1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com>
4 ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
5 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
6 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
7 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
8 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
10 ;;; This file is part of GNU Guix.
12 ;;; GNU Guix is free software; you can redistribute it and/or modify it
13 ;;; under the terms of the GNU General Public License as published by
14 ;;; the Free Software Foundation; either version 3 of the License, or (at
15 ;;; your option) any later version.
17 ;;; GNU Guix is distributed in the hope that it will be useful, but
18 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
19 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
20 ;;; GNU General Public License for more details.
22 ;;; You should have received a copy of the GNU General Public License
23 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
25 (define-module (gnu packages statistics)
26 #:use-module ((guix licenses) #:prefix license:)
27 #:use-module (guix packages)
28 #:use-module (guix download)
29 #:use-module (guix utils)
30 #:use-module (guix build-system gnu)
31 #:use-module (guix build-system r)
32 #:use-module (guix build-system python)
33 #:use-module (gnu packages)
34 #:use-module (gnu packages compression)
35 #:use-module (gnu packages curl)
36 #:use-module (gnu packages gcc)
37 #:use-module (gnu packages gtk)
38 #:use-module (gnu packages gettext)
39 #:use-module (gnu packages glib)
40 #:use-module (gnu packages haskell)
41 #:use-module (gnu packages icu4c)
42 #:use-module (gnu packages image)
43 #:use-module (gnu packages java)
44 #:use-module (gnu packages maths)
45 #:use-module (gnu packages multiprecision)
46 #:use-module (gnu packages pcre)
47 #:use-module (gnu packages perl)
48 #:use-module (gnu packages pkg-config)
49 #:use-module (gnu packages python)
50 #:use-module (gnu packages readline)
51 #:use-module (gnu packages ssh)
52 #:use-module (gnu packages texinfo)
53 #:use-module (gnu packages tls)
54 #:use-module (gnu packages base)
55 #:use-module (gnu packages web)
56 #:use-module (gnu packages xml)
57 #:use-module (gnu packages xorg)
58 #:use-module (gnu packages zip)
59 #:use-module (srfi srfi-1))
69 (uri (string-append "mirror://gnu/pspp/pspp-"
73 "0xw61kq0hxh7f6a4yjhnqbhc0fj9r3wb3qnpq05qhdp79n30ik24"))))
74 (build-system gnu-build-system)
77 ("gettext" ,gnu-gettext)
81 ("readline" ,readline)
83 ("gtksourceview" ,gtksourceview)
86 `(("glib" ,glib "bin") ;for glib-genmarshal
88 ("pkg-config" ,pkg-config)))
89 (home-page "http://www.gnu.org/software/pspp/")
90 (synopsis "Statistical analysis")
92 "GNU PSPP is a statistical analysis program. It can perform
93 descriptive statistics, T-tests, linear regression and non-parametric tests.
94 It features both a graphical interface as well as command-line input. PSPP
95 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
96 can be imported from spreadsheets, text files and database sources and it can
97 be output in text, PostScript, PDF or HTML.")
98 (license license:gpl3+)))
106 (uri (string-append "mirror://cran/src/base/R-"
107 (version-prefix version 1) "/R-"
111 "1r0i0cqs3p0vrpiwq0zg5kbrmja9rmaijyzf9f23v6d5n5ab2mlj"))))
112 (build-system gnu-build-system)
115 (list (string-append "LDFLAGS=-Wl,-rpath="
116 (assoc-ref %outputs "out")
119 (modify-phases %standard-phases
121 'configure 'set-default-pager
122 ;; Set default pager to "cat", because otherwise it is "false",
123 ;; making "help()" print nothing at all.
124 (lambda _ (setenv "PAGER" "cat") #t))
125 (add-before 'check 'set-timezone
126 ;; Some tests require the timezone to be set.
127 (lambda* (#:key inputs #:allow-other-keys)
130 (string-append (assoc-ref inputs "tzdata")
133 (add-after 'build 'make-info
134 (lambda _ (zero? (system* "make" "info"))))
135 (add-after 'build 'install-info
136 (lambda _ (zero? (system* "make" "install-info")))))
144 "--enable-BLAS-shlib"
146 "--with-system-bzlib"
149 "--with-system-xz")))
150 ;; R has some support for Java. When the JDK is available at configure
151 ;; time environment variables pointing to the JDK will be recorded under
152 ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
153 ;; CMD javareconf". "R CMD javareconf" appears to only be used to update
154 ;; the recorded environment variables in $R_HOME/etc. Refer to
155 ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
156 ;; for additional information.
158 ;; As the JDK is a rather large input with only very limited effects on R,
159 ;; we decided to drop it.
163 ("pkg-config" ,pkg-config)
164 ("texinfo" ,texinfo) ; for building HTML manuals
165 ("which" ,which) ; for tests/Examples/base-Ex.R
171 ("gfortran" ,gfortran)
178 ("readline" ,readline)
181 (list (search-path-specification
182 (variable "R_LIBS_SITE")
183 (files (list "site-library/")))))
184 (home-page "http://www.r-project.org/")
185 (synopsis "Environment for statistical computing and graphics")
187 "R is a language and environment for statistical computing and graphics.
188 It provides a variety of statistical techniques, such as linear and nonlinear
189 modeling, classical statistical tests, time-series analysis, classification
190 and clustering. It also provides robust support for producing
191 publication-quality data plots. A large amount of 3rd-party packages are
192 available, greatly increasing its breadth and scope.")
193 (license license:gpl3+)))
195 (define-public r-colorspace
197 (name "r-colorspace")
202 (uri (cran-uri "colorspace" version))
204 (base32 "0y8n4ljwhbdvkysdwgqzcnpv107pb3px1jip3k6svv86p72nacds"))))
205 (build-system r-build-system)
206 (home-page "http://cran.r-project.org/web/packages/colorspace")
207 (synopsis "Color space manipulation")
209 "This package carries out a mapping between assorted color spaces
210 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
211 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
212 colors are provided.")
213 (license license:bsd-3)))
215 (define-public r-dichromat
222 (uri (cran-uri "dichromat" version))
224 (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
225 (build-system r-build-system)
226 (home-page "http://cran.r-project.org/web/packages/dichromat")
227 (synopsis "Color schemes for dichromats")
229 "Dichromat collapses red-green or green-blue distinctions to simulate the
230 effects of different types of color-blindness.")
231 (license license:gpl2+)))
233 (define-public r-digest
240 (uri (cran-uri "digest" version))
242 (base32 "0ixy1mb7kfl20lkckqiilpw03g1ip4ibihs03gicz7w625hc7zcm"))))
243 (build-system r-build-system)
244 ;; Vignettes require r-knitr, which requires r-digest, so we have to
245 ;; disable them and the tests.
248 #:configure-flags (list "--no-build-vignettes")))
249 (home-page "http://dirk.eddelbuettel.com/code/digest.html")
250 (synopsis "Create cryptographic hash digests of R objects")
252 "This package contains an implementation of a function 'digest()' for the
253 creation of hash digests of arbitrary R objects (using the md5, sha-1,
254 sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
255 of R language objects, as well as a function 'hmac()' to create hash-based
256 message authentication code.
258 Please note that this package is not meant to be deployed for cryptographic
259 purposes for which more comprehensive (and widely tested) libraries such as
260 OpenSSL should be used.")
261 (license license:gpl2+)))
263 (define-public r-estimability
265 (name "r-estimability")
269 (uri (cran-uri "estimability" version))
272 "049adh8i0ad0m0qln2ylqdxcs5v2q9zfignn2a50r5f93ip2ay6w"))))
273 (build-system r-build-system)
274 (home-page "http://cran.r-project.org/web/packages/estimability")
275 (synopsis "Tools for assessing estimability of linear predictions")
276 (description "Provides tools for determining estimability of linear
277 functions of regression coefficients, and 'epredict' methods that handle
278 non-estimable cases correctly.")
279 (license license:gpl2+)))
281 (define-public r-gtable
288 (uri (cran-uri "gtable" version))
290 (base32 "0k9hfj6r5y238gqh92s3cbdn34biczx3zfh79ix5xq0c5vkai2xh"))))
291 (build-system r-build-system)
292 (home-page "https://cran.r-project.org/web/packages/gtable")
293 (synopsis "R library to arrange grobs in tables")
295 "Gtable is a collection of tools to make it easier to work with
296 \"tables\" of grobs.")
297 (license license:gpl2+)))
299 (define-public r-labeling
306 (uri (cran-uri "labeling" version))
308 (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
309 (build-system r-build-system)
310 (home-page "http://cran.r-project.org/web/packages/labeling")
311 (synopsis "Axis labeling algorithms")
312 (description "The labeling package provides a range of axis labeling
314 (license license:expat)))
316 (define-public r-magrittr
323 (uri (cran-uri "magrittr" version))
325 (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
326 (build-system r-build-system)
327 (home-page "http://cran.r-project.org/web/packages/magrittr/index.html")
328 (synopsis "A forward-pipe operator for R")
330 "Magrittr provides a mechanism for chaining commands with a new
331 forward-pipe operator, %>%. This operator will forward a value, or the result
332 of an expression, into the next function call/expression. There is flexible
333 support for the type of right-hand side expressions. For more information,
334 see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
335 (license license:expat)))
337 (define-public r-munsell
344 (uri (cran-uri "munsell" version))
346 (base32 "0jdxlbjslkzaqgp058da1cgm85qvqi09wpcgpvp4hvwnmy83qz1r"))))
347 (build-system r-build-system)
349 `(("r-colorspace" ,r-colorspace)))
350 (home-page "http://cran.r-project.org/web/packages/munsell")
351 (synopsis "Munsell colour system")
353 "The Munsell package contains Functions for exploring and using the
354 Munsell colour system.")
355 (license license:expat)))
357 (define-public r-rcpp
364 (uri (cran-uri "Rcpp" version))
366 (base32 "1vw0zbd6zhqixqg7h8ahn1dr1hb492365x419nrp2lhvr60r8i0k"))))
367 (build-system r-build-system)
368 (home-page "http://www.rcpp.org")
369 (synopsis "Seamless R and C++ Integration")
371 "The Rcpp package provides R functions as well as C++ classes which offer
372 a seamless integration of R and C++. Many R data types and objects can be
373 mapped back and forth to C++ equivalents which facilitates both writing of new
374 code as well as easier integration of third-party libraries. Documentation
375 about Rcpp is provided by several vignettes included in this package, via the
376 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
377 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
378 'citation(\"Rcpp\")' for details on these last two.")
379 (license license:gpl2+)))
381 (define-public r-plyr
388 (uri (cran-uri "plyr" version))
390 (base32 "06v4zxawpjz37rp2q2ii5q43g664z9s29j4ydn0cz3crn7lzl6pk"))))
391 (build-system r-build-system)
392 (native-inputs `(("r-rcpp" ,r-rcpp)))
393 (home-page "http://had.co.nz/plyr")
394 (synopsis "Tools for Splitting, Applying and Combining Data")
396 "Plyr is a set of tools that solves a common set of problems: you need to
397 break a big problem down into manageable pieces, operate on each piece and
398 then put all the pieces back together. For example, you might want to fit a
399 model to each spatial location or time point in your study, summarise data by
400 panels or collapse high-dimensional arrays to simpler summary statistics.")
401 (license license:expat)))
403 (define-public r-proto
410 (uri (cran-uri "proto" version))
412 (base32 "03mvzi529y6kjcp9bkpk7zlgpcakb3iz73hca6rpjy14pyzl3nfh"))))
413 (build-system r-build-system)
414 (home-page "http://r-proto.googlecode.com")
415 (synopsis "Prototype object-based programming")
417 "Proto is an object oriented system using object-based, also called
418 prototype-based, rather than class-based object oriented ideas.")
419 (license license:gpl2+)))
421 (define-public r-rcolorbrewer
423 (name "r-rcolorbrewer")
428 (uri (cran-uri "RColorBrewer" version))
430 (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
431 (build-system r-build-system)
432 (home-page "http://cran.r-project.org/web/packages/RColorBrewer")
433 (synopsis "ColorBrewer palettes")
435 "This package provides color schemes for maps (and other graphics)
436 designed by Cynthia Brewer as described at http://colorbrewer2.org")
437 ;; Includes code licensed under bsd-4
438 (license license:asl2.0)))
440 (define-public r-stringi
447 (uri (cran-uri "stringi" version))
450 "1ld38536sswyywp6pyys3v8vkngbk5cksrhdxp8jyr6bz7qf8j77"))))
451 (build-system r-build-system)
452 (inputs `(("icu4c" ,icu4c)))
453 (native-inputs `(("pkg-config" ,pkg-config)))
454 (home-page "http://stringi.rexamine.com/")
455 (synopsis "Character string processing facilities")
457 "This package allows for fast, correct, consistent, portable, as well as
458 convenient character string/text processing in every locale and any native
459 encoding. Owing to the use of the ICU library, the package provides R users
460 with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
461 programmers. Among available features there are: pattern searching
462 (e.g. via regular expressions), random string generation, string collation,
463 transliteration, concatenation, date-time formatting and parsing, etc.")
464 (license license:bsd-3)))
466 (define-public r-stringr
473 (uri (cran-uri "stringr" version))
475 (base32 "0jnz6r9yqyf7dschr2fnn1slg4wn6b4ik5q00j4zrh43bfw7s9pq"))))
476 (build-system r-build-system)
478 `(("r-magrittr" ,r-magrittr)
479 ("r-stringi" ,r-stringi)))
480 (home-page "https://github.com/hadley/stringr")
481 (synopsis "Simple, consistent wrappers for common string operations")
483 "Stringr is a consistent, simple and easy to use set of wrappers around
484 the fantastic 'stringi' package. All function and argument names (and
485 positions) are consistent, all functions deal with \"NA\"'s and zero length
486 vectors in the same way, and the output from one function is easy to feed into
487 the input of another.")
488 (license license:gpl2+)))
490 (define-public r-reshape2
497 (uri (cran-uri "reshape2" version))
499 (base32 "0hl082dyk3pk07nqprpn5dvnrkqhnf6zjnjig1ijddxhlmsrzm7v"))))
500 (build-system r-build-system)
504 ("r-stringr" ,r-stringr)))
505 (home-page "https://github.com/hadley/reshape")
506 (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
508 "Reshape2 is an R library to flexibly restructure and aggregate data
509 using just two functions: melt and dcast (or acast).")
510 (license license:expat)))
512 (define-public r-scales
519 (uri (cran-uri "scales" version))
521 (base32 "19y6q4j8vpmc73dnn4ncp5wj44gri7m77ys3z2rn3crrcc9zc7l5"))))
522 (build-system r-build-system)
524 `(("r-dichromat" ,r-dichromat)
525 ("r-labeling" ,r-labeling)
526 ("r-munsell" ,r-munsell)
528 ("r-rcolorbrewer" ,r-rcolorbrewer)
530 (home-page "https://github.com/hadley/scales")
531 (synopsis "Scale functions for visualization")
533 "This package provides graphical scales that map data to aesthetics, and
534 provides methods for automatically determining breaks and labels for axes and
536 (license license:expat)))
538 (define-public r-ggplot2
545 (uri (cran-uri "ggplot2" version))
547 (base32 "0s9rvp0f736ji6p9xpxq54agxf95pjkql4sj7ag0hv2xhnp27hzj"))))
548 (build-system r-build-system)
550 `(("r-digest" ,r-digest)
551 ("r-gtable" ,r-gtable)
554 ("r-reshape2" ,r-reshape2)
555 ("r-scales" ,r-scales)))
556 (home-page "http://ggplot2.org")
557 (synopsis "An implementation of the grammar of graphics")
559 "Ggplot2 is an implementation of the grammar of graphics in R. It
560 combines the advantages of both base and lattice graphics: conditioning and
561 shared axes are handled automatically, and you can still build up a plot step
562 by step from multiple data sources. It also implements a sophisticated
563 multidimensional conditioning system and a consistent interface to map data to
564 aesthetic attributes.")
565 (license license:gpl2+)))
567 (define-public r-assertthat
569 (name "r-assertthat")
573 (uri (cran-uri "assertthat" version))
576 "0dwsqajyglfscqilj843qfqn1ndbqpswa7b4l1d633qjk9d68qqk"))))
577 (build-system r-build-system)
578 (home-page "https://github.com/hadley/assertthat")
579 (synopsis "Easy pre and post assertions")
581 "Assertthat is an extension to stopifnot() that makes it easy to declare
582 the pre and post conditions that your code should satisfy, while also
583 producing friendly error messages so that your users know what they've done
585 (license license:gpl3+)))
587 (define-public r-lazyeval
593 (uri (cran-uri "lazyeval" version))
596 "02qfpn2fmy78vx4jxr7g7rhqzcm1kcivfwai7lbh0vvpawia0qwh"))))
597 (build-system r-build-system)
598 (home-page "https://github.com/hadley/lazyeval")
599 (synopsis "Lazy (non-standard) evaluation in R")
601 "This package provides the tools necessary to do non-standard
602 evaluation (NSE) in R.")
603 (license license:gpl3+)))
611 (uri (cran-uri "DBI" version))
614 "13n6ibmrma42qmq17qgkyjsc0ciwqf17sd7lw7w26pwpyjd4mwgg"))))
615 (build-system r-build-system)
616 (home-page "https://github.com/rstats-db/DBI")
617 (synopsis "R database interface")
619 "The DBI package provides a database interface (DBI) definition for
620 communication between R and relational database management systems. All
621 classes in this package are virtual and need to be extended by the various
622 R/DBMS implementations.")
623 (license license:lgpl2.0+)))
631 (uri (cran-uri "BH" version))
634 "136497fng9bcvrf8favpj8inz96pxdwp1rrb2k00sxjxjbgawhg4"))))
635 (build-system r-build-system)
636 (home-page "https://github.com/eddelbuettel/bh")
637 (synopsis "R package providing subset of Boost headers")
639 "This package aims to provide the most useful subset of Boost libraries
640 for template use among CRAN packages.")
641 (license license:boost1.0)))
643 (define-public r-evaluate
649 (uri (cran-uri "evaluate" version))
652 "1bn6bympg9prr8d16g1g530bddii8i04hf4i2bkw0yf4dsfqq4g8"))))
653 (build-system r-build-system)
655 `(("r-stringr" ,r-stringr)))
656 (home-page "https://github.com/hadley/evaluate")
657 (synopsis "Parsing and evaluation tools for R")
659 "This package provides tools that allow you to recreate the parsing,
660 evaluation and display of R code, with enough information that you can
661 accurately recreate what happens at the command line. The tools can easily be
662 adapted for other output formats, such as HTML or LaTeX.")
663 (license license:gpl3+)))
665 (define-public r-formatr
671 (uri (cran-uri "formatR" version))
674 "1fvynq0fj1r9grg9vvfdh5fl2riv6qki9f2rfpyvbvqq3xxpmi3f"))))
675 (build-system r-build-system)
676 (home-page "http://yihui.name/formatR")
677 (synopsis "Format R code automatically")
679 "This package provides a function to format R source code. Spaces and
680 indent will be added to the code automatically, and comments will be preserved
681 under certain conditions, so that R code will be more human-readable and tidy.
682 There is also a Shiny app as a user interface in this package.")
683 (license license:gpl3+)))
685 (define-public r-highr
691 (uri (cran-uri "highr" version))
694 "0n9v44dxdy5fhkdmpbpa2p78whyd9z3rhhy42ipdz5m5vsr55qa3"))))
695 (build-system r-build-system)
696 (home-page "https://github.com/yihui/highr")
697 (synopsis "Syntax highlighting for R source code")
699 "This package provides syntax highlighting for R source code. Currently
700 it supports LaTeX and HTML output. Source code of other languages is
701 supported via Andre Simon's highlight package.")
702 (license license:gpl3+)))
704 (define-public r-mime
710 (uri (cran-uri "mime" version))
713 "145cdcg252w2zsq67dmvmsqka60msfp7agymlxs3gl3ihgiwg46p"))))
714 (build-system r-build-system)
715 (home-page "https://github.com/yihui/mime")
716 (synopsis "R package to map filenames to MIME types")
718 "This package guesses the MIME type from a filename extension using the
719 data derived from /etc/mime.types in UNIX-type systems.")
720 (license license:gpl2)))
722 (define-public r-markdown
728 (uri (cran-uri "markdown" version))
731 "00j1hlib3il50azs2vlcyhi0bjpx1r50mxr9w9dl5g1bwjjc71hb"))))
732 (build-system r-build-system)
733 ;; Skip check phase because the tests require the r-knitr package to be
734 ;; installed. This prevents installation failures. Knitr normally
735 ;; shouldn't be available since r-markdown is a dependency of the r-knitr
737 (arguments `(#:tests? #f))
739 `(("r-mime" ,r-mime)))
740 (home-page "https://github.com/rstudio/markdown")
741 (synopsis "Markdown rendering for R")
743 "This package provides R bindings to the Sundown Markdown rendering
744 library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
745 syntax that can be converted to XHTML or other formats.")
746 (license license:gpl2)))
748 (define-public r-yaml
754 (uri (cran-uri "yaml" version))
757 "18kz5mfn7qpif5pn91w4vbrc5bkycsj85vwm5wxwzjlb02i9mxi6"))))
758 (build-system r-build-system)
759 (home-page "https://cran.r-project.org/web/packages/yaml/")
760 (synopsis "Methods to convert R data to YAML and back")
762 "This package implements the libyaml YAML 1.1 parser and
763 emitter (http://pyyaml.org/wiki/LibYAML) for R.")
764 (license license:bsd-3)))
766 (define-public r-knitr
772 (uri (cran-uri "knitr" version))
775 "0v69846myi4fbjp8wiik4295fhba67s3i6ccysghm6x031i2f26q"))))
776 (build-system r-build-system)
778 `(("r-evaluate" ,r-evaluate)
779 ("r-digest" ,r-digest)
780 ("r-formatr" ,r-formatr)
782 ("r-markdown" ,r-markdown)
783 ("r-stringr" ,r-stringr)
785 (home-page "http://yihui.name/knitr/")
786 (synopsis "General-purpose package for dynamic report generation in R")
788 "This package provides a general-purpose tool for dynamic report
789 generation in R using Literate Programming techniques.")
790 ;; The code is released under any version of the GPL. As it is used by
791 ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
793 (license license:gpl2+)))
795 (define-public r-microbenchmark
797 (name "r-microbenchmark")
801 (uri (cran-uri "microbenchmark" version))
804 "0qn5r1a6qidghcisc2hpbdmj62pnixc3zz6p4ipk8mvakf0hdsvg"))))
805 (build-system r-build-system)
807 `(("r-ggplot2" ,r-ggplot2)))
808 (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
809 (synopsis "Accurate timing functions for R")
811 "This package provides infrastructure to accurately measure and compare
812 the execution time of R expressions.")
813 (license license:bsd-2)))
815 (define-public r-codetools
821 (uri (cran-uri "codetools" version))
824 "0y9r4m2b8xgavr89sc179knzwpz54xljbc1dinpq2q07i4xn0397"))))
825 (build-system r-build-system)
826 (home-page "https://cran.r-project.org/web/packages/codetools/index.html")
827 (synopsis "Code analysis tools for R")
828 (description "This package provides code analysis tools for R.")
829 (license license:gpl3+)))
831 (define-public r-pryr
837 (uri (cran-uri "pryr" version))
840 "1in350a8hxwf580afavasvn3jc7x2p1b7nlwmj1scakfz74vghk5"))))
841 (build-system r-build-system)
843 `(("r-stringr" ,r-stringr)
844 ("r-codetools" ,r-codetools)))
846 `(("r-rcpp" ,r-rcpp)))
847 (home-page "https://github.com/hadley/pryr")
848 (synopsis "Tools for computing on the R language")
850 "This package provides useful tools to pry back the covers of R and
851 understand the language at a deeper level.")
852 (license license:gpl2)))
854 (define-public r-memoise
860 (uri (cran-uri "memoise" version))
863 "0sq2dhpvxy17v1baj256r0jnygdy3m5a8x4zh6vhv29957qnq6zx"))))
864 (build-system r-build-system)
866 `(("r-digest" ,r-digest)))
867 (home-page "http://github.com/hadley/memoise")
868 (synopsis "Memoise functions for R")
870 "This R package allows to cache the results of a function so that when
871 you call it again with the same arguments it returns the pre-computed value.")
872 (license license:expat)))
874 (define-public r-crayon
880 (uri (cran-uri "crayon" version))
883 "0d38fm06h272a8iqlc0d45m2rh36giwqw7mwq4z8hkp4vs975fmm"))))
884 (build-system r-build-system)
886 `(("r-memoise" ,r-memoise)))
887 (home-page "https://github.com/gaborcsardi/crayon")
888 (synopsis "Colored terminal output for R")
890 "Colored terminal output on terminals that support ANSI color and
891 highlight codes. It also works in Emacs ESS. ANSI color support is
892 automatically detected. Colors and highlighting can be combined and nested.
893 New styles can also be created easily. This package was inspired by the
894 \"chalk\" JavaScript project.")
895 (license license:expat)))
897 (define-public r-praise
904 (uri (cran-uri "praise" version))
907 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
908 (build-system r-build-system)
909 (home-page "https://github.com/gaborcsardi/praise")
910 (synopsis "Functions to praise users")
912 "This package provides template functions to assist in building friendly
913 R packages that praise their users.")
914 (license license:expat)))
916 (define-public r-testthat
922 (uri (cran-uri "testthat" version))
925 "0pj1r01x4ny4capr83dfa19hi5i2sjjxky99schzip8zrq5dzxqf"))))
926 (build-system r-build-system)
928 `(("r-digest" ,r-digest)
929 ("r-crayon" ,r-crayon)
930 ("r-magrittr" ,r-magrittr)
931 ("r-praise" ,r-praise)
933 (home-page "https://github.com/hadley/testthat")
934 (synopsis "Unit testing for R")
936 "This package provides a unit testing system for R designed to be fun,
937 flexible and easy to set up.")
938 (license license:expat)))
946 (uri (cran-uri "R6" version))
949 "0yad91i9p4r8bbz6nq8zny39y767n9an7ak5p275ynx8km6v3yqv"))))
950 (build-system r-build-system)
951 (home-page "https://github.com/wch/R6/")
952 (synopsis "Classes with reference semantics in R")
954 "The R6 package allows the creation of classes with reference semantics,
955 similar to R's built-in reference classes. Compared to reference classes, R6
956 classes are simpler and lighter-weight, and they are not built on S4 classes
957 so they do not require the methods package. These classes allow public and
958 private members, and they support inheritance, even when the classes are
959 defined in different packages.")
960 (license license:expat)))
962 (define-public r-dplyr
968 (uri (cran-uri "dplyr" version))
971 "1p8rbn4p4yrx2840dapwiahf9iqa8gnvd35nyc200wfhmrxlqdlc"))))
972 (build-system r-build-system)
974 `(("r-assertthat" ,r-assertthat)
976 ("r-magrittr" ,r-magrittr)
977 ("r-lazyeval" ,r-lazyeval)
982 (home-page "https://github.com/hadley/dplyr")
983 (synopsis "Tools for working with data frames in R")
985 "dplyr is the next iteration of plyr. It is focussed on tools for
986 working with data frames. It has three main goals: 1) identify the most
987 important data manipulation tools needed for data analysis and make them easy
988 to use in R; 2) provide fast performance for in-memory data by writing key
989 pieces of code in C++; 3) use the same code interface to work with data no
990 matter where it is stored, whether in a data frame, a data table or
992 (license license:expat)))
994 (define-public r-acepack
1001 (uri (cran-uri "acepack" version))
1004 "13ry3vyys12iplb14jfhmkrl9g5fxg3iijiggq4s4zb5m5436b1y"))))
1005 (build-system r-build-system)
1007 `(("gfortran" ,gfortran)))
1008 (home-page "http://cran.r-project.org/web/packages/acepack")
1009 (synopsis "Functions for regression transformations")
1011 "This package provides ACE and AVAS methods for choosing regression
1013 (license license:expat)))
1015 (define-public r-cluster
1022 (uri (cran-uri "cluster" version))
1025 "1r669aaaia05i8sv8hxiig1ddah7hm8qw869wgig5i0zzk22bnfl"))))
1026 (build-system r-build-system)
1028 `(("gfortran" ,gfortran)))
1029 (home-page "http://cran.r-project.org/web/packages/cluster")
1030 (synopsis "Methods for data cluster analysis")
1032 "This package provides tools that are useful in finding groups in data.
1033 It is based on the methods described in Kaufman and Rousseeuw (1990) \"Finding
1035 (license license:gpl2+)))
1037 (define-public r-foreign
1044 (uri (cran-uri "foreign" version))
1047 "19278jm85728zb20800w6hq9q8jy8ywdn81mgmlnxkmrr9giwh6p"))))
1048 (build-system r-build-system)
1049 (home-page "http://cran.r-project.org/web/packages/foreign")
1050 (synopsis "Read data stored by other statistics software in R")
1052 "This package provides functions for reading and writing data stored by
1053 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka, and
1054 for reading and writing some dBase files.")
1055 (license license:gpl2+)))
1057 (define-public r-formula
1064 (uri (cran-uri "Formula" version))
1067 "02in5325zzrqbhlygx6s0dinj6ymw845q70y56frqacv25ayzcax"))))
1068 (properties `((upstream-name . "Formula")))
1069 (build-system r-build-system)
1070 (home-page "http://cran.r-project.org/web/packages/Formula")
1071 (synopsis "Extended model formulas")
1073 "This package provides a new class @code{Formula}, which extends the base
1074 class @code{formula}. It supports extended formulas with multiple parts of
1075 regressors on the right-hand side and/or multiple responses on the left-hand
1077 (license (list license:gpl2+ license:gpl3+))))
1079 (define-public r-locfit
1086 (uri (cran-uri "locfit" version))
1089 "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
1090 (build-system r-build-system)
1091 (home-page "http://cran.r-project.org/web/packages/locfit")
1092 (synopsis "Local regression, likelihood and density estimation")
1094 "This package provides functions used for local regression, likelihood
1095 and density estimation.")
1096 (license (list license:gpl2+ license:gpl3+))))
1098 (define-public r-chron
1104 (uri (cran-uri "chron" version))
1107 "1xj50kk8b8mbjpszp8i0wbripb5a4b36jcscwlbyap8n4487g34s"))))
1108 (build-system r-build-system)
1109 (home-page "http://cran.r-project.org/web/packages/chron")
1110 (synopsis "Chronological R objects which can handle dates and times")
1112 "This package provides chronological R objects which can handle dates and
1114 (license license:gpl2)))
1116 (define-public r-data-table
1118 (name "r-data-table")
1122 (uri (cran-uri "data.table" version))
1125 "0vi3zplpxqbg78z9ifjfs1kl2i8qhkqxr7l9ysp2663kq54w6x3g"))))
1126 (build-system r-build-system)
1128 `(("r-chron" ,r-chron)))
1129 (home-page "https://github.com/Rdatatable/data.table/wiki")
1130 (synopsis "Enhanced version of data.frame R object")
1132 "The R package @code{data.table} is an extension of @code{data.frame}
1133 providing functions for fast aggregation of large data (e.g. 100GB in RAM),
1134 fast ordered joins, fast add/modify/delete of columns by group, column listing
1135 and fast file reading.")
1136 (license license:gpl3+)))
1138 (define-public r-xtable
1145 (uri (cran-uri "xtable" version))
1148 "0398qkpvlw3dv0myz4mjcyqwpwc2m31l127r8vdzwc71wb6s28qn"))))
1149 (build-system r-build-system)
1151 `(("r-knitr" ,r-knitr)))
1152 (home-page "http://xtable.r-forge.r-project.org/")
1153 (synopsis "Export R tables to LaTeX or HTML")
1155 "This package provides tools to export R data as LaTeX and HTML tables.")
1156 (license license:gpl2+)))
1158 (define-public python-patsy
1160 (name "python-patsy")
1164 (uri (pypi-uri "patsy" version ".zip"))
1167 "1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w"))))
1168 (build-system python-build-system)
1171 (modify-phases %standard-phases
1172 (replace 'check (lambda _ (zero? (system* "nosetests" "-v"))))
1173 (add-after 'unpack 'prevent-generation-of-egg-archive
1175 (substitute* "setup.py"
1176 (("from setuptools import setup")
1177 "from distutils.core import setup"))
1180 `(("python-numpy" ,python-numpy)
1181 ("python-scipy" ,python-scipy)
1182 ("python-six" ,python-six)))
1184 `(("python-nose" ,python-nose)
1186 (home-page "https://github.com/pydata/patsy")
1187 (synopsis "Describe statistical models and build design matrices")
1189 "Patsy is a Python package for describing statistical models and for
1190 building design matrices.")
1191 ;; The majority of the code is distributed under BSD-2. The module
1192 ;; patsy.compat contains code derived from the Python standard library,
1193 ;; and is covered by the PSFL.
1194 (license (list license:bsd-2 license:psfl))
1195 (properties `((python2-variant . ,(delay python2-patsy))))))
1197 (define-public python2-patsy
1198 (let ((patsy (package-with-python2 (strip-python2-variant python-patsy))))
1199 (package (inherit patsy)
1201 `(("python2-setuptools" ,python2-setuptools)
1202 ,@(package-native-inputs patsy))))))
1204 (define-public python-statsmodels
1206 (name "python-statsmodels")
1211 (uri (string-append "https://pypi.python.org/packages/source/"
1212 "s/statsmodels/statsmodels-" version ".tar.gz"))
1215 "0xn67sqr0cc1lmlhzm71352hrb4hw7g318p5ff5q97pc98vl8kmy"))))
1216 (build-system python-build-system)
1219 (modify-phases %standard-phases
1220 ;; tests must be run after installation
1222 (add-after 'unpack 'set-matplotlib-backend-to-agg
1224 ;; Set the matplotlib backend to Agg to avoid problems using the
1225 ;; GTK backend without a display.
1226 (substitute* (find-files "statsmodels/graphics/tests" "\\.py")
1227 (("import matplotlib\\.pyplot as plt" line)
1228 (string-append "import matplotlib;matplotlib.use('Agg');"
1231 (add-after 'install 'check
1233 (with-directory-excursion "/tmp"
1234 (zero? (system* "nosetests"
1236 "-v" "statsmodels"))))))))
1238 `(("python-numpy" ,python-numpy)
1239 ("python-scipy" ,python-scipy)
1240 ("python-pandas" ,python-pandas)
1241 ("python-patsy" ,python-patsy)
1242 ("python-matplotlib" ,python-matplotlib)))
1244 `(("python-cython" ,python-cython)
1245 ("python-nose" ,python-nose)
1246 ("python-sphinx" ,python-sphinx)))
1247 (home-page "http://statsmodels.sourceforge.net/")
1248 (synopsis "Statistical modeling and econometrics in Python")
1250 "Statsmodels is a Python package that provides a complement to scipy for
1251 statistical computations including descriptive statistics and estimation and
1252 inference for statistical models.")
1253 (license license:bsd-3)))
1255 (define-public python2-statsmodels
1256 (let ((stats (package-with-python2 python-statsmodels)))
1257 (package (inherit stats)
1259 `(("python2-numpy" ,python2-numpy)
1260 ("python2-scipy" ,python2-scipy)
1261 ("python2-pandas" ,python2-pandas)
1262 ("python2-patsy" ,python2-patsy)
1263 ("python2-matplotlib" ,python2-matplotlib)))
1265 `(("python2-setuptools" ,python2-setuptools)
1266 ,@(package-native-inputs stats))))))
1268 (define-public r-coda
1274 (uri (cran-uri "coda" version))
1277 "03sc780734zj2kqcm8lkyvf76fql0jbfhkblpn8l58zmb6cqi958"))))
1278 (build-system r-build-system)
1280 `(("r-lattice" ,r-lattice)))
1281 (home-page "http://cran.r-project.org/web/packages/coda")
1282 (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
1283 (description "This package provides functions for summarizing and plotting
1284 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
1285 diagnostic tests of convergence to the equilibrium distribution of the Markov
1287 (license license:gpl2+)))
1289 (define-public r-xml2
1296 (uri (cran-uri "xml2" version))
1299 "0jjilz36h7vbdbkpvjnja1vgjf6d1imql3z4glqn2m2b74w5qm4c"))))
1300 (build-system r-build-system)
1302 `(("libxml2" ,libxml2)))
1304 `(("r-rcpp" ,r-rcpp)
1306 (home-page "https://github.com/hadley/xml2")
1307 (synopsis "Parse XML with R")
1309 "This package provides a simple, consistent interface to working with XML
1310 files in R. It is built on top of the libxml2 C library.")
1311 (license license:gpl2+)))
1313 (define-public r-rversions
1315 (name "r-rversions")
1319 (uri (cran-uri "rversions" version))
1322 "0xmi461g1rf5ngb7r1sri798jn6icld1xq25wj9jii2ca8j8xv68"))))
1323 (build-system r-build-system)
1325 `(("r-curl" ,r-curl)
1326 ("r-xml2" ,r-xml2)))
1327 (home-page "https://github.com/metacran/rversions")
1328 (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
1330 "This package provides functions to query the main R repository to find
1331 the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
1332 previous R versions and their release dates.")
1333 (license license:expat)))
1335 (define-public r-whisker
1341 (uri (cran-uri "whisker" version))
1344 "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28"))))
1345 (build-system r-build-system)
1346 (home-page "http://github.com/edwindj/whisker")
1347 (synopsis "Logicless mustache templating for R")
1349 "This package provides logicless templating, with a syntax that is not
1351 (license license:gpl3+)))
1353 (define-public r-brew
1359 (uri (cran-uri "brew" version))
1362 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
1363 (build-system r-build-system)
1364 (home-page "http://cran.r-project.org/web/packages/brew")
1365 (synopsis "Templating framework for report generation")
1367 "The brew package implements a templating framework for mixing text and R
1368 code for report generation. The template syntax is similar to PHP, Ruby's erb
1369 module, Java Server Pages, and Python's psp module.")
1370 (license license:gpl2+)))
1372 (define-public r-roxygen2
1378 (uri (cran-uri "roxygen2" version))
1381 "19gblyrrn29msbpawcb1hn5m1rshiqwxy0lby0vf92rm13fmsxcz"))))
1382 (build-system r-build-system)
1384 `(("r-brew" ,r-brew)
1385 ("r-digest" ,r-digest)
1387 ("r-stringi" ,r-stringi)
1388 ("r-stringr" ,r-stringr)))
1389 (home-page "https://github.com/klutometis/roxygen")
1390 (synopsis "In-source documentation system for R")
1392 "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
1393 collation, and NAMESPACE files.")
1394 (license license:gpl2+)))
1396 (define-public r-openssl
1403 (uri (cran-uri "openssl" version))
1406 "0ldqam7d9fyxwhr651ld6lsh05lg4v2y8ajxwzq9ywzjmfb3vlpz"))))
1407 (build-system r-build-system)
1409 `(("openssl" ,openssl)))
1410 (home-page "https://github.com/jeroenooms/openssl")
1411 (synopsis "Toolkit for encryption, signatures and certificates")
1413 "This package provides R bindings to OpenSSL libssl and libcrypto, plus
1414 custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
1415 and P-521. Cryptographic signatures can either be created and verified
1416 manually or via x509 certificates. AES block cipher is used in CBC mode for
1417 symmetric encryption; RSA for asymmetric (public key) encryption. High-level
1418 envelope functions combine RSA and AES for encrypting arbitrary sized data.
1419 Other utilities include key generators, hash functions (md5, sha1, sha256,
1420 etc), base64 encoder, a secure random number generator, and @code{bignum} math
1421 methods for manually performing crypto calculations on large multibyte
1423 (license license:expat)))
1425 (define-public r-httr
1431 (uri (cran-uri "httr" version))
1434 "08sq34pknsfcy8lm06nydi12mbaxpqpgb025ahr33v9d3g0wvh6p"))))
1435 (build-system r-build-system)
1437 `(("r-curl" ,r-curl)
1438 ("r-digest" ,r-digest)
1439 ("r-jsonlite" ,r-jsonlite)
1440 ("r-openssl" ,r-openssl)
1443 ("r-stringr" ,r-stringr)))
1444 (home-page "https://github.com/hadley/httr")
1445 (synopsis "Tools for working with URLs and HTTP")
1447 "The aim of httr is to provide a wrapper for RCurl customised to the
1448 demands of modern web APIs. It provides useful tools for working with HTTP
1449 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
1450 functions make it easy to control additional request components.")
1451 (license license:expat)))
1453 (define-public r-git2r
1459 (uri (cran-uri "git2r" version))
1462 "1rpdf85wy9fp456ypvbhl3p9whkb7kgl0n7rkqxd2bhvyzkvjak8"))))
1463 (build-system r-build-system)
1464 ;; This R package contains modified sources of libgit2. This modified
1465 ;; version of libgit2 is built as the package is built. Hence libgit2 is
1466 ;; not among the inputs of this package.
1468 `(("libssh2" ,libssh2)
1469 ("openssl" ,openssl)
1471 (home-page "https://github.com/ropensci/git2r")
1472 (synopsis "Access Git repositories with R")
1474 "This package provides an R interface to the libgit2 library, which is a
1475 pure C implementation of the Git core methods.")
1476 ;; GPLv2 only with linking exception.
1477 (license license:gpl2)))
1479 (define-public r-rstudioapi
1481 (name "r-rstudioapi")
1485 (uri (cran-uri "rstudioapi" version))
1488 "0sgnqfx0m3hzh57k10s7ndrbw7yqjjjcgfikafya98jcc7wmpwym"))))
1489 (build-system r-build-system)
1490 (home-page "http://cran.r-project.org/web/packages/rstudioapi")
1491 (synopsis "Safely access the RStudio API")
1493 "This package provides functions to access the RStudio API and provide
1494 informative error messages when it's not available.")
1495 (license license:expat)))
1497 (define-public r-devtools
1503 (uri (cran-uri "devtools" version))
1506 "0ik3l3q62sspdph613f9ik5yz36s8q5nrc50dqgn3pxzvpwpdj2i"))))
1507 (build-system r-build-system)
1509 `(("r-curl" ,r-curl)
1510 ("r-digest" ,r-digest)
1511 ("r-evaluate" ,r-evaluate)
1512 ("r-git2r" ,r-git2r)
1514 ("r-jsonlite" ,r-jsonlite)
1515 ("r-memoise" ,r-memoise)
1516 ("r-roxygen2" ,r-roxygen2)
1517 ("r-rstudioapi" ,r-rstudioapi)
1518 ("r-rversions" ,r-rversions)
1519 ("r-whisker" ,r-whisker)
1520 ("r-withr" ,r-withr)))
1521 (home-page "https://github.com/hadley/devtools")
1522 (synopsis "Tools to make developing R packages easier")
1523 (description "The devtools package is a collection of package development
1524 tools to simplify the devolpment of R packages.")
1525 (license license:gpl2+)))
1527 (define-public r-withr
1533 (uri (cran-uri "withr" version))
1536 "0zbj3rd7dc0ycknmay7y7rm1qvnh9n05jw93gjggz46j2zfmy93y"))))
1537 (build-system r-build-system)
1538 (home-page "https://github.com/jimhester/withr")
1539 (synopsis "Run code with temporarily modified global state")
1541 "This package provides a set of functions to run R code in an environment
1542 in which global state has been temporarily modified. Many of these functions
1543 were originally a part of the r-devtools package.")
1544 (license license:gpl2+)))
1546 (define-public r-readr
1552 (uri (cran-uri "readr" version))
1555 "156422xwvskynna5kjc8h1qqnn50kxgjrihl2h2b7vm9sxxdyr2m"))))
1556 (build-system r-build-system)
1558 `(("r-curl" ,r-curl)
1561 (home-page "https://github.com/hadley/readr")
1562 (synopsis "Read tabular data")
1564 "This package provides functions to read flat or tabular text files from
1565 disk (or a connection).")
1566 (license license:gpl2+)))
1568 (define-public r-plotrix
1574 (uri (cran-uri "plotrix" version))
1577 "1jn1k3skmlgyvpijj6vlcn5m2zgrsdh00g1fq8n5dqs1pkl1sqrw"))))
1578 (build-system r-build-system)
1579 (home-page "http://cran.r-project.org/web/packages/plotrix")
1580 (synopsis "Various plotting functions")
1582 "This package provides lots of plotting, various labeling, axis and color
1583 scaling functions for R.")
1584 (license license:gpl2+)))
1586 (define-public r-gridbase
1592 (uri (cran-uri "gridBase" version))
1595 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
1596 (build-system r-build-system)
1597 (home-page "http://cran.r-project.org/web/packages/gridBase")
1598 (synopsis "Integration of base and grid graphics")
1600 "This package provides an integration of base and grid graphics for R.")
1601 (license license:gpl2+)))
1603 (define-public r-lattice
1609 (uri (cran-uri "lattice" version))
1612 "0car12x5vl9k180i9pc86lq3cvwqakdpqn3lgdf98k9n2h52cilg"))))
1613 (build-system r-build-system)
1614 (home-page "http://lattice.r-forge.r-project.org/")
1615 (synopsis "High-level data visualization system")
1617 "The lattice package provides a powerful and elegant high-level data
1618 visualization system inspired by Trellis graphics, with an emphasis on
1619 multivariate data. Lattice is sufficient for typical graphics needs, and is
1620 also flexible enough to handle most nonstandard requirements.")
1621 (license license:gpl2+)))
1623 (define-public r-latticeextra
1625 (name "r-latticeextra")
1630 (uri (cran-uri "latticeExtra" version))
1633 "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq"))))
1634 (properties `((upstream-name . "latticeExtra")))
1635 (build-system r-build-system)
1637 `(("r-lattice" ,r-lattice)
1638 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1639 (home-page "http://latticeextra.r-forge.r-project.org/")
1640 (synopsis "Extra graphical utilities based on lattice")
1642 "Building on the infrastructure provided by the lattice package, this
1643 package provides several new high-level graphics functions and methods, as
1644 well as additional utilities such as panel and axis annotation functions.")
1645 (license license:gpl2+)))
1647 (define-public r-rcpparmadillo
1649 (name "r-rcpparmadillo")
1650 (version "0.6.700.3.0")
1653 (uri (cran-uri "RcppArmadillo" version))
1656 "1mc62b6my568ni18w4clgs6l6ggqrwzsm3lgx0c1prf4rap69s8w"))
1657 (modules '((guix build utils)))
1658 ;; Remove bundled armadillo sources
1661 (delete-file-recursively "inst/include/armadillo_bits")
1662 (delete-file "inst/include/armadillo")))))
1663 (properties `((upstream-name . "RcppArmadillo")))
1664 (build-system r-build-system)
1667 (modify-phases %standard-phases
1668 (add-after 'unpack 'link-against-armadillo
1670 (substitute* "src/Makevars"
1671 (("PKG_LIBS=" prefix)
1672 (string-append prefix "-larmadillo"))))))))
1674 `(("r-rcpp" ,r-rcpp)
1675 ("armadillo" ,armadillo-for-rcpparmadillo)))
1676 (home-page "https://github.com/RcppCore/RcppArmadillo")
1677 (synopsis "Rcpp integration for the Armadillo linear algebra library")
1679 "Armadillo is a templated C++ linear algebra library that aims towards a
1680 good balance between speed and ease of use. Integer, floating point and
1681 complex numbers are supported, as well as a subset of trigonometric and
1682 statistics functions. Various matrix decompositions are provided through
1683 optional integration with LAPACK and ATLAS libraries. This package includes
1684 the header files from the templated Armadillo library.")
1685 ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
1686 ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
1687 ;; later, as is the rest of 'Rcpp'.
1688 (license license:gpl2+)))
1690 (define-public r-bitops
1696 (uri (cran-uri "bitops" version))
1699 "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
1700 (build-system r-build-system)
1701 (home-page "http://cran.r-project.org/web/packages/bitops")
1702 (synopsis "Bitwise operations")
1704 "This package provides functions for bitwise operations on integer
1706 (license license:gpl2+)))
1708 (define-public r-catools
1714 (uri (cran-uri "caTools" version))
1717 "1x4szsn2qmbzpyjfdaiz2q7jwhap2gky9wq0riah74q0pzz76ank"))))
1718 (properties `((upstream-name . "caTools")))
1719 (build-system r-build-system)
1721 `(("r-bitops" ,r-bitops)))
1722 (home-page "http://cran.r-project.org/web/packages/caTools")
1723 (synopsis "Various tools including functions for moving window statistics")
1725 "This package contains several basic utility functions including:
1726 moving (rolling, running) window statistic functions, read/write for GIF and
1727 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
1728 encoder/decoder, round-off-error-free sum and cumsum, etc.")
1729 (license license:gpl3+)))
1731 (define-public r-rmarkdown
1733 (name "r-rmarkdown")
1738 (uri (cran-uri "rmarkdown" version))
1741 "09ajq5miqzz46q0i9svvbh93dbi7xbjn4702d6z3scdz272gx7l2"))))
1742 (properties `((upstream-name . "rmarkdown")))
1743 (build-system r-build-system)
1745 `(("r-catools" ,r-catools)
1746 ("r-htmltools" ,r-htmltools)
1747 ("r-knitr" ,r-knitr)
1749 ("ghc-pandoc" ,ghc-pandoc)))
1750 (home-page "http://rmarkdown.rstudio.com")
1751 (synopsis "Convert R Markdown documents into a variety of formats")
1753 "This package provides tools to convert R Markdown documents into a
1754 variety of formats.")
1755 (license license:gpl3+)))
1757 (define-public r-gtable
1763 (uri (cran-uri "gtable" version))
1766 "0vz7073m0a2q12qzzihrfh5c2kx5jqi5l7z470fxmwqghdllh7l0"))))
1767 (properties `((upstream-name . "gtable")))
1768 (build-system r-build-system)
1769 (home-page "http://cran.r-project.org/web/packages/gtable")
1770 (synopsis "Arrange grobs in tables")
1772 "This package provides tools to make it easier to work with tables of
1774 (license license:gpl2+)))
1776 (define-public r-gridextra
1778 (name "r-gridextra")
1782 (uri (cran-uri "gridExtra" version))
1785 "0638ihwl00j76ivaxxhxvi8z573lwy1jym3srr78mx6dbdd4bzj4"))))
1786 (properties `((upstream-name . "gridExtra")))
1787 (build-system r-build-system)
1789 `(("r-gtable" ,r-gtable)))
1791 `(("r-knitr" ,r-knitr))) ;for building vignettes
1792 (home-page "https://github.com/baptiste/gridextra")
1793 (synopsis "Miscellaneous functions for \"Grid\" graphics")
1795 "This package provides a number of user-level functions to work with
1796 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
1798 (license license:gpl2+)))
1800 (define-public r-rsqlite
1806 (uri (cran-uri "RSQLite" version))
1809 "08b1syv8z887gxiw8i09dpqh0zisfb6ihq6qqr01zipvkahzq34f"))))
1810 (properties `((upstream-name . "RSQLite")))
1811 (build-system r-build-system)
1813 `(("r-dbi" ,r-dbi)))
1814 (home-page "https://github.com/rstats-db/RSQLite")
1815 (synopsis "SQLite interface for R")
1817 "This package embeds the SQLite database engine in R and provides an
1818 interface compliant with the DBI package. The source for the SQLite
1819 engine (version 3.8.6) is included.")
1820 (license license:lgpl2.0+)))
1822 (define-public r-rcurl
1825 (version "1.95-0.1.2")
1828 (uri (string-append "http://www.bioconductor.org/packages/"
1829 "release/extra/src/"
1830 "contrib/RCurl_" version ".tar.gz"))
1833 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
1834 (properties `((upstream-name . "RCurl")))
1835 (build-system r-build-system)
1837 `(("libcurl" ,curl)))
1839 `(("r-bitops" ,r-bitops)))
1840 (home-page "http://www.omegahat.org/RCurl")
1841 (synopsis "General network client interface for R")
1843 "The package allows one to compose general HTTP requests and provides
1844 convenient functions to fetch URIs, GET and POST forms, etc. and process the
1845 results returned by the Web server. This provides a great deal of control
1846 over the HTTP/FTP/... connection and the form of the request while providing a
1847 higher-level interface than is available just using R socket connections.
1848 Additionally, the underlying implementation is robust and extensive,
1849 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
1850 ldap, and also supports cookies, redirects, authentication, etc.")
1851 (license license:bsd-3)))
1853 (define-public r-xml
1856 (version "3.98-1.4")
1859 (uri (cran-uri "XML" version))
1862 "09hiy5a875v2fhsgrsfymrwccn9249wnnsr6ck2slrig65svq2lw"))))
1864 `((upstream-name . "XML")))
1865 (build-system r-build-system)
1867 `(("libxml2" ,libxml2)))
1869 `(("r-rcurl" ,r-rcurl)))
1870 (home-page "http://www.omegahat.org/RSXML")
1871 (synopsis "Tools for parsing and generating XML within R")
1873 "Many approaches for both reading and creating XML (and HTML)
1874 documents (including DTDs), both local and accessible via HTTP or FTP. Also
1875 offers access to an XPath \"interpreter\".")
1876 (license license:bsd-2)))
1878 (define-public r-xnomial
1883 (origin (method url-fetch)
1884 (uri (cran-uri "XNomial" version))
1887 "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
1888 (properties (quasiquote ((upstream-name . "XNomial"))))
1889 (build-system r-build-system)
1890 (home-page "http://cran.r-project.org/web/packages/XNomial")
1891 (synopsis "Goodness-of-Fit test for multinomial data")
1893 "This package provides an exact Goodness-of-Fit test for
1894 multinomial data with fixed probabilities. It can be used to
1895 determine whether a set of counts fits a given expected ratio. To see
1896 whether a set of observed counts fits an expectation, one can examine
1897 all possible outcomes with @code{xmulti()} or a random sample of them
1898 with @code{xmonte()} and find the probability of an observation
1899 deviating from the expectation by at least as much as the observed.
1900 As a measure of deviation from the expected, one can use the
1901 log-likelihood ratio, the multinomial probability, or the classic
1902 chi-square statistic. A histogram of the test statistic can also be
1903 plotted and compared with the asymptotic curve.")
1904 (license (list license:gpl2+ license:gpl3+))))
1906 (define-public r-lambda-r
1912 (uri (cran-uri "lambda.r" version))
1915 "1lxzrwyminc3dfb07pbn1rmj45kplxgsb17b06pzflj728knbqwa"))))
1916 (properties `((upstream-name . "lambda.r")))
1917 (build-system r-build-system)
1918 (home-page "http://cran.r-project.org/web/packages/lambda.r")
1919 (synopsis "Functional programming extension for R")
1921 "This package provides a language extension to efficiently write
1922 functional programs in R. Syntax extensions include multi-part function
1923 definitions, pattern matching, guard statements, built-in (optional) type
1925 (license license:lgpl3+)))
1927 (define-public r-futile-options
1929 (name "r-futile-options")
1933 (uri (cran-uri "futile.options" version))
1936 "1hp82h6xqq5cck67h7lpf22n3j7mg3v1mla5y5ivnzrrb7iyr17f"))))
1938 `((upstream-name . "futile.options")))
1939 (build-system r-build-system)
1940 (home-page "http://cran.r-project.org/web/packages/futile.options")
1941 (synopsis "Options management framework")
1943 "The futile.options subsystem provides an easy user-defined options
1944 management system that is properly scoped. This means that options created
1945 via @code{futile.options} are fully self-contained and will not collide with
1946 options defined in other packages.")
1947 (license license:lgpl3+)))
1949 (define-public r-futile-logger
1951 (name "r-futile-logger")
1955 (uri (cran-uri "futile.logger" version))
1958 "1plld1icxrcay7llplbd4i8inpg97crpnczk58mbk26j8glqbr51"))))
1959 (properties `((upstream-name . "futile.logger")))
1960 (build-system r-build-system)
1962 `(("r-futile-options" ,r-futile-options)
1963 ("r-lambda-r" ,r-lambda-r)))
1964 (home-page "http://cran.r-project.org/web/packages/futile.logger")
1965 (synopsis "Logging utility for R")
1967 "This package provides a simple yet powerful logging utility. Based
1968 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
1969 convenient and easy to use replacement for @code{cat} and @code{print}
1971 (license license:lgpl3+)))
1973 (define-public r-snow
1979 (uri (cran-uri "snow" version))
1982 "19r2yq8aqw99vwyx81p6ay4afsfqffal1wzvizk3dj882s2n4j8w"))))
1983 (build-system r-build-system)
1984 (home-page "http://cran.r-project.org/web/packages/snow")
1985 (synopsis "Support for simple parallel computing in R")
1987 "The snow package provides support for simple parallel computing on a
1988 network of workstations using R. A master R process calls @code{makeCluster}
1989 to start a cluster of worker processes; the master process then uses functions
1990 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
1991 worker processes and collect and return the results on the master.")
1992 (license (list license:gpl2+ license:gpl3+))))
1994 (define-public r-sparsem
2000 (uri (cran-uri "SparseM" version))
2003 "0s9kab5khk7daqf6nfp1wm1qnhkssnnwnymisfwyk3kz4q5maqfz"))))
2005 `((upstream-name . "SparseM")))
2007 `(("gfortran" ,gfortran)))
2008 (build-system r-build-system)
2009 (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
2010 (synopsis "Sparse linear algebra")
2012 "This package provides some basic linear algebra functionality for sparse
2013 matrices. It includes Cholesky decomposition and backsolving as well as
2014 standard R subsetting and Kronecker products.")
2015 (license license:gpl2+)))
2017 (define-public r-iterators
2019 (name "r-iterators")
2024 (uri (cran-uri "iterators" version))
2027 "1f057pabs7ss9h1n244can26qsi5n2k3salrdk0b0vkphlrs4kmf"))))
2028 (build-system r-build-system)
2029 (home-page "http://cran.r-project.org/web/packages/iterators")
2030 (synopsis "Iterator construct for R")
2032 "This package provides support for iterators, which allow a programmer to
2033 traverse through all the elements of a vector, list, or other collection of
2035 (license license:asl2.0)))
2037 (define-public r-codetools
2039 (name "r-codetools")
2044 (uri (cran-uri "codetools" version))
2047 "0y9r4m2b8xgavr89sc179knzwpz54xljbc1dinpq2q07i4xn0397"))))
2048 (build-system r-build-system)
2049 (home-page "http://cran.r-project.org/web/packages/codetools")
2050 (synopsis "Code analysis tools for R")
2051 (description "This package provides code analysis tools for R to check R
2052 code for possible problems.")
2053 (license (list license:gpl2+ license:gpl3+))))
2055 (define-public r-foreach
2062 (uri (cran-uri "foreach" version))
2065 "10aqsd3rxz03s1qdb6gsb1cj89mj4vmh491zfpin4skj1xvkzw0y"))))
2066 (build-system r-build-system)
2068 `(("r-codetools" ,r-codetools)
2069 ("r-iterators" ,r-iterators)))
2070 (home-page "http://cran.r-project.org/web/packages/foreach")
2071 (synopsis "Foreach looping construct for R")
2073 "This package provides support for the @code{foreach} looping construct.
2074 @code{foreach} is an idiom that allows for iterating over elements in a
2075 collection, without the use of an explicit loop counter. This package in
2076 particular is intended to be used for its return value, rather than for its
2077 side effects. In that sense, it is similar to the standard @code{lapply}
2078 function, but doesn't require the evaluation of a function. Using
2079 @code{foreach} without side effects also facilitates executing the loop in
2081 (license license:asl2.0)))
2083 (define-public r-doparallel
2085 (name "r-doparallel")
2090 (uri (cran-uri "doParallel" version))
2093 "1mddx25l25pw9d0csnx2q203dbg5hbrhkr1f08kw0p02a1lln0kh"))))
2094 (properties `((upstream-name . "doParallel")))
2095 (build-system r-build-system)
2097 `(("r-foreach" ,r-foreach)
2098 ("r-iterators" ,r-iterators)))
2099 (home-page "http://cran.r-project.org/web/packages/doParallel")
2100 (synopsis "Foreach parallel adaptor for the 'parallel' package")
2102 "This package provides a parallel backend for the @code{%dopar%} function
2103 using the parallel package.")
2104 (license license:gpl2+)))
2112 (uri (cran-uri "DT" version))
2115 "0mj7iiy1gglw7kixybmb7kr1bcl5r006zcb3klkw7p6vvvzdm6qj"))))
2117 `((upstream-name . "DT")))
2118 (build-system r-build-system)
2120 `(("r-htmltools" ,r-htmltools)
2121 ("r-htmlwidgets" ,r-htmlwidgets)
2122 ("r-magrittr" ,r-magrittr)))
2123 (home-page "http://rstudio.github.io/DT")
2124 (synopsis "R wrapper of the DataTables JavaScript library")
2126 "This package allows for data objects in R to be rendered as HTML tables
2127 using the JavaScript library 'DataTables' (typically via R Markdown or Shiny).
2128 The 'DataTables' library has been included in this R package.")
2129 ;; The DT package as a whole is distributed under GPLv3. The DT package
2130 ;; inludes other software components under different licenses:
2132 ;; * Expat: jQuery, jquery.highlight.js, DataTables
2133 ;; * ASL2.0: selectize.js
2134 ;; * WTFPL: noUiSlider
2135 (license (list license:gpl3
2138 (license:non-copyleft "http://www.wtfpl.net/txt/copying/")))))
2140 (define-public r-base64enc
2142 (name "r-base64enc")
2146 (uri (cran-uri "base64enc" version))
2149 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
2150 (build-system r-build-system)
2151 (home-page "http://www.rforge.net/base64enc")
2152 (synopsis "Tools for Base64 encoding")
2154 "This package provides tools for handling Base64 encoding. It is more
2155 flexible than the orphaned \"base64\" package.")
2156 (license license:gpl2+)))
2158 (define-public r-irlba
2165 (uri (cran-uri "irlba" version))
2168 "1gms3rxrm24ri4vjvnpl4v47m7bx0zk63z8y85rbhsvx230xdy0m"))))
2169 (build-system r-build-system)
2170 (home-page "http://cran.r-project.org/web/packages/irlba")
2171 (synopsis "Methods for eigendecomposition of large matrices")
2173 "This package provides fast and memory efficient methods for truncated
2174 singular and eigenvalue decompositions, as well as for principal component
2175 analysis of large sparse or dense matrices.")
2176 (license (list license:gpl2+ license:gpl3+))))
2178 (define-public r-pkgmaker
2185 (uri (cran-uri "pkgmaker" version))
2188 "0vrqnd3kg6liqvpbd969jjsdx0f0rvmmxgdbwwrp6xfmdg0pib8r"))))
2189 (build-system r-build-system)
2191 `(("r-codetools" ,r-codetools)
2192 ("r-digest" ,r-digest)
2193 ("r-registry" ,r-registry)
2194 ("r-stringr" ,r-stringr)
2195 ("r-xtable" ,r-xtable)))
2196 (home-page "https://renozao.github.io/pkgmaker")
2197 (synopsis "Package development utilities")
2199 "This package provides some low-level utilities to use for R package
2200 development. It currently provides managers for multiple package specific
2201 options and registries, vignette, unit test and bibtex related utilities.")
2202 (license license:gpl2+)))
2204 (define-public r-registry
2211 (uri (cran-uri "registry" version))
2214 "0c7lscfxncwwd8zp46h2xfw9gw14dypqv6m2kx85xjhjh0xw99aq"))))
2215 (build-system r-build-system)
2216 (home-page "http://cran.r-project.org/web/packages/registry")
2217 (synopsis "Infrastructure for R package registries")
2219 "This package provides a generic infrastructure for creating and using R
2220 package registries.")
2221 (license license:gpl2+)))
2223 (define-public r-rngtools
2230 (uri (cran-uri "rngtools" version))
2233 "1fcgfqrrb48z37xgy8sffx91p9irp39yqzxv7nqp1x2hnwsrh097"))))
2234 (build-system r-build-system)
2236 `(("r-digest" ,r-digest)
2237 ("r-pkgmaker" ,r-pkgmaker)
2238 ("r-stringr" ,r-stringr)))
2239 (home-page "https://renozao.github.io/rngtools")
2240 (synopsis "Utility functions for working with random number generators")
2242 "This package contains a set of functions for working with Random Number
2243 Generators (RNGs). In particular, it defines a generic S4 framework for
2244 getting/setting the current RNG, or RNG data that are embedded into objects
2245 for reproducibility. Notably, convenient default methods greatly facilitate
2246 the way current RNG settings can be changed.")
2247 (license license:gpl3+)))
2249 (define-public r-nmf
2256 (uri (cran-uri "NMF" version))
2259 "0mmh9bz0zjwd8h9jplz4rq3g94npaqj8s4px51vcv47csssd9k6z"))))
2260 (properties `((upstream-name . "NMF")))
2261 (build-system r-build-system)
2263 `(("r-cluster" ,r-cluster)
2264 ("r-colorspace" ,r-colorspace)
2265 ("r-digest" ,r-digest)
2266 ("r-doparallel" ,r-doparallel)
2267 ("r-foreach" ,r-foreach)
2268 ("r-ggplot2" ,r-ggplot2)
2269 ("r-gridbase" ,r-gridbase)
2270 ("r-pkgmaker" ,r-pkgmaker)
2271 ("r-rcolorbrewer" ,r-rcolorbrewer)
2272 ("r-registry" ,r-registry)
2273 ("r-reshape2" ,r-reshape2)
2274 ("r-rngtools" ,r-rngtools)
2275 ("r-stringr" ,r-stringr)))
2276 (home-page "http://renozao.github.io/NMF")
2277 (synopsis "Algorithms and framework for nonnegative matrix factorization")
2279 "This package provides a framework to perform Non-negative Matrix
2280 Factorization (NMF). The package implements a set of already published
2281 algorithms and seeding methods, and provides a framework to test, develop and
2282 plug new or custom algorithms. Most of the built-in algorithms have been
2283 optimized in C++, and the main interface function provides an easy way of
2284 performing parallel computations on multicore machines.")
2285 (license license:gpl2+)))
2287 (define-public r-igraph
2294 (uri (cran-uri "igraph" version))
2297 "00jnm8v3kvxpxav5klld2z2nnkcpj4sdwv4ksipddy5mp04ysr6w"))))
2298 (build-system r-build-system)
2300 `(("gfortran" ,gfortran)))
2303 ("libxml2" ,libxml2)))
2305 `(("r-irlba" ,r-irlba)
2306 ("r-magrittr" ,r-magrittr)
2308 (home-page "http://igraph.org")
2309 (synopsis "Network analysis and visualization")
2311 "This package provides routines for simple graphs and network analysis.
2312 It can handle large graphs very well and provides functions for generating
2313 random and regular graphs, graph visualization, centrality methods and much
2315 (license license:gpl2+)))
2317 (define-public r-r-methodss3
2319 (name "r-r-methodss3")
2323 (uri (cran-uri "R.methodsS3" version))
2326 "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24"))))
2327 (properties `((upstream-name . "R.methodsS3")))
2328 (build-system r-build-system)
2329 (home-page "http://cran.r-project.org/web/packages/R.methodsS3")
2330 (synopsis "S3 methods simplified")
2332 "This package provides methods that simplify the setup of S3 generic
2333 functions and S3 methods. Major effort has been made in making definition of
2334 methods as simple as possible with a minimum of maintenance for package
2335 developers. For example, generic functions are created automatically, if
2336 missing, and naming conflict are automatically solved, if possible. The
2337 method @code{setMethodS3()} is a good start for those who in the future may
2338 want to migrate to S4.")
2339 (license license:lgpl2.1+)))
2341 (define-public r-r-oo
2347 (uri (cran-uri "R.oo" version))
2350 "1l1x4r69mdchjyi6sq52p580fz3b3bqv6dpn1706y9n4vq47qx24"))))
2351 (properties `((upstream-name . "R.oo")))
2352 (build-system r-build-system)
2354 `(("r-r-methodss3" ,r-r-methodss3)))
2355 (home-page "https://github.com/HenrikBengtsson/R.oo")
2356 (synopsis "R object-oriented programming with or without references")
2358 "This package provides methods and classes for object-oriented
2359 programming in R with or without references. Large effort has been made on
2360 making definition of methods as simple as possible with a minimum of
2361 maintenance for package developers.")
2362 (license license:lgpl2.1+)))
2364 (define-public r-r-utils
2370 (uri (cran-uri "R.utils" version))
2373 "0f4z7ka1wb7bgxc5wyqihqxsnqwgyyzbglwvfwmx0gn8i0wzi647"))))
2374 (properties `((upstream-name . "R.utils")))
2375 (build-system r-build-system)
2377 `(("r-r-methodss3" ,r-r-methodss3)
2378 ("r-r-oo" ,r-r-oo)))
2379 (home-page "https://github.com/HenrikBengtsson/R.utils")
2380 (synopsis "Various programming utilities")
2382 "This package provides utility functions useful when programming and
2383 developing R packages.")
2384 (license license:lgpl2.1+)))
2386 (define-public r-r-cache
2392 (uri (cran-uri "R.cache" version))
2395 "006x52w9r8phw5hgqmyp0bz8z42vn8p5yibibnzi1sfa1xlw8iyx"))))
2396 (properties `((upstream-name . "R.cache")))
2397 (build-system r-build-system)
2399 `(("r-digest" ,r-digest)
2400 ("r-r-methodss3" ,r-r-methodss3)
2402 ("r-r-utils" ,r-r-utils)))
2403 (home-page "https://github.com/HenrikBengtsson/R.cache")
2404 (synopsis "Light-weight caching of objects and results")
2406 "This package provides methods for caching or memoization of objects and
2407 results. With this package, any R object can be cached in a key-value storage
2408 where the key can be an arbitrary set of R objects. The cache memory is
2409 persistent (on the file system).")
2410 (license license:lgpl2.1+)))
2412 (define-public r-r-rsp
2418 (uri (cran-uri "R.rsp" version))
2421 "0snc6ps75s3ci6sy8mil1wg2i9xmlr1ygh9n244y1brdvp43dfsw"))))
2422 (properties `((upstream-name . "R.rsp")))
2423 (build-system r-build-system)
2425 `(("r-r-cache" ,r-r-cache)
2426 ("r-r-methodss3" ,r-r-methodss3)
2428 ("r-r-utils" ,r-r-utils)))
2429 (home-page "https://github.com/HenrikBengtsson/R.rsp")
2430 (synopsis "Dynamic generation of scientific reports")
2432 "The RSP markup language provides a powerful markup for controlling the
2433 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
2434 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
2435 to many other literate programming languages, with RSP it is straightforward
2436 to loop over mixtures of code and text sections, e.g. in month-by-month
2437 summaries. RSP has also several preprocessing directives for incorporating
2438 static and dynamic contents of external files (local or online) among other
2439 things. RSP is ideal for self-contained scientific reports and R package
2441 (license license:lgpl2.1+)))
2443 (define-public r-mvtnorm
2449 (uri (cran-uri "mvtnorm" version))
2452 "1pc1mi2h063gh4a40009xk5j6pf5bm4274i5kycln38dixsry3yh"))))
2453 (build-system r-build-system)
2455 `(("gfortran" ,gfortran)))
2456 (home-page "http://mvtnorm.R-forge.R-project.org")
2457 (synopsis "Package for multivariate normal and t-distributions")
2458 (description "This package can compute multivariate normal and
2459 t-probabilities, quantiles, random deviates and densities.")
2460 (license license:gpl2)))
2462 (define-public r-matrixstats
2464 (name "r-matrixstats")
2468 (uri (cran-uri "matrixStats" version))
2471 "08l32abp7dfnsc49ca4hzznh934y60n5z01x5ga2ixky5961s57c"))))
2472 (properties `((upstream-name . "matrixStats")))
2473 (build-system r-build-system)
2475 `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
2476 (home-page "https://github.com/HenrikBengtsson/matrixStats")
2477 (synopsis "Methods applying to vectors and matrix rows and columns")
2479 "This package provides methods operating on rows and columns of matrices,
2480 e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
2481 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
2482 @code{weightedMedians()}. All methods have been optimized for speed and
2484 (license license:artistic2.0)))
2486 (define-public r-viridis
2492 (uri (cran-uri "viridis" version))
2495 "1a9hqn2pccpc51vh8ghw698ni6xzdnp8v0n8kgjh51nlz5hhc87j"))))
2496 (build-system r-build-system)
2498 `(("r-ggplot2" ,r-ggplot2)
2499 ("r-gridextra" ,r-gridextra)))
2500 (home-page "https://github.com/sjmgarnier/viridis")
2501 (synopsis "Matplotlib default color map")
2503 "This package is a port of the new @url{matplotlib,
2504 http://matplotlib.org/} color maps (@code{viridis}--the default--,
2505 @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
2506 designed in such a way that they will analytically be perfectly
2507 perceptually-uniform, both in regular form and also when converted to
2508 black-and-white. They are also designed to be perceived by readers with the
2509 most common form of color blindness.")
2510 (license license:x11)))
2512 (define-public r-tidyr
2519 (uri (cran-uri "tidyr" version))
2522 "0xp6lyr2l4ix2mrilx4qmca7wm5qmbhvi24m4nf7qsgwp54gnv2h"))))
2523 (build-system r-build-system)
2525 `(("r-dplyr" ,r-dplyr)
2526 ("r-lazyeval" ,r-lazyeval)
2527 ("r-magrittr" ,r-magrittr)
2529 ("r-stringi" ,r-stringi)))
2530 (home-page "https://github.com/hadley/tidyr")
2531 (synopsis "Tidy data with `spread()` and `gather()` functions")
2533 "tidyr is a reframing of the reshape2 package designed to accompany the
2534 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
2535 a solid pipeline for data analysis. It is designed specifically for tidying
2536 data, not the general reshaping that reshape2 does, or the general aggregation
2537 that reshape did. In particular, built-in methods only work for data frames,
2538 and tidyr provides no margins or aggregation.")
2539 (license license:expat)))
2541 (define-public r-hexbin
2548 (uri (cran-uri "hexbin" version))
2551 "0xi6fbf1fvyn2gffr052n3viibqzpr3603sgi4xaminbzja4syjh"))))
2552 (build-system r-build-system)
2554 `(("r-lattice" ,r-lattice)))
2556 `(("gfortran" ,gfortran)))
2557 (home-page "http://github.com/edzer/hexbin")
2558 (synopsis "Hexagonal binning routines")
2560 "This package provides binning and plotting functions for hexagonal bins.
2561 It uses and relies on grid graphics and formal (S4) classes and methods.")
2562 (license license:gpl2+)))
2564 (define-public r-plotly
2570 (uri (cran-uri "plotly" version))
2573 "1pfl9w35iwin8a1hfwcihajyps2ngjbyrmvi61b9lspcdbk39lf8"))))
2574 (build-system r-build-system)
2576 `(("r-base64enc" ,r-base64enc)
2577 ("r-digest" ,r-digest)
2578 ("r-ggplot2" ,r-ggplot2)
2579 ("r-hexbin" ,r-hexbin)
2580 ("r-htmlwidgets" ,r-htmlwidgets)
2582 ("r-jsonlite" ,r-jsonlite)
2583 ("r-magrittr" ,r-magrittr)
2585 ("r-scales" ,r-scales)
2586 ("r-tidyr" ,r-tidyr)
2587 ("r-viridis" ,r-viridis)))
2588 (home-page "https://plot.ly/r")
2589 (synopsis "Create interactive web graphics")
2591 "This package enables the translation of ggplot2 graphs to an interactive
2592 web-based version and/or the creation of custom web-based visualizations
2593 directly from R. Once uploaded to a plotly account, plotly graphs (and the
2594 data behind them) can be viewed and modified in a web browser.")
2595 (license license:x11)))
2597 (define-public r-biased-urn
2599 (name "r-biased-urn")
2604 (uri (cran-uri "BiasedUrn" version))
2607 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
2608 (properties `((upstream-name . "BiasedUrn")))
2609 (build-system r-build-system)
2610 (home-page "http://www.agner.org/random/")
2611 (synopsis "Biased urn model distributions")
2613 "This package provides statistical models of biased sampling in the form
2614 of univariate and multivariate noncentral hypergeometric distributions,
2615 including Wallenius' noncentral hypergeometric distribution and Fisher's
2616 noncentral hypergeometric distribution (also called extended hypergeometric
2618 (license license:gpl3+)))
2620 (define-public r-ztable
2626 (uri (cran-uri "ztable" version))
2629 "1jfqnqy9544gfvz3bsb48v4177nwp4b4n9l2743asq8sbq305b5r"))))
2630 (build-system r-build-system)
2631 (home-page "http://cran.r-project.org/web/packages/ztable")
2632 (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
2634 "This package provides functions to make zebra-striped tables (tables
2635 with alternating row colors) in LaTeX and HTML formats easily from
2636 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
2637 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
2638 @code{cbind.mytable} objects.")
2639 (license license:gpl2+)))