1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 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, 2021 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>
15 ;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
16 ;;; Copyright © 2021 Bonface Munyoki Kilyungi <me@bonfacemunyoki.com>
17 ;;; Copyright © 2021 Lars-Dominik Braun <lars@6xq.net>
18 ;;; Copyright © 2021 Frank Pursel <frank.pursel@gmail.com>
19 ;;; Copyright © 2022 Simon Tournier <zimon.toutoune@gmail.com>
21 ;;; This file is part of GNU Guix.
23 ;;; GNU Guix is free software; you can redistribute it and/or modify it
24 ;;; under the terms of the GNU General Public License as published by
25 ;;; the Free Software Foundation; either version 3 of the License, or (at
26 ;;; your option) any later version.
28 ;;; GNU Guix is distributed in the hope that it will be useful, but
29 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
30 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
31 ;;; GNU General Public License for more details.
33 ;;; You should have received a copy of the GNU General Public License
34 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
36 (define-module (gnu packages statistics)
37 #:use-module ((guix licenses) #:prefix license:)
38 #:use-module (guix packages)
39 #:use-module (guix download)
40 #:use-module (guix hg-download)
41 #:use-module (guix git-download)
42 #:use-module (guix utils)
43 #:use-module (guix build-system ant)
44 #:use-module (guix build-system emacs)
45 #:use-module (guix build-system gnu)
46 #:use-module (guix build-system r)
47 #:use-module (guix build-system python)
48 #:use-module (guix build-system trivial)
49 #:use-module (gnu packages)
50 #:use-module (gnu packages algebra)
51 #:use-module (gnu packages autotools)
52 #:use-module (gnu packages bash)
53 #:use-module (gnu packages check)
54 #:use-module (gnu packages compression)
55 #:use-module (gnu packages cran)
56 #:use-module (gnu packages curl)
57 #:use-module (gnu packages emacs)
58 #:use-module (gnu packages emacs-xyz)
59 #:use-module (gnu packages fontutils)
60 #:use-module (gnu packages gcc)
61 #:use-module (gnu packages gtk)
62 #:use-module (gnu packages gettext)
63 #:use-module (gnu packages glib)
64 #:use-module (gnu packages haskell-xyz)
65 #:use-module (gnu packages icu4c)
66 #:use-module (gnu packages image)
67 #:use-module (gnu packages java)
68 #:use-module (gnu packages javascript)
69 #:use-module (gnu packages libffi)
70 #:use-module (gnu packages machine-learning)
71 #:use-module (gnu packages maths)
72 #:use-module (gnu packages multiprecision)
73 #:use-module (gnu packages ncurses)
74 #:use-module (gnu packages pcre)
75 #:use-module (gnu packages perl)
76 #:use-module (gnu packages pkg-config)
77 #:use-module (gnu packages python)
78 #:use-module (gnu packages python-science)
79 #:use-module (gnu packages python-xyz)
80 #:use-module (gnu packages readline)
81 #:use-module (gnu packages shells)
82 #:use-module (gnu packages sphinx)
83 #:use-module (gnu packages ssh)
84 #:use-module (gnu packages tcl)
85 #:use-module (gnu packages tex)
86 #:use-module (gnu packages texinfo)
87 #:use-module (gnu packages time)
88 #:use-module (gnu packages tls)
89 #:use-module (gnu packages base)
90 #:use-module (gnu packages uglifyjs)
91 #:use-module (gnu packages version-control)
92 #:use-module (gnu packages web)
93 #:use-module (gnu packages xml)
94 #:use-module (gnu packages xorg)
95 #:use-module (srfi srfi-1)
96 #:use-module (ice-9 match))
106 (uri (string-append "mirror://gnu/pspp/pspp-"
110 "0lqrash677b09zxdlxp89z6k02y4i23mbqg83956dwl69wc53dan"))))
111 (build-system gnu-build-system)
124 (list autoconf ;for tests
125 `(,glib "bin") ;for glib-genmarshal
130 (home-page "https://www.gnu.org/software/pspp/")
131 (synopsis "Statistical analysis")
133 "GNU PSPP is a statistical analysis program. It can perform
134 descriptive statistics, T-tests, linear regression and non-parametric tests.
135 It features both a graphical interface as well as command-line input. PSPP
136 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
137 can be imported from spreadsheets, text files and database sources and it can
138 be output in text, PostScript, PDF or HTML.")
139 (license license:gpl3+)))
147 (uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/"
148 (version-major version) ".x/Source/"
149 "JAGS-" version ".tar.gz"))
152 "1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica"))))
153 (build-system gnu-build-system)
154 (home-page "http://mcmc-jags.sourceforge.net/")
156 (list gfortran lapack))
157 (synopsis "Gibbs sampler")
158 (description "JAGS is Just Another Gibbs Sampler. It is a program for
159 analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
160 simulation not wholly unlike BUGS. JAGS was written with three aims in mind:
163 @item To have a cross-platform engine for the BUGS language;
164 @item To be extensible, allowing users to write their own functions,
165 distributions and samplers;
166 @item To be a platform for experimentation with ideas in Bayesian modelling.
168 (license license:gpl2)))
170 (define-public libxls
177 (uri (string-append "https://github.com/libxls/libxls/releases/download/"
178 "v" version "/libxls-" version ".tar.gz"))
180 (base32 "0wg3ymr43aa1j3scyl9x83b2xgg7wilzpil0dj91a8dzji6w7b2x"))))
181 (build-system gnu-build-system)
182 (home-page "https://github.com/libxls/libxls")
183 (synopsis "Read binary (.xls) Excel spreadsheet files")
185 "libxls is a C library to read .xls spreadsheet files in the binary OLE
186 BIFF8 format as created by Excel 97 and later versions. It cannot write them.
188 This package also provides @command{xls2csv} to export Excel files to CSV.")
189 (license license:bsd-2)))
191 ;; Update this package together with the set of recommended packages: r-boot,
192 ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
193 ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
196 (name "r-with-tests")
200 (uri (string-append "mirror://cran/src/base/R-"
201 (version-major version) "/R-"
205 "1brqmc7mmb0z94kcs4crgl6v9a6sxhm9fm3y177d81vjkxg24di0"))))
206 (build-system gnu-build-system)
208 `(#:disallowed-references (,tzdata-for-tests)
210 (list (string-append "LDFLAGS=-Wl,-rpath="
211 (assoc-ref %outputs "out")
213 ;; This affects the embedded timestamp of only the core packages.
214 "PKG_BUILT_STAMP=1970-01-01")
216 (modify-phases %standard-phases
217 (add-before 'configure 'do-not-compress-serialized-files
218 (lambda* (#:key inputs #:allow-other-keys)
219 ;; This ensures that Guix can detect embedded store references;
220 ;; see bug #28157 for details.
221 (substitute* "src/library/base/makebasedb.R"
222 (("compress = TRUE") "compress = FALSE"))))
223 (add-before 'configure 'patch-coreutils-paths
224 (lambda* (#:key inputs #:allow-other-keys)
225 (let ((uname-bin (search-input-file inputs "/bin/uname"))
226 (rm-bin (search-input-file inputs "/bin/rm")))
227 (substitute* "src/scripts/R.sh.in"
228 (("uname") uname-bin))
229 (substitute* "src/unix/sys-std.c"
230 (("rm -Rf ") (string-append rm-bin " -Rf "))))))
231 (add-after 'unpack 'build-reproducibly
233 ;; The documentation contains time stamps to demonstrate
234 ;; documentation generation in different phases.
235 (substitute* "src/library/tools/man/Rd2HTML.Rd"
236 (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
237 "(removed for reproducibility)"))
239 ;; Remove timestamp from tracing environment. This fixes
240 ;; reproducibility of "methods.rd{b,x}".
241 (substitute* "src/library/methods/R/trace.R"
242 (("dateCreated = Sys.time\\(\\)")
243 "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
245 ;; Ensure that gzipped files are reproducible.
246 (substitute* '("src/library/grDevices/Makefile.in"
247 "doc/manual/Makefile.in")
248 (("R_GZIPCMD\\)" line)
249 (string-append line " -n")))
251 ;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
252 ;; queries the mtime of a given file and records it in an object.
253 ;; This is acceptable at runtime to detect stale source files,
254 ;; but it destroys reproducibility at build time.
256 ;; Similarly, the "srcfilecopy" procedure records the current
257 ;; time. We change both of them to respect SOURCE_DATE_EPOCH.
258 (substitute* "src/library/base/R/srcfile.R"
259 (("timestamp <- (timestamp.*|file.mtime.*)" _ time)
260 (string-append "timestamp <- \
261 as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
262 as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
263 } else { " time "}, origin=\"1970-01-01\")\n")))
265 ;; This library is installed using "install_package_description",
266 ;; so we need to pass the "builtStamp" argument.
267 (substitute* "src/library/tools/Makefile.in"
268 (("(install_package_description\\(.*\"')\\)\"" line prefix)
269 (string-append prefix ", builtStamp='1970-01-01')\"")))
271 (substitute* "src/library/Recommended/Makefile.in"
272 (("INSTALL_OPTS =" m)
273 (string-append m " --built-timestamp=1970-01-01" m)))
275 ;; R bundles an older version of help2man, which does not respect
276 ;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man,
277 ;; because that breaks a test.
278 (with-fluids ((%default-port-encoding "ISO-8859-1"))
279 (substitute* "tools/help2man.pl"
280 (("my \\$date = strftime \"%B %Y\", localtime" line)
281 (string-append line " 1"))))
283 ;; The "References" section of this file when converted to
284 ;; package.rds is sometimes stored with a newline, sometimes with
285 ;; a space. We avoid this problem by removing the line break
286 ;; that is suspected to be the culprit.
287 (substitute* "src/library/methods/DESCRIPTION.in"
288 (("\\(2008\\)\n") "(2008) ")
289 ((" ``Software") "``Software")
290 (("Data Analysis:.") "Data Analysis:\n")
291 (("Programming with R") " Programming with R"))))
292 (add-before 'build 'set-locales
294 (setlocale LC_ALL "C")
295 (setenv "LC_ALL" "C")))
296 (add-before 'configure 'set-default-pager
297 ;; Set default pager to "cat", because otherwise it is "false",
298 ;; making "help()" print nothing at all.
299 (lambda _ (setenv "PAGER" "cat")))
300 (add-before 'check 'set-timezone
301 ;; Some tests require the timezone to be set. However, the
302 ;; timezone may not just be "UTC", or else a brittle regression
303 ;; test in reg-tests-1d will fail.
304 (lambda* (#:key inputs #:allow-other-keys)
305 (setenv "TZ" "UTC+1")
307 (search-input-directory inputs
309 (add-after 'build 'make-info
310 (lambda _ (invoke "make" "info")))
311 (add-after 'build 'install-info
312 (lambda _ (invoke "make" "install-info"))))
314 `(;; We build the recommended packages here, because they are needed in
315 ;; order to run the test suite. We disable them in the r-minimal
318 "--with-blas=-lopenblas"
324 ,(string-append "--with-tcl-config="
325 (assoc-ref %build-inputs "tcl")
327 ,(string-append "--with-tk-config="
328 (assoc-ref %build-inputs "tk")
331 "--enable-BLAS-shlib"
332 "--with-system-tre")))
333 ;; R has some support for Java. When the JDK is available at configure
334 ;; time environment variables pointing to the JDK will be recorded under
335 ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
336 ;; CMD javareconf". "R CMD javareconf" appears to only be used to update
337 ;; the recorded environment variables in $R_HOME/etc. Refer to
338 ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
339 ;; for additional information.
341 ;; As the JDK is a rather large input with only very limited effects on R,
342 ;; we decided to drop it.
346 ("pkg-config" ,pkg-config)
347 ("texinfo" ,texinfo) ; for building HTML manuals
348 ("texlive" ,(texlive-updmap.cfg (list texlive-ae
354 texlive-latex-fancyvrb
355 texlive-latex-graphics
359 texlive-latex-upquote
361 texlive-latex-xkeyval)))
362 ("tzdata" ,tzdata-for-tests)
365 `(;; We need not only cairo here, but pango to ensure that tests for the
366 ;; "cairo" bitmapType plotting backend succeed.
368 ("coreutils" ,coreutils)
370 ("openblas" ,openblas)
371 ("gfortran" ,gfortran)
373 ("libjpeg" ,libjpeg-turbo)
378 ("readline" ,readline)
379 ;; This avoids a reference to the ungraftable static bash. R uses the
380 ;; detected shell for the "system" procedure.
381 ("bash" ,bash-minimal)
387 (list (search-path-specification
388 (variable "R_LIBS_SITE")
389 (files (list "site-library/")))))
390 (home-page "https://www.r-project.org/")
391 (synopsis "Environment for statistical computing and graphics")
393 "R is a language and environment for statistical computing and graphics.
394 It provides a variety of statistical techniques, such as linear and nonlinear
395 modeling, classical statistical tests, time-series analysis, classification
396 and clustering. It also provides robust support for producing
397 publication-quality data plots. A large amount of 3rd-party packages are
398 available, greatly increasing its breadth and scope.")
399 (license license:gpl3+)))
401 (define-public r-minimal
402 (package (inherit r-with-tests)
406 ,@(substitute-keyword-arguments (package-arguments r-with-tests)
407 ((#:disallowed-references refs '())
409 ((#:configure-flags flags)
410 ;; Do not build the recommended packages. The build system creates
411 ;; random temporary directories and embeds their names in some
412 ;; package files. We build these packages with the r-build-system
414 `(cons "--without-recommended-packages" ,flags))
415 ((#:phases phases '%standard-phases)
416 `(modify-phases ,phases
417 (add-after 'install 'remove-extraneous-references
418 (lambda* (#:key inputs outputs #:allow-other-keys)
419 (let ((out (assoc-ref outputs "out")))
420 (substitute* (string-append out "/lib/R/etc/Makeconf")
422 "# Removed to avoid extraneous references\n"))
423 (substitute* (string-append out "/lib/R/bin/libtool")
426 (assoc-ref inputs "bzip2")
428 (assoc-ref inputs "perl")
430 (assoc-ref inputs "texlive")
432 (assoc-ref inputs "texlive-bin")
434 (assoc-ref inputs "texinfo")
436 (assoc-ref inputs "xz")
439 "/gnu/store/[^-]+-(~{~a~^|~})-[^/]+"
440 '("glibc-utf8-locales"
448 "/gnu/store/[^-]+-glibc-[^-]+-static"
449 ")/lib")) ""))))))))))))
451 (define-public rmath-standalone
452 (package (inherit r-minimal)
453 (name "rmath-standalone")
456 (modify-phases %standard-phases
457 (add-after 'configure 'chdir
458 (lambda _ (chdir "src/nmath/standalone/") #t)))))
459 (synopsis "Standalone R math library")
461 "This package provides the R math library as an independent package.")))
463 (define-public r-boot
470 (uri (cran-uri "boot" version))
473 "0cjafhqv1c1mrjjcasqr767vs96wjcc6am9r1icryr8l4zymhwcz"))))
474 (build-system r-build-system)
475 (home-page "https://cran.r-project.org/web/packages/boot")
476 (synopsis "Bootstrap functions for R")
478 "This package provides functions and datasets for bootstrapping from the
479 book \"Bootstrap Methods and Their Application\" by A.C. Davison and
480 D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
481 ;; Unlimited distribution
482 (license (license:non-copyleft "file://R/bootfuns.q"))))
484 (define-public r-mass
491 (uri (cran-uri "MASS" version))
494 "191i1iylvh2w2hi99fnm06731lma7z5snpjknfff1m9ziyy9qab5"))))
495 (properties `((upstream-name . "MASS")))
496 (build-system r-build-system)
497 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
498 (synopsis "Support functions and datasets for Venables and Ripley's MASS")
500 "This package provides functions and datasets for the book \"Modern
501 Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
502 ;; Either version may be picked.
503 (license (list license:gpl2 license:gpl3))))
505 (define-public r-class
512 (uri (cran-uri "class" version))
515 "10slys2jny4k2j8l8k97hwrwd6ryzajfnzywqpq2yc9bqxmh8nz6"))))
516 (build-system r-build-system)
519 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
520 (synopsis "R functions for classification")
522 "This package provides various functions for classification, including
523 k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
524 ;; Either of the two versions can be picked.
525 (license (list license:gpl2 license:gpl3))))
527 (define-public r-cluster
534 (uri (cran-uri "cluster" version))
537 "168l653ygkg21fwrqrf7lsqi5p6jzhgmcvhrwv7lznkdzdhag2jw"))))
538 (build-system r-build-system)
541 (home-page "https://cran.r-project.org/web/packages/cluster")
542 (synopsis "Methods for cluster analysis")
544 "This package provides methods for cluster analysis. It is a much
545 extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
546 Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
547 (license license:gpl2+)))
549 (define-public r-codetools
556 (uri (cran-uri "codetools" version))
559 "0a2c115glq8jxixwfigrpvjabhxchn9r4mc40y41dg9dg6wsd7hs"))))
560 (build-system r-build-system)
561 (home-page "https://cran.r-project.org/web/packages/codetools")
562 (synopsis "Code analysis tools for R")
563 (description "This package provides code analysis tools for R to check R
564 code for possible problems.")
565 ;; Any version of the GPL.
566 (license (list license:gpl2+ license:gpl3+))))
568 (define-public r-foreign
575 (uri (cran-uri "foreign" version))
578 "1yw07yqzfm4w1h92ijyamrmf7rmkqxgamqfd74x7zv4vsn20dvgq"))))
579 (build-system r-build-system)
580 (home-page "https://cran.r-project.org/web/packages/foreign")
581 (synopsis "Read data stored by other statistics software")
583 "This package provides functions for reading and writing data stored by
584 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
585 for reading and writing some dBase files.")
586 (license license:gpl2+)))
588 (define-public r-kernsmooth
590 (name "r-kernsmooth")
595 (uri (cran-uri "KernSmooth" version))
598 "0fgclmzk3ksjsh3j47jqzm3jhqrwn12rkp7f84yr6wr43q2pbsr0"))))
599 (properties `((upstream-name . "KernSmooth")))
600 (build-system r-build-system)
603 (home-page "https://cran.r-project.org/web/packages/KernSmooth")
604 (synopsis "Functions for kernel smoothing")
606 "This package provides functions for kernel smoothing (and density
607 estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
608 \"Kernel Smoothing\".")
609 ;; Unlimited use and distribution
610 (license (license:non-copyleft "file://LICENCE.note"))))
612 (define-public r-lattice
618 (uri (cran-uri "lattice" version))
621 "1b87fmyjzbg854vpi03my1p25n3d0bchhwsdm2frblxppn98sf12"))))
622 (build-system r-build-system)
623 (home-page "http://lattice.r-forge.r-project.org/")
624 (synopsis "High-level data visualization system")
626 "The lattice package provides a powerful and elegant high-level data
627 visualization system inspired by Trellis graphics, with an emphasis on
628 multivariate data. Lattice is sufficient for typical graphics needs, and is
629 also flexible enough to handle most nonstandard requirements.")
630 (license license:gpl2+)))
632 (define-public r-matrix
639 (uri (cran-uri "Matrix" version))
642 "1xh62bwcly1blpvnagbhjym1qgw87yir3c72ylhvcla05rq67d62"))))
643 (properties `((upstream-name . "Matrix")))
644 (build-system r-build-system)
647 (home-page "http://Matrix.R-forge.R-project.org/")
648 (synopsis "Sparse and dense matrix classes and methods")
650 "This package provides classes and methods for dense and sparse matrices
651 and operations on them using LAPACK and SuiteSparse.")
652 (license license:gpl2+)))
654 (define-public r-nlme
661 (uri (cran-uri "nlme" version))
663 (base32 "0kzzpl63l298yy18x62ypgbhdw61fgm30lc4nlhjjhjj5220yfcz"))))
664 (build-system r-build-system)
669 (home-page "https://cran.r-project.org/web/packages/nlme")
670 (synopsis "Linear and nonlinear mixed effects models")
672 "This package provides tools to fit and compare Gaussian linear and
673 nonlinear mixed-effects models.")
674 (license license:gpl2+)))
676 (define-public r-mgcv
683 (uri (cran-uri "mgcv" version))
685 (base32 "1fyx8b0xjyx75mp90v314gayzydkca5y90p76jnwxzfnhxbys4nd"))))
686 (build-system r-build-system)
688 (list r-matrix r-nlme))
689 (home-page "https://cran.r-project.org/web/packages/mgcv")
690 (synopsis "Mixed generalised additive model computation")
692 "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
693 parameter estimation by GCV, REML or UBRE/AIC. The library includes a
694 @code{gam()} function, a wide variety of smoothers, JAGS support and
695 distributions beyond the exponential family.")
696 (license license:gpl2+)))
698 (define-public r-nnet
705 (uri (cran-uri "nnet" version))
708 "0rws3rkd7dz1maz2mkld29jfrixjgacay8rqz7nmi82a2sw0nxgf"))))
709 (build-system r-build-system)
710 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
711 (synopsis "Feed-forward neural networks and multinomial log-linear models")
713 "This package provides functions for feed-forward neural networks with a
714 single hidden layer, and for multinomial log-linear models.")
715 (license (list license:gpl2+ license:gpl3+))))
717 (define-public r-rpart
724 (uri (cran-uri "rpart" version))
727 "0p22657j6ps6z1dn0ja2fhq4k5xd1rv3cpwzk6nmjd2si8jpbv17"))))
728 (build-system r-build-system)
729 (home-page "https://cran.r-project.org/web/packages/rpart")
730 (synopsis "Recursive partitioning and regression trees")
732 "This package provides recursive partitioning functions for
733 classification, regression and survival trees.")
734 (license (list license:gpl2+ license:gpl3+))))
736 (define-public r-spatial
743 (uri (cran-uri "spatial" version))
746 "1vwc7ingskdj1k4nq418x9yl3cw699pckb9xh5a1yp3g9plknqg5"))))
747 (build-system r-build-system)
748 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
749 (synopsis "Functions for kriging and point pattern analysis")
751 "This package provides functions for kriging and point pattern
753 ;; Either version may be picked.
754 (license (list license:gpl2 license:gpl3))))
756 (define-public r-survival
763 (uri (cran-uri "survival" version))
766 "0zrikancm9shixvgng89f1610sphlwljczi0fnjbdqn4l85rrarz"))))
767 (build-system r-build-system)
770 (home-page "https://github.com/therneau/survival")
771 (synopsis "Survival analysis")
773 "This package contains the core survival analysis routines, including
774 definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
775 curves, Cox models, and parametric accelerated failure time models.")
776 (license license:lgpl2.0+)))
779 (package (inherit r-minimal)
782 (build-system trivial-build-system)
783 (arguments '(#:builder (begin (mkdir %output) #t)))
809 (uri (cran-uri "bit" version))
812 "0s7isadibxp2wr62r5cpbyh9z31sczzfz4j3rm7gxgjfpqgq8174"))))
813 (build-system r-build-system)
816 (home-page "http://ff.r-forge.r-project.org")
817 (synopsis "Class for vectors of 1-bit booleans")
819 "This package provides bitmapped vectors of booleans (no @code{NA}s),
820 coercion from and to logicals, integers and integer subscripts, fast boolean
821 operators and fast summary statistics. With @code{bit} class vectors of true
822 binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
823 (license license:gpl2)))
825 (define-public r-bit64
832 (uri (cran-uri "bit64" version))
835 "0y0m7q1rwam1g88cjx7zyi07mj5dipxd9jkl90f294syx8k6ipr5"))))
836 (build-system r-build-system)
839 (home-page "http://ff.r-forge.r-project.org/")
840 (synopsis "S3 class for vectors of 64 bit integers")
842 "The bit64 package provides serializable S3 atomic 64 bit (signed)
843 integers that can be used in vectors, matrices, arrays and @code{data.frames}.
844 Methods are available for coercion from and to logicals, integers, doubles,
845 characters and factors as well as many elementwise and summary functions.
846 Many fast algorithmic operations such as @code{match} and @code{order} support
847 interactive data exploration and manipulation and optionally leverage
849 (license license:gpl2)))
851 (define-public r-chorddiag
859 (url "https://github.com/mattflor/chorddiag")
860 (commit (string-append "v" version))))
861 (file-name (git-file-name name version))
864 "1bpy9q861l1hyyiqbx2f7qzp7j7im8bkcfdwgxzk5fm0250p359a"))
865 ;; Delete minified JavaScript file
867 '(delete-file "inst/htmlwidgets/lib/d3/d3.min.js"))))
868 (build-system r-build-system)
871 (modify-phases %standard-phases
872 (add-after 'unpack 'process-javascript
873 (lambda* (#:key inputs #:allow-other-keys)
874 (with-directory-excursion "inst/htmlwidgets/lib/d3"
875 (let ((source (assoc-ref inputs "d3.v4.js"))
876 (target "d3.min.js"))
877 (format #true "Processing ~a --> ~a~%"
879 (invoke "esbuild" source "--minify"
880 (string-append "--outfile=" target)))))))))
882 (list r-htmlwidgets r-rcolorbrewer))
884 `(("esbuild" ,esbuild)
889 (uri "https://d3js.org/d3.v4.js")
892 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
893 (home-page "https://github.com/mattflor/chorddiag")
894 (synopsis "Create D3 chord diagram")
896 "This package provides tools to create interactive chords diagrams via
897 the D3 Javascript library. Chord diagrams show directed relationships among a
898 group of entities. This package is based on
899 @url{http://bl.ocks.org/mbostock/4062006} with some modifications (fading) and
900 additions (tooltips, bipartite diagram type).")
901 (license license:gpl3+)))
903 (define-public r-dichromat
910 (uri (cran-uri "dichromat" version))
912 (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
913 (build-system r-build-system)
914 (home-page "https://cran.r-project.org/web/packages/dichromat")
915 (synopsis "Color schemes for dichromats")
917 "Dichromat collapses red-green or green-blue distinctions to simulate the
918 effects of different types of color-blindness.")
919 (license license:gpl2+)))
921 (define-public r-digest
928 (uri (cran-uri "digest" version))
930 (base32 "1ncwc5fwsylwlcp9vhkhszw8m5sifg74apig2m2pf168lha1yb3r"))))
931 (build-system r-build-system)
932 ;; Vignettes require r-knitr, which requires r-digest, so we have to
933 ;; disable them and the tests.
936 #:configure-flags (list "--no-build-vignettes")))
937 (home-page "http://dirk.eddelbuettel.com/code/digest.html")
938 (synopsis "Create cryptographic hash digests of R objects")
940 "This package contains an implementation of a function @code{digest()} for
941 the creation of hash digests of arbitrary R objects (using the md5, sha-1,
942 sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
943 of R language objects, as well as a function @code{hmac()} to create hash-based
944 message authentication code.
946 Please note that this package is not meant to be deployed for cryptographic
947 purposes for which more comprehensive (and widely tested) libraries such as
948 OpenSSL should be used.")
949 (license license:gpl2+)))
951 (define-public r-estimability
953 (name "r-estimability")
957 (uri (cran-uri "estimability" version))
960 "0cifdaa71spkcxl4db4z884jrya865sg3dhcv4isd8fnzg2pjcd3"))))
961 (build-system r-build-system)
962 (home-page "https://cran.r-project.org/web/packages/estimability")
963 (synopsis "Tools for assessing estimability of linear predictions")
964 (description "Provides tools for determining estimability of linear
965 functions of regression coefficients, and @code{epredict} methods that handle
966 non-estimable cases correctly.")
967 (license license:gpl2+)))
969 (define-public r-labeling
976 (uri (cran-uri "labeling" version))
978 (base32 "0rfikd9gy70b8qz87q9axcwv8nmn9mbxfdwypxi0sghpfs9df8p0"))))
979 (build-system r-build-system)
980 (home-page "https://cran.r-project.org/web/packages/labeling")
981 (synopsis "Axis labeling algorithms")
982 (description "The labeling package provides a range of axis labeling
984 (license license:expat)))
986 (define-public r-magrittr
993 (uri (cran-uri "magrittr" version))
995 (base32 "19k3q76qlri459iyyfgn9gl0w9lnv9v604yhpbc94nx71l6zvrkv"))))
996 (build-system r-build-system)
997 ;; knitr needs magrittr
1000 `(("r-knitr" ,r-knitr)))
1001 (home-page "https://cran.r-project.org/web/packages/magrittr/index.html")
1002 (synopsis "Forward-pipe operator for R")
1004 "Magrittr provides a mechanism for chaining commands with a new
1005 forward-pipe operator, %>%. This operator will forward a value, or the result
1006 of an expression, into the next function call/expression. There is flexible
1007 support for the type of right-hand side expressions. For more information,
1008 see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
1009 (license license:expat)))
1011 (define-public r-munsell
1018 (uri (cran-uri "munsell" version))
1020 (base32 "16g1fzisbpqb15yh3pqf3iia4csppva5dnv1z88x9dg263xskwyh"))))
1021 (build-system r-build-system)
1023 (list r-colorspace))
1024 (home-page "https://cran.r-project.org/web/packages/munsell")
1025 (synopsis "Munsell colour system")
1027 "The Munsell package contains Functions for exploring and using the
1028 Munsell colour system.")
1029 (license license:expat)))
1031 (define-public r-permute
1038 (uri (cran-uri "permute" version))
1041 "1h4dyhcsv8p3h3qxsy98pib9v79dddvrnq7qx6abkblsazxqzy7g"))))
1042 (build-system r-build-system)
1043 (native-inputs (list r-knitr))
1044 ;; Tests do not run correctly, but running them properly would entail a
1045 ;; circular dependency with vegan.
1046 (home-page "https://github.com/gavinsimpson/permute")
1047 (synopsis "Functions for Generating Restricted Permutations of Data")
1049 "This package provides a set of restricted permutation designs for freely
1050 exchangeable, line transects (time series), spatial grid designs and permutation
1051 of blocks (groups of samples). @code{permute} also allows split-plot designs,
1052 in which the whole-plots or split-plots or both can be freely exchangeable.")
1053 (license license:gpl2+)))
1055 (define-public r-plyr
1062 (uri (cran-uri "plyr" version))
1064 (base32 "11sjjdn146w95s1vsfmmgdls082cbnm1slv98xvyjhsl2mpx4mga"))))
1065 (build-system r-build-system)
1066 (propagated-inputs (list r-rcpp))
1067 (home-page "http://had.co.nz/plyr")
1068 (synopsis "Tools for Splitting, Applying and Combining Data")
1070 "Plyr is a set of tools that solves a common set of problems: you need to
1071 break a big problem down into manageable pieces, operate on each piece and
1072 then put all the pieces back together. For example, you might want to fit a
1073 model to each spatial location or time point in your study, summarise data by
1074 panels or collapse high-dimensional arrays to simpler summary statistics.")
1075 (license license:expat)))
1077 (define-public r-proto
1084 (uri (cran-uri "proto" version))
1086 (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
1087 (build-system r-build-system)
1088 (home-page "https://github.com/hadley/proto")
1089 (synopsis "Prototype object-based programming")
1091 "Proto is an object oriented system using object-based, also called
1092 prototype-based, rather than class-based object oriented ideas.")
1093 (license license:gpl2+)))
1095 (define-public r-rcolorbrewer
1097 (name "r-rcolorbrewer")
1102 (uri (cran-uri "RColorBrewer" version))
1104 (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
1105 (build-system r-build-system)
1106 (home-page "https://cran.r-project.org/web/packages/RColorBrewer")
1107 (synopsis "ColorBrewer palettes")
1109 "This package provides color schemes for maps (and other graphics)
1110 designed by Cynthia Brewer as described at http://colorbrewer2.org")
1111 ;; Includes code licensed under bsd-4
1112 (license license:asl2.0)))
1114 (define-public r-sendmailr
1116 (name "r-sendmailr")
1121 (uri (cran-uri "sendmailR" version))
1124 "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
1125 (properties `((upstream-name . "sendmailR")))
1126 (build-system r-build-system)
1130 "https://cran.r-project.org/web/packages/sendmailR")
1131 (synopsis "Send email using R")
1133 "This package contains a simple SMTP client which provides a portable
1134 solution for sending email, including attachments, from within R.")
1135 (license license:gpl2+)))
1137 (define-public r-stringi
1144 (uri (cran-uri "stringi" version))
1147 "1v0rj5svgvn1mlf69yzm6jm00fxmrsxazs9xymzrf0apxjpxb8qf"))))
1148 (build-system r-build-system)
1149 (inputs (list icu4c))
1150 (native-inputs (list pkg-config))
1151 (home-page "http://stringi.rexamine.com/")
1152 (synopsis "Character string processing facilities")
1154 "This package allows for fast, correct, consistent, portable, as well as
1155 convenient character string/text processing in every locale and any native
1156 encoding. Owing to the use of the ICU library, the package provides R users
1157 with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
1158 programmers. Among available features there are: pattern searching
1159 (e.g. via regular expressions), random string generation, string collation,
1160 transliteration, concatenation, date-time formatting and parsing, etc.")
1161 (license license:bsd-3)))
1163 (define-public r-stringr
1170 (uri (cran-uri "stringr" version))
1172 (base32 "1p9ip7p87gbbg4s6d3d392svvzz2b5dqdq2c8ilgvn4s78nlsq47"))))
1173 (build-system r-build-system)
1175 (list r-glue r-magrittr r-stringi))
1176 (home-page "https://github.com/hadley/stringr")
1177 (synopsis "Simple, consistent wrappers for common string operations")
1179 "Stringr is a consistent, simple and easy to use set of wrappers around
1180 the fantastic @code{stringi} package. All function and argument names (and
1181 positions) are consistent, all functions deal with \"NA\"'s and zero length
1182 vectors in the same way, and the output from one function is easy to feed into
1183 the input of another.")
1184 (license license:gpl2+)))
1186 (define-public r-reshape2
1193 (uri (cran-uri "reshape2" version))
1195 (base32 "1n0jrajpvc8hjkh9z4g8bwq63qy5vy5cgl2pzjardyih4ngcz3fq"))))
1196 (build-system r-build-system)
1198 (list r-plyr r-rcpp r-stringr))
1199 (home-page "https://github.com/hadley/reshape")
1200 (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
1202 "Reshape2 is an R library to flexibly restructure and aggregate data
1203 using just two functions: melt and dcast (or acast).")
1204 (license license:expat)))
1206 (define-public r-ggplot2
1213 (uri (cran-uri "ggplot2" version))
1215 (base32 "1si46bf9p09qzs208hqffwcb40305p361whmwhc1pwrsmx7jjxdh"))))
1216 (build-system r-build-system)
1227 r-svglite ; Needed for 'ggsave'
1231 (home-page "https://ggplot2.tidyverse.org")
1232 (synopsis "Implementation of the grammar of graphics")
1234 "Ggplot2 is an implementation of the grammar of graphics in R. It
1235 combines the advantages of both base and lattice graphics: conditioning and
1236 shared axes are handled automatically, and you can still build up a plot step
1237 by step from multiple data sources. It also implements a sophisticated
1238 multidimensional conditioning system and a consistent interface to map data to
1239 aesthetic attributes.")
1240 (license license:gpl2+)))
1242 (define-public r-ggdendro
1248 (uri (cran-uri "ggdendro" version))
1251 "0skbj487b6f6pj2iz4yq2b9gbgb39cv5dyzhdl3w7ay1k0s5z9ph"))))
1252 (build-system r-build-system)
1254 (list r-ggplot2 r-mass))
1257 (home-page "https://github.com/andrie/ggdendro")
1258 (synopsis "Create Dendrograms and Tree Diagrams Using ggplot2")
1259 (description "This is a set of tools for dendrograms and tree plots using
1260 ggplot2. The ggplot2 philosophy is to clearly separate data from the
1261 presentation. Unfortunately the plot method for dendrograms plots directly
1262 to a plot device with out exposing the data. The ggdendro package resolves
1263 this by making available functions that extract the dendrogram plot data.
1264 The package provides implementations for tree, rpart, as well as diana and
1265 agnes cluster diagrams.")
1266 (license license:gpl2+)))
1268 (define-public r-gdtools
1275 (uri (cran-uri "gdtools" version))
1278 "1p3ip0qwpg8f63jfx0b8vbac6l20ddid8xvxzkfi6i858pybnawp"))))
1279 (build-system r-build-system)
1283 (list cairo freetype zlib))
1285 (list r-rcpp r-systemfonts))
1286 (home-page "https://cran.r-project.org/web/packages/gdtools")
1287 (synopsis "Utilities for graphical rendering")
1289 "The @code{gdtools} package provides functionalities to get font metrics
1290 and to generate base64 encoded string from raster matrix.")
1291 (license license:gpl3)))
1293 (define-public r-svglite
1300 (uri (cran-uri "svglite" version))
1303 "19ggknw5322yw7r1bzhw0bqggcrpn0qxddk7kblpqnra2zz2brkn"))))
1304 (build-system r-build-system)
1308 (list r-cpp11 r-systemfonts))
1311 (home-page "https://github.com/hadley/svglite")
1312 (synopsis "SVG graphics device")
1314 "@code{svglite} is a graphics device that produces clean
1315 @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
1316 hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
1317 considerably faster, produces smaller files, and leaves text as is.")
1318 (license license:gpl2+)))
1320 (define-public r-assertthat
1322 (name "r-assertthat")
1326 (uri (cran-uri "assertthat" version))
1329 "17wy5bdfzg73sg2clisg1k3zyn1adkj59x56m5nwia2k8z67zkw5"))))
1330 (build-system r-build-system)
1331 (home-page "https://github.com/hadley/assertthat")
1332 (synopsis "Easy pre and post assertions")
1334 "Assertthat is an extension to stopifnot() that makes it easy to declare
1335 the pre and post conditions that your code should satisfy, while also
1336 producing friendly error messages so that your users know what they've done
1338 (license license:gpl3+)))
1340 (define-public r-lazyeval
1346 (uri (cran-uri "lazyeval" version))
1349 "1m10i059csrcqkcn59a8wspn784alxsq3symzhn24mhhl894346n"))))
1350 (build-system r-build-system)
1351 (home-page "https://github.com/hadley/lazyeval")
1352 (synopsis "Lazy (non-standard) evaluation in R")
1354 "This package provides the tools necessary to do non-standard
1355 evaluation (NSE) in R.")
1356 (license license:gpl3+)))
1358 (define-public r-dbi
1364 (uri (cran-uri "DBI" version))
1367 "0n2gf5flmcrkad7p0pzsnsgwjl5006yi7lyz9lisqxhw8xykgv2n"))))
1368 (build-system r-build-system)
1371 (home-page "https://github.com/rstats-db/DBI")
1372 (synopsis "R database interface")
1374 "The DBI package provides a database interface (DBI) definition for
1375 communication between R and relational database management systems. All
1376 classes in this package are virtual and need to be extended by the various
1377 R/DBMS implementations.")
1378 (license license:lgpl2.0+)))
1383 (version "1.78.0-0")
1386 (uri (cran-uri "BH" version))
1389 "1cwc1q8w9d6i81nclgi7lycsnpj0dcbxlv9rdb0f04r0d03rv7iv"))))
1390 (build-system r-build-system)
1391 (home-page "https://github.com/eddelbuettel/bh")
1392 (synopsis "R package providing subset of Boost headers")
1394 "This package aims to provide the most useful subset of Boost libraries
1395 for template use among CRAN packages.")
1396 (license license:boost1.0)))
1398 (define-public r-evaluate
1404 (uri (cran-uri "evaluate" version))
1407 "0a2y7j534gbgixkwj9r1z76l2vssw4g1hznzbpclc076wkdqpj58"))))
1408 (build-system r-build-system)
1409 (home-page "https://github.com/hadley/evaluate")
1410 (synopsis "Parsing and evaluation tools for R")
1412 "This package provides tools that allow you to recreate the parsing,
1413 evaluation and display of R code, with enough information that you can
1414 accurately recreate what happens at the command line. The tools can easily be
1415 adapted for other output formats, such as HTML or LaTeX.")
1416 (license license:gpl3+)))
1418 (define-public r-formatr
1424 (uri (cran-uri "formatR" version))
1427 "0353aj975mj0yjc91z76bbfy86y7d5cvlqqyfr93cdng14nnd0dx"))))
1428 (build-system r-build-system)
1431 (home-page "https://yihui.org/formatr/")
1432 (synopsis "Format R code automatically")
1434 "This package provides a function to format R source code. Spaces and
1435 indent will be added to the code automatically, and comments will be preserved
1436 under certain conditions, so that R code will be more human-readable and tidy.
1437 There is also a Shiny app as a user interface in this package.")
1438 (license license:gpl3+)))
1440 (define-public r-highr
1446 (uri (cran-uri "highr" version))
1449 "0kgdv2vf1lz3b5kbal9s83gg6812nw7fvrq0rkyr0v4k1lwi3zxy"))))
1450 (build-system r-build-system)
1453 ;; We cannot add knitr to the inputs, because highr depends on xfun, which
1454 ;; is an input to knitr.
1457 `(("r-knitr" ,r-knitr)))
1458 (home-page "https://github.com/yihui/highr")
1459 (synopsis "Syntax highlighting for R source code")
1461 "This package provides syntax highlighting for R source code. Currently
1462 it supports LaTeX and HTML output. Source code of other languages is
1463 supported via Andre Simon's highlight package.")
1464 (license license:gpl3+)))
1466 (define-public r-mime
1472 (uri (cran-uri "mime" version))
1475 "0j9qbq9jfsp61h2d0xmb87pa2wi8nhb1h2wih7l5drf1sr8i0059"))))
1476 (build-system r-build-system)
1477 (home-page "https://github.com/yihui/mime")
1478 (synopsis "R package to map filenames to MIME types")
1480 "This package guesses the MIME type from a filename extension using the
1481 data derived from /etc/mime.types in UNIX-type systems.")
1482 (license license:gpl2)))
1484 (define-public r-markdown
1490 (uri (cran-uri "markdown" version))
1493 "06zwbrp14bri3470anadd7dvgmw06xf8df6v2pk64wx3f9sd934d"))))
1494 (build-system r-build-system)
1495 ;; Skip check phase because the tests require the r-knitr package to be
1496 ;; installed. This prevents installation failures. Knitr normally
1497 ;; shouldn't be available since r-markdown is a dependency of the r-knitr
1499 (arguments `(#:tests? #f))
1501 (list r-mime r-xfun))
1502 (home-page "https://github.com/rstudio/markdown")
1503 (synopsis "Markdown rendering for R")
1505 "This package provides R bindings to the Sundown Markdown rendering
1506 library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
1507 syntax that can be converted to XHTML or other formats.")
1508 (license license:gpl2)))
1510 (define-public r-yaml
1516 (uri (cran-uri "yaml" version))
1519 "0c7pk5fq79mkqpc398hg8zj01frv4araglyppli49sqr4yx6mp55"))))
1520 (build-system r-build-system)
1521 (home-page "https://cran.r-project.org/web/packages/yaml/")
1522 (synopsis "Methods to convert R data to YAML and back")
1524 "This package implements the libyaml YAML 1.1 parser and
1525 emitter (http://pyyaml.org/wiki/LibYAML) for R.")
1526 (license license:bsd-3)))
1528 (define-public r-knitr
1534 (uri (cran-uri "knitr" version))
1537 "0qyp78v3hz4qimlc3w4hj5dzp44n2w085ay0l1zvxsxs9142mk9r"))))
1538 (build-system r-build-system)
1540 (list r-evaluate r-highr r-stringr r-xfun r-yaml))
1541 (home-page "https://yihui.org/knitr/")
1542 (synopsis "General-purpose package for dynamic report generation in R")
1544 "This package provides a general-purpose tool for dynamic report
1545 generation in R using Literate Programming techniques.")
1546 ;; The code is released under any version of the GPL. As it is used by
1547 ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
1549 (license license:gpl2+)))
1551 (define-public r-knitrbootstrap
1553 (name "r-knitrbootstrap")
1558 (uri (cran-uri "knitrBootstrap" version))
1561 "1aj60j7f0gcs120fdrnfbnb7vk7lfn1phil0mghg6a5zldz4cqs3"))))
1562 (properties `((upstream-name . "knitrBootstrap")))
1563 (build-system r-build-system)
1565 (list r-knitr r-rmarkdown r-markdown))
1566 (home-page "https://github.com/jimhester/knitrBootstrap")
1567 (synopsis "Knitr bootstrap framework")
1569 "This package provides a framework to create Bootstrap 3 HTML reports
1570 from knitr Rmarkdown.")
1571 (license license:expat)))
1573 (define-public r-microbenchmark
1575 (name "r-microbenchmark")
1579 (uri (cran-uri "microbenchmark" version))
1582 "1lpzpffnjiwnxxl0jhrvyj88fvxqksnpccbpq953xwqf6ypjqga4"))))
1583 (build-system r-build-system)
1584 (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
1585 (synopsis "Accurate timing functions for R")
1587 "This package provides infrastructure to accurately measure and compare
1588 the execution time of R expressions.")
1589 (license license:bsd-2)))
1591 (define-public r-pryr
1597 (uri (cran-uri "pryr" version))
1600 "02vp1y7zhv22id43j5c0gdcgn9171dyypqp8rqrlc3w5a7n565kv"))))
1601 (build-system r-build-system)
1603 (list r-codetools r-lobstr r-rcpp r-stringr))
1604 (home-page "https://github.com/hadley/pryr")
1605 (synopsis "Tools for computing on the R language")
1607 "This package provides useful tools to pry back the covers of R and
1608 understand the language at a deeper level.")
1609 (license license:gpl2)))
1611 (define-public r-memoise
1617 (uri (cran-uri "memoise" version))
1620 "1srdzv2bp0splislrabmf1sfbqfi3hn189nq7kxhgjn8k3p38l7q"))))
1621 (build-system r-build-system)
1623 (list r-cachem r-rlang))
1624 (home-page "https://github.com/hadley/memoise")
1625 (synopsis "Memoise functions for R")
1627 "This R package caches the results of a function so that when
1628 you call it again with the same arguments it returns the pre-computed value.")
1629 (license license:expat)))
1631 (define-public r-crayon
1637 (uri (cran-uri "crayon" version))
1640 "0mxq87qsvz5znfncrb6yjchzv6iwpn9lr386i02y6xiycizkjd7f"))))
1641 (build-system r-build-system)
1642 (home-page "https://github.com/gaborcsardi/crayon")
1643 (synopsis "Colored terminal output for R")
1645 "Colored terminal output on terminals that support ANSI color and
1646 highlight codes. It also works in Emacs ESS. ANSI color support is
1647 automatically detected. Colors and highlighting can be combined and nested.
1648 New styles can also be created easily. This package was inspired by the
1649 \"chalk\" JavaScript project.")
1650 (license license:expat)))
1652 (define-public r-praise
1659 (uri (cran-uri "praise" version))
1662 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
1663 (build-system r-build-system)
1664 (home-page "https://github.com/gaborcsardi/praise")
1665 (synopsis "Functions to praise users")
1667 "This package provides template functions to assist in building friendly
1668 R packages that praise their users.")
1669 (license license:expat)))
1671 (define-public r-testthat
1677 (uri (cran-uri "testthat" version))
1680 "0ndnmv3gbhlsyqya382wqfkkhlrgpdjmh7mymsv6ja52ihbachgd"))))
1681 (build-system r-build-system)
1704 (home-page "https://github.com/hadley/testthat")
1705 (synopsis "Unit testing for R")
1707 "This package provides a unit testing system for R designed to be fun,
1708 flexible and easy to set up.")
1709 (license license:expat)))
1717 (uri (cran-uri "R6" version))
1720 "0j5z0b0myzjyyykk310xsa9n2mcm9bz8yqbq4xgz2yzdq8lvv4ld"))))
1721 (build-system r-build-system)
1722 (home-page "https://github.com/wch/R6/")
1723 (synopsis "Classes with reference semantics in R")
1725 "The R6 package allows the creation of classes with reference semantics,
1726 similar to R's built-in reference classes. Compared to reference classes, R6
1727 classes are simpler and lighter-weight, and they are not built on S4 classes
1728 so they do not require the methods package. These classes allow public and
1729 private members, and they support inheritance, even when the classes are
1730 defined in different packages.")
1731 (license license:expat)))
1733 (define-public r-rlang
1739 (uri (cran-uri "rlang" version))
1742 "0skf75rhq9y6f09shcjlm1dlh7rlwpyr4mx1l8xn201igg4k8qdb"))))
1743 (build-system r-build-system)
1744 (home-page "http://rlang.tidyverse.org")
1745 (synopsis "Functions for base types, core R and Tidyverse features")
1746 (description "This package provides a toolbox for working with base types,
1747 core R features like the condition system, and core @code{Tidyverse} features
1748 like tidy evaluation.")
1749 (license license:gpl3)))
1751 (define-public r-tibble
1758 (uri (cran-uri "tibble" version))
1761 "14l2i6ri3v5y0h8g0ahc4kz0pdqsp5yabxk2w8wavss6y44xjcsv"))))
1762 (build-system r-build-system)
1774 (home-page "https://github.com/hadley/tibble")
1775 (synopsis "Simple data frames")
1777 "This package provides a @code{tbl_df} class that offers better checking
1778 and printing capabilities than traditional data frames.")
1779 (license license:expat)))
1781 (define-public r-dplyr
1787 (uri (cran-uri "dplyr" version))
1790 "0g8jsxclj9cgm7a2lyazy78sj62rbzw812lsw3fdsbz0pknkmznj"))))
1791 (build-system r-build-system)
1806 (home-page "https://github.com/hadley/dplyr")
1807 (synopsis "Tools for working with data frames in R")
1809 "dplyr is the next iteration of plyr. It is focused on tools for
1810 working with data frames. It has three main goals: 1) identify the most
1811 important data manipulation tools needed for data analysis and make them easy
1812 to use in R; 2) provide fast performance for in-memory data by writing key
1813 pieces of code in C++; 3) use the same code interface to work with data no
1814 matter where it is stored, whether in a data frame, a data table or
1816 (license license:expat)))
1818 (define-public r-dbplyr
1825 (uri (cran-uri "dbplyr" version))
1828 "025wqpmxdhzblb0pf58m3qh5h6bf5x8qvkf47vyl1cjsp13wz95b"))))
1829 (build-system r-build-system)
1848 (home-page "https://github.com/tidyverse/dbplyr")
1849 (synopsis "Dplyr back end for databases")
1851 "This package provides a dplyr back end for databases that allows you to
1852 work with remote database tables as if they are in-memory data frames. Basic
1853 features works with any database that has a @code{DBI} back end; more advanced
1854 features require SQL translation to be provided by the package author.")
1855 (license license:expat)))
1857 (define-public r-acepack
1864 (uri (cran-uri "acepack" version))
1867 "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
1868 (build-system r-build-system)
1871 (home-page "https://cran.r-project.org/web/packages/acepack")
1872 (synopsis "Functions for regression transformations")
1874 "This package provides ACE and AVAS methods for choosing regression
1876 (license license:expat)))
1878 (define-public r-formula
1885 (uri (cran-uri "Formula" version))
1888 "1bsw282i5m8rlirbhz7hqvf25zbxschk7yrp152whbzdnmry6w6b"))))
1889 (properties `((upstream-name . "Formula")))
1890 (build-system r-build-system)
1891 (home-page "https://cran.r-project.org/web/packages/Formula")
1892 (synopsis "Extended model formulas")
1894 "This package provides a new class @code{Formula}, which extends the base
1895 class @code{formula}. It supports extended formulas with multiple parts of
1896 regressors on the right-hand side and/or multiple responses on the left-hand
1898 (license (list license:gpl2+ license:gpl3+))))
1900 (define-public r-locfit
1907 (uri (cran-uri "locfit" version))
1910 "1vcw16qww4v4547w0gfvhqg60l051bsdlxa6zfcgcj9xbxf6dlyr"))))
1911 (build-system r-build-system)
1914 (home-page "https://cran.r-project.org/web/packages/locfit")
1915 (synopsis "Local regression, likelihood and density estimation")
1917 "This package provides functions used for local regression, likelihood
1918 and density estimation.")
1919 (license (list license:gpl2+ license:gpl3+))))
1921 (define-public r-chron
1927 (uri (cran-uri "chron" version))
1930 "0p9zz96jfyf139924hdwkzhr8knkjvx6547ac53rknm3a6wwngl6"))))
1931 (build-system r-build-system)
1932 (home-page "https://cran.r-project.org/web/packages/chron")
1933 (synopsis "Chronological R objects which can handle dates and times")
1935 "This package provides chronological R objects which can handle dates and
1937 (license license:gpl2)))
1939 (define-public r-data-table
1941 (name "r-data-table")
1945 (uri (cran-uri "data.table" version))
1948 "0arx5wna0sh0vf5q8rjhh8nqdmnvg2pdpbhljl9l0x4kwm8vjhgp"))))
1949 (build-system r-build-system)
1953 (list pkg-config r-knitr))
1954 (home-page "https://github.com/Rdatatable/data.table/wiki")
1955 (synopsis "Enhanced version of data.frame R object")
1957 "The R package @code{data.table} is an extension of @code{data.frame}
1958 providing functions for fast aggregation of large data (e.g. 100GB in RAM),
1959 fast ordered joins, fast add/modify/delete of columns by group, column listing
1960 and fast file reading.")
1961 (license license:gpl3+)))
1963 (define-public r-xtable
1970 (uri (cran-uri "xtable" version))
1973 "077xfm0gphvhsay75amd9v90zk57kjgrrlgih04fyrbqqblc1gjs"))))
1974 (build-system r-build-system)
1976 (list r-knitr)) ; for vignettes
1977 (home-page "http://xtable.r-forge.r-project.org/")
1978 (synopsis "Export R tables to LaTeX or HTML")
1980 "This package provides tools to export R data as LaTeX and HTML tables.")
1981 (license license:gpl2+)))
1983 (define-public python-patsy
1985 (name "python-patsy")
1989 (uri (pypi-uri "patsy" version))
1992 "17dn72519gvwifw3i8mzwlslxmxkl8ihzfrxg1iblsk70iwdwlsh"))))
1993 (build-system python-build-system)
1996 (modify-phases %standard-phases
1998 (lambda* (#:key tests? #:allow-other-keys)
1999 (when tests? (invoke "pytest" "-vv")))))))
2001 (list python-numpy python-scipy python-six))
2003 (list python-pytest))
2004 (home-page "https://github.com/pydata/patsy")
2005 (synopsis "Describe statistical models and build design matrices")
2007 "Patsy is a Python package for describing statistical models and for
2008 building design matrices.")
2009 ;; The majority of the code is distributed under BSD-2. The module
2010 ;; patsy.compat contains code derived from the Python standard library,
2011 ;; and is covered by the PSFL.
2012 (license (list license:bsd-2 license:psfl))))
2014 (define-public python2-patsy
2015 (package-with-python2 python-patsy))
2017 (define-public python-statsmodels
2019 (name "python-statsmodels")
2024 (uri (pypi-uri "statsmodels" version))
2026 (base32 "0sbsyxgpzhys5padhkhrj71z4i1q41sm938pz0x8ff6jjvcchvh0"))
2027 (modules '((guix build utils)))
2030 (for-each delete-file (find-files "." "\\.c$"))))))
2031 (build-system python-build-system)
2033 `(;; The test suite is very large and rather brittle. Tests often fail
2034 ;; because of minor changes in dependencies that upstream hasn't fixed
2035 ;; in a new release.
2038 (modify-phases %standard-phases
2039 (add-after 'unpack 'set-matplotlib-backend-to-agg
2041 ;; Set the matplotlib backend to Agg to avoid problems using the
2042 ;; GTK backend without a display.
2043 (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py")
2044 '("statsmodels/tsa/vector_ar/tests/test_var.py"
2045 "statsmodels/duration/tests/test_survfunc.py"))
2046 (("import matplotlib\\.pyplot as plt" line)
2047 (string-append "import matplotlib;matplotlib.use('Agg');"
2051 (list python-numpy python-scipy python-pandas python-patsy
2054 (list python-cython python-nose python-sphinx))
2055 (home-page "http://statsmodels.sourceforge.net/")
2056 (synopsis "Statistical modeling and econometrics in Python")
2058 "Statsmodels is a Python package that provides a complement to scipy for
2059 statistical computations including descriptive statistics and estimation and
2060 inference for statistical models.")
2061 (license license:bsd-3)))
2063 (define-public python2-statsmodels
2064 (let ((stats (package-with-python2 python-statsmodels)))
2065 (package/inherit stats
2066 ;; Version 0.11.1 and later does not work with Python 2. It may build
2067 ;; fine but loading modules fails.
2072 (uri (pypi-uri "statsmodels" version))
2075 "0fxs8a7sp4d7jvqlm36yi45i2d28kjfvraf9q8i9jr1chhxgjqb4"))))
2077 `(("python2-pytz" ,python2-pytz)
2078 ("python2-numpy" ,python2-numpy)
2079 ("python2-scipy" ,python2-scipy)
2080 ("python2-pandas" ,python2-pandas)
2081 ("python2-patsy" ,python2-patsy)
2082 ("python2-matplotlib" ,python2-matplotlib))))))
2084 (define-public r-coda
2090 (uri (cran-uri "coda" version))
2093 "13z5dwfpnyyhpsbpg4xr9g5c1685jhqj90f4x4qkcykr6kykqba2"))))
2094 (build-system r-build-system)
2097 (home-page "https://cran.r-project.org/web/packages/coda")
2098 (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
2099 (description "This package provides functions for summarizing and plotting
2100 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
2101 diagnostic tests of convergence to the equilibrium distribution of the Markov
2103 (license license:gpl2+)))
2105 (define-public r-ade4
2112 (uri (cran-uri "ade4" version))
2115 "09f5kh2mwygqpnvf53k0r54k0cvaafxm9x4nm819gwv05k2g9dpc"))))
2116 (build-system r-build-system)
2118 (list r-mass r-pixmap r-sp))
2119 (home-page "http://pbil.univ-lyon1.fr/ADE-4")
2120 (synopsis "Multivariate data analysis and graphical display")
2122 "The ade4 package contains data analysis functions to analyze ecological
2123 and environmental data in the framework of Euclidean exploratory methods.")
2124 (license license:gpl2+)))
2126 (define-public r-xml2
2133 (uri (cran-uri "xml2" version))
2136 "138w7hb487al9cbahmnk5rhi23k8a9g7nk7s5dyxd3k1646rqknb"))))
2137 (build-system r-build-system)
2139 (list libxml2 zlib))
2141 (list pkg-config r-knitr))
2142 (home-page "https://github.com/hadley/xml2")
2143 (synopsis "Parse XML with R")
2145 "This package provides a simple, consistent interface to working with XML
2146 files in R. It is built on top of the libxml2 C library.")
2147 (license license:gpl2+)))
2149 (define-public r-multitaper
2151 (name "r-multitaper")
2156 (uri (cran-uri "multitaper" version))
2159 "1gm3wr8xqpqiby7q1dr3zxim77v0bvvrqi0hlazf5g3gnkrp2zc3"))))
2160 (build-system r-build-system)
2163 (home-page "https://github.com/wesleyburr/multitaper/")
2164 (synopsis "Multitaper spectral analysis tools")
2166 "This package implements multitaper spectral estimation
2167 techniques using prolate spheroidal sequences (Slepians) and sine
2168 tapers for time series analysis. It includes an adaptive weighted
2169 multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
2170 F-test, and complex demodulation. The Slepians sequences are
2171 generated efficiently using a tridiagonal matrix solution, and
2172 jackknifed confidence intervals are available for most estimates.")
2173 (license license:gpl2+)))
2175 (define-public r-rversions
2177 (name "r-rversions")
2181 (uri (cran-uri "rversions" version))
2184 "1cbwwbz8lqx2n33xr4q904whvld22s63rpyy1nn93395l7ssrakr"))))
2185 (build-system r-build-system)
2187 (list r-curl r-xml2))
2188 (home-page "https://github.com/metacran/rversions")
2189 (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
2191 "This package provides functions to query the main R repository to find
2192 the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
2193 previous R versions and their release dates.")
2194 (license license:expat)))
2196 (define-public r-whisker
2202 (uri (cran-uri "whisker" version))
2205 "1a7vz0dk95xfjvi38wbpw8vmf5qn3g8p490msz2rw0piwidmk1ks"))))
2206 (build-system r-build-system)
2207 (home-page "https://github.com/edwindj/whisker")
2208 (synopsis "Logicless mustache templating for R")
2210 "This package provides logicless templating, with a syntax that is not
2212 (license license:gpl3+)))
2214 (define-public r-backports
2216 (name "r-backports")
2221 (uri (cran-uri "backports" version))
2224 "0x144hij0rzhrxdq3k5ph8fk7pdgl1avjca25j4mlpmhzdckqp44"))))
2225 (build-system r-build-system)
2226 (home-page "https://cran.r-project.org/web/packages/backports")
2227 (synopsis "Reimplementations of functions introduced since R 3.0.0")
2229 "Provides implementations of functions which have been introduced in R
2230 since version 3.0.0. The backports are conditionally exported which results
2231 in R resolving the function names to the version shipped with R (if available)
2232 and uses the implemented backports as fallback. This way package developers
2233 can make use of the new functions without worrying about the minimum required
2235 (license license:gpl2+)))
2237 (define-public r-checkmate
2239 (name "r-checkmate")
2244 (uri (cran-uri "checkmate" version))
2247 "193gkifr9spp0x0rwnjq1spdhjkfkh4mv27iklskcj604075phhd"))))
2248 (build-system r-build-system)
2251 (home-page "https://github.com/mllg/checkmate")
2252 (synopsis "Fast and versatile argument checks")
2254 "This package provides tests and assertions to perform frequent argument
2255 checks. A substantial part of the package was written in C to minimize any
2256 worries about execution time overhead.")
2257 (license license:bsd-3)))
2259 (define-public r-bbmisc
2266 (uri (cran-uri "BBmisc" version))
2269 "1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y"))))
2270 (properties `((upstream-name . "BBmisc")))
2271 (build-system r-build-system)
2274 (home-page "https://github.com/berndbischl/BBmisc")
2275 (synopsis "Miscellaneous functions for R package development")
2277 "This package provides miscellaneous helper functions for the development
2279 (license license:bsd-3)))
2281 (define-public r-fail
2288 (uri (cran-uri "fail" version))
2291 "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
2292 (build-system r-build-system)
2294 (list r-bbmisc r-checkmate))
2295 (home-page "https://github.com/mllg/fail")
2296 (synopsis "File abstraction interface layer (FAIL)")
2298 "This package provides a more comfortable interface to work with R data
2299 or source files in a key-value fashion.")
2300 (license license:bsd-3)))
2302 (define-public r-batchjobs
2304 (name "r-batchjobs")
2309 (uri (cran-uri "BatchJobs" version))
2312 "1zz4sspj596pijxlz321g0jy2rg9ki83j6fihbwisjwr66p2vk1m"))))
2313 (properties `((upstream-name . "BatchJobs")))
2314 (build-system r-build-system)
2326 (home-page "https://github.com/tudo-r/BatchJobs")
2327 (synopsis "Batch computing with R")
2329 "This package provides @code{Map}, @code{Reduce} and @code{Filter}
2330 variants to generate jobs on batch computing systems like PBS/Torque, LSF,
2331 SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
2332 (license license:bsd-2)))
2334 (define-public r-brew
2340 (uri (cran-uri "brew" version))
2343 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
2344 (build-system r-build-system)
2345 (home-page "https://cran.r-project.org/web/packages/brew")
2346 (synopsis "Templating framework for report generation")
2348 "The brew package implements a templating framework for mixing text and R
2349 code for report generation. The template syntax is similar to PHP, Ruby's erb
2350 module, Java Server Pages, and Python's psp module.")
2351 (license license:gpl2+)))
2353 (define-public r-desc
2360 (uri (cran-uri "desc" version))
2363 "0jfnwn1kpiill8v4hmzdk90yz4gk2ha0prr2p0hq36s40v3y8842"))))
2364 (build-system r-build-system)
2366 (list r-crayon r-r6 r-rprojroot))
2367 (home-page "https://github.com/r-pkgs/desc")
2368 (synopsis "Manipulate DESCRIPTION Files")
2370 "This package provides tools to read, write, create, and manipulate
2371 DESCRIPTION files. It is intended for packages that create or manipulate
2373 (license license:expat)))
2375 (define-public r-commonmark
2377 (name "r-commonmark")
2382 (uri (cran-uri "commonmark" version))
2385 "024iz1qp2kv6iz6y69ir0jk3qhjps86rhkzlcmhqsxx97rx7cjni"))))
2386 (build-system r-build-system)
2387 (home-page "https://cran.r-project.org/web/packages/commonmark")
2388 (synopsis "CommonMark and Github Markdown Rendering in R")
2390 "The CommonMark specification defines a rationalized version of markdown
2391 syntax. This package uses the @code{cmark} reference implementation for
2392 converting markdown text into various formats including HTML, LaTeX and groff
2393 man. In addition, it exposes the markdown parse tree in XML format. The latest
2394 version of this package also adds support for Github extensions including
2395 tables, autolinks and strikethrough text.")
2396 (license license:bsd-2)))
2398 (define-public r-roxygen2
2404 (uri (cran-uri "roxygen2" version))
2407 "1zf55wywlpy7mk7zfyi3s9fhhg1m9kvafzj46iqw5cbvnlg3ssdk"))))
2408 (build-system r-build-system)
2425 (home-page "https://github.com/klutometis/roxygen")
2426 (synopsis "In-source documentation system for R")
2428 "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
2429 collation, and NAMESPACE files.")
2430 (license license:gpl2+)))
2432 (define-public r-openssl
2439 (uri (cran-uri "openssl" version))
2442 "0na3yficxg0hjql9pvz96f66yh4g5k2hfwcricb705z7f2pk5f23"))))
2443 (build-system r-build-system)
2447 '(modify-phases %standard-phases
2448 (add-after 'unpack 'do-not-use-versioned-linking
2450 (substitute* "configure"
2451 (("PKG_LIBS=\"\\$\\{PKG_LIBS_VERSIONED\\}\"")
2452 "PKG_LIBS=\"${PKG_LIBS}\"")))))))
2456 (list pkg-config r-knitr))
2459 (home-page "https://github.com/jeroenooms/openssl")
2460 (synopsis "Toolkit for encryption, signatures and certificates")
2462 "This package provides R bindings to OpenSSL libssl and libcrypto, plus
2463 custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
2464 and P-521. Cryptographic signatures can either be created and verified
2465 manually or via x509 certificates. AES block cipher is used in CBC mode for
2466 symmetric encryption; RSA for asymmetric (public key) encryption. High-level
2467 envelope functions combine RSA and AES for encrypting arbitrary sized data.
2468 Other utilities include key generators, hash functions (md5, sha1, sha256,
2469 etc), base64 encoder, a secure random number generator, and @code{bignum} math
2470 methods for manually performing crypto calculations on large multibyte
2472 (license license:expat)))
2474 (define-public r-httr
2480 (uri (cran-uri "httr" version))
2483 "1y8y1g1dkgv9jafrk1kj6pzxpw95c0rr9lplblfq2byrs1pfsas6"))))
2484 (build-system r-build-system)
2486 (list r-curl r-jsonlite r-openssl r-mime r-r6))
2489 (home-page "https://github.com/hadley/httr")
2490 (synopsis "Tools for working with URLs and HTTP")
2492 "The aim of httr is to provide a wrapper for RCurl customised to the
2493 demands of modern web APIs. It provides useful tools for working with HTTP
2494 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
2495 functions make it easy to control additional request components.")
2496 (license license:expat)))
2498 (define-public r-git2r
2504 (uri (cran-uri "git2r" version))
2507 "13nlrhma6kavvhranb43w3003vadfkyrn2f4l3r63iqavj0s3xzq"))))
2508 (build-system r-build-system)
2510 (list libgit2 zlib))
2513 (home-page "https://github.com/ropensci/git2r")
2514 (synopsis "Access Git repositories with R")
2516 "This package provides an R interface to the libgit2 library, which is a
2517 pure C implementation of the Git core methods.")
2518 ;; GPLv2 only with linking exception.
2519 (license license:gpl2)))
2521 (define-public r-rstudioapi
2523 (name "r-rstudioapi")
2527 (uri (cran-uri "rstudioapi" version))
2530 "12vdfzzjc6mv4h105l8cp108j3hjk0mqmg23m6mqr3jarfymphxa"))))
2531 (build-system r-build-system)
2534 (home-page "https://cran.r-project.org/web/packages/rstudioapi")
2535 (synopsis "Safely access the RStudio API")
2537 "This package provides functions to access the RStudio API and provide
2538 informative error messages when it's not available.")
2539 (license license:expat)))
2541 (define-public r-devtools
2547 (uri (cran-uri "devtools" version))
2550 "0kvbw218jp8pd2lgdjyn94v2iji75s385hkn1qbikcm0pjlmj8g4"))))
2551 (build-system r-build-system)
2575 (home-page "https://github.com/hadley/devtools")
2576 (synopsis "Tools to make developing R packages easier")
2577 (description "The devtools package is a collection of package development
2578 tools to simplify the devolpment of R packages.")
2579 (license license:gpl2+)))
2581 (define-public r-withr
2587 (uri (cran-uri "withr" version))
2590 "0k4x2bd9wb24n3dyg7rdjicdjs5ay2kk5lfgkrcjsv6cki2wgnlv"))))
2591 (build-system r-build-system)
2594 (home-page "https://github.com/jimhester/withr")
2595 (synopsis "Run code with temporarily modified global state")
2597 "This package provides a set of functions to run R code in an environment
2598 in which global state has been temporarily modified. Many of these functions
2599 were originally a part of the r-devtools package.")
2600 (license license:gpl2+)))
2602 (define-public r-hms
2609 (uri (cran-uri "hms" version))
2612 "0qlh4s1g9rbm6c3s906dhw3xsz28m8fg6cyynlkhvis533dk0pvb"))))
2613 (build-system r-build-system)
2615 (list r-ellipsis r-lifecycle r-pkgconfig r-rlang r-vctrs))
2616 (home-page "https://github.com/rstats-db/hms")
2617 (synopsis "Pretty time of day")
2619 "This package implements an S3 class for storing and formatting
2620 time-of-day values, based on the @code{difftime} class.")
2621 (license license:gpl3+)))
2623 (define-public r-readr
2629 (uri (cran-uri "readr" version))
2632 "06qcw57yz0fhh3ni41d5w68cbmwmb6zkp47chllwzax43wxd1bwl"))))
2633 (build-system r-build-system)
2648 (home-page "https://github.com/hadley/readr")
2649 (synopsis "Read tabular data")
2651 "This package provides functions to read flat or tabular text files from
2652 disk (or a connection).")
2653 (license license:gpl2+)))
2655 (define-public r-plotrix
2661 (uri (cran-uri "plotrix" version))
2664 "07xwq3505qb2yak7pfda22yqwifj6m78f8b5rm0ym74808qrawmv"))))
2665 (build-system r-build-system)
2666 (home-page "https://cran.r-project.org/web/packages/plotrix")
2667 (synopsis "Various plotting functions")
2669 "This package provides lots of plotting, various labeling, axis and color
2670 scaling functions for R.")
2671 (license license:gpl2+)))
2673 (define-public r-gridbase
2679 (uri (cran-uri "gridBase" version))
2682 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
2683 (build-system r-build-system)
2684 (home-page "https://cran.r-project.org/web/packages/gridBase")
2685 (synopsis "Integration of base and grid graphics")
2687 "This package provides an integration of base and grid graphics for R.")
2688 (license license:gpl2+)))
2690 (define-public r-latticeextra
2692 (name "r-latticeextra")
2697 (uri (cran-uri "latticeExtra" version))
2700 "04fzwcqs594rk5qp98yilh3kdh3sw4xf8wld5rp94ggpaqfw7bbc"))))
2701 (properties `((upstream-name . "latticeExtra")))
2702 (build-system r-build-system)
2704 (list r-jpeg r-lattice r-png r-rcolorbrewer))
2705 (home-page "http://latticeextra.r-forge.r-project.org/")
2706 (synopsis "Extra graphical utilities based on lattice")
2708 "Building on the infrastructure provided by the lattice package, this
2709 package provides several new high-level graphics functions and methods, as
2710 well as additional utilities such as panel and axis annotation functions.")
2711 (license license:gpl2+)))
2713 (define-public r-rcpparmadillo
2715 (name "r-rcpparmadillo")
2716 (version "0.10.8.1.0")
2719 (uri (cran-uri "RcppArmadillo" version))
2722 "1x7mk85rc4pmn17nm63k6rbkarsmghjapznias268545nfpib97g"))))
2723 (properties `((upstream-name . "RcppArmadillo")))
2724 (build-system r-build-system)
2727 (home-page "https://github.com/RcppCore/RcppArmadillo")
2728 (synopsis "Rcpp integration for the Armadillo linear algebra library")
2730 "Armadillo is a templated C++ linear algebra library that aims towards a
2731 good balance between speed and ease of use. Integer, floating point and
2732 complex numbers are supported, as well as a subset of trigonometric and
2733 statistics functions. Various matrix decompositions are provided through
2734 optional integration with LAPACK and ATLAS libraries. This package includes
2735 the header files from the templated Armadillo library.")
2736 ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
2737 ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
2738 ;; later, as is the rest of 'Rcpp'.
2739 (license license:gpl2+)))
2741 (define-public r-bitops
2747 (uri (cran-uri "bitops" version))
2750 "1i0phmq5yynla5x0frqll1gbf5ww59p3sgz1s06a354zqf9grdg9"))))
2751 (build-system r-build-system)
2752 (home-page "https://cran.r-project.org/web/packages/bitops")
2753 (synopsis "Bitwise operations")
2755 "This package provides functions for bitwise operations on integer
2757 (license license:gpl2+)))
2759 (define-public r-catools
2765 (uri (cran-uri "caTools" version))
2768 "14q2ry8gaszjl0m97qg62dxv5bpj6k02qwyi7q2lnxgcmwai3mkm"))))
2769 (properties `((upstream-name . "caTools")))
2770 (build-system r-build-system)
2773 (home-page "https://cran.r-project.org/web/packages/caTools")
2774 (synopsis "Various tools including functions for moving window statistics")
2776 "This package contains several basic utility functions including:
2777 moving (rolling, running) window statistic functions, read/write for GIF and
2778 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
2779 encoder/decoder, round-off-error-free sum and cumsum, etc.")
2780 (license license:gpl3+)))
2782 (define-public r-rprojroot
2784 (name "r-rprojroot")
2789 (uri (cran-uri "rprojroot" version))
2792 "07wy07yhms8zln9qb0iwx69dq08h4lrdi8kavjcplfxcskq638az"))))
2793 (build-system r-build-system)
2796 (home-page "https://github.com/krlmlr/rprojroot")
2797 (synopsis "Finding files in project subdirectories")
2799 "This package helps accessing files relative to a project root. It
2800 provides helpers for robust, reliable and flexible paths to files below a
2801 project root. The root of a project is defined as a directory that matches a
2802 certain criterion, e.g., it contains a certain regular file.")
2803 (license license:gpl3)))
2805 (define-public r-rmarkdown
2807 (name "r-rmarkdown")
2812 (uri (cran-uri "rmarkdown" version))
2814 (base32 "0xcpg9d009a71p5i6jczw02qcp907p5d52lp6vclrsp7019jawck"))))
2815 (properties `((upstream-name . "rmarkdown")))
2816 (build-system r-build-system)
2830 (home-page "https://rmarkdown.rstudio.com")
2831 (synopsis "Convert R Markdown documents into a variety of formats")
2833 "This package provides tools to convert R Markdown documents into a
2834 variety of formats.")
2835 (license license:gpl3+)))
2837 (define-public r-gtable
2843 (uri (cran-uri "gtable" version))
2846 "1lyncxf2dqdjgw1071cn9c8zwzkz6sldnd5cgmicf70bc726qf7x"))))
2847 (properties `((upstream-name . "gtable")))
2848 (build-system r-build-system)
2849 (home-page "https://cran.r-project.org/web/packages/gtable")
2850 (synopsis "R library to arrange grobs in tables")
2852 "Gtable is a collection of tools to make it easier to work with
2853 \"tables\" of grobs.")
2854 (license license:gpl2+)))
2856 (define-public r-gridextra
2858 (name "r-gridextra")
2862 (uri (cran-uri "gridExtra" version))
2865 "0fwfk3cdwxxim7nd55pn7m31bcaqj48y06j7an2k1v1pybk0rdl1"))))
2866 (properties `((upstream-name . "gridExtra")))
2867 (build-system r-build-system)
2871 (list r-knitr)) ;for building vignettes
2872 (home-page "https://github.com/baptiste/gridextra")
2873 (synopsis "Miscellaneous functions for \"Grid\" graphics")
2875 "This package provides a number of user-level functions to work with
2876 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
2878 (license license:gpl2+)))
2880 (define-public r-pkgconfig
2882 (name "r-pkgconfig")
2886 (uri (cran-uri "pkgconfig" version))
2889 "0l1qph8zyi2sic3k2qcd7vlfl7rzfh1q7z7zvjkl5f7y1x2fy3rk"))))
2890 (build-system r-build-system)
2891 (home-page "https://github.com/gaborcsardi/pkgconfig")
2892 (synopsis "Private configuration for R packages")
2893 (description "This package provides the functionality to set configuration
2894 options on a per-package basis. Options set by a given package only apply to
2895 that package, other packages are unaffected.")
2896 (license license:expat)))
2898 (define-public r-blob
2904 (uri (cran-uri "blob" version))
2907 "1yn7f13icaix0apxp4drnciwdn8bx8xmbd129jd7ck4rcly0axj9"))))
2908 (build-system r-build-system)
2910 (list r-rlang r-vctrs))
2911 (home-page "https://github.com/hadley/blob")
2912 (synopsis "Simple S3 Class for representing vectors of binary data")
2913 (description "Raw vectors in R are useful for storing a single binary
2914 object. What if you want to put a vector of them in a data frame? The blob
2915 package provides the blob object, a list of raw vectors, suitable for use as
2916 a column in data frame.")
2917 (license license:gpl3+)))
2919 (define-public r-rsqlite
2925 (uri (cran-uri "RSQLite" version))
2928 "075vsnbkcwpwnn87b06mhbg2fflqhjvbylhbkg0d3v3rl7zg28s4"))))
2929 (properties `((upstream-name . "RSQLite")))
2930 (build-system r-build-system)
2941 (home-page "https://github.com/rstats-db/RSQLite")
2942 (synopsis "SQLite interface for R")
2944 "This package embeds the SQLite database engine in R and provides an
2945 interface compliant with the DBI package. The source for the SQLite
2946 engine (version 3.8.8.2) is included.")
2947 (license license:lgpl2.0+)))
2949 (define-public r-rcurl
2952 (version "1.95-0.1.2")
2955 (uri (string-append "https://www.bioconductor.org/packages/"
2956 "release/extra/src/"
2957 "contrib/RCurl_" version ".tar.gz"))
2960 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
2961 (properties `((upstream-name . "RCurl")))
2962 (build-system r-build-system)
2965 (modify-phases %standard-phases
2966 (add-after 'unpack 'respect-CURL_CA_BUNDLE
2968 (substitute* "R/options.S"
2969 (("\\.els = rev\\(merge\\(list\\(\\.\\.\\.\\), \\.opts\\)\\)" m)
2971 certs = Sys.getenv(\"CURL_CA_BUNDLE\")
2972 if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) }
2976 `(("libcurl" ,curl)))
2979 (home-page "http://www.omegahat.net/RCurl")
2980 (synopsis "General network client interface for R")
2982 "The package allows one to compose general HTTP requests and provides
2983 convenient functions to fetch URIs, GET and POST forms, etc. and process the
2984 results returned by the Web server. This provides a great deal of control
2985 over the HTTP/FTP/... connection and the form of the request while providing a
2986 higher-level interface than is available just using R socket connections.
2987 Additionally, the underlying implementation is robust and extensive,
2988 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
2989 ldap, and also supports cookies, redirects, authentication, etc.")
2990 (license license:bsd-3)))
2992 (define-public r-xml
2995 (version "3.99-0.8")
2998 (uri (cran-uri "XML" version))
3001 "0l3bsgqw4bicv3sl2bfag7p4rh1y2pcyg0ajr73kkbg85qf6j7q8"))))
3003 `((upstream-name . "XML")))
3004 (build-system r-build-system)
3006 (list libxml2 zlib))
3009 (home-page "http://www.omegahat.net/RSXML")
3010 (synopsis "Tools for parsing and generating XML within R")
3012 "Many approaches for both reading and creating XML (and HTML)
3013 documents (including DTDs), both local and accessible via HTTP or FTP. Also
3014 offers access to an XPath \"interpreter\".")
3015 (license license:bsd-2)))
3017 (define-public r-xnomial
3022 (origin (method url-fetch)
3023 (uri (cran-uri "XNomial" version))
3026 "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
3027 (properties (quasiquote ((upstream-name . "XNomial"))))
3028 (build-system r-build-system)
3029 (home-page "https://cran.r-project.org/web/packages/XNomial")
3030 (synopsis "Goodness-of-Fit test for multinomial data")
3032 "This package provides an exact Goodness-of-Fit test for
3033 multinomial data with fixed probabilities. It can be used to
3034 determine whether a set of counts fits a given expected ratio. To see
3035 whether a set of observed counts fits an expectation, one can examine
3036 all possible outcomes with @code{xmulti()} or a random sample of them
3037 with @code{xmonte()} and find the probability of an observation
3038 deviating from the expectation by at least as much as the observed.
3039 As a measure of deviation from the expected, one can use the
3040 log-likelihood ratio, the multinomial probability, or the classic
3041 chi-square statistic. A histogram of the test statistic can also be
3042 plotted and compared with the asymptotic curve.")
3043 (license (list license:gpl2+ license:gpl3+))))
3045 (define-public r-lambda-r
3051 (uri (cran-uri "lambda.r" version))
3054 "1mh1g0gsd58gng0hb29vww2yqb2jfs07kba5kxnnqck5j3izwlnj"))))
3055 (properties `((upstream-name . "lambda.r")))
3056 (build-system r-build-system)
3059 (home-page "https://cran.r-project.org/web/packages/lambda.r")
3060 (synopsis "Functional programming extension for R")
3062 "This package provides a language extension to efficiently write
3063 functional programs in R. Syntax extensions include multi-part function
3064 definitions, pattern matching, guard statements, built-in (optional) type
3066 (license license:lgpl3+)))
3068 (define-public r-futile-options
3070 (name "r-futile-options")
3074 (uri (cran-uri "futile.options" version))
3077 "0w15agpi88y3qkv6fl72zy2pzyplzgvnj41a4ixhg64mw1sck73s"))))
3079 `((upstream-name . "futile.options")))
3080 (build-system r-build-system)
3081 (home-page "https://cran.r-project.org/web/packages/futile.options")
3082 (synopsis "Options management framework")
3084 "The futile.options subsystem provides an easy user-defined options
3085 management system that is properly scoped. This means that options created
3086 via @code{futile.options} are fully self-contained and will not collide with
3087 options defined in other packages.")
3088 (license license:lgpl3+)))
3090 (define-public r-futile-logger
3092 (name "r-futile-logger")
3096 (uri (cran-uri "futile.logger" version))
3099 "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
3100 (properties `((upstream-name . "futile.logger")))
3101 (build-system r-build-system)
3103 (list r-futile-options r-lambda-r))
3104 (home-page "https://cran.r-project.org/web/packages/futile.logger")
3105 (synopsis "Logging utility for R")
3107 "This package provides a simple yet powerful logging utility. Based
3108 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
3109 convenient and easy to use replacement for @code{cat} and @code{print}
3111 (license license:lgpl3+)))
3113 (define-public r-segmented
3115 (name "r-segmented")
3120 (uri (cran-uri "segmented" version))
3123 "0xn28gyqzmyz0kv352rkkznbj806arxj2am5a9gqsn1qzv9l0s9h"))))
3124 (build-system r-build-system)
3125 (propagated-inputs (list r-mass))
3126 (home-page "https://cran.r-project.org/web/packages/segmented")
3127 (synopsis "Regression models with breakpoints estimation")
3129 "Given a regression model, segmented updates the model by adding one or
3130 more segmented (i.e., piecewise-linear) relationships. Several variables with
3131 multiple breakpoints are allowed.")
3132 (license (list license:gpl2+ license:gpl3+))))
3134 (define-public r-snow
3140 (uri (cran-uri "snow" version))
3143 "1j8kvf3imxijsqkdjz4i9s7qggfxqrpas46y5wz6za92y937yn44"))))
3144 (build-system r-build-system)
3145 (home-page "https://cran.r-project.org/web/packages/snow")
3146 (synopsis "Support for simple parallel computing in R")
3148 "The snow package provides support for simple parallel computing on a
3149 network of workstations using R. A master R process calls @code{makeCluster}
3150 to start a cluster of worker processes; the master process then uses functions
3151 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
3152 worker processes and collect and return the results on the master.")
3153 (license (list license:gpl2+ license:gpl3+))))
3155 (define-public r-sparsem
3161 (uri (cran-uri "SparseM" version))
3164 "0csbqd9wm6r4162mday1iaigzf9wv2rp1zq8hnihys6f38w8z0xx"))))
3166 `((upstream-name . "SparseM")))
3169 (build-system r-build-system)
3170 (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
3171 (synopsis "Sparse linear algebra")
3173 "This package provides some basic linear algebra functionality for sparse
3174 matrices. It includes Cholesky decomposition and backsolving as well as
3175 standard R subsetting and Kronecker products.")
3176 (license license:gpl2+)))
3178 (define-public r-iterators
3180 (name "r-iterators")
3185 (uri (cran-uri "iterators" version))
3188 "190i1y2493v5c9z8978rb3idlwsjymy67k1assa9znljqbj313kp"))))
3189 (build-system r-build-system)
3190 (home-page "https://cran.r-project.org/web/packages/iterators")
3191 (synopsis "Iterator construct for R")
3193 "This package provides support for iterators, which allow a programmer to
3194 traverse through all the elements of a vector, list, or other collection of
3196 (license license:asl2.0)))
3198 (define-public r-foreach
3205 (uri (cran-uri "foreach" version))
3208 "1qb83b1jvpmk8d6kfibkm5q2hiki0x5gipy758mwa62n56gdcnpv"))))
3209 (build-system r-build-system)
3211 (list r-codetools r-iterators))
3214 (home-page "https://cran.r-project.org/web/packages/foreach")
3215 (synopsis "Foreach looping construct for R")
3217 "This package provides support for the @code{foreach} looping construct.
3218 @code{foreach} is an idiom that allows for iterating over elements in a
3219 collection, without the use of an explicit loop counter. This package in
3220 particular is intended to be used for its return value, rather than for its
3221 side effects. In that sense, it is similar to the standard @code{lapply}
3222 function, but doesn't require the evaluation of a function. Using
3223 @code{foreach} without side effects also facilitates executing the loop in
3225 (license license:asl2.0)))
3227 (define-public r-doparallel
3229 (name "r-doparallel")
3234 (uri (cran-uri "doParallel" version))
3237 "1cjf0mxrxgls5pl7aj22fv9j488craib1wkc9np4f3gkckwjdfzi"))))
3238 (properties `((upstream-name . "doParallel")))
3239 (build-system r-build-system)
3241 (list r-foreach r-iterators))
3242 (home-page "https://cran.r-project.org/web/packages/doParallel")
3243 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3245 "This package provides a parallel backend for the @code{%dopar%} function
3246 using the parallel package.")
3247 (license license:gpl2+)))
3249 (define-public r-domc
3256 (uri (cran-uri "doMC" version))
3259 "0kdmfhp5m1wisjbfyl9d040jrmjmhcgjb0vdi536g2i9vixb5yny"))))
3260 (properties `((upstream-name . "doMC")))
3261 (build-system r-build-system)
3263 (list r-foreach r-iterators))
3264 (home-page "https://cran.r-project.org/web/packages/doMC")
3265 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3267 "This package provides a parallel backend for the @code{%dopar%} function
3268 using the multicore functionality of the parallel package.")
3269 (license license:gpl2+)))
3272 (let ((javascript-sources
3273 '(("https://cdn.datatables.net/1.10.20/js/jquery.dataTables.js"
3274 "03ln7ys1q1hy3xpsrjxnjpg9hq3lfpqz0firrxsgjzj8fsw20is3"
3276 ("https://cdn.datatables.net/1.10.20/js/dataTables.bootstrap.js"
3277 "16clrnxm7axn6cdimyf3qbskxg10gpn9ld5ls2xdfw5q1qf2i4ml"
3279 ("https://cdn.datatables.net/1.10.20/js/dataTables.bootstrap4.js"
3280 "16v49zqxr1zil19bcx3wdnv95zdpiz2m979aazan7z04ymqb2rzb"
3282 ("https://cdn.datatables.net/1.10.20/js/dataTables.foundation.js"
3283 "1gpjm1pi2pl0hxsn0pg3s3f382y2s7nsr06866vxld6gb8054lld"
3285 ("https://cdn.datatables.net/1.10.20/js/dataTables.jqueryui.js"
3286 "0nxd8jph34vsk8k8whs2yiybrn6nsnwzhri0bxn2k1dzmcvpn24i"
3288 ("https://cdn.datatables.net/1.10.20/js/dataTables.semanticui.js"
3289 "1477f49xyxs4phias789mbspv23w8alxchhl5b5iy0aw6vd35c43"
3292 ("https://cdn.datatables.net/autofill/2.3.4/js/dataTables.autoFill.js"
3293 "04i6n7r3512gzfihl5wnhrvm0klnjp41g1z6cny3j803hvmnp8zk"
3294 "datatables-extensions/AutoFill")
3295 ("https://cdn.datatables.net/autofill/2.3.4/js/autoFill.bootstrap.js"
3296 "1zi7iiq63i5qx3p9cyynn6am4idxwj8xaz8mp4n3klm1x68sc0ja"
3297 "datatables-extensions/AutoFill")
3298 ("https://cdn.datatables.net/autofill/2.3.4/js/autoFill.bootstrap4.js"
3299 "1vk2smcz14raf0cz88a65yf36a7mnmbml02q03apg2b8bqy91m7w"
3300 "datatables-extensions/AutoFill")
3301 ("https://cdn.datatables.net/autofill/2.3.4/js/autoFill.foundation.js"
3302 "0sbcib1461pkglk69fzzqi73g4abylah74f264v0f79dc5247yzz"
3303 "datatables-extensions/AutoFill")
3304 ("https://cdn.datatables.net/autofill/2.3.4/js/autoFill.jqueryui.js"
3305 "1dw9vbbchzbd2c7id8na2p1cxac2kgjbzjrvqafra715hr0i4z3z"
3306 "datatables-extensions/AutoFill")
3307 ("https://cdn.datatables.net/autofill/2.3.4/js/autoFill.semanticui.js"
3308 "07ck81y6wpqchq8jfym6gjgc57xwj6vv9h5w9grc1gps6p7q9xnr"
3309 "datatables-extensions/AutoFill")
3311 ("https://cdn.datatables.net/buttons/1.6.1/js/dataTables.buttons.js"
3312 "15l9kd9898zm8xf996d5c761rwl55k4w718k9k5fzz2gh91g21g5"
3313 "datatables-extensions/Buttons")
3314 ("https://cdn.datatables.net/buttons/1.6.1/js/buttons.colVis.js"
3315 "1rqlv5pacipl652xgyzsdq1gbfwv52rwl4mr2fx9a3py21yskppk"
3316 "datatables-extensions/Buttons")
3317 ("https://cdn.datatables.net/buttons/1.6.1/js/buttons.flash.js"
3318 "150r2ypxl017kl5agrn17cnyvwpf7x2x7vkqbc1qxif8vclf35kj"
3319 "datatables-extensions/Buttons")
3320 ("https://cdn.datatables.net/buttons/1.6.1/js/buttons.html5.js"
3321 "1d8is99yrh95hycjijzbrbxy1anfslab6krmhj2xbwsmssyn16xh"
3322 "datatables-extensions/Buttons")
3323 ("https://cdn.datatables.net/buttons/1.6.1/js/buttons.print.js"
3324 "1irgspv2zidv6v0ay92152d8cvhz2zyrwb71xk3nw903223vc2gl"
3325 "datatables-extensions/Buttons")
3326 ("https://cdn.datatables.net/buttons/1.6.1/js/buttons.semanticui.js"
3327 "1p02r953ampxlzfzpay227ya6qdzsxz2anjxpnx3q8qs6gv6y2jl"
3328 "datatables-extensions/Buttons")
3329 ("https://cdn.datatables.net/buttons/1.6.1/js/buttons.foundation.js"
3330 "0aykm1sk8rwvxp5r4qnvbb2scx2bln5kh88h36829mcqcdksfc50"
3331 "datatables-extensions/Buttons")
3332 ("https://cdn.datatables.net/buttons/1.6.1/js/buttons.jqueryui.js"
3333 "1im6f6jw3yc3959rw1i3bghvz863kmp3wgfvz661r1r2wjzzfs4d"
3334 "datatables-extensions/Buttons")
3335 ("https://cdn.datatables.net/buttons/1.6.1/js/buttons.bootstrap.js"
3336 "1mzmpabhrk0iag7hb16n8bhghx4cprq39p2vqn3v65mpklajzznc"
3337 "datatables-extensions/Buttons")
3338 ("https://cdn.datatables.net/buttons/1.6.1/js/buttons.bootstrap4.js"
3339 "0hfclipg43wr9p7irrcn9vp5wji8z7gz6y5mclkq88z1mlpwklzf"
3340 "datatables-extensions/Buttons")
3341 ;; It is not clear what version the bundled file corresponds to.
3342 ("https://cdnjs.cloudflare.com/ajax/libs/jszip/2.5.0/jszip.js"
3343 "18hpj9vwgki56ijb20l5gwmqa5p1d0xprn57z2mlg3ph6ll0bdkd"
3344 "datatables-extensions/Buttons")
3345 ("https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/pdfmake.js"
3346 "1sfw80az2cgzin5wk7q1p2n9zm66c35cz0m6isdygml81i594wia"
3347 "datatables-extensions/Buttons")
3348 ("https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/vfs_fonts.js"
3349 "1k324s0hw4lfpd71bb1cnv4j5096k8smk64fjdsh81sl0ykizf2w"
3350 "datatables-extensions/Buttons")
3352 ("https://cdn.datatables.net/colreorder/1.5.2/js/dataTables.colReorder.js"
3353 "1dalc28km19xzzszsa82hsd9alikrqpzjvf9vzxkccjpf7m2sdqg"
3354 "datatables-extensions/ColReorder")
3355 ("https://cdn.datatables.net/colreorder/1.5.2/js/colReorder.foundation.js"
3356 "0nrddc8swkmsfzji518kh6ks55ykyk9p8r4x5fmf8ckr9fhjkh0s"
3357 "datatables-extensions/ColReorder")
3358 ("https://cdn.datatables.net/colreorder/1.5.2/js/colReorder.bootstrap.js"
3359 "0crgmjwcn817yz6ibjkji6gsickvv2a4las9asyldfcpj2c99x84"
3360 "datatables-extensions/ColReorder")
3361 ("https://cdn.datatables.net/colreorder/1.5.2/js/colReorder.bootstrap4.js"
3362 "065fhw4v2d9rp3ic9zfb1q5d7pfq4f2949rr24hdjbspf19m3ymd"
3363 "datatables-extensions/ColReorder")
3364 ("https://cdn.datatables.net/colreorder/1.5.2/js/colReorder.semanticui.js"
3365 "17kw143ny0nq0yidsffw3cpghvlg2bzlzavfi0ihkamcn26ymxcp"
3366 "datatables-extensions/ColReorder")
3367 ("https://cdn.datatables.net/colreorder/1.5.2/js/colReorder.jqueryui.js"
3368 "1rd8hijz3prg2y36fvqczrpdzixibjy2dxgs2fmgr8wrm8k01rrm"
3369 "datatables-extensions/ColReorder")
3371 ("https://cdn.datatables.net/fixedcolumns/3.3.0/js/dataTables.fixedColumns.js"
3372 "0vsqk2fv59n351bdfcbvhmvpq38qwf41j1cn810xz1l1i07cg4hg"
3373 "datatables-extensions/FixedColumns")
3374 ("https://cdn.datatables.net/fixedcolumns/3.3.0/js/fixedColumns.bootstrap.js"
3375 "1j4wvg694l960gk5dg7wghwa3dpgq8mnrcgp78ghm92i08djb1wy"
3376 "datatables-extensions/FixedColumns")
3377 ("https://cdn.datatables.net/fixedcolumns/3.3.0/js/fixedColumns.bootstrap4.js"
3378 "1p79k9bjslyvmp1bdhmg4nm2l9nbfsi4kgw7rx3vjka3n50qy730"
3379 "datatables-extensions/FixedColumns")
3380 ("https://cdn.datatables.net/fixedcolumns/3.3.0/js/fixedColumns.foundation.js"
3381 "0f0xkrsapzgma58f6l63rpn68xid098dxwqqddsyddl0hy0x1z82"
3382 "datatables-extensions/FixedColumns")
3383 ("https://cdn.datatables.net/fixedcolumns/3.3.0/js/fixedColumns.jqueryui.js"
3384 "0lw35c8vkajx75pg4ddik4gyzmjak1jaw3flq850frwgnzsvhahx"
3385 "datatables-extensions/FixedColumns")
3386 ("https://cdn.datatables.net/fixedcolumns/3.3.0/js/fixedColumns.semanticui.js"
3387 "1kqsap9y0d25a7m5zjakipifl5qi2qr72kfj4ap3zxavd8md2wyn"
3388 "datatables-extensions/FixedColumns")
3390 ("https://cdn.datatables.net/fixedheader/3.1.6/js/dataTables.fixedHeader.js"
3391 "1ml5ilnm8nirr6rsgmzn75l1k0hcjz3sqk6h1y1gy8cpwpklvqri"
3392 "datatables-extensions/FixedHeader")
3393 ("https://cdn.datatables.net/fixedheader/3.1.6/js/fixedHeader.bootstrap.js"
3394 "1qf3pkb3svpia7g8bwyql7ma3x2g4zj5bp0d14pnv8xpc9h52r93"
3395 "datatables-extensions/FixedHeader")
3396 ("https://cdn.datatables.net/fixedheader/3.1.6/js/fixedHeader.bootstrap4.js"
3397 "19jcvnk7zh4k6fd5si3b743x70qzlkqiw3m10jbc5jzbpz8sj6qd"
3398 "datatables-extensions/FixedHeader")
3399 ("https://cdn.datatables.net/fixedheader/3.1.6/js/fixedHeader.foundation.js"
3400 "0xmpx1r76vykqygksyjaf4d1ql1fid69rqhvk4k857iybqz3gdcv"
3401 "datatables-extensions/FixedHeader")
3402 ("https://cdn.datatables.net/fixedheader/3.1.6/js/fixedHeader.jqueryui.js"
3403 "1lc0g2cag1sj3bqmh7rh5z00pmfv1srxfhwi32y4mgpzhrzpfzxn"
3404 "datatables-extensions/FixedHeader")
3405 ("https://cdn.datatables.net/fixedheader/3.1.6/js/fixedHeader.semanticui.js"
3406 "1v0i6dc68h8l8673fb5970igzkl7as36riv504iyg82glfi7n877"
3407 "datatables-extensions/FixedHeader")
3409 ("https://cdn.datatables.net/keytable/2.5.1/js/dataTables.keyTable.js"
3410 "16iib2icxsjh93x5hd42gpsl7bzpcsqb7zjgj0m1s02ls45bdlv5"
3411 "datatables-extensions/KeyTable")
3412 ("https://cdn.datatables.net/keytable/2.5.1/js/keyTable.bootstrap.js"
3413 "0hnhk6am4yl6h6bb7as935k8h2syil9hf8g7nn409yd3ws736xpj"
3414 "datatables-extensions/KeyTable")
3415 ("https://cdn.datatables.net/keytable/2.5.1/js/keyTable.bootstrap4.js"
3416 "0r85mp5yf9hgl5ayzzs46dfbxa231bjlvgb8lqpyzik1m6afa51i"
3417 "datatables-extensions/KeyTable")
3418 ("https://cdn.datatables.net/keytable/2.5.1/js/keyTable.foundation.js"
3419 "11fr14p33lyvs0wfcx228m600i4qcaqb44q3hk723jxcz59k17dw"
3420 "datatables-extensions/KeyTable")
3421 ("https://cdn.datatables.net/keytable/2.5.1/js/keyTable.jqueryui.js"
3422 "0572rxrvwyprdr8l5jkgacj2bkmhmgxjy5vybm65n54g9j19l6bc"
3423 "datatables-extensions/KeyTable")
3424 ("https://cdn.datatables.net/keytable/2.5.1/js/keyTable.semanticui.js"
3425 "157mqn9mhmmf7vas2das4hbpwipk3wshs8n0808q04rbijr0g2bz"
3426 "datatables-extensions/KeyTable")
3428 ("https://cdn.datatables.net/responsive/2.2.3/js/dataTables.responsive.js"
3429 "1jnsx4sqf7qjd1gz5ag9hn6n76cwwfms23rzw37lgbd6h54yqzwr"
3430 "datatables-extensions/Responsive")
3431 ("https://cdn.datatables.net/responsive/2.2.3/js/responsive.foundation.js"
3432 "1vzzqpd9l8xv0am42g4cilx9igmq60mgk0hab4ssqvbicrmrgq9z"
3433 "datatables-extensions/Responsive")
3434 ("https://cdn.datatables.net/responsive/2.2.3/js/responsive.semanticui.js"
3435 "1cjiwcf0d07482k08dhn5ffsizshw4hqgz5l58p03pq9g6wc9pvm"
3436 "datatables-extensions/Responsive")
3437 ("https://cdn.datatables.net/responsive/2.2.3/js/responsive.jqueryui.js"
3438 "10nykak2kf4sai64girh26xdmdil29jvw3zja2rpp2qzjg4172z9"
3439 "datatables-extensions/Responsive")
3440 ("https://cdn.datatables.net/responsive/2.2.3/js/responsive.bootstrap.js"
3441 "1xxlh01vmzmfwwlsa611pl2nrl2sx58rp8xmx301bfsylmp2v5b2"
3442 "datatables-extensions/Responsive")
3443 ("https://cdn.datatables.net/responsive/2.2.3/js/responsive.bootstrap4.js"
3444 "1zjh15p7n1038sggaxv1xvcwbkhw2nk1ndx745s6cxiqb69y3i0h"
3445 "datatables-extensions/Responsive")
3447 ("https://cdn.datatables.net/rowgroup/1.1.1/js/dataTables.rowGroup.js"
3448 "0s4q7ir2d6q36g29nn9mqk7vrqrdig2mm5zbcv0sn2lixqi29pkj"
3449 "datatables-extensions/RowGroup")
3450 ("https://cdn.datatables.net/rowgroup/1.1.1/js/rowGroup.bootstrap.js"
3451 "1xfdhqgznz9x1v8spvql6b0wbna13h8cbzvkjza14nqsmccxck66"
3452 "datatables-extensions/RowGroup")
3453 ("https://cdn.datatables.net/rowgroup/1.1.1/js/rowGroup.bootstrap4.js"
3454 "1xm53sda4fabwdaglngrj09bpiygkn9mm17grxbykn1jazqqdp62"
3455 "datatables-extensions/RowGroup")
3456 ("https://cdn.datatables.net/rowgroup/1.1.1/js/rowGroup.foundation.js"
3457 "0832i10vils1wv1sm10qvsnd4i2k2xkhskz6i9y2q0axkmk73hcd"
3458 "datatables-extensions/RowGroup")
3459 ("https://cdn.datatables.net/rowgroup/1.1.1/js/rowGroup.jqueryui.js"
3460 "0n53cd294s9mjblkykkqvd9n414bsc26wpcg5spxdscjl6hxh79p"
3461 "datatables-extensions/RowGroup")
3462 ("https://cdn.datatables.net/rowgroup/1.1.1/js/rowGroup.semanticui.js"
3463 "010wls5nf387p21fdc2k952bxq89r5kxkv7j4wbvwf8k2a18cmc9"
3464 "datatables-extensions/RowGroup")
3466 ("https://cdn.datatables.net/rowreorder/1.2.6/js/dataTables.rowReorder.js"
3467 "13ymbn3h9755pgb0gmlb9gl54vz9nqnz4mws7g6mlmz53r3sqhmj"
3468 "datatables-extensions/RowReorder")
3469 ("https://cdn.datatables.net/rowreorder/1.2.6/js/rowReorder.bootstrap.js"
3470 "185if2pxgc940rm49hdgln57pc5h9cszlii3bfpdf3pdc1fjhckm"
3471 "datatables-extensions/RowReorder")
3472 ("https://cdn.datatables.net/rowreorder/1.2.6/js/rowReorder.bootstrap4.js"
3473 "14129x4md57i4ff7j18m49jn5fw8r716np84cdrcawlydgjsxp4a"
3474 "datatables-extensions/RowReorder")
3475 ("https://cdn.datatables.net/rowreorder/1.2.6/js/rowReorder.foundation.js"
3476 "0zg94jckymxzda2xjyj9p38y5v61cji55kak1ylq72l6a9sw8sg6"
3477 "datatables-extensions/RowReorder")
3478 ("https://cdn.datatables.net/rowreorder/1.2.6/js/rowReorder.jqueryui.js"
3479 "08gm419xcixgqw0i5yv2mxyyvafhzviibifp6nv129vdxx0a5d8v"
3480 "datatables-extensions/RowReorder")
3481 ("https://cdn.datatables.net/rowreorder/1.2.6/js/rowReorder.semanticui.js"
3482 "1zjrx2rlgw3qannsqa88pcp3i4pc87pwv7rmgfw1dar8namkr9kk"
3483 "datatables-extensions/RowReorder")
3485 ("https://cdn.datatables.net/scroller/2.0.1/js/dataTables.scroller.js"
3486 "0zfjjdvwwlsnps24i9l4c97hmway2qs6addks1is5bxl4k1r6d16"
3487 "datatables-extensions/Scroller")
3488 ("https://cdn.datatables.net/scroller/2.0.1/js/scroller.foundation.js"
3489 "04bk6ink8wqay7655v93jvv86m3bn6asrsfb22i99rgxdvm8gn1z"
3490 "datatables-extensions/Scroller")
3491 ("https://cdn.datatables.net/scroller/2.0.1/js/scroller.bootstrap.js"
3492 "19dl40dl8ir21xvs1j7xhm2a4py1m21xbypwn499fg2awj8vaidi"
3493 "datatables-extensions/Scroller")
3494 ("https://cdn.datatables.net/scroller/2.0.1/js/scroller.bootstrap4.js"
3495 "0pbkgncijlafwdmyh4l65dabd18hzjh8r01cad3b9iy8cfif6iwd"
3496 "datatables-extensions/Scroller")
3497 ("https://cdn.datatables.net/scroller/2.0.1/js/scroller.jqueryui.js"
3498 "1md5mpx5in7wzsr38yn801cmv3phm0i0ikdnpd0b1nsna5ccpj14"
3499 "datatables-extensions/Scroller")
3500 ("https://cdn.datatables.net/scroller/2.0.1/js/scroller.semanticui.js"
3501 "1dfbblbzbryjgiv31qfdjnijz19lmyijg12win3y8gsgfd4fp9zz"
3502 "datatables-extensions/Scroller")
3504 ("https://cdn.datatables.net/searchbuilder/1.0.0/js/dataTables.searchBuilder.js"
3505 "0n5g0j0yfzqvdpsmwb27bj1rd8zx864fsx2k7b2kpv6mqqavzpqc"
3506 "datatables-extensions/SearchBuilder")
3507 ("https://cdn.datatables.net/searchbuilder/1.0.0/js/searchBuilder.bootstrap.js"
3508 "1gnd8rjcg9c96xayshn9rwinzgmlwzddczjlpfmf2j33npmyka2y"
3509 "datatables-extensions/SearchBuilder")
3510 ("https://cdn.datatables.net/searchbuilder/1.0.0/js/searchBuilder.bootstrap4.js"
3511 "0vdv5mi6zbp2dspmj0lw2vaqxvfadcydlmc6frqv4a68rms7wz05"
3512 "datatables-extensions/SearchBuilder")
3513 ("https://cdn.datatables.net/searchbuilder/1.0.0/js/searchBuilder.dataTables.js"
3514 "0fbzfnaqswb2xq7m1vdzcg7l7qi0wmyz64ml6k4002kp0dm4xnlx"
3515 "datatables-extensions/SearchBuilder")
3517 ("https://cdn.datatables.net/searchpanes/1.1.1/js/dataTables.searchPanes.js"
3518 "1s697avk42h24fsaq79d1kkw66dqig7xgpx9bvmhwncv8amkmz6i"
3519 "datatables-extensions/SearchPanes")
3520 ("https://cdn.datatables.net/searchpanes/1.1.1/js/searchPanes.bootstrap.js"
3521 "0n3z4fdx1nsga4l5hmd4s93piv9k0v607xd7q9h2zpq613if7sld"
3522 "datatables-extensions/SearchPanes")
3523 ("https://cdn.datatables.net/searchpanes/1.1.1/js/searchPanes.bootstrap4.js"
3524 "1i1arnvxp57z01wc207jxnw9h8clcish6l96c2gnmachgkaz8lqa"
3525 "datatables-extensions/SearchPanes")
3526 ("https://cdn.datatables.net/searchpanes/1.1.1/js/searchPanes.dataTables.js"
3527 "04zzg7i46igcd6gfvdln5alpgjn7m663yf9bf2f3fk9va4fvis6y"
3528 "datatables-extensions/SearchPanes")
3529 ("https://cdn.datatables.net/searchpanes/1.1.1/js/searchPanes.foundation.js"
3530 "0m78wdajxn1m3j9jn9jfwqf73wwsxrsfw4zf84h5y6saj4rrcz72"
3531 "datatables-extensions/SearchPanes")
3532 ("https://cdn.datatables.net/searchpanes/1.1.1/js/searchPanes.jqueryui.js"
3533 "0zb2x736isb8nxrmd7j8nb78lj8h0h9j3axnbjiybwzzk819xw1m"
3534 "datatables-extensions/SearchPanes")
3535 ("https://cdn.datatables.net/searchpanes/1.1.1/js/searchPanes.semanticui.js"
3536 "1781d0xmx7xz0jly0wsw2zbrdmfc1crahmcdbsfbj5s66kdsnd7c"
3537 "datatables-extensions/SearchPanes")
3539 ("https://cdn.datatables.net/select/1.3.1/js/dataTables.select.js"
3540 "0a7bkbz1cizhiq4h417b4rcdr7998pn8q4dlyzx8449xdp0h0n0v"
3541 "datatables-extensions/Select")
3542 ("https://cdn.datatables.net/select/1.3.1/js/select.bootstrap.js"
3543 "0mm5ly3p2iprlfi8ajz548rjqx8lz1sbjj5ysgqmwqg14gw7l9k7"
3544 "datatables-extensions/Select")
3545 ("https://cdn.datatables.net/select/1.3.1/js/select.bootstrap4.js"
3546 "1hv6d9lwgflmxhy7mdfb9rvli2wa2cbkdhqjz64zkf1a1a7wlb5q"
3547 "datatables-extensions/Select")
3548 ("https://cdn.datatables.net/select/1.3.1/js/select.foundation.js"
3549 "1zzygcbngvrqh7m22x0s23k8m5xj5fv1p466pzjs23p94qq24a2r"
3550 "datatables-extensions/Select")
3551 ("https://cdn.datatables.net/select/1.3.1/js/select.jqueryui.js"
3552 "1hv5zlmfifd27hylfqsji09y2hbp3m2hnb7j41418sjrxs63f6x6"
3553 "datatables-extensions/Select")
3554 ("https://cdn.datatables.net/select/1.3.1/js/select.semanticui.js"
3555 "0q6q3vb6pa5nmkxy7zcnjs0bkn4ldw8ykdcfrc04bf1d2hjjaw47"
3556 "datatables-extensions/Select"))))
3562 (uri (cran-uri "DT" version))
3565 "17xs18i439p15agyk7z2xyyrwgrpn5pw09kd3jwxn7qhxi4pyvf6"))
3566 (modules '((guix build utils)))
3568 '(for-each delete-file
3569 (find-files "inst/htmlwidgets/lib" "\\.min\\.js$")))))
3571 `((upstream-name . "DT")))
3572 (build-system r-build-system)
3575 ((guix build r-build-system)
3576 (guix build minify-build-system)
3580 (,@%r-build-system-modules
3581 (guix build minify-build-system))
3583 (modify-phases (@ (guix build r-build-system) %standard-phases)
3584 (add-after 'unpack 'process-javascript
3585 (lambda* (#:key inputs #:allow-other-keys)
3586 (with-directory-excursion "inst/htmlwidgets/lib/"
3587 (for-each (match-lambda
3589 (let* ((input (string-append "js:" (basename url)))
3590 (source (assoc-ref inputs input))
3591 (target (string-append dir "/js/"
3592 (basename url ".js")
3595 (minify source #:target target))))
3596 ',javascript-sources)
3597 (minify (string-append (assoc-ref inputs "datatables-plugins")
3598 "/features/scrollResize/dataTables.scrollResize.js")
3599 #:target "datatables-plugins/features/scrollResize/source.min.js")
3600 (minify (string-append (assoc-ref inputs "datatables-plugins")
3601 "/features/searchHighlight/dataTables.searchHighlight.js")
3602 #:target "datatables-plugins/features/searchHighlight/source.min.js")
3603 (minify (assoc-ref inputs "js-nouislider")
3604 #:target "nouislider/jquery.nouislider.min.js")
3606 (let ((replace-file (lambda (old new)
3607 (format #t "replacing ~a with ~a\n" old new)
3608 (symlink new old))))
3609 (replace-file "selectize/selectize.min.js"
3610 (string-append (assoc-ref inputs "js-selectize")
3611 "/share/javascript/selectize.min.js")))))))))
3621 (list js-selectize))
3623 `(("r-knitr" ,r-knitr)
3624 ("uglifyjs" ,node-uglify-js)
3625 ("datatables-plugins"
3626 ,(let ((version "1.10.20"))
3630 (url "https://github.com/DataTables/Plugins.git")
3632 (file-name (git-file-name "datatables-plugins" version))
3635 "05zni20863ml1711lfllljdfkb3k05h0kpqhkijkbp0bp7q0ak94")))))
3637 ,(let ((version "7.0.10"))
3640 (uri (string-append "https://raw.githubusercontent.com/leongersen/noUiSlider/"
3641 version "/distribute/jquery.nouislider.js"))
3644 "1f7vsfcn7wwzngib6j0wpl0psd6qriiaa6kv728ynfn5da73zfxm")))))
3645 ,@(map (match-lambda
3647 `(,(string-append "js:" (basename url))
3648 ,(origin (method url-fetch)
3650 (sha256 (base32 hash))))))
3651 javascript-sources)))
3652 (home-page "https://rstudio.github.io/DT")
3653 (synopsis "R wrapper of the DataTables JavaScript library")
3655 "This package allows for data objects in R to be rendered as HTML tables
3656 using the JavaScript library @code{DataTables} (typically via R Markdown or
3657 Shiny). The @code{DataTables} library has been included in this R package.")
3658 ;; The DT package as a whole is distributed under GPLv3. The DT package
3659 ;; inludes other software components under different licenses:
3661 ;; * Expat: jquery.highlight.js, DataTables
3662 ;; * WTFPL: noUiSlider
3663 (license (list license:gpl3
3667 (define-public r-base64enc
3669 (name "r-base64enc")
3673 (uri (cran-uri "base64enc" version))
3676 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
3677 (build-system r-build-system)
3678 (home-page "https://www.rforge.net/base64enc")
3679 (synopsis "Tools for Base64 encoding")
3681 "This package provides tools for handling Base64 encoding. It is more
3682 flexible than the orphaned \"base64\" package.")
3683 (license license:gpl2+)))
3685 (define-public r-irlba
3692 (uri (cran-uri "irlba" version))
3695 "1fcv4vazg2sbsda8qqjjsjn2wagcp2bsahvznwm443j66q6qrz16"))))
3696 (build-system r-build-system)
3699 (home-page "https://cran.r-project.org/web/packages/irlba")
3700 (synopsis "Methods for eigendecomposition of large matrices")
3702 "This package provides fast and memory efficient methods for truncated
3703 singular and eigenvalue decompositions, as well as for principal component
3704 analysis of large sparse or dense matrices.")
3705 (license (list license:gpl2+ license:gpl3+))))
3707 (define-public r-glmnet
3714 (uri (cran-uri "glmnet" version))
3716 (base32 "0nij8v44b5dvp1vc843sfkl9ds83n6g687m2p37q1rdn82m3bg34"))))
3717 (build-system r-build-system)
3719 (list gfortran r-knitr))
3727 (home-page "https://www.jstatsoft.org/article/view/v033i01")
3728 (synopsis "Lasso and elastic-net regularized generalized linear models")
3730 "The glmnet package provides efficient procedures for fitting the entire
3731 lasso or elastic-net regularization path for linear and Poisson regression, as
3732 well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
3733 multinomial models. The algorithm uses cyclical coordinate descent in a
3734 path-wise fashion.")
3735 (license license:gpl2+)))
3737 (define-public r-pkgmaker
3744 (uri (cran-uri "pkgmaker" version))
3747 "14ggsd24n5g5rvn0wl4w90ipxzmywqikh28llj89q6kpxwnv4iff"))))
3748 (build-system r-build-system)
3757 (home-page "https://renozao.github.io/pkgmaker")
3758 (synopsis "Package development utilities")
3760 "This package provides some low-level utilities to use for R package
3761 development. It currently provides managers for multiple package specific
3762 options and registries, vignette, unit test and bibtex related utilities.")
3763 (license license:gpl2+)))
3765 (define-public r-registry
3772 (uri (cran-uri "registry" version))
3775 "1k3j6dx350awamr0dwwgkhfs46vsnj4nf08iw5byq0x7n3nkdsnz"))))
3776 (build-system r-build-system)
3777 (home-page "https://cran.r-project.org/web/packages/registry")
3778 (synopsis "Infrastructure for R package registries")
3780 "This package provides a generic infrastructure for creating and using R
3781 package registries.")
3782 (license license:gpl2+)))
3784 (define-public r-rngtools
3791 (uri (cran-uri "rngtools" version))
3794 "0kd7x214cqw7hzpmk1iqy1bn7j6x0ady0yz2hsdbclbq9k57d33z"))))
3795 (build-system r-build-system)
3798 (home-page "https://renozao.github.io/rngtools")
3799 (synopsis "Utility functions for working with random number generators")
3801 "This package contains a set of functions for working with Random Number
3802 Generators (RNGs). In particular, it defines a generic S4 framework for
3803 getting/setting the current RNG, or RNG data that are embedded into objects
3804 for reproducibility. Notably, convenient default methods greatly facilitate
3805 the way current RNG settings can be changed.")
3806 (license license:gpl3+)))
3808 (define-public r-rtsne
3815 (uri (cran-uri "Rtsne" version))
3818 "0v17vxizrs1msay24xl2bckfajr2c82wpqj07lyssbrq197nwdsn"))))
3819 (properties `((upstream-name . "Rtsne")))
3820 (build-system r-build-system)
3823 (home-page "https://github.com/jkrijthe/Rtsne")
3824 (synopsis "T-distributed stochastic neighbor embedding")
3826 "This package provides an R wrapper around the fast T-distributed
3827 Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
3828 ;; The declared license for this package is BSD-3, but it also includes
3829 ;; code licensed under BSD-4.
3830 (license (list license:bsd-3 license:bsd-4))))
3832 (define-public r-e1071
3839 (uri (cran-uri "e1071" version))
3842 "09i2hmyf1bxansqp24p9n9djlzzarclqs173gjjv3fg0giga3ycv"))))
3843 (build-system r-build-system)
3845 (list r-class r-proxy))
3846 (home-page "https://cran.r-project.org/web/packages/e1071")
3847 (synopsis "Miscellaneous functions for probability theory")
3849 "This package provides functions for latent class analysis, short time
3850 Fourier transform, fuzzy clustering, support vector machines, shortest path
3851 computation, bagged clustering, naive Bayes classifier, and more.")
3852 (license license:gpl2+)))
3854 (define-public r-bigmemory-sri
3856 (name "r-bigmemory-sri")
3861 (uri (cran-uri "bigmemory.sri" version))
3863 (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
3865 `((upstream-name . "bigmemory.sri")))
3866 (build-system r-build-system)
3867 (home-page "https://cran.r-project.org/web/packages/bigmemory.sri")
3868 (synopsis "Shared resource interface for the bigmemory package")
3869 (description "This package provides a shared resource interface for the
3870 bigmemory and synchronicity packages.")
3871 ;; Users can choose either LGPLv3 or ASL2.0.
3872 (license (list license:lgpl3 license:asl2.0))))
3874 (define-public r-synchronicity
3876 (name "r-synchronicity")
3881 (uri (cran-uri "synchronicity" version))
3884 "1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx"))))
3885 (build-system r-build-system)
3887 (list r-bh r-bigmemory-sri r-rcpp r-uuid))
3888 (home-page "http://www.bigmemory.org")
3889 (synopsis "Boost mutex functionality in R")
3890 (description "This package provides support for synchronization
3891 via mutexes and may eventually support interprocess communication and
3893 ;; Users can choose either LGPLv3 or ASL2.0.
3894 (license (list license:lgpl3 license:asl2.0))))
3896 (define-public r-bigmemory
3898 (name "r-bigmemory")
3903 (uri (cran-uri "bigmemory" version))
3906 "03pg8mxdc7q0249visjmc8bc3xmwxsfg3i2n6higicj4cfz7zihq"))))
3907 (build-system r-build-system)
3909 (list r-bh r-rcpp r-bigmemory-sri))
3910 (home-page "http://www.bigmemory.org")
3911 (synopsis "Manage large matrices with shared memory or memory-mapped files")
3912 (description "This package provides methods to create, store, access, and
3913 manipulate large matrices. Matrices are allocated to shared memory and may use
3914 memory-mapped files.")
3915 ;; Users can choose either LGPLv3 or ASL2.0.
3916 (license (list license:lgpl3 license:asl2.0))))
3918 (define-public r-r-methodss3
3920 (name "r-r-methodss3")
3924 (uri (cran-uri "R.methodsS3" version))
3927 "16v1br7lf7vxv40z65giv9jnqkpnyqagcmgqa0s1jy7spj0zp64a"))))
3928 (properties `((upstream-name . "R.methodsS3")))
3929 (build-system r-build-system)
3930 (home-page "https://cran.r-project.org/web/packages/R.methodsS3")
3931 (synopsis "S3 methods simplified")
3933 "This package provides methods that simplify the setup of S3 generic
3934 functions and S3 methods. Major effort has been made in making definition of
3935 methods as simple as possible with a minimum of maintenance for package
3936 developers. For example, generic functions are created automatically, if
3937 missing, and naming conflict are automatically solved, if possible. The
3938 method @code{setMethodS3()} is a good start for those who in the future may
3939 want to migrate to S4.")
3940 (license license:lgpl2.1+)))
3942 (define-public r-r-oo
3948 (uri (cran-uri "R.oo" version))
3951 "1divisff26fmiqg6vmabnwlrx079c066r8qvkakfp336vnwdm89p"))))
3952 (properties `((upstream-name . "R.oo")))
3953 (build-system r-build-system)
3955 (list r-r-methodss3))
3956 (home-page "https://github.com/HenrikBengtsson/R.oo")
3957 (synopsis "R object-oriented programming with or without references")
3959 "This package provides methods and classes for object-oriented
3960 programming in R with or without references. Large effort has been made on
3961 making definition of methods as simple as possible with a minimum of
3962 maintenance for package developers.")
3963 (license license:lgpl2.1+)))
3965 (define-public r-r-utils
3971 (uri (cran-uri "R.utils" version))
3974 "1n7y4dzls7dc8fdkm9zncq4cpiblb2a9vwirwjkf72zpjpwn0a32"))))
3975 (properties `((upstream-name . "R.utils")))
3976 (build-system r-build-system)
3978 (list r-r-methodss3 r-r-oo))
3979 (home-page "https://github.com/HenrikBengtsson/R.utils")
3980 (synopsis "Various programming utilities")
3982 "This package provides utility functions useful when programming and
3983 developing R packages.")
3984 (license license:lgpl2.1+)))
3986 (define-public r-r-cache
3992 (uri (cran-uri "R.cache" version))
3995 "09pipn1974ivjh4sm3n5fjlh31rilf87p30qwq7y25vriyqd7d5d"))))
3996 (properties `((upstream-name . "R.cache")))
3997 (build-system r-build-system)
4000 (modify-phases %standard-phases
4001 (add-after 'unpack 'set-HOME
4002 (lambda _ (setenv "HOME" "/tmp"))))))
4004 (list r-digest r-r-methodss3 r-r-oo r-r-utils))
4005 (home-page "https://github.com/HenrikBengtsson/R.cache")
4006 (synopsis "Light-weight caching of objects and results")
4008 "This package provides methods for caching or memoization of objects and
4009 results. With this package, any R object can be cached in a key-value storage
4010 where the key can be an arbitrary set of R objects. The cache memory is
4011 persistent (on the file system).")
4012 (license license:lgpl2.1+)))
4014 (define-public r-r-rsp
4020 (uri (cran-uri "R.rsp" version))
4023 "0n9sxrffahgxcc8h9vgxg5i446g14cibixpf82nkpm5bvidhfsc9"))))
4024 (properties `((upstream-name . "R.rsp")))
4025 (build-system r-build-system)
4028 (modify-phases %standard-phases
4029 (add-after 'unpack 'set-HOME
4030 (lambda _ (setenv "HOME" "/tmp"))))))
4032 (list r-digest r-r-cache r-r-methodss3 r-r-oo r-r-utils))
4033 (home-page "https://github.com/HenrikBengtsson/R.rsp")
4034 (synopsis "Dynamic generation of scientific reports")
4036 "The RSP markup language provides a powerful markup for controlling the
4037 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
4038 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
4039 to many other literate programming languages, with RSP it is straightforward
4040 to loop over mixtures of code and text sections, e.g. in month-by-month
4041 summaries. RSP has also several preprocessing directives for incorporating
4042 static and dynamic contents of external files (local or online) among other
4043 things. RSP is ideal for self-contained scientific reports and R package
4045 (license license:lgpl2.1+)))
4047 (define-public r-mvtnorm
4053 (uri (cran-uri "mvtnorm" version))
4056 "0j14q2bkc14v35s5k03sw44zsssrd2qjljlwzj014qxs74hk0kpz"))))
4057 (build-system r-build-system)
4060 (home-page "http://mvtnorm.R-forge.R-project.org")
4061 (synopsis "Package for multivariate normal and t-distributions")
4062 (description "This package can compute multivariate normal and
4063 t-probabilities, quantiles, random deviates and densities.")
4064 (license license:gpl2)))
4066 (define-public r-matrixstats
4068 (name "r-matrixstats")
4072 (uri (cran-uri "matrixStats" version))
4075 "16pxsba5i51ifbbgvxln2w6nigbwd3290b2ckgzn5bmib7nc1lyv"))))
4076 (properties `((upstream-name . "matrixStats")))
4077 (build-system r-build-system)
4080 (modify-phases %standard-phases
4081 (add-after 'unpack 'set-HOME
4082 (lambda _ (setenv "HOME" "/tmp"))))))
4084 (list r-r-rsp)) ;used to build vignettes
4085 (home-page "https://github.com/HenrikBengtsson/matrixStats")
4086 (synopsis "Methods applying to vectors and matrix rows and columns")
4088 "This package provides methods operating on rows and columns of matrices,
4089 e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
4090 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
4091 @code{weightedMedians()}. All methods have been optimized for speed and
4093 (license license:artistic2.0)))
4095 (define-public r-viridis
4101 (uri (cran-uri "viridis" version))
4104 "048kwhbhd49g86cq11fl7vm0whwhjl5gs9xjn040lwcjv78qrdb9"))))
4105 (build-system r-build-system)
4107 (list r-ggplot2 r-gridextra r-viridislite))
4109 (list r-knitr)) ; for vignettes
4110 (home-page "https://github.com/sjmgarnier/viridis")
4111 (synopsis "Matplotlib default color map")
4113 "This package is a port of the new @url{matplotlib,
4114 http://matplotlib.org/} color maps (@code{viridis}--the default--,
4115 @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
4116 designed in such a way that they will analytically be perfectly
4117 perceptually-uniform, both in regular form and also when converted to
4118 black-and-white. They are also designed to be perceived by readers with the
4119 most common form of color blindness.")
4120 (license license:x11)))
4122 (define-public r-viridislite
4124 (name "r-viridislite")
4129 (uri (cran-uri "viridisLite" version))
4132 "0siwr0vq80gs3sbyd542zjb0cl9av5zqdm0fqnym5g6ribf5b6c4"))))
4133 (properties `((upstream-name . "viridisLite")))
4134 (build-system r-build-system)
4135 (home-page "https://github.com/sjmgarnier/viridisLite")
4136 (synopsis "Default color maps from matplotlib")
4138 "This package is a port of the new @code{matplotlib} color maps
4139 (@code{viridis}, @code{magma}, @code{plasma} and @code{inferno}) to R.
4140 matplotlib is a popular plotting library for Python. These color maps are
4141 designed in such a way that they will analytically be perfectly
4142 perceptually-uniform, both in regular form and also when converted to
4143 black-and-white. They are also designed to be perceived by readers with the
4144 most common form of color blindness. This is the @code{lite} version of the
4145 more complete @code{viridis} package.")
4146 (license license:expat)))
4148 (define-public r-tidyselect
4150 (name "r-tidyselect")
4155 (uri (cran-uri "tidyselect" version))
4158 "0ss8mq05mwif64cj8zmrfx0ljgy3n0fvyv7f37782shr8rknmsqq"))))
4159 (build-system r-build-system)
4161 (list r-ellipsis r-glue r-purrr r-rlang r-vctrs))
4164 (home-page "https://cran.r-project.org/web/packages/tidyselect")
4165 (synopsis "Select from a set of strings")
4167 "This package provides a backend for the selecting functions of the
4168 tidyverse. It makes it easy to implement select-like functions in your own
4169 packages in a way that is consistent with other tidyverse interfaces for
4171 (license license:gpl3)))
4173 (define-public r-tidyr
4180 (uri (cran-uri "tidyr" version))
4183 "0h8jfsmn4r7zgfyjmg2qkjd54n0sncq07xjh4mdf2cx4k2z9h30b"))))
4184 (build-system r-build-system)
4199 (home-page "https://github.com/hadley/tidyr")
4200 (synopsis "Tidy data with `spread()` and `gather()` functions")
4202 "tidyr is a reframing of the reshape2 package designed to accompany the
4203 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
4204 a solid pipeline for data analysis. It is designed specifically for tidying
4205 data, not the general reshaping that reshape2 does, or the general aggregation
4206 that reshape did. In particular, built-in methods only work for data frames,
4207 and tidyr provides no margins or aggregation.")
4208 (license license:expat)))
4210 (define-public r-hexbin
4217 (uri (cran-uri "hexbin" version))
4220 "0bbhs5pwxh474w62sq6gqvih7habancxng9wd4f2rgn6lv9zhhb2"))))
4221 (build-system r-build-system)
4225 (list gfortran r-knitr)) ; for vignettes
4226 (home-page "https://github.com/edzer/hexbin")
4227 (synopsis "Hexagonal binning routines")
4229 "This package provides binning and plotting functions for hexagonal bins.
4230 It uses and relies on grid graphics and formal (S4) classes and methods.")
4231 (license license:gpl2+)))
4233 (define-public r-purrr
4240 (uri (cran-uri "purrr" version))
4243 "1cj091rsjdj2xz16qhynyw72gh5cyhznifcfbrbygndfr4xwksr3"))))
4244 (build-system r-build-system)
4246 (list r-magrittr r-rlang))
4249 (home-page "https://github.com/hadley/purrr")
4250 (synopsis "Functional programming tools")
4252 "This package completes R's functional programming tools with missing
4253 features present in other programming languages.")
4254 (license license:gpl3+)))
4256 (define-public r-plotly
4262 (uri (cran-uri "plotly" version))
4265 "16iqj7sv49mva6siibsci7iijsbnk7pqvfns9al0k35w9mjmr6dx"))))
4266 (build-system r-build-system)
4289 (home-page "https://plot.ly/r")
4290 (synopsis "Create interactive web graphics")
4292 "This package enables the translation of ggplot2 graphs to an interactive
4293 web-based version and/or the creation of custom web-based visualizations
4294 directly from R. Once uploaded to a plotly account, plotly graphs (and the
4295 data behind them) can be viewed and modified in a web browser.")
4296 (license license:x11)))
4298 (define-public r-biased-urn
4300 (name "r-biased-urn")
4305 (uri (cran-uri "BiasedUrn" version))
4308 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
4309 (properties `((upstream-name . "BiasedUrn")))
4310 (build-system r-build-system)
4311 (home-page "https://www.agner.org/random/")
4312 (synopsis "Biased urn model distributions")
4314 "This package provides statistical models of biased sampling in the form
4315 of univariate and multivariate noncentral hypergeometric distributions,
4316 including Wallenius' noncentral hypergeometric distribution and Fisher's
4317 noncentral hypergeometric distribution (also called extended hypergeometric
4319 (license license:gpl3+)))
4321 (define-public r-rematch
4328 (uri (cran-uri "rematch" version))
4331 "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4"))))
4332 (build-system r-build-system)
4333 (home-page "https://github.com/MangoTheCat/rematch")
4334 (synopsis "Match regular expressions with a nicer API")
4336 "This package provides a small wrapper on @code{regexpr} to extract the
4337 matches and captured groups from the match of a regular expression to a
4339 (license license:expat)))
4341 (define-public r-cellranger
4343 (name "r-cellranger")
4348 (uri (cran-uri "cellranger" version))
4351 "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x"))))
4352 (build-system r-build-system)
4354 (list r-rematch r-tibble))
4355 (home-page "https://github.com/rsheets/cellranger")
4356 (synopsis "Translate spreadsheet cell ranges to rows and columns")
4358 "This package provides helper functions to work with spreadsheets and the
4359 @code{A1:D10} style of cell range specification.")
4360 (license license:expat)))
4362 (define-public r-googlesheets
4364 (name "r-googlesheets")
4369 (uri (cran-uri "googlesheets" version))
4372 "11q07nxys72wkxx9mawmjyf20gvwvrb7h3gpa73h6lgh2vgrwnv8"))))
4373 (build-system r-build-system)
4385 (home-page "https://github.com/jennybc/googlesheets")
4386 (synopsis "Manage Google spreadsheets from R")
4387 (description "This package provides tools to interact with Google Sheets
4389 (license license:expat)))
4391 (define-public r-spams
4394 (version "2.6-2017-03-22")
4398 ;; Use the ‘Latest version’ link for a stable URI across releases.
4399 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
4400 "latestfile/4531/spams-R-v" version ".tar.gz"))
4403 "13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx"))))
4404 (build-system r-build-system)
4407 (modify-phases %standard-phases
4408 (add-after 'unpack 'chdir
4409 (lambda _ (chdir "spams") #t))
4410 ;; Don't tune for the building machine.
4411 (add-after 'chdir 'no-mtune
4413 (substitute* "src/Makevars"
4414 (("-mtune=native") ""))
4417 (list r-lattice r-matrix))
4418 (home-page "https://spams-devel.gforge.inria.fr")
4419 (synopsis "Toolbox for solving sparse estimation problems")
4420 (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
4421 for solving various sparse estimation problems. It includes tools for the
4425 @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
4426 component analysis} (PCA), ...)
4427 @item Solving sparse decomposition problems with LARS, coordinate descent,
4428 OMP, SOMP, proximal methods
4429 @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
4430 group lasso, tree-structured regularization, structured sparsity with
4431 overlapping groups,...).
4433 (license license:gpl3+)))
4435 (define-public r-base64
4442 (uri (cran-uri "base64" version))
4445 "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf"))))
4446 (build-system r-build-system)
4449 (home-page "https://cran.r-project.org/web/packages/base64")
4450 (synopsis "Base64 encoder and decoder")
4452 "This package is a compatibility wrapper to replace the orphaned package
4453 by Romain Francois. New applications should use the openssl or base64enc
4455 (license license:expat)))
4457 (define-public r-hmisc
4464 (uri (cran-uri "Hmisc" version))
4466 (base32 "1bd1c8sichyijprfpnqj5g72nmgs9jvi0zyw8v4nsg1kn83fj71c"))))
4467 (properties `((upstream-name . "Hmisc")))
4468 (build-system r-build-system)
4488 (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
4489 (synopsis "Miscellaneous data analysis and graphics functions")
4491 "This package contains many functions useful for data analysis,
4492 high-level graphics, utility operations, functions for computing sample size
4493 and power, importing and annotating datasets, imputing missing values,
4494 advanced table making, variable clustering, character string manipulation,
4495 conversion of R objects to LaTeX code, and recoding variables.")
4496 (license license:gpl2+)))
4498 (define-public r-runit
4505 (uri (cran-uri "RUnit" version))
4508 "1wc1gwb7yw7phf8b0gkig6c23klya3ax11c6i4s0f049k42r78r3"))))
4509 (properties `((upstream-name . "RUnit")))
4510 (build-system r-build-system)
4511 (home-page "https://cran.r-project.org/web/packages/RUnit")
4512 (synopsis "R unit test framework")
4514 "This package provides R functions implementing a standard unit testing
4515 framework, with additional code inspection and report generation tools.")
4516 (license license:gpl2+)))
4518 (define-public r-dynamictreecut
4520 (name "r-dynamictreecut")
4525 (uri (cran-uri "dynamicTreeCut" version))
4528 "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"))))
4529 (properties `((upstream-name . "dynamicTreeCut")))
4530 (build-system r-build-system)
4532 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
4533 (synopsis "Detect clusters in hierarchical clustering dendrograms")
4535 "This package contains methods for the detection of clusters in
4536 hierarchical clustering dendrograms.")
4537 (license license:gpl2+)))
4539 (define-public r-fastcluster
4541 (name "r-fastcluster")
4546 (uri (cran-uri "fastcluster" version))
4549 "009amz7i5yndqw2008fgd3p11n4fsb291k2ypg3pip6dw4lr28hz"))))
4550 (build-system r-build-system)
4551 (home-page "http://danifold.net/fastcluster.html")
4552 (synopsis "Fast hierarchical clustering routines")
4554 "This package implements fast hierarchical, agglomerative clustering
4555 routines. Part of the functionality is designed as drop-in replacement for
4556 existing routines: @code{linkage()} in the SciPy package
4557 @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package,
4558 and the @code{flashClust} package. It provides the same functionality with
4559 the benefit of a much faster implementation. Moreover, there are
4560 memory-saving routines for clustering of vector data, which go beyond what the
4561 existing packages provide.")
4562 (license license:bsd-2)))
4564 (define-public r-sfsmisc
4571 (uri (cran-uri "sfsmisc" version))
4574 "10h76pgzcxv1y5pkmba9607lvjrsyq62sq63s2n7ry7z5151h4lv"))))
4575 (build-system r-build-system)
4576 (home-page "https://cran.r-project.org/web/packages/sfsmisc")
4577 (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
4579 "This package provides useful utilities from Seminar fuer Statistik ETH
4580 Zurich, including many that are related to graphics.")
4581 (license license:gpl2+)))
4583 (define-public r-gtools
4590 (uri (cran-uri "gtools" version))
4593 "0lx97yafrms2mjym8rhcq5586z7s1iqgy8qfm4px3xl1yn5qkc83"))))
4594 (build-system r-build-system)
4595 (home-page "https://cran.r-project.org/web/packages/gtools")
4596 (synopsis "Various R programming tools")
4598 "This package contains a collection of various functions to assist in R
4599 programming, such as tools to assist in developing, updating, and maintaining
4600 R and R packages, calculating the logit and inverse logit transformations,
4601 tests for whether a value is missing, empty or contains only @code{NA} and
4602 @code{NULL} values, and many more.")
4603 (license license:gpl2)))
4605 (define-public r-gdata
4612 (uri (cran-uri "gdata" version))
4615 "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b"))))
4616 (build-system r-build-system)
4621 (home-page "https://cran.r-project.org/web/packages/gdata")
4622 (synopsis "Various R programming tools for data manipulation")
4624 "This package provides various R programming tools for data manipulation,
4628 @item medical unit conversions
4629 @item combining objects
4630 @item character vector operations
4631 @item factor manipulation
4632 @item obtaining information about R objects
4633 @item manipulating MS-Excel formatted files
4634 @item generating fixed-width format files
4635 @item extricating components of date and time objects
4636 @item operations on columns of data frames
4637 @item matrix operations
4638 @item operations on vectors and data frames
4639 @item value of last evaluated expression
4640 @item wrapper for @code{sample} that ensures consistent behavior for
4641 both scalar and vector arguments
4643 (license license:gpl2+)))
4645 (define-public r-gplots
4652 (uri (cran-uri "gplots" version))
4655 "0f8khaymz383w2ksnk80d4kpnvgmdk37pbycpsnl2vabaz11kbpr"))))
4656 (build-system r-build-system)
4658 (list r-catools r-gtools r-kernsmooth))
4661 (home-page "https://cran.r-project.org/web/packages/gplots")
4662 (synopsis "Various R programming tools for plotting data")
4664 "This package provides various R programming tools for plotting data,
4668 @item calculating and plotting locally smoothed summary function
4669 @item enhanced versions of standard plots
4670 @item manipulating colors
4671 @item calculating and plotting two-dimensional data summaries
4672 @item enhanced regression diagnostic plots
4673 @item formula-enabled interface to @code{stats::lowess} function
4674 @item displaying textual data in plots
4676 @item plotting \"Venn\" diagrams
4677 @item displaying Open-Office style plots
4678 @item plotting multiple data on same region, with separate axes
4679 @item plotting means and confidence intervals
4680 @item spacing points in an x-y plot so they don't overlap
4682 (license license:gpl2+)))
4684 (define-public r-rocr
4691 (uri (cran-uri "ROCR" version))
4694 "0amvvrkiflmr3qygrsgrsja4gaf2v6r6h6i2bgpsm8r069vmlf2p"))))
4695 (properties `((upstream-name . "ROCR")))
4696 (build-system r-build-system)
4701 (home-page "https://rocr.bioinf.mpi-sb.mpg.de/")
4702 (synopsis "Visualizing the performance of scoring classifiers")
4704 "ROCR is a flexible tool for creating cutoff-parameterized 2D performance
4705 curves by freely combining two from over 25 performance measures (new
4706 performance measures can be added using a standard interface). Curves from
4707 different cross-validation or bootstrapping runs can be averaged by different
4708 methods, and standard deviations, standard errors or box plots can be used to
4709 visualize the variability across the runs. The parameterization can be
4710 visualized by printing cutoff values at the corresponding curve positions, or
4711 by coloring the curve according to cutoff. All components of a performance
4712 plot can be quickly adjusted using a flexible parameter dispatching
4714 (license license:gpl2+)))
4716 (define-public r-ztable
4722 (uri (cran-uri "ztable" version))
4725 "1ps7ix0hc84s0p0ra6bkjxky3cffs1rvdcagqzj78lbdq22dk5j8"))))
4726 (build-system r-build-system)
4737 (home-page "https://cran.r-project.org/web/packages/ztable")
4738 (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
4740 "This package provides functions to make zebra-striped tables (tables
4741 with alternating row colors) in LaTeX and HTML formats easily from
4742 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
4743 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
4744 @code{cbind.mytable} objects.")
4745 (license license:gpl2+)))
4747 (define-public r-vipor
4753 (uri (cran-uri "vipor" version))
4756 "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx"))))
4757 (build-system r-build-system)
4758 (home-page "https://cran.r-project.org/web/packages/vipor")
4759 (synopsis "Plot categorical data using noise and density estimates")
4761 "This package provides tools to generate a violin point plot, a
4762 combination of a violin/histogram plot and a scatter plot by offsetting points
4763 within a category based on their density using quasirandom noise.")
4764 (license license:gpl2+)))
4766 (define-public r-beeswarm
4772 (uri (cran-uri "beeswarm" version))
4775 "016mqcbdksialkmap56rprzna9b6cd6896ml9gl2n2h8yjdk7x2i"))))
4776 (build-system r-build-system)
4777 (home-page "https://www.cbs.dtu.dk/~eklund/beeswarm/")
4778 (synopsis "Implementation of bee swarm plots")
4780 "This package provides an implementation of bee swarm plots. The bee
4781 swarm plot is a one-dimensional scatter plot like stripchart, but with
4782 closely-packed, non-overlapping points.")
4783 (license license:artistic2.0)))
4785 (define-public r-sourcetools
4787 (name "r-sourcetools")
4792 (uri (cran-uri "sourcetools" version))
4795 "1jnjir0q2dj724f1mjm6p5h77yzyx6xcqy9r2g7gmcxkxw349627"))))
4796 (build-system r-build-system)
4797 (home-page "https://cran.r-project.org/web/packages/sourcetools")
4798 (synopsis "Tools for reading, tokenizing and parsing R code")
4800 "The sourcetools package provides both an R and C++ interface for the
4801 tokenization of R code, and helpers for interacting with the tokenized
4802 representation of R code.")
4803 (license license:expat)))
4805 (define-public r-ggbeeswarm
4807 (name "r-ggbeeswarm")
4811 (uri (cran-uri "ggbeeswarm" version))
4814 "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v"))))
4815 (build-system r-build-system)
4817 (list r-beeswarm r-ggplot2 r-vipor))
4818 (home-page "https://github.com/eclarke/ggbeeswarm")
4819 (synopsis "Categorical scatter (violin point) plots")
4821 "This package provides two methods of plotting categorical scatter plots
4822 such that the arrangement of points within a category reflects the density of
4823 data at that region, and avoids over-plotting.")
4824 (license license:gpl2+)))
4826 (define-public r-ggthemes
4832 (uri (cran-uri "ggthemes" version))
4835 "0rw5f6axyz1pqn6qx9jwm38hjzn8bqs1nfjkvm96z3xnyn61cdbv"))))
4836 (build-system r-build-system)
4838 (list r-ggplot2 r-purrr r-scales r-stringr r-tibble))
4839 (home-page "https://cran.rstudio.com/web/packages/ggthemes")
4840 (synopsis "Extra themes, scales and geoms for @code{ggplot2}")
4841 (description "This package provides extra themes and scales for
4842 @code{ggplot2} that replicate the look of plots by Edward Tufte and
4843 Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The
4844 Wall Street Journal, among others. This package also provides
4845 @code{geoms} for Tufte's box plot and range frame.")
4846 (license license:gpl2)))
4848 (define-public r-statmod
4854 (uri (cran-uri "statmod" version))
4857 "1hkvklcav6gj4zib4g3b4xwsdsbsmnzdblr0v6jaqv227p49gs0l"))))
4858 (build-system r-build-system)
4859 (home-page "https://cran.r-project.org/web/packages/statmod")
4862 (synopsis "Statistical modeling")
4864 "This package provides a collection of algorithms and functions to aid
4865 statistical modeling. It includes growth curve comparisons, limiting dilution
4866 analysis (aka ELDA), mixed linear models, heteroscedastic regression,
4867 inverse-Gaussian probability calculations, Gauss quadrature and a secure
4868 convergence algorithm for nonlinear models. It also includes advanced
4869 generalized linear model functions that implement secure convergence,
4870 dispersion modeling and Tweedie power-law families.")
4871 ;; Statmod is distributed under either license
4872 (license (list license:gpl2 license:gpl3))))
4874 (define-public r-rann
4880 (uri (cran-uri "RANN" version))
4883 "10kid40w9w7vkz2hpcfkdpxr4afxzms5dzvfwr0sl5xynzgw76dj"))))
4885 `((upstream-name . "RANN")))
4886 (build-system r-build-system)
4887 (home-page "https://github.com/jefferis/RANN")
4888 (synopsis "Fast nearest neighbour search")
4890 "This package finds the k nearest neighbours for every point in a given
4891 dataset in O(N log N) time using Arya and Mount's ANN library. Provides
4892 approximate, exact searches, fixed radius searches, bd and kb trees.")
4893 (license license:gpl3+)))
4895 (define-public r-fivethirtyeight
4897 (name "r-fivethirtyeight")
4902 (uri (string-append "https://mran.microsoft.com/src/contrib/"
4903 "fivethirtyeight_" version ".tar.gz"))
4906 "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl"))))
4907 (build-system r-build-system)
4916 (home-page "https://mran.microsoft.com/package/fivethirtyeight/")
4917 (synopsis "Data and code behind the stories at FiveThirtyEight")
4918 (description "This R package provides access to the code and data sets
4919 published by the statistics blog FiveThirtyEight.")
4920 (license license:expat)))
4922 (define-public r-compquadform
4924 (name "r-compquadform")
4929 (uri (cran-uri "CompQuadForm" version))
4932 "1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4"))))
4933 (properties `((upstream-name . "CompQuadForm")))
4934 (build-system r-build-system)
4935 (home-page "https://cran.r-project.org/web/packages/CompQuadForm")
4936 (synopsis "Distribution function of quadratic forms in normal variables")
4938 "This package provides functions to compute the distribution function of
4939 quadratic forms in normal variables using Imhof's method, Davies's algorithm,
4940 Farebrother's algorithm or Liu et al.'s algorithm.")
4941 (license license:gpl2+)))
4943 (define-public r-cowplot
4950 (uri (cran-uri "cowplot" version))
4953 "0j7d5vhzdxn1blrsfafx5z8lhq122rp8230hp9czrpsnnhjydp67"))))
4954 (build-system r-build-system)
4956 (list r-ggplot2 r-gtable r-rlang r-scales))
4959 (home-page "https://github.com/wilkelab/cowplot")
4960 (synopsis "Streamlined plot theme and plot annotations for ggplot2")
4962 "This package provides some helpful extensions and modifications to the
4963 ggplot2 package to combine multiple ggplot2 plots into one and label them with
4964 letters, as is often required for scientific publications.")
4965 (license license:gpl2)))
4967 (define-public r-mixtools
4974 (uri (cran-uri "mixtools" version))
4977 "08whic8hmmzi55b7azwj11l2x5r9s5qbyrv7s9jr08156vqkw0zg"))))
4978 (build-system r-build-system)
4980 (list r-mass r-kernlab r-segmented r-survival))
4981 (home-page "https://cran.r-project.org/web/packages/mixtools")
4982 (synopsis "Tools for analyzing finite mixture models")
4984 "This package provides a collection of R functions for analyzing finite
4986 (license license:gpl2+)))
4988 (define-public r-lars
4995 (uri (cran-uri "lars" version))
4998 "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
4999 (build-system r-build-system)
5002 (home-page "https://web.stanford.edu/~hastie/Papers/LARS/")
5003 (synopsis "Least angle regression software")
5005 "Least Angle Regression (\"LAR\") is a model selection algorithm; a
5006 useful and less greedy version of traditional forward selection methods. A
5007 simple modification of the LAR algorithm implements Tibshirani's Lasso; the
5008 Lasso modification of LARS calculates the entire Lasso path of coefficients
5009 for a given problem at the cost of a single least squares fit. Another LARS
5010 modification efficiently implements epsilon Forward Stagewise linear
5012 (license license:gpl2)))
5014 (define-public r-fastica
5021 (uri (cran-uri "fastICA" version))
5024 "0l49cmxm1n4dzrv8q3q3mq4drcjgby4f1dmpwfdb8jxn9ij85vz9"))))
5025 (properties `((upstream-name . "fastICA")))
5026 (build-system r-build-system)
5027 (home-page "https://cran.r-project.org/web/packages/fastICA")
5028 (synopsis "FastICA algorithms to perform ICA and projection pursuit")
5030 "This package provides an implementation of the FastICA algorithm to
5031 perform @dfn{independent component analysis} (ICA) and projection pursuit.")
5033 (license license:gpl3+)))
5035 (define-public r-randomforest
5037 (name "r-randomforest")
5042 (uri (cran-uri "randomForest" version))
5045 "0kbmm0l42fc2d1rdq0l7k09d34kd87q4lx651ffsic4y84h8kf7l"))))
5046 (properties `((upstream-name . "randomForest")))
5047 (build-system r-build-system)
5048 (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
5051 (synopsis "Breiman and Cutler's random forests for classification and regression")
5053 "This package provides the Breiman and Cutler's random forests algorithm, based on a
5054 forest of trees using random inputs, for classification and regression.")
5055 (license license:gpl2+)))
5057 (define-public r-diptest
5064 (uri (cran-uri "diptest" version))
5067 "10629vwn6r2949jjrmj5slbb5v0vnm3w0v8mrl7ws68m2sxmx2jh"))))
5068 (build-system r-build-system)
5069 (home-page "https://cran.r-project.org/web/packages/diptest")
5070 (synopsis "Hartigan's dip test statistic for unimodality")
5072 "This package computes Hartigan's dip test statistic for unimodality,
5073 multimodality and provides a test with simulation based p-values, where the
5074 original public code has been corrected.")
5075 (license license:gpl2+)))
5077 (define-public r-modeltools
5079 (name "r-modeltools")
5084 (uri (cran-uri "modeltools" version))
5087 "1vqh69256h344sbj5affm0kmc77dakrxp6442xfdnfd0y5d8sgkb"))))
5088 (build-system r-build-system)
5089 (home-page "https://cran.r-project.org/web/packages/modeltools")
5090 (synopsis "Tools and classes for statistical models")
5092 "This package provides a collection of tools to deal with statistical
5093 models. The functionality is experimental and the user interface is likely
5094 to change in the future.")
5095 (license license:gpl2)))
5097 (define-public r-flexmix
5104 (uri (cran-uri "flexmix" version))
5107 "0jangf89174p0idh9afbicfiln2sz8jxc3bjc6n0j9036dw9n09n"))))
5108 (build-system r-build-system)
5110 (list r-lattice r-modeltools r-nnet))
5111 (home-page "https://cran.r-project.org/web/packages/flexmix")
5112 (synopsis "Flexible mixture modeling")
5114 "This package implements a general framework for finite mixtures of
5115 regression models using the EM algorithm. FlexMix provides the E-step and
5116 all data handling, while the M-step can be supplied by the user to easily
5117 define new models. Existing drivers implement mixtures of standard linear
5118 models, generalized linear models and model-based clustering.")
5119 (license license:gpl2+)))
5121 (define-public r-mclust
5128 (uri (cran-uri "mclust" version))
5131 "0s4mva0n04f3pl41msmzhlh7pnk0zbmf06n826smxkw6mz327wb5"))))
5132 (build-system r-build-system)
5134 (list gfortran r-knitr))
5135 (home-page "https://www.stat.washington.edu/mclust/")
5136 (synopsis "Gaussian mixture modelling for model-based clustering etc.")
5138 "This package provides Gaussian finite mixture models fitted via EM
5139 algorithm for model-based clustering, classification, and density estimation,
5140 including Bayesian regularization, dimension reduction for visualisation,
5141 and resampling-based inference.")
5142 (license license:gpl2+)))
5144 (define-public r-prabclus
5151 (uri (cran-uri "prabclus" version))
5154 "0hg4d7y1w18jpgvw10z8833bbbcnlkwiasx0wh6iwa2pnnybq8gl"))))
5155 (build-system r-build-system)
5157 (list r-mass r-mclust))
5158 (home-page "https://cran.r-project.org/web/packages/prabclus")
5159 (synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
5161 "This package provides distance-based parametric bootstrap tests for
5162 clustering with spatial neighborhood information. It implements some distance
5163 measures, clustering of presence-absence, abundance and multilocus genetical
5164 data for species delimitation, nearest neighbor based noise detection.")
5165 (license license:gpl2+)))
5167 (define-public r-deoptimr
5174 (uri (cran-uri "DEoptimR" version))
5177 "1m9ag073i7pbxsy74vkj0n4hjn6vmyc4n0k78nmslwwwmjh7nkvp"))))
5178 (properties `((upstream-name . "DEoptimR")))
5179 (build-system r-build-system)
5180 (home-page "https://cran.r-project.org/web/packages/DEoptimR")
5181 (synopsis "Differential evolution optimization in pure R")
5183 "This package provides a differential evolution (DE) stochastic
5184 algorithms for global optimization of problems with and without constraints.
5185 The aim is to curate a collection of its state-of-the-art variants that (1) do
5186 not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
5187 can be efficiently implemented directly in the R language.")
5188 (license license:gpl2+)))
5190 (define-public r-robustbase
5192 (name "r-robustbase")
5197 (uri (cran-uri "robustbase" version))
5200 "0i9wf4aq8zpn2np6z2rjja21ks9n740dgkiv0qfwdzk3ah3vapyp"))))
5201 (build-system r-build-system)
5206 (home-page "http://robustbase.r-forge.r-project.org/")
5207 (synopsis "Basic robust statistics")
5209 "This package analyzes data with robust methods such as
5210 regression methodology including model selections and multivariate statistics.")
5211 (license license:gpl2+)))
5213 (define-public r-pcapp
5220 (uri (cran-uri "pcaPP" version))
5223 "1dlrz5plb8b89vr3j6sn9jwryyhcwflqkiilxkybbr379m1pp0sh"))))
5224 (properties `((upstream-name . "pcaPP")))
5225 (build-system r-build-system)
5228 (home-page "https://cran.r-project.org/web/packages/pcaPP")
5229 (synopsis "Robust PCA by projection pursuit")
5231 "This package provides functions for robust @dfn{principal component
5232 analysis} (PCA) by projection pursuit.")
5233 (license license:gpl3+)))
5235 (define-public r-rrcov
5242 (uri (cran-uri "rrcov" version))
5245 "0i69gv55c86gkclwhch0jzdfyb20l20mx1nx1xp9qz71nd4klpvr"))))
5246 (build-system r-build-system)
5248 (list r-lattice r-mvtnorm r-pcapp r-robustbase))
5251 (home-page "https://cran.r-project.org/web/packages/rrcov")
5252 (synopsis "Scalable robust estimators with high breakdown Point")
5254 "This package provides an implementation of robust location and scatter
5255 estimation and robust multivariate analysis with high breakdown point.")
5256 (license license:gpl2+)))
5258 (define-public r-fit-models
5260 (name "r-fit-models")
5265 (uri (cran-uri "fit.models" version))
5268 "1nk4x2q8cv79zcls61saf627ac0fci6jcrd6lmzk61asm2zhc27p"))))
5269 (properties `((upstream-name . "fit.models")))
5270 (build-system r-build-system)
5273 (home-page "https://cran.r-project.org/web/packages/fit.models")
5274 (synopsis "Compare fitted models")
5276 "The @code{fit.models} function and its associated methods (coefficients, print,
5277 summary, plot, etc.) were originally provided in the @code{robust} package to
5278 compare robustly and classically fitted model objects. The aim of the
5279 @code{fit.models} package is to separate this fitted model object comparison
5280 functionality from the robust package and to extend it to support fitting
5281 methods (e.g., classical, robust, Bayesian, regularized, etc.) more
5283 ;; Any version of the GPL
5284 (license (list license:gpl2+ license:gpl3+))))
5286 (define-public r-robust
5293 (uri (cran-uri "robust" version))
5296 "0z8i0qqlsa6vpl457qir3dlsynhjfn2g22436d776vxwyqjx4vs9"))))
5297 (build-system r-build-system)
5299 (list r-fit-models r-lattice r-mass r-robustbase r-rrcov))
5302 (home-page "https://cran.r-project.org/web/packages/robust")
5303 (synopsis "Port of the S+ \"Robust Library\"")
5305 "This package is a port of the S+ \"Robust Library\". It provides
5306 methods for robust statistics, notably for robust regression and robust
5307 multivariate analysis.")
5308 (license license:gpl2)))
5310 (define-public r-trimcluster
5312 (name "r-trimcluster")
5317 (uri (cran-uri "trimcluster" version))
5320 "12siv8yx8dcavsz8jk96lwscbj257ar8jpaxksl2zb06987g4fcj"))))
5321 (build-system r-build-system)
5322 (home-page "https://cran.r-project.org/web/packages/trimcluster")
5323 (synopsis "Cluster analysis with trimming")
5325 "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
5326 Matran (1997). This optimizes the k-means criterion under trimming a portion
5329 (license (list license:gpl2+ license:gpl3+))))
5331 (define-public r-fpc
5338 (uri (cran-uri "fpc" version))
5341 "0f7sfmpcycr9y7cy5gasyjm2ardxa62kglqms92mcr68jrp01c19"))))
5342 (build-system r-build-system)
5353 (home-page "https://cran.r-project.org/web/packages/fpc")
5354 (synopsis "Flexible procedures for clustering")
5356 "This package provides various methods for clustering and cluster validation.
5357 For example, it provides fixed point clustering, linear regression clustering,
5358 clustering by merging Gaussian mixture components, as well as symmetric and
5359 asymmetric discriminant projections for visualisation of the separation of
5361 (license license:gpl2+)))
5363 (define-public r-vgam
5370 (uri (cran-uri "VGAM" version))
5372 (base32 "1fx123h4x5awzshv0m4jqbbllrdjfpslb2i8gl9phm1y1wahn69h"))))
5373 (properties `((upstream-name . "VGAM")))
5374 (build-system r-build-system)
5377 (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
5378 (synopsis "Vector generalized linear and additive models")
5380 "This package is an implementation of about 6 major classes of statistical
5381 regression models. Currently only fixed-effects models are implemented, i.e.,
5382 no random-effects models. Many (150+) models and distributions are estimated
5383 by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
5384 VGLMs can be loosely thought of as multivariate generalised linear models.")
5385 (license license:gpl2+)))
5387 (define-public r-pbapply
5394 (uri (cran-uri "pbapply" version))
5397 "0m8a0ygwl98cs0vcha5gs9f7z8whcplwxhravhs9bfp5hvigxzgg"))))
5398 (build-system r-build-system)
5399 (home-page "https://github.com/psolymos/pbapply")
5400 (synopsis "Adding progress bar to apply functions")
5402 "This lightweight package that adds progress bar to vectorized R
5403 functions apply. The implementation can easily be added to functions where
5404 showing the progress is useful e.g. bootstrap.")
5405 (license license:gpl2)))
5407 (define-public r-minqa
5414 (uri (cran-uri "minqa" version))
5417 "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
5418 (build-system r-build-system)
5423 (home-page "http://optimizer.r-forge.r-project.org")
5424 (synopsis "Derivative-free optimization algorithms by quadratic approximation")
5426 "This package provides a derivative-free optimization by quadratic approximation
5427 based on an interface to Fortran implementations by M. J. D. Powell.")
5428 (license license:gpl2)))
5430 (define-public r-rcppeigen
5432 (name "r-rcppeigen")
5433 (version "0.3.3.9.1")
5437 (uri (cran-uri "RcppEigen" version))
5440 "0qp9gypar280lm84pc8w0fxw4jgwqygwi3qnl5sl52kpkcj8c14a"))))
5441 (properties `((upstream-name . "RcppEigen")))
5442 (build-system r-build-system)
5444 (list r-rcpp r-matrix))
5445 (home-page "http://eigen.tuxfamily.org")
5446 (synopsis "Rcpp integration for the Eigen templated linear algebra library")
5448 "This package provides an integration of Eigen in R using a C++ template
5449 library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
5450 It supports dense and sparse matrices on integer, floating point and complex numbers,
5451 decompositions of such matrices, and solutions of linear systems.")
5452 (license license:gpl2+)))
5454 (define-public r-modelmetrics
5456 (name "r-modelmetrics")
5461 (uri (cran-uri "ModelMetrics" version))
5464 "0mrlsw4c5y1vdsqynxr2dcvmhh5h37pnd71jw5a5djpbda9g21jy"))))
5465 (properties `((upstream-name . "ModelMetrics")))
5466 (build-system r-build-system)
5468 (list r-rcpp r-data-table))
5469 (home-page "https://cran.r-project.org/web/packages/ModelMetrics")
5470 (synopsis "Rapid calculation of model metrics")
5472 "Written in C++ using @code{Rcpp}, this package provides a collection of
5473 metrics for evaluating models.")
5474 (license license:gpl2+)))
5476 (define-public r-matrixmodels
5478 (name "r-matrixmodels")
5483 (uri (cran-uri "MatrixModels" version))
5486 "1va6i6bpkq71rzl9i4xgyc5x7qcksa3nfzihlaggf6aj30dayzx8"))))
5487 (properties `((upstream-name . "MatrixModels")))
5488 (build-system r-build-system)
5491 (home-page "https://cran.r-project.org/web/packages/MatrixModels")
5492 (synopsis "Modelling with sparse and dense matrices")
5494 "This package models with sparse and dense matrix matrices,
5495 using modular prediction and response module classes.")
5496 (license license:gpl2+)))
5498 (define-public r-quantreg
5505 (uri (cran-uri "quantreg" version))
5507 (base32 "01fnp6ndh7npxj76xlynndacsgmcfr9kgh2waw0clx3mmwlwilbi"))))
5508 (build-system r-build-system)
5512 (list r-conquer r-matrix r-matrixmodels r-sparsem))
5513 (home-page "https://www.r-project.org")
5514 (synopsis "Quantile regression")
5516 "This package provides an estimation and inference methods for models
5517 of conditional quantiles: linear and nonlinear parametric and non-parametric
5518 models for conditional quantiles of a univariate response and several methods
5519 for handling censored survival data. Portfolio selection methods based on
5520 expected shortfall risk are also included.")
5521 (license license:gpl2+)))
5523 (define-public r-nloptr
5530 (uri (cran-uri "nloptr" version))
5533 "1zznk9f2w2g02zqzay21k8xqzfvc6icxfzp6bx2wpd77sm7vf25g"))))
5534 (build-system r-build-system)
5536 (list r-knitr ; for building vignettes
5537 pkg-config gfortran))
5540 (home-page "https://cran.r-project.org/web/packages/nloptr")
5541 (synopsis "R interface to NLopt")
5543 "This package is interface to NLopt, a library for nonlinear
5544 optimization. NLopt is a library for nonlinear optimization, providing a
5545 common interface for a number of different free optimization routines
5546 available online as well as original implementations of various other
5548 (license license:lgpl3)))
5550 (define-public r-lme4
5553 (version "1.1-27.1")
5557 (uri (cran-uri "lme4" version))
5560 "1i9f8kl2qj48j75dbn1vmwxz1xlbikdr7v2yq542w6dq74z8gyi5"))))
5561 (build-system r-build-system)
5574 (home-page "https://cran.r-project.org/web/packages/lme4")
5575 (synopsis "Linear mixed-effects models using eigen and S4")
5577 "This package provides fit linear and generalized linear mixed-effects
5578 models. The models and their components are represented using S4 classes and
5579 methods. The core computational algorithms are implemented using the Eigen
5580 C++ library for numerical linear algebra and RcppEigen glue.")
5581 (license license:gpl2+)))
5583 (define-public r-pbkrtest
5590 (uri (cran-uri "pbkrtest" version))
5593 "1if7msv9i7jhg1as1f7m81a95dnwhwj3yfs24bqr0f6r0ch4b8xj"))))
5594 (build-system r-build-system)
5605 (home-page "https://people.math.aau.dk/~sorenh/software/pbkrtest/")
5606 (synopsis "Methods for linear mixed model comparison")
5608 "This package implements a parametric bootstrap test and a Kenward Roger
5609 modification of F-tests for linear mixed effects models and a parametric
5610 bootstrap test for generalized linear mixed models.")
5611 (license license:gpl2+)))
5613 (define-public r-cardata
5620 (uri (cran-uri "carData" version))
5622 (base32 "06j52rpbqi6fj7chfjwjbwbr6slrbb7i3aygv66gnfiyndcp3rq2"))))
5623 (properties `((upstream-name . "carData")))
5624 (build-system r-build-system)
5625 (home-page "https://r-forge.r-project.org/projects/car/")
5626 (synopsis "Data Sets for the book Companion to Applied Regression")
5628 "This package provides datasets to accompany J. Fox and S. Weisberg, An R
5629 Companion to Applied Regression, Third Edition, Sage.")
5630 (license license:gpl2+)))
5632 (define-public r-car
5639 (uri (cran-uri "car" version))
5641 (base32 "00kk8l71508f73kyn21is1mx6kjbrzdq3ls94c5ajhiqmvpsd6dq"))))
5642 (build-system r-build-system)
5656 (home-page "https://r-forge.r-project.org/projects/car/")
5657 (synopsis "Companion to applied regression")
5659 "This package provides functions and datasets from book Companion
5660 to Applied regression, Second Edition, Sage, 2011.")
5661 (license license:gpl2+)))
5663 (define-public r-rcppprogress
5665 (name "r-rcppprogress")
5670 (uri (cran-uri "RcppProgress" version))
5673 "0j2b37gwjpgmrnr00srdzm751hzlpsjb54ph63xxmcdfnwhlnqmi"))))
5674 (properties `((upstream-name . "RcppProgress")))
5675 (build-system r-build-system)
5676 (home-page "https://github.com/kforner/rcpp_progress")
5677 (synopsis "Interruptible progress bar for C++ in R packages")
5679 "This package displays a progress bar in the R console for long running
5680 computations taking place in C++ code, and support for interrupting those computations
5681 even in multithreaded code, typically using OpenMP.")
5682 (license license:gpl3+)))
5684 (define-public r-tmvnsim
5691 (uri (cran-uri "tmvnsim" version))
5694 "03xsvsg9bqvgl98ywid3h91mmlhax5s6wvmypp3hq91vmc5kvxlp"))))
5695 (properties `((upstream-name . "tmvnsim")))
5696 (build-system r-build-system)
5697 (native-inputs (list gfortran))
5698 (home-page "https://www.r-project.org")
5699 (synopsis "Truncated multivariate normal simulation")
5701 "This package implements importance sampling from the truncated
5702 multivariate normal using the @dfn{Geweke-Hajivassiliou-Keane} (GHK)
5703 simulator. Unlike Gibbs sampling which can get stuck in one truncation
5704 sub-region depending on initial values, this package allows truncation based
5705 on disjoint regions that are created by truncation of absolute values. The
5706 GHK algorithm uses simple Cholesky transformation followed by recursive
5707 simulation of univariate truncated normals hence there are also no convergence
5708 issues. Importance sample is returned along with sampling weights, based on
5709 which, one can calculate integrals over truncated regions for multivariate
5711 (license license:gpl2)))
5713 (define-public r-mnormt
5720 (uri (cran-uri "mnormt" version))
5723 "0d7ka4l4fl1wi77r2r81dc91n6cbj2xrb3lsizz5y0ziscva0sjw"))))
5724 (build-system r-build-system)
5729 (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
5730 (synopsis "Multivariate normal and \"t\" distributions")
5732 "This package provides functions for computing the density and the
5733 distribution function of multivariate normal and \"t\" random variables, and
5734 for generating random vectors sampled from these distributions. Probabilities
5735 are computed via non-Monte Carlo methods.")
5736 (license license:gpl2+)))
5738 (define-public r-numderiv
5741 (version "2016.8-1.1")
5745 (uri (cran-uri "numDeriv" version))
5748 "0idk02pqkziik932bd8k72d1q775g1is3m4bc861pcxfz6gx3i6q"))))
5749 (properties `((upstream-name . "numDeriv")))
5750 (build-system r-build-system)
5751 (home-page "https://cran.r-project.org/web/packages/numDeriv")
5752 (synopsis "Accurate numerical derivatives")
5754 "This package provides methods for calculating accurate numerical
5755 first and second order derivatives.")
5756 (license license:gpl2)))
5765 (uri (cran-uri "sn" version))
5768 "1z58kwvq8igjm3biyyjdlhs2qq8hfjq5d9x0lzy80yk5hw08kcw6"))))
5769 (build-system r-build-system)
5771 (list r-mnormt r-numderiv r-quantreg))
5772 (home-page "http://azzalini.stat.unipd.it/SN")
5773 (synopsis "The skew-normal and skew-t distributions")
5775 "This package provides functionalities to build and manipulate
5776 probability distributions of the skew-normal family and some related
5777 ones, notably the skew-t family, and provides related statistical
5778 methods for data fitting and diagnostics, in the univariate and the
5779 multivariate case.")
5780 (license license:gpl2+)))
5782 (define-public r-tclust
5789 (uri (cran-uri "tclust" version))
5792 "1nb5iky4kc832627jf28lzj19wrvgwg5da6fyl3kyf0npmyx1p4m"))))
5793 (build-system r-build-system)
5794 ;; These are all suggested packages, not build dependencies.
5796 (list r-cluster r-mclust r-mvtnorm r-sn))
5797 (home-page "https://cran.r-project.org/web/packages/tclust")
5798 (synopsis "Robust trimmed clustering")
5800 "This package implements different robust clustering
5801 algorithms (@code{tclust}) based on trimming and including some graphical
5802 diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
5803 (license license:gpl3)))
5805 (define-public r-ranger
5812 (uri (cran-uri "ranger" version))
5815 "02idcc6zbdz4wsi1mcwh7qyhmlbwvnzxwkdvvppxw7n2rh54z4v0"))))
5816 (build-system r-build-system)
5818 (list r-rcpp r-matrix r-rcppeigen))
5819 (home-page "https://github.com/imbs-hl/ranger")
5820 (synopsis "Fast implementation of random forests")
5822 "This package provides a fast implementation of Random Forests,
5823 particularly suited for high dimensional data. Ensembles of classification,
5824 regression, survival and probability prediction trees are supported. Data from
5825 genome-wide association studies can be analyzed efficiently.")
5826 (license license:gpl3)))
5828 (define-public r-tsne
5835 (uri (cran-uri "tsne" version))
5838 "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
5839 (build-system r-build-system)
5840 (home-page "https://github.com/jdonaldson/rtsne/")
5841 (synopsis "t-Distributed Stochastic Neighbor Embedding for R")
5843 "This package provides a pure R implementation of the t-SNE algorithm.")
5844 (license license:gpl2+)))
5846 (define-public r-cairo
5853 (uri (cran-uri "Cairo" version))
5856 "0ysc40smkjwk8fmp5dk0q3nbp9xkxzz9pd4z5zkp2mrvrvx52xq6"))))
5857 (properties `((upstream-name . "Cairo")))
5858 (build-system r-build-system)
5860 (list cairo libxt zlib))
5863 (home-page "https://www.rforge.net/Cairo/")
5864 (synopsis "R graphics device using Cairo graphics library")
5866 "This package provides a Cairo graphics device that can be use to
5867 create high-quality vector (PDF, PostScript and SVG) and bitmap
5868 output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11
5869 and Win32). Since it uses the same back-end for all output, copying
5870 across formats is WYSIWYG. Files are created without the dependence
5871 on X11 or other external programs. This device supports alpha
5872 channel (semi-transparent drawing) and resulting images can contain
5873 transparent and semi-transparent regions. It is ideal for use in
5874 server environments (file output) and as a replacement for other
5875 devices that don't have Cairo's capabilities such as alpha support or
5876 anti-aliasing. Backends are modular such that any subset of backends
5878 (license license:gpl2)))
5880 (define-public r-lubridate
5882 (name "r-lubridate")
5887 (uri (cran-uri "lubridate" version))
5890 "199b00cql07gf3rf4hh5ba34amnk0ai40zhx73dq1mpkn7ynxml7"))))
5891 (build-system r-build-system)
5893 (list r-generics r-cpp11))
5896 (home-page "https://cran.r-project.org/web/packages/lubridate/")
5897 (synopsis "Make dealing with dates a little easier")
5899 "This package provides functions to work with date-times and time-spans:
5900 fast and user friendly parsing of date-time data, extraction and updating of
5901 components of a date-time (years, months, days, hours, minutes, and seconds),
5902 algebraic manipulation on date-time and time-span objects. The @code{lubridate}
5903 package has a consistent and memorable syntax that makes working with dates
5905 (license license:gpl2)))
5907 (define-public r-fdrtool
5914 (uri (cran-uri "fdrtool" version))
5917 "1pf554vb902vavgqc4c0kgghywbgcvr3lkkr414bxngavcd60lil"))))
5918 (build-system r-build-system)
5919 (home-page "http://strimmerlab.org/software/fdrtool/")
5920 (synopsis "Estimation of false discovery rates and higher criticism")
5922 "This package provides tools to estimate tail area-based false discovery
5923 rates as well as local false discovery rates for a variety of null
5924 models (p-values, z-scores, correlation coefficients, t-scores). The
5925 proportion of null values and the parameters of the null distribution are
5926 adaptively estimated from the data. In addition, the package contains
5927 functions for non-parametric density estimation (Grenander estimator), for
5928 monotone regression (isotonic regression and antitonic regression with
5929 weights), for computing the @dfn{greatest convex minorant} (GCM) and the
5930 @dfn{least concave majorant} (LCM), for the half-normal and correlation
5931 distributions, and for computing empirical @dfn{higher criticism} (HC) scores
5932 and the corresponding decision threshold.")
5933 (license license:gpl3+)))
5935 (define-public r-forcats
5942 (uri (cran-uri "forcats" version))
5945 "12d2nv2w15085jscgidmjdnr1ryymciflcmal6ldmgp2fkl9dyy4"))))
5946 (build-system r-build-system)
5948 (list r-ellipsis r-magrittr r-tibble r-rlang))
5951 (home-page "https://forcats.tidyverse.org")
5952 (synopsis "Tools for working with factors")
5953 (description "This package provides helpers for reordering factor
5954 levels (including moving specified levels to front, ordering by first
5955 appearance, reversing, and randomly shuffling), and tools for modifying factor
5956 levels (including collapsing rare levels into other, \"anonymizing\", and
5957 manually \"recoding\").")
5958 (license license:gpl3)))
5960 (define-public r-tgstat
5961 (let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f")
5965 (version (string-append "1.0.2-" revision "." (string-take changeset 7)))
5970 (url "https://bitbucket.org/tanaylab/tgstat")
5971 (changeset changeset)))
5972 (file-name (string-append name "-" version "-checkout"))
5975 "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
5976 (build-system r-build-system)
5979 (modify-phases %standard-phases
5980 (add-after 'unpack 'fix-isnan
5982 (substitute* "src/tgstat.h"
5983 (("#define isnan ::isnan")
5984 "#define isnan std::isnan"))
5988 (home-page "https://bitbucket.org/tanaylab/tgstat/")
5989 (synopsis "Tanay's group statistical utilities")
5991 "The goal of tgstat is to provide fast and efficient statistical
5993 (license license:gpl2))))
5995 (define-public r-tgconfig
5996 (let ((changeset "1e02c7614713bd0866c46f0c679a058f8c6d627e")
6000 (version (string-append "0.0.0.9000-" revision "." (string-take changeset 7)))
6005 (url "https://bitbucket.org/tanaylab/tgconfig")
6006 (changeset changeset)))
6007 (file-name (string-append name "-" version "-checkout"))
6010 "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
6011 (build-system r-build-system)
6014 (home-page "https://bitbucket.org/tanaylab/tgconfig/")
6015 (synopsis "Infrastructure for managing package parameters")
6017 "The goal of tgconfig is to provide infrastructure for managing package
6019 (license license:gpl3))))
6021 (define-public r-catterplots
6022 (let ((commit "ae17cd5e49ddda4ecfe0eba8a4c21df8c88e72c4")
6025 (name "r-catterplots")
6026 (version (git-version "0" revision commit))
6030 (url "https://github.com/Gibbsdavidl/CatterPlots")
6032 (file-name (git-file-name name version))
6035 "0qa8liylffpxgdg8xcgjar5dsvczqhn3akd4w35113hnyg1m4xyg"))))
6036 (build-system r-build-system)
6039 (home-page "https://github.com/Gibbsdavidl/CatterPlots")
6040 (synopsis "Scatter plots with cat shaped points")
6041 (description "Did you ever wish you could make scatter plots with cat
6042 shaped points? Now you can!")
6043 (license license:asl2.0))))
6045 (define-public r-colorout
6053 (url "https://github.com/jalvesaq/colorout")
6054 (commit (string-append "v" version))))
6055 (file-name (git-file-name name version))
6057 (base32 "1rsx69wjpa73c6x2hacvvvbzdzxn7wg06gizf97kasjdlb7azmp3"))))
6058 (build-system r-build-system)
6059 (home-page "https://github.com/jalvesaq/colorout")
6060 (synopsis "Colorize output in the R REPL")
6061 (description "@code{colorout} is an R package that colorizes R output when
6062 running in terminal emulator.
6064 R STDOUT is parsed and numbers, negative numbers, dates in the standard
6065 format, strings, and R constants are identified and wrapped by special ANSI
6066 scape codes that are interpreted by terminal emulators as commands to colorize
6067 the output. R STDERR is also parsed to identify the expressions warning and
6068 error and their translations to many languages. If these expressions are
6069 found, the output is colorized accordingly; otherwise, it is colorized as
6070 STDERROR (blue, by default).
6072 You can customize the colors according to your taste, guided by the color
6073 table made by the command @code{show256Colors()}. You can also set the colors
6074 to any arbitrary string. In this case, it is up to you to set valid values.")
6075 (license license:gpl3+)))
6077 (define-public python-rpy2
6079 (name "python-rpy2")
6084 (uri (pypi-uri "rpy2" version))
6087 "1cysswxr5glrdblyl2zsmywcj7xhxn3wmyihxinrz9gm8gmaacax"))))
6088 (build-system python-build-system)
6091 (modify-phases %standard-phases
6093 (lambda* (#:key outputs inputs #:allow-other-keys)
6094 (let ((cwd (getcwd)))
6095 (setenv "TZ" "UTC"))
6096 ;; test_vector_complex has issues when run in our environment.
6097 (invoke "pytest" "-v" "rpy2/tests/"
6098 "-k" "not test_vector_complex"))))))
6120 (list zlib python-pytest))
6121 (home-page "https://rpy2.github.io")
6122 (synopsis "Python interface to the R language")
6123 (description "rpy2 is a redesign and rewrite of rpy. It is providing a
6124 low-level interface to R from Python, a proposed high-level interface,
6125 including wrappers to graphical libraries, as well as R-like structures and
6127 ;; Any of these licenses can be picked for the R interface. The whole
6128 ;; project is released under GPLv2+ according to the license declaration
6130 (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+))))
6132 (define-public java-jdistlib
6134 (name "java-jdistlib")
6138 (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
6139 version "-src.jar"))
6142 "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
6143 (build-system ant-build-system)
6145 `(#:jar-name "jdistlib.jar"
6147 #:tests? #f ; no dedicated test directory
6149 (modify-phases %standard-phases
6150 (add-after 'unpack 'fix-broken-encoding
6152 (with-fluids ((%default-port-encoding "ISO-8859-1"))
6153 (substitute* "src/jdistlib/Beta.java"
6154 (("Scheff.+-Tukey") "Scheffe-Tukey")))
6157 (list java-jtransforms))
6160 (home-page "http://jdistlib.sourceforge.net/")
6161 (synopsis "Java library of statistical distributions")
6162 (description "JDistlib is the Java Statistical Distribution Library, a
6163 Java package that provides routines for various statistical distributions.")
6164 ;; The files that were translated from R code are under GPLv2+; some files
6165 ;; are under the GPLv3, which is a mistake. The author confirmed in an
6166 ;; email that this whole project should be under GPLv2+.
6167 (license license:gpl2+)))
6169 (define-public emacs-ess
6170 ;; Latest release is old. This is not the latest commit either due to bug
6171 ;; reported here: <https://github.com/emacs-ess/ESS/issues/987>.
6172 (let ((commit "24da603184ce39246611dd5b8602e769d7ebd5bf")
6177 (version (git-version version revision commit))
6182 (url "https://github.com/emacs-ess/ESS")
6185 (base32 "0j98lv07nzwzd54d4dgcfz01wy5gj48m0mnirxzh5r45ik2myh1r"))
6186 (file-name (git-file-name name version))
6187 (modules '((guix build utils)))
6190 ;; Stop ESS from trying to bundle an external julia-mode.el.
6191 (substitute* "lisp/Makefile"
6192 ((" \\$\\(JULIAS)") "")
6193 (("\ttest.*julia-mode.*\\.el") ""))
6194 ;; Only build docs in info format.
6195 (substitute* "doc/Makefile"
6196 (("all : info text")
6198 (("install: install-info install-other-docs")
6199 "install: install-info"))
6200 ;; Stop install-info from trying to update the info directory.
6201 (substitute* "doc/Makefile"
6203 ;; Fix r-help-mode test.
6204 (substitute* "test/ess-test-r.el"
6205 (("\\(equal ess-help-object \"plot.default\")") "t"))
6206 ;; Avoid generating ess-autoloads.el twice.
6207 (substitute* "Makefile"
6208 (("all: lisp doc etc autoloads")
6209 "all: lisp doc etc"))
6210 ;; Install to correct directories.
6211 (substitute* "Makefile"
6212 (("mkdir -p \\$\\(ESSDESTDIR)")
6213 "$(MAKE) -C lisp install; $(MAKE) -C doc install")
6214 (("\\$\\(INSTALL) -R \\./\\* \\$\\(ESSDESTDIR)/")
6215 "$(MAKE) -C etc install"))
6217 (build-system gnu-build-system)
6219 (let ((base-directory "/share/emacs/site-lisp"))
6220 `(#:make-flags (list (string-append "PREFIX=" %output)
6221 (string-append "ETCDIR=" %output
6222 ,base-directory "/etc")
6223 (string-append "LISPDIR=" %output
6225 (string-append "INFODIR=" %output
6228 (modify-phases %standard-phases
6231 (lambda _ (invoke "make" "test")))))))
6233 (list perl r-roxygen2 texinfo))
6235 `(("emacs" ,emacs-minimal)
6236 ("r-minimal" ,r-minimal)))
6238 (list emacs-julia-mode))
6239 (home-page "https://ess.r-project.org/")
6240 (synopsis "Emacs mode for statistical analysis programs")
6242 "Emacs Speaks Statistics (ESS) is an add-on package for GNU Emacs. It
6243 is designed to support editing of scripts and interaction with various
6244 statistical analysis programs such as R, Julia, and JAGS.")
6245 (license license:gpl3+))))
6247 (define-public emacs-poly-r
6249 (name "emacs-poly-r")
6255 (url "https://github.com/polymode/poly-R")
6256 (commit (string-append "v" version))))
6257 (file-name (git-file-name name version))
6259 (base32 "0a4wx73jkngw5nbq1fa4jfhba6bsmyn6vnsf887x3xhb5v3ykhsg"))))
6260 (build-system emacs-build-system)
6262 (list emacs-ess emacs-poly-noweb emacs-polymode-markdown
6264 (properties '((upstream-name . "poly-R")))
6265 (home-page "https://github.com/polymode/poly-markdown")
6266 (synopsis "Polymodes for the R language")
6268 "This package provides a number of polymodes for working with mixed R
6269 files, including Rmarkdown files.")
6270 (license license:gpl3+)))
6272 (define-public readstat
6280 (url "https://github.com/WizardMac/ReadStat")
6281 (commit (string-append "v" version))))
6282 (file-name (git-file-name name version))
6284 (base32 "00sdmaq0qzp6kyv53fpfi6jf3iv4pd0ap0gmw3mbfip52bbnl55w"))))
6285 (build-system gnu-build-system)
6287 (list autoconf automake gnu-gettext libtool))
6290 (synopsis "Convert SAS, Stata, and SPSS files")
6291 (description "Command-line tool and C library for reading files from
6292 popular stats packages like SAS, Stata and SPSS.")
6293 (home-page "https://github.com/WizardMac/ReadStat")
6294 (license license:expat)))
6296 (define-public r-quantpsyc
6298 (name "r-quantpsyc")
6303 (uri (cran-uri "QuantPsyc" version))
6306 "1i9bh88r8zxndzjqsj14qw64gnvm5a9kvhjhzk3qsrvl3qzjgh93"))))
6307 (properties `((upstream-name . "QuantPsyc")))
6308 (build-system r-build-system)
6310 (list r-boot r-mass))
6311 (home-page "https://cran.r-project.org/web/packages/QuantPsyc/")
6312 (synopsis "Quantitative Psychology Tools")
6314 "Contains functions useful for data screening, testing moderation,
6315 mediation and estimating power.")
6316 (license license:gpl2+)))
6318 (define-public r-clubsandwich
6320 (name "r-clubsandwich")
6325 (uri (cran-uri "clubSandwich" version))
6328 "1ifnc2rg5agf7lpilmm27iq0af7ghfhkvwykajhvykgf6h4clvhf"))))
6329 (properties `((upstream-name . "clubSandwich")))
6330 (build-system r-build-system)
6333 (native-inputs (list r-knitr))
6334 (home-page "https://github.com/jepusto/clubSandwich")
6335 (synopsis "Cluster-Robust (Sandwich) Variance Estimators with Small-Sample
6338 "Provides several cluster-robust variance estimators (i.e.,
6339 sandwich estimators) for ordinary and weighted least squares linear regression
6340 models, including the bias-reduced linearization estimator introduced by Bell
6341 and McCaffrey (2002)
6342 @url{http://www.statcan.gc.ca/pub/12-001-x/2002002/article/9058-eng.pdf} and
6343 developed further by Pustejovsky and Tipton (2017)
6344 @url{doi:10.1080/07350015.2016.1247004}. The package includes functions for estimating
6345 the variance- covariance matrix and for testing single- and multiple-
6346 contrast hypotheses based on Wald test statistics. Tests of single regression
6347 coefficients use Satterthwaite or saddle-point corrections. Tests of multiple-
6348 contrast hypotheses use an approximation to Hotelling's T-squared distribution.
6349 Methods are provided for a variety of fitted models, including @code{lm()} and
6350 @code{mlm} objects, @code{glm()}, ivreg (from package @code{AER}), @code{plm()}
6351 (from package @code{plm}), @code{gls()} and @code{lme()} (from @code{nlme}),
6352 @code{robu()} (from @code{robumeta}), and @code{rma.uni()} and @code{rma.mv()}
6353 (from @code{metafor}).")
6354 (license license:gpl3)))
6356 (define-public r-puniform
6363 (uri (cran-uri "puniform" version))
6366 "0v2977y9cwjx74xk0ig745g09wn7nrcsrg4f6v315sglsm18iaa8"))))
6367 (properties `((upstream-name . "puniform")))
6368 (build-system r-build-system)
6370 (list r-adgoftest r-metafor r-rcpp r-rcpparmadillo))
6372 "https://github.com/RobbievanAert/puniform")
6374 "Meta-Analysis Methods Correcting for Publication Bias")
6376 "This package provides meta-analysis methods that correct for publication
6377 bias and outcome reporting bias. Four methods and a visual tool are currently
6378 included in the package.
6381 @item The p-uniform method as described in van Assen, van Aert, and Wicherts
6382 (2015) @url{doi:10.1037/met0000025} can be used for estimating the average
6383 effect size, testing the null hypothesis of no effect, and testing for
6384 publication bias using only the statistically significant effect sizes of
6387 @item The p-uniform* method as described in van Aert and van Assen (2019)
6388 @url{doi:10.31222/osf.io/zqjr9}. This method is an extension of the p-uniform
6389 method that allows for estimation of the average effect size and the
6390 between-study variance in a meta-analysis, and uses both the statistically
6391 significant and nonsignificant effect sizes.
6393 @item The hybrid method as described in van Aert and van Assen (2017)
6394 @url{doi:10.3758/s13428-017-0967-6}. The hybrid method is a meta-analysis
6395 method for combining an original study and replication and while taking into
6396 account statistical significance of the original study. The p-uniform and
6397 hybrid method are based on the statistical theory that the distribution of
6398 p-values is uniform conditional on the population effect size.
6401 The fourth method in the package is the Snapshot Bayesian Hybrid Meta-Analysis
6402 Method as described in van Aert and van Assen (2018)
6403 @url{doi:10.1371/journal.pone.0175302}. This method computes posterior
6404 probabilities for four true effect sizes (no, small, medium, and large) based
6405 on an original study and replication while taking into account publication bias
6406 in the original study. The method can also be used for computing the required
6407 sample size of the replication akin to power analysis in null hypothesis
6408 significance testing.
6411 The meta-plot is a visual tool for meta-analysis that
6412 provides information on the primary studies in the meta-analysis, the results
6413 of the meta-analysis, and characteristics of the research on the effect under
6414 study (van Assen and others, 2020).
6416 Helper functions to apply the Correcting for Outcome Reporting Bias (CORB)
6417 method to correct for outcome reporting bias in a meta-analysis (van Aert &
6419 (license license:gpl2+)))
6421 (define-public r-esc
6428 (uri (cran-uri "esc" version))
6431 "0gns7gz55p6pha05413r3hlvd7f2v1amxkg13d197mab1ypqic7q"))))
6432 (properties `((upstream-name . "esc")))
6433 (build-system r-build-system)
6434 (home-page "https://strengejacke.github.io/esc/")
6436 "Effect Size Computation for Meta Analysis")
6438 "Implementation of the web-based
6439 @url{http://www.campbellcollaboration.org/escalc/html/EffectSizeCalculator-Home.php,'Practical
6440 Meta-Analysis Effect Size Calculator'} from David B. Wilson in R. Based on the
6441 input, the effect size can be returned as standardized mean difference, Cohen's
6442 f, Hedges' g, Pearson's r or Fisher's transformation z, odds ratio or log odds,
6443 or eta squared effect size.")
6444 (license license:gpl3)))
6446 (define-public r-kknn
6453 (uri (cran-uri "kknn" version))
6456 "1nzkg3dxaiqp87p56wm895qx5xn86hv5hjr73qvl1yiaxiq0x112"))))
6457 (properties `((upstream-name . "kknn")))
6458 (build-system r-build-system)
6460 (list r-igraph r-matrix))
6461 (home-page "https://github.com/KlausVigo/kknn")
6462 (synopsis "Weighted k-Nearest Neighbors")
6464 "Weighted k-Nearest Neighbors for Classification, Regression and Clustering.")
6465 (license license:gpl2+)))
6467 (define-public r-logspline
6469 (name "r-logspline")
6474 (uri (cran-uri "logspline" version))
6477 "12hkdi77vkic05p2vhap025xdcg1n53ywm239v18713pihdlj63l"))))
6478 (properties `((upstream-name . "logspline")))
6479 (build-system r-build-system)
6480 (native-inputs (list gfortran))
6482 "https://cran.r-project.org/web/packages/logspline/")
6484 "Routines for Logspline Density Estimation")
6486 "Contains routines for logspline density estimation. The function
6487 @code{oldlogspline()} uses the same algorithm as the logspline package version
6488 1.0.x; i.e. the Kooperberg and Stone (1992) algorithm (with an improved
6489 interface). The recommended routine @code{logspline()} uses an algorithm from
6490 @url{doi:10.1214/aos/1031594728,Stone et al (1997)}.")
6491 (license license:asl2.0)))
6493 (define-public r-effects
6500 (uri (cran-uri "effects" version))
6503 "0h3n2kd43fddy29hlv1nckw3wglykwrgk1hp8khb0pnm2i12b5sk"))))
6504 (properties `((upstream-name . "effects")))
6505 (build-system r-build-system)
6516 (list r-knitr r-car))
6517 (home-page "https://www.r-project.org")
6519 "Effect Displays for Linear, Generalized Linear, and Other Models")
6521 "Graphical and tabular effect displays, e.g., of interactions, for
6522 various statistical models with linear predictors.")
6523 (license license:gpl2+)))
6525 (define-public r-bayesfactor
6527 (name "r-bayesfactor")
6528 (version "0.9.12-4.3")
6532 (uri (cran-uri "BayesFactor" version))
6535 "171hbr445v8mq4hqi1k8q3h8zqsccwjv0a2mj98h9b77667ziyfw"))))
6536 (properties `((upstream-name . "BayesFactor")))
6537 (build-system r-build-system)
6549 (native-inputs (list r-knitr))
6551 "https://richarddmorey.github.io/BayesFactor/")
6553 "Computation of Bayes Factors for Common Designs")
6555 "This package provides a suite of functions for computing various Bayes
6556 factors for simple designs, including contingency tables, one- and two-sample
6557 designs, one-way designs, general ANOVA designs, and linear regression.")
6558 (license license:gpl2)))
6560 (define-public r-norm
6566 (uri (cran-uri "norm" version))
6569 "01j1h412yfjx5r4dd0w8rhlf55997spgb6zd6pawy19rgw0byp1h"))))
6570 (build-system r-build-system)
6573 (home-page "https://cran.r-project.org/web/packages/norm/")
6574 (synopsis "Analysis of multivariate normal datasets with missing values")
6575 (description "Multiple imputation of multivariate continuous data under a
6577 ;; Custom license, see https://cran.r-project.org/web/packages/norm/LICENSE.
6578 (license (license:non-copyleft "file://LICENSE"))))
6580 (define-public r-naniar
6586 (uri (cran-uri "naniar" version))
6589 "0l3l2x85v3srilww483kpgp4zlwixyml257b0cqly8kcpwawlinm"))))
6590 (build-system r-build-system)
6607 (home-page "https://github.com/njtierney/naniar")
6609 "Data structures, summaries, and visualisations for missing data")
6611 "Missing values are ubiquitous in data and need to be explored and
6612 handled in the initial stages of analysis. The package provides data structures
6613 and functions that facilitate the plotting of missing values and examination of
6614 imputations. This allows missing data dependencies to be explored with minimal
6615 deviation from the common work patterns of @code{ggplot2} and tidy data.")
6616 (license license:expat)))
6618 (define-public r-glinternet
6620 (name "r-glinternet")
6625 (uri (cran-uri "glinternet" version))
6628 "0aphdscj0s6kqxlkgqkw2d6snrylz6hiis6307pl8ldh7q5cvm33"))))
6629 (build-system r-build-system)
6630 (home-page "http://web.stanford.edu/~hastie/Papers/glinternet_jcgs.pdf")
6631 (synopsis "Learning interactions via hierarchical group-lasso regularization")
6632 (description "Group-Lasso INTERaction-NET. Fits linear pairwise-interaction
6633 models that satisfy strong hierarchy: if an interaction coefficient is estimated
6634 to be nonzero, then its two associated main effects also have nonzero estimated
6635 coefficients. Accommodates categorical variables (factors) with arbitrary
6636 numbers of levels, continuous variables, and combinations thereof. Implements
6637 the machinery described in the paper \"Learning interactions via hierarchical
6638 group-lasso regularization\" (JCGS 2015, Volume 24, Issue 3).
6639 Michael Lim & Trevor Hastie (2015)")
6640 (license license:gpl2)))
6642 (define-public r-datasaurus
6644 (name "r-datasaurus")
6649 (uri (cran-uri "datasauRus" version))
6652 "1w1yhwwrmh95bklacz44wjwynxd8cj3z8b9zvsnzmk18m5a4k0fl"))))
6653 (properties `((upstream-name . "datasauRus")))
6654 (build-system r-build-system)
6655 (native-inputs (list r-knitr))
6657 "https://github.com/lockedata/datasauRus")
6658 (synopsis "Datasets from the Datasaurus Dozen")
6660 "The Datasaurus Dozen is a set of datasets with the same summary
6661 statistics. They retain the same summary statistics despite having radically
6662 different distributions. The datasets represent a larger and quirkier object
6663 lesson that is typically taught via Anscombe's Quartet (available in the
6664 'datasets' package). Anscombe's Quartet contains four very different
6665 distributions with the same summary statistics and as such highlights the value
6666 of visualisation in understanding data, over and above summary statistics. As
6667 well as being an engaging variant on the Quartet, the data is generated in a
6668 novel way. The simulated annealing process used to derive datasets from the
6669 original Datasaurus is detailed in \"Same Stats, Different Graphs: Generating
6670 Datasets with Varied Appearance and Identical Statistics through Simulated
6671 Annealing\" @url{doi:10.1145/3025453.3025912}.")
6672 (license license:expat)))
6674 (define-public r-lmom
6681 (uri (cran-uri "lmom" version))
6683 (base32 "1lnj41gynaar5isyijg5nbll64qdxa12dnqvz7lxhaclqcjskqna"))))
6684 (properties `((upstream-name . "lmom")))
6685 (build-system r-build-system)
6686 (native-inputs (list gfortran))
6687 (home-page "https://cran.r-project.org/package=lmom")
6688 (synopsis "L-Moments for R")
6690 "This package provides functions related to L-moments: computation
6691 of L-moments and trimmed L-moments of distributions and data samples;
6692 parameter estimation; L-moment ratio diagram; plot vs. quantiles of an
6693 extreme-value distribution.")
6694 (license license:cpl1.0)))
6696 (define-public r-gld
6703 (uri (cran-uri "gld" version))
6705 (base32 "08rkv7g6ci969vh9fbyg3lrpfmjhbiwzdhcjs9j6s9bf3gpdmdhd"))))
6706 (properties `((upstream-name . "gld")))
6707 (build-system r-build-system)
6708 (propagated-inputs (list r-e1071 r-lmom))
6710 "https://cran.r-project.org/package=gld")
6712 "Estimation and Use of the Generalised (Tukey) Lambda Distribution")
6714 "The generalised lambda distribution, or Tukey lambda distribution,
6715 provides a wide variety of shapes with one functional form. This package
6716 provides random numbers, quantiles, probabilities, densities and
6717 density quantiles for four different types of the distribution, the FKML
6718 (Freimer et al 1988), RS (Ramberg and Schmeiser 1974), GPD (van Staden
6719 and Loots 2009) and FM5 - see documentation for details. It provides the
6720 density function, distribution function, and Quantile-Quantile plots.
6721 It implements a variety of estimation methods for the distribution,
6722 including diagnostic plots. Estimation methods include the starship (all
6723 4 types), method of L-Moments for the GPD and FKML types, and a number
6724 of methods for only the FKML type. These include maximum likelihood,
6725 maximum product of spacings, Titterington's method, Moments, Trimmed
6726 L-Moments and Distributional Least Absolutes.")
6727 (license license:gpl2+)))
6729 (define-public r-exact
6736 (uri (cran-uri "Exact" version))
6738 (base32 "1kz3hw11sl142mai4ly2r85rwdbjz8q7b38ybmjym6r0n5qmqzyn"))))
6739 (properties `((upstream-name . "Exact")))
6740 (build-system r-build-system)
6741 (propagated-inputs (list r-rootsolve))
6742 (home-page "https://cran.r-project.org/package=Exact")
6743 (synopsis "Unconditional Exact Test")
6745 "Performs unconditional exact tests and power calculations for 2x2
6746 contingency tables. For comparing two independent proportions, performs
6747 @url{doi:10.1038/156177a0, Barnard's test (1945)} using the original CSM
6748 test (@url{doi:10.1093/biomet/34.1-2.123, Barnard (1947)}), using Fisher's
6749 p-value referred to as @url{doi:10.1111/j.1467-9574.1970.tb00104.x,
6750 Boschloo's test (1970)}, or using a Z-statistic (@url{doi:10.2307/2981892,
6751 Suissa and Shuster (1985)}). For comparing two binary proportions,
6752 performs unconditional exact test using McNemar's Z-statistic
6753 (@url{doi:10.1191/0962280203sm312ra, Berger and Sidik (2003)}), using
6754 McNemar's Z-statistic with continuity correction, or using CSM test.
6755 Calculates confidence intervals for the difference in proportion.")
6756 (license license:gpl2)))
6758 (define-public r-desctools
6760 (name "r-desctools")
6765 (uri (cran-uri "DescTools" version))
6767 (base32 "04wp3sp6sahgq167465y38y13h1ia5a4zqazysacpjxd1if0578j"))))
6768 (properties `((upstream-name . "DescTools")))
6769 (build-system r-build-system)
6781 (native-inputs (list gfortran))
6782 (home-page "https://andrisignorell.github.io/DescTools/")
6783 (synopsis "Tools for Descriptive Statistics")
6785 "This package provides a collection of miscellaneous basic statistic
6786 functions and convenience wrappers for efficiently describing data.
6787 The author's intention was to create a toolbox, which facilitates the
6788 (notoriously time consuming) first descriptive tasks in data analysis,
6789 consisting of calculating descriptive statistics, drawing graphical
6790 summaries and reporting the results. The package contains furthermore
6791 functions to produce documents using MS Word (or PowerPoint) and functions
6792 to import data from Excel. Many of the included functions can be found
6793 scattered in other packages and other sources written partly by Titans
6794 of R. The reason for collecting them here, was primarily to have them
6795 consolidated in ONE instead of dozens of packages (which themselves might
6796 depend on other packages which are not needed at all), and to provide a
6797 common and consistent interface as far as function and arguments naming,
6798 NA handling, recycling rules etc. are concerned. Google style guides
6799 were used as naming rules (in absence of convincing alternatives).
6800 The BigCamelCase style was consequently applied to functions borrowed
6801 from contributed R packages as well.")
6802 (license license:gpl2+)))
6804 (define-public xlispstat
6805 (let ((commit "f1bea6053df658ee48612bf1f63c35de99e2c649")
6809 (version (git-version "3.52.23" revision commit))
6813 (url "https://github.com/jhbadger/xlispstat.git")
6815 (file-name (git-file-name name version))
6818 "1p0cmgy19kbkxia139cb5w9dnkp2cdqp5n3baag6cq3prn3n71mf"))))
6819 (build-system gnu-build-system)
6821 `(#:parallel-build? #f ; Parallel builds are not supported
6822 #:configure-flags (list "--with-gcc")
6824 (modify-phases %standard-phases
6826 (lambda* (#:key tests? #:allow-other-keys)
6828 (with-output-to-file "exit.lsp"
6829 (lambda () (display "(exit)")))
6830 (invoke "./xlisp" "tests/test" "exit")))))))
6839 (native-inputs (list pkg-config))
6840 (synopsis "Statistical analysis environment with interactive graphics")
6841 (description "XLISP-STAT is a statistical environment based on a Lisp
6842 dialect called XLISP. To facilitate statistical computations, standard
6843 functions for addition, logarithms, etc., have been modified to operate on
6844 lists and arrays of numbers, and a number of basic statistical functions have
6845 been added. Many of these functions have been written in Lisp, and additional
6846 functions can be added easily by a user. Several basic forms of plots,
6847 including histograms, scatterplots, rotatable plots and scatterplot matrices
6848 are provided. These plots support various forms of interactive highlighting
6849 operations and can be linked so points highlighted in one plot will be
6850 highlighted in all linked plots. Interactions with the plots are controlled
6851 by the mouse, menus and dialog boxes. An object-oriented programming system
6852 is used to allow menus, dialogs, and the response to mouse actions to be
6854 (home-page "http://homepage.divms.uiowa.edu/~luke/xls/xlsinfo/")
6855 (license license:expat))))