1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 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, 2017, 2019 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>
10 ;;; Copyright © 2017 Kyle Meyer <kyle@kyleam.com>
11 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
12 ;;; Copyright © 2017 Alex Kost <alezost@gmail.com>
13 ;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com>
15 ;;; This file is part of GNU Guix.
17 ;;; GNU Guix is free software; you can redistribute it and/or modify it
18 ;;; under the terms of the GNU General Public License as published by
19 ;;; the Free Software Foundation; either version 3 of the License, or (at
20 ;;; your option) any later version.
22 ;;; GNU Guix is distributed in the hope that it will be useful, but
23 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
24 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
25 ;;; GNU General Public License for more details.
27 ;;; You should have received a copy of the GNU General Public License
28 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
30 (define-module (gnu packages statistics)
31 #:use-module ((guix licenses) #:prefix license:)
32 #:use-module (guix packages)
33 #:use-module (guix download)
34 #:use-module (guix hg-download)
35 #:use-module (guix git-download)
36 #:use-module (guix utils)
37 #:use-module (guix build-system ant)
38 #:use-module (guix build-system gnu)
39 #:use-module (guix build-system r)
40 #:use-module (guix build-system python)
41 #:use-module (guix build-system trivial)
42 #:use-module (gnu packages)
43 #:use-module (gnu packages algebra)
44 #:use-module (gnu packages autotools)
45 #:use-module (gnu packages bash)
46 #:use-module (gnu packages check)
47 #:use-module (gnu packages compression)
48 #:use-module (gnu packages cran)
49 #:use-module (gnu packages curl)
50 #:use-module (gnu packages emacs)
51 #:use-module (gnu packages emacs-xyz)
52 #:use-module (gnu packages gcc)
53 #:use-module (gnu packages gtk)
54 #:use-module (gnu packages gettext)
55 #:use-module (gnu packages glib)
56 #:use-module (gnu packages haskell)
57 #:use-module (gnu packages icu4c)
58 #:use-module (gnu packages image)
59 #:use-module (gnu packages java)
60 #:use-module (gnu packages libffi)
61 #:use-module (gnu packages machine-learning)
62 #:use-module (gnu packages maths)
63 #:use-module (gnu packages multiprecision)
64 #:use-module (gnu packages pcre)
65 #:use-module (gnu packages perl)
66 #:use-module (gnu packages pkg-config)
67 #:use-module (gnu packages python)
68 #:use-module (gnu packages python-xyz)
69 #:use-module (gnu packages readline)
70 #:use-module (gnu packages sphinx)
71 #:use-module (gnu packages ssh)
72 #:use-module (gnu packages tcl)
73 #:use-module (gnu packages tex)
74 #:use-module (gnu packages texinfo)
75 #:use-module (gnu packages time)
76 #:use-module (gnu packages tls)
77 #:use-module (gnu packages base)
78 #:use-module (gnu packages web)
79 #:use-module (gnu packages xml)
80 #:use-module (gnu packages xorg)
81 #:use-module (srfi srfi-1))
91 (uri (string-append "mirror://gnu/pspp/pspp-"
95 "07pp27zycrb5x927jwaj9r3q7hy915jh51xs85zxby6gfiwl63m5"))))
96 (build-system gnu-build-system)
99 ("gettext" ,gettext-minimal)
103 ("readline" ,readline)
105 ("gtksourceview" ,gtksourceview)
106 ("spread-sheet-widget" ,spread-sheet-widget)
109 `(("autoconf" ,autoconf) ;for tests
110 ("glib" ,glib "bin") ;for glib-genmarshal
112 ("pkg-config" ,pkg-config)
113 ("python" ,python-2) ;for tests
114 ("texinfo" ,texinfo)))
115 (home-page "https://www.gnu.org/software/pspp/")
116 (synopsis "Statistical analysis")
118 "GNU PSPP is a statistical analysis program. It can perform
119 descriptive statistics, T-tests, linear regression and non-parametric tests.
120 It features both a graphical interface as well as command-line input. PSPP
121 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
122 can be imported from spreadsheets, text files and database sources and it can
123 be output in text, PostScript, PDF or HTML.")
124 (license license:gpl3+)))
132 (uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/"
133 (version-major version) ".x/Source/"
134 "JAGS-" version ".tar.gz"))
137 "1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica"))))
138 (build-system gnu-build-system)
139 (home-page "http://mcmc-jags.sourceforge.net/")
141 `(("gfortran" ,gfortran)
143 (synopsis "Gibbs sampler")
144 (description "JAGS is Just Another Gibbs Sampler. It is a program for
145 analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
146 simulation not wholly unlike BUGS. JAGS was written with three aims in mind:
149 @item To have a cross-platform engine for the BUGS language;
150 @item To be extensible, allowing users to write their own functions,
151 distributions and samplers;
152 @item To be a platform for experimentation with ideas in Bayesian modelling.
154 (license license:gpl2)))
156 (define-public libxls
163 (uri (string-append "https://github.com/libxls/libxls/releases/download/"
164 "v" version "/libxls-" version ".tar.gz"))
166 (base32 "00j2lrcvvhclmh3z9vy7myqq1br1jnnqkz2wzgk4a1gbg8c5afn5"))))
167 (build-system gnu-build-system)
168 (home-page "https://github.com/libxls/libxls")
169 (synopsis "Read binary (.xls) Excel spreadsheet files")
171 "libxls is a C library to read .xls spreadsheet files in the binary OLE
172 BIFF8 format as created by Excel 97 and later versions. It cannot write them.
174 This package also provides @command{xls2csv} to export Excel files to CSV.")
175 (license license:bsd-2)))
177 ;; Update this package together with the set of recommended packages: r-boot,
178 ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
179 ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
182 (name "r-with-tests")
186 (uri (string-append "mirror://cran/src/base/R-"
187 (version-major version) "/R-"
191 "02bmylmzrm9sdidirmwy233lghmd2346z725ca71ari68lzarz1n"))))
192 (build-system gnu-build-system)
194 `(#:disallowed-references (,tzdata-for-tests)
196 (list (string-append "LDFLAGS=-Wl,-rpath="
197 (assoc-ref %outputs "out")
199 ;; This affects the embedded timestamp of only the core packages.
200 "PKG_BUILT_STAMP=1970-01-01")
202 (modify-phases %standard-phases
203 (add-before 'configure 'do-not-compress-serialized-files
204 (lambda* (#:key inputs #:allow-other-keys)
205 ;; This ensures that Guix can detect embedded store references;
206 ;; see bug #28157 for details.
207 (substitute* "src/library/base/makebasedb.R"
208 (("compress = TRUE") "compress = FALSE"))
210 (add-before 'configure 'patch-uname
211 (lambda* (#:key inputs #:allow-other-keys)
212 (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
214 (substitute* "src/scripts/R.sh.in"
215 (("uname") uname-bin)))
217 (add-after 'unpack 'build-reproducibly
219 ;; The documentation contains time stamps to demonstrate
220 ;; documentation generation in different phases.
221 (substitute* "src/library/tools/man/Rd2HTML.Rd"
222 (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
223 "(removed for reproducibility)"))
225 ;; Remove timestamp from tracing environment. This fixes
226 ;; reproducibility of "methods.rd{b,x}".
227 (substitute* "src/library/methods/R/trace.R"
228 (("dateCreated = Sys.time\\(\\)")
229 "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
231 ;; Ensure that gzipped files are reproducible.
232 (substitute* '("src/library/grDevices/Makefile.in"
233 "doc/manual/Makefile.in")
234 (("R_GZIPCMD\\)" line)
235 (string-append line " -n")))
237 ;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
238 ;; queries the mtime of a given file and records it in an object.
239 ;; This is acceptable at runtime to detect stale source files,
240 ;; but it destroys reproducibility at build time.
242 ;; Similarly, the "srcfilecopy" procedure records the current
243 ;; time. We change both of them to respect SOURCE_DATE_EPOCH.
244 (substitute* "src/library/base/R/srcfile.R"
245 (("timestamp <- (timestamp.*|file.mtime.*)" _ time)
246 (string-append "timestamp <- \
247 as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
248 as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
249 } else { " time "}, origin=\"1970-01-01\")\n")))
251 ;; This library is installed using "install_package_description",
252 ;; so we need to pass the "builtStamp" argument.
253 (substitute* "src/library/tools/Makefile.in"
254 (("(install_package_description\\(.*\"')\\)\"" line prefix)
255 (string-append prefix ", builtStamp='1970-01-01')\"")))
257 (substitute* "src/library/Recommended/Makefile.in"
258 (("INSTALL_OPTS =" m)
259 (string-append m " --built-timestamp=1970-01-01" m)))
261 ;; R bundles an older version of help2man, which does not respect
262 ;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man,
263 ;; because that breaks a test.
264 (with-fluids ((%default-port-encoding "ISO-8859-1"))
265 (substitute* "tools/help2man.pl"
266 (("my \\$date = strftime \"%B %Y\", localtime" line)
267 (string-append line " 1"))))
269 (add-before 'configure 'set-default-pager
270 ;; Set default pager to "cat", because otherwise it is "false",
271 ;; making "help()" print nothing at all.
272 (lambda _ (setenv "PAGER" "cat") #t))
273 (add-before 'check 'set-timezone
274 ;; Some tests require the timezone to be set. However, the
275 ;; timezone may not just be "UTC", or else a brittle regression
276 ;; test in reg-tests-1d will fail.
277 (lambda* (#:key inputs #:allow-other-keys)
278 (setenv "TZ" "UTC+1")
280 (string-append (assoc-ref inputs "tzdata")
283 (add-after 'build 'make-info
284 (lambda _ (invoke "make" "info")))
285 (add-after 'build 'install-info
286 (lambda _ (invoke "make" "install-info"))))
288 `(;; We build the recommended packages here, because they are needed in
289 ;; order to run the test suite. We disable them in the r-minimal
292 "--with-blas=-lopenblas"
298 ,(string-append "--with-tcl-config="
299 (assoc-ref %build-inputs "tcl")
301 ,(string-append "--with-tk-config="
302 (assoc-ref %build-inputs "tk")
305 "--enable-BLAS-shlib"
306 "--with-system-tre")))
307 ;; R has some support for Java. When the JDK is available at configure
308 ;; time environment variables pointing to the JDK will be recorded under
309 ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
310 ;; CMD javareconf". "R CMD javareconf" appears to only be used to update
311 ;; the recorded environment variables in $R_HOME/etc. Refer to
312 ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
313 ;; for additional information.
315 ;; As the JDK is a rather large input with only very limited effects on R,
316 ;; we decided to drop it.
320 ("pkg-config" ,pkg-config)
321 ("texinfo" ,texinfo) ; for building HTML manuals
322 ("texlive" ,(texlive-union (list texlive-fonts-amsfonts
324 texlive-latex-amsfonts
326 texlive-latex-fancyvrb
327 texlive-latex-graphics
328 texlive-latex-hyperref
329 texlive-latex-oberdiek
331 texlive-latex-upquote
333 ("tzdata" ,tzdata-for-tests)
336 `(;; We need not only cairo here, but pango to ensure that tests for the
337 ;; "cairo" bitmapType plotting backend succeed.
339 ("coreutils" ,coreutils)
341 ("openblas" ,openblas)
342 ("gfortran" ,gfortran)
349 ("readline" ,readline)
350 ;; This avoids a reference to the ungraftable static bash. R uses the
351 ;; detected shell for the "system" procedure.
352 ("bash" ,bash-minimal)
358 (list (search-path-specification
359 (variable "R_LIBS_SITE")
360 (files (list "site-library/")))))
361 (home-page "https://www.r-project.org/")
362 (synopsis "Environment for statistical computing and graphics")
364 "R is a language and environment for statistical computing and graphics.
365 It provides a variety of statistical techniques, such as linear and nonlinear
366 modeling, classical statistical tests, time-series analysis, classification
367 and clustering. It also provides robust support for producing
368 publication-quality data plots. A large amount of 3rd-party packages are
369 available, greatly increasing its breadth and scope.")
370 (license license:gpl3+)))
372 (define-public r-minimal
373 (package (inherit r-with-tests)
377 ,@(substitute-keyword-arguments (package-arguments r-with-tests)
378 ((#:configure-flags flags)
379 ;; Do not build the recommended packages. The build system creates
380 ;; random temporary directories and embeds their names in some
381 ;; package files. We build these packages with the r-build-system
383 `(cons "--without-recommended-packages" ,flags)))))))
385 (define-public rmath-standalone
386 (package (inherit r-minimal)
387 (name "rmath-standalone")
390 (modify-phases %standard-phases
391 (add-after 'configure 'chdir
392 (lambda _ (chdir "src/nmath/standalone/") #t)))))
393 (synopsis "Standalone R math library")
395 "This package provides the R math library as an independent package.")))
397 (define-public r-boot
404 (uri (cran-uri "boot" version))
407 "0bx07zbb5nfz2xfgnzbspg7r5vxz4bjdz1ry4d1vk434vlcrxj1h"))))
408 (build-system r-build-system)
409 (home-page "https://cran.r-project.org/web/packages/boot")
410 (synopsis "Bootstrap functions for R")
412 "This package provides functions and datasets for bootstrapping from the
413 book \"Bootstrap Methods and Their Application\" by A.C. Davison and
414 D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
415 ;; Unlimited distribution
416 (license (license:non-copyleft "file://R/bootfuns.q"))))
418 (define-public r-mass
425 (uri (cran-uri "MASS" version))
428 "0x1ckf51y851g0kvbhsgdxb26vfpmbw3xdbcnh3ck7fjm13da4cr"))))
429 (properties `((upstream-name . "MASS")))
430 (build-system r-build-system)
431 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
432 (synopsis "Support functions and datasets for Venables and Ripley's MASS")
434 "This package provides functions and datasets for the book \"Modern
435 Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
436 ;; Either version may be picked.
437 (license (list license:gpl2 license:gpl3))))
439 (define-public r-class
446 (uri (cran-uri "class" version))
449 "1x1hqz8xyhbpq4krsh02glqnlzcch25agkmn4a3da9n723b37gzn"))))
450 (build-system r-build-system)
452 `(("r-mass" ,r-mass)))
453 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
454 (synopsis "R functions for classification")
456 "This package provides various functions for classification, including
457 k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
458 ;; Either of the two versions can be picked.
459 (license (list license:gpl2 license:gpl3))))
461 (define-public r-cluster
468 (uri (cran-uri "cluster" version))
471 "055af3yz2biqbsbwm4arwr1yqnj4gicpzv2i6dbfl5pnz2z5byga"))))
472 (build-system r-build-system)
474 `(("gfortran" ,gfortran)))
475 (home-page "https://cran.r-project.org/web/packages/cluster")
476 (synopsis "Methods for cluster analysis")
478 "This package provides methods for cluster analysis. It is a much
479 extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
480 Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
481 (license license:gpl2+)))
483 (define-public r-codetools
490 (uri (cran-uri "codetools" version))
493 "00bmhzqprqfn3w6ghx7sakai6s7il8gbksfiawj8in5mbhbncypn"))))
494 (build-system r-build-system)
495 (home-page "https://cran.r-project.org/web/packages/codetools")
496 (synopsis "Code analysis tools for R")
497 (description "This package provides code analysis tools for R to check R
498 code for possible problems.")
499 ;; Any version of the GPL.
500 (license (list license:gpl2+ license:gpl3+))))
502 (define-public r-foreign
509 (uri (cran-uri "foreign" version))
512 "124c9229is44p2rv7xyh2q86nsfi7vzyyh5n3c5ihziqrp4ig723"))))
513 (build-system r-build-system)
514 (home-page "https://cran.r-project.org/web/packages/foreign")
515 (synopsis "Read data stored by other statistics software")
517 "This package provides functions for reading and writing data stored by
518 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
519 for reading and writing some dBase files.")
520 (license license:gpl2+)))
522 (define-public r-kernsmooth
524 (name "r-kernsmooth")
529 (uri (cran-uri "KernSmooth" version))
532 "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb"))))
533 (properties `((upstream-name . "KernSmooth")))
534 (build-system r-build-system)
536 `(("gfortran" ,gfortran)))
537 (home-page "https://cran.r-project.org/web/packages/KernSmooth")
538 (synopsis "Functions for kernel smoothing")
540 "This package provides functions for kernel smoothing (and density
541 estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
542 \"Kernel Smoothing\".")
543 ;; Unlimited use and distribution
544 (license (license:non-copyleft "file://LICENCE.note"))))
546 (define-public r-lattice
552 (uri (cran-uri "lattice" version))
555 "0b8abkz7syscq883mrgv63pkwaqkcpwfx8rgbqy9vgfva0z5xszx"))))
556 (build-system r-build-system)
557 (home-page "http://lattice.r-forge.r-project.org/")
558 (synopsis "High-level data visualization system")
560 "The lattice package provides a powerful and elegant high-level data
561 visualization system inspired by Trellis graphics, with an emphasis on
562 multivariate data. Lattice is sufficient for typical graphics needs, and is
563 also flexible enough to handle most nonstandard requirements.")
564 (license license:gpl2+)))
566 (define-public r-matrix
573 (uri (cran-uri "Matrix" version))
576 "1k1zf92ycqr7fz44w7bp1p354ww7jg0wm23ybb8dzmbg37qfchyv"))))
577 (properties `((upstream-name . "Matrix")))
578 (build-system r-build-system)
580 `(("r-lattice" ,r-lattice)))
581 (home-page "http://Matrix.R-forge.R-project.org/")
582 (synopsis "Sparse and dense matrix classes and methods")
584 "This package provides classes and methods for dense and sparse matrices
585 and operations on them using LAPACK and SuiteSparse.")
586 (license license:gpl2+)))
588 (define-public r-nlme
595 (uri (cran-uri "nlme" version))
598 "0ml00g79bimjcl0sgn6h55l5b4gfmnsnc1vvmivggn0318k4c04i"))))
599 (build-system r-build-system)
601 `(("r-lattice" ,r-lattice)))
603 `(("gfortran" ,gfortran)))
604 (home-page "https://cran.r-project.org/web/packages/nlme")
605 (synopsis "Linear and nonlinear mixed effects models")
607 "This package provides tools to fit and compare Gaussian linear and
608 nonlinear mixed-effects models.")
609 (license license:gpl2+)))
611 (define-public r-mgcv
618 (uri (cran-uri "mgcv" version))
621 "1snkpnkkigwrj9zm31j1nlivv9ls56imz263cv167hnmghiahpmm"))))
622 (build-system r-build-system)
624 `(("r-matrix" ,r-matrix)
626 (home-page "https://cran.r-project.org/web/packages/mgcv")
627 (synopsis "Mixed generalised additive model computation")
629 "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
630 parameter estimation by GCV, REML or UBRE/AIC. The library includes a
631 @code{gam()} function, a wide variety of smoothers, JAGS support and
632 distributions beyond the exponential family.")
633 (license license:gpl2+)))
635 (define-public r-nnet
642 (uri (cran-uri "nnet" version))
645 "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7"))))
646 (build-system r-build-system)
647 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
648 (synopsis "Feed-forward neural networks and multinomial log-linear models")
650 "This package provides functions for feed-forward neural networks with a
651 single hidden layer, and for multinomial log-linear models.")
652 (license (list license:gpl2+ license:gpl3+))))
654 (define-public r-rpart
661 (uri (cran-uri "rpart" version))
664 "0p5frya963ppn476p5dxs2mnarsalksr6gw9zzmjsn8ikq7bx3ib"))))
665 (build-system r-build-system)
666 (home-page "https://cran.r-project.org/web/packages/rpart")
667 (synopsis "Recursive partitioning and regression trees")
669 "This package provides recursive partitioning functions for
670 classification, regression and survival trees.")
671 (license (list license:gpl2+ license:gpl3+))))
673 (define-public r-spatial
680 (uri (cran-uri "spatial" version))
683 "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
684 (build-system r-build-system)
685 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
686 (synopsis "Functions for kriging and point pattern analysis")
688 "This package provides functions for kriging and point pattern
690 ;; Either version may be picked.
691 (license (list license:gpl2 license:gpl3))))
693 (define-public r-survival
700 (uri (cran-uri "survival" version))
703 "1faiwyg7x8y2kfzb66l4yc8br0mdlz4k20znmjrwq96dbzhm3cam"))))
704 (build-system r-build-system)
706 `(("r-matrix" ,r-matrix)))
707 (home-page "https://github.com/therneau/survival")
708 (synopsis "Survival analysis")
710 "This package contains the core survival analysis routines, including
711 definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
712 curves, Cox models, and parametric accelerated failure time models.")
713 (license license:lgpl2.0+)))
716 (package (inherit r-minimal)
719 (build-system trivial-build-system)
720 (arguments '(#:builder (begin (mkdir %output) #t)))
722 `(("r-minimal" ,r-minimal)
725 ("r-cluster" ,r-cluster)
726 ("r-codetools" ,r-codetools)
727 ("r-foreign" ,r-foreign)
728 ("r-kernsmooth" ,r-kernsmooth)
729 ("r-lattice" ,r-lattice)
731 ("r-matrix" ,r-matrix)
736 ("r-spatial" ,r-spatial)
737 ("r-survival" ,r-survival)))))
746 (uri (cran-uri "bit" version))
749 "0m7jrqzpa1pk8ixcl814x06jf96nlvvr16x6did6cfk4zghsrfjw"))))
750 (build-system r-build-system)
751 (home-page "http://ff.r-forge.r-project.org")
752 (synopsis "Class for vectors of 1-bit booleans")
754 "This package provides bitmapped vectors of booleans (no @code{NA}s),
755 coercion from and to logicals, integers and integer subscripts, fast boolean
756 operators and fast summary statistics. With @code{bit} class vectors of true
757 binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
758 (license license:gpl2)))
760 (define-public r-bit64
767 (uri (cran-uri "bit64" version))
770 "07znvz9vp1nz1y5ljng4qyskvm943cdbmy996s67560ijxzsm6kv"))))
771 (build-system r-build-system)
774 (home-page "http://ff.r-forge.r-project.org/")
775 (synopsis "S3 class for vectors of 64 bit integers")
777 "The bit64 package provides serializable S3 atomic 64 bit (signed)
778 integers that can be used in vectors, matrices, arrays and @code{data.frames}.
779 Methods are available for coercion from and to logicals, integers, doubles,
780 characters and factors as well as many elementwise and summary functions.
781 Many fast algorithmic operations such as @code{match} and @code{order} support
782 interactive data exploration and manipulation and optionally leverage
784 (license license:gpl2)))
786 (define-public r-dichromat
793 (uri (cran-uri "dichromat" version))
795 (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
796 (build-system r-build-system)
797 (home-page "https://cran.r-project.org/web/packages/dichromat")
798 (synopsis "Color schemes for dichromats")
800 "Dichromat collapses red-green or green-blue distinctions to simulate the
801 effects of different types of color-blindness.")
802 (license license:gpl2+)))
804 (define-public r-digest
811 (uri (cran-uri "digest" version))
813 (base32 "1irhk2jaj9cg57cxprgyn1if06x121xwcxh1fzzn3148bl5lnrq5"))))
814 (build-system r-build-system)
815 ;; Vignettes require r-knitr, which requires r-digest, so we have to
816 ;; disable them and the tests.
819 #:configure-flags (list "--no-build-vignettes")))
820 (home-page "http://dirk.eddelbuettel.com/code/digest.html")
821 (synopsis "Create cryptographic hash digests of R objects")
823 "This package contains an implementation of a function @code{digest()} for
824 the creation of hash digests of arbitrary R objects (using the md5, sha-1,
825 sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
826 of R language objects, as well as a function @code{hmac()} to create hash-based
827 message authentication code.
829 Please note that this package is not meant to be deployed for cryptographic
830 purposes for which more comprehensive (and widely tested) libraries such as
831 OpenSSL should be used.")
832 (license license:gpl2+)))
834 (define-public r-estimability
836 (name "r-estimability")
840 (uri (cran-uri "estimability" version))
843 "0cifdaa71spkcxl4db4z884jrya865sg3dhcv4isd8fnzg2pjcd3"))))
844 (build-system r-build-system)
845 (home-page "https://cran.r-project.org/web/packages/estimability")
846 (synopsis "Tools for assessing estimability of linear predictions")
847 (description "Provides tools for determining estimability of linear
848 functions of regression coefficients, and @code{epredict} methods that handle
849 non-estimable cases correctly.")
850 (license license:gpl2+)))
852 (define-public r-pheatmap
859 (uri (cran-uri "pheatmap" version))
862 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
863 (build-system r-build-system)
865 `(("r-gtable" ,r-gtable)
866 ("r-rcolorbrewer" ,r-rcolorbrewer)
867 ("r-scales" ,r-scales)))
869 "https://cran.r-project.org/web/packages/pheatmap")
870 (synopsis "Pretty heatmaps")
872 "This package provides an implementation of heatmaps that offers more
873 control over dimensions and appearance.")
874 (license license:gpl2+)))
876 (define-public r-labeling
883 (uri (cran-uri "labeling" version))
885 (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
886 (build-system r-build-system)
887 (home-page "https://cran.r-project.org/web/packages/labeling")
888 (synopsis "Axis labeling algorithms")
889 (description "The labeling package provides a range of axis labeling
891 (license license:expat)))
893 (define-public r-magrittr
900 (uri (cran-uri "magrittr" version))
902 (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
903 (build-system r-build-system)
904 (home-page "https://cran.r-project.org/web/packages/magrittr/index.html")
905 (synopsis "A forward-pipe operator for R")
907 "Magrittr provides a mechanism for chaining commands with a new
908 forward-pipe operator, %>%. This operator will forward a value, or the result
909 of an expression, into the next function call/expression. There is flexible
910 support for the type of right-hand side expressions. For more information,
911 see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
912 (license license:expat)))
914 (define-public r-munsell
921 (uri (cran-uri "munsell" version))
923 (base32 "16g1fzisbpqb15yh3pqf3iia4csppva5dnv1z88x9dg263xskwyh"))))
924 (build-system r-build-system)
926 `(("r-colorspace" ,r-colorspace)))
927 (home-page "https://cran.r-project.org/web/packages/munsell")
928 (synopsis "Munsell colour system")
930 "The Munsell package contains Functions for exploring and using the
931 Munsell colour system.")
932 (license license:expat)))
934 (define-public r-permute
941 (uri (cran-uri "permute" version))
944 "0ra8p5mf2590azrkas8z2ry7mif77xqxd29n4zgyi5vll225726j"))))
945 (build-system r-build-system)
946 ;; Tests do not run correctly, but running them properly would entail a
947 ;; circular dependency with vegan.
948 (home-page "https://github.com/gavinsimpson/permute")
949 (synopsis "Functions for Generating Restricted Permutations of Data")
951 "This package provides a set of restricted permutation designs for freely
952 exchangeable, line transects (time series), spatial grid designs and permutation
953 of blocks (groups of samples). @code{permute} also allows split-plot designs,
954 in which the whole-plots or split-plots or both can be freely exchangeable.")
955 (license license:gpl2+)))
957 (define-public r-plyr
964 (uri (cran-uri "plyr" version))
966 (base32 "1igar5pcjqh0jyxv0z3jah8rz617vfa86vw0r5c7c031b7bj5db0"))))
967 (build-system r-build-system)
968 (native-inputs `(("r-rcpp" ,r-rcpp)))
969 (home-page "http://had.co.nz/plyr")
970 (synopsis "Tools for Splitting, Applying and Combining Data")
972 "Plyr is a set of tools that solves a common set of problems: you need to
973 break a big problem down into manageable pieces, operate on each piece and
974 then put all the pieces back together. For example, you might want to fit a
975 model to each spatial location or time point in your study, summarise data by
976 panels or collapse high-dimensional arrays to simpler summary statistics.")
977 (license license:expat)))
979 (define-public r-proto
986 (uri (cran-uri "proto" version))
988 (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
989 (build-system r-build-system)
990 (home-page "https://github.com/hadley/proto")
991 (synopsis "Prototype object-based programming")
993 "Proto is an object oriented system using object-based, also called
994 prototype-based, rather than class-based object oriented ideas.")
995 (license license:gpl2+)))
997 (define-public r-rcolorbrewer
999 (name "r-rcolorbrewer")
1004 (uri (cran-uri "RColorBrewer" version))
1006 (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
1007 (build-system r-build-system)
1008 (home-page "https://cran.r-project.org/web/packages/RColorBrewer")
1009 (synopsis "ColorBrewer palettes")
1011 "This package provides color schemes for maps (and other graphics)
1012 designed by Cynthia Brewer as described at http://colorbrewer2.org")
1013 ;; Includes code licensed under bsd-4
1014 (license license:asl2.0)))
1016 (define-public r-sendmailr
1018 (name "r-sendmailr")
1023 (uri (cran-uri "sendmailR" version))
1026 "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
1027 (properties `((upstream-name . "sendmailR")))
1028 (build-system r-build-system)
1030 `(("r-base64enc" ,r-base64enc)))
1032 "https://cran.r-project.org/web/packages/sendmailR")
1033 (synopsis "Send email using R")
1035 "This package contains a simple SMTP client which provides a portable
1036 solution for sending email, including attachments, from within R.")
1037 (license license:gpl2+)))
1039 (define-public r-stringi
1046 (uri (cran-uri "stringi" version))
1049 "1vbr6g9p1iyzdj7wfw6afyizvnd1a2srfvkl72pq23vhdcwwpkhk"))))
1050 (build-system r-build-system)
1051 (inputs `(("icu4c" ,icu4c)))
1052 (native-inputs `(("pkg-config" ,pkg-config)))
1053 (home-page "http://stringi.rexamine.com/")
1054 (synopsis "Character string processing facilities")
1056 "This package allows for fast, correct, consistent, portable, as well as
1057 convenient character string/text processing in every locale and any native
1058 encoding. Owing to the use of the ICU library, the package provides R users
1059 with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
1060 programmers. Among available features there are: pattern searching
1061 (e.g. via regular expressions), random string generation, string collation,
1062 transliteration, concatenation, date-time formatting and parsing, etc.")
1063 (license license:bsd-3)))
1065 (define-public r-stringr
1072 (uri (cran-uri "stringr" version))
1074 (base32 "1p9ip7p87gbbg4s6d3d392svvzz2b5dqdq2c8ilgvn4s78nlsq47"))))
1075 (build-system r-build-system)
1077 `(("r-glue" ,r-glue)
1078 ("r-magrittr" ,r-magrittr)
1079 ("r-stringi" ,r-stringi)))
1080 (home-page "https://github.com/hadley/stringr")
1081 (synopsis "Simple, consistent wrappers for common string operations")
1083 "Stringr is a consistent, simple and easy to use set of wrappers around
1084 the fantastic @code{stringi} package. All function and argument names (and
1085 positions) are consistent, all functions deal with \"NA\"'s and zero length
1086 vectors in the same way, and the output from one function is easy to feed into
1087 the input of another.")
1088 (license license:gpl2+)))
1090 (define-public r-reshape2
1097 (uri (cran-uri "reshape2" version))
1099 (base32 "03ki5ka1dj208fc0dclbm0b4xp9d769pah2j9cs34l776p4r9zwa"))))
1100 (build-system r-build-system)
1102 `(("r-plyr" ,r-plyr)
1104 ("r-stringr" ,r-stringr)))
1105 (home-page "https://github.com/hadley/reshape")
1106 (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
1108 "Reshape2 is an R library to flexibly restructure and aggregate data
1109 using just two functions: melt and dcast (or acast).")
1110 (license license:expat)))
1112 (define-public r-scales
1119 (uri (cran-uri "scales" version))
1121 (base32 "0353dkh3d7x78463c6ds80hcml59lrqwr8rlv82a8dnkxla4l7qc"))))
1122 (build-system r-build-system)
1124 `(("r-labeling" ,r-labeling)
1125 ("r-munsell" ,r-munsell)
1126 ("r-rcolorbrewer" ,r-rcolorbrewer)
1129 ("r-viridislite" ,r-viridislite)))
1130 (home-page "https://github.com/hadley/scales")
1131 (synopsis "Scale functions for visualization")
1133 "This package provides graphical scales that map data to aesthetics, and
1134 provides methods for automatically determining breaks and labels for axes and
1136 (license license:expat)))
1138 (define-public r-ggplot2
1145 (uri (cran-uri "ggplot2" version))
1147 (base32 "1cvk9pw59kxx19kamqwa15h26rbznp0vvqpn7y8kgjssnrzqkdii"))))
1148 (build-system r-build-system)
1150 `(("r-digest" ,r-digest)
1151 ("r-gtable" ,r-gtable)
1152 ("r-lazyeval" ,r-lazyeval)
1155 ("r-tibble" ,r-tibble)
1156 ("r-reshape2" ,r-reshape2)
1157 ("r-rlang" ,r-rlang)
1158 ("r-scales" ,r-scales)
1159 ("r-svglite" ,r-svglite) ; Needed for 'ggsave'
1160 ("r-viridislite" ,r-viridislite)
1161 ("r-withr" ,r-withr)))
1162 (home-page "https://ggplot2.tidyverse.org")
1163 (synopsis "An implementation of the grammar of graphics")
1165 "Ggplot2 is an implementation of the grammar of graphics in R. It
1166 combines the advantages of both base and lattice graphics: conditioning and
1167 shared axes are handled automatically, and you can still build up a plot step
1168 by step from multiple data sources. It also implements a sophisticated
1169 multidimensional conditioning system and a consistent interface to map data to
1170 aesthetic attributes.")
1171 (license license:gpl2+)))
1173 (define-public r-ggdendro
1179 (uri (cran-uri "ggdendro" version))
1182 "1zzq1hxd0d1qa5hrzwfkdw6fzscpcafbwbpkrb62dm559y8awp0j"))))
1183 (build-system r-build-system)
1185 `(("r-ggplot2" ,r-ggplot2)
1187 ("r-knitr" ,r-knitr)))
1188 (home-page "https://github.com/andrie/ggdendro")
1189 (synopsis "Create Dendrograms and Tree Diagrams Using ggplot2")
1190 (description "This is a set of tools for dendrograms and tree plots using
1191 ggplot2. The ggplot2 philosophy is to clearly separate data from the
1192 presentation. Unfortunately the plot method for dendrograms plots directly
1193 to a plot device with out exposing the data. The ggdendro package resolves
1194 this by making available functions that extract the dendrogram plot data.
1195 The package provides implementations for tree, rpart, as well as diana and
1196 agnes cluster diagrams.")
1197 (license license:gpl2+)))
1199 (define-public r-gdtools
1206 (uri (cran-uri "gdtools" version))
1209 "0w4fihf52q5qxxk0lg36x6yvjjl8vw66y60ncdjs5fvnxqn5z2vb"))))
1210 (build-system r-build-system)
1212 `(("pkg-config" ,pkg-config)))
1217 `(("r-rcpp" ,r-rcpp)
1218 ("r-withr" ,r-withr)))
1219 (home-page "https://cran.r-project.org/web/packages/gdtools")
1220 (synopsis "Utilities for graphical rendering")
1222 "The @code{gdtools} package provides functionalities to get font metrics
1223 and to generate base64 encoded string from raster matrix.")
1224 (license license:gpl3)))
1226 (define-public r-svglite
1233 (uri (cran-uri "svglite" version))
1236 "1gwv51wqp6pgm2f9gavsiq65njs77fr49n8y6y9ax60k3a4vvg14"))))
1237 (build-system r-build-system)
1240 ("r-gdtools" ,r-gdtools)
1241 ("r-rcpp" ,r-rcpp)))
1242 (home-page "https://github.com/hadley/svglite")
1243 (synopsis "SVG graphics device")
1245 "@code{svglite} is a graphics device that produces clean
1246 @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
1247 hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
1248 considerably faster, produces smaller files, and leaves text as is.")
1249 (license license:gpl2+)))
1251 (define-public r-assertthat
1253 (name "r-assertthat")
1257 (uri (cran-uri "assertthat" version))
1260 "17wy5bdfzg73sg2clisg1k3zyn1adkj59x56m5nwia2k8z67zkw5"))))
1261 (build-system r-build-system)
1262 (home-page "https://github.com/hadley/assertthat")
1263 (synopsis "Easy pre and post assertions")
1265 "Assertthat is an extension to stopifnot() that makes it easy to declare
1266 the pre and post conditions that your code should satisfy, while also
1267 producing friendly error messages so that your users know what they've done
1269 (license license:gpl3+)))
1271 (define-public r-lazyeval
1277 (uri (cran-uri "lazyeval" version))
1280 "1m10i059csrcqkcn59a8wspn784alxsq3symzhn24mhhl894346n"))))
1281 (build-system r-build-system)
1282 (home-page "https://github.com/hadley/lazyeval")
1283 (synopsis "Lazy (non-standard) evaluation in R")
1285 "This package provides the tools necessary to do non-standard
1286 evaluation (NSE) in R.")
1287 (license license:gpl3+)))
1289 (define-public r-dbi
1295 (uri (cran-uri "DBI" version))
1298 "1x8wy2vg2gcgd9bww04qmf0dsn3kp0rfjd8q8j1r2x9zxccg25pz"))))
1299 (build-system r-build-system)
1300 (home-page "https://github.com/rstats-db/DBI")
1301 (synopsis "R database interface")
1303 "The DBI package provides a database interface (DBI) definition for
1304 communication between R and relational database management systems. All
1305 classes in this package are virtual and need to be extended by the various
1306 R/DBMS implementations.")
1307 (license license:lgpl2.0+)))
1312 (version "1.69.0-1")
1315 (uri (cran-uri "BH" version))
1318 "18mckfwxxv8m8rzaz03mg2h6vhaj7y131h6yasfg0s73nxj47zd0"))))
1319 (build-system r-build-system)
1320 (home-page "https://github.com/eddelbuettel/bh")
1321 (synopsis "R package providing subset of Boost headers")
1323 "This package aims to provide the most useful subset of Boost libraries
1324 for template use among CRAN packages.")
1325 (license license:boost1.0)))
1327 (define-public r-evaluate
1333 (uri (cran-uri "evaluate" version))
1336 "0a2y7j534gbgixkwj9r1z76l2vssw4g1hznzbpclc076wkdqpj58"))))
1337 (build-system r-build-system)
1338 (home-page "https://github.com/hadley/evaluate")
1339 (synopsis "Parsing and evaluation tools for R")
1341 "This package provides tools that allow you to recreate the parsing,
1342 evaluation and display of R code, with enough information that you can
1343 accurately recreate what happens at the command line. The tools can easily be
1344 adapted for other output formats, such as HTML or LaTeX.")
1345 (license license:gpl3+)))
1347 (define-public r-formatr
1353 (uri (cran-uri "formatR" version))
1356 "1nsxbrx31k3y6yql30qkrvdfyznlia2qfvwv95mfiy7m7wdn4rm3"))))
1357 (build-system r-build-system)
1358 (home-page "http://yihui.name/formatR")
1359 (synopsis "Format R code automatically")
1361 "This package provides a function to format R source code. Spaces and
1362 indent will be added to the code automatically, and comments will be preserved
1363 under certain conditions, so that R code will be more human-readable and tidy.
1364 There is also a Shiny app as a user interface in this package.")
1365 (license license:gpl3+)))
1367 (define-public r-highr
1373 (uri (cran-uri "highr" version))
1376 "0my6idnhmmgs4q1vs40y2lh56yij2p59mpwvm53wjs2zk6x1zl2b"))))
1377 (build-system r-build-system)
1378 (home-page "https://github.com/yihui/highr")
1379 (synopsis "Syntax highlighting for R source code")
1381 "This package provides syntax highlighting for R source code. Currently
1382 it supports LaTeX and HTML output. Source code of other languages is
1383 supported via Andre Simon's highlight package.")
1384 (license license:gpl3+)))
1386 (define-public r-mime
1392 (uri (cran-uri "mime" version))
1395 "12vpip67ajb90b8p96w43ir7mavrw2i61bwvpfnrlmlj9kj3w20i"))))
1396 (build-system r-build-system)
1397 (home-page "https://github.com/yihui/mime")
1398 (synopsis "R package to map filenames to MIME types")
1400 "This package guesses the MIME type from a filename extension using the
1401 data derived from /etc/mime.types in UNIX-type systems.")
1402 (license license:gpl2)))
1404 (define-public r-markdown
1410 (uri (cran-uri "markdown" version))
1413 "19nrz0ba1yd5kicd65crkkz2r3kialm2hm6zdkp495l2s5r80b8p"))))
1414 (build-system r-build-system)
1415 ;; Skip check phase because the tests require the r-knitr package to be
1416 ;; installed. This prevents installation failures. Knitr normally
1417 ;; shouldn't be available since r-markdown is a dependency of the r-knitr
1419 (arguments `(#:tests? #f))
1421 `(("r-mime" ,r-mime)))
1422 (home-page "https://github.com/rstudio/markdown")
1423 (synopsis "Markdown rendering for R")
1425 "This package provides R bindings to the Sundown Markdown rendering
1426 library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
1427 syntax that can be converted to XHTML or other formats.")
1428 (license license:gpl2)))
1430 (define-public r-yaml
1436 (uri (cran-uri "yaml" version))
1439 "0in562nd0i23cg91a8kdbqgim656fgscykwi0icsnq53xj3srg2m"))))
1440 (build-system r-build-system)
1441 (home-page "https://cran.r-project.org/web/packages/yaml/")
1442 (synopsis "Methods to convert R data to YAML and back")
1444 "This package implements the libyaml YAML 1.1 parser and
1445 emitter (http://pyyaml.org/wiki/LibYAML) for R.")
1446 (license license:bsd-3)))
1448 (define-public r-knitr
1454 (uri (cran-uri "knitr" version))
1457 "16ba4258c915xydhniw4cw7fvv1vp4cnwd1w49ykx7zw00rznfq6"))))
1458 (build-system r-build-system)
1460 `(("r-evaluate" ,r-evaluate)
1461 ("r-highr" ,r-highr)
1462 ("r-markdown" ,r-markdown)
1463 ("r-stringr" ,r-stringr)
1465 ("r-yaml" ,r-yaml)))
1466 (home-page "http://yihui.name/knitr/")
1467 (synopsis "General-purpose package for dynamic report generation in R")
1469 "This package provides a general-purpose tool for dynamic report
1470 generation in R using Literate Programming techniques.")
1471 ;; The code is released under any version of the GPL. As it is used by
1472 ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
1474 (license license:gpl2+)))
1476 (define-public r-knitrbootstrap
1478 (name "r-knitrbootstrap")
1483 (uri (cran-uri "knitrBootstrap" version))
1486 "1aj60j7f0gcs120fdrnfbnb7vk7lfn1phil0mghg6a5zldz4cqs3"))))
1487 (properties `((upstream-name . "knitrBootstrap")))
1488 (build-system r-build-system)
1490 `(("r-knitr" ,r-knitr)
1491 ("r-rmarkdown" ,r-rmarkdown)
1492 ("r-markdown" ,r-markdown)))
1493 (home-page "https://github.com/jimhester/knitrBootstrap")
1494 (synopsis "Knitr bootstrap framework")
1496 "This package provides a framework to create Bootstrap 3 HTML reports
1497 from knitr Rmarkdown.")
1498 (license license:expat)))
1500 (define-public r-microbenchmark
1502 (name "r-microbenchmark")
1506 (uri (cran-uri "microbenchmark" version))
1509 "1sn1fxgzakm5iqbgc35g3k4yi0iqrkmwz33cvdrphrzh1lxnmi3s"))))
1510 (build-system r-build-system)
1511 (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
1512 (synopsis "Accurate timing functions for R")
1514 "This package provides infrastructure to accurately measure and compare
1515 the execution time of R expressions.")
1516 (license license:bsd-2)))
1518 (define-public r-pryr
1524 (uri (cran-uri "pryr" version))
1527 "06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k"))))
1528 (build-system r-build-system)
1530 `(("r-stringr" ,r-stringr)
1531 ("r-codetools" ,r-codetools)))
1533 `(("r-rcpp" ,r-rcpp)))
1534 (home-page "https://github.com/hadley/pryr")
1535 (synopsis "Tools for computing on the R language")
1537 "This package provides useful tools to pry back the covers of R and
1538 understand the language at a deeper level.")
1539 (license license:gpl2)))
1541 (define-public r-memoise
1547 (uri (cran-uri "memoise" version))
1550 "034qfc2xlh30x1q2vya239w34a3ir3y2fwnx2agbgbi6592zjxmj"))))
1551 (build-system r-build-system)
1553 `(("r-digest" ,r-digest)))
1554 (home-page "https://github.com/hadley/memoise")
1555 (synopsis "Memoise functions for R")
1557 "This R package allows to cache the results of a function so that when
1558 you call it again with the same arguments it returns the pre-computed value.")
1559 (license license:expat)))
1561 (define-public r-crayon
1567 (uri (cran-uri "crayon" version))
1570 "0s7s6vc3ww8pzanpjisym4jjvwcc5pi2qg8srx7jqlz9j3wrnvpw"))))
1571 (build-system r-build-system)
1573 `(("r-memoise" ,r-memoise)))
1574 (home-page "https://github.com/gaborcsardi/crayon")
1575 (synopsis "Colored terminal output for R")
1577 "Colored terminal output on terminals that support ANSI color and
1578 highlight codes. It also works in Emacs ESS. ANSI color support is
1579 automatically detected. Colors and highlighting can be combined and nested.
1580 New styles can also be created easily. This package was inspired by the
1581 \"chalk\" JavaScript project.")
1582 (license license:expat)))
1584 (define-public r-praise
1591 (uri (cran-uri "praise" version))
1594 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
1595 (build-system r-build-system)
1596 (home-page "https://github.com/gaborcsardi/praise")
1597 (synopsis "Functions to praise users")
1599 "This package provides template functions to assist in building friendly
1600 R packages that praise their users.")
1601 (license license:expat)))
1603 (define-public r-testthat
1609 (uri (cran-uri "testthat" version))
1612 "0y0bvggm4pzkzp6xn7b8cf3ybqp9ijxkhhyp3z49a9iipc90bvk7"))))
1613 (build-system r-build-system)
1616 ("r-crayon" ,r-crayon)
1617 ("r-digest" ,r-digest)
1618 ("r-evaluate" ,r-evaluate)
1619 ("r-magrittr" ,r-magrittr)
1620 ("r-praise" ,r-praise)
1622 ("r-rlang" ,r-rlang)
1623 ("r-withr" ,r-withr)))
1624 (home-page "https://github.com/hadley/testthat")
1625 (synopsis "Unit testing for R")
1627 "This package provides a unit testing system for R designed to be fun,
1628 flexible and easy to set up.")
1629 (license license:expat)))
1637 (uri (cran-uri "R6" version))
1640 "1kmbw2k5vvzwh3wwmn66mszpfny0z6k8dca980qgbxgvfh0i3gkh"))))
1641 (build-system r-build-system)
1642 (home-page "https://github.com/wch/R6/")
1643 (synopsis "Classes with reference semantics in R")
1645 "The R6 package allows the creation of classes with reference semantics,
1646 similar to R's built-in reference classes. Compared to reference classes, R6
1647 classes are simpler and lighter-weight, and they are not built on S4 classes
1648 so they do not require the methods package. These classes allow public and
1649 private members, and they support inheritance, even when the classes are
1650 defined in different packages.")
1651 (license license:expat)))
1653 (define-public r-rlang
1659 (uri (cran-uri "rlang" version))
1662 "038mmbmklw17ncgz53vrdx2506c1jj6di3y165bbx2sl2yia8j4p"))))
1663 (build-system r-build-system)
1664 (home-page "http://rlang.tidyverse.org")
1665 (synopsis "Functions for base types, core R and Tidyverse features")
1666 (description "This package provides a toolbox for working with base types,
1667 core R features like the condition system, and core @code{Tidyverse} features
1668 like tidy evaluation.")
1669 (license license:gpl3)))
1671 (define-public r-tibble
1678 (uri (cran-uri "tibble" version))
1681 "06jfayiip8j8ibdhw3fvxn4n8aqbqhwanrszpzlsf92xdfgfm34s"))))
1682 (build-system r-build-system)
1685 ("r-crayon" ,r-crayon)
1686 ("r-fansi" ,r-fansi)
1687 ("r-pkgconfig" ,r-pkgconfig)
1688 ("r-pillar" ,r-pillar)
1689 ("r-rlang" ,r-rlang)))
1690 (home-page "https://github.com/hadley/tibble")
1691 (synopsis "Simple data frames")
1693 "This package provides a @code{tbl_df} class that offers better checking
1694 and printing capabilities than traditional data frames.")
1695 (license license:expat)))
1697 (define-public r-dplyr
1703 (uri (cran-uri "dplyr" version))
1706 "032c89wa04g9rih9shyvwl3il0bsrv3xk489x6867sk9bb3amd38"))))
1707 (build-system r-build-system)
1709 `(("r-assertthat" ,r-assertthat)
1712 ("r-magrittr" ,r-magrittr)
1713 ("r-pkgconfig" ,r-pkgconfig)
1714 ("r-plogr" ,r-plogr)
1717 ("r-rlang" ,r-rlang)
1718 ("r-tibble" ,r-tibble)
1719 ("r-tidyselect" ,r-tidyselect)))
1720 (home-page "https://github.com/hadley/dplyr")
1721 (synopsis "Tools for working with data frames in R")
1723 "dplyr is the next iteration of plyr. It is focussed on tools for
1724 working with data frames. It has three main goals: 1) identify the most
1725 important data manipulation tools needed for data analysis and make them easy
1726 to use in R; 2) provide fast performance for in-memory data by writing key
1727 pieces of code in C++; 3) use the same code interface to work with data no
1728 matter where it is stored, whether in a data frame, a data table or
1730 (license license:expat)))
1732 (define-public r-dbplyr
1739 (uri (cran-uri "dbplyr" version))
1742 "1q2dflr88s5a1amzfld3087q422vf70052qn84zyd8895kdg10xp"))))
1743 (build-system r-build-system)
1745 `(("r-assertthat" ,r-assertthat)
1747 ("r-dplyr" ,r-dplyr)
1749 ("r-purrr" ,r-purrr)
1751 ("r-rlang" ,r-rlang)
1752 ("r-tibble" ,r-tibble)
1753 ("r-tidyselect" ,r-tidyselect)))
1754 (home-page "https://github.com/tidyverse/dbplyr")
1755 (synopsis "Dplyr back end for databases")
1757 "This package provides a dplyr back end for databases that allows you to
1758 work with remote database tables as if they are in-memory data frames. Basic
1759 features works with any database that has a @code{DBI} back end; more advanced
1760 features require SQL translation to be provided by the package author.")
1761 (license license:expat)))
1763 (define-public r-acepack
1770 (uri (cran-uri "acepack" version))
1773 "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
1774 (build-system r-build-system)
1776 `(("gfortran" ,gfortran)))
1777 (home-page "https://cran.r-project.org/web/packages/acepack")
1778 (synopsis "Functions for regression transformations")
1780 "This package provides ACE and AVAS methods for choosing regression
1782 (license license:expat)))
1784 (define-public r-formula
1791 (uri (cran-uri "Formula" version))
1794 "0wiqh8rr9d5ciy80wj8f5fnmiiw0ywanvvnhkwd622dx42dk848l"))))
1795 (properties `((upstream-name . "Formula")))
1796 (build-system r-build-system)
1797 (home-page "https://cran.r-project.org/web/packages/Formula")
1798 (synopsis "Extended model formulas")
1800 "This package provides a new class @code{Formula}, which extends the base
1801 class @code{formula}. It supports extended formulas with multiple parts of
1802 regressors on the right-hand side and/or multiple responses on the left-hand
1804 (license (list license:gpl2+ license:gpl3+))))
1806 (define-public r-locfit
1813 (uri (cran-uri "locfit" version))
1816 "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
1817 (build-system r-build-system)
1819 `(("r-lattice" ,r-lattice)))
1820 (home-page "https://cran.r-project.org/web/packages/locfit")
1821 (synopsis "Local regression, likelihood and density estimation")
1823 "This package provides functions used for local regression, likelihood
1824 and density estimation.")
1825 (license (list license:gpl2+ license:gpl3+))))
1827 (define-public r-chron
1833 (uri (cran-uri "chron" version))
1836 "02bkywwsxwrxc035hv51dxgdm1fjxdm7dn19ivifln59dfs1862j"))))
1837 (build-system r-build-system)
1838 (home-page "https://cran.r-project.org/web/packages/chron")
1839 (synopsis "Chronological R objects which can handle dates and times")
1841 "This package provides chronological R objects which can handle dates and
1843 (license license:gpl2)))
1845 (define-public r-data-table
1847 (name "r-data-table")
1851 (uri (cran-uri "data.table" version))
1854 "1x929lwhai6nkppm4zvicyw5qh5va5sizp86r30qnfkh1n7w2mfv"))))
1855 (build-system r-build-system)
1856 (home-page "https://github.com/Rdatatable/data.table/wiki")
1857 (synopsis "Enhanced version of data.frame R object")
1859 "The R package @code{data.table} is an extension of @code{data.frame}
1860 providing functions for fast aggregation of large data (e.g. 100GB in RAM),
1861 fast ordered joins, fast add/modify/delete of columns by group, column listing
1862 and fast file reading.")
1863 (license license:gpl3+)))
1865 (define-public r-xtable
1872 (uri (cran-uri "xtable" version))
1875 "077xfm0gphvhsay75amd9v90zk57kjgrrlgih04fyrbqqblc1gjs"))))
1876 (build-system r-build-system)
1878 `(("r-knitr" ,r-knitr))) ; for vignettes
1879 (home-page "http://xtable.r-forge.r-project.org/")
1880 (synopsis "Export R tables to LaTeX or HTML")
1882 "This package provides tools to export R data as LaTeX and HTML tables.")
1883 (license license:gpl2+)))
1885 (define-public python-patsy
1887 (name "python-patsy")
1891 (uri (pypi-uri "patsy" version ".zip"))
1894 "1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w"))))
1895 (build-system python-build-system)
1898 (modify-phases %standard-phases
1900 (lambda _ (invoke "nosetests" "-v"))))))
1902 `(("python-numpy" ,python-numpy)
1903 ("python-scipy" ,python-scipy)
1904 ("python-six" ,python-six)))
1906 `(("python-nose" ,python-nose)
1908 (home-page "https://github.com/pydata/patsy")
1909 (synopsis "Describe statistical models and build design matrices")
1911 "Patsy is a Python package for describing statistical models and for
1912 building design matrices.")
1913 ;; The majority of the code is distributed under BSD-2. The module
1914 ;; patsy.compat contains code derived from the Python standard library,
1915 ;; and is covered by the PSFL.
1916 (license (list license:bsd-2 license:psfl))))
1918 (define-public python2-patsy
1919 (package-with-python2 python-patsy))
1921 (define-public python-statsmodels
1923 (name "python-statsmodels")
1928 (uri (pypi-uri "statsmodels" version))
1931 "0fxs8a7sp4d7jvqlm36yi45i2d28kjfvraf9q8i9jr1chhxgjqb4"))))
1932 (build-system python-build-system)
1934 `(;; The test suite is very large and rather brittle. Tests often fail
1935 ;; because of minor changes in dependencies that upstream hasn't fixed
1936 ;; in a new release.
1939 (modify-phases %standard-phases
1940 (add-after 'unpack 'set-matplotlib-backend-to-agg
1942 ;; Set the matplotlib backend to Agg to avoid problems using the
1943 ;; GTK backend without a display.
1944 (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py")
1945 '("statsmodels/tsa/vector_ar/tests/test_var.py"
1946 "statsmodels/duration/tests/test_survfunc.py"))
1947 (("import matplotlib\\.pyplot as plt" line)
1948 (string-append "import matplotlib;matplotlib.use('Agg');"
1952 `(("python-numpy" ,python-numpy)
1953 ("python-scipy" ,python-scipy)
1954 ("python-pandas" ,python-pandas)
1955 ("python-patsy" ,python-patsy)
1956 ("python-matplotlib" ,python-matplotlib)))
1958 `(("python-cython" ,python-cython)
1959 ("python-nose" ,python-nose)
1960 ("python-sphinx" ,python-sphinx)))
1961 (home-page "http://statsmodels.sourceforge.net/")
1962 (synopsis "Statistical modeling and econometrics in Python")
1964 "Statsmodels is a Python package that provides a complement to scipy for
1965 statistical computations including descriptive statistics and estimation and
1966 inference for statistical models.")
1967 (license license:bsd-3)))
1969 (define-public python2-statsmodels
1970 (let ((stats (package-with-python2 python-statsmodels)))
1971 (package (inherit stats)
1973 `(("python2-pytz" ,python2-pytz)
1974 ("python2-numpy" ,python2-numpy)
1975 ("python2-scipy" ,python2-scipy)
1976 ("python2-pandas" ,python2-pandas)
1977 ("python2-patsy" ,python2-patsy)
1978 ("python2-matplotlib" ,python2-matplotlib))))))
1980 (define-public r-coda
1986 (uri (cran-uri "coda" version))
1989 "1mn50bshky968gn4nf6vnkaa768fnvm1xmhkms7szwdw9341zpyk"))))
1990 (build-system r-build-system)
1992 `(("r-lattice" ,r-lattice)))
1993 (home-page "https://cran.r-project.org/web/packages/coda")
1994 (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
1995 (description "This package provides functions for summarizing and plotting
1996 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
1997 diagnostic tests of convergence to the equilibrium distribution of the Markov
1999 (license license:gpl2+)))
2001 (define-public r-ade4
2008 (uri (cran-uri "ade4" version))
2011 "16z9jk4qj35ghsk4lwmq241dgc770y8a70dlmp9q4gz6d8ssgl7m"))))
2012 (build-system r-build-system)
2014 `(("r-mass" ,r-mass)))
2015 (home-page "http://pbil.univ-lyon1.fr/ADE-4")
2016 (synopsis "Multivariate data analysis and graphical display")
2018 "The ade4 package contains data analysis functions to analyze ecological
2019 and environmental data in the framework of Euclidean exploratory methods.")
2020 (license license:gpl2+)))
2022 (define-public r-xml2
2029 (uri (cran-uri "xml2" version))
2032 "0186d7r36xw1z9f8ajz35a0dz4ch6hmrjl9536yc7vq78v4vn5an"))))
2033 (build-system r-build-system)
2035 `(("libxml2" ,libxml2)
2038 `(("pkg-config" ,pkg-config)))
2040 `(("r-rcpp" ,r-rcpp)))
2041 (home-page "https://github.com/hadley/xml2")
2042 (synopsis "Parse XML with R")
2044 "This package provides a simple, consistent interface to working with XML
2045 files in R. It is built on top of the libxml2 C library.")
2046 (license license:gpl2+)))
2048 (define-public r-multitaper
2050 (name "r-multitaper")
2055 (uri (cran-uri "multitaper" version))
2058 "04wd9bbhyx7697pfy0fpj02v1csr48hkpqj62h9p8a6w84ji4k68"))))
2059 (build-system r-build-system)
2061 `(("gfortran" ,gfortran)))
2062 (home-page "https://github.com/wesleyburr/multitaper/")
2063 (synopsis "Multitaper spectral analysis tools")
2065 "This package implements multitaper spectral estimation
2066 techniques using prolate spheroidal sequences (Slepians) and sine
2067 tapers for time series analysis. It includes an adaptive weighted
2068 multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
2069 F-test, and complex demodulation. The Slepians sequences are
2070 generated efficiently using a tridiagonal matrix solution, and
2071 jackknifed confidence intervals are available for most estimates.")
2072 (license license:gpl2+)))
2074 (define-public r-rversions
2076 (name "r-rversions")
2080 (uri (cran-uri "rversions" version))
2083 "0mkg9zrjxlbwqzijiysivrs523x48syqj30xdfp88clpkqfk435m"))))
2084 (build-system r-build-system)
2086 `(("r-curl" ,r-curl)
2087 ("r-xml2" ,r-xml2)))
2088 (home-page "https://github.com/metacran/rversions")
2089 (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
2091 "This package provides functions to query the main R repository to find
2092 the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
2093 previous R versions and their release dates.")
2094 (license license:expat)))
2096 (define-public r-whisker
2102 (uri (cran-uri "whisker" version))
2105 "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28"))))
2106 (build-system r-build-system)
2107 (home-page "https://github.com/edwindj/whisker")
2108 (synopsis "Logicless mustache templating for R")
2110 "This package provides logicless templating, with a syntax that is not
2112 (license license:gpl3+)))
2114 (define-public r-backports
2116 (name "r-backports")
2121 (uri (cran-uri "backports" version))
2124 "00zz969vc2gfi5p9q65pzghq2bxm3p9zqgwqswkyz9rgybz5wjzf"))))
2125 (build-system r-build-system)
2126 (home-page "https://cran.r-project.org/web/packages/backports")
2127 (synopsis "Reimplementations of functions introduced since R 3.0.0")
2129 "Provides implementations of functions which have been introduced in R
2130 since version 3.0.0. The backports are conditionally exported which results
2131 in R resolving the function names to the version shipped with R (if available)
2132 and uses the implemented backports as fallback. This way package developers
2133 can make use of the new functions without worrying about the minimum required
2135 (license license:gpl2+)))
2137 (define-public r-checkmate
2139 (name "r-checkmate")
2144 (uri (cran-uri "checkmate" version))
2147 "08ddpgs4mv5d5y4j054pm8drmxkn7yvhfpbghwxlizjpnxa5g8ps"))))
2148 (build-system r-build-system)
2150 `(("r-backports" ,r-backports)))
2151 (home-page "https://github.com/mllg/checkmate")
2152 (synopsis "Fast and versatile argument checks")
2154 "This package provides tests and assertions to perform frequent argument
2155 checks. A substantial part of the package was written in C to minimize any
2156 worries about execution time overhead.")
2157 (license license:bsd-3)))
2159 (define-public r-bbmisc
2166 (uri (cran-uri "BBmisc" version))
2169 "1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y"))))
2170 (properties `((upstream-name . "BBmisc")))
2171 (build-system r-build-system)
2173 `(("r-checkmate" ,r-checkmate)))
2174 (home-page "https://github.com/berndbischl/BBmisc")
2175 (synopsis "Miscellaneous functions for R package development")
2177 "This package provides miscellaneous helper functions for the development
2179 (license license:bsd-3)))
2181 (define-public r-fail
2188 (uri (cran-uri "fail" version))
2191 "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
2192 (build-system r-build-system)
2194 `(("r-bbmisc" ,r-bbmisc)
2195 ("r-checkmate" ,r-checkmate)))
2196 (home-page "https://github.com/mllg/fail")
2197 (synopsis "File abstraction interface layer (FAIL)")
2199 "This package provides a more comfortable interface to work with R data
2200 or source files in a key-value fashion.")
2201 (license license:bsd-3)))
2203 (define-public r-batchjobs
2205 (name "r-batchjobs")
2210 (uri (cran-uri "BatchJobs" version))
2213 "1zz4sspj596pijxlz321g0jy2rg9ki83j6fihbwisjwr66p2vk1m"))))
2214 (properties `((upstream-name . "BatchJobs")))
2215 (build-system r-build-system)
2217 `(("r-backports" ,r-backports)
2218 ("r-bbmisc" ,r-bbmisc)
2220 ("r-checkmate" ,r-checkmate)
2221 ("r-data-table" ,r-data-table)
2223 ("r-digest" ,r-digest)
2224 ("r-rsqlite" ,r-rsqlite)
2225 ("r-sendmailr" ,r-sendmailr)
2226 ("r-stringi" ,r-stringi)))
2227 (home-page "https://github.com/tudo-r/BatchJobs")
2228 (synopsis "Batch computing with R")
2230 "This package provides @code{Map}, @code{Reduce} and @code{Filter}
2231 variants to generate jobs on batch computing systems like PBS/Torque, LSF,
2232 SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
2233 (license license:bsd-2)))
2235 (define-public r-brew
2241 (uri (cran-uri "brew" version))
2244 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
2245 (build-system r-build-system)
2246 (home-page "https://cran.r-project.org/web/packages/brew")
2247 (synopsis "Templating framework for report generation")
2249 "The brew package implements a templating framework for mixing text and R
2250 code for report generation. The template syntax is similar to PHP, Ruby's erb
2251 module, Java Server Pages, and Python's psp module.")
2252 (license license:gpl2+)))
2254 (define-public r-desc
2261 (uri (cran-uri "desc" version))
2264 "1s6s13fk6sxwcj8wzkwxl9vr33153xx11p5wi9avqx3rzkabavz6"))))
2265 (build-system r-build-system)
2267 `(("r-assertthat" ,r-assertthat)
2268 ("r-crayon" ,r-crayon)
2270 ("r-rprojroot" ,r-rprojroot)))
2271 (home-page "https://github.com/r-pkgs/desc")
2272 (synopsis "Manipulate DESCRIPTION Files")
2274 "This package provides tools to read, write, create, and manipulate
2275 DESCRIPTION files. It is intended for packages that create or manipulate
2277 (license license:expat)))
2279 (define-public r-commonmark
2281 (name "r-commonmark")
2286 (uri (cran-uri "commonmark" version))
2289 "024iz1qp2kv6iz6y69ir0jk3qhjps86rhkzlcmhqsxx97rx7cjni"))))
2290 (build-system r-build-system)
2291 (home-page "https://cran.r-project.org/web/packages/commonmark")
2292 (synopsis "CommonMark and Github Markdown Rendering in R")
2294 "The CommonMark specification defines a rationalized version of markdown
2295 syntax. This package uses the @code{cmark} reference implementation for
2296 converting markdown text into various formats including HTML, LaTeX and groff
2297 man. In addition, it exposes the markdown parse tree in XML format. The latest
2298 version of this package also adds support for Github extensions including
2299 tables, autolinks and strikethrough text.")
2300 (license license:bsd-2)))
2302 (define-public r-roxygen2
2308 (uri (cran-uri "roxygen2" version))
2311 "0wq29ilqas8yn2z8v49fk0hbgchg29nmyyhwczgdipz0cbhbfipd"))))
2312 (build-system r-build-system)
2314 `(("r-brew" ,r-brew)
2315 ("r-commonmark" ,r-commonmark)
2317 ("r-digest" ,r-digest)
2318 ("r-pkgload" ,r-pkgload)
2319 ("r-purrr" ,r-purrr)
2322 ("r-stringi" ,r-stringi)
2323 ("r-stringr" ,r-stringr)
2324 ("r-xml2" ,r-xml2)))
2326 `(("r-knitr" ,r-knitr))) ; for vignettes
2327 (home-page "https://github.com/klutometis/roxygen")
2328 (synopsis "In-source documentation system for R")
2330 "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
2331 collation, and NAMESPACE files.")
2332 (license license:gpl2+)))
2334 (define-public r-openssl
2341 (uri (cran-uri "openssl" version))
2344 "1ihz2qi33lhngl19xdanq0pbmfaacy63794mg8ll7z2lab3yryzp"))))
2345 (build-system r-build-system)
2347 `(("libressl" ,libressl)))
2349 `(("pkg-config" ,pkg-config)))
2351 `(("r-askpass" ,r-askpass)))
2352 (home-page "https://github.com/jeroenooms/openssl")
2353 (synopsis "Toolkit for encryption, signatures and certificates")
2355 "This package provides R bindings to OpenSSL libssl and libcrypto, plus
2356 custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
2357 and P-521. Cryptographic signatures can either be created and verified
2358 manually or via x509 certificates. AES block cipher is used in CBC mode for
2359 symmetric encryption; RSA for asymmetric (public key) encryption. High-level
2360 envelope functions combine RSA and AES for encrypting arbitrary sized data.
2361 Other utilities include key generators, hash functions (md5, sha1, sha256,
2362 etc), base64 encoder, a secure random number generator, and @code{bignum} math
2363 methods for manually performing crypto calculations on large multibyte
2365 (license license:expat)))
2367 (define-public r-httr
2373 (uri (cran-uri "httr" version))
2376 "0mp1il13q6n49n2hv1p2p8x6avjan6dr5az19ql4hb78pc3pwp37"))))
2377 (build-system r-build-system)
2379 `(("r-curl" ,r-curl)
2380 ("r-jsonlite" ,r-jsonlite)
2381 ("r-openssl" ,r-openssl)
2384 (home-page "https://github.com/hadley/httr")
2385 (synopsis "Tools for working with URLs and HTTP")
2387 "The aim of httr is to provide a wrapper for RCurl customised to the
2388 demands of modern web APIs. It provides useful tools for working with HTTP
2389 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
2390 functions make it easy to control additional request components.")
2391 (license license:expat)))
2393 (define-public r-git2r
2399 (uri (cran-uri "git2r" version))
2402 "15kpvz6ry2r8ii5hzinjwkggc5kgmkbcpsdwzahsf8gha52w80p0"))))
2403 (build-system r-build-system)
2404 ;; This R package contains modified sources of libgit2. This modified
2405 ;; version of libgit2 is built as the package is built. Hence libgit2 is
2406 ;; not among the inputs of this package.
2408 `(("libssh2" ,libssh2) ; for SSH transport
2409 ("openssl" ,openssl)
2412 `(("pkg-config" ,pkg-config)))
2413 (home-page "https://github.com/ropensci/git2r")
2414 (synopsis "Access Git repositories with R")
2416 "This package provides an R interface to the libgit2 library, which is a
2417 pure C implementation of the Git core methods.")
2418 ;; GPLv2 only with linking exception.
2419 (license license:gpl2)))
2421 (define-public r-rstudioapi
2423 (name "r-rstudioapi")
2427 (uri (cran-uri "rstudioapi" version))
2430 "15mbw607ncdf53mgga76n3va5zzdcjqz14nb0jcn9axwccqamic0"))))
2431 (build-system r-build-system)
2432 (home-page "https://cran.r-project.org/web/packages/rstudioapi")
2433 (synopsis "Safely access the RStudio API")
2435 "This package provides functions to access the RStudio API and provide
2436 informative error messages when it's not available.")
2437 (license license:expat)))
2439 (define-public r-devtools
2445 (uri (cran-uri "devtools" version))
2448 "028pppj39ng7q17k27531s8k00lmw982vz5krn74n9b8f2azm8lr"))))
2449 (build-system r-build-system)
2451 `(("r-callr" ,r-callr)
2453 ("r-digest" ,r-digest)
2454 ("r-git2r" ,r-git2r)
2456 ("r-jsonlite" ,r-jsonlite)
2457 ("r-memoise" ,r-memoise)
2458 ("r-pkgbuild" ,r-pkgbuild)
2459 ("r-pkgload" ,r-pkgload)
2460 ("r-rcmdcheck" ,r-rcmdcheck)
2461 ("r-remotes" ,r-remotes)
2462 ("r-rstudioapi" ,r-rstudioapi)
2463 ("r-sessioninfo" ,r-sessioninfo)
2464 ("r-usethis" ,r-usethis)
2465 ("r-withr" ,r-withr)))
2466 (home-page "https://github.com/hadley/devtools")
2467 (synopsis "Tools to make developing R packages easier")
2468 (description "The devtools package is a collection of package development
2469 tools to simplify the devolpment of R packages.")
2470 (license license:gpl2+)))
2472 (define-public r-withr
2478 (uri (cran-uri "withr" version))
2481 "11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1"))))
2482 (build-system r-build-system)
2483 (home-page "https://github.com/jimhester/withr")
2484 (synopsis "Run code with temporarily modified global state")
2486 "This package provides a set of functions to run R code in an environment
2487 in which global state has been temporarily modified. Many of these functions
2488 were originally a part of the r-devtools package.")
2489 (license license:gpl2+)))
2491 (define-public r-hms
2498 (uri (cran-uri "hms" version))
2501 "1g6hslk3z0xga38r71irxq802wskg6nv804mp8y9f7i2wfrj0y55"))))
2502 (build-system r-build-system)
2504 `(("r-rlang" ,r-rlang)
2505 ("r-pkgconfig" ,r-pkgconfig)))
2506 (home-page "https://github.com/rstats-db/hms")
2507 (synopsis "Pretty time of day")
2509 "This package implements an S3 class for storing and formatting
2510 time-of-day values, based on the @code{difftime} class.")
2511 (license license:gpl3+)))
2513 (define-public r-readr
2519 (uri (cran-uri "readr" version))
2522 "1wz496rw0ah433p755n3xac8gh7yzid4xgdjzd1a7wmpkgilvy9k"))))
2523 (build-system r-build-system)
2525 `(("r-clipr" ,r-clipr)
2526 ("r-crayon" ,r-crayon)
2529 ("r-tibble" ,r-tibble)
2532 (home-page "https://github.com/hadley/readr")
2533 (synopsis "Read tabular data")
2535 "This package provides functions to read flat or tabular text files from
2536 disk (or a connection).")
2537 (license license:gpl2+)))
2539 (define-public r-plotrix
2545 (uri (cran-uri "plotrix" version))
2548 "0ijfjlr7ls5hvfyzdmwab6bx0w3nvp0c8fgynj4355cj8mbzgmc3"))))
2549 (build-system r-build-system)
2550 (home-page "https://cran.r-project.org/web/packages/plotrix")
2551 (synopsis "Various plotting functions")
2553 "This package provides lots of plotting, various labeling, axis and color
2554 scaling functions for R.")
2555 (license license:gpl2+)))
2557 (define-public r-gridbase
2563 (uri (cran-uri "gridBase" version))
2566 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
2567 (build-system r-build-system)
2568 (home-page "https://cran.r-project.org/web/packages/gridBase")
2569 (synopsis "Integration of base and grid graphics")
2571 "This package provides an integration of base and grid graphics for R.")
2572 (license license:gpl2+)))
2574 (define-public r-latticeextra
2576 (name "r-latticeextra")
2581 (uri (cran-uri "latticeExtra" version))
2584 "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq"))))
2585 (properties `((upstream-name . "latticeExtra")))
2586 (build-system r-build-system)
2588 `(("r-lattice" ,r-lattice)
2589 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2590 (home-page "http://latticeextra.r-forge.r-project.org/")
2591 (synopsis "Extra graphical utilities based on lattice")
2593 "Building on the infrastructure provided by the lattice package, this
2594 package provides several new high-level graphics functions and methods, as
2595 well as additional utilities such as panel and axis annotation functions.")
2596 (license license:gpl2+)))
2598 (define-public r-rcpparmadillo
2600 (name "r-rcpparmadillo")
2601 (version "0.9.500.2.0")
2604 (uri (cran-uri "RcppArmadillo" version))
2607 "1lyvpb7n54ijlqns29qiixqr39334knf67cnixvlic58945glrhv"))))
2608 (properties `((upstream-name . "RcppArmadillo")))
2609 (build-system r-build-system)
2610 ;; All needed for vignettes
2612 `(("r-knitr" ,r-knitr)
2613 ("r-rmarkdown" ,r-rmarkdown)
2614 ("ghc-pandoc" ,ghc-pandoc)
2615 ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)))
2617 `(("r-rcpp" ,r-rcpp)))
2618 (home-page "https://github.com/RcppCore/RcppArmadillo")
2619 (synopsis "Rcpp integration for the Armadillo linear algebra library")
2621 "Armadillo is a templated C++ linear algebra library that aims towards a
2622 good balance between speed and ease of use. Integer, floating point and
2623 complex numbers are supported, as well as a subset of trigonometric and
2624 statistics functions. Various matrix decompositions are provided through
2625 optional integration with LAPACK and ATLAS libraries. This package includes
2626 the header files from the templated Armadillo library.")
2627 ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
2628 ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
2629 ;; later, as is the rest of 'Rcpp'.
2630 (license license:gpl2+)))
2632 (define-public r-bitops
2638 (uri (cran-uri "bitops" version))
2641 "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
2642 (build-system r-build-system)
2643 (home-page "https://cran.r-project.org/web/packages/bitops")
2644 (synopsis "Bitwise operations")
2646 "This package provides functions for bitwise operations on integer
2648 (license license:gpl2+)))
2650 (define-public r-catools
2653 (version "1.17.1.2")
2656 (uri (cran-uri "caTools" version))
2659 "0svj31y7h8vimvliygmmbl7pk850qk80k1vn38mlcxsnmcpm9k39"))))
2660 (properties `((upstream-name . "caTools")))
2661 (build-system r-build-system)
2663 `(("r-bitops" ,r-bitops)))
2664 (home-page "https://cran.r-project.org/web/packages/caTools")
2665 (synopsis "Various tools including functions for moving window statistics")
2667 "This package contains several basic utility functions including:
2668 moving (rolling, running) window statistic functions, read/write for GIF and
2669 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
2670 encoder/decoder, round-off-error-free sum and cumsum, etc.")
2671 (license license:gpl3+)))
2673 (define-public r-rprojroot
2675 (name "r-rprojroot")
2680 (uri (cran-uri "rprojroot" version))
2683 "12r3fdxmi2pmwn6ic3rhg0b20ll5z420m0d8fziv1n21961namnz"))))
2684 (build-system r-build-system)
2686 `(("r-backports" ,r-backports)))
2687 (home-page "https://github.com/krlmlr/rprojroot")
2688 (synopsis "Finding files in project subdirectories")
2690 "This package helps accessing files relative to a project root. It
2691 provides helpers for robust, reliable and flexible paths to files below a
2692 project root. The root of a project is defined as a directory that matches a
2693 certain criterion, e.g., it contains a certain regular file.")
2694 (license license:gpl3)))
2696 (define-public r-rmarkdown
2698 (name "r-rmarkdown")
2703 (uri (cran-uri "rmarkdown" version))
2706 "1vv3b8nlw8ra19492rjg3na42lwh3xr5a2jy2ia81fvvs846pywn"))))
2707 (properties `((upstream-name . "rmarkdown")))
2708 (build-system r-build-system)
2710 `(("r-base64enc" ,r-base64enc)
2711 ("r-evaluate" ,r-evaluate)
2712 ("r-htmltools" ,r-htmltools)
2713 ("r-jsonlite" ,r-jsonlite)
2714 ("r-knitr" ,r-knitr)
2716 ("r-stringr" ,r-stringr)
2717 ("r-tinytex" ,r-tinytex)
2720 ("ghc-pandoc" ,ghc-pandoc)))
2721 (home-page "http://rmarkdown.rstudio.com")
2722 (synopsis "Convert R Markdown documents into a variety of formats")
2724 "This package provides tools to convert R Markdown documents into a
2725 variety of formats.")
2726 (license license:gpl3+)))
2728 (define-public r-gtable
2734 (uri (cran-uri "gtable" version))
2737 "1lyncxf2dqdjgw1071cn9c8zwzkz6sldnd5cgmicf70bc726qf7x"))))
2738 (properties `((upstream-name . "gtable")))
2739 (build-system r-build-system)
2740 (home-page "https://cran.r-project.org/web/packages/gtable")
2741 (synopsis "R library to arrange grobs in tables")
2743 "Gtable is a collection of tools to make it easier to work with
2744 \"tables\" of grobs.")
2745 (license license:gpl2+)))
2747 (define-public r-gridextra
2749 (name "r-gridextra")
2753 (uri (cran-uri "gridExtra" version))
2756 "0fwfk3cdwxxim7nd55pn7m31bcaqj48y06j7an2k1v1pybk0rdl1"))))
2757 (properties `((upstream-name . "gridExtra")))
2758 (build-system r-build-system)
2760 `(("r-gtable" ,r-gtable)))
2762 `(("r-knitr" ,r-knitr))) ;for building vignettes
2763 (home-page "https://github.com/baptiste/gridextra")
2764 (synopsis "Miscellaneous functions for \"Grid\" graphics")
2766 "This package provides a number of user-level functions to work with
2767 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
2769 (license license:gpl2+)))
2771 (define-public r-pkgconfig
2773 (name "r-pkgconfig")
2777 (uri (cran-uri "pkgconfig" version))
2780 "1jk9ip549xphb3anfixqv1yx5kidnndqgy9v3qjpmgmds5a7g695"))))
2781 (build-system r-build-system)
2782 (home-page "https://github.com/gaborcsardi/pkgconfig")
2783 (synopsis "Private configuration for R packages")
2784 (description "This package provides the functionality to set configuration
2785 options on a per-package basis. Options set by a given package only apply to
2786 that package, other packages are unaffected.")
2787 (license license:expat)))
2789 (define-public r-blob
2795 (uri (cran-uri "blob" version))
2798 "0lsg91hk508dd95ivig2lwg62qafwnarjw68110kx63cfk4zkjxc"))))
2799 (build-system r-build-system)
2801 `(("r-prettyunits" ,r-prettyunits)
2802 ("r-tibble" ,r-tibble)))
2803 (home-page "https://github.com/hadley/blob")
2804 (synopsis "Simple S3 Class for representing vectors of binary data")
2805 (description "Raw vectors in R are useful for storing a single binary
2806 object. What if you want to put a vector of them in a data frame? The blob
2807 package provides the blob object, a list of raw vectors, suitable for use as
2808 a column in data frame.")
2809 (license license:gpl3+)))
2811 (define-public r-rsqlite
2817 (uri (cran-uri "RSQLite" version))
2820 "1giwk4335sc6yhj3rs8h070g1mwy38kyqyqv6vcfxvskykj7vp6z"))))
2821 (properties `((upstream-name . "RSQLite")))
2822 (build-system r-build-system)
2826 ("r-memoise" ,r-memoise)
2827 ("r-plogr" ,r-plogr)
2829 ("r-bit64" ,r-bit64)
2831 ("r-pkgconfig" ,r-pkgconfig)))
2832 (home-page "https://github.com/rstats-db/RSQLite")
2833 (synopsis "SQLite interface for R")
2835 "This package embeds the SQLite database engine in R and provides an
2836 interface compliant with the DBI package. The source for the SQLite
2837 engine (version 3.8.8.2) is included.")
2838 (license license:lgpl2.0+)))
2840 (define-public r-rcurl
2843 (version "1.95-0.1.2")
2846 (uri (string-append "https://www.bioconductor.org/packages/"
2847 "release/extra/src/"
2848 "contrib/RCurl_" version ".tar.gz"))
2851 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
2852 (properties `((upstream-name . "RCurl")))
2853 (build-system r-build-system)
2856 (modify-phases %standard-phases
2857 (add-after 'unpack 'respect-CURL_CA_BUNDLE
2859 (substitute* "R/options.S"
2860 (("\\.els = rev\\(merge\\(list\\(\\.\\.\\.\\), \\.opts\\)\\)" m)
2862 certs = Sys.getenv(\"CURL_CA_BUNDLE\")
2863 if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) }
2867 `(("libcurl" ,curl)))
2869 `(("r-bitops" ,r-bitops)))
2870 (home-page "http://www.omegahat.org/RCurl")
2871 (synopsis "General network client interface for R")
2873 "The package allows one to compose general HTTP requests and provides
2874 convenient functions to fetch URIs, GET and POST forms, etc. and process the
2875 results returned by the Web server. This provides a great deal of control
2876 over the HTTP/FTP/... connection and the form of the request while providing a
2877 higher-level interface than is available just using R socket connections.
2878 Additionally, the underlying implementation is robust and extensive,
2879 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
2880 ldap, and also supports cookies, redirects, authentication, etc.")
2881 (license license:bsd-3)))
2883 (define-public r-xml
2886 (version "3.98-1.20")
2889 (uri (cran-uri "XML" version))
2892 "0n28m8iz1wfgixr7fjswl238c5w9kggsrw0c8hdzp859dqvqdbs6"))))
2894 `((upstream-name . "XML")))
2895 (build-system r-build-system)
2897 `(("libxml2" ,libxml2)
2900 `(("pkg-config" ,pkg-config)))
2901 (home-page "http://www.omegahat.org/RSXML")
2902 (synopsis "Tools for parsing and generating XML within R")
2904 "Many approaches for both reading and creating XML (and HTML)
2905 documents (including DTDs), both local and accessible via HTTP or FTP. Also
2906 offers access to an XPath \"interpreter\".")
2907 (license license:bsd-2)))
2909 (define-public r-xnomial
2914 (origin (method url-fetch)
2915 (uri (cran-uri "XNomial" version))
2918 "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
2919 (properties (quasiquote ((upstream-name . "XNomial"))))
2920 (build-system r-build-system)
2921 (home-page "https://cran.r-project.org/web/packages/XNomial")
2922 (synopsis "Goodness-of-Fit test for multinomial data")
2924 "This package provides an exact Goodness-of-Fit test for
2925 multinomial data with fixed probabilities. It can be used to
2926 determine whether a set of counts fits a given expected ratio. To see
2927 whether a set of observed counts fits an expectation, one can examine
2928 all possible outcomes with @code{xmulti()} or a random sample of them
2929 with @code{xmonte()} and find the probability of an observation
2930 deviating from the expectation by at least as much as the observed.
2931 As a measure of deviation from the expected, one can use the
2932 log-likelihood ratio, the multinomial probability, or the classic
2933 chi-square statistic. A histogram of the test statistic can also be
2934 plotted and compared with the asymptotic curve.")
2935 (license (list license:gpl2+ license:gpl3+))))
2937 (define-public r-lambda-r
2943 (uri (cran-uri "lambda.r" version))
2946 "0cc6pszs6yccn0hgjpyn9gspv9aiva9d91ba0640i5m0l5xy7n0c"))))
2947 (properties `((upstream-name . "lambda.r")))
2948 (build-system r-build-system)
2950 `(("r-formatr" ,r-formatr)))
2951 (home-page "https://cran.r-project.org/web/packages/lambda.r")
2952 (synopsis "Functional programming extension for R")
2954 "This package provides a language extension to efficiently write
2955 functional programs in R. Syntax extensions include multi-part function
2956 definitions, pattern matching, guard statements, built-in (optional) type
2958 (license license:lgpl3+)))
2960 (define-public r-futile-options
2962 (name "r-futile-options")
2966 (uri (cran-uri "futile.options" version))
2969 "0w15agpi88y3qkv6fl72zy2pzyplzgvnj41a4ixhg64mw1sck73s"))))
2971 `((upstream-name . "futile.options")))
2972 (build-system r-build-system)
2973 (home-page "https://cran.r-project.org/web/packages/futile.options")
2974 (synopsis "Options management framework")
2976 "The futile.options subsystem provides an easy user-defined options
2977 management system that is properly scoped. This means that options created
2978 via @code{futile.options} are fully self-contained and will not collide with
2979 options defined in other packages.")
2980 (license license:lgpl3+)))
2982 (define-public r-futile-logger
2984 (name "r-futile-logger")
2988 (uri (cran-uri "futile.logger" version))
2991 "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
2992 (properties `((upstream-name . "futile.logger")))
2993 (build-system r-build-system)
2995 `(("r-futile-options" ,r-futile-options)
2996 ("r-lambda-r" ,r-lambda-r)))
2997 (home-page "https://cran.r-project.org/web/packages/futile.logger")
2998 (synopsis "Logging utility for R")
3000 "This package provides a simple yet powerful logging utility. Based
3001 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
3002 convenient and easy to use replacement for @code{cat} and @code{print}
3004 (license license:lgpl3+)))
3006 (define-public r-segmented
3008 (name "r-segmented")
3013 (uri (cran-uri "segmented" version))
3016 "1igsfkffpa60zn6j45lhw1zgr5pz6rjknv2f3sylnx5l9fdwibgf"))))
3017 (build-system r-build-system)
3018 (home-page "https://cran.r-project.org/web/packages/segmented")
3019 (synopsis "Regression models with breakpoints estimation")
3021 "Given a regression model, segmented updates the model by adding one or
3022 more segmented (i.e., piecewise-linear) relationships. Several variables with
3023 multiple breakpoints are allowed.")
3024 (license (list license:gpl2+ license:gpl3+))))
3026 (define-public r-snow
3032 (uri (cran-uri "snow" version))
3035 "1n3n8pva9s34fvlw32yng0x416lmbv7q1fsd0ywa4kikmxym64l5"))))
3036 (build-system r-build-system)
3037 (home-page "https://cran.r-project.org/web/packages/snow")
3038 (synopsis "Support for simple parallel computing in R")
3040 "The snow package provides support for simple parallel computing on a
3041 network of workstations using R. A master R process calls @code{makeCluster}
3042 to start a cluster of worker processes; the master process then uses functions
3043 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
3044 worker processes and collect and return the results on the master.")
3045 (license (list license:gpl2+ license:gpl3+))))
3047 (define-public r-sparsem
3053 (uri (cran-uri "SparseM" version))
3056 "0p6ljma2h12cq1xmy0cxb48ih8dhxxbnwkqzvx3cckxf2kprycm9"))))
3058 `((upstream-name . "SparseM")))
3060 `(("gfortran" ,gfortran)))
3061 (build-system r-build-system)
3062 (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
3063 (synopsis "Sparse linear algebra")
3065 "This package provides some basic linear algebra functionality for sparse
3066 matrices. It includes Cholesky decomposition and backsolving as well as
3067 standard R subsetting and Kronecker products.")
3068 (license license:gpl2+)))
3070 (define-public r-iterators
3072 (name "r-iterators")
3077 (uri (cran-uri "iterators" version))
3080 "1s3iykfvccpnzs73z90rx18qvbvgw2dgl4nfcrvm5m1850qb5qd9"))))
3081 (build-system r-build-system)
3082 (home-page "https://cran.r-project.org/web/packages/iterators")
3083 (synopsis "Iterator construct for R")
3085 "This package provides support for iterators, which allow a programmer to
3086 traverse through all the elements of a vector, list, or other collection of
3088 (license license:asl2.0)))
3090 (define-public r-foreach
3097 (uri (cran-uri "foreach" version))
3100 "0j2yj0rn0d5nbzz9nq5rqqgnxhp9pbd92q4klsarl2xpsn8119y0"))))
3101 (build-system r-build-system)
3103 `(("r-codetools" ,r-codetools)
3104 ("r-iterators" ,r-iterators)))
3105 (home-page "https://cran.r-project.org/web/packages/foreach")
3106 (synopsis "Foreach looping construct for R")
3108 "This package provides support for the @code{foreach} looping construct.
3109 @code{foreach} is an idiom that allows for iterating over elements in a
3110 collection, without the use of an explicit loop counter. This package in
3111 particular is intended to be used for its return value, rather than for its
3112 side effects. In that sense, it is similar to the standard @code{lapply}
3113 function, but doesn't require the evaluation of a function. Using
3114 @code{foreach} without side effects also facilitates executing the loop in
3116 (license license:asl2.0)))
3118 (define-public r-doparallel
3120 (name "r-doparallel")
3125 (uri (cran-uri "doParallel" version))
3128 "01qjs4iw9f1kgymcypj0m2s4pvgqhxaycpli0fb8lq3dc0vpzfyb"))))
3129 (properties `((upstream-name . "doParallel")))
3130 (build-system r-build-system)
3132 `(("r-foreach" ,r-foreach)
3133 ("r-iterators" ,r-iterators)))
3134 (home-page "https://cran.r-project.org/web/packages/doParallel")
3135 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3137 "This package provides a parallel backend for the @code{%dopar%} function
3138 using the parallel package.")
3139 (license license:gpl2+)))
3141 (define-public r-domc
3148 (uri (cran-uri "doMC" version))
3151 "1vfrykvfvsyq12mypd266867ml1dcwc3rj5k9c3wrn5bddcm88kr"))))
3152 (properties `((upstream-name . "doMC")))
3153 (build-system r-build-system)
3155 `(("r-foreach" ,r-foreach)
3156 ("r-iterators" ,r-iterators)))
3157 (home-page "https://cran.r-project.org/web/packages/doMC")
3158 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3160 "This package provides a parallel backend for the @code{%dopar%} function
3161 using the multicore functionality of the parallel package.")
3162 (license license:gpl2+)))
3170 (uri (cran-uri "DT" version))
3173 "0b6ywgzk9b35y5f69zwfz3vv7qwqqj3xsmy0xymf7nfcvrqg3qqx"))))
3175 `((upstream-name . "DT")))
3176 (build-system r-build-system)
3178 `(("r-crosstalk" ,r-crosstalk)
3179 ("r-htmltools" ,r-htmltools)
3180 ("r-htmlwidgets" ,r-htmlwidgets)
3181 ("r-magrittr" ,r-magrittr)
3182 ("r-promises" ,r-promises)))
3183 (home-page "http://rstudio.github.io/DT")
3184 (synopsis "R wrapper of the DataTables JavaScript library")
3186 "This package allows for data objects in R to be rendered as HTML tables
3187 using the JavaScript library @code{DataTables} (typically via R Markdown or
3188 Shiny). The @code{DataTables} library has been included in this R package.")
3189 ;; The DT package as a whole is distributed under GPLv3. The DT package
3190 ;; inludes other software components under different licenses:
3192 ;; * Expat: jQuery, jquery.highlight.js, DataTables
3193 ;; * ASL2.0: selectize.js
3194 ;; * WTFPL: noUiSlider
3195 (license (list license:gpl3
3198 (license:non-copyleft "http://www.wtfpl.net/txt/copying/")))))
3200 (define-public r-base64enc
3202 (name "r-base64enc")
3206 (uri (cran-uri "base64enc" version))
3209 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
3210 (build-system r-build-system)
3211 (home-page "http://www.rforge.net/base64enc")
3212 (synopsis "Tools for Base64 encoding")
3214 "This package provides tools for handling Base64 encoding. It is more
3215 flexible than the orphaned \"base64\" package.")
3216 (license license:gpl2+)))
3218 (define-public r-irlba
3225 (uri (cran-uri "irlba" version))
3228 "1h7mzrqdjc41814cf6c93sbyl7nxwvsf3x8apl9rhmydgdlk7qkf"))))
3229 (build-system r-build-system)
3231 `(("r-matrix" ,r-matrix)))
3232 (home-page "https://cran.r-project.org/web/packages/irlba")
3233 (synopsis "Methods for eigendecomposition of large matrices")
3235 "This package provides fast and memory efficient methods for truncated
3236 singular and eigenvalue decompositions, as well as for principal component
3237 analysis of large sparse or dense matrices.")
3238 (license (list license:gpl2+ license:gpl3+))))
3240 (define-public r-glmnet
3247 (uri (cran-uri "glmnet" version))
3250 "0sr5akaiaab1sdh9c8gfmc4kp9b4vqhd90d9ig0rqpqhp3bykp78"))))
3251 (build-system r-build-system)
3253 `(("gfortran" ,gfortran)))
3255 `(("r-foreach" ,r-foreach)
3256 ("r-matrix" ,r-matrix)))
3257 (home-page "http://www.jstatsoft.org/v33/i01")
3258 (synopsis "Lasso and elastic-net regularized generalized linear models")
3260 "The glmnet package provides efficient procedures for fitting the entire
3261 lasso or elastic-net regularization path for linear and Poisson regression, as
3262 well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
3263 multinomial models. The algorithm uses cyclical coordinate descent in a
3264 path-wise fashion.")
3265 (license license:gpl2+)))
3267 (define-public r-pkgmaker
3274 (uri (cran-uri "pkgmaker" version))
3277 "0spcamjncj78kzjps2rw4v1a4494yazv6xvhn0vmdflnypc8k8hp"))))
3278 (build-system r-build-system)
3280 `(("r-bibtex" ,r-bibtex)
3281 ("r-codetools" ,r-codetools)
3282 ("r-digest" ,r-digest)
3283 ("r-magrittr" ,r-magrittr)
3284 ("r-registry" ,r-registry)
3285 ("r-stringi" ,r-stringi)
3286 ("r-stringr" ,r-stringr)
3287 ("r-withr" ,r-withr)
3288 ("r-xtable" ,r-xtable)))
3289 (home-page "https://renozao.github.io/pkgmaker")
3290 (synopsis "Package development utilities")
3292 "This package provides some low-level utilities to use for R package
3293 development. It currently provides managers for multiple package specific
3294 options and registries, vignette, unit test and bibtex related utilities.")
3295 (license license:gpl2+)))
3297 (define-public r-registry
3304 (uri (cran-uri "registry" version))
3307 "1k3j6dx350awamr0dwwgkhfs46vsnj4nf08iw5byq0x7n3nkdsnz"))))
3308 (build-system r-build-system)
3309 (home-page "https://cran.r-project.org/web/packages/registry")
3310 (synopsis "Infrastructure for R package registries")
3312 "This package provides a generic infrastructure for creating and using R
3313 package registries.")
3314 (license license:gpl2+)))
3316 (define-public r-rngtools
3323 (uri (cran-uri "rngtools" version))
3326 "0k1nlcxggflq0043m15dfclnqnzchkpw2ik7jk82h4dqwvysiqcr"))))
3327 (build-system r-build-system)
3329 `(("r-digest" ,r-digest)
3330 ("r-pkgmaker" ,r-pkgmaker)
3331 ("r-stringr" ,r-stringr)))
3332 (home-page "https://renozao.github.io/rngtools")
3333 (synopsis "Utility functions for working with random number generators")
3335 "This package contains a set of functions for working with Random Number
3336 Generators (RNGs). In particular, it defines a generic S4 framework for
3337 getting/setting the current RNG, or RNG data that are embedded into objects
3338 for reproducibility. Notably, convenient default methods greatly facilitate
3339 the way current RNG settings can be changed.")
3340 (license license:gpl3+)))
3342 (define-public r-rtsne
3349 (uri (cran-uri "Rtsne" version))
3352 "0v17vxizrs1msay24xl2bckfajr2c82wpqj07lyssbrq197nwdsn"))))
3353 (properties `((upstream-name . "Rtsne")))
3354 (build-system r-build-system)
3356 `(("r-rcpp" ,r-rcpp)))
3357 (home-page "https://github.com/jkrijthe/Rtsne")
3358 (synopsis "T-distributed stochastic neighbor embedding")
3360 "This package provides an R wrapper around the fast T-distributed
3361 Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
3362 ;; The declared license for this package is BSD-3, but it also includes
3363 ;; code licensed under BSD-4.
3364 (license (list license:bsd-3 license:bsd-4))))
3366 (define-public r-e1071
3373 (uri (cran-uri "e1071" version))
3376 "0lipj692rjjw8rrhqh2k9i5dh8y2sjrw9q53rwm32irhx2f2j73j"))))
3377 (build-system r-build-system)
3379 `(("r-class" ,r-class)))
3380 (home-page "https://cran.r-project.org/web/packages/e1071")
3381 (synopsis "Miscellaneous functions for probability theory")
3383 "This package provides functions for latent class analysis, short time
3384 Fourier transform, fuzzy clustering, support vector machines, shortest path
3385 computation, bagged clustering, naive Bayes classifier, and more.")
3386 (license license:gpl2+)))
3388 (define-public r-bigmemory-sri
3390 (name "r-bigmemory-sri")
3395 (uri (cran-uri "bigmemory.sri" version))
3397 (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
3399 `((upstream-name . "bigmemory.sri")))
3400 (build-system r-build-system)
3401 (home-page "https://cran.r-project.org/web/packages/bigmemory.sri")
3402 (synopsis "Shared resource interface for the bigmemory package")
3403 (description "This package provides a shared resource interface for the
3404 bigmemory and synchronicity packages.")
3405 ;; Users can choose either LGPLv3 or ASL2.0.
3406 (license (list license:lgpl3 license:asl2.0))))
3408 (define-public r-synchronicity
3410 (name "r-synchronicity")
3415 (uri (cran-uri "synchronicity" version))
3418 "1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx"))))
3419 (build-system r-build-system)
3422 ("r-bigmemory-sri" ,r-bigmemory-sri)
3424 ("r-uuid" ,r-uuid)))
3425 (home-page "http://www.bigmemory.org")
3426 (synopsis "Boost mutex functionality in R")
3427 (description "This package provides support for synchronization
3428 via mutexes and may eventually support interprocess communication and
3430 ;; Users can choose either LGPLv3 or ASL2.0.
3431 (license (list license:lgpl3 license:asl2.0))))
3433 (define-public r-bigmemory
3435 (name "r-bigmemory")
3440 (uri (cran-uri "bigmemory" version))
3443 "0ycl9dzm3drpyas625h34rir5bnbjlncxlvawfsfmqwcbmwdjdvj"))))
3444 (build-system r-build-system)
3448 ("r-bigmemory-sri" ,r-bigmemory-sri)))
3449 (home-page "http://www.bigmemory.org")
3450 (synopsis "Manage large matrices with shared memory or memory-mapped files")
3451 (description "This package provides methods to create, store, access, and
3452 manipulate large matrices. Matrices are allocated to shared memory and may use
3453 memory-mapped files.")
3454 ;; Users can choose either LGPLv3 or ASL2.0.
3455 (license (list license:lgpl3 license:asl2.0))))
3457 (define-public r-nmf
3464 (uri (cran-uri "NMF" version))
3467 "1qq25n3k5sgh3srlshb3ic6q92s12c1ilqf5cd5anvq6cqfchc1v"))))
3468 (properties `((upstream-name . "NMF")))
3469 (build-system r-build-system)
3471 `(("r-cluster" ,r-cluster)
3472 ("r-bigmemory" ,r-bigmemory) ; suggested
3473 ("r-synchronicity" ,r-synchronicity) ; suggested
3474 ("r-colorspace" ,r-colorspace)
3475 ("r-digest" ,r-digest)
3476 ("r-doparallel" ,r-doparallel)
3477 ("r-foreach" ,r-foreach)
3478 ("r-ggplot2" ,r-ggplot2)
3479 ("r-gridbase" ,r-gridbase)
3480 ("r-pkgmaker" ,r-pkgmaker)
3481 ("r-rcolorbrewer" ,r-rcolorbrewer)
3482 ("r-registry" ,r-registry)
3483 ("r-reshape2" ,r-reshape2)
3484 ("r-rngtools" ,r-rngtools)
3485 ("r-stringr" ,r-stringr)))
3486 (home-page "http://renozao.github.io/NMF")
3487 (synopsis "Algorithms and framework for nonnegative matrix factorization")
3489 "This package provides a framework to perform Non-negative Matrix
3490 Factorization (NMF). The package implements a set of already published
3491 algorithms and seeding methods, and provides a framework to test, develop and
3492 plug new or custom algorithms. Most of the built-in algorithms have been
3493 optimized in C++, and the main interface function provides an easy way of
3494 performing parallel computations on multicore machines.")
3495 (license license:gpl2+)))
3497 (define-public r-r-methodss3
3499 (name "r-r-methodss3")
3503 (uri (cran-uri "R.methodsS3" version))
3506 "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24"))))
3507 (properties `((upstream-name . "R.methodsS3")))
3508 (build-system r-build-system)
3509 (home-page "https://cran.r-project.org/web/packages/R.methodsS3")
3510 (synopsis "S3 methods simplified")
3512 "This package provides methods that simplify the setup of S3 generic
3513 functions and S3 methods. Major effort has been made in making definition of
3514 methods as simple as possible with a minimum of maintenance for package
3515 developers. For example, generic functions are created automatically, if
3516 missing, and naming conflict are automatically solved, if possible. The
3517 method @code{setMethodS3()} is a good start for those who in the future may
3518 want to migrate to S4.")
3519 (license license:lgpl2.1+)))
3521 (define-public r-r-oo
3527 (uri (cran-uri "R.oo" version))
3530 "0k6xwy93fpb2p7bs76lzk52br9rv5xnd9524xj8qyazv1132x1n0"))))
3531 (properties `((upstream-name . "R.oo")))
3532 (build-system r-build-system)
3534 `(("r-r-methodss3" ,r-r-methodss3)))
3535 (home-page "https://github.com/HenrikBengtsson/R.oo")
3536 (synopsis "R object-oriented programming with or without references")
3538 "This package provides methods and classes for object-oriented
3539 programming in R with or without references. Large effort has been made on
3540 making definition of methods as simple as possible with a minimum of
3541 maintenance for package developers.")
3542 (license license:lgpl2.1+)))
3544 (define-public r-r-utils
3550 (uri (cran-uri "R.utils" version))
3553 "1w4zn2db15bggfnh64fbyi2z2sj47rcd4xn53b28dsnkamdcramj"))))
3554 (properties `((upstream-name . "R.utils")))
3555 (build-system r-build-system)
3557 `(("r-r-methodss3" ,r-r-methodss3)
3558 ("r-r-oo" ,r-r-oo)))
3559 (home-page "https://github.com/HenrikBengtsson/R.utils")
3560 (synopsis "Various programming utilities")
3562 "This package provides utility functions useful when programming and
3563 developing R packages.")
3564 (license license:lgpl2.1+)))
3566 (define-public r-r-cache
3572 (uri (cran-uri "R.cache" version))
3575 "1hf5cb7xvnca5zlh9245b5g62sgsaxwdhiv7x59yld37cydakm6k"))))
3576 (properties `((upstream-name . "R.cache")))
3577 (build-system r-build-system)
3579 `(("r-digest" ,r-digest)
3580 ("r-r-methodss3" ,r-r-methodss3)
3582 ("r-r-utils" ,r-r-utils)))
3583 (home-page "https://github.com/HenrikBengtsson/R.cache")
3584 (synopsis "Light-weight caching of objects and results")
3586 "This package provides methods for caching or memoization of objects and
3587 results. With this package, any R object can be cached in a key-value storage
3588 where the key can be an arbitrary set of R objects. The cache memory is
3589 persistent (on the file system).")
3590 (license license:lgpl2.1+)))
3592 (define-public r-r-rsp
3598 (uri (cran-uri "R.rsp" version))
3601 "0i01p8jxc4j4zl2v2ykvvpfnm5hv650zj1wi1dh8hq0c98xi2yfr"))))
3602 (properties `((upstream-name . "R.rsp")))
3603 (build-system r-build-system)
3605 `(("r-digest" ,r-digest)
3606 ("r-r-cache" ,r-r-cache)
3607 ("r-r-methodss3" ,r-r-methodss3)
3609 ("r-r-utils" ,r-r-utils)))
3610 (home-page "https://github.com/HenrikBengtsson/R.rsp")
3611 (synopsis "Dynamic generation of scientific reports")
3613 "The RSP markup language provides a powerful markup for controlling the
3614 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
3615 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
3616 to many other literate programming languages, with RSP it is straightforward
3617 to loop over mixtures of code and text sections, e.g. in month-by-month
3618 summaries. RSP has also several preprocessing directives for incorporating
3619 static and dynamic contents of external files (local or online) among other
3620 things. RSP is ideal for self-contained scientific reports and R package
3622 (license license:lgpl2.1+)))
3624 (define-public r-mvtnorm
3630 (uri (cran-uri "mvtnorm" version))
3633 "0lkjph661blc1nwfzg9w48a60wvj6ffh4zjwlisvracsx4nn2883"))))
3634 (build-system r-build-system)
3636 `(("gfortran" ,gfortran)))
3637 (home-page "http://mvtnorm.R-forge.R-project.org")
3638 (synopsis "Package for multivariate normal and t-distributions")
3639 (description "This package can compute multivariate normal and
3640 t-probabilities, quantiles, random deviates and densities.")
3641 (license license:gpl2)))
3643 (define-public r-matrixstats
3645 (name "r-matrixstats")
3649 (uri (cran-uri "matrixStats" version))
3652 "0vx00ldsg2zvdrjn49jxczk2c9iaabgvzgpdka5j02ihh7hv83cg"))))
3653 (properties `((upstream-name . "matrixStats")))
3654 (build-system r-build-system)
3656 `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
3657 (home-page "https://github.com/HenrikBengtsson/matrixStats")
3658 (synopsis "Methods applying to vectors and matrix rows and columns")
3660 "This package provides methods operating on rows and columns of matrices,
3661 e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
3662 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
3663 @code{weightedMedians()}. All methods have been optimized for speed and
3665 (license license:artistic2.0)))
3667 (define-public r-viridis
3673 (uri (cran-uri "viridis" version))
3676 "060rf1jn29dq53y3nhb0hykvcap6rqsk04rq544ypiiqb18ngwnx"))))
3677 (build-system r-build-system)
3679 `(("r-ggplot2" ,r-ggplot2)
3680 ("r-gridextra" ,r-gridextra)
3681 ("r-viridislite" ,r-viridislite)))
3682 (home-page "https://github.com/sjmgarnier/viridis")
3683 (synopsis "Matplotlib default color map")
3685 "This package is a port of the new @url{matplotlib,
3686 http://matplotlib.org/} color maps (@code{viridis}--the default--,
3687 @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
3688 designed in such a way that they will analytically be perfectly
3689 perceptually-uniform, both in regular form and also when converted to
3690 black-and-white. They are also designed to be perceived by readers with the
3691 most common form of color blindness.")
3692 (license license:x11)))
3694 (define-public r-viridislite
3696 (name "r-viridislite")
3701 (uri (cran-uri "viridisLite" version))
3704 "1by2l05f0yabwvv64lhnv7bbhx0w683s3wr9j2xda920ghpa23kq"))))
3705 (properties `((upstream-name . "viridisLite")))
3706 (build-system r-build-system)
3707 (home-page "https://github.com/sjmgarnier/viridisLite")
3708 (synopsis "Default color maps from matplotlib")
3710 "This package is a port of the new @code{matplotlib} color maps
3711 (@code{viridis}, @code{magma}, @code{plasma} and @code{inferno}) to R.
3712 matplotlib is a popular plotting library for Python. These color maps are
3713 designed in such a way that they will analytically be perfectly
3714 perceptually-uniform, both in regular form and also when converted to
3715 black-and-white. They are also designed to be perceived by readers with the
3716 most common form of color blindness. This is the @code{lite} version of the
3717 more complete @code{viridis} package.")
3718 (license license:expat)))
3720 (define-public r-tidyselect
3722 (name "r-tidyselect")
3727 (uri (cran-uri "tidyselect" version))
3730 "0x3cp36byhfjajikr1lwffjm85ayw3bcs7d7kb0cydgs61ifiqjw"))))
3731 (build-system r-build-system)
3733 `(("r-glue" ,r-glue)
3734 ("r-purrr" ,r-purrr)
3736 ("r-rlang" ,r-rlang)))
3737 (home-page "https://cran.r-project.org/web/packages/tidyselect")
3738 (synopsis "Select from a set of strings")
3740 "This package provides a backend for the selecting functions of the
3741 tidyverse. It makes it easy to implement select-like functions in your own
3742 packages in a way that is consistent with other tidyverse interfaces for
3744 (license license:gpl3)))
3746 (define-public r-tidyr
3753 (uri (cran-uri "tidyr" version))
3756 "0dyc4b03wi65bk7j0ma0y188syh37h57wgxji82i0h8j6pn593x1"))))
3757 (build-system r-build-system)
3759 `(("r-dplyr" ,r-dplyr)
3760 ("r-magrittr" ,r-magrittr)
3762 ("r-purrr" ,r-purrr)
3763 ("r-rlang" ,r-rlang)
3764 ("r-tidyselect" ,r-tidyselect)
3766 ("r-stringi" ,r-stringi)
3767 ("r-tibble" ,r-tibble)))
3768 (home-page "https://github.com/hadley/tidyr")
3769 (synopsis "Tidy data with `spread()` and `gather()` functions")
3771 "tidyr is a reframing of the reshape2 package designed to accompany the
3772 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
3773 a solid pipeline for data analysis. It is designed specifically for tidying
3774 data, not the general reshaping that reshape2 does, or the general aggregation
3775 that reshape did. In particular, built-in methods only work for data frames,
3776 and tidyr provides no margins or aggregation.")
3777 (license license:expat)))
3779 (define-public r-hexbin
3786 (uri (cran-uri "hexbin" version))
3789 "14f181lw6sj5xhfxbrpyyinsjfl0nzqilq6z80lgrhj2cnkj593y"))))
3790 (build-system r-build-system)
3792 `(("r-lattice" ,r-lattice)))
3794 `(("gfortran" ,gfortran)))
3795 (home-page "https://github.com/edzer/hexbin")
3796 (synopsis "Hexagonal binning routines")
3798 "This package provides binning and plotting functions for hexagonal bins.
3799 It uses and relies on grid graphics and formal (S4) classes and methods.")
3800 (license license:gpl2+)))
3802 (define-public r-purrr
3809 (uri (cran-uri "purrr" version))
3812 "0ccs78a2ylr60f3z0f7iywi8h1pwr8mz4ga78bs4pwgnwkclvir7"))))
3813 (build-system r-build-system)
3815 `(("r-magrittr" ,r-magrittr)
3816 ("r-rlang" ,r-rlang)))
3817 (home-page "https://github.com/hadley/purrr")
3818 (synopsis "Functional programming tools")
3820 "This package completes R's functional programming tools with missing
3821 features present in other programming languages.")
3822 (license license:gpl3+)))
3824 (define-public r-plotly
3830 (uri (cran-uri "plotly" version))
3833 "1kz2hm7vnkn4clxr6yyxxnmdmkz9zwjq6bzysw7j27r3721i8qgp"))))
3834 (build-system r-build-system)
3836 `(("r-base64enc" ,r-base64enc)
3837 ("r-crosstalk" ,r-crosstalk)
3838 ("r-digest" ,r-digest)
3839 ("r-data-table" ,r-data-table)
3840 ("r-dplyr" ,r-dplyr)
3841 ("r-ggplot2" ,r-ggplot2)
3842 ("r-hexbin" ,r-hexbin)
3843 ("r-htmltools" ,r-htmltools)
3844 ("r-htmlwidgets" ,r-htmlwidgets)
3846 ("r-jsonlite" ,r-jsonlite)
3847 ("r-lazyeval" ,r-lazyeval)
3848 ("r-magrittr" ,r-magrittr)
3849 ("r-promises" ,r-promises)
3850 ("r-purrr" ,r-purrr)
3851 ("r-rcolorbrewer" ,r-rcolorbrewer)
3852 ("r-rlang" ,r-rlang)
3853 ("r-scales" ,r-scales)
3854 ("r-tibble" ,r-tibble)
3855 ("r-tidyr" ,r-tidyr)
3856 ("r-viridislite" ,r-viridislite)))
3857 (home-page "https://plot.ly/r")
3858 (synopsis "Create interactive web graphics")
3860 "This package enables the translation of ggplot2 graphs to an interactive
3861 web-based version and/or the creation of custom web-based visualizations
3862 directly from R. Once uploaded to a plotly account, plotly graphs (and the
3863 data behind them) can be viewed and modified in a web browser.")
3864 (license license:x11)))
3866 (define-public r-biased-urn
3868 (name "r-biased-urn")
3873 (uri (cran-uri "BiasedUrn" version))
3876 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
3877 (properties `((upstream-name . "BiasedUrn")))
3878 (build-system r-build-system)
3879 (home-page "http://www.agner.org/random/")
3880 (synopsis "Biased urn model distributions")
3882 "This package provides statistical models of biased sampling in the form
3883 of univariate and multivariate noncentral hypergeometric distributions,
3884 including Wallenius' noncentral hypergeometric distribution and Fisher's
3885 noncentral hypergeometric distribution (also called extended hypergeometric
3887 (license license:gpl3+)))
3889 (define-public r-rematch
3896 (uri (cran-uri "rematch" version))
3899 "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4"))))
3900 (build-system r-build-system)
3901 (home-page "https://github.com/MangoTheCat/rematch")
3902 (synopsis "Match regular expressions with a nicer API")
3904 "This package provides a small wrapper on @code{regexpr} to extract the
3905 matches and captured groups from the match of a regular expression to a
3907 (license license:expat)))
3909 (define-public r-cellranger
3911 (name "r-cellranger")
3916 (uri (cran-uri "cellranger" version))
3919 "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x"))))
3920 (build-system r-build-system)
3922 `(("r-rematch" ,r-rematch)
3923 ("r-tibble" ,r-tibble)))
3924 (home-page "https://github.com/rsheets/cellranger")
3925 (synopsis "Translate spreadsheet cell ranges to rows and columns")
3927 "This package provides helper functions to work with spreadsheets and the
3928 @code{A1:D10} style of cell range specification.")
3929 (license license:expat)))
3931 (define-public r-googlesheets
3933 (name "r-googlesheets")
3938 (uri (cran-uri "googlesheets" version))
3941 "11q07nxys72wkxx9mawmjyf20gvwvrb7h3gpa73h6lgh2vgrwnv8"))))
3942 (build-system r-build-system)
3944 `(("r-cellranger" ,r-cellranger)
3945 ("r-dplyr" ,r-dplyr)
3947 ("r-jsonlite" ,r-jsonlite)
3948 ("r-purrr" ,r-purrr)
3949 ("r-readr" ,r-readr)
3950 ("r-stringr" ,r-stringr)
3951 ("r-tibble" ,r-tibble)
3952 ("r-tidyr" ,r-tidyr)
3953 ("r-xml2" ,r-xml2)))
3954 (home-page "https://github.com/jennybc/googlesheets")
3955 (synopsis "Manage Google spreadsheets from R")
3956 (description "This package provides tools to interact with Google Sheets
3958 (license license:expat)))
3960 (define-public r-spams
3963 (version "2.6-2017-03-22")
3967 ;; Use the ‘Latest version’ link for a stable URI across releases.
3968 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
3969 "latestfile/4531/spams-R-v" version ".tar.gz"))
3972 "13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx"))))
3973 (build-system r-build-system)
3976 (modify-phases %standard-phases
3977 (add-after 'unpack 'chdir
3978 (lambda _ (chdir "spams") #t))
3979 ;; Don't tune for the building machine.
3980 (add-after 'chdir 'no-mtune
3982 (substitute* "src/Makevars"
3983 (("-mtune=native") ""))
3986 `(("r-lattice" ,r-lattice)
3987 ("r-matrix" ,r-matrix)))
3988 (home-page "http://spams-devel.gforge.inria.fr")
3989 (synopsis "Toolbox for solving sparse estimation problems")
3990 (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
3991 for solving various sparse estimation problems. It includes tools for the
3995 @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
3996 component analysis} (PCA), ...)
3997 @item Solving sparse decomposition problems with LARS, coordinate descent,
3998 OMP, SOMP, proximal methods
3999 @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
4000 group lasso, tree-structured regularization, structured sparsity with
4001 overlapping groups,...).
4003 (license license:gpl3+)))
4005 (define-public r-base64
4012 (uri (cran-uri "base64" version))
4015 "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf"))))
4016 (build-system r-build-system)
4018 `(("r-openssl" ,r-openssl)))
4019 (home-page "https://cran.r-project.org/web/packages/base64")
4020 (synopsis "Base64 encoder and decoder")
4022 "This package is a compatibility wrapper to replace the orphaned package
4023 by Romain Francois. New applications should use the openssl or base64enc
4025 (license license:expat)))
4027 (define-public r-hmisc
4034 (uri (cran-uri "Hmisc" version))
4037 "1n8i2jhc308hd6bvys9cd7nrz7pwjszs03r5bwlh1pc869ki95ly"))))
4038 (properties `((upstream-name . "Hmisc")))
4039 (build-system r-build-system)
4041 `(("gfortran" ,gfortran)))
4043 `(("r-acepack" ,r-acepack)
4044 ("r-base64enc" ,r-base64enc)
4045 ("r-cluster" ,r-cluster)
4046 ("r-data-table" ,r-data-table)
4047 ("r-foreign" ,r-foreign)
4048 ("r-formula" ,r-formula)
4049 ("r-ggplot2" ,r-ggplot2)
4050 ("r-gridextra" ,r-gridextra)
4051 ("r-gtable" ,r-gtable)
4052 ("r-lattice" ,r-lattice)
4053 ("r-latticeextra" ,r-latticeextra)
4054 ("r-htmltable" ,r-htmltable)
4055 ("r-htmltools" ,r-htmltools)
4057 ("r-rpart" ,r-rpart)
4058 ("r-survival" ,r-survival)
4059 ("r-viridis" ,r-viridis)))
4060 (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
4061 (synopsis "Miscellaneous data analysis and graphics functions")
4063 "This package contains many functions useful for data analysis,
4064 high-level graphics, utility operations, functions for computing sample size
4065 and power, importing and annotating datasets, imputing missing values,
4066 advanced table making, variable clustering, character string manipulation,
4067 conversion of R objects to LaTeX code, and recoding variables.")
4068 (license license:gpl2+)))
4070 (define-public r-runit
4077 (uri (cran-uri "RUnit" version))
4080 "1wc1gwb7yw7phf8b0gkig6c23klya3ax11c6i4s0f049k42r78r3"))))
4081 (properties `((upstream-name . "RUnit")))
4082 (build-system r-build-system)
4083 (home-page "https://cran.r-project.org/web/packages/RUnit")
4084 (synopsis "R unit test framework")
4086 "This package provides R functions implementing a standard unit testing
4087 framework, with additional code inspection and report generation tools.")
4088 (license license:gpl2+)))
4090 (define-public r-dynamictreecut
4092 (name "r-dynamictreecut")
4097 (uri (cran-uri "dynamicTreeCut" version))
4100 "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"))))
4101 (properties `((upstream-name . "dynamicTreeCut")))
4102 (build-system r-build-system)
4104 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
4105 (synopsis "Detect clusters in hierarchical clustering dendrograms")
4107 "This package contains methods for the detection of clusters in
4108 hierarchical clustering dendrograms.")
4109 (license license:gpl2+)))
4111 (define-public r-preprocesscore
4113 (name "r-preprocesscore")
4118 (uri (bioconductor-uri "preprocessCore" version))
4121 "0iiyn42hlvmc5vabg5x15mls11124i23sh4qijwk0narh438cqm0"))))
4123 `((upstream-name . "preprocessCore")))
4124 (build-system r-build-system)
4125 (home-page "https://github.com/bmbolstad/preprocessCore")
4126 (synopsis "Collection of pre-processing functions")
4128 "This package provides a library of core pre-processing and normalization
4130 (license license:lgpl2.0+)))
4132 (define-public r-fastcluster
4134 (name "r-fastcluster")
4139 (uri (cran-uri "fastcluster" version))
4142 "01a2xnhhvv1swd4g8p4lzyn7ww7kg49jlnzc7kfz60jqjzpisrpk"))))
4143 (build-system r-build-system)
4144 (home-page "http://danifold.net/fastcluster.html")
4145 (synopsis "Fast hierarchical clustering routines")
4147 "This package implements fast hierarchical, agglomerative clustering
4148 routines. Part of the functionality is designed as drop-in replacement for
4149 existing routines: @code{linkage()} in the SciPy package
4150 @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package,
4151 and the @code{flashClust} package. It provides the same functionality with
4152 the benefit of a much faster implementation. Moreover, there are
4153 memory-saving routines for clustering of vector data, which go beyond what the
4154 existing packages provide.")
4155 (license license:bsd-2)))
4157 (define-public r-sfsmisc
4164 (uri (cran-uri "sfsmisc" version))
4167 "0zaw617zarmwir8l60riky0z6r1j3mwfnm1f32vqcbljb74akdj4"))))
4168 (build-system r-build-system)
4169 (home-page "https://cran.r-project.org/web/packages/sfsmisc")
4170 (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
4172 "This package provides useful utilities from Seminar fuer Statistik ETH
4173 Zurich, including many that are related to graphics.")
4174 (license license:gpl2+)))
4176 (define-public r-gtools
4183 (uri (cran-uri "gtools" version))
4186 "0f5syk1qq6cjq6hwymvkiyhzwa389z94722v881ipbfqkd2q8505"))))
4187 (build-system r-build-system)
4190 (modify-phases %standard-phases
4191 (add-after 'unpack 'make-deterministic
4193 (substitute* "R/checkReverseDependencies.R"
4194 (("tempdir\\(\\)") "\"/tmp\""))
4196 (home-page "https://cran.r-project.org/web/packages/gtools")
4197 (synopsis "Various R programming tools")
4199 "This package contains a collection of various functions to assist in R
4200 programming, such as tools to assist in developing, updating, and maintaining
4201 R and R packages, calculating the logit and inverse logit transformations,
4202 tests for whether a value is missing, empty or contains only @code{NA} and
4203 @code{NULL} values, and many more.")
4204 (license license:gpl2)))
4206 (define-public r-gdata
4213 (uri (cran-uri "gdata" version))
4216 "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b"))))
4217 (build-system r-build-system)
4221 `(("r-gtools" ,r-gtools)))
4222 (home-page "https://cran.r-project.org/web/packages/gdata")
4223 (synopsis "Various R programming tools for data manipulation")
4225 "This package provides various R programming tools for data manipulation,
4229 @item medical unit conversions
4230 @item combining objects
4231 @item character vector operations
4232 @item factor manipulation
4233 @item obtaining information about R objects
4234 @item manipulating MS-Excel formatted files
4235 @item generating fixed-width format files
4236 @item extricating components of date and time objects
4237 @item operations on columns of data frames
4238 @item matrix operations
4239 @item operations on vectors and data frames
4240 @item value of last evaluated expression
4241 @item wrapper for @code{sample} that ensures consistent behavior for
4242 both scalar and vector arguments
4244 (license license:gpl2+)))
4246 (define-public r-gplots
4253 (uri (cran-uri "gplots" version))
4256 "033plcfs9w8pmn84n24mdhiixdirc2a7pz6dvm61fpd20gwh7cbx"))))
4257 (build-system r-build-system)
4259 `(("r-catools" ,r-catools)
4260 ("r-gdata" ,r-gdata)
4261 ("r-gtools" ,r-gtools)
4262 ("r-kernsmooth" ,r-kernsmooth)))
4263 (home-page "https://cran.r-project.org/web/packages/gplots")
4264 (synopsis "Various R programming tools for plotting data")
4266 "This package provides various R programming tools for plotting data,
4270 @item calculating and plotting locally smoothed summary function
4271 @item enhanced versions of standard plots
4272 @item manipulating colors
4273 @item calculating and plotting two-dimensional data summaries
4274 @item enhanced regression diagnostic plots
4275 @item formula-enabled interface to @code{stats::lowess} function
4276 @item displaying textual data in plots
4278 @item plotting \"Venn\" diagrams
4279 @item displaying Open-Office style plots
4280 @item plotting multiple data on same region, with separate axes
4281 @item plotting means and confidence intervals
4282 @item spacing points in an x-y plot so they don't overlap
4284 (license license:gpl2+)))
4286 (define-public r-rocr
4293 (uri (cran-uri "ROCR" version))
4296 "1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7"))))
4297 (properties `((upstream-name . "ROCR")))
4298 (build-system r-build-system)
4300 `(("r-gplots" ,r-gplots)))
4301 (home-page "http://rocr.bioinf.mpi-sb.mpg.de/")
4302 (synopsis "Visualizing the performance of scoring classifiers")
4304 "ROCR is a flexible tool for creating cutoff-parameterized 2D performance
4305 curves by freely combining two from over 25 performance measures (new
4306 performance measures can be added using a standard interface). Curves from
4307 different cross-validation or bootstrapping runs can be averaged by different
4308 methods, and standard deviations, standard errors or box plots can be used to
4309 visualize the variability across the runs. The parameterization can be
4310 visualized by printing cutoff values at the corresponding curve positions, or
4311 by coloring the curve according to cutoff. All components of a performance
4312 plot can be quickly adjusted using a flexible parameter dispatching
4314 (license license:gpl2+)))
4316 (define-public r-zoo
4322 (uri (cran-uri "zoo" version))
4325 "1k1pmzr9nfwbxq1xf0jzn3nawv4sgnkxkgzxnm1i887jcbrs85r2"))))
4326 (build-system r-build-system)
4328 `(("r-lattice" ,r-lattice)))
4329 (home-page "http://zoo.R-Forge.R-project.org/")
4330 (synopsis "S3 infrastructure for regular and irregular time series")
4331 (description "This package contains an S3 class with methods for totally
4332 ordered indexed observations. It is particularly aimed at irregular time
4333 series of numeric vectors/matrices and factors.")
4334 (license license:gpl2+)))
4336 (define-public r-ztable
4342 (uri (cran-uri "ztable" version))
4345 "0g7khk5ifsdh9p31wlwh2l5mn1hzxzpv6qcn1wh34vsfjdmijjwy"))))
4346 (build-system r-build-system)
4348 `(("r-flextable" ,r-flextable)
4349 ("r-magrittr" ,r-magrittr)
4350 ("r-moonbook" ,r-moonbook)
4351 ("r-officer" ,r-officer)
4352 ("r-rcolorbrewer" ,r-rcolorbrewer)
4353 ("r-scales" ,r-scales)
4354 ("r-stringr" ,r-stringr)))
4355 (home-page "https://cran.r-project.org/web/packages/ztable")
4356 (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
4358 "This package provides functions to make zebra-striped tables (tables
4359 with alternating row colors) in LaTeX and HTML formats easily from
4360 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
4361 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
4362 @code{cbind.mytable} objects.")
4363 (license license:gpl2+)))
4365 (define-public r-vipor
4371 (uri (cran-uri "vipor" version))
4374 "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx"))))
4375 (build-system r-build-system)
4376 (home-page "https://cran.r-project.org/web/packages/vipor")
4377 (synopsis "Plot categorical data using noise and density estimates")
4379 "This package provides tools to generate a violin point plot, a
4380 combination of a violin/histogram plot and a scatter plot by offsetting points
4381 within a category based on their density using quasirandom noise.")
4382 (license license:gpl2+)))
4384 (define-public r-beeswarm
4390 (uri (cran-uri "beeswarm" version))
4393 "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
4394 (build-system r-build-system)
4395 (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/")
4396 (synopsis "Implementation of bee swarm plots")
4398 "This package provides an implementation of bee swarm plots. The bee
4399 swarm plot is a one-dimensional scatter plot like stripchart, but with
4400 closely-packed, non-overlapping points.")
4401 (license license:artistic2.0)))
4403 (define-public r-sourcetools
4405 (name "r-sourcetools")
4410 (uri (cran-uri "sourcetools" version))
4413 "1jnjir0q2dj724f1mjm6p5h77yzyx6xcqy9r2g7gmcxkxw349627"))))
4414 (build-system r-build-system)
4415 (home-page "https://cran.r-project.org/web/packages/sourcetools")
4416 (synopsis "Tools for reading, tokenizing and parsing R code")
4418 "The sourcetools package provides both an R and C++ interface for the
4419 tokenization of R code, and helpers for interacting with the tokenized
4420 representation of R code.")
4421 (license license:expat)))
4423 (define-public r-ggbeeswarm
4425 (name "r-ggbeeswarm")
4429 (uri (cran-uri "ggbeeswarm" version))
4432 "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v"))))
4433 (build-system r-build-system)
4435 `(("r-beeswarm" ,r-beeswarm)
4436 ("r-ggplot2" ,r-ggplot2)
4437 ("r-vipor" ,r-vipor)))
4438 (home-page "https://github.com/eclarke/ggbeeswarm")
4439 (synopsis "Categorical scatter (violin point) plots")
4441 "This package provides two methods of plotting categorical scatter plots
4442 such that the arrangement of points within a category reflects the density of
4443 data at that region, and avoids over-plotting.")
4444 (license license:gpl2+)))
4446 (define-public r-ggthemes
4452 (uri (cran-uri "ggthemes" version))
4455 "0rrkzfggc1nlda1w1lbqdycx6nawxbkac1szhvkwrqlzh6agxcsv"))))
4456 (build-system r-build-system)
4458 `(("r-ggplot2" ,r-ggplot2)
4459 ("r-purrr" ,r-purrr)
4460 ("r-scales" ,r-scales)
4461 ("r-stringr" ,r-stringr)
4462 ("r-tibble" ,r-tibble)))
4463 (home-page "https://cran.rstudio.com/web/packages/ggthemes")
4464 (synopsis "Extra themes, scales and geoms for @code{ggplot2}")
4465 (description "This package provides extra themes and scales for
4466 @code{ggplot2} that replicate the look of plots by Edward Tufte and
4467 Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The
4468 Wall Street Journal, among others. This package also provides
4469 @code{geoms} for Tufte's box plot and range frame.")
4470 (license license:gpl2)))
4472 (define-public r-statmod
4478 (uri (cran-uri "statmod" version))
4481 "083yyp84xj85zg4bhz7i90bqzl3p6155ch4abwsfc9k1lv7s2rrg"))))
4482 (build-system r-build-system)
4483 (home-page "https://cran.r-project.org/web/packages/statmod")
4485 `(("gfortran" ,gfortran)))
4486 (synopsis "Statistical modeling")
4488 "This package provides a collection of algorithms and functions to aid
4489 statistical modeling. It includes growth curve comparisons, limiting dilution
4490 analysis (aka ELDA), mixed linear models, heteroscedastic regression,
4491 inverse-Gaussian probability calculations, Gauss quadrature and a secure
4492 convergence algorithm for nonlinear models. It also includes advanced
4493 generalized linear model functions that implement secure convergence,
4494 dispersion modeling and Tweedie power-law families.")
4495 ;; Statmod is distributed under either license
4496 (license (list license:gpl2 license:gpl3))))
4498 (define-public r-rann
4504 (uri (cran-uri "RANN" version))
4507 "10kid40w9w7vkz2hpcfkdpxr4afxzms5dzvfwr0sl5xynzgw76dj"))))
4509 `((upstream-name . "RANN")))
4510 (build-system r-build-system)
4511 (home-page "https://github.com/jefferis/RANN")
4512 (synopsis "Fast nearest neighbour search")
4514 "This package finds the k nearest neighbours for every point in a given
4515 dataset in O(N log N) time using Arya and Mount's ANN library. Provides
4516 approximate, exact searches, fixed radius searches, bd and kb trees.")
4517 (license license:gpl3+)))
4519 (define-public r-fivethirtyeight
4521 (name "r-fivethirtyeight")
4526 (uri (string-append "https://mran.microsoft.com/src/contrib/"
4527 "fivethirtyeight_" version ".tar.gz"))
4530 "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl"))))
4531 (build-system r-build-system)
4533 `(("r-knitr" ,r-knitr)
4534 ("r-rmarkdown" ,r-rmarkdown)
4535 ("r-dplyr" ,r-dplyr)
4536 ("r-readr" ,r-readr)
4537 ("r-ggplot2" ,r-ggplot2)
4538 ("r-magrittr" ,r-magrittr)
4539 ("r-stringr" ,r-stringr)))
4540 (home-page "https://mran.microsoft.com/package/fivethirtyeight/")
4541 (synopsis "Data and code behind the stories at FiveThirtyEight")
4542 (description "This R package provides access to the code and data sets
4543 published by the statistics blog FiveThirtyEight.")
4544 (license license:expat)))
4546 (define-public r-compquadform
4548 (name "r-compquadform")
4553 (uri (cran-uri "CompQuadForm" version))
4556 "1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4"))))
4557 (properties `((upstream-name . "CompQuadForm")))
4558 (build-system r-build-system)
4559 (home-page "https://cran.r-project.org/web/packages/CompQuadForm")
4560 (synopsis "Distribution function of quadratic forms in normal variables")
4562 "This package provides functions to compute the distribution function of
4563 quadratic forms in normal variables using Imhof's method, Davies's algorithm,
4564 Farebrother's algorithm or Liu et al.'s algorithm.")
4565 (license license:gpl2+)))
4567 (define-public r-cowplot
4574 (uri (cran-uri "cowplot" version))
4577 "0yvalwalvyddyqk0q66y8361nxlh2cvp3ssazax9g5q89lghjmzv"))))
4578 (build-system r-build-system)
4580 `(("r-ggplot2" ,r-ggplot2)
4581 ("r-gtable" ,r-gtable)
4583 ("r-scales" ,r-scales)))
4584 (home-page "https://github.com/wilkelab/cowplot")
4585 (synopsis "Streamlined plot theme and plot annotations for ggplot2")
4587 "This package provides some helpful extensions and modifications to the
4588 ggplot2 package to combine multiple ggplot2 plots into one and label them with
4589 letters, as is often required for scientific publications.")
4590 (license license:gpl2)))
4592 (define-public r-mixtools
4599 (uri (cran-uri "mixtools" version))
4602 "13wdm0xs5bakhpa8ypg6lvhjaqkxyabwz4glxdwn0jwdvkcdhgsl"))))
4603 (build-system r-build-system)
4605 `(("r-mass" ,r-mass)
4606 ("r-segmented" ,r-segmented)
4607 ("r-survival" ,r-survival)))
4608 (home-page "https://cran.r-project.org/web/packages/mixtools")
4609 (synopsis "Tools for analyzing finite mixture models")
4611 "This package provides a collection of R functions for analyzing finite
4613 (license license:gpl2+)))
4615 (define-public r-lars
4622 (uri (cran-uri "lars" version))
4625 "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
4626 (build-system r-build-system)
4628 `(("gfortran" ,gfortran)))
4629 (home-page "http://www-stat.stanford.edu/~hastie/Papers/#LARS")
4630 (synopsis "Least angle regression software")
4632 "Least Angle Regression (\"LAR\") is a model selection algorithm; a
4633 useful and less greedy version of traditional forward selection methods. A
4634 simple modification of the LAR algorithm implements Tibshirani's Lasso; the
4635 Lasso modification of LARS calculates the entire Lasso path of coefficients
4636 for a given problem at the cost of a single least squares fit. Another LARS
4637 modification efficiently implements epsilon Forward Stagewise linear
4639 (license license:gpl2)))
4641 (define-public r-fastica
4648 (uri (cran-uri "fastICA" version))
4651 "108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg"))))
4652 (properties `((upstream-name . "fastICA")))
4653 (build-system r-build-system)
4654 (home-page "https://cran.r-project.org/web/packages/fastICA")
4655 (synopsis "FastICA algorithms to perform ICA and projection pursuit")
4657 "This package provides an implementation of the FastICA algorithm to
4658 perform @dfn{independent component analysis} (ICA) and projection pursuit.")
4660 (license license:gpl3+)))
4662 (define-public r-randomforest
4664 (name "r-randomforest")
4669 (uri (cran-uri "randomForest" version))
4672 "0kbmm0l42fc2d1rdq0l7k09d34kd87q4lx651ffsic4y84h8kf7l"))))
4673 (properties `((upstream-name . "randomForest")))
4674 (build-system r-build-system)
4675 (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
4677 `(("gfortran" ,gfortran)))
4678 (synopsis "Breiman and Cutler's random forests for classification and regression")
4680 "This package provides the Breiman and Cutler's random forests algorithm, based on a
4681 forest of trees using random inputs, for classification and regression.")
4682 (license license:gpl2+)))
4684 (define-public r-diptest
4691 (uri (cran-uri "diptest" version))
4694 "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
4695 (build-system r-build-system)
4696 (home-page "https://cran.r-project.org/web/packages/diptest")
4697 (synopsis "Hartigan's dip test statistic for unimodality")
4699 "This package computes Hartigan's dip test statistic for unimodality,
4700 multimodality and provides a test with simulation based p-values, where the
4701 original public code has been corrected.")
4702 (license license:gpl2+)))
4704 (define-public r-modeltools
4706 (name "r-modeltools")
4711 (uri (cran-uri "modeltools" version))
4714 "1s9lmkac3rl0nknf4wizfhg7ryq7c8yvvyc4z619238br27hhsi5"))))
4715 (build-system r-build-system)
4716 (home-page "https://cran.r-project.org/web/packages/modeltools")
4717 (synopsis "Tools and classes for statistical models")
4719 "This package provides a collection of tools to deal with statistical
4720 models. The functionality is experimental and the user interface is likely
4721 to change in the future.")
4722 (license license:gpl2)))
4724 (define-public r-flexmix
4731 (uri (cran-uri "flexmix" version))
4734 "0hrz2axp2c9548b1r0bmrl57219nn030qndb83a8garkzq5lqi5s"))))
4735 (build-system r-build-system)
4737 `(("r-lattice" ,r-lattice)
4738 ("r-modeltools" ,r-modeltools)
4739 ("r-nnet" ,r-nnet)))
4740 (home-page "https://cran.r-project.org/web/packages/flexmix")
4741 (synopsis "Flexible mixture modeling")
4743 "This package implements a general framework for finite mixtures of
4744 regression models using the EM algorithm. FlexMix provides the E-step and
4745 all data handling, while the M-step can be supplied by the user to easily
4746 define new models. Existing drivers implement mixtures of standard linear
4747 models, generalized linear models and model-based clustering.")
4748 (license license:gpl2+)))
4750 (define-public r-mclust
4757 (uri (cran-uri "mclust" version))
4760 "039ymr57bq5327gypizw0v2qb81j6bkqhjdh8yj23qa5sh51phyc"))))
4761 (build-system r-build-system)
4763 `(("gfortran" ,gfortran)))
4764 (home-page "http://www.stat.washington.edu/mclust/")
4765 (synopsis "Gaussian mixture modelling for model-based clustering etc.")
4767 "This package provides Gaussian finite mixture models fitted via EM
4768 algorithm for model-based clustering, classification, and density estimation,
4769 including Bayesian regularization, dimension reduction for visualisation,
4770 and resampling-based inference.")
4771 (license license:gpl2+)))
4773 (define-public r-prabclus
4780 (uri (cran-uri "prabclus" version))
4783 "1h5k13w8mmmdy74l145zh64f339wy78z1nlg8xr3zg23gmv98cpg"))))
4784 (build-system r-build-system)
4786 `(("r-mass" ,r-mass)
4787 ("r-mclust" ,r-mclust)))
4788 (home-page "https://cran.r-project.org/web/packages/prabclus")
4789 (synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
4791 "This package provides distance-based parametric bootstrap tests for
4792 clustering with spatial neighborhood information. It implements some distance
4793 measures, clustering of presence-absence, abundance and multilocus genetical
4794 data for species delimitation, nearest neighbor based noise detection.")
4795 (license license:gpl2+)))
4797 (define-public r-deoptimr
4804 (uri (cran-uri "DEoptimR" version))
4807 "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
4808 (properties `((upstream-name . "DEoptimR")))
4809 (build-system r-build-system)
4810 (home-page "https://cran.r-project.org/web/packages/DEoptimR")
4811 (synopsis "Differential evolution optimization in pure R")
4813 "This package provides a differential evolution (DE) stochastic
4814 algorithms for global optimization of problems with and without constraints.
4815 The aim is to curate a collection of its state-of-the-art variants that (1) do
4816 not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
4817 can be efficiently implemented directly in the R language.")
4818 (license license:gpl2+)))
4820 (define-public r-robustbase
4822 (name "r-robustbase")
4827 (uri (cran-uri "robustbase" version))
4830 "0mkzbsjl5nihyj7mzks14p6kr3spp44xvygjz4ran11gspdn9rdx"))))
4831 (build-system r-build-system)
4833 `(("gfortran" ,gfortran)))
4835 `(("r-deoptimr" ,r-deoptimr)))
4836 (home-page "http://robustbase.r-forge.r-project.org/")
4837 (synopsis "Basic robust statistics")
4839 "This package allows to analyze data with robust methods such as
4840 regression methodology including model selections and multivariate statistics.")
4841 (license license:gpl2+)))
4843 (define-public r-pcapp
4850 (uri (cran-uri "pcaPP" version))
4853 "1z2kdf9gfp965xbcd4rg6vf20d1bl443na0qjkpq7gmzpaq6cifa"))))
4854 (properties `((upstream-name . "pcaPP")))
4855 (build-system r-build-system)
4857 `(("r-mvtnorm" ,r-mvtnorm)))
4858 (home-page "https://cran.r-project.org/web/packages/pcaPP")
4859 (synopsis "Robust PCA by projection pursuit")
4861 "This package provides functions for robust @dfn{principal component
4862 analysis} (PCA) by projection pursuit.")
4863 (license license:gpl3+)))
4865 (define-public r-rrcov
4872 (uri (cran-uri "rrcov" version))
4875 "14zjyqcdiqx6js99nx5s8hmyx564ixy2d8s6i7wa50xmx368rl6b"))))
4876 (build-system r-build-system)
4878 `(("r-cluster" ,r-cluster)
4879 ("r-lattice" ,r-lattice)
4880 ("r-mvtnorm" ,r-mvtnorm)
4881 ("r-pcapp" ,r-pcapp)
4882 ("r-robustbase" ,r-robustbase)))
4884 `(("gfortran" ,gfortran)))
4885 (home-page "https://cran.r-project.org/web/packages/rrcov")
4886 (synopsis "Scalable robust estimators with high breakdown Point")
4888 "This package provides an implementation of robust location and scatter
4889 estimation and robust multivariate analysis with high breakdown point.")
4890 (license license:gpl2+)))
4892 (define-public r-fit-models
4894 (name "r-fit-models")
4899 (uri (cran-uri "fit.models" version))
4902 "0vjbzmx0ambm6yzidb4vbgmhclwzwv2iz2cwl54ccdkvx4cx3fck"))))
4903 (properties `((upstream-name . "fit.models")))
4904 (build-system r-build-system)
4906 `(("r-lattice" ,r-lattice)))
4907 (home-page "https://cran.r-project.org/web/packages/fit.models")
4908 (synopsis "Compare fitted models")
4910 "The @code{fit.models} function and its associated methods (coefficients, print,
4911 summary, plot, etc.) were originally provided in the @code{robust} package to
4912 compare robustly and classically fitted model objects. The aim of the
4913 @code{fit.models} package is to separate this fitted model object comparison
4914 functionality from the robust package and to extend it to support fitting
4915 methods (e.g., classical, robust, Bayesian, regularized, etc.) more
4917 ;; Any version of the GPL
4918 (license (list license:gpl2+ license:gpl3+))))
4920 (define-public r-robust
4927 (uri (cran-uri "robust" version))
4930 "1b7qh1aff500nd6dh4y2ipmjgdiq8991shflb63pc39vpc0ny6g4"))))
4931 (build-system r-build-system)
4933 `(("r-fit-models" ,r-fit-models)
4934 ("r-lattice" ,r-lattice)
4936 ("r-robustbase" ,r-robustbase)
4937 ("r-rrcov" ,r-rrcov)))
4939 `(("gfortran" ,gfortran)))
4940 (home-page "https://cran.r-project.org/web/packages/robust")
4941 (synopsis "Port of the S+ \"Robust Library\"")
4943 "This package is a port of the S+ \"Robust Library\". It provides
4944 methods for robust statistics, notably for robust regression and robust
4945 multivariate analysis.")
4946 (license license:gpl2)))
4948 (define-public r-trimcluster
4950 (name "r-trimcluster")
4955 (uri (cran-uri "trimcluster" version))
4958 "0013bpyq6mkvjn38qsmwnsxfiwxgwngnqxycxvgpgmiadhm8fjmn"))))
4959 (build-system r-build-system)
4960 (home-page "https://cran.r-project.org/web/packages/trimcluster")
4961 (synopsis "Cluster analysis with trimming")
4963 "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
4964 Matran (1997). This optimizes the k-means criterion under trimming a portion
4967 (license (list license:gpl2+ license:gpl3+))))
4969 (define-public r-fpc
4976 (uri (cran-uri "fpc" version))
4979 "1dy3pla4jjgs46izqg2kxajlxr80sbr9896jbzb1qszrdx7af041"))))
4980 (build-system r-build-system)
4982 `(("r-class" ,r-class)
4983 ("r-cluster" ,r-cluster)
4984 ("r-diptest" ,r-diptest)
4985 ("r-flexmix" ,r-flexmix)
4986 ("r-kernlab" ,r-kernlab)
4988 ("r-mclust" ,r-mclust)
4989 ("r-prabclus" ,r-prabclus)
4990 ("r-robustbase" ,r-robustbase)))
4991 (home-page "https://cran.r-project.org/web/packages/fpc")
4992 (synopsis "Flexible procedures for clustering")
4994 "This package provides various methods for clustering and cluster validation.
4995 For example, it provides fixed point clustering, linear regression clustering,
4996 clustering by merging Gaussian mixture components, as well as symmetric and
4997 asymmetric discriminant projections for visualisation of the separation of
4999 (license license:gpl2+)))
5001 (define-public r-vgam
5008 (uri (cran-uri "VGAM" version))
5011 "0lnsqx3q3k0c7sj8gj0n6shn2fyxwrh8xph8h1r1i23ybbb2n6fy"))))
5012 (properties `((upstream-name . "VGAM")))
5013 (build-system r-build-system)
5015 `(("gfortran" ,gfortran)))
5016 (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
5017 (synopsis "Vector generalized linear and additive models")
5019 "This package is an implementation of about 6 major classes of statistical
5020 regression models. Currently only fixed-effects models are implemented, i.e.,
5021 no random-effects models. Many (150+) models and distributions are estimated
5022 by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
5023 VGLMs can be loosely thought of as multivariate generalised linear models.")
5024 (license license:gpl2+)))
5026 (define-public r-pbapply
5033 (uri (cran-uri "pbapply" version))
5036 "0bn7a9ni36xy5acnrl9ky3gd1k8jr5kxgazzh3pzd1q6bri1nx7k"))))
5037 (build-system r-build-system)
5038 (home-page "https://github.com/psolymos/pbapply")
5039 (synopsis "Adding progress bar to apply functions")
5041 "This lightweight package that adds progress bar to vectorized R
5042 functions apply. The implementation can easily be added to functions where
5043 showing the progress is useful e.g. bootstrap.")
5044 (license license:gpl2)))
5046 (define-public r-minqa
5053 (uri (cran-uri "minqa" version))
5056 "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
5057 (build-system r-build-system)
5059 `(("r-rcpp" ,r-rcpp)))
5061 `(("gfortran" ,gfortran)))
5062 (home-page "http://optimizer.r-forge.r-project.org")
5063 (synopsis "Derivative-free optimization algorithms by quadratic approximation")
5065 "This package provides a derivative-free optimization by quadratic approximation
5066 based on an interface to Fortran implementations by M. J. D. Powell.")
5067 (license license:gpl2)))
5069 (define-public r-rcppeigen
5071 (name "r-rcppeigen")
5072 (version "0.3.3.5.0")
5076 (uri (cran-uri "RcppEigen" version))
5079 "01bz41c29591ybzqn4z88ss036ai3anh9figryvmfpqcfwbszip5"))))
5080 (properties `((upstream-name . "RcppEigen")))
5081 (build-system r-build-system)
5083 `(("r-rcpp" ,r-rcpp)
5084 ("r-matrix" ,r-matrix)))
5085 (home-page "http://eigen.tuxfamily.org")
5086 (synopsis "Rcpp integration for the Eigen templated linear algebra library")
5088 "This package provides an integration of Eigen in R using a C++ template
5089 library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
5090 It supports dense and sparse matrices on integer, floating point and complex numbers,
5091 decompositions of such matrices, and solutions of linear systems.")
5092 (license license:gpl2+)))
5094 (define-public r-modelmetrics
5096 (name "r-modelmetrics")
5101 (uri (cran-uri "ModelMetrics" version))
5104 "158ddbw2snlyzd2q6mdaif5i67kq4qfvadylwjxgv1w2cmszrmk6"))))
5105 (properties `((upstream-name . "ModelMetrics")))
5106 (build-system r-build-system)
5108 `(("r-rcpp" ,r-rcpp)
5109 ("r-data-table" ,r-data-table)))
5110 (home-page "https://cran.r-project.org/web/packages/ModelMetrics")
5111 (synopsis "Rapid calculation of model metrics")
5113 "Written in C++ using @code{Rcpp}, this package provides a collection of
5114 metrics for evaluating models.")
5115 (license license:gpl2+)))
5117 (define-public r-matrixmodels
5119 (name "r-matrixmodels")
5124 (uri (cran-uri "MatrixModels" version))
5127 "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
5128 (properties `((upstream-name . "MatrixModels")))
5129 (build-system r-build-system)
5131 `(("r-matrix" ,r-matrix)))
5132 (home-page "https://cran.r-project.org/web/packages/MatrixModels")
5133 (synopsis "Modelling with sparse and dense matrices")
5135 "This package models with sparse and dense matrix matrices,
5136 using modular prediction and response module classes.")
5137 (license license:gpl2+)))
5139 (define-public r-quantreg
5146 (uri (cran-uri "quantreg" version))
5149 "110ax3ngn6i94h7iw7ha67kfsmj94hycp7lk62nmyvkp34vpfykh"))))
5150 (build-system r-build-system)
5152 `(("gfortran" ,gfortran)))
5154 `(("r-matrix" ,r-matrix)
5155 ("r-matrixmodels" ,r-matrixmodels)
5156 ("r-sparsem" ,r-sparsem)))
5157 (home-page "https://www.r-project.org")
5158 (synopsis "Quantile regression")
5160 "This package provides an estimation and inference methods for models
5161 of conditional quantiles: linear and nonlinear parametric and non-parametric
5162 models for conditional quantiles of a univariate response and several methods
5163 for handling censored survival data. Portfolio selection methods based on
5164 expected shortfall risk are also included.")
5165 (license license:gpl2+)))
5167 (define-public r-nloptr
5174 (uri (cran-uri "nloptr" version))
5177 "15yz60kljxwnhm2m3gryjzxl3ynhkhd5jiwc179b1hz6rlzf71hz"))))
5178 (build-system r-build-system)
5180 `(("r-knitr" ,r-knitr) ; for building vignettes
5181 ("pkg-config" ,pkg-config)
5182 ("gfortran" ,gfortran)))
5184 `(("nlopt" ,nlopt)))
5185 (home-page "https://cran.r-project.org/web/packages/nloptr")
5186 (synopsis "R interface to NLopt")
5188 "This package is interface to NLopt, a library for nonlinear
5189 optimization. NLopt is a library for nonlinear optimization, providing a
5190 common interface for a number of different free optimization routines
5191 available online as well as original implementations of various other
5193 (license license:lgpl3)))
5195 (define-public r-lme4
5202 (uri (cran-uri "lme4" version))
5205 "035j2hqkwv939xl07pm2vykvf3wlx8qj317846n9pkpqkyv58mbz"))))
5206 (build-system r-build-system)
5208 `(("r-boot" ,r-boot)
5209 ("r-lattice" ,r-lattice)
5211 ("r-matrix" ,r-matrix)
5212 ("r-minqa" ,r-minqa)
5213 ("r-nloptr" ,r-nloptr)
5216 ("r-rcppeigen" ,r-rcppeigen)))
5217 (home-page "https://cran.r-project.org/web/packages/lme4")
5218 (synopsis "Linear mixed-effects models using eigen and S4")
5220 "This package provides fit linear and generalized linear mixed-effects
5221 models. The models and their components are represented using S4 classes and
5222 methods. The core computational algorithms are implemented using the Eigen
5223 C++ library for numerical linear algebra and RcppEigen glue.")
5224 (license license:gpl2+)))
5226 (define-public r-pbkrtest
5233 (uri (cran-uri "pbkrtest" version))
5236 "1si3bhi59xc51a0pgjjglccq3h4aljyhw2k1b8574s145fnh7fsw"))))
5237 (build-system r-build-system)
5239 `(("r-lme4" ,r-lme4)
5241 ("r-matrix" ,r-matrix)))
5242 (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
5243 (synopsis "Methods for linear mixed model comparison")
5245 "This package implements a parametric bootstrap test and a Kenward Roger
5246 modification of F-tests for linear mixed effects models and a parametric
5247 bootstrap test for generalized linear mixed models.")
5248 (license license:gpl2+)))
5250 (define-public r-cardata
5257 (uri (cran-uri "carData" version))
5260 "152lfgaspgx6x2wzdb5p3zv6r87a0d2pg10h6fjmdr613kzlwp1v"))))
5261 (properties `((upstream-name . "carData")))
5262 (build-system r-build-system)
5263 (home-page "https://r-forge.r-project.org/projects/car/")
5264 (synopsis "Data Sets for the book Companion to Applied Regression")
5266 "This package provides datasets to accompany J. Fox and S. Weisberg, An R
5267 Companion to Applied Regression, Third Edition, Sage.")
5268 (license license:gpl2+)))
5270 (define-public r-car
5277 (uri (cran-uri "car" version))
5280 "0vy3g3bjljd2al8xb9qr45f98is7yppc9jilqn7b6zvf5yqpr07s"))))
5281 (build-system r-build-system)
5283 `(("r-abind" ,r-abind)
5284 ("r-cardata" ,r-cardata)
5286 ("r-maptools" ,r-maptools)
5291 ("r-pbkrtest" ,r-pbkrtest)
5292 ("r-quantreg" ,r-quantreg)
5294 (home-page "https://r-forge.r-project.org/projects/car/")
5295 (synopsis "Companion to applied regression")
5297 "This package provides functions and datasets from book Companion
5298 to Applied regression, Second Edition, Sage, 2011.")
5299 (license license:gpl2+)))
5301 (define-public r-caret
5308 (uri (cran-uri "caret" version))
5311 "03898irgb70q0p01kq99yb6q6xji0jx4jmj0yxlv8wcwd841r0x1"))))
5312 (build-system r-build-system)
5314 `(("r-foreach" ,r-foreach)
5315 ("r-ggplot2" ,r-ggplot2)
5316 ("r-lattice" ,r-lattice)
5317 ("r-modelmetrics" ,r-modelmetrics)
5320 ("r-recipes" ,r-recipes)
5321 ("r-reshape2" ,r-reshape2)
5322 ("r-withr" ,r-withr)))
5323 (home-page "https://github.com/topepo/caret")
5324 (synopsis "Classification and regression training")
5326 "This package provides misc functions for training and plotting
5327 classification and regression models.")
5328 (license license:gpl2+)))
5330 (define-public r-rcppprogress
5332 (name "r-rcppprogress")
5337 (uri (cran-uri "RcppProgress" version))
5340 "0yk01hfv961zyp569682k9igvhnwqyg5j0n5fm63sxigj82l2xhi"))))
5341 (properties `((upstream-name . "RcppProgress")))
5342 (build-system r-build-system)
5344 `(("r-devtools" ,r-devtools)
5345 ("r-rcpp" ,r-rcpp)))
5346 (home-page "https://github.com/kforner/rcpp_progress")
5347 (synopsis "Interruptible progress bar for C++ in R packages")
5349 "This package allows to display a progress bar in the R console for long running
5350 computations taking place in C++ code, and support for interrupting those computations
5351 even in multithreaded code, typically using OpenMP.")
5352 (license license:gpl3+)))
5354 (define-public r-mnormt
5361 (uri (cran-uri "mnormt" version))
5364 "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z"))))
5365 (build-system r-build-system)
5367 `(("gfortran" ,gfortran)))
5368 (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
5369 (synopsis "Multivariate normal and \"t\" distributions")
5371 "This package provides functions for computing the density and the
5372 distribution function of multivariate normal and \"t\" random variables, and
5373 for generating random vectors sampled from these distributions. Probabilities
5374 are computed via non-Monte Carlo methods.")
5375 (license license:gpl2+)))
5377 (define-public r-numderiv
5380 (version "2016.8-1.1")
5384 (uri (cran-uri "numDeriv" version))
5387 "0idk02pqkziik932bd8k72d1q775g1is3m4bc861pcxfz6gx3i6q"))))
5388 (properties `((upstream-name . "numDeriv")))
5389 (build-system r-build-system)
5390 (home-page "https://cran.r-project.org/web/packages/numDeriv")
5391 (synopsis "Accurate numerical derivatives")
5393 "This package provides methods for calculating accurate numerical
5394 first and second order derivatives.")
5395 (license license:gpl2)))
5404 (uri (cran-uri "sn" version))
5407 "0x46gxkplxbnhaqbpiav1r4xlv4ib7n57kxmca7scqwj22y7wrs6"))))
5408 (build-system r-build-system)
5410 `(("r-mnormt" ,r-mnormt)
5411 ("r-numderiv" ,r-numderiv)))
5412 (home-page "http://azzalini.stat.unipd.it/SN")
5413 (synopsis "The skew-normal and skew-t distributions")
5415 "This package provides functionalities to build and manipulate
5416 probability distributions of the skew-normal family and some related
5417 ones, notably the skew-t family, and provides related statistical
5418 methods for data fitting and diagnostics, in the univariate and the
5419 multivariate case.")
5420 (license license:gpl2+)))
5422 (define-public r-tclust
5429 (uri (cran-uri "tclust" version))
5432 "17md6l9v9dl9b72l84df01b52h2xiynbcjm437mv9mzcr09fc2sb"))))
5433 (build-system r-build-system)
5434 ;; These are all suggested packages, not build dependencies.
5436 `(("r-cluster" ,r-cluster)
5437 ("r-mclust" ,r-mclust)
5438 ("r-mvtnorm" ,r-mvtnorm)
5440 (home-page "https://cran.r-project.org/web/packages/tclust")
5441 (synopsis "Robust trimmed clustering")
5443 "This package implements different robust clustering
5444 algorithms (@code{tclust}) based on trimming and including some graphical
5445 diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
5446 (license license:gpl3)))
5448 (define-public r-ranger
5455 (uri (cran-uri "ranger" version))
5458 "1sxyzxmjc6lm8wcmq15j6sscnza7aay4mr3dyri2zngx6fa8mb0k"))))
5459 (build-system r-build-system)
5461 `(("r-rcpp" ,r-rcpp)
5462 ("r-matrix" ,r-matrix)
5463 ("r-rcppeigen" ,r-rcppeigen)))
5464 (home-page "https://github.com/imbs-hl/ranger")
5465 (synopsis "Fast implementation of random forests")
5467 "This package provides a fast implementation of Random Forests,
5468 particularly suited for high dimensional data. Ensembles of classification,
5469 regression, survival and probability prediction trees are supported. Data from
5470 genome-wide association studies can be analyzed efficiently.")
5471 (license license:gpl3)))
5473 (define-public r-tsne
5480 (uri (cran-uri "tsne" version))
5483 "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
5484 (build-system r-build-system)
5485 (home-page "https://github.com/jdonaldson/rtsne/")
5486 (synopsis "t-Distributed Stochastic Neighbor Embedding for R")
5488 "This package provides a pure R implementation of the t-SNE algorithm.")
5489 (license license:gpl2+)))
5491 (define-public r-cairo
5498 (uri (cran-uri "Cairo" version))
5501 "1mdmd5zmjkh1b0x928zizgzh42x8swbajffb88rvnjfdhk1z0dvq"))))
5502 (properties `((upstream-name . "Cairo")))
5503 (build-system r-build-system)
5509 `(("pkg-config" ,pkg-config)))
5510 (home-page "http://www.rforge.net/Cairo/")
5511 (synopsis "R graphics device using Cairo graphics library")
5513 "This package provides a Cairo graphics device that can be use to
5514 create high-quality vector (PDF, PostScript and SVG) and bitmap
5515 output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11
5516 and Win32). Since it uses the same back-end for all output, copying
5517 across formats is WYSIWYG. Files are created without the dependence
5518 on X11 or other external programs. This device supports alpha
5519 channel (semi-transparent drawing) and resulting images can contain
5520 transparent and semi-transparent regions. It is ideal for use in
5521 server environments (file output) and as a replacement for other
5522 devices that don't have Cairo's capabilities such as alpha support or
5523 anti-aliasing. Backends are modular such that any subset of backends
5525 (license license:gpl2)))
5527 (define-public r-lubridate
5529 (name "r-lubridate")
5534 (uri (cran-uri "lubridate" version))
5537 "14a823il77w3wmmnzr89vwrqp50y56dh5raycnaw6c8nv5xsh32i"))))
5538 (build-system r-build-system)
5540 `(("r-rcpp" ,r-rcpp)
5541 ("r-stringr" ,r-stringr)))
5543 "https://cran.r-project.org/web/packages/lubridate")
5544 (synopsis "Make dealing with dates a little easier")
5546 "This package provides functions to work with date-times and time-spans:
5547 fast and user friendly parsing of date-time data, extraction and updating of
5548 components of a date-time (years, months, days, hours, minutes, and seconds),
5549 algebraic manipulation on date-time and time-span objects. The @code{lubridate}
5550 package has a consistent and memorable syntax that makes working with dates
5552 (license license:gpl2)))
5554 (define-public r-fdrtool
5561 (uri (cran-uri "fdrtool" version))
5564 "1h46frlk7d9f4qx0bg6p55nrm9wwwz2sv6d1nz7061wdfsm69yb5"))))
5565 (build-system r-build-system)
5566 (home-page "http://strimmerlab.org/software/fdrtool/")
5567 (synopsis "Estimation of false discovery rates and higher criticism")
5569 "This package provides tools to estimate tail area-based false discovery
5570 rates as well as local false discovery rates for a variety of null
5571 models (p-values, z-scores, correlation coefficients, t-scores). The
5572 proportion of null values and the parameters of the null distribution are
5573 adaptively estimated from the data. In addition, the package contains
5574 functions for non-parametric density estimation (Grenander estimator), for
5575 monotone regression (isotonic regression and antitonic regression with
5576 weights), for computing the @dfn{greatest convex minorant} (GCM) and the
5577 @dfn{least concave majorant} (LCM), for the half-normal and correlation
5578 distributions, and for computing empirical @dfn{higher criticism} (HC) scores
5579 and the corresponding decision threshold.")
5580 (license license:gpl3+)))
5582 (define-public r-forcats
5589 (uri (cran-uri "forcats" version))
5592 "1cnjh23z59fhbjmy7y95425hcq3m5wrwqvahsxwi7zm6d9bwp0vw"))))
5593 (build-system r-build-system)
5595 `(("r-ellipsis" ,r-ellipsis)
5596 ("r-magrittr" ,r-magrittr)
5597 ("r-tibble" ,r-tibble)
5598 ("r-rlang" ,r-rlang)))
5599 (home-page "http://forcats.tidyverse.org")
5600 (synopsis "Tools for working with factors")
5601 (description "This package provides helpers for reordering factor
5602 levels (including moving specified levels to front, ordering by first
5603 appearance, reversing, and randomly shuffling), and tools for modifying factor
5604 levels (including collapsing rare levels into other, \"anonymizing\", and
5605 manually \"recoding\").")
5606 (license license:gpl3)))
5608 (define-public r-tgstat
5609 (let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f")
5613 (version (string-append "1.0.2-" revision "." (string-take changeset 7)))
5618 (url "https://bitbucket.org/tanaylab/tgstat")
5619 (changeset changeset)))
5620 (file-name (string-append name "-" version "-checkout"))
5623 "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
5624 (build-system r-build-system)
5627 (modify-phases %standard-phases
5628 (add-after 'unpack 'fix-isnan
5630 (substitute* "src/tgstat.h"
5631 (("#define isnan ::isnan")
5632 "#define isnan std::isnan"))
5635 `(("r-rcpp" ,r-rcpp)))
5636 (home-page "https://bitbucket.org/tanaylab/tgstat/")
5637 (synopsis "Tanay's group statistical utilities")
5639 "The goal of tgstat is to provide fast and efficient statistical
5641 (license license:gpl2))))
5643 (define-public r-tgconfig
5644 (let ((changeset "1e02c7614713bd0866c46f0c679a058f8c6d627e")
5648 (version (string-append "0.0.0.9000-" revision "." (string-take changeset 7)))
5653 (url "https://bitbucket.org/tanaylab/tgconfig")
5654 (changeset changeset)))
5655 (file-name (string-append name "-" version "-checkout"))
5658 "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
5659 (build-system r-build-system)
5661 `(("r-yaml" ,r-yaml)))
5662 (home-page "https://bitbucket.org/tanaylab/tgconfig/")
5663 (synopsis "Infrastructure for managing package parameters")
5665 "The goal of tgconfig is to provide infrastructure for managing package
5667 (license license:gpl3))))
5669 (define-public r-directlabels
5671 (name "r-directlabels")
5672 (version "2018.05.22")
5676 (uri (cran-uri "directlabels" version))
5679 "0xcpc56ssb9430b0xcdhayk3qaak2qcakyss2pz14y5w2027hblv"))))
5680 (build-system r-build-system)
5682 `(("r-quadprog" ,r-quadprog)))
5683 (home-page "http://directlabels.r-forge.r-project.org/")
5684 (synopsis "Direct labels for multicolor plots")
5686 "This package provides an extensible framework for automatically placing
5687 direct labels onto multicolor plots. Label positions are described using
5688 positioning methods that can be re-used across several different plots. There
5689 are heuristics for examining @code{trellis} and @code{ggplot} objects and
5690 inferring an appropriate positioning method.")
5691 (license license:gpl3)))
5693 (define-public r-catterplots
5694 (let ((commit "40063ec57f9515d231508f135ca0ec769614efb9")
5697 (name "r-catterplots")
5698 (version (string-append "0-" revision "." (string-take commit 9)))
5702 (url "https://github.com/Gibbsdavidl/CatterPlots.git")
5704 (file-name (string-append name "-" version "-checkout"))
5707 "1wl80pgbz8d9kfpffvkh439hlgz2qldm9m75wqjfrgrg8lcjzrxg"))))
5708 (build-system r-build-system)
5710 `(("r-png" ,r-png)))
5711 (home-page "https://github.com/Gibbsdavidl/CatterPlots")
5712 (synopsis "Scatter plots with cat shaped points")
5713 (description "Did you ever wish you could make scatter plots with cat
5714 shaped points? Now you can!")
5715 (license license:asl2.0))))
5717 (define-public r-colorout
5724 (uri (string-append "https://github.com/jalvesaq/colorout/archive/"
5725 "v" version ".tar.gz"))
5726 (file-name (string-append name "-" version ".tar.gz"))
5729 "07vqx5ihgnq4dzn5jnfjfhdm3957v4prvf8vhnb3cwvlly4l7p9v"))))
5730 (build-system r-build-system)
5731 (home-page "https://github.com/jalvesaq/colorout")
5732 (synopsis "Colorize output in the R REPL")
5733 (description "@code{colorout} is an R package that colorizes R output when
5734 running in terminal emulator.
5736 R STDOUT is parsed and numbers, negative numbers, dates in the standard
5737 format, strings, and R constants are identified and wrapped by special ANSI
5738 scape codes that are interpreted by terminal emulators as commands to colorize
5739 the output. R STDERR is also parsed to identify the expressions warning and
5740 error and their translations to many languages. If these expressions are
5741 found, the output is colorized accordingly; otherwise, it is colorized as
5742 STDERROR (blue, by default).
5744 You can customize the colors according to your taste, guided by the color
5745 table made by the command @code{show256Colors()}. You can also set the colors
5746 to any arbitrary string. In this case, it is up to you to set valid values.")
5747 (license license:gpl3+)))
5749 (define-public r-txtplot
5756 (uri (cran-uri "txtplot" version))
5759 "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h"))))
5760 (build-system r-build-system)
5761 (home-page "https://cran.r-project.org/web/packages/txtplot/")
5762 (synopsis "Text-based plotting")
5763 (description "This package provides functions to produce rudimentary ASCII
5764 graphics directly in the terminal window. This package provides a basic
5765 plotting function (and equivalents of curve, density, acf and barplot) as well
5766 as a boxplot function.")
5767 (license license:lgpl3+)))
5769 (define-public python-rpy2
5770 ;; We need to take this changeset instead of the RELEASE_3_0_4 tag, because
5771 ;; it fixes a regression when using ggplot 3.2.0.
5772 (let ((changeset "19868a8")
5775 (name "python-rpy2")
5776 (version (git-version "3.0.4" revision changeset))
5781 (url "https://bitbucket.org/rpy2/rpy2")
5782 (changeset changeset)))
5783 (file-name (git-file-name name version))
5786 "1bb0wslcbj3wjvyk3jb9yyzdi6adfqh5vfgcvn22dyzxzbhcs8kk"))))
5787 (build-system python-build-system)
5789 '(#:modules ((ice-9 ftw)
5793 (guix build python-build-system))
5795 (modify-phases %standard-phases
5797 (lambda* (#:key outputs inputs #:allow-other-keys)
5798 (let ((cwd (getcwd)))
5800 (setenv "PYTHONPATH"
5801 (string-append cwd "/build/"
5802 (find (cut string-prefix? "lib" <>)
5803 (scandir (string-append cwd "/build")))
5805 (getenv "PYTHONPATH"))))
5806 (invoke "pytest" "-v" "rpy/tests/"))))))
5808 `(("python-cffi" ,python-cffi)
5809 ("python-six" ,python-six)
5810 ("python-jinja2" ,python-jinja2)
5811 ("python-numpy" ,python-numpy)
5812 ("python-pandas" ,python-pandas)
5813 ("python-pytz" ,python-pytz)
5814 ("python-ipython" ,python-ipython)
5815 ("python-tzlocal" ,python-tzlocal)))
5817 `(("readline" ,readline)
5820 ("r-minimal" ,r-minimal)
5821 ("r-survival" ,r-survival)
5822 ("r-ggplot2" ,r-ggplot2)
5823 ("r-rsqlite" ,r-rsqlite)
5824 ("r-dplyr" ,r-dplyr)
5825 ("r-dbplyr" ,r-dbplyr)
5826 ("python-numpy" ,python-numpy)))
5829 ("python-pytest" ,python-pytest)))
5830 (home-page "https://rpy2.bitbucket.io/")
5831 (synopsis "Python interface to the R language")
5832 (description "rpy2 is a redesign and rewrite of rpy. It is providing a
5833 low-level interface to R from Python, a proposed high-level interface,
5834 including wrappers to graphical libraries, as well as R-like structures and
5836 ;; Any of these licenses can be picked for the R interface. The whole
5837 ;; project is released under GPLv2+ according to the license declaration
5839 (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+)))))
5841 (define-public java-jdistlib
5843 (name "java-jdistlib")
5847 (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
5848 version "-src.jar"))
5851 "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
5852 (build-system ant-build-system)
5854 `(#:jar-name "jdistlib.jar"
5856 #:tests? #f ; no dedicated test directory
5858 (modify-phases %standard-phases
5859 (add-after 'unpack 'fix-broken-encoding
5861 (with-fluids ((%default-port-encoding "ISO-8859-1"))
5862 (substitute* "src/jdistlib/Beta.java"
5863 (("Scheff.+-Tukey") "Scheffe-Tukey")))
5866 `(("java-jtransforms" ,java-jtransforms)))
5868 `(("java-junit" ,java-junit)))
5869 (home-page "http://jdistlib.sourceforge.net/")
5870 (synopsis "Java library of statistical distributions")
5871 (description "JDistlib is the Java Statistical Distribution Library, a
5872 Java package that provides routines for various statistical distributions.")
5873 ;; The files that were translated from R code are under GPLv2+; some files
5874 ;; are under the GPLv3, which is a mistake. The author confirmed in an
5875 ;; email that this whole project should be under GPLv2+.
5876 (license license:gpl2+)))
5878 (define-public emacs-ess
5884 (uri (string-append "https://github.com/emacs-ess/ESS/archive/v"
5888 "0cbilbsiwvcyf6d5y24mymp57m3ana5dkzab3knfs83w4a3a4c5c"))
5889 (file-name (string-append name "-" version ".tar.gz"))
5890 (modules '((guix build utils)))
5893 ;; Stop ESS from trying to bundle an external julia-mode.el.
5894 (substitute* "lisp/Makefile"
5895 (("^\tjulia-mode.elc\\\\\n") "")
5896 (("^dist: all julia-mode.el")
5898 ;; No need to build docs in so many formats. Also, skipping
5899 ;; pdf lets us not pull in texlive.
5900 (substitute* "doc/Makefile"
5901 (("all : info text html pdf")
5903 (("install: install-info install-other-docs")
5904 "install: install-info"))
5905 ;; Test fails upstream
5906 (substitute* "test/ess-r-tests.el"
5907 (("ert-deftest ess-r-namespaced-eval-no-srcref-in-errors ()")
5908 "ert-deftest ess-r-namespaced-eval-no-srcref-in-errors () :expected-result :failed"))
5910 (build-system gnu-build-system)
5912 (let ((base-directory "/share/emacs/site-lisp/guix.d/ess"))
5913 `(#:make-flags (list (string-append "PREFIX=" %output)
5914 (string-append "ETCDIR=" %output "/"
5915 ,base-directory "/etc")
5916 (string-append "LISPDIR=" %output "/"
5919 (modify-phases %standard-phases
5921 (add-before 'build 'more-shebang-patching
5922 (lambda* (#:key inputs #:allow-other-keys)
5923 (substitute* "Makeconf"
5924 (("SHELL = /bin/sh")
5925 (string-append "SHELL = " (which "sh"))))
5929 (invoke "make" "test")))))))
5931 `(("emacs" ,emacs-minimal)
5932 ("r-minimal" ,r-minimal)))
5935 ("texinfo" ,texinfo)))
5937 `(("emacs-julia-mode" ,emacs-julia-mode)))
5938 (home-page "https://ess.r-project.org/")
5939 (synopsis "Emacs mode for statistical analysis programs")
5940 (description "Emacs Speaks Statistics (ESS) is an add-on package for GNU
5941 Emacs. It is designed to support editing of scripts and interaction with
5942 various statistical analysis programs such as R, Julia, and JAGS.")
5943 (license license:gpl2+)))