1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com>
4 ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
5 ;;; Copyright © 2016, 2017, 2019 Efraim Flashner <efraim@flashner.co.il>
6 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
7 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
8 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
9 ;;; Copyright © 2016, 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
10 ;;; Copyright © 2017 Kyle Meyer <kyle@kyleam.com>
11 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
12 ;;; Copyright © 2017 Alex Kost <alezost@gmail.com>
13 ;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com>
15 ;;; This file is part of GNU Guix.
17 ;;; GNU Guix is free software; you can redistribute it and/or modify it
18 ;;; under the terms of the GNU General Public License as published by
19 ;;; the Free Software Foundation; either version 3 of the License, or (at
20 ;;; your option) any later version.
22 ;;; GNU Guix is distributed in the hope that it will be useful, but
23 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
24 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
25 ;;; GNU General Public License for more details.
27 ;;; You should have received a copy of the GNU General Public License
28 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
30 (define-module (gnu packages statistics)
31 #:use-module ((guix licenses) #:prefix license:)
32 #:use-module (guix packages)
33 #:use-module (guix download)
34 #:use-module (guix hg-download)
35 #:use-module (guix git-download)
36 #:use-module (guix utils)
37 #:use-module (guix build-system ant)
38 #:use-module (guix build-system gnu)
39 #:use-module (guix build-system r)
40 #:use-module (guix build-system python)
41 #:use-module (guix build-system trivial)
42 #:use-module (gnu packages)
43 #:use-module (gnu packages algebra)
44 #:use-module (gnu packages autotools)
45 #:use-module (gnu packages bash)
46 #:use-module (gnu packages check)
47 #:use-module (gnu packages compression)
48 #:use-module (gnu packages cran)
49 #:use-module (gnu packages curl)
50 #:use-module (gnu packages emacs)
51 #:use-module (gnu packages emacs-xyz)
52 #:use-module (gnu packages fontutils)
53 #:use-module (gnu packages gcc)
54 #:use-module (gnu packages gtk)
55 #:use-module (gnu packages gettext)
56 #:use-module (gnu packages glib)
57 #:use-module (gnu packages haskell-xyz)
58 #:use-module (gnu packages icu4c)
59 #:use-module (gnu packages image)
60 #:use-module (gnu packages java)
61 #:use-module (gnu packages libffi)
62 #:use-module (gnu packages machine-learning)
63 #:use-module (gnu packages maths)
64 #:use-module (gnu packages multiprecision)
65 #:use-module (gnu packages pcre)
66 #:use-module (gnu packages perl)
67 #:use-module (gnu packages pkg-config)
68 #:use-module (gnu packages python)
69 #:use-module (gnu packages python-science)
70 #:use-module (gnu packages python-xyz)
71 #:use-module (gnu packages readline)
72 #:use-module (gnu packages sphinx)
73 #:use-module (gnu packages ssh)
74 #:use-module (gnu packages tcl)
75 #:use-module (gnu packages tex)
76 #:use-module (gnu packages texinfo)
77 #:use-module (gnu packages time)
78 #:use-module (gnu packages tls)
79 #:use-module (gnu packages base)
80 #:use-module (gnu packages version-control)
81 #:use-module (gnu packages web)
82 #:use-module (gnu packages xml)
83 #:use-module (gnu packages xorg)
84 #:use-module (srfi srfi-1))
94 (uri (string-append "mirror://gnu/pspp/pspp-"
98 "07pp27zycrb5x927jwaj9r3q7hy915jh51xs85zxby6gfiwl63m5"))))
99 (build-system gnu-build-system)
102 ("gettext" ,gettext-minimal)
106 ("readline" ,readline)
108 ("gtksourceview" ,gtksourceview)
109 ("spread-sheet-widget" ,spread-sheet-widget)
112 `(("autoconf" ,autoconf) ;for tests
113 ("glib" ,glib "bin") ;for glib-genmarshal
115 ("pkg-config" ,pkg-config)
116 ("python" ,python-2) ;for tests
117 ("texinfo" ,texinfo)))
118 (home-page "https://www.gnu.org/software/pspp/")
119 (synopsis "Statistical analysis")
121 "GNU PSPP is a statistical analysis program. It can perform
122 descriptive statistics, T-tests, linear regression and non-parametric tests.
123 It features both a graphical interface as well as command-line input. PSPP
124 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
125 can be imported from spreadsheets, text files and database sources and it can
126 be output in text, PostScript, PDF or HTML.")
127 (license license:gpl3+)))
135 (uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/"
136 (version-major version) ".x/Source/"
137 "JAGS-" version ".tar.gz"))
140 "1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica"))))
141 (build-system gnu-build-system)
142 (home-page "http://mcmc-jags.sourceforge.net/")
144 `(("gfortran" ,gfortran)
146 (synopsis "Gibbs sampler")
147 (description "JAGS is Just Another Gibbs Sampler. It is a program for
148 analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
149 simulation not wholly unlike BUGS. JAGS was written with three aims in mind:
152 @item To have a cross-platform engine for the BUGS language;
153 @item To be extensible, allowing users to write their own functions,
154 distributions and samplers;
155 @item To be a platform for experimentation with ideas in Bayesian modelling.
157 (license license:gpl2)))
159 (define-public libxls
166 (uri (string-append "https://github.com/libxls/libxls/releases/download/"
167 "v" version "/libxls-" version ".tar.gz"))
169 (base32 "1akadsyl10rp101ccjmrxr7933c3v641k377bn74jv6cdkcm4zld"))))
170 (build-system gnu-build-system)
171 (home-page "https://github.com/libxls/libxls")
172 (synopsis "Read binary (.xls) Excel spreadsheet files")
174 "libxls is a C library to read .xls spreadsheet files in the binary OLE
175 BIFF8 format as created by Excel 97 and later versions. It cannot write them.
177 This package also provides @command{xls2csv} to export Excel files to CSV.")
178 (license license:bsd-2)))
180 ;; Update this package together with the set of recommended packages: r-boot,
181 ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
182 ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
185 (name "r-with-tests")
189 (uri (string-append "mirror://cran/src/base/R-"
190 (version-major version) "/R-"
194 "0m69pfi0nxyriyb2yz74xfzaxwfkinnf9kpvf1rz727vvmfa8rdx"))))
195 (build-system gnu-build-system)
197 `(#:disallowed-references (,tzdata-for-tests)
199 (list (string-append "LDFLAGS=-Wl,-rpath="
200 (assoc-ref %outputs "out")
202 ;; This affects the embedded timestamp of only the core packages.
203 "PKG_BUILT_STAMP=1970-01-01")
205 (modify-phases %standard-phases
206 (add-before 'configure 'do-not-compress-serialized-files
207 (lambda* (#:key inputs #:allow-other-keys)
208 ;; This ensures that Guix can detect embedded store references;
209 ;; see bug #28157 for details.
210 (substitute* "src/library/base/makebasedb.R"
211 (("compress = TRUE") "compress = FALSE"))
213 (add-before 'configure 'patch-uname
214 (lambda* (#:key inputs #:allow-other-keys)
215 (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
217 (substitute* "src/scripts/R.sh.in"
218 (("uname") uname-bin)))
220 (add-after 'unpack 'build-reproducibly
222 ;; The documentation contains time stamps to demonstrate
223 ;; documentation generation in different phases.
224 (substitute* "src/library/tools/man/Rd2HTML.Rd"
225 (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
226 "(removed for reproducibility)"))
228 ;; Remove timestamp from tracing environment. This fixes
229 ;; reproducibility of "methods.rd{b,x}".
230 (substitute* "src/library/methods/R/trace.R"
231 (("dateCreated = Sys.time\\(\\)")
232 "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
234 ;; Ensure that gzipped files are reproducible.
235 (substitute* '("src/library/grDevices/Makefile.in"
236 "doc/manual/Makefile.in")
237 (("R_GZIPCMD\\)" line)
238 (string-append line " -n")))
240 ;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
241 ;; queries the mtime of a given file and records it in an object.
242 ;; This is acceptable at runtime to detect stale source files,
243 ;; but it destroys reproducibility at build time.
245 ;; Similarly, the "srcfilecopy" procedure records the current
246 ;; time. We change both of them to respect SOURCE_DATE_EPOCH.
247 (substitute* "src/library/base/R/srcfile.R"
248 (("timestamp <- (timestamp.*|file.mtime.*)" _ time)
249 (string-append "timestamp <- \
250 as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
251 as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
252 } else { " time "}, origin=\"1970-01-01\")\n")))
254 ;; This library is installed using "install_package_description",
255 ;; so we need to pass the "builtStamp" argument.
256 (substitute* "src/library/tools/Makefile.in"
257 (("(install_package_description\\(.*\"')\\)\"" line prefix)
258 (string-append prefix ", builtStamp='1970-01-01')\"")))
260 (substitute* "src/library/Recommended/Makefile.in"
261 (("INSTALL_OPTS =" m)
262 (string-append m " --built-timestamp=1970-01-01" m)))
264 ;; R bundles an older version of help2man, which does not respect
265 ;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man,
266 ;; because that breaks a test.
267 (with-fluids ((%default-port-encoding "ISO-8859-1"))
268 (substitute* "tools/help2man.pl"
269 (("my \\$date = strftime \"%B %Y\", localtime" line)
270 (string-append line " 1"))))
272 (add-before 'configure 'set-default-pager
273 ;; Set default pager to "cat", because otherwise it is "false",
274 ;; making "help()" print nothing at all.
275 (lambda _ (setenv "PAGER" "cat") #t))
276 (add-before 'check 'set-timezone
277 ;; Some tests require the timezone to be set. However, the
278 ;; timezone may not just be "UTC", or else a brittle regression
279 ;; test in reg-tests-1d will fail.
280 (lambda* (#:key inputs #:allow-other-keys)
281 (setenv "TZ" "UTC+1")
283 (string-append (assoc-ref inputs "tzdata")
286 (add-after 'build 'make-info
287 (lambda _ (invoke "make" "info")))
288 (add-after 'build 'install-info
289 (lambda _ (invoke "make" "install-info"))))
291 `(;; We build the recommended packages here, because they are needed in
292 ;; order to run the test suite. We disable them in the r-minimal
295 "--with-blas=-lopenblas"
301 ,(string-append "--with-tcl-config="
302 (assoc-ref %build-inputs "tcl")
304 ,(string-append "--with-tk-config="
305 (assoc-ref %build-inputs "tk")
308 "--enable-BLAS-shlib"
309 "--with-system-tre")))
310 ;; R has some support for Java. When the JDK is available at configure
311 ;; time environment variables pointing to the JDK will be recorded under
312 ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
313 ;; CMD javareconf". "R CMD javareconf" appears to only be used to update
314 ;; the recorded environment variables in $R_HOME/etc. Refer to
315 ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
316 ;; for additional information.
318 ;; As the JDK is a rather large input with only very limited effects on R,
319 ;; we decided to drop it.
323 ("pkg-config" ,pkg-config)
324 ("texinfo" ,texinfo) ; for building HTML manuals
325 ("texlive" ,(texlive-union (list texlive-fonts-ec
328 texlive-latex-fancyvrb
329 texlive-latex-graphics
330 texlive-latex-hyperref
331 texlive-latex-oberdiek
333 texlive-latex-upquote
335 ("tzdata" ,tzdata-for-tests)
338 `(;; We need not only cairo here, but pango to ensure that tests for the
339 ;; "cairo" bitmapType plotting backend succeed.
341 ("coreutils" ,coreutils)
343 ("openblas" ,openblas)
344 ("gfortran" ,gfortran)
351 ("readline" ,readline)
352 ;; This avoids a reference to the ungraftable static bash. R uses the
353 ;; detected shell for the "system" procedure.
354 ("bash" ,bash-minimal)
360 (list (search-path-specification
361 (variable "R_LIBS_SITE")
362 (files (list "site-library/")))))
363 (home-page "https://www.r-project.org/")
364 (synopsis "Environment for statistical computing and graphics")
366 "R is a language and environment for statistical computing and graphics.
367 It provides a variety of statistical techniques, such as linear and nonlinear
368 modeling, classical statistical tests, time-series analysis, classification
369 and clustering. It also provides robust support for producing
370 publication-quality data plots. A large amount of 3rd-party packages are
371 available, greatly increasing its breadth and scope.")
372 (license license:gpl3+)))
374 (define-public r-minimal
375 (package (inherit r-with-tests)
379 ,@(substitute-keyword-arguments (package-arguments r-with-tests)
380 ((#:configure-flags flags)
381 ;; Do not build the recommended packages. The build system creates
382 ;; random temporary directories and embeds their names in some
383 ;; package files. We build these packages with the r-build-system
385 `(cons "--without-recommended-packages" ,flags)))))))
387 (define-public rmath-standalone
388 (package (inherit r-minimal)
389 (name "rmath-standalone")
392 (modify-phases %standard-phases
393 (add-after 'configure 'chdir
394 (lambda _ (chdir "src/nmath/standalone/") #t)))))
395 (synopsis "Standalone R math library")
397 "This package provides the R math library as an independent package.")))
399 (define-public r-boot
406 (uri (cran-uri "boot" version))
409 "0yv0l55kjmlfdx1xhgyjdi0bskxhfal74wr5jxaib1qj99nmkm49"))))
410 (build-system r-build-system)
411 (home-page "https://cran.r-project.org/web/packages/boot")
412 (synopsis "Bootstrap functions for R")
414 "This package provides functions and datasets for bootstrapping from the
415 book \"Bootstrap Methods and Their Application\" by A.C. Davison and
416 D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
417 ;; Unlimited distribution
418 (license (license:non-copyleft "file://R/bootfuns.q"))))
420 (define-public r-mass
427 (uri (cran-uri "MASS" version))
430 "1k0m7pa4gb5apzrrkb5kx5d7bmkm2pl5g15vwb6j067hrqahck26"))))
431 (properties `((upstream-name . "MASS")))
432 (build-system r-build-system)
433 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
434 (synopsis "Support functions and datasets for Venables and Ripley's MASS")
436 "This package provides functions and datasets for the book \"Modern
437 Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
438 ;; Either version may be picked.
439 (license (list license:gpl2 license:gpl3))))
441 (define-public r-class
448 (uri (cran-uri "class" version))
451 "1x1hqz8xyhbpq4krsh02glqnlzcch25agkmn4a3da9n723b37gzn"))))
452 (build-system r-build-system)
454 `(("r-mass" ,r-mass)))
455 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
456 (synopsis "R functions for classification")
458 "This package provides various functions for classification, including
459 k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
460 ;; Either of the two versions can be picked.
461 (license (list license:gpl2 license:gpl3))))
463 (define-public r-cluster
470 (uri (cran-uri "cluster" version))
473 "055af3yz2biqbsbwm4arwr1yqnj4gicpzv2i6dbfl5pnz2z5byga"))))
474 (build-system r-build-system)
476 `(("gfortran" ,gfortran)))
477 (home-page "https://cran.r-project.org/web/packages/cluster")
478 (synopsis "Methods for cluster analysis")
480 "This package provides methods for cluster analysis. It is a much
481 extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
482 Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
483 (license license:gpl2+)))
485 (define-public r-codetools
492 (uri (cran-uri "codetools" version))
495 "00bmhzqprqfn3w6ghx7sakai6s7il8gbksfiawj8in5mbhbncypn"))))
496 (build-system r-build-system)
497 (home-page "https://cran.r-project.org/web/packages/codetools")
498 (synopsis "Code analysis tools for R")
499 (description "This package provides code analysis tools for R to check R
500 code for possible problems.")
501 ;; Any version of the GPL.
502 (license (list license:gpl2+ license:gpl3+))))
504 (define-public r-foreign
511 (uri (cran-uri "foreign" version))
514 "0g4mi101srjbl17ydb2hl3854m3xj0llj6861lfr30sp08nkqavl"))))
515 (build-system r-build-system)
516 (home-page "https://cran.r-project.org/web/packages/foreign")
517 (synopsis "Read data stored by other statistics software")
519 "This package provides functions for reading and writing data stored by
520 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
521 for reading and writing some dBase files.")
522 (license license:gpl2+)))
524 (define-public r-kernsmooth
526 (name "r-kernsmooth")
531 (uri (cran-uri "KernSmooth" version))
534 "1acrkbdn3a74y4dndkcdl1njnpfqz7gk3bsz03g8lfj8l7z53hmq"))))
535 (properties `((upstream-name . "KernSmooth")))
536 (build-system r-build-system)
538 `(("gfortran" ,gfortran)))
539 (home-page "https://cran.r-project.org/web/packages/KernSmooth")
540 (synopsis "Functions for kernel smoothing")
542 "This package provides functions for kernel smoothing (and density
543 estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
544 \"Kernel Smoothing\".")
545 ;; Unlimited use and distribution
546 (license (license:non-copyleft "file://LICENCE.note"))))
548 (define-public r-lattice
554 (uri (cran-uri "lattice" version))
557 "0b8abkz7syscq883mrgv63pkwaqkcpwfx8rgbqy9vgfva0z5xszx"))))
558 (build-system r-build-system)
559 (home-page "http://lattice.r-forge.r-project.org/")
560 (synopsis "High-level data visualization system")
562 "The lattice package provides a powerful and elegant high-level data
563 visualization system inspired by Trellis graphics, with an emphasis on
564 multivariate data. Lattice is sufficient for typical graphics needs, and is
565 also flexible enough to handle most nonstandard requirements.")
566 (license license:gpl2+)))
568 (define-public r-matrix
575 (uri (cran-uri "Matrix" version))
578 "06b1rc1vq65b271f2wpzhqkvhng8hwwnvjflzxkng50i52603zzp"))))
579 (properties `((upstream-name . "Matrix")))
580 (build-system r-build-system)
582 `(("r-lattice" ,r-lattice)))
583 (home-page "http://Matrix.R-forge.R-project.org/")
584 (synopsis "Sparse and dense matrix classes and methods")
586 "This package provides classes and methods for dense and sparse matrices
587 and operations on them using LAPACK and SuiteSparse.")
588 (license license:gpl2+)))
590 (define-public r-nlme
597 (uri (cran-uri "nlme" version))
599 (base32 "13iixbs2ibldc75rl7rav5n5kx33zwm33xnfw1yvlkpcqf38bd22"))))
600 (build-system r-build-system)
602 `(("r-lattice" ,r-lattice)))
604 `(("gfortran" ,gfortran)))
605 (home-page "https://cran.r-project.org/web/packages/nlme")
606 (synopsis "Linear and nonlinear mixed effects models")
608 "This package provides tools to fit and compare Gaussian linear and
609 nonlinear mixed-effects models.")
610 (license license:gpl2+)))
612 (define-public r-mgcv
619 (uri (cran-uri "mgcv" version))
621 (base32 "1if34mqsn9r7g0l82lxvvx0wjhi9paqdymyd73nschxcl1if8vbk"))))
622 (build-system r-build-system)
624 `(("r-matrix" ,r-matrix)
626 (home-page "https://cran.r-project.org/web/packages/mgcv")
627 (synopsis "Mixed generalised additive model computation")
629 "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
630 parameter estimation by GCV, REML or UBRE/AIC. The library includes a
631 @code{gam()} function, a wide variety of smoothers, JAGS support and
632 distributions beyond the exponential family.")
633 (license license:gpl2+)))
635 (define-public r-nnet
642 (uri (cran-uri "nnet" version))
645 "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7"))))
646 (build-system r-build-system)
647 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
648 (synopsis "Feed-forward neural networks and multinomial log-linear models")
650 "This package provides functions for feed-forward neural networks with a
651 single hidden layer, and for multinomial log-linear models.")
652 (license (list license:gpl2+ license:gpl3+))))
654 (define-public r-rpart
661 (uri (cran-uri "rpart" version))
664 "0p5frya963ppn476p5dxs2mnarsalksr6gw9zzmjsn8ikq7bx3ib"))))
665 (build-system r-build-system)
666 (home-page "https://cran.r-project.org/web/packages/rpart")
667 (synopsis "Recursive partitioning and regression trees")
669 "This package provides recursive partitioning functions for
670 classification, regression and survival trees.")
671 (license (list license:gpl2+ license:gpl3+))))
673 (define-public r-spatial
680 (uri (cran-uri "spatial" version))
683 "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
684 (build-system r-build-system)
685 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
686 (synopsis "Functions for kriging and point pattern analysis")
688 "This package provides functions for kriging and point pattern
690 ;; Either version may be picked.
691 (license (list license:gpl2 license:gpl3))))
693 (define-public r-survival
700 (uri (cran-uri "survival" version))
703 "15fj4y8c107bwq22amx88r5hw7qndlcbr9sapzrpkpr7iqz3kkyf"))))
704 (build-system r-build-system)
706 `(("r-matrix" ,r-matrix)))
707 (home-page "https://github.com/therneau/survival")
708 (synopsis "Survival analysis")
710 "This package contains the core survival analysis routines, including
711 definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
712 curves, Cox models, and parametric accelerated failure time models.")
713 (license license:lgpl2.0+)))
716 (package (inherit r-minimal)
719 (build-system trivial-build-system)
720 (arguments '(#:builder (begin (mkdir %output) #t)))
722 `(("r-minimal" ,r-minimal)
725 ("r-cluster" ,r-cluster)
726 ("r-codetools" ,r-codetools)
727 ("r-foreign" ,r-foreign)
728 ("r-kernsmooth" ,r-kernsmooth)
729 ("r-lattice" ,r-lattice)
731 ("r-matrix" ,r-matrix)
736 ("r-spatial" ,r-spatial)
737 ("r-survival" ,r-survival)))))
746 (uri (cran-uri "bit" version))
749 "0y351ajlrn9ywbiai46mjpwmw5pqc9ik2z24rf0bnbdcvaxdr7r8"))))
750 (build-system r-build-system)
751 (home-page "http://ff.r-forge.r-project.org")
752 (synopsis "Class for vectors of 1-bit booleans")
754 "This package provides bitmapped vectors of booleans (no @code{NA}s),
755 coercion from and to logicals, integers and integer subscripts, fast boolean
756 operators and fast summary statistics. With @code{bit} class vectors of true
757 binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
758 (license license:gpl2)))
760 (define-public r-bit64
767 (uri (cran-uri "bit64" version))
770 "07znvz9vp1nz1y5ljng4qyskvm943cdbmy996s67560ijxzsm6kv"))))
771 (build-system r-build-system)
774 (home-page "http://ff.r-forge.r-project.org/")
775 (synopsis "S3 class for vectors of 64 bit integers")
777 "The bit64 package provides serializable S3 atomic 64 bit (signed)
778 integers that can be used in vectors, matrices, arrays and @code{data.frames}.
779 Methods are available for coercion from and to logicals, integers, doubles,
780 characters and factors as well as many elementwise and summary functions.
781 Many fast algorithmic operations such as @code{match} and @code{order} support
782 interactive data exploration and manipulation and optionally leverage
784 (license license:gpl2)))
786 (define-public r-dichromat
793 (uri (cran-uri "dichromat" version))
795 (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
796 (build-system r-build-system)
797 (home-page "https://cran.r-project.org/web/packages/dichromat")
798 (synopsis "Color schemes for dichromats")
800 "Dichromat collapses red-green or green-blue distinctions to simulate the
801 effects of different types of color-blindness.")
802 (license license:gpl2+)))
804 (define-public r-digest
811 (uri (cran-uri "digest" version))
813 (base32 "18h5s8vkdcz2vhpsx6g3ig00zalrihr03skn95zw3lr2y56pafmp"))))
814 (build-system r-build-system)
815 ;; Vignettes require r-knitr, which requires r-digest, so we have to
816 ;; disable them and the tests.
819 #:configure-flags (list "--no-build-vignettes")))
820 (home-page "http://dirk.eddelbuettel.com/code/digest.html")
821 (synopsis "Create cryptographic hash digests of R objects")
823 "This package contains an implementation of a function @code{digest()} for
824 the creation of hash digests of arbitrary R objects (using the md5, sha-1,
825 sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
826 of R language objects, as well as a function @code{hmac()} to create hash-based
827 message authentication code.
829 Please note that this package is not meant to be deployed for cryptographic
830 purposes for which more comprehensive (and widely tested) libraries such as
831 OpenSSL should be used.")
832 (license license:gpl2+)))
834 (define-public r-estimability
836 (name "r-estimability")
840 (uri (cran-uri "estimability" version))
843 "0cifdaa71spkcxl4db4z884jrya865sg3dhcv4isd8fnzg2pjcd3"))))
844 (build-system r-build-system)
845 (home-page "https://cran.r-project.org/web/packages/estimability")
846 (synopsis "Tools for assessing estimability of linear predictions")
847 (description "Provides tools for determining estimability of linear
848 functions of regression coefficients, and @code{epredict} methods that handle
849 non-estimable cases correctly.")
850 (license license:gpl2+)))
852 (define-public r-labeling
859 (uri (cran-uri "labeling" version))
861 (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
862 (build-system r-build-system)
863 (home-page "https://cran.r-project.org/web/packages/labeling")
864 (synopsis "Axis labeling algorithms")
865 (description "The labeling package provides a range of axis labeling
867 (license license:expat)))
869 (define-public r-magrittr
876 (uri (cran-uri "magrittr" version))
878 (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
879 (build-system r-build-system)
880 (home-page "https://cran.r-project.org/web/packages/magrittr/index.html")
881 (synopsis "A forward-pipe operator for R")
883 "Magrittr provides a mechanism for chaining commands with a new
884 forward-pipe operator, %>%. This operator will forward a value, or the result
885 of an expression, into the next function call/expression. There is flexible
886 support for the type of right-hand side expressions. For more information,
887 see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
888 (license license:expat)))
890 (define-public r-munsell
897 (uri (cran-uri "munsell" version))
899 (base32 "16g1fzisbpqb15yh3pqf3iia4csppva5dnv1z88x9dg263xskwyh"))))
900 (build-system r-build-system)
902 `(("r-colorspace" ,r-colorspace)))
903 (home-page "https://cran.r-project.org/web/packages/munsell")
904 (synopsis "Munsell colour system")
906 "The Munsell package contains Functions for exploring and using the
907 Munsell colour system.")
908 (license license:expat)))
910 (define-public r-permute
917 (uri (cran-uri "permute" version))
920 "0ra8p5mf2590azrkas8z2ry7mif77xqxd29n4zgyi5vll225726j"))))
921 (build-system r-build-system)
922 ;; Tests do not run correctly, but running them properly would entail a
923 ;; circular dependency with vegan.
924 (home-page "https://github.com/gavinsimpson/permute")
925 (synopsis "Functions for Generating Restricted Permutations of Data")
927 "This package provides a set of restricted permutation designs for freely
928 exchangeable, line transects (time series), spatial grid designs and permutation
929 of blocks (groups of samples). @code{permute} also allows split-plot designs,
930 in which the whole-plots or split-plots or both can be freely exchangeable.")
931 (license license:gpl2+)))
933 (define-public r-plyr
940 (uri (cran-uri "plyr" version))
942 (base32 "0x4mbb3rgv1ayxqidw0p9i10khbg51fz5r62vw4il8d7licqq07a"))))
943 (build-system r-build-system)
944 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
945 (home-page "http://had.co.nz/plyr")
946 (synopsis "Tools for Splitting, Applying and Combining Data")
948 "Plyr is a set of tools that solves a common set of problems: you need to
949 break a big problem down into manageable pieces, operate on each piece and
950 then put all the pieces back together. For example, you might want to fit a
951 model to each spatial location or time point in your study, summarise data by
952 panels or collapse high-dimensional arrays to simpler summary statistics.")
953 (license license:expat)))
955 (define-public r-proto
962 (uri (cran-uri "proto" version))
964 (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
965 (build-system r-build-system)
966 (home-page "https://github.com/hadley/proto")
967 (synopsis "Prototype object-based programming")
969 "Proto is an object oriented system using object-based, also called
970 prototype-based, rather than class-based object oriented ideas.")
971 (license license:gpl2+)))
973 (define-public r-rcolorbrewer
975 (name "r-rcolorbrewer")
980 (uri (cran-uri "RColorBrewer" version))
982 (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
983 (build-system r-build-system)
984 (home-page "https://cran.r-project.org/web/packages/RColorBrewer")
985 (synopsis "ColorBrewer palettes")
987 "This package provides color schemes for maps (and other graphics)
988 designed by Cynthia Brewer as described at http://colorbrewer2.org")
989 ;; Includes code licensed under bsd-4
990 (license license:asl2.0)))
992 (define-public r-sendmailr
999 (uri (cran-uri "sendmailR" version))
1002 "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
1003 (properties `((upstream-name . "sendmailR")))
1004 (build-system r-build-system)
1006 `(("r-base64enc" ,r-base64enc)))
1008 "https://cran.r-project.org/web/packages/sendmailR")
1009 (synopsis "Send email using R")
1011 "This package contains a simple SMTP client which provides a portable
1012 solution for sending email, including attachments, from within R.")
1013 (license license:gpl2+)))
1015 (define-public r-stringi
1022 (uri (cran-uri "stringi" version))
1025 "0gdmdf4i3ik8rcs7af1vlsfnilcmw3z28jx4278rpq2asigps89k"))))
1026 (build-system r-build-system)
1027 (inputs `(("icu4c" ,icu4c)))
1028 (native-inputs `(("pkg-config" ,pkg-config)))
1029 (home-page "http://stringi.rexamine.com/")
1030 (synopsis "Character string processing facilities")
1032 "This package allows for fast, correct, consistent, portable, as well as
1033 convenient character string/text processing in every locale and any native
1034 encoding. Owing to the use of the ICU library, the package provides R users
1035 with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
1036 programmers. Among available features there are: pattern searching
1037 (e.g. via regular expressions), random string generation, string collation,
1038 transliteration, concatenation, date-time formatting and parsing, etc.")
1039 (license license:bsd-3)))
1041 (define-public r-stringr
1048 (uri (cran-uri "stringr" version))
1050 (base32 "1p9ip7p87gbbg4s6d3d392svvzz2b5dqdq2c8ilgvn4s78nlsq47"))))
1051 (build-system r-build-system)
1053 `(("r-glue" ,r-glue)
1054 ("r-magrittr" ,r-magrittr)
1055 ("r-stringi" ,r-stringi)))
1056 (home-page "https://github.com/hadley/stringr")
1057 (synopsis "Simple, consistent wrappers for common string operations")
1059 "Stringr is a consistent, simple and easy to use set of wrappers around
1060 the fantastic @code{stringi} package. All function and argument names (and
1061 positions) are consistent, all functions deal with \"NA\"'s and zero length
1062 vectors in the same way, and the output from one function is easy to feed into
1063 the input of another.")
1064 (license license:gpl2+)))
1066 (define-public r-reshape2
1073 (uri (cran-uri "reshape2" version))
1075 (base32 "03ki5ka1dj208fc0dclbm0b4xp9d769pah2j9cs34l776p4r9zwa"))))
1076 (build-system r-build-system)
1078 `(("r-plyr" ,r-plyr)
1080 ("r-stringr" ,r-stringr)))
1081 (home-page "https://github.com/hadley/reshape")
1082 (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
1084 "Reshape2 is an R library to flexibly restructure and aggregate data
1085 using just two functions: melt and dcast (or acast).")
1086 (license license:expat)))
1088 (define-public r-ggplot2
1095 (uri (cran-uri "ggplot2" version))
1097 (base32 "0mjswqiqcwm0aqxll16bx2kwa6c9km3aql87bdj4347n1ali94g3"))))
1098 (build-system r-build-system)
1100 `(("r-digest" ,r-digest)
1101 ("r-gtable" ,r-gtable)
1102 ("r-lazyeval" ,r-lazyeval)
1105 ("r-tibble" ,r-tibble)
1106 ("r-reshape2" ,r-reshape2)
1107 ("r-rlang" ,r-rlang)
1108 ("r-scales" ,r-scales)
1109 ("r-svglite" ,r-svglite) ; Needed for 'ggsave'
1110 ("r-viridislite" ,r-viridislite)
1111 ("r-withr" ,r-withr)))
1112 (home-page "https://ggplot2.tidyverse.org")
1113 (synopsis "An implementation of the grammar of graphics")
1115 "Ggplot2 is an implementation of the grammar of graphics in R. It
1116 combines the advantages of both base and lattice graphics: conditioning and
1117 shared axes are handled automatically, and you can still build up a plot step
1118 by step from multiple data sources. It also implements a sophisticated
1119 multidimensional conditioning system and a consistent interface to map data to
1120 aesthetic attributes.")
1121 (license license:gpl2+)))
1123 (define-public r-ggdendro
1129 (uri (cran-uri "ggdendro" version))
1132 "1zzq1hxd0d1qa5hrzwfkdw6fzscpcafbwbpkrb62dm559y8awp0j"))))
1133 (build-system r-build-system)
1135 `(("r-ggplot2" ,r-ggplot2)
1137 ("r-knitr" ,r-knitr)))
1138 (home-page "https://github.com/andrie/ggdendro")
1139 (synopsis "Create Dendrograms and Tree Diagrams Using ggplot2")
1140 (description "This is a set of tools for dendrograms and tree plots using
1141 ggplot2. The ggplot2 philosophy is to clearly separate data from the
1142 presentation. Unfortunately the plot method for dendrograms plots directly
1143 to a plot device with out exposing the data. The ggdendro package resolves
1144 this by making available functions that extract the dendrogram plot data.
1145 The package provides implementations for tree, rpart, as well as diana and
1146 agnes cluster diagrams.")
1147 (license license:gpl2+)))
1149 (define-public r-gdtools
1156 (uri (cran-uri "gdtools" version))
1159 "1aax50wyrs4336zpf247l8wmp4spab2n70msziy1ip4gbjn26wa1"))))
1160 (build-system r-build-system)
1162 `(("pkg-config" ,pkg-config)))
1165 ("freetype2" ,freetype)
1168 `(("r-rcpp" ,r-rcpp)
1169 ("r-systemfonts" ,r-systemfonts)))
1170 (home-page "https://cran.r-project.org/web/packages/gdtools")
1171 (synopsis "Utilities for graphical rendering")
1173 "The @code{gdtools} package provides functionalities to get font metrics
1174 and to generate base64 encoded string from raster matrix.")
1175 (license license:gpl3)))
1177 (define-public r-svglite
1184 (uri (cran-uri "svglite" version))
1187 "1gwv51wqp6pgm2f9gavsiq65njs77fr49n8y6y9ax60k3a4vvg14"))))
1188 (build-system r-build-system)
1191 ("r-gdtools" ,r-gdtools)
1192 ("r-rcpp" ,r-rcpp)))
1193 (home-page "https://github.com/hadley/svglite")
1194 (synopsis "SVG graphics device")
1196 "@code{svglite} is a graphics device that produces clean
1197 @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
1198 hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
1199 considerably faster, produces smaller files, and leaves text as is.")
1200 (license license:gpl2+)))
1202 (define-public r-assertthat
1204 (name "r-assertthat")
1208 (uri (cran-uri "assertthat" version))
1211 "17wy5bdfzg73sg2clisg1k3zyn1adkj59x56m5nwia2k8z67zkw5"))))
1212 (build-system r-build-system)
1213 (home-page "https://github.com/hadley/assertthat")
1214 (synopsis "Easy pre and post assertions")
1216 "Assertthat is an extension to stopifnot() that makes it easy to declare
1217 the pre and post conditions that your code should satisfy, while also
1218 producing friendly error messages so that your users know what they've done
1220 (license license:gpl3+)))
1222 (define-public r-lazyeval
1228 (uri (cran-uri "lazyeval" version))
1231 "1m10i059csrcqkcn59a8wspn784alxsq3symzhn24mhhl894346n"))))
1232 (build-system r-build-system)
1233 (home-page "https://github.com/hadley/lazyeval")
1234 (synopsis "Lazy (non-standard) evaluation in R")
1236 "This package provides the tools necessary to do non-standard
1237 evaluation (NSE) in R.")
1238 (license license:gpl3+)))
1240 (define-public r-dbi
1246 (uri (cran-uri "DBI" version))
1249 "1r03j9rdcxb9bhxk40dkmy10ikz4yzsxhy3f9k9ix3x577xbfvd9"))))
1250 (build-system r-build-system)
1251 (home-page "https://github.com/rstats-db/DBI")
1252 (synopsis "R database interface")
1254 "The DBI package provides a database interface (DBI) definition for
1255 communication between R and relational database management systems. All
1256 classes in this package are virtual and need to be extended by the various
1257 R/DBMS implementations.")
1258 (license license:lgpl2.0+)))
1263 (version "1.72.0-3")
1266 (uri (cran-uri "BH" version))
1269 "1ay8vb6i730lipg8b8g3893vqglhw2kqpc29lwdrxdkb66iw33l8"))))
1270 (build-system r-build-system)
1271 (home-page "https://github.com/eddelbuettel/bh")
1272 (synopsis "R package providing subset of Boost headers")
1274 "This package aims to provide the most useful subset of Boost libraries
1275 for template use among CRAN packages.")
1276 (license license:boost1.0)))
1278 (define-public r-evaluate
1284 (uri (cran-uri "evaluate" version))
1287 "0a2y7j534gbgixkwj9r1z76l2vssw4g1hznzbpclc076wkdqpj58"))))
1288 (build-system r-build-system)
1289 (home-page "https://github.com/hadley/evaluate")
1290 (synopsis "Parsing and evaluation tools for R")
1292 "This package provides tools that allow you to recreate the parsing,
1293 evaluation and display of R code, with enough information that you can
1294 accurately recreate what happens at the command line. The tools can easily be
1295 adapted for other output formats, such as HTML or LaTeX.")
1296 (license license:gpl3+)))
1298 (define-public r-formatr
1304 (uri (cran-uri "formatR" version))
1307 "1nsxbrx31k3y6yql30qkrvdfyznlia2qfvwv95mfiy7m7wdn4rm3"))))
1308 (build-system r-build-system)
1309 (home-page "https://yihui.org/formatr/")
1310 (synopsis "Format R code automatically")
1312 "This package provides a function to format R source code. Spaces and
1313 indent will be added to the code automatically, and comments will be preserved
1314 under certain conditions, so that R code will be more human-readable and tidy.
1315 There is also a Shiny app as a user interface in this package.")
1316 (license license:gpl3+)))
1318 (define-public r-highr
1324 (uri (cran-uri "highr" version))
1327 "0my6idnhmmgs4q1vs40y2lh56yij2p59mpwvm53wjs2zk6x1zl2b"))))
1328 (build-system r-build-system)
1329 (home-page "https://github.com/yihui/highr")
1330 (synopsis "Syntax highlighting for R source code")
1332 "This package provides syntax highlighting for R source code. Currently
1333 it supports LaTeX and HTML output. Source code of other languages is
1334 supported via Andre Simon's highlight package.")
1335 (license license:gpl3+)))
1337 (define-public r-mime
1343 (uri (cran-uri "mime" version))
1346 "18w98prfbivvygiyamsf9yg090kzbnvw2fn9b27823gmis4d08ny"))))
1347 (build-system r-build-system)
1348 (home-page "https://github.com/yihui/mime")
1349 (synopsis "R package to map filenames to MIME types")
1351 "This package guesses the MIME type from a filename extension using the
1352 data derived from /etc/mime.types in UNIX-type systems.")
1353 (license license:gpl2)))
1355 (define-public r-markdown
1361 (uri (cran-uri "markdown" version))
1364 "06zwbrp14bri3470anadd7dvgmw06xf8df6v2pk64wx3f9sd934d"))))
1365 (build-system r-build-system)
1366 ;; Skip check phase because the tests require the r-knitr package to be
1367 ;; installed. This prevents installation failures. Knitr normally
1368 ;; shouldn't be available since r-markdown is a dependency of the r-knitr
1370 (arguments `(#:tests? #f))
1372 `(("r-mime" ,r-mime)
1373 ("r-xfun" ,r-xfun)))
1374 (home-page "https://github.com/rstudio/markdown")
1375 (synopsis "Markdown rendering for R")
1377 "This package provides R bindings to the Sundown Markdown rendering
1378 library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
1379 syntax that can be converted to XHTML or other formats.")
1380 (license license:gpl2)))
1382 (define-public r-yaml
1388 (uri (cran-uri "yaml" version))
1391 "0in562nd0i23cg91a8kdbqgim656fgscykwi0icsnq53xj3srg2m"))))
1392 (build-system r-build-system)
1393 (home-page "https://cran.r-project.org/web/packages/yaml/")
1394 (synopsis "Methods to convert R data to YAML and back")
1396 "This package implements the libyaml YAML 1.1 parser and
1397 emitter (http://pyyaml.org/wiki/LibYAML) for R.")
1398 (license license:bsd-3)))
1400 (define-public r-knitr
1406 (uri (cran-uri "knitr" version))
1409 "02nysgnx6xv0kd351s1d59yx4g0drsd9lmcgxs0rsw5f1jiycgdg"))))
1410 (build-system r-build-system)
1412 `(("r-evaluate" ,r-evaluate)
1413 ("r-highr" ,r-highr)
1414 ("r-markdown" ,r-markdown)
1415 ("r-stringr" ,r-stringr)
1417 ("r-yaml" ,r-yaml)))
1418 (home-page "http://yihui.name/knitr/")
1419 (synopsis "General-purpose package for dynamic report generation in R")
1421 "This package provides a general-purpose tool for dynamic report
1422 generation in R using Literate Programming techniques.")
1423 ;; The code is released under any version of the GPL. As it is used by
1424 ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
1426 (license license:gpl2+)))
1428 (define-public r-knitrbootstrap
1430 (name "r-knitrbootstrap")
1435 (uri (cran-uri "knitrBootstrap" version))
1438 "1aj60j7f0gcs120fdrnfbnb7vk7lfn1phil0mghg6a5zldz4cqs3"))))
1439 (properties `((upstream-name . "knitrBootstrap")))
1440 (build-system r-build-system)
1442 `(("r-knitr" ,r-knitr)
1443 ("r-rmarkdown" ,r-rmarkdown)
1444 ("r-markdown" ,r-markdown)))
1445 (home-page "https://github.com/jimhester/knitrBootstrap")
1446 (synopsis "Knitr bootstrap framework")
1448 "This package provides a framework to create Bootstrap 3 HTML reports
1449 from knitr Rmarkdown.")
1450 (license license:expat)))
1452 (define-public r-microbenchmark
1454 (name "r-microbenchmark")
1458 (uri (cran-uri "microbenchmark" version))
1461 "1xl4m4yl4h2zcjiz8wsa7f3sh55qg2xr3sgpvz18rlix6b3173r6"))))
1462 (build-system r-build-system)
1463 (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
1464 (synopsis "Accurate timing functions for R")
1466 "This package provides infrastructure to accurately measure and compare
1467 the execution time of R expressions.")
1468 (license license:bsd-2)))
1470 (define-public r-pryr
1476 (uri (cran-uri "pryr" version))
1479 "06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k"))))
1480 (build-system r-build-system)
1482 `(("r-stringr" ,r-stringr)
1483 ("r-codetools" ,r-codetools)))
1485 `(("r-rcpp" ,r-rcpp)))
1486 (home-page "https://github.com/hadley/pryr")
1487 (synopsis "Tools for computing on the R language")
1489 "This package provides useful tools to pry back the covers of R and
1490 understand the language at a deeper level.")
1491 (license license:gpl2)))
1493 (define-public r-memoise
1499 (uri (cran-uri "memoise" version))
1502 "034qfc2xlh30x1q2vya239w34a3ir3y2fwnx2agbgbi6592zjxmj"))))
1503 (build-system r-build-system)
1505 `(("r-digest" ,r-digest)))
1506 (home-page "https://github.com/hadley/memoise")
1507 (synopsis "Memoise functions for R")
1509 "This R package allows to cache the results of a function so that when
1510 you call it again with the same arguments it returns the pre-computed value.")
1511 (license license:expat)))
1513 (define-public r-crayon
1519 (uri (cran-uri "crayon" version))
1522 "0s7s6vc3ww8pzanpjisym4jjvwcc5pi2qg8srx7jqlz9j3wrnvpw"))))
1523 (build-system r-build-system)
1525 `(("r-memoise" ,r-memoise)))
1526 (home-page "https://github.com/gaborcsardi/crayon")
1527 (synopsis "Colored terminal output for R")
1529 "Colored terminal output on terminals that support ANSI color and
1530 highlight codes. It also works in Emacs ESS. ANSI color support is
1531 automatically detected. Colors and highlighting can be combined and nested.
1532 New styles can also be created easily. This package was inspired by the
1533 \"chalk\" JavaScript project.")
1534 (license license:expat)))
1536 (define-public r-praise
1543 (uri (cran-uri "praise" version))
1546 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
1547 (build-system r-build-system)
1548 (home-page "https://github.com/gaborcsardi/praise")
1549 (synopsis "Functions to praise users")
1551 "This package provides template functions to assist in building friendly
1552 R packages that praise their users.")
1553 (license license:expat)))
1555 (define-public r-testthat
1561 (uri (cran-uri "testthat" version))
1564 "0m8xchdpgn9iwj6gb2qw46zr85v9zf1gkbr9nnahmy5sp1s9bbky"))))
1565 (build-system r-build-system)
1568 ("r-crayon" ,r-crayon)
1569 ("r-digest" ,r-digest)
1570 ("r-ellipsis" ,r-ellipsis)
1571 ("r-evaluate" ,r-evaluate)
1572 ("r-magrittr" ,r-magrittr)
1573 ("r-pkgload" ,r-pkgload)
1574 ("r-praise" ,r-praise)
1576 ("r-rlang" ,r-rlang)
1577 ("r-withr" ,r-withr)))
1578 (home-page "https://github.com/hadley/testthat")
1579 (synopsis "Unit testing for R")
1581 "This package provides a unit testing system for R designed to be fun,
1582 flexible and easy to set up.")
1583 (license license:expat)))
1591 (uri (cran-uri "R6" version))
1594 "0gma5z41mx02ka9h96xdyf3p6i1rx0izczrzj26c4mbnh9jgvc16"))))
1595 (build-system r-build-system)
1596 (home-page "https://github.com/wch/R6/")
1597 (synopsis "Classes with reference semantics in R")
1599 "The R6 package allows the creation of classes with reference semantics,
1600 similar to R's built-in reference classes. Compared to reference classes, R6
1601 classes are simpler and lighter-weight, and they are not built on S4 classes
1602 so they do not require the methods package. These classes allow public and
1603 private members, and they support inheritance, even when the classes are
1604 defined in different packages.")
1605 (license license:expat)))
1607 (define-public r-rlang
1613 (uri (cran-uri "rlang" version))
1616 "0qsqfikbsj55x5brghnkzzp7pz0japr4xnzm993f668mlls3f6i4"))))
1617 (build-system r-build-system)
1618 (home-page "http://rlang.tidyverse.org")
1619 (synopsis "Functions for base types, core R and Tidyverse features")
1620 (description "This package provides a toolbox for working with base types,
1621 core R features like the condition system, and core @code{Tidyverse} features
1622 like tidy evaluation.")
1623 (license license:gpl3)))
1625 (define-public r-tibble
1632 (uri (cran-uri "tibble" version))
1635 "06jfayiip8j8ibdhw3fvxn4n8aqbqhwanrszpzlsf92xdfgfm34s"))))
1636 (build-system r-build-system)
1639 ("r-crayon" ,r-crayon)
1640 ("r-fansi" ,r-fansi)
1641 ("r-pkgconfig" ,r-pkgconfig)
1642 ("r-pillar" ,r-pillar)
1643 ("r-rlang" ,r-rlang)))
1644 (home-page "https://github.com/hadley/tibble")
1645 (synopsis "Simple data frames")
1647 "This package provides a @code{tbl_df} class that offers better checking
1648 and printing capabilities than traditional data frames.")
1649 (license license:expat)))
1651 (define-public r-dplyr
1657 (uri (cran-uri "dplyr" version))
1660 "032c89wa04g9rih9shyvwl3il0bsrv3xk489x6867sk9bb3amd38"))))
1661 (build-system r-build-system)
1663 `(("r-assertthat" ,r-assertthat)
1666 ("r-magrittr" ,r-magrittr)
1667 ("r-pkgconfig" ,r-pkgconfig)
1668 ("r-plogr" ,r-plogr)
1671 ("r-rlang" ,r-rlang)
1672 ("r-tibble" ,r-tibble)
1673 ("r-tidyselect" ,r-tidyselect)))
1674 (home-page "https://github.com/hadley/dplyr")
1675 (synopsis "Tools for working with data frames in R")
1677 "dplyr is the next iteration of plyr. It is focussed on tools for
1678 working with data frames. It has three main goals: 1) identify the most
1679 important data manipulation tools needed for data analysis and make them easy
1680 to use in R; 2) provide fast performance for in-memory data by writing key
1681 pieces of code in C++; 3) use the same code interface to work with data no
1682 matter where it is stored, whether in a data frame, a data table or
1684 (license license:expat)))
1686 (define-public r-dbplyr
1693 (uri (cran-uri "dbplyr" version))
1696 "1q2dflr88s5a1amzfld3087q422vf70052qn84zyd8895kdg10xp"))))
1697 (build-system r-build-system)
1699 `(("r-assertthat" ,r-assertthat)
1701 ("r-dplyr" ,r-dplyr)
1703 ("r-purrr" ,r-purrr)
1705 ("r-rlang" ,r-rlang)
1706 ("r-tibble" ,r-tibble)
1707 ("r-tidyselect" ,r-tidyselect)))
1708 (home-page "https://github.com/tidyverse/dbplyr")
1709 (synopsis "Dplyr back end for databases")
1711 "This package provides a dplyr back end for databases that allows you to
1712 work with remote database tables as if they are in-memory data frames. Basic
1713 features works with any database that has a @code{DBI} back end; more advanced
1714 features require SQL translation to be provided by the package author.")
1715 (license license:expat)))
1717 (define-public r-acepack
1724 (uri (cran-uri "acepack" version))
1727 "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
1728 (build-system r-build-system)
1730 `(("gfortran" ,gfortran)))
1731 (home-page "https://cran.r-project.org/web/packages/acepack")
1732 (synopsis "Functions for regression transformations")
1734 "This package provides ACE and AVAS methods for choosing regression
1736 (license license:expat)))
1738 (define-public r-formula
1745 (uri (cran-uri "Formula" version))
1748 "0wiqh8rr9d5ciy80wj8f5fnmiiw0ywanvvnhkwd622dx42dk848l"))))
1749 (properties `((upstream-name . "Formula")))
1750 (build-system r-build-system)
1751 (home-page "https://cran.r-project.org/web/packages/Formula")
1752 (synopsis "Extended model formulas")
1754 "This package provides a new class @code{Formula}, which extends the base
1755 class @code{formula}. It supports extended formulas with multiple parts of
1756 regressors on the right-hand side and/or multiple responses on the left-hand
1758 (license (list license:gpl2+ license:gpl3+))))
1760 (define-public r-locfit
1767 (uri (cran-uri "locfit" version))
1770 "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
1771 (build-system r-build-system)
1773 `(("r-lattice" ,r-lattice)))
1774 (home-page "https://cran.r-project.org/web/packages/locfit")
1775 (synopsis "Local regression, likelihood and density estimation")
1777 "This package provides functions used for local regression, likelihood
1778 and density estimation.")
1779 (license (list license:gpl2+ license:gpl3+))))
1781 (define-public r-chron
1787 (uri (cran-uri "chron" version))
1790 "0vc7dxqwx0jqzwszax6di3091npsxnhnbvr7sy7rlip0jqzarwqd"))))
1791 (build-system r-build-system)
1792 (home-page "https://cran.r-project.org/web/packages/chron")
1793 (synopsis "Chronological R objects which can handle dates and times")
1795 "This package provides chronological R objects which can handle dates and
1797 (license license:gpl2)))
1799 (define-public r-data-table
1801 (name "r-data-table")
1805 (uri (cran-uri "data.table" version))
1808 "1p7rf4v3ysflpgcmy9krkwmcy7z22wb08xm443649waz6lx5z9yk"))))
1809 (build-system r-build-system)
1813 `(("pkg-config" ,pkg-config)))
1814 (home-page "https://github.com/Rdatatable/data.table/wiki")
1815 (synopsis "Enhanced version of data.frame R object")
1817 "The R package @code{data.table} is an extension of @code{data.frame}
1818 providing functions for fast aggregation of large data (e.g. 100GB in RAM),
1819 fast ordered joins, fast add/modify/delete of columns by group, column listing
1820 and fast file reading.")
1821 (license license:gpl3+)))
1823 (define-public r-xtable
1830 (uri (cran-uri "xtable" version))
1833 "077xfm0gphvhsay75amd9v90zk57kjgrrlgih04fyrbqqblc1gjs"))))
1834 (build-system r-build-system)
1836 `(("r-knitr" ,r-knitr))) ; for vignettes
1837 (home-page "http://xtable.r-forge.r-project.org/")
1838 (synopsis "Export R tables to LaTeX or HTML")
1840 "This package provides tools to export R data as LaTeX and HTML tables.")
1841 (license license:gpl2+)))
1843 (define-public python-patsy
1845 (name "python-patsy")
1849 (uri (pypi-uri "patsy" version))
1852 "149rbrdzwns0ay88caf1zsm1r53v1q5np1mrb36na50y432cw5gi"))))
1853 (build-system python-build-system)
1856 (modify-phases %standard-phases
1858 (lambda _ (invoke "nosetests" "-v"))))))
1860 `(("python-numpy" ,python-numpy)
1861 ("python-scipy" ,python-scipy)
1862 ("python-six" ,python-six)))
1864 `(("python-nose" ,python-nose)))
1865 (home-page "https://github.com/pydata/patsy")
1866 (synopsis "Describe statistical models and build design matrices")
1868 "Patsy is a Python package for describing statistical models and for
1869 building design matrices.")
1870 ;; The majority of the code is distributed under BSD-2. The module
1871 ;; patsy.compat contains code derived from the Python standard library,
1872 ;; and is covered by the PSFL.
1873 (license (list license:bsd-2 license:psfl))))
1875 (define-public python2-patsy
1876 (package-with-python2 python-patsy))
1878 (define-public python-statsmodels
1880 (name "python-statsmodels")
1885 (uri (pypi-uri "statsmodels" version))
1888 "0fxs8a7sp4d7jvqlm36yi45i2d28kjfvraf9q8i9jr1chhxgjqb4"))))
1889 (build-system python-build-system)
1891 `(;; The test suite is very large and rather brittle. Tests often fail
1892 ;; because of minor changes in dependencies that upstream hasn't fixed
1893 ;; in a new release.
1896 (modify-phases %standard-phases
1897 (add-after 'unpack 'set-matplotlib-backend-to-agg
1899 ;; Set the matplotlib backend to Agg to avoid problems using the
1900 ;; GTK backend without a display.
1901 (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py")
1902 '("statsmodels/tsa/vector_ar/tests/test_var.py"
1903 "statsmodels/duration/tests/test_survfunc.py"))
1904 (("import matplotlib\\.pyplot as plt" line)
1905 (string-append "import matplotlib;matplotlib.use('Agg');"
1909 `(("python-numpy" ,python-numpy)
1910 ("python-scipy" ,python-scipy)
1911 ("python-pandas" ,python-pandas)
1912 ("python-patsy" ,python-patsy)
1913 ("python-matplotlib" ,python-matplotlib)))
1915 `(("python-cython" ,python-cython)
1916 ("python-nose" ,python-nose)
1917 ("python-sphinx" ,python-sphinx)))
1918 (home-page "http://statsmodels.sourceforge.net/")
1919 (synopsis "Statistical modeling and econometrics in Python")
1921 "Statsmodels is a Python package that provides a complement to scipy for
1922 statistical computations including descriptive statistics and estimation and
1923 inference for statistical models.")
1924 (license license:bsd-3)))
1926 (define-public python2-statsmodels
1927 (let ((stats (package-with-python2 python-statsmodels)))
1928 (package (inherit stats)
1930 `(("python2-pytz" ,python2-pytz)
1931 ("python2-numpy" ,python2-numpy)
1932 ("python2-scipy" ,python2-scipy)
1933 ("python2-pandas" ,python2-pandas)
1934 ("python2-patsy" ,python2-patsy)
1935 ("python2-matplotlib" ,python2-matplotlib))))))
1937 (define-public r-coda
1943 (uri (cran-uri "coda" version))
1946 "1mn50bshky968gn4nf6vnkaa768fnvm1xmhkms7szwdw9341zpyk"))))
1947 (build-system r-build-system)
1949 `(("r-lattice" ,r-lattice)))
1950 (home-page "https://cran.r-project.org/web/packages/coda")
1951 (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
1952 (description "This package provides functions for summarizing and plotting
1953 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
1954 diagnostic tests of convergence to the equilibrium distribution of the Markov
1956 (license license:gpl2+)))
1958 (define-public r-ade4
1965 (uri (cran-uri "ade4" version))
1968 "16z9jk4qj35ghsk4lwmq241dgc770y8a70dlmp9q4gz6d8ssgl7m"))))
1969 (build-system r-build-system)
1971 `(("r-mass" ,r-mass)))
1972 (home-page "http://pbil.univ-lyon1.fr/ADE-4")
1973 (synopsis "Multivariate data analysis and graphical display")
1975 "The ade4 package contains data analysis functions to analyze ecological
1976 and environmental data in the framework of Euclidean exploratory methods.")
1977 (license license:gpl2+)))
1979 (define-public r-xml2
1986 (uri (cran-uri "xml2" version))
1989 "1x3q3a0xv8j0nx3hs4d3pfjm5g9nvaxmfrapba9f4nrkqi3z2l1h"))))
1990 (build-system r-build-system)
1992 `(("libxml2" ,libxml2)
1995 `(("pkg-config" ,pkg-config)))
1997 `(("r-rcpp" ,r-rcpp)))
1998 (home-page "https://github.com/hadley/xml2")
1999 (synopsis "Parse XML with R")
2001 "This package provides a simple, consistent interface to working with XML
2002 files in R. It is built on top of the libxml2 C library.")
2003 (license license:gpl2+)))
2005 (define-public r-multitaper
2007 (name "r-multitaper")
2012 (uri (cran-uri "multitaper" version))
2015 "04wd9bbhyx7697pfy0fpj02v1csr48hkpqj62h9p8a6w84ji4k68"))))
2016 (build-system r-build-system)
2018 `(("gfortran" ,gfortran)))
2019 (home-page "https://github.com/wesleyburr/multitaper/")
2020 (synopsis "Multitaper spectral analysis tools")
2022 "This package implements multitaper spectral estimation
2023 techniques using prolate spheroidal sequences (Slepians) and sine
2024 tapers for time series analysis. It includes an adaptive weighted
2025 multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
2026 F-test, and complex demodulation. The Slepians sequences are
2027 generated efficiently using a tridiagonal matrix solution, and
2028 jackknifed confidence intervals are available for most estimates.")
2029 (license license:gpl2+)))
2031 (define-public r-rversions
2033 (name "r-rversions")
2037 (uri (cran-uri "rversions" version))
2040 "1ic6sxnyya24d5xsxjg3fba73fhya9fhs0kaf66yha6nwxj1zv2i"))))
2041 (build-system r-build-system)
2043 `(("r-curl" ,r-curl)
2044 ("r-xml2" ,r-xml2)))
2045 (home-page "https://github.com/metacran/rversions")
2046 (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
2048 "This package provides functions to query the main R repository to find
2049 the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
2050 previous R versions and their release dates.")
2051 (license license:expat)))
2053 (define-public r-whisker
2059 (uri (cran-uri "whisker" version))
2062 "1a7vz0dk95xfjvi38wbpw8vmf5qn3g8p490msz2rw0piwidmk1ks"))))
2063 (build-system r-build-system)
2064 (home-page "https://github.com/edwindj/whisker")
2065 (synopsis "Logicless mustache templating for R")
2067 "This package provides logicless templating, with a syntax that is not
2069 (license license:gpl3+)))
2071 (define-public r-backports
2073 (name "r-backports")
2078 (uri (cran-uri "backports" version))
2081 "0k19w68b2aihyj5mflw3732gkkzs78sssqdns960pdw3yfnkiv33"))))
2082 (build-system r-build-system)
2083 (home-page "https://cran.r-project.org/web/packages/backports")
2084 (synopsis "Reimplementations of functions introduced since R 3.0.0")
2086 "Provides implementations of functions which have been introduced in R
2087 since version 3.0.0. The backports are conditionally exported which results
2088 in R resolving the function names to the version shipped with R (if available)
2089 and uses the implemented backports as fallback. This way package developers
2090 can make use of the new functions without worrying about the minimum required
2092 (license license:gpl2+)))
2094 (define-public r-checkmate
2096 (name "r-checkmate")
2101 (uri (cran-uri "checkmate" version))
2104 "08ddpgs4mv5d5y4j054pm8drmxkn7yvhfpbghwxlizjpnxa5g8ps"))))
2105 (build-system r-build-system)
2107 `(("r-backports" ,r-backports)))
2108 (home-page "https://github.com/mllg/checkmate")
2109 (synopsis "Fast and versatile argument checks")
2111 "This package provides tests and assertions to perform frequent argument
2112 checks. A substantial part of the package was written in C to minimize any
2113 worries about execution time overhead.")
2114 (license license:bsd-3)))
2116 (define-public r-bbmisc
2123 (uri (cran-uri "BBmisc" version))
2126 "1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y"))))
2127 (properties `((upstream-name . "BBmisc")))
2128 (build-system r-build-system)
2130 `(("r-checkmate" ,r-checkmate)))
2131 (home-page "https://github.com/berndbischl/BBmisc")
2132 (synopsis "Miscellaneous functions for R package development")
2134 "This package provides miscellaneous helper functions for the development
2136 (license license:bsd-3)))
2138 (define-public r-fail
2145 (uri (cran-uri "fail" version))
2148 "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
2149 (build-system r-build-system)
2151 `(("r-bbmisc" ,r-bbmisc)
2152 ("r-checkmate" ,r-checkmate)))
2153 (home-page "https://github.com/mllg/fail")
2154 (synopsis "File abstraction interface layer (FAIL)")
2156 "This package provides a more comfortable interface to work with R data
2157 or source files in a key-value fashion.")
2158 (license license:bsd-3)))
2160 (define-public r-batchjobs
2162 (name "r-batchjobs")
2167 (uri (cran-uri "BatchJobs" version))
2170 "1zz4sspj596pijxlz321g0jy2rg9ki83j6fihbwisjwr66p2vk1m"))))
2171 (properties `((upstream-name . "BatchJobs")))
2172 (build-system r-build-system)
2174 `(("r-backports" ,r-backports)
2175 ("r-bbmisc" ,r-bbmisc)
2177 ("r-checkmate" ,r-checkmate)
2178 ("r-data-table" ,r-data-table)
2180 ("r-digest" ,r-digest)
2181 ("r-rsqlite" ,r-rsqlite)
2182 ("r-sendmailr" ,r-sendmailr)
2183 ("r-stringi" ,r-stringi)))
2184 (home-page "https://github.com/tudo-r/BatchJobs")
2185 (synopsis "Batch computing with R")
2187 "This package provides @code{Map}, @code{Reduce} and @code{Filter}
2188 variants to generate jobs on batch computing systems like PBS/Torque, LSF,
2189 SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
2190 (license license:bsd-2)))
2192 (define-public r-brew
2198 (uri (cran-uri "brew" version))
2201 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
2202 (build-system r-build-system)
2203 (home-page "https://cran.r-project.org/web/packages/brew")
2204 (synopsis "Templating framework for report generation")
2206 "The brew package implements a templating framework for mixing text and R
2207 code for report generation. The template syntax is similar to PHP, Ruby's erb
2208 module, Java Server Pages, and Python's psp module.")
2209 (license license:gpl2+)))
2211 (define-public r-desc
2218 (uri (cran-uri "desc" version))
2221 "1s6s13fk6sxwcj8wzkwxl9vr33153xx11p5wi9avqx3rzkabavz6"))))
2222 (build-system r-build-system)
2224 `(("r-assertthat" ,r-assertthat)
2225 ("r-crayon" ,r-crayon)
2227 ("r-rprojroot" ,r-rprojroot)))
2228 (home-page "https://github.com/r-pkgs/desc")
2229 (synopsis "Manipulate DESCRIPTION Files")
2231 "This package provides tools to read, write, create, and manipulate
2232 DESCRIPTION files. It is intended for packages that create or manipulate
2234 (license license:expat)))
2236 (define-public r-commonmark
2238 (name "r-commonmark")
2243 (uri (cran-uri "commonmark" version))
2246 "024iz1qp2kv6iz6y69ir0jk3qhjps86rhkzlcmhqsxx97rx7cjni"))))
2247 (build-system r-build-system)
2248 (home-page "https://cran.r-project.org/web/packages/commonmark")
2249 (synopsis "CommonMark and Github Markdown Rendering in R")
2251 "The CommonMark specification defines a rationalized version of markdown
2252 syntax. This package uses the @code{cmark} reference implementation for
2253 converting markdown text into various formats including HTML, LaTeX and groff
2254 man. In addition, it exposes the markdown parse tree in XML format. The latest
2255 version of this package also adds support for Github extensions including
2256 tables, autolinks and strikethrough text.")
2257 (license license:bsd-2)))
2259 (define-public r-roxygen2
2265 (uri (cran-uri "roxygen2" version))
2268 "162xag27hwwyadfwm5zpyy15nxwhw2vbhwapx3jmi9cfyryr68sq"))))
2269 (build-system r-build-system)
2271 `(("r-brew" ,r-brew)
2272 ("r-commonmark" ,r-commonmark)
2274 ("r-digest" ,r-digest)
2275 ("r-pkgload" ,r-pkgload)
2276 ("r-purrr" ,r-purrr)
2279 ("r-rlang" ,r-rlang)
2280 ("r-stringi" ,r-stringi)
2281 ("r-stringr" ,r-stringr)
2282 ("r-xml2" ,r-xml2)))
2284 `(("r-knitr" ,r-knitr))) ; for vignettes
2285 (home-page "https://github.com/klutometis/roxygen")
2286 (synopsis "In-source documentation system for R")
2288 "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
2289 collation, and NAMESPACE files.")
2290 (license license:gpl2+)))
2292 (define-public r-openssl
2299 (uri (cran-uri "openssl" version))
2302 "1ihz2qi33lhngl19xdanq0pbmfaacy63794mg8ll7z2lab3yryzp"))))
2303 (build-system r-build-system)
2305 `(("libressl" ,libressl)))
2307 `(("pkg-config" ,pkg-config)))
2309 `(("r-askpass" ,r-askpass)))
2310 (home-page "https://github.com/jeroenooms/openssl")
2311 (synopsis "Toolkit for encryption, signatures and certificates")
2313 "This package provides R bindings to OpenSSL libssl and libcrypto, plus
2314 custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
2315 and P-521. Cryptographic signatures can either be created and verified
2316 manually or via x509 certificates. AES block cipher is used in CBC mode for
2317 symmetric encryption; RSA for asymmetric (public key) encryption. High-level
2318 envelope functions combine RSA and AES for encrypting arbitrary sized data.
2319 Other utilities include key generators, hash functions (md5, sha1, sha256,
2320 etc), base64 encoder, a secure random number generator, and @code{bignum} math
2321 methods for manually performing crypto calculations on large multibyte
2323 (license license:expat)))
2325 (define-public r-httr
2331 (uri (cran-uri "httr" version))
2334 "0mp1il13q6n49n2hv1p2p8x6avjan6dr5az19ql4hb78pc3pwp37"))))
2335 (build-system r-build-system)
2337 `(("r-curl" ,r-curl)
2338 ("r-jsonlite" ,r-jsonlite)
2339 ("r-openssl" ,r-openssl)
2342 (home-page "https://github.com/hadley/httr")
2343 (synopsis "Tools for working with URLs and HTTP")
2345 "The aim of httr is to provide a wrapper for RCurl customised to the
2346 demands of modern web APIs. It provides useful tools for working with HTTP
2347 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
2348 functions make it easy to control additional request components.")
2349 (license license:expat)))
2351 (define-public r-git2r
2357 (uri (cran-uri "git2r" version))
2360 "0dbl845sahv2i641ncaf06w06djravwc5wknp9syzx0ad8l0kmhk"))))
2361 (build-system r-build-system)
2363 `(("libgit2" ,libgit2)
2366 `(("pkg-config" ,pkg-config)))
2367 (home-page "https://github.com/ropensci/git2r")
2368 (synopsis "Access Git repositories with R")
2370 "This package provides an R interface to the libgit2 library, which is a
2371 pure C implementation of the Git core methods.")
2372 ;; GPLv2 only with linking exception.
2373 (license license:gpl2)))
2375 (define-public r-rstudioapi
2377 (name "r-rstudioapi")
2381 (uri (cran-uri "rstudioapi" version))
2384 "15mbw607ncdf53mgga76n3va5zzdcjqz14nb0jcn9axwccqamic0"))))
2385 (build-system r-build-system)
2386 (home-page "https://cran.r-project.org/web/packages/rstudioapi")
2387 (synopsis "Safely access the RStudio API")
2389 "This package provides functions to access the RStudio API and provide
2390 informative error messages when it's not available.")
2391 (license license:expat)))
2393 (define-public r-devtools
2399 (uri (cran-uri "devtools" version))
2402 "0i2f549hxkn0j1x1avkhwy68c9r48v9284j7x9cak2q6dfsqz61f"))))
2403 (build-system r-build-system)
2405 `(("r-callr" ,r-callr)
2408 ("r-crayon" ,r-crayon)
2410 ("r-digest" ,r-digest)
2412 ("r-ellipsis" ,r-ellipsis)
2414 ("r-git2r" ,r-git2r)
2416 ("r-jsonlite" ,r-jsonlite)
2417 ("r-memoise" ,r-memoise)
2418 ("r-pkgbuild" ,r-pkgbuild)
2419 ("r-pkgload" ,r-pkgload)
2420 ("r-rcmdcheck" ,r-rcmdcheck)
2421 ("r-remotes" ,r-remotes)
2422 ("r-rlang" ,r-rlang)
2423 ("r-roxygen2" ,r-roxygen2)
2424 ("r-rstudioapi" ,r-rstudioapi)
2425 ("r-rversions" ,r-rversions)
2426 ("r-sessioninfo" ,r-sessioninfo)
2427 ("r-testthat" ,r-testthat)
2428 ("r-usethis" ,r-usethis)
2429 ("r-withr" ,r-withr)))
2430 (home-page "https://github.com/hadley/devtools")
2431 (synopsis "Tools to make developing R packages easier")
2432 (description "The devtools package is a collection of package development
2433 tools to simplify the devolpment of R packages.")
2434 (license license:gpl2+)))
2436 (define-public r-withr
2442 (uri (cran-uri "withr" version))
2445 "11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1"))))
2446 (build-system r-build-system)
2447 (home-page "https://github.com/jimhester/withr")
2448 (synopsis "Run code with temporarily modified global state")
2450 "This package provides a set of functions to run R code in an environment
2451 in which global state has been temporarily modified. Many of these functions
2452 were originally a part of the r-devtools package.")
2453 (license license:gpl2+)))
2455 (define-public r-hms
2462 (uri (cran-uri "hms" version))
2465 "1baki0qw5ijgiflvsdvqj3apg4yanf12vx14kwbqdzk5rz46fasf"))))
2466 (build-system r-build-system)
2468 `(("r-rlang" ,r-rlang)
2469 ("r-pkgconfig" ,r-pkgconfig)
2470 ("r-vctrs" ,r-vctrs)))
2471 (home-page "https://github.com/rstats-db/hms")
2472 (synopsis "Pretty time of day")
2474 "This package implements an S3 class for storing and formatting
2475 time-of-day values, based on the @code{difftime} class.")
2476 (license license:gpl3+)))
2478 (define-public r-readr
2484 (uri (cran-uri "readr" version))
2487 "1wz496rw0ah433p755n3xac8gh7yzid4xgdjzd1a7wmpkgilvy9k"))))
2488 (build-system r-build-system)
2490 `(("r-clipr" ,r-clipr)
2491 ("r-crayon" ,r-crayon)
2494 ("r-tibble" ,r-tibble)
2497 (home-page "https://github.com/hadley/readr")
2498 (synopsis "Read tabular data")
2500 "This package provides functions to read flat or tabular text files from
2501 disk (or a connection).")
2502 (license license:gpl2+)))
2504 (define-public r-plotrix
2510 (uri (cran-uri "plotrix" version))
2513 "1x92mmyfry127zzr6cmcj6kjsc4zhxrrdlr0jcxn3bb0hpdfps54"))))
2514 (build-system r-build-system)
2515 (home-page "https://cran.r-project.org/web/packages/plotrix")
2516 (synopsis "Various plotting functions")
2518 "This package provides lots of plotting, various labeling, axis and color
2519 scaling functions for R.")
2520 (license license:gpl2+)))
2522 (define-public r-gridbase
2528 (uri (cran-uri "gridBase" version))
2531 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
2532 (build-system r-build-system)
2533 (home-page "https://cran.r-project.org/web/packages/gridBase")
2534 (synopsis "Integration of base and grid graphics")
2536 "This package provides an integration of base and grid graphics for R.")
2537 (license license:gpl2+)))
2539 (define-public r-latticeextra
2541 (name "r-latticeextra")
2546 (uri (cran-uri "latticeExtra" version))
2549 "04fzwcqs594rk5qp98yilh3kdh3sw4xf8wld5rp94ggpaqfw7bbc"))))
2550 (properties `((upstream-name . "latticeExtra")))
2551 (build-system r-build-system)
2553 `(("r-jpeg" ,r-jpeg)
2554 ("r-lattice" ,r-lattice)
2556 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2557 (home-page "http://latticeextra.r-forge.r-project.org/")
2558 (synopsis "Extra graphical utilities based on lattice")
2560 "Building on the infrastructure provided by the lattice package, this
2561 package provides several new high-level graphics functions and methods, as
2562 well as additional utilities such as panel and axis annotation functions.")
2563 (license license:gpl2+)))
2565 (define-public r-rcpparmadillo
2567 (name "r-rcpparmadillo")
2568 (version "0.9.800.4.0")
2571 (uri (cran-uri "RcppArmadillo" version))
2574 "1csh54v4d0ccwmk4bqj4rca1d5rqpafvb4459x3q6k9sys0charx"))))
2575 (properties `((upstream-name . "RcppArmadillo")))
2576 (build-system r-build-system)
2577 ;; All needed for vignettes
2579 `(("r-knitr" ,r-knitr)
2580 ("r-rmarkdown" ,r-rmarkdown)
2581 ("ghc-pandoc" ,ghc-pandoc)
2582 ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)))
2584 `(("r-rcpp" ,r-rcpp)))
2585 (home-page "https://github.com/RcppCore/RcppArmadillo")
2586 (synopsis "Rcpp integration for the Armadillo linear algebra library")
2588 "Armadillo is a templated C++ linear algebra library that aims towards a
2589 good balance between speed and ease of use. Integer, floating point and
2590 complex numbers are supported, as well as a subset of trigonometric and
2591 statistics functions. Various matrix decompositions are provided through
2592 optional integration with LAPACK and ATLAS libraries. This package includes
2593 the header files from the templated Armadillo library.")
2594 ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
2595 ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
2596 ;; later, as is the rest of 'Rcpp'.
2597 (license license:gpl2+)))
2599 (define-public r-bitops
2605 (uri (cran-uri "bitops" version))
2608 "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
2609 (build-system r-build-system)
2610 (home-page "https://cran.r-project.org/web/packages/bitops")
2611 (synopsis "Bitwise operations")
2613 "This package provides functions for bitwise operations on integer
2615 (license license:gpl2+)))
2617 (define-public r-catools
2623 (uri (cran-uri "caTools" version))
2626 "0y1kgyiy322yhb0phzwvf2zgjz9awp13lhzhk9v1ddg88656jhq3"))))
2627 (properties `((upstream-name . "caTools")))
2628 (build-system r-build-system)
2630 `(("r-bitops" ,r-bitops)))
2631 (home-page "https://cran.r-project.org/web/packages/caTools")
2632 (synopsis "Various tools including functions for moving window statistics")
2634 "This package contains several basic utility functions including:
2635 moving (rolling, running) window statistic functions, read/write for GIF and
2636 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
2637 encoder/decoder, round-off-error-free sum and cumsum, etc.")
2638 (license license:gpl3+)))
2640 (define-public r-rprojroot
2642 (name "r-rprojroot")
2647 (uri (cran-uri "rprojroot" version))
2650 "12r3fdxmi2pmwn6ic3rhg0b20ll5z420m0d8fziv1n21961namnz"))))
2651 (build-system r-build-system)
2653 `(("r-backports" ,r-backports)))
2654 (home-page "https://github.com/krlmlr/rprojroot")
2655 (synopsis "Finding files in project subdirectories")
2657 "This package helps accessing files relative to a project root. It
2658 provides helpers for robust, reliable and flexible paths to files below a
2659 project root. The root of a project is defined as a directory that matches a
2660 certain criterion, e.g., it contains a certain regular file.")
2661 (license license:gpl3)))
2663 (define-public r-rmarkdown
2665 (name "r-rmarkdown")
2670 (uri (cran-uri "rmarkdown" version))
2672 (base32 "0pa5xs0vzwn9vsgysjqbks9v5lbqphxh5agciskllibc40hhwigg"))))
2673 (properties `((upstream-name . "rmarkdown")))
2674 (build-system r-build-system)
2676 `(("r-base64enc" ,r-base64enc)
2677 ("r-evaluate" ,r-evaluate)
2678 ("r-htmltools" ,r-htmltools)
2679 ("r-jsonlite" ,r-jsonlite)
2680 ("r-knitr" ,r-knitr)
2682 ("r-stringr" ,r-stringr)
2683 ("r-tinytex" ,r-tinytex)
2686 ("ghc-pandoc" ,ghc-pandoc)))
2687 (home-page "https://rmarkdown.rstudio.com")
2688 (synopsis "Convert R Markdown documents into a variety of formats")
2690 "This package provides tools to convert R Markdown documents into a
2691 variety of formats.")
2692 (license license:gpl3+)))
2694 (define-public r-gtable
2700 (uri (cran-uri "gtable" version))
2703 "1lyncxf2dqdjgw1071cn9c8zwzkz6sldnd5cgmicf70bc726qf7x"))))
2704 (properties `((upstream-name . "gtable")))
2705 (build-system r-build-system)
2706 (home-page "https://cran.r-project.org/web/packages/gtable")
2707 (synopsis "R library to arrange grobs in tables")
2709 "Gtable is a collection of tools to make it easier to work with
2710 \"tables\" of grobs.")
2711 (license license:gpl2+)))
2713 (define-public r-gridextra
2715 (name "r-gridextra")
2719 (uri (cran-uri "gridExtra" version))
2722 "0fwfk3cdwxxim7nd55pn7m31bcaqj48y06j7an2k1v1pybk0rdl1"))))
2723 (properties `((upstream-name . "gridExtra")))
2724 (build-system r-build-system)
2726 `(("r-gtable" ,r-gtable)))
2728 `(("r-knitr" ,r-knitr))) ;for building vignettes
2729 (home-page "https://github.com/baptiste/gridextra")
2730 (synopsis "Miscellaneous functions for \"Grid\" graphics")
2732 "This package provides a number of user-level functions to work with
2733 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
2735 (license license:gpl2+)))
2737 (define-public r-pkgconfig
2739 (name "r-pkgconfig")
2743 (uri (cran-uri "pkgconfig" version))
2746 "0l1qph8zyi2sic3k2qcd7vlfl7rzfh1q7z7zvjkl5f7y1x2fy3rk"))))
2747 (build-system r-build-system)
2748 (home-page "https://github.com/gaborcsardi/pkgconfig")
2749 (synopsis "Private configuration for R packages")
2750 (description "This package provides the functionality to set configuration
2751 options on a per-package basis. Options set by a given package only apply to
2752 that package, other packages are unaffected.")
2753 (license license:expat)))
2755 (define-public r-blob
2761 (uri (cran-uri "blob" version))
2764 "1slb5mvxfyi92i8ifx2qa31hp57inilwhq1g9lzvgha6jrxbqm7g"))))
2765 (build-system r-build-system)
2767 `(("r-rlang" ,r-rlang)
2768 ("r-vctrs" ,r-vctrs)))
2769 (home-page "https://github.com/hadley/blob")
2770 (synopsis "Simple S3 Class for representing vectors of binary data")
2771 (description "Raw vectors in R are useful for storing a single binary
2772 object. What if you want to put a vector of them in a data frame? The blob
2773 package provides the blob object, a list of raw vectors, suitable for use as
2774 a column in data frame.")
2775 (license license:gpl3+)))
2777 (define-public r-rsqlite
2783 (uri (cran-uri "RSQLite" version))
2786 "1m38sj8rwbf3p2lhqabcp7c7djk7s9ng37cz39yxk706v9pi4380"))))
2787 (properties `((upstream-name . "RSQLite")))
2788 (build-system r-build-system)
2792 ("r-memoise" ,r-memoise)
2793 ("r-plogr" ,r-plogr)
2795 ("r-bit64" ,r-bit64)
2797 ("r-pkgconfig" ,r-pkgconfig)))
2798 (home-page "https://github.com/rstats-db/RSQLite")
2799 (synopsis "SQLite interface for R")
2801 "This package embeds the SQLite database engine in R and provides an
2802 interface compliant with the DBI package. The source for the SQLite
2803 engine (version 3.8.8.2) is included.")
2804 (license license:lgpl2.0+)))
2806 (define-public r-rcurl
2809 (version "1.95-0.1.2")
2812 (uri (string-append "https://www.bioconductor.org/packages/"
2813 "release/extra/src/"
2814 "contrib/RCurl_" version ".tar.gz"))
2817 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
2818 (properties `((upstream-name . "RCurl")))
2819 (build-system r-build-system)
2822 (modify-phases %standard-phases
2823 (add-after 'unpack 'respect-CURL_CA_BUNDLE
2825 (substitute* "R/options.S"
2826 (("\\.els = rev\\(merge\\(list\\(\\.\\.\\.\\), \\.opts\\)\\)" m)
2828 certs = Sys.getenv(\"CURL_CA_BUNDLE\")
2829 if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) }
2833 `(("libcurl" ,curl)))
2835 `(("r-bitops" ,r-bitops)))
2836 (home-page "http://www.omegahat.org/RCurl")
2837 (synopsis "General network client interface for R")
2839 "The package allows one to compose general HTTP requests and provides
2840 convenient functions to fetch URIs, GET and POST forms, etc. and process the
2841 results returned by the Web server. This provides a great deal of control
2842 over the HTTP/FTP/... connection and the form of the request while providing a
2843 higher-level interface than is available just using R socket connections.
2844 Additionally, the underlying implementation is robust and extensive,
2845 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
2846 ldap, and also supports cookies, redirects, authentication, etc.")
2847 (license license:bsd-3)))
2849 (define-public r-xml
2852 (version "3.99-0.3")
2855 (uri (cran-uri "XML" version))
2858 "0lzpqwajs5xaqdna50vl24qkp9xvh00zypjjzy6kgdzk11isgdw1"))))
2860 `((upstream-name . "XML")))
2861 (build-system r-build-system)
2863 `(("libxml2" ,libxml2)
2866 `(("pkg-config" ,pkg-config)))
2867 (home-page "http://www.omegahat.org/RSXML")
2868 (synopsis "Tools for parsing and generating XML within R")
2870 "Many approaches for both reading and creating XML (and HTML)
2871 documents (including DTDs), both local and accessible via HTTP or FTP. Also
2872 offers access to an XPath \"interpreter\".")
2873 (license license:bsd-2)))
2875 (define-public r-xnomial
2880 (origin (method url-fetch)
2881 (uri (cran-uri "XNomial" version))
2884 "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
2885 (properties (quasiquote ((upstream-name . "XNomial"))))
2886 (build-system r-build-system)
2887 (home-page "https://cran.r-project.org/web/packages/XNomial")
2888 (synopsis "Goodness-of-Fit test for multinomial data")
2890 "This package provides an exact Goodness-of-Fit test for
2891 multinomial data with fixed probabilities. It can be used to
2892 determine whether a set of counts fits a given expected ratio. To see
2893 whether a set of observed counts fits an expectation, one can examine
2894 all possible outcomes with @code{xmulti()} or a random sample of them
2895 with @code{xmonte()} and find the probability of an observation
2896 deviating from the expectation by at least as much as the observed.
2897 As a measure of deviation from the expected, one can use the
2898 log-likelihood ratio, the multinomial probability, or the classic
2899 chi-square statistic. A histogram of the test statistic can also be
2900 plotted and compared with the asymptotic curve.")
2901 (license (list license:gpl2+ license:gpl3+))))
2903 (define-public r-lambda-r
2909 (uri (cran-uri "lambda.r" version))
2912 "1mh1g0gsd58gng0hb29vww2yqb2jfs07kba5kxnnqck5j3izwlnj"))))
2913 (properties `((upstream-name . "lambda.r")))
2914 (build-system r-build-system)
2916 `(("r-formatr" ,r-formatr)))
2917 (home-page "https://cran.r-project.org/web/packages/lambda.r")
2918 (synopsis "Functional programming extension for R")
2920 "This package provides a language extension to efficiently write
2921 functional programs in R. Syntax extensions include multi-part function
2922 definitions, pattern matching, guard statements, built-in (optional) type
2924 (license license:lgpl3+)))
2926 (define-public r-futile-options
2928 (name "r-futile-options")
2932 (uri (cran-uri "futile.options" version))
2935 "0w15agpi88y3qkv6fl72zy2pzyplzgvnj41a4ixhg64mw1sck73s"))))
2937 `((upstream-name . "futile.options")))
2938 (build-system r-build-system)
2939 (home-page "https://cran.r-project.org/web/packages/futile.options")
2940 (synopsis "Options management framework")
2942 "The futile.options subsystem provides an easy user-defined options
2943 management system that is properly scoped. This means that options created
2944 via @code{futile.options} are fully self-contained and will not collide with
2945 options defined in other packages.")
2946 (license license:lgpl3+)))
2948 (define-public r-futile-logger
2950 (name "r-futile-logger")
2954 (uri (cran-uri "futile.logger" version))
2957 "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
2958 (properties `((upstream-name . "futile.logger")))
2959 (build-system r-build-system)
2961 `(("r-futile-options" ,r-futile-options)
2962 ("r-lambda-r" ,r-lambda-r)))
2963 (home-page "https://cran.r-project.org/web/packages/futile.logger")
2964 (synopsis "Logging utility for R")
2966 "This package provides a simple yet powerful logging utility. Based
2967 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
2968 convenient and easy to use replacement for @code{cat} and @code{print}
2970 (license license:lgpl3+)))
2972 (define-public r-segmented
2974 (name "r-segmented")
2979 (uri (cran-uri "segmented" version))
2982 "06cxdrqgnpk5fvbam5i7qa4n71wry0yvlj0jpwbxf267mvpx10fh"))))
2983 (build-system r-build-system)
2984 (home-page "https://cran.r-project.org/web/packages/segmented")
2985 (synopsis "Regression models with breakpoints estimation")
2987 "Given a regression model, segmented updates the model by adding one or
2988 more segmented (i.e., piecewise-linear) relationships. Several variables with
2989 multiple breakpoints are allowed.")
2990 (license (list license:gpl2+ license:gpl3+))))
2992 (define-public r-snow
2998 (uri (cran-uri "snow" version))
3001 "1n3n8pva9s34fvlw32yng0x416lmbv7q1fsd0ywa4kikmxym64l5"))))
3002 (build-system r-build-system)
3003 (home-page "https://cran.r-project.org/web/packages/snow")
3004 (synopsis "Support for simple parallel computing in R")
3006 "The snow package provides support for simple parallel computing on a
3007 network of workstations using R. A master R process calls @code{makeCluster}
3008 to start a cluster of worker processes; the master process then uses functions
3009 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
3010 worker processes and collect and return the results on the master.")
3011 (license (list license:gpl2+ license:gpl3+))))
3013 (define-public r-sparsem
3019 (uri (cran-uri "SparseM" version))
3022 "0cmlm0lps3daalvp5jzjnjfys388hgkyc8yw0g5r2351h749xdyn"))))
3024 `((upstream-name . "SparseM")))
3026 `(("gfortran" ,gfortran)))
3027 (build-system r-build-system)
3028 (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
3029 (synopsis "Sparse linear algebra")
3031 "This package provides some basic linear algebra functionality for sparse
3032 matrices. It includes Cholesky decomposition and backsolving as well as
3033 standard R subsetting and Kronecker products.")
3034 (license license:gpl2+)))
3036 (define-public r-iterators
3038 (name "r-iterators")
3043 (uri (cran-uri "iterators" version))
3046 "0jwzxaa3jm1xzgfv5pn0xqkk7rhm0xwvgn85w7xaw8xx1vb33gwn"))))
3047 (build-system r-build-system)
3048 (home-page "https://cran.r-project.org/web/packages/iterators")
3049 (synopsis "Iterator construct for R")
3051 "This package provides support for iterators, which allow a programmer to
3052 traverse through all the elements of a vector, list, or other collection of
3054 (license license:asl2.0)))
3056 (define-public r-foreach
3063 (uri (cran-uri "foreach" version))
3066 "0q7iyniw5iri4hl57bhil3r69s5wnaijzn0q0x4h3z42245jqqwm"))))
3067 (build-system r-build-system)
3069 `(("r-codetools" ,r-codetools)
3070 ("r-iterators" ,r-iterators)))
3071 (home-page "https://cran.r-project.org/web/packages/foreach")
3072 (synopsis "Foreach looping construct for R")
3074 "This package provides support for the @code{foreach} looping construct.
3075 @code{foreach} is an idiom that allows for iterating over elements in a
3076 collection, without the use of an explicit loop counter. This package in
3077 particular is intended to be used for its return value, rather than for its
3078 side effects. In that sense, it is similar to the standard @code{lapply}
3079 function, but doesn't require the evaluation of a function. Using
3080 @code{foreach} without side effects also facilitates executing the loop in
3082 (license license:asl2.0)))
3084 (define-public r-doparallel
3086 (name "r-doparallel")
3091 (uri (cran-uri "doParallel" version))
3094 "0vnqbha3gig3awbfvsfx3ni5jir398md1n7xmsb8jihnjsk7xbbi"))))
3095 (properties `((upstream-name . "doParallel")))
3096 (build-system r-build-system)
3098 `(("r-foreach" ,r-foreach)
3099 ("r-iterators" ,r-iterators)))
3100 (home-page "https://cran.r-project.org/web/packages/doParallel")
3101 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3103 "This package provides a parallel backend for the @code{%dopar%} function
3104 using the parallel package.")
3105 (license license:gpl2+)))
3107 (define-public r-domc
3114 (uri (cran-uri "doMC" version))
3117 "1cn9gxavhvjswip8pwvkpi7q6wpzdllcsdjabga8akf55nggqxr9"))))
3118 (properties `((upstream-name . "doMC")))
3119 (build-system r-build-system)
3121 `(("r-foreach" ,r-foreach)
3122 ("r-iterators" ,r-iterators)))
3123 (home-page "https://cran.r-project.org/web/packages/doMC")
3124 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3126 "This package provides a parallel backend for the @code{%dopar%} function
3127 using the multicore functionality of the parallel package.")
3128 (license license:gpl2+)))
3136 (uri (cran-uri "DT" version))
3139 "09k9s07aah1apc308sj1abvr27mky6fkpl9j6lxl2x55n4immvkg"))))
3141 `((upstream-name . "DT")))
3142 (build-system r-build-system)
3144 `(("r-crosstalk" ,r-crosstalk)
3145 ("r-htmltools" ,r-htmltools)
3146 ("r-htmlwidgets" ,r-htmlwidgets)
3147 ("r-jsonlite" ,r-jsonlite)
3148 ("r-magrittr" ,r-magrittr)
3149 ("r-promises" ,r-promises)))
3150 (home-page "http://rstudio.github.io/DT")
3151 (synopsis "R wrapper of the DataTables JavaScript library")
3153 "This package allows for data objects in R to be rendered as HTML tables
3154 using the JavaScript library @code{DataTables} (typically via R Markdown or
3155 Shiny). The @code{DataTables} library has been included in this R package.")
3156 ;; The DT package as a whole is distributed under GPLv3. The DT package
3157 ;; inludes other software components under different licenses:
3159 ;; * Expat: jQuery, jquery.highlight.js, DataTables
3160 ;; * ASL2.0: selectize.js
3161 ;; * WTFPL: noUiSlider
3162 (license (list license:gpl3
3165 (license:non-copyleft "http://www.wtfpl.net/txt/copying/")))))
3167 (define-public r-base64enc
3169 (name "r-base64enc")
3173 (uri (cran-uri "base64enc" version))
3176 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
3177 (build-system r-build-system)
3178 (home-page "http://www.rforge.net/base64enc")
3179 (synopsis "Tools for Base64 encoding")
3181 "This package provides tools for handling Base64 encoding. It is more
3182 flexible than the orphaned \"base64\" package.")
3183 (license license:gpl2+)))
3185 (define-public r-irlba
3192 (uri (cran-uri "irlba" version))
3195 "1h7mzrqdjc41814cf6c93sbyl7nxwvsf3x8apl9rhmydgdlk7qkf"))))
3196 (build-system r-build-system)
3198 `(("r-matrix" ,r-matrix)))
3199 (home-page "https://cran.r-project.org/web/packages/irlba")
3200 (synopsis "Methods for eigendecomposition of large matrices")
3202 "This package provides fast and memory efficient methods for truncated
3203 singular and eigenvalue decompositions, as well as for principal component
3204 analysis of large sparse or dense matrices.")
3205 (license (list license:gpl2+ license:gpl3+))))
3207 (define-public r-glmnet
3214 (uri (cran-uri "glmnet" version))
3216 (base32 "0b3nnfzp8dxcdkvxr0yvy6d58yk3xg4kz1wqa42bxqppbakmd2gl"))))
3217 (build-system r-build-system)
3219 `(("gfortran" ,gfortran)))
3221 `(("r-foreach" ,r-foreach)
3222 ("r-matrix" ,r-matrix)
3223 ("r-shape" ,r-shape)))
3224 (home-page "https://www.jstatsoft.org/article/view/v033i01")
3225 (synopsis "Lasso and elastic-net regularized generalized linear models")
3227 "The glmnet package provides efficient procedures for fitting the entire
3228 lasso or elastic-net regularization path for linear and Poisson regression, as
3229 well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
3230 multinomial models. The algorithm uses cyclical coordinate descent in a
3231 path-wise fashion.")
3232 (license license:gpl2+)))
3234 (define-public r-pkgmaker
3241 (uri (cran-uri "pkgmaker" version))
3244 "0cc6v6kpwxwwh7k7zyw13wqdp0f9qzzr1a7vv02lskgii54aa4nb"))))
3245 (build-system r-build-system)
3247 `(("r-assertthat" ,r-assertthat)
3248 ("r-bibtex" ,r-bibtex)
3249 ("r-codetools" ,r-codetools)
3250 ("r-digest" ,r-digest)
3251 ("r-magrittr" ,r-magrittr)
3252 ("r-registry" ,r-registry)
3253 ("r-stringi" ,r-stringi)
3254 ("r-stringr" ,r-stringr)
3255 ("r-withr" ,r-withr)
3256 ("r-xtable" ,r-xtable)))
3257 (home-page "https://renozao.github.io/pkgmaker")
3258 (synopsis "Package development utilities")
3260 "This package provides some low-level utilities to use for R package
3261 development. It currently provides managers for multiple package specific
3262 options and registries, vignette, unit test and bibtex related utilities.")
3263 (license license:gpl2+)))
3265 (define-public r-registry
3272 (uri (cran-uri "registry" version))
3275 "1k3j6dx350awamr0dwwgkhfs46vsnj4nf08iw5byq0x7n3nkdsnz"))))
3276 (build-system r-build-system)
3277 (home-page "https://cran.r-project.org/web/packages/registry")
3278 (synopsis "Infrastructure for R package registries")
3280 "This package provides a generic infrastructure for creating and using R
3281 package registries.")
3282 (license license:gpl2+)))
3284 (define-public r-rngtools
3291 (uri (cran-uri "rngtools" version))
3294 "0xgmg3qb6insc157as47mcm9sdjdpy9jirh7w06bxb7pfcxqfx42"))))
3295 (build-system r-build-system)
3297 `(("r-digest" ,r-digest)))
3298 (home-page "https://renozao.github.io/rngtools")
3299 (synopsis "Utility functions for working with random number generators")
3301 "This package contains a set of functions for working with Random Number
3302 Generators (RNGs). In particular, it defines a generic S4 framework for
3303 getting/setting the current RNG, or RNG data that are embedded into objects
3304 for reproducibility. Notably, convenient default methods greatly facilitate
3305 the way current RNG settings can be changed.")
3306 (license license:gpl3+)))
3308 (define-public r-rtsne
3315 (uri (cran-uri "Rtsne" version))
3318 "0v17vxizrs1msay24xl2bckfajr2c82wpqj07lyssbrq197nwdsn"))))
3319 (properties `((upstream-name . "Rtsne")))
3320 (build-system r-build-system)
3322 `(("r-rcpp" ,r-rcpp)))
3323 (home-page "https://github.com/jkrijthe/Rtsne")
3324 (synopsis "T-distributed stochastic neighbor embedding")
3326 "This package provides an R wrapper around the fast T-distributed
3327 Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
3328 ;; The declared license for this package is BSD-3, but it also includes
3329 ;; code licensed under BSD-4.
3330 (license (list license:bsd-3 license:bsd-4))))
3332 (define-public r-e1071
3339 (uri (cran-uri "e1071" version))
3342 "0pf2pjb590z0jikgv1037xcp7dq06mg3dzmyffjw6gk7dd9blbdv"))))
3343 (build-system r-build-system)
3345 `(("r-class" ,r-class)))
3346 (home-page "https://cran.r-project.org/web/packages/e1071")
3347 (synopsis "Miscellaneous functions for probability theory")
3349 "This package provides functions for latent class analysis, short time
3350 Fourier transform, fuzzy clustering, support vector machines, shortest path
3351 computation, bagged clustering, naive Bayes classifier, and more.")
3352 (license license:gpl2+)))
3354 (define-public r-bigmemory-sri
3356 (name "r-bigmemory-sri")
3361 (uri (cran-uri "bigmemory.sri" version))
3363 (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
3365 `((upstream-name . "bigmemory.sri")))
3366 (build-system r-build-system)
3367 (home-page "https://cran.r-project.org/web/packages/bigmemory.sri")
3368 (synopsis "Shared resource interface for the bigmemory package")
3369 (description "This package provides a shared resource interface for the
3370 bigmemory and synchronicity packages.")
3371 ;; Users can choose either LGPLv3 or ASL2.0.
3372 (license (list license:lgpl3 license:asl2.0))))
3374 (define-public r-synchronicity
3376 (name "r-synchronicity")
3381 (uri (cran-uri "synchronicity" version))
3384 "1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx"))))
3385 (build-system r-build-system)
3388 ("r-bigmemory-sri" ,r-bigmemory-sri)
3390 ("r-uuid" ,r-uuid)))
3391 (home-page "http://www.bigmemory.org")
3392 (synopsis "Boost mutex functionality in R")
3393 (description "This package provides support for synchronization
3394 via mutexes and may eventually support interprocess communication and
3396 ;; Users can choose either LGPLv3 or ASL2.0.
3397 (license (list license:lgpl3 license:asl2.0))))
3399 (define-public r-bigmemory
3401 (name "r-bigmemory")
3406 (uri (cran-uri "bigmemory" version))
3409 "03pg8mxdc7q0249visjmc8bc3xmwxsfg3i2n6higicj4cfz7zihq"))))
3410 (build-system r-build-system)
3414 ("r-bigmemory-sri" ,r-bigmemory-sri)))
3415 (home-page "http://www.bigmemory.org")
3416 (synopsis "Manage large matrices with shared memory or memory-mapped files")
3417 (description "This package provides methods to create, store, access, and
3418 manipulate large matrices. Matrices are allocated to shared memory and may use
3419 memory-mapped files.")
3420 ;; Users can choose either LGPLv3 or ASL2.0.
3421 (license (list license:lgpl3 license:asl2.0))))
3423 (define-public r-nmf
3430 (uri (cran-uri "NMF" version))
3433 "1qq25n3k5sgh3srlshb3ic6q92s12c1ilqf5cd5anvq6cqfchc1v"))))
3434 (properties `((upstream-name . "NMF")))
3435 (build-system r-build-system)
3437 `(("r-cluster" ,r-cluster)
3438 ("r-bigmemory" ,r-bigmemory) ; suggested
3439 ("r-synchronicity" ,r-synchronicity) ; suggested
3440 ("r-colorspace" ,r-colorspace)
3441 ("r-digest" ,r-digest)
3442 ("r-doparallel" ,r-doparallel)
3443 ("r-foreach" ,r-foreach)
3444 ("r-ggplot2" ,r-ggplot2)
3445 ("r-gridbase" ,r-gridbase)
3446 ("r-pkgmaker" ,r-pkgmaker)
3447 ("r-rcolorbrewer" ,r-rcolorbrewer)
3448 ("r-registry" ,r-registry)
3449 ("r-reshape2" ,r-reshape2)
3450 ("r-rngtools" ,r-rngtools)
3451 ("r-stringr" ,r-stringr)))
3452 (home-page "http://renozao.github.io/NMF")
3453 (synopsis "Algorithms and framework for nonnegative matrix factorization")
3455 "This package provides a framework to perform Non-negative Matrix
3456 Factorization (NMF). The package implements a set of already published
3457 algorithms and seeding methods, and provides a framework to test, develop and
3458 plug new or custom algorithms. Most of the built-in algorithms have been
3459 optimized in C++, and the main interface function provides an easy way of
3460 performing parallel computations on multicore machines.")
3461 (license license:gpl2+)))
3463 (define-public r-r-methodss3
3465 (name "r-r-methodss3")
3469 (uri (cran-uri "R.methodsS3" version))
3472 "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24"))))
3473 (properties `((upstream-name . "R.methodsS3")))
3474 (build-system r-build-system)
3475 (home-page "https://cran.r-project.org/web/packages/R.methodsS3")
3476 (synopsis "S3 methods simplified")
3478 "This package provides methods that simplify the setup of S3 generic
3479 functions and S3 methods. Major effort has been made in making definition of
3480 methods as simple as possible with a minimum of maintenance for package
3481 developers. For example, generic functions are created automatically, if
3482 missing, and naming conflict are automatically solved, if possible. The
3483 method @code{setMethodS3()} is a good start for those who in the future may
3484 want to migrate to S4.")
3485 (license license:lgpl2.1+)))
3487 (define-public r-r-oo
3493 (uri (cran-uri "R.oo" version))
3496 "189fb7mmyzwg6nn8rza8iip7fbyws7i2vkmzy672x9mhvgilq4pm"))))
3497 (properties `((upstream-name . "R.oo")))
3498 (build-system r-build-system)
3500 `(("r-r-methodss3" ,r-r-methodss3)))
3501 (home-page "https://github.com/HenrikBengtsson/R.oo")
3502 (synopsis "R object-oriented programming with or without references")
3504 "This package provides methods and classes for object-oriented
3505 programming in R with or without references. Large effort has been made on
3506 making definition of methods as simple as possible with a minimum of
3507 maintenance for package developers.")
3508 (license license:lgpl2.1+)))
3510 (define-public r-r-utils
3516 (uri (cran-uri "R.utils" version))
3519 "1krj1ny7y43lpm2q8c7swxfdc3ngy2j8knzv71f8bfsgh673nsxc"))))
3520 (properties `((upstream-name . "R.utils")))
3521 (build-system r-build-system)
3523 `(("r-r-methodss3" ,r-r-methodss3)
3524 ("r-r-oo" ,r-r-oo)))
3525 (home-page "https://github.com/HenrikBengtsson/R.utils")
3526 (synopsis "Various programming utilities")
3528 "This package provides utility functions useful when programming and
3529 developing R packages.")
3530 (license license:lgpl2.1+)))
3532 (define-public r-r-cache
3538 (uri (cran-uri "R.cache" version))
3541 "1n8n5ihkryrbxv630dwhz4r048nyv676qd3i9f5z5fa04hvlxbqq"))))
3542 (properties `((upstream-name . "R.cache")))
3543 (build-system r-build-system)
3545 `(("r-digest" ,r-digest)
3546 ("r-r-methodss3" ,r-r-methodss3)
3548 ("r-r-utils" ,r-r-utils)))
3549 (home-page "https://github.com/HenrikBengtsson/R.cache")
3550 (synopsis "Light-weight caching of objects and results")
3552 "This package provides methods for caching or memoization of objects and
3553 results. With this package, any R object can be cached in a key-value storage
3554 where the key can be an arbitrary set of R objects. The cache memory is
3555 persistent (on the file system).")
3556 (license license:lgpl2.1+)))
3558 (define-public r-r-rsp
3564 (uri (cran-uri "R.rsp" version))
3567 "128zqyvbq9hm9gy86jzhj609lkfw57vr24mdxgh46ncmx66ag4gj"))))
3568 (properties `((upstream-name . "R.rsp")))
3569 (build-system r-build-system)
3571 `(("r-digest" ,r-digest)
3572 ("r-r-cache" ,r-r-cache)
3573 ("r-r-methodss3" ,r-r-methodss3)
3575 ("r-r-utils" ,r-r-utils)))
3576 (home-page "https://github.com/HenrikBengtsson/R.rsp")
3577 (synopsis "Dynamic generation of scientific reports")
3579 "The RSP markup language provides a powerful markup for controlling the
3580 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
3581 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
3582 to many other literate programming languages, with RSP it is straightforward
3583 to loop over mixtures of code and text sections, e.g. in month-by-month
3584 summaries. RSP has also several preprocessing directives for incorporating
3585 static and dynamic contents of external files (local or online) among other
3586 things. RSP is ideal for self-contained scientific reports and R package
3588 (license license:lgpl2.1+)))
3590 (define-public r-mvtnorm
3596 (uri (cran-uri "mvtnorm" version))
3599 "03rfmii9j8x8fjv7hp8qd28z0svl4w0x54k2f4jpwv4qa7079i24"))))
3600 (build-system r-build-system)
3602 `(("gfortran" ,gfortran)))
3603 (home-page "http://mvtnorm.R-forge.R-project.org")
3604 (synopsis "Package for multivariate normal and t-distributions")
3605 (description "This package can compute multivariate normal and
3606 t-probabilities, quantiles, random deviates and densities.")
3607 (license license:gpl2)))
3609 (define-public r-matrixstats
3611 (name "r-matrixstats")
3615 (uri (cran-uri "matrixStats" version))
3618 "06fvx0rlaz80k0lkqq2n7v0309xpz7h7ss0m9kgyikp4xs8bvmhn"))))
3619 (properties `((upstream-name . "matrixStats")))
3620 (build-system r-build-system)
3622 `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
3623 (home-page "https://github.com/HenrikBengtsson/matrixStats")
3624 (synopsis "Methods applying to vectors and matrix rows and columns")
3626 "This package provides methods operating on rows and columns of matrices,
3627 e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
3628 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
3629 @code{weightedMedians()}. All methods have been optimized for speed and
3631 (license license:artistic2.0)))
3633 (define-public r-viridis
3639 (uri (cran-uri "viridis" version))
3642 "060rf1jn29dq53y3nhb0hykvcap6rqsk04rq544ypiiqb18ngwnx"))))
3643 (build-system r-build-system)
3645 `(("r-ggplot2" ,r-ggplot2)
3646 ("r-gridextra" ,r-gridextra)
3647 ("r-viridislite" ,r-viridislite)))
3648 (home-page "https://github.com/sjmgarnier/viridis")
3649 (synopsis "Matplotlib default color map")
3651 "This package is a port of the new @url{matplotlib,
3652 http://matplotlib.org/} color maps (@code{viridis}--the default--,
3653 @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
3654 designed in such a way that they will analytically be perfectly
3655 perceptually-uniform, both in regular form and also when converted to
3656 black-and-white. They are also designed to be perceived by readers with the
3657 most common form of color blindness.")
3658 (license license:x11)))
3660 (define-public r-viridislite
3662 (name "r-viridislite")
3667 (uri (cran-uri "viridisLite" version))
3670 "1by2l05f0yabwvv64lhnv7bbhx0w683s3wr9j2xda920ghpa23kq"))))
3671 (properties `((upstream-name . "viridisLite")))
3672 (build-system r-build-system)
3673 (home-page "https://github.com/sjmgarnier/viridisLite")
3674 (synopsis "Default color maps from matplotlib")
3676 "This package is a port of the new @code{matplotlib} color maps
3677 (@code{viridis}, @code{magma}, @code{plasma} and @code{inferno}) to R.
3678 matplotlib is a popular plotting library for Python. These color maps are
3679 designed in such a way that they will analytically be perfectly
3680 perceptually-uniform, both in regular form and also when converted to
3681 black-and-white. They are also designed to be perceived by readers with the
3682 most common form of color blindness. This is the @code{lite} version of the
3683 more complete @code{viridis} package.")
3684 (license license:expat)))
3686 (define-public r-tidyselect
3688 (name "r-tidyselect")
3693 (uri (cran-uri "tidyselect" version))
3696 "0x3cp36byhfjajikr1lwffjm85ayw3bcs7d7kb0cydgs61ifiqjw"))))
3697 (build-system r-build-system)
3699 `(("r-glue" ,r-glue)
3700 ("r-purrr" ,r-purrr)
3702 ("r-rlang" ,r-rlang)))
3703 (home-page "https://cran.r-project.org/web/packages/tidyselect")
3704 (synopsis "Select from a set of strings")
3706 "This package provides a backend for the selecting functions of the
3707 tidyverse. It makes it easy to implement select-like functions in your own
3708 packages in a way that is consistent with other tidyverse interfaces for
3710 (license license:gpl3)))
3712 (define-public r-tidyr
3719 (uri (cran-uri "tidyr" version))
3722 "0safj8bcf8libwr0jx4059bmarngvhfddrcv8k5iw39m9lpxs0r4"))))
3723 (build-system r-build-system)
3725 `(("r-dplyr" ,r-dplyr)
3726 ("r-ellipsis" ,r-ellipsis)
3727 ("r-magrittr" ,r-magrittr)
3729 ("r-lifecycle" ,r-lifecycle)
3730 ("r-purrr" ,r-purrr)
3731 ("r-rlang" ,r-rlang)
3732 ("r-tidyselect" ,r-tidyselect)
3734 ("r-stringi" ,r-stringi)
3735 ("r-tibble" ,r-tibble)
3736 ("r-vctrs" ,r-vctrs)))
3737 (home-page "https://github.com/hadley/tidyr")
3738 (synopsis "Tidy data with `spread()` and `gather()` functions")
3740 "tidyr is a reframing of the reshape2 package designed to accompany the
3741 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
3742 a solid pipeline for data analysis. It is designed specifically for tidying
3743 data, not the general reshaping that reshape2 does, or the general aggregation
3744 that reshape did. In particular, built-in methods only work for data frames,
3745 and tidyr provides no margins or aggregation.")
3746 (license license:expat)))
3748 (define-public r-hexbin
3755 (uri (cran-uri "hexbin" version))
3758 "0b58jb1kz39wzrnkv077cfzns889xly7psvhxnm3xmnx6yvd986d"))))
3759 (build-system r-build-system)
3761 `(("r-lattice" ,r-lattice)))
3763 `(("gfortran" ,gfortran)))
3764 (home-page "https://github.com/edzer/hexbin")
3765 (synopsis "Hexagonal binning routines")
3767 "This package provides binning and plotting functions for hexagonal bins.
3768 It uses and relies on grid graphics and formal (S4) classes and methods.")
3769 (license license:gpl2+)))
3771 (define-public r-purrr
3778 (uri (cran-uri "purrr" version))
3781 "17lyys7dxjrwsfkq7a7hw65iy3qn3pp1sn70srdy64jf8adahc8g"))))
3782 (build-system r-build-system)
3784 `(("r-magrittr" ,r-magrittr)
3785 ("r-rlang" ,r-rlang)))
3786 (home-page "https://github.com/hadley/purrr")
3787 (synopsis "Functional programming tools")
3789 "This package completes R's functional programming tools with missing
3790 features present in other programming languages.")
3791 (license license:gpl3+)))
3793 (define-public r-plotly
3799 (uri (cran-uri "plotly" version))
3802 "0gadam4qw81q9gpjp7sqrpd7ikmcdsc78d8vjn39g0xzs5j8r845"))))
3803 (build-system r-build-system)
3805 `(("r-base64enc" ,r-base64enc)
3806 ("r-crosstalk" ,r-crosstalk)
3807 ("r-digest" ,r-digest)
3808 ("r-data-table" ,r-data-table)
3809 ("r-dplyr" ,r-dplyr)
3810 ("r-ggplot2" ,r-ggplot2)
3811 ("r-hexbin" ,r-hexbin)
3812 ("r-htmltools" ,r-htmltools)
3813 ("r-htmlwidgets" ,r-htmlwidgets)
3815 ("r-jsonlite" ,r-jsonlite)
3816 ("r-lazyeval" ,r-lazyeval)
3817 ("r-magrittr" ,r-magrittr)
3818 ("r-promises" ,r-promises)
3819 ("r-purrr" ,r-purrr)
3820 ("r-rcolorbrewer" ,r-rcolorbrewer)
3821 ("r-rlang" ,r-rlang)
3822 ("r-scales" ,r-scales)
3823 ("r-tibble" ,r-tibble)
3824 ("r-tidyr" ,r-tidyr)
3825 ("r-viridislite" ,r-viridislite)))
3826 (home-page "https://plot.ly/r")
3827 (synopsis "Create interactive web graphics")
3829 "This package enables the translation of ggplot2 graphs to an interactive
3830 web-based version and/or the creation of custom web-based visualizations
3831 directly from R. Once uploaded to a plotly account, plotly graphs (and the
3832 data behind them) can be viewed and modified in a web browser.")
3833 (license license:x11)))
3835 (define-public r-biased-urn
3837 (name "r-biased-urn")
3842 (uri (cran-uri "BiasedUrn" version))
3845 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
3846 (properties `((upstream-name . "BiasedUrn")))
3847 (build-system r-build-system)
3848 (home-page "http://www.agner.org/random/")
3849 (synopsis "Biased urn model distributions")
3851 "This package provides statistical models of biased sampling in the form
3852 of univariate and multivariate noncentral hypergeometric distributions,
3853 including Wallenius' noncentral hypergeometric distribution and Fisher's
3854 noncentral hypergeometric distribution (also called extended hypergeometric
3856 (license license:gpl3+)))
3858 (define-public r-rematch
3865 (uri (cran-uri "rematch" version))
3868 "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4"))))
3869 (build-system r-build-system)
3870 (home-page "https://github.com/MangoTheCat/rematch")
3871 (synopsis "Match regular expressions with a nicer API")
3873 "This package provides a small wrapper on @code{regexpr} to extract the
3874 matches and captured groups from the match of a regular expression to a
3876 (license license:expat)))
3878 (define-public r-cellranger
3880 (name "r-cellranger")
3885 (uri (cran-uri "cellranger" version))
3888 "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x"))))
3889 (build-system r-build-system)
3891 `(("r-rematch" ,r-rematch)
3892 ("r-tibble" ,r-tibble)))
3893 (home-page "https://github.com/rsheets/cellranger")
3894 (synopsis "Translate spreadsheet cell ranges to rows and columns")
3896 "This package provides helper functions to work with spreadsheets and the
3897 @code{A1:D10} style of cell range specification.")
3898 (license license:expat)))
3900 (define-public r-googlesheets
3902 (name "r-googlesheets")
3907 (uri (cran-uri "googlesheets" version))
3910 "11q07nxys72wkxx9mawmjyf20gvwvrb7h3gpa73h6lgh2vgrwnv8"))))
3911 (build-system r-build-system)
3913 `(("r-cellranger" ,r-cellranger)
3914 ("r-dplyr" ,r-dplyr)
3916 ("r-jsonlite" ,r-jsonlite)
3917 ("r-purrr" ,r-purrr)
3918 ("r-readr" ,r-readr)
3919 ("r-stringr" ,r-stringr)
3920 ("r-tibble" ,r-tibble)
3921 ("r-tidyr" ,r-tidyr)
3922 ("r-xml2" ,r-xml2)))
3923 (home-page "https://github.com/jennybc/googlesheets")
3924 (synopsis "Manage Google spreadsheets from R")
3925 (description "This package provides tools to interact with Google Sheets
3927 (license license:expat)))
3929 (define-public r-spams
3932 (version "2.6-2017-03-22")
3936 ;; Use the ‘Latest version’ link for a stable URI across releases.
3937 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
3938 "latestfile/4531/spams-R-v" version ".tar.gz"))
3941 "13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx"))))
3942 (build-system r-build-system)
3945 (modify-phases %standard-phases
3946 (add-after 'unpack 'chdir
3947 (lambda _ (chdir "spams") #t))
3948 ;; Don't tune for the building machine.
3949 (add-after 'chdir 'no-mtune
3951 (substitute* "src/Makevars"
3952 (("-mtune=native") ""))
3955 `(("r-lattice" ,r-lattice)
3956 ("r-matrix" ,r-matrix)))
3957 (home-page "http://spams-devel.gforge.inria.fr")
3958 (synopsis "Toolbox for solving sparse estimation problems")
3959 (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
3960 for solving various sparse estimation problems. It includes tools for the
3964 @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
3965 component analysis} (PCA), ...)
3966 @item Solving sparse decomposition problems with LARS, coordinate descent,
3967 OMP, SOMP, proximal methods
3968 @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
3969 group lasso, tree-structured regularization, structured sparsity with
3970 overlapping groups,...).
3972 (license license:gpl3+)))
3974 (define-public r-base64
3981 (uri (cran-uri "base64" version))
3984 "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf"))))
3985 (build-system r-build-system)
3987 `(("r-openssl" ,r-openssl)))
3988 (home-page "https://cran.r-project.org/web/packages/base64")
3989 (synopsis "Base64 encoder and decoder")
3991 "This package is a compatibility wrapper to replace the orphaned package
3992 by Romain Francois. New applications should use the openssl or base64enc
3994 (license license:expat)))
3996 (define-public r-hmisc
4003 (uri (cran-uri "Hmisc" version))
4005 (base32 "0rb1m6138lqzb46nss9ggvhghipd10vdnwsy6iq2wzynrynzkwkz"))))
4006 (properties `((upstream-name . "Hmisc")))
4007 (build-system r-build-system)
4009 `(("gfortran" ,gfortran)))
4011 `(("r-acepack" ,r-acepack)
4012 ("r-base64enc" ,r-base64enc)
4013 ("r-cluster" ,r-cluster)
4014 ("r-data-table" ,r-data-table)
4015 ("r-foreign" ,r-foreign)
4016 ("r-formula" ,r-formula)
4017 ("r-ggplot2" ,r-ggplot2)
4018 ("r-gridextra" ,r-gridextra)
4019 ("r-gtable" ,r-gtable)
4020 ("r-lattice" ,r-lattice)
4021 ("r-latticeextra" ,r-latticeextra)
4022 ("r-htmltable" ,r-htmltable)
4023 ("r-htmltools" ,r-htmltools)
4025 ("r-rpart" ,r-rpart)
4026 ("r-survival" ,r-survival)
4027 ("r-viridis" ,r-viridis)))
4028 (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
4029 (synopsis "Miscellaneous data analysis and graphics functions")
4031 "This package contains many functions useful for data analysis,
4032 high-level graphics, utility operations, functions for computing sample size
4033 and power, importing and annotating datasets, imputing missing values,
4034 advanced table making, variable clustering, character string manipulation,
4035 conversion of R objects to LaTeX code, and recoding variables.")
4036 (license license:gpl2+)))
4038 (define-public r-runit
4045 (uri (cran-uri "RUnit" version))
4048 "1wc1gwb7yw7phf8b0gkig6c23klya3ax11c6i4s0f049k42r78r3"))))
4049 (properties `((upstream-name . "RUnit")))
4050 (build-system r-build-system)
4051 (home-page "https://cran.r-project.org/web/packages/RUnit")
4052 (synopsis "R unit test framework")
4054 "This package provides R functions implementing a standard unit testing
4055 framework, with additional code inspection and report generation tools.")
4056 (license license:gpl2+)))
4058 (define-public r-dynamictreecut
4060 (name "r-dynamictreecut")
4065 (uri (cran-uri "dynamicTreeCut" version))
4068 "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"))))
4069 (properties `((upstream-name . "dynamicTreeCut")))
4070 (build-system r-build-system)
4072 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
4073 (synopsis "Detect clusters in hierarchical clustering dendrograms")
4075 "This package contains methods for the detection of clusters in
4076 hierarchical clustering dendrograms.")
4077 (license license:gpl2+)))
4079 (define-public r-preprocesscore
4081 (name "r-preprocesscore")
4086 (uri (bioconductor-uri "preprocessCore" version))
4089 "0zrb9hx60vppkg0priczdb301nhq5f0dj8lkc8rcc4xrqqr915qm"))))
4091 `((upstream-name . "preprocessCore")))
4092 (build-system r-build-system)
4093 (home-page "https://github.com/bmbolstad/preprocessCore")
4094 (synopsis "Collection of pre-processing functions")
4096 "This package provides a library of core pre-processing and normalization
4098 (license license:lgpl2.0+)))
4100 (define-public r-fastcluster
4102 (name "r-fastcluster")
4107 (uri (cran-uri "fastcluster" version))
4110 "01a2xnhhvv1swd4g8p4lzyn7ww7kg49jlnzc7kfz60jqjzpisrpk"))))
4111 (build-system r-build-system)
4112 (home-page "http://danifold.net/fastcluster.html")
4113 (synopsis "Fast hierarchical clustering routines")
4115 "This package implements fast hierarchical, agglomerative clustering
4116 routines. Part of the functionality is designed as drop-in replacement for
4117 existing routines: @code{linkage()} in the SciPy package
4118 @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package,
4119 and the @code{flashClust} package. It provides the same functionality with
4120 the benefit of a much faster implementation. Moreover, there are
4121 memory-saving routines for clustering of vector data, which go beyond what the
4122 existing packages provide.")
4123 (license license:bsd-2)))
4125 (define-public r-sfsmisc
4132 (uri (cran-uri "sfsmisc" version))
4135 "0zaw617zarmwir8l60riky0z6r1j3mwfnm1f32vqcbljb74akdj4"))))
4136 (build-system r-build-system)
4137 (home-page "https://cran.r-project.org/web/packages/sfsmisc")
4138 (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
4140 "This package provides useful utilities from Seminar fuer Statistik ETH
4141 Zurich, including many that are related to graphics.")
4142 (license license:gpl2+)))
4144 (define-public r-gtools
4151 (uri (cran-uri "gtools" version))
4154 "0f5syk1qq6cjq6hwymvkiyhzwa389z94722v881ipbfqkd2q8505"))))
4155 (build-system r-build-system)
4158 (modify-phases %standard-phases
4159 (add-after 'unpack 'make-deterministic
4161 (substitute* "R/checkReverseDependencies.R"
4162 (("tempdir\\(\\)") "\"/tmp\""))
4164 (home-page "https://cran.r-project.org/web/packages/gtools")
4165 (synopsis "Various R programming tools")
4167 "This package contains a collection of various functions to assist in R
4168 programming, such as tools to assist in developing, updating, and maintaining
4169 R and R packages, calculating the logit and inverse logit transformations,
4170 tests for whether a value is missing, empty or contains only @code{NA} and
4171 @code{NULL} values, and many more.")
4172 (license license:gpl2)))
4174 (define-public r-gdata
4181 (uri (cran-uri "gdata" version))
4184 "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b"))))
4185 (build-system r-build-system)
4189 `(("r-gtools" ,r-gtools)))
4190 (home-page "https://cran.r-project.org/web/packages/gdata")
4191 (synopsis "Various R programming tools for data manipulation")
4193 "This package provides various R programming tools for data manipulation,
4197 @item medical unit conversions
4198 @item combining objects
4199 @item character vector operations
4200 @item factor manipulation
4201 @item obtaining information about R objects
4202 @item manipulating MS-Excel formatted files
4203 @item generating fixed-width format files
4204 @item extricating components of date and time objects
4205 @item operations on columns of data frames
4206 @item matrix operations
4207 @item operations on vectors and data frames
4208 @item value of last evaluated expression
4209 @item wrapper for @code{sample} that ensures consistent behavior for
4210 both scalar and vector arguments
4212 (license license:gpl2+)))
4214 (define-public r-gplots
4221 (uri (cran-uri "gplots" version))
4224 "0vrm7wqrmqsmfrc070r9chpzb0vv60pay2lyar9qxfry6bsrvx86"))))
4225 (build-system r-build-system)
4227 `(("r-catools" ,r-catools)
4228 ("r-gdata" ,r-gdata)
4229 ("r-gtools" ,r-gtools)
4230 ("r-kernsmooth" ,r-kernsmooth)))
4231 (home-page "https://cran.r-project.org/web/packages/gplots")
4232 (synopsis "Various R programming tools for plotting data")
4234 "This package provides various R programming tools for plotting data,
4238 @item calculating and plotting locally smoothed summary function
4239 @item enhanced versions of standard plots
4240 @item manipulating colors
4241 @item calculating and plotting two-dimensional data summaries
4242 @item enhanced regression diagnostic plots
4243 @item formula-enabled interface to @code{stats::lowess} function
4244 @item displaying textual data in plots
4246 @item plotting \"Venn\" diagrams
4247 @item displaying Open-Office style plots
4248 @item plotting multiple data on same region, with separate axes
4249 @item plotting means and confidence intervals
4250 @item spacing points in an x-y plot so they don't overlap
4252 (license license:gpl2+)))
4254 (define-public r-rocr
4261 (uri (cran-uri "ROCR" version))
4264 "1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7"))))
4265 (properties `((upstream-name . "ROCR")))
4266 (build-system r-build-system)
4268 `(("r-gplots" ,r-gplots)))
4269 (home-page "http://rocr.bioinf.mpi-sb.mpg.de/")
4270 (synopsis "Visualizing the performance of scoring classifiers")
4272 "ROCR is a flexible tool for creating cutoff-parameterized 2D performance
4273 curves by freely combining two from over 25 performance measures (new
4274 performance measures can be added using a standard interface). Curves from
4275 different cross-validation or bootstrapping runs can be averaged by different
4276 methods, and standard deviations, standard errors or box plots can be used to
4277 visualize the variability across the runs. The parameterization can be
4278 visualized by printing cutoff values at the corresponding curve positions, or
4279 by coloring the curve according to cutoff. All components of a performance
4280 plot can be quickly adjusted using a flexible parameter dispatching
4282 (license license:gpl2+)))
4284 (define-public r-zoo
4290 (uri (cran-uri "zoo" version))
4293 "1w4542zs53bm261g95086a60576v334g1jrhnbgdqni4izf2s1wy"))))
4294 (build-system r-build-system)
4296 `(("r-lattice" ,r-lattice)))
4297 (home-page "http://zoo.R-Forge.R-project.org/")
4298 (synopsis "S3 infrastructure for regular and irregular time series")
4299 (description "This package contains an S3 class with methods for totally
4300 ordered indexed observations. It is particularly aimed at irregular time
4301 series of numeric vectors/matrices and factors.")
4302 (license license:gpl2+)))
4304 (define-public r-ztable
4310 (uri (cran-uri "ztable" version))
4313 "0g7khk5ifsdh9p31wlwh2l5mn1hzxzpv6qcn1wh34vsfjdmijjwy"))))
4314 (build-system r-build-system)
4316 `(("r-flextable" ,r-flextable)
4317 ("r-magrittr" ,r-magrittr)
4318 ("r-moonbook" ,r-moonbook)
4319 ("r-officer" ,r-officer)
4320 ("r-rcolorbrewer" ,r-rcolorbrewer)
4321 ("r-scales" ,r-scales)
4322 ("r-stringr" ,r-stringr)))
4323 (home-page "https://cran.r-project.org/web/packages/ztable")
4324 (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
4326 "This package provides functions to make zebra-striped tables (tables
4327 with alternating row colors) in LaTeX and HTML formats easily from
4328 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
4329 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
4330 @code{cbind.mytable} objects.")
4331 (license license:gpl2+)))
4333 (define-public r-vipor
4339 (uri (cran-uri "vipor" version))
4342 "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx"))))
4343 (build-system r-build-system)
4344 (home-page "https://cran.r-project.org/web/packages/vipor")
4345 (synopsis "Plot categorical data using noise and density estimates")
4347 "This package provides tools to generate a violin point plot, a
4348 combination of a violin/histogram plot and a scatter plot by offsetting points
4349 within a category based on their density using quasirandom noise.")
4350 (license license:gpl2+)))
4352 (define-public r-beeswarm
4358 (uri (cran-uri "beeswarm" version))
4361 "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
4362 (build-system r-build-system)
4363 (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/")
4364 (synopsis "Implementation of bee swarm plots")
4366 "This package provides an implementation of bee swarm plots. The bee
4367 swarm plot is a one-dimensional scatter plot like stripchart, but with
4368 closely-packed, non-overlapping points.")
4369 (license license:artistic2.0)))
4371 (define-public r-sourcetools
4373 (name "r-sourcetools")
4378 (uri (cran-uri "sourcetools" version))
4381 "1jnjir0q2dj724f1mjm6p5h77yzyx6xcqy9r2g7gmcxkxw349627"))))
4382 (build-system r-build-system)
4383 (home-page "https://cran.r-project.org/web/packages/sourcetools")
4384 (synopsis "Tools for reading, tokenizing and parsing R code")
4386 "The sourcetools package provides both an R and C++ interface for the
4387 tokenization of R code, and helpers for interacting with the tokenized
4388 representation of R code.")
4389 (license license:expat)))
4391 (define-public r-ggbeeswarm
4393 (name "r-ggbeeswarm")
4397 (uri (cran-uri "ggbeeswarm" version))
4400 "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v"))))
4401 (build-system r-build-system)
4403 `(("r-beeswarm" ,r-beeswarm)
4404 ("r-ggplot2" ,r-ggplot2)
4405 ("r-vipor" ,r-vipor)))
4406 (home-page "https://github.com/eclarke/ggbeeswarm")
4407 (synopsis "Categorical scatter (violin point) plots")
4409 "This package provides two methods of plotting categorical scatter plots
4410 such that the arrangement of points within a category reflects the density of
4411 data at that region, and avoids over-plotting.")
4412 (license license:gpl2+)))
4414 (define-public r-ggthemes
4420 (uri (cran-uri "ggthemes" version))
4423 "0rrkzfggc1nlda1w1lbqdycx6nawxbkac1szhvkwrqlzh6agxcsv"))))
4424 (build-system r-build-system)
4426 `(("r-ggplot2" ,r-ggplot2)
4427 ("r-purrr" ,r-purrr)
4428 ("r-scales" ,r-scales)
4429 ("r-stringr" ,r-stringr)
4430 ("r-tibble" ,r-tibble)))
4431 (home-page "https://cran.rstudio.com/web/packages/ggthemes")
4432 (synopsis "Extra themes, scales and geoms for @code{ggplot2}")
4433 (description "This package provides extra themes and scales for
4434 @code{ggplot2} that replicate the look of plots by Edward Tufte and
4435 Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The
4436 Wall Street Journal, among others. This package also provides
4437 @code{geoms} for Tufte's box plot and range frame.")
4438 (license license:gpl2)))
4440 (define-public r-statmod
4446 (uri (cran-uri "statmod" version))
4449 "1fbi5m4c0lingm2vvi0g6jf8f2mg1h01xwyz5rnymrq7gs0ibiks"))))
4450 (build-system r-build-system)
4451 (home-page "https://cran.r-project.org/web/packages/statmod")
4453 `(("gfortran" ,gfortran)))
4454 (synopsis "Statistical modeling")
4456 "This package provides a collection of algorithms and functions to aid
4457 statistical modeling. It includes growth curve comparisons, limiting dilution
4458 analysis (aka ELDA), mixed linear models, heteroscedastic regression,
4459 inverse-Gaussian probability calculations, Gauss quadrature and a secure
4460 convergence algorithm for nonlinear models. It also includes advanced
4461 generalized linear model functions that implement secure convergence,
4462 dispersion modeling and Tweedie power-law families.")
4463 ;; Statmod is distributed under either license
4464 (license (list license:gpl2 license:gpl3))))
4466 (define-public r-rann
4472 (uri (cran-uri "RANN" version))
4475 "10kid40w9w7vkz2hpcfkdpxr4afxzms5dzvfwr0sl5xynzgw76dj"))))
4477 `((upstream-name . "RANN")))
4478 (build-system r-build-system)
4479 (home-page "https://github.com/jefferis/RANN")
4480 (synopsis "Fast nearest neighbour search")
4482 "This package finds the k nearest neighbours for every point in a given
4483 dataset in O(N log N) time using Arya and Mount's ANN library. Provides
4484 approximate, exact searches, fixed radius searches, bd and kb trees.")
4485 (license license:gpl3+)))
4487 (define-public r-fivethirtyeight
4489 (name "r-fivethirtyeight")
4494 (uri (string-append "https://mran.microsoft.com/src/contrib/"
4495 "fivethirtyeight_" version ".tar.gz"))
4498 "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl"))))
4499 (build-system r-build-system)
4501 `(("r-knitr" ,r-knitr)
4502 ("r-rmarkdown" ,r-rmarkdown)
4503 ("r-dplyr" ,r-dplyr)
4504 ("r-readr" ,r-readr)
4505 ("r-ggplot2" ,r-ggplot2)
4506 ("r-magrittr" ,r-magrittr)
4507 ("r-stringr" ,r-stringr)))
4508 (home-page "https://mran.microsoft.com/package/fivethirtyeight/")
4509 (synopsis "Data and code behind the stories at FiveThirtyEight")
4510 (description "This R package provides access to the code and data sets
4511 published by the statistics blog FiveThirtyEight.")
4512 (license license:expat)))
4514 (define-public r-compquadform
4516 (name "r-compquadform")
4521 (uri (cran-uri "CompQuadForm" version))
4524 "1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4"))))
4525 (properties `((upstream-name . "CompQuadForm")))
4526 (build-system r-build-system)
4527 (home-page "https://cran.r-project.org/web/packages/CompQuadForm")
4528 (synopsis "Distribution function of quadratic forms in normal variables")
4530 "This package provides functions to compute the distribution function of
4531 quadratic forms in normal variables using Imhof's method, Davies's algorithm,
4532 Farebrother's algorithm or Liu et al.'s algorithm.")
4533 (license license:gpl2+)))
4535 (define-public r-cowplot
4542 (uri (cran-uri "cowplot" version))
4545 "19cqdhgfyr1wj0fz0c5ly8f0aiy9sfgzq6lzb78hkx0hdp2agybh"))))
4546 (build-system r-build-system)
4548 `(("r-ggplot2" ,r-ggplot2)
4549 ("r-gtable" ,r-gtable)
4550 ("r-rlang" ,r-rlang)
4551 ("r-scales" ,r-scales)))
4552 (home-page "https://github.com/wilkelab/cowplot")
4553 (synopsis "Streamlined plot theme and plot annotations for ggplot2")
4555 "This package provides some helpful extensions and modifications to the
4556 ggplot2 package to combine multiple ggplot2 plots into one and label them with
4557 letters, as is often required for scientific publications.")
4558 (license license:gpl2)))
4560 (define-public r-mixtools
4567 (uri (cran-uri "mixtools" version))
4570 "13wdm0xs5bakhpa8ypg6lvhjaqkxyabwz4glxdwn0jwdvkcdhgsl"))))
4571 (build-system r-build-system)
4573 `(("r-mass" ,r-mass)
4574 ("r-segmented" ,r-segmented)
4575 ("r-survival" ,r-survival)))
4576 (home-page "https://cran.r-project.org/web/packages/mixtools")
4577 (synopsis "Tools for analyzing finite mixture models")
4579 "This package provides a collection of R functions for analyzing finite
4581 (license license:gpl2+)))
4583 (define-public r-lars
4590 (uri (cran-uri "lars" version))
4593 "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
4594 (build-system r-build-system)
4596 `(("gfortran" ,gfortran)))
4597 (home-page "http://www-stat.stanford.edu/~hastie/Papers/#LARS")
4598 (synopsis "Least angle regression software")
4600 "Least Angle Regression (\"LAR\") is a model selection algorithm; a
4601 useful and less greedy version of traditional forward selection methods. A
4602 simple modification of the LAR algorithm implements Tibshirani's Lasso; the
4603 Lasso modification of LARS calculates the entire Lasso path of coefficients
4604 for a given problem at the cost of a single least squares fit. Another LARS
4605 modification efficiently implements epsilon Forward Stagewise linear
4607 (license license:gpl2)))
4609 (define-public r-fastica
4616 (uri (cran-uri "fastICA" version))
4619 "1zpijqcipm0aa3rxj0mys06lskqy4dbppjpxr1aby0j16y9ka8ij"))))
4620 (properties `((upstream-name . "fastICA")))
4621 (build-system r-build-system)
4622 (home-page "https://cran.r-project.org/web/packages/fastICA")
4623 (synopsis "FastICA algorithms to perform ICA and projection pursuit")
4625 "This package provides an implementation of the FastICA algorithm to
4626 perform @dfn{independent component analysis} (ICA) and projection pursuit.")
4628 (license license:gpl3+)))
4630 (define-public r-randomforest
4632 (name "r-randomforest")
4637 (uri (cran-uri "randomForest" version))
4640 "0kbmm0l42fc2d1rdq0l7k09d34kd87q4lx651ffsic4y84h8kf7l"))))
4641 (properties `((upstream-name . "randomForest")))
4642 (build-system r-build-system)
4643 (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
4645 `(("gfortran" ,gfortran)))
4646 (synopsis "Breiman and Cutler's random forests for classification and regression")
4648 "This package provides the Breiman and Cutler's random forests algorithm, based on a
4649 forest of trees using random inputs, for classification and regression.")
4650 (license license:gpl2+)))
4652 (define-public r-diptest
4659 (uri (cran-uri "diptest" version))
4662 "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
4663 (build-system r-build-system)
4664 (home-page "https://cran.r-project.org/web/packages/diptest")
4665 (synopsis "Hartigan's dip test statistic for unimodality")
4667 "This package computes Hartigan's dip test statistic for unimodality,
4668 multimodality and provides a test with simulation based p-values, where the
4669 original public code has been corrected.")
4670 (license license:gpl2+)))
4672 (define-public r-modeltools
4674 (name "r-modeltools")
4679 (uri (cran-uri "modeltools" version))
4682 "1s9lmkac3rl0nknf4wizfhg7ryq7c8yvvyc4z619238br27hhsi5"))))
4683 (build-system r-build-system)
4684 (home-page "https://cran.r-project.org/web/packages/modeltools")
4685 (synopsis "Tools and classes for statistical models")
4687 "This package provides a collection of tools to deal with statistical
4688 models. The functionality is experimental and the user interface is likely
4689 to change in the future.")
4690 (license license:gpl2)))
4692 (define-public r-flexmix
4699 (uri (cran-uri "flexmix" version))
4702 "0hrz2axp2c9548b1r0bmrl57219nn030qndb83a8garkzq5lqi5s"))))
4703 (build-system r-build-system)
4705 `(("r-lattice" ,r-lattice)
4706 ("r-modeltools" ,r-modeltools)
4707 ("r-nnet" ,r-nnet)))
4708 (home-page "https://cran.r-project.org/web/packages/flexmix")
4709 (synopsis "Flexible mixture modeling")
4711 "This package implements a general framework for finite mixtures of
4712 regression models using the EM algorithm. FlexMix provides the E-step and
4713 all data handling, while the M-step can be supplied by the user to easily
4714 define new models. Existing drivers implement mixtures of standard linear
4715 models, generalized linear models and model-based clustering.")
4716 (license license:gpl2+)))
4718 (define-public r-mclust
4725 (uri (cran-uri "mclust" version))
4728 "0whandnda1fnjn5k3hgxdbp3b0xr7nlzy1j37saqb536h8q9dwkm"))))
4729 (build-system r-build-system)
4731 `(("gfortran" ,gfortran)))
4732 (home-page "http://www.stat.washington.edu/mclust/")
4733 (synopsis "Gaussian mixture modelling for model-based clustering etc.")
4735 "This package provides Gaussian finite mixture models fitted via EM
4736 algorithm for model-based clustering, classification, and density estimation,
4737 including Bayesian regularization, dimension reduction for visualisation,
4738 and resampling-based inference.")
4739 (license license:gpl2+)))
4741 (define-public r-prabclus
4748 (uri (cran-uri "prabclus" version))
4751 "0hg4d7y1w18jpgvw10z8833bbbcnlkwiasx0wh6iwa2pnnybq8gl"))))
4752 (build-system r-build-system)
4754 `(("r-mass" ,r-mass)
4755 ("r-mclust" ,r-mclust)))
4756 (home-page "https://cran.r-project.org/web/packages/prabclus")
4757 (synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
4759 "This package provides distance-based parametric bootstrap tests for
4760 clustering with spatial neighborhood information. It implements some distance
4761 measures, clustering of presence-absence, abundance and multilocus genetical
4762 data for species delimitation, nearest neighbor based noise detection.")
4763 (license license:gpl2+)))
4765 (define-public r-deoptimr
4772 (uri (cran-uri "DEoptimR" version))
4775 "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
4776 (properties `((upstream-name . "DEoptimR")))
4777 (build-system r-build-system)
4778 (home-page "https://cran.r-project.org/web/packages/DEoptimR")
4779 (synopsis "Differential evolution optimization in pure R")
4781 "This package provides a differential evolution (DE) stochastic
4782 algorithms for global optimization of problems with and without constraints.
4783 The aim is to curate a collection of its state-of-the-art variants that (1) do
4784 not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
4785 can be efficiently implemented directly in the R language.")
4786 (license license:gpl2+)))
4788 (define-public r-robustbase
4790 (name "r-robustbase")
4795 (uri (cran-uri "robustbase" version))
4798 "0mkzbsjl5nihyj7mzks14p6kr3spp44xvygjz4ran11gspdn9rdx"))))
4799 (build-system r-build-system)
4801 `(("gfortran" ,gfortran)))
4803 `(("r-deoptimr" ,r-deoptimr)))
4804 (home-page "http://robustbase.r-forge.r-project.org/")
4805 (synopsis "Basic robust statistics")
4807 "This package allows to analyze data with robust methods such as
4808 regression methodology including model selections and multivariate statistics.")
4809 (license license:gpl2+)))
4811 (define-public r-pcapp
4818 (uri (cran-uri "pcaPP" version))
4821 "1z2kdf9gfp965xbcd4rg6vf20d1bl443na0qjkpq7gmzpaq6cifa"))))
4822 (properties `((upstream-name . "pcaPP")))
4823 (build-system r-build-system)
4825 `(("r-mvtnorm" ,r-mvtnorm)))
4826 (home-page "https://cran.r-project.org/web/packages/pcaPP")
4827 (synopsis "Robust PCA by projection pursuit")
4829 "This package provides functions for robust @dfn{principal component
4830 analysis} (PCA) by projection pursuit.")
4831 (license license:gpl3+)))
4833 (define-public r-rrcov
4840 (uri (cran-uri "rrcov" version))
4843 "0m62k58nabw7hjz1qyyf9a0d6lvcz5vcvpksjnq93zcfra9inr57"))))
4844 (build-system r-build-system)
4846 `(("r-lattice" ,r-lattice)
4847 ("r-mvtnorm" ,r-mvtnorm)
4848 ("r-pcapp" ,r-pcapp)
4849 ("r-robustbase" ,r-robustbase)))
4851 `(("gfortran" ,gfortran)))
4852 (home-page "https://cran.r-project.org/web/packages/rrcov")
4853 (synopsis "Scalable robust estimators with high breakdown Point")
4855 "This package provides an implementation of robust location and scatter
4856 estimation and robust multivariate analysis with high breakdown point.")
4857 (license license:gpl2+)))
4859 (define-public r-fit-models
4861 (name "r-fit-models")
4866 (uri (cran-uri "fit.models" version))
4869 "0vjbzmx0ambm6yzidb4vbgmhclwzwv2iz2cwl54ccdkvx4cx3fck"))))
4870 (properties `((upstream-name . "fit.models")))
4871 (build-system r-build-system)
4873 `(("r-lattice" ,r-lattice)))
4874 (home-page "https://cran.r-project.org/web/packages/fit.models")
4875 (synopsis "Compare fitted models")
4877 "The @code{fit.models} function and its associated methods (coefficients, print,
4878 summary, plot, etc.) were originally provided in the @code{robust} package to
4879 compare robustly and classically fitted model objects. The aim of the
4880 @code{fit.models} package is to separate this fitted model object comparison
4881 functionality from the robust package and to extend it to support fitting
4882 methods (e.g., classical, robust, Bayesian, regularized, etc.) more
4884 ;; Any version of the GPL
4885 (license (list license:gpl2+ license:gpl3+))))
4887 (define-public r-robust
4890 (version "0.4-18.2")
4894 (uri (cran-uri "robust" version))
4897 "02x7d6dgx3skiadvx5m3c44b4bhz37ycpfhc25dhhv50y1db6l3k"))))
4898 (build-system r-build-system)
4900 `(("r-fit-models" ,r-fit-models)
4901 ("r-lattice" ,r-lattice)
4903 ("r-robustbase" ,r-robustbase)
4904 ("r-rrcov" ,r-rrcov)))
4906 `(("gfortran" ,gfortran)))
4907 (home-page "https://cran.r-project.org/web/packages/robust")
4908 (synopsis "Port of the S+ \"Robust Library\"")
4910 "This package is a port of the S+ \"Robust Library\". It provides
4911 methods for robust statistics, notably for robust regression and robust
4912 multivariate analysis.")
4913 (license license:gpl2)))
4915 (define-public r-trimcluster
4917 (name "r-trimcluster")
4922 (uri (cran-uri "trimcluster" version))
4925 "0013bpyq6mkvjn38qsmwnsxfiwxgwngnqxycxvgpgmiadhm8fjmn"))))
4926 (build-system r-build-system)
4927 (home-page "https://cran.r-project.org/web/packages/trimcluster")
4928 (synopsis "Cluster analysis with trimming")
4930 "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
4931 Matran (1997). This optimizes the k-means criterion under trimming a portion
4934 (license (list license:gpl2+ license:gpl3+))))
4936 (define-public r-fpc
4943 (uri (cran-uri "fpc" version))
4946 "1gsnl5sbdg86b2wdrsy6wq83xj6mrziiq7rxa8cqksgljc7gp6yf"))))
4947 (build-system r-build-system)
4949 `(("r-class" ,r-class)
4950 ("r-cluster" ,r-cluster)
4951 ("r-diptest" ,r-diptest)
4952 ("r-flexmix" ,r-flexmix)
4953 ("r-kernlab" ,r-kernlab)
4955 ("r-mclust" ,r-mclust)
4956 ("r-prabclus" ,r-prabclus)
4957 ("r-robustbase" ,r-robustbase)))
4958 (home-page "https://cran.r-project.org/web/packages/fpc")
4959 (synopsis "Flexible procedures for clustering")
4961 "This package provides various methods for clustering and cluster validation.
4962 For example, it provides fixed point clustering, linear regression clustering,
4963 clustering by merging Gaussian mixture components, as well as symmetric and
4964 asymmetric discriminant projections for visualisation of the separation of
4966 (license license:gpl2+)))
4968 (define-public r-vgam
4975 (uri (cran-uri "VGAM" version))
4977 (base32 "0kyan3a4ys2xbg9kf167cyf1gk7g963id62cjm2ij4i7y4wi61zq"))))
4978 (properties `((upstream-name . "VGAM")))
4979 (build-system r-build-system)
4981 `(("gfortran" ,gfortran)))
4982 (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
4983 (synopsis "Vector generalized linear and additive models")
4985 "This package is an implementation of about 6 major classes of statistical
4986 regression models. Currently only fixed-effects models are implemented, i.e.,
4987 no random-effects models. Many (150+) models and distributions are estimated
4988 by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
4989 VGLMs can be loosely thought of as multivariate generalised linear models.")
4990 (license license:gpl2+)))
4992 (define-public r-pbapply
4999 (uri (cran-uri "pbapply" version))
5002 "1xmk4p006v8gij26rs6kp5prjyf2n32nqjxiyp8a6kvgyc4z46dc"))))
5003 (build-system r-build-system)
5004 (home-page "https://github.com/psolymos/pbapply")
5005 (synopsis "Adding progress bar to apply functions")
5007 "This lightweight package that adds progress bar to vectorized R
5008 functions apply. The implementation can easily be added to functions where
5009 showing the progress is useful e.g. bootstrap.")
5010 (license license:gpl2)))
5012 (define-public r-minqa
5019 (uri (cran-uri "minqa" version))
5022 "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
5023 (build-system r-build-system)
5025 `(("r-rcpp" ,r-rcpp)))
5027 `(("gfortran" ,gfortran)))
5028 (home-page "http://optimizer.r-forge.r-project.org")
5029 (synopsis "Derivative-free optimization algorithms by quadratic approximation")
5031 "This package provides a derivative-free optimization by quadratic approximation
5032 based on an interface to Fortran implementations by M. J. D. Powell.")
5033 (license license:gpl2)))
5035 (define-public r-rcppeigen
5037 (name "r-rcppeigen")
5038 (version "0.3.3.7.0")
5042 (uri (cran-uri "RcppEigen" version))
5045 "1b78qcjim0n9klgkr82n794d6bj9r9f33g0kcsszsns2hir65sk2"))))
5046 (properties `((upstream-name . "RcppEigen")))
5047 (build-system r-build-system)
5049 `(("r-rcpp" ,r-rcpp)
5050 ("r-matrix" ,r-matrix)))
5051 (home-page "http://eigen.tuxfamily.org")
5052 (synopsis "Rcpp integration for the Eigen templated linear algebra library")
5054 "This package provides an integration of Eigen in R using a C++ template
5055 library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
5056 It supports dense and sparse matrices on integer, floating point and complex numbers,
5057 decompositions of such matrices, and solutions of linear systems.")
5058 (license license:gpl2+)))
5060 (define-public r-modelmetrics
5062 (name "r-modelmetrics")
5067 (uri (cran-uri "ModelMetrics" version))
5070 "17yw46yr0n9hddvlhh73jdpmpdlpa581n5xjpwkr6cpr2f7xxpqc"))))
5071 (properties `((upstream-name . "ModelMetrics")))
5072 (build-system r-build-system)
5074 `(("r-rcpp" ,r-rcpp)
5075 ("r-data-table" ,r-data-table)))
5076 (home-page "https://cran.r-project.org/web/packages/ModelMetrics")
5077 (synopsis "Rapid calculation of model metrics")
5079 "Written in C++ using @code{Rcpp}, this package provides a collection of
5080 metrics for evaluating models.")
5081 (license license:gpl2+)))
5083 (define-public r-matrixmodels
5085 (name "r-matrixmodels")
5090 (uri (cran-uri "MatrixModels" version))
5093 "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
5094 (properties `((upstream-name . "MatrixModels")))
5095 (build-system r-build-system)
5097 `(("r-matrix" ,r-matrix)))
5098 (home-page "https://cran.r-project.org/web/packages/MatrixModels")
5099 (synopsis "Modelling with sparse and dense matrices")
5101 "This package models with sparse and dense matrix matrices,
5102 using modular prediction and response module classes.")
5103 (license license:gpl2+)))
5105 (define-public r-quantreg
5112 (uri (cran-uri "quantreg" version))
5114 (base32 "19nh79qrkb75q348nk148l8wqjwnq5jgq29wpzqym5cfv1kjqfvh"))))
5115 (build-system r-build-system)
5117 `(("gfortran" ,gfortran)))
5119 `(("r-matrix" ,r-matrix)
5120 ("r-matrixmodels" ,r-matrixmodels)
5121 ("r-sparsem" ,r-sparsem)))
5122 (home-page "https://www.r-project.org")
5123 (synopsis "Quantile regression")
5125 "This package provides an estimation and inference methods for models
5126 of conditional quantiles: linear and nonlinear parametric and non-parametric
5127 models for conditional quantiles of a univariate response and several methods
5128 for handling censored survival data. Portfolio selection methods based on
5129 expected shortfall risk are also included.")
5130 (license license:gpl2+)))
5132 (define-public r-nloptr
5139 (uri (cran-uri "nloptr" version))
5142 "15yz60kljxwnhm2m3gryjzxl3ynhkhd5jiwc179b1hz6rlzf71hz"))))
5143 (build-system r-build-system)
5145 `(("r-knitr" ,r-knitr) ; for building vignettes
5146 ("pkg-config" ,pkg-config)
5147 ("gfortran" ,gfortran)))
5149 `(("nlopt" ,nlopt)))
5150 (home-page "https://cran.r-project.org/web/packages/nloptr")
5151 (synopsis "R interface to NLopt")
5153 "This package is interface to NLopt, a library for nonlinear
5154 optimization. NLopt is a library for nonlinear optimization, providing a
5155 common interface for a number of different free optimization routines
5156 available online as well as original implementations of various other
5158 (license license:lgpl3)))
5160 (define-public r-lme4
5167 (uri (cran-uri "lme4" version))
5170 "035j2hqkwv939xl07pm2vykvf3wlx8qj317846n9pkpqkyv58mbz"))))
5171 (build-system r-build-system)
5173 `(("r-boot" ,r-boot)
5174 ("r-lattice" ,r-lattice)
5176 ("r-matrix" ,r-matrix)
5177 ("r-minqa" ,r-minqa)
5178 ("r-nloptr" ,r-nloptr)
5181 ("r-rcppeigen" ,r-rcppeigen)))
5182 (home-page "https://cran.r-project.org/web/packages/lme4")
5183 (synopsis "Linear mixed-effects models using eigen and S4")
5185 "This package provides fit linear and generalized linear mixed-effects
5186 models. The models and their components are represented using S4 classes and
5187 methods. The core computational algorithms are implemented using the Eigen
5188 C++ library for numerical linear algebra and RcppEigen glue.")
5189 (license license:gpl2+)))
5191 (define-public r-pbkrtest
5198 (uri (cran-uri "pbkrtest" version))
5201 "1si3bhi59xc51a0pgjjglccq3h4aljyhw2k1b8574s145fnh7fsw"))))
5202 (build-system r-build-system)
5204 `(("r-lme4" ,r-lme4)
5206 ("r-matrix" ,r-matrix)))
5207 (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
5208 (synopsis "Methods for linear mixed model comparison")
5210 "This package implements a parametric bootstrap test and a Kenward Roger
5211 modification of F-tests for linear mixed effects models and a parametric
5212 bootstrap test for generalized linear mixed models.")
5213 (license license:gpl2+)))
5215 (define-public r-cardata
5222 (uri (cran-uri "carData" version))
5224 (base32 "0cg2yxzn0pdjqykr60my1fzpfkqac21fll5hv3m9w5c9sayq8swq"))))
5225 (properties `((upstream-name . "carData")))
5226 (build-system r-build-system)
5227 (home-page "https://r-forge.r-project.org/projects/car/")
5228 (synopsis "Data Sets for the book Companion to Applied Regression")
5230 "This package provides datasets to accompany J. Fox and S. Weisberg, An R
5231 Companion to Applied Regression, Third Edition, Sage.")
5232 (license license:gpl2+)))
5234 (define-public r-car
5241 (uri (cran-uri "car" version))
5243 (base32 "0yv5mwaa0ymrbis9590mx0zcj3w6j4drhs6ab13zhx4zc3x1b7b6"))))
5244 (build-system r-build-system)
5246 `(("r-abind" ,r-abind)
5247 ("r-cardata" ,r-cardata)
5249 ("r-maptools" ,r-maptools)
5254 ("r-pbkrtest" ,r-pbkrtest)
5255 ("r-quantreg" ,r-quantreg)
5257 (home-page "https://r-forge.r-project.org/projects/car/")
5258 (synopsis "Companion to applied regression")
5260 "This package provides functions and datasets from book Companion
5261 to Applied regression, Second Edition, Sage, 2011.")
5262 (license license:gpl2+)))
5264 (define-public r-rcppprogress
5266 (name "r-rcppprogress")
5271 (uri (cran-uri "RcppProgress" version))
5274 "0yk01hfv961zyp569682k9igvhnwqyg5j0n5fm63sxigj82l2xhi"))))
5275 (properties `((upstream-name . "RcppProgress")))
5276 (build-system r-build-system)
5278 `(("r-devtools" ,r-devtools)
5279 ("r-rcpp" ,r-rcpp)))
5280 (home-page "https://github.com/kforner/rcpp_progress")
5281 (synopsis "Interruptible progress bar for C++ in R packages")
5283 "This package allows to display a progress bar in the R console for long running
5284 computations taking place in C++ code, and support for interrupting those computations
5285 even in multithreaded code, typically using OpenMP.")
5286 (license license:gpl3+)))
5288 (define-public r-mnormt
5295 (uri (cran-uri "mnormt" version))
5298 "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z"))))
5299 (build-system r-build-system)
5301 `(("gfortran" ,gfortran)))
5302 (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
5303 (synopsis "Multivariate normal and \"t\" distributions")
5305 "This package provides functions for computing the density and the
5306 distribution function of multivariate normal and \"t\" random variables, and
5307 for generating random vectors sampled from these distributions. Probabilities
5308 are computed via non-Monte Carlo methods.")
5309 (license license:gpl2+)))
5311 (define-public r-numderiv
5314 (version "2016.8-1.1")
5318 (uri (cran-uri "numDeriv" version))
5321 "0idk02pqkziik932bd8k72d1q775g1is3m4bc861pcxfz6gx3i6q"))))
5322 (properties `((upstream-name . "numDeriv")))
5323 (build-system r-build-system)
5324 (home-page "https://cran.r-project.org/web/packages/numDeriv")
5325 (synopsis "Accurate numerical derivatives")
5327 "This package provides methods for calculating accurate numerical
5328 first and second order derivatives.")
5329 (license license:gpl2)))
5338 (uri (cran-uri "sn" version))
5341 "0x46gxkplxbnhaqbpiav1r4xlv4ib7n57kxmca7scqwj22y7wrs6"))))
5342 (build-system r-build-system)
5344 `(("r-mnormt" ,r-mnormt)
5345 ("r-numderiv" ,r-numderiv)))
5346 (home-page "http://azzalini.stat.unipd.it/SN")
5347 (synopsis "The skew-normal and skew-t distributions")
5349 "This package provides functionalities to build and manipulate
5350 probability distributions of the skew-normal family and some related
5351 ones, notably the skew-t family, and provides related statistical
5352 methods for data fitting and diagnostics, in the univariate and the
5353 multivariate case.")
5354 (license license:gpl2+)))
5356 (define-public r-tclust
5363 (uri (cran-uri "tclust" version))
5366 "17md6l9v9dl9b72l84df01b52h2xiynbcjm437mv9mzcr09fc2sb"))))
5367 (build-system r-build-system)
5368 ;; These are all suggested packages, not build dependencies.
5370 `(("r-cluster" ,r-cluster)
5371 ("r-mclust" ,r-mclust)
5372 ("r-mvtnorm" ,r-mvtnorm)
5374 (home-page "https://cran.r-project.org/web/packages/tclust")
5375 (synopsis "Robust trimmed clustering")
5377 "This package implements different robust clustering
5378 algorithms (@code{tclust}) based on trimming and including some graphical
5379 diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
5380 (license license:gpl3)))
5382 (define-public r-ranger
5389 (uri (cran-uri "ranger" version))
5392 "1vr5akgh388iivrxi0g4pl2npq9dc4cim3ljk4kjf637q058wc7w"))))
5393 (build-system r-build-system)
5395 `(("r-rcpp" ,r-rcpp)
5396 ("r-matrix" ,r-matrix)
5397 ("r-rcppeigen" ,r-rcppeigen)))
5398 (home-page "https://github.com/imbs-hl/ranger")
5399 (synopsis "Fast implementation of random forests")
5401 "This package provides a fast implementation of Random Forests,
5402 particularly suited for high dimensional data. Ensembles of classification,
5403 regression, survival and probability prediction trees are supported. Data from
5404 genome-wide association studies can be analyzed efficiently.")
5405 (license license:gpl3)))
5407 (define-public r-tsne
5414 (uri (cran-uri "tsne" version))
5417 "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
5418 (build-system r-build-system)
5419 (home-page "https://github.com/jdonaldson/rtsne/")
5420 (synopsis "t-Distributed Stochastic Neighbor Embedding for R")
5422 "This package provides a pure R implementation of the t-SNE algorithm.")
5423 (license license:gpl2+)))
5425 (define-public r-cairo
5432 (uri (cran-uri "Cairo" version))
5435 "1mdmd5zmjkh1b0x928zizgzh42x8swbajffb88rvnjfdhk1z0dvq"))))
5436 (properties `((upstream-name . "Cairo")))
5437 (build-system r-build-system)
5443 `(("pkg-config" ,pkg-config)))
5444 (home-page "https://www.rforge.net/Cairo/")
5445 (synopsis "R graphics device using Cairo graphics library")
5447 "This package provides a Cairo graphics device that can be use to
5448 create high-quality vector (PDF, PostScript and SVG) and bitmap
5449 output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11
5450 and Win32). Since it uses the same back-end for all output, copying
5451 across formats is WYSIWYG. Files are created without the dependence
5452 on X11 or other external programs. This device supports alpha
5453 channel (semi-transparent drawing) and resulting images can contain
5454 transparent and semi-transparent regions. It is ideal for use in
5455 server environments (file output) and as a replacement for other
5456 devices that don't have Cairo's capabilities such as alpha support or
5457 anti-aliasing. Backends are modular such that any subset of backends
5459 (license license:gpl2)))
5461 (define-public r-lubridate
5463 (name "r-lubridate")
5468 (uri (cran-uri "lubridate" version))
5471 "14a823il77w3wmmnzr89vwrqp50y56dh5raycnaw6c8nv5xsh32i"))))
5472 (build-system r-build-system)
5474 `(("r-rcpp" ,r-rcpp)
5475 ("r-stringr" ,r-stringr)))
5477 "https://cran.r-project.org/web/packages/lubridate")
5478 (synopsis "Make dealing with dates a little easier")
5480 "This package provides functions to work with date-times and time-spans:
5481 fast and user friendly parsing of date-time data, extraction and updating of
5482 components of a date-time (years, months, days, hours, minutes, and seconds),
5483 algebraic manipulation on date-time and time-span objects. The @code{lubridate}
5484 package has a consistent and memorable syntax that makes working with dates
5486 (license license:gpl2)))
5488 (define-public r-fdrtool
5495 (uri (cran-uri "fdrtool" version))
5498 "1h46frlk7d9f4qx0bg6p55nrm9wwwz2sv6d1nz7061wdfsm69yb5"))))
5499 (build-system r-build-system)
5500 (home-page "http://strimmerlab.org/software/fdrtool/")
5501 (synopsis "Estimation of false discovery rates and higher criticism")
5503 "This package provides tools to estimate tail area-based false discovery
5504 rates as well as local false discovery rates for a variety of null
5505 models (p-values, z-scores, correlation coefficients, t-scores). The
5506 proportion of null values and the parameters of the null distribution are
5507 adaptively estimated from the data. In addition, the package contains
5508 functions for non-parametric density estimation (Grenander estimator), for
5509 monotone regression (isotonic regression and antitonic regression with
5510 weights), for computing the @dfn{greatest convex minorant} (GCM) and the
5511 @dfn{least concave majorant} (LCM), for the half-normal and correlation
5512 distributions, and for computing empirical @dfn{higher criticism} (HC) scores
5513 and the corresponding decision threshold.")
5514 (license license:gpl3+)))
5516 (define-public r-forcats
5523 (uri (cran-uri "forcats" version))
5526 "1cnjh23z59fhbjmy7y95425hcq3m5wrwqvahsxwi7zm6d9bwp0vw"))))
5527 (build-system r-build-system)
5529 `(("r-ellipsis" ,r-ellipsis)
5530 ("r-magrittr" ,r-magrittr)
5531 ("r-tibble" ,r-tibble)
5532 ("r-rlang" ,r-rlang)))
5533 (home-page "http://forcats.tidyverse.org")
5534 (synopsis "Tools for working with factors")
5535 (description "This package provides helpers for reordering factor
5536 levels (including moving specified levels to front, ordering by first
5537 appearance, reversing, and randomly shuffling), and tools for modifying factor
5538 levels (including collapsing rare levels into other, \"anonymizing\", and
5539 manually \"recoding\").")
5540 (license license:gpl3)))
5542 (define-public r-tgstat
5543 (let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f")
5547 (version (string-append "1.0.2-" revision "." (string-take changeset 7)))
5552 (url "https://bitbucket.org/tanaylab/tgstat")
5553 (changeset changeset)))
5554 (file-name (string-append name "-" version "-checkout"))
5557 "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
5558 (build-system r-build-system)
5561 (modify-phases %standard-phases
5562 (add-after 'unpack 'fix-isnan
5564 (substitute* "src/tgstat.h"
5565 (("#define isnan ::isnan")
5566 "#define isnan std::isnan"))
5569 `(("r-rcpp" ,r-rcpp)))
5570 (home-page "https://bitbucket.org/tanaylab/tgstat/")
5571 (synopsis "Tanay's group statistical utilities")
5573 "The goal of tgstat is to provide fast and efficient statistical
5575 (license license:gpl2))))
5577 (define-public r-tgconfig
5578 (let ((changeset "1e02c7614713bd0866c46f0c679a058f8c6d627e")
5582 (version (string-append "0.0.0.9000-" revision "." (string-take changeset 7)))
5587 (url "https://bitbucket.org/tanaylab/tgconfig")
5588 (changeset changeset)))
5589 (file-name (string-append name "-" version "-checkout"))
5592 "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
5593 (build-system r-build-system)
5595 `(("r-yaml" ,r-yaml)))
5596 (home-page "https://bitbucket.org/tanaylab/tgconfig/")
5597 (synopsis "Infrastructure for managing package parameters")
5599 "The goal of tgconfig is to provide infrastructure for managing package
5601 (license license:gpl3))))
5603 (define-public r-directlabels
5605 (name "r-directlabels")
5606 (version "2018.05.22")
5610 (uri (cran-uri "directlabels" version))
5613 "0xcpc56ssb9430b0xcdhayk3qaak2qcakyss2pz14y5w2027hblv"))))
5614 (build-system r-build-system)
5616 `(("r-quadprog" ,r-quadprog)))
5617 (home-page "http://directlabels.r-forge.r-project.org/")
5618 (synopsis "Direct labels for multicolor plots")
5620 "This package provides an extensible framework for automatically placing
5621 direct labels onto multicolor plots. Label positions are described using
5622 positioning methods that can be re-used across several different plots. There
5623 are heuristics for examining @code{trellis} and @code{ggplot} objects and
5624 inferring an appropriate positioning method.")
5625 (license license:gpl3)))
5627 (define-public r-catterplots
5628 (let ((commit "ae17cd5e49ddda4ecfe0eba8a4c21df8c88e72c4")
5631 (name "r-catterplots")
5632 (version (git-version "0" revision commit))
5636 (url "https://github.com/Gibbsdavidl/CatterPlots.git")
5638 (file-name (git-file-name name version))
5641 "0qa8liylffpxgdg8xcgjar5dsvczqhn3akd4w35113hnyg1m4xyg"))))
5642 (build-system r-build-system)
5644 `(("r-png" ,r-png)))
5645 (home-page "https://github.com/Gibbsdavidl/CatterPlots")
5646 (synopsis "Scatter plots with cat shaped points")
5647 (description "Did you ever wish you could make scatter plots with cat
5648 shaped points? Now you can!")
5649 (license license:asl2.0))))
5651 (define-public r-colorout
5659 (url "https://github.com/jalvesaq/colorout.git")
5660 (commit (string-append "v" version))))
5661 (file-name (git-file-name name version))
5663 (base32 "1rsx69wjpa73c6x2hacvvvbzdzxn7wg06gizf97kasjdlb7azmp3"))))
5664 (build-system r-build-system)
5665 (home-page "https://github.com/jalvesaq/colorout")
5666 (synopsis "Colorize output in the R REPL")
5667 (description "@code{colorout} is an R package that colorizes R output when
5668 running in terminal emulator.
5670 R STDOUT is parsed and numbers, negative numbers, dates in the standard
5671 format, strings, and R constants are identified and wrapped by special ANSI
5672 scape codes that are interpreted by terminal emulators as commands to colorize
5673 the output. R STDERR is also parsed to identify the expressions warning and
5674 error and their translations to many languages. If these expressions are
5675 found, the output is colorized accordingly; otherwise, it is colorized as
5676 STDERROR (blue, by default).
5678 You can customize the colors according to your taste, guided by the color
5679 table made by the command @code{show256Colors()}. You can also set the colors
5680 to any arbitrary string. In this case, it is up to you to set valid values.")
5681 (license license:gpl3+)))
5683 (define-public python-rpy2
5684 ;; We need to take this changeset instead of the RELEASE_3_0_4 tag, because
5685 ;; it fixes a regression when using ggplot 3.2.0.
5686 (let ((changeset "19868a8")
5689 (name "python-rpy2")
5690 (version (git-version "3.0.4" revision changeset))
5695 (url "https://bitbucket.org/rpy2/rpy2")
5696 (changeset changeset)))
5697 (file-name (git-file-name name version))
5700 "1bb0wslcbj3wjvyk3jb9yyzdi6adfqh5vfgcvn22dyzxzbhcs8kk"))))
5701 (build-system python-build-system)
5703 '(#:modules ((ice-9 ftw)
5707 (guix build python-build-system))
5709 (modify-phases %standard-phases
5711 (lambda* (#:key outputs inputs #:allow-other-keys)
5712 (let ((cwd (getcwd)))
5714 (setenv "PYTHONPATH"
5715 (string-append cwd "/build/"
5716 (find (cut string-prefix? "lib" <>)
5717 (scandir (string-append cwd "/build")))
5719 (getenv "PYTHONPATH"))))
5720 (invoke "pytest" "-v" "rpy/tests/"))))))
5722 `(("python-cffi" ,python-cffi)
5723 ("python-six" ,python-six)
5724 ("python-jinja2" ,python-jinja2)
5725 ("python-numpy" ,python-numpy)
5726 ("python-pandas" ,python-pandas)
5727 ("python-pytz" ,python-pytz)
5728 ("python-ipython" ,python-ipython)
5729 ("python-tzlocal" ,python-tzlocal)))
5731 `(("readline" ,readline)
5734 ("r-minimal" ,r-minimal)
5735 ("r-survival" ,r-survival)
5736 ("r-ggplot2" ,r-ggplot2)
5737 ("r-rsqlite" ,r-rsqlite)
5738 ("r-dplyr" ,r-dplyr)
5739 ("r-dbplyr" ,r-dbplyr)
5740 ("python-numpy" ,python-numpy)))
5743 ("python-pytest" ,python-pytest)))
5744 (home-page "https://rpy2.bitbucket.io/")
5745 (synopsis "Python interface to the R language")
5746 (description "rpy2 is a redesign and rewrite of rpy. It is providing a
5747 low-level interface to R from Python, a proposed high-level interface,
5748 including wrappers to graphical libraries, as well as R-like structures and
5750 ;; Any of these licenses can be picked for the R interface. The whole
5751 ;; project is released under GPLv2+ according to the license declaration
5753 (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+)))))
5755 (define-public java-jdistlib
5757 (name "java-jdistlib")
5761 (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
5762 version "-src.jar"))
5765 "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
5766 (build-system ant-build-system)
5768 `(#:jar-name "jdistlib.jar"
5770 #:tests? #f ; no dedicated test directory
5772 (modify-phases %standard-phases
5773 (add-after 'unpack 'fix-broken-encoding
5775 (with-fluids ((%default-port-encoding "ISO-8859-1"))
5776 (substitute* "src/jdistlib/Beta.java"
5777 (("Scheff.+-Tukey") "Scheffe-Tukey")))
5780 `(("java-jtransforms" ,java-jtransforms)))
5782 `(("java-junit" ,java-junit)))
5783 (home-page "http://jdistlib.sourceforge.net/")
5784 (synopsis "Java library of statistical distributions")
5785 (description "JDistlib is the Java Statistical Distribution Library, a
5786 Java package that provides routines for various statistical distributions.")
5787 ;; The files that were translated from R code are under GPLv2+; some files
5788 ;; are under the GPLv3, which is a mistake. The author confirmed in an
5789 ;; email that this whole project should be under GPLv2+.
5790 (license license:gpl2+)))
5792 (define-public emacs-ess
5798 (uri (string-append "https://github.com/emacs-ess/ESS/archive/v"
5802 "0cbilbsiwvcyf6d5y24mymp57m3ana5dkzab3knfs83w4a3a4c5c"))
5803 (file-name (string-append name "-" version ".tar.gz"))
5804 (modules '((guix build utils)))
5807 ;; Stop ESS from trying to bundle an external julia-mode.el.
5808 (substitute* "lisp/Makefile"
5809 (("^\tjulia-mode.elc\\\\\n") "")
5810 (("^dist: all julia-mode.el")
5812 ;; No need to build docs in so many formats. Also, skipping
5813 ;; pdf lets us not pull in texlive.
5814 (substitute* "doc/Makefile"
5815 (("all : info text html pdf")
5817 (("install: install-info install-other-docs")
5818 "install: install-info"))
5819 ;; Test fails upstream
5820 (substitute* "test/ess-r-tests.el"
5821 (("ert-deftest ess-r-namespaced-eval-no-srcref-in-errors ()")
5822 "ert-deftest ess-r-namespaced-eval-no-srcref-in-errors () :expected-result :failed"))
5824 (build-system gnu-build-system)
5826 (let ((base-directory "/share/emacs/site-lisp/guix.d/ess"))
5827 `(#:make-flags (list (string-append "PREFIX=" %output)
5828 (string-append "ETCDIR=" %output "/"
5829 ,base-directory "/etc")
5830 (string-append "LISPDIR=" %output "/"
5833 (modify-phases %standard-phases
5835 (add-before 'build 'more-shebang-patching
5836 (lambda* (#:key inputs #:allow-other-keys)
5837 (substitute* "Makeconf"
5838 (("SHELL = /bin/sh")
5839 (string-append "SHELL = " (which "sh"))))
5843 (invoke "make" "test")))))))
5845 `(("emacs" ,emacs-minimal)
5846 ("r-minimal" ,r-minimal)))
5849 ("texinfo" ,texinfo)))
5851 `(("emacs-julia-mode" ,emacs-julia-mode)))
5852 (home-page "https://ess.r-project.org/")
5853 (synopsis "Emacs mode for statistical analysis programs")
5854 (description "Emacs Speaks Statistics (ESS) is an add-on package for GNU
5855 Emacs. It is designed to support editing of scripts and interaction with
5856 various statistical analysis programs such as R, Julia, and JAGS.")
5857 (license license:gpl2+)))