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 "03cypg2qf7v9mq9mr9alz9w5y9m5kdgwbc97bp26pyymg253m609"))))
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 adding characters to break
276 ;; up the series of line break and spaces that is suspected to be
278 (substitute* "src/library/methods/DESCRIPTION.in"
282 (add-before 'build 'set-locales
284 (setlocale LC_ALL "C")
285 (setenv "LC_ALL" "C")
287 (add-before 'configure 'set-default-pager
288 ;; Set default pager to "cat", because otherwise it is "false",
289 ;; making "help()" print nothing at all.
290 (lambda _ (setenv "PAGER" "cat") #t))
291 (add-before 'check 'set-timezone
292 ;; Some tests require the timezone to be set. However, the
293 ;; timezone may not just be "UTC", or else a brittle regression
294 ;; test in reg-tests-1d will fail.
295 (lambda* (#:key inputs #:allow-other-keys)
296 (setenv "TZ" "UTC+1")
298 (string-append (assoc-ref inputs "tzdata")
301 (add-after 'build 'make-info
302 (lambda _ (invoke "make" "info")))
303 (add-after 'build 'install-info
304 (lambda _ (invoke "make" "install-info"))))
306 `(;; We build the recommended packages here, because they are needed in
307 ;; order to run the test suite. We disable them in the r-minimal
310 "--with-blas=-lopenblas"
316 ,(string-append "--with-tcl-config="
317 (assoc-ref %build-inputs "tcl")
319 ,(string-append "--with-tk-config="
320 (assoc-ref %build-inputs "tk")
323 "--enable-BLAS-shlib"
324 "--with-system-tre")))
325 ;; R has some support for Java. When the JDK is available at configure
326 ;; time environment variables pointing to the JDK will be recorded under
327 ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
328 ;; CMD javareconf". "R CMD javareconf" appears to only be used to update
329 ;; the recorded environment variables in $R_HOME/etc. Refer to
330 ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
331 ;; for additional information.
333 ;; As the JDK is a rather large input with only very limited effects on R,
334 ;; we decided to drop it.
338 ("pkg-config" ,pkg-config)
339 ("texinfo" ,texinfo) ; for building HTML manuals
340 ("texlive" ,(texlive-union (list texlive-ae
345 texlive-latex-fancyvrb
346 texlive-latex-graphics
347 texlive-latex-hyperref
348 texlive-latex-oberdiek
350 texlive-latex-upquote
352 texlive-latex-xkeyval)))
353 ("tzdata" ,tzdata-for-tests)
356 `(;; We need not only cairo here, but pango to ensure that tests for the
357 ;; "cairo" bitmapType plotting backend succeed.
359 ("coreutils" ,coreutils)
361 ("openblas" ,openblas)
362 ("gfortran" ,gfortran)
364 ("libjpeg" ,libjpeg-turbo)
369 ("readline" ,readline)
370 ;; This avoids a reference to the ungraftable static bash. R uses the
371 ;; detected shell for the "system" procedure.
372 ("bash" ,bash-minimal)
378 (list (search-path-specification
379 (variable "R_LIBS_SITE")
380 (files (list "site-library/")))))
381 (home-page "https://www.r-project.org/")
382 (synopsis "Environment for statistical computing and graphics")
384 "R is a language and environment for statistical computing and graphics.
385 It provides a variety of statistical techniques, such as linear and nonlinear
386 modeling, classical statistical tests, time-series analysis, classification
387 and clustering. It also provides robust support for producing
388 publication-quality data plots. A large amount of 3rd-party packages are
389 available, greatly increasing its breadth and scope.")
390 (license license:gpl3+)))
392 (define-public r-minimal
393 (package (inherit r-with-tests)
397 ,@(substitute-keyword-arguments (package-arguments r-with-tests)
398 ((#:configure-flags flags)
399 ;; Do not build the recommended packages. The build system creates
400 ;; random temporary directories and embeds their names in some
401 ;; package files. We build these packages with the r-build-system
403 `(cons "--without-recommended-packages" ,flags)))))))
405 (define-public rmath-standalone
406 (package (inherit r-minimal)
407 (name "rmath-standalone")
410 (modify-phases %standard-phases
411 (add-after 'configure 'chdir
412 (lambda _ (chdir "src/nmath/standalone/") #t)))))
413 (synopsis "Standalone R math library")
415 "This package provides the R math library as an independent package.")))
417 (define-public r-boot
424 (uri (cran-uri "boot" version))
427 "1gpvi1h3nqhnnsfy96rlhakdpj84iqqsxr29rr3261sknky3aj26"))))
428 (build-system r-build-system)
429 (home-page "https://cran.r-project.org/web/packages/boot")
430 (synopsis "Bootstrap functions for R")
432 "This package provides functions and datasets for bootstrapping from the
433 book \"Bootstrap Methods and Their Application\" by A.C. Davison and
434 D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
435 ;; Unlimited distribution
436 (license (license:non-copyleft "file://R/bootfuns.q"))))
438 (define-public r-mass
445 (uri (cran-uri "MASS" version))
448 "0f2bwsbqr3nzsqxva051lg8wd068naqif3vc48hac0m3mmq4x0j1"))))
449 (properties `((upstream-name . "MASS")))
450 (build-system r-build-system)
451 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
452 (synopsis "Support functions and datasets for Venables and Ripley's MASS")
454 "This package provides functions and datasets for the book \"Modern
455 Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
456 ;; Either version may be picked.
457 (license (list license:gpl2 license:gpl3))))
459 (define-public r-class
466 (uri (cran-uri "class" version))
469 "04qk8qia0qr8893fizmkbd5hsqn6m8383c0cyn9xnmkmvyv8a7xy"))))
470 (build-system r-build-system)
472 `(("r-mass" ,r-mass)))
473 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
474 (synopsis "R functions for classification")
476 "This package provides various functions for classification, including
477 k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
478 ;; Either of the two versions can be picked.
479 (license (list license:gpl2 license:gpl3))))
481 (define-public r-cluster
488 (uri (cran-uri "cluster" version))
491 "055af3yz2biqbsbwm4arwr1yqnj4gicpzv2i6dbfl5pnz2z5byga"))))
492 (build-system r-build-system)
494 `(("gfortran" ,gfortran)))
495 (home-page "https://cran.r-project.org/web/packages/cluster")
496 (synopsis "Methods for cluster analysis")
498 "This package provides methods for cluster analysis. It is a much
499 extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
500 Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
501 (license license:gpl2+)))
503 (define-public r-codetools
510 (uri (cran-uri "codetools" version))
513 "0a2c115glq8jxixwfigrpvjabhxchn9r4mc40y41dg9dg6wsd7hs"))))
514 (build-system r-build-system)
515 (home-page "https://cran.r-project.org/web/packages/codetools")
516 (synopsis "Code analysis tools for R")
517 (description "This package provides code analysis tools for R to check R
518 code for possible problems.")
519 ;; Any version of the GPL.
520 (license (list license:gpl2+ license:gpl3+))))
522 (define-public r-foreign
529 (uri (cran-uri "foreign" version))
532 "0b4rca1bl8xxna05057hchbwfmgjgx0n140szabpc0raizqzks0s"))))
533 (build-system r-build-system)
534 (home-page "https://cran.r-project.org/web/packages/foreign")
535 (synopsis "Read data stored by other statistics software")
537 "This package provides functions for reading and writing data stored by
538 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
539 for reading and writing some dBase files.")
540 (license license:gpl2+)))
542 (define-public r-kernsmooth
544 (name "r-kernsmooth")
549 (uri (cran-uri "KernSmooth" version))
552 "14640ddvxmczd5xjg1xsd51gll2glfg946vks8wmac6jb8680d43"))))
553 (properties `((upstream-name . "KernSmooth")))
554 (build-system r-build-system)
556 `(("gfortran" ,gfortran)))
557 (home-page "https://cran.r-project.org/web/packages/KernSmooth")
558 (synopsis "Functions for kernel smoothing")
560 "This package provides functions for kernel smoothing (and density
561 estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
562 \"Kernel Smoothing\".")
563 ;; Unlimited use and distribution
564 (license (license:non-copyleft "file://LICENCE.note"))))
566 (define-public r-lattice
572 (uri (cran-uri "lattice" version))
575 "1dapkmh4jlb9sxfrpvapvlfhczl4s8p3r20bn47gcgdk1izmbjjl"))))
576 (build-system r-build-system)
577 (home-page "http://lattice.r-forge.r-project.org/")
578 (synopsis "High-level data visualization system")
580 "The lattice package provides a powerful and elegant high-level data
581 visualization system inspired by Trellis graphics, with an emphasis on
582 multivariate data. Lattice is sufficient for typical graphics needs, and is
583 also flexible enough to handle most nonstandard requirements.")
584 (license license:gpl2+)))
586 (define-public r-matrix
593 (uri (cran-uri "Matrix" version))
596 "0ccmmfd0lbvrhzjzr28k4yfawiywa1m4ics34zyi3rqq23csa2wm"))))
597 (properties `((upstream-name . "Matrix")))
598 (build-system r-build-system)
600 `(("r-lattice" ,r-lattice)))
601 (home-page "http://Matrix.R-forge.R-project.org/")
602 (synopsis "Sparse and dense matrix classes and methods")
604 "This package provides classes and methods for dense and sparse matrices
605 and operations on them using LAPACK and SuiteSparse.")
606 (license license:gpl2+)))
608 (define-public r-nlme
615 (uri (cran-uri "nlme" version))
617 (base32 "1jl6x0glpyszy6bkbcggm3f10jl4kldhs5q561k85xcbssx2dim2"))))
618 (build-system r-build-system)
620 `(("r-lattice" ,r-lattice)))
622 `(("gfortran" ,gfortran)))
623 (home-page "https://cran.r-project.org/web/packages/nlme")
624 (synopsis "Linear and nonlinear mixed effects models")
626 "This package provides tools to fit and compare Gaussian linear and
627 nonlinear mixed-effects models.")
628 (license license:gpl2+)))
630 (define-public r-mgcv
637 (uri (cran-uri "mgcv" version))
639 (base32 "1x1bdzz2b2f05626xygwqp30b4rhblgg76hs15j9ab4fjan7pjwq"))))
640 (build-system r-build-system)
642 `(("r-matrix" ,r-matrix)
644 (home-page "https://cran.r-project.org/web/packages/mgcv")
645 (synopsis "Mixed generalised additive model computation")
647 "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
648 parameter estimation by GCV, REML or UBRE/AIC. The library includes a
649 @code{gam()} function, a wide variety of smoothers, JAGS support and
650 distributions beyond the exponential family.")
651 (license license:gpl2+)))
653 (define-public r-nnet
660 (uri (cran-uri "nnet" version))
663 "1bzl62p5awva5kxcncs6lrdrkqp9ljd993zia731ckfpcjbrw6sx"))))
664 (build-system r-build-system)
665 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
666 (synopsis "Feed-forward neural networks and multinomial log-linear models")
668 "This package provides functions for feed-forward neural networks with a
669 single hidden layer, and for multinomial log-linear models.")
670 (license (list license:gpl2+ license:gpl3+))))
672 (define-public r-rpart
679 (uri (cran-uri "rpart" version))
682 "0p5frya963ppn476p5dxs2mnarsalksr6gw9zzmjsn8ikq7bx3ib"))))
683 (build-system r-build-system)
684 (home-page "https://cran.r-project.org/web/packages/rpart")
685 (synopsis "Recursive partitioning and regression trees")
687 "This package provides recursive partitioning functions for
688 classification, regression and survival trees.")
689 (license (list license:gpl2+ license:gpl3+))))
691 (define-public r-spatial
698 (uri (cran-uri "spatial" version))
701 "0qrdhzd5r78iwi46nk8jr56dzz5l5imkflxjw64d0ys0wyg06fbn"))))
702 (build-system r-build-system)
703 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
704 (synopsis "Functions for kriging and point pattern analysis")
706 "This package provides functions for kriging and point pattern
708 ;; Either version may be picked.
709 (license (list license:gpl2 license:gpl3))))
711 (define-public r-survival
718 (uri (cran-uri "survival" version))
721 "0ila864g5b9yhjhk3jirgdpi06sksc0axa78890dmkvyv9rwsmjk"))))
722 (build-system r-build-system)
724 `(("r-matrix" ,r-matrix)))
725 (home-page "https://github.com/therneau/survival")
726 (synopsis "Survival analysis")
728 "This package contains the core survival analysis routines, including
729 definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
730 curves, Cox models, and parametric accelerated failure time models.")
731 (license license:lgpl2.0+)))
734 (package (inherit r-minimal)
737 (build-system trivial-build-system)
738 (arguments '(#:builder (begin (mkdir %output) #t)))
740 `(("r-minimal" ,r-minimal)
743 ("r-cluster" ,r-cluster)
744 ("r-codetools" ,r-codetools)
745 ("r-foreign" ,r-foreign)
746 ("r-kernsmooth" ,r-kernsmooth)
747 ("r-lattice" ,r-lattice)
749 ("r-matrix" ,r-matrix)
754 ("r-spatial" ,r-spatial)
755 ("r-survival" ,r-survival)))))
764 (uri (cran-uri "bit" version))
767 "0s7isadibxp2wr62r5cpbyh9z31sczzfz4j3rm7gxgjfpqgq8174"))))
768 (build-system r-build-system)
770 `(("r-knitr" ,r-knitr)))
771 (home-page "http://ff.r-forge.r-project.org")
772 (synopsis "Class for vectors of 1-bit booleans")
774 "This package provides bitmapped vectors of booleans (no @code{NA}s),
775 coercion from and to logicals, integers and integer subscripts, fast boolean
776 operators and fast summary statistics. With @code{bit} class vectors of true
777 binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
778 (license license:gpl2)))
780 (define-public r-bit64
787 (uri (cran-uri "bit64" version))
790 "0y0m7q1rwam1g88cjx7zyi07mj5dipxd9jkl90f294syx8k6ipr5"))))
791 (build-system r-build-system)
794 (home-page "http://ff.r-forge.r-project.org/")
795 (synopsis "S3 class for vectors of 64 bit integers")
797 "The bit64 package provides serializable S3 atomic 64 bit (signed)
798 integers that can be used in vectors, matrices, arrays and @code{data.frames}.
799 Methods are available for coercion from and to logicals, integers, doubles,
800 characters and factors as well as many elementwise and summary functions.
801 Many fast algorithmic operations such as @code{match} and @code{order} support
802 interactive data exploration and manipulation and optionally leverage
804 (license license:gpl2)))
806 (define-public r-dichromat
813 (uri (cran-uri "dichromat" version))
815 (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
816 (build-system r-build-system)
817 (home-page "https://cran.r-project.org/web/packages/dichromat")
818 (synopsis "Color schemes for dichromats")
820 "Dichromat collapses red-green or green-blue distinctions to simulate the
821 effects of different types of color-blindness.")
822 (license license:gpl2+)))
824 (define-public r-digest
831 (uri (cran-uri "digest" version))
833 (base32 "0gr503pinailfglpfbzxprqw7w1jla8jr9nl856a4zch498zg1gl"))))
834 (build-system r-build-system)
835 ;; Vignettes require r-knitr, which requires r-digest, so we have to
836 ;; disable them and the tests.
839 #:configure-flags (list "--no-build-vignettes")))
840 (home-page "http://dirk.eddelbuettel.com/code/digest.html")
841 (synopsis "Create cryptographic hash digests of R objects")
843 "This package contains an implementation of a function @code{digest()} for
844 the creation of hash digests of arbitrary R objects (using the md5, sha-1,
845 sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
846 of R language objects, as well as a function @code{hmac()} to create hash-based
847 message authentication code.
849 Please note that this package is not meant to be deployed for cryptographic
850 purposes for which more comprehensive (and widely tested) libraries such as
851 OpenSSL should be used.")
852 (license license:gpl2+)))
854 (define-public r-estimability
856 (name "r-estimability")
860 (uri (cran-uri "estimability" version))
863 "0cifdaa71spkcxl4db4z884jrya865sg3dhcv4isd8fnzg2pjcd3"))))
864 (build-system r-build-system)
865 (home-page "https://cran.r-project.org/web/packages/estimability")
866 (synopsis "Tools for assessing estimability of linear predictions")
867 (description "Provides tools for determining estimability of linear
868 functions of regression coefficients, and @code{epredict} methods that handle
869 non-estimable cases correctly.")
870 (license license:gpl2+)))
872 (define-public r-labeling
879 (uri (cran-uri "labeling" version))
881 (base32 "0rfikd9gy70b8qz87q9axcwv8nmn9mbxfdwypxi0sghpfs9df8p0"))))
882 (build-system r-build-system)
883 (home-page "https://cran.r-project.org/web/packages/labeling")
884 (synopsis "Axis labeling algorithms")
885 (description "The labeling package provides a range of axis labeling
887 (license license:expat)))
889 (define-public r-magrittr
896 (uri (cran-uri "magrittr" version))
898 (base32 "0pxd99fvg406whqsk9wh756rayrwh84xn3h44zmlpcy23kanbhkm"))))
899 (build-system r-build-system)
900 ;; knitr needs magrittr
903 `(("r-knitr" ,r-knitr)))
904 (home-page "https://cran.r-project.org/web/packages/magrittr/index.html")
905 (synopsis "A forward-pipe operator for R")
907 "Magrittr provides a mechanism for chaining commands with a new
908 forward-pipe operator, %>%. This operator will forward a value, or the result
909 of an expression, into the next function call/expression. There is flexible
910 support for the type of right-hand side expressions. For more information,
911 see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
912 (license license:expat)))
914 (define-public r-munsell
921 (uri (cran-uri "munsell" version))
923 (base32 "16g1fzisbpqb15yh3pqf3iia4csppva5dnv1z88x9dg263xskwyh"))))
924 (build-system r-build-system)
926 `(("r-colorspace" ,r-colorspace)))
927 (home-page "https://cran.r-project.org/web/packages/munsell")
928 (synopsis "Munsell colour system")
930 "The Munsell package contains Functions for exploring and using the
931 Munsell colour system.")
932 (license license:expat)))
934 (define-public r-permute
941 (uri (cran-uri "permute" version))
944 "0ra8p5mf2590azrkas8z2ry7mif77xqxd29n4zgyi5vll225726j"))))
945 (build-system r-build-system)
946 ;; Tests do not run correctly, but running them properly would entail a
947 ;; circular dependency with vegan.
948 (home-page "https://github.com/gavinsimpson/permute")
949 (synopsis "Functions for Generating Restricted Permutations of Data")
951 "This package provides a set of restricted permutation designs for freely
952 exchangeable, line transects (time series), spatial grid designs and permutation
953 of blocks (groups of samples). @code{permute} also allows split-plot designs,
954 in which the whole-plots or split-plots or both can be freely exchangeable.")
955 (license license:gpl2+)))
957 (define-public r-plyr
964 (uri (cran-uri "plyr" version))
966 (base32 "11sjjdn146w95s1vsfmmgdls082cbnm1slv98xvyjhsl2mpx4mga"))))
967 (build-system r-build-system)
968 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
969 (home-page "http://had.co.nz/plyr")
970 (synopsis "Tools for Splitting, Applying and Combining Data")
972 "Plyr is a set of tools that solves a common set of problems: you need to
973 break a big problem down into manageable pieces, operate on each piece and
974 then put all the pieces back together. For example, you might want to fit a
975 model to each spatial location or time point in your study, summarise data by
976 panels or collapse high-dimensional arrays to simpler summary statistics.")
977 (license license:expat)))
979 (define-public r-proto
986 (uri (cran-uri "proto" version))
988 (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
989 (build-system r-build-system)
990 (home-page "https://github.com/hadley/proto")
991 (synopsis "Prototype object-based programming")
993 "Proto is an object oriented system using object-based, also called
994 prototype-based, rather than class-based object oriented ideas.")
995 (license license:gpl2+)))
997 (define-public r-rcolorbrewer
999 (name "r-rcolorbrewer")
1004 (uri (cran-uri "RColorBrewer" version))
1006 (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
1007 (build-system r-build-system)
1008 (home-page "https://cran.r-project.org/web/packages/RColorBrewer")
1009 (synopsis "ColorBrewer palettes")
1011 "This package provides color schemes for maps (and other graphics)
1012 designed by Cynthia Brewer as described at http://colorbrewer2.org")
1013 ;; Includes code licensed under bsd-4
1014 (license license:asl2.0)))
1016 (define-public r-sendmailr
1018 (name "r-sendmailr")
1023 (uri (cran-uri "sendmailR" version))
1026 "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
1027 (properties `((upstream-name . "sendmailR")))
1028 (build-system r-build-system)
1030 `(("r-base64enc" ,r-base64enc)))
1032 "https://cran.r-project.org/web/packages/sendmailR")
1033 (synopsis "Send email using R")
1035 "This package contains a simple SMTP client which provides a portable
1036 solution for sending email, including attachments, from within R.")
1037 (license license:gpl2+)))
1039 (define-public r-stringi
1046 (uri (cran-uri "stringi" version))
1049 "0420f7zn5knyyvd3a3xa7059l4kadw0m67rfpivacqn9xn6iwkr2"))))
1050 (build-system r-build-system)
1051 (inputs `(("icu4c" ,icu4c)))
1052 (native-inputs `(("pkg-config" ,pkg-config)))
1053 (home-page "http://stringi.rexamine.com/")
1054 (synopsis "Character string processing facilities")
1056 "This package allows for fast, correct, consistent, portable, as well as
1057 convenient character string/text processing in every locale and any native
1058 encoding. Owing to the use of the ICU library, the package provides R users
1059 with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
1060 programmers. Among available features there are: pattern searching
1061 (e.g. via regular expressions), random string generation, string collation,
1062 transliteration, concatenation, date-time formatting and parsing, etc.")
1063 (license license:bsd-3)))
1065 (define-public r-stringr
1072 (uri (cran-uri "stringr" version))
1074 (base32 "1p9ip7p87gbbg4s6d3d392svvzz2b5dqdq2c8ilgvn4s78nlsq47"))))
1075 (build-system r-build-system)
1077 `(("r-glue" ,r-glue)
1078 ("r-magrittr" ,r-magrittr)
1079 ("r-stringi" ,r-stringi)))
1080 (home-page "https://github.com/hadley/stringr")
1081 (synopsis "Simple, consistent wrappers for common string operations")
1083 "Stringr is a consistent, simple and easy to use set of wrappers around
1084 the fantastic @code{stringi} package. All function and argument names (and
1085 positions) are consistent, all functions deal with \"NA\"'s and zero length
1086 vectors in the same way, and the output from one function is easy to feed into
1087 the input of another.")
1088 (license license:gpl2+)))
1090 (define-public r-reshape2
1097 (uri (cran-uri "reshape2" version))
1099 (base32 "1n0jrajpvc8hjkh9z4g8bwq63qy5vy5cgl2pzjardyih4ngcz3fq"))))
1100 (build-system r-build-system)
1102 `(("r-plyr" ,r-plyr)
1104 ("r-stringr" ,r-stringr)))
1105 (home-page "https://github.com/hadley/reshape")
1106 (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
1108 "Reshape2 is an R library to flexibly restructure and aggregate data
1109 using just two functions: melt and dcast (or acast).")
1110 (license license:expat)))
1112 (define-public r-ggplot2
1119 (uri (cran-uri "ggplot2" version))
1121 (base32 "1k136k1sr6dq1xvx6gs6gzji6hbnnwnsb5qivsxrblfv90irxhj5"))))
1122 (build-system r-build-system)
1124 `(("r-digest" ,r-digest)
1126 ("r-gtable" ,r-gtable)
1127 ("r-isoband" ,r-isoband)
1130 ("r-tibble" ,r-tibble)
1131 ("r-rlang" ,r-rlang)
1132 ("r-scales" ,r-scales)
1133 ("r-svglite" ,r-svglite) ; Needed for 'ggsave'
1134 ("r-withr" ,r-withr)))
1136 `(("r-knitr" ,r-knitr)))
1137 (home-page "https://ggplot2.tidyverse.org")
1138 (synopsis "An implementation of the grammar of graphics")
1140 "Ggplot2 is an implementation of the grammar of graphics in R. It
1141 combines the advantages of both base and lattice graphics: conditioning and
1142 shared axes are handled automatically, and you can still build up a plot step
1143 by step from multiple data sources. It also implements a sophisticated
1144 multidimensional conditioning system and a consistent interface to map data to
1145 aesthetic attributes.")
1146 (license license:gpl2+)))
1148 (define-public r-ggdendro
1154 (uri (cran-uri "ggdendro" version))
1157 "0skbj487b6f6pj2iz4yq2b9gbgb39cv5dyzhdl3w7ay1k0s5z9ph"))))
1158 (build-system r-build-system)
1160 `(("r-ggplot2" ,r-ggplot2)
1161 ("r-mass" ,r-mass)))
1163 `(("r-knitr" ,r-knitr)))
1164 (home-page "https://github.com/andrie/ggdendro")
1165 (synopsis "Create Dendrograms and Tree Diagrams Using ggplot2")
1166 (description "This is a set of tools for dendrograms and tree plots using
1167 ggplot2. The ggplot2 philosophy is to clearly separate data from the
1168 presentation. Unfortunately the plot method for dendrograms plots directly
1169 to a plot device with out exposing the data. The ggdendro package resolves
1170 this by making available functions that extract the dendrogram plot data.
1171 The package provides implementations for tree, rpart, as well as diana and
1172 agnes cluster diagrams.")
1173 (license license:gpl2+)))
1175 (define-public r-gdtools
1182 (uri (cran-uri "gdtools" version))
1185 "1p3ip0qwpg8f63jfx0b8vbac6l20ddid8xvxzkfi6i858pybnawp"))))
1186 (build-system r-build-system)
1188 `(("pkg-config" ,pkg-config)))
1191 ("freetype2" ,freetype)
1194 `(("r-rcpp" ,r-rcpp)
1195 ("r-systemfonts" ,r-systemfonts)))
1196 (home-page "https://cran.r-project.org/web/packages/gdtools")
1197 (synopsis "Utilities for graphical rendering")
1199 "The @code{gdtools} package provides functionalities to get font metrics
1200 and to generate base64 encoded string from raster matrix.")
1201 (license license:gpl3)))
1203 (define-public r-svglite
1210 (uri (cran-uri "svglite" version))
1213 "00n8bg4iligl0h24v42cka417w26zmcxrr4r6k8wdal1riwhgmi5"))))
1214 (build-system r-build-system)
1217 ("r-gdtools" ,r-gdtools)
1218 ("r-rcpp" ,r-rcpp)))
1220 `(("r-knitr" ,r-knitr)))
1221 (home-page "https://github.com/hadley/svglite")
1222 (synopsis "SVG graphics device")
1224 "@code{svglite} is a graphics device that produces clean
1225 @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
1226 hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
1227 considerably faster, produces smaller files, and leaves text as is.")
1228 (license license:gpl2+)))
1230 (define-public r-assertthat
1232 (name "r-assertthat")
1236 (uri (cran-uri "assertthat" version))
1239 "17wy5bdfzg73sg2clisg1k3zyn1adkj59x56m5nwia2k8z67zkw5"))))
1240 (build-system r-build-system)
1241 (home-page "https://github.com/hadley/assertthat")
1242 (synopsis "Easy pre and post assertions")
1244 "Assertthat is an extension to stopifnot() that makes it easy to declare
1245 the pre and post conditions that your code should satisfy, while also
1246 producing friendly error messages so that your users know what they've done
1248 (license license:gpl3+)))
1250 (define-public r-lazyeval
1256 (uri (cran-uri "lazyeval" version))
1259 "1m10i059csrcqkcn59a8wspn784alxsq3symzhn24mhhl894346n"))))
1260 (build-system r-build-system)
1261 (home-page "https://github.com/hadley/lazyeval")
1262 (synopsis "Lazy (non-standard) evaluation in R")
1264 "This package provides the tools necessary to do non-standard
1265 evaluation (NSE) in R.")
1266 (license license:gpl3+)))
1268 (define-public r-dbi
1274 (uri (cran-uri "DBI" version))
1277 "0i0kfyg43nryyka2bjlgz4x75w965224qp36wz1hl7a2lswb6ajp"))))
1278 (build-system r-build-system)
1280 `(("r-knitr" ,r-knitr)))
1281 (home-page "https://github.com/rstats-db/DBI")
1282 (synopsis "R database interface")
1284 "The DBI package provides a database interface (DBI) definition for
1285 communication between R and relational database management systems. All
1286 classes in this package are virtual and need to be extended by the various
1287 R/DBMS implementations.")
1288 (license license:lgpl2.0+)))
1293 (version "1.75.0-0")
1296 (uri (cran-uri "BH" version))
1299 "0nkgvl5qjs2a7jv0ncsrl4fqaw2pdaj7a1pncdv6kp874sci0k5f"))))
1300 (build-system r-build-system)
1301 (home-page "https://github.com/eddelbuettel/bh")
1302 (synopsis "R package providing subset of Boost headers")
1304 "This package aims to provide the most useful subset of Boost libraries
1305 for template use among CRAN packages.")
1306 (license license:boost1.0)))
1308 (define-public r-evaluate
1314 (uri (cran-uri "evaluate" version))
1317 "0a2y7j534gbgixkwj9r1z76l2vssw4g1hznzbpclc076wkdqpj58"))))
1318 (build-system r-build-system)
1319 (home-page "https://github.com/hadley/evaluate")
1320 (synopsis "Parsing and evaluation tools for R")
1322 "This package provides tools that allow you to recreate the parsing,
1323 evaluation and display of R code, with enough information that you can
1324 accurately recreate what happens at the command line. The tools can easily be
1325 adapted for other output formats, such as HTML or LaTeX.")
1326 (license license:gpl3+)))
1328 (define-public r-formatr
1334 (uri (cran-uri "formatR" version))
1337 "1nsxbrx31k3y6yql30qkrvdfyznlia2qfvwv95mfiy7m7wdn4rm3"))))
1338 (build-system r-build-system)
1339 (home-page "https://yihui.org/formatr/")
1340 (synopsis "Format R code automatically")
1342 "This package provides a function to format R source code. Spaces and
1343 indent will be added to the code automatically, and comments will be preserved
1344 under certain conditions, so that R code will be more human-readable and tidy.
1345 There is also a Shiny app as a user interface in this package.")
1346 (license license:gpl3+)))
1348 (define-public r-highr
1354 (uri (cran-uri "highr" version))
1357 "0my6idnhmmgs4q1vs40y2lh56yij2p59mpwvm53wjs2zk6x1zl2b"))))
1358 (build-system r-build-system)
1359 (home-page "https://github.com/yihui/highr")
1360 (synopsis "Syntax highlighting for R source code")
1362 "This package provides syntax highlighting for R source code. Currently
1363 it supports LaTeX and HTML output. Source code of other languages is
1364 supported via Andre Simon's highlight package.")
1365 (license license:gpl3+)))
1367 (define-public r-mime
1373 (uri (cran-uri "mime" version))
1376 "107sqarmyhxlch5nrg796i5z03p9mshskisiq2fm628ajk99gkrc"))))
1377 (build-system r-build-system)
1378 (home-page "https://github.com/yihui/mime")
1379 (synopsis "R package to map filenames to MIME types")
1381 "This package guesses the MIME type from a filename extension using the
1382 data derived from /etc/mime.types in UNIX-type systems.")
1383 (license license:gpl2)))
1385 (define-public r-markdown
1391 (uri (cran-uri "markdown" version))
1394 "06zwbrp14bri3470anadd7dvgmw06xf8df6v2pk64wx3f9sd934d"))))
1395 (build-system r-build-system)
1396 ;; Skip check phase because the tests require the r-knitr package to be
1397 ;; installed. This prevents installation failures. Knitr normally
1398 ;; shouldn't be available since r-markdown is a dependency of the r-knitr
1400 (arguments `(#:tests? #f))
1402 `(("r-mime" ,r-mime)
1403 ("r-xfun" ,r-xfun)))
1404 (home-page "https://github.com/rstudio/markdown")
1405 (synopsis "Markdown rendering for R")
1407 "This package provides R bindings to the Sundown Markdown rendering
1408 library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
1409 syntax that can be converted to XHTML or other formats.")
1410 (license license:gpl2)))
1412 (define-public r-yaml
1418 (uri (cran-uri "yaml" version))
1421 "10r7g26x73am45niigm3k466030nymnr3v3fjljafzrr5aybf58i"))))
1422 (build-system r-build-system)
1423 (home-page "https://cran.r-project.org/web/packages/yaml/")
1424 (synopsis "Methods to convert R data to YAML and back")
1426 "This package implements the libyaml YAML 1.1 parser and
1427 emitter (http://pyyaml.org/wiki/LibYAML) for R.")
1428 (license license:bsd-3)))
1430 (define-public r-knitr
1436 (uri (cran-uri "knitr" version))
1439 "0gn9qwc5762a6j0iywfwhalni52g228dcy4bl4di6d52cqsv3ars"))))
1440 (build-system r-build-system)
1442 `(("r-evaluate" ,r-evaluate)
1443 ("r-highr" ,r-highr)
1444 ("r-markdown" ,r-markdown)
1445 ("r-stringr" ,r-stringr)
1447 ("r-yaml" ,r-yaml)))
1448 (home-page "https://yihui.org/knitr/")
1449 (synopsis "General-purpose package for dynamic report generation in R")
1451 "This package provides a general-purpose tool for dynamic report
1452 generation in R using Literate Programming techniques.")
1453 ;; The code is released under any version of the GPL. As it is used by
1454 ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
1456 (license license:gpl2+)))
1458 (define-public r-knitrbootstrap
1460 (name "r-knitrbootstrap")
1465 (uri (cran-uri "knitrBootstrap" version))
1468 "1aj60j7f0gcs120fdrnfbnb7vk7lfn1phil0mghg6a5zldz4cqs3"))))
1469 (properties `((upstream-name . "knitrBootstrap")))
1470 (build-system r-build-system)
1472 `(("r-knitr" ,r-knitr)
1473 ("r-rmarkdown" ,r-rmarkdown)
1474 ("r-markdown" ,r-markdown)))
1475 (home-page "https://github.com/jimhester/knitrBootstrap")
1476 (synopsis "Knitr bootstrap framework")
1478 "This package provides a framework to create Bootstrap 3 HTML reports
1479 from knitr Rmarkdown.")
1480 (license license:expat)))
1482 (define-public r-microbenchmark
1484 (name "r-microbenchmark")
1488 (uri (cran-uri "microbenchmark" version))
1491 "1xl4m4yl4h2zcjiz8wsa7f3sh55qg2xr3sgpvz18rlix6b3173r6"))))
1492 (build-system r-build-system)
1493 (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
1494 (synopsis "Accurate timing functions for R")
1496 "This package provides infrastructure to accurately measure and compare
1497 the execution time of R expressions.")
1498 (license license:bsd-2)))
1500 (define-public r-pryr
1506 (uri (cran-uri "pryr" version))
1509 "06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k"))))
1510 (build-system r-build-system)
1512 `(("r-stringr" ,r-stringr)
1513 ("r-codetools" ,r-codetools)))
1515 `(("r-rcpp" ,r-rcpp)))
1516 (home-page "https://github.com/hadley/pryr")
1517 (synopsis "Tools for computing on the R language")
1519 "This package provides useful tools to pry back the covers of R and
1520 understand the language at a deeper level.")
1521 (license license:gpl2)))
1523 (define-public r-memoise
1529 (uri (cran-uri "memoise" version))
1532 "034qfc2xlh30x1q2vya239w34a3ir3y2fwnx2agbgbi6592zjxmj"))))
1533 (build-system r-build-system)
1535 `(("r-digest" ,r-digest)))
1536 (home-page "https://github.com/hadley/memoise")
1537 (synopsis "Memoise functions for R")
1539 "This R package caches the results of a function so that when
1540 you call it again with the same arguments it returns the pre-computed value.")
1541 (license license:expat)))
1543 (define-public r-crayon
1549 (uri (cran-uri "crayon" version))
1552 "0s7s6vc3ww8pzanpjisym4jjvwcc5pi2qg8srx7jqlz9j3wrnvpw"))))
1553 (build-system r-build-system)
1555 `(("r-memoise" ,r-memoise)))
1556 (home-page "https://github.com/gaborcsardi/crayon")
1557 (synopsis "Colored terminal output for R")
1559 "Colored terminal output on terminals that support ANSI color and
1560 highlight codes. It also works in Emacs ESS. ANSI color support is
1561 automatically detected. Colors and highlighting can be combined and nested.
1562 New styles can also be created easily. This package was inspired by the
1563 \"chalk\" JavaScript project.")
1564 (license license:expat)))
1566 (define-public r-praise
1573 (uri (cran-uri "praise" version))
1576 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
1577 (build-system r-build-system)
1578 (home-page "https://github.com/gaborcsardi/praise")
1579 (synopsis "Functions to praise users")
1581 "This package provides template functions to assist in building friendly
1582 R packages that praise their users.")
1583 (license license:expat)))
1585 (define-public r-testthat
1591 (uri (cran-uri "testthat" version))
1594 "1l1s4jgmgbsf711ma5i58ssgkz98an7hijcxvwfz314nf5fc8zr9"))))
1595 (build-system r-build-system)
1597 `(("r-brio" ,r-brio)
1598 ("r-callr" ,r-callr)
1600 ("r-crayon" ,r-crayon)
1602 ("r-digest" ,r-digest)
1603 ("r-ellipsis" ,r-ellipsis)
1604 ("r-evaluate" ,r-evaluate)
1605 ("r-jsonlite" ,r-jsonlite)
1606 ("r-lifecycle" ,r-lifecycle)
1607 ("r-magrittr" ,r-magrittr)
1608 ("r-pkgload" ,r-pkgload)
1609 ("r-praise" ,r-praise)
1610 ("r-processx" ,r-processx)
1613 ("r-rlang" ,r-rlang)
1614 ("r-waldo" ,r-waldo)
1615 ("r-withr" ,r-withr)))
1617 `(("r-knitr" ,r-knitr)))
1618 (home-page "https://github.com/hadley/testthat")
1619 (synopsis "Unit testing for R")
1621 "This package provides a unit testing system for R designed to be fun,
1622 flexible and easy to set up.")
1623 (license license:expat)))
1631 (uri (cran-uri "R6" version))
1634 "00ifi2kwa7kn67xf0z1w6jfdicjczygbyi5mhfw2qlzc4sbazhdf"))))
1635 (build-system r-build-system)
1636 (home-page "https://github.com/wch/R6/")
1637 (synopsis "Classes with reference semantics in R")
1639 "The R6 package allows the creation of classes with reference semantics,
1640 similar to R's built-in reference classes. Compared to reference classes, R6
1641 classes are simpler and lighter-weight, and they are not built on S4 classes
1642 so they do not require the methods package. These classes allow public and
1643 private members, and they support inheritance, even when the classes are
1644 defined in different packages.")
1645 (license license:expat)))
1647 (define-public r-rlang
1653 (uri (cran-uri "rlang" version))
1656 "0ximv89f6zymnwms121k1jfvvflrdm3pmmf5xyvz56f1qiq04lq7"))))
1657 (build-system r-build-system)
1658 (home-page "http://rlang.tidyverse.org")
1659 (synopsis "Functions for base types, core R and Tidyverse features")
1660 (description "This package provides a toolbox for working with base types,
1661 core R features like the condition system, and core @code{Tidyverse} features
1662 like tidy evaluation.")
1663 (license license:gpl3)))
1665 (define-public r-tibble
1672 (uri (cran-uri "tibble" version))
1675 "142i34h53b8w8jkh3l8y3xsqfvvgp7ybfbv830bjky7cymxjvj8w"))))
1676 (build-system r-build-system)
1679 ("r-crayon" ,r-crayon)
1680 ("r-ellipsis" ,r-ellipsis)
1681 ("r-fansi" ,r-fansi)
1682 ("r-lifecycle" ,r-lifecycle)
1683 ("r-magrittr" ,r-magrittr)
1684 ("r-pkgconfig" ,r-pkgconfig)
1685 ("r-pillar" ,r-pillar)
1686 ("r-rlang" ,r-rlang)
1687 ("r-vctrs" ,r-vctrs)))
1689 `(("r-knitr" ,r-knitr)))
1690 (home-page "https://github.com/hadley/tibble")
1691 (synopsis "Simple data frames")
1693 "This package provides a @code{tbl_df} class that offers better checking
1694 and printing capabilities than traditional data frames.")
1695 (license license:expat)))
1697 (define-public r-dplyr
1703 (uri (cran-uri "dplyr" version))
1706 "0hc4wnx70mrsb3s0k5ywffhnky3hznlrvvs22m6ls5crgvcak898"))))
1707 (build-system r-build-system)
1709 `(("r-ellipsis" ,r-ellipsis)
1710 ("r-generics" ,r-generics)
1712 ("r-lifecycle" ,r-lifecycle)
1713 ("r-magrittr" ,r-magrittr)
1715 ("r-rlang" ,r-rlang)
1716 ("r-tibble" ,r-tibble)
1717 ("r-tidyselect" ,r-tidyselect)
1718 ("r-vctrs" ,r-vctrs)))
1720 `(("r-knitr" ,r-knitr)))
1721 (home-page "https://github.com/hadley/dplyr")
1722 (synopsis "Tools for working with data frames in R")
1724 "dplyr is the next iteration of plyr. It is focussed on tools for
1725 working with data frames. It has three main goals: 1) identify the most
1726 important data manipulation tools needed for data analysis and make them easy
1727 to use in R; 2) provide fast performance for in-memory data by writing key
1728 pieces of code in C++; 3) use the same code interface to work with data no
1729 matter where it is stored, whether in a data frame, a data table or
1731 (license license:expat)))
1733 (define-public r-dbplyr
1740 (uri (cran-uri "dbplyr" version))
1743 "0sa0ggirvfn8j9y4cvhj04z93h6979jm4knjzahdvyzyxhv1kmzc"))))
1744 (build-system r-build-system)
1746 `(("r-assertthat" ,r-assertthat)
1749 ("r-dplyr" ,r-dplyr)
1751 ("r-lifecycle" ,r-lifecycle)
1752 ("r-magrittr" ,r-magrittr)
1753 ("r-purrr" ,r-purrr)
1755 ("r-rlang" ,r-rlang)
1756 ("r-tibble" ,r-tibble)
1757 ("r-tidyselect" ,r-tidyselect)
1758 ("r-withr" ,r-withr)))
1760 `(("r-knitr" ,r-knitr)))
1761 (home-page "https://github.com/tidyverse/dbplyr")
1762 (synopsis "Dplyr back end for databases")
1764 "This package provides a dplyr back end for databases that allows you to
1765 work with remote database tables as if they are in-memory data frames. Basic
1766 features works with any database that has a @code{DBI} back end; more advanced
1767 features require SQL translation to be provided by the package author.")
1768 (license license:expat)))
1770 (define-public r-acepack
1777 (uri (cran-uri "acepack" version))
1780 "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
1781 (build-system r-build-system)
1783 `(("gfortran" ,gfortran)))
1784 (home-page "https://cran.r-project.org/web/packages/acepack")
1785 (synopsis "Functions for regression transformations")
1787 "This package provides ACE and AVAS methods for choosing regression
1789 (license license:expat)))
1791 (define-public r-formula
1798 (uri (cran-uri "Formula" version))
1801 "1bsw282i5m8rlirbhz7hqvf25zbxschk7yrp152whbzdnmry6w6b"))))
1802 (properties `((upstream-name . "Formula")))
1803 (build-system r-build-system)
1804 (home-page "https://cran.r-project.org/web/packages/Formula")
1805 (synopsis "Extended model formulas")
1807 "This package provides a new class @code{Formula}, which extends the base
1808 class @code{formula}. It supports extended formulas with multiple parts of
1809 regressors on the right-hand side and/or multiple responses on the left-hand
1811 (license (list license:gpl2+ license:gpl3+))))
1813 (define-public r-locfit
1820 (uri (cran-uri "locfit" version))
1823 "1vcw16qww4v4547w0gfvhqg60l051bsdlxa6zfcgcj9xbxf6dlyr"))))
1824 (build-system r-build-system)
1826 `(("r-lattice" ,r-lattice)))
1827 (home-page "https://cran.r-project.org/web/packages/locfit")
1828 (synopsis "Local regression, likelihood and density estimation")
1830 "This package provides functions used for local regression, likelihood
1831 and density estimation.")
1832 (license (list license:gpl2+ license:gpl3+))))
1834 (define-public r-chron
1840 (uri (cran-uri "chron" version))
1843 "0p9zz96jfyf139924hdwkzhr8knkjvx6547ac53rknm3a6wwngl6"))))
1844 (build-system r-build-system)
1845 (home-page "https://cran.r-project.org/web/packages/chron")
1846 (synopsis "Chronological R objects which can handle dates and times")
1848 "This package provides chronological R objects which can handle dates and
1850 (license license:gpl2)))
1852 (define-public r-data-table
1854 (name "r-data-table")
1858 (uri (cran-uri "data.table" version))
1861 "16ryrpzl86krww5nx7a97i09y5xqld4lw4d9pa1vzjl99x6ds36m"))))
1862 (build-system r-build-system)
1866 `(("pkg-config" ,pkg-config)
1867 ("r-knitr" ,r-knitr)))
1868 (home-page "https://github.com/Rdatatable/data.table/wiki")
1869 (synopsis "Enhanced version of data.frame R object")
1871 "The R package @code{data.table} is an extension of @code{data.frame}
1872 providing functions for fast aggregation of large data (e.g. 100GB in RAM),
1873 fast ordered joins, fast add/modify/delete of columns by group, column listing
1874 and fast file reading.")
1875 (license license:gpl3+)))
1877 (define-public r-xtable
1884 (uri (cran-uri "xtable" version))
1887 "077xfm0gphvhsay75amd9v90zk57kjgrrlgih04fyrbqqblc1gjs"))))
1888 (build-system r-build-system)
1890 `(("r-knitr" ,r-knitr))) ; for vignettes
1891 (home-page "http://xtable.r-forge.r-project.org/")
1892 (synopsis "Export R tables to LaTeX or HTML")
1894 "This package provides tools to export R data as LaTeX and HTML tables.")
1895 (license license:gpl2+)))
1897 (define-public python-patsy
1899 (name "python-patsy")
1903 (uri (pypi-uri "patsy" version))
1906 "149rbrdzwns0ay88caf1zsm1r53v1q5np1mrb36na50y432cw5gi"))))
1907 (build-system python-build-system)
1910 (modify-phases %standard-phases
1912 (lambda _ (invoke "nosetests" "-v"))))))
1914 `(("python-numpy" ,python-numpy)
1915 ("python-scipy" ,python-scipy)
1916 ("python-six" ,python-six)))
1918 `(("python-nose" ,python-nose)))
1919 (home-page "https://github.com/pydata/patsy")
1920 (synopsis "Describe statistical models and build design matrices")
1922 "Patsy is a Python package for describing statistical models and for
1923 building design matrices.")
1924 ;; The majority of the code is distributed under BSD-2. The module
1925 ;; patsy.compat contains code derived from the Python standard library,
1926 ;; and is covered by the PSFL.
1927 (license (list license:bsd-2 license:psfl))))
1929 (define-public python2-patsy
1930 (package-with-python2 python-patsy))
1932 (define-public python-statsmodels
1934 (name "python-statsmodels")
1939 (uri (pypi-uri "statsmodels" version))
1942 "1w6mf8b86vizi2895j11szqryr2v1ckjig3wp9fv94aslfh3zpjv"))))
1943 (build-system python-build-system)
1945 `(;; The test suite is very large and rather brittle. Tests often fail
1946 ;; because of minor changes in dependencies that upstream hasn't fixed
1947 ;; in a new release.
1950 (modify-phases %standard-phases
1951 (add-after 'unpack 'set-matplotlib-backend-to-agg
1953 ;; Set the matplotlib backend to Agg to avoid problems using the
1954 ;; GTK backend without a display.
1955 (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py")
1956 '("statsmodels/tsa/vector_ar/tests/test_var.py"
1957 "statsmodels/duration/tests/test_survfunc.py"))
1958 (("import matplotlib\\.pyplot as plt" line)
1959 (string-append "import matplotlib;matplotlib.use('Agg');"
1963 `(("python-numpy" ,python-numpy)
1964 ("python-scipy" ,python-scipy)
1965 ("python-pandas" ,python-pandas)
1966 ("python-patsy" ,python-patsy)
1967 ("python-matplotlib" ,python-matplotlib)))
1969 `(("python-cython" ,python-cython)
1970 ("python-nose" ,python-nose)
1971 ("python-sphinx" ,python-sphinx)))
1972 (home-page "http://statsmodels.sourceforge.net/")
1973 (synopsis "Statistical modeling and econometrics in Python")
1975 "Statsmodels is a Python package that provides a complement to scipy for
1976 statistical computations including descriptive statistics and estimation and
1977 inference for statistical models.")
1978 (license license:bsd-3)))
1980 (define-public python2-statsmodels
1981 (let ((stats (package-with-python2 python-statsmodels)))
1982 (package (inherit stats)
1984 `(("python2-pytz" ,python2-pytz)
1985 ("python2-numpy" ,python2-numpy)
1986 ("python2-scipy" ,python2-scipy)
1987 ("python2-pandas" ,python2-pandas)
1988 ("python2-patsy" ,python2-patsy)
1989 ("python2-matplotlib" ,python2-matplotlib))))))
1991 (define-public r-coda
1997 (uri (cran-uri "coda" version))
2000 "13z5dwfpnyyhpsbpg4xr9g5c1685jhqj90f4x4qkcykr6kykqba2"))))
2001 (build-system r-build-system)
2003 `(("r-lattice" ,r-lattice)))
2004 (home-page "https://cran.r-project.org/web/packages/coda")
2005 (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
2006 (description "This package provides functions for summarizing and plotting
2007 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
2008 diagnostic tests of convergence to the equilibrium distribution of the Markov
2010 (license license:gpl2+)))
2012 (define-public r-ade4
2019 (uri (cran-uri "ade4" version))
2022 "142m70im8yd4q01q7z02y3ia0f66yh4ikdznv0ps6c7yyigs5mwv"))))
2023 (build-system r-build-system)
2025 `(("r-mass" ,r-mass)
2026 ("r-pixmap" ,r-pixmap)
2027 ("r-progress" ,r-progress)
2029 (home-page "http://pbil.univ-lyon1.fr/ADE-4")
2030 (synopsis "Multivariate data analysis and graphical display")
2032 "The ade4 package contains data analysis functions to analyze ecological
2033 and environmental data in the framework of Euclidean exploratory methods.")
2034 (license license:gpl2+)))
2036 (define-public r-xml2
2043 (uri (cran-uri "xml2" version))
2046 "1kx400v62xkd5xal7rzz7jcarz94ac8g1sh4i2dqr78qwgkzj8nz"))))
2047 (build-system r-build-system)
2049 `(("libxml2" ,libxml2)
2052 `(("pkg-config" ,pkg-config)
2053 ("r-knitr" ,r-knitr)))
2054 (home-page "https://github.com/hadley/xml2")
2055 (synopsis "Parse XML with R")
2057 "This package provides a simple, consistent interface to working with XML
2058 files in R. It is built on top of the libxml2 C library.")
2059 (license license:gpl2+)))
2061 (define-public r-multitaper
2063 (name "r-multitaper")
2068 (uri (cran-uri "multitaper" version))
2071 "1gm3wr8xqpqiby7q1dr3zxim77v0bvvrqi0hlazf5g3gnkrp2zc3"))))
2072 (build-system r-build-system)
2074 `(("gfortran" ,gfortran)))
2075 (home-page "https://github.com/wesleyburr/multitaper/")
2076 (synopsis "Multitaper spectral analysis tools")
2078 "This package implements multitaper spectral estimation
2079 techniques using prolate spheroidal sequences (Slepians) and sine
2080 tapers for time series analysis. It includes an adaptive weighted
2081 multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
2082 F-test, and complex demodulation. The Slepians sequences are
2083 generated efficiently using a tridiagonal matrix solution, and
2084 jackknifed confidence intervals are available for most estimates.")
2085 (license license:gpl2+)))
2087 (define-public r-rversions
2089 (name "r-rversions")
2093 (uri (cran-uri "rversions" version))
2096 "0ghpla5r3d6zh5dn6d6ii5p0a952lcdv004m88fk8r9k76vz88rm"))))
2097 (build-system r-build-system)
2099 `(("r-curl" ,r-curl)
2100 ("r-xml2" ,r-xml2)))
2101 (home-page "https://github.com/metacran/rversions")
2102 (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
2104 "This package provides functions to query the main R repository to find
2105 the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
2106 previous R versions and their release dates.")
2107 (license license:expat)))
2109 (define-public r-whisker
2115 (uri (cran-uri "whisker" version))
2118 "1a7vz0dk95xfjvi38wbpw8vmf5qn3g8p490msz2rw0piwidmk1ks"))))
2119 (build-system r-build-system)
2120 (home-page "https://github.com/edwindj/whisker")
2121 (synopsis "Logicless mustache templating for R")
2123 "This package provides logicless templating, with a syntax that is not
2125 (license license:gpl3+)))
2127 (define-public r-backports
2129 (name "r-backports")
2134 (uri (cran-uri "backports" version))
2137 "1mf2nz78l97lbxyagv55bcxrny51ds8g28h307cfa1g3ayylp0x2"))))
2138 (build-system r-build-system)
2139 (home-page "https://cran.r-project.org/web/packages/backports")
2140 (synopsis "Reimplementations of functions introduced since R 3.0.0")
2142 "Provides implementations of functions which have been introduced in R
2143 since version 3.0.0. The backports are conditionally exported which results
2144 in R resolving the function names to the version shipped with R (if available)
2145 and uses the implemented backports as fallback. This way package developers
2146 can make use of the new functions without worrying about the minimum required
2148 (license license:gpl2+)))
2150 (define-public r-checkmate
2152 (name "r-checkmate")
2157 (uri (cran-uri "checkmate" version))
2160 "193gkifr9spp0x0rwnjq1spdhjkfkh4mv27iklskcj604075phhd"))))
2161 (build-system r-build-system)
2163 `(("r-backports" ,r-backports)))
2164 (home-page "https://github.com/mllg/checkmate")
2165 (synopsis "Fast and versatile argument checks")
2167 "This package provides tests and assertions to perform frequent argument
2168 checks. A substantial part of the package was written in C to minimize any
2169 worries about execution time overhead.")
2170 (license license:bsd-3)))
2172 (define-public r-bbmisc
2179 (uri (cran-uri "BBmisc" version))
2182 "1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y"))))
2183 (properties `((upstream-name . "BBmisc")))
2184 (build-system r-build-system)
2186 `(("r-checkmate" ,r-checkmate)))
2187 (home-page "https://github.com/berndbischl/BBmisc")
2188 (synopsis "Miscellaneous functions for R package development")
2190 "This package provides miscellaneous helper functions for the development
2192 (license license:bsd-3)))
2194 (define-public r-fail
2201 (uri (cran-uri "fail" version))
2204 "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
2205 (build-system r-build-system)
2207 `(("r-bbmisc" ,r-bbmisc)
2208 ("r-checkmate" ,r-checkmate)))
2209 (home-page "https://github.com/mllg/fail")
2210 (synopsis "File abstraction interface layer (FAIL)")
2212 "This package provides a more comfortable interface to work with R data
2213 or source files in a key-value fashion.")
2214 (license license:bsd-3)))
2216 (define-public r-batchjobs
2218 (name "r-batchjobs")
2223 (uri (cran-uri "BatchJobs" version))
2226 "1zz4sspj596pijxlz321g0jy2rg9ki83j6fihbwisjwr66p2vk1m"))))
2227 (properties `((upstream-name . "BatchJobs")))
2228 (build-system r-build-system)
2230 `(("r-backports" ,r-backports)
2231 ("r-bbmisc" ,r-bbmisc)
2233 ("r-checkmate" ,r-checkmate)
2234 ("r-data-table" ,r-data-table)
2236 ("r-digest" ,r-digest)
2237 ("r-rsqlite" ,r-rsqlite)
2238 ("r-sendmailr" ,r-sendmailr)
2239 ("r-stringi" ,r-stringi)))
2240 (home-page "https://github.com/tudo-r/BatchJobs")
2241 (synopsis "Batch computing with R")
2243 "This package provides @code{Map}, @code{Reduce} and @code{Filter}
2244 variants to generate jobs on batch computing systems like PBS/Torque, LSF,
2245 SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
2246 (license license:bsd-2)))
2248 (define-public r-brew
2254 (uri (cran-uri "brew" version))
2257 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
2258 (build-system r-build-system)
2259 (home-page "https://cran.r-project.org/web/packages/brew")
2260 (synopsis "Templating framework for report generation")
2262 "The brew package implements a templating framework for mixing text and R
2263 code for report generation. The template syntax is similar to PHP, Ruby's erb
2264 module, Java Server Pages, and Python's psp module.")
2265 (license license:gpl2+)))
2267 (define-public r-desc
2274 (uri (cran-uri "desc" version))
2277 "1s6s13fk6sxwcj8wzkwxl9vr33153xx11p5wi9avqx3rzkabavz6"))))
2278 (build-system r-build-system)
2280 `(("r-assertthat" ,r-assertthat)
2281 ("r-crayon" ,r-crayon)
2283 ("r-rprojroot" ,r-rprojroot)))
2284 (home-page "https://github.com/r-pkgs/desc")
2285 (synopsis "Manipulate DESCRIPTION Files")
2287 "This package provides tools to read, write, create, and manipulate
2288 DESCRIPTION files. It is intended for packages that create or manipulate
2290 (license license:expat)))
2292 (define-public r-commonmark
2294 (name "r-commonmark")
2299 (uri (cran-uri "commonmark" version))
2302 "024iz1qp2kv6iz6y69ir0jk3qhjps86rhkzlcmhqsxx97rx7cjni"))))
2303 (build-system r-build-system)
2304 (home-page "https://cran.r-project.org/web/packages/commonmark")
2305 (synopsis "CommonMark and Github Markdown Rendering in R")
2307 "The CommonMark specification defines a rationalized version of markdown
2308 syntax. This package uses the @code{cmark} reference implementation for
2309 converting markdown text into various formats including HTML, LaTeX and groff
2310 man. In addition, it exposes the markdown parse tree in XML format. The latest
2311 version of this package also adds support for Github extensions including
2312 tables, autolinks and strikethrough text.")
2313 (license license:bsd-2)))
2315 (define-public r-roxygen2
2321 (uri (cran-uri "roxygen2" version))
2324 "0qc8akwfwmaqsjaza87f5fi0zk6sh3l6j3assbs6chvx0gnmvidx"))))
2325 (build-system r-build-system)
2327 `(("r-brew" ,r-brew)
2328 ("r-commonmark" ,r-commonmark)
2330 ("r-digest" ,r-digest)
2331 ("r-knitr" ,r-knitr)
2332 ("r-pkgload" ,r-pkgload)
2333 ("r-purrr" ,r-purrr)
2336 ("r-rlang" ,r-rlang)
2337 ("r-stringi" ,r-stringi)
2338 ("r-stringr" ,r-stringr)
2339 ("r-xml2" ,r-xml2)))
2341 `(("r-knitr" ,r-knitr)))
2342 (home-page "https://github.com/klutometis/roxygen")
2343 (synopsis "In-source documentation system for R")
2345 "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
2346 collation, and NAMESPACE files.")
2347 (license license:gpl2+)))
2349 (define-public r-openssl
2356 (uri (cran-uri "openssl" version))
2359 "0sc2skh1nz7jj65p0pq4a6bl8jza6lyi4zvmvwndzxfgivgh281l"))))
2360 (build-system r-build-system)
2362 `(("libressl" ,libressl)))
2364 `(("pkg-config" ,pkg-config)
2365 ("r-knitr" ,r-knitr)))
2367 `(("r-askpass" ,r-askpass)))
2368 (home-page "https://github.com/jeroenooms/openssl")
2369 (synopsis "Toolkit for encryption, signatures and certificates")
2371 "This package provides R bindings to OpenSSL libssl and libcrypto, plus
2372 custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
2373 and P-521. Cryptographic signatures can either be created and verified
2374 manually or via x509 certificates. AES block cipher is used in CBC mode for
2375 symmetric encryption; RSA for asymmetric (public key) encryption. High-level
2376 envelope functions combine RSA and AES for encrypting arbitrary sized data.
2377 Other utilities include key generators, hash functions (md5, sha1, sha256,
2378 etc), base64 encoder, a secure random number generator, and @code{bignum} math
2379 methods for manually performing crypto calculations on large multibyte
2381 (license license:expat)))
2383 (define-public r-httr
2389 (uri (cran-uri "httr" version))
2392 "1y8y1g1dkgv9jafrk1kj6pzxpw95c0rr9lplblfq2byrs1pfsas6"))))
2393 (build-system r-build-system)
2395 `(("r-curl" ,r-curl)
2396 ("r-jsonlite" ,r-jsonlite)
2397 ("r-openssl" ,r-openssl)
2401 `(("r-knitr" ,r-knitr)))
2402 (home-page "https://github.com/hadley/httr")
2403 (synopsis "Tools for working with URLs and HTTP")
2405 "The aim of httr is to provide a wrapper for RCurl customised to the
2406 demands of modern web APIs. It provides useful tools for working with HTTP
2407 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
2408 functions make it easy to control additional request components.")
2409 (license license:expat)))
2411 (define-public r-git2r
2417 (uri (cran-uri "git2r" version))
2420 "1wjmbs9cmm16pm3g0rmqp7cxxyh95m5lgx4fx5bpgj6j466i8vff"))))
2421 (build-system r-build-system)
2423 `(("libgit2" ,libgit2)
2426 `(("pkg-config" ,pkg-config)))
2427 (home-page "https://github.com/ropensci/git2r")
2428 (synopsis "Access Git repositories with R")
2430 "This package provides an R interface to the libgit2 library, which is a
2431 pure C implementation of the Git core methods.")
2432 ;; GPLv2 only with linking exception.
2433 (license license:gpl2)))
2435 (define-public r-rstudioapi
2437 (name "r-rstudioapi")
2441 (uri (cran-uri "rstudioapi" version))
2444 "12vdfzzjc6mv4h105l8cp108j3hjk0mqmg23m6mqr3jarfymphxa"))))
2445 (build-system r-build-system)
2447 `(("r-knitr" ,r-knitr)))
2448 (home-page "https://cran.r-project.org/web/packages/rstudioapi")
2449 (synopsis "Safely access the RStudio API")
2451 "This package provides functions to access the RStudio API and provide
2452 informative error messages when it's not available.")
2453 (license license:expat)))
2455 (define-public r-devtools
2461 (uri (cran-uri "devtools" version))
2464 "0vcqs4c5dfjs2ddkclv3z7zzix2zrnrxvzax8hjvjszgp8362275"))))
2465 (build-system r-build-system)
2467 `(("r-callr" ,r-callr)
2472 ("r-ellipsis" ,r-ellipsis)
2474 ("r-jsonlite" ,r-jsonlite)
2475 ("r-memoise" ,r-memoise)
2476 ("r-pkgbuild" ,r-pkgbuild)
2477 ("r-pkgload" ,r-pkgload)
2478 ("r-rcmdcheck" ,r-rcmdcheck)
2479 ("r-remotes" ,r-remotes)
2480 ("r-rlang" ,r-rlang)
2481 ("r-roxygen2" ,r-roxygen2)
2482 ("r-rstudioapi" ,r-rstudioapi)
2483 ("r-rversions" ,r-rversions)
2484 ("r-sessioninfo" ,r-sessioninfo)
2485 ("r-testthat" ,r-testthat)
2486 ("r-usethis" ,r-usethis)
2487 ("r-withr" ,r-withr)))
2489 `(("r-knitr" ,r-knitr)))
2490 (home-page "https://github.com/hadley/devtools")
2491 (synopsis "Tools to make developing R packages easier")
2492 (description "The devtools package is a collection of package development
2493 tools to simplify the devolpment of R packages.")
2494 (license license:gpl2+)))
2496 (define-public r-withr
2502 (uri (cran-uri "withr" version))
2505 "1y0l6zbpg0wix60r58yk452aqvx4rd0bk7zw9b90lzniwk3wvr7d"))))
2506 (build-system r-build-system)
2508 `(("r-knitr" ,r-knitr)))
2509 (home-page "https://github.com/jimhester/withr")
2510 (synopsis "Run code with temporarily modified global state")
2512 "This package provides a set of functions to run R code in an environment
2513 in which global state has been temporarily modified. Many of these functions
2514 were originally a part of the r-devtools package.")
2515 (license license:gpl2+)))
2517 (define-public r-hms
2524 (uri (cran-uri "hms" version))
2527 "0qn9lvpkqrpxck88nf0zbff43vd7d6s1ibg58qfr3w14sw1yj14p"))))
2528 (build-system r-build-system)
2530 `(("r-ellipsis" ,r-ellipsis)
2531 ("r-lifecycle" ,r-lifecycle)
2532 ("r-pkgconfig" ,r-pkgconfig)
2533 ("r-rlang" ,r-rlang)
2534 ("r-vctrs" ,r-vctrs)))
2535 (home-page "https://github.com/rstats-db/hms")
2536 (synopsis "Pretty time of day")
2538 "This package implements an S3 class for storing and formatting
2539 time-of-day values, based on the @code{difftime} class.")
2540 (license license:gpl3+)))
2542 (define-public r-readr
2548 (uri (cran-uri "readr" version))
2551 "1fa67h4l9d30ig460xizgzl115i9pm3bk9dvsbrw6awbmf51ic82"))))
2552 (build-system r-build-system)
2555 ("r-clipr" ,r-clipr)
2556 ("r-cpp11" ,r-cpp11)
2557 ("r-crayon" ,r-crayon)
2559 ("r-lifecycle" ,r-lifecycle)
2560 ("r-tibble" ,r-tibble)
2562 ("r-rlang" ,r-rlang)
2565 `(("r-knitr" ,r-knitr)))
2566 (home-page "https://github.com/hadley/readr")
2567 (synopsis "Read tabular data")
2569 "This package provides functions to read flat or tabular text files from
2570 disk (or a connection).")
2571 (license license:gpl2+)))
2573 (define-public r-plotrix
2579 (uri (cran-uri "plotrix" version))
2582 "104llmr6dvlcnfpmd8zbdlv63k79djc4qqgadjavj4v4cmz1zkcc"))))
2583 (build-system r-build-system)
2584 (home-page "https://cran.r-project.org/web/packages/plotrix")
2585 (synopsis "Various plotting functions")
2587 "This package provides lots of plotting, various labeling, axis and color
2588 scaling functions for R.")
2589 (license license:gpl2+)))
2591 (define-public r-gridbase
2597 (uri (cran-uri "gridBase" version))
2600 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
2601 (build-system r-build-system)
2602 (home-page "https://cran.r-project.org/web/packages/gridBase")
2603 (synopsis "Integration of base and grid graphics")
2605 "This package provides an integration of base and grid graphics for R.")
2606 (license license:gpl2+)))
2608 (define-public r-latticeextra
2610 (name "r-latticeextra")
2615 (uri (cran-uri "latticeExtra" version))
2618 "04fzwcqs594rk5qp98yilh3kdh3sw4xf8wld5rp94ggpaqfw7bbc"))))
2619 (properties `((upstream-name . "latticeExtra")))
2620 (build-system r-build-system)
2622 `(("r-jpeg" ,r-jpeg)
2623 ("r-lattice" ,r-lattice)
2625 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2626 (home-page "http://latticeextra.r-forge.r-project.org/")
2627 (synopsis "Extra graphical utilities based on lattice")
2629 "Building on the infrastructure provided by the lattice package, this
2630 package provides several new high-level graphics functions and methods, as
2631 well as additional utilities such as panel and axis annotation functions.")
2632 (license license:gpl2+)))
2634 (define-public r-rcpparmadillo
2636 (name "r-rcpparmadillo")
2637 (version "0.10.1.2.2")
2640 (uri (cran-uri "RcppArmadillo" version))
2643 "0sfhk4mh39ab1y7pmlnijg4w65yz7pfsyjlqy931zdpjzh1kfciq"))))
2644 (properties `((upstream-name . "RcppArmadillo")))
2645 (build-system r-build-system)
2647 `(("r-rcpp" ,r-rcpp)))
2648 (home-page "https://github.com/RcppCore/RcppArmadillo")
2649 (synopsis "Rcpp integration for the Armadillo linear algebra library")
2651 "Armadillo is a templated C++ linear algebra library that aims towards a
2652 good balance between speed and ease of use. Integer, floating point and
2653 complex numbers are supported, as well as a subset of trigonometric and
2654 statistics functions. Various matrix decompositions are provided through
2655 optional integration with LAPACK and ATLAS libraries. This package includes
2656 the header files from the templated Armadillo library.")
2657 ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
2658 ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
2659 ;; later, as is the rest of 'Rcpp'.
2660 (license license:gpl2+)))
2662 (define-public r-bitops
2668 (uri (cran-uri "bitops" version))
2671 "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
2672 (build-system r-build-system)
2673 (home-page "https://cran.r-project.org/web/packages/bitops")
2674 (synopsis "Bitwise operations")
2676 "This package provides functions for bitwise operations on integer
2678 (license license:gpl2+)))
2680 (define-public r-catools
2686 (uri (cran-uri "caTools" version))
2689 "1yf98x2gaf84y9m32xrg84g384zlfwsdw7wvywdljpgdpvzs9szz"))))
2690 (properties `((upstream-name . "caTools")))
2691 (build-system r-build-system)
2693 `(("r-bitops" ,r-bitops)))
2694 (home-page "https://cran.r-project.org/web/packages/caTools")
2695 (synopsis "Various tools including functions for moving window statistics")
2697 "This package contains several basic utility functions including:
2698 moving (rolling, running) window statistic functions, read/write for GIF and
2699 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
2700 encoder/decoder, round-off-error-free sum and cumsum, etc.")
2701 (license license:gpl3+)))
2703 (define-public r-rprojroot
2705 (name "r-rprojroot")
2710 (uri (cran-uri "rprojroot" version))
2713 "07wy07yhms8zln9qb0iwx69dq08h4lrdi8kavjcplfxcskq638az"))))
2714 (build-system r-build-system)
2716 `(("r-knitr" ,r-knitr)))
2717 (home-page "https://github.com/krlmlr/rprojroot")
2718 (synopsis "Finding files in project subdirectories")
2720 "This package helps accessing files relative to a project root. It
2721 provides helpers for robust, reliable and flexible paths to files below a
2722 project root. The root of a project is defined as a directory that matches a
2723 certain criterion, e.g., it contains a certain regular file.")
2724 (license license:gpl3)))
2726 (define-public r-rmarkdown
2728 (name "r-rmarkdown")
2733 (uri (cran-uri "rmarkdown" version))
2735 (base32 "1c7nrpnv2v43msv7nia90rjh6s5x9m5wlb3mpiwy04fyfb29krz6"))))
2736 (properties `((upstream-name . "rmarkdown")))
2737 (build-system r-build-system)
2739 `(("r-evaluate" ,r-evaluate)
2740 ("r-htmltools" ,r-htmltools)
2741 ("r-jsonlite" ,r-jsonlite)
2742 ("r-knitr" ,r-knitr)
2743 ("r-stringr" ,r-stringr)
2744 ("r-tinytex" ,r-tinytex)
2748 ("pandoc-citeproc" ,pandoc-citeproc)))
2750 `(("r-knitr" ,r-knitr)))
2751 (home-page "https://rmarkdown.rstudio.com")
2752 (synopsis "Convert R Markdown documents into a variety of formats")
2754 "This package provides tools to convert R Markdown documents into a
2755 variety of formats.")
2756 (license license:gpl3+)))
2758 (define-public r-gtable
2764 (uri (cran-uri "gtable" version))
2767 "1lyncxf2dqdjgw1071cn9c8zwzkz6sldnd5cgmicf70bc726qf7x"))))
2768 (properties `((upstream-name . "gtable")))
2769 (build-system r-build-system)
2770 (home-page "https://cran.r-project.org/web/packages/gtable")
2771 (synopsis "R library to arrange grobs in tables")
2773 "Gtable is a collection of tools to make it easier to work with
2774 \"tables\" of grobs.")
2775 (license license:gpl2+)))
2777 (define-public r-gridextra
2779 (name "r-gridextra")
2783 (uri (cran-uri "gridExtra" version))
2786 "0fwfk3cdwxxim7nd55pn7m31bcaqj48y06j7an2k1v1pybk0rdl1"))))
2787 (properties `((upstream-name . "gridExtra")))
2788 (build-system r-build-system)
2790 `(("r-gtable" ,r-gtable)))
2792 `(("r-knitr" ,r-knitr))) ;for building vignettes
2793 (home-page "https://github.com/baptiste/gridextra")
2794 (synopsis "Miscellaneous functions for \"Grid\" graphics")
2796 "This package provides a number of user-level functions to work with
2797 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
2799 (license license:gpl2+)))
2801 (define-public r-pkgconfig
2803 (name "r-pkgconfig")
2807 (uri (cran-uri "pkgconfig" version))
2810 "0l1qph8zyi2sic3k2qcd7vlfl7rzfh1q7z7zvjkl5f7y1x2fy3rk"))))
2811 (build-system r-build-system)
2812 (home-page "https://github.com/gaborcsardi/pkgconfig")
2813 (synopsis "Private configuration for R packages")
2814 (description "This package provides the functionality to set configuration
2815 options on a per-package basis. Options set by a given package only apply to
2816 that package, other packages are unaffected.")
2817 (license license:expat)))
2819 (define-public r-blob
2825 (uri (cran-uri "blob" version))
2828 "1slb5mvxfyi92i8ifx2qa31hp57inilwhq1g9lzvgha6jrxbqm7g"))))
2829 (build-system r-build-system)
2831 `(("r-rlang" ,r-rlang)
2832 ("r-vctrs" ,r-vctrs)))
2833 (home-page "https://github.com/hadley/blob")
2834 (synopsis "Simple S3 Class for representing vectors of binary data")
2835 (description "Raw vectors in R are useful for storing a single binary
2836 object. What if you want to put a vector of them in a data frame? The blob
2837 package provides the blob object, a list of raw vectors, suitable for use as
2838 a column in data frame.")
2839 (license license:gpl3+)))
2841 (define-public r-rsqlite
2847 (uri (cran-uri "RSQLite" version))
2850 "0wx8awxfd4q4mb5dk261rf7zd7y2lcm121fplay0vxl697yym719"))))
2851 (properties `((upstream-name . "RSQLite")))
2852 (build-system r-build-system)
2856 ("r-memoise" ,r-memoise)
2857 ("r-plogr" ,r-plogr)
2859 ("r-bit64" ,r-bit64)
2861 ("r-pkgconfig" ,r-pkgconfig)))
2863 `(("r-knitr" ,r-knitr)))
2864 (home-page "https://github.com/rstats-db/RSQLite")
2865 (synopsis "SQLite interface for R")
2867 "This package embeds the SQLite database engine in R and provides an
2868 interface compliant with the DBI package. The source for the SQLite
2869 engine (version 3.8.8.2) is included.")
2870 (license license:lgpl2.0+)))
2872 (define-public r-rcurl
2875 (version "1.95-0.1.2")
2878 (uri (string-append "https://www.bioconductor.org/packages/"
2879 "release/extra/src/"
2880 "contrib/RCurl_" version ".tar.gz"))
2883 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
2884 (properties `((upstream-name . "RCurl")))
2885 (build-system r-build-system)
2888 (modify-phases %standard-phases
2889 (add-after 'unpack 'respect-CURL_CA_BUNDLE
2891 (substitute* "R/options.S"
2892 (("\\.els = rev\\(merge\\(list\\(\\.\\.\\.\\), \\.opts\\)\\)" m)
2894 certs = Sys.getenv(\"CURL_CA_BUNDLE\")
2895 if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) }
2899 `(("libcurl" ,curl)))
2901 `(("r-bitops" ,r-bitops)))
2902 (home-page "http://www.omegahat.org/RCurl")
2903 (synopsis "General network client interface for R")
2905 "The package allows one to compose general HTTP requests and provides
2906 convenient functions to fetch URIs, GET and POST forms, etc. and process the
2907 results returned by the Web server. This provides a great deal of control
2908 over the HTTP/FTP/... connection and the form of the request while providing a
2909 higher-level interface than is available just using R socket connections.
2910 Additionally, the underlying implementation is robust and extensive,
2911 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
2912 ldap, and also supports cookies, redirects, authentication, etc.")
2913 (license license:bsd-3)))
2915 (define-public r-xml
2918 (version "3.99-0.5")
2921 (uri (cran-uri "XML" version))
2924 "19jkpnbjx2ij0h7rxi13sqnjnwsap6wywmd4gnhfnqpic1rrnlk0"))))
2926 `((upstream-name . "XML")))
2927 (build-system r-build-system)
2929 `(("libxml2" ,libxml2)
2932 `(("pkg-config" ,pkg-config)))
2933 (home-page "http://www.omegahat.org/RSXML")
2934 (synopsis "Tools for parsing and generating XML within R")
2936 "Many approaches for both reading and creating XML (and HTML)
2937 documents (including DTDs), both local and accessible via HTTP or FTP. Also
2938 offers access to an XPath \"interpreter\".")
2939 (license license:bsd-2)))
2941 (define-public r-xnomial
2946 (origin (method url-fetch)
2947 (uri (cran-uri "XNomial" version))
2950 "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
2951 (properties (quasiquote ((upstream-name . "XNomial"))))
2952 (build-system r-build-system)
2953 (home-page "https://cran.r-project.org/web/packages/XNomial")
2954 (synopsis "Goodness-of-Fit test for multinomial data")
2956 "This package provides an exact Goodness-of-Fit test for
2957 multinomial data with fixed probabilities. It can be used to
2958 determine whether a set of counts fits a given expected ratio. To see
2959 whether a set of observed counts fits an expectation, one can examine
2960 all possible outcomes with @code{xmulti()} or a random sample of them
2961 with @code{xmonte()} and find the probability of an observation
2962 deviating from the expectation by at least as much as the observed.
2963 As a measure of deviation from the expected, one can use the
2964 log-likelihood ratio, the multinomial probability, or the classic
2965 chi-square statistic. A histogram of the test statistic can also be
2966 plotted and compared with the asymptotic curve.")
2967 (license (list license:gpl2+ license:gpl3+))))
2969 (define-public r-lambda-r
2975 (uri (cran-uri "lambda.r" version))
2978 "1mh1g0gsd58gng0hb29vww2yqb2jfs07kba5kxnnqck5j3izwlnj"))))
2979 (properties `((upstream-name . "lambda.r")))
2980 (build-system r-build-system)
2982 `(("r-formatr" ,r-formatr)))
2983 (home-page "https://cran.r-project.org/web/packages/lambda.r")
2984 (synopsis "Functional programming extension for R")
2986 "This package provides a language extension to efficiently write
2987 functional programs in R. Syntax extensions include multi-part function
2988 definitions, pattern matching, guard statements, built-in (optional) type
2990 (license license:lgpl3+)))
2992 (define-public r-futile-options
2994 (name "r-futile-options")
2998 (uri (cran-uri "futile.options" version))
3001 "0w15agpi88y3qkv6fl72zy2pzyplzgvnj41a4ixhg64mw1sck73s"))))
3003 `((upstream-name . "futile.options")))
3004 (build-system r-build-system)
3005 (home-page "https://cran.r-project.org/web/packages/futile.options")
3006 (synopsis "Options management framework")
3008 "The futile.options subsystem provides an easy user-defined options
3009 management system that is properly scoped. This means that options created
3010 via @code{futile.options} are fully self-contained and will not collide with
3011 options defined in other packages.")
3012 (license license:lgpl3+)))
3014 (define-public r-futile-logger
3016 (name "r-futile-logger")
3020 (uri (cran-uri "futile.logger" version))
3023 "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
3024 (properties `((upstream-name . "futile.logger")))
3025 (build-system r-build-system)
3027 `(("r-futile-options" ,r-futile-options)
3028 ("r-lambda-r" ,r-lambda-r)))
3029 (home-page "https://cran.r-project.org/web/packages/futile.logger")
3030 (synopsis "Logging utility for R")
3032 "This package provides a simple yet powerful logging utility. Based
3033 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
3034 convenient and easy to use replacement for @code{cat} and @code{print}
3036 (license license:lgpl3+)))
3038 (define-public r-segmented
3040 (name "r-segmented")
3045 (uri (cran-uri "segmented" version))
3048 "0g8l1i31zfqamvwc5j537k3ld6dr5z81p84grdlqq41gywmyidmr"))))
3049 (build-system r-build-system)
3050 (home-page "https://cran.r-project.org/web/packages/segmented")
3051 (synopsis "Regression models with breakpoints estimation")
3053 "Given a regression model, segmented updates the model by adding one or
3054 more segmented (i.e., piecewise-linear) relationships. Several variables with
3055 multiple breakpoints are allowed.")
3056 (license (list license:gpl2+ license:gpl3+))))
3058 (define-public r-snow
3064 (uri (cran-uri "snow" version))
3067 "1n3n8pva9s34fvlw32yng0x416lmbv7q1fsd0ywa4kikmxym64l5"))))
3068 (build-system r-build-system)
3069 (home-page "https://cran.r-project.org/web/packages/snow")
3070 (synopsis "Support for simple parallel computing in R")
3072 "The snow package provides support for simple parallel computing on a
3073 network of workstations using R. A master R process calls @code{makeCluster}
3074 to start a cluster of worker processes; the master process then uses functions
3075 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
3076 worker processes and collect and return the results on the master.")
3077 (license (list license:gpl2+ license:gpl3+))))
3079 (define-public r-sparsem
3085 (uri (cran-uri "SparseM" version))
3088 "0cmlm0lps3daalvp5jzjnjfys388hgkyc8yw0g5r2351h749xdyn"))))
3090 `((upstream-name . "SparseM")))
3092 `(("gfortran" ,gfortran)))
3093 (build-system r-build-system)
3094 (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
3095 (synopsis "Sparse linear algebra")
3097 "This package provides some basic linear algebra functionality for sparse
3098 matrices. It includes Cholesky decomposition and backsolving as well as
3099 standard R subsetting and Kronecker products.")
3100 (license license:gpl2+)))
3102 (define-public r-iterators
3104 (name "r-iterators")
3109 (uri (cran-uri "iterators" version))
3112 "190i1y2493v5c9z8978rb3idlwsjymy67k1assa9znljqbj313kp"))))
3113 (build-system r-build-system)
3114 (home-page "https://cran.r-project.org/web/packages/iterators")
3115 (synopsis "Iterator construct for R")
3117 "This package provides support for iterators, which allow a programmer to
3118 traverse through all the elements of a vector, list, or other collection of
3120 (license license:asl2.0)))
3122 (define-public r-foreach
3129 (uri (cran-uri "foreach" version))
3132 "1qb83b1jvpmk8d6kfibkm5q2hiki0x5gipy758mwa62n56gdcnpv"))))
3133 (build-system r-build-system)
3135 `(("r-codetools" ,r-codetools)
3136 ("r-iterators" ,r-iterators)))
3138 `(("r-knitr" ,r-knitr)))
3139 (home-page "https://cran.r-project.org/web/packages/foreach")
3140 (synopsis "Foreach looping construct for R")
3142 "This package provides support for the @code{foreach} looping construct.
3143 @code{foreach} is an idiom that allows for iterating over elements in a
3144 collection, without the use of an explicit loop counter. This package in
3145 particular is intended to be used for its return value, rather than for its
3146 side effects. In that sense, it is similar to the standard @code{lapply}
3147 function, but doesn't require the evaluation of a function. Using
3148 @code{foreach} without side effects also facilitates executing the loop in
3150 (license license:asl2.0)))
3152 (define-public r-doparallel
3154 (name "r-doparallel")
3159 (uri (cran-uri "doParallel" version))
3162 "1cjf0mxrxgls5pl7aj22fv9j488craib1wkc9np4f3gkckwjdfzi"))))
3163 (properties `((upstream-name . "doParallel")))
3164 (build-system r-build-system)
3166 `(("r-foreach" ,r-foreach)
3167 ("r-iterators" ,r-iterators)))
3168 (home-page "https://cran.r-project.org/web/packages/doParallel")
3169 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3171 "This package provides a parallel backend for the @code{%dopar%} function
3172 using the parallel package.")
3173 (license license:gpl2+)))
3175 (define-public r-domc
3182 (uri (cran-uri "doMC" version))
3185 "0kdmfhp5m1wisjbfyl9d040jrmjmhcgjb0vdi536g2i9vixb5yny"))))
3186 (properties `((upstream-name . "doMC")))
3187 (build-system r-build-system)
3189 `(("r-foreach" ,r-foreach)
3190 ("r-iterators" ,r-iterators)))
3191 (home-page "https://cran.r-project.org/web/packages/doMC")
3192 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3194 "This package provides a parallel backend for the @code{%dopar%} function
3195 using the multicore functionality of the parallel package.")
3196 (license license:gpl2+)))
3204 (uri (cran-uri "DT" version))
3207 "0mpvyfmi2viyhdqx11hznd7dl0q6kxrdmppjsmm2pk0x8a904hz3"))))
3209 `((upstream-name . "DT")))
3210 (build-system r-build-system)
3212 `(("r-crosstalk" ,r-crosstalk)
3213 ("r-htmltools" ,r-htmltools)
3214 ("r-htmlwidgets" ,r-htmlwidgets)
3215 ("r-jsonlite" ,r-jsonlite)
3216 ("r-magrittr" ,r-magrittr)
3217 ("r-promises" ,r-promises)))
3219 `(("r-knitr" ,r-knitr)))
3220 (home-page "https://rstudio.github.io/DT")
3221 (synopsis "R wrapper of the DataTables JavaScript library")
3223 "This package allows for data objects in R to be rendered as HTML tables
3224 using the JavaScript library @code{DataTables} (typically via R Markdown or
3225 Shiny). The @code{DataTables} library has been included in this R package.")
3226 ;; The DT package as a whole is distributed under GPLv3. The DT package
3227 ;; inludes other software components under different licenses:
3229 ;; * Expat: jQuery, jquery.highlight.js, DataTables
3230 ;; * ASL2.0: selectize.js
3231 ;; * WTFPL: noUiSlider
3232 (license (list license:gpl3
3237 (define-public r-base64enc
3239 (name "r-base64enc")
3243 (uri (cran-uri "base64enc" version))
3246 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
3247 (build-system r-build-system)
3248 (home-page "https://www.rforge.net/base64enc")
3249 (synopsis "Tools for Base64 encoding")
3251 "This package provides tools for handling Base64 encoding. It is more
3252 flexible than the orphaned \"base64\" package.")
3253 (license license:gpl2+)))
3255 (define-public r-irlba
3262 (uri (cran-uri "irlba" version))
3265 "1h7mzrqdjc41814cf6c93sbyl7nxwvsf3x8apl9rhmydgdlk7qkf"))))
3266 (build-system r-build-system)
3268 `(("r-matrix" ,r-matrix)))
3269 (home-page "https://cran.r-project.org/web/packages/irlba")
3270 (synopsis "Methods for eigendecomposition of large matrices")
3272 "This package provides fast and memory efficient methods for truncated
3273 singular and eigenvalue decompositions, as well as for principal component
3274 analysis of large sparse or dense matrices.")
3275 (license (list license:gpl2+ license:gpl3+))))
3277 (define-public r-glmnet
3284 (uri (cran-uri "glmnet" version))
3286 (base32 "1js01qnznm20h4pslaw1ragxhrzk0w4nw7r6ryg7i27l344za2lg"))))
3287 (build-system r-build-system)
3289 `(("gfortran" ,gfortran)
3290 ("r-knitr" ,r-knitr)))
3292 `(("r-foreach" ,r-foreach)
3293 ("r-matrix" ,r-matrix)
3294 ("r-shape" ,r-shape)
3295 ("r-survival" ,r-survival)))
3296 (home-page "https://www.jstatsoft.org/article/view/v033i01")
3297 (synopsis "Lasso and elastic-net regularized generalized linear models")
3299 "The glmnet package provides efficient procedures for fitting the entire
3300 lasso or elastic-net regularization path for linear and Poisson regression, as
3301 well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
3302 multinomial models. The algorithm uses cyclical coordinate descent in a
3303 path-wise fashion.")
3304 (license license:gpl2+)))
3306 (define-public r-pkgmaker
3313 (uri (cran-uri "pkgmaker" version))
3316 "14ggsd24n5g5rvn0wl4w90ipxzmywqikh28llj89q6kpxwnv4iff"))))
3317 (build-system r-build-system)
3319 `(("r-assertthat" ,r-assertthat)
3320 ("r-codetools" ,r-codetools)
3321 ("r-digest" ,r-digest)
3322 ("r-registry" ,r-registry)
3323 ("r-stringr" ,r-stringr)
3324 ("r-withr" ,r-withr)
3325 ("r-xtable" ,r-xtable)))
3326 (home-page "https://renozao.github.io/pkgmaker")
3327 (synopsis "Package development utilities")
3329 "This package provides some low-level utilities to use for R package
3330 development. It currently provides managers for multiple package specific
3331 options and registries, vignette, unit test and bibtex related utilities.")
3332 (license license:gpl2+)))
3334 (define-public r-registry
3341 (uri (cran-uri "registry" version))
3344 "1k3j6dx350awamr0dwwgkhfs46vsnj4nf08iw5byq0x7n3nkdsnz"))))
3345 (build-system r-build-system)
3346 (home-page "https://cran.r-project.org/web/packages/registry")
3347 (synopsis "Infrastructure for R package registries")
3349 "This package provides a generic infrastructure for creating and using R
3350 package registries.")
3351 (license license:gpl2+)))
3353 (define-public r-rngtools
3360 (uri (cran-uri "rngtools" version))
3363 "0xgmg3qb6insc157as47mcm9sdjdpy9jirh7w06bxb7pfcxqfx42"))))
3364 (build-system r-build-system)
3366 `(("r-digest" ,r-digest)))
3367 (home-page "https://renozao.github.io/rngtools")
3368 (synopsis "Utility functions for working with random number generators")
3370 "This package contains a set of functions for working with Random Number
3371 Generators (RNGs). In particular, it defines a generic S4 framework for
3372 getting/setting the current RNG, or RNG data that are embedded into objects
3373 for reproducibility. Notably, convenient default methods greatly facilitate
3374 the way current RNG settings can be changed.")
3375 (license license:gpl3+)))
3377 (define-public r-rtsne
3384 (uri (cran-uri "Rtsne" version))
3387 "0v17vxizrs1msay24xl2bckfajr2c82wpqj07lyssbrq197nwdsn"))))
3388 (properties `((upstream-name . "Rtsne")))
3389 (build-system r-build-system)
3391 `(("r-rcpp" ,r-rcpp)))
3392 (home-page "https://github.com/jkrijthe/Rtsne")
3393 (synopsis "T-distributed stochastic neighbor embedding")
3395 "This package provides an R wrapper around the fast T-distributed
3396 Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
3397 ;; The declared license for this package is BSD-3, but it also includes
3398 ;; code licensed under BSD-4.
3399 (license (list license:bsd-3 license:bsd-4))))
3401 (define-public r-e1071
3408 (uri (cran-uri "e1071" version))
3411 "02935xcscjhb0jmnvh44hxlpjcgladrcr0gpz1jxq07m0qdqgaz6"))))
3412 (build-system r-build-system)
3414 `(("r-class" ,r-class)))
3415 (home-page "https://cran.r-project.org/web/packages/e1071")
3416 (synopsis "Miscellaneous functions for probability theory")
3418 "This package provides functions for latent class analysis, short time
3419 Fourier transform, fuzzy clustering, support vector machines, shortest path
3420 computation, bagged clustering, naive Bayes classifier, and more.")
3421 (license license:gpl2+)))
3423 (define-public r-bigmemory-sri
3425 (name "r-bigmemory-sri")
3430 (uri (cran-uri "bigmemory.sri" version))
3432 (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
3434 `((upstream-name . "bigmemory.sri")))
3435 (build-system r-build-system)
3436 (home-page "https://cran.r-project.org/web/packages/bigmemory.sri")
3437 (synopsis "Shared resource interface for the bigmemory package")
3438 (description "This package provides a shared resource interface for the
3439 bigmemory and synchronicity packages.")
3440 ;; Users can choose either LGPLv3 or ASL2.0.
3441 (license (list license:lgpl3 license:asl2.0))))
3443 (define-public r-synchronicity
3445 (name "r-synchronicity")
3450 (uri (cran-uri "synchronicity" version))
3453 "1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx"))))
3454 (build-system r-build-system)
3457 ("r-bigmemory-sri" ,r-bigmemory-sri)
3459 ("r-uuid" ,r-uuid)))
3460 (home-page "http://www.bigmemory.org")
3461 (synopsis "Boost mutex functionality in R")
3462 (description "This package provides support for synchronization
3463 via mutexes and may eventually support interprocess communication and
3465 ;; Users can choose either LGPLv3 or ASL2.0.
3466 (license (list license:lgpl3 license:asl2.0))))
3468 (define-public r-bigmemory
3470 (name "r-bigmemory")
3475 (uri (cran-uri "bigmemory" version))
3478 "03pg8mxdc7q0249visjmc8bc3xmwxsfg3i2n6higicj4cfz7zihq"))))
3479 (build-system r-build-system)
3483 ("r-bigmemory-sri" ,r-bigmemory-sri)))
3484 (home-page "http://www.bigmemory.org")
3485 (synopsis "Manage large matrices with shared memory or memory-mapped files")
3486 (description "This package provides methods to create, store, access, and
3487 manipulate large matrices. Matrices are allocated to shared memory and may use
3488 memory-mapped files.")
3489 ;; Users can choose either LGPLv3 or ASL2.0.
3490 (license (list license:lgpl3 license:asl2.0))))
3492 (define-public r-r-methodss3
3494 (name "r-r-methodss3")
3498 (uri (cran-uri "R.methodsS3" version))
3501 "16v1br7lf7vxv40z65giv9jnqkpnyqagcmgqa0s1jy7spj0zp64a"))))
3502 (properties `((upstream-name . "R.methodsS3")))
3503 (build-system r-build-system)
3504 (home-page "https://cran.r-project.org/web/packages/R.methodsS3")
3505 (synopsis "S3 methods simplified")
3507 "This package provides methods that simplify the setup of S3 generic
3508 functions and S3 methods. Major effort has been made in making definition of
3509 methods as simple as possible with a minimum of maintenance for package
3510 developers. For example, generic functions are created automatically, if
3511 missing, and naming conflict are automatically solved, if possible. The
3512 method @code{setMethodS3()} is a good start for those who in the future may
3513 want to migrate to S4.")
3514 (license license:lgpl2.1+)))
3516 (define-public r-r-oo
3522 (uri (cran-uri "R.oo" version))
3525 "1divisff26fmiqg6vmabnwlrx079c066r8qvkakfp336vnwdm89p"))))
3526 (properties `((upstream-name . "R.oo")))
3527 (build-system r-build-system)
3529 `(("r-r-methodss3" ,r-r-methodss3)))
3530 (home-page "https://github.com/HenrikBengtsson/R.oo")
3531 (synopsis "R object-oriented programming with or without references")
3533 "This package provides methods and classes for object-oriented
3534 programming in R with or without references. Large effort has been made on
3535 making definition of methods as simple as possible with a minimum of
3536 maintenance for package developers.")
3537 (license license:lgpl2.1+)))
3539 (define-public r-r-utils
3545 (uri (cran-uri "R.utils" version))
3548 "1gssnk73nhisc20by9kvfl4byfsmwrk6597na0x40ycck58lyylm"))))
3549 (properties `((upstream-name . "R.utils")))
3550 (build-system r-build-system)
3552 `(("r-r-methodss3" ,r-r-methodss3)
3553 ("r-r-oo" ,r-r-oo)))
3554 (home-page "https://github.com/HenrikBengtsson/R.utils")
3555 (synopsis "Various programming utilities")
3557 "This package provides utility functions useful when programming and
3558 developing R packages.")
3559 (license license:lgpl2.1+)))
3561 (define-public r-r-cache
3567 (uri (cran-uri "R.cache" version))
3570 "1n8n5ihkryrbxv630dwhz4r048nyv676qd3i9f5z5fa04hvlxbqq"))))
3571 (properties `((upstream-name . "R.cache")))
3572 (build-system r-build-system)
3574 `(("r-digest" ,r-digest)
3575 ("r-r-methodss3" ,r-r-methodss3)
3577 ("r-r-utils" ,r-r-utils)))
3578 (home-page "https://github.com/HenrikBengtsson/R.cache")
3579 (synopsis "Light-weight caching of objects and results")
3581 "This package provides methods for caching or memoization of objects and
3582 results. With this package, any R object can be cached in a key-value storage
3583 where the key can be an arbitrary set of R objects. The cache memory is
3584 persistent (on the file system).")
3585 (license license:lgpl2.1+)))
3587 (define-public r-r-rsp
3593 (uri (cran-uri "R.rsp" version))
3596 "0n9sxrffahgxcc8h9vgxg5i446g14cibixpf82nkpm5bvidhfsc9"))))
3597 (properties `((upstream-name . "R.rsp")))
3598 (build-system r-build-system)
3600 `(("r-digest" ,r-digest)
3601 ("r-r-cache" ,r-r-cache)
3602 ("r-r-methodss3" ,r-r-methodss3)
3604 ("r-r-utils" ,r-r-utils)))
3605 (home-page "https://github.com/HenrikBengtsson/R.rsp")
3606 (synopsis "Dynamic generation of scientific reports")
3608 "The RSP markup language provides a powerful markup for controlling the
3609 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
3610 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
3611 to many other literate programming languages, with RSP it is straightforward
3612 to loop over mixtures of code and text sections, e.g. in month-by-month
3613 summaries. RSP has also several preprocessing directives for incorporating
3614 static and dynamic contents of external files (local or online) among other
3615 things. RSP is ideal for self-contained scientific reports and R package
3617 (license license:lgpl2.1+)))
3619 (define-public r-mvtnorm
3625 (uri (cran-uri "mvtnorm" version))
3628 "1pj51mi0g6ip7a2nhzc93yv9289kaayvspjvsbgbgarvx7axlrg9"))))
3629 (build-system r-build-system)
3631 `(("gfortran" ,gfortran)))
3632 (home-page "http://mvtnorm.R-forge.R-project.org")
3633 (synopsis "Package for multivariate normal and t-distributions")
3634 (description "This package can compute multivariate normal and
3635 t-probabilities, quantiles, random deviates and densities.")
3636 (license license:gpl2)))
3638 (define-public r-matrixstats
3640 (name "r-matrixstats")
3644 (uri (cran-uri "matrixStats" version))
3647 "0hzkx7yi9ira476izsgw7r2bhv72ra4z2m9zr1i1f4ivrn3ihs7r"))))
3648 (properties `((upstream-name . "matrixStats")))
3649 (build-system r-build-system)
3651 `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
3652 (home-page "https://github.com/HenrikBengtsson/matrixStats")
3653 (synopsis "Methods applying to vectors and matrix rows and columns")
3655 "This package provides methods operating on rows and columns of matrices,
3656 e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
3657 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
3658 @code{weightedMedians()}. All methods have been optimized for speed and
3660 (license license:artistic2.0)))
3662 (define-public r-viridis
3668 (uri (cran-uri "viridis" version))
3671 "060rf1jn29dq53y3nhb0hykvcap6rqsk04rq544ypiiqb18ngwnx"))))
3672 (build-system r-build-system)
3674 `(("r-ggplot2" ,r-ggplot2)
3675 ("r-gridextra" ,r-gridextra)
3676 ("r-viridislite" ,r-viridislite)))
3678 `(("r-knitr" ,r-knitr))) ; for vignettes
3679 (home-page "https://github.com/sjmgarnier/viridis")
3680 (synopsis "Matplotlib default color map")
3682 "This package is a port of the new @url{matplotlib,
3683 http://matplotlib.org/} color maps (@code{viridis}--the default--,
3684 @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
3685 designed in such a way that they will analytically be perfectly
3686 perceptually-uniform, both in regular form and also when converted to
3687 black-and-white. They are also designed to be perceived by readers with the
3688 most common form of color blindness.")
3689 (license license:x11)))
3691 (define-public r-viridislite
3693 (name "r-viridislite")
3698 (uri (cran-uri "viridisLite" version))
3701 "1by2l05f0yabwvv64lhnv7bbhx0w683s3wr9j2xda920ghpa23kq"))))
3702 (properties `((upstream-name . "viridisLite")))
3703 (build-system r-build-system)
3704 (home-page "https://github.com/sjmgarnier/viridisLite")
3705 (synopsis "Default color maps from matplotlib")
3707 "This package is a port of the new @code{matplotlib} color maps
3708 (@code{viridis}, @code{magma}, @code{plasma} and @code{inferno}) to R.
3709 matplotlib is a popular plotting library for Python. These color maps are
3710 designed in such a way that they will analytically be perfectly
3711 perceptually-uniform, both in regular form and also when converted to
3712 black-and-white. They are also designed to be perceived by readers with the
3713 most common form of color blindness. This is the @code{lite} version of the
3714 more complete @code{viridis} package.")
3715 (license license:expat)))
3717 (define-public r-tidyselect
3719 (name "r-tidyselect")
3724 (uri (cran-uri "tidyselect" version))
3727 "14rqx4dq574hilmdwrr34wyjg8rlw4rvndpsqd9plgxm3wwfsdg6"))))
3728 (build-system r-build-system)
3730 `(("r-ellipsis" ,r-ellipsis)
3732 ("r-purrr" ,r-purrr)
3733 ("r-rlang" ,r-rlang)
3734 ("r-vctrs" ,r-vctrs)))
3736 `(("r-knitr" ,r-knitr)))
3737 (home-page "https://cran.r-project.org/web/packages/tidyselect")
3738 (synopsis "Select from a set of strings")
3740 "This package provides a backend for the selecting functions of the
3741 tidyverse. It makes it easy to implement select-like functions in your own
3742 packages in a way that is consistent with other tidyverse interfaces for
3744 (license license:gpl3)))
3746 (define-public r-tidyr
3753 (uri (cran-uri "tidyr" version))
3756 "0v7x1pgmwmjypzdr4j2ig2klgrrgryi3qvw8hwqv65a5h9kwpz08"))))
3757 (build-system r-build-system)
3759 `(("r-cpp11" ,r-cpp11)
3760 ("r-dplyr" ,r-dplyr)
3761 ("r-ellipsis" ,r-ellipsis)
3762 ("r-magrittr" ,r-magrittr)
3764 ("r-lifecycle" ,r-lifecycle)
3765 ("r-purrr" ,r-purrr)
3766 ("r-rlang" ,r-rlang)
3767 ("r-tidyselect" ,r-tidyselect)
3768 ("r-tibble" ,r-tibble)
3769 ("r-vctrs" ,r-vctrs)))
3771 `(("r-knitr" ,r-knitr)))
3772 (home-page "https://github.com/hadley/tidyr")
3773 (synopsis "Tidy data with `spread()` and `gather()` functions")
3775 "tidyr is a reframing of the reshape2 package designed to accompany the
3776 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
3777 a solid pipeline for data analysis. It is designed specifically for tidying
3778 data, not the general reshaping that reshape2 does, or the general aggregation
3779 that reshape did. In particular, built-in methods only work for data frames,
3780 and tidyr provides no margins or aggregation.")
3781 (license license:expat)))
3783 (define-public r-hexbin
3790 (uri (cran-uri "hexbin" version))
3793 "0bbhs5pwxh474w62sq6gqvih7habancxng9wd4f2rgn6lv9zhhb2"))))
3794 (build-system r-build-system)
3796 `(("r-lattice" ,r-lattice)))
3798 `(("gfortran" ,gfortran)
3799 ("r-knitr" ,r-knitr))) ; for vignettes
3800 (home-page "https://github.com/edzer/hexbin")
3801 (synopsis "Hexagonal binning routines")
3803 "This package provides binning and plotting functions for hexagonal bins.
3804 It uses and relies on grid graphics and formal (S4) classes and methods.")
3805 (license license:gpl2+)))
3807 (define-public r-purrr
3814 (uri (cran-uri "purrr" version))
3817 "1cj091rsjdj2xz16qhynyw72gh5cyhznifcfbrbygndfr4xwksr3"))))
3818 (build-system r-build-system)
3820 `(("r-magrittr" ,r-magrittr)
3821 ("r-rlang" ,r-rlang)))
3823 `(("r-knitr" ,r-knitr)))
3824 (home-page "https://github.com/hadley/purrr")
3825 (synopsis "Functional programming tools")
3827 "This package completes R's functional programming tools with missing
3828 features present in other programming languages.")
3829 (license license:gpl3+)))
3831 (define-public r-plotly
3837 (uri (cran-uri "plotly" version))
3840 "0801i2q7sw62x734d58h9p2fwpi1hirqj73gsg18pqkdv4b1lkfl"))))
3841 (build-system r-build-system)
3843 `(("r-base64enc" ,r-base64enc)
3844 ("r-crosstalk" ,r-crosstalk)
3845 ("r-digest" ,r-digest)
3846 ("r-data-table" ,r-data-table)
3847 ("r-dplyr" ,r-dplyr)
3848 ("r-ggplot2" ,r-ggplot2)
3849 ("r-htmltools" ,r-htmltools)
3850 ("r-htmlwidgets" ,r-htmlwidgets)
3852 ("r-jsonlite" ,r-jsonlite)
3853 ("r-lazyeval" ,r-lazyeval)
3854 ("r-magrittr" ,r-magrittr)
3855 ("r-promises" ,r-promises)
3856 ("r-purrr" ,r-purrr)
3857 ("r-rcolorbrewer" ,r-rcolorbrewer)
3858 ("r-rlang" ,r-rlang)
3859 ("r-scales" ,r-scales)
3860 ("r-tibble" ,r-tibble)
3861 ("r-tidyr" ,r-tidyr)
3862 ("r-vctrs" ,r-vctrs)
3863 ("r-viridislite" ,r-viridislite)))
3864 (home-page "https://plot.ly/r")
3865 (synopsis "Create interactive web graphics")
3867 "This package enables the translation of ggplot2 graphs to an interactive
3868 web-based version and/or the creation of custom web-based visualizations
3869 directly from R. Once uploaded to a plotly account, plotly graphs (and the
3870 data behind them) can be viewed and modified in a web browser.")
3871 (license license:x11)))
3873 (define-public r-biased-urn
3875 (name "r-biased-urn")
3880 (uri (cran-uri "BiasedUrn" version))
3883 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
3884 (properties `((upstream-name . "BiasedUrn")))
3885 (build-system r-build-system)
3886 (home-page "http://www.agner.org/random/")
3887 (synopsis "Biased urn model distributions")
3889 "This package provides statistical models of biased sampling in the form
3890 of univariate and multivariate noncentral hypergeometric distributions,
3891 including Wallenius' noncentral hypergeometric distribution and Fisher's
3892 noncentral hypergeometric distribution (also called extended hypergeometric
3894 (license license:gpl3+)))
3896 (define-public r-rematch
3903 (uri (cran-uri "rematch" version))
3906 "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4"))))
3907 (build-system r-build-system)
3908 (home-page "https://github.com/MangoTheCat/rematch")
3909 (synopsis "Match regular expressions with a nicer API")
3911 "This package provides a small wrapper on @code{regexpr} to extract the
3912 matches and captured groups from the match of a regular expression to a
3914 (license license:expat)))
3916 (define-public r-cellranger
3918 (name "r-cellranger")
3923 (uri (cran-uri "cellranger" version))
3926 "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x"))))
3927 (build-system r-build-system)
3929 `(("r-rematch" ,r-rematch)
3930 ("r-tibble" ,r-tibble)))
3931 (home-page "https://github.com/rsheets/cellranger")
3932 (synopsis "Translate spreadsheet cell ranges to rows and columns")
3934 "This package provides helper functions to work with spreadsheets and the
3935 @code{A1:D10} style of cell range specification.")
3936 (license license:expat)))
3938 (define-public r-googlesheets
3940 (name "r-googlesheets")
3945 (uri (cran-uri "googlesheets" version))
3948 "11q07nxys72wkxx9mawmjyf20gvwvrb7h3gpa73h6lgh2vgrwnv8"))))
3949 (build-system r-build-system)
3951 `(("r-cellranger" ,r-cellranger)
3952 ("r-dplyr" ,r-dplyr)
3954 ("r-jsonlite" ,r-jsonlite)
3955 ("r-purrr" ,r-purrr)
3956 ("r-readr" ,r-readr)
3957 ("r-stringr" ,r-stringr)
3958 ("r-tibble" ,r-tibble)
3959 ("r-tidyr" ,r-tidyr)
3960 ("r-xml2" ,r-xml2)))
3961 (home-page "https://github.com/jennybc/googlesheets")
3962 (synopsis "Manage Google spreadsheets from R")
3963 (description "This package provides tools to interact with Google Sheets
3965 (license license:expat)))
3967 (define-public r-spams
3970 (version "2.6-2017-03-22")
3974 ;; Use the ‘Latest version’ link for a stable URI across releases.
3975 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
3976 "latestfile/4531/spams-R-v" version ".tar.gz"))
3979 "13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx"))))
3980 (build-system r-build-system)
3983 (modify-phases %standard-phases
3984 (add-after 'unpack 'chdir
3985 (lambda _ (chdir "spams") #t))
3986 ;; Don't tune for the building machine.
3987 (add-after 'chdir 'no-mtune
3989 (substitute* "src/Makevars"
3990 (("-mtune=native") ""))
3993 `(("r-lattice" ,r-lattice)
3994 ("r-matrix" ,r-matrix)))
3995 (home-page "https://spams-devel.gforge.inria.fr")
3996 (synopsis "Toolbox for solving sparse estimation problems")
3997 (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
3998 for solving various sparse estimation problems. It includes tools for the
4002 @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
4003 component analysis} (PCA), ...)
4004 @item Solving sparse decomposition problems with LARS, coordinate descent,
4005 OMP, SOMP, proximal methods
4006 @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
4007 group lasso, tree-structured regularization, structured sparsity with
4008 overlapping groups,...).
4010 (license license:gpl3+)))
4012 (define-public r-base64
4019 (uri (cran-uri "base64" version))
4022 "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf"))))
4023 (build-system r-build-system)
4025 `(("r-openssl" ,r-openssl)))
4026 (home-page "https://cran.r-project.org/web/packages/base64")
4027 (synopsis "Base64 encoder and decoder")
4029 "This package is a compatibility wrapper to replace the orphaned package
4030 by Romain Francois. New applications should use the openssl or base64enc
4032 (license license:expat)))
4034 (define-public r-hmisc
4041 (uri (cran-uri "Hmisc" version))
4043 (base32 "1j7vkckmahdh90ndcl646sjpxq82y4x55ngxqvkni22mv16wc2j9"))))
4044 (properties `((upstream-name . "Hmisc")))
4045 (build-system r-build-system)
4047 `(("gfortran" ,gfortran)))
4049 `(("r-base64enc" ,r-base64enc)
4050 ("r-cluster" ,r-cluster)
4051 ("r-data-table" ,r-data-table)
4052 ("r-foreign" ,r-foreign)
4053 ("r-formula" ,r-formula)
4054 ("r-ggplot2" ,r-ggplot2)
4055 ("r-gridextra" ,r-gridextra)
4056 ("r-gtable" ,r-gtable)
4057 ("r-lattice" ,r-lattice)
4058 ("r-latticeextra" ,r-latticeextra)
4059 ("r-htmltable" ,r-htmltable)
4060 ("r-htmltools" ,r-htmltools)
4062 ("r-rpart" ,r-rpart)
4063 ("r-survival" ,r-survival)
4064 ("r-viridis" ,r-viridis)))
4065 (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
4066 (synopsis "Miscellaneous data analysis and graphics functions")
4068 "This package contains many functions useful for data analysis,
4069 high-level graphics, utility operations, functions for computing sample size
4070 and power, importing and annotating datasets, imputing missing values,
4071 advanced table making, variable clustering, character string manipulation,
4072 conversion of R objects to LaTeX code, and recoding variables.")
4073 (license license:gpl2+)))
4075 (define-public r-runit
4082 (uri (cran-uri "RUnit" version))
4085 "1wc1gwb7yw7phf8b0gkig6c23klya3ax11c6i4s0f049k42r78r3"))))
4086 (properties `((upstream-name . "RUnit")))
4087 (build-system r-build-system)
4088 (home-page "https://cran.r-project.org/web/packages/RUnit")
4089 (synopsis "R unit test framework")
4091 "This package provides R functions implementing a standard unit testing
4092 framework, with additional code inspection and report generation tools.")
4093 (license license:gpl2+)))
4095 (define-public r-dynamictreecut
4097 (name "r-dynamictreecut")
4102 (uri (cran-uri "dynamicTreeCut" version))
4105 "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"))))
4106 (properties `((upstream-name . "dynamicTreeCut")))
4107 (build-system r-build-system)
4109 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
4110 (synopsis "Detect clusters in hierarchical clustering dendrograms")
4112 "This package contains methods for the detection of clusters in
4113 hierarchical clustering dendrograms.")
4114 (license license:gpl2+)))
4116 (define-public r-fastcluster
4118 (name "r-fastcluster")
4123 (uri (cran-uri "fastcluster" version))
4126 "01a2xnhhvv1swd4g8p4lzyn7ww7kg49jlnzc7kfz60jqjzpisrpk"))))
4127 (build-system r-build-system)
4128 (home-page "http://danifold.net/fastcluster.html")
4129 (synopsis "Fast hierarchical clustering routines")
4131 "This package implements fast hierarchical, agglomerative clustering
4132 routines. Part of the functionality is designed as drop-in replacement for
4133 existing routines: @code{linkage()} in the SciPy package
4134 @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package,
4135 and the @code{flashClust} package. It provides the same functionality with
4136 the benefit of a much faster implementation. Moreover, there are
4137 memory-saving routines for clustering of vector data, which go beyond what the
4138 existing packages provide.")
4139 (license license:bsd-2)))
4141 (define-public r-sfsmisc
4148 (uri (cran-uri "sfsmisc" version))
4151 "198zpkz1gvw954ym8669svrk81yb49j6fyk5i6a7dw07z3snlmdn"))))
4152 (build-system r-build-system)
4153 (home-page "https://cran.r-project.org/web/packages/sfsmisc")
4154 (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
4156 "This package provides useful utilities from Seminar fuer Statistik ETH
4157 Zurich, including many that are related to graphics.")
4158 (license license:gpl2+)))
4160 (define-public r-gtools
4167 (uri (cran-uri "gtools" version))
4170 "1pnwy412wvhhvnnx8qg6s9hrgcnsfhnfcpf2560ipipk845acfsh"))))
4171 (build-system r-build-system)
4174 (modify-phases %standard-phases
4175 (add-after 'unpack 'make-deterministic
4177 (substitute* "R/checkReverseDependencies.R"
4178 (("tempdir\\(\\)") "\"/tmp\""))
4180 (home-page "https://cran.r-project.org/web/packages/gtools")
4181 (synopsis "Various R programming tools")
4183 "This package contains a collection of various functions to assist in R
4184 programming, such as tools to assist in developing, updating, and maintaining
4185 R and R packages, calculating the logit and inverse logit transformations,
4186 tests for whether a value is missing, empty or contains only @code{NA} and
4187 @code{NULL} values, and many more.")
4188 (license license:gpl2)))
4190 (define-public r-gdata
4197 (uri (cran-uri "gdata" version))
4200 "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b"))))
4201 (build-system r-build-system)
4205 `(("r-gtools" ,r-gtools)))
4206 (home-page "https://cran.r-project.org/web/packages/gdata")
4207 (synopsis "Various R programming tools for data manipulation")
4209 "This package provides various R programming tools for data manipulation,
4213 @item medical unit conversions
4214 @item combining objects
4215 @item character vector operations
4216 @item factor manipulation
4217 @item obtaining information about R objects
4218 @item manipulating MS-Excel formatted files
4219 @item generating fixed-width format files
4220 @item extricating components of date and time objects
4221 @item operations on columns of data frames
4222 @item matrix operations
4223 @item operations on vectors and data frames
4224 @item value of last evaluated expression
4225 @item wrapper for @code{sample} that ensures consistent behavior for
4226 both scalar and vector arguments
4228 (license license:gpl2+)))
4230 (define-public r-gplots
4237 (uri (cran-uri "gplots" version))
4240 "0f8khaymz383w2ksnk80d4kpnvgmdk37pbycpsnl2vabaz11kbpr"))))
4241 (build-system r-build-system)
4243 `(("r-catools" ,r-catools)
4244 ("r-gtools" ,r-gtools)
4245 ("r-kernsmooth" ,r-kernsmooth)))
4247 `(("r-knitr" ,r-knitr)))
4248 (home-page "https://cran.r-project.org/web/packages/gplots")
4249 (synopsis "Various R programming tools for plotting data")
4251 "This package provides various R programming tools for plotting data,
4255 @item calculating and plotting locally smoothed summary function
4256 @item enhanced versions of standard plots
4257 @item manipulating colors
4258 @item calculating and plotting two-dimensional data summaries
4259 @item enhanced regression diagnostic plots
4260 @item formula-enabled interface to @code{stats::lowess} function
4261 @item displaying textual data in plots
4263 @item plotting \"Venn\" diagrams
4264 @item displaying Open-Office style plots
4265 @item plotting multiple data on same region, with separate axes
4266 @item plotting means and confidence intervals
4267 @item spacing points in an x-y plot so they don't overlap
4269 (license license:gpl2+)))
4271 (define-public r-rocr
4278 (uri (cran-uri "ROCR" version))
4281 "0amvvrkiflmr3qygrsgrsja4gaf2v6r6h6i2bgpsm8r069vmlf2p"))))
4282 (properties `((upstream-name . "ROCR")))
4283 (build-system r-build-system)
4285 `(("r-gplots" ,r-gplots)))
4287 `(("r-knitr" ,r-knitr)))
4288 (home-page "https://rocr.bioinf.mpi-sb.mpg.de/")
4289 (synopsis "Visualizing the performance of scoring classifiers")
4291 "ROCR is a flexible tool for creating cutoff-parameterized 2D performance
4292 curves by freely combining two from over 25 performance measures (new
4293 performance measures can be added using a standard interface). Curves from
4294 different cross-validation or bootstrapping runs can be averaged by different
4295 methods, and standard deviations, standard errors or box plots can be used to
4296 visualize the variability across the runs. The parameterization can be
4297 visualized by printing cutoff values at the corresponding curve positions, or
4298 by coloring the curve according to cutoff. All components of a performance
4299 plot can be quickly adjusted using a flexible parameter dispatching
4301 (license license:gpl2+)))
4303 (define-public r-ztable
4309 (uri (cran-uri "ztable" version))
4312 "0wxcdb7yp2r6w5iznz1k49npp5sn4jiybfcj30s3198hkcnv0r8y"))))
4313 (build-system r-build-system)
4315 `(("r-flextable" ,r-flextable)
4316 ("r-magrittr" ,r-magrittr)
4317 ("r-officer" ,r-officer)
4318 ("r-rcolorbrewer" ,r-rcolorbrewer)
4319 ("r-rstudioapi" ,r-rstudioapi)
4320 ("r-scales" ,r-scales)
4321 ("r-stringr" ,r-stringr)))
4323 `(("r-knitr" ,r-knitr)))
4324 (home-page "https://cran.r-project.org/web/packages/ztable")
4325 (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
4327 "This package provides functions to make zebra-striped tables (tables
4328 with alternating row colors) in LaTeX and HTML formats easily from
4329 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
4330 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
4331 @code{cbind.mytable} objects.")
4332 (license license:gpl2+)))
4334 (define-public r-vipor
4340 (uri (cran-uri "vipor" version))
4343 "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx"))))
4344 (build-system r-build-system)
4345 (home-page "https://cran.r-project.org/web/packages/vipor")
4346 (synopsis "Plot categorical data using noise and density estimates")
4348 "This package provides tools to generate a violin point plot, a
4349 combination of a violin/histogram plot and a scatter plot by offsetting points
4350 within a category based on their density using quasirandom noise.")
4351 (license license:gpl2+)))
4353 (define-public r-beeswarm
4359 (uri (cran-uri "beeswarm" version))
4362 "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
4363 (build-system r-build-system)
4364 (home-page "https://www.cbs.dtu.dk/~eklund/beeswarm/")
4365 (synopsis "Implementation of bee swarm plots")
4367 "This package provides an implementation of bee swarm plots. The bee
4368 swarm plot is a one-dimensional scatter plot like stripchart, but with
4369 closely-packed, non-overlapping points.")
4370 (license license:artistic2.0)))
4372 (define-public r-sourcetools
4374 (name "r-sourcetools")
4379 (uri (cran-uri "sourcetools" version))
4382 "1jnjir0q2dj724f1mjm6p5h77yzyx6xcqy9r2g7gmcxkxw349627"))))
4383 (build-system r-build-system)
4384 (home-page "https://cran.r-project.org/web/packages/sourcetools")
4385 (synopsis "Tools for reading, tokenizing and parsing R code")
4387 "The sourcetools package provides both an R and C++ interface for the
4388 tokenization of R code, and helpers for interacting with the tokenized
4389 representation of R code.")
4390 (license license:expat)))
4392 (define-public r-ggbeeswarm
4394 (name "r-ggbeeswarm")
4398 (uri (cran-uri "ggbeeswarm" version))
4401 "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v"))))
4402 (build-system r-build-system)
4404 `(("r-beeswarm" ,r-beeswarm)
4405 ("r-ggplot2" ,r-ggplot2)
4406 ("r-vipor" ,r-vipor)))
4407 (home-page "https://github.com/eclarke/ggbeeswarm")
4408 (synopsis "Categorical scatter (violin point) plots")
4410 "This package provides two methods of plotting categorical scatter plots
4411 such that the arrangement of points within a category reflects the density of
4412 data at that region, and avoids over-plotting.")
4413 (license license:gpl2+)))
4415 (define-public r-ggthemes
4421 (uri (cran-uri "ggthemes" version))
4424 "0rrkzfggc1nlda1w1lbqdycx6nawxbkac1szhvkwrqlzh6agxcsv"))))
4425 (build-system r-build-system)
4427 `(("r-ggplot2" ,r-ggplot2)
4428 ("r-purrr" ,r-purrr)
4429 ("r-scales" ,r-scales)
4430 ("r-stringr" ,r-stringr)
4431 ("r-tibble" ,r-tibble)))
4432 (home-page "https://cran.rstudio.com/web/packages/ggthemes")
4433 (synopsis "Extra themes, scales and geoms for @code{ggplot2}")
4434 (description "This package provides extra themes and scales for
4435 @code{ggplot2} that replicate the look of plots by Edward Tufte and
4436 Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The
4437 Wall Street Journal, among others. This package also provides
4438 @code{geoms} for Tufte's box plot and range frame.")
4439 (license license:gpl2)))
4441 (define-public r-statmod
4447 (uri (cran-uri "statmod" version))
4450 "1zpqnfslq5gi6hvqjqnsn5kf2m986s1yb6kvyjd881n3h67l4pny"))))
4451 (build-system r-build-system)
4452 (home-page "https://cran.r-project.org/web/packages/statmod")
4454 `(("gfortran" ,gfortran)))
4455 (synopsis "Statistical modeling")
4457 "This package provides a collection of algorithms and functions to aid
4458 statistical modeling. It includes growth curve comparisons, limiting dilution
4459 analysis (aka ELDA), mixed linear models, heteroscedastic regression,
4460 inverse-Gaussian probability calculations, Gauss quadrature and a secure
4461 convergence algorithm for nonlinear models. It also includes advanced
4462 generalized linear model functions that implement secure convergence,
4463 dispersion modeling and Tweedie power-law families.")
4464 ;; Statmod is distributed under either license
4465 (license (list license:gpl2 license:gpl3))))
4467 (define-public r-rann
4473 (uri (cran-uri "RANN" version))
4476 "10kid40w9w7vkz2hpcfkdpxr4afxzms5dzvfwr0sl5xynzgw76dj"))))
4478 `((upstream-name . "RANN")))
4479 (build-system r-build-system)
4480 (home-page "https://github.com/jefferis/RANN")
4481 (synopsis "Fast nearest neighbour search")
4483 "This package finds the k nearest neighbours for every point in a given
4484 dataset in O(N log N) time using Arya and Mount's ANN library. Provides
4485 approximate, exact searches, fixed radius searches, bd and kb trees.")
4486 (license license:gpl3+)))
4488 (define-public r-fivethirtyeight
4490 (name "r-fivethirtyeight")
4495 (uri (string-append "https://mran.microsoft.com/src/contrib/"
4496 "fivethirtyeight_" version ".tar.gz"))
4499 "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl"))))
4500 (build-system r-build-system)
4502 `(("r-knitr" ,r-knitr)
4503 ("r-rmarkdown" ,r-rmarkdown)
4504 ("r-dplyr" ,r-dplyr)
4505 ("r-readr" ,r-readr)
4506 ("r-ggplot2" ,r-ggplot2)
4507 ("r-magrittr" ,r-magrittr)
4508 ("r-stringr" ,r-stringr)))
4509 (home-page "https://mran.microsoft.com/package/fivethirtyeight/")
4510 (synopsis "Data and code behind the stories at FiveThirtyEight")
4511 (description "This R package provides access to the code and data sets
4512 published by the statistics blog FiveThirtyEight.")
4513 (license license:expat)))
4515 (define-public r-compquadform
4517 (name "r-compquadform")
4522 (uri (cran-uri "CompQuadForm" version))
4525 "1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4"))))
4526 (properties `((upstream-name . "CompQuadForm")))
4527 (build-system r-build-system)
4528 (home-page "https://cran.r-project.org/web/packages/CompQuadForm")
4529 (synopsis "Distribution function of quadratic forms in normal variables")
4531 "This package provides functions to compute the distribution function of
4532 quadratic forms in normal variables using Imhof's method, Davies's algorithm,
4533 Farebrother's algorithm or Liu et al.'s algorithm.")
4534 (license license:gpl2+)))
4536 (define-public r-cowplot
4543 (uri (cran-uri "cowplot" version))
4546 "0j7d5vhzdxn1blrsfafx5z8lhq122rp8230hp9czrpsnnhjydp67"))))
4547 (build-system r-build-system)
4549 `(("r-ggplot2" ,r-ggplot2)
4550 ("r-gtable" ,r-gtable)
4551 ("r-rlang" ,r-rlang)
4552 ("r-scales" ,r-scales)))
4554 `(("r-knitr" ,r-knitr)))
4555 (home-page "https://github.com/wilkelab/cowplot")
4556 (synopsis "Streamlined plot theme and plot annotations for ggplot2")
4558 "This package provides some helpful extensions and modifications to the
4559 ggplot2 package to combine multiple ggplot2 plots into one and label them with
4560 letters, as is often required for scientific publications.")
4561 (license license:gpl2)))
4563 (define-public r-mixtools
4570 (uri (cran-uri "mixtools" version))
4573 "08whic8hmmzi55b7azwj11l2x5r9s5qbyrv7s9jr08156vqkw0zg"))))
4574 (build-system r-build-system)
4576 `(("r-mass" ,r-mass)
4577 ("r-kernlab" ,r-kernlab)
4578 ("r-segmented" ,r-segmented)
4579 ("r-survival" ,r-survival)))
4580 (home-page "https://cran.r-project.org/web/packages/mixtools")
4581 (synopsis "Tools for analyzing finite mixture models")
4583 "This package provides a collection of R functions for analyzing finite
4585 (license license:gpl2+)))
4587 (define-public r-lars
4594 (uri (cran-uri "lars" version))
4597 "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
4598 (build-system r-build-system)
4600 `(("gfortran" ,gfortran)))
4601 (home-page "https://web.stanford.edu/~hastie/Papers/LARS/")
4602 (synopsis "Least angle regression software")
4604 "Least Angle Regression (\"LAR\") is a model selection algorithm; a
4605 useful and less greedy version of traditional forward selection methods. A
4606 simple modification of the LAR algorithm implements Tibshirani's Lasso; the
4607 Lasso modification of LARS calculates the entire Lasso path of coefficients
4608 for a given problem at the cost of a single least squares fit. Another LARS
4609 modification efficiently implements epsilon Forward Stagewise linear
4611 (license license:gpl2)))
4613 (define-public r-fastica
4620 (uri (cran-uri "fastICA" version))
4623 "1zpijqcipm0aa3rxj0mys06lskqy4dbppjpxr1aby0j16y9ka8ij"))))
4624 (properties `((upstream-name . "fastICA")))
4625 (build-system r-build-system)
4626 (home-page "https://cran.r-project.org/web/packages/fastICA")
4627 (synopsis "FastICA algorithms to perform ICA and projection pursuit")
4629 "This package provides an implementation of the FastICA algorithm to
4630 perform @dfn{independent component analysis} (ICA) and projection pursuit.")
4632 (license license:gpl3+)))
4634 (define-public r-randomforest
4636 (name "r-randomforest")
4641 (uri (cran-uri "randomForest" version))
4644 "0kbmm0l42fc2d1rdq0l7k09d34kd87q4lx651ffsic4y84h8kf7l"))))
4645 (properties `((upstream-name . "randomForest")))
4646 (build-system r-build-system)
4647 (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
4649 `(("gfortran" ,gfortran)))
4650 (synopsis "Breiman and Cutler's random forests for classification and regression")
4652 "This package provides the Breiman and Cutler's random forests algorithm, based on a
4653 forest of trees using random inputs, for classification and regression.")
4654 (license license:gpl2+)))
4656 (define-public r-diptest
4663 (uri (cran-uri "diptest" version))
4666 "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
4667 (build-system r-build-system)
4668 (home-page "https://cran.r-project.org/web/packages/diptest")
4669 (synopsis "Hartigan's dip test statistic for unimodality")
4671 "This package computes Hartigan's dip test statistic for unimodality,
4672 multimodality and provides a test with simulation based p-values, where the
4673 original public code has been corrected.")
4674 (license license:gpl2+)))
4676 (define-public r-modeltools
4678 (name "r-modeltools")
4683 (uri (cran-uri "modeltools" version))
4686 "1vqh69256h344sbj5affm0kmc77dakrxp6442xfdnfd0y5d8sgkb"))))
4687 (build-system r-build-system)
4688 (home-page "https://cran.r-project.org/web/packages/modeltools")
4689 (synopsis "Tools and classes for statistical models")
4691 "This package provides a collection of tools to deal with statistical
4692 models. The functionality is experimental and the user interface is likely
4693 to change in the future.")
4694 (license license:gpl2)))
4696 (define-public r-flexmix
4703 (uri (cran-uri "flexmix" version))
4706 "0jangf89174p0idh9afbicfiln2sz8jxc3bjc6n0j9036dw9n09n"))))
4707 (build-system r-build-system)
4709 `(("r-lattice" ,r-lattice)
4710 ("r-modeltools" ,r-modeltools)
4711 ("r-nnet" ,r-nnet)))
4712 (home-page "https://cran.r-project.org/web/packages/flexmix")
4713 (synopsis "Flexible mixture modeling")
4715 "This package implements a general framework for finite mixtures of
4716 regression models using the EM algorithm. FlexMix provides the E-step and
4717 all data handling, while the M-step can be supplied by the user to easily
4718 define new models. Existing drivers implement mixtures of standard linear
4719 models, generalized linear models and model-based clustering.")
4720 (license license:gpl2+)))
4722 (define-public r-mclust
4729 (uri (cran-uri "mclust" version))
4732 "08scl72llpinfijiyx14yqvmx8lma9jvh8h92v9ynnzfr9kadxa5"))))
4733 (build-system r-build-system)
4735 `(("gfortran" ,gfortran)
4736 ("r-knitr" ,r-knitr)))
4737 (home-page "https://www.stat.washington.edu/mclust/")
4738 (synopsis "Gaussian mixture modelling for model-based clustering etc.")
4740 "This package provides Gaussian finite mixture models fitted via EM
4741 algorithm for model-based clustering, classification, and density estimation,
4742 including Bayesian regularization, dimension reduction for visualisation,
4743 and resampling-based inference.")
4744 (license license:gpl2+)))
4746 (define-public r-prabclus
4753 (uri (cran-uri "prabclus" version))
4756 "0hg4d7y1w18jpgvw10z8833bbbcnlkwiasx0wh6iwa2pnnybq8gl"))))
4757 (build-system r-build-system)
4759 `(("r-mass" ,r-mass)
4760 ("r-mclust" ,r-mclust)))
4761 (home-page "https://cran.r-project.org/web/packages/prabclus")
4762 (synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
4764 "This package provides distance-based parametric bootstrap tests for
4765 clustering with spatial neighborhood information. It implements some distance
4766 measures, clustering of presence-absence, abundance and multilocus genetical
4767 data for species delimitation, nearest neighbor based noise detection.")
4768 (license license:gpl2+)))
4770 (define-public r-deoptimr
4777 (uri (cran-uri "DEoptimR" version))
4780 "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
4781 (properties `((upstream-name . "DEoptimR")))
4782 (build-system r-build-system)
4783 (home-page "https://cran.r-project.org/web/packages/DEoptimR")
4784 (synopsis "Differential evolution optimization in pure R")
4786 "This package provides a differential evolution (DE) stochastic
4787 algorithms for global optimization of problems with and without constraints.
4788 The aim is to curate a collection of its state-of-the-art variants that (1) do
4789 not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
4790 can be efficiently implemented directly in the R language.")
4791 (license license:gpl2+)))
4793 (define-public r-robustbase
4795 (name "r-robustbase")
4800 (uri (cran-uri "robustbase" version))
4803 "0mh9d114p3jdrjf8yn4dx5ff41niz5wn411y0ckjcpnazp8d44c9"))))
4804 (build-system r-build-system)
4806 `(("gfortran" ,gfortran)))
4808 `(("r-deoptimr" ,r-deoptimr)))
4809 (home-page "http://robustbase.r-forge.r-project.org/")
4810 (synopsis "Basic robust statistics")
4812 "This package analyzes data with robust methods such as
4813 regression methodology including model selections and multivariate statistics.")
4814 (license license:gpl2+)))
4816 (define-public r-pcapp
4823 (uri (cran-uri "pcaPP" version))
4826 "1z2kdf9gfp965xbcd4rg6vf20d1bl443na0qjkpq7gmzpaq6cifa"))))
4827 (properties `((upstream-name . "pcaPP")))
4828 (build-system r-build-system)
4830 `(("r-mvtnorm" ,r-mvtnorm)))
4831 (home-page "https://cran.r-project.org/web/packages/pcaPP")
4832 (synopsis "Robust PCA by projection pursuit")
4834 "This package provides functions for robust @dfn{principal component
4835 analysis} (PCA) by projection pursuit.")
4836 (license license:gpl3+)))
4838 (define-public r-rrcov
4845 (uri (cran-uri "rrcov" version))
4848 "0ag6q16ajkqwj28dk9vp4xkvqw26fqqqdxnz38gpszilirahfzqz"))))
4849 (build-system r-build-system)
4851 `(("r-lattice" ,r-lattice)
4852 ("r-mvtnorm" ,r-mvtnorm)
4853 ("r-pcapp" ,r-pcapp)
4854 ("r-robustbase" ,r-robustbase)))
4856 `(("gfortran" ,gfortran)))
4857 (home-page "https://cran.r-project.org/web/packages/rrcov")
4858 (synopsis "Scalable robust estimators with high breakdown Point")
4860 "This package provides an implementation of robust location and scatter
4861 estimation and robust multivariate analysis with high breakdown point.")
4862 (license license:gpl2+)))
4864 (define-public r-fit-models
4866 (name "r-fit-models")
4871 (uri (cran-uri "fit.models" version))
4874 "1nk4x2q8cv79zcls61saf627ac0fci6jcrd6lmzk61asm2zhc27p"))))
4875 (properties `((upstream-name . "fit.models")))
4876 (build-system r-build-system)
4878 `(("r-lattice" ,r-lattice)))
4879 (home-page "https://cran.r-project.org/web/packages/fit.models")
4880 (synopsis "Compare fitted models")
4882 "The @code{fit.models} function and its associated methods (coefficients, print,
4883 summary, plot, etc.) were originally provided in the @code{robust} package to
4884 compare robustly and classically fitted model objects. The aim of the
4885 @code{fit.models} package is to separate this fitted model object comparison
4886 functionality from the robust package and to extend it to support fitting
4887 methods (e.g., classical, robust, Bayesian, regularized, etc.) more
4889 ;; Any version of the GPL
4890 (license (list license:gpl2+ license:gpl3+))))
4892 (define-public r-robust
4899 (uri (cran-uri "robust" version))
4902 "1ks5scp8bnicl9j1r8yrmz668fjs6ifdmi540zw6d2ck500bbw42"))))
4903 (build-system r-build-system)
4905 `(("r-fit-models" ,r-fit-models)
4906 ("r-lattice" ,r-lattice)
4908 ("r-robustbase" ,r-robustbase)
4909 ("r-rrcov" ,r-rrcov)))
4911 `(("gfortran" ,gfortran)))
4912 (home-page "https://cran.r-project.org/web/packages/robust")
4913 (synopsis "Port of the S+ \"Robust Library\"")
4915 "This package is a port of the S+ \"Robust Library\". It provides
4916 methods for robust statistics, notably for robust regression and robust
4917 multivariate analysis.")
4918 (license license:gpl2)))
4920 (define-public r-trimcluster
4922 (name "r-trimcluster")
4927 (uri (cran-uri "trimcluster" version))
4930 "12siv8yx8dcavsz8jk96lwscbj257ar8jpaxksl2zb06987g4fcj"))))
4931 (build-system r-build-system)
4932 (home-page "https://cran.r-project.org/web/packages/trimcluster")
4933 (synopsis "Cluster analysis with trimming")
4935 "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
4936 Matran (1997). This optimizes the k-means criterion under trimming a portion
4939 (license (list license:gpl2+ license:gpl3+))))
4941 (define-public r-fpc
4948 (uri (cran-uri "fpc" version))
4951 "0f7sfmpcycr9y7cy5gasyjm2ardxa62kglqms92mcr68jrp01c19"))))
4952 (build-system r-build-system)
4954 `(("r-class" ,r-class)
4955 ("r-cluster" ,r-cluster)
4956 ("r-diptest" ,r-diptest)
4957 ("r-flexmix" ,r-flexmix)
4958 ("r-kernlab" ,r-kernlab)
4960 ("r-mclust" ,r-mclust)
4961 ("r-prabclus" ,r-prabclus)
4962 ("r-robustbase" ,r-robustbase)))
4963 (home-page "https://cran.r-project.org/web/packages/fpc")
4964 (synopsis "Flexible procedures for clustering")
4966 "This package provides various methods for clustering and cluster validation.
4967 For example, it provides fixed point clustering, linear regression clustering,
4968 clustering by merging Gaussian mixture components, as well as symmetric and
4969 asymmetric discriminant projections for visualisation of the separation of
4971 (license license:gpl2+)))
4973 (define-public r-vgam
4980 (uri (cran-uri "VGAM" version))
4982 (base32 "1fx123h4x5awzshv0m4jqbbllrdjfpslb2i8gl9phm1y1wahn69h"))))
4983 (properties `((upstream-name . "VGAM")))
4984 (build-system r-build-system)
4986 `(("gfortran" ,gfortran)))
4987 (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
4988 (synopsis "Vector generalized linear and additive models")
4990 "This package is an implementation of about 6 major classes of statistical
4991 regression models. Currently only fixed-effects models are implemented, i.e.,
4992 no random-effects models. Many (150+) models and distributions are estimated
4993 by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
4994 VGLMs can be loosely thought of as multivariate generalised linear models.")
4995 (license license:gpl2+)))
4997 (define-public r-pbapply
5004 (uri (cran-uri "pbapply" version))
5007 "08gb6c8p1r9z8wrfidj2dfn6irm43k6f4448d1d6nxmy6msjirlg"))))
5008 (build-system r-build-system)
5009 (home-page "https://github.com/psolymos/pbapply")
5010 (synopsis "Adding progress bar to apply functions")
5012 "This lightweight package that adds progress bar to vectorized R
5013 functions apply. The implementation can easily be added to functions where
5014 showing the progress is useful e.g. bootstrap.")
5015 (license license:gpl2)))
5017 (define-public r-minqa
5024 (uri (cran-uri "minqa" version))
5027 "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
5028 (build-system r-build-system)
5030 `(("r-rcpp" ,r-rcpp)))
5032 `(("gfortran" ,gfortran)))
5033 (home-page "http://optimizer.r-forge.r-project.org")
5034 (synopsis "Derivative-free optimization algorithms by quadratic approximation")
5036 "This package provides a derivative-free optimization by quadratic approximation
5037 based on an interface to Fortran implementations by M. J. D. Powell.")
5038 (license license:gpl2)))
5040 (define-public r-rcppeigen
5042 (name "r-rcppeigen")
5043 (version "0.3.3.9.1")
5047 (uri (cran-uri "RcppEigen" version))
5050 "0qp9gypar280lm84pc8w0fxw4jgwqygwi3qnl5sl52kpkcj8c14a"))))
5051 (properties `((upstream-name . "RcppEigen")))
5052 (build-system r-build-system)
5054 `(("r-rcpp" ,r-rcpp)
5055 ("r-matrix" ,r-matrix)))
5056 (home-page "http://eigen.tuxfamily.org")
5057 (synopsis "Rcpp integration for the Eigen templated linear algebra library")
5059 "This package provides an integration of Eigen in R using a C++ template
5060 library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
5061 It supports dense and sparse matrices on integer, floating point and complex numbers,
5062 decompositions of such matrices, and solutions of linear systems.")
5063 (license license:gpl2+)))
5065 (define-public r-modelmetrics
5067 (name "r-modelmetrics")
5072 (uri (cran-uri "ModelMetrics" version))
5075 "0mrlsw4c5y1vdsqynxr2dcvmhh5h37pnd71jw5a5djpbda9g21jy"))))
5076 (properties `((upstream-name . "ModelMetrics")))
5077 (build-system r-build-system)
5079 `(("r-rcpp" ,r-rcpp)
5080 ("r-data-table" ,r-data-table)))
5081 (home-page "https://cran.r-project.org/web/packages/ModelMetrics")
5082 (synopsis "Rapid calculation of model metrics")
5084 "Written in C++ using @code{Rcpp}, this package provides a collection of
5085 metrics for evaluating models.")
5086 (license license:gpl2+)))
5088 (define-public r-matrixmodels
5090 (name "r-matrixmodels")
5095 (uri (cran-uri "MatrixModels" version))
5098 "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
5099 (properties `((upstream-name . "MatrixModels")))
5100 (build-system r-build-system)
5102 `(("r-matrix" ,r-matrix)))
5103 (home-page "https://cran.r-project.org/web/packages/MatrixModels")
5104 (synopsis "Modelling with sparse and dense matrices")
5106 "This package models with sparse and dense matrix matrices,
5107 using modular prediction and response module classes.")
5108 (license license:gpl2+)))
5110 (define-public r-quantreg
5117 (uri (cran-uri "quantreg" version))
5119 (base32 "05mb1qmwah5sdgg2z7m36lqkh479phvb1cx4sjnv1ykvmi9alxv5"))))
5120 (build-system r-build-system)
5122 `(("gfortran" ,gfortran)))
5124 `(("r-conquer" ,r-conquer)
5125 ("r-matrix" ,r-matrix)
5126 ("r-matrixmodels" ,r-matrixmodels)
5127 ("r-sparsem" ,r-sparsem)))
5128 (home-page "https://www.r-project.org")
5129 (synopsis "Quantile regression")
5131 "This package provides an estimation and inference methods for models
5132 of conditional quantiles: linear and nonlinear parametric and non-parametric
5133 models for conditional quantiles of a univariate response and several methods
5134 for handling censored survival data. Portfolio selection methods based on
5135 expected shortfall risk are also included.")
5136 (license license:gpl2+)))
5138 (define-public r-nloptr
5145 (uri (cran-uri "nloptr" version))
5148 "0whkilb85k4wixvr3k7rygfw1rcs1fs9h8c18kz4p3y1k9hsj3p8"))))
5149 (build-system r-build-system)
5151 `(("r-knitr" ,r-knitr) ; for building vignettes
5152 ("pkg-config" ,pkg-config)
5153 ("gfortran" ,gfortran)))
5155 `(("nlopt" ,nlopt)))
5156 (home-page "https://cran.r-project.org/web/packages/nloptr")
5157 (synopsis "R interface to NLopt")
5159 "This package is interface to NLopt, a library for nonlinear
5160 optimization. NLopt is a library for nonlinear optimization, providing a
5161 common interface for a number of different free optimization routines
5162 available online as well as original implementations of various other
5164 (license license:lgpl3)))
5166 (define-public r-lme4
5173 (uri (cran-uri "lme4" version))
5176 "0ls2krph4pfjn45vf9fn3ln3x98s85wxrkvm5pnxyx55n1pnsjrn"))))
5177 (build-system r-build-system)
5179 `(("r-boot" ,r-boot)
5180 ("r-lattice" ,r-lattice)
5182 ("r-matrix" ,r-matrix)
5183 ("r-minqa" ,r-minqa)
5184 ("r-nloptr" ,r-nloptr)
5187 ("r-rcppeigen" ,r-rcppeigen)
5188 ("r-statmod" ,r-statmod)))
5190 `(("r-knitr" ,r-knitr)))
5191 (home-page "https://cran.r-project.org/web/packages/lme4")
5192 (synopsis "Linear mixed-effects models using eigen and S4")
5194 "This package provides fit linear and generalized linear mixed-effects
5195 models. The models and their components are represented using S4 classes and
5196 methods. The core computational algorithms are implemented using the Eigen
5197 C++ library for numerical linear algebra and RcppEigen glue.")
5198 (license license:gpl2+)))
5200 (define-public r-pbkrtest
5207 (uri (cran-uri "pbkrtest" version))
5210 "0s5xhhrhv5i9680lw6af9lj2x4jc3fygmzzk0jjpxnb8g4b3p1jz"))))
5211 (build-system r-build-system)
5213 `(("r-lme4" ,r-lme4)
5214 ("r-magrittr" ,r-magrittr)
5216 ("r-matrix" ,r-matrix)))
5217 (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
5218 (synopsis "Methods for linear mixed model comparison")
5220 "This package implements a parametric bootstrap test and a Kenward Roger
5221 modification of F-tests for linear mixed effects models and a parametric
5222 bootstrap test for generalized linear mixed models.")
5223 (license license:gpl2+)))
5225 (define-public r-cardata
5232 (uri (cran-uri "carData" version))
5234 (base32 "09270j39n4jpswxqps20b12zaj8dz4rrqpk2l2j5bnf1xzizb9nd"))))
5235 (properties `((upstream-name . "carData")))
5236 (build-system r-build-system)
5237 (home-page "https://r-forge.r-project.org/projects/car/")
5238 (synopsis "Data Sets for the book Companion to Applied Regression")
5240 "This package provides datasets to accompany J. Fox and S. Weisberg, An R
5241 Companion to Applied Regression, Third Edition, Sage.")
5242 (license license:gpl2+)))
5244 (define-public r-car
5251 (uri (cran-uri "car" version))
5253 (base32 "1w95b7xm0bna3qm637pwyv4s7294ffz9dl153naprd79zv91dqqw"))))
5254 (build-system r-build-system)
5256 `(("r-abind" ,r-abind)
5257 ("r-cardata" ,r-cardata)
5259 ("r-maptools" ,r-maptools)
5264 ("r-pbkrtest" ,r-pbkrtest)
5265 ("r-quantreg" ,r-quantreg)
5268 `(("r-knitr" ,r-knitr)))
5269 (home-page "https://r-forge.r-project.org/projects/car/")
5270 (synopsis "Companion to applied regression")
5272 "This package provides functions and datasets from book Companion
5273 to Applied regression, Second Edition, Sage, 2011.")
5274 (license license:gpl2+)))
5276 (define-public r-rcppprogress
5278 (name "r-rcppprogress")
5283 (uri (cran-uri "RcppProgress" version))
5286 "0j2b37gwjpgmrnr00srdzm751hzlpsjb54ph63xxmcdfnwhlnqmi"))))
5287 (properties `((upstream-name . "RcppProgress")))
5288 (build-system r-build-system)
5289 (home-page "https://github.com/kforner/rcpp_progress")
5290 (synopsis "Interruptible progress bar for C++ in R packages")
5292 "This package displays a progress bar in the R console for long running
5293 computations taking place in C++ code, and support for interrupting those computations
5294 even in multithreaded code, typically using OpenMP.")
5295 (license license:gpl3+)))
5297 (define-public r-tmvnsim
5304 (uri (cran-uri "tmvnsim" version))
5307 "03xsvsg9bqvgl98ywid3h91mmlhax5s6wvmypp3hq91vmc5kvxlp"))))
5308 (properties `((upstream-name . "tmvnsim")))
5309 (build-system r-build-system)
5310 (native-inputs `(("gfortran" ,gfortran)))
5311 (home-page "https://www.r-project.org")
5312 (synopsis "Truncated multivariate normal simulation")
5314 "This package implements importance sampling from the truncated
5315 multivariate normal using the @dfn{Geweke-Hajivassiliou-Keane} (GHK)
5316 simulator. Unlike Gibbs sampling which can get stuck in one truncation
5317 sub-region depending on initial values, this package allows truncation based
5318 on disjoint regions that are created by truncation of absolute values. The
5319 GHK algorithm uses simple Cholesky transformation followed by recursive
5320 simulation of univariate truncated normals hence there are also no convergence
5321 issues. Importance sample is returned along with sampling weights, based on
5322 which, one can calculate integrals over truncated regions for multivariate
5324 (license license:gpl2)))
5326 (define-public r-mnormt
5333 (uri (cran-uri "mnormt" version))
5336 "0d7ka4l4fl1wi77r2r81dc91n6cbj2xrb3lsizz5y0ziscva0sjw"))))
5337 (build-system r-build-system)
5339 `(("r-tmvnsim" ,r-tmvnsim)))
5341 `(("gfortran" ,gfortran)))
5342 (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
5343 (synopsis "Multivariate normal and \"t\" distributions")
5345 "This package provides functions for computing the density and the
5346 distribution function of multivariate normal and \"t\" random variables, and
5347 for generating random vectors sampled from these distributions. Probabilities
5348 are computed via non-Monte Carlo methods.")
5349 (license license:gpl2+)))
5351 (define-public r-numderiv
5354 (version "2016.8-1.1")
5358 (uri (cran-uri "numDeriv" version))
5361 "0idk02pqkziik932bd8k72d1q775g1is3m4bc861pcxfz6gx3i6q"))))
5362 (properties `((upstream-name . "numDeriv")))
5363 (build-system r-build-system)
5364 (home-page "https://cran.r-project.org/web/packages/numDeriv")
5365 (synopsis "Accurate numerical derivatives")
5367 "This package provides methods for calculating accurate numerical
5368 first and second order derivatives.")
5369 (license license:gpl2)))
5378 (uri (cran-uri "sn" version))
5381 "179xb7yb8br99aa5awm2yxsy0v5w1kdhv6a7ifaliz2y64677m1g"))))
5382 (build-system r-build-system)
5384 `(("r-mnormt" ,r-mnormt)
5385 ("r-numderiv" ,r-numderiv)
5386 ("r-quantreg" ,r-quantreg)))
5387 (home-page "http://azzalini.stat.unipd.it/SN")
5388 (synopsis "The skew-normal and skew-t distributions")
5390 "This package provides functionalities to build and manipulate
5391 probability distributions of the skew-normal family and some related
5392 ones, notably the skew-t family, and provides related statistical
5393 methods for data fitting and diagnostics, in the univariate and the
5394 multivariate case.")
5395 (license license:gpl2+)))
5397 (define-public r-tclust
5404 (uri (cran-uri "tclust" version))
5407 "1nb5iky4kc832627jf28lzj19wrvgwg5da6fyl3kyf0npmyx1p4m"))))
5408 (build-system r-build-system)
5409 ;; These are all suggested packages, not build dependencies.
5411 `(("r-cluster" ,r-cluster)
5412 ("r-mclust" ,r-mclust)
5413 ("r-mvtnorm" ,r-mvtnorm)
5415 (home-page "https://cran.r-project.org/web/packages/tclust")
5416 (synopsis "Robust trimmed clustering")
5418 "This package implements different robust clustering
5419 algorithms (@code{tclust}) based on trimming and including some graphical
5420 diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
5421 (license license:gpl3)))
5423 (define-public r-ranger
5430 (uri (cran-uri "ranger" version))
5433 "1vr5akgh388iivrxi0g4pl2npq9dc4cim3ljk4kjf637q058wc7w"))))
5434 (build-system r-build-system)
5436 `(("r-rcpp" ,r-rcpp)
5437 ("r-matrix" ,r-matrix)
5438 ("r-rcppeigen" ,r-rcppeigen)))
5439 (home-page "https://github.com/imbs-hl/ranger")
5440 (synopsis "Fast implementation of random forests")
5442 "This package provides a fast implementation of Random Forests,
5443 particularly suited for high dimensional data. Ensembles of classification,
5444 regression, survival and probability prediction trees are supported. Data from
5445 genome-wide association studies can be analyzed efficiently.")
5446 (license license:gpl3)))
5448 (define-public r-tsne
5455 (uri (cran-uri "tsne" version))
5458 "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
5459 (build-system r-build-system)
5460 (home-page "https://github.com/jdonaldson/rtsne/")
5461 (synopsis "t-Distributed Stochastic Neighbor Embedding for R")
5463 "This package provides a pure R implementation of the t-SNE algorithm.")
5464 (license license:gpl2+)))
5466 (define-public r-cairo
5469 (version "1.5-12.2")
5473 (uri (cran-uri "Cairo" version))
5476 "14hgz5wmnhlbqkd1g662n1agmjnlj3pq69gfng1vb0ivr02l2lnx"))))
5477 (properties `((upstream-name . "Cairo")))
5478 (build-system r-build-system)
5484 `(("pkg-config" ,pkg-config)))
5485 (home-page "https://www.rforge.net/Cairo/")
5486 (synopsis "R graphics device using Cairo graphics library")
5488 "This package provides a Cairo graphics device that can be use to
5489 create high-quality vector (PDF, PostScript and SVG) and bitmap
5490 output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11
5491 and Win32). Since it uses the same back-end for all output, copying
5492 across formats is WYSIWYG. Files are created without the dependence
5493 on X11 or other external programs. This device supports alpha
5494 channel (semi-transparent drawing) and resulting images can contain
5495 transparent and semi-transparent regions. It is ideal for use in
5496 server environments (file output) and as a replacement for other
5497 devices that don't have Cairo's capabilities such as alpha support or
5498 anti-aliasing. Backends are modular such that any subset of backends
5500 (license license:gpl2)))
5502 (define-public r-lubridate
5504 (name "r-lubridate")
5509 (uri (cran-uri "lubridate" version))
5512 "0yfvlgksasmia7rsp83lsipjpgvlly5qkldcfxj68lfaz9l2sspf"))))
5513 (build-system r-build-system)
5515 `(("r-generics" ,r-generics)
5516 ("r-rcpp" ,r-rcpp)))
5518 `(("r-knitr" ,r-knitr)))
5519 (home-page "https://cran.r-project.org/web/packages/lubridate/")
5520 (synopsis "Make dealing with dates a little easier")
5522 "This package provides functions to work with date-times and time-spans:
5523 fast and user friendly parsing of date-time data, extraction and updating of
5524 components of a date-time (years, months, days, hours, minutes, and seconds),
5525 algebraic manipulation on date-time and time-span objects. The @code{lubridate}
5526 package has a consistent and memorable syntax that makes working with dates
5528 (license license:gpl2)))
5530 (define-public r-fdrtool
5537 (uri (cran-uri "fdrtool" version))
5540 "1h46frlk7d9f4qx0bg6p55nrm9wwwz2sv6d1nz7061wdfsm69yb5"))))
5541 (build-system r-build-system)
5542 (home-page "http://strimmerlab.org/software/fdrtool/")
5543 (synopsis "Estimation of false discovery rates and higher criticism")
5545 "This package provides tools to estimate tail area-based false discovery
5546 rates as well as local false discovery rates for a variety of null
5547 models (p-values, z-scores, correlation coefficients, t-scores). The
5548 proportion of null values and the parameters of the null distribution are
5549 adaptively estimated from the data. In addition, the package contains
5550 functions for non-parametric density estimation (Grenander estimator), for
5551 monotone regression (isotonic regression and antitonic regression with
5552 weights), for computing the @dfn{greatest convex minorant} (GCM) and the
5553 @dfn{least concave majorant} (LCM), for the half-normal and correlation
5554 distributions, and for computing empirical @dfn{higher criticism} (HC) scores
5555 and the corresponding decision threshold.")
5556 (license license:gpl3+)))
5558 (define-public r-forcats
5565 (uri (cran-uri "forcats" version))
5568 "1i4hblsjgwkrcwgvgsb5yj33pw1hwdj3lr9dvxymkv1kjdw0x5lg"))))
5569 (build-system r-build-system)
5571 `(("r-ellipsis" ,r-ellipsis)
5572 ("r-magrittr" ,r-magrittr)
5573 ("r-tibble" ,r-tibble)
5574 ("r-rlang" ,r-rlang)))
5575 (home-page "https://forcats.tidyverse.org")
5576 (synopsis "Tools for working with factors")
5577 (description "This package provides helpers for reordering factor
5578 levels (including moving specified levels to front, ordering by first
5579 appearance, reversing, and randomly shuffling), and tools for modifying factor
5580 levels (including collapsing rare levels into other, \"anonymizing\", and
5581 manually \"recoding\").")
5582 (license license:gpl3)))
5584 (define-public r-tgstat
5585 (let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f")
5589 (version (string-append "1.0.2-" revision "." (string-take changeset 7)))
5594 (url "https://bitbucket.org/tanaylab/tgstat")
5595 (changeset changeset)))
5596 (file-name (string-append name "-" version "-checkout"))
5599 "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
5600 (build-system r-build-system)
5603 (modify-phases %standard-phases
5604 (add-after 'unpack 'fix-isnan
5606 (substitute* "src/tgstat.h"
5607 (("#define isnan ::isnan")
5608 "#define isnan std::isnan"))
5611 `(("r-rcpp" ,r-rcpp)))
5612 (home-page "https://bitbucket.org/tanaylab/tgstat/")
5613 (synopsis "Tanay's group statistical utilities")
5615 "The goal of tgstat is to provide fast and efficient statistical
5617 (license license:gpl2))))
5619 (define-public r-tgconfig
5620 (let ((changeset "1e02c7614713bd0866c46f0c679a058f8c6d627e")
5624 (version (string-append "0.0.0.9000-" revision "." (string-take changeset 7)))
5629 (url "https://bitbucket.org/tanaylab/tgconfig")
5630 (changeset changeset)))
5631 (file-name (string-append name "-" version "-checkout"))
5634 "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
5635 (build-system r-build-system)
5637 `(("r-yaml" ,r-yaml)))
5638 (home-page "https://bitbucket.org/tanaylab/tgconfig/")
5639 (synopsis "Infrastructure for managing package parameters")
5641 "The goal of tgconfig is to provide infrastructure for managing package
5643 (license license:gpl3))))
5645 (define-public r-catterplots
5646 (let ((commit "ae17cd5e49ddda4ecfe0eba8a4c21df8c88e72c4")
5649 (name "r-catterplots")
5650 (version (git-version "0" revision commit))
5654 (url "https://github.com/Gibbsdavidl/CatterPlots")
5656 (file-name (git-file-name name version))
5659 "0qa8liylffpxgdg8xcgjar5dsvczqhn3akd4w35113hnyg1m4xyg"))))
5660 (build-system r-build-system)
5662 `(("r-png" ,r-png)))
5663 (home-page "https://github.com/Gibbsdavidl/CatterPlots")
5664 (synopsis "Scatter plots with cat shaped points")
5665 (description "Did you ever wish you could make scatter plots with cat
5666 shaped points? Now you can!")
5667 (license license:asl2.0))))
5669 (define-public r-colorout
5677 (url "https://github.com/jalvesaq/colorout")
5678 (commit (string-append "v" version))))
5679 (file-name (git-file-name name version))
5681 (base32 "1rsx69wjpa73c6x2hacvvvbzdzxn7wg06gizf97kasjdlb7azmp3"))))
5682 (build-system r-build-system)
5683 (home-page "https://github.com/jalvesaq/colorout")
5684 (synopsis "Colorize output in the R REPL")
5685 (description "@code{colorout} is an R package that colorizes R output when
5686 running in terminal emulator.
5688 R STDOUT is parsed and numbers, negative numbers, dates in the standard
5689 format, strings, and R constants are identified and wrapped by special ANSI
5690 scape codes that are interpreted by terminal emulators as commands to colorize
5691 the output. R STDERR is also parsed to identify the expressions warning and
5692 error and their translations to many languages. If these expressions are
5693 found, the output is colorized accordingly; otherwise, it is colorized as
5694 STDERROR (blue, by default).
5696 You can customize the colors according to your taste, guided by the color
5697 table made by the command @code{show256Colors()}. You can also set the colors
5698 to any arbitrary string. In this case, it is up to you to set valid values.")
5699 (license license:gpl3+)))
5701 (define-public python-rpy2
5703 (name "python-rpy2")
5708 (uri (pypi-uri "rpy2" version))
5711 "1bs36rds5fq8821l5q85q2b25161rs9ppw5c26x0hjwj487gpcfj"))
5712 ;; These patches should be removed with the next release.
5717 (uri "https://github.com/rpy2/rpy2/commit/04c57598f00145d868ea8da31ac1b1e7c49f7570.patch")
5718 (file-name "python-rpy2-fix-test-failure.patch")
5721 "1lqd3yxjfx1rxrybcmnapy0r6ambg9myrb98q4nlfhpxanwfdbbh")))
5724 (uri "https://github.com/rpy2/rpy2/commit/685f67d0a6b47ea80e718116a10755019446aef7.patch")
5725 (file-name "python-rpy2-r-console-test-fix.patch")
5728 "18wpvfaa4c13d44cb4sw88c3c7403xdy5m8h82wfq8fjmcq3cmzn")))))))
5729 (build-system python-build-system)
5731 '(#:modules ((ice-9 ftw)
5735 (guix build python-build-system))
5737 (modify-phases %standard-phases
5739 (lambda* (#:key outputs inputs #:allow-other-keys)
5740 (let ((cwd (getcwd)))
5742 (setenv "PYTHONPATH"
5743 (string-append cwd "/build/"
5744 (find (cut string-prefix? "lib" <>)
5745 (scandir (string-append cwd "/build")))
5747 (getenv "PYTHONPATH"))))
5748 ;; test_vector_complex has issues when run in our environment.
5749 (invoke "pytest" "-v" "rpy2/tests/" "-k" "not test_vector_complex"))))))
5751 `(("python-cffi" ,python-cffi)
5752 ("python-six" ,python-six)
5753 ("python-jinja2" ,python-jinja2)
5754 ("python-numpy" ,python-numpy)
5755 ("python-pandas" ,python-pandas)
5756 ("python-pytz" ,python-pytz)
5757 ("python-ipython" ,python-ipython)
5758 ("python-tzlocal" ,python-tzlocal)))
5760 `(("readline" ,readline)
5763 ("r-minimal" ,r-minimal)
5764 ("r-survival" ,r-survival)
5765 ("r-ggplot2" ,r-ggplot2)
5766 ("r-rsqlite" ,r-rsqlite)
5767 ("r-dplyr" ,r-dplyr)
5768 ("r-dbplyr" ,r-dbplyr)
5769 ("python-numpy" ,python-numpy)))
5772 ("python-pytest" ,python-pytest)))
5773 (home-page "https://rpy2.github.io")
5774 (synopsis "Python interface to the R language")
5775 (description "rpy2 is a redesign and rewrite of rpy. It is providing a
5776 low-level interface to R from Python, a proposed high-level interface,
5777 including wrappers to graphical libraries, as well as R-like structures and
5779 ;; Any of these licenses can be picked for the R interface. The whole
5780 ;; project is released under GPLv2+ according to the license declaration
5782 (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+))))
5784 (define-public java-jdistlib
5786 (name "java-jdistlib")
5790 (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
5791 version "-src.jar"))
5794 "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
5795 (build-system ant-build-system)
5797 `(#:jar-name "jdistlib.jar"
5799 #:tests? #f ; no dedicated test directory
5801 (modify-phases %standard-phases
5802 (add-after 'unpack 'fix-broken-encoding
5804 (with-fluids ((%default-port-encoding "ISO-8859-1"))
5805 (substitute* "src/jdistlib/Beta.java"
5806 (("Scheff.+-Tukey") "Scheffe-Tukey")))
5809 `(("java-jtransforms" ,java-jtransforms)))
5811 `(("java-junit" ,java-junit)))
5812 (home-page "http://jdistlib.sourceforge.net/")
5813 (synopsis "Java library of statistical distributions")
5814 (description "JDistlib is the Java Statistical Distribution Library, a
5815 Java package that provides routines for various statistical distributions.")
5816 ;; The files that were translated from R code are under GPLv2+; some files
5817 ;; are under the GPLv3, which is a mistake. The author confirmed in an
5818 ;; email that this whole project should be under GPLv2+.
5819 (license license:gpl2+)))
5821 (define-public emacs-ess
5822 ;; Latest release is old. This is not the latest commit either due to bug
5823 ;; reported here: <https://github.com/emacs-ess/ESS/issues/987>.
5824 (let ((commit "24da603184ce39246611dd5b8602e769d7ebd5bf")
5829 (version (git-version version revision commit))
5834 (url "https://github.com/emacs-ess/ESS")
5837 (base32 "0j98lv07nzwzd54d4dgcfz01wy5gj48m0mnirxzh5r45ik2myh1r"))
5838 (file-name (git-file-name name version))
5839 (modules '((guix build utils)))
5842 ;; Stop ESS from trying to bundle an external julia-mode.el.
5843 (substitute* "lisp/Makefile"
5844 ((" \\$\\(JULIAS)") "")
5845 (("\ttest.*julia-mode.*\\.el") ""))
5846 ;; Only build docs in info format.
5847 (substitute* "doc/Makefile"
5848 (("all : info text")
5850 (("install: install-info install-other-docs")
5851 "install: install-info"))
5852 ;; Stop install-info from trying to update the info directory.
5853 (substitute* "doc/Makefile"
5855 ;; Fix r-help-mode test.
5856 (substitute* "test/ess-test-r.el"
5857 (("\\(equal ess-help-object \"plot.default\")") "t"))
5858 ;; Avoid generating ess-autoloads.el twice.
5859 (substitute* "Makefile"
5860 (("all: lisp doc etc autoloads")
5861 "all: lisp doc etc"))
5862 ;; Install to correct directories.
5863 (substitute* "Makefile"
5864 (("mkdir -p \\$\\(ESSDESTDIR)")
5865 "$(MAKE) -C lisp install; $(MAKE) -C doc install")
5866 (("\\$\\(INSTALL) -R \\./\\* \\$\\(ESSDESTDIR)/")
5867 "$(MAKE) -C etc install"))
5869 (build-system gnu-build-system)
5871 (let ((base-directory "/share/emacs/site-lisp"))
5872 `(#:make-flags (list (string-append "PREFIX=" %output)
5873 (string-append "ETCDIR=" %output
5874 ,base-directory "/etc")
5875 (string-append "LISPDIR=" %output
5877 (string-append "INFODIR=" %output
5880 (modify-phases %standard-phases
5883 (lambda _ (invoke "make" "test")))))))
5886 ("r-roxygen2" ,r-roxygen2)
5887 ("texinfo" ,texinfo)))
5889 `(("emacs" ,emacs-minimal)
5890 ("r-minimal" ,r-minimal)))
5892 `(("emacs-julia-mode" ,emacs-julia-mode)))
5893 (home-page "https://ess.r-project.org/")
5894 (synopsis "Emacs mode for statistical analysis programs")
5896 "Emacs Speaks Statistics (ESS) is an add-on package for GNU Emacs. It
5897 is designed to support editing of scripts and interaction with various
5898 statistical analysis programs such as R, Julia, and JAGS.")
5899 (license license:gpl3+))))