1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com>
4 ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
5 ;;; Copyright © 2016, 2017, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
6 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
7 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
8 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
9 ;;; Copyright © 2016, 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
10 ;;; Copyright © 2017 Kyle Meyer <kyle@kyleam.com>
11 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
12 ;;; Copyright © 2017 Alex Kost <alezost@gmail.com>
13 ;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com>
14 ;;; Copyright © 2020 Tim Howes <timhowes@lavabit.com>
16 ;;; This file is part of GNU Guix.
18 ;;; GNU Guix is free software; you can redistribute it and/or modify it
19 ;;; under the terms of the GNU General Public License as published by
20 ;;; the Free Software Foundation; either version 3 of the License, or (at
21 ;;; your option) any later version.
23 ;;; GNU Guix is distributed in the hope that it will be useful, but
24 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
25 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
26 ;;; GNU General Public License for more details.
28 ;;; You should have received a copy of the GNU General Public License
29 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
31 (define-module (gnu packages statistics)
32 #:use-module ((guix licenses) #:prefix license:)
33 #:use-module (guix packages)
34 #:use-module (guix download)
35 #:use-module (guix hg-download)
36 #:use-module (guix git-download)
37 #:use-module (guix utils)
38 #:use-module (guix build-system ant)
39 #:use-module (guix build-system gnu)
40 #:use-module (guix build-system r)
41 #:use-module (guix build-system python)
42 #:use-module (guix build-system trivial)
43 #:use-module (gnu packages)
44 #:use-module (gnu packages algebra)
45 #:use-module (gnu packages autotools)
46 #:use-module (gnu packages bash)
47 #:use-module (gnu packages check)
48 #:use-module (gnu packages compression)
49 #:use-module (gnu packages cran)
50 #:use-module (gnu packages curl)
51 #:use-module (gnu packages emacs)
52 #:use-module (gnu packages emacs-xyz)
53 #:use-module (gnu packages fontutils)
54 #:use-module (gnu packages gcc)
55 #:use-module (gnu packages gtk)
56 #:use-module (gnu packages gettext)
57 #:use-module (gnu packages glib)
58 #:use-module (gnu packages haskell-xyz)
59 #:use-module (gnu packages icu4c)
60 #:use-module (gnu packages image)
61 #:use-module (gnu packages java)
62 #:use-module (gnu packages libffi)
63 #:use-module (gnu packages machine-learning)
64 #:use-module (gnu packages maths)
65 #:use-module (gnu packages multiprecision)
66 #:use-module (gnu packages pcre)
67 #:use-module (gnu packages perl)
68 #:use-module (gnu packages pkg-config)
69 #:use-module (gnu packages python)
70 #:use-module (gnu packages python-science)
71 #:use-module (gnu packages python-xyz)
72 #:use-module (gnu packages readline)
73 #:use-module (gnu packages sphinx)
74 #:use-module (gnu packages ssh)
75 #:use-module (gnu packages tcl)
76 #:use-module (gnu packages tex)
77 #:use-module (gnu packages texinfo)
78 #:use-module (gnu packages time)
79 #:use-module (gnu packages tls)
80 #:use-module (gnu packages base)
81 #:use-module (gnu packages version-control)
82 #:use-module (gnu packages web)
83 #:use-module (gnu packages xml)
84 #:use-module (gnu packages xorg)
85 #:use-module (srfi srfi-1))
95 (uri (string-append "mirror://gnu/pspp/pspp-"
99 "0lqrash677b09zxdlxp89z6k02y4i23mbqg83956dwl69wc53dan"))))
100 (build-system gnu-build-system)
103 ("gettext" ,gettext-minimal)
107 ("readline" ,readline)
109 ("gtksourceview" ,gtksourceview-3)
110 ("spread-sheet-widget" ,spread-sheet-widget)
113 `(("autoconf" ,autoconf) ;for tests
114 ("glib" ,glib "bin") ;for glib-genmarshal
116 ("pkg-config" ,pkg-config)
117 ("python" ,python-2) ;for tests
118 ("texinfo" ,texinfo)))
119 (home-page "https://www.gnu.org/software/pspp/")
120 (synopsis "Statistical analysis")
122 "GNU PSPP is a statistical analysis program. It can perform
123 descriptive statistics, T-tests, linear regression and non-parametric tests.
124 It features both a graphical interface as well as command-line input. PSPP
125 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
126 can be imported from spreadsheets, text files and database sources and it can
127 be output in text, PostScript, PDF or HTML.")
128 (license license:gpl3+)))
136 (uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/"
137 (version-major version) ".x/Source/"
138 "JAGS-" version ".tar.gz"))
141 "1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica"))))
142 (build-system gnu-build-system)
143 (home-page "http://mcmc-jags.sourceforge.net/")
145 `(("gfortran" ,gfortran)
147 (synopsis "Gibbs sampler")
148 (description "JAGS is Just Another Gibbs Sampler. It is a program for
149 analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
150 simulation not wholly unlike BUGS. JAGS was written with three aims in mind:
153 @item To have a cross-platform engine for the BUGS language;
154 @item To be extensible, allowing users to write their own functions,
155 distributions and samplers;
156 @item To be a platform for experimentation with ideas in Bayesian modelling.
158 (license license:gpl2)))
160 (define-public libxls
167 (uri (string-append "https://github.com/libxls/libxls/releases/download/"
168 "v" version "/libxls-" version ".tar.gz"))
170 (base32 "0wg3ymr43aa1j3scyl9x83b2xgg7wilzpil0dj91a8dzji6w7b2x"))))
171 (build-system gnu-build-system)
172 (home-page "https://github.com/libxls/libxls")
173 (synopsis "Read binary (.xls) Excel spreadsheet files")
175 "libxls is a C library to read .xls spreadsheet files in the binary OLE
176 BIFF8 format as created by Excel 97 and later versions. It cannot write them.
178 This package also provides @command{xls2csv} to export Excel files to CSV.")
179 (license license:bsd-2)))
181 ;; Update this package together with the set of recommended packages: r-boot,
182 ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
183 ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
186 (name "r-with-tests")
190 (uri (string-append "mirror://cran/src/base/R-"
191 (version-major version) "/R-"
195 "0bl098xcv8v316kqnf43v6gb4kcsv31ydqfm1f7qr824jzb2fgsj"))))
196 (build-system gnu-build-system)
198 `(#:disallowed-references (,tzdata-for-tests)
200 (list (string-append "LDFLAGS=-Wl,-rpath="
201 (assoc-ref %outputs "out")
203 ;; This affects the embedded timestamp of only the core packages.
204 "PKG_BUILT_STAMP=1970-01-01")
206 (modify-phases %standard-phases
207 (add-before 'configure 'do-not-compress-serialized-files
208 (lambda* (#:key inputs #:allow-other-keys)
209 ;; This ensures that Guix can detect embedded store references;
210 ;; see bug #28157 for details.
211 (substitute* "src/library/base/makebasedb.R"
212 (("compress = TRUE") "compress = FALSE"))
214 (add-before 'configure 'patch-uname
215 (lambda* (#:key inputs #:allow-other-keys)
216 (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
218 (substitute* "src/scripts/R.sh.in"
219 (("uname") uname-bin)))
221 (add-after 'unpack 'build-reproducibly
223 ;; The documentation contains time stamps to demonstrate
224 ;; documentation generation in different phases.
225 (substitute* "src/library/tools/man/Rd2HTML.Rd"
226 (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
227 "(removed for reproducibility)"))
229 ;; Remove timestamp from tracing environment. This fixes
230 ;; reproducibility of "methods.rd{b,x}".
231 (substitute* "src/library/methods/R/trace.R"
232 (("dateCreated = Sys.time\\(\\)")
233 "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
235 ;; Ensure that gzipped files are reproducible.
236 (substitute* '("src/library/grDevices/Makefile.in"
237 "doc/manual/Makefile.in")
238 (("R_GZIPCMD\\)" line)
239 (string-append line " -n")))
241 ;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
242 ;; queries the mtime of a given file and records it in an object.
243 ;; This is acceptable at runtime to detect stale source files,
244 ;; but it destroys reproducibility at build time.
246 ;; Similarly, the "srcfilecopy" procedure records the current
247 ;; time. We change both of them to respect SOURCE_DATE_EPOCH.
248 (substitute* "src/library/base/R/srcfile.R"
249 (("timestamp <- (timestamp.*|file.mtime.*)" _ time)
250 (string-append "timestamp <- \
251 as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
252 as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
253 } else { " time "}, origin=\"1970-01-01\")\n")))
255 ;; This library is installed using "install_package_description",
256 ;; so we need to pass the "builtStamp" argument.
257 (substitute* "src/library/tools/Makefile.in"
258 (("(install_package_description\\(.*\"')\\)\"" line prefix)
259 (string-append prefix ", builtStamp='1970-01-01')\"")))
261 (substitute* "src/library/Recommended/Makefile.in"
262 (("INSTALL_OPTS =" m)
263 (string-append m " --built-timestamp=1970-01-01" m)))
265 ;; R bundles an older version of help2man, which does not respect
266 ;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man,
267 ;; because that breaks a test.
268 (with-fluids ((%default-port-encoding "ISO-8859-1"))
269 (substitute* "tools/help2man.pl"
270 (("my \\$date = strftime \"%B %Y\", localtime" line)
271 (string-append line " 1"))))
273 ;; The "References" section of this file when converted to
274 ;; package.rds is sometimes stored with a newline, sometimes with
275 ;; a space. We avoid this problem by removing the line break
276 ;; that is suspected to be the culprit.
277 (substitute* "src/library/methods/DESCRIPTION.in"
278 (("\\(2008\\)\n") "(2008) ")
279 ((" ``Software") "``Software"))
281 (add-before 'build 'set-locales
283 (setlocale LC_ALL "C")
284 (setenv "LC_ALL" "C")
286 (add-before 'configure 'set-default-pager
287 ;; Set default pager to "cat", because otherwise it is "false",
288 ;; making "help()" print nothing at all.
289 (lambda _ (setenv "PAGER" "cat") #t))
290 (add-before 'check 'set-timezone
291 ;; Some tests require the timezone to be set. However, the
292 ;; timezone may not just be "UTC", or else a brittle regression
293 ;; test in reg-tests-1d will fail.
294 (lambda* (#:key inputs #:allow-other-keys)
295 (setenv "TZ" "UTC+1")
297 (string-append (assoc-ref inputs "tzdata")
300 (add-after 'build 'make-info
301 (lambda _ (invoke "make" "info")))
302 (add-after 'build 'install-info
303 (lambda _ (invoke "make" "install-info"))))
305 `(;; We build the recommended packages here, because they are needed in
306 ;; order to run the test suite. We disable them in the r-minimal
309 "--with-blas=-lopenblas"
315 ,(string-append "--with-tcl-config="
316 (assoc-ref %build-inputs "tcl")
318 ,(string-append "--with-tk-config="
319 (assoc-ref %build-inputs "tk")
322 "--enable-BLAS-shlib"
323 "--with-system-tre")))
324 ;; R has some support for Java. When the JDK is available at configure
325 ;; time environment variables pointing to the JDK will be recorded under
326 ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
327 ;; CMD javareconf". "R CMD javareconf" appears to only be used to update
328 ;; the recorded environment variables in $R_HOME/etc. Refer to
329 ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
330 ;; for additional information.
332 ;; As the JDK is a rather large input with only very limited effects on R,
333 ;; we decided to drop it.
337 ("pkg-config" ,pkg-config)
338 ("texinfo" ,texinfo) ; for building HTML manuals
339 ("texlive" ,(texlive-union (list texlive-ae
344 texlive-latex-fancyvrb
345 texlive-latex-graphics
346 texlive-latex-hyperref
347 texlive-latex-oberdiek
349 texlive-latex-upquote
351 texlive-latex-xkeyval)))
352 ("tzdata" ,tzdata-for-tests)
355 `(;; We need not only cairo here, but pango to ensure that tests for the
356 ;; "cairo" bitmapType plotting backend succeed.
358 ("coreutils" ,coreutils)
360 ("openblas" ,openblas)
361 ("gfortran" ,gfortran)
363 ("libjpeg" ,libjpeg-turbo)
368 ("readline" ,readline)
369 ;; This avoids a reference to the ungraftable static bash. R uses the
370 ;; detected shell for the "system" procedure.
371 ("bash" ,bash-minimal)
377 (list (search-path-specification
378 (variable "R_LIBS_SITE")
379 (files (list "site-library/")))))
380 (home-page "https://www.r-project.org/")
381 (synopsis "Environment for statistical computing and graphics")
383 "R is a language and environment for statistical computing and graphics.
384 It provides a variety of statistical techniques, such as linear and nonlinear
385 modeling, classical statistical tests, time-series analysis, classification
386 and clustering. It also provides robust support for producing
387 publication-quality data plots. A large amount of 3rd-party packages are
388 available, greatly increasing its breadth and scope.")
389 (license license:gpl3+)))
391 (define-public r-minimal
392 (package (inherit r-with-tests)
396 ,@(substitute-keyword-arguments (package-arguments r-with-tests)
397 ((#:configure-flags flags)
398 ;; Do not build the recommended packages. The build system creates
399 ;; random temporary directories and embeds their names in some
400 ;; package files. We build these packages with the r-build-system
402 `(cons "--without-recommended-packages" ,flags)))))))
404 (define-public rmath-standalone
405 (package (inherit r-minimal)
406 (name "rmath-standalone")
409 (modify-phases %standard-phases
410 (add-after 'configure 'chdir
411 (lambda _ (chdir "src/nmath/standalone/") #t)))))
412 (synopsis "Standalone R math library")
414 "This package provides the R math library as an independent package.")))
416 (define-public r-boot
423 (uri (cran-uri "boot" version))
426 "0cjafhqv1c1mrjjcasqr767vs96wjcc6am9r1icryr8l4zymhwcz"))))
427 (build-system r-build-system)
428 (home-page "https://cran.r-project.org/web/packages/boot")
429 (synopsis "Bootstrap functions for R")
431 "This package provides functions and datasets for bootstrapping from the
432 book \"Bootstrap Methods and Their Application\" by A.C. Davison and
433 D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
434 ;; Unlimited distribution
435 (license (license:non-copyleft "file://R/bootfuns.q"))))
437 (define-public r-mass
444 (uri (cran-uri "MASS" version))
447 "08g8ashbcas3ac98kxvchbwc8da9dq9anpngb4arnw62npawq05q"))))
448 (properties `((upstream-name . "MASS")))
449 (build-system r-build-system)
450 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
451 (synopsis "Support functions and datasets for Venables and Ripley's MASS")
453 "This package provides functions and datasets for the book \"Modern
454 Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
455 ;; Either version may be picked.
456 (license (list license:gpl2 license:gpl3))))
458 (define-public r-class
465 (uri (cran-uri "class" version))
468 "0dxyxk59fs90713qisanlvk4p0d3l8n8n7zdd4d5c290naaaw83q"))))
469 (build-system r-build-system)
471 `(("r-mass" ,r-mass)))
472 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
473 (synopsis "R functions for classification")
475 "This package provides various functions for classification, including
476 k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
477 ;; Either of the two versions can be picked.
478 (license (list license:gpl2 license:gpl3))))
480 (define-public r-cluster
487 (uri (cran-uri "cluster" version))
490 "168l653ygkg21fwrqrf7lsqi5p6jzhgmcvhrwv7lznkdzdhag2jw"))))
491 (build-system r-build-system)
493 `(("gfortran" ,gfortran)))
494 (home-page "https://cran.r-project.org/web/packages/cluster")
495 (synopsis "Methods for cluster analysis")
497 "This package provides methods for cluster analysis. It is a much
498 extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
499 Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
500 (license license:gpl2+)))
502 (define-public r-codetools
509 (uri (cran-uri "codetools" version))
512 "0a2c115glq8jxixwfigrpvjabhxchn9r4mc40y41dg9dg6wsd7hs"))))
513 (build-system r-build-system)
514 (home-page "https://cran.r-project.org/web/packages/codetools")
515 (synopsis "Code analysis tools for R")
516 (description "This package provides code analysis tools for R to check R
517 code for possible problems.")
518 ;; Any version of the GPL.
519 (license (list license:gpl2+ license:gpl3+))))
521 (define-public r-foreign
528 (uri (cran-uri "foreign" version))
531 "0b4rca1bl8xxna05057hchbwfmgjgx0n140szabpc0raizqzks0s"))))
532 (build-system r-build-system)
533 (home-page "https://cran.r-project.org/web/packages/foreign")
534 (synopsis "Read data stored by other statistics software")
536 "This package provides functions for reading and writing data stored by
537 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
538 for reading and writing some dBase files.")
539 (license license:gpl2+)))
541 (define-public r-kernsmooth
543 (name "r-kernsmooth")
548 (uri (cran-uri "KernSmooth" version))
551 "0fgclmzk3ksjsh3j47jqzm3jhqrwn12rkp7f84yr6wr43q2pbsr0"))))
552 (properties `((upstream-name . "KernSmooth")))
553 (build-system r-build-system)
555 `(("gfortran" ,gfortran)))
556 (home-page "https://cran.r-project.org/web/packages/KernSmooth")
557 (synopsis "Functions for kernel smoothing")
559 "This package provides functions for kernel smoothing (and density
560 estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
561 \"Kernel Smoothing\".")
562 ;; Unlimited use and distribution
563 (license (license:non-copyleft "file://LICENCE.note"))))
565 (define-public r-lattice
571 (uri (cran-uri "lattice" version))
574 "16yvdklwgjfclayh15axknjwzygx8i7y8zl5mlw8m85dqzihifap"))))
575 (build-system r-build-system)
576 (home-page "http://lattice.r-forge.r-project.org/")
577 (synopsis "High-level data visualization system")
579 "The lattice package provides a powerful and elegant high-level data
580 visualization system inspired by Trellis graphics, with an emphasis on
581 multivariate data. Lattice is sufficient for typical graphics needs, and is
582 also flexible enough to handle most nonstandard requirements.")
583 (license license:gpl2+)))
585 (define-public r-matrix
592 (uri (cran-uri "Matrix" version))
595 "0ccmmfd0lbvrhzjzr28k4yfawiywa1m4ics34zyi3rqq23csa2wm"))))
596 (properties `((upstream-name . "Matrix")))
597 (build-system r-build-system)
599 `(("r-lattice" ,r-lattice)))
600 (home-page "http://Matrix.R-forge.R-project.org/")
601 (synopsis "Sparse and dense matrix classes and methods")
603 "This package provides classes and methods for dense and sparse matrices
604 and operations on them using LAPACK and SuiteSparse.")
605 (license license:gpl2+)))
607 (define-public r-nlme
614 (uri (cran-uri "nlme" version))
616 (base32 "0pji9vvmjqyk8b7lhxsixnagsrz2hmnwy6ilc2gg5ji1y6qx2rav"))))
617 (build-system r-build-system)
619 `(("r-lattice" ,r-lattice)))
621 `(("gfortran" ,gfortran)))
622 (home-page "https://cran.r-project.org/web/packages/nlme")
623 (synopsis "Linear and nonlinear mixed effects models")
625 "This package provides tools to fit and compare Gaussian linear and
626 nonlinear mixed-effects models.")
627 (license license:gpl2+)))
629 (define-public r-mgcv
636 (uri (cran-uri "mgcv" version))
638 (base32 "1dyphss1bw5rd8apgxsb364rcrkdbc9pcbsa0jy95mg9g5434wvk"))))
639 (build-system r-build-system)
641 `(("r-matrix" ,r-matrix)
643 (home-page "https://cran.r-project.org/web/packages/mgcv")
644 (synopsis "Mixed generalised additive model computation")
646 "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
647 parameter estimation by GCV, REML or UBRE/AIC. The library includes a
648 @code{gam()} function, a wide variety of smoothers, JAGS support and
649 distributions beyond the exponential family.")
650 (license license:gpl2+)))
652 (define-public r-nnet
659 (uri (cran-uri "nnet" version))
662 "0smmyx4vhlz99vy4w238y913gq74845v0l1p0g1kgydsp9lijlcr"))))
663 (build-system r-build-system)
664 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
665 (synopsis "Feed-forward neural networks and multinomial log-linear models")
667 "This package provides functions for feed-forward neural networks with a
668 single hidden layer, and for multinomial log-linear models.")
669 (license (list license:gpl2+ license:gpl3+))))
671 (define-public r-rpart
678 (uri (cran-uri "rpart" version))
681 "0p5frya963ppn476p5dxs2mnarsalksr6gw9zzmjsn8ikq7bx3ib"))))
682 (build-system r-build-system)
683 (home-page "https://cran.r-project.org/web/packages/rpart")
684 (synopsis "Recursive partitioning and regression trees")
686 "This package provides recursive partitioning functions for
687 classification, regression and survival trees.")
688 (license (list license:gpl2+ license:gpl3+))))
690 (define-public r-spatial
697 (uri (cran-uri "spatial" version))
700 "0dlafq744mahxpb13llmsrg54fzww8ld1nbxmr7m851gff11kk2j"))))
701 (build-system r-build-system)
702 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
703 (synopsis "Functions for kriging and point pattern analysis")
705 "This package provides functions for kriging and point pattern
707 ;; Either version may be picked.
708 (license (list license:gpl2 license:gpl3))))
710 (define-public r-survival
717 (uri (cran-uri "survival" version))
720 "0w0gkni1w8rbmfw7yl08bl1s9lij1yhbkj4dvmxcarkkw26sjjzs"))))
721 (build-system r-build-system)
723 `(("r-matrix" ,r-matrix)))
724 (home-page "https://github.com/therneau/survival")
725 (synopsis "Survival analysis")
727 "This package contains the core survival analysis routines, including
728 definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
729 curves, Cox models, and parametric accelerated failure time models.")
730 (license license:lgpl2.0+)))
733 (package (inherit r-minimal)
736 (build-system trivial-build-system)
737 (arguments '(#:builder (begin (mkdir %output) #t)))
739 `(("r-minimal" ,r-minimal)
742 ("r-cluster" ,r-cluster)
743 ("r-codetools" ,r-codetools)
744 ("r-foreign" ,r-foreign)
745 ("r-kernsmooth" ,r-kernsmooth)
746 ("r-lattice" ,r-lattice)
748 ("r-matrix" ,r-matrix)
753 ("r-spatial" ,r-spatial)
754 ("r-survival" ,r-survival)))))
763 (uri (cran-uri "bit" version))
766 "0s7isadibxp2wr62r5cpbyh9z31sczzfz4j3rm7gxgjfpqgq8174"))))
767 (build-system r-build-system)
769 `(("r-knitr" ,r-knitr)))
770 (home-page "http://ff.r-forge.r-project.org")
771 (synopsis "Class for vectors of 1-bit booleans")
773 "This package provides bitmapped vectors of booleans (no @code{NA}s),
774 coercion from and to logicals, integers and integer subscripts, fast boolean
775 operators and fast summary statistics. With @code{bit} class vectors of true
776 binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
777 (license license:gpl2)))
779 (define-public r-bit64
786 (uri (cran-uri "bit64" version))
789 "0y0m7q1rwam1g88cjx7zyi07mj5dipxd9jkl90f294syx8k6ipr5"))))
790 (build-system r-build-system)
793 (home-page "http://ff.r-forge.r-project.org/")
794 (synopsis "S3 class for vectors of 64 bit integers")
796 "The bit64 package provides serializable S3 atomic 64 bit (signed)
797 integers that can be used in vectors, matrices, arrays and @code{data.frames}.
798 Methods are available for coercion from and to logicals, integers, doubles,
799 characters and factors as well as many elementwise and summary functions.
800 Many fast algorithmic operations such as @code{match} and @code{order} support
801 interactive data exploration and manipulation and optionally leverage
803 (license license:gpl2)))
805 (define-public r-dichromat
812 (uri (cran-uri "dichromat" version))
814 (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
815 (build-system r-build-system)
816 (home-page "https://cran.r-project.org/web/packages/dichromat")
817 (synopsis "Color schemes for dichromats")
819 "Dichromat collapses red-green or green-blue distinctions to simulate the
820 effects of different types of color-blindness.")
821 (license license:gpl2+)))
823 (define-public r-digest
830 (uri (cran-uri "digest" version))
832 (base32 "0gr503pinailfglpfbzxprqw7w1jla8jr9nl856a4zch498zg1gl"))))
833 (build-system r-build-system)
834 ;; Vignettes require r-knitr, which requires r-digest, so we have to
835 ;; disable them and the tests.
838 #:configure-flags (list "--no-build-vignettes")))
839 (home-page "http://dirk.eddelbuettel.com/code/digest.html")
840 (synopsis "Create cryptographic hash digests of R objects")
842 "This package contains an implementation of a function @code{digest()} for
843 the creation of hash digests of arbitrary R objects (using the md5, sha-1,
844 sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
845 of R language objects, as well as a function @code{hmac()} to create hash-based
846 message authentication code.
848 Please note that this package is not meant to be deployed for cryptographic
849 purposes for which more comprehensive (and widely tested) libraries such as
850 OpenSSL should be used.")
851 (license license:gpl2+)))
853 (define-public r-estimability
855 (name "r-estimability")
859 (uri (cran-uri "estimability" version))
862 "0cifdaa71spkcxl4db4z884jrya865sg3dhcv4isd8fnzg2pjcd3"))))
863 (build-system r-build-system)
864 (home-page "https://cran.r-project.org/web/packages/estimability")
865 (synopsis "Tools for assessing estimability of linear predictions")
866 (description "Provides tools for determining estimability of linear
867 functions of regression coefficients, and @code{epredict} methods that handle
868 non-estimable cases correctly.")
869 (license license:gpl2+)))
871 (define-public r-labeling
878 (uri (cran-uri "labeling" version))
880 (base32 "0rfikd9gy70b8qz87q9axcwv8nmn9mbxfdwypxi0sghpfs9df8p0"))))
881 (build-system r-build-system)
882 (home-page "https://cran.r-project.org/web/packages/labeling")
883 (synopsis "Axis labeling algorithms")
884 (description "The labeling package provides a range of axis labeling
886 (license license:expat)))
888 (define-public r-magrittr
895 (uri (cran-uri "magrittr" version))
897 (base32 "0pxd99fvg406whqsk9wh756rayrwh84xn3h44zmlpcy23kanbhkm"))))
898 (build-system r-build-system)
899 ;; knitr needs magrittr
902 `(("r-knitr" ,r-knitr)))
903 (home-page "https://cran.r-project.org/web/packages/magrittr/index.html")
904 (synopsis "A forward-pipe operator for R")
906 "Magrittr provides a mechanism for chaining commands with a new
907 forward-pipe operator, %>%. This operator will forward a value, or the result
908 of an expression, into the next function call/expression. There is flexible
909 support for the type of right-hand side expressions. For more information,
910 see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
911 (license license:expat)))
913 (define-public r-munsell
920 (uri (cran-uri "munsell" version))
922 (base32 "16g1fzisbpqb15yh3pqf3iia4csppva5dnv1z88x9dg263xskwyh"))))
923 (build-system r-build-system)
925 `(("r-colorspace" ,r-colorspace)))
926 (home-page "https://cran.r-project.org/web/packages/munsell")
927 (synopsis "Munsell colour system")
929 "The Munsell package contains Functions for exploring and using the
930 Munsell colour system.")
931 (license license:expat)))
933 (define-public r-permute
940 (uri (cran-uri "permute" version))
943 "0ra8p5mf2590azrkas8z2ry7mif77xqxd29n4zgyi5vll225726j"))))
944 (build-system r-build-system)
945 ;; Tests do not run correctly, but running them properly would entail a
946 ;; circular dependency with vegan.
947 (home-page "https://github.com/gavinsimpson/permute")
948 (synopsis "Functions for Generating Restricted Permutations of Data")
950 "This package provides a set of restricted permutation designs for freely
951 exchangeable, line transects (time series), spatial grid designs and permutation
952 of blocks (groups of samples). @code{permute} also allows split-plot designs,
953 in which the whole-plots or split-plots or both can be freely exchangeable.")
954 (license license:gpl2+)))
956 (define-public r-plyr
963 (uri (cran-uri "plyr" version))
965 (base32 "11sjjdn146w95s1vsfmmgdls082cbnm1slv98xvyjhsl2mpx4mga"))))
966 (build-system r-build-system)
967 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
968 (home-page "http://had.co.nz/plyr")
969 (synopsis "Tools for Splitting, Applying and Combining Data")
971 "Plyr is a set of tools that solves a common set of problems: you need to
972 break a big problem down into manageable pieces, operate on each piece and
973 then put all the pieces back together. For example, you might want to fit a
974 model to each spatial location or time point in your study, summarise data by
975 panels or collapse high-dimensional arrays to simpler summary statistics.")
976 (license license:expat)))
978 (define-public r-proto
985 (uri (cran-uri "proto" version))
987 (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
988 (build-system r-build-system)
989 (home-page "https://github.com/hadley/proto")
990 (synopsis "Prototype object-based programming")
992 "Proto is an object oriented system using object-based, also called
993 prototype-based, rather than class-based object oriented ideas.")
994 (license license:gpl2+)))
996 (define-public r-rcolorbrewer
998 (name "r-rcolorbrewer")
1003 (uri (cran-uri "RColorBrewer" version))
1005 (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
1006 (build-system r-build-system)
1007 (home-page "https://cran.r-project.org/web/packages/RColorBrewer")
1008 (synopsis "ColorBrewer palettes")
1010 "This package provides color schemes for maps (and other graphics)
1011 designed by Cynthia Brewer as described at http://colorbrewer2.org")
1012 ;; Includes code licensed under bsd-4
1013 (license license:asl2.0)))
1015 (define-public r-sendmailr
1017 (name "r-sendmailr")
1022 (uri (cran-uri "sendmailR" version))
1025 "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
1026 (properties `((upstream-name . "sendmailR")))
1027 (build-system r-build-system)
1029 `(("r-base64enc" ,r-base64enc)))
1031 "https://cran.r-project.org/web/packages/sendmailR")
1032 (synopsis "Send email using R")
1034 "This package contains a simple SMTP client which provides a portable
1035 solution for sending email, including attachments, from within R.")
1036 (license license:gpl2+)))
1038 (define-public r-stringi
1045 (uri (cran-uri "stringi" version))
1048 "0420f7zn5knyyvd3a3xa7059l4kadw0m67rfpivacqn9xn6iwkr2"))))
1049 (build-system r-build-system)
1050 (inputs `(("icu4c" ,icu4c)))
1051 (native-inputs `(("pkg-config" ,pkg-config)))
1052 (home-page "http://stringi.rexamine.com/")
1053 (synopsis "Character string processing facilities")
1055 "This package allows for fast, correct, consistent, portable, as well as
1056 convenient character string/text processing in every locale and any native
1057 encoding. Owing to the use of the ICU library, the package provides R users
1058 with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
1059 programmers. Among available features there are: pattern searching
1060 (e.g. via regular expressions), random string generation, string collation,
1061 transliteration, concatenation, date-time formatting and parsing, etc.")
1062 (license license:bsd-3)))
1064 (define-public r-stringr
1071 (uri (cran-uri "stringr" version))
1073 (base32 "1p9ip7p87gbbg4s6d3d392svvzz2b5dqdq2c8ilgvn4s78nlsq47"))))
1074 (build-system r-build-system)
1076 `(("r-glue" ,r-glue)
1077 ("r-magrittr" ,r-magrittr)
1078 ("r-stringi" ,r-stringi)))
1079 (home-page "https://github.com/hadley/stringr")
1080 (synopsis "Simple, consistent wrappers for common string operations")
1082 "Stringr is a consistent, simple and easy to use set of wrappers around
1083 the fantastic @code{stringi} package. All function and argument names (and
1084 positions) are consistent, all functions deal with \"NA\"'s and zero length
1085 vectors in the same way, and the output from one function is easy to feed into
1086 the input of another.")
1087 (license license:gpl2+)))
1089 (define-public r-reshape2
1096 (uri (cran-uri "reshape2" version))
1098 (base32 "1n0jrajpvc8hjkh9z4g8bwq63qy5vy5cgl2pzjardyih4ngcz3fq"))))
1099 (build-system r-build-system)
1101 `(("r-plyr" ,r-plyr)
1103 ("r-stringr" ,r-stringr)))
1104 (home-page "https://github.com/hadley/reshape")
1105 (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
1107 "Reshape2 is an R library to flexibly restructure and aggregate data
1108 using just two functions: melt and dcast (or acast).")
1109 (license license:expat)))
1111 (define-public r-ggplot2
1118 (uri (cran-uri "ggplot2" version))
1120 (base32 "1k136k1sr6dq1xvx6gs6gzji6hbnnwnsb5qivsxrblfv90irxhj5"))))
1121 (build-system r-build-system)
1123 `(("r-digest" ,r-digest)
1125 ("r-gtable" ,r-gtable)
1126 ("r-isoband" ,r-isoband)
1129 ("r-tibble" ,r-tibble)
1130 ("r-rlang" ,r-rlang)
1131 ("r-scales" ,r-scales)
1132 ("r-svglite" ,r-svglite) ; Needed for 'ggsave'
1133 ("r-withr" ,r-withr)))
1135 `(("r-knitr" ,r-knitr)))
1136 (home-page "https://ggplot2.tidyverse.org")
1137 (synopsis "An implementation of the grammar of graphics")
1139 "Ggplot2 is an implementation of the grammar of graphics in R. It
1140 combines the advantages of both base and lattice graphics: conditioning and
1141 shared axes are handled automatically, and you can still build up a plot step
1142 by step from multiple data sources. It also implements a sophisticated
1143 multidimensional conditioning system and a consistent interface to map data to
1144 aesthetic attributes.")
1145 (license license:gpl2+)))
1147 (define-public r-ggdendro
1153 (uri (cran-uri "ggdendro" version))
1156 "0skbj487b6f6pj2iz4yq2b9gbgb39cv5dyzhdl3w7ay1k0s5z9ph"))))
1157 (build-system r-build-system)
1159 `(("r-ggplot2" ,r-ggplot2)
1160 ("r-mass" ,r-mass)))
1162 `(("r-knitr" ,r-knitr)))
1163 (home-page "https://github.com/andrie/ggdendro")
1164 (synopsis "Create Dendrograms and Tree Diagrams Using ggplot2")
1165 (description "This is a set of tools for dendrograms and tree plots using
1166 ggplot2. The ggplot2 philosophy is to clearly separate data from the
1167 presentation. Unfortunately the plot method for dendrograms plots directly
1168 to a plot device with out exposing the data. The ggdendro package resolves
1169 this by making available functions that extract the dendrogram plot data.
1170 The package provides implementations for tree, rpart, as well as diana and
1171 agnes cluster diagrams.")
1172 (license license:gpl2+)))
1174 (define-public r-gdtools
1181 (uri (cran-uri "gdtools" version))
1184 "1p3ip0qwpg8f63jfx0b8vbac6l20ddid8xvxzkfi6i858pybnawp"))))
1185 (build-system r-build-system)
1187 `(("pkg-config" ,pkg-config)))
1190 ("freetype2" ,freetype)
1193 `(("r-rcpp" ,r-rcpp)
1194 ("r-systemfonts" ,r-systemfonts)))
1195 (home-page "https://cran.r-project.org/web/packages/gdtools")
1196 (synopsis "Utilities for graphical rendering")
1198 "The @code{gdtools} package provides functionalities to get font metrics
1199 and to generate base64 encoded string from raster matrix.")
1200 (license license:gpl3)))
1202 (define-public r-svglite
1209 (uri (cran-uri "svglite" version))
1212 "19ggknw5322yw7r1bzhw0bqggcrpn0qxddk7kblpqnra2zz2brkn"))))
1213 (build-system r-build-system)
1215 `(("libpng" ,libpng)
1218 `(("r-cpp11" ,r-cpp11)
1219 ("r-systemfonts" ,r-systemfonts)))
1221 `(("r-knitr" ,r-knitr)))
1222 (home-page "https://github.com/hadley/svglite")
1223 (synopsis "SVG graphics device")
1225 "@code{svglite} is a graphics device that produces clean
1226 @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
1227 hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
1228 considerably faster, produces smaller files, and leaves text as is.")
1229 (license license:gpl2+)))
1231 (define-public r-assertthat
1233 (name "r-assertthat")
1237 (uri (cran-uri "assertthat" version))
1240 "17wy5bdfzg73sg2clisg1k3zyn1adkj59x56m5nwia2k8z67zkw5"))))
1241 (build-system r-build-system)
1242 (home-page "https://github.com/hadley/assertthat")
1243 (synopsis "Easy pre and post assertions")
1245 "Assertthat is an extension to stopifnot() that makes it easy to declare
1246 the pre and post conditions that your code should satisfy, while also
1247 producing friendly error messages so that your users know what they've done
1249 (license license:gpl3+)))
1251 (define-public r-lazyeval
1257 (uri (cran-uri "lazyeval" version))
1260 "1m10i059csrcqkcn59a8wspn784alxsq3symzhn24mhhl894346n"))))
1261 (build-system r-build-system)
1262 (home-page "https://github.com/hadley/lazyeval")
1263 (synopsis "Lazy (non-standard) evaluation in R")
1265 "This package provides the tools necessary to do non-standard
1266 evaluation (NSE) in R.")
1267 (license license:gpl3+)))
1269 (define-public r-dbi
1275 (uri (cran-uri "DBI" version))
1278 "0i0kfyg43nryyka2bjlgz4x75w965224qp36wz1hl7a2lswb6ajp"))))
1279 (build-system r-build-system)
1281 `(("r-knitr" ,r-knitr)))
1282 (home-page "https://github.com/rstats-db/DBI")
1283 (synopsis "R database interface")
1285 "The DBI package provides a database interface (DBI) definition for
1286 communication between R and relational database management systems. All
1287 classes in this package are virtual and need to be extended by the various
1288 R/DBMS implementations.")
1289 (license license:lgpl2.0+)))
1294 (version "1.75.0-0")
1297 (uri (cran-uri "BH" version))
1300 "0nkgvl5qjs2a7jv0ncsrl4fqaw2pdaj7a1pncdv6kp874sci0k5f"))))
1301 (build-system r-build-system)
1302 (home-page "https://github.com/eddelbuettel/bh")
1303 (synopsis "R package providing subset of Boost headers")
1305 "This package aims to provide the most useful subset of Boost libraries
1306 for template use among CRAN packages.")
1307 (license license:boost1.0)))
1309 (define-public r-evaluate
1315 (uri (cran-uri "evaluate" version))
1318 "0a2y7j534gbgixkwj9r1z76l2vssw4g1hznzbpclc076wkdqpj58"))))
1319 (build-system r-build-system)
1320 (home-page "https://github.com/hadley/evaluate")
1321 (synopsis "Parsing and evaluation tools for R")
1323 "This package provides tools that allow you to recreate the parsing,
1324 evaluation and display of R code, with enough information that you can
1325 accurately recreate what happens at the command line. The tools can easily be
1326 adapted for other output formats, such as HTML or LaTeX.")
1327 (license license:gpl3+)))
1329 (define-public r-formatr
1335 (uri (cran-uri "formatR" version))
1338 "0vbzvb91y5cxjbnwpww0r40r6m1l9w1qa979sv7ghhalzr7bib3i"))))
1339 (build-system r-build-system)
1341 `(("r-knitr" ,r-knitr)))
1342 (home-page "https://yihui.org/formatr/")
1343 (synopsis "Format R code automatically")
1345 "This package provides a function to format R source code. Spaces and
1346 indent will be added to the code automatically, and comments will be preserved
1347 under certain conditions, so that R code will be more human-readable and tidy.
1348 There is also a Shiny app as a user interface in this package.")
1349 (license license:gpl3+)))
1351 (define-public r-highr
1357 (uri (cran-uri "highr" version))
1360 "0kgdv2vf1lz3b5kbal9s83gg6812nw7fvrq0rkyr0v4k1lwi3zxy"))))
1361 (build-system r-build-system)
1363 `(("r-xfun" ,r-xfun)))
1364 ;; We cannot add knitr to the inputs, because highr depends on xfun, which
1365 ;; is an input to knitr.
1368 `(("r-knitr" ,r-knitr)))
1369 (home-page "https://github.com/yihui/highr")
1370 (synopsis "Syntax highlighting for R source code")
1372 "This package provides syntax highlighting for R source code. Currently
1373 it supports LaTeX and HTML output. Source code of other languages is
1374 supported via Andre Simon's highlight package.")
1375 (license license:gpl3+)))
1377 (define-public r-mime
1383 (uri (cran-uri "mime" version))
1386 "1xz37fizlx4w3g8kbim7vr5slqd6cmaq5sa0s4q7ayl1bahk6ckq"))))
1387 (build-system r-build-system)
1388 (home-page "https://github.com/yihui/mime")
1389 (synopsis "R package to map filenames to MIME types")
1391 "This package guesses the MIME type from a filename extension using the
1392 data derived from /etc/mime.types in UNIX-type systems.")
1393 (license license:gpl2)))
1395 (define-public r-markdown
1401 (uri (cran-uri "markdown" version))
1404 "06zwbrp14bri3470anadd7dvgmw06xf8df6v2pk64wx3f9sd934d"))))
1405 (build-system r-build-system)
1406 ;; Skip check phase because the tests require the r-knitr package to be
1407 ;; installed. This prevents installation failures. Knitr normally
1408 ;; shouldn't be available since r-markdown is a dependency of the r-knitr
1410 (arguments `(#:tests? #f))
1412 `(("r-mime" ,r-mime)
1413 ("r-xfun" ,r-xfun)))
1414 (home-page "https://github.com/rstudio/markdown")
1415 (synopsis "Markdown rendering for R")
1417 "This package provides R bindings to the Sundown Markdown rendering
1418 library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
1419 syntax that can be converted to XHTML or other formats.")
1420 (license license:gpl2)))
1422 (define-public r-yaml
1428 (uri (cran-uri "yaml" version))
1431 "10r7g26x73am45niigm3k466030nymnr3v3fjljafzrr5aybf58i"))))
1432 (build-system r-build-system)
1433 (home-page "https://cran.r-project.org/web/packages/yaml/")
1434 (synopsis "Methods to convert R data to YAML and back")
1436 "This package implements the libyaml YAML 1.1 parser and
1437 emitter (http://pyyaml.org/wiki/LibYAML) for R.")
1438 (license license:bsd-3)))
1440 (define-public r-knitr
1446 (uri (cran-uri "knitr" version))
1449 "0289dj7h4wppn4xc4ids7xlrfb46gzd1n9r2wpmfc3c818mk70rg"))))
1450 (build-system r-build-system)
1452 `(("r-evaluate" ,r-evaluate)
1453 ("r-highr" ,r-highr)
1454 ("r-markdown" ,r-markdown)
1455 ("r-stringr" ,r-stringr)
1457 ("r-yaml" ,r-yaml)))
1458 (home-page "https://yihui.org/knitr/")
1459 (synopsis "General-purpose package for dynamic report generation in R")
1461 "This package provides a general-purpose tool for dynamic report
1462 generation in R using Literate Programming techniques.")
1463 ;; The code is released under any version of the GPL. As it is used by
1464 ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
1466 (license license:gpl2+)))
1468 (define-public r-knitrbootstrap
1470 (name "r-knitrbootstrap")
1475 (uri (cran-uri "knitrBootstrap" version))
1478 "1aj60j7f0gcs120fdrnfbnb7vk7lfn1phil0mghg6a5zldz4cqs3"))))
1479 (properties `((upstream-name . "knitrBootstrap")))
1480 (build-system r-build-system)
1482 `(("r-knitr" ,r-knitr)
1483 ("r-rmarkdown" ,r-rmarkdown)
1484 ("r-markdown" ,r-markdown)))
1485 (home-page "https://github.com/jimhester/knitrBootstrap")
1486 (synopsis "Knitr bootstrap framework")
1488 "This package provides a framework to create Bootstrap 3 HTML reports
1489 from knitr Rmarkdown.")
1490 (license license:expat)))
1492 (define-public r-microbenchmark
1494 (name "r-microbenchmark")
1498 (uri (cran-uri "microbenchmark" version))
1501 "1xl4m4yl4h2zcjiz8wsa7f3sh55qg2xr3sgpvz18rlix6b3173r6"))))
1502 (build-system r-build-system)
1503 (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
1504 (synopsis "Accurate timing functions for R")
1506 "This package provides infrastructure to accurately measure and compare
1507 the execution time of R expressions.")
1508 (license license:bsd-2)))
1510 (define-public r-pryr
1516 (uri (cran-uri "pryr" version))
1519 "06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k"))))
1520 (build-system r-build-system)
1522 `(("r-stringr" ,r-stringr)
1523 ("r-codetools" ,r-codetools)))
1525 `(("r-rcpp" ,r-rcpp)))
1526 (home-page "https://github.com/hadley/pryr")
1527 (synopsis "Tools for computing on the R language")
1529 "This package provides useful tools to pry back the covers of R and
1530 understand the language at a deeper level.")
1531 (license license:gpl2)))
1533 (define-public r-memoise
1539 (uri (cran-uri "memoise" version))
1542 "1bzcv7pmls3bx2w5ccv1pm20wycbfqba1v76k0fjgmjsm6hy76pz"))))
1543 (build-system r-build-system)
1545 `(("r-cachem" ,r-cachem)
1546 ("r-rlang" ,r-rlang)))
1547 (home-page "https://github.com/hadley/memoise")
1548 (synopsis "Memoise functions for R")
1550 "This R package caches the results of a function so that when
1551 you call it again with the same arguments it returns the pre-computed value.")
1552 (license license:expat)))
1554 (define-public r-crayon
1560 (uri (cran-uri "crayon" version))
1563 "1ir963s6zk9l32fw257y54p7898cd7z7yazkn9h6j2cdfhpf9dh8"))))
1564 (build-system r-build-system)
1565 (home-page "https://github.com/gaborcsardi/crayon")
1566 (synopsis "Colored terminal output for R")
1568 "Colored terminal output on terminals that support ANSI color and
1569 highlight codes. It also works in Emacs ESS. ANSI color support is
1570 automatically detected. Colors and highlighting can be combined and nested.
1571 New styles can also be created easily. This package was inspired by the
1572 \"chalk\" JavaScript project.")
1573 (license license:expat)))
1575 (define-public r-praise
1582 (uri (cran-uri "praise" version))
1585 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
1586 (build-system r-build-system)
1587 (home-page "https://github.com/gaborcsardi/praise")
1588 (synopsis "Functions to praise users")
1590 "This package provides template functions to assist in building friendly
1591 R packages that praise their users.")
1592 (license license:expat)))
1594 (define-public r-testthat
1600 (uri (cran-uri "testthat" version))
1603 "03sbk36vrjhzfap6a9czxw93r7h06rh3mb01inbrhrh5r2pd00qq"))))
1604 (build-system r-build-system)
1606 `(("r-brio" ,r-brio)
1607 ("r-callr" ,r-callr)
1609 ("r-crayon" ,r-crayon)
1611 ("r-digest" ,r-digest)
1612 ("r-ellipsis" ,r-ellipsis)
1613 ("r-evaluate" ,r-evaluate)
1614 ("r-jsonlite" ,r-jsonlite)
1615 ("r-lifecycle" ,r-lifecycle)
1616 ("r-magrittr" ,r-magrittr)
1617 ("r-pkgload" ,r-pkgload)
1618 ("r-praise" ,r-praise)
1619 ("r-processx" ,r-processx)
1622 ("r-rlang" ,r-rlang)
1623 ("r-waldo" ,r-waldo)
1624 ("r-withr" ,r-withr)))
1626 `(("r-knitr" ,r-knitr)))
1627 (home-page "https://github.com/hadley/testthat")
1628 (synopsis "Unit testing for R")
1630 "This package provides a unit testing system for R designed to be fun,
1631 flexible and easy to set up.")
1632 (license license:expat)))
1640 (uri (cran-uri "R6" version))
1643 "00ifi2kwa7kn67xf0z1w6jfdicjczygbyi5mhfw2qlzc4sbazhdf"))))
1644 (build-system r-build-system)
1645 (home-page "https://github.com/wch/R6/")
1646 (synopsis "Classes with reference semantics in R")
1648 "The R6 package allows the creation of classes with reference semantics,
1649 similar to R's built-in reference classes. Compared to reference classes, R6
1650 classes are simpler and lighter-weight, and they are not built on S4 classes
1651 so they do not require the methods package. These classes allow public and
1652 private members, and they support inheritance, even when the classes are
1653 defined in different packages.")
1654 (license license:expat)))
1656 (define-public r-rlang
1662 (uri (cran-uri "rlang" version))
1665 "1pfm24jjkxzdb5qcbc05dcjxyk69zpfr5jv4xakqh1xh41mr43kl"))))
1666 (build-system r-build-system)
1667 (home-page "http://rlang.tidyverse.org")
1668 (synopsis "Functions for base types, core R and Tidyverse features")
1669 (description "This package provides a toolbox for working with base types,
1670 core R features like the condition system, and core @code{Tidyverse} features
1671 like tidy evaluation.")
1672 (license license:gpl3)))
1674 (define-public r-tibble
1681 (uri (cran-uri "tibble" version))
1684 "0qqfiwy7i2zjxwmz0xp1j1p88yycdg3lh377jkzz6zs6gsbd89ln"))))
1685 (build-system r-build-system)
1687 `(("r-ellipsis" ,r-ellipsis)
1688 ("r-fansi" ,r-fansi)
1689 ("r-lifecycle" ,r-lifecycle)
1690 ("r-magrittr" ,r-magrittr)
1691 ("r-pkgconfig" ,r-pkgconfig)
1692 ("r-pillar" ,r-pillar)
1693 ("r-rlang" ,r-rlang)
1694 ("r-vctrs" ,r-vctrs)))
1696 `(("r-knitr" ,r-knitr)))
1697 (home-page "https://github.com/hadley/tibble")
1698 (synopsis "Simple data frames")
1700 "This package provides a @code{tbl_df} class that offers better checking
1701 and printing capabilities than traditional data frames.")
1702 (license license:expat)))
1704 (define-public r-dplyr
1710 (uri (cran-uri "dplyr" version))
1713 "0w3fr6sn0mw5mjs27669czpc8vpjj6ayrjavw8v0gd7ccsfa0hbm"))))
1714 (build-system r-build-system)
1716 `(("r-ellipsis" ,r-ellipsis)
1717 ("r-generics" ,r-generics)
1719 ("r-lifecycle" ,r-lifecycle)
1720 ("r-magrittr" ,r-magrittr)
1722 ("r-rlang" ,r-rlang)
1723 ("r-tibble" ,r-tibble)
1724 ("r-tidyselect" ,r-tidyselect)
1725 ("r-vctrs" ,r-vctrs)))
1727 `(("r-knitr" ,r-knitr)))
1728 (home-page "https://github.com/hadley/dplyr")
1729 (synopsis "Tools for working with data frames in R")
1731 "dplyr is the next iteration of plyr. It is focussed on tools for
1732 working with data frames. It has three main goals: 1) identify the most
1733 important data manipulation tools needed for data analysis and make them easy
1734 to use in R; 2) provide fast performance for in-memory data by writing key
1735 pieces of code in C++; 3) use the same code interface to work with data no
1736 matter where it is stored, whether in a data frame, a data table or
1738 (license license:expat)))
1740 (define-public r-dbplyr
1747 (uri (cran-uri "dbplyr" version))
1750 "025wqpmxdhzblb0pf58m3qh5h6bf5x8qvkf47vyl1cjsp13wz95b"))))
1751 (build-system r-build-system)
1753 `(("r-assertthat" ,r-assertthat)
1756 ("r-dplyr" ,r-dplyr)
1757 ("r-ellipsis" ,r-ellipsis)
1759 ("r-lifecycle" ,r-lifecycle)
1760 ("r-magrittr" ,r-magrittr)
1761 ("r-purrr" ,r-purrr)
1763 ("r-rlang" ,r-rlang)
1764 ("r-tibble" ,r-tibble)
1765 ("r-tidyselect" ,r-tidyselect)
1766 ("r-vctrs" ,r-vctrs)
1767 ("r-withr" ,r-withr)))
1769 `(("r-knitr" ,r-knitr)))
1770 (home-page "https://github.com/tidyverse/dbplyr")
1771 (synopsis "Dplyr back end for databases")
1773 "This package provides a dplyr back end for databases that allows you to
1774 work with remote database tables as if they are in-memory data frames. Basic
1775 features works with any database that has a @code{DBI} back end; more advanced
1776 features require SQL translation to be provided by the package author.")
1777 (license license:expat)))
1779 (define-public r-acepack
1786 (uri (cran-uri "acepack" version))
1789 "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
1790 (build-system r-build-system)
1792 `(("gfortran" ,gfortran)))
1793 (home-page "https://cran.r-project.org/web/packages/acepack")
1794 (synopsis "Functions for regression transformations")
1796 "This package provides ACE and AVAS methods for choosing regression
1798 (license license:expat)))
1800 (define-public r-formula
1807 (uri (cran-uri "Formula" version))
1810 "1bsw282i5m8rlirbhz7hqvf25zbxschk7yrp152whbzdnmry6w6b"))))
1811 (properties `((upstream-name . "Formula")))
1812 (build-system r-build-system)
1813 (home-page "https://cran.r-project.org/web/packages/Formula")
1814 (synopsis "Extended model formulas")
1816 "This package provides a new class @code{Formula}, which extends the base
1817 class @code{formula}. It supports extended formulas with multiple parts of
1818 regressors on the right-hand side and/or multiple responses on the left-hand
1820 (license (list license:gpl2+ license:gpl3+))))
1822 (define-public r-locfit
1829 (uri (cran-uri "locfit" version))
1832 "1vcw16qww4v4547w0gfvhqg60l051bsdlxa6zfcgcj9xbxf6dlyr"))))
1833 (build-system r-build-system)
1835 `(("r-lattice" ,r-lattice)))
1836 (home-page "https://cran.r-project.org/web/packages/locfit")
1837 (synopsis "Local regression, likelihood and density estimation")
1839 "This package provides functions used for local regression, likelihood
1840 and density estimation.")
1841 (license (list license:gpl2+ license:gpl3+))))
1843 (define-public r-chron
1849 (uri (cran-uri "chron" version))
1852 "0p9zz96jfyf139924hdwkzhr8knkjvx6547ac53rknm3a6wwngl6"))))
1853 (build-system r-build-system)
1854 (home-page "https://cran.r-project.org/web/packages/chron")
1855 (synopsis "Chronological R objects which can handle dates and times")
1857 "This package provides chronological R objects which can handle dates and
1859 (license license:gpl2)))
1861 (define-public r-data-table
1863 (name "r-data-table")
1867 (uri (cran-uri "data.table" version))
1870 "0kgbvap5v2spnkz3dwfm4jh4qcpvbzdn9s8bzfnhzabz9qjdxw8k"))))
1871 (build-system r-build-system)
1875 `(("pkg-config" ,pkg-config)
1876 ("r-knitr" ,r-knitr)))
1877 (home-page "https://github.com/Rdatatable/data.table/wiki")
1878 (synopsis "Enhanced version of data.frame R object")
1880 "The R package @code{data.table} is an extension of @code{data.frame}
1881 providing functions for fast aggregation of large data (e.g. 100GB in RAM),
1882 fast ordered joins, fast add/modify/delete of columns by group, column listing
1883 and fast file reading.")
1884 (license license:gpl3+)))
1886 (define-public r-xtable
1893 (uri (cran-uri "xtable" version))
1896 "077xfm0gphvhsay75amd9v90zk57kjgrrlgih04fyrbqqblc1gjs"))))
1897 (build-system r-build-system)
1899 `(("r-knitr" ,r-knitr))) ; for vignettes
1900 (home-page "http://xtable.r-forge.r-project.org/")
1901 (synopsis "Export R tables to LaTeX or HTML")
1903 "This package provides tools to export R data as LaTeX and HTML tables.")
1904 (license license:gpl2+)))
1906 (define-public python-patsy
1908 (name "python-patsy")
1912 (uri (pypi-uri "patsy" version))
1915 "149rbrdzwns0ay88caf1zsm1r53v1q5np1mrb36na50y432cw5gi"))))
1916 (build-system python-build-system)
1919 (modify-phases %standard-phases
1921 (lambda _ (invoke "nosetests" "-v"))))))
1923 `(("python-numpy" ,python-numpy)
1924 ("python-scipy" ,python-scipy)
1925 ("python-six" ,python-six)))
1927 `(("python-nose" ,python-nose)))
1928 (home-page "https://github.com/pydata/patsy")
1929 (synopsis "Describe statistical models and build design matrices")
1931 "Patsy is a Python package for describing statistical models and for
1932 building design matrices.")
1933 ;; The majority of the code is distributed under BSD-2. The module
1934 ;; patsy.compat contains code derived from the Python standard library,
1935 ;; and is covered by the PSFL.
1936 (license (list license:bsd-2 license:psfl))))
1938 (define-public python2-patsy
1939 (package-with-python2 python-patsy))
1941 (define-public python-statsmodels
1943 (name "python-statsmodels")
1948 (uri (pypi-uri "statsmodels" version))
1951 "1w6mf8b86vizi2895j11szqryr2v1ckjig3wp9fv94aslfh3zpjv"))))
1952 (build-system python-build-system)
1954 `(;; The test suite is very large and rather brittle. Tests often fail
1955 ;; because of minor changes in dependencies that upstream hasn't fixed
1956 ;; in a new release.
1959 (modify-phases %standard-phases
1960 (add-after 'unpack 'set-matplotlib-backend-to-agg
1962 ;; Set the matplotlib backend to Agg to avoid problems using the
1963 ;; GTK backend without a display.
1964 (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py")
1965 '("statsmodels/tsa/vector_ar/tests/test_var.py"
1966 "statsmodels/duration/tests/test_survfunc.py"))
1967 (("import matplotlib\\.pyplot as plt" line)
1968 (string-append "import matplotlib;matplotlib.use('Agg');"
1972 `(("python-numpy" ,python-numpy)
1973 ("python-scipy" ,python-scipy)
1974 ("python-pandas" ,python-pandas)
1975 ("python-patsy" ,python-patsy)
1976 ("python-matplotlib" ,python-matplotlib)))
1978 `(("python-cython" ,python-cython)
1979 ("python-nose" ,python-nose)
1980 ("python-sphinx" ,python-sphinx)))
1981 (home-page "http://statsmodels.sourceforge.net/")
1982 (synopsis "Statistical modeling and econometrics in Python")
1984 "Statsmodels is a Python package that provides a complement to scipy for
1985 statistical computations including descriptive statistics and estimation and
1986 inference for statistical models.")
1987 (license license:bsd-3)))
1989 (define-public python2-statsmodels
1990 (let ((stats (package-with-python2 python-statsmodels)))
1991 (package/inherit stats
1993 `(("python2-pytz" ,python2-pytz)
1994 ("python2-numpy" ,python2-numpy)
1995 ("python2-scipy" ,python2-scipy)
1996 ("python2-pandas" ,python2-pandas)
1997 ("python2-patsy" ,python2-patsy)
1998 ("python2-matplotlib" ,python2-matplotlib))))))
2000 (define-public r-coda
2006 (uri (cran-uri "coda" version))
2009 "13z5dwfpnyyhpsbpg4xr9g5c1685jhqj90f4x4qkcykr6kykqba2"))))
2010 (build-system r-build-system)
2012 `(("r-lattice" ,r-lattice)))
2013 (home-page "https://cran.r-project.org/web/packages/coda")
2014 (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
2015 (description "This package provides functions for summarizing and plotting
2016 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
2017 diagnostic tests of convergence to the equilibrium distribution of the Markov
2019 (license license:gpl2+)))
2021 (define-public r-ade4
2028 (uri (cran-uri "ade4" version))
2031 "142m70im8yd4q01q7z02y3ia0f66yh4ikdznv0ps6c7yyigs5mwv"))))
2032 (build-system r-build-system)
2034 `(("r-mass" ,r-mass)
2035 ("r-pixmap" ,r-pixmap)
2036 ("r-progress" ,r-progress)
2038 (home-page "http://pbil.univ-lyon1.fr/ADE-4")
2039 (synopsis "Multivariate data analysis and graphical display")
2041 "The ade4 package contains data analysis functions to analyze ecological
2042 and environmental data in the framework of Euclidean exploratory methods.")
2043 (license license:gpl2+)))
2045 (define-public r-xml2
2052 (uri (cran-uri "xml2" version))
2055 "1kx400v62xkd5xal7rzz7jcarz94ac8g1sh4i2dqr78qwgkzj8nz"))))
2056 (build-system r-build-system)
2058 `(("libxml2" ,libxml2)
2061 `(("pkg-config" ,pkg-config)
2062 ("r-knitr" ,r-knitr)))
2063 (home-page "https://github.com/hadley/xml2")
2064 (synopsis "Parse XML with R")
2066 "This package provides a simple, consistent interface to working with XML
2067 files in R. It is built on top of the libxml2 C library.")
2068 (license license:gpl2+)))
2070 (define-public r-multitaper
2072 (name "r-multitaper")
2077 (uri (cran-uri "multitaper" version))
2080 "1gm3wr8xqpqiby7q1dr3zxim77v0bvvrqi0hlazf5g3gnkrp2zc3"))))
2081 (build-system r-build-system)
2083 `(("gfortran" ,gfortran)))
2084 (home-page "https://github.com/wesleyburr/multitaper/")
2085 (synopsis "Multitaper spectral analysis tools")
2087 "This package implements multitaper spectral estimation
2088 techniques using prolate spheroidal sequences (Slepians) and sine
2089 tapers for time series analysis. It includes an adaptive weighted
2090 multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
2091 F-test, and complex demodulation. The Slepians sequences are
2092 generated efficiently using a tridiagonal matrix solution, and
2093 jackknifed confidence intervals are available for most estimates.")
2094 (license license:gpl2+)))
2096 (define-public r-rversions
2098 (name "r-rversions")
2102 (uri (cran-uri "rversions" version))
2105 "0ghpla5r3d6zh5dn6d6ii5p0a952lcdv004m88fk8r9k76vz88rm"))))
2106 (build-system r-build-system)
2108 `(("r-curl" ,r-curl)
2109 ("r-xml2" ,r-xml2)))
2110 (home-page "https://github.com/metacran/rversions")
2111 (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
2113 "This package provides functions to query the main R repository to find
2114 the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
2115 previous R versions and their release dates.")
2116 (license license:expat)))
2118 (define-public r-whisker
2124 (uri (cran-uri "whisker" version))
2127 "1a7vz0dk95xfjvi38wbpw8vmf5qn3g8p490msz2rw0piwidmk1ks"))))
2128 (build-system r-build-system)
2129 (home-page "https://github.com/edwindj/whisker")
2130 (synopsis "Logicless mustache templating for R")
2132 "This package provides logicless templating, with a syntax that is not
2134 (license license:gpl3+)))
2136 (define-public r-backports
2138 (name "r-backports")
2143 (uri (cran-uri "backports" version))
2146 "1mf2nz78l97lbxyagv55bcxrny51ds8g28h307cfa1g3ayylp0x2"))))
2147 (build-system r-build-system)
2148 (home-page "https://cran.r-project.org/web/packages/backports")
2149 (synopsis "Reimplementations of functions introduced since R 3.0.0")
2151 "Provides implementations of functions which have been introduced in R
2152 since version 3.0.0. The backports are conditionally exported which results
2153 in R resolving the function names to the version shipped with R (if available)
2154 and uses the implemented backports as fallback. This way package developers
2155 can make use of the new functions without worrying about the minimum required
2157 (license license:gpl2+)))
2159 (define-public r-checkmate
2161 (name "r-checkmate")
2166 (uri (cran-uri "checkmate" version))
2169 "193gkifr9spp0x0rwnjq1spdhjkfkh4mv27iklskcj604075phhd"))))
2170 (build-system r-build-system)
2172 `(("r-backports" ,r-backports)))
2173 (home-page "https://github.com/mllg/checkmate")
2174 (synopsis "Fast and versatile argument checks")
2176 "This package provides tests and assertions to perform frequent argument
2177 checks. A substantial part of the package was written in C to minimize any
2178 worries about execution time overhead.")
2179 (license license:bsd-3)))
2181 (define-public r-bbmisc
2188 (uri (cran-uri "BBmisc" version))
2191 "1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y"))))
2192 (properties `((upstream-name . "BBmisc")))
2193 (build-system r-build-system)
2195 `(("r-checkmate" ,r-checkmate)))
2196 (home-page "https://github.com/berndbischl/BBmisc")
2197 (synopsis "Miscellaneous functions for R package development")
2199 "This package provides miscellaneous helper functions for the development
2201 (license license:bsd-3)))
2203 (define-public r-fail
2210 (uri (cran-uri "fail" version))
2213 "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
2214 (build-system r-build-system)
2216 `(("r-bbmisc" ,r-bbmisc)
2217 ("r-checkmate" ,r-checkmate)))
2218 (home-page "https://github.com/mllg/fail")
2219 (synopsis "File abstraction interface layer (FAIL)")
2221 "This package provides a more comfortable interface to work with R data
2222 or source files in a key-value fashion.")
2223 (license license:bsd-3)))
2225 (define-public r-batchjobs
2227 (name "r-batchjobs")
2232 (uri (cran-uri "BatchJobs" version))
2235 "1zz4sspj596pijxlz321g0jy2rg9ki83j6fihbwisjwr66p2vk1m"))))
2236 (properties `((upstream-name . "BatchJobs")))
2237 (build-system r-build-system)
2239 `(("r-backports" ,r-backports)
2240 ("r-bbmisc" ,r-bbmisc)
2242 ("r-checkmate" ,r-checkmate)
2243 ("r-data-table" ,r-data-table)
2245 ("r-digest" ,r-digest)
2246 ("r-rsqlite" ,r-rsqlite)
2247 ("r-sendmailr" ,r-sendmailr)
2248 ("r-stringi" ,r-stringi)))
2249 (home-page "https://github.com/tudo-r/BatchJobs")
2250 (synopsis "Batch computing with R")
2252 "This package provides @code{Map}, @code{Reduce} and @code{Filter}
2253 variants to generate jobs on batch computing systems like PBS/Torque, LSF,
2254 SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
2255 (license license:bsd-2)))
2257 (define-public r-brew
2263 (uri (cran-uri "brew" version))
2266 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
2267 (build-system r-build-system)
2268 (home-page "https://cran.r-project.org/web/packages/brew")
2269 (synopsis "Templating framework for report generation")
2271 "The brew package implements a templating framework for mixing text and R
2272 code for report generation. The template syntax is similar to PHP, Ruby's erb
2273 module, Java Server Pages, and Python's psp module.")
2274 (license license:gpl2+)))
2276 (define-public r-desc
2283 (uri (cran-uri "desc" version))
2286 "1sw4vya3l971gpccq4gnjywgbl73bgx8la18l0wy617qv94f905y"))))
2287 (build-system r-build-system)
2289 `(("r-crayon" ,r-crayon)
2291 ("r-rprojroot" ,r-rprojroot)))
2292 (home-page "https://github.com/r-pkgs/desc")
2293 (synopsis "Manipulate DESCRIPTION Files")
2295 "This package provides tools to read, write, create, and manipulate
2296 DESCRIPTION files. It is intended for packages that create or manipulate
2298 (license license:expat)))
2300 (define-public r-commonmark
2302 (name "r-commonmark")
2307 (uri (cran-uri "commonmark" version))
2310 "024iz1qp2kv6iz6y69ir0jk3qhjps86rhkzlcmhqsxx97rx7cjni"))))
2311 (build-system r-build-system)
2312 (home-page "https://cran.r-project.org/web/packages/commonmark")
2313 (synopsis "CommonMark and Github Markdown Rendering in R")
2315 "The CommonMark specification defines a rationalized version of markdown
2316 syntax. This package uses the @code{cmark} reference implementation for
2317 converting markdown text into various formats including HTML, LaTeX and groff
2318 man. In addition, it exposes the markdown parse tree in XML format. The latest
2319 version of this package also adds support for Github extensions including
2320 tables, autolinks and strikethrough text.")
2321 (license license:bsd-2)))
2323 (define-public r-roxygen2
2329 (uri (cran-uri "roxygen2" version))
2332 "0qc8akwfwmaqsjaza87f5fi0zk6sh3l6j3assbs6chvx0gnmvidx"))))
2333 (build-system r-build-system)
2335 `(("r-brew" ,r-brew)
2336 ("r-commonmark" ,r-commonmark)
2338 ("r-digest" ,r-digest)
2339 ("r-knitr" ,r-knitr)
2340 ("r-pkgload" ,r-pkgload)
2341 ("r-purrr" ,r-purrr)
2344 ("r-rlang" ,r-rlang)
2345 ("r-stringi" ,r-stringi)
2346 ("r-stringr" ,r-stringr)
2347 ("r-xml2" ,r-xml2)))
2349 `(("r-knitr" ,r-knitr)))
2350 (home-page "https://github.com/klutometis/roxygen")
2351 (synopsis "In-source documentation system for R")
2353 "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
2354 collation, and NAMESPACE files.")
2355 (license license:gpl2+)))
2357 (define-public r-openssl
2364 (uri (cran-uri "openssl" version))
2367 "0x68di44vrqvikr419mgh9wlvbhxs52zda9pb6spikx69m4v83wj"))))
2368 (build-system r-build-system)
2370 `(("libressl" ,libressl)))
2372 `(("pkg-config" ,pkg-config)
2373 ("r-knitr" ,r-knitr)))
2375 `(("r-askpass" ,r-askpass)))
2376 (home-page "https://github.com/jeroenooms/openssl")
2377 (synopsis "Toolkit for encryption, signatures and certificates")
2379 "This package provides R bindings to OpenSSL libssl and libcrypto, plus
2380 custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
2381 and P-521. Cryptographic signatures can either be created and verified
2382 manually or via x509 certificates. AES block cipher is used in CBC mode for
2383 symmetric encryption; RSA for asymmetric (public key) encryption. High-level
2384 envelope functions combine RSA and AES for encrypting arbitrary sized data.
2385 Other utilities include key generators, hash functions (md5, sha1, sha256,
2386 etc), base64 encoder, a secure random number generator, and @code{bignum} math
2387 methods for manually performing crypto calculations on large multibyte
2389 (license license:expat)))
2391 (define-public r-httr
2397 (uri (cran-uri "httr" version))
2400 "1y8y1g1dkgv9jafrk1kj6pzxpw95c0rr9lplblfq2byrs1pfsas6"))))
2401 (build-system r-build-system)
2403 `(("r-curl" ,r-curl)
2404 ("r-jsonlite" ,r-jsonlite)
2405 ("r-openssl" ,r-openssl)
2409 `(("r-knitr" ,r-knitr)))
2410 (home-page "https://github.com/hadley/httr")
2411 (synopsis "Tools for working with URLs and HTTP")
2413 "The aim of httr is to provide a wrapper for RCurl customised to the
2414 demands of modern web APIs. It provides useful tools for working with HTTP
2415 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
2416 functions make it easy to control additional request components.")
2417 (license license:expat)))
2419 (define-public r-git2r
2425 (uri (cran-uri "git2r" version))
2428 "1wjmbs9cmm16pm3g0rmqp7cxxyh95m5lgx4fx5bpgj6j466i8vff"))))
2429 (build-system r-build-system)
2431 `(("libgit2" ,libgit2)
2434 `(("pkg-config" ,pkg-config)))
2435 (home-page "https://github.com/ropensci/git2r")
2436 (synopsis "Access Git repositories with R")
2438 "This package provides an R interface to the libgit2 library, which is a
2439 pure C implementation of the Git core methods.")
2440 ;; GPLv2 only with linking exception.
2441 (license license:gpl2)))
2443 (define-public r-rstudioapi
2445 (name "r-rstudioapi")
2449 (uri (cran-uri "rstudioapi" version))
2452 "12vdfzzjc6mv4h105l8cp108j3hjk0mqmg23m6mqr3jarfymphxa"))))
2453 (build-system r-build-system)
2455 `(("r-knitr" ,r-knitr)))
2456 (home-page "https://cran.r-project.org/web/packages/rstudioapi")
2457 (synopsis "Safely access the RStudio API")
2459 "This package provides functions to access the RStudio API and provide
2460 informative error messages when it's not available.")
2461 (license license:expat)))
2463 (define-public r-devtools
2469 (uri (cran-uri "devtools" version))
2472 "094kl4d07kvmn1dcvq73mn4r30c4vpshrqj4998azh7garjlz3kj"))))
2473 (build-system r-build-system)
2475 `(("r-callr" ,r-callr)
2478 ("r-ellipsis" ,r-ellipsis)
2481 ("r-jsonlite" ,r-jsonlite)
2482 ("r-lifecycle" ,r-lifecycle)
2483 ("r-memoise" ,r-memoise)
2484 ("r-pkgbuild" ,r-pkgbuild)
2485 ("r-pkgload" ,r-pkgload)
2486 ("r-rcmdcheck" ,r-rcmdcheck)
2487 ("r-remotes" ,r-remotes)
2488 ("r-rlang" ,r-rlang)
2489 ("r-roxygen2" ,r-roxygen2)
2490 ("r-rstudioapi" ,r-rstudioapi)
2491 ("r-rversions" ,r-rversions)
2492 ("r-sessioninfo" ,r-sessioninfo)
2493 ("r-testthat" ,r-testthat)
2494 ("r-usethis" ,r-usethis)
2495 ("r-withr" ,r-withr)))
2497 `(("r-knitr" ,r-knitr)))
2498 (home-page "https://github.com/hadley/devtools")
2499 (synopsis "Tools to make developing R packages easier")
2500 (description "The devtools package is a collection of package development
2501 tools to simplify the devolpment of R packages.")
2502 (license license:gpl2+)))
2504 (define-public r-withr
2510 (uri (cran-uri "withr" version))
2513 "1j5srffi748yxphwli56lkbh4cga0kmz38dyzganzkw0nx66mya8"))))
2514 (build-system r-build-system)
2516 `(("r-knitr" ,r-knitr)))
2517 (home-page "https://github.com/jimhester/withr")
2518 (synopsis "Run code with temporarily modified global state")
2520 "This package provides a set of functions to run R code in an environment
2521 in which global state has been temporarily modified. Many of these functions
2522 were originally a part of the r-devtools package.")
2523 (license license:gpl2+)))
2525 (define-public r-hms
2532 (uri (cran-uri "hms" version))
2535 "0qn9lvpkqrpxck88nf0zbff43vd7d6s1ibg58qfr3w14sw1yj14p"))))
2536 (build-system r-build-system)
2538 `(("r-ellipsis" ,r-ellipsis)
2539 ("r-lifecycle" ,r-lifecycle)
2540 ("r-pkgconfig" ,r-pkgconfig)
2541 ("r-rlang" ,r-rlang)
2542 ("r-vctrs" ,r-vctrs)))
2543 (home-page "https://github.com/rstats-db/hms")
2544 (synopsis "Pretty time of day")
2546 "This package implements an S3 class for storing and formatting
2547 time-of-day values, based on the @code{difftime} class.")
2548 (license license:gpl3+)))
2550 (define-public r-readr
2556 (uri (cran-uri "readr" version))
2559 "1fa67h4l9d30ig460xizgzl115i9pm3bk9dvsbrw6awbmf51ic82"))))
2560 (build-system r-build-system)
2563 ("r-clipr" ,r-clipr)
2564 ("r-cpp11" ,r-cpp11)
2565 ("r-crayon" ,r-crayon)
2567 ("r-lifecycle" ,r-lifecycle)
2568 ("r-tibble" ,r-tibble)
2570 ("r-rlang" ,r-rlang)
2573 `(("r-knitr" ,r-knitr)))
2574 (home-page "https://github.com/hadley/readr")
2575 (synopsis "Read tabular data")
2577 "This package provides functions to read flat or tabular text files from
2578 disk (or a connection).")
2579 (license license:gpl2+)))
2581 (define-public r-plotrix
2587 (uri (cran-uri "plotrix" version))
2590 "0pxfaalwwmnpv19nff0cg6b871m6gjhhmx63fpxm7730z75qh663"))))
2591 (build-system r-build-system)
2592 (home-page "https://cran.r-project.org/web/packages/plotrix")
2593 (synopsis "Various plotting functions")
2595 "This package provides lots of plotting, various labeling, axis and color
2596 scaling functions for R.")
2597 (license license:gpl2+)))
2599 (define-public r-gridbase
2605 (uri (cran-uri "gridBase" version))
2608 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
2609 (build-system r-build-system)
2610 (home-page "https://cran.r-project.org/web/packages/gridBase")
2611 (synopsis "Integration of base and grid graphics")
2613 "This package provides an integration of base and grid graphics for R.")
2614 (license license:gpl2+)))
2616 (define-public r-latticeextra
2618 (name "r-latticeextra")
2623 (uri (cran-uri "latticeExtra" version))
2626 "04fzwcqs594rk5qp98yilh3kdh3sw4xf8wld5rp94ggpaqfw7bbc"))))
2627 (properties `((upstream-name . "latticeExtra")))
2628 (build-system r-build-system)
2630 `(("r-jpeg" ,r-jpeg)
2631 ("r-lattice" ,r-lattice)
2633 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2634 (home-page "http://latticeextra.r-forge.r-project.org/")
2635 (synopsis "Extra graphical utilities based on lattice")
2637 "Building on the infrastructure provided by the lattice package, this
2638 package provides several new high-level graphics functions and methods, as
2639 well as additional utilities such as panel and axis annotation functions.")
2640 (license license:gpl2+)))
2642 (define-public r-rcpparmadillo
2644 (name "r-rcpparmadillo")
2645 (version "0.10.4.0.0")
2648 (uri (cran-uri "RcppArmadillo" version))
2651 "00nc7wfrra645mp7dl4j451m3pk3a0b3lrhgf8ydnw862avr9s6v"))))
2652 (properties `((upstream-name . "RcppArmadillo")))
2653 (build-system r-build-system)
2655 `(("r-rcpp" ,r-rcpp)))
2656 (home-page "https://github.com/RcppCore/RcppArmadillo")
2657 (synopsis "Rcpp integration for the Armadillo linear algebra library")
2659 "Armadillo is a templated C++ linear algebra library that aims towards a
2660 good balance between speed and ease of use. Integer, floating point and
2661 complex numbers are supported, as well as a subset of trigonometric and
2662 statistics functions. Various matrix decompositions are provided through
2663 optional integration with LAPACK and ATLAS libraries. This package includes
2664 the header files from the templated Armadillo library.")
2665 ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
2666 ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
2667 ;; later, as is the rest of 'Rcpp'.
2668 (license license:gpl2+)))
2670 (define-public r-bitops
2676 (uri (cran-uri "bitops" version))
2679 "1i0phmq5yynla5x0frqll1gbf5ww59p3sgz1s06a354zqf9grdg9"))))
2680 (build-system r-build-system)
2681 (home-page "https://cran.r-project.org/web/packages/bitops")
2682 (synopsis "Bitwise operations")
2684 "This package provides functions for bitwise operations on integer
2686 (license license:gpl2+)))
2688 (define-public r-catools
2694 (uri (cran-uri "caTools" version))
2697 "14q2ry8gaszjl0m97qg62dxv5bpj6k02qwyi7q2lnxgcmwai3mkm"))))
2698 (properties `((upstream-name . "caTools")))
2699 (build-system r-build-system)
2701 `(("r-bitops" ,r-bitops)))
2702 (home-page "https://cran.r-project.org/web/packages/caTools")
2703 (synopsis "Various tools including functions for moving window statistics")
2705 "This package contains several basic utility functions including:
2706 moving (rolling, running) window statistic functions, read/write for GIF and
2707 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
2708 encoder/decoder, round-off-error-free sum and cumsum, etc.")
2709 (license license:gpl3+)))
2711 (define-public r-rprojroot
2713 (name "r-rprojroot")
2718 (uri (cran-uri "rprojroot" version))
2721 "07wy07yhms8zln9qb0iwx69dq08h4lrdi8kavjcplfxcskq638az"))))
2722 (build-system r-build-system)
2724 `(("r-knitr" ,r-knitr)))
2725 (home-page "https://github.com/krlmlr/rprojroot")
2726 (synopsis "Finding files in project subdirectories")
2728 "This package helps accessing files relative to a project root. It
2729 provides helpers for robust, reliable and flexible paths to files below a
2730 project root. The root of a project is defined as a directory that matches a
2731 certain criterion, e.g., it contains a certain regular file.")
2732 (license license:gpl3)))
2734 (define-public r-rmarkdown
2736 (name "r-rmarkdown")
2741 (uri (cran-uri "rmarkdown" version))
2743 (base32 "0shj637qhpcf30il3lhl3k5bxi5l3x3gf612hbqlakp1qrgrf8lm"))))
2744 (properties `((upstream-name . "rmarkdown")))
2745 (build-system r-build-system)
2747 `(("r-evaluate" ,r-evaluate)
2748 ("r-htmltools" ,r-htmltools)
2749 ("r-jsonlite" ,r-jsonlite)
2750 ("r-knitr" ,r-knitr)
2751 ("r-stringr" ,r-stringr)
2752 ("r-tinytex" ,r-tinytex)
2756 ("pandoc-citeproc" ,pandoc-citeproc)))
2758 `(("r-knitr" ,r-knitr)))
2759 (home-page "https://rmarkdown.rstudio.com")
2760 (synopsis "Convert R Markdown documents into a variety of formats")
2762 "This package provides tools to convert R Markdown documents into a
2763 variety of formats.")
2764 (license license:gpl3+)))
2766 (define-public r-gtable
2772 (uri (cran-uri "gtable" version))
2775 "1lyncxf2dqdjgw1071cn9c8zwzkz6sldnd5cgmicf70bc726qf7x"))))
2776 (properties `((upstream-name . "gtable")))
2777 (build-system r-build-system)
2778 (home-page "https://cran.r-project.org/web/packages/gtable")
2779 (synopsis "R library to arrange grobs in tables")
2781 "Gtable is a collection of tools to make it easier to work with
2782 \"tables\" of grobs.")
2783 (license license:gpl2+)))
2785 (define-public r-gridextra
2787 (name "r-gridextra")
2791 (uri (cran-uri "gridExtra" version))
2794 "0fwfk3cdwxxim7nd55pn7m31bcaqj48y06j7an2k1v1pybk0rdl1"))))
2795 (properties `((upstream-name . "gridExtra")))
2796 (build-system r-build-system)
2798 `(("r-gtable" ,r-gtable)))
2800 `(("r-knitr" ,r-knitr))) ;for building vignettes
2801 (home-page "https://github.com/baptiste/gridextra")
2802 (synopsis "Miscellaneous functions for \"Grid\" graphics")
2804 "This package provides a number of user-level functions to work with
2805 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
2807 (license license:gpl2+)))
2809 (define-public r-pkgconfig
2811 (name "r-pkgconfig")
2815 (uri (cran-uri "pkgconfig" version))
2818 "0l1qph8zyi2sic3k2qcd7vlfl7rzfh1q7z7zvjkl5f7y1x2fy3rk"))))
2819 (build-system r-build-system)
2820 (home-page "https://github.com/gaborcsardi/pkgconfig")
2821 (synopsis "Private configuration for R packages")
2822 (description "This package provides the functionality to set configuration
2823 options on a per-package basis. Options set by a given package only apply to
2824 that package, other packages are unaffected.")
2825 (license license:expat)))
2827 (define-public r-blob
2833 (uri (cran-uri "blob" version))
2836 "1slb5mvxfyi92i8ifx2qa31hp57inilwhq1g9lzvgha6jrxbqm7g"))))
2837 (build-system r-build-system)
2839 `(("r-rlang" ,r-rlang)
2840 ("r-vctrs" ,r-vctrs)))
2841 (home-page "https://github.com/hadley/blob")
2842 (synopsis "Simple S3 Class for representing vectors of binary data")
2843 (description "Raw vectors in R are useful for storing a single binary
2844 object. What if you want to put a vector of them in a data frame? The blob
2845 package provides the blob object, a list of raw vectors, suitable for use as
2846 a column in data frame.")
2847 (license license:gpl3+)))
2849 (define-public r-rsqlite
2855 (uri (cran-uri "RSQLite" version))
2858 "1j89n4ydv42y5hqqv8nz72sa5wncws074kg527s902k1a67s69ii"))))
2859 (properties `((upstream-name . "RSQLite")))
2860 (build-system r-build-system)
2863 ("r-memoise" ,r-memoise)
2864 ("r-plogr" ,r-plogr)
2866 ("r-bit64" ,r-bit64)
2868 ("r-pkgconfig" ,r-pkgconfig)))
2870 `(("r-knitr" ,r-knitr)))
2871 (home-page "https://github.com/rstats-db/RSQLite")
2872 (synopsis "SQLite interface for R")
2874 "This package embeds the SQLite database engine in R and provides an
2875 interface compliant with the DBI package. The source for the SQLite
2876 engine (version 3.8.8.2) is included.")
2877 (license license:lgpl2.0+)))
2879 (define-public r-rcurl
2882 (version "1.95-0.1.2")
2885 (uri (string-append "https://www.bioconductor.org/packages/"
2886 "release/extra/src/"
2887 "contrib/RCurl_" version ".tar.gz"))
2890 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
2891 (properties `((upstream-name . "RCurl")))
2892 (build-system r-build-system)
2895 (modify-phases %standard-phases
2896 (add-after 'unpack 'respect-CURL_CA_BUNDLE
2898 (substitute* "R/options.S"
2899 (("\\.els = rev\\(merge\\(list\\(\\.\\.\\.\\), \\.opts\\)\\)" m)
2901 certs = Sys.getenv(\"CURL_CA_BUNDLE\")
2902 if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) }
2906 `(("libcurl" ,curl)))
2908 `(("r-bitops" ,r-bitops)))
2909 (home-page "http://www.omegahat.net/RCurl")
2910 (synopsis "General network client interface for R")
2912 "The package allows one to compose general HTTP requests and provides
2913 convenient functions to fetch URIs, GET and POST forms, etc. and process the
2914 results returned by the Web server. This provides a great deal of control
2915 over the HTTP/FTP/... connection and the form of the request while providing a
2916 higher-level interface than is available just using R socket connections.
2917 Additionally, the underlying implementation is robust and extensive,
2918 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
2919 ldap, and also supports cookies, redirects, authentication, etc.")
2920 (license license:bsd-3)))
2922 (define-public r-xml
2925 (version "3.99-0.6")
2928 (uri (cran-uri "XML" version))
2931 "0qibvacbfm7gl41ylway3vdyi1qbpa211d48rg3k5i30d48rbf58"))))
2933 `((upstream-name . "XML")))
2934 (build-system r-build-system)
2936 `(("libxml2" ,libxml2)
2939 `(("pkg-config" ,pkg-config)))
2940 (home-page "http://www.omegahat.net/RSXML")
2941 (synopsis "Tools for parsing and generating XML within R")
2943 "Many approaches for both reading and creating XML (and HTML)
2944 documents (including DTDs), both local and accessible via HTTP or FTP. Also
2945 offers access to an XPath \"interpreter\".")
2946 (license license:bsd-2)))
2948 (define-public r-xnomial
2953 (origin (method url-fetch)
2954 (uri (cran-uri "XNomial" version))
2957 "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
2958 (properties (quasiquote ((upstream-name . "XNomial"))))
2959 (build-system r-build-system)
2960 (home-page "https://cran.r-project.org/web/packages/XNomial")
2961 (synopsis "Goodness-of-Fit test for multinomial data")
2963 "This package provides an exact Goodness-of-Fit test for
2964 multinomial data with fixed probabilities. It can be used to
2965 determine whether a set of counts fits a given expected ratio. To see
2966 whether a set of observed counts fits an expectation, one can examine
2967 all possible outcomes with @code{xmulti()} or a random sample of them
2968 with @code{xmonte()} and find the probability of an observation
2969 deviating from the expectation by at least as much as the observed.
2970 As a measure of deviation from the expected, one can use the
2971 log-likelihood ratio, the multinomial probability, or the classic
2972 chi-square statistic. A histogram of the test statistic can also be
2973 plotted and compared with the asymptotic curve.")
2974 (license (list license:gpl2+ license:gpl3+))))
2976 (define-public r-lambda-r
2982 (uri (cran-uri "lambda.r" version))
2985 "1mh1g0gsd58gng0hb29vww2yqb2jfs07kba5kxnnqck5j3izwlnj"))))
2986 (properties `((upstream-name . "lambda.r")))
2987 (build-system r-build-system)
2989 `(("r-formatr" ,r-formatr)))
2990 (home-page "https://cran.r-project.org/web/packages/lambda.r")
2991 (synopsis "Functional programming extension for R")
2993 "This package provides a language extension to efficiently write
2994 functional programs in R. Syntax extensions include multi-part function
2995 definitions, pattern matching, guard statements, built-in (optional) type
2997 (license license:lgpl3+)))
2999 (define-public r-futile-options
3001 (name "r-futile-options")
3005 (uri (cran-uri "futile.options" version))
3008 "0w15agpi88y3qkv6fl72zy2pzyplzgvnj41a4ixhg64mw1sck73s"))))
3010 `((upstream-name . "futile.options")))
3011 (build-system r-build-system)
3012 (home-page "https://cran.r-project.org/web/packages/futile.options")
3013 (synopsis "Options management framework")
3015 "The futile.options subsystem provides an easy user-defined options
3016 management system that is properly scoped. This means that options created
3017 via @code{futile.options} are fully self-contained and will not collide with
3018 options defined in other packages.")
3019 (license license:lgpl3+)))
3021 (define-public r-futile-logger
3023 (name "r-futile-logger")
3027 (uri (cran-uri "futile.logger" version))
3030 "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
3031 (properties `((upstream-name . "futile.logger")))
3032 (build-system r-build-system)
3034 `(("r-futile-options" ,r-futile-options)
3035 ("r-lambda-r" ,r-lambda-r)))
3036 (home-page "https://cran.r-project.org/web/packages/futile.logger")
3037 (synopsis "Logging utility for R")
3039 "This package provides a simple yet powerful logging utility. Based
3040 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
3041 convenient and easy to use replacement for @code{cat} and @code{print}
3043 (license license:lgpl3+)))
3045 (define-public r-segmented
3047 (name "r-segmented")
3052 (uri (cran-uri "segmented" version))
3055 "0bchqcy308kbywavgyg9kb4543rbkfn753q9c6d7l7aw7sxvyxl2"))))
3056 (build-system r-build-system)
3057 (home-page "https://cran.r-project.org/web/packages/segmented")
3058 (synopsis "Regression models with breakpoints estimation")
3060 "Given a regression model, segmented updates the model by adding one or
3061 more segmented (i.e., piecewise-linear) relationships. Several variables with
3062 multiple breakpoints are allowed.")
3063 (license (list license:gpl2+ license:gpl3+))))
3065 (define-public r-snow
3071 (uri (cran-uri "snow" version))
3074 "1n3n8pva9s34fvlw32yng0x416lmbv7q1fsd0ywa4kikmxym64l5"))))
3075 (build-system r-build-system)
3076 (home-page "https://cran.r-project.org/web/packages/snow")
3077 (synopsis "Support for simple parallel computing in R")
3079 "The snow package provides support for simple parallel computing on a
3080 network of workstations using R. A master R process calls @code{makeCluster}
3081 to start a cluster of worker processes; the master process then uses functions
3082 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
3083 worker processes and collect and return the results on the master.")
3084 (license (list license:gpl2+ license:gpl3+))))
3086 (define-public r-sparsem
3092 (uri (cran-uri "SparseM" version))
3095 "0csbqd9wm6r4162mday1iaigzf9wv2rp1zq8hnihys6f38w8z0xx"))))
3097 `((upstream-name . "SparseM")))
3099 `(("gfortran" ,gfortran)))
3100 (build-system r-build-system)
3101 (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
3102 (synopsis "Sparse linear algebra")
3104 "This package provides some basic linear algebra functionality for sparse
3105 matrices. It includes Cholesky decomposition and backsolving as well as
3106 standard R subsetting and Kronecker products.")
3107 (license license:gpl2+)))
3109 (define-public r-iterators
3111 (name "r-iterators")
3116 (uri (cran-uri "iterators" version))
3119 "190i1y2493v5c9z8978rb3idlwsjymy67k1assa9znljqbj313kp"))))
3120 (build-system r-build-system)
3121 (home-page "https://cran.r-project.org/web/packages/iterators")
3122 (synopsis "Iterator construct for R")
3124 "This package provides support for iterators, which allow a programmer to
3125 traverse through all the elements of a vector, list, or other collection of
3127 (license license:asl2.0)))
3129 (define-public r-foreach
3136 (uri (cran-uri "foreach" version))
3139 "1qb83b1jvpmk8d6kfibkm5q2hiki0x5gipy758mwa62n56gdcnpv"))))
3140 (build-system r-build-system)
3142 `(("r-codetools" ,r-codetools)
3143 ("r-iterators" ,r-iterators)))
3145 `(("r-knitr" ,r-knitr)))
3146 (home-page "https://cran.r-project.org/web/packages/foreach")
3147 (synopsis "Foreach looping construct for R")
3149 "This package provides support for the @code{foreach} looping construct.
3150 @code{foreach} is an idiom that allows for iterating over elements in a
3151 collection, without the use of an explicit loop counter. This package in
3152 particular is intended to be used for its return value, rather than for its
3153 side effects. In that sense, it is similar to the standard @code{lapply}
3154 function, but doesn't require the evaluation of a function. Using
3155 @code{foreach} without side effects also facilitates executing the loop in
3157 (license license:asl2.0)))
3159 (define-public r-doparallel
3161 (name "r-doparallel")
3166 (uri (cran-uri "doParallel" version))
3169 "1cjf0mxrxgls5pl7aj22fv9j488craib1wkc9np4f3gkckwjdfzi"))))
3170 (properties `((upstream-name . "doParallel")))
3171 (build-system r-build-system)
3173 `(("r-foreach" ,r-foreach)
3174 ("r-iterators" ,r-iterators)))
3175 (home-page "https://cran.r-project.org/web/packages/doParallel")
3176 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3178 "This package provides a parallel backend for the @code{%dopar%} function
3179 using the parallel package.")
3180 (license license:gpl2+)))
3182 (define-public r-domc
3189 (uri (cran-uri "doMC" version))
3192 "0kdmfhp5m1wisjbfyl9d040jrmjmhcgjb0vdi536g2i9vixb5yny"))))
3193 (properties `((upstream-name . "doMC")))
3194 (build-system r-build-system)
3196 `(("r-foreach" ,r-foreach)
3197 ("r-iterators" ,r-iterators)))
3198 (home-page "https://cran.r-project.org/web/packages/doMC")
3199 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3201 "This package provides a parallel backend for the @code{%dopar%} function
3202 using the multicore functionality of the parallel package.")
3203 (license license:gpl2+)))
3211 (uri (cran-uri "DT" version))
3214 "1vxqmj01504k9639m2cig1s4qflz3dj54h9rgx5qa72fpkvkk411"))))
3216 `((upstream-name . "DT")))
3217 (build-system r-build-system)
3219 `(("r-crosstalk" ,r-crosstalk)
3220 ("r-htmltools" ,r-htmltools)
3221 ("r-htmlwidgets" ,r-htmlwidgets)
3222 ("r-jsonlite" ,r-jsonlite)
3223 ("r-magrittr" ,r-magrittr)
3224 ("r-promises" ,r-promises)))
3226 `(("r-knitr" ,r-knitr)))
3227 (home-page "https://rstudio.github.io/DT")
3228 (synopsis "R wrapper of the DataTables JavaScript library")
3230 "This package allows for data objects in R to be rendered as HTML tables
3231 using the JavaScript library @code{DataTables} (typically via R Markdown or
3232 Shiny). The @code{DataTables} library has been included in this R package.")
3233 ;; The DT package as a whole is distributed under GPLv3. The DT package
3234 ;; inludes other software components under different licenses:
3236 ;; * Expat: jQuery, jquery.highlight.js, DataTables
3237 ;; * ASL2.0: selectize.js
3238 ;; * WTFPL: noUiSlider
3239 (license (list license:gpl3
3244 (define-public r-base64enc
3246 (name "r-base64enc")
3250 (uri (cran-uri "base64enc" version))
3253 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
3254 (build-system r-build-system)
3255 (home-page "https://www.rforge.net/base64enc")
3256 (synopsis "Tools for Base64 encoding")
3258 "This package provides tools for handling Base64 encoding. It is more
3259 flexible than the orphaned \"base64\" package.")
3260 (license license:gpl2+)))
3262 (define-public r-irlba
3269 (uri (cran-uri "irlba" version))
3272 "1h7mzrqdjc41814cf6c93sbyl7nxwvsf3x8apl9rhmydgdlk7qkf"))))
3273 (build-system r-build-system)
3275 `(("r-matrix" ,r-matrix)))
3276 (home-page "https://cran.r-project.org/web/packages/irlba")
3277 (synopsis "Methods for eigendecomposition of large matrices")
3279 "This package provides fast and memory efficient methods for truncated
3280 singular and eigenvalue decompositions, as well as for principal component
3281 analysis of large sparse or dense matrices.")
3282 (license (list license:gpl2+ license:gpl3+))))
3284 (define-public r-glmnet
3291 (uri (cran-uri "glmnet" version))
3293 (base32 "0zpfq0m1y5zks5p9r28553ykywwrhrb3ds8m6b7sm6hj4n1c4csd"))))
3294 (build-system r-build-system)
3296 `(("gfortran" ,gfortran)
3297 ("r-knitr" ,r-knitr)))
3299 `(("r-foreach" ,r-foreach)
3300 ("r-matrix" ,r-matrix)
3301 ("r-shape" ,r-shape)
3302 ("r-survival" ,r-survival)))
3303 (home-page "https://www.jstatsoft.org/article/view/v033i01")
3304 (synopsis "Lasso and elastic-net regularized generalized linear models")
3306 "The glmnet package provides efficient procedures for fitting the entire
3307 lasso or elastic-net regularization path for linear and Poisson regression, as
3308 well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
3309 multinomial models. The algorithm uses cyclical coordinate descent in a
3310 path-wise fashion.")
3311 (license license:gpl2+)))
3313 (define-public r-pkgmaker
3320 (uri (cran-uri "pkgmaker" version))
3323 "14ggsd24n5g5rvn0wl4w90ipxzmywqikh28llj89q6kpxwnv4iff"))))
3324 (build-system r-build-system)
3326 `(("r-assertthat" ,r-assertthat)
3327 ("r-codetools" ,r-codetools)
3328 ("r-digest" ,r-digest)
3329 ("r-registry" ,r-registry)
3330 ("r-stringr" ,r-stringr)
3331 ("r-withr" ,r-withr)
3332 ("r-xtable" ,r-xtable)))
3333 (home-page "https://renozao.github.io/pkgmaker")
3334 (synopsis "Package development utilities")
3336 "This package provides some low-level utilities to use for R package
3337 development. It currently provides managers for multiple package specific
3338 options and registries, vignette, unit test and bibtex related utilities.")
3339 (license license:gpl2+)))
3341 (define-public r-registry
3348 (uri (cran-uri "registry" version))
3351 "1k3j6dx350awamr0dwwgkhfs46vsnj4nf08iw5byq0x7n3nkdsnz"))))
3352 (build-system r-build-system)
3353 (home-page "https://cran.r-project.org/web/packages/registry")
3354 (synopsis "Infrastructure for R package registries")
3356 "This package provides a generic infrastructure for creating and using R
3357 package registries.")
3358 (license license:gpl2+)))
3360 (define-public r-rngtools
3367 (uri (cran-uri "rngtools" version))
3370 "0xgmg3qb6insc157as47mcm9sdjdpy9jirh7w06bxb7pfcxqfx42"))))
3371 (build-system r-build-system)
3373 `(("r-digest" ,r-digest)))
3374 (home-page "https://renozao.github.io/rngtools")
3375 (synopsis "Utility functions for working with random number generators")
3377 "This package contains a set of functions for working with Random Number
3378 Generators (RNGs). In particular, it defines a generic S4 framework for
3379 getting/setting the current RNG, or RNG data that are embedded into objects
3380 for reproducibility. Notably, convenient default methods greatly facilitate
3381 the way current RNG settings can be changed.")
3382 (license license:gpl3+)))
3384 (define-public r-rtsne
3391 (uri (cran-uri "Rtsne" version))
3394 "0v17vxizrs1msay24xl2bckfajr2c82wpqj07lyssbrq197nwdsn"))))
3395 (properties `((upstream-name . "Rtsne")))
3396 (build-system r-build-system)
3398 `(("r-rcpp" ,r-rcpp)))
3399 (home-page "https://github.com/jkrijthe/Rtsne")
3400 (synopsis "T-distributed stochastic neighbor embedding")
3402 "This package provides an R wrapper around the fast T-distributed
3403 Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
3404 ;; The declared license for this package is BSD-3, but it also includes
3405 ;; code licensed under BSD-4.
3406 (license (list license:bsd-3 license:bsd-4))))
3408 (define-public r-e1071
3415 (uri (cran-uri "e1071" version))
3418 "0blfnv3m5k5xm9bfx1v5awvagqlhqaqpabrvzplf4244c3j259qa"))))
3419 (build-system r-build-system)
3421 `(("r-class" ,r-class)
3422 ("r-proxy" ,r-proxy)))
3423 (home-page "https://cran.r-project.org/web/packages/e1071")
3424 (synopsis "Miscellaneous functions for probability theory")
3426 "This package provides functions for latent class analysis, short time
3427 Fourier transform, fuzzy clustering, support vector machines, shortest path
3428 computation, bagged clustering, naive Bayes classifier, and more.")
3429 (license license:gpl2+)))
3431 (define-public r-bigmemory-sri
3433 (name "r-bigmemory-sri")
3438 (uri (cran-uri "bigmemory.sri" version))
3440 (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
3442 `((upstream-name . "bigmemory.sri")))
3443 (build-system r-build-system)
3444 (home-page "https://cran.r-project.org/web/packages/bigmemory.sri")
3445 (synopsis "Shared resource interface for the bigmemory package")
3446 (description "This package provides a shared resource interface for the
3447 bigmemory and synchronicity packages.")
3448 ;; Users can choose either LGPLv3 or ASL2.0.
3449 (license (list license:lgpl3 license:asl2.0))))
3451 (define-public r-synchronicity
3453 (name "r-synchronicity")
3458 (uri (cran-uri "synchronicity" version))
3461 "1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx"))))
3462 (build-system r-build-system)
3465 ("r-bigmemory-sri" ,r-bigmemory-sri)
3467 ("r-uuid" ,r-uuid)))
3468 (home-page "http://www.bigmemory.org")
3469 (synopsis "Boost mutex functionality in R")
3470 (description "This package provides support for synchronization
3471 via mutexes and may eventually support interprocess communication and
3473 ;; Users can choose either LGPLv3 or ASL2.0.
3474 (license (list license:lgpl3 license:asl2.0))))
3476 (define-public r-bigmemory
3478 (name "r-bigmemory")
3483 (uri (cran-uri "bigmemory" version))
3486 "03pg8mxdc7q0249visjmc8bc3xmwxsfg3i2n6higicj4cfz7zihq"))))
3487 (build-system r-build-system)
3491 ("r-bigmemory-sri" ,r-bigmemory-sri)))
3492 (home-page "http://www.bigmemory.org")
3493 (synopsis "Manage large matrices with shared memory or memory-mapped files")
3494 (description "This package provides methods to create, store, access, and
3495 manipulate large matrices. Matrices are allocated to shared memory and may use
3496 memory-mapped files.")
3497 ;; Users can choose either LGPLv3 or ASL2.0.
3498 (license (list license:lgpl3 license:asl2.0))))
3500 (define-public r-r-methodss3
3502 (name "r-r-methodss3")
3506 (uri (cran-uri "R.methodsS3" version))
3509 "16v1br7lf7vxv40z65giv9jnqkpnyqagcmgqa0s1jy7spj0zp64a"))))
3510 (properties `((upstream-name . "R.methodsS3")))
3511 (build-system r-build-system)
3512 (home-page "https://cran.r-project.org/web/packages/R.methodsS3")
3513 (synopsis "S3 methods simplified")
3515 "This package provides methods that simplify the setup of S3 generic
3516 functions and S3 methods. Major effort has been made in making definition of
3517 methods as simple as possible with a minimum of maintenance for package
3518 developers. For example, generic functions are created automatically, if
3519 missing, and naming conflict are automatically solved, if possible. The
3520 method @code{setMethodS3()} is a good start for those who in the future may
3521 want to migrate to S4.")
3522 (license license:lgpl2.1+)))
3524 (define-public r-r-oo
3530 (uri (cran-uri "R.oo" version))
3533 "1divisff26fmiqg6vmabnwlrx079c066r8qvkakfp336vnwdm89p"))))
3534 (properties `((upstream-name . "R.oo")))
3535 (build-system r-build-system)
3537 `(("r-r-methodss3" ,r-r-methodss3)))
3538 (home-page "https://github.com/HenrikBengtsson/R.oo")
3539 (synopsis "R object-oriented programming with or without references")
3541 "This package provides methods and classes for object-oriented
3542 programming in R with or without references. Large effort has been made on
3543 making definition of methods as simple as possible with a minimum of
3544 maintenance for package developers.")
3545 (license license:lgpl2.1+)))
3547 (define-public r-r-utils
3553 (uri (cran-uri "R.utils" version))
3556 "1gssnk73nhisc20by9kvfl4byfsmwrk6597na0x40ycck58lyylm"))))
3557 (properties `((upstream-name . "R.utils")))
3558 (build-system r-build-system)
3560 `(("r-r-methodss3" ,r-r-methodss3)
3561 ("r-r-oo" ,r-r-oo)))
3562 (home-page "https://github.com/HenrikBengtsson/R.utils")
3563 (synopsis "Various programming utilities")
3565 "This package provides utility functions useful when programming and
3566 developing R packages.")
3567 (license license:lgpl2.1+)))
3569 (define-public r-r-cache
3575 (uri (cran-uri "R.cache" version))
3578 "09pipn1974ivjh4sm3n5fjlh31rilf87p30qwq7y25vriyqd7d5d"))))
3579 (properties `((upstream-name . "R.cache")))
3580 (build-system r-build-system)
3583 (modify-phases %standard-phases
3584 (add-after 'unpack 'set-HOME
3585 (lambda _ (setenv "HOME" "/tmp"))))))
3587 `(("r-digest" ,r-digest)
3588 ("r-r-methodss3" ,r-r-methodss3)
3590 ("r-r-utils" ,r-r-utils)))
3591 (home-page "https://github.com/HenrikBengtsson/R.cache")
3592 (synopsis "Light-weight caching of objects and results")
3594 "This package provides methods for caching or memoization of objects and
3595 results. With this package, any R object can be cached in a key-value storage
3596 where the key can be an arbitrary set of R objects. The cache memory is
3597 persistent (on the file system).")
3598 (license license:lgpl2.1+)))
3600 (define-public r-r-rsp
3606 (uri (cran-uri "R.rsp" version))
3609 "0n9sxrffahgxcc8h9vgxg5i446g14cibixpf82nkpm5bvidhfsc9"))))
3610 (properties `((upstream-name . "R.rsp")))
3611 (build-system r-build-system)
3613 `(("r-digest" ,r-digest)
3614 ("r-r-cache" ,r-r-cache)
3615 ("r-r-methodss3" ,r-r-methodss3)
3617 ("r-r-utils" ,r-r-utils)))
3618 (home-page "https://github.com/HenrikBengtsson/R.rsp")
3619 (synopsis "Dynamic generation of scientific reports")
3621 "The RSP markup language provides a powerful markup for controlling the
3622 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
3623 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
3624 to many other literate programming languages, with RSP it is straightforward
3625 to loop over mixtures of code and text sections, e.g. in month-by-month
3626 summaries. RSP has also several preprocessing directives for incorporating
3627 static and dynamic contents of external files (local or online) among other
3628 things. RSP is ideal for self-contained scientific reports and R package
3630 (license license:lgpl2.1+)))
3632 (define-public r-mvtnorm
3638 (uri (cran-uri "mvtnorm" version))
3641 "1pj51mi0g6ip7a2nhzc93yv9289kaayvspjvsbgbgarvx7axlrg9"))))
3642 (build-system r-build-system)
3644 `(("gfortran" ,gfortran)))
3645 (home-page "http://mvtnorm.R-forge.R-project.org")
3646 (synopsis "Package for multivariate normal and t-distributions")
3647 (description "This package can compute multivariate normal and
3648 t-probabilities, quantiles, random deviates and densities.")
3649 (license license:gpl2)))
3651 (define-public r-matrixstats
3653 (name "r-matrixstats")
3657 (uri (cran-uri "matrixStats" version))
3660 "0jab3xk56vqqzgz8jbsvxvsvr83sj0gb3cic0906wjyjijwv8rw3"))))
3661 (properties `((upstream-name . "matrixStats")))
3662 (build-system r-build-system)
3664 `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
3665 (home-page "https://github.com/HenrikBengtsson/matrixStats")
3666 (synopsis "Methods applying to vectors and matrix rows and columns")
3668 "This package provides methods operating on rows and columns of matrices,
3669 e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
3670 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
3671 @code{weightedMedians()}. All methods have been optimized for speed and
3673 (license license:artistic2.0)))
3675 (define-public r-viridis
3681 (uri (cran-uri "viridis" version))
3684 "060rf1jn29dq53y3nhb0hykvcap6rqsk04rq544ypiiqb18ngwnx"))))
3685 (build-system r-build-system)
3687 `(("r-ggplot2" ,r-ggplot2)
3688 ("r-gridextra" ,r-gridextra)
3689 ("r-viridislite" ,r-viridislite)))
3691 `(("r-knitr" ,r-knitr))) ; for vignettes
3692 (home-page "https://github.com/sjmgarnier/viridis")
3693 (synopsis "Matplotlib default color map")
3695 "This package is a port of the new @url{matplotlib,
3696 http://matplotlib.org/} color maps (@code{viridis}--the default--,
3697 @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
3698 designed in such a way that they will analytically be perfectly
3699 perceptually-uniform, both in regular form and also when converted to
3700 black-and-white. They are also designed to be perceived by readers with the
3701 most common form of color blindness.")
3702 (license license:x11)))
3704 (define-public r-viridislite
3706 (name "r-viridislite")
3711 (uri (cran-uri "viridisLite" version))
3714 "1by2l05f0yabwvv64lhnv7bbhx0w683s3wr9j2xda920ghpa23kq"))))
3715 (properties `((upstream-name . "viridisLite")))
3716 (build-system r-build-system)
3717 (home-page "https://github.com/sjmgarnier/viridisLite")
3718 (synopsis "Default color maps from matplotlib")
3720 "This package is a port of the new @code{matplotlib} color maps
3721 (@code{viridis}, @code{magma}, @code{plasma} and @code{inferno}) to R.
3722 matplotlib is a popular plotting library for Python. These color maps are
3723 designed in such a way that they will analytically be perfectly
3724 perceptually-uniform, both in regular form and also when converted to
3725 black-and-white. They are also designed to be perceived by readers with the
3726 most common form of color blindness. This is the @code{lite} version of the
3727 more complete @code{viridis} package.")
3728 (license license:expat)))
3730 (define-public r-tidyselect
3732 (name "r-tidyselect")
3737 (uri (cran-uri "tidyselect" version))
3740 "14rqx4dq574hilmdwrr34wyjg8rlw4rvndpsqd9plgxm3wwfsdg6"))))
3741 (build-system r-build-system)
3743 `(("r-ellipsis" ,r-ellipsis)
3745 ("r-purrr" ,r-purrr)
3746 ("r-rlang" ,r-rlang)
3747 ("r-vctrs" ,r-vctrs)))
3749 `(("r-knitr" ,r-knitr)))
3750 (home-page "https://cran.r-project.org/web/packages/tidyselect")
3751 (synopsis "Select from a set of strings")
3753 "This package provides a backend for the selecting functions of the
3754 tidyverse. It makes it easy to implement select-like functions in your own
3755 packages in a way that is consistent with other tidyverse interfaces for
3757 (license license:gpl3)))
3759 (define-public r-tidyr
3766 (uri (cran-uri "tidyr" version))
3769 "0cpbrvr759z8p7r9lpkjhj2dcdymsbnaib0rma9b4jb7i3qzmh2a"))))
3770 (build-system r-build-system)
3772 `(("r-cpp11" ,r-cpp11)
3773 ("r-dplyr" ,r-dplyr)
3774 ("r-ellipsis" ,r-ellipsis)
3775 ("r-magrittr" ,r-magrittr)
3777 ("r-lifecycle" ,r-lifecycle)
3778 ("r-purrr" ,r-purrr)
3779 ("r-rlang" ,r-rlang)
3780 ("r-tidyselect" ,r-tidyselect)
3781 ("r-tibble" ,r-tibble)
3782 ("r-vctrs" ,r-vctrs)))
3784 `(("r-knitr" ,r-knitr)))
3785 (home-page "https://github.com/hadley/tidyr")
3786 (synopsis "Tidy data with `spread()` and `gather()` functions")
3788 "tidyr is a reframing of the reshape2 package designed to accompany the
3789 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
3790 a solid pipeline for data analysis. It is designed specifically for tidying
3791 data, not the general reshaping that reshape2 does, or the general aggregation
3792 that reshape did. In particular, built-in methods only work for data frames,
3793 and tidyr provides no margins or aggregation.")
3794 (license license:expat)))
3796 (define-public r-hexbin
3803 (uri (cran-uri "hexbin" version))
3806 "0bbhs5pwxh474w62sq6gqvih7habancxng9wd4f2rgn6lv9zhhb2"))))
3807 (build-system r-build-system)
3809 `(("r-lattice" ,r-lattice)))
3811 `(("gfortran" ,gfortran)
3812 ("r-knitr" ,r-knitr))) ; for vignettes
3813 (home-page "https://github.com/edzer/hexbin")
3814 (synopsis "Hexagonal binning routines")
3816 "This package provides binning and plotting functions for hexagonal bins.
3817 It uses and relies on grid graphics and formal (S4) classes and methods.")
3818 (license license:gpl2+)))
3820 (define-public r-purrr
3827 (uri (cran-uri "purrr" version))
3830 "1cj091rsjdj2xz16qhynyw72gh5cyhznifcfbrbygndfr4xwksr3"))))
3831 (build-system r-build-system)
3833 `(("r-magrittr" ,r-magrittr)
3834 ("r-rlang" ,r-rlang)))
3836 `(("r-knitr" ,r-knitr)))
3837 (home-page "https://github.com/hadley/purrr")
3838 (synopsis "Functional programming tools")
3840 "This package completes R's functional programming tools with missing
3841 features present in other programming languages.")
3842 (license license:gpl3+)))
3844 (define-public r-plotly
3850 (uri (cran-uri "plotly" version))
3853 "0801i2q7sw62x734d58h9p2fwpi1hirqj73gsg18pqkdv4b1lkfl"))))
3854 (build-system r-build-system)
3856 `(("r-base64enc" ,r-base64enc)
3857 ("r-crosstalk" ,r-crosstalk)
3858 ("r-digest" ,r-digest)
3859 ("r-data-table" ,r-data-table)
3860 ("r-dplyr" ,r-dplyr)
3861 ("r-ggplot2" ,r-ggplot2)
3862 ("r-htmltools" ,r-htmltools)
3863 ("r-htmlwidgets" ,r-htmlwidgets)
3865 ("r-jsonlite" ,r-jsonlite)
3866 ("r-lazyeval" ,r-lazyeval)
3867 ("r-magrittr" ,r-magrittr)
3868 ("r-promises" ,r-promises)
3869 ("r-purrr" ,r-purrr)
3870 ("r-rcolorbrewer" ,r-rcolorbrewer)
3871 ("r-rlang" ,r-rlang)
3872 ("r-scales" ,r-scales)
3873 ("r-tibble" ,r-tibble)
3874 ("r-tidyr" ,r-tidyr)
3875 ("r-vctrs" ,r-vctrs)
3876 ("r-viridislite" ,r-viridislite)))
3877 (home-page "https://plot.ly/r")
3878 (synopsis "Create interactive web graphics")
3880 "This package enables the translation of ggplot2 graphs to an interactive
3881 web-based version and/or the creation of custom web-based visualizations
3882 directly from R. Once uploaded to a plotly account, plotly graphs (and the
3883 data behind them) can be viewed and modified in a web browser.")
3884 (license license:x11)))
3886 (define-public r-biased-urn
3888 (name "r-biased-urn")
3893 (uri (cran-uri "BiasedUrn" version))
3896 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
3897 (properties `((upstream-name . "BiasedUrn")))
3898 (build-system r-build-system)
3899 (home-page "https://www.agner.org/random/")
3900 (synopsis "Biased urn model distributions")
3902 "This package provides statistical models of biased sampling in the form
3903 of univariate and multivariate noncentral hypergeometric distributions,
3904 including Wallenius' noncentral hypergeometric distribution and Fisher's
3905 noncentral hypergeometric distribution (also called extended hypergeometric
3907 (license license:gpl3+)))
3909 (define-public r-rematch
3916 (uri (cran-uri "rematch" version))
3919 "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4"))))
3920 (build-system r-build-system)
3921 (home-page "https://github.com/MangoTheCat/rematch")
3922 (synopsis "Match regular expressions with a nicer API")
3924 "This package provides a small wrapper on @code{regexpr} to extract the
3925 matches and captured groups from the match of a regular expression to a
3927 (license license:expat)))
3929 (define-public r-cellranger
3931 (name "r-cellranger")
3936 (uri (cran-uri "cellranger" version))
3939 "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x"))))
3940 (build-system r-build-system)
3942 `(("r-rematch" ,r-rematch)
3943 ("r-tibble" ,r-tibble)))
3944 (home-page "https://github.com/rsheets/cellranger")
3945 (synopsis "Translate spreadsheet cell ranges to rows and columns")
3947 "This package provides helper functions to work with spreadsheets and the
3948 @code{A1:D10} style of cell range specification.")
3949 (license license:expat)))
3951 (define-public r-googlesheets
3953 (name "r-googlesheets")
3958 (uri (cran-uri "googlesheets" version))
3961 "11q07nxys72wkxx9mawmjyf20gvwvrb7h3gpa73h6lgh2vgrwnv8"))))
3962 (build-system r-build-system)
3964 `(("r-cellranger" ,r-cellranger)
3965 ("r-dplyr" ,r-dplyr)
3967 ("r-jsonlite" ,r-jsonlite)
3968 ("r-purrr" ,r-purrr)
3969 ("r-readr" ,r-readr)
3970 ("r-stringr" ,r-stringr)
3971 ("r-tibble" ,r-tibble)
3972 ("r-tidyr" ,r-tidyr)
3973 ("r-xml2" ,r-xml2)))
3974 (home-page "https://github.com/jennybc/googlesheets")
3975 (synopsis "Manage Google spreadsheets from R")
3976 (description "This package provides tools to interact with Google Sheets
3978 (license license:expat)))
3980 (define-public r-spams
3983 (version "2.6-2017-03-22")
3987 ;; Use the ‘Latest version’ link for a stable URI across releases.
3988 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
3989 "latestfile/4531/spams-R-v" version ".tar.gz"))
3992 "13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx"))))
3993 (build-system r-build-system)
3996 (modify-phases %standard-phases
3997 (add-after 'unpack 'chdir
3998 (lambda _ (chdir "spams") #t))
3999 ;; Don't tune for the building machine.
4000 (add-after 'chdir 'no-mtune
4002 (substitute* "src/Makevars"
4003 (("-mtune=native") ""))
4006 `(("r-lattice" ,r-lattice)
4007 ("r-matrix" ,r-matrix)))
4008 (home-page "https://spams-devel.gforge.inria.fr")
4009 (synopsis "Toolbox for solving sparse estimation problems")
4010 (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
4011 for solving various sparse estimation problems. It includes tools for the
4015 @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
4016 component analysis} (PCA), ...)
4017 @item Solving sparse decomposition problems with LARS, coordinate descent,
4018 OMP, SOMP, proximal methods
4019 @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
4020 group lasso, tree-structured regularization, structured sparsity with
4021 overlapping groups,...).
4023 (license license:gpl3+)))
4025 (define-public r-base64
4032 (uri (cran-uri "base64" version))
4035 "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf"))))
4036 (build-system r-build-system)
4038 `(("r-openssl" ,r-openssl)))
4039 (home-page "https://cran.r-project.org/web/packages/base64")
4040 (synopsis "Base64 encoder and decoder")
4042 "This package is a compatibility wrapper to replace the orphaned package
4043 by Romain Francois. New applications should use the openssl or base64enc
4045 (license license:expat)))
4047 (define-public r-hmisc
4054 (uri (cran-uri "Hmisc" version))
4056 (base32 "11qj73zj16p113jpwn2vv06l99kqlcxcmrldbpyi5s7pwing9jnx"))))
4057 (properties `((upstream-name . "Hmisc")))
4058 (build-system r-build-system)
4060 `(("gfortran" ,gfortran)))
4062 `(("r-base64enc" ,r-base64enc)
4063 ("r-cluster" ,r-cluster)
4064 ("r-data-table" ,r-data-table)
4065 ("r-foreign" ,r-foreign)
4066 ("r-formula" ,r-formula)
4067 ("r-ggplot2" ,r-ggplot2)
4068 ("r-gridextra" ,r-gridextra)
4069 ("r-gtable" ,r-gtable)
4070 ("r-lattice" ,r-lattice)
4071 ("r-latticeextra" ,r-latticeextra)
4072 ("r-htmltable" ,r-htmltable)
4073 ("r-htmltools" ,r-htmltools)
4075 ("r-rpart" ,r-rpart)
4076 ("r-survival" ,r-survival)
4077 ("r-viridis" ,r-viridis)))
4078 (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
4079 (synopsis "Miscellaneous data analysis and graphics functions")
4081 "This package contains many functions useful for data analysis,
4082 high-level graphics, utility operations, functions for computing sample size
4083 and power, importing and annotating datasets, imputing missing values,
4084 advanced table making, variable clustering, character string manipulation,
4085 conversion of R objects to LaTeX code, and recoding variables.")
4086 (license license:gpl2+)))
4088 (define-public r-runit
4095 (uri (cran-uri "RUnit" version))
4098 "1wc1gwb7yw7phf8b0gkig6c23klya3ax11c6i4s0f049k42r78r3"))))
4099 (properties `((upstream-name . "RUnit")))
4100 (build-system r-build-system)
4101 (home-page "https://cran.r-project.org/web/packages/RUnit")
4102 (synopsis "R unit test framework")
4104 "This package provides R functions implementing a standard unit testing
4105 framework, with additional code inspection and report generation tools.")
4106 (license license:gpl2+)))
4108 (define-public r-dynamictreecut
4110 (name "r-dynamictreecut")
4115 (uri (cran-uri "dynamicTreeCut" version))
4118 "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"))))
4119 (properties `((upstream-name . "dynamicTreeCut")))
4120 (build-system r-build-system)
4122 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
4123 (synopsis "Detect clusters in hierarchical clustering dendrograms")
4125 "This package contains methods for the detection of clusters in
4126 hierarchical clustering dendrograms.")
4127 (license license:gpl2+)))
4129 (define-public r-fastcluster
4131 (name "r-fastcluster")
4136 (uri (cran-uri "fastcluster" version))
4139 "01a2xnhhvv1swd4g8p4lzyn7ww7kg49jlnzc7kfz60jqjzpisrpk"))))
4140 (build-system r-build-system)
4141 (home-page "http://danifold.net/fastcluster.html")
4142 (synopsis "Fast hierarchical clustering routines")
4144 "This package implements fast hierarchical, agglomerative clustering
4145 routines. Part of the functionality is designed as drop-in replacement for
4146 existing routines: @code{linkage()} in the SciPy package
4147 @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package,
4148 and the @code{flashClust} package. It provides the same functionality with
4149 the benefit of a much faster implementation. Moreover, there are
4150 memory-saving routines for clustering of vector data, which go beyond what the
4151 existing packages provide.")
4152 (license license:bsd-2)))
4154 (define-public r-sfsmisc
4161 (uri (cran-uri "sfsmisc" version))
4164 "1skxahq5jgqdsllpsavzrcpz8l0yj3mfzcf70as8d33jxbiaa4s4"))))
4165 (build-system r-build-system)
4166 (home-page "https://cran.r-project.org/web/packages/sfsmisc")
4167 (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
4169 "This package provides useful utilities from Seminar fuer Statistik ETH
4170 Zurich, including many that are related to graphics.")
4171 (license license:gpl2+)))
4173 (define-public r-gtools
4180 (uri (cran-uri "gtools" version))
4183 "1pnwy412wvhhvnnx8qg6s9hrgcnsfhnfcpf2560ipipk845acfsh"))))
4184 (build-system r-build-system)
4187 (modify-phases %standard-phases
4188 (add-after 'unpack 'make-deterministic
4190 (substitute* "R/checkReverseDependencies.R"
4191 (("tempdir\\(\\)") "\"/tmp\""))
4193 (home-page "https://cran.r-project.org/web/packages/gtools")
4194 (synopsis "Various R programming tools")
4196 "This package contains a collection of various functions to assist in R
4197 programming, such as tools to assist in developing, updating, and maintaining
4198 R and R packages, calculating the logit and inverse logit transformations,
4199 tests for whether a value is missing, empty or contains only @code{NA} and
4200 @code{NULL} values, and many more.")
4201 (license license:gpl2)))
4203 (define-public r-gdata
4210 (uri (cran-uri "gdata" version))
4213 "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b"))))
4214 (build-system r-build-system)
4218 `(("r-gtools" ,r-gtools)))
4219 (home-page "https://cran.r-project.org/web/packages/gdata")
4220 (synopsis "Various R programming tools for data manipulation")
4222 "This package provides various R programming tools for data manipulation,
4226 @item medical unit conversions
4227 @item combining objects
4228 @item character vector operations
4229 @item factor manipulation
4230 @item obtaining information about R objects
4231 @item manipulating MS-Excel formatted files
4232 @item generating fixed-width format files
4233 @item extricating components of date and time objects
4234 @item operations on columns of data frames
4235 @item matrix operations
4236 @item operations on vectors and data frames
4237 @item value of last evaluated expression
4238 @item wrapper for @code{sample} that ensures consistent behavior for
4239 both scalar and vector arguments
4241 (license license:gpl2+)))
4243 (define-public r-gplots
4250 (uri (cran-uri "gplots" version))
4253 "0f8khaymz383w2ksnk80d4kpnvgmdk37pbycpsnl2vabaz11kbpr"))))
4254 (build-system r-build-system)
4256 `(("r-catools" ,r-catools)
4257 ("r-gtools" ,r-gtools)
4258 ("r-kernsmooth" ,r-kernsmooth)))
4260 `(("r-knitr" ,r-knitr)))
4261 (home-page "https://cran.r-project.org/web/packages/gplots")
4262 (synopsis "Various R programming tools for plotting data")
4264 "This package provides various R programming tools for plotting data,
4268 @item calculating and plotting locally smoothed summary function
4269 @item enhanced versions of standard plots
4270 @item manipulating colors
4271 @item calculating and plotting two-dimensional data summaries
4272 @item enhanced regression diagnostic plots
4273 @item formula-enabled interface to @code{stats::lowess} function
4274 @item displaying textual data in plots
4276 @item plotting \"Venn\" diagrams
4277 @item displaying Open-Office style plots
4278 @item plotting multiple data on same region, with separate axes
4279 @item plotting means and confidence intervals
4280 @item spacing points in an x-y plot so they don't overlap
4282 (license license:gpl2+)))
4284 (define-public r-rocr
4291 (uri (cran-uri "ROCR" version))
4294 "0amvvrkiflmr3qygrsgrsja4gaf2v6r6h6i2bgpsm8r069vmlf2p"))))
4295 (properties `((upstream-name . "ROCR")))
4296 (build-system r-build-system)
4298 `(("r-gplots" ,r-gplots)))
4300 `(("r-knitr" ,r-knitr)))
4301 (home-page "https://rocr.bioinf.mpi-sb.mpg.de/")
4302 (synopsis "Visualizing the performance of scoring classifiers")
4304 "ROCR is a flexible tool for creating cutoff-parameterized 2D performance
4305 curves by freely combining two from over 25 performance measures (new
4306 performance measures can be added using a standard interface). Curves from
4307 different cross-validation or bootstrapping runs can be averaged by different
4308 methods, and standard deviations, standard errors or box plots can be used to
4309 visualize the variability across the runs. The parameterization can be
4310 visualized by printing cutoff values at the corresponding curve positions, or
4311 by coloring the curve according to cutoff. All components of a performance
4312 plot can be quickly adjusted using a flexible parameter dispatching
4314 (license license:gpl2+)))
4316 (define-public r-ztable
4322 (uri (cran-uri "ztable" version))
4325 "0wxcdb7yp2r6w5iznz1k49npp5sn4jiybfcj30s3198hkcnv0r8y"))))
4326 (build-system r-build-system)
4328 `(("r-flextable" ,r-flextable)
4329 ("r-magrittr" ,r-magrittr)
4330 ("r-officer" ,r-officer)
4331 ("r-rcolorbrewer" ,r-rcolorbrewer)
4332 ("r-rstudioapi" ,r-rstudioapi)
4333 ("r-scales" ,r-scales)
4334 ("r-stringr" ,r-stringr)))
4336 `(("r-knitr" ,r-knitr)))
4337 (home-page "https://cran.r-project.org/web/packages/ztable")
4338 (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
4340 "This package provides functions to make zebra-striped tables (tables
4341 with alternating row colors) in LaTeX and HTML formats easily from
4342 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
4343 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
4344 @code{cbind.mytable} objects.")
4345 (license license:gpl2+)))
4347 (define-public r-vipor
4353 (uri (cran-uri "vipor" version))
4356 "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx"))))
4357 (build-system r-build-system)
4358 (home-page "https://cran.r-project.org/web/packages/vipor")
4359 (synopsis "Plot categorical data using noise and density estimates")
4361 "This package provides tools to generate a violin point plot, a
4362 combination of a violin/histogram plot and a scatter plot by offsetting points
4363 within a category based on their density using quasirandom noise.")
4364 (license license:gpl2+)))
4366 (define-public r-beeswarm
4372 (uri (cran-uri "beeswarm" version))
4375 "1jsggypyww77hkcic03kdb3fp8h938qs142xi0lapzh62bkn2pjj"))))
4376 (build-system r-build-system)
4377 (home-page "https://www.cbs.dtu.dk/~eklund/beeswarm/")
4378 (synopsis "Implementation of bee swarm plots")
4380 "This package provides an implementation of bee swarm plots. The bee
4381 swarm plot is a one-dimensional scatter plot like stripchart, but with
4382 closely-packed, non-overlapping points.")
4383 (license license:artistic2.0)))
4385 (define-public r-sourcetools
4387 (name "r-sourcetools")
4392 (uri (cran-uri "sourcetools" version))
4395 "1jnjir0q2dj724f1mjm6p5h77yzyx6xcqy9r2g7gmcxkxw349627"))))
4396 (build-system r-build-system)
4397 (home-page "https://cran.r-project.org/web/packages/sourcetools")
4398 (synopsis "Tools for reading, tokenizing and parsing R code")
4400 "The sourcetools package provides both an R and C++ interface for the
4401 tokenization of R code, and helpers for interacting with the tokenized
4402 representation of R code.")
4403 (license license:expat)))
4405 (define-public r-ggbeeswarm
4407 (name "r-ggbeeswarm")
4411 (uri (cran-uri "ggbeeswarm" version))
4414 "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v"))))
4415 (build-system r-build-system)
4417 `(("r-beeswarm" ,r-beeswarm)
4418 ("r-ggplot2" ,r-ggplot2)
4419 ("r-vipor" ,r-vipor)))
4420 (home-page "https://github.com/eclarke/ggbeeswarm")
4421 (synopsis "Categorical scatter (violin point) plots")
4423 "This package provides two methods of plotting categorical scatter plots
4424 such that the arrangement of points within a category reflects the density of
4425 data at that region, and avoids over-plotting.")
4426 (license license:gpl2+)))
4428 (define-public r-ggthemes
4434 (uri (cran-uri "ggthemes" version))
4437 "0rw5f6axyz1pqn6qx9jwm38hjzn8bqs1nfjkvm96z3xnyn61cdbv"))))
4438 (build-system r-build-system)
4440 `(("r-ggplot2" ,r-ggplot2)
4441 ("r-purrr" ,r-purrr)
4442 ("r-scales" ,r-scales)
4443 ("r-stringr" ,r-stringr)
4444 ("r-tibble" ,r-tibble)))
4445 (home-page "https://cran.rstudio.com/web/packages/ggthemes")
4446 (synopsis "Extra themes, scales and geoms for @code{ggplot2}")
4447 (description "This package provides extra themes and scales for
4448 @code{ggplot2} that replicate the look of plots by Edward Tufte and
4449 Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The
4450 Wall Street Journal, among others. This package also provides
4451 @code{geoms} for Tufte's box plot and range frame.")
4452 (license license:gpl2)))
4454 (define-public r-statmod
4460 (uri (cran-uri "statmod" version))
4463 "1zpqnfslq5gi6hvqjqnsn5kf2m986s1yb6kvyjd881n3h67l4pny"))))
4464 (build-system r-build-system)
4465 (home-page "https://cran.r-project.org/web/packages/statmod")
4467 `(("gfortran" ,gfortran)))
4468 (synopsis "Statistical modeling")
4470 "This package provides a collection of algorithms and functions to aid
4471 statistical modeling. It includes growth curve comparisons, limiting dilution
4472 analysis (aka ELDA), mixed linear models, heteroscedastic regression,
4473 inverse-Gaussian probability calculations, Gauss quadrature and a secure
4474 convergence algorithm for nonlinear models. It also includes advanced
4475 generalized linear model functions that implement secure convergence,
4476 dispersion modeling and Tweedie power-law families.")
4477 ;; Statmod is distributed under either license
4478 (license (list license:gpl2 license:gpl3))))
4480 (define-public r-rann
4486 (uri (cran-uri "RANN" version))
4489 "10kid40w9w7vkz2hpcfkdpxr4afxzms5dzvfwr0sl5xynzgw76dj"))))
4491 `((upstream-name . "RANN")))
4492 (build-system r-build-system)
4493 (home-page "https://github.com/jefferis/RANN")
4494 (synopsis "Fast nearest neighbour search")
4496 "This package finds the k nearest neighbours for every point in a given
4497 dataset in O(N log N) time using Arya and Mount's ANN library. Provides
4498 approximate, exact searches, fixed radius searches, bd and kb trees.")
4499 (license license:gpl3+)))
4501 (define-public r-fivethirtyeight
4503 (name "r-fivethirtyeight")
4508 (uri (string-append "https://mran.microsoft.com/src/contrib/"
4509 "fivethirtyeight_" version ".tar.gz"))
4512 "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl"))))
4513 (build-system r-build-system)
4515 `(("r-knitr" ,r-knitr)
4516 ("r-rmarkdown" ,r-rmarkdown)
4517 ("r-dplyr" ,r-dplyr)
4518 ("r-readr" ,r-readr)
4519 ("r-ggplot2" ,r-ggplot2)
4520 ("r-magrittr" ,r-magrittr)
4521 ("r-stringr" ,r-stringr)))
4522 (home-page "https://mran.microsoft.com/package/fivethirtyeight/")
4523 (synopsis "Data and code behind the stories at FiveThirtyEight")
4524 (description "This R package provides access to the code and data sets
4525 published by the statistics blog FiveThirtyEight.")
4526 (license license:expat)))
4528 (define-public r-compquadform
4530 (name "r-compquadform")
4535 (uri (cran-uri "CompQuadForm" version))
4538 "1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4"))))
4539 (properties `((upstream-name . "CompQuadForm")))
4540 (build-system r-build-system)
4541 (home-page "https://cran.r-project.org/web/packages/CompQuadForm")
4542 (synopsis "Distribution function of quadratic forms in normal variables")
4544 "This package provides functions to compute the distribution function of
4545 quadratic forms in normal variables using Imhof's method, Davies's algorithm,
4546 Farebrother's algorithm or Liu et al.'s algorithm.")
4547 (license license:gpl2+)))
4549 (define-public r-cowplot
4556 (uri (cran-uri "cowplot" version))
4559 "0j7d5vhzdxn1blrsfafx5z8lhq122rp8230hp9czrpsnnhjydp67"))))
4560 (build-system r-build-system)
4562 `(("r-ggplot2" ,r-ggplot2)
4563 ("r-gtable" ,r-gtable)
4564 ("r-rlang" ,r-rlang)
4565 ("r-scales" ,r-scales)))
4567 `(("r-knitr" ,r-knitr)))
4568 (home-page "https://github.com/wilkelab/cowplot")
4569 (synopsis "Streamlined plot theme and plot annotations for ggplot2")
4571 "This package provides some helpful extensions and modifications to the
4572 ggplot2 package to combine multiple ggplot2 plots into one and label them with
4573 letters, as is often required for scientific publications.")
4574 (license license:gpl2)))
4576 (define-public r-mixtools
4583 (uri (cran-uri "mixtools" version))
4586 "08whic8hmmzi55b7azwj11l2x5r9s5qbyrv7s9jr08156vqkw0zg"))))
4587 (build-system r-build-system)
4589 `(("r-mass" ,r-mass)
4590 ("r-kernlab" ,r-kernlab)
4591 ("r-segmented" ,r-segmented)
4592 ("r-survival" ,r-survival)))
4593 (home-page "https://cran.r-project.org/web/packages/mixtools")
4594 (synopsis "Tools for analyzing finite mixture models")
4596 "This package provides a collection of R functions for analyzing finite
4598 (license license:gpl2+)))
4600 (define-public r-lars
4607 (uri (cran-uri "lars" version))
4610 "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
4611 (build-system r-build-system)
4613 `(("gfortran" ,gfortran)))
4614 (home-page "https://web.stanford.edu/~hastie/Papers/LARS/")
4615 (synopsis "Least angle regression software")
4617 "Least Angle Regression (\"LAR\") is a model selection algorithm; a
4618 useful and less greedy version of traditional forward selection methods. A
4619 simple modification of the LAR algorithm implements Tibshirani's Lasso; the
4620 Lasso modification of LARS calculates the entire Lasso path of coefficients
4621 for a given problem at the cost of a single least squares fit. Another LARS
4622 modification efficiently implements epsilon Forward Stagewise linear
4624 (license license:gpl2)))
4626 (define-public r-fastica
4633 (uri (cran-uri "fastICA" version))
4636 "1zpijqcipm0aa3rxj0mys06lskqy4dbppjpxr1aby0j16y9ka8ij"))))
4637 (properties `((upstream-name . "fastICA")))
4638 (build-system r-build-system)
4639 (home-page "https://cran.r-project.org/web/packages/fastICA")
4640 (synopsis "FastICA algorithms to perform ICA and projection pursuit")
4642 "This package provides an implementation of the FastICA algorithm to
4643 perform @dfn{independent component analysis} (ICA) and projection pursuit.")
4645 (license license:gpl3+)))
4647 (define-public r-randomforest
4649 (name "r-randomforest")
4654 (uri (cran-uri "randomForest" version))
4657 "0kbmm0l42fc2d1rdq0l7k09d34kd87q4lx651ffsic4y84h8kf7l"))))
4658 (properties `((upstream-name . "randomForest")))
4659 (build-system r-build-system)
4660 (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
4662 `(("gfortran" ,gfortran)))
4663 (synopsis "Breiman and Cutler's random forests for classification and regression")
4665 "This package provides the Breiman and Cutler's random forests algorithm, based on a
4666 forest of trees using random inputs, for classification and regression.")
4667 (license license:gpl2+)))
4669 (define-public r-diptest
4676 (uri (cran-uri "diptest" version))
4679 "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
4680 (build-system r-build-system)
4681 (home-page "https://cran.r-project.org/web/packages/diptest")
4682 (synopsis "Hartigan's dip test statistic for unimodality")
4684 "This package computes Hartigan's dip test statistic for unimodality,
4685 multimodality and provides a test with simulation based p-values, where the
4686 original public code has been corrected.")
4687 (license license:gpl2+)))
4689 (define-public r-modeltools
4691 (name "r-modeltools")
4696 (uri (cran-uri "modeltools" version))
4699 "1vqh69256h344sbj5affm0kmc77dakrxp6442xfdnfd0y5d8sgkb"))))
4700 (build-system r-build-system)
4701 (home-page "https://cran.r-project.org/web/packages/modeltools")
4702 (synopsis "Tools and classes for statistical models")
4704 "This package provides a collection of tools to deal with statistical
4705 models. The functionality is experimental and the user interface is likely
4706 to change in the future.")
4707 (license license:gpl2)))
4709 (define-public r-flexmix
4716 (uri (cran-uri "flexmix" version))
4719 "0jangf89174p0idh9afbicfiln2sz8jxc3bjc6n0j9036dw9n09n"))))
4720 (build-system r-build-system)
4722 `(("r-lattice" ,r-lattice)
4723 ("r-modeltools" ,r-modeltools)
4724 ("r-nnet" ,r-nnet)))
4725 (home-page "https://cran.r-project.org/web/packages/flexmix")
4726 (synopsis "Flexible mixture modeling")
4728 "This package implements a general framework for finite mixtures of
4729 regression models using the EM algorithm. FlexMix provides the E-step and
4730 all data handling, while the M-step can be supplied by the user to easily
4731 define new models. Existing drivers implement mixtures of standard linear
4732 models, generalized linear models and model-based clustering.")
4733 (license license:gpl2+)))
4735 (define-public r-mclust
4742 (uri (cran-uri "mclust" version))
4745 "08scl72llpinfijiyx14yqvmx8lma9jvh8h92v9ynnzfr9kadxa5"))))
4746 (build-system r-build-system)
4748 `(("gfortran" ,gfortran)
4749 ("r-knitr" ,r-knitr)))
4750 (home-page "https://www.stat.washington.edu/mclust/")
4751 (synopsis "Gaussian mixture modelling for model-based clustering etc.")
4753 "This package provides Gaussian finite mixture models fitted via EM
4754 algorithm for model-based clustering, classification, and density estimation,
4755 including Bayesian regularization, dimension reduction for visualisation,
4756 and resampling-based inference.")
4757 (license license:gpl2+)))
4759 (define-public r-prabclus
4766 (uri (cran-uri "prabclus" version))
4769 "0hg4d7y1w18jpgvw10z8833bbbcnlkwiasx0wh6iwa2pnnybq8gl"))))
4770 (build-system r-build-system)
4772 `(("r-mass" ,r-mass)
4773 ("r-mclust" ,r-mclust)))
4774 (home-page "https://cran.r-project.org/web/packages/prabclus")
4775 (synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
4777 "This package provides distance-based parametric bootstrap tests for
4778 clustering with spatial neighborhood information. It implements some distance
4779 measures, clustering of presence-absence, abundance and multilocus genetical
4780 data for species delimitation, nearest neighbor based noise detection.")
4781 (license license:gpl2+)))
4783 (define-public r-deoptimr
4790 (uri (cran-uri "DEoptimR" version))
4793 "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
4794 (properties `((upstream-name . "DEoptimR")))
4795 (build-system r-build-system)
4796 (home-page "https://cran.r-project.org/web/packages/DEoptimR")
4797 (synopsis "Differential evolution optimization in pure R")
4799 "This package provides a differential evolution (DE) stochastic
4800 algorithms for global optimization of problems with and without constraints.
4801 The aim is to curate a collection of its state-of-the-art variants that (1) do
4802 not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
4803 can be efficiently implemented directly in the R language.")
4804 (license license:gpl2+)))
4806 (define-public r-robustbase
4808 (name "r-robustbase")
4813 (uri (cran-uri "robustbase" version))
4816 "0mh9d114p3jdrjf8yn4dx5ff41niz5wn411y0ckjcpnazp8d44c9"))))
4817 (build-system r-build-system)
4819 `(("gfortran" ,gfortran)))
4821 `(("r-deoptimr" ,r-deoptimr)))
4822 (home-page "http://robustbase.r-forge.r-project.org/")
4823 (synopsis "Basic robust statistics")
4825 "This package analyzes data with robust methods such as
4826 regression methodology including model selections and multivariate statistics.")
4827 (license license:gpl2+)))
4829 (define-public r-pcapp
4836 (uri (cran-uri "pcaPP" version))
4839 "1z2kdf9gfp965xbcd4rg6vf20d1bl443na0qjkpq7gmzpaq6cifa"))))
4840 (properties `((upstream-name . "pcaPP")))
4841 (build-system r-build-system)
4843 `(("r-mvtnorm" ,r-mvtnorm)))
4844 (home-page "https://cran.r-project.org/web/packages/pcaPP")
4845 (synopsis "Robust PCA by projection pursuit")
4847 "This package provides functions for robust @dfn{principal component
4848 analysis} (PCA) by projection pursuit.")
4849 (license license:gpl3+)))
4851 (define-public r-rrcov
4858 (uri (cran-uri "rrcov" version))
4861 "0ag6q16ajkqwj28dk9vp4xkvqw26fqqqdxnz38gpszilirahfzqz"))))
4862 (build-system r-build-system)
4864 `(("r-lattice" ,r-lattice)
4865 ("r-mvtnorm" ,r-mvtnorm)
4866 ("r-pcapp" ,r-pcapp)
4867 ("r-robustbase" ,r-robustbase)))
4869 `(("gfortran" ,gfortran)))
4870 (home-page "https://cran.r-project.org/web/packages/rrcov")
4871 (synopsis "Scalable robust estimators with high breakdown Point")
4873 "This package provides an implementation of robust location and scatter
4874 estimation and robust multivariate analysis with high breakdown point.")
4875 (license license:gpl2+)))
4877 (define-public r-fit-models
4879 (name "r-fit-models")
4884 (uri (cran-uri "fit.models" version))
4887 "1nk4x2q8cv79zcls61saf627ac0fci6jcrd6lmzk61asm2zhc27p"))))
4888 (properties `((upstream-name . "fit.models")))
4889 (build-system r-build-system)
4891 `(("r-lattice" ,r-lattice)))
4892 (home-page "https://cran.r-project.org/web/packages/fit.models")
4893 (synopsis "Compare fitted models")
4895 "The @code{fit.models} function and its associated methods (coefficients, print,
4896 summary, plot, etc.) were originally provided in the @code{robust} package to
4897 compare robustly and classically fitted model objects. The aim of the
4898 @code{fit.models} package is to separate this fitted model object comparison
4899 functionality from the robust package and to extend it to support fitting
4900 methods (e.g., classical, robust, Bayesian, regularized, etc.) more
4902 ;; Any version of the GPL
4903 (license (list license:gpl2+ license:gpl3+))))
4905 (define-public r-robust
4912 (uri (cran-uri "robust" version))
4915 "1ks5scp8bnicl9j1r8yrmz668fjs6ifdmi540zw6d2ck500bbw42"))))
4916 (build-system r-build-system)
4918 `(("r-fit-models" ,r-fit-models)
4919 ("r-lattice" ,r-lattice)
4921 ("r-robustbase" ,r-robustbase)
4922 ("r-rrcov" ,r-rrcov)))
4924 `(("gfortran" ,gfortran)))
4925 (home-page "https://cran.r-project.org/web/packages/robust")
4926 (synopsis "Port of the S+ \"Robust Library\"")
4928 "This package is a port of the S+ \"Robust Library\". It provides
4929 methods for robust statistics, notably for robust regression and robust
4930 multivariate analysis.")
4931 (license license:gpl2)))
4933 (define-public r-trimcluster
4935 (name "r-trimcluster")
4940 (uri (cran-uri "trimcluster" version))
4943 "12siv8yx8dcavsz8jk96lwscbj257ar8jpaxksl2zb06987g4fcj"))))
4944 (build-system r-build-system)
4945 (home-page "https://cran.r-project.org/web/packages/trimcluster")
4946 (synopsis "Cluster analysis with trimming")
4948 "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
4949 Matran (1997). This optimizes the k-means criterion under trimming a portion
4952 (license (list license:gpl2+ license:gpl3+))))
4954 (define-public r-fpc
4961 (uri (cran-uri "fpc" version))
4964 "0f7sfmpcycr9y7cy5gasyjm2ardxa62kglqms92mcr68jrp01c19"))))
4965 (build-system r-build-system)
4967 `(("r-class" ,r-class)
4968 ("r-cluster" ,r-cluster)
4969 ("r-diptest" ,r-diptest)
4970 ("r-flexmix" ,r-flexmix)
4971 ("r-kernlab" ,r-kernlab)
4973 ("r-mclust" ,r-mclust)
4974 ("r-prabclus" ,r-prabclus)
4975 ("r-robustbase" ,r-robustbase)))
4976 (home-page "https://cran.r-project.org/web/packages/fpc")
4977 (synopsis "Flexible procedures for clustering")
4979 "This package provides various methods for clustering and cluster validation.
4980 For example, it provides fixed point clustering, linear regression clustering,
4981 clustering by merging Gaussian mixture components, as well as symmetric and
4982 asymmetric discriminant projections for visualisation of the separation of
4984 (license license:gpl2+)))
4986 (define-public r-vgam
4993 (uri (cran-uri "VGAM" version))
4995 (base32 "1fx123h4x5awzshv0m4jqbbllrdjfpslb2i8gl9phm1y1wahn69h"))))
4996 (properties `((upstream-name . "VGAM")))
4997 (build-system r-build-system)
4999 `(("gfortran" ,gfortran)))
5000 (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
5001 (synopsis "Vector generalized linear and additive models")
5003 "This package is an implementation of about 6 major classes of statistical
5004 regression models. Currently only fixed-effects models are implemented, i.e.,
5005 no random-effects models. Many (150+) models and distributions are estimated
5006 by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
5007 VGLMs can be loosely thought of as multivariate generalised linear models.")
5008 (license license:gpl2+)))
5010 (define-public r-pbapply
5017 (uri (cran-uri "pbapply" version))
5020 "08gb6c8p1r9z8wrfidj2dfn6irm43k6f4448d1d6nxmy6msjirlg"))))
5021 (build-system r-build-system)
5022 (home-page "https://github.com/psolymos/pbapply")
5023 (synopsis "Adding progress bar to apply functions")
5025 "This lightweight package that adds progress bar to vectorized R
5026 functions apply. The implementation can easily be added to functions where
5027 showing the progress is useful e.g. bootstrap.")
5028 (license license:gpl2)))
5030 (define-public r-minqa
5037 (uri (cran-uri "minqa" version))
5040 "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
5041 (build-system r-build-system)
5043 `(("r-rcpp" ,r-rcpp)))
5045 `(("gfortran" ,gfortran)))
5046 (home-page "http://optimizer.r-forge.r-project.org")
5047 (synopsis "Derivative-free optimization algorithms by quadratic approximation")
5049 "This package provides a derivative-free optimization by quadratic approximation
5050 based on an interface to Fortran implementations by M. J. D. Powell.")
5051 (license license:gpl2)))
5053 (define-public r-rcppeigen
5055 (name "r-rcppeigen")
5056 (version "0.3.3.9.1")
5060 (uri (cran-uri "RcppEigen" version))
5063 "0qp9gypar280lm84pc8w0fxw4jgwqygwi3qnl5sl52kpkcj8c14a"))))
5064 (properties `((upstream-name . "RcppEigen")))
5065 (build-system r-build-system)
5067 `(("r-rcpp" ,r-rcpp)
5068 ("r-matrix" ,r-matrix)))
5069 (home-page "http://eigen.tuxfamily.org")
5070 (synopsis "Rcpp integration for the Eigen templated linear algebra library")
5072 "This package provides an integration of Eigen in R using a C++ template
5073 library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
5074 It supports dense and sparse matrices on integer, floating point and complex numbers,
5075 decompositions of such matrices, and solutions of linear systems.")
5076 (license license:gpl2+)))
5078 (define-public r-modelmetrics
5080 (name "r-modelmetrics")
5085 (uri (cran-uri "ModelMetrics" version))
5088 "0mrlsw4c5y1vdsqynxr2dcvmhh5h37pnd71jw5a5djpbda9g21jy"))))
5089 (properties `((upstream-name . "ModelMetrics")))
5090 (build-system r-build-system)
5092 `(("r-rcpp" ,r-rcpp)
5093 ("r-data-table" ,r-data-table)))
5094 (home-page "https://cran.r-project.org/web/packages/ModelMetrics")
5095 (synopsis "Rapid calculation of model metrics")
5097 "Written in C++ using @code{Rcpp}, this package provides a collection of
5098 metrics for evaluating models.")
5099 (license license:gpl2+)))
5101 (define-public r-matrixmodels
5103 (name "r-matrixmodels")
5108 (uri (cran-uri "MatrixModels" version))
5111 "1va6i6bpkq71rzl9i4xgyc5x7qcksa3nfzihlaggf6aj30dayzx8"))))
5112 (properties `((upstream-name . "MatrixModels")))
5113 (build-system r-build-system)
5115 `(("r-matrix" ,r-matrix)))
5116 (home-page "https://cran.r-project.org/web/packages/MatrixModels")
5117 (synopsis "Modelling with sparse and dense matrices")
5119 "This package models with sparse and dense matrix matrices,
5120 using modular prediction and response module classes.")
5121 (license license:gpl2+)))
5123 (define-public r-quantreg
5130 (uri (cran-uri "quantreg" version))
5132 (base32 "1y8sgl16yby1k7g23y6bdnfllwnxj3iik3fqp96iwm5jd8blb7q4"))))
5133 (build-system r-build-system)
5135 `(("gfortran" ,gfortran)))
5137 `(("r-conquer" ,r-conquer)
5138 ("r-matrix" ,r-matrix)
5139 ("r-matrixmodels" ,r-matrixmodels)
5140 ("r-sparsem" ,r-sparsem)))
5141 (home-page "https://www.r-project.org")
5142 (synopsis "Quantile regression")
5144 "This package provides an estimation and inference methods for models
5145 of conditional quantiles: linear and nonlinear parametric and non-parametric
5146 models for conditional quantiles of a univariate response and several methods
5147 for handling censored survival data. Portfolio selection methods based on
5148 expected shortfall risk are also included.")
5149 (license license:gpl2+)))
5151 (define-public r-nloptr
5158 (uri (cran-uri "nloptr" version))
5161 "0whkilb85k4wixvr3k7rygfw1rcs1fs9h8c18kz4p3y1k9hsj3p8"))))
5162 (build-system r-build-system)
5164 `(("r-knitr" ,r-knitr) ; for building vignettes
5165 ("pkg-config" ,pkg-config)
5166 ("gfortran" ,gfortran)))
5168 `(("nlopt" ,nlopt)))
5169 (home-page "https://cran.r-project.org/web/packages/nloptr")
5170 (synopsis "R interface to NLopt")
5172 "This package is interface to NLopt, a library for nonlinear
5173 optimization. NLopt is a library for nonlinear optimization, providing a
5174 common interface for a number of different free optimization routines
5175 available online as well as original implementations of various other
5177 (license license:lgpl3)))
5179 (define-public r-lme4
5186 (uri (cran-uri "lme4" version))
5189 "0ls2krph4pfjn45vf9fn3ln3x98s85wxrkvm5pnxyx55n1pnsjrn"))))
5190 (build-system r-build-system)
5192 `(("r-boot" ,r-boot)
5193 ("r-lattice" ,r-lattice)
5195 ("r-matrix" ,r-matrix)
5196 ("r-minqa" ,r-minqa)
5197 ("r-nloptr" ,r-nloptr)
5200 ("r-rcppeigen" ,r-rcppeigen)
5201 ("r-statmod" ,r-statmod)))
5203 `(("r-knitr" ,r-knitr)))
5204 (home-page "https://cran.r-project.org/web/packages/lme4")
5205 (synopsis "Linear mixed-effects models using eigen and S4")
5207 "This package provides fit linear and generalized linear mixed-effects
5208 models. The models and their components are represented using S4 classes and
5209 methods. The core computational algorithms are implemented using the Eigen
5210 C++ library for numerical linear algebra and RcppEigen glue.")
5211 (license license:gpl2+)))
5213 (define-public r-pbkrtest
5220 (uri (cran-uri "pbkrtest" version))
5223 "1if7msv9i7jhg1as1f7m81a95dnwhwj3yfs24bqr0f6r0ch4b8xj"))))
5224 (build-system r-build-system)
5226 `(("r-broom" ,r-broom)
5227 ("r-dplyr" ,r-dplyr)
5229 ("r-magrittr" ,r-magrittr)
5231 ("r-matrix" ,r-matrix)
5232 ("r-numderiv" ,r-numderiv)))
5234 `(("r-knitr" ,r-knitr)))
5235 (home-page "https://people.math.aau.dk/~sorenh/software/pbkrtest/")
5236 (synopsis "Methods for linear mixed model comparison")
5238 "This package implements a parametric bootstrap test and a Kenward Roger
5239 modification of F-tests for linear mixed effects models and a parametric
5240 bootstrap test for generalized linear mixed models.")
5241 (license license:gpl2+)))
5243 (define-public r-cardata
5250 (uri (cran-uri "carData" version))
5252 (base32 "09270j39n4jpswxqps20b12zaj8dz4rrqpk2l2j5bnf1xzizb9nd"))))
5253 (properties `((upstream-name . "carData")))
5254 (build-system r-build-system)
5255 (home-page "https://r-forge.r-project.org/projects/car/")
5256 (synopsis "Data Sets for the book Companion to Applied Regression")
5258 "This package provides datasets to accompany J. Fox and S. Weisberg, An R
5259 Companion to Applied Regression, Third Edition, Sage.")
5260 (license license:gpl2+)))
5262 (define-public r-car
5269 (uri (cran-uri "car" version))
5271 (base32 "1w95b7xm0bna3qm637pwyv4s7294ffz9dl153naprd79zv91dqqw"))))
5272 (build-system r-build-system)
5274 `(("r-abind" ,r-abind)
5275 ("r-cardata" ,r-cardata)
5277 ("r-maptools" ,r-maptools)
5282 ("r-pbkrtest" ,r-pbkrtest)
5283 ("r-quantreg" ,r-quantreg)
5286 `(("r-knitr" ,r-knitr)))
5287 (home-page "https://r-forge.r-project.org/projects/car/")
5288 (synopsis "Companion to applied regression")
5290 "This package provides functions and datasets from book Companion
5291 to Applied regression, Second Edition, Sage, 2011.")
5292 (license license:gpl2+)))
5294 (define-public r-rcppprogress
5296 (name "r-rcppprogress")
5301 (uri (cran-uri "RcppProgress" version))
5304 "0j2b37gwjpgmrnr00srdzm751hzlpsjb54ph63xxmcdfnwhlnqmi"))))
5305 (properties `((upstream-name . "RcppProgress")))
5306 (build-system r-build-system)
5307 (home-page "https://github.com/kforner/rcpp_progress")
5308 (synopsis "Interruptible progress bar for C++ in R packages")
5310 "This package displays a progress bar in the R console for long running
5311 computations taking place in C++ code, and support for interrupting those computations
5312 even in multithreaded code, typically using OpenMP.")
5313 (license license:gpl3+)))
5315 (define-public r-tmvnsim
5322 (uri (cran-uri "tmvnsim" version))
5325 "03xsvsg9bqvgl98ywid3h91mmlhax5s6wvmypp3hq91vmc5kvxlp"))))
5326 (properties `((upstream-name . "tmvnsim")))
5327 (build-system r-build-system)
5328 (native-inputs `(("gfortran" ,gfortran)))
5329 (home-page "https://www.r-project.org")
5330 (synopsis "Truncated multivariate normal simulation")
5332 "This package implements importance sampling from the truncated
5333 multivariate normal using the @dfn{Geweke-Hajivassiliou-Keane} (GHK)
5334 simulator. Unlike Gibbs sampling which can get stuck in one truncation
5335 sub-region depending on initial values, this package allows truncation based
5336 on disjoint regions that are created by truncation of absolute values. The
5337 GHK algorithm uses simple Cholesky transformation followed by recursive
5338 simulation of univariate truncated normals hence there are also no convergence
5339 issues. Importance sample is returned along with sampling weights, based on
5340 which, one can calculate integrals over truncated regions for multivariate
5342 (license license:gpl2)))
5344 (define-public r-mnormt
5351 (uri (cran-uri "mnormt" version))
5354 "0d7ka4l4fl1wi77r2r81dc91n6cbj2xrb3lsizz5y0ziscva0sjw"))))
5355 (build-system r-build-system)
5357 `(("r-tmvnsim" ,r-tmvnsim)))
5359 `(("gfortran" ,gfortran)))
5360 (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
5361 (synopsis "Multivariate normal and \"t\" distributions")
5363 "This package provides functions for computing the density and the
5364 distribution function of multivariate normal and \"t\" random variables, and
5365 for generating random vectors sampled from these distributions. Probabilities
5366 are computed via non-Monte Carlo methods.")
5367 (license license:gpl2+)))
5369 (define-public r-numderiv
5372 (version "2016.8-1.1")
5376 (uri (cran-uri "numDeriv" version))
5379 "0idk02pqkziik932bd8k72d1q775g1is3m4bc861pcxfz6gx3i6q"))))
5380 (properties `((upstream-name . "numDeriv")))
5381 (build-system r-build-system)
5382 (home-page "https://cran.r-project.org/web/packages/numDeriv")
5383 (synopsis "Accurate numerical derivatives")
5385 "This package provides methods for calculating accurate numerical
5386 first and second order derivatives.")
5387 (license license:gpl2)))
5396 (uri (cran-uri "sn" version))
5399 "0sl8qzy9isy5fq8qxh1fg5285jzgy895nbgz8gdq5d0r6zdwrmmb"))))
5400 (build-system r-build-system)
5402 `(("r-mnormt" ,r-mnormt)
5403 ("r-numderiv" ,r-numderiv)
5404 ("r-quantreg" ,r-quantreg)))
5405 (home-page "http://azzalini.stat.unipd.it/SN")
5406 (synopsis "The skew-normal and skew-t distributions")
5408 "This package provides functionalities to build and manipulate
5409 probability distributions of the skew-normal family and some related
5410 ones, notably the skew-t family, and provides related statistical
5411 methods for data fitting and diagnostics, in the univariate and the
5412 multivariate case.")
5413 (license license:gpl2+)))
5415 (define-public r-tclust
5422 (uri (cran-uri "tclust" version))
5425 "1nb5iky4kc832627jf28lzj19wrvgwg5da6fyl3kyf0npmyx1p4m"))))
5426 (build-system r-build-system)
5427 ;; These are all suggested packages, not build dependencies.
5429 `(("r-cluster" ,r-cluster)
5430 ("r-mclust" ,r-mclust)
5431 ("r-mvtnorm" ,r-mvtnorm)
5433 (home-page "https://cran.r-project.org/web/packages/tclust")
5434 (synopsis "Robust trimmed clustering")
5436 "This package implements different robust clustering
5437 algorithms (@code{tclust}) based on trimming and including some graphical
5438 diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
5439 (license license:gpl3)))
5441 (define-public r-ranger
5448 (uri (cran-uri "ranger" version))
5451 "1vr5akgh388iivrxi0g4pl2npq9dc4cim3ljk4kjf637q058wc7w"))))
5452 (build-system r-build-system)
5454 `(("r-rcpp" ,r-rcpp)
5455 ("r-matrix" ,r-matrix)
5456 ("r-rcppeigen" ,r-rcppeigen)))
5457 (home-page "https://github.com/imbs-hl/ranger")
5458 (synopsis "Fast implementation of random forests")
5460 "This package provides a fast implementation of Random Forests,
5461 particularly suited for high dimensional data. Ensembles of classification,
5462 regression, survival and probability prediction trees are supported. Data from
5463 genome-wide association studies can be analyzed efficiently.")
5464 (license license:gpl3)))
5466 (define-public r-tsne
5473 (uri (cran-uri "tsne" version))
5476 "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
5477 (build-system r-build-system)
5478 (home-page "https://github.com/jdonaldson/rtsne/")
5479 (synopsis "t-Distributed Stochastic Neighbor Embedding for R")
5481 "This package provides a pure R implementation of the t-SNE algorithm.")
5482 (license license:gpl2+)))
5484 (define-public r-cairo
5487 (version "1.5-12.2")
5491 (uri (cran-uri "Cairo" version))
5494 "14hgz5wmnhlbqkd1g662n1agmjnlj3pq69gfng1vb0ivr02l2lnx"))))
5495 (properties `((upstream-name . "Cairo")))
5496 (build-system r-build-system)
5502 `(("pkg-config" ,pkg-config)))
5503 (home-page "https://www.rforge.net/Cairo/")
5504 (synopsis "R graphics device using Cairo graphics library")
5506 "This package provides a Cairo graphics device that can be use to
5507 create high-quality vector (PDF, PostScript and SVG) and bitmap
5508 output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11
5509 and Win32). Since it uses the same back-end for all output, copying
5510 across formats is WYSIWYG. Files are created without the dependence
5511 on X11 or other external programs. This device supports alpha
5512 channel (semi-transparent drawing) and resulting images can contain
5513 transparent and semi-transparent regions. It is ideal for use in
5514 server environments (file output) and as a replacement for other
5515 devices that don't have Cairo's capabilities such as alpha support or
5516 anti-aliasing. Backends are modular such that any subset of backends
5518 (license license:gpl2)))
5520 (define-public r-lubridate
5522 (name "r-lubridate")
5527 (uri (cran-uri "lubridate" version))
5530 "1s653d6rnpf9bkynxmbq4fdjdcz7r9ma19aph8f5y9ck70his4hm"))))
5531 (build-system r-build-system)
5533 `(("r-generics" ,r-generics)
5534 ("r-rcpp" ,r-rcpp)))
5536 `(("r-knitr" ,r-knitr)))
5537 (home-page "https://cran.r-project.org/web/packages/lubridate/")
5538 (synopsis "Make dealing with dates a little easier")
5540 "This package provides functions to work with date-times and time-spans:
5541 fast and user friendly parsing of date-time data, extraction and updating of
5542 components of a date-time (years, months, days, hours, minutes, and seconds),
5543 algebraic manipulation on date-time and time-span objects. The @code{lubridate}
5544 package has a consistent and memorable syntax that makes working with dates
5546 (license license:gpl2)))
5548 (define-public r-fdrtool
5555 (uri (cran-uri "fdrtool" version))
5558 "1aap4k1l3a9m43374xq688mqnzkgqx8l021li262r3h1xr4adpp7"))))
5559 (build-system r-build-system)
5560 (home-page "http://strimmerlab.org/software/fdrtool/")
5561 (synopsis "Estimation of false discovery rates and higher criticism")
5563 "This package provides tools to estimate tail area-based false discovery
5564 rates as well as local false discovery rates for a variety of null
5565 models (p-values, z-scores, correlation coefficients, t-scores). The
5566 proportion of null values and the parameters of the null distribution are
5567 adaptively estimated from the data. In addition, the package contains
5568 functions for non-parametric density estimation (Grenander estimator), for
5569 monotone regression (isotonic regression and antitonic regression with
5570 weights), for computing the @dfn{greatest convex minorant} (GCM) and the
5571 @dfn{least concave majorant} (LCM), for the half-normal and correlation
5572 distributions, and for computing empirical @dfn{higher criticism} (HC) scores
5573 and the corresponding decision threshold.")
5574 (license license:gpl3+)))
5576 (define-public r-forcats
5583 (uri (cran-uri "forcats" version))
5586 "12d2nv2w15085jscgidmjdnr1ryymciflcmal6ldmgp2fkl9dyy4"))))
5587 (build-system r-build-system)
5589 `(("r-ellipsis" ,r-ellipsis)
5590 ("r-magrittr" ,r-magrittr)
5591 ("r-tibble" ,r-tibble)
5592 ("r-rlang" ,r-rlang)))
5594 `(("r-knitr" ,r-knitr)))
5595 (home-page "https://forcats.tidyverse.org")
5596 (synopsis "Tools for working with factors")
5597 (description "This package provides helpers for reordering factor
5598 levels (including moving specified levels to front, ordering by first
5599 appearance, reversing, and randomly shuffling), and tools for modifying factor
5600 levels (including collapsing rare levels into other, \"anonymizing\", and
5601 manually \"recoding\").")
5602 (license license:gpl3)))
5604 (define-public r-tgstat
5605 (let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f")
5609 (version (string-append "1.0.2-" revision "." (string-take changeset 7)))
5614 (url "https://bitbucket.org/tanaylab/tgstat")
5615 (changeset changeset)))
5616 (file-name (string-append name "-" version "-checkout"))
5619 "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
5620 (build-system r-build-system)
5623 (modify-phases %standard-phases
5624 (add-after 'unpack 'fix-isnan
5626 (substitute* "src/tgstat.h"
5627 (("#define isnan ::isnan")
5628 "#define isnan std::isnan"))
5631 `(("r-rcpp" ,r-rcpp)))
5632 (home-page "https://bitbucket.org/tanaylab/tgstat/")
5633 (synopsis "Tanay's group statistical utilities")
5635 "The goal of tgstat is to provide fast and efficient statistical
5637 (license license:gpl2))))
5639 (define-public r-tgconfig
5640 (let ((changeset "1e02c7614713bd0866c46f0c679a058f8c6d627e")
5644 (version (string-append "0.0.0.9000-" revision "." (string-take changeset 7)))
5649 (url "https://bitbucket.org/tanaylab/tgconfig")
5650 (changeset changeset)))
5651 (file-name (string-append name "-" version "-checkout"))
5654 "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
5655 (build-system r-build-system)
5657 `(("r-yaml" ,r-yaml)))
5658 (home-page "https://bitbucket.org/tanaylab/tgconfig/")
5659 (synopsis "Infrastructure for managing package parameters")
5661 "The goal of tgconfig is to provide infrastructure for managing package
5663 (license license:gpl3))))
5665 (define-public r-catterplots
5666 (let ((commit "ae17cd5e49ddda4ecfe0eba8a4c21df8c88e72c4")
5669 (name "r-catterplots")
5670 (version (git-version "0" revision commit))
5674 (url "https://github.com/Gibbsdavidl/CatterPlots")
5676 (file-name (git-file-name name version))
5679 "0qa8liylffpxgdg8xcgjar5dsvczqhn3akd4w35113hnyg1m4xyg"))))
5680 (build-system r-build-system)
5682 `(("r-png" ,r-png)))
5683 (home-page "https://github.com/Gibbsdavidl/CatterPlots")
5684 (synopsis "Scatter plots with cat shaped points")
5685 (description "Did you ever wish you could make scatter plots with cat
5686 shaped points? Now you can!")
5687 (license license:asl2.0))))
5689 (define-public r-colorout
5697 (url "https://github.com/jalvesaq/colorout")
5698 (commit (string-append "v" version))))
5699 (file-name (git-file-name name version))
5701 (base32 "1rsx69wjpa73c6x2hacvvvbzdzxn7wg06gizf97kasjdlb7azmp3"))))
5702 (build-system r-build-system)
5703 (home-page "https://github.com/jalvesaq/colorout")
5704 (synopsis "Colorize output in the R REPL")
5705 (description "@code{colorout} is an R package that colorizes R output when
5706 running in terminal emulator.
5708 R STDOUT is parsed and numbers, negative numbers, dates in the standard
5709 format, strings, and R constants are identified and wrapped by special ANSI
5710 scape codes that are interpreted by terminal emulators as commands to colorize
5711 the output. R STDERR is also parsed to identify the expressions warning and
5712 error and their translations to many languages. If these expressions are
5713 found, the output is colorized accordingly; otherwise, it is colorized as
5714 STDERROR (blue, by default).
5716 You can customize the colors according to your taste, guided by the color
5717 table made by the command @code{show256Colors()}. You can also set the colors
5718 to any arbitrary string. In this case, it is up to you to set valid values.")
5719 (license license:gpl3+)))
5721 (define-public python-rpy2
5723 (name "python-rpy2")
5728 (uri (pypi-uri "rpy2" version))
5731 "1bs36rds5fq8821l5q85q2b25161rs9ppw5c26x0hjwj487gpcfj"))
5732 ;; These patches should be removed with the next release.
5737 (uri "https://github.com/rpy2/rpy2/commit/04c57598f00145d868ea8da31ac1b1e7c49f7570.patch")
5738 (file-name "python-rpy2-fix-test-failure.patch")
5741 "1lqd3yxjfx1rxrybcmnapy0r6ambg9myrb98q4nlfhpxanwfdbbh")))
5744 (uri "https://github.com/rpy2/rpy2/commit/685f67d0a6b47ea80e718116a10755019446aef7.patch")
5745 (file-name "python-rpy2-r-console-test-fix.patch")
5748 "18wpvfaa4c13d44cb4sw88c3c7403xdy5m8h82wfq8fjmcq3cmzn")))))))
5749 (build-system python-build-system)
5751 '(#:modules ((ice-9 ftw)
5755 (guix build python-build-system))
5757 (modify-phases %standard-phases
5759 (lambda* (#:key outputs inputs #:allow-other-keys)
5760 (let ((cwd (getcwd)))
5762 (setenv "PYTHONPATH"
5763 (string-append cwd "/build/"
5764 (find (cut string-prefix? "lib" <>)
5765 (scandir (string-append cwd "/build")))
5767 (getenv "PYTHONPATH"))))
5768 ;; test_vector_complex has issues when run in our environment.
5769 (invoke "pytest" "-v" "rpy2/tests/" "-k" "not test_vector_complex"))))))
5771 `(("python-cffi" ,python-cffi)
5772 ("python-six" ,python-six)
5773 ("python-jinja2" ,python-jinja2)
5774 ("python-numpy" ,python-numpy)
5775 ("python-pandas" ,python-pandas)
5776 ("python-pytz" ,python-pytz)
5777 ("python-ipython" ,python-ipython)
5778 ("python-tzlocal" ,python-tzlocal)))
5780 `(("readline" ,readline)
5783 ("r-minimal" ,r-minimal)
5784 ("r-survival" ,r-survival)
5785 ("r-ggplot2" ,r-ggplot2)
5786 ("r-rsqlite" ,r-rsqlite)
5787 ("r-dplyr" ,r-dplyr)
5788 ("r-dbplyr" ,r-dbplyr)
5789 ("python-numpy" ,python-numpy)))
5792 ("python-pytest" ,python-pytest)))
5793 (home-page "https://rpy2.github.io")
5794 (synopsis "Python interface to the R language")
5795 (description "rpy2 is a redesign and rewrite of rpy. It is providing a
5796 low-level interface to R from Python, a proposed high-level interface,
5797 including wrappers to graphical libraries, as well as R-like structures and
5799 ;; Any of these licenses can be picked for the R interface. The whole
5800 ;; project is released under GPLv2+ according to the license declaration
5802 (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+))))
5804 (define-public java-jdistlib
5806 (name "java-jdistlib")
5810 (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
5811 version "-src.jar"))
5814 "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
5815 (build-system ant-build-system)
5817 `(#:jar-name "jdistlib.jar"
5819 #:tests? #f ; no dedicated test directory
5821 (modify-phases %standard-phases
5822 (add-after 'unpack 'fix-broken-encoding
5824 (with-fluids ((%default-port-encoding "ISO-8859-1"))
5825 (substitute* "src/jdistlib/Beta.java"
5826 (("Scheff.+-Tukey") "Scheffe-Tukey")))
5829 `(("java-jtransforms" ,java-jtransforms)))
5831 `(("java-junit" ,java-junit)))
5832 (home-page "http://jdistlib.sourceforge.net/")
5833 (synopsis "Java library of statistical distributions")
5834 (description "JDistlib is the Java Statistical Distribution Library, a
5835 Java package that provides routines for various statistical distributions.")
5836 ;; The files that were translated from R code are under GPLv2+; some files
5837 ;; are under the GPLv3, which is a mistake. The author confirmed in an
5838 ;; email that this whole project should be under GPLv2+.
5839 (license license:gpl2+)))
5841 (define-public emacs-ess
5842 ;; Latest release is old. This is not the latest commit either due to bug
5843 ;; reported here: <https://github.com/emacs-ess/ESS/issues/987>.
5844 (let ((commit "24da603184ce39246611dd5b8602e769d7ebd5bf")
5849 (version (git-version version revision commit))
5854 (url "https://github.com/emacs-ess/ESS")
5857 (base32 "0j98lv07nzwzd54d4dgcfz01wy5gj48m0mnirxzh5r45ik2myh1r"))
5858 (file-name (git-file-name name version))
5859 (modules '((guix build utils)))
5862 ;; Stop ESS from trying to bundle an external julia-mode.el.
5863 (substitute* "lisp/Makefile"
5864 ((" \\$\\(JULIAS)") "")
5865 (("\ttest.*julia-mode.*\\.el") ""))
5866 ;; Only build docs in info format.
5867 (substitute* "doc/Makefile"
5868 (("all : info text")
5870 (("install: install-info install-other-docs")
5871 "install: install-info"))
5872 ;; Stop install-info from trying to update the info directory.
5873 (substitute* "doc/Makefile"
5875 ;; Fix r-help-mode test.
5876 (substitute* "test/ess-test-r.el"
5877 (("\\(equal ess-help-object \"plot.default\")") "t"))
5878 ;; Avoid generating ess-autoloads.el twice.
5879 (substitute* "Makefile"
5880 (("all: lisp doc etc autoloads")
5881 "all: lisp doc etc"))
5882 ;; Install to correct directories.
5883 (substitute* "Makefile"
5884 (("mkdir -p \\$\\(ESSDESTDIR)")
5885 "$(MAKE) -C lisp install; $(MAKE) -C doc install")
5886 (("\\$\\(INSTALL) -R \\./\\* \\$\\(ESSDESTDIR)/")
5887 "$(MAKE) -C etc install"))
5889 (build-system gnu-build-system)
5891 (let ((base-directory "/share/emacs/site-lisp"))
5892 `(#:make-flags (list (string-append "PREFIX=" %output)
5893 (string-append "ETCDIR=" %output
5894 ,base-directory "/etc")
5895 (string-append "LISPDIR=" %output
5897 (string-append "INFODIR=" %output
5900 (modify-phases %standard-phases
5903 (lambda _ (invoke "make" "test")))))))
5906 ("r-roxygen2" ,r-roxygen2)
5907 ("texinfo" ,texinfo)))
5909 `(("emacs" ,emacs-minimal)
5910 ("r-minimal" ,r-minimal)))
5912 `(("emacs-julia-mode" ,emacs-julia-mode)))
5913 (home-page "https://ess.r-project.org/")
5914 (synopsis "Emacs mode for statistical analysis programs")
5916 "Emacs Speaks Statistics (ESS) is an add-on package for GNU Emacs. It
5917 is designed to support editing of scripts and interaction with various
5918 statistical analysis programs such as R, Julia, and JAGS.")
5919 (license license:gpl3+))))
5921 (define-public readstat
5929 (url "https://github.com/WizardMac/ReadStat")
5930 (commit (string-append "v" version))))
5931 (file-name (git-file-name name version))
5933 (base32 "00sdmaq0qzp6kyv53fpfi6jf3iv4pd0ap0gmw3mbfip52bbnl55w"))))
5934 (build-system gnu-build-system)
5936 `(("autoconf" ,autoconf)
5937 ("automake" ,automake)
5938 ("gettext" ,gnu-gettext)
5939 ("libtool" ,libtool)))
5941 `(("zlib" ,zlib))) ; libz
5942 (synopsis "Convert SAS, Stata, and SPSS files")
5943 (description "Command-line tool and C library for reading files from
5944 popular stats packages like SAS, Stata and SPSS.")
5945 (home-page "https://github.com/WizardMac/ReadStat")
5946 (license license:expat)))
5948 (define-public r-quantpsyc
5950 (name "r-quantpsyc")
5955 (uri (cran-uri "QuantPsyc" version))
5958 "1i9bh88r8zxndzjqsj14qw64gnvm5a9kvhjhzk3qsrvl3qzjgh93"))))
5959 (properties `((upstream-name . "QuantPsyc")))
5960 (build-system r-build-system)
5962 `(("r-boot" ,r-boot) ("r-mass" ,r-mass)))
5963 (home-page "https://cran.r-project.org/web/packages/QuantPsyc/")
5964 (synopsis "Quantitative Psychology Tools")
5966 "Contains functions useful for data screening, testing moderation,
5967 mediation and estimating power.")
5968 (license license:gpl2+)))
5970 (define-public r-clubsandwich
5972 (name "r-clubsandwich")
5977 (uri (cran-uri "clubSandwich" version))
5980 "0jazgka18bb5n58d5sn94q7rc9sac82qrpl2i5b4rkx9q2pb39cn"))))
5981 (properties `((upstream-name . "clubSandwich")))
5982 (build-system r-build-system)
5984 `(("r-sandwich" ,r-sandwich)))
5985 (native-inputs `(("r-knitr" ,r-knitr)))
5986 (home-page "https://github.com/jepusto/clubSandwich")
5987 (synopsis "Cluster-Robust (Sandwich) Variance Estimators with Small-Sample
5990 "Provides several cluster-robust variance estimators (i.e.,
5991 sandwich estimators) for ordinary and weighted least squares linear regression
5992 models, including the bias-reduced linearization estimator introduced by Bell
5993 and McCaffrey (2002)
5994 @url{http://www.statcan.gc.ca/pub/12-001-x/2002002/article/9058-eng.pdf} and
5995 developed further by Pustejovsky and Tipton (2017)
5996 @url{doi:10.1080/07350015.2016.1247004}. The package includes functions for estimating
5997 the variance- covariance matrix and for testing single- and multiple-
5998 contrast hypotheses based on Wald test statistics. Tests of single regression
5999 coefficients use Satterthwaite or saddle-point corrections. Tests of multiple-
6000 contrast hypotheses use an approximation to Hotelling's T-squared distribution.
6001 Methods are provided for a variety of fitted models, including @code{lm()} and
6002 @code{mlm} objects, @code{glm()}, ivreg (from package @code{AER}), @code{plm()}
6003 (from package @code{plm}), @code{gls()} and @code{lme()} (from @code{nlme}),
6004 @code{robu()} (from @code{robumeta}), and @code{rma.uni()} and @code{rma.mv()}
6005 (from @code{metafor}).")
6006 (license license:gpl3)))
6008 (define-public r-puniform
6015 (uri (cran-uri "puniform" version))
6018 "0v2977y9cwjx74xk0ig745g09wn7nrcsrg4f6v315sglsm18iaa8"))))
6019 (properties `((upstream-name . "puniform")))
6020 (build-system r-build-system)
6022 `(("r-adgoftest" ,r-adgoftest)
6023 ("r-metafor" ,r-metafor)
6025 ("r-rcpparmadillo" ,r-rcpparmadillo)))
6027 "https://github.com/RobbievanAert/puniform")
6029 "Meta-Analysis Methods Correcting for Publication Bias")
6031 "This package provides meta-analysis methods that correct for publication
6032 bias and outcome reporting bias. Four methods and a visual tool are currently
6033 included in the package.
6036 @item The p-uniform method as described in van Assen, van Aert, and Wicherts
6037 (2015) @url{doi:10.1037/met0000025} can be used for estimating the average
6038 effect size, testing the null hypothesis of no effect, and testing for
6039 publication bias using only the statistically significant effect sizes of
6042 @item The p-uniform* method as described in van Aert and van Assen (2019)
6043 @url{doi:10.31222/osf.io/zqjr9}. This method is an extension of the p-uniform
6044 method that allows for estimation of the average effect size and the
6045 between-study variance in a meta-analysis, and uses both the statistically
6046 significant and nonsignificant effect sizes.
6048 @item The hybrid method as described in van Aert and van Assen (2017)
6049 @url{doi:10.3758/s13428-017-0967-6}. The hybrid method is a meta-analysis
6050 method for combining an original study and replication and while taking into
6051 account statistical significance of the original study. The p-uniform and
6052 hybrid method are based on the statistical theory that the distribution of
6053 p-values is uniform conditional on the population effect size.
6056 The fourth method in the package is the Snapshot Bayesian Hybrid Meta-Analysis
6057 Method as described in van Aert and van Assen (2018)
6058 @url{doi:10.1371/journal.pone.0175302}. This method computes posterior
6059 probabilities for four true effect sizes (no, small, medium, and large) based
6060 on an original study and replication while taking into account publication bias
6061 in the original study. The method can also be used for computing the required
6062 sample size of the replication akin to power analysis in null hypothesis
6063 significance testing.
6066 The meta-plot is a visual tool for meta-analysis that
6067 provides information on the primary studies in the meta-analysis, the results
6068 of the meta-analysis, and characteristics of the research on the effect under
6069 study (van Assen and others, 2020).
6071 Helper functions to apply the Correcting for Outcome Reporting Bias (CORB)
6072 method to correct for outcome reporting bias in a meta-analysis (van Aert &
6074 (license license:gpl2+)))
6076 (define-public r-esc
6083 (uri (cran-uri "esc" version))
6086 "0gns7gz55p6pha05413r3hlvd7f2v1amxkg13d197mab1ypqic7q"))))
6087 (properties `((upstream-name . "esc")))
6088 (build-system r-build-system)
6089 (home-page "https://strengejacke.github.io/esc/")
6091 "Effect Size Computation for Meta Analysis")
6093 "Implementation of the web-based
6094 @url{http://www.campbellcollaboration.org/escalc/html/EffectSizeCalculator-Home.php,'Practical
6095 Meta-Analysis Effect Size Calculator'} from David B. Wilson in R. Based on the
6096 input, the effect size can be returned as standardized mean difference, Cohen's
6097 f, Hedges' g, Pearson's r or Fisher's transformation z, odds ratio or log odds,
6098 or eta squared effect size.")
6099 (license license:gpl3)))