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056468dc RW |
1 | ;;; GNU Guix --- Functional package management for GNU |
2 | ;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net> | |
94989d4b | 3 | ;;; Copyright © 2017 Roel Janssen <roel@gnu.org> |
0796954b | 4 | ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr> |
056468dc RW |
5 | ;;; |
6 | ;;; This file is part of GNU Guix. | |
7 | ;;; | |
8 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
9 | ;;; under the terms of the GNU General Public License as published by | |
10 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
11 | ;;; your option) any later version. | |
12 | ;;; | |
13 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
14 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
15 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
16 | ;;; GNU General Public License for more details. | |
17 | ;;; | |
18 | ;;; You should have received a copy of the GNU General Public License | |
19 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
20 | ||
21 | (define-module (gnu packages cran) | |
22 | #:use-module ((guix licenses) #:prefix license:) | |
23 | #:use-module (guix packages) | |
24 | #:use-module (guix download) | |
25 | #:use-module (guix utils) | |
c69d27db | 26 | #:use-module (guix build-system r) |
062b6dbd | 27 | #:use-module (gnu packages gcc) |
f97ce815 | 28 | #:use-module (gnu packages machine-learning) |
521e0703 | 29 | #:use-module (gnu packages maths) |
94989d4b | 30 | #:use-module (gnu packages mpi) |
e0268ff2 RW |
31 | #:use-module (gnu packages perl) |
32 | #:use-module (gnu packages statistics) | |
33 | #:use-module (gnu packages web)) | |
056468dc RW |
34 | |
35 | (define-public r-colorspace | |
36 | (package | |
37 | (name "r-colorspace") | |
38 | (version "1.3-2") | |
39 | (source | |
40 | (origin | |
41 | (method url-fetch) | |
42 | (uri (cran-uri "colorspace" version)) | |
43 | (sha256 | |
44 | (base32 "0d1ya7hx4y58n5ivwmdmq2zgh0g2sbv7ykh13n85c1355csd57yx")))) | |
45 | (build-system r-build-system) | |
e9960d8c | 46 | (home-page "https://cran.r-project.org/web/packages/colorspace") |
056468dc RW |
47 | (synopsis "Color space manipulation") |
48 | (description | |
49 | "This package carries out a mapping between assorted color spaces | |
50 | including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar | |
51 | CIELAB. Qualitative, sequential, and diverging color palettes based on HCL | |
52 | colors are provided.") | |
53 | (license license:bsd-3))) | |
5bee6bf4 RW |
54 | |
55 | (define-public r-glue | |
56 | (package | |
57 | (name "r-glue") | |
a8a2871f | 58 | (version "1.2.0") |
5bee6bf4 RW |
59 | (source |
60 | (origin | |
61 | (method url-fetch) | |
62 | (uri (cran-uri "glue" version)) | |
63 | (sha256 | |
64 | (base32 | |
a8a2871f | 65 | "0vi9y8ix95g6hjqdz9c9y4119apbdjcypdv0ag8cl6vaxqs5n9qr")))) |
5bee6bf4 RW |
66 | (build-system r-build-system) |
67 | (home-page "https://github.com/tidyverse/glue") | |
68 | (synopsis "Interpreted string literals") | |
69 | (description | |
70 | "This package provides an implementation of interpreted string literals, | |
71 | inspired by Python's Literal String Interpolation (PEP-0498) and | |
72 | Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.") | |
73 | (license license:expat))) | |
847b4572 RW |
74 | |
75 | (define-public r-plogr | |
76 | (package | |
77 | (name "r-plogr") | |
78 | (version "0.1-1") | |
79 | (source | |
80 | (origin | |
81 | (method url-fetch) | |
82 | (uri (cran-uri "plogr" version)) | |
83 | (sha256 | |
84 | (base32 | |
85 | "13zliqlbkl8b04k9ga0sx5jsh7k867gracgl84l2a9kcqy9mqx92")))) | |
86 | (build-system r-build-system) | |
87 | (home-page "https://github.com/krlmlr/plogr") | |
88 | (synopsis "R bindings for the plog C++ logging library") | |
89 | (description | |
90 | "This package provides the header files for a stripped-down version of | |
91 | the plog header-only C++ logging library, and a method to log to R's standard | |
92 | error stream.") | |
93 | (license license:expat))) | |
a8cba9dd RW |
94 | |
95 | (define-public r-rcpp | |
96 | (package | |
97 | (name "r-rcpp") | |
d76f987c | 98 | (version "0.12.14") |
a8cba9dd RW |
99 | (source |
100 | (origin | |
101 | (method url-fetch) | |
102 | (uri (cran-uri "Rcpp" version)) | |
103 | (sha256 | |
d76f987c | 104 | (base32 "0qvyxggddyg87lza45hjl0a2prabdyshkqzkz418vi777zygqa6s")))) |
a8cba9dd RW |
105 | (build-system r-build-system) |
106 | (home-page "http://www.rcpp.org") | |
107 | (synopsis "Seamless R and C++ integration") | |
108 | (description | |
109 | "The Rcpp package provides R functions as well as C++ classes which offer | |
110 | a seamless integration of R and C++. Many R data types and objects can be | |
111 | mapped back and forth to C++ equivalents which facilitates both writing of new | |
112 | code as well as easier integration of third-party libraries. Documentation | |
113 | about Rcpp is provided by several vignettes included in this package, via the | |
114 | 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel | |
115 | and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see | |
116 | 'citation(\"Rcpp\")' for details on these last two.") | |
117 | (license license:gpl2+))) | |
eed58a08 RW |
118 | |
119 | (define-public r-bindr | |
120 | (package | |
121 | (name "r-bindr") | |
122 | (version "0.1") | |
123 | (source | |
124 | (origin | |
125 | (method url-fetch) | |
126 | (uri (cran-uri "bindr" version)) | |
127 | (sha256 | |
128 | (base32 | |
129 | "0d95ifm0x4mrfzi20xf39f5pzd7rfzqsld0vjqf6xzga5rhnd8fc")))) | |
130 | (build-system r-build-system) | |
131 | (home-page "https://github.com/krlmlr/bindr") | |
132 | (synopsis "Parametrized active bindings") | |
133 | (description | |
134 | "This package provides a simple interface for creating active bindings | |
135 | where the bound function accepts additional arguments.") | |
136 | (license license:expat))) | |
4bb0b4cc RW |
137 | |
138 | (define-public r-bindrcpp | |
139 | (package | |
140 | (name "r-bindrcpp") | |
141 | (version "0.2") | |
142 | (source | |
143 | (origin | |
144 | (method url-fetch) | |
145 | (uri (cran-uri "bindrcpp" version)) | |
146 | (sha256 | |
147 | (base32 | |
148 | "0l1l22zl87wiyl79m3gj2vlxmkhxvrkl4alhyy08h55q7hqs3vyh")))) | |
149 | (build-system r-build-system) | |
150 | (propagated-inputs | |
151 | `(("r-bindr" ,r-bindr) | |
152 | ("r-plogr" ,r-plogr) | |
153 | ("r-rcpp" ,r-rcpp))) | |
154 | (home-page "https://github.com/krlmlr/bindrcpp") | |
155 | (synopsis "Rcpp interface to active bindings") | |
156 | (description | |
157 | "This package provides an easy way to fill an environment with active | |
158 | bindings that call a C++ function.") | |
159 | (license license:expat))) | |
33ce12e2 RW |
160 | |
161 | (define-public r-auc | |
162 | (package | |
163 | (name "r-auc") | |
164 | (version "0.3.0") | |
165 | (source | |
166 | (origin | |
167 | (method url-fetch) | |
168 | (uri (cran-uri "AUC" version)) | |
169 | (sha256 | |
170 | (base32 | |
171 | "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7")))) | |
172 | (properties `((upstream-name . "AUC"))) | |
173 | (build-system r-build-system) | |
e9960d8c | 174 | (home-page "https://cran.r-project.org/web/packages/AUC") |
33ce12e2 RW |
175 | (synopsis "Compute the area under the curve of selected measures") |
176 | (description | |
177 | "This package includes functions to compute the area under the curve of | |
178 | selected measures: the area under the sensitivity curve (AUSEC), the area | |
179 | under the specificity curve (AUSPC), the area under the accuracy | |
180 | curve (AUACC), and the area under the receiver operating characteristic | |
181 | curve (AUROC). The curves can also be visualized. Support for partial areas | |
182 | is provided.") | |
183 | (license license:gpl2+))) | |
c69d27db RW |
184 | |
185 | (define-public r-calibrate | |
186 | (package | |
187 | (name "r-calibrate") | |
188 | (version "1.7.2") | |
189 | (source | |
190 | (origin | |
191 | (method url-fetch) | |
192 | (uri (cran-uri "calibrate" version)) | |
193 | (sha256 | |
194 | (base32 | |
195 | "010nb1nb9y7zhw2k6d2i2drwy5brp7b83mjj2w7i3wjp9xb6l1kq")))) | |
196 | (build-system r-build-system) | |
197 | (propagated-inputs | |
198 | `(("r-mass" ,r-mass))) | |
e9960d8c | 199 | (home-page "https://cran.r-project.org/web/packages/calibrate") |
c69d27db RW |
200 | (synopsis "Calibration of scatterplot and biplot axes") |
201 | (description | |
202 | "This is a package for drawing calibrated scales with tick marks | |
203 | on (non-orthogonal) variable vectors in scatterplots and biplots.") | |
204 | (license license:gpl2))) | |
2bdb5c3f RW |
205 | |
206 | (define-public r-shape | |
207 | (package | |
208 | (name "r-shape") | |
ea4d4f76 | 209 | (version "1.4.3") |
2bdb5c3f RW |
210 | (source |
211 | (origin | |
212 | (method url-fetch) | |
213 | (uri (cran-uri "shape" version)) | |
214 | (sha256 | |
215 | (base32 | |
ea4d4f76 | 216 | "1v9xp60p813rnx41vchkh32qmcb4z2zp9l7r1a8a6f8aqylnq3vj")))) |
2bdb5c3f | 217 | (build-system r-build-system) |
e9960d8c | 218 | (home-page "https://cran.r-project.org/web/packages/shape") |
2bdb5c3f RW |
219 | (synopsis "Functions for plotting graphical shapes") |
220 | (description | |
221 | "This package provides functions for plotting graphical shapes such as | |
222 | ellipses, circles, cylinders, arrows, ...") | |
223 | (license license:gpl3+))) | |
4847a62e RW |
224 | |
225 | (define-public r-globaloptions | |
226 | (package | |
227 | (name "r-globaloptions") | |
228 | (version "0.0.12") | |
229 | (source | |
230 | (origin | |
231 | (method url-fetch) | |
232 | (uri (cran-uri "GlobalOptions" version)) | |
233 | (sha256 | |
234 | (base32 | |
235 | "1abpc03cfvazbwj2sx6qgngs5pgpzysvxkana20hyvb4n7ws77f0")))) | |
236 | (properties `((upstream-name . "GlobalOptions"))) | |
237 | (build-system r-build-system) | |
238 | (home-page "https://github.com/jokergoo/GlobalOptions") | |
239 | (synopsis "Generate functions to get or set global options") | |
240 | (description | |
241 | "This package provides more controls on the option values such as | |
242 | validation and filtering on the values, making options invisible or private.") | |
243 | (license license:gpl2+))) | |
2856369f RW |
244 | |
245 | (define-public r-circlize | |
246 | (package | |
247 | (name "r-circlize") | |
afa427e3 | 248 | (version "0.4.3") |
2856369f RW |
249 | (source |
250 | (origin | |
251 | (method url-fetch) | |
252 | (uri (cran-uri "circlize" version)) | |
253 | (sha256 | |
254 | (base32 | |
afa427e3 | 255 | "0pg947gkryygikfbv6admx8gsg02b6g219j6a1sdnqij2908yxna")))) |
2856369f RW |
256 | (build-system r-build-system) |
257 | (propagated-inputs | |
258 | `(("r-colorspace" ,r-colorspace) | |
259 | ("r-globaloptions" ,r-globaloptions) | |
260 | ("r-shape" ,r-shape))) | |
261 | (home-page "https://github.com/jokergoo/circlize") | |
262 | (synopsis "Circular visualization") | |
263 | (description | |
031462ba TGR |
264 | "Circular layout is an efficient way to visualise huge amounts of |
265 | information. This package provides an implementation of circular layout | |
266 | generation in R as well as an enhancement of available software. Its | |
267 | flexibility is based on the usage of low-level graphics functions such that | |
268 | self-defined high-level graphics can be easily implemented by users for | |
269 | specific purposes. Together with the seamless connection between the powerful | |
270 | computational and visual environment in R, it gives users more convenience and | |
271 | freedom to design figures for better understanding complex patterns behind | |
272 | multi-dimensional data.") | |
2856369f | 273 | (license license:gpl2+))) |
5cc79c9c RW |
274 | |
275 | (define-public r-powerlaw | |
276 | (package | |
277 | (name "r-powerlaw") | |
eeb54328 | 278 | (version "0.70.1") |
5cc79c9c RW |
279 | (source |
280 | (origin | |
281 | (method url-fetch) | |
282 | (uri (cran-uri "poweRlaw" version)) | |
283 | (sha256 | |
284 | (base32 | |
eeb54328 | 285 | "04sr0nhdd1v915m0zf5gasznzgi08ykcy20kkwdw0l5mvvdbic8m")))) |
5cc79c9c RW |
286 | (properties `((upstream-name . "poweRlaw"))) |
287 | (build-system r-build-system) | |
288 | (propagated-inputs | |
289 | `(("r-vgam" ,r-vgam))) | |
290 | (home-page "https://github.com/csgillespie/poweRlaw") | |
291 | (synopsis "Tools for the analysis of heavy tailed distributions") | |
292 | (description | |
293 | "This package provides an implementation of maximum likelihood estimators | |
294 | for a variety of heavy tailed distributions, including both the discrete and | |
295 | continuous power law distributions. Additionally, a goodness-of-fit based | |
296 | approach is used to estimate the lower cut-off for the scaling region.") | |
297 | ;; Any of these GPL versions. | |
298 | (license (list license:gpl2 license:gpl3)))) | |
05486604 RW |
299 | |
300 | (define-public r-compare | |
301 | (package | |
302 | (name "r-compare") | |
303 | (version "0.2-6") | |
304 | (source | |
305 | (origin | |
306 | (method url-fetch) | |
307 | (uri (cran-uri "compare" version)) | |
308 | (sha256 | |
309 | (base32 | |
310 | "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw")))) | |
311 | (build-system r-build-system) | |
e9960d8c | 312 | (home-page "https://cran.r-project.org/web/packages/compare") |
05486604 RW |
313 | (synopsis "Comparing objects for differences") |
314 | (description | |
315 | "This package provides functions to compare a model object to a | |
316 | comparison object. If the objects are not identical, the functions can be | |
317 | instructed to explore various modifications of the objects (e.g., sorting | |
318 | rows, dropping names) to see if the modified versions are identical.") | |
319 | (license license:gpl2+))) | |
d3c67e1b RW |
320 | |
321 | (define-public r-dendextend | |
322 | (package | |
323 | (name "r-dendextend") | |
6c84c735 | 324 | (version "1.6.0") |
d3c67e1b RW |
325 | (source |
326 | (origin | |
327 | (method url-fetch) | |
328 | (uri (cran-uri "dendextend" version)) | |
329 | (sha256 | |
330 | (base32 | |
6c84c735 | 331 | "0pichh08zi12lpxzc061dmv4smj6lizygd1xymln8wfz18sf7923")))) |
d3c67e1b RW |
332 | (build-system r-build-system) |
333 | (propagated-inputs | |
334 | `(("r-fpc" ,r-fpc) | |
335 | ("r-ggplot2" ,r-ggplot2) | |
336 | ("r-magrittr" ,r-magrittr) | |
337 | ("r-viridis" ,r-viridis) | |
338 | ("r-whisker" ,r-whisker))) | |
339 | (home-page "https://cran.r-project.org/web/packages/dendextend") | |
340 | (synopsis "Extending 'dendrogram' functionality in R") | |
341 | (description | |
342 | "This package offers a set of functions for extending @code{dendrogram} | |
343 | objects in R, letting you visualize and compare trees of hierarchical | |
344 | clusterings. You can adjust a tree's graphical parameters (the color, size, | |
345 | type, etc of its branches, nodes and labels) and visually and statistically | |
346 | compare different dendrograms to one another.") | |
347 | ;; Any of these versions | |
348 | (license (list license:gpl2 license:gpl3)))) | |
e0268ff2 RW |
349 | |
350 | (define-public r-getoptlong | |
351 | (package | |
352 | (name "r-getoptlong") | |
353 | (version "0.1.6") | |
354 | (source | |
355 | (origin | |
356 | (method url-fetch) | |
357 | (uri (cran-uri "GetoptLong" version)) | |
358 | (sha256 | |
359 | (base32 | |
360 | "1d98gcvlvp9nz5lbnzr0kkpc2hbkx74hlhrnybqhg1gdwc3g09pm")))) | |
361 | (properties `((upstream-name . "GetoptLong"))) | |
362 | (build-system r-build-system) | |
363 | (inputs | |
364 | `(("perl" ,perl))) | |
365 | (propagated-inputs | |
366 | `(("r-globaloptions" ,r-globaloptions) | |
367 | ("r-rjson" ,r-rjson))) | |
368 | (home-page "https://github.com/jokergoo/GetoptLong") | |
369 | (synopsis "Parsing command-line arguments and variable interpolation") | |
370 | (description | |
371 | "This is yet another command-line argument parser which wraps the | |
372 | powerful Perl module @code{Getopt::Long} and with some adaptation for easier | |
373 | use in R. It also provides a simple way for variable interpolation in R.") | |
374 | (license license:gpl2+))) | |
f2e974e1 RW |
375 | |
376 | (define-public r-fastmatch | |
377 | (package | |
378 | (name "r-fastmatch") | |
379 | (version "1.1-0") | |
380 | (source | |
381 | (origin | |
382 | (method url-fetch) | |
383 | (uri (cran-uri "fastmatch" version)) | |
384 | (sha256 | |
385 | (base32 | |
386 | "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90")))) | |
387 | (build-system r-build-system) | |
388 | (home-page "http://www.rforge.net/fastmatch") | |
389 | (synopsis "Fast match function") | |
390 | (description | |
391 | "This package provides a fast @code{match} replacement for cases that | |
392 | require repeated look-ups. It is slightly faster that R's built-in | |
393 | @code{match} function on first match against a table, but extremely fast on | |
394 | any subsequent lookup as it keeps the hash table in memory.") | |
395 | (license license:gpl2))) | |
a7f0faa2 RW |
396 | |
397 | (define-public r-ff | |
398 | (package | |
399 | (name "r-ff") | |
400 | (version "2.2-13") | |
401 | (source | |
402 | (origin | |
403 | (method url-fetch) | |
404 | (uri (cran-uri "ff" version)) | |
405 | (sha256 | |
406 | (base32 | |
407 | "1nvd6kx46xzyc99a44mgynd94pvd2h495m5a7b1g67k5w2phiywb")))) | |
408 | (build-system r-build-system) | |
409 | (propagated-inputs `(("r-bit" ,r-bit))) | |
410 | (home-page "http://ff.r-forge.r-project.org/") | |
411 | (synopsis "Memory-efficient storage of large data on disk and access functions") | |
412 | (description | |
413 | "This package provides data structures that are stored on disk but | |
414 | behave (almost) as if they were in RAM by transparently mapping only a section | |
415 | in main memory.") | |
a6e67d86 EF |
416 | ;; error Architecture not supported. |
417 | (supported-systems (delete "aarch64-linux" %supported-systems)) | |
a7f0faa2 | 418 | (license license:gpl2))) |
49c9c297 RW |
419 | |
420 | (define-public r-ffbase | |
421 | (package | |
422 | (name "r-ffbase") | |
423 | (version "0.12.3") | |
424 | (source | |
425 | (origin | |
426 | (method url-fetch) | |
427 | (uri (cran-uri "ffbase" version)) | |
428 | (sha256 | |
429 | (base32 | |
430 | "1nz97bndxxkzp8rq6va8ff5ky9vkaib1jybm6j852awwb3n9had5")))) | |
431 | (build-system r-build-system) | |
432 | (propagated-inputs | |
433 | `(("r-bit" ,r-bit) | |
434 | ("r-fastmatch" ,r-fastmatch) | |
435 | ("r-ff" ,r-ff))) | |
436 | (home-page "http://github.com/edwindj/ffbase") | |
437 | (synopsis "Basic statistical functions for package 'ff'") | |
438 | (description | |
439 | "This package extends the out of memory vectors of @code{ff} with | |
440 | statistical functions and other utilities to ease their usage.") | |
441 | (license license:gpl3))) | |
18a16ceb RW |
442 | |
443 | (define-public r-prettyunits | |
444 | (package | |
445 | (name "r-prettyunits") | |
446 | (version "1.0.2") | |
447 | (source | |
448 | (origin | |
449 | (method url-fetch) | |
450 | (uri (cran-uri "prettyunits" version)) | |
451 | (sha256 | |
452 | (base32 | |
453 | "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m")))) | |
454 | (build-system r-build-system) | |
455 | (propagated-inputs | |
456 | `(("r-assertthat" ,r-assertthat) | |
457 | ("r-magrittr" ,r-magrittr))) | |
458 | (home-page "https://github.com/gaborcsardi/prettyunits") | |
459 | (synopsis "Pretty, human readable formatting of quantities") | |
460 | (description | |
461 | "This package provides tools for pretty, human readable formatting of | |
462 | quantities.") | |
463 | (license license:expat))) | |
71be51d5 RW |
464 | |
465 | (define-public r-reshape | |
466 | (package | |
467 | (name "r-reshape") | |
38ea6cfa | 468 | (version "0.8.7") |
71be51d5 RW |
469 | (source |
470 | (origin | |
471 | (method url-fetch) | |
472 | (uri (cran-uri "reshape" version)) | |
473 | (sha256 | |
474 | (base32 | |
38ea6cfa | 475 | "14ir3w4bb3bsz8jsak27nj7kpn227pdgr9653gjq5wc93rywi9ig")))) |
71be51d5 RW |
476 | (build-system r-build-system) |
477 | (propagated-inputs | |
478 | `(("r-plyr" ,r-plyr) | |
479 | ("r-rcpp" ,r-rcpp))) | |
480 | (home-page "http://had.co.nz/reshape") | |
481 | (synopsis "Flexibly reshape data") | |
482 | (description | |
483 | "Flexibly restructure and aggregate data using just two functions: | |
484 | @code{melt} and @code{cast}. This package provides them.") | |
485 | (license license:expat))) | |
c9c6f4b5 RW |
486 | |
487 | (define-public r-progress | |
488 | (package | |
489 | (name "r-progress") | |
490 | (version "1.1.2") | |
491 | (source | |
492 | (origin | |
493 | (method url-fetch) | |
494 | (uri (cran-uri "progress" version)) | |
495 | (sha256 | |
496 | (base32 | |
497 | "1fxakchfjr5vj59s9sxynd7crpz97xj42438rmkhkf3rjpyspx59")))) | |
498 | (build-system r-build-system) | |
499 | (propagated-inputs | |
500 | `(("r-prettyunits" ,r-prettyunits) | |
501 | ("r-r6" ,r-r6))) | |
502 | (home-page "https://github.com/gaborcsardi/progress") | |
503 | (synopsis "Terminal progress bars") | |
504 | (description | |
505 | "This package provides configurable progress bars. They may include | |
506 | percentage, elapsed time, and/or the estimated completion time. They work in | |
507 | terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The | |
508 | package also provides a C++ API, that works with or without Rcpp.") | |
509 | (license license:expat))) | |
ac840207 RW |
510 | |
511 | (define-public r-ggally | |
512 | (package | |
513 | (name "r-ggally") | |
bf958fcd | 514 | (version "1.3.2") |
ac840207 RW |
515 | (source |
516 | (origin | |
517 | (method url-fetch) | |
518 | (uri (cran-uri "GGally" version)) | |
519 | (sha256 | |
520 | (base32 | |
bf958fcd | 521 | "02px7j28wzbhcgcwm2m0pxb6g7s5zvphl64ix55pkvag4m2ky57l")))) |
ac840207 RW |
522 | (properties `((upstream-name . "GGally"))) |
523 | (build-system r-build-system) | |
524 | (propagated-inputs | |
525 | `(("r-ggplot2" ,r-ggplot2) | |
526 | ("r-gtable" ,r-gtable) | |
527 | ("r-plyr" ,r-plyr) | |
528 | ("r-progress" ,r-progress) | |
529 | ("r-rcolorbrewer" ,r-rcolorbrewer) | |
530 | ("r-reshape" ,r-reshape))) | |
531 | (home-page "https://ggobi.github.io/ggally") | |
532 | (synopsis "Extension to ggplot2") | |
533 | (description | |
534 | "The R package ggplot2 is a plotting system based on the grammar of | |
535 | graphics. GGally extends ggplot2 by adding several functions to reduce the | |
536 | complexity of combining geometric objects with transformed data. Some of | |
537 | these functions include a pairwise plot matrix, a two group pairwise plot | |
538 | matrix, a parallel coordinates plot, a survival plot, and several functions to | |
539 | plot networks.") | |
540 | (license license:gpl2+))) | |
3349faec RW |
541 | |
542 | (define-public r-proxy | |
543 | (package | |
544 | (name "r-proxy") | |
f46a74e9 | 545 | (version "0.4-20") |
3349faec RW |
546 | (source |
547 | (origin | |
548 | (method url-fetch) | |
549 | (uri (cran-uri "proxy" version)) | |
550 | (sha256 | |
551 | (base32 | |
f46a74e9 | 552 | "15g6dacdmlbkcnimblscghl23aj732cn6qwbs583r4im9v5nvbla")))) |
3349faec | 553 | (build-system r-build-system) |
e9960d8c | 554 | (home-page "https://cran.r-project.org/web/packages/proxy") |
3349faec RW |
555 | (synopsis "Distance and similarity measures") |
556 | (description | |
557 | "This package provides an extensible framework for the efficient | |
558 | calculation of auto- and cross-proximities, along with implementations of the | |
559 | most popular ones.") | |
560 | (license license:gpl2))) | |
bc0081e7 RW |
561 | |
562 | (define-public r-sp | |
563 | (package | |
564 | (name "r-sp") | |
f7b17218 | 565 | (version "1.2-5") |
bc0081e7 RW |
566 | (source |
567 | (origin | |
568 | (method url-fetch) | |
569 | (uri (cran-uri "sp" version)) | |
570 | (sha256 | |
571 | (base32 | |
f7b17218 | 572 | "09yydnacp33yx0kn537k96fjlbf75fjafqfknpa5gvci4l888bqd")))) |
bc0081e7 RW |
573 | (build-system r-build-system) |
574 | (propagated-inputs | |
575 | `(("r-lattice" ,r-lattice))) | |
e9960d8c | 576 | (home-page "https://cran.r-project.org/web/packages/sp") |
bc0081e7 RW |
577 | (synopsis "Classes and methods for spatial data") |
578 | (description | |
579 | "This package provides classes and methods for spatial data; the classes | |
580 | document where the spatial location information resides, for 2D or 3D data. | |
581 | Utility functions are provided, e.g. for plotting data as maps, spatial | |
582 | selection, as well as methods for retrieving coordinates, for subsetting, | |
583 | print, summary, etc.") | |
584 | (license license:gpl2+))) | |
e389d10f RW |
585 | |
586 | (define-public r-rmtstat | |
587 | (package | |
588 | (name "r-rmtstat") | |
589 | (version "0.3") | |
590 | (source | |
591 | (origin | |
592 | (method url-fetch) | |
593 | (uri (cran-uri "RMTstat" version)) | |
594 | (sha256 | |
595 | (base32 | |
596 | "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1")))) | |
597 | (properties `((upstream-name . "RMTstat"))) | |
598 | (build-system r-build-system) | |
e9960d8c | 599 | (home-page "https://cran.r-project.org/web/packages/RMTstat") |
e389d10f RW |
600 | (synopsis "Distributions, statistics and tests derived from random matrix theory") |
601 | (description | |
602 | "This package provides functions for working with the Tracy-Widom laws | |
603 | and other distributions related to the eigenvalues of large Wishart | |
604 | matrices.") | |
605 | (license license:bsd-3))) | |
6427e620 | 606 | |
94989d4b RJ |
607 | (define-public r-rmpi |
608 | (package | |
609 | (name "r-rmpi") | |
610 | (version "0.6-6") | |
611 | (source (origin | |
612 | (method url-fetch) | |
613 | (uri (cran-uri "Rmpi" version)) | |
614 | (sha256 | |
615 | (base32 | |
616 | "0fm6z049aaq2c9xagm8n64d9560hg9d8hyb0m359fii672nhkz6q")))) | |
617 | (properties `((upstream-name . "Rmpi"))) | |
618 | (build-system r-build-system) | |
619 | (arguments | |
620 | `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\""))) | |
621 | (inputs | |
622 | `(("openmpi" ,openmpi))) | |
623 | (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi") | |
624 | (synopsis "R interface to message-passing interface (MPI)") | |
625 | (description | |
626 | "This package provides an interface (wrapper) to MPI APIs. It also | |
627 | provides an interactive R manager and worker environment.") | |
628 | (license license:gpl2+))) | |
629 | ||
6427e620 RW |
630 | (define-public r-lmoments |
631 | (package | |
632 | (name "r-lmoments") | |
633 | (version "1.2-3") | |
634 | (source | |
635 | (origin | |
636 | (method url-fetch) | |
637 | (uri (cran-uri "Lmoments" version)) | |
638 | (sha256 | |
639 | (base32 | |
640 | "13p0r4w16jvjnyjmkhkp3dwdfr1gap2l0k4k5jy41m8nc5fvcx79")))) | |
641 | (properties `((upstream-name . "Lmoments"))) | |
642 | (build-system r-build-system) | |
643 | (home-page "http://www.tilastotiede.fi/juha_karvanen.html") | |
644 | (synopsis "L-moments and quantile mixtures") | |
645 | (description | |
646 | "This package contains functions to estimate L-moments and trimmed | |
647 | L-moments from the data. It also contains functions to estimate the | |
648 | parameters of the normal polynomial quantile mixture and the Cauchy polynomial | |
649 | quantile mixture from L-moments and trimmed L-moments.") | |
650 | (license license:gpl2))) | |
28476b4b RW |
651 | |
652 | (define-public r-distillery | |
653 | (package | |
654 | (name "r-distillery") | |
28f2f893 | 655 | (version "1.0-4") |
28476b4b RW |
656 | (source |
657 | (origin | |
658 | (method url-fetch) | |
659 | (uri (cran-uri "distillery" version)) | |
660 | (sha256 | |
661 | (base32 | |
28f2f893 | 662 | "1m0pgmlvk7bsb6q3kxagnq422babk61sf73naavac68v8x2q8fix")))) |
28476b4b RW |
663 | (build-system r-build-system) |
664 | (home-page "http://www.ral.ucar.edu/staff/ericg") | |
665 | (synopsis "Functions for confidence intervals and object information") | |
666 | (description | |
667 | "This package provides some very simple method functions for confidence | |
668 | interval calculation and to distill pertinent information from a potentially | |
669 | complex object; primarily used in common with the packages extRemes and | |
670 | SpatialVx.") | |
671 | (license license:gpl2+))) | |
58db98c9 RW |
672 | |
673 | (define-public r-extremes | |
674 | (package | |
675 | (name "r-extremes") | |
676 | (version "2.0-8") | |
677 | (source | |
678 | (origin | |
679 | (method url-fetch) | |
680 | (uri (cran-uri "extRemes" version)) | |
681 | (sha256 | |
682 | (base32 | |
683 | "0pnpib3g2r9x8hfqhvq23j8m3jh62lp28ipnqir5yadnzv850gfm")))) | |
684 | (properties `((upstream-name . "extRemes"))) | |
685 | (build-system r-build-system) | |
686 | (propagated-inputs | |
687 | `(("r-car" ,r-car) | |
688 | ("r-distillery" ,r-distillery) | |
689 | ("r-lmoments" ,r-lmoments))) | |
690 | (home-page "http://www.assessment.ucar.edu/toolkit/") | |
691 | (synopsis "Extreme value analysis") | |
692 | (description | |
693 | "ExtRemes is a suite of functions for carrying out analyses on the | |
694 | extreme values of a process of interest; be they block maxima over long blocks | |
695 | or excesses over a high threshold.") | |
696 | (license license:gpl2+))) | |
062b6dbd RW |
697 | |
698 | (define-public r-lmtest | |
699 | (package | |
700 | (name "r-lmtest") | |
701 | (version "0.9-35") | |
702 | (source | |
703 | (origin | |
704 | (method url-fetch) | |
705 | (uri (cran-uri "lmtest" version)) | |
706 | (sha256 | |
707 | (base32 | |
708 | "107br1l7p52wxvazs031f4h5ryply97qywg9dzrkw4ydnvqq4j9g")))) | |
709 | (build-system r-build-system) | |
710 | (propagated-inputs | |
711 | `(("r-zoo" ,r-zoo))) | |
712 | (native-inputs | |
713 | `(("gfortran" ,gfortran))) | |
e9960d8c | 714 | (home-page "https://cran.r-project.org/web/packages/lmtest") |
062b6dbd RW |
715 | (synopsis "Testing linear regression models") |
716 | (description | |
717 | "This package provides a collection of tests, data sets, and examples for | |
718 | diagnostic checking in linear regression models. Furthermore, some generic | |
719 | tools for inference in parametric models are provided.") | |
720 | ;; Either version is okay | |
721 | (license (list license:gpl2 license:gpl3)))) | |
d6b156dc RW |
722 | |
723 | (define-public r-inline | |
724 | (package | |
725 | (name "r-inline") | |
726 | (version "0.3.14") | |
727 | (source (origin | |
728 | (method url-fetch) | |
729 | (uri (cran-uri "inline" version)) | |
730 | (sha256 | |
731 | (base32 | |
732 | "0cf9vya9h4znwgp6s1nayqqmh6mwyw7jl0isk1nx4j2ijszxcd7x")))) | |
733 | (build-system r-build-system) | |
e9960d8c | 734 | (home-page "https://cran.r-project.org/web/packages/inline") |
d6b156dc RW |
735 | (synopsis "Functions to inline C, C++, Fortran function calls from R") |
736 | (description | |
737 | "This package provides functionality to dynamically define R functions | |
738 | and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and | |
739 | @code{.Call} calling conventions.") | |
740 | ;; Any version of the LGPL. | |
741 | (license license:lgpl3+))) | |
8c72b830 RW |
742 | |
743 | (define-public r-bbmle | |
744 | (package | |
745 | (name "r-bbmle") | |
84078220 | 746 | (version "1.0.20") |
8c72b830 RW |
747 | (source |
748 | (origin | |
749 | (method url-fetch) | |
750 | (uri (cran-uri "bbmle" version)) | |
751 | (sha256 | |
752 | (base32 | |
84078220 | 753 | "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc")))) |
8c72b830 RW |
754 | (build-system r-build-system) |
755 | (propagated-inputs | |
756 | `(("r-lattice" ,r-lattice) | |
757 | ("r-mass" ,r-mass) | |
758 | ("r-numderiv" ,r-numderiv))) | |
e9960d8c | 759 | (home-page "https://cran.r-project.org/web/packages/bbmle") |
8c72b830 RW |
760 | (synopsis "Tools for General Maximum Likelihood Estimation") |
761 | (description | |
c151b0b6 RW |
762 | "This package provides methods and functions for fitting maximum |
763 | likelihood models in R. This package modifies and extends the @code{mle} | |
764 | classes in the @code{stats4} package.") | |
8c72b830 | 765 | ;; Any version of the GPL |
c151b0b6 | 766 | (license license:gpl2+))) |
b31e4a96 RW |
767 | |
768 | (define-public r-emdbook | |
769 | (package | |
770 | (name "r-emdbook") | |
771 | (version "1.3.9") | |
772 | (source | |
773 | (origin | |
774 | (method url-fetch) | |
775 | (uri (cran-uri "emdbook" version)) | |
776 | (sha256 | |
777 | (base32 | |
778 | "09xbdyw8a4pvrsg3ryr8drby0njy4avc5wsjj4ffibdaicpchy69")))) | |
779 | (build-system r-build-system) | |
780 | (propagated-inputs | |
781 | `(("r-bbmle" ,r-bbmle) | |
782 | ("r-coda" ,r-coda) | |
783 | ("r-lattice" ,r-lattice) | |
784 | ("r-mass" ,r-mass) | |
785 | ("r-plyr" ,r-plyr) | |
786 | ("r-rcpp" ,r-rcpp))) | |
787 | (home-page "http://www.math.mcmaster.ca/bolker/emdbook") | |
788 | (synopsis "Support functions and data for \"Ecological Models and Data\"") | |
789 | (description | |
790 | "This package provides auxiliary functions and data sets for \"Ecological | |
791 | Models and Data\", a book presenting maximum likelihood estimation and related | |
792 | topics for ecologists (ISBN 978-0-691-12522-0).") | |
793 | ;; Any GPL version | |
794 | (license (list license:gpl2 license:gpl3)))) | |
a3e36d37 RW |
795 | |
796 | (define-public r-lpsolve | |
797 | (package | |
798 | (name "r-lpsolve") | |
799 | (version "5.6.13") | |
800 | (source | |
801 | (origin | |
802 | (method url-fetch) | |
803 | (uri (cran-uri "lpSolve" version)) | |
804 | (sha256 | |
805 | (base32 | |
806 | "13a9ry8xf5j1f2j6imqrxdgxqz3nqp9sj9b4ivyx9sid459irm6m")))) | |
807 | (properties `((upstream-name . "lpSolve"))) | |
808 | (build-system r-build-system) | |
e9960d8c | 809 | (home-page "https://cran.r-project.org/web/packages/lpSolve") |
a3e36d37 RW |
810 | (synopsis "R interface to Lp_solve to solve linear/integer programs") |
811 | (description | |
812 | "Lp_solve is software for solving linear, integer and mixed integer | |
813 | programs. This implementation supplies a \"wrapper\" function in C and some R | |
814 | functions that solve general linear/integer problems, assignment problems, and | |
815 | transportation problems.") | |
816 | (license license:lgpl2.0))) | |
521e0703 RW |
817 | |
818 | (define-public r-limsolve | |
819 | (package | |
820 | (name "r-limsolve") | |
821 | (version "1.5.5.3") | |
822 | (source | |
823 | (origin | |
824 | (method url-fetch) | |
825 | (uri (cran-uri "limSolve" version)) | |
826 | (sha256 | |
827 | (base32 | |
828 | "1ll6ir42h3g2fzf0wqai213bm82gpwjj2hfma2np3mz024sc09rg")))) | |
829 | (properties `((upstream-name . "limSolve"))) | |
830 | (build-system r-build-system) | |
831 | (propagated-inputs | |
832 | `(("r-lpsolve" ,r-lpsolve) | |
833 | ("r-mass" ,r-mass) | |
834 | ("r-quadprog" ,r-quadprog))) | |
835 | (native-inputs `(("gfortran" ,gfortran))) | |
e9960d8c | 836 | (home-page "https://cran.r-project.org/web/packages/limSolve") |
521e0703 RW |
837 | (synopsis "Solving linear inverse models") |
838 | (description | |
839 | "This package provides functions that: | |
840 | ||
841 | @enumerate | |
842 | @item find the minimum/maximum of a linear or quadratic function, | |
843 | @item sample an underdetermined or overdetermined system, | |
844 | @item solve a linear system Ax=B for the unknown x. | |
845 | @end enumerate | |
846 | ||
847 | It includes banded and tridiagonal linear systems. The package calls Fortran | |
848 | functions from LINPACK.") | |
849 | ;; Any GPL version. | |
850 | (license (list license:gpl2+ license:gpl3+)))) | |
6b4a9aec RW |
851 | |
852 | (define-public r-fitdistrplus | |
853 | (package | |
854 | (name "r-fitdistrplus") | |
855 | (version "1.0-9") | |
856 | (source | |
857 | (origin | |
858 | (method url-fetch) | |
859 | (uri (cran-uri "fitdistrplus" version)) | |
860 | (sha256 | |
861 | (base32 | |
862 | "18x9454g598d54763k3hvi33iszifk7sxvhd1zg5r8z1vpixx3z6")))) | |
863 | (build-system r-build-system) | |
864 | (propagated-inputs | |
865 | `(("r-mass" ,r-mass) | |
866 | ("r-survival" ,r-survival))) | |
867 | (home-page "http://riskassessment.r-forge.r-project.org") | |
868 | (synopsis "Fitting a parametric distribution from data") | |
869 | (description | |
870 | "This package extends the @code{fitdistr} function of the MASS package | |
871 | with several functions to help the fit of a parametric distribution to | |
872 | non-censored or censored data. Censored data may contain left-censored, | |
873 | right-censored and interval-censored values, with several lower and upper | |
874 | bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package | |
875 | provides moment matching (MME), quantile matching (QME) and maximum | |
876 | goodness-of-fit estimation (MGE) methods (available only for non-censored | |
877 | data). Weighted versions of MLE, MME and QME are available.") | |
878 | (license license:gpl2+))) | |
8d220073 RW |
879 | |
880 | (define-public r-energy | |
881 | (package | |
882 | (name "r-energy") | |
65eb1c4a | 883 | (version "1.7-2") |
8d220073 RW |
884 | (source |
885 | (origin | |
886 | (method url-fetch) | |
887 | (uri (cran-uri "energy" version)) | |
888 | (sha256 | |
889 | (base32 | |
65eb1c4a | 890 | "19c7bgjnm4ggf7w5mk64c5shkma3sa9wc8x117iqv7pk1bvvyy3p")))) |
8d220073 RW |
891 | (build-system r-build-system) |
892 | (propagated-inputs | |
893 | `(("r-boot" ,r-boot) | |
894 | ("r-rcpp" ,r-rcpp))) | |
e9960d8c | 895 | (home-page "https://cran.r-project.org/web/packages/energy") |
8d220073 RW |
896 | (synopsis "Multivariate inference via the energy of data") |
897 | (description | |
898 | "This package provides e-statistics (energy) tests and statistics for | |
899 | multivariate and univariate inference, including distance correlation, | |
900 | one-sample, two-sample, and multi-sample tests for comparing multivariate | |
901 | distributions, are implemented. Measuring and testing multivariate | |
902 | independence based on distance correlation, partial distance correlation, | |
903 | multivariate goodness-of-fit tests, clustering based on energy distance, | |
904 | testing for multivariate normality, distance components (disco) for | |
905 | non-parametric analysis of structured data, and other energy | |
906 | statistics/methods are implemented.") | |
907 | (license license:gpl2+))) | |
abcb8494 RW |
908 | |
909 | (define-public r-suppdists | |
910 | (package | |
911 | (name "r-suppdists") | |
912 | (version "1.1-9.4") | |
913 | (source | |
914 | (origin | |
915 | (method url-fetch) | |
916 | (uri (cran-uri "SuppDists" version)) | |
917 | (sha256 | |
918 | (base32 | |
919 | "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw")))) | |
920 | (properties `((upstream-name . "SuppDists"))) | |
921 | (build-system r-build-system) | |
e9960d8c | 922 | (home-page "https://cran.r-project.org/web/packages/SuppDists") |
abcb8494 RW |
923 | (synopsis "Supplementary distributions") |
924 | (description | |
925 | "This package provides ten distributions supplementing those built into | |
926 | R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, | |
927 | Spearman's rho, maximum F ratio, the Pearson product moment correlation | |
928 | coefficient, Johnson distributions, normal scores and generalized | |
929 | hypergeometric distributions. In addition two random number generators of | |
930 | George Marsaglia are included.") | |
931 | (license license:gpl2+))) | |
05e8a3ef RW |
932 | |
933 | (define-public r-ksamples | |
934 | (package | |
935 | (name "r-ksamples") | |
c62276b2 | 936 | (version "1.2-7") |
05e8a3ef RW |
937 | (source |
938 | (origin | |
939 | (method url-fetch) | |
940 | (uri (cran-uri "kSamples" version)) | |
941 | (sha256 | |
942 | (base32 | |
c62276b2 | 943 | "0f19rjngk0lg6s8c6h5l55qpxp8sl4vxj3kpi05cizzncny9b9bj")))) |
05e8a3ef RW |
944 | (properties `((upstream-name . "kSamples"))) |
945 | (build-system r-build-system) | |
946 | (propagated-inputs | |
947 | `(("r-suppdists" ,r-suppdists))) | |
e9960d8c | 948 | (home-page "https://cran.r-project.org/web/packages/kSamples") |
05e8a3ef RW |
949 | (synopsis "K-Sample rank tests and their combinations") |
950 | (description | |
951 | "This package provides tools to compares k samples using the | |
952 | Anderson-Darling test, Kruskal-Wallis type tests with different rank score | |
953 | criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT) | |
954 | test. It computes asymptotic, simulated or (limited) exact P-values, all | |
955 | valid under randomization, with or without ties, or conditionally under random | |
956 | sampling from populations, given the observed tie pattern. Except for Steel's | |
957 | test and the JT test it also combines these tests across several blocks of | |
958 | samples.") | |
959 | (license license:gpl2+))) | |
f97ce815 RW |
960 | |
961 | (define-public r-cvst | |
962 | (package | |
963 | (name "r-cvst") | |
964 | (version "0.2-1") | |
965 | (source | |
966 | (origin | |
967 | (method url-fetch) | |
968 | (uri (cran-uri "CVST" version)) | |
969 | (sha256 | |
970 | (base32 | |
971 | "17xacyi8cf37rr2xswx96qy7pwkaqq394awdlswykz3qlyzx4zx2")))) | |
972 | (properties `((upstream-name . "CVST"))) | |
973 | (build-system r-build-system) | |
974 | (propagated-inputs | |
975 | `(("r-kernlab" ,r-kernlab) | |
976 | ("r-matrix" ,r-matrix))) | |
e9960d8c | 977 | (home-page "https://cran.r-project.org/web/packages/CVST") |
f97ce815 RW |
978 | (synopsis "Fast cross-validation via sequential testing") |
979 | (description | |
980 | "This package implements the fast cross-validation via sequential | |
981 | testing (CVST) procedure. CVST is an improved cross-validation procedure | |
982 | which uses non-parametric testing coupled with sequential analysis to | |
983 | determine the best parameter set on linearly increasing subsets of the data. | |
984 | Additionally to the CVST the package contains an implementation of the | |
985 | ordinary k-fold cross-validation with a flexible and powerful set of helper | |
986 | objects and methods to handle the overall model selection process. The | |
987 | implementations of the Cochran's Q test with permutations and the sequential | |
988 | testing framework of Wald are generic and can therefore also be used in other | |
989 | contexts.") | |
990 | (license license:gpl2+))) | |
797e1dfb RW |
991 | |
992 | (define-public r-lava | |
993 | (package | |
994 | (name "r-lava") | |
7ef9e146 | 995 | (version "1.5.1") |
797e1dfb RW |
996 | (source |
997 | (origin | |
998 | (method url-fetch) | |
999 | (uri (cran-uri "lava" version)) | |
1000 | (sha256 | |
1001 | (base32 | |
7ef9e146 | 1002 | "1vcm04h9i39gmf2prl5d4j4il4gs6skzr6y2fvl1vn4hklna87f4")))) |
797e1dfb RW |
1003 | (build-system r-build-system) |
1004 | (propagated-inputs | |
1005 | `(("r-numderiv" ,r-numderiv) | |
1006 | ("r-survival" ,r-survival))) | |
1007 | (home-page "https://github.com/kkholst/lava") | |
1008 | (synopsis "Latent variable models") | |
1009 | (description | |
1010 | "This package provides tools for the estimation and simulation of latent | |
1011 | variable models.") | |
1012 | (license license:gpl3))) | |
d26b7c1b RW |
1013 | |
1014 | (define-public r-drr | |
1015 | (package | |
1016 | (name "r-drr") | |
1017 | (version "0.0.2") | |
1018 | (source | |
1019 | (origin | |
1020 | (method url-fetch) | |
1021 | (uri (cran-uri "DRR" version)) | |
1022 | (sha256 | |
1023 | (base32 | |
1024 | "1scfwp6ry6apxzqjclsmn2frxp9qfw6zxsxn5w0j0q3sz42hz1h2")))) | |
1025 | (properties `((upstream-name . "DRR"))) | |
1026 | (build-system r-build-system) | |
1027 | (propagated-inputs | |
1028 | `(("r-cvst" ,r-cvst) | |
1029 | ("r-kernlab" ,r-kernlab) | |
1030 | ("r-matrix" ,r-matrix))) | |
e9960d8c | 1031 | (home-page "https://cran.r-project.org/web/packages/DRR") |
d26b7c1b RW |
1032 | (synopsis "Dimensionality reduction via regression") |
1033 | (description | |
1034 | "This package provides an implementation of dimensionality reduction via | |
1035 | regression using Kernel Ridge Regression.") | |
1036 | (license license:gpl3))) | |
9dd707f0 RW |
1037 | |
1038 | (define-public r-prodlim | |
1039 | (package | |
1040 | (name "r-prodlim") | |
1041 | (version "1.6.1") | |
1042 | (source | |
1043 | (origin | |
1044 | (method url-fetch) | |
1045 | (uri (cran-uri "prodlim" version)) | |
1046 | (sha256 | |
1047 | (base32 | |
1048 | "0m51rkivx1zr6whdqwj66jpnkmp4385m06kkha3dp8qqf4jna9iz")))) | |
1049 | (build-system r-build-system) | |
1050 | (propagated-inputs | |
1051 | `(("r-kernsmooth" ,r-kernsmooth) | |
1052 | ("r-lava" ,r-lava) | |
1053 | ("r-rcpp" ,r-rcpp) | |
1054 | ("r-survival" ,r-survival))) | |
e9960d8c | 1055 | (home-page "https://cran.r-project.org/web/packages/prodlim") |
9dd707f0 RW |
1056 | (synopsis "Product-limit estimation for censored event history analysis") |
1057 | (description | |
1058 | "This package provides a fast and user-friendly implementation of | |
1059 | nonparametric estimators for censored event history (survival) analysis with | |
1060 | the Kaplan-Meier and Aalen-Johansen methods.") | |
1061 | (license license:gpl2+))) | |
b561f563 RW |
1062 | |
1063 | (define-public r-dimred | |
1064 | (package | |
1065 | (name "r-dimred") | |
1066 | (version "0.1.0") | |
1067 | (source | |
1068 | (origin | |
1069 | (method url-fetch) | |
1070 | (uri (cran-uri "dimRed" version)) | |
1071 | (sha256 | |
1072 | (base32 | |
1073 | "0fasca5fsbrxdwv30hch7vb9snb844l7l8p5fjf239dq45xfy37v")))) | |
1074 | (properties `((upstream-name . "dimRed"))) | |
1075 | (build-system r-build-system) | |
1076 | (propagated-inputs `(("r-drr" ,r-drr))) | |
1077 | (home-page "https://github.com/gdkrmr/dimRed") | |
1078 | (synopsis "Framework for dimensionality reduction") | |
1079 | (description | |
1080 | "This package provides a collection of dimensionality reduction | |
1081 | techniques from R packages and provides a common interface for calling the | |
1082 | methods.") | |
1083 | (license license:gpl3))) | |
1b663184 RW |
1084 | |
1085 | (define-public r-timedate | |
1086 | (package | |
1087 | (name "r-timedate") | |
26007cd5 | 1088 | (version "3042.101") |
1b663184 RW |
1089 | (source |
1090 | (origin | |
1091 | (method url-fetch) | |
1092 | (uri (cran-uri "timeDate" version)) | |
1093 | (sha256 | |
1094 | (base32 | |
26007cd5 | 1095 | "0vcckaw1gqz3j4v69r9jn41vlmk5a5c7572xam1nl75ki5v4r3bc")))) |
1b663184 RW |
1096 | (properties `((upstream-name . "timeDate"))) |
1097 | (build-system r-build-system) | |
1098 | (home-page "https://www.rmetrics.org") | |
1099 | (synopsis "Chronological and calendar objects") | |
1100 | (description | |
1101 | "This package provides an environment for teaching \"Financial | |
1102 | Engineering and Computational Finance\" and for managing chronological and | |
1103 | calendar objects.") | |
1104 | (license license:gpl2+))) | |
f57b883e RW |
1105 | |
1106 | (define-public r-ddalpha | |
1107 | (package | |
1108 | (name "r-ddalpha") | |
e90456b9 | 1109 | (version "1.3.1") |
f57b883e RW |
1110 | (source |
1111 | (origin | |
1112 | (method url-fetch) | |
1113 | (uri (cran-uri "ddalpha" version)) | |
1114 | (sha256 | |
1115 | (base32 | |
e90456b9 | 1116 | "0pczw9543y7f92m7gyk7rxcjn8vsjaldc5vl0r56ywip9i374zbh")))) |
f57b883e RW |
1117 | (build-system r-build-system) |
1118 | (propagated-inputs | |
1119 | `(("r-bh" ,r-bh) | |
1120 | ("r-class" ,r-class) | |
1121 | ("r-mass" ,r-mass) | |
1122 | ("r-rcpp" ,r-rcpp) | |
e90456b9 RW |
1123 | ("r-robustbase" ,r-robustbase) |
1124 | ("r-sfsmisc" ,r-sfsmisc))) | |
1125 | (native-inputs | |
1126 | `(("gfortran" ,gfortran))) | |
e9960d8c | 1127 | (home-page "https://cran.r-project.org/web/packages/ddalpha") |
f57b883e RW |
1128 | (synopsis "Depth-Based classification and calculation of data depth") |
1129 | (description | |
1130 | "This package contains procedures for depth-based supervised learning, | |
1131 | which are entirely non-parametric, in particular the DDalpha-procedure (Lange, | |
1132 | Mosler and Mozharovskyi, 2014). The training data sample is transformed by a | |
1133 | statistical depth function to a compact low-dimensional space, where the final | |
1134 | classification is done. It also offers an extension to functional data and | |
1135 | routines for calculating certain notions of statistical depth functions. 50 | |
1136 | multivariate and 5 functional classification problems are included.") | |
1137 | (license license:gpl2))) | |
5a87093f RW |
1138 | |
1139 | (define-public r-gower | |
1140 | (package | |
1141 | (name "r-gower") | |
1142 | (version "0.1.2") | |
1143 | (source | |
1144 | (origin | |
1145 | (method url-fetch) | |
1146 | (uri (cran-uri "gower" version)) | |
1147 | (sha256 | |
1148 | (base32 | |
1149 | "1mbrj1lam3jfbby2j32shmmj5cn09zx3rkxbamq7q8sdg39b54gb")))) | |
1150 | (build-system r-build-system) | |
1151 | (native-inputs | |
1152 | `(("r-knitr" ,r-knitr))) | |
1153 | (home-page "https://github.com/markvanderloo/gower") | |
1154 | (synopsis "Gower's distance") | |
1155 | (description | |
1156 | "This package provides tools to compute Gower's distance (or similarity) | |
1157 | coefficient between records, and to compute the top-n matches between records. | |
1158 | Core algorithms are executed in parallel on systems supporting OpenMP.") | |
1159 | (license license:gpl3))) | |
649cf27c RW |
1160 | |
1161 | (define-public r-rcpproll | |
1162 | (package | |
1163 | (name "r-rcpproll") | |
1164 | (version "0.2.2") | |
1165 | (source | |
1166 | (origin | |
1167 | (method url-fetch) | |
1168 | (uri (cran-uri "RcppRoll" version)) | |
1169 | (sha256 | |
1170 | (base32 | |
1171 | "19xzvxym8zbighndygkq4imfwc0abh4hqyq3qrr8aakyd096iisi")))) | |
1172 | (properties `((upstream-name . "RcppRoll"))) | |
1173 | (build-system r-build-system) | |
1174 | (propagated-inputs | |
1175 | `(("r-rcpp" ,r-rcpp))) | |
e9960d8c | 1176 | (home-page "https://cran.r-project.org/web/packages/RcppRoll") |
649cf27c RW |
1177 | (synopsis "Efficient rolling and windowed operations") |
1178 | (description | |
1179 | "This package provides fast and efficient routines for common rolling / | |
1180 | windowed operations. Routines for the efficient computation of windowed mean, | |
1181 | median, sum, product, minimum, maximum, standard deviation and variance are | |
1182 | provided.") | |
1183 | (license license:gpl2+))) | |
6c3d42d6 RW |
1184 | |
1185 | (define-public r-ipred | |
1186 | (package | |
1187 | (name "r-ipred") | |
1188 | (version "0.9-6") | |
1189 | (source | |
1190 | (origin | |
1191 | (method url-fetch) | |
1192 | (uri (cran-uri "ipred" version)) | |
1193 | (sha256 | |
1194 | (base32 | |
1195 | "1vrw1pqcpnc04x1r2h9grdfm6bivs358sww5gg90jwlvxcw69lxq")))) | |
1196 | (build-system r-build-system) | |
1197 | (propagated-inputs | |
1198 | `(("r-class" ,r-class) | |
1199 | ("r-mass" ,r-mass) | |
1200 | ("r-nnet" ,r-nnet) | |
1201 | ("r-prodlim" ,r-prodlim) | |
1202 | ("r-rpart" ,r-rpart) | |
1203 | ("r-survival" ,r-survival))) | |
e9960d8c | 1204 | (home-page "https://cran.r-project.org/web/packages/ipred") |
6c3d42d6 RW |
1205 | (synopsis "Improved predictors") |
1206 | (description | |
1207 | "This package provides improved predictive models by indirect | |
1208 | classification and bagging for classification, regression and survival | |
1209 | problems as well as resampling based estimators of prediction error.") | |
1210 | (license license:gpl2+))) | |
ba4527ab | 1211 | |
cdc129dc RW |
1212 | (define-public r-psych |
1213 | (package | |
1214 | (name "r-psych") | |
1215 | (version "1.7.8") | |
1216 | (source | |
1217 | (origin | |
1218 | (method url-fetch) | |
1219 | (uri (cran-uri "psych" version)) | |
1220 | (sha256 | |
1221 | (base32 | |
1222 | "0daismb8pdk392vdy304hqx0m3jx62gx3a0hygjygc125rhfla7k")))) | |
1223 | (build-system r-build-system) | |
1224 | (propagated-inputs | |
1225 | `(("r-foreign" ,r-foreign) | |
1226 | ("r-lattice" ,r-lattice) | |
1227 | ("r-mnormt" ,r-mnormt) | |
1228 | ("r-nlme" ,r-nlme))) | |
e9960d8c | 1229 | (home-page "https://cran.r-project.org/web/packages/psych/") |
cdc129dc RW |
1230 | (synopsis "Procedures for psychological, psychometric, and personality research") |
1231 | (description | |
1232 | "This package provides a general purpose toolbox for personality, | |
1233 | psychometric theory and experimental psychology. Functions are primarily for | |
1234 | multivariate analysis and scale construction using factor analysis, principal | |
1235 | component analysis, cluster analysis and reliability analysis, although others | |
1236 | provide basic descriptive statistics. Item Response Theory is done using | |
1237 | factor analysis of tetrachoric and polychoric correlations. Functions for | |
1238 | analyzing data at multiple levels include within and between group statistics, | |
1239 | including correlations and factor analysis. Functions for simulating and | |
1240 | testing particular item and test structures are included. Several functions | |
1241 | serve as a useful front end for structural equation modeling. Graphical | |
1242 | displays of path diagrams, factor analysis and structural equation models are | |
1243 | created using basic graphics.") | |
1244 | (license license:gpl2+))) | |
1245 | ||
6c8c8c6b RW |
1246 | (define-public r-broom |
1247 | (package | |
1248 | (name "r-broom") | |
1249 | (version "0.4.3") | |
1250 | (source | |
1251 | (origin | |
1252 | (method url-fetch) | |
1253 | (uri (cran-uri "broom" version)) | |
1254 | (sha256 | |
1255 | (base32 | |
1256 | "119pc2jnxvm13cvd77c7d14p3bn68f4jm310vj3yfck40101n9if")))) | |
1257 | (build-system r-build-system) | |
1258 | (propagated-inputs | |
1259 | `(("r-dplyr" ,r-dplyr) | |
1260 | ("r-nlme" ,r-nlme) | |
1261 | ("r-plyr" ,r-plyr) | |
1262 | ("r-psych" ,r-psych) | |
1263 | ("r-reshape2" ,r-reshape2) | |
1264 | ("r-stringr" ,r-stringr) | |
1265 | ("r-tidyr" ,r-tidyr))) | |
1266 | (home-page "http://github.com/tidyverse/broom") | |
1267 | (synopsis "Convert statistical analysis objects into tidy data frames") | |
1268 | (description | |
1269 | "This package provides tools to convert statistical analysis objects from | |
1270 | R into tidy data frames, so that they can more easily be combined, reshaped | |
1271 | and otherwise processed with tools like @code{dplyr}, @code{tidyr} and | |
1272 | @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which | |
1273 | summarizes a model's statistical findings such as coefficients of a | |
1274 | regression; @code{augment}, which adds columns to the original data such as | |
1275 | predictions, residuals and cluster assignments; and @code{glance}, which | |
1276 | provides a one-row summary of model-level statistics.") | |
1277 | (license license:expat))) | |
1278 | ||
ba4527ab RW |
1279 | (define-public r-recipes |
1280 | (package | |
1281 | (name "r-recipes") | |
18a11c6d | 1282 | (version "0.1.1") |
ba4527ab RW |
1283 | (source |
1284 | (origin | |
1285 | (method url-fetch) | |
1286 | (uri (cran-uri "recipes" version)) | |
1287 | (sha256 | |
1288 | (base32 | |
18a11c6d | 1289 | "0id46c7iaf49miw4kxpidsbg3hdywav43n1lh2zd1vg5946bzg04")))) |
ba4527ab RW |
1290 | (build-system r-build-system) |
1291 | (propagated-inputs | |
18a11c6d RW |
1292 | `(("r-broom" ,r-broom) |
1293 | ("r-ddalpha" ,r-ddalpha) | |
ba4527ab RW |
1294 | ("r-dimred" ,r-dimred) |
1295 | ("r-dplyr" ,r-dplyr) | |
1296 | ("r-gower" ,r-gower) | |
1297 | ("r-ipred" ,r-ipred) | |
1298 | ("r-lubridate" ,r-lubridate) | |
1299 | ("r-magrittr" ,r-magrittr) | |
18a11c6d | 1300 | ("r-matrix" ,r-matrix) |
ba4527ab RW |
1301 | ("r-purrr" ,r-purrr) |
1302 | ("r-rcpproll" ,r-rcpproll) | |
1303 | ("r-rlang" ,r-rlang) | |
1304 | ("r-tibble" ,r-tibble) | |
1305 | ("r-tidyselect" ,r-tidyselect) | |
1306 | ("r-timedate" ,r-timedate))) | |
1307 | (home-page "https://github.com/topepo/recipes") | |
1308 | (synopsis "Preprocessing tools to create design matrices") | |
1309 | (description | |
1310 | "Recipes is an extensible framework to create and preprocess design | |
1311 | matrices. Recipes consist of one or more data manipulation and analysis | |
1312 | \"steps\". Statistical parameters for the steps can be estimated from an | |
1313 | initial data set and then applied to other data sets. The resulting design | |
1314 | matrices can then be used as inputs into statistical or machine learning | |
1315 | models.") | |
1316 | (license license:gpl2))) | |
1ab867be RW |
1317 | |
1318 | (define-public r-pdist | |
1319 | (package | |
1320 | (name "r-pdist") | |
1321 | (version "1.2") | |
1322 | (source | |
1323 | (origin | |
1324 | (method url-fetch) | |
1325 | (uri (cran-uri "pdist" version)) | |
1326 | (sha256 | |
1327 | (base32 | |
1328 | "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd")))) | |
1329 | (build-system r-build-system) | |
1330 | (home-page "https://github.com/jeffwong/pdist") | |
1331 | (synopsis "Partitioned distance function") | |
1332 | (description | |
1333 | "Pdist computes the euclidean distance between rows of a matrix X and | |
1334 | rows of another matrix Y. Previously, this could be done by binding the two | |
1335 | matrices together and calling @code{dist}, but this creates unnecessary | |
1336 | computation by computing the distances between a row of X and another row of | |
1337 | X, and likewise for Y. Pdist strictly computes distances across the two | |
1338 | matrices, not within the same matrix, making computations significantly faster | |
1339 | for certain use cases.") | |
1340 | (license license:gpl3+))) | |
81e0b625 RW |
1341 | |
1342 | (define-public r-ggrepel | |
1343 | (package | |
1344 | (name "r-ggrepel") | |
1345 | (version "0.7.0") | |
1346 | (source | |
1347 | (origin | |
1348 | (method url-fetch) | |
1349 | (uri (cran-uri "ggrepel" version)) | |
1350 | (sha256 | |
1351 | (base32 | |
1352 | "0g0qfm6g71rv27423c1x846ipilnj213knyzrcr09vrpxc87l618")))) | |
1353 | (build-system r-build-system) | |
1354 | (propagated-inputs | |
1355 | `(("r-ggplot2" ,r-ggplot2) | |
1356 | ("r-rcpp" ,r-rcpp) | |
1357 | ("r-scales" ,r-scales))) | |
1358 | (home-page "http://github.com/slowkow/ggrepel") | |
1359 | (synopsis "Repulsive text and label geometries for ggplot2") | |
1360 | (description | |
1361 | "This package provides text and label geometries for ggplot2 that help to | |
1362 | avoid overlapping text labels. Labels repel away from each other and away | |
1363 | from the data points.") | |
1364 | (license license:gpl3))) | |
6b968c4c RW |
1365 | |
1366 | (define-public r-corrplot | |
1367 | (package | |
1368 | (name "r-corrplot") | |
1369 | (version "0.84") | |
1370 | (source | |
1371 | (origin | |
1372 | (method url-fetch) | |
1373 | (uri (cran-uri "corrplot" version)) | |
1374 | (sha256 | |
1375 | (base32 | |
1376 | "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd")))) | |
1377 | (build-system r-build-system) | |
1378 | (home-page "https://github.com/taiyun/corrplot") | |
1379 | (synopsis "Visualization of a correlation matrix") | |
1380 | (description | |
1381 | "This package provides a graphical display of a correlation matrix or | |
1382 | general matrix. It also contains some algorithms to do matrix reordering. In | |
1383 | addition, corrplot is good at details, including choosing color, text labels, | |
1384 | color labels, layout, etc.") | |
1385 | ;; Any version of the GPL | |
1386 | (license license:gpl2+))) | |
a40a04fd RW |
1387 | |
1388 | (define-public r-stringdist | |
1389 | (package | |
1390 | (name "r-stringdist") | |
1391 | (version "0.9.4.6") | |
1392 | (source | |
1393 | (origin | |
1394 | (method url-fetch) | |
1395 | (uri (cran-uri "stringdist" version)) | |
1396 | (sha256 | |
1397 | (base32 | |
1398 | "0j5b7hr53nr9xq44famkpwzi4khix93ffani5pwldqkf8bpdvhci")))) | |
1399 | (build-system r-build-system) | |
1400 | (home-page "https://github.com/markvanderloo/stringdist") | |
1401 | (synopsis "Approximate string matching and string distance functions") | |
1402 | (description | |
1403 | "This package implements an approximate string matching version of R's | |
1404 | native @code{match} function. It can calculate various string distances based | |
1405 | on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), | |
1406 | qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro, | |
1407 | Jaro-Winkler). An implementation of soundex is provided as well. Distances | |
1408 | can be computed between character vectors while taking proper care of encoding | |
1409 | or between integer vectors representing generic sequences.") | |
1410 | (license license:gpl3+))) | |
10e16fa9 RW |
1411 | |
1412 | (define-public r-mice | |
1413 | (package | |
1414 | (name "r-mice") | |
1415 | (version "2.46.0") | |
1416 | (source | |
1417 | (origin | |
1418 | (method url-fetch) | |
1419 | (uri (cran-uri "mice" version)) | |
1420 | (sha256 | |
1421 | (base32 | |
1422 | "1gjvlk67zvgipfczsca8zqk97vg3sivv82hblsdwp14s7smhjcax")))) | |
1423 | (build-system r-build-system) | |
1424 | (propagated-inputs | |
1425 | `(("r-lattice" ,r-lattice) | |
1426 | ("r-mass" ,r-mass) | |
1427 | ("r-nnet" ,r-nnet) | |
1428 | ("r-rcpp" ,r-rcpp) | |
1429 | ("r-rpart" ,r-rpart) | |
1430 | ("r-survival" ,r-survival))) | |
1431 | (home-page "https://cran.r-project.org/web/packages/mice/") | |
1432 | (synopsis "Multivariate imputation by chained equations") | |
1433 | (description | |
1434 | "Multiple imputation using @dfn{Fully Conditional Specification} (FCS) | |
1435 | implemented by the MICE algorithm as described in @url{Van Buuren and | |
1436 | Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each | |
1437 | variable has its own imputation model. Built-in imputation models are | |
1438 | provided for continuous data (predictive mean matching, normal), binary | |
1439 | data (logistic regression), unordered categorical data (polytomous logistic | |
1440 | regression) and ordered categorical data (proportional odds). MICE can also | |
1441 | impute continuous two-level data (normal model, pan, second-level variables). | |
1442 | Passive imputation can be used to maintain consistency between variables. | |
1443 | Various diagnostic plots are available to inspect the quality of the | |
1444 | imputations.") | |
1445 | ;; Any of these two versions. | |
1446 | (license (list license:gpl2 license:gpl3)))) | |
7fd5f60b | 1447 | |
02cdb45f RW |
1448 | (define-public r-truncnorm |
1449 | (package | |
1450 | (name "r-truncnorm") | |
1451 | (version "1.0-7") | |
1452 | (source | |
1453 | (origin | |
1454 | (method url-fetch) | |
1455 | (uri (cran-uri "truncnorm" version)) | |
1456 | (sha256 | |
1457 | (base32 | |
1458 | "1qac05z50618y4bw1d7yznsli1bv82s0g8h37iacrjrdkv87bmy7")))) | |
1459 | (build-system r-build-system) | |
e9960d8c | 1460 | (home-page "https://cran.r-project.org/web/packages/truncnorm/") |
02cdb45f RW |
1461 | (synopsis "Truncated normal distribution") |
1462 | (description "This package provides functions for the truncated normal | |
1463 | distribution with mean equal to @code{mean} and standard deviation equal to | |
1464 | @code{sd}. It includes density, distribution, quantile, and expected value | |
1465 | functions, as well as a random generation function.") | |
1466 | (license license:gpl2))) | |
1467 | ||
cb8b4c11 RW |
1468 | (define-public r-rsolnp |
1469 | (package | |
1470 | (name "r-rsolnp") | |
1471 | (version "1.16") | |
1472 | (source | |
1473 | (origin | |
1474 | (method url-fetch) | |
1475 | (uri (cran-uri "Rsolnp" version)) | |
1476 | (sha256 | |
1477 | (base32 | |
1478 | "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii")))) | |
1479 | (properties `((upstream-name . "Rsolnp"))) | |
1480 | (build-system r-build-system) | |
1481 | (propagated-inputs | |
1482 | `(("r-truncnorm" ,r-truncnorm))) | |
e9960d8c | 1483 | (home-page "https://cran.r-project.org/web/packages/Rsolnp/") |
cb8b4c11 RW |
1484 | (synopsis "General non-linear optimization") |
1485 | (description "The Rsolnp package implements a general non-linear augmented | |
1486 | Lagrange multiplier method solver, a @dfn{sequential quadratic | |
1487 | programming} (SQP) based solver).") | |
1488 | ;; Any version of the GPL. | |
1489 | (license license:gpl2+))) | |
1490 | ||
7fd5f60b RW |
1491 | (define-public r-hardyweinberg |
1492 | (package | |
1493 | (name "r-hardyweinberg") | |
d0394944 | 1494 | (version "1.5.9") |
7fd5f60b RW |
1495 | (source |
1496 | (origin | |
1497 | (method url-fetch) | |
1498 | (uri (cran-uri "HardyWeinberg" version)) | |
1499 | (sha256 | |
1500 | (base32 | |
d0394944 | 1501 | "0qk3lly5qczn61rj0q9xzscppspvk238yjgr4p71pkzkjhiv40jz")))) |
7fd5f60b RW |
1502 | (properties `((upstream-name . "HardyWeinberg"))) |
1503 | (build-system r-build-system) | |
1504 | (propagated-inputs | |
1505 | `(("r-mice" ,r-mice) | |
d0394944 RW |
1506 | ("r-rcpp" ,r-rcpp) |
1507 | ("r-rsolnp" ,r-rsolnp))) | |
7fd5f60b RW |
1508 | (home-page "https://cran.r-project.org/package=HardyWeinberg") |
1509 | (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium") | |
1510 | (description | |
1511 | "This package contains tools for exploring Hardy-Weinberg equilibrium for | |
1512 | diallelic genetic marker data. All classical tests (chi-square, exact, | |
1513 | likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are | |
1514 | included in the package, as well as functions for power computation and for | |
1515 | the simulation of marker data under equilibrium and disequilibrium. Routines | |
1516 | for dealing with markers on the X-chromosome are included. Functions for | |
1517 | testing equilibrium in the presence of missing data by using multiple | |
1518 | imputation are also provided. Implements several graphics for exploring the | |
1519 | equilibrium status of a large set of diallelic markers: ternary plots with | |
1520 | acceptance regions, log-ratio plots and Q-Q plots.") | |
1521 | (license license:gpl2+))) | |
3a22732c RW |
1522 | |
1523 | (define-public r-sm | |
1524 | (package | |
1525 | (name "r-sm") | |
1526 | (version "2.2-5.4") | |
1527 | (source | |
1528 | (origin | |
1529 | (method url-fetch) | |
1530 | (uri (cran-uri "sm" version)) | |
1531 | (sha256 | |
1532 | (base32 | |
1533 | "0hnq5s2fv94gaj0nyqc1vjdjd64vsp9z23nqa8hxvjcaf996rwj9")))) | |
1534 | (build-system r-build-system) | |
1535 | (native-inputs `(("gfortran" ,gfortran))) | |
1536 | (home-page "http://www.stats.gla.ac.uk/~adrian/sm/") | |
1537 | (synopsis "Smoothing methods for nonparametric regression and density estimation") | |
1538 | (description | |
1539 | "This is software accompanying the book 'Applied Smoothing Techniques for | |
1540 | Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford | |
1541 | University Press. It provides smoothing methods for nonparametric regression | |
1542 | and density estimation") | |
1543 | (license license:gpl2+))) | |
9232cac4 RW |
1544 | |
1545 | (define-public r-vioplot | |
1546 | (package | |
1547 | (name "r-vioplot") | |
1548 | (version "0.2") | |
1549 | (source | |
1550 | (origin | |
1551 | (method url-fetch) | |
1552 | (uri (cran-uri "vioplot" version)) | |
1553 | (sha256 | |
1554 | (base32 | |
1555 | "16wkb26kv6qr34hv5zgqmgq6zzgysg9i78pvy2c097lr60v087v0")))) | |
1556 | (build-system r-build-system) | |
1557 | (propagated-inputs `(("r-sm" ,r-sm))) | |
1558 | (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler") | |
1559 | (synopsis "Violin plot") | |
1560 | (description | |
1561 | "This package provides a violin plot, which is a combination of a box | |
1562 | plot and a kernel density plot.") | |
1563 | (license license:bsd-3))) | |
7b0569c0 RW |
1564 | |
1565 | (define-public r-rsofia | |
1566 | (package | |
1567 | (name "r-rsofia") | |
1568 | (version "1.1") | |
1569 | (source (origin | |
1570 | (method url-fetch) | |
1571 | ;; This package has been removed from CRAN, so we can | |
1572 | ;; only fetch it from the archives. | |
1573 | (uri (string-append "https://cran.r-project.org/src/" | |
1574 | "contrib/Archive/RSofia/RSofia_" | |
1575 | version ".tar.gz")) | |
1576 | (sha256 | |
1577 | (base32 | |
1578 | "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn")))) | |
1579 | (properties `((upstream-name . "RSofia"))) | |
1580 | (build-system r-build-system) | |
1581 | (propagated-inputs | |
1582 | `(("r-rcpp" ,r-rcpp))) | |
1583 | (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia") | |
1584 | (synopsis "Port of sofia-ml to R") | |
1585 | (description "This package is a port of sofia-ml to R. Sofia-ml is a | |
1586 | suite of fast incremental algorithms for machine learning that can be used for | |
1587 | training models for classification or ranking.") | |
1588 | (license license:asl2.0))) | |
738dda83 | 1589 | |
3699383e RW |
1590 | (define-public r-xts |
1591 | (package | |
1592 | (name "r-xts") | |
0796954b | 1593 | (version "0.10-1") |
3699383e RW |
1594 | (source |
1595 | (origin | |
1596 | (method url-fetch) | |
1597 | (uri (cran-uri "xts" version)) | |
1598 | (sha256 | |
1599 | (base32 | |
0796954b | 1600 | "1j9ddh9v9081zrqlpylsk13fldilhjdyaw6r6pa726fhgnrsf8a2")))) |
3699383e RW |
1601 | (build-system r-build-system) |
1602 | (propagated-inputs `(("r-zoo" ,r-zoo))) | |
1603 | (native-inputs `(("gfortran" ,gfortran))) | |
1604 | (home-page "https://github.com/joshuaulrich/xts") | |
1605 | (synopsis "Extensible time series") | |
1606 | (description | |
1607 | "This package provides for uniform handling of R's different time-based | |
1608 | data classes by extending @code{zoo}, maximizing native format information | |
1609 | preservation and allowing for user-level customization and extension, while | |
1610 | simplifying cross-class interoperability.") | |
1611 | (license license:gpl2+))) | |
b72b42cf RW |
1612 | |
1613 | (define-public r-performanceanalytics | |
1614 | (package | |
1615 | (name "r-performanceanalytics") | |
1616 | (version "1.4.3541") | |
1617 | (source | |
1618 | (origin | |
1619 | (method url-fetch) | |
1620 | (uri (cran-uri "PerformanceAnalytics" version)) | |
1621 | (sha256 | |
1622 | (base32 | |
1623 | "1czchsccsbdfjw743j6rm101q2q01pggyl8zmlva213pwm86zb3v")))) | |
1624 | (properties | |
1625 | `((upstream-name . "PerformanceAnalytics"))) | |
1626 | (build-system r-build-system) | |
1627 | (propagated-inputs | |
1628 | `(("r-xts" ,r-xts) | |
1629 | ("r-zoo" ,r-zoo))) | |
1630 | (native-inputs `(("gfortran" ,gfortran))) | |
1631 | (home-page "http://r-forge.r-project.org/projects/returnanalytics/") | |
1632 | (synopsis "Econometric tools for performance and risk analysis") | |
1633 | (description "This is a collection of econometric functions for | |
1634 | performance and risk analysis. This package aims to aid practitioners and | |
1635 | researchers in utilizing the latest research in analysis of non-normal return | |
1636 | streams. In general, it is most tested on return (rather than price) data on | |
1637 | a regular scale, but most functions will work with irregular return data as | |
1638 | well, and increasing numbers of functions will work with P&L or price data | |
1639 | where possible.") | |
1640 | ;; Either version may be picked. | |
1641 | (license (list license:gpl2 license:gpl3)))) | |
018cf270 RW |
1642 | |
1643 | (define-public r-laeken | |
1644 | (package | |
1645 | (name "r-laeken") | |
1646 | (version "0.4.6") | |
1647 | (source | |
1648 | (origin | |
1649 | (method url-fetch) | |
1650 | (uri (cran-uri "laeken" version)) | |
1651 | (sha256 | |
1652 | (base32 | |
1653 | "1rhkv1kk508pwln1d325iq4fink2ncssps0ypxi52j9d7wk78la6")))) | |
1654 | (build-system r-build-system) | |
1655 | (propagated-inputs | |
1656 | `(("r-boot" ,r-boot) | |
1657 | ("r-mass" ,r-mass))) | |
e9960d8c | 1658 | (home-page "https://cran.r-project.org/web/packages/laeken/") |
018cf270 RW |
1659 | (synopsis "Estimation of indicators on social exclusion and poverty") |
1660 | (description "This package provides tools for the estimation of indicators | |
1661 | on social exclusion and poverty, as well as an implementation of Pareto tail | |
1662 | modeling for empirical income distributions.") | |
1663 | (license license:gpl2+))) | |
e5c17b8d RW |
1664 | |
1665 | (define-public r-vcd | |
1666 | (package | |
1667 | (name "r-vcd") | |
2960f965 | 1668 | (version "1.4-4") |
e5c17b8d RW |
1669 | (source |
1670 | (origin | |
1671 | (method url-fetch) | |
1672 | (uri (cran-uri "vcd" version)) | |
1673 | (sha256 | |
1674 | (base32 | |
2960f965 | 1675 | "1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5")))) |
e5c17b8d RW |
1676 | (build-system r-build-system) |
1677 | (propagated-inputs | |
1678 | `(("r-colorspace" ,r-colorspace) | |
1679 | ("r-lmtest" ,r-lmtest) | |
1680 | ("r-mass" ,r-mass))) | |
e9960d8c | 1681 | (home-page "https://cran.r-project.org/web/packages/vcd/") |
e5c17b8d RW |
1682 | (synopsis "Visualizing categorical data") |
1683 | (description "This package provides visualization techniques, data sets, | |
1684 | summary and inference procedures aimed particularly at categorical data. | |
1685 | Special emphasis is given to highly extensible grid graphics. The package was | |
1686 | originally inspired by the book \"Visualizing Categorical Data\" by Michael | |
1687 | Friendly and is now the main support package for a new book, \"Discrete Data | |
1688 | Analysis with R\" by Michael Friendly and David Meyer (2015).") | |
1689 | (license license:gpl2))) | |
ae164260 RW |
1690 | |
1691 | (define-public r-ica | |
1692 | (package | |
1693 | (name "r-ica") | |
1694 | (version "1.0-1") | |
1695 | (source | |
1696 | (origin | |
1697 | (method url-fetch) | |
1698 | (uri (cran-uri "ica" version)) | |
1699 | (sha256 | |
1700 | (base32 | |
1701 | "1bkl4a72l0k6gm82l3jxnib898z20cw17zg81jj39l9dn65rlmcq")))) | |
1702 | (build-system r-build-system) | |
e9960d8c | 1703 | (home-page "https://cran.r-project.org/web/packages/ica/") |
ae164260 RW |
1704 | (synopsis "Independent component analysis") |
1705 | (description "This package provides tools for @dfn{Independent Component | |
1706 | Analysis} (ICA) using various algorithms: FastICA, | |
1707 | Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization | |
1708 | of Eigenmatrices} (JADE).") | |
1709 | (license license:gpl2+))) | |
bf025ff6 RW |
1710 | |
1711 | (define-public r-dtw | |
1712 | (package | |
1713 | (name "r-dtw") | |
1714 | (version "1.18-1") | |
1715 | (source | |
1716 | (origin | |
1717 | (method url-fetch) | |
1718 | (uri (cran-uri "dtw" version)) | |
1719 | (sha256 | |
1720 | (base32 | |
1721 | "1b91vahba09cqlb8b1ry4dlv4rbldb4s2p6w52gmyw31vxdv5nnr")))) | |
1722 | (build-system r-build-system) | |
1723 | (propagated-inputs `(("r-proxy" ,r-proxy))) | |
1724 | (home-page "http://dtw.r-forge.r-project.org/") | |
1725 | (synopsis "Dynamic Time Warping Algorithms") | |
1726 | (description "This package provides a comprehensive implementation of | |
1727 | @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the | |
1728 | optimal (least cumulative distance) alignment between points of two time | |
1729 | series. Common DTW variants covered include local (slope) and global (window) | |
1730 | constraints, subsequence matches, arbitrary distance definitions, | |
1731 | normalizations, minimum variance matching, and so on.") | |
1732 | (license license:gpl2+))) | |
15ef07f0 RW |
1733 | |
1734 | (define-public r-sdmtools | |
1735 | (package | |
1736 | (name "r-sdmtools") | |
1737 | (version "1.1-221") | |
1738 | (source | |
1739 | (origin | |
1740 | (method url-fetch) | |
1741 | (uri (cran-uri "SDMTools" version)) | |
1742 | (sha256 | |
1743 | (base32 | |
1744 | "1kacrpamshv7wz83yn45sfbw4m9c44xrrngzcklnwx8gcxx2knm6")))) | |
1745 | (properties `((upstream-name . "SDMTools"))) | |
1746 | (build-system r-build-system) | |
1747 | (propagated-inputs `(("r-r-utils" ,r-r-utils))) | |
1748 | (home-page "http://www.rforge.net/SDMTools/") | |
1749 | (synopsis "Species distribution modelling tools") | |
1750 | (description "This packages provides a set of tools for post processing | |
1751 | the outcomes of species distribution modeling exercises. It includes novel | |
1752 | methods for comparing models and tracking changes in distributions through | |
1753 | time. It further includes methods for visualizing outcomes, selecting | |
1754 | thresholds, calculating measures of accuracy and landscape fragmentation | |
1755 | statistics, etc.") | |
1756 | (license license:gpl3+))) | |
ae3f2079 RW |
1757 | |
1758 | (define-public r-scatterplot3d | |
1759 | (package | |
1760 | (name "r-scatterplot3d") | |
1761 | (version "0.3-40") | |
1762 | (source | |
1763 | (origin | |
1764 | (method url-fetch) | |
1765 | (uri (cran-uri "scatterplot3d" version)) | |
1766 | (sha256 | |
1767 | (base32 | |
1768 | "0ababcj87kx7860mica9y2ydlhskxmgj9n46crx036cila512jc2")))) | |
1769 | (build-system r-build-system) | |
e9960d8c | 1770 | (home-page "https://cran.r-project.org/web/packages/scatterplot3d/") |
ae3f2079 RW |
1771 | (synopsis "3D scatter plot") |
1772 | (description "This package provides an implementation of scatter plots for | |
1773 | plotting. a three dimensional point cloud.") | |
1774 | (license license:gpl2))) | |
f90018e5 RW |
1775 | |
1776 | (define-public r-ggridges | |
1777 | (package | |
1778 | (name "r-ggridges") | |
1779 | (version "0.4.1") | |
1780 | (source | |
1781 | (origin | |
1782 | (method url-fetch) | |
1783 | (uri (cran-uri "ggridges" version)) | |
1784 | (sha256 | |
1785 | (base32 | |
1786 | "0kfa3icqdalqdg1klxjrhfl7if35d3wnsiyl86bprw5dyqyh3lh3")))) | |
1787 | (build-system r-build-system) | |
1788 | (propagated-inputs | |
1789 | `(("r-ggplot2" ,r-ggplot2) | |
1790 | ("r-plyr" ,r-plyr) | |
1791 | ("r-scales" ,r-scales))) | |
1792 | (home-page "https://github.com/clauswilke/ggridges") | |
1793 | (synopsis "Ridgeline plots in ggplot2") | |
1794 | (description | |
1795 | "Ridgeline plots provide a convenient way of visualizing changes in | |
1796 | distributions over time or space. This package enables the creation of such | |
1797 | plots in @code{ggplot2}.") | |
1798 | (license license:gpl2))) | |
007f6d98 RW |
1799 | |
1800 | (define-public r-ggjoy | |
1801 | (package | |
1802 | (name "r-ggjoy") | |
1803 | (version "0.4.0") | |
1804 | (source | |
1805 | (origin | |
1806 | (method url-fetch) | |
1807 | (uri (cran-uri "ggjoy" version)) | |
1808 | (sha256 | |
1809 | (base32 | |
1810 | "1s24zn7gmk52bvjjhanxby7rxbnc2yfl0nx5nv7x7z0zja8gg7nb")))) | |
1811 | (build-system r-build-system) | |
1812 | (propagated-inputs | |
1813 | `(("r-ggplot2" ,r-ggplot2) | |
1814 | ("r-ggridges" ,r-ggridges))) | |
1815 | (home-page "https://github.com/clauswilke/ggjoy") | |
1816 | (synopsis "Joyplots in ggplot2") | |
1817 | (description "Joyplots provide a convenient way of visualizing changes in | |
1818 | distributions over time or space. This package enables the creation of such | |
1819 | plots in @code{ggplot2}.") | |
1820 | (license license:gpl2))) | |
2976f304 RW |
1821 | |
1822 | (define-public r-cli | |
1823 | (package | |
1824 | (name "r-cli") | |
1825 | (version "1.0.0") | |
1826 | (source | |
1827 | (origin | |
1828 | (method url-fetch) | |
1829 | (uri (cran-uri "cli" version)) | |
1830 | (sha256 | |
1831 | (base32 | |
1832 | "07as3dr7vwx02p3qgzlmxz1dlrd3x3lysrzp222ip9jcjpydp8wg")))) | |
1833 | (build-system r-build-system) | |
1834 | (propagated-inputs | |
1835 | `(("r-assertthat" ,r-assertthat) | |
1836 | ("r-crayon" ,r-crayon))) | |
1837 | (home-page "https://github.com/r-lib/cli#readme") | |
1838 | (synopsis "Helpers for developing command line interfaces") | |
1839 | (description "This package provides a suite of tools designed to build | |
1840 | attractive command line interfaces (CLIs). It includes tools for drawing | |
1841 | rules, boxes, trees, and Unicode symbols with ASCII alternatives.") | |
1842 | (license license:expat))) | |
55577393 RW |
1843 | |
1844 | (define-public r-argparser | |
1845 | (package | |
1846 | (name "r-argparser") | |
1847 | (version "0.4") | |
1848 | (source | |
1849 | (origin | |
1850 | (method url-fetch) | |
1851 | (uri (cran-uri "argparser" version)) | |
1852 | (sha256 | |
1853 | (base32 | |
1854 | "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9")))) | |
1855 | (build-system r-build-system) | |
1856 | (home-page "https://bitbucket.org/djhshih/argparser") | |
1857 | (synopsis "Command-line argument parser") | |
1858 | (description | |
1859 | "This package provides a cross-platform command-line argument parser | |
1860 | written purely in R with no external dependencies. It is useful with the | |
1861 | Rscript front-end and facilitates turning an R script into an executable | |
1862 | script.") | |
1863 | (license license:gpl3+))) |