1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017 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>
9 ;;; Copyright © 2016, 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
11 ;;; This file is part of GNU Guix.
13 ;;; GNU Guix is free software; you can redistribute it and/or modify it
14 ;;; under the terms of the GNU General Public License as published by
15 ;;; the Free Software Foundation; either version 3 of the License, or (at
16 ;;; your option) any later version.
18 ;;; GNU Guix is distributed in the hope that it will be useful, but
19 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
20 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21 ;;; GNU General Public License for more details.
23 ;;; You should have received a copy of the GNU General Public License
24 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
26 (define-module (gnu packages statistics)
27 #:use-module ((guix licenses) #:prefix license:)
28 #:use-module (guix packages)
29 #:use-module (guix download)
30 #:use-module (guix utils)
31 #:use-module (guix build-system gnu)
32 #:use-module (guix build-system r)
33 #:use-module (guix build-system python)
34 #:use-module (guix build-system trivial)
35 #:use-module (gnu packages)
36 #:use-module (gnu packages compression)
37 #:use-module (gnu packages curl)
38 #:use-module (gnu packages gcc)
39 #:use-module (gnu packages gtk)
40 #:use-module (gnu packages gettext)
41 #:use-module (gnu packages glib)
42 #:use-module (gnu packages haskell)
43 #:use-module (gnu packages icu4c)
44 #:use-module (gnu packages image)
45 #:use-module (gnu packages java)
46 #:use-module (gnu packages machine-learning)
47 #:use-module (gnu packages maths)
48 #:use-module (gnu packages multiprecision)
49 #:use-module (gnu packages pcre)
50 #:use-module (gnu packages perl)
51 #:use-module (gnu packages pkg-config)
52 #:use-module (gnu packages python)
53 #:use-module (gnu packages readline)
54 #:use-module (gnu packages ssh)
55 #:use-module (gnu packages texinfo)
56 #:use-module (gnu packages tls)
57 #:use-module (gnu packages base)
58 #:use-module (gnu packages web)
59 #:use-module (gnu packages xml)
60 #:use-module (gnu packages xorg)
61 #:use-module (gnu packages zip)
62 #:use-module (srfi srfi-1))
72 (uri (string-append "mirror://gnu/pspp/pspp-"
76 "1afsq0a3iij64qacczvwhk81qg0q5rfqm055y5h9ls28d6paqz7p"))))
77 (build-system gnu-build-system)
80 ("gettext" ,gettext-minimal)
84 ("readline" ,readline)
86 ("gtksourceview" ,gtksourceview)
89 `(("glib" ,glib "bin") ;for glib-genmarshal
91 ("pkg-config" ,pkg-config)))
92 (home-page "https://www.gnu.org/software/pspp/")
93 (synopsis "Statistical analysis")
95 "GNU PSPP is a statistical analysis program. It can perform
96 descriptive statistics, T-tests, linear regression and non-parametric tests.
97 It features both a graphical interface as well as command-line input. PSPP
98 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
99 can be imported from spreadsheets, text files and database sources and it can
100 be output in text, PostScript, PDF or HTML.")
101 (license license:gpl3+)))
103 ;; Update this package together with the set of recommended packages: r-boot,
104 ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
105 ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
106 (define-public r-minimal
112 (uri (string-append "mirror://cran/src/base/R-"
113 (version-prefix version 1) "/R-"
117 "0v7wpj89b0i3ad3fi1wak5c93hywmbxv8sdnixhq8l17782nidss"))))
118 (build-system gnu-build-system)
121 (list (string-append "LDFLAGS=-Wl,-rpath="
122 (assoc-ref %outputs "out")
124 ;; This affects the embedded timestamp of only the core packages.
125 "PKG_BUILT_STAMP=1970-01-01")
127 (modify-phases %standard-phases
128 (add-before 'configure 'patch-uname
129 (lambda* (#:key inputs #:allow-other-keys)
130 (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
132 (substitute* "src/scripts/R.sh.in"
133 (("uname") uname-bin)))
135 (add-after 'unpack 'build-reproducibly
137 ;; The documentation contains time stamps to demonstrate
138 ;; documentation generation in different phases.
139 (substitute* "src/library/tools/man/Rd2HTML.Rd"
140 (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
141 "(removed for reproducibility)"))
143 ;; Remove timestamp from tracing environment. This fixes
144 ;; reproducibility of "methods.rd{b,x}".
145 (substitute* "src/library/methods/R/trace.R"
146 (("dateCreated = Sys.time\\(\\)")
147 "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
149 ;; Ensure that gzipped files are reproducible.
150 (substitute* '("src/library/grDevices/Makefile.in"
151 "doc/manual/Makefile.in")
152 (("R_GZIPCMD\\)" line)
153 (string-append line " -n")))
155 ;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
156 ;; queries the mtime of a given file and records it in an object.
157 ;; This is acceptable at runtime to detect stale source files,
158 ;; but it destroys reproducibility at build time.
160 ;; Instead of disabling this feature, which may have unexpected
161 ;; consequences, we reset the mtime of generated files before
162 ;; passing them to the "srcfile" procedure.
163 (substitute* "src/library/Makefile.in"
164 (("@\\(cd base && \\$\\(MAKE\\) mkdesc\\)" line)
165 (string-append line "\n find $(top_builddir)/library/tools | xargs touch -d '1970-01-01'; \n"))
166 (("@\\$\\(MAKE\\) Rdobjects" line)
167 (string-append "@find $(srcdir)/tools | xargs touch -d '1970-01-01'; \n "
169 (substitute* "src/library/tools/Makefile.in"
170 (("@\\$\\(INSTALL_DATA\\) all.R \\$\\(top_builddir\\)/library/\\$\\(pkg\\)/R/\\$\\(pkg\\)" line)
173 "\n find $(srcdir)/$(pkg) $(top_builddir)/library/$(pkg) | xargs touch -d \"1970-01-01\"; \n")))
175 ;; This library is installed using "install_package_description",
176 ;; so we need to pass the "builtStamp" argument.
177 (substitute* "src/library/tools/Makefile.in"
178 (("(install_package_description\\(.*\"')\\)\"" line prefix)
179 (string-append prefix ", builtStamp='1970-01-01')\"")))
181 (add-before 'configure 'set-default-pager
182 ;; Set default pager to "cat", because otherwise it is "false",
183 ;; making "help()" print nothing at all.
184 (lambda _ (setenv "PAGER" "cat") #t))
185 (add-before 'check 'set-timezone
186 ;; Some tests require the timezone to be set.
187 (lambda* (#:key inputs #:allow-other-keys)
190 (string-append (assoc-ref inputs "tzdata")
193 (add-after 'build 'make-info
194 (lambda _ (zero? (system* "make" "info"))))
195 (add-after 'build 'install-info
196 (lambda _ (zero? (system* "make" "install-info")))))
198 '(;; Do not build the recommended packages. The build system creates
199 ;; random temporary directories and embeds their names in some
200 ;; package files. We build these packages with the r-build-system
202 "--without-recommended-packages"
204 "--with-blas=-lopenblas"
210 "--enable-BLAS-shlib"
211 "--with-system-tre")))
212 ;; R has some support for Java. When the JDK is available at configure
213 ;; time environment variables pointing to the JDK will be recorded under
214 ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
215 ;; CMD javareconf". "R CMD javareconf" appears to only be used to update
216 ;; the recorded environment variables in $R_HOME/etc. Refer to
217 ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
218 ;; for additional information.
220 ;; As the JDK is a rather large input with only very limited effects on R,
221 ;; we decided to drop it.
225 ("pkg-config" ,pkg-config)
226 ("texinfo" ,texinfo) ; for building HTML manuals
227 ("which" ,which) ; for tests/Examples/base-Ex.R
230 `(;; We need not only cairo here, but pango to ensure that tests for the
231 ;; "cairo" bitmapType plotting backend succeed.
233 ("coreutils" ,coreutils)
236 ("openblas" ,openblas)
237 ("gfortran" ,gfortran)
244 ("readline" ,readline)
247 (list (search-path-specification
248 (variable "R_LIBS_SITE")
249 (files (list "site-library/")))))
250 (home-page "http://www.r-project.org/")
251 (synopsis "Environment for statistical computing and graphics")
253 "R is a language and environment for statistical computing and graphics.
254 It provides a variety of statistical techniques, such as linear and nonlinear
255 modeling, classical statistical tests, time-series analysis, classification
256 and clustering. It also provides robust support for producing
257 publication-quality data plots. A large amount of 3rd-party packages are
258 available, greatly increasing its breadth and scope.")
259 (license license:gpl3+)))
261 (define-public r-boot
268 (uri (cran-uri "boot" version))
271 "0pi348vvgzn1ny54yxhw6kq6nl7rx9bpr9ji1a6wqs8ah5zj7z8j"))))
272 (build-system r-build-system)
273 (home-page "http://cran.r-project.org/web/packages/boot")
274 (synopsis "Bootstrap functions for R")
276 "This package provides functions and datasets for bootstrapping from the
277 book \"Bootstrap Methods and Their Application\" by A.C. Davison and
278 D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
279 ;; Unlimited distribution
280 (license (license:non-copyleft "file://R/bootfuns.q"))))
282 (define-public r-mass
289 (uri (cran-uri "MASS" version))
292 "13lp5919h2bnpmf8rbmkar8a41yx62fnx66pkvljvqf60wa29qsx"))))
293 (properties `((upstream-name . "MASS")))
294 (build-system r-build-system)
295 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
296 (synopsis "Support functions and datasets for Venables and Ripley's MASS")
298 "This package provides functions and datasets for the book \"Modern
299 Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
300 ;; Either version may be picked.
301 (license (list license:gpl2 license:gpl3))))
303 (define-public r-class
310 (uri (cran-uri "class" version))
313 "173b8a16lh1i0zjmr784l0xr0azp9v8bgslh12hfdswbq7dpdf0q"))))
314 (build-system r-build-system)
316 `(("r-mass" ,r-mass)))
317 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
318 (synopsis "R functions for classification")
320 "This package provides various functions for classification, including
321 k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
322 ;; Either of the two versions can be picked.
323 (license (list license:gpl2 license:gpl3))))
325 (define-public r-cluster
332 (uri (cran-uri "cluster" version))
335 "1bkvqmv8h2c423q9ag2afb6s9j2vcdlxsf559zzbimraphrr2c2b"))))
336 (build-system r-build-system)
337 (home-page "http://cran.r-project.org/web/packages/cluster")
338 (synopsis "Methods for cluster analysis")
340 "This package provides methods for cluster analysis. It is a much
341 extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
342 Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
343 (license license:gpl2+)))
345 (define-public r-codetools
352 (uri (cran-uri "codetools" version))
355 "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf"))))
356 (build-system r-build-system)
357 (home-page "http://cran.r-project.org/web/packages/codetools")
358 (synopsis "Code analysis tools for R")
359 (description "This package provides code analysis tools for R.")
360 ;; Any version of the GPL.
361 (license (list license:gpl2+ license:gpl3+))))
363 (define-public r-foreign
370 (uri (cran-uri "foreign" version))
373 "1mcrm2pydimbyjhkrw5h380bifj1jhwzifph1xgh90asf3lvd1xd"))))
374 (build-system r-build-system)
375 (home-page "http://cran.r-project.org/web/packages/foreign")
376 (synopsis "Read data stored by other statistics software")
378 "This package provides functions for reading and writing data stored by
379 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
380 for reading and writing some dBase files.")
381 (license license:gpl2+)))
383 (define-public r-kernsmooth
385 (name "r-kernsmooth")
390 (uri (cran-uri "KernSmooth" version))
393 "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb"))))
394 (properties `((upstream-name . "KernSmooth")))
395 (build-system r-build-system)
396 (home-page "http://cran.r-project.org/web/packages/KernSmooth")
397 (synopsis "Functions for kernel smoothing")
399 "This package provides functions for kernel smoothing (and density
400 estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
401 \"Kernel Smoothing\".")
402 ;; Unlimited distribution
403 (license (license:non-copyleft "file://LICENCE.note"))))
405 (define-public r-lattice
411 (uri (cran-uri "lattice" version))
414 "0615h69czr73k47whhzimf1qxv5qk0cabcrkljwhyrn6m6piq6ja"))))
415 (build-system r-build-system)
416 (home-page "http://lattice.r-forge.r-project.org/")
417 (synopsis "High-level data visualization system")
419 "The lattice package provides a powerful and elegant high-level data
420 visualization system inspired by Trellis graphics, with an emphasis on
421 multivariate data. Lattice is sufficient for typical graphics needs, and is
422 also flexible enough to handle most nonstandard requirements.")
423 (license license:gpl2+)))
425 (define-public r-matrix
432 (uri (cran-uri "Matrix" version))
435 "09rd51na9spz0lm1lylkfhw43w7c922b83m4jsggmpg3pbd6dssa"))))
436 (properties `((upstream-name . "Matrix")))
437 (build-system r-build-system)
439 `(("r-lattice" ,r-lattice)))
440 (home-page "http://Matrix.R-forge.R-project.org/")
441 (synopsis "Sparse and dense matrix classes and methods")
443 "This package provides classes and methods for dense and sparse matrices
444 and operations on them using LAPACK and SuiteSparse.")
445 (license license:gpl2+)))
447 (define-public r-nlme
454 (uri (cran-uri "nlme" version))
457 "0k2nvdzhic6bzhfsbq6la6q6a1i5nlj4pnh6lpdxiiwvxdks3nkr"))))
458 (build-system r-build-system)
460 `(("r-lattice" ,r-lattice)))
462 `(("gfortran" ,gfortran)))
463 (home-page "http://cran.r-project.org/web/packages/nlme")
464 (synopsis "Linear and nonlinear mixed effects models")
466 "This package provides tools to fit and compare Gaussian linear and
467 nonlinear mixed-effects models.")
468 (license license:gpl2+)))
470 (define-public r-mgcv
477 (uri (cran-uri "mgcv" version))
480 "0pj31gdwra7nv8spys4pfcbmsik99q1y1d0d2g37ywc3sz5s0rlj"))))
481 (build-system r-build-system)
483 `(("r-matrix" ,r-matrix)
485 (home-page "http://cran.r-project.org/web/packages/mgcv")
486 (synopsis "Mixed generalised additive model computation")
488 "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
489 parameter estimation by GCV, REML or UBRE/AIC. The library includes a
490 @code{gam()} function, a wide variety of smoothers, JAGS support and
491 distributions beyond the exponential family.")
492 (license license:gpl2+)))
494 (define-public r-nnet
501 (uri (cran-uri "nnet" version))
504 "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7"))))
505 (build-system r-build-system)
506 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
507 (synopsis "Feed-forward neural networks and multinomial log-linear models")
509 "This package provides functions for feed-forward neural networks with a
510 single hidden layer, and for multinomial log-linear models.")
511 (license (list license:gpl2+ license:gpl3+))))
513 (define-public r-rpart
520 (uri (cran-uri "rpart" version))
523 "119dvh2cpab4vq9blvbkil5hgq6w018amiwlda3ii0fki39axpf5"))))
524 (build-system r-build-system)
525 (home-page "http://cran.r-project.org/web/packages/rpart")
526 (synopsis "Recursive partitioning and regression trees")
528 "This package provides recursive partitioning functions for
529 classification, regression and survival trees.")
530 (license (list license:gpl2+ license:gpl3+))))
532 (define-public r-spatial
539 (uri (cran-uri "spatial" version))
542 "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
543 (build-system r-build-system)
544 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
545 (synopsis "Functions for kriging and point pattern analysis")
547 "This package provides functions for kriging and point pattern
549 ;; Either version may be picked.
550 (license (list license:gpl2 license:gpl3))))
552 (define-public r-survival
559 (uri (cran-uri "survival" version))
562 "10pf0kq0g66k5rgizrvh29mq3r84acljw2jgrv5yp6z38xw23mci"))))
563 (build-system r-build-system)
565 `(("r-matrix" ,r-matrix)))
566 (home-page "https://github.com/therneau/survival")
567 (synopsis "Survival analysis")
569 "This package contains the core survival analysis routines, including
570 definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
571 curves, Cox models, and parametric accelerated failure time models.")
572 (license license:lgpl2.0+)))
575 (package (inherit r-minimal)
578 (build-system trivial-build-system)
579 (arguments '(#:builder (mkdir %output)))
581 `(("r-minimal" ,r-minimal)
584 ("r-cluster" ,r-cluster)
585 ("r-codetools" ,r-codetools)
586 ("r-foreign" ,r-foreign)
587 ("r-kernsmooth" ,r-kernsmooth)
588 ("r-lattice" ,r-lattice)
590 ("r-matrix" ,r-matrix)
595 ("r-spatial" ,r-spatial)
596 ("r-survival" ,r-survival)))))
605 (uri (cran-uri "bit" version))
608 "0a6ig6nnjzq80r2ll4hc74za3xwzbzig6wlyb4dby0knzf3iqa6f"))))
609 (build-system r-build-system)
610 (home-page "http://ff.r-forge.r-project.org")
611 (synopsis "Class for vectors of 1-bit booleans")
613 "This package provides bitmapped vectors of booleans (no @code{NA}s),
614 coercion from and to logicals, integers and integer subscripts, fast boolean
615 operators and fast summary statistics. With @code{bit} class vectors of true
616 binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
617 (license license:gpl2)))
619 (define-public r-bit64
626 (uri (cran-uri "bit64" version))
629 "0fz5m3fhvxgwjl76maag7yn0zdw24rx34gy6v77378fajag9yllg"))))
630 (build-system r-build-system)
633 (home-page "http://ff.r-forge.r-project.org/")
634 (synopsis "S3 class for vectors of 64 bit integers")
636 "The bit64 package provides serializable S3 atomic 64 bit (signed)
637 integers that can be used in vectors, matrices, arrays and @code{data.frames}.
638 Methods are available for coercion from and to logicals, integers, doubles,
639 characters and factors as well as many elementwise and summary functions.
640 Many fast algorithmic operations such as @code{match} and @code{order} support
641 interactive data exploration and manipulation and optionally leverage
643 (license license:gpl2)))
645 (define-public r-colorspace
647 (name "r-colorspace")
652 (uri (cran-uri "colorspace" version))
654 (base32 "0d1ya7hx4y58n5ivwmdmq2zgh0g2sbv7ykh13n85c1355csd57yx"))))
655 (build-system r-build-system)
656 (home-page "http://cran.r-project.org/web/packages/colorspace")
657 (synopsis "Color space manipulation")
659 "This package carries out a mapping between assorted color spaces
660 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
661 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
662 colors are provided.")
663 (license license:bsd-3)))
665 (define-public r-dichromat
672 (uri (cran-uri "dichromat" version))
674 (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
675 (build-system r-build-system)
676 (home-page "http://cran.r-project.org/web/packages/dichromat")
677 (synopsis "Color schemes for dichromats")
679 "Dichromat collapses red-green or green-blue distinctions to simulate the
680 effects of different types of color-blindness.")
681 (license license:gpl2+)))
683 (define-public r-digest
690 (uri (cran-uri "digest" version))
692 (base32 "07825781nl85gx3pqskc04ywgs0f874qj9z2nyrwz7h0aqks0l8c"))))
693 (build-system r-build-system)
694 ;; Vignettes require r-knitr, which requires r-digest, so we have to
695 ;; disable them and the tests.
698 #:configure-flags (list "--no-build-vignettes")))
699 (home-page "http://dirk.eddelbuettel.com/code/digest.html")
700 (synopsis "Create cryptographic hash digests of R objects")
702 "This package contains an implementation of a function 'digest()' for the
703 creation of hash digests of arbitrary R objects (using the md5, sha-1,
704 sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
705 of R language objects, as well as a function 'hmac()' to create hash-based
706 message authentication code.
708 Please note that this package is not meant to be deployed for cryptographic
709 purposes for which more comprehensive (and widely tested) libraries such as
710 OpenSSL should be used.")
711 (license license:gpl2+)))
713 (define-public r-estimability
715 (name "r-estimability")
719 (uri (cran-uri "estimability" version))
722 "13b80bpnbrarazjvnpnk91ljjsqgfm2fm3gy66aj09cmmsmv199h"))))
723 (build-system r-build-system)
724 (home-page "http://cran.r-project.org/web/packages/estimability")
725 (synopsis "Tools for assessing estimability of linear predictions")
726 (description "Provides tools for determining estimability of linear
727 functions of regression coefficients, and 'epredict' methods that handle
728 non-estimable cases correctly.")
729 (license license:gpl2+)))
731 (define-public r-pheatmap
738 (uri (cran-uri "pheatmap" version))
741 "1ik0k69kb4n7xl3bkx4p09kw08ri93855zcsxq1c668171jqfiji"))))
742 (build-system r-build-system)
744 `(("r-gtable" ,r-gtable)
745 ("r-rcolorbrewer" ,r-rcolorbrewer)
746 ("r-scales" ,r-scales)))
748 "http://cran.r-project.org/web/packages/pheatmap")
749 (synopsis "Pretty heatmaps")
751 "This package provides an implementation of heatmaps that offers more
752 control over dimensions and appearance.")
753 (license license:gpl2+)))
755 (define-public r-labeling
762 (uri (cran-uri "labeling" version))
764 (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
765 (build-system r-build-system)
766 (home-page "http://cran.r-project.org/web/packages/labeling")
767 (synopsis "Axis labeling algorithms")
768 (description "The labeling package provides a range of axis labeling
770 (license license:expat)))
772 (define-public r-magrittr
779 (uri (cran-uri "magrittr" version))
781 (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
782 (build-system r-build-system)
783 (home-page "http://cran.r-project.org/web/packages/magrittr/index.html")
784 (synopsis "A forward-pipe operator for R")
786 "Magrittr provides a mechanism for chaining commands with a new
787 forward-pipe operator, %>%. This operator will forward a value, or the result
788 of an expression, into the next function call/expression. There is flexible
789 support for the type of right-hand side expressions. For more information,
790 see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
791 (license license:expat)))
793 (define-public r-munsell
800 (uri (cran-uri "munsell" version))
802 (base32 "0jdxlbjslkzaqgp058da1cgm85qvqi09wpcgpvp4hvwnmy83qz1r"))))
803 (build-system r-build-system)
805 `(("r-colorspace" ,r-colorspace)))
806 (home-page "http://cran.r-project.org/web/packages/munsell")
807 (synopsis "Munsell colour system")
809 "The Munsell package contains Functions for exploring and using the
810 Munsell colour system.")
811 (license license:expat)))
813 (define-public r-rcpp
820 (uri (cran-uri "Rcpp" version))
822 (base32 "0is1vql1q82g7yakad4skx707ip0fx3rgdwv9a8mi8259gly2qji"))))
823 (build-system r-build-system)
824 (home-page "http://www.rcpp.org")
825 (synopsis "Seamless R and C++ Integration")
827 "The Rcpp package provides R functions as well as C++ classes which offer
828 a seamless integration of R and C++. Many R data types and objects can be
829 mapped back and forth to C++ equivalents which facilitates both writing of new
830 code as well as easier integration of third-party libraries. Documentation
831 about Rcpp is provided by several vignettes included in this package, via the
832 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
833 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
834 'citation(\"Rcpp\")' for details on these last two.")
835 (license license:gpl2+)))
837 (define-public r-permute
844 (uri (cran-uri "permute" version))
847 "1w8wzk1fg9q7wvisnfp2js70dg0m9wi12gkdhpyngpbdcgssahd5"))))
848 (build-system r-build-system)
849 ;; Tests do not run correctly, but running them properly would entail a
850 ;; circular dependency with vegan.
851 (home-page "https://github.com/gavinsimpson/permute")
852 (synopsis "Functions for Generating Restricted Permutations of Data")
854 "This package provides a set of restricted permutation designs for freely
855 exchangeable, line transects (time series), spatial grid designs and permutation
856 of blocks (groups of samples). @code{permute} also allows split-plot designs,
857 in which the whole-plots or split-plots or both can be freely exchangeable.")
858 (license license:gpl2+)))
860 (define-public r-plyr
867 (uri (cran-uri "plyr" version))
869 (base32 "1igar5pcjqh0jyxv0z3jah8rz617vfa86vw0r5c7c031b7bj5db0"))))
870 (build-system r-build-system)
871 (native-inputs `(("r-rcpp" ,r-rcpp)))
872 (home-page "http://had.co.nz/plyr")
873 (synopsis "Tools for Splitting, Applying and Combining Data")
875 "Plyr is a set of tools that solves a common set of problems: you need to
876 break a big problem down into manageable pieces, operate on each piece and
877 then put all the pieces back together. For example, you might want to fit a
878 model to each spatial location or time point in your study, summarise data by
879 panels or collapse high-dimensional arrays to simpler summary statistics.")
880 (license license:expat)))
882 (define-public r-proto
889 (uri (cran-uri "proto" version))
891 (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
892 (build-system r-build-system)
893 (home-page "https://github.com/hadley/proto")
894 (synopsis "Prototype object-based programming")
896 "Proto is an object oriented system using object-based, also called
897 prototype-based, rather than class-based object oriented ideas.")
898 (license license:gpl2+)))
900 (define-public r-rcolorbrewer
902 (name "r-rcolorbrewer")
907 (uri (cran-uri "RColorBrewer" version))
909 (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
910 (build-system r-build-system)
911 (home-page "http://cran.r-project.org/web/packages/RColorBrewer")
912 (synopsis "ColorBrewer palettes")
914 "This package provides color schemes for maps (and other graphics)
915 designed by Cynthia Brewer as described at http://colorbrewer2.org")
916 ;; Includes code licensed under bsd-4
917 (license license:asl2.0)))
919 (define-public r-sendmailr
926 (uri (cran-uri "sendmailR" version))
929 "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
930 (properties `((upstream-name . "sendmailR")))
931 (build-system r-build-system)
933 `(("r-base64enc" ,r-base64enc)))
935 "http://cran.r-project.org/web/packages/sendmailR")
936 (synopsis "Send email using R")
938 "This package contains a simple SMTP client which provides a portable
939 solution for sending email, including attachments, from within R.")
940 (license license:gpl2+)))
942 (define-public r-stringi
949 (uri (cran-uri "stringi" version))
952 "13i1p6j8mx31hsw2s4c2phm2llrrdakzixkm6i0axsxprri722z5"))))
953 (build-system r-build-system)
954 (inputs `(("icu4c" ,icu4c)))
955 (native-inputs `(("pkg-config" ,pkg-config)))
956 (home-page "http://stringi.rexamine.com/")
957 (synopsis "Character string processing facilities")
959 "This package allows for fast, correct, consistent, portable, as well as
960 convenient character string/text processing in every locale and any native
961 encoding. Owing to the use of the ICU library, the package provides R users
962 with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
963 programmers. Among available features there are: pattern searching
964 (e.g. via regular expressions), random string generation, string collation,
965 transliteration, concatenation, date-time formatting and parsing, etc.")
966 (license license:bsd-3)))
968 (define-public r-stringr
975 (uri (cran-uri "stringr" version))
977 (base32 "0css5j4psl80br75chg6s1s3ipzf89f71bnbys34flp9yghg1cfc"))))
978 (build-system r-build-system)
980 `(("r-magrittr" ,r-magrittr)
981 ("r-stringi" ,r-stringi)))
982 (home-page "https://github.com/hadley/stringr")
983 (synopsis "Simple, consistent wrappers for common string operations")
985 "Stringr is a consistent, simple and easy to use set of wrappers around
986 the fantastic 'stringi' package. All function and argument names (and
987 positions) are consistent, all functions deal with \"NA\"'s and zero length
988 vectors in the same way, and the output from one function is easy to feed into
989 the input of another.")
990 (license license:gpl2+)))
992 (define-public r-reshape2
999 (uri (cran-uri "reshape2" version))
1001 (base32 "0swvjmc9f8cvkrsz463cp6snd8bncbv6q8yrfrb4rgkr0dhq6dvd"))))
1002 (build-system r-build-system)
1004 `(("r-plyr" ,r-plyr)
1006 ("r-stringr" ,r-stringr)))
1007 (home-page "https://github.com/hadley/reshape")
1008 (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
1010 "Reshape2 is an R library to flexibly restructure and aggregate data
1011 using just two functions: melt and dcast (or acast).")
1012 (license license:expat)))
1014 (define-public r-scales
1021 (uri (cran-uri "scales" version))
1023 (base32 "1lqccfmqdwrw0cjyqvw2zvgpk2jvnqrfb303l1raqyyf3zxqhav4"))))
1024 (build-system r-build-system)
1026 `(("r-dichromat" ,r-dichromat)
1027 ("r-labeling" ,r-labeling)
1028 ("r-munsell" ,r-munsell)
1030 ("r-rcolorbrewer" ,r-rcolorbrewer)
1031 ("r-rcpp" ,r-rcpp)))
1032 (home-page "https://github.com/hadley/scales")
1033 (synopsis "Scale functions for visualization")
1035 "This package provides graphical scales that map data to aesthetics, and
1036 provides methods for automatically determining breaks and labels for axes and
1038 (license license:expat)))
1040 (define-public r-ggplot2
1047 (uri (cran-uri "ggplot2" version))
1049 (base32 "0543782ddv2hp6s0l702mnxfg8n7a6qlbm8bm55x22hnqgz8kg2z"))))
1050 (build-system r-build-system)
1052 `(("r-digest" ,r-digest)
1053 ("r-gtable" ,r-gtable)
1055 ("r-lazyeval" ,r-lazyeval)
1057 ("r-tibble" ,r-tibble)
1058 ("r-reshape2" ,r-reshape2)
1059 ("r-scales" ,r-scales)
1060 ("r-svglite" ,r-svglite))) ; Needed for 'ggsave'
1061 (home-page "http://ggplot2.org")
1062 (synopsis "An implementation of the grammar of graphics")
1064 "Ggplot2 is an implementation of the grammar of graphics in R. It
1065 combines the advantages of both base and lattice graphics: conditioning and
1066 shared axes are handled automatically, and you can still build up a plot step
1067 by step from multiple data sources. It also implements a sophisticated
1068 multidimensional conditioning system and a consistent interface to map data to
1069 aesthetic attributes.")
1070 (license license:gpl2+)))
1072 (define-public r-gdtools
1079 (uri (cran-uri "gdtools" version))
1082 "1prh814lw3qkgnf0760cvpic1k68jhlkpcxlksv8chjkvsrnnf09"))))
1083 (build-system r-build-system)
1085 `(("r-rcpp" ,r-rcpp)
1086 ("pkg-config" ,pkg-config)))
1088 `(("cairo" ,cairo)))
1090 `(("r-withr" ,r-withr)))
1091 (home-page "http://cran.r-project.org/web/packages/gdtools")
1092 (synopsis "Utilities for graphical rendering")
1094 "The @code{gdtools} package provides functionalities to get font metrics
1095 and to generate base64 encoded string from raster matrix.")
1096 (license license:gpl3)))
1098 (define-public r-svglite
1105 (uri (cran-uri "svglite" version))
1108 "1s1gvmlmmna5y4jsn9h6438pg5b86fl4nwfvkgm6n4h6ljfgqyx3"))))
1109 (build-system r-build-system)
1110 (native-inputs `(("r-rcpp" ,r-rcpp)))
1113 ("r-gdtools" ,r-gdtools)))
1114 (home-page "https://github.com/hadley/svglite")
1115 (synopsis "SVG graphics device")
1117 "@code{svglite} is a graphics device that produces clean
1118 @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
1119 hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
1120 considerably faster, produces smaller files, and leaves text as is.")
1121 (license license:gpl2+)))
1123 (define-public r-assertthat
1125 (name "r-assertthat")
1129 (uri (cran-uri "assertthat" version))
1132 "0dwsqajyglfscqilj843qfqn1ndbqpswa7b4l1d633qjk9d68qqk"))))
1133 (build-system r-build-system)
1134 (home-page "https://github.com/hadley/assertthat")
1135 (synopsis "Easy pre and post assertions")
1137 "Assertthat is an extension to stopifnot() that makes it easy to declare
1138 the pre and post conditions that your code should satisfy, while also
1139 producing friendly error messages so that your users know what they've done
1141 (license license:gpl3+)))
1143 (define-public r-lazyeval
1149 (uri (cran-uri "lazyeval" version))
1152 "1jwdz40nznlc44hpjli7h98gnpa4d98ifggmj7z88h84n9aqywqk"))))
1153 (build-system r-build-system)
1154 (home-page "https://github.com/hadley/lazyeval")
1155 (synopsis "Lazy (non-standard) evaluation in R")
1157 "This package provides the tools necessary to do non-standard
1158 evaluation (NSE) in R.")
1159 (license license:gpl3+)))
1161 (define-public r-dbi
1167 (uri (cran-uri "DBI" version))
1170 "1idwm9lkmz6ns6h0vvgml18mg0k7vjqiv9p5svrdcmx7r1rirpdi"))))
1171 (build-system r-build-system)
1172 (home-page "https://github.com/rstats-db/DBI")
1173 (synopsis "R database interface")
1175 "The DBI package provides a database interface (DBI) definition for
1176 communication between R and relational database management systems. All
1177 classes in this package are virtual and need to be extended by the various
1178 R/DBMS implementations.")
1179 (license license:lgpl2.0+)))
1184 (version "1.62.0-1")
1187 (uri (cran-uri "BH" version))
1190 "01vfdpfznd4ynqql33z238xr262mvy3i80lyi8l3a3p3hi0a262p"))))
1191 (build-system r-build-system)
1192 (home-page "https://github.com/eddelbuettel/bh")
1193 (synopsis "R package providing subset of Boost headers")
1195 "This package aims to provide the most useful subset of Boost libraries
1196 for template use among CRAN packages.")
1197 (license license:boost1.0)))
1199 (define-public r-evaluate
1205 (uri (cran-uri "evaluate" version))
1208 "0mwna7rjyrmc76651a1fm7c76ippdsc2wsp3sj3iwb1c73mvlqv1"))))
1209 (build-system r-build-system)
1211 `(("r-stringr" ,r-stringr)))
1212 (home-page "https://github.com/hadley/evaluate")
1213 (synopsis "Parsing and evaluation tools for R")
1215 "This package provides tools that allow you to recreate the parsing,
1216 evaluation and display of R code, with enough information that you can
1217 accurately recreate what happens at the command line. The tools can easily be
1218 adapted for other output formats, such as HTML or LaTeX.")
1219 (license license:gpl3+)))
1221 (define-public r-formatr
1227 (uri (cran-uri "formatR" version))
1230 "1fvynq0fj1r9grg9vvfdh5fl2riv6qki9f2rfpyvbvqq3xxpmi3f"))))
1231 (build-system r-build-system)
1232 (home-page "http://yihui.name/formatR")
1233 (synopsis "Format R code automatically")
1235 "This package provides a function to format R source code. Spaces and
1236 indent will be added to the code automatically, and comments will be preserved
1237 under certain conditions, so that R code will be more human-readable and tidy.
1238 There is also a Shiny app as a user interface in this package.")
1239 (license license:gpl3+)))
1241 (define-public r-highr
1247 (uri (cran-uri "highr" version))
1250 "0n9v44dxdy5fhkdmpbpa2p78whyd9z3rhhy42ipdz5m5vsr55qa3"))))
1251 (build-system r-build-system)
1252 (home-page "https://github.com/yihui/highr")
1253 (synopsis "Syntax highlighting for R source code")
1255 "This package provides syntax highlighting for R source code. Currently
1256 it supports LaTeX and HTML output. Source code of other languages is
1257 supported via Andre Simon's highlight package.")
1258 (license license:gpl3+)))
1260 (define-public r-mime
1266 (uri (cran-uri "mime" version))
1269 "0i91m3ivaja1k33jwcvz16pfjypkci27awm8glil7sxhmwaj3izw"))))
1270 (build-system r-build-system)
1271 (home-page "https://github.com/yihui/mime")
1272 (synopsis "R package to map filenames to MIME types")
1274 "This package guesses the MIME type from a filename extension using the
1275 data derived from /etc/mime.types in UNIX-type systems.")
1276 (license license:gpl2)))
1278 (define-public r-markdown
1284 (uri (cran-uri "markdown" version))
1287 "00j1hlib3il50azs2vlcyhi0bjpx1r50mxr9w9dl5g1bwjjc71hb"))))
1288 (build-system r-build-system)
1289 ;; Skip check phase because the tests require the r-knitr package to be
1290 ;; installed. This prevents installation failures. Knitr normally
1291 ;; shouldn't be available since r-markdown is a dependency of the r-knitr
1293 (arguments `(#:tests? #f))
1295 `(("r-mime" ,r-mime)))
1296 (home-page "https://github.com/rstudio/markdown")
1297 (synopsis "Markdown rendering for R")
1299 "This package provides R bindings to the Sundown Markdown rendering
1300 library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
1301 syntax that can be converted to XHTML or other formats.")
1302 (license license:gpl2)))
1304 (define-public r-yaml
1310 (uri (cran-uri "yaml" version))
1313 "0x88xicrf7vwp77xgan27mnpdljhpkn0pz5kphnwqi3ddy25k9a1"))))
1314 (build-system r-build-system)
1315 (home-page "https://cran.r-project.org/web/packages/yaml/")
1316 (synopsis "Methods to convert R data to YAML and back")
1318 "This package implements the libyaml YAML 1.1 parser and
1319 emitter (http://pyyaml.org/wiki/LibYAML) for R.")
1320 (license license:bsd-3)))
1322 (define-public r-knitr
1328 (uri (cran-uri "knitr" version))
1331 "1pbxd3k7kv5sa1a5gxm0zc2bhjxdgx2nfch9xap5k85djmgsfqc1"))))
1332 (build-system r-build-system)
1334 `(("r-evaluate" ,r-evaluate)
1335 ("r-digest" ,r-digest)
1336 ("r-highr" ,r-highr)
1337 ("r-markdown" ,r-markdown)
1338 ("r-stringr" ,r-stringr)
1339 ("r-yaml" ,r-yaml)))
1340 (home-page "http://yihui.name/knitr/")
1341 (synopsis "General-purpose package for dynamic report generation in R")
1343 "This package provides a general-purpose tool for dynamic report
1344 generation in R using Literate Programming techniques.")
1345 ;; The code is released under any version of the GPL. As it is used by
1346 ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
1348 (license license:gpl2+)))
1350 (define-public r-knitrbootstrap
1352 (name "r-knitrbootstrap")
1357 (uri (cran-uri "knitrBootstrap" version))
1360 "0pshn2slzqwpryklslsxwh1dmqcnwv6bwi7yfm6m342wjybpk0wl"))))
1361 (properties `((upstream-name . "knitrBootstrap")))
1362 (build-system r-build-system)
1364 `(("r-knitr" ,r-knitr)
1365 ("r-rmarkdown" ,r-rmarkdown)))
1366 (home-page "https://github.com/jimhester/knitrBootstrap")
1367 (synopsis "Knitr bootstrap framework")
1369 "This package provides a framework to create Bootstrap 3 HTML reports
1370 from knitr Rmarkdown.")
1371 (license license:expat)))
1373 (define-public r-microbenchmark
1375 (name "r-microbenchmark")
1379 (uri (cran-uri "microbenchmark" version))
1382 "0qn5r1a6qidghcisc2hpbdmj62pnixc3zz6p4ipk8mvakf0hdsvg"))))
1383 (build-system r-build-system)
1385 `(("r-ggplot2" ,r-ggplot2)))
1386 (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
1387 (synopsis "Accurate timing functions for R")
1389 "This package provides infrastructure to accurately measure and compare
1390 the execution time of R expressions.")
1391 (license license:bsd-2)))
1393 (define-public r-pryr
1399 (uri (cran-uri "pryr" version))
1402 "1in350a8hxwf580afavasvn3jc7x2p1b7nlwmj1scakfz74vghk5"))))
1403 (build-system r-build-system)
1405 `(("r-stringr" ,r-stringr)
1406 ("r-codetools" ,r-codetools)))
1408 `(("r-rcpp" ,r-rcpp)))
1409 (home-page "https://github.com/hadley/pryr")
1410 (synopsis "Tools for computing on the R language")
1412 "This package provides useful tools to pry back the covers of R and
1413 understand the language at a deeper level.")
1414 (license license:gpl2)))
1416 (define-public r-memoise
1422 (uri (cran-uri "memoise" version))
1425 "0sq2dhpvxy17v1baj256r0jnygdy3m5a8x4zh6vhv29957qnq6zx"))))
1426 (build-system r-build-system)
1428 `(("r-digest" ,r-digest)))
1429 (home-page "http://github.com/hadley/memoise")
1430 (synopsis "Memoise functions for R")
1432 "This R package allows to cache the results of a function so that when
1433 you call it again with the same arguments it returns the pre-computed value.")
1434 (license license:expat)))
1436 (define-public r-crayon
1442 (uri (cran-uri "crayon" version))
1445 "0s2yam18slph7xsw4pyc9f92gdyf609r5w92yax69zh57kb7asws"))))
1446 (build-system r-build-system)
1448 `(("r-memoise" ,r-memoise)))
1449 (home-page "https://github.com/gaborcsardi/crayon")
1450 (synopsis "Colored terminal output for R")
1452 "Colored terminal output on terminals that support ANSI color and
1453 highlight codes. It also works in Emacs ESS. ANSI color support is
1454 automatically detected. Colors and highlighting can be combined and nested.
1455 New styles can also be created easily. This package was inspired by the
1456 \"chalk\" JavaScript project.")
1457 (license license:expat)))
1459 (define-public r-praise
1466 (uri (cran-uri "praise" version))
1469 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
1470 (build-system r-build-system)
1471 (home-page "https://github.com/gaborcsardi/praise")
1472 (synopsis "Functions to praise users")
1474 "This package provides template functions to assist in building friendly
1475 R packages that praise their users.")
1476 (license license:expat)))
1478 (define-public r-testthat
1484 (uri (cran-uri "testthat" version))
1487 "0pj1r01x4ny4capr83dfa19hi5i2sjjxky99schzip8zrq5dzxqf"))))
1488 (build-system r-build-system)
1490 `(("r-digest" ,r-digest)
1491 ("r-crayon" ,r-crayon)
1492 ("r-magrittr" ,r-magrittr)
1493 ("r-praise" ,r-praise)
1495 (home-page "https://github.com/hadley/testthat")
1496 (synopsis "Unit testing for R")
1498 "This package provides a unit testing system for R designed to be fun,
1499 flexible and easy to set up.")
1500 (license license:expat)))
1508 (uri (cran-uri "R6" version))
1511 "1ir51pb0y6yj05qaxsflk4a6hv8n73cwlb0qajcskbrz632dsyvx"))))
1512 (build-system r-build-system)
1513 (home-page "https://github.com/wch/R6/")
1514 (synopsis "Classes with reference semantics in R")
1516 "The R6 package allows the creation of classes with reference semantics,
1517 similar to R's built-in reference classes. Compared to reference classes, R6
1518 classes are simpler and lighter-weight, and they are not built on S4 classes
1519 so they do not require the methods package. These classes allow public and
1520 private members, and they support inheritance, even when the classes are
1521 defined in different packages.")
1522 (license license:expat)))
1524 (define-public r-tibble
1531 (uri (cran-uri "tibble" version))
1534 "011i352ylq9b4xfcj7h10h7qsqd9qkc1rzc0pr1gf8qjb788p2pd"))))
1535 (build-system r-build-system)
1537 `(("r-assertthat" ,r-assertthat)
1538 ("r-lazyeval" ,r-lazyeval)
1539 ("r-rcpp" ,r-rcpp)))
1540 (home-page "https://github.com/hadley/tibble")
1541 (synopsis "Simple data frames")
1543 "This package provides a @code{tbl_df} class that offers better checking
1544 and printing capabilities than traditional data frames.")
1545 (license license:expat)))
1547 (define-public r-dplyr
1553 (uri (cran-uri "dplyr" version))
1556 "0ks5cklb03laqf5ygcw986g1lv7wk1ipvypjlha8xly2y4lvilwk"))))
1557 (build-system r-build-system)
1559 `(("r-assertthat" ,r-assertthat)
1561 ("r-magrittr" ,r-magrittr)
1562 ("r-lazyeval" ,r-lazyeval)
1564 ("r-tibble" ,r-tibble)))
1566 `(("r-rcpp" ,r-rcpp)
1568 (home-page "https://github.com/hadley/dplyr")
1569 (synopsis "Tools for working with data frames in R")
1571 "dplyr is the next iteration of plyr. It is focussed on tools for
1572 working with data frames. It has three main goals: 1) identify the most
1573 important data manipulation tools needed for data analysis and make them easy
1574 to use in R; 2) provide fast performance for in-memory data by writing key
1575 pieces of code in C++; 3) use the same code interface to work with data no
1576 matter where it is stored, whether in a data frame, a data table or
1578 (license license:expat)))
1580 (define-public r-acepack
1587 (uri (cran-uri "acepack" version))
1590 "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
1591 (build-system r-build-system)
1593 `(("gfortran" ,gfortran)))
1594 (home-page "http://cran.r-project.org/web/packages/acepack")
1595 (synopsis "Functions for regression transformations")
1597 "This package provides ACE and AVAS methods for choosing regression
1599 (license license:expat)))
1601 (define-public r-cluster
1608 (uri (cran-uri "cluster" version))
1611 "1bkvqmv8h2c423q9ag2afb6s9j2vcdlxsf559zzbimraphrr2c2b"))))
1612 (build-system r-build-system)
1614 `(("gfortran" ,gfortran)))
1615 (home-page "http://cran.r-project.org/web/packages/cluster")
1616 (synopsis "Methods for data cluster analysis")
1618 "This package provides tools that are useful in finding groups in data.
1619 It is based on the methods described in Kaufman and Rousseeuw (1990) \"Finding
1621 (license license:gpl2+)))
1623 (define-public r-foreign
1630 (uri (cran-uri "foreign" version))
1633 "1mcrm2pydimbyjhkrw5h380bifj1jhwzifph1xgh90asf3lvd1xd"))))
1634 (build-system r-build-system)
1635 (home-page "http://cran.r-project.org/web/packages/foreign")
1636 (synopsis "Read data stored by other statistics software in R")
1638 "This package provides functions for reading and writing data stored by
1639 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka, and
1640 for reading and writing some dBase files.")
1641 (license license:gpl2+)))
1643 (define-public r-formula
1650 (uri (cran-uri "Formula" version))
1653 "02in5325zzrqbhlygx6s0dinj6ymw845q70y56frqacv25ayzcax"))))
1654 (properties `((upstream-name . "Formula")))
1655 (build-system r-build-system)
1656 (home-page "http://cran.r-project.org/web/packages/Formula")
1657 (synopsis "Extended model formulas")
1659 "This package provides a new class @code{Formula}, which extends the base
1660 class @code{formula}. It supports extended formulas with multiple parts of
1661 regressors on the right-hand side and/or multiple responses on the left-hand
1663 (license (list license:gpl2+ license:gpl3+))))
1665 (define-public r-locfit
1672 (uri (cran-uri "locfit" version))
1675 "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
1676 (build-system r-build-system)
1678 `(("r-lattice" ,r-lattice)))
1679 (home-page "http://cran.r-project.org/web/packages/locfit")
1680 (synopsis "Local regression, likelihood and density estimation")
1682 "This package provides functions used for local regression, likelihood
1683 and density estimation.")
1684 (license (list license:gpl2+ license:gpl3+))))
1686 (define-public r-chron
1692 (uri (cran-uri "chron" version))
1695 "1q1d0p2wq19w3mpfqnrg8nmspxqmhv4ap52r393s6y3abl36ccac"))))
1696 (build-system r-build-system)
1697 (home-page "http://cran.r-project.org/web/packages/chron")
1698 (synopsis "Chronological R objects which can handle dates and times")
1700 "This package provides chronological R objects which can handle dates and
1702 (license license:gpl2)))
1704 (define-public r-data-table
1706 (name "r-data-table")
1710 (uri (cran-uri "data.table" version))
1713 "1168arn4wjd1jj7kgr4sb8xd52hr8p8iqp85g5jwp3mkz4p76qfg"))))
1714 (build-system r-build-system)
1715 (home-page "https://github.com/Rdatatable/data.table/wiki")
1716 (synopsis "Enhanced version of data.frame R object")
1718 "The R package @code{data.table} is an extension of @code{data.frame}
1719 providing functions for fast aggregation of large data (e.g. 100GB in RAM),
1720 fast ordered joins, fast add/modify/delete of columns by group, column listing
1721 and fast file reading.")
1722 (license license:gpl3+)))
1724 (define-public r-xtable
1731 (uri (cran-uri "xtable" version))
1734 "0398qkpvlw3dv0myz4mjcyqwpwc2m31l127r8vdzwc71wb6s28qn"))))
1735 (build-system r-build-system)
1737 `(("r-knitr" ,r-knitr)))
1738 (home-page "http://xtable.r-forge.r-project.org/")
1739 (synopsis "Export R tables to LaTeX or HTML")
1741 "This package provides tools to export R data as LaTeX and HTML tables.")
1742 (license license:gpl2+)))
1744 (define-public python-patsy
1746 (name "python-patsy")
1750 (uri (pypi-uri "patsy" version ".zip"))
1753 "1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w"))))
1754 (build-system python-build-system)
1757 (modify-phases %standard-phases
1758 (replace 'check (lambda _ (zero? (system* "nosetests" "-v")))))))
1760 `(("python-numpy" ,python-numpy)
1761 ("python-scipy" ,python-scipy)
1762 ("python-six" ,python-six)))
1764 `(("python-nose" ,python-nose)
1766 (home-page "https://github.com/pydata/patsy")
1767 (synopsis "Describe statistical models and build design matrices")
1769 "Patsy is a Python package for describing statistical models and for
1770 building design matrices.")
1771 ;; The majority of the code is distributed under BSD-2. The module
1772 ;; patsy.compat contains code derived from the Python standard library,
1773 ;; and is covered by the PSFL.
1774 (license (list license:bsd-2 license:psfl))))
1776 (define-public python2-patsy
1777 (package-with-python2 python-patsy))
1779 (define-public python-statsmodels
1781 (name "python-statsmodels")
1786 (uri (pypi-uri "statsmodels" version))
1789 "0j30v3932shnj9368c9jr3svkyrvfj90h2l7nxnqkbpv0svilhr6"))
1790 (patches (search-patches "python-statsmodels-fix-tests.patch"))))
1791 (build-system python-build-system)
1794 (modify-phases %standard-phases
1795 ;; tests must be run after installation
1797 (add-after 'unpack 'set-matplotlib-backend-to-agg
1799 ;; Set the matplotlib backend to Agg to avoid problems using the
1800 ;; GTK backend without a display.
1801 (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py")
1802 '("statsmodels/tsa/vector_ar/tests/test_var.py"
1803 "statsmodels/duration/tests/test_survfunc.py"))
1804 (("import matplotlib\\.pyplot as plt" line)
1805 (string-append "import matplotlib;matplotlib.use('Agg');"
1808 (add-after 'install 'check
1809 (lambda* (#:key inputs outputs #:allow-other-keys)
1810 ;; Make installed package available for running the tests
1811 (add-installed-pythonpath inputs outputs)
1812 (with-directory-excursion "/tmp"
1813 (zero? (system* "nosetests"
1815 "-v" "statsmodels"))))))))
1817 `(("python-numpy" ,python-numpy)
1818 ("python-scipy" ,python-scipy)
1819 ("python-pandas" ,python-pandas)
1820 ("python-patsy" ,python-patsy)
1821 ("python-matplotlib" ,python-matplotlib)))
1823 `(("python-cython" ,python-cython)
1824 ("python-nose" ,python-nose)
1825 ("python-sphinx" ,python-sphinx)))
1826 (home-page "http://statsmodels.sourceforge.net/")
1827 (synopsis "Statistical modeling and econometrics in Python")
1829 "Statsmodels is a Python package that provides a complement to scipy for
1830 statistical computations including descriptive statistics and estimation and
1831 inference for statistical models.")
1832 (license license:bsd-3)))
1834 (define-public python2-statsmodels
1835 (let ((stats (package-with-python2 python-statsmodels)))
1836 (package (inherit stats)
1838 `(("python2-pytz" ,python2-pytz)
1839 ("python2-numpy" ,python2-numpy)
1840 ("python2-scipy" ,python2-scipy)
1841 ("python2-pandas" ,python2-pandas)
1842 ("python2-patsy" ,python2-patsy)
1843 ("python2-matplotlib" ,python2-matplotlib))))))
1845 (define-public r-coda
1851 (uri (cran-uri "coda" version))
1854 "14a4a8df4ygj05h37chmdn8kzcqs07fpbflxfrq530563mrza7yl"))))
1855 (build-system r-build-system)
1857 `(("r-lattice" ,r-lattice)))
1858 (home-page "http://cran.r-project.org/web/packages/coda")
1859 (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
1860 (description "This package provides functions for summarizing and plotting
1861 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
1862 diagnostic tests of convergence to the equilibrium distribution of the Markov
1864 (license license:gpl2+)))
1866 (define-public r-ade4
1873 (uri (cran-uri "ade4" version))
1876 "0aaqbnydm5fb37nrvqj4bx6hxax7255j426cwh2lh88nyvznbq37"))))
1877 (build-system r-build-system)
1878 (home-page "http://pbil.univ-lyon1.fr/ADE-4")
1879 (synopsis "Multivariate data analysis and graphical display")
1881 "The ade4 package contains data analysis functions to analyze ecological
1882 and environmental data in the framework of Euclidean exploratory methods.")
1883 (license license:gpl2+)))
1885 (define-public r-xml2
1892 (uri (cran-uri "xml2" version))
1895 "0f2alsrk3yykznbhnz4pcsg9mb72cv607vbapqx5kqfv39772kgr"))))
1896 (build-system r-build-system)
1898 `(("libxml2" ,libxml2)))
1900 `(("r-rcpp" ,r-rcpp)
1902 (home-page "https://github.com/hadley/xml2")
1903 (synopsis "Parse XML with R")
1905 "This package provides a simple, consistent interface to working with XML
1906 files in R. It is built on top of the libxml2 C library.")
1907 (license license:gpl2+)))
1909 (define-public r-multitaper
1911 (name "r-multitaper")
1916 (uri (cran-uri "multitaper" version))
1919 "011qpkwpjclfc24y2qqigmdnikqwdnanflfhihigh5b5k7qwgm5j"))))
1920 (build-system r-build-system)
1922 `(("gfortran" ,gfortran)))
1923 (home-page "http://github.com/wesleyburr/multitaper/")
1924 (synopsis "Multitaper spectral analysis tools")
1926 "This package implements multitaper spectral estimation
1927 techniques using prolate spheroidal sequences (Slepians) and sine
1928 tapers for time series analysis. It includes an adaptive weighted
1929 multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
1930 F-test, and complex demodulation. The Slepians sequences are
1931 generated efficiently using a tridiagonal matrix solution, and
1932 jackknifed confidence intervals are available for most estimates.")
1933 (license license:gpl2+)))
1935 (define-public r-rversions
1937 (name "r-rversions")
1941 (uri (cran-uri "rversions" version))
1944 "0i2gi05nrvknr7g89rbppkswyfcwwd4r9gp75fdfhpah8sgq1l11"))))
1945 (build-system r-build-system)
1947 `(("r-curl" ,r-curl)
1948 ("r-xml2" ,r-xml2)))
1949 (home-page "https://github.com/metacran/rversions")
1950 (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
1952 "This package provides functions to query the main R repository to find
1953 the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
1954 previous R versions and their release dates.")
1955 (license license:expat)))
1957 (define-public r-whisker
1963 (uri (cran-uri "whisker" version))
1966 "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28"))))
1967 (build-system r-build-system)
1968 (home-page "http://github.com/edwindj/whisker")
1969 (synopsis "Logicless mustache templating for R")
1971 "This package provides logicless templating, with a syntax that is not
1973 (license license:gpl3+)))
1975 (define-public r-backports
1977 (name "r-backports")
1982 (uri (cran-uri "backports" version))
1985 "0fssh5rnnvpp8wm0ml9gk765idwrgj07xyxpkhpidl9zwydxzif2"))))
1986 (build-system r-build-system)
1987 (home-page "http://cran.r-project.org/web/packages/backports")
1988 (synopsis "Reimplementations of functions introduced since R 3.0.0")
1990 "Provides implementations of functions which have been introduced in R
1991 since version 3.0.0. The backports are conditionally exported which results
1992 in R resolving the function names to the version shipped with R (if available)
1993 and uses the implemented backports as fallback. This way package developers
1994 can make use of the new functions without worrying about the minimum required
1996 (license license:gpl2+)))
1998 (define-public r-checkmate
2000 (name "r-checkmate")
2005 (uri (cran-uri "checkmate" version))
2008 "1zqcggl9m7slvc0q6zyhssdypb7jzf3l9byl5vxh1qdwjiw2y64g"))))
2009 (build-system r-build-system)
2011 `(("r-backports" ,r-backports)))
2012 (home-page "https://github.com/mllg/checkmate")
2013 (synopsis "Fast and versatile argument checks")
2015 "This package provides tests and assertions to perform frequent argument
2016 checks. A substantial part of the package was written in C to minimize any
2017 worries about execution time overhead.")
2018 (license license:bsd-3)))
2020 (define-public r-bbmisc
2027 (uri (cran-uri "BBmisc" version))
2030 "0cw2mhw7qhdrx91zzd5iwyh7ch9fy4wxga8j63731q6sxr1airjl"))))
2031 (properties `((upstream-name . "BBmisc")))
2032 (build-system r-build-system)
2034 `(("r-checkmate" ,r-checkmate)))
2035 (home-page "https://github.com/berndbischl/BBmisc")
2036 (synopsis "Miscellaneous functions for R package development")
2038 "This package provides miscellaneous helper functions for the development
2040 (license license:bsd-3)))
2042 (define-public r-fail
2049 (uri (cran-uri "fail" version))
2052 "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
2053 (build-system r-build-system)
2055 `(("r-bbmisc" ,r-bbmisc)
2056 ("r-checkmate" ,r-checkmate)))
2057 (home-page "https://github.com/mllg/fail")
2058 (synopsis "File abstraction interface layer (FAIL)")
2060 "This package provides a more comfortable interface to work with R data
2061 or source files in a key-value fashion.")
2062 (license license:bsd-3)))
2064 (define-public r-batchjobs
2066 (name "r-batchjobs")
2071 (uri (cran-uri "BatchJobs" version))
2074 "1kb99024jih5bycc226bl4jyvbbl1sg72q3m2wnlshl7s8p6vva0"))))
2075 (properties `((upstream-name . "BatchJobs")))
2076 (build-system r-build-system)
2078 `(("r-bbmisc" ,r-bbmisc)
2080 ("r-checkmate" ,r-checkmate)
2082 ("r-digest" ,r-digest)
2084 ("r-rsqlite" ,r-rsqlite)
2085 ("r-sendmailr" ,r-sendmailr)
2086 ("r-stringr" ,r-stringr)))
2087 (home-page "https://github.com/tudo-r/BatchJobs")
2088 (synopsis "Batch computing with R")
2090 "This package provides @code{Map}, @code{Reduce} and @code{Filter}
2091 variants to generate jobs on batch computing systems like PBS/Torque, LSF,
2092 SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
2093 (license license:bsd-2)))
2095 (define-public r-brew
2101 (uri (cran-uri "brew" version))
2104 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
2105 (build-system r-build-system)
2106 (home-page "http://cran.r-project.org/web/packages/brew")
2107 (synopsis "Templating framework for report generation")
2109 "The brew package implements a templating framework for mixing text and R
2110 code for report generation. The template syntax is similar to PHP, Ruby's erb
2111 module, Java Server Pages, and Python's psp module.")
2112 (license license:gpl2+)))
2114 (define-public r-roxygen2
2120 (uri (cran-uri "roxygen2" version))
2123 "19gblyrrn29msbpawcb1hn5m1rshiqwxy0lby0vf92rm13fmsxcz"))))
2124 (build-system r-build-system)
2126 `(("r-brew" ,r-brew)
2127 ("r-digest" ,r-digest)
2129 ("r-stringi" ,r-stringi)
2130 ("r-stringr" ,r-stringr)))
2131 (home-page "https://github.com/klutometis/roxygen")
2132 (synopsis "In-source documentation system for R")
2134 "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
2135 collation, and NAMESPACE files.")
2136 (license license:gpl2+)))
2138 (define-public r-openssl
2145 (uri (cran-uri "openssl" version))
2148 "0ffwllii8xl6sa2v66134g0fwaw1y3zn3mvaa4nrc120vv5d3mkd"))))
2149 (build-system r-build-system)
2151 `(("openssl" ,openssl)))
2152 (home-page "https://github.com/jeroenooms/openssl")
2153 (synopsis "Toolkit for encryption, signatures and certificates")
2155 "This package provides R bindings to OpenSSL libssl and libcrypto, plus
2156 custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
2157 and P-521. Cryptographic signatures can either be created and verified
2158 manually or via x509 certificates. AES block cipher is used in CBC mode for
2159 symmetric encryption; RSA for asymmetric (public key) encryption. High-level
2160 envelope functions combine RSA and AES for encrypting arbitrary sized data.
2161 Other utilities include key generators, hash functions (md5, sha1, sha256,
2162 etc), base64 encoder, a secure random number generator, and @code{bignum} math
2163 methods for manually performing crypto calculations on large multibyte
2165 (license license:expat)))
2167 (define-public r-httr
2173 (uri (cran-uri "httr" version))
2176 "03kkjlhyvvi5znwaxfm6cmdsg3q7ivwsvkzgabhjdj2jxs80pfg7"))))
2177 (build-system r-build-system)
2179 `(("r-curl" ,r-curl)
2180 ("r-digest" ,r-digest)
2181 ("r-jsonlite" ,r-jsonlite)
2182 ("r-openssl" ,r-openssl)
2185 ("r-stringr" ,r-stringr)))
2186 (home-page "https://github.com/hadley/httr")
2187 (synopsis "Tools for working with URLs and HTTP")
2189 "The aim of httr is to provide a wrapper for RCurl customised to the
2190 demands of modern web APIs. It provides useful tools for working with HTTP
2191 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
2192 functions make it easy to control additional request components.")
2193 (license license:expat)))
2195 (define-public r-git2r
2201 (uri (cran-uri "git2r" version))
2204 "0bgzdsdi9n6l8pchivs6a2g4ksa56qs8hygpyv2c0ndqmx4jxcwi"))))
2205 (build-system r-build-system)
2206 ;; This R package contains modified sources of libgit2. This modified
2207 ;; version of libgit2 is built as the package is built. Hence libgit2 is
2208 ;; not among the inputs of this package.
2210 `(("libssh2" ,libssh2)
2211 ("openssl" ,openssl)
2213 (home-page "https://github.com/ropensci/git2r")
2214 (synopsis "Access Git repositories with R")
2216 "This package provides an R interface to the libgit2 library, which is a
2217 pure C implementation of the Git core methods.")
2218 ;; GPLv2 only with linking exception.
2219 (license license:gpl2)))
2221 (define-public r-rstudioapi
2223 (name "r-rstudioapi")
2227 (uri (cran-uri "rstudioapi" version))
2230 "1zkvz72z6nw0xc8bhb21y5x1nk6avijs0w8n4vsbvw9sn76wc96s"))))
2231 (build-system r-build-system)
2232 (home-page "http://cran.r-project.org/web/packages/rstudioapi")
2233 (synopsis "Safely access the RStudio API")
2235 "This package provides functions to access the RStudio API and provide
2236 informative error messages when it's not available.")
2237 (license license:expat)))
2239 (define-public r-devtools
2245 (uri (cran-uri "devtools" version))
2248 "16l18szmj482vf3dvl2fqwwa4zaqylmic1pk7dwh428cp0d86mzi"))))
2249 (build-system r-build-system)
2251 `(("r-curl" ,r-curl)
2252 ("r-digest" ,r-digest)
2253 ("r-evaluate" ,r-evaluate)
2254 ("r-git2r" ,r-git2r)
2256 ("r-jsonlite" ,r-jsonlite)
2257 ("r-memoise" ,r-memoise)
2258 ("r-roxygen2" ,r-roxygen2)
2259 ("r-rstudioapi" ,r-rstudioapi)
2260 ("r-rversions" ,r-rversions)
2261 ("r-whisker" ,r-whisker)
2262 ("r-withr" ,r-withr)))
2263 (home-page "https://github.com/hadley/devtools")
2264 (synopsis "Tools to make developing R packages easier")
2265 (description "The devtools package is a collection of package development
2266 tools to simplify the devolpment of R packages.")
2267 (license license:gpl2+)))
2269 (define-public r-withr
2275 (uri (cran-uri "withr" version))
2278 "042z8nmqqilgrvhmbqrjc05qys3gzwq1rqy2wxp2bi5d41859493"))))
2279 (build-system r-build-system)
2280 (home-page "https://github.com/jimhester/withr")
2281 (synopsis "Run code with temporarily modified global state")
2283 "This package provides a set of functions to run R code in an environment
2284 in which global state has been temporarily modified. Many of these functions
2285 were originally a part of the r-devtools package.")
2286 (license license:gpl2+)))
2288 (define-public r-hms
2295 (uri (cran-uri "hms" version))
2298 "127znf522r5mn3k6frhdd7pqh063bs3l85gn9h7cx50hpjf2as4k"))))
2299 (build-system r-build-system)
2300 (home-page "https://github.com/rstats-db/hms")
2301 (synopsis "Pretty time of day")
2303 "This package implements an S3 class for storing and formatting
2304 time-of-day values, based on the @code{difftime} class.")
2305 (license license:gpl3+)))
2307 (define-public r-readr
2313 (uri (cran-uri "readr" version))
2316 "0xji0dbal6xcxnsmjj678fw29n7wrj45wrd5ng99yhqqijcm9f6g"))))
2317 (build-system r-build-system)
2319 `(("r-curl" ,r-curl)
2322 ("r-tibble" ,r-tibble)
2325 (home-page "https://github.com/hadley/readr")
2326 (synopsis "Read tabular data")
2328 "This package provides functions to read flat or tabular text files from
2329 disk (or a connection).")
2330 (license license:gpl2+)))
2332 (define-public r-plotrix
2338 (uri (cran-uri "plotrix" version))
2341 "1wxzjnzvkl3aga51ad2xhv4s7v46kvnp4z0nz4cb9cn10057sfw8"))))
2342 (build-system r-build-system)
2343 (home-page "http://cran.r-project.org/web/packages/plotrix")
2344 (synopsis "Various plotting functions")
2346 "This package provides lots of plotting, various labeling, axis and color
2347 scaling functions for R.")
2348 (license license:gpl2+)))
2350 (define-public r-gridbase
2356 (uri (cran-uri "gridBase" version))
2359 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
2360 (build-system r-build-system)
2361 (home-page "http://cran.r-project.org/web/packages/gridBase")
2362 (synopsis "Integration of base and grid graphics")
2364 "This package provides an integration of base and grid graphics for R.")
2365 (license license:gpl2+)))
2367 (define-public r-latticeextra
2369 (name "r-latticeextra")
2374 (uri (cran-uri "latticeExtra" version))
2377 "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq"))))
2378 (properties `((upstream-name . "latticeExtra")))
2379 (build-system r-build-system)
2381 `(("r-lattice" ,r-lattice)
2382 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2383 (home-page "http://latticeextra.r-forge.r-project.org/")
2384 (synopsis "Extra graphical utilities based on lattice")
2386 "Building on the infrastructure provided by the lattice package, this
2387 package provides several new high-level graphics functions and methods, as
2388 well as additional utilities such as panel and axis annotation functions.")
2389 (license license:gpl2+)))
2391 (define-public r-rcpparmadillo
2393 (name "r-rcpparmadillo")
2394 (version "0.7.600.1.0")
2397 (uri (cran-uri "RcppArmadillo" version))
2400 "0k1wniip184j0ckcg9kcjy2q4mcfj5jpd1nkk4l0ab75ad8znywv"))
2401 (modules '((guix build utils)))
2402 ;; Remove bundled armadillo sources
2405 (delete-file-recursively "inst/include/armadillo_bits")
2406 (delete-file "inst/include/armadillo")))))
2407 (properties `((upstream-name . "RcppArmadillo")))
2408 (build-system r-build-system)
2411 (modify-phases %standard-phases
2412 (add-after 'unpack 'link-against-armadillo
2414 (substitute* "src/Makevars"
2415 (("PKG_LIBS=" prefix)
2416 (string-append prefix "-larmadillo"))))))))
2418 `(("r-rcpp" ,r-rcpp)
2419 ("armadillo" ,armadillo-for-rcpparmadillo)))
2420 (home-page "https://github.com/RcppCore/RcppArmadillo")
2421 (synopsis "Rcpp integration for the Armadillo linear algebra library")
2423 "Armadillo is a templated C++ linear algebra library that aims towards a
2424 good balance between speed and ease of use. Integer, floating point and
2425 complex numbers are supported, as well as a subset of trigonometric and
2426 statistics functions. Various matrix decompositions are provided through
2427 optional integration with LAPACK and ATLAS libraries. This package includes
2428 the header files from the templated Armadillo library.")
2429 ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
2430 ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
2431 ;; later, as is the rest of 'Rcpp'.
2432 (license license:gpl2+)))
2434 (define-public r-bitops
2440 (uri (cran-uri "bitops" version))
2443 "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
2444 (build-system r-build-system)
2445 (home-page "http://cran.r-project.org/web/packages/bitops")
2446 (synopsis "Bitwise operations")
2448 "This package provides functions for bitwise operations on integer
2450 (license license:gpl2+)))
2452 (define-public r-catools
2458 (uri (cran-uri "caTools" version))
2461 "1x4szsn2qmbzpyjfdaiz2q7jwhap2gky9wq0riah74q0pzz76ank"))))
2462 (properties `((upstream-name . "caTools")))
2463 (build-system r-build-system)
2465 `(("r-bitops" ,r-bitops)))
2466 (home-page "http://cran.r-project.org/web/packages/caTools")
2467 (synopsis "Various tools including functions for moving window statistics")
2469 "This package contains several basic utility functions including:
2470 moving (rolling, running) window statistic functions, read/write for GIF and
2471 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
2472 encoder/decoder, round-off-error-free sum and cumsum, etc.")
2473 (license license:gpl3+)))
2475 (define-public r-rprojroot
2477 (name "r-rprojroot")
2482 (uri (cran-uri "rprojroot" version))
2485 "04ywfpar4d2hyi4rh4fbixrbzd665gpa2jhx67g8857cr70pp0nh"))))
2486 (build-system r-build-system)
2488 `(("r-backports" ,r-backports)))
2489 (home-page "https://github.com/krlmlr/rprojroot")
2490 (synopsis "Finding files in project subdirectories")
2492 "This package helps accessing files relative to a project root. It
2493 provides helpers for robust, reliable and flexible paths to files below a
2494 project root. The root of a project is defined as a directory that matches a
2495 certain criterion, e.g., it contains a certain regular file.")
2496 (license license:gpl3)))
2498 (define-public r-rmarkdown
2500 (name "r-rmarkdown")
2505 (uri (cran-uri "rmarkdown" version))
2508 "1vvxyf3zhyxx6k697lia299456hryp8nh3zr0fc27f3107a8mcjf"))))
2509 (properties `((upstream-name . "rmarkdown")))
2510 (build-system r-build-system)
2512 `(("r-catools" ,r-catools)
2513 ("r-evaluate" ,r-evaluate)
2514 ("r-htmltools" ,r-htmltools)
2515 ("r-jsonlite" ,r-jsonlite)
2516 ("r-base64enc" ,r-base64enc)
2517 ("r-knitr" ,r-knitr)
2518 ("r-rprojroot" ,r-rprojroot)
2520 ("ghc-pandoc" ,ghc-pandoc)))
2521 (home-page "http://rmarkdown.rstudio.com")
2522 (synopsis "Convert R Markdown documents into a variety of formats")
2524 "This package provides tools to convert R Markdown documents into a
2525 variety of formats.")
2526 (license license:gpl3+)))
2528 (define-public r-gtable
2534 (uri (cran-uri "gtable" version))
2537 "0vz7073m0a2q12qzzihrfh5c2kx5jqi5l7z470fxmwqghdllh7l0"))))
2538 (properties `((upstream-name . "gtable")))
2539 (build-system r-build-system)
2540 (home-page "https://cran.r-project.org/web/packages/gtable")
2541 (synopsis "R library to arrange grobs in tables")
2543 "Gtable is a collection of tools to make it easier to work with
2544 \"tables\" of grobs.")
2545 (license license:gpl2+)))
2547 (define-public r-gridextra
2549 (name "r-gridextra")
2553 (uri (cran-uri "gridExtra" version))
2556 "0638ihwl00j76ivaxxhxvi8z573lwy1jym3srr78mx6dbdd4bzj4"))))
2557 (properties `((upstream-name . "gridExtra")))
2558 (build-system r-build-system)
2560 `(("r-gtable" ,r-gtable)))
2562 `(("r-knitr" ,r-knitr))) ;for building vignettes
2563 (home-page "https://github.com/baptiste/gridextra")
2564 (synopsis "Miscellaneous functions for \"Grid\" graphics")
2566 "This package provides a number of user-level functions to work with
2567 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
2569 (license license:gpl2+)))
2571 (define-public r-plogr
2578 (uri (cran-uri "plogr" version))
2581 "13zliqlbkl8b04k9ga0sx5jsh7k867gracgl84l2a9kcqy9mqx92"))))
2582 (build-system r-build-system)
2583 (home-page "https://github.com/krlmlr/plogr")
2584 (synopsis "R bindings for the plog C++ logging library")
2586 "This package provides the header files for a stripped-down version of
2587 the plog header-only C++ logging library, and a method to log to R's standard
2589 (license license:expat)))
2591 (define-public r-rsqlite
2597 (uri (cran-uri "RSQLite" version))
2600 "11vnzds5gidgakdmsbdn0bvnsz064ym1savwb7l6gc1bjn7xa2k4"))))
2601 (properties `((upstream-name . "RSQLite")))
2602 (build-system r-build-system)
2606 ("r-memoise" ,r-memoise)
2607 ("r-plogr" ,r-plogr)
2608 ("r-rcpp" ,r-rcpp)))
2609 (home-page "https://github.com/rstats-db/RSQLite")
2610 (synopsis "SQLite interface for R")
2612 "This package embeds the SQLite database engine in R and provides an
2613 interface compliant with the DBI package. The source for the SQLite
2614 engine (version 3.8.6) is included.")
2615 (license license:lgpl2.0+)))
2617 (define-public r-rcurl
2620 (version "1.95-0.1.2")
2623 (uri (string-append "http://www.bioconductor.org/packages/"
2624 "release/extra/src/"
2625 "contrib/RCurl_" version ".tar.gz"))
2628 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
2629 (properties `((upstream-name . "RCurl")))
2630 (build-system r-build-system)
2632 `(("libcurl" ,curl)))
2634 `(("r-bitops" ,r-bitops)))
2635 (home-page "http://www.omegahat.org/RCurl")
2636 (synopsis "General network client interface for R")
2638 "The package allows one to compose general HTTP requests and provides
2639 convenient functions to fetch URIs, GET and POST forms, etc. and process the
2640 results returned by the Web server. This provides a great deal of control
2641 over the HTTP/FTP/... connection and the form of the request while providing a
2642 higher-level interface than is available just using R socket connections.
2643 Additionally, the underlying implementation is robust and extensive,
2644 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
2645 ldap, and also supports cookies, redirects, authentication, etc.")
2646 (license license:bsd-3)))
2648 (define-public r-xml
2651 (version "3.98-1.5")
2654 (uri (cran-uri "XML" version))
2657 "0dcdj7ryn8lm7wmv4hqhh9jxa5k97l6ad8xyvb932yfkwj1g1byy"))))
2659 `((upstream-name . "XML")))
2660 (build-system r-build-system)
2662 `(("libxml2" ,libxml2)))
2663 (home-page "http://www.omegahat.org/RSXML")
2664 (synopsis "Tools for parsing and generating XML within R")
2666 "Many approaches for both reading and creating XML (and HTML)
2667 documents (including DTDs), both local and accessible via HTTP or FTP. Also
2668 offers access to an XPath \"interpreter\".")
2669 (license license:bsd-2)))
2671 (define-public r-xnomial
2676 (origin (method url-fetch)
2677 (uri (cran-uri "XNomial" version))
2680 "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
2681 (properties (quasiquote ((upstream-name . "XNomial"))))
2682 (build-system r-build-system)
2683 (home-page "http://cran.r-project.org/web/packages/XNomial")
2684 (synopsis "Goodness-of-Fit test for multinomial data")
2686 "This package provides an exact Goodness-of-Fit test for
2687 multinomial data with fixed probabilities. It can be used to
2688 determine whether a set of counts fits a given expected ratio. To see
2689 whether a set of observed counts fits an expectation, one can examine
2690 all possible outcomes with @code{xmulti()} or a random sample of them
2691 with @code{xmonte()} and find the probability of an observation
2692 deviating from the expectation by at least as much as the observed.
2693 As a measure of deviation from the expected, one can use the
2694 log-likelihood ratio, the multinomial probability, or the classic
2695 chi-square statistic. A histogram of the test statistic can also be
2696 plotted and compared with the asymptotic curve.")
2697 (license (list license:gpl2+ license:gpl3+))))
2699 (define-public r-lambda-r
2705 (uri (cran-uri "lambda.r" version))
2708 "1j6287iqvs3ill6r5g6ksf5809qp0l0nf20ib8266m1r09lc9j14"))))
2709 (properties `((upstream-name . "lambda.r")))
2710 (build-system r-build-system)
2711 (home-page "http://cran.r-project.org/web/packages/lambda.r")
2712 (synopsis "Functional programming extension for R")
2714 "This package provides a language extension to efficiently write
2715 functional programs in R. Syntax extensions include multi-part function
2716 definitions, pattern matching, guard statements, built-in (optional) type
2718 (license license:lgpl3+)))
2720 (define-public r-futile-options
2722 (name "r-futile-options")
2726 (uri (cran-uri "futile.options" version))
2729 "1hp82h6xqq5cck67h7lpf22n3j7mg3v1mla5y5ivnzrrb7iyr17f"))))
2731 `((upstream-name . "futile.options")))
2732 (build-system r-build-system)
2733 (home-page "http://cran.r-project.org/web/packages/futile.options")
2734 (synopsis "Options management framework")
2736 "The futile.options subsystem provides an easy user-defined options
2737 management system that is properly scoped. This means that options created
2738 via @code{futile.options} are fully self-contained and will not collide with
2739 options defined in other packages.")
2740 (license license:lgpl3+)))
2742 (define-public r-futile-logger
2744 (name "r-futile-logger")
2748 (uri (cran-uri "futile.logger" version))
2751 "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
2752 (properties `((upstream-name . "futile.logger")))
2753 (build-system r-build-system)
2755 `(("r-futile-options" ,r-futile-options)
2756 ("r-lambda-r" ,r-lambda-r)))
2757 (home-page "http://cran.r-project.org/web/packages/futile.logger")
2758 (synopsis "Logging utility for R")
2760 "This package provides a simple yet powerful logging utility. Based
2761 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
2762 convenient and easy to use replacement for @code{cat} and @code{print}
2764 (license license:lgpl3+)))
2766 (define-public r-segmented
2768 (name "r-segmented")
2773 (uri (cran-uri "segmented" version))
2776 "1740cvx2q4v23g4q0zkvg50s5bv8jcrlzzhm7fac4xn0riwmzp5i"))))
2777 (build-system r-build-system)
2778 (home-page "http://cran.r-project.org/web/packages/segmented")
2779 (synopsis "Regression models with breakpoints estimation")
2781 "Given a regression model, segmented updates the model by adding one or
2782 more segmented (i.e., piecewise-linear) relationships. Several variables with
2783 multiple breakpoints are allowed.")
2784 (license (list license:gpl2+ license:gpl3+))))
2786 (define-public r-snow
2792 (uri (cran-uri "snow" version))
2795 "1mxbrkpnmq32x4wd0194d541661yvfrrjlr3lsf7qq53ms3h21zf"))))
2796 (build-system r-build-system)
2797 (home-page "http://cran.r-project.org/web/packages/snow")
2798 (synopsis "Support for simple parallel computing in R")
2800 "The snow package provides support for simple parallel computing on a
2801 network of workstations using R. A master R process calls @code{makeCluster}
2802 to start a cluster of worker processes; the master process then uses functions
2803 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
2804 worker processes and collect and return the results on the master.")
2805 (license (list license:gpl2+ license:gpl3+))))
2807 (define-public r-sparsem
2813 (uri (cran-uri "SparseM" version))
2816 "1fpfhld887y5lyb8jydprmv5krqm1fk6n53z942b4g4z1v4g04j7"))))
2818 `((upstream-name . "SparseM")))
2820 `(("gfortran" ,gfortran)))
2821 (build-system r-build-system)
2822 (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
2823 (synopsis "Sparse linear algebra")
2825 "This package provides some basic linear algebra functionality for sparse
2826 matrices. It includes Cholesky decomposition and backsolving as well as
2827 standard R subsetting and Kronecker products.")
2828 (license license:gpl2+)))
2830 (define-public r-iterators
2832 (name "r-iterators")
2837 (uri (cran-uri "iterators" version))
2840 "1f057pabs7ss9h1n244can26qsi5n2k3salrdk0b0vkphlrs4kmf"))))
2841 (build-system r-build-system)
2842 (home-page "http://cran.r-project.org/web/packages/iterators")
2843 (synopsis "Iterator construct for R")
2845 "This package provides support for iterators, which allow a programmer to
2846 traverse through all the elements of a vector, list, or other collection of
2848 (license license:asl2.0)))
2850 (define-public r-codetools
2852 (name "r-codetools")
2857 (uri (cran-uri "codetools" version))
2860 "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf"))))
2861 (build-system r-build-system)
2862 (home-page "https://cran.r-project.org/web/packages/codetools")
2863 (synopsis "Code analysis tools for R")
2864 (description "This package provides code analysis tools for R to check R
2865 code for possible problems.")
2866 (license (list license:gpl2+ license:gpl3+))))
2868 (define-public r-foreach
2875 (uri (cran-uri "foreach" version))
2878 "10aqsd3rxz03s1qdb6gsb1cj89mj4vmh491zfpin4skj1xvkzw0y"))))
2879 (build-system r-build-system)
2881 `(("r-codetools" ,r-codetools)
2882 ("r-iterators" ,r-iterators)))
2883 (home-page "http://cran.r-project.org/web/packages/foreach")
2884 (synopsis "Foreach looping construct for R")
2886 "This package provides support for the @code{foreach} looping construct.
2887 @code{foreach} is an idiom that allows for iterating over elements in a
2888 collection, without the use of an explicit loop counter. This package in
2889 particular is intended to be used for its return value, rather than for its
2890 side effects. In that sense, it is similar to the standard @code{lapply}
2891 function, but doesn't require the evaluation of a function. Using
2892 @code{foreach} without side effects also facilitates executing the loop in
2894 (license license:asl2.0)))
2896 (define-public r-doparallel
2898 (name "r-doparallel")
2903 (uri (cran-uri "doParallel" version))
2906 "1mddx25l25pw9d0csnx2q203dbg5hbrhkr1f08kw0p02a1lln0kh"))))
2907 (properties `((upstream-name . "doParallel")))
2908 (build-system r-build-system)
2910 `(("r-foreach" ,r-foreach)
2911 ("r-iterators" ,r-iterators)))
2912 (home-page "http://cran.r-project.org/web/packages/doParallel")
2913 (synopsis "Foreach parallel adaptor for the 'parallel' package")
2915 "This package provides a parallel backend for the @code{%dopar%} function
2916 using the parallel package.")
2917 (license license:gpl2+)))
2919 (define-public r-domc
2926 (uri (cran-uri "doMC" version))
2929 "0y47jl6g4f83r14pj8bafdzq1phj7bxy5dwyz3k43d2rr8phk8bn"))))
2930 (properties `((upstream-name . "doMC")))
2931 (build-system r-build-system)
2933 `(("r-foreach" ,r-foreach)
2934 ("r-iterators" ,r-iterators)))
2935 (home-page "http://cran.r-project.org/web/packages/doMC")
2936 (synopsis "Foreach parallel adaptor for the 'parallel' package")
2938 "This package provides a parallel backend for the @code{%dopar%} function
2939 using the multicore functionality of the parallel package.")
2940 (license license:gpl2+)))
2948 (uri (cran-uri "DT" version))
2951 "1g86p0jcjqi2ph5rhm45jkzibsa6yfcj8n5cg3giy90sqgjzkdx1"))))
2953 `((upstream-name . "DT")))
2954 (build-system r-build-system)
2956 `(("r-htmltools" ,r-htmltools)
2957 ("r-htmlwidgets" ,r-htmlwidgets)
2958 ("r-magrittr" ,r-magrittr)))
2959 (home-page "http://rstudio.github.io/DT")
2960 (synopsis "R wrapper of the DataTables JavaScript library")
2962 "This package allows for data objects in R to be rendered as HTML tables
2963 using the JavaScript library 'DataTables' (typically via R Markdown or Shiny).
2964 The 'DataTables' library has been included in this R package.")
2965 ;; The DT package as a whole is distributed under GPLv3. The DT package
2966 ;; inludes other software components under different licenses:
2968 ;; * Expat: jQuery, jquery.highlight.js, DataTables
2969 ;; * ASL2.0: selectize.js
2970 ;; * WTFPL: noUiSlider
2971 (license (list license:gpl3
2974 (license:non-copyleft "http://www.wtfpl.net/txt/copying/")))))
2976 (define-public r-base64enc
2978 (name "r-base64enc")
2982 (uri (cran-uri "base64enc" version))
2985 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
2986 (build-system r-build-system)
2987 (home-page "http://www.rforge.net/base64enc")
2988 (synopsis "Tools for Base64 encoding")
2990 "This package provides tools for handling Base64 encoding. It is more
2991 flexible than the orphaned \"base64\" package.")
2992 (license license:gpl2+)))
2994 (define-public r-irlba
3001 (uri (cran-uri "irlba" version))
3004 "1qbcn0ix85pmk296jhpi419kvh06vxm5cq24yk013ps3g7fyi0si"))))
3005 (build-system r-build-system)
3007 `(("r-matrix" ,r-matrix)))
3008 (home-page "http://cran.r-project.org/web/packages/irlba")
3009 (synopsis "Methods for eigendecomposition of large matrices")
3011 "This package provides fast and memory efficient methods for truncated
3012 singular and eigenvalue decompositions, as well as for principal component
3013 analysis of large sparse or dense matrices.")
3014 (license (list license:gpl2+ license:gpl3+))))
3016 (define-public r-glmnet
3023 (uri (cran-uri "glmnet" version))
3026 "1cbpzmbv837fvq88rgn6mgzgr9f1wqp9fg8gh2kkmngvr1957a9c"))))
3027 (build-system r-build-system)
3029 `(("gfortran" ,gfortran)))
3031 `(("r-foreach" ,r-foreach)
3032 ("r-matrix" ,r-matrix)))
3033 (home-page "http://www.jstatsoft.org/v33/i01")
3034 (synopsis "Lasso and elastic-net regularized generalized linear models")
3036 "The glmnet package provides efficient procedures for fitting the entire
3037 lasso or elastic-net regularization path for linear and Poisson regression, as
3038 well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
3039 multinomial models. The algorithm uses cyclical coordinate descent in a
3040 path-wise fashion.")
3041 (license license:gpl2+)))
3043 (define-public r-pkgmaker
3050 (uri (cran-uri "pkgmaker" version))
3053 "0vrqnd3kg6liqvpbd969jjsdx0f0rvmmxgdbwwrp6xfmdg0pib8r"))))
3054 (build-system r-build-system)
3056 `(("r-codetools" ,r-codetools)
3057 ("r-digest" ,r-digest)
3058 ("r-registry" ,r-registry)
3059 ("r-stringr" ,r-stringr)
3060 ("r-xtable" ,r-xtable)))
3061 (home-page "https://renozao.github.io/pkgmaker")
3062 (synopsis "Package development utilities")
3064 "This package provides some low-level utilities to use for R package
3065 development. It currently provides managers for multiple package specific
3066 options and registries, vignette, unit test and bibtex related utilities.")
3067 (license license:gpl2+)))
3069 (define-public r-registry
3076 (uri (cran-uri "registry" version))
3079 "0c7lscfxncwwd8zp46h2xfw9gw14dypqv6m2kx85xjhjh0xw99aq"))))
3080 (build-system r-build-system)
3081 (home-page "http://cran.r-project.org/web/packages/registry")
3082 (synopsis "Infrastructure for R package registries")
3084 "This package provides a generic infrastructure for creating and using R
3085 package registries.")
3086 (license license:gpl2+)))
3088 (define-public r-rngtools
3095 (uri (cran-uri "rngtools" version))
3098 "1fcgfqrrb48z37xgy8sffx91p9irp39yqzxv7nqp1x2hnwsrh097"))))
3099 (build-system r-build-system)
3101 `(("r-digest" ,r-digest)
3102 ("r-pkgmaker" ,r-pkgmaker)
3103 ("r-stringr" ,r-stringr)))
3104 (home-page "https://renozao.github.io/rngtools")
3105 (synopsis "Utility functions for working with random number generators")
3107 "This package contains a set of functions for working with Random Number
3108 Generators (RNGs). In particular, it defines a generic S4 framework for
3109 getting/setting the current RNG, or RNG data that are embedded into objects
3110 for reproducibility. Notably, convenient default methods greatly facilitate
3111 the way current RNG settings can be changed.")
3112 (license license:gpl3+)))
3114 (define-public r-rtsne
3121 (uri (cran-uri "Rtsne" version))
3124 "0zi4nxgpiv1gpdmcnqdhz5kymzp8m5xj02zpf290p1yyydl76bhy"))))
3125 (properties `((upstream-name . "Rtsne")))
3126 (build-system r-build-system)
3128 `(("r-rcpp" ,r-rcpp)))
3129 (home-page "https://github.com/jkrijthe/Rtsne")
3130 (synopsis "T-distributed stochastic neighbor embedding")
3132 "This package provides an R wrapper around the fast T-distributed
3133 Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
3134 ;; The declared license for this package is BSD-3, but it also includes
3135 ;; code licensed under BSD-4.
3136 (license (list license:bsd-3 license:bsd-4))))
3138 (define-public r-e1071
3145 (uri (cran-uri "e1071" version))
3148 "1069qwj9gsjq6par2cgfah8nn5x2w38830761x1f7mqpmk0gnj3h"))))
3149 (build-system r-build-system)
3151 `(("r-class" ,r-class)))
3152 (home-page "http://cran.r-project.org/web/packages/e1071")
3153 (synopsis "Miscellaneous functions for probability theory")
3155 "This package provides functions for latent class analysis, short time
3156 Fourier transform, fuzzy clustering, support vector machines, shortest path
3157 computation, bagged clustering, naive Bayes classifier, and more.")
3158 (license license:gpl2+)))
3160 (define-public r-bigmemory-sri
3162 (name "r-bigmemory-sri")
3167 (uri (cran-uri "bigmemory.sri" version))
3169 (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
3171 `((upstream-name . "bigmemory.sri")))
3172 (build-system r-build-system)
3173 (home-page "http://cran.r-project.org/web/packages/bigmemory.sri")
3174 (synopsis "Shared resource interface for the bigmemory package")
3175 (description "This package provides a shared resource interface for the
3176 bigmemory and synchronicity packages.")
3177 ;; Users can choose either LGPLv3 or ASL2.0.
3178 (license (list license:lgpl3 license:asl2.0))))
3180 (define-public r-synchronicity
3182 (name "r-synchronicity")
3187 (uri (cran-uri "synchronicity" version))
3190 "0d9skpwmsnkn4xb3f2kgyyv8bhdi0r9p1kj3cvi0s92fjjnpi00c"))))
3191 (build-system r-build-system)
3194 ("r-bigmemory-sri" ,r-bigmemory-sri)
3195 ("r-rcpp" ,r-rcpp)))
3196 (home-page "http://www.bigmemory.org")
3197 (synopsis "Boost mutex functionality in R")
3198 (description "This package provides support for synchronization
3199 via mutexes and may eventually support interprocess communication and
3201 ;; Users can choose either LGPLv3 or ASL2.0.
3202 (license (list license:lgpl3 license:asl2.0))))
3204 (define-public r-bigmemory
3206 (name "r-bigmemory")
3211 (uri (cran-uri "bigmemory" version))
3214 "191gbzca557kpk7mdsg716vfyqpr7j5din6qb8hin4g1nkzzwmg6"))))
3215 (build-system r-build-system)
3219 ("r-bigmemory-sri" ,r-bigmemory-sri)
3220 ("r-r-utils" ,r-r-utils)))
3221 (home-page "http://www.bigmemory.org")
3222 (synopsis "Manage large matrices with shared memory or memory-mapped files")
3223 (description "This package provides methods to create, store, access, and
3224 manipulate large matrices. Matrices are allocated to shared memory and may use
3225 memory-mapped files.")
3226 ;; Users can choose either LGPLv3 or ASL2.0.
3227 (license (list license:lgpl3 license:asl2.0))))
3229 (define-public r-nmf
3236 (uri (cran-uri "NMF" version))
3239 "0mmh9bz0zjwd8h9jplz4rq3g94npaqj8s4px51vcv47csssd9k6z"))))
3240 (properties `((upstream-name . "NMF")))
3241 (build-system r-build-system)
3243 `(("r-cluster" ,r-cluster)
3244 ("r-bigmemory" ,r-bigmemory)
3245 ("r-synchronicity" ,r-synchronicity)
3246 ("r-colorspace" ,r-colorspace)
3247 ("r-digest" ,r-digest)
3248 ("r-doparallel" ,r-doparallel)
3249 ("r-foreach" ,r-foreach)
3250 ("r-ggplot2" ,r-ggplot2)
3251 ("r-gridbase" ,r-gridbase)
3252 ("r-pkgmaker" ,r-pkgmaker)
3253 ("r-rcolorbrewer" ,r-rcolorbrewer)
3254 ("r-registry" ,r-registry)
3255 ("r-reshape2" ,r-reshape2)
3256 ("r-rngtools" ,r-rngtools)
3257 ("r-stringr" ,r-stringr)))
3258 (home-page "http://renozao.github.io/NMF")
3259 (synopsis "Algorithms and framework for nonnegative matrix factorization")
3261 "This package provides a framework to perform Non-negative Matrix
3262 Factorization (NMF). The package implements a set of already published
3263 algorithms and seeding methods, and provides a framework to test, develop and
3264 plug new or custom algorithms. Most of the built-in algorithms have been
3265 optimized in C++, and the main interface function provides an easy way of
3266 performing parallel computations on multicore machines.")
3267 (license license:gpl2+)))
3269 (define-public r-igraph
3276 (uri (cran-uri "igraph" version))
3279 "00jnm8v3kvxpxav5klld2z2nnkcpj4sdwv4ksipddy5mp04ysr6w"))))
3280 (build-system r-build-system)
3282 `(("gfortran" ,gfortran)))
3285 ("libxml2" ,libxml2)))
3287 `(("r-irlba" ,r-irlba)
3288 ("r-magrittr" ,r-magrittr)
3290 (home-page "http://igraph.org")
3291 (synopsis "Network analysis and visualization")
3293 "This package provides routines for simple graphs and network analysis.
3294 It can handle large graphs very well and provides functions for generating
3295 random and regular graphs, graph visualization, centrality methods and much
3297 (license license:gpl2+)))
3299 (define-public r-r-methodss3
3301 (name "r-r-methodss3")
3305 (uri (cran-uri "R.methodsS3" version))
3308 "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24"))))
3309 (properties `((upstream-name . "R.methodsS3")))
3310 (build-system r-build-system)
3311 (home-page "http://cran.r-project.org/web/packages/R.methodsS3")
3312 (synopsis "S3 methods simplified")
3314 "This package provides methods that simplify the setup of S3 generic
3315 functions and S3 methods. Major effort has been made in making definition of
3316 methods as simple as possible with a minimum of maintenance for package
3317 developers. For example, generic functions are created automatically, if
3318 missing, and naming conflict are automatically solved, if possible. The
3319 method @code{setMethodS3()} is a good start for those who in the future may
3320 want to migrate to S4.")
3321 (license license:lgpl2.1+)))
3323 (define-public r-r-oo
3329 (uri (cran-uri "R.oo" version))
3332 "0723gxjazgqq7v3lwnl7axw3brzcnizvhbd71ijkkv8mz31fwp34"))))
3333 (properties `((upstream-name . "R.oo")))
3334 (build-system r-build-system)
3336 `(("r-r-methodss3" ,r-r-methodss3)))
3337 (home-page "https://github.com/HenrikBengtsson/R.oo")
3338 (synopsis "R object-oriented programming with or without references")
3340 "This package provides methods and classes for object-oriented
3341 programming in R with or without references. Large effort has been made on
3342 making definition of methods as simple as possible with a minimum of
3343 maintenance for package developers.")
3344 (license license:lgpl2.1+)))
3346 (define-public r-r-utils
3352 (uri (cran-uri "R.utils" version))
3355 "17q3w5dlly5xl2srrzsmf9s7vs5d576vqbcs6sr2p5x4qvqa1q8s"))))
3356 (properties `((upstream-name . "R.utils")))
3357 (build-system r-build-system)
3359 `(("r-r-methodss3" ,r-r-methodss3)
3360 ("r-r-oo" ,r-r-oo)))
3361 (home-page "https://github.com/HenrikBengtsson/R.utils")
3362 (synopsis "Various programming utilities")
3364 "This package provides utility functions useful when programming and
3365 developing R packages.")
3366 (license license:lgpl2.1+)))
3368 (define-public r-r-cache
3374 (uri (cran-uri "R.cache" version))
3377 "006x52w9r8phw5hgqmyp0bz8z42vn8p5yibibnzi1sfa1xlw8iyx"))))
3378 (properties `((upstream-name . "R.cache")))
3379 (build-system r-build-system)
3381 `(("r-digest" ,r-digest)
3382 ("r-r-methodss3" ,r-r-methodss3)
3384 ("r-r-utils" ,r-r-utils)))
3385 (home-page "https://github.com/HenrikBengtsson/R.cache")
3386 (synopsis "Light-weight caching of objects and results")
3388 "This package provides methods for caching or memoization of objects and
3389 results. With this package, any R object can be cached in a key-value storage
3390 where the key can be an arbitrary set of R objects. The cache memory is
3391 persistent (on the file system).")
3392 (license license:lgpl2.1+)))
3394 (define-public r-r-rsp
3400 (uri (cran-uri "R.rsp" version))
3403 "1hz5fnxz30m3cc7x7ha1swx4pn8c2244z6ka6v9m3l5lpdgc1367"))))
3404 (properties `((upstream-name . "R.rsp")))
3405 (build-system r-build-system)
3407 `(("r-r-cache" ,r-r-cache)
3408 ("r-r-methodss3" ,r-r-methodss3)
3410 ("r-r-utils" ,r-r-utils)))
3411 (home-page "https://github.com/HenrikBengtsson/R.rsp")
3412 (synopsis "Dynamic generation of scientific reports")
3414 "The RSP markup language provides a powerful markup for controlling the
3415 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
3416 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
3417 to many other literate programming languages, with RSP it is straightforward
3418 to loop over mixtures of code and text sections, e.g. in month-by-month
3419 summaries. RSP has also several preprocessing directives for incorporating
3420 static and dynamic contents of external files (local or online) among other
3421 things. RSP is ideal for self-contained scientific reports and R package
3423 (license license:lgpl2.1+)))
3425 (define-public r-mvtnorm
3431 (uri (cran-uri "mvtnorm" version))
3434 "1pc1mi2h063gh4a40009xk5j6pf5bm4274i5kycln38dixsry3yh"))))
3435 (build-system r-build-system)
3437 `(("gfortran" ,gfortran)))
3438 (home-page "http://mvtnorm.R-forge.R-project.org")
3439 (synopsis "Package for multivariate normal and t-distributions")
3440 (description "This package can compute multivariate normal and
3441 t-probabilities, quantiles, random deviates and densities.")
3442 (license license:gpl2)))
3444 (define-public r-matrixstats
3446 (name "r-matrixstats")
3450 (uri (cran-uri "matrixStats" version))
3453 "0bsalx605kgb9nl7mfnq1qinkyd9s97p8plymsyfja1gmcnjrcpj"))))
3454 (properties `((upstream-name . "matrixStats")))
3455 (build-system r-build-system)
3457 `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
3458 (home-page "https://github.com/HenrikBengtsson/matrixStats")
3459 (synopsis "Methods applying to vectors and matrix rows and columns")
3461 "This package provides methods operating on rows and columns of matrices,
3462 e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
3463 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
3464 @code{weightedMedians()}. All methods have been optimized for speed and
3466 (license license:artistic2.0)))
3468 (define-public r-viridis
3474 (uri (cran-uri "viridis" version))
3477 "1a9hqn2pccpc51vh8ghw698ni6xzdnp8v0n8kgjh51nlz5hhc87j"))))
3478 (build-system r-build-system)
3480 `(("r-ggplot2" ,r-ggplot2)
3481 ("r-gridextra" ,r-gridextra)))
3482 (home-page "https://github.com/sjmgarnier/viridis")
3483 (synopsis "Matplotlib default color map")
3485 "This package is a port of the new @url{matplotlib,
3486 http://matplotlib.org/} color maps (@code{viridis}--the default--,
3487 @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
3488 designed in such a way that they will analytically be perfectly
3489 perceptually-uniform, both in regular form and also when converted to
3490 black-and-white. They are also designed to be perceived by readers with the
3491 most common form of color blindness.")
3492 (license license:x11)))
3494 (define-public r-viridislite
3496 (name "r-viridislite")
3501 (uri (cran-uri "viridisLite" version))
3504 "1b0fhj8i1m9jsz91gzag60k7vy7kk5xkdg31rc3h3spq96l66psp"))))
3505 (properties `((upstream-name . "viridisLite")))
3506 (build-system r-build-system)
3507 (home-page "https://github.com/sjmgarnier/viridisLite")
3508 (synopsis "Default color maps from matplotlib")
3510 "This package is a port of the new @code{matplotlib} color maps ('viridis',
3511 'magma', 'plasma' and 'inferno') to R. matplotlib is a popular plotting
3512 library for Python. These color maps are designed in such a way that they
3513 will analytically be perfectly perceptually-uniform, both in regular form and
3514 also when converted to black-and-white. They are also designed to be
3515 perceived by readers with the most common form of color blindness. This is
3516 the 'lite' version of the more complete @code{viridis} package.")
3517 (license license:expat)))
3519 (define-public r-tidyr
3526 (uri (cran-uri "tidyr" version))
3529 "1bpwbphgl43ym433b0nrshwhr7pprmj1wkpkamdzix1zvf9dcbc2"))))
3530 (build-system r-build-system)
3532 `(("r-dplyr" ,r-dplyr)
3533 ("r-lazyeval" ,r-lazyeval)
3534 ("r-magrittr" ,r-magrittr)
3536 ("r-stringi" ,r-stringi)))
3537 (home-page "https://github.com/hadley/tidyr")
3538 (synopsis "Tidy data with `spread()` and `gather()` functions")
3540 "tidyr is a reframing of the reshape2 package designed to accompany the
3541 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
3542 a solid pipeline for data analysis. It is designed specifically for tidying
3543 data, not the general reshaping that reshape2 does, or the general aggregation
3544 that reshape did. In particular, built-in methods only work for data frames,
3545 and tidyr provides no margins or aggregation.")
3546 (license license:expat)))
3548 (define-public r-hexbin
3551 ;; The package tarball was updated in place, resulting in a change in the
3552 ;; hash value. We decided to bump the version to 1.27.1-1 instead of
3553 ;; keeping the version at upstream's 1.27.1.
3554 (version "1.27.1-1")
3558 (uri (cran-uri "hexbin" "1.27.1"))
3561 "025d609z1nyy684hwvp34b9mjzkgvild7fvfr95f941dmsikan87"))))
3562 (build-system r-build-system)
3564 `(("r-lattice" ,r-lattice)))
3566 `(("gfortran" ,gfortran)))
3567 (home-page "http://github.com/edzer/hexbin")
3568 (synopsis "Hexagonal binning routines")
3570 "This package provides binning and plotting functions for hexagonal bins.
3571 It uses and relies on grid graphics and formal (S4) classes and methods.")
3572 (license license:gpl2+)))
3574 (define-public r-purrr
3581 (uri (cran-uri "purrr" version))
3584 "0lss8q733nv7s154wargm6vnxq55qygnxakib8xdj4jv0y86sxc3"))))
3585 (build-system r-build-system)
3588 ("r-dplyr" ,r-dplyr)
3589 ("r-lazyeval" ,r-lazyeval)
3590 ("r-magrittr" ,r-magrittr)
3591 ("r-rcpp" ,r-rcpp)))
3592 (home-page "https://github.com/hadley/purrr")
3593 (synopsis "Functional programming tools")
3595 "This package completes R's functional programming tools with missing
3596 features present in other programming languages.")
3597 (license license:gpl3+)))
3599 (define-public r-plotly
3605 (uri (cran-uri "plotly" version))
3608 "09yw977yxlcxv57kni3q899zrxyxa6pznr06cylr9lqkyr7llfhx"))))
3609 (build-system r-build-system)
3611 `(("r-base64enc" ,r-base64enc)
3612 ("r-digest" ,r-digest)
3613 ("r-dplyr" ,r-dplyr)
3614 ("r-ggplot2" ,r-ggplot2)
3615 ("r-hexbin" ,r-hexbin)
3616 ("r-htmlwidgets" ,r-htmlwidgets)
3618 ("r-jsonlite" ,r-jsonlite)
3619 ("r-lazyeval" ,r-lazyeval)
3620 ("r-magrittr" ,r-magrittr)
3621 ("r-purrr" ,r-purrr)
3622 ("r-scales" ,r-scales)
3623 ("r-tibble" ,r-tibble)
3624 ("r-tidyr" ,r-tidyr)
3625 ("r-viridislite" ,r-viridislite)))
3626 (home-page "https://plot.ly/r")
3627 (synopsis "Create interactive web graphics")
3629 "This package enables the translation of ggplot2 graphs to an interactive
3630 web-based version and/or the creation of custom web-based visualizations
3631 directly from R. Once uploaded to a plotly account, plotly graphs (and the
3632 data behind them) can be viewed and modified in a web browser.")
3633 (license license:x11)))
3635 (define-public r-biased-urn
3637 (name "r-biased-urn")
3642 (uri (cran-uri "BiasedUrn" version))
3645 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
3646 (properties `((upstream-name . "BiasedUrn")))
3647 (build-system r-build-system)
3648 (home-page "http://www.agner.org/random/")
3649 (synopsis "Biased urn model distributions")
3651 "This package provides statistical models of biased sampling in the form
3652 of univariate and multivariate noncentral hypergeometric distributions,
3653 including Wallenius' noncentral hypergeometric distribution and Fisher's
3654 noncentral hypergeometric distribution (also called extended hypergeometric
3656 (license license:gpl3+)))
3658 (define-public r-rematch
3665 (uri (cran-uri "rematch" version))
3668 "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4"))))
3669 (build-system r-build-system)
3670 (home-page "https://github.com/MangoTheCat/rematch")
3671 (synopsis "Match regular expressions with a nicer API")
3673 "This package provides a small wrapper on @code{regexpr} to extract the
3674 matches and captured groups from the match of a regular expression to a
3676 (license license:expat)))
3678 (define-public r-cellranger
3680 (name "r-cellranger")
3685 (uri (cran-uri "cellranger" version))
3688 "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x"))))
3689 (build-system r-build-system)
3691 `(("r-rematch" ,r-rematch)
3692 ("r-tibble" ,r-tibble)))
3693 (home-page "https://github.com/rsheets/cellranger")
3694 (synopsis "Translate spreadsheet cell ranges to rows and columns")
3696 "This package provides helper functions to work with spreadsheets and the
3697 @code{A1:D10} style of cell range specification.")
3698 (license license:expat)))
3700 (define-public r-googlesheets
3702 (name "r-googlesheets")
3707 (uri (cran-uri "googlesheets" version))
3710 "0ps13h1cv7fj5dh8s4nvwi64wnnyqdsadcaa4iizq1c5s615cwk3"))))
3711 (build-system r-build-system)
3713 `(("r-cellranger" ,r-cellranger)
3714 ("r-dplyr" ,r-dplyr)
3716 ("r-jsonlite" ,r-jsonlite)
3717 ("r-purrr" ,r-purrr)
3718 ("r-readr" ,r-readr)
3719 ("r-stringr" ,r-stringr)
3720 ("r-tidyr" ,r-tidyr)
3721 ("r-xml2" ,r-xml2)))
3722 (home-page "https://github.com/jennybc/googlesheets")
3723 (synopsis "Manage Google spreadsheets from R")
3724 (description "This package provides tools to interact with Google Sheets
3726 (license license:expat)))
3728 (define-public r-spams
3731 (version "2.5-svn2014-07-04")
3735 (uri (string-append "https://gforge.inria.fr/frs/download.php/33815/"
3736 "spams-R-v" version ".tar.gz"))
3739 "1k459jg9a334slkw31w63l4d39xszjzsng7dv5j1mp78zifz7hvx"))))
3740 (build-system r-build-system)
3743 (modify-phases %standard-phases
3744 (add-after 'unpack 'chdir
3745 (lambda _ (chdir "spams") #t))
3746 ;; Since R 3.3.0 including R headers inside of an extern "C" block
3747 ;; causes C headers to be included, which results in a lot of
3748 ;; duplicate definitions. This can be avoided by defining
3749 ;; NO_C_HEADERS before including the R headers.
3750 (add-after 'chdir 'patch-use-of-R-headers
3752 (substitute* "src/spams.cpp"
3753 (("#include <R.h>" line)
3754 (string-append "#define NO_C_HEADERS\n" line)))
3756 ;; This looks like a syntax error.
3757 (add-after 'chdir 'patch-isnan
3759 (substitute* '"src/spams/linalg/linalg.h"
3760 (("if isnan\\(lambda\\) \\{")
3761 "if (isnan(lambda)) {"))
3764 `(("r-lattice" ,r-lattice)
3765 ("r-matrix" ,r-matrix)))
3766 (home-page "http://spams-devel.gforge.inria.fr")
3767 (synopsis "Toolbox for solving sparse estimation problems")
3768 (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
3769 for solving various sparse estimation problems. It includes tools for the
3773 @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
3774 component analysis} (PCA), ...)
3775 @item Solving sparse decomposition problems with LARS, coordinate descent,
3776 OMP, SOMP, proximal methods
3777 @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
3778 group lasso, tree-structured regularization, structured sparsity with
3779 overlapping groups,...).
3781 (license license:gpl3+)))
3783 (define-public r-base64
3790 (uri (cran-uri "base64" version))
3793 "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf"))))
3794 (build-system r-build-system)
3796 `(("r-openssl" ,r-openssl)))
3797 (home-page "http://cran.r-project.org/web/packages/base64")
3798 (synopsis "Base64 encoder and decoder")
3800 "This package is a compatibility wrapper to replace the orphaned package
3801 by Romain Francois. New applications should use the openssl or base64enc
3803 (license license:expat)))
3805 (define-public r-hmisc
3812 (uri (cran-uri "Hmisc" version))
3815 "1lg9k0kj803wsm3h0a991q9l2lrgsqryzfv2z79b88kjbfapqpqr"))))
3816 (properties `((upstream-name . "Hmisc")))
3817 (build-system r-build-system)
3819 `(("gfortran" ,gfortran)))
3821 `(("r-acepack" ,r-acepack)
3822 ("r-base64" ,r-base64)
3823 ("r-base64enc" ,r-base64enc)
3824 ("r-cluster" ,r-cluster)
3825 ("r-data-table" ,r-data-table)
3826 ("r-foreign" ,r-foreign)
3827 ("r-formula" ,r-formula)
3828 ("r-ggplot2" ,r-ggplot2)
3829 ("r-gridextra" ,r-gridextra)
3830 ("r-gtable" ,r-gtable)
3831 ("r-lattice" ,r-lattice)
3832 ("r-latticeextra" ,r-latticeextra)
3833 ("r-htmltable" ,r-htmltable)
3834 ("r-htmltools" ,r-htmltools)
3836 ("r-rpart" ,r-rpart)
3837 ("r-survival" ,r-survival)
3838 ("r-viridis" ,r-viridis)))
3839 (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
3840 (synopsis "Miscellaneous data analysis and graphics functions")
3842 "This package contains many functions useful for data analysis,
3843 high-level graphics, utility operations, functions for computing sample size
3844 and power, importing and annotating datasets, imputing missing values,
3845 advanced table making, variable clustering, character string manipulation,
3846 conversion of R objects to LaTeX code, and recoding variables.")
3847 (license license:gpl2+)))
3849 (define-public r-runit
3856 (uri (cran-uri "RUnit" version))
3859 "1jqr871jkll2xmk7wk5hv1z3a36hyn2ibgivw7bwk4b346940xlx"))))
3860 (properties `((upstream-name . "RUnit")))
3861 (build-system r-build-system)
3862 (home-page "http://cran.r-project.org/web/packages/RUnit")
3863 (synopsis "R unit test framework")
3865 "This package provides R functions implementing a standard unit testing
3866 framework, with additional code inspection and report generation tools.")
3867 (license license:gpl2+)))
3869 (define-public r-dynamictreecut
3871 (name "r-dynamictreecut")
3876 (uri (cran-uri "dynamicTreeCut" version))
3879 "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"))))
3880 (properties `((upstream-name . "dynamicTreeCut")))
3881 (build-system r-build-system)
3883 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
3884 (synopsis "Detect clusters in hierarchical clustering dendrograms")
3886 "This package contains methods for the detection of clusters in
3887 hierarchical clustering dendrograms.")
3888 (license license:gpl2+)))
3890 (define-public r-preprocesscore
3892 (name "r-preprocesscore")
3897 (uri (bioconductor-uri "preprocessCore" version))
3900 "1n8y12q7145f385gm2k3c6y3vwvin7jlb47la4mnl7mar6pq9kmp"))))
3902 `((upstream-name . "preprocessCore")))
3903 (build-system r-build-system)
3904 (home-page "https://github.com/bmbolstad/preprocessCore")
3905 (synopsis "Collection of pre-processing functions")
3907 "This package provides a library of core pre-processing and normalization
3909 (license license:lgpl2.0+)))
3911 (define-public r-fastcluster
3913 (name "r-fastcluster")
3918 (uri (cran-uri "fastcluster" version))
3921 "006k9isra5biyavqwci61avladw19mhp6kmkjj3777rl1r4r8b9z"))))
3922 (build-system r-build-system)
3923 (home-page "http://danifold.net/fastcluster.html")
3924 (synopsis "Fast hierarchical clustering routines")
3926 "This package implements fast hierarchical, agglomerative clustering
3927 routines. Part of the functionality is designed as drop-in replacement for
3928 existing routines: @code{linkage()} in the SciPy package
3929 @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package,
3930 and the @code{flashClust} package. It provides the same functionality with
3931 the benefit of a much faster implementation. Moreover, there are
3932 memory-saving routines for clustering of vector data, which go beyond what the
3933 existing packages provide.")
3934 (license license:bsd-2)))
3936 (define-public r-sfsmisc
3943 (uri (cran-uri "sfsmisc" version))
3946 "0580piv4n1nispl3pa8nfjjfnb8iwaqky2dzdy0aqnxrxgrhqhvz"))))
3947 (build-system r-build-system)
3948 (home-page "http://cran.r-project.org/web/packages/sfsmisc")
3949 (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
3951 "This package provides useful utilities from Seminar fuer Statistik ETH
3952 Zurich, including many that are related to graphics.")
3953 (license license:gpl2+)))
3955 (define-public r-gtools
3962 (uri (cran-uri "gtools" version))
3965 "1xknwk9xlsj027pg0nwiizigcrsc84hdrig0jn0cgcyxj8dabdl6"))))
3966 (build-system r-build-system)
3967 (home-page "http://cran.r-project.org/web/packages/gtools")
3968 (synopsis "Various R programming tools")
3970 "This package contains a collection of various functions to assist in R
3971 programming, such as tools to assist in developing, updating, and maintaining
3972 R and R packages, calculating the logit and inverse logit transformations,
3973 tests for whether a value is missing, empty or contains only @code{NA} and
3974 @code{NULL} values, and many more.")
3975 (license license:gpl2)))
3977 (define-public r-gdata
3984 (uri (cran-uri "gdata" version))
3987 "0kiy3jbcszlpmarg311spdsfi5pn89wgy742dxsbzxk8907fr5w0"))))
3988 (build-system r-build-system)
3992 `(("r-gtools" ,r-gtools)))
3993 (home-page "http://cran.r-project.org/web/packages/gdata")
3994 (synopsis "Various R programming tools for data manipulation")
3996 "This package provides various R programming tools for data manipulation,
4000 @item medical unit conversions
4001 @item combining objects
4002 @item character vector operations
4003 @item factor manipulation
4004 @item obtaining information about R objects
4005 @item manipulating MS-Excel formatted files
4006 @item generating fixed-width format files
4007 @item extricating components of date and time objects
4008 @item operations on columns of data frames
4009 @item matrix operations
4010 @item operations on vectors and data frames
4011 @item value of last evaluated expression
4012 @item wrapper for @code{sample} that ensures consistent behavior for
4013 both scalar and vector arguments
4015 (license license:gpl2+)))
4017 (define-public r-gplots
4024 (uri (cran-uri "gplots" version))
4027 "02nb8n3s7c1zxq2s7ycaq2ys72y7mzirxrwj954h6gdc4x1zhg9l"))))
4028 (build-system r-build-system)
4030 `(("r-catools" ,r-catools)
4031 ("r-gdata" ,r-gdata)
4032 ("r-gtools" ,r-gtools)
4033 ("r-kernsmooth" ,r-kernsmooth)))
4034 (home-page "http://cran.r-project.org/web/packages/gplots")
4035 (synopsis "Various R programming tools for plotting data")
4037 "This package provides various R programming tools for plotting data,
4041 @item calculating and plotting locally smoothed summary function
4042 @item enhanced versions of standard plots
4043 @item manipulating colors
4044 @item calculating and plotting two-dimensional data summaries
4045 @item enhanced regression diagnostic plots
4046 @item formula-enabled interface to @code{stats::lowess} function
4047 @item displaying textual data in plots
4049 @item plotting \"Venn\" diagrams
4050 @item displaying Open-Office style plots
4051 @item plotting multiple data on same region, with separate axes
4052 @item plotting means and confidence intervals
4053 @item spacing points in an x-y plot so they don't overlap
4055 (license license:gpl2+)))
4057 (define-public r-rocr
4064 (uri (cran-uri "ROCR" version))
4067 "1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7"))))
4068 (properties `((upstream-name . "ROCR")))
4069 (build-system r-build-system)
4071 `(("r-gplots" ,r-gplots)))
4072 (home-page "http://rocr.bioinf.mpi-sb.mpg.de/")
4073 (synopsis "Visualizing the performance of scoring classifiers")
4075 "ROCR is a flexible tool for creating cutoff-parameterized 2D performance
4076 curves by freely combining two from over 25 performance measures (new
4077 performance measures can be added using a standard interface). Curves from
4078 different cross-validation or bootstrapping runs can be averaged by different
4079 methods, and standard deviations, standard errors or box plots can be used to
4080 visualize the variability across the runs. The parameterization can be
4081 visualized by printing cutoff values at the corresponding curve positions, or
4082 by coloring the curve according to cutoff. All components of a performance
4083 plot can be quickly adjusted using a flexible parameter dispatching
4085 (license license:gpl2+)))
4087 (define-public r-kernsmooth
4089 (name "r-kernsmooth")
4094 (uri (cran-uri "KernSmooth" version))
4097 "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb"))))
4098 (properties `((upstream-name . "KernSmooth")))
4099 (build-system r-build-system)
4101 `(("gfortran" ,gfortran)))
4102 (home-page "http://cran.r-project.org/web/packages/KernSmooth")
4103 (synopsis "Functions for kernel smoothing")
4105 "This package provides functions for kernel smoothing (and density
4106 estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
4107 \"Kernel Smoothing\".")
4108 ;; Unlimited use and distribution
4109 (license (license:non-copyleft "file://LICENSE.note"))))
4111 (define-public r-zoo
4117 (uri (cran-uri "zoo" version))
4120 "167m142rwwfy8b9hnfc3fi28dcsdjk61g1crqhll6sh5xmgnfn28"))))
4121 (build-system r-build-system)
4123 `(("r-lattice" ,r-lattice)))
4124 (home-page "http://zoo.R-Forge.R-project.org/")
4125 (synopsis "S3 infrastructure for regular and irregular time series")
4126 (description "This package contains an S3 class with methods for totally
4127 ordered indexed observations. It is particularly aimed at irregular time
4128 series of numeric vectors/matrices and factors.")
4129 (license license:gpl2+)))
4131 (define-public r-ztable
4137 (uri (cran-uri "ztable" version))
4140 "1jfqnqy9544gfvz3bsb48v4177nwp4b4n9l2743asq8sbq305b5r"))))
4141 (build-system r-build-system)
4142 (home-page "http://cran.r-project.org/web/packages/ztable")
4143 (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
4145 "This package provides functions to make zebra-striped tables (tables
4146 with alternating row colors) in LaTeX and HTML formats easily from
4147 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
4148 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
4149 @code{cbind.mytable} objects.")
4150 (license license:gpl2+)))
4152 (define-public r-vipor
4158 (uri (cran-uri "vipor" version))
4161 "0p1z9a3fazl78pj8a1i2n62v8hrs8cinq82j9wpawhmfkn3dggss"))))
4162 (build-system r-build-system)
4163 (home-page "http://cran.r-project.org/web/packages/vipor")
4164 (synopsis "Plot categorical data using noise and density estimates")
4166 "This package provides tools to generate a violin point plot, a
4167 combination of a violin/histogram plot and a scatter plot by offsetting points
4168 within a category based on their density using quasirandom noise.")
4169 (license license:gpl2+)))
4171 (define-public r-beeswarm
4177 (uri (cran-uri "beeswarm" version))
4180 "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
4181 (build-system r-build-system)
4182 (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/")
4183 (synopsis "Implementation of bee swarm plots")
4185 "This package provides an implementation of bee swarm plots. The bee
4186 swarm plot is a one-dimensional scatter plot like stripchart, but with
4187 closely-packed, non-overlapping points.")
4188 (license license:artistic2.0)))
4190 (define-public r-sourcetools
4192 (name "r-sourcetools")
4197 (uri (cran-uri "sourcetools" version))
4200 "0jx6kslygfqaic3cmjwag3dy98q1a2dw20cz7z8agsknmmbk6dy2"))))
4201 (build-system r-build-system)
4202 (home-page "http://cran.r-project.org/web/packages/sourcetools")
4203 (synopsis "Tools for reading, tokenizing and parsing R code")
4205 "The sourcetools package provides both an R and C++ interface for the
4206 tokenization of R code, and helpers for interacting with the tokenized
4207 representation of R code.")
4208 (license license:expat)))
4210 (define-public r-ggbeeswarm
4212 (name "r-ggbeeswarm")
4216 (uri (cran-uri "ggbeeswarm" version))
4219 "1jgp55rvmzc4agcrlsjn8m5lk85di9c4wj94xzikqkql4lvq3qpd"))))
4220 (build-system r-build-system)
4222 `(("r-beeswarm" ,r-beeswarm)
4223 ("r-ggplot2" ,r-ggplot2)
4224 ("r-vipor" ,r-vipor)))
4225 (home-page "https://github.com/eclarke/ggbeeswarm")
4226 (synopsis "Categorical scatter (violin point) plots")
4228 "This package provides two methods of plotting categorical scatter plots
4229 such that the arrangement of points within a category reflects the density of
4230 data at that region, and avoids over-plotting.")
4231 (license license:gpl2+)))
4233 (define-public r-ggthemes
4239 (uri (cran-uri "ggthemes" version))
4242 "1qdxg2siwsiq32fmgcxn4vihgxad9v8q0aqigl7a94c26bwxs7y2"))))
4243 (build-system r-build-system)
4245 `(("r-assertthat" ,r-assertthat)
4246 ("r-colorspace" ,r-colorspace)
4247 ("r-ggplot2" ,r-ggplot2)
4248 ("r-scales" ,r-scales)))
4249 (home-page "https://cran.rstudio.com/web/packages/ggthemes")
4250 (synopsis "Extra themes, scales and geoms for @code{ggplot2}")
4251 (description "This package provides extra themes and scales for
4252 @code{ggplot2} that replicate the look of plots by Edward Tufte and
4253 Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The
4254 Wall Street Journal, among others. This package also provides
4255 @code{geoms} for Tufte's box plot and range frame.")
4256 (license license:gpl2)))
4258 (define-public r-statmod
4264 (uri (cran-uri "statmod" version))
4267 "14yilq9d3z20hig4rs8bjqyydw3dfx90mhmzvw9w8p16h0s595sn"))))
4268 (build-system r-build-system)
4269 (home-page "http://cran.r-project.org/web/packages/statmod")
4271 `(("gfortran" ,gfortran)))
4272 (synopsis "Statistical modeling")
4274 "This package provides a collection of algorithms and functions to aid
4275 statistical modeling. It includes growth curve comparisons, limiting dilution
4276 analysis (aka ELDA), mixed linear models, heteroscedastic regression,
4277 inverse-Gaussian probability calculations, Gauss quadrature and a secure
4278 convergence algorithm for nonlinear models. It also includes advanced
4279 generalized linear model functions that implement secure convergence,
4280 dispersion modeling and Tweedie power-law families.")
4281 ;; Statmod is distributed under either license
4282 (license (list license:gpl2 license:gpl3))))
4284 (define-public r-rann
4290 (uri (cran-uri "RANN" version))
4293 "007cgqg9bybg2zlljbv5m6cmlm3r6i251018rpgjcn0xnm9sjsj7"))))
4295 `((upstream-name . "RANN")))
4296 (build-system r-build-system)
4297 (home-page "https://github.com/jefferis/RANN")
4298 (synopsis "Fast nearest neighbour search")
4300 "This package finds the k nearest neighbours for every point in a given
4301 dataset in O(N log N) time using Arya and Mount's ANN library. Provides
4302 approximate, exact searches, fixed radius searches, bd and kb trees.")
4303 (license license:gpl3+)))
4305 (define-public r-fivethirtyeight
4307 (name "r-fivethirtyeight")
4312 (uri (string-append "https://mran.microsoft.com/src/contrib/"
4313 "fivethirtyeight_" version ".tar.gz"))
4316 "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl"))))
4317 (build-system r-build-system)
4319 `(("r-knitr" ,r-knitr)
4320 ("r-rmarkdown" ,r-rmarkdown)
4321 ("r-dplyr" ,r-dplyr)
4322 ("r-readr" ,r-readr)
4323 ("r-ggplot2" ,r-ggplot2)
4324 ("r-magrittr" ,r-magrittr)
4325 ("r-stringr" ,r-stringr)))
4326 (home-page "https://mran.microsoft.com/package/fivethirtyeight/")
4327 (synopsis "Data and code behind the stories at FiveThirtyEight")
4328 (description "This R package provides access to the code and data sets
4329 published by the statistics blog FiveThirtyEight.")
4330 (license license:expat)))
4332 (define-public r-compquadform
4334 (name "r-compquadform")
4339 (uri (cran-uri "CompQuadForm" version))
4342 "0bsgbdblxpv57mbwnf51xyiydp2bqyxkg4zzwqki85cv5xqlrq1n"))))
4343 (properties `((upstream-name . "CompQuadForm")))
4344 (build-system r-build-system)
4345 (home-page "http://cran.r-project.org/web/packages/CompQuadForm")
4346 (synopsis "Distribution function of quadratic forms in normal variables")
4348 "This package provides functions to compute the distribution function of
4349 quadratic forms in normal variables using Imhof's method, Davies's algorithm,
4350 Farebrother's algorithm or Liu et al.'s algorithm.")
4351 (license license:gpl2+)))
4353 (define-public r-cowplot
4360 (uri (cran-uri "cowplot" version))
4363 "03iimcsh1pk7iqzjdlfcj43b8khijdk4hg00j4jdllv19xsfb0hx"))))
4364 (build-system r-build-system)
4366 `(("r-ggplot2" ,r-ggplot2)
4367 ("r-gtable" ,r-gtable)
4368 ("r-plyr" ,r-plyr)))
4369 (home-page "https://github.com/wilkelab/cowplot")
4370 (synopsis "Streamlined plot theme and plot annotations for ggplot2")
4372 "This package provides some helpful extensions and modifications to the
4373 ggplot2 package to combine multiple ggplot2 plots into one and label them with
4374 letters, as is often required for scientific publications.")
4375 (license license:gpl2)))
4377 (define-public r-mixtools
4384 (uri (cran-uri "mixtools" version))
4387 "133rr17ywmlhsc6457hs8qxi8ng443ql9ashxpwc8875gjhv1x32"))))
4388 (build-system r-build-system)
4390 `(("r-boot" ,r-boot)
4392 ("r-segmented" ,r-segmented)))
4393 (home-page "http://cran.r-project.org/web/packages/mixtools")
4394 (synopsis "Tools for analyzing finite mixture models")
4396 "This package provides a collection of R functions for analyzing finite
4398 (license license:gpl2+)))
4400 (define-public r-lars
4407 (uri (cran-uri "lars" version))
4410 "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
4411 (build-system r-build-system)
4413 `(("gfortran" ,gfortran)))
4414 (home-page "http://www-stat.stanford.edu/~hastie/Papers/#LARS")
4415 (synopsis "Least angle regression software")
4417 "Least Angle Regression (\"LAR\") is a model selection algorithm; a
4418 useful and less greedy version of traditional forward selection methods. A
4419 simple modification of the LAR algorithm implements Tibshirani's Lasso; the
4420 Lasso modification of LARS calculates the entire Lasso path of coefficients
4421 for a given problem at the cost of a single least squares fit. Another LARS
4422 modification efficiently implements epsilon Forward Stagewise linear
4424 (license license:gpl2)))
4426 (define-public r-fastica
4433 (uri (cran-uri "fastICA" version))
4436 "0ykk78fsk5da2g16i4wji85bvji7nayjvkfp07hyaxq9d15jmf0r"))))
4437 (properties `((upstream-name . "fastICA")))
4438 (build-system r-build-system)
4439 (home-page "http://cran.r-project.org/web/packages/fastICA")
4440 (synopsis "FastICA algorithms to perform ICA and projection pursuit")
4442 "This package provides an implementation of the FastICA algorithm to
4443 perform @dfn{independent component analysis} (ICA) and projection pursuit.")
4445 (license license:gpl3+)))
4447 (define-public r-randomforest
4449 (name "r-randomforest")
4454 (uri (cran-uri "randomForest" version))
4457 "1i43idaihhl6nwqw42v9dqpl6f8z3ykcn2in32lh2755i27jylbf"))))
4458 (properties `((upstream-name . "randomForest")))
4459 (build-system r-build-system)
4460 (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
4462 `(("gfortran" ,gfortran)))
4463 (synopsis "Breiman and Cutler's random forests for classification and regression")
4465 "This package provides the Breiman and Cutler's random forests algorithm, based on a
4466 forest of trees using random inputs, for classification and regression.")
4467 (license license:gpl2+)))
4469 (define-public r-diptest
4476 (uri (cran-uri "diptest" version))
4479 "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
4480 (build-system r-build-system)
4481 (home-page "http://cran.r-project.org/web/packages/diptest")
4482 (synopsis "Hartigan's dip test statistic for unimodality")
4484 "This package computes Hartigan's dip test statistic for unimodality,
4485 multimodality and provides a test with simulation based p-values, where the
4486 original public code has been corrected.")
4487 (license license:gpl2+)))
4489 (define-public r-modeltools
4491 (name "r-modeltools")
4496 (uri (cran-uri "modeltools" version))
4499 "0ynds453xprxv0jqqzi3blnv5w6vrdww9pvd1sq4lrr5ar3k3cq7"))))
4500 (build-system r-build-system)
4501 (home-page "http://cran.r-project.org/web/packages/modeltools")
4502 (synopsis "Tools and classes for statistical models")
4504 "This package provides a collection of tools to deal with statistical
4505 models. The functionality is experimental and the user interface is likely
4506 to change in the future.")
4507 (license license:gpl2)))
4509 (define-public r-flexmix
4516 (uri (cran-uri "flexmix" version))
4519 "1i205yw3kkxs27gqcs6zx0c2mh16p332a2p06wq6fdzb20bazg3z"))))
4520 (build-system r-build-system)
4522 `(("r-lattice" ,r-lattice)
4523 ("r-modeltools" ,r-modeltools)
4524 ("r-nnet" ,r-nnet)))
4525 (home-page "http://cran.r-project.org/web/packages/flexmix")
4526 (synopsis "Flexible mixture modeling")
4528 "This package implements a general framework for finite mixtures of
4529 regression models using the EM algorithm. FlexMix provides the E-step and
4530 all data handling, while the M-step can be supplied by the user to easily
4531 define new models. Existing drivers implement mixtures of standard linear
4532 models, generalized linear models and model-based clustering.")
4533 (license license:gpl2+)))
4535 (define-public r-mclust
4542 (uri (cran-uri "mclust" version))
4545 "19cbg7p5h2b6h9mvcx9rjppyd3awma18ymaljakbnclpvhwbqpwd"))))
4546 (build-system r-build-system)
4548 `(("gfortran" ,gfortran)))
4549 (home-page "http://www.stat.washington.edu/mclust/")
4550 (synopsis "Gaussian mixture modelling for model-based clustering etc.")
4552 "This package provides Gaussian finite mixture models fitted via EM
4553 algorithm for model-based clustering, classification, and density estimation,
4554 including Bayesian regularization, dimension reduction for visualisation,
4555 and resampling-based inference.")
4556 (license license:gpl2+)))
4558 (define-public r-prabclus
4565 (uri (cran-uri "prabclus" version))
4568 "0qjsxrx6yv338bxm4ki0w9h8hind1l98abdrz828588bwj02jya1"))))
4569 (build-system r-build-system)
4571 `(("r-mass" ,r-mass)
4572 ("r-mclust" ,r-mclust)))
4573 (home-page "https://cran.r-project.org/web/packages/prabclus")
4574 (synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
4576 "This package provides a distance-based parametric bootstrap tests
4577 for clustering with spatial neighborhood information. Some distance measures,
4578 clustering of presence-absence, abundance and multilocus genetical data for
4579 species delimitation, nearest neighbor based noise detection.")
4580 (license license:gpl2+)))
4582 (define-public r-deoptimr
4589 (uri (cran-uri "DEoptimR" version))
4592 "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
4593 (properties `((upstream-name . "DEoptimR")))
4594 (build-system r-build-system)
4595 (home-page "http://cran.r-project.org/web/packages/DEoptimR")
4596 (synopsis "Differential evolution optimization in pure R")
4598 "This package provides a differential evolution (DE) stochastic
4599 algorithms for global optimization of problems with and without constraints.
4600 The aim is to curate a collection of its state-of-the-art variants that (1) do
4601 not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
4602 can be efficiently implemented directly in the R language.")
4603 (license license:gpl2+)))
4605 (define-public r-robustbase
4607 (name "r-robustbase")
4612 (uri (cran-uri "robustbase" version))
4615 "13xz4am7y0s0kl5bmbcw3dlhl7ji8h9sjx56wsgmj6r9n35nrggw"))))
4616 (build-system r-build-system)
4618 `(("gfortran" ,gfortran)))
4620 `(("r-deoptimr" ,r-deoptimr)))
4621 (home-page "http://robustbase.r-forge.r-project.org/")
4622 (synopsis "Basic robust statistics")
4624 "This packages allows to analyze data with robust methods such as
4625 regression methodology including model selections and multivariate statistics.")
4626 (license license:gpl2+)))
4628 (define-public r-trimcluster
4630 (name "r-trimcluster")
4635 (uri (cran-uri "trimcluster" version))
4638 "0lsgbg93hm0w1rdb813ry0ks2l0jfpyqzqkf3h3bj6fch0avcbv2"))))
4639 (build-system r-build-system)
4640 (home-page "http://cran.r-project.org/web/packages/trimcluster")
4641 (synopsis "Cluster analysis with trimming")
4643 "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
4644 Matran (1997). This optimizes the k-means criterion under trimming a portion
4646 (license license:gpl2+)))
4648 (define-public r-fpc
4655 (uri (cran-uri "fpc" version))
4658 "15m0p9l9w2v7sl0cnzyg81i2fmx3hrhvr3371544mwn3fpsca5sx"))))
4659 (build-system r-build-system)
4661 `(("r-class" ,r-class)
4662 ("r-cluster" ,r-cluster)
4663 ("r-diptest" ,r-diptest)
4664 ("r-flexmix" ,r-flexmix)
4665 ("r-kernlab" ,r-kernlab)
4667 ("r-mclust" ,r-mclust)
4668 ("r-mvtnorm" ,r-mvtnorm)
4669 ("r-prabclus" ,r-prabclus)
4670 ("r-robustbase" ,r-robustbase)
4671 ("r-trimcluster" ,r-trimcluster)))
4672 (home-page "http://cran.r-project.org/web/packages/fpc")
4673 (synopsis "Flexible procedures for clustering")
4675 "This package provides various methods for clustering and cluster validation.
4676 For example, it provides fixed point clustering, linear regression clustering,
4677 clustering by merging Gaussian mixture components, as well as symmetric and
4678 asymmetric discriminant projections for visualisation of the separation of
4680 (license license:gpl2+)))
4682 (define-public r-vgam
4689 (uri (cran-uri "VGAM" version))
4692 "0wr6szcpj8r4a1rlzgd6iym7khin69fmvxcf37iyvs8mms86dfr3"))))
4693 (properties `((upstream-name . "VGAM")))
4694 (build-system r-build-system)
4696 `(("gfortran" ,gfortran)))
4697 (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
4698 (synopsis "Vector generalized linear and additive models")
4700 "This package is an implementation of about 6 major classes of statistical
4701 regression models. Currently only fixed-effects models are implemented, i.e.,
4702 no random-effects models. Many (150+) models and distributions are estimated
4703 by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
4704 VGLMs can be loosely thought of as multivariate generalised linear models.")
4705 (license license:gpl2+)))
4707 (define-public r-pbapply
4714 (uri (cran-uri "pbapply" version))
4717 "1sdmjlnwxb99f95g5v8k8mirrkzw99yig377v0qi9lzwjgd6fqqr"))))
4718 (build-system r-build-system)
4719 (home-page "https://github.com/psolymos/pbapply")
4720 (synopsis "Adding progress bar to apply functions")
4722 "This lightweight package that adds progress bar to vectorized R
4723 functions apply. The implementation can easily be added to functions where
4724 showing the progress is useful e.g. bootstrap.")
4725 (license license:gpl2)))
4727 (define-public r-fnn
4734 (uri (cran-uri "FNN" version))
4737 "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj"))))
4738 (properties `((upstream-name . "FNN")))
4739 (build-system r-build-system)
4740 (home-page "http://cran.r-project.org/web/packages/FNN")
4741 (synopsis "Fast nearest neighbor search algorithms and applications")
4743 "This package provides cover-tree and kd-tree fast k-nearest neighbor
4744 search algorithms and related applications including KNN classification,
4745 regression and information measures.")
4746 (license license:gpl2+)))
4748 (define-public r-minqa
4755 (uri (cran-uri "minqa" version))
4758 "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
4759 (build-system r-build-system)
4761 `(("r-rcpp" ,r-rcpp)))
4763 `(("gfortran" ,gfortran)))
4764 (home-page "http://optimizer.r-forge.r-project.org")
4765 (synopsis "Derivative-free optimization algorithms by quadratic approximation")
4767 "This package provides a derivative-free optimization by quadratic approximation
4768 based on an interface to Fortran implementations by M. J. D. Powell.")
4769 (license license:gpl2)))
4771 (define-public r-rcppeigen
4773 (name "r-rcppeigen")
4774 (version "0.3.2.9.0")
4778 (uri (cran-uri "RcppEigen" version))
4781 "0fy9kr03160f1ywzff3p380s8a59jz7d2d0rggb14g2y0slzpbr5"))))
4782 (properties `((upstream-name . "RcppEigen")))
4783 (build-system r-build-system)
4785 `(("r-rcpp" ,r-rcpp)
4786 ("r-matrix" ,r-matrix)))
4787 (home-page "http://eigen.tuxfamily.org")
4788 (synopsis "Rcpp integration for the Eigen templated linear algebra library")
4790 "This package provides an integration of Eigen in R using a C++ template
4791 library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
4792 It supports dense and sparse matrices on integer, floating point and complex numbers,
4793 decompositions of such matrices, and solutions of linear systems.")
4794 (license license:gpl2+)))
4796 (define-public r-modelmetrics
4798 (name "r-modelmetrics")
4803 (uri (cran-uri "ModelMetrics" version))
4806 "119xxmzb5biq7k1yxqsf0jmmarmfn6lds9x9hfgv593xlpym6za8"))))
4807 (properties `((upstream-name . "ModelMetrics")))
4808 (build-system r-build-system)
4810 `(("r-rcpp" ,r-rcpp)))
4811 (home-page "http://cran.r-project.org/web/packages/ModelMetrics")
4812 (synopsis "Rapid calculation of model metrics")
4814 "Written in C++ using @code{Rcpp}, this package provides a collection of
4815 metrics for evaluating models.")
4816 (license license:gpl2+)))
4818 (define-public r-matrixmodels
4820 (name "r-matrixmodels")
4825 (uri (cran-uri "MatrixModels" version))
4828 "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
4829 (properties `((upstream-name . "MatrixModels")))
4830 (build-system r-build-system)
4832 `(("r-matrix" ,r-matrix)))
4833 (home-page "https://cran.r-project.org/web/packages/MatrixModels")
4834 (synopsis "Modelling with sparse and dense matrices")
4836 "This package models with sparse and dense matrix matrices,
4837 using modular prediction and response module classes.")
4838 (license license:gpl2+)))
4840 (define-public r-quantreg
4847 (uri (cran-uri "quantreg" version))
4850 "098gy8xv9kcl5y0cm93b8chr5sm6crrdxi20bkx9lmwmybl3himv"))))
4851 (build-system r-build-system)
4853 `(("gfortran" ,gfortran)))
4855 `(("r-matrixmodels" ,r-matrixmodels)
4856 ("r-sparsem" ,r-sparsem)))
4857 (home-page "http://www.r-project.org")
4858 (synopsis "Quantile regression")
4860 "This package provides an estimation and inference methods for models
4861 of conditional quantiles: linear and nonlinear parametric and non-parametric
4862 models for conditional quantiles of a univariate response and several methods
4863 for handling censored survival data. Portfolio selection methods based on
4864 expected shortfall risk are also included.")
4865 (license license:gpl2+)))
4867 (define-public r-nloptr
4874 (uri (cran-uri "nloptr" version))
4877 "1cypz91z28vhvwq2rzqjrbdc6a2lvfr2g16vid2sax618q6ai089"))))
4878 (build-system r-build-system)
4880 `(("pkg-config" ,pkg-config)))
4882 `(("nlopt" ,nlopt)))
4883 (home-page "http://cran.r-project.org/web/packages/nloptr")
4884 (synopsis "R interface to NLopt")
4886 "This package is interface to NLopt, a library for nonlinear
4887 optimization. NLopt is a library for nonlinear optimization, providing a
4888 common interface for a number of different free optimization routines
4889 available online as well as original implementations of various other
4891 (license license:lgpl3)))
4893 (define-public r-lme4
4900 (uri (cran-uri "lme4" version))
4903 "0j60l5kgx1wvw2wm3jwfqwi63hammaq8gfcxzwa4h552likvaxi9"))))
4904 (build-system r-build-system)
4906 `(("r-rcpp" ,r-rcpp)
4907 ("r-rcppeigen" ,r-rcppeigen)))
4909 `(("r-minqa" ,r-minqa)
4910 ("r-nloptr" ,r-nloptr)
4912 ("r-nlme" ,r-nlme)))
4913 (home-page "http://cran.r-project.org/web/packages/lme4")
4914 (synopsis "Linear mixed-effects models using eigen and S4")
4916 "This package provides fit linear and generalized linear mixed-effects
4917 models. The models and their components are represented using S4 classes and
4918 methods. The core computational algorithms are implemented using the Eigen
4919 C++ library for numerical linear algebra and RcppEigen glue.")
4920 (license license:gpl2+)))
4922 (define-public r-pbkrtest
4929 (uri (cran-uri "pbkrtest" version))
4932 "00cw18q7wvddzjrbxz917wkix6r7672vi2wmsp4gwgzady8vha4x"))))
4933 (build-system r-build-system)
4935 `(("r-lme4" ,r-lme4)
4937 ("r-matrix" ,r-matrix)))
4938 (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
4939 (synopsis "Methods for linear mixed model comparison")
4941 "This package implements a parametric bootstrap test and a Kenward Roger
4942 modification of F-tests for linear mixed effects models and a parametric
4943 bootstrap test for generalized linear mixed models.")
4944 (license license:gpl2+)))
4946 (define-public r-car
4953 (uri (cran-uri "car" version))
4956 "0a6v7rsd1xsdyapnfqy37m7c4kx9wslkzsizc9k0lmnba0bwyfgx"))))
4957 (build-system r-build-system)
4959 `(("r-mass" ,r-mass)
4962 ("r-pbkrtest" ,r-pbkrtest)
4963 ("r-quantreg" ,r-quantreg)))
4964 (home-page "https://r-forge.r-project.org/projects/car/")
4965 (synopsis "Companion to applied regression")
4967 "This package provides functions and datasets from book Companion
4968 to Applied regression, Second Edition, Sage, 2011.")
4969 (license license:gpl2+)))
4971 (define-public r-caret
4978 (uri (cran-uri "caret" version))
4981 "1jzaqwv4glyqqnfbpalgajd0ag866247vvdh5i83ffqs1yhs984h"))))
4982 (build-system r-build-system)
4985 ("r-foreach" ,r-foreach)
4986 ("r-ggplot2" ,r-ggplot2)
4987 ("r-modelmetrics" ,r-modelmetrics)
4989 ("r-reshape2" ,r-reshape2)))
4990 (home-page "https://github.com/topepo/caret")
4991 (synopsis "Classification and regression training")
4993 "This package provides misc functions for training and plotting
4994 classification and regression models.")
4995 (license license:gpl2+)))
4997 (define-public r-rcppprogress
4999 (name "r-rcppprogress")
5004 (uri (cran-uri "RcppProgress" version))
5007 "0796g11w7iv3ix1wfm3fh09qq7jki4r4cp1mjagq77igri3xrr9x"))))
5008 (properties `((upstream-name . "RcppProgress")))
5009 (build-system r-build-system)
5011 `(("r-rcpp" ,r-rcpp)))
5012 (home-page "https://github.com/kforner/rcpp_progress")
5013 (synopsis "Interruptible progress bar for C++ in R packages")
5015 "This package allows to display a progress bar in the R console for long running
5016 computations taking place in C++ code, and support for interrupting those computations
5017 even in multithreaded code, typically using OpenMP.")
5018 (license license:gpl3+)))
5020 (define-public r-mnormt
5027 (uri (cran-uri "mnormt" version))
5030 "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z"))))
5031 (build-system r-build-system)
5033 `(("gfortran" ,gfortran)))
5034 (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
5035 (synopsis "Multivariate normal and \"t\" distributions")
5037 "This package provides functions for computing the density and the
5038 distribution function of multivariate normal and \"t\" random variables, and
5039 for generating random vectors sampled from these distributions. Probabilities
5040 are computed via non-Monte Carlo methods.")
5041 (license license:gpl2+)))
5043 (define-public r-numderiv
5046 (version "2016.8-1")
5050 (uri (cran-uri "numDeriv" version))
5053 "07ni52rwiap4wilfz94w5mrqaxr59axxmgn57857ip4p6qkiss0v"))))
5054 (properties `((upstream-name . "numDeriv")))
5055 (build-system r-build-system)
5056 (home-page "https://cran.r-project.org/web/packages/numDeriv")
5057 (synopsis "Accurate numerical derivatives")
5059 "This package provides methods for calculating accurate numerical
5060 first and second order derivatives.")
5061 (license license:gpl2)))
5070 (uri (cran-uri "sn" version))
5073 "0fh7xjsfd2x8d9lbnss7raldh24b72b3pvcv7zqa1qprzg7zfr01"))))
5074 (build-system r-build-system)
5076 `(("r-mnormt" ,r-mnormt)
5077 ("r-numderiv" ,r-numderiv)))
5078 (home-page "http://azzalini.stat.unipd.it/SN")
5079 (synopsis "The skew-normal and skew-t distributions")
5081 "This packages provides functionalities to build and manipulate
5082 probability distributions of the skew-normal family and some related
5083 ones, notably the skew-t family, and provides related statistical
5084 methods for data fitting and diagnostics, in the univariate and the
5085 multivariate case.")
5086 (license license:gpl2+)))
5088 (define-public r-tclust
5095 (uri (cran-uri "tclust" version))
5098 "0a1b7yp4l9wf6ic5czizyl2cnxrc1virj0icr8i6m1vv23jd8jfp"))))
5099 (build-system r-build-system)
5101 `(("r-cluster" ,r-cluster)
5102 ("r-mclust" ,r-mclust)
5103 ("r-mvtnorm" ,r-mvtnorm)
5105 (home-page "http://cran.r-project.org/web/packages/tclust")
5106 (synopsis "Robust trimmed clustering")
5108 "This package implements different robust clustering
5109 algorithms (@code{tclust}) based on trimming and including some graphical
5110 diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
5111 (license license:gpl3)))
5113 (define-public r-ranger
5120 (uri (cran-uri "ranger" version))
5123 "1fwqwbi0dnla16x6zj14rf95qr5gmilfmlrwnv7s960h4yiw4n97"))))
5124 (build-system r-build-system)
5126 `(("r-rcpp" ,r-rcpp)))
5127 (home-page "https://github.com/imbs-hl/ranger")
5128 (synopsis "Fast implementation of random forests")
5130 "This package provides a fast implementation of Random Forests,
5131 particularly suited for high dimensional data. Ensembles of classification,
5132 regression, survival and probability prediction trees are supported. Data from
5133 genome-wide association studies can be analyzed efficiently.")
5134 (license license:gpl3)))
5136 (define-public r-tsne
5143 (uri (cran-uri "tsne" version))
5146 "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
5147 (build-system r-build-system)
5148 (home-page "https://github.com/jdonaldson/rtsne/")
5149 (synopsis "t-Distributed Stochastic Neighbor Embedding for R")
5151 "This package provides a pure R implementation of the t-SNE algorithm.")
5152 (license license:gpl2+)))
5154 (define-public r-cairo
5161 (uri (cran-uri "Cairo" version))
5164 "1x1q99r3r978rlkkm5gixkv03p0mcr6k7ydcqdmisrwnmrn7p1ia"))))
5165 (properties `((upstream-name . "Cairo")))
5166 (build-system r-build-system)
5171 `(("pkg-config" ,pkg-config)))
5172 (home-page "http://www.rforge.net/Cairo/")
5173 (synopsis "R graphics device using Cairo graphics library")
5175 "This package provides a Cairo graphics device that can be use to
5176 create high-quality vector (PDF, PostScript and SVG) and bitmap
5177 output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11
5178 and Win32). Since it uses the same back-end for all output, copying
5179 across formats is WYSIWYG. Files are created without the dependence
5180 on X11 or other external programs. This device supports alpha
5181 channel (semi-transparent drawing) and resulting images can contain
5182 transparent and semi-transparent regions. It is ideal for use in
5183 server environments (file output) and as a replacement for other
5184 devices that don't have Cairo's capabilities such as alpha support or
5185 anti-aliasing. Backends are modular such that any subset of backends
5187 (license license:gpl2)))