gnu: sbcl-cl-cffi-gtk: Update to 20200417.
[jackhill/guix/guix.git] / gnu / packages / cran.scm
1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
4 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
5 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
6 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
7 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
8 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
9 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
10 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
11 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
12 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
13 ;;; Copyright © 2018, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
14 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
15 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
16 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
17 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
18 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
19 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
20 ;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
21 ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
22 ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
23 ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
24 ;;;
25 ;;; This file is part of GNU Guix.
26 ;;;
27 ;;; GNU Guix is free software; you can redistribute it and/or modify it
28 ;;; under the terms of the GNU General Public License as published by
29 ;;; the Free Software Foundation; either version 3 of the License, or (at
30 ;;; your option) any later version.
31 ;;;
32 ;;; GNU Guix is distributed in the hope that it will be useful, but
33 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
34 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
35 ;;; GNU General Public License for more details.
36 ;;;
37 ;;; You should have received a copy of the GNU General Public License
38 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
39
40 (define-module (gnu packages cran)
41 #:use-module ((guix licenses) #:prefix license:)
42 #:use-module (guix packages)
43 #:use-module (guix download)
44 #:use-module (guix git-download)
45 #:use-module (guix utils)
46 #:use-module (guix build-system r)
47 #:use-module (gnu packages algebra)
48 #:use-module (gnu packages autotools)
49 #:use-module (gnu packages base)
50 #:use-module (gnu packages bioinformatics)
51 #:use-module (gnu packages c)
52 #:use-module (gnu packages compression)
53 #:use-module (gnu packages curl)
54 #:use-module (gnu packages databases)
55 #:use-module (gnu packages fontutils)
56 #:use-module (gnu packages gcc)
57 #:use-module (gnu packages geo)
58 #:use-module (gnu packages ghostscript)
59 #:use-module (gnu packages gl)
60 #:use-module (gnu packages gnome)
61 #:use-module (gnu packages graph)
62 #:use-module (gnu packages gtk)
63 #:use-module (gnu packages haskell-xyz)
64 #:use-module (gnu packages icu4c)
65 #:use-module (gnu packages image)
66 #:use-module (gnu packages imagemagick)
67 #:use-module (gnu packages java)
68 #:use-module (gnu packages javascript)
69 #:use-module (gnu packages lisp-xyz)
70 #:use-module (gnu packages machine-learning)
71 #:use-module (gnu packages maths)
72 #:use-module (gnu packages mpi)
73 #:use-module (gnu packages multiprecision)
74 #:use-module (gnu packages networking)
75 #:use-module (gnu packages pcre)
76 #:use-module (gnu packages perl)
77 #:use-module (gnu packages pkg-config)
78 #:use-module (gnu packages python)
79 #:use-module (gnu packages python-xyz)
80 #:use-module (gnu packages statistics)
81 #:use-module (gnu packages tcl)
82 #:use-module (gnu packages tls)
83 #:use-module (gnu packages web)
84 #:use-module (gnu packages xorg))
85
86 (define-public r-bezier
87 (package
88 (name "r-bezier")
89 (version "1.1.2")
90 (source (origin
91 (method url-fetch)
92 (uri (cran-uri "bezier" version))
93 (sha256
94 (base32
95 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
96 (build-system r-build-system)
97 (home-page "https://cran.r-project.org/web/packages/bezier/")
98 (synopsis "Bezier curve and spline toolkit")
99 (description
100 "This package is a toolkit for working with Bezier curves and splines.
101 The package provides functions for point generation, arc length estimation,
102 degree elevation and curve fitting.")
103 (license license:gpl2+)))
104
105 (define-public r-clipr
106 (package
107 (name "r-clipr")
108 (version "0.7.0")
109 (source
110 (origin
111 (method url-fetch)
112 (uri (cran-uri "clipr" version))
113 (sha256
114 (base32
115 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
116 (build-system r-build-system)
117 (home-page "https://github.com/mdlincoln/clipr")
118 (synopsis "Read and write from the system clipboard")
119 (description
120 "This package provides simple utility functions to read from and write to
121 the system clipboards.")
122 (license license:gpl3)))
123
124 (define-public r-ggpmisc
125 (package
126 (name "r-ggpmisc")
127 (version "0.3.4")
128 (source (origin
129 (method url-fetch)
130 (uri (cran-uri "ggpmisc" version))
131 (sha256
132 (base32
133 "0xc1yp0kphipq23ri4ij93garx1x2nrf4i0lhs6m10pp9yz7fbmj"))))
134 (build-system r-build-system)
135 (propagated-inputs
136 `(("r-broom" ,r-broom)
137 ("r-dplyr" ,r-dplyr)
138 ("r-ggplot2" ,r-ggplot2)
139 ("r-gridextra" ,r-gridextra)
140 ("r-lubridate" ,r-lubridate)
141 ("r-mass" ,r-mass)
142 ("r-plyr" ,r-plyr)
143 ("r-polynom" ,r-polynom)
144 ("r-splus2r" ,r-splus2r)
145 ("r-tibble" ,r-tibble)
146 ("r-xts" ,r-xts)
147 ("r-zoo" ,r-zoo)))
148 (home-page "https://www.r4photobiology.info/")
149 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
150 (description "This package provides extensions to @code{ggplot2},
151 respecting the grammar of its graphics paradigm.")
152 (license license:gpl2+)))
153
154 (define-public r-oenb
155 (package
156 (name "r-oenb")
157 (version "0.0.1")
158 (source
159 (origin
160 (method url-fetch)
161 (uri (cran-uri "oenb" version))
162 (sha256
163 (base32
164 "1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz"))))
165 (properties `((upstream-name . "oenb")))
166 (build-system r-build-system)
167 (propagated-inputs
168 `(("r-dplyr" ,r-dplyr)
169 ("r-xml" ,r-xml)))
170 (native-inputs `(("r-knitr" ,r-knitr)))
171 (home-page "https://github.com/franzmohr/oenb")
172 (synopsis "Tools for the OeNB Data Web Service")
173 (description
174 "Tools to access data from the data web service of the
175 @acronym{OeNB, Oesterreichische Nationalbank},
176 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
177 (license license:gpl2+)))
178
179 (define-public r-scales
180 (package
181 (name "r-scales")
182 (version "1.1.0")
183 (source
184 (origin
185 (method url-fetch)
186 (uri (cran-uri "scales" version))
187 (sha256
188 (base32 "00rdbfj5mwc3kr8pskidn3n2zkp4ms6cx36xazz54pxw3pysdr0y"))))
189 (build-system r-build-system)
190 (propagated-inputs
191 `(("r-farver" ,r-farver)
192 ("r-labeling" ,r-labeling)
193 ("r-lifecycle" ,r-lifecycle)
194 ("r-munsell" ,r-munsell)
195 ("r-rcolorbrewer" ,r-rcolorbrewer)
196 ("r-r6" ,r-r6)
197 ("r-viridislite" ,r-viridislite)))
198 (home-page "https://github.com/hadley/scales")
199 (synopsis "Scale functions for visualization")
200 (description
201 "This package provides graphical scales that map data to aesthetics, and
202 provides methods for automatically determining breaks and labels for axes and
203 legends.")
204 (license license:expat)))
205
206 (define-public r-pheatmap
207 (package
208 (name "r-pheatmap")
209 (version "1.0.12")
210 (source
211 (origin
212 (method url-fetch)
213 (uri (cran-uri "pheatmap" version))
214 (sha256
215 (base32
216 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
217 (build-system r-build-system)
218 (propagated-inputs
219 `(("r-gtable" ,r-gtable)
220 ("r-rcolorbrewer" ,r-rcolorbrewer)
221 ("r-scales" ,r-scales)))
222 (home-page "https://cran.r-project.org/web/packages/pheatmap")
223 (synopsis "Pretty heatmaps")
224 (description
225 "This package provides an implementation of heatmaps that offers more
226 control over dimensions and appearance.")
227 (license license:gpl2+)))
228
229 (define-public r-ecp
230 (package
231 (name "r-ecp")
232 (version "3.1.2")
233 (source (origin
234 (method url-fetch)
235 (uri (cran-uri "ecp" version))
236 (sha256
237 (base32
238 "11f9p869xr0zg779i46gmflxlq4xclk9wxbab0nj2fan26pn4sfy"))))
239 (build-system r-build-system)
240 (propagated-inputs
241 `(("r-rcpp" ,r-rcpp)))
242 (home-page "https://cran.r-project.org/web/packages/ecp/")
243 (synopsis "Multiple change-point analysis of multivariate data")
244 (description
245 "This package implements various procedures for finding multiple
246 change-points. Two methods make use of dynamic programming and pruning, with
247 no distributional assumptions other than the existence of certain absolute
248 moments in one method. Hierarchical and exact search methods are included.
249 All methods return the set of estimated change-points as well as other summary
250 information.")
251 (license license:gpl2+)))
252
253 (define-public r-ellipsis
254 (package
255 (name "r-ellipsis")
256 (version "0.3.0")
257 (source
258 (origin
259 (method url-fetch)
260 (uri (cran-uri "ellipsis" version))
261 (sha256
262 (base32
263 "01z9gq311nzwv3a0sa49jhm5ylqd59srip4vjkrf23hzgb5i9y0b"))))
264 (build-system r-build-system)
265 (propagated-inputs
266 `(("r-rlang" ,r-rlang)))
267 (home-page "https://github.com/hadley/ellipsis")
268 (synopsis "Tools for working with additional arguments")
269 (description
270 "In S3 generics, it's useful to take @code{...} so that methods can have
271 additional arguments. But this flexibility comes at a cost: misspelled
272 arguments will be silently ignored. The @code{ellipsis} package is an
273 experiment that allows a generic to warn if any arguments passed in @code{...}
274 are not used.")
275 (license license:gpl3)))
276
277 (define-public r-grr
278 (package
279 (name "r-grr")
280 (version "0.9.5")
281 (source
282 (origin
283 (method url-fetch)
284 (uri (cran-uri "grr" version))
285 (sha256
286 (base32
287 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
288 (build-system r-build-system)
289 (home-page "https://cran.r-project.org/web/packages/grr")
290 (synopsis "Alternative implementations of base R functions")
291 (description
292 "This package provides alternative implementations of some base R
293 functions, including @code{sort}, @code{order}, and @code{match}. The
294 functions are simplified but can be faster or have other advantages.")
295 (license license:gpl3)))
296
297 (define-public r-matrix-utils
298 (package
299 (name "r-matrix-utils")
300 (version "0.9.8")
301 (source
302 (origin
303 (method url-fetch)
304 (uri (cran-uri "Matrix.utils" version))
305 (sha256
306 (base32
307 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
308 (properties `((upstream-name . "Matrix.utils")))
309 (build-system r-build-system)
310 (propagated-inputs
311 `(("r-grr" ,r-grr)
312 ("r-matrix" ,r-matrix)))
313 (home-page "https://github.com/cvarrichio/Matrix.utils")
314 (synopsis
315 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
316 (description
317 "This package implements data manipulation methods such as @code{cast},
318 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
319 objects.")
320 (license license:gpl3)))
321
322 (define-public r-sys
323 (package
324 (name "r-sys")
325 (version "3.3")
326 (source
327 (origin
328 (method url-fetch)
329 (uri (cran-uri "sys" version))
330 (sha256
331 (base32
332 "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6"))))
333 (build-system r-build-system)
334 (home-page "https://github.com/jeroen/sys")
335 (synopsis "Powerful and reliable tools for running system commands in R")
336 (description
337 "This package provides drop-in replacements for the base @code{system2()}
338 function with fine control and consistent behavior across platforms. It
339 supports clean interruption, timeout, background tasks, and streaming STDIN /
340 STDOUT / STDERR over binary or text connections. The package also provides
341 functions for evaluating expressions inside a temporary fork. Such
342 evaluations have no side effects on the main R process, and support reliable
343 interrupts and timeouts. This provides the basis for a sandboxing
344 mechanism.")
345 (license license:expat)))
346
347 (define-public r-askpass
348 (package
349 (name "r-askpass")
350 (version "1.1")
351 (source
352 (origin
353 (method url-fetch)
354 (uri (cran-uri "askpass" version))
355 (sha256
356 (base32
357 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
358 (build-system r-build-system)
359 (propagated-inputs `(("r-sys" ,r-sys)))
360 (home-page "https://github.com/jeroen/askpass")
361 (synopsis "Safe password entry for R")
362 (description
363 "This package provides cross-platform utilities for prompting the user
364 for credentials or a passphrase, for example to authenticate with a server or
365 read a protected key.")
366 (license license:expat)))
367
368 (define-public r-vegan
369 (package
370 (name "r-vegan")
371 (version "2.5-6")
372 (source
373 (origin
374 (method url-fetch)
375 (uri (cran-uri "vegan" version))
376 (sha256
377 (base32
378 "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
379 (build-system r-build-system)
380 (native-inputs
381 `(("gfortran" ,gfortran)))
382 (propagated-inputs
383 `(("r-cluster" ,r-cluster)
384 ("r-knitr" ,r-knitr) ; needed for vignettes
385 ("r-lattice" ,r-lattice)
386 ("r-mass" ,r-mass)
387 ("r-mgcv" ,r-mgcv)
388 ("r-permute" ,r-permute)))
389 (home-page "https://cran.r-project.org/web/packages/vegan")
390 (synopsis "Functions for community ecology")
391 (description
392 "The vegan package provides tools for descriptive community ecology. It
393 has most basic functions of diversity analysis, community ordination and
394 dissimilarity analysis. Most of its multivariate tools can be used for other
395 data types as well.")
396 (license license:gpl2+)))
397
398 (define-public r-tidyverse
399 (package
400 (name "r-tidyverse")
401 (version "1.3.0")
402 (source
403 (origin
404 (method url-fetch)
405 (uri (cran-uri "tidyverse" version))
406 (sha256
407 (base32
408 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
409 (build-system r-build-system)
410 (propagated-inputs
411 `(("r-broom" ,r-broom)
412 ("r-cli" ,r-cli)
413 ("r-crayon" ,r-crayon)
414 ("r-dbplyr" ,r-dbplyr)
415 ("r-dplyr" ,r-dplyr)
416 ("r-forcats" ,r-forcats)
417 ("r-ggplot2" ,r-ggplot2)
418 ("r-haven" ,r-haven)
419 ("r-hms" ,r-hms)
420 ("r-httr" ,r-httr)
421 ("r-jsonlite" ,r-jsonlite)
422 ("r-lubridate" ,r-lubridate)
423 ("r-magrittr" ,r-magrittr)
424 ("r-modelr" ,r-modelr)
425 ("r-pillar" ,r-pillar)
426 ("r-purrr" ,r-purrr)
427 ("r-readr" ,r-readr)
428 ("r-readxl" ,r-readxl)
429 ("r-reprex" ,r-reprex)
430 ("r-rlang" ,r-rlang)
431 ("r-rstudioapi" ,r-rstudioapi)
432 ("r-rvest" ,r-rvest)
433 ("r-stringr" ,r-stringr)
434 ("r-tibble" ,r-tibble)
435 ("r-tidyr" ,r-tidyr)
436 ("r-xml2" ,r-xml2)))
437 (home-page "https://tidyverse.tidyverse.org")
438 (synopsis "Install and load packages from the \"Tidyverse\"")
439 (description
440 "The @code{tidyverse} is a set of packages that work in harmony because
441 they share common data representations and API design. This package is
442 designed to make it easy to install and load multiple tidyverse packages in a
443 single step.")
444 (license license:gpl3)))
445
446 (define-public r-rvest
447 (package
448 (name "r-rvest")
449 (version "0.3.5")
450 (source
451 (origin
452 (method url-fetch)
453 (uri (cran-uri "rvest" version))
454 (sha256
455 (base32 "0r0a5jic09xw5pk0x42pr99r3zab5m9s4x85ymx1sl769jz42zqf"))))
456 (build-system r-build-system)
457 (propagated-inputs
458 `(("r-httr" ,r-httr)
459 ("r-magrittr" ,r-magrittr)
460 ("r-selectr" ,r-selectr)
461 ("r-xml2" ,r-xml2)))
462 (home-page "https://github.com/hadley/rvest")
463 (synopsis "Simple web scraping for R")
464 (description
465 "@code{r-rvest} helps you scrape information from web pages. It is
466 designed to work with @code{magrittr} to make it easy to express common web
467 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
468 (license license:gpl3)))
469
470 (define-public r-selectr
471 (package
472 (name "r-selectr")
473 (version "0.4-2")
474 (source
475 (origin
476 (method url-fetch)
477 (uri (cran-uri "selectr" version))
478 (sha256
479 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
480 (build-system r-build-system)
481 (propagated-inputs
482 `(("r-stringr" ,r-stringr)
483 ("r-r6" ,r-r6)))
484 (home-page "https://sjp.co.nz/projects/selectr/")
485 (synopsis "Translate CSS selectors to XPath expressions")
486 (description
487 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
488 expression. This allows you to use CSS selectors when working with the XML
489 package as it can only evaluate XPath expressions. Also provided are
490 convenience functions useful for using CSS selectors on XML nodes. This
491 package is a port of the Python package @code{cssselect}.")
492 (license license:bsd-3)))
493
494 (define-public r-reprex
495 (package
496 (name "r-reprex")
497 (version "0.3.0")
498 (source
499 (origin
500 (method url-fetch)
501 (uri (cran-uri "reprex" version))
502 (sha256
503 (base32
504 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
505 (build-system r-build-system)
506 (propagated-inputs
507 `(("r-callr" ,r-callr)
508 ("r-clipr" ,r-clipr)
509 ("r-fs" ,r-fs)
510 ("r-rlang" ,r-rlang)
511 ("r-rmarkdown" ,r-rmarkdown)
512 ("r-whisker" ,r-whisker)
513 ("r-withr" ,r-withr)))
514 (home-page "https://github.com/tidyverse/reprex")
515 (synopsis "Prepare reproducible R code examples for sharing")
516 (description
517 "This package provides a convenience wrapper that uses the
518 @code{rmarkdown} package to render small snippets of code to target formats
519 that include both code and output. The goal is to encourage the sharing of
520 small, reproducible, and runnable examples on code-oriented websites or email.
521 @code{reprex} also extracts clean, runnable R code from various common formats,
522 such as copy/paste from an R session.")
523 (license license:expat)))
524
525 (define-public r-reordercluster
526 (package
527 (name "r-reordercluster")
528 (version "1.0")
529 (source (origin
530 (method url-fetch)
531 (uri (cran-uri "ReorderCluster" version))
532 (sha256
533 (base32
534 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
535 (build-system r-build-system)
536 (propagated-inputs
537 `(("r-gplots" ,r-gplots)
538 ("r-rcpp" ,r-rcpp)))
539 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
540 (synopsis "Reordering the dendrogram according to the class labels")
541 (description "This package provides tools for performing the leaf reordering
542 for the dendrogram that preserves the hierarchical clustering result and at the
543 same time tries to group instances from the same class together.")
544 (license license:gpl3+)))
545
546 (define-public r-callr
547 (package
548 (name "r-callr")
549 (version "3.4.3")
550 (source
551 (origin
552 (method url-fetch)
553 (uri (cran-uri "callr" version))
554 (sha256
555 (base32
556 "1dc20gdawy9mhnc452qlshv2p4krs6c2gymvpv365mn141zjgdq1"))))
557 (build-system r-build-system)
558 (propagated-inputs
559 `(("r-r6" ,r-r6)
560 ("r-processx" ,r-processx)))
561 (home-page "https://github.com/r-lib/callr#readme")
562 (synopsis "Call R from R")
563 (description
564 "It is sometimes useful to perform a computation in a separate R process,
565 without affecting the current R process at all. This package does exactly
566 that.")
567 (license license:expat)))
568
569 (define-public r-readxl
570 (package
571 (name "r-readxl")
572 (version "1.3.1")
573 (source
574 (origin
575 (method url-fetch)
576 (uri (cran-uri "readxl" version))
577 (sha256
578 (base32
579 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
580 (build-system r-build-system)
581 (propagated-inputs
582 `(("r-cellranger" ,r-cellranger)
583 ("r-progress" ,r-progress)
584 ("r-rcpp" ,r-rcpp)
585 ("r-tibble" ,r-tibble)))
586 (home-page "https://readxl.tidyverse.org")
587 (synopsis "Read Excel files")
588 (description
589 "This package lets you import Excel files into R. It supports
590 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
591 the embedded @code{RapidXML} C++ library.")
592 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
593 ;; 'rapidxml' which is Boost.
594 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
595
596 (define-public r-modelr
597 (package
598 (name "r-modelr")
599 (version "0.1.6")
600 (source
601 (origin
602 (method url-fetch)
603 (uri (cran-uri "modelr" version))
604 (sha256
605 (base32
606 "1x2m34m4qirb401krmgc5wg3g7ndbcglfab2l0655rmky3fz7rfp"))))
607 (build-system r-build-system)
608 (propagated-inputs
609 `(("r-broom" ,r-broom)
610 ("r-dplyr" ,r-dplyr)
611 ("r-magrittr" ,r-magrittr)
612 ("r-purrr" ,r-purrr)
613 ("r-rlang" ,r-rlang)
614 ("r-tibble" ,r-tibble)
615 ("r-tidyr" ,r-tidyr)
616 ("r-tidyselect" ,r-tidyselect)))
617 (home-page "https://github.com/tidyverse/modelr")
618 (synopsis "Helper functions for modelling in pipelines")
619 (description
620 "Functions for modelling that help you seamlessly integrate modelling
621 into a pipeline of data manipulation and visualisation.")
622 (license license:gpl3)))
623
624 (define-public r-httpuv
625 (package
626 (name "r-httpuv")
627 (version "1.5.2")
628 (source (origin
629 (method url-fetch)
630 (uri (cran-uri "httpuv" version))
631 (sha256
632 (base32
633 "13ax0hs2lc39ilznh1zarwqdzahcbhb8adilrfik3xg0fkljpcwk"))))
634 (build-system r-build-system)
635 (propagated-inputs
636 `(("r-bh" ,r-bh)
637 ("r-later" ,r-later)
638 ("r-promises" ,r-promises)
639 ("r-r6" ,r-r6)
640 ("r-rcpp" ,r-rcpp)))
641 (home-page "https://github.com/rstudio/httpuv")
642 (synopsis "HTTP and WebSocket server library for R")
643 (description
644 "The httpuv package provides low-level socket and protocol support for
645 handling HTTP and WebSocket requests directly from within R. It is primarily
646 intended as a building block for other packages, rather than making it
647 particularly easy to create complete web applications using httpuv alone.")
648 ;; This package includes third-party code that was originally released
649 ;; under various non-copyleft licenses. Full licensing information can be
650 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
651 (license license:gpl3+)))
652
653 (define-public r-jsonlite
654 (package
655 (name "r-jsonlite")
656 (version "1.6.1")
657 (source (origin
658 (method url-fetch)
659 (uri (cran-uri "jsonlite" version))
660 (sha256
661 (base32
662 "0xrki07wc17bkmhz0h7jay784j1sls2i9bf1mfpj6yl59791v4kl"))))
663 (build-system r-build-system)
664 (home-page "https://arxiv.org/abs/1403.2805")
665 (synopsis "Robust, high performance JSON parser and generator for R")
666 (description
667 "The jsonlite package provides a fast JSON parser and generator optimized
668 for statistical data and the web. It offers flexible, robust, high
669 performance tools for working with JSON in R and is particularly powerful for
670 building pipelines and interacting with a web API. In addition to converting
671 JSON data from/to R objects, jsonlite contains functions to stream, validate,
672 and prettify JSON data. The unit tests included with the package verify that
673 all edge cases are encoded and decoded consistently for use with dynamic data
674 in systems and applications.")
675 (license license:expat)))
676
677 (define-public r-servr
678 (package
679 (name "r-servr")
680 (version "0.16")
681 (source (origin
682 (method url-fetch)
683 (uri (cran-uri "servr" version))
684 (sha256
685 (base32
686 "106skz04iq4dkblr17idxsxfcfqic6rcaz8mahydkwjjppnhp5fc"))))
687 (build-system r-build-system)
688 (propagated-inputs
689 `(("r-httpuv" ,r-httpuv)
690 ("r-jsonlite" ,r-jsonlite)
691 ("r-mime" ,r-mime)
692 ("r-xfun" ,r-xfun)))
693 (home-page "https://github.com/yihui/servr")
694 (synopsis "Simple HTTP server to serve static files or dynamic documents")
695 (description
696 "Servr provides an HTTP server in R to serve static files, or dynamic
697 documents that can be converted to HTML files (e.g., R Markdown) under a given
698 directory.")
699 (license license:expat)))
700
701 (define-public r-htmltools
702 (package
703 (name "r-htmltools")
704 (version "0.4.0")
705 (source (origin
706 (method url-fetch)
707 (uri (cran-uri "htmltools" version))
708 (sha256
709 (base32
710 "06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v"))))
711 (build-system r-build-system)
712 (propagated-inputs
713 `(("r-digest" ,r-digest)
714 ("r-rcpp" ,r-rcpp)
715 ("r-rlang" ,r-rlang)))
716 (home-page "https://cran.r-project.org/web/packages/htmltools")
717 (synopsis "R tools for HTML")
718 (description
719 "This package provides tools for HTML generation and output in R.")
720 (license license:expat)))
721
722 (define-public r-htmlwidgets
723 (package
724 (name "r-htmlwidgets")
725 (version "1.5.1")
726 (source (origin
727 (method url-fetch)
728 (uri (cran-uri "htmlwidgets" version))
729 (sha256
730 (base32
731 "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
732 (build-system r-build-system)
733 (propagated-inputs
734 `(("r-htmltools" ,r-htmltools)
735 ("r-jsonlite" ,r-jsonlite)
736 ("r-yaml" ,r-yaml)))
737 (home-page "https://github.com/ramnathv/htmlwidgets")
738 (synopsis "HTML Widgets for R")
739 (description
740 "HTML widgets is a framework for creating HTML widgets that render in
741 various contexts including the R console, R Markdown documents, and Shiny web
742 applications.")
743 (license license:expat)))
744
745 (define-public r-htmltable
746 (package
747 (name "r-htmltable")
748 (version "1.13.3")
749 (source
750 (origin
751 (method url-fetch)
752 (uri (cran-uri "htmlTable" version))
753 (sha256
754 (base32
755 "0g9r156k9yl1f092hfw3b9wjx11akf0shbi3x0d0mvpnflvc8nfl"))))
756 (properties `((upstream-name . "htmlTable")))
757 (build-system r-build-system)
758 (propagated-inputs
759 `(("r-checkmate" ,r-checkmate)
760 ("r-htmltools" ,r-htmltools)
761 ("r-htmlwidgets" ,r-htmlwidgets)
762 ("r-knitr" ,r-knitr)
763 ("r-magrittr" ,r-magrittr)
764 ("r-rstudioapi" ,r-rstudioapi)
765 ("r-stringr" ,r-stringr)))
766 (home-page "http://gforge.se/packages/")
767 (synopsis "Advanced tables for Markdown/HTML")
768 (description
769 "This package provides functions to build tables with advanced layout
770 elements such as row spanners, column spanners, table spanners, zebra
771 striping, and more. While allowing advanced layout, the underlying
772 CSS-structure is simple in order to maximize compatibility with word
773 processors such as LibreOffice. The package also contains a few text
774 formatting functions that help outputting text compatible with HTML or
775 LaTeX.")
776 (license license:gpl3+)))
777
778 (define-public r-curl
779 (package
780 (name "r-curl")
781 (version "4.3")
782 (source (origin
783 (method url-fetch)
784 (uri (cran-uri "curl" version))
785 (sha256
786 (base32
787 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
788 (build-system r-build-system)
789 (arguments
790 `(#:phases
791 (modify-phases %standard-phases
792 ;; The environment variable CURL_CA_BUNDLE is only respected when
793 ;; running Windows, so we disable the platform checks.
794 ;; This can be removed once the libcurl has been patched.
795 (add-after 'unpack 'allow-CURL_CA_BUNDLE
796 (lambda _
797 (substitute* "R/onload.R"
798 (("if \\(!grepl\\(\"mingw\".*")
799 "if (FALSE)\n"))
800 (substitute* "src/handle.c"
801 (("/\\* Only set" m)
802 (string-append "\
803 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
804 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
805 " m)))
806 #t)))))
807 (inputs
808 `(("libcurl" ,curl)
809 ("zlib" ,zlib)))
810 (native-inputs
811 `(("pkg-config" ,pkg-config)))
812 (home-page "https://github.com/jeroenooms/curl")
813 (synopsis "HTTP client for R")
814 (description
815 "The @code{curl()} and @code{curl_download()} functions provide highly
816 configurable drop-in replacements for base @code{url()} and
817 @code{download.file()} with better performance, support for encryption, gzip
818 compression, authentication, and other @code{libcurl} goodies. The core of
819 the package implements a framework for performing fully customized requests
820 where data can be processed either in memory, on disk, or streaming via the
821 callback or connection interfaces.")
822 (license license:expat)))
823
824 (define-public r-hwriter
825 (package
826 (name "r-hwriter")
827 (version "1.3.2")
828 (source
829 (origin
830 (method url-fetch)
831 (uri (cran-uri "hwriter" version))
832 (sha256
833 (base32
834 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
835 (build-system r-build-system)
836 (home-page "https://cran.r-project.org/web/packages/hwriter")
837 (synopsis "Output R objects in HTML format")
838 (description
839 "This package provides easy-to-use and versatile functions to output R
840 objects in HTML format.")
841 (license license:lgpl2.1+)))
842
843 (define-public r-rjson
844 (package
845 (name "r-rjson")
846 (version "0.2.20")
847 (source
848 (origin
849 (method url-fetch)
850 (uri (cran-uri "rjson" version))
851 (sha256
852 (base32
853 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
854 (build-system r-build-system)
855 (home-page "https://cran.r-project.org/web/packages/rjson")
856 (synopsis "JSON library for R")
857 (description
858 "This package provides functions to convert R objects into JSON objects
859 and vice-versa.")
860 (license license:gpl2+)))
861
862 (define-public r-fastmap
863 (package
864 (name "r-fastmap")
865 (version "1.0.1")
866 (source
867 (origin
868 (method url-fetch)
869 (uri (cran-uri "fastmap" version))
870 (sha256
871 (base32
872 "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
873 (properties `((upstream-name . "fastmap")))
874 (build-system r-build-system)
875 (home-page "https://r-lib.github.io/fastmap/")
876 (synopsis "Fast implementation of a key-value store")
877 (description
878 "This package provides a fast implementation of a key-value store.
879 Environments are commonly used as key-value stores, but every time a new key
880 is used, it is added to R's global symbol table, causing a small amount of
881 memory leakage. This can be problematic in cases where many different keys
882 are used. Fastmap avoids this memory leak issue by implementing the map using
883 data structures in C++.")
884 (license license:expat)))
885
886 (define-public r-shiny
887 (package
888 (name "r-shiny")
889 (version "1.4.0.2")
890 (source
891 (origin
892 (method git-fetch)
893 (uri (git-reference
894 (url "https://github.com/rstudio/shiny.git")
895 (commit (string-append "v" version))))
896 (file-name (git-file-name name version))
897 (sha256
898 (base32
899 "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs"))))
900 (build-system r-build-system)
901 (arguments
902 `(#:modules ((guix build r-build-system)
903 (guix build minify-build-system)
904 (guix build utils)
905 (ice-9 match))
906 #:imported-modules (,@%r-build-system-modules
907 (guix build minify-build-system))
908 #:phases
909 (modify-phases (@ (guix build r-build-system) %standard-phases)
910 (add-after 'unpack 'replace-bundled-minified-JavaScript
911 (lambda* (#:key inputs #:allow-other-keys)
912 (let ((replace-file (lambda (old new)
913 (format #t "replacing ~a with ~a\n" old new)
914 (delete-file old)
915 (symlink new old))))
916 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
917 ;; contain just data. They are not minified code, so we don't
918 ;; replace them.
919 (with-directory-excursion "inst/www/shared"
920 (replace-file "bootstrap/shim/respond.min.js"
921 (string-append (assoc-ref inputs "js-respond")
922 "/share/javascript/respond.min.js"))
923 (replace-file "bootstrap/shim/html5shiv.min.js"
924 (string-append (assoc-ref inputs "js-html5shiv")
925 "/share/javascript/html5shiv.min.js"))
926 (replace-file "json2-min.js"
927 (string-append (assoc-ref inputs "js-json2")
928 "/share/javascript/json2-min.js"))
929 (replace-file "strftime/strftime-min.js"
930 (string-append (assoc-ref inputs "js-strftime")
931 "/share/javascript/strftime.min.js"))
932 (replace-file "highlight/highlight.pack.js"
933 (string-append (assoc-ref inputs "js-highlight")
934 "/share/javascript/highlight.min.js"))
935 (replace-file "datatables/js/jquery.dataTables.min.js"
936 (string-append (assoc-ref inputs "js-datatables")
937 "/share/javascript/jquery.dataTables.min.js"))
938 (replace-file "selectize/js/selectize.min.js"
939 (string-append (assoc-ref inputs "js-selectize")
940 "/share/javascript/selectize.min.js"))
941 (replace-file "selectize/js/es5-shim.min.js"
942 (string-append (assoc-ref inputs "js-es5-shim")
943 "/share/javascript/es5-shim.min.js"))
944 (for-each (match-lambda
945 ((source . target)
946 (delete-file target)
947 (minify source #:target target)))
948 '(("jqueryui/jquery-ui.js" .
949 "jqueryui/jquery-ui.min.js")
950 ("datepicker/js/bootstrap-datepicker.js" .
951 "datepicker/js/bootstrap-datepicker.min.js")
952 ("ionrangeslider/js/ion.rangeSlider.js" .
953 "ionrangeslider/js/ion.rangeSlider.min.js")
954 ("bootstrap/js/bootstrap.js" .
955 "bootstrap/js/bootstrap.min.js")
956 ("shiny.js" .
957 "shiny.min.js")
958 ("jquery.js" .
959 "jquery.min.js")
960 ("legacy/jquery.js" .
961 "legacy/jquery.min.js")
962 ("showdown/src/showdown.js" .
963 "showdown/compressed/showdown.js")))))
964 #t)))))
965 (propagated-inputs
966 `(("r-crayon" ,r-crayon)
967 ("r-digest" ,r-digest)
968 ("r-fastmap" ,r-fastmap)
969 ("r-htmltools" ,r-htmltools)
970 ("r-httpuv" ,r-httpuv)
971 ("r-jsonlite" ,r-jsonlite)
972 ("r-later" ,r-later)
973 ("r-mime" ,r-mime)
974 ("r-promises" ,r-promises)
975 ("r-r6" ,r-r6)
976 ("r-rlang" ,r-rlang)
977 ("r-sourcetools" ,r-sourcetools)
978 ("r-withr" ,r-withr)
979 ("r-xtable" ,r-xtable)))
980 (inputs
981 `(("js-datatables" ,js-datatables)
982 ("js-html5shiv" ,js-html5shiv)
983 ("js-json2" ,js-json2)
984 ("js-respond" ,js-respond)
985 ("js-selectize" ,js-selectize)
986 ("js-strftime" ,js-strftime)
987 ("js-highlight" ,js-highlight)
988 ("js-es5-shim" ,js-es5-shim)))
989 (native-inputs
990 `(("uglify-js" ,uglify-js)
991 ("gfortran" ,gfortran)))
992 (home-page "http://shiny.rstudio.com")
993 (synopsis "Easy interactive web applications with R")
994 (description
995 "Makes it incredibly easy to build interactive web applications
996 with R. Automatic \"reactive\" binding between inputs and outputs and
997 extensive prebuilt widgets make it possible to build beautiful,
998 responsive, and powerful applications with minimal effort.")
999 (license license:artistic2.0)))
1000
1001 ;; This package includes minified JavaScript files. When upgrading please
1002 ;; check that there are no new minified JavaScript files.
1003 (define-public r-shinytree
1004 (package
1005 (name "r-shinytree")
1006 (version "0.2.7")
1007 (source
1008 (origin
1009 (method url-fetch)
1010 (uri (cran-uri "shinyTree" version))
1011 (sha256
1012 (base32
1013 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1014 (modules '((guix build utils)))
1015 (snippet
1016 '(begin
1017 ;; Delete minified JavaScript
1018 (for-each delete-file
1019 '("inst/www/jsTree-3.3.7/libs/require.js"
1020 "inst/www/jsTree-3.3.7/libs/jquery.js"
1021 "inst/www/jsTree-3.3.7/jstree.min.js"))
1022 #t))))
1023 (properties `((upstream-name . "shinyTree")))
1024 (build-system r-build-system)
1025 (arguments
1026 `(#:modules ((guix build utils)
1027 (guix build r-build-system)
1028 (srfi srfi-1)
1029 (ice-9 popen))
1030 #:phases
1031 (modify-phases %standard-phases
1032 (add-after 'unpack 'replace-minified-javascript
1033 (lambda* (#:key inputs #:allow-other-keys)
1034 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1035 (symlink (string-append (assoc-ref inputs "js-requirejs")
1036 "/share/javascript/require.min.js")
1037 "libs/require.js")
1038 (call-with-values
1039 (lambda ()
1040 (unzip2
1041 `((,(assoc-ref inputs "js-jquery")
1042 "libs/jquery.js")
1043 ("jstree.js"
1044 "jstree.min.js"))))
1045 (lambda (sources targets)
1046 (for-each (lambda (source target)
1047 (format #t "Processing ~a --> ~a~%"
1048 source target)
1049 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1050 (call-with-output-file target
1051 (lambda (port)
1052 (dump-port minified port)))))
1053 sources targets))))
1054 #t)))))
1055 (propagated-inputs
1056 `(("r-htmlwidgets" ,r-htmlwidgets)
1057 ("r-jsonlite" ,r-jsonlite)
1058 ("r-promises" ,r-promises)
1059 ("r-shiny" ,r-shiny)
1060 ("r-stringr" ,r-stringr)))
1061 (inputs
1062 `(("js-requirejs" ,js-requirejs)))
1063 (native-inputs
1064 `(("uglify-js" ,uglify-js)
1065 ("js-jquery"
1066 ,(origin
1067 (method url-fetch)
1068 (uri "https://code.jquery.com/jquery-3.3.1.js")
1069 (sha256
1070 (base32
1071 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1072 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1073 (synopsis "jsTree bindings for Shiny")
1074 (description
1075 "This package exposes R bindings to jsTree, a JavaScript library that
1076 supports interactive trees, to enable rich, editable trees in Shiny.")
1077 (license license:expat)))
1078
1079 (define-public r-shinydashboard
1080 (package
1081 (name "r-shinydashboard")
1082 (version "0.7.1")
1083 (source (origin
1084 (method url-fetch)
1085 (uri (cran-uri "shinydashboard" version))
1086 (sha256
1087 (base32
1088 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1089 (build-system r-build-system)
1090 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1091 ;; Regenerate it from the included sources.
1092 (arguments
1093 `(#:modules ((guix build utils)
1094 (guix build r-build-system)
1095 (ice-9 popen))
1096 #:phases
1097 (modify-phases %standard-phases
1098 (add-after 'unpack 'generate-minified-javascript
1099 (lambda _
1100 (with-directory-excursion "inst/AdminLTE"
1101 (delete-file "app.min.js")
1102 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1103 (call-with-output-file "app.min.js"
1104 (lambda (port)
1105 (dump-port minified port))))))))))
1106 (propagated-inputs
1107 `(("r-htmltools" ,r-htmltools)
1108 ("r-promises" ,r-promises)
1109 ("r-shiny" ,r-shiny)))
1110 (native-inputs
1111 `(("uglify-js" ,uglify-js)))
1112 (home-page "https://rstudio.github.io/shinydashboard/")
1113 (synopsis "Create dashboards with shiny")
1114 (description "This package provides an extension to the Shiny web
1115 application framework for R, making it easy to create attractive dashboards.")
1116 ;; This package includes software that was released under the Expat
1117 ;; license, but the whole package is released under GPL version 2 or
1118 ;; later.
1119 (license license:gpl2+)))
1120
1121 (define-public r-shinyfiles
1122 (package
1123 (name "r-shinyfiles")
1124 (version "0.8.0")
1125 (source
1126 (origin
1127 (method url-fetch)
1128 (uri (cran-uri "shinyFiles" version))
1129 (sha256
1130 (base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w"))))
1131 (properties `((upstream-name . "shinyFiles")))
1132 (build-system r-build-system)
1133 (propagated-inputs
1134 `(("r-fs" ,r-fs)
1135 ("r-htmltools" ,r-htmltools)
1136 ("r-jsonlite" ,r-jsonlite)
1137 ("r-shiny" ,r-shiny)
1138 ("r-tibble" ,r-tibble)))
1139 (home-page "https://github.com/thomasp85/shinyFiles")
1140 (synopsis "Server-side file system viewer for Shiny")
1141 (description
1142 "This package provides functionality for client-side navigation of the
1143 server side file system in shiny apps. In case the app is running locally
1144 this gives the user direct access to the file system without the need to
1145 \"download\" files to a temporary location. Both file and folder selection as
1146 well as file saving is available.")
1147 (license license:gpl2+)))
1148
1149 (define-public r-shinythemes
1150 (package
1151 (name "r-shinythemes")
1152 (version "1.1.2")
1153 (source
1154 (origin
1155 (method url-fetch)
1156 (uri (cran-uri "shinythemes" version))
1157 (sha256
1158 (base32
1159 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
1160 (properties `((upstream-name . "shinythemes")))
1161 (build-system r-build-system)
1162 (propagated-inputs `(("r-shiny" ,r-shiny)))
1163 (home-page "https://rstudio.github.io/shinythemes/")
1164 (synopsis "Themes for Shiny")
1165 (description
1166 "This package provides themes for use with Shiny. It includes several
1167 Bootstrap themes, which are packaged for use with Shiny applications.")
1168 ;; The package is released under version 3 of the GPL, but it includes
1169 ;; source files that are covered by the Expat license. It also includes
1170 ;; fonts under SIL or the ASL.
1171 (license (list license:gpl3 license:expat
1172 license:silofl1.1 license:asl2.0))))
1173
1174 ;; The package sources include minified variants of d3.js and non-minified
1175 ;; source code of d3-jetpack.
1176 (define-public r-d3r
1177 (package
1178 (name "r-d3r")
1179 (version "0.8.7")
1180 (source
1181 (origin
1182 (method url-fetch)
1183 (uri (cran-uri "d3r" version))
1184 (sha256
1185 (base32
1186 "0xl3im76lp7pd5lhp8jfyqdm4j4zvjrx5a5fl81xv2cf7x3n4f2a"))))
1187 (build-system r-build-system)
1188 (arguments
1189 `(#:modules ((guix build utils)
1190 (guix build r-build-system)
1191 (srfi srfi-1)
1192 (ice-9 popen))
1193 #:phases
1194 (modify-phases %standard-phases
1195 (add-after 'unpack 'process-javascript
1196 (lambda* (#:key inputs #:allow-other-keys)
1197 (with-directory-excursion "inst/www/d3/"
1198 (call-with-values
1199 (lambda ()
1200 (unzip2
1201 `((,(assoc-ref inputs "d3.v3.js")
1202 "v3/dist/d3.min.js")
1203 (,(assoc-ref inputs "d3.v4.js")
1204 "v4/dist/d3.min.js")
1205 (,(assoc-ref inputs "d3.v5.js")
1206 "v5/dist/d3.min.js"))))
1207 (lambda (sources targets)
1208 (for-each (lambda (source target)
1209 (format #t "Processing ~a --> ~a~%"
1210 source target)
1211 (delete-file target)
1212 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1213 (call-with-output-file target
1214 (lambda (port)
1215 (dump-port minified port)))))
1216 sources targets))))
1217 #t)))))
1218 (propagated-inputs
1219 `(("r-dplyr" ,r-dplyr)
1220 ("r-htmltools" ,r-htmltools)
1221 ("r-tidyr" ,r-tidyr)))
1222 (native-inputs
1223 `(("uglify-js" ,uglify-js)
1224 ("d3.v3.js"
1225 ,(origin
1226 (method url-fetch)
1227 (uri "https://d3js.org/d3.v3.js")
1228 (sha256
1229 (base32
1230 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1231 ("d3.v4.js"
1232 ,(origin
1233 (method url-fetch)
1234 (uri "https://d3js.org/d3.v4.js")
1235 (sha256
1236 (base32
1237 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1238 ("d3.v5.js"
1239 ,(origin
1240 (method url-fetch)
1241 (uri "https://d3js.org/d3.v5.js")
1242 (sha256
1243 (base32
1244 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1245 (home-page "https://github.com/timelyportfolio/d3r")
1246 (synopsis "d3.js utilities for R")
1247 (description
1248 "This package provides a suite of functions to help ease the use of the
1249 d3.js visualization library in R. These helpers include
1250 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1251 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1252 R objects into the JSON format that the d3.js library expects.")
1253 (license license:bsd-3)))
1254
1255 ;; We use the latest commit here because the last release was in 2016 while
1256 ;; the latest commit was in 2018.
1257 (define-public r-sankeyd3
1258 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1259 (revision "1"))
1260 (package
1261 (name "r-sankeyd3")
1262 (version (git-version "0.3.2" revision commit))
1263 (source
1264 (origin
1265 (method git-fetch)
1266 (uri (git-reference
1267 (url "https://github.com/fbreitwieser/sankeyD3.git")
1268 (commit commit)))
1269 (file-name (git-file-name name version))
1270 (sha256
1271 (base32
1272 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1273 (build-system r-build-system)
1274 (propagated-inputs
1275 `(("r-d3r" ,r-d3r)
1276 ("r-htmlwidgets" ,r-htmlwidgets)
1277 ("r-shiny" ,r-shiny)
1278 ("r-magrittr" ,r-magrittr)))
1279 (home-page "https://github.com/fbreitwieser/sankeyD3")
1280 (synopsis "Sankey network graphs from R")
1281 (description
1282 "This package provides an R library to generate Sankey network graphs
1283 in R and Shiny via the D3 visualization library.")
1284 ;; The R code is licensed under GPLv3+. It includes the non-minified
1285 ;; JavaScript source code of d3-sankey, which is released under the
1286 ;; 3-clause BSD license.
1287 (license (list license:gpl3+ license:bsd-3)))))
1288
1289 (define-public r-crosstalk
1290 (package
1291 (name "r-crosstalk")
1292 (version "1.1.0.1")
1293 (source
1294 (origin
1295 (method url-fetch)
1296 (uri (cran-uri "crosstalk" version))
1297 (sha256
1298 (base32
1299 "03ihj7cimkklrbad9zic78xsrfcisygmgy859hqnx0hiph80p9rn"))))
1300 (build-system r-build-system)
1301 (propagated-inputs
1302 `(("r-htmltools" ,r-htmltools)
1303 ("r-jsonlite" ,r-jsonlite)
1304 ("r-lazyeval" ,r-lazyeval)
1305 ("r-r6" ,r-r6)))
1306 (home-page "https://rstudio.github.io/crosstalk/")
1307 (synopsis "Inter-widget interactivity for HTML widgets")
1308 (description
1309 "This package provides building blocks for allowing HTML widgets to
1310 communicate with each other, with Shiny or without (i.e. static @code{.html}
1311 files). It currently supports linked brushing and filtering.")
1312 (license license:expat)))
1313
1314 (define-public r-rook
1315 (package
1316 (name "r-rook")
1317 (version "1.1-1")
1318 (source
1319 (origin
1320 (method url-fetch)
1321 (uri (cran-uri "Rook" version))
1322 (sha256
1323 (base32
1324 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1325 (properties `((upstream-name . "Rook")))
1326 (build-system r-build-system)
1327 (propagated-inputs `(("r-brew" ,r-brew)))
1328 (home-page "https://cran.r-project.org/web/packages/Rook")
1329 (synopsis "Web server interface for R")
1330 (description
1331 "This package contains the Rook specification and convenience software
1332 for building and running Rook applications. A Rook application is an R
1333 reference class object that implements a @code{call} method or an R closure
1334 that takes exactly one argument, an environment, and returns a list with three
1335 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1336 (license license:gpl2)))
1337
1338 (define-public r-miniui
1339 (package
1340 (name "r-miniui")
1341 (version "0.1.1.1")
1342 (source
1343 (origin
1344 (method url-fetch)
1345 (uri (cran-uri "miniUI" version))
1346 (sha256
1347 (base32
1348 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1349 (properties `((upstream-name . "miniUI")))
1350 (build-system r-build-system)
1351 (propagated-inputs
1352 `(("r-htmltools" ,r-htmltools)
1353 ("r-shiny" ,r-shiny)))
1354 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1355 (synopsis "Shiny UI widgets for small screens")
1356 (description
1357 "This package provides UI widget and layout functions for writing Shiny apps that
1358 work well on small screens.")
1359 (license license:gpl3)))
1360
1361 (define-public r-feather
1362 (package
1363 (name "r-feather")
1364 (version "0.3.5")
1365 (source
1366 (origin
1367 (method url-fetch)
1368 (uri (cran-uri "feather" version))
1369 (sha256
1370 (base32
1371 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1372 (build-system r-build-system)
1373 (propagated-inputs
1374 `(("r-hms" ,r-hms)
1375 ("r-rcpp" ,r-rcpp)
1376 ("r-tibble" ,r-tibble)))
1377 (home-page "https://github.com/wesm/feather")
1378 (synopsis "R Bindings to the Feather API")
1379 (description "Read and write feather files, a lightweight binary columnar
1380 data store designed for maximum speed.")
1381 (license license:asl2.0)))
1382
1383 (define-public r-maps
1384 (package
1385 (name "r-maps")
1386 (version "3.3.0")
1387 (source
1388 (origin
1389 (method url-fetch)
1390 (uri (cran-uri "maps" version))
1391 (sha256
1392 (base32
1393 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1394 (build-system r-build-system)
1395 (home-page "https://cran.r-project.org/web/packages/maps")
1396 (synopsis "Draw geographical maps")
1397 (description "This package provides an R module for display of maps.
1398 Projection code and larger maps are in separate packages (@code{mapproj} and
1399 @code{mapdata}).")
1400 (license license:gpl2)))
1401
1402 (define-public r-mapproj
1403 (package
1404 (name "r-mapproj")
1405 (version "1.2.7")
1406 (source
1407 (origin
1408 (method url-fetch)
1409 (uri (cran-uri "mapproj" version))
1410 (sha256
1411 (base32
1412 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
1413 (build-system r-build-system)
1414 (propagated-inputs `(("r-maps" ,r-maps)))
1415 (home-page "https://cran.r-project.org/web/packages/mapproj")
1416 (synopsis "Map projection in R")
1417 (description "This package converts latitude/longitude into projected
1418 coordinates.")
1419 (license (list license:gpl2 ; The R interface
1420 (license:non-copyleft ; The C code
1421 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1422 "Lucent Public License Version 1.02")))))
1423
1424 (define-public r-rgooglemaps
1425 (package
1426 (name "r-rgooglemaps")
1427 (version "1.4.5.3")
1428 (source
1429 (origin
1430 (method url-fetch)
1431 (uri (cran-uri "RgoogleMaps" version))
1432 (sha256
1433 (base32
1434 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
1435 (properties `((upstream-name . "RgoogleMaps")))
1436 (build-system r-build-system)
1437 (propagated-inputs
1438 `(("r-png" ,r-png)
1439 ("r-sp" ,r-sp)))
1440 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1441 (synopsis "Use Google Maps in R")
1442 (description "This package serves two purposes:
1443 @enumerate
1444 @item Provide a comfortable R interface to query the Google server for static
1445 maps, and
1446 @item Use the map as a background image to overlay plots within R. This
1447 requires proper coordinate scaling.
1448 @end enumerate\n")
1449 (license license:gpl2+)))
1450
1451 (define-public r-geosphere
1452 (package
1453 (name "r-geosphere")
1454 (version "1.5-10")
1455 (source
1456 (origin
1457 (method url-fetch)
1458 (uri (cran-uri "geosphere" version))
1459 (sha256
1460 (base32
1461 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1462 (build-system r-build-system)
1463 (propagated-inputs `(("r-sp" ,r-sp)))
1464 (home-page "https://cran.r-project.org/web/packages/geosphere")
1465 (synopsis "Spherical trigonometry")
1466 (description "This package computes spherical trigonometry for geographic
1467 applications. That is, compute distances and related measures for angular
1468 (longitude/latitude) locations.")
1469 (license license:gpl3+)))
1470
1471 (define-public r-jpeg
1472 (package
1473 (name "r-jpeg")
1474 (version "0.1-8.1")
1475 (source
1476 (origin
1477 (method url-fetch)
1478 (uri (cran-uri "jpeg" version))
1479 (sha256
1480 (base32
1481 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1482 (build-system r-build-system)
1483 (inputs `(("libjpeg" ,libjpeg)))
1484 (home-page "https://www.rforge.net/jpeg/")
1485 (synopsis "Read and write JPEG images with R")
1486 (description "This package provides a way to read, write and display
1487 bitmap images stored in the JPEG format with R. It can read and write both
1488 files and in-memory raw vectors.")
1489 (license license:gpl2+)))
1490
1491 (define-public r-ggmap
1492 (package
1493 (name "r-ggmap")
1494 (version "3.0.0")
1495 (source
1496 (origin
1497 (method url-fetch)
1498 (uri (cran-uri "ggmap" version))
1499 (sha256
1500 (base32
1501 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1502 (build-system r-build-system)
1503 (propagated-inputs
1504 `(("r-bitops" ,r-bitops)
1505 ("r-digest" ,r-digest)
1506 ("r-dplyr" ,r-dplyr)
1507 ("r-ggplot2" ,r-ggplot2)
1508 ("r-glue" ,r-glue)
1509 ("r-httr" ,r-httr)
1510 ("r-jpeg" ,r-jpeg)
1511 ("r-magrittr" ,r-magrittr)
1512 ("r-plyr" ,r-plyr)
1513 ("r-png" ,r-png)
1514 ("r-purrr" ,r-purrr)
1515 ("r-rgooglemaps" ,r-rgooglemaps)
1516 ("r-rjson" ,r-rjson)
1517 ("r-scales" ,r-scales)
1518 ("r-stringr" ,r-stringr)
1519 ("r-tibble" ,r-tibble)
1520 ("r-tidyr" ,r-tidyr)))
1521 (home-page "https://github.com/dkahle/ggmap")
1522 (synopsis "Spatial visualization with ggplot2")
1523 (description "This package provides a collection of functions to visualize
1524 spatial data and models on top of static maps from various online sources (e.g
1525 Google Maps and Stamen Maps). It includes tools common to those tasks,
1526 including functions for geolocation and routing.")
1527 (license license:gpl2)))
1528
1529 (define-public r-haven
1530 (package
1531 (name "r-haven")
1532 (version "2.2.0")
1533 (source
1534 (origin
1535 (method url-fetch)
1536 (uri (cran-uri "haven" version))
1537 (sha256
1538 (base32
1539 "0g9d6mxqmrw2zdms78jpx2sx73pczlyy771v1h5hmxqz9sqyk7hr"))))
1540 (build-system r-build-system)
1541 (inputs
1542 `(("zlib" ,zlib)))
1543 (propagated-inputs
1544 `(("r-forcats" ,r-forcats)
1545 ("r-hms" ,r-hms)
1546 ("r-rcpp" ,r-rcpp)
1547 ("r-rlang" ,r-rlang)
1548 ("r-readr" ,r-readr)
1549 ("r-tibble" ,r-tibble)
1550 ("r-tidyselect" ,r-tidyselect)))
1551 (home-page "https://haven.tidyverse.org")
1552 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1553 (description
1554 "This package lets you mport foreign statistical formats into R via the
1555 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1556 (license license:expat)))
1557
1558 (define-public r-amap
1559 (package
1560 (name "r-amap")
1561 (version "0.8-18")
1562 (source (origin
1563 (method url-fetch)
1564 (uri (cran-uri "amap" version))
1565 (sha256
1566 (base32
1567 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
1568 (build-system r-build-system)
1569 (native-inputs
1570 `(("gfortran" ,gfortran)))
1571 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1572 (synopsis "Another multidimensional analysis package")
1573 (description "This package provides tools for clustering and principal
1574 component analysis (with robust methods, and parallelized functions).")
1575 (license license:gpl2+)))
1576
1577 (define-public r-ape
1578 (package
1579 (name "r-ape")
1580 (version "5.3")
1581 (source
1582 (origin
1583 (method url-fetch)
1584 (uri (cran-uri "ape" version))
1585 (sha256
1586 (base32
1587 "08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08"))))
1588 (build-system r-build-system)
1589 (propagated-inputs
1590 `(("r-lattice" ,r-lattice)
1591 ("r-nlme" ,r-nlme)
1592 ("r-rcpp" ,r-rcpp)))
1593 (home-page "http://ape-package.ird.fr/")
1594 (synopsis "Analyses of phylogenetics and evolution")
1595 (description
1596 "This package provides functions for reading, writing, plotting, and
1597 manipulating phylogenetic trees, analyses of comparative data in a
1598 phylogenetic framework, ancestral character analyses, analyses of
1599 diversification and macroevolution, computing distances from DNA sequences,
1600 and several other tools.")
1601 (license license:gpl2+)))
1602
1603 (define-public r-abbyyr
1604 (package
1605 (name "r-abbyyr")
1606 (version "0.5.5")
1607 (source
1608 (origin
1609 (method url-fetch)
1610 (uri (cran-uri "abbyyR" version))
1611 (sha256
1612 (base32
1613 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1614 (properties `((upstream-name . "abbyyR")))
1615 (build-system r-build-system)
1616 (propagated-inputs
1617 `(("r-curl" ,r-curl)
1618 ("r-httr" ,r-httr)
1619 ("r-plyr" ,r-plyr)
1620 ("r-progress" ,r-progress)
1621 ("r-readr" ,r-readr)
1622 ("r-xml" ,r-xml)))
1623 (home-page "https://github.com/soodoku/abbyyR")
1624 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1625 (description
1626 "This package provides tools to get text from images of text using Abbyy
1627 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1628 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1629 passports and get the results in a variety of formats including plain text and
1630 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1631 (license license:expat)))
1632
1633 (define-public r-colorspace
1634 (package
1635 (name "r-colorspace")
1636 (version "1.4-1")
1637 (source
1638 (origin
1639 (method url-fetch)
1640 (uri (cran-uri "colorspace" version))
1641 (sha256
1642 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1643 (build-system r-build-system)
1644 (home-page "https://cran.r-project.org/web/packages/colorspace")
1645 (synopsis "Color space manipulation")
1646 (description
1647 "This package carries out a mapping between assorted color spaces
1648 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1649 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1650 colors are provided.")
1651 (license license:bsd-3)))
1652
1653 (define-public r-glue
1654 (package
1655 (name "r-glue")
1656 (version "1.4.0")
1657 (source
1658 (origin
1659 (method url-fetch)
1660 (uri (cran-uri "glue" version))
1661 (sha256
1662 (base32
1663 "1hb9j2519jv9zgkgjb25hnqi22i7zxnaksqd16m4nxa1f6gl0v7a"))))
1664 (build-system r-build-system)
1665 ;; knitr depends on glue, so we can't add knitr here to build the
1666 ;; vignettes.
1667 #;
1668 (native-inputs
1669 `(("r-knitr" ,r-knitr)))
1670 (home-page "https://github.com/tidyverse/glue")
1671 (synopsis "Interpreted string literals")
1672 (description
1673 "This package provides an implementation of interpreted string literals,
1674 inspired by Python's Literal String Interpolation (PEP-0498) and
1675 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1676 (license license:expat)))
1677
1678 (define-public r-pastecs
1679 (package
1680 (name "r-pastecs")
1681 (version "1.3.21")
1682 (source (origin
1683 (method url-fetch)
1684 (uri (cran-uri "pastecs" version))
1685 (sha256
1686 (base32
1687 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1688 (build-system r-build-system)
1689 (propagated-inputs
1690 `(("r-boot" ,r-boot)))
1691 (home-page "http://www.sciviews.org/pastecs")
1692 (synopsis "Analysis of space-time ecological series")
1693 (description
1694 "This package provides functions for regulation, decomposition and analysis
1695 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1696 initiative to bring PASSTEC 2000 functionalities to R.")
1697 (license license:gpl2+)))
1698
1699 (define-public r-plogr
1700 (package
1701 (name "r-plogr")
1702 (version "0.2.0")
1703 (source
1704 (origin
1705 (method url-fetch)
1706 (uri (cran-uri "plogr" version))
1707 (sha256
1708 (base32
1709 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1710 (build-system r-build-system)
1711 (home-page "https://github.com/krlmlr/plogr")
1712 (synopsis "R bindings for the plog C++ logging library")
1713 (description
1714 "This package provides the header files for a stripped-down version of
1715 the plog header-only C++ logging library, and a method to log to R's standard
1716 error stream.")
1717 (license license:expat)))
1718
1719 (define-public r-pls
1720 (package
1721 (name "r-pls")
1722 (version "2.7-2")
1723 (source
1724 (origin
1725 (method url-fetch)
1726 (uri (cran-uri "pls" version))
1727 (sha256
1728 (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
1729 (build-system r-build-system)
1730 (home-page "https://mevik.net/work/software/pls.html")
1731 (synopsis "Partial Least Squares and Principal Component Regression")
1732 (description
1733 "The pls package implements multivariate regression methods: Partial Least
1734 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1735 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1736
1737 @itemize
1738 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1739 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1740 @item multi-response models (or @dfn{PLS2})
1741 @item flexible cross-validation
1742 @item Jackknife variance estimates of regression coefficients
1743 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1744 (R)MSEP, R², and correlation loadings
1745 @item formula interface, modelled after @code{lm()}, with methods for predict,
1746 print, summary, plot, update, etc.
1747 @item extraction functions for coefficients, scores, and loadings
1748 @item MSEP, RMSEP, and R² estimates
1749 @item multiplicative scatter correction (@dfn{MSC})
1750 @end itemize\n")
1751 (license license:gpl2)))
1752
1753 (define-public r-ps
1754 (package
1755 (name "r-ps")
1756 (version "1.3.2")
1757 (source
1758 (origin
1759 (method url-fetch)
1760 (uri (cran-uri "ps" version))
1761 (sha256
1762 (base32 "0127q6pw9iw8hhcfp231gmdh29nahh2n5jzc38avrzy7yrm4bwl9"))))
1763 (build-system r-build-system)
1764 (home-page "https://ps.r-lib.org")
1765 (synopsis "List, query, and manipulate system processes")
1766 (description
1767 "The ps package implements an API to list, query, and manipulate system
1768 processes. Most of its code is based on the @code{psutil} Python package.")
1769 (license license:bsd-3)))
1770
1771 (define-public r-pkgbuild
1772 (package
1773 (name "r-pkgbuild")
1774 (version "1.0.7")
1775 (source
1776 (origin
1777 (method url-fetch)
1778 (uri (cran-uri "pkgbuild" version))
1779 (sha256
1780 (base32 "0wd9678yp6yi73n92f58wi9jc19gdq5cmbj65l6pifh2haikifr9"))))
1781 (build-system r-build-system)
1782 (propagated-inputs
1783 `(("r-callr" ,r-callr)
1784 ("r-cli" ,r-cli)
1785 ("r-crayon" ,r-crayon)
1786 ("r-desc" ,r-desc)
1787 ("r-prettyunits" ,r-prettyunits)
1788 ("r-r6" ,r-r6)
1789 ("r-rprojroot" ,r-rprojroot)
1790 ("r-withr" ,r-withr)))
1791 (home-page "https://github.com/r-pkgs/pkgbuild")
1792 (synopsis "Find tools needed to build R packages")
1793 (description
1794 "This package provides functions used to build R packages. It locates
1795 compilers needed to build R packages on various platforms and ensures the PATH
1796 is configured appropriately so R can use them.")
1797 (license license:gpl3)))
1798
1799 (define-public r-pkgload
1800 (package
1801 (name "r-pkgload")
1802 (version "1.0.2")
1803 (source
1804 (origin
1805 (method url-fetch)
1806 (uri (cran-uri "pkgload" version))
1807 (sha256
1808 (base32
1809 "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
1810 (build-system r-build-system)
1811 (propagated-inputs
1812 `(("r-desc" ,r-desc)
1813 ("r-pkgbuild" ,r-pkgbuild)
1814 ("r-rlang" ,r-rlang)
1815 ("r-rprojroot" ,r-rprojroot)
1816 ("r-rstudioapi" ,r-rstudioapi)
1817 ("r-withr" ,r-withr)))
1818 (home-page "https://github.com/r-lib/pkgload")
1819 (synopsis "Simulate package installation and attach")
1820 (description
1821 "This package simulates the process of installing a package and then
1822 attaching it. This is a key part of the @code{devtools} package as it allows
1823 you to rapidly iterate while developing a package.")
1824 (license license:gpl3)))
1825
1826 (define-public r-rcpp
1827 (package
1828 (name "r-rcpp")
1829 (version "1.0.4.6")
1830 (source
1831 (origin
1832 (method url-fetch)
1833 (uri (cran-uri "Rcpp" version))
1834 (sha256
1835 (base32 "00mk23zmrqn1c4mk9d6csjcbnl12wd7yicjk2ikmw5dyvdfngbs5"))))
1836 (build-system r-build-system)
1837 (home-page "http://www.rcpp.org")
1838 (synopsis "Seamless R and C++ integration")
1839 (description
1840 "The Rcpp package provides R functions as well as C++ classes which offer
1841 a seamless integration of R and C++. Many R data types and objects can be
1842 mapped back and forth to C++ equivalents which facilitates both writing of new
1843 code as well as easier integration of third-party libraries. Documentation
1844 about Rcpp is provided by several vignettes included in this package, via the
1845 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
1846 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
1847 @code{citation(\"Rcpp\")} for details on these last two.")
1848 (license license:gpl2+)))
1849
1850 (define-public r-bindr
1851 (package
1852 (name "r-bindr")
1853 (version "0.1.1")
1854 (source
1855 (origin
1856 (method url-fetch)
1857 (uri (cran-uri "bindr" version))
1858 (sha256
1859 (base32
1860 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
1861 (build-system r-build-system)
1862 (home-page "https://github.com/krlmlr/bindr")
1863 (synopsis "Parametrized active bindings")
1864 (description
1865 "This package provides a simple interface for creating active bindings
1866 where the bound function accepts additional arguments.")
1867 (license license:expat)))
1868
1869 (define-public r-bindrcpp
1870 (package
1871 (name "r-bindrcpp")
1872 (version "0.2.2")
1873 (source
1874 (origin
1875 (method url-fetch)
1876 (uri (cran-uri "bindrcpp" version))
1877 (sha256
1878 (base32
1879 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
1880 (build-system r-build-system)
1881 (propagated-inputs
1882 `(("r-bindr" ,r-bindr)
1883 ("r-plogr" ,r-plogr)
1884 ("r-rcpp" ,r-rcpp)))
1885 (home-page "https://github.com/krlmlr/bindrcpp")
1886 (synopsis "Rcpp interface to active bindings")
1887 (description
1888 "This package provides an easy way to fill an environment with active
1889 bindings that call a C++ function.")
1890 (license license:expat)))
1891
1892 (define-public r-auc
1893 (package
1894 (name "r-auc")
1895 (version "0.3.0")
1896 (source
1897 (origin
1898 (method url-fetch)
1899 (uri (cran-uri "AUC" version))
1900 (sha256
1901 (base32
1902 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
1903 (properties `((upstream-name . "AUC")))
1904 (build-system r-build-system)
1905 (home-page "https://cran.r-project.org/web/packages/AUC")
1906 (synopsis "Compute the area under the curve of selected measures")
1907 (description
1908 "This package includes functions to compute the area under the curve of
1909 selected measures: the area under the sensitivity curve (AUSEC), the area
1910 under the specificity curve (AUSPC), the area under the accuracy
1911 curve (AUACC), and the area under the receiver operating characteristic
1912 curve (AUROC). The curves can also be visualized. Support for partial areas
1913 is provided.")
1914 (license license:gpl2+)))
1915
1916 (define-public r-calibrate
1917 (package
1918 (name "r-calibrate")
1919 (version "1.7.5")
1920 (source
1921 (origin
1922 (method url-fetch)
1923 (uri (cran-uri "calibrate" version))
1924 (sha256
1925 (base32 "1s423nr176l2sc66wp7hzgqkv7c2bq8d2bjrrvrrm5qa9y3zdx1k"))))
1926 (build-system r-build-system)
1927 (propagated-inputs
1928 `(("r-mass" ,r-mass)))
1929 (home-page "https://cran.r-project.org/web/packages/calibrate")
1930 (synopsis "Calibration of scatterplot and biplot axes")
1931 (description
1932 "This is a package for drawing calibrated scales with tick marks
1933 on (non-orthogonal) variable vectors in scatterplots and biplots.")
1934 (license license:gpl2)))
1935
1936 (define-public r-shape
1937 (package
1938 (name "r-shape")
1939 (version "1.4.4")
1940 (source
1941 (origin
1942 (method url-fetch)
1943 (uri (cran-uri "shape" version))
1944 (sha256
1945 (base32
1946 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
1947 (build-system r-build-system)
1948 (home-page "https://cran.r-project.org/web/packages/shape")
1949 (synopsis "Functions for plotting graphical shapes")
1950 (description
1951 "This package provides functions for plotting graphical shapes such as
1952 ellipses, circles, cylinders, arrows, ...")
1953 (license license:gpl3+)))
1954
1955 (define-public r-globaloptions
1956 (package
1957 (name "r-globaloptions")
1958 (version "0.1.1")
1959 (source
1960 (origin
1961 (method url-fetch)
1962 (uri (cran-uri "GlobalOptions" version))
1963 (sha256
1964 (base32 "0x89hfz80avq4zcskxl71i4zi0mgniqqxfrvz050aa2189wfyja2"))))
1965 (properties `((upstream-name . "GlobalOptions")))
1966 (build-system r-build-system)
1967 (home-page "https://github.com/jokergoo/GlobalOptions")
1968 (synopsis "Generate functions to get or set global options")
1969 (description
1970 "This package provides more controls on the option values such as
1971 validation and filtering on the values, making options invisible or private.")
1972 (license license:gpl2+)))
1973
1974 (define-public r-circlize
1975 (package
1976 (name "r-circlize")
1977 (version "0.4.8")
1978 (source
1979 (origin
1980 (method url-fetch)
1981 (uri (cran-uri "circlize" version))
1982 (sha256
1983 (base32
1984 "0jvr9hmxyhg0zx101iiqkrg8wfaj86kp62xpv42n2j9fkn5r1mi2"))))
1985 (build-system r-build-system)
1986 (propagated-inputs
1987 `(("r-colorspace" ,r-colorspace)
1988 ("r-globaloptions" ,r-globaloptions)
1989 ("r-shape" ,r-shape)))
1990 (home-page "https://github.com/jokergoo/circlize")
1991 (synopsis "Circular visualization")
1992 (description
1993 "Circular layout is an efficient way to visualise huge amounts of
1994 information. This package provides an implementation of circular layout
1995 generation in R as well as an enhancement of available software. Its
1996 flexibility is based on the usage of low-level graphics functions such that
1997 self-defined high-level graphics can be easily implemented by users for
1998 specific purposes. Together with the seamless connection between the powerful
1999 computational and visual environment in R, it gives users more convenience and
2000 freedom to design figures for better understanding complex patterns behind
2001 multi-dimensional data.")
2002 (license license:gpl2+)))
2003
2004 (define-public r-powerlaw
2005 (package
2006 (name "r-powerlaw")
2007 (version "0.70.6")
2008 (source
2009 (origin
2010 (method url-fetch)
2011 (uri (cran-uri "poweRlaw" version))
2012 (sha256
2013 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2014 (properties `((upstream-name . "poweRlaw")))
2015 (build-system r-build-system)
2016 (propagated-inputs
2017 `(("r-pracma" ,r-pracma)))
2018 (native-inputs
2019 `(("r-knitr" ,r-knitr)))
2020 (home-page "https://github.com/csgillespie/poweRlaw")
2021 (synopsis "Tools for the analysis of heavy tailed distributions")
2022 (description
2023 "This package provides an implementation of maximum likelihood estimators
2024 for a variety of heavy tailed distributions, including both the discrete and
2025 continuous power law distributions. Additionally, a goodness-of-fit based
2026 approach is used to estimate the lower cut-off for the scaling region.")
2027 ;; Any of these GPL versions.
2028 (license (list license:gpl2 license:gpl3))))
2029
2030 (define-public r-compare
2031 (package
2032 (name "r-compare")
2033 (version "0.2-6")
2034 (source
2035 (origin
2036 (method url-fetch)
2037 (uri (cran-uri "compare" version))
2038 (sha256
2039 (base32
2040 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
2041 (build-system r-build-system)
2042 (home-page "https://cran.r-project.org/web/packages/compare")
2043 (synopsis "Comparing objects for differences")
2044 (description
2045 "This package provides functions to compare a model object to a
2046 comparison object. If the objects are not identical, the functions can be
2047 instructed to explore various modifications of the objects (e.g., sorting
2048 rows, dropping names) to see if the modified versions are identical.")
2049 (license license:gpl2+)))
2050
2051 (define-public r-dendextend
2052 (package
2053 (name "r-dendextend")
2054 (version "1.13.4")
2055 (source
2056 (origin
2057 (method url-fetch)
2058 (uri (cran-uri "dendextend" version))
2059 (sha256
2060 (base32
2061 "1pjbz6sb4pgh3d5pm53vmf3q8y6lq3hrgjd6547xxs3m63sb8mn4"))))
2062 (build-system r-build-system)
2063 (propagated-inputs
2064 `(("r-ggplot2" ,r-ggplot2)
2065 ("r-magrittr" ,r-magrittr)
2066 ("r-viridis" ,r-viridis)))
2067 (home-page "https://cran.r-project.org/web/packages/dendextend")
2068 (synopsis "Extending 'dendrogram' functionality in R")
2069 (description
2070 "This package offers a set of functions for extending @code{dendrogram}
2071 objects in R, letting you visualize and compare trees of hierarchical
2072 clusterings. You can adjust a tree's graphical parameters (the color, size,
2073 type, etc of its branches, nodes and labels) and visually and statistically
2074 compare different dendrograms to one another.")
2075 ;; Any of these versions
2076 (license (list license:gpl2 license:gpl3))))
2077
2078 (define-public r-getoptlong
2079 (package
2080 (name "r-getoptlong")
2081 (version "0.1.8")
2082 (source
2083 (origin
2084 (method url-fetch)
2085 (uri (cran-uri "GetoptLong" version))
2086 (sha256
2087 (base32
2088 "1l8xkvyl152bsyvxazsvx2sm1vkygn75x0lsg3sbg7xp6drdn3kc"))))
2089 (properties `((upstream-name . "GetoptLong")))
2090 (build-system r-build-system)
2091 (inputs
2092 `(("perl" ,perl)))
2093 (propagated-inputs
2094 `(("r-globaloptions" ,r-globaloptions)
2095 ("r-rjson" ,r-rjson)))
2096 (home-page "https://github.com/jokergoo/GetoptLong")
2097 (synopsis "Parsing command-line arguments and variable interpolation")
2098 (description
2099 "This is yet another command-line argument parser which wraps the
2100 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
2101 use in R. It also provides a simple way for variable interpolation in R.")
2102 (license license:gpl2+)))
2103
2104 (define-public r-fastmatch
2105 (package
2106 (name "r-fastmatch")
2107 (version "1.1-0")
2108 (source
2109 (origin
2110 (method url-fetch)
2111 (uri (cran-uri "fastmatch" version))
2112 (sha256
2113 (base32
2114 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
2115 (build-system r-build-system)
2116 (home-page "https://www.rforge.net/fastmatch")
2117 (synopsis "Fast match function")
2118 (description
2119 "This package provides a fast @code{match} replacement for cases that
2120 require repeated look-ups. It is slightly faster that R's built-in
2121 @code{match} function on first match against a table, but extremely fast on
2122 any subsequent lookup as it keeps the hash table in memory.")
2123 (license license:gpl2)))
2124
2125 (define-public r-ff
2126 (package
2127 (name "r-ff")
2128 (version "2.2-14.2")
2129 (source
2130 (origin
2131 (method url-fetch)
2132 (uri (cran-uri "ff" version))
2133 (sha256
2134 (base32
2135 "1r1pbrf5s4rdm3msxxr8fy1f2xjihqciclsnvxf59qzz6g1nmh7q"))))
2136 (build-system r-build-system)
2137 (propagated-inputs `(("r-bit" ,r-bit)))
2138 (home-page "http://ff.r-forge.r-project.org/")
2139 (synopsis "Memory-efficient storage of large data on disk and access functions")
2140 (description
2141 "This package provides data structures that are stored on disk but
2142 behave (almost) as if they were in RAM by transparently mapping only a section
2143 in main memory.")
2144 ;; error Architecture not supported.
2145 (supported-systems (delete "aarch64-linux" %supported-systems))
2146 (license license:gpl2)))
2147
2148 (define-public r-ffbase
2149 (package
2150 (name "r-ffbase")
2151 (version "0.12.8")
2152 (source
2153 (origin
2154 (method url-fetch)
2155 (uri (cran-uri "ffbase" version))
2156 (sha256
2157 (base32
2158 "0mjk7dkq1ginqqfvngzny747ggf9a8fd7kblq96n5ys1jrwjyqhq"))))
2159 (build-system r-build-system)
2160 (propagated-inputs
2161 `(("r-bit" ,r-bit)
2162 ("r-fastmatch" ,r-fastmatch)
2163 ("r-ff" ,r-ff)))
2164 (home-page "http://github.com/edwindj/ffbase")
2165 (synopsis "Basic statistical functions for package 'ff'")
2166 (description
2167 "This package extends the out of memory vectors of @code{ff} with
2168 statistical functions and other utilities to ease their usage.")
2169 (license license:gpl3)))
2170
2171 (define-public r-prettyunits
2172 (package
2173 (name "r-prettyunits")
2174 (version "1.1.1")
2175 (source
2176 (origin
2177 (method url-fetch)
2178 (uri (cran-uri "prettyunits" version))
2179 (sha256
2180 (base32
2181 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
2182 (build-system r-build-system)
2183 (home-page "https://github.com/gaborcsardi/prettyunits")
2184 (synopsis "Pretty, human readable formatting of quantities")
2185 (description
2186 "This package provides tools for pretty, human readable formatting of
2187 quantities.")
2188 (license license:expat)))
2189
2190 (define-public r-reshape
2191 (package
2192 (name "r-reshape")
2193 (version "0.8.8")
2194 (source
2195 (origin
2196 (method url-fetch)
2197 (uri (cran-uri "reshape" version))
2198 (sha256
2199 (base32
2200 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2201 (build-system r-build-system)
2202 (propagated-inputs
2203 `(("r-plyr" ,r-plyr)
2204 ("r-rcpp" ,r-rcpp)))
2205 (home-page "http://had.co.nz/reshape")
2206 (synopsis "Flexibly reshape data")
2207 (description
2208 "Flexibly restructure and aggregate data using just two functions:
2209 @code{melt} and @code{cast}. This package provides them.")
2210 (license license:expat)))
2211
2212 (define-public r-progress
2213 (package
2214 (name "r-progress")
2215 (version "1.2.2")
2216 (source
2217 (origin
2218 (method url-fetch)
2219 (uri (cran-uri "progress" version))
2220 (sha256
2221 (base32
2222 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2223 (build-system r-build-system)
2224 (propagated-inputs
2225 `(("r-crayon" ,r-crayon)
2226 ("r-hms" ,r-hms)
2227 ("r-prettyunits" ,r-prettyunits)
2228 ("r-r6" ,r-r6)))
2229 (home-page "https://github.com/gaborcsardi/progress")
2230 (synopsis "Terminal progress bars")
2231 (description
2232 "This package provides configurable progress bars. They may include
2233 percentage, elapsed time, and/or the estimated completion time. They work in
2234 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2235 package also provides a C++ API, that works with or without Rcpp.")
2236 (license license:expat)))
2237
2238 (define-public r-ggally
2239 (package
2240 (name "r-ggally")
2241 (version "1.5.0")
2242 (source
2243 (origin
2244 (method url-fetch)
2245 (uri (cran-uri "GGally" version))
2246 (sha256
2247 (base32
2248 "082s321zspg5al6acigwrhg4fsrmkkk5caabg662qbcy8v6n34h6"))))
2249 (properties `((upstream-name . "GGally")))
2250 (build-system r-build-system)
2251 (inputs
2252 `(("libressl" ,libressl)))
2253 (propagated-inputs
2254 `(("r-ggplot2" ,r-ggplot2)
2255 ("r-gtable" ,r-gtable)
2256 ("r-plyr" ,r-plyr)
2257 ("r-progress" ,r-progress)
2258 ("r-rcolorbrewer" ,r-rcolorbrewer)
2259 ("r-reshape" ,r-reshape)
2260 ("r-rlang" ,r-rlang)))
2261 (home-page "https://ggobi.github.io/ggally")
2262 (synopsis "Extension to ggplot2")
2263 (description
2264 "The R package ggplot2 is a plotting system based on the grammar of
2265 graphics. GGally extends ggplot2 by adding several functions to reduce the
2266 complexity of combining geometric objects with transformed data. Some of
2267 these functions include a pairwise plot matrix, a two group pairwise plot
2268 matrix, a parallel coordinates plot, a survival plot, and several functions to
2269 plot networks.")
2270 (license license:gpl2+)))
2271
2272 (define-public r-proxy
2273 (package
2274 (name "r-proxy")
2275 (version "0.4-24")
2276 (source
2277 (origin
2278 (method url-fetch)
2279 (uri (cran-uri "proxy" version))
2280 (sha256
2281 (base32
2282 "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
2283 (build-system r-build-system)
2284 (home-page "https://cran.r-project.org/web/packages/proxy")
2285 (synopsis "Distance and similarity measures")
2286 (description
2287 "This package provides an extensible framework for the efficient
2288 calculation of auto- and cross-proximities, along with implementations of the
2289 most popular ones.")
2290 (license license:gpl2)))
2291
2292 (define-public r-sp
2293 (package
2294 (name "r-sp")
2295 (version "1.4-1")
2296 (source
2297 (origin
2298 (method url-fetch)
2299 (uri (cran-uri "sp" version))
2300 (sha256
2301 (base32 "0fbh865r4py89g6ln8bslig2vbxxwa642p5k5g02rskyhajg35lg"))))
2302 (build-system r-build-system)
2303 (propagated-inputs
2304 `(("r-lattice" ,r-lattice)))
2305 (home-page "https://cran.r-project.org/web/packages/sp")
2306 (synopsis "Classes and methods for spatial data")
2307 (description
2308 "This package provides classes and methods for spatial data; the classes
2309 document where the spatial location information resides, for 2D or 3D data.
2310 Utility functions are provided, e.g. for plotting data as maps, spatial
2311 selection, as well as methods for retrieving coordinates, for subsetting,
2312 print, summary, etc.")
2313 (license license:gpl2+)))
2314
2315 (define-public r-rmtstat
2316 (package
2317 (name "r-rmtstat")
2318 (version "0.3")
2319 (source
2320 (origin
2321 (method url-fetch)
2322 (uri (cran-uri "RMTstat" version))
2323 (sha256
2324 (base32
2325 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2326 (properties `((upstream-name . "RMTstat")))
2327 (build-system r-build-system)
2328 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2329 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2330 (description
2331 "This package provides functions for working with the Tracy-Widom laws
2332 and other distributions related to the eigenvalues of large Wishart
2333 matrices.")
2334 (license license:bsd-3)))
2335
2336 (define-public r-rmpi
2337 (package
2338 (name "r-rmpi")
2339 (version "0.6-9")
2340 (source (origin
2341 (method url-fetch)
2342 (uri (cran-uri "Rmpi" version))
2343 (sha256
2344 (base32
2345 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2346 (properties `((upstream-name . "Rmpi")))
2347 (build-system r-build-system)
2348 (arguments
2349 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2350 #:phases (modify-phases %standard-phases
2351 (add-before 'install 'mpi-setup
2352 ,%openmpi-setup))))
2353 (inputs
2354 `(("openmpi" ,openmpi)))
2355 (native-inputs
2356 `(("pkg-config" ,pkg-config)))
2357 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2358 (synopsis "R interface to message-passing interface (MPI)")
2359 (description
2360 "This package provides an interface (wrapper) to MPI APIs. It also
2361 provides an interactive R manager and worker environment.")
2362 (license license:gpl2+)))
2363
2364 (define-public r-lmoments
2365 (package
2366 (name "r-lmoments")
2367 (version "1.3-1")
2368 (source
2369 (origin
2370 (method url-fetch)
2371 (uri (cran-uri "Lmoments" version))
2372 (sha256
2373 (base32
2374 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2375 (properties `((upstream-name . "Lmoments")))
2376 (build-system r-build-system)
2377 (propagated-inputs
2378 `(("r-rcpp" ,r-rcpp)
2379 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2380 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2381 (synopsis "L-moments and quantile mixtures")
2382 (description
2383 "This package contains functions to estimate L-moments and trimmed
2384 L-moments from the data. It also contains functions to estimate the
2385 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2386 quantile mixture from L-moments and trimmed L-moments.")
2387 (license license:gpl2)))
2388
2389 (define-public r-distillery
2390 (package
2391 (name "r-distillery")
2392 (version "1.0-7")
2393 (source
2394 (origin
2395 (method url-fetch)
2396 (uri (cran-uri "distillery" version))
2397 (sha256
2398 (base32
2399 "0w72vb3p51m0hwms9icwgy1xg3dplmpjrxibl2s92lpdrv737249"))))
2400 (build-system r-build-system)
2401 (home-page "https://ral.ucar.edu/staff/ericg/")
2402 (synopsis "Functions for confidence intervals and object information")
2403 (description
2404 "This package provides some very simple method functions for confidence
2405 interval calculation and to distill pertinent information from a potentially
2406 complex object; primarily used in common with the packages extRemes and
2407 SpatialVx.")
2408 (license license:gpl2+)))
2409
2410 (define-public r-extremes
2411 (package
2412 (name "r-extremes")
2413 (version "2.0-11")
2414 (source
2415 (origin
2416 (method url-fetch)
2417 (uri (cran-uri "extRemes" version))
2418 (sha256
2419 (base32
2420 "0hmgynxhzswqnhwb2sxrkczgam8c17s3vpxqc5bcz0bwczpxxyvm"))))
2421 (properties `((upstream-name . "extRemes")))
2422 (build-system r-build-system)
2423 (propagated-inputs
2424 `(("r-distillery" ,r-distillery)
2425 ("r-lmoments" ,r-lmoments)))
2426 (home-page "https://www.assessment.ucar.edu/toolkit/")
2427 (synopsis "Extreme value analysis")
2428 (description
2429 "ExtRemes is a suite of functions for carrying out analyses on the
2430 extreme values of a process of interest; be they block maxima over long blocks
2431 or excesses over a high threshold.")
2432 (license license:gpl2+)))
2433
2434 (define-public r-lmtest
2435 (package
2436 (name "r-lmtest")
2437 (version "0.9-37")
2438 (source
2439 (origin
2440 (method url-fetch)
2441 (uri (cran-uri "lmtest" version))
2442 (sha256
2443 (base32
2444 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2445 (build-system r-build-system)
2446 (propagated-inputs
2447 `(("r-zoo" ,r-zoo)))
2448 (native-inputs
2449 `(("gfortran" ,gfortran)))
2450 (home-page "https://cran.r-project.org/web/packages/lmtest")
2451 (synopsis "Testing linear regression models")
2452 (description
2453 "This package provides a collection of tests, data sets, and examples for
2454 diagnostic checking in linear regression models. Furthermore, some generic
2455 tools for inference in parametric models are provided.")
2456 ;; Either version is okay
2457 (license (list license:gpl2 license:gpl3))))
2458
2459 (define-public r-idr
2460 (package
2461 (name "r-idr")
2462 (version "1.2")
2463 (source (origin
2464 (method url-fetch)
2465 (uri (cran-uri "idr" version))
2466 (sha256
2467 (base32
2468 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2469 (build-system r-build-system)
2470 (home-page "https://cran.r-project.org/web/packages/idr/")
2471 (synopsis "Irreproducible discovery rate")
2472 (description
2473 "This is a package for estimating the copula mixture model and plotting
2474 correspondence curves in \"Measuring reproducibility of high-throughput
2475 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2476 by Li, Brown, Huang, and Bickel")
2477 (license license:gpl2+)))
2478
2479 (define-public r-inline
2480 (package
2481 (name "r-inline")
2482 (version "0.3.15")
2483 (source (origin
2484 (method url-fetch)
2485 (uri (cran-uri "inline" version))
2486 (sha256
2487 (base32
2488 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2489 (build-system r-build-system)
2490 (home-page "https://cran.r-project.org/web/packages/inline")
2491 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2492 (description
2493 "This package provides functionality to dynamically define R functions
2494 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2495 @code{.Call} calling conventions.")
2496 ;; Any version of the LGPL.
2497 (license license:lgpl3+)))
2498
2499 (define-public r-inum
2500 (package
2501 (name "r-inum")
2502 (version "1.0-1")
2503 (source (origin
2504 (method url-fetch)
2505 (uri (cran-uri "inum" version))
2506 (sha256
2507 (base32
2508 "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
2509 (build-system r-build-system)
2510 (propagated-inputs
2511 `(("r-libcoin" ,r-libcoin)))
2512 (home-page "https://cran.r-project.org/web/packages/inum/")
2513 (synopsis "Interval and enum-type representation of vectors")
2514 (description
2515 "This package provides an enum-type representation of vectors and
2516 representation of intervals, including a method of coercing variables
2517 in data frames.")
2518 (license license:gpl2)))
2519
2520 (define-public r-bdsmatrix
2521 (package
2522 (name "r-bdsmatrix")
2523 (version "1.3-4")
2524 (source
2525 (origin
2526 (method url-fetch)
2527 (uri (cran-uri "bdsmatrix" version))
2528 (sha256
2529 (base32
2530 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
2531 (properties `((upstream-name . "bdsmatrix")))
2532 (build-system r-build-system)
2533 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
2534 (synopsis "Routines for block diagonal symmetric matrices")
2535 (description
2536 "This package provides procedures to work with block diagonal symmetric
2537 matrices, a special case of sparse matrices.")
2538 (license license:lgpl2.0)))
2539
2540 (define-public r-bbmle
2541 (package
2542 (name "r-bbmle")
2543 (version "1.0.23.1")
2544 (source
2545 (origin
2546 (method url-fetch)
2547 (uri (cran-uri "bbmle" version))
2548 (sha256
2549 (base32
2550 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
2551 (build-system r-build-system)
2552 (propagated-inputs
2553 `(("r-bdsmatrix" ,r-bdsmatrix)
2554 ("r-lattice" ,r-lattice)
2555 ("r-mass" ,r-mass)
2556 ("r-matrix" ,r-matrix)
2557 ("r-mvtnorm" ,r-mvtnorm)
2558 ("r-numderiv" ,r-numderiv)))
2559 (home-page "https://cran.r-project.org/web/packages/bbmle")
2560 (synopsis "Tools for General Maximum Likelihood Estimation")
2561 (description
2562 "This package provides methods and functions for fitting maximum
2563 likelihood models in R. This package modifies and extends the @code{mle}
2564 classes in the @code{stats4} package.")
2565 ;; Any version of the GPL
2566 (license license:gpl2+)))
2567
2568 (define-public r-emdbook
2569 (package
2570 (name "r-emdbook")
2571 (version "1.3.12")
2572 (source
2573 (origin
2574 (method url-fetch)
2575 (uri (cran-uri "emdbook" version))
2576 (sha256
2577 (base32
2578 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
2579 (build-system r-build-system)
2580 (propagated-inputs
2581 `(("r-bbmle" ,r-bbmle)
2582 ("r-coda" ,r-coda)
2583 ("r-lattice" ,r-lattice)
2584 ("r-mass" ,r-mass)
2585 ("r-plyr" ,r-plyr)))
2586 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2587 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2588 (description
2589 "This package provides auxiliary functions and data sets for \"Ecological
2590 Models and Data\", a book presenting maximum likelihood estimation and related
2591 topics for ecologists (ISBN 978-0-691-12522-0).")
2592 ;; Any GPL version
2593 (license (list license:gpl2 license:gpl3))))
2594
2595 (define-public r-lpsolve
2596 (package
2597 (name "r-lpsolve")
2598 (version "5.6.15")
2599 (source
2600 (origin
2601 (method url-fetch)
2602 (uri (cran-uri "lpSolve" version))
2603 (sha256
2604 (base32
2605 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
2606 (properties `((upstream-name . "lpSolve")))
2607 (build-system r-build-system)
2608 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2609 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2610 (description
2611 "Lp_solve is software for solving linear, integer and mixed integer
2612 programs. This implementation supplies a \"wrapper\" function in C and some R
2613 functions that solve general linear/integer problems, assignment problems, and
2614 transportation problems.")
2615 (license license:lgpl2.0)))
2616
2617 (define-public r-limsolve
2618 (package
2619 (name "r-limsolve")
2620 (version "1.5.6")
2621 (source
2622 (origin
2623 (method url-fetch)
2624 (uri (cran-uri "limSolve" version))
2625 (sha256
2626 (base32
2627 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2628 (properties `((upstream-name . "limSolve")))
2629 (build-system r-build-system)
2630 (propagated-inputs
2631 `(("r-lpsolve" ,r-lpsolve)
2632 ("r-mass" ,r-mass)
2633 ("r-quadprog" ,r-quadprog)))
2634 (native-inputs `(("gfortran" ,gfortran)))
2635 (home-page "https://cran.r-project.org/web/packages/limSolve")
2636 (synopsis "Solving linear inverse models")
2637 (description
2638 "This package provides functions that:
2639
2640 @enumerate
2641 @item find the minimum/maximum of a linear or quadratic function,
2642 @item sample an underdetermined or overdetermined system,
2643 @item solve a linear system Ax=B for the unknown x.
2644 @end enumerate
2645
2646 It includes banded and tridiagonal linear systems. The package calls Fortran
2647 functions from LINPACK.")
2648 ;; Any GPL version.
2649 (license (list license:gpl2+ license:gpl3+))))
2650
2651 (define-public r-fitdistrplus
2652 (package
2653 (name "r-fitdistrplus")
2654 (version "1.0-14")
2655 (source
2656 (origin
2657 (method url-fetch)
2658 (uri (cran-uri "fitdistrplus" version))
2659 (sha256
2660 (base32
2661 "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245"))))
2662 (build-system r-build-system)
2663 (propagated-inputs
2664 `(("r-mass" ,r-mass)
2665 ("r-npsurv" ,r-npsurv)
2666 ("r-survival" ,r-survival)))
2667 (home-page "http://riskassessment.r-forge.r-project.org")
2668 (synopsis "Fitting a parametric distribution from data")
2669 (description
2670 "This package extends the @code{fitdistr} function of the MASS package
2671 with several functions to help the fit of a parametric distribution to
2672 non-censored or censored data. Censored data may contain left-censored,
2673 right-censored and interval-censored values, with several lower and upper
2674 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2675 provides moment matching (MME), quantile matching (QME) and maximum
2676 goodness-of-fit estimation (MGE) methods (available only for non-censored
2677 data). Weighted versions of MLE, MME and QME are available.")
2678 (license license:gpl2+)))
2679
2680 (define-public r-energy
2681 (package
2682 (name "r-energy")
2683 (version "1.7-7")
2684 (source
2685 (origin
2686 (method url-fetch)
2687 (uri (cran-uri "energy" version))
2688 (sha256
2689 (base32
2690 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
2691 (build-system r-build-system)
2692 (propagated-inputs
2693 `(("r-boot" ,r-boot)
2694 ("r-rcpp" ,r-rcpp)))
2695 (home-page "https://cran.r-project.org/web/packages/energy")
2696 (synopsis "Multivariate inference via the energy of data")
2697 (description
2698 "This package provides e-statistics (energy) tests and statistics for
2699 multivariate and univariate inference, including distance correlation,
2700 one-sample, two-sample, and multi-sample tests for comparing multivariate
2701 distributions, are implemented. Measuring and testing multivariate
2702 independence based on distance correlation, partial distance correlation,
2703 multivariate goodness-of-fit tests, clustering based on energy distance,
2704 testing for multivariate normality, distance components (disco) for
2705 non-parametric analysis of structured data, and other energy
2706 statistics/methods are implemented.")
2707 (license license:gpl2+)))
2708
2709 (define-public r-suppdists
2710 (package
2711 (name "r-suppdists")
2712 (version "1.1-9.5")
2713 (source
2714 (origin
2715 (method url-fetch)
2716 (uri (cran-uri "SuppDists" version))
2717 (sha256
2718 (base32
2719 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
2720 (properties `((upstream-name . "SuppDists")))
2721 (build-system r-build-system)
2722 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2723 (synopsis "Supplementary distributions")
2724 (description
2725 "This package provides ten distributions supplementing those built into
2726 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2727 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2728 coefficient, Johnson distributions, normal scores and generalized
2729 hypergeometric distributions. In addition two random number generators of
2730 George Marsaglia are included.")
2731 (license license:gpl2+)))
2732
2733 (define-public r-ksamples
2734 (package
2735 (name "r-ksamples")
2736 (version "1.2-9")
2737 (source
2738 (origin
2739 (method url-fetch)
2740 (uri (cran-uri "kSamples" version))
2741 (sha256
2742 (base32
2743 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2744 (properties `((upstream-name . "kSamples")))
2745 (build-system r-build-system)
2746 (propagated-inputs
2747 `(("r-suppdists" ,r-suppdists)))
2748 (home-page "https://cran.r-project.org/web/packages/kSamples")
2749 (synopsis "K-Sample rank tests and their combinations")
2750 (description
2751 "This package provides tools to compares k samples using the
2752 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2753 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2754 test. It computes asymptotic, simulated or (limited) exact P-values, all
2755 valid under randomization, with or without ties, or conditionally under random
2756 sampling from populations, given the observed tie pattern. Except for Steel's
2757 test and the JT test it also combines these tests across several blocks of
2758 samples.")
2759 (license license:gpl2+)))
2760
2761 (define-public r-cvst
2762 (package
2763 (name "r-cvst")
2764 (version "0.2-2")
2765 (source
2766 (origin
2767 (method url-fetch)
2768 (uri (cran-uri "CVST" version))
2769 (sha256
2770 (base32
2771 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2772 (properties `((upstream-name . "CVST")))
2773 (build-system r-build-system)
2774 (propagated-inputs
2775 `(("r-kernlab" ,r-kernlab)
2776 ("r-matrix" ,r-matrix)))
2777 (home-page "https://cran.r-project.org/web/packages/CVST")
2778 (synopsis "Fast cross-validation via sequential testing")
2779 (description
2780 "This package implements the fast cross-validation via sequential
2781 testing (CVST) procedure. CVST is an improved cross-validation procedure
2782 which uses non-parametric testing coupled with sequential analysis to
2783 determine the best parameter set on linearly increasing subsets of the data.
2784 Additionally to the CVST the package contains an implementation of the
2785 ordinary k-fold cross-validation with a flexible and powerful set of helper
2786 objects and methods to handle the overall model selection process. The
2787 implementations of the Cochran's Q test with permutations and the sequential
2788 testing framework of Wald are generic and can therefore also be used in other
2789 contexts.")
2790 (license license:gpl2+)))
2791
2792 (define-public r-squarem
2793 (package
2794 (name "r-squarem")
2795 (version "2020.2")
2796 (source
2797 (origin
2798 (method url-fetch)
2799 (uri (cran-uri "SQUAREM" version))
2800 (sha256
2801 (base32
2802 "1j6sa93xjvynnzx9jx79a3fysbykmbqyknknsqif5bcha6xp6cvf"))))
2803 (properties `((upstream-name . "SQUAREM")))
2804 (build-system r-build-system)
2805 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
2806 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2807 (description
2808 "This package provides algorithms for accelerating the convergence of
2809 slow, monotone sequences from smooth, contraction mapping such as the EM
2810 algorithm. It can be used to accelerate any smooth, linearly convergent
2811 acceleration scheme. A tutorial style introduction to this package is
2812 available in a vignette.")
2813 (license license:gpl2+)))
2814
2815 (define-public r-lava
2816 (package
2817 (name "r-lava")
2818 (version "1.6.7")
2819 (source
2820 (origin
2821 (method url-fetch)
2822 (uri (cran-uri "lava" version))
2823 (sha256
2824 (base32
2825 "0ffzxbb8pvfh1m6j61az4ga37snyhylq2941fyc76w7w9i2sixv3"))))
2826 (build-system r-build-system)
2827 (propagated-inputs
2828 `(("r-numderiv" ,r-numderiv)
2829 ("r-squarem" ,r-squarem)
2830 ("r-survival" ,r-survival)))
2831 (home-page "https://github.com/kkholst/lava")
2832 (synopsis "Latent variable models")
2833 (description
2834 "This package provides tools for the estimation and simulation of latent
2835 variable models.")
2836 (license license:gpl3)))
2837
2838 (define-public r-drr
2839 (package
2840 (name "r-drr")
2841 (version "0.0.4")
2842 (source
2843 (origin
2844 (method url-fetch)
2845 (uri (cran-uri "DRR" version))
2846 (sha256
2847 (base32
2848 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
2849 (properties `((upstream-name . "DRR")))
2850 (build-system r-build-system)
2851 (propagated-inputs
2852 `(("r-cvst" ,r-cvst)
2853 ("r-kernlab" ,r-kernlab)
2854 ("r-matrix" ,r-matrix)))
2855 (home-page "https://cran.r-project.org/web/packages/DRR")
2856 (synopsis "Dimensionality reduction via regression")
2857 (description
2858 "This package provides an implementation of dimensionality reduction via
2859 regression using Kernel Ridge Regression.")
2860 (license license:gpl3)))
2861
2862 (define-public r-prodlim
2863 (package
2864 (name "r-prodlim")
2865 (version "2019.11.13")
2866 (source
2867 (origin
2868 (method url-fetch)
2869 (uri (cran-uri "prodlim" version))
2870 (sha256
2871 (base32
2872 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
2873 (build-system r-build-system)
2874 (propagated-inputs
2875 `(("r-kernsmooth" ,r-kernsmooth)
2876 ("r-lava" ,r-lava)
2877 ("r-rcpp" ,r-rcpp)
2878 ("r-survival" ,r-survival)))
2879 (home-page "https://cran.r-project.org/web/packages/prodlim")
2880 (synopsis "Product-limit estimation for censored event history analysis")
2881 (description
2882 "This package provides a fast and user-friendly implementation of
2883 nonparametric estimators for censored event history (survival) analysis with
2884 the Kaplan-Meier and Aalen-Johansen methods.")
2885 (license license:gpl2+)))
2886
2887 (define-public r-dimred
2888 (package
2889 (name "r-dimred")
2890 (version "0.2.3")
2891 (source
2892 (origin
2893 (method url-fetch)
2894 (uri (cran-uri "dimRed" version))
2895 (sha256
2896 (base32
2897 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
2898 (properties `((upstream-name . "dimRed")))
2899 (build-system r-build-system)
2900 (propagated-inputs
2901 `(("r-drr" ,r-drr)
2902 ("r-magrittr" ,r-magrittr)))
2903 (home-page "https://github.com/gdkrmr/dimRed")
2904 (synopsis "Framework for dimensionality reduction")
2905 (description
2906 "This package provides a collection of dimensionality reduction
2907 techniques from R packages and provides a common interface for calling the
2908 methods.")
2909 (license license:gpl3)))
2910
2911 (define-public r-timedate
2912 (package
2913 (name "r-timedate")
2914 (version "3043.102")
2915 (source
2916 (origin
2917 (method url-fetch)
2918 (uri (cran-uri "timeDate" version))
2919 (sha256
2920 (base32
2921 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
2922 (properties `((upstream-name . "timeDate")))
2923 (build-system r-build-system)
2924 (home-page "https://www.rmetrics.org")
2925 (synopsis "Chronological and calendar objects")
2926 (description
2927 "This package provides an environment for teaching \"Financial
2928 Engineering and Computational Finance\" and for managing chronological and
2929 calendar objects.")
2930 (license license:gpl2+)))
2931
2932 (define-public r-magic
2933 (package
2934 (name "r-magic")
2935 (version "1.5-9")
2936 (source
2937 (origin
2938 (method url-fetch)
2939 (uri (cran-uri "magic" version))
2940 (sha256
2941 (base32
2942 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
2943 (build-system r-build-system)
2944 (propagated-inputs
2945 `(("r-abind" ,r-abind)))
2946 (home-page "https://github.com/RobinHankin/magic.git")
2947 (synopsis "Create and investigate magic squares")
2948 (description
2949 "This package provides a collection of efficient, vectorized algorithms
2950 for the creation and investigation of magic squares and hypercubes, including
2951 a variety of functions for the manipulation and analysis of arbitrarily
2952 dimensioned arrays.")
2953 (license license:gpl2)))
2954
2955 (define-public r-rmysql
2956 (package
2957 (name "r-rmysql")
2958 (version "0.10.20")
2959 (source
2960 (origin
2961 (method url-fetch)
2962 (uri (cran-uri "RMySQL" version))
2963 (sha256
2964 (base32
2965 "0lv9m6zpm8dgv7yixr6xhw379vbq45d7n7gkrmjrppdj8vcih77i"))))
2966 (properties `((upstream-name . "RMySQL")))
2967 (build-system r-build-system)
2968 (inputs
2969 `(("mariadb" ,mariadb "lib")
2970 ("mariadb-dev" ,mariadb "dev")
2971 ("zlib" ,zlib)))
2972 (propagated-inputs
2973 `(("r-dbi" ,r-dbi)))
2974 (home-page "https://github.com/r-dbi/RMySQL")
2975 (synopsis "Database interface and MySQL driver for R")
2976 (description
2977 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
2978 package contains an old implementation based on legacy code from S-PLUS which
2979 is being phased out. A modern MySQL client based on Rcpp is available from
2980 the RMariaDB package.")
2981 (license license:gpl2)))
2982
2983 (define-public r-rpostgresql
2984 (package
2985 (name "r-rpostgresql")
2986 (version "0.6-2")
2987 (source
2988 (origin
2989 (method url-fetch)
2990 (uri (cran-uri "RPostgreSQL" version))
2991 (sha256
2992 (base32
2993 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
2994 (properties `((upstream-name . "RPostgreSQL")))
2995 (build-system r-build-system)
2996 (inputs
2997 `(("postgresql" ,postgresql)))
2998 (propagated-inputs
2999 `(("r-dbi" ,r-dbi)))
3000 (home-page "https://github.com/tomoakin/RPostgreSQL")
3001 (synopsis "R interface to the PostgreSQL database system")
3002 (description
3003 "This package provides a Database Interface (DBI) compliant driver for R
3004 to access PostgreSQL database systems.")
3005 ;; The whole package is released under GPL version 2. It includes code
3006 ;; under the PostgreSQL license.
3007 (license license:gpl2)))
3008
3009 (define-public r-linprog
3010 (package
3011 (name "r-linprog")
3012 (version "0.9-2")
3013 (source
3014 (origin
3015 (method url-fetch)
3016 (uri (cran-uri "linprog" version))
3017 (sha256
3018 (base32
3019 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
3020 (build-system r-build-system)
3021 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
3022 (home-page "http://linprog.r-forge.r-project.org/")
3023 (synopsis "Linear programming and optimization")
3024 (description
3025 "This package can be used to solve Linear Programming / Linear
3026 Optimization problems by using the simplex algorithm.")
3027 (license license:gpl2+)))
3028
3029 (define-public r-geometry
3030 (package
3031 (name "r-geometry")
3032 (version "0.4.5")
3033 (source
3034 (origin
3035 (method url-fetch)
3036 (uri (cran-uri "geometry" version))
3037 (sha256
3038 (base32
3039 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
3040 (build-system r-build-system)
3041 (propagated-inputs
3042 `(("r-magic" ,r-magic)
3043 ("r-linprog" ,r-linprog)
3044 ("r-lpsolve" ,r-lpsolve)
3045 ("r-rcpp" ,r-rcpp)
3046 ("r-rcppprogress" ,r-rcppprogress)))
3047 (home-page "http://geometry.r-forge.r-project.org/")
3048 (synopsis "Mesh generation and surface tesselation")
3049 (description
3050 "This package makes the qhull library available in R, in a similar manner
3051 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
3052 intersections about a point, Voronoi diagrams, furthest-site Delaunay
3053 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
3054 and higher dimensions. It implements the Quickhull algorithm for computing
3055 the convex hull. Qhull does not support constrained Delaunay triangulations,
3056 or mesh generation of non-convex objects, but the package does include some R
3057 functions that allow for this. Currently the package only gives access to
3058 Delaunay triangulation and convex hull computation.")
3059 ;; The Qhull sources are included and are distributed under a custom
3060 ;; non-copyleft license. The R sources are released under GPL version 2.
3061 (license (list license:gpl2
3062 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
3063
3064 (define-public r-ddalpha
3065 (package
3066 (name "r-ddalpha")
3067 (version "1.3.11")
3068 (source
3069 (origin
3070 (method url-fetch)
3071 (uri (cran-uri "ddalpha" version))
3072 (sha256
3073 (base32
3074 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
3075 (build-system r-build-system)
3076 (propagated-inputs
3077 `(("r-bh" ,r-bh)
3078 ("r-class" ,r-class)
3079 ("r-geometry" ,r-geometry)
3080 ("r-mass" ,r-mass)
3081 ("r-rcpp" ,r-rcpp)
3082 ("r-robustbase" ,r-robustbase)
3083 ("r-sfsmisc" ,r-sfsmisc)))
3084 (native-inputs
3085 `(("gfortran" ,gfortran)))
3086 (home-page "https://cran.r-project.org/web/packages/ddalpha")
3087 (synopsis "Depth-Based classification and calculation of data depth")
3088 (description
3089 "This package contains procedures for depth-based supervised learning,
3090 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
3091 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
3092 statistical depth function to a compact low-dimensional space, where the final
3093 classification is done. It also offers an extension to functional data and
3094 routines for calculating certain notions of statistical depth functions. 50
3095 multivariate and 5 functional classification problems are included.")
3096 (license license:gpl2)))
3097
3098 (define-public r-gower
3099 (package
3100 (name "r-gower")
3101 (version "0.2.1")
3102 (source
3103 (origin
3104 (method url-fetch)
3105 (uri (cran-uri "gower" version))
3106 (sha256
3107 (base32
3108 "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
3109 (build-system r-build-system)
3110 (home-page "https://github.com/markvanderloo/gower")
3111 (synopsis "Gower's distance")
3112 (description
3113 "This package provides tools to compute Gower's distance (or similarity)
3114 coefficient between records, and to compute the top-n matches between records.
3115 Core algorithms are executed in parallel on systems supporting OpenMP.")
3116 (license license:gpl3)))
3117
3118 (define-public r-rcpproll
3119 (package
3120 (name "r-rcpproll")
3121 (version "0.3.0")
3122 (source
3123 (origin
3124 (method url-fetch)
3125 (uri (cran-uri "RcppRoll" version))
3126 (sha256
3127 (base32
3128 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
3129 (properties `((upstream-name . "RcppRoll")))
3130 (build-system r-build-system)
3131 (propagated-inputs
3132 `(("r-rcpp" ,r-rcpp)))
3133 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
3134 (synopsis "Efficient rolling and windowed operations")
3135 (description
3136 "This package provides fast and efficient routines for common rolling /
3137 windowed operations. Routines for the efficient computation of windowed mean,
3138 median, sum, product, minimum, maximum, standard deviation and variance are
3139 provided.")
3140 (license license:gpl2+)))
3141
3142 (define-public r-ipred
3143 (package
3144 (name "r-ipred")
3145 (version "0.9-9")
3146 (source
3147 (origin
3148 (method url-fetch)
3149 (uri (cran-uri "ipred" version))
3150 (sha256
3151 (base32
3152 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
3153 (build-system r-build-system)
3154 (propagated-inputs
3155 `(("r-class" ,r-class)
3156 ("r-mass" ,r-mass)
3157 ("r-nnet" ,r-nnet)
3158 ("r-prodlim" ,r-prodlim)
3159 ("r-rpart" ,r-rpart)
3160 ("r-survival" ,r-survival)))
3161 (home-page "https://cran.r-project.org/web/packages/ipred")
3162 (synopsis "Improved predictors")
3163 (description
3164 "This package provides improved predictive models by indirect
3165 classification and bagging for classification, regression and survival
3166 problems as well as resampling based estimators of prediction error.")
3167 (license license:gpl2+)))
3168
3169 (define-public r-psych
3170 (package
3171 (name "r-psych")
3172 (version "1.9.12.31")
3173 (source
3174 (origin
3175 (method url-fetch)
3176 (uri (cran-uri "psych" version))
3177 (sha256
3178 (base32
3179 "02i9p6appf15hjdsi58g39bzs9as40f9qhy8m7ki30hd1fz1vrr5"))))
3180 (build-system r-build-system)
3181 (propagated-inputs
3182 `(("r-lattice" ,r-lattice)
3183 ("r-mnormt" ,r-mnormt)
3184 ("r-nlme" ,r-nlme)))
3185 (home-page "https://cran.r-project.org/web/packages/psych/")
3186 (synopsis "Procedures for psychological, psychometric, and personality research")
3187 (description
3188 "This package provides a general purpose toolbox for personality,
3189 psychometric theory and experimental psychology. Functions are primarily for
3190 multivariate analysis and scale construction using factor analysis, principal
3191 component analysis, cluster analysis and reliability analysis, although others
3192 provide basic descriptive statistics. Item Response Theory is done using
3193 factor analysis of tetrachoric and polychoric correlations. Functions for
3194 analyzing data at multiple levels include within and between group statistics,
3195 including correlations and factor analysis. Functions for simulating and
3196 testing particular item and test structures are included. Several functions
3197 serve as a useful front end for structural equation modeling. Graphical
3198 displays of path diagrams, factor analysis and structural equation models are
3199 created using basic graphics.")
3200 (license license:gpl2+)))
3201
3202 (define-public r-generics
3203 (package
3204 (name "r-generics")
3205 (version "0.0.2")
3206 (source
3207 (origin
3208 (method url-fetch)
3209 (uri (cran-uri "generics" version))
3210 (sha256
3211 (base32
3212 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3213 (build-system r-build-system)
3214 (home-page "https://github.com/r-lib/generics")
3215 (synopsis "Common S3 generics not provided by base R methods")
3216 (description
3217 "In order to reduce potential package dependencies and conflicts,
3218 generics provides a number of commonly used S3 generics that are not provided
3219 by base R methods related to model fitting.")
3220 (license license:gpl2)))
3221
3222 (define-public r-broom
3223 (package
3224 (name "r-broom")
3225 (version "0.5.6")
3226 (source
3227 (origin
3228 (method url-fetch)
3229 (uri (cran-uri "broom" version))
3230 (sha256
3231 (base32
3232 "0da3jsb02xckrk6alznicn6l5lnyvdhc64qklyarnd77miqgc1hb"))))
3233 (build-system r-build-system)
3234 (propagated-inputs
3235 `(("r-backports" ,r-backports)
3236 ("r-dplyr" ,r-dplyr)
3237 ("r-generics" ,r-generics)
3238 ("r-nlme" ,r-nlme)
3239 ("r-purrr" ,r-purrr)
3240 ("r-reshape2" ,r-reshape2)
3241 ("r-stringr" ,r-stringr)
3242 ("r-tibble" ,r-tibble)
3243 ("r-tidyr" ,r-tidyr)))
3244 (native-inputs
3245 `(("r-knitr" ,r-knitr)))
3246 (home-page "https://github.com/tidyverse/broom")
3247 (synopsis "Convert statistical analysis objects into tidy data frames")
3248 (description
3249 "This package provides tools to convert statistical analysis objects from
3250 R into tidy data frames, so that they can more easily be combined, reshaped
3251 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3252 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3253 summarizes a model's statistical findings such as coefficients of a
3254 regression; @code{augment}, which adds columns to the original data such as
3255 predictions, residuals and cluster assignments; and @code{glance}, which
3256 provides a one-row summary of model-level statistics.")
3257 (license license:expat)))
3258
3259 (define-public r-recipes
3260 (package
3261 (name "r-recipes")
3262 (version "0.1.10")
3263 (source
3264 (origin
3265 (method url-fetch)
3266 (uri (cran-uri "recipes" version))
3267 (sha256
3268 (base32
3269 "11f96aanrzi2v6cn49fhvf9y4cmhra63wcy6nvpv6hcfaqqmwd2g"))))
3270 (build-system r-build-system)
3271 (propagated-inputs
3272 `(("r-dplyr" ,r-dplyr)
3273 ("r-generics" ,r-generics)
3274 ("r-glue" ,r-glue)
3275 ("r-gower" ,r-gower)
3276 ("r-ipred" ,r-ipred)
3277 ("r-lubridate" ,r-lubridate)
3278 ("r-magrittr" ,r-magrittr)
3279 ("r-matrix" ,r-matrix)
3280 ("r-purrr" ,r-purrr)
3281 ("r-rlang" ,r-rlang)
3282 ("r-tibble" ,r-tibble)
3283 ("r-tidyr" ,r-tidyr)
3284 ("r-tidyselect" ,r-tidyselect)
3285 ("r-timedate" ,r-timedate)
3286 ("r-withr" ,r-withr)))
3287 (native-inputs
3288 `(("r-knitr" ,r-knitr)))
3289 (home-page "https://github.com/topepo/recipes")
3290 (synopsis "Preprocessing tools to create design matrices")
3291 (description
3292 "Recipes is an extensible framework to create and preprocess design
3293 matrices. Recipes consist of one or more data manipulation and analysis
3294 \"steps\". Statistical parameters for the steps can be estimated from an
3295 initial data set and then applied to other data sets. The resulting design
3296 matrices can then be used as inputs into statistical or machine learning
3297 models.")
3298 (license license:gpl2)))
3299
3300 (define-public r-pdist
3301 (package
3302 (name "r-pdist")
3303 (version "1.2")
3304 (source
3305 (origin
3306 (method url-fetch)
3307 (uri (cran-uri "pdist" version))
3308 (sha256
3309 (base32
3310 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3311 (build-system r-build-system)
3312 (home-page "https://github.com/jeffwong/pdist")
3313 (synopsis "Partitioned distance function")
3314 (description
3315 "Pdist computes the euclidean distance between rows of a matrix X and
3316 rows of another matrix Y. Previously, this could be done by binding the two
3317 matrices together and calling @code{dist}, but this creates unnecessary
3318 computation by computing the distances between a row of X and another row of
3319 X, and likewise for Y. Pdist strictly computes distances across the two
3320 matrices, not within the same matrix, making computations significantly faster
3321 for certain use cases.")
3322 (license license:gpl3+)))
3323
3324 (define-public r-ggrepel
3325 (package
3326 (name "r-ggrepel")
3327 (version "0.8.2")
3328 (source
3329 (origin
3330 (method url-fetch)
3331 (uri (cran-uri "ggrepel" version))
3332 (sha256
3333 (base32
3334 "1qaifn3dazdqbqlii210xhw7yf142iw7g9p2axmmxbz90p0by08d"))))
3335 (build-system r-build-system)
3336 (propagated-inputs
3337 `(("r-ggplot2" ,r-ggplot2)
3338 ("r-rcpp" ,r-rcpp)
3339 ("r-scales" ,r-scales)))
3340 (native-inputs
3341 `(("r-knitr" ,r-knitr))) ; for vignettes
3342 (home-page "http://github.com/slowkow/ggrepel")
3343 (synopsis "Repulsive text and label geometries for ggplot2")
3344 (description
3345 "This package provides text and label geometries for ggplot2 that help to
3346 avoid overlapping text labels. Labels repel away from each other and away
3347 from the data points.")
3348 (license license:gpl3)))
3349
3350 (define-public r-corrplot
3351 (package
3352 (name "r-corrplot")
3353 (version "0.84")
3354 (source
3355 (origin
3356 (method url-fetch)
3357 (uri (cran-uri "corrplot" version))
3358 (sha256
3359 (base32
3360 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3361 (build-system r-build-system)
3362 (home-page "https://github.com/taiyun/corrplot")
3363 (synopsis "Visualization of a correlation matrix")
3364 (description
3365 "This package provides a graphical display of a correlation matrix or
3366 general matrix. It also contains some algorithms to do matrix reordering. In
3367 addition, corrplot is good at details, including choosing color, text labels,
3368 color labels, layout, etc.")
3369 ;; Any version of the GPL
3370 (license license:gpl2+)))
3371
3372 (define-public r-stringdist
3373 (package
3374 (name "r-stringdist")
3375 (version "0.9.5.5")
3376 (source
3377 (origin
3378 (method url-fetch)
3379 (uri (cran-uri "stringdist" version))
3380 (sha256
3381 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi"))))
3382 (build-system r-build-system)
3383 (home-page "https://github.com/markvanderloo/stringdist")
3384 (synopsis "Approximate string matching and string distance functions")
3385 (description
3386 "This package implements an approximate string matching version of R's
3387 native @code{match} function. It can calculate various string distances based
3388 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3389 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3390 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3391 can be computed between character vectors while taking proper care of encoding
3392 or between integer vectors representing generic sequences.")
3393 (license license:gpl3+)))
3394
3395 (define-public r-ucminf
3396 (package
3397 (name "r-ucminf")
3398 (version "1.1-4")
3399 (source
3400 (origin
3401 (method url-fetch)
3402 (uri (cran-uri "ucminf" version))
3403 (sha256
3404 (base32
3405 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3406 (build-system r-build-system)
3407 (native-inputs `(("gfortran" ,gfortran)))
3408 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3409 (synopsis "General-purpose unconstrained non-linear optimization")
3410 (description
3411 "This package provides an implementation of an algorithm for
3412 general-purpose unconstrained non-linear optimization. The algorithm is of
3413 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3414 search with a trust region type monitoring of the input to the line search
3415 algorithm. The interface of @code{ucminf} is designed for easy interchange
3416 with the package @code{optim}.")
3417 (license license:gpl2+)))
3418
3419 (define-public r-ordinal
3420 (package
3421 (name "r-ordinal")
3422 (version "2019.12-10")
3423 (source
3424 (origin
3425 (method url-fetch)
3426 (uri (cran-uri "ordinal" version))
3427 (sha256
3428 (base32
3429 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
3430 (build-system r-build-system)
3431 (propagated-inputs
3432 `(("r-mass" ,r-mass)
3433 ("r-matrix" ,r-matrix)
3434 ("r-numderiv" ,r-numderiv)
3435 ("r-ucminf" ,r-ucminf)))
3436 (home-page "https://github.com/runehaubo/ordinal")
3437 (synopsis "Regression models for ordinal data")
3438 (description
3439 "This package provides an implementation of cumulative link (mixed)
3440 models also known as ordered regression models, proportional odds models,
3441 proportional hazards models for grouped survival times and ordered models.
3442 Estimation is via maximum likelihood and mixed models are fitted with the
3443 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3444 (license license:gpl2+)))
3445
3446 (define-public r-jomo
3447 (package
3448 (name "r-jomo")
3449 (version "2.6-10")
3450 (source
3451 (origin
3452 (method url-fetch)
3453 (uri (cran-uri "jomo" version))
3454 (sha256
3455 (base32
3456 "1k9l4290g350zbw1pjs871q9bxj3j2h1dilxpp06v4wy4n7d8qs0"))))
3457 (build-system r-build-system)
3458 (propagated-inputs
3459 `(("r-lme4" ,r-lme4)
3460 ("r-mass" ,r-mass)
3461 ("r-ordinal" ,r-ordinal)
3462 ("r-survival" ,r-survival)))
3463 (home-page "https://cran.r-project.org/web/packages/jomo/")
3464 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3465 (description
3466 "Similarly to Schafer's package pan, jomo is a package for multilevel
3467 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3468 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3469 possibility of handling binary and categorical data through latent normal
3470 variables, the option to use cluster-specific covariance matrices and to
3471 impute compatibly with the substantive model.")
3472 (license license:gpl2)))
3473
3474 (define-public r-pan
3475 (package
3476 (name "r-pan")
3477 (version "1.6")
3478 (source
3479 (origin
3480 (method url-fetch)
3481 (uri (cran-uri "pan" version))
3482 (sha256
3483 (base32
3484 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3485 (build-system r-build-system)
3486 (native-inputs `(("gfortran" ,gfortran)))
3487 (home-page "https://cran.r-project.org/web/packages/pan/")
3488 (synopsis "Multiple imputation for multivariate panel or clustered data")
3489 (description
3490 "This package implements multiple imputation for multivariate panel or
3491 clustered data.")
3492 (license license:gpl3)))
3493
3494 (define-public r-mitml
3495 (package
3496 (name "r-mitml")
3497 (version "0.3-7")
3498 (source
3499 (origin
3500 (method url-fetch)
3501 (uri (cran-uri "mitml" version))
3502 (sha256
3503 (base32
3504 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3505 (build-system r-build-system)
3506 (propagated-inputs
3507 `(("r-haven" ,r-haven)
3508 ("r-jomo" ,r-jomo)
3509 ("r-pan" ,r-pan)))
3510 (home-page "https://cran.r-project.org/web/packages/mitml/")
3511 (synopsis "Tools for multiple imputation in multilevel modeling")
3512 (description
3513 "This package provides tools for multiple imputation of missing data in
3514 multilevel modeling. It includes a user-friendly interface to the packages
3515 pan and jomo, and several functions for visualization, data management and the
3516 analysis of multiply imputed data sets.")
3517 (license license:gpl2+)))
3518
3519 (define-public r-mice
3520 (package
3521 (name "r-mice")
3522 (version "3.8.0")
3523 (source
3524 (origin
3525 (method url-fetch)
3526 (uri (cran-uri "mice" version))
3527 (sha256
3528 (base32
3529 "1ibybvigqkkla4xwhqs2w4m6c68alfcdsljx99nn4p92rzb1ig04"))))
3530 (build-system r-build-system)
3531 (propagated-inputs
3532 `(("r-broom" ,r-broom)
3533 ("r-dplyr" ,r-dplyr)
3534 ("r-lattice" ,r-lattice)
3535 ("r-rcpp" ,r-rcpp)
3536 ("r-tidyr" ,r-tidyr)))
3537 (home-page "https://cran.r-project.org/web/packages/mice/")
3538 (synopsis "Multivariate imputation by chained equations")
3539 (description
3540 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3541 implemented by the MICE algorithm as described in @url{Van Buuren and
3542 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3543 variable has its own imputation model. Built-in imputation models are
3544 provided for continuous data (predictive mean matching, normal), binary
3545 data (logistic regression), unordered categorical data (polytomous logistic
3546 regression) and ordered categorical data (proportional odds). MICE can also
3547 impute continuous two-level data (normal model, pan, second-level variables).
3548 Passive imputation can be used to maintain consistency between variables.
3549 Various diagnostic plots are available to inspect the quality of the
3550 imputations.")
3551 ;; Any of these two versions.
3552 (license (list license:gpl2 license:gpl3))))
3553
3554 (define-public r-truncnorm
3555 (package
3556 (name "r-truncnorm")
3557 (version "1.0-8")
3558 (source
3559 (origin
3560 (method url-fetch)
3561 (uri (cran-uri "truncnorm" version))
3562 (sha256
3563 (base32
3564 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3565 (build-system r-build-system)
3566 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3567 (synopsis "Truncated normal distribution")
3568 (description "This package provides functions for the truncated normal
3569 distribution with mean equal to @code{mean} and standard deviation equal to
3570 @code{sd}. It includes density, distribution, quantile, and expected value
3571 functions, as well as a random generation function.")
3572 (license license:gpl2)))
3573
3574 (define-public r-rsolnp
3575 (package
3576 (name "r-rsolnp")
3577 (version "1.16")
3578 (source
3579 (origin
3580 (method url-fetch)
3581 (uri (cran-uri "Rsolnp" version))
3582 (sha256
3583 (base32
3584 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3585 (properties `((upstream-name . "Rsolnp")))
3586 (build-system r-build-system)
3587 (propagated-inputs
3588 `(("r-truncnorm" ,r-truncnorm)))
3589 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3590 (synopsis "General non-linear optimization")
3591 (description "The Rsolnp package implements a general non-linear augmented
3592 Lagrange multiplier method solver, a @dfn{sequential quadratic
3593 programming} (SQP) based solver).")
3594 ;; Any version of the GPL.
3595 (license license:gpl2+)))
3596
3597 (define-public r-hardyweinberg
3598 (package
3599 (name "r-hardyweinberg")
3600 (version "1.6.3")
3601 (source
3602 (origin
3603 (method url-fetch)
3604 (uri (cran-uri "HardyWeinberg" version))
3605 (sha256
3606 (base32
3607 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3608 (properties `((upstream-name . "HardyWeinberg")))
3609 (build-system r-build-system)
3610 (propagated-inputs
3611 `(("r-mice" ,r-mice)
3612 ("r-rcpp" ,r-rcpp)
3613 ("r-rsolnp" ,r-rsolnp)))
3614 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3615 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3616 (description
3617 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3618 diallelic genetic marker data. All classical tests (chi-square, exact,
3619 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3620 included in the package, as well as functions for power computation and for
3621 the simulation of marker data under equilibrium and disequilibrium. Routines
3622 for dealing with markers on the X-chromosome are included. Functions for
3623 testing equilibrium in the presence of missing data by using multiple
3624 imputation are also provided. Implements several graphics for exploring the
3625 equilibrium status of a large set of diallelic markers: ternary plots with
3626 acceptance regions, log-ratio plots and Q-Q plots.")
3627 (license license:gpl2+)))
3628
3629 (define-public r-sm
3630 (package
3631 (name "r-sm")
3632 (version "2.2-5.6")
3633 (source
3634 (origin
3635 (method url-fetch)
3636 (uri (cran-uri "sm" version))
3637 (sha256
3638 (base32
3639 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3640 (build-system r-build-system)
3641 (native-inputs `(("gfortran" ,gfortran)))
3642 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3643 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3644 (description
3645 "This is software accompanying the book 'Applied Smoothing Techniques for
3646 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3647 University Press. It provides smoothing methods for nonparametric regression
3648 and density estimation")
3649 (license license:gpl2+)))
3650
3651 (define-public r-venndiagram
3652 (package
3653 (name "r-venndiagram")
3654 (version "1.6.20")
3655 (source (origin
3656 (method url-fetch)
3657 (uri (cran-uri "VennDiagram" version))
3658 (sha256
3659 (base32
3660 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3661 (properties `((upstream-name . "VennDiagram")))
3662 (build-system r-build-system)
3663 (propagated-inputs
3664 `(("r-futile-logger" ,r-futile-logger)))
3665 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3666 (synopsis "Generate High-Resolution Venn and Euler Plots")
3667 (description
3668 "This package provides a set of functions to generate high-resolution
3669 Venn and Euler plots. It includes handling for several special cases,
3670 including two-case scaling, and extensive customization of plot shape and
3671 structure.")
3672 (license license:gpl2+)))
3673
3674 (define-public r-vioplot
3675 (package
3676 (name "r-vioplot")
3677 (version "0.3.4")
3678 (source
3679 (origin
3680 (method url-fetch)
3681 (uri (cran-uri "vioplot" version))
3682 (sha256
3683 (base32
3684 "1fsklymilspzz5fzlj7666x09aglaw0v4x0yfjjzy4vr5qpjc529"))))
3685 (build-system r-build-system)
3686 (propagated-inputs
3687 `(("r-sm" ,r-sm)
3688 ("r-zoo" ,r-zoo)))
3689 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3690 (synopsis "Violin plot")
3691 (description
3692 "This package provides a violin plot, which is a combination of a box
3693 plot and a kernel density plot.")
3694 (license license:bsd-3)))
3695
3696 (define-public r-rsofia
3697 (package
3698 (name "r-rsofia")
3699 (version "1.1")
3700 (source (origin
3701 (method url-fetch)
3702 ;; This package has been removed from CRAN, so we can
3703 ;; only fetch it from the archives.
3704 (uri (string-append "https://cran.r-project.org/src/"
3705 "contrib/Archive/RSofia/RSofia_"
3706 version ".tar.gz"))
3707 (sha256
3708 (base32
3709 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3710 (properties `((upstream-name . "RSofia")))
3711 (build-system r-build-system)
3712 (propagated-inputs
3713 `(("r-rcpp" ,r-rcpp)))
3714 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3715 (synopsis "Port of sofia-ml to R")
3716 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3717 suite of fast incremental algorithms for machine learning that can be used for
3718 training models for classification or ranking.")
3719 (license license:asl2.0)))
3720
3721 (define-public r-xts
3722 (package
3723 (name "r-xts")
3724 (version "0.12-0")
3725 (source
3726 (origin
3727 (method url-fetch)
3728 (uri (cran-uri "xts" version))
3729 (sha256
3730 (base32
3731 "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz"))))
3732 (build-system r-build-system)
3733 (propagated-inputs `(("r-zoo" ,r-zoo)))
3734 (home-page "https://github.com/joshuaulrich/xts")
3735 (synopsis "Extensible time series")
3736 (description
3737 "This package provides for uniform handling of R's different time-based
3738 data classes by extending @code{zoo}, maximizing native format information
3739 preservation and allowing for user-level customization and extension, while
3740 simplifying cross-class interoperability.")
3741 (license license:gpl2+)))
3742
3743 (define-public r-performanceanalytics
3744 (package
3745 (name "r-performanceanalytics")
3746 (version "2.0.4")
3747 (source
3748 (origin
3749 (method url-fetch)
3750 (uri (cran-uri "PerformanceAnalytics" version))
3751 (sha256
3752 (base32
3753 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
3754 (properties
3755 `((upstream-name . "PerformanceAnalytics")))
3756 (build-system r-build-system)
3757 (propagated-inputs
3758 `(("r-quadprog" ,r-quadprog)
3759 ("r-xts" ,r-xts)
3760 ("r-zoo" ,r-zoo)))
3761 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3762 (synopsis "Econometric tools for performance and risk analysis")
3763 (description "This is a collection of econometric functions for
3764 performance and risk analysis. This package aims to aid practitioners and
3765 researchers in utilizing the latest research in analysis of non-normal return
3766 streams. In general, it is most tested on return (rather than price) data on
3767 a regular scale, but most functions will work with irregular return data as
3768 well, and increasing numbers of functions will work with P&L or price data
3769 where possible.")
3770 ;; Either version may be picked.
3771 (license (list license:gpl2 license:gpl3))))
3772
3773 (define-public r-laeken
3774 (package
3775 (name "r-laeken")
3776 (version "0.5.1")
3777 (source
3778 (origin
3779 (method url-fetch)
3780 (uri (cran-uri "laeken" version))
3781 (sha256
3782 (base32
3783 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
3784 (build-system r-build-system)
3785 (propagated-inputs
3786 `(("r-boot" ,r-boot)
3787 ("r-mass" ,r-mass)))
3788 (home-page "https://cran.r-project.org/web/packages/laeken/")
3789 (synopsis "Estimation of indicators on social exclusion and poverty")
3790 (description "This package provides tools for the estimation of indicators
3791 on social exclusion and poverty, as well as an implementation of Pareto tail
3792 modeling for empirical income distributions.")
3793 (license license:gpl2+)))
3794
3795 (define-public r-vcd
3796 (package
3797 (name "r-vcd")
3798 (version "1.4-7")
3799 (source
3800 (origin
3801 (method url-fetch)
3802 (uri (cran-uri "vcd" version))
3803 (sha256
3804 (base32
3805 "16aj688nhlcvdxzfsqh4s375v8f8vl8997dl8h1xg29b42nv52gc"))))
3806 (build-system r-build-system)
3807 (propagated-inputs
3808 `(("r-colorspace" ,r-colorspace)
3809 ("r-lmtest" ,r-lmtest)
3810 ("r-mass" ,r-mass)))
3811 (home-page "https://cran.r-project.org/web/packages/vcd/")
3812 (synopsis "Visualizing categorical data")
3813 (description "This package provides visualization techniques, data sets,
3814 summary and inference procedures aimed particularly at categorical data.
3815 Special emphasis is given to highly extensible grid graphics. The package was
3816 originally inspired by the book \"Visualizing Categorical Data\" by Michael
3817 Friendly and is now the main support package for a new book, \"Discrete Data
3818 Analysis with R\" by Michael Friendly and David Meyer (2015).")
3819 (license license:gpl2)))
3820
3821 (define-public r-ica
3822 (package
3823 (name "r-ica")
3824 (version "1.0-2")
3825 (source
3826 (origin
3827 (method url-fetch)
3828 (uri (cran-uri "ica" version))
3829 (sha256
3830 (base32
3831 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
3832 (build-system r-build-system)
3833 (home-page "https://cran.r-project.org/web/packages/ica/")
3834 (synopsis "Independent component analysis")
3835 (description "This package provides tools for @dfn{Independent Component
3836 Analysis} (ICA) using various algorithms: FastICA,
3837 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
3838 of Eigenmatrices} (JADE).")
3839 (license license:gpl2+)))
3840
3841 (define-public r-dtw
3842 (package
3843 (name "r-dtw")
3844 (version "1.21-3")
3845 (source
3846 (origin
3847 (method url-fetch)
3848 (uri (cran-uri "dtw" version))
3849 (sha256
3850 (base32
3851 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
3852 (build-system r-build-system)
3853 (propagated-inputs `(("r-proxy" ,r-proxy)))
3854 (home-page "http://dtw.r-forge.r-project.org/")
3855 (synopsis "Dynamic Time Warping Algorithms")
3856 (description "This package provides a comprehensive implementation of
3857 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
3858 optimal (least cumulative distance) alignment between points of two time
3859 series. Common DTW variants covered include local (slope) and global (window)
3860 constraints, subsequence matches, arbitrary distance definitions,
3861 normalizations, minimum variance matching, and so on.")
3862 (license license:gpl2+)))
3863
3864 (define-public r-sdmtools
3865 (package
3866 (name "r-sdmtools")
3867 (version "1.1-221.2")
3868 (source
3869 (origin
3870 (method url-fetch)
3871 (uri (cran-uri "SDMTools" version))
3872 (sha256
3873 (base32
3874 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
3875 (properties `((upstream-name . "SDMTools")))
3876 (build-system r-build-system)
3877 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
3878 (home-page "https://www.rforge.net/SDMTools/")
3879 (synopsis "Species distribution modelling tools")
3880 (description "This package provides a set of tools for post processing
3881 the outcomes of species distribution modeling exercises. It includes novel
3882 methods for comparing models and tracking changes in distributions through
3883 time. It further includes methods for visualizing outcomes, selecting
3884 thresholds, calculating measures of accuracy and landscape fragmentation
3885 statistics, etc.")
3886 (license license:gpl3+)))
3887
3888 (define-public r-scatterplot3d
3889 (package
3890 (name "r-scatterplot3d")
3891 (version "0.3-41")
3892 (source
3893 (origin
3894 (method url-fetch)
3895 (uri (cran-uri "scatterplot3d" version))
3896 (sha256
3897 (base32
3898 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
3899 (build-system r-build-system)
3900 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
3901 (synopsis "3D scatter plot")
3902 (description "This package provides an implementation of scatter plots for
3903 plotting. a three dimensional point cloud.")
3904 (license license:gpl2)))
3905
3906 (define-public r-ggridges
3907 (package
3908 (name "r-ggridges")
3909 (version "0.5.2")
3910 (source
3911 (origin
3912 (method url-fetch)
3913 (uri (cran-uri "ggridges" version))
3914 (sha256
3915 (base32
3916 "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh"))))
3917 (build-system r-build-system)
3918 (propagated-inputs
3919 `(("r-ggplot2" ,r-ggplot2)
3920 ("r-plyr" ,r-plyr)
3921 ("r-scales" ,r-scales)
3922 ("r-withr" ,r-withr)))
3923 (home-page "https://github.com/clauswilke/ggridges")
3924 (synopsis "Ridgeline plots in ggplot2")
3925 (description
3926 "Ridgeline plots provide a convenient way of visualizing changes in
3927 distributions over time or space. This package enables the creation of such
3928 plots in @code{ggplot2}.")
3929 (license license:gpl2)))
3930
3931 (define-public r-ggjoy
3932 (package
3933 (name "r-ggjoy")
3934 (version "0.4.1")
3935 (source
3936 (origin
3937 (method url-fetch)
3938 (uri (cran-uri "ggjoy" version))
3939 (sha256
3940 (base32
3941 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
3942 (build-system r-build-system)
3943 (propagated-inputs
3944 `(("r-ggplot2" ,r-ggplot2)
3945 ("r-ggridges" ,r-ggridges)))
3946 (home-page "https://github.com/clauswilke/ggjoy")
3947 (synopsis "Joyplots in ggplot2")
3948 (description "Joyplots provide a convenient way of visualizing changes in
3949 distributions over time or space. This package enables the creation of such
3950 plots in @code{ggplot2}.")
3951 (license license:gpl2)))
3952
3953 (define-public r-cli
3954 (package
3955 (name "r-cli")
3956 (version "2.0.2")
3957 (source
3958 (origin
3959 (method url-fetch)
3960 (uri (cran-uri "cli" version))
3961 (sha256
3962 (base32
3963 "1dhkah6jvr96k4h4agcc2rfls75bpjb0j58fzaz3dc0fp3jk8229"))))
3964 (build-system r-build-system)
3965 (propagated-inputs
3966 `(("r-assertthat" ,r-assertthat)
3967 ("r-crayon" ,r-crayon)
3968 ("r-fansi" ,r-fansi)
3969 ("r-glue" ,r-glue)))
3970 (home-page "https://github.com/r-lib/cli#readme")
3971 (synopsis "Helpers for developing command line interfaces")
3972 (description "This package provides a suite of tools designed to build
3973 attractive command line interfaces (CLIs). It includes tools for drawing
3974 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
3975 (license license:expat)))
3976
3977 (define-public r-argparser
3978 (package
3979 (name "r-argparser")
3980 (version "0.6")
3981 (source
3982 (origin
3983 (method url-fetch)
3984 (uri (cran-uri "argparser" version))
3985 (sha256
3986 (base32
3987 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
3988 (build-system r-build-system)
3989 (home-page "https://bitbucket.org/djhshih/argparser")
3990 (synopsis "Command-line argument parser")
3991 (description
3992 "This package provides a cross-platform command-line argument parser
3993 written purely in R with no external dependencies. It is useful with the
3994 Rscript front-end and facilitates turning an R script into an executable
3995 script.")
3996 (license license:gpl3+)))
3997
3998 (define-public r-debugme
3999 (package
4000 (name "r-debugme")
4001 (version "1.1.0")
4002 (source
4003 (origin
4004 (method url-fetch)
4005 (uri (cran-uri "debugme" version))
4006 (sha256
4007 (base32
4008 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
4009 (build-system r-build-system)
4010 (propagated-inputs `(("r-crayon" ,r-crayon)))
4011 (home-page "https://github.com/r-lib/debugme#readme")
4012 (synopsis "Debug R packages")
4013 (description
4014 "This package allows the user to specify debug messages as special string
4015 constants, and control debugging of packages via environment variables.")
4016 (license license:expat)))
4017
4018 (define-public r-processx
4019 (package
4020 (name "r-processx")
4021 (version "3.4.2")
4022 (source
4023 (origin
4024 (method url-fetch)
4025 (uri (cran-uri "processx" version))
4026 (sha256
4027 (base32
4028 "02awswxq6wh3rl99dncw5n6c1xmd0v81xcdp2dfyi6vm6b3gz84l"))))
4029 (build-system r-build-system)
4030 (propagated-inputs
4031 `(("r-ps" ,r-ps)
4032 ("r-r6" ,r-r6)))
4033 (home-page "https://github.com/r-lib/processx3")
4034 (synopsis "Execute and control system processes")
4035 (description
4036 "This package provides portable tools to run system processes in the
4037 background. It can check if a background process is running; wait on a
4038 background process to finish; get the exit status of finished processes; kill
4039 background processes and their children; restart processes. It can read the
4040 standard output and error of the processes, using non-blocking connections.
4041 @code{processx} can poll a process for standard output or error, with a
4042 timeout. It can also poll several processes at once.")
4043 (license license:expat)))
4044
4045 (define-public r-tsp
4046 (package
4047 (name "r-tsp")
4048 (version "1.1-10")
4049 (source
4050 (origin
4051 (method url-fetch)
4052 (uri (cran-uri "TSP" version))
4053 (sha256
4054 (base32
4055 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
4056 (properties `((upstream-name . "TSP")))
4057 (build-system r-build-system)
4058 (propagated-inputs `(("r-foreach" ,r-foreach)))
4059 (home-page "https://cran.r-project.org/web/packages/TSP/")
4060 (synopsis "Traveling salesperson problem (TSP)")
4061 (description "This package provides basic infrastructure and some
4062 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
4063 traveling salesman problem).")
4064 (license license:gpl3)))
4065
4066 (define-public r-qap
4067 (package
4068 (name "r-qap")
4069 (version "0.1-1")
4070 (source
4071 (origin
4072 (method url-fetch)
4073 (uri (cran-uri "qap" version))
4074 (sha256
4075 (base32
4076 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
4077 (build-system r-build-system)
4078 (native-inputs `(("gfortran" ,gfortran)))
4079 (home-page "https://cran.r-project.org/web/packages/qap/")
4080 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
4081 (description "This package implements heuristics for the @dfn{quadratic
4082 assignment problem} (QAP). Currently only a simulated annealing heuristic is
4083 available.")
4084 (license license:gpl3)))
4085
4086 (define-public r-gclus
4087 (package
4088 (name "r-gclus")
4089 (version "1.3.2")
4090 (source
4091 (origin
4092 (method url-fetch)
4093 (uri (cran-uri "gclus" version))
4094 (sha256
4095 (base32
4096 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
4097 (build-system r-build-system)
4098 (propagated-inputs `(("r-cluster" ,r-cluster)))
4099 (home-page "https://cran.r-project.org/web/packages/gclus/")
4100 (synopsis "Clustering graphics")
4101 (description "This package orders panels in scatterplot matrices and
4102 parallel coordinate displays by some merit index. It contains various indices
4103 of merit, ordering functions, and enhanced versions of @code{pairs} and
4104 @code{parcoord} which color panels according to their merit level.")
4105 (license license:gpl2+)))
4106
4107 (define-public r-webshot
4108 (package
4109 (name "r-webshot")
4110 (version "0.5.2")
4111 (source
4112 (origin
4113 (method url-fetch)
4114 (uri (cran-uri "webshot" version))
4115 (sha256
4116 (base32
4117 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
4118 (build-system r-build-system)
4119 (propagated-inputs
4120 `(("r-callr" ,r-callr)
4121 ("r-jsonlite" ,r-jsonlite)
4122 ("r-magrittr" ,r-magrittr)))
4123 (home-page "https://github.com/wch/webshot/")
4124 (synopsis "Take screenshots of web pages")
4125 (description
4126 "Webshot makes it easy to take screenshots of web pages from within R.
4127 It can also run Shiny applications locally and take screenshots of the
4128 application; and it can render and screenshot static as well as interactive R
4129 Markdown documents.")
4130 (license license:gpl2)))
4131
4132 (define-public r-seriation
4133 (package
4134 (name "r-seriation")
4135 (version "1.2-8")
4136 (source
4137 (origin
4138 (method url-fetch)
4139 (uri (cran-uri "seriation" version))
4140 (sha256
4141 (base32
4142 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
4143 (build-system r-build-system)
4144 (propagated-inputs
4145 `(("r-cluster" ,r-cluster)
4146 ("r-colorspace" ,r-colorspace)
4147 ("r-dendextend" ,r-dendextend)
4148 ("r-gclus" ,r-gclus)
4149 ("r-gplots" ,r-gplots)
4150 ("r-mass" ,r-mass)
4151 ("r-qap" ,r-qap)
4152 ("r-registry" ,r-registry)
4153 ("r-tsp" ,r-tsp)))
4154 (native-inputs `(("gfortran" ,gfortran)))
4155 (home-page "https://s2.smu.edu/IDA/seriation/")
4156 (synopsis "Infrastructure for ordering objects using seriation")
4157 (description
4158 "This package provides infrastructure for seriation with an
4159 implementation of several seriation/sequencing techniques to reorder matrices,
4160 dissimilarity matrices, and dendrograms. It also provides (optimally)
4161 reordered heatmaps, color images and clustering visualizations like
4162 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4163 iVAT).")
4164 (license license:gpl3)))
4165
4166 (define-public r-xfun
4167 (package
4168 (name "r-xfun")
4169 (version "0.13")
4170 (source
4171 (origin
4172 (method url-fetch)
4173 (uri (cran-uri "xfun" version))
4174 (sha256
4175 (base32 "03iyqgx9mmdbd3qih70qzijjqcdg7k7ps5r1y6q8praanx9qvnm3"))))
4176 (build-system r-build-system)
4177 ;; knitr itself depends on xfun
4178 #;
4179 (native-inputs
4180 `(("r-knitr" ,r-knitr)))
4181 (home-page "https://github.com/yihui/xfun")
4182 (synopsis "Miscellaneous functions")
4183 (description
4184 "This package provides miscellaneous functions commonly used in other
4185 packages maintained by Yihui Xie.")
4186 (license license:expat)))
4187
4188 (define-public r-utf8
4189 (package
4190 (name "r-utf8")
4191 (version "1.1.4")
4192 (source
4193 (origin
4194 (method url-fetch)
4195 (uri (cran-uri "utf8" version))
4196 (sha256
4197 (base32
4198 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4199 (build-system r-build-system)
4200 (home-page "https://github.com/patperry/r-utf8")
4201 (synopsis "Unicode text processing")
4202 (description
4203 "This package provides tools to process and print UTF-8 encoded
4204 international text (Unicode). Input, validate, normalize, encode, format, and
4205 display.")
4206 (license license:asl2.0)))
4207
4208 (define-public r-zeallot
4209 (package
4210 (name "r-zeallot")
4211 (version "0.1.0")
4212 (source
4213 (origin
4214 (method url-fetch)
4215 (uri (cran-uri "zeallot" version))
4216 (sha256
4217 (base32
4218 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4219 (build-system r-build-system)
4220 (home-page "https://github.com/nteetor/zeallot")
4221 (synopsis "Multiple, unpacking, and destructuring assignment")
4222 (description
4223 "This package provides a @code{%<-%} operator to perform multiple,
4224 unpacking, and destructuring assignment in R. The operator unpacks the
4225 right-hand side of an assignment into multiple values and assigns these values
4226 to variables on the left-hand side of the assignment.")
4227 (license license:expat)))
4228
4229 (define-public r-vctrs
4230 (package
4231 (name "r-vctrs")
4232 (version "0.2.4")
4233 (source
4234 (origin
4235 (method url-fetch)
4236 (uri (cran-uri "vctrs" version))
4237 (sha256
4238 (base32
4239 "15sgzs6afvmhssk6jcg41rn3bvmzmbm4sgca6f6x8lfrsazvdj6w"))))
4240 (build-system r-build-system)
4241 (propagated-inputs
4242 `(("r-digest" ,r-digest)
4243 ("r-ellipsis" ,r-ellipsis)
4244 ("r-glue" ,r-glue)
4245 ("r-rlang" ,r-rlang)))
4246 (native-inputs
4247 `(("r-knitr" ,r-knitr)))
4248 (home-page "https://github.com/r-lib/vctrs")
4249 (synopsis "Vector helpers")
4250 (description
4251 "There are three main goals to the @code{vctrs} package:
4252
4253 @enumerate
4254 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4255 @code{length()} and @code{class()}. These definitions are paired with a
4256 framework for type-coercion and size-recycling.
4257 @item To define type- and size-stability as desirable function properties, use
4258 them to analyse existing base function, and to propose better alternatives.
4259 This work has been particularly motivated by thinking about the ideal
4260 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4261 @item To provide a new @code{vctr} base class that makes it easy to create new
4262 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4263 a few new @code{vctrs} generics, making implementation considerably simpler
4264 and more robust.
4265 @end enumerate\n")
4266 (license license:gpl3)))
4267
4268 (define-public r-pillar
4269 (package
4270 (name "r-pillar")
4271 (version "1.4.3")
4272 (source
4273 (origin
4274 (method url-fetch)
4275 (uri (cran-uri "pillar" version))
4276 (sha256
4277 (base32
4278 "02sn7zw80wq33jgxk2i6m5jb83sk7y72dfhgyy0apfinv05w92ss"))))
4279 (build-system r-build-system)
4280 (propagated-inputs
4281 `(("r-cli" ,r-cli)
4282 ("r-crayon" ,r-crayon)
4283 ("r-fansi" ,r-fansi)
4284 ("r-rlang" ,r-rlang)
4285 ("r-utf8" ,r-utf8)
4286 ("r-vctrs" ,r-vctrs)))
4287 (home-page "https://github.com/r-lib/pillar")
4288 (synopsis "Coloured formatting for columns")
4289 (description
4290 "This package provides a @code{pillar} generic designed for formatting
4291 columns of data using the full range of colours provided by modern
4292 terminals.")
4293 (license license:gpl3)))
4294
4295 (define-public r-uuid
4296 (package
4297 (name "r-uuid")
4298 (version "0.1-4")
4299 (source
4300 (origin
4301 (method url-fetch)
4302 (uri (cran-uri "uuid" version))
4303 (sha256
4304 (base32
4305 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
4306 (build-system r-build-system)
4307 (home-page "https://www.rforge.net/uuid")
4308 (synopsis "Tools for generating and handling of UUIDs")
4309 (description
4310 "This package provides tools for generating and handling of
4311 @dfn{Universally Unique Identifiers} (UUIDs).")
4312 (license license:expat)))
4313
4314 (define-public r-tinytex
4315 (package
4316 (name "r-tinytex")
4317 (version "0.22")
4318 (source
4319 (origin
4320 (method url-fetch)
4321 (uri (cran-uri "tinytex" version))
4322 (sha256
4323 (base32
4324 "0s9f62v3ps5f8903ar6kxlf1z3b4v78vlw1nb05bq55dgj8brg3b"))))
4325 (build-system r-build-system)
4326 (propagated-inputs
4327 `(("r-xfun" ,r-xfun)))
4328 (home-page "https://github.com/yihui/tinytex")
4329 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4330 (description
4331 "This package provides helper functions to install and maintain the LaTeX
4332 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4333 easy-to-maintain version of TeX Live. This package also contains helper
4334 functions to compile LaTeX documents, and install missing LaTeX packages
4335 automatically.")
4336 (license license:expat)))
4337
4338 (define-public r-network
4339 (package
4340 (name "r-network")
4341 (version "1.16.0")
4342 (source
4343 (origin
4344 (method url-fetch)
4345 (uri (cran-uri "network" version))
4346 (sha256
4347 (base32
4348 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4349 (build-system r-build-system)
4350 (propagated-inputs
4351 `(("r-magrittr" ,r-magrittr)
4352 ("r-tibble" ,r-tibble)))
4353 (home-page "https://statnet.org/")
4354 (synopsis "Classes for relational data")
4355 (description
4356 "This package provides tools to create and modify network objects. The
4357 @code{network} class can represent a range of relational data types, and
4358 supports arbitrary vertex/edge/graph attributes.")
4359 (license license:gpl2+)))
4360
4361 (define-public r-statnet-common
4362 (package
4363 (name "r-statnet-common")
4364 (version "4.3.0")
4365 (source
4366 (origin
4367 (method url-fetch)
4368 (uri (cran-uri "statnet.common" version))
4369 (sha256
4370 (base32
4371 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4372 (properties
4373 `((upstream-name . "statnet.common")))
4374 (build-system r-build-system)
4375 (propagated-inputs
4376 `(("r-coda" ,r-coda)))
4377 (home-page "https://statnet.org")
4378 (synopsis "R scripts and utilities used by the Statnet software")
4379 (description "This package provides non-statistical utilities used by the
4380 software developed by the Statnet Project.")
4381 (license license:gpl3)))
4382
4383 (define-public r-statcheck
4384 (package
4385 (name "r-statcheck")
4386 (version "1.3.0")
4387 (source
4388 (origin
4389 (method url-fetch)
4390 (uri (cran-uri "statcheck" version))
4391 (sha256
4392 (base32
4393 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4394 (build-system r-build-system)
4395 (propagated-inputs
4396 `(("r-ggplot2" ,r-ggplot2)
4397 ("r-plyr" ,r-plyr)
4398 ("r-rmarkdown" ,r-rmarkdown)))
4399 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4400 (synopsis "Extract statistics from articles and recompute p-values")
4401 (description "This package can automatically extract statistical
4402 null-hypothesis significant testing (NHST) results from articles and recompute
4403 the p-values based on the reported test statistic and degrees of freedom to
4404 detect possible inconsistencies.")
4405 (license license:gpl2)))
4406
4407 (define-public r-sna
4408 (package
4409 (name "r-sna")
4410 (version "2.5")
4411 (source
4412 (origin
4413 (method url-fetch)
4414 (uri (cran-uri "sna" version))
4415 (sha256
4416 (base32
4417 "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
4418 (build-system r-build-system)
4419 (propagated-inputs
4420 `(("r-network" ,r-network)
4421 ("r-statnet-common" ,r-statnet-common)))
4422 (home-page "https://statnet.org")
4423 (synopsis "Tools for social network analysis")
4424 (description
4425 "This package provides a range of tools for social network analysis,
4426 including node and graph-level indices, structural distance and covariance
4427 methods, structural equivalence detection, network regression, random graph
4428 generation, and 2D/3D network visualization.")
4429 (license license:gpl2+)))
4430
4431 (define-public r-tfisher
4432 (package
4433 (name "r-tfisher")
4434 (version "0.2.0")
4435 (source
4436 (origin
4437 (method url-fetch)
4438 (uri (cran-uri "TFisher" version))
4439 (sha256
4440 (base32
4441 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4442 (properties `((upstream-name . "TFisher")))
4443 (build-system r-build-system)
4444 (propagated-inputs
4445 `(("r-matrix" ,r-matrix)
4446 ("r-mvtnorm" ,r-mvtnorm)
4447 ("r-sn" ,r-sn)))
4448 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4449 (synopsis "Optimal thresholding Fisher's p-value combination method")
4450 (description
4451 "This package provides the @dfn{cumulative distribution function} (CDF),
4452 quantile, and statistical power calculator for a collection of thresholding
4453 Fisher's p-value combination methods, including Fisher's p-value combination
4454 method, truncated product method and, in particular, soft-thresholding
4455 Fisher's p-value combination method which is proven to be optimal in some
4456 context of signal detection. The p-value calculator for the omnibus version
4457 of these tests are also included.")
4458 (license license:gpl2)))
4459
4460 (define-public r-ttr
4461 (package
4462 (name "r-ttr")
4463 (version "0.23-6")
4464 (source
4465 (origin
4466 (method url-fetch)
4467 (uri (cran-uri "TTR" version))
4468 (sha256
4469 (base32
4470 "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg"))))
4471 (properties `((upstream-name . "TTR")))
4472 (build-system r-build-system)
4473 (propagated-inputs
4474 `(("r-curl" ,r-curl)
4475 ("r-xts" ,r-xts)
4476 ("r-zoo" ,r-zoo)))
4477 (home-page "https://github.com/joshuaulrich/TTR")
4478 (synopsis "Technical trading rules")
4479 (description
4480 "This package provides functions and data to construct technical trading
4481 rules with R.")
4482 (license license:gpl2)))
4483
4484 (define-public r-leaps
4485 (package
4486 (name "r-leaps")
4487 (version "3.1")
4488 (source
4489 (origin
4490 (method url-fetch)
4491 (uri (cran-uri "leaps" version))
4492 (sha256
4493 (base32
4494 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
4495 (build-system r-build-system)
4496 (native-inputs `(("gfortran" ,gfortran)))
4497 (home-page "https://cran.r-project.org/web/packages/leaps/")
4498 (synopsis "Regression subset selection")
4499 (description
4500 "This package provides tools for regression subset selection, including
4501 exhaustive search.")
4502 (license license:gpl2+)))
4503
4504 (define-public r-splus2r
4505 (package
4506 (name "r-splus2r")
4507 (version "1.2-2")
4508 (source
4509 (origin
4510 (method url-fetch)
4511 (uri (cran-uri "splus2R" version))
4512 (sha256
4513 (base32
4514 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4515 (properties `((upstream-name . "splus2R")))
4516 (build-system r-build-system)
4517 (native-inputs `(("gfortran" ,gfortran)))
4518 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4519 (synopsis "Supplemental S-PLUS functionality in R")
4520 (description
4521 "Currently there are many functions in S-PLUS that are missing in R. To
4522 facilitate the conversion of S-PLUS packages to R packages, this package
4523 provides some missing S-PLUS functionality in R.")
4524 (license license:gpl2)))
4525
4526 (define-public r-ifultools
4527 (package
4528 (name "r-ifultools")
4529 (version "2.0-5")
4530 (source
4531 (origin
4532 (method url-fetch)
4533 (uri (cran-uri "ifultools" version))
4534 (sha256
4535 (base32
4536 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4537 (build-system r-build-system)
4538 (propagated-inputs
4539 `(("r-mass" ,r-mass)
4540 ("r-splus2r" ,r-splus2r)))
4541 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4542 (synopsis "Insightful research tools")
4543 (description "This package provides C code used by the wmtsa, fractal, and
4544 sapa R packages.")
4545 (license license:gpl2)))
4546
4547 (define-public r-sapa
4548 (package
4549 (name "r-sapa")
4550 (version "2.0-2")
4551 (source
4552 (origin
4553 (method url-fetch)
4554 (uri (cran-uri "sapa" version))
4555 (sha256
4556 (base32
4557 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4558 (build-system r-build-system)
4559 (propagated-inputs
4560 `(("r-ifultools" ,r-ifultools)
4561 ("r-splus2r" ,r-splus2r)))
4562 (home-page "https://cran.r-project.org/web/packages/sapa/")
4563 (synopsis "Spectral analysis for physical applications")
4564 (description "This package provides software for the book Spectral
4565 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4566 Cambridge University Press, 1993.")
4567 (license license:gpl2)))
4568
4569 (define-public r-aggregation
4570 (package
4571 (name "r-aggregation")
4572 (version "1.0.1")
4573 (source
4574 (origin
4575 (method url-fetch)
4576 (uri (cran-uri "aggregation" version))
4577 (sha256
4578 (base32
4579 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4580 (build-system r-build-system)
4581 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4582 (synopsis "Methods for p-value aggregation")
4583 (description
4584 "This package contains functionality for performing the following methods
4585 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4586 Fisher's method), and Sidak correction.")
4587 (license license:gpl3)))
4588
4589 (define-public r-quantmod
4590 (package
4591 (name "r-quantmod")
4592 (version "0.4.17")
4593 (source
4594 (origin
4595 (method url-fetch)
4596 (uri (cran-uri "quantmod" version))
4597 (sha256
4598 (base32
4599 "1ss441rwlr88kz212m0wgx0hwgwi41rhy1jncg2lgqzqfvr5dzqa"))))
4600 (build-system r-build-system)
4601 (propagated-inputs
4602 `(("r-curl" ,r-curl)
4603 ("r-ttr" ,r-ttr)
4604 ("r-xts" ,r-xts)
4605 ("r-zoo" ,r-zoo)))
4606 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4607 (synopsis "Quantitative financial modelling framework")
4608 (description "This package provides a quantitative financial modelling
4609 framework to allow users to specify, build, trade, and analyse quantitative
4610 financial trading strategies.")
4611 (license license:gpl3)))
4612
4613 (define-public r-tseries
4614 (package
4615 (name "r-tseries")
4616 (version "0.10-47")
4617 (source
4618 (origin
4619 (method url-fetch)
4620 (uri (cran-uri "tseries" version))
4621 (sha256
4622 (base32
4623 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4624 (build-system r-build-system)
4625 (propagated-inputs
4626 `(("r-quadprog" ,r-quadprog)
4627 ("r-quantmod" ,r-quantmod)
4628 ("r-zoo" ,r-zoo)))
4629 (native-inputs
4630 `(("gfortran" ,gfortran)))
4631 (home-page "https://cran.r-project.org/web/packages/tseries/")
4632 (synopsis "Time series analysis and computational finance")
4633 (description
4634 "This package provides functions relating to time series analysis and
4635 computational finance.")
4636 (license license:gpl2)))
4637
4638 (define-public r-wmtsa
4639 (package
4640 (name "r-wmtsa")
4641 (version "2.0-3")
4642 (source
4643 (origin
4644 (method url-fetch)
4645 (uri (cran-uri "wmtsa" version))
4646 (sha256
4647 (base32
4648 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4649 (build-system r-build-system)
4650 (propagated-inputs
4651 `(("r-ifultools" ,r-ifultools)
4652 ("r-mass" ,r-mass)
4653 ("r-splus2r" ,r-splus2r)))
4654 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4655 (synopsis "Wavelet methods for time series analysis")
4656 (description
4657 "This package provides software to accompany the book \"Wavelet Methods
4658 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4659 University Press, 2000.")
4660 (license license:gpl2)))
4661
4662 (define-public r-tsa
4663 (package
4664 (name "r-tsa")
4665 (version "1.2")
4666 (source
4667 (origin
4668 (method url-fetch)
4669 (uri (cran-uri "TSA" version))
4670 (sha256
4671 (base32
4672 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4673 (properties `((upstream-name . "TSA")))
4674 (build-system r-build-system)
4675 (propagated-inputs
4676 `(("r-leaps" ,r-leaps)
4677 ("r-locfit" ,r-locfit)
4678 ("r-mgcv" ,r-mgcv)))
4679 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
4680 (synopsis "Time series analysis")
4681 (description
4682 "This package contains R functions and datasets detailed in the book
4683 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4684 Cryer and Kung-Sik Chan.")
4685 (license license:gpl2+)))
4686
4687 (define-public r-extradistr
4688 (package
4689 (name "r-extradistr")
4690 (version "1.8.11")
4691 (source
4692 (origin
4693 (method url-fetch)
4694 (uri (cran-uri "extraDistr" version))
4695 (sha256
4696 (base32
4697 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4698 (properties `((upstream-name . "extraDistr")))
4699 (build-system r-build-system)
4700 (propagated-inputs
4701 `(("r-rcpp" ,r-rcpp)))
4702 (home-page "https://github.com/twolodzko/extraDistr")
4703 (synopsis "Additional univariate and multivariate distributions")
4704 (description
4705 "This package implements density, distribution functions, quantile
4706 functions and random generation functions for a large number of univariate and
4707 multivariate distributions.")
4708 (license license:gpl2)))
4709
4710 (define-public r-fractal
4711 (package
4712 (name "r-fractal")
4713 (version "2.0-4")
4714 (source
4715 (origin
4716 (method url-fetch)
4717 (uri (cran-uri "fractal" version))
4718 (sha256
4719 (base32
4720 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4721 (build-system r-build-system)
4722 (propagated-inputs
4723 `(("r-ifultools" ,r-ifultools)
4724 ("r-mass" ,r-mass)
4725 ("r-sapa" ,r-sapa)
4726 ("r-scatterplot3d" ,r-scatterplot3d)
4727 ("r-splus2r" ,r-splus2r)
4728 ("r-wmtsa" ,r-wmtsa)))
4729 (home-page "https://cran.r-project.org/web/packages/fractal/")
4730 (synopsis "Fractal time series modeling and analysis")
4731 (description
4732 "This package provides tools for stochastic fractal and deterministic
4733 chaotic time series analysis.")
4734 (license license:gpl2)))
4735
4736 (define-public r-urca
4737 (package
4738 (name "r-urca")
4739 (version "1.3-0")
4740 (source
4741 (origin
4742 (method url-fetch)
4743 (uri (cran-uri "urca" version))
4744 (sha256
4745 (base32
4746 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4747 (build-system r-build-system)
4748 (propagated-inputs `(("r-nlme" ,r-nlme)))
4749 (native-inputs `(("gfortran" ,gfortran)))
4750 (home-page "https://cran.r-project.org/web/packages/urca/")
4751 (synopsis "Unit root and cointegration tests for time series data")
4752 (description
4753 "This package provides unit root and cointegration tests encountered in
4754 applied econometric analysis.")
4755 (license license:gpl2+)))
4756
4757 (define-public r-cubature
4758 (package
4759 (name "r-cubature")
4760 (version "2.0.4")
4761 (source
4762 (origin
4763 (method url-fetch)
4764 (uri (cran-uri "cubature" version))
4765 (sha256
4766 (base32
4767 "0jpyq8j7x06dpiz29w48av879ygldzgls9z810192hsymkmfaz6r"))))
4768 (build-system r-build-system)
4769 (propagated-inputs
4770 `(("r-rcpp" ,r-rcpp)))
4771 (home-page "https://github.com/bnaras/cubature")
4772 (synopsis "Adaptive multivariate integration over hypercubes")
4773 (description
4774 "This package is an R wrapper around the cubature C library for adaptive
4775 multivariate integration over hypercubes. This version provides both
4776 @code{hcubature} and @code{pcubature} routines in addition to a vector
4777 interface.")
4778 ;; The included cubature C library is released under GPLv2+, but the
4779 ;; wrapper declares the license to be GPLv3+.
4780 (license (list license:gpl2+ license:gpl3+))))
4781
4782 (define-public r-trend
4783 (package
4784 (name "r-trend")
4785 (version "1.1.2")
4786 (source
4787 (origin
4788 (method url-fetch)
4789 (uri (cran-uri "trend" version))
4790 (sha256
4791 (base32
4792 "09b6ycyfgs4xlhx6kn6qm5rl2acp58hzhv8qclzn3kb1wjjyvxy5"))))
4793 (build-system r-build-system)
4794 (propagated-inputs
4795 `(("r-extradistr" ,r-extradistr)))
4796 (native-inputs
4797 `(("gfortran" ,gfortran)))
4798 (home-page "https://cran.r-project.org/web/packages/trend/")
4799 (synopsis "Non-parametric trend tests and change-point detection")
4800 (description
4801 "The analysis of environmental data often requires the detection of
4802 trends and change-points. This package includes tests for trend
4803 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4804 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4805 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4806 correlation trend test), change-point detection (Lanzante's test procedures,
4807 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4808 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4809 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
4810 sample Robust Rank-Order Distributional Test.")
4811 (license license:gpl3)))
4812
4813 (define-public r-expm
4814 (package
4815 (name "r-expm")
4816 (version "0.999-4")
4817 (source
4818 (origin
4819 (method url-fetch)
4820 (uri (cran-uri "expm" version))
4821 (sha256
4822 (base32
4823 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
4824 (build-system r-build-system)
4825 (propagated-inputs `(("r-matrix" ,r-matrix)))
4826 (native-inputs `(("gfortran" ,gfortran)))
4827 (home-page "https://r-forge.r-project.org/projects/expm/")
4828 (synopsis "Tools for matrix exponentials and related quantities")
4829 (description
4830 "This package provides tools for the computation of the matrix
4831 exponential, logarithm, square root, and related quantities.")
4832 (license license:gpl2+)))
4833
4834 (define-public r-complexplus
4835 (package
4836 (name "r-complexplus")
4837 (version "2.1")
4838 (source
4839 (origin
4840 (method url-fetch)
4841 (uri (cran-uri "complexplus" version))
4842 (sha256
4843 (base32
4844 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
4845 (build-system r-build-system)
4846 (propagated-inputs
4847 `(("r-expm" ,r-expm)
4848 ("r-matrix" ,r-matrix)))
4849 (home-page "https://cran.r-project.org/web/packages/complexplus/")
4850 (synopsis "Functions of complex or real variables")
4851 (description
4852 "This package extends several functions to the complex domain, including
4853 the matrix exponential and logarithm, and the determinant.")
4854 (license license:gpl2)))
4855
4856 (define-public r-phontools
4857 (package
4858 (name "r-phontools")
4859 (version "0.2-2.1")
4860 (source
4861 (origin
4862 (method url-fetch)
4863 (uri (cran-uri "phonTools" version))
4864 (sha256
4865 (base32
4866 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
4867 (properties `((upstream-name . "phonTools")))
4868 (build-system r-build-system)
4869 (home-page "http://www.santiagobarreda.com/rscripts.html")
4870 (synopsis "Tools for phonetic and acoustic analyses")
4871 (description
4872 "This package contains tools for the organization, display, and analysis
4873 of the sorts of data frequently encountered in phonetics research and
4874 experimentation, including the easy creation of IPA vowel plots, and the
4875 creation and manipulation of WAVE audio files.")
4876 (license license:bsd-2)))
4877
4878 (define-public r-np
4879 (package
4880 (name "r-np")
4881 (version "0.60-10")
4882 (source
4883 (origin
4884 (method url-fetch)
4885 (uri (cran-uri "np" version))
4886 (sha256
4887 (base32
4888 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
4889 (build-system r-build-system)
4890 (propagated-inputs
4891 `(("r-boot" ,r-boot)
4892 ("r-cubature" ,r-cubature)
4893 ("r-quadprog" ,r-quadprog)
4894 ("r-quantreg" ,r-quantreg)))
4895 (home-page "https://github.com/JeffreyRacine/R-Package-np")
4896 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
4897 (description "This package provides non-parametric (and semi-parametric)
4898 kernel methods that seamlessly handle a mix of continuous, unordered, and
4899 ordered factor data types.")
4900 ;; Any version of the GPL.
4901 (license license:gpl3+)))
4902
4903 (define-public r-powerplus
4904 (package
4905 (name "r-powerplus")
4906 (version "3.1")
4907 (source
4908 (origin
4909 (method url-fetch)
4910 (uri (cran-uri "powerplus" version))
4911 (sha256
4912 (base32
4913 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
4914 (build-system r-build-system)
4915 (propagated-inputs
4916 `(("r-complexplus" ,r-complexplus)
4917 ("r-expm" ,r-expm)
4918 ("r-mass" ,r-mass)
4919 ("r-matrix" ,r-matrix)
4920 ("r-phontools" ,r-phontools)))
4921 (home-page "https://cran.r-project.org/web/packages/powerplus/")
4922 (synopsis "Exponentiation operations")
4923 (description
4924 "This package provides tools for the computation of matrix and scalar
4925 exponentiation.")
4926 (license license:gpl2)))
4927
4928 (define-public r-egg
4929 (package
4930 (name "r-egg")
4931 (version "0.4.5")
4932 (source
4933 (origin
4934 (method url-fetch)
4935 (uri (cran-uri "egg" version))
4936 (sha256
4937 (base32
4938 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
4939 (properties `((upstream-name . "egg")))
4940 (build-system r-build-system)
4941 (propagated-inputs
4942 `(("r-ggplot2" ,r-ggplot2)
4943 ("r-gridextra" ,r-gridextra)
4944 ("r-gtable" ,r-gtable)))
4945 (home-page "https://cran.r-project.org/web/packages/egg")
4946 (synopsis "Extensions for ggplot2")
4947 (description
4948 "This package provides miscellaneous functions to help customize ggplot2
4949 objects. High-level functions are provided to post-process ggplot2 layouts
4950 and allow alignment between plot panels, as well as setting panel sizes to
4951 fixed values. Other functions include a custom @code{geom}, and helper
4952 functions to enforce symmetric scales or add tags to facetted plots.")
4953 (license license:gpl3)))
4954
4955 (define-public r-heatmaply
4956 (package
4957 (name "r-heatmaply")
4958 (version "1.1.0")
4959 (source
4960 (origin
4961 (method url-fetch)
4962 (uri (cran-uri "heatmaply" version))
4963 (sha256
4964 (base32
4965 "133q8ir45vhfxs2lnd96k97g21ihg2arfhp349kmk339pk32fcxz"))))
4966 (build-system r-build-system)
4967 (propagated-inputs
4968 `(("r-assertthat" ,r-assertthat)
4969 ("r-colorspace" ,r-colorspace)
4970 ("r-dendextend" ,r-dendextend)
4971 ("r-egg" ,r-egg)
4972 ("r-ggplot2" ,r-ggplot2)
4973 ("r-htmlwidgets" ,r-htmlwidgets)
4974 ("r-magrittr" ,r-magrittr)
4975 ("r-plotly" ,r-plotly)
4976 ("r-rcolorbrewer" ,r-rcolorbrewer)
4977 ("r-reshape2" ,r-reshape2)
4978 ("r-scales" ,r-scales)
4979 ("r-seriation" ,r-seriation)
4980 ("r-viridis" ,r-viridis)
4981 ("r-webshot" ,r-webshot)))
4982 (native-inputs
4983 `(("r-knitr" ,r-knitr)))
4984 (home-page "https://cran.r-project.org/package=heatmaply")
4985 (synopsis "Interactive cluster heat maps using plotly")
4986 (description
4987 "This package enables you to create interactive cluster heatmaps that can
4988 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
4989 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
4990 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
4991 a popular graphical method for visualizing high-dimensional data, in which a
4992 table of numbers is encoded as a grid of colored cells. The rows and columns
4993 of the matrix are ordered to highlight patterns and are often accompanied by
4994 dendrograms.")
4995 ;; Either version of the license.
4996 (license (list license:gpl2 license:gpl3))))
4997
4998 (define-public r-h5
4999 (package
5000 (name "r-h5")
5001 (version "0.9.9")
5002 (source
5003 (origin
5004 (method url-fetch)
5005 (uri (cran-uri "h5" version))
5006 (sha256
5007 (base32
5008 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
5009 (build-system r-build-system)
5010 (inputs
5011 `(("zlib" ,zlib)
5012 ("hdf5" ,hdf5)))
5013 (native-inputs
5014 `(("which" ,which)))
5015 (propagated-inputs
5016 `(("r-rcpp" ,r-rcpp)))
5017 (home-page "https://github.com/mannau/h5")
5018 (synopsis "Interface to the HDF5 Library")
5019 (description
5020 "This package provides an S4 interface to the HDF5 library supporting
5021 fast storage and retrieval of R-objects like vectors, matrices and arrays to
5022 binary files in a language independent format. The HDF5 format can therefore
5023 be used as an alternative to R's save/load mechanism. Since h5 is able to
5024 access only subsets of stored data it can also handle data sets which do not
5025 fit into memory.")
5026 (license license:bsd-2)))
5027
5028 (define-public r-cgdsr
5029 (package
5030 (name "r-cgdsr")
5031 (version "1.3.0")
5032 (source
5033 (origin
5034 (method url-fetch)
5035 (uri (cran-uri "cgdsr" version))
5036 (sha256
5037 (base32
5038 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
5039 (build-system r-build-system)
5040 (propagated-inputs
5041 `(("r-httr" ,r-httr)
5042 ("r-r-methodss3" ,r-r-methodss3)
5043 ("r-r-oo" ,r-r-oo)))
5044 (home-page "https://github.com/cBioPortal/cgdsr")
5045 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
5046 (description
5047 "This package provides a basic set of R functions for querying the Cancer
5048 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
5049 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
5050 (license license:lgpl3)))
5051
5052 (define-public r-import
5053 (package
5054 (name "r-import")
5055 (version "1.1.0")
5056 (source
5057 (origin
5058 (method url-fetch)
5059 (uri (cran-uri "import" version))
5060 (sha256
5061 (base32
5062 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
5063 (build-system r-build-system)
5064 (home-page "https://github.com/smbache/import")
5065 (synopsis "Import mechanism for R")
5066 (description
5067 "This is an alternative mechanism for importing objects from packages.
5068 The syntax allows for importing multiple objects from a package with a single
5069 command in an expressive way. The import package bridges some of the gap
5070 between using @code{library} (or @code{require}) and direct (single-object)
5071 imports. Furthermore the imported objects are not placed in the current
5072 environment. It is also possible to import objects from stand-alone @code{.R}
5073 files.")
5074 (license license:expat)))
5075
5076 (define-public r-shinyace
5077 (package
5078 (name "r-shinyace")
5079 (version "0.4.1")
5080 (source
5081 (origin
5082 (method url-fetch)
5083 (uri (cran-uri "shinyAce" version))
5084 (sha256
5085 (base32
5086 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
5087 (properties `((upstream-name . "shinyAce")))
5088 (build-system r-build-system)
5089 (propagated-inputs
5090 `(("r-shiny" ,r-shiny)
5091 ("r-jsonlite" ,r-jsonlite)))
5092 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
5093 (synopsis "Ace editor bindings for Shiny")
5094 (description
5095 "This package provides Ace editor bindings to enable a rich text editing
5096 environment within Shiny.")
5097 (license license:expat)))
5098
5099 (define-public r-randomizr
5100 (package
5101 (name "r-randomizr")
5102 (version "0.20.0")
5103 (source
5104 (origin
5105 (method url-fetch)
5106 (uri (cran-uri "randomizr" version))
5107 (sha256
5108 (base32
5109 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
5110 (properties `((upstream-name . "randomizr")))
5111 (build-system r-build-system)
5112 (native-inputs
5113 `(("r-knitr" ,r-knitr)))
5114 (home-page "https://declaredesign.org/r/randomizr/")
5115 (synopsis "Tools for common forms of random assignment and sampling")
5116 (description
5117 "This package provides tools for generating random assignments for common
5118 experimental designs and random samples for common sampling designs.")
5119 (license license:expat)))
5120
5121 (define-public r-base64url
5122 (package
5123 (name "r-base64url")
5124 (version "1.4")
5125 (source
5126 (origin
5127 (method url-fetch)
5128 (uri (cran-uri "base64url" version))
5129 (sha256
5130 (base32
5131 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
5132 (build-system r-build-system)
5133 (propagated-inputs
5134 `(("r-backports" ,r-backports)))
5135 (home-page "https://github.com/mllg/base64url")
5136 (synopsis "Fast and URL-safe base64 encoder and decoder")
5137 (description
5138 "This package provides a URL-safe base64 encoder and decoder. In
5139 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
5140 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
5141 encoder does not fill the string with trailing @code{=}. The resulting
5142 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
5143 and thus are safe to use in URLs or for file names. The package also comes
5144 with a simple base32 encoder/decoder suited for case insensitive file
5145 systems.")
5146 (license license:gpl3)))
5147
5148 (define-public r-radiant-data
5149 (package
5150 (name "r-radiant-data")
5151 (version "1.3.4")
5152 (source
5153 (origin
5154 (method url-fetch)
5155 (uri (cran-uri "radiant.data" version))
5156 (sha256
5157 (base32
5158 "19sjjb49inrfl7jzq4zpwhdslni0zrp30bl58pisin29ka3ylpzs"))
5159 (modules '((guix build utils)))
5160 (snippet
5161 '(begin
5162 ;; Delete files that are under CC-NC-SA.
5163 (delete-file-recursively "inst/app/tools/help")
5164 #t))))
5165 (properties `((upstream-name . "radiant.data")))
5166 (build-system r-build-system)
5167 (propagated-inputs
5168 `(("r-base64enc" ,r-base64enc)
5169 ("r-broom" ,r-broom)
5170 ("r-car" ,r-car)
5171 ("r-curl" ,r-curl)
5172 ("r-dplyr" ,r-dplyr)
5173 ("r-dt" ,r-dt)
5174 ("r-glue" ,r-glue)
5175 ("r-ggplot2" ,r-ggplot2)
5176 ("r-import" ,r-import)
5177 ("r-jsonlite" ,r-jsonlite)
5178 ("r-knitr" ,r-knitr)
5179 ("r-lubridate" ,r-lubridate)
5180 ("r-magrittr" ,r-magrittr)
5181 ("r-markdown" ,r-markdown)
5182 ("r-mass" ,r-mass)
5183 ("r-patchwork" ,r-patchwork)
5184 ("r-plotly" ,r-plotly)
5185 ("r-psych" ,r-psych)
5186 ("r-randomizr" ,r-randomizr)
5187 ("r-readr" ,r-readr)
5188 ("r-readxl" ,r-readxl)
5189 ("r-rlang" ,r-rlang)
5190 ("r-rmarkdown" ,r-rmarkdown)
5191 ("r-rstudioapi" ,r-rstudioapi)
5192 ("r-scales" ,r-scales)
5193 ("r-shiny" ,r-shiny)
5194 ("r-shinyfiles" ,r-shinyfiles)
5195 ("r-shinyace" ,r-shinyace)
5196 ("r-stringi" ,r-stringi)
5197 ("r-tibble" ,r-tibble)
5198 ("r-tidyr" ,r-tidyr)
5199 ("r-writexl" ,r-writexl)))
5200 (home-page "https://github.com/radiant-rstats/radiant.data")
5201 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5202 (description
5203 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5204 visualizing, summarizing, transforming, and combining data. It also contains
5205 functionality to generate reproducible reports of the analyses conducted in
5206 the application.")
5207 (license license:agpl3)))
5208
5209 (define-public r-algdesign
5210 (package
5211 (name "r-algdesign")
5212 (version "1.2.0")
5213 (source
5214 (origin
5215 (method url-fetch)
5216 (uri (cran-uri "AlgDesign" version))
5217 (sha256
5218 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5219 (properties `((upstream-name . "AlgDesign")))
5220 (build-system r-build-system)
5221 (home-page "https://github.com/jvbraun/AlgDesign")
5222 (synopsis "Algorithmic experimental design")
5223 (description
5224 "This package provides tools to calculate exact and approximate theory
5225 experimental designs for D, A, and I criteria. Very large designs may be
5226 created. Experimental designs may be blocked or blocked designs created from
5227 a candidate list, using several criteria. The blocking can be done when whole
5228 and within plot factors interact.")
5229 (license license:gpl2+)))
5230
5231 (define-public r-signal
5232 (package
5233 (name "r-signal")
5234 (version "0.7-6")
5235 (source
5236 (origin
5237 (method url-fetch)
5238 (uri (cran-uri "signal" version))
5239 (sha256
5240 (base32
5241 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5242 (build-system r-build-system)
5243 (propagated-inputs `(("r-mass" ,r-mass)))
5244 (native-inputs `(("gfortran" ,gfortran)))
5245 (home-page "https://cran.r-project.org/web/packages/signal/")
5246 (synopsis "Signal processing")
5247 (description
5248 "This package provides a set of signal processing functions originally
5249 written for Matlab and GNU Octave. It includes filter generation utilities,
5250 filtering functions, resampling routines, and visualization of filter models.
5251 It also includes interpolation functions.")
5252 (license license:gpl2)))
5253
5254 (define-public r-gsubfn
5255 (package
5256 (name "r-gsubfn")
5257 (version "0.7")
5258 (source
5259 (origin
5260 (method url-fetch)
5261 (uri (cran-uri "gsubfn" version))
5262 (sha256
5263 (base32
5264 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5265 (build-system r-build-system)
5266 (propagated-inputs `(("r-proto" ,r-proto)))
5267 (home-page "https://code.google.com/archive/p/gsubfn/")
5268 (synopsis "Utilities for strings and function arguments.")
5269 (description
5270 "This package provides @code{gsubfn} which is like @code{gsub} but can
5271 take a replacement function or certain other objects instead of the
5272 replacement string. Matches and back references are input to the replacement
5273 function and replaced by the function output. @code{gsubfn} can be used to
5274 split strings based on content rather than delimiters and for quasi-perl-style
5275 string interpolation. The package also has facilities for translating
5276 formulas to functions and allowing such formulas in function calls instead of
5277 functions.")
5278 (license license:gpl2+)))
5279
5280 (define-public r-sqldf
5281 (package
5282 (name "r-sqldf")
5283 (version "0.4-11")
5284 (source
5285 (origin
5286 (method url-fetch)
5287 (uri (cran-uri "sqldf" version))
5288 (sha256
5289 (base32
5290 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5291 (build-system r-build-system)
5292 (propagated-inputs
5293 `(("r-chron" ,r-chron)
5294 ("r-dbi" ,r-dbi)
5295 ("r-gsubfn" ,r-gsubfn)
5296 ("r-proto" ,r-proto)
5297 ("r-rsqlite" ,r-rsqlite)))
5298 (home-page "https://github.com/ggrothendieck/sqldf")
5299 (synopsis "Manipulate R data frames using SQL")
5300 (description
5301 "The @code{sqldf} function is typically passed a single argument which is
5302 an SQL select statement where the table names are ordinary R data frame names.
5303 @code{sqldf} transparently sets up a database, imports the data frames into
5304 that database, performs the SQL statement and returns the result using a
5305 heuristic to determine which class to assign to each column of the returned
5306 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5307 used to read filtered files into R even if the original files are larger than
5308 R itself can handle.")
5309 (license license:gpl2)))
5310
5311 (define-public r-abind
5312 (package
5313 (name "r-abind")
5314 (version "1.4-5")
5315 (source
5316 (origin
5317 (method url-fetch)
5318 (uri (cran-uri "abind" version))
5319 (sha256
5320 (base32
5321 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5322 (build-system r-build-system)
5323 (home-page "https://cran.r-project.org/web/packages/abind/")
5324 (synopsis "Combine multidimensional arrays")
5325 (description
5326 "This package provides tools to combine multidimensional arrays into a
5327 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5328 works with vectors, matrices, and higher-dimensional arrays. It also provides
5329 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5330 extracting and replacing data in arrays.")
5331 (license license:lgpl2.0+)))
5332
5333 (define-public r-prroc
5334 (package
5335 (name "r-prroc")
5336 (version "1.3.1")
5337 (source
5338 (origin
5339 (method url-fetch)
5340 (uri (cran-uri "PRROC" version))
5341 (sha256
5342 (base32
5343 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5344 (properties `((upstream-name . "PRROC")))
5345 (build-system r-build-system)
5346 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5347 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5348 (description
5349 "This package computes the areas under the @dfn{precision-recall} (PR)
5350 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5351 contrast to other implementations, the interpolation between points of the PR
5352 curve is done by a non-linear piecewise function. In addition to the areas
5353 under the curves, the curves themselves can also be computed and plotted by a
5354 specific S3-method.")
5355 (license license:gpl3)))
5356
5357 (define-public r-vim
5358 (package
5359 (name "r-vim")
5360 (version "5.1.1")
5361 (source
5362 (origin
5363 (method url-fetch)
5364 (uri (cran-uri "VIM" version))
5365 (sha256
5366 (base32
5367 "0w22ir0gvym7gqd6nw2j7w5ivlb3az1dkfxv33imimkb7c83056a"))))
5368 (properties `((upstream-name . "VIM")))
5369 (build-system r-build-system)
5370 (propagated-inputs
5371 `(("r-car" ,r-car)
5372 ("r-colorspace" ,r-colorspace)
5373 ("r-data-table" ,r-data-table)
5374 ("r-e1071" ,r-e1071)
5375 ("r-laeken" ,r-laeken)
5376 ("r-magrittr" ,r-magrittr)
5377 ("r-mass" ,r-mass)
5378 ("r-nnet" ,r-nnet)
5379 ("r-ranger" ,r-ranger)
5380 ("r-rcpp" ,r-rcpp)
5381 ("r-robustbase" ,r-robustbase)
5382 ("r-sp" ,r-sp)
5383 ("r-vcd" ,r-vcd)))
5384 (home-page "https://github.com/alexkowa/VIM")
5385 (synopsis "Visualization and imputation of missing values")
5386 (description
5387 "This package provides tools for the visualization of missing and/or
5388 imputed values are introduced, which can be used for exploring the data and
5389 the structure of the missing and/or imputed values. Depending on this
5390 structure of the missing values, the corresponding methods may help to
5391 identify the mechanism generating the missing values and allows to explore the
5392 data including missing values. In addition, the quality of imputation can be
5393 visually explored using various univariate, bivariate, multiple and
5394 multivariate plot methods.")
5395 (license license:gpl2+)))
5396
5397 (define-public r-fnn
5398 (package
5399 (name "r-fnn")
5400 (version "1.1.3")
5401 (source
5402 (origin
5403 (method url-fetch)
5404 (uri (cran-uri "FNN" version))
5405 (sha256
5406 (base32
5407 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5408 (properties `((upstream-name . "FNN")))
5409 (build-system r-build-system)
5410 (home-page "https://cran.r-project.org/web/packages/FNN")
5411 (synopsis "Fast nearest neighbor search algorithms and applications")
5412 (description
5413 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5414 search algorithms. Related applications including KNN classification,
5415 regression and information measures are implemented.")
5416 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5417 ;; later can be used.
5418 (license license:gpl2+)))
5419
5420 (define-public r-smoother
5421 (package
5422 (name "r-smoother")
5423 (version "1.1")
5424 (source
5425 (origin
5426 (method url-fetch)
5427 (uri (cran-uri "smoother" version))
5428 (sha256
5429 (base32
5430 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5431 (build-system r-build-system)
5432 (propagated-inputs
5433 `(("r-ttr" ,r-ttr)))
5434 (home-page "https://cran.r-project.org/web/packages/smoother")
5435 (synopsis "Functions relating to the smoothing of numerical data")
5436 (description
5437 "This package provides a collection of methods for smoothing numerical
5438 data, commencing with a port of the Matlab gaussian window smoothing function.
5439 In addition, several functions typically used in smoothing of financial data
5440 are included.")
5441 (license license:gpl2)))
5442
5443 (define-public r-riverplot
5444 (package
5445 (name "r-riverplot")
5446 (version "0.6")
5447 (source
5448 (origin
5449 (method url-fetch)
5450 (uri (cran-uri "riverplot" version))
5451 (sha256
5452 (base32
5453 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5454 (build-system r-build-system)
5455 (home-page "https://logfc.wordpress.com")
5456 (synopsis "Sankey or ribbon plots")
5457 (description
5458 "Sankey plots are a type of diagram that is convenient to illustrate how
5459 flow of information, resources etc. separates and joins, much like observing
5460 how rivers split and merge. For example, they can be used to compare
5461 different clusterings. This package provides an implementation of Sankey
5462 plots for R.")
5463 (license license:gpl2+)))
5464
5465 (define-public r-dyn
5466 (package
5467 (name "r-dyn")
5468 (version "0.2-9.6")
5469 (source
5470 (origin
5471 (method url-fetch)
5472 (uri (cran-uri "dyn" version))
5473 (sha256
5474 (base32
5475 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5476 (build-system r-build-system)
5477 (propagated-inputs
5478 `(("r-zoo" ,r-zoo)))
5479 (home-page "https://cran.r-project.org/web/packages/dyn")
5480 (synopsis "Time series regression")
5481 (description
5482 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5483 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5484 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5485 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5486 @code{randomForest::randomForest()} and other regression functions, allowing
5487 those functions to be used with time series including specifications that may
5488 contain lags, diffs and missing values.")
5489 ;; Any GPL version.
5490 (license license:gpl2+)))
5491
5492 (define-public r-catdap
5493 (package
5494 (name "r-catdap")
5495 (version "1.3.5")
5496 (source
5497 (origin
5498 (method url-fetch)
5499 (uri (cran-uri "catdap" version))
5500 (sha256
5501 (base32
5502 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
5503 (build-system r-build-system)
5504 (native-inputs
5505 `(("gfortran" ,gfortran)))
5506 (home-page "https://cran.r-project.org/web/packages/catdap/")
5507 (synopsis "Tools for categorical data analysis")
5508 (description
5509 "This package provides functions for analyzing multivariate data.
5510 Dependencies of the distribution of the specified variable (response
5511 variable) to other variables (explanatory variables) are derived and
5512 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5513 (license license:gpl2+)))
5514
5515 (define-public r-arules
5516 (package
5517 (name "r-arules")
5518 (version "1.6-5")
5519 (source
5520 (origin
5521 (method url-fetch)
5522 (uri (cran-uri "arules" version))
5523 (sha256
5524 (base32
5525 "0bcvfn8lvcv74vv9z3kgg7yq5hm7wjqhmzadi55cbm8zxd76g84v"))))
5526 (build-system r-build-system)
5527 (propagated-inputs
5528 `(("r-matrix" ,r-matrix)))
5529 (home-page "https://github.com/mhahsler/arules")
5530 (synopsis "Mining association rules and frequent itemsets")
5531 (description
5532 "This package provides an infrastructure for representing, manipulating
5533 and analyzing transaction data and patterns (frequent itemsets and association rules).
5534 It also provides C implementations of the association mining algorithms Apriori
5535 and Eclat.")
5536 (license license:gpl3)))
5537
5538 (define-public r-parsedate
5539 (package
5540 (name "r-parsedate")
5541 (version "1.2.0")
5542 (source
5543 (origin
5544 (method url-fetch)
5545 (uri (cran-uri "parsedate" version))
5546 (sha256
5547 (base32
5548 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5549 (build-system r-build-system)
5550 (propagated-inputs
5551 `(("r-rematch2" ,r-rematch2)))
5552 (home-page "https://github.com/gaborcsardi/parsedate")
5553 (synopsis
5554 "Recognize and parse dates in various formats")
5555 (description
5556 "This package provides three functions for dealing with dates:
5557 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5558 time formats, @code{parse_date} parses dates in unspecified formats,
5559 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5560 (license license:gpl2)))
5561
5562 (define-public r-abc-data
5563 (package
5564 (name "r-abc-data")
5565 (version "1.0")
5566 (source
5567 (origin
5568 (method url-fetch)
5569 (uri (cran-uri "abc.data" version))
5570 (sha256
5571 (base32
5572 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5573 (properties `((upstream-name . "abc.data")))
5574 (build-system r-build-system)
5575 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5576 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5577 (description
5578 "This package contains data which are used by functions of the abc
5579 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5580 algorithms for performing parameter estimation, model selection, and
5581 goodness-of-fit.")
5582 (license license:gpl3+)))
5583
5584 (define-public r-abc
5585 (package
5586 (name "r-abc")
5587 (version "2.1")
5588 (source
5589 (origin
5590 (method url-fetch)
5591 (uri (cran-uri "abc" version))
5592 (sha256
5593 (base32
5594 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5595 (build-system r-build-system)
5596 (propagated-inputs
5597 `(("r-abc-data" ,r-abc-data)
5598 ("r-locfit" ,r-locfit)
5599 ("r-mass" ,r-mass)
5600 ("r-nnet" ,r-nnet)
5601 ("r-quantreg" ,r-quantreg)))
5602 (home-page "https://cran.r-project.org/web/packages/abc/")
5603 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5604 (description
5605 "This package implements several @dfn{Approximate Bayesian
5606 Computation} (ABC) algorithms for performing parameter estimation, model
5607 selection, and goodness-of-fit. Cross-validation tools are also available for
5608 measuring the accuracy of ABC estimates, and to calculate the
5609 misclassification probabilities of different models.")
5610 (license license:gpl3+)))
5611
5612 (define-public r-zip
5613 (package
5614 (name "r-zip")
5615 (version "2.0.4")
5616 (source
5617 (origin
5618 (method url-fetch)
5619 (uri (cran-uri "zip" version))
5620 (sha256
5621 (base32
5622 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
5623 (build-system r-build-system)
5624 (home-page "https://github.com/gaborcsardi/zip")
5625 (synopsis "Cross-platform Zip compression")
5626 (description
5627 "This package provides a cross-platform Zip compression library for R.
5628 It is a replacement for the @code{zip} function, that does not require any
5629 additional external tools on any platform.")
5630 (license license:cc0)))
5631
5632 (define-public r-openxlsx
5633 (package
5634 (name "r-openxlsx")
5635 (version "4.1.4")
5636 (source
5637 (origin
5638 (method url-fetch)
5639 (uri (cran-uri "openxlsx" version))
5640 (sha256
5641 (base32
5642 "1mwxldw9i9nfksx1i6h1kfs7vmsz9fgyllbsipar4vnfyqhqp8q7"))))
5643 (build-system r-build-system)
5644 (propagated-inputs
5645 `(("r-rcpp" ,r-rcpp)
5646 ("r-stringi" ,r-stringi)
5647 ("r-zip" ,r-zip)))
5648 (home-page "https://github.com/awalker89/openxlsx")
5649 (synopsis "Read, write and edit XLSX files")
5650 (description
5651 "This package simplifies the creation of Excel @code{.xlsx} files by
5652 providing a high level interface to writing, styling and editing worksheets.
5653 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5654 and @code{XLConnect} packages with the added benefit of removing the
5655 dependency on Java.")
5656 (license license:gpl3)))
5657
5658 (define-public r-rio
5659 (package
5660 (name "r-rio")
5661 (version "0.5.16")
5662 (source
5663 (origin
5664 (method url-fetch)
5665 (uri (cran-uri "rio" version))
5666 (sha256
5667 (base32
5668 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5669 (build-system r-build-system)
5670 (propagated-inputs
5671 `(("r-curl" ,r-curl)
5672 ("r-data-table" ,r-data-table)
5673 ("r-foreign" ,r-foreign)
5674 ("r-haven" ,r-haven)
5675 ("r-openxlsx" ,r-openxlsx)
5676 ("r-readxl" ,r-readxl)
5677 ("r-tibble" ,r-tibble)))
5678 (home-page "https://github.com/leeper/rio")
5679 (synopsis "Swiss-army knife for data I/O")
5680 (description
5681 "This package provides streamlined data import and export infrastructure
5682 by making assumptions that the user is probably willing to make: @code{import}
5683 and @code{export} determine the data structure from the file extension,
5684 reasonable defaults are used for data import and export (e.g.,
5685 @code{stringsAsFactors=FALSE}), web-based import is natively
5686 supported (including from SSL/HTTPS), compressed files can be read directly
5687 without explicit decompression, and fast import packages are used where
5688 appropriate. An additional convenience function, @code{convert}, provides a
5689 simple method for converting between file types.")
5690 (license license:gpl2)))
5691
5692 (define-public r-maptools
5693 (package
5694 (name "r-maptools")
5695 (version "0.9-9")
5696 (source
5697 (origin
5698 (method url-fetch)
5699 (uri (cran-uri "maptools" version))
5700 (sha256
5701 (base32
5702 "0v4llkxk8qs61vq4ykvaim4k23aagdaz0p62ns7zfq02sln3pfk9"))))
5703 (build-system r-build-system)
5704 (propagated-inputs
5705 `(("r-foreign" ,r-foreign)
5706 ("r-lattice" ,r-lattice)
5707 ("r-sp" ,r-sp)))
5708 (home-page "https://r-forge.r-project.org/projects/maptools/")
5709 (synopsis "Tools for reading and handling spatial objects")
5710 (description
5711 "This package provides a set of tools for manipulating and reading
5712 geographic data, in particular ESRI Shapefiles. It includes binary access to
5713 GSHHG shoreline files. The package also provides interface wrappers for
5714 exchanging spatial objects with other R packages.")
5715 ;; The C source files from shapelib are released under the Expat license.
5716 ;; The R code is released under GPL version 2 or later.
5717 (license (list license:gpl2+
5718 license:expat))))
5719
5720 (define-public r-later
5721 (package
5722 (name "r-later")
5723 (version "1.0.0")
5724 (source
5725 (origin
5726 (method url-fetch)
5727 (uri (cran-uri "later" version))
5728 (sha256
5729 (base32
5730 "11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7"))))
5731 (build-system r-build-system)
5732 (propagated-inputs
5733 `(("r-bh" ,r-bh)
5734 ("r-rcpp" ,r-rcpp)
5735 ("r-rlang" ,r-rlang)))
5736 (home-page "https://github.com/r-lib/later")
5737 (synopsis "Utilities for delaying function execution")
5738 (description
5739 "This package provides tools to execute arbitrary R or C functions some
5740 time after the current time, after the R execution stack has emptied.")
5741 (license license:gpl2+)))
5742
5743 (define-public r-promises
5744 (package
5745 (name "r-promises")
5746 (version "1.1.0")
5747 (source
5748 (origin
5749 (method url-fetch)
5750 (uri (cran-uri "promises" version))
5751 (sha256
5752 (base32
5753 "01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8"))))
5754 (build-system r-build-system)
5755 (propagated-inputs
5756 `(("r-later" ,r-later)
5757 ("r-magrittr" ,r-magrittr)
5758 ("r-r6" ,r-r6)
5759 ("r-rcpp" ,r-rcpp)
5760 ("r-rlang" ,r-rlang)))
5761 (home-page "https://rstudio.github.io/promises")
5762 (synopsis "Abstractions for promise-based asynchronous programming")
5763 (description
5764 "This package provides fundamental abstractions for doing asynchronous
5765 programming in R using promises. Asynchronous programming is useful for
5766 allowing a single R process to orchestrate multiple tasks in the background
5767 while also attending to something else. Semantics are similar to JavaScript
5768 promises, but with a syntax that is idiomatic R.")
5769 (license license:expat)))
5770
5771 (define-public r-dosnow
5772 (package
5773 (name "r-dosnow")
5774 (version "1.0.18")
5775 (source
5776 (origin
5777 (method url-fetch)
5778 (uri (cran-uri "doSNOW" version))
5779 (sha256
5780 (base32
5781 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
5782 (properties `((upstream-name . "doSNOW")))
5783 (build-system r-build-system)
5784 (propagated-inputs
5785 `(("r-foreach" ,r-foreach)
5786 ("r-iterators" ,r-iterators)
5787 ("r-snow" ,r-snow)))
5788 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5789 (synopsis "Foreach parallel adaptor for the snow package")
5790 (description
5791 "This package provides a parallel backend for the @code{%dopar%} function
5792 using the @code{snow} package.")
5793 (license license:gpl2)))
5794
5795 (define-public r-snowfall
5796 (package
5797 (name "r-snowfall")
5798 (version "1.84-6.1")
5799 (source (origin
5800 (method url-fetch)
5801 (uri (cran-uri "snowfall" version))
5802 (sha256
5803 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
5804 (build-system r-build-system)
5805 (propagated-inputs
5806 `(("r-snow" ,r-snow)))
5807 (home-page "https://cran.r-project.org/web/packages/snowfall/")
5808 (synopsis "Easier cluster computing")
5809 (description "This package is a usability wrapper around snow for easier
5810 development of parallel R programs. This package offers e.g. extended error
5811 checks, and additional functions. All functions work in sequential mode, too,
5812 if no cluster is present or wished. The package is also designed as connector
5813 to the cluster management tool @code{sfCluster}, but can also used without
5814 it.")
5815 (license license:gpl2+)))
5816
5817 (define-public r-rappdirs
5818 (package
5819 (name "r-rappdirs")
5820 (version "0.3.1")
5821 (source
5822 (origin
5823 (method url-fetch)
5824 (uri (cran-uri "rappdirs" version))
5825 (sha256
5826 (base32
5827 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
5828 (build-system r-build-system)
5829 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
5830 (synopsis "Determine where to save data, caches, and logs")
5831 (description
5832 "This package provides an easy way to determine which directories on the
5833 user's computer should be used to save data, caches and logs. It is a port of
5834 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
5835 (license license:expat)))
5836
5837 (define-public r-renv
5838 (package
5839 (name "r-renv")
5840 (version "0.9.3")
5841 (source
5842 (origin
5843 (method url-fetch)
5844 (uri (cran-uri "renv" version))
5845 (sha256
5846 (base32
5847 "02ayfgbpw4b58148dcxz31anaxncwczmxs1zzkskwj0rzhb2x60r"))))
5848 (properties `((upstream-name . "renv")))
5849 (build-system r-build-system)
5850 (home-page "https://rstudio.github.io/renv")
5851 (synopsis "Project environments")
5852 (description
5853 "This package provides a dependency management toolkit for R. Using
5854 renv, you can create and manage project-local R libraries, save the state of
5855 these libraries to a lockfile, and later restore your library as required.
5856 Together, these tools can help make your projects more isolated, portable, and
5857 reproducible.")
5858 (license license:expat)))
5859
5860 (define-public r-learnr
5861 (package
5862 (name "r-learnr")
5863 (version "0.10.1")
5864 (source
5865 (origin
5866 (method url-fetch)
5867 (uri (cran-uri "learnr" version))
5868 (sha256
5869 (base32
5870 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
5871 (build-system r-build-system)
5872 (propagated-inputs
5873 `(("r-checkmate" ,r-checkmate)
5874 ("r-ellipsis" ,r-ellipsis)
5875 ("r-evaluate" ,r-evaluate)
5876 ("r-htmltools" ,r-htmltools)
5877 ("r-htmlwidgets" ,r-htmlwidgets)
5878 ("r-jsonlite" ,r-jsonlite)
5879 ("r-knitr" ,r-knitr)
5880 ("r-markdown" ,r-markdown)
5881 ("r-rappdirs" ,r-rappdirs)
5882 ("r-renv" ,r-renv)
5883 ("r-rmarkdown" ,r-rmarkdown)
5884 ("r-rprojroot" ,r-rprojroot)
5885 ("r-shiny" ,r-shiny)
5886 ("r-withr" ,r-withr)))
5887 (home-page "https://rstudio.github.io/learnr/")
5888 (synopsis "Interactive tutorials for R")
5889 (description
5890 "This package provides tools to create interactive tutorials using R
5891 Markdown. Use a combination of narrative, figures, videos, exercises, and
5892 quizzes to create self-paced tutorials for learning about R and R packages.")
5893 (license license:asl2.0)))
5894
5895 (define-public r-analytics
5896 (package
5897 (name "r-analytics")
5898 (version "3.0")
5899 (source
5900 (origin
5901 (method url-fetch)
5902 (uri (cran-uri "analytics" version))
5903 (sha256
5904 (base32
5905 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
5906 (build-system r-build-system)
5907 (propagated-inputs
5908 `(("r-car" ,r-car)
5909 ("r-cluster" ,r-cluster)
5910 ("r-fractal" ,r-fractal)
5911 ("r-lmtest" ,r-lmtest)
5912 ("r-mass" ,r-mass)
5913 ("r-np" ,r-np)
5914 ("r-powerplus" ,r-powerplus)
5915 ("r-robust" ,r-robust)
5916 ("r-trend" ,r-trend)
5917 ("r-tsa" ,r-tsa)
5918 ("r-urca" ,r-urca)
5919 ("r-vim" ,r-vim)))
5920 (home-page "https://cran.r-project.org/web/packages/analytics/")
5921 (synopsis "Collection of data analysis tools")
5922 (description
5923 "This package is a collection of data analysis tools. It includes tools
5924 for regression outlier detection in a fitted linear model, stationary
5925 bootstrap using a truncated geometric distribution, a comprehensive test for
5926 weak stationarity, column means by group, weighted biplots, and a heuristic to
5927 obtain a better initial configuration in non-metric MDS.")
5928 (license license:gpl2)))
5929
5930 (define-public r-reticulate
5931 (package
5932 (name "r-reticulate")
5933 (version "1.15")
5934 (source
5935 (origin
5936 (method url-fetch)
5937 (uri (cran-uri "reticulate" version))
5938 (sha256
5939 (base32
5940 "03dmnx9jhxx6vfbv2i5n6sln38kb9zkshz982pg3l9i4jjf3xns7"))))
5941 (build-system r-build-system)
5942 (inputs `(("python" ,python)))
5943 (propagated-inputs
5944 `(("r-rappdirs" ,r-rappdirs)
5945 ("r-jsonlite" ,r-jsonlite)
5946 ("r-matrix" ,r-matrix)
5947 ("r-rcpp" ,r-rcpp)))
5948 (native-inputs
5949 `(("r-knitr" ,r-knitr)))
5950 (home-page "https://github.com/rstudio/reticulate")
5951 (synopsis "R interface to Python")
5952 (description
5953 "This package provides an interface from R to Python modules, classes,
5954 and functions. When calling into Python, R data types are automatically
5955 converted to their equivalent Python types. When values are returned from
5956 Python to R they are converted back to R types.")
5957 (license license:asl2.0)))
5958
5959 (define-public r-bibtex
5960 (package
5961 (name "r-bibtex")
5962 (version "0.4.2.2")
5963 (source
5964 (origin
5965 (method url-fetch)
5966 (uri (cran-uri "bibtex" version))
5967 (sha256
5968 (base32
5969 "140hkjzdp3033cvji861rd06z1ixgpnn4n5amygqsmhnixk8ff07"))))
5970 (build-system r-build-system)
5971 (propagated-inputs `(("r-stringr" ,r-stringr)))
5972 (home-page "https://github.com/romainfrancois/bibtex")
5973 (synopsis "Bibtex parser")
5974 (description "This package provides a utility for R to parse a bibtex
5975 file.")
5976 (license license:gpl2+)))
5977
5978 (define-public r-ggseqlogo
5979 (package
5980 (name "r-ggseqlogo")
5981 (version "0.1")
5982 (source
5983 (origin
5984 (method url-fetch)
5985 (uri (cran-uri "ggseqlogo" version))
5986 (sha256
5987 (base32
5988 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
5989 (build-system r-build-system)
5990 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
5991 (home-page "https://github.com/omarwagih/ggseqlogo")
5992 (synopsis "ggplot2 extension for drawing genetic sequence logos")
5993 (description
5994 "The range of functions provided by this package makes it possible to
5995 draw highly versatile genomic sequence logos. Features include, but are not
5996 limited to, modifying colour schemes and fonts used to draw the logo,
5997 generating multiple logo plots, and aiding the visualisation with annotations.
5998 Sequence logos can easily be combined with other ggplot2 plots.")
5999 ;; Unspecified version of the LGPL.
6000 (license license:lgpl3+)))
6001
6002 (define-public r-ggsci
6003 (package
6004 (name "r-ggsci")
6005 (version "2.9")
6006 (source
6007 (origin
6008 (method url-fetch)
6009 (uri (cran-uri "ggsci" version))
6010 (sha256
6011 (base32
6012 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
6013 (build-system r-build-system)
6014 (propagated-inputs
6015 `(("r-ggplot2" ,r-ggplot2)
6016 ("r-scales" ,r-scales)))
6017 (home-page "https://nanx.me/ggsci/")
6018 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
6019 (description
6020 "This package provides a collection of ggplot2 color palettes inspired by
6021 plots in scientific journals, data visualization libraries, science fiction
6022 movies, and TV shows.")
6023 (license license:gpl3)))
6024
6025 (define-public r-ggsignif
6026 (package
6027 (name "r-ggsignif")
6028 (version "0.6.0")
6029 (source
6030 (origin
6031 (method url-fetch)
6032 (uri (cran-uri "ggsignif" version))
6033 (sha256
6034 (base32
6035 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
6036 (build-system r-build-system)
6037 (native-inputs
6038 `(("r-knitr" ,r-knitr)))
6039 (propagated-inputs
6040 `(("r-ggplot2" ,r-ggplot2)))
6041 (home-page "https://github.com/const-ae/ggsignif")
6042 (synopsis "Significance brackets for ggplot2")
6043 (description
6044 "Enrich your ggplots with group-wise comparisons. This package provides
6045 an easy way to indicate if two groups are significantly different. Commonly
6046 this is shown by a bracket on top connecting the groups of interest which
6047 itself is annotated with the level of significance. The package provides a
6048 single layer that takes the groups for comparison and the test as arguments
6049 and adds the annotation to the plot.")
6050 (license license:gpl3)))
6051
6052 (define-public r-ggpubr
6053 (package
6054 (name "r-ggpubr")
6055 (version "0.2.5")
6056 (source
6057 (origin
6058 (method url-fetch)
6059 (uri (cran-uri "ggpubr" version))
6060 (sha256
6061 (base32
6062 "0kb3hpmnhj4mkbx1kx0kv5y22himr8dijqx7ra0h8hi0pf2l2ha7"))))
6063 (build-system r-build-system)
6064 (propagated-inputs
6065 `(("r-cowplot" ,r-cowplot)
6066 ("r-dplyr" ,r-dplyr)
6067 ("r-ggplot2" ,r-ggplot2)
6068 ("r-ggrepel" ,r-ggrepel)
6069 ("r-ggsci" ,r-ggsci)
6070 ("r-ggsignif" ,r-ggsignif)
6071 ("r-glue" ,r-glue)
6072 ("r-gridextra" ,r-gridextra)
6073 ("r-magrittr" ,r-magrittr)
6074 ("r-polynom" ,r-polynom)
6075 ("r-purrr" ,r-purrr)
6076 ("r-rlang" ,r-rlang)
6077 ("r-scales" ,r-scales)
6078 ("r-tidyr" ,r-tidyr)))
6079 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
6080 (synopsis "ggplot2-based publication-ready plots")
6081 (description
6082 "The ggplot2 package is an excellent and flexible package for elegant
6083 data visualization in R. However the default generated plots require some
6084 formatting before we can send them for publication. The ggpubr package
6085 provides some easy-to-use functions for creating and customizing ggplot2-based
6086 publication-ready plots.")
6087 (license license:gpl2)))
6088
6089 (define-public r-ellipse
6090 (package
6091 (name "r-ellipse")
6092 (version "0.4.1")
6093 (source
6094 (origin
6095 (method url-fetch)
6096 (uri (cran-uri "ellipse" version))
6097 (sha256
6098 (base32
6099 "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
6100 (build-system r-build-system)
6101 (home-page "https://cran.r-project.org/web/packages/ellipse/")
6102 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
6103 (description
6104 "This package contains various routines for drawing ellipses and
6105 ellipse-like confidence regions, implementing the plots described in Murdoch
6106 and Chow (1996), A graphical display of large correlation matrices, The
6107 American Statistician 50, 178-180. There are also routines implementing the
6108 profile plots described in Bates and Watts (1988), Nonlinear Regression
6109 Analysis and its Applications.")
6110 (license license:gpl2+)))
6111
6112 (define-public r-flashclust
6113 (package
6114 (name "r-flashclust")
6115 (version "1.01-2")
6116 (source
6117 (origin
6118 (method url-fetch)
6119 (uri (cran-uri "flashClust" version))
6120 (sha256
6121 (base32
6122 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
6123 (properties `((upstream-name . "flashClust")))
6124 (build-system r-build-system)
6125 (native-inputs `(("gfortran" ,gfortran)))
6126 (home-page "https://cran.r-project.org/web/packages/flashClust/")
6127 (synopsis "Implementation of optimal hierarchical clustering")
6128 (description
6129 "This package provides a fast implementation of hierarchical
6130 clustering.")
6131 (license license:gpl2+)))
6132
6133 (define-public r-factominer
6134 (package
6135 (name "r-factominer")
6136 (version "2.3")
6137 (source
6138 (origin
6139 (method url-fetch)
6140 (uri (cran-uri "FactoMineR" version))
6141 (sha256
6142 (base32
6143 "0ldgf3daksh6lpblhqys67m4mxqx3q9s9n5plfam6dwshfik0ky6"))))
6144 (properties `((upstream-name . "FactoMineR")))
6145 (build-system r-build-system)
6146 (propagated-inputs
6147 `(("r-car" ,r-car)
6148 ("r-cluster" ,r-cluster)
6149 ("r-ellipse" ,r-ellipse)
6150 ("r-flashclust" ,r-flashclust)
6151 ("r-ggplot2" ,r-ggplot2)
6152 ("r-ggrepel" ,r-ggrepel)
6153 ("r-lattice" ,r-lattice)
6154 ("r-leaps" ,r-leaps)
6155 ("r-mass" ,r-mass)
6156 ("r-scatterplot3d" ,r-scatterplot3d)))
6157 (home-page "http://factominer.free.fr")
6158 (synopsis "Multivariate exploratory data analysis and data mining")
6159 (description
6160 "This package provides exploratory data analysis methods to summarize,
6161 visualize and describe datasets. The main principal component methods are
6162 available, those with the largest potential in terms of applications:
6163 principal component analysis (PCA) when variables are quantitative,
6164 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
6165 variables are categorical, Multiple Factor Analysis when variables are
6166 structured in groups, etc. and hierarchical cluster analysis.")
6167 (license license:gpl2+)))
6168
6169 (define-public r-factoextra
6170 (package
6171 (name "r-factoextra")
6172 (version "1.0.7")
6173 (source
6174 (origin
6175 (method url-fetch)
6176 (uri (cran-uri "factoextra" version))
6177 (sha256
6178 (base32
6179 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
6180 (build-system r-build-system)
6181 (propagated-inputs
6182 `(("r-abind" ,r-abind)
6183 ("r-cluster" ,r-cluster)
6184 ("r-dendextend" ,r-dendextend)
6185 ("r-factominer" ,r-factominer)
6186 ("r-ggplot2" ,r-ggplot2)
6187 ("r-ggpubr" ,r-ggpubr)
6188 ("r-ggrepel" ,r-ggrepel)
6189 ("r-reshape2" ,r-reshape2)
6190 ("r-tidyr" ,r-tidyr)))
6191 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
6192 (synopsis "Extract and visualize the results of multivariate data analyses")
6193 (description
6194 "This package provides some easy-to-use functions to extract and
6195 visualize the output of multivariate data analyses, including
6196 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6197 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6198 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6199 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6200 packages. It contains also functions for simplifying some clustering analysis
6201 steps and provides ggplot2-based elegant data visualization.")
6202 (license license:gpl2)))
6203
6204 (define-public r-fansi
6205 (package
6206 (name "r-fansi")
6207 (version "0.4.1")
6208 (source
6209 (origin
6210 (method url-fetch)
6211 (uri (cran-uri "fansi" version))
6212 (sha256
6213 (base32
6214 "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w"))))
6215 (build-system r-build-system)
6216 (native-inputs
6217 `(("r-knitr" ,r-knitr))) ; for vignettes
6218 (home-page "https://github.com/brodieG/fansi")
6219 (synopsis "ANSI control sequence aware string functions")
6220 (description
6221 "This package provides counterparts to R string manipulation functions
6222 that account for the effects of ANSI text formatting control sequences.")
6223 (license license:gpl2+)))
6224
6225 (define-public r-nbclust
6226 (package
6227 (name "r-nbclust")
6228 (version "3.0")
6229 (source
6230 (origin
6231 (method url-fetch)
6232 (uri (cran-uri "NbClust" version))
6233 (sha256
6234 (base32
6235 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6236 (properties `((upstream-name . "NbClust")))
6237 (build-system r-build-system)
6238 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6239 (synopsis "Determine the best number of clusters in a data set")
6240 (description
6241 "NbClust provides 30 indexes for determining the optimal number of
6242 clusters in a data set and offers the best clustering scheme from different
6243 results to the user.")
6244 (license license:gpl2)))
6245
6246 (define-public r-hdf5r
6247 (package
6248 (name "r-hdf5r")
6249 (version "1.3.2")
6250 (source
6251 (origin
6252 (method url-fetch)
6253 (uri (cran-uri "hdf5r" version))
6254 (sha256
6255 (base32
6256 "0c2p06k9bp9rf0fyavnxw5d8jr2bbgx3gjblahz581cpvsfksj9i"))))
6257 (build-system r-build-system)
6258 (inputs
6259 `(("hdf5" ,hdf5)
6260 ("zlib" ,zlib)))
6261 (propagated-inputs
6262 `(("r-bit64" ,r-bit64)
6263 ("r-r6" ,r-r6)))
6264 (native-inputs
6265 `(("r-knitr" ,r-knitr)))
6266 (home-page "https://hhoeflin.github.io/hdf5r")
6267 (synopsis "Interface to the HDF5 binary data format")
6268 (description
6269 "HDF5 is a data model, library and file format for storing and managing
6270 large amounts of data. This package provides a nearly feature complete,
6271 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6272 functionality is added so that HDF5 objects behave very similar to their
6273 corresponding R counterparts.")
6274 (license license:asl2.0)))
6275
6276 (define-public r-itertools
6277 (package
6278 (name "r-itertools")
6279 (version "0.1-3")
6280 (source
6281 (origin
6282 (method url-fetch)
6283 (uri (cran-uri "itertools" version))
6284 (sha256
6285 (base32
6286 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6287 (build-system r-build-system)
6288 (propagated-inputs
6289 `(("r-iterators" ,r-iterators)))
6290 (home-page "https://cran.r-project.org/web/packages/itertools/")
6291 (synopsis "Iterator tools")
6292 (description
6293 "This package provides various tools for creating iterators, many
6294 patterned after functions in the Python @code{itertools} module, and others
6295 patterned after functions in the snow package.")
6296 (license license:gpl2)))
6297
6298 (define-public r-polynom
6299 (package
6300 (name "r-polynom")
6301 (version "1.4-0")
6302 (source
6303 (origin
6304 (method url-fetch)
6305 (uri (cran-uri "polynom" version))
6306 (sha256
6307 (base32
6308 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6309 (build-system r-build-system)
6310 (home-page "https://cran.r-project.org/web/packages/polynom/")
6311 (synopsis "Functions for univariate polynomial manipulations")
6312 (description
6313 "This package provides a collection of functions to implement a class for
6314 univariate polynomial manipulations.")
6315 (license license:gpl2)))
6316
6317 (define-public r-gbrd
6318 (package
6319 (name "r-gbrd")
6320 (version "0.4-11")
6321 (source
6322 (origin
6323 (method url-fetch)
6324 (uri (cran-uri "gbRd" version))
6325 (sha256
6326 (base32
6327 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6328 (properties `((upstream-name . "gbRd")))
6329 (build-system r-build-system)
6330 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6331 (synopsis "Utilities for processing Rd objects and files")
6332 (description
6333 "This package provides utilities for processing Rd objects and files.
6334 Extract argument descriptions and other parts of the help pages of
6335 functions.")
6336 (license license:gpl2+)))
6337
6338 (define-public r-rjags
6339 (package
6340 (name "r-rjags")
6341 (version "4-10")
6342 (source
6343 (origin
6344 (method url-fetch)
6345 (uri (cran-uri "rjags" version))
6346 (sha256
6347 (base32
6348 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6349 (build-system r-build-system)
6350 (propagated-inputs
6351 `(("r-coda" ,r-coda)))
6352 (inputs
6353 `(("jags" ,jags)))
6354 (native-inputs
6355 `(("pkg-config" ,pkg-config)))
6356 (home-page "http://mcmc-jags.sourceforge.net")
6357 (synopsis "Bayesian graphical models using MCMC")
6358 (description
6359 "This package provides an R interface to the JAGS MCMC library. JAGS is
6360 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6361 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6362 (license license:gpl2)))
6363
6364 (define-public r-rdpack
6365 (package
6366 (name "r-rdpack")
6367 (version "0.11-1")
6368 (source
6369 (origin
6370 (method url-fetch)
6371 (uri (cran-uri "Rdpack" version))
6372 (sha256
6373 (base32
6374 "080y15p2hl4jsq91ak2f1y2kx1iqq5c5wzyx3zyhjwp01cahy0jq"))))
6375 (properties `((upstream-name . "Rdpack")))
6376 (build-system r-build-system)
6377 (propagated-inputs
6378 `(("r-bibtex" ,r-bibtex)
6379 ("r-gbrd" ,r-gbrd)))
6380 (home-page "https://github.com/GeoBosh/Rdpack")
6381 (synopsis "Update and manipulate Rd documentation objects")
6382 (description
6383 "This package provides functions for manipulation of R documentation
6384 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6385 updating Rd documentation for functions, methods and classes; it also includes
6386 Rd macros for citations and import of references from bibtex files for use in
6387 Rd files and roxygen2 comments, as well as many functions for manipulation of
6388 references and Rd files.")
6389 (license license:gpl2+)))
6390
6391 (define-public r-officer
6392 (package
6393 (name "r-officer")
6394 (version "0.3.8")
6395 (source
6396 (origin
6397 (method url-fetch)
6398 (uri (cran-uri "officer" version))
6399 (sha256
6400 (base32
6401 "0xhx5n6qksyh2s9hvwhnc8y0hn362asc5y94ld06snad786hz0rw"))))
6402 (build-system r-build-system)
6403 (propagated-inputs
6404 `(("r-magrittr" ,r-magrittr)
6405 ("r-r6" ,r-r6)
6406 ("r-uuid" ,r-uuid)
6407 ("r-xml2" ,r-xml2)
6408 ("r-zip" ,r-zip)))
6409 (native-inputs
6410 `(("r-knitr" ,r-knitr)))
6411 (home-page "https://davidgohel.github.io/officer")
6412 (synopsis "Manipulation of Word and PowerPoint documents")
6413 (description
6414 "This package provides tools to access and manipulate Word and PowerPoint
6415 documents from R. The package focuses on tabular and graphical reporting from
6416 R; it also provides two functions that let users get document content into
6417 data objects. A set of functions lets add and remove images, tables and
6418 paragraphs of text in new or existing documents. When working with PowerPoint
6419 presentations, slides can be added or removed; shapes inside slides can also
6420 be added or removed. When working with Word documents, a cursor can be used
6421 to help insert or delete content at a specific location in the document.")
6422 (license license:gpl3)))
6423
6424 (define-public r-abn
6425 (package
6426 (name "r-abn")
6427 (version "2.2")
6428 (source
6429 (origin
6430 (method url-fetch)
6431 (uri (cran-uri "abn" version))
6432 (sha256
6433 (base32
6434 "19w6bdjyp4zwqs6p0flry4qxqynf9rh8ykdrfrp61wrdf7kysw0d"))))
6435 (build-system r-build-system)
6436 (inputs
6437 `(("gsl" ,gsl)))
6438 (propagated-inputs
6439 `(("r-lme4" ,r-lme4)
6440 ("r-mass" ,r-mass)
6441 ("r-nnet" ,r-nnet)
6442 ("r-rcpp" ,r-rcpp)
6443 ("r-rcpparmadillo" ,r-rcpparmadillo)
6444 ("r-rjags" ,r-rjags)))
6445 (home-page "https://r-bayesian-networks.org/")
6446 (synopsis "Modelling multivariate data with additive bayesian networks")
6447 (description
6448 "Bayesian network analysis is a form of probabilistic graphical models
6449 which derives from empirical data a directed acyclic graph, DAG, describing
6450 the dependency structure between random variables. An additive Bayesian
6451 network model consists of a form of a DAG where each node comprises a
6452 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6453 equivalent to Bayesian multivariate regression using graphical modelling, they
6454 generalises the usual multivariable regression, GLM, to multiple dependent
6455 variables. This package provides routines to help determine optimal Bayesian
6456 network models for a given data set, where these models are used to identify
6457 statistical dependencies in messy, complex data.")
6458 (license license:gpl2+)))
6459
6460 (define-public r-acd
6461 (package
6462 (name "r-acd")
6463 (version "1.5.3")
6464 (source
6465 (origin
6466 (method url-fetch)
6467 (uri (cran-uri "ACD" version))
6468 (sha256
6469 (base32
6470 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6471 (properties `((upstream-name . "ACD")))
6472 (build-system r-build-system)
6473 (home-page "https://cran.r-project.org/web/packages/ACD/")
6474 (synopsis "Categorical data analysis with complete or missing responses")
6475 (description
6476 "This package provides tools for categorical data analysis with complete
6477 or missing responses.")
6478 (license license:gpl2+)))
6479
6480 (define-public r-acdm
6481 (package
6482 (name "r-acdm")
6483 (version "1.0.4")
6484 (source
6485 (origin
6486 (method url-fetch)
6487 (uri (cran-uri "ACDm" version))
6488 (sha256
6489 (base32
6490 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6491 (properties `((upstream-name . "ACDm")))
6492 (build-system r-build-system)
6493 (propagated-inputs
6494 `(("r-dplyr" ,r-dplyr)
6495 ("r-ggplot2" ,r-ggplot2)
6496 ("r-plyr" ,r-plyr)
6497 ("r-rsolnp" ,r-rsolnp)
6498 ("r-zoo" ,r-zoo)))
6499 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6500 (synopsis "Tools for Autoregressive Conditional Duration Models")
6501 (description
6502 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6503 and Russell, 1998) models. It creates trade, price or volume durations from
6504 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6505 and tests them.")
6506 (license license:gpl2+)))
6507
6508 (define-public r-overlap
6509 (package
6510 (name "r-overlap")
6511 (version "0.3.2")
6512 (source
6513 (origin
6514 (method url-fetch)
6515 (uri (cran-uri "overlap" version))
6516 (sha256
6517 (base32
6518 "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
6519 (build-system r-build-system)
6520 (home-page "https://cran.r-project.org/web/packages/overlap/")
6521 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6522 (description
6523 "This package provides functions to fit kernel density functions to data
6524 on temporal activity patterns of animals; estimate coefficients of overlapping
6525 of densities for two species; and calculate bootstrap estimates of confidence
6526 intervals.")
6527 (license license:gpl3+)))
6528
6529 (define-public r-snakecase
6530 (package
6531 (name "r-snakecase")
6532 (version "0.11.0")
6533 (source
6534 (origin
6535 (method url-fetch)
6536 (uri (cran-uri "snakecase" version))
6537 (sha256
6538 (base32
6539 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6540 (build-system r-build-system)
6541 (propagated-inputs
6542 `(("r-stringi" ,r-stringi)
6543 ("r-stringr" ,r-stringr)))
6544 (home-page "https://github.com/Tazinho/snakecase")
6545 (synopsis "Convert strings into any case")
6546 (description
6547 "This package provides a consistent, flexible and easy to use tool to
6548 parse and convert strings into cases like snake or camel among others.")
6549 (license license:gpl3)))
6550
6551 (define-public r-prediction
6552 (package
6553 (name "r-prediction")
6554 (version "0.3.14")
6555 (source
6556 (origin
6557 (method url-fetch)
6558 (uri (cran-uri "prediction" version))
6559 (sha256
6560 (base32
6561 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6562 (build-system r-build-system)
6563 (propagated-inputs
6564 `(("r-data-table" ,r-data-table)))
6565 (home-page "https://github.com/leeper/prediction")
6566 (synopsis "Tidy, type-safe prediction methods")
6567 (description
6568 "This package provides the @code{prediction()} function, a type-safe
6569 alternative to @code{predict()} that always returns a data frame. The package
6570 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6571 from the @code{stats} package, as well as numerous other model classes from
6572 other add-on packages.")
6573 (license license:expat)))
6574
6575 (define-public r-insight
6576 (package
6577 (name "r-insight")
6578 (version "0.8.3")
6579 (source
6580 (origin
6581 (method url-fetch)
6582 (uri (cran-uri "insight" version))
6583 (sha256
6584 (base32
6585 "0lm5a4r368mq1pwmxjk2xnz25lb9j4v7mdkl1bahk2alklxgb8yj"))))
6586 (build-system r-build-system)
6587 (native-inputs
6588 `(("r-knitr" ,r-knitr)))
6589 (home-page "https://easystats.github.io/insight/")
6590 (synopsis "Easy access to model information for various model objects")
6591 (description
6592 "This package provides a tool to provide an easy, intuitive and
6593 consistent access to information contained in various R models, like model
6594 formulas, model terms, information about random effects, data that was used to
6595 fit the model or data from response variables. The package mainly revolves
6596 around two types of functions: Functions that find (the names of) information,
6597 starting with @code{find_}, and functions that get the underlying data,
6598 starting with @code{get_}. The package has a consistent syntax and works with
6599 many different model objects, where otherwise functions to access these
6600 information are missing.")
6601 (license license:gpl3)))
6602
6603 (define-public r-sjlabelled
6604 (package
6605 (name "r-sjlabelled")
6606 (version "1.1.3")
6607 (source
6608 (origin
6609 (method url-fetch)
6610 (uri (cran-uri "sjlabelled" version))
6611 (sha256
6612 (base32
6613 "1amq7i9sxf0pkxhskqc53xq5wvc9rdxm7cxyb4b6xh6qsskjnlsj"))))
6614 (build-system r-build-system)
6615 (propagated-inputs
6616 `(("r-haven" ,r-haven)
6617 ("r-insight" ,r-insight)))
6618 (home-page "https://github.com/strengejacke/sjlabelled")
6619 (synopsis "Labelled data utility functions")
6620 (description
6621 "This package provides a collection of functions dealing with labelled
6622 data, like reading and writing data between R and other statistical software
6623 packages. This includes easy ways to get, set or change value and variable
6624 label attributes, to convert labelled vectors into factors or numeric (and
6625 vice versa), or to deal with multiple declared missing values.")
6626 (license license:gpl3)))
6627
6628 (define-public r-sjmisc
6629 (package
6630 (name "r-sjmisc")
6631 (version "2.8.4")
6632 (source
6633 (origin
6634 (method url-fetch)
6635 (uri (cran-uri "sjmisc" version))
6636 (sha256
6637 (base32
6638 "1ad7ca71w0v9ja4wb47aygczc987zz1lnjljhh2n497nzrpzzv64"))))
6639 (build-system r-build-system)
6640 (propagated-inputs
6641 `(("r-dplyr" ,r-dplyr)
6642 ("r-insight" ,r-insight)
6643 ("r-magrittr" ,r-magrittr)
6644 ("r-purrr" ,r-purrr)
6645 ("r-rlang" ,r-rlang)
6646 ("r-sjlabelled" ,r-sjlabelled)
6647 ("r-tidyselect" ,r-tidyselect)))
6648 (native-inputs
6649 `(("r-knitr" ,r-knitr)))
6650 (home-page "https://github.com/strengejacke/sjmisc")
6651 (synopsis "Data and variable transformation functions")
6652 (description
6653 "This package is a collection of miscellaneous utility functions,
6654 supporting data transformation tasks like recoding, dichotomizing or grouping
6655 variables, setting and replacing missing values. The data transformation
6656 functions also support labelled data, and all integrate seamlessly into a
6657 tidyverse workflow.")
6658 (license license:gpl3)))
6659
6660 (define-public r-nortest
6661 (package
6662 (name "r-nortest")
6663 (version "1.0-4")
6664 (source
6665 (origin
6666 (method url-fetch)
6667 (uri (cran-uri "nortest" version))
6668 (sha256
6669 (base32
6670 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6671 (build-system r-build-system)
6672 (home-page "https://cran.r-project.org/web/packages/nortest/")
6673 (synopsis "Tests for normality")
6674 (description
6675 "This package provides five omnibus tests for testing the composite
6676 hypothesis of normality.")
6677 (license license:gpl2+)))
6678
6679 (define-public r-moonbook
6680 (package
6681 (name "r-moonbook")
6682 (version "0.2.3")
6683 (source
6684 (origin
6685 (method url-fetch)
6686 (uri (cran-uri "moonBook" version))
6687 (sha256
6688 (base32
6689 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
6690 (properties `((upstream-name . "moonBook")))
6691 (build-system r-build-system)
6692 (propagated-inputs
6693 `(("r-magrittr" ,r-magrittr)
6694 ("r-nortest" ,r-nortest)
6695 ("r-purrr" ,r-purrr)
6696 ("r-sjmisc" ,r-sjmisc)
6697 ("r-stringr" ,r-stringr)
6698 ("r-survival" ,r-survival)))
6699 (home-page "https://github.com/cardiomoon/moonBook")
6700 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
6701 (description
6702 "This package provides several analysis-related functions for the book
6703 entitled \"R statistics and graph for medical articles\" (written in Korean),
6704 version 1, by Keon-Woong Moon with Korean demographic data with several plot
6705 functions.")
6706 (license license:gpl2)))
6707
6708 (define-public r-flextable
6709 (package
6710 (name "r-flextable")
6711 (version "0.5.9")
6712 (source
6713 (origin
6714 (method url-fetch)
6715 (uri (cran-uri "flextable" version))
6716 (sha256
6717 (base32
6718 "1rkz0nhwjy1l8sb0kmna5v492n2ydnk7gydswnmf88r8vfyjczhw"))))
6719 (build-system r-build-system)
6720 (propagated-inputs
6721 `(("r-base64enc" ,r-base64enc)
6722 ("r-data-table" ,r-data-table)
6723 ("r-gdtools" ,r-gdtools)
6724 ("r-htmltools" ,r-htmltools)
6725 ("r-knitr" ,r-knitr)
6726 ("r-officer" ,r-officer)
6727 ("r-rlang" ,r-rlang)
6728 ("r-rmarkdown" ,r-rmarkdown)
6729 ("r-xml2" ,r-xml2)))
6730 (home-page "https://davidgohel.github.io/flextable")
6731 (synopsis "Functions for tabular reporting")
6732 (description
6733 "This package provides tools to create pretty tables for HTML documents
6734 and other formats. Functions are provided to let users create tables, modify
6735 and format their content. It extends the @code{officer} package and can be
6736 used within R markdown documents when rendering to HTML and to Word
6737 documents.")
6738 (license license:gpl3)))
6739
6740 (define-public r-writexl
6741 (package
6742 (name "r-writexl")
6743 (version "1.2")
6744 (source
6745 (origin
6746 (method url-fetch)
6747 (uri (cran-uri "writexl" version))
6748 (sha256
6749 (base32
6750 "09fhdip6igcg97fjx4c7727cx2lb49l4d74l4i8rg2bag2s5lrj3"))))
6751 (build-system r-build-system)
6752 (inputs `(("zlib" ,zlib)))
6753 (home-page "https://github.com/ropensci/writexl")
6754 (synopsis "Export data frames to xlsx format")
6755 (description
6756 "This package provides a data frame to xlsx exporter based on
6757 libxlsxwriter.")
6758 (license license:bsd-2)))
6759
6760 (define-public r-biasedurn
6761 (package
6762 (name "r-biasedurn")
6763 (version "1.07")
6764 (source
6765 (origin
6766 (method url-fetch)
6767 (uri (cran-uri "BiasedUrn" version))
6768 (sha256
6769 (base32
6770 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
6771 (properties `((upstream-name . "BiasedUrn")))
6772 (build-system r-build-system)
6773 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
6774 (synopsis "Biased Urn model distributions")
6775 (description
6776 "This package provides statistical models of biased sampling in the form
6777 of univariate and multivariate noncentral hypergeometric distributions,
6778 including Wallenius' noncentral hypergeometric distribution and Fisher's
6779 noncentral hypergeometric distribution (also called extended hypergeometric
6780 distribution).")
6781 (license license:gpl3)))
6782
6783 (define-public r-goplot
6784 (package
6785 (name "r-goplot")
6786 (version "1.0.2")
6787 (source
6788 (origin
6789 (method url-fetch)
6790 (uri (cran-uri "GOplot" version))
6791 (sha256
6792 (base32
6793 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
6794 (properties `((upstream-name . "GOplot")))
6795 (build-system r-build-system)
6796 (propagated-inputs
6797 `(("r-ggdendro" ,r-ggdendro)
6798 ("r-ggplot2" ,r-ggplot2)
6799 ("r-gridextra" ,r-gridextra)
6800 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6801 (home-page "https://github.com/wencke/wencke.github.io")
6802 (synopsis "Visualization of functional analysis data")
6803 (description
6804 "This package provides an implementation of multilayered visualizations
6805 for enhanced graphical representation of functional analysis data. It
6806 combines and integrates omics data derived from expression and functional
6807 annotation enrichment analyses. Its plotting functions have been developed
6808 with an hierarchical structure in mind: starting from a general overview to
6809 identify the most enriched categories (modified bar plot, bubble plot) to a
6810 more detailed one displaying different types of relevant information for the
6811 molecules in a given set of categories (circle plot, chord plot, cluster plot,
6812 Venn diagram, heatmap).")
6813 (license license:gpl2)))
6814
6815 (define-public r-getopt
6816 (package
6817 (name "r-getopt")
6818 (version "1.20.3")
6819 (source
6820 (origin
6821 (method url-fetch)
6822 (uri (cran-uri "getopt" version))
6823 (sha256
6824 (base32
6825 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
6826 (build-system r-build-system)
6827 (home-page "https://github.com/trevorld/getopt")
6828 (synopsis "Command-line option processor for R")
6829 (description
6830 "This package is designed to be used with Rscript to write shebang
6831 scripts that accept short and long options. Many users will prefer to
6832 use the packages @code{optparse} or @code{argparse} which add extra
6833 features like automatically generated help options and usage texts,
6834 support for default values, positional argument support, etc.")
6835 (license license:gpl2+)))
6836
6837 (define-public r-findpython
6838 (package
6839 (name "r-findpython")
6840 (version "1.0.5")
6841 (source
6842 (origin
6843 (method url-fetch)
6844 (uri (cran-uri "findpython" version))
6845 (sha256
6846 (base32
6847 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
6848 (build-system r-build-system)
6849 (home-page "https://github.com/trevorld/findpython")
6850 (synopsis "Functions to find an acceptable Python binary")
6851 (description
6852 "This package was designed to find an acceptable Python binary that
6853 matches version and feature constraints.")
6854 (license license:expat)))
6855
6856 ;; This in not the same as "r-argparser"
6857 (define-public r-argparse
6858 (package
6859 (name "r-argparse")
6860 (version "2.0.1")
6861 (source
6862 (origin
6863 (method url-fetch)
6864 (uri (cran-uri "argparse" version))
6865 (sha256
6866 (base32
6867 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
6868 (build-system r-build-system)
6869 (inputs `(("python" ,python)))
6870 (propagated-inputs
6871 `(("r-findpython" ,r-findpython)
6872 ("r-jsonlite" ,r-jsonlite)
6873 ("r-r6" ,r-r6)))
6874 (home-page "https://github.com/trevorld/argparse")
6875 (synopsis "Command line optional and positional argument parser")
6876 (description
6877 "This package provides a command line parser to be used with Rscript to
6878 write shebang scripts that gracefully accept positional and optional arguments
6879 and automatically generate usage notices.")
6880 (license license:gpl2+)))
6881
6882 (define-public r-hash
6883 (package
6884 (name "r-hash")
6885 (version "2.2.6.1")
6886 (source
6887 (origin
6888 (method url-fetch)
6889 (uri (cran-uri "hash" version))
6890 (sha256
6891 (base32
6892 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
6893 (build-system r-build-system)
6894 (home-page "https://cran.r-project.org/web/packages/hash/")
6895 (synopsis "Implementation of hash/associated arrays/dictionaries")
6896 (description
6897 "This package implements a data structure similar to hashes in Perl and
6898 dictionaries in Python but with a purposefully R flavor. For objects of
6899 appreciable size, access using hashes outperforms native named lists and
6900 vectors.")
6901 (license license:gpl2+)))
6902
6903 (define-public r-orddom
6904 (package
6905 (name "r-orddom")
6906 (version "3.1")
6907 (source
6908 (origin
6909 (method url-fetch)
6910 (uri (cran-uri "orddom" version))
6911 (sha256
6912 (base32
6913 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
6914 (build-system r-build-system)
6915 (propagated-inputs `(("r-psych" ,r-psych)))
6916 (home-page "https://cran.r-project.org/web/packages/orddom/")
6917 (synopsis "Ordinal dominance statistics")
6918 (description
6919 "This package provides tools to compute ordinal, statistics and effect
6920 sizes as an alternative to mean comparison: Cliff's delta or success rate
6921 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
6922 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
6923 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
6924 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
6925 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
6926 Group (Non-)Overlap considerations.")
6927 (license license:gpl2)))
6928
6929 (define-public r-deriv
6930 (package
6931 (name "r-deriv")
6932 (version "4.0")
6933 (source
6934 (origin
6935 (method url-fetch)
6936 (uri (cran-uri "Deriv" version))
6937 (sha256
6938 (base32
6939 "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n"))))
6940 (properties `((upstream-name . "Deriv")))
6941 (build-system r-build-system)
6942 (home-page "https://cran.r-project.org/web/packages/Deriv")
6943 (synopsis "Symbolic differentiation")
6944 (description
6945 "This package provides an R-based solution for symbolic differentiation.
6946 It admits user-defined functions as well as function substitution in arguments
6947 of functions to be differentiated. Some symbolic simplification is part of
6948 the work.")
6949 (license license:gpl3+)))
6950
6951 (define-public r-doby
6952 (package
6953 (name "r-doby")
6954 (version "4.6.5")
6955 (source
6956 (origin
6957 (method url-fetch)
6958 (uri (cran-uri "doBy" version))
6959 (sha256
6960 (base32
6961 "1ckazh701b4ilg8bj17ji903538jmb49d997gm49ah5j5jc1x0g7"))))
6962 (properties `((upstream-name . "doBy")))
6963 (build-system r-build-system)
6964 (propagated-inputs
6965 `(("r-broom" ,r-broom)
6966 ("r-deriv" ,r-deriv)
6967 ("r-dplyr" ,r-dplyr)
6968 ("r-magrittr" ,r-magrittr)
6969 ("r-mass" ,r-mass)
6970 ("r-matrix" ,r-matrix)
6971 ("r-plyr" ,r-plyr)
6972 ("r-pbkrtest" ,r-pbkrtest)
6973 ("r-tibble" ,r-tibble)))
6974 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
6975 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
6976 (description
6977 "This package contains:
6978
6979 @itemize
6980 @item facilities for working with grouped data: @code{do}
6981 something to data stratified @code{by} some variables.
6982 @item implementations of least-squares means, general linear contrasts, and
6983 @item miscellaneous other utilities.
6984 @end itemize\n")
6985 (license license:gpl2+)))
6986
6987 (define-public r-refgenome
6988 (package
6989 (name "r-refgenome")
6990 (version "1.7.7")
6991 (source
6992 (origin
6993 (method url-fetch)
6994 (uri (cran-uri "refGenome" version))
6995 (sha256
6996 (base32
6997 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
6998 (properties `((upstream-name . "refGenome")))
6999 (build-system r-build-system)
7000 (propagated-inputs
7001 `(("r-dbi" ,r-dbi)
7002 ("r-doby" ,r-doby)
7003 ("r-rsqlite" ,r-rsqlite)))
7004 (home-page "https://cran.r-project.org/web/packages/refGenome/")
7005 (synopsis
7006 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
7007 (description
7008 "This package contains functionality for importing and managing of
7009 downloaded genome annotation data from the Ensembl genome browser (European
7010 Bioinformatics Institute) and from the UCSC genome browser (University of
7011 California, Santa Cruz) and annotation routines for genomic positions and
7012 splice site positions.")
7013 (license license:gpl2)))
7014
7015 (define-public r-basix
7016 (package
7017 (name "r-basix")
7018 (version "1.1")
7019 (source
7020 (origin
7021 (method url-fetch)
7022 (uri (cran-uri "BASIX" version))
7023 (sha256
7024 (base32
7025 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
7026 (properties `((upstream-name . "BASIX")))
7027 (build-system r-build-system)
7028 (home-page "https://cran.r-project.org/web/packages/BASIX/")
7029 (synopsis "Efficient C/C++ toolset for R")
7030 (description
7031 "BASIX provides some efficient C/C++ implementations of native R
7032 procedures to speed up calculations in R.")
7033 (license license:gpl2)))
7034
7035 (define-public r-blockfest
7036 (package
7037 (name "r-blockfest")
7038 (version "1.6")
7039 (source
7040 (origin
7041 (method url-fetch)
7042 (uri (cran-uri "BlockFeST" version))
7043 (sha256
7044 (base32
7045 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
7046 (properties `((upstream-name . "BlockFeST")))
7047 (build-system r-build-system)
7048 (propagated-inputs `(("r-basix" ,r-basix)))
7049 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
7050 (synopsis "Bayesian calculation of region-specific fixation index")
7051 (description
7052 "This package provides an R implementation of an extension of the
7053 BayeScan software for codominant markers, adding the option to group
7054 individual SNPs into pre-defined blocks. A typical application of this new
7055 approach is the identification of genomic regions, genes, or gene sets
7056 containing one or more SNPs that evolved under directional selection.")
7057 (license license:gpl2)))
7058
7059 (define-public r-proc
7060 (package
7061 (name "r-proc")
7062 (version "1.16.2")
7063 (source
7064 (origin
7065 (method url-fetch)
7066 (uri (cran-uri "pROC" version))
7067 (sha256
7068 (base32
7069 "0apwa5zzqh74pjnvf5a1s5qf6i9r5h44jdllfrwymkd2v479d2xn"))))
7070 (properties `((upstream-name . "pROC")))
7071 (build-system r-build-system)
7072 (propagated-inputs
7073 `(("r-plyr" ,r-plyr)
7074 ("r-rcpp" ,r-rcpp)))
7075 (home-page "https://web.expasy.org/pROC/")
7076 (synopsis "Display and analyze ROC curves")
7077 (description
7078 "This package provides tools for visualizing, smoothing and comparing
7079 receiver operating characteristic (ROC curves). The area under the
7080 curve (AUC) can be compared with statistical tests based on U-statistics or
7081 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
7082 (license license:gpl3+)))
7083
7084 (define-public r-rootsolve
7085 (package
7086 (name "r-rootsolve")
7087 (version "1.8.2.1")
7088 (source
7089 (origin
7090 (method url-fetch)
7091 (uri (cran-uri "rootSolve" version))
7092 (sha256
7093 (base32
7094 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
7095 (properties `((upstream-name . "rootSolve")))
7096 (build-system r-build-system)
7097 (native-inputs `(("gfortran" ,gfortran)))
7098 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
7099 (synopsis "Tools for the analysis of ordinary differential equations")
7100 (description
7101 "This package provides routines to find the root of nonlinear functions,
7102 and to perform steady-state and equilibrium analysis of @dfn{ordinary
7103 differential equations} (ODE). It includes routines that:
7104
7105 @enumerate
7106 @item generate gradient and jacobian matrices (full and banded),
7107 @item find roots of non-linear equations by the Newton-Raphson method,
7108 @item estimate steady-state conditions of a system of (differential) equations
7109 in full, banded or sparse form, using the Newton-Raphson method, or by
7110 dynamically running,
7111 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
7112 and 3-D partial differential equations, that have been converted to ordinary
7113 differential equations by numerical differencing (using the method-of-lines
7114 approach).
7115 @end enumerate\n")
7116 (license license:gpl2+)))
7117
7118 (define-public r-abcanalysis
7119 (package
7120 (name "r-abcanalysis")
7121 (version "1.2.1")
7122 (source
7123 (origin
7124 (method url-fetch)
7125 (uri (cran-uri "ABCanalysis" version))
7126 (sha256
7127 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
7128 (properties `((upstream-name . "ABCanalysis")))
7129 (build-system r-build-system)
7130 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
7131 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
7132 (synopsis "Computed ABC Analysis")
7133 (description
7134 "Multivariate data sets often differ in several factors or derived statistical
7135 parameters, which have to be selected for a valid interpretation. Basing this
7136 selection on traditional statistical limits leads occasionally to the perception
7137 of losing information from a data set. This package provides tools to calculate
7138 these limits on the basis of the mathematical properties of the distribution of
7139 the analyzed items.")
7140 (license license:gpl3)))
7141
7142 (define-public r-slam
7143 (package
7144 (name "r-slam")
7145 (version "0.1-47")
7146 (source
7147 (origin
7148 (method url-fetch)
7149 (uri (cran-uri "slam" version))
7150 (sha256
7151 (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
7152 (build-system r-build-system)
7153 (home-page "https://cran.r-project.org/web/packages/slam/")
7154 (synopsis "Sparse lightweight arrays and matrices")
7155 (description
7156 "This package contains data structures and algorithms for sparse arrays and matrices,
7157 based on index arrays and simple triplet representations, respectively.")
7158 (license license:gpl2)))
7159
7160 (define-public r-manipulatewidget
7161 (package
7162 (name "r-manipulatewidget")
7163 (version "0.10.1")
7164 (source
7165 (origin
7166 (method url-fetch)
7167 (uri (cran-uri "manipulateWidget" version))
7168 (sha256
7169 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
7170 (properties
7171 `((upstream-name . "manipulateWidget")))
7172 (build-system r-build-system)
7173 (propagated-inputs
7174 `(("r-base64enc" ,r-base64enc)
7175 ("r-codetools" ,r-codetools)
7176 ("r-htmltools" ,r-htmltools)
7177 ("r-htmlwidgets" ,r-htmlwidgets)
7178 ("r-knitr" ,r-knitr)
7179 ("r-miniui" ,r-miniui)
7180 ("r-shiny" ,r-shiny)
7181 ("r-webshot" ,r-webshot)))
7182 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
7183 (synopsis "Add even more interactivity to interactive charts")
7184 (description
7185 "This package lets you create in just a few lines of R code a nice user interface to
7186 modify the data or the graphical parameters of one or multiple interactive
7187 charts. It is useful to quickly explore visually some data or for package
7188 developers to generate user interfaces easy to maintain.")
7189 (license license:gpl2+)))
7190
7191 (define-public r-a3
7192 (package
7193 (name "r-a3")
7194 (version "1.0.0")
7195 (source
7196 (origin
7197 (method url-fetch)
7198 (uri (cran-uri "A3" version))
7199 (sha256
7200 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
7201 (properties `((upstream-name . "A3")))
7202 (build-system r-build-system)
7203 (propagated-inputs
7204 `(("r-pbapply" ,r-pbapply)
7205 ("r-xtable" ,r-xtable)))
7206 (home-page "https://cran.r-project.org/web/packages/A3/")
7207 (synopsis "Error metrics for predictive models")
7208 (description
7209 "This package supplies tools for tabulating and analyzing the results of predictive
7210 models. The methods employed are applicable to virtually any predictive model
7211 and make comparisons between different methodologies straightforward.")
7212 (license license:gpl2+)))
7213
7214 (define-public r-infotheo
7215 (package
7216 (name "r-infotheo")
7217 (version "1.2.0")
7218 (source
7219 (origin
7220 (method url-fetch)
7221 (uri (cran-uri "infotheo" version))
7222 (sha256
7223 (base32
7224 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7225 (build-system r-build-system)
7226 (home-page "http://homepage.meyerp.com/software")
7227 (synopsis "Information-theoretic measures")
7228 (description
7229 "This package implements various measures of information theory based on
7230 several entropy estimators.")
7231 (license license:gpl3+)))
7232
7233 (define-public r-abcoptim
7234 (package
7235 (name "r-abcoptim")
7236 (version "0.15.0")
7237 (source
7238 (origin
7239 (method url-fetch)
7240 (uri (cran-uri "ABCoptim" version))
7241 (sha256
7242 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7243 (properties `((upstream-name . "ABCoptim")))
7244 (build-system r-build-system)
7245 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7246 (home-page "https://github.com/gvegayon/ABCoptim/")
7247 (synopsis "Optimization of Artificial Bee Colony algorithm")
7248 (description
7249 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7250 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7251 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7252 algorithms, and uses only common control parameters such as colony size and
7253 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7254 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7255 This version is a work-in-progress and is written in R code.")
7256 (license license:expat)))
7257
7258 (define-public r-abcp2
7259 (package
7260 (name "r-abcp2")
7261 (version "1.2")
7262 (source
7263 (origin
7264 (method url-fetch)
7265 (uri (cran-uri "ABCp2" version))
7266 (sha256
7267 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7268 (properties `((upstream-name . "ABCp2")))
7269 (build-system r-build-system)
7270 (propagated-inputs `(("r-mass" ,r-mass)))
7271 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7272 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7273 (description
7274 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7275 Poisson, and Gamma distribution and estimates the proportional paternity of the
7276 second male (P2) based on the best fit distribution.")
7277 (license license:gpl2)))
7278
7279 (define-public r-abcrf
7280 (package
7281 (name "r-abcrf")
7282 (version "1.8.1")
7283 (source
7284 (origin
7285 (method url-fetch)
7286 (uri (cran-uri "abcrf" version))
7287 (sha256
7288 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7289 (build-system r-build-system)
7290 (propagated-inputs
7291 `(("r-doparallel" ,r-doparallel)
7292 ("r-foreach" ,r-foreach)
7293 ("r-mass" ,r-mass)
7294 ("r-matrixstats" ,r-matrixstats)
7295 ("r-ranger" ,r-ranger)
7296 ("r-rcpp" ,r-rcpp)
7297 ("r-rcpparmadillo" ,r-rcpparmadillo)
7298 ("r-readr" ,r-readr)
7299 ("r-stringr" ,r-stringr)))
7300 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7301 (synopsis "Approximate bayesian computation via random forests")
7302 (description
7303 "This package performs approximate bayesian computation (ABC) model choice and
7304 parameter inference via random forests. This machine learning tool named random
7305 forests (RF) can conduct selection among the highly complex models covered by
7306 ABC algorithms.")
7307 (license license:gpl2+)))
7308
7309 (define-public r-abctools
7310 (package
7311 (name "r-abctools")
7312 (version "1.1.3")
7313 (source
7314 (origin
7315 (method url-fetch)
7316 (uri (cran-uri "abctools" version))
7317 (sha256
7318 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7319 (build-system r-build-system)
7320 (propagated-inputs
7321 `(("r-abc" ,r-abc)
7322 ("r-abind" ,r-abind)
7323 ("r-hmisc" ,r-hmisc)
7324 ("r-plyr" ,r-plyr)))
7325 (home-page "https://github.com/dennisprangle/abctools/")
7326 (synopsis "Tools for ABC analyses")
7327 (description
7328 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7329 including summary statistic selection and assessing coverage. This includes
7330 recent dimension reduction algorithms to tune the choice of summary statistics,
7331 and coverage methods to tune the choice of threshold.")
7332 (license license:gpl2+)))
7333
7334 (define-public r-ggstance
7335 (package
7336 (name "r-ggstance")
7337 (version "0.3.4")
7338 (source
7339 (origin
7340 (method url-fetch)
7341 (uri (cran-uri "ggstance" version))
7342 (sha256
7343 (base32 "0aqz3dn02cgij018a4sglqwrwr9dzzj12l8xr1064q7hfd4f64m1"))))
7344 (build-system r-build-system)
7345 (propagated-inputs
7346 `(("r-ggplot2" ,r-ggplot2)
7347 ("r-plyr" ,r-plyr)
7348 ("r-rlang" ,r-rlang)
7349 ("r-withr" ,r-withr)))
7350 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7351 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7352 (description
7353 "This package is a @code{r-ggplot2} extension that provides flipped components:
7354 @enumerate
7355 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7356 @item vertical versions of @code{r-ggplot2} positions.
7357 @end enumerate")
7358 (license license:gpl3)))
7359
7360 (define-public r-mosaiccore
7361 (package
7362 (name "r-mosaiccore")
7363 (version "0.6.0")
7364 (source
7365 (origin
7366 (method url-fetch)
7367 (uri (cran-uri "mosaicCore" version))
7368 (sha256
7369 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7370 (properties `((upstream-name . "mosaicCore")))
7371 (build-system r-build-system)
7372 (propagated-inputs
7373 `(("r-dplyr" ,r-dplyr)
7374 ("r-lazyeval" ,r-lazyeval)
7375 ("r-mass" ,r-mass)
7376 ("r-rlang" ,r-rlang)
7377 ("r-tidyr" ,r-tidyr)))
7378 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7379 (synopsis "Common utilities for mosaic family packages")
7380 (description
7381 "Common utilities used in other Mosaic family packages are collected here.")
7382 (license license:gpl2+)))
7383
7384 (define-public r-ggformula
7385 (package
7386 (name "r-ggformula")
7387 (version "0.9.4")
7388 (source
7389 (origin
7390 (method url-fetch)
7391 (uri (cran-uri "ggformula" version))
7392 (sha256
7393 (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f"))))
7394 (build-system r-build-system)
7395 (propagated-inputs
7396 `(("r-ggforce" ,r-ggforce)
7397 ("r-ggplot2" ,r-ggplot2)
7398 ("r-ggstance" ,r-ggstance)
7399 ("r-magrittr" ,r-magrittr)
7400 ("r-mosaiccore" ,r-mosaiccore)
7401 ("r-rlang" ,r-rlang)
7402 ("r-stringr" ,r-stringr)
7403 ("r-tibble" ,r-tibble)))
7404 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7405 (synopsis "Formula interface for the @code{r-ggplot2}")
7406 (description
7407 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7408 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7409 and extends the excellent simplicity of the lattice-graphics formula interface,
7410 while providing the intuitive capabilities of @code{r-ggplot2}.")
7411 (license license:expat)))
7412
7413 (define-public r-mosaicdata
7414 (package
7415 (name "r-mosaicdata")
7416 (version "0.17.0")
7417 (source
7418 (origin
7419 (method url-fetch)
7420 (uri (cran-uri "mosaicData" version))
7421 (sha256
7422 (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9"))))
7423 (properties `((upstream-name . "mosaicData")))
7424 (build-system r-build-system)
7425 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7426 (synopsis "Data sets for project Mosaic")
7427 (description
7428 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7429 used to teach mathematics, statistics, computation and modeling.")
7430 (license license:gpl2+)))
7431
7432 (define-public r-raster
7433 (package
7434 (name "r-raster")
7435 (version "3.1-5")
7436 (source
7437 (origin
7438 (method url-fetch)
7439 (uri (cran-uri "raster" version))
7440 (sha256
7441 (base32
7442 "010sq00ijpmwac280ip9rryw0pxk0al8g675v2lc9rdrbgaj4rnv"))))
7443 (build-system r-build-system)
7444 (propagated-inputs
7445 `(("r-rcpp" ,r-rcpp)
7446 ("r-sp" ,r-sp)))
7447 (home-page "https://www.rspatial.org/")
7448 (synopsis "Geographic data analysis and modeling")
7449 (description
7450 "The package implements basic and high-level functions for reading,
7451 writing, manipulating, analyzing and modeling of gridded spatial data.
7452 Processing of very large files is supported.")
7453 (license license:gpl3+)))
7454
7455 (define-public r-mosaic
7456 (package
7457 (name "r-mosaic")
7458 (version "1.4.0")
7459 (source
7460 (origin
7461 (method url-fetch)
7462 (uri (cran-uri "mosaic" version))
7463 (sha256
7464 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7465 (build-system r-build-system)
7466 (propagated-inputs
7467 `(("r-broom" ,r-broom)
7468 ("r-dplyr" ,r-dplyr)
7469 ("r-ggdendro" ,r-ggdendro)
7470 ("r-ggformula" ,r-ggformula)
7471 ("r-ggplot2" ,r-ggplot2)
7472 ("r-ggrepel" ,r-ggrepel)
7473 ("r-glue" ,r-glue)
7474 ("r-gridextra" ,r-gridextra)
7475 ("r-lattice" ,r-lattice)
7476 ("r-latticeextra" ,r-latticeextra)
7477 ("r-lazyeval" ,r-lazyeval)
7478 ("r-mass" ,r-mass)
7479 ("r-matrix" ,r-matrix)
7480 ("r-mosaiccore" ,r-mosaiccore)
7481 ("r-mosaicdata" ,r-mosaicdata)
7482 ("r-readr" ,r-readr)
7483 ("r-tidyr" ,r-tidyr)))
7484 (native-inputs
7485 `(("r-knitr" ,r-knitr)))
7486 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7487 (synopsis "Mathematics, statistics, and computation teaching utilities")
7488 (description
7489 "This package contain data sets and utilities from
7490 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7491 statistics, computation and modeling. Project MOSAIC is a community of
7492 educators working to tie together aspects of quantitative work that students
7493 in science, technology, engineering and mathematics will need in their
7494 professional lives, but which are usually taught in isolation, if at all.")
7495 (license license:gpl2+)))
7496
7497 (define-public r-abd
7498 (package
7499 (name "r-abd")
7500 (version "0.2-8")
7501 (source
7502 (origin
7503 (method url-fetch)
7504 (uri (cran-uri "abd" version))
7505 (sha256
7506 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7507 (build-system r-build-system)
7508 (propagated-inputs
7509 `(("r-lattice" ,r-lattice)
7510 ("r-mosaic" ,r-mosaic)
7511 ("r-nlme" ,r-nlme)))
7512 (home-page "https://cran.r-project.org/web/packages/abd/")
7513 (synopsis "Analysis of biological data")
7514 (description
7515 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7516 biological data by Michael Whitlock and Dolph Schluter.")
7517 (license license:gpl2)))
7518
7519 (define-public r-svgui
7520 (package
7521 (name "r-svgui")
7522 (version "1.0.0")
7523 (source
7524 (origin
7525 (method url-fetch)
7526 (uri (cran-uri "svGUI" version))
7527 (sha256
7528 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7529 (properties `((upstream-name . "svGUI")))
7530 (build-system r-build-system)
7531 (home-page "https://github.com/SciViews/svGUI/")
7532 (synopsis "Functions for managing GUI clients in R")
7533 (description
7534 "The SciViews @code{svGUI} package eases the management of Graphical User
7535 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7536 centralizes info about GUI elements currently used, and it dispatches GUI
7537 calls to the particular toolkits in use in function of the context.")
7538 (license license:gpl2)))
7539
7540 (define-public r-svdialogs
7541 (package
7542 (name "r-svdialogs")
7543 (version "1.0.0")
7544 (source
7545 (origin
7546 (method url-fetch)
7547 (uri (cran-uri "svDialogs" version))
7548 (sha256
7549 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7550 (properties `((upstream-name . "svDialogs")))
7551 (build-system r-build-system)
7552 (inputs
7553 `(("yad" ,yad)
7554 ("zenity" ,zenity)))
7555 (propagated-inputs
7556 `(("r-rstudioapi" ,r-rstudioapi)
7557 ("r-svgui" ,r-svgui)))
7558 (home-page "https://github.com/SciViews/svDialogs/")
7559 (synopsis "Portable dialog boxes")
7560 (description
7561 "This package helps to construct standard dialog boxes for your GUI, including
7562 message boxes, input boxes, list, file or directory selection, and others. In
7563 case R cannot display GUI dialog boxes, a simpler command line version of these
7564 interactive elements is also provided as a fallback solution.")
7565 (license license:gpl2)))
7566
7567 (define-public r-abe
7568 (package
7569 (name "r-abe")
7570 (version "3.0.1")
7571 (source
7572 (origin
7573 (method url-fetch)
7574 (uri (cran-uri "abe" version))
7575 (sha256
7576 (base32
7577 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7578 (build-system r-build-system)
7579 (home-page "https://cran.r-project.org/web/packages/abe/")
7580 (synopsis "Augmented backward elimination")
7581 (description
7582 "This package performs augmented backward elimination and checks the
7583 stability of the obtained model. Augmented backward elimination combines
7584 significance or information based criteria with the change in estimate to
7585 either select the optimal model for prediction purposes or to serve as a tool
7586 to obtain a practically sound, highly interpretable model.")
7587 (license license:gpl2+)))
7588
7589 (define-public r-abf2
7590 (package
7591 (name "r-abf2")
7592 (version "0.7-1")
7593 (source
7594 (origin
7595 (method url-fetch)
7596 (uri (cran-uri "abf2" version))
7597 (sha256
7598 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7599 (build-system r-build-system)
7600 (home-page "https://cran.r-project.org/web/packages/abf2/")
7601 (synopsis "Load gap-free axon @code{r-abf2} files")
7602 (description
7603 "This package loads electrophysiology data from ABF2 files, as created by
7604 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7605 mode are currently supported.")
7606 (license license:artistic2.0)))
7607
7608 (define-public r-abhgenotyper
7609 (package
7610 (name "r-abhgenotyper")
7611 (version "1.0.1")
7612 (source
7613 (origin
7614 (method url-fetch)
7615 (uri (cran-uri "ABHgenotypeR" version))
7616 (sha256
7617 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7618 (properties `((upstream-name . "ABHgenotypeR")))
7619 (build-system r-build-system)
7620 (propagated-inputs
7621 `(("r-ggplot2" ,r-ggplot2)
7622 ("r-reshape2" ,r-reshape2)))
7623 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7624 (synopsis "Visualize and manipulate ABH genotypes")
7625 (description
7626 "The @code{r-abhgenotyper} package provides simple imputation,
7627 error-correction and plotting capacities for genotype data. The package is
7628 supposed to serve as an intermediate but independent analysis tool between the
7629 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7630 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7631 genotypes as \"graphical genotypes\".")
7632 (license license:gpl3)))
7633
7634 (define-public r-furrr
7635 (package
7636 (name "r-furrr")
7637 (version "0.1.0")
7638 (source
7639 (origin
7640 (method url-fetch)
7641 (uri (cran-uri "furrr" version))
7642 (sha256
7643 (base32
7644 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
7645 (build-system r-build-system)
7646 (propagated-inputs
7647 `(("r-future" ,r-future)
7648 ("r-globals" ,r-globals)
7649 ("r-purrr" ,r-purrr)
7650 ("r-rlang" ,r-rlang)))
7651 (home-page "https://github.com/DavisVaughan/furrr")
7652 (synopsis "Apply mapping functions in parallel using futures")
7653 (description
7654 "This package provides implementations of the family of @code{map()}
7655 functions from the @code{purrr} package that can be resolved using any
7656 @code{future}-supported backend, e.g. parallel on the local machine or
7657 distributed on a compute cluster.")
7658 (license license:lgpl2.1+)))
7659
7660 (define-public r-abjutils
7661 (package
7662 (name "r-abjutils")
7663 (version "0.2.3")
7664 (source
7665 (origin
7666 (method url-fetch)
7667 (uri (cran-uri "abjutils" version))
7668 (sha256
7669 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
7670 (build-system r-build-system)
7671 (propagated-inputs
7672 `(("r-devtools" ,r-devtools)
7673 ("r-dplyr" ,r-dplyr)
7674 ("r-furrr" ,r-furrr)
7675 ("r-future" ,r-future)
7676 ("r-glue" ,r-glue)
7677 ("r-httr" ,r-httr)
7678 ("r-magrittr" ,r-magrittr)
7679 ("r-progress" ,r-progress)
7680 ("r-purrr" ,r-purrr)
7681 ("r-readr" ,r-readr)
7682 ("r-rlang" ,r-rlang)
7683 ("r-rstudioapi" ,r-rstudioapi)
7684 ("r-scales" ,r-scales)
7685 ("r-stringi" ,r-stringi)
7686 ("r-stringr" ,r-stringr)
7687 ("r-tibble" ,r-tibble)
7688 ("r-tidyr" ,r-tidyr)))
7689 (home-page "https://github.com/abjur/abjutils/")
7690 (synopsis "Collection of tools for jurimetrical analysis")
7691 (description
7692 "This package implements general purpose tools, such as functions for
7693 sampling and basic manipulation of Brazilian lawsuits identification number.
7694 It also implements functions for text cleaning, such as accentuation
7695 removal.")
7696 (license license:expat)))
7697
7698 (define-public r-abnormality
7699 (package
7700 (name "r-abnormality")
7701 (version "0.1.0")
7702 (source
7703 (origin
7704 (method url-fetch)
7705 (uri (cran-uri "abnormality" version))
7706 (sha256
7707 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
7708 (build-system r-build-system)
7709 (propagated-inputs
7710 `(("r-mass" ,r-mass)
7711 ("r-matrix" ,r-matrix)))
7712 (home-page "https://cran.r-project.org/web/packages/abnormality/")
7713 (synopsis "Measure a subject's abnormality with respect to a reference population")
7714 (description
7715 "This package contains functions to implement the methodology and
7716 considerations laid out by Marks et al. in the article \"Measuring abnormality
7717 in high dimensional spaces: applications in biomechanical gait analysis\".
7718 Using high-dimensional datasets to measure a subject's overall level of
7719 abnormality as compared to a reference population is often needed in outcomes
7720 research.")
7721 (license license:expat)))
7722
7723 (define-public r-abodoutlier
7724 (package
7725 (name "r-abodoutlier")
7726 (version "0.1")
7727 (source
7728 (origin
7729 (method url-fetch)
7730 (uri (cran-uri "abodOutlier" version))
7731 (sha256
7732 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
7733 (properties `((upstream-name . "abodOutlier")))
7734 (build-system r-build-system)
7735 (propagated-inputs
7736 `(("r-cluster" ,r-cluster)))
7737 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
7738 (synopsis "Angle-based outlier detection")
7739 (description
7740 "This package performs angle-based outlier detection on a given data
7741 frame. It offers three methods to process data:
7742 @enumerate
7743 @item full but slow implementation using all the data that has cubic
7744 complexity;
7745 @item a fully randomized method;
7746 @item a method using k-nearest neighbours.
7747 @end enumerate
7748 These algorithms are well suited for high dimensional data outlier
7749 detection.")
7750 (license license:expat)))
7751
7752 (define-public r-abps
7753 (package
7754 (name "r-abps")
7755 (version "0.3")
7756 (source
7757 (origin
7758 (method url-fetch)
7759 (uri (cran-uri "ABPS" version))
7760 (sha256
7761 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
7762 (properties `((upstream-name . "ABPS")))
7763 (build-system r-build-system)
7764 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
7765 (home-page "https://cran.r-project.org/web/packages/ABPS/")
7766 (synopsis "Abnormal blood profile score to detect blood doping")
7767 (description
7768 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
7769 The ABPS is a part of the Athlete biological passport program of the World
7770 anti-doping agency, which combines several blood parameters into a single
7771 score in order to detect blood doping. The package also contains functions to
7772 calculate other scores used in anti-doping programs, such as the ratio of
7773 hemoglobin to reticulocytes (OFF-score), as well as example data.")
7774 (license license:gpl2+)))
7775
7776 (define-public r-parmigene
7777 (package
7778 (name "r-parmigene")
7779 (version "1.0.2")
7780 (source
7781 (origin
7782 (method url-fetch)
7783 (uri (cran-uri "parmigene" version))
7784 (sha256
7785 (base32
7786 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
7787 (build-system r-build-system)
7788 (home-page "https://cran.r-project.org/web/packages/parmigene/")
7789 (synopsis "Mutual information estimation for gene network reconstruction")
7790 (description
7791 "This package provides a parallel estimation of the mutual information
7792 based on entropy estimates from k-nearest neighbors distances and algorithms
7793 for the reconstruction of gene regulatory networks.")
7794 (license license:agpl3+)))
7795
7796 (define-public r-pscl
7797 (package
7798 (name "r-pscl")
7799 (version "1.5.5")
7800 (source
7801 (origin
7802 (method url-fetch)
7803 (uri (cran-uri "pscl" version))
7804 (sha256
7805 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
7806 (build-system r-build-system)
7807 (propagated-inputs
7808 `(("r-mass" ,r-mass)))
7809 (home-page "https://github.com/atahk/pscl/")
7810 (synopsis "Political science computational laboratory")
7811 (description
7812 "The @code{pscl} is an R package providing classes and methods for:
7813 @enumerate
7814 @item Bayesian analysis of roll call data (item-response models);
7815 @item elementary Bayesian statistics;
7816 @item maximum likelihood estimation of zero-inflated and hurdle models for count
7817 data;
7818 @item utility functions.
7819 @end enumerate")
7820 (license license:gpl2)))
7821
7822 (define-public r-accelmissing
7823 (package
7824 (name "r-accelmissing")
7825 (version "1.4")
7826 (source
7827 (origin
7828 (method url-fetch)
7829 (uri (cran-uri "accelmissing" version))
7830 (sha256
7831 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
7832 (build-system r-build-system)
7833 (propagated-inputs
7834 `(("r-mice" ,r-mice)
7835 ("r-pscl" ,r-pscl)))
7836 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
7837 (synopsis "Missing value imputation for accelerometer data")
7838 (description
7839 "This package provides a statistical method to impute the missing values in
7840 accelerometer data. The methodology includes both parametric and
7841 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
7842 model. It also provides multiple functions to preprocess the accelerometer data
7843 previous to the missing data imputation. These include detecting the wearing
7844 and the non-wearing time, selecting valid days and subjects, and creating plots.")
7845 (license license:gpl2+)))
7846
7847 (define-public r-mhsmm
7848 (package
7849 (name "r-mhsmm")
7850 (version "0.4.16")
7851 (source
7852 (origin
7853 (method url-fetch)
7854 (uri (cran-uri "mhsmm" version))
7855 (sha256
7856 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
7857 (build-system r-build-system)
7858 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7859 (home-page "https://github.com/jaredo/mhsmm/")
7860 (synopsis "Inference for hidden Markov and semi-Markov models")
7861 (description
7862 "The @code{r-mhsmm} package implements estimation and prediction methods for
7863 hidden Markov and semi-Markov models for multiple observation sequences. Such
7864 techniques are of interest when observed data is thought to be dependent on some
7865 unobserved (or hidden) state. Also, this package is suitable for equidistant
7866 time series data, with multivariate and/or missing data. Allows user defined
7867 emission distributions.")
7868 (license license:gpl2+)))
7869
7870 (define-public r-nleqslv
7871 (package
7872 (name "r-nleqslv")
7873 (version "3.3.2")
7874 (source
7875 (origin
7876 (method url-fetch)
7877 (uri (cran-uri "nleqslv" version))
7878 (sha256
7879 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
7880 (build-system r-build-system)
7881 (native-inputs `(("gfortran" ,gfortran)))
7882 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
7883 (synopsis "Solve systems of nonlinear equations")
7884 (description
7885 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
7886 Broyden or a Newton method with a choice of global strategies such as line
7887 search and trust region. There are options for using a numerical or user
7888 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
7889 singular or ill-conditioned Jacobian.")
7890 (license license:gpl2+)))
7891
7892 (define-public r-physicalactivity
7893 (package
7894 (name "r-physicalactivity")
7895 (version "0.2-2")
7896 (source
7897 (origin
7898 (method url-fetch)
7899 (uri (cran-uri "PhysicalActivity" version))
7900 (sha256
7901 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
7902 (properties
7903 `((upstream-name . "PhysicalActivity")))
7904 (build-system r-build-system)
7905 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
7906 (synopsis "Procesing accelerometer data for physical activity measurement")
7907 (description
7908 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
7909 for classification of monitor wear and nonwear time intervals in accelerometer
7910 data collected to assess physical activity. The package also contains functions
7911 for making plots of accelerometer data and obtaining the summary of various
7912 information including daily monitor wear time and the mean monitor wear time
7913 during valid days. The revised package version 0.2-1 improved the functions
7914 regarding speed, robustness and add better support for time zones and daylight
7915 saving. In addition, several functions were added:
7916 @enumerate
7917 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
7918 @item the @code{markPAI} can categorize physical activity intensity level based
7919 on user-defined cut-points of accelerometer counts.
7920 @end enumerate
7921 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
7922 @code{queryActigraph} functions.")
7923 (license license:gpl3+)))
7924
7925 (define-public r-acc
7926 (package
7927 (name "r-acc")
7928 (version "1.3.3")
7929 (source
7930 (origin
7931 (method url-fetch)
7932 (uri (cran-uri "acc" version))
7933 (sha256
7934 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
7935 (build-system r-build-system)
7936 (propagated-inputs
7937 `(("r-circlize" ,r-circlize)
7938 ("r-dbi" ,r-dbi)
7939 ("r-ggplot2" ,r-ggplot2)
7940 ("r-iterators" ,r-iterators)
7941 ("r-mhsmm" ,r-mhsmm)
7942 ("r-nleqslv" ,r-nleqslv)
7943 ("r-physicalactivity" ,r-physicalactivity)
7944 ("r-plyr" ,r-plyr)
7945 ("r-r-utils" ,r-r-utils)
7946 ("r-rcpp" ,r-rcpp)
7947 ("r-rcpparmadillo" ,r-rcpparmadillo)
7948 ("r-rsqlite" ,r-rsqlite)
7949 ("r-zoo" ,r-zoo)))
7950 (home-page "https://cran.r-project.org/web/packages/acc/")
7951 (synopsis "Exploring accelerometer data")
7952 (description
7953 "This package processes accelerometer data from uni-axial and tri-axial devices
7954 and generates data summaries. Also, includes functions to plot, analyze, and
7955 simulate accelerometer data.")
7956 (license license:gpl2+)))
7957
7958 (define-public r-rbenchmark
7959 (package
7960 (name "r-rbenchmark")
7961 (version "1.0.0")
7962 (source
7963 (origin
7964 (method url-fetch)
7965 (uri (cran-uri "rbenchmark" version))
7966 (sha256
7967 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
7968 (build-system r-build-system)
7969 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
7970 (synopsis "Benchmarking routine for R")
7971 (description
7972 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
7973 and is intended to facilitate benchmarking of arbitrary R code. The library
7974 consists of just one function, benchmark, which is a simple wrapper around
7975 system.time. Given a specification of the benchmarking process (counts of
7976 replications, evaluation environment) and an arbitrary number of expressions,
7977 benchmark evaluates each of the expressions in the specified environment,
7978 replicating the evaluation as many times as specified, and returning the results
7979 conveniently wrapped into a data frame.")
7980 (license license:gpl2+)))
7981
7982 (define-public r-mitools
7983 (package
7984 (name "r-mitools")
7985 (version "2.4")
7986 (source
7987 (origin
7988 (method url-fetch)
7989 (uri (cran-uri "mitools" version))
7990 (sha256
7991 (base32
7992 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
7993 (build-system r-build-system)
7994 (propagated-inputs `(("r-dbi" ,r-dbi)))
7995 (home-page "https://cran.r-project.org/web/packages/mitools/")
7996 (synopsis "Tools for multiple imputation of missing data")
7997 (description
7998 "This package provides tools to perform analyses and combine results from
7999 multiple-imputation datasets.")
8000 (license license:gpl2)))
8001
8002 (define-public r-magick
8003 (package
8004 (name "r-magick")
8005 (version "2.3")
8006 (source
8007 (origin
8008 (method url-fetch)
8009 (uri (cran-uri "magick" version))
8010 (sha256
8011 (base32
8012 "182b4wahkq9q0scn99mql4vm9fp92nja0r5yizc4x9rjl492ahd8"))))
8013 (build-system r-build-system)
8014 (inputs
8015 `(("imagemagick" ,imagemagick)
8016 ("zlib" ,zlib)))
8017 (propagated-inputs
8018 `(("r-curl" ,r-curl)
8019 ("r-magrittr" ,r-magrittr)
8020 ("r-rcpp" ,r-rcpp)))
8021 (native-inputs
8022 `(("pkg-config" ,pkg-config)))
8023 (home-page "https://github.com/ropensci/magick")
8024 (synopsis "Advanced graphics and image-processing in R")
8025 (description
8026 "This package provides bindings to ImageMagick, a comprehensive image
8027 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
8028 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
8029 operations are vectorized via the Magick++ STL meaning they operate either on
8030 a single frame or a series of frames for working with layers, collages, or
8031 animation. In RStudio, images are automatically previewed when printed to the
8032 console, resulting in an interactive editing environment.")
8033 (license license:expat)))
8034
8035 (define-public r-survey
8036 (package
8037 (name "r-survey")
8038 (version "4.0")
8039 (source
8040 (origin
8041 (method url-fetch)
8042 (uri (cran-uri "survey" version))
8043 (sha256
8044 (base32
8045 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
8046 (build-system r-build-system)
8047 (propagated-inputs
8048 `(("r-lattice" ,r-lattice)
8049 ("r-matrix" ,r-matrix)
8050 ("r-minqa" ,r-minqa)
8051 ("r-mitools" ,r-mitools)
8052 ("r-numderiv" ,r-numderiv)
8053 ("r-survival" ,r-survival)))
8054 (home-page "http://r-survey.r-forge.r-project.org/survey/")
8055 (synopsis "Analysis of complex survey samples")
8056 (description
8057 "This package provides tools for the analysis of complex survey samples.
8058 The provided features include: summary statistics, two-sample tests, rank
8059 tests, generalised linear models, cumulative link models, Cox models,
8060 loglinear models, and general maximum pseudolikelihood estimation for
8061 multistage stratified, cluster-sampled, unequally weighted survey samples;
8062 variances by Taylor series linearisation or replicate weights;
8063 post-stratification, calibration, and raking; two-phase subsampling designs;
8064 graphics; PPS sampling without replacement; principal components, and factor
8065 analysis.")
8066 ;; Either version of the GPL.
8067 (license (list license:gpl2 license:gpl3))))
8068
8069 (define-public r-gee
8070 (package
8071 (name "r-gee")
8072 (version "4.13-20")
8073 (source
8074 (origin
8075 (method url-fetch)
8076 (uri (cran-uri "gee" version))
8077 (sha256
8078 (base32
8079 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
8080 (properties `((upstream-name . "gee")))
8081 (build-system r-build-system)
8082 (native-inputs
8083 `(("gfortran" ,gfortran)))
8084 (home-page "https://cran.r-project.org/web/packages/gee/")
8085 (synopsis "Generalized estimation equation solver")
8086 (description
8087 "This package provides a solver for generalized estimation equations.")
8088 (license license:gpl2)))
8089
8090 (define-public r-tab
8091 (package
8092 (name "r-tab")
8093 (version "4.1.1")
8094 (source
8095 (origin
8096 (method url-fetch)
8097 (uri (cran-uri "tab" version))
8098 (sha256
8099 (base32
8100 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
8101 (properties `((upstream-name . "tab")))
8102 (build-system r-build-system)
8103 (propagated-inputs
8104 `(("r-dplyr" ,r-dplyr)
8105 ("r-gee" ,r-gee)
8106 ("r-knitr" ,r-knitr)
8107 ("r-mass" ,r-mass)
8108 ("r-survey" ,r-survey)
8109 ("r-survival" ,r-survival)
8110 ("r-xtable" ,r-xtable)))
8111 (home-page "https://cran.r-project.org/web/packages/tab/")
8112 (synopsis "Create summary tables for statistical reports")
8113 (description
8114 "This package contains functions for creating various types of summary
8115 tables, e.g. comparing characteristics across levels of a categorical variable
8116 and summarizing fitted generalized linear models, generalized estimating
8117 equations, and Cox proportional hazards models. Functions are available to
8118 handle data from simple random samples as well as complex surveys.")
8119 (license license:gpl3+)))
8120
8121 (define-public r-dvmisc
8122 (package
8123 (name "r-dvmisc")
8124 (version "1.1.4")
8125 (source
8126 (origin
8127 (method url-fetch)
8128 (uri (cran-uri "dvmisc" version))
8129 (sha256
8130 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
8131 (build-system r-build-system)
8132 (propagated-inputs
8133 `(("r-cubature" ,r-cubature)
8134 ("r-data-table" ,r-data-table)
8135 ("r-dplyr" ,r-dplyr)
8136 ("r-ggplot2" ,r-ggplot2)
8137 ("r-mass" ,r-mass)
8138 ("r-mvtnorm" ,r-mvtnorm)
8139 ("r-pracma" ,r-pracma)
8140 ("r-rbenchmark" ,r-rbenchmark)
8141 ("r-rcpp" ,r-rcpp)
8142 ("r-survey" ,r-survey)
8143 ("r-tab" ,r-tab)))
8144 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
8145 (synopsis "Faster computation of common statistics and miscellaneous functions")
8146 (description
8147 "This package implements faster versions of base R functions (e.g. mean, standard
8148 deviation, covariance, weighted mean), mostly written in C++, along with
8149 miscellaneous functions for various purposes (e.g. create the histogram with
8150 fitted probability density function or probability mass function curve, create
8151 the body mass index groups, assess the linearity assumption in logistic
8152 regression).")
8153 (license license:gpl2)))
8154
8155 (define-public r-accelerometry
8156 (package
8157 (name "r-accelerometry")
8158 (version "3.1.2")
8159 (source
8160 (origin
8161 (method url-fetch)
8162 (uri (cran-uri "accelerometry" version))
8163 (sha256
8164 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
8165 (build-system r-build-system)
8166 (propagated-inputs
8167 `(("r-dvmisc" ,r-dvmisc)
8168 ("r-rcpp" ,r-rcpp)))
8169 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
8170 (synopsis "Functions for processing accelerometer data")
8171 (description
8172 "This package provides a collection of functions that perform operations on
8173 time-series accelerometer data, such as identify the non-wear time, flag minutes
8174 that are part of an activity bout, and find the maximum 10-minute average count
8175 value. The functions are generally very flexible, allowing for a variety of
8176 algorithms to be implemented.")
8177 (license license:gpl3)))
8178
8179 (define-public r-absim
8180 (package
8181 (name "r-absim")
8182 (version "0.2.6")
8183 (source
8184 (origin
8185 (method url-fetch)
8186 (uri (cran-uri "AbSim" version))
8187 (sha256
8188 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
8189 (properties `((upstream-name . "AbSim")))
8190 (build-system r-build-system)
8191 (propagated-inputs
8192 `(("r-ape" ,r-ape)
8193 ("r-powerlaw" ,r-powerlaw)))
8194 (home-page "https://cran.r-project.org/web/packages/AbSim/")
8195 (synopsis "Time resolved simulations of antibody repertoires")
8196 (description
8197 "This package provides simulation methods for the evolution of antibody repertoires.
8198 The heavy and light chain variable region of both human and C57BL/6 mice can
8199 be simulated in a time-dependent fashion. Both single lineages using one set of
8200 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8201 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8202 Upon completion, the main loop of the algorithm begins, with each iteration
8203 representing one simulated time step. Various mutation events are possible at
8204 each time step, contributing to a diverse final repertoire.")
8205 (license license:gpl2)))
8206
8207 (define-public r-quic
8208 (package
8209 (name "r-quic")
8210 (version "1.1")
8211 (source
8212 (origin
8213 (method url-fetch)
8214 (uri (cran-uri "QUIC" version))
8215 (sha256
8216 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8217 (properties `((upstream-name . "QUIC")))
8218 (build-system r-build-system)
8219 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8220 (synopsis "Regularized sparse inverse covariance matrix estimation")
8221 (description
8222 "This package implements the regularized Gaussian maximum likelihood
8223 estimation of the inverse of a covariance matrix. It uses Newton's method and
8224 coordinate descent to solve the regularized inverse covariance matrix
8225 estimation problem.")
8226 ;; The project home page states that the release is under GPLv3 or later.
8227 ;; The CRAN page only says GPL-3.
8228 (license license:gpl3+)))
8229
8230 (define-public r-abundant
8231 (package
8232 (name "r-abundant")
8233 (version "1.1")
8234 (source
8235 (origin
8236 (method url-fetch)
8237 (uri (cran-uri "abundant" version))
8238 (sha256
8239 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8240 (build-system r-build-system)
8241 (propagated-inputs
8242 `(("r-quic" ,r-quic)))
8243 (home-page "https://cran.r-project.org/web/packages/abundant/")
8244 (synopsis "Abundant regression and high-dimensional principal fitted components")
8245 (description
8246 "This package provides tools to fit and predict with the high-dimensional
8247 principal fitted components model. This model is described by Cook, Forzani,
8248 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8249 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8250 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8251 (license license:gpl2+)))
8252
8253 (define-public r-ac3net
8254 (package
8255 (name "r-ac3net")
8256 (version "1.2.2")
8257 (source
8258 (origin
8259 (method url-fetch)
8260 (uri (cran-uri "Ac3net" version))
8261 (sha256
8262 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8263 (properties `((upstream-name . "Ac3net")))
8264 (build-system r-build-system)
8265 (propagated-inputs
8266 `(("r-data-table" ,r-data-table)))
8267 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8268 (synopsis "Inferring directional conservative causal core gene networks")
8269 (description "This package infers directional Conservative causal core
8270 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8271 directional network.")
8272 (license license:gpl3+)))
8273
8274 (define-public r-aca
8275 (package
8276 (name "r-aca")
8277 (version "1.1")
8278 (source
8279 (origin
8280 (method url-fetch)
8281 (uri (cran-uri "ACA" version))
8282 (sha256
8283 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8284 (properties `((upstream-name . "ACA")))
8285 (build-system r-build-system)
8286 (home-page "https://cran.r-project.org/web/packages/ACA/")
8287 (synopsis "Abrupt change-point or aberration detection in point series")
8288 (description
8289 "This package offers an interactive function for the detection of breakpoints in
8290 series.")
8291 ;; Any version of the GPL
8292 (license (list license:gpl2+ license:gpl3+))))
8293
8294 (define-public r-acceptancesampling
8295 (package
8296 (name "r-acceptancesampling")
8297 (version "1.0-6")
8298 (source
8299 (origin
8300 (method url-fetch)
8301 (uri (cran-uri "AcceptanceSampling" version))
8302 (sha256
8303 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8304 (properties
8305 `((upstream-name . "AcceptanceSampling")))
8306 (build-system r-build-system)
8307 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8308 (synopsis "Creation and evaluation of acceptance sampling plans")
8309 (description
8310 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8311 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8312 in quality control and improvement. International standards of acceptance
8313 sampling provide sampling plans for specific circumstances. The aim of this
8314 package is to provide an easy-to-use interface to visualize single, double or
8315 multiple sampling plans. In addition, methods have been provided to enable the
8316 user to assess sampling plans against pre-specified levels of performance, as
8317 measured by the probability of acceptance for a given level of quality in the
8318 lot.")
8319 (license license:gpl3+)))
8320
8321 (define-public r-acclma
8322 (package
8323 (name "r-acclma")
8324 (version "1.0")
8325 (source
8326 (origin
8327 (method url-fetch)
8328 (uri (cran-uri "ACCLMA" version))
8329 (sha256
8330 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8331 (properties `((upstream-name . "ACCLMA")))
8332 (build-system r-build-system)
8333 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8334 (synopsis "ACC & LMA graph plotting")
8335 (description
8336 "This package contains a function that imports data from a @acronym{CSV,
8337 Comma-Separated Values} file, or uses manually entered data from the format (x,
8338 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8339 Curve} vs @acronym{LOI, Line of Independence} graph and
8340 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8341 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8342 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8343 string) was passed, a manual data entry window is opened. The header parameter
8344 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8345 a header row or not. The dataset should contain only one independent variable
8346 (x) and one dependent variable (y) and can contain a weight for each
8347 observation.")
8348 (license license:gpl2)))
8349
8350 (define-public r-aspi
8351 (package
8352 (name "r-aspi")
8353 (version "0.2.0")
8354 (source
8355 (origin
8356 (method url-fetch)
8357 (uri (cran-uri "aspi" version))
8358 (sha256
8359 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8360 (build-system r-build-system)
8361 (home-page
8362 "https://cran.r-project.org/web/packages/aspi/")
8363 (synopsis
8364 "Analysis of symmetry of parasitic infections")
8365 (description
8366 "This package provides tools for the analysis and visualization of bilateral
8367 asymmetry in parasitic infections.")
8368 (license license:gpl3+)))
8369
8370 (define-public r-sandwich
8371 (package
8372 (name "r-sandwich")
8373 (version "2.5-1")
8374 (source
8375 (origin
8376 (method url-fetch)
8377 (uri (cran-uri "sandwich" version))
8378 (sha256
8379 (base32
8380 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8381 (build-system r-build-system)
8382 (propagated-inputs
8383 `(("r-zoo" ,r-zoo)))
8384 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8385 (synopsis "Robust Covariance Matrix Estimators")
8386 (description
8387 "This package provides model-robust standard error estimators for
8388 cross-sectional, time series, clustered, panel, and longitudinal data.")
8389 ;; Either version of the license.
8390 (license (list license:gpl2 license:gpl3))))
8391
8392 (define-public r-th-data
8393 (package
8394 (name "r-th-data")
8395 (version "1.0-10")
8396 (source
8397 (origin
8398 (method url-fetch)
8399 (uri (cran-uri "TH.data" version))
8400 (sha256
8401 (base32
8402 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8403 (properties `((upstream-name . "TH.data")))
8404 (build-system r-build-system)
8405 (propagated-inputs
8406 `(("r-mass" ,r-mass)
8407 ("r-survival" ,r-survival)))
8408 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8409 (synopsis "Shared data sets")
8410 (description
8411 "This package contains supporting data sets that are used in other
8412 packages maintained by Torsten Hothorn.")
8413 (license license:gpl3)))
8414
8415 (define-public r-multcomp
8416 (package
8417 (name "r-multcomp")
8418 (version "1.4-13")
8419 (source
8420 (origin
8421 (method url-fetch)
8422 (uri (cran-uri "multcomp" version))
8423 (sha256
8424 (base32
8425 "1nszi22rcc551yc75h9cdfkdqsxw1rz30vadazmpyzihp1bh63yk"))))
8426 (build-system r-build-system)
8427 (propagated-inputs
8428 `(("r-codetools" ,r-codetools)
8429 ("r-mvtnorm" ,r-mvtnorm)
8430 ("r-sandwich" ,r-sandwich)
8431 ("r-survival" ,r-survival)
8432 ("r-th-data" ,r-th-data)))
8433 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8434 (synopsis "Simultaneous inference in general parametric models")
8435 (description
8436 "Simultaneous tests and confidence intervals for general linear
8437 hypotheses in parametric models, including linear, generalized linear, linear
8438 mixed effects, and survival models. The package includes demos reproducing
8439 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8440 Hothorn, Westfall, 2010, CRC Press).")
8441 (license license:gpl2)))
8442
8443 (define-public r-emmeans
8444 (package
8445 (name "r-emmeans")
8446 (version "1.4.6")
8447 (source
8448 (origin
8449 (method url-fetch)
8450 (uri (cran-uri "emmeans" version))
8451 (sha256
8452 (base32
8453 "0mxk7ghlv4r6sna4897q1la2xgyn1dw3r9srhm9x4h5l4701avfa"))))
8454 (build-system r-build-system)
8455 (propagated-inputs
8456 `(("r-estimability" ,r-estimability)
8457 ("r-mvtnorm" ,r-mvtnorm)
8458 ("r-numderiv" ,r-numderiv)
8459 ("r-plyr" ,r-plyr)
8460 ("r-xtable" ,r-xtable)))
8461 (native-inputs
8462 `(("r-knitr" ,r-knitr)))
8463 (home-page "https://github.com/rvlenth/emmeans")
8464 (synopsis "Estimated marginal means, aka least-squares means")
8465 (description
8466 "This package provides tools to obtain @dfn{estimated marginal
8467 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8468 be used to compute contrasts or linear functions of EMMs, trends, and
8469 comparisons of slopes.")
8470 ;; Either version of the license.
8471 (license (list license:gpl2 license:gpl3))))
8472
8473 (define-public r-pwr
8474 (package
8475 (name "r-pwr")
8476 (version "1.3-0")
8477 (source
8478 (origin
8479 (method url-fetch)
8480 (uri (cran-uri "pwr" version))
8481 (sha256
8482 (base32
8483 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
8484 (build-system r-build-system)
8485 (native-inputs
8486 `(("r-knitr" ,r-knitr)))
8487 (home-page "https://github.com/heliosdrm/pwr")
8488 (synopsis "Basic functions for power analysis")
8489 (description
8490 "This package provides power analysis functions along the lines of
8491 Cohen (1988).")
8492 (license license:gpl3+)))
8493
8494 (define-public r-libcoin
8495 (package
8496 (name "r-libcoin")
8497 (version "1.0-5")
8498 (source
8499 (origin
8500 (method url-fetch)
8501 (uri (cran-uri "libcoin" version))
8502 (sha256
8503 (base32
8504 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
8505 (build-system r-build-system)
8506 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8507 (home-page "https://cran.r-project.org/web/packages/libcoin")
8508 (synopsis "Linear test statistics for permutation inference")
8509 (description
8510 "This package provides basic infrastructure for linear test statistics
8511 and permutation inference in the framework of Strasser and Weber (1999).")
8512 (license license:gpl2)))
8513
8514 (define-public r-coin
8515 (package
8516 (name "r-coin")
8517 (version "1.3-1")
8518 (source
8519 (origin
8520 (method url-fetch)
8521 (uri (cran-uri "coin" version))
8522 (sha256
8523 (base32
8524 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8525 (build-system r-build-system)
8526 (propagated-inputs
8527 `(("r-libcoin" ,r-libcoin)
8528 ("r-matrixstats" ,r-matrixstats)
8529 ("r-modeltools" ,r-modeltools)
8530 ("r-multcomp" ,r-multcomp)
8531 ("r-mvtnorm" ,r-mvtnorm)
8532 ("r-survival" ,r-survival)))
8533 (home-page "http://coin.r-forge.r-project.org")
8534 (synopsis "Conditional inference procedures in a permutation test framework")
8535 (description
8536 "This package provides conditional inference procedures for the general
8537 independence problem including two-sample, K-sample (non-parametric ANOVA),
8538 correlation, censored, ordered and multivariate problems.")
8539 (license license:gpl2)))
8540
8541 (define-public r-bayesplot
8542 (package
8543 (name "r-bayesplot")
8544 (version "1.7.1")
8545 (source
8546 (origin
8547 (method url-fetch)
8548 (uri (cran-uri "bayesplot" version))
8549 (sha256
8550 (base32
8551 "0sq0ajnm96hmlqf1cv5n2gshh3qdij4n1zbm7qrniz2q6b5aj342"))))
8552 (build-system r-build-system)
8553 (inputs
8554 `(("pandoc" ,ghc-pandoc)
8555 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
8556 (propagated-inputs
8557 `(("r-dplyr" ,r-dplyr)
8558 ("r-ggplot2" ,r-ggplot2)
8559 ("r-ggridges" ,r-ggridges)
8560 ("r-glue" ,r-glue)
8561 ("r-reshape2" ,r-reshape2)
8562 ("r-rlang" ,r-rlang)
8563 ("r-tibble" ,r-tibble)
8564 ("r-tidyselect" ,r-tidyselect)))
8565 (home-page "https://mc-stan.org/bayesplot")
8566 (synopsis "Plotting for Bayesian models")
8567 (description
8568 "This package provides plotting functions for posterior analysis, model
8569 checking, and MCMC diagnostics. The package is designed not only to provide
8570 convenient functionality for users, but also a common set of functions that
8571 can be easily used by developers working on a variety of R packages for
8572 Bayesian modeling.")
8573 (license license:gpl3+)))
8574
8575 (define-public r-tmb
8576 (package
8577 (name "r-tmb")
8578 (version "1.7.16")
8579 (source
8580 (origin
8581 (method url-fetch)
8582 (uri (cran-uri "TMB" version))
8583 (sha256
8584 (base32
8585 "0lly12hdi99iklwr0vg9xkyhi038w4gncbf895qcwbndmqp0lx44"))))
8586 (properties `((upstream-name . "TMB")))
8587 (build-system r-build-system)
8588 (propagated-inputs
8589 `(("r-matrix" ,r-matrix)
8590 ("r-rcppeigen" ,r-rcppeigen)))
8591 (home-page "http://tmb-project.org")
8592 (synopsis "Template model builder: a general random effect tool")
8593 (description
8594 "With this tool, a user should be able to quickly implement complex
8595 random effect models through simple C++ templates. The package combines
8596 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8597 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8598 from R) to obtain an efficient implementation of the applied Laplace
8599 approximation with exact derivatives. Key features are: Automatic sparseness
8600 detection, parallelism through BLAS and parallel user templates.")
8601 (license license:gpl2)))
8602
8603 (define-public r-sjstats
8604 (package
8605 (name "r-sjstats")
8606 (version "0.17.9")
8607 (source
8608 (origin
8609 (method url-fetch)
8610 (uri (cran-uri "sjstats" version))
8611 (sha256
8612 (base32 "0938ac6ixvkif07azd2msa8g3qnn9rabj6jg17almbysl83kg4nm"))))
8613 (build-system r-build-system)
8614 (propagated-inputs
8615 `(("r-bayestestr" ,r-bayestestr)
8616 ("r-broom" ,r-broom)
8617 ("r-dplyr" ,r-dplyr)
8618 ("r-effectsize" ,r-effectsize)
8619 ("r-emmeans" ,r-emmeans)
8620 ("r-insight" ,r-insight)
8621 ("r-lme4" ,r-lme4)
8622 ("r-magrittr" ,r-magrittr)
8623 ("r-mass" ,r-mass)
8624 ("r-modelr" ,r-modelr)
8625 ("r-parameters" ,r-parameters)
8626 ("r-performance" ,r-performance)
8627 ("r-purrr" ,r-purrr)
8628 ("r-rlang" ,r-rlang)
8629 ("r-sjlabelled" ,r-sjlabelled)
8630 ("r-sjmisc" ,r-sjmisc)
8631 ("r-tidyr" ,r-tidyr)))
8632 (home-page "https://github.com/strengejacke/sjstats")
8633 (synopsis "Functions for common statistical computations")
8634 (description
8635 "This package provides a collection of convenient functions for common
8636 statistical computations, which are not directly provided by R's @code{base}
8637 or @code{stats} packages. This package aims at providing, first, shortcuts
8638 for statistical measures, which otherwise could only be calculated with
8639 additional effort. Second, these shortcut functions are generic, and can be
8640 applied not only to vectors, but also to other objects as well. The focus of
8641 most functions lies on summary statistics or fit measures for regression
8642 models, including generalized linear models, mixed effects models and Bayesian
8643 models.")
8644 (license license:gpl3)))
8645
8646 (define-public r-glmmtmb
8647 (package
8648 (name "r-glmmtmb")
8649 (version "1.0.1")
8650 (source
8651 (origin
8652 (method url-fetch)
8653 (uri (cran-uri "glmmTMB" version))
8654 (sha256
8655 (base32
8656 "0sdx1q7wc7895xh8747r4p0wkij0xjgn5ij62ipi9423zd0sr0mm"))))
8657 (properties `((upstream-name . "glmmTMB")))
8658 (build-system r-build-system)
8659 (propagated-inputs
8660 `(("r-lme4" ,r-lme4)
8661 ("r-matrix" ,r-matrix)
8662 ("r-nlme" ,r-nlme)
8663 ("r-rcppeigen" ,r-rcppeigen)
8664 ("r-tmb" ,r-tmb)))
8665 (native-inputs
8666 `(("r-knitr" ,r-knitr))) ; for vignettes
8667 (home-page "https://github.com/glmmTMB")
8668 (synopsis "Generalized linear mixed models")
8669 (description
8670 "Fit linear and generalized linear mixed models with various extensions,
8671 including zero-inflation. The models are fitted using maximum likelihood
8672 estimation via the Template Model Builder. Random effects are assumed to be
8673 Gaussian on the scale of the linear predictor and are integrated out using the
8674 Laplace approximation. Gradients are calculated using automatic
8675 differentiation.")
8676 (license license:agpl3+)))
8677
8678 (define-public r-bayestestr
8679 (package
8680 (name "r-bayestestr")
8681 (version "0.6.0")
8682 (source
8683 (origin
8684 (method url-fetch)
8685 (uri (cran-uri "bayestestR" version))
8686 (sha256
8687 (base32
8688 "0s7wdmk8avgaqk2b7fcf4bsh13isrkl1q4y7z2y8jhdagxxxnzd1"))))
8689 (properties `((upstream-name . "bayestestR")))
8690 (build-system r-build-system)
8691 (propagated-inputs
8692 `(("r-insight" ,r-insight)))
8693 (native-inputs
8694 `(("r-knitr" ,r-knitr)))
8695 (home-page "https://github.com/easystats/bayestestR")
8696 (synopsis "Describe Bayesian models and posterior distributions")
8697 (description
8698 "This package provides utilities to understand and describe posterior
8699 distributions and Bayesian models. It includes point-estimates such as
8700 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
8701 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
8702 ROPE percentage and pd).")
8703 (license license:gpl3)))
8704
8705 (define-public r-performance
8706 (package
8707 (name "r-performance")
8708 (version "0.4.5")
8709 (source
8710 (origin
8711 (method url-fetch)
8712 (uri (cran-uri "performance" version))
8713 (sha256
8714 (base32
8715 "0j6wmnwhfdd3v1a17qmg491q50579knjzscmyr4yk3xr0jbsbg8x"))))
8716 (build-system r-build-system)
8717 (propagated-inputs
8718 `(("r-bayestestr" ,r-bayestestr)
8719 ("r-insight" ,r-insight)))
8720 (home-page "https://easystats.github.io/performance/")
8721 (synopsis "Assessment of regression models performance")
8722 (description
8723 "This package provides utilities for computing measures to assess model
8724 quality, which are not directly provided by R's @code{base} or @code{stats}
8725 packages. These include e.g. measures like r-squared, intraclass correlation
8726 coefficient, root mean squared error or functions to check models for
8727 overdispersion, singularity or zero-inflation and more. Functions apply to a
8728 large variety of regression models, including generalized linear models, mixed
8729 effects models and Bayesian models.")
8730 (license license:gpl3)))
8731
8732 (define-public r-ggeffects
8733 (package
8734 (name "r-ggeffects")
8735 (version "0.14.3")
8736 (source
8737 (origin
8738 (method url-fetch)
8739 (uri (cran-uri "ggeffects" version))
8740 (sha256
8741 (base32
8742 "06p80bgjhjknzlb4vs4n41i9n9vv5agncakl9f92zkaahgyzd6sd"))))
8743 (build-system r-build-system)
8744 (propagated-inputs
8745 `(("r-insight" ,r-insight)
8746 ("r-mass" ,r-mass)
8747 ("r-sjlabelled" ,r-sjlabelled)))
8748 (native-inputs
8749 `(("r-knitr" ,r-knitr)))
8750 (home-page "https://github.com/strengejacke/ggeffects")
8751 (synopsis "Create tidy data frames of marginal effects for ggplot")
8752 (description
8753 "This package provides tools to compute marginal effects from statistical
8754 models and return the result as tidy data frames. These data frames are ready
8755 to use with the @code{ggplot2} package. Marginal effects can be calculated
8756 for many different models. Interaction terms, splines and polynomial terms
8757 are also supported. The two main functions are @code{ggpredict()} and
8758 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
8759 results using @code{ggplot2}.")
8760 (license license:gpl3)))
8761
8762 (define-public r-effectsize
8763 (package
8764 (name "r-effectsize")
8765 (version "0.3.0")
8766 (source
8767 (origin
8768 (method url-fetch)
8769 (uri (cran-uri "effectsize" version))
8770 (sha256
8771 (base32
8772 "0kijp4wamkidaxysc11dd4vhvnm4wnbi87871wcbwn27k5b6i5dg"))))
8773 (properties `((upstream-name . "effectsize")))
8774 (build-system r-build-system)
8775 (propagated-inputs
8776 `(("r-bayestestr" ,r-bayestestr)
8777 ("r-insight" ,r-insight)
8778 ("r-parameters" ,r-parameters)))
8779 (native-inputs
8780 `(("r-knitr" ,r-knitr)))
8781 (home-page "https://github.com/easystats/effectsize")
8782 (synopsis "Indices of effect size and standardized parameters")
8783 (description
8784 "This package provides utilities to work with indices of effect size and
8785 standardized parameters for a wide variety of models, allowing computation and
8786 conversion of indices such as Cohen's d, r, odds, etc.")
8787 (license license:gpl3)))
8788
8789 (define-public r-sjplot
8790 (package
8791 (name "r-sjplot")
8792 (version "2.8.3")
8793 (source
8794 (origin
8795 (method url-fetch)
8796 (uri (cran-uri "sjPlot" version))
8797 (sha256
8798 (base32 "0ip1rkjlhyf3axlc8qqss1qq1f0xrda890c1jmcbhm98wwjw264f"))))
8799 (properties `((upstream-name . "sjPlot")))
8800 (build-system r-build-system)
8801 (propagated-inputs
8802 `(("r-bayestestr" ,r-bayestestr)
8803 ("r-dplyr" ,r-dplyr)
8804 ("r-effectsize" ,r-effectsize)
8805 ("r-ggeffects" ,r-ggeffects)
8806 ("r-ggplot2" ,r-ggplot2)
8807 ("r-insight" ,r-insight)
8808 ("r-knitr" ,r-knitr)
8809 ("r-mass" ,r-mass)
8810 ("r-parameters" ,r-parameters)
8811 ("r-performance" ,r-performance)
8812 ("r-purrr" ,r-purrr)
8813 ("r-rlang" ,r-rlang)
8814 ("r-scales" ,r-scales)
8815 ("r-sjlabelled" ,r-sjlabelled)
8816 ("r-sjmisc" ,r-sjmisc)
8817 ("r-sjstats" ,r-sjstats)
8818 ("r-tidyr" ,r-tidyr)))
8819 (native-inputs
8820 `(("r-knitr" ,r-knitr)))
8821 (home-page "https://strengejacke.github.io/sjPlot/")
8822 (synopsis "Data visualization for statistics in social science")
8823 (description
8824 "This package represents a collection of plotting and table output
8825 functions for data visualization. Results of various statistical
8826 analyses (that are commonly used in social sciences) can be visualized using
8827 this package, including simple and cross tabulated frequencies, histograms,
8828 box plots, (generalized) linear models, mixed effects models, principal
8829 component analysis and correlation matrices, cluster analyses, scatter plots,
8830 stacked scales, effects plots of regression models (including interaction
8831 terms) and much more. This package supports labelled data.")
8832 (license license:gpl3)))
8833
8834 (define-public r-ini
8835 (package
8836 (name "r-ini")
8837 (version "0.3.1")
8838 (source
8839 (origin
8840 (method url-fetch)
8841 (uri (cran-uri "ini" version))
8842 (sha256
8843 (base32
8844 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
8845 (build-system r-build-system)
8846 (home-page "https://github.com/dvdscripter/ini")
8847 (synopsis "Read and write configuration files")
8848 (description
8849 "This package provides tools to parse simple @code{.ini} configuration
8850 files to an structured list. Users can manipulate this resulting list with
8851 @code{lapply()} functions. This same structured list can be used to write
8852 back to file after modifications.")
8853 (license license:gpl3)))
8854
8855 (define-public r-gh
8856 (package
8857 (name "r-gh")
8858 (version "1.1.0")
8859 (source
8860 (origin
8861 (method url-fetch)
8862 (uri (cran-uri "gh" version))
8863 (sha256
8864 (base32
8865 "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
8866 (build-system r-build-system)
8867 (propagated-inputs
8868 `(("r-cli" ,r-cli)
8869 ("r-httr" ,r-httr)
8870 ("r-ini" ,r-ini)
8871 ("r-jsonlite" ,r-jsonlite)))
8872 (home-page "https://github.com/r-lib/gh#readme")
8873 (synopsis "Access the GitHub API via R")
8874 (description
8875 "This package provides a minimal R client to access the GitHub API.")
8876 (license license:expat)))
8877
8878 (define-public r-fs
8879 (package
8880 (name "r-fs")
8881 (version "1.4.1")
8882 (source
8883 (origin
8884 (method url-fetch)
8885 (uri (cran-uri "fs" version))
8886 (sha256
8887 (base32
8888 "0kksig9pk8aid9l6r250na8z8j9919jvs20lj0s6m9bcybgh74df"))))
8889 (build-system r-build-system)
8890 (native-inputs
8891 `(("pkg-config" ,pkg-config)
8892 ("r-knitr" ,r-knitr)))
8893 (home-page "https://fs.r-lib.org")
8894 (synopsis "Cross-platform file system operations based on libuv")
8895 (description
8896 "This package provides a cross-platform interface to file system
8897 operations, built on top of the libuv C library.")
8898 (license license:gpl3)))
8899
8900 (define-public r-clisymbols
8901 (package
8902 (name "r-clisymbols")
8903 (version "1.2.0")
8904 (source
8905 (origin
8906 (method url-fetch)
8907 (uri (cran-uri "clisymbols" version))
8908 (sha256
8909 (base32
8910 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
8911 (build-system r-build-system)
8912 (home-page "https://github.com/gaborcsardi/clisymbols")
8913 (synopsis "Unicode symbols at the R prompt")
8914 (description
8915 "This package provides a small subset of Unicode symbols, that are useful
8916 when building command line applications. They fall back to alternatives on
8917 terminals that do not support Unicode.")
8918 (license license:expat)))
8919
8920 (define-public r-usethis
8921 (package
8922 (name "r-usethis")
8923 (version "1.6.1")
8924 (source
8925 (origin
8926 (method url-fetch)
8927 (uri (cran-uri "usethis" version))
8928 (sha256
8929 (base32
8930 "0vwxsnq615mwc706a4a71gyy0hmvnllbh249gzm7vl3ym5cr0cv0"))))
8931 (build-system r-build-system)
8932 (propagated-inputs
8933 `(("r-cli" ,r-cli)
8934 ("r-clipr" ,r-clipr)
8935 ("r-crayon" ,r-crayon)
8936 ("r-curl" ,r-curl)
8937 ("r-desc" ,r-desc)
8938 ("r-fs" ,r-fs)
8939 ("r-gh" ,r-gh)
8940 ("r-git2r" ,r-git2r)
8941 ("r-glue" ,r-glue)
8942 ("r-purrr" ,r-purrr)
8943 ("r-rematch2" ,r-rematch2)
8944 ("r-rlang" ,r-rlang)
8945 ("r-rprojroot" ,r-rprojroot)
8946 ("r-rstudioapi" ,r-rstudioapi)
8947 ("r-whisker" ,r-whisker)
8948 ("r-withr" ,r-withr)
8949 ("r-yaml" ,r-yaml)))
8950 (home-page "https://github.com/r-lib/usethis")
8951 (synopsis "Automate R package and project setup")
8952 (description
8953 "This package helps you to automate R package and project setup tasks
8954 that are otherwise performed manually. This includes setting up unit testing,
8955 test coverage, continuous integration, Git, GitHub integration, licenses,
8956 Rcpp, RStudio projects, and more.")
8957 (license license:gpl3)))
8958
8959 (define-public r-sessioninfo
8960 (package
8961 (name "r-sessioninfo")
8962 (version "1.1.1")
8963 (source
8964 (origin
8965 (method url-fetch)
8966 (uri (cran-uri "sessioninfo" version))
8967 (sha256
8968 (base32
8969 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
8970 (build-system r-build-system)
8971 (propagated-inputs
8972 `(("r-cli" ,r-cli)
8973 ("r-withr" ,r-withr)))
8974 (home-page "https://github.com/r-lib/sessioninfo#readme")
8975 (synopsis "R session information")
8976 (description
8977 "This package provides tools to query and print information about the
8978 current R session. It is similar to @code{utils::sessionInfo()}, but includes
8979 more information about packages, and where they were installed from.")
8980 (license license:gpl2)))
8981
8982 (define-public r-remotes
8983 (package
8984 (name "r-remotes")
8985 (version "2.1.1")
8986 (source
8987 (origin
8988 (method url-fetch)
8989 (uri (cran-uri "remotes" version))
8990 (sha256
8991 (base32
8992 "12qinl7jv54f2524ri13gcrv6d523rg1harpi500j676zi30fnaf"))))
8993 (build-system r-build-system)
8994 (home-page "https://github.com/r-lib/remotes#readme")
8995 (synopsis "R package installation from remote repositories")
8996 (description
8997 "Download and install R packages stored in GitHub, BitBucket, or plain
8998 subversion or git repositories. This package is a lightweight replacement of
8999 the @code{install_*} functions in the @code{devtools} package. Indeed most of
9000 the code was copied over from @code{devtools}.")
9001 (license license:gpl2+)))
9002
9003 (define-public r-xopen
9004 (package
9005 (name "r-xopen")
9006 (version "1.0.0")
9007 (source
9008 (origin
9009 (method url-fetch)
9010 (uri (cran-uri "xopen" version))
9011 (sha256
9012 (base32
9013 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
9014 (build-system r-build-system)
9015 (propagated-inputs
9016 `(("r-processx" ,r-processx)))
9017 (home-page "https://github.com/r-lib/xopen#readme")
9018 (synopsis "Open system files, URLs, anything")
9019 (description
9020 "This package provides a cross-platform solution to open files,
9021 directories or URLs with their associated programs.")
9022 (license license:expat)))
9023
9024 (define-public r-rcmdcheck
9025 (package
9026 (name "r-rcmdcheck")
9027 (version "1.3.3")
9028 (source
9029 (origin
9030 (method url-fetch)
9031 (uri (cran-uri "rcmdcheck" version))
9032 (sha256
9033 (base32
9034 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
9035 (build-system r-build-system)
9036 (propagated-inputs
9037 `(("r-callr" ,r-callr)
9038 ("r-cli" ,r-cli)
9039 ("r-crayon" ,r-crayon)
9040 ("r-desc" ,r-desc)
9041 ("r-digest" ,r-digest)
9042 ("r-pkgbuild" ,r-pkgbuild)
9043 ("r-prettyunits" ,r-prettyunits)
9044 ("r-r6" ,r-r6)
9045 ("r-rprojroot" ,r-rprojroot)
9046 ("r-sessioninfo" ,r-sessioninfo)
9047 ("r-withr" ,r-withr)
9048 ("r-xopen" ,r-xopen)))
9049 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
9050 (synopsis "Run R CMD check from R and capture results")
9051 (description
9052 "Run @code{R CMD check} from R programmatically, and capture the results
9053 of the individual checks.")
9054 (license license:expat)))
9055
9056 (define-public r-rapportools
9057 (package
9058 (name "r-rapportools")
9059 (version "1.0")
9060 (source
9061 (origin
9062 (method url-fetch)
9063 (uri (cran-uri "rapportools" version))
9064 (sha256
9065 (base32
9066 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
9067 (build-system r-build-system)
9068 (propagated-inputs
9069 `(("r-pander" ,r-pander)
9070 ("r-plyr" ,r-plyr)
9071 ("r-reshape" ,r-reshape)))
9072 (home-page "https://cran.r-project.org/web/packages/rapportools/")
9073 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
9074 (description
9075 "This package provides helper functions that act as wrappers to more
9076 advanced statistical methods with the advantage of having sane defaults for
9077 quick reporting.")
9078 (license license:agpl3+)))
9079
9080 (define-public r-pander
9081 (package
9082 (name "r-pander")
9083 (version "0.6.3")
9084 (source
9085 (origin
9086 (method url-fetch)
9087 (uri (cran-uri "pander" version))
9088 (sha256
9089 (base32
9090 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
9091 (build-system r-build-system)
9092 (propagated-inputs
9093 `(("r-digest" ,r-digest)
9094 ("r-rcpp" ,r-rcpp)))
9095 (home-page "https://rapporter.github.io/pander")
9096 (synopsis "Render R objects into Pandoc's markdown")
9097 (description
9098 "The main aim of the pander R package is to provide a minimal and easy
9099 tool for rendering R objects into Pandoc's markdown. The package is also
9100 capable of exporting/converting complex Pandoc documents (reports) in various
9101 ways.")
9102 ;; This package is licensed under either the AGPLv3+ or the very rarely
9103 ;; used OSL 3.0.
9104 (license license:agpl3+)))
9105
9106 (define-public r-summarytools
9107 (package
9108 (name "r-summarytools")
9109 (version "0.9.6")
9110 (source
9111 (origin
9112 (method url-fetch)
9113 (uri (cran-uri "summarytools" version))
9114 (sha256
9115 (base32
9116 "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2"))))
9117 (build-system r-build-system)
9118 (propagated-inputs
9119 `(("r-base64enc" ,r-base64enc)
9120 ("r-checkmate" ,r-checkmate)
9121 ("r-dplyr" ,r-dplyr)
9122 ("r-htmltools" ,r-htmltools)
9123 ("r-lubridate" ,r-lubridate)
9124 ("r-magick" ,r-magick)
9125 ("r-matrixstats" ,r-matrixstats)
9126 ("r-pander" ,r-pander)
9127 ("r-pryr" ,r-pryr)
9128 ("r-rapportools" ,r-rapportools)
9129 ("r-tibble" ,r-tibble)
9130 ("r-tidyr" ,r-tidyr)))
9131 (home-page "https://github.com/dcomtois/summarytools")
9132 (synopsis "Tools to quickly and neatly summarize data")
9133 (description
9134 "This package provides tools for data frame summaries, cross-tabulations,
9135 weight-enabled frequency tables and common univariate statistics in concise
9136 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
9137 good point-of-entry for exploring data, both for experienced and new R
9138 users.")
9139 (license license:gpl2)))
9140
9141 (define-public r-lsei
9142 (package
9143 (name "r-lsei")
9144 (version "1.2-0")
9145 (source
9146 (origin
9147 (method url-fetch)
9148 (uri (cran-uri "lsei" version))
9149 (sha256
9150 (base32
9151 "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7"))))
9152 (build-system r-build-system)
9153 (native-inputs
9154 `(("gfortran" ,gfortran)))
9155 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9156 (synopsis "Solve regression problems under equality/inequality constraints")
9157 (description
9158 "It contains functions that solve least squares linear regression
9159 problems under linear equality/inequality constraints. Functions for solving
9160 quadratic programming problems are also available, which transform such
9161 problems into least squares ones first.")
9162 (license license:gpl2+)))
9163
9164 (define-public r-npsurv
9165 (package
9166 (name "r-npsurv")
9167 (version "0.4-0")
9168 (source
9169 (origin
9170 (method url-fetch)
9171 (uri (cran-uri "npsurv" version))
9172 (sha256
9173 (base32
9174 "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20"))))
9175 (build-system r-build-system)
9176 (propagated-inputs
9177 `(("r-lsei" ,r-lsei)))
9178 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9179 (synopsis "Nonparametric survival analysis")
9180 (description
9181 "This package contains functions for non-parametric survival analysis of
9182 exact and interval-censored observations.")
9183 (license license:gpl2+)))
9184
9185 (define-public r-clusteval
9186 (package
9187 (name "r-clusteval")
9188 (version "0.1")
9189 (source
9190 (origin
9191 (method url-fetch)
9192 (uri (cran-uri "clusteval" version))
9193 (sha256
9194 (base32
9195 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
9196 (build-system r-build-system)
9197 (propagated-inputs
9198 `(("r-mvtnorm" ,r-mvtnorm)
9199 ("r-rcpp" ,r-rcpp)))
9200 (home-page "https://cran.r-project.org/web/packages/clusteval/")
9201 (synopsis "Evaluation of clustering algorithms")
9202 (description
9203 "This R package provides a suite of tools to evaluate clustering
9204 algorithms, clusterings, and individual clusters.")
9205 (license license:expat)))
9206
9207 (define-public r-tweedie
9208 (package
9209 (name "r-tweedie")
9210 (version "2.3.2")
9211 (source
9212 (origin
9213 (method url-fetch)
9214 (uri (cran-uri "tweedie" version))
9215 (sha256
9216 (base32
9217 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9218 (build-system r-build-system)
9219 (native-inputs `(("gfortran" ,gfortran)))
9220 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9221 (synopsis "Evaluation of Tweedie exponential family models")
9222 (description
9223 "Maximum likelihood computations for Tweedie families, including the
9224 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9225 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9226 and related methods.")
9227 (license license:gpl2+)))
9228
9229 (define-public r-rcppgsl
9230 (package
9231 (name "r-rcppgsl")
9232 (version "0.3.7")
9233 (source
9234 (origin
9235 (method url-fetch)
9236 (uri (cran-uri "RcppGSL" version))
9237 (sha256
9238 (base32 "0cnw2k7cfqrm79r6j283aybflxig80x4n4rjkfp2317wf10mrsa5"))))
9239 (properties `((upstream-name . "RcppGSL")))
9240 (build-system r-build-system)
9241 (propagated-inputs
9242 `(("r-rcpp" ,r-rcpp)
9243 ("gsl" ,gsl)))
9244 (native-inputs
9245 `(("r-knitr" ,r-knitr))) ; for vignettes
9246 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9247 (synopsis "Rcpp integration for GSL vectors and matrices")
9248 (description
9249 "The GNU Scientific Library (or GSL) is a collection of numerical
9250 routines for scientific computing. It is particularly useful for C and C++
9251 programs as it provides a standard C interface to a wide range of mathematical
9252 routines. There are over 1000 functions in total with an extensive test
9253 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9254 structures and R using concepts from Rcpp which is itself a package that eases
9255 the interfaces between R and C++.")
9256 (license license:gpl2+)))
9257
9258 (define-public r-mvabund
9259 (package
9260 (name "r-mvabund")
9261 (version "4.1.3")
9262 (source
9263 (origin
9264 (method url-fetch)
9265 (uri (cran-uri "mvabund" version))
9266 (sha256
9267 (base32
9268 "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b"))))
9269 (build-system r-build-system)
9270 (propagated-inputs
9271 `(("r-mass" ,r-mass)
9272 ("r-rcpp" ,r-rcpp)
9273 ("r-rcppgsl" ,r-rcppgsl)
9274 ("r-statmod" ,r-statmod)
9275 ("r-tweedie" ,r-tweedie)))
9276 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9277 (synopsis "Statistical methods for analysing multivariate abundance data")
9278 (description
9279 "This package provides a set of tools for displaying, modeling and
9280 analysing multivariate abundance data in community ecology.")
9281 (license license:lgpl2.1+)))
9282
9283 (define-public r-afex
9284 (package
9285 (name "r-afex")
9286 (version "0.27-2")
9287 (source
9288 (origin
9289 (method url-fetch)
9290 (uri (cran-uri "afex" version))
9291 (sha256
9292 (base32
9293 "0qsmcddy4449qjj3ajmqvdiqdkhkswmz5dqf150wxwq897p3bvf2"))))
9294 (build-system r-build-system)
9295 (propagated-inputs
9296 `(("r-car" ,r-car)
9297 ("r-lme4" ,r-lme4)
9298 ("r-lmertest" ,r-lmertest)
9299 ("r-pbkrtest" ,r-pbkrtest)
9300 ("r-reshape2" ,r-reshape2)))
9301 (native-inputs
9302 `(("r-knitr" ,r-knitr)))
9303 (home-page "https://afex.singmann.science/")
9304 (synopsis "Analysis of factorial experiments")
9305 (description
9306 "This package provides convenience functions for analyzing factorial
9307 experiments using ANOVA or mixed models.")
9308 (license license:gpl2+)))
9309
9310 (define-public r-lmertest
9311 (package
9312 (name "r-lmertest")
9313 (version "3.1-2")
9314 (source
9315 (origin
9316 (method url-fetch)
9317 (uri (cran-uri "lmerTest" version))
9318 (sha256
9319 (base32
9320 "1qkdxx5sri65zgpb9gw4nkfkdam51kgy4hxclk5c40yk7y3p0n1q"))))
9321 (properties `((upstream-name . "lmerTest")))
9322 (build-system r-build-system)
9323 (propagated-inputs
9324 `(("r-ggplot2" ,r-ggplot2)
9325 ("r-lme4" ,r-lme4)
9326 ("r-mass" ,r-mass)
9327 ("r-numderiv" ,r-numderiv)))
9328 (home-page "https://github.com/runehaubo/lmerTestR")
9329 (synopsis "Tests in linear mixed effects models")
9330 (description
9331 "This package provides p-values in type I, II or III anova and summary
9332 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9333 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9334 package. Model selection methods include step, drop1 and anova-like tables
9335 for random effects (ranova). Methods for Least-Square means (LS-means) and
9336 tests of linear contrasts of fixed effects are also available.")
9337 (license license:gpl2+)))
9338
9339 (define-public r-r2glmm
9340 (package
9341 (name "r-r2glmm")
9342 (version "0.1.2")
9343 (source
9344 (origin
9345 (method url-fetch)
9346 (uri (cran-uri "r2glmm" version))
9347 (sha256
9348 (base32
9349 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9350 (build-system r-build-system)
9351 (propagated-inputs
9352 `(("r-afex" ,r-afex)
9353 ("r-data-table" ,r-data-table)
9354 ("r-dplyr" ,r-dplyr)
9355 ("r-ggplot2" ,r-ggplot2)
9356 ("r-gridextra" ,r-gridextra)
9357 ("r-lmertest" ,r-lmertest)
9358 ("r-mass" ,r-mass)
9359 ("r-matrix" ,r-matrix)
9360 ("r-mgcv" ,r-mgcv)
9361 ("r-pbkrtest" ,r-pbkrtest)))
9362 (home-page "https://github.com/bcjaeger/r2glmm")
9363 (synopsis "Compute R squared for mixed (multilevel) models")
9364 (description
9365 "This package computes model and semi partial R squared with confidence
9366 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9367 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9368 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9369 al. (2016)).")
9370 (license license:gpl2)))
9371
9372 (define-public r-weights
9373 (package
9374 (name "r-weights")
9375 (version "1.0.1")
9376 (source
9377 (origin
9378 (method url-fetch)
9379 (uri (cran-uri "weights" version))
9380 (sha256
9381 (base32
9382 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
9383 (build-system r-build-system)
9384 (propagated-inputs
9385 `(("r-gdata" ,r-gdata)
9386 ("r-hmisc" ,r-hmisc)
9387 ("r-mice" ,r-mice)))
9388 (home-page
9389 "https://cran.r-project.org/web/packages/weights/")
9390 (synopsis "Weighting and weighted statistics")
9391 (description "This package Provides a variety of functions for producing
9392 simple weighted statistics, such as weighted Pearson's correlations, partial
9393 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9394 includes some software for quickly recoding survey data and plotting point
9395 estimates from interaction terms in regressions (and multiply imputed
9396 regressions). NOTE: Weighted partial correlation calculations pulled to
9397 address a bug.")
9398 (license license:gpl2+)))
9399
9400 (define-public r-rcppannoy
9401 (package
9402 (name "r-rcppannoy")
9403 (version "0.0.16")
9404 (source
9405 (origin
9406 (method url-fetch)
9407 (uri (cran-uri "RcppAnnoy" version))
9408 (sha256
9409 (base32
9410 "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr"))))
9411 (properties `((upstream-name . "RcppAnnoy")))
9412 (build-system r-build-system)
9413 (propagated-inputs
9414 `(("r-rcpp" ,r-rcpp)))
9415 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9416 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9417 (description
9418 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9419 for efficient memory usage as well an ability to load from and save to disk.
9420 This package provides an R interface.")
9421 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9422 ;; GPLv2+.
9423 (license (list license:gpl2+ license:asl2.0))))
9424
9425 (define-public r-rcpphnsw
9426 (package
9427 (name "r-rcpphnsw")
9428 (version "0.2.0")
9429 (source
9430 (origin
9431 (method url-fetch)
9432 (uri (cran-uri "RcppHNSW" version))
9433 (sha256
9434 (base32
9435 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9436 (properties `((upstream-name . "RcppHNSW")))
9437 (build-system r-build-system)
9438 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9439 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9440 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9441 (description
9442 "Hnswlib is a C++ library for approximate nearest neighbors. This
9443 package provides a minimal R interface by relying on the Rcpp package.")
9444 ;; hnswlib is released under Version 2.0 of the Apache License.
9445 (license (list license:gpl3 license:asl2.0))))
9446
9447 (define-public r-rcppparallel
9448 (package
9449 (name "r-rcppparallel")
9450 (version "5.0.0")
9451 (source
9452 (origin
9453 (method url-fetch)
9454 (uri (cran-uri "RcppParallel" version))
9455 (sha256
9456 (base32
9457 "1mhd6vp47xmfw533h0pkvydv96m57fspvd85g8m7iqb5rcxvhhdb"))))
9458 (properties `((upstream-name . "RcppParallel")))
9459 (build-system r-build-system)
9460 (home-page "https://rcppcore.github.io/RcppParallel/")
9461 (synopsis "Parallel programming tools for Rcpp")
9462 (description
9463 "This package provides high level functions for parallel programming with
9464 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9465 the work of a standard serial @code{for} loop into a parallel one and the
9466 @code{parallelReduce()} function can be used for accumulating aggregates or
9467 other values.")
9468 (license license:gpl2)))
9469
9470 (define-public r-ncdf4
9471 (package
9472 (name "r-ncdf4")
9473 (version "1.17")
9474 (source
9475 (origin
9476 (method url-fetch)
9477 (uri (cran-uri "ncdf4" version))
9478 (sha256
9479 (base32
9480 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9481 (build-system r-build-system)
9482 (inputs
9483 `(("netcdf" ,netcdf)
9484 ("zlib" ,zlib)))
9485 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9486 (synopsis "R interface to Unidata netCDF format data files")
9487 (description
9488 "This package provides a high-level R interface to data files written
9489 using Unidata's netCDF library (version 4 or earlier), which are binary data
9490 files that are portable across platforms and include metadata information in
9491 addition to the data sets. Using this package, netCDF files can be opened and
9492 data sets read in easily. It is also easy to create new netCDF dimensions,
9493 variables, and files, in either version 3 or 4 format, and manipulate existing
9494 netCDF files.")
9495 (license license:gpl3+)))
9496
9497 (define-public r-biocmanager
9498 (package
9499 (name "r-biocmanager")
9500 (version "1.30.10")
9501 (source
9502 (origin
9503 (method url-fetch)
9504 (uri (cran-uri "BiocManager" version))
9505 (sha256
9506 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9507 (properties `((upstream-name . "BiocManager")))
9508 (build-system r-build-system)
9509 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9510 (synopsis "Access the Bioconductor project package repository")
9511 (description
9512 "This package provides a convenient tool to install and update
9513 Bioconductor packages.")
9514 (license license:artistic2.0)))
9515
9516 (define-public r-rgl
9517 (package
9518 (name "r-rgl")
9519 (version "0.100.54")
9520 (source
9521 (origin
9522 (method url-fetch)
9523 (uri (cran-uri "rgl" version))
9524 (sha256
9525 (base32
9526 "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp"))))
9527 (build-system r-build-system)
9528 (native-inputs
9529 `(("pkg-config" ,pkg-config)))
9530 (inputs
9531 `(("freetype" ,freetype)
9532 ("libpng" ,libpng)
9533 ("glu" ,glu)
9534 ("libx11" ,libx11)
9535 ("ghc-pandoc" ,ghc-pandoc)
9536 ("zlib" ,zlib)))
9537 (propagated-inputs
9538 `(("r-crosstalk" ,r-crosstalk)
9539 ("r-htmltools" ,r-htmltools)
9540 ("r-htmlwidgets" ,r-htmlwidgets)
9541 ("r-jsonlite" ,r-jsonlite)
9542 ("r-knitr" ,r-knitr)
9543 ("r-magrittr" ,r-magrittr)
9544 ("r-manipulatewidget" ,r-manipulatewidget)
9545 ("r-shiny" ,r-shiny)))
9546 (home-page "https://r-forge.r-project.org/projects/rgl/")
9547 (synopsis "3D visualization using OpenGL")
9548 (description
9549 "This package provides medium to high level functions for 3D interactive graphics,
9550 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9551 as functions for constructing representations of geometric
9552 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9553 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9554 image formats, including PNG, Postscript, SVG, PGF.")
9555 ;; Any version of the GPL.
9556 (license (list license:gpl2+ license:gpl3+))))
9557
9558 (define-public r-multicool
9559 (package
9560 (name "r-multicool")
9561 (version "0.1-11")
9562 (source
9563 (origin
9564 (method url-fetch)
9565 (uri (cran-uri "multicool" version))
9566 (sha256
9567 (base32
9568 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
9569 (build-system r-build-system)
9570 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9571 (home-page "https://cran.r-project.org/web/packages/multicool/")
9572 (synopsis "Permutations of multisets in cool-lex order")
9573 (description
9574 "This package provides a set of tools to permute multisets without loops
9575 or hash tables and to generate integer partitions. Cool-lex order is similar
9576 to colexicographical order.")
9577 (license license:gpl2)))
9578
9579 (define-public r-misc3d
9580 (package
9581 (name "r-misc3d")
9582 (version "0.8-4")
9583 (source
9584 (origin
9585 (method url-fetch)
9586 (uri (cran-uri "misc3d" version))
9587 (sha256
9588 (base32
9589 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9590 (build-system r-build-system)
9591 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9592 (synopsis "Miscellaneous 3D Plots")
9593 (description
9594 "This package provides a collection of miscellaneous 3d plots, including
9595 isosurfaces.")
9596 ;; Any version of the GPL.
9597 (license (list license:gpl2+ license:gpl3+))))
9598
9599 (define-public r-ks
9600 (package
9601 (name "r-ks")
9602 (version "1.11.7")
9603 (source
9604 (origin
9605 (method url-fetch)
9606 (uri (cran-uri "ks" version))
9607 (sha256
9608 (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
9609 (build-system r-build-system)
9610 (propagated-inputs
9611 `(("r-fnn" ,r-fnn)
9612 ("r-kernlab" ,r-kernlab)
9613 ("r-kernsmooth" ,r-kernsmooth)
9614 ("r-matrix" ,r-matrix)
9615 ("r-mclust" ,r-mclust)
9616 ("r-mgcv" ,r-mgcv)
9617 ("r-multicool" ,r-multicool)
9618 ("r-mvtnorm" ,r-mvtnorm)))
9619 (home-page "http://www.mvstat.net/tduong/")
9620 (synopsis "Kernel smoothing")
9621 (description
9622 "This package provides kernel smoothers for univariate and multivariate
9623 data, including density functions, density derivatives, cumulative
9624 distributions, modal clustering, discriminant analysis, and two-sample
9625 hypothesis testing.")
9626 ;; Either version of the GPL.
9627 (license (list license:gpl2 license:gpl3))))
9628
9629 (define-public r-feature
9630 (package
9631 (name "r-feature")
9632 (version "1.2.13")
9633 (source
9634 (origin
9635 (method url-fetch)
9636 (uri (cran-uri "feature" version))
9637 (sha256
9638 (base32
9639 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9640 (build-system r-build-system)
9641 (propagated-inputs
9642 `(("r-ks" ,r-ks)
9643 ("r-misc3d" ,r-misc3d)
9644 ("r-rgl" ,r-rgl)))
9645 (home-page "http://www.mvstat.net/tduong/")
9646 (synopsis "Inferential feature significance for kernel density estimation")
9647 (description
9648 "The feature package contains functions to display and compute kernel
9649 density estimates, significant gradient and significant curvature regions.
9650 Significant gradient and/or curvature regions often correspond to significant
9651 features (e.g. local modes).")
9652 ;; Either version of the GPL.
9653 (license (list license:gpl2 license:gpl3))))
9654
9655 (define-public r-arm
9656 (package
9657 (name "r-arm")
9658 (version "1.11-1")
9659 (source
9660 (origin
9661 (method url-fetch)
9662 (uri (cran-uri "arm" version))
9663 (sha256
9664 (base32
9665 "0i2lnm09bqy1qw0ms5pw0rzw196xmnk5dxha3g8lc58lqpldp0kv"))))
9666 (build-system r-build-system)
9667 (propagated-inputs
9668 `(("r-abind" ,r-abind)
9669 ("r-coda" ,r-coda)
9670 ("r-lme4" ,r-lme4)
9671 ("r-mass" ,r-mass)
9672 ("r-matrix" ,r-matrix)
9673 ("r-nlme" ,r-nlme)))
9674 (home-page "https://cran.r-project.org/web/packages/arm/")
9675 (synopsis "Data analysis using regression and multilevel/hierarchical models")
9676 (description
9677 "This package provides functions to accompany A. Gelman and J. Hill,
9678 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
9679 University Press, 2007.")
9680 (license license:gpl3+)))
9681
9682 (define-public r-circular
9683 (package
9684 (name "r-circular")
9685 (version "0.4-93")
9686 (source
9687 (origin
9688 (method url-fetch)
9689 (uri (cran-uri "circular" version))
9690 (sha256
9691 (base32
9692 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
9693 (build-system r-build-system)
9694 (propagated-inputs
9695 `(("r-boot" ,r-boot)
9696 ("r-mvtnorm" ,r-mvtnorm)))
9697 (native-inputs
9698 `(("gfortran" ,gfortran)))
9699 (home-page "https://cran.r-project.org/web/packages/circular/")
9700 (synopsis "Circular statistics")
9701 (description
9702 "This package provides tools for circular statistics, from \"Topics in
9703 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
9704 Scientific.")
9705 (license license:gpl2+)))
9706
9707 (define-public r-activity
9708 (package
9709 (name "r-activity")
9710 (version "1.3")
9711 (source
9712 (origin
9713 (method url-fetch)
9714 (uri (cran-uri "activity" version))
9715 (sha256
9716 (base32
9717 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
9718 (build-system r-build-system)
9719 (propagated-inputs
9720 `(("r-circular" ,r-circular)
9721 ("r-insol" ,r-insol)
9722 ("r-pbapply" ,r-pbapply)))
9723 (home-page "https://cran.r-project.org/web/packages/activity/")
9724 (synopsis "Animal activity statistics")
9725 (description
9726 "This package provides functions to fit kernel density functions to
9727 animal activity time data; plot activity distributions; quantify overall
9728 levels of activity; statistically compare activity metrics through
9729 bootstrapping; and evaluate variation in linear variables with time (or other
9730 circular variables).")
9731 (license license:gpl3)))
9732
9733 (define-public r-ouch
9734 (package
9735 (name "r-ouch")
9736 (version "2.14-1")
9737 (source
9738 (origin
9739 (method url-fetch)
9740 (uri (cran-uri "ouch" version))
9741 (sha256
9742 (base32
9743 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
9744 (build-system r-build-system)
9745 (propagated-inputs `(("r-subplex" ,r-subplex)))
9746 (home-page "https://kingaa.github.io/ouch/")
9747 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
9748 (description
9749 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
9750 for evolution along a phylogenetic tree.")
9751 (license license:gpl2+)))
9752
9753 (define-public r-fmsb
9754 (package
9755 (name "r-fmsb")
9756 (version "0.7.0")
9757 (source
9758 (origin
9759 (method url-fetch)
9760 (uri (cran-uri "fmsb" version))
9761 (sha256
9762 (base32
9763 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
9764 (build-system r-build-system)
9765 (home-page "http://minato.sip21c.org/msb/")
9766 (synopsis "Functions for medical statistics book with demographic data")
9767 (description
9768 "This package provides several utility functions for the book entitled
9769 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
9770 Japan, 2007) with Japanese demographic data and some demographic analysis
9771 related functions.")
9772 (license license:gpl2+)))
9773
9774 (define-public r-stabledist
9775 (package
9776 (name "r-stabledist")
9777 (version "0.7-1")
9778 (source
9779 (origin
9780 (method url-fetch)
9781 (uri (cran-uri "stabledist" version))
9782 (sha256
9783 (base32
9784 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
9785 (build-system r-build-system)
9786 (home-page "https://www.rmetrics.org")
9787 (synopsis "Stable distribution functions")
9788 (description
9789 "This package provides density, probability and quantile functions, and
9790 random number generation for (skew) stable distributions, using the
9791 parametrizations of Nolan.")
9792 (license license:gpl2+)))
9793
9794 (define-public r-gsl
9795 (package
9796 (name "r-gsl")
9797 (version "2.1-6")
9798 (source
9799 (origin
9800 (method url-fetch)
9801 (uri (cran-uri "gsl" version))
9802 (sha256
9803 (base32
9804 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
9805 (build-system r-build-system)
9806 (inputs
9807 `(("gsl" ,gsl)))
9808 (home-page "https://cran.r-project.org/web/packages/gsl")
9809 (synopsis "Wrapper for the GNU Scientific Library")
9810 (description
9811 "This package provides an R wrapper for the special functions and quasi
9812 random number generators of the GNU Scientific Library.")
9813 (license license:gpl2+)))
9814
9815 (define-public r-adgoftest
9816 (package
9817 (name "r-adgoftest")
9818 (version "0.3")
9819 (source
9820 (origin
9821 (method url-fetch)
9822 (uri (cran-uri "ADGofTest" version))
9823 (sha256
9824 (base32
9825 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
9826 (properties `((upstream-name . "ADGofTest")))
9827 (build-system r-build-system)
9828 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
9829 (synopsis "Anderson-Darling GoF test")
9830 (description
9831 "This package provides an implementation of the Anderson-Darling GoF test
9832 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
9833 Anderson-Darling Distribution\".")
9834 ;; Any version of the GPL.
9835 (license license:gpl3+)))
9836
9837 (define-public r-softimpute
9838 (package
9839 (name "r-softimpute")
9840 (version "1.4")
9841 (source
9842 (origin
9843 (method url-fetch)
9844 (uri (cran-uri "softImpute" version))
9845 (sha256
9846 (base32
9847 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
9848 (properties `((upstream-name . "softImpute")))
9849 (build-system r-build-system)
9850 (propagated-inputs
9851 `(("r-matrix" ,r-matrix)))
9852 (native-inputs
9853 `(("gfortran" ,gfortran)))
9854 (home-page "https://cran.r-project.org/web/packages/softImpute")
9855 (synopsis "Matrix completion via iterative soft-thresholded SVD")
9856 (description
9857 "This package provides iterative methods for matrix completion that use
9858 nuclear-norm regularization. The package includes procedures for centering
9859 and scaling rows, columns or both, and for computing low-rank @dfn{single
9860 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
9861 components).")
9862 (license license:gpl2)))
9863
9864 (define-public r-fftwtools
9865 (package
9866 (name "r-fftwtools")
9867 (version "0.9-8")
9868 (source
9869 (origin
9870 (method url-fetch)
9871 (uri (cran-uri "fftwtools" version))
9872 (sha256
9873 (base32
9874 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
9875 (build-system r-build-system)
9876 (inputs `(("fftw" ,fftw)))
9877 (home-page "https://github.com/krahim/fftwtools")
9878 (synopsis "Wrapper for FFTW3")
9879 (description
9880 "This package provides a wrapper for several FFTW functions. It provides
9881 access to the two-dimensional FFT, the multivariate FFT, and the
9882 one-dimensional real to complex FFT using the FFTW3 library. The package
9883 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
9884 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
9885 The FFT functions have a parameter that allows them to not return the
9886 redundant complex conjugate when the input is real data.")
9887 (license license:gpl2+)))
9888
9889 (define-public r-tiff
9890 (package
9891 (name "r-tiff")
9892 (version "0.1-5")
9893 (source
9894 (origin
9895 (method url-fetch)
9896 (uri (cran-uri "tiff" version))
9897 (sha256
9898 (base32
9899 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
9900 (build-system r-build-system)
9901 (inputs
9902 `(("libtiff" ,libtiff)
9903 ("libjpeg" ,libjpeg)
9904 ("zlib" ,zlib)))
9905 (home-page "https://www.rforge.net/tiff/")
9906 (synopsis "Read and write TIFF images")
9907 (description
9908 "This package provides an easy and simple way to read, write and display
9909 bitmap images stored in the TIFF format. It can read and write both files and
9910 in-memory raw vectors.")
9911 ;; Either of these two license versions.
9912 (license (list license:gpl2 license:gpl3))))
9913
9914 (define-public r-nlp
9915 (package
9916 (name "r-nlp")
9917 (version "0.2-0")
9918 (source
9919 (origin
9920 (method url-fetch)
9921 (uri (cran-uri "NLP" version))
9922 (sha256
9923 (base32
9924 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
9925 (properties `((upstream-name . "NLP")))
9926 (build-system r-build-system)
9927 (home-page "https://cran.r-project.org/web/packages/NLP/")
9928 (synopsis "Natural language processing infrastructure")
9929 (description
9930 "This package provides basic classes and methods for Natural Language
9931 Processing.")
9932 (license license:gpl3)))
9933
9934 (define-public r-tm
9935 (package
9936 (name "r-tm")
9937 (version "0.7-7")
9938 (source
9939 (origin
9940 (method url-fetch)
9941 (uri (cran-uri "tm" version))
9942 (sha256
9943 (base32
9944 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
9945 (properties `((upstream-name . "tm")))
9946 (build-system r-build-system)
9947 (propagated-inputs
9948 `(("r-bh" ,r-bh)
9949 ("r-nlp" ,r-nlp)
9950 ("r-rcpp" ,r-rcpp)
9951 ("r-slam" ,r-slam)
9952 ("r-xml2" ,r-xml2)))
9953 (home-page "http://tm.r-forge.r-project.org/")
9954 (synopsis "Text mining package")
9955 (description
9956 "This package provides a framework for text mining applications within R.")
9957 (license license:gpl3)))
9958
9959 (define-public r-waveslim
9960 (package
9961 (name "r-waveslim")
9962 (version "1.8.2")
9963 (source
9964 (origin
9965 (method url-fetch)
9966 (uri (cran-uri "waveslim" version))
9967 (sha256
9968 (base32
9969 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
9970 (build-system r-build-system)
9971 (native-inputs
9972 `(("gfortran" ,gfortran)))
9973 (home-page "http://waveslim.blogspot.com")
9974 (synopsis "Basic wavelet routines for signal processing")
9975 (description
9976 "This package provides basic wavelet routines for time series (1D),
9977 image (2D) and array (3D) analysis. The code provided here is based on
9978 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
9979 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
9980 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
9981 pairs (Selesnick 2001, 2002).")
9982 (license license:bsd-3)))
9983
9984 (define-public r-wordcloud
9985 (package
9986 (name "r-wordcloud")
9987 (version "2.6")
9988 (source
9989 (origin
9990 (method url-fetch)
9991 (uri (cran-uri "wordcloud" version))
9992 (sha256
9993 (base32
9994 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
9995 (build-system r-build-system)
9996 (propagated-inputs
9997 `(("r-rcolorbrewer" ,r-rcolorbrewer)
9998 ("r-rcpp" ,r-rcpp)
9999 ;; The "tm" package is only "suggested" according to CRAN, but the
10000 ;; wordcloud package cannot be loaded without it.
10001 ("r-tm" ,r-tm)))
10002 (home-page "https://cran.r-project.org/web/packages/wordcloud")
10003 (synopsis "Word clouds")
10004 (description
10005 "This package provides functionality to create pretty word clouds,
10006 visualize differences and similarity between documents, and avoid
10007 over-plotting in scatter plots with text.")
10008 (license license:lgpl2.1)))
10009
10010 (define-public r-colorramps
10011 (package
10012 (name "r-colorramps")
10013 (version "2.3")
10014 (source
10015 (origin
10016 (method url-fetch)
10017 (uri (cran-uri "colorRamps" version))
10018 (sha256
10019 (base32
10020 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
10021 (properties `((upstream-name . "colorRamps")))
10022 (build-system r-build-system)
10023 (home-page "https://cran.r-project.org/web/packages/colorRamps")
10024 (synopsis "Build color tables")
10025 (description "This package provides features to build gradient color
10026 maps.")
10027 ;; Any version of the GPL
10028 (license license:gpl3+)))
10029
10030 (define-public r-tidytree
10031 (package
10032 (name "r-tidytree")
10033 (version "0.3.3")
10034 (source
10035 (origin
10036 (method url-fetch)
10037 (uri (cran-uri "tidytree" version))
10038 (sha256
10039 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
10040 (build-system r-build-system)
10041 (propagated-inputs
10042 `(("r-ape" ,r-ape)
10043 ("r-dplyr" ,r-dplyr)
10044 ("r-lazyeval" ,r-lazyeval)
10045 ("r-magrittr" ,r-magrittr)
10046 ("r-rlang" ,r-rlang)
10047 ("r-tibble" ,r-tibble)))
10048 (native-inputs
10049 `(("r-knitr" ,r-knitr)))
10050 (home-page "https://github.com/GuangchuangYu/tidytree")
10051 (synopsis "Tidy tool for phylogenetic tree data manipulation")
10052 (description
10053 "Phylogenetic trees generally contain multiple components including nodes,
10054 edges, branches and associated data. This package provides an approach to
10055 convert tree objects to tidy data frames. It also provides tidy interfaces to
10056 manipulate tree data.")
10057 (license license:artistic2.0)))
10058
10059 (define-public r-rvcheck
10060 (package
10061 (name "r-rvcheck")
10062 (version "0.1.8")
10063 (source
10064 (origin
10065 (method url-fetch)
10066 (uri (cran-uri "rvcheck" version))
10067 (sha256
10068 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
10069 (build-system r-build-system)
10070 (propagated-inputs
10071 `(("r-biocmanager" ,r-biocmanager)
10072 ("r-rlang" ,r-rlang)))
10073 (home-page "https://cran.r-project.org/web/packages/rvcheck")
10074 (synopsis "R package version check")
10075 (description
10076 "This package provides tools to check the latest release version of R and
10077 R packages (on CRAN, Bioconductor or Github).")
10078 (license license:artistic2.0)))
10079
10080 (define-public r-docopt
10081 (package
10082 (name "r-docopt")
10083 (version "0.6.1")
10084 (source
10085 (origin
10086 (method url-fetch)
10087 (uri (cran-uri "docopt" version))
10088 (sha256
10089 (base32
10090 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
10091 (build-system r-build-system)
10092 (home-page "https://github.com/docopt/docopt.R")
10093 (synopsis "Command-line interface specification language")
10094 (description
10095 "This package enables you to define a command-line interface by just
10096 giving it a description in the specific format.")
10097 (license license:expat)))
10098
10099 (define-public r-sparsesvd
10100 (package
10101 (name "r-sparsesvd")
10102 (version "0.2")
10103 (source
10104 (origin
10105 (method url-fetch)
10106 (uri (cran-uri "sparsesvd" version))
10107 (sha256
10108 (base32
10109 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
10110 (build-system r-build-system)
10111 (propagated-inputs `(("r-matrix" ,r-matrix)))
10112 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
10113 (synopsis "Sparse truncated singular value decomposition")
10114 (description
10115 "This package provides a Wrapper around the SVDLIBC library
10116 for (truncated) singular value decomposition of a sparse matrix. Currently,
10117 only sparse real matrices in Matrix package format are supported.")
10118 ;; SVDLIBC is released under BSD-2. The R interface is released under
10119 ;; BSD-3.
10120 (license (list license:bsd-3 license:bsd-2))))
10121
10122 (define-public r-speedglm
10123 (package
10124 (name "r-speedglm")
10125 (version "0.3-2")
10126 (source
10127 (origin
10128 (method url-fetch)
10129 (uri (cran-uri "speedglm" version))
10130 (sha256
10131 (base32
10132 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
10133 (build-system r-build-system)
10134 (propagated-inputs
10135 `(("r-mass" ,r-mass)
10136 ("r-matrix" ,r-matrix)))
10137 (home-page "https://cran.r-project.org/web/packages/speedglm")
10138 (synopsis "Fit linear and generalized linear models to large data sets")
10139 (description
10140 "This package provides tools for fitting linear models and generalized
10141 linear models to large data sets by updating algorithms.")
10142 ;; Any version of the GPL
10143 (license license:gpl2+)))
10144
10145 (define-public r-densityclust
10146 (package
10147 (name "r-densityclust")
10148 (version "0.3")
10149 (source
10150 (origin
10151 (method url-fetch)
10152 (uri (cran-uri "densityClust" version))
10153 (sha256
10154 (base32
10155 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
10156 (properties `((upstream-name . "densityClust")))
10157 (build-system r-build-system)
10158 (propagated-inputs
10159 `(("r-fnn" ,r-fnn)
10160 ("r-ggplot2" ,r-ggplot2)
10161 ("r-ggrepel" ,r-ggrepel)
10162 ("r-gridextra" ,r-gridextra)
10163 ("r-rcolorbrewer" ,r-rcolorbrewer)
10164 ("r-rcpp" ,r-rcpp)
10165 ("r-rtsne" ,r-rtsne)))
10166 (home-page "https://cran.r-project.org/web/packages/densityClust")
10167 (synopsis "Clustering by fast search and find of density peaks")
10168 (description
10169 "This package provides an improved implementation (based on k-nearest
10170 neighbors) of the density peak clustering algorithm, originally described by
10171 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
10172 large datasets (> 100,000 samples) very efficiently.")
10173 (license license:gpl2+)))
10174
10175 (define-public r-combinat
10176 (package
10177 (name "r-combinat")
10178 (version "0.0-8")
10179 (source
10180 (origin
10181 (method url-fetch)
10182 (uri (cran-uri "combinat" version))
10183 (sha256
10184 (base32
10185 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
10186 (build-system r-build-system)
10187 (home-page "https://cran.r-project.org/web/packages/combinat")
10188 (synopsis "Combinatorics utilities")
10189 (description "This package provides assorted routines for combinatorics.")
10190 (license license:gpl2)))
10191
10192 (define-public r-qlcmatrix
10193 (package
10194 (name "r-qlcmatrix")
10195 (version "0.9.7")
10196 (source
10197 (origin
10198 (method url-fetch)
10199 (uri (cran-uri "qlcMatrix" version))
10200 (sha256
10201 (base32
10202 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
10203 (properties `((upstream-name . "qlcMatrix")))
10204 (build-system r-build-system)
10205 (propagated-inputs
10206 `(("r-docopt" ,r-docopt)
10207 ("r-matrix" ,r-matrix)
10208 ("r-slam" ,r-slam)
10209 ("r-sparsesvd" ,r-sparsesvd)))
10210 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10211 (synopsis "Sparse matrix functions for quantitative language comparison")
10212 (description
10213 "This package provides an extension of the functionality of the Matrix
10214 package for using sparse matrices. Some of the functions are very general,
10215 while other are highly specific for the special data format used for
10216 @dfn{quantitative language comparison} (QLC).")
10217 (license license:gpl3)))
10218
10219 (define-public r-ddrtree
10220 (package
10221 (name "r-ddrtree")
10222 (version "0.1.5")
10223 (source
10224 (origin
10225 (method url-fetch)
10226 (uri (cran-uri "DDRTree" version))
10227 (sha256
10228 (base32
10229 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10230 (properties `((upstream-name . "DDRTree")))
10231 (build-system r-build-system)
10232 (propagated-inputs
10233 `(("r-bh" ,r-bh)
10234 ("r-irlba" ,r-irlba)
10235 ("r-rcpp" ,r-rcpp)
10236 ("r-rcppeigen" ,r-rcppeigen)))
10237 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10238 (synopsis "Learning principal graphs with DDRTree")
10239 (description
10240 "This package provides an implementation of the framework of
10241 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10242 dimensional space while constructs a principal tree which passes through the
10243 middle of the data simultaneously. DDRTree shows superiority to
10244 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10245 intrinsic structure of single cell genomics data. In general, it could be
10246 used to reconstruct the temporal progression as well as the bifurcation
10247 structure of any data type.")
10248 (license license:asl2.0)))
10249
10250 (define-public r-corpcor
10251 (package
10252 (name "r-corpcor")
10253 (version "1.6.9")
10254 (source
10255 (origin
10256 (method url-fetch)
10257 (uri (cran-uri "corpcor" version))
10258 (sha256
10259 (base32
10260 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10261 (build-system r-build-system)
10262 (home-page "http://strimmerlab.org/software/corpcor/")
10263 (synopsis "Efficient estimation of covariance and (partial) correlation")
10264 (description
10265 "This package implements a James-Stein-type shrinkage estimator for the
10266 covariance matrix, with separate shrinkage for variances and correlations.
10267 Furthermore, functions are available for fast singular value decomposition,
10268 for computing the pseudoinverse, and for checking the rank and positive
10269 definiteness of a matrix.")
10270 (license license:gpl3+)))
10271
10272 (define-public r-rspectra
10273 (package
10274 (name "r-rspectra")
10275 (version "0.16-0")
10276 (source
10277 (origin
10278 (method url-fetch)
10279 (uri (cran-uri "RSpectra" version))
10280 (sha256
10281 (base32
10282 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10283 (properties `((upstream-name . "RSpectra")))
10284 (build-system r-build-system)
10285 (propagated-inputs
10286 `(("r-matrix" ,r-matrix)
10287 ("r-rcpp" ,r-rcpp)
10288 ("r-rcppeigen" ,r-rcppeigen)))
10289 (home-page "https://github.com/yixuan/RSpectra")
10290 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10291 (description
10292 "This package provides an R interface to the Spectra library for
10293 large-scale eigenvalue and SVD problems. It is typically used to compute a
10294 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10295 which is usually more efficient than @code{eigen()} if k << n.")
10296 ;; MPL 2 or later.
10297 (license license:mpl2.0)))
10298
10299 (define-public r-vbsr
10300 (package
10301 (name "r-vbsr")
10302 (version "0.0.5")
10303 (source
10304 (origin
10305 (method url-fetch)
10306 (uri (cran-uri "vbsr" version))
10307 (sha256
10308 (base32
10309 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10310 (build-system r-build-system)
10311 (home-page "https://cran.r-project.org/web/packages/vbsr")
10312 (synopsis "Variational Bayes spike regression regularized linear models")
10313 (description
10314 "This package provides an efficient algorithm for solving ultra-sparse
10315 regularized regression models using a variational Bayes algorithm with a spike
10316 prior. The algorithm is solved on a path, with coordinate updates, and is
10317 capable of generating very sparse models. Very general model
10318 diagnostics for controlling type-1 errors are also provided.")
10319 (license license:gpl2)))
10320
10321 (define-public r-flare
10322 (package
10323 (name "r-flare")
10324 (version "1.6.0.2")
10325 (source
10326 (origin
10327 (method url-fetch)
10328 (uri (cran-uri "flare" version))
10329 (sha256
10330 (base32
10331 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10332 (build-system r-build-system)
10333 (propagated-inputs
10334 `(("r-igraph" ,r-igraph)
10335 ("r-lattice" ,r-lattice)
10336 ("r-mass" ,r-mass)
10337 ("r-matrix" ,r-matrix)))
10338 (home-page "https://cran.r-project.org/web/packages/flare")
10339 (synopsis "Family of Lasso regression implementations")
10340 (description
10341 "This package provides implementations of a family of Lasso variants
10342 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10343 high dimensional sparse linear models.")
10344 (license license:gpl2)))
10345
10346 (define-public r-lassopv
10347 (package
10348 (name "r-lassopv")
10349 (version "0.2.0")
10350 (source
10351 (origin
10352 (method url-fetch)
10353 (uri (cran-uri "lassopv" version))
10354 (sha256
10355 (base32
10356 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10357 (build-system r-build-system)
10358 (propagated-inputs `(("r-lars" ,r-lars)))
10359 (home-page "https://github.com/lingfeiwang/lassopv")
10360 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10361 (description
10362 "This package enables you to estimate the p-values for predictors x
10363 against target variable y in Lasso regression, using the regularization
10364 strength when each predictor enters the active set of regularization path for
10365 the first time as the statistic.")
10366 (license license:gpl3)))
10367
10368 (define-public r-splitstackshape
10369 (package
10370 (name "r-splitstackshape")
10371 (version "1.4.8")
10372 (source
10373 (origin
10374 (method url-fetch)
10375 (uri (cran-uri "splitstackshape" version))
10376 (sha256
10377 (base32
10378 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10379 (build-system r-build-system)
10380 (propagated-inputs
10381 `(("r-data-table" ,r-data-table)))
10382 (home-page "https://github.com/mrdwab/splitstackshape")
10383 (synopsis "Stack and reshape datasets after splitting concatenated values")
10384 (description
10385 "Online data collection tools like Google Forms often export
10386 multiple-response questions with data concatenated in cells. The
10387 @code{concat.split} (cSplit) family of functions provided by this package
10388 splits such data into separate cells. This package also includes functions to
10389 stack groups of columns and to reshape wide data, even when the data are
10390 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10391 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10392 handle.")
10393 (license license:gpl3)))
10394
10395 (define-public r-tfmpvalue
10396 (package
10397 (name "r-tfmpvalue")
10398 (version "0.0.8")
10399 (source
10400 (origin
10401 (method url-fetch)
10402 (uri (cran-uri "TFMPvalue" version))
10403 (sha256
10404 (base32
10405 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10406 (properties `((upstream-name . "TFMPvalue")))
10407 (build-system r-build-system)
10408 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10409 (home-page "https://github.com/ge11232002/TFMPvalue")
10410 (synopsis "P-value computation for position weight matrices")
10411 (description
10412 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10413 identification from sequence/alignments, we are interested in the significance
10414 of certain match scores. TFMPvalue provides the accurate calculation of a
10415 p-value with a score threshold for position weight matrices, or the score with
10416 a given p-value. It is an interface to code originally made available by
10417 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10418 Touzet and Varre (2007).")
10419 (license license:gpl2)))
10420
10421 (define-public r-rnifti
10422 (package
10423 (name "r-rnifti")
10424 (version "1.1.0")
10425 (source
10426 (origin
10427 (method url-fetch)
10428 (uri (cran-uri "RNifti" version))
10429 (sha256
10430 (base32
10431 "1z8ninp3aq18w0slcfn8r2fp48cdz8l0k0namsrnvgyp8lzcpqpn"))))
10432 (properties `((upstream-name . "RNifti")))
10433 (build-system r-build-system)
10434 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10435 (home-page "https://github.com/jonclayden/RNifti")
10436 (synopsis "Fast R and C++ access to NIfTI images")
10437 (description
10438 "This package provides very fast read and write access to images stored
10439 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10440 compiled C and interpreted R code. It also provides a C/C++ API that can be
10441 used by other packages.")
10442 (license license:gpl2)))
10443
10444 (define-public r-shades
10445 (package
10446 (name "r-shades")
10447 (version "1.4.0")
10448 (source
10449 (origin
10450 (method url-fetch)
10451 (uri (cran-uri "shades" version))
10452 (sha256
10453 (base32
10454 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10455 (build-system r-build-system)
10456 (home-page "https://github.com/jonclayden/shades")
10457 (synopsis "Simple color manipulation")
10458 (description
10459 "This package provides functions for easily manipulating colors,
10460 creating color scales and calculating color distances.")
10461 (license license:bsd-3)))
10462
10463 (define-public r-ore
10464 (package
10465 (name "r-ore")
10466 (version "1.6.3")
10467 (source
10468 (origin
10469 (method url-fetch)
10470 (uri (cran-uri "ore" version))
10471 (sha256
10472 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10473 (build-system r-build-system)
10474 (home-page "https://github.com/jonclayden/ore")
10475 (synopsis "R interface to the Onigmo regular expression library")
10476 (description
10477 "This package provides an alternative to R's built-in functionality for
10478 handling regular expressions, based on the Onigmo library. It offers
10479 first-class compiled regex objects, partial matching and function-based
10480 substitutions, amongst other features.")
10481 (license license:bsd-3)))
10482
10483 (define-public r-reportr
10484 (package
10485 (name "r-reportr")
10486 (version "1.3.0")
10487 (source
10488 (origin
10489 (method url-fetch)
10490 (uri (cran-uri "reportr" version))
10491 (sha256
10492 (base32
10493 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10494 (build-system r-build-system)
10495 (propagated-inputs `(("r-ore" ,r-ore)))
10496 (home-page "https://github.com/jonclayden/reportr")
10497 (synopsis "General message and error reporting system")
10498 (description
10499 "This package provides a system for reporting messages, which offers
10500 certain useful features over the standard R system, such as the incorporation
10501 of output consolidation, message filtering, assertions, expression
10502 substitution, automatic generation of stack traces for debugging, and
10503 conditional reporting based on the current \"output level\".")
10504 (license license:gpl2)))
10505
10506 (define-public r-tractor-base
10507 (package
10508 (name "r-tractor-base")
10509 (version "3.3.2")
10510 (source
10511 (origin
10512 (method url-fetch)
10513 (uri (cran-uri "tractor.base" version))
10514 (sha256
10515 (base32
10516 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10517 (properties `((upstream-name . "tractor.base")))
10518 (build-system r-build-system)
10519 (propagated-inputs
10520 `(("r-ore" ,r-ore)
10521 ("r-reportr" ,r-reportr)
10522 ("r-rnifti" ,r-rnifti)
10523 ("r-shades" ,r-shades)))
10524 (home-page "https://www.tractor-mri.org.uk")
10525 (synopsis "Read, manipulate and visualize magnetic resonance images")
10526 (description
10527 "This package provides functions for working with magnetic resonance
10528 images. It supports reading and writing of popular file formats (DICOM,
10529 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10530 visualization; flexible image manipulation; metadata and sparse image
10531 handling.")
10532 (license license:gpl2)))
10533
10534 (define-public r-grimport
10535 (package
10536 (name "r-grimport")
10537 (version "0.9-3")
10538 (source
10539 (origin
10540 (method url-fetch)
10541 (uri (cran-uri "grImport" version))
10542 (sha256
10543 (base32
10544 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
10545 (properties `((upstream-name . "grImport")))
10546 (build-system r-build-system)
10547 (inputs
10548 `(("ghostscript" ,ghostscript)))
10549 (propagated-inputs
10550 `(("r-xml" ,r-xml)))
10551 (home-page "https://cran.r-project.org/web/packages/grImport")
10552 (synopsis "Convert, import, and draw PostScript pictures")
10553 (description
10554 "This package provides functions for converting, importing, and drawing
10555 PostScript pictures in R plots.")
10556 (license license:gpl2+)))
10557
10558 (define-public r-grimport2
10559 (package
10560 (name "r-grimport2")
10561 (version "0.2-0")
10562 (source
10563 (origin
10564 (method url-fetch)
10565 (uri (cran-uri "grImport2" version))
10566 (sha256
10567 (base32
10568 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
10569 (properties `((upstream-name . "grImport2")))
10570 (build-system r-build-system)
10571 (propagated-inputs
10572 `(("r-base64enc" ,r-base64enc)
10573 ("r-jpeg" ,r-jpeg)
10574 ("r-png" ,r-png)
10575 ("r-xml" ,r-xml)))
10576 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10577 (synopsis "Import SVG graphics")
10578 (description
10579 "This package provides functions for importing external vector images and
10580 drawing them as part of R plots. This package is different from the
10581 @code{grImport} package because, where that package imports PostScript format
10582 images, this package imports SVG format images. Furthermore, this package
10583 imports a specific subset of SVG, so external images must be preprocessed
10584 using a package like @code{rsvg} to produce SVG that this package can import.
10585 SVG features that are not supported by R graphics, such as gradient fills, can
10586 be imported and then exported via the @code{gridSVG} package.")
10587 (license license:gpl2+)))
10588
10589 (define-public r-kohonen
10590 (package
10591 (name "r-kohonen")
10592 (version "3.0.10")
10593 (source
10594 (origin
10595 (method url-fetch)
10596 (uri (cran-uri "kohonen" version))
10597 (sha256
10598 (base32
10599 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
10600 (build-system r-build-system)
10601 (propagated-inputs
10602 `(("r-rcpp" ,r-rcpp)))
10603 (home-page "https://cran.r-project.org/web/packages/kohonen")
10604 (synopsis "Supervised and unsupervised self-organising maps")
10605 (description
10606 "This package provides functions to train @dfn{self-organising
10607 maps} (SOMs). Also interrogation of the maps and prediction using trained
10608 maps are supported. The name of the package refers to Teuvo Kohonen, the
10609 inventor of the SOM.")
10610 (license license:gpl2+)))
10611
10612 (define-public r-nnls
10613 (package
10614 (name "r-nnls")
10615 (version "1.4")
10616 (source
10617 (origin
10618 (method url-fetch)
10619 (uri (cran-uri "nnls" version))
10620 (sha256
10621 (base32
10622 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10623 (build-system r-build-system)
10624 (native-inputs `(("gfortran" ,gfortran)))
10625 (home-page "https://cran.r-project.org/web/packages/nnls")
10626 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10627 (description
10628 "This package provides an R interface to the Lawson-Hanson implementation
10629 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10630 the combination of non-negative and non-positive constraints.")
10631 (license license:gpl2+)))
10632
10633 (define-public r-iso
10634 (package
10635 (name "r-iso")
10636 (version "0.0-18")
10637 (source
10638 (origin
10639 (method url-fetch)
10640 (uri (cran-uri "Iso" version))
10641 (sha256
10642 (base32
10643 "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
10644 (properties `((upstream-name . "Iso")))
10645 (build-system r-build-system)
10646 (native-inputs `(("gfortran" ,gfortran)))
10647 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
10648 (synopsis "Functions to perform isotonic regression")
10649 (description
10650 "This package provides support for linear order and unimodal
10651 order (univariate) isotonic regression and bivariate isotonic regression with
10652 linear order on both variables.")
10653 (license license:gpl2+)))
10654
10655 (define-public r-chemometricswithr
10656 (package
10657 (name "r-chemometricswithr")
10658 (version "0.1.13")
10659 (source
10660 (origin
10661 (method url-fetch)
10662 (uri (cran-uri "ChemometricsWithR" version))
10663 (sha256
10664 (base32
10665 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
10666 (properties
10667 `((upstream-name . "ChemometricsWithR")))
10668 (build-system r-build-system)
10669 (propagated-inputs
10670 `(("r-devtools" ,r-devtools)
10671 ("r-kohonen" ,r-kohonen)
10672 ("r-mass" ,r-mass)
10673 ("r-pls" ,r-pls)))
10674 (home-page "https://github.com/rwehrens/CWR")
10675 (synopsis "Chemometrics with R")
10676 (description
10677 "This package provides functions and scripts used in the book
10678 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
10679 Life Sciences\" by Ron Wehrens, Springer (2011).")
10680 (license license:gpl2+)))
10681
10682 (define-public r-als
10683 (package
10684 (name "r-als")
10685 (version "0.0.6")
10686 (source
10687 (origin
10688 (method url-fetch)
10689 (uri (cran-uri "ALS" version))
10690 (sha256
10691 (base32
10692 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
10693 (properties `((upstream-name . "ALS")))
10694 (build-system r-build-system)
10695 (propagated-inputs
10696 `(("r-iso" ,r-iso)
10697 ("r-nnls" ,r-nnls)))
10698 (home-page "https://cran.r-project.org/web/packages/ALS")
10699 (synopsis "Multivariate curve resolution alternating least squares")
10700 (description
10701 "Alternating least squares is often used to resolve components
10702 contributing to data with a bilinear structure; the basic technique may be
10703 extended to alternating constrained least squares. This package provides an
10704 implementation of @dfn{multivariate curve resolution alternating least
10705 squares} (MCR-ALS).
10706
10707 Commonly applied constraints include unimodality, non-negativity, and
10708 normalization of components. Several data matrices may be decomposed
10709 simultaneously by assuming that one of the two matrices in the bilinear
10710 decomposition is shared between datasets.")
10711 (license license:gpl2+)))
10712
10713 (define-public r-strucchange
10714 (package
10715 (name "r-strucchange")
10716 (version "1.5-2")
10717 (source
10718 (origin
10719 (method url-fetch)
10720 (uri (cran-uri "strucchange" version))
10721 (sha256
10722 (base32
10723 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
10724 (build-system r-build-system)
10725 (propagated-inputs
10726 `(("r-sandwich" ,r-sandwich)
10727 ("r-zoo" ,r-zoo)))
10728 (home-page "https://cran.r-project.org/web/packages/strucchange")
10729 (synopsis "Testing, monitoring, and dating structural changes")
10730 (description
10731 "This package provides tools for testing, monitoring and dating
10732 structural changes in (linear) regression models. It features tests/methods
10733 from the generalized fluctuation test framework as well as from the F
10734 test (Chow test) framework. This includes methods to fit, plot and test
10735 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
10736 statistics, respectively. It is possible to monitor incoming data online
10737 using fluctuation processes. Finally, the breakpoints in regression models
10738 with structural changes can be estimated together with confidence intervals.
10739 Emphasis is always given to methods for visualizing the data.")
10740 ;; Either of these two GPL versions
10741 (license (list license:gpl2 license:gpl3))))
10742
10743 (define-public r-pixmap
10744 (package
10745 (name "r-pixmap")
10746 (version "0.4-11")
10747 (source
10748 (origin
10749 (method url-fetch)
10750 (uri (cran-uri "pixmap" version))
10751 (sha256
10752 (base32
10753 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
10754 (build-system r-build-system)
10755 (home-page "https://cran.r-project.org/web/packages/pixmap")
10756 (synopsis "Tools for bitmap images")
10757 (description
10758 "This package provides functions for importing, exporting, plotting and
10759 other manipulations of bitmapped images.")
10760 (license license:gpl2)))
10761
10762 (define-public r-rapidjsonr
10763 (package
10764 (name "r-rapidjsonr")
10765 (version "1.2.0")
10766 (source
10767 (origin
10768 (method url-fetch)
10769 (uri (cran-uri "rapidjsonr" version))
10770 (sha256
10771 (base32
10772 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
10773 (build-system r-build-system)
10774 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
10775 (synopsis "JSON parser")
10776 (description
10777 "This package provides JSON parsing capability through the Rapidjson
10778 library.")
10779 (license license:expat)))
10780
10781 (define-public r-ontologyindex
10782 (package
10783 (name "r-ontologyindex")
10784 (version "2.5")
10785 (source
10786 (origin
10787 (method url-fetch)
10788 (uri (cran-uri "ontologyIndex" version))
10789 (sha256
10790 (base32
10791 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
10792 (properties `((upstream-name . "ontologyIndex")))
10793 (build-system r-build-system)
10794 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
10795 (synopsis "Functions for processing ontologies in R")
10796 (description
10797 "This package provides functions for reading ontologies into R as lists
10798 and manipulating sets of ontological terms.")
10799 (license license:gpl2+)))
10800
10801 (define-public r-gargle
10802 (package
10803 (name "r-gargle")
10804 (version "0.4.0")
10805 (source
10806 (origin
10807 (method url-fetch)
10808 (uri (cran-uri "gargle" version))
10809 (sha256
10810 (base32
10811 "08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx"))))
10812 (build-system r-build-system)
10813 (propagated-inputs
10814 `(("r-fs" ,r-fs)
10815 ("r-glue" ,r-glue)
10816 ("r-httr" ,r-httr)
10817 ("r-jsonlite" ,r-jsonlite)
10818 ("r-rlang" ,r-rlang)
10819 ("r-withr" ,r-withr)))
10820 (home-page "https://gargle.r-lib.org")
10821 (synopsis "Utilities for working with Google APIs")
10822 (description
10823 "This package provides utilities for working with Google APIs. This
10824 includes functions and classes for handling common credential types and for
10825 preparing, executing, and processing HTTP requests.")
10826 (license license:expat)))
10827
10828 (define-public r-bigrquery
10829 (package
10830 (name "r-bigrquery")
10831 (version "1.2.0")
10832 (source
10833 (origin
10834 (method url-fetch)
10835 (uri (cran-uri "bigrquery" version))
10836 (sha256
10837 (base32
10838 "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb"))))
10839 (build-system r-build-system)
10840 (propagated-inputs
10841 `(("r-assertthat" ,r-assertthat)
10842 ("r-bit64" ,r-bit64)
10843 ("r-curl" ,r-curl)
10844 ("r-dbi" ,r-dbi)
10845 ("r-gargle" ,r-gargle)
10846 ("r-glue" ,r-glue)
10847 ("r-httr" ,r-httr)
10848 ("r-jsonlite" ,r-jsonlite)
10849 ("r-prettyunits" ,r-prettyunits)
10850 ("r-progress" ,r-progress)
10851 ("r-rapidjsonr" ,r-rapidjsonr)
10852 ("r-rcpp" ,r-rcpp)
10853 ("r-rlang" ,r-rlang)
10854 ("r-tibble" ,r-tibble)))
10855 (home-page "https://github.com/rstats-db/bigrquery")
10856 (synopsis "R interface to Google's BigQuery API")
10857 (description
10858 "This package provides an R interface to Google's BigQuery database.")
10859 (license license:gpl3)))
10860
10861 (define-public r-gmp
10862 (package
10863 (name "r-gmp")
10864 (version "0.5-13.6")
10865 (source
10866 (origin
10867 (method url-fetch)
10868 (uri (cran-uri "gmp" version))
10869 (sha256
10870 (base32
10871 "0j2sz2nw41y9306rl1b8hbn0spz7453z5iawcq0bvslyrhc1d9ir"))))
10872 (build-system r-build-system)
10873 (arguments
10874 '(#:phases
10875 (modify-phases %standard-phases
10876 (add-after 'unpack 'set-CC
10877 (lambda _ (setenv "CC" "gcc") #t)))))
10878 (inputs `(("gmp" ,gmp)))
10879 (home-page "https://cran.r-project.org/web/packages/gmp")
10880 (synopsis "Multiple precision arithmetic")
10881 (description
10882 "This package supports multiple precision arithmetic (big integers and
10883 rationals, prime number tests, matrix computation), \"arithmetic without
10884 limitations\" using the GNU Multiple Precision library.")
10885 ;; Any version of the GPL.
10886 (license license:gpl3+)))
10887
10888 (define-public r-rmpfr
10889 (package
10890 (name "r-rmpfr")
10891 (version "0.8-1")
10892 (source
10893 (origin
10894 (method url-fetch)
10895 (uri (cran-uri "Rmpfr" version))
10896 (sha256
10897 (base32
10898 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
10899 (properties `((upstream-name . "Rmpfr")))
10900 (build-system r-build-system)
10901 (inputs
10902 `(("mpfr" ,mpfr)
10903 ("gmp" ,gmp)))
10904 (propagated-inputs
10905 `(("r-gmp" ,r-gmp)))
10906 (native-inputs
10907 `(("pkg-config" ,pkg-config)))
10908 (home-page "http://rmpfr.r-forge.r-project.org/")
10909 (synopsis "R bindings to the MPFR library")
10910 (description
10911 "This package supports arithmetic (via S4 classes and methods) for
10912 arbitrary precision floating point numbers, including transcendental
10913 functions. To this end, the package interfaces with the @dfn{Multiple
10914 Precision Floating-Point Reliable} (MPFR) library.")
10915 (license license:gpl2+)))
10916
10917 (define-public r-assertive-base
10918 (package
10919 (name "r-assertive-base")
10920 (version "0.0-7")
10921 (source
10922 (origin
10923 (method url-fetch)
10924 (uri (cran-uri "assertive.base" version))
10925 (sha256
10926 (base32
10927 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
10928 (properties
10929 `((upstream-name . "assertive.base")))
10930 (build-system r-build-system)
10931 (home-page "https://bitbucket.org/richierocks/assertive.base")
10932 (synopsis "Core of the assertive package")
10933 (description
10934 "This package provides a minimal set of predicates and assertions used by
10935 the assertive package. This is mainly for use by other package developers who
10936 want to include run-time testing features in their own packages.")
10937 (license license:gpl3+)))
10938
10939 (define-public r-assertive-properties
10940 (package
10941 (name "r-assertive-properties")
10942 (version "0.0-4")
10943 (source
10944 (origin
10945 (method url-fetch)
10946 (uri (cran-uri "assertive.properties" version))
10947 (sha256
10948 (base32
10949 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
10950 (properties
10951 `((upstream-name . "assertive.properties")))
10952 (build-system r-build-system)
10953 (propagated-inputs
10954 `(("r-assertive-base" ,r-assertive-base)))
10955 (home-page "https://bitbucket.org/richierocks/assertive.properties")
10956 (synopsis "Assertions to check properties of variables")
10957 (description
10958 "This package provides a set of predicates and assertions for checking
10959 the properties of variables, such as length, names and attributes. This is
10960 mainly for use by other package developers who want to include run-time
10961 testing features in their own packages.")
10962 (license license:gpl3+)))
10963
10964 (define-public r-assertive-numbers
10965 (package
10966 (name "r-assertive-numbers")
10967 (version "0.0-2")
10968 (source
10969 (origin
10970 (method url-fetch)
10971 (uri (cran-uri "assertive.numbers" version))
10972 (sha256
10973 (base32
10974 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
10975 (properties
10976 `((upstream-name . "assertive.numbers")))
10977 (build-system r-build-system)
10978 (propagated-inputs
10979 `(("r-assertive-base" ,r-assertive-base)))
10980 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
10981 (synopsis "Assertions to check properties of numbers")
10982 (description
10983 "This package provides a set of predicates and assertions for checking
10984 the properties of numbers. This is mainly for use by other package developers
10985 who want to include run-time testing features in their own packages.")
10986 (license license:gpl3+)))
10987
10988 (define-public r-assertive-sets
10989 (package
10990 (name "r-assertive-sets")
10991 (version "0.0-3")
10992 (source
10993 (origin
10994 (method url-fetch)
10995 (uri (cran-uri "assertive.sets" version))
10996 (sha256
10997 (base32
10998 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
10999 (properties
11000 `((upstream-name . "assertive.sets")))
11001 (build-system r-build-system)
11002 (propagated-inputs
11003 `(("r-assertive-base" ,r-assertive-base)))
11004 (home-page "https://bitbucket.org/richierocks/assertive.sets")
11005 (synopsis "Assertions to check properties of sets")
11006 (description
11007 "This package provides a set of predicates and assertions for checking
11008 the properties of sets. This is mainly for use by other package developers
11009 who want to include run-time testing features in their own packages.")
11010 (license license:gpl3+)))
11011
11012 (define-public r-assertive-matrices
11013 (package
11014 (name "r-assertive-matrices")
11015 (version "0.0-2")
11016 (source
11017 (origin
11018 (method url-fetch)
11019 (uri (cran-uri "assertive.matrices" version))
11020 (sha256
11021 (base32
11022 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
11023 (properties
11024 `((upstream-name . "assertive.matrices")))
11025 (build-system r-build-system)
11026 (propagated-inputs
11027 `(("r-assertive-base" ,r-assertive-base)))
11028 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
11029 (synopsis "Assertions to check properties of matrices")
11030 (description
11031 "This package provides a set of predicates and assertions for checking
11032 the properties of matrices. This is mainly for use by other package
11033 developers who want to include run-time testing features in their own
11034 packages.")
11035 (license license:gpl3+)))
11036
11037 (define-public r-assertive-models
11038 (package
11039 (name "r-assertive-models")
11040 (version "0.0-2")
11041 (source
11042 (origin
11043 (method url-fetch)
11044 (uri (cran-uri "assertive.models" version))
11045 (sha256
11046 (base32
11047 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
11048 (properties
11049 `((upstream-name . "assertive.models")))
11050 (build-system r-build-system)
11051 (propagated-inputs
11052 `(("r-assertive-base" ,r-assertive-base)))
11053 (home-page "https://bitbucket.org/richierocks/assertive.models")
11054 (synopsis "Assertions to check properties of models")
11055 (description
11056 "This package provides a set of predicates and assertions for checking
11057 the properties of models. This is mainly for use by other package developers
11058 who want to include run-time testing features in their own packages.")
11059 (license license:gpl3+)))
11060
11061 (define-public r-assertive-reflection
11062 (package
11063 (name "r-assertive-reflection")
11064 (version "0.0-4")
11065 (source
11066 (origin
11067 (method url-fetch)
11068 (uri (cran-uri "assertive.reflection" version))
11069 (sha256
11070 (base32
11071 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
11072 (properties
11073 `((upstream-name . "assertive.reflection")))
11074 (build-system r-build-system)
11075 (propagated-inputs
11076 `(("r-assertive-base" ,r-assertive-base)))
11077 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
11078 (synopsis "Assertions for checking the state of R")
11079 (description
11080 "This package provides a set of predicates and assertions for checking
11081 the state and capabilities of R, the operating system it is running on, and
11082 the IDE being used. This is mainly for use by other package developers who
11083 want to include run-time testing features in their own packages.")
11084 (license license:gpl3+)))
11085
11086 (define-public r-assertive-types
11087 (package
11088 (name "r-assertive-types")
11089 (version "0.0-3")
11090 (source
11091 (origin
11092 (method url-fetch)
11093 (uri (cran-uri "assertive.types" version))
11094 (sha256
11095 (base32
11096 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
11097 (properties
11098 `((upstream-name . "assertive.types")))
11099 (build-system r-build-system)
11100 (propagated-inputs
11101 `(("r-assertive-base" ,r-assertive-base)
11102 ("r-assertive-properties" ,r-assertive-properties)
11103 ("r-codetools" ,r-codetools)))
11104 (home-page "https://bitbucket.org/richierocks/assertive.types")
11105 (synopsis "Assertions to check types of variables")
11106 (description
11107 "This package provides a set of predicates and assertions for checking
11108 the types of variables. This is mainly for use by other package developers
11109 who want to include run-time testing features in their own packages.")
11110 (license license:gpl3+)))
11111
11112 (define-public r-assertive-files
11113 (package
11114 (name "r-assertive-files")
11115 (version "0.0-2")
11116 (source
11117 (origin
11118 (method url-fetch)
11119 (uri (cran-uri "assertive.files" version))
11120 (sha256
11121 (base32
11122 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
11123 (properties
11124 `((upstream-name . "assertive.files")))
11125 (build-system r-build-system)
11126 (propagated-inputs
11127 `(("r-assertive-base" ,r-assertive-base)
11128 ("r-assertive-numbers" ,r-assertive-numbers)))
11129 (home-page "https://bitbucket.org/richierocks/assertive.files")
11130 (synopsis "Assertions to check properties of files")
11131 (description
11132 "This package provides a set of predicates and assertions for checking
11133 the properties of files and connections. This is mainly for use by other
11134 package developers who want to include run-time testing features in their own
11135 packages.")
11136 (license license:gpl3+)))
11137
11138 (define-public r-assertive-code
11139 (package
11140 (name "r-assertive-code")
11141 (version "0.0-3")
11142 (source
11143 (origin
11144 (method url-fetch)
11145 (uri (cran-uri "assertive.code" version))
11146 (sha256
11147 (base32
11148 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
11149 (properties
11150 `((upstream-name . "assertive.code")))
11151 (build-system r-build-system)
11152 (propagated-inputs
11153 `(("r-assertive-base" ,r-assertive-base)
11154 ("r-assertive-properties" ,r-assertive-properties)
11155 ("r-assertive-types" ,r-assertive-types)))
11156 (home-page "https://bitbucket.org/richierocks/assertive.code")
11157 (synopsis "Assertions to check properties of code")
11158 (description
11159 "This package provides a set of predicates and assertions for checking
11160 the properties of code. This is mainly for use by other package developers
11161 who want to include run-time testing features in their own packages.")
11162 (license license:gpl3+)))
11163
11164 (define-public r-assertive-datetimes
11165 (package
11166 (name "r-assertive-datetimes")
11167 (version "0.0-2")
11168 (source
11169 (origin
11170 (method url-fetch)
11171 (uri (cran-uri "assertive.datetimes" version))
11172 (sha256
11173 (base32
11174 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
11175 (properties
11176 `((upstream-name . "assertive.datetimes")))
11177 (build-system r-build-system)
11178 (propagated-inputs
11179 `(("r-assertive-base" ,r-assertive-base)
11180 ("r-assertive-types" ,r-assertive-types)))
11181 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
11182 (synopsis "Assertions to check properties of dates and times")
11183 (description
11184 "This package provides a set of predicates and assertions for checking
11185 the properties of dates and times. This is mainly for use by other package
11186 developers who want to include run-time testing features in their own
11187 packages.")
11188 (license license:gpl3+)))
11189
11190 (define-public r-assertive-strings
11191 (package
11192 (name "r-assertive-strings")
11193 (version "0.0-3")
11194 (source
11195 (origin
11196 (method url-fetch)
11197 (uri (cran-uri "assertive.strings" version))
11198 (sha256
11199 (base32
11200 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
11201 (properties
11202 `((upstream-name . "assertive.strings")))
11203 (build-system r-build-system)
11204 (propagated-inputs
11205 `(("r-assertive-base" ,r-assertive-base)
11206 ("r-assertive-types" ,r-assertive-types)
11207 ("r-stringi" ,r-stringi)))
11208 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11209 (synopsis "Assertions to check properties of strings")
11210 (description
11211 "This package provides a set of predicates and assertions for checking
11212 the properties of strings. This is mainly for use by other package developers
11213 who want to include run-time testing features in their own packages.")
11214 (license license:gpl3+)))
11215
11216 (define-public r-assertive-data-us
11217 (package
11218 (name "r-assertive-data-us")
11219 (version "0.0-2")
11220 (source
11221 (origin
11222 (method url-fetch)
11223 (uri (cran-uri "assertive.data.us" version))
11224 (sha256
11225 (base32
11226 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11227 (properties
11228 `((upstream-name . "assertive.data.us")))
11229 (build-system r-build-system)
11230 (propagated-inputs
11231 `(("r-assertive-base" ,r-assertive-base)
11232 ("r-assertive-strings" ,r-assertive-strings)))
11233 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11234 (synopsis "Assertions to check properties of strings")
11235 (description
11236 "This package provides a set of predicates and assertions for checking
11237 the properties of US-specific complex data types. This is mainly for use by
11238 other package developers who want to include run-time testing features in
11239 their own packages.")
11240 (license license:gpl3+)))
11241
11242 (define-public r-assertive-data-uk
11243 (package
11244 (name "r-assertive-data-uk")
11245 (version "0.0-2")
11246 (source
11247 (origin
11248 (method url-fetch)
11249 (uri (cran-uri "assertive.data.uk" version))
11250 (sha256
11251 (base32
11252 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11253 (properties
11254 `((upstream-name . "assertive.data.uk")))
11255 (build-system r-build-system)
11256 (propagated-inputs
11257 `(("r-assertive-base" ,r-assertive-base)
11258 ("r-assertive-strings" ,r-assertive-strings)))
11259 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11260 (synopsis "Assertions to check properties of strings")
11261 (description
11262 "This package provides a set of predicates and assertions for checking
11263 the properties of UK-specific complex data types. This is mainly for use by
11264 other package developers who want to include run-time testing features in
11265 their own packages.")
11266 (license license:gpl3+)))
11267
11268 (define-public r-assertive-data
11269 (package
11270 (name "r-assertive-data")
11271 (version "0.0-3")
11272 (source
11273 (origin
11274 (method url-fetch)
11275 (uri (cran-uri "assertive.data" version))
11276 (sha256
11277 (base32
11278 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11279 (properties
11280 `((upstream-name . "assertive.data")))
11281 (build-system r-build-system)
11282 (propagated-inputs
11283 `(("r-assertive-base" ,r-assertive-base)
11284 ("r-assertive-strings" ,r-assertive-strings)))
11285 (home-page "https://bitbucket.org/richierocks/assertive.data")
11286 (synopsis "Assertions to check properties of data")
11287 (description
11288 "This package provides a set of predicates and assertions for checking
11289 the properties of (country independent) complex data types. This is mainly
11290 for use by other package developers who want to include run-time testing
11291 features in their own packages.")
11292 (license license:gpl3+)))
11293
11294 (define-public r-assertive
11295 (package
11296 (name "r-assertive")
11297 (version "0.3-5")
11298 (source
11299 (origin
11300 (method url-fetch)
11301 (uri (cran-uri "assertive" version))
11302 (sha256
11303 (base32
11304 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
11305 (build-system r-build-system)
11306 (propagated-inputs
11307 `(("r-assertive-base" ,r-assertive-base)
11308 ("r-assertive-code" ,r-assertive-code)
11309 ("r-assertive-data" ,r-assertive-data)
11310 ("r-assertive-data-uk" ,r-assertive-data-uk)
11311 ("r-assertive-data-us" ,r-assertive-data-us)
11312 ("r-assertive-datetimes" ,r-assertive-datetimes)
11313 ("r-assertive-files" ,r-assertive-files)
11314 ("r-assertive-matrices" ,r-assertive-matrices)
11315 ("r-assertive-models" ,r-assertive-models)
11316 ("r-assertive-numbers" ,r-assertive-numbers)
11317 ("r-assertive-properties" ,r-assertive-properties)
11318 ("r-assertive-reflection" ,r-assertive-reflection)
11319 ("r-assertive-sets" ,r-assertive-sets)
11320 ("r-assertive-strings" ,r-assertive-strings)
11321 ("r-assertive-types" ,r-assertive-types)
11322 ("r-knitr" ,r-knitr)))
11323 (home-page "https://bitbucket.org/richierocks/assertive")
11324 (synopsis "Readable check functions to ensure code integrity")
11325 (description
11326 "This package provides lots of predicates (@code{is_*} functions) to
11327 check the state of your variables, and assertions (@code{assert_*} functions)
11328 to throw errors if they aren't in the right form.")
11329 (license license:gpl3+)))
11330
11331 (define-public r-dotcall64
11332 (package
11333 (name "r-dotcall64")
11334 (version "1.0-0")
11335 (source
11336 (origin
11337 (method url-fetch)
11338 (uri (cran-uri "dotCall64" version))
11339 (sha256
11340 (base32
11341 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11342 (properties `((upstream-name . "dotCall64")))
11343 (build-system r-build-system)
11344 (native-inputs `(("gfortran" ,gfortran)))
11345 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11346 (synopsis "Enhanced foreign function interface supporting long vectors")
11347 (description
11348 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11349 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11350 supports long vectors, arguments of type 64-bit integer, and provides a
11351 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11352 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11353 (license license:gpl2+)))
11354
11355 (define-public r-spam
11356 (package
11357 (name "r-spam")
11358 (version "2.5-1")
11359 (source
11360 (origin
11361 (method url-fetch)
11362 (uri (cran-uri "spam" version))
11363 (sha256
11364 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11365 (build-system r-build-system)
11366 (propagated-inputs
11367 `(("r-dotcall64" ,r-dotcall64)))
11368 (native-inputs `(("gfortran" ,gfortran)))
11369 (home-page "https://www.math.uzh.ch/pages/spam/")
11370 (synopsis "Sparse matrix algebra")
11371 (description
11372 "This package provides a set of functions for sparse matrix algebra.
11373 Differences with other sparse matrix packages are:
11374
11375 @enumerate
11376 @item it only supports (essentially) one sparse matrix format;
11377 @item it is based on transparent and simple structure(s);
11378 @item it is tailored for MCMC calculations within G(M)RF;
11379 @item and it is fast and scalable (with the extension package @code{spam64}).
11380 @end enumerate\n")
11381 ;; Either of these licenses
11382 (license (list license:bsd-3 license:lgpl2.0))))
11383
11384 (define-public r-fields
11385 (package
11386 (name "r-fields")
11387 (version "10.3")
11388 (source
11389 (origin
11390 (method url-fetch)
11391 (uri (cran-uri "fields" version))
11392 (sha256
11393 (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9"))))
11394 (build-system r-build-system)
11395 (propagated-inputs
11396 `(("r-maps" ,r-maps)
11397 ("r-spam" ,r-spam)))
11398 (native-inputs
11399 `(("gfortran" ,gfortran)))
11400 (home-page "https://www.image.ucar.edu/fields")
11401 (synopsis "Tools for spatial data")
11402 (description
11403 "This is a package for curve, surface and function fitting with an
11404 emphasis on splines, spatial data and spatial statistics. The major methods
11405 include cubic, and thin plate splines, Kriging, and compactly supported
11406 covariance functions for large data sets.")
11407 (license license:gpl2+)))
11408
11409 (define-public r-spatialextremes
11410 (package
11411 (name "r-spatialextremes")
11412 (version "2.0-8")
11413 (source
11414 (origin
11415 (method url-fetch)
11416 (uri (cran-uri "SpatialExtremes" version))
11417 (sha256
11418 (base32
11419 "0r2byz5xxc46zqnigdax28q7446ibmzmsmi10lmm2hdks3ml6sl3"))))
11420 (properties
11421 `((upstream-name . "SpatialExtremes")))
11422 (build-system r-build-system)
11423 (propagated-inputs
11424 `(("r-fields" ,r-fields)
11425 ("r-maps" ,r-maps)))
11426 (home-page "http://spatialextremes.r-forge.r-project.org/")
11427 (synopsis "Modelling spatial extremes")
11428 (description
11429 "This package provides tools for the statistical modelling of spatial
11430 extremes using max-stable processes, copula or Bayesian hierarchical models.
11431 More precisely, this package allows (conditional) simulations from various
11432 parametric max-stable models, analysis of the extremal spatial dependence, the
11433 fitting of such processes using composite likelihoods or least square (simple
11434 max-stable processes only), model checking and selection and prediction.")
11435 (license license:gpl2+)))
11436
11437 (define-public r-drc
11438 (package
11439 (name "r-drc")
11440 (version "3.0-1")
11441 (source
11442 (origin
11443 (method url-fetch)
11444 (uri (cran-uri "drc" version))
11445 (sha256
11446 (base32
11447 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11448 (build-system r-build-system)
11449 (propagated-inputs
11450 `(("r-car" ,r-car)
11451 ("r-gtools" ,r-gtools)
11452 ("r-mass" ,r-mass)
11453 ("r-multcomp" ,r-multcomp)
11454 ("r-plotrix" ,r-plotrix)
11455 ("r-scales" ,r-scales)))
11456 (home-page "https://cran.r-project.org/web/packages/drc")
11457 (synopsis "Analysis of dose-response curves")
11458 (description
11459 "This package provides a suite of flexible and versatile model fitting
11460 and after-fitting functions for the analysis of dose-response data.")
11461 (license license:gpl2+)))
11462
11463 (define-public r-rmeta
11464 (package
11465 (name "r-rmeta")
11466 (version "3.0")
11467 (source
11468 (origin
11469 (method url-fetch)
11470 (uri (cran-uri "rmeta" version))
11471 (sha256
11472 (base32
11473 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11474 (build-system r-build-system)
11475 (home-page "https://cran.r-project.org/web/packages/rmeta")
11476 (synopsis "Tools for meta-analysis")
11477 (description
11478 "This package provides functions for simple fixed and random effects
11479 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11480 draws standard summary plots, funnel plots, and computes summaries and tests
11481 for association and heterogeneity.")
11482 (license license:gpl2)))
11483
11484 (define-public r-bootstrap
11485 (package
11486 (name "r-bootstrap")
11487 (version "2019.6")
11488 (source
11489 (origin
11490 (method url-fetch)
11491 (uri (cran-uri "bootstrap" version))
11492 (sha256
11493 (base32
11494 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11495 (build-system r-build-system)
11496 (native-inputs `(("gfortran" ,gfortran)))
11497 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11498 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11499 (description
11500 "This package provides software and data for the book \"An Introduction
11501 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11502 This package is primarily provided for projects already based on it, and for
11503 support of the book. New projects should preferentially use the recommended
11504 package \"boot\".")
11505 (license license:bsd-3)))
11506
11507 (define-public r-survivalroc
11508 (package
11509 (name "r-survivalroc")
11510 (version "1.0.3")
11511 (source
11512 (origin
11513 (method url-fetch)
11514 (uri (cran-uri "survivalROC" version))
11515 (sha256
11516 (base32
11517 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11518 (properties `((upstream-name . "survivalROC")))
11519 (build-system r-build-system)
11520 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11521 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11522 (description
11523 "Compute time-dependent ROC curve from censored survival data using
11524 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11525 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11526 (license license:gpl2+)))
11527
11528 (define-public r-longitudinal
11529 (package
11530 (name "r-longitudinal")
11531 (version "1.1.12")
11532 (source
11533 (origin
11534 (method url-fetch)
11535 (uri (cran-uri "longitudinal" version))
11536 (sha256
11537 (base32
11538 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11539 (build-system r-build-system)
11540 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11541 (home-page "http://strimmerlab.org/software/longitudinal/")
11542 (synopsis "Analysis of multiple time course data")
11543 (description
11544 "This package contains general data structures and functions for
11545 longitudinal data with multiple variables, repeated measurements, and
11546 irregularly spaced time points. It also implements a shrinkage estimator of
11547 dynamical correlation and dynamical covariance.")
11548 (license license:gpl3+)))
11549
11550 (define-public r-genenet
11551 (package
11552 (name "r-genenet")
11553 (version "1.2.14")
11554 (source
11555 (origin
11556 (method url-fetch)
11557 (uri (cran-uri "GeneNet" version))
11558 (sha256
11559 (base32
11560 "0cdhrj15rz0w0pyw3r8mikrzsdh95y5i1c0pa3cn0c2bjnjx3x3n"))))
11561 (properties `((upstream-name . "GeneNet")))
11562 (build-system r-build-system)
11563 (propagated-inputs
11564 `(("r-corpcor" ,r-corpcor)
11565 ("r-fdrtool" ,r-fdrtool)
11566 ("r-longitudinal" ,r-longitudinal)))
11567 (home-page "http://strimmerlab.org/software/genenet/")
11568 (synopsis "Modeling and inferring gene networks")
11569 (description
11570 "This package analyzes gene expression (time series) data with focus on
11571 the inference of gene networks. In particular, GeneNet implements the methods
11572 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11573 for learning large-scale gene association networks (including assignment of
11574 putative directions).")
11575 (license license:gpl3+)))
11576
11577 (define-public r-rbamtools
11578 (package
11579 (name "r-rbamtools")
11580 (version "2.16.17")
11581 (source
11582 (origin
11583 (method url-fetch)
11584 (uri (cran-uri "rbamtools" version))
11585 (sha256
11586 (base32
11587 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11588 (build-system r-build-system)
11589 (inputs `(("zlib" ,zlib)))
11590 (propagated-inputs
11591 `(("r-refgenome" ,r-refgenome)))
11592 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11593 (synopsis "Read and write BAM (binary alignment) files")
11594 (description
11595 "This package provides an R interface to functions of the SAMtools
11596 library.")
11597 (license license:artistic2.0)))
11598
11599 (define-public r-protviz
11600 (package
11601 (name "r-protviz")
11602 (version "0.6.4")
11603 (source
11604 (origin
11605 (method url-fetch)
11606 (uri (cran-uri "protViz" version))
11607 (sha256
11608 (base32
11609 "1qq9bf4485x8cviry9fmhnv4hw9aw657w134003myzcv42c4pml6"))))
11610 (properties `((upstream-name . "protViz")))
11611 (build-system r-build-system)
11612 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11613 (home-page "https://github.com/protViz/protViz/")
11614 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11615 (description
11616 "This package helps with quality checks, visualizations and analysis of
11617 mass spectrometry data, coming from proteomics experiments. The package is
11618 developed, tested and used at the Functional Genomics Center Zurich, where it
11619 is used mainly for prototyping, teaching, and having fun with proteomics data.
11620 But it can also be used to do data analysis for small scale data sets.")
11621 (license license:gpl3)))
11622
11623 (define-public r-cmprsk
11624 (package
11625 (name "r-cmprsk")
11626 (version "2.2-9")
11627 (source
11628 (origin
11629 (method url-fetch)
11630 (uri (cran-uri "cmprsk" version))
11631 (sha256
11632 (base32 "0xhgfg5b4i9skkaxp7gzkafgg5bqs5q1rp4hpw2jjmykg2nifn99"))))
11633 (build-system r-build-system)
11634 (propagated-inputs
11635 `(("r-survival" ,r-survival)))
11636 (native-inputs
11637 `(("gfortran" ,gfortran)))
11638 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11639 (synopsis "Subdistribution analysis of competing risks")
11640 (description
11641 "This package provides tool for estimation, testing and regression
11642 modeling of subdistribution functions in competing risks, as described in
11643 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
11644 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
11645 A proportional hazards model for the subdistribution of a competing risk,
11646 JASA, 94:496-509.")
11647 (license license:gpl2+)))
11648
11649 (define-public r-etm
11650 (package
11651 (name "r-etm")
11652 (version "1.1")
11653 (source
11654 (origin
11655 (method url-fetch)
11656 (uri (cran-uri "etm" version))
11657 (sha256
11658 (base32
11659 "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd"))))
11660 (build-system r-build-system)
11661 (propagated-inputs
11662 `(("r-data-table" ,r-data-table)
11663 ("r-lattice" ,r-lattice)
11664 ("r-rcpp" ,r-rcpp)
11665 ("r-rcpparmadillo" ,r-rcpparmadillo)
11666 ("r-survival" ,r-survival)))
11667 (home-page "https://cran.r-project.org/web/packages/etm")
11668 (synopsis "Empirical transition matrix")
11669 (description
11670 "The @dfn{empirical transition matrix} (etm) package estimates
11671 the matrix of transition probabilities for any time-inhomogeneous multistate
11672 model with finite state space using the Aalen-Johansen estimator.")
11673 (license license:expat)))
11674
11675 (define-public r-epi
11676 (package
11677 (name "r-epi")
11678 (version "2.40")
11679 (source
11680 (origin
11681 (method url-fetch)
11682 (uri (cran-uri "Epi" version))
11683 (sha256
11684 (base32
11685 "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5"))))
11686 (properties `((upstream-name . "Epi")))
11687 (build-system r-build-system)
11688 (propagated-inputs
11689 `(("r-cmprsk" ,r-cmprsk)
11690 ("r-data-table" ,r-data-table)
11691 ("r-etm" ,r-etm)
11692 ("r-mass" ,r-mass)
11693 ("r-matrix" ,r-matrix)
11694 ("r-mgcv" ,r-mgcv)
11695 ("r-numderiv" ,r-numderiv)
11696 ("r-plyr" ,r-plyr)
11697 ("r-survival" ,r-survival)
11698 ("r-zoo" ,r-zoo)))
11699 (home-page "https://BendixCarstensen.com/Epi/")
11700 (synopsis "Statistical analysis in epidemiology")
11701 (description
11702 "This package provides functions for demographic and epidemiological
11703 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
11704 particular representation, manipulation and simulation of multistate data -
11705 the Lexis suite of functions, which includes interfaces to the @code{mstate},
11706 @code{etm} and @code{cmprsk} packages. It also contains functions for
11707 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
11708 data and some useful functions for tabulation and plotting, as well as a
11709 number of epidemiological data sets.")
11710 (license license:gpl2)))
11711
11712 (define-public r-ppls
11713 (package
11714 (name "r-ppls")
11715 (version "1.6-1.1")
11716 (source
11717 (origin
11718 (method url-fetch)
11719 (uri (cran-uri "ppls" version))
11720 (sha256
11721 (base32
11722 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
11723 (build-system r-build-system)
11724 (propagated-inputs `(("r-mass" ,r-mass)))
11725 (home-page "https://cran.r-project.org/web/packages/ppls")
11726 (synopsis "Penalized partial least squares")
11727 (description
11728 "This package contains linear and nonlinear regression methods based on
11729 partial least squares and penalization techniques. Model parameters are
11730 selected via cross-validation, and confidence intervals ans tests for the
11731 regression coefficients can be conducted via jackknifing.")
11732 (license license:gpl2+)))
11733
11734 (define-public r-huge
11735 (package
11736 (name "r-huge")
11737 (version "1.3.4.1")
11738 (source
11739 (origin
11740 (method url-fetch)
11741 (uri (cran-uri "huge" version))
11742 (sha256
11743 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
11744 (build-system r-build-system)
11745 (propagated-inputs
11746 `(("r-igraph" ,r-igraph)
11747 ("r-mass" ,r-mass)
11748 ("r-matrix" ,r-matrix)
11749 ("r-rcpp" ,r-rcpp)
11750 ("r-rcppeigen" ,r-rcppeigen)))
11751 (home-page "https://cran.r-project.org/web/packages/huge")
11752 (synopsis "High-dimensional undirected graph estimation")
11753 (description
11754 "This package provides a general framework for high-dimensional
11755 undirected graph estimation. It integrates data preprocessing, neighborhood
11756 screening, graph estimation, and model selection techniques into a pipeline.")
11757 (license license:gpl2)))
11758
11759 (define-public r-parcor
11760 (package
11761 (name "r-parcor")
11762 (version "0.2-6")
11763 (source
11764 (origin
11765 (method url-fetch)
11766 (uri (cran-uri "parcor" version))
11767 (sha256
11768 (base32
11769 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
11770 (build-system r-build-system)
11771 (propagated-inputs
11772 `(("r-epi" ,r-epi)
11773 ("r-genenet" ,r-genenet)
11774 ("r-glmnet" ,r-glmnet)
11775 ("r-mass" ,r-mass)
11776 ("r-ppls" ,r-ppls)))
11777 (home-page "https://cran.r-project.org/web/packages/parcor")
11778 (synopsis "Regularized estimation of partial correlation matrices")
11779 (description
11780 "This package estimates the matrix of partial correlations based on
11781 different regularized regression methods: lasso, adaptive lasso, PLS, and
11782 Ridge Regression. In addition, the package provides model selection for
11783 lasso, adaptive lasso and Ridge regression based on cross-validation.")
11784 (license license:gpl2+)))
11785
11786 (define-public r-mcmc
11787 (package
11788 (name "r-mcmc")
11789 (version "0.9-7")
11790 (source
11791 (origin
11792 (method url-fetch)
11793 (uri (cran-uri "mcmc" version))
11794 (sha256
11795 (base32
11796 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
11797 (build-system r-build-system)
11798 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
11799 (synopsis "Markov chain Monte Carlo")
11800 (description
11801 "This package simulates continuous distributions of random vectors using
11802 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
11803 function that evaluates the log unnormalized density. Algorithms are random
11804 walk Metropolis algorithm (function @code{metrop}), simulated
11805 tempering (function @code{temper}), and morphometric random walk
11806 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
11807 by change of variable.")
11808 (license license:expat)))
11809
11810 (define-public r-listenv
11811 (package
11812 (name "r-listenv")
11813 (version "0.8.0")
11814 (source
11815 (origin
11816 (method url-fetch)
11817 (uri (cran-uri "listenv" version))
11818 (sha256
11819 (base32
11820 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
11821 (build-system r-build-system)
11822 (native-inputs
11823 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11824 (home-page "https://github.com/HenrikBengtsson/listenv")
11825 (synopsis "Environments behaving (almost) as lists")
11826 (description
11827 "This package implements list environments. List environments are
11828 environments that have list-like properties. For instance, the elements of a
11829 list environment are ordered and can be accessed and iterated over using index
11830 subsetting.")
11831 (license license:lgpl2.1+)))
11832
11833 (define-public r-globals
11834 (package
11835 (name "r-globals")
11836 (version "0.12.5")
11837 (source
11838 (origin
11839 (method url-fetch)
11840 (uri (cran-uri "globals" version))
11841 (sha256
11842 (base32
11843 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
11844 (build-system r-build-system)
11845 (propagated-inputs
11846 `(("r-codetools" ,r-codetools)))
11847 (home-page "https://github.com/HenrikBengtsson/globals")
11848 (synopsis "Identify global objects in R expressions")
11849 (description
11850 "This package provides tools to identify global (\"unknown\" or \"free\")
11851 objects in R expressions by code inspection using various strategies, e.g.
11852 conservative or liberal. The objective of this package is to make it as
11853 simple as possible to identify global objects for the purpose of exporting
11854 them in distributed compute environments.")
11855 (license license:lgpl2.1+)))
11856
11857 (define-public r-future
11858 (package
11859 (name "r-future")
11860 (version "1.17.0")
11861 (source
11862 (origin
11863 (method url-fetch)
11864 (uri (cran-uri "future" version))
11865 (sha256
11866 (base32
11867 "0d4y7gwcgqx2z0y6h5bh4lrz0m7b0inii5cjcq0kk8za762bi8rg"))))
11868 (build-system r-build-system)
11869 (propagated-inputs
11870 `(("r-digest" ,r-digest)
11871 ("r-globals" ,r-globals)
11872 ("r-listenv" ,r-listenv)))
11873 (native-inputs
11874 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11875 (home-page "https://github.com/HenrikBengtsson/future")
11876 (synopsis "Unified parallel and distributed processing in R")
11877 (description
11878 "The purpose of this package is to provide a lightweight and unified
11879 Future API for sequential and parallel processing of R expression via futures.
11880 This package implements sequential, multicore, multisession, and cluster
11881 futures. With these, R expressions can be evaluated on the local machine, in
11882 parallel a set of local machines, or distributed on a mix of local and remote
11883 machines. Extensions to this package implement additional backends for
11884 processing futures via compute cluster schedulers etc. Because of its unified
11885 API, there is no need to modify any code in order to switch from sequential on
11886 the local machine to, say, distributed processing on a remote compute cluster.")
11887 (license license:lgpl2.1+)))
11888
11889 (define-public r-future-apply
11890 (package
11891 (name "r-future-apply")
11892 (version "1.5.0")
11893 (source
11894 (origin
11895 (method url-fetch)
11896 (uri (cran-uri "future.apply" version))
11897 (sha256
11898 (base32
11899 "095a681ngbwbp7v53ladwya7ar8fgwnlgr3r1yklf3vdxwd54xll"))))
11900 (properties `((upstream-name . "future.apply")))
11901 (build-system r-build-system)
11902 (propagated-inputs
11903 `(("r-future" ,r-future)
11904 ("r-globals" ,r-globals)))
11905 (native-inputs
11906 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11907 (home-page "https://github.com/HenrikBengtsson/future.apply")
11908 (synopsis "Apply function to elements in parallel using futures")
11909 (description
11910 "This package provides implementations of @code{apply()},
11911 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
11912 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
11913 can be resolved using any future-supported backend, e.g. parallel on the local
11914 machine or distributed on a compute cluster.")
11915 (license license:gpl2+)))
11916
11917 (define-public r-rsvd
11918 (package
11919 (name "r-rsvd")
11920 (version "1.0.3")
11921 (source
11922 (origin
11923 (method url-fetch)
11924 (uri (cran-uri "rsvd" version))
11925 (sha256
11926 (base32
11927 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
11928 (build-system r-build-system)
11929 (propagated-inputs
11930 `(("r-matrix" ,r-matrix)))
11931 (home-page "https://github.com/erichson/rSVD")
11932 (synopsis "Randomized singular value decomposition")
11933 (description
11934 "Low-rank matrix decompositions are fundamental tools and widely used for
11935 data analysis, dimension reduction, and data compression. Classically, highly
11936 accurate deterministic matrix algorithms are used for this task. However, the
11937 emergence of large-scale data has severely challenged our computational
11938 ability to analyze big data. The concept of randomness has been demonstrated
11939 as an effective strategy to quickly produce approximate answers to familiar
11940 problems such as the @dfn{singular value decomposition} (SVD). This package
11941 provides several randomized matrix algorithms such as the randomized singular
11942 value decomposition (@code{rsvd}), randomized principal component
11943 analysis (@code{rpca}), randomized robust principal component
11944 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
11945 and the randomized CUR decomposition (@code{rcur}). In addition several plot
11946 functions are provided.")
11947 (license license:gpl3+)))
11948
11949 (define-public r-sloop
11950 (package
11951 (name "r-sloop")
11952 (version "1.0.1")
11953 (source
11954 (origin
11955 (method url-fetch)
11956 (uri (cran-uri "sloop" version))
11957 (sha256
11958 (base32
11959 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
11960 (build-system r-build-system)
11961 (propagated-inputs
11962 `(("r-codetools" ,r-codetools)
11963 ("r-crayon" ,r-crayon)
11964 ("r-purrr" ,r-purrr)
11965 ("r-rlang" ,r-rlang)
11966 ("r-tibble" ,r-tibble)))
11967 (home-page "https://github.com/r-lib/sloop")
11968 (synopsis "Helpers for object-oriented programming in R")
11969 (description
11970 "This package provides a collection of helper functions designed to
11971 help you to better understand object oriented programming in R, particularly
11972 using @code{S3}.")
11973 (license license:gpl3)))
11974
11975 (define-public r-capushe
11976 (package
11977 (name "r-capushe")
11978 (version "1.1.1")
11979 (source
11980 (origin
11981 (method url-fetch)
11982 (uri (cran-uri "capushe" version))
11983 (sha256
11984 (base32
11985 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
11986 (build-system r-build-system)
11987 (propagated-inputs `(("r-mass" ,r-mass)))
11988 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
11989 (synopsis "Calibrating penalties using slope heuristics")
11990 (description
11991 "This package provides tools for the calibration of penalized criteria
11992 for model selection. The calibration methods available are based on the slope
11993 heuristics.")
11994 (license license:gpl2+)))
11995
11996 (define-public r-dorng
11997 (package
11998 (name "r-dorng")
11999 (version "1.8.2")
12000 (source
12001 (origin
12002 (method url-fetch)
12003 (uri (cran-uri "doRNG" version))
12004 (sha256
12005 (base32
12006 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
12007 (properties `((upstream-name . "doRNG")))
12008 (build-system r-build-system)
12009 (propagated-inputs
12010 `(("r-foreach" ,r-foreach)
12011 ("r-iterators" ,r-iterators)
12012 ("r-rngtools" ,r-rngtools)))
12013 (home-page "https://renozao.github.io/doRNG/")
12014 (synopsis "Generic reproducible parallel backend for foreach loops")
12015 (description
12016 "This package provides functions to perform reproducible parallel
12017 @code{foreach} loops, using independent random streams as generated by
12018 L'Ecuyer's combined multiple-recursive generator. It enables to easily
12019 convert standard @code{%dopar%} loops into fully reproducible loops,
12020 independently of the number of workers, the task scheduling strategy, or the
12021 chosen parallel environment and associated foreach backend.")
12022 (license license:gpl2+)))
12023
12024 (define-public r-blockmodeling
12025 (package
12026 (name "r-blockmodeling")
12027 (version "0.3.6")
12028 (source
12029 (origin
12030 (method url-fetch)
12031 (uri (cran-uri "blockmodeling" version))
12032 (sha256
12033 (base32
12034 "12paf76l3wlxad14bkxn37lw9rg6ka473m86wlcf3yhriw8kbaiz"))))
12035 (build-system r-build-system)
12036 (propagated-inputs
12037 `(("r-matrix" ,r-matrix)))
12038 (native-inputs `(("gfortran" ,gfortran)))
12039 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
12040 (synopsis "Generalized and classical blockmodeling of valued networks")
12041 (description
12042 "This package is primarily meant as an implementation of generalized
12043 blockmodeling for valued networks. In addition, measures of similarity or
12044 dissimilarity based on structural equivalence and regular equivalence (REGE
12045 algorithms) can be computed and partitioned matrices can be plotted.")
12046 (license license:gpl2+)))
12047
12048 (define-public r-upsetr
12049 (package
12050 (name "r-upsetr")
12051 (version "1.4.0")
12052 (source
12053 (origin
12054 (method url-fetch)
12055 (uri (cran-uri "UpSetR" version))
12056 (sha256
12057 (base32
12058 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
12059 (properties `((upstream-name . "UpSetR")))
12060 (build-system r-build-system)
12061 (propagated-inputs
12062 `(("r-ggplot2" ,r-ggplot2)
12063 ("r-gridextra" ,r-gridextra)
12064 ("r-plyr" ,r-plyr)
12065 ("r-scales" ,r-scales)))
12066 (home-page "https://github.com/hms-dbmi/UpSetR")
12067 (synopsis "Visualize intersecting sets")
12068 (description
12069 "This package provides a more scalable alternative to Venn and Euler
12070 diagrams for visualizing intersecting sets. Create visualizations of
12071 intersecting sets using a novel matrix design, along with visualizations of
12072 several common set, element and attribute related tasks.")
12073 (license license:expat)))
12074
12075 ;; This package includes a JavaScript file, which is not minified. When
12076 ;; upgrading please check that there are no new minified JavaScript files.
12077 (define-public r-shinybs
12078 (package
12079 (name "r-shinybs")
12080 (version "0.61")
12081 (source
12082 (origin
12083 (method url-fetch)
12084 (uri (cran-uri "shinyBS" version))
12085 (sha256
12086 (base32
12087 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
12088 (properties `((upstream-name . "shinyBS")))
12089 (build-system r-build-system)
12090 ;; The tests spawn Shiny browser apps. They cannot be run
12091 ;; non-interactively.
12092 (arguments '(#:tests? #f))
12093 (propagated-inputs
12094 `(("r-htmltools" ,r-htmltools)
12095 ("r-shiny" ,r-shiny)))
12096 (home-page "https://ebailey78.github.io/shinyBS/")
12097 (synopsis "Twitter Bootstrap components for Shiny")
12098 (description
12099 "This package adds additional Twitter Bootstrap components to Shiny.")
12100 (license license:gpl3)))
12101
12102 (define-public r-outliers
12103 (package
12104 (name "r-outliers")
12105 (version "0.14")
12106 (source
12107 (origin
12108 (method url-fetch)
12109 (uri (cran-uri "outliers" version))
12110 (sha256
12111 (base32
12112 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
12113 (build-system r-build-system)
12114 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
12115 (synopsis "Tests for outliers")
12116 (description
12117 "This package provides a collection of some tests commonly used for
12118 identifying outliers.")
12119 (license license:gpl2+)))
12120
12121 (define-public r-bayesm
12122 (package
12123 (name "r-bayesm")
12124 (version "3.1-4")
12125 (source
12126 (origin
12127 (method url-fetch)
12128 (uri (cran-uri "bayesm" version))
12129 (sha256
12130 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
12131 (build-system r-build-system)
12132 (propagated-inputs
12133 `(("r-rcpp" ,r-rcpp)
12134 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12135 (home-page "http://www.perossi.org/home/bsm-1")
12136 (synopsis "Bayesian inference for marketing/micro-econometrics")
12137 (description
12138 "This package covers many important models used in marketing and
12139 micro-econometrics applications, including Bayes Regression (univariate or
12140 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
12141 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
12142 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
12143 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
12144 Estimation with normal base, Hierarchical Linear Models with normal prior and
12145 covariates, Hierarchical Linear Models with a mixture of normals prior and
12146 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
12147 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
12148 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
12149 analysis of choice-based conjoint data, Bayesian treatment of linear
12150 instrumental variables models, Analysis of Multivariate Ordinal survey data
12151 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
12152 Coefficient Logit Models.")
12153 (license license:gpl2+)))
12154
12155 (define-public r-tensora
12156 (package
12157 (name "r-tensora")
12158 (version "0.36.1")
12159 (source
12160 (origin
12161 (method url-fetch)
12162 (uri (cran-uri "tensorA" version))
12163 (sha256
12164 (base32
12165 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
12166 (properties `((upstream-name . "tensorA")))
12167 (build-system r-build-system)
12168 (home-page "http://www.stat.boogaart.de/tensorA")
12169 (synopsis "Advanced tensor arithmetic with named indices")
12170 (description
12171 "This package provides convenience functions for advanced linear algebra
12172 with tensors and computation with datasets of tensors on a higher level
12173 abstraction. It includes Einstein and Riemann summing conventions, dragging,
12174 co- and contravariate indices, and parallel computations on sequences of
12175 tensors.")
12176 (license license:gpl2+)))
12177
12178 (define-public r-rarpack
12179 (package
12180 (name "r-rarpack")
12181 (version "0.11-0")
12182 (source
12183 (origin
12184 (method url-fetch)
12185 (uri (cran-uri "rARPACK" version))
12186 (sha256
12187 (base32
12188 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
12189 (properties `((upstream-name . "rARPACK")))
12190 (build-system r-build-system)
12191 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
12192 (home-page "https://github.com/yixuan/rARPACK")
12193 (synopsis "Solvers for large scale eigenvalue and SVD problems")
12194 (description
12195 "This package was previously an R wrapper of the ARPACK library, and now
12196 a shell of the R package RSpectra, an R interface to the Spectra library for
12197 solving large scale eigenvalue/vector problems. The current version of
12198 rARPACK simply imports and exports the functions provided by RSpectra. New
12199 users of rARPACK are advised to switch to the RSpectra package.")
12200 (license license:bsd-3)))
12201
12202 (define-public r-compositions
12203 (package
12204 (name "r-compositions")
12205 (version "1.40-5")
12206 (source
12207 (origin
12208 (method url-fetch)
12209 (uri (cran-uri "compositions" version))
12210 (sha256
12211 (base32
12212 "0l9ayz2nb2wqhl7v9hkfl7pd950ba0h6hma8zqncbcxh6xh2k7l7"))))
12213 (build-system r-build-system)
12214 (propagated-inputs
12215 `(("r-bayesm" ,r-bayesm)
12216 ("r-robustbase" ,r-robustbase)
12217 ("r-tensora" ,r-tensora)))
12218 (home-page "http://www.stat.boogaart.de/compositions")
12219 (synopsis "Compositional data analysis")
12220 (description
12221 "This package provides functions for the consistent analysis of
12222 compositional data (e.g. portions of substances) and positive
12223 numbers (e.g. concentrations).")
12224 (license license:gpl2+)))
12225
12226 (define-public r-cobs
12227 (package
12228 (name "r-cobs")
12229 (version "1.3-4")
12230 (source
12231 (origin
12232 (method url-fetch)
12233 (uri (cran-uri "cobs" version))
12234 (sha256
12235 (base32
12236 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
12237 (build-system r-build-system)
12238 (propagated-inputs
12239 `(("r-quantreg" ,r-quantreg)
12240 ("r-sparsem" ,r-sparsem)))
12241 (home-page "https://cran.r-project.org/web/packages/cobs")
12242 (synopsis "Constrained B-Splines (sparse matrix based)")
12243 (description
12244 "This package provides qualitatively constrained (regression) smoothing
12245 splines via linear programming and sparse matrices.")
12246 (license license:gpl2+)))
12247
12248 (define-public r-drimpute
12249 (package
12250 (name "r-drimpute")
12251 (version "1.0")
12252 (source
12253 (origin
12254 (method url-fetch)
12255 (uri (cran-uri "DrImpute" version))
12256 (sha256
12257 (base32
12258 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12259 (properties `((upstream-name . "DrImpute")))
12260 (build-system r-build-system)
12261 (propagated-inputs
12262 `(("r-rcpp" ,r-rcpp)
12263 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12264 (home-page "https://github.com/ikwak2/DrImpute")
12265 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12266 (description
12267 "This is an R package for imputing dropout events. Many statistical
12268 methods in cell type identification, visualization and lineage reconstruction
12269 do not account for dropout events. DrImpute can improve the performance of
12270 such software by imputing dropout events.")
12271 (license license:gpl3)))
12272
12273 (define-public r-gamlss-dist
12274 (package
12275 (name "r-gamlss-dist")
12276 (version "5.1-6")
12277 (source
12278 (origin
12279 (method url-fetch)
12280 (uri (cran-uri "gamlss.dist" version))
12281 (sha256
12282 (base32 "1p904x0b07z4amaqdn2xhs7qzbq8lisr6lqc844s3pkxzmny7w1z"))))
12283 (properties `((upstream-name . "gamlss.dist")))
12284 (build-system r-build-system)
12285 (propagated-inputs `(("r-mass" ,r-mass)))
12286 (home-page "http://www.gamlss.org/")
12287 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12288 (description
12289 "This package provides a set of distributions which can be used for
12290 modelling the response variables in Generalized Additive Models for Location
12291 Scale and Shape. The distributions can be continuous, discrete or mixed
12292 distributions. Extra distributions can be created, by transforming, any
12293 continuous distribution defined on the real line, to a distribution defined on
12294 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12295 transformation, respectively.")
12296 ;; Either version of the GPL.
12297 (license (list license:gpl2 license:gpl3))))
12298
12299 ;; This package includes JavaScript files, which are not minified. When
12300 ;; upgrading please check that there are no new minified JavaScript files.
12301 (define-public r-shinyjs
12302 (package
12303 (name "r-shinyjs")
12304 (version "1.1")
12305 (source
12306 (origin
12307 (method url-fetch)
12308 (uri (cran-uri "shinyjs" version))
12309 (sha256
12310 (base32
12311 "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9"))))
12312 (build-system r-build-system)
12313 (propagated-inputs
12314 `(("r-digest" ,r-digest)
12315 ("r-htmltools" ,r-htmltools)
12316 ("r-jsonlite" ,r-jsonlite)
12317 ("r-shiny" ,r-shiny)))
12318 (home-page "https://deanattali.com/shinyjs")
12319 (synopsis "Improve the user experience of your Shiny apps")
12320 (description
12321 "Perform common useful JavaScript operations in Shiny apps that will
12322 greatly improve your apps without having to know any JavaScript. Examples
12323 include: hiding an element, disabling an input, resetting an input back to its
12324 original value, delaying code execution by a few seconds, and many more useful
12325 functions for both the end user and the developer. Shinyjs can also be used
12326 to easily call your own custom JavaScript functions from R.")
12327 (license license:agpl3+)))
12328
12329 ;; This package includes minified JavaScript files. When upgrading please
12330 ;; check that there are no new minified JavaScript files.
12331 (define-public r-colourpicker
12332 (package
12333 (name "r-colourpicker")
12334 (version "1.0")
12335 (source
12336 (origin
12337 (method url-fetch)
12338 (uri (cran-uri "colourpicker" version))
12339 (sha256
12340 (base32
12341 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12342 (build-system r-build-system)
12343 (arguments
12344 `(#:modules ((guix build utils)
12345 (guix build r-build-system)
12346 (srfi srfi-1)
12347 (ice-9 popen))
12348 #:phases
12349 (modify-phases %standard-phases
12350 (add-after 'unpack 'process-javascript
12351 (lambda* (#:key inputs #:allow-other-keys)
12352 (with-directory-excursion "inst"
12353 (call-with-values
12354 (lambda ()
12355 (unzip2
12356 `((,(assoc-ref inputs "js-salvattore")
12357 "examples/colourInput/www/salvattore.min.js")
12358 (,(assoc-ref inputs "js-jquery")
12359 "htmlwidgets/lib/jquery/jquery.min.js")
12360 ("www/shared/colourpicker/js/colourpicker.js"
12361 "www/shared/colourpicker/js/colourpicker.min.js"))))
12362 (lambda (sources targets)
12363 (for-each (lambda (source target)
12364 (format #t "Processing ~a --> ~a~%"
12365 source target)
12366 (delete-file target)
12367 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12368 (call-with-output-file target
12369 (lambda (port)
12370 (dump-port minified port)))))
12371 sources targets))))
12372 #t)))))
12373 (propagated-inputs
12374 `(("r-ggplot2" ,r-ggplot2)
12375 ("r-htmltools" ,r-htmltools)
12376 ("r-htmlwidgets" ,r-htmlwidgets)
12377 ("r-jsonlite" ,r-jsonlite)
12378 ("r-miniui" ,r-miniui)
12379 ("r-shiny" ,r-shiny)
12380 ("r-shinyjs" ,r-shinyjs)))
12381 (native-inputs
12382 `(("uglify-js" ,uglify-js)
12383 ("js-jquery"
12384 ,(origin
12385 (method url-fetch)
12386 (uri "https://code.jquery.com/jquery-3.3.1.js")
12387 (sha256
12388 (base32
12389 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12390 ("js-salvattore"
12391 ,(origin
12392 (method url-fetch)
12393 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12394 (sha256
12395 (base32
12396 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12397 (home-page "https://github.com/daattali/colourpicker")
12398 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12399 (description
12400 "This package provides a color picker that can be used as an input in
12401 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12402 custom color palettes, and many more options. A plot color helper tool is
12403 available as an RStudio Addin, which helps you pick colors to use in your
12404 plots. A more generic color picker RStudio Addin is also provided to let you
12405 select colors to use in your R code.")
12406 (license license:expat)))
12407
12408 (define-public r-ggextra
12409 (package
12410 (name "r-ggextra")
12411 (version "0.9")
12412 (source
12413 (origin
12414 (method url-fetch)
12415 (uri (cran-uri "ggExtra" version))
12416 (sha256
12417 (base32
12418 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12419 (properties `((upstream-name . "ggExtra")))
12420 (build-system r-build-system)
12421 (propagated-inputs
12422 `(("r-colourpicker" ,r-colourpicker)
12423 ("r-ggplot2" ,r-ggplot2)
12424 ("r-gtable" ,r-gtable)
12425 ("r-miniui" ,r-miniui)
12426 ("r-r6" ,r-r6)
12427 ("r-scales" ,r-scales)
12428 ("r-shiny" ,r-shiny)
12429 ("r-shinyjs" ,r-shinyjs)))
12430 (native-inputs
12431 `(("r-knitr" ,r-knitr)))
12432 (home-page "https://github.com/daattali/ggExtra")
12433 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12434 (description
12435 "This package is a collection of functions and layers to enhance ggplot2.
12436 The flagship function is @code{ggMarginal()}, which can be used to add
12437 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12438 (license license:expat)))
12439
12440 (define-public r-minpack-lm
12441 (package
12442 (name "r-minpack-lm")
12443 (version "1.2-1")
12444 (source
12445 (origin
12446 (method url-fetch)
12447 (uri (cran-uri "minpack.lm" version))
12448 (sha256
12449 (base32
12450 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12451 (properties `((upstream-name . "minpack.lm")))
12452 (build-system r-build-system)
12453 (native-inputs `(("gfortran" ,gfortran)))
12454 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12455 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12456 (description
12457 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12458 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12459 problems by a modification of the Levenberg-Marquardt algorithm, with support
12460 for lower and upper parameter bounds. The implementation can be used via
12461 @code{nls}-like calls using the @code{nlsLM} function.")
12462 (license license:gpl3)))
12463
12464 (define-public r-moments
12465 (package
12466 (name "r-moments")
12467 (version "0.14")
12468 (source
12469 (origin
12470 (method url-fetch)
12471 (uri (cran-uri "moments" version))
12472 (sha256
12473 (base32
12474 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12475 (build-system r-build-system)
12476 (home-page "https://cran.r-project.org/web/packages/moments")
12477 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12478 (description
12479 "This package provides functions to calculate: moments, Pearson's
12480 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12481 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12482 (license license:gpl2+)))
12483
12484 (define-public r-msir
12485 (package
12486 (name "r-msir")
12487 (version "1.3.2")
12488 (source
12489 (origin
12490 (method url-fetch)
12491 (uri (cran-uri "msir" version))
12492 (sha256
12493 (base32
12494 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12495 (build-system r-build-system)
12496 (propagated-inputs
12497 `(("r-mclust" ,r-mclust)))
12498 (home-page "https://cran.r-project.org/web/packages/msir")
12499 (synopsis "Model-based sliced inverse regression")
12500 (description
12501 "This is an R package for dimension reduction based on finite Gaussian
12502 mixture modeling of inverse regression.")
12503 (license license:gpl2+)))
12504
12505 (define-public r-pbivnorm
12506 (package
12507 (name "r-pbivnorm")
12508 (version "0.6.0")
12509 (source
12510 (origin
12511 (method url-fetch)
12512 (uri (cran-uri "pbivnorm" version))
12513 (sha256
12514 (base32
12515 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12516 (build-system r-build-system)
12517 (native-inputs `(("gfortran" ,gfortran)))
12518 (home-page "https://github.com/brentonk/pbivnorm")
12519 (synopsis "Vectorized bivariate normal CDF")
12520 (description
12521 "This package provides a vectorized R function for calculating
12522 probabilities from a standard bivariate normal CDF.")
12523 (license license:gpl2+)))
12524
12525 (define-public r-lavaan
12526 (package
12527 (name "r-lavaan")
12528 (version "0.6-5")
12529 (source
12530 (origin
12531 (method url-fetch)
12532 (uri (cran-uri "lavaan" version))
12533 (sha256
12534 (base32
12535 "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy"))))
12536 (build-system r-build-system)
12537 (propagated-inputs
12538 `(("r-mass" ,r-mass)
12539 ("r-mnormt" ,r-mnormt)
12540 ("r-numderiv" ,r-numderiv)
12541 ("r-pbivnorm" ,r-pbivnorm)))
12542 (home-page "http://lavaan.ugent.be")
12543 (synopsis "Latent variable analysis")
12544 (description
12545 "This package provides tools to fit a variety of latent variable models,
12546 including confirmatory factor analysis, structural equation modeling and
12547 latent growth curve models.")
12548 (license license:gpl2+)))
12549
12550 (define-public r-nonnest2
12551 (package
12552 (name "r-nonnest2")
12553 (version "0.5-3")
12554 (source
12555 (origin
12556 (method url-fetch)
12557 (uri (cran-uri "nonnest2" version))
12558 (sha256
12559 (base32
12560 "1mnv4pa583ir9s03h952hk40lwdywr3g88g76sk1zsa54rcmn82c"))))
12561 (build-system r-build-system)
12562 (propagated-inputs
12563 `(("r-compquadform" ,r-compquadform)
12564 ("r-lavaan" ,r-lavaan)
12565 ("r-mvtnorm" ,r-mvtnorm)
12566 ("r-sandwich" ,r-sandwich)))
12567 (native-inputs
12568 `(("r-knitr" ,r-knitr)))
12569 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12570 (synopsis "Tests of non-nested models")
12571 (description
12572 "This package allows for testing of non-nested models. It includes tests
12573 of model distinguishability and of model fit that can be applied to both
12574 nested and non-nested models. The package also includes functionality to
12575 obtain confidence intervals associated with AIC and BIC.")
12576 ;; Either version of the GPL.
12577 (license (list license:gpl2 license:gpl3))))
12578
12579 (define-public r-penalized
12580 (package
12581 (name "r-penalized")
12582 (version "0.9-51")
12583 (source
12584 (origin
12585 (method url-fetch)
12586 (uri (cran-uri "penalized" version))
12587 (sha256
12588 (base32
12589 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12590 (build-system r-build-system)
12591 (propagated-inputs
12592 `(("r-rcpp" ,r-rcpp)
12593 ("r-rcpparmadillo" ,r-rcpparmadillo)
12594 ("r-survival" ,r-survival)))
12595 (home-page "https://cran.r-project.org/web/packages/penalized/")
12596 (synopsis "Penalized estimation in GLMs and in the Cox model")
12597 (description
12598 "This package provides tools for fitting possibly high dimensional
12599 penalized regression models. The penalty structure can be any combination of
12600 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12601 constraint on the regression coefficients. The supported regression models
12602 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12603 model. Cross-validation routines allow optimization of the tuning
12604 parameters.")
12605 (license license:gpl2+)))
12606
12607 (define-public r-zim
12608 (package
12609 (name "r-zim")
12610 (version "1.1.0")
12611 (source
12612 (origin
12613 (method url-fetch)
12614 (uri (cran-uri "ZIM" version))
12615 (sha256
12616 (base32
12617 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12618 (properties `((upstream-name . "ZIM")))
12619 (build-system r-build-system)
12620 (propagated-inputs `(("r-mass" ,r-mass)))
12621 (home-page "https://github.com/biostatstudio/ZIM")
12622 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12623 (description
12624 "Analyze count time series with excess zeros. Two types of statistical
12625 models are supported: Markov regression and state-space models. They are also
12626 known as observation-driven and parameter-driven models respectively in the
12627 time series literature. The functions used for Markov regression or
12628 observation-driven models can also be used to fit ordinary regression models
12629 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12630 negative binomial (ZINB) assumption. The package also contains miscellaneous
12631 functions to compute density, distribution, quantile, and generate random
12632 numbers from ZIP and ZINB distributions.")
12633 (license license:gpl3)))
12634
12635 (define-public r-nor1mix
12636 (package
12637 (name "r-nor1mix")
12638 (version "1.3-0")
12639 (source
12640 (origin
12641 (method url-fetch)
12642 (uri (cran-uri "nor1mix" version))
12643 (sha256
12644 (base32
12645 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
12646 (build-system r-build-system)
12647 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
12648 (synopsis "Normal (1-d) mixture models")
12649 (description
12650 "This package provides S3 classes and methods for one-dimensional normal
12651 mixture models, for, e.g., density estimation or clustering algorithms
12652 research and teaching; it provides the widely used Marron-Wand densities. It
12653 also provides tools for efficient random number generation and graphics.")
12654 (license license:gpl2+)))
12655
12656 (define-public r-beanplot
12657 (package
12658 (name "r-beanplot")
12659 (version "1.2")
12660 (source
12661 (origin
12662 (method url-fetch)
12663 (uri (cran-uri "beanplot" version))
12664 (sha256
12665 (base32
12666 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
12667 (build-system r-build-system)
12668 (home-page "https://cran.r-project.org/web/packages/beanplot/")
12669 (synopsis "Visualization via beanplots")
12670 (description
12671 "This package provides beanplots, an alternative to
12672 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
12673 graphs.")
12674 (license license:gpl2)))
12675
12676 (define-public r-pbdzmq
12677 (package
12678 (name "r-pbdzmq")
12679 (version "0.3-3")
12680 (source
12681 (origin
12682 (method url-fetch)
12683 (uri (cran-uri "pbdZMQ" version))
12684 (sha256
12685 (base32
12686 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
12687 (properties `((upstream-name . "pbdZMQ")))
12688 (build-system r-build-system)
12689 (inputs
12690 `(("zeromq" ,zeromq)
12691 ("zlib" ,zlib)))
12692 (native-inputs
12693 `(("pkg-config" ,pkg-config)))
12694 (home-page "https://pbdr.org/")
12695 (synopsis "R interface to ZeroMQ")
12696 (description
12697 "ZeroMQ is a well-known library for high-performance asynchronous
12698 messaging in scalable, distributed applications. This package provides high
12699 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
12700 interactive client/server programming frameworks. A few wrapper functions
12701 compatible with @code{rzmq} are also provided.")
12702 (license license:gpl3)))
12703
12704 (define-public r-repr
12705 (package
12706 (name "r-repr")
12707 (version "1.1.0")
12708 (source
12709 (origin
12710 (method url-fetch)
12711 (uri (cran-uri "repr" version))
12712 (sha256
12713 (base32
12714 "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
12715 (build-system r-build-system)
12716 (propagated-inputs
12717 `(("r-base64enc" ,r-base64enc)
12718 ("r-htmltools" ,r-htmltools)
12719 ("r-jsonlite" ,r-jsonlite)
12720 ("r-pillar" ,r-pillar)))
12721 (home-page "https://cran.r-project.org/web/packages/repr/")
12722 (synopsis "Serializable representations")
12723 (description
12724 "This package provides string and binary representations of objects for
12725 several formats and MIME types.")
12726 (license license:gpl3)))
12727
12728 (define-public r-irdisplay
12729 (package
12730 (name "r-irdisplay")
12731 (version "0.7.0")
12732 (source
12733 (origin
12734 (method url-fetch)
12735 (uri (cran-uri "IRdisplay" version))
12736 (sha256
12737 (base32
12738 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
12739 (properties `((upstream-name . "IRdisplay")))
12740 (build-system r-build-system)
12741 (propagated-inputs
12742 `(("r-repr" ,r-repr)))
12743 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
12744 (synopsis "Jupyter display machinery")
12745 (description
12746 "This package provides an interface to the rich display capabilities of
12747 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
12748 running IRkernel session.")
12749 (license license:expat)))
12750
12751 (define-public r-irkernel
12752 (package
12753 (name "r-irkernel")
12754 (version "1.1")
12755 (source
12756 (origin
12757 (method url-fetch)
12758 (uri (cran-uri "IRkernel" version))
12759 (sha256
12760 (base32
12761 "1viqxs91dys1z4cf7gb59rmqvzb8lc7jdp4azrpmhgwa8qf46s94"))))
12762 (properties `((upstream-name . "IRkernel")))
12763 (build-system r-build-system)
12764 (arguments
12765 `(#:phases
12766 (modify-phases %standard-phases
12767 (add-after 'install 'install-kernelspec
12768 (lambda* (#:key outputs #:allow-other-keys)
12769 (let ((out (assoc-ref outputs "out")))
12770 (setenv "HOME" "/tmp")
12771 (invoke "jupyter" "kernelspec" "install"
12772 "--name" "ir"
12773 "--prefix" out
12774 (string-append out "/site-library/IRkernel/kernelspec"))
12775 ;; Record the absolute file name of the 'R' executable in
12776 ;; 'kernel.json'.
12777 (substitute* (string-append out "/share/jupyter"
12778 "/kernels/ir/kernel.json")
12779 (("\\[\"R\",")
12780 (string-append "[\"" (which "R") "\",")))
12781 #t))))))
12782 (inputs
12783 `(("jupyter" ,jupyter)))
12784 (propagated-inputs
12785 `(("r-crayon" ,r-crayon)
12786 ("r-digest" ,r-digest)
12787 ("r-evaluate" ,r-evaluate)
12788 ("r-irdisplay" ,r-irdisplay)
12789 ("r-jsonlite" ,r-jsonlite)
12790 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
12791 ("r-minimal" ,r-minimal)
12792 ("r-pbdzmq" ,r-pbdzmq)
12793 ("r-repr" ,r-repr)
12794 ("r-uuid" ,r-uuid)))
12795 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
12796 (synopsis "Native R kernel for Jupyter")
12797 (description
12798 "The R kernel for the Jupyter environment executes R code which the
12799 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
12800 network.")
12801 (license license:expat)))
12802
12803 (define-public r-gmodels
12804 (package
12805 (name "r-gmodels")
12806 (version "2.18.1")
12807 (source
12808 (origin
12809 (method url-fetch)
12810 (uri (cran-uri "gmodels" version))
12811 (sha256
12812 (base32
12813 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
12814 (build-system r-build-system)
12815 (propagated-inputs
12816 `(("r-gdata" ,r-gdata)
12817 ("r-mass" ,r-mass)))
12818 (home-page "https://cran.r-project.org/web/packages/gmodels/")
12819 (synopsis "Various R programming tools for model fitting")
12820 (description
12821 "This package provides various R programming tools for model fitting.")
12822 (license license:gpl2)))
12823
12824 (define-public r-apcluster
12825 (package
12826 (name "r-apcluster")
12827 (version "1.4.8")
12828 (source
12829 (origin
12830 (method url-fetch)
12831 (uri (cran-uri "apcluster" version))
12832 (sha256
12833 (base32
12834 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
12835 (build-system r-build-system)
12836 (propagated-inputs
12837 `(("r-matrix" ,r-matrix)
12838 ("r-rcpp" ,r-rcpp)))
12839 (home-page "https://cran.r-project.org/web/packages/apcluster/")
12840 (synopsis "Affinity propagation clustering")
12841 (description
12842 "This package implements affinity propagation clustering introduced by
12843 Frey and Dueck (2007). The package further provides leveraged affinity
12844 propagation and an algorithm for exemplar-based agglomerative clustering that
12845 can also be used to join clusters obtained from affinity propagation. Various
12846 plotting functions are available for analyzing clustering results.")
12847 (license license:gpl2+)))
12848
12849 (define-public r-valr
12850 (package
12851 (name "r-valr")
12852 (version "0.5.0")
12853 (source
12854 (origin
12855 (method url-fetch)
12856 (uri (cran-uri "valr" version))
12857 (sha256
12858 (base32
12859 "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
12860 (build-system r-build-system)
12861 (propagated-inputs
12862 `(("r-broom" ,r-broom)
12863 ("r-dplyr" ,r-dplyr)
12864 ("r-ggplot2" ,r-ggplot2)
12865 ("r-rcpp" ,r-rcpp)
12866 ("r-readr" ,r-readr)
12867 ("r-rlang" ,r-rlang)
12868 ("r-stringr" ,r-stringr)
12869 ("r-tibble" ,r-tibble)))
12870 (home-page "http://github.com/rnabioco/valr")
12871 (synopsis "Genome interval arithmetic in R")
12872 (description
12873 "This package enables you to read and manipulate genome intervals and
12874 signals. It provides functionality similar to command-line tool suites within
12875 R, enabling interactive analysis and visualization of genome-scale data.")
12876 (license license:expat)))
12877
12878 (define-public r-rematch2
12879 (package
12880 (name "r-rematch2")
12881 (version "2.1.1")
12882 (source
12883 (origin
12884 (method url-fetch)
12885 (uri (cran-uri "rematch2" version))
12886 (sha256
12887 (base32
12888 "13siaa8s2ji9q6hykhb2r34ag76335ypmbqr90xaqilbir0klhnh"))))
12889 (build-system r-build-system)
12890 (propagated-inputs
12891 `(("r-tibble" ,r-tibble)))
12892 (home-page "https://github.com/r-lib/rematch2")
12893 (synopsis "Tidy output from regular expression matching")
12894 (description
12895 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
12896 return the match results in tidy data frames.")
12897 (license license:expat)))
12898
12899 (define-public r-picante
12900 (package
12901 (name "r-picante")
12902 (version "1.8.1")
12903 (source
12904 (origin
12905 (method url-fetch)
12906 (uri (cran-uri "picante" version))
12907 (sha256
12908 (base32
12909 "1b16zm8zjjsl181b8krkdcrbcw347kf772c4w7y5332qmfi7jhz0"))))
12910 (build-system r-build-system)
12911 (propagated-inputs
12912 `(("r-ape" ,r-ape)
12913 ("r-nlme" ,r-nlme)
12914 ("r-vegan" ,r-vegan)))
12915 (home-page "https://cran.r-project.org/web/packages/picante/")
12916 (synopsis "Integrating phylogenies and ecology")
12917 (description
12918 "This package provides functions for phylocom integration, community
12919 analyses, null-models, traits and evolution. It implements numerous
12920 ecophylogenetic approaches including measures of community phylogenetic and
12921 trait diversity, phylogenetic signal, estimation of trait values for
12922 unobserved taxa, null models for community and phylogeny randomizations, and
12923 utility functions for data input/output and phylogeny plotting. A full
12924 description of package functionality and methods are provided by Kembel et
12925 al. (2010).")
12926 (license license:gpl2)))
12927
12928 (define-public r-reinforcelearn
12929 (package
12930 (name "r-reinforcelearn")
12931 (version "0.2.1")
12932 (source
12933 (origin
12934 (method url-fetch)
12935 (uri (cran-uri "reinforcelearn" version))
12936 (sha256
12937 (base32
12938 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
12939 (build-system r-build-system)
12940 (propagated-inputs
12941 `(("r-checkmate" ,r-checkmate)
12942 ("r-nnet" ,r-nnet)
12943 ("r-purrr" ,r-purrr)
12944 ("r-r6" ,r-r6)))
12945 (home-page "https://markusdumke.github.io/reinforcelearn")
12946 (synopsis "Reinforcement learning")
12947 (description
12948 "This package implements reinforcement learning environments and
12949 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
12950 can be used with function approximation, eligibility traces (Singh & Sutton,
12951 1996) and experience replay (Mnih et al., 2013).")
12952 (license license:expat)))
12953
12954 (define-public r-lemon
12955 (package
12956 (name "r-lemon")
12957 (version "0.4.4")
12958 (source
12959 (origin
12960 (method url-fetch)
12961 (uri (cran-uri "lemon" version))
12962 (sha256
12963 (base32
12964 "0m9hqwi709j9iwsxn8jh63741jiyr7ppwgqaw2zkv285p3m5wvd5"))))
12965 (build-system r-build-system)
12966 (propagated-inputs
12967 `(("r-ggplot2" ,r-ggplot2)
12968 ("r-gridextra" ,r-gridextra)
12969 ("r-gtable" ,r-gtable)
12970 ("r-knitr" ,r-knitr)
12971 ("r-lattice" ,r-lattice)
12972 ("r-plyr" ,r-plyr)
12973 ("r-rlang" ,r-rlang)
12974 ("r-scales" ,r-scales)))
12975 (home-page "https://github.com/stefanedwards/lemon")
12976 (synopsis "Freshen up your ggplot2 plots")
12977 (description
12978 "This package provides functions for working with legends and axis lines
12979 of ggplot2, facets that repeat axis lines on all panels, and some knitr
12980 extensions.")
12981 (license license:gpl3)))
12982
12983 (define-public r-wgaim
12984 (package
12985 (name "r-wgaim")
12986 (version "2.0-1")
12987 (source
12988 (origin
12989 (method url-fetch)
12990 (uri (cran-uri "wgaim" version))
12991 (sha256
12992 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
12993 (build-system r-build-system)
12994 (propagated-inputs
12995 `(("r-ggplot2" ,r-ggplot2)
12996 ("r-qtl" ,r-qtl)))
12997 (home-page "https://cran.r-project.org/web/packages/wgaim")
12998 (synopsis "Whole genome average interval mapping for QTL detection")
12999 (description
13000 "This package integrates sophisticated mixed modelling methods with a
13001 whole genome approach to detecting significant QTL in linkage maps.")
13002 (license license:gpl2+)))
13003
13004 (define-public r-bedr
13005 (package
13006 (name "r-bedr")
13007 (version "1.0.7")
13008 (source
13009 (origin
13010 (method url-fetch)
13011 (uri (cran-uri "bedr" version))
13012 (sha256
13013 (base32
13014 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
13015 (build-system r-build-system)
13016 (propagated-inputs
13017 `(("r-data-table" ,r-data-table)
13018 ("r-r-utils" ,r-r-utils)
13019 ("r-testthat" ,r-testthat)
13020 ("r-venndiagram" ,r-venndiagram)
13021 ("r-yaml" ,r-yaml)
13022 ("bedops" ,bedops)
13023 ("bedtools" ,bedtools)
13024 ("htslib" ,htslib))) ; for tabix
13025 (native-inputs
13026 `(("r-knitr" ,r-knitr))) ; for vignettes
13027 (home-page "https://cran.r-project.org/web/packages/bedr")
13028 (synopsis "Genomic region processing")
13029 (description
13030 "This package is for genomic regions processing using command line tools
13031 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
13032 utilities to perform genome arithmetic e.g indexing, formatting and merging.
13033 The bedr package's API enhances access to these tools as well as offers
13034 additional utilities for genomic regions processing.")
13035 (license license:gpl2)))
13036
13037 (define-public r-sets
13038 (package
13039 (name "r-sets")
13040 (version "1.0-18")
13041 (source
13042 (origin
13043 (method url-fetch)
13044 (uri (cran-uri "sets" version))
13045 (sha256
13046 (base32
13047 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
13048 (properties `((upstream-name . "sets")))
13049 (build-system r-build-system)
13050 (home-page "https://cran.r-project.org/web/packages/sets")
13051 (synopsis "Sets, generalized sets, customizable sets and intervals")
13052 (description
13053 "This package provides data structures and basic operations for ordinary
13054 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
13055 customizable sets, and intervals.")
13056 (license license:gpl2)))
13057
13058 (define-public r-partitions
13059 (package
13060 (name "r-partitions")
13061 (version "1.9-22")
13062 (source
13063 (origin
13064 (method url-fetch)
13065 (uri (cran-uri "partitions" version))
13066 (sha256
13067 (base32
13068 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
13069 (build-system r-build-system)
13070 (propagated-inputs
13071 `(("r-gmp" ,r-gmp)
13072 ("r-polynom" ,r-polynom)
13073 ("r-sets" ,r-sets)))
13074 (home-page "https://cran.r-project.org/web/packages/partitions")
13075 (synopsis "Additive partitions of integers")
13076 (description
13077 "This package provides tools to enumerates the partitions, unequal
13078 partitions, and restricted partitions of an integer; the three corresponding
13079 partition functions are also given.")
13080 ;; Any version of the GPL
13081 (license license:gpl2+)))
13082
13083 (define-public r-brobdingnag
13084 (package
13085 (name "r-brobdingnag")
13086 (version "1.2-6")
13087 (source
13088 (origin
13089 (method url-fetch)
13090 (uri (cran-uri "Brobdingnag" version))
13091 (sha256
13092 (base32
13093 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
13094 (properties `((upstream-name . "Brobdingnag")))
13095 (build-system r-build-system)
13096 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
13097 (synopsis "Very large numbers in R")
13098 (description
13099 "This package handles very large numbers in R. Real numbers are held
13100 using their natural logarithms, plus a logical flag indicating sign. The
13101 package includes a vignette that gives a step-by-step introduction to using S4
13102 methods.")
13103 ;; Any version of the GPL
13104 (license license:gpl2+)))
13105
13106 (define-public r-untb
13107 (package
13108 (name "r-untb")
13109 (version "1.7-4")
13110 (source
13111 (origin
13112 (method url-fetch)
13113 (uri (cran-uri "untb" version))
13114 (sha256
13115 (base32
13116 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
13117 (build-system r-build-system)
13118 (propagated-inputs
13119 `(("r-brobdingnag" ,r-brobdingnag)
13120 ("r-partitions" ,r-partitions)
13121 ("r-polynom" ,r-polynom)))
13122 (home-page "https://github.com/RobinHankin/untb.git")
13123 (synopsis "Ecological drift under the UNTB")
13124 (description
13125 "This package provides numerical simulations, and visualizations, of
13126 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
13127 (license license:gpl2+)))
13128
13129 (define-public r-stepwise
13130 (package
13131 (name "r-stepwise")
13132 (version "0.3")
13133 (source
13134 (origin
13135 (method url-fetch)
13136 (uri (cran-uri "stepwise" version))
13137 (sha256
13138 (base32
13139 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
13140 (build-system r-build-system)
13141 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
13142 (synopsis "Stepwise detection of recombination breakpoints")
13143 (description
13144 "This package provides a stepwise approach to identifying recombination
13145 breakpoints in a genomic sequence alignment.")
13146 (license license:gpl2+)))
13147
13148 (define-public r-snpmaxsel
13149 (package
13150 (name "r-snpmaxsel")
13151 (version "1.0-3")
13152 (source
13153 (origin
13154 (method url-fetch)
13155 (uri (cran-uri "SNPmaxsel" version))
13156 (sha256
13157 (base32
13158 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
13159 (properties `((upstream-name . "SNPmaxsel")))
13160 (build-system r-build-system)
13161 (propagated-inputs
13162 `(("r-combinat" ,r-combinat)
13163 ("r-mvtnorm" ,r-mvtnorm)))
13164 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
13165 (synopsis "Maximally selected statistics for SNP data")
13166 (description
13167 "This package implements asymptotic methods related to maximally selected
13168 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
13169 data.")
13170 (license license:gpl2+)))
13171
13172 (define-public r-acsnminer
13173 (package
13174 (name "r-acsnminer")
13175 (version "0.16.8.25")
13176 (source (origin
13177 (method url-fetch)
13178 (uri (cran-uri "ACSNMineR" version))
13179 (sha256
13180 (base32
13181 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
13182 (properties `((upstream-name . "ACSNMineR")))
13183 (build-system r-build-system)
13184 (propagated-inputs
13185 `(("r-ggplot2" ,r-ggplot2)
13186 ("r-gridextra" ,r-gridextra)))
13187 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
13188 (synopsis "Gene enrichment analysis")
13189 (description
13190 "This package provides tools to compute and represent gene set enrichment
13191 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
13192 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
13193 enrichment can be run with hypergeometric test or Fisher exact test, and can
13194 use multiple corrections. Visualization of data can be done either by
13195 barplots or heatmaps.")
13196 (license license:gpl2+)))
13197
13198 (define-public r-seqinr
13199 (package
13200 (name "r-seqinr")
13201 (version "3.6-1")
13202 (source
13203 (origin
13204 (method url-fetch)
13205 (uri (cran-uri "seqinr" version))
13206 (sha256
13207 (base32
13208 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
13209 (build-system r-build-system)
13210 (propagated-inputs
13211 `(("r-ade4" ,r-ade4)
13212 ("r-segmented" ,r-segmented)))
13213 (inputs
13214 `(("zlib" ,zlib)))
13215 (home-page "http://seqinr.r-forge.r-project.org/")
13216 (synopsis "Biological sequences retrieval and analysis")
13217 (description
13218 "This package provides tools for exploratory data analysis and data
13219 visualization of biological sequence (DNA and protein) data. It also includes
13220 utilities for sequence data management under the ACNUC system.")
13221 (license license:gpl2+)))
13222
13223 (define-public r-units
13224 (package
13225 (name "r-units")
13226 (version "0.6-6")
13227 (source
13228 (origin
13229 (method url-fetch)
13230 (uri (cran-uri "units" version))
13231 (sha256
13232 (base32
13233 "11x6xz1fbml28xmrhgn4sii9vfyj3gyfc1dfxahdg9cszdmcgdnh"))))
13234 (build-system r-build-system)
13235 (inputs
13236 `(("udunits" ,udunits)))
13237 (propagated-inputs
13238 `(("r-rcpp" ,r-rcpp)))
13239 (native-inputs
13240 `(("r-knitr" ,r-knitr)))
13241 (home-page "https://github.com/r-quantities/units/")
13242 (synopsis "Measurement Units for R Vectors")
13243 (description
13244 "This package provides support for measurement units in R vectors,
13245 matrices and arrays: automatic propagation, conversion, derivation and
13246 simplification of units; raising errors in case of unit incompatibility. It
13247 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13248 classes.")
13249 (license license:gpl2)))
13250
13251 (define-public r-classint
13252 (package
13253 (name "r-classint")
13254 (version "0.4-3")
13255 (source
13256 (origin
13257 (method url-fetch)
13258 (uri (cran-uri "classInt" version))
13259 (sha256
13260 (base32
13261 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
13262 (properties `((upstream-name . "classInt")))
13263 (build-system r-build-system)
13264 (propagated-inputs
13265 `(("r-class" ,r-class)
13266 ("r-e1071" ,r-e1071)
13267 ("r-kernsmooth" ,r-kernsmooth)))
13268 (native-inputs
13269 `(("gfortran" ,gfortran)
13270 ("r-knitr" ,r-knitr)))
13271 (home-page "https://github.com/r-spatial/classInt/")
13272 (synopsis "Choose univariate class intervals")
13273 (description
13274 "This package provides selected commonly used methods for choosing
13275 univariate class intervals for mapping or other graphics purposes.")
13276 (license license:gpl2+)))
13277
13278 (define-public r-spdata
13279 (package
13280 (name "r-spdata")
13281 (version "0.3.5")
13282 (source
13283 (origin
13284 (method url-fetch)
13285 (uri (cran-uri "spData" version))
13286 (sha256
13287 (base32
13288 "09l9j1vjbfyc8mikb8kliqmdjkg4xigq3zhdx98mv51flh5q87lh"))))
13289 (properties `((upstream-name . "spData")))
13290 (build-system r-build-system)
13291 (propagated-inputs
13292 `(("r-raster" ,r-raster)
13293 ("r-sp" ,r-sp)))
13294 (home-page "https://github.com/Nowosad/spData")
13295 (synopsis "Datasets for spatial analysis")
13296 (description
13297 "This a package containing diverse spatial datasets for demonstrating,
13298 benchmarking and teaching spatial data analysis. It includes R data of class
13299 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13300 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13301 of the datasets are designed to illustrate specific analysis techniques.
13302 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13303 illustrate point pattern analysis techniques.")
13304 (license license:cc0)))
13305
13306 (define-public r-learnbayes
13307 (package
13308 (name "r-learnbayes")
13309 (version "2.15.1")
13310 (source
13311 (origin
13312 (method url-fetch)
13313 (uri (cran-uri "LearnBayes" version))
13314 (sha256
13315 (base32
13316 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13317 (properties `((upstream-name . "LearnBayes")))
13318 (build-system r-build-system)
13319 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13320 (synopsis "Functions for learning Bayesian inference")
13321 (description
13322 "This package provides a collection of functions helpful in learning the
13323 basic tenets of Bayesian statistical inference. It contains functions for
13324 summarizing basic one and two parameter posterior distributions and predictive
13325 distributions. It contains MCMC algorithms for summarizing posterior
13326 distributions defined by the user. It also contains functions for regression
13327 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13328 sampling.")
13329 (license license:gpl2+)))
13330
13331 (define-public r-deldir
13332 (package
13333 (name "r-deldir")
13334 (version "0.1-25")
13335 (source
13336 (origin
13337 (method url-fetch)
13338 (uri (cran-uri "deldir" version))
13339 (sha256
13340 (base32
13341 "0kdglv8rc1pb4ilcid4xc9wpv5kkj2y6x6wg7919k3hya7mz58ph"))))
13342 (build-system r-build-system)
13343 (native-inputs `(("gfortran" ,gfortran)))
13344 (home-page "https://cran.r-project.org/web/packages/deldir")
13345 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13346 (description
13347 "This package provides tools for calculating the Delaunay triangulation
13348 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13349 of a planar point set. It plots triangulations and tessellations in various
13350 ways, clips tessellations to sub-windows, calculates perimeters of
13351 tessellations, and summarizes information about the tiles of the
13352 tessellation.")
13353 (license license:gpl2+)))
13354
13355 (define-public r-sf
13356 (package
13357 (name "r-sf")
13358 (version "0.9-2")
13359 (source
13360 (origin
13361 (method url-fetch)
13362 (uri (cran-uri "sf" version))
13363 (sha256
13364 (base32
13365 "01xplgy5nlwy3ajfch4h1ssa1xhm7q0jzscpz04dmvgqfzwhhdfh"))))
13366 (build-system r-build-system)
13367 (inputs
13368 `(("gdal" ,gdal)
13369 ("geos" ,geos)
13370 ("proj" ,proj.4)
13371 ("zlib" ,zlib)))
13372 (propagated-inputs
13373 `(("r-classint" ,r-classint)
13374 ("r-dbi" ,r-dbi)
13375 ("r-magrittr" ,r-magrittr)
13376 ("r-rcpp" ,r-rcpp)
13377 ("r-units" ,r-units)))
13378 (native-inputs
13379 `(("pkg-config" ,pkg-config)
13380 ("r-knitr" ,r-knitr)))
13381 (home-page "https://github.com/r-spatial/sf/")
13382 (synopsis "Simple features for R")
13383 (description
13384 "This package provides support for simple features, a standardized way to
13385 encode spatial vector data. It binds to GDAL for reading and writing data, to
13386 GEOS for geometrical operations, and to PROJ for projection conversions and
13387 datum transformations.")
13388 ;; Either of these licenses
13389 (license (list license:gpl2 license:expat))))
13390
13391 (define-public r-spdep
13392 (package
13393 (name "r-spdep")
13394 (version "1.1-3")
13395 (source
13396 (origin
13397 (method url-fetch)
13398 (uri (cran-uri "spdep" version))
13399 (sha256
13400 (base32
13401 "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk"))))
13402 (build-system r-build-system)
13403 (propagated-inputs
13404 `(("r-boot" ,r-boot)
13405 ("r-coda" ,r-coda)
13406 ("r-deldir" ,r-deldir)
13407 ("r-expm" ,r-expm)
13408 ("r-gmodels" ,r-gmodels)
13409 ("r-learnbayes" ,r-learnbayes)
13410 ("r-mass" ,r-mass)
13411 ("r-matrix" ,r-matrix)
13412 ("r-nlme" ,r-nlme)
13413 ("r-sf" ,r-sf)
13414 ("r-sp" ,r-sp)
13415 ("r-spdata" ,r-spdata)))
13416 (home-page "https://github.com/r-spatial/spdep/")
13417 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13418 (description
13419 "This package provides a collection of functions to create spatial
13420 weights matrix objects from polygon contiguities, from point patterns by
13421 distance and tessellations, for summarizing these objects, and for permitting
13422 their use in spatial data analysis, including regional aggregation by minimum
13423 spanning tree.")
13424 (license license:gpl2+)))
13425
13426 (define-public r-adegenet
13427 (package
13428 (name "r-adegenet")
13429 (version "2.1.2")
13430 (source
13431 (origin
13432 (method url-fetch)
13433 (uri (cran-uri "adegenet" version))
13434 (sha256
13435 (base32
13436 "01fgrgbiddz2q4l3mx637hhwbs7r0c43yw7vpwl8p8pwbm3nykz0"))))
13437 (build-system r-build-system)
13438 (propagated-inputs
13439 `(("r-ade4" ,r-ade4)
13440 ("r-ape" ,r-ape)
13441 ("r-boot" ,r-boot)
13442 ("r-dplyr" ,r-dplyr)
13443 ("r-ggplot2" ,r-ggplot2)
13444 ("r-igraph" ,r-igraph)
13445 ("r-mass" ,r-mass)
13446 ("r-reshape2" ,r-reshape2)
13447 ("r-seqinr" ,r-seqinr)
13448 ("r-shiny" ,r-shiny)
13449 ("r-spdep" ,r-spdep)
13450 ("r-vegan" ,r-vegan)))
13451 (home-page "https://github.com/thibautjombart/adegenet")
13452 (synopsis "Exploratory analysis of genetic and genomic data")
13453 (description
13454 "This package provides a toolset for the exploration of genetic and
13455 genomic data. Adegenet provides formal (S4) classes for storing and handling
13456 various genetic data, including genetic markers with varying ploidy and
13457 hierarchical population structure (@code{genind} class), alleles counts by
13458 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13459 also implements original multivariate methods (DAPC, sPCA), graphics,
13460 statistical tests, simulation tools, distance and similarity measures, and
13461 several spatial methods. A range of both empirical and simulated datasets is
13462 also provided to illustrate various methods.")
13463 (license license:gpl2+)))
13464
13465 (define-public r-pegas
13466 (package
13467 (name "r-pegas")
13468 (version "0.13")
13469 (source
13470 (origin
13471 (method url-fetch)
13472 (uri (cran-uri "pegas" version))
13473 (sha256
13474 (base32 "002i7s4g0nhnq0v05gs0yssqiyhpq2f7rw2rhn31hsbgxc86frvy"))))
13475 (build-system r-build-system)
13476 (propagated-inputs
13477 `(("r-adegenet" ,r-adegenet)
13478 ("r-ape" ,r-ape)))
13479 (home-page "http://ape-package.ird.fr/pegas.html")
13480 (synopsis "Population and evolutionary genetics analysis system")
13481 (description
13482 "This package provides functions for reading, writing, plotting,
13483 analysing, and manipulating allelic and haplotypic data, including from VCF
13484 files, and for the analysis of population nucleotide sequences and
13485 micro-satellites including coalescent analyses, linkage disequilibrium,
13486 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13487 minimum spanning tree and network, and median-joining networks.")
13488 (license license:gpl2+)))
13489
13490 (define-public r-rmetasim
13491 (package
13492 (name "r-rmetasim")
13493 (version "3.1.14")
13494 (source
13495 (origin
13496 (method url-fetch)
13497 (uri (cran-uri "rmetasim" version))
13498 (sha256
13499 (base32
13500 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
13501 (build-system r-build-system)
13502 (propagated-inputs
13503 `(("r-ade4" ,r-ade4)
13504 ("r-adegenet" ,r-adegenet)
13505 ("r-gtools" ,r-gtools)
13506 ("r-pegas" ,r-pegas)))
13507 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13508 (synopsis "Individual-based population genetic simulation environment")
13509 (description
13510 "This package provides an interface between R and the metasim simulation
13511 engine. The simulation environment is documented in: Strand, A.(2002),
13512 Metasim 1.0: an individual-based environment for simulating population
13513 genetics of complex population dynamics.")
13514 ;; Any GPL version
13515 (license license:gpl2+)))
13516
13517 (define-public r-genetics
13518 (package
13519 (name "r-genetics")
13520 (version "1.3.8.1.2")
13521 (source
13522 (origin
13523 (method url-fetch)
13524 (uri (cran-uri "genetics" version))
13525 (sha256
13526 (base32
13527 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13528 (build-system r-build-system)
13529 (propagated-inputs
13530 `(("r-combinat" ,r-combinat)
13531 ("r-gdata" ,r-gdata)
13532 ("r-gtools" ,r-gtools)
13533 ("r-mass" ,r-mass)
13534 ("r-mvtnorm" ,r-mvtnorm)))
13535 (home-page "https://cran.r-project.org/web/packages/genetics/")
13536 (synopsis "Population genetics")
13537 (description
13538 "This package provides classes and methods for handling genetic data.
13539 It includes classes to represent genotypes and haplotypes at single markers up
13540 to multiple markers on multiple chromosomes. Function include allele
13541 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13542 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13543 and testing for linkage disequilibrium, ...")
13544 ;; Any GPL version.
13545 (license license:gpl2+)))
13546
13547 (define-public r-snp-plotter
13548 (package
13549 (name "r-snp-plotter")
13550 (version "0.5.1")
13551 (source
13552 (origin
13553 (method url-fetch)
13554 (uri (cran-uri "snp.plotter" version))
13555 (sha256
13556 (base32
13557 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13558 (properties `((upstream-name . "snp.plotter")))
13559 (build-system r-build-system)
13560 (propagated-inputs `(("r-genetics" ,r-genetics)))
13561 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13562 (synopsis "Plot p-values using single SNP and/or haplotype data")
13563 (description
13564 "This package helps you create plots of p-values using single SNP and/or
13565 haplotype data. Main features of the package include options to display a
13566 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13567 datasets simultaneously. Plots can be created using global and/or individual
13568 haplotype p-values along with single SNP p-values. Images are created as
13569 either PDF/EPS files.")
13570 (license license:gpl2+)))
13571
13572 (define-public r-polspline
13573 (package
13574 (name "r-polspline")
13575 (version "1.1.17")
13576 (source
13577 (origin
13578 (method url-fetch)
13579 (uri (cran-uri "polspline" version))
13580 (sha256
13581 (base32 "0c7fnxpqpy3hibiim4yib6l6bq363s97wwvllxp4lp8h06fjcyyn"))))
13582 (build-system r-build-system)
13583 (native-inputs `(("gfortran" ,gfortran)))
13584 (home-page "https://cran.r-project.org/web/packages/polspline/")
13585 (synopsis "Polynomial spline routines")
13586 (description
13587 "This package provides routines for the polynomial spline fitting
13588 routines hazard regression, hazard estimation with flexible tails, logspline,
13589 lspec, polyclass, and polymars.")
13590 (license license:gpl2+)))
13591
13592 (define-public r-rms
13593 (package
13594 (name "r-rms")
13595 (version "5.1-4")
13596 (source
13597 (origin
13598 (method url-fetch)
13599 (uri (cran-uri "rms" version))
13600 (sha256
13601 (base32 "19knh1sw0icw6jh9wfb2hq5jf49i2qfvp9myvqm5paa495689x9q"))))
13602 (build-system r-build-system)
13603 (propagated-inputs
13604 `(("r-ggplot2" ,r-ggplot2)
13605 ("r-hmisc" ,r-hmisc)
13606 ("r-htmltable" ,r-htmltable)
13607 ("r-htmltools" ,r-htmltools)
13608 ("r-lattice" ,r-lattice)
13609 ("r-multcomp" ,r-multcomp)
13610 ("r-nlme" ,r-nlme)
13611 ("r-polspline" ,r-polspline)
13612 ("r-quantreg" ,r-quantreg)
13613 ("r-rpart" ,r-rpart)
13614 ("r-sparsem" ,r-sparsem)
13615 ("r-survival" ,r-survival)))
13616 (native-inputs `(("gfortran" ,gfortran)))
13617 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13618 (synopsis "Regression modeling strategies")
13619 (description
13620 "This is a package for regression modeling, testing, estimation,
13621 validation, graphics, prediction, and typesetting by storing enhanced model
13622 design attributes in the fit. The rms package is a collection of functions
13623 that assist with and streamline modeling. It also contains functions for
13624 binary and ordinal logistic regression models, ordinal models for continuous Y
13625 with a variety of distribution families, and the Buckley-James multiple
13626 regression model for right-censored responses, and implements penalized
13627 maximum likelihood estimation for logistic and ordinary linear models. The
13628 package works with almost any regression model, but it was especially written
13629 to work with binary or ordinal regression models, Cox regression, accelerated
13630 failure time models, ordinary linear models, the Buckley-James model,
13631 generalized least squares for serially or spatially correlated observations,
13632 generalized linear models, and quantile regression.")
13633 (license license:gpl2+)))
13634
13635 (define-public r-haplo-stats
13636 (package
13637 (name "r-haplo-stats")
13638 (version "1.7.9")
13639 (source
13640 (origin
13641 (method url-fetch)
13642 (uri (cran-uri "haplo.stats" version))
13643 (sha256
13644 (base32
13645 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
13646 (properties `((upstream-name . "haplo.stats")))
13647 (build-system r-build-system)
13648 (propagated-inputs
13649 `(("r-rms" ,r-rms)))
13650 (native-inputs
13651 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
13652 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
13653 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
13654 (description
13655 "This package provides routines for the analysis of indirectly measured
13656 haplotypes. The statistical methods assume that all subjects are unrelated
13657 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
13658 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
13659 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
13660 examples in the vignette.")
13661 (license license:gpl2+)))
13662
13663 (define-public r-bqtl
13664 (package
13665 (name "r-bqtl")
13666 (version "1.0-32")
13667 (source
13668 (origin
13669 (method url-fetch)
13670 (uri (cran-uri "bqtl" version))
13671 (sha256
13672 (base32
13673 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
13674 (build-system r-build-system)
13675 (native-inputs `(("gfortran" ,gfortran)))
13676 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
13677 (synopsis "Bayesian QTL mapping toolkit")
13678 (description
13679 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
13680 lines. It includes maximum likelihood and Bayesian tools.")
13681 (license license:gpl2+)))
13682
13683 (define-public r-ibdreg
13684 (package
13685 (name "r-ibdreg")
13686 (version "0.2.5")
13687 (source
13688 (origin
13689 (method url-fetch)
13690 (uri (cran-uri "ibdreg" version))
13691 (sha256
13692 (base32
13693 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
13694 (build-system r-build-system)
13695 (home-page "https://www.mayo.edu/research/labs/\
13696 statistical-genetics-genetic-epidemiology/software")
13697 (synopsis "Regression methods for IBD linkage with covariates")
13698 (description
13699 "This package provides a method to test genetic linkage with covariates
13700 by regression methods with response IBD sharing for relative pairs. Account
13701 for correlations of IBD statistics and covariates for relative pairs within
13702 the same pedigree.")
13703 (license license:gpl2+)))
13704
13705 (define-public r-dlmap
13706 (package
13707 (name "r-dlmap")
13708 (version "1.13")
13709 (source
13710 (origin
13711 (method url-fetch)
13712 (uri (cran-uri "dlmap" version))
13713 (sha256
13714 (base32
13715 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
13716 (build-system r-build-system)
13717 (propagated-inputs
13718 `(("r-ibdreg" ,r-ibdreg)
13719 ("r-mgcv" ,r-mgcv)
13720 ("r-nlme" ,r-nlme)
13721 ("r-qtl" ,r-qtl)
13722 ("r-wgaim" ,r-wgaim)))
13723 (home-page "https://cran.r-project.org/web/packages/dlmap/")
13724 (synopsis "Detection localization mapping for QTL")
13725 (description
13726 "This is package for QTL mapping in a mixed model framework with separate
13727 detection and localization stages. The first stage detects the number of QTL
13728 on each chromosome based on the genetic variation due to grouped markers on
13729 the chromosome; the second stage uses this information to determine the most
13730 likely QTL positions. The mixed model can accommodate general fixed and
13731 random effects, including spatial effects in field trials and pedigree
13732 effects. It is applicable to backcrosses, doubled haploids, recombinant
13733 inbred lines, F2 intercrosses, and association mapping populations.")
13734 (license license:gpl2)))
13735
13736 (define-public r-ldheatmap
13737 (package
13738 (name "r-ldheatmap")
13739 (version "0.99-7")
13740 (source
13741 (origin
13742 (method url-fetch)
13743 (uri (cran-uri "LDheatmap" version))
13744 (sha256
13745 (base32
13746 "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
13747 (properties `((upstream-name . "LDheatmap")))
13748 (build-system r-build-system)
13749 (propagated-inputs
13750 `(("r-genetics" ,r-genetics)
13751 ("r-rcpp" ,r-rcpp)
13752 ("r-snpstats" ,r-snpstats)))
13753 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
13754 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
13755 (description
13756 "This package provides tools to produce a graphical display, as a heat
13757 map, of measures of pairwise linkage disequilibria between SNPs. Users may
13758 optionally include the physical locations or genetic map distances of each SNP
13759 on the plot.")
13760 (license license:gpl3)))
13761
13762 (define-public r-hwde
13763 (package
13764 (name "r-hwde")
13765 (version "0.67")
13766 (source
13767 (origin
13768 (method url-fetch)
13769 (uri (cran-uri "hwde" version))
13770 (sha256
13771 (base32
13772 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
13773 (build-system r-build-system)
13774 (home-page "https://cran.r-project.org/web/packages/hwde/")
13775 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
13776 (description
13777 "This package fits models for genotypic disequilibria, as described in
13778 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
13779 terms are available that account for first order interactions between loci.
13780 It also implements, for a single locus in a single population, a conditional
13781 exact test for Hardy-Weinberg equilibrium.")
13782 (license license:gpl2+)))
13783
13784 (define-public r-tdthap
13785 (package
13786 (name "r-tdthap")
13787 (version "1.1-11")
13788 (source
13789 (origin
13790 (method url-fetch)
13791 (uri (cran-uri "tdthap" version))
13792 (sha256
13793 (base32
13794 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
13795 (build-system r-build-system)
13796 (home-page "https://cran.r-project.org/web/packages/tdthap/")
13797 (synopsis "TDT tests for extended haplotypes")
13798 (description
13799 "Functions and examples are provided for transmission/disequilibrium
13800 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
13801 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
13802 (license license:artistic2.0)))
13803
13804 (define-public r-sparql
13805 (package
13806 (name "r-sparql")
13807 (version "1.16")
13808 (source (origin
13809 (method url-fetch)
13810 (uri (cran-uri "SPARQL" version))
13811 (sha256
13812 (base32
13813 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
13814 (properties `((upstream-name . "SPARQL")))
13815 (build-system r-build-system)
13816 (propagated-inputs
13817 `(("r-rcurl" ,r-rcurl)
13818 ("r-xml" ,r-xml)))
13819 (home-page "https://cran.r-project.org/web/packages/SPARQL")
13820 (synopsis "SPARQL client for R")
13821 (description "This package provides an interface to use SPARQL to pose
13822 SELECT or UPDATE queries to an end-point.")
13823 ;; The only license indication is found in the DESCRIPTION file,
13824 ;; which states GPL-3. So we cannot assume GPLv3+.
13825 (license license:gpl3)))
13826
13827 (define-public r-bookdown
13828 (package
13829 (name "r-bookdown")
13830 (version "0.18")
13831 (source (origin
13832 (method url-fetch)
13833 (uri (cran-uri "bookdown" version))
13834 (sha256
13835 (base32
13836 "1my6g16phx21v5cvfqcnjibh3zcv02xkix347aafd6a7r3hnxpq5"))))
13837 (build-system r-build-system)
13838 (propagated-inputs
13839 `(("r-htmltools" ,r-htmltools)
13840 ("r-knitr" ,r-knitr)
13841 ("r-rmarkdown" ,r-rmarkdown)
13842 ("r-tinytex" ,r-tinytex)
13843 ("r-xfun" ,r-xfun)
13844 ("pandoc" ,ghc-pandoc)))
13845 (home-page "https://github.com/rstudio/bookdown")
13846 (synopsis "Authoring books and technical documents with R markdown")
13847 (description "This package provides output formats and utilities for
13848 authoring books and technical documents with R Markdown.")
13849 (license license:gpl3)))
13850
13851 (define-public r-optparse
13852 (package
13853 (name "r-optparse")
13854 (version "1.6.6")
13855 (source
13856 (origin
13857 (method url-fetch)
13858 (uri (cran-uri "optparse" version))
13859 (sha256
13860 (base32
13861 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
13862 (build-system r-build-system)
13863 (propagated-inputs
13864 `(("r-getopt" ,r-getopt)))
13865 (native-inputs
13866 `(("r-knitr" ,r-knitr)))
13867 (home-page "https://github.com/trevorld/optparse")
13868 (synopsis "Command line option parser")
13869 (description
13870 "This package provides a command line parser inspired by Python's
13871 @code{optparse} library to be used with Rscript to write shebang scripts
13872 that accept short and long options.")
13873 (license license:gpl2+)))
13874
13875 (define-public r-wgcna
13876 (package
13877 (name "r-wgcna")
13878 (version "1.69")
13879 (source
13880 (origin
13881 (method url-fetch)
13882 (uri (cran-uri "WGCNA" version))
13883 (sha256
13884 (base32
13885 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
13886 (properties `((upstream-name . "WGCNA")))
13887 (build-system r-build-system)
13888 (propagated-inputs
13889 `(("r-annotationdbi" ,r-annotationdbi)
13890 ("r-doparallel" ,r-doparallel)
13891 ("r-dynamictreecut" ,r-dynamictreecut)
13892 ("r-fastcluster" ,r-fastcluster)
13893 ("r-foreach" ,r-foreach)
13894 ("r-go-db" ,r-go-db)
13895 ("r-hmisc" ,r-hmisc)
13896 ("r-impute" ,r-impute)
13897 ("r-rcpp" ,r-rcpp)
13898 ("r-survival" ,r-survival)
13899 ("r-matrixstats" ,r-matrixstats)
13900 ("r-preprocesscore" ,r-preprocesscore)))
13901 (home-page
13902 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
13903 (synopsis "Weighted correlation network analysis")
13904 (description
13905 "This package provides functions necessary to perform Weighted
13906 Correlation Network Analysis on high-dimensional data. It includes functions
13907 for rudimentary data cleaning, construction and summarization of correlation
13908 networks, module identification and functions for relating both variables and
13909 modules to sample traits. It also includes a number of utility functions for
13910 data manipulation and visualization.")
13911 (license license:gpl2+)))
13912
13913 (define-public r-kernlab
13914 (package
13915 (name "r-kernlab")
13916 (version "0.9-29")
13917 (source
13918 (origin
13919 (method url-fetch)
13920 (uri (cran-uri "kernlab" version))
13921 (sha256
13922 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
13923 (build-system r-build-system)
13924 (home-page "https://cran.r-project.org/web/packages/kernlab")
13925 (synopsis "Kernel-based machine learning tools")
13926 (description
13927 "This package provides kernel-based machine learning methods for
13928 classification, regression, clustering, novelty detection, quantile regression
13929 and dimensionality reduction. Among other methods @code{kernlab} includes
13930 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
13931 and a QP solver.")
13932 (license license:gpl2)))
13933
13934 (define-public r-hierfstat
13935 (package
13936 (name "r-hierfstat")
13937 (version "0.04-22")
13938 (source
13939 (origin
13940 (method url-fetch)
13941 (uri (cran-uri "hierfstat" version))
13942 (sha256
13943 (base32
13944 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
13945 (build-system r-build-system)
13946 (propagated-inputs
13947 `(("r-ade4" ,r-ade4)
13948 ("r-adegenet" ,r-adegenet)
13949 ("r-gtools" ,r-gtools)))
13950 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
13951 (synopsis "Estimation and tests of hierarchical F-statistics")
13952 (description
13953 "This package allows the estimation of hierarchical F-statistics from
13954 haploid or diploid genetic data with any numbers of levels in the hierarchy,
13955 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
13956 are also given to test via randomisations the significance of each F and
13957 variance components, using the likelihood-ratio statistics G.")
13958 (license license:gpl2+)))
13959
13960 (define-public r-hapassoc
13961 (package
13962 (name "r-hapassoc")
13963 (version "1.2-8")
13964 (source
13965 (origin
13966 (method url-fetch)
13967 (uri (cran-uri "hapassoc" version))
13968 (sha256
13969 (base32
13970 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
13971 (build-system r-build-system)
13972 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
13973 (synopsis "Inference of trait associations with SNP haplotypes")
13974 (description
13975 "Hapassoc performs likelihood inference of trait associations with
13976 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
13977 functions are developed primarily for data collected in cohort or
13978 cross-sectional studies. They can accommodate uncertain haplotype phase and
13979 handle missing genotypes at some SNPs.")
13980 (license license:gpl2)))
13981
13982 (define-public r-sampling
13983 (package
13984 (name "r-sampling")
13985 (version "2.8")
13986 (source
13987 (origin
13988 (method url-fetch)
13989 (uri (cran-uri "sampling" version))
13990 (sha256
13991 (base32
13992 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
13993 (build-system r-build-system)
13994 (propagated-inputs
13995 `(("r-lpsolve" ,r-lpsolve)
13996 ("r-mass" ,r-mass)))
13997 (home-page "https://cran.r-project.org/web/packages/sampling/")
13998 (synopsis "Survey sampling")
13999 (description
14000 "This package provides functions for drawing and calibrating samples.")
14001 (license license:gpl2+)))
14002
14003 (define-public r-r2html
14004 (package
14005 (name "r-r2html")
14006 (version "2.3.2")
14007 (source
14008 (origin
14009 (method url-fetch)
14010 (uri (cran-uri "R2HTML" version))
14011 (sha256
14012 (base32
14013 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
14014 (properties `((upstream-name . "R2HTML")))
14015 (build-system r-build-system)
14016 (home-page "https://github.com/nalimilan/R2HTML")
14017 (synopsis "HTML export for R objects")
14018 (description
14019 "This package includes HTML functions and methods to write in an HTML
14020 file. Thus, making HTML reports is easy. It includes a function that allows
14021 redirection on the fly, which appears to be very useful for teaching purposes,
14022 as the student can keep a copy of the produced output to keep all that they
14023 did during the course. The package comes with a vignette describing how to
14024 write HTML reports for statistical analysis. Finally, a driver for Sweave
14025 parses HTML flat files containing R code and to automatically write
14026 the corresponding outputs (tables and graphs).")
14027 (license license:gpl2+)))
14028
14029 (define-public r-rjava
14030 (package
14031 (name "r-rjava")
14032 (version "0.9-12")
14033 (source
14034 (origin
14035 (method url-fetch)
14036 (uri (cran-uri "rJava" version))
14037 (sha256
14038 (base32
14039 "03vv0pj6san03c51iyqsyb1rwh3097dfpl2s8iswzzmc7k3shj12"))))
14040 (properties `((upstream-name . "rJava")))
14041 (build-system r-build-system)
14042 (arguments
14043 `(#:modules ((guix build utils)
14044 (guix build r-build-system)
14045 (ice-9 match))
14046 #:phases
14047 (modify-phases %standard-phases
14048 (add-after 'unpack 'set-JAVA_HOME
14049 (lambda* (#:key inputs #:allow-other-keys)
14050 (let ((jdk (assoc-ref inputs "jdk")))
14051 (setenv "JAVA_HOME" jdk)
14052 (setenv "JAVA" (which "java"))
14053 (setenv "JAR" (which "jar"))
14054 (setenv "JAVAC" (which "javac"))
14055 (setenv "JAVAH" (which "javah"))
14056 (setenv "JAVA_CPPFLAGS"
14057 (string-append "-I" jdk "/include "
14058 "-I" jdk "/include/linux"))
14059 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
14060 ((lib) (setenv "JAVA_LIBS" lib))
14061 (_ (error "Could not find libjvm.so"))))
14062 #t)))))
14063 (inputs
14064 `(("icu4c" ,icu4c)
14065 ("jdk" ,icedtea-8 "jdk")
14066 ("pcre" ,pcre)
14067 ("zlib" ,zlib)))
14068 (home-page "https://www.rforge.net/rJava/")
14069 (synopsis "Low-Level R to Java interface")
14070 (description
14071 "This package provides a low-level interface to the Java VM very much
14072 like .C/.Call and friends. It allows the creation of objects, calling methods
14073 and accessing fields.")
14074 (license license:gpl2)))
14075
14076 (define-public r-svmisc
14077 (package
14078 (name "r-svmisc")
14079 (version "1.1.0")
14080 (source
14081 (origin
14082 (method url-fetch)
14083 (uri (cran-uri "svMisc" version))
14084 (sha256
14085 (base32
14086 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
14087 (properties `((upstream-name . "svMisc")))
14088 (build-system r-build-system)
14089 (home-page "https://github.com/SciViews/svMisc")
14090 (synopsis "Miscellaneous functions for SciViews")
14091 (description
14092 "This package provides miscellaneous functions for SciViews or general
14093 use, including tools to manage a temporary environment attached to the search
14094 path for temporary variables you do not want to @code{save()} or
14095 @code{load()}; test the current platform; showing progress bars, etc.")
14096 (license license:gpl2)))
14097
14098 (define-public r-xyz
14099 (package
14100 (name "r-xyz")
14101 (version "0.2")
14102 (source
14103 (origin
14104 (method url-fetch)
14105 (uri (cran-uri "xyz" version))
14106 (sha256
14107 (base32
14108 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
14109 (build-system r-build-system)
14110 (propagated-inputs
14111 `(("r-rcpp" ,r-rcpp)))
14112 (home-page "https://cran.r-project.org/web/packages/xyz/")
14113 (synopsis "Algorithm for fast interaction search in high-dimensional data")
14114 (description
14115 "High dimensional interaction search by brute force requires a quadratic
14116 computational cost in the number of variables. The xyz algorithm provably
14117 finds strong interactions in almost linear time. For details of the algorithm
14118 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
14119 interaction search in high-dimensional data.")
14120 ;; Any version of the GPL.
14121 (license license:gpl2+)))
14122
14123 (define-public r-rttf2pt1
14124 (package
14125 (name "r-rttf2pt1")
14126 (version "1.3.8")
14127 (source
14128 (origin
14129 (method url-fetch)
14130 (uri (cran-uri "Rttf2pt1" version))
14131 (sha256
14132 (base32
14133 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
14134 (properties `((upstream-name . "Rttf2pt1")))
14135 (build-system r-build-system)
14136 (home-page "https://github.com/wch/Rttf2pt1")
14137 (synopsis "Font conversion utility")
14138 (description
14139 "This package contains the program @code{ttf2pt1}, for use with the
14140 @code{extrafont} package.")
14141 ;; Most of the files are covered under the Expat license. Some files are
14142 ;; covered under BSD-3. Deviations for individual files are recorded in
14143 ;; the LICENSE file.
14144 (license (list license:bsd-3 license:expat
14145 (license:non-copyleft "file://LICENSE")))))
14146
14147 (define-public r-extrafontdb
14148 (package
14149 (name "r-extrafontdb")
14150 (version "1.0")
14151 (source
14152 (origin
14153 (method url-fetch)
14154 (uri (cran-uri "extrafontdb" version))
14155 (sha256
14156 (base32
14157 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
14158 (build-system r-build-system)
14159 (home-page "https://github.com/wch/extrafontdb")
14160 (synopsis "Database for the extrafont package")
14161 (description
14162 "This package holds the database for the @code{extrafont} package.")
14163 (license license:gpl2)))
14164
14165 (define-public r-extrafont
14166 (package
14167 (name "r-extrafont")
14168 (version "0.17")
14169 (source
14170 (origin
14171 (method url-fetch)
14172 (uri (cran-uri "extrafont" version))
14173 (sha256
14174 (base32
14175 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
14176 (build-system r-build-system)
14177 (propagated-inputs
14178 `(("r-extrafontdb" ,r-extrafontdb)
14179 ("r-rttf2pt1" ,r-rttf2pt1)))
14180 (home-page "https://github.com/wch/extrafont")
14181 (synopsis "Tools for using fonts in R")
14182 (description
14183 "The extrafont package makes it easier to use fonts other than the basic
14184 PostScript fonts that R uses. Fonts that are imported into extrafont can be
14185 used with PDF or PostScript output files. There are two hurdles for using
14186 fonts in PDF (or Postscript) output files:
14187
14188 @enumerate
14189 @item Making R aware of the font and the dimensions of the characters.
14190 @item Embedding the fonts in the PDF file so that the PDF can be displayed
14191 properly on a device that doesn't have the font. This is usually needed if
14192 you want to print the PDF file or share it with others.
14193 @end enumerate
14194
14195 The extrafont package makes both of these things easier.")
14196 (license license:gpl2)))
14197
14198 (define-public r-xkcd
14199 (package
14200 (name "r-xkcd")
14201 (version "0.0.6")
14202 (source
14203 (origin
14204 (method url-fetch)
14205 (uri (cran-uri "xkcd" version))
14206 (sha256
14207 (base32
14208 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
14209 (build-system r-build-system)
14210 (propagated-inputs
14211 `(("r-extrafont" ,r-extrafont)
14212 ("r-ggplot2" ,r-ggplot2)
14213 ("r-hmisc" ,r-hmisc)))
14214 (home-page "https://cran.r-project.org/web/packages/xkcd/")
14215 (synopsis "Plot ggplot2 graphics in the XKCD style")
14216 (description
14217 "This package provides the means to plot ggplot2 graphs in the style of
14218 the XKCD web comic.")
14219 (license license:gpl3)))
14220
14221 (define-public r-msigdbr
14222 (package
14223 (name "r-msigdbr")
14224 (version "7.0.1")
14225 (source
14226 (origin
14227 (method url-fetch)
14228 (uri (cran-uri "msigdbr" version))
14229 (sha256
14230 (base32
14231 "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd"))))
14232 (build-system r-build-system)
14233 (propagated-inputs
14234 `(("r-dplyr" ,r-dplyr)
14235 ("r-magrittr" ,r-magrittr)
14236 ("r-rlang" ,r-rlang)
14237 ("r-tibble" ,r-tibble)))
14238 (home-page "https://github.com/igordot/msigdbr")
14239 (synopsis "MSigDB gene sets for multiple organisms")
14240 (description
14241 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14242 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14243 software in a standard R data frame with key-value pairs. Included are the
14244 original human gene symbols and Entrez IDs as well as the equivalents for
14245 various frequently studied model organisms such as mouse, rat, pig, fly, and
14246 yeast.")
14247 ;; The package is covered under the Expat license, but the upstream MSigDB
14248 ;; files are made available under the Creative Commons Attribution 4.0
14249 ;; International license.
14250 (license (list license:expat license:cc-by4.0))))
14251
14252 (define-public r-gridgraphics
14253 (package
14254 (name "r-gridgraphics")
14255 (version "0.5-0")
14256 (source
14257 (origin
14258 (method url-fetch)
14259 (uri (cran-uri "gridGraphics" version))
14260 (sha256
14261 (base32
14262 "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r"))))
14263 (properties `((upstream-name . "gridGraphics")))
14264 (build-system r-build-system)
14265 (home-page "https://github.com/pmur002/gridgraphics")
14266 (synopsis "Redraw base graphics using @code{grid} graphics")
14267 (description
14268 "This package provides functions to convert a page of plots drawn with
14269 the @code{graphics} package into identical output drawn with the @code{grid}
14270 package. The result looks like the original @code{graphics}-based plot, but
14271 consists of @code{grid} grobs and viewports that can then be manipulated with
14272 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14273 (license license:gpl2+)))
14274
14275 (define-public r-farver
14276 (package
14277 (name "r-farver")
14278 (version "2.0.3")
14279 (source
14280 (origin
14281 (method url-fetch)
14282 (uri (cran-uri "farver" version))
14283 (sha256
14284 (base32
14285 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
14286 (build-system r-build-system)
14287 (home-page "https://github.com/thomasp85/farver")
14288 (synopsis "Vectorized color conversion and comparison")
14289 (description
14290 "The encoding of color can be handled in many different ways, using
14291 different color spaces. As different color spaces have different uses,
14292 efficient conversion between these representations are important. This
14293 package provides a set of functions that gives access to very fast color space
14294 conversion and comparisons implemented in C++, and offers 100-fold speed
14295 improvements over the @code{convertColor} function in the @code{grDevices}
14296 package.")
14297 (license license:expat)))
14298
14299 (define-public r-ggplotify
14300 (package
14301 (name "r-ggplotify")
14302 (version "0.0.5")
14303 (source
14304 (origin
14305 (method url-fetch)
14306 (uri (cran-uri "ggplotify" version))
14307 (sha256
14308 (base32
14309 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
14310 (build-system r-build-system)
14311 (propagated-inputs
14312 `(("r-ggplot2" ,r-ggplot2)
14313 ("r-gridgraphics" ,r-gridgraphics)
14314 ("r-rvcheck" ,r-rvcheck)))
14315 (native-inputs
14316 `(("r-knitr" ,r-knitr)))
14317 (home-page "https://github.com/GuangchuangYu/ggplotify")
14318 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14319 (description
14320 "This package provides tools to convert plot function calls (using
14321 expression or formula) to @code{grob} or @code{ggplot} objects that are
14322 compatible with the @code{grid} and @code{ggplot2} environment. With this
14323 package, we are able to e.g. use @code{cowplot} to align plots produced by
14324 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14325 converting them to @code{ggplot} objects.")
14326 (license license:artistic2.0)))
14327
14328 (define-public r-triebeard
14329 (package
14330 (name "r-triebeard")
14331 (version "0.3.0")
14332 (source
14333 (origin
14334 (method url-fetch)
14335 (uri (cran-uri "triebeard" version))
14336 (sha256
14337 (base32
14338 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14339 (build-system r-build-system)
14340 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14341 (home-page "https://github.com/Ironholds/triebeard/")
14342 (synopsis "Radix trees in Rcpp")
14343 (description
14344 "Radix trees, or tries, are key-value data structures optimized for
14345 efficient lookups, similar in purpose to hash tables. This package provides
14346 an implementation of radix trees for use in R programming and in developing
14347 packages with Rcpp.")
14348 (license license:expat)))
14349
14350 (define-public r-tweenr
14351 (package
14352 (name "r-tweenr")
14353 (version "1.0.1")
14354 (source
14355 (origin
14356 (method url-fetch)
14357 (uri (cran-uri "tweenr" version))
14358 (sha256
14359 (base32
14360 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14361 (build-system r-build-system)
14362 (propagated-inputs
14363 `(("r-farver" ,r-farver)
14364 ("r-magrittr" ,r-magrittr)
14365 ("r-rcpp" ,r-rcpp)
14366 ("r-rlang" ,r-rlang)))
14367 (home-page "https://github.com/thomasp85/tweenr")
14368 (synopsis "Interpolate data for smooth animations")
14369 (description
14370 "In order to create smooth animation between states of data, tweening is
14371 necessary. This package provides a range of functions for creating tweened
14372 data that can be used as basis for animation. Furthermore it adds a number of
14373 vectorized interpolaters for common R data types such as numeric, date and
14374 color.")
14375 (license license:expat)))
14376
14377 (define-public r-polyclip
14378 (package
14379 (name "r-polyclip")
14380 (version "1.10-0")
14381 (source
14382 (origin
14383 (method url-fetch)
14384 (uri (cran-uri "polyclip" version))
14385 (sha256
14386 (base32
14387 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14388 (build-system r-build-system)
14389 (native-inputs `(("pkg-config" ,pkg-config)))
14390 (home-page "http://www.angusj.com/delphi/clipper.php")
14391 (synopsis "Polygon clipping")
14392 (description
14393 "This package provides an R port of the library Clipper. It performs
14394 polygon clipping operations (intersection, union, set minus, set difference)
14395 for polygonal regions of arbitrary complexity, including holes. It computes
14396 offset polygons (spatial buffer zones, morphological dilations, Minkowski
14397 dilations) for polygonal regions and polygonal lines. It computes the
14398 Minkowski Sum of general polygons. There is a function for removing
14399 self-intersections from polygon data.")
14400 (license license:boost1.0)))
14401
14402 (define-public r-urltools
14403 (package
14404 (name "r-urltools")
14405 (version "1.7.3")
14406 (source
14407 (origin
14408 (method url-fetch)
14409 (uri (cran-uri "urltools" version))
14410 (sha256
14411 (base32
14412 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14413 (build-system r-build-system)
14414 (propagated-inputs
14415 `(("r-rcpp" ,r-rcpp)
14416 ("r-triebeard" ,r-triebeard)))
14417 (home-page "https://github.com/Ironholds/urltools/")
14418 (synopsis "Vectorized tools for URL handling and parsing")
14419 (description
14420 "This package provides a toolkit for all URL-handling needs, including
14421 encoding and decoding, parsing, parameter extraction and modification. All
14422 functions are designed to be both fast and entirely vectorized. It is
14423 intended to be useful for people dealing with web-related datasets, such as
14424 server-side logs, although may be useful for other situations involving large
14425 sets of URLs.")
14426 (license license:expat)))
14427
14428 (define-public r-ggforce
14429 (package
14430 (name "r-ggforce")
14431 (version "0.3.1")
14432 (source
14433 (origin
14434 (method url-fetch)
14435 (uri (cran-uri "ggforce" version))
14436 (sha256
14437 (base32
14438 "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
14439 (build-system r-build-system)
14440 (propagated-inputs
14441 `(("r-ggplot2" ,r-ggplot2)
14442 ("r-gtable" ,r-gtable)
14443 ("r-mass" ,r-mass)
14444 ("r-polyclip" ,r-polyclip)
14445 ("r-rcpp" ,r-rcpp)
14446 ("r-rcppeigen" ,r-rcppeigen)
14447 ("r-rlang" ,r-rlang)
14448 ("r-scales" ,r-scales)
14449 ("r-tidyselect" ,r-tidyselect)
14450 ("r-tweenr" ,r-tweenr)
14451 ("r-withr" ,r-withr)))
14452 (home-page "https://ggforce.data-imaginist.com")
14453 (synopsis "Accelerating ggplot2")
14454 (description
14455 "The aim of the ggplot2 package is to aid in visual data investigations.
14456 This focus has led to a lack of facilities for composing specialized plots.
14457 Thi package aims to be a collection of mainly new statistics and geometries
14458 that fills this gap.")
14459 (license license:expat)))
14460
14461 (define-public r-europepmc
14462 (package
14463 (name "r-europepmc")
14464 (version "0.3")
14465 (source
14466 (origin
14467 (method url-fetch)
14468 (uri (cran-uri "europepmc" version))
14469 (sha256
14470 (base32
14471 "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h"))))
14472 (build-system r-build-system)
14473 (propagated-inputs
14474 `(("r-dplyr" ,r-dplyr)
14475 ("r-httr" ,r-httr)
14476 ("r-jsonlite" ,r-jsonlite)
14477 ("r-plyr" ,r-plyr)
14478 ("r-progress" ,r-progress)
14479 ("r-purrr" ,r-purrr)
14480 ("r-urltools" ,r-urltools)
14481 ("r-xml2" ,r-xml2)))
14482 (home-page "https://github.com/ropensci/europepmc/")
14483 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14484 (description
14485 "This package provides an R Client for the
14486 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14487 Service}. It gives access to both metadata on life science literature and
14488 open access full texts. Europe PMC indexes all PubMed content and other
14489 literature sources including Agricola, a bibliographic database of citations
14490 to the agricultural literature, or Biological Patents. In addition to
14491 bibliographic metadata, the client allows users to fetch citations and
14492 reference lists. Links between life-science literature and other EBI
14493 databases, including ENA, PDB or ChEMBL are also accessible.")
14494 (license license:gpl3)))
14495
14496 (define-public r-ggraph
14497 (package
14498 (name "r-ggraph")
14499 (version "2.0.2")
14500 (source
14501 (origin
14502 (method url-fetch)
14503 (uri (cran-uri "ggraph" version))
14504 (sha256
14505 (base32
14506 "1ckq82hg52vr2wydkqv2wrppgjyvddd6bwqzrngqlm7j71xapjl0"))))
14507 (build-system r-build-system)
14508 (propagated-inputs
14509 `(("r-digest" ,r-digest)
14510 ("r-dplyr" ,r-dplyr)
14511 ("r-ggforce" ,r-ggforce)
14512 ("r-ggplot2" ,r-ggplot2)
14513 ("r-ggrepel" ,r-ggrepel)
14514 ("r-graphlayouts" ,r-graphlayouts)
14515 ("r-gtable" ,r-gtable)
14516 ("r-igraph" ,r-igraph)
14517 ("r-mass" ,r-mass)
14518 ("r-rcpp" ,r-rcpp)
14519 ("r-rlang" ,r-rlang)
14520 ("r-scales" ,r-scales)
14521 ("r-tidygraph" ,r-tidygraph)
14522 ("r-viridis" ,r-viridis)))
14523 (native-inputs
14524 `(("r-knitr" ,r-knitr)))
14525 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14526 (synopsis "Implementation of grammar of graphics for graphs and networks")
14527 (description
14528 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14529 graph and network visualizations due to its reliance on tabular data input.
14530 The ggraph package is an extension of the ggplot2 API tailored to graph
14531 visualizations and provides the same flexible approach to building up plots
14532 layer by layer.")
14533 (license license:gpl3)))
14534
14535 (define-public r-varselrf
14536 (package
14537 (name "r-varselrf")
14538 (version "0.7-8")
14539 (source
14540 (origin
14541 (method url-fetch)
14542 (uri (cran-uri "varSelRF" version))
14543 (sha256
14544 (base32
14545 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14546 (properties `((upstream-name . "varSelRF")))
14547 (build-system r-build-system)
14548 (propagated-inputs
14549 `(("r-randomforest" ,r-randomforest)))
14550 (home-page "https://www.ligarto.org/rdiaz/software/software")
14551 (synopsis "Variable selection using random forests")
14552 (description
14553 "This package provides tools for the variable selection from random
14554 forests using both backwards variable elimination (for the selection of small
14555 sets of non-redundant variables) and selection based on the importance
14556 spectrum (somewhat similar to scree plots; for the selection of large,
14557 potentially highly-correlated variables). The main applications are in
14558 high-dimensional data (e.g., microarray data, and other genomics and
14559 proteomics applications).")
14560 (license license:gpl2+)))
14561
14562 (define-public r-pamr
14563 (package
14564 (name "r-pamr")
14565 (version "1.56.1")
14566 (source
14567 (origin
14568 (method url-fetch)
14569 (uri (cran-uri "pamr" version))
14570 (sha256
14571 (base32
14572 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14573 (build-system r-build-system)
14574 (propagated-inputs
14575 `(("r-cluster" ,r-cluster)
14576 ("r-survival" ,r-survival)))
14577 (native-inputs `(("gfortran" ,gfortran)))
14578 (home-page "https://cran.r-project.org/web/packages/pamr/")
14579 (synopsis "Prediction Analysis for Microarrays")
14580 (description
14581 "This package provides some functions for sample classification in
14582 microarrays.")
14583 (license license:gpl2)))
14584
14585 (define-public r-rda
14586 (package
14587 (name "r-rda")
14588 (version "1.0.2-2.1")
14589 (source
14590 (origin
14591 (method url-fetch)
14592 (uri (cran-uri "rda" version))
14593 (sha256
14594 (base32
14595 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
14596 (build-system r-build-system)
14597 (home-page "https://cran.r-project.org/web/packages/rda/")
14598 (synopsis "Shrunken centroids regularized discriminant analysis")
14599 (description
14600 "This package provides tools for shrunken centroids regularized
14601 discriminant analysis for the purpose of classifying high dimensional data.")
14602 (license license:gpl2+)))
14603
14604 (define-public r-ggvis
14605 (package
14606 (name "r-ggvis")
14607 (version "0.4.5")
14608 (source
14609 (origin
14610 (method url-fetch)
14611 (uri (cran-uri "ggvis" version))
14612 (sha256
14613 (base32
14614 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
14615 (build-system r-build-system)
14616 (propagated-inputs
14617 `(("r-assertthat" ,r-assertthat)
14618 ("r-dplyr" ,r-dplyr)
14619 ("r-htmltools" ,r-htmltools)
14620 ("r-jsonlite" ,r-jsonlite)
14621 ("r-lazyeval" ,r-lazyeval)
14622 ("r-magrittr" ,r-magrittr)
14623 ("r-shiny" ,r-shiny)))
14624 (home-page "https://ggvis.rstudio.com/")
14625 (synopsis "Interactive grammar of graphics")
14626 (description
14627 "This package is a data visualization package for R providing an
14628 implementation of an interactive grammar of graphics, taking the best parts of
14629 ggplot2, combining them with the reactive framework of Shiny and drawing web
14630 graphics using Vega.")
14631 (license license:gpl2)))
14632
14633 (define-public r-gbm
14634 (package
14635 (name "r-gbm")
14636 (version "2.1.5")
14637 (source
14638 (origin
14639 (method url-fetch)
14640 (uri (cran-uri "gbm" version))
14641 (sha256
14642 (base32
14643 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
14644 (build-system r-build-system)
14645 (propagated-inputs
14646 `(("r-gridextra" ,r-gridextra)
14647 ("r-lattice" ,r-lattice)
14648 ("r-survival" ,r-survival)))
14649 (home-page "https://github.com/gbm-developers/gbm")
14650 (synopsis "Generalized boosted regression models")
14651 (description
14652 "This package is an implementation of extensions to Freund and Schapire's
14653 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
14654 regression methods for least squares, absolute loss, t-distribution loss,
14655 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
14656 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
14657 and Learning to Rank measures (LambdaMart).")
14658 (license license:gpl2+)))
14659
14660 (define-public r-threejs
14661 (package
14662 (name "r-threejs")
14663 (version "0.3.3")
14664 (source
14665 (origin
14666 (method url-fetch)
14667 (uri (cran-uri "threejs" version))
14668 (sha256
14669 (base32
14670 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
14671 (build-system r-build-system)
14672 (arguments
14673 `(#:modules ((guix build utils)
14674 (guix build r-build-system)
14675 (srfi srfi-1)
14676 (ice-9 popen))
14677 #:phases
14678 (modify-phases %standard-phases
14679 (add-after 'unpack 'process-javascript
14680 (lambda* (#:key inputs #:allow-other-keys)
14681 (with-directory-excursion "inst"
14682 (call-with-values
14683 (lambda ()
14684 (unzip2
14685 `((,(assoc-ref inputs "js-jquery")
14686 "htmlwidgets/lib/jquery/jquery.min.js")
14687 (,(assoc-ref inputs "js-threejs-111")
14688 "htmlwidgets/lib/threejs-111/three.min.js"))))
14689 (lambda (sources targets)
14690 (for-each (lambda (source target)
14691 (format #t "Processing ~a --> ~a~%"
14692 source target)
14693 (delete-file target)
14694 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14695 (call-with-output-file target
14696 (lambda (port)
14697 (dump-port minified port)))))
14698 sources targets))))
14699 #t)))))
14700 (propagated-inputs
14701 `(("r-base64enc" ,r-base64enc)
14702 ("r-crosstalk" ,r-crosstalk)
14703 ("r-htmlwidgets" ,r-htmlwidgets)
14704 ("r-igraph" ,r-igraph)))
14705 (native-inputs
14706 `(("uglify-js" ,uglify-js)
14707 ("js-jquery"
14708 ,(origin
14709 (method url-fetch)
14710 (uri "https://code.jquery.com/jquery-1.12.4.js")
14711 (sha256
14712 (base32
14713 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
14714 ("js-threejs-111"
14715 ,(origin
14716 (method url-fetch)
14717 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
14718 (sha256
14719 (base32
14720 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
14721 (home-page "https://bwlewis.github.io/rthreejs")
14722 (synopsis "Interactive 3D scatter plots, networks and globes")
14723 (description
14724 "Create interactive 3D scatter plots, network plots, and globes in R
14725 using the three.js visualization library.")
14726 (license license:expat)))
14727
14728 (define-public r-mlbench
14729 (package
14730 (name "r-mlbench")
14731 (version "2.1-1")
14732 (source
14733 (origin
14734 (method url-fetch)
14735 (uri (cran-uri "mlbench" version))
14736 (sha256
14737 (base32
14738 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
14739 (build-system r-build-system)
14740 (home-page "https://cran.r-project.org/web/packages/mlbench/")
14741 (synopsis "Machine learning benchmark problems")
14742 (description
14743 "This package provides a collection of artificial and real-world machine
14744 learning benchmark problems, including, e.g., several data sets from the UCI
14745 repository.")
14746 (license license:gpl2)))
14747
14748 (define-public r-mpm
14749 (package
14750 (name "r-mpm")
14751 (version "1.0-22")
14752 (source
14753 (origin
14754 (method url-fetch)
14755 (uri (cran-uri "mpm" version))
14756 (sha256
14757 (base32
14758 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
14759 (build-system r-build-system)
14760 (propagated-inputs
14761 `(("r-kernsmooth" ,r-kernsmooth)
14762 ("r-mass" ,r-mass)))
14763 (home-page "http://mpm.r-forge.r-project.org")
14764 (synopsis "Multivariate projection methods")
14765 (description
14766 "This is a package for exploratory graphical analysis of multivariate
14767 data, specifically gene expression data with different projection methods:
14768 principal component analysis, correspondence analysis, spectral map
14769 analysis.")
14770 (license license:gpl2+)))
14771
14772 (define-public r-png
14773 (package
14774 (name "r-png")
14775 (version "0.1-7")
14776 (source (origin
14777 (method url-fetch)
14778 (uri (cran-uri "png" version))
14779 (sha256
14780 (base32
14781 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
14782 (build-system r-build-system)
14783 (inputs
14784 `(("libpng" ,libpng)
14785 ("zlib" ,zlib)))
14786 (home-page "https://www.rforge.net/png/")
14787 (synopsis "Read and write PNG images")
14788 (description
14789 "This package provides an easy and simple way to read, write and display
14790 bitmap images stored in the PNG format. It can read and write both files and
14791 in-memory raw vectors.")
14792 ;; Any of these GPL versions.
14793 (license (list license:gpl2 license:gpl3))))
14794
14795 (define-public r-ggcorrplot
14796 (package
14797 (name "r-ggcorrplot")
14798 (version "0.1.3")
14799 (source
14800 (origin
14801 (method url-fetch)
14802 (uri (cran-uri "ggcorrplot" version))
14803 (sha256
14804 (base32
14805 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
14806 (build-system r-build-system)
14807 (propagated-inputs
14808 `(("r-ggplot2" ,r-ggplot2)
14809 ("r-reshape2" ,r-reshape2)))
14810 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
14811 (synopsis "Visualization of a correlation matrix using ggplot2")
14812 (description
14813 "The ggcorrplot package can be used to visualize easily a correlation
14814 matrix using ggplot2. It provides a solution for reordering the correlation
14815 matrix and displays the significance level on the plot. It also includes a
14816 function for computing a matrix of correlation p-values.")
14817 (license license:gpl2)))
14818
14819 (define-public r-flexdashboard
14820 (package
14821 (name "r-flexdashboard")
14822 (version "0.5.1.1")
14823 (source
14824 (origin
14825 (method url-fetch)
14826 (uri (cran-uri "flexdashboard" version))
14827 (sha256
14828 (base32
14829 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
14830 (build-system r-build-system)
14831 (arguments
14832 `(#:modules ((guix build utils)
14833 (guix build r-build-system)
14834 (srfi srfi-1)
14835 (srfi srfi-26)
14836 (ice-9 popen)
14837 (ice-9 textual-ports))
14838 #:phases
14839 (modify-phases %standard-phases
14840 (add-after 'unpack 'process-javascript
14841 (lambda* (#:key inputs #:allow-other-keys)
14842 (with-directory-excursion "inst"
14843 ;; Concatenate all components of prism.js
14844 (let ((contents (string-join
14845 (map (lambda (name)
14846 (call-with-input-file
14847 (assoc-ref inputs name)
14848 get-string-all))
14849 (list "js-prism"
14850 "js-prism-r"
14851 "js-prism-line-numbers"))
14852 "\n")))
14853 (call-with-output-file "prism-src.js"
14854 (cut display contents <>)))
14855 (call-with-values
14856 (lambda ()
14857 (unzip2
14858 `(("www/stickytableheaders/jquery.stickytableheaders.js"
14859 "www/stickytableheaders/jquery.stickytableheaders.min.js")
14860 ("www/sly/sly.js"
14861 "www/sly/sly.min.js")
14862 ("prism-src.js"
14863 "www/prism/prism.js")
14864 (,(assoc-ref inputs "js-raphael")
14865 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
14866 (,(assoc-ref inputs "js-featherlight")
14867 "www/featherlight/featherlight.min.js"))))
14868 (lambda (sources targets)
14869 (for-each (lambda (source target)
14870 (format #t "Processing ~a --> ~a~%"
14871 source target)
14872 (delete-file target)
14873 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14874 (call-with-output-file target
14875 (lambda (port)
14876 (dump-port minified port)))))
14877 sources targets))))
14878 #t)))))
14879 (propagated-inputs
14880 `(("r-htmltools" ,r-htmltools)
14881 ("r-htmlwidgets" ,r-htmlwidgets)
14882 ("r-jsonlite" ,r-jsonlite)
14883 ("r-knitr" ,r-knitr)
14884 ("r-rmarkdown" ,r-rmarkdown)
14885 ("r-shiny" ,r-shiny)))
14886 (native-inputs
14887 `(("uglify-js" ,uglify-js)
14888 ("js-raphael"
14889 ,(origin
14890 (method url-fetch)
14891 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
14892 (sha256
14893 (base32
14894 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
14895 ("js-prism"
14896 ,(origin
14897 (method url-fetch)
14898 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
14899 (sha256
14900 (base32
14901 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
14902 ("js-prism-r"
14903 ,(origin
14904 (method url-fetch)
14905 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
14906 (sha256
14907 (base32
14908 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
14909 ("js-prism-line-numbers"
14910 ,(origin
14911 (method url-fetch)
14912 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
14913 (sha256
14914 (base32
14915 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
14916 ("js-featherlight"
14917 ,(origin
14918 (method url-fetch)
14919 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
14920 (sha256
14921 (base32
14922 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
14923 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
14924 (synopsis "R Markdown format for flexible dashboards")
14925 (description
14926 "This package provides an R Markdown format for converting an R Markdown
14927 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
14928 of its components to the containing web page.")
14929 (license license:expat)))
14930
14931 (define-public r-preseqr
14932 (package
14933 (name "r-preseqr")
14934 (version "4.0.0")
14935 (source
14936 (origin
14937 (method url-fetch)
14938 (uri (cran-uri "preseqR" version))
14939 (sha256
14940 (base32
14941 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
14942 (properties `((upstream-name . "preseqR")))
14943 (build-system r-build-system)
14944 (propagated-inputs
14945 `(("r-polynom" ,r-polynom)))
14946 (home-page "https://cran.r-project.org/web/packages/preseqR/")
14947 (synopsis "Predicting species accumulation curves")
14948 (description
14949 "This package can be used to predict the r-species accumulation
14950 curve (r-SAC), which is the number of species represented at least r times as
14951 a function of the sampling effort. When r = 1, the curve is known as the
14952 species accumulation curve, or the library complexity curve in high-throughput
14953 genomic sequencing. The package includes both parametric and nonparametric
14954 methods, as described by Deng C, et al. (2018).")
14955 (license license:gpl3)))
14956
14957 (define-public r-mapplots
14958 (package
14959 (name "r-mapplots")
14960 (version "1.5.1")
14961 (source
14962 (origin
14963 (method url-fetch)
14964 (uri (cran-uri "mapplots" version))
14965 (sha256
14966 (base32
14967 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
14968 (build-system r-build-system)
14969 (home-page "https://cran.r-project.org/web/packages/mapplots/")
14970 (synopsis "Data visualization on maps")
14971 (description
14972 "This package helps you create simple maps; add sub-plots like pie plots
14973 to a map or any other plot; format, plot and export gridded data. The package
14974 was developed for displaying fisheries data but most functions can be used for
14975 more generic data visualisation.")
14976 (license license:gpl2+)))
14977
14978 (define-public r-pmcmr
14979 (package
14980 (name "r-pmcmr")
14981 (version "4.3")
14982 (source
14983 (origin
14984 (method url-fetch)
14985 (uri (cran-uri "PMCMR" version))
14986 (sha256
14987 (base32
14988 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
14989 (properties `((upstream-name . "PMCMR")))
14990 (build-system r-build-system)
14991 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
14992 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
14993 (description
14994 "This is a deprecated package for calculating pairwise multiple
14995 comparisons of mean rank sums. This package is superseded by the novel
14996 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
14997 compatibility of dependent packages for some time.")
14998 (license license:gpl3+)))
14999
15000 (define-public r-downloader
15001 (package
15002 (name "r-downloader")
15003 (version "0.4")
15004 (source
15005 (origin
15006 (method url-fetch)
15007 (uri (cran-uri "downloader" version))
15008 (sha256
15009 (base32
15010 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
15011 (build-system r-build-system)
15012 (propagated-inputs
15013 `(("r-digest" ,r-digest)))
15014 (home-page "https://github.com/wch/downloader")
15015 (synopsis "Download files over HTTP and HTTPS")
15016 (description
15017 "This package provides a wrapper for the @code{download.file} function,
15018 making it possible to download files over HTTPS across platforms. The
15019 @code{RCurl} package provides this functionality (and much more) but has
15020 external dependencies. This package has is implemented purely in R.")
15021 (license license:gpl2)))
15022
15023 (define-public r-rex
15024 (package
15025 (name "r-rex")
15026 (version "1.2.0")
15027 (source
15028 (origin
15029 (method url-fetch)
15030 (uri (cran-uri "rex" version))
15031 (sha256
15032 (base32
15033 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
15034 (build-system r-build-system)
15035 (propagated-inputs
15036 `(("r-lazyeval" ,r-lazyeval)))
15037 (native-inputs
15038 `(("r-knitr" ,r-knitr)))
15039 (home-page "https://github.com/kevinushey/rex")
15040 (synopsis "Friendly regular expressions")
15041 (description
15042 "This package provides a friendly interface for the construction of
15043 regular expressions. Regular expressions are a very powerful feature, however
15044 they are often difficult to interpret. Rex allows you to build complex
15045 regular expressions from human readable expressions")
15046 (license license:expat)))
15047
15048 (define-public r-xmlparsedata
15049 (package
15050 (name "r-xmlparsedata")
15051 (version "1.0.3")
15052 (source
15053 (origin
15054 (method url-fetch)
15055 (uri (cran-uri "xmlparsedata" version))
15056 (sha256
15057 (base32
15058 "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh"))))
15059 (properties `((upstream-name . "xmlparsedata")))
15060 (build-system r-build-system)
15061 (home-page "https://github.com/r-lib/xmlparsedata#readme")
15062 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
15063 (description
15064 "This package provides tools to convert the output of
15065 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
15066 @code{XPath}, and is easier to manipulate in general.")
15067 (license license:expat)))
15068
15069 (define-public r-cyclocomp
15070 (package
15071 (name "r-cyclocomp")
15072 (version "1.1.0")
15073 (source
15074 (origin
15075 (method url-fetch)
15076 (uri (cran-uri "cyclocomp" version))
15077 (sha256
15078 (base32
15079 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
15080 (properties `((upstream-name . "cyclocomp")))
15081 (build-system r-build-system)
15082 (propagated-inputs
15083 `(("r-callr" ,r-callr)
15084 ("r-crayon" ,r-crayon)
15085 ("r-desc" ,r-desc)
15086 ("r-remotes" ,r-remotes)
15087 ("r-withr" ,r-withr)))
15088 (home-page "https://github.com/MangoTheCat/cyclocomp")
15089 (synopsis "Cyclomatic complexity of R code")
15090 (description
15091 "Cyclomatic complexity is a software metric, used to indicate the
15092 complexity of a program. It is a quantitative measure of the number of
15093 linearly independent paths through a program's source code. This package
15094 provides tools to compute this metric.")
15095 (license license:expat)))
15096
15097 (define-public r-lintr
15098 (package
15099 (name "r-lintr")
15100 (version "2.0.1")
15101 (source
15102 (origin
15103 (method url-fetch)
15104 (uri (cran-uri "lintr" version))
15105 (sha256
15106 (base32
15107 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
15108 (properties `((upstream-name . "lintr")))
15109 (build-system r-build-system)
15110 (propagated-inputs
15111 `(("r-codetools" ,r-codetools)
15112 ("r-crayon" ,r-crayon)
15113 ("r-cyclocomp" ,r-cyclocomp)
15114 ("r-digest" ,r-digest)
15115 ("r-httr" ,r-httr)
15116 ("r-jsonlite" ,r-jsonlite)
15117 ("r-knitr" ,r-knitr)
15118 ("r-rex" ,r-rex)
15119 ("r-rstudioapi" ,r-rstudioapi)
15120 ("r-testthat" ,r-testthat)
15121 ("r-xml2" ,r-xml2)
15122 ("r-xmlparsedata" ,r-xmlparsedata)))
15123 (home-page "https://github.com/jimhester/lintr")
15124 (synopsis "Linter for R code")
15125 (description "This package checks adherence to a given style, syntax
15126 errors and possible semantic issues. It supports on the fly checking of R
15127 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
15128 (license license:expat)))
15129
15130 (define-public r-sctransform
15131 (package
15132 (name "r-sctransform")
15133 (version "0.2.1")
15134 (source
15135 (origin
15136 (method url-fetch)
15137 (uri (cran-uri "sctransform" version))
15138 (sha256
15139 (base32
15140 "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
15141 (build-system r-build-system)
15142 (propagated-inputs
15143 `(("r-future-apply" ,r-future-apply)
15144 ("r-ggplot2" ,r-ggplot2)
15145 ("r-gridextra" ,r-gridextra)
15146 ("r-mass" ,r-mass)
15147 ("r-matrix" ,r-matrix)
15148 ("r-rcpp" ,r-rcpp)
15149 ("r-rcppeigen" ,r-rcppeigen)
15150 ("r-reshape2" ,r-reshape2)))
15151 (home-page "https://github.com/ChristophH/sctransform")
15152 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
15153 (description
15154 "This package provides a normalization method for single-cell UMI count
15155 data using a variance stabilizing transformation. The transformation is based
15156 on a negative binomial regression model with regularized parameters. As part
15157 of the same regression framework, this package also provides functions for
15158 batch correction, and data correction.")
15159 (license license:gpl3)))
15160
15161 (define-public r-styler
15162 (package
15163 (name "r-styler")
15164 (version "1.3.2")
15165 (source
15166 (origin
15167 (method url-fetch)
15168 (uri (cran-uri "styler" version))
15169 (sha256
15170 (base32
15171 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
15172 (build-system r-build-system)
15173 (propagated-inputs
15174 `(("r-backports" ,r-backports)
15175 ("r-cli" ,r-cli)
15176 ("r-magrittr" ,r-magrittr)
15177 ("r-purrr" ,r-purrr)
15178 ("r-r-cache" ,r-r-cache)
15179 ("r-rematch2" ,r-rematch2)
15180 ("r-rlang" ,r-rlang)
15181 ("r-rprojroot" ,r-rprojroot)
15182 ("r-tibble" ,r-tibble)
15183 ("r-withr" ,r-withr)
15184 ("r-xfun" ,r-xfun)))
15185 (home-page "https://github.com/r-lib/styler")
15186 (synopsis "Non-invasive pretty printing of R code")
15187 (description
15188 "This is a package for pretty-printing R code without changing the user's
15189 formatting intent.")
15190 (license license:gpl3)))
15191
15192 (define-public r-scrime
15193 (package
15194 (name "r-scrime")
15195 (version "1.3.5")
15196 (source
15197 (origin
15198 (method url-fetch)
15199 (uri (cran-uri "scrime" version))
15200 (sha256
15201 (base32
15202 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
15203 (build-system r-build-system)
15204 (home-page "https://cran.r-project.org/web/packages/scrime/")
15205 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
15206 (description
15207 "This package provides tools for the analysis of high-dimensional data
15208 developed/implemented at the group \"Statistical Complexity Reduction In
15209 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
15210 the functions can also be applied to other types of categorical data.")
15211 (license license:gpl2)))
15212
15213 (define-public r-pbmcapply
15214 (package
15215 (name "r-pbmcapply")
15216 (version "1.5.0")
15217 (source
15218 (origin
15219 (method url-fetch)
15220 (uri (cran-uri "pbmcapply" version))
15221 (sha256
15222 (base32
15223 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
15224 (build-system r-build-system)
15225 (home-page "https://github.com/kvnkuang/pbmcapply")
15226 (synopsis "Track the progress of apply procedures with a progress bar")
15227 (description
15228 "This light-weight package helps you track and visualize the progress of
15229 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15230 (license license:expat)))
15231
15232 (define-public r-blme
15233 (package
15234 (name "r-blme")
15235 (version "1.0-4")
15236 (source
15237 (origin
15238 (method url-fetch)
15239 (uri (cran-uri "blme" version))
15240 (sha256
15241 (base32
15242 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15243 (build-system r-build-system)
15244 (propagated-inputs `(("r-lme4" ,r-lme4)))
15245 (home-page "https://github.com/vdorie/blme")
15246 (synopsis "Bayesian linear mixed-effects models")
15247 (description
15248 "This package provides tools for maximum a posteriori estimation for
15249 linear and generalized linear mixed-effects models in a Bayesian setting. It
15250 extends the lme4 package.")
15251 (license license:gpl2+)))
15252
15253 (define-public r-batchtools
15254 (package
15255 (name "r-batchtools")
15256 (version "0.9.13")
15257 (source
15258 (origin
15259 (method url-fetch)
15260 (uri (cran-uri "batchtools" version))
15261 (sha256
15262 (base32
15263 "02bwfinwgn5nl638997javig61jmr0ci0qybmprz13jnvmam1yns"))))
15264 (build-system r-build-system)
15265 (propagated-inputs
15266 `(("r-backports" ,r-backports)
15267 ("r-base64url" ,r-base64url)
15268 ("r-brew" ,r-brew)
15269 ("r-checkmate" ,r-checkmate)
15270 ("r-data-table" ,r-data-table)
15271 ("r-digest" ,r-digest)
15272 ("r-fs" ,r-fs)
15273 ("r-progress" ,r-progress)
15274 ("r-r6" ,r-r6)
15275 ("r-rappdirs" ,r-rappdirs)
15276 ("r-stringi" ,r-stringi)
15277 ("r-withr" ,r-withr)))
15278 (native-inputs
15279 `(("r-knitr" ,r-knitr)))
15280 (home-page "https://github.com/mllg/batchtools")
15281 (synopsis "Tools for computation on batch systems")
15282 (description
15283 "As a successor of the packages BatchJobs and BatchExperiments, this
15284 package provides a parallel implementation of the Map function for high
15285 performance computing systems managed by various schedulers. A multicore and
15286 socket mode allow the parallelization on a local machines, and multiple
15287 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15288 the package provides an abstraction mechanism to define large-scale computer
15289 experiments in a well-organized and reproducible way.")
15290 (license license:lgpl3)))
15291
15292 (define-public r-clue
15293 (package
15294 (name "r-clue")
15295 (version "0.3-57")
15296 (source
15297 (origin
15298 (method url-fetch)
15299 (uri (cran-uri "clue" version))
15300 (sha256
15301 (base32
15302 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15303 (build-system r-build-system)
15304 (propagated-inputs `(("r-cluster" ,r-cluster)))
15305 (home-page "https://cran.r-project.org/web/packages/clue/")
15306 (synopsis "Tools for analyzing cluster ensembles")
15307 (description "Cluster ensembles are collections of individual solutions to
15308 a given clustering problem which are useful or necessary to consider in a wide
15309 range of applications. This R package provides an extensible computational
15310 environment for creating and analyzing cluster ensembles, with basic data
15311 structures for representing partitions and hierarchies, and facilities for
15312 computing on them, including methods for measuring proximity and obtaining
15313 consensus and secondary clusterings.")
15314 (license license:gpl2)))
15315
15316 (define-public r-sitmo
15317 (package
15318 (name "r-sitmo")
15319 (version "2.0.1")
15320 (source
15321 (origin
15322 (method url-fetch)
15323 (uri (cran-uri "sitmo" version))
15324 (sha256
15325 (base32
15326 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15327 (build-system r-build-system)
15328 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15329 (home-page "https://github.com/coatless/sitmo/")
15330 (synopsis "Parallel pseudo random number generator header files")
15331 (description
15332 "This package provides two high quality and fast PPRNGs that may be used
15333 in an OpenMP parallel environment. In addition, there is a generator for one
15334 dimensional low-discrepancy sequence.")
15335 (license license:expat)))
15336
15337 (define-public r-dqrng
15338 (package
15339 (name "r-dqrng")
15340 (version "0.2.1")
15341 (source
15342 (origin
15343 (method url-fetch)
15344 (uri (cran-uri "dqrng" version))
15345 (sha256
15346 (base32
15347 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15348 (build-system r-build-system)
15349 (propagated-inputs
15350 `(("r-bh" ,r-bh)
15351 ("r-rcpp" ,r-rcpp)
15352 ("r-sitmo" ,r-sitmo)))
15353 (home-page "https://www.daqana.org/dqrng")
15354 (synopsis "Fast pseudo random number generators")
15355 (description
15356 "Several fast random number generators are provided as C++ header-only
15357 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15358 Additionally, fast functions for generating random numbers according to a
15359 uniform, normal and exponential distribution are included. The latter two use
15360 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15361 functions are exported to R and as a C++ interface and are enabled for use
15362 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15363 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15364 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15365 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15366 ;; whole is distributed under the terms of the AGPL 3.
15367 (license license:agpl3)))
15368
15369 (define-public r-ingredients
15370 (package
15371 (name "r-ingredients")
15372 (version "1.2.0")
15373 (source
15374 (origin
15375 (method url-fetch)
15376 (uri (cran-uri "ingredients" version))
15377 (sha256
15378 (base32
15379 "1q196y9xzn4wk44fa1bvh0hcbizgm93rwir82nyk31k5pgixk967"))))
15380 (properties `((upstream-name . "ingredients")))
15381 (build-system r-build-system)
15382 (propagated-inputs
15383 `(("r-ggplot2" ,r-ggplot2)
15384 ("r-gridextra" ,r-gridextra)
15385 ("r-scales" ,r-scales)))
15386 (native-inputs `(("r-knitr" ,r-knitr)))
15387 (home-page "https://ModelOriented.github.io/ingredients/")
15388 (synopsis "Effects and importances of model ingredients")
15389 (description
15390 "This is a collection of tools for assessment of feature importance and
15391 feature effects. Key functions are:
15392
15393 @itemize
15394 @item @code{feature_importance()} for assessment of global level feature
15395 importance,
15396 @item @code{ceteris_paribus()} for calculation of the what-if plots,
15397 @item @code{partial_dependence()} for partial dependence plots,
15398 @item @code{conditional_dependence()} for conditional dependence plots,
15399 @item @code{accumulated_dependence()} for accumulated local effects plots,
15400 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
15401 aggregation of ceteris paribus profiles,
15402 @item generic @code{print()} and @code{plot()} for better usability of
15403 selected explainers,
15404 @item generic @code{plotD3()} for interactive, D3 based explanations, and
15405 @item generic @code{describe()} for explanations in natural language.
15406 @end itemize\n")
15407 (license license:gpl3)))
15408
15409 (define-public r-ibreakdown
15410 (package
15411 (name "r-ibreakdown")
15412 (version "1.2.0")
15413 (source
15414 (origin
15415 (method url-fetch)
15416 (uri (cran-uri "iBreakDown" version))
15417 (sha256
15418 (base32
15419 "0y4zjpyn8j76jrs5phjzs5lfq3lqjspmrwcksqv9wq0rbdgh14vk"))))
15420 (properties `((upstream-name . "iBreakDown")))
15421 (build-system r-build-system)
15422 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
15423 (native-inputs `(("r-knitr" ,r-knitr)))
15424 (home-page "https://ModelOriented.github.io/iBreakDown/")
15425 (synopsis "Model agnostic instance level variable attributions")
15426 (description
15427 "This package provides a model agnostic tool for decomposition of
15428 predictions from black boxes. It supports additive attributions and
15429 attributions with interactions. The Break Down Table shows contributions of
15430 every variable to a final prediction. The Break Down Plot presents variable
15431 contributions in a concise graphical way. This package works for
15432 classification and regression models.")
15433 (license license:gpl3)))
15434
15435 (define-public r-dalex
15436 (package
15437 (name "r-dalex")
15438 (version "1.2.1")
15439 (source
15440 (origin
15441 (method url-fetch)
15442 (uri (cran-uri "DALEX" version))
15443 (sha256
15444 (base32
15445 "0lx8nasm1zgh1ckz8nw3ysp6xjv3dsj39hzhr6k3xhh6i8pm9rxk"))))
15446 (properties `((upstream-name . "DALEX")))
15447 (build-system r-build-system)
15448 (propagated-inputs
15449 `(("r-ggplot2" ,r-ggplot2)
15450 ("r-ibreakdown" ,r-ibreakdown)
15451 ("r-ingredients" ,r-ingredients)))
15452 (home-page "https://pbiecek.github.io/DALEX/")
15453 (synopsis "Descriptive machine learning explanations")
15454 (description
15455 "Machine Learning models are widely used and have various applications in
15456 classification or regression. Models created with boosting, bagging, stacking
15457 or similar techniques are often used due to their high performance, but such
15458 black-box models usually lack interpretability. The DALEX package contains
15459 various explainers that help to understand the link between input variables
15460 and model output.")
15461 ;; Any version of the GPL
15462 (license license:gpl3+)))
15463
15464 (define-public r-enrichr
15465 (package
15466 (name "r-enrichr")
15467 (version "2.1")
15468 (source
15469 (origin
15470 (method url-fetch)
15471 (uri (cran-uri "enrichR" version))
15472 (sha256
15473 (base32
15474 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
15475 (properties `((upstream-name . "enrichR")))
15476 (build-system r-build-system)
15477 (propagated-inputs
15478 `(("r-httr" ,r-httr)
15479 ("r-rjson" ,r-rjson)))
15480 (home-page "https://cran.r-project.org/web/packages/enrichR/")
15481 (synopsis "R Interface to Enrichr database for analyzing gene sets")
15482 (description
15483 "This package provides an R interface to all Enrichr databases, a
15484 web-based tool for analyzing gene sets and returns any enrichment of common
15485 annotated biological functions.")
15486 (license license:gpl2+)))
15487
15488 (define-public r-plot3d
15489 (package
15490 (name "r-plot3d")
15491 (version "1.3")
15492 (source
15493 (origin
15494 (method url-fetch)
15495 (uri (cran-uri "plot3D" version))
15496 (sha256
15497 (base32
15498 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
15499 (properties `((upstream-name . "plot3D")))
15500 (build-system r-build-system)
15501 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
15502 (home-page "https://cran.r-project.org/web/packages/plot3D")
15503 (synopsis "Plot multi-dimensional data")
15504 (description
15505 "This package provides functions for viewing 2D and 3D data, including
15506 perspective plots, slice plots, surface plots, scatter plots, etc. It
15507 includes data sets from oceanography.")
15508 (license license:gpl3+)))
15509
15510 (define-public r-ggfortify
15511 (package
15512 (name "r-ggfortify")
15513 (version "0.4.10")
15514 (source
15515 (origin
15516 (method url-fetch)
15517 (uri (cran-uri "ggfortify" version))
15518 (sha256
15519 (base32
15520 "0wmcwp63h90v3f00ixszvis4z28im621jickvc0wgi6qvjvnayq0"))))
15521 (build-system r-build-system)
15522 (propagated-inputs
15523 `(("r-dplyr" ,r-dplyr)
15524 ("r-ggplot2" ,r-ggplot2)
15525 ("r-gridextra" ,r-gridextra)
15526 ("r-scales" ,r-scales)
15527 ("r-stringr" ,r-stringr)
15528 ("r-tibble" ,r-tibble)
15529 ("r-tidyr" ,r-tidyr)))
15530 (native-inputs
15531 `(("r-knitr" ,r-knitr)))
15532 (home-page "https://github.com/sinhrks/ggfortify")
15533 (synopsis "Data visualization tools for statistical analysis results")
15534 (description
15535 "This package provides unified plotting tools for statistics commonly
15536 used, such as GLM, time series, PCA families, clustering and survival
15537 analysis. The package offers a single plotting interface for these analysis
15538 results and plots in a unified style using the @code{ggplot2} package.")
15539 (license license:gpl2)))
15540
15541 (define-public r-refmanager
15542 (package
15543 (name "r-refmanager")
15544 (version "1.2.12")
15545 (source
15546 (origin
15547 (method url-fetch)
15548 (uri (cran-uri "RefManageR" version))
15549 (sha256
15550 (base32
15551 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
15552 (properties `((upstream-name . "RefManageR")))
15553 (build-system r-build-system)
15554 (propagated-inputs
15555 `(("r-bibtex" ,r-bibtex)
15556 ("r-httr" ,r-httr)
15557 ("r-jsonlite" ,r-jsonlite)
15558 ("r-lubridate" ,r-lubridate)
15559 ("r-plyr" ,r-plyr)
15560 ("r-stringr" ,r-stringr)
15561 ("r-xml2" ,r-xml2)))
15562 (home-page "https://github.com/ropensci/RefManageR/")
15563 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
15564 (description
15565 "This package provides tools for importing and working with bibliographic
15566 references. It greatly enhances the @code{bibentry} class by providing a
15567 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
15568 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
15569 by various formats for name lists (author by last names, translator by full
15570 names, etc.). Entries can be updated, combined, sorted, printed in a number
15571 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
15572 into R and converted to @code{BibEntry} objects.")
15573 ;; Any of these licenses may be picked.
15574 (license (list license:gpl2 license:gpl3 license:bsd-3))))
15575
15576 (define-public r-citr
15577 (package
15578 (name "r-citr")
15579 (version "0.3.2")
15580 (source
15581 (origin
15582 (method url-fetch)
15583 (uri (cran-uri "citr" version))
15584 (sha256
15585 (base32
15586 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
15587 (build-system r-build-system)
15588 (propagated-inputs
15589 `(("r-assertthat" ,r-assertthat)
15590 ("r-curl" ,r-curl)
15591 ("r-httr" ,r-httr)
15592 ("r-miniui" ,r-miniui)
15593 ("r-refmanager" ,r-refmanager)
15594 ("r-rstudioapi" ,r-rstudioapi)
15595 ("r-shiny" ,r-shiny)
15596 ("r-shinyjs" ,r-shinyjs)
15597 ("r-yaml" ,r-yaml)))
15598 (home-page "https://github.com/crsh/citr")
15599 (synopsis "RStudio add-in to insert Markdown citations")
15600 (description
15601 "This package provides functions and an RStudio add-in that search a
15602 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
15603 the current document.")
15604 (license license:expat)))
15605
15606 (define-public r-xgboost
15607 (package
15608 (name "r-xgboost")
15609 (version "1.0.0.2")
15610 (source
15611 (origin
15612 (method url-fetch)
15613 (uri (cran-uri "xgboost" version))
15614 (sha256
15615 (base32
15616 "1ld2w51c5fy3bl0kvjn1iplffc4lmin9s9zz5xx7xsm44d6j6kzd"))))
15617 (build-system r-build-system)
15618 (propagated-inputs
15619 `(("r-data-table" ,r-data-table)
15620 ("r-magrittr" ,r-magrittr)
15621 ("r-matrix" ,r-matrix)
15622 ("r-stringi" ,r-stringi)))
15623 (native-inputs
15624 `(("r-knitr" ,r-knitr)))
15625 (home-page "https://github.com/dmlc/xgboost")
15626 (synopsis "Extreme gradient boosting")
15627 (description
15628 "This package provides an R interface to Extreme Gradient Boosting, which
15629 is an efficient implementation of the gradient boosting framework from Chen
15630 and Guestrin (2016). The package includes efficient linear model solver and
15631 tree learning algorithms. The package can automatically do parallel
15632 computation on a single machine. It supports various objective functions,
15633 including regression, classification and ranking. The package is made to be
15634 extensible, so that users are also allowed to define their own objectives
15635 easily.")
15636 (license license:asl2.0)))
15637
15638 (define-public r-umap
15639 (package
15640 (name "r-umap")
15641 (version "0.2.5.0")
15642 (source
15643 (origin
15644 (method url-fetch)
15645 (uri (cran-uri "umap" version))
15646 (sha256
15647 (base32
15648 "0qp8zbh6fn8kn6q2h2lyjgmq3pr6gqwsd8ymqx25px13zjhxch9d"))))
15649 (build-system r-build-system)
15650 (propagated-inputs
15651 `(("r-openssl" ,r-openssl)
15652 ("r-rcpp" ,r-rcpp)
15653 ("r-reticulate" ,r-reticulate)
15654 ("r-rspectra" ,r-rspectra)))
15655 (native-inputs
15656 `(("r-knitr" ,r-knitr)))
15657 (home-page "https://github.com/tkonopka/umap")
15658 (synopsis "Uniform manifold approximation and projection")
15659 (description
15660 "Uniform manifold approximation and projection is a technique for
15661 dimension reduction. This package provides an interface to the UMAP algorithm
15662 in R, including a translation of the original algorithm into R.")
15663 (license license:expat)))
15664
15665 (define-public r-uwot
15666 (package
15667 (name "r-uwot")
15668 (version "0.1.8")
15669 (source
15670 (origin
15671 (method url-fetch)
15672 (uri (cran-uri "uwot" version))
15673 (sha256
15674 (base32
15675 "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd"))))
15676 (build-system r-build-system)
15677 (propagated-inputs
15678 `(("r-dqrng" ,r-dqrng)
15679 ("r-fnn" ,r-fnn)
15680 ("r-irlba" ,r-irlba)
15681 ("r-matrix" ,r-matrix)
15682 ("r-rcpp" ,r-rcpp)
15683 ("r-rcppannoy" ,r-rcppannoy)
15684 ("r-rcppprogress" ,r-rcppprogress)
15685 ("r-rspectra" ,r-rspectra)))
15686 (home-page "https://github.com/jlmelville/uwot")
15687 (synopsis "Uniform manifold approximation and projection")
15688 (description
15689 "This package provides an implementation of the Uniform Manifold
15690 Approximation and Projection dimensionality reduction by McInnes et
15691 al. (2018). It also provides means to transform new data and to carry out
15692 supervised dimensionality reduction. An implementation of the related
15693 LargeVis method of Tang et al. (2016) is also provided.")
15694 (license license:gpl3)))
15695
15696 (define-public r-kableextra
15697 (package
15698 (name "r-kableextra")
15699 (version "1.1.0")
15700 (source
15701 (origin
15702 (method url-fetch)
15703 (uri (cran-uri "kableExtra" version))
15704 (sha256
15705 (base32
15706 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
15707 (properties `((upstream-name . "kableExtra")))
15708 (build-system r-build-system)
15709 (propagated-inputs
15710 `(("r-digest" ,r-digest)
15711 ("r-glue" ,r-glue)
15712 ("r-htmltools" ,r-htmltools)
15713 ("r-knitr" ,r-knitr)
15714 ("r-magrittr" ,r-magrittr)
15715 ("r-readr" ,r-readr)
15716 ("r-rmarkdown" ,r-rmarkdown)
15717 ("r-rstudioapi" ,r-rstudioapi)
15718 ("r-rvest" ,r-rvest)
15719 ("r-scales" ,r-scales)
15720 ("r-stringr" ,r-stringr)
15721 ("r-viridislite" ,r-viridislite)
15722 ("r-webshot" ,r-webshot)
15723 ("r-xml2" ,r-xml2)))
15724 (home-page "https://haozhu233.github.io/kableExtra/")
15725 (synopsis "Construct complex tables with pipe syntax")
15726 (description
15727 "Build complex HTML or LaTeX tables using @code{kable()} from
15728 @code{knitr} and the piping syntax from @code{magrittr}. The function
15729 @code{kable()} is a light weight table generator coming from @code{knitr}.
15730 This package simplifies the way to manipulate the HTML or LaTeX codes
15731 generated by @code{kable()} and allows users to construct complex tables and
15732 customize styles using a readable syntax.")
15733 (license license:expat)))
15734
15735 (define-public r-glasso
15736 (package
15737 (name "r-glasso")
15738 (version "1.11")
15739 (source
15740 (origin
15741 (method url-fetch)
15742 (uri (cran-uri "glasso" version))
15743 (sha256
15744 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
15745 (build-system r-build-system)
15746 (native-inputs `(("gfortran" ,gfortran)))
15747 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
15748 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
15749 (description
15750 "This is a package for estimation of a sparse inverse covariance matrix
15751 using a lasso (L1) penalty. Facilities are provided for estimates along a
15752 path of values for the regularization parameter.")
15753 (license license:gpl2)))
15754
15755 (define-public r-rhpcblasctl
15756 (package
15757 (name "r-rhpcblasctl")
15758 (version "0.20-17")
15759 (source
15760 (origin
15761 (method url-fetch)
15762 (uri (cran-uri "RhpcBLASctl" version))
15763 (sha256
15764 (base32
15765 "0iwc06blr5sx7rylwczi2jrha8sk8qs0jklflwpidl0zj1jxdggp"))))
15766 (properties `((upstream-name . "RhpcBLASctl")))
15767 (build-system r-build-system)
15768 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
15769 (synopsis "Control the number of threads on BLAS")
15770 (description
15771 "This package allows you to control the number of threads the BLAS
15772 library uses. It is also possible to control the number of threads in
15773 OpenMP.")
15774 (license license:agpl3+)))
15775
15776 (define-public r-lda
15777 (package
15778 (name "r-lda")
15779 (version "1.4.2")
15780 (source
15781 (origin
15782 (method url-fetch)
15783 (uri (cran-uri "lda" version))
15784 (sha256
15785 (base32
15786 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
15787 (build-system r-build-system)
15788 (home-page "https://cran.r-project.org/web/packages/lda/")
15789 (synopsis "Collapsed Gibbs sampling methods for topic models")
15790 (description
15791 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
15792 related models. This includes (but is not limited to) sLDA, corrLDA, and the
15793 mixed-membership stochastic blockmodel. Inference for all of these models is
15794 implemented via a fast collapsed Gibbs sampler written in C. Utility
15795 functions for reading/writing data typically used in topic models, as well as
15796 tools for examining posterior distributions are also included.")
15797 ;; Any version of the LGPL
15798 (license license:lgpl3+)))
15799
15800 (define-public r-rann-l1
15801 (package
15802 (name "r-rann-l1")
15803 (version "2.5.2")
15804 (source
15805 (origin
15806 (method url-fetch)
15807 (uri (cran-uri "RANN.L1" version))
15808 (sha256
15809 (base32
15810 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
15811 (properties `((upstream-name . "RANN.L1")))
15812 (build-system r-build-system)
15813 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
15814 (synopsis "Fast nearest neighbour search using L1 metric")
15815 (description
15816 "This package provides tools to find the k nearest neighbours for every
15817 point in a given dataset in O(N log N) time using Arya and Mount's ANN
15818 library. There is support for approximate as well as exact searches, fixed
15819 radius searches and @code{bd} as well as @code{kd} trees. The distance is
15820 computed using the L1 (Manhattan, taxicab) metric.")
15821 (license license:gpl3+)))
15822
15823 (define-public r-leiden
15824 (package
15825 (name "r-leiden")
15826 (version "0.3.3")
15827 (source
15828 (origin
15829 (method url-fetch)
15830 (uri (cran-uri "leiden" version))
15831 (sha256
15832 (base32
15833 "1hh6bmbz6cpqwl4i94gxylgv9x92zbqdg81r8r4ymfy8c70f3df2"))))
15834 (properties `((upstream-name . "leiden")))
15835 (build-system r-build-system)
15836 (propagated-inputs
15837 `(("r-igraph" ,r-igraph)
15838 ("r-matrix" ,r-matrix)
15839 ("r-reticulate" ,r-reticulate)))
15840 (home-page "https://github.com/TomKellyGenetics/leiden")
15841 (synopsis "R implementation of Leiden clustering algorithm")
15842 (description
15843 "This package implements the Python @code{leidenalg} module to be called
15844 in R. It enables clustering using the Leiden algorithm for partitioning a
15845 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
15846 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
15847 (license license:gpl3)))
15848
15849 (define-public r-patchwork
15850 (package
15851 (name "r-patchwork")
15852 (version "1.0.0")
15853 (source
15854 (origin
15855 (method url-fetch)
15856 (uri (cran-uri "patchwork" version))
15857 (sha256
15858 (base32
15859 "0qrwbcswh7ylrmghi17k6wk7w51cz6mcmvcyyd41hy3m2ywmkywb"))))
15860 (build-system r-build-system)
15861 (propagated-inputs
15862 `(("r-ggplot2" ,r-ggplot2)
15863 ("r-gtable" ,r-gtable)))
15864 (native-inputs
15865 `(("r-knitr" ,r-knitr)))
15866 (home-page "https://github.com/thomasp85/patchwork")
15867 (synopsis "Compose ggplot2 plots")
15868 (description
15869 "The @code{ggplot2} package provides a strong API for sequentially
15870 building up a plot, but does not concern itself with composition of multiple
15871 plots. Patchwork is a package that expands the API to allow for arbitrarily
15872 complex composition of plots by providing mathmatical operators for combining
15873 multiple plots.")
15874 (license license:expat)))
15875
15876 (define-public r-liger
15877 (package
15878 (name "r-liger")
15879 (version "0.4.2")
15880 (source
15881 (origin
15882 (method git-fetch)
15883 (uri (git-reference
15884 (url "https://github.com/MacoskoLab/liger.git")
15885 (commit (string-append "v" version))))
15886 (file-name (git-file-name name version))
15887 (sha256
15888 (base32
15889 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
15890 (modules '((guix build utils)))
15891 (snippet
15892 '(begin
15893 (delete-file "inst/java/ModularityOptimizer.jar")
15894 #t))))
15895 (build-system r-build-system)
15896 (arguments
15897 `(#:phases
15898 (modify-phases %standard-phases
15899 (add-after 'unpack 'build-java-part
15900 (lambda* (#:key inputs #:allow-other-keys)
15901 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
15902 (for-each (lambda (file) (invoke "javac" file))
15903 (find-files "." "\\.java$"))
15904 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
15905 (find-files "." "\\.class$"))
15906 #t)))))
15907 (propagated-inputs
15908 `(("r-cowplot" ,r-cowplot)
15909 ("r-dosnow" ,r-dosnow)
15910 ("r-dplyr" ,r-dplyr)
15911 ("r-fnn" ,r-fnn)
15912 ("r-foreach" ,r-foreach)
15913 ("r-ggplot2" ,r-ggplot2)
15914 ("r-ggrepel" ,r-ggrepel)
15915 ("r-hmisc" ,r-hmisc)
15916 ("r-ica" ,r-ica)
15917 ("r-irlba" ,r-irlba)
15918 ("r-matrix" ,r-matrix)
15919 ("r-mclust" ,r-mclust)
15920 ("r-patchwork" ,r-patchwork)
15921 ("r-plyr" ,r-plyr)
15922 ("r-rann-l1" ,r-rann-l1)
15923 ("r-rcpp" ,r-rcpp)
15924 ("r-rcpparmadillo" ,r-rcpparmadillo)
15925 ("r-riverplot" ,r-riverplot)
15926 ("r-rtsne" ,r-rtsne)
15927 ("r-snow" ,r-snow)))
15928 (native-inputs
15929 `(("jdk" ,icedtea "jdk")
15930 ;; See https://github.com/MacoskoLab/liger/issues/96
15931 ;; The optimizer is released under the Expat license.
15932 ("optimizer-src"
15933 ,(origin
15934 (method url-fetch)
15935 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
15936 (sha256
15937 (base32
15938 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
15939 ("unzip" ,unzip)
15940 ("r-knitr" ,r-knitr))) ; for vignettes
15941 (home-page "https://github.com/MacoskoLab/liger")
15942 (synopsis "Integrate and analyze multiple single-cell datasets")
15943 (description
15944 "LIGER is a package for integrating and analyzing multiple single-cell
15945 datasets, developed and maintained by the Macosko lab. It relies on
15946 integrative non-negative matrix factorization to identify shared and
15947 dataset-specific factors.")
15948 (license license:gpl3)))
15949
15950 (define-public r-harmony
15951 (package
15952 (name "r-harmony")
15953 (version "0.1")
15954 (source
15955 (origin
15956 (method git-fetch)
15957 (uri (git-reference
15958 (url "https://github.com/immunogenomics/harmony")
15959 (commit version)))
15960 (file-name (git-file-name name version))
15961 (sha256
15962 (base32
15963 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
15964 (modules '((guix build utils)))
15965 (snippet
15966 '(begin
15967 (for-each delete-file '("config.status" "configure"))
15968 #t))))
15969 (build-system r-build-system)
15970 (propagated-inputs
15971 `(("r-cowplot" ,r-cowplot)
15972 ("r-dplyr" ,r-dplyr)
15973 ("r-ggplot2" ,r-ggplot2)
15974 ("r-irlba" ,r-irlba)
15975 ("r-matrix" ,r-matrix)
15976 ("r-rcpp" ,r-rcpp)
15977 ("r-rcpparmadillo" ,r-rcpparmadillo)
15978 ("r-rcppprogress" ,r-rcppprogress)
15979 ("r-rlang" ,r-rlang)
15980 ("r-tibble" ,r-tibble)
15981 ("r-tidyr" ,r-tidyr)))
15982 (native-inputs
15983 `(("autoconf" ,autoconf)))
15984 (home-page "https://github.com/immunogenomics/harmony")
15985 (synopsis "Integration of single cell sequencing data")
15986 (description
15987 "This package provides an implementation of the Harmony algorithm for
15988 single cell integration, described in Korsunsky et al
15989 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
15990 function and interfaces to external frameworks.")
15991 (license license:gpl3)))
15992
15993 (define-public r-covr
15994 (package
15995 (name "r-covr")
15996 (version "3.5.0")
15997 (source
15998 (origin
15999 (method url-fetch)
16000 (uri (cran-uri "covr" version))
16001 (sha256
16002 (base32 "1pvr95h7jg9hqq1qq1cccy323pkxldrwafl08151cc410499k4fb"))))
16003 (properties `((upstream-name . "covr")))
16004 (build-system r-build-system)
16005 (propagated-inputs
16006 `(("r-crayon" ,r-crayon)
16007 ("r-digest" ,r-digest)
16008 ("r-httr" ,r-httr)
16009 ("r-jsonlite" ,r-jsonlite)
16010 ("r-rex" ,r-rex)
16011 ("r-withr" ,r-withr)
16012 ("r-yaml" ,r-yaml)))
16013 (native-inputs
16014 `(("r-knitr" ,r-knitr))) ; for vignettes
16015 (home-page "https://github.com/r-lib/covr")
16016 (synopsis "Test coverage for R packages")
16017 (description
16018 "Thisp package enables you to track and report code coverage for your
16019 package and (optionally) upload the results to a coverage service. Code
16020 coverage is a measure of the amount of code being exercised by a set of tests.
16021 It is an indirect measure of test quality and completeness. This package is
16022 compatible with any testing methodology or framework and tracks coverage of
16023 both R code and compiled C/C++/FORTRAN code.")
16024 (license license:gpl3)))
16025
16026 (define-public r-systemfonts
16027 (package
16028 (name "r-systemfonts")
16029 (version "0.2.1")
16030 (source
16031 (origin
16032 (method url-fetch)
16033 (uri (cran-uri "systemfonts" version))
16034 (sha256
16035 (base32
16036 "0dna00xai0pw76b4830yy4r5j1hq7f7kla67v0iz39cjm4rq4ygq"))))
16037 (properties `((upstream-name . "systemfonts")))
16038 (build-system r-build-system)
16039 (inputs
16040 `(("fontconfig" ,fontconfig)
16041 ("zlib" ,zlib)))
16042 (native-inputs
16043 `(("pkg-config" ,pkg-config)
16044 ("r-knitr" ,r-knitr)))
16045 (home-page "https://github.com/r-lib/systemfonts")
16046 (synopsis "System native font finding")
16047 (description
16048 "This package provides system native access to the font catalogue. As
16049 font handling varies between systems it is difficult to correctly locate
16050 installed fonts across different operating systems. The 'systemfonts' package
16051 provides bindings to the native libraries for finding font files that can then
16052 be used further by e.g. graphic devices.")
16053 (license license:expat)))
16054
16055 (define-public r-graphlayouts
16056 (package
16057 (name "r-graphlayouts")
16058 (version "0.7.0")
16059 (source
16060 (origin
16061 (method url-fetch)
16062 (uri (cran-uri "graphlayouts" version))
16063 (sha256
16064 (base32
16065 "17lc75k8i3c696hfj44zj7j1a5sb0nap8spc5r98v7vd6xh4nii0"))))
16066 (properties `((upstream-name . "graphlayouts")))
16067 (build-system r-build-system)
16068 (propagated-inputs
16069 `(("r-igraph" ,r-igraph)
16070 ("r-rcpp" ,r-rcpp)
16071 ("r-rcpparmadillo" ,r-rcpparmadillo)))
16072 (home-page "https://github.com/schochastics/graphlayouts")
16073 (synopsis "Additional layout algorithms for network visualizations")
16074 (description
16075 "This package provides several layout algorithms to visualize networks
16076 which are not part of the igraph library. Most are based on the concept of
16077 stress majorization by Gansner et al. (2004)
16078 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
16079 emphasize hidden group structures in networks or focus on specific nodes.")
16080 (license license:expat)))
16081
16082 (define-public r-tidygraph
16083 (package
16084 (name "r-tidygraph")
16085 (version "1.1.2")
16086 (source
16087 (origin
16088 (method url-fetch)
16089 (uri (cran-uri "tidygraph" version))
16090 (sha256
16091 (base32
16092 "1zpsarm74afbc7p5dlyb0whc09670qdcddw1ckb25cfc9hfh0hjn"))))
16093 (properties `((upstream-name . "tidygraph")))
16094 (build-system r-build-system)
16095 (propagated-inputs
16096 `(("r-dplyr" ,r-dplyr)
16097 ("r-igraph" ,r-igraph)
16098 ("r-magrittr" ,r-magrittr)
16099 ("r-pillar" ,r-pillar)
16100 ("r-r6" ,r-r6)
16101 ("r-rcpp" ,r-rcpp)
16102 ("r-rlang" ,r-rlang)
16103 ("r-tibble" ,r-tibble)
16104 ("r-tidyr" ,r-tidyr)))
16105 (home-page "https://github.com/thomasp85/tidygraph")
16106 (synopsis "Tidy API for graph manipulation")
16107 (description
16108 "This package provides a graph implementation that can be thought of as
16109 two tidy data frames describing node and edge data respectively. It provides
16110 an approach to manipulate these two virtual data frames using the API defined
16111 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
16112 common graph algorithms.")
16113 (license license:expat)))
16114
16115 (define-public r-soupx
16116 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
16117 (revision "1"))
16118 (package
16119 (name "r-soupx")
16120 (version (git-version "0.3.1" revision commit))
16121 (source
16122 (origin
16123 (method git-fetch)
16124 (uri (git-reference
16125 (url "https://github.com/constantAmateur/SoupX")
16126 (commit commit)))
16127 (file-name (git-file-name name version))
16128 (sha256
16129 (base32
16130 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
16131 (properties `((upstream-name . "SoupX")))
16132 (build-system r-build-system)
16133 (propagated-inputs
16134 `(("r-ggplot2" ,r-ggplot2)
16135 ("r-matrix" ,r-matrix)
16136 ("r-seurat" ,r-seurat)))
16137 (home-page "https://github.com/constantAmateur/SoupX")
16138 (synopsis "Single cell mRNA Soup eXterminator")
16139 (description
16140 "This package provides a package for quantifying, profiling and
16141 removing cell free mRNA contamination (the \"soup\") from droplet based single
16142 cell RNA-seq experiments.")
16143 (license license:gpl2))))
16144
16145 (define-public r-assertr
16146 (package
16147 (name "r-assertr")
16148 (version "2.7")
16149 (source
16150 (origin
16151 (method url-fetch)
16152 (uri (cran-uri "assertr" version))
16153 (sha256
16154 (base32
16155 "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
16156 (build-system r-build-system)
16157 (propagated-inputs
16158 `(("r-dplyr" ,r-dplyr)
16159 ("r-mass" ,r-mass)
16160 ("r-rlang" ,r-rlang)))
16161 (native-inputs
16162 `(("r-knitr" ,r-knitr))) ; needed for vignette
16163 (home-page "https://github.com/ropensci/assertr")
16164 (synopsis "Assertive programming for R analysis pipelines")
16165 (description
16166 "This package provides functionality to assert conditions that have to be
16167 met so that errors in data used in analysis pipelines can fail quickly. It is
16168 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
16169 in pipelines.")
16170 (license license:expat)))
16171
16172 (define-public r-parameters
16173 (package
16174 (name "r-parameters")
16175 (version "0.6.1")
16176 (source
16177 (origin
16178 (method url-fetch)
16179 (uri (cran-uri "parameters" version))
16180 (sha256
16181 (base32
16182 "0mylxkf1y6mk4kf6c57x102sf4c800pfasjcfbf1hnsh6ya0m6dy"))))
16183 (properties `((upstream-name . "parameters")))
16184 (build-system r-build-system)
16185 (propagated-inputs
16186 `(("r-bayestestr" ,r-bayestestr)
16187 ("r-insight" ,r-insight)))
16188 (native-inputs
16189 `(("r-knitr" ,r-knitr)))
16190 (home-page "https://cran.r-project.org/web/packages/parameters")
16191 (synopsis "Processing of model parameters")
16192 (description
16193 "This package provides utilities for processing the parameters of various
16194 statistical models. Beyond computing p values, CIs, and other indices for a
16195 wide variety of models, this package implements features like standardization
16196 or bootstrapping of parameters and models, feature reduction (feature
16197 extraction and variable selection) as well as conversion between indices of
16198 effect size.")
16199 (license license:gpl3)))
16200
16201 (define-public r-rgdal
16202 (package
16203 (name "r-rgdal")
16204 (version "1.4-8")
16205 (source
16206 (origin
16207 (method url-fetch)
16208 (uri (cran-uri "rgdal" version))
16209 (sha256
16210 (base32 "1jd691amf3ghznq5im15gvhl6v6k25klpl75m4ngrqf9xlxaa3as"))))
16211 (properties `((upstream-name . "rgdal")))
16212 (build-system r-build-system)
16213 (inputs
16214 `(("gdal" ,gdal)
16215 ("proj.4" ,proj.4)
16216 ("zlib" ,zlib)))
16217 (propagated-inputs
16218 `(("r-sp" ,r-sp)))
16219 (native-inputs
16220 `(("pkg-config" ,pkg-config)))
16221 (home-page "http://rgdal.r-forge.r-project.org")
16222 (synopsis "Bindings for the Geospatial Data Abstraction Library")
16223 (description
16224 "This package provides bindings to the Geospatial Data Abstraction
16225 Library (GDAL) and access to projection/transformation operations from the
16226 PROJ.4 library.")
16227 (license license:gpl2+)))
16228
16229 (define-public r-insol
16230 (package
16231 (name "r-insol")
16232 (version "1.2.1")
16233 (source
16234 (origin
16235 (method url-fetch)
16236 (uri (cran-uri "insol" version))
16237 (sha256
16238 (base32
16239 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
16240 (properties `((upstream-name . "insol")))
16241 (build-system r-build-system)
16242 (propagated-inputs
16243 `(("r-raster" ,r-raster)))
16244 (native-inputs
16245 `(("gfortran" ,gfortran)))
16246 (home-page "https://meteoexploration.com/R/insol/index.html")
16247 (synopsis "Tools for calculating solar radiation")
16248 (description
16249 "This package provides functions to compute insolation on tilted
16250 surfaces, computes atmospheric transmittance and related parameters such as:
16251 Earth radius vector, declination, sunset and sunrise, daylength, equation of
16252 time, vector in the direction of the sun, vector normal to surface, and some
16253 atmospheric physics.")
16254 (license license:gpl2+)))
16255
16256 (define-public r-lifecycle
16257 (package
16258 (name "r-lifecycle")
16259 (version "0.2.0")
16260 (source
16261 (origin
16262 (method url-fetch)
16263 (uri (cran-uri "lifecycle" version))
16264 (sha256
16265 (base32
16266 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
16267 (properties `((upstream-name . "lifecycle")))
16268 (build-system r-build-system)
16269 (propagated-inputs
16270 `(("r-glue" ,r-glue)
16271 ("r-rlang" ,r-rlang)))
16272 (native-inputs
16273 `(("r-knitr" ,r-knitr))) ; for vignettes
16274 (home-page "https://github.com/r-lib/lifecycle")
16275 (synopsis "Manage the life cycle of your package functions")
16276 (description
16277 "Manage the life cycle of your exported functions with shared
16278 conventions, documentation badges, and non-invasive deprecation warnings. The
16279 lifecycle package defines four development stages (experimental, maturing,
16280 stable, and questioning) and three deprecation stages (soft-deprecated,
16281 deprecated, and defunct). It makes it easy to insert badges corresponding to
16282 these stages in your documentation. Usage of deprecated functions are
16283 signalled with increasing levels of non-invasive verbosity.")
16284 (license license:gpl3)))
16285
16286 (define-public r-assertable
16287 (package
16288 (name "r-assertable")
16289 (version "0.2.7")
16290 (source
16291 (origin
16292 (method url-fetch)
16293 (uri (cran-uri "assertable" version))
16294 (sha256
16295 (base32
16296 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
16297 (build-system r-build-system)
16298 (propagated-inputs
16299 `(("r-data-table" ,r-data-table)))
16300 (home-page "https://cran.r-project.org/web/packages/assertable/")
16301 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
16302 (description "This package provides simple, flexible assertions on
16303 data.frame or data.table objects with verbose output for vetting. While other
16304 assertion packages apply towards more general use-cases, @code{assertable} is
16305 tailored towards tabular data. It includes functions to check variable names
16306 and values, whether the dataset contains all combinations of a given set of
16307 unique identifiers, and whether it is a certain length. In addition,
16308 @code{assertable} includes utility functions to check the existence of target
16309 files and to efficiently import multiple tabular data files into one
16310 data.table.")
16311 (license license:gpl3)))
16312
16313 (define-public r-quadprog
16314 (package
16315 (name "r-quadprog")
16316 (version "1.5-8")
16317 (source
16318 (origin
16319 (method url-fetch)
16320 (uri (cran-uri "quadprog" version))
16321 (sha256
16322 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
16323 (build-system r-build-system)
16324 (native-inputs
16325 `(("gfortran" ,gfortran)))
16326 (home-page "https://cran.r-project.org/web/packages/quadprog")
16327 (synopsis "Functions to solve quadratic programming problems")
16328 (description
16329 "This package contains routines and documentation for solving quadratic
16330 programming problems.")
16331 (license license:gpl3+)))
16332
16333 (define-public r-desolve
16334 (package
16335 (name "r-desolve")
16336 (version "1.28")
16337 (source
16338 (origin
16339 (method url-fetch)
16340 (uri (cran-uri "deSolve" version))
16341 (sha256
16342 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
16343 (properties `((upstream-name . "deSolve")))
16344 (build-system r-build-system)
16345 (native-inputs
16346 `(("gfortran" ,gfortran)))
16347 (home-page "https://desolve.r-forge.r-project.org/")
16348 (synopsis "Solvers for initial value problems of differential equations")
16349 (description "This package provides functions that solve initial value
16350 problems of a system of first-order @dfn{ordinary differential
16351 equations} (ODE), of @dfn{partial differential equations} (PDE), of
16352 @dfn{differential algebraic equations} (DAE), and of delay differential
16353 equations. The functions provide an interface to the FORTRAN functions
16354 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
16355 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
16356 C-implementation of solvers of the Runge-Kutta family with fixed or variable
16357 time steps. The package contains routines designed for solving ODEs resulting
16358 from 1-D, 2-D and 3-D partial differential equations that have been converted
16359 to ODEs by numerical differencing.")
16360 (license license:gpl2+)))
16361
16362 (define-public r-pracma
16363 (package
16364 (name "r-pracma")
16365 (version "2.2.9")
16366 (source (origin
16367 (method url-fetch)
16368 (uri (cran-uri "pracma" version))
16369 (sha256
16370 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
16371 (build-system r-build-system)
16372 (home-page "https://cran.r-project.org/web/packages/pracma/")
16373 (synopsis "Practical numerical math functions")
16374 (description "This package provides functions for numerical analysis and
16375 linear algebra, numerical optimization, differential equations, plus some
16376 special functions. It uses Matlab function names where appropriate to simplify
16377 porting.")
16378 (license license:gpl3+)))
16379
16380 (define-public r-subplex
16381 (package
16382 (name "r-subplex")
16383 (version "1.6")
16384 (source
16385 (origin
16386 (method url-fetch)
16387 (uri (cran-uri "subplex" version))
16388 (sha256
16389 (base32
16390 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
16391 (build-system r-build-system)
16392 (native-inputs
16393 `(("gfortran" ,gfortran)))
16394 (home-page "https://cran.r-project.org/web/packages/subplex")
16395 (synopsis "Unconstrained optimization using the subplex algorithm")
16396 (description
16397 "This package implements the Subplex optimization algorithm.
16398 It solves unconstrained optimization problems using a simplex method on
16399 subspaces. The method is well suited for optimizing objective functions that
16400 are noisy or are discontinuous at the solution.")
16401 (license license:gpl3+)))
16402
16403 (define-public r-txtplot
16404 (package
16405 (name "r-txtplot")
16406 (version "1.0-4")
16407 (source
16408 (origin
16409 (method url-fetch)
16410 (uri (cran-uri "txtplot" version))
16411 (sha256
16412 (base32
16413 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
16414 (build-system r-build-system)
16415 (home-page "https://cran.r-project.org/web/packages/txtplot/")
16416 (synopsis "Text-based plotting")
16417 (description "This package provides functions to produce rudimentary ASCII
16418 graphics directly in the terminal window. This package provides a basic
16419 plotting function (and equivalents of curve, density, acf and barplot) as well
16420 as a boxplot function.")
16421 (license license:lgpl3+)))
16422
16423 (define-public r-bio3d
16424 (package
16425 (name "r-bio3d")
16426 (version "2.4-1")
16427 (source
16428 (origin
16429 (method url-fetch)
16430 (uri (cran-uri "bio3d" version))
16431 (sha256
16432 (base32
16433 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
16434 (properties `((upstream-name . "bio3d")))
16435 (build-system r-build-system)
16436 (inputs `(("zlib" ,zlib)))
16437 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16438 (home-page "http://thegrantlab.org/bio3d/")
16439 (synopsis "Biological structure analysis")
16440 (description
16441 "This package provides utilities to process, organize and explore protein
16442 structure, sequence and dynamics data. Features include the ability to read
16443 and write structure, sequence and dynamic trajectory data, perform sequence
16444 and structure database searches, data summaries, atom selection, alignment,
16445 superposition, rigid core identification, clustering, torsion analysis,
16446 distance matrix analysis, structure and sequence conservation analysis, normal
16447 mode analysis, principal component analysis of heterogeneous structure data,
16448 and correlation network analysis from normal mode and molecular dynamics data.
16449 In addition, various utility functions are provided to enable the statistical
16450 and graphical power of the R environment to work with biological sequence and
16451 structural data.")
16452 (license license:gpl2+)))
16453
16454 (define-public r-bios2cor
16455 (package
16456 (name "r-bios2cor")
16457 (version "2.1")
16458 (source
16459 (origin
16460 (method url-fetch)
16461 (uri (cran-uri "Bios2cor" version))
16462 (sha256
16463 (base32
16464 "04wk1cjrrxhpv1kdhd67r1qvjv268xxi0z0r105wy912110z9m6x"))))
16465 (properties `((upstream-name . "Bios2cor")))
16466 (build-system r-build-system)
16467 (propagated-inputs
16468 `(("r-bigmemory" ,r-bigmemory)
16469 ("r-bio3d" ,r-bio3d)
16470 ("r-circular" ,r-circular)
16471 ("r-igraph" ,r-igraph)))
16472 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
16473 (synopsis "From biological sequences and simulations to correlation analysis")
16474 (description
16475 "This package provides utilities for computation and analysis of
16476 correlation/covariation in multiple sequence alignments and in side chain
16477 motions during molecular dynamics simulations. Features include the
16478 computation of correlation/covariation scores using a variety of scoring
16479 functions between either sequence positions in alignments or side chain
16480 dihedral angles in molecular dynamics simulations and utilities to analyze the
16481 correlation/covariation matrix through a variety of tools including network
16482 representation and principal components analysis. In addition, several
16483 utility functions are based on the R graphical environment to provide friendly
16484 tools for help in data interpretation.")
16485 (license license:gpl2+)))
16486
16487 ;; This package includes minified JavaScript files. When upgrading please
16488 ;; check that there are no new minified JavaScript files.
16489 (define-public r-networkd3
16490 (package
16491 (name "r-networkd3")
16492 (version "0.4")
16493 (source
16494 (origin
16495 (method url-fetch)
16496 (uri (cran-uri "networkD3" version))
16497 (sha256
16498 (base32
16499 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
16500 (snippet
16501 '(begin
16502 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
16503 #t))))
16504 (properties `((upstream-name . "networkD3")))
16505 (build-system r-build-system)
16506 (arguments
16507 `(#:modules ((guix build utils)
16508 (guix build r-build-system)
16509 (srfi srfi-1)
16510 (ice-9 popen))
16511 #:phases
16512 (modify-phases %standard-phases
16513 (add-after 'unpack 'process-javascript
16514 (lambda* (#:key inputs #:allow-other-keys)
16515 (with-directory-excursion "inst/htmlwidgets/lib/"
16516 (call-with-values
16517 (lambda ()
16518 (unzip2
16519 `((,(assoc-ref inputs "d3.v4.js")
16520 "d3-4.5.0/d3.min.js"))))
16521 (lambda (sources targets)
16522 (for-each (lambda (source target)
16523 (format #t "Processing ~a --> ~a~%"
16524 source target)
16525 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16526 (call-with-output-file target
16527 (lambda (port)
16528 (dump-port minified port)))))
16529 sources targets))))
16530 #t)))))
16531 (native-inputs
16532 `(("uglify-js" ,uglify-js)
16533 ;; NOTE: Make sure that this version of d3 is still valid when
16534 ;; upgrading the package.
16535 ("d3.v4.js"
16536 ,(origin
16537 (method url-fetch)
16538 (uri "https://d3js.org/d3.v4.js")
16539 (sha256
16540 (base32
16541 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
16542 (propagated-inputs
16543 `(("r-htmlwidgets" ,r-htmlwidgets)
16544 ("r-igraph" ,r-igraph)
16545 ("r-magrittr" ,r-magrittr)))
16546 (home-page "https://cran.r-project.org/package=networkD3")
16547 (synopsis "D3 JavaScript network graphs from R")
16548 (description
16549 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
16550 graphs from R.")
16551 (license license:gpl3+)))
16552
16553 (define-public r-aasea
16554 (package
16555 (name "r-aasea")
16556 (version "1.1.0")
16557 (source
16558 (origin
16559 (method url-fetch)
16560 (uri (cran-uri "aaSEA" version))
16561 (sha256
16562 (base32
16563 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
16564 (properties `((upstream-name . "aaSEA")))
16565 (build-system r-build-system)
16566 (propagated-inputs
16567 `(("r-bios2cor" ,r-bios2cor)
16568 ("r-dt" ,r-dt)
16569 ("r-hmisc" ,r-hmisc)
16570 ("r-magrittr" ,r-magrittr)
16571 ("r-networkd3" ,r-networkd3)
16572 ("r-plotly" ,r-plotly)
16573 ("r-seqinr" ,r-seqinr)
16574 ("r-shiny" ,r-shiny)
16575 ("r-shinydashboard" ,r-shinydashboard)))
16576 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
16577 (synopsis "Amino acid substitution effect analyzer")
16578 (description
16579 "Given a protein multiple sequence alignment, it is a daunting task to
16580 assess the effects of substitutions along sequence length. The aaSEA package
16581 is intended to help researchers to rapidly analyze property changes caused by
16582 single, multiple and correlated amino acid substitutions in proteins.")
16583 (license license:gpl3)))
16584
16585 (define-public r-abacus
16586 (package
16587 (name "r-abacus")
16588 (version "1.0.0")
16589 (source
16590 (origin
16591 (method url-fetch)
16592 (uri (cran-uri "ABACUS" version))
16593 (sha256
16594 (base32
16595 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
16596 (properties `((upstream-name . "ABACUS")))
16597 (build-system r-build-system)
16598 (propagated-inputs
16599 `(("r-ggplot2" ,r-ggplot2)
16600 ("r-shiny" ,r-shiny)))
16601 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
16602 (synopsis "Apps-based activities for communicating and understanding statistics")
16603 (description
16604 "This package provides a set of Shiny apps for effective communication
16605 and understanding in statistics. The current version includes properties of
16606 normal distribution, properties of sampling distribution, one-sample z and t
16607 tests, two samples independent (unpaired) t test and analysis of variance.")
16608 (license license:gpl3)))
16609
16610 (define-public r-abc-rap
16611 (package
16612 (name "r-abc-rap")
16613 (version "0.9.0")
16614 (source
16615 (origin
16616 (method url-fetch)
16617 (uri (cran-uri "ABC.RAP" version))
16618 (sha256
16619 (base32
16620 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
16621 (properties `((upstream-name . "ABC.RAP")))
16622 (build-system r-build-system)
16623 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
16624 (synopsis "Array-based CpG region analysis pipeline")
16625 (description
16626 "This package aims to identify candidate genes that are differentially
16627 methylated between cases and controls. It applies Student's t-test and delta
16628 beta analysis to identify candidate genes containing multiple CpG sites.")
16629 (license license:gpl3)))
16630
16631 (define-public r-abcadm
16632 (package
16633 (name "r-abcadm")
16634 (version "1.0")
16635 (source
16636 (origin
16637 (method url-fetch)
16638 (uri (cran-uri "abcADM" version))
16639 (sha256
16640 (base32
16641 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
16642 (properties `((upstream-name . "abcADM")))
16643 (build-system r-build-system)
16644 (propagated-inputs
16645 `(("r-bh" ,r-bh)
16646 ("r-rcpp" ,r-rcpp)))
16647 (home-page "https://cran.r-project.org/web/packages/abcADM/")
16648 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
16649 (description
16650 "This package provides tools to estimate parameters of accumulated
16651 damage (load duration) models based on failure time data under a Bayesian
16652 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
16653 long-term reliability under stochastic load profiles.")
16654 (license license:gpl3)))
16655
16656 (define-public r-rglpk
16657 (package
16658 (name "r-rglpk")
16659 (version "0.6-4")
16660 (source
16661 (origin
16662 (method url-fetch)
16663 (uri (cran-uri "Rglpk" version))
16664 (sha256
16665 (base32
16666 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
16667 (properties `((upstream-name . "Rglpk")))
16668 (build-system r-build-system)
16669 (propagated-inputs
16670 `(("r-slam" ,r-slam)))
16671 (inputs
16672 `(("glpk" ,glpk)))
16673 (home-page "https://r-forge.r-project.org/projects/rglp/")
16674 (synopsis "R interface to the GNU Linear Programming Kit")
16675 (description
16676 "This package provides an R interface to the GNU Linear Programming Kit,
16677 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
16678 integer linear programming} (MILP) and other related problems.")
16679 ;; Either license
16680 (license (list license:gpl2 license:gpl3))))
16681
16682 (define-public r-abcdefba
16683 (package
16684 (name "r-abcdefba")
16685 (version "0.4")
16686 (source
16687 (origin
16688 (method url-fetch)
16689 (uri (cran-uri "abcdeFBA" version))
16690 (sha256
16691 (base32
16692 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
16693 (properties `((upstream-name . "abcdeFBA")))
16694 (build-system r-build-system)
16695 (propagated-inputs
16696 `(("r-corrplot" ,r-corrplot)
16697 ("r-lattice" ,r-lattice)
16698 ("r-rgl" ,r-rgl)
16699 ("r-rglpk" ,r-rglpk)))
16700 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
16701 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
16702 (description
16703 "This package provides functions for Constraint Based Simulation using
16704 Flux Balance Analysis and informative analysis of the data generated during
16705 simulation.")
16706 (license license:gpl2)))
16707
16708 (define-public r-abcrlda
16709 (package
16710 (name "r-abcrlda")
16711 (version "1.0.2")
16712 (source
16713 (origin
16714 (method url-fetch)
16715 (uri (cran-uri "abcrlda" version))
16716 (sha256
16717 (base32
16718 "0zjdrbg3zx0znqnh0dvmifs9c12b8vjhbaf3nbwab9xh25nsmg75"))))
16719 (properties `((upstream-name . "abcrlda")))
16720 (build-system r-build-system)
16721 (home-page "https://ieeexplore.ieee.org/document/8720003/")
16722 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
16723 (description
16724 "This package offers methods to perform @dfn{asymptotically
16725 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
16726 cost-sensitive binary classification. The bias-correction is an estimate of
16727 the bias term added to regularized discriminant analysis that minimizes the
16728 overall risk.")
16729 (license license:gpl3)))
16730
16731 (define-public r-abemus
16732 (package
16733 (name "r-abemus")
16734 (version "1.0.1")
16735 (source
16736 (origin
16737 (method url-fetch)
16738 (uri (cran-uri "abemus" version))
16739 (sha256
16740 (base32
16741 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
16742 (properties `((upstream-name . "abemus")))
16743 (build-system r-build-system)
16744 (propagated-inputs
16745 `(("r-data-table" ,r-data-table)))
16746 (home-page "https://cran.r-project.org/web/packages/abemus/")
16747 (synopsis "Adaptive base error model in ultra-deep sequencing data")
16748 (description
16749 "This package provides an implementation of @dfn{Adaptive Base Error
16750 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
16751 platform-specific genetic knowledge and empirical signal to readily detect and
16752 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
16753 cell free DNA} (cfDNA).")
16754 (license license:gpl3)))
16755
16756 ;; This package includes minified JavaScript files. When upgrading please
16757 ;; check that there are no new minified JavaScript files.
16758 (define-public r-rintrojs
16759 (package
16760 (name "r-rintrojs")
16761 (version "0.2.2")
16762 (source
16763 (origin
16764 (method url-fetch)
16765 (uri (cran-uri "rintrojs" version))
16766 (sha256
16767 (base32
16768 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
16769 (properties `((upstream-name . "rintrojs")))
16770 (build-system r-build-system)
16771 (arguments
16772 `(#:modules ((guix build utils)
16773 (guix build r-build-system)
16774 (srfi srfi-1)
16775 (ice-9 popen))
16776 #:phases
16777 (modify-phases %standard-phases
16778 (add-after 'unpack 'process-javascript
16779 (lambda* (#:key inputs #:allow-other-keys)
16780 (with-directory-excursion "inst/javascript/introjs/"
16781 (call-with-values
16782 (lambda ()
16783 (unzip2
16784 `((,(assoc-ref inputs "intro.js")
16785 "intro.min.js"))))
16786 (lambda (sources targets)
16787 (for-each (lambda (source target)
16788 (format #t "Processing ~a --> ~a~%"
16789 source target)
16790 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16791 (call-with-output-file target
16792 (lambda (port)
16793 (dump-port minified port)))))
16794 sources targets))))
16795 #t)))))
16796 (native-inputs
16797 `(("uglify-js" ,uglify-js)
16798 ("intro.js"
16799 ,(origin
16800 (method url-fetch)
16801 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
16802 (sha256
16803 (base32
16804 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
16805 (propagated-inputs
16806 `(("r-jsonlite" ,r-jsonlite)
16807 ("r-shiny" ,r-shiny)))
16808 (home-page "https://github.com/carlganz/rintrojs")
16809 (synopsis "Wrapper for the Intro.js library")
16810 (description
16811 "This package provides a wrapper for the @url{http://www.introjs.com,
16812 Intro.js} library. This package makes it easy to include step-by-step
16813 introductions, and clickable hints in a Shiny application. It supports both
16814 static introductions in the UI, and programmatic introductions from the
16815 server-side.")
16816 (license license:agpl3+)))
16817
16818 (define-public r-sysfonts
16819 (package
16820 (name "r-sysfonts")
16821 (version "0.8")
16822 (source
16823 (origin
16824 (method url-fetch)
16825 (uri (cran-uri "sysfonts" version))
16826 (sha256
16827 (base32
16828 "0wng902plryf2d8fc7k7m3jx11acz51kb2d91cqbyhq7xpk06z43"))))
16829 (properties `((upstream-name . "sysfonts")))
16830 (build-system r-build-system)
16831 (inputs
16832 `(("freetype" ,freetype)
16833 ("libpng" ,libpng)
16834 ("zlib" ,zlib)))
16835 (native-inputs
16836 `(("pkg-config" ,pkg-config)))
16837 (home-page "https://github.com/yixuan/sysfonts")
16838 (synopsis "Loading fonts into R")
16839 (description
16840 "This is a package to simplify loading of system fonts and Google Fonts
16841 into R, in order to support other packages.")
16842 (license license:gpl2)))
16843
16844 (define-public r-showtextdb
16845 (package
16846 (name "r-showtextdb")
16847 (version "2.0")
16848 (source
16849 (origin
16850 (method url-fetch)
16851 (uri (cran-uri "showtextdb" version))
16852 (sha256
16853 (base32
16854 "1qwwj9x2jvadvwn60h75k99c9xi7yhqjsgaakahz5paxgj583bsh"))))
16855 (properties `((upstream-name . "showtextdb")))
16856 (build-system r-build-system)
16857 (propagated-inputs
16858 `(("r-sysfonts" ,r-sysfonts)))
16859 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
16860 (synopsis "Font files for the 'showtext' package")
16861 (description
16862 "This package provides font files that can be used by the @code{showtext}
16863 package.")
16864 (license license:asl2.0)))
16865
16866 (define-public r-showtext
16867 (package
16868 (name "r-showtext")
16869 (version "0.7-1")
16870 (source
16871 (origin
16872 (method url-fetch)
16873 (uri (cran-uri "showtext" version))
16874 (sha256
16875 (base32
16876 "0a5gg72bfrc7wm0phj1aflj1wc08kfi81ac32na6ya9s2ivyimw5"))))
16877 (properties `((upstream-name . "showtext")))
16878 (build-system r-build-system)
16879 (inputs
16880 `(("freetype" ,freetype)
16881 ("libpng" ,libpng)
16882 ("zlib" ,zlib)))
16883 (propagated-inputs
16884 `(("r-showtextdb" ,r-showtextdb)
16885 ("r-sysfonts" ,r-sysfonts)))
16886 (native-inputs `(("pkg-config" ,pkg-config)))
16887 (home-page "https://github.com/yixuan/showtext")
16888 (synopsis "Using fonts more easily in R graphs")
16889 (description
16890 "This package aims to make it easy to use various types of
16891 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
16892 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
16893 will be converted into polygons or raster images, hence after the plot has
16894 been created, it no longer relies on the font files. No external software
16895 such as Ghostscript is needed to use this package.")
16896 (license license:asl2.0)))
16897
16898 (define-public r-emojifont
16899 (package
16900 (name "r-emojifont")
16901 (version "0.5.3")
16902 (source
16903 (origin
16904 (method url-fetch)
16905 (uri (cran-uri "emojifont" version))
16906 (sha256
16907 (base32
16908 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
16909 (properties `((upstream-name . "emojifont")))
16910 (build-system r-build-system)
16911 (propagated-inputs
16912 `(("r-ggplot2" ,r-ggplot2)
16913 ("r-proto" ,r-proto)
16914 ("r-showtext" ,r-showtext)
16915 ("r-sysfonts" ,r-sysfonts)))
16916 (home-page "https://guangchuangyu.github.io/emojifont")
16917 (synopsis "Emoji and Font Awesome in R graphics")
16918 (description
16919 "This package enables the use of emoji and the Font Awesome glyphs in
16920 both base and ggplot2 graphics.")
16921 (license license:artistic2.0)))
16922
16923 (define-public r-abstractr
16924 (package
16925 (name "r-abstractr")
16926 (version "0.1.0")
16927 (source
16928 (origin
16929 (method url-fetch)
16930 (uri (cran-uri "abstractr" version))
16931 (sha256
16932 (base32
16933 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
16934 (properties `((upstream-name . "abstractr")))
16935 (build-system r-build-system)
16936 (propagated-inputs
16937 `(("r-colourpicker" ,r-colourpicker)
16938 ("r-emojifont" ,r-emojifont)
16939 ("r-ggplot2" ,r-ggplot2)
16940 ("r-gridextra" ,r-gridextra)
16941 ("r-rintrojs" ,r-rintrojs)
16942 ("r-shiny" ,r-shiny)
16943 ("r-shinythemes" ,r-shinythemes)))
16944 (home-page "https://matt-kumar.shinyapps.io/portfolio")
16945 (synopsis "R-Shiny application for creating visual abstracts")
16946 (description
16947 "This package provides an R Shiny application to create visual abstracts
16948 for original research. A variety of user defined options and formatting are
16949 included.")
16950 (license license:gpl3)))
16951
16952 (define-public r-qgam
16953 (package
16954 (name "r-qgam")
16955 (version "1.3.2")
16956 (source
16957 (origin
16958 (method url-fetch)
16959 (uri (cran-uri "qgam" version))
16960 (sha256
16961 (base32
16962 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
16963 (properties `((upstream-name . "qgam")))
16964 (build-system r-build-system)
16965 (propagated-inputs
16966 `(("r-doparallel" ,r-doparallel)
16967 ("r-mgcv" ,r-mgcv)
16968 ("r-plyr" ,r-plyr)
16969 ("r-shiny" ,r-shiny)))
16970 (native-inputs `(("r-knitr" ,r-knitr)))
16971 (home-page "https://cran.r-project.org/web/packages/qgam/")
16972 (synopsis "Smooth additive quantile regression models")
16973 (description
16974 "This package provides smooth additive quantile regression models, fitted
16975 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
16976 the smoothing parameters are estimated automatically by marginal loss
16977 minimization, while the regression coefficients are estimated using either
16978 PIRLS or Newton algorithm. The learning rate is determined so that the
16979 Bayesian credible intervals of the estimated effects have approximately the
16980 correct coverage. The main function is @code{qgam()} which is similar to
16981 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
16982 regression models.")
16983 (license license:gpl2+)))
16984
16985 (define-public r-abtest
16986 (package
16987 (name "r-abtest")
16988 (version "0.2.1")
16989 (source
16990 (origin
16991 (method url-fetch)
16992 (uri (cran-uri "abtest" version))
16993 (sha256
16994 (base32
16995 "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
16996 (properties `((upstream-name . "abtest")))
16997 (build-system r-build-system)
16998 (propagated-inputs
16999 `(("r-matrix" ,r-matrix)
17000 ("r-mvtnorm" ,r-mvtnorm)
17001 ("r-plotrix" ,r-plotrix)
17002 ("r-qgam" ,r-qgam)
17003 ("r-rcolorbrewer" ,r-rcolorbrewer)
17004 ("r-rcpp" ,r-rcpp)
17005 ("r-sn" ,r-sn)
17006 ("r-truncnorm" ,r-truncnorm)))
17007 (home-page "https://cran.r-project.org/web/packages/abtest/")
17008 (synopsis "Bayesian A/B testing")
17009 (description
17010 "This package provides functions for Bayesian A/B testing including prior
17011 elicitation options based on Kass and Vaidyanathan (1992)
17012 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
17013 (license license:gpl2+)))
17014
17015 (define-public r-accept
17016 (package
17017 (name "r-accept")
17018 (version "0.7.1")
17019 (source
17020 (origin
17021 (method url-fetch)
17022 (uri (cran-uri "accept" version))
17023 (sha256
17024 (base32
17025 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
17026 (properties `((upstream-name . "accept")))
17027 (build-system r-build-system)
17028 (propagated-inputs
17029 `(("r-dplyr" ,r-dplyr)
17030 ("r-extrafont" ,r-extrafont)
17031 ("r-mass" ,r-mass)
17032 ("r-plotly" ,r-plotly)
17033 ("r-stringr" ,r-stringr)
17034 ("r-viridis" ,r-viridis)))
17035 (home-page "https://cran.r-project.org/web/packages/accept/")
17036 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
17037 (description
17038 "This package allows clinicians to predict the rate and severity of
17039 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
17040 Disease} (COPD) patients, based on the clinical prediction model published in
17041 Adibi et al. (2019) @url{doi:10.1101/651901}.")
17042 (license license:gpl3)))
17043
17044 (define-public r-smpracticals
17045 (package
17046 (name "r-smpracticals")
17047 (version "1.4-3")
17048 (source
17049 (origin
17050 (method url-fetch)
17051 (uri (cran-uri "SMPracticals" version))
17052 (sha256
17053 (base32
17054 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
17055 (properties `((upstream-name . "SMPracticals")))
17056 (build-system r-build-system)
17057 (propagated-inputs
17058 `(("r-ellipse" ,r-ellipse)
17059 ("r-mass" ,r-mass)
17060 ("r-nlme" ,r-nlme)
17061 ("r-survival" ,r-survival)))
17062 (home-page "http://statwww.epfl.ch/davison/SM/")
17063 (synopsis "Practicals for use with Davison (2003) Statistical Models")
17064 (description
17065 "This package contains the datasets and a few functions for use with the
17066 practicals outlined in Appendix A of the book Statistical Models (Davison,
17067 2003, Cambridge University Press). The practicals themselves can be found at
17068 @url{http://statwww.epfl.ch/davison/SM/}.")
17069 (license license:gpl2+)))
17070
17071 (define-public r-fgui
17072 (package
17073 (name "r-fgui")
17074 (version "1.0-8")
17075 (source
17076 (origin
17077 (method url-fetch)
17078 (uri (cran-uri "fgui" version))
17079 (sha256
17080 (base32
17081 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
17082 (properties `((upstream-name . "fgui")))
17083 (build-system r-build-system)
17084 (home-page
17085 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
17086 (synopsis "Create GUI for R functions")
17087 (description
17088 "Rapidly create a GUI for a function you created by automatically
17089 creating widgets for arguments of the function. This package automatically
17090 parses help routines for context-sensitive help to these arguments. The
17091 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
17092 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
17093 incorporated into the interface for greater customization for the more
17094 experienced.")
17095 ;; Any version of the GPL.
17096 (license (list license:gpl2+ license:gpl3+))))
17097
17098 (define-public r-tcltk2
17099 (package
17100 (name "r-tcltk2")
17101 (version "1.2-11")
17102 (source
17103 (origin
17104 (method url-fetch)
17105 (uri (cran-uri "tcltk2" version))
17106 (sha256
17107 (base32
17108 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
17109 (properties `((upstream-name . "tcltk2")))
17110 (build-system r-build-system)
17111 (inputs
17112 `(("tcl" ,tcl)
17113 ("tk" ,tk)))
17114 (home-page "https://www.sciviews.org/SciViews-R")
17115 (synopsis "Tcl/Tk additions")
17116 (description
17117 "This package provides a series of additional Tcl commands and Tk widgets
17118 with style and various functions to supplement the tcltk package")
17119 (license license:lgpl3)))
17120
17121 (define-public r-accrual
17122 (package
17123 (name "r-accrual")
17124 (version "1.3")
17125 (source
17126 (origin
17127 (method url-fetch)
17128 (uri (cran-uri "accrual" version))
17129 (sha256
17130 (base32
17131 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
17132 (properties `((upstream-name . "accrual")))
17133 (build-system r-build-system)
17134 (propagated-inputs
17135 `(("r-fgui" ,r-fgui)
17136 ("r-smpracticals" ,r-smpracticals)
17137 ("r-tcltk2" ,r-tcltk2)))
17138 (home-page "https://cran.r-project.org/web/packages/accrual/")
17139 (synopsis "Bayesian accrual prediction")
17140 (description
17141 "Subject recruitment for medical research is challenging. Slow patient
17142 accrual leads to delay in research. Accrual monitoring during the process of
17143 recruitment is critical. Researchers need reliable tools to manage the
17144 accrual rate. This package provides an implementation of a Bayesian method
17145 that integrates researcher's experience on previous trials and data from the
17146 current study, providing reliable prediction on accrual rate for clinical
17147 studies. It provides functions for Bayesian accrual prediction which can be
17148 easily used by statisticians and clinical researchers.")
17149 (license license:gpl2)))
17150
17151 (define-public r-accrued
17152 (package
17153 (name "r-accrued")
17154 (version "1.4.1")
17155 (source
17156 (origin
17157 (method url-fetch)
17158 (uri (cran-uri "accrued" version))
17159 (sha256
17160 (base32
17161 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
17162 (properties `((upstream-name . "accrued")))
17163 (build-system r-build-system)
17164 (home-page "https://cran.r-project.org/web/packages/accrued/")
17165 (synopsis "Data quality visualization tools for partially accruing data")
17166 (description
17167 "This is a package for visualizing data quality of partially accruing
17168 data.")
17169 (license license:gpl3)))
17170
17171 (define-public r-mda
17172 (package
17173 (name "r-mda")
17174 (version "0.4-10")
17175 (source
17176 (origin
17177 (method url-fetch)
17178 (uri (cran-uri "mda" version))
17179 (sha256
17180 (base32
17181 "19g6kn6g0shidrjfffklbmzc5w7mcimrxhagx4nmpslg59ibqdkh"))))
17182 (properties `((upstream-name . "mda")))
17183 (build-system r-build-system)
17184 (propagated-inputs `(("r-class" ,r-class)))
17185 (native-inputs `(("gfortran" ,gfortran)))
17186 (home-page "https://cran.r-project.org/web/packages/mda/")
17187 (synopsis "Mixture and flexible discriminant analysis")
17188 (description
17189 "This is a package for mixture and flexible discriminant analysis,
17190 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
17191 (license license:gpl2)))
17192
17193 (define-public r-elasticnet
17194 (package
17195 (name "r-elasticnet")
17196 (version "1.1.1")
17197 (source
17198 (origin
17199 (method url-fetch)
17200 (uri (cran-uri "elasticnet" version))
17201 (sha256
17202 (base32
17203 "0p9dplnsp28z4s2fl6afbwrgd0aj339fak8mmndicmrh7bb7rpmb"))))
17204 (properties `((upstream-name . "elasticnet")))
17205 (build-system r-build-system)
17206 (propagated-inputs
17207 `(("r-lars" ,r-lars)))
17208 (home-page "http://users.stat.umn.edu/~zouxx019/")
17209 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
17210 (description
17211 "This package provides functions for fitting the entire solution path of
17212 the Elastic-Net and also provides functions for estimating sparse Principal
17213 Components. The Lasso solution paths can be computed by the same function.")
17214 (license license:gpl2+)))
17215
17216 (define-public r-sparselda
17217 (package
17218 (name "r-sparselda")
17219 (version "0.1-9")
17220 (source
17221 (origin
17222 (method url-fetch)
17223 (uri (cran-uri "sparseLDA" version))
17224 (sha256
17225 (base32
17226 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
17227 (properties `((upstream-name . "sparseLDA")))
17228 (build-system r-build-system)
17229 (propagated-inputs
17230 `(("r-elasticnet" ,r-elasticnet)
17231 ("r-mass" ,r-mass)
17232 ("r-mda" ,r-mda)))
17233 (home-page "https://www.imm.dtu.dk/~lkhc/")
17234 (synopsis "Sparse discriminant analysis")
17235 (description
17236 "This package performs sparse linear discriminant analysis for Gaussians
17237 and mixture of Gaussian models.")
17238 (license license:gpl2+)))
17239
17240 (define-public r-accsda
17241 (package
17242 (name "r-accsda")
17243 (version "1.0.0")
17244 (source
17245 (origin
17246 (method url-fetch)
17247 (uri (cran-uri "accSDA" version))
17248 (sha256
17249 (base32
17250 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
17251 (properties `((upstream-name . "accSDA")))
17252 (build-system r-build-system)
17253 (propagated-inputs
17254 `(("r-ggplot2" ,r-ggplot2)
17255 ("r-ggthemes" ,r-ggthemes)
17256 ("r-gridextra" ,r-gridextra)
17257 ("r-mass" ,r-mass)
17258 ("r-rarpack" ,r-rarpack)
17259 ("r-sparselda" ,r-sparselda)))
17260 (home-page "https://github.com/gumeo/accSDA/wiki")
17261 (synopsis "Accelerated sparse discriminant analysis")
17262 (description
17263 "This package provides an implementation of sparse linear discriminant
17264 analysis, which is a supervised classification method for multiple classes.
17265 Various novel optimization approaches to this problem are implemented
17266 including @dfn{alternating direction method of multipliers} (ADMM),
17267 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
17268 Functions for performing cross validation are also supplied along with basic
17269 prediction and plotting functions. @dfn{Sparse zero variance
17270 discriminant} (SZVD) analysis is also included in the package.")
17271 (license license:gpl2+)))
17272
17273 (define-public r-ace2fastq
17274 (package
17275 (name "r-ace2fastq")
17276 (version "0.6.0")
17277 (source
17278 (origin
17279 (method url-fetch)
17280 (uri (cran-uri "ace2fastq" version))
17281 (sha256
17282 (base32
17283 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
17284 (properties `((upstream-name . "ace2fastq")))
17285 (build-system r-build-system)
17286 (propagated-inputs
17287 `(("r-stringr" ,r-stringr)))
17288 (home-page "https://github.com/c5sire/ace2fastq")
17289 (synopsis "ACE file to FASTQ converter")
17290 (description
17291 "The ACE file format is used in genomics to store contigs from sequencing
17292 machines. This tools converts it into FASTQ format. Both formats contain the
17293 sequence characters and their corresponding quality information. Unlike the
17294 FASTQ file, the ACE file stores the quality values numerically. The
17295 conversion algorithm uses the standard Sanger formula. The package
17296 facilitates insertion into pipelines, and content inspection.")
17297 (license license:gpl3)))
17298
17299 (define-public r-rngwell
17300 (package
17301 (name "r-rngwell")
17302 (version "0.10-6")
17303 (source
17304 (origin
17305 (method url-fetch)
17306 (uri (cran-uri "rngWELL" version))
17307 (sha256
17308 (base32
17309 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
17310 (properties `((upstream-name . "rngWELL")))
17311 (build-system r-build-system)
17312 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
17313 (synopsis "Toolbox for WELL random number generators")
17314 (description
17315 "This is a dedicated package to WELL pseudo random generators, which were
17316 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
17317 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
17318 (license license:bsd-3)))
17319
17320 (define-public r-randtoolbox
17321 (package
17322 (name "r-randtoolbox")
17323 (version "1.30.1")
17324 (source
17325 (origin
17326 (method url-fetch)
17327 (uri (cran-uri "randtoolbox" version))
17328 (sha256
17329 (base32
17330 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
17331 (properties `((upstream-name . "randtoolbox")))
17332 (build-system r-build-system)
17333 (propagated-inputs
17334 `(("r-rngwell" ,r-rngwell)))
17335 (native-inputs
17336 `(("gfortran" ,gfortran)))
17337 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
17338 (synopsis "Toolbox for pseudo and quasi random number generation")
17339 (description
17340 "This package provides
17341
17342 @enumerate
17343 @item pseudo random generators, such as general linear
17344 congruential generators, multiple recursive generators and generalized
17345 feedback shift register (SF-Mersenne Twister algorithm and WELL
17346 generators)
17347
17348 @item quasi random generators, such as the Torus algorithm, the Sobol
17349 sequence, the Halton sequence (including the Van der Corput sequence), and
17350
17351 @item some generator tests: the gap test, the serial test, the poker test.
17352 @end enumerate
17353
17354 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
17355 (license license:bsd-3)))
17356
17357 (define-public r-lhs
17358 (package
17359 (name "r-lhs")
17360 (version "1.0.2")
17361 (source
17362 (origin
17363 (method url-fetch)
17364 (uri (cran-uri "lhs" version))
17365 (sha256
17366 (base32
17367 "0n0i1hr9gmc0hfcs2cvpjvdfgm6k26rhcq3q22r8ic0gfj953572"))))
17368 (properties `((upstream-name . "lhs")))
17369 (build-system r-build-system)
17370 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17371 (native-inputs
17372 `(("r-knitr" ,r-knitr)))
17373 (home-page "https://github.com/bertcarnell/lhs")
17374 (synopsis "Latin Hypercube Samples")
17375 (description
17376 "This package provides a number of methods for creating and augmenting
17377 Latin Hypercube Samples.")
17378 (license license:gpl3)))
17379
17380 (define-public r-acebayes
17381 (package
17382 (name "r-acebayes")
17383 (version "1.9")
17384 (source
17385 (origin
17386 (method url-fetch)
17387 (uri (cran-uri "acebayes" version))
17388 (sha256
17389 (base32
17390 "1imfwm1vpbb24vfmfn1nljhmaz8429mwjihw34892p387s8h7xz2"))))
17391 (properties `((upstream-name . "acebayes")))
17392 (build-system r-build-system)
17393 (propagated-inputs
17394 `(("r-compare" ,r-compare)
17395 ("r-lhs" ,r-lhs)
17396 ("r-randtoolbox" ,r-randtoolbox)
17397 ("r-rcpp" ,r-rcpp)
17398 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17399 (home-page "https://cran.r-project.org/web/packages/acebayes/")
17400 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
17401 (description
17402 "Finding an optimal Bayesian experimental design involves maximizing an
17403 objective function given by the expectation of some appropriately chosen
17404 utility function with respect to the joint distribution of unknown
17405 quantities (including responses). This objective function is usually not
17406 available in closed form and the design space can be continuous and of high
17407 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
17408 to maximise an approximation to the expectation of the utility function.")
17409 (license license:gpl2)))
17410
17411 (define-public r-acet
17412 (package
17413 (name "r-acet")
17414 (version "1.8.0")
17415 (source
17416 (origin
17417 (method url-fetch)
17418 (uri (cran-uri "ACEt" version))
17419 (sha256
17420 (base32
17421 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
17422 (properties `((upstream-name . "ACEt")))
17423 (build-system r-build-system)
17424 (propagated-inputs
17425 `(("r-bh" ,r-bh)
17426 ("r-mass" ,r-mass)
17427 ("r-rcpp" ,r-rcpp)
17428 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17429 (home-page "https://cran.r-project.org/web/packages/ACEt/")
17430 (synopsis "Estimating dynamic heritability and twin model comparison")
17431 (description
17432 "This package supports twin models that are able to estimate the dynamic
17433 behaviour of the variance components in the classical twin models with respect
17434 to age using B-splines and P-splines.")
17435 (license license:gpl2+)))
17436
17437 (define-public r-acfmperiod
17438 (package
17439 (name "r-acfmperiod")
17440 (version "1.0.0")
17441 (source
17442 (origin
17443 (method url-fetch)
17444 (uri (cran-uri "acfMPeriod" version))
17445 (sha256
17446 (base32
17447 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
17448 (properties `((upstream-name . "acfMPeriod")))
17449 (build-system r-build-system)
17450 (propagated-inputs
17451 `(("r-mass" ,r-mass)))
17452 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
17453 (synopsis "Estimation of the ACF from the M-periodogram")
17454 (description
17455 "This package support non-robust and robust computations of the sample
17456 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
17457 univariate and multivariate processes. The methodology consists in reversing
17458 the diagonalization procedure involving the periodogram or the
17459 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
17460 ACOVF or the ACF as discussed in Fuller (1995)
17461 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
17462 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
17463 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
17464 (license license:gpl2+)))
17465
17466 (define-public r-gamlss-data
17467 (package
17468 (name "r-gamlss-data")
17469 (version "5.1-4")
17470 (source
17471 (origin
17472 (method url-fetch)
17473 (uri (cran-uri "gamlss.data" version))
17474 (sha256
17475 (base32
17476 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
17477 (properties `((upstream-name . "gamlss.data")))
17478 (build-system r-build-system)
17479 (home-page "http://www.gamlss.org/")
17480 (synopsis "GAMLSS data")
17481 (description
17482 "This package provides data used as examples to demonstrate GAMLSS
17483 models.")
17484 ;; Either version of the license
17485 (license (list license:gpl2 license:gpl3))))
17486
17487 (define-public r-gamlss
17488 (package
17489 (name "r-gamlss")
17490 (version "5.1-6")
17491 (source
17492 (origin
17493 (method url-fetch)
17494 (uri (cran-uri "gamlss" version))
17495 (sha256
17496 (base32
17497 "16b7ick1khvldbvfmmpw9cjs1vznnrisvifq7717fxzd8c9s5jdr"))))
17498 (properties `((upstream-name . "gamlss")))
17499 (build-system r-build-system)
17500 (propagated-inputs
17501 `(("r-gamlss-data" ,r-gamlss-data)
17502 ("r-gamlss-dist" ,r-gamlss-dist)
17503 ("r-mass" ,r-mass)
17504 ("r-nlme" ,r-nlme)
17505 ("r-survival" ,r-survival)))
17506 (home-page "http://www.gamlss.org/")
17507 (synopsis "Generalized additive models for location scale and shape")
17508 (description
17509 "This package provides functions for fitting the generalized additive
17510 models for location scale and shape introduced by Rigby and
17511 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
17512 use a distributional regression approach where all the parameters of the
17513 conditional distribution of the response variable are modelled using
17514 explanatory variables.")
17515 ;; Either version of the license
17516 (license (list license:gpl2 license:gpl3))))
17517
17518 (define-public r-acid
17519 (package
17520 (name "r-acid")
17521 (version "1.1")
17522 (source
17523 (origin
17524 (method url-fetch)
17525 (uri (cran-uri "acid" version))
17526 (sha256
17527 (base32
17528 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
17529 (properties `((upstream-name . "acid")))
17530 (build-system r-build-system)
17531 (propagated-inputs
17532 `(("r-gamlss" ,r-gamlss)
17533 ("r-gamlss-dist" ,r-gamlss-dist)
17534 ("r-hmisc" ,r-hmisc)))
17535 (home-page "https://cran.r-project.org/web/packages/acid/")
17536 (synopsis "Analysing conditional income distributions")
17537 (description
17538 "This package provides functions for the analysis of income distributions
17539 for subgroups of the population as defined by a set of variables like age,
17540 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
17541 distribution as well as functions for moments, inequality measures, entropy
17542 measures and polarisation measures of income distributions. This package thus
17543 aides the analysis of income inequality by offering tools for the exploratory
17544 analysis of income distributions at the disaggregated level.")
17545 (license license:gpl3)))
17546
17547 (define-public r-acm4r
17548 (package
17549 (name "r-acm4r")
17550 (version "1.0")
17551 (source
17552 (origin
17553 (method url-fetch)
17554 (uri (cran-uri "acm4r" version))
17555 (sha256
17556 (base32
17557 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
17558 (properties `((upstream-name . "acm4r")))
17559 (build-system r-build-system)
17560 (propagated-inputs `(("r-mass" ,r-mass)))
17561 (home-page "https://cran.r-project.org/web/packages/acm4r/")
17562 (synopsis "Align-and-count method comparisons of RFLP data")
17563 (description
17564 "This is a package to compare sequence fragment lengths or molecular
17565 weights from pairs of lanes. The number of matching bands in the
17566 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
17567 the align-and-count method.")
17568 ;; Any version of the GPL
17569 (license (list license:gpl2+ license:gpl3+))))
17570
17571 (define-public r-filematrix
17572 (package
17573 (name "r-filematrix")
17574 (version "1.3")
17575 (source
17576 (origin
17577 (method url-fetch)
17578 (uri (cran-uri "filematrix" version))
17579 (sha256
17580 (base32
17581 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
17582 (properties `((upstream-name . "filematrix")))
17583 (build-system r-build-system)
17584 ;; These inputs are needed for vignettes
17585 (native-inputs
17586 `(("r-knitr" ,r-knitr)
17587 ("r-rmarkdown" ,r-rmarkdown)
17588 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
17589 (home-page "https://github.com/andreyshabalin/filematrix")
17590 (synopsis "File-backed matrix class with convenient read and write access")
17591 (description
17592 "This package provides an interface for working with large matrices
17593 stored in files, not in computer memory. It supports multiple non-character
17594 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
17595 byte real values). Access to parts of the matrix is done by indexing, exactly
17596 as with usual R matrices. It supports very large matrices; the package has
17597 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
17598 columns, ad allows for quick addition of extra columns to a filematrix.")
17599 (license license:lgpl3)))
17600
17601 (define-public r-acmeeqtl
17602 (package
17603 (name "r-acmeeqtl")
17604 (version "1.6")
17605 (source
17606 (origin
17607 (method url-fetch)
17608 (uri (cran-uri "ACMEeqtl" version))
17609 (sha256
17610 (base32
17611 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
17612 (properties `((upstream-name . "ACMEeqtl")))
17613 (build-system r-build-system)
17614 (propagated-inputs
17615 `(("r-filematrix" ,r-filematrix)))
17616 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
17617 (synopsis "Estimation of interpretable eQTL effect sizes")
17618 (description
17619 "This package provides a non-linear model, termed ACME, that reflects a
17620 parsimonious biological model for allelic contributions of cis-acting eQTLs.
17621 With non-linear least-squares algorithm the maximum likelihood parameters can
17622 be estimated. The ACME model provides interpretable effect size estimates and
17623 p-values with well controlled Type-I error.")
17624 (license license:lgpl3)))
17625
17626 (define-public r-acmer
17627 (package
17628 (name "r-acmer")
17629 (version "1.1.0")
17630 (source
17631 (origin
17632 (method url-fetch)
17633 (uri (cran-uri "acmeR" version))
17634 (sha256
17635 (base32
17636 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
17637 (properties `((upstream-name . "acmeR")))
17638 (build-system r-build-system)
17639 (propagated-inputs `(("r-foreign" ,r-foreign)))
17640 (home-page "https://cran.r-project.org/web/packages/acmeR/")
17641 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
17642 (description
17643 "This package provides an implementation of the ACME estimator, described
17644 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
17645 Mortality at Wind Turbines. Unlike most other models, this estimator supports
17646 decreasing-hazard Weibull model for persistence; decreasing search proficiency
17647 as carcasses age; variable bleed-through at successive searches; and interval
17648 mortality estimates. The package provides, based on search data, functions
17649 for estimating the mortality inflation factor in Frequentist and Bayesian
17650 settings.")
17651 (license license:expat)))
17652
17653 (define-public r-r-huge
17654 (package
17655 (name "r-r-huge")
17656 (version "0.9.0")
17657 (source
17658 (origin
17659 (method url-fetch)
17660 (uri (cran-uri "R.huge" version))
17661 (sha256
17662 (base32
17663 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
17664 (properties `((upstream-name . "R.huge")))
17665 (build-system r-build-system)
17666 (propagated-inputs
17667 `(("r-r-methodss3" ,r-r-methodss3)
17668 ("r-r-oo" ,r-r-oo)
17669 ("r-r-utils" ,r-r-utils)))
17670 (home-page "https://github.com/HenrikBengtsson/R.huge")
17671 (synopsis "Methods for accessing huge amounts of data")
17672 (description
17673 "This is a deprecated package for accessing huge amounts of data.
17674 Cross-platform alternatives are the following packages: bigmemory (CRAN),
17675 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
17676 the @code{aroma.affymetrix} package.")
17677 (license license:lgpl2.1+)))
17678
17679 (define-public r-r-filesets
17680 (package
17681 (name "r-r-filesets")
17682 (version "2.13.0")
17683 (source
17684 (origin
17685 (method url-fetch)
17686 (uri (cran-uri "R.filesets" version))
17687 (sha256
17688 (base32
17689 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
17690 (properties `((upstream-name . "R.filesets")))
17691 (build-system r-build-system)
17692 (propagated-inputs
17693 `(("r-digest" ,r-digest)
17694 ("r-r-cache" ,r-r-cache)
17695 ("r-r-methodss3" ,r-r-methodss3)
17696 ("r-r-oo" ,r-r-oo)
17697 ("r-r-utils" ,r-r-utils)))
17698 (home-page "https://github.com/HenrikBengtsson/R.filesets")
17699 (synopsis "Easy handling of and access to files")
17700 (description
17701 "This package provides classes and methods to locate, setup, subset,
17702 navigate and iterate file sets, i.e. sets of files located in one or more
17703 directories on the file system. The API is designed such that these classes
17704 can be extended via inheritance to provide a richer API for special file
17705 formats. Moreover, a specific name format is defined such that filenames and
17706 directories can be considered to have full names which consists of a name
17707 followed by comma-separated tags. This adds additional flexibility to
17708 identify file sets and individual files.")
17709 (license license:lgpl2.1+)))
17710
17711 (define-public r-r-devices
17712 (package
17713 (name "r-r-devices")
17714 (version "2.16.1")
17715 (source
17716 (origin
17717 (method url-fetch)
17718 (uri (cran-uri "R.devices" version))
17719 (sha256
17720 (base32
17721 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
17722 (properties `((upstream-name . "R.devices")))
17723 (build-system r-build-system)
17724 (propagated-inputs
17725 `(("r-base64enc" ,r-base64enc)
17726 ("r-r-methodss3" ,r-r-methodss3)
17727 ("r-r-oo" ,r-r-oo)
17728 ("r-r-utils" ,r-r-utils)))
17729 (home-page "https://github.com/HenrikBengtsson/R.devices")
17730 (synopsis "Unified handling of graphics devices")
17731 (description
17732 "This package provides functions for creating plots and image files in a
17733 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
17734 Default device options as well as scales and aspect ratios are controlled in a
17735 uniform way across all device types. Switching output format requires minimal
17736 changes in code. This package is ideal for large-scale batch processing,
17737 because it will never leave open graphics devices or incomplete image files
17738 behind, even on errors or user interrupts.")
17739 (license license:lgpl2.1+)))
17740
17741 (define-public r-acnr
17742 (package
17743 (name "r-acnr")
17744 (version "1.0.0")
17745 (source
17746 (origin
17747 (method url-fetch)
17748 (uri (cran-uri "acnr" version))
17749 (sha256
17750 (base32
17751 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
17752 (properties `((upstream-name . "acnr")))
17753 (build-system r-build-system)
17754 (home-page "https://github.com/mpierrejean/acnr")
17755 (synopsis "Annotated copy-number regions")
17756 (description
17757 "This package provides SNP array data from different types of copy-number
17758 regions. These regions were identified manually by the authors of the package
17759 and may be used to generate realistic data sets with known truth.")
17760 (license license:lgpl2.1+)))
17761
17762 (define-public r-acopula
17763 (package
17764 (name "r-acopula")
17765 (version "0.9.3")
17766 (source
17767 (origin
17768 (method url-fetch)
17769 (uri (cran-uri "acopula" version))
17770 (sha256
17771 (base32
17772 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
17773 (properties `((upstream-name . "acopula")))
17774 (build-system r-build-system)
17775 (home-page "https://cran.r-project.org/web/packages/acopula/")
17776 (synopsis "Modelling dependence with multivariate Archimax copulas")
17777 (description
17778 "Archimax copulas are a mixture of Archimedean and EV copulas. This
17779 package provides definitions of several parametric families of generator and
17780 dependence function, computes CDF and PDF, estimates parameters, tests for
17781 goodness of fit, generates random sample and checks copula properties for
17782 custom constructs. In the 2-dimensional case explicit formulas for density
17783 are used, contrary to higher dimensions when all derivatives are linearly
17784 approximated. Several non-archimax families (normal, FGM, Plackett) are
17785 provided as well.")
17786 (license license:gpl2)))
17787
17788 (define-public r-tuner
17789 (package
17790 (name "r-tuner")
17791 (version "1.3.3")
17792 (source
17793 (origin
17794 (method url-fetch)
17795 (uri (cran-uri "tuneR" version))
17796 (sha256
17797 (base32
17798 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
17799 (properties `((upstream-name . "tuneR")))
17800 (build-system r-build-system)
17801 (propagated-inputs `(("r-signal" ,r-signal)))
17802 (home-page "https://cran.r-project.org/web/packages/tuneR/")
17803 (synopsis "Analysis of music and speech")
17804 (description
17805 "This is a package for the analysis of music and speech. Analyze music
17806 and speech, extract features like MFCCs, handle wave files and their
17807 representation in various ways, read MP3, read MIDI, perform steps of a
17808 transcription, ...")
17809 ;; Either of these versions.
17810 (license (list license:gpl2 license:gpl3))))
17811
17812 (define-public r-seewave
17813 (package
17814 (name "r-seewave")
17815 (version "2.1.5")
17816 (source
17817 (origin
17818 (method url-fetch)
17819 (uri (cran-uri "seewave" version))
17820 (sha256
17821 (base32
17822 "1qg8f5gik9pw6f9mcxqmrc9x3003s8vdm6g01pjjpyc9qaqiz2vi"))))
17823 (properties `((upstream-name . "seewave")))
17824 (build-system r-build-system)
17825 (propagated-inputs
17826 `(("r-tuner" ,r-tuner)))
17827 (home-page "http://rug.mnhn.fr/seewave")
17828 (synopsis "Sound analysis and synthesis")
17829 (description
17830 "This package provides functions for analysing, manipulating, displaying,
17831 editing and synthesizing time waves (particularly sound). This package
17832 processes time analysis (oscillograms and envelopes), spectral content,
17833 resonance quality factor, entropy, cross correlation and autocorrelation,
17834 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
17835 and 3D spectrograms and many other analyses.")
17836 (license license:gpl2+)))
17837
17838 (define-public r-acousticndlcoder
17839 (package
17840 (name "r-acousticndlcoder")
17841 (version "1.0.2")
17842 (source
17843 (origin
17844 (method url-fetch)
17845 (uri (cran-uri "AcousticNDLCodeR" version))
17846 (sha256
17847 (base32
17848 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
17849 (properties
17850 `((upstream-name . "AcousticNDLCodeR")))
17851 (build-system r-build-system)
17852 (propagated-inputs
17853 `(("r-seewave" ,r-seewave)
17854 ("r-tuner" ,r-tuner)
17855 ("r-zoo" ,r-zoo)))
17856 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
17857 (synopsis "Coding sound files for use with NDL")
17858 (description
17859 "Make acoustic cues to use with the R package @code{ndl}.
17860 The package implements functions used in the PLoS ONE paper \"Words from
17861 spontaneous conversational speech can be recognized with human-like accuracy
17862 by an error-driven learning algorithm that discriminates between meanings
17863 straight from smart acoustic features, bypassing the phoneme as recognition
17864 unit.\" @url{doi:10.1371/journal.pone.0174623}")
17865 (license license:gpl2+)))
17866
17867 (define-public r-acp
17868 (package
17869 (name "r-acp")
17870 (version "2.1")
17871 (source
17872 (origin
17873 (method url-fetch)
17874 (uri (cran-uri "acp" version))
17875 (sha256
17876 (base32
17877 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
17878 (properties `((upstream-name . "acp")))
17879 (build-system r-build-system)
17880 (propagated-inputs
17881 `(("r-quantmod" ,r-quantmod)
17882 ("r-tseries" ,r-tseries)))
17883 (home-page "https://cran.r-project.org/web/packages/acp/")
17884 (synopsis "Autoregressive conditional Poisson")
17885 (description
17886 "This package supports the analysis of count data exhibiting
17887 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
17888 model (ACP(p,q)) proposed by Heinen (2003).")
17889 (license license:gpl2)))
17890
17891 (define-public r-ada
17892 (package
17893 (name "r-ada")
17894 (version "2.0-5")
17895 (source
17896 (origin
17897 (method url-fetch)
17898 (uri (cran-uri "ada" version))
17899 (sha256
17900 (base32
17901 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
17902 (properties `((upstream-name . "ada")))
17903 (build-system r-build-system)
17904 (propagated-inputs `(("r-rpart" ,r-rpart)))
17905 (home-page "https://cran.r-project.org/web/packages/ada/")
17906 (synopsis "Stochastic boosting")
17907 (description
17908 "This package provides a straightforward, well-documented, and broad
17909 boosting routine for classification, ideally suited for small to
17910 moderate-sized data sets. It performs discrete, real, and gentle boost under
17911 both exponential and logistic loss on a given data set.")
17912 ;; Any version of the GPL.
17913 (license (list license:gpl2+ license:gpl3+))))
17914
17915 (define-public r-genalg
17916 (package
17917 (name "r-genalg")
17918 (version "0.2.0")
17919 (source
17920 (origin
17921 (method url-fetch)
17922 (uri (cran-uri "genalg" version))
17923 (sha256
17924 (base32
17925 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
17926 (properties `((upstream-name . "genalg")))
17927 (build-system r-build-system)
17928 (home-page "https://github.com/egonw/genalg")
17929 (synopsis "R based genetic algorithm")
17930 (description
17931 "This package provides an R based genetic algorithm for binary and
17932 floating point chromosomes.")
17933 (license license:gpl2)))
17934
17935 (define-public r-kernelfactory
17936 (package
17937 (name "r-kernelfactory")
17938 (version "0.3.0")
17939 (source
17940 (origin
17941 (method url-fetch)
17942 (uri (cran-uri "kernelFactory" version))
17943 (sha256
17944 (base32
17945 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
17946 (properties `((upstream-name . "kernelFactory")))
17947 (build-system r-build-system)
17948 (propagated-inputs
17949 `(("r-auc" ,r-auc)
17950 ("r-genalg" ,r-genalg)
17951 ("r-kernlab" ,r-kernlab)
17952 ("r-randomforest" ,r-randomforest)))
17953 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
17954 (synopsis "Ensemble of kernel machines")
17955 (description
17956 "Kernel factory is an ensemble method where each base classifier (random
17957 forest) is fit on the kernel matrix of a subset of the training data.")
17958 (license license:gpl2+)))
17959
17960 (define-public r-dummies
17961 (package
17962 (name "r-dummies")
17963 (version "1.5.6")
17964 (source
17965 (origin
17966 (method url-fetch)
17967 (uri (cran-uri "dummies" version))
17968 (sha256
17969 (base32
17970 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
17971 (properties `((upstream-name . "dummies")))
17972 (build-system r-build-system)
17973 (home-page "https://decisionpatterns.com")
17974 (synopsis "Create dummy/indicator variables flexibly and efficiently")
17975 (description
17976 "This package lets you expand factors, characters and other eligible
17977 classes into dummy/indicator variables.")
17978 (license license:gpl2+)))
17979
17980 (define-public r-acrm
17981 (package
17982 (name "r-acrm")
17983 (version "0.1.1")
17984 (source
17985 (origin
17986 (method url-fetch)
17987 (uri (cran-uri "aCRM" version))
17988 (sha256
17989 (base32
17990 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
17991 (properties `((upstream-name . "aCRM")))
17992 (build-system r-build-system)
17993 (propagated-inputs
17994 `(("r-ada" ,r-ada)
17995 ("r-dummies" ,r-dummies)
17996 ("r-kernelfactory" ,r-kernelfactory)
17997 ("r-randomforest" ,r-randomforest)))
17998 (home-page "https://cran.r-project.org/web/packages/aCRM/")
17999 (synopsis "Convenience functions for analytical customer relationship management")
18000 (description
18001 "This package provides convenience functions for data preparation and
18002 modeling often used in @dfn{analytical customer relationship
18003 management} (aCRM).")
18004 (license license:gpl2+)))
18005
18006 (define-public r-treeclust
18007 (package
18008 (name "r-treeclust")
18009 (version "1.1-7")
18010 (source
18011 (origin
18012 (method url-fetch)
18013 (uri (cran-uri "treeClust" version))
18014 (sha256
18015 (base32
18016 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
18017 (properties `((upstream-name . "treeClust")))
18018 (build-system r-build-system)
18019 (propagated-inputs
18020 `(("r-cluster" ,r-cluster)
18021 ("r-rpart" ,r-rpart)))
18022 (home-page "https://cran.r-project.org/web/packages/treeClust/")
18023 (synopsis "Cluster distances through trees")
18024 (description
18025 "This package provides tools to create a measure of inter-point
18026 dissimilarity useful for clustering mixed data, and, optionally, perform the
18027 clustering.")
18028 (license license:gpl2+)))
18029
18030 (define-public r-acrosstic
18031 (package
18032 (name "r-acrosstic")
18033 (version "1.0-3")
18034 (source
18035 (origin
18036 (method url-fetch)
18037 (uri (cran-uri "AcrossTic" version))
18038 (sha256
18039 (base32
18040 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
18041 (properties `((upstream-name . "AcrossTic")))
18042 (build-system r-build-system)
18043 (propagated-inputs
18044 `(("r-lpsolve" ,r-lpsolve)
18045 ("r-treeclust" ,r-treeclust)))
18046 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
18047 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
18048 (description
18049 "This is a package for constructing minimum-cost regular spanning
18050 subgraph as part of a non-parametric two-sample test for equality of
18051 distribution.")
18052 (license license:gpl2+)))
18053
18054 (define-public r-acrt
18055 (package
18056 (name "r-acrt")
18057 (version "1.0.1")
18058 (source
18059 (origin
18060 (method url-fetch)
18061 (uri (cran-uri "acrt" version))
18062 (sha256
18063 (base32
18064 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
18065 (properties `((upstream-name . "acrt")))
18066 (build-system r-build-system)
18067 (propagated-inputs
18068 `(("r-rcpp" ,r-rcpp)
18069 ("r-rcppeigen" ,r-rcppeigen)
18070 ("r-sandwich" ,r-sandwich)))
18071 (home-page "https://cran.r-project.org/web/packages/acrt/")
18072 (synopsis "Autocorrelation robust testing")
18073 (description
18074 "This package provides functions for testing affine hypotheses on the
18075 regression coefficient vector in regression models with autocorrelated
18076 errors.")
18077 (license license:gpl2)))
18078
18079 (define-public r-acs
18080 (package
18081 (name "r-acs")
18082 (version "2.1.4")
18083 (source
18084 (origin
18085 (method url-fetch)
18086 (uri (cran-uri "acs" version))
18087 (sha256
18088 (base32
18089 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
18090 (properties `((upstream-name . "acs")))
18091 (build-system r-build-system)
18092 (propagated-inputs
18093 `(("r-httr" ,r-httr)
18094 ("r-plyr" ,r-plyr)
18095 ("r-rcpp" ,r-rcpp)
18096 ("r-stringr" ,r-stringr)
18097 ("r-xml" ,r-xml)))
18098 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
18099 (synopsis "Work with data from the US Census")
18100 (description
18101 "This package provides a general toolkit for downloading, managing,
18102 analyzing, and presenting data from the
18103 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
18104 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
18105 American Community Survey (ACS). Confidence intervals provided with ACS data
18106 are converted to standard errors to be bundled with estimates in complex
18107 @code{acs} objects. The package provides new methods to conduct standard
18108 operations on @code{acs} objects and present/plot data in statistically
18109 appropriate ways.")
18110 (license license:gpl3)))
18111
18112 (define-public r-acss-data
18113 (package
18114 (name "r-acss-data")
18115 (version "1.0")
18116 (source
18117 (origin
18118 (method url-fetch)
18119 (uri (cran-uri "acss.data" version))
18120 (sha256
18121 (base32
18122 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
18123 (properties `((upstream-name . "acss.data")))
18124 (build-system r-build-system)
18125 (home-page "http://complexitycalculator.com/methodology.html")
18126 (synopsis "Data for algorithmic complexity of short strings")
18127 (description
18128 "This is a data only package providing the algorithmic complexity of
18129 short strings, computed using the coding theorem method. For a given set of
18130 symbols in a string, all possible or a large number of random samples of
18131 Turing machines with a given number of states (e.g., 5) and number of symbols
18132 corresponding to the number of symbols in the strings were simulated until
18133 they reached a halting state or failed to end. This package contains data on
18134 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
18135 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
18136 distribution of the halting states.")
18137 (license license:gpl2+)))
18138
18139 (define-public r-acss
18140 (package
18141 (name "r-acss")
18142 (version "0.2-5")
18143 (source
18144 (origin
18145 (method url-fetch)
18146 (uri (cran-uri "acss" version))
18147 (sha256
18148 (base32
18149 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
18150 (properties `((upstream-name . "acss")))
18151 (build-system r-build-system)
18152 (propagated-inputs
18153 `(("r-acss-data" ,r-acss-data)
18154 ("r-zoo" ,r-zoo)))
18155 (home-page "http://complexitycalculator.com/methodology.html")
18156 (synopsis "Algorithmic complexity for short strings")
18157 (description
18158 "The main purpose of this package is to provide the algorithmic
18159 complexity for short strings, an approximation of the Kolmogorov Complexity of
18160 a short string using the coding theorem method. While the database containing
18161 the complexity is provided in the data only package @code{acss.data}, this
18162 package provides functions accessing the data such as @code{prob_random}
18163 returning the posterior probability that a given string was produced by a
18164 random process. In addition, two traditional (but problematic) measures of
18165 complexity are also provided: entropy and change complexity.")
18166 (license license:gpl2+)))
18167
18168 (define-public r-acswr
18169 (package
18170 (name "r-acswr")
18171 (version "1.0")
18172 (source
18173 (origin
18174 (method url-fetch)
18175 (uri (cran-uri "ACSWR" version))
18176 (sha256
18177 (base32
18178 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
18179 (properties `((upstream-name . "ACSWR")))
18180 (build-system r-build-system)
18181 (propagated-inputs
18182 `(("r-mass" ,r-mass)))
18183 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
18184 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
18185 (description
18186 "This is a companion package for the book \"A Course in Statistics with
18187 R\" (ISBN 978-1-119-15272-9.)")
18188 (license license:gpl2)))
18189
18190 (define-public r-alabama
18191 (package
18192 (name "r-alabama")
18193 (version "2015.3-1")
18194 (source
18195 (origin
18196 (method url-fetch)
18197 (uri (cran-uri "alabama" version))
18198 (sha256
18199 (base32
18200 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
18201 (properties `((upstream-name . "alabama")))
18202 (build-system r-build-system)
18203 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
18204 (home-page "https://cran.r-project.org/web/packages/alabama/")
18205 (synopsis "Constrained nonlinear optimization")
18206 (description
18207 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
18208 Algorithm; it is used for optimizing smooth nonlinear objective functions with
18209 constraints. Linear or nonlinear equality and inequality constraints are
18210 allowed.")
18211 (license license:gpl2+)))
18212
18213 (define-public r-gdina
18214 (package
18215 (name "r-gdina")
18216 (version "2.7.9")
18217 (source
18218 (origin
18219 (method url-fetch)
18220 (uri (cran-uri "GDINA" version))
18221 (sha256
18222 (base32
18223 "13pmj069r04h38hg61ibyn1ab15zdy9m0qv60vi25ahgsmg6ccvx"))))
18224 (properties `((upstream-name . "GDINA")))
18225 (build-system r-build-system)
18226 (propagated-inputs
18227 `(("r-alabama" ,r-alabama)
18228 ("r-ggplot2" ,r-ggplot2)
18229 ("r-mass" ,r-mass)
18230 ("r-nloptr" ,r-nloptr)
18231 ("r-numderiv" ,r-numderiv)
18232 ("r-rcpp" ,r-rcpp)
18233 ("r-rcpparmadillo" ,r-rcpparmadillo)
18234 ("r-rsolnp" ,r-rsolnp)
18235 ("r-shiny" ,r-shiny)
18236 ("r-shinydashboard" ,r-shinydashboard)))
18237 (native-inputs
18238 `(("r-knitr" ,r-knitr)))
18239 (home-page "https://github.com/Wenchao-Ma/GDINA")
18240 (synopsis "Generalized DINA model framework")
18241 (description
18242 "This package provides a set of psychometric tools for cognitive
18243 diagnosis modeling based on the generalized deterministic inputs, noisy and
18244 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
18245 and its extensions, including the sequential G-DINA model by Ma and de la
18246 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
18247 polytomous G-DINA model by Chen and de la Torre
18248 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
18249 distribution can be independent, saturated, higher-order, loglinear smoothed
18250 or structured. Q-matrix validation, item and model fit statistics, model
18251 comparison at test and item level and differential item functioning can also
18252 be conducted. A graphical user interface is also provided.")
18253 (license license:gpl3)))
18254
18255 (define-public r-actcd
18256 (package
18257 (name "r-actcd")
18258 (version "1.2-0")
18259 (source
18260 (origin
18261 (method url-fetch)
18262 (uri (cran-uri "ACTCD" version))
18263 (sha256
18264 (base32
18265 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
18266 (properties `((upstream-name . "ACTCD")))
18267 (build-system r-build-system)
18268 (propagated-inputs
18269 `(("r-gdina" ,r-gdina)
18270 ("r-r-methodss3" ,r-r-methodss3)))
18271 (native-inputs
18272 `(("gfortran" ,gfortran)))
18273 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
18274 (synopsis "Asymptotic classification theory for cognitive diagnosis")
18275 (description
18276 "This is a package supporting cluster analysis for cognitive diagnosis
18277 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
18278 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
18279 sum-scores, cluster analysis techniques can be used to classify examinees into
18280 latent classes based on their attribute patterns. In addition to the
18281 algorithms used to classify data, three labeling approaches are proposed to
18282 label clusters so that examinees' attribute profiles can be obtained.")
18283 (license license:gpl2+)))
18284
18285 (define-public r-ineq
18286 (package
18287 (name "r-ineq")
18288 (version "0.2-13")
18289 (source
18290 (origin
18291 (method url-fetch)
18292 (uri (cran-uri "ineq" version))
18293 (sha256
18294 (base32
18295 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
18296 (properties `((upstream-name . "ineq")))
18297 (build-system r-build-system)
18298 (home-page "https://cran.r-project.org/web/packages/ineq/")
18299 (synopsis "Measuring inequality, concentration, and poverty")
18300 (description
18301 "This package provides tools for measuring inequality, concentration, and
18302 poverty measures. It provides both empirical and theoretical Lorenz curves.")
18303 ;; Either of these two versions.
18304 (license (list license:gpl2 license:gpl3))))
18305
18306 (define-public r-actfrag
18307 (package
18308 (name "r-actfrag")
18309 (version "0.1.1")
18310 (source
18311 (origin
18312 (method url-fetch)
18313 (uri (cran-uri "ActFrag" version))
18314 (sha256
18315 (base32
18316 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
18317 (properties `((upstream-name . "ActFrag")))
18318 (build-system r-build-system)
18319 (propagated-inputs
18320 `(("r-accelerometry" ,r-accelerometry)
18321 ("r-dplyr" ,r-dplyr)
18322 ("r-ineq" ,r-ineq)
18323 ("r-survival" ,r-survival)
18324 ("r-tidyr" ,r-tidyr)))
18325 (home-page "https://github.com/junruidi/ActFrag")
18326 (synopsis "Activity fragmentation metrics extraction")
18327 (description
18328 "This package provides functions to extract commonly used fragmentation
18329 metrics to quantify time accumulation strategies based on minute level
18330 actigraphy-measured activity counts data.")
18331 (license license:gpl3)))
18332
18333 (define-public r-fda
18334 (package
18335 (name "r-fda")
18336 (version "5.1.4")
18337 (source
18338 (origin
18339 (method url-fetch)
18340 (uri (cran-uri "fda" version))
18341 (sha256
18342 (base32
18343 "0js4ggl3aiwsqk6npwz72yhcznkb63smddds24ngf6a0p8yp5p2x"))))
18344 (properties `((upstream-name . "fda")))
18345 (build-system r-build-system)
18346 (propagated-inputs
18347 `(("r-matrix" ,r-matrix)))
18348 (home-page "https://www.functionaldata.org")
18349 (synopsis "Functional data analysis")
18350 (description
18351 "These functions were developed to support functional data analysis as
18352 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
18353 Analysis. The package includes data sets and script files working many
18354 examples.")
18355 (license license:gpl2+)))
18356
18357 (define-public r-actigraphy
18358 (package
18359 (name "r-actigraphy")
18360 (version "1.4.0")
18361 (source
18362 (origin
18363 (method url-fetch)
18364 (uri (cran-uri "Actigraphy" version))
18365 (sha256
18366 (base32
18367 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
18368 (properties `((upstream-name . "Actigraphy")))
18369 (build-system r-build-system)
18370 (propagated-inputs
18371 `(("r-fda" ,r-fda)))
18372 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
18373 (synopsis "Actigraphy data analysis")
18374 (description
18375 "This package provides tools for functional linear modeling and analysis
18376 of actigraphy data.")
18377 (license license:asl2.0)))
18378
18379 (define-public r-activedriver
18380 (package
18381 (name "r-activedriver")
18382 (version "1.0.0")
18383 (source
18384 (origin
18385 (method url-fetch)
18386 (uri (cran-uri "ActiveDriver" version))
18387 (sha256
18388 (base32
18389 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
18390 (properties `((upstream-name . "ActiveDriver")))
18391 (build-system r-build-system)
18392 (propagated-inputs
18393 `(("r-mass" ,r-mass)))
18394 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
18395 (synopsis "Tools for finding cancer driver proteins")
18396 (description
18397 "This package provides a mutation analysis tool that discovers cancer
18398 driver genes with frequent mutations in protein signalling sites such as
18399 post-translational modifications (phosphorylation, ubiquitination, etc). The
18400 Poisson generalized linear regression model identifies genes where cancer
18401 mutations in signalling sites are more frequent than expected from the
18402 sequence of the entire gene. Integration of mutations with signalling
18403 information helps find new driver genes and propose candidate mechanisms to
18404 known drivers.")
18405 (license license:gpl2+)))
18406
18407 (define-public r-activitycounts
18408 (package
18409 (name "r-activitycounts")
18410 (version "0.1.2")
18411 (source
18412 (origin
18413 (method url-fetch)
18414 (uri (cran-uri "activityCounts" version))
18415 (sha256
18416 (base32
18417 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
18418 (properties
18419 `((upstream-name . "activityCounts")))
18420 (build-system r-build-system)
18421 (propagated-inputs
18422 `(("r-lubridate" ,r-lubridate)
18423 ("r-magrittr" ,r-magrittr)
18424 ("r-seewave" ,r-seewave)
18425 ("r-signal" ,r-signal)
18426 ("r-tibble" ,r-tibble)))
18427 (home-page "https://github.com/walkabillylab/activityCounts")
18428 (synopsis "Generate ActiLife counts")
18429 (description
18430 "ActiLife generates activity counts from data collected by Actigraph
18431 accelerometers. Actigraph is one of the most common research-grade
18432 accelerometers. There is considerable research validating and developing
18433 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
18434 counts are proprietary and difficult to implement if researchers use different
18435 accelerometer brands. The code creates ActiLife counts from raw acceleration
18436 data for different accelerometer brands.")
18437 (license license:gpl3)))
18438
18439 (define-public r-activityindex
18440 (package
18441 (name "r-activityindex")
18442 (version "0.3.6")
18443 (source
18444 (origin
18445 (method url-fetch)
18446 (uri (cran-uri "ActivityIndex" version))
18447 (sha256
18448 (base32
18449 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
18450 (properties `((upstream-name . "ActivityIndex")))
18451 (build-system r-build-system)
18452 (propagated-inputs
18453 `(("r-data-table" ,r-data-table)
18454 ("r-matrixstats" ,r-matrixstats)
18455 ("r-r-utils" ,r-r-utils)))
18456 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
18457 (synopsis "Activity Index calculation using raw accelerometry data")
18458 (description
18459 "This is a package to read raw accelerometry from GT3X+ accelerometry
18460 data and plain table data to calculate the Activity Index from Bai et
18461 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
18462 (license license:gpl3)))
18463
18464 (define-public r-activpal
18465 (package
18466 (name "r-activpal")
18467 (version "0.1.3")
18468 (source
18469 (origin
18470 (method url-fetch)
18471 (uri (cran-uri "activPAL" version))
18472 (sha256
18473 (base32
18474 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
18475 (properties `((upstream-name . "activPAL")))
18476 (build-system r-build-system)
18477 (propagated-inputs
18478 `(("r-devtools" ,r-devtools)
18479 ("r-dplyr" ,r-dplyr)
18480 ("r-ggplot2" ,r-ggplot2)
18481 ("r-lubridate" ,r-lubridate)
18482 ("r-magrittr" ,r-magrittr)
18483 ("r-tidyr" ,r-tidyr)))
18484 (home-page "https://cran.r-project.org/web/packages/activPAL")
18485 (synopsis "Processing and chart generation from activPAL events files")
18486 (description
18487 "This package contains functions to generate pre-defined summary
18488 statistics from activPAL events files. The package also contains functions to
18489 produce informative graphics that visualize physical activity behaviour and
18490 trends. This includes generating graphs that align physical activity
18491 behaviour with additional time based observations described by other data
18492 sets, such as sleep diaries and continuous glucose monitoring data.")
18493 (license license:gpl3)))
18494
18495 (define-public r-activpalprocessing
18496 (package
18497 (name "r-activpalprocessing")
18498 (version "1.0.2")
18499 (source
18500 (origin
18501 (method url-fetch)
18502 (uri (cran-uri "activpalProcessing" version))
18503 (sha256
18504 (base32
18505 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
18506 (properties
18507 `((upstream-name . "activpalProcessing")))
18508 (build-system r-build-system)
18509 (propagated-inputs
18510 `(("r-chron" ,r-chron)))
18511 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
18512 (synopsis "Process activPAL events files")
18513 (description
18514 "This package performs estimation of physical activity and sedentary
18515 behavior variables from activPAL events files.")
18516 ;; Either version of the GPL.
18517 (license (list license:gpl2 license:gpl3))))
18518
18519 (define-public r-actogrammr
18520 (package
18521 (name "r-actogrammr")
18522 (version "0.2.3")
18523 (source
18524 (origin
18525 (method url-fetch)
18526 (uri (cran-uri "actogrammr" version))
18527 (sha256
18528 (base32
18529 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
18530 (properties `((upstream-name . "actogrammr")))
18531 (build-system r-build-system)
18532 (propagated-inputs
18533 `(("r-dplyr" ,r-dplyr)
18534 ("r-ggplot2" ,r-ggplot2)
18535 ("r-lubridate" ,r-lubridate)
18536 ("r-readr" ,r-readr)
18537 ("r-tidyr" ,r-tidyr)))
18538 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
18539 (synopsis "Read in activity data and plot actograms")
18540 (description
18541 "Read in activity measurements from standard file formats used by
18542 circadian rhythm researchers, currently only ClockLab format, and process and
18543 plot the data. The central type of plot is the actogram, as first described
18544 in \"Activity and distribution of certain wild mice in relation to biotic
18545 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
18546 (license license:gpl3)))
18547
18548 (define-public r-expint
18549 (package
18550 (name "r-expint")
18551 (version "0.1-6")
18552 (source
18553 (origin
18554 (method url-fetch)
18555 (uri (cran-uri "expint" version))
18556 (sha256
18557 (base32
18558 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
18559 (properties `((upstream-name . "expint")))
18560 (build-system r-build-system)
18561 (home-page "https://gitlab.com/vigou3/expint")
18562 (synopsis "Exponential integral and incomplete Gamma function")
18563 (description
18564 "This package provides the exponential integrals @code{E_1(x)},
18565 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
18566 function @code{G(a, x)} defined for negative values of its first argument.
18567 The package also gives easy access to the underlying C routines through an
18568 API; see the package vignette for details.")
18569 (license license:gpl2+)))
18570
18571 (define-public r-actuar
18572 (package
18573 (name "r-actuar")
18574 (version "2.3-3")
18575 (source
18576 (origin
18577 (method url-fetch)
18578 (uri (cran-uri "actuar" version))
18579 (sha256
18580 (base32
18581 "0aw3hlan5y22mdqk1wvnw9ksqhwp4yy5hi0dpv21p7s0hyxhphih"))))
18582 (properties `((upstream-name . "actuar")))
18583 (build-system r-build-system)
18584 (propagated-inputs `(("r-expint" ,r-expint)))
18585 (home-page "https://gitlab.com/vigou3/actuar")
18586 (synopsis "Actuarial functions and heavy tailed distributions")
18587 (description
18588 "This package provides functions and data sets for actuarial science:
18589 modeling of loss distributions; risk theory and ruin theory; simulation of
18590 compound models, discrete mixtures and compound hierarchical models;
18591 credibility theory. It boasts support for many additional probability
18592 distributions to model insurance loss amounts and loss frequency: 19
18593 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
18594 distribution; zero-truncated and zero-modified extensions of the standard
18595 discrete distributions. It also supports phase-type distributions commonly
18596 used to compute ruin probabilities.")
18597 (license license:gpl2+)))
18598
18599 (define-public r-bmp
18600 (package
18601 (name "r-bmp")
18602 (version "0.3")
18603 (source
18604 (origin
18605 (method url-fetch)
18606 (uri (cran-uri "bmp" version))
18607 (sha256
18608 (base32
18609 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
18610 (properties `((upstream-name . "bmp")))
18611 (build-system r-build-system)
18612 (home-page "https://cran.r-project.org/web/packages/bmp/")
18613 (synopsis "Read Bitmap (BMP) images")
18614 (description
18615 "This package provides pure R tools to read BMP format images. It is
18616 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
18617 (license license:gpl2+)))
18618
18619 (define-public r-readbitmap
18620 (package
18621 (name "r-readbitmap")
18622 (version "0.1.5")
18623 (source
18624 (origin
18625 (method url-fetch)
18626 (uri (cran-uri "readbitmap" version))
18627 (sha256
18628 (base32
18629 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
18630 (properties `((upstream-name . "readbitmap")))
18631 (build-system r-build-system)
18632 (inputs
18633 `(("libjpeg" ,libjpeg)
18634 ("libpng" ,libpng)))
18635 (propagated-inputs
18636 `(("r-bmp" ,r-bmp)
18637 ("r-jpeg" ,r-jpeg)
18638 ("r-png" ,r-png)
18639 ("r-tiff" ,r-tiff)))
18640 (home-page "https://github.com/jefferis/readbitmap")
18641 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
18642 (description
18643 "This package provides tools to identify and read BMP, JPEG, PNG, and
18644 TIFF format bitmap images. Identification defaults to the use of the magic
18645 number embedded in the file rather than the file extension.")
18646 (license license:gpl2+)))
18647
18648 (define-public r-imager
18649 (package
18650 (name "r-imager")
18651 (version "0.42.1")
18652 (source
18653 (origin
18654 (method url-fetch)
18655 (uri (cran-uri "imager" version))
18656 (sha256
18657 (base32
18658 "1d7a49lcna77wyfjf5q1b89jck3p3vnysnkgz4drb0qkpy6hz76b"))))
18659 (properties `((upstream-name . "imager")))
18660 (build-system r-build-system)
18661 (inputs
18662 `(("fftw" ,fftw)
18663 ("libtiff" ,libtiff)
18664 ("libx11" ,libx11)
18665 ("zlib" ,zlib)))
18666 (propagated-inputs
18667 `(("r-downloader" ,r-downloader)
18668 ("r-igraph" ,r-igraph)
18669 ("r-jpeg" ,r-jpeg)
18670 ("r-magrittr" ,r-magrittr)
18671 ("r-png" ,r-png)
18672 ("r-purrr" ,r-purrr)
18673 ("r-rcpp" ,r-rcpp)
18674 ("r-readbitmap" ,r-readbitmap)
18675 ("r-stringr" ,r-stringr)))
18676 (native-inputs `(("pkg-config" ,pkg-config)))
18677 (home-page "https://dahtah.github.io/imager/")
18678 (synopsis "Image processing library")
18679 (description
18680 "This is a package for fast image processing for images in up to 4
18681 dimensions (two spatial dimensions, one time/depth dimension, one color
18682 dimension). It provides most traditional image processing tools (filtering,
18683 morphology, transformations, etc.) as well as various functions for easily
18684 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
18685 simple, modern C++ library for image processing.")
18686 (license license:lgpl3)))
18687
18688 (define-public r-acuityview
18689 (package
18690 (name "r-acuityview")
18691 (version "0.1")
18692 (source
18693 (origin
18694 (method url-fetch)
18695 (uri (cran-uri "AcuityView" version))
18696 (sha256
18697 (base32
18698 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
18699 (properties `((upstream-name . "AcuityView")))
18700 (build-system r-build-system)
18701 (propagated-inputs
18702 `(("r-fftwtools" ,r-fftwtools)
18703 ("r-imager" ,r-imager)
18704 ("r-plotrix" ,r-plotrix)))
18705 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
18706 (synopsis "Display scenes as seen by an animal with less acute vision")
18707 (description
18708 "This package provides a simple method for representing a visual scene as
18709 it may be seen by an animal with less acute vision.")
18710 (license license:gpl2+)))
18711
18712 (define-public r-caret
18713 (package
18714 (name "r-caret")
18715 (version "6.0-86")
18716 (source
18717 (origin
18718 (method url-fetch)
18719 (uri (cran-uri "caret" version))
18720 (sha256
18721 (base32
18722 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
18723 (build-system r-build-system)
18724 (propagated-inputs
18725 `(("r-foreach" ,r-foreach)
18726 ("r-ggplot2" ,r-ggplot2)
18727 ("r-lattice" ,r-lattice)
18728 ("r-modelmetrics" ,r-modelmetrics)
18729 ("r-nlme" ,r-nlme)
18730 ("r-plyr" ,r-plyr)
18731 ("r-proc" ,r-proc)
18732 ("r-recipes" ,r-recipes)
18733 ("r-reshape2" ,r-reshape2)
18734 ("r-withr" ,r-withr)))
18735 (native-inputs
18736 `(("r-knitr" ,r-knitr)))
18737 (home-page "https://github.com/topepo/caret")
18738 (synopsis "Classification and regression training")
18739 (description
18740 "This package provides miscellaneous functions for training and plotting
18741 classification and regression models.")
18742 (license license:gpl2+)))
18743
18744 (define-public r-adabag
18745 (package
18746 (name "r-adabag")
18747 (version "4.2")
18748 (source
18749 (origin
18750 (method url-fetch)
18751 (uri (cran-uri "adabag" version))
18752 (sha256
18753 (base32
18754 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
18755 (properties `((upstream-name . "adabag")))
18756 (build-system r-build-system)
18757 (propagated-inputs
18758 `(("r-caret" ,r-caret)
18759 ("r-doparallel" ,r-doparallel)
18760 ("r-foreach" ,r-foreach)
18761 ("r-rpart" ,r-rpart)))
18762 (home-page "https://cran.r-project.org/web/packages/adabag/")
18763 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
18764 (description
18765 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
18766 Breiman's Bagging algorithm using classification trees as individual
18767 classifiers. Once these classifiers have been trained, they can be used to
18768 predict on new data. Also, cross validation estimation of the error can be
18769 done.")
18770 (license license:gpl2+)))
18771
18772 (define-public r-adagio
18773 (package
18774 (name "r-adagio")
18775 (version "0.7.1")
18776 (source
18777 (origin
18778 (method url-fetch)
18779 (uri (cran-uri "adagio" version))
18780 (sha256
18781 (base32
18782 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
18783 (properties `((upstream-name . "adagio")))
18784 (build-system r-build-system)
18785 (native-inputs `(("gfortran" ,gfortran)))
18786 (home-page "https://cran.r-project.org/web/packages/adagio/")
18787 (synopsis "Discrete and global optimization routines")
18788 (description
18789 "This package provides methods and algorithms for discrete optimization,
18790 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
18791 Hooke-Jeeves minimization, and some (evolutionary) global optimization
18792 functions.")
18793 (license license:gpl3+)))
18794
18795 (define-public r-univoutl
18796 (package
18797 (name "r-univoutl")
18798 (version "0.2")
18799 (source
18800 (origin
18801 (method url-fetch)
18802 (uri (cran-uri "univOutl" version))
18803 (sha256
18804 (base32
18805 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
18806 (properties `((upstream-name . "univOutl")))
18807 (build-system r-build-system)
18808 (propagated-inputs
18809 `(("r-hmisc" ,r-hmisc)
18810 ("r-robustbase" ,r-robustbase)))
18811 (home-page "https://github.com/marcellodo/univOutl")
18812 (synopsis "Detection of univariate outliers")
18813 (description
18814 "This package provides well-known outlier detection techniques in the
18815 univariate case. Methods to deal with skewed distribution are included too.
18816 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
18817 historical data is implemented as well. When available, survey weights can be
18818 used in outliers detection.")
18819 (license license:gpl2+)))
18820
18821 (define-public r-tolerance
18822 (package
18823 (name "r-tolerance")
18824 (version "2.0.0")
18825 (source
18826 (origin
18827 (method url-fetch)
18828 (uri (cran-uri "tolerance" version))
18829 (sha256
18830 (base32
18831 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
18832 (properties `((upstream-name . "tolerance")))
18833 (build-system r-build-system)
18834 (propagated-inputs
18835 `(("r-mass" ,r-mass)
18836 ("r-rgl" ,r-rgl)))
18837 (home-page "https://cran.r-project.org/web/packages/tolerance/")
18838 (synopsis "Statistical tolerance intervals and regions")
18839 (description
18840 "This package provides functions for estimating tolerance
18841 limits (intervals) for various univariate distributions (binomial, Cauchy,
18842 discrete Pareto, exponential, two-parameter exponential, extreme value,
18843 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
18844 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
18845 Bayesian normal tolerance limits, multivariate normal tolerance regions,
18846 nonparametric tolerance intervals, tolerance bands for regression
18847 settings (linear regression, nonlinear regression, nonparametric regression,
18848 and multivariate regression), and analysis of variance tolerance intervals.
18849 Visualizations are also available for most of these settings.")
18850 (license license:gpl2+)))
18851
18852 (define-public r-additivitytests
18853 (package
18854 (name "r-additivitytests")
18855 (version "1.1-4")
18856 (source
18857 (origin
18858 (method url-fetch)
18859 (uri (cran-uri "additivityTests" version))
18860 (sha256
18861 (base32
18862 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
18863 (properties
18864 `((upstream-name . "additivityTests")))
18865 (build-system r-build-system)
18866 (home-page "https://github.com/simecek/additivityTests")
18867 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
18868 (description
18869 "This package provides an implementation of the Tukey, Mandel,
18870 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
18871 (license license:gpl3)))
18872
18873 (define-public r-flexclust
18874 (package
18875 (name "r-flexclust")
18876 (version "1.4-0")
18877 (source
18878 (origin
18879 (method url-fetch)
18880 (uri (cran-uri "flexclust" version))
18881 (sha256
18882 (base32
18883 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
18884 (properties `((upstream-name . "flexclust")))
18885 (build-system r-build-system)
18886 (propagated-inputs
18887 `(("r-class" ,r-class)
18888 ("r-lattice" ,r-lattice)
18889 ("r-modeltools" ,r-modeltools)))
18890 (home-page "https://cran.r-project.org/web/packages/flexclust/")
18891 (synopsis "Flexible cluster algorithms")
18892 (description
18893 "The main function @code{kcca} implements a general framework for
18894 k-centroids cluster analysis supporting arbitrary distance measures and
18895 centroid computation. Further cluster methods include hard competitive
18896 learning, neural gas, and QT clustering. There are numerous visualization
18897 methods for cluster results (neighborhood graphs, convex cluster hulls,
18898 barcharts of centroids, ...), and bootstrap methods for the analysis of
18899 cluster stability.")
18900 (license license:gpl2)))
18901
18902 (define-public r-biclust
18903 (package
18904 (name "r-biclust")
18905 (version "2.0.2")
18906 (source
18907 (origin
18908 (method url-fetch)
18909 (uri (cran-uri "biclust" version))
18910 (sha256
18911 (base32
18912 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
18913 (properties `((upstream-name . "biclust")))
18914 (build-system r-build-system)
18915 (propagated-inputs
18916 `(("r-additivitytests" ,r-additivitytests)
18917 ("r-colorspace" ,r-colorspace)
18918 ("r-flexclust" ,r-flexclust)
18919 ("r-ggplot2" ,r-ggplot2)
18920 ("r-lattice" ,r-lattice)
18921 ("r-mass" ,r-mass)
18922 ("r-tidyr" ,r-tidyr)))
18923 (home-page "https://cran.r-project.org/web/packages/biclust/")
18924 (synopsis "BiCluster algorithms")
18925 (description
18926 "The main function @code{biclust()} provides several algorithms to find
18927 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
18928 In addition, the package provides methods for data
18929 preprocessing (normalization and discretization), visualization, and
18930 validation of bicluster solutions.")
18931 (license license:gpl3)))
18932
18933 (define-public r-icge
18934 (package
18935 (name "r-icge")
18936 (version "0.3")
18937 (source
18938 (origin
18939 (method url-fetch)
18940 (uri (cran-uri "ICGE" version))
18941 (sha256
18942 (base32
18943 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
18944 (properties `((upstream-name . "ICGE")))
18945 (build-system r-build-system)
18946 (propagated-inputs
18947 `(("r-cluster" ,r-cluster)
18948 ("r-mass" ,r-mass)))
18949 (home-page "https://cran.r-project.org/web/packages/ICGE/")
18950 (synopsis "Cluster estimation and identification of atypical units")
18951 (description
18952 "ICGE is a package that helps to estimate the number of real clusters in
18953 data as well as to identify atypical units. The underlying methods are based
18954 on distances rather than on unit x variables.")
18955 (license license:gpl2+)))
18956
18957 (define-public r-depth
18958 (package
18959 (name "r-depth")
18960 (version "2.1-1.1")
18961 (source
18962 (origin
18963 (method url-fetch)
18964 (uri (cran-uri "depth" version))
18965 (sha256
18966 (base32
18967 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
18968 (properties `((upstream-name . "depth")))
18969 (build-system r-build-system)
18970 (propagated-inputs
18971 `(("r-abind" ,r-abind)
18972 ("r-circular" ,r-circular)
18973 ("r-rgl" ,r-rgl)))
18974 (native-inputs
18975 `(("gfortran" ,gfortran)))
18976 (home-page "https://cran.r-project.org/web/packages/depth/")
18977 (synopsis "Nonparametric depth functions for multivariate analysis")
18978 (description
18979 "This package provides tools for depth functions methodology applied to
18980 multivariate analysis. Besides allowing calculation of depth values and
18981 depth-based location estimators, the package includes functions or drawing
18982 contour plots and perspective plots of depth functions. Euclidian and
18983 spherical depths are supported.")
18984 (license license:gpl2)))
18985
18986 (define-public r-archetypes
18987 (package
18988 (name "r-archetypes")
18989 (version "2.2-0.1")
18990 (source
18991 (origin
18992 (method url-fetch)
18993 (uri (cran-uri "archetypes" version))
18994 (sha256
18995 (base32
18996 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
18997 (properties `((upstream-name . "archetypes")))
18998 (build-system r-build-system)
18999 (propagated-inputs
19000 `(("r-modeltools" ,r-modeltools)
19001 ("r-nnls" ,r-nnls)))
19002 (home-page "https://cran.r-project.org/web/packages/archetypes")
19003 (synopsis "Archetypal analysis")
19004 (description
19005 "The main function @code{archetypes} implements a framework for
19006 archetypal analysis supporting arbitrary problem solving mechanisms for the
19007 different conceptual parts of the algorithm.")
19008 (license license:gpl2+)))
19009
19010 (define-public r-shapes
19011 (package
19012 (name "r-shapes")
19013 (version "1.2.5")
19014 (source
19015 (origin
19016 (method url-fetch)
19017 (uri (cran-uri "shapes" version))
19018 (sha256
19019 (base32
19020 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
19021 (properties `((upstream-name . "shapes")))
19022 (build-system r-build-system)
19023 (propagated-inputs
19024 `(("r-mass" ,r-mass)
19025 ("r-minpack-lm" ,r-minpack-lm)
19026 ("r-rgl" ,r-rgl)
19027 ("r-scatterplot3d" ,r-scatterplot3d)))
19028 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
19029 (synopsis "Statistical shape analysis")
19030 (description
19031 "This package provides routines for the statistical analysis of landmark
19032 shapes, including Procrustes analysis, graphical displays, principal
19033 components analysis, permutation and bootstrap tests, thin-plate spline
19034 transformation grids and comparing covariance matrices. See Dryden, I.L. and
19035 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
19036 Edition), John Wiley and Sons.")
19037 (license license:gpl2)))
19038
19039 (define-public r-anthropometry
19040 (package
19041 (name "r-anthropometry")
19042 (version "1.14")
19043 (source
19044 (origin
19045 (method url-fetch)
19046 (uri (cran-uri "Anthropometry" version))
19047 (sha256
19048 (base32
19049 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
19050 (properties `((upstream-name . "Anthropometry")))
19051 (build-system r-build-system)
19052 (propagated-inputs
19053 `(("r-archetypes" ,r-archetypes)
19054 ("r-biclust" ,r-biclust)
19055 ("r-cluster" ,r-cluster)
19056 ("r-depth" ,r-depth)
19057 ("r-fnn" ,r-fnn)
19058 ("r-icge" ,r-icge)
19059 ("r-nnls" ,r-nnls)
19060 ("r-rgl" ,r-rgl)
19061 ("r-shapes" ,r-shapes)))
19062 (native-inputs
19063 `(("r-knitr" ,r-knitr)))
19064 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
19065 (synopsis "Statistical methods for anthropometric data")
19066 (description
19067 "This package provides statistical methods especially developed to
19068 analyze anthropometric data. These methods are aimed at providing effective
19069 solutions to some commons problems related to Ergonomics and Anthropometry.
19070 They are based on clustering, the statistical concept of data depth,
19071 statistical shape analysis and archetypal analysis.")
19072 (license license:gpl2+)))
19073
19074 (define-public r-adamethods
19075 (package
19076 (name "r-adamethods")
19077 (version "1.2")
19078 (source
19079 (origin
19080 (method url-fetch)
19081 (uri (cran-uri "adamethods" version))
19082 (sha256
19083 (base32
19084 "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh"))))
19085 (properties `((upstream-name . "adamethods")))
19086 (build-system r-build-system)
19087 (propagated-inputs
19088 `(("r-anthropometry" ,r-anthropometry)
19089 ("r-archetypes" ,r-archetypes)
19090 ("r-fnn" ,r-fnn)
19091 ("r-foreach" ,r-foreach)
19092 ("r-nnls" ,r-nnls)
19093 ("r-tolerance" ,r-tolerance)
19094 ("r-univoutl" ,r-univoutl)))
19095 (home-page "https://cran.r-project.org/web/packages/adamethods/")
19096 (synopsis "Archetypoid algorithms and anomaly detection")
19097 (description
19098 "This package is a collection of several algorithms to obtain
19099 archetypoids with small and large databases and with both classical
19100 multivariate data and functional data (univariate and multivariate). Some of
19101 these algorithms also allow to detect anomalies (outliers).")
19102 (license license:gpl2+)))
19103
19104 (define-public r-idpmisc
19105 (package
19106 (name "r-idpmisc")
19107 (version "1.1.20")
19108 (source
19109 (origin
19110 (method url-fetch)
19111 (uri (cran-uri "IDPmisc" version))
19112 (sha256
19113 (base32
19114 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
19115 (properties `((upstream-name . "IDPmisc")))
19116 (build-system r-build-system)
19117 (propagated-inputs
19118 `(("r-lattice" ,r-lattice)))
19119 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
19120 (synopsis "Functions for data analyses and visualization")
19121 (description
19122 "This package provides different high-level graphics functions for
19123 displaying large datasets, displaying circular data in a very flexible way,
19124 finding local maxima, brewing color ramps, drawing nice arrows, zooming
19125 2D-plots, creating figures with differently colored margin and plot region.
19126 In addition, the package contains auxiliary functions for data manipulation
19127 like omitting observations with irregular values or selecting data by logical
19128 vectors, which include NAs. Other functions are especially useful in
19129 spectroscopy and analyses of environmental data: robust baseline fitting,
19130 finding peaks in spectra, converting humidity measures.")
19131 (license license:gpl3+)))
19132
19133 (define-public r-qqman
19134 (package
19135 (name "r-qqman")
19136 (version "0.1.4")
19137 (source
19138 (origin
19139 (method url-fetch)
19140 (uri (cran-uri "qqman" version))
19141 (sha256
19142 (base32
19143 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
19144 (properties `((upstream-name . "qqman")))
19145 (build-system r-build-system)
19146 (propagated-inputs
19147 `(("r-calibrate" ,r-calibrate)))
19148 (home-page "https://cran.r-project.org/web/packages/qqman/")
19149 (synopsis "Q-Q and Manhattan plots for GWAS data")
19150 (description
19151 "This package allows you to create Q-Q and Manhattan plots for GWAS data
19152 from PLINK results.")
19153 (license license:gpl3)))
19154
19155 (define-public r-ggplot-multistats
19156 (package
19157 (name "r-ggplot-multistats")
19158 (version "1.0.0")
19159 (source
19160 (origin
19161 (method url-fetch)
19162 (uri (cran-uri "ggplot.multistats" version))
19163 (sha256
19164 (base32
19165 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
19166 (properties
19167 `((upstream-name . "ggplot.multistats")))
19168 (build-system r-build-system)
19169 (propagated-inputs
19170 `(("r-ggplot2" ,r-ggplot2)
19171 ("r-hexbin" ,r-hexbin)
19172 ("r-rlang" ,r-rlang)
19173 ("r-scales" ,r-scales)))
19174 (home-page "https://github.com/flying-sheep/ggplot.multistats")
19175 (synopsis "Multiple summary statistics for binned stats/geometries")
19176 (description
19177 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
19178 which functions similar to its singular form, but allows the use of multiple
19179 statistics per bin. Those statistics can be mapped to multiple bin
19180 aesthetics.")
19181 (license license:gpl3)))
19182
19183 (define-public r-knn-covertree
19184 (package
19185 (name "r-knn-covertree")
19186 (version "1.0")
19187 (source
19188 (origin
19189 (method url-fetch)
19190 (uri (cran-uri "knn.covertree" version))
19191 (sha256
19192 (base32
19193 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
19194 (properties `((upstream-name . "knn.covertree")))
19195 (build-system r-build-system)
19196 (propagated-inputs
19197 `(("r-matrix" ,r-matrix)
19198 ("r-rcpp" ,r-rcpp)
19199 ("r-rcppeigen" ,r-rcppeigen)))
19200 (home-page "https://github.com/flying-sheep/knn.covertree")
19201 (synopsis "Accurate kNN Implementation with multiple distance measures")
19202 (description
19203 "Similarly to the FNN package, this package allows calculation of the k
19204 nearest neighbors (kNN) of a data matrix. The implementation is based on
19205 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
19206 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
19207 (license license:agpl3+)))
19208
19209 (define-public r-poibin
19210 (package
19211 (name "r-poibin")
19212 (version "1.5")
19213 (source
19214 (origin
19215 (method url-fetch)
19216 (uri (cran-uri "poibin" version))
19217 (sha256
19218 (base32
19219 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
19220 (properties `((upstream-name . "poibin")))
19221 (build-system r-build-system)
19222 (home-page "https://cran.r-project.org/web/packages/poibin/")
19223 (synopsis "Poisson binomial distribution")
19224 (description
19225 "This package provides an implementation of both the exact and
19226 approximation methods for computing the @dfn{cumulative distribution
19227 function} (CDF) of the Poisson binomial distribution. It also provides the
19228 @dfn{probability mass function} (PMF), quantile function, and random number
19229 generation for the Poisson binomial distribution.")
19230 (license license:gpl2)))
19231
19232 (define-public r-diagram
19233 (package
19234 (name "r-diagram")
19235 (version "1.6.4")
19236 (source
19237 (origin
19238 (method url-fetch)
19239 (uri (cran-uri "diagram" version))
19240 (sha256
19241 (base32
19242 "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
19243 (properties `((upstream-name . "diagram")))
19244 (build-system r-build-system)
19245 (propagated-inputs
19246 `(("r-shape" ,r-shape)))
19247 (home-page "https://cran.r-project.org/web/packages/diagram/")
19248 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
19249 (description
19250 "This package provides tools to visualize simple graphs (networks) based
19251 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
19252 electrical networks, etc. It also includes supporting material for the book
19253 \"A practical guide to ecological modelling - using R as a simulation
19254 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
19255 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
19256 Francesca Mazzia (2012).")
19257 (license license:gpl2+)))
19258
19259 (define-public r-lim
19260 (package
19261 (name "r-lim")
19262 (version "1.4.6")
19263 (source
19264 (origin
19265 (method url-fetch)
19266 (uri (cran-uri "LIM" version))
19267 (sha256
19268 (base32
19269 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
19270 (properties `((upstream-name . "LIM")))
19271 (build-system r-build-system)
19272 (propagated-inputs
19273 `(("r-diagram" ,r-diagram)
19274 ("r-limsolve" ,r-limsolve)))
19275 (home-page "https://cran.r-project.org/web/packages/LIM/")
19276 (synopsis "Linear inverse model examples and solution methods")
19277 (description
19278 "This package provides functions that read and solve linear inverse
19279 problems (food web problems, linear programming problems).")
19280 (license license:gpl2+)))
19281
19282 (define-public r-shinycssloaders
19283 (package
19284 (name "r-shinycssloaders")
19285 (version "0.3")
19286 (source
19287 (origin
19288 (method url-fetch)
19289 (uri (cran-uri "shinycssloaders" version))
19290 (sha256
19291 (base32
19292 "1gzq1lhcnhqd145ys3ixf0l13l560fiqr2sc3m2nrijwxlgcw54d"))))
19293 (properties
19294 `((upstream-name . "shinycssloaders")))
19295 (build-system r-build-system)
19296 (propagated-inputs
19297 `(("r-digest" ,r-digest)
19298 ("r-glue" ,r-glue)
19299 ("r-shiny" ,r-shiny)))
19300 (home-page "https://github.com/andrewsali/shinycssloaders")
19301 (synopsis "Add CSS loading animations to Shiny outputs")
19302 (description
19303 "This package provides tools to create a lightweight Shiny wrapper for
19304 the css-loaders created by Luke Hass
19305 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
19306 automatically show a loader when the output is (re)calculating.")
19307 (license license:gpl3)))
19308
19309 (define-public r-rsvg
19310 (package
19311 (name "r-rsvg")
19312 (version "1.3")
19313 (source
19314 (origin
19315 (method url-fetch)
19316 (uri (cran-uri "rsvg" version))
19317 (sha256
19318 (base32
19319 "11mccgf6hfskg45wqc114sx3qy2r494y6axdf73z6xwhs1wpm97g"))))
19320 (properties `((upstream-name . "rsvg")))
19321 (build-system r-build-system)
19322 (inputs
19323 `(("librsvg" ,librsvg)
19324 ("zlib" ,zlib)))
19325 (native-inputs
19326 `(("pkg-config" ,pkg-config)))
19327 (home-page "https://github.com/jeroen/rsvg#readme")
19328 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
19329 (description
19330 "This package allows you to render vector-based SVG images into
19331 high-quality custom-size bitmap arrays using the librsvg2 library. The
19332 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
19333 addition, the package can convert images directly to various formats such as
19334 PDF or PostScript.")
19335 (license license:expat)))
19336
19337 (define-public r-influencer
19338 (package
19339 (name "r-influencer")
19340 (version "0.1.0")
19341 (source
19342 (origin
19343 (method url-fetch)
19344 (uri (cran-uri "influenceR" version))
19345 (sha256
19346 (base32
19347 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
19348 (properties `((upstream-name . "influenceR")))
19349 (build-system r-build-system)
19350 (propagated-inputs
19351 `(("r-igraph" ,r-igraph)
19352 ("r-matrix" ,r-matrix)))
19353 (home-page "https://github.com/rcc-uchicago/influenceR")
19354 (synopsis "Tools to quantify structural importance of nodes in a network")
19355 (description
19356 "This package provides functionality to compute various node centrality
19357 measures on networks. Included are functions to compute betweenness
19358 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
19359 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
19360 algorithm to identify key players, and Valente's bridging metric. The
19361 betweenness, Key Players, and bridging implementations are parallelized with
19362 OpenMP.")
19363 (license license:gpl2)))
19364
19365 (define-public r-emplik
19366 (package
19367 (name "r-emplik")
19368 (version "1.0-4.3")
19369 (source
19370 (origin
19371 (method url-fetch)
19372 (uri (cran-uri "emplik" version))
19373 (sha256
19374 (base32
19375 "1g4hz85bvw29c77zs0ig487z92jjl682vv457x81l077h0psvk7c"))))
19376 (properties `((upstream-name . "emplik")))
19377 (build-system r-build-system)
19378 (propagated-inputs
19379 `(("r-quantreg" ,r-quantreg)))
19380 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
19381 (synopsis "Empirical likelihood ratio for censored/truncated data")
19382 (description
19383 "This package provides empirical likelihood ratio tests for
19384 means/quantiles/hazards from possibly censored and/or truncated data. It also
19385 does regression.")
19386 (license license:gpl2+)))
19387
19388 (define-public r-imputeyn
19389 (package
19390 (name "r-imputeyn")
19391 (version "1.3")
19392 (source
19393 (origin
19394 (method url-fetch)
19395 (uri (cran-uri "imputeYn" version))
19396 (sha256
19397 (base32
19398 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
19399 (properties `((upstream-name . "imputeYn")))
19400 (build-system r-build-system)
19401 (propagated-inputs
19402 `(("r-boot" ,r-boot)
19403 ("r-emplik" ,r-emplik)
19404 ("r-mvtnorm" ,r-mvtnorm)
19405 ("r-quadprog" ,r-quadprog)
19406 ("r-survival" ,r-survival)))
19407 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
19408 (synopsis "Impute last largest censored observation under weighted least squares")
19409 (description
19410 "This package allows for the imputation of the last largest censored
19411 observantions. This method brings less bias and more efficient estimates for
19412 AFT models.")
19413 (license license:gpl2)))
19414
19415 (define-public r-adapenetclass
19416 (package
19417 (name "r-adapenetclass")
19418 (version "1.2")
19419 (source
19420 (origin
19421 (method url-fetch)
19422 (uri (cran-uri "AdapEnetClass" version))
19423 (sha256
19424 (base32
19425 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
19426 (properties `((upstream-name . "AdapEnetClass")))
19427 (build-system r-build-system)
19428 (propagated-inputs
19429 `(("r-glmnet" ,r-glmnet)
19430 ("r-imputeyn" ,r-imputeyn)
19431 ("r-lars" ,r-lars)
19432 ("r-quadprog" ,r-quadprog)))
19433 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
19434 (synopsis "Class of adaptive elastic net methods for censored data")
19435 (description
19436 "This package provides methods for variable selection for AFT models.")
19437 (license license:gpl2)))
19438
19439 (define-public r-flock
19440 (package
19441 (name "r-flock")
19442 (version "0.7")
19443 (source
19444 (origin
19445 (method url-fetch)
19446 (uri (cran-uri "flock" version))
19447 (sha256
19448 (base32
19449 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
19450 (properties `((upstream-name . "flock")))
19451 (build-system r-build-system)
19452 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19453 (home-page "https://cran.r-project.org/web/packages/flock/")
19454 (synopsis "Process synchronization using file locks")
19455 (description
19456 "This package implements synchronization between R processes (spawned by
19457 using the @code{parallel} package for instance) using file locks. It supports
19458 both exclusive and shared locking.")
19459 (license license:asl2.0)))
19460
19461 (define-public r-archivist
19462 (package
19463 (name "r-archivist")
19464 (version "2.3.4")
19465 (source
19466 (origin
19467 (method url-fetch)
19468 (uri (cran-uri "archivist" version))
19469 (sha256
19470 (base32
19471 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
19472 (properties `((upstream-name . "archivist")))
19473 (build-system r-build-system)
19474 (propagated-inputs
19475 `(("r-dbi" ,r-dbi)
19476 ("r-digest" ,r-digest)
19477 ("r-flock" ,r-flock)
19478 ("r-httr" ,r-httr)
19479 ("r-lubridate" ,r-lubridate)
19480 ("r-magrittr" ,r-magrittr)
19481 ("r-rcurl" ,r-rcurl)
19482 ("r-rsqlite" ,r-rsqlite)))
19483 (home-page "https://pbiecek.github.io/archivist/")
19484 (synopsis "Tools for storing, restoring and searching for R objects")
19485 (description
19486 "Data exploration and modelling is a process in which a lot of data
19487 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
19488 statistical models, different versions of data sets and different versions of
19489 results. Archivist helps to store and manage artifacts created in R. It
19490 allows you to store selected artifacts as binary files together with their
19491 metadata and relations. Archivist allows sharing artifacts with others. It
19492 can look for already created artifacts by using its class, name, date of the
19493 creation or other properties. It also makes it easy to restore such
19494 artifacts.")
19495 (license license:gpl2)))
19496
19497 (define-public r-versions
19498 (package
19499 (name "r-versions")
19500 (version "0.3")
19501 (source
19502 (origin
19503 (method url-fetch)
19504 (uri (cran-uri "versions" version))
19505 (sha256
19506 (base32
19507 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
19508 (properties `((upstream-name . "versions")))
19509 (build-system r-build-system)
19510 (home-page "https://cran.r-project.org/web/packages/versions/")
19511 (synopsis "Query and install specific versions of CRAN packages")
19512 (description
19513 "This package allows you to install specified versions of R packages
19514 hosted on CRAN and provides functions to list available versions and the
19515 versions of currently installed packages.")
19516 (license license:bsd-3)))
19517
19518 (define-public r-adapr
19519 (package
19520 (name "r-adapr")
19521 (version "2.0.0")
19522 (source
19523 (origin
19524 (method url-fetch)
19525 (uri (cran-uri "adapr" version))
19526 (sha256
19527 (base32
19528 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
19529 (properties `((upstream-name . "adapr")))
19530 (build-system r-build-system)
19531 (propagated-inputs
19532 `(("r-archivist" ,r-archivist)
19533 ("r-devtools" ,r-devtools)
19534 ("r-digest" ,r-digest)
19535 ("r-doparallel" ,r-doparallel)
19536 ("r-gdata" ,r-gdata)
19537 ("r-ggplot2" ,r-ggplot2)
19538 ("r-git2r" ,r-git2r)
19539 ("r-igraph" ,r-igraph)
19540 ("r-knitr" ,r-knitr)
19541 ("r-plotly" ,r-plotly)
19542 ("r-plyr" ,r-plyr)
19543 ("r-rmarkdown" ,r-rmarkdown)
19544 ("r-shiny" ,r-shiny)
19545 ("r-shinydashboard" ,r-shinydashboard)
19546 ("r-versions" ,r-versions)))
19547 (home-page "https://cran.r-project.org/web/packages/adapr/")
19548 (synopsis "Implementation of an accountable data analysis process")
19549 (description
19550 "This package tracks reading and writing within R scripts that are
19551 organized into a directed acyclic graph. It contains an interactive Shiny
19552 application @code{adaprApp()}. It uses Git and file hashes to track version
19553 histories of inputs and outputs.")
19554 (license license:lgpl2.0)))
19555
19556 (define-public r-adapsamp
19557 (package
19558 (name "r-adapsamp")
19559 (version "1.1.1")
19560 (source
19561 (origin
19562 (method url-fetch)
19563 (uri (cran-uri "AdapSamp" version))
19564 (sha256
19565 (base32
19566 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
19567 (properties `((upstream-name . "AdapSamp")))
19568 (build-system r-build-system)
19569 (propagated-inputs `(("r-pracma" ,r-pracma)))
19570 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
19571 (synopsis "Adaptive sampling algorithms")
19572 (description
19573 "For distributions whose probability density functions are log-concave,
19574 the adaptive rejection sampling algorithm can be used to build envelope
19575 functions for sampling. For others, the modified adaptive rejection sampling
19576 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
19577 adaptive slice sampling algorithm can be used. This R package mainly includes
19578 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
19579 @code{rASS()}. These functions can realize sampling based on the algorithms
19580 above.")
19581 (license license:gpl2)))
19582
19583 (define-public r-adaptalint
19584 (package
19585 (name "r-adaptalint")
19586 (version "0.2.4")
19587 (source
19588 (origin
19589 (method url-fetch)
19590 (uri (cran-uri "adaptalint" version))
19591 (sha256
19592 (base32
19593 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
19594 (properties `((upstream-name . "adaptalint")))
19595 (build-system r-build-system)
19596 (propagated-inputs
19597 `(("r-dplyr" ,r-dplyr)
19598 ("r-lintr" ,r-lintr)
19599 ("r-purrr" ,r-purrr)))
19600 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
19601 (synopsis "Check R code style")
19602 (description
19603 "This package provides tools to infer the code style (which style rules
19604 are followed and which ones are not) from one package and use it to check
19605 another. This makes it easier to find and correct the most important problems
19606 first.")
19607 (license license:gpl3)))
19608
19609 (define-public r-fracdiff
19610 (package
19611 (name "r-fracdiff")
19612 (version "1.5-1")
19613 (source
19614 (origin
19615 (method url-fetch)
19616 (uri (cran-uri "fracdiff" version))
19617 (sha256
19618 (base32
19619 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
19620 (properties `((upstream-name . "fracdiff")))
19621 (build-system r-build-system)
19622 (home-page "https://github.com/mmaechler/fracdiff")
19623 (synopsis
19624 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
19625 (description
19626 "This package provides tools for the maximum likelihood estimation of the
19627 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
19628 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
19629 (license license:gpl2+)))
19630
19631 (define-public r-forecast
19632 (package
19633 (name "r-forecast")
19634 (version "8.12")
19635 (source
19636 (origin
19637 (method url-fetch)
19638 (uri (cran-uri "forecast" version))
19639 (sha256
19640 (base32
19641 "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b"))))
19642 (properties `((upstream-name . "forecast")))
19643 (build-system r-build-system)
19644 (propagated-inputs
19645 `(("r-colorspace" ,r-colorspace)
19646 ("r-fracdiff" ,r-fracdiff)
19647 ("r-ggplot2" ,r-ggplot2)
19648 ("r-lmtest" ,r-lmtest)
19649 ("r-magrittr" ,r-magrittr)
19650 ("r-nnet" ,r-nnet)
19651 ("r-rcpp" ,r-rcpp)
19652 ("r-rcpparmadillo" ,r-rcpparmadillo)
19653 ("r-timedate" ,r-timedate)
19654 ("r-tseries" ,r-tseries)
19655 ("r-urca" ,r-urca)
19656 ("r-zoo" ,r-zoo)))
19657 (native-inputs
19658 `(("r-knitr" ,r-knitr))) ; needed for vignettes
19659 (home-page "https://pkg.robjhyndman.com/forecast/")
19660 (synopsis "Forecasting functions for time series and linear models")
19661 (description
19662 "This package provides methods and tools for displaying and analysing
19663 univariate time series forecasts including exponential smoothing via state
19664 space models and automatic ARIMA modelling.")
19665 (license license:gpl3)))
19666
19667 (define-public r-xmisc
19668 (package
19669 (name "r-xmisc")
19670 (version "0.2.1")
19671 (source
19672 (origin
19673 (method url-fetch)
19674 (uri (cran-uri "Xmisc" version))
19675 (sha256
19676 (base32
19677 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
19678 (properties `((upstream-name . "Xmisc")))
19679 (build-system r-build-system)
19680 (home-page "https://cran.r-project.org/package=Xmisc")
19681 (synopsis
19682 "Xiaobei's miscellaneous classes and functions")
19683 (description
19684 "This package provides Xiaobei's miscellaneous classes and functions,
19685 which are useful when developing R packages for @dfn{object oriented
19686 programming} (OOP) using R Reference Class.")
19687 (license license:gpl2+)))
19688
19689 (define-public r-proxyc
19690 (package
19691 (name "r-proxyc")
19692 (version "0.1.5")
19693 (source
19694 (origin
19695 (method url-fetch)
19696 (uri (cran-uri "proxyC" version))
19697 (sha256
19698 (base32
19699 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
19700 (properties `((upstream-name . "proxyC")))
19701 (build-system r-build-system)
19702 (propagated-inputs
19703 `(("r-matrix" ,r-matrix)
19704 ("r-rcpp" ,r-rcpp)
19705 ("r-rcpparmadillo" ,r-rcpparmadillo)
19706 ("r-rcppparallel" ,r-rcppparallel)))
19707 (home-page "https://cran.r-project.org/package=proxyC")
19708 (synopsis "Compute proximity in large sparse matrices")
19709 (description
19710 "This package provides efficient tools to compute the proximity between
19711 rows or columns of large matrices. Functions are optimised for large sparse
19712 matrices using the Armadillo and Intel TBB libraries. Among several built-in
19713 similarity/distance measures, computation of correlation, cosine similarity
19714 and Euclidean distance is particularly fast.")
19715 (license license:gpl3)))
19716
19717 (define-public r-isocodes
19718 (package
19719 (name "r-isocodes")
19720 (version "2020.03.16")
19721 (source
19722 (origin
19723 (method url-fetch)
19724 (uri (cran-uri "ISOcodes" version))
19725 (sha256
19726 (base32
19727 "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn"))))
19728 (properties `((upstream-name . "ISOcodes")))
19729 (build-system r-build-system)
19730 (home-page "https://cran.r-project.org/package=ISOcodes")
19731 (synopsis "Selected ISO codes")
19732 (description
19733 "This package provides ISO language, territory, currency, script and
19734 character codes. It provides ISO 639 language codes, ISO 3166 territory
19735 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
19736 character codes as well as the UN M.49 area codes.")
19737 (license license:gpl2)))
19738
19739 (define-public r-stopwords
19740 (package
19741 (name "r-stopwords")
19742 (version "2.0")
19743 (source
19744 (origin
19745 (method url-fetch)
19746 (uri (cran-uri "stopwords" version))
19747 (sha256
19748 (base32
19749 "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
19750 (properties `((upstream-name . "stopwords")))
19751 (build-system r-build-system)
19752 (propagated-inputs
19753 `(("r-desc" ,r-desc)
19754 ("r-isocodes" ,r-isocodes)
19755 ("r-usethis" ,r-usethis)))
19756 (home-page "https://github.com/quanteda/stopwords")
19757 (synopsis "Multilingual stopword lists")
19758 (description
19759 "This package provides multiple sources of stopwords, for use in text
19760 analysis and natural language processing.")
19761 (license license:expat)))
19762
19763 (define-public r-spacyr
19764 (package
19765 (name "r-spacyr")
19766 (version "1.2.1")
19767 (source
19768 (origin
19769 (method url-fetch)
19770 (uri (cran-uri "spacyr" version))
19771 (sha256
19772 (base32
19773 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
19774 (properties `((upstream-name . "spacyr")))
19775 (build-system r-build-system)
19776 (propagated-inputs
19777 `(("r-data-table" ,r-data-table)
19778 ("r-reticulate" ,r-reticulate)))
19779 (home-page "https://spacyr.quanteda.io")
19780 (synopsis "R wrapper for the spaCy NLP library")
19781 (description
19782 "This package provides an R wrapper to the Python @dfn{natural language
19783 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
19784 (license license:gpl3)))
19785
19786 (define-public r-snowballc
19787 (package
19788 (name "r-snowballc")
19789 (version "0.7.0")
19790 (source
19791 (origin
19792 (method url-fetch)
19793 (uri (cran-uri "SnowballC" version))
19794 (sha256
19795 (base32
19796 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
19797 (properties `((upstream-name . "SnowballC")))
19798 (build-system r-build-system)
19799 (home-page "https://r-forge.r-project.org/projects/r-temis/")
19800 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
19801 (description
19802 "This package provides an R interface to the C @code{libstemmer} library
19803 that implements Porter's word stemming algorithm for collapsing words to a
19804 common root to aid comparison of vocabulary. Currently supported languages
19805 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
19806 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
19807 (license license:bsd-3)))
19808
19809 (define-public r-quanteda
19810 (package
19811 (name "r-quanteda")
19812 (version "2.0.1")
19813 (source
19814 (origin
19815 (method url-fetch)
19816 (uri (cran-uri "quanteda" version))
19817 (sha256
19818 (base32
19819 "0pym6vdzqbkyj87m3pla229092xvvx4j830x67qflxzzdmc9dzhz"))))
19820 (properties `((upstream-name . "quanteda")))
19821 (build-system r-build-system)
19822 (propagated-inputs
19823 `(("r-data-table" ,r-data-table)
19824 ("r-extrafont" ,r-extrafont)
19825 ("r-fastmatch" ,r-fastmatch)
19826 ("r-ggplot2" ,r-ggplot2)
19827 ("r-ggrepel" ,r-ggrepel)
19828 ("r-jsonlite" ,r-jsonlite)
19829 ("r-magrittr" ,r-magrittr)
19830 ("r-matrix" ,r-matrix)
19831 ("r-network" ,r-network)
19832 ("r-proxyc" ,r-proxyc)
19833 ("r-rcpp" ,r-rcpp)
19834 ("r-rcpparmadillo" ,r-rcpparmadillo)
19835 ("r-rcppparallel" ,r-rcppparallel)
19836 ("r-sna" ,r-sna)
19837 ("r-snowballc" ,r-snowballc)
19838 ("r-stopwords" ,r-stopwords)
19839 ("r-stringi" ,r-stringi)
19840 ("r-xml2" ,r-xml2)
19841 ("r-yaml" ,r-yaml)))
19842 (native-inputs
19843 `(("r-knitr" ,r-knitr)))
19844 (home-page "https://quanteda.io")
19845 (synopsis "Quantitative analysis of textual data")
19846 (description
19847 "This package provides a fast, flexible, and comprehensive framework for
19848 quantitative text analysis in R. It provides functionality for corpus
19849 management, creating and manipulating tokens and ngrams, exploring keywords in
19850 context, forming and manipulating sparse matrices of documents by features and
19851 feature co-occurrences, analyzing keywords, computing feature similarities and
19852 distances, applying content dictionaries, applying supervised and unsupervised
19853 machine learning, visually representing text and text analyses, and more.")
19854 (license license:gpl3)))
19855
19856 (define-public r-topicmodels
19857 (package
19858 (name "r-topicmodels")
19859 (version "0.2-11")
19860 (source
19861 (origin
19862 (method url-fetch)
19863 (uri (cran-uri "topicmodels" version))
19864 (sha256
19865 (base32
19866 "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
19867 (properties `((upstream-name . "topicmodels")))
19868 (build-system r-build-system)
19869 (native-inputs
19870 `(("gsl" ,gsl)))
19871 (propagated-inputs
19872 `(("r-modeltools" ,r-modeltools)
19873 ("r-slam" ,r-slam)
19874 ("r-tm" ,r-tm)))
19875 (home-page "https://cran.r-project.org/package=topicmodels")
19876 (synopsis "Topic models")
19877 (description
19878 "This package provides an interface to the C code for @dfn{Latent
19879 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
19880 David M. Blei and co-authors and the C++ code for fitting LDA models using
19881 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
19882 (license license:gpl2)))
19883
19884 (define-public r-stm
19885 (package
19886 (name "r-stm")
19887 (version "1.3.5")
19888 (source
19889 (origin
19890 (method url-fetch)
19891 (uri (cran-uri "stm" version))
19892 (sha256
19893 (base32
19894 "1yyfxaxqc6yq0yq68zhdnhpwpvsyp71dlmivn7zxixfmp932s6cn"))))
19895 (properties `((upstream-name . "stm")))
19896 (build-system r-build-system)
19897 (propagated-inputs
19898 `(("r-data-table" ,r-data-table)
19899 ("r-glmnet" ,r-glmnet)
19900 ("r-lda" ,r-lda)
19901 ("r-matrix" ,r-matrix)
19902 ("r-matrixstats" ,r-matrixstats)
19903 ("r-quadprog" ,r-quadprog)
19904 ("r-quanteda" ,r-quanteda)
19905 ("r-rcpp" ,r-rcpp)
19906 ("r-rcpparmadillo" ,r-rcpparmadillo)
19907 ("r-slam" ,r-slam)
19908 ("r-stringr" ,r-stringr)))
19909 (home-page "http://www.structuraltopicmodel.com/")
19910 (synopsis "Estimation of the Structural Topic Model")
19911 (description
19912 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
19913 topic models with document-level covariates. The package also includes tools
19914 for model selection, visualization, and estimation of topic-covariate
19915 regressions.")
19916 (license license:expat)))
19917
19918 (define-public r-polycor
19919 (package
19920 (name "r-polycor")
19921 (version "0.7-10")
19922 (source
19923 (origin
19924 (method url-fetch)
19925 (uri (cran-uri "polycor" version))
19926 (sha256
19927 (base32
19928 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
19929 (properties `((upstream-name . "polycor")))
19930 (build-system r-build-system)
19931 (propagated-inputs
19932 `(("r-matrix" ,r-matrix)
19933 ("r-mvtnorm" ,r-mvtnorm)))
19934 (home-page "https://r-forge.r-project.org/projects/polycor/")
19935 (synopsis "Polychoric and polyserial correlations")
19936 (description
19937 "This package provides tools to compute polychoric and polyserial
19938 correlations by quick \"two-step\" methods or ML, optionally with standard
19939 errors; tetrachoric and biserial correlations are special cases.")
19940 (license license:gpl2+)))
19941
19942 (define-public r-msm
19943 (package
19944 (name "r-msm")
19945 (version "1.6.8")
19946 (source
19947 (origin
19948 (method url-fetch)
19949 (uri (cran-uri "msm" version))
19950 (sha256
19951 (base32
19952 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
19953 (properties `((upstream-name . "msm")))
19954 (build-system r-build-system)
19955 (propagated-inputs
19956 `(("r-expm" ,r-expm)
19957 ("r-mvtnorm" ,r-mvtnorm)
19958 ("r-survival" ,r-survival)))
19959 (home-page "https://github.com/chjackson/msm")
19960 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
19961 (description
19962 "This package provides functions for fitting continuous-time Markov and
19963 hidden Markov multi-state models to longitudinal data. It was designed for
19964 processes observed at arbitrary times in continuous time (panel data) but some
19965 other observation schemes are supported. Both Markov transition rates and the
19966 hidden Markov output process can be modelled in terms of covariates, which may
19967 be constant or piecewise-constant in time.")
19968 (license license:gpl2+)))
19969
19970 (define-public r-ltm
19971 (package
19972 (name "r-ltm")
19973 (version "1.1-1")
19974 (source
19975 (origin
19976 (method url-fetch)
19977 (uri (cran-uri "ltm" version))
19978 (sha256
19979 (base32
19980 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
19981 (properties `((upstream-name . "ltm")))
19982 (build-system r-build-system)
19983 (propagated-inputs
19984 `(("r-mass" ,r-mass)
19985 ("r-msm" ,r-msm)
19986 ("r-polycor" ,r-polycor)))
19987 (home-page "https://github.com/drizopoulos/ltm")
19988 (synopsis "Latent trait models under IRT")
19989 (description
19990 "This is a package supporting the analysis of multivariate dichotomous
19991 and polytomous data using latent trait models under the Item Response Theory
19992 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
19993 Three-Parameter, the Graded Response, and the Generalized Partial Credit
19994 Models.")
19995 (license license:gpl2+)))
19996
19997 (define-public r-mi
19998 (package
19999 (name "r-mi")
20000 (version "1.0")
20001 (source
20002 (origin
20003 (method url-fetch)
20004 (uri (cran-uri "mi" version))
20005 (sha256
20006 (base32
20007 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
20008 (properties `((upstream-name . "mi")))
20009 (build-system r-build-system)
20010 (propagated-inputs
20011 `(("r-arm" ,r-arm)
20012 ("r-matrix" ,r-matrix)))
20013 (home-page "http://www.stat.columbia.edu/~gelman/")
20014 (synopsis "Missing data imputation and model checking")
20015 (description
20016 "This package provides functions for data manipulation, imputing missing
20017 values in an approximate Bayesian framework, diagnostics of the models used to
20018 generate the imputations, confidence-building mechanisms to validate some of
20019 the assumptions of the imputation algorithm, and functions to analyze multiply
20020 imputed data sets with the appropriate degree of sampling uncertainty.")
20021 (license license:gpl2+)))
20022
20023 (define-public r-matrixcalc
20024 (package
20025 (name "r-matrixcalc")
20026 (version "1.0-3")
20027 (source
20028 (origin
20029 (method url-fetch)
20030 (uri (cran-uri "matrixcalc" version))
20031 (sha256
20032 (base32
20033 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
20034 (properties `((upstream-name . "matrixcalc")))
20035 (build-system r-build-system)
20036 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
20037 (synopsis "Collection of functions for matrix calculations")
20038 (description
20039 "This package provides a collection of functions to support matrix
20040 calculations for probability, econometric and numerical analysis. There are
20041 additional functions that are comparable to APL functions which are useful for
20042 actuarial models such as pension mathematics.")
20043 (license license:gpl2+)))
20044
20045 (define-public r-sem
20046 (package
20047 (name "r-sem")
20048 (version "3.1-9")
20049 (source
20050 (origin
20051 (method url-fetch)
20052 (uri (cran-uri "sem" version))
20053 (sha256
20054 (base32
20055 "1f9c6g6pfx66gd2pappcsqh484ah6a0x4z47hpd46rah0817hcsa"))))
20056 (properties `((upstream-name . "sem")))
20057 (build-system r-build-system)
20058 (propagated-inputs
20059 `(("r-boot" ,r-boot)
20060 ("r-mass" ,r-mass)
20061 ("r-matrixcalc" ,r-matrixcalc)
20062 ("r-mi" ,r-mi)))
20063 (home-page "https://cran.r-project.org/package=sem")
20064 (synopsis "Structural equation models")
20065 (description
20066 "This package provides functions for fitting general linear structural
20067 equation models (with observed and latent variables) using the RAM approach,
20068 and for fitting structural equations in observed-variable models by two-stage
20069 least squares.")
20070 (license license:gpl2+)))
20071
20072 (define-public r-semtools
20073 (package
20074 (name "r-semtools")
20075 (version "0.5-2")
20076 (source
20077 (origin
20078 (method url-fetch)
20079 (uri (cran-uri "semTools" version))
20080 (sha256
20081 (base32
20082 "1zj841pszfsikzp82cmh463qyc4xhdrqjqcnhc2r8mcflv12irv6"))))
20083 (properties `((upstream-name . "semTools")))
20084 (build-system r-build-system)
20085 (propagated-inputs
20086 `(("r-lavaan" ,r-lavaan)))
20087 (home-page "https://github.com/simsem/semTools/wiki")
20088 (synopsis "Useful tools for structural equation modeling")
20089 (description
20090 "This package provides useful tools for structural equation modeling.")
20091 (license license:gpl2+)))
20092
20093 (define-public r-regsem
20094 (package
20095 (name "r-regsem")
20096 (version "1.5.2")
20097 (source
20098 (origin
20099 (method url-fetch)
20100 (uri (cran-uri "regsem" version))
20101 (sha256
20102 (base32
20103 "0ch057010xfsw0nqcsarzakdbiplvxaldyqlbbacspqs65ax1yk7"))))
20104 (properties `((upstream-name . "regsem")))
20105 (build-system r-build-system)
20106 (propagated-inputs
20107 `(("r-lavaan" ,r-lavaan)
20108 ("r-rcpp" ,r-rcpp)
20109 ("r-rcpparmadillo" ,r-rcpparmadillo)
20110 ("r-rsolnp" ,r-rsolnp)))
20111 (home-page "https://cran.r-project.org/package=regsem")
20112 (synopsis "Regularized structural equation modeling")
20113 (description
20114 "This package uses both ridge and lasso penalties (and extensions) to
20115 penalize specific parameters in structural equation models. The package
20116 offers additional cost functions, cross validation, and other extensions
20117 beyond traditional structural equation models. It also contains a function to
20118 perform @dfn{exploratory mediation} (XMed).")
20119 (license license:gpl2+)))
20120
20121 (define-public r-stanheaders
20122 (package
20123 (name "r-stanheaders")
20124 (version "2.19.2")
20125 (source
20126 (origin
20127 (method url-fetch)
20128 (uri (cran-uri "StanHeaders" version))
20129 (sha256
20130 (base32
20131 "0cmk0fzczx7dcywcw1dhm6gfq84qlsx77qrsk4z3bf3dhr4bznam"))))
20132 (properties `((upstream-name . "StanHeaders")))
20133 (build-system r-build-system)
20134 (inputs `(("pandoc" ,ghc-pandoc)))
20135 (native-inputs
20136 `(("gfortran" ,gfortran)
20137 ("r-knitr" ,r-knitr))) ; for vignettes
20138 (home-page "https://mc-stan.org/")
20139 (synopsis "C++ header files for Stan")
20140 (description
20141 "The C++ header files of the Stan project are provided by this package.
20142 There is a shared object containing part of the @code{CVODES} library, but it
20143 is not accessible from R. @code{r-stanheaders} is only useful for developers
20144 who want to utilize the @code{LinkingTo} directive of their package's
20145 DESCRIPTION file to build on the Stan library without incurring unnecessary
20146 dependencies.
20147
20148 The Stan project develops a probabilistic programming language that implements
20149 full or approximate Bayesian statistical inference via Markov Chain Monte
20150 Carlo or variational methods and implements (optionally penalized) maximum
20151 likelihood estimation via optimization. The Stan library includes an advanced
20152 automatic differentiation scheme, templated statistical and linear algebra
20153 functions that can handle the automatically differentiable scalar types (and
20154 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
20155 package provides user-facing R functions to parse, compile, test, estimate,
20156 and analyze Stan models.")
20157 (license license:bsd-3)))
20158
20159 (define-public r-rpf
20160 (package
20161 (name "r-rpf")
20162 (version "1.0.3")
20163 (source
20164 (origin
20165 (method url-fetch)
20166 (uri (cran-uri "rpf" version))
20167 (sha256
20168 (base32
20169 "1i2kqd7nx55nn35qnw89xmnqk23x9c8xhkh736c2xg7k2ai84ybl"))))
20170 (properties `((upstream-name . "rpf")))
20171 (build-system r-build-system)
20172 (propagated-inputs
20173 `(("r-lifecycle" ,r-lifecycle)
20174 ("r-mvtnorm" ,r-mvtnorm)
20175 ("r-rcpp" ,r-rcpp)
20176 ("r-rcppeigen" ,r-rcppeigen)))
20177 (home-page "https://github.com/jpritikin/rpf")
20178 (synopsis "Response probability functions")
20179 (description
20180 "The purpose of this package is to factor out logic and math common to
20181 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
20182 core support code suitable for more specialized IRT packages to build upon.
20183 Complete access to optimized C functions is made available with
20184 @code{R_RegisterCCallable()}.")
20185 (license license:gpl3+)))
20186
20187 (define-public r-openmx
20188 (package
20189 (name "r-openmx")
20190 (version "2.17.3")
20191 (source
20192 (origin
20193 (method url-fetch)
20194 (uri (cran-uri "OpenMx" version))
20195 (sha256
20196 (base32
20197 "1s2pcg281ag3qz2wz8yi826f2d3kj3qg916js7zz0nsrljcyv5bc"))))
20198 (properties `((upstream-name . "OpenMx")))
20199 (build-system r-build-system)
20200 (propagated-inputs
20201 `(("r-bh" ,r-bh)
20202 ("r-digest" ,r-digest)
20203 ("r-mass" ,r-mass)
20204 ("r-matrix" ,r-matrix)
20205 ("r-rcpp" ,r-rcpp)
20206 ("r-rcppeigen" ,r-rcppeigen)
20207 ("r-rpf" ,r-rpf)
20208 ("r-stanheaders" ,r-stanheaders)))
20209 (native-inputs `(("gfortran" ,gfortran)))
20210 (home-page "http://openmx.ssri.psu.edu")
20211 (synopsis "Extended structural equation modelling")
20212 (description
20213 "This package allows for the estimation of a wide variety of advanced
20214 multivariate statistical models. It consists of a library of functions and
20215 optimizers that allow you to quickly and flexibly define an SEM model and
20216 estimate parameters given observed data.")
20217 (license license:asl2.0)))
20218
20219 (define-public r-kutils
20220 (package
20221 (name "r-kutils")
20222 (version "1.70")
20223 (source
20224 (origin
20225 (method url-fetch)
20226 (uri (cran-uri "kutils" version))
20227 (sha256
20228 (base32
20229 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
20230 (properties `((upstream-name . "kutils")))
20231 (build-system r-build-system)
20232 (propagated-inputs
20233 `(("r-foreign" ,r-foreign)
20234 ("r-openxlsx" ,r-openxlsx)
20235 ("r-plyr" ,r-plyr)
20236 ("r-runit" ,r-runit)
20237 ("r-xtable" ,r-xtable)))
20238 (home-page "https://cran.r-project.org/package=kutils")
20239 (synopsis "Project management tools")
20240 (description
20241 "This package provides tools for data importation, recoding, and
20242 inspection. There are functions to create new project folders, R code
20243 templates, create uniquely named output directories, and to quickly obtain a
20244 visual summary for each variable in a data frame. The main feature here is
20245 the systematic implementation of the \"variable key\" framework for data
20246 importation and recoding.")
20247 (license license:gpl2)))
20248
20249 (define-public r-rockchalk
20250 (package
20251 (name "r-rockchalk")
20252 (version "1.8.144")
20253 (source
20254 (origin
20255 (method url-fetch)
20256 (uri (cran-uri "rockchalk" version))
20257 (sha256
20258 (base32
20259 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
20260 (properties `((upstream-name . "rockchalk")))
20261 (build-system r-build-system)
20262 (propagated-inputs
20263 `(("r-cardata" ,r-cardata)
20264 ("r-kutils" ,r-kutils)
20265 ("r-lme4" ,r-lme4)
20266 ("r-mass" ,r-mass)))
20267 (home-page "https://cran.r-project.org/package=rockchalk")
20268 (synopsis "Regression estimation and presentation")
20269 (description
20270 "This package provides a collection of functions for interpretation and
20271 presentation of regression analysis. These functions are used to produce the
20272 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
20273 includes regression diagnostics, regression tables, and plots of interactions
20274 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
20275 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
20276 fairly comprehensive overview.")
20277 (license license:gpl3+)))
20278
20279 (define-public r-lisreltor
20280 (package
20281 (name "r-lisreltor")
20282 (version "0.1.4")
20283 (source
20284 (origin
20285 (method url-fetch)
20286 (uri (cran-uri "lisrelToR" version))
20287 (sha256
20288 (base32
20289 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
20290 (properties `((upstream-name . "lisrelToR")))
20291 (build-system r-build-system)
20292 (home-page "https://cran.r-project.org/package=lisrelToR")
20293 (synopsis "Import output from LISREL into R")
20294 (description
20295 "This is an unofficial package aimed at automating the import of LISREL
20296 output in R.")
20297 (license license:gpl2)))
20298
20299 (define-public r-bdgraph
20300 (package
20301 (name "r-bdgraph")
20302 (version "2.62")
20303 (source
20304 (origin
20305 (method url-fetch)
20306 (uri (cran-uri "BDgraph" version))
20307 (sha256
20308 (base32
20309 "1b1vfar940swvn3pcil848qsp8ji50fjjll8jjzp6y2adx0f8pby"))))
20310 (properties `((upstream-name . "BDgraph")))
20311 (build-system r-build-system)
20312 (propagated-inputs
20313 `(("r-igraph" ,r-igraph)))
20314 (home-page "https://www.uva.nl/profile/a.mohammadi")
20315 (synopsis "Bayesian structure learning in graphical models")
20316 (description
20317 "This package provides statistical tools for Bayesian structure learning
20318 in undirected graphical models for continuous, discrete, and mixed data. It
20319 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
20320 on a continuous-time birth-death process.")
20321 (license license:gpl2+)))
20322
20323 (define-public r-d3network
20324 (package
20325 (name "r-d3network")
20326 (version "0.5.2.1")
20327 (source
20328 (origin
20329 (method url-fetch)
20330 (uri (cran-uri "d3Network" version))
20331 (sha256
20332 (base32
20333 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
20334 (properties `((upstream-name . "d3Network")))
20335 (build-system r-build-system)
20336 (propagated-inputs
20337 `(("r-plyr" ,r-plyr)
20338 ("r-rjson" ,r-rjson)
20339 ("r-whisker" ,r-whisker)))
20340 (home-page "http://christophergandrud.github.io/d3Network/")
20341 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
20342 (description
20343 "This package is intended to make it easy to create D3 JavaScript
20344 network, tree, dendrogram, and Sankey graphs from R using data frames.")
20345 (license license:gpl3+)))
20346
20347 (define-public r-qgraph
20348 (package
20349 (name "r-qgraph")
20350 (version "1.6.5")
20351 (source
20352 (origin
20353 (method url-fetch)
20354 (uri (cran-uri "qgraph" version))
20355 (sha256
20356 (base32
20357 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
20358 (properties `((upstream-name . "qgraph")))
20359 (build-system r-build-system)
20360 (propagated-inputs
20361 `(("r-abind" ,r-abind)
20362 ("r-bdgraph" ,r-bdgraph)
20363 ("r-colorspace" ,r-colorspace)
20364 ("r-corpcor" ,r-corpcor)
20365 ("r-d3network" ,r-d3network)
20366 ("r-dplyr" ,r-dplyr)
20367 ("r-fdrtool" ,r-fdrtool)
20368 ("r-ggplot2" ,r-ggplot2)
20369 ("r-ggraph" ,r-ggraph)
20370 ("r-glasso" ,r-glasso)
20371 ("r-gtools" ,r-gtools)
20372 ("r-hmisc" ,r-hmisc)
20373 ("r-huge" ,r-huge)
20374 ("r-igraph" ,r-igraph)
20375 ("r-jpeg" ,r-jpeg)
20376 ("r-lavaan" ,r-lavaan)
20377 ("r-matrix" ,r-matrix)
20378 ("r-pbapply" ,r-pbapply)
20379 ("r-plyr" ,r-plyr)
20380 ("r-png" ,r-png)
20381 ("r-psych" ,r-psych)
20382 ("r-rcpp" ,r-rcpp)
20383 ("r-reshape2" ,r-reshape2)
20384 ("r-tidygraph" ,r-tidygraph)))
20385 (home-page "http://sachaepskamp.com/qgraph/")
20386 (synopsis "Weighted network visualization and analysis")
20387 (description
20388 "This package implements tools for weighted network visualization and
20389 analysis, as well as Gaussian graphical model computation. It contains graph
20390 plotting methods, and tools for psychometric data visualization and graphical
20391 model estimation. See Epskamp et al. (2012)
20392 @url{doi:10.18637/jss.v048.i04}.")
20393 (license license:gpl2)))
20394
20395 (define-public r-semplot
20396 (package
20397 (name "r-semplot")
20398 (version "1.1.2")
20399 (source
20400 (origin
20401 (method url-fetch)
20402 (uri (cran-uri "semPlot" version))
20403 (sha256
20404 (base32
20405 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
20406 (properties `((upstream-name . "semPlot")))
20407 (build-system r-build-system)
20408 (propagated-inputs
20409 `(("r-colorspace" ,r-colorspace)
20410 ("r-corpcor" ,r-corpcor)
20411 ("r-igraph" ,r-igraph)
20412 ("r-lavaan" ,r-lavaan)
20413 ("r-lisreltor" ,r-lisreltor)
20414 ("r-openmx" ,r-openmx)
20415 ("r-plyr" ,r-plyr)
20416 ("r-qgraph" ,r-qgraph)
20417 ("r-regsem" ,r-regsem)
20418 ("r-rockchalk" ,r-rockchalk)
20419 ("r-sem" ,r-sem)
20420 ("r-xml" ,r-xml)))
20421 (home-page "https://github.com/SachaEpskamp/semPlot")
20422 (synopsis "Unified visualizations of structural equation models")
20423 (description
20424 "Structural equation modeling (SEM) has a long history of representing
20425 models graphically as path diagrams. The semPlot package for R fills the gap
20426 between advanced, but time-consuming, graphical software and the limited
20427 graphics produced automatically by SEM software. In addition, semPlot offers
20428 more functionality than drawing path diagrams: it can act as a common ground
20429 for importing SEM results into R. Any result usable as input to semPlot can
20430 also be represented in any of the three popular SEM frame-works, as well as
20431 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
20432 (license license:gpl2)))
20433
20434 (define-public r-cdm
20435 (package
20436 (name "r-cdm")
20437 (version "7.5-15")
20438 (source
20439 (origin
20440 (method url-fetch)
20441 (uri (cran-uri "CDM" version))
20442 (sha256
20443 (base32
20444 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
20445 (properties `((upstream-name . "CDM")))
20446 (build-system r-build-system)
20447 (propagated-inputs
20448 `(("r-mvtnorm" ,r-mvtnorm)
20449 ("r-polycor" ,r-polycor)
20450 ("r-rcpp" ,r-rcpp)
20451 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20452 (home-page
20453 "https://github.com/alexanderrobitzsch/CDM")
20454 (synopsis "Cognitive diagnosis modeling")
20455 (description
20456 "This package provides functions for cognitive diagnosis modeling and
20457 multidimensional item response modeling for dichotomous and polytomous item
20458 responses. It enables the estimation of the DINA and DINO model, the multiple
20459 group (polytomous) GDINA model, the multiple choice DINA model, the general
20460 diagnostic model (GDM), the structured latent class model (SLCA), and
20461 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
20462 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
20463 estimation and the package structure. For tutorials on how to use the CDM
20464 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
20465 well as Ravand and Robitzsch (2015).")
20466 (license license:gpl2+)))
20467
20468 (define-public r-tam
20469 (package
20470 (name "r-tam")
20471 (version "3.4-26")
20472 (source
20473 (origin
20474 (method url-fetch)
20475 (uri (cran-uri "TAM" version))
20476 (sha256
20477 (base32
20478 "111d7qkxhwh1lfvldyh9d61pdb5vb6x8lr8n9h95ssvw07vjqvk9"))))
20479 (properties `((upstream-name . "TAM")))
20480 (build-system r-build-system)
20481 (propagated-inputs
20482 `(("r-cdm" ,r-cdm)
20483 ("r-rcpp" ,r-rcpp)
20484 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20485 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
20486 (synopsis "Test analysis modules")
20487 (description
20488 "This package includes tools for marginal maximum likelihood estimation
20489 and joint maximum likelihood estimation for unidimensional and
20490 multidimensional item response models. The package functionality covers the
20491 Rasch model, 2PL model, 3PL model, generalized partial credit model,
20492 multi-faceted Rasch model, nominal item response model, structured latent
20493 class model, mixture distribution IRT models, and located latent class models.
20494 Latent regression models and plausible value imputation are also supported.")
20495 (license license:gpl2+)))
20496
20497 (define-public r-erm
20498 (package
20499 (name "r-erm")
20500 (version "1.0-1")
20501 (source
20502 (origin
20503 (method url-fetch)
20504 (uri (cran-uri "eRm" version))
20505 (sha256
20506 (base32
20507 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
20508 (properties `((upstream-name . "eRm")))
20509 (build-system r-build-system)
20510 (propagated-inputs
20511 `(("r-colorspace" ,r-colorspace)
20512 ("r-lattice" ,r-lattice)
20513 ("r-mass" ,r-mass)
20514 ("r-matrix" ,r-matrix)
20515 ("r-psych" ,r-psych)))
20516 (native-inputs `(("gfortran" ,gfortran)))
20517 (home-page "https://cran.r-project.org/package=eRm")
20518 (synopsis "Extended Rasch modeling")
20519 (description
20520 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
20521 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
20522 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
20523 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
20524 data matrix. Additional features are the ML estimation of the person
20525 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
20526 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
20527 infit and outfit measures, ICC and other plots, automated stepwise item
20528 elimination, and a simulation module for various binary data matrices.")
20529 (license license:gpl3)))
20530
20531 (define-public r-irtoys
20532 (package
20533 (name "r-irtoys")
20534 (version "0.2.1")
20535 (source
20536 (origin
20537 (method url-fetch)
20538 (uri (cran-uri "irtoys" version))
20539 (sha256
20540 (base32
20541 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
20542 (properties `((upstream-name . "irtoys")))
20543 (build-system r-build-system)
20544 (propagated-inputs
20545 `(("r-ltm" ,r-ltm)
20546 ("r-sm" ,r-sm)))
20547 (home-page "https://cran.r-project.org/package=irtoys")
20548 (synopsis "Collection of functions related to Item Response Theory (IRT)")
20549 (description
20550 "This package provides a collection of functions useful in learning and
20551 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
20552 programs. It provides basic CTT analysis, a simple common interface to the
20553 estimation of item parameters in IRT models for binary responses with three
20554 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
20555 EAP, WLE, plausible values), item and person fit statistics, scaling
20556 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
20557 array of parametric and non-parametric (kernel) plots. It estimates and plots
20558 Haberman's interaction model when all items are dichotomously scored.")
20559 (license license:gpl2+)))
20560
20561 (define-public r-iheatmapr
20562 (package
20563 (name "r-iheatmapr")
20564 (version "0.4.12")
20565 (source
20566 (origin
20567 (method url-fetch)
20568 (uri (cran-uri "iheatmapr" version))
20569 (sha256
20570 (base32
20571 "0s479j9l35xiss599vablxgvg6i2j9zq9sxphsq4vdk3bafg84bw"))))
20572 (properties `((upstream-name . "iheatmapr")))
20573 (build-system r-build-system)
20574 (propagated-inputs
20575 `(("r-fastcluster" ,r-fastcluster)
20576 ("r-ggdendro" ,r-ggdendro)
20577 ("r-htmlwidgets" ,r-htmlwidgets)
20578 ("r-jsonlite" ,r-jsonlite)
20579 ("r-knitr" ,r-knitr)
20580 ("r-magrittr" ,r-magrittr)
20581 ("r-plyr" ,r-plyr)
20582 ("r-rcolorbrewer" ,r-rcolorbrewer)
20583 ("r-s4vectors" ,r-s4vectors)
20584 ("r-scales" ,r-scales)))
20585 (home-page "https://docs.ropensci.org/iheatmapr")
20586 (synopsis "Interactive, Complex Heatmaps")
20587 (description
20588 "iheatmapr is an R package for building complex, interactive heatmaps
20589 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
20590 subplots along the rows or columns of the main heatmap add more information
20591 about each row or column. For example, a one column additional heatmap may
20592 indicate what group a particular row or column belongs to. Complex heatmaps
20593 may also include multiple side by side heatmaps which show different types of
20594 data for the same conditions. Interactivity can improve complex heatmaps by
20595 providing tooltips with information about each cell and enabling zooming into
20596 interesting features. iheatmapr uses the plotly library for interactivity.")
20597 (license license:expat)))
20598
20599 (define-public r-packrat
20600 (package
20601 (name "r-packrat")
20602 (version "0.5.0")
20603 (source
20604 (origin
20605 (method url-fetch)
20606 (uri (cran-uri "packrat" version))
20607 (sha256
20608 (base32
20609 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
20610 (properties `((upstream-name . "packrat")))
20611 (build-system r-build-system)
20612 (home-page "https://github.com/rstudio/packrat/")
20613 (synopsis "Dependency management R projects")
20614 (description
20615 "This package provides a dependency manager for R projects that allows
20616 you to manage the R packages your project depends on in an isolated, portable,
20617 and reproducible way.")
20618 (license license:gpl2)))
20619
20620 (define-public r-rsconnect
20621 (package
20622 (name "r-rsconnect")
20623 (version "0.8.16")
20624 (source
20625 (origin
20626 (method url-fetch)
20627 (uri (cran-uri "rsconnect" version))
20628 (sha256
20629 (base32
20630 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
20631 (properties `((upstream-name . "rsconnect")))
20632 (build-system r-build-system)
20633 (propagated-inputs
20634 `(("r-curl" ,r-curl)
20635 ("r-digest" ,r-digest)
20636 ("r-jsonlite" ,r-jsonlite)
20637 ("r-openssl" ,r-openssl)
20638 ("r-packrat" ,r-packrat)
20639 ("r-rstudioapi" ,r-rstudioapi)
20640 ("r-yaml" ,r-yaml)))
20641 (home-page "https://github.com/rstudio/rsconnect")
20642 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
20643 (description
20644 "This package provides a programmatic deployment interface for RPubs,
20645 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
20646 documents, Shiny applications, Plumber APIs, plots, and static web content.")
20647 (license license:gpl2)))
20648
20649 ;; This package includes minified JavaScript files. When upgrading please
20650 ;; check that there are no new minified JavaScript files.
20651 (define-public r-dygraphs
20652 (package
20653 (name "r-dygraphs")
20654 (version "1.1.1.6")
20655 (source
20656 (origin
20657 (method url-fetch)
20658 (uri (cran-uri "dygraphs" version))
20659 (sha256
20660 (base32
20661 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
20662 (properties `((upstream-name . "dygraphs")))
20663 (build-system r-build-system)
20664 (arguments
20665 `(#:modules ((guix build utils)
20666 (guix build r-build-system)
20667 (srfi srfi-1)
20668 (ice-9 popen))
20669 #:phases
20670 (modify-phases %standard-phases
20671 (add-after 'unpack 'process-javascript
20672 (lambda* (#:key inputs #:allow-other-keys)
20673 (with-directory-excursion "inst/htmlwidgets/lib/"
20674 (call-with-values
20675 (lambda ()
20676 (unzip2
20677 `(("dygraphs/dygraph-combined-dev.js"
20678 "dygraph-combined.js")
20679 (,(assoc-ref inputs "js-jquery")
20680 "jquery/jquery.min.js")
20681 (,(assoc-ref inputs "js-fquarter")
20682 "fquarter/moment-fquarter.min.js"))))
20683 (lambda (sources targets)
20684 (for-each (lambda (source target)
20685 (format #t "Processing ~a --> ~a~%"
20686 source target)
20687 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
20688 (call-with-output-file target
20689 (lambda (port)
20690 (dump-port minified port)))))
20691 sources targets))))
20692 #t)))))
20693 (native-inputs
20694 `(("uglify-js" ,uglify-js)
20695 ;; They actually use version 1.11.1, but this more recent version
20696 ;; should be just fine.
20697 ("js-jquery"
20698 ,(origin
20699 (method url-fetch)
20700 (uri "https://code.jquery.com/jquery-1.12.4.js")
20701 (sha256
20702 (base32
20703 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
20704 ("js-fquarter"
20705 ,(origin
20706 (method url-fetch)
20707 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
20708 "moment-fquarter/1.0.1/moment-fquarter.js"))
20709 (sha256
20710 (base32
20711 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
20712 (propagated-inputs
20713 `(("r-htmltools" ,r-htmltools)
20714 ("r-htmlwidgets" ,r-htmlwidgets)
20715 ("r-magrittr" ,r-magrittr)
20716 ("r-xts" ,r-xts)
20717 ("r-zoo" ,r-zoo)))
20718 (home-page "https://github.com/rstudio/dygraphs")
20719 (synopsis "Interface to Dygraphs interactive time series charting library")
20720 (description
20721 "This package provides an R interface to the dygraphs JavaScript charting
20722 library (a copy of which is included in the package). It provides rich
20723 facilities for charting time-series data in R, including highly configurable
20724 series- and axis-display and interactive features like zoom/pan and
20725 series/point highlighting.")
20726 (license license:expat)))
20727
20728 (define-public r-shinystan
20729 (package
20730 (name "r-shinystan")
20731 (version "2.5.0")
20732 (source
20733 (origin
20734 (method url-fetch)
20735 (uri (cran-uri "shinystan" version))
20736 (sha256
20737 (base32
20738 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
20739 (properties `((upstream-name . "shinystan")))
20740 (build-system r-build-system)
20741 (propagated-inputs
20742 `(("r-bayesplot" ,r-bayesplot)
20743 ("r-colourpicker" ,r-colourpicker)
20744 ("r-dt" ,r-dt)
20745 ("r-dygraphs" ,r-dygraphs)
20746 ("r-ggplot2" ,r-ggplot2)
20747 ("r-gridextra" ,r-gridextra)
20748 ("r-gtools" ,r-gtools)
20749 ("r-markdown" ,r-markdown)
20750 ("r-reshape2" ,r-reshape2)
20751 ("r-rsconnect" ,r-rsconnect)
20752 ("r-rstan" ,r-rstan)
20753 ("r-shiny" ,r-shiny)
20754 ("r-shinyjs" ,r-shinyjs)
20755 ("r-shinythemes" ,r-shinythemes)
20756 ("r-threejs" ,r-threejs)
20757 ("r-xtable" ,r-xtable)
20758 ("r-xts" ,r-xts)))
20759 (home-page "https://mc-stan.org/")
20760 (synopsis "Interactive visual and numerical analysis for Bayesian models")
20761 (description
20762 "This package provides a graphical user interface for interactive
20763 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
20764 for analyzing a posterior sample. The interface is powered by the Shiny web
20765 application framework and works with the output of MCMC programs written in
20766 any programming language (and has extended functionality for Stan models fit
20767 using the @code{rstan} and @code{rstanarm} packages).")
20768 (license license:gpl3+)))
20769
20770 (define-public r-rstantools
20771 (package
20772 (name "r-rstantools")
20773 (version "2.0.0")
20774 (source
20775 (origin
20776 (method url-fetch)
20777 (uri (cran-uri "rstantools" version))
20778 (sha256
20779 (base32
20780 "1il0pn4ksbdkska5fmhvgaicvwnnc6cs08g6ags9fj1xkjiqmrsa"))))
20781 (properties `((upstream-name . "rstantools")))
20782 (build-system r-build-system)
20783 (inputs `(("pandoc" ,ghc-pandoc)))
20784 (propagated-inputs
20785 `(("r-desc" ,r-desc)
20786 ("r-rcpp" ,r-rcpp)))
20787 (home-page "https://mc-stan.org/rstantools/")
20788 (synopsis "Tools for developing R packages interfacing with Stan")
20789 (description
20790 "This package provides various tools for developers of R packages
20791 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
20792 up the required package structure, S3 generics and default methods to unify
20793 function naming across Stan-based R packages, and vignettes with
20794 recommendations for developers.")
20795 (license license:gpl3+)))
20796
20797 (define-public r-loo
20798 (package
20799 (name "r-loo")
20800 (version "2.2.0")
20801 (source
20802 (origin
20803 (method url-fetch)
20804 (uri (cran-uri "loo" version))
20805 (sha256
20806 (base32
20807 "1hq1zcj76x55z9kic6cwf7mfq9pzqfbr341jbc9wp7x8ac4zcva6"))))
20808 (properties `((upstream-name . "loo")))
20809 (build-system r-build-system)
20810 (inputs
20811 `(("pandoc" ,ghc-pandoc)
20812 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
20813 (propagated-inputs
20814 `(("r-checkmate" ,r-checkmate)
20815 ("r-matrixstats" ,r-matrixstats)))
20816 (home-page "https://mc-stan.org/loo/")
20817 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
20818 (description
20819 "This package provides an implementation of efficient approximate
20820 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
20821 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
20822 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
20823 procedure for regularizing importance weights. As a byproduct of the
20824 calculations, we also obtain approximate standard errors for estimated
20825 predictive errors and for the comparison of predictive errors between models.
20826 The package also provides methods for using stacking and other model weighting
20827 techniques to average Bayesian predictive distributions.")
20828 (license license:gpl3+)))
20829
20830 (define-public r-rstan
20831 (package
20832 (name "r-rstan")
20833 (version "2.19.3")
20834 (source
20835 (origin
20836 (method url-fetch)
20837 (uri (cran-uri "rstan" version))
20838 (sha256
20839 (base32
20840 "128ndwjrhf8b1qvvqz4bl13qlm8718z9qs5ryc6gsdr3vk65s0np"))))
20841 (properties `((upstream-name . "rstan")))
20842 (build-system r-build-system)
20843 (arguments
20844 `(#:phases
20845 (modify-phases %standard-phases
20846 (add-before 'install 'set-timezone
20847 ;; This package is picky about timezones.
20848 (lambda* (#:key inputs #:allow-other-keys)
20849 (setenv "TZ" "UTC+1")
20850 (setenv "TZDIR"
20851 (string-append (assoc-ref inputs "tzdata")
20852 "/share/zoneinfo"))
20853 #t)))))
20854 (native-inputs
20855 `(("tzdata" ,tzdata-for-tests)
20856 ("pandoc" ,ghc-pandoc)))
20857 (propagated-inputs
20858 `(("r-bh" ,r-bh)
20859 ("r-ggplot2" ,r-ggplot2)
20860 ("r-gridextra" ,r-gridextra)
20861 ("r-inline" ,r-inline)
20862 ("r-loo" ,r-loo)
20863 ("r-pkgbuild" ,r-pkgbuild)
20864 ("r-rcpp" ,r-rcpp)
20865 ("r-rcppeigen" ,r-rcppeigen)
20866 ("r-stanheaders" ,r-stanheaders)))
20867 (home-page "https://discourse.mc-stan.org/")
20868 (synopsis "R interface to Stan")
20869 (description
20870 "User-facing R functions are provided to parse, compile, test, estimate,
20871 and analyze Stan models by accessing the header-only Stan library provided by
20872 the StanHeaders package. The Stan project develops a probabilistic
20873 programming language that implements full Bayesian statistical inference via
20874 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
20875 approximation, and (optionally penalized) maximum likelihood estimation via
20876 optimization. In all three cases, automatic differentiation is used to
20877 quickly and accurately evaluate gradients without burdening the user with the
20878 need to derive the partial derivatives.")
20879 (license license:gpl3+)))
20880
20881 (define-public r-rstanarm
20882 (package
20883 (name "r-rstanarm")
20884 (version "2.19.3")
20885 (source
20886 (origin
20887 (method url-fetch)
20888 (uri (cran-uri "rstanarm" version))
20889 (sha256
20890 (base32
20891 "0gxjq8bdlvdd8kn3dhp12xlymdab036r7n12lzmd3xlkl4cnxq3s"))))
20892 (properties `((upstream-name . "rstanarm")))
20893 (build-system r-build-system)
20894 (inputs
20895 `(("pandoc" ,ghc-pandoc)
20896 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
20897 (propagated-inputs
20898 `(("r-bayesplot" ,r-bayesplot)
20899 ("r-bh" ,r-bh)
20900 ("r-ggplot2" ,r-ggplot2)
20901 ("r-lme4" ,r-lme4)
20902 ("r-loo" ,r-loo)
20903 ("r-matrix" ,r-matrix)
20904 ("r-nlme" ,r-nlme)
20905 ("r-rcpp" ,r-rcpp)
20906 ("r-rcppeigen" ,r-rcppeigen)
20907 ("r-rcppparallel" ,r-rcppparallel)
20908 ("r-rstan" ,r-rstan)
20909 ("r-rstantools" ,r-rstantools)
20910 ("r-shinystan" ,r-shinystan)
20911 ("r-stanheaders" ,r-stanheaders)
20912 ("r-survival" ,r-survival)))
20913 (home-page "https://mc-stan.org/rstanarm/")
20914 (synopsis "Bayesian applied regression modeling via Stan")
20915 (description
20916 "This package estimates previously compiled regression models using the
20917 @code{rstan} package, which provides the R interface to the Stan C++ library
20918 for Bayesian estimation. Users specify models via the customary R syntax with
20919 a formula and @code{data.frame} plus some additional arguments for priors.")
20920 (license license:gpl3+)))
20921
20922 (define-public r-kendall
20923 (package
20924 (name "r-kendall")
20925 (version "2.2")
20926 (source
20927 (origin
20928 (method url-fetch)
20929 (uri (cran-uri "Kendall" version))
20930 (sha256
20931 (base32
20932 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
20933 (properties `((upstream-name . "Kendall")))
20934 (build-system r-build-system)
20935 (propagated-inputs
20936 `(("r-boot" ,r-boot)))
20937 (native-inputs
20938 `(("gfortran" ,gfortran)))
20939 (home-page "https://cran.r-project.org/web/packages/Kendall/")
20940 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
20941 (description
20942 "This package computes the Kendall rank correlation and Mann-Kendall
20943 trend test.")
20944 (license license:gpl2+)))
20945
20946 (define-public r-zyp
20947 (package
20948 (name "r-zyp")
20949 (version "0.10-1.1")
20950 (source
20951 (origin
20952 (method url-fetch)
20953 (uri (cran-uri "zyp" version))
20954 (sha256
20955 (base32
20956 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
20957 (properties `((upstream-name . "zyp")))
20958 (build-system r-build-system)
20959 (propagated-inputs
20960 `(("r-kendall" ,r-kendall)))
20961 (home-page "https://cran.r-project.org/web/packages/zyp/")
20962 (synopsis "Zhang + Yue-Pilon Trends Package")
20963 (description
20964 "This package contains an efficient implementation of Sen's slope
20965 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
20966 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
20967 climate data.")
20968 (license license:lgpl2.1)))
20969
20970 (define-public r-zvcv
20971 (package
20972 (name "r-zvcv")
20973 (version "1.0.0")
20974 (source
20975 (origin
20976 (method url-fetch)
20977 (uri (cran-uri "ZVCV" version))
20978 (sha256
20979 (base32
20980 "1npw836q2skx54843lgxvb0rfwafckjc8k8dljykm60ad3z7zak8"))))
20981 (properties `((upstream-name . "ZVCV")))
20982 (build-system r-build-system)
20983 (propagated-inputs
20984 `(("r-abind" ,r-abind)
20985 ("r-glmnet" ,r-glmnet)
20986 ("r-mvtnorm" ,r-mvtnorm)
20987 ("r-partitions" ,r-partitions)
20988 ("r-rcpp" ,r-rcpp)
20989 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20990 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
20991 (synopsis "Zero-Variance Control Variates")
20992 (description
20993 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
20994 to reduce the variance of Monte Carlo estimators of expectations using the
20995 derivatives of the log target. Once the derivatives are available, the only
20996 additional computational effort is in solving a linear regression problem.
20997 This method has been extended to higher dimensions using regularisation. This
20998 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
20999 samples, derivatives and function evaluations are available. Additional
21000 functions for applying ZV-CV to two estimators for the normalising constant of
21001 the posterior distribution in Bayesian statistics are also supplied.")
21002 (license license:gpl2+)))
21003
21004 (define-public r-ztype
21005 (package
21006 (name "r-ztype")
21007 (version "0.1.0")
21008 (source
21009 (origin
21010 (method url-fetch)
21011 (uri (cran-uri "ztype" version))
21012 (sha256
21013 (base32
21014 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
21015 (properties `((upstream-name . "ztype")))
21016 (build-system r-build-system)
21017 (propagated-inputs
21018 `(("r-assertthat" ,r-assertthat)
21019 ("r-dplyr" ,r-dplyr)
21020 ("r-ggplot2" ,r-ggplot2)
21021 ("r-lubridate" ,r-lubridate)
21022 ("r-magrittr" ,r-magrittr)
21023 ("r-rvest" ,r-rvest)
21024 ("r-stringr" ,r-stringr)))
21025 (home-page "https://cran.r-project.org/web/packages/ztype/")
21026 (synopsis "Run a Ztype game loaded with R functions")
21027 (description
21028 "How fast can you type R functions on your keyboard? Find out by running
21029 a @code{zty.pe} game: export R functions as instructions to type to destroy
21030 opponents' vessels.")
21031 (license license:gpl3)))
21032
21033 (define-public r-zseq
21034 (package
21035 (name "r-zseq")
21036 (version "0.2.0")
21037 (source
21038 (origin
21039 (method url-fetch)
21040 (uri (cran-uri "Zseq" version))
21041 (sha256
21042 (base32
21043 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
21044 (properties `((upstream-name . "Zseq")))
21045 (build-system r-build-system)
21046 (propagated-inputs
21047 `(("r-gmp" ,r-gmp)))
21048 (home-page "https://cran.r-project.org/web/packages/Zseq/")
21049 (synopsis "Integer sequence generator")
21050 (description
21051 "This package generates well-known integer sequences. The @code{gmp}
21052 package is adopted for computing with arbitrarily large numbers. Every
21053 function has a hyperlink to its corresponding item in the @dfn{On-Line
21054 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
21055 (license license:gpl3+)))
21056
21057 (define-public r-isoband
21058 (package
21059 (name "r-isoband")
21060 (version "0.2.1")
21061 (source
21062 (origin
21063 (method url-fetch)
21064 (uri (cran-uri "isoband" version))
21065 (sha256
21066 (base32
21067 "1ndlnv4g9pbd02y50sx4ffg2ccwqbi7fm2v1lh22wdd8pq33d20q"))))
21068 (properties `((upstream-name . "isoband")))
21069 (build-system r-build-system)
21070 (propagated-inputs
21071 `(("r-rcpp" ,r-rcpp)
21072 ("r-testthat" ,r-testthat)))
21073 (native-inputs
21074 `(("r-knitr" ,r-knitr)))
21075 (home-page "https://github.com/wilkelab/isoband")
21076 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
21077 (description
21078 "This package provides a fast C++ implementation to generate contour
21079 lines (isolines) and contour polygons (isobands) from regularly spaced grids
21080 containing elevation data.")
21081 (license license:expat)))
21082
21083 (define-public r-ppcor
21084 (package
21085 (name "r-ppcor")
21086 (version "1.1")
21087 (source
21088 (origin
21089 (method url-fetch)
21090 (uri (cran-uri "ppcor" version))
21091 (sha256
21092 (base32
21093 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
21094 (properties `((upstream-name . "ppcor")))
21095 (build-system r-build-system)
21096 (propagated-inputs
21097 `(("r-mass" ,r-mass)))
21098 (home-page "https://cran.r-project.org/web/packages/ppcor/")
21099 (synopsis "Partial and semi-partial correlation")
21100 (description
21101 "This package provides users not only with a function to readily
21102 calculate the higher-order partial and semi-partial correlations but also with
21103 statistics and p-values of the correlation coefficients.")
21104 (license license:gpl2)))
21105
21106 (define-public r-hrbrthemes
21107 (package
21108 (name "r-hrbrthemes")
21109 (version "0.8.0")
21110 (source
21111 (origin
21112 (method url-fetch)
21113 (uri (cran-uri "hrbrthemes" version))
21114 (sha256
21115 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
21116 (properties `((upstream-name . "hrbrthemes")))
21117 (build-system r-build-system)
21118 (propagated-inputs
21119 `(("r-extrafont" ,r-extrafont)
21120 ("r-gdtools" ,r-gdtools)
21121 ("r-ggplot2" ,r-ggplot2)
21122 ("r-htmltools" ,r-htmltools)
21123 ("r-knitr" ,r-knitr)
21124 ("r-magrittr" ,r-magrittr)
21125 ("r-rmarkdown" ,r-rmarkdown)
21126 ("r-scales" ,r-scales)))
21127 (native-inputs
21128 `(("r-knitr" ,r-knitr)))
21129 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
21130 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
21131 (description
21132 "This package provides a compilation of extra @code{ggplot2} themes,
21133 scales and utilities, including a spell check function for plot label fields
21134 and an overall emphasis on typography.")
21135 (license license:expat)))
21136
21137 (define-public r-crochet
21138 (package
21139 (name "r-crochet")
21140 (version "2.2.0")
21141 (source
21142 (origin
21143 (method url-fetch)
21144 (uri (cran-uri "crochet" version))
21145 (sha256
21146 (base32
21147 "1cbv79nyycxk6f8ldcsnn2pvgxqlnrj0qs19nhafnq2clxy863k6"))))
21148 (build-system r-build-system)
21149 (home-page "https://github.com/agrueneberg/crochet")
21150 (synopsis "Implementation Helper for Matrix-Like Types")
21151 (description
21152 "Functions to help implement the extraction / subsetting / indexing
21153 function @code{[} and replacement function @code{[<-} of custom matrix-like
21154 types (based on S3, S4, etc.), modeled as closely to the base matrix class
21155 as possible (with tests to prove it).")
21156 (license license:expat)))
21157
21158 (define-public r-boa
21159 (package
21160 (name "r-boa")
21161 (version "1.1.8-2")
21162 (source
21163 (origin
21164 (method url-fetch)
21165 (uri (cran-uri "boa" version))
21166 (sha256
21167 (base32
21168 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
21169 (properties `((upstream-name . "boa")))
21170 (build-system r-build-system)
21171 (home-page "http://www.jstatsoft.org/v21/i11")
21172 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
21173 (description
21174 "This package provides a menu-driven program and library of functions for
21175 carrying out convergence diagnostics and statistical and graphical analysis of
21176 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
21177 (license license:gpl2+)))
21178
21179 (define-public r-httpcode
21180 (package
21181 (name "r-httpcode")
21182 (version "0.3.0")
21183 (source (origin
21184 (method url-fetch)
21185 (uri (cran-uri "httpcode" version))
21186 (sha256
21187 (base32
21188 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
21189 (build-system r-build-system)
21190 (home-page "https://github.com/sckott/httpcode")
21191 (synopsis "HTTP status code helper")
21192 (description "@code{httpcode} provides functionality for finding and
21193 explaining the meaning of @code{HTTP} status codes. Functions are included for
21194 searching for codes by full or partial number, by message, and to get
21195 appropriate dog and cat images for many status codes.")
21196 (license license:expat)))
21197
21198 (define-public r-latex2exp
21199 (package
21200 (name "r-latex2exp")
21201 (version "0.4.0")
21202 (source (origin
21203 (method url-fetch)
21204 (uri (cran-uri "latex2exp" version))
21205 (sha256
21206 (base32
21207 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
21208 (build-system r-build-system)
21209 (propagated-inputs
21210 `(("r-stringr" ,r-stringr)
21211 ("r-magrittr", r-magrittr)))
21212 (home-page "https://github.com/stefano-meschiari/latex2exp/")
21213 (synopsis "Use LaTeX expressions in plots")
21214 (description "@code{latex2exp} parses and converts LaTeX math formulas to
21215 R's plotmath expressions, used to enter mathematical formulas and symbols to be
21216 rendered as text, axis labels, etc. throughout R's plotting system.")
21217 (license license:expat)))
21218
21219 (define-public r-oai
21220 (package
21221 (name "r-oai")
21222 (version "0.3.0")
21223 (source (origin
21224 (method url-fetch)
21225 (uri (cran-uri "oai" version))
21226 (sha256
21227 (base32
21228 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
21229 (build-system r-build-system)
21230 (propagated-inputs
21231 `(("r-xml2" ,r-xml2)
21232 ("r-httr" ,r-httr)
21233 ("r-plyr" ,r-plyr)
21234 ("r-stringr" ,r-stringr)
21235 ("r-tibble" ,r-tibble)))
21236 (home-page "https://github.com/ropensci/oai/")
21237 (synopsis "General purpose OAI-PMH services client")
21238 (description "@code{oai} provides a general purpose client to work with
21239 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
21240 service. Functions are provided to work with the OAI-PMH verbs:
21241 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
21242 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
21243 (license license:expat)))
21244
21245 (define-public r-argon2
21246 (package
21247 (name "r-argon2")
21248 (version "0.2-0")
21249 (source
21250 (origin
21251 (method url-fetch)
21252 (uri (cran-uri "argon2" version))
21253 (sha256
21254 (base32
21255 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
21256 (properties `((upstream-name . "argon2")))
21257 (build-system r-build-system)
21258 (home-page "https://github.com/wrathematics/argon2")
21259 (synopsis "Secure password hashing based on the argon2 algorithm")
21260 (description
21261 "This package provides utilities for secure password hashing via the
21262 argon2 algorithm.")
21263 (license license:bsd-2)))
21264
21265 (define-public r-getpass
21266 (package
21267 (name "r-getpass")
21268 (version "0.2-2")
21269 (source
21270 (origin
21271 (method url-fetch)
21272 (uri (cran-uri "getPass" version))
21273 (sha256
21274 (base32
21275 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
21276 (properties `((upstream-name . "getPass")))
21277 (build-system r-build-system)
21278 (propagated-inputs
21279 `(("r-rstudioapi" ,r-rstudioapi)))
21280 (home-page "https://github.com/wrathematics/getPass")
21281 (synopsis "Masked user input")
21282 (description
21283 "This package provides a micro-package for reading \"passwords\", i.e.
21284 reading user input with masking, so that the input is not displayed as it is
21285 typed. Currently, RStudio, the command line (every OS), and any platform
21286 where tcltk is present are supported.")
21287 (license license:bsd-2)))
21288
21289 (define-public r-remoter
21290 (package
21291 (name "r-remoter")
21292 (version "0.4-0")
21293 (source
21294 (origin
21295 (method url-fetch)
21296 (uri (cran-uri "remoter" version))
21297 (sha256
21298 (base32
21299 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
21300 (properties `((upstream-name . "remoter")))
21301 (build-system r-build-system)
21302 (propagated-inputs
21303 `(("r-argon2" ,r-argon2)
21304 ("r-getpass" ,r-getpass)
21305 ("r-pbdzmq" ,r-pbdzmq)
21306 ("r-png" ,r-png)))
21307 (home-page "https://github.com/RBigData/remoter")
21308 (synopsis "Control a remote R session from a local one")
21309 (description
21310 "This package provides a set of utilities for client/server computing
21311 with R, controlling a remote R session (the server) from a local one (the
21312 client).")
21313 (license license:bsd-2)))
21314
21315 (define-public r-asd
21316 (package
21317 (name "r-asd")
21318 (version "2.2")
21319 (source
21320 (origin
21321 (method url-fetch)
21322 (uri (cran-uri "asd" version))
21323 (sha256
21324 (base32
21325 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
21326 (properties `((upstream-name . "asd")))
21327 (build-system r-build-system)
21328 (propagated-inputs
21329 `(("r-mvtnorm" ,r-mvtnorm)))
21330 (home-page "https://cran.r-project.org/web/packages/asd")
21331 (synopsis "Simulations for Adaptive Seamless Designs")
21332 (description
21333 "This package provdes means to run simulations for adaptive seamless
21334 designs with and without early outcomes for treatment selection and
21335 subpopulation type designs.")
21336 (license license:gpl3)))
21337
21338 (define-public r-nbconvertr
21339 (package
21340 (name "r-nbconvertr")
21341 (version "1.3.2")
21342 (source
21343 (origin
21344 (method url-fetch)
21345 (uri (cran-uri "nbconvertR" version))
21346 (sha256
21347 (base32
21348 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
21349 (properties `((upstream-name . "nbconvertR")))
21350 (build-system r-build-system)
21351 (inputs
21352 `(("jupyter" ,python-nbconvert)
21353 ("pandoc" ,ghc-pandoc)))
21354 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
21355 (synopsis "Vignette engine wrapping Jupyter notebooks")
21356 (description
21357 "This package calls the Jupyter script @code{nbconvert} to create
21358 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
21359 containing rich text, code, and its output. Code cells can be edited and
21360 evaluated interactively.")
21361 (license license:gpl3)))
21362
21363 (define-public r-bridgesampling
21364 (package
21365 (name "r-bridgesampling")
21366 (version "1.0-0")
21367 (source
21368 (origin
21369 (method url-fetch)
21370 (uri (cran-uri "bridgesampling" version))
21371 (sha256
21372 (base32
21373 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
21374 (properties
21375 `((upstream-name . "bridgesampling")))
21376 (build-system r-build-system)
21377 (propagated-inputs
21378 `(("r-brobdingnag" ,r-brobdingnag)
21379 ("r-coda" ,r-coda)
21380 ("r-matrix" ,r-matrix)
21381 ("r-mvtnorm" ,r-mvtnorm)
21382 ("r-scales" ,r-scales)
21383 ("r-stringr" ,r-stringr)))
21384 (native-inputs
21385 `(("r-knitr" ,r-knitr)))
21386 (home-page "https://github.com/quentingronau/bridgesampling")
21387 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
21388 (description
21389 "This package provides functions for estimating marginal likelihoods,
21390 Bayes factors, posterior model probabilities, and normalizing constants in
21391 general, via different versions of bridge sampling.")
21392 (license license:gpl2+)))
21393
21394 (define-public r-tea
21395 (package
21396 (name "r-tea")
21397 (version "1.1")
21398 (source
21399 (origin
21400 (method url-fetch)
21401 (uri (cran-uri "tea" version))
21402 (sha256
21403 (base32
21404 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
21405 (properties
21406 `((upstream-name . "tea")))
21407 (build-system r-build-system)
21408 (propagated-inputs
21409 `(("r-matrix" ,r-matrix)))
21410 (home-page "https://cran.r-project.org/web/packages/tea/")
21411 (synopsis "Threshold estimation approaches")
21412 (description
21413 "This package provides different approaches for selecting the threshold
21414 in generalized Pareto distributions. Most of them are based on minimizing the
21415 AMSE-criterion or atleast by reducing the bias of the assumed GPD-model.
21416 Others are heuristically motivated by searching for stable sample paths, i.e.
21417 a nearly constant region of the tail index estimator with respect to k, which
21418 is the number of data in the tail. The third class is motivated by graphical
21419 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
21420 is also implemented here.")
21421 (license license:gpl3)))
21422
21423 (define-public r-awsmethods
21424 (package
21425 (name "r-awsmethods")
21426 (version "1.1-1")
21427 (source
21428 (origin
21429 (method url-fetch)
21430 (uri (cran-uri "awsMethods" version))
21431 (sha256
21432 (base32
21433 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
21434 (properties
21435 `((upstream-name . "awsMethods")))
21436 (build-system r-build-system)
21437 (home-page "http://www.wias-berlin.de/software/imaging/")
21438 (synopsis "Class and methods definitions")
21439 (description
21440 "This package defines the generic method @code{extract} and provides
21441 @code{openMP} support as needed in several packages like
21442 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
21443 (license license:gpl2+)))
21444
21445 (define-public r-aws
21446 (package
21447 (name "r-aws")
21448 (version "2.4-2")
21449 (source
21450 (origin
21451 (method url-fetch)
21452 (uri (cran-uri "aws" version))
21453 (sha256
21454 (base32
21455 "1czlsy64nx6j7h1smgb561yyv3f98pwqwglk77yla4mx3fp14bvq"))))
21456 (properties
21457 `((upstream-name . "aws")))
21458 (build-system r-build-system)
21459 (propagated-inputs
21460 `(("r-awsmethods" ,r-awsmethods)
21461 ("r-gsl" ,r-gsl)))
21462 (native-inputs
21463 `(("gfortran" ,gfortran)))
21464 (home-page "https://cran.r-project.org/web/packages/aws/")
21465 (synopsis "Adaptive weights smoothing")
21466 (description
21467 "This package provides a collection of R-functions implementing adaptive
21468 smoothing procedures in 1D, 2D and 3D. This includes the
21469 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
21470 Confidence Intervals} (ICI), variational approaches, and a non-local means
21471 filter.")
21472 (license license:gpl2+)))
21473
21474 (define-public r-sgloptim
21475 (package
21476 (name "r-sgloptim")
21477 (version "1.3.8")
21478 (source
21479 (origin
21480 (method url-fetch)
21481 (uri (cran-uri "sglOptim" version))
21482 (sha256
21483 (base32
21484 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
21485 (properties
21486 `((upstream-name . "sglOptim")))
21487 (build-system r-build-system)
21488 (propagated-inputs
21489 `(("r-bh" ,r-bh)
21490 ("r-doparallel" ,r-doparallel)
21491 ("r-foreach" ,r-foreach)
21492 ("r-matrix" ,r-matrix)
21493 ("r-rcpp" ,r-rcpp)
21494 ("r-rcpparmadillo" ,r-rcpparmadillo)
21495 ("r-rcppprogress" ,r-rcppprogress)))
21496 (native-inputs
21497 `(("r-knitr" ,r-knitr)))
21498 (home-page "https://github.com/nielsrhansen/sglOptim")
21499 (synopsis "Generic sparse group Lasso solver")
21500 (description
21501 "This package provides a fast generic solver for sparse group lasso
21502 optimization problems. The loss (objective) function must be defined in a C++
21503 module. The optimization problem is solved using a coordinate gradient
21504 descent algorithm. Convergence of the algorithm is established and the
21505 algorithm is applicable to a broad class of loss functions. Use of parallel
21506 computing for cross validation and subsampling is supported through the
21507 @code{foreach} and @code{doParallel} packages.")
21508 (license license:gpl2+)))
21509
21510 (define-public r-grouped
21511 (package
21512 (name "r-grouped")
21513 (version "0.6-0")
21514 (source
21515 (origin
21516 (method url-fetch)
21517 (uri (cran-uri "grouped" version))
21518 (sha256
21519 (base32
21520 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
21521 (properties
21522 `((upstream-name . "grouped")))
21523 (build-system r-build-system)
21524 (propagated-inputs
21525 `(("r-mass" ,r-mass)))
21526 (home-page "https://cran.r-project.org/web/packages/grouped/")
21527 (synopsis "Regression analysis of grouped and coarse data")
21528 (description
21529 "This package provides regression models for grouped and coarse data,
21530 under the coarsened at random assumption.")
21531 (license license:gpl2+)))
21532
21533 (define-public r-stam
21534 (package
21535 (name "r-stam")
21536 (version "0.0-1")
21537 (source
21538 (origin
21539 (method url-fetch)
21540 (uri (cran-uri "stam" version))
21541 (sha256
21542 (base32
21543 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
21544 (properties
21545 `((upstream-name . "stam")))
21546 (build-system r-build-system)
21547 (propagated-inputs
21548 `(("r-np" ,r-np)
21549 ("r-sp" ,r-sp)))
21550 (home-page "https://cran.r-project.org/web/packages/stam")
21551 (synopsis "Spatio-temporal analysis and modelling")
21552 (description
21553 "This package provides various methods to conduct Spatio-Temporal
21554 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
21555 Inferred Spatio-Temporal Modelling.")
21556 (license license:gpl2+)))
21557
21558 (define-public r-dcv
21559 (package
21560 (name "r-dcv")
21561 (version "0.1.1")
21562 (source
21563 (origin
21564 (method url-fetch)
21565 (uri (cran-uri "dcv" version))
21566 (sha256
21567 (base32
21568 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
21569 (properties
21570 `((upstream-name . "dcv")))
21571 (build-system r-build-system)
21572 (propagated-inputs
21573 `(("r-lmtest" ,r-lmtest)))
21574 (home-page "https://cran.r-project.org/web/packages/dcv/")
21575 (synopsis "Conventional cross-validation statistics for climate-growth model")
21576 (description
21577 "This package performs several conventional cross-validation statistical
21578 methods for climate-growth model in the climate reconstruction from tree
21579 rings, including Sign Test statistic, Reduction of Error statistic, Product
21580 Mean Test, Durbin-Watson statistic etc.")
21581 (license license:gpl2)))
21582
21583 (define-public r-rcdd
21584 (package
21585 (name "r-rcdd")
21586 (version "1.2-2")
21587 (source
21588 (origin
21589 (method url-fetch)
21590 (uri (cran-uri "rcdd" version))
21591 (sha256
21592 (base32
21593 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
21594 (properties
21595 `((upstream-name . "rcdd")))
21596 (build-system r-build-system)
21597 (inputs
21598 `(("gmp" ,gmp)))
21599 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
21600 (synopsis "Computational geometry")
21601 (description
21602 "This package converts back and forth between two representations of a
21603 convex polytope: as solution of a set of linear equalities and inequalities
21604 and as convex hull of set of points and rays. Also does linear programming
21605 and redundant generator elimination. All functions can use exact
21606 infinite-precision rational arithmetic.")
21607 (license license:gpl2)))
21608
21609 (define-public r-rxnat
21610 (package
21611 (name "r-rxnat")
21612 (version "1.0.8")
21613 (source
21614 (origin
21615 (method url-fetch)
21616 (uri (cran-uri "Rxnat" version))
21617 (sha256
21618 (base32
21619 "12xcs2l6vn50bwzfmv60j1qahjw2npfm1a3yjhffcxzh6p8chwbg"))))
21620 (properties
21621 `((upstream-name . "Rxnat")))
21622 (build-system r-build-system)
21623 (propagated-inputs
21624 `(("r-httr" ,r-httr)
21625 ("r-rcurl" ,r-rcurl)))
21626 (native-inputs
21627 `(("r-knitr" ,r-knitr)))
21628 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
21629 (synopsis "Queries and extracts images from neuroimaging datasets")
21630 (description
21631 "This package allows communication with the Extensible Neuroimaging
21632 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
21633 download images.")
21634 (license license:gpl2)))
21635
21636 (define-public r-rserve
21637 (package
21638 (name "r-rserve")
21639 (version "1.8-6")
21640 (source
21641 (origin
21642 (method url-fetch)
21643 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
21644 version ".tar.gz"))
21645 (sha256
21646 (base32
21647 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
21648 (build-system r-build-system)
21649 (propagated-inputs
21650 `(("r-checkmate" ,r-checkmate)
21651 ("r-mime" ,r-mime)
21652 ("r-jsonlite" ,r-jsonlite)
21653 ("r-knitr" ,r-knitr)
21654 ("r-r6" ,r-r6)
21655 ("r-rcpp" ,r-rcpp)
21656 ("r-uuid" ,r-uuid)))
21657 (inputs
21658 `(("openssl" ,openssl)
21659 ("zlib" ,zlib)))
21660 (home-page "https://github.com/s-u/Rserve")
21661 (synopsis
21662 "Server providing access to R from many languages and systems")
21663 (description
21664 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
21665 binary requests to be sent to R. Every connection has a separate workspace
21666 and working directory. Client-side implementations are available for popular
21667 languages such as C/C++ and Java, allowing any application to use facilities
21668 of R without the need of linking to R code. Rserve supports remote
21669 connection, user authentication and file transfer. A simple R client is
21670 included in this package as well.")
21671 (license license:gpl2)))