aboutsummaryrefslogtreecommitdiff
path: root/gnu/packages/statistics.scm
blob: 9acc20b5eb879355b21d541ba1e059b4b301315f (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages statistics)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix utils)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system r)
  #:use-module (gnu packages)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages icu4c)
  #:use-module (gnu packages image)
  #:use-module (gnu packages java)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages pcre)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages readline)
  #:use-module (gnu packages texlive)
  #:use-module (gnu packages texinfo)
  #:use-module (gnu packages base)
  #:use-module (gnu packages xorg))

(define-public r
  (package
    (name "r")
    (version "3.2.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://cran/src/base/R-"
                                  (version-prefix version 1) "/R-"
                                  version ".tar.gz"))
              (sha256
               (base32
                "07a6s865bjnh7w0fqsrkv1pva76w99v86w0w787qpdil87km54cw"))))
    (build-system gnu-build-system)
    (arguments
     `(#:make-flags
       (list (string-append "LDFLAGS=-Wl,-rpath="
                            (assoc-ref %outputs "out")
                            "/lib/R/lib"))
       #:phases
       (modify-phases %standard-phases
         (add-before
          'configure 'set-default-pager
          ;; Set default pager to "cat", because otherwise it is "false",
          ;; making "help()" print nothing at all.
          (lambda _ (setenv "PAGER" "cat") #t))
         (add-before
          'check 'set-timezone
          ;; Some tests require the timezone to be set.
          (lambda _ (setenv "TZ" "UTC") #t))
         (add-after 'build 'make-info
          (lambda _ (zero? (system* "make" "info"))))
         (add-after 'build 'install-info
          (lambda _ (zero? (system* "make" "install-info")))))
       #:configure-flags
       '("--with-blas=openblas"
         "--with-lapack"
         "--with-cairo"
         "--with-libpng"
         "--with-jpeglib"
         "--with-libtiff"
         "--with-ICU"
         "--enable-R-shlib"
         "--enable-BLAS-shlib"
         "--with-system-zlib"
         "--with-system-bzlib"
         "--with-system-pcre"
         "--with-system-tre"
         "--with-system-xz")))
    ;; R has some support for Java.  When the JDK is available at configure
    ;; time environment variables pointing to the JDK will be recorded under
    ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
    ;; CMD javareconf".  "R CMD javareconf" appears to only be used to update
    ;; the recorded environment variables in $R_HOME/etc.  Refer to
    ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
    ;; for additional information.

    ;; As the JDK is a rather large input with only very limited effects on R,
    ;; we decided to drop it.
    (native-inputs
     `(("bzip2" ,bzip2)
       ("perl" ,perl)
       ("pkg-config" ,pkg-config)
       ("texinfo" ,texinfo) ; for building HTML manuals
       ("which" ,which) ; for tests/Examples/base-Ex.R
       ("xz" ,xz)))
    (inputs
     `(("openblas" ,openblas)
       ("cairo" ,cairo)
       ("gfortran" ,gfortran)
       ("icu4c" ,icu4c)
       ("lapack" ,lapack)
       ("libjpeg" ,libjpeg)
       ("libpng" ,libpng)
       ("libtiff" ,libtiff)
       ("libxt" ,libxt)
       ("pcre" ,pcre)
       ("readline" ,readline)
       ("zlib" ,zlib)))
    (native-search-paths
     (list (search-path-specification
            (variable "R_LIBS_SITE")
            (files (list "site-library/")))))
    (home-page "http://www.r-project.org/")
    (synopsis "Environment for statistical computing and graphics")
    (description
     "R is a language and environment for statistical computing and graphics.
It provides a variety of statistical techniques, such as linear and nonlinear
modeling, classical statistical tests, time-series analysis, classification
and clustering.  It also provides robust support for producing
publication-quality data plots.  A large amount of 3rd-party packages are
available, greatly increasing its breadth and scope.")
    (license license:gpl3+)))

(define-public r-colorspace
  (package
    (name "r-colorspace")
    (version "1.2-6")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "colorspace" version))
       (sha256
        (base32 "0y8n4ljwhbdvkysdwgqzcnpv107pb3px1jip3k6svv86p72nacds"))))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/colorspace")
    (synopsis "Color space manipulation")
    (description
     "This package carries out a mapping between assorted color spaces
including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
CIELAB.  Qualitative, sequential, and diverging color palettes based on HCL
colors are provided.")
    (license license:bsd-3)))

(define-public r-dichromat
  (package
    (name "r-dichromat")
    (version "2.0-0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "dichromat" version))
       (sha256
        (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/dichromat")
    (synopsis "Color schemes for dichromats")
    (description
     "Dichromat collapses red-green or green-blue distinctions to simulate the
effects of different types of color-blindness.")
    (license license:gpl2+)))

(define-public r-digest
  (package
    (name "r-digest")
    (version "0.6.8")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "digest" version))
       (sha256
        (base32 "0m9grqv67hhf51lz10whymhw0g0d98466ka694kya5x95hn44qih"))))
    (build-system r-build-system)
    (home-page "http://dirk.eddelbuettel.com/code/digest.html")
    (synopsis "Create cryptographic hash digests of R objects")
    (description
     "This package contains an implementation of a function 'digest()' for the
creation of hash digests of arbitrary R objects (using the md5, sha-1,
sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
of R language objects, as well as a function 'hmac()' to create hash-based
message authentication code.

Please note that this package is not meant to be deployed for cryptographic
purposes for which more comprehensive (and widely tested) libraries such as
OpenSSL should be used.")
    (license license:gpl2+)))

(define-public r-gtable
  (package
    (name "r-gtable")
    (version "0.1.2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "gtable" version))
       (sha256
        (base32 "0k9hfj6r5y238gqh92s3cbdn34biczx3zfh79ix5xq0c5vkai2xh"))))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/gtable")
    (synopsis "R library to arrange grobs in tables")
    (description
     "Gtable is a collection of tools to make it easier to work with
\"tables\" of grobs.")
    (license license:gpl2+)))

(define-public r-labeling
  (package
    (name "r-labeling")
    (version "0.3")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "labeling" version))
       (sha256
        (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/labeling")
    (synopsis "Axis labeling algorithms")
    (description "The labeling package provides a range of axis labeling
algorithms.")
    (license license:expat)))

(define-public r-magrittr
  (package
    (name "r-magrittr")
    (version "1.5")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "magrittr" version))
       (sha256
        (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/magrittr/index.html")
    (synopsis "A forward-pipe operator for R")
    (description
     "Magrittr provides a mechanism for chaining commands with a new
forward-pipe operator, %>%.  This operator will forward a value, or the result
of an expression, into the next function call/expression.  There is flexible
support for the type of right-hand side expressions.  For more information,
see package vignette.  To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
    (license license:expat)))

(define-public r-munsell
  (package
    (name "r-munsell")
    (version "0.4.2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "munsell" version))
       (sha256
        (base32 "1bi5yi0i80778bbzx2rm4f0glpc34kvh24pwwfhm4v32izsqgrw4"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-colorspace" ,r-colorspace)))
    (home-page "http://cran.r-project.org/web/packages/munsell")
    (synopsis "Munsell colour system")
    (description
     "The Munsell package contains Functions for exploring and using the
Munsell colour system.")
    (license license:expat)))

(define-public r-rcpp
  (package
    (name "r-rcpp")
    (version "0.12.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "Rcpp" version))
       (sha256
        (base32 "182109z0yc1snqgd833ssl2cix6cbq83bcxmy5344b15ym820y38"))))
    (build-system r-build-system)
    (home-page "http://www.rcpp.org")
    (synopsis "Seamless R and C++ Integration")
    (description
     "The Rcpp package provides R functions as well as C++ classes which offer
a seamless integration of R and C++.  Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries.  Documentation
about Rcpp is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
'citation(\"Rcpp\")' for details on these last two.")
    (license license:gpl2+)))

(define-public r-plyr
  (package
    (name "r-plyr")
    (version "1.8.3")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "plyr" version))
       (sha256
        (base32 "06v4zxawpjz37rp2q2ii5q43g664z9s29j4ydn0cz3crn7lzl6pk"))))
    (build-system r-build-system)
    (native-inputs `(("r-rcpp" ,r-rcpp)))
    (home-page "http://had.co.nz/plyr")
    (synopsis "Tools for Splitting, Applying and Combining Data")
    (description
     "Plyr is a set of tools that solves a common set of problems: you need to
break a big problem down into manageable pieces, operate on each piece and
then put all the pieces back together.  For example, you might want to fit a
model to each spatial location or time point in your study, summarise data by
panels or collapse high-dimensional arrays to simpler summary statistics.")
    (license license:expat)))

(define-public r-proto
  (package
    (name "r-proto")
    (version "0.3-10")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "proto" version))
       (sha256
        (base32 "03mvzi529y6kjcp9bkpk7zlgpcakb3iz73hca6rpjy14pyzl3nfh"))))
    (build-system r-build-system)
    (home-page "http://r-proto.googlecode.com")
    (synopsis "Prototype object-based programming")
    (description
     "Proto is an object oriented system using object-based, also called
prototype-based, rather than class-based object oriented ideas.")
    (license license:gpl2+)))

(define-public r-rcolorbrewer
  (package
    (name "r-rcolorbrewer")
    (version "1.1-2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "RColorBrewer" version))
       (sha256
        (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/RColorBrewer")
    (synopsis "ColorBrewer palettes")
    (description
     "This package provides color schemes for maps (and other graphics)
designed by Cynthia Brewer as described at http://colorbrewer2.org")
    ;; Includes code licensed under bsd-4
    (license license:asl2.0)))

(define-public r-stringi
  (package
    (name "r-stringi")
    (version "0.5-5")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "stringi" version))
       (sha256
        (base32
         "183wrrjhpgl1wbnn9lhghyvhz7l2mc64mpcmzplckal7y9j7pmhw"))))
    (build-system r-build-system)
    (inputs `(("icu4c" ,icu4c)))
    (native-inputs `(("pkg-config" ,pkg-config)))
    (home-page "http://stringi.rexamine.com/")
    (synopsis "Character string processing facilities")
    (description
     "This package allows for fast, correct, consistent, portable, as well as
convenient character string/text processing in every locale and any native
encoding.  Owing to the use of the ICU library, the package provides R users
with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
programmers.  Among available features there are: pattern searching
 (e.g.  via regular expressions), random string generation, string collation,
transliteration, concatenation, date-time formatting and parsing, etc.")
    (license license:bsd-3)))

(define-public r-stringr
  (package
    (name "r-stringr")
    (version "1.0.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "stringr" version))
       (sha256
        (base32 "0jnz6r9yqyf7dschr2fnn1slg4wn6b4ik5q00j4zrh43bfw7s9pq"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-magrittr" ,r-magrittr)
       ("r-stringi" ,r-stringi)))
    (home-page "https://github.com/hadley/stringr")
    (synopsis "Simple, consistent wrappers for common string operations")
    (description
     "Stringr is a consistent, simple and easy to use set of wrappers around
the fantastic 'stringi' package.  All function and argument names (and
positions) are consistent, all functions deal with \"NA\"'s and zero length
vectors in the same way, and the output from one function is easy to feed into
the input of another.")
    (license license:gpl2+)))

(define-public r-reshape2
  (package
    (name "r-reshape2")
    (version "1.4.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "reshape2" version))
       (sha256
        (base32 "0hl082dyk3pk07nqprpn5dvnrkqhnf6zjnjig1ijddxhlmsrzm7v"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-plyr" ,r-plyr)
       ("r-rcpp" ,r-rcpp)
       ("r-stringr" ,r-stringr)))
    (home-page "https://github.com/hadley/reshape")
    (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
    (description
     "Reshape2 is an R library to flexibly restructure and aggregate data
using just two functions: melt and dcast (or acast).")
    (license license:expat)))

(define-public r-scales
  (package
    (name "r-scales")
    (version "0.2.5")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "scales" version))
       (sha256
        (base32 "12xrmn1vh64dl46bq7n7pa427aicb2ifjrby9in3m32nyvir0kac"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-dichromat" ,r-dichromat)
       ("r-labeling" ,r-labeling)
       ("r-munsell" ,r-munsell)
       ("r-plyr" ,r-plyr)
       ("r-rcolorbrewer" ,r-rcolorbrewer)
       ("r-rcpp" ,r-rcpp)))
    (home-page "https://github.com/hadley/scales")
    (synopsis "Scale functions for visualization")
    (description
     "This package provides graphical scales that map data to aesthetics, and
provides methods for automatically determining breaks and labels for axes and
legends.")
    (license license:expat)))

(define-public r-ggplot2
  (package
    (name "r-ggplot2")
    (version "1.0.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "ggplot2" version))
       (sha256
        (base32 "0794kjqi3lrxb33lr1mykd58959hlgkhdn259vj8fxrh65mqw920"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-digest" ,r-digest)
       ("r-gtable" ,r-gtable)
       ("r-plyr" ,r-plyr)
       ("r-proto" ,r-proto)
       ("r-reshape2" ,r-reshape2)
       ("r-scales" ,r-scales)))
    (home-page "http://ggplot2.org")
    (synopsis "An implementation of the grammar of graphics")
    (description
     "Ggplot2 is an implementation of the grammar of graphics in R.  It
combines the advantages of both base and lattice graphics: conditioning and
shared axes are handled automatically, and you can still build up a plot step
by step from multiple data sources.  It also implements a sophisticated
multidimensional conditioning system and a consistent interface to map data to
aesthetic attributes.")
    (license license:gpl2+)))

(define-public r-assertthat
  (package
    (name "r-assertthat")
    (version "0.1")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "assertthat" version))
              (sha256
               (base32
                "0dwsqajyglfscqilj843qfqn1ndbqpswa7b4l1d633qjk9d68qqk"))))
    (build-system r-build-system)
    (home-page "https://github.com/hadley/assertthat")
    (synopsis "Easy pre and post assertions")
    (description
     "Assertthat is an extension to stopifnot() that makes it easy to declare
the pre and post conditions that your code should satisfy, while also
producing friendly error messages so that your users know what they've done
wrong.")
    (license license:gpl3+)))

(define-public r-lazyeval
  (package
    (name "r-lazyeval")
    (version "0.1.10")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "lazyeval" version))
              (sha256
               (base32
                "02qfpn2fmy78vx4jxr7g7rhqzcm1kcivfwai7lbh0vvpawia0qwh"))))
    (build-system r-build-system)
    (home-page "https://github.com/hadley/lazyeval")
    (synopsis "Lazy (non-standard) evaluation in R")
    (description
     "This package provides the tools necessary to do non-standard
evaluation (NSE) in R.")
    (license license:gpl3+)))

(define-public r-dbi
  (package
    (name "r-dbi")
    (version "0.3.1")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "DBI" version))
              (sha256
               (base32
                "0xj5baxwnhl23rd5nskhjvranrwrc68f3xlyrklglipi41bm69hw"))))
    (build-system r-build-system)
    (home-page "https://github.com/rstats-db/DBI")
    (synopsis "R database interface")
    (description
     "The DBI package provides a database interface (DBI) definition for
communication between R and relational database management systems.  All
classes in this package are virtual and need to be extended by the various
R/DBMS implementations.")
    (license license:lgpl2.0+)))

(define-public r-bh
  (package
    (name "r-bh")
    (version "1.58.0-1")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "BH" version))
              (sha256
               (base32
                "17rnwyw9ib2pvm60iixzkbz7ff4fslpifp1nlx4czp42hy67kqpf"))))
    (build-system r-build-system)
    (home-page "https://github.com/eddelbuettel/bh")
    (synopsis "R package providing subset of Boost headers")
    (description
     "This package aims to provide the most useful subset of Boost libraries
for template use among CRAN packages.")
    (license license:boost1.0)))

(define-public r-evaluate
  (package
    (name "r-evaluate")
    (version "0.8")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "evaluate" version))
              (sha256
               (base32
                "137gc35jlizhqnx19mxim3llrkm403abj8ghb2b7v5ls9rvd40pq"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-stringr" ,r-stringr)))
    (home-page "https://github.com/hadley/evaluate")
    (synopsis "Parsing and evaluation tools for R")
    (description
     "This package provides tools that allow you to recreate the parsing,
evaluation and display of R code, with enough information that you can
accurately recreate what happens at the command line.  The tools can easily be
adapted for other output formats, such as HTML or LaTeX.")
    (license license:gpl3+)))