1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 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, 2020 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, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
12 ;;; Copyright © 2017 Alex Kost <alezost@gmail.com>
13 ;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com>
14 ;;; Copyright © 2020 Tim Howes <timhowes@lavabit.com>
16 ;;; This file is part of GNU Guix.
18 ;;; GNU Guix is free software; you can redistribute it and/or modify it
19 ;;; under the terms of the GNU General Public License as published by
20 ;;; the Free Software Foundation; either version 3 of the License, or (at
21 ;;; your option) any later version.
23 ;;; GNU Guix is distributed in the hope that it will be useful, but
24 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
25 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
26 ;;; GNU General Public License for more details.
28 ;;; You should have received a copy of the GNU General Public License
29 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
31 (define-module (gnu packages statistics)
32 #:use-module ((guix licenses) #:prefix license:)
33 #:use-module (guix packages)
34 #:use-module (guix download)
35 #:use-module (guix hg-download)
36 #:use-module (guix git-download)
37 #:use-module (guix utils)
38 #:use-module (guix build-system ant)
39 #:use-module (guix build-system gnu)
40 #:use-module (guix build-system r)
41 #:use-module (guix build-system python)
42 #:use-module (guix build-system trivial)
43 #:use-module (gnu packages)
44 #:use-module (gnu packages algebra)
45 #:use-module (gnu packages autotools)
46 #:use-module (gnu packages bash)
47 #:use-module (gnu packages check)
48 #:use-module (gnu packages compression)
49 #:use-module (gnu packages cran)
50 #:use-module (gnu packages curl)
51 #:use-module (gnu packages emacs)
52 #:use-module (gnu packages emacs-xyz)
53 #:use-module (gnu packages fontutils)
54 #:use-module (gnu packages gcc)
55 #:use-module (gnu packages gtk)
56 #:use-module (gnu packages gettext)
57 #:use-module (gnu packages glib)
58 #:use-module (gnu packages haskell-xyz)
59 #:use-module (gnu packages icu4c)
60 #:use-module (gnu packages image)
61 #:use-module (gnu packages java)
62 #:use-module (gnu packages libffi)
63 #:use-module (gnu packages machine-learning)
64 #:use-module (gnu packages maths)
65 #:use-module (gnu packages multiprecision)
66 #:use-module (gnu packages pcre)
67 #:use-module (gnu packages perl)
68 #:use-module (gnu packages pkg-config)
69 #:use-module (gnu packages python)
70 #:use-module (gnu packages python-science)
71 #:use-module (gnu packages python-xyz)
72 #:use-module (gnu packages readline)
73 #:use-module (gnu packages sphinx)
74 #:use-module (gnu packages ssh)
75 #:use-module (gnu packages tcl)
76 #:use-module (gnu packages tex)
77 #:use-module (gnu packages texinfo)
78 #:use-module (gnu packages time)
79 #:use-module (gnu packages tls)
80 #:use-module (gnu packages base)
81 #:use-module (gnu packages version-control)
82 #:use-module (gnu packages web)
83 #:use-module (gnu packages xml)
84 #:use-module (gnu packages xorg)
85 #:use-module (srfi srfi-1))
95 (uri (string-append "mirror://gnu/pspp/pspp-"
99 "07pp27zycrb5x927jwaj9r3q7hy915jh51xs85zxby6gfiwl63m5"))))
100 (build-system gnu-build-system)
103 ("gettext" ,gettext-minimal)
107 ("readline" ,readline)
109 ("gtksourceview" ,gtksourceview)
110 ("spread-sheet-widget" ,spread-sheet-widget)
113 `(("autoconf" ,autoconf) ;for tests
114 ("glib" ,glib "bin") ;for glib-genmarshal
116 ("pkg-config" ,pkg-config)
117 ("python" ,python-2) ;for tests
118 ("texinfo" ,texinfo)))
119 (home-page "https://www.gnu.org/software/pspp/")
120 (synopsis "Statistical analysis")
122 "GNU PSPP is a statistical analysis program. It can perform
123 descriptive statistics, T-tests, linear regression and non-parametric tests.
124 It features both a graphical interface as well as command-line input. PSPP
125 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
126 can be imported from spreadsheets, text files and database sources and it can
127 be output in text, PostScript, PDF or HTML.")
128 (license license:gpl3+)))
136 (uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/"
137 (version-major version) ".x/Source/"
138 "JAGS-" version ".tar.gz"))
141 "1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica"))))
142 (build-system gnu-build-system)
143 (home-page "http://mcmc-jags.sourceforge.net/")
145 `(("gfortran" ,gfortran)
147 (synopsis "Gibbs sampler")
148 (description "JAGS is Just Another Gibbs Sampler. It is a program for
149 analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
150 simulation not wholly unlike BUGS. JAGS was written with three aims in mind:
153 @item To have a cross-platform engine for the BUGS language;
154 @item To be extensible, allowing users to write their own functions,
155 distributions and samplers;
156 @item To be a platform for experimentation with ideas in Bayesian modelling.
158 (license license:gpl2)))
160 (define-public libxls
167 (uri (string-append "https://github.com/libxls/libxls/releases/download/"
168 "v" version "/libxls-" version ".tar.gz"))
170 (base32 "0rl513wpq5qh7wkmdk4g9c68rzffv3mcbz48p4xyg4969zrx8lnm"))))
171 (build-system gnu-build-system)
172 (home-page "https://github.com/libxls/libxls")
173 (synopsis "Read binary (.xls) Excel spreadsheet files")
175 "libxls is a C library to read .xls spreadsheet files in the binary OLE
176 BIFF8 format as created by Excel 97 and later versions. It cannot write them.
178 This package also provides @command{xls2csv} to export Excel files to CSV.")
179 (license license:bsd-2)))
181 ;; Update this package together with the set of recommended packages: r-boot,
182 ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
183 ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
186 (name "r-with-tests")
190 (uri (string-append "mirror://cran/src/base/R-"
191 (version-major version) "/R-"
195 "0xdy3dy2bzdiba8z94hjykyra8si8a5q15s0bri7c26scjrymg6k"))))
196 (build-system gnu-build-system)
198 `(#:disallowed-references (,tzdata-for-tests)
200 (list (string-append "LDFLAGS=-Wl,-rpath="
201 (assoc-ref %outputs "out")
203 ;; This affects the embedded timestamp of only the core packages.
204 "PKG_BUILT_STAMP=1970-01-01")
206 (modify-phases %standard-phases
207 (add-before 'configure 'do-not-compress-serialized-files
208 (lambda* (#:key inputs #:allow-other-keys)
209 ;; This ensures that Guix can detect embedded store references;
210 ;; see bug #28157 for details.
211 (substitute* "src/library/base/makebasedb.R"
212 (("compress = TRUE") "compress = FALSE"))
214 (add-before 'configure 'patch-uname
215 (lambda* (#:key inputs #:allow-other-keys)
216 (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
218 (substitute* "src/scripts/R.sh.in"
219 (("uname") uname-bin)))
221 (add-after 'unpack 'build-reproducibly
223 ;; The documentation contains time stamps to demonstrate
224 ;; documentation generation in different phases.
225 (substitute* "src/library/tools/man/Rd2HTML.Rd"
226 (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
227 "(removed for reproducibility)"))
229 ;; Remove timestamp from tracing environment. This fixes
230 ;; reproducibility of "methods.rd{b,x}".
231 (substitute* "src/library/methods/R/trace.R"
232 (("dateCreated = Sys.time\\(\\)")
233 "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
235 ;; Ensure that gzipped files are reproducible.
236 (substitute* '("src/library/grDevices/Makefile.in"
237 "doc/manual/Makefile.in")
238 (("R_GZIPCMD\\)" line)
239 (string-append line " -n")))
241 ;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
242 ;; queries the mtime of a given file and records it in an object.
243 ;; This is acceptable at runtime to detect stale source files,
244 ;; but it destroys reproducibility at build time.
246 ;; Similarly, the "srcfilecopy" procedure records the current
247 ;; time. We change both of them to respect SOURCE_DATE_EPOCH.
248 (substitute* "src/library/base/R/srcfile.R"
249 (("timestamp <- (timestamp.*|file.mtime.*)" _ time)
250 (string-append "timestamp <- \
251 as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
252 as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
253 } else { " time "}, origin=\"1970-01-01\")\n")))
255 ;; This library is installed using "install_package_description",
256 ;; so we need to pass the "builtStamp" argument.
257 (substitute* "src/library/tools/Makefile.in"
258 (("(install_package_description\\(.*\"')\\)\"" line prefix)
259 (string-append prefix ", builtStamp='1970-01-01')\"")))
261 (substitute* "src/library/Recommended/Makefile.in"
262 (("INSTALL_OPTS =" m)
263 (string-append m " --built-timestamp=1970-01-01" m)))
265 ;; R bundles an older version of help2man, which does not respect
266 ;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man,
267 ;; because that breaks a test.
268 (with-fluids ((%default-port-encoding "ISO-8859-1"))
269 (substitute* "tools/help2man.pl"
270 (("my \\$date = strftime \"%B %Y\", localtime" line)
271 (string-append line " 1"))))
273 (add-before 'build 'set-locales
275 (setlocale LC_ALL "C")
276 (setenv "LC_ALL" "C")
278 (add-before 'configure 'set-default-pager
279 ;; Set default pager to "cat", because otherwise it is "false",
280 ;; making "help()" print nothing at all.
281 (lambda _ (setenv "PAGER" "cat") #t))
282 (add-before 'check 'set-timezone
283 ;; Some tests require the timezone to be set. However, the
284 ;; timezone may not just be "UTC", or else a brittle regression
285 ;; test in reg-tests-1d will fail.
286 (lambda* (#:key inputs #:allow-other-keys)
287 (setenv "TZ" "UTC+1")
289 (string-append (assoc-ref inputs "tzdata")
292 (add-after 'build 'make-info
293 (lambda _ (invoke "make" "info")))
294 (add-after 'build 'install-info
295 (lambda _ (invoke "make" "install-info"))))
297 `(;; We build the recommended packages here, because they are needed in
298 ;; order to run the test suite. We disable them in the r-minimal
301 "--with-blas=-lopenblas"
307 ,(string-append "--with-tcl-config="
308 (assoc-ref %build-inputs "tcl")
310 ,(string-append "--with-tk-config="
311 (assoc-ref %build-inputs "tk")
314 "--enable-BLAS-shlib"
315 "--with-system-tre")))
316 ;; R has some support for Java. When the JDK is available at configure
317 ;; time environment variables pointing to the JDK will be recorded under
318 ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
319 ;; CMD javareconf". "R CMD javareconf" appears to only be used to update
320 ;; the recorded environment variables in $R_HOME/etc. Refer to
321 ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
322 ;; for additional information.
324 ;; As the JDK is a rather large input with only very limited effects on R,
325 ;; we decided to drop it.
329 ("pkg-config" ,pkg-config)
330 ("texinfo" ,texinfo) ; for building HTML manuals
331 ("texlive" ,(texlive-union (list texlive-ae
336 texlive-latex-fancyvrb
337 texlive-latex-graphics
338 texlive-latex-hyperref
339 texlive-latex-oberdiek
341 texlive-latex-upquote
343 texlive-latex-xkeyval)))
344 ("tzdata" ,tzdata-for-tests)
347 `(;; We need not only cairo here, but pango to ensure that tests for the
348 ;; "cairo" bitmapType plotting backend succeed.
350 ("coreutils" ,coreutils)
352 ("openblas" ,openblas)
353 ("gfortran" ,gfortran)
355 ("libjpeg" ,libjpeg-turbo)
360 ("readline" ,readline)
361 ;; This avoids a reference to the ungraftable static bash. R uses the
362 ;; detected shell for the "system" procedure.
363 ("bash" ,bash-minimal)
369 (list (search-path-specification
370 (variable "R_LIBS_SITE")
371 (files (list "site-library/")))))
372 (home-page "https://www.r-project.org/")
373 (synopsis "Environment for statistical computing and graphics")
375 "R is a language and environment for statistical computing and graphics.
376 It provides a variety of statistical techniques, such as linear and nonlinear
377 modeling, classical statistical tests, time-series analysis, classification
378 and clustering. It also provides robust support for producing
379 publication-quality data plots. A large amount of 3rd-party packages are
380 available, greatly increasing its breadth and scope.")
381 (license license:gpl3+)))
383 (define-public r-minimal
384 (package (inherit r-with-tests)
388 ,@(substitute-keyword-arguments (package-arguments r-with-tests)
389 ((#:configure-flags flags)
390 ;; Do not build the recommended packages. The build system creates
391 ;; random temporary directories and embeds their names in some
392 ;; package files. We build these packages with the r-build-system
394 `(cons "--without-recommended-packages" ,flags)))))))
396 (define-public rmath-standalone
397 (package (inherit r-minimal)
398 (name "rmath-standalone")
401 (modify-phases %standard-phases
402 (add-after 'configure 'chdir
403 (lambda _ (chdir "src/nmath/standalone/") #t)))))
404 (synopsis "Standalone R math library")
406 "This package provides the R math library as an independent package.")))
408 (define-public r-boot
415 (uri (cran-uri "boot" version))
418 "1gpvi1h3nqhnnsfy96rlhakdpj84iqqsxr29rr3261sknky3aj26"))))
419 (build-system r-build-system)
420 (home-page "https://cran.r-project.org/web/packages/boot")
421 (synopsis "Bootstrap functions for R")
423 "This package provides functions and datasets for bootstrapping from the
424 book \"Bootstrap Methods and Their Application\" by A.C. Davison and
425 D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
426 ;; Unlimited distribution
427 (license (license:non-copyleft "file://R/bootfuns.q"))))
429 (define-public r-mass
436 (uri (cran-uri "MASS" version))
439 "1viyxy22qp8abzzzlbck55b0i81rrdygim1dq2pm52s2v13mq0z2"))))
440 (properties `((upstream-name . "MASS")))
441 (build-system r-build-system)
442 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
443 (synopsis "Support functions and datasets for Venables and Ripley's MASS")
445 "This package provides functions and datasets for the book \"Modern
446 Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
447 ;; Either version may be picked.
448 (license (list license:gpl2 license:gpl3))))
450 (define-public r-class
457 (uri (cran-uri "class" version))
460 "04qk8qia0qr8893fizmkbd5hsqn6m8383c0cyn9xnmkmvyv8a7xy"))))
461 (build-system r-build-system)
463 `(("r-mass" ,r-mass)))
464 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
465 (synopsis "R functions for classification")
467 "This package provides various functions for classification, including
468 k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
469 ;; Either of the two versions can be picked.
470 (license (list license:gpl2 license:gpl3))))
472 (define-public r-cluster
479 (uri (cran-uri "cluster" version))
482 "055af3yz2biqbsbwm4arwr1yqnj4gicpzv2i6dbfl5pnz2z5byga"))))
483 (build-system r-build-system)
485 `(("gfortran" ,gfortran)))
486 (home-page "https://cran.r-project.org/web/packages/cluster")
487 (synopsis "Methods for cluster analysis")
489 "This package provides methods for cluster analysis. It is a much
490 extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
491 Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
492 (license license:gpl2+)))
494 (define-public r-codetools
501 (uri (cran-uri "codetools" version))
504 "00bmhzqprqfn3w6ghx7sakai6s7il8gbksfiawj8in5mbhbncypn"))))
505 (build-system r-build-system)
506 (home-page "https://cran.r-project.org/web/packages/codetools")
507 (synopsis "Code analysis tools for R")
508 (description "This package provides code analysis tools for R to check R
509 code for possible problems.")
510 ;; Any version of the GPL.
511 (license (list license:gpl2+ license:gpl3+))))
513 (define-public r-foreign
520 (uri (cran-uri "foreign" version))
523 "0wjdi3qn9famsxmpdyyahidaid0yhxlpx4ad9k8vrxhxd6xspasp"))))
524 (build-system r-build-system)
525 (home-page "https://cran.r-project.org/web/packages/foreign")
526 (synopsis "Read data stored by other statistics software")
528 "This package provides functions for reading and writing data stored by
529 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
530 for reading and writing some dBase files.")
531 (license license:gpl2+)))
533 (define-public r-kernsmooth
535 (name "r-kernsmooth")
540 (uri (cran-uri "KernSmooth" version))
543 "11g6b0q67vasxag6v9m4px33qqxpmnx47c73yv1dninv2pz76g9b"))))
544 (properties `((upstream-name . "KernSmooth")))
545 (build-system r-build-system)
547 `(("gfortran" ,gfortran)))
548 (home-page "https://cran.r-project.org/web/packages/KernSmooth")
549 (synopsis "Functions for kernel smoothing")
551 "This package provides functions for kernel smoothing (and density
552 estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
553 \"Kernel Smoothing\".")
554 ;; Unlimited use and distribution
555 (license (license:non-copyleft "file://LICENCE.note"))))
557 (define-public r-lattice
563 (uri (cran-uri "lattice" version))
566 "1dapkmh4jlb9sxfrpvapvlfhczl4s8p3r20bn47gcgdk1izmbjjl"))))
567 (build-system r-build-system)
568 (home-page "http://lattice.r-forge.r-project.org/")
569 (synopsis "High-level data visualization system")
571 "The lattice package provides a powerful and elegant high-level data
572 visualization system inspired by Trellis graphics, with an emphasis on
573 multivariate data. Lattice is sufficient for typical graphics needs, and is
574 also flexible enough to handle most nonstandard requirements.")
575 (license license:gpl2+)))
577 (define-public r-matrix
584 (uri (cran-uri "Matrix" version))
587 "06b1rc1vq65b271f2wpzhqkvhng8hwwnvjflzxkng50i52603zzp"))))
588 (properties `((upstream-name . "Matrix")))
589 (build-system r-build-system)
591 `(("r-lattice" ,r-lattice)))
592 (home-page "http://Matrix.R-forge.R-project.org/")
593 (synopsis "Sparse and dense matrix classes and methods")
595 "This package provides classes and methods for dense and sparse matrices
596 and operations on them using LAPACK and SuiteSparse.")
597 (license license:gpl2+)))
599 (define-public r-nlme
606 (uri (cran-uri "nlme" version))
608 (base32 "1cmf43r82kar1hpj9dhqfi3rbjka0z5s6cbdy7fklwh99xj3phkp"))))
609 (build-system r-build-system)
611 `(("r-lattice" ,r-lattice)))
613 `(("gfortran" ,gfortran)))
614 (home-page "https://cran.r-project.org/web/packages/nlme")
615 (synopsis "Linear and nonlinear mixed effects models")
617 "This package provides tools to fit and compare Gaussian linear and
618 nonlinear mixed-effects models.")
619 (license license:gpl2+)))
621 (define-public r-mgcv
628 (uri (cran-uri "mgcv" version))
630 (base32 "1if34mqsn9r7g0l82lxvvx0wjhi9paqdymyd73nschxcl1if8vbk"))))
631 (build-system r-build-system)
633 `(("r-matrix" ,r-matrix)
635 (home-page "https://cran.r-project.org/web/packages/mgcv")
636 (synopsis "Mixed generalised additive model computation")
638 "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
639 parameter estimation by GCV, REML or UBRE/AIC. The library includes a
640 @code{gam()} function, a wide variety of smoothers, JAGS support and
641 distributions beyond the exponential family.")
642 (license license:gpl2+)))
644 (define-public r-nnet
651 (uri (cran-uri "nnet" version))
654 "1bzl62p5awva5kxcncs6lrdrkqp9ljd993zia731ckfpcjbrw6sx"))))
655 (build-system r-build-system)
656 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
657 (synopsis "Feed-forward neural networks and multinomial log-linear models")
659 "This package provides functions for feed-forward neural networks with a
660 single hidden layer, and for multinomial log-linear models.")
661 (license (list license:gpl2+ license:gpl3+))))
663 (define-public r-rpart
670 (uri (cran-uri "rpart" version))
673 "0p5frya963ppn476p5dxs2mnarsalksr6gw9zzmjsn8ikq7bx3ib"))))
674 (build-system r-build-system)
675 (home-page "https://cran.r-project.org/web/packages/rpart")
676 (synopsis "Recursive partitioning and regression trees")
678 "This package provides recursive partitioning functions for
679 classification, regression and survival trees.")
680 (license (list license:gpl2+ license:gpl3+))))
682 (define-public r-spatial
689 (uri (cran-uri "spatial" version))
692 "0qrdhzd5r78iwi46nk8jr56dzz5l5imkflxjw64d0ys0wyg06fbn"))))
693 (build-system r-build-system)
694 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
695 (synopsis "Functions for kriging and point pattern analysis")
697 "This package provides functions for kriging and point pattern
699 ;; Either version may be picked.
700 (license (list license:gpl2 license:gpl3))))
702 (define-public r-survival
709 (uri (cran-uri "survival" version))
712 "07h76r2y23w889257krlijcw4n4d7ssx92x7i5qb1xyv5gyvl3rx"))))
713 (build-system r-build-system)
715 `(("r-matrix" ,r-matrix)))
716 (home-page "https://github.com/therneau/survival")
717 (synopsis "Survival analysis")
719 "This package contains the core survival analysis routines, including
720 definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
721 curves, Cox models, and parametric accelerated failure time models.")
722 (license license:lgpl2.0+)))
725 (package (inherit r-minimal)
728 (build-system trivial-build-system)
729 (arguments '(#:builder (begin (mkdir %output) #t)))
731 `(("r-minimal" ,r-minimal)
734 ("r-cluster" ,r-cluster)
735 ("r-codetools" ,r-codetools)
736 ("r-foreign" ,r-foreign)
737 ("r-kernsmooth" ,r-kernsmooth)
738 ("r-lattice" ,r-lattice)
740 ("r-matrix" ,r-matrix)
745 ("r-spatial" ,r-spatial)
746 ("r-survival" ,r-survival)))))
755 (uri (cran-uri "bit" version))
758 "12xjkkkmflkz8s435by4r23b57cz7z67z84907f6qg99hn1yg0qb"))))
759 (build-system r-build-system)
760 (home-page "http://ff.r-forge.r-project.org")
761 (synopsis "Class for vectors of 1-bit booleans")
763 "This package provides bitmapped vectors of booleans (no @code{NA}s),
764 coercion from and to logicals, integers and integer subscripts, fast boolean
765 operators and fast summary statistics. With @code{bit} class vectors of true
766 binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
767 (license license:gpl2)))
769 (define-public r-bit64
776 (uri (cran-uri "bit64" version))
779 "07znvz9vp1nz1y5ljng4qyskvm943cdbmy996s67560ijxzsm6kv"))))
780 (build-system r-build-system)
783 (home-page "http://ff.r-forge.r-project.org/")
784 (synopsis "S3 class for vectors of 64 bit integers")
786 "The bit64 package provides serializable S3 atomic 64 bit (signed)
787 integers that can be used in vectors, matrices, arrays and @code{data.frames}.
788 Methods are available for coercion from and to logicals, integers, doubles,
789 characters and factors as well as many elementwise and summary functions.
790 Many fast algorithmic operations such as @code{match} and @code{order} support
791 interactive data exploration and manipulation and optionally leverage
793 (license license:gpl2)))
795 (define-public r-dichromat
802 (uri (cran-uri "dichromat" version))
804 (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
805 (build-system r-build-system)
806 (home-page "https://cran.r-project.org/web/packages/dichromat")
807 (synopsis "Color schemes for dichromats")
809 "Dichromat collapses red-green or green-blue distinctions to simulate the
810 effects of different types of color-blindness.")
811 (license license:gpl2+)))
813 (define-public r-digest
820 (uri (cran-uri "digest" version))
822 (base32 "1r9dkq0kxkps54gkmgcdngsd068p054va2vhnqhs5jmwp2vsvk0m"))))
823 (build-system r-build-system)
824 ;; Vignettes require r-knitr, which requires r-digest, so we have to
825 ;; disable them and the tests.
828 #:configure-flags (list "--no-build-vignettes")))
829 (home-page "http://dirk.eddelbuettel.com/code/digest.html")
830 (synopsis "Create cryptographic hash digests of R objects")
832 "This package contains an implementation of a function @code{digest()} for
833 the creation of hash digests of arbitrary R objects (using the md5, sha-1,
834 sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
835 of R language objects, as well as a function @code{hmac()} to create hash-based
836 message authentication code.
838 Please note that this package is not meant to be deployed for cryptographic
839 purposes for which more comprehensive (and widely tested) libraries such as
840 OpenSSL should be used.")
841 (license license:gpl2+)))
843 (define-public r-estimability
845 (name "r-estimability")
849 (uri (cran-uri "estimability" version))
852 "0cifdaa71spkcxl4db4z884jrya865sg3dhcv4isd8fnzg2pjcd3"))))
853 (build-system r-build-system)
854 (home-page "https://cran.r-project.org/web/packages/estimability")
855 (synopsis "Tools for assessing estimability of linear predictions")
856 (description "Provides tools for determining estimability of linear
857 functions of regression coefficients, and @code{epredict} methods that handle
858 non-estimable cases correctly.")
859 (license license:gpl2+)))
861 (define-public r-labeling
868 (uri (cran-uri "labeling" version))
870 (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
871 (build-system r-build-system)
872 (home-page "https://cran.r-project.org/web/packages/labeling")
873 (synopsis "Axis labeling algorithms")
874 (description "The labeling package provides a range of axis labeling
876 (license license:expat)))
878 (define-public r-magrittr
885 (uri (cran-uri "magrittr" version))
887 (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
888 (build-system r-build-system)
889 (home-page "https://cran.r-project.org/web/packages/magrittr/index.html")
890 (synopsis "A forward-pipe operator for R")
892 "Magrittr provides a mechanism for chaining commands with a new
893 forward-pipe operator, %>%. This operator will forward a value, or the result
894 of an expression, into the next function call/expression. There is flexible
895 support for the type of right-hand side expressions. For more information,
896 see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
897 (license license:expat)))
899 (define-public r-munsell
906 (uri (cran-uri "munsell" version))
908 (base32 "16g1fzisbpqb15yh3pqf3iia4csppva5dnv1z88x9dg263xskwyh"))))
909 (build-system r-build-system)
911 `(("r-colorspace" ,r-colorspace)))
912 (home-page "https://cran.r-project.org/web/packages/munsell")
913 (synopsis "Munsell colour system")
915 "The Munsell package contains Functions for exploring and using the
916 Munsell colour system.")
917 (license license:expat)))
919 (define-public r-permute
926 (uri (cran-uri "permute" version))
929 "0ra8p5mf2590azrkas8z2ry7mif77xqxd29n4zgyi5vll225726j"))))
930 (build-system r-build-system)
931 ;; Tests do not run correctly, but running them properly would entail a
932 ;; circular dependency with vegan.
933 (home-page "https://github.com/gavinsimpson/permute")
934 (synopsis "Functions for Generating Restricted Permutations of Data")
936 "This package provides a set of restricted permutation designs for freely
937 exchangeable, line transects (time series), spatial grid designs and permutation
938 of blocks (groups of samples). @code{permute} also allows split-plot designs,
939 in which the whole-plots or split-plots or both can be freely exchangeable.")
940 (license license:gpl2+)))
942 (define-public r-plyr
949 (uri (cran-uri "plyr" version))
951 (base32 "11sjjdn146w95s1vsfmmgdls082cbnm1slv98xvyjhsl2mpx4mga"))))
952 (build-system r-build-system)
953 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
954 (home-page "http://had.co.nz/plyr")
955 (synopsis "Tools for Splitting, Applying and Combining Data")
957 "Plyr is a set of tools that solves a common set of problems: you need to
958 break a big problem down into manageable pieces, operate on each piece and
959 then put all the pieces back together. For example, you might want to fit a
960 model to each spatial location or time point in your study, summarise data by
961 panels or collapse high-dimensional arrays to simpler summary statistics.")
962 (license license:expat)))
964 (define-public r-proto
971 (uri (cran-uri "proto" version))
973 (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
974 (build-system r-build-system)
975 (home-page "https://github.com/hadley/proto")
976 (synopsis "Prototype object-based programming")
978 "Proto is an object oriented system using object-based, also called
979 prototype-based, rather than class-based object oriented ideas.")
980 (license license:gpl2+)))
982 (define-public r-rcolorbrewer
984 (name "r-rcolorbrewer")
989 (uri (cran-uri "RColorBrewer" version))
991 (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
992 (build-system r-build-system)
993 (home-page "https://cran.r-project.org/web/packages/RColorBrewer")
994 (synopsis "ColorBrewer palettes")
996 "This package provides color schemes for maps (and other graphics)
997 designed by Cynthia Brewer as described at http://colorbrewer2.org")
998 ;; Includes code licensed under bsd-4
999 (license license:asl2.0)))
1001 (define-public r-sendmailr
1003 (name "r-sendmailr")
1008 (uri (cran-uri "sendmailR" version))
1011 "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
1012 (properties `((upstream-name . "sendmailR")))
1013 (build-system r-build-system)
1015 `(("r-base64enc" ,r-base64enc)))
1017 "https://cran.r-project.org/web/packages/sendmailR")
1018 (synopsis "Send email using R")
1020 "This package contains a simple SMTP client which provides a portable
1021 solution for sending email, including attachments, from within R.")
1022 (license license:gpl2+)))
1024 (define-public r-stringi
1031 (uri (cran-uri "stringi" version))
1034 "1mkgxzf000zdgbbbvg2vf4md4l501n5lfksffq8vdg6pbgd6fgv3"))))
1035 (build-system r-build-system)
1036 (inputs `(("icu4c" ,icu4c)))
1037 (native-inputs `(("pkg-config" ,pkg-config)))
1038 (home-page "http://stringi.rexamine.com/")
1039 (synopsis "Character string processing facilities")
1041 "This package allows for fast, correct, consistent, portable, as well as
1042 convenient character string/text processing in every locale and any native
1043 encoding. Owing to the use of the ICU library, the package provides R users
1044 with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
1045 programmers. Among available features there are: pattern searching
1046 (e.g. via regular expressions), random string generation, string collation,
1047 transliteration, concatenation, date-time formatting and parsing, etc.")
1048 (license license:bsd-3)))
1050 (define-public r-stringr
1057 (uri (cran-uri "stringr" version))
1059 (base32 "1p9ip7p87gbbg4s6d3d392svvzz2b5dqdq2c8ilgvn4s78nlsq47"))))
1060 (build-system r-build-system)
1062 `(("r-glue" ,r-glue)
1063 ("r-magrittr" ,r-magrittr)
1064 ("r-stringi" ,r-stringi)))
1065 (home-page "https://github.com/hadley/stringr")
1066 (synopsis "Simple, consistent wrappers for common string operations")
1068 "Stringr is a consistent, simple and easy to use set of wrappers around
1069 the fantastic @code{stringi} package. All function and argument names (and
1070 positions) are consistent, all functions deal with \"NA\"'s and zero length
1071 vectors in the same way, and the output from one function is easy to feed into
1072 the input of another.")
1073 (license license:gpl2+)))
1075 (define-public r-reshape2
1082 (uri (cran-uri "reshape2" version))
1084 (base32 "1n0jrajpvc8hjkh9z4g8bwq63qy5vy5cgl2pzjardyih4ngcz3fq"))))
1085 (build-system r-build-system)
1087 `(("r-plyr" ,r-plyr)
1089 ("r-stringr" ,r-stringr)))
1090 (home-page "https://github.com/hadley/reshape")
1091 (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
1093 "Reshape2 is an R library to flexibly restructure and aggregate data
1094 using just two functions: melt and dcast (or acast).")
1095 (license license:expat)))
1097 (define-public r-ggplot2
1104 (uri (cran-uri "ggplot2" version))
1106 (base32 "0wsib5qpzn4d0w1ss3x158xmrawkms8vvsfvr3mh40pvd8g2ibad"))))
1107 (build-system r-build-system)
1109 `(("r-digest" ,r-digest)
1111 ("r-gtable" ,r-gtable)
1112 ("r-isoband" ,r-isoband)
1115 ("r-tibble" ,r-tibble)
1116 ("r-rlang" ,r-rlang)
1117 ("r-scales" ,r-scales)
1118 ("r-svglite" ,r-svglite) ; Needed for 'ggsave'
1119 ("r-withr" ,r-withr)))
1121 `(("r-knitr" ,r-knitr)))
1122 (home-page "https://ggplot2.tidyverse.org")
1123 (synopsis "An implementation of the grammar of graphics")
1125 "Ggplot2 is an implementation of the grammar of graphics in R. It
1126 combines the advantages of both base and lattice graphics: conditioning and
1127 shared axes are handled automatically, and you can still build up a plot step
1128 by step from multiple data sources. It also implements a sophisticated
1129 multidimensional conditioning system and a consistent interface to map data to
1130 aesthetic attributes.")
1131 (license license:gpl2+)))
1133 (define-public r-ggdendro
1139 (uri (cran-uri "ggdendro" version))
1142 "1zzq1hxd0d1qa5hrzwfkdw6fzscpcafbwbpkrb62dm559y8awp0j"))))
1143 (build-system r-build-system)
1145 `(("r-ggplot2" ,r-ggplot2)
1147 ("r-knitr" ,r-knitr)))
1148 (home-page "https://github.com/andrie/ggdendro")
1149 (synopsis "Create Dendrograms and Tree Diagrams Using ggplot2")
1150 (description "This is a set of tools for dendrograms and tree plots using
1151 ggplot2. The ggplot2 philosophy is to clearly separate data from the
1152 presentation. Unfortunately the plot method for dendrograms plots directly
1153 to a plot device with out exposing the data. The ggdendro package resolves
1154 this by making available functions that extract the dendrogram plot data.
1155 The package provides implementations for tree, rpart, as well as diana and
1156 agnes cluster diagrams.")
1157 (license license:gpl2+)))
1159 (define-public r-gdtools
1166 (uri (cran-uri "gdtools" version))
1169 "08njzin0c6biw62j5w30r9j85vr1m2cg4hmv5d76nym860yrlqjf"))))
1170 (build-system r-build-system)
1172 `(("pkg-config" ,pkg-config)))
1175 ("freetype2" ,freetype)
1178 `(("r-rcpp" ,r-rcpp)
1179 ("r-systemfonts" ,r-systemfonts)))
1180 (home-page "https://cran.r-project.org/web/packages/gdtools")
1181 (synopsis "Utilities for graphical rendering")
1183 "The @code{gdtools} package provides functionalities to get font metrics
1184 and to generate base64 encoded string from raster matrix.")
1185 (license license:gpl3)))
1187 (define-public r-svglite
1194 (uri (cran-uri "svglite" version))
1197 "1zivykbi1pxdxhrkc1if1ihdn5p27j0nai2q0abca1dwry3wg2yl"))))
1198 (build-system r-build-system)
1201 ("r-gdtools" ,r-gdtools)
1202 ("r-rcpp" ,r-rcpp)))
1203 (home-page "https://github.com/hadley/svglite")
1204 (synopsis "SVG graphics device")
1206 "@code{svglite} is a graphics device that produces clean
1207 @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
1208 hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
1209 considerably faster, produces smaller files, and leaves text as is.")
1210 (license license:gpl2+)))
1212 (define-public r-assertthat
1214 (name "r-assertthat")
1218 (uri (cran-uri "assertthat" version))
1221 "17wy5bdfzg73sg2clisg1k3zyn1adkj59x56m5nwia2k8z67zkw5"))))
1222 (build-system r-build-system)
1223 (home-page "https://github.com/hadley/assertthat")
1224 (synopsis "Easy pre and post assertions")
1226 "Assertthat is an extension to stopifnot() that makes it easy to declare
1227 the pre and post conditions that your code should satisfy, while also
1228 producing friendly error messages so that your users know what they've done
1230 (license license:gpl3+)))
1232 (define-public r-lazyeval
1238 (uri (cran-uri "lazyeval" version))
1241 "1m10i059csrcqkcn59a8wspn784alxsq3symzhn24mhhl894346n"))))
1242 (build-system r-build-system)
1243 (home-page "https://github.com/hadley/lazyeval")
1244 (synopsis "Lazy (non-standard) evaluation in R")
1246 "This package provides the tools necessary to do non-standard
1247 evaluation (NSE) in R.")
1248 (license license:gpl3+)))
1250 (define-public r-dbi
1256 (uri (cran-uri "DBI" version))
1259 "1r03j9rdcxb9bhxk40dkmy10ikz4yzsxhy3f9k9ix3x577xbfvd9"))))
1260 (build-system r-build-system)
1261 (home-page "https://github.com/rstats-db/DBI")
1262 (synopsis "R database interface")
1264 "The DBI package provides a database interface (DBI) definition for
1265 communication between R and relational database management systems. All
1266 classes in this package are virtual and need to be extended by the various
1267 R/DBMS implementations.")
1268 (license license:lgpl2.0+)))
1273 (version "1.72.0-3")
1276 (uri (cran-uri "BH" version))
1279 "1ay8vb6i730lipg8b8g3893vqglhw2kqpc29lwdrxdkb66iw33l8"))))
1280 (build-system r-build-system)
1281 (home-page "https://github.com/eddelbuettel/bh")
1282 (synopsis "R package providing subset of Boost headers")
1284 "This package aims to provide the most useful subset of Boost libraries
1285 for template use among CRAN packages.")
1286 (license license:boost1.0)))
1288 (define-public r-evaluate
1294 (uri (cran-uri "evaluate" version))
1297 "0a2y7j534gbgixkwj9r1z76l2vssw4g1hznzbpclc076wkdqpj58"))))
1298 (build-system r-build-system)
1299 (home-page "https://github.com/hadley/evaluate")
1300 (synopsis "Parsing and evaluation tools for R")
1302 "This package provides tools that allow you to recreate the parsing,
1303 evaluation and display of R code, with enough information that you can
1304 accurately recreate what happens at the command line. The tools can easily be
1305 adapted for other output formats, such as HTML or LaTeX.")
1306 (license license:gpl3+)))
1308 (define-public r-formatr
1314 (uri (cran-uri "formatR" version))
1317 "1nsxbrx31k3y6yql30qkrvdfyznlia2qfvwv95mfiy7m7wdn4rm3"))))
1318 (build-system r-build-system)
1319 (home-page "https://yihui.org/formatr/")
1320 (synopsis "Format R code automatically")
1322 "This package provides a function to format R source code. Spaces and
1323 indent will be added to the code automatically, and comments will be preserved
1324 under certain conditions, so that R code will be more human-readable and tidy.
1325 There is also a Shiny app as a user interface in this package.")
1326 (license license:gpl3+)))
1328 (define-public r-highr
1334 (uri (cran-uri "highr" version))
1337 "0my6idnhmmgs4q1vs40y2lh56yij2p59mpwvm53wjs2zk6x1zl2b"))))
1338 (build-system r-build-system)
1339 (home-page "https://github.com/yihui/highr")
1340 (synopsis "Syntax highlighting for R source code")
1342 "This package provides syntax highlighting for R source code. Currently
1343 it supports LaTeX and HTML output. Source code of other languages is
1344 supported via Andre Simon's highlight package.")
1345 (license license:gpl3+)))
1347 (define-public r-mime
1353 (uri (cran-uri "mime" version))
1356 "107sqarmyhxlch5nrg796i5z03p9mshskisiq2fm628ajk99gkrc"))))
1357 (build-system r-build-system)
1358 (home-page "https://github.com/yihui/mime")
1359 (synopsis "R package to map filenames to MIME types")
1361 "This package guesses the MIME type from a filename extension using the
1362 data derived from /etc/mime.types in UNIX-type systems.")
1363 (license license:gpl2)))
1365 (define-public r-markdown
1371 (uri (cran-uri "markdown" version))
1374 "06zwbrp14bri3470anadd7dvgmw06xf8df6v2pk64wx3f9sd934d"))))
1375 (build-system r-build-system)
1376 ;; Skip check phase because the tests require the r-knitr package to be
1377 ;; installed. This prevents installation failures. Knitr normally
1378 ;; shouldn't be available since r-markdown is a dependency of the r-knitr
1380 (arguments `(#:tests? #f))
1382 `(("r-mime" ,r-mime)
1383 ("r-xfun" ,r-xfun)))
1384 (home-page "https://github.com/rstudio/markdown")
1385 (synopsis "Markdown rendering for R")
1387 "This package provides R bindings to the Sundown Markdown rendering
1388 library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
1389 syntax that can be converted to XHTML or other formats.")
1390 (license license:gpl2)))
1392 (define-public r-yaml
1398 (uri (cran-uri "yaml" version))
1401 "10r7g26x73am45niigm3k466030nymnr3v3fjljafzrr5aybf58i"))))
1402 (build-system r-build-system)
1403 (home-page "https://cran.r-project.org/web/packages/yaml/")
1404 (synopsis "Methods to convert R data to YAML and back")
1406 "This package implements the libyaml YAML 1.1 parser and
1407 emitter (http://pyyaml.org/wiki/LibYAML) for R.")
1408 (license license:bsd-3)))
1410 (define-public r-knitr
1416 (uri (cran-uri "knitr" version))
1419 "00rcwiq8znmk5h4qgrwd0639xyb38iwbjykqjk3disz3kvrcvbn1"))))
1420 (build-system r-build-system)
1422 `(("r-evaluate" ,r-evaluate)
1423 ("r-highr" ,r-highr)
1424 ("r-markdown" ,r-markdown)
1425 ("r-stringr" ,r-stringr)
1427 ("r-yaml" ,r-yaml)))
1428 (home-page "https://yihui.org/knitr/")
1429 (synopsis "General-purpose package for dynamic report generation in R")
1431 "This package provides a general-purpose tool for dynamic report
1432 generation in R using Literate Programming techniques.")
1433 ;; The code is released under any version of the GPL. As it is used by
1434 ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
1436 (license license:gpl2+)))
1438 (define-public r-knitrbootstrap
1440 (name "r-knitrbootstrap")
1445 (uri (cran-uri "knitrBootstrap" version))
1448 "1aj60j7f0gcs120fdrnfbnb7vk7lfn1phil0mghg6a5zldz4cqs3"))))
1449 (properties `((upstream-name . "knitrBootstrap")))
1450 (build-system r-build-system)
1452 `(("r-knitr" ,r-knitr)
1453 ("r-rmarkdown" ,r-rmarkdown)
1454 ("r-markdown" ,r-markdown)))
1455 (home-page "https://github.com/jimhester/knitrBootstrap")
1456 (synopsis "Knitr bootstrap framework")
1458 "This package provides a framework to create Bootstrap 3 HTML reports
1459 from knitr Rmarkdown.")
1460 (license license:expat)))
1462 (define-public r-microbenchmark
1464 (name "r-microbenchmark")
1468 (uri (cran-uri "microbenchmark" version))
1471 "1xl4m4yl4h2zcjiz8wsa7f3sh55qg2xr3sgpvz18rlix6b3173r6"))))
1472 (build-system r-build-system)
1473 (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
1474 (synopsis "Accurate timing functions for R")
1476 "This package provides infrastructure to accurately measure and compare
1477 the execution time of R expressions.")
1478 (license license:bsd-2)))
1480 (define-public r-pryr
1486 (uri (cran-uri "pryr" version))
1489 "06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k"))))
1490 (build-system r-build-system)
1492 `(("r-stringr" ,r-stringr)
1493 ("r-codetools" ,r-codetools)))
1495 `(("r-rcpp" ,r-rcpp)))
1496 (home-page "https://github.com/hadley/pryr")
1497 (synopsis "Tools for computing on the R language")
1499 "This package provides useful tools to pry back the covers of R and
1500 understand the language at a deeper level.")
1501 (license license:gpl2)))
1503 (define-public r-memoise
1509 (uri (cran-uri "memoise" version))
1512 "034qfc2xlh30x1q2vya239w34a3ir3y2fwnx2agbgbi6592zjxmj"))))
1513 (build-system r-build-system)
1515 `(("r-digest" ,r-digest)))
1516 (home-page "https://github.com/hadley/memoise")
1517 (synopsis "Memoise functions for R")
1519 "This R package caches the results of a function so that when
1520 you call it again with the same arguments it returns the pre-computed value.")
1521 (license license:expat)))
1523 (define-public r-crayon
1529 (uri (cran-uri "crayon" version))
1532 "0s7s6vc3ww8pzanpjisym4jjvwcc5pi2qg8srx7jqlz9j3wrnvpw"))))
1533 (build-system r-build-system)
1535 `(("r-memoise" ,r-memoise)))
1536 (home-page "https://github.com/gaborcsardi/crayon")
1537 (synopsis "Colored terminal output for R")
1539 "Colored terminal output on terminals that support ANSI color and
1540 highlight codes. It also works in Emacs ESS. ANSI color support is
1541 automatically detected. Colors and highlighting can be combined and nested.
1542 New styles can also be created easily. This package was inspired by the
1543 \"chalk\" JavaScript project.")
1544 (license license:expat)))
1546 (define-public r-praise
1553 (uri (cran-uri "praise" version))
1556 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
1557 (build-system r-build-system)
1558 (home-page "https://github.com/gaborcsardi/praise")
1559 (synopsis "Functions to praise users")
1561 "This package provides template functions to assist in building friendly
1562 R packages that praise their users.")
1563 (license license:expat)))
1565 (define-public r-testthat
1571 (uri (cran-uri "testthat" version))
1574 "0v70v2fs0f2ir962z9csbjlj8snrq9mbjfyhhb9dhz3zy26qs9hs"))))
1575 (build-system r-build-system)
1578 ("r-crayon" ,r-crayon)
1579 ("r-digest" ,r-digest)
1580 ("r-ellipsis" ,r-ellipsis)
1581 ("r-evaluate" ,r-evaluate)
1582 ("r-magrittr" ,r-magrittr)
1583 ("r-pkgload" ,r-pkgload)
1584 ("r-praise" ,r-praise)
1586 ("r-rlang" ,r-rlang)
1587 ("r-withr" ,r-withr)))
1588 (home-page "https://github.com/hadley/testthat")
1589 (synopsis "Unit testing for R")
1591 "This package provides a unit testing system for R designed to be fun,
1592 flexible and easy to set up.")
1593 (license license:expat)))
1601 (uri (cran-uri "R6" version))
1604 "0gma5z41mx02ka9h96xdyf3p6i1rx0izczrzj26c4mbnh9jgvc16"))))
1605 (build-system r-build-system)
1606 (home-page "https://github.com/wch/R6/")
1607 (synopsis "Classes with reference semantics in R")
1609 "The R6 package allows the creation of classes with reference semantics,
1610 similar to R's built-in reference classes. Compared to reference classes, R6
1611 classes are simpler and lighter-weight, and they are not built on S4 classes
1612 so they do not require the methods package. These classes allow public and
1613 private members, and they support inheritance, even when the classes are
1614 defined in different packages.")
1615 (license license:expat)))
1617 (define-public r-rlang
1623 (uri (cran-uri "rlang" version))
1626 "1jik4lywg4688dfi5fh8jbnmsxvq3382ii0nsw5armjzfq3v309s"))))
1627 (build-system r-build-system)
1628 (home-page "http://rlang.tidyverse.org")
1629 (synopsis "Functions for base types, core R and Tidyverse features")
1630 (description "This package provides a toolbox for working with base types,
1631 core R features like the condition system, and core @code{Tidyverse} features
1632 like tidy evaluation.")
1633 (license license:gpl3)))
1635 (define-public r-tibble
1642 (uri (cran-uri "tibble" version))
1645 "17m7xvn423snq9dmr0bhx42j5rbc53w1viizxx4bvq37nz7m4i8m"))))
1646 (build-system r-build-system)
1649 ("r-crayon" ,r-crayon)
1650 ("r-ellipsis" ,r-ellipsis)
1651 ("r-fansi" ,r-fansi)
1652 ("r-lifecycle" ,r-lifecycle)
1653 ("r-magrittr" ,r-magrittr)
1654 ("r-pkgconfig" ,r-pkgconfig)
1655 ("r-pillar" ,r-pillar)
1656 ("r-rlang" ,r-rlang)
1657 ("r-vctrs" ,r-vctrs)))
1659 `(("r-knitr" ,r-knitr)))
1660 (home-page "https://github.com/hadley/tibble")
1661 (synopsis "Simple data frames")
1663 "This package provides a @code{tbl_df} class that offers better checking
1664 and printing capabilities than traditional data frames.")
1665 (license license:expat)))
1667 (define-public r-dplyr
1673 (uri (cran-uri "dplyr" version))
1676 "1wxi7pzw1mqkgay2s9hwlkpkxfzydngf56wrf7k93n14rlqm3dmz"))))
1677 (build-system r-build-system)
1679 `(("r-ellipsis" ,r-ellipsis)
1680 ("r-generics" ,r-generics)
1682 ("r-lifecycle" ,r-lifecycle)
1683 ("r-magrittr" ,r-magrittr)
1685 ("r-rlang" ,r-rlang)
1686 ("r-tibble" ,r-tibble)
1687 ("r-tidyselect" ,r-tidyselect)
1688 ("r-vctrs" ,r-vctrs)))
1690 `(("r-knitr" ,r-knitr)))
1691 (home-page "https://github.com/hadley/dplyr")
1692 (synopsis "Tools for working with data frames in R")
1694 "dplyr is the next iteration of plyr. It is focussed on tools for
1695 working with data frames. It has three main goals: 1) identify the most
1696 important data manipulation tools needed for data analysis and make them easy
1697 to use in R; 2) provide fast performance for in-memory data by writing key
1698 pieces of code in C++; 3) use the same code interface to work with data no
1699 matter where it is stored, whether in a data frame, a data table or
1701 (license license:expat)))
1703 (define-public r-dbplyr
1710 (uri (cran-uri "dbplyr" version))
1713 "1v0p0557n6bz84nq9jc4182k00mdd1hvz7h4w3bbg81z0fmpj0d8"))))
1714 (build-system r-build-system)
1716 `(("r-assertthat" ,r-assertthat)
1719 ("r-dplyr" ,r-dplyr)
1721 ("r-lifecycle" ,r-lifecycle)
1722 ("r-magrittr" ,r-magrittr)
1723 ("r-purrr" ,r-purrr)
1725 ("r-rlang" ,r-rlang)
1726 ("r-tibble" ,r-tibble)
1727 ("r-tidyselect" ,r-tidyselect)))
1729 `(("r-knitr" ,r-knitr)))
1730 (home-page "https://github.com/tidyverse/dbplyr")
1731 (synopsis "Dplyr back end for databases")
1733 "This package provides a dplyr back end for databases that allows you to
1734 work with remote database tables as if they are in-memory data frames. Basic
1735 features works with any database that has a @code{DBI} back end; more advanced
1736 features require SQL translation to be provided by the package author.")
1737 (license license:expat)))
1739 (define-public r-acepack
1746 (uri (cran-uri "acepack" version))
1749 "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
1750 (build-system r-build-system)
1752 `(("gfortran" ,gfortran)))
1753 (home-page "https://cran.r-project.org/web/packages/acepack")
1754 (synopsis "Functions for regression transformations")
1756 "This package provides ACE and AVAS methods for choosing regression
1758 (license license:expat)))
1760 (define-public r-formula
1767 (uri (cran-uri "Formula" version))
1770 "0wiqh8rr9d5ciy80wj8f5fnmiiw0ywanvvnhkwd622dx42dk848l"))))
1771 (properties `((upstream-name . "Formula")))
1772 (build-system r-build-system)
1773 (home-page "https://cran.r-project.org/web/packages/Formula")
1774 (synopsis "Extended model formulas")
1776 "This package provides a new class @code{Formula}, which extends the base
1777 class @code{formula}. It supports extended formulas with multiple parts of
1778 regressors on the right-hand side and/or multiple responses on the left-hand
1780 (license (list license:gpl2+ license:gpl3+))))
1782 (define-public r-locfit
1789 (uri (cran-uri "locfit" version))
1792 "1vcw16qww4v4547w0gfvhqg60l051bsdlxa6zfcgcj9xbxf6dlyr"))))
1793 (build-system r-build-system)
1795 `(("r-lattice" ,r-lattice)))
1796 (home-page "https://cran.r-project.org/web/packages/locfit")
1797 (synopsis "Local regression, likelihood and density estimation")
1799 "This package provides functions used for local regression, likelihood
1800 and density estimation.")
1801 (license (list license:gpl2+ license:gpl3+))))
1803 (define-public r-chron
1809 (uri (cran-uri "chron" version))
1812 "09gbs7c1ynlg0kl1m6nkbn75ysk16g13r17snnaws64qwywiywqg"))))
1813 (build-system r-build-system)
1814 (home-page "https://cran.r-project.org/web/packages/chron")
1815 (synopsis "Chronological R objects which can handle dates and times")
1817 "This package provides chronological R objects which can handle dates and
1819 (license license:gpl2)))
1821 (define-public r-data-table
1823 (name "r-data-table")
1827 (uri (cran-uri "data.table" version))
1830 "1p7rf4v3ysflpgcmy9krkwmcy7z22wb08xm443649waz6lx5z9yk"))))
1831 (build-system r-build-system)
1835 `(("pkg-config" ,pkg-config)))
1836 (home-page "https://github.com/Rdatatable/data.table/wiki")
1837 (synopsis "Enhanced version of data.frame R object")
1839 "The R package @code{data.table} is an extension of @code{data.frame}
1840 providing functions for fast aggregation of large data (e.g. 100GB in RAM),
1841 fast ordered joins, fast add/modify/delete of columns by group, column listing
1842 and fast file reading.")
1843 (license license:gpl3+)))
1845 (define-public r-xtable
1852 (uri (cran-uri "xtable" version))
1855 "077xfm0gphvhsay75amd9v90zk57kjgrrlgih04fyrbqqblc1gjs"))))
1856 (build-system r-build-system)
1858 `(("r-knitr" ,r-knitr))) ; for vignettes
1859 (home-page "http://xtable.r-forge.r-project.org/")
1860 (synopsis "Export R tables to LaTeX or HTML")
1862 "This package provides tools to export R data as LaTeX and HTML tables.")
1863 (license license:gpl2+)))
1865 (define-public python-patsy
1867 (name "python-patsy")
1871 (uri (pypi-uri "patsy" version))
1874 "149rbrdzwns0ay88caf1zsm1r53v1q5np1mrb36na50y432cw5gi"))))
1875 (build-system python-build-system)
1878 (modify-phases %standard-phases
1880 (lambda _ (invoke "nosetests" "-v"))))))
1882 `(("python-numpy" ,python-numpy)
1883 ("python-scipy" ,python-scipy)
1884 ("python-six" ,python-six)))
1886 `(("python-nose" ,python-nose)))
1887 (home-page "https://github.com/pydata/patsy")
1888 (synopsis "Describe statistical models and build design matrices")
1890 "Patsy is a Python package for describing statistical models and for
1891 building design matrices.")
1892 ;; The majority of the code is distributed under BSD-2. The module
1893 ;; patsy.compat contains code derived from the Python standard library,
1894 ;; and is covered by the PSFL.
1895 (license (list license:bsd-2 license:psfl))))
1897 (define-public python2-patsy
1898 (package-with-python2 python-patsy))
1900 (define-public python-statsmodels
1902 (name "python-statsmodels")
1907 (uri (pypi-uri "statsmodels" version))
1910 "1w6mf8b86vizi2895j11szqryr2v1ckjig3wp9fv94aslfh3zpjv"))))
1911 (build-system python-build-system)
1913 `(;; The test suite is very large and rather brittle. Tests often fail
1914 ;; because of minor changes in dependencies that upstream hasn't fixed
1915 ;; in a new release.
1918 (modify-phases %standard-phases
1919 (add-after 'unpack 'set-matplotlib-backend-to-agg
1921 ;; Set the matplotlib backend to Agg to avoid problems using the
1922 ;; GTK backend without a display.
1923 (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py")
1924 '("statsmodels/tsa/vector_ar/tests/test_var.py"
1925 "statsmodels/duration/tests/test_survfunc.py"))
1926 (("import matplotlib\\.pyplot as plt" line)
1927 (string-append "import matplotlib;matplotlib.use('Agg');"
1931 `(("python-numpy" ,python-numpy)
1932 ("python-scipy" ,python-scipy)
1933 ("python-pandas" ,python-pandas)
1934 ("python-patsy" ,python-patsy)
1935 ("python-matplotlib" ,python-matplotlib)))
1937 `(("python-cython" ,python-cython)
1938 ("python-nose" ,python-nose)
1939 ("python-sphinx" ,python-sphinx)))
1940 (home-page "http://statsmodels.sourceforge.net/")
1941 (synopsis "Statistical modeling and econometrics in Python")
1943 "Statsmodels is a Python package that provides a complement to scipy for
1944 statistical computations including descriptive statistics and estimation and
1945 inference for statistical models.")
1946 (license license:bsd-3)))
1948 (define-public python2-statsmodels
1949 (let ((stats (package-with-python2 python-statsmodels)))
1950 (package (inherit stats)
1952 `(("python2-pytz" ,python2-pytz)
1953 ("python2-numpy" ,python2-numpy)
1954 ("python2-scipy" ,python2-scipy)
1955 ("python2-pandas" ,python2-pandas)
1956 ("python2-patsy" ,python2-patsy)
1957 ("python2-matplotlib" ,python2-matplotlib))))))
1959 (define-public r-coda
1965 (uri (cran-uri "coda" version))
1968 "1mn50bshky968gn4nf6vnkaa768fnvm1xmhkms7szwdw9341zpyk"))))
1969 (build-system r-build-system)
1971 `(("r-lattice" ,r-lattice)))
1972 (home-page "https://cran.r-project.org/web/packages/coda")
1973 (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
1974 (description "This package provides functions for summarizing and plotting
1975 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
1976 diagnostic tests of convergence to the equilibrium distribution of the Markov
1978 (license license:gpl2+)))
1980 (define-public r-ade4
1987 (uri (cran-uri "ade4" version))
1990 "1xpxznlqm8wb4d5z2dcrl0wi3jjciq2hr5rcx2b5aaipiiyzm1ij"))))
1991 (build-system r-build-system)
1993 `(("r-mass" ,r-mass)
1994 ("r-pixmap" ,r-pixmap)
1996 (home-page "http://pbil.univ-lyon1.fr/ADE-4")
1997 (synopsis "Multivariate data analysis and graphical display")
1999 "The ade4 package contains data analysis functions to analyze ecological
2000 and environmental data in the framework of Euclidean exploratory methods.")
2001 (license license:gpl2+)))
2003 (define-public r-xml2
2010 (uri (cran-uri "xml2" version))
2013 "1kx400v62xkd5xal7rzz7jcarz94ac8g1sh4i2dqr78qwgkzj8nz"))))
2014 (build-system r-build-system)
2016 `(("libxml2" ,libxml2)
2019 `(("pkg-config" ,pkg-config)
2020 ("r-knitr" ,r-knitr)))
2021 (home-page "https://github.com/hadley/xml2")
2022 (synopsis "Parse XML with R")
2024 "This package provides a simple, consistent interface to working with XML
2025 files in R. It is built on top of the libxml2 C library.")
2026 (license license:gpl2+)))
2028 (define-public r-multitaper
2030 (name "r-multitaper")
2035 (uri (cran-uri "multitaper" version))
2038 "04wd9bbhyx7697pfy0fpj02v1csr48hkpqj62h9p8a6w84ji4k68"))))
2039 (build-system r-build-system)
2041 `(("gfortran" ,gfortran)))
2042 (home-page "https://github.com/wesleyburr/multitaper/")
2043 (synopsis "Multitaper spectral analysis tools")
2045 "This package implements multitaper spectral estimation
2046 techniques using prolate spheroidal sequences (Slepians) and sine
2047 tapers for time series analysis. It includes an adaptive weighted
2048 multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
2049 F-test, and complex demodulation. The Slepians sequences are
2050 generated efficiently using a tridiagonal matrix solution, and
2051 jackknifed confidence intervals are available for most estimates.")
2052 (license license:gpl2+)))
2054 (define-public r-rversions
2056 (name "r-rversions")
2060 (uri (cran-uri "rversions" version))
2063 "0ghpla5r3d6zh5dn6d6ii5p0a952lcdv004m88fk8r9k76vz88rm"))))
2064 (build-system r-build-system)
2066 `(("r-curl" ,r-curl)
2067 ("r-xml2" ,r-xml2)))
2068 (home-page "https://github.com/metacran/rversions")
2069 (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
2071 "This package provides functions to query the main R repository to find
2072 the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
2073 previous R versions and their release dates.")
2074 (license license:expat)))
2076 (define-public r-whisker
2082 (uri (cran-uri "whisker" version))
2085 "1a7vz0dk95xfjvi38wbpw8vmf5qn3g8p490msz2rw0piwidmk1ks"))))
2086 (build-system r-build-system)
2087 (home-page "https://github.com/edwindj/whisker")
2088 (synopsis "Logicless mustache templating for R")
2090 "This package provides logicless templating, with a syntax that is not
2092 (license license:gpl3+)))
2094 (define-public r-backports
2096 (name "r-backports")
2101 (uri (cran-uri "backports" version))
2104 "1irc9c23hwliwkky1b3hi0dkzwalhb7zgjj08562ff1k8dqv4qf6"))))
2105 (build-system r-build-system)
2106 (home-page "https://cran.r-project.org/web/packages/backports")
2107 (synopsis "Reimplementations of functions introduced since R 3.0.0")
2109 "Provides implementations of functions which have been introduced in R
2110 since version 3.0.0. The backports are conditionally exported which results
2111 in R resolving the function names to the version shipped with R (if available)
2112 and uses the implemented backports as fallback. This way package developers
2113 can make use of the new functions without worrying about the minimum required
2115 (license license:gpl2+)))
2117 (define-public r-checkmate
2119 (name "r-checkmate")
2124 (uri (cran-uri "checkmate" version))
2127 "193gkifr9spp0x0rwnjq1spdhjkfkh4mv27iklskcj604075phhd"))))
2128 (build-system r-build-system)
2130 `(("r-backports" ,r-backports)))
2131 (home-page "https://github.com/mllg/checkmate")
2132 (synopsis "Fast and versatile argument checks")
2134 "This package provides tests and assertions to perform frequent argument
2135 checks. A substantial part of the package was written in C to minimize any
2136 worries about execution time overhead.")
2137 (license license:bsd-3)))
2139 (define-public r-bbmisc
2146 (uri (cran-uri "BBmisc" version))
2149 "1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y"))))
2150 (properties `((upstream-name . "BBmisc")))
2151 (build-system r-build-system)
2153 `(("r-checkmate" ,r-checkmate)))
2154 (home-page "https://github.com/berndbischl/BBmisc")
2155 (synopsis "Miscellaneous functions for R package development")
2157 "This package provides miscellaneous helper functions for the development
2159 (license license:bsd-3)))
2161 (define-public r-fail
2168 (uri (cran-uri "fail" version))
2171 "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
2172 (build-system r-build-system)
2174 `(("r-bbmisc" ,r-bbmisc)
2175 ("r-checkmate" ,r-checkmate)))
2176 (home-page "https://github.com/mllg/fail")
2177 (synopsis "File abstraction interface layer (FAIL)")
2179 "This package provides a more comfortable interface to work with R data
2180 or source files in a key-value fashion.")
2181 (license license:bsd-3)))
2183 (define-public r-batchjobs
2185 (name "r-batchjobs")
2190 (uri (cran-uri "BatchJobs" version))
2193 "1zz4sspj596pijxlz321g0jy2rg9ki83j6fihbwisjwr66p2vk1m"))))
2194 (properties `((upstream-name . "BatchJobs")))
2195 (build-system r-build-system)
2197 `(("r-backports" ,r-backports)
2198 ("r-bbmisc" ,r-bbmisc)
2200 ("r-checkmate" ,r-checkmate)
2201 ("r-data-table" ,r-data-table)
2203 ("r-digest" ,r-digest)
2204 ("r-rsqlite" ,r-rsqlite)
2205 ("r-sendmailr" ,r-sendmailr)
2206 ("r-stringi" ,r-stringi)))
2207 (home-page "https://github.com/tudo-r/BatchJobs")
2208 (synopsis "Batch computing with R")
2210 "This package provides @code{Map}, @code{Reduce} and @code{Filter}
2211 variants to generate jobs on batch computing systems like PBS/Torque, LSF,
2212 SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
2213 (license license:bsd-2)))
2215 (define-public r-brew
2221 (uri (cran-uri "brew" version))
2224 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
2225 (build-system r-build-system)
2226 (home-page "https://cran.r-project.org/web/packages/brew")
2227 (synopsis "Templating framework for report generation")
2229 "The brew package implements a templating framework for mixing text and R
2230 code for report generation. The template syntax is similar to PHP, Ruby's erb
2231 module, Java Server Pages, and Python's psp module.")
2232 (license license:gpl2+)))
2234 (define-public r-desc
2241 (uri (cran-uri "desc" version))
2244 "1s6s13fk6sxwcj8wzkwxl9vr33153xx11p5wi9avqx3rzkabavz6"))))
2245 (build-system r-build-system)
2247 `(("r-assertthat" ,r-assertthat)
2248 ("r-crayon" ,r-crayon)
2250 ("r-rprojroot" ,r-rprojroot)))
2251 (home-page "https://github.com/r-pkgs/desc")
2252 (synopsis "Manipulate DESCRIPTION Files")
2254 "This package provides tools to read, write, create, and manipulate
2255 DESCRIPTION files. It is intended for packages that create or manipulate
2257 (license license:expat)))
2259 (define-public r-commonmark
2261 (name "r-commonmark")
2266 (uri (cran-uri "commonmark" version))
2269 "024iz1qp2kv6iz6y69ir0jk3qhjps86rhkzlcmhqsxx97rx7cjni"))))
2270 (build-system r-build-system)
2271 (home-page "https://cran.r-project.org/web/packages/commonmark")
2272 (synopsis "CommonMark and Github Markdown Rendering in R")
2274 "The CommonMark specification defines a rationalized version of markdown
2275 syntax. This package uses the @code{cmark} reference implementation for
2276 converting markdown text into various formats including HTML, LaTeX and groff
2277 man. In addition, it exposes the markdown parse tree in XML format. The latest
2278 version of this package also adds support for Github extensions including
2279 tables, autolinks and strikethrough text.")
2280 (license license:bsd-2)))
2282 (define-public r-roxygen2
2288 (uri (cran-uri "roxygen2" version))
2291 "0qc8akwfwmaqsjaza87f5fi0zk6sh3l6j3assbs6chvx0gnmvidx"))))
2292 (build-system r-build-system)
2294 `(("r-brew" ,r-brew)
2295 ("r-commonmark" ,r-commonmark)
2297 ("r-digest" ,r-digest)
2298 ("r-knitr" ,r-knitr)
2299 ("r-pkgload" ,r-pkgload)
2300 ("r-purrr" ,r-purrr)
2303 ("r-rlang" ,r-rlang)
2304 ("r-stringi" ,r-stringi)
2305 ("r-stringr" ,r-stringr)
2306 ("r-xml2" ,r-xml2)))
2308 `(("r-knitr" ,r-knitr)))
2309 (home-page "https://github.com/klutometis/roxygen")
2310 (synopsis "In-source documentation system for R")
2312 "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
2313 collation, and NAMESPACE files.")
2314 (license license:gpl2+)))
2316 (define-public r-openssl
2323 (uri (cran-uri "openssl" version))
2326 "17fkc6pr8w5z3rpadg692a689p1v4j7xl5ak0y64is7c74cxgljx"))))
2327 (build-system r-build-system)
2329 `(("libressl" ,libressl)))
2331 `(("pkg-config" ,pkg-config)
2332 ("r-knitr" ,r-knitr)))
2334 `(("r-askpass" ,r-askpass)))
2335 (home-page "https://github.com/jeroenooms/openssl")
2336 (synopsis "Toolkit for encryption, signatures and certificates")
2338 "This package provides R bindings to OpenSSL libssl and libcrypto, plus
2339 custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
2340 and P-521. Cryptographic signatures can either be created and verified
2341 manually or via x509 certificates. AES block cipher is used in CBC mode for
2342 symmetric encryption; RSA for asymmetric (public key) encryption. High-level
2343 envelope functions combine RSA and AES for encrypting arbitrary sized data.
2344 Other utilities include key generators, hash functions (md5, sha1, sha256,
2345 etc), base64 encoder, a secure random number generator, and @code{bignum} math
2346 methods for manually performing crypto calculations on large multibyte
2348 (license license:expat)))
2350 (define-public r-httr
2356 (uri (cran-uri "httr" version))
2359 "0mp1il13q6n49n2hv1p2p8x6avjan6dr5az19ql4hb78pc3pwp37"))))
2360 (build-system r-build-system)
2362 `(("r-curl" ,r-curl)
2363 ("r-jsonlite" ,r-jsonlite)
2364 ("r-openssl" ,r-openssl)
2367 (home-page "https://github.com/hadley/httr")
2368 (synopsis "Tools for working with URLs and HTTP")
2370 "The aim of httr is to provide a wrapper for RCurl customised to the
2371 demands of modern web APIs. It provides useful tools for working with HTTP
2372 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
2373 functions make it easy to control additional request components.")
2374 (license license:expat)))
2376 (define-public r-git2r
2382 (uri (cran-uri "git2r" version))
2385 "1h1vfzym6hi1fqs9p5z5v0f4xldggr425frw8k6dsidah3qhg4h9"))))
2386 (build-system r-build-system)
2388 `(("libgit2" ,libgit2)
2391 `(("pkg-config" ,pkg-config)))
2392 (home-page "https://github.com/ropensci/git2r")
2393 (synopsis "Access Git repositories with R")
2395 "This package provides an R interface to the libgit2 library, which is a
2396 pure C implementation of the Git core methods.")
2397 ;; GPLv2 only with linking exception.
2398 (license license:gpl2)))
2400 (define-public r-rstudioapi
2402 (name "r-rstudioapi")
2406 (uri (cran-uri "rstudioapi" version))
2409 "0srh0m4mw4k6s7spwb84l4cx4xnn04cp5cjxi0fwza7bwavpzq0k"))))
2410 (build-system r-build-system)
2411 (home-page "https://cran.r-project.org/web/packages/rstudioapi")
2412 (synopsis "Safely access the RStudio API")
2414 "This package provides functions to access the RStudio API and provide
2415 informative error messages when it's not available.")
2416 (license license:expat)))
2418 (define-public r-devtools
2424 (uri (cran-uri "devtools" version))
2427 "1l6w765q180bg5mmdq5k2ymf6apz7ldhnknzf6ynfp1kf70pbhsg"))))
2428 (build-system r-build-system)
2430 `(("r-callr" ,r-callr)
2433 ("r-crayon" ,r-crayon)
2435 ("r-digest" ,r-digest)
2437 ("r-ellipsis" ,r-ellipsis)
2439 ("r-git2r" ,r-git2r)
2441 ("r-jsonlite" ,r-jsonlite)
2442 ("r-memoise" ,r-memoise)
2443 ("r-pkgbuild" ,r-pkgbuild)
2444 ("r-pkgload" ,r-pkgload)
2445 ("r-rcmdcheck" ,r-rcmdcheck)
2446 ("r-remotes" ,r-remotes)
2447 ("r-rlang" ,r-rlang)
2448 ("r-roxygen2" ,r-roxygen2)
2449 ("r-rstudioapi" ,r-rstudioapi)
2450 ("r-rversions" ,r-rversions)
2451 ("r-sessioninfo" ,r-sessioninfo)
2452 ("r-testthat" ,r-testthat)
2453 ("r-usethis" ,r-usethis)
2454 ("r-withr" ,r-withr)))
2456 `(("r-knitr" ,r-knitr)))
2457 (home-page "https://github.com/hadley/devtools")
2458 (synopsis "Tools to make developing R packages easier")
2459 (description "The devtools package is a collection of package development
2460 tools to simplify the devolpment of R packages.")
2461 (license license:gpl2+)))
2463 (define-public r-withr
2469 (uri (cran-uri "withr" version))
2472 "10mmfffjbnb2zq5x0kqhhb4z6va4micc6pjzvlfji34gyhffa8ac"))))
2473 (build-system r-build-system)
2475 `(("r-knitr" ,r-knitr)))
2476 (home-page "https://github.com/jimhester/withr")
2477 (synopsis "Run code with temporarily modified global state")
2479 "This package provides a set of functions to run R code in an environment
2480 in which global state has been temporarily modified. Many of these functions
2481 were originally a part of the r-devtools package.")
2482 (license license:gpl2+)))
2484 (define-public r-hms
2491 (uri (cran-uri "hms" version))
2494 "1baki0qw5ijgiflvsdvqj3apg4yanf12vx14kwbqdzk5rz46fasf"))))
2495 (build-system r-build-system)
2497 `(("r-rlang" ,r-rlang)
2498 ("r-pkgconfig" ,r-pkgconfig)
2499 ("r-vctrs" ,r-vctrs)))
2500 (home-page "https://github.com/rstats-db/hms")
2501 (synopsis "Pretty time of day")
2503 "This package implements an S3 class for storing and formatting
2504 time-of-day values, based on the @code{difftime} class.")
2505 (license license:gpl3+)))
2507 (define-public r-readr
2513 (uri (cran-uri "readr" version))
2516 "1wz496rw0ah433p755n3xac8gh7yzid4xgdjzd1a7wmpkgilvy9k"))))
2517 (build-system r-build-system)
2519 `(("r-clipr" ,r-clipr)
2520 ("r-crayon" ,r-crayon)
2523 ("r-tibble" ,r-tibble)
2526 (home-page "https://github.com/hadley/readr")
2527 (synopsis "Read tabular data")
2529 "This package provides functions to read flat or tabular text files from
2530 disk (or a connection).")
2531 (license license:gpl2+)))
2533 (define-public r-plotrix
2539 (uri (cran-uri "plotrix" version))
2542 "104llmr6dvlcnfpmd8zbdlv63k79djc4qqgadjavj4v4cmz1zkcc"))))
2543 (build-system r-build-system)
2544 (home-page "https://cran.r-project.org/web/packages/plotrix")
2545 (synopsis "Various plotting functions")
2547 "This package provides lots of plotting, various labeling, axis and color
2548 scaling functions for R.")
2549 (license license:gpl2+)))
2551 (define-public r-gridbase
2557 (uri (cran-uri "gridBase" version))
2560 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
2561 (build-system r-build-system)
2562 (home-page "https://cran.r-project.org/web/packages/gridBase")
2563 (synopsis "Integration of base and grid graphics")
2565 "This package provides an integration of base and grid graphics for R.")
2566 (license license:gpl2+)))
2568 (define-public r-latticeextra
2570 (name "r-latticeextra")
2575 (uri (cran-uri "latticeExtra" version))
2578 "04fzwcqs594rk5qp98yilh3kdh3sw4xf8wld5rp94ggpaqfw7bbc"))))
2579 (properties `((upstream-name . "latticeExtra")))
2580 (build-system r-build-system)
2582 `(("r-jpeg" ,r-jpeg)
2583 ("r-lattice" ,r-lattice)
2585 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2586 (home-page "http://latticeextra.r-forge.r-project.org/")
2587 (synopsis "Extra graphical utilities based on lattice")
2589 "Building on the infrastructure provided by the lattice package, this
2590 package provides several new high-level graphics functions and methods, as
2591 well as additional utilities such as panel and axis annotation functions.")
2592 (license license:gpl2+)))
2594 (define-public r-rcpparmadillo
2596 (name "r-rcpparmadillo")
2597 (version "0.9.900.1.0")
2600 (uri (cran-uri "RcppArmadillo" version))
2603 "1zisw2yrb9qmmrs7q8y83mrm7lh1c2786h70gs8jwc0si16x0lq5"))))
2604 (properties `((upstream-name . "RcppArmadillo")))
2605 (build-system r-build-system)
2607 `(("r-rcpp" ,r-rcpp)))
2608 (home-page "https://github.com/RcppCore/RcppArmadillo")
2609 (synopsis "Rcpp integration for the Armadillo linear algebra library")
2611 "Armadillo is a templated C++ linear algebra library that aims towards a
2612 good balance between speed and ease of use. Integer, floating point and
2613 complex numbers are supported, as well as a subset of trigonometric and
2614 statistics functions. Various matrix decompositions are provided through
2615 optional integration with LAPACK and ATLAS libraries. This package includes
2616 the header files from the templated Armadillo library.")
2617 ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
2618 ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
2619 ;; later, as is the rest of 'Rcpp'.
2620 (license license:gpl2+)))
2622 (define-public r-bitops
2628 (uri (cran-uri "bitops" version))
2631 "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
2632 (build-system r-build-system)
2633 (home-page "https://cran.r-project.org/web/packages/bitops")
2634 (synopsis "Bitwise operations")
2636 "This package provides functions for bitwise operations on integer
2638 (license license:gpl2+)))
2640 (define-public r-catools
2646 (uri (cran-uri "caTools" version))
2649 "0y1kgyiy322yhb0phzwvf2zgjz9awp13lhzhk9v1ddg88656jhq3"))))
2650 (properties `((upstream-name . "caTools")))
2651 (build-system r-build-system)
2653 `(("r-bitops" ,r-bitops)))
2654 (home-page "https://cran.r-project.org/web/packages/caTools")
2655 (synopsis "Various tools including functions for moving window statistics")
2657 "This package contains several basic utility functions including:
2658 moving (rolling, running) window statistic functions, read/write for GIF and
2659 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
2660 encoder/decoder, round-off-error-free sum and cumsum, etc.")
2661 (license license:gpl3+)))
2663 (define-public r-rprojroot
2665 (name "r-rprojroot")
2670 (uri (cran-uri "rprojroot" version))
2673 "12r3fdxmi2pmwn6ic3rhg0b20ll5z420m0d8fziv1n21961namnz"))))
2674 (build-system r-build-system)
2676 `(("r-backports" ,r-backports)))
2677 (home-page "https://github.com/krlmlr/rprojroot")
2678 (synopsis "Finding files in project subdirectories")
2680 "This package helps accessing files relative to a project root. It
2681 provides helpers for robust, reliable and flexible paths to files below a
2682 project root. The root of a project is defined as a directory that matches a
2683 certain criterion, e.g., it contains a certain regular file.")
2684 (license license:gpl3)))
2686 (define-public r-rmarkdown
2688 (name "r-rmarkdown")
2693 (uri (cran-uri "rmarkdown" version))
2695 (base32 "0vdjq4kcyxkr2m27588kk6yi5g53symjshj4jz4n0j18wz53shji"))))
2696 (properties `((upstream-name . "rmarkdown")))
2697 (build-system r-build-system)
2699 `(("r-base64enc" ,r-base64enc)
2700 ("r-evaluate" ,r-evaluate)
2701 ("r-htmltools" ,r-htmltools)
2702 ("r-jsonlite" ,r-jsonlite)
2703 ("r-knitr" ,r-knitr)
2705 ("r-stringr" ,r-stringr)
2706 ("r-tinytex" ,r-tinytex)
2709 ("ghc-pandoc" ,ghc-pandoc)))
2711 `(("r-knitr" ,r-knitr)))
2712 (home-page "https://rmarkdown.rstudio.com")
2713 (synopsis "Convert R Markdown documents into a variety of formats")
2715 "This package provides tools to convert R Markdown documents into a
2716 variety of formats.")
2717 (license license:gpl3+)))
2719 (define-public r-gtable
2725 (uri (cran-uri "gtable" version))
2728 "1lyncxf2dqdjgw1071cn9c8zwzkz6sldnd5cgmicf70bc726qf7x"))))
2729 (properties `((upstream-name . "gtable")))
2730 (build-system r-build-system)
2731 (home-page "https://cran.r-project.org/web/packages/gtable")
2732 (synopsis "R library to arrange grobs in tables")
2734 "Gtable is a collection of tools to make it easier to work with
2735 \"tables\" of grobs.")
2736 (license license:gpl2+)))
2738 (define-public r-gridextra
2740 (name "r-gridextra")
2744 (uri (cran-uri "gridExtra" version))
2747 "0fwfk3cdwxxim7nd55pn7m31bcaqj48y06j7an2k1v1pybk0rdl1"))))
2748 (properties `((upstream-name . "gridExtra")))
2749 (build-system r-build-system)
2751 `(("r-gtable" ,r-gtable)))
2753 `(("r-knitr" ,r-knitr))) ;for building vignettes
2754 (home-page "https://github.com/baptiste/gridextra")
2755 (synopsis "Miscellaneous functions for \"Grid\" graphics")
2757 "This package provides a number of user-level functions to work with
2758 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
2760 (license license:gpl2+)))
2762 (define-public r-pkgconfig
2764 (name "r-pkgconfig")
2768 (uri (cran-uri "pkgconfig" version))
2771 "0l1qph8zyi2sic3k2qcd7vlfl7rzfh1q7z7zvjkl5f7y1x2fy3rk"))))
2772 (build-system r-build-system)
2773 (home-page "https://github.com/gaborcsardi/pkgconfig")
2774 (synopsis "Private configuration for R packages")
2775 (description "This package provides the functionality to set configuration
2776 options on a per-package basis. Options set by a given package only apply to
2777 that package, other packages are unaffected.")
2778 (license license:expat)))
2780 (define-public r-blob
2786 (uri (cran-uri "blob" version))
2789 "1slb5mvxfyi92i8ifx2qa31hp57inilwhq1g9lzvgha6jrxbqm7g"))))
2790 (build-system r-build-system)
2792 `(("r-rlang" ,r-rlang)
2793 ("r-vctrs" ,r-vctrs)))
2794 (home-page "https://github.com/hadley/blob")
2795 (synopsis "Simple S3 Class for representing vectors of binary data")
2796 (description "Raw vectors in R are useful for storing a single binary
2797 object. What if you want to put a vector of them in a data frame? The blob
2798 package provides the blob object, a list of raw vectors, suitable for use as
2799 a column in data frame.")
2800 (license license:gpl3+)))
2802 (define-public r-rsqlite
2808 (uri (cran-uri "RSQLite" version))
2811 "1m38sj8rwbf3p2lhqabcp7c7djk7s9ng37cz39yxk706v9pi4380"))))
2812 (properties `((upstream-name . "RSQLite")))
2813 (build-system r-build-system)
2817 ("r-memoise" ,r-memoise)
2818 ("r-plogr" ,r-plogr)
2820 ("r-bit64" ,r-bit64)
2822 ("r-pkgconfig" ,r-pkgconfig)))
2823 (home-page "https://github.com/rstats-db/RSQLite")
2824 (synopsis "SQLite interface for R")
2826 "This package embeds the SQLite database engine in R and provides an
2827 interface compliant with the DBI package. The source for the SQLite
2828 engine (version 3.8.8.2) is included.")
2829 (license license:lgpl2.0+)))
2831 (define-public r-rcurl
2834 (version "1.95-0.1.2")
2837 (uri (string-append "https://www.bioconductor.org/packages/"
2838 "release/extra/src/"
2839 "contrib/RCurl_" version ".tar.gz"))
2842 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
2843 (properties `((upstream-name . "RCurl")))
2844 (build-system r-build-system)
2847 (modify-phases %standard-phases
2848 (add-after 'unpack 'respect-CURL_CA_BUNDLE
2850 (substitute* "R/options.S"
2851 (("\\.els = rev\\(merge\\(list\\(\\.\\.\\.\\), \\.opts\\)\\)" m)
2853 certs = Sys.getenv(\"CURL_CA_BUNDLE\")
2854 if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) }
2858 `(("libcurl" ,curl)))
2860 `(("r-bitops" ,r-bitops)))
2861 (home-page "http://www.omegahat.org/RCurl")
2862 (synopsis "General network client interface for R")
2864 "The package allows one to compose general HTTP requests and provides
2865 convenient functions to fetch URIs, GET and POST forms, etc. and process the
2866 results returned by the Web server. This provides a great deal of control
2867 over the HTTP/FTP/... connection and the form of the request while providing a
2868 higher-level interface than is available just using R socket connections.
2869 Additionally, the underlying implementation is robust and extensive,
2870 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
2871 ldap, and also supports cookies, redirects, authentication, etc.")
2872 (license license:bsd-3)))
2874 (define-public r-xml
2877 (version "3.99-0.3")
2880 (uri (cran-uri "XML" version))
2883 "0lzpqwajs5xaqdna50vl24qkp9xvh00zypjjzy6kgdzk11isgdw1"))))
2885 `((upstream-name . "XML")))
2886 (build-system r-build-system)
2888 `(("libxml2" ,libxml2)
2891 `(("pkg-config" ,pkg-config)))
2892 (home-page "http://www.omegahat.org/RSXML")
2893 (synopsis "Tools for parsing and generating XML within R")
2895 "Many approaches for both reading and creating XML (and HTML)
2896 documents (including DTDs), both local and accessible via HTTP or FTP. Also
2897 offers access to an XPath \"interpreter\".")
2898 (license license:bsd-2)))
2900 (define-public r-xnomial
2905 (origin (method url-fetch)
2906 (uri (cran-uri "XNomial" version))
2909 "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
2910 (properties (quasiquote ((upstream-name . "XNomial"))))
2911 (build-system r-build-system)
2912 (home-page "https://cran.r-project.org/web/packages/XNomial")
2913 (synopsis "Goodness-of-Fit test for multinomial data")
2915 "This package provides an exact Goodness-of-Fit test for
2916 multinomial data with fixed probabilities. It can be used to
2917 determine whether a set of counts fits a given expected ratio. To see
2918 whether a set of observed counts fits an expectation, one can examine
2919 all possible outcomes with @code{xmulti()} or a random sample of them
2920 with @code{xmonte()} and find the probability of an observation
2921 deviating from the expectation by at least as much as the observed.
2922 As a measure of deviation from the expected, one can use the
2923 log-likelihood ratio, the multinomial probability, or the classic
2924 chi-square statistic. A histogram of the test statistic can also be
2925 plotted and compared with the asymptotic curve.")
2926 (license (list license:gpl2+ license:gpl3+))))
2928 (define-public r-lambda-r
2934 (uri (cran-uri "lambda.r" version))
2937 "1mh1g0gsd58gng0hb29vww2yqb2jfs07kba5kxnnqck5j3izwlnj"))))
2938 (properties `((upstream-name . "lambda.r")))
2939 (build-system r-build-system)
2941 `(("r-formatr" ,r-formatr)))
2942 (home-page "https://cran.r-project.org/web/packages/lambda.r")
2943 (synopsis "Functional programming extension for R")
2945 "This package provides a language extension to efficiently write
2946 functional programs in R. Syntax extensions include multi-part function
2947 definitions, pattern matching, guard statements, built-in (optional) type
2949 (license license:lgpl3+)))
2951 (define-public r-futile-options
2953 (name "r-futile-options")
2957 (uri (cran-uri "futile.options" version))
2960 "0w15agpi88y3qkv6fl72zy2pzyplzgvnj41a4ixhg64mw1sck73s"))))
2962 `((upstream-name . "futile.options")))
2963 (build-system r-build-system)
2964 (home-page "https://cran.r-project.org/web/packages/futile.options")
2965 (synopsis "Options management framework")
2967 "The futile.options subsystem provides an easy user-defined options
2968 management system that is properly scoped. This means that options created
2969 via @code{futile.options} are fully self-contained and will not collide with
2970 options defined in other packages.")
2971 (license license:lgpl3+)))
2973 (define-public r-futile-logger
2975 (name "r-futile-logger")
2979 (uri (cran-uri "futile.logger" version))
2982 "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
2983 (properties `((upstream-name . "futile.logger")))
2984 (build-system r-build-system)
2986 `(("r-futile-options" ,r-futile-options)
2987 ("r-lambda-r" ,r-lambda-r)))
2988 (home-page "https://cran.r-project.org/web/packages/futile.logger")
2989 (synopsis "Logging utility for R")
2991 "This package provides a simple yet powerful logging utility. Based
2992 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
2993 convenient and easy to use replacement for @code{cat} and @code{print}
2995 (license license:lgpl3+)))
2997 (define-public r-segmented
2999 (name "r-segmented")
3004 (uri (cran-uri "segmented" version))
3007 "0r83p36l6m5sy4lxfjbfajn4gcqb0wv9zh7arny02s6c7fb4756y"))))
3008 (build-system r-build-system)
3009 (home-page "https://cran.r-project.org/web/packages/segmented")
3010 (synopsis "Regression models with breakpoints estimation")
3012 "Given a regression model, segmented updates the model by adding one or
3013 more segmented (i.e., piecewise-linear) relationships. Several variables with
3014 multiple breakpoints are allowed.")
3015 (license (list license:gpl2+ license:gpl3+))))
3017 (define-public r-snow
3023 (uri (cran-uri "snow" version))
3026 "1n3n8pva9s34fvlw32yng0x416lmbv7q1fsd0ywa4kikmxym64l5"))))
3027 (build-system r-build-system)
3028 (home-page "https://cran.r-project.org/web/packages/snow")
3029 (synopsis "Support for simple parallel computing in R")
3031 "The snow package provides support for simple parallel computing on a
3032 network of workstations using R. A master R process calls @code{makeCluster}
3033 to start a cluster of worker processes; the master process then uses functions
3034 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
3035 worker processes and collect and return the results on the master.")
3036 (license (list license:gpl2+ license:gpl3+))))
3038 (define-public r-sparsem
3044 (uri (cran-uri "SparseM" version))
3047 "0cmlm0lps3daalvp5jzjnjfys388hgkyc8yw0g5r2351h749xdyn"))))
3049 `((upstream-name . "SparseM")))
3051 `(("gfortran" ,gfortran)))
3052 (build-system r-build-system)
3053 (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
3054 (synopsis "Sparse linear algebra")
3056 "This package provides some basic linear algebra functionality for sparse
3057 matrices. It includes Cholesky decomposition and backsolving as well as
3058 standard R subsetting and Kronecker products.")
3059 (license license:gpl2+)))
3061 (define-public r-iterators
3063 (name "r-iterators")
3068 (uri (cran-uri "iterators" version))
3071 "0jwzxaa3jm1xzgfv5pn0xqkk7rhm0xwvgn85w7xaw8xx1vb33gwn"))))
3072 (build-system r-build-system)
3073 (home-page "https://cran.r-project.org/web/packages/iterators")
3074 (synopsis "Iterator construct for R")
3076 "This package provides support for iterators, which allow a programmer to
3077 traverse through all the elements of a vector, list, or other collection of
3079 (license license:asl2.0)))
3081 (define-public r-foreach
3088 (uri (cran-uri "foreach" version))
3091 "0584nv49x8d8m1cak5drb54sxs3y594gd521kjsdwk4c849sgy8s"))))
3092 (build-system r-build-system)
3094 `(("r-codetools" ,r-codetools)
3095 ("r-iterators" ,r-iterators)))
3097 `(("r-knitr" ,r-knitr)))
3098 (home-page "https://cran.r-project.org/web/packages/foreach")
3099 (synopsis "Foreach looping construct for R")
3101 "This package provides support for the @code{foreach} looping construct.
3102 @code{foreach} is an idiom that allows for iterating over elements in a
3103 collection, without the use of an explicit loop counter. This package in
3104 particular is intended to be used for its return value, rather than for its
3105 side effects. In that sense, it is similar to the standard @code{lapply}
3106 function, but doesn't require the evaluation of a function. Using
3107 @code{foreach} without side effects also facilitates executing the loop in
3109 (license license:asl2.0)))
3111 (define-public r-doparallel
3113 (name "r-doparallel")
3118 (uri (cran-uri "doParallel" version))
3121 "0vnqbha3gig3awbfvsfx3ni5jir398md1n7xmsb8jihnjsk7xbbi"))))
3122 (properties `((upstream-name . "doParallel")))
3123 (build-system r-build-system)
3125 `(("r-foreach" ,r-foreach)
3126 ("r-iterators" ,r-iterators)))
3127 (home-page "https://cran.r-project.org/web/packages/doParallel")
3128 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3130 "This package provides a parallel backend for the @code{%dopar%} function
3131 using the parallel package.")
3132 (license license:gpl2+)))
3134 (define-public r-domc
3141 (uri (cran-uri "doMC" version))
3144 "1cn9gxavhvjswip8pwvkpi7q6wpzdllcsdjabga8akf55nggqxr9"))))
3145 (properties `((upstream-name . "doMC")))
3146 (build-system r-build-system)
3148 `(("r-foreach" ,r-foreach)
3149 ("r-iterators" ,r-iterators)))
3150 (home-page "https://cran.r-project.org/web/packages/doMC")
3151 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3153 "This package provides a parallel backend for the @code{%dopar%} function
3154 using the multicore functionality of the parallel package.")
3155 (license license:gpl2+)))
3163 (uri (cran-uri "DT" version))
3166 "0xhinw7wasrai5wfswp3r48qfv7ppdfd9jc7py2rp63dn0bnvbab"))))
3168 `((upstream-name . "DT")))
3169 (build-system r-build-system)
3171 `(("r-crosstalk" ,r-crosstalk)
3172 ("r-htmltools" ,r-htmltools)
3173 ("r-htmlwidgets" ,r-htmlwidgets)
3174 ("r-jsonlite" ,r-jsonlite)
3175 ("r-magrittr" ,r-magrittr)
3176 ("r-promises" ,r-promises)))
3178 `(("r-knitr" ,r-knitr)))
3179 (home-page "https://rstudio.github.io/DT")
3180 (synopsis "R wrapper of the DataTables JavaScript library")
3182 "This package allows for data objects in R to be rendered as HTML tables
3183 using the JavaScript library @code{DataTables} (typically via R Markdown or
3184 Shiny). The @code{DataTables} library has been included in this R package.")
3185 ;; The DT package as a whole is distributed under GPLv3. The DT package
3186 ;; inludes other software components under different licenses:
3188 ;; * Expat: jQuery, jquery.highlight.js, DataTables
3189 ;; * ASL2.0: selectize.js
3190 ;; * WTFPL: noUiSlider
3191 (license (list license:gpl3
3196 (define-public r-base64enc
3198 (name "r-base64enc")
3202 (uri (cran-uri "base64enc" version))
3205 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
3206 (build-system r-build-system)
3207 (home-page "https://www.rforge.net/base64enc")
3208 (synopsis "Tools for Base64 encoding")
3210 "This package provides tools for handling Base64 encoding. It is more
3211 flexible than the orphaned \"base64\" package.")
3212 (license license:gpl2+)))
3214 (define-public r-irlba
3221 (uri (cran-uri "irlba" version))
3224 "1h7mzrqdjc41814cf6c93sbyl7nxwvsf3x8apl9rhmydgdlk7qkf"))))
3225 (build-system r-build-system)
3227 `(("r-matrix" ,r-matrix)))
3228 (home-page "https://cran.r-project.org/web/packages/irlba")
3229 (synopsis "Methods for eigendecomposition of large matrices")
3231 "This package provides fast and memory efficient methods for truncated
3232 singular and eigenvalue decompositions, as well as for principal component
3233 analysis of large sparse or dense matrices.")
3234 (license (list license:gpl2+ license:gpl3+))))
3236 (define-public r-glmnet
3243 (uri (cran-uri "glmnet" version))
3245 (base32 "0qdswxvdwjcnw0by15p9yfzw8laq4f2j0ivpma6q8c5zywldpxxc"))))
3246 (build-system r-build-system)
3248 `(("gfortran" ,gfortran)
3249 ("r-knitr" ,r-knitr)))
3251 `(("r-foreach" ,r-foreach)
3252 ("r-matrix" ,r-matrix)
3253 ("r-shape" ,r-shape)
3254 ("r-survival" ,r-survival)))
3255 (home-page "https://www.jstatsoft.org/article/view/v033i01")
3256 (synopsis "Lasso and elastic-net regularized generalized linear models")
3258 "The glmnet package provides efficient procedures for fitting the entire
3259 lasso or elastic-net regularization path for linear and Poisson regression, as
3260 well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
3261 multinomial models. The algorithm uses cyclical coordinate descent in a
3262 path-wise fashion.")
3263 (license license:gpl2+)))
3265 (define-public r-pkgmaker
3272 (uri (cran-uri "pkgmaker" version))
3275 "0r0ga20dy25v9y5gjbds4y6kaa5a7qknh503qdkzllcpzbibh0hp"))))
3276 (build-system r-build-system)
3278 `(("r-assertthat" ,r-assertthat)
3279 ("r-bibtex" ,r-bibtex)
3280 ("r-codetools" ,r-codetools)
3281 ("r-digest" ,r-digest)
3282 ("r-magrittr" ,r-magrittr)
3283 ("r-registry" ,r-registry)
3284 ("r-stringi" ,r-stringi)
3285 ("r-stringr" ,r-stringr)
3286 ("r-withr" ,r-withr)
3287 ("r-xtable" ,r-xtable)))
3288 (home-page "https://renozao.github.io/pkgmaker")
3289 (synopsis "Package development utilities")
3291 "This package provides some low-level utilities to use for R package
3292 development. It currently provides managers for multiple package specific
3293 options and registries, vignette, unit test and bibtex related utilities.")
3294 (license license:gpl2+)))
3296 (define-public r-registry
3303 (uri (cran-uri "registry" version))
3306 "1k3j6dx350awamr0dwwgkhfs46vsnj4nf08iw5byq0x7n3nkdsnz"))))
3307 (build-system r-build-system)
3308 (home-page "https://cran.r-project.org/web/packages/registry")
3309 (synopsis "Infrastructure for R package registries")
3311 "This package provides a generic infrastructure for creating and using R
3312 package registries.")
3313 (license license:gpl2+)))
3315 (define-public r-rngtools
3322 (uri (cran-uri "rngtools" version))
3325 "0xgmg3qb6insc157as47mcm9sdjdpy9jirh7w06bxb7pfcxqfx42"))))
3326 (build-system r-build-system)
3328 `(("r-digest" ,r-digest)))
3329 (home-page "https://renozao.github.io/rngtools")
3330 (synopsis "Utility functions for working with random number generators")
3332 "This package contains a set of functions for working with Random Number
3333 Generators (RNGs). In particular, it defines a generic S4 framework for
3334 getting/setting the current RNG, or RNG data that are embedded into objects
3335 for reproducibility. Notably, convenient default methods greatly facilitate
3336 the way current RNG settings can be changed.")
3337 (license license:gpl3+)))
3339 (define-public r-rtsne
3346 (uri (cran-uri "Rtsne" version))
3349 "0v17vxizrs1msay24xl2bckfajr2c82wpqj07lyssbrq197nwdsn"))))
3350 (properties `((upstream-name . "Rtsne")))
3351 (build-system r-build-system)
3353 `(("r-rcpp" ,r-rcpp)))
3354 (home-page "https://github.com/jkrijthe/Rtsne")
3355 (synopsis "T-distributed stochastic neighbor embedding")
3357 "This package provides an R wrapper around the fast T-distributed
3358 Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
3359 ;; The declared license for this package is BSD-3, but it also includes
3360 ;; code licensed under BSD-4.
3361 (license (list license:bsd-3 license:bsd-4))))
3363 (define-public r-e1071
3370 (uri (cran-uri "e1071" version))
3373 "0pf2pjb590z0jikgv1037xcp7dq06mg3dzmyffjw6gk7dd9blbdv"))))
3374 (build-system r-build-system)
3376 `(("r-class" ,r-class)))
3377 (home-page "https://cran.r-project.org/web/packages/e1071")
3378 (synopsis "Miscellaneous functions for probability theory")
3380 "This package provides functions for latent class analysis, short time
3381 Fourier transform, fuzzy clustering, support vector machines, shortest path
3382 computation, bagged clustering, naive Bayes classifier, and more.")
3383 (license license:gpl2+)))
3385 (define-public r-bigmemory-sri
3387 (name "r-bigmemory-sri")
3392 (uri (cran-uri "bigmemory.sri" version))
3394 (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
3396 `((upstream-name . "bigmemory.sri")))
3397 (build-system r-build-system)
3398 (home-page "https://cran.r-project.org/web/packages/bigmemory.sri")
3399 (synopsis "Shared resource interface for the bigmemory package")
3400 (description "This package provides a shared resource interface for the
3401 bigmemory and synchronicity packages.")
3402 ;; Users can choose either LGPLv3 or ASL2.0.
3403 (license (list license:lgpl3 license:asl2.0))))
3405 (define-public r-synchronicity
3407 (name "r-synchronicity")
3412 (uri (cran-uri "synchronicity" version))
3415 "1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx"))))
3416 (build-system r-build-system)
3419 ("r-bigmemory-sri" ,r-bigmemory-sri)
3421 ("r-uuid" ,r-uuid)))
3422 (home-page "http://www.bigmemory.org")
3423 (synopsis "Boost mutex functionality in R")
3424 (description "This package provides support for synchronization
3425 via mutexes and may eventually support interprocess communication and
3427 ;; Users can choose either LGPLv3 or ASL2.0.
3428 (license (list license:lgpl3 license:asl2.0))))
3430 (define-public r-bigmemory
3432 (name "r-bigmemory")
3437 (uri (cran-uri "bigmemory" version))
3440 "03pg8mxdc7q0249visjmc8bc3xmwxsfg3i2n6higicj4cfz7zihq"))))
3441 (build-system r-build-system)
3445 ("r-bigmemory-sri" ,r-bigmemory-sri)))
3446 (home-page "http://www.bigmemory.org")
3447 (synopsis "Manage large matrices with shared memory or memory-mapped files")
3448 (description "This package provides methods to create, store, access, and
3449 manipulate large matrices. Matrices are allocated to shared memory and may use
3450 memory-mapped files.")
3451 ;; Users can choose either LGPLv3 or ASL2.0.
3452 (license (list license:lgpl3 license:asl2.0))))
3454 (define-public r-r-methodss3
3456 (name "r-r-methodss3")
3460 (uri (cran-uri "R.methodsS3" version))
3463 "19c5870v7b59fs6xk58bh3rfkmhfralmgsax86zzpdmz47pga1g0"))))
3464 (properties `((upstream-name . "R.methodsS3")))
3465 (build-system r-build-system)
3466 (home-page "https://cran.r-project.org/web/packages/R.methodsS3")
3467 (synopsis "S3 methods simplified")
3469 "This package provides methods that simplify the setup of S3 generic
3470 functions and S3 methods. Major effort has been made in making definition of
3471 methods as simple as possible with a minimum of maintenance for package
3472 developers. For example, generic functions are created automatically, if
3473 missing, and naming conflict are automatically solved, if possible. The
3474 method @code{setMethodS3()} is a good start for those who in the future may
3475 want to migrate to S4.")
3476 (license license:lgpl2.1+)))
3478 (define-public r-r-oo
3484 (uri (cran-uri "R.oo" version))
3487 "189fb7mmyzwg6nn8rza8iip7fbyws7i2vkmzy672x9mhvgilq4pm"))))
3488 (properties `((upstream-name . "R.oo")))
3489 (build-system r-build-system)
3491 `(("r-r-methodss3" ,r-r-methodss3)))
3492 (home-page "https://github.com/HenrikBengtsson/R.oo")
3493 (synopsis "R object-oriented programming with or without references")
3495 "This package provides methods and classes for object-oriented
3496 programming in R with or without references. Large effort has been made on
3497 making definition of methods as simple as possible with a minimum of
3498 maintenance for package developers.")
3499 (license license:lgpl2.1+)))
3501 (define-public r-r-utils
3507 (uri (cran-uri "R.utils" version))
3510 "1krj1ny7y43lpm2q8c7swxfdc3ngy2j8knzv71f8bfsgh673nsxc"))))
3511 (properties `((upstream-name . "R.utils")))
3512 (build-system r-build-system)
3514 `(("r-r-methodss3" ,r-r-methodss3)
3515 ("r-r-oo" ,r-r-oo)))
3516 (home-page "https://github.com/HenrikBengtsson/R.utils")
3517 (synopsis "Various programming utilities")
3519 "This package provides utility functions useful when programming and
3520 developing R packages.")
3521 (license license:lgpl2.1+)))
3523 (define-public r-r-cache
3529 (uri (cran-uri "R.cache" version))
3532 "1n8n5ihkryrbxv630dwhz4r048nyv676qd3i9f5z5fa04hvlxbqq"))))
3533 (properties `((upstream-name . "R.cache")))
3534 (build-system r-build-system)
3536 `(("r-digest" ,r-digest)
3537 ("r-r-methodss3" ,r-r-methodss3)
3539 ("r-r-utils" ,r-r-utils)))
3540 (home-page "https://github.com/HenrikBengtsson/R.cache")
3541 (synopsis "Light-weight caching of objects and results")
3543 "This package provides methods for caching or memoization of objects and
3544 results. With this package, any R object can be cached in a key-value storage
3545 where the key can be an arbitrary set of R objects. The cache memory is
3546 persistent (on the file system).")
3547 (license license:lgpl2.1+)))
3549 (define-public r-r-rsp
3555 (uri (cran-uri "R.rsp" version))
3558 "128zqyvbq9hm9gy86jzhj609lkfw57vr24mdxgh46ncmx66ag4gj"))))
3559 (properties `((upstream-name . "R.rsp")))
3560 (build-system r-build-system)
3562 `(("r-digest" ,r-digest)
3563 ("r-r-cache" ,r-r-cache)
3564 ("r-r-methodss3" ,r-r-methodss3)
3566 ("r-r-utils" ,r-r-utils)))
3567 (home-page "https://github.com/HenrikBengtsson/R.rsp")
3568 (synopsis "Dynamic generation of scientific reports")
3570 "The RSP markup language provides a powerful markup for controlling the
3571 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
3572 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
3573 to many other literate programming languages, with RSP it is straightforward
3574 to loop over mixtures of code and text sections, e.g. in month-by-month
3575 summaries. RSP has also several preprocessing directives for incorporating
3576 static and dynamic contents of external files (local or online) among other
3577 things. RSP is ideal for self-contained scientific reports and R package
3579 (license license:lgpl2.1+)))
3581 (define-public r-mvtnorm
3587 (uri (cran-uri "mvtnorm" version))
3590 "1pj51mi0g6ip7a2nhzc93yv9289kaayvspjvsbgbgarvx7axlrg9"))))
3591 (build-system r-build-system)
3593 `(("gfortran" ,gfortran)))
3594 (home-page "http://mvtnorm.R-forge.R-project.org")
3595 (synopsis "Package for multivariate normal and t-distributions")
3596 (description "This package can compute multivariate normal and
3597 t-probabilities, quantiles, random deviates and densities.")
3598 (license license:gpl2)))
3600 (define-public r-matrixstats
3602 (name "r-matrixstats")
3606 (uri (cran-uri "matrixStats" version))
3609 "09qgfv9x32x6ncgf19iy7yjp26fwy6p5wm8spc2xzfc0qhylmqrr"))))
3610 (properties `((upstream-name . "matrixStats")))
3611 (build-system r-build-system)
3613 `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
3614 (home-page "https://github.com/HenrikBengtsson/matrixStats")
3615 (synopsis "Methods applying to vectors and matrix rows and columns")
3617 "This package provides methods operating on rows and columns of matrices,
3618 e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
3619 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
3620 @code{weightedMedians()}. All methods have been optimized for speed and
3622 (license license:artistic2.0)))
3624 (define-public r-viridis
3630 (uri (cran-uri "viridis" version))
3633 "060rf1jn29dq53y3nhb0hykvcap6rqsk04rq544ypiiqb18ngwnx"))))
3634 (build-system r-build-system)
3636 `(("r-ggplot2" ,r-ggplot2)
3637 ("r-gridextra" ,r-gridextra)
3638 ("r-viridislite" ,r-viridislite)))
3640 `(("r-knitr" ,r-knitr))) ; for vignettes
3641 (home-page "https://github.com/sjmgarnier/viridis")
3642 (synopsis "Matplotlib default color map")
3644 "This package is a port of the new @url{matplotlib,
3645 http://matplotlib.org/} color maps (@code{viridis}--the default--,
3646 @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
3647 designed in such a way that they will analytically be perfectly
3648 perceptually-uniform, both in regular form and also when converted to
3649 black-and-white. They are also designed to be perceived by readers with the
3650 most common form of color blindness.")
3651 (license license:x11)))
3653 (define-public r-viridislite
3655 (name "r-viridislite")
3660 (uri (cran-uri "viridisLite" version))
3663 "1by2l05f0yabwvv64lhnv7bbhx0w683s3wr9j2xda920ghpa23kq"))))
3664 (properties `((upstream-name . "viridisLite")))
3665 (build-system r-build-system)
3666 (home-page "https://github.com/sjmgarnier/viridisLite")
3667 (synopsis "Default color maps from matplotlib")
3669 "This package is a port of the new @code{matplotlib} color maps
3670 (@code{viridis}, @code{magma}, @code{plasma} and @code{inferno}) to R.
3671 matplotlib is a popular plotting library for Python. These color maps are
3672 designed in such a way that they will analytically be perfectly
3673 perceptually-uniform, both in regular form and also when converted to
3674 black-and-white. They are also designed to be perceived by readers with the
3675 most common form of color blindness. This is the @code{lite} version of the
3676 more complete @code{viridis} package.")
3677 (license license:expat)))
3679 (define-public r-tidyselect
3681 (name "r-tidyselect")
3686 (uri (cran-uri "tidyselect" version))
3689 "14rqx4dq574hilmdwrr34wyjg8rlw4rvndpsqd9plgxm3wwfsdg6"))))
3690 (build-system r-build-system)
3692 `(("r-ellipsis" ,r-ellipsis)
3694 ("r-purrr" ,r-purrr)
3695 ("r-rlang" ,r-rlang)
3696 ("r-vctrs" ,r-vctrs)))
3698 `(("r-knitr" ,r-knitr)))
3699 (home-page "https://cran.r-project.org/web/packages/tidyselect")
3700 (synopsis "Select from a set of strings")
3702 "This package provides a backend for the selecting functions of the
3703 tidyverse. It makes it easy to implement select-like functions in your own
3704 packages in a way that is consistent with other tidyverse interfaces for
3706 (license license:gpl3)))
3708 (define-public r-tidyr
3715 (uri (cran-uri "tidyr" version))
3718 "0vqj5dakb35axv4l0yrihpa16vnz2b5bhaaqg7l0gsqbb04qcb00"))))
3719 (build-system r-build-system)
3721 `(("r-dplyr" ,r-dplyr)
3722 ("r-ellipsis" ,r-ellipsis)
3723 ("r-magrittr" ,r-magrittr)
3725 ("r-lifecycle" ,r-lifecycle)
3726 ("r-purrr" ,r-purrr)
3727 ("r-rlang" ,r-rlang)
3728 ("r-tidyselect" ,r-tidyselect)
3730 ("r-stringi" ,r-stringi)
3731 ("r-tibble" ,r-tibble)
3732 ("r-vctrs" ,r-vctrs)))
3734 `(("r-knitr" ,r-knitr)))
3735 (home-page "https://github.com/hadley/tidyr")
3736 (synopsis "Tidy data with `spread()` and `gather()` functions")
3738 "tidyr is a reframing of the reshape2 package designed to accompany the
3739 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
3740 a solid pipeline for data analysis. It is designed specifically for tidying
3741 data, not the general reshaping that reshape2 does, or the general aggregation
3742 that reshape did. In particular, built-in methods only work for data frames,
3743 and tidyr provides no margins or aggregation.")
3744 (license license:expat)))
3746 (define-public r-hexbin
3753 (uri (cran-uri "hexbin" version))
3756 "1ry6jm3lqz3mj0s5rzbs6mpkz2hxpnvbw8c1vwc4pj7b173r5l22"))))
3757 (build-system r-build-system)
3759 `(("r-lattice" ,r-lattice)))
3761 `(("gfortran" ,gfortran)
3762 ("r-knitr" ,r-knitr))) ; for vignettes
3763 (home-page "https://github.com/edzer/hexbin")
3764 (synopsis "Hexagonal binning routines")
3766 "This package provides binning and plotting functions for hexagonal bins.
3767 It uses and relies on grid graphics and formal (S4) classes and methods.")
3768 (license license:gpl2+)))
3770 (define-public r-purrr
3777 (uri (cran-uri "purrr" version))
3780 "1cj091rsjdj2xz16qhynyw72gh5cyhznifcfbrbygndfr4xwksr3"))))
3781 (build-system r-build-system)
3783 `(("r-magrittr" ,r-magrittr)
3784 ("r-rlang" ,r-rlang)))
3786 `(("r-knitr" ,r-knitr)))
3787 (home-page "https://github.com/hadley/purrr")
3788 (synopsis "Functional programming tools")
3790 "This package completes R's functional programming tools with missing
3791 features present in other programming languages.")
3792 (license license:gpl3+)))
3794 (define-public r-plotly
3800 (uri (cran-uri "plotly" version))
3803 "1f0x83a2s7200iqi6gpngijks06fcvcbm6701d5r5rxpb8rawppl"))))
3804 (build-system r-build-system)
3806 `(("r-base64enc" ,r-base64enc)
3807 ("r-crosstalk" ,r-crosstalk)
3808 ("r-digest" ,r-digest)
3809 ("r-data-table" ,r-data-table)
3810 ("r-dplyr" ,r-dplyr)
3811 ("r-ggplot2" ,r-ggplot2)
3812 ("r-hexbin" ,r-hexbin)
3813 ("r-htmltools" ,r-htmltools)
3814 ("r-htmlwidgets" ,r-htmlwidgets)
3816 ("r-jsonlite" ,r-jsonlite)
3817 ("r-lazyeval" ,r-lazyeval)
3818 ("r-magrittr" ,r-magrittr)
3819 ("r-promises" ,r-promises)
3820 ("r-purrr" ,r-purrr)
3821 ("r-rcolorbrewer" ,r-rcolorbrewer)
3822 ("r-rlang" ,r-rlang)
3823 ("r-scales" ,r-scales)
3824 ("r-tibble" ,r-tibble)
3825 ("r-tidyr" ,r-tidyr)
3826 ("r-viridislite" ,r-viridislite)))
3827 (home-page "https://plot.ly/r")
3828 (synopsis "Create interactive web graphics")
3830 "This package enables the translation of ggplot2 graphs to an interactive
3831 web-based version and/or the creation of custom web-based visualizations
3832 directly from R. Once uploaded to a plotly account, plotly graphs (and the
3833 data behind them) can be viewed and modified in a web browser.")
3834 (license license:x11)))
3836 (define-public r-biased-urn
3838 (name "r-biased-urn")
3843 (uri (cran-uri "BiasedUrn" version))
3846 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
3847 (properties `((upstream-name . "BiasedUrn")))
3848 (build-system r-build-system)
3849 (home-page "http://www.agner.org/random/")
3850 (synopsis "Biased urn model distributions")
3852 "This package provides statistical models of biased sampling in the form
3853 of univariate and multivariate noncentral hypergeometric distributions,
3854 including Wallenius' noncentral hypergeometric distribution and Fisher's
3855 noncentral hypergeometric distribution (also called extended hypergeometric
3857 (license license:gpl3+)))
3859 (define-public r-rematch
3866 (uri (cran-uri "rematch" version))
3869 "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4"))))
3870 (build-system r-build-system)
3871 (home-page "https://github.com/MangoTheCat/rematch")
3872 (synopsis "Match regular expressions with a nicer API")
3874 "This package provides a small wrapper on @code{regexpr} to extract the
3875 matches and captured groups from the match of a regular expression to a
3877 (license license:expat)))
3879 (define-public r-cellranger
3881 (name "r-cellranger")
3886 (uri (cran-uri "cellranger" version))
3889 "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x"))))
3890 (build-system r-build-system)
3892 `(("r-rematch" ,r-rematch)
3893 ("r-tibble" ,r-tibble)))
3894 (home-page "https://github.com/rsheets/cellranger")
3895 (synopsis "Translate spreadsheet cell ranges to rows and columns")
3897 "This package provides helper functions to work with spreadsheets and the
3898 @code{A1:D10} style of cell range specification.")
3899 (license license:expat)))
3901 (define-public r-googlesheets
3903 (name "r-googlesheets")
3908 (uri (cran-uri "googlesheets" version))
3911 "11q07nxys72wkxx9mawmjyf20gvwvrb7h3gpa73h6lgh2vgrwnv8"))))
3912 (build-system r-build-system)
3914 `(("r-cellranger" ,r-cellranger)
3915 ("r-dplyr" ,r-dplyr)
3917 ("r-jsonlite" ,r-jsonlite)
3918 ("r-purrr" ,r-purrr)
3919 ("r-readr" ,r-readr)
3920 ("r-stringr" ,r-stringr)
3921 ("r-tibble" ,r-tibble)
3922 ("r-tidyr" ,r-tidyr)
3923 ("r-xml2" ,r-xml2)))
3924 (home-page "https://github.com/jennybc/googlesheets")
3925 (synopsis "Manage Google spreadsheets from R")
3926 (description "This package provides tools to interact with Google Sheets
3928 (license license:expat)))
3930 (define-public r-spams
3933 (version "2.6-2017-03-22")
3937 ;; Use the ‘Latest version’ link for a stable URI across releases.
3938 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
3939 "latestfile/4531/spams-R-v" version ".tar.gz"))
3942 "13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx"))))
3943 (build-system r-build-system)
3946 (modify-phases %standard-phases
3947 (add-after 'unpack 'chdir
3948 (lambda _ (chdir "spams") #t))
3949 ;; Don't tune for the building machine.
3950 (add-after 'chdir 'no-mtune
3952 (substitute* "src/Makevars"
3953 (("-mtune=native") ""))
3956 `(("r-lattice" ,r-lattice)
3957 ("r-matrix" ,r-matrix)))
3958 (home-page "https://spams-devel.gforge.inria.fr")
3959 (synopsis "Toolbox for solving sparse estimation problems")
3960 (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
3961 for solving various sparse estimation problems. It includes tools for the
3965 @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
3966 component analysis} (PCA), ...)
3967 @item Solving sparse decomposition problems with LARS, coordinate descent,
3968 OMP, SOMP, proximal methods
3969 @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
3970 group lasso, tree-structured regularization, structured sparsity with
3971 overlapping groups,...).
3973 (license license:gpl3+)))
3975 (define-public r-base64
3982 (uri (cran-uri "base64" version))
3985 "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf"))))
3986 (build-system r-build-system)
3988 `(("r-openssl" ,r-openssl)))
3989 (home-page "https://cran.r-project.org/web/packages/base64")
3990 (synopsis "Base64 encoder and decoder")
3992 "This package is a compatibility wrapper to replace the orphaned package
3993 by Romain Francois. New applications should use the openssl or base64enc
3995 (license license:expat)))
3997 (define-public r-hmisc
4004 (uri (cran-uri "Hmisc" version))
4006 (base32 "1ivfamwghd2z408fkhs7jy5zl3q0z1a2la16yi8js872br6cyvpi"))))
4007 (properties `((upstream-name . "Hmisc")))
4008 (build-system r-build-system)
4010 `(("gfortran" ,gfortran)))
4012 `(("r-acepack" ,r-acepack)
4013 ("r-base64enc" ,r-base64enc)
4014 ("r-cluster" ,r-cluster)
4015 ("r-data-table" ,r-data-table)
4016 ("r-foreign" ,r-foreign)
4017 ("r-formula" ,r-formula)
4018 ("r-ggplot2" ,r-ggplot2)
4019 ("r-gridextra" ,r-gridextra)
4020 ("r-gtable" ,r-gtable)
4021 ("r-lattice" ,r-lattice)
4022 ("r-latticeextra" ,r-latticeextra)
4023 ("r-htmltable" ,r-htmltable)
4024 ("r-htmltools" ,r-htmltools)
4026 ("r-rpart" ,r-rpart)
4027 ("r-survival" ,r-survival)
4028 ("r-viridis" ,r-viridis)))
4029 (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
4030 (synopsis "Miscellaneous data analysis and graphics functions")
4032 "This package contains many functions useful for data analysis,
4033 high-level graphics, utility operations, functions for computing sample size
4034 and power, importing and annotating datasets, imputing missing values,
4035 advanced table making, variable clustering, character string manipulation,
4036 conversion of R objects to LaTeX code, and recoding variables.")
4037 (license license:gpl2+)))
4039 (define-public r-runit
4046 (uri (cran-uri "RUnit" version))
4049 "1wc1gwb7yw7phf8b0gkig6c23klya3ax11c6i4s0f049k42r78r3"))))
4050 (properties `((upstream-name . "RUnit")))
4051 (build-system r-build-system)
4052 (home-page "https://cran.r-project.org/web/packages/RUnit")
4053 (synopsis "R unit test framework")
4055 "This package provides R functions implementing a standard unit testing
4056 framework, with additional code inspection and report generation tools.")
4057 (license license:gpl2+)))
4059 (define-public r-dynamictreecut
4061 (name "r-dynamictreecut")
4066 (uri (cran-uri "dynamicTreeCut" version))
4069 "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"))))
4070 (properties `((upstream-name . "dynamicTreeCut")))
4071 (build-system r-build-system)
4073 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
4074 (synopsis "Detect clusters in hierarchical clustering dendrograms")
4076 "This package contains methods for the detection of clusters in
4077 hierarchical clustering dendrograms.")
4078 (license license:gpl2+)))
4080 (define-public r-preprocesscore
4082 (name "r-preprocesscore")
4087 (uri (bioconductor-uri "preprocessCore" version))
4090 "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl"))))
4092 `((upstream-name . "preprocessCore")))
4093 (build-system r-build-system)
4094 (home-page "https://github.com/bmbolstad/preprocessCore")
4095 (synopsis "Collection of pre-processing functions")
4097 "This package provides a library of core pre-processing and normalization
4099 (license license:lgpl2.0+)))
4101 (define-public r-fastcluster
4103 (name "r-fastcluster")
4108 (uri (cran-uri "fastcluster" version))
4111 "01a2xnhhvv1swd4g8p4lzyn7ww7kg49jlnzc7kfz60jqjzpisrpk"))))
4112 (build-system r-build-system)
4113 (home-page "http://danifold.net/fastcluster.html")
4114 (synopsis "Fast hierarchical clustering routines")
4116 "This package implements fast hierarchical, agglomerative clustering
4117 routines. Part of the functionality is designed as drop-in replacement for
4118 existing routines: @code{linkage()} in the SciPy package
4119 @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package,
4120 and the @code{flashClust} package. It provides the same functionality with
4121 the benefit of a much faster implementation. Moreover, there are
4122 memory-saving routines for clustering of vector data, which go beyond what the
4123 existing packages provide.")
4124 (license license:bsd-2)))
4126 (define-public r-sfsmisc
4133 (uri (cran-uri "sfsmisc" version))
4136 "12g6m8sf17q3qmm133nm4fa296w5n5d9ly3fvb2nvc0w4llkif3l"))))
4137 (build-system r-build-system)
4138 (home-page "https://cran.r-project.org/web/packages/sfsmisc")
4139 (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
4141 "This package provides useful utilities from Seminar fuer Statistik ETH
4142 Zurich, including many that are related to graphics.")
4143 (license license:gpl2+)))
4145 (define-public r-gtools
4152 (uri (cran-uri "gtools" version))
4155 "1pnwy412wvhhvnnx8qg6s9hrgcnsfhnfcpf2560ipipk845acfsh"))))
4156 (build-system r-build-system)
4159 (modify-phases %standard-phases
4160 (add-after 'unpack 'make-deterministic
4162 (substitute* "R/checkReverseDependencies.R"
4163 (("tempdir\\(\\)") "\"/tmp\""))
4165 (home-page "https://cran.r-project.org/web/packages/gtools")
4166 (synopsis "Various R programming tools")
4168 "This package contains a collection of various functions to assist in R
4169 programming, such as tools to assist in developing, updating, and maintaining
4170 R and R packages, calculating the logit and inverse logit transformations,
4171 tests for whether a value is missing, empty or contains only @code{NA} and
4172 @code{NULL} values, and many more.")
4173 (license license:gpl2)))
4175 (define-public r-gdata
4182 (uri (cran-uri "gdata" version))
4185 "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b"))))
4186 (build-system r-build-system)
4190 `(("r-gtools" ,r-gtools)))
4191 (home-page "https://cran.r-project.org/web/packages/gdata")
4192 (synopsis "Various R programming tools for data manipulation")
4194 "This package provides various R programming tools for data manipulation,
4198 @item medical unit conversions
4199 @item combining objects
4200 @item character vector operations
4201 @item factor manipulation
4202 @item obtaining information about R objects
4203 @item manipulating MS-Excel formatted files
4204 @item generating fixed-width format files
4205 @item extricating components of date and time objects
4206 @item operations on columns of data frames
4207 @item matrix operations
4208 @item operations on vectors and data frames
4209 @item value of last evaluated expression
4210 @item wrapper for @code{sample} that ensures consistent behavior for
4211 both scalar and vector arguments
4213 (license license:gpl2+)))
4215 (define-public r-gplots
4222 (uri (cran-uri "gplots" version))
4225 "0hs6mk48i9yd43rg9wfjc2nxsjjwrnpifxqvxkv8ah18kvpd6xnp"))))
4226 (build-system r-build-system)
4228 `(("r-catools" ,r-catools)
4229 ("r-gdata" ,r-gdata)
4230 ("r-gtools" ,r-gtools)
4231 ("r-kernsmooth" ,r-kernsmooth)))
4232 (home-page "https://cran.r-project.org/web/packages/gplots")
4233 (synopsis "Various R programming tools for plotting data")
4235 "This package provides various R programming tools for plotting data,
4239 @item calculating and plotting locally smoothed summary function
4240 @item enhanced versions of standard plots
4241 @item manipulating colors
4242 @item calculating and plotting two-dimensional data summaries
4243 @item enhanced regression diagnostic plots
4244 @item formula-enabled interface to @code{stats::lowess} function
4245 @item displaying textual data in plots
4247 @item plotting \"Venn\" diagrams
4248 @item displaying Open-Office style plots
4249 @item plotting multiple data on same region, with separate axes
4250 @item plotting means and confidence intervals
4251 @item spacing points in an x-y plot so they don't overlap
4253 (license license:gpl2+)))
4255 (define-public r-rocr
4262 (uri (cran-uri "ROCR" version))
4265 "0amvvrkiflmr3qygrsgrsja4gaf2v6r6h6i2bgpsm8r069vmlf2p"))))
4266 (properties `((upstream-name . "ROCR")))
4267 (build-system r-build-system)
4269 `(("r-gplots" ,r-gplots)))
4271 `(("r-knitr" ,r-knitr)))
4272 (home-page "https://rocr.bioinf.mpi-sb.mpg.de/")
4273 (synopsis "Visualizing the performance of scoring classifiers")
4275 "ROCR is a flexible tool for creating cutoff-parameterized 2D performance
4276 curves by freely combining two from over 25 performance measures (new
4277 performance measures can be added using a standard interface). Curves from
4278 different cross-validation or bootstrapping runs can be averaged by different
4279 methods, and standard deviations, standard errors or box plots can be used to
4280 visualize the variability across the runs. The parameterization can be
4281 visualized by printing cutoff values at the corresponding curve positions, or
4282 by coloring the curve according to cutoff. All components of a performance
4283 plot can be quickly adjusted using a flexible parameter dispatching
4285 (license license:gpl2+)))
4287 (define-public r-ztable
4293 (uri (cran-uri "ztable" version))
4296 "0g7khk5ifsdh9p31wlwh2l5mn1hzxzpv6qcn1wh34vsfjdmijjwy"))))
4297 (build-system r-build-system)
4299 `(("r-flextable" ,r-flextable)
4300 ("r-magrittr" ,r-magrittr)
4301 ("r-moonbook" ,r-moonbook)
4302 ("r-officer" ,r-officer)
4303 ("r-rcolorbrewer" ,r-rcolorbrewer)
4304 ("r-scales" ,r-scales)
4305 ("r-stringr" ,r-stringr)))
4306 (home-page "https://cran.r-project.org/web/packages/ztable")
4307 (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
4309 "This package provides functions to make zebra-striped tables (tables
4310 with alternating row colors) in LaTeX and HTML formats easily from
4311 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
4312 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
4313 @code{cbind.mytable} objects.")
4314 (license license:gpl2+)))
4316 (define-public r-vipor
4322 (uri (cran-uri "vipor" version))
4325 "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx"))))
4326 (build-system r-build-system)
4327 (home-page "https://cran.r-project.org/web/packages/vipor")
4328 (synopsis "Plot categorical data using noise and density estimates")
4330 "This package provides tools to generate a violin point plot, a
4331 combination of a violin/histogram plot and a scatter plot by offsetting points
4332 within a category based on their density using quasirandom noise.")
4333 (license license:gpl2+)))
4335 (define-public r-beeswarm
4341 (uri (cran-uri "beeswarm" version))
4344 "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
4345 (build-system r-build-system)
4346 (home-page "https://www.cbs.dtu.dk/~eklund/beeswarm/")
4347 (synopsis "Implementation of bee swarm plots")
4349 "This package provides an implementation of bee swarm plots. The bee
4350 swarm plot is a one-dimensional scatter plot like stripchart, but with
4351 closely-packed, non-overlapping points.")
4352 (license license:artistic2.0)))
4354 (define-public r-sourcetools
4356 (name "r-sourcetools")
4361 (uri (cran-uri "sourcetools" version))
4364 "1jnjir0q2dj724f1mjm6p5h77yzyx6xcqy9r2g7gmcxkxw349627"))))
4365 (build-system r-build-system)
4366 (home-page "https://cran.r-project.org/web/packages/sourcetools")
4367 (synopsis "Tools for reading, tokenizing and parsing R code")
4369 "The sourcetools package provides both an R and C++ interface for the
4370 tokenization of R code, and helpers for interacting with the tokenized
4371 representation of R code.")
4372 (license license:expat)))
4374 (define-public r-ggbeeswarm
4376 (name "r-ggbeeswarm")
4380 (uri (cran-uri "ggbeeswarm" version))
4383 "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v"))))
4384 (build-system r-build-system)
4386 `(("r-beeswarm" ,r-beeswarm)
4387 ("r-ggplot2" ,r-ggplot2)
4388 ("r-vipor" ,r-vipor)))
4389 (home-page "https://github.com/eclarke/ggbeeswarm")
4390 (synopsis "Categorical scatter (violin point) plots")
4392 "This package provides two methods of plotting categorical scatter plots
4393 such that the arrangement of points within a category reflects the density of
4394 data at that region, and avoids over-plotting.")
4395 (license license:gpl2+)))
4397 (define-public r-ggthemes
4403 (uri (cran-uri "ggthemes" version))
4406 "0rrkzfggc1nlda1w1lbqdycx6nawxbkac1szhvkwrqlzh6agxcsv"))))
4407 (build-system r-build-system)
4409 `(("r-ggplot2" ,r-ggplot2)
4410 ("r-purrr" ,r-purrr)
4411 ("r-scales" ,r-scales)
4412 ("r-stringr" ,r-stringr)
4413 ("r-tibble" ,r-tibble)))
4414 (home-page "https://cran.rstudio.com/web/packages/ggthemes")
4415 (synopsis "Extra themes, scales and geoms for @code{ggplot2}")
4416 (description "This package provides extra themes and scales for
4417 @code{ggplot2} that replicate the look of plots by Edward Tufte and
4418 Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The
4419 Wall Street Journal, among others. This package also provides
4420 @code{geoms} for Tufte's box plot and range frame.")
4421 (license license:gpl2)))
4423 (define-public r-statmod
4429 (uri (cran-uri "statmod" version))
4432 "0yklg64aw5y8kfq5piafnrj1v3jv563iwzzl75g3kllrw23c508s"))))
4433 (build-system r-build-system)
4434 (home-page "https://cran.r-project.org/web/packages/statmod")
4436 `(("gfortran" ,gfortran)))
4437 (synopsis "Statistical modeling")
4439 "This package provides a collection of algorithms and functions to aid
4440 statistical modeling. It includes growth curve comparisons, limiting dilution
4441 analysis (aka ELDA), mixed linear models, heteroscedastic regression,
4442 inverse-Gaussian probability calculations, Gauss quadrature and a secure
4443 convergence algorithm for nonlinear models. It also includes advanced
4444 generalized linear model functions that implement secure convergence,
4445 dispersion modeling and Tweedie power-law families.")
4446 ;; Statmod is distributed under either license
4447 (license (list license:gpl2 license:gpl3))))
4449 (define-public r-rann
4455 (uri (cran-uri "RANN" version))
4458 "10kid40w9w7vkz2hpcfkdpxr4afxzms5dzvfwr0sl5xynzgw76dj"))))
4460 `((upstream-name . "RANN")))
4461 (build-system r-build-system)
4462 (home-page "https://github.com/jefferis/RANN")
4463 (synopsis "Fast nearest neighbour search")
4465 "This package finds the k nearest neighbours for every point in a given
4466 dataset in O(N log N) time using Arya and Mount's ANN library. Provides
4467 approximate, exact searches, fixed radius searches, bd and kb trees.")
4468 (license license:gpl3+)))
4470 (define-public r-fivethirtyeight
4472 (name "r-fivethirtyeight")
4477 (uri (string-append "https://mran.microsoft.com/src/contrib/"
4478 "fivethirtyeight_" version ".tar.gz"))
4481 "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl"))))
4482 (build-system r-build-system)
4484 `(("r-knitr" ,r-knitr)
4485 ("r-rmarkdown" ,r-rmarkdown)
4486 ("r-dplyr" ,r-dplyr)
4487 ("r-readr" ,r-readr)
4488 ("r-ggplot2" ,r-ggplot2)
4489 ("r-magrittr" ,r-magrittr)
4490 ("r-stringr" ,r-stringr)))
4491 (home-page "https://mran.microsoft.com/package/fivethirtyeight/")
4492 (synopsis "Data and code behind the stories at FiveThirtyEight")
4493 (description "This R package provides access to the code and data sets
4494 published by the statistics blog FiveThirtyEight.")
4495 (license license:expat)))
4497 (define-public r-compquadform
4499 (name "r-compquadform")
4504 (uri (cran-uri "CompQuadForm" version))
4507 "1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4"))))
4508 (properties `((upstream-name . "CompQuadForm")))
4509 (build-system r-build-system)
4510 (home-page "https://cran.r-project.org/web/packages/CompQuadForm")
4511 (synopsis "Distribution function of quadratic forms in normal variables")
4513 "This package provides functions to compute the distribution function of
4514 quadratic forms in normal variables using Imhof's method, Davies's algorithm,
4515 Farebrother's algorithm or Liu et al.'s algorithm.")
4516 (license license:gpl2+)))
4518 (define-public r-cowplot
4525 (uri (cran-uri "cowplot" version))
4528 "19cqdhgfyr1wj0fz0c5ly8f0aiy9sfgzq6lzb78hkx0hdp2agybh"))))
4529 (build-system r-build-system)
4531 `(("r-ggplot2" ,r-ggplot2)
4532 ("r-gtable" ,r-gtable)
4533 ("r-rlang" ,r-rlang)
4534 ("r-scales" ,r-scales)))
4535 (home-page "https://github.com/wilkelab/cowplot")
4536 (synopsis "Streamlined plot theme and plot annotations for ggplot2")
4538 "This package provides some helpful extensions and modifications to the
4539 ggplot2 package to combine multiple ggplot2 plots into one and label them with
4540 letters, as is often required for scientific publications.")
4541 (license license:gpl2)))
4543 (define-public r-mixtools
4550 (uri (cran-uri "mixtools" version))
4553 "08whic8hmmzi55b7azwj11l2x5r9s5qbyrv7s9jr08156vqkw0zg"))))
4554 (build-system r-build-system)
4556 `(("r-mass" ,r-mass)
4557 ("r-kernlab" ,r-kernlab)
4558 ("r-segmented" ,r-segmented)
4559 ("r-survival" ,r-survival)))
4560 (home-page "https://cran.r-project.org/web/packages/mixtools")
4561 (synopsis "Tools for analyzing finite mixture models")
4563 "This package provides a collection of R functions for analyzing finite
4565 (license license:gpl2+)))
4567 (define-public r-lars
4574 (uri (cran-uri "lars" version))
4577 "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
4578 (build-system r-build-system)
4580 `(("gfortran" ,gfortran)))
4581 (home-page "https://web.stanford.edu/~hastie/Papers/LARS/")
4582 (synopsis "Least angle regression software")
4584 "Least Angle Regression (\"LAR\") is a model selection algorithm; a
4585 useful and less greedy version of traditional forward selection methods. A
4586 simple modification of the LAR algorithm implements Tibshirani's Lasso; the
4587 Lasso modification of LARS calculates the entire Lasso path of coefficients
4588 for a given problem at the cost of a single least squares fit. Another LARS
4589 modification efficiently implements epsilon Forward Stagewise linear
4591 (license license:gpl2)))
4593 (define-public r-fastica
4600 (uri (cran-uri "fastICA" version))
4603 "1zpijqcipm0aa3rxj0mys06lskqy4dbppjpxr1aby0j16y9ka8ij"))))
4604 (properties `((upstream-name . "fastICA")))
4605 (build-system r-build-system)
4606 (home-page "https://cran.r-project.org/web/packages/fastICA")
4607 (synopsis "FastICA algorithms to perform ICA and projection pursuit")
4609 "This package provides an implementation of the FastICA algorithm to
4610 perform @dfn{independent component analysis} (ICA) and projection pursuit.")
4612 (license license:gpl3+)))
4614 (define-public r-randomforest
4616 (name "r-randomforest")
4621 (uri (cran-uri "randomForest" version))
4624 "0kbmm0l42fc2d1rdq0l7k09d34kd87q4lx651ffsic4y84h8kf7l"))))
4625 (properties `((upstream-name . "randomForest")))
4626 (build-system r-build-system)
4627 (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
4629 `(("gfortran" ,gfortran)))
4630 (synopsis "Breiman and Cutler's random forests for classification and regression")
4632 "This package provides the Breiman and Cutler's random forests algorithm, based on a
4633 forest of trees using random inputs, for classification and regression.")
4634 (license license:gpl2+)))
4636 (define-public r-diptest
4643 (uri (cran-uri "diptest" version))
4646 "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
4647 (build-system r-build-system)
4648 (home-page "https://cran.r-project.org/web/packages/diptest")
4649 (synopsis "Hartigan's dip test statistic for unimodality")
4651 "This package computes Hartigan's dip test statistic for unimodality,
4652 multimodality and provides a test with simulation based p-values, where the
4653 original public code has been corrected.")
4654 (license license:gpl2+)))
4656 (define-public r-modeltools
4658 (name "r-modeltools")
4663 (uri (cran-uri "modeltools" version))
4666 "1vqh69256h344sbj5affm0kmc77dakrxp6442xfdnfd0y5d8sgkb"))))
4667 (build-system r-build-system)
4668 (home-page "https://cran.r-project.org/web/packages/modeltools")
4669 (synopsis "Tools and classes for statistical models")
4671 "This package provides a collection of tools to deal with statistical
4672 models. The functionality is experimental and the user interface is likely
4673 to change in the future.")
4674 (license license:gpl2)))
4676 (define-public r-flexmix
4683 (uri (cran-uri "flexmix" version))
4686 "0hrz2axp2c9548b1r0bmrl57219nn030qndb83a8garkzq5lqi5s"))))
4687 (build-system r-build-system)
4689 `(("r-lattice" ,r-lattice)
4690 ("r-modeltools" ,r-modeltools)
4691 ("r-nnet" ,r-nnet)))
4692 (home-page "https://cran.r-project.org/web/packages/flexmix")
4693 (synopsis "Flexible mixture modeling")
4695 "This package implements a general framework for finite mixtures of
4696 regression models using the EM algorithm. FlexMix provides the E-step and
4697 all data handling, while the M-step can be supplied by the user to easily
4698 define new models. Existing drivers implement mixtures of standard linear
4699 models, generalized linear models and model-based clustering.")
4700 (license license:gpl2+)))
4702 (define-public r-mclust
4709 (uri (cran-uri "mclust" version))
4712 "1z46qask09x3xpv0wzvhn09218vwyrip4f5jrhnx96khpwvczzyl"))))
4713 (build-system r-build-system)
4715 `(("gfortran" ,gfortran)
4716 ("r-knitr" ,r-knitr)))
4717 (home-page "https://www.stat.washington.edu/mclust/")
4718 (synopsis "Gaussian mixture modelling for model-based clustering etc.")
4720 "This package provides Gaussian finite mixture models fitted via EM
4721 algorithm for model-based clustering, classification, and density estimation,
4722 including Bayesian regularization, dimension reduction for visualisation,
4723 and resampling-based inference.")
4724 (license license:gpl2+)))
4726 (define-public r-prabclus
4733 (uri (cran-uri "prabclus" version))
4736 "0hg4d7y1w18jpgvw10z8833bbbcnlkwiasx0wh6iwa2pnnybq8gl"))))
4737 (build-system r-build-system)
4739 `(("r-mass" ,r-mass)
4740 ("r-mclust" ,r-mclust)))
4741 (home-page "https://cran.r-project.org/web/packages/prabclus")
4742 (synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
4744 "This package provides distance-based parametric bootstrap tests for
4745 clustering with spatial neighborhood information. It implements some distance
4746 measures, clustering of presence-absence, abundance and multilocus genetical
4747 data for species delimitation, nearest neighbor based noise detection.")
4748 (license license:gpl2+)))
4750 (define-public r-deoptimr
4757 (uri (cran-uri "DEoptimR" version))
4760 "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
4761 (properties `((upstream-name . "DEoptimR")))
4762 (build-system r-build-system)
4763 (home-page "https://cran.r-project.org/web/packages/DEoptimR")
4764 (synopsis "Differential evolution optimization in pure R")
4766 "This package provides a differential evolution (DE) stochastic
4767 algorithms for global optimization of problems with and without constraints.
4768 The aim is to curate a collection of its state-of-the-art variants that (1) do
4769 not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
4770 can be efficiently implemented directly in the R language.")
4771 (license license:gpl2+)))
4773 (define-public r-robustbase
4775 (name "r-robustbase")
4780 (uri (cran-uri "robustbase" version))
4783 "1cr478xi4n9jwsdpbq182a7ig47rpb413q28dz6d1am08sk6657a"))))
4784 (build-system r-build-system)
4786 `(("gfortran" ,gfortran)))
4788 `(("r-deoptimr" ,r-deoptimr)))
4789 (home-page "http://robustbase.r-forge.r-project.org/")
4790 (synopsis "Basic robust statistics")
4792 "This package analyzes data with robust methods such as
4793 regression methodology including model selections and multivariate statistics.")
4794 (license license:gpl2+)))
4796 (define-public r-pcapp
4803 (uri (cran-uri "pcaPP" version))
4806 "1z2kdf9gfp965xbcd4rg6vf20d1bl443na0qjkpq7gmzpaq6cifa"))))
4807 (properties `((upstream-name . "pcaPP")))
4808 (build-system r-build-system)
4810 `(("r-mvtnorm" ,r-mvtnorm)))
4811 (home-page "https://cran.r-project.org/web/packages/pcaPP")
4812 (synopsis "Robust PCA by projection pursuit")
4814 "This package provides functions for robust @dfn{principal component
4815 analysis} (PCA) by projection pursuit.")
4816 (license license:gpl3+)))
4818 (define-public r-rrcov
4825 (uri (cran-uri "rrcov" version))
4828 "0m62k58nabw7hjz1qyyf9a0d6lvcz5vcvpksjnq93zcfra9inr57"))))
4829 (build-system r-build-system)
4831 `(("r-lattice" ,r-lattice)
4832 ("r-mvtnorm" ,r-mvtnorm)
4833 ("r-pcapp" ,r-pcapp)
4834 ("r-robustbase" ,r-robustbase)))
4836 `(("gfortran" ,gfortran)))
4837 (home-page "https://cran.r-project.org/web/packages/rrcov")
4838 (synopsis "Scalable robust estimators with high breakdown Point")
4840 "This package provides an implementation of robust location and scatter
4841 estimation and robust multivariate analysis with high breakdown point.")
4842 (license license:gpl2+)))
4844 (define-public r-fit-models
4846 (name "r-fit-models")
4851 (uri (cran-uri "fit.models" version))
4854 "0wrrfsgngsfrqnm247f0h6g01807i7lbf5chpyx7hkfdfmm4xbxn"))))
4855 (properties `((upstream-name . "fit.models")))
4856 (build-system r-build-system)
4858 `(("r-lattice" ,r-lattice)))
4859 (home-page "https://cran.r-project.org/web/packages/fit.models")
4860 (synopsis "Compare fitted models")
4862 "The @code{fit.models} function and its associated methods (coefficients, print,
4863 summary, plot, etc.) were originally provided in the @code{robust} package to
4864 compare robustly and classically fitted model objects. The aim of the
4865 @code{fit.models} package is to separate this fitted model object comparison
4866 functionality from the robust package and to extend it to support fitting
4867 methods (e.g., classical, robust, Bayesian, regularized, etc.) more
4869 ;; Any version of the GPL
4870 (license (list license:gpl2+ license:gpl3+))))
4872 (define-public r-robust
4879 (uri (cran-uri "robust" version))
4882 "1ks5scp8bnicl9j1r8yrmz668fjs6ifdmi540zw6d2ck500bbw42"))))
4883 (build-system r-build-system)
4885 `(("r-fit-models" ,r-fit-models)
4886 ("r-lattice" ,r-lattice)
4888 ("r-robustbase" ,r-robustbase)
4889 ("r-rrcov" ,r-rrcov)))
4891 `(("gfortran" ,gfortran)))
4892 (home-page "https://cran.r-project.org/web/packages/robust")
4893 (synopsis "Port of the S+ \"Robust Library\"")
4895 "This package is a port of the S+ \"Robust Library\". It provides
4896 methods for robust statistics, notably for robust regression and robust
4897 multivariate analysis.")
4898 (license license:gpl2)))
4900 (define-public r-trimcluster
4902 (name "r-trimcluster")
4907 (uri (cran-uri "trimcluster" version))
4910 "12siv8yx8dcavsz8jk96lwscbj257ar8jpaxksl2zb06987g4fcj"))))
4911 (build-system r-build-system)
4912 (home-page "https://cran.r-project.org/web/packages/trimcluster")
4913 (synopsis "Cluster analysis with trimming")
4915 "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
4916 Matran (1997). This optimizes the k-means criterion under trimming a portion
4919 (license (list license:gpl2+ license:gpl3+))))
4921 (define-public r-fpc
4928 (uri (cran-uri "fpc" version))
4931 "1xnp3j36hggfg675v39mnr6rgvp7i11pfng7nmyy3k2ldgklz0j9"))))
4932 (build-system r-build-system)
4934 `(("r-class" ,r-class)
4935 ("r-cluster" ,r-cluster)
4936 ("r-diptest" ,r-diptest)
4937 ("r-flexmix" ,r-flexmix)
4938 ("r-kernlab" ,r-kernlab)
4940 ("r-mclust" ,r-mclust)
4941 ("r-prabclus" ,r-prabclus)
4942 ("r-robustbase" ,r-robustbase)))
4943 (home-page "https://cran.r-project.org/web/packages/fpc")
4944 (synopsis "Flexible procedures for clustering")
4946 "This package provides various methods for clustering and cluster validation.
4947 For example, it provides fixed point clustering, linear regression clustering,
4948 clustering by merging Gaussian mixture components, as well as symmetric and
4949 asymmetric discriminant projections for visualisation of the separation of
4951 (license license:gpl2+)))
4953 (define-public r-vgam
4960 (uri (cran-uri "VGAM" version))
4962 (base32 "1hwlrdx3nhdp83pvy1h23i16vbbhi4kizdhr58c8nvg7kqdzb7qc"))))
4963 (properties `((upstream-name . "VGAM")))
4964 (build-system r-build-system)
4966 `(("gfortran" ,gfortran)))
4967 (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
4968 (synopsis "Vector generalized linear and additive models")
4970 "This package is an implementation of about 6 major classes of statistical
4971 regression models. Currently only fixed-effects models are implemented, i.e.,
4972 no random-effects models. Many (150+) models and distributions are estimated
4973 by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
4974 VGLMs can be loosely thought of as multivariate generalised linear models.")
4975 (license license:gpl2+)))
4977 (define-public r-pbapply
4984 (uri (cran-uri "pbapply" version))
4987 "1xmk4p006v8gij26rs6kp5prjyf2n32nqjxiyp8a6kvgyc4z46dc"))))
4988 (build-system r-build-system)
4989 (home-page "https://github.com/psolymos/pbapply")
4990 (synopsis "Adding progress bar to apply functions")
4992 "This lightweight package that adds progress bar to vectorized R
4993 functions apply. The implementation can easily be added to functions where
4994 showing the progress is useful e.g. bootstrap.")
4995 (license license:gpl2)))
4997 (define-public r-minqa
5004 (uri (cran-uri "minqa" version))
5007 "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
5008 (build-system r-build-system)
5010 `(("r-rcpp" ,r-rcpp)))
5012 `(("gfortran" ,gfortran)))
5013 (home-page "http://optimizer.r-forge.r-project.org")
5014 (synopsis "Derivative-free optimization algorithms by quadratic approximation")
5016 "This package provides a derivative-free optimization by quadratic approximation
5017 based on an interface to Fortran implementations by M. J. D. Powell.")
5018 (license license:gpl2)))
5020 (define-public r-rcppeigen
5022 (name "r-rcppeigen")
5023 (version "0.3.3.7.0")
5027 (uri (cran-uri "RcppEigen" version))
5030 "1b78qcjim0n9klgkr82n794d6bj9r9f33g0kcsszsns2hir65sk2"))))
5031 (properties `((upstream-name . "RcppEigen")))
5032 (build-system r-build-system)
5034 `(("r-rcpp" ,r-rcpp)
5035 ("r-matrix" ,r-matrix)))
5036 (home-page "http://eigen.tuxfamily.org")
5037 (synopsis "Rcpp integration for the Eigen templated linear algebra library")
5039 "This package provides an integration of Eigen in R using a C++ template
5040 library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
5041 It supports dense and sparse matrices on integer, floating point and complex numbers,
5042 decompositions of such matrices, and solutions of linear systems.")
5043 (license license:gpl2+)))
5045 (define-public r-modelmetrics
5047 (name "r-modelmetrics")
5052 (uri (cran-uri "ModelMetrics" version))
5055 "0mrlsw4c5y1vdsqynxr2dcvmhh5h37pnd71jw5a5djpbda9g21jy"))))
5056 (properties `((upstream-name . "ModelMetrics")))
5057 (build-system r-build-system)
5059 `(("r-rcpp" ,r-rcpp)
5060 ("r-data-table" ,r-data-table)))
5061 (home-page "https://cran.r-project.org/web/packages/ModelMetrics")
5062 (synopsis "Rapid calculation of model metrics")
5064 "Written in C++ using @code{Rcpp}, this package provides a collection of
5065 metrics for evaluating models.")
5066 (license license:gpl2+)))
5068 (define-public r-matrixmodels
5070 (name "r-matrixmodels")
5075 (uri (cran-uri "MatrixModels" version))
5078 "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
5079 (properties `((upstream-name . "MatrixModels")))
5080 (build-system r-build-system)
5082 `(("r-matrix" ,r-matrix)))
5083 (home-page "https://cran.r-project.org/web/packages/MatrixModels")
5084 (synopsis "Modelling with sparse and dense matrices")
5086 "This package models with sparse and dense matrix matrices,
5087 using modular prediction and response module classes.")
5088 (license license:gpl2+)))
5090 (define-public r-quantreg
5097 (uri (cran-uri "quantreg" version))
5099 (base32 "1zjc8p95kb0ypxa6nxp0lkdq8armkjmmhf8484m25n5f14a59qfb"))))
5100 (build-system r-build-system)
5102 `(("gfortran" ,gfortran)))
5104 `(("r-matrix" ,r-matrix)
5105 ("r-matrixmodels" ,r-matrixmodels)
5106 ("r-sparsem" ,r-sparsem)))
5107 (home-page "https://www.r-project.org")
5108 (synopsis "Quantile regression")
5110 "This package provides an estimation and inference methods for models
5111 of conditional quantiles: linear and nonlinear parametric and non-parametric
5112 models for conditional quantiles of a univariate response and several methods
5113 for handling censored survival data. Portfolio selection methods based on
5114 expected shortfall risk are also included.")
5115 (license license:gpl2+)))
5117 (define-public r-nloptr
5124 (uri (cran-uri "nloptr" version))
5127 "0whkilb85k4wixvr3k7rygfw1rcs1fs9h8c18kz4p3y1k9hsj3p8"))))
5128 (build-system r-build-system)
5130 `(("r-knitr" ,r-knitr) ; for building vignettes
5131 ("pkg-config" ,pkg-config)
5132 ("gfortran" ,gfortran)))
5134 `(("nlopt" ,nlopt)))
5135 (home-page "https://cran.r-project.org/web/packages/nloptr")
5136 (synopsis "R interface to NLopt")
5138 "This package is interface to NLopt, a library for nonlinear
5139 optimization. NLopt is a library for nonlinear optimization, providing a
5140 common interface for a number of different free optimization routines
5141 available online as well as original implementations of various other
5143 (license license:lgpl3)))
5145 (define-public r-lme4
5152 (uri (cran-uri "lme4" version))
5155 "0qh29kqli0l3naylgb6jha6jllx4nwryr3hv9yk37blgyyql5mcr"))))
5156 (build-system r-build-system)
5158 `(("r-boot" ,r-boot)
5159 ("r-lattice" ,r-lattice)
5161 ("r-matrix" ,r-matrix)
5162 ("r-minqa" ,r-minqa)
5163 ("r-nloptr" ,r-nloptr)
5166 ("r-rcppeigen" ,r-rcppeigen)
5167 ("r-statmod" ,r-statmod)))
5169 `(("r-knitr" ,r-knitr)))
5170 (home-page "https://cran.r-project.org/web/packages/lme4")
5171 (synopsis "Linear mixed-effects models using eigen and S4")
5173 "This package provides fit linear and generalized linear mixed-effects
5174 models. The models and their components are represented using S4 classes and
5175 methods. The core computational algorithms are implemented using the Eigen
5176 C++ library for numerical linear algebra and RcppEigen glue.")
5177 (license license:gpl2+)))
5179 (define-public r-pbkrtest
5186 (uri (cran-uri "pbkrtest" version))
5189 "0s5xhhrhv5i9680lw6af9lj2x4jc3fygmzzk0jjpxnb8g4b3p1jz"))))
5190 (build-system r-build-system)
5192 `(("r-lme4" ,r-lme4)
5193 ("r-magrittr" ,r-magrittr)
5195 ("r-matrix" ,r-matrix)))
5196 (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
5197 (synopsis "Methods for linear mixed model comparison")
5199 "This package implements a parametric bootstrap test and a Kenward Roger
5200 modification of F-tests for linear mixed effects models and a parametric
5201 bootstrap test for generalized linear mixed models.")
5202 (license license:gpl2+)))
5204 (define-public r-cardata
5211 (uri (cran-uri "carData" version))
5213 (base32 "09270j39n4jpswxqps20b12zaj8dz4rrqpk2l2j5bnf1xzizb9nd"))))
5214 (properties `((upstream-name . "carData")))
5215 (build-system r-build-system)
5216 (home-page "https://r-forge.r-project.org/projects/car/")
5217 (synopsis "Data Sets for the book Companion to Applied Regression")
5219 "This package provides datasets to accompany J. Fox and S. Weisberg, An R
5220 Companion to Applied Regression, Third Edition, Sage.")
5221 (license license:gpl2+)))
5223 (define-public r-car
5230 (uri (cran-uri "car" version))
5232 (base32 "0ig1691kxbzkrsq8xi5a6fq2f0vq22j1dn54jxdkldqr5vri1m57"))))
5233 (build-system r-build-system)
5235 `(("r-abind" ,r-abind)
5236 ("r-cardata" ,r-cardata)
5238 ("r-maptools" ,r-maptools)
5243 ("r-pbkrtest" ,r-pbkrtest)
5244 ("r-quantreg" ,r-quantreg)
5247 `(("r-knitr" ,r-knitr)))
5248 (home-page "https://r-forge.r-project.org/projects/car/")
5249 (synopsis "Companion to applied regression")
5251 "This package provides functions and datasets from book Companion
5252 to Applied regression, Second Edition, Sage, 2011.")
5253 (license license:gpl2+)))
5255 (define-public r-rcppprogress
5257 (name "r-rcppprogress")
5262 (uri (cran-uri "RcppProgress" version))
5265 "0j2b37gwjpgmrnr00srdzm751hzlpsjb54ph63xxmcdfnwhlnqmi"))))
5266 (properties `((upstream-name . "RcppProgress")))
5267 (build-system r-build-system)
5268 (home-page "https://github.com/kforner/rcpp_progress")
5269 (synopsis "Interruptible progress bar for C++ in R packages")
5271 "This package displays a progress bar in the R console for long running
5272 computations taking place in C++ code, and support for interrupting those computations
5273 even in multithreaded code, typically using OpenMP.")
5274 (license license:gpl3+)))
5276 (define-public r-tmvnsim
5283 (uri (cran-uri "tmvnsim" version))
5286 "03xsvsg9bqvgl98ywid3h91mmlhax5s6wvmypp3hq91vmc5kvxlp"))))
5287 (properties `((upstream-name . "tmvnsim")))
5288 (build-system r-build-system)
5289 (native-inputs `(("gfortran" ,gfortran)))
5290 (home-page "https://www.r-project.org")
5291 (synopsis "Truncated multivariate normal simulation")
5293 "This package implements importance sampling from the truncated
5294 multivariate normal using the @dfn{Geweke-Hajivassiliou-Keane} (GHK)
5295 simulator. Unlike Gibbs sampling which can get stuck in one truncation
5296 sub-region depending on initial values, this package allows truncation based
5297 on disjoint regions that are created by truncation of absolute values. The
5298 GHK algorithm uses simple Cholesky transformation followed by recursive
5299 simulation of univariate truncated normals hence there are also no convergence
5300 issues. Importance sample is returned along with sampling weights, based on
5301 which, one can calculate integrals over truncated regions for multivariate
5303 (license license:gpl2)))
5305 (define-public r-mnormt
5312 (uri (cran-uri "mnormt" version))
5315 "00nn0b6nksn2jbpg0np5wphryp4f9v95vqxf5v628yysnawgkcwq"))))
5316 (build-system r-build-system)
5318 `(("r-tmvnsim" ,r-tmvnsim)))
5320 `(("gfortran" ,gfortran)))
5321 (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
5322 (synopsis "Multivariate normal and \"t\" distributions")
5324 "This package provides functions for computing the density and the
5325 distribution function of multivariate normal and \"t\" random variables, and
5326 for generating random vectors sampled from these distributions. Probabilities
5327 are computed via non-Monte Carlo methods.")
5328 (license license:gpl2+)))
5330 (define-public r-numderiv
5333 (version "2016.8-1.1")
5337 (uri (cran-uri "numDeriv" version))
5340 "0idk02pqkziik932bd8k72d1q775g1is3m4bc861pcxfz6gx3i6q"))))
5341 (properties `((upstream-name . "numDeriv")))
5342 (build-system r-build-system)
5343 (home-page "https://cran.r-project.org/web/packages/numDeriv")
5344 (synopsis "Accurate numerical derivatives")
5346 "This package provides methods for calculating accurate numerical
5347 first and second order derivatives.")
5348 (license license:gpl2)))
5357 (uri (cran-uri "sn" version))
5360 "179xb7yb8br99aa5awm2yxsy0v5w1kdhv6a7ifaliz2y64677m1g"))))
5361 (build-system r-build-system)
5363 `(("r-mnormt" ,r-mnormt)
5364 ("r-numderiv" ,r-numderiv)
5365 ("r-quantreg" ,r-quantreg)))
5366 (home-page "http://azzalini.stat.unipd.it/SN")
5367 (synopsis "The skew-normal and skew-t distributions")
5369 "This package provides functionalities to build and manipulate
5370 probability distributions of the skew-normal family and some related
5371 ones, notably the skew-t family, and provides related statistical
5372 methods for data fitting and diagnostics, in the univariate and the
5373 multivariate case.")
5374 (license license:gpl2+)))
5376 (define-public r-tclust
5383 (uri (cran-uri "tclust" version))
5386 "17md6l9v9dl9b72l84df01b52h2xiynbcjm437mv9mzcr09fc2sb"))))
5387 (build-system r-build-system)
5388 ;; These are all suggested packages, not build dependencies.
5390 `(("r-cluster" ,r-cluster)
5391 ("r-mclust" ,r-mclust)
5392 ("r-mvtnorm" ,r-mvtnorm)
5394 (home-page "https://cran.r-project.org/web/packages/tclust")
5395 (synopsis "Robust trimmed clustering")
5397 "This package implements different robust clustering
5398 algorithms (@code{tclust}) based on trimming and including some graphical
5399 diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
5400 (license license:gpl3)))
5402 (define-public r-ranger
5409 (uri (cran-uri "ranger" version))
5412 "1vr5akgh388iivrxi0g4pl2npq9dc4cim3ljk4kjf637q058wc7w"))))
5413 (build-system r-build-system)
5415 `(("r-rcpp" ,r-rcpp)
5416 ("r-matrix" ,r-matrix)
5417 ("r-rcppeigen" ,r-rcppeigen)))
5418 (home-page "https://github.com/imbs-hl/ranger")
5419 (synopsis "Fast implementation of random forests")
5421 "This package provides a fast implementation of Random Forests,
5422 particularly suited for high dimensional data. Ensembles of classification,
5423 regression, survival and probability prediction trees are supported. Data from
5424 genome-wide association studies can be analyzed efficiently.")
5425 (license license:gpl3)))
5427 (define-public r-tsne
5434 (uri (cran-uri "tsne" version))
5437 "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
5438 (build-system r-build-system)
5439 (home-page "https://github.com/jdonaldson/rtsne/")
5440 (synopsis "t-Distributed Stochastic Neighbor Embedding for R")
5442 "This package provides a pure R implementation of the t-SNE algorithm.")
5443 (license license:gpl2+)))
5445 (define-public r-cairo
5452 (uri (cran-uri "Cairo" version))
5455 "02v29am4fac3fyq6y1w6r89zwbqqkxjsxrafcwb5s124ikxyl22f"))))
5456 (properties `((upstream-name . "Cairo")))
5457 (build-system r-build-system)
5463 `(("pkg-config" ,pkg-config)))
5464 (home-page "https://www.rforge.net/Cairo/")
5465 (synopsis "R graphics device using Cairo graphics library")
5467 "This package provides a Cairo graphics device that can be use to
5468 create high-quality vector (PDF, PostScript and SVG) and bitmap
5469 output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11
5470 and Win32). Since it uses the same back-end for all output, copying
5471 across formats is WYSIWYG. Files are created without the dependence
5472 on X11 or other external programs. This device supports alpha
5473 channel (semi-transparent drawing) and resulting images can contain
5474 transparent and semi-transparent regions. It is ideal for use in
5475 server environments (file output) and as a replacement for other
5476 devices that don't have Cairo's capabilities such as alpha support or
5477 anti-aliasing. Backends are modular such that any subset of backends
5479 (license license:gpl2)))
5481 (define-public r-lubridate
5483 (name "r-lubridate")
5488 (uri (cran-uri "lubridate" version))
5491 "0wnjzvfkrgp2hkr8g5r5vcgcxmsq8bhdmkzkk0m93wr3fgh5xyfb"))))
5492 (build-system r-build-system)
5494 `(("r-generics" ,r-generics)
5495 ("r-rcpp" ,r-rcpp)))
5497 `(("r-knitr" ,r-knitr)))
5498 (home-page "https://cran.r-project.org/web/packages/lubridate/")
5499 (synopsis "Make dealing with dates a little easier")
5501 "This package provides functions to work with date-times and time-spans:
5502 fast and user friendly parsing of date-time data, extraction and updating of
5503 components of a date-time (years, months, days, hours, minutes, and seconds),
5504 algebraic manipulation on date-time and time-span objects. The @code{lubridate}
5505 package has a consistent and memorable syntax that makes working with dates
5507 (license license:gpl2)))
5509 (define-public r-fdrtool
5516 (uri (cran-uri "fdrtool" version))
5519 "1h46frlk7d9f4qx0bg6p55nrm9wwwz2sv6d1nz7061wdfsm69yb5"))))
5520 (build-system r-build-system)
5521 (home-page "http://strimmerlab.org/software/fdrtool/")
5522 (synopsis "Estimation of false discovery rates and higher criticism")
5524 "This package provides tools to estimate tail area-based false discovery
5525 rates as well as local false discovery rates for a variety of null
5526 models (p-values, z-scores, correlation coefficients, t-scores). The
5527 proportion of null values and the parameters of the null distribution are
5528 adaptively estimated from the data. In addition, the package contains
5529 functions for non-parametric density estimation (Grenander estimator), for
5530 monotone regression (isotonic regression and antitonic regression with
5531 weights), for computing the @dfn{greatest convex minorant} (GCM) and the
5532 @dfn{least concave majorant} (LCM), for the half-normal and correlation
5533 distributions, and for computing empirical @dfn{higher criticism} (HC) scores
5534 and the corresponding decision threshold.")
5535 (license license:gpl3+)))
5537 (define-public r-forcats
5544 (uri (cran-uri "forcats" version))
5547 "1i4hblsjgwkrcwgvgsb5yj33pw1hwdj3lr9dvxymkv1kjdw0x5lg"))))
5548 (build-system r-build-system)
5550 `(("r-ellipsis" ,r-ellipsis)
5551 ("r-magrittr" ,r-magrittr)
5552 ("r-tibble" ,r-tibble)
5553 ("r-rlang" ,r-rlang)))
5554 (home-page "https://forcats.tidyverse.org")
5555 (synopsis "Tools for working with factors")
5556 (description "This package provides helpers for reordering factor
5557 levels (including moving specified levels to front, ordering by first
5558 appearance, reversing, and randomly shuffling), and tools for modifying factor
5559 levels (including collapsing rare levels into other, \"anonymizing\", and
5560 manually \"recoding\").")
5561 (license license:gpl3)))
5563 (define-public r-tgstat
5564 (let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f")
5568 (version (string-append "1.0.2-" revision "." (string-take changeset 7)))
5573 (url "https://bitbucket.org/tanaylab/tgstat")
5574 (changeset changeset)))
5575 (file-name (string-append name "-" version "-checkout"))
5578 "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
5579 (build-system r-build-system)
5582 (modify-phases %standard-phases
5583 (add-after 'unpack 'fix-isnan
5585 (substitute* "src/tgstat.h"
5586 (("#define isnan ::isnan")
5587 "#define isnan std::isnan"))
5590 `(("r-rcpp" ,r-rcpp)))
5591 (home-page "https://bitbucket.org/tanaylab/tgstat/")
5592 (synopsis "Tanay's group statistical utilities")
5594 "The goal of tgstat is to provide fast and efficient statistical
5596 (license license:gpl2))))
5598 (define-public r-tgconfig
5599 (let ((changeset "1e02c7614713bd0866c46f0c679a058f8c6d627e")
5603 (version (string-append "0.0.0.9000-" revision "." (string-take changeset 7)))
5608 (url "https://bitbucket.org/tanaylab/tgconfig")
5609 (changeset changeset)))
5610 (file-name (string-append name "-" version "-checkout"))
5613 "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
5614 (build-system r-build-system)
5616 `(("r-yaml" ,r-yaml)))
5617 (home-page "https://bitbucket.org/tanaylab/tgconfig/")
5618 (synopsis "Infrastructure for managing package parameters")
5620 "The goal of tgconfig is to provide infrastructure for managing package
5622 (license license:gpl3))))
5624 (define-public r-catterplots
5625 (let ((commit "ae17cd5e49ddda4ecfe0eba8a4c21df8c88e72c4")
5628 (name "r-catterplots")
5629 (version (git-version "0" revision commit))
5633 (url "https://github.com/Gibbsdavidl/CatterPlots")
5635 (file-name (git-file-name name version))
5638 "0qa8liylffpxgdg8xcgjar5dsvczqhn3akd4w35113hnyg1m4xyg"))))
5639 (build-system r-build-system)
5641 `(("r-png" ,r-png)))
5642 (home-page "https://github.com/Gibbsdavidl/CatterPlots")
5643 (synopsis "Scatter plots with cat shaped points")
5644 (description "Did you ever wish you could make scatter plots with cat
5645 shaped points? Now you can!")
5646 (license license:asl2.0))))
5648 (define-public r-colorout
5656 (url "https://github.com/jalvesaq/colorout")
5657 (commit (string-append "v" version))))
5658 (file-name (git-file-name name version))
5660 (base32 "1rsx69wjpa73c6x2hacvvvbzdzxn7wg06gizf97kasjdlb7azmp3"))))
5661 (build-system r-build-system)
5662 (home-page "https://github.com/jalvesaq/colorout")
5663 (synopsis "Colorize output in the R REPL")
5664 (description "@code{colorout} is an R package that colorizes R output when
5665 running in terminal emulator.
5667 R STDOUT is parsed and numbers, negative numbers, dates in the standard
5668 format, strings, and R constants are identified and wrapped by special ANSI
5669 scape codes that are interpreted by terminal emulators as commands to colorize
5670 the output. R STDERR is also parsed to identify the expressions warning and
5671 error and their translations to many languages. If these expressions are
5672 found, the output is colorized accordingly; otherwise, it is colorized as
5673 STDERROR (blue, by default).
5675 You can customize the colors according to your taste, guided by the color
5676 table made by the command @code{show256Colors()}. You can also set the colors
5677 to any arbitrary string. In this case, it is up to you to set valid values.")
5678 (license license:gpl3+)))
5680 (define-public python-rpy2
5681 ;; We need to take this changeset instead of the RELEASE_3_0_4 tag, because
5682 ;; it fixes a regression when using ggplot 3.2.0.
5683 (let ((changeset "19868a8")
5686 (name "python-rpy2")
5687 (version (git-version "3.0.4" revision changeset))
5692 (url "https://bitbucket.org/rpy2/rpy2")
5693 (changeset changeset)))
5694 (file-name (git-file-name name version))
5697 "1bb0wslcbj3wjvyk3jb9yyzdi6adfqh5vfgcvn22dyzxzbhcs8kk"))))
5698 (build-system python-build-system)
5700 '(#:modules ((ice-9 ftw)
5704 (guix build python-build-system))
5706 (modify-phases %standard-phases
5708 (lambda* (#:key outputs inputs #:allow-other-keys)
5709 (let ((cwd (getcwd)))
5711 (setenv "PYTHONPATH"
5712 (string-append cwd "/build/"
5713 (find (cut string-prefix? "lib" <>)
5714 (scandir (string-append cwd "/build")))
5716 (getenv "PYTHONPATH"))))
5717 (invoke "pytest" "-v" "rpy/tests/"))))))
5719 `(("python-cffi" ,python-cffi)
5720 ("python-six" ,python-six)
5721 ("python-jinja2" ,python-jinja2)
5722 ("python-numpy" ,python-numpy)
5723 ("python-pandas" ,python-pandas)
5724 ("python-pytz" ,python-pytz)
5725 ("python-ipython" ,python-ipython)
5726 ("python-tzlocal" ,python-tzlocal)))
5728 `(("readline" ,readline)
5731 ("r-minimal" ,r-minimal)
5732 ("r-survival" ,r-survival)
5733 ("r-ggplot2" ,r-ggplot2)
5734 ("r-rsqlite" ,r-rsqlite)
5735 ("r-dplyr" ,r-dplyr)
5736 ("r-dbplyr" ,r-dbplyr)
5737 ("python-numpy" ,python-numpy)))
5740 ("python-pytest" ,python-pytest)))
5741 (home-page "https://rpy2.bitbucket.io/")
5742 (synopsis "Python interface to the R language")
5743 (description "rpy2 is a redesign and rewrite of rpy. It is providing a
5744 low-level interface to R from Python, a proposed high-level interface,
5745 including wrappers to graphical libraries, as well as R-like structures and
5747 ;; Any of these licenses can be picked for the R interface. The whole
5748 ;; project is released under GPLv2+ according to the license declaration
5750 (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+)))))
5752 (define-public java-jdistlib
5754 (name "java-jdistlib")
5758 (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
5759 version "-src.jar"))
5762 "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
5763 (build-system ant-build-system)
5765 `(#:jar-name "jdistlib.jar"
5767 #:tests? #f ; no dedicated test directory
5769 (modify-phases %standard-phases
5770 (add-after 'unpack 'fix-broken-encoding
5772 (with-fluids ((%default-port-encoding "ISO-8859-1"))
5773 (substitute* "src/jdistlib/Beta.java"
5774 (("Scheff.+-Tukey") "Scheffe-Tukey")))
5777 `(("java-jtransforms" ,java-jtransforms)))
5779 `(("java-junit" ,java-junit)))
5780 (home-page "http://jdistlib.sourceforge.net/")
5781 (synopsis "Java library of statistical distributions")
5782 (description "JDistlib is the Java Statistical Distribution Library, a
5783 Java package that provides routines for various statistical distributions.")
5784 ;; The files that were translated from R code are under GPLv2+; some files
5785 ;; are under the GPLv3, which is a mistake. The author confirmed in an
5786 ;; email that this whole project should be under GPLv2+.
5787 (license license:gpl2+)))
5789 (define-public emacs-ess
5796 (url "https://github.com/emacs-ess/ESS")
5797 (commit (string-append "v" version))))
5800 "1yq41l2bicwjrc0b731iic20cpcnz6ppigri1jn621qv2qv22vy3"))
5801 (file-name (git-file-name name version))
5802 (modules '((guix build utils)))
5805 ;; Stop ESS from trying to bundle an external julia-mode.el.
5806 (substitute* "lisp/Makefile"
5807 (("^ess-julia.elc: julia-mode.elc") "")
5808 (("^all: julia-mode.el")
5810 ;; Include *.el files in install target.
5811 (substitute* "lisp/Makefile"
5812 (("\t\\$\\(INSTALL) \\$\\(ELC\\) \\$\\(LISPDIR\\)" elc)
5813 (string-append "\t$(INSTALL) $(ELS) ess-autoloads.el "
5814 "$(LISPDIR)\n" elc)))
5815 ;; Only build docs in info format.
5816 (substitute* "doc/Makefile"
5817 (("all : info text")
5819 (("install: install-info install-other-docs")
5820 "install: install-info"))
5821 ;; Stop install-info from trying to update the info directory.
5822 (substitute* "doc/Makefile"
5823 ((".*\\$\\(INFODIR\\)/dir.*") ""))
5824 ;; Fix roxygen preview test.
5825 (substitute* "test/ess-r-tests.el"
5826 (("Add together two numbers.\n")
5827 "Add together two numbers. ")
5828 (("##' add\\(10, 1\\)") "add(10, 1)"))
5830 (build-system gnu-build-system)
5832 (let ((base-directory "/share/emacs/site-lisp"))
5833 `(#:make-flags (list (string-append "PREFIX=" %output)
5834 (string-append "ETCDIR=" %output
5835 ,base-directory "/etc")
5836 (string-append "LISPDIR=" %output
5839 (modify-phases %standard-phases
5841 (add-before 'build 'more-shebang-patching
5842 (lambda* (#:key inputs #:allow-other-keys)
5843 (substitute* "Makeconf"
5844 (("SHELL = /bin/sh")
5845 (string-append "SHELL = " (which "sh"))))
5849 (invoke "make" "test")))))))
5851 `(("emacs" ,emacs-minimal)
5852 ("r-minimal" ,r-minimal)))
5855 ("r-roxygen2" ,r-roxygen2)
5856 ("texinfo" ,texinfo)))
5858 `(("emacs-julia-mode" ,emacs-julia-mode)))
5859 (home-page "https://ess.r-project.org/")
5860 (synopsis "Emacs mode for statistical analysis programs")
5861 (description "Emacs Speaks Statistics (ESS) is an add-on package for GNU
5862 Emacs. It is designed to support editing of scripts and interaction with
5863 various statistical analysis programs such as R, Julia, and JAGS.")
5864 (license license:gpl2+)))