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 "1afsq0a3iij64qacczvwhk81qg0q5rfqm055y5h9ls28d6paqz7p"))))
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
168 `(;; We need not only cairo here, but pango to ensure that tests for the
169 ;; "cairo" bitmapType plotting backend succeed.
173 ("gfortran" ,gfortran)
180 ("readline" ,readline)
183 (list (search-path-specification
184 (variable "R_LIBS_SITE")
185 (files (list "site-library/")))))
186 (home-page "http://www.r-project.org/")
187 (synopsis "Environment for statistical computing and graphics")
189 "R is a language and environment for statistical computing and graphics.
190 It provides a variety of statistical techniques, such as linear and nonlinear
191 modeling, classical statistical tests, time-series analysis, classification
192 and clustering. It also provides robust support for producing
193 publication-quality data plots. A large amount of 3rd-party packages are
194 available, greatly increasing its breadth and scope.")
195 (license license:gpl3+)))
197 (define-public r-colorspace
199 (name "r-colorspace")
204 (uri (cran-uri "colorspace" version))
206 (base32 "0y8n4ljwhbdvkysdwgqzcnpv107pb3px1jip3k6svv86p72nacds"))))
207 (build-system r-build-system)
208 (home-page "http://cran.r-project.org/web/packages/colorspace")
209 (synopsis "Color space manipulation")
211 "This package carries out a mapping between assorted color spaces
212 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
213 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
214 colors are provided.")
215 (license license:bsd-3)))
217 (define-public r-dichromat
224 (uri (cran-uri "dichromat" version))
226 (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
227 (build-system r-build-system)
228 (home-page "http://cran.r-project.org/web/packages/dichromat")
229 (synopsis "Color schemes for dichromats")
231 "Dichromat collapses red-green or green-blue distinctions to simulate the
232 effects of different types of color-blindness.")
233 (license license:gpl2+)))
235 (define-public r-digest
242 (uri (cran-uri "digest" version))
244 (base32 "0ixy1mb7kfl20lkckqiilpw03g1ip4ibihs03gicz7w625hc7zcm"))))
245 (build-system r-build-system)
246 ;; Vignettes require r-knitr, which requires r-digest, so we have to
247 ;; disable them and the tests.
250 #:configure-flags (list "--no-build-vignettes")))
251 (home-page "http://dirk.eddelbuettel.com/code/digest.html")
252 (synopsis "Create cryptographic hash digests of R objects")
254 "This package contains an implementation of a function 'digest()' for the
255 creation of hash digests of arbitrary R objects (using the md5, sha-1,
256 sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
257 of R language objects, as well as a function 'hmac()' to create hash-based
258 message authentication code.
260 Please note that this package is not meant to be deployed for cryptographic
261 purposes for which more comprehensive (and widely tested) libraries such as
262 OpenSSL should be used.")
263 (license license:gpl2+)))
265 (define-public r-estimability
267 (name "r-estimability")
271 (uri (cran-uri "estimability" version))
274 "049adh8i0ad0m0qln2ylqdxcs5v2q9zfignn2a50r5f93ip2ay6w"))))
275 (build-system r-build-system)
276 (home-page "http://cran.r-project.org/web/packages/estimability")
277 (synopsis "Tools for assessing estimability of linear predictions")
278 (description "Provides tools for determining estimability of linear
279 functions of regression coefficients, and 'epredict' methods that handle
280 non-estimable cases correctly.")
281 (license license:gpl2+)))
283 (define-public r-gtable
290 (uri (cran-uri "gtable" version))
292 (base32 "0k9hfj6r5y238gqh92s3cbdn34biczx3zfh79ix5xq0c5vkai2xh"))))
293 (build-system r-build-system)
294 (home-page "https://cran.r-project.org/web/packages/gtable")
295 (synopsis "R library to arrange grobs in tables")
297 "Gtable is a collection of tools to make it easier to work with
298 \"tables\" of grobs.")
299 (license license:gpl2+)))
301 (define-public r-labeling
308 (uri (cran-uri "labeling" version))
310 (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
311 (build-system r-build-system)
312 (home-page "http://cran.r-project.org/web/packages/labeling")
313 (synopsis "Axis labeling algorithms")
314 (description "The labeling package provides a range of axis labeling
316 (license license:expat)))
318 (define-public r-magrittr
325 (uri (cran-uri "magrittr" version))
327 (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
328 (build-system r-build-system)
329 (home-page "http://cran.r-project.org/web/packages/magrittr/index.html")
330 (synopsis "A forward-pipe operator for R")
332 "Magrittr provides a mechanism for chaining commands with a new
333 forward-pipe operator, %>%. This operator will forward a value, or the result
334 of an expression, into the next function call/expression. There is flexible
335 support for the type of right-hand side expressions. For more information,
336 see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
337 (license license:expat)))
339 (define-public r-munsell
346 (uri (cran-uri "munsell" version))
348 (base32 "0jdxlbjslkzaqgp058da1cgm85qvqi09wpcgpvp4hvwnmy83qz1r"))))
349 (build-system r-build-system)
351 `(("r-colorspace" ,r-colorspace)))
352 (home-page "http://cran.r-project.org/web/packages/munsell")
353 (synopsis "Munsell colour system")
355 "The Munsell package contains Functions for exploring and using the
356 Munsell colour system.")
357 (license license:expat)))
359 (define-public r-rcpp
366 (uri (cran-uri "Rcpp" version))
368 (base32 "1vw0zbd6zhqixqg7h8ahn1dr1hb492365x419nrp2lhvr60r8i0k"))))
369 (build-system r-build-system)
370 (home-page "http://www.rcpp.org")
371 (synopsis "Seamless R and C++ Integration")
373 "The Rcpp package provides R functions as well as C++ classes which offer
374 a seamless integration of R and C++. Many R data types and objects can be
375 mapped back and forth to C++ equivalents which facilitates both writing of new
376 code as well as easier integration of third-party libraries. Documentation
377 about Rcpp is provided by several vignettes included in this package, via the
378 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
379 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
380 'citation(\"Rcpp\")' for details on these last two.")
381 (license license:gpl2+)))
383 (define-public r-mgcv
390 (uri (cran-uri "mgcv" version))
393 "1khzy36nn6xbnzqfc2953ng0sv8w91mns1ymhibaqn1150x1qid0"))))
394 (build-system r-build-system)
395 (home-page "http://cran.r-project.org/web/packages/mgcv")
396 (synopsis "Mixed generalised additive model computation")
398 "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
399 parameter estimation by GCV, REML or UBRE/AIC. The library includes a
400 @code{gam()} function, a wide variety of smoothers, JAGS support and
401 distributions beyond the exponential family.")
402 (license license:gpl2+)))
404 (define-public r-permute
411 (uri (cran-uri "permute" version))
414 "0w68cqw6s4pixix8bh1qzsy1pm64jqh1cjznw74h82ygp8sj7p73"))))
415 (build-system r-build-system)
416 ;; Tests do not run correctly, but running them properly would entail a
417 ;; circular dependency with vegan.
418 (home-page "https://github.com/gavinsimpson/permute")
419 (synopsis "Functions for Generating Restricted Permutations of Data")
421 "This package provides a set of restricted permutation designs for freely
422 exchangeable, line transects (time series), spatial grid designs and permutation
423 of blocks (groups of samples). @code{permute} also allows split-plot designs,
424 in which the whole-plots or split-plots or both can be freely exchangeable.")
425 (license license:gpl2+)))
427 (define-public r-plyr
434 (uri (cran-uri "plyr" version))
436 (base32 "06v4zxawpjz37rp2q2ii5q43g664z9s29j4ydn0cz3crn7lzl6pk"))))
437 (build-system r-build-system)
438 (native-inputs `(("r-rcpp" ,r-rcpp)))
439 (home-page "http://had.co.nz/plyr")
440 (synopsis "Tools for Splitting, Applying and Combining Data")
442 "Plyr is a set of tools that solves a common set of problems: you need to
443 break a big problem down into manageable pieces, operate on each piece and
444 then put all the pieces back together. For example, you might want to fit a
445 model to each spatial location or time point in your study, summarise data by
446 panels or collapse high-dimensional arrays to simpler summary statistics.")
447 (license license:expat)))
449 (define-public r-proto
456 (uri (cran-uri "proto" version))
458 (base32 "03mvzi529y6kjcp9bkpk7zlgpcakb3iz73hca6rpjy14pyzl3nfh"))))
459 (build-system r-build-system)
460 (home-page "http://r-proto.googlecode.com")
461 (synopsis "Prototype object-based programming")
463 "Proto is an object oriented system using object-based, also called
464 prototype-based, rather than class-based object oriented ideas.")
465 (license license:gpl2+)))
467 (define-public r-rcolorbrewer
469 (name "r-rcolorbrewer")
474 (uri (cran-uri "RColorBrewer" version))
476 (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
477 (build-system r-build-system)
478 (home-page "http://cran.r-project.org/web/packages/RColorBrewer")
479 (synopsis "ColorBrewer palettes")
481 "This package provides color schemes for maps (and other graphics)
482 designed by Cynthia Brewer as described at http://colorbrewer2.org")
483 ;; Includes code licensed under bsd-4
484 (license license:asl2.0)))
486 (define-public r-stringi
493 (uri (cran-uri "stringi" version))
496 "1ld38536sswyywp6pyys3v8vkngbk5cksrhdxp8jyr6bz7qf8j77"))))
497 (build-system r-build-system)
498 (inputs `(("icu4c" ,icu4c)))
499 (native-inputs `(("pkg-config" ,pkg-config)))
500 (home-page "http://stringi.rexamine.com/")
501 (synopsis "Character string processing facilities")
503 "This package allows for fast, correct, consistent, portable, as well as
504 convenient character string/text processing in every locale and any native
505 encoding. Owing to the use of the ICU library, the package provides R users
506 with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
507 programmers. Among available features there are: pattern searching
508 (e.g. via regular expressions), random string generation, string collation,
509 transliteration, concatenation, date-time formatting and parsing, etc.")
510 (license license:bsd-3)))
512 (define-public r-stringr
519 (uri (cran-uri "stringr" version))
521 (base32 "0jnz6r9yqyf7dschr2fnn1slg4wn6b4ik5q00j4zrh43bfw7s9pq"))))
522 (build-system r-build-system)
524 `(("r-magrittr" ,r-magrittr)
525 ("r-stringi" ,r-stringi)))
526 (home-page "https://github.com/hadley/stringr")
527 (synopsis "Simple, consistent wrappers for common string operations")
529 "Stringr is a consistent, simple and easy to use set of wrappers around
530 the fantastic 'stringi' package. All function and argument names (and
531 positions) are consistent, all functions deal with \"NA\"'s and zero length
532 vectors in the same way, and the output from one function is easy to feed into
533 the input of another.")
534 (license license:gpl2+)))
536 (define-public r-reshape2
543 (uri (cran-uri "reshape2" version))
545 (base32 "0hl082dyk3pk07nqprpn5dvnrkqhnf6zjnjig1ijddxhlmsrzm7v"))))
546 (build-system r-build-system)
550 ("r-stringr" ,r-stringr)))
551 (home-page "https://github.com/hadley/reshape")
552 (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
554 "Reshape2 is an R library to flexibly restructure and aggregate data
555 using just two functions: melt and dcast (or acast).")
556 (license license:expat)))
558 (define-public r-scales
565 (uri (cran-uri "scales" version))
567 (base32 "19y6q4j8vpmc73dnn4ncp5wj44gri7m77ys3z2rn3crrcc9zc7l5"))))
568 (build-system r-build-system)
570 `(("r-dichromat" ,r-dichromat)
571 ("r-labeling" ,r-labeling)
572 ("r-munsell" ,r-munsell)
574 ("r-rcolorbrewer" ,r-rcolorbrewer)
576 (home-page "https://github.com/hadley/scales")
577 (synopsis "Scale functions for visualization")
579 "This package provides graphical scales that map data to aesthetics, and
580 provides methods for automatically determining breaks and labels for axes and
582 (license license:expat)))
584 (define-public r-ggplot2
591 (uri (cran-uri "ggplot2" version))
593 (base32 "0s9rvp0f736ji6p9xpxq54agxf95pjkql4sj7ag0hv2xhnp27hzj"))))
594 (build-system r-build-system)
596 `(("r-digest" ,r-digest)
597 ("r-gtable" ,r-gtable)
600 ("r-reshape2" ,r-reshape2)
601 ("r-scales" ,r-scales)
602 ("r-svglite" ,r-svglite)))
603 (home-page "http://ggplot2.org")
604 (synopsis "An implementation of the grammar of graphics")
606 "Ggplot2 is an implementation of the grammar of graphics in R. It
607 combines the advantages of both base and lattice graphics: conditioning and
608 shared axes are handled automatically, and you can still build up a plot step
609 by step from multiple data sources. It also implements a sophisticated
610 multidimensional conditioning system and a consistent interface to map data to
611 aesthetic attributes.")
612 (license license:gpl2+)))
614 (define-public r-gdtools
621 (uri (cran-uri "gdtools" version))
624 "1bmnf9d677f2jy8jnb9ymjz1qzm4yrd0qp6k5qrrly06jfffyx7g"))))
625 (build-system r-build-system)
628 ("pkg-config" ,pkg-config)))
631 (home-page "http://cran.r-project.org/web/packages/gdtools")
632 (synopsis "Utilities for graphical rendering")
634 "The @code{gdtools} package provides functionalities to get font metrics
635 and to generate base64 encoded string from raster matrix.")
636 (license license:gpl3)))
638 (define-public r-svglite
645 (uri (cran-uri "svglite" version))
648 "11ryicjglfi6jvkk4jgg5kra42qbs5z2zid7jjhlslpjcljfwc70"))))
649 (build-system r-build-system)
650 (native-inputs `(("r-rcpp" ,r-rcpp)))
653 ("r-gdtools" ,r-gdtools)))
654 (home-page "https://github.com/hadley/svglite")
655 (synopsis "SVG graphics device")
657 "@code{svglite} is a graphics device that produces clean
658 @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
659 hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
660 considerably faster, produces smaller files, and leaves text as is.")
661 (license license:gpl2+)))
663 (define-public r-assertthat
665 (name "r-assertthat")
669 (uri (cran-uri "assertthat" version))
672 "0dwsqajyglfscqilj843qfqn1ndbqpswa7b4l1d633qjk9d68qqk"))))
673 (build-system r-build-system)
674 (home-page "https://github.com/hadley/assertthat")
675 (synopsis "Easy pre and post assertions")
677 "Assertthat is an extension to stopifnot() that makes it easy to declare
678 the pre and post conditions that your code should satisfy, while also
679 producing friendly error messages so that your users know what they've done
681 (license license:gpl3+)))
683 (define-public r-lazyeval
689 (uri (cran-uri "lazyeval" version))
692 "02qfpn2fmy78vx4jxr7g7rhqzcm1kcivfwai7lbh0vvpawia0qwh"))))
693 (build-system r-build-system)
694 (home-page "https://github.com/hadley/lazyeval")
695 (synopsis "Lazy (non-standard) evaluation in R")
697 "This package provides the tools necessary to do non-standard
698 evaluation (NSE) in R.")
699 (license license:gpl3+)))
707 (uri (cran-uri "DBI" version))
710 "13n6ibmrma42qmq17qgkyjsc0ciwqf17sd7lw7w26pwpyjd4mwgg"))))
711 (build-system r-build-system)
712 (home-page "https://github.com/rstats-db/DBI")
713 (synopsis "R database interface")
715 "The DBI package provides a database interface (DBI) definition for
716 communication between R and relational database management systems. All
717 classes in this package are virtual and need to be extended by the various
718 R/DBMS implementations.")
719 (license license:lgpl2.0+)))
727 (uri (cran-uri "BH" version))
730 "136497fng9bcvrf8favpj8inz96pxdwp1rrb2k00sxjxjbgawhg4"))))
731 (build-system r-build-system)
732 (home-page "https://github.com/eddelbuettel/bh")
733 (synopsis "R package providing subset of Boost headers")
735 "This package aims to provide the most useful subset of Boost libraries
736 for template use among CRAN packages.")
737 (license license:boost1.0)))
739 (define-public r-evaluate
745 (uri (cran-uri "evaluate" version))
748 "1bn6bympg9prr8d16g1g530bddii8i04hf4i2bkw0yf4dsfqq4g8"))))
749 (build-system r-build-system)
751 `(("r-stringr" ,r-stringr)))
752 (home-page "https://github.com/hadley/evaluate")
753 (synopsis "Parsing and evaluation tools for R")
755 "This package provides tools that allow you to recreate the parsing,
756 evaluation and display of R code, with enough information that you can
757 accurately recreate what happens at the command line. The tools can easily be
758 adapted for other output formats, such as HTML or LaTeX.")
759 (license license:gpl3+)))
761 (define-public r-formatr
767 (uri (cran-uri "formatR" version))
770 "1fvynq0fj1r9grg9vvfdh5fl2riv6qki9f2rfpyvbvqq3xxpmi3f"))))
771 (build-system r-build-system)
772 (home-page "http://yihui.name/formatR")
773 (synopsis "Format R code automatically")
775 "This package provides a function to format R source code. Spaces and
776 indent will be added to the code automatically, and comments will be preserved
777 under certain conditions, so that R code will be more human-readable and tidy.
778 There is also a Shiny app as a user interface in this package.")
779 (license license:gpl3+)))
781 (define-public r-highr
787 (uri (cran-uri "highr" version))
790 "0n9v44dxdy5fhkdmpbpa2p78whyd9z3rhhy42ipdz5m5vsr55qa3"))))
791 (build-system r-build-system)
792 (home-page "https://github.com/yihui/highr")
793 (synopsis "Syntax highlighting for R source code")
795 "This package provides syntax highlighting for R source code. Currently
796 it supports LaTeX and HTML output. Source code of other languages is
797 supported via Andre Simon's highlight package.")
798 (license license:gpl3+)))
800 (define-public r-mime
806 (uri (cran-uri "mime" version))
809 "145cdcg252w2zsq67dmvmsqka60msfp7agymlxs3gl3ihgiwg46p"))))
810 (build-system r-build-system)
811 (home-page "https://github.com/yihui/mime")
812 (synopsis "R package to map filenames to MIME types")
814 "This package guesses the MIME type from a filename extension using the
815 data derived from /etc/mime.types in UNIX-type systems.")
816 (license license:gpl2)))
818 (define-public r-markdown
824 (uri (cran-uri "markdown" version))
827 "00j1hlib3il50azs2vlcyhi0bjpx1r50mxr9w9dl5g1bwjjc71hb"))))
828 (build-system r-build-system)
829 ;; Skip check phase because the tests require the r-knitr package to be
830 ;; installed. This prevents installation failures. Knitr normally
831 ;; shouldn't be available since r-markdown is a dependency of the r-knitr
833 (arguments `(#:tests? #f))
835 `(("r-mime" ,r-mime)))
836 (home-page "https://github.com/rstudio/markdown")
837 (synopsis "Markdown rendering for R")
839 "This package provides R bindings to the Sundown Markdown rendering
840 library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
841 syntax that can be converted to XHTML or other formats.")
842 (license license:gpl2)))
844 (define-public r-yaml
850 (uri (cran-uri "yaml" version))
853 "18kz5mfn7qpif5pn91w4vbrc5bkycsj85vwm5wxwzjlb02i9mxi6"))))
854 (build-system r-build-system)
855 (home-page "https://cran.r-project.org/web/packages/yaml/")
856 (synopsis "Methods to convert R data to YAML and back")
858 "This package implements the libyaml YAML 1.1 parser and
859 emitter (http://pyyaml.org/wiki/LibYAML) for R.")
860 (license license:bsd-3)))
862 (define-public r-knitr
868 (uri (cran-uri "knitr" version))
871 "0v69846myi4fbjp8wiik4295fhba67s3i6ccysghm6x031i2f26q"))))
872 (build-system r-build-system)
874 `(("r-evaluate" ,r-evaluate)
875 ("r-digest" ,r-digest)
876 ("r-formatr" ,r-formatr)
878 ("r-markdown" ,r-markdown)
879 ("r-stringr" ,r-stringr)
881 (home-page "http://yihui.name/knitr/")
882 (synopsis "General-purpose package for dynamic report generation in R")
884 "This package provides a general-purpose tool for dynamic report
885 generation in R using Literate Programming techniques.")
886 ;; The code is released under any version of the GPL. As it is used by
887 ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
889 (license license:gpl2+)))
891 (define-public r-knitrbootstrap
893 (name "r-knitrbootstrap")
898 (uri (cran-uri "knitrBootstrap" version))
901 "0pshn2slzqwpryklslsxwh1dmqcnwv6bwi7yfm6m342wjybpk0wl"))))
902 (properties `((upstream-name . "knitrBootstrap")))
903 (build-system r-build-system)
905 `(("r-knitr" ,r-knitr)
906 ("r-rmarkdown" ,r-rmarkdown)))
907 (home-page "https://github.com/jimhester/knitrBootstrap")
908 (synopsis "Knitr bootstrap framework")
910 "This package provides a framework to create Bootstrap 3 HTML reports
911 from knitr Rmarkdown.")
912 (license license:expat)))
914 (define-public r-microbenchmark
916 (name "r-microbenchmark")
920 (uri (cran-uri "microbenchmark" version))
923 "0qn5r1a6qidghcisc2hpbdmj62pnixc3zz6p4ipk8mvakf0hdsvg"))))
924 (build-system r-build-system)
926 `(("r-ggplot2" ,r-ggplot2)))
927 (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
928 (synopsis "Accurate timing functions for R")
930 "This package provides infrastructure to accurately measure and compare
931 the execution time of R expressions.")
932 (license license:bsd-2)))
934 (define-public r-codetools
940 (uri (cran-uri "codetools" version))
943 "0y9r4m2b8xgavr89sc179knzwpz54xljbc1dinpq2q07i4xn0397"))))
944 (build-system r-build-system)
945 (home-page "https://cran.r-project.org/web/packages/codetools/index.html")
946 (synopsis "Code analysis tools for R")
947 (description "This package provides code analysis tools for R.")
948 (license license:gpl3+)))
950 (define-public r-pryr
956 (uri (cran-uri "pryr" version))
959 "1in350a8hxwf580afavasvn3jc7x2p1b7nlwmj1scakfz74vghk5"))))
960 (build-system r-build-system)
962 `(("r-stringr" ,r-stringr)
963 ("r-codetools" ,r-codetools)))
965 `(("r-rcpp" ,r-rcpp)))
966 (home-page "https://github.com/hadley/pryr")
967 (synopsis "Tools for computing on the R language")
969 "This package provides useful tools to pry back the covers of R and
970 understand the language at a deeper level.")
971 (license license:gpl2)))
973 (define-public r-memoise
979 (uri (cran-uri "memoise" version))
982 "0sq2dhpvxy17v1baj256r0jnygdy3m5a8x4zh6vhv29957qnq6zx"))))
983 (build-system r-build-system)
985 `(("r-digest" ,r-digest)))
986 (home-page "http://github.com/hadley/memoise")
987 (synopsis "Memoise functions for R")
989 "This R package allows to cache the results of a function so that when
990 you call it again with the same arguments it returns the pre-computed value.")
991 (license license:expat)))
993 (define-public r-crayon
999 (uri (cran-uri "crayon" version))
1002 "0d38fm06h272a8iqlc0d45m2rh36giwqw7mwq4z8hkp4vs975fmm"))))
1003 (build-system r-build-system)
1005 `(("r-memoise" ,r-memoise)))
1006 (home-page "https://github.com/gaborcsardi/crayon")
1007 (synopsis "Colored terminal output for R")
1009 "Colored terminal output on terminals that support ANSI color and
1010 highlight codes. It also works in Emacs ESS. ANSI color support is
1011 automatically detected. Colors and highlighting can be combined and nested.
1012 New styles can also be created easily. This package was inspired by the
1013 \"chalk\" JavaScript project.")
1014 (license license:expat)))
1016 (define-public r-praise
1023 (uri (cran-uri "praise" version))
1026 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
1027 (build-system r-build-system)
1028 (home-page "https://github.com/gaborcsardi/praise")
1029 (synopsis "Functions to praise users")
1031 "This package provides template functions to assist in building friendly
1032 R packages that praise their users.")
1033 (license license:expat)))
1035 (define-public r-testthat
1041 (uri (cran-uri "testthat" version))
1044 "0pj1r01x4ny4capr83dfa19hi5i2sjjxky99schzip8zrq5dzxqf"))))
1045 (build-system r-build-system)
1047 `(("r-digest" ,r-digest)
1048 ("r-crayon" ,r-crayon)
1049 ("r-magrittr" ,r-magrittr)
1050 ("r-praise" ,r-praise)
1052 (home-page "https://github.com/hadley/testthat")
1053 (synopsis "Unit testing for R")
1055 "This package provides a unit testing system for R designed to be fun,
1056 flexible and easy to set up.")
1057 (license license:expat)))
1065 (uri (cran-uri "R6" version))
1068 "0yad91i9p4r8bbz6nq8zny39y767n9an7ak5p275ynx8km6v3yqv"))))
1069 (build-system r-build-system)
1070 (home-page "https://github.com/wch/R6/")
1071 (synopsis "Classes with reference semantics in R")
1073 "The R6 package allows the creation of classes with reference semantics,
1074 similar to R's built-in reference classes. Compared to reference classes, R6
1075 classes are simpler and lighter-weight, and they are not built on S4 classes
1076 so they do not require the methods package. These classes allow public and
1077 private members, and they support inheritance, even when the classes are
1078 defined in different packages.")
1079 (license license:expat)))
1081 (define-public r-dplyr
1087 (uri (cran-uri "dplyr" version))
1090 "1p8rbn4p4yrx2840dapwiahf9iqa8gnvd35nyc200wfhmrxlqdlc"))))
1091 (build-system r-build-system)
1093 `(("r-assertthat" ,r-assertthat)
1095 ("r-magrittr" ,r-magrittr)
1096 ("r-lazyeval" ,r-lazyeval)
1099 `(("r-rcpp" ,r-rcpp)
1101 (home-page "https://github.com/hadley/dplyr")
1102 (synopsis "Tools for working with data frames in R")
1104 "dplyr is the next iteration of plyr. It is focussed on tools for
1105 working with data frames. It has three main goals: 1) identify the most
1106 important data manipulation tools needed for data analysis and make them easy
1107 to use in R; 2) provide fast performance for in-memory data by writing key
1108 pieces of code in C++; 3) use the same code interface to work with data no
1109 matter where it is stored, whether in a data frame, a data table or
1111 (license license:expat)))
1113 (define-public r-acepack
1120 (uri (cran-uri "acepack" version))
1123 "13ry3vyys12iplb14jfhmkrl9g5fxg3iijiggq4s4zb5m5436b1y"))))
1124 (build-system r-build-system)
1126 `(("gfortran" ,gfortran)))
1127 (home-page "http://cran.r-project.org/web/packages/acepack")
1128 (synopsis "Functions for regression transformations")
1130 "This package provides ACE and AVAS methods for choosing regression
1132 (license license:expat)))
1134 (define-public r-cluster
1141 (uri (cran-uri "cluster" version))
1144 "1r669aaaia05i8sv8hxiig1ddah7hm8qw869wgig5i0zzk22bnfl"))))
1145 (build-system r-build-system)
1147 `(("gfortran" ,gfortran)))
1148 (home-page "http://cran.r-project.org/web/packages/cluster")
1149 (synopsis "Methods for data cluster analysis")
1151 "This package provides tools that are useful in finding groups in data.
1152 It is based on the methods described in Kaufman and Rousseeuw (1990) \"Finding
1154 (license license:gpl2+)))
1156 (define-public r-foreign
1163 (uri (cran-uri "foreign" version))
1166 "19278jm85728zb20800w6hq9q8jy8ywdn81mgmlnxkmrr9giwh6p"))))
1167 (build-system r-build-system)
1168 (home-page "http://cran.r-project.org/web/packages/foreign")
1169 (synopsis "Read data stored by other statistics software in R")
1171 "This package provides functions for reading and writing data stored by
1172 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka, and
1173 for reading and writing some dBase files.")
1174 (license license:gpl2+)))
1176 (define-public r-formula
1183 (uri (cran-uri "Formula" version))
1186 "02in5325zzrqbhlygx6s0dinj6ymw845q70y56frqacv25ayzcax"))))
1187 (properties `((upstream-name . "Formula")))
1188 (build-system r-build-system)
1189 (home-page "http://cran.r-project.org/web/packages/Formula")
1190 (synopsis "Extended model formulas")
1192 "This package provides a new class @code{Formula}, which extends the base
1193 class @code{formula}. It supports extended formulas with multiple parts of
1194 regressors on the right-hand side and/or multiple responses on the left-hand
1196 (license (list license:gpl2+ license:gpl3+))))
1198 (define-public r-locfit
1205 (uri (cran-uri "locfit" version))
1208 "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
1209 (build-system r-build-system)
1210 (home-page "http://cran.r-project.org/web/packages/locfit")
1211 (synopsis "Local regression, likelihood and density estimation")
1213 "This package provides functions used for local regression, likelihood
1214 and density estimation.")
1215 (license (list license:gpl2+ license:gpl3+))))
1217 (define-public r-chron
1223 (uri (cran-uri "chron" version))
1226 "1xj50kk8b8mbjpszp8i0wbripb5a4b36jcscwlbyap8n4487g34s"))))
1227 (build-system r-build-system)
1228 (home-page "http://cran.r-project.org/web/packages/chron")
1229 (synopsis "Chronological R objects which can handle dates and times")
1231 "This package provides chronological R objects which can handle dates and
1233 (license license:gpl2)))
1235 (define-public r-data-table
1237 (name "r-data-table")
1241 (uri (cran-uri "data.table" version))
1244 "0vi3zplpxqbg78z9ifjfs1kl2i8qhkqxr7l9ysp2663kq54w6x3g"))))
1245 (build-system r-build-system)
1247 `(("r-chron" ,r-chron)))
1248 (home-page "https://github.com/Rdatatable/data.table/wiki")
1249 (synopsis "Enhanced version of data.frame R object")
1251 "The R package @code{data.table} is an extension of @code{data.frame}
1252 providing functions for fast aggregation of large data (e.g. 100GB in RAM),
1253 fast ordered joins, fast add/modify/delete of columns by group, column listing
1254 and fast file reading.")
1255 (license license:gpl3+)))
1257 (define-public r-xtable
1264 (uri (cran-uri "xtable" version))
1267 "0398qkpvlw3dv0myz4mjcyqwpwc2m31l127r8vdzwc71wb6s28qn"))))
1268 (build-system r-build-system)
1270 `(("r-knitr" ,r-knitr)))
1271 (home-page "http://xtable.r-forge.r-project.org/")
1272 (synopsis "Export R tables to LaTeX or HTML")
1274 "This package provides tools to export R data as LaTeX and HTML tables.")
1275 (license license:gpl2+)))
1277 (define-public python-patsy
1279 (name "python-patsy")
1283 (uri (pypi-uri "patsy" version ".zip"))
1286 "1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w"))))
1287 (build-system python-build-system)
1290 (modify-phases %standard-phases
1291 (replace 'check (lambda _ (zero? (system* "nosetests" "-v"))))
1292 (add-after 'unpack 'prevent-generation-of-egg-archive
1294 (substitute* "setup.py"
1295 (("from setuptools import setup")
1296 "from distutils.core import setup"))
1299 `(("python-numpy" ,python-numpy)
1300 ("python-scipy" ,python-scipy)
1301 ("python-six" ,python-six)))
1303 `(("python-nose" ,python-nose)
1305 (home-page "https://github.com/pydata/patsy")
1306 (synopsis "Describe statistical models and build design matrices")
1308 "Patsy is a Python package for describing statistical models and for
1309 building design matrices.")
1310 ;; The majority of the code is distributed under BSD-2. The module
1311 ;; patsy.compat contains code derived from the Python standard library,
1312 ;; and is covered by the PSFL.
1313 (license (list license:bsd-2 license:psfl))
1314 (properties `((python2-variant . ,(delay python2-patsy))))))
1316 (define-public python2-patsy
1317 (let ((patsy (package-with-python2 (strip-python2-variant python-patsy))))
1318 (package (inherit patsy)
1320 `(("python2-setuptools" ,python2-setuptools)
1321 ,@(package-native-inputs patsy))))))
1323 (define-public python-statsmodels
1325 (name "python-statsmodels")
1330 (uri (string-append "https://pypi.python.org/packages/source/"
1331 "s/statsmodels/statsmodels-" version ".tar.gz"))
1334 "0xn67sqr0cc1lmlhzm71352hrb4hw7g318p5ff5q97pc98vl8kmy"))
1335 (patches (search-patches "python-statsmodels-fix-tests.patch"))))
1336 (build-system python-build-system)
1339 (modify-phases %standard-phases
1340 ;; tests must be run after installation
1342 (add-after 'unpack 'set-matplotlib-backend-to-agg
1344 ;; Set the matplotlib backend to Agg to avoid problems using the
1345 ;; GTK backend without a display.
1346 (substitute* (find-files "statsmodels/graphics/tests" "\\.py")
1347 (("import matplotlib\\.pyplot as plt" line)
1348 (string-append "import matplotlib;matplotlib.use('Agg');"
1351 (add-after 'install 'check
1353 (with-directory-excursion "/tmp"
1354 (zero? (system* "nosetests"
1356 "-v" "statsmodels"))))))))
1358 `(("python-numpy" ,python-numpy)
1359 ("python-scipy" ,python-scipy)
1360 ("python-pandas" ,python-pandas)
1361 ("python-patsy" ,python-patsy)
1362 ("python-matplotlib" ,python-matplotlib)))
1364 `(("python-cython" ,python-cython)
1365 ("python-nose" ,python-nose)
1366 ("python-sphinx" ,python-sphinx)))
1367 (home-page "http://statsmodels.sourceforge.net/")
1368 (synopsis "Statistical modeling and econometrics in Python")
1370 "Statsmodels is a Python package that provides a complement to scipy for
1371 statistical computations including descriptive statistics and estimation and
1372 inference for statistical models.")
1373 (license license:bsd-3)))
1375 (define-public python2-statsmodels
1376 (let ((stats (package-with-python2 python-statsmodels)))
1377 (package (inherit stats)
1379 `(("python2-pytz" ,python2-pytz)
1380 ("python2-numpy" ,python2-numpy)
1381 ("python2-scipy" ,python2-scipy)
1382 ("python2-pandas" ,python2-pandas)
1383 ("python2-patsy" ,python2-patsy)
1384 ("python2-matplotlib" ,python2-matplotlib)))
1386 `(("python2-setuptools" ,python2-setuptools)
1387 ,@(package-native-inputs stats))))))
1389 (define-public r-coda
1395 (uri (cran-uri "coda" version))
1398 "03sc780734zj2kqcm8lkyvf76fql0jbfhkblpn8l58zmb6cqi958"))))
1399 (build-system r-build-system)
1401 `(("r-lattice" ,r-lattice)))
1402 (home-page "http://cran.r-project.org/web/packages/coda")
1403 (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
1404 (description "This package provides functions for summarizing and plotting
1405 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
1406 diagnostic tests of convergence to the equilibrium distribution of the Markov
1408 (license license:gpl2+)))
1410 (define-public r-ade4
1417 (uri (cran-uri "ade4" version))
1420 "17sbicash7z4b63dlrbaf8xx2pbwh62vykzvhdjs43h8jkl881y7"))))
1421 (build-system r-build-system)
1422 (home-page "http://pbil.univ-lyon1.fr/ADE-4")
1423 (synopsis "Multivariate data analysis and graphical display")
1425 "The ade4 package contains data analysis functions to analyze ecological
1426 and environmental data in the framework of Euclidean exploratory methods.")
1427 (license license:gpl2+)))
1429 (define-public r-xml2
1436 (uri (cran-uri "xml2" version))
1439 "0jjilz36h7vbdbkpvjnja1vgjf6d1imql3z4glqn2m2b74w5qm4c"))))
1440 (build-system r-build-system)
1442 `(("libxml2" ,libxml2)))
1444 `(("r-rcpp" ,r-rcpp)
1446 (home-page "https://github.com/hadley/xml2")
1447 (synopsis "Parse XML with R")
1449 "This package provides a simple, consistent interface to working with XML
1450 files in R. It is built on top of the libxml2 C library.")
1451 (license license:gpl2+)))
1453 (define-public r-multitaper
1455 (name "r-multitaper")
1460 (uri (cran-uri "multitaper" version))
1463 "1s0lmjzpyd7zmc2p1ywv5fm7qkq357p70b76gw9wjlms6d81j1n4"))))
1464 (build-system r-build-system)
1466 `(("gfortran" ,gfortran)))
1467 (home-page "http://github.com/wesleyburr/multitaper/")
1468 (synopsis "Multitaper spectral analysis tools")
1470 "This package implements multitaper spectral estimation
1471 techniques using prolate spheroidal sequences (Slepians) and sine
1472 tapers for time series analysis. It includes an adaptive weighted
1473 multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
1474 F-test, and complex demodulation. The Slepians sequences are
1475 generated efficiently using a tridiagonal matrix solution, and
1476 jackknifed confidence intervals are available for most estimates.")
1477 (license license:gpl2+)))
1479 (define-public r-rversions
1481 (name "r-rversions")
1485 (uri (cran-uri "rversions" version))
1488 "0xmi461g1rf5ngb7r1sri798jn6icld1xq25wj9jii2ca8j8xv68"))))
1489 (build-system r-build-system)
1491 `(("r-curl" ,r-curl)
1492 ("r-xml2" ,r-xml2)))
1493 (home-page "https://github.com/metacran/rversions")
1494 (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
1496 "This package provides functions to query the main R repository to find
1497 the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
1498 previous R versions and their release dates.")
1499 (license license:expat)))
1501 (define-public r-whisker
1507 (uri (cran-uri "whisker" version))
1510 "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28"))))
1511 (build-system r-build-system)
1512 (home-page "http://github.com/edwindj/whisker")
1513 (synopsis "Logicless mustache templating for R")
1515 "This package provides logicless templating, with a syntax that is not
1517 (license license:gpl3+)))
1519 (define-public r-brew
1525 (uri (cran-uri "brew" version))
1528 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
1529 (build-system r-build-system)
1530 (home-page "http://cran.r-project.org/web/packages/brew")
1531 (synopsis "Templating framework for report generation")
1533 "The brew package implements a templating framework for mixing text and R
1534 code for report generation. The template syntax is similar to PHP, Ruby's erb
1535 module, Java Server Pages, and Python's psp module.")
1536 (license license:gpl2+)))
1538 (define-public r-roxygen2
1544 (uri (cran-uri "roxygen2" version))
1547 "19gblyrrn29msbpawcb1hn5m1rshiqwxy0lby0vf92rm13fmsxcz"))))
1548 (build-system r-build-system)
1550 `(("r-brew" ,r-brew)
1551 ("r-digest" ,r-digest)
1553 ("r-stringi" ,r-stringi)
1554 ("r-stringr" ,r-stringr)))
1555 (home-page "https://github.com/klutometis/roxygen")
1556 (synopsis "In-source documentation system for R")
1558 "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
1559 collation, and NAMESPACE files.")
1560 (license license:gpl2+)))
1562 (define-public r-openssl
1569 (uri (cran-uri "openssl" version))
1572 "0ldqam7d9fyxwhr651ld6lsh05lg4v2y8ajxwzq9ywzjmfb3vlpz"))))
1573 (build-system r-build-system)
1575 `(("openssl" ,openssl)))
1576 (home-page "https://github.com/jeroenooms/openssl")
1577 (synopsis "Toolkit for encryption, signatures and certificates")
1579 "This package provides R bindings to OpenSSL libssl and libcrypto, plus
1580 custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
1581 and P-521. Cryptographic signatures can either be created and verified
1582 manually or via x509 certificates. AES block cipher is used in CBC mode for
1583 symmetric encryption; RSA for asymmetric (public key) encryption. High-level
1584 envelope functions combine RSA and AES for encrypting arbitrary sized data.
1585 Other utilities include key generators, hash functions (md5, sha1, sha256,
1586 etc), base64 encoder, a secure random number generator, and @code{bignum} math
1587 methods for manually performing crypto calculations on large multibyte
1589 (license license:expat)))
1591 (define-public r-httr
1597 (uri (cran-uri "httr" version))
1600 "08sq34pknsfcy8lm06nydi12mbaxpqpgb025ahr33v9d3g0wvh6p"))))
1601 (build-system r-build-system)
1603 `(("r-curl" ,r-curl)
1604 ("r-digest" ,r-digest)
1605 ("r-jsonlite" ,r-jsonlite)
1606 ("r-openssl" ,r-openssl)
1609 ("r-stringr" ,r-stringr)))
1610 (home-page "https://github.com/hadley/httr")
1611 (synopsis "Tools for working with URLs and HTTP")
1613 "The aim of httr is to provide a wrapper for RCurl customised to the
1614 demands of modern web APIs. It provides useful tools for working with HTTP
1615 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
1616 functions make it easy to control additional request components.")
1617 (license license:expat)))
1619 (define-public r-git2r
1625 (uri (cran-uri "git2r" version))
1628 "1rpdf85wy9fp456ypvbhl3p9whkb7kgl0n7rkqxd2bhvyzkvjak8"))))
1629 (build-system r-build-system)
1630 ;; This R package contains modified sources of libgit2. This modified
1631 ;; version of libgit2 is built as the package is built. Hence libgit2 is
1632 ;; not among the inputs of this package.
1634 `(("libssh2" ,libssh2)
1635 ("openssl" ,openssl)
1637 (home-page "https://github.com/ropensci/git2r")
1638 (synopsis "Access Git repositories with R")
1640 "This package provides an R interface to the libgit2 library, which is a
1641 pure C implementation of the Git core methods.")
1642 ;; GPLv2 only with linking exception.
1643 (license license:gpl2)))
1645 (define-public r-rstudioapi
1647 (name "r-rstudioapi")
1651 (uri (cran-uri "rstudioapi" version))
1654 "0sgnqfx0m3hzh57k10s7ndrbw7yqjjjcgfikafya98jcc7wmpwym"))))
1655 (build-system r-build-system)
1656 (home-page "http://cran.r-project.org/web/packages/rstudioapi")
1657 (synopsis "Safely access the RStudio API")
1659 "This package provides functions to access the RStudio API and provide
1660 informative error messages when it's not available.")
1661 (license license:expat)))
1663 (define-public r-devtools
1669 (uri (cran-uri "devtools" version))
1672 "0ik3l3q62sspdph613f9ik5yz36s8q5nrc50dqgn3pxzvpwpdj2i"))))
1673 (build-system r-build-system)
1675 `(("r-curl" ,r-curl)
1676 ("r-digest" ,r-digest)
1677 ("r-evaluate" ,r-evaluate)
1678 ("r-git2r" ,r-git2r)
1680 ("r-jsonlite" ,r-jsonlite)
1681 ("r-memoise" ,r-memoise)
1682 ("r-roxygen2" ,r-roxygen2)
1683 ("r-rstudioapi" ,r-rstudioapi)
1684 ("r-rversions" ,r-rversions)
1685 ("r-whisker" ,r-whisker)
1686 ("r-withr" ,r-withr)))
1687 (home-page "https://github.com/hadley/devtools")
1688 (synopsis "Tools to make developing R packages easier")
1689 (description "The devtools package is a collection of package development
1690 tools to simplify the devolpment of R packages.")
1691 (license license:gpl2+)))
1693 (define-public r-withr
1699 (uri (cran-uri "withr" version))
1702 "0zbj3rd7dc0ycknmay7y7rm1qvnh9n05jw93gjggz46j2zfmy93y"))))
1703 (build-system r-build-system)
1704 (home-page "https://github.com/jimhester/withr")
1705 (synopsis "Run code with temporarily modified global state")
1707 "This package provides a set of functions to run R code in an environment
1708 in which global state has been temporarily modified. Many of these functions
1709 were originally a part of the r-devtools package.")
1710 (license license:gpl2+)))
1712 (define-public r-readr
1718 (uri (cran-uri "readr" version))
1721 "156422xwvskynna5kjc8h1qqnn50kxgjrihl2h2b7vm9sxxdyr2m"))))
1722 (build-system r-build-system)
1724 `(("r-curl" ,r-curl)
1727 (home-page "https://github.com/hadley/readr")
1728 (synopsis "Read tabular data")
1730 "This package provides functions to read flat or tabular text files from
1731 disk (or a connection).")
1732 (license license:gpl2+)))
1734 (define-public r-plotrix
1740 (uri (cran-uri "plotrix" version))
1743 "1jn1k3skmlgyvpijj6vlcn5m2zgrsdh00g1fq8n5dqs1pkl1sqrw"))))
1744 (build-system r-build-system)
1745 (home-page "http://cran.r-project.org/web/packages/plotrix")
1746 (synopsis "Various plotting functions")
1748 "This package provides lots of plotting, various labeling, axis and color
1749 scaling functions for R.")
1750 (license license:gpl2+)))
1752 (define-public r-gridbase
1758 (uri (cran-uri "gridBase" version))
1761 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
1762 (build-system r-build-system)
1763 (home-page "http://cran.r-project.org/web/packages/gridBase")
1764 (synopsis "Integration of base and grid graphics")
1766 "This package provides an integration of base and grid graphics for R.")
1767 (license license:gpl2+)))
1769 (define-public r-lattice
1775 (uri (cran-uri "lattice" version))
1778 "0car12x5vl9k180i9pc86lq3cvwqakdpqn3lgdf98k9n2h52cilg"))))
1779 (build-system r-build-system)
1780 (home-page "http://lattice.r-forge.r-project.org/")
1781 (synopsis "High-level data visualization system")
1783 "The lattice package provides a powerful and elegant high-level data
1784 visualization system inspired by Trellis graphics, with an emphasis on
1785 multivariate data. Lattice is sufficient for typical graphics needs, and is
1786 also flexible enough to handle most nonstandard requirements.")
1787 (license license:gpl2+)))
1789 (define-public r-latticeextra
1791 (name "r-latticeextra")
1796 (uri (cran-uri "latticeExtra" version))
1799 "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq"))))
1800 (properties `((upstream-name . "latticeExtra")))
1801 (build-system r-build-system)
1803 `(("r-lattice" ,r-lattice)
1804 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1805 (home-page "http://latticeextra.r-forge.r-project.org/")
1806 (synopsis "Extra graphical utilities based on lattice")
1808 "Building on the infrastructure provided by the lattice package, this
1809 package provides several new high-level graphics functions and methods, as
1810 well as additional utilities such as panel and axis annotation functions.")
1811 (license license:gpl2+)))
1813 (define-public r-rcpparmadillo
1815 (name "r-rcpparmadillo")
1816 (version "0.6.700.6.0")
1819 (uri (cran-uri "RcppArmadillo" version))
1822 "0x736cjg1pbvn8c6h91c88qmmz4pddvvqg88k9c9kwhn24fjrra0"))
1823 (modules '((guix build utils)))
1824 ;; Remove bundled armadillo sources
1827 (delete-file-recursively "inst/include/armadillo_bits")
1828 (delete-file "inst/include/armadillo")))))
1829 (properties `((upstream-name . "RcppArmadillo")))
1830 (build-system r-build-system)
1833 (modify-phases %standard-phases
1834 (add-after 'unpack 'link-against-armadillo
1836 (substitute* "src/Makevars"
1837 (("PKG_LIBS=" prefix)
1838 (string-append prefix "-larmadillo"))))))))
1840 `(("r-rcpp" ,r-rcpp)
1841 ("armadillo" ,armadillo-for-rcpparmadillo)))
1842 (home-page "https://github.com/RcppCore/RcppArmadillo")
1843 (synopsis "Rcpp integration for the Armadillo linear algebra library")
1845 "Armadillo is a templated C++ linear algebra library that aims towards a
1846 good balance between speed and ease of use. Integer, floating point and
1847 complex numbers are supported, as well as a subset of trigonometric and
1848 statistics functions. Various matrix decompositions are provided through
1849 optional integration with LAPACK and ATLAS libraries. This package includes
1850 the header files from the templated Armadillo library.")
1851 ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
1852 ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
1853 ;; later, as is the rest of 'Rcpp'.
1854 (license license:gpl2+)))
1856 (define-public r-bitops
1862 (uri (cran-uri "bitops" version))
1865 "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
1866 (build-system r-build-system)
1867 (home-page "http://cran.r-project.org/web/packages/bitops")
1868 (synopsis "Bitwise operations")
1870 "This package provides functions for bitwise operations on integer
1872 (license license:gpl2+)))
1874 (define-public r-catools
1880 (uri (cran-uri "caTools" version))
1883 "1x4szsn2qmbzpyjfdaiz2q7jwhap2gky9wq0riah74q0pzz76ank"))))
1884 (properties `((upstream-name . "caTools")))
1885 (build-system r-build-system)
1887 `(("r-bitops" ,r-bitops)))
1888 (home-page "http://cran.r-project.org/web/packages/caTools")
1889 (synopsis "Various tools including functions for moving window statistics")
1891 "This package contains several basic utility functions including:
1892 moving (rolling, running) window statistic functions, read/write for GIF and
1893 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
1894 encoder/decoder, round-off-error-free sum and cumsum, etc.")
1895 (license license:gpl3+)))
1897 (define-public r-rmarkdown
1899 (name "r-rmarkdown")
1904 (uri (cran-uri "rmarkdown" version))
1907 "09ajq5miqzz46q0i9svvbh93dbi7xbjn4702d6z3scdz272gx7l2"))))
1908 (properties `((upstream-name . "rmarkdown")))
1909 (build-system r-build-system)
1911 `(("r-catools" ,r-catools)
1912 ("r-htmltools" ,r-htmltools)
1913 ("r-knitr" ,r-knitr)
1915 ("ghc-pandoc" ,ghc-pandoc)))
1916 (home-page "http://rmarkdown.rstudio.com")
1917 (synopsis "Convert R Markdown documents into a variety of formats")
1919 "This package provides tools to convert R Markdown documents into a
1920 variety of formats.")
1921 (license license:gpl3+)))
1923 (define-public r-gtable
1929 (uri (cran-uri "gtable" version))
1932 "0vz7073m0a2q12qzzihrfh5c2kx5jqi5l7z470fxmwqghdllh7l0"))))
1933 (properties `((upstream-name . "gtable")))
1934 (build-system r-build-system)
1935 (home-page "http://cran.r-project.org/web/packages/gtable")
1936 (synopsis "Arrange grobs in tables")
1938 "This package provides tools to make it easier to work with tables of
1940 (license license:gpl2+)))
1942 (define-public r-gridextra
1944 (name "r-gridextra")
1948 (uri (cran-uri "gridExtra" version))
1951 "0638ihwl00j76ivaxxhxvi8z573lwy1jym3srr78mx6dbdd4bzj4"))))
1952 (properties `((upstream-name . "gridExtra")))
1953 (build-system r-build-system)
1955 `(("r-gtable" ,r-gtable)))
1957 `(("r-knitr" ,r-knitr))) ;for building vignettes
1958 (home-page "https://github.com/baptiste/gridextra")
1959 (synopsis "Miscellaneous functions for \"Grid\" graphics")
1961 "This package provides a number of user-level functions to work with
1962 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
1964 (license license:gpl2+)))
1966 (define-public r-rsqlite
1972 (uri (cran-uri "RSQLite" version))
1975 "08b1syv8z887gxiw8i09dpqh0zisfb6ihq6qqr01zipvkahzq34f"))))
1976 (properties `((upstream-name . "RSQLite")))
1977 (build-system r-build-system)
1979 `(("r-dbi" ,r-dbi)))
1980 (home-page "https://github.com/rstats-db/RSQLite")
1981 (synopsis "SQLite interface for R")
1983 "This package embeds the SQLite database engine in R and provides an
1984 interface compliant with the DBI package. The source for the SQLite
1985 engine (version 3.8.6) is included.")
1986 (license license:lgpl2.0+)))
1988 (define-public r-rcurl
1991 (version "1.95-0.1.2")
1994 (uri (string-append "http://www.bioconductor.org/packages/"
1995 "release/extra/src/"
1996 "contrib/RCurl_" version ".tar.gz"))
1999 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
2000 (properties `((upstream-name . "RCurl")))
2001 (build-system r-build-system)
2003 `(("libcurl" ,curl)))
2005 `(("r-bitops" ,r-bitops)))
2006 (home-page "http://www.omegahat.org/RCurl")
2007 (synopsis "General network client interface for R")
2009 "The package allows one to compose general HTTP requests and provides
2010 convenient functions to fetch URIs, GET and POST forms, etc. and process the
2011 results returned by the Web server. This provides a great deal of control
2012 over the HTTP/FTP/... connection and the form of the request while providing a
2013 higher-level interface than is available just using R socket connections.
2014 Additionally, the underlying implementation is robust and extensive,
2015 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
2016 ldap, and also supports cookies, redirects, authentication, etc.")
2017 (license license:bsd-3)))
2019 (define-public r-xml
2022 (version "3.98-1.4")
2025 (uri (cran-uri "XML" version))
2028 "09hiy5a875v2fhsgrsfymrwccn9249wnnsr6ck2slrig65svq2lw"))))
2030 `((upstream-name . "XML")))
2031 (build-system r-build-system)
2033 `(("libxml2" ,libxml2)))
2035 `(("r-rcurl" ,r-rcurl)))
2036 (home-page "http://www.omegahat.org/RSXML")
2037 (synopsis "Tools for parsing and generating XML within R")
2039 "Many approaches for both reading and creating XML (and HTML)
2040 documents (including DTDs), both local and accessible via HTTP or FTP. Also
2041 offers access to an XPath \"interpreter\".")
2042 (license license:bsd-2)))
2044 (define-public r-xnomial
2049 (origin (method url-fetch)
2050 (uri (cran-uri "XNomial" version))
2053 "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
2054 (properties (quasiquote ((upstream-name . "XNomial"))))
2055 (build-system r-build-system)
2056 (home-page "http://cran.r-project.org/web/packages/XNomial")
2057 (synopsis "Goodness-of-Fit test for multinomial data")
2059 "This package provides an exact Goodness-of-Fit test for
2060 multinomial data with fixed probabilities. It can be used to
2061 determine whether a set of counts fits a given expected ratio. To see
2062 whether a set of observed counts fits an expectation, one can examine
2063 all possible outcomes with @code{xmulti()} or a random sample of them
2064 with @code{xmonte()} and find the probability of an observation
2065 deviating from the expectation by at least as much as the observed.
2066 As a measure of deviation from the expected, one can use the
2067 log-likelihood ratio, the multinomial probability, or the classic
2068 chi-square statistic. A histogram of the test statistic can also be
2069 plotted and compared with the asymptotic curve.")
2070 (license (list license:gpl2+ license:gpl3+))))
2072 (define-public r-lambda-r
2078 (uri (cran-uri "lambda.r" version))
2081 "1lxzrwyminc3dfb07pbn1rmj45kplxgsb17b06pzflj728knbqwa"))))
2082 (properties `((upstream-name . "lambda.r")))
2083 (build-system r-build-system)
2084 (home-page "http://cran.r-project.org/web/packages/lambda.r")
2085 (synopsis "Functional programming extension for R")
2087 "This package provides a language extension to efficiently write
2088 functional programs in R. Syntax extensions include multi-part function
2089 definitions, pattern matching, guard statements, built-in (optional) type
2091 (license license:lgpl3+)))
2093 (define-public r-futile-options
2095 (name "r-futile-options")
2099 (uri (cran-uri "futile.options" version))
2102 "1hp82h6xqq5cck67h7lpf22n3j7mg3v1mla5y5ivnzrrb7iyr17f"))))
2104 `((upstream-name . "futile.options")))
2105 (build-system r-build-system)
2106 (home-page "http://cran.r-project.org/web/packages/futile.options")
2107 (synopsis "Options management framework")
2109 "The futile.options subsystem provides an easy user-defined options
2110 management system that is properly scoped. This means that options created
2111 via @code{futile.options} are fully self-contained and will not collide with
2112 options defined in other packages.")
2113 (license license:lgpl3+)))
2115 (define-public r-futile-logger
2117 (name "r-futile-logger")
2121 (uri (cran-uri "futile.logger" version))
2124 "1plld1icxrcay7llplbd4i8inpg97crpnczk58mbk26j8glqbr51"))))
2125 (properties `((upstream-name . "futile.logger")))
2126 (build-system r-build-system)
2128 `(("r-futile-options" ,r-futile-options)
2129 ("r-lambda-r" ,r-lambda-r)))
2130 (home-page "http://cran.r-project.org/web/packages/futile.logger")
2131 (synopsis "Logging utility for R")
2133 "This package provides a simple yet powerful logging utility. Based
2134 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
2135 convenient and easy to use replacement for @code{cat} and @code{print}
2137 (license license:lgpl3+)))
2139 (define-public r-snow
2145 (uri (cran-uri "snow" version))
2148 "19r2yq8aqw99vwyx81p6ay4afsfqffal1wzvizk3dj882s2n4j8w"))))
2149 (build-system r-build-system)
2150 (home-page "http://cran.r-project.org/web/packages/snow")
2151 (synopsis "Support for simple parallel computing in R")
2153 "The snow package provides support for simple parallel computing on a
2154 network of workstations using R. A master R process calls @code{makeCluster}
2155 to start a cluster of worker processes; the master process then uses functions
2156 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
2157 worker processes and collect and return the results on the master.")
2158 (license (list license:gpl2+ license:gpl3+))))
2160 (define-public r-sparsem
2166 (uri (cran-uri "SparseM" version))
2169 "0s9kab5khk7daqf6nfp1wm1qnhkssnnwnymisfwyk3kz4q5maqfz"))))
2171 `((upstream-name . "SparseM")))
2173 `(("gfortran" ,gfortran)))
2174 (build-system r-build-system)
2175 (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
2176 (synopsis "Sparse linear algebra")
2178 "This package provides some basic linear algebra functionality for sparse
2179 matrices. It includes Cholesky decomposition and backsolving as well as
2180 standard R subsetting and Kronecker products.")
2181 (license license:gpl2+)))
2183 (define-public r-iterators
2185 (name "r-iterators")
2190 (uri (cran-uri "iterators" version))
2193 "1f057pabs7ss9h1n244can26qsi5n2k3salrdk0b0vkphlrs4kmf"))))
2194 (build-system r-build-system)
2195 (home-page "http://cran.r-project.org/web/packages/iterators")
2196 (synopsis "Iterator construct for R")
2198 "This package provides support for iterators, which allow a programmer to
2199 traverse through all the elements of a vector, list, or other collection of
2201 (license license:asl2.0)))
2203 (define-public r-codetools
2205 (name "r-codetools")
2210 (uri (cran-uri "codetools" version))
2213 "0y9r4m2b8xgavr89sc179knzwpz54xljbc1dinpq2q07i4xn0397"))))
2214 (build-system r-build-system)
2215 (home-page "http://cran.r-project.org/web/packages/codetools")
2216 (synopsis "Code analysis tools for R")
2217 (description "This package provides code analysis tools for R to check R
2218 code for possible problems.")
2219 (license (list license:gpl2+ license:gpl3+))))
2221 (define-public r-foreach
2228 (uri (cran-uri "foreach" version))
2231 "10aqsd3rxz03s1qdb6gsb1cj89mj4vmh491zfpin4skj1xvkzw0y"))))
2232 (build-system r-build-system)
2234 `(("r-codetools" ,r-codetools)
2235 ("r-iterators" ,r-iterators)))
2236 (home-page "http://cran.r-project.org/web/packages/foreach")
2237 (synopsis "Foreach looping construct for R")
2239 "This package provides support for the @code{foreach} looping construct.
2240 @code{foreach} is an idiom that allows for iterating over elements in a
2241 collection, without the use of an explicit loop counter. This package in
2242 particular is intended to be used for its return value, rather than for its
2243 side effects. In that sense, it is similar to the standard @code{lapply}
2244 function, but doesn't require the evaluation of a function. Using
2245 @code{foreach} without side effects also facilitates executing the loop in
2247 (license license:asl2.0)))
2249 (define-public r-doparallel
2251 (name "r-doparallel")
2256 (uri (cran-uri "doParallel" version))
2259 "1mddx25l25pw9d0csnx2q203dbg5hbrhkr1f08kw0p02a1lln0kh"))))
2260 (properties `((upstream-name . "doParallel")))
2261 (build-system r-build-system)
2263 `(("r-foreach" ,r-foreach)
2264 ("r-iterators" ,r-iterators)))
2265 (home-page "http://cran.r-project.org/web/packages/doParallel")
2266 (synopsis "Foreach parallel adaptor for the 'parallel' package")
2268 "This package provides a parallel backend for the @code{%dopar%} function
2269 using the parallel package.")
2270 (license license:gpl2+)))
2272 (define-public r-domc
2279 (uri (cran-uri "doMC" version))
2282 "0y47jl6g4f83r14pj8bafdzq1phj7bxy5dwyz3k43d2rr8phk8bn"))))
2283 (properties `((upstream-name . "doMC")))
2284 (build-system r-build-system)
2286 `(("r-foreach" ,r-foreach)
2287 ("r-iterators" ,r-iterators)))
2288 (home-page "http://cran.r-project.org/web/packages/doMC")
2289 (synopsis "Foreach parallel adaptor for the 'parallel' package")
2291 "This package provides a parallel backend for the @code{%dopar%} function
2292 using the multicore functionality of the parallel package.")
2293 (license license:gpl2+)))
2301 (uri (cran-uri "DT" version))
2304 "0mj7iiy1gglw7kixybmb7kr1bcl5r006zcb3klkw7p6vvvzdm6qj"))))
2306 `((upstream-name . "DT")))
2307 (build-system r-build-system)
2309 `(("r-htmltools" ,r-htmltools)
2310 ("r-htmlwidgets" ,r-htmlwidgets)
2311 ("r-magrittr" ,r-magrittr)))
2312 (home-page "http://rstudio.github.io/DT")
2313 (synopsis "R wrapper of the DataTables JavaScript library")
2315 "This package allows for data objects in R to be rendered as HTML tables
2316 using the JavaScript library 'DataTables' (typically via R Markdown or Shiny).
2317 The 'DataTables' library has been included in this R package.")
2318 ;; The DT package as a whole is distributed under GPLv3. The DT package
2319 ;; inludes other software components under different licenses:
2321 ;; * Expat: jQuery, jquery.highlight.js, DataTables
2322 ;; * ASL2.0: selectize.js
2323 ;; * WTFPL: noUiSlider
2324 (license (list license:gpl3
2327 (license:non-copyleft "http://www.wtfpl.net/txt/copying/")))))
2329 (define-public r-base64enc
2331 (name "r-base64enc")
2335 (uri (cran-uri "base64enc" version))
2338 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
2339 (build-system r-build-system)
2340 (home-page "http://www.rforge.net/base64enc")
2341 (synopsis "Tools for Base64 encoding")
2343 "This package provides tools for handling Base64 encoding. It is more
2344 flexible than the orphaned \"base64\" package.")
2345 (license license:gpl2+)))
2347 (define-public r-irlba
2354 (uri (cran-uri "irlba" version))
2357 "1gms3rxrm24ri4vjvnpl4v47m7bx0zk63z8y85rbhsvx230xdy0m"))))
2358 (build-system r-build-system)
2359 (home-page "http://cran.r-project.org/web/packages/irlba")
2360 (synopsis "Methods for eigendecomposition of large matrices")
2362 "This package provides fast and memory efficient methods for truncated
2363 singular and eigenvalue decompositions, as well as for principal component
2364 analysis of large sparse or dense matrices.")
2365 (license (list license:gpl2+ license:gpl3+))))
2367 (define-public r-glmnet
2374 (uri (cran-uri "glmnet" version))
2377 "1cbpzmbv837fvq88rgn6mgzgr9f1wqp9fg8gh2kkmngvr1957a9c"))))
2378 (build-system r-build-system)
2380 `(("gfortran" ,gfortran)))
2382 `(("r-foreach" ,r-foreach)))
2383 (home-page "http://www.jstatsoft.org/v33/i01")
2384 (synopsis "Lasso and elastic-net regularized generalized linear models")
2386 "The glmnet package provides efficient procedures for fitting the entire
2387 lasso or elastic-net regularization path for linear and Poisson regression, as
2388 well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
2389 multinomial models. The algorithm uses cyclical coordinate descent in a
2390 path-wise fashion.")
2391 (license license:gpl2+)))
2393 (define-public r-pkgmaker
2400 (uri (cran-uri "pkgmaker" version))
2403 "0vrqnd3kg6liqvpbd969jjsdx0f0rvmmxgdbwwrp6xfmdg0pib8r"))))
2404 (build-system r-build-system)
2406 `(("r-codetools" ,r-codetools)
2407 ("r-digest" ,r-digest)
2408 ("r-registry" ,r-registry)
2409 ("r-stringr" ,r-stringr)
2410 ("r-xtable" ,r-xtable)))
2411 (home-page "https://renozao.github.io/pkgmaker")
2412 (synopsis "Package development utilities")
2414 "This package provides some low-level utilities to use for R package
2415 development. It currently provides managers for multiple package specific
2416 options and registries, vignette, unit test and bibtex related utilities.")
2417 (license license:gpl2+)))
2419 (define-public r-registry
2426 (uri (cran-uri "registry" version))
2429 "0c7lscfxncwwd8zp46h2xfw9gw14dypqv6m2kx85xjhjh0xw99aq"))))
2430 (build-system r-build-system)
2431 (home-page "http://cran.r-project.org/web/packages/registry")
2432 (synopsis "Infrastructure for R package registries")
2434 "This package provides a generic infrastructure for creating and using R
2435 package registries.")
2436 (license license:gpl2+)))
2438 (define-public r-rngtools
2445 (uri (cran-uri "rngtools" version))
2448 "1fcgfqrrb48z37xgy8sffx91p9irp39yqzxv7nqp1x2hnwsrh097"))))
2449 (build-system r-build-system)
2451 `(("r-digest" ,r-digest)
2452 ("r-pkgmaker" ,r-pkgmaker)
2453 ("r-stringr" ,r-stringr)))
2454 (home-page "https://renozao.github.io/rngtools")
2455 (synopsis "Utility functions for working with random number generators")
2457 "This package contains a set of functions for working with Random Number
2458 Generators (RNGs). In particular, it defines a generic S4 framework for
2459 getting/setting the current RNG, or RNG data that are embedded into objects
2460 for reproducibility. Notably, convenient default methods greatly facilitate
2461 the way current RNG settings can be changed.")
2462 (license license:gpl3+)))
2464 (define-public r-nmf
2471 (uri (cran-uri "NMF" version))
2474 "0mmh9bz0zjwd8h9jplz4rq3g94npaqj8s4px51vcv47csssd9k6z"))))
2475 (properties `((upstream-name . "NMF")))
2476 (build-system r-build-system)
2478 `(("r-cluster" ,r-cluster)
2479 ("r-colorspace" ,r-colorspace)
2480 ("r-digest" ,r-digest)
2481 ("r-doparallel" ,r-doparallel)
2482 ("r-foreach" ,r-foreach)
2483 ("r-ggplot2" ,r-ggplot2)
2484 ("r-gridbase" ,r-gridbase)
2485 ("r-pkgmaker" ,r-pkgmaker)
2486 ("r-rcolorbrewer" ,r-rcolorbrewer)
2487 ("r-registry" ,r-registry)
2488 ("r-reshape2" ,r-reshape2)
2489 ("r-rngtools" ,r-rngtools)
2490 ("r-stringr" ,r-stringr)))
2491 (home-page "http://renozao.github.io/NMF")
2492 (synopsis "Algorithms and framework for nonnegative matrix factorization")
2494 "This package provides a framework to perform Non-negative Matrix
2495 Factorization (NMF). The package implements a set of already published
2496 algorithms and seeding methods, and provides a framework to test, develop and
2497 plug new or custom algorithms. Most of the built-in algorithms have been
2498 optimized in C++, and the main interface function provides an easy way of
2499 performing parallel computations on multicore machines.")
2500 (license license:gpl2+)))
2502 (define-public r-igraph
2509 (uri (cran-uri "igraph" version))
2512 "00jnm8v3kvxpxav5klld2z2nnkcpj4sdwv4ksipddy5mp04ysr6w"))))
2513 (build-system r-build-system)
2515 `(("gfortran" ,gfortran)))
2518 ("libxml2" ,libxml2)))
2520 `(("r-irlba" ,r-irlba)
2521 ("r-magrittr" ,r-magrittr)
2523 (home-page "http://igraph.org")
2524 (synopsis "Network analysis and visualization")
2526 "This package provides routines for simple graphs and network analysis.
2527 It can handle large graphs very well and provides functions for generating
2528 random and regular graphs, graph visualization, centrality methods and much
2530 (license license:gpl2+)))
2532 (define-public r-r-methodss3
2534 (name "r-r-methodss3")
2538 (uri (cran-uri "R.methodsS3" version))
2541 "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24"))))
2542 (properties `((upstream-name . "R.methodsS3")))
2543 (build-system r-build-system)
2544 (home-page "http://cran.r-project.org/web/packages/R.methodsS3")
2545 (synopsis "S3 methods simplified")
2547 "This package provides methods that simplify the setup of S3 generic
2548 functions and S3 methods. Major effort has been made in making definition of
2549 methods as simple as possible with a minimum of maintenance for package
2550 developers. For example, generic functions are created automatically, if
2551 missing, and naming conflict are automatically solved, if possible. The
2552 method @code{setMethodS3()} is a good start for those who in the future may
2553 want to migrate to S4.")
2554 (license license:lgpl2.1+)))
2556 (define-public r-r-oo
2562 (uri (cran-uri "R.oo" version))
2565 "1l1x4r69mdchjyi6sq52p580fz3b3bqv6dpn1706y9n4vq47qx24"))))
2566 (properties `((upstream-name . "R.oo")))
2567 (build-system r-build-system)
2569 `(("r-r-methodss3" ,r-r-methodss3)))
2570 (home-page "https://github.com/HenrikBengtsson/R.oo")
2571 (synopsis "R object-oriented programming with or without references")
2573 "This package provides methods and classes for object-oriented
2574 programming in R with or without references. Large effort has been made on
2575 making definition of methods as simple as possible with a minimum of
2576 maintenance for package developers.")
2577 (license license:lgpl2.1+)))
2579 (define-public r-r-utils
2585 (uri (cran-uri "R.utils" version))
2588 "0f4z7ka1wb7bgxc5wyqihqxsnqwgyyzbglwvfwmx0gn8i0wzi647"))))
2589 (properties `((upstream-name . "R.utils")))
2590 (build-system r-build-system)
2592 `(("r-r-methodss3" ,r-r-methodss3)
2593 ("r-r-oo" ,r-r-oo)))
2594 (home-page "https://github.com/HenrikBengtsson/R.utils")
2595 (synopsis "Various programming utilities")
2597 "This package provides utility functions useful when programming and
2598 developing R packages.")
2599 (license license:lgpl2.1+)))
2601 (define-public r-r-cache
2607 (uri (cran-uri "R.cache" version))
2610 "006x52w9r8phw5hgqmyp0bz8z42vn8p5yibibnzi1sfa1xlw8iyx"))))
2611 (properties `((upstream-name . "R.cache")))
2612 (build-system r-build-system)
2614 `(("r-digest" ,r-digest)
2615 ("r-r-methodss3" ,r-r-methodss3)
2617 ("r-r-utils" ,r-r-utils)))
2618 (home-page "https://github.com/HenrikBengtsson/R.cache")
2619 (synopsis "Light-weight caching of objects and results")
2621 "This package provides methods for caching or memoization of objects and
2622 results. With this package, any R object can be cached in a key-value storage
2623 where the key can be an arbitrary set of R objects. The cache memory is
2624 persistent (on the file system).")
2625 (license license:lgpl2.1+)))
2627 (define-public r-r-rsp
2633 (uri (cran-uri "R.rsp" version))
2636 "1ssykygqkxzx9qblxhavxlf2z6r5bhk0s47yw1dllfiyc8zy7jv2"))))
2637 (properties `((upstream-name . "R.rsp")))
2638 (build-system r-build-system)
2640 `(("r-r-cache" ,r-r-cache)
2641 ("r-r-methodss3" ,r-r-methodss3)
2643 ("r-r-utils" ,r-r-utils)))
2644 (home-page "https://github.com/HenrikBengtsson/R.rsp")
2645 (synopsis "Dynamic generation of scientific reports")
2647 "The RSP markup language provides a powerful markup for controlling the
2648 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
2649 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
2650 to many other literate programming languages, with RSP it is straightforward
2651 to loop over mixtures of code and text sections, e.g. in month-by-month
2652 summaries. RSP has also several preprocessing directives for incorporating
2653 static and dynamic contents of external files (local or online) among other
2654 things. RSP is ideal for self-contained scientific reports and R package
2656 (license license:lgpl2.1+)))
2658 (define-public r-mvtnorm
2664 (uri (cran-uri "mvtnorm" version))
2667 "1pc1mi2h063gh4a40009xk5j6pf5bm4274i5kycln38dixsry3yh"))))
2668 (build-system r-build-system)
2670 `(("gfortran" ,gfortran)))
2671 (home-page "http://mvtnorm.R-forge.R-project.org")
2672 (synopsis "Package for multivariate normal and t-distributions")
2673 (description "This package can compute multivariate normal and
2674 t-probabilities, quantiles, random deviates and densities.")
2675 (license license:gpl2)))
2677 (define-public r-matrixstats
2679 (name "r-matrixstats")
2683 (uri (cran-uri "matrixStats" version))
2686 "0zj27xxx9cyrq16rn4g3l0krqg68p8f2qp18w1w4i767j87amlbj"))))
2687 (properties `((upstream-name . "matrixStats")))
2688 (build-system r-build-system)
2690 `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
2691 (home-page "https://github.com/HenrikBengtsson/matrixStats")
2692 (synopsis "Methods applying to vectors and matrix rows and columns")
2694 "This package provides methods operating on rows and columns of matrices,
2695 e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
2696 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
2697 @code{weightedMedians()}. All methods have been optimized for speed and
2699 (license license:artistic2.0)))
2701 (define-public r-viridis
2707 (uri (cran-uri "viridis" version))
2710 "1a9hqn2pccpc51vh8ghw698ni6xzdnp8v0n8kgjh51nlz5hhc87j"))))
2711 (build-system r-build-system)
2713 `(("r-ggplot2" ,r-ggplot2)
2714 ("r-gridextra" ,r-gridextra)))
2715 (home-page "https://github.com/sjmgarnier/viridis")
2716 (synopsis "Matplotlib default color map")
2718 "This package is a port of the new @url{matplotlib,
2719 http://matplotlib.org/} color maps (@code{viridis}--the default--,
2720 @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
2721 designed in such a way that they will analytically be perfectly
2722 perceptually-uniform, both in regular form and also when converted to
2723 black-and-white. They are also designed to be perceived by readers with the
2724 most common form of color blindness.")
2725 (license license:x11)))
2727 (define-public r-tidyr
2734 (uri (cran-uri "tidyr" version))
2737 "0xp6lyr2l4ix2mrilx4qmca7wm5qmbhvi24m4nf7qsgwp54gnv2h"))))
2738 (build-system r-build-system)
2740 `(("r-dplyr" ,r-dplyr)
2741 ("r-lazyeval" ,r-lazyeval)
2742 ("r-magrittr" ,r-magrittr)
2744 ("r-stringi" ,r-stringi)))
2745 (home-page "https://github.com/hadley/tidyr")
2746 (synopsis "Tidy data with `spread()` and `gather()` functions")
2748 "tidyr is a reframing of the reshape2 package designed to accompany the
2749 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
2750 a solid pipeline for data analysis. It is designed specifically for tidying
2751 data, not the general reshaping that reshape2 does, or the general aggregation
2752 that reshape did. In particular, built-in methods only work for data frames,
2753 and tidyr provides no margins or aggregation.")
2754 (license license:expat)))
2756 (define-public r-hexbin
2763 (uri (cran-uri "hexbin" version))
2766 "0xi6fbf1fvyn2gffr052n3viibqzpr3603sgi4xaminbzja4syjh"))))
2767 (build-system r-build-system)
2769 `(("r-lattice" ,r-lattice)))
2771 `(("gfortran" ,gfortran)))
2772 (home-page "http://github.com/edzer/hexbin")
2773 (synopsis "Hexagonal binning routines")
2775 "This package provides binning and plotting functions for hexagonal bins.
2776 It uses and relies on grid graphics and formal (S4) classes and methods.")
2777 (license license:gpl2+)))
2779 (define-public r-plotly
2785 (uri (cran-uri "plotly" version))
2788 "15hvqa0sf4z6l6vvr614zjszfphwpv66zpc665iyiynq0pd1jv2c"))))
2789 (build-system r-build-system)
2791 `(("r-base64enc" ,r-base64enc)
2792 ("r-digest" ,r-digest)
2793 ("r-ggplot2" ,r-ggplot2)
2794 ("r-hexbin" ,r-hexbin)
2795 ("r-htmlwidgets" ,r-htmlwidgets)
2797 ("r-jsonlite" ,r-jsonlite)
2798 ("r-magrittr" ,r-magrittr)
2800 ("r-scales" ,r-scales)
2801 ("r-tidyr" ,r-tidyr)
2802 ("r-viridis" ,r-viridis)))
2803 (home-page "https://plot.ly/r")
2804 (synopsis "Create interactive web graphics")
2806 "This package enables the translation of ggplot2 graphs to an interactive
2807 web-based version and/or the creation of custom web-based visualizations
2808 directly from R. Once uploaded to a plotly account, plotly graphs (and the
2809 data behind them) can be viewed and modified in a web browser.")
2810 (license license:x11)))
2812 (define-public r-biased-urn
2814 (name "r-biased-urn")
2819 (uri (cran-uri "BiasedUrn" version))
2822 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
2823 (properties `((upstream-name . "BiasedUrn")))
2824 (build-system r-build-system)
2825 (home-page "http://www.agner.org/random/")
2826 (synopsis "Biased urn model distributions")
2828 "This package provides statistical models of biased sampling in the form
2829 of univariate and multivariate noncentral hypergeometric distributions,
2830 including Wallenius' noncentral hypergeometric distribution and Fisher's
2831 noncentral hypergeometric distribution (also called extended hypergeometric
2833 (license license:gpl3+)))
2835 (define-public r-runit
2842 (uri (cran-uri "RUnit" version))
2845 "1jqr871jkll2xmk7wk5hv1z3a36hyn2ibgivw7bwk4b346940xlx"))))
2846 (properties `((upstream-name . "RUnit")))
2847 (build-system r-build-system)
2848 (home-page "http://cran.r-project.org/web/packages/RUnit")
2849 (synopsis "R unit test framework")
2851 "This package provides R functions implementing a standard unit testing
2852 framework, with additional code inspection and report generation tools.")
2853 (license license:gpl2+)))
2855 (define-public r-zoo
2861 (uri (cran-uri "zoo" version))
2864 "0m67bnrg7r1jxvs9p7rpa430szp5qfp65r056yb8bivpc16jd98c"))))
2865 (build-system r-build-system)
2867 `(("r-lattice" ,r-lattice)))
2868 (home-page "http://zoo.R-Forge.R-project.org/")
2869 (synopsis "S3 infrastructure for regular and irregular time series")
2870 (description "This package contains an S3 class with methods for totally
2871 ordered indexed observations. It is particularly aimed at irregular time
2872 series of numeric vectors/matrices and factors.")
2873 (license license:gpl2+)))
2875 (define-public r-ztable
2881 (uri (cran-uri "ztable" version))
2884 "1jfqnqy9544gfvz3bsb48v4177nwp4b4n9l2743asq8sbq305b5r"))))
2885 (build-system r-build-system)
2886 (home-page "http://cran.r-project.org/web/packages/ztable")
2887 (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
2889 "This package provides functions to make zebra-striped tables (tables
2890 with alternating row colors) in LaTeX and HTML formats easily from
2891 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
2892 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
2893 @code{cbind.mytable} objects.")
2894 (license license:gpl2+)))