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 machine-learning)
45 #:use-module (gnu packages maths)
46 #:use-module (gnu packages multiprecision)
47 #:use-module (gnu packages pcre)
48 #:use-module (gnu packages perl)
49 #:use-module (gnu packages pkg-config)
50 #:use-module (gnu packages python)
51 #:use-module (gnu packages readline)
52 #:use-module (gnu packages ssh)
53 #:use-module (gnu packages texinfo)
54 #:use-module (gnu packages tls)
55 #:use-module (gnu packages base)
56 #:use-module (gnu packages web)
57 #:use-module (gnu packages xml)
58 #:use-module (gnu packages xorg)
59 #:use-module (gnu packages zip)
60 #:use-module (srfi srfi-1))
70 (uri (string-append "mirror://gnu/pspp/pspp-"
74 "1afsq0a3iij64qacczvwhk81qg0q5rfqm055y5h9ls28d6paqz7p"))))
75 (build-system gnu-build-system)
78 ("gettext" ,gettext-minimal)
82 ("readline" ,readline)
84 ("gtksourceview" ,gtksourceview)
87 `(("glib" ,glib "bin") ;for glib-genmarshal
89 ("pkg-config" ,pkg-config)))
90 (home-page "http://www.gnu.org/software/pspp/")
91 (synopsis "Statistical analysis")
93 "GNU PSPP is a statistical analysis program. It can perform
94 descriptive statistics, T-tests, linear regression and non-parametric tests.
95 It features both a graphical interface as well as command-line input. PSPP
96 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
97 can be imported from spreadsheets, text files and database sources and it can
98 be output in text, PostScript, PDF or HTML.")
99 (license license:gpl3+)))
107 (uri (string-append "mirror://cran/src/base/R-"
108 (version-prefix version 1) "/R-"
112 "1qm9znh8akfy9fkzzi6f1vz2w1dd0chsr6qn7kw80lqzhgjrmi9x"))))
113 (build-system gnu-build-system)
116 (list (string-append "LDFLAGS=-Wl,-rpath="
117 (assoc-ref %outputs "out")
120 (modify-phases %standard-phases
121 (add-before 'configure 'patch-uname
122 (lambda* (#:key inputs #:allow-other-keys)
123 (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
125 (substitute* "src/scripts/R.sh.in"
126 (("uname") uname-bin)))
129 'configure 'set-default-pager
130 ;; Set default pager to "cat", because otherwise it is "false",
131 ;; making "help()" print nothing at all.
132 (lambda _ (setenv "PAGER" "cat") #t))
133 (add-before 'check 'set-timezone
134 ;; Some tests require the timezone to be set.
135 (lambda* (#:key inputs #:allow-other-keys)
138 (string-append (assoc-ref inputs "tzdata")
141 (add-after 'build 'make-info
142 (lambda _ (zero? (system* "make" "info"))))
143 (add-after 'build 'install-info
144 (lambda _ (zero? (system* "make" "install-info")))))
147 "--with-blas=-lopenblas"
153 "--enable-BLAS-shlib"
155 "--with-system-bzlib"
158 "--with-system-xz")))
159 ;; R has some support for Java. When the JDK is available at configure
160 ;; time environment variables pointing to the JDK will be recorded under
161 ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
162 ;; CMD javareconf". "R CMD javareconf" appears to only be used to update
163 ;; the recorded environment variables in $R_HOME/etc. Refer to
164 ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
165 ;; for additional information.
167 ;; As the JDK is a rather large input with only very limited effects on R,
168 ;; we decided to drop it.
172 ("pkg-config" ,pkg-config)
173 ("texinfo" ,texinfo) ; for building HTML manuals
174 ("which" ,which) ; for tests/Examples/base-Ex.R
177 `(;; We need not only cairo here, but pango to ensure that tests for the
178 ;; "cairo" bitmapType plotting backend succeed.
180 ("coreutils" ,coreutils)
183 ("openblas" ,openblas)
184 ("gfortran" ,gfortran)
191 ("readline" ,readline)
194 (list (search-path-specification
195 (variable "R_LIBS_SITE")
196 (files (list "site-library/")))))
197 (home-page "http://www.r-project.org/")
198 (synopsis "Environment for statistical computing and graphics")
200 "R is a language and environment for statistical computing and graphics.
201 It provides a variety of statistical techniques, such as linear and nonlinear
202 modeling, classical statistical tests, time-series analysis, classification
203 and clustering. It also provides robust support for producing
204 publication-quality data plots. A large amount of 3rd-party packages are
205 available, greatly increasing its breadth and scope.")
206 (license license:gpl3+)))
208 (define-public r-colorspace
210 (name "r-colorspace")
215 (uri (cran-uri "colorspace" version))
217 (base32 "0flw97iwwpkxy6si9cn982jhl61wb1rxi3r0nz2xxf0c3fzw18d5"))))
218 (build-system r-build-system)
219 (home-page "http://cran.r-project.org/web/packages/colorspace")
220 (synopsis "Color space manipulation")
222 "This package carries out a mapping between assorted color spaces
223 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
224 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
225 colors are provided.")
226 (license license:bsd-3)))
228 (define-public r-dichromat
235 (uri (cran-uri "dichromat" version))
237 (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
238 (build-system r-build-system)
239 (home-page "http://cran.r-project.org/web/packages/dichromat")
240 (synopsis "Color schemes for dichromats")
242 "Dichromat collapses red-green or green-blue distinctions to simulate the
243 effects of different types of color-blindness.")
244 (license license:gpl2+)))
246 (define-public r-digest
253 (uri (cran-uri "digest" version))
255 (base32 "07825781nl85gx3pqskc04ywgs0f874qj9z2nyrwz7h0aqks0l8c"))))
256 (build-system r-build-system)
257 ;; Vignettes require r-knitr, which requires r-digest, so we have to
258 ;; disable them and the tests.
261 #:configure-flags (list "--no-build-vignettes")))
262 (home-page "http://dirk.eddelbuettel.com/code/digest.html")
263 (synopsis "Create cryptographic hash digests of R objects")
265 "This package contains an implementation of a function 'digest()' for the
266 creation of hash digests of arbitrary R objects (using the md5, sha-1,
267 sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
268 of R language objects, as well as a function 'hmac()' to create hash-based
269 message authentication code.
271 Please note that this package is not meant to be deployed for cryptographic
272 purposes for which more comprehensive (and widely tested) libraries such as
273 OpenSSL should be used.")
274 (license license:gpl2+)))
276 (define-public r-estimability
278 (name "r-estimability")
282 (uri (cran-uri "estimability" version))
285 "049adh8i0ad0m0qln2ylqdxcs5v2q9zfignn2a50r5f93ip2ay6w"))))
286 (build-system r-build-system)
287 (home-page "http://cran.r-project.org/web/packages/estimability")
288 (synopsis "Tools for assessing estimability of linear predictions")
289 (description "Provides tools for determining estimability of linear
290 functions of regression coefficients, and 'epredict' methods that handle
291 non-estimable cases correctly.")
292 (license license:gpl2+)))
294 (define-public r-gtable
301 (uri (cran-uri "gtable" version))
303 (base32 "0k9hfj6r5y238gqh92s3cbdn34biczx3zfh79ix5xq0c5vkai2xh"))))
304 (build-system r-build-system)
305 (home-page "https://cran.r-project.org/web/packages/gtable")
306 (synopsis "R library to arrange grobs in tables")
308 "Gtable is a collection of tools to make it easier to work with
309 \"tables\" of grobs.")
310 (license license:gpl2+)))
312 (define-public r-pheatmap
319 (uri (cran-uri "pheatmap" version))
322 "1ik0k69kb4n7xl3bkx4p09kw08ri93855zcsxq1c668171jqfiji"))))
323 (build-system r-build-system)
325 `(("r-gtable" ,r-gtable)
326 ("r-rcolorbrewer" ,r-rcolorbrewer)
327 ("r-scales" ,r-scales)))
329 "http://cran.r-project.org/web/packages/pheatmap")
330 (synopsis "Pretty heatmaps")
332 "This package provides an implementation of heatmaps that offers more
333 control over dimensions and appearance.")
334 (license license:gpl2+)))
336 (define-public r-labeling
343 (uri (cran-uri "labeling" version))
345 (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
346 (build-system r-build-system)
347 (home-page "http://cran.r-project.org/web/packages/labeling")
348 (synopsis "Axis labeling algorithms")
349 (description "The labeling package provides a range of axis labeling
351 (license license:expat)))
353 (define-public r-magrittr
360 (uri (cran-uri "magrittr" version))
362 (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
363 (build-system r-build-system)
364 (home-page "http://cran.r-project.org/web/packages/magrittr/index.html")
365 (synopsis "A forward-pipe operator for R")
367 "Magrittr provides a mechanism for chaining commands with a new
368 forward-pipe operator, %>%. This operator will forward a value, or the result
369 of an expression, into the next function call/expression. There is flexible
370 support for the type of right-hand side expressions. For more information,
371 see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
372 (license license:expat)))
374 (define-public r-munsell
381 (uri (cran-uri "munsell" version))
383 (base32 "0jdxlbjslkzaqgp058da1cgm85qvqi09wpcgpvp4hvwnmy83qz1r"))))
384 (build-system r-build-system)
386 `(("r-colorspace" ,r-colorspace)))
387 (home-page "http://cran.r-project.org/web/packages/munsell")
388 (synopsis "Munsell colour system")
390 "The Munsell package contains Functions for exploring and using the
391 Munsell colour system.")
392 (license license:expat)))
394 (define-public r-rcpp
401 (uri (cran-uri "Rcpp" version))
403 (base32 "1ipid4yfqp1k5c70f7bz7izzq63srmrcxhiqrnyilk2wgrvd7ypb"))))
404 (build-system r-build-system)
405 (home-page "http://www.rcpp.org")
406 (synopsis "Seamless R and C++ Integration")
408 "The Rcpp package provides R functions as well as C++ classes which offer
409 a seamless integration of R and C++. Many R data types and objects can be
410 mapped back and forth to C++ equivalents which facilitates both writing of new
411 code as well as easier integration of third-party libraries. Documentation
412 about Rcpp is provided by several vignettes included in this package, via the
413 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
414 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
415 'citation(\"Rcpp\")' for details on these last two.")
416 (license license:gpl2+)))
418 (define-public r-matrix
425 (uri (cran-uri "Matrix" version))
428 "09rd51na9spz0lm1lylkfhw43w7c922b83m4jsggmpg3pbd6dssa"))))
429 (properties `((upstream-name . "Matrix")))
430 (build-system r-build-system)
432 `(("r-lattice" ,r-lattice)))
433 (home-page "http://Matrix.R-forge.R-project.org/")
434 (synopsis "Sparse and dense matrix classes and methods")
436 "This package provides classes and methods for dense and sparse matrices
437 and operations on them using LAPACK and SuiteSparse.")
438 (license license:gpl2+)))
440 (define-public r-mgcv
447 (uri (cran-uri "mgcv" version))
450 "05xzmsx51y92c0r0yihac8m9d3v1sqnn8ahcgm3q75j8z6zybsjs"))))
451 (build-system r-build-system)
452 (home-page "http://cran.r-project.org/web/packages/mgcv")
453 (synopsis "Mixed generalised additive model computation")
455 "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
456 parameter estimation by GCV, REML or UBRE/AIC. The library includes a
457 @code{gam()} function, a wide variety of smoothers, JAGS support and
458 distributions beyond the exponential family.")
459 (license license:gpl2+)))
461 (define-public r-permute
468 (uri (cran-uri "permute" version))
471 "1w8wzk1fg9q7wvisnfp2js70dg0m9wi12gkdhpyngpbdcgssahd5"))))
472 (build-system r-build-system)
473 ;; Tests do not run correctly, but running them properly would entail a
474 ;; circular dependency with vegan.
475 (home-page "https://github.com/gavinsimpson/permute")
476 (synopsis "Functions for Generating Restricted Permutations of Data")
478 "This package provides a set of restricted permutation designs for freely
479 exchangeable, line transects (time series), spatial grid designs and permutation
480 of blocks (groups of samples). @code{permute} also allows split-plot designs,
481 in which the whole-plots or split-plots or both can be freely exchangeable.")
482 (license license:gpl2+)))
484 (define-public r-plyr
491 (uri (cran-uri "plyr" version))
493 (base32 "1igar5pcjqh0jyxv0z3jah8rz617vfa86vw0r5c7c031b7bj5db0"))))
494 (build-system r-build-system)
495 (native-inputs `(("r-rcpp" ,r-rcpp)))
496 (home-page "http://had.co.nz/plyr")
497 (synopsis "Tools for Splitting, Applying and Combining Data")
499 "Plyr is a set of tools that solves a common set of problems: you need to
500 break a big problem down into manageable pieces, operate on each piece and
501 then put all the pieces back together. For example, you might want to fit a
502 model to each spatial location or time point in your study, summarise data by
503 panels or collapse high-dimensional arrays to simpler summary statistics.")
504 (license license:expat)))
506 (define-public r-proto
513 (uri (cran-uri "proto" version))
515 (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
516 (build-system r-build-system)
517 (home-page "https://github.com/hadley/proto")
518 (synopsis "Prototype object-based programming")
520 "Proto is an object oriented system using object-based, also called
521 prototype-based, rather than class-based object oriented ideas.")
522 (license license:gpl2+)))
524 (define-public r-rcolorbrewer
526 (name "r-rcolorbrewer")
531 (uri (cran-uri "RColorBrewer" version))
533 (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
534 (build-system r-build-system)
535 (home-page "http://cran.r-project.org/web/packages/RColorBrewer")
536 (synopsis "ColorBrewer palettes")
538 "This package provides color schemes for maps (and other graphics)
539 designed by Cynthia Brewer as described at http://colorbrewer2.org")
540 ;; Includes code licensed under bsd-4
541 (license license:asl2.0)))
543 (define-public r-sendmailr
550 (uri (cran-uri "sendmailR" version))
553 "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
554 (properties `((upstream-name . "sendmailR")))
555 (build-system r-build-system)
557 `(("r-base64enc" ,r-base64enc)))
559 "http://cran.r-project.org/web/packages/sendmailR")
560 (synopsis "Send email using R")
562 "This package contains a simple SMTP client which provides a portable
563 solution for sending email, including attachments, from within R.")
564 (license license:gpl2+)))
566 (define-public r-stringi
573 (uri (cran-uri "stringi" version))
576 "13i1p6j8mx31hsw2s4c2phm2llrrdakzixkm6i0axsxprri722z5"))))
577 (build-system r-build-system)
578 (inputs `(("icu4c" ,icu4c)))
579 (native-inputs `(("pkg-config" ,pkg-config)))
580 (home-page "http://stringi.rexamine.com/")
581 (synopsis "Character string processing facilities")
583 "This package allows for fast, correct, consistent, portable, as well as
584 convenient character string/text processing in every locale and any native
585 encoding. Owing to the use of the ICU library, the package provides R users
586 with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
587 programmers. Among available features there are: pattern searching
588 (e.g. via regular expressions), random string generation, string collation,
589 transliteration, concatenation, date-time formatting and parsing, etc.")
590 (license license:bsd-3)))
592 (define-public r-stringr
599 (uri (cran-uri "stringr" version))
601 (base32 "0css5j4psl80br75chg6s1s3ipzf89f71bnbys34flp9yghg1cfc"))))
602 (build-system r-build-system)
604 `(("r-magrittr" ,r-magrittr)
605 ("r-stringi" ,r-stringi)))
606 (home-page "https://github.com/hadley/stringr")
607 (synopsis "Simple, consistent wrappers for common string operations")
609 "Stringr is a consistent, simple and easy to use set of wrappers around
610 the fantastic 'stringi' package. All function and argument names (and
611 positions) are consistent, all functions deal with \"NA\"'s and zero length
612 vectors in the same way, and the output from one function is easy to feed into
613 the input of another.")
614 (license license:gpl2+)))
616 (define-public r-reshape2
623 (uri (cran-uri "reshape2" version))
625 (base32 "0swvjmc9f8cvkrsz463cp6snd8bncbv6q8yrfrb4rgkr0dhq6dvd"))))
626 (build-system r-build-system)
630 ("r-stringr" ,r-stringr)))
631 (home-page "https://github.com/hadley/reshape")
632 (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
634 "Reshape2 is an R library to flexibly restructure and aggregate data
635 using just two functions: melt and dcast (or acast).")
636 (license license:expat)))
638 (define-public r-scales
645 (uri (cran-uri "scales" version))
647 (base32 "19y6q4j8vpmc73dnn4ncp5wj44gri7m77ys3z2rn3crrcc9zc7l5"))))
648 (build-system r-build-system)
650 `(("r-dichromat" ,r-dichromat)
651 ("r-labeling" ,r-labeling)
652 ("r-munsell" ,r-munsell)
654 ("r-rcolorbrewer" ,r-rcolorbrewer)
656 (home-page "https://github.com/hadley/scales")
657 (synopsis "Scale functions for visualization")
659 "This package provides graphical scales that map data to aesthetics, and
660 provides methods for automatically determining breaks and labels for axes and
662 (license license:expat)))
664 (define-public r-ggplot2
671 (uri (cran-uri "ggplot2" version))
673 (base32 "0s9rvp0f736ji6p9xpxq54agxf95pjkql4sj7ag0hv2xhnp27hzj"))))
674 (build-system r-build-system)
676 `(("r-digest" ,r-digest)
677 ("r-gtable" ,r-gtable)
680 ("r-reshape2" ,r-reshape2)
681 ("r-scales" ,r-scales)
682 ("r-svglite" ,r-svglite)))
683 (home-page "http://ggplot2.org")
684 (synopsis "An implementation of the grammar of graphics")
686 "Ggplot2 is an implementation of the grammar of graphics in R. It
687 combines the advantages of both base and lattice graphics: conditioning and
688 shared axes are handled automatically, and you can still build up a plot step
689 by step from multiple data sources. It also implements a sophisticated
690 multidimensional conditioning system and a consistent interface to map data to
691 aesthetic attributes.")
692 (license license:gpl2+)))
694 (define-public r-gdtools
701 (uri (cran-uri "gdtools" version))
704 "1l9d759x9s4ddz51sls8kcjps2i9kwfbc72dnagrdavh82h0al8n"))))
705 (build-system r-build-system)
708 ("pkg-config" ,pkg-config)))
712 `(("r-withr" ,r-withr)))
713 (home-page "http://cran.r-project.org/web/packages/gdtools")
714 (synopsis "Utilities for graphical rendering")
716 "The @code{gdtools} package provides functionalities to get font metrics
717 and to generate base64 encoded string from raster matrix.")
718 (license license:gpl3)))
720 (define-public r-svglite
727 (uri (cran-uri "svglite" version))
730 "11ryicjglfi6jvkk4jgg5kra42qbs5z2zid7jjhlslpjcljfwc70"))))
731 (build-system r-build-system)
732 (native-inputs `(("r-rcpp" ,r-rcpp)))
735 ("r-gdtools" ,r-gdtools)))
736 (home-page "https://github.com/hadley/svglite")
737 (synopsis "SVG graphics device")
739 "@code{svglite} is a graphics device that produces clean
740 @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
741 hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
742 considerably faster, produces smaller files, and leaves text as is.")
743 (license license:gpl2+)))
745 (define-public r-assertthat
747 (name "r-assertthat")
751 (uri (cran-uri "assertthat" version))
754 "0dwsqajyglfscqilj843qfqn1ndbqpswa7b4l1d633qjk9d68qqk"))))
755 (build-system r-build-system)
756 (home-page "https://github.com/hadley/assertthat")
757 (synopsis "Easy pre and post assertions")
759 "Assertthat is an extension to stopifnot() that makes it easy to declare
760 the pre and post conditions that your code should satisfy, while also
761 producing friendly error messages so that your users know what they've done
763 (license license:gpl3+)))
765 (define-public r-lazyeval
771 (uri (cran-uri "lazyeval" version))
774 "1jwdz40nznlc44hpjli7h98gnpa4d98ifggmj7z88h84n9aqywqk"))))
775 (build-system r-build-system)
776 (home-page "https://github.com/hadley/lazyeval")
777 (synopsis "Lazy (non-standard) evaluation in R")
779 "This package provides the tools necessary to do non-standard
780 evaluation (NSE) in R.")
781 (license license:gpl3+)))
789 (uri (cran-uri "DBI" version))
792 "1idwm9lkmz6ns6h0vvgml18mg0k7vjqiv9p5svrdcmx7r1rirpdi"))))
793 (build-system r-build-system)
794 (home-page "https://github.com/rstats-db/DBI")
795 (synopsis "R database interface")
797 "The DBI package provides a database interface (DBI) definition for
798 communication between R and relational database management systems. All
799 classes in this package are virtual and need to be extended by the various
800 R/DBMS implementations.")
801 (license license:lgpl2.0+)))
809 (uri (cran-uri "BH" version))
812 "136497fng9bcvrf8favpj8inz96pxdwp1rrb2k00sxjxjbgawhg4"))))
813 (build-system r-build-system)
814 (home-page "https://github.com/eddelbuettel/bh")
815 (synopsis "R package providing subset of Boost headers")
817 "This package aims to provide the most useful subset of Boost libraries
818 for template use among CRAN packages.")
819 (license license:boost1.0)))
821 (define-public r-evaluate
827 (uri (cran-uri "evaluate" version))
830 "0mwna7rjyrmc76651a1fm7c76ippdsc2wsp3sj3iwb1c73mvlqv1"))))
831 (build-system r-build-system)
833 `(("r-stringr" ,r-stringr)))
834 (home-page "https://github.com/hadley/evaluate")
835 (synopsis "Parsing and evaluation tools for R")
837 "This package provides tools that allow you to recreate the parsing,
838 evaluation and display of R code, with enough information that you can
839 accurately recreate what happens at the command line. The tools can easily be
840 adapted for other output formats, such as HTML or LaTeX.")
841 (license license:gpl3+)))
843 (define-public r-formatr
849 (uri (cran-uri "formatR" version))
852 "1fvynq0fj1r9grg9vvfdh5fl2riv6qki9f2rfpyvbvqq3xxpmi3f"))))
853 (build-system r-build-system)
854 (home-page "http://yihui.name/formatR")
855 (synopsis "Format R code automatically")
857 "This package provides a function to format R source code. Spaces and
858 indent will be added to the code automatically, and comments will be preserved
859 under certain conditions, so that R code will be more human-readable and tidy.
860 There is also a Shiny app as a user interface in this package.")
861 (license license:gpl3+)))
863 (define-public r-highr
869 (uri (cran-uri "highr" version))
872 "0n9v44dxdy5fhkdmpbpa2p78whyd9z3rhhy42ipdz5m5vsr55qa3"))))
873 (build-system r-build-system)
874 (home-page "https://github.com/yihui/highr")
875 (synopsis "Syntax highlighting for R source code")
877 "This package provides syntax highlighting for R source code. Currently
878 it supports LaTeX and HTML output. Source code of other languages is
879 supported via Andre Simon's highlight package.")
880 (license license:gpl3+)))
882 (define-public r-mime
888 (uri (cran-uri "mime" version))
891 "0i91m3ivaja1k33jwcvz16pfjypkci27awm8glil7sxhmwaj3izw"))))
892 (build-system r-build-system)
893 (home-page "https://github.com/yihui/mime")
894 (synopsis "R package to map filenames to MIME types")
896 "This package guesses the MIME type from a filename extension using the
897 data derived from /etc/mime.types in UNIX-type systems.")
898 (license license:gpl2)))
900 (define-public r-markdown
906 (uri (cran-uri "markdown" version))
909 "00j1hlib3il50azs2vlcyhi0bjpx1r50mxr9w9dl5g1bwjjc71hb"))))
910 (build-system r-build-system)
911 ;; Skip check phase because the tests require the r-knitr package to be
912 ;; installed. This prevents installation failures. Knitr normally
913 ;; shouldn't be available since r-markdown is a dependency of the r-knitr
915 (arguments `(#:tests? #f))
917 `(("r-mime" ,r-mime)))
918 (home-page "https://github.com/rstudio/markdown")
919 (synopsis "Markdown rendering for R")
921 "This package provides R bindings to the Sundown Markdown rendering
922 library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
923 syntax that can be converted to XHTML or other formats.")
924 (license license:gpl2)))
926 (define-public r-yaml
932 (uri (cran-uri "yaml" version))
935 "18kz5mfn7qpif5pn91w4vbrc5bkycsj85vwm5wxwzjlb02i9mxi6"))))
936 (build-system r-build-system)
937 (home-page "https://cran.r-project.org/web/packages/yaml/")
938 (synopsis "Methods to convert R data to YAML and back")
940 "This package implements the libyaml YAML 1.1 parser and
941 emitter (http://pyyaml.org/wiki/LibYAML) for R.")
942 (license license:bsd-3)))
944 (define-public r-knitr
950 (uri (cran-uri "knitr" version))
953 "1v0s0knb294p7a2xkwy35bhg0w8p3qcgyphd748sj86hh8a30vds"))))
954 (build-system r-build-system)
956 `(("r-evaluate" ,r-evaluate)
957 ("r-digest" ,r-digest)
958 ("r-formatr" ,r-formatr)
960 ("r-markdown" ,r-markdown)
961 ("r-stringr" ,r-stringr)
963 (home-page "http://yihui.name/knitr/")
964 (synopsis "General-purpose package for dynamic report generation in R")
966 "This package provides a general-purpose tool for dynamic report
967 generation in R using Literate Programming techniques.")
968 ;; The code is released under any version of the GPL. As it is used by
969 ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
971 (license license:gpl2+)))
973 (define-public r-knitrbootstrap
975 (name "r-knitrbootstrap")
980 (uri (cran-uri "knitrBootstrap" version))
983 "0pshn2slzqwpryklslsxwh1dmqcnwv6bwi7yfm6m342wjybpk0wl"))))
984 (properties `((upstream-name . "knitrBootstrap")))
985 (build-system r-build-system)
987 `(("r-knitr" ,r-knitr)
988 ("r-rmarkdown" ,r-rmarkdown)))
989 (home-page "https://github.com/jimhester/knitrBootstrap")
990 (synopsis "Knitr bootstrap framework")
992 "This package provides a framework to create Bootstrap 3 HTML reports
993 from knitr Rmarkdown.")
994 (license license:expat)))
996 (define-public r-microbenchmark
998 (name "r-microbenchmark")
1002 (uri (cran-uri "microbenchmark" version))
1005 "0qn5r1a6qidghcisc2hpbdmj62pnixc3zz6p4ipk8mvakf0hdsvg"))))
1006 (build-system r-build-system)
1008 `(("r-ggplot2" ,r-ggplot2)))
1009 (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
1010 (synopsis "Accurate timing functions for R")
1012 "This package provides infrastructure to accurately measure and compare
1013 the execution time of R expressions.")
1014 (license license:bsd-2)))
1016 (define-public r-codetools
1018 (name "r-codetools")
1022 (uri (cran-uri "codetools" version))
1025 "0y9r4m2b8xgavr89sc179knzwpz54xljbc1dinpq2q07i4xn0397"))))
1026 (build-system r-build-system)
1027 (home-page "https://cran.r-project.org/web/packages/codetools/index.html")
1028 (synopsis "Code analysis tools for R")
1029 (description "This package provides code analysis tools for R.")
1030 (license license:gpl3+)))
1032 (define-public r-pryr
1038 (uri (cran-uri "pryr" version))
1041 "1in350a8hxwf580afavasvn3jc7x2p1b7nlwmj1scakfz74vghk5"))))
1042 (build-system r-build-system)
1044 `(("r-stringr" ,r-stringr)
1045 ("r-codetools" ,r-codetools)))
1047 `(("r-rcpp" ,r-rcpp)))
1048 (home-page "https://github.com/hadley/pryr")
1049 (synopsis "Tools for computing on the R language")
1051 "This package provides useful tools to pry back the covers of R and
1052 understand the language at a deeper level.")
1053 (license license:gpl2)))
1055 (define-public r-memoise
1061 (uri (cran-uri "memoise" version))
1064 "0sq2dhpvxy17v1baj256r0jnygdy3m5a8x4zh6vhv29957qnq6zx"))))
1065 (build-system r-build-system)
1067 `(("r-digest" ,r-digest)))
1068 (home-page "http://github.com/hadley/memoise")
1069 (synopsis "Memoise functions for R")
1071 "This R package allows to cache the results of a function so that when
1072 you call it again with the same arguments it returns the pre-computed value.")
1073 (license license:expat)))
1075 (define-public r-crayon
1081 (uri (cran-uri "crayon" version))
1084 "0s2yam18slph7xsw4pyc9f92gdyf609r5w92yax69zh57kb7asws"))))
1085 (build-system r-build-system)
1087 `(("r-memoise" ,r-memoise)))
1088 (home-page "https://github.com/gaborcsardi/crayon")
1089 (synopsis "Colored terminal output for R")
1091 "Colored terminal output on terminals that support ANSI color and
1092 highlight codes. It also works in Emacs ESS. ANSI color support is
1093 automatically detected. Colors and highlighting can be combined and nested.
1094 New styles can also be created easily. This package was inspired by the
1095 \"chalk\" JavaScript project.")
1096 (license license:expat)))
1098 (define-public r-praise
1105 (uri (cran-uri "praise" version))
1108 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
1109 (build-system r-build-system)
1110 (home-page "https://github.com/gaborcsardi/praise")
1111 (synopsis "Functions to praise users")
1113 "This package provides template functions to assist in building friendly
1114 R packages that praise their users.")
1115 (license license:expat)))
1117 (define-public r-testthat
1123 (uri (cran-uri "testthat" version))
1126 "0pj1r01x4ny4capr83dfa19hi5i2sjjxky99schzip8zrq5dzxqf"))))
1127 (build-system r-build-system)
1129 `(("r-digest" ,r-digest)
1130 ("r-crayon" ,r-crayon)
1131 ("r-magrittr" ,r-magrittr)
1132 ("r-praise" ,r-praise)
1134 (home-page "https://github.com/hadley/testthat")
1135 (synopsis "Unit testing for R")
1137 "This package provides a unit testing system for R designed to be fun,
1138 flexible and easy to set up.")
1139 (license license:expat)))
1147 (uri (cran-uri "R6" version))
1150 "1ir51pb0y6yj05qaxsflk4a6hv8n73cwlb0qajcskbrz632dsyvx"))))
1151 (build-system r-build-system)
1152 (home-page "https://github.com/wch/R6/")
1153 (synopsis "Classes with reference semantics in R")
1155 "The R6 package allows the creation of classes with reference semantics,
1156 similar to R's built-in reference classes. Compared to reference classes, R6
1157 classes are simpler and lighter-weight, and they are not built on S4 classes
1158 so they do not require the methods package. These classes allow public and
1159 private members, and they support inheritance, even when the classes are
1160 defined in different packages.")
1161 (license license:expat)))
1163 (define-public r-tibble
1170 (uri (cran-uri "tibble" version))
1173 "011i352ylq9b4xfcj7h10h7qsqd9qkc1rzc0pr1gf8qjb788p2pd"))))
1174 (build-system r-build-system)
1176 `(("r-assertthat" ,r-assertthat)
1177 ("r-lazyeval" ,r-lazyeval)
1178 ("r-rcpp" ,r-rcpp)))
1179 (home-page "https://github.com/hadley/tibble")
1180 (synopsis "Simple data frames")
1182 "This package provides a @code{tbl_df} class that offers better checking
1183 and printing capabilities than traditional data frames.")
1184 (license license:expat)))
1186 (define-public r-dplyr
1192 (uri (cran-uri "dplyr" version))
1195 "0ks5cklb03laqf5ygcw986g1lv7wk1ipvypjlha8xly2y4lvilwk"))))
1196 (build-system r-build-system)
1198 `(("r-assertthat" ,r-assertthat)
1200 ("r-magrittr" ,r-magrittr)
1201 ("r-lazyeval" ,r-lazyeval)
1203 ("r-tibble" ,r-tibble)))
1205 `(("r-rcpp" ,r-rcpp)
1207 (home-page "https://github.com/hadley/dplyr")
1208 (synopsis "Tools for working with data frames in R")
1210 "dplyr is the next iteration of plyr. It is focussed on tools for
1211 working with data frames. It has three main goals: 1) identify the most
1212 important data manipulation tools needed for data analysis and make them easy
1213 to use in R; 2) provide fast performance for in-memory data by writing key
1214 pieces of code in C++; 3) use the same code interface to work with data no
1215 matter where it is stored, whether in a data frame, a data table or
1217 (license license:expat)))
1219 (define-public r-acepack
1226 (uri (cran-uri "acepack" version))
1229 "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
1230 (build-system r-build-system)
1232 `(("gfortran" ,gfortran)))
1233 (home-page "http://cran.r-project.org/web/packages/acepack")
1234 (synopsis "Functions for regression transformations")
1236 "This package provides ACE and AVAS methods for choosing regression
1238 (license license:expat)))
1240 (define-public r-cluster
1247 (uri (cran-uri "cluster" version))
1250 "1bkvqmv8h2c423q9ag2afb6s9j2vcdlxsf559zzbimraphrr2c2b"))))
1251 (build-system r-build-system)
1253 `(("gfortran" ,gfortran)))
1254 (home-page "http://cran.r-project.org/web/packages/cluster")
1255 (synopsis "Methods for data cluster analysis")
1257 "This package provides tools that are useful in finding groups in data.
1258 It is based on the methods described in Kaufman and Rousseeuw (1990) \"Finding
1260 (license license:gpl2+)))
1262 (define-public r-foreign
1269 (uri (cran-uri "foreign" version))
1272 "1mcrm2pydimbyjhkrw5h380bifj1jhwzifph1xgh90asf3lvd1xd"))))
1273 (build-system r-build-system)
1274 (home-page "http://cran.r-project.org/web/packages/foreign")
1275 (synopsis "Read data stored by other statistics software in R")
1277 "This package provides functions for reading and writing data stored by
1278 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka, and
1279 for reading and writing some dBase files.")
1280 (license license:gpl2+)))
1282 (define-public r-formula
1289 (uri (cran-uri "Formula" version))
1292 "02in5325zzrqbhlygx6s0dinj6ymw845q70y56frqacv25ayzcax"))))
1293 (properties `((upstream-name . "Formula")))
1294 (build-system r-build-system)
1295 (home-page "http://cran.r-project.org/web/packages/Formula")
1296 (synopsis "Extended model formulas")
1298 "This package provides a new class @code{Formula}, which extends the base
1299 class @code{formula}. It supports extended formulas with multiple parts of
1300 regressors on the right-hand side and/or multiple responses on the left-hand
1302 (license (list license:gpl2+ license:gpl3+))))
1304 (define-public r-locfit
1311 (uri (cran-uri "locfit" version))
1314 "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
1315 (build-system r-build-system)
1316 (home-page "http://cran.r-project.org/web/packages/locfit")
1317 (synopsis "Local regression, likelihood and density estimation")
1319 "This package provides functions used for local regression, likelihood
1320 and density estimation.")
1321 (license (list license:gpl2+ license:gpl3+))))
1323 (define-public r-chron
1329 (uri (cran-uri "chron" version))
1332 "1xj50kk8b8mbjpszp8i0wbripb5a4b36jcscwlbyap8n4487g34s"))))
1333 (build-system r-build-system)
1334 (home-page "http://cran.r-project.org/web/packages/chron")
1335 (synopsis "Chronological R objects which can handle dates and times")
1337 "This package provides chronological R objects which can handle dates and
1339 (license license:gpl2)))
1341 (define-public r-data-table
1343 (name "r-data-table")
1347 (uri (cran-uri "data.table" version))
1350 "0vi3zplpxqbg78z9ifjfs1kl2i8qhkqxr7l9ysp2663kq54w6x3g"))))
1351 (build-system r-build-system)
1353 `(("r-chron" ,r-chron)))
1354 (home-page "https://github.com/Rdatatable/data.table/wiki")
1355 (synopsis "Enhanced version of data.frame R object")
1357 "The R package @code{data.table} is an extension of @code{data.frame}
1358 providing functions for fast aggregation of large data (e.g. 100GB in RAM),
1359 fast ordered joins, fast add/modify/delete of columns by group, column listing
1360 and fast file reading.")
1361 (license license:gpl3+)))
1363 (define-public r-xtable
1370 (uri (cran-uri "xtable" version))
1373 "0398qkpvlw3dv0myz4mjcyqwpwc2m31l127r8vdzwc71wb6s28qn"))))
1374 (build-system r-build-system)
1376 `(("r-knitr" ,r-knitr)))
1377 (home-page "http://xtable.r-forge.r-project.org/")
1378 (synopsis "Export R tables to LaTeX or HTML")
1380 "This package provides tools to export R data as LaTeX and HTML tables.")
1381 (license license:gpl2+)))
1383 (define-public python-patsy
1385 (name "python-patsy")
1389 (uri (pypi-uri "patsy" version ".zip"))
1392 "1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w"))))
1393 (build-system python-build-system)
1396 (modify-phases %standard-phases
1397 (replace 'check (lambda _ (zero? (system* "nosetests" "-v"))))
1398 (add-after 'unpack 'prevent-generation-of-egg-archive
1400 (substitute* "setup.py"
1401 (("from setuptools import setup")
1402 "from distutils.core import setup"))
1405 `(("python-numpy" ,python-numpy)
1406 ("python-scipy" ,python-scipy)
1407 ("python-six" ,python-six)))
1409 `(("python-nose" ,python-nose)
1411 (home-page "https://github.com/pydata/patsy")
1412 (synopsis "Describe statistical models and build design matrices")
1414 "Patsy is a Python package for describing statistical models and for
1415 building design matrices.")
1416 ;; The majority of the code is distributed under BSD-2. The module
1417 ;; patsy.compat contains code derived from the Python standard library,
1418 ;; and is covered by the PSFL.
1419 (license (list license:bsd-2 license:psfl))
1420 (properties `((python2-variant . ,(delay python2-patsy))))))
1422 (define-public python2-patsy
1423 (let ((patsy (package-with-python2 (strip-python2-variant python-patsy))))
1424 (package (inherit patsy)
1426 `(("python2-setuptools" ,python2-setuptools)
1427 ,@(package-native-inputs patsy))))))
1429 (define-public python-statsmodels
1431 (name "python-statsmodels")
1436 (uri (string-append "https://pypi.python.org/packages/source/"
1437 "s/statsmodels/statsmodels-" version ".tar.gz"))
1440 "0xn67sqr0cc1lmlhzm71352hrb4hw7g318p5ff5q97pc98vl8kmy"))
1441 (patches (search-patches "python-statsmodels-fix-tests.patch"))))
1442 (build-system python-build-system)
1445 (modify-phases %standard-phases
1446 ;; tests must be run after installation
1448 (add-after 'unpack 'set-matplotlib-backend-to-agg
1450 ;; Set the matplotlib backend to Agg to avoid problems using the
1451 ;; GTK backend without a display.
1452 (substitute* (find-files "statsmodels/graphics/tests" "\\.py")
1453 (("import matplotlib\\.pyplot as plt" line)
1454 (string-append "import matplotlib;matplotlib.use('Agg');"
1457 (add-after 'install 'check
1459 (with-directory-excursion "/tmp"
1460 (zero? (system* "nosetests"
1462 "-v" "statsmodels"))))))))
1464 `(("python-numpy" ,python-numpy)
1465 ("python-scipy" ,python-scipy)
1466 ("python-pandas" ,python-pandas)
1467 ("python-patsy" ,python-patsy)
1468 ("python-matplotlib" ,python-matplotlib)))
1470 `(("python-cython" ,python-cython)
1471 ("python-nose" ,python-nose)
1472 ("python-sphinx" ,python-sphinx)))
1473 (home-page "http://statsmodels.sourceforge.net/")
1474 (synopsis "Statistical modeling and econometrics in Python")
1476 "Statsmodels is a Python package that provides a complement to scipy for
1477 statistical computations including descriptive statistics and estimation and
1478 inference for statistical models.")
1479 (license license:bsd-3)))
1481 (define-public python2-statsmodels
1482 (let ((stats (package-with-python2 python-statsmodels)))
1483 (package (inherit stats)
1485 `(("python2-pytz" ,python2-pytz)
1486 ("python2-numpy" ,python2-numpy)
1487 ("python2-scipy" ,python2-scipy)
1488 ("python2-pandas" ,python2-pandas)
1489 ("python2-patsy" ,python2-patsy)
1490 ("python2-matplotlib" ,python2-matplotlib)))
1492 `(("python2-setuptools" ,python2-setuptools)
1493 ,@(package-native-inputs stats))))))
1495 (define-public r-coda
1501 (uri (cran-uri "coda" version))
1504 "03sc780734zj2kqcm8lkyvf76fql0jbfhkblpn8l58zmb6cqi958"))))
1505 (build-system r-build-system)
1507 `(("r-lattice" ,r-lattice)))
1508 (home-page "http://cran.r-project.org/web/packages/coda")
1509 (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
1510 (description "This package provides functions for summarizing and plotting
1511 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
1512 diagnostic tests of convergence to the equilibrium distribution of the Markov
1514 (license license:gpl2+)))
1516 (define-public r-ade4
1523 (uri (cran-uri "ade4" version))
1526 "17sbicash7z4b63dlrbaf8xx2pbwh62vykzvhdjs43h8jkl881y7"))))
1527 (build-system r-build-system)
1528 (home-page "http://pbil.univ-lyon1.fr/ADE-4")
1529 (synopsis "Multivariate data analysis and graphical display")
1531 "The ade4 package contains data analysis functions to analyze ecological
1532 and environmental data in the framework of Euclidean exploratory methods.")
1533 (license license:gpl2+)))
1535 (define-public r-xml2
1542 (uri (cran-uri "xml2" version))
1545 "0f2alsrk3yykznbhnz4pcsg9mb72cv607vbapqx5kqfv39772kgr"))))
1546 (build-system r-build-system)
1548 `(("libxml2" ,libxml2)))
1550 `(("r-rcpp" ,r-rcpp)
1552 (home-page "https://github.com/hadley/xml2")
1553 (synopsis "Parse XML with R")
1555 "This package provides a simple, consistent interface to working with XML
1556 files in R. It is built on top of the libxml2 C library.")
1557 (license license:gpl2+)))
1559 (define-public r-multitaper
1561 (name "r-multitaper")
1566 (uri (cran-uri "multitaper" version))
1569 "011qpkwpjclfc24y2qqigmdnikqwdnanflfhihigh5b5k7qwgm5j"))))
1570 (build-system r-build-system)
1572 `(("gfortran" ,gfortran)))
1573 (home-page "http://github.com/wesleyburr/multitaper/")
1574 (synopsis "Multitaper spectral analysis tools")
1576 "This package implements multitaper spectral estimation
1577 techniques using prolate spheroidal sequences (Slepians) and sine
1578 tapers for time series analysis. It includes an adaptive weighted
1579 multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
1580 F-test, and complex demodulation. The Slepians sequences are
1581 generated efficiently using a tridiagonal matrix solution, and
1582 jackknifed confidence intervals are available for most estimates.")
1583 (license license:gpl2+)))
1585 (define-public r-rversions
1587 (name "r-rversions")
1591 (uri (cran-uri "rversions" version))
1594 "0i2gi05nrvknr7g89rbppkswyfcwwd4r9gp75fdfhpah8sgq1l11"))))
1595 (build-system r-build-system)
1597 `(("r-curl" ,r-curl)
1598 ("r-xml2" ,r-xml2)))
1599 (home-page "https://github.com/metacran/rversions")
1600 (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
1602 "This package provides functions to query the main R repository to find
1603 the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
1604 previous R versions and their release dates.")
1605 (license license:expat)))
1607 (define-public r-whisker
1613 (uri (cran-uri "whisker" version))
1616 "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28"))))
1617 (build-system r-build-system)
1618 (home-page "http://github.com/edwindj/whisker")
1619 (synopsis "Logicless mustache templating for R")
1621 "This package provides logicless templating, with a syntax that is not
1623 (license license:gpl3+)))
1625 (define-public r-backports
1627 (name "r-backports")
1632 (uri (cran-uri "backports" version))
1635 "0fssh5rnnvpp8wm0ml9gk765idwrgj07xyxpkhpidl9zwydxzif2"))))
1636 (build-system r-build-system)
1637 (home-page "http://cran.r-project.org/web/packages/backports")
1638 (synopsis "Reimplementations of functions introduced since R 3.0.0")
1640 "Provides implementations of functions which have been introduced in R
1641 since version 3.0.0. The backports are conditionally exported which results
1642 in R resolving the function names to the version shipped with R (if available)
1643 and uses the implemented backports as fallback. This way package developers
1644 can make use of the new functions without worrying about the minimum required
1646 (license license:gpl2+)))
1648 (define-public r-checkmate
1650 (name "r-checkmate")
1655 (uri (cran-uri "checkmate" version))
1658 "1zqcggl9m7slvc0q6zyhssdypb7jzf3l9byl5vxh1qdwjiw2y64g"))))
1659 (build-system r-build-system)
1661 `(("r-backports" ,r-backports)))
1662 (home-page "https://github.com/mllg/checkmate")
1663 (synopsis "Fast and versatile argument checks")
1665 "This package provides tests and assertions to perform frequent argument
1666 checks. A substantial part of the package was written in C to minimize any
1667 worries about execution time overhead.")
1668 (license license:bsd-3)))
1670 (define-public r-bbmisc
1677 (uri (cran-uri "BBmisc" version))
1680 "0cw2mhw7qhdrx91zzd5iwyh7ch9fy4wxga8j63731q6sxr1airjl"))))
1681 (properties `((upstream-name . "BBmisc")))
1682 (build-system r-build-system)
1684 `(("r-checkmate" ,r-checkmate)))
1685 (home-page "https://github.com/berndbischl/BBmisc")
1686 (synopsis "Miscellaneous functions for R package development")
1688 "This package provides miscellaneous helper functions for the development
1690 (license license:bsd-3)))
1692 (define-public r-fail
1699 (uri (cran-uri "fail" version))
1702 "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
1703 (build-system r-build-system)
1705 `(("r-bbmisc" ,r-bbmisc)
1706 ("r-checkmate" ,r-checkmate)))
1707 (home-page "https://github.com/mllg/fail")
1708 (synopsis "File abstraction interface layer (FAIL)")
1710 "This package provides a more comfortable interface to work with R data
1711 or source files in a key-value fashion.")
1712 (license license:bsd-3)))
1714 (define-public r-batchjobs
1716 (name "r-batchjobs")
1721 (uri (cran-uri "BatchJobs" version))
1724 "1kb99024jih5bycc226bl4jyvbbl1sg72q3m2wnlshl7s8p6vva0"))))
1725 (properties `((upstream-name . "BatchJobs")))
1726 (build-system r-build-system)
1728 `(("r-bbmisc" ,r-bbmisc)
1730 ("r-checkmate" ,r-checkmate)
1732 ("r-digest" ,r-digest)
1734 ("r-rsqlite" ,r-rsqlite)
1735 ("r-sendmailr" ,r-sendmailr)
1736 ("r-stringr" ,r-stringr)))
1737 (home-page "https://github.com/tudo-r/BatchJobs")
1738 (synopsis "Batch computing with R")
1740 "This package provides @code{Map}, @code{Reduce} and @code{Filter}
1741 variants to generate jobs on batch computing systems like PBS/Torque, LSF,
1742 SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
1743 (license license:bsd-2)))
1745 (define-public r-brew
1751 (uri (cran-uri "brew" version))
1754 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
1755 (build-system r-build-system)
1756 (home-page "http://cran.r-project.org/web/packages/brew")
1757 (synopsis "Templating framework for report generation")
1759 "The brew package implements a templating framework for mixing text and R
1760 code for report generation. The template syntax is similar to PHP, Ruby's erb
1761 module, Java Server Pages, and Python's psp module.")
1762 (license license:gpl2+)))
1764 (define-public r-roxygen2
1770 (uri (cran-uri "roxygen2" version))
1773 "19gblyrrn29msbpawcb1hn5m1rshiqwxy0lby0vf92rm13fmsxcz"))))
1774 (build-system r-build-system)
1776 `(("r-brew" ,r-brew)
1777 ("r-digest" ,r-digest)
1779 ("r-stringi" ,r-stringi)
1780 ("r-stringr" ,r-stringr)))
1781 (home-page "https://github.com/klutometis/roxygen")
1782 (synopsis "In-source documentation system for R")
1784 "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
1785 collation, and NAMESPACE files.")
1786 (license license:gpl2+)))
1788 (define-public r-openssl
1795 (uri (cran-uri "openssl" version))
1798 "1lal8mmcwjhhln10mfi96ipv3d364k0wiviiln220wvhddcpr9pp"))))
1799 (build-system r-build-system)
1801 `(("openssl" ,openssl)))
1802 (home-page "https://github.com/jeroenooms/openssl")
1803 (synopsis "Toolkit for encryption, signatures and certificates")
1805 "This package provides R bindings to OpenSSL libssl and libcrypto, plus
1806 custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
1807 and P-521. Cryptographic signatures can either be created and verified
1808 manually or via x509 certificates. AES block cipher is used in CBC mode for
1809 symmetric encryption; RSA for asymmetric (public key) encryption. High-level
1810 envelope functions combine RSA and AES for encrypting arbitrary sized data.
1811 Other utilities include key generators, hash functions (md5, sha1, sha256,
1812 etc), base64 encoder, a secure random number generator, and @code{bignum} math
1813 methods for manually performing crypto calculations on large multibyte
1815 (license license:expat)))
1817 (define-public r-httr
1823 (uri (cran-uri "httr" version))
1826 "03kkjlhyvvi5znwaxfm6cmdsg3q7ivwsvkzgabhjdj2jxs80pfg7"))))
1827 (build-system r-build-system)
1829 `(("r-curl" ,r-curl)
1830 ("r-digest" ,r-digest)
1831 ("r-jsonlite" ,r-jsonlite)
1832 ("r-openssl" ,r-openssl)
1835 ("r-stringr" ,r-stringr)))
1836 (home-page "https://github.com/hadley/httr")
1837 (synopsis "Tools for working with URLs and HTTP")
1839 "The aim of httr is to provide a wrapper for RCurl customised to the
1840 demands of modern web APIs. It provides useful tools for working with HTTP
1841 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
1842 functions make it easy to control additional request components.")
1843 (license license:expat)))
1845 (define-public r-git2r
1851 (uri (cran-uri "git2r" version))
1854 "1rpdf85wy9fp456ypvbhl3p9whkb7kgl0n7rkqxd2bhvyzkvjak8"))))
1855 (build-system r-build-system)
1856 ;; This R package contains modified sources of libgit2. This modified
1857 ;; version of libgit2 is built as the package is built. Hence libgit2 is
1858 ;; not among the inputs of this package.
1860 `(("libssh2" ,libssh2)
1861 ("openssl" ,openssl)
1863 (home-page "https://github.com/ropensci/git2r")
1864 (synopsis "Access Git repositories with R")
1866 "This package provides an R interface to the libgit2 library, which is a
1867 pure C implementation of the Git core methods.")
1868 ;; GPLv2 only with linking exception.
1869 (license license:gpl2)))
1871 (define-public r-rstudioapi
1873 (name "r-rstudioapi")
1877 (uri (cran-uri "rstudioapi" version))
1880 "1zkvz72z6nw0xc8bhb21y5x1nk6avijs0w8n4vsbvw9sn76wc96s"))))
1881 (build-system r-build-system)
1882 (home-page "http://cran.r-project.org/web/packages/rstudioapi")
1883 (synopsis "Safely access the RStudio API")
1885 "This package provides functions to access the RStudio API and provide
1886 informative error messages when it's not available.")
1887 (license license:expat)))
1889 (define-public r-devtools
1895 (uri (cran-uri "devtools" version))
1898 "16l18szmj482vf3dvl2fqwwa4zaqylmic1pk7dwh428cp0d86mzi"))))
1899 (build-system r-build-system)
1901 `(("r-curl" ,r-curl)
1902 ("r-digest" ,r-digest)
1903 ("r-evaluate" ,r-evaluate)
1904 ("r-git2r" ,r-git2r)
1906 ("r-jsonlite" ,r-jsonlite)
1907 ("r-memoise" ,r-memoise)
1908 ("r-roxygen2" ,r-roxygen2)
1909 ("r-rstudioapi" ,r-rstudioapi)
1910 ("r-rversions" ,r-rversions)
1911 ("r-whisker" ,r-whisker)
1912 ("r-withr" ,r-withr)))
1913 (home-page "https://github.com/hadley/devtools")
1914 (synopsis "Tools to make developing R packages easier")
1915 (description "The devtools package is a collection of package development
1916 tools to simplify the devolpment of R packages.")
1917 (license license:gpl2+)))
1919 (define-public r-withr
1925 (uri (cran-uri "withr" version))
1928 "042z8nmqqilgrvhmbqrjc05qys3gzwq1rqy2wxp2bi5d41859493"))))
1929 (build-system r-build-system)
1930 (home-page "https://github.com/jimhester/withr")
1931 (synopsis "Run code with temporarily modified global state")
1933 "This package provides a set of functions to run R code in an environment
1934 in which global state has been temporarily modified. Many of these functions
1935 were originally a part of the r-devtools package.")
1936 (license license:gpl2+)))
1938 (define-public r-hms
1945 (uri (cran-uri "hms" version))
1948 "0ln1dc26mkl5pc26vvyf01d35x75q6cjaj39cccxp67chbwbdlds"))))
1949 (build-system r-build-system)
1950 (home-page "https://github.com/rstats-db/hms")
1951 (synopsis "Pretty time of day")
1953 "This package implements an S3 class for storing and formatting
1954 time-of-day values, based on the @code{difftime} class.")
1955 (license license:gpl3+)))
1957 (define-public r-readr
1963 (uri (cran-uri "readr" version))
1966 "0xji0dbal6xcxnsmjj678fw29n7wrj45wrd5ng99yhqqijcm9f6g"))))
1967 (build-system r-build-system)
1969 `(("r-curl" ,r-curl)
1972 ("r-tibble" ,r-tibble)
1975 (home-page "https://github.com/hadley/readr")
1976 (synopsis "Read tabular data")
1978 "This package provides functions to read flat or tabular text files from
1979 disk (or a connection).")
1980 (license license:gpl2+)))
1982 (define-public r-plotrix
1988 (uri (cran-uri "plotrix" version))
1991 "0h97jra8zqssi9j4i0psa6c7ya49ya8jd2qc18lc61a4s2yn8w91"))))
1992 (build-system r-build-system)
1993 (home-page "http://cran.r-project.org/web/packages/plotrix")
1994 (synopsis "Various plotting functions")
1996 "This package provides lots of plotting, various labeling, axis and color
1997 scaling functions for R.")
1998 (license license:gpl2+)))
2000 (define-public r-gridbase
2006 (uri (cran-uri "gridBase" version))
2009 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
2010 (build-system r-build-system)
2011 (home-page "http://cran.r-project.org/web/packages/gridBase")
2012 (synopsis "Integration of base and grid graphics")
2014 "This package provides an integration of base and grid graphics for R.")
2015 (license license:gpl2+)))
2017 (define-public r-lattice
2023 (uri (cran-uri "lattice" version))
2026 "0615h69czr73k47whhzimf1qxv5qk0cabcrkljwhyrn6m6piq6ja"))))
2027 (build-system r-build-system)
2028 (home-page "http://lattice.r-forge.r-project.org/")
2029 (synopsis "High-level data visualization system")
2031 "The lattice package provides a powerful and elegant high-level data
2032 visualization system inspired by Trellis graphics, with an emphasis on
2033 multivariate data. Lattice is sufficient for typical graphics needs, and is
2034 also flexible enough to handle most nonstandard requirements.")
2035 (license license:gpl2+)))
2037 (define-public r-latticeextra
2039 (name "r-latticeextra")
2044 (uri (cran-uri "latticeExtra" version))
2047 "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq"))))
2048 (properties `((upstream-name . "latticeExtra")))
2049 (build-system r-build-system)
2051 `(("r-lattice" ,r-lattice)
2052 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2053 (home-page "http://latticeextra.r-forge.r-project.org/")
2054 (synopsis "Extra graphical utilities based on lattice")
2056 "Building on the infrastructure provided by the lattice package, this
2057 package provides several new high-level graphics functions and methods, as
2058 well as additional utilities such as panel and axis annotation functions.")
2059 (license license:gpl2+)))
2061 (define-public r-rcpparmadillo
2063 (name "r-rcpparmadillo")
2064 (version "0.7.500.0.0")
2067 (uri (cran-uri "RcppArmadillo" version))
2070 "06qb6877c5qd8lvnc4b27z8fwb5r5pyylkj0g6kj1rn868zkh5ps"))
2071 (modules '((guix build utils)))
2072 ;; Remove bundled armadillo sources
2075 (delete-file-recursively "inst/include/armadillo_bits")
2076 (delete-file "inst/include/armadillo")))))
2077 (properties `((upstream-name . "RcppArmadillo")))
2078 (build-system r-build-system)
2081 (modify-phases %standard-phases
2082 (add-after 'unpack 'link-against-armadillo
2084 (substitute* "src/Makevars"
2085 (("PKG_LIBS=" prefix)
2086 (string-append prefix "-larmadillo"))))))))
2088 `(("r-rcpp" ,r-rcpp)
2089 ("armadillo" ,armadillo-for-rcpparmadillo)))
2090 (home-page "https://github.com/RcppCore/RcppArmadillo")
2091 (synopsis "Rcpp integration for the Armadillo linear algebra library")
2093 "Armadillo is a templated C++ linear algebra library that aims towards a
2094 good balance between speed and ease of use. Integer, floating point and
2095 complex numbers are supported, as well as a subset of trigonometric and
2096 statistics functions. Various matrix decompositions are provided through
2097 optional integration with LAPACK and ATLAS libraries. This package includes
2098 the header files from the templated Armadillo library.")
2099 ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
2100 ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
2101 ;; later, as is the rest of 'Rcpp'.
2102 (license license:gpl2+)))
2104 (define-public r-bitops
2110 (uri (cran-uri "bitops" version))
2113 "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
2114 (build-system r-build-system)
2115 (home-page "http://cran.r-project.org/web/packages/bitops")
2116 (synopsis "Bitwise operations")
2118 "This package provides functions for bitwise operations on integer
2120 (license license:gpl2+)))
2122 (define-public r-catools
2128 (uri (cran-uri "caTools" version))
2131 "1x4szsn2qmbzpyjfdaiz2q7jwhap2gky9wq0riah74q0pzz76ank"))))
2132 (properties `((upstream-name . "caTools")))
2133 (build-system r-build-system)
2135 `(("r-bitops" ,r-bitops)))
2136 (home-page "http://cran.r-project.org/web/packages/caTools")
2137 (synopsis "Various tools including functions for moving window statistics")
2139 "This package contains several basic utility functions including:
2140 moving (rolling, running) window statistic functions, read/write for GIF and
2141 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
2142 encoder/decoder, round-off-error-free sum and cumsum, etc.")
2143 (license license:gpl3+)))
2145 (define-public r-rmarkdown
2147 (name "r-rmarkdown")
2152 (uri (cran-uri "rmarkdown" version))
2155 "1czvkaz1ji3jyj6qrvbswisqs9d05ljqc4vjkfdrf6hygix7azd0"))))
2156 (properties `((upstream-name . "rmarkdown")))
2157 (build-system r-build-system)
2159 `(("r-catools" ,r-catools)
2160 ("r-evaluate" ,r-evaluate)
2161 ("r-tibble" ,r-tibble)
2162 ("r-htmltools" ,r-htmltools)
2163 ("r-jsonlite" ,r-jsonlite)
2164 ("r-base64enc" ,r-base64enc)
2165 ("r-knitr" ,r-knitr)
2167 ("ghc-pandoc" ,ghc-pandoc)))
2168 (home-page "http://rmarkdown.rstudio.com")
2169 (synopsis "Convert R Markdown documents into a variety of formats")
2171 "This package provides tools to convert R Markdown documents into a
2172 variety of formats.")
2173 (license license:gpl3+)))
2175 (define-public r-gtable
2181 (uri (cran-uri "gtable" version))
2184 "0vz7073m0a2q12qzzihrfh5c2kx5jqi5l7z470fxmwqghdllh7l0"))))
2185 (properties `((upstream-name . "gtable")))
2186 (build-system r-build-system)
2187 (home-page "http://cran.r-project.org/web/packages/gtable")
2188 (synopsis "Arrange grobs in tables")
2190 "This package provides tools to make it easier to work with tables of
2192 (license license:gpl2+)))
2194 (define-public r-gridextra
2196 (name "r-gridextra")
2200 (uri (cran-uri "gridExtra" version))
2203 "0638ihwl00j76ivaxxhxvi8z573lwy1jym3srr78mx6dbdd4bzj4"))))
2204 (properties `((upstream-name . "gridExtra")))
2205 (build-system r-build-system)
2207 `(("r-gtable" ,r-gtable)))
2209 `(("r-knitr" ,r-knitr))) ;for building vignettes
2210 (home-page "https://github.com/baptiste/gridextra")
2211 (synopsis "Miscellaneous functions for \"Grid\" graphics")
2213 "This package provides a number of user-level functions to work with
2214 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
2216 (license license:gpl2+)))
2218 (define-public r-rsqlite
2224 (uri (cran-uri "RSQLite" version))
2227 "08b1syv8z887gxiw8i09dpqh0zisfb6ihq6qqr01zipvkahzq34f"))))
2228 (properties `((upstream-name . "RSQLite")))
2229 (build-system r-build-system)
2231 `(("r-dbi" ,r-dbi)))
2232 (home-page "https://github.com/rstats-db/RSQLite")
2233 (synopsis "SQLite interface for R")
2235 "This package embeds the SQLite database engine in R and provides an
2236 interface compliant with the DBI package. The source for the SQLite
2237 engine (version 3.8.6) is included.")
2238 (license license:lgpl2.0+)))
2240 (define-public r-rcurl
2243 (version "1.95-0.1.2")
2246 (uri (string-append "http://www.bioconductor.org/packages/"
2247 "release/extra/src/"
2248 "contrib/RCurl_" version ".tar.gz"))
2251 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
2252 (properties `((upstream-name . "RCurl")))
2253 (build-system r-build-system)
2255 `(("libcurl" ,curl)))
2257 `(("r-bitops" ,r-bitops)))
2258 (home-page "http://www.omegahat.org/RCurl")
2259 (synopsis "General network client interface for R")
2261 "The package allows one to compose general HTTP requests and provides
2262 convenient functions to fetch URIs, GET and POST forms, etc. and process the
2263 results returned by the Web server. This provides a great deal of control
2264 over the HTTP/FTP/... connection and the form of the request while providing a
2265 higher-level interface than is available just using R socket connections.
2266 Additionally, the underlying implementation is robust and extensive,
2267 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
2268 ldap, and also supports cookies, redirects, authentication, etc.")
2269 (license license:bsd-3)))
2271 (define-public r-xml
2274 (version "3.98-1.4")
2277 (uri (cran-uri "XML" version))
2280 "09hiy5a875v2fhsgrsfymrwccn9249wnnsr6ck2slrig65svq2lw"))))
2282 `((upstream-name . "XML")))
2283 (build-system r-build-system)
2285 `(("libxml2" ,libxml2)))
2287 `(("r-rcurl" ,r-rcurl)))
2288 (home-page "http://www.omegahat.org/RSXML")
2289 (synopsis "Tools for parsing and generating XML within R")
2291 "Many approaches for both reading and creating XML (and HTML)
2292 documents (including DTDs), both local and accessible via HTTP or FTP. Also
2293 offers access to an XPath \"interpreter\".")
2294 (license license:bsd-2)))
2296 (define-public r-xnomial
2301 (origin (method url-fetch)
2302 (uri (cran-uri "XNomial" version))
2305 "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
2306 (properties (quasiquote ((upstream-name . "XNomial"))))
2307 (build-system r-build-system)
2308 (home-page "http://cran.r-project.org/web/packages/XNomial")
2309 (synopsis "Goodness-of-Fit test for multinomial data")
2311 "This package provides an exact Goodness-of-Fit test for
2312 multinomial data with fixed probabilities. It can be used to
2313 determine whether a set of counts fits a given expected ratio. To see
2314 whether a set of observed counts fits an expectation, one can examine
2315 all possible outcomes with @code{xmulti()} or a random sample of them
2316 with @code{xmonte()} and find the probability of an observation
2317 deviating from the expectation by at least as much as the observed.
2318 As a measure of deviation from the expected, one can use the
2319 log-likelihood ratio, the multinomial probability, or the classic
2320 chi-square statistic. A histogram of the test statistic can also be
2321 plotted and compared with the asymptotic curve.")
2322 (license (list license:gpl2+ license:gpl3+))))
2324 (define-public r-lambda-r
2330 (uri (cran-uri "lambda.r" version))
2333 "1j6287iqvs3ill6r5g6ksf5809qp0l0nf20ib8266m1r09lc9j14"))))
2334 (properties `((upstream-name . "lambda.r")))
2335 (build-system r-build-system)
2336 (home-page "http://cran.r-project.org/web/packages/lambda.r")
2337 (synopsis "Functional programming extension for R")
2339 "This package provides a language extension to efficiently write
2340 functional programs in R. Syntax extensions include multi-part function
2341 definitions, pattern matching, guard statements, built-in (optional) type
2343 (license license:lgpl3+)))
2345 (define-public r-futile-options
2347 (name "r-futile-options")
2351 (uri (cran-uri "futile.options" version))
2354 "1hp82h6xqq5cck67h7lpf22n3j7mg3v1mla5y5ivnzrrb7iyr17f"))))
2356 `((upstream-name . "futile.options")))
2357 (build-system r-build-system)
2358 (home-page "http://cran.r-project.org/web/packages/futile.options")
2359 (synopsis "Options management framework")
2361 "The futile.options subsystem provides an easy user-defined options
2362 management system that is properly scoped. This means that options created
2363 via @code{futile.options} are fully self-contained and will not collide with
2364 options defined in other packages.")
2365 (license license:lgpl3+)))
2367 (define-public r-futile-logger
2369 (name "r-futile-logger")
2373 (uri (cran-uri "futile.logger" version))
2376 "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
2377 (properties `((upstream-name . "futile.logger")))
2378 (build-system r-build-system)
2380 `(("r-futile-options" ,r-futile-options)
2381 ("r-lambda-r" ,r-lambda-r)))
2382 (home-page "http://cran.r-project.org/web/packages/futile.logger")
2383 (synopsis "Logging utility for R")
2385 "This package provides a simple yet powerful logging utility. Based
2386 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
2387 convenient and easy to use replacement for @code{cat} and @code{print}
2389 (license license:lgpl3+)))
2391 (define-public r-segmented
2393 (name "r-segmented")
2398 (uri (cran-uri "segmented" version))
2401 "1740cvx2q4v23g4q0zkvg50s5bv8jcrlzzhm7fac4xn0riwmzp5i"))))
2402 (build-system r-build-system)
2403 (home-page "http://cran.r-project.org/web/packages/segmented")
2404 (synopsis "Regression models with breakpoints estimation")
2406 "Given a regression model, segmented updates the model by adding one or
2407 more segmented (i.e., piecewise-linear) relationships. Several variables with
2408 multiple breakpoints are allowed.")
2409 (license (list license:gpl2+ license:gpl3+))))
2411 (define-public r-snow
2417 (uri (cran-uri "snow" version))
2420 "1mxbrkpnmq32x4wd0194d541661yvfrrjlr3lsf7qq53ms3h21zf"))))
2421 (build-system r-build-system)
2422 (home-page "http://cran.r-project.org/web/packages/snow")
2423 (synopsis "Support for simple parallel computing in R")
2425 "The snow package provides support for simple parallel computing on a
2426 network of workstations using R. A master R process calls @code{makeCluster}
2427 to start a cluster of worker processes; the master process then uses functions
2428 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
2429 worker processes and collect and return the results on the master.")
2430 (license (list license:gpl2+ license:gpl3+))))
2432 (define-public r-sparsem
2438 (uri (cran-uri "SparseM" version))
2441 "0zpb1swn9xjkb22sky10ixff7vqfiz9m36nkbc1qqbm9frcldnka"))))
2443 `((upstream-name . "SparseM")))
2445 `(("gfortran" ,gfortran)))
2446 (build-system r-build-system)
2447 (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
2448 (synopsis "Sparse linear algebra")
2450 "This package provides some basic linear algebra functionality for sparse
2451 matrices. It includes Cholesky decomposition and backsolving as well as
2452 standard R subsetting and Kronecker products.")
2453 (license license:gpl2+)))
2455 (define-public r-iterators
2457 (name "r-iterators")
2462 (uri (cran-uri "iterators" version))
2465 "1f057pabs7ss9h1n244can26qsi5n2k3salrdk0b0vkphlrs4kmf"))))
2466 (build-system r-build-system)
2467 (home-page "http://cran.r-project.org/web/packages/iterators")
2468 (synopsis "Iterator construct for R")
2470 "This package provides support for iterators, which allow a programmer to
2471 traverse through all the elements of a vector, list, or other collection of
2473 (license license:asl2.0)))
2475 (define-public r-codetools
2477 (name "r-codetools")
2482 (uri (cran-uri "codetools" version))
2485 "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf"))))
2486 (build-system r-build-system)
2487 (home-page "http://cran.r-project.org/web/packages/codetools")
2488 (synopsis "Code analysis tools for R")
2489 (description "This package provides code analysis tools for R to check R
2490 code for possible problems.")
2491 (license (list license:gpl2+ license:gpl3+))))
2493 (define-public r-foreach
2500 (uri (cran-uri "foreach" version))
2503 "10aqsd3rxz03s1qdb6gsb1cj89mj4vmh491zfpin4skj1xvkzw0y"))))
2504 (build-system r-build-system)
2506 `(("r-codetools" ,r-codetools)
2507 ("r-iterators" ,r-iterators)))
2508 (home-page "http://cran.r-project.org/web/packages/foreach")
2509 (synopsis "Foreach looping construct for R")
2511 "This package provides support for the @code{foreach} looping construct.
2512 @code{foreach} is an idiom that allows for iterating over elements in a
2513 collection, without the use of an explicit loop counter. This package in
2514 particular is intended to be used for its return value, rather than for its
2515 side effects. In that sense, it is similar to the standard @code{lapply}
2516 function, but doesn't require the evaluation of a function. Using
2517 @code{foreach} without side effects also facilitates executing the loop in
2519 (license license:asl2.0)))
2521 (define-public r-doparallel
2523 (name "r-doparallel")
2528 (uri (cran-uri "doParallel" version))
2531 "1mddx25l25pw9d0csnx2q203dbg5hbrhkr1f08kw0p02a1lln0kh"))))
2532 (properties `((upstream-name . "doParallel")))
2533 (build-system r-build-system)
2535 `(("r-foreach" ,r-foreach)
2536 ("r-iterators" ,r-iterators)))
2537 (home-page "http://cran.r-project.org/web/packages/doParallel")
2538 (synopsis "Foreach parallel adaptor for the 'parallel' package")
2540 "This package provides a parallel backend for the @code{%dopar%} function
2541 using the parallel package.")
2542 (license license:gpl2+)))
2544 (define-public r-domc
2551 (uri (cran-uri "doMC" version))
2554 "0y47jl6g4f83r14pj8bafdzq1phj7bxy5dwyz3k43d2rr8phk8bn"))))
2555 (properties `((upstream-name . "doMC")))
2556 (build-system r-build-system)
2558 `(("r-foreach" ,r-foreach)
2559 ("r-iterators" ,r-iterators)))
2560 (home-page "http://cran.r-project.org/web/packages/doMC")
2561 (synopsis "Foreach parallel adaptor for the 'parallel' package")
2563 "This package provides a parallel backend for the @code{%dopar%} function
2564 using the multicore functionality of the parallel package.")
2565 (license license:gpl2+)))
2573 (uri (cran-uri "DT" version))
2576 "1g86p0jcjqi2ph5rhm45jkzibsa6yfcj8n5cg3giy90sqgjzkdx1"))))
2578 `((upstream-name . "DT")))
2579 (build-system r-build-system)
2581 `(("r-htmltools" ,r-htmltools)
2582 ("r-htmlwidgets" ,r-htmlwidgets)
2583 ("r-magrittr" ,r-magrittr)))
2584 (home-page "http://rstudio.github.io/DT")
2585 (synopsis "R wrapper of the DataTables JavaScript library")
2587 "This package allows for data objects in R to be rendered as HTML tables
2588 using the JavaScript library 'DataTables' (typically via R Markdown or Shiny).
2589 The 'DataTables' library has been included in this R package.")
2590 ;; The DT package as a whole is distributed under GPLv3. The DT package
2591 ;; inludes other software components under different licenses:
2593 ;; * Expat: jQuery, jquery.highlight.js, DataTables
2594 ;; * ASL2.0: selectize.js
2595 ;; * WTFPL: noUiSlider
2596 (license (list license:gpl3
2599 (license:non-copyleft "http://www.wtfpl.net/txt/copying/")))))
2601 (define-public r-base64enc
2603 (name "r-base64enc")
2607 (uri (cran-uri "base64enc" version))
2610 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
2611 (build-system r-build-system)
2612 (home-page "http://www.rforge.net/base64enc")
2613 (synopsis "Tools for Base64 encoding")
2615 "This package provides tools for handling Base64 encoding. It is more
2616 flexible than the orphaned \"base64\" package.")
2617 (license license:gpl2+)))
2619 (define-public r-irlba
2626 (uri (cran-uri "irlba" version))
2629 "1qbcn0ix85pmk296jhpi419kvh06vxm5cq24yk013ps3g7fyi0si"))))
2630 (build-system r-build-system)
2631 (home-page "http://cran.r-project.org/web/packages/irlba")
2632 (synopsis "Methods for eigendecomposition of large matrices")
2634 "This package provides fast and memory efficient methods for truncated
2635 singular and eigenvalue decompositions, as well as for principal component
2636 analysis of large sparse or dense matrices.")
2637 (license (list license:gpl2+ license:gpl3+))))
2639 (define-public r-glmnet
2646 (uri (cran-uri "glmnet" version))
2649 "1cbpzmbv837fvq88rgn6mgzgr9f1wqp9fg8gh2kkmngvr1957a9c"))))
2650 (build-system r-build-system)
2652 `(("gfortran" ,gfortran)))
2654 `(("r-foreach" ,r-foreach)))
2655 (home-page "http://www.jstatsoft.org/v33/i01")
2656 (synopsis "Lasso and elastic-net regularized generalized linear models")
2658 "The glmnet package provides efficient procedures for fitting the entire
2659 lasso or elastic-net regularization path for linear and Poisson regression, as
2660 well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
2661 multinomial models. The algorithm uses cyclical coordinate descent in a
2662 path-wise fashion.")
2663 (license license:gpl2+)))
2665 (define-public r-pkgmaker
2672 (uri (cran-uri "pkgmaker" version))
2675 "0vrqnd3kg6liqvpbd969jjsdx0f0rvmmxgdbwwrp6xfmdg0pib8r"))))
2676 (build-system r-build-system)
2678 `(("r-codetools" ,r-codetools)
2679 ("r-digest" ,r-digest)
2680 ("r-registry" ,r-registry)
2681 ("r-stringr" ,r-stringr)
2682 ("r-xtable" ,r-xtable)))
2683 (home-page "https://renozao.github.io/pkgmaker")
2684 (synopsis "Package development utilities")
2686 "This package provides some low-level utilities to use for R package
2687 development. It currently provides managers for multiple package specific
2688 options and registries, vignette, unit test and bibtex related utilities.")
2689 (license license:gpl2+)))
2691 (define-public r-registry
2698 (uri (cran-uri "registry" version))
2701 "0c7lscfxncwwd8zp46h2xfw9gw14dypqv6m2kx85xjhjh0xw99aq"))))
2702 (build-system r-build-system)
2703 (home-page "http://cran.r-project.org/web/packages/registry")
2704 (synopsis "Infrastructure for R package registries")
2706 "This package provides a generic infrastructure for creating and using R
2707 package registries.")
2708 (license license:gpl2+)))
2710 (define-public r-rngtools
2717 (uri (cran-uri "rngtools" version))
2720 "1fcgfqrrb48z37xgy8sffx91p9irp39yqzxv7nqp1x2hnwsrh097"))))
2721 (build-system r-build-system)
2723 `(("r-digest" ,r-digest)
2724 ("r-pkgmaker" ,r-pkgmaker)
2725 ("r-stringr" ,r-stringr)))
2726 (home-page "https://renozao.github.io/rngtools")
2727 (synopsis "Utility functions for working with random number generators")
2729 "This package contains a set of functions for working with Random Number
2730 Generators (RNGs). In particular, it defines a generic S4 framework for
2731 getting/setting the current RNG, or RNG data that are embedded into objects
2732 for reproducibility. Notably, convenient default methods greatly facilitate
2733 the way current RNG settings can be changed.")
2734 (license license:gpl3+)))
2736 (define-public r-rtsne
2743 (uri (cran-uri "Rtsne" version))
2746 "0zi4nxgpiv1gpdmcnqdhz5kymzp8m5xj02zpf290p1yyydl76bhy"))))
2747 (properties `((upstream-name . "Rtsne")))
2748 (build-system r-build-system)
2750 `(("r-rcpp" ,r-rcpp)))
2751 (home-page "https://github.com/jkrijthe/Rtsne")
2752 (synopsis "T-distributed stochastic neighbor embedding")
2754 "This package provides an R wrapper around the fast T-distributed
2755 Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
2756 ;; The declared license for this package is BSD-3, but it also includes
2757 ;; code licensed under BSD-4.
2758 (license (list license:bsd-3 license:bsd-4))))
2760 (define-public r-e1071
2767 (uri (cran-uri "e1071" version))
2770 "1069qwj9gsjq6par2cgfah8nn5x2w38830761x1f7mqpmk0gnj3h"))))
2771 (build-system r-build-system)
2772 (home-page "http://cran.r-project.org/web/packages/e1071")
2773 (synopsis "Miscellaneous functions for probability theory")
2775 "This package provides functions for latent class analysis, short time
2776 Fourier transform, fuzzy clustering, support vector machines, shortest path
2777 computation, bagged clustering, naive Bayes classifier, and more.")
2778 (license license:gpl2+)))
2780 (define-public r-bigmemory-sri
2782 (name "r-bigmemory-sri")
2787 (uri (cran-uri "bigmemory.sri" version))
2789 (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
2791 `((upstream-name . "bigmemory.sri")))
2792 (build-system r-build-system)
2793 (home-page "http://cran.r-project.org/web/packages/bigmemory.sri")
2794 (synopsis "Shared resource interface for the bigmemory package")
2795 (description "This package provides a shared resource interface for the
2796 bigmemory and synchronicity packages.")
2797 ;; Users can choose either LGPLv3 or ASL2.0.
2798 (license (list license:lgpl3 license:asl2.0))))
2800 (define-public r-synchronicity
2802 (name "r-synchronicity")
2807 (uri (cran-uri "synchronicity" version))
2810 "0d9skpwmsnkn4xb3f2kgyyv8bhdi0r9p1kj3cvi0s92fjjnpi00c"))))
2811 (build-system r-build-system)
2814 ("r-bigmemory-sri" ,r-bigmemory-sri)
2815 ("r-rcpp" ,r-rcpp)))
2816 (home-page "http://www.bigmemory.org")
2817 (synopsis "Boost mutex functionality in R")
2818 (description "This package provides support for synchronization
2819 via mutexes and may eventually support interprocess communication and
2821 ;; Users can choose either LGPLv3 or ASL2.0.
2822 (license (list license:lgpl3 license:asl2.0))))
2824 (define-public r-bigmemory
2826 (name "r-bigmemory")
2831 (uri (cran-uri "bigmemory" version))
2834 "191gbzca557kpk7mdsg716vfyqpr7j5din6qb8hin4g1nkzzwmg6"))))
2835 (build-system r-build-system)
2839 ("r-bigmemory-sri" ,r-bigmemory-sri)
2840 ("r-r-utils" ,r-r-utils)))
2841 (home-page "http://www.bigmemory.org")
2842 (synopsis "Manage large matrices with shared memory or memory-mapped files")
2843 (description "This package provides methods to create, store, access, and
2844 manipulate large matrices. Matrices are allocated to shared memory and may use
2845 memory-mapped files.")
2846 ;; Users can choose either LGPLv3 or ASL2.0.
2847 (license (list license:lgpl3 license:asl2.0))))
2849 (define-public r-nmf
2856 (uri (cran-uri "NMF" version))
2859 "0mmh9bz0zjwd8h9jplz4rq3g94npaqj8s4px51vcv47csssd9k6z"))))
2860 (properties `((upstream-name . "NMF")))
2861 (build-system r-build-system)
2863 `(("r-cluster" ,r-cluster)
2864 ("r-bigmemory" ,r-bigmemory)
2865 ("r-synchronicity" ,r-synchronicity)
2866 ("r-colorspace" ,r-colorspace)
2867 ("r-digest" ,r-digest)
2868 ("r-doparallel" ,r-doparallel)
2869 ("r-foreach" ,r-foreach)
2870 ("r-ggplot2" ,r-ggplot2)
2871 ("r-gridbase" ,r-gridbase)
2872 ("r-pkgmaker" ,r-pkgmaker)
2873 ("r-rcolorbrewer" ,r-rcolorbrewer)
2874 ("r-registry" ,r-registry)
2875 ("r-reshape2" ,r-reshape2)
2876 ("r-rngtools" ,r-rngtools)
2877 ("r-stringr" ,r-stringr)))
2878 (home-page "http://renozao.github.io/NMF")
2879 (synopsis "Algorithms and framework for nonnegative matrix factorization")
2881 "This package provides a framework to perform Non-negative Matrix
2882 Factorization (NMF). The package implements a set of already published
2883 algorithms and seeding methods, and provides a framework to test, develop and
2884 plug new or custom algorithms. Most of the built-in algorithms have been
2885 optimized in C++, and the main interface function provides an easy way of
2886 performing parallel computations on multicore machines.")
2887 (license license:gpl2+)))
2889 (define-public r-igraph
2896 (uri (cran-uri "igraph" version))
2899 "00jnm8v3kvxpxav5klld2z2nnkcpj4sdwv4ksipddy5mp04ysr6w"))))
2900 (build-system r-build-system)
2902 `(("gfortran" ,gfortran)))
2905 ("libxml2" ,libxml2)))
2907 `(("r-irlba" ,r-irlba)
2908 ("r-magrittr" ,r-magrittr)
2910 (home-page "http://igraph.org")
2911 (synopsis "Network analysis and visualization")
2913 "This package provides routines for simple graphs and network analysis.
2914 It can handle large graphs very well and provides functions for generating
2915 random and regular graphs, graph visualization, centrality methods and much
2917 (license license:gpl2+)))
2919 (define-public r-r-methodss3
2921 (name "r-r-methodss3")
2925 (uri (cran-uri "R.methodsS3" version))
2928 "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24"))))
2929 (properties `((upstream-name . "R.methodsS3")))
2930 (build-system r-build-system)
2931 (home-page "http://cran.r-project.org/web/packages/R.methodsS3")
2932 (synopsis "S3 methods simplified")
2934 "This package provides methods that simplify the setup of S3 generic
2935 functions and S3 methods. Major effort has been made in making definition of
2936 methods as simple as possible with a minimum of maintenance for package
2937 developers. For example, generic functions are created automatically, if
2938 missing, and naming conflict are automatically solved, if possible. The
2939 method @code{setMethodS3()} is a good start for those who in the future may
2940 want to migrate to S4.")
2941 (license license:lgpl2.1+)))
2943 (define-public r-r-oo
2949 (uri (cran-uri "R.oo" version))
2952 "0723gxjazgqq7v3lwnl7axw3brzcnizvhbd71ijkkv8mz31fwp34"))))
2953 (properties `((upstream-name . "R.oo")))
2954 (build-system r-build-system)
2956 `(("r-r-methodss3" ,r-r-methodss3)))
2957 (home-page "https://github.com/HenrikBengtsson/R.oo")
2958 (synopsis "R object-oriented programming with or without references")
2960 "This package provides methods and classes for object-oriented
2961 programming in R with or without references. Large effort has been made on
2962 making definition of methods as simple as possible with a minimum of
2963 maintenance for package developers.")
2964 (license license:lgpl2.1+)))
2966 (define-public r-r-utils
2972 (uri (cran-uri "R.utils" version))
2975 "0cn0wlmgwclmqak05825wrk9q894xa4qjqa7rn0i9p4ss7k6vifj"))))
2976 (properties `((upstream-name . "R.utils")))
2977 (build-system r-build-system)
2979 `(("r-r-methodss3" ,r-r-methodss3)
2980 ("r-r-oo" ,r-r-oo)))
2981 (home-page "https://github.com/HenrikBengtsson/R.utils")
2982 (synopsis "Various programming utilities")
2984 "This package provides utility functions useful when programming and
2985 developing R packages.")
2986 (license license:lgpl2.1+)))
2988 (define-public r-r-cache
2994 (uri (cran-uri "R.cache" version))
2997 "006x52w9r8phw5hgqmyp0bz8z42vn8p5yibibnzi1sfa1xlw8iyx"))))
2998 (properties `((upstream-name . "R.cache")))
2999 (build-system r-build-system)
3001 `(("r-digest" ,r-digest)
3002 ("r-r-methodss3" ,r-r-methodss3)
3004 ("r-r-utils" ,r-r-utils)))
3005 (home-page "https://github.com/HenrikBengtsson/R.cache")
3006 (synopsis "Light-weight caching of objects and results")
3008 "This package provides methods for caching or memoization of objects and
3009 results. With this package, any R object can be cached in a key-value storage
3010 where the key can be an arbitrary set of R objects. The cache memory is
3011 persistent (on the file system).")
3012 (license license:lgpl2.1+)))
3014 (define-public r-r-rsp
3020 (uri (cran-uri "R.rsp" version))
3023 "1ssykygqkxzx9qblxhavxlf2z6r5bhk0s47yw1dllfiyc8zy7jv2"))))
3024 (properties `((upstream-name . "R.rsp")))
3025 (build-system r-build-system)
3027 `(("r-r-cache" ,r-r-cache)
3028 ("r-r-methodss3" ,r-r-methodss3)
3030 ("r-r-utils" ,r-r-utils)))
3031 (home-page "https://github.com/HenrikBengtsson/R.rsp")
3032 (synopsis "Dynamic generation of scientific reports")
3034 "The RSP markup language provides a powerful markup for controlling the
3035 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
3036 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
3037 to many other literate programming languages, with RSP it is straightforward
3038 to loop over mixtures of code and text sections, e.g. in month-by-month
3039 summaries. RSP has also several preprocessing directives for incorporating
3040 static and dynamic contents of external files (local or online) among other
3041 things. RSP is ideal for self-contained scientific reports and R package
3043 (license license:lgpl2.1+)))
3045 (define-public r-mvtnorm
3051 (uri (cran-uri "mvtnorm" version))
3054 "1pc1mi2h063gh4a40009xk5j6pf5bm4274i5kycln38dixsry3yh"))))
3055 (build-system r-build-system)
3057 `(("gfortran" ,gfortran)))
3058 (home-page "http://mvtnorm.R-forge.R-project.org")
3059 (synopsis "Package for multivariate normal and t-distributions")
3060 (description "This package can compute multivariate normal and
3061 t-probabilities, quantiles, random deviates and densities.")
3062 (license license:gpl2)))
3064 (define-public r-matrixstats
3066 (name "r-matrixstats")
3070 (uri (cran-uri "matrixStats" version))
3073 "0bsalx605kgb9nl7mfnq1qinkyd9s97p8plymsyfja1gmcnjrcpj"))))
3074 (properties `((upstream-name . "matrixStats")))
3075 (build-system r-build-system)
3077 `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
3078 (home-page "https://github.com/HenrikBengtsson/matrixStats")
3079 (synopsis "Methods applying to vectors and matrix rows and columns")
3081 "This package provides methods operating on rows and columns of matrices,
3082 e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
3083 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
3084 @code{weightedMedians()}. All methods have been optimized for speed and
3086 (license license:artistic2.0)))
3088 (define-public r-viridis
3094 (uri (cran-uri "viridis" version))
3097 "1a9hqn2pccpc51vh8ghw698ni6xzdnp8v0n8kgjh51nlz5hhc87j"))))
3098 (build-system r-build-system)
3100 `(("r-ggplot2" ,r-ggplot2)
3101 ("r-gridextra" ,r-gridextra)))
3102 (home-page "https://github.com/sjmgarnier/viridis")
3103 (synopsis "Matplotlib default color map")
3105 "This package is a port of the new @url{matplotlib,
3106 http://matplotlib.org/} color maps (@code{viridis}--the default--,
3107 @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
3108 designed in such a way that they will analytically be perfectly
3109 perceptually-uniform, both in regular form and also when converted to
3110 black-and-white. They are also designed to be perceived by readers with the
3111 most common form of color blindness.")
3112 (license license:x11)))
3114 (define-public r-viridislite
3116 (name "r-viridislite")
3121 (uri (cran-uri "viridisLite" version))
3124 "1b0fhj8i1m9jsz91gzag60k7vy7kk5xkdg31rc3h3spq96l66psp"))))
3125 (properties `((upstream-name . "viridisLite")))
3126 (build-system r-build-system)
3127 (home-page "https://github.com/sjmgarnier/viridisLite")
3128 (synopsis "Default color maps from matplotlib")
3130 "This package is a port of the new @code{matplotlib} color maps ('viridis',
3131 'magma', 'plasma' and 'inferno') to R. matplotlib is a popular plotting
3132 library for Python. These color maps are designed in such a way that they
3133 will analytically be perfectly perceptually-uniform, both in regular form and
3134 also when converted to black-and-white. They are also designed to be
3135 perceived by readers with the most common form of color blindness. This is
3136 the 'lite' version of the more complete @code{viridis} package.")
3137 (license license:expat)))
3139 (define-public r-tidyr
3146 (uri (cran-uri "tidyr" version))
3149 "1bpwbphgl43ym433b0nrshwhr7pprmj1wkpkamdzix1zvf9dcbc2"))))
3150 (build-system r-build-system)
3152 `(("r-dplyr" ,r-dplyr)
3153 ("r-lazyeval" ,r-lazyeval)
3154 ("r-magrittr" ,r-magrittr)
3156 ("r-stringi" ,r-stringi)))
3157 (home-page "https://github.com/hadley/tidyr")
3158 (synopsis "Tidy data with `spread()` and `gather()` functions")
3160 "tidyr is a reframing of the reshape2 package designed to accompany the
3161 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
3162 a solid pipeline for data analysis. It is designed specifically for tidying
3163 data, not the general reshaping that reshape2 does, or the general aggregation
3164 that reshape did. In particular, built-in methods only work for data frames,
3165 and tidyr provides no margins or aggregation.")
3166 (license license:expat)))
3168 (define-public r-hexbin
3175 (uri (cran-uri "hexbin" version))
3178 "0xi6fbf1fvyn2gffr052n3viibqzpr3603sgi4xaminbzja4syjh"))))
3179 (build-system r-build-system)
3181 `(("r-lattice" ,r-lattice)))
3183 `(("gfortran" ,gfortran)))
3184 (home-page "http://github.com/edzer/hexbin")
3185 (synopsis "Hexagonal binning routines")
3187 "This package provides binning and plotting functions for hexagonal bins.
3188 It uses and relies on grid graphics and formal (S4) classes and methods.")
3189 (license license:gpl2+)))
3191 (define-public r-purrr
3198 (uri (cran-uri "purrr" version))
3201 "0lss8q733nv7s154wargm6vnxq55qygnxakib8xdj4jv0y86sxc3"))))
3202 (build-system r-build-system)
3205 ("r-dplyr" ,r-dplyr)
3206 ("r-lazyeval" ,r-lazyeval)
3207 ("r-magrittr" ,r-magrittr)
3208 ("r-rcpp" ,r-rcpp)))
3209 (home-page "https://github.com/hadley/purrr")
3210 (synopsis "Functional programming tools")
3212 "This package completes R's functional programming tools with missing
3213 features present in other programming languages.")
3214 (license license:gpl3+)))
3216 (define-public r-plotly
3222 (uri (cran-uri "plotly" version))
3225 "08shs0qhy9js0fpj3d4rzfbwmw11ki3z5vg8jszfm6m69mfkgzw1"))))
3226 (build-system r-build-system)
3228 `(("r-base64enc" ,r-base64enc)
3229 ("r-digest" ,r-digest)
3230 ("r-dplyr" ,r-dplyr)
3231 ("r-ggplot2" ,r-ggplot2)
3232 ("r-hexbin" ,r-hexbin)
3233 ("r-htmlwidgets" ,r-htmlwidgets)
3235 ("r-jsonlite" ,r-jsonlite)
3236 ("r-lazyeval" ,r-lazyeval)
3237 ("r-magrittr" ,r-magrittr)
3238 ("r-purrr" ,r-purrr)
3239 ("r-scales" ,r-scales)
3240 ("r-tibble" ,r-tibble)
3241 ("r-tidyr" ,r-tidyr)
3242 ("r-viridislite" ,r-viridislite)))
3243 (home-page "https://plot.ly/r")
3244 (synopsis "Create interactive web graphics")
3246 "This package enables the translation of ggplot2 graphs to an interactive
3247 web-based version and/or the creation of custom web-based visualizations
3248 directly from R. Once uploaded to a plotly account, plotly graphs (and the
3249 data behind them) can be viewed and modified in a web browser.")
3250 (license license:x11)))
3252 (define-public r-biased-urn
3254 (name "r-biased-urn")
3259 (uri (cran-uri "BiasedUrn" version))
3262 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
3263 (properties `((upstream-name . "BiasedUrn")))
3264 (build-system r-build-system)
3265 (home-page "http://www.agner.org/random/")
3266 (synopsis "Biased urn model distributions")
3268 "This package provides statistical models of biased sampling in the form
3269 of univariate and multivariate noncentral hypergeometric distributions,
3270 including Wallenius' noncentral hypergeometric distribution and Fisher's
3271 noncentral hypergeometric distribution (also called extended hypergeometric
3273 (license license:gpl3+)))
3275 (define-public r-rpart
3282 (uri (cran-uri "rpart" version))
3285 "119dvh2cpab4vq9blvbkil5hgq6w018amiwlda3ii0fki39axpf5"))))
3286 (build-system r-build-system)
3287 (home-page "http://cran.r-project.org/web/packages/rpart")
3288 (synopsis "Recursive partitioning and regression trees")
3290 "This package provides recursive partitioning functions for
3291 classification, regression and survival trees.")
3292 (license (list license:gpl2+ license:gpl3+))))
3294 (define-public r-survival
3301 (uri (cran-uri "survival" version))
3304 "10pf0kq0g66k5rgizrvh29mq3r84acljw2jgrv5yp6z38xw23mci"))))
3305 (build-system r-build-system)
3306 (home-page "https://github.com/therneau/survival")
3307 (synopsis "Survival analysis")
3309 "This package contains the core survival analysis routines, including
3310 definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
3311 curves, Cox models, and parametric accelerated failure time models.")
3312 (license license:lgpl2.0+)))
3314 (define-public r-hmisc
3321 (uri (cran-uri "Hmisc" version))
3324 "0azxmg9h9c456biydc0wpi9xhljmd37m8bv0zaadbvc93g7x0l4b"))))
3325 (properties `((upstream-name . "Hmisc")))
3326 (build-system r-build-system)
3328 `(("gfortran" ,gfortran)))
3330 `(("r-acepack" ,r-acepack)
3331 ("r-cluster" ,r-cluster)
3332 ("r-data-table" ,r-data-table)
3333 ("r-foreign" ,r-foreign)
3334 ("r-formula" ,r-formula)
3335 ("r-ggplot2" ,r-ggplot2)
3336 ("r-gridextra" ,r-gridextra)
3337 ("r-gtable" ,r-gtable)
3338 ("r-lattice" ,r-lattice)
3339 ;; Hmisc needs survival >= 2.40.1, so it cannot use the survival
3340 ;; package that comes with R 3.3.1.
3341 ("r-survival" ,r-survival)
3342 ("r-latticeextra" ,r-latticeextra)
3343 ("r-htmltable" ,r-htmltable)
3344 ("r-htmltools" ,r-htmltools)
3345 ("r-viridis" ,r-viridis)
3347 ("r-rpart" ,r-rpart)))
3348 (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
3349 (synopsis "Miscellaneous data analysis and graphics functions")
3351 "This package contains many functions useful for data analysis,
3352 high-level graphics, utility operations, functions for computing sample size
3353 and power, importing and annotating datasets, imputing missing values,
3354 advanced table making, variable clustering, character string manipulation,
3355 conversion of R objects to LaTeX code, and recoding variables.")
3356 (license license:gpl2+)))
3358 (define-public r-runit
3365 (uri (cran-uri "RUnit" version))
3368 "1jqr871jkll2xmk7wk5hv1z3a36hyn2ibgivw7bwk4b346940xlx"))))
3369 (properties `((upstream-name . "RUnit")))
3370 (build-system r-build-system)
3371 (home-page "http://cran.r-project.org/web/packages/RUnit")
3372 (synopsis "R unit test framework")
3374 "This package provides R functions implementing a standard unit testing
3375 framework, with additional code inspection and report generation tools.")
3376 (license license:gpl2+)))
3378 (define-public r-kernsmooth
3380 (name "r-kernsmooth")
3385 (uri (cran-uri "KernSmooth" version))
3388 "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb"))))
3389 (properties `((upstream-name . "KernSmooth")))
3390 (build-system r-build-system)
3392 `(("gfortran" ,gfortran)))
3393 (home-page "http://cran.r-project.org/web/packages/KernSmooth")
3394 (synopsis "Functions for kernel smoothing")
3396 "This package provides functions for kernel smoothing (and density
3397 estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
3398 \"Kernel Smoothing\".")
3399 ;; Unlimited use and distribution
3400 (license (license:non-copyleft "file://LICENSE.note"))))
3402 (define-public r-zoo
3408 (uri (cran-uri "zoo" version))
3411 "0m67bnrg7r1jxvs9p7rpa430szp5qfp65r056yb8bivpc16jd98c"))))
3412 (build-system r-build-system)
3414 `(("r-lattice" ,r-lattice)))
3415 (home-page "http://zoo.R-Forge.R-project.org/")
3416 (synopsis "S3 infrastructure for regular and irregular time series")
3417 (description "This package contains an S3 class with methods for totally
3418 ordered indexed observations. It is particularly aimed at irregular time
3419 series of numeric vectors/matrices and factors.")
3420 (license license:gpl2+)))
3422 (define-public r-ztable
3428 (uri (cran-uri "ztable" version))
3431 "1jfqnqy9544gfvz3bsb48v4177nwp4b4n9l2743asq8sbq305b5r"))))
3432 (build-system r-build-system)
3433 (home-page "http://cran.r-project.org/web/packages/ztable")
3434 (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
3436 "This package provides functions to make zebra-striped tables (tables
3437 with alternating row colors) in LaTeX and HTML formats easily from
3438 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
3439 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
3440 @code{cbind.mytable} objects.")
3441 (license license:gpl2+)))