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 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 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 gcc)
53 #:use-module (gnu packages gtk)
54 #:use-module (gnu packages gettext)
55 #:use-module (gnu packages glib)
56 #:use-module (gnu packages haskell)
57 #:use-module (gnu packages icu4c)
58 #:use-module (gnu packages image)
59 #:use-module (gnu packages java)
60 #:use-module (gnu packages machine-learning)
61 #:use-module (gnu packages maths)
62 #:use-module (gnu packages multiprecision)
63 #:use-module (gnu packages pcre)
64 #:use-module (gnu packages perl)
65 #:use-module (gnu packages pkg-config)
66 #:use-module (gnu packages python)
67 #:use-module (gnu packages python-xyz)
68 #:use-module (gnu packages readline)
69 #:use-module (gnu packages ssh)
70 #:use-module (gnu packages tcl)
71 #:use-module (gnu packages texinfo)
72 #:use-module (gnu packages time)
73 #:use-module (gnu packages tls)
74 #:use-module (gnu packages base)
75 #:use-module (gnu packages web)
76 #:use-module (gnu packages xml)
77 #:use-module (gnu packages xorg)
78 #:use-module (srfi srfi-1))
88 (uri (string-append "mirror://gnu/pspp/pspp-"
92 "07pp27zycrb5x927jwaj9r3q7hy915jh51xs85zxby6gfiwl63m5"))))
93 (build-system gnu-build-system)
96 ("gettext" ,gettext-minimal)
100 ("readline" ,readline)
102 ("gtksourceview" ,gtksourceview)
103 ("spread-sheet-widget" ,spread-sheet-widget)
106 `(("autoconf" ,autoconf) ;for tests
107 ("glib" ,glib "bin") ;for glib-genmarshal
109 ("pkg-config" ,pkg-config)
110 ("python" ,python-2) ;for tests
111 ("texinfo" ,texinfo)))
112 (home-page "https://www.gnu.org/software/pspp/")
113 (synopsis "Statistical analysis")
115 "GNU PSPP is a statistical analysis program. It can perform
116 descriptive statistics, T-tests, linear regression and non-parametric tests.
117 It features both a graphical interface as well as command-line input. PSPP
118 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
119 can be imported from spreadsheets, text files and database sources and it can
120 be output in text, PostScript, PDF or HTML.")
121 (license license:gpl3+)))
129 (uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/"
130 (version-major version) ".x/Source/"
131 "JAGS-" version ".tar.gz"))
134 "1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica"))))
135 (build-system gnu-build-system)
136 (home-page "http://mcmc-jags.sourceforge.net/")
138 `(("gfortran" ,gfortran)
140 (synopsis "Gibbs sampler")
141 (description "JAGS is Just Another Gibbs Sampler. It is a program for
142 analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
143 simulation not wholly unlike BUGS. JAGS was written with three aims in mind:
146 @item To have a cross-platform engine for the BUGS language;
147 @item To be extensible, allowing users to write their own functions,
148 distributions and samplers;
149 @item To be a platform for experimentation with ideas in Bayesian modelling.
151 (license license:gpl2)))
153 ;; Update this package together with the set of recommended packages: r-boot,
154 ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
155 ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
158 (name "r-with-tests")
162 (uri (string-append "mirror://cran/src/base/R-"
163 (version-major version) "/R-"
167 "1vap2k8kj5icy9naw61f9zyphf4rs0c9rxvil0zxkwx0xvsvyqq4"))))
168 (build-system gnu-build-system)
170 `(#:disallowed-references (,tzdata-for-tests)
172 (list (string-append "LDFLAGS=-Wl,-rpath="
173 (assoc-ref %outputs "out")
175 ;; This affects the embedded timestamp of only the core packages.
176 "PKG_BUILT_STAMP=1970-01-01")
178 (modify-phases %standard-phases
179 (add-before 'configure 'do-not-compress-serialized-files
180 (lambda* (#:key inputs #:allow-other-keys)
181 ;; This ensures that Guix can detect embedded store references;
182 ;; see bug #28157 for details.
183 (substitute* "src/library/base/makebasedb.R"
184 (("compress = TRUE") "compress = FALSE"))
186 (add-before 'configure 'patch-uname
187 (lambda* (#:key inputs #:allow-other-keys)
188 (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
190 (substitute* "src/scripts/R.sh.in"
191 (("uname") uname-bin)))
193 (add-after 'unpack 'build-reproducibly
195 ;; The documentation contains time stamps to demonstrate
196 ;; documentation generation in different phases.
197 (substitute* "src/library/tools/man/Rd2HTML.Rd"
198 (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
199 "(removed for reproducibility)"))
201 ;; Remove timestamp from tracing environment. This fixes
202 ;; reproducibility of "methods.rd{b,x}".
203 (substitute* "src/library/methods/R/trace.R"
204 (("dateCreated = Sys.time\\(\\)")
205 "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
207 ;; Ensure that gzipped files are reproducible.
208 (substitute* '("src/library/grDevices/Makefile.in"
209 "doc/manual/Makefile.in")
210 (("R_GZIPCMD\\)" line)
211 (string-append line " -n")))
213 ;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
214 ;; queries the mtime of a given file and records it in an object.
215 ;; This is acceptable at runtime to detect stale source files,
216 ;; but it destroys reproducibility at build time.
218 ;; Similarly, the "srcfilecopy" procedure records the current
219 ;; time. We change both of them to respect SOURCE_DATE_EPOCH.
220 (substitute* "src/library/base/R/srcfile.R"
221 (("timestamp <- (timestamp.*|file.mtime.*)" _ time)
222 (string-append "timestamp <- \
223 as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
224 as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
225 } else { " time "}, origin=\"1970-01-01\")\n")))
227 ;; This library is installed using "install_package_description",
228 ;; so we need to pass the "builtStamp" argument.
229 (substitute* "src/library/tools/Makefile.in"
230 (("(install_package_description\\(.*\"')\\)\"" line prefix)
231 (string-append prefix ", builtStamp='1970-01-01')\"")))
233 ;; R bundles an older version of help2man, which does not respect
234 ;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man,
235 ;; because that breaks a test.
236 (with-fluids ((%default-port-encoding "ISO-8859-1"))
237 (substitute* "tools/help2man.pl"
238 (("my \\$date = strftime \"%B %Y\", localtime" line)
239 (string-append line " 1"))))
241 (add-before 'configure 'set-default-pager
242 ;; Set default pager to "cat", because otherwise it is "false",
243 ;; making "help()" print nothing at all.
244 (lambda _ (setenv "PAGER" "cat") #t))
245 (add-before 'check 'set-timezone
246 ;; Some tests require the timezone to be set. However, the
247 ;; timezone may not just be "UTC", or else a brittle regression
248 ;; test in reg-tests-1d will fail.
249 (lambda* (#:key inputs #:allow-other-keys)
250 (setenv "TZ" "UTC+1")
252 (string-append (assoc-ref inputs "tzdata")
255 (add-after 'build 'make-info
256 (lambda _ (invoke "make" "info")))
257 (add-after 'build 'install-info
258 (lambda _ (invoke "make" "install-info"))))
260 `(;; We build the recommended packages here, because they are needed in
261 ;; order to run the test suite. We disable them in the r-minimal
264 "--with-blas=-lopenblas"
270 ,(string-append "--with-tcl-config="
271 (assoc-ref %build-inputs "tcl")
273 ,(string-append "--with-tk-config="
274 (assoc-ref %build-inputs "tk")
277 "--enable-BLAS-shlib"
278 "--with-system-tre")))
279 ;; R has some support for Java. When the JDK is available at configure
280 ;; time environment variables pointing to the JDK will be recorded under
281 ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
282 ;; CMD javareconf". "R CMD javareconf" appears to only be used to update
283 ;; the recorded environment variables in $R_HOME/etc. Refer to
284 ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
285 ;; for additional information.
287 ;; As the JDK is a rather large input with only very limited effects on R,
288 ;; we decided to drop it.
292 ("pkg-config" ,pkg-config)
293 ("texinfo" ,texinfo) ; for building HTML manuals
294 ("tzdata" ,tzdata-for-tests)
297 `(;; We need not only cairo here, but pango to ensure that tests for the
298 ;; "cairo" bitmapType plotting backend succeed.
300 ("coreutils" ,coreutils)
302 ("openblas" ,openblas)
303 ("gfortran" ,gfortran)
310 ("readline" ,readline)
311 ;; This avoids a reference to the ungraftable static bash. R uses the
312 ;; detected shell for the "system" procedure.
313 ("bash" ,bash-minimal)
319 (list (search-path-specification
320 (variable "R_LIBS_SITE")
321 (files (list "site-library/")))))
322 (home-page "https://www.r-project.org/")
323 (synopsis "Environment for statistical computing and graphics")
325 "R is a language and environment for statistical computing and graphics.
326 It provides a variety of statistical techniques, such as linear and nonlinear
327 modeling, classical statistical tests, time-series analysis, classification
328 and clustering. It also provides robust support for producing
329 publication-quality data plots. A large amount of 3rd-party packages are
330 available, greatly increasing its breadth and scope.")
331 (license license:gpl3+)))
333 (define-public r-minimal
334 (package (inherit r-with-tests)
338 ,@(substitute-keyword-arguments (package-arguments r-with-tests)
339 ((#:configure-flags flags)
340 ;; Do not build the recommended packages. The build system creates
341 ;; random temporary directories and embeds their names in some
342 ;; package files. We build these packages with the r-build-system
344 `(cons "--without-recommended-packages" ,flags)))))))
346 (define-public rmath-standalone
347 (package (inherit r-minimal)
348 (name "rmath-standalone")
351 (modify-phases %standard-phases
352 (add-after 'configure 'chdir
353 (lambda _ (chdir "src/nmath/standalone/") #t)))))
354 (synopsis "Standalone R math library")
356 "This package provides the R math library as an independent package.")))
358 (define-public r-boot
365 (uri (cran-uri "boot" version))
368 "0ai1qpm0p4z07xr0dvag8sdn9jrxcwanrsk9khzmww094jvr1jxd"))))
369 (build-system r-build-system)
370 (home-page "https://cran.r-project.org/web/packages/boot")
371 (synopsis "Bootstrap functions for R")
373 "This package provides functions and datasets for bootstrapping from the
374 book \"Bootstrap Methods and Their Application\" by A.C. Davison and
375 D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
376 ;; Unlimited distribution
377 (license (license:non-copyleft "file://R/bootfuns.q"))))
379 (define-public r-mass
386 (uri (cran-uri "MASS" version))
389 "14907ia8418mp3p1rs1i2f1x5b6kk5z998dk353a29j3xqf3ybyq"))))
390 (properties `((upstream-name . "MASS")))
391 (build-system r-build-system)
392 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
393 (synopsis "Support functions and datasets for Venables and Ripley's MASS")
395 "This package provides functions and datasets for the book \"Modern
396 Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
397 ;; Either version may be picked.
398 (license (list license:gpl2 license:gpl3))))
400 (define-public r-class
407 (uri (cran-uri "class" version))
410 "1x1hqz8xyhbpq4krsh02glqnlzcch25agkmn4a3da9n723b37gzn"))))
411 (build-system r-build-system)
413 `(("r-mass" ,r-mass)))
414 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
415 (synopsis "R functions for classification")
417 "This package provides various functions for classification, including
418 k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
419 ;; Either of the two versions can be picked.
420 (license (list license:gpl2 license:gpl3))))
422 (define-public r-cluster
429 (uri (cran-uri "cluster" version))
432 "1grxbifbc4nwig25dmjgkympnbzb4al0w6k1c0ibdhpk1h4l20di"))))
433 (build-system r-build-system)
435 `(("gfortran" ,gfortran)))
436 (home-page "https://cran.r-project.org/web/packages/cluster")
437 (synopsis "Methods for cluster analysis")
439 "This package provides methods for cluster analysis. It is a much
440 extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
441 Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
442 (license license:gpl2+)))
444 (define-public r-codetools
451 (uri (cran-uri "codetools" version))
454 "00bmhzqprqfn3w6ghx7sakai6s7il8gbksfiawj8in5mbhbncypn"))))
455 (build-system r-build-system)
456 (home-page "https://cran.r-project.org/web/packages/codetools")
457 (synopsis "Code analysis tools for R")
458 (description "This package provides code analysis tools for R to check R
459 code for possible problems.")
460 ;; Any version of the GPL.
461 (license (list license:gpl2+ license:gpl3+))))
463 (define-public r-foreign
470 (uri (cran-uri "foreign" version))
473 "1mv04w3ycz0ymsszn8aa87k6k5sb8mg8lhf1b8w4zpfrphpkkliv"))))
474 (build-system r-build-system)
475 (home-page "https://cran.r-project.org/web/packages/foreign")
476 (synopsis "Read data stored by other statistics software")
478 "This package provides functions for reading and writing data stored by
479 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
480 for reading and writing some dBase files.")
481 (license license:gpl2+)))
483 (define-public r-kernsmooth
485 (name "r-kernsmooth")
490 (uri (cran-uri "KernSmooth" version))
493 "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb"))))
494 (properties `((upstream-name . "KernSmooth")))
495 (build-system r-build-system)
497 `(("gfortran" ,gfortran)))
498 (home-page "https://cran.r-project.org/web/packages/KernSmooth")
499 (synopsis "Functions for kernel smoothing")
501 "This package provides functions for kernel smoothing (and density
502 estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
503 \"Kernel Smoothing\".")
504 ;; Unlimited use and distribution
505 (license (license:non-copyleft "file://LICENCE.note"))))
507 (define-public r-lattice
513 (uri (cran-uri "lattice" version))
516 "0b8abkz7syscq883mrgv63pkwaqkcpwfx8rgbqy9vgfva0z5xszx"))))
517 (build-system r-build-system)
518 (home-page "http://lattice.r-forge.r-project.org/")
519 (synopsis "High-level data visualization system")
521 "The lattice package provides a powerful and elegant high-level data
522 visualization system inspired by Trellis graphics, with an emphasis on
523 multivariate data. Lattice is sufficient for typical graphics needs, and is
524 also flexible enough to handle most nonstandard requirements.")
525 (license license:gpl2+)))
527 (define-public r-matrix
534 (uri (cran-uri "Matrix" version))
537 "1mshhyia6imh939p8labxi0wv21lal7csmccxi42klpgdh1j89kv"))))
538 (properties `((upstream-name . "Matrix")))
539 (build-system r-build-system)
541 `(("r-lattice" ,r-lattice)))
542 (home-page "http://Matrix.R-forge.R-project.org/")
543 (synopsis "Sparse and dense matrix classes and methods")
545 "This package provides classes and methods for dense and sparse matrices
546 and operations on them using LAPACK and SuiteSparse.")
547 (license license:gpl2+)))
549 (define-public r-nlme
556 (uri (cran-uri "nlme" version))
559 "11vyxxc0n36vb8d8g02zr0402ymicvbifwdsqm7gy9iqqnwrn101"))))
560 (build-system r-build-system)
562 `(("r-lattice" ,r-lattice)))
564 `(("gfortran" ,gfortran)))
565 (home-page "https://cran.r-project.org/web/packages/nlme")
566 (synopsis "Linear and nonlinear mixed effects models")
568 "This package provides tools to fit and compare Gaussian linear and
569 nonlinear mixed-effects models.")
570 (license license:gpl2+)))
572 (define-public r-mgcv
579 (uri (cran-uri "mgcv" version))
582 "02bsz455fr5hyhpmgcrd266qafs2wbz3ygdipxg9gfazbdvq2v4q"))))
583 (build-system r-build-system)
585 `(("r-matrix" ,r-matrix)
587 (home-page "https://cran.r-project.org/web/packages/mgcv")
588 (synopsis "Mixed generalised additive model computation")
590 "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
591 parameter estimation by GCV, REML or UBRE/AIC. The library includes a
592 @code{gam()} function, a wide variety of smoothers, JAGS support and
593 distributions beyond the exponential family.")
594 (license license:gpl2+)))
596 (define-public r-nnet
603 (uri (cran-uri "nnet" version))
606 "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7"))))
607 (build-system r-build-system)
608 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
609 (synopsis "Feed-forward neural networks and multinomial log-linear models")
611 "This package provides functions for feed-forward neural networks with a
612 single hidden layer, and for multinomial log-linear models.")
613 (license (list license:gpl2+ license:gpl3+))))
615 (define-public r-rpart
622 (uri (cran-uri "rpart" version))
625 "0k29qx3k3pj5sgrpg0p47yd8i811rmdakaw57bigpq1449asc4cf"))))
626 (build-system r-build-system)
627 (home-page "https://cran.r-project.org/web/packages/rpart")
628 (synopsis "Recursive partitioning and regression trees")
630 "This package provides recursive partitioning functions for
631 classification, regression and survival trees.")
632 (license (list license:gpl2+ license:gpl3+))))
634 (define-public r-spatial
641 (uri (cran-uri "spatial" version))
644 "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
645 (build-system r-build-system)
646 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
647 (synopsis "Functions for kriging and point pattern analysis")
649 "This package provides functions for kriging and point pattern
651 ;; Either version may be picked.
652 (license (list license:gpl2 license:gpl3))))
654 (define-public r-survival
661 (uri (cran-uri "survival" version))
664 "0ldrjja1dj4n1ic0lbggm7jvk52sl5h85i8m23nrgndi60acsv4r"))))
665 (build-system r-build-system)
667 `(("r-matrix" ,r-matrix)))
668 (home-page "https://github.com/therneau/survival")
669 (synopsis "Survival analysis")
671 "This package contains the core survival analysis routines, including
672 definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
673 curves, Cox models, and parametric accelerated failure time models.")
674 (license license:lgpl2.0+)))
677 (package (inherit r-minimal)
680 (build-system trivial-build-system)
681 (arguments '(#:builder (begin (mkdir %output) #t)))
683 `(("r-minimal" ,r-minimal)
686 ("r-cluster" ,r-cluster)
687 ("r-codetools" ,r-codetools)
688 ("r-foreign" ,r-foreign)
689 ("r-kernsmooth" ,r-kernsmooth)
690 ("r-lattice" ,r-lattice)
692 ("r-matrix" ,r-matrix)
697 ("r-spatial" ,r-spatial)
698 ("r-survival" ,r-survival)))))
707 (uri (cran-uri "bit" version))
710 "0m7jrqzpa1pk8ixcl814x06jf96nlvvr16x6did6cfk4zghsrfjw"))))
711 (build-system r-build-system)
712 (home-page "http://ff.r-forge.r-project.org")
713 (synopsis "Class for vectors of 1-bit booleans")
715 "This package provides bitmapped vectors of booleans (no @code{NA}s),
716 coercion from and to logicals, integers and integer subscripts, fast boolean
717 operators and fast summary statistics. With @code{bit} class vectors of true
718 binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
719 (license license:gpl2)))
721 (define-public r-bit64
728 (uri (cran-uri "bit64" version))
731 "07znvz9vp1nz1y5ljng4qyskvm943cdbmy996s67560ijxzsm6kv"))))
732 (build-system r-build-system)
735 (home-page "http://ff.r-forge.r-project.org/")
736 (synopsis "S3 class for vectors of 64 bit integers")
738 "The bit64 package provides serializable S3 atomic 64 bit (signed)
739 integers that can be used in vectors, matrices, arrays and @code{data.frames}.
740 Methods are available for coercion from and to logicals, integers, doubles,
741 characters and factors as well as many elementwise and summary functions.
742 Many fast algorithmic operations such as @code{match} and @code{order} support
743 interactive data exploration and manipulation and optionally leverage
745 (license license:gpl2)))
747 (define-public r-dichromat
754 (uri (cran-uri "dichromat" version))
756 (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
757 (build-system r-build-system)
758 (home-page "https://cran.r-project.org/web/packages/dichromat")
759 (synopsis "Color schemes for dichromats")
761 "Dichromat collapses red-green or green-blue distinctions to simulate the
762 effects of different types of color-blindness.")
763 (license license:gpl2+)))
765 (define-public r-digest
772 (uri (cran-uri "digest" version))
774 (base32 "0k3iv0r8wy8w7zchmgrnrqv3bc149075j4817kf0q521vi4f6vbj"))))
775 (build-system r-build-system)
776 ;; Vignettes require r-knitr, which requires r-digest, so we have to
777 ;; disable them and the tests.
780 #:configure-flags (list "--no-build-vignettes")))
781 (home-page "http://dirk.eddelbuettel.com/code/digest.html")
782 (synopsis "Create cryptographic hash digests of R objects")
784 "This package contains an implementation of a function 'digest()' for the
785 creation of hash digests of arbitrary R objects (using the md5, sha-1,
786 sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
787 of R language objects, as well as a function 'hmac()' to create hash-based
788 message authentication code.
790 Please note that this package is not meant to be deployed for cryptographic
791 purposes for which more comprehensive (and widely tested) libraries such as
792 OpenSSL should be used.")
793 (license license:gpl2+)))
795 (define-public r-estimability
797 (name "r-estimability")
801 (uri (cran-uri "estimability" version))
804 "0cifdaa71spkcxl4db4z884jrya865sg3dhcv4isd8fnzg2pjcd3"))))
805 (build-system r-build-system)
806 (home-page "https://cran.r-project.org/web/packages/estimability")
807 (synopsis "Tools for assessing estimability of linear predictions")
808 (description "Provides tools for determining estimability of linear
809 functions of regression coefficients, and 'epredict' methods that handle
810 non-estimable cases correctly.")
811 (license license:gpl2+)))
813 (define-public r-pheatmap
820 (uri (cran-uri "pheatmap" version))
823 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
824 (build-system r-build-system)
826 `(("r-gtable" ,r-gtable)
827 ("r-rcolorbrewer" ,r-rcolorbrewer)
828 ("r-scales" ,r-scales)))
830 "https://cran.r-project.org/web/packages/pheatmap")
831 (synopsis "Pretty heatmaps")
833 "This package provides an implementation of heatmaps that offers more
834 control over dimensions and appearance.")
835 (license license:gpl2+)))
837 (define-public r-labeling
844 (uri (cran-uri "labeling" version))
846 (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
847 (build-system r-build-system)
848 (home-page "https://cran.r-project.org/web/packages/labeling")
849 (synopsis "Axis labeling algorithms")
850 (description "The labeling package provides a range of axis labeling
852 (license license:expat)))
854 (define-public r-magrittr
861 (uri (cran-uri "magrittr" version))
863 (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
864 (build-system r-build-system)
865 (home-page "https://cran.r-project.org/web/packages/magrittr/index.html")
866 (synopsis "A forward-pipe operator for R")
868 "Magrittr provides a mechanism for chaining commands with a new
869 forward-pipe operator, %>%. This operator will forward a value, or the result
870 of an expression, into the next function call/expression. There is flexible
871 support for the type of right-hand side expressions. For more information,
872 see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
873 (license license:expat)))
875 (define-public r-munsell
882 (uri (cran-uri "munsell" version))
884 (base32 "16g1fzisbpqb15yh3pqf3iia4csppva5dnv1z88x9dg263xskwyh"))))
885 (build-system r-build-system)
887 `(("r-colorspace" ,r-colorspace)))
888 (home-page "https://cran.r-project.org/web/packages/munsell")
889 (synopsis "Munsell colour system")
891 "The Munsell package contains Functions for exploring and using the
892 Munsell colour system.")
893 (license license:expat)))
895 (define-public r-permute
902 (uri (cran-uri "permute" version))
905 "1w8wzk1fg9q7wvisnfp2js70dg0m9wi12gkdhpyngpbdcgssahd5"))))
906 (build-system r-build-system)
907 ;; Tests do not run correctly, but running them properly would entail a
908 ;; circular dependency with vegan.
909 (home-page "https://github.com/gavinsimpson/permute")
910 (synopsis "Functions for Generating Restricted Permutations of Data")
912 "This package provides a set of restricted permutation designs for freely
913 exchangeable, line transects (time series), spatial grid designs and permutation
914 of blocks (groups of samples). @code{permute} also allows split-plot designs,
915 in which the whole-plots or split-plots or both can be freely exchangeable.")
916 (license license:gpl2+)))
918 (define-public r-plyr
925 (uri (cran-uri "plyr" version))
927 (base32 "1igar5pcjqh0jyxv0z3jah8rz617vfa86vw0r5c7c031b7bj5db0"))))
928 (build-system r-build-system)
929 (native-inputs `(("r-rcpp" ,r-rcpp)))
930 (home-page "http://had.co.nz/plyr")
931 (synopsis "Tools for Splitting, Applying and Combining Data")
933 "Plyr is a set of tools that solves a common set of problems: you need to
934 break a big problem down into manageable pieces, operate on each piece and
935 then put all the pieces back together. For example, you might want to fit a
936 model to each spatial location or time point in your study, summarise data by
937 panels or collapse high-dimensional arrays to simpler summary statistics.")
938 (license license:expat)))
940 (define-public r-proto
947 (uri (cran-uri "proto" version))
949 (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
950 (build-system r-build-system)
951 (home-page "https://github.com/hadley/proto")
952 (synopsis "Prototype object-based programming")
954 "Proto is an object oriented system using object-based, also called
955 prototype-based, rather than class-based object oriented ideas.")
956 (license license:gpl2+)))
958 (define-public r-rcolorbrewer
960 (name "r-rcolorbrewer")
965 (uri (cran-uri "RColorBrewer" version))
967 (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
968 (build-system r-build-system)
969 (home-page "https://cran.r-project.org/web/packages/RColorBrewer")
970 (synopsis "ColorBrewer palettes")
972 "This package provides color schemes for maps (and other graphics)
973 designed by Cynthia Brewer as described at http://colorbrewer2.org")
974 ;; Includes code licensed under bsd-4
975 (license license:asl2.0)))
977 (define-public r-sendmailr
984 (uri (cran-uri "sendmailR" version))
987 "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
988 (properties `((upstream-name . "sendmailR")))
989 (build-system r-build-system)
991 `(("r-base64enc" ,r-base64enc)))
993 "https://cran.r-project.org/web/packages/sendmailR")
994 (synopsis "Send email using R")
996 "This package contains a simple SMTP client which provides a portable
997 solution for sending email, including attachments, from within R.")
998 (license license:gpl2+)))
1000 (define-public r-stringi
1007 (uri (cran-uri "stringi" version))
1010 "1y46xab7g1lsjmilp4hbl7pjad6pcxp66hdj8wnfdg9518h0lmq1"))))
1011 (build-system r-build-system)
1012 (inputs `(("icu4c" ,icu4c)))
1013 (native-inputs `(("pkg-config" ,pkg-config)))
1014 (home-page "http://stringi.rexamine.com/")
1015 (synopsis "Character string processing facilities")
1017 "This package allows for fast, correct, consistent, portable, as well as
1018 convenient character string/text processing in every locale and any native
1019 encoding. Owing to the use of the ICU library, the package provides R users
1020 with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
1021 programmers. Among available features there are: pattern searching
1022 (e.g. via regular expressions), random string generation, string collation,
1023 transliteration, concatenation, date-time formatting and parsing, etc.")
1024 (license license:bsd-3)))
1026 (define-public r-stringr
1033 (uri (cran-uri "stringr" version))
1035 (base32 "0hq3ybz7clnifi5wdm2s6p2i0kzljdkv26blg6yphng472h8x2vs"))))
1036 (build-system r-build-system)
1038 `(("r-glue" ,r-glue)
1039 ("r-magrittr" ,r-magrittr)
1040 ("r-stringi" ,r-stringi)))
1041 (home-page "https://github.com/hadley/stringr")
1042 (synopsis "Simple, consistent wrappers for common string operations")
1044 "Stringr is a consistent, simple and easy to use set of wrappers around
1045 the fantastic 'stringi' package. All function and argument names (and
1046 positions) are consistent, all functions deal with \"NA\"'s and zero length
1047 vectors in the same way, and the output from one function is easy to feed into
1048 the input of another.")
1049 (license license:gpl2+)))
1051 (define-public r-reshape2
1058 (uri (cran-uri "reshape2" version))
1060 (base32 "03ki5ka1dj208fc0dclbm0b4xp9d769pah2j9cs34l776p4r9zwa"))))
1061 (build-system r-build-system)
1063 `(("r-plyr" ,r-plyr)
1065 ("r-stringr" ,r-stringr)))
1066 (home-page "https://github.com/hadley/reshape")
1067 (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
1069 "Reshape2 is an R library to flexibly restructure and aggregate data
1070 using just two functions: melt and dcast (or acast).")
1071 (license license:expat)))
1073 (define-public r-scales
1080 (uri (cran-uri "scales" version))
1082 (base32 "0353dkh3d7x78463c6ds80hcml59lrqwr8rlv82a8dnkxla4l7qc"))))
1083 (build-system r-build-system)
1085 `(("r-labeling" ,r-labeling)
1086 ("r-munsell" ,r-munsell)
1087 ("r-rcolorbrewer" ,r-rcolorbrewer)
1090 ("r-viridislite" ,r-viridislite)))
1091 (home-page "https://github.com/hadley/scales")
1092 (synopsis "Scale functions for visualization")
1094 "This package provides graphical scales that map data to aesthetics, and
1095 provides methods for automatically determining breaks and labels for axes and
1097 (license license:expat)))
1099 (define-public r-ggplot2
1106 (uri (cran-uri "ggplot2" version))
1108 (base32 "1msy36r21nlmnpyaw2m9k0ykmnd19b9il01b65w457pfw75prrs9"))))
1109 (build-system r-build-system)
1111 `(("r-digest" ,r-digest)
1112 ("r-gtable" ,r-gtable)
1114 ("r-lazyeval" ,r-lazyeval)
1117 ("r-tibble" ,r-tibble)
1118 ("r-reshape2" ,r-reshape2)
1119 ("r-rlang" ,r-rlang)
1120 ("r-scales" ,r-scales)
1121 ("r-svglite" ,r-svglite) ; Needed for 'ggsave'
1122 ("r-viridislite" ,r-viridislite)
1123 ("r-withr" ,r-withr)))
1124 (home-page "https://ggplot2.tidyverse.org")
1125 (synopsis "An implementation of the grammar of graphics")
1127 "Ggplot2 is an implementation of the grammar of graphics in R. It
1128 combines the advantages of both base and lattice graphics: conditioning and
1129 shared axes are handled automatically, and you can still build up a plot step
1130 by step from multiple data sources. It also implements a sophisticated
1131 multidimensional conditioning system and a consistent interface to map data to
1132 aesthetic attributes.")
1133 (license license:gpl2+)))
1135 (define-public r-ggdendro
1141 (uri (cran-uri "ggdendro" version))
1144 "1zzq1hxd0d1qa5hrzwfkdw6fzscpcafbwbpkrb62dm559y8awp0j"))))
1145 (build-system r-build-system)
1147 `(("r-ggplot2" ,r-ggplot2)
1149 ("r-knitr" ,r-knitr)))
1150 (home-page "https://github.com/andrie/ggdendro")
1151 (synopsis "Create Dendrograms and Tree Diagrams Using ggplot2")
1152 (description "This is a set of tools for dendrograms and tree plots using
1153 ggplot2. The ggplot2 philosophy is to clearly separate data from the
1154 presentation. Unfortunately the plot method for dendrograms plots directly
1155 to a plot device with out exposing the data. The ggdendro package resolves
1156 this by making available functions that extract the dendrogram plot data.
1157 The package provides implementations for tree, rpart, as well as diana and
1158 agnes cluster diagrams.")
1159 (license license:gpl2+)))
1161 (define-public r-gdtools
1168 (uri (cran-uri "gdtools" version))
1171 "122k9spymawfnfyksxyapwq9cigydy5nrjwhrwrhy3qkax3aycf6"))))
1172 (build-system r-build-system)
1174 `(("r-rcpp" ,r-rcpp)
1175 ("pkg-config" ,pkg-config)))
1180 `(("r-withr" ,r-withr)))
1181 (home-page "https://cran.r-project.org/web/packages/gdtools")
1182 (synopsis "Utilities for graphical rendering")
1184 "The @code{gdtools} package provides functionalities to get font metrics
1185 and to generate base64 encoded string from raster matrix.")
1186 (license license:gpl3)))
1188 (define-public r-svglite
1195 (uri (cran-uri "svglite" version))
1198 "1bws3lc4hlhln11zd7lalhiyc43yk6c6vrzy41fkxk1dkjazfx51"))))
1199 (build-system r-build-system)
1200 (native-inputs `(("r-rcpp" ,r-rcpp)))
1203 ("r-gdtools" ,r-gdtools)))
1204 (home-page "https://github.com/hadley/svglite")
1205 (synopsis "SVG graphics device")
1207 "@code{svglite} is a graphics device that produces clean
1208 @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
1209 hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
1210 considerably faster, produces smaller files, and leaves text as is.")
1211 (license license:gpl2+)))
1213 (define-public r-assertthat
1215 (name "r-assertthat")
1219 (uri (cran-uri "assertthat" version))
1222 "1wp5znk3xy338x6hknppk702jn596yr735d9i7c3wabm3sdzfgnp"))))
1223 (build-system r-build-system)
1224 (home-page "https://github.com/hadley/assertthat")
1225 (synopsis "Easy pre and post assertions")
1227 "Assertthat is an extension to stopifnot() that makes it easy to declare
1228 the pre and post conditions that your code should satisfy, while also
1229 producing friendly error messages so that your users know what they've done
1231 (license license:gpl3+)))
1233 (define-public r-lazyeval
1239 (uri (cran-uri "lazyeval" version))
1242 "0q9zx78ncy2ffzrf9sh053069kd3w1xn1ss3gsbyf3y4jhza9cw3"))))
1243 (build-system r-build-system)
1244 (home-page "https://github.com/hadley/lazyeval")
1245 (synopsis "Lazy (non-standard) evaluation in R")
1247 "This package provides the tools necessary to do non-standard
1248 evaluation (NSE) in R.")
1249 (license license:gpl3+)))
1251 (define-public r-dbi
1257 (uri (cran-uri "DBI" version))
1260 "1x8wy2vg2gcgd9bww04qmf0dsn3kp0rfjd8q8j1r2x9zxccg25pz"))))
1261 (build-system r-build-system)
1262 (home-page "https://github.com/rstats-db/DBI")
1263 (synopsis "R database interface")
1265 "The DBI package provides a database interface (DBI) definition for
1266 communication between R and relational database management systems. All
1267 classes in this package are virtual and need to be extended by the various
1268 R/DBMS implementations.")
1269 (license license:lgpl2.0+)))
1274 (version "1.69.0-1")
1277 (uri (cran-uri "BH" version))
1280 "18mckfwxxv8m8rzaz03mg2h6vhaj7y131h6yasfg0s73nxj47zd0"))))
1281 (build-system r-build-system)
1282 (home-page "https://github.com/eddelbuettel/bh")
1283 (synopsis "R package providing subset of Boost headers")
1285 "This package aims to provide the most useful subset of Boost libraries
1286 for template use among CRAN packages.")
1287 (license license:boost1.0)))
1289 (define-public r-evaluate
1295 (uri (cran-uri "evaluate" version))
1298 "11rpn40153kcvqqrfhg2ldqfs68frg6yzsl0k3rxnlnv4c0v008g"))))
1299 (build-system r-build-system)
1300 (home-page "https://github.com/hadley/evaluate")
1301 (synopsis "Parsing and evaluation tools for R")
1303 "This package provides tools that allow you to recreate the parsing,
1304 evaluation and display of R code, with enough information that you can
1305 accurately recreate what happens at the command line. The tools can easily be
1306 adapted for other output formats, such as HTML or LaTeX.")
1307 (license license:gpl3+)))
1309 (define-public r-formatr
1315 (uri (cran-uri "formatR" version))
1318 "19sd23vgs4ac0fwlw40j3676k6mramb0ajlq8hdw23kjwdx1jk47"))))
1319 (build-system r-build-system)
1320 (home-page "http://yihui.name/formatR")
1321 (synopsis "Format R code automatically")
1323 "This package provides a function to format R source code. Spaces and
1324 indent will be added to the code automatically, and comments will be preserved
1325 under certain conditions, so that R code will be more human-readable and tidy.
1326 There is also a Shiny app as a user interface in this package.")
1327 (license license:gpl3+)))
1329 (define-public r-highr
1335 (uri (cran-uri "highr" version))
1338 "1dzknqk4x7iiiq1jkh9bqm5qcvs7mbqxbkn5955050payavabfya"))))
1339 (build-system r-build-system)
1340 (home-page "https://github.com/yihui/highr")
1341 (synopsis "Syntax highlighting for R source code")
1343 "This package provides syntax highlighting for R source code. Currently
1344 it supports LaTeX and HTML output. Source code of other languages is
1345 supported via Andre Simon's highlight package.")
1346 (license license:gpl3+)))
1348 (define-public r-mime
1354 (uri (cran-uri "mime" version))
1357 "00f4gw4sg1kn03s67gficxgb7a7fb6pwhlvrxrml05q1mc2vcxa7"))))
1358 (build-system r-build-system)
1359 (home-page "https://github.com/yihui/mime")
1360 (synopsis "R package to map filenames to MIME types")
1362 "This package guesses the MIME type from a filename extension using the
1363 data derived from /etc/mime.types in UNIX-type systems.")
1364 (license license:gpl2)))
1366 (define-public r-markdown
1372 (uri (cran-uri "markdown" version))
1375 "08xzs4bcf12jxp0276m6xqvq8kcgg5qp6fxrvsz6r9x73jjccs1h"))))
1376 (build-system r-build-system)
1377 ;; Skip check phase because the tests require the r-knitr package to be
1378 ;; installed. This prevents installation failures. Knitr normally
1379 ;; shouldn't be available since r-markdown is a dependency of the r-knitr
1381 (arguments `(#:tests? #f))
1383 `(("r-mime" ,r-mime)))
1384 (home-page "https://github.com/rstudio/markdown")
1385 (synopsis "Markdown rendering for R")
1387 "This package provides R bindings to the Sundown Markdown rendering
1388 library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
1389 syntax that can be converted to XHTML or other formats.")
1390 (license license:gpl2)))
1392 (define-public r-yaml
1398 (uri (cran-uri "yaml" version))
1401 "0in562nd0i23cg91a8kdbqgim656fgscykwi0icsnq53xj3srg2m"))))
1402 (build-system r-build-system)
1403 (home-page "https://cran.r-project.org/web/packages/yaml/")
1404 (synopsis "Methods to convert R data to YAML and back")
1406 "This package implements the libyaml YAML 1.1 parser and
1407 emitter (http://pyyaml.org/wiki/LibYAML) for R.")
1408 (license license:bsd-3)))
1410 (define-public r-knitr
1416 (uri (cran-uri "knitr" version))
1419 "0xzymi4gkilqaa5b2ay9zk1advavzkwxf7mb064bqfb09y8rak0j"))))
1420 (build-system r-build-system)
1422 `(("r-evaluate" ,r-evaluate)
1423 ("r-highr" ,r-highr)
1424 ("r-markdown" ,r-markdown)
1425 ("r-stringr" ,r-stringr)
1427 ("r-yaml" ,r-yaml)))
1428 (home-page "http://yihui.name/knitr/")
1429 (synopsis "General-purpose package for dynamic report generation in R")
1431 "This package provides a general-purpose tool for dynamic report
1432 generation in R using Literate Programming techniques.")
1433 ;; The code is released under any version of the GPL. As it is used by
1434 ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
1436 (license license:gpl2+)))
1438 (define-public r-knitrbootstrap
1440 (name "r-knitrbootstrap")
1445 (uri (cran-uri "knitrBootstrap" version))
1448 "1aj60j7f0gcs120fdrnfbnb7vk7lfn1phil0mghg6a5zldz4cqs3"))))
1449 (properties `((upstream-name . "knitrBootstrap")))
1450 (build-system r-build-system)
1452 `(("r-knitr" ,r-knitr)
1453 ("r-rmarkdown" ,r-rmarkdown)
1454 ("r-markdown" ,r-markdown)))
1455 (home-page "https://github.com/jimhester/knitrBootstrap")
1456 (synopsis "Knitr bootstrap framework")
1458 "This package provides a framework to create Bootstrap 3 HTML reports
1459 from knitr Rmarkdown.")
1460 (license license:expat)))
1462 (define-public r-microbenchmark
1464 (name "r-microbenchmark")
1468 (uri (cran-uri "microbenchmark" version))
1471 "1sn1fxgzakm5iqbgc35g3k4yi0iqrkmwz33cvdrphrzh1lxnmi3s"))))
1472 (build-system r-build-system)
1473 (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
1474 (synopsis "Accurate timing functions for R")
1476 "This package provides infrastructure to accurately measure and compare
1477 the execution time of R expressions.")
1478 (license license:bsd-2)))
1480 (define-public r-pryr
1486 (uri (cran-uri "pryr" version))
1489 "06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k"))))
1490 (build-system r-build-system)
1492 `(("r-stringr" ,r-stringr)
1493 ("r-codetools" ,r-codetools)))
1495 `(("r-rcpp" ,r-rcpp)))
1496 (home-page "https://github.com/hadley/pryr")
1497 (synopsis "Tools for computing on the R language")
1499 "This package provides useful tools to pry back the covers of R and
1500 understand the language at a deeper level.")
1501 (license license:gpl2)))
1503 (define-public r-memoise
1509 (uri (cran-uri "memoise" version))
1512 "034qfc2xlh30x1q2vya239w34a3ir3y2fwnx2agbgbi6592zjxmj"))))
1513 (build-system r-build-system)
1515 `(("r-digest" ,r-digest)))
1516 (home-page "https://github.com/hadley/memoise")
1517 (synopsis "Memoise functions for R")
1519 "This R package allows to cache the results of a function so that when
1520 you call it again with the same arguments it returns the pre-computed value.")
1521 (license license:expat)))
1523 (define-public r-crayon
1529 (uri (cran-uri "crayon" version))
1532 "0s7s6vc3ww8pzanpjisym4jjvwcc5pi2qg8srx7jqlz9j3wrnvpw"))))
1533 (build-system r-build-system)
1535 `(("r-memoise" ,r-memoise)))
1536 (home-page "https://github.com/gaborcsardi/crayon")
1537 (synopsis "Colored terminal output for R")
1539 "Colored terminal output on terminals that support ANSI color and
1540 highlight codes. It also works in Emacs ESS. ANSI color support is
1541 automatically detected. Colors and highlighting can be combined and nested.
1542 New styles can also be created easily. This package was inspired by the
1543 \"chalk\" JavaScript project.")
1544 (license license:expat)))
1546 (define-public r-praise
1553 (uri (cran-uri "praise" version))
1556 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
1557 (build-system r-build-system)
1558 (home-page "https://github.com/gaborcsardi/praise")
1559 (synopsis "Functions to praise users")
1561 "This package provides template functions to assist in building friendly
1562 R packages that praise their users.")
1563 (license license:expat)))
1565 (define-public r-testthat
1571 (uri (cran-uri "testthat" version))
1574 "1cafy5xsjx6m08s45456mjsal7mfxzwpbrds0p4z3gwam948gpzy"))))
1575 (build-system r-build-system)
1578 ("r-crayon" ,r-crayon)
1579 ("r-digest" ,r-digest)
1580 ("r-magrittr" ,r-magrittr)
1581 ("r-praise" ,r-praise)
1583 ("r-rlang" ,r-rlang)
1584 ("r-withr" ,r-withr)))
1585 (home-page "https://github.com/hadley/testthat")
1586 (synopsis "Unit testing for R")
1588 "This package provides a unit testing system for R designed to be fun,
1589 flexible and easy to set up.")
1590 (license license:expat)))
1598 (uri (cran-uri "R6" version))
1601 "1jgshp0x8a65rwyvk31slnfp7l153dk5826y2rxcd5lpclby3d85"))))
1602 (build-system r-build-system)
1603 (home-page "https://github.com/wch/R6/")
1604 (synopsis "Classes with reference semantics in R")
1606 "The R6 package allows the creation of classes with reference semantics,
1607 similar to R's built-in reference classes. Compared to reference classes, R6
1608 classes are simpler and lighter-weight, and they are not built on S4 classes
1609 so they do not require the methods package. These classes allow public and
1610 private members, and they support inheritance, even when the classes are
1611 defined in different packages.")
1612 (license license:expat)))
1614 (define-public r-rlang
1620 (uri (cran-uri "rlang" version))
1623 "0lbi66bavca866k26dnpkxj3l106xr4a6khcsfn8i3i8w8mpnhih"))))
1624 (build-system r-build-system)
1625 (home-page "http://rlang.tidyverse.org")
1626 (synopsis "Functions for base types, core R and Tidyverse features")
1627 (description "This package provides a toolbox for working with base types,
1628 core R features like the condition system, and core @code{Tidyverse} features
1629 like tidy evaluation.")
1630 (license license:gpl3)))
1632 (define-public r-tibble
1639 (uri (cran-uri "tibble" version))
1642 "04rxf5x9awwa9c00v9p7d3a2lqnn7j2rjg4r219hmw7cbqlwrcks"))))
1643 (build-system r-build-system)
1646 ("r-crayon" ,r-crayon)
1647 ("r-fansi" ,r-fansi)
1648 ("r-pkgconfig" ,r-pkgconfig)
1649 ("r-pillar" ,r-pillar)
1650 ("r-rlang" ,r-rlang)))
1651 (home-page "https://github.com/hadley/tibble")
1652 (synopsis "Simple data frames")
1654 "This package provides a @code{tbl_df} class that offers better checking
1655 and printing capabilities than traditional data frames.")
1656 (license license:expat)))
1658 (define-public r-dplyr
1664 (uri (cran-uri "dplyr" version))
1667 "06p59nhli8c1sarghzxq0y4pk6lyyz3xwkarp55b252dfg2rly9p"))))
1668 (build-system r-build-system)
1670 `(("r-assertthat" ,r-assertthat)
1672 ("r-magrittr" ,r-magrittr)
1673 ("r-rlang" ,r-rlang)
1674 ("r-plogr" ,r-plogr)
1676 ("r-pkgconfig" ,r-pkgconfig)
1677 ("r-bindrcpp" ,r-bindrcpp)
1678 ("r-tibble" ,r-tibble)
1679 ("r-tidyselect" ,r-tidyselect)))
1681 `(("r-rcpp" ,r-rcpp)
1683 (home-page "https://github.com/hadley/dplyr")
1684 (synopsis "Tools for working with data frames in R")
1686 "dplyr is the next iteration of plyr. It is focussed on tools for
1687 working with data frames. It has three main goals: 1) identify the most
1688 important data manipulation tools needed for data analysis and make them easy
1689 to use in R; 2) provide fast performance for in-memory data by writing key
1690 pieces of code in C++; 3) use the same code interface to work with data no
1691 matter where it is stored, whether in a data frame, a data table or
1693 (license license:expat)))
1695 (define-public r-dbplyr
1702 (uri (cran-uri "dbplyr" version))
1705 "07p23vyvi7s4abldhkyir05kcf7xnfc18igfryq12j67xd0jql0m"))))
1706 (build-system r-build-system)
1708 `(("r-assertthat" ,r-assertthat)
1710 ("r-dplyr" ,r-dplyr)
1712 ("r-purrr" ,r-purrr)
1714 ("r-rlang" ,r-rlang)
1715 ("r-tibble" ,r-tibble)
1716 ("r-tidyselect" ,r-tidyselect)))
1717 (home-page "https://github.com/tidyverse/dbplyr")
1718 (synopsis "Dplyr back end for databases")
1720 "This package provides a dplyr back end for databases that allows you to
1721 work with remote database tables as if they are in-memory data frames. Basic
1722 features works with any database that has a @code{DBI} back end; more advanced
1723 features require SQL translation to be provided by the package author.")
1724 (license license:expat)))
1726 (define-public r-acepack
1733 (uri (cran-uri "acepack" version))
1736 "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
1737 (build-system r-build-system)
1739 `(("gfortran" ,gfortran)))
1740 (home-page "https://cran.r-project.org/web/packages/acepack")
1741 (synopsis "Functions for regression transformations")
1743 "This package provides ACE and AVAS methods for choosing regression
1745 (license license:expat)))
1747 (define-public r-formula
1754 (uri (cran-uri "Formula" version))
1757 "0wiqh8rr9d5ciy80wj8f5fnmiiw0ywanvvnhkwd622dx42dk848l"))))
1758 (properties `((upstream-name . "Formula")))
1759 (build-system r-build-system)
1760 (home-page "https://cran.r-project.org/web/packages/Formula")
1761 (synopsis "Extended model formulas")
1763 "This package provides a new class @code{Formula}, which extends the base
1764 class @code{formula}. It supports extended formulas with multiple parts of
1765 regressors on the right-hand side and/or multiple responses on the left-hand
1767 (license (list license:gpl2+ license:gpl3+))))
1769 (define-public r-locfit
1776 (uri (cran-uri "locfit" version))
1779 "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
1780 (build-system r-build-system)
1782 `(("r-lattice" ,r-lattice)))
1783 (home-page "https://cran.r-project.org/web/packages/locfit")
1784 (synopsis "Local regression, likelihood and density estimation")
1786 "This package provides functions used for local regression, likelihood
1787 and density estimation.")
1788 (license (list license:gpl2+ license:gpl3+))))
1790 (define-public r-chron
1796 (uri (cran-uri "chron" version))
1799 "02bkywwsxwrxc035hv51dxgdm1fjxdm7dn19ivifln59dfs1862j"))))
1800 (build-system r-build-system)
1801 (home-page "https://cran.r-project.org/web/packages/chron")
1802 (synopsis "Chronological R objects which can handle dates and times")
1804 "This package provides chronological R objects which can handle dates and
1806 (license license:gpl2)))
1808 (define-public r-data-table
1810 (name "r-data-table")
1814 (uri (cran-uri "data.table" version))
1817 "1xz388khklqqc39r1cmjvqm65azambgzqw0743aypm6v4chi26v1"))))
1818 (build-system r-build-system)
1819 (home-page "https://github.com/Rdatatable/data.table/wiki")
1820 (synopsis "Enhanced version of data.frame R object")
1822 "The R package @code{data.table} is an extension of @code{data.frame}
1823 providing functions for fast aggregation of large data (e.g. 100GB in RAM),
1824 fast ordered joins, fast add/modify/delete of columns by group, column listing
1825 and fast file reading.")
1826 (license license:gpl3+)))
1828 (define-public r-xtable
1835 (uri (cran-uri "xtable" version))
1838 "09f311gq9g7dzf8jdvcx72j11xb7p00jlg066jjbpa6pz3zv1cjk"))))
1839 (build-system r-build-system)
1841 `(("r-knitr" ,r-knitr))) ; for vignettes
1842 (home-page "http://xtable.r-forge.r-project.org/")
1843 (synopsis "Export R tables to LaTeX or HTML")
1845 "This package provides tools to export R data as LaTeX and HTML tables.")
1846 (license license:gpl2+)))
1848 (define-public python-patsy
1850 (name "python-patsy")
1854 (uri (pypi-uri "patsy" version ".zip"))
1857 "1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w"))))
1858 (build-system python-build-system)
1861 (modify-phases %standard-phases
1863 (lambda _ (invoke "nosetests" "-v"))))))
1865 `(("python-numpy" ,python-numpy)
1866 ("python-scipy" ,python-scipy)
1867 ("python-six" ,python-six)))
1869 `(("python-nose" ,python-nose)
1871 (home-page "https://github.com/pydata/patsy")
1872 (synopsis "Describe statistical models and build design matrices")
1874 "Patsy is a Python package for describing statistical models and for
1875 building design matrices.")
1876 ;; The majority of the code is distributed under BSD-2. The module
1877 ;; patsy.compat contains code derived from the Python standard library,
1878 ;; and is covered by the PSFL.
1879 (license (list license:bsd-2 license:psfl))))
1881 (define-public python2-patsy
1882 (package-with-python2 python-patsy))
1884 (define-public python-statsmodels
1886 (name "python-statsmodels")
1891 (uri (pypi-uri "statsmodels" version))
1894 "0fxs8a7sp4d7jvqlm36yi45i2d28kjfvraf9q8i9jr1chhxgjqb4"))))
1895 (build-system python-build-system)
1897 `(;; The test suite is very large and rather brittle. Tests often fail
1898 ;; because of minor changes in dependencies that upstream hasn't fixed
1899 ;; in a new release.
1902 (modify-phases %standard-phases
1903 (add-after 'unpack 'set-matplotlib-backend-to-agg
1905 ;; Set the matplotlib backend to Agg to avoid problems using the
1906 ;; GTK backend without a display.
1907 (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py")
1908 '("statsmodels/tsa/vector_ar/tests/test_var.py"
1909 "statsmodels/duration/tests/test_survfunc.py"))
1910 (("import matplotlib\\.pyplot as plt" line)
1911 (string-append "import matplotlib;matplotlib.use('Agg');"
1915 `(("python-numpy" ,python-numpy)
1916 ("python-scipy" ,python-scipy)
1917 ("python-pandas" ,python-pandas)
1918 ("python-patsy" ,python-patsy)
1919 ("python-matplotlib" ,python-matplotlib)))
1921 `(("python-cython" ,python-cython)
1922 ("python-nose" ,python-nose)
1923 ("python-sphinx" ,python-sphinx)))
1924 (home-page "http://statsmodels.sourceforge.net/")
1925 (synopsis "Statistical modeling and econometrics in Python")
1927 "Statsmodels is a Python package that provides a complement to scipy for
1928 statistical computations including descriptive statistics and estimation and
1929 inference for statistical models.")
1930 (license license:bsd-3)))
1932 (define-public python2-statsmodels
1933 (let ((stats (package-with-python2 python-statsmodels)))
1934 (package (inherit stats)
1936 `(("python2-pytz" ,python2-pytz)
1937 ("python2-numpy" ,python2-numpy)
1938 ("python2-scipy" ,python2-scipy)
1939 ("python2-pandas" ,python2-pandas)
1940 ("python2-patsy" ,python2-patsy)
1941 ("python2-matplotlib" ,python2-matplotlib))))))
1943 (define-public r-coda
1949 (uri (cran-uri "coda" version))
1952 "03fs3sdrrym3is92dgpa6ydk3m63gaihwy7bva4k0wm2hxm7x2k7"))))
1953 (build-system r-build-system)
1955 `(("r-lattice" ,r-lattice)))
1956 (home-page "https://cran.r-project.org/web/packages/coda")
1957 (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
1958 (description "This package provides functions for summarizing and plotting
1959 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
1960 diagnostic tests of convergence to the equilibrium distribution of the Markov
1962 (license license:gpl2+)))
1964 (define-public r-ade4
1971 (uri (cran-uri "ade4" version))
1974 "16z9jk4qj35ghsk4lwmq241dgc770y8a70dlmp9q4gz6d8ssgl7m"))))
1975 (build-system r-build-system)
1977 `(("r-mass" ,r-mass)))
1978 (home-page "http://pbil.univ-lyon1.fr/ADE-4")
1979 (synopsis "Multivariate data analysis and graphical display")
1981 "The ade4 package contains data analysis functions to analyze ecological
1982 and environmental data in the framework of Euclidean exploratory methods.")
1983 (license license:gpl2+)))
1985 (define-public r-xml2
1992 (uri (cran-uri "xml2" version))
1995 "154lmksfiwkhnlmryas25mjhfg6k4mmnnk7bbb29mnn5x5pr2yha"))))
1996 (build-system r-build-system)
1998 `(("libxml2" ,libxml2)
2001 `(("pkg-config" ,pkg-config)))
2003 `(("r-rcpp" ,r-rcpp)))
2004 (home-page "https://github.com/hadley/xml2")
2005 (synopsis "Parse XML with R")
2007 "This package provides a simple, consistent interface to working with XML
2008 files in R. It is built on top of the libxml2 C library.")
2009 (license license:gpl2+)))
2011 (define-public r-multitaper
2013 (name "r-multitaper")
2018 (uri (cran-uri "multitaper" version))
2021 "04wd9bbhyx7697pfy0fpj02v1csr48hkpqj62h9p8a6w84ji4k68"))))
2022 (build-system r-build-system)
2024 `(("gfortran" ,gfortran)))
2025 (home-page "https://github.com/wesleyburr/multitaper/")
2026 (synopsis "Multitaper spectral analysis tools")
2028 "This package implements multitaper spectral estimation
2029 techniques using prolate spheroidal sequences (Slepians) and sine
2030 tapers for time series analysis. It includes an adaptive weighted
2031 multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
2032 F-test, and complex demodulation. The Slepians sequences are
2033 generated efficiently using a tridiagonal matrix solution, and
2034 jackknifed confidence intervals are available for most estimates.")
2035 (license license:gpl2+)))
2037 (define-public r-rversions
2039 (name "r-rversions")
2043 (uri (cran-uri "rversions" version))
2046 "0i2gi05nrvknr7g89rbppkswyfcwwd4r9gp75fdfhpah8sgq1l11"))))
2047 (build-system r-build-system)
2049 `(("r-curl" ,r-curl)
2050 ("r-xml2" ,r-xml2)))
2051 (home-page "https://github.com/metacran/rversions")
2052 (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
2054 "This package provides functions to query the main R repository to find
2055 the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
2056 previous R versions and their release dates.")
2057 (license license:expat)))
2059 (define-public r-whisker
2065 (uri (cran-uri "whisker" version))
2068 "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28"))))
2069 (build-system r-build-system)
2070 (home-page "https://github.com/edwindj/whisker")
2071 (synopsis "Logicless mustache templating for R")
2073 "This package provides logicless templating, with a syntax that is not
2075 (license license:gpl3+)))
2077 (define-public r-backports
2079 (name "r-backports")
2084 (uri (cran-uri "backports" version))
2087 "1hac46xaawnqajlsfb5k7pfkc2ya9h76s5qv9ycj3jafh93d26z4"))))
2088 (build-system r-build-system)
2089 (home-page "https://cran.r-project.org/web/packages/backports")
2090 (synopsis "Reimplementations of functions introduced since R 3.0.0")
2092 "Provides implementations of functions which have been introduced in R
2093 since version 3.0.0. The backports are conditionally exported which results
2094 in R resolving the function names to the version shipped with R (if available)
2095 and uses the implemented backports as fallback. This way package developers
2096 can make use of the new functions without worrying about the minimum required
2098 (license license:gpl2+)))
2100 (define-public r-checkmate
2102 (name "r-checkmate")
2107 (uri (cran-uri "checkmate" version))
2110 "1y4ylzn55kpyfpzcx9rxb9413d3ck6hair36ldl0ak61ia5kc75p"))))
2111 (build-system r-build-system)
2113 `(("r-backports" ,r-backports)))
2114 (home-page "https://github.com/mllg/checkmate")
2115 (synopsis "Fast and versatile argument checks")
2117 "This package provides tests and assertions to perform frequent argument
2118 checks. A substantial part of the package was written in C to minimize any
2119 worries about execution time overhead.")
2120 (license license:bsd-3)))
2122 (define-public r-bbmisc
2129 (uri (cran-uri "BBmisc" version))
2132 "1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y"))))
2133 (properties `((upstream-name . "BBmisc")))
2134 (build-system r-build-system)
2136 `(("r-checkmate" ,r-checkmate)))
2137 (home-page "https://github.com/berndbischl/BBmisc")
2138 (synopsis "Miscellaneous functions for R package development")
2140 "This package provides miscellaneous helper functions for the development
2142 (license license:bsd-3)))
2144 (define-public r-fail
2151 (uri (cran-uri "fail" version))
2154 "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
2155 (build-system r-build-system)
2157 `(("r-bbmisc" ,r-bbmisc)
2158 ("r-checkmate" ,r-checkmate)))
2159 (home-page "https://github.com/mllg/fail")
2160 (synopsis "File abstraction interface layer (FAIL)")
2162 "This package provides a more comfortable interface to work with R data
2163 or source files in a key-value fashion.")
2164 (license license:bsd-3)))
2166 (define-public r-batchjobs
2168 (name "r-batchjobs")
2173 (uri (cran-uri "BatchJobs" version))
2176 "035658marnw57p4f38g99rwmvmb6hpbq0fhlxp3qbw22zfnnkvs9"))))
2177 (properties `((upstream-name . "BatchJobs")))
2178 (build-system r-build-system)
2180 `(("r-backports" ,r-backports)
2181 ("r-bbmisc" ,r-bbmisc)
2183 ("r-checkmate" ,r-checkmate)
2184 ("r-data-table" ,r-data-table)
2186 ("r-digest" ,r-digest)
2187 ("r-rsqlite" ,r-rsqlite)
2188 ("r-sendmailr" ,r-sendmailr)
2189 ("r-stringi" ,r-stringi)))
2190 (home-page "https://github.com/tudo-r/BatchJobs")
2191 (synopsis "Batch computing with R")
2193 "This package provides @code{Map}, @code{Reduce} and @code{Filter}
2194 variants to generate jobs on batch computing systems like PBS/Torque, LSF,
2195 SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
2196 (license license:bsd-2)))
2198 (define-public r-brew
2204 (uri (cran-uri "brew" version))
2207 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
2208 (build-system r-build-system)
2209 (home-page "https://cran.r-project.org/web/packages/brew")
2210 (synopsis "Templating framework for report generation")
2212 "The brew package implements a templating framework for mixing text and R
2213 code for report generation. The template syntax is similar to PHP, Ruby's erb
2214 module, Java Server Pages, and Python's psp module.")
2215 (license license:gpl2+)))
2217 (define-public r-desc
2224 (uri (cran-uri "desc" version))
2227 "1s6s13fk6sxwcj8wzkwxl9vr33153xx11p5wi9avqx3rzkabavz6"))))
2228 (build-system r-build-system)
2230 `(("r-assertthat" ,r-assertthat)
2231 ("r-crayon" ,r-crayon)
2233 ("r-rprojroot" ,r-rprojroot)))
2234 (home-page "https://github.com/r-pkgs/desc")
2235 (synopsis "Manipulate DESCRIPTION Files")
2237 "This package provides tools to read, write, create, and manipulate
2238 DESCRIPTION files. It is intended for packages that create or manipulate
2240 (license license:expat)))
2242 (define-public r-commonmark
2244 (name "r-commonmark")
2249 (uri (cran-uri "commonmark" version))
2252 "024iz1qp2kv6iz6y69ir0jk3qhjps86rhkzlcmhqsxx97rx7cjni"))))
2253 (build-system r-build-system)
2254 (home-page "https://cran.r-project.org/web/packages/commonmark")
2255 (synopsis "CommonMark and Github Markdown Rendering in R")
2257 "The CommonMark specification defines a rationalized version of markdown
2258 syntax. This package uses the 'cmark' reference implementation for converting
2259 markdown text into various formats including HTML, LaTeX and groff man. In
2260 addition, it exposes the markdown parse tree in XML format. The latest
2261 version of this package also adds support for Github extensions including
2262 tables, autolinks and strikethrough text.")
2263 (license license:bsd-2)))
2265 (define-public r-roxygen2
2271 (uri (cran-uri "roxygen2" version))
2274 "0wq29ilqas8yn2z8v49fk0hbgchg29nmyyhwczgdipz0cbhbfipd"))))
2275 (build-system r-build-system)
2277 `(("r-brew" ,r-brew)
2278 ("r-commonmark" ,r-commonmark)
2280 ("r-digest" ,r-digest)
2281 ("r-pkgload" ,r-pkgload)
2282 ("r-purrr" ,r-purrr)
2285 ("r-stringi" ,r-stringi)
2286 ("r-stringr" ,r-stringr)
2287 ("r-xml2" ,r-xml2)))
2289 `(("r-knitr" ,r-knitr))) ; for vignettes
2290 (home-page "https://github.com/klutometis/roxygen")
2291 (synopsis "In-source documentation system for R")
2293 "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
2294 collation, and NAMESPACE files.")
2295 (license license:gpl2+)))
2297 (define-public r-openssl
2304 (uri (cran-uri "openssl" version))
2307 "0ypa41qr58jgipzkqn3wjqdsjyi7qk57i46s5wy88xy3j8jl9jkv"))))
2308 (build-system r-build-system)
2310 `(("libressl" ,libressl)))
2312 `(("pkg-config" ,pkg-config)))
2314 `(("r-askpass" ,r-askpass)))
2315 (home-page "https://github.com/jeroenooms/openssl")
2316 (synopsis "Toolkit for encryption, signatures and certificates")
2318 "This package provides R bindings to OpenSSL libssl and libcrypto, plus
2319 custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
2320 and P-521. Cryptographic signatures can either be created and verified
2321 manually or via x509 certificates. AES block cipher is used in CBC mode for
2322 symmetric encryption; RSA for asymmetric (public key) encryption. High-level
2323 envelope functions combine RSA and AES for encrypting arbitrary sized data.
2324 Other utilities include key generators, hash functions (md5, sha1, sha256,
2325 etc), base64 encoder, a secure random number generator, and @code{bignum} math
2326 methods for manually performing crypto calculations on large multibyte
2328 (license license:expat)))
2330 (define-public r-httr
2336 (uri (cran-uri "httr" version))
2339 "0j6vknwyvkjpjsxwch4q02aik4dnm3h4l0wc7dgzc555bm1g2cyn"))))
2340 (build-system r-build-system)
2342 `(("r-curl" ,r-curl)
2343 ("r-jsonlite" ,r-jsonlite)
2344 ("r-openssl" ,r-openssl)
2347 (home-page "https://github.com/hadley/httr")
2348 (synopsis "Tools for working with URLs and HTTP")
2350 "The aim of httr is to provide a wrapper for RCurl customised to the
2351 demands of modern web APIs. It provides useful tools for working with HTTP
2352 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
2353 functions make it easy to control additional request components.")
2354 (license license:expat)))
2356 (define-public r-git2r
2362 (uri (cran-uri "git2r" version))
2365 "0vfc25z4j53pc49cnp3zjwzjb72kvc0aq96wgyg10xpgvhl3z0gg"))))
2366 (build-system r-build-system)
2367 ;; This R package contains modified sources of libgit2. This modified
2368 ;; version of libgit2 is built as the package is built. Hence libgit2 is
2369 ;; not among the inputs of this package.
2371 `(("libssh2" ,libssh2) ; for SSH transport
2372 ("openssl" ,openssl)
2375 `(("pkg-config" ,pkg-config)))
2376 (home-page "https://github.com/ropensci/git2r")
2377 (synopsis "Access Git repositories with R")
2379 "This package provides an R interface to the libgit2 library, which is a
2380 pure C implementation of the Git core methods.")
2381 ;; GPLv2 only with linking exception.
2382 (license license:gpl2)))
2384 (define-public r-rstudioapi
2386 (name "r-rstudioapi")
2390 (uri (cran-uri "rstudioapi" version))
2393 "0gn1pvaxfh2gh2ikvxcr8f6k97ygcfr68iz6dhwlq4z71a1s4jai"))))
2394 (build-system r-build-system)
2395 (home-page "https://cran.r-project.org/web/packages/rstudioapi")
2396 (synopsis "Safely access the RStudio API")
2398 "This package provides functions to access the RStudio API and provide
2399 informative error messages when it's not available.")
2400 (license license:expat)))
2402 (define-public r-devtools
2408 (uri (cran-uri "devtools" version))
2411 "1nyspqicn9zd1rgq3k07b3179i8w5ys6jbd65g9q8qczrb7z3x8f"))))
2412 (build-system r-build-system)
2414 `(("r-callr" ,r-callr)
2416 ("r-digest" ,r-digest)
2417 ("r-git2r" ,r-git2r)
2419 ("r-jsonlite" ,r-jsonlite)
2420 ("r-memoise" ,r-memoise)
2421 ("r-pkgbuild" ,r-pkgbuild)
2422 ("r-pkgload" ,r-pkgload)
2423 ("r-rcmdcheck" ,r-rcmdcheck)
2424 ("r-remotes" ,r-remotes)
2425 ("r-rstudioapi" ,r-rstudioapi)
2426 ("r-sessioninfo" ,r-sessioninfo)
2427 ("r-usethis" ,r-usethis)
2428 ("r-withr" ,r-withr)))
2429 (home-page "https://github.com/hadley/devtools")
2430 (synopsis "Tools to make developing R packages easier")
2431 (description "The devtools package is a collection of package development
2432 tools to simplify the devolpment of R packages.")
2433 (license license:gpl2+)))
2435 (define-public r-withr
2441 (uri (cran-uri "withr" version))
2444 "11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1"))))
2445 (build-system r-build-system)
2446 (home-page "https://github.com/jimhester/withr")
2447 (synopsis "Run code with temporarily modified global state")
2449 "This package provides a set of functions to run R code in an environment
2450 in which global state has been temporarily modified. Many of these functions
2451 were originally a part of the r-devtools package.")
2452 (license license:gpl2+)))
2454 (define-public r-hms
2461 (uri (cran-uri "hms" version))
2464 "1g6hslk3z0xga38r71irxq802wskg6nv804mp8y9f7i2wfrj0y55"))))
2465 (build-system r-build-system)
2467 `(("r-rlang" ,r-rlang)
2468 ("r-pkgconfig" ,r-pkgconfig)))
2469 (home-page "https://github.com/rstats-db/hms")
2470 (synopsis "Pretty time of day")
2472 "This package implements an S3 class for storing and formatting
2473 time-of-day values, based on the @code{difftime} class.")
2474 (license license:gpl3+)))
2476 (define-public r-readr
2482 (uri (cran-uri "readr" version))
2485 "1wz496rw0ah433p755n3xac8gh7yzid4xgdjzd1a7wmpkgilvy9k"))))
2486 (build-system r-build-system)
2488 `(("r-clipr" ,r-clipr)
2489 ("r-crayon" ,r-crayon)
2492 ("r-tibble" ,r-tibble)
2495 (home-page "https://github.com/hadley/readr")
2496 (synopsis "Read tabular data")
2498 "This package provides functions to read flat or tabular text files from
2499 disk (or a connection).")
2500 (license license:gpl2+)))
2502 (define-public r-plotrix
2508 (uri (cran-uri "plotrix" version))
2511 "1hs0zwaqs34559girinvysjfbvznyn8znp9cwvkqx6k2cqvcjinj"))))
2512 (build-system r-build-system)
2513 (home-page "https://cran.r-project.org/web/packages/plotrix")
2514 (synopsis "Various plotting functions")
2516 "This package provides lots of plotting, various labeling, axis and color
2517 scaling functions for R.")
2518 (license license:gpl2+)))
2520 (define-public r-gridbase
2526 (uri (cran-uri "gridBase" version))
2529 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
2530 (build-system r-build-system)
2531 (home-page "https://cran.r-project.org/web/packages/gridBase")
2532 (synopsis "Integration of base and grid graphics")
2534 "This package provides an integration of base and grid graphics for R.")
2535 (license license:gpl2+)))
2537 (define-public r-latticeextra
2539 (name "r-latticeextra")
2544 (uri (cran-uri "latticeExtra" version))
2547 "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq"))))
2548 (properties `((upstream-name . "latticeExtra")))
2549 (build-system r-build-system)
2551 `(("r-lattice" ,r-lattice)
2552 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2553 (home-page "http://latticeextra.r-forge.r-project.org/")
2554 (synopsis "Extra graphical utilities based on lattice")
2556 "Building on the infrastructure provided by the lattice package, this
2557 package provides several new high-level graphics functions and methods, as
2558 well as additional utilities such as panel and axis annotation functions.")
2559 (license license:gpl2+)))
2561 (define-public r-rcpparmadillo
2563 (name "r-rcpparmadillo")
2564 (version "0.9.200.7.0")
2567 (uri (cran-uri "RcppArmadillo" version))
2570 "11m04yvdh6086567dzzxchbf68fl5hxf2y32acf3f43bjqgwbv2p"))))
2571 (properties `((upstream-name . "RcppArmadillo")))
2572 (build-system r-build-system)
2574 `(("r-knitr" ,r-knitr))) ; needed for vignettes
2576 `(("r-rcpp" ,r-rcpp)))
2577 (home-page "https://github.com/RcppCore/RcppArmadillo")
2578 (synopsis "Rcpp integration for the Armadillo linear algebra library")
2580 "Armadillo is a templated C++ linear algebra library that aims towards a
2581 good balance between speed and ease of use. Integer, floating point and
2582 complex numbers are supported, as well as a subset of trigonometric and
2583 statistics functions. Various matrix decompositions are provided through
2584 optional integration with LAPACK and ATLAS libraries. This package includes
2585 the header files from the templated Armadillo library.")
2586 ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
2587 ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
2588 ;; later, as is the rest of 'Rcpp'.
2589 (license license:gpl2+)))
2591 (define-public r-bitops
2597 (uri (cran-uri "bitops" version))
2600 "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
2601 (build-system r-build-system)
2602 (home-page "https://cran.r-project.org/web/packages/bitops")
2603 (synopsis "Bitwise operations")
2605 "This package provides functions for bitwise operations on integer
2607 (license license:gpl2+)))
2609 (define-public r-catools
2612 (version "1.17.1.1")
2615 (uri (cran-uri "caTools" version))
2618 "01hccp05gz25vhz9nnxv1c91lrxlr7drcw9xf124gggifxf2qgnm"))))
2619 (properties `((upstream-name . "caTools")))
2620 (build-system r-build-system)
2622 `(("r-bitops" ,r-bitops)))
2623 (home-page "https://cran.r-project.org/web/packages/caTools")
2624 (synopsis "Various tools including functions for moving window statistics")
2626 "This package contains several basic utility functions including:
2627 moving (rolling, running) window statistic functions, read/write for GIF and
2628 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
2629 encoder/decoder, round-off-error-free sum and cumsum, etc.")
2630 (license license:gpl3+)))
2632 (define-public r-rprojroot
2634 (name "r-rprojroot")
2639 (uri (cran-uri "rprojroot" version))
2642 "12r3fdxmi2pmwn6ic3rhg0b20ll5z420m0d8fziv1n21961namnz"))))
2643 (build-system r-build-system)
2645 `(("r-backports" ,r-backports)))
2646 (home-page "https://github.com/krlmlr/rprojroot")
2647 (synopsis "Finding files in project subdirectories")
2649 "This package helps accessing files relative to a project root. It
2650 provides helpers for robust, reliable and flexible paths to files below a
2651 project root. The root of a project is defined as a directory that matches a
2652 certain criterion, e.g., it contains a certain regular file.")
2653 (license license:gpl3)))
2655 (define-public r-rmarkdown
2657 (name "r-rmarkdown")
2662 (uri (cran-uri "rmarkdown" version))
2665 "0yyjbh891mdqzpjkblz8510ng71i7mxmyiqr69x3rwlwk2vakk79"))))
2666 (properties `((upstream-name . "rmarkdown")))
2667 (build-system r-build-system)
2669 `(("r-base64enc" ,r-base64enc)
2670 ("r-evaluate" ,r-evaluate)
2671 ("r-htmltools" ,r-htmltools)
2672 ("r-jsonlite" ,r-jsonlite)
2673 ("r-knitr" ,r-knitr)
2675 ("r-stringr" ,r-stringr)
2676 ("r-tinytex" ,r-tinytex)
2678 ("ghc-pandoc" ,ghc-pandoc)))
2679 (home-page "http://rmarkdown.rstudio.com")
2680 (synopsis "Convert R Markdown documents into a variety of formats")
2682 "This package provides tools to convert R Markdown documents into a
2683 variety of formats.")
2684 (license license:gpl3+)))
2686 (define-public r-gtable
2692 (uri (cran-uri "gtable" version))
2695 "0vz7073m0a2q12qzzihrfh5c2kx5jqi5l7z470fxmwqghdllh7l0"))))
2696 (properties `((upstream-name . "gtable")))
2697 (build-system r-build-system)
2698 (home-page "https://cran.r-project.org/web/packages/gtable")
2699 (synopsis "R library to arrange grobs in tables")
2701 "Gtable is a collection of tools to make it easier to work with
2702 \"tables\" of grobs.")
2703 (license license:gpl2+)))
2705 (define-public r-gridextra
2707 (name "r-gridextra")
2711 (uri (cran-uri "gridExtra" version))
2714 "0fwfk3cdwxxim7nd55pn7m31bcaqj48y06j7an2k1v1pybk0rdl1"))))
2715 (properties `((upstream-name . "gridExtra")))
2716 (build-system r-build-system)
2718 `(("r-gtable" ,r-gtable)))
2720 `(("r-knitr" ,r-knitr))) ;for building vignettes
2721 (home-page "https://github.com/baptiste/gridextra")
2722 (synopsis "Miscellaneous functions for \"Grid\" graphics")
2724 "This package provides a number of user-level functions to work with
2725 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
2727 (license license:gpl2+)))
2729 (define-public r-pkgconfig
2731 (name "r-pkgconfig")
2735 (uri (cran-uri "pkgconfig" version))
2738 "1jk9ip549xphb3anfixqv1yx5kidnndqgy9v3qjpmgmds5a7g695"))))
2739 (build-system r-build-system)
2740 (home-page "https://github.com/gaborcsardi/pkgconfig")
2741 (synopsis "Private configuration for R packages")
2742 (description "This package provides the functionality to set configuration
2743 options on a per-package basis. Options set by a given package only apply to
2744 that package, other packages are unaffected.")
2745 (license license:expat)))
2747 (define-public r-blob
2753 (uri (cran-uri "blob" version))
2756 "0lsg91hk508dd95ivig2lwg62qafwnarjw68110kx63cfk4zkjxc"))))
2757 (build-system r-build-system)
2759 `(("r-prettyunits" ,r-prettyunits)
2760 ("r-tibble" ,r-tibble)))
2761 (home-page "https://github.com/hadley/blob")
2762 (synopsis "Simple S3 Class for representing vectors of binary data")
2763 (description "Raw vectors in R are useful for storing a single binary
2764 object. What if you want to put a vector of them in a data frame? The blob
2765 package provides the blob object, a list of raw vectors, suitable for use as
2766 a column in data frame.")
2767 (license license:gpl3+)))
2769 (define-public r-rsqlite
2775 (uri (cran-uri "RSQLite" version))
2778 "1giwk4335sc6yhj3rs8h070g1mwy38kyqyqv6vcfxvskykj7vp6z"))))
2779 (properties `((upstream-name . "RSQLite")))
2780 (build-system r-build-system)
2784 ("r-memoise" ,r-memoise)
2785 ("r-plogr" ,r-plogr)
2787 ("r-bit64" ,r-bit64)
2789 ("r-pkgconfig" ,r-pkgconfig)))
2790 (home-page "https://github.com/rstats-db/RSQLite")
2791 (synopsis "SQLite interface for R")
2793 "This package embeds the SQLite database engine in R and provides an
2794 interface compliant with the DBI package. The source for the SQLite
2795 engine (version 3.8.8.2) is included.")
2796 (license license:lgpl2.0+)))
2798 (define-public r-rcurl
2801 (version "1.95-0.1.2")
2804 (uri (string-append "https://www.bioconductor.org/packages/"
2805 "release/extra/src/"
2806 "contrib/RCurl_" version ".tar.gz"))
2809 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
2810 (properties `((upstream-name . "RCurl")))
2811 (build-system r-build-system)
2814 (modify-phases %standard-phases
2815 (add-after 'unpack 'respect-CURL_CA_BUNDLE
2817 (substitute* "R/options.S"
2818 (("\\.els = rev\\(merge\\(list\\(\\.\\.\\.\\), \\.opts\\)\\)" m)
2820 certs = Sys.getenv(\"CURL_CA_BUNDLE\")
2821 if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) }
2825 `(("libcurl" ,curl)))
2827 `(("r-bitops" ,r-bitops)))
2828 (home-page "http://www.omegahat.org/RCurl")
2829 (synopsis "General network client interface for R")
2831 "The package allows one to compose general HTTP requests and provides
2832 convenient functions to fetch URIs, GET and POST forms, etc. and process the
2833 results returned by the Web server. This provides a great deal of control
2834 over the HTTP/FTP/... connection and the form of the request while providing a
2835 higher-level interface than is available just using R socket connections.
2836 Additionally, the underlying implementation is robust and extensive,
2837 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
2838 ldap, and also supports cookies, redirects, authentication, etc.")
2839 (license license:bsd-3)))
2841 (define-public r-xml
2844 (version "3.98-1.16")
2847 (uri (cran-uri "XML" version))
2850 "0nl1kk354r8snhj6p9mc74m7awvqc6akmd4y3a46y78yv3g15njp"))))
2852 `((upstream-name . "XML")))
2853 (build-system r-build-system)
2855 `(("libxml2" ,libxml2)
2858 `(("pkg-config" ,pkg-config)))
2859 (home-page "http://www.omegahat.org/RSXML")
2860 (synopsis "Tools for parsing and generating XML within R")
2862 "Many approaches for both reading and creating XML (and HTML)
2863 documents (including DTDs), both local and accessible via HTTP or FTP. Also
2864 offers access to an XPath \"interpreter\".")
2865 (license license:bsd-2)))
2867 (define-public r-xnomial
2872 (origin (method url-fetch)
2873 (uri (cran-uri "XNomial" version))
2876 "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
2877 (properties (quasiquote ((upstream-name . "XNomial"))))
2878 (build-system r-build-system)
2879 (home-page "https://cran.r-project.org/web/packages/XNomial")
2880 (synopsis "Goodness-of-Fit test for multinomial data")
2882 "This package provides an exact Goodness-of-Fit test for
2883 multinomial data with fixed probabilities. It can be used to
2884 determine whether a set of counts fits a given expected ratio. To see
2885 whether a set of observed counts fits an expectation, one can examine
2886 all possible outcomes with @code{xmulti()} or a random sample of them
2887 with @code{xmonte()} and find the probability of an observation
2888 deviating from the expectation by at least as much as the observed.
2889 As a measure of deviation from the expected, one can use the
2890 log-likelihood ratio, the multinomial probability, or the classic
2891 chi-square statistic. A histogram of the test statistic can also be
2892 plotted and compared with the asymptotic curve.")
2893 (license (list license:gpl2+ license:gpl3+))))
2895 (define-public r-lambda-r
2901 (uri (cran-uri "lambda.r" version))
2904 "0cc6pszs6yccn0hgjpyn9gspv9aiva9d91ba0640i5m0l5xy7n0c"))))
2905 (properties `((upstream-name . "lambda.r")))
2906 (build-system r-build-system)
2908 `(("r-formatr" ,r-formatr)))
2909 (home-page "https://cran.r-project.org/web/packages/lambda.r")
2910 (synopsis "Functional programming extension for R")
2912 "This package provides a language extension to efficiently write
2913 functional programs in R. Syntax extensions include multi-part function
2914 definitions, pattern matching, guard statements, built-in (optional) type
2916 (license license:lgpl3+)))
2918 (define-public r-futile-options
2920 (name "r-futile-options")
2924 (uri (cran-uri "futile.options" version))
2927 "0w15agpi88y3qkv6fl72zy2pzyplzgvnj41a4ixhg64mw1sck73s"))))
2929 `((upstream-name . "futile.options")))
2930 (build-system r-build-system)
2931 (home-page "https://cran.r-project.org/web/packages/futile.options")
2932 (synopsis "Options management framework")
2934 "The futile.options subsystem provides an easy user-defined options
2935 management system that is properly scoped. This means that options created
2936 via @code{futile.options} are fully self-contained and will not collide with
2937 options defined in other packages.")
2938 (license license:lgpl3+)))
2940 (define-public r-futile-logger
2942 (name "r-futile-logger")
2946 (uri (cran-uri "futile.logger" version))
2949 "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
2950 (properties `((upstream-name . "futile.logger")))
2951 (build-system r-build-system)
2953 `(("r-futile-options" ,r-futile-options)
2954 ("r-lambda-r" ,r-lambda-r)))
2955 (home-page "https://cran.r-project.org/web/packages/futile.logger")
2956 (synopsis "Logging utility for R")
2958 "This package provides a simple yet powerful logging utility. Based
2959 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
2960 convenient and easy to use replacement for @code{cat} and @code{print}
2962 (license license:lgpl3+)))
2964 (define-public r-segmented
2966 (name "r-segmented")
2971 (uri (cran-uri "segmented" version))
2974 "0nrik5fyq59hwiwjcpbi4p5yfavgfjq6wyrynhkrbm4k6v1g1wlq"))))
2975 (build-system r-build-system)
2976 (home-page "https://cran.r-project.org/web/packages/segmented")
2977 (synopsis "Regression models with breakpoints estimation")
2979 "Given a regression model, segmented updates the model by adding one or
2980 more segmented (i.e., piecewise-linear) relationships. Several variables with
2981 multiple breakpoints are allowed.")
2982 (license (list license:gpl2+ license:gpl3+))))
2984 (define-public r-snow
2990 (uri (cran-uri "snow" version))
2993 "1n3n8pva9s34fvlw32yng0x416lmbv7q1fsd0ywa4kikmxym64l5"))))
2994 (build-system r-build-system)
2995 (home-page "https://cran.r-project.org/web/packages/snow")
2996 (synopsis "Support for simple parallel computing in R")
2998 "The snow package provides support for simple parallel computing on a
2999 network of workstations using R. A master R process calls @code{makeCluster}
3000 to start a cluster of worker processes; the master process then uses functions
3001 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
3002 worker processes and collect and return the results on the master.")
3003 (license (list license:gpl2+ license:gpl3+))))
3005 (define-public r-sparsem
3011 (uri (cran-uri "SparseM" version))
3014 "0p6ljma2h12cq1xmy0cxb48ih8dhxxbnwkqzvx3cckxf2kprycm9"))))
3016 `((upstream-name . "SparseM")))
3018 `(("gfortran" ,gfortran)))
3019 (build-system r-build-system)
3020 (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
3021 (synopsis "Sparse linear algebra")
3023 "This package provides some basic linear algebra functionality for sparse
3024 matrices. It includes Cholesky decomposition and backsolving as well as
3025 standard R subsetting and Kronecker products.")
3026 (license license:gpl2+)))
3028 (define-public r-iterators
3030 (name "r-iterators")
3035 (uri (cran-uri "iterators" version))
3038 "1s3iykfvccpnzs73z90rx18qvbvgw2dgl4nfcrvm5m1850qb5qd9"))))
3039 (build-system r-build-system)
3040 (home-page "https://cran.r-project.org/web/packages/iterators")
3041 (synopsis "Iterator construct for R")
3043 "This package provides support for iterators, which allow a programmer to
3044 traverse through all the elements of a vector, list, or other collection of
3046 (license license:asl2.0)))
3048 (define-public r-foreach
3055 (uri (cran-uri "foreach" version))
3058 "0j2yj0rn0d5nbzz9nq5rqqgnxhp9pbd92q4klsarl2xpsn8119y0"))))
3059 (build-system r-build-system)
3061 `(("r-codetools" ,r-codetools)
3062 ("r-iterators" ,r-iterators)))
3063 (home-page "https://cran.r-project.org/web/packages/foreach")
3064 (synopsis "Foreach looping construct for R")
3066 "This package provides support for the @code{foreach} looping construct.
3067 @code{foreach} is an idiom that allows for iterating over elements in a
3068 collection, without the use of an explicit loop counter. This package in
3069 particular is intended to be used for its return value, rather than for its
3070 side effects. In that sense, it is similar to the standard @code{lapply}
3071 function, but doesn't require the evaluation of a function. Using
3072 @code{foreach} without side effects also facilitates executing the loop in
3074 (license license:asl2.0)))
3076 (define-public r-doparallel
3078 (name "r-doparallel")
3083 (uri (cran-uri "doParallel" version))
3086 "01qjs4iw9f1kgymcypj0m2s4pvgqhxaycpli0fb8lq3dc0vpzfyb"))))
3087 (properties `((upstream-name . "doParallel")))
3088 (build-system r-build-system)
3090 `(("r-foreach" ,r-foreach)
3091 ("r-iterators" ,r-iterators)))
3092 (home-page "https://cran.r-project.org/web/packages/doParallel")
3093 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3095 "This package provides a parallel backend for the @code{%dopar%} function
3096 using the parallel package.")
3097 (license license:gpl2+)))
3099 (define-public r-domc
3106 (uri (cran-uri "doMC" version))
3109 "1vfrykvfvsyq12mypd266867ml1dcwc3rj5k9c3wrn5bddcm88kr"))))
3110 (properties `((upstream-name . "doMC")))
3111 (build-system r-build-system)
3113 `(("r-foreach" ,r-foreach)
3114 ("r-iterators" ,r-iterators)))
3115 (home-page "https://cran.r-project.org/web/packages/doMC")
3116 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3118 "This package provides a parallel backend for the @code{%dopar%} function
3119 using the multicore functionality of the parallel package.")
3120 (license license:gpl2+)))
3128 (uri (cran-uri "DT" version))
3131 "1s5d3sld4l8zygpkvprvlbqa0pm2cv1bm7h7p999wxlap28vnnqf"))))
3133 `((upstream-name . "DT")))
3134 (build-system r-build-system)
3136 `(("r-crosstalk" ,r-crosstalk)
3137 ("r-htmltools" ,r-htmltools)
3138 ("r-htmlwidgets" ,r-htmlwidgets)
3139 ("r-magrittr" ,r-magrittr)
3140 ("r-promises" ,r-promises)))
3141 (home-page "http://rstudio.github.io/DT")
3142 (synopsis "R wrapper of the DataTables JavaScript library")
3144 "This package allows for data objects in R to be rendered as HTML tables
3145 using the JavaScript library 'DataTables' (typically via R Markdown or Shiny).
3146 The 'DataTables' library has been included in this R package.")
3147 ;; The DT package as a whole is distributed under GPLv3. The DT package
3148 ;; inludes other software components under different licenses:
3150 ;; * Expat: jQuery, jquery.highlight.js, DataTables
3151 ;; * ASL2.0: selectize.js
3152 ;; * WTFPL: noUiSlider
3153 (license (list license:gpl3
3156 (license:non-copyleft "http://www.wtfpl.net/txt/copying/")))))
3158 (define-public r-base64enc
3160 (name "r-base64enc")
3164 (uri (cran-uri "base64enc" version))
3167 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
3168 (build-system r-build-system)
3169 (home-page "http://www.rforge.net/base64enc")
3170 (synopsis "Tools for Base64 encoding")
3172 "This package provides tools for handling Base64 encoding. It is more
3173 flexible than the orphaned \"base64\" package.")
3174 (license license:gpl2+)))
3176 (define-public r-irlba
3183 (uri (cran-uri "irlba" version))
3186 "0f7wb12wa0zbyllk5adcf4f517wgjpkhsx4j176i9ax6xy7jvprz"))))
3187 (build-system r-build-system)
3189 `(("r-matrix" ,r-matrix)))
3190 (home-page "https://cran.r-project.org/web/packages/irlba")
3191 (synopsis "Methods for eigendecomposition of large matrices")
3193 "This package provides fast and memory efficient methods for truncated
3194 singular and eigenvalue decompositions, as well as for principal component
3195 analysis of large sparse or dense matrices.")
3196 (license (list license:gpl2+ license:gpl3+))))
3198 (define-public r-glmnet
3205 (uri (cran-uri "glmnet" version))
3208 "1brr51z1fzbpyj6myyir4g6dhbp6xwl7nx4xnvrjarnf5y0csk55"))))
3209 (build-system r-build-system)
3211 `(("gfortran" ,gfortran)))
3213 `(("r-foreach" ,r-foreach)
3214 ("r-matrix" ,r-matrix)))
3215 (home-page "http://www.jstatsoft.org/v33/i01")
3216 (synopsis "Lasso and elastic-net regularized generalized linear models")
3218 "The glmnet package provides efficient procedures for fitting the entire
3219 lasso or elastic-net regularization path for linear and Poisson regression, as
3220 well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
3221 multinomial models. The algorithm uses cyclical coordinate descent in a
3222 path-wise fashion.")
3223 (license license:gpl2+)))
3225 (define-public r-pkgmaker
3232 (uri (cran-uri "pkgmaker" version))
3235 "0spcamjncj78kzjps2rw4v1a4494yazv6xvhn0vmdflnypc8k8hp"))))
3236 (build-system r-build-system)
3238 `(("r-bibtex" ,r-bibtex)
3239 ("r-codetools" ,r-codetools)
3240 ("r-digest" ,r-digest)
3241 ("r-magrittr" ,r-magrittr)
3242 ("r-registry" ,r-registry)
3243 ("r-stringi" ,r-stringi)
3244 ("r-stringr" ,r-stringr)
3245 ("r-withr" ,r-withr)
3246 ("r-xtable" ,r-xtable)))
3247 (home-page "https://renozao.github.io/pkgmaker")
3248 (synopsis "Package development utilities")
3250 "This package provides some low-level utilities to use for R package
3251 development. It currently provides managers for multiple package specific
3252 options and registries, vignette, unit test and bibtex related utilities.")
3253 (license license:gpl2+)))
3255 (define-public r-registry
3262 (uri (cran-uri "registry" version))
3265 "1yqfl1g6vsl28zn8brzc39659k8lqsmfms7900j7p64ilydyb2sx"))))
3266 (build-system r-build-system)
3267 (home-page "https://cran.r-project.org/web/packages/registry")
3268 (synopsis "Infrastructure for R package registries")
3270 "This package provides a generic infrastructure for creating and using R
3271 package registries.")
3272 (license license:gpl2+)))
3274 (define-public r-rngtools
3281 (uri (cran-uri "rngtools" version))
3284 "097215qcfw6ybllpzmp1532r59h2srvch3aca4z4s6l2rf9w8gvn"))))
3285 (build-system r-build-system)
3287 `(("r-digest" ,r-digest)
3288 ("r-pkgmaker" ,r-pkgmaker)
3289 ("r-stringr" ,r-stringr)))
3290 (home-page "https://renozao.github.io/rngtools")
3291 (synopsis "Utility functions for working with random number generators")
3293 "This package contains a set of functions for working with Random Number
3294 Generators (RNGs). In particular, it defines a generic S4 framework for
3295 getting/setting the current RNG, or RNG data that are embedded into objects
3296 for reproducibility. Notably, convenient default methods greatly facilitate
3297 the way current RNG settings can be changed.")
3298 (license license:gpl3+)))
3300 (define-public r-rtsne
3307 (uri (cran-uri "Rtsne" version))
3310 "0v17vxizrs1msay24xl2bckfajr2c82wpqj07lyssbrq197nwdsn"))))
3311 (properties `((upstream-name . "Rtsne")))
3312 (build-system r-build-system)
3314 `(("r-rcpp" ,r-rcpp)))
3315 (home-page "https://github.com/jkrijthe/Rtsne")
3316 (synopsis "T-distributed stochastic neighbor embedding")
3318 "This package provides an R wrapper around the fast T-distributed
3319 Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
3320 ;; The declared license for this package is BSD-3, but it also includes
3321 ;; code licensed under BSD-4.
3322 (license (list license:bsd-3 license:bsd-4))))
3324 (define-public r-e1071
3331 (uri (cran-uri "e1071" version))
3334 "11fqm4shmksalkazcwvzfknp3amigw7fr8wdwanqa5v5kx7ihyq9"))))
3335 (build-system r-build-system)
3337 `(("r-class" ,r-class)))
3338 (home-page "https://cran.r-project.org/web/packages/e1071")
3339 (synopsis "Miscellaneous functions for probability theory")
3341 "This package provides functions for latent class analysis, short time
3342 Fourier transform, fuzzy clustering, support vector machines, shortest path
3343 computation, bagged clustering, naive Bayes classifier, and more.")
3344 (license license:gpl2+)))
3346 (define-public r-bigmemory-sri
3348 (name "r-bigmemory-sri")
3353 (uri (cran-uri "bigmemory.sri" version))
3355 (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
3357 `((upstream-name . "bigmemory.sri")))
3358 (build-system r-build-system)
3359 (home-page "https://cran.r-project.org/web/packages/bigmemory.sri")
3360 (synopsis "Shared resource interface for the bigmemory package")
3361 (description "This package provides a shared resource interface for the
3362 bigmemory and synchronicity packages.")
3363 ;; Users can choose either LGPLv3 or ASL2.0.
3364 (license (list license:lgpl3 license:asl2.0))))
3366 (define-public r-synchronicity
3368 (name "r-synchronicity")
3373 (uri (cran-uri "synchronicity" version))
3376 "1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx"))))
3377 (build-system r-build-system)
3380 ("r-bigmemory-sri" ,r-bigmemory-sri)
3382 ("r-uuid" ,r-uuid)))
3383 (home-page "http://www.bigmemory.org")
3384 (synopsis "Boost mutex functionality in R")
3385 (description "This package provides support for synchronization
3386 via mutexes and may eventually support interprocess communication and
3388 ;; Users can choose either LGPLv3 or ASL2.0.
3389 (license (list license:lgpl3 license:asl2.0))))
3391 (define-public r-bigmemory
3393 (name "r-bigmemory")
3398 (uri (cran-uri "bigmemory" version))
3401 "0ycl9dzm3drpyas625h34rir5bnbjlncxlvawfsfmqwcbmwdjdvj"))))
3402 (build-system r-build-system)
3406 ("r-bigmemory-sri" ,r-bigmemory-sri)))
3407 (home-page "http://www.bigmemory.org")
3408 (synopsis "Manage large matrices with shared memory or memory-mapped files")
3409 (description "This package provides methods to create, store, access, and
3410 manipulate large matrices. Matrices are allocated to shared memory and may use
3411 memory-mapped files.")
3412 ;; Users can choose either LGPLv3 or ASL2.0.
3413 (license (list license:lgpl3 license:asl2.0))))
3415 (define-public r-nmf
3422 (uri (cran-uri "NMF" version))
3425 "1qq25n3k5sgh3srlshb3ic6q92s12c1ilqf5cd5anvq6cqfchc1v"))))
3426 (properties `((upstream-name . "NMF")))
3427 (build-system r-build-system)
3429 `(("r-cluster" ,r-cluster)
3430 ("r-bigmemory" ,r-bigmemory) ; suggested
3431 ("r-synchronicity" ,r-synchronicity) ; suggested
3432 ("r-colorspace" ,r-colorspace)
3433 ("r-digest" ,r-digest)
3434 ("r-doparallel" ,r-doparallel)
3435 ("r-foreach" ,r-foreach)
3436 ("r-ggplot2" ,r-ggplot2)
3437 ("r-gridbase" ,r-gridbase)
3438 ("r-pkgmaker" ,r-pkgmaker)
3439 ("r-rcolorbrewer" ,r-rcolorbrewer)
3440 ("r-registry" ,r-registry)
3441 ("r-reshape2" ,r-reshape2)
3442 ("r-rngtools" ,r-rngtools)
3443 ("r-stringr" ,r-stringr)))
3444 (home-page "http://renozao.github.io/NMF")
3445 (synopsis "Algorithms and framework for nonnegative matrix factorization")
3447 "This package provides a framework to perform Non-negative Matrix
3448 Factorization (NMF). The package implements a set of already published
3449 algorithms and seeding methods, and provides a framework to test, develop and
3450 plug new or custom algorithms. Most of the built-in algorithms have been
3451 optimized in C++, and the main interface function provides an easy way of
3452 performing parallel computations on multicore machines.")
3453 (license license:gpl2+)))
3455 (define-public r-r-methodss3
3457 (name "r-r-methodss3")
3461 (uri (cran-uri "R.methodsS3" version))
3464 "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24"))))
3465 (properties `((upstream-name . "R.methodsS3")))
3466 (build-system r-build-system)
3467 (home-page "https://cran.r-project.org/web/packages/R.methodsS3")
3468 (synopsis "S3 methods simplified")
3470 "This package provides methods that simplify the setup of S3 generic
3471 functions and S3 methods. Major effort has been made in making definition of
3472 methods as simple as possible with a minimum of maintenance for package
3473 developers. For example, generic functions are created automatically, if
3474 missing, and naming conflict are automatically solved, if possible. The
3475 method @code{setMethodS3()} is a good start for those who in the future may
3476 want to migrate to S4.")
3477 (license license:lgpl2.1+)))
3479 (define-public r-r-oo
3485 (uri (cran-uri "R.oo" version))
3488 "0k6xwy93fpb2p7bs76lzk52br9rv5xnd9524xj8qyazv1132x1n0"))))
3489 (properties `((upstream-name . "R.oo")))
3490 (build-system r-build-system)
3492 `(("r-r-methodss3" ,r-r-methodss3)))
3493 (home-page "https://github.com/HenrikBengtsson/R.oo")
3494 (synopsis "R object-oriented programming with or without references")
3496 "This package provides methods and classes for object-oriented
3497 programming in R with or without references. Large effort has been made on
3498 making definition of methods as simple as possible with a minimum of
3499 maintenance for package developers.")
3500 (license license:lgpl2.1+)))
3502 (define-public r-r-utils
3508 (uri (cran-uri "R.utils" version))
3511 "0cxhn14a57x4gcyrwpfz1d6dw4xh0jcpqkb33hx8imnr340blh7n"))))
3512 (properties `((upstream-name . "R.utils")))
3513 (build-system r-build-system)
3515 `(("r-r-methodss3" ,r-r-methodss3)
3516 ("r-r-oo" ,r-r-oo)))
3517 (home-page "https://github.com/HenrikBengtsson/R.utils")
3518 (synopsis "Various programming utilities")
3520 "This package provides utility functions useful when programming and
3521 developing R packages.")
3522 (license license:lgpl2.1+)))
3524 (define-public r-r-cache
3530 (uri (cran-uri "R.cache" version))
3533 "1hf5cb7xvnca5zlh9245b5g62sgsaxwdhiv7x59yld37cydakm6k"))))
3534 (properties `((upstream-name . "R.cache")))
3535 (build-system r-build-system)
3537 `(("r-digest" ,r-digest)
3538 ("r-r-methodss3" ,r-r-methodss3)
3540 ("r-r-utils" ,r-r-utils)))
3541 (home-page "https://github.com/HenrikBengtsson/R.cache")
3542 (synopsis "Light-weight caching of objects and results")
3544 "This package provides methods for caching or memoization of objects and
3545 results. With this package, any R object can be cached in a key-value storage
3546 where the key can be an arbitrary set of R objects. The cache memory is
3547 persistent (on the file system).")
3548 (license license:lgpl2.1+)))
3550 (define-public r-r-rsp
3556 (uri (cran-uri "R.rsp" version))
3559 "0ax6781kfylx0acz0i3sqnpkxmrq73x29wwfic59ng7vj0ws0gyd"))))
3560 (properties `((upstream-name . "R.rsp")))
3561 (build-system r-build-system)
3563 `(("r-digest" ,r-digest)
3564 ("r-r-cache" ,r-r-cache)
3565 ("r-r-methodss3" ,r-r-methodss3)
3567 ("r-r-utils" ,r-r-utils)))
3568 (home-page "https://github.com/HenrikBengtsson/R.rsp")
3569 (synopsis "Dynamic generation of scientific reports")
3571 "The RSP markup language provides a powerful markup for controlling the
3572 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
3573 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
3574 to many other literate programming languages, with RSP it is straightforward
3575 to loop over mixtures of code and text sections, e.g. in month-by-month
3576 summaries. RSP has also several preprocessing directives for incorporating
3577 static and dynamic contents of external files (local or online) among other
3578 things. RSP is ideal for self-contained scientific reports and R package
3580 (license license:lgpl2.1+)))
3582 (define-public r-mvtnorm
3588 (uri (cran-uri "mvtnorm" version))
3591 "0la42lylb7cjrcrc285bn69bz9kyg556xw317iz139dp1yswl410"))))
3592 (build-system r-build-system)
3594 `(("gfortran" ,gfortran)))
3595 (home-page "http://mvtnorm.R-forge.R-project.org")
3596 (synopsis "Package for multivariate normal and t-distributions")
3597 (description "This package can compute multivariate normal and
3598 t-probabilities, quantiles, random deviates and densities.")
3599 (license license:gpl2)))
3601 (define-public r-matrixstats
3603 (name "r-matrixstats")
3607 (uri (cran-uri "matrixStats" version))
3610 "0vx00ldsg2zvdrjn49jxczk2c9iaabgvzgpdka5j02ihh7hv83cg"))))
3611 (properties `((upstream-name . "matrixStats")))
3612 (build-system r-build-system)
3614 `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
3615 (home-page "https://github.com/HenrikBengtsson/matrixStats")
3616 (synopsis "Methods applying to vectors and matrix rows and columns")
3618 "This package provides methods operating on rows and columns of matrices,
3619 e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
3620 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
3621 @code{weightedMedians()}. All methods have been optimized for speed and
3623 (license license:artistic2.0)))
3625 (define-public r-viridis
3631 (uri (cran-uri "viridis" version))
3634 "060rf1jn29dq53y3nhb0hykvcap6rqsk04rq544ypiiqb18ngwnx"))))
3635 (build-system r-build-system)
3637 `(("r-ggplot2" ,r-ggplot2)
3638 ("r-gridextra" ,r-gridextra)
3639 ("r-viridislite" ,r-viridislite)))
3640 (home-page "https://github.com/sjmgarnier/viridis")
3641 (synopsis "Matplotlib default color map")
3643 "This package is a port of the new @url{matplotlib,
3644 http://matplotlib.org/} color maps (@code{viridis}--the default--,
3645 @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
3646 designed in such a way that they will analytically be perfectly
3647 perceptually-uniform, both in regular form and also when converted to
3648 black-and-white. They are also designed to be perceived by readers with the
3649 most common form of color blindness.")
3650 (license license:x11)))
3652 (define-public r-viridislite
3654 (name "r-viridislite")
3659 (uri (cran-uri "viridisLite" version))
3662 "1by2l05f0yabwvv64lhnv7bbhx0w683s3wr9j2xda920ghpa23kq"))))
3663 (properties `((upstream-name . "viridisLite")))
3664 (build-system r-build-system)
3665 (home-page "https://github.com/sjmgarnier/viridisLite")
3666 (synopsis "Default color maps from matplotlib")
3668 "This package is a port of the new @code{matplotlib} color maps ('viridis',
3669 'magma', 'plasma' and 'inferno') to R. matplotlib is a popular plotting
3670 library for Python. These color maps are designed in such a way that they
3671 will analytically be perfectly perceptually-uniform, both in regular form and
3672 also when converted to black-and-white. They are also designed to be
3673 perceived by readers with the most common form of color blindness. This is
3674 the 'lite' version of the more complete @code{viridis} package.")
3675 (license license:expat)))
3677 (define-public r-tidyselect
3679 (name "r-tidyselect")
3684 (uri (cran-uri "tidyselect" version))
3687 "0x3cp36byhfjajikr1lwffjm85ayw3bcs7d7kb0cydgs61ifiqjw"))))
3688 (build-system r-build-system)
3690 `(("r-glue" ,r-glue)
3691 ("r-purrr" ,r-purrr)
3693 ("r-rlang" ,r-rlang)))
3694 (home-page "https://cran.r-project.org/web/packages/tidyselect")
3695 (synopsis "Select from a set of strings")
3697 "This package provides a backend for the selecting functions of the
3698 tidyverse. It makes it easy to implement select-like functions in your own
3699 packages in a way that is consistent with other tidyverse interfaces for
3701 (license license:gpl3)))
3703 (define-public r-tidyr
3710 (uri (cran-uri "tidyr" version))
3713 "03s9dv6c2dj65a769h8fgy9878y46rdq7x65i53kd44kag80i9cr"))))
3714 (build-system r-build-system)
3716 `(("r-dplyr" ,r-dplyr)
3717 ("r-magrittr" ,r-magrittr)
3719 ("r-purrr" ,r-purrr)
3720 ("r-rlang" ,r-rlang)
3721 ("r-tidyselect" ,r-tidyselect)
3723 ("r-stringi" ,r-stringi)
3724 ("r-tibble" ,r-tibble)))
3725 (home-page "https://github.com/hadley/tidyr")
3726 (synopsis "Tidy data with `spread()` and `gather()` functions")
3728 "tidyr is a reframing of the reshape2 package designed to accompany the
3729 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
3730 a solid pipeline for data analysis. It is designed specifically for tidying
3731 data, not the general reshaping that reshape2 does, or the general aggregation
3732 that reshape did. In particular, built-in methods only work for data frames,
3733 and tidyr provides no margins or aggregation.")
3734 (license license:expat)))
3736 (define-public r-hexbin
3743 (uri (cran-uri "hexbin" version))
3746 "0lpfl0015lg5x7lvv9dr302bca22c7fs91pnd896ypgpzqg7pm26"))))
3747 (build-system r-build-system)
3749 `(("r-lattice" ,r-lattice)))
3751 `(("gfortran" ,gfortran)))
3752 (home-page "https://github.com/edzer/hexbin")
3753 (synopsis "Hexagonal binning routines")
3755 "This package provides binning and plotting functions for hexagonal bins.
3756 It uses and relies on grid graphics and formal (S4) classes and methods.")
3757 (license license:gpl2+)))
3759 (define-public r-purrr
3766 (uri (cran-uri "purrr" version))
3769 "0mzbf9ca8qdrqkrh9x7yzqxiab9bk10ql46qr1wl2bgbflminzda"))))
3770 (build-system r-build-system)
3772 `(("r-magrittr" ,r-magrittr)
3773 ("r-rlang" ,r-rlang)))
3774 (home-page "https://github.com/hadley/purrr")
3775 (synopsis "Functional programming tools")
3777 "This package completes R's functional programming tools with missing
3778 features present in other programming languages.")
3779 (license license:gpl3+)))
3781 (define-public r-plotly
3787 (uri (cran-uri "plotly" version))
3790 "19p8pa03q9mw5vaan7r56xgd13d90ssiz0flbrkvpfrir2105ybq"))))
3791 (build-system r-build-system)
3793 `(("r-base64enc" ,r-base64enc)
3794 ("r-crosstalk" ,r-crosstalk)
3795 ("r-digest" ,r-digest)
3796 ("r-data-table" ,r-data-table)
3797 ("r-dplyr" ,r-dplyr)
3798 ("r-ggplot2" ,r-ggplot2)
3799 ("r-hexbin" ,r-hexbin)
3800 ("r-htmltools" ,r-htmltools)
3801 ("r-htmlwidgets" ,r-htmlwidgets)
3803 ("r-jsonlite" ,r-jsonlite)
3804 ("r-lazyeval" ,r-lazyeval)
3805 ("r-magrittr" ,r-magrittr)
3806 ("r-promises" ,r-promises)
3807 ("r-purrr" ,r-purrr)
3808 ("r-rcolorbrewer" ,r-rcolorbrewer)
3809 ("r-rlang" ,r-rlang)
3810 ("r-scales" ,r-scales)
3811 ("r-tibble" ,r-tibble)
3812 ("r-tidyr" ,r-tidyr)
3813 ("r-viridislite" ,r-viridislite)))
3814 (home-page "https://plot.ly/r")
3815 (synopsis "Create interactive web graphics")
3817 "This package enables the translation of ggplot2 graphs to an interactive
3818 web-based version and/or the creation of custom web-based visualizations
3819 directly from R. Once uploaded to a plotly account, plotly graphs (and the
3820 data behind them) can be viewed and modified in a web browser.")
3821 (license license:x11)))
3823 (define-public r-biased-urn
3825 (name "r-biased-urn")
3830 (uri (cran-uri "BiasedUrn" version))
3833 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
3834 (properties `((upstream-name . "BiasedUrn")))
3835 (build-system r-build-system)
3836 (home-page "http://www.agner.org/random/")
3837 (synopsis "Biased urn model distributions")
3839 "This package provides statistical models of biased sampling in the form
3840 of univariate and multivariate noncentral hypergeometric distributions,
3841 including Wallenius' noncentral hypergeometric distribution and Fisher's
3842 noncentral hypergeometric distribution (also called extended hypergeometric
3844 (license license:gpl3+)))
3846 (define-public r-rematch
3853 (uri (cran-uri "rematch" version))
3856 "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4"))))
3857 (build-system r-build-system)
3858 (home-page "https://github.com/MangoTheCat/rematch")
3859 (synopsis "Match regular expressions with a nicer API")
3861 "This package provides a small wrapper on @code{regexpr} to extract the
3862 matches and captured groups from the match of a regular expression to a
3864 (license license:expat)))
3866 (define-public r-cellranger
3868 (name "r-cellranger")
3873 (uri (cran-uri "cellranger" version))
3876 "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x"))))
3877 (build-system r-build-system)
3879 `(("r-rematch" ,r-rematch)
3880 ("r-tibble" ,r-tibble)))
3881 (home-page "https://github.com/rsheets/cellranger")
3882 (synopsis "Translate spreadsheet cell ranges to rows and columns")
3884 "This package provides helper functions to work with spreadsheets and the
3885 @code{A1:D10} style of cell range specification.")
3886 (license license:expat)))
3888 (define-public r-googlesheets
3890 (name "r-googlesheets")
3895 (uri (cran-uri "googlesheets" version))
3898 "11q07nxys72wkxx9mawmjyf20gvwvrb7h3gpa73h6lgh2vgrwnv8"))))
3899 (build-system r-build-system)
3901 `(("r-cellranger" ,r-cellranger)
3902 ("r-dplyr" ,r-dplyr)
3904 ("r-jsonlite" ,r-jsonlite)
3905 ("r-purrr" ,r-purrr)
3906 ("r-readr" ,r-readr)
3907 ("r-stringr" ,r-stringr)
3908 ("r-tibble" ,r-tibble)
3909 ("r-tidyr" ,r-tidyr)
3910 ("r-xml2" ,r-xml2)))
3911 (home-page "https://github.com/jennybc/googlesheets")
3912 (synopsis "Manage Google spreadsheets from R")
3913 (description "This package provides tools to interact with Google Sheets
3915 (license license:expat)))
3917 (define-public r-spams
3920 (version "2.6-2017-03-22")
3924 ;; Use the ‘Latest version’ link for a stable URI across releases.
3925 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
3926 "latestfile/4531/spams-R-v" version ".tar.gz"))
3929 "13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx"))))
3930 (build-system r-build-system)
3933 (modify-phases %standard-phases
3934 (add-after 'unpack 'chdir
3935 (lambda _ (chdir "spams") #t))
3936 ;; Don't tune for the building machine.
3937 (add-after 'chdir 'no-mtune
3939 (substitute* "src/Makevars"
3940 (("-mtune=native") ""))
3943 `(("r-lattice" ,r-lattice)
3944 ("r-matrix" ,r-matrix)))
3945 (home-page "http://spams-devel.gforge.inria.fr")
3946 (synopsis "Toolbox for solving sparse estimation problems")
3947 (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
3948 for solving various sparse estimation problems. It includes tools for the
3952 @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
3953 component analysis} (PCA), ...)
3954 @item Solving sparse decomposition problems with LARS, coordinate descent,
3955 OMP, SOMP, proximal methods
3956 @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
3957 group lasso, tree-structured regularization, structured sparsity with
3958 overlapping groups,...).
3960 (license license:gpl3+)))
3962 (define-public r-base64
3969 (uri (cran-uri "base64" version))
3972 "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf"))))
3973 (build-system r-build-system)
3975 `(("r-openssl" ,r-openssl)))
3976 (home-page "https://cran.r-project.org/web/packages/base64")
3977 (synopsis "Base64 encoder and decoder")
3979 "This package is a compatibility wrapper to replace the orphaned package
3980 by Romain Francois. New applications should use the openssl or base64enc
3982 (license license:expat)))
3984 (define-public r-hmisc
3991 (uri (cran-uri "Hmisc" version))
3994 "1n8i2jhc308hd6bvys9cd7nrz7pwjszs03r5bwlh1pc869ki95ly"))))
3995 (properties `((upstream-name . "Hmisc")))
3996 (build-system r-build-system)
3998 `(("gfortran" ,gfortran)))
4000 `(("r-acepack" ,r-acepack)
4001 ("r-base64enc" ,r-base64enc)
4002 ("r-cluster" ,r-cluster)
4003 ("r-data-table" ,r-data-table)
4004 ("r-foreign" ,r-foreign)
4005 ("r-formula" ,r-formula)
4006 ("r-ggplot2" ,r-ggplot2)
4007 ("r-gridextra" ,r-gridextra)
4008 ("r-gtable" ,r-gtable)
4009 ("r-lattice" ,r-lattice)
4010 ("r-latticeextra" ,r-latticeextra)
4011 ("r-htmltable" ,r-htmltable)
4012 ("r-htmltools" ,r-htmltools)
4014 ("r-rpart" ,r-rpart)
4015 ("r-survival" ,r-survival)
4016 ("r-viridis" ,r-viridis)))
4017 (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
4018 (synopsis "Miscellaneous data analysis and graphics functions")
4020 "This package contains many functions useful for data analysis,
4021 high-level graphics, utility operations, functions for computing sample size
4022 and power, importing and annotating datasets, imputing missing values,
4023 advanced table making, variable clustering, character string manipulation,
4024 conversion of R objects to LaTeX code, and recoding variables.")
4025 (license license:gpl2+)))
4027 (define-public r-runit
4034 (uri (cran-uri "RUnit" version))
4037 "1wc1gwb7yw7phf8b0gkig6c23klya3ax11c6i4s0f049k42r78r3"))))
4038 (properties `((upstream-name . "RUnit")))
4039 (build-system r-build-system)
4040 (home-page "https://cran.r-project.org/web/packages/RUnit")
4041 (synopsis "R unit test framework")
4043 "This package provides R functions implementing a standard unit testing
4044 framework, with additional code inspection and report generation tools.")
4045 (license license:gpl2+)))
4047 (define-public r-dynamictreecut
4049 (name "r-dynamictreecut")
4054 (uri (cran-uri "dynamicTreeCut" version))
4057 "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"))))
4058 (properties `((upstream-name . "dynamicTreeCut")))
4059 (build-system r-build-system)
4061 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
4062 (synopsis "Detect clusters in hierarchical clustering dendrograms")
4064 "This package contains methods for the detection of clusters in
4065 hierarchical clustering dendrograms.")
4066 (license license:gpl2+)))
4068 (define-public r-preprocesscore
4070 (name "r-preprocesscore")
4075 (uri (bioconductor-uri "preprocessCore" version))
4078 "0ijyjqi8mxxf350dhvgp36swwww5ag7ac9a6r6ymihc5syjr4w4j"))))
4080 `((upstream-name . "preprocessCore")))
4081 (build-system r-build-system)
4082 (home-page "https://github.com/bmbolstad/preprocessCore")
4083 (synopsis "Collection of pre-processing functions")
4085 "This package provides a library of core pre-processing and normalization
4087 (license license:lgpl2.0+)))
4089 (define-public r-fastcluster
4091 (name "r-fastcluster")
4096 (uri (cran-uri "fastcluster" version))
4099 "01a2xnhhvv1swd4g8p4lzyn7ww7kg49jlnzc7kfz60jqjzpisrpk"))))
4100 (build-system r-build-system)
4101 (home-page "http://danifold.net/fastcluster.html")
4102 (synopsis "Fast hierarchical clustering routines")
4104 "This package implements fast hierarchical, agglomerative clustering
4105 routines. Part of the functionality is designed as drop-in replacement for
4106 existing routines: @code{linkage()} in the SciPy package
4107 @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package,
4108 and the @code{flashClust} package. It provides the same functionality with
4109 the benefit of a much faster implementation. Moreover, there are
4110 memory-saving routines for clustering of vector data, which go beyond what the
4111 existing packages provide.")
4112 (license license:bsd-2)))
4114 (define-public r-sfsmisc
4121 (uri (cran-uri "sfsmisc" version))
4124 "1y25nnw09qfm66523w1z4q766lv15a6ykvsq30r154n7m7aggvsq"))))
4125 (build-system r-build-system)
4126 (home-page "https://cran.r-project.org/web/packages/sfsmisc")
4127 (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
4129 "This package provides useful utilities from Seminar fuer Statistik ETH
4130 Zurich, including many that are related to graphics.")
4131 (license license:gpl2+)))
4133 (define-public r-gtools
4140 (uri (cran-uri "gtools" version))
4143 "0f5syk1qq6cjq6hwymvkiyhzwa389z94722v881ipbfqkd2q8505"))))
4144 (build-system r-build-system)
4147 (modify-phases %standard-phases
4148 (add-after 'unpack 'make-deterministic
4150 (substitute* "R/checkReverseDependencies.R"
4151 (("tempdir\\(\\)") "\"/tmp\""))
4153 (home-page "https://cran.r-project.org/web/packages/gtools")
4154 (synopsis "Various R programming tools")
4156 "This package contains a collection of various functions to assist in R
4157 programming, such as tools to assist in developing, updating, and maintaining
4158 R and R packages, calculating the logit and inverse logit transformations,
4159 tests for whether a value is missing, empty or contains only @code{NA} and
4160 @code{NULL} values, and many more.")
4161 (license license:gpl2)))
4163 (define-public r-gdata
4170 (uri (cran-uri "gdata" version))
4173 "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b"))))
4174 (build-system r-build-system)
4178 `(("r-gtools" ,r-gtools)))
4179 (home-page "https://cran.r-project.org/web/packages/gdata")
4180 (synopsis "Various R programming tools for data manipulation")
4182 "This package provides various R programming tools for data manipulation,
4186 @item medical unit conversions
4187 @item combining objects
4188 @item character vector operations
4189 @item factor manipulation
4190 @item obtaining information about R objects
4191 @item manipulating MS-Excel formatted files
4192 @item generating fixed-width format files
4193 @item extricating components of date and time objects
4194 @item operations on columns of data frames
4195 @item matrix operations
4196 @item operations on vectors and data frames
4197 @item value of last evaluated expression
4198 @item wrapper for @code{sample} that ensures consistent behavior for
4199 both scalar and vector arguments
4201 (license license:gpl2+)))
4203 (define-public r-gplots
4210 (uri (cran-uri "gplots" version))
4213 "033plcfs9w8pmn84n24mdhiixdirc2a7pz6dvm61fpd20gwh7cbx"))))
4214 (build-system r-build-system)
4216 `(("r-catools" ,r-catools)
4217 ("r-gdata" ,r-gdata)
4218 ("r-gtools" ,r-gtools)
4219 ("r-kernsmooth" ,r-kernsmooth)))
4220 (home-page "https://cran.r-project.org/web/packages/gplots")
4221 (synopsis "Various R programming tools for plotting data")
4223 "This package provides various R programming tools for plotting data,
4227 @item calculating and plotting locally smoothed summary function
4228 @item enhanced versions of standard plots
4229 @item manipulating colors
4230 @item calculating and plotting two-dimensional data summaries
4231 @item enhanced regression diagnostic plots
4232 @item formula-enabled interface to @code{stats::lowess} function
4233 @item displaying textual data in plots
4235 @item plotting \"Venn\" diagrams
4236 @item displaying Open-Office style plots
4237 @item plotting multiple data on same region, with separate axes
4238 @item plotting means and confidence intervals
4239 @item spacing points in an x-y plot so they don't overlap
4241 (license license:gpl2+)))
4243 (define-public r-rocr
4250 (uri (cran-uri "ROCR" version))
4253 "1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7"))))
4254 (properties `((upstream-name . "ROCR")))
4255 (build-system r-build-system)
4257 `(("r-gplots" ,r-gplots)))
4258 (home-page "http://rocr.bioinf.mpi-sb.mpg.de/")
4259 (synopsis "Visualizing the performance of scoring classifiers")
4261 "ROCR is a flexible tool for creating cutoff-parameterized 2D performance
4262 curves by freely combining two from over 25 performance measures (new
4263 performance measures can be added using a standard interface). Curves from
4264 different cross-validation or bootstrapping runs can be averaged by different
4265 methods, and standard deviations, standard errors or box plots can be used to
4266 visualize the variability across the runs. The parameterization can be
4267 visualized by printing cutoff values at the corresponding curve positions, or
4268 by coloring the curve according to cutoff. All components of a performance
4269 plot can be quickly adjusted using a flexible parameter dispatching
4271 (license license:gpl2+)))
4273 (define-public r-zoo
4279 (uri (cran-uri "zoo" version))
4282 "1pywcp86kqijdrvl42qwdy75szrag9pzj0p88zbrj2r1klb8rn5i"))))
4283 (build-system r-build-system)
4285 `(("r-lattice" ,r-lattice)))
4286 (home-page "http://zoo.R-Forge.R-project.org/")
4287 (synopsis "S3 infrastructure for regular and irregular time series")
4288 (description "This package contains an S3 class with methods for totally
4289 ordered indexed observations. It is particularly aimed at irregular time
4290 series of numeric vectors/matrices and factors.")
4291 (license license:gpl2+)))
4293 (define-public r-ztable
4299 (uri (cran-uri "ztable" version))
4302 "0g7khk5ifsdh9p31wlwh2l5mn1hzxzpv6qcn1wh34vsfjdmijjwy"))))
4303 (build-system r-build-system)
4305 `(("r-flextable" ,r-flextable)
4306 ("r-magrittr" ,r-magrittr)
4307 ("r-moonbook" ,r-moonbook)
4308 ("r-officer" ,r-officer)
4309 ("r-rcolorbrewer" ,r-rcolorbrewer)
4310 ("r-scales" ,r-scales)
4311 ("r-stringr" ,r-stringr)))
4312 (home-page "https://cran.r-project.org/web/packages/ztable")
4313 (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
4315 "This package provides functions to make zebra-striped tables (tables
4316 with alternating row colors) in LaTeX and HTML formats easily from
4317 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
4318 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
4319 @code{cbind.mytable} objects.")
4320 (license license:gpl2+)))
4322 (define-public r-vipor
4328 (uri (cran-uri "vipor" version))
4331 "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx"))))
4332 (build-system r-build-system)
4333 (home-page "https://cran.r-project.org/web/packages/vipor")
4334 (synopsis "Plot categorical data using noise and density estimates")
4336 "This package provides tools to generate a violin point plot, a
4337 combination of a violin/histogram plot and a scatter plot by offsetting points
4338 within a category based on their density using quasirandom noise.")
4339 (license license:gpl2+)))
4341 (define-public r-beeswarm
4347 (uri (cran-uri "beeswarm" version))
4350 "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
4351 (build-system r-build-system)
4352 (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/")
4353 (synopsis "Implementation of bee swarm plots")
4355 "This package provides an implementation of bee swarm plots. The bee
4356 swarm plot is a one-dimensional scatter plot like stripchart, but with
4357 closely-packed, non-overlapping points.")
4358 (license license:artistic2.0)))
4360 (define-public r-sourcetools
4362 (name "r-sourcetools")
4367 (uri (cran-uri "sourcetools" version))
4370 "1jnjir0q2dj724f1mjm6p5h77yzyx6xcqy9r2g7gmcxkxw349627"))))
4371 (build-system r-build-system)
4372 (home-page "https://cran.r-project.org/web/packages/sourcetools")
4373 (synopsis "Tools for reading, tokenizing and parsing R code")
4375 "The sourcetools package provides both an R and C++ interface for the
4376 tokenization of R code, and helpers for interacting with the tokenized
4377 representation of R code.")
4378 (license license:expat)))
4380 (define-public r-ggbeeswarm
4382 (name "r-ggbeeswarm")
4386 (uri (cran-uri "ggbeeswarm" version))
4389 "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v"))))
4390 (build-system r-build-system)
4392 `(("r-beeswarm" ,r-beeswarm)
4393 ("r-ggplot2" ,r-ggplot2)
4394 ("r-vipor" ,r-vipor)))
4395 (home-page "https://github.com/eclarke/ggbeeswarm")
4396 (synopsis "Categorical scatter (violin point) plots")
4398 "This package provides two methods of plotting categorical scatter plots
4399 such that the arrangement of points within a category reflects the density of
4400 data at that region, and avoids over-plotting.")
4401 (license license:gpl2+)))
4403 (define-public r-ggthemes
4409 (uri (cran-uri "ggthemes" version))
4412 "0y6570wv135sf7pv57l7bqilzw47rziaqx4vsk45pf1w4lmj0w8b"))))
4413 (build-system r-build-system)
4415 `(("r-ggplot2" ,r-ggplot2)
4416 ("r-purrr" ,r-purrr)
4417 ("r-scales" ,r-scales)
4418 ("r-stringr" ,r-stringr)
4419 ("r-tibble" ,r-tibble)))
4420 (home-page "https://cran.rstudio.com/web/packages/ggthemes")
4421 (synopsis "Extra themes, scales and geoms for @code{ggplot2}")
4422 (description "This package provides extra themes and scales for
4423 @code{ggplot2} that replicate the look of plots by Edward Tufte and
4424 Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The
4425 Wall Street Journal, among others. This package also provides
4426 @code{geoms} for Tufte's box plot and range frame.")
4427 (license license:gpl2)))
4429 (define-public r-statmod
4435 (uri (cran-uri "statmod" version))
4438 "07v4x8af60alcw6vbiwf5fp25bhra61kvxz9kqx64lszm0i1fb4x"))))
4439 (build-system r-build-system)
4440 (home-page "https://cran.r-project.org/web/packages/statmod")
4442 `(("gfortran" ,gfortran)))
4443 (synopsis "Statistical modeling")
4445 "This package provides a collection of algorithms and functions to aid
4446 statistical modeling. It includes growth curve comparisons, limiting dilution
4447 analysis (aka ELDA), mixed linear models, heteroscedastic regression,
4448 inverse-Gaussian probability calculations, Gauss quadrature and a secure
4449 convergence algorithm for nonlinear models. It also includes advanced
4450 generalized linear model functions that implement secure convergence,
4451 dispersion modeling and Tweedie power-law families.")
4452 ;; Statmod is distributed under either license
4453 (license (list license:gpl2 license:gpl3))))
4455 (define-public r-rann
4461 (uri (cran-uri "RANN" version))
4464 "10kid40w9w7vkz2hpcfkdpxr4afxzms5dzvfwr0sl5xynzgw76dj"))))
4466 `((upstream-name . "RANN")))
4467 (build-system r-build-system)
4468 (home-page "https://github.com/jefferis/RANN")
4469 (synopsis "Fast nearest neighbour search")
4471 "This package finds the k nearest neighbours for every point in a given
4472 dataset in O(N log N) time using Arya and Mount's ANN library. Provides
4473 approximate, exact searches, fixed radius searches, bd and kb trees.")
4474 (license license:gpl3+)))
4476 (define-public r-fivethirtyeight
4478 (name "r-fivethirtyeight")
4483 (uri (string-append "https://mran.microsoft.com/src/contrib/"
4484 "fivethirtyeight_" version ".tar.gz"))
4487 "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl"))))
4488 (build-system r-build-system)
4490 `(("r-knitr" ,r-knitr)
4491 ("r-rmarkdown" ,r-rmarkdown)
4492 ("r-dplyr" ,r-dplyr)
4493 ("r-readr" ,r-readr)
4494 ("r-ggplot2" ,r-ggplot2)
4495 ("r-magrittr" ,r-magrittr)
4496 ("r-stringr" ,r-stringr)))
4497 (home-page "https://mran.microsoft.com/package/fivethirtyeight/")
4498 (synopsis "Data and code behind the stories at FiveThirtyEight")
4499 (description "This R package provides access to the code and data sets
4500 published by the statistics blog FiveThirtyEight.")
4501 (license license:expat)))
4503 (define-public r-compquadform
4505 (name "r-compquadform")
4510 (uri (cran-uri "CompQuadForm" version))
4513 "1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4"))))
4514 (properties `((upstream-name . "CompQuadForm")))
4515 (build-system r-build-system)
4516 (home-page "https://cran.r-project.org/web/packages/CompQuadForm")
4517 (synopsis "Distribution function of quadratic forms in normal variables")
4519 "This package provides functions to compute the distribution function of
4520 quadratic forms in normal variables using Imhof's method, Davies's algorithm,
4521 Farebrother's algorithm or Liu et al.'s algorithm.")
4522 (license license:gpl2+)))
4524 (define-public r-cowplot
4531 (uri (cran-uri "cowplot" version))
4534 "0yvalwalvyddyqk0q66y8361nxlh2cvp3ssazax9g5q89lghjmzv"))))
4535 (build-system r-build-system)
4537 `(("r-ggplot2" ,r-ggplot2)
4538 ("r-gtable" ,r-gtable)
4540 ("r-scales" ,r-scales)))
4541 (home-page "https://github.com/wilkelab/cowplot")
4542 (synopsis "Streamlined plot theme and plot annotations for ggplot2")
4544 "This package provides some helpful extensions and modifications to the
4545 ggplot2 package to combine multiple ggplot2 plots into one and label them with
4546 letters, as is often required for scientific publications.")
4547 (license license:gpl2)))
4549 (define-public r-mixtools
4556 (uri (cran-uri "mixtools" version))
4559 "13wdm0xs5bakhpa8ypg6lvhjaqkxyabwz4glxdwn0jwdvkcdhgsl"))))
4560 (build-system r-build-system)
4562 `(("r-mass" ,r-mass)
4563 ("r-segmented" ,r-segmented)
4564 ("r-survival" ,r-survival)))
4565 (home-page "https://cran.r-project.org/web/packages/mixtools")
4566 (synopsis "Tools for analyzing finite mixture models")
4568 "This package provides a collection of R functions for analyzing finite
4570 (license license:gpl2+)))
4572 (define-public r-lars
4579 (uri (cran-uri "lars" version))
4582 "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
4583 (build-system r-build-system)
4585 `(("gfortran" ,gfortran)))
4586 (home-page "http://www-stat.stanford.edu/~hastie/Papers/#LARS")
4587 (synopsis "Least angle regression software")
4589 "Least Angle Regression (\"LAR\") is a model selection algorithm; a
4590 useful and less greedy version of traditional forward selection methods. A
4591 simple modification of the LAR algorithm implements Tibshirani's Lasso; the
4592 Lasso modification of LARS calculates the entire Lasso path of coefficients
4593 for a given problem at the cost of a single least squares fit. Another LARS
4594 modification efficiently implements epsilon Forward Stagewise linear
4596 (license license:gpl2)))
4598 (define-public r-fastica
4605 (uri (cran-uri "fastICA" version))
4608 "108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg"))))
4609 (properties `((upstream-name . "fastICA")))
4610 (build-system r-build-system)
4611 (home-page "https://cran.r-project.org/web/packages/fastICA")
4612 (synopsis "FastICA algorithms to perform ICA and projection pursuit")
4614 "This package provides an implementation of the FastICA algorithm to
4615 perform @dfn{independent component analysis} (ICA) and projection pursuit.")
4617 (license license:gpl3+)))
4619 (define-public r-randomforest
4621 (name "r-randomforest")
4626 (uri (cran-uri "randomForest" version))
4629 "0kbmm0l42fc2d1rdq0l7k09d34kd87q4lx651ffsic4y84h8kf7l"))))
4630 (properties `((upstream-name . "randomForest")))
4631 (build-system r-build-system)
4632 (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
4634 `(("gfortran" ,gfortran)))
4635 (synopsis "Breiman and Cutler's random forests for classification and regression")
4637 "This package provides the Breiman and Cutler's random forests algorithm, based on a
4638 forest of trees using random inputs, for classification and regression.")
4639 (license license:gpl2+)))
4641 (define-public r-diptest
4648 (uri (cran-uri "diptest" version))
4651 "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
4652 (build-system r-build-system)
4653 (home-page "https://cran.r-project.org/web/packages/diptest")
4654 (synopsis "Hartigan's dip test statistic for unimodality")
4656 "This package computes Hartigan's dip test statistic for unimodality,
4657 multimodality and provides a test with simulation based p-values, where the
4658 original public code has been corrected.")
4659 (license license:gpl2+)))
4661 (define-public r-modeltools
4663 (name "r-modeltools")
4668 (uri (cran-uri "modeltools" version))
4671 "1s9lmkac3rl0nknf4wizfhg7ryq7c8yvvyc4z619238br27hhsi5"))))
4672 (build-system r-build-system)
4673 (home-page "https://cran.r-project.org/web/packages/modeltools")
4674 (synopsis "Tools and classes for statistical models")
4676 "This package provides a collection of tools to deal with statistical
4677 models. The functionality is experimental and the user interface is likely
4678 to change in the future.")
4679 (license license:gpl2)))
4681 (define-public r-flexmix
4688 (uri (cran-uri "flexmix" version))
4691 "0sl4zxh1sb2sr5q7svjw9ihrm219jzn82yrc9d43q6r1b8bpyz43"))))
4692 (build-system r-build-system)
4694 `(("r-lattice" ,r-lattice)
4695 ("r-modeltools" ,r-modeltools)
4696 ("r-nnet" ,r-nnet)))
4697 (home-page "https://cran.r-project.org/web/packages/flexmix")
4698 (synopsis "Flexible mixture modeling")
4700 "This package implements a general framework for finite mixtures of
4701 regression models using the EM algorithm. FlexMix provides the E-step and
4702 all data handling, while the M-step can be supplied by the user to easily
4703 define new models. Existing drivers implement mixtures of standard linear
4704 models, generalized linear models and model-based clustering.")
4705 (license license:gpl2+)))
4707 (define-public r-mclust
4714 (uri (cran-uri "mclust" version))
4717 "09152swfpa3fzhmrq5cwb5kxgvrxvigv1m4v6rhcibrdhfd1x8x4"))))
4718 (build-system r-build-system)
4720 `(("gfortran" ,gfortran)))
4721 (home-page "http://www.stat.washington.edu/mclust/")
4722 (synopsis "Gaussian mixture modelling for model-based clustering etc.")
4724 "This package provides Gaussian finite mixture models fitted via EM
4725 algorithm for model-based clustering, classification, and density estimation,
4726 including Bayesian regularization, dimension reduction for visualisation,
4727 and resampling-based inference.")
4728 (license license:gpl2+)))
4730 (define-public r-prabclus
4737 (uri (cran-uri "prabclus" version))
4740 "0h2nml8ri27mhfs2p6ngb6kfd6lyq30sc6813yybpskkrb6gs1pb"))))
4741 (build-system r-build-system)
4743 `(("r-mass" ,r-mass)
4744 ("r-mclust" ,r-mclust)))
4745 (home-page "https://cran.r-project.org/web/packages/prabclus")
4746 (synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
4748 "This package provides distance-based parametric bootstrap tests for
4749 clustering with spatial neighborhood information. It implements some distance
4750 measures, clustering of presence-absence, abundance and multilocus genetical
4751 data for species delimitation, nearest neighbor based noise detection.")
4752 (license license:gpl2+)))
4754 (define-public r-deoptimr
4761 (uri (cran-uri "DEoptimR" version))
4764 "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
4765 (properties `((upstream-name . "DEoptimR")))
4766 (build-system r-build-system)
4767 (home-page "https://cran.r-project.org/web/packages/DEoptimR")
4768 (synopsis "Differential evolution optimization in pure R")
4770 "This package provides a differential evolution (DE) stochastic
4771 algorithms for global optimization of problems with and without constraints.
4772 The aim is to curate a collection of its state-of-the-art variants that (1) do
4773 not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
4774 can be efficiently implemented directly in the R language.")
4775 (license license:gpl2+)))
4777 (define-public r-robustbase
4779 (name "r-robustbase")
4784 (uri (cran-uri "robustbase" version))
4787 "1nqh1qg1qd1qrxl1w585dqx7ql55qzjny1r4f9hqxpwd7lml07cc"))))
4788 (build-system r-build-system)
4790 `(("gfortran" ,gfortran)))
4792 `(("r-deoptimr" ,r-deoptimr)))
4793 (home-page "http://robustbase.r-forge.r-project.org/")
4794 (synopsis "Basic robust statistics")
4796 "This packages allows to analyze data with robust methods such as
4797 regression methodology including model selections and multivariate statistics.")
4798 (license license:gpl2+)))
4800 (define-public r-pcapp
4807 (uri (cran-uri "pcaPP" version))
4810 "1z2kdf9gfp965xbcd4rg6vf20d1bl443na0qjkpq7gmzpaq6cifa"))))
4811 (properties `((upstream-name . "pcaPP")))
4812 (build-system r-build-system)
4814 `(("r-mvtnorm" ,r-mvtnorm)))
4815 (home-page "https://cran.r-project.org/web/packages/pcaPP")
4816 (synopsis "Robust PCA by projection pursuit")
4818 "This package provides functions for robust @dfn{principal component
4819 analysis} (PCA) by projection pursuit.")
4820 (license license:gpl3+)))
4822 (define-public r-rrcov
4829 (uri (cran-uri "rrcov" version))
4832 "14zjyqcdiqx6js99nx5s8hmyx564ixy2d8s6i7wa50xmx368rl6b"))))
4833 (build-system r-build-system)
4835 `(("r-cluster" ,r-cluster)
4836 ("r-lattice" ,r-lattice)
4837 ("r-mvtnorm" ,r-mvtnorm)
4838 ("r-pcapp" ,r-pcapp)
4839 ("r-robustbase" ,r-robustbase)))
4841 `(("gfortran" ,gfortran)))
4842 (home-page "https://cran.r-project.org/web/packages/rrcov")
4843 (synopsis "Scalable robust estimators with high breakdown Point")
4845 "This package provides an implementation of robust location and scatter
4846 estimation and robust multivariate analysis with high breakdown point.")
4847 (license license:gpl2+)))
4849 (define-public r-fit-models
4851 (name "r-fit-models")
4856 (uri (cran-uri "fit.models" version))
4859 "0vjbzmx0ambm6yzidb4vbgmhclwzwv2iz2cwl54ccdkvx4cx3fck"))))
4860 (properties `((upstream-name . "fit.models")))
4861 (build-system r-build-system)
4863 `(("r-lattice" ,r-lattice)))
4864 (home-page "https://cran.r-project.org/web/packages/fit.models")
4865 (synopsis "Compare fitted models")
4867 "The @code{fit.models} function and its associated methods (coefficients, print,
4868 summary, plot, etc.) were originally provided in the @code{robust} package to
4869 compare robustly and classically fitted model objects. The aim of the
4870 @code{fit.models} package is to separate this fitted model object comparison
4871 functionality from the robust package and to extend it to support fitting
4872 methods (e.g., classical, robust, Bayesian, regularized, etc.) more
4874 ;; Any version of the GPL
4875 (license (list license:gpl2+ license:gpl3+))))
4877 (define-public r-robust
4884 (uri (cran-uri "robust" version))
4887 "1b7qh1aff500nd6dh4y2ipmjgdiq8991shflb63pc39vpc0ny6g4"))))
4888 (build-system r-build-system)
4890 `(("r-fit-models" ,r-fit-models)
4891 ("r-lattice" ,r-lattice)
4893 ("r-robustbase" ,r-robustbase)
4894 ("r-rrcov" ,r-rrcov)))
4896 `(("gfortran" ,gfortran)))
4897 (home-page "https://cran.r-project.org/web/packages/robust")
4898 (synopsis "Port of the S+ \"Robust Library\"")
4900 "This package is a port of the S+ \"Robust Library\". It provides
4901 methods for robust statistics, notably for robust regression and robust
4902 multivariate analysis.")
4903 (license license:gpl2)))
4905 (define-public r-trimcluster
4907 (name "r-trimcluster")
4912 (uri (cran-uri "trimcluster" version))
4915 "0013bpyq6mkvjn38qsmwnsxfiwxgwngnqxycxvgpgmiadhm8fjmn"))))
4916 (build-system r-build-system)
4917 (home-page "https://cran.r-project.org/web/packages/trimcluster")
4918 (synopsis "Cluster analysis with trimming")
4920 "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
4921 Matran (1997). This optimizes the k-means criterion under trimming a portion
4924 (license (list license:gpl2+ license:gpl3+))))
4926 (define-public r-fpc
4929 (version "2.1-11.1")
4933 (uri (cran-uri "fpc" version))
4936 "1ari57hkgqsxh6khr6j52cfrzc0096cnn1q7ghxk2z4brdd4rznc"))))
4937 (build-system r-build-system)
4939 `(("r-class" ,r-class)
4940 ("r-cluster" ,r-cluster)
4941 ("r-diptest" ,r-diptest)
4942 ("r-flexmix" ,r-flexmix)
4943 ("r-kernlab" ,r-kernlab)
4945 ("r-mclust" ,r-mclust)
4946 ("r-mvtnorm" ,r-mvtnorm)
4947 ("r-prabclus" ,r-prabclus)
4948 ("r-robustbase" ,r-robustbase)
4949 ("r-trimcluster" ,r-trimcluster)))
4950 (home-page "https://cran.r-project.org/web/packages/fpc")
4951 (synopsis "Flexible procedures for clustering")
4953 "This package provides various methods for clustering and cluster validation.
4954 For example, it provides fixed point clustering, linear regression clustering,
4955 clustering by merging Gaussian mixture components, as well as symmetric and
4956 asymmetric discriminant projections for visualisation of the separation of
4958 (license license:gpl2+)))
4960 (define-public r-vgam
4967 (uri (cran-uri "VGAM" version))
4970 "1fg31xz86jblqraifiy3q36d0hjqnll01jxx85xq87j1cyhj060j"))))
4971 (properties `((upstream-name . "VGAM")))
4972 (build-system r-build-system)
4974 `(("gfortran" ,gfortran)))
4975 (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
4976 (synopsis "Vector generalized linear and additive models")
4978 "This package is an implementation of about 6 major classes of statistical
4979 regression models. Currently only fixed-effects models are implemented, i.e.,
4980 no random-effects models. Many (150+) models and distributions are estimated
4981 by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
4982 VGLMs can be loosely thought of as multivariate generalised linear models.")
4983 (license license:gpl2+)))
4985 (define-public r-pbapply
4992 (uri (cran-uri "pbapply" version))
4995 "0lk5kxac09xzdv6vf7ix6r5bfrm7cnpyr2l5mkd4igpciadszzfd"))))
4996 (build-system r-build-system)
4997 (home-page "https://github.com/psolymos/pbapply")
4998 (synopsis "Adding progress bar to apply functions")
5000 "This lightweight package that adds progress bar to vectorized R
5001 functions apply. The implementation can easily be added to functions where
5002 showing the progress is useful e.g. bootstrap.")
5003 (license license:gpl2)))
5005 (define-public r-minqa
5012 (uri (cran-uri "minqa" version))
5015 "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
5016 (build-system r-build-system)
5018 `(("r-rcpp" ,r-rcpp)))
5020 `(("gfortran" ,gfortran)))
5021 (home-page "http://optimizer.r-forge.r-project.org")
5022 (synopsis "Derivative-free optimization algorithms by quadratic approximation")
5024 "This package provides a derivative-free optimization by quadratic approximation
5025 based on an interface to Fortran implementations by M. J. D. Powell.")
5026 (license license:gpl2)))
5028 (define-public r-rcppeigen
5030 (name "r-rcppeigen")
5031 (version "0.3.3.5.0")
5035 (uri (cran-uri "RcppEigen" version))
5038 "01bz41c29591ybzqn4z88ss036ai3anh9figryvmfpqcfwbszip5"))))
5039 (properties `((upstream-name . "RcppEigen")))
5040 (build-system r-build-system)
5042 `(("r-rcpp" ,r-rcpp)
5043 ("r-matrix" ,r-matrix)))
5044 (home-page "http://eigen.tuxfamily.org")
5045 (synopsis "Rcpp integration for the Eigen templated linear algebra library")
5047 "This package provides an integration of Eigen in R using a C++ template
5048 library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
5049 It supports dense and sparse matrices on integer, floating point and complex numbers,
5050 decompositions of such matrices, and solutions of linear systems.")
5051 (license license:gpl2+)))
5053 (define-public r-modelmetrics
5055 (name "r-modelmetrics")
5060 (uri (cran-uri "ModelMetrics" version))
5063 "158ddbw2snlyzd2q6mdaif5i67kq4qfvadylwjxgv1w2cmszrmk6"))))
5064 (properties `((upstream-name . "ModelMetrics")))
5065 (build-system r-build-system)
5067 `(("r-rcpp" ,r-rcpp)
5068 ("r-data-table" ,r-data-table)))
5069 (home-page "https://cran.r-project.org/web/packages/ModelMetrics")
5070 (synopsis "Rapid calculation of model metrics")
5072 "Written in C++ using @code{Rcpp}, this package provides a collection of
5073 metrics for evaluating models.")
5074 (license license:gpl2+)))
5076 (define-public r-matrixmodels
5078 (name "r-matrixmodels")
5083 (uri (cran-uri "MatrixModels" version))
5086 "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
5087 (properties `((upstream-name . "MatrixModels")))
5088 (build-system r-build-system)
5090 `(("r-matrix" ,r-matrix)))
5091 (home-page "https://cran.r-project.org/web/packages/MatrixModels")
5092 (synopsis "Modelling with sparse and dense matrices")
5094 "This package models with sparse and dense matrix matrices,
5095 using modular prediction and response module classes.")
5096 (license license:gpl2+)))
5098 (define-public r-quantreg
5105 (uri (cran-uri "quantreg" version))
5108 "1vvvnk291f0dccg04l3nsnk585gq75sk0b2vdbrqv3lczvv18nw1"))))
5109 (build-system r-build-system)
5111 `(("gfortran" ,gfortran)))
5113 `(("r-matrix" ,r-matrix)
5114 ("r-matrixmodels" ,r-matrixmodels)
5115 ("r-sparsem" ,r-sparsem)))
5116 (home-page "https://www.r-project.org")
5117 (synopsis "Quantile regression")
5119 "This package provides an estimation and inference methods for models
5120 of conditional quantiles: linear and nonlinear parametric and non-parametric
5121 models for conditional quantiles of a univariate response and several methods
5122 for handling censored survival data. Portfolio selection methods based on
5123 expected shortfall risk are also included.")
5124 (license license:gpl2+)))
5126 (define-public r-nloptr
5133 (uri (cran-uri "nloptr" version))
5136 "15yz60kljxwnhm2m3gryjzxl3ynhkhd5jiwc179b1hz6rlzf71hz"))))
5137 (build-system r-build-system)
5139 `(("r-knitr" ,r-knitr) ; for building vignettes
5140 ("pkg-config" ,pkg-config)
5141 ("gfortran" ,gfortran)))
5143 `(("nlopt" ,nlopt)))
5144 (home-page "https://cran.r-project.org/web/packages/nloptr")
5145 (synopsis "R interface to NLopt")
5147 "This package is interface to NLopt, a library for nonlinear
5148 optimization. NLopt is a library for nonlinear optimization, providing a
5149 common interface for a number of different free optimization routines
5150 available online as well as original implementations of various other
5152 (license license:lgpl3)))
5154 (define-public r-lme4
5161 (uri (cran-uri "lme4" version))
5164 "0j8xhkkcdv45ilab960s9jrcjk6jbzvd7w7myswv5fmalrpq52pf"))))
5165 (build-system r-build-system)
5167 `(("r-rcpp" ,r-rcpp)
5168 ("r-rcppeigen" ,r-rcppeigen)))
5170 `(("r-lattice" ,r-lattice)
5171 ("r-matrix" ,r-matrix)
5172 ("r-minqa" ,r-minqa)
5173 ("r-nloptr" ,r-nloptr)
5175 ("r-nlme" ,r-nlme)))
5176 (home-page "https://cran.r-project.org/web/packages/lme4")
5177 (synopsis "Linear mixed-effects models using eigen and S4")
5179 "This package provides fit linear and generalized linear mixed-effects
5180 models. The models and their components are represented using S4 classes and
5181 methods. The core computational algorithms are implemented using the Eigen
5182 C++ library for numerical linear algebra and RcppEigen glue.")
5183 (license license:gpl2+)))
5185 (define-public r-pbkrtest
5192 (uri (cran-uri "pbkrtest" version))
5195 "1si3bhi59xc51a0pgjjglccq3h4aljyhw2k1b8574s145fnh7fsw"))))
5196 (build-system r-build-system)
5198 `(("r-lme4" ,r-lme4)
5200 ("r-matrix" ,r-matrix)))
5201 (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
5202 (synopsis "Methods for linear mixed model comparison")
5204 "This package implements a parametric bootstrap test and a Kenward Roger
5205 modification of F-tests for linear mixed effects models and a parametric
5206 bootstrap test for generalized linear mixed models.")
5207 (license license:gpl2+)))
5209 (define-public r-cardata
5216 (uri (cran-uri "carData" version))
5219 "152lfgaspgx6x2wzdb5p3zv6r87a0d2pg10h6fjmdr613kzlwp1v"))))
5220 (properties `((upstream-name . "carData")))
5221 (build-system r-build-system)
5222 (home-page "https://r-forge.r-project.org/projects/car/")
5223 (synopsis "Data Sets for the book Companion to Applied Regression")
5225 "This package provides datasets to accompany J. Fox and S. Weisberg, An R
5226 Companion to Applied Regression, Third Edition, Sage.")
5227 (license license:gpl2+)))
5229 (define-public r-car
5236 (uri (cran-uri "car" version))
5239 "0l3wyc9ia0ypcbap2p39slazfpbl84mjzydqvpsywrzdiyxajnfz"))))
5240 (build-system r-build-system)
5242 `(("r-abind" ,r-abind)
5243 ("r-cardata" ,r-cardata)
5245 ("r-maptools" ,r-maptools)
5250 ("r-pbkrtest" ,r-pbkrtest)
5251 ("r-quantreg" ,r-quantreg)
5253 (home-page "https://r-forge.r-project.org/projects/car/")
5254 (synopsis "Companion to applied regression")
5256 "This package provides functions and datasets from book Companion
5257 to Applied regression, Second Edition, Sage, 2011.")
5258 (license license:gpl2+)))
5260 (define-public r-caret
5267 (uri (cran-uri "caret" version))
5270 "1fibrskjzq2f06b8gbrfp3263svfc5s5apsjwaqdg9qzs7sy7fpc"))))
5271 (build-system r-build-system)
5273 `(("r-foreach" ,r-foreach)
5274 ("r-ggplot2" ,r-ggplot2)
5275 ("r-lattice" ,r-lattice)
5276 ("r-modelmetrics" ,r-modelmetrics)
5279 ("r-recipes" ,r-recipes)
5280 ("r-reshape2" ,r-reshape2)
5281 ("r-withr" ,r-withr)))
5282 (home-page "https://github.com/topepo/caret")
5283 (synopsis "Classification and regression training")
5285 "This package provides misc functions for training and plotting
5286 classification and regression models.")
5287 (license license:gpl2+)))
5289 (define-public r-rcppprogress
5291 (name "r-rcppprogress")
5296 (uri (cran-uri "RcppProgress" version))
5299 "0yk01hfv961zyp569682k9igvhnwqyg5j0n5fm63sxigj82l2xhi"))))
5300 (properties `((upstream-name . "RcppProgress")))
5301 (build-system r-build-system)
5303 `(("r-devtools" ,r-devtools)
5304 ("r-rcpp" ,r-rcpp)))
5305 (home-page "https://github.com/kforner/rcpp_progress")
5306 (synopsis "Interruptible progress bar for C++ in R packages")
5308 "This package allows to display a progress bar in the R console for long running
5309 computations taking place in C++ code, and support for interrupting those computations
5310 even in multithreaded code, typically using OpenMP.")
5311 (license license:gpl3+)))
5313 (define-public r-mnormt
5320 (uri (cran-uri "mnormt" version))
5323 "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z"))))
5324 (build-system r-build-system)
5326 `(("gfortran" ,gfortran)))
5327 (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
5328 (synopsis "Multivariate normal and \"t\" distributions")
5330 "This package provides functions for computing the density and the
5331 distribution function of multivariate normal and \"t\" random variables, and
5332 for generating random vectors sampled from these distributions. Probabilities
5333 are computed via non-Monte Carlo methods.")
5334 (license license:gpl2+)))
5336 (define-public r-numderiv
5339 (version "2016.8-1")
5343 (uri (cran-uri "numDeriv" version))
5346 "07ni52rwiap4wilfz94w5mrqaxr59axxmgn57857ip4p6qkiss0v"))))
5347 (properties `((upstream-name . "numDeriv")))
5348 (build-system r-build-system)
5349 (home-page "https://cran.r-project.org/web/packages/numDeriv")
5350 (synopsis "Accurate numerical derivatives")
5352 "This package provides methods for calculating accurate numerical
5353 first and second order derivatives.")
5354 (license license:gpl2)))
5363 (uri (cran-uri "sn" version))
5366 "10via4lg0vx9pzq350vwhz5wv1dhzxr2l3r6jq99nk37vmyvj8fc"))))
5367 (build-system r-build-system)
5369 `(("r-mnormt" ,r-mnormt)
5370 ("r-numderiv" ,r-numderiv)))
5371 (home-page "http://azzalini.stat.unipd.it/SN")
5372 (synopsis "The skew-normal and skew-t distributions")
5374 "This packages provides functionalities to build and manipulate
5375 probability distributions of the skew-normal family and some related
5376 ones, notably the skew-t family, and provides related statistical
5377 methods for data fitting and diagnostics, in the univariate and the
5378 multivariate case.")
5379 (license license:gpl2+)))
5381 (define-public r-tclust
5388 (uri (cran-uri "tclust" version))
5391 "17md6l9v9dl9b72l84df01b52h2xiynbcjm437mv9mzcr09fc2sb"))))
5392 (build-system r-build-system)
5393 ;; These are all suggested packages, not build dependencies.
5395 `(("r-cluster" ,r-cluster)
5396 ("r-mclust" ,r-mclust)
5397 ("r-mvtnorm" ,r-mvtnorm)
5399 (home-page "https://cran.r-project.org/web/packages/tclust")
5400 (synopsis "Robust trimmed clustering")
5402 "This package implements different robust clustering
5403 algorithms (@code{tclust}) based on trimming and including some graphical
5404 diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
5405 (license license:gpl3)))
5407 (define-public r-ranger
5414 (uri (cran-uri "ranger" version))
5417 "1yyg1nppq76jngzffd44brppqrlxqdhv92pyy0gn09rfc0ab37wr"))))
5418 (build-system r-build-system)
5420 `(("r-rcpp" ,r-rcpp)
5421 ("r-matrix" ,r-matrix)
5422 ("r-rcppeigen" ,r-rcppeigen)))
5423 (home-page "https://github.com/imbs-hl/ranger")
5424 (synopsis "Fast implementation of random forests")
5426 "This package provides a fast implementation of Random Forests,
5427 particularly suited for high dimensional data. Ensembles of classification,
5428 regression, survival and probability prediction trees are supported. Data from
5429 genome-wide association studies can be analyzed efficiently.")
5430 (license license:gpl3)))
5432 (define-public r-tsne
5439 (uri (cran-uri "tsne" version))
5442 "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
5443 (build-system r-build-system)
5444 (home-page "https://github.com/jdonaldson/rtsne/")
5445 (synopsis "t-Distributed Stochastic Neighbor Embedding for R")
5447 "This package provides a pure R implementation of the t-SNE algorithm.")
5448 (license license:gpl2+)))
5450 (define-public r-cairo
5457 (uri (cran-uri "Cairo" version))
5460 "1x1q99r3r978rlkkm5gixkv03p0mcr6k7ydcqdmisrwnmrn7p1ia"))))
5461 (properties `((upstream-name . "Cairo")))
5462 (build-system r-build-system)
5467 `(("pkg-config" ,pkg-config)))
5468 (home-page "http://www.rforge.net/Cairo/")
5469 (synopsis "R graphics device using Cairo graphics library")
5471 "This package provides a Cairo graphics device that can be use to
5472 create high-quality vector (PDF, PostScript and SVG) and bitmap
5473 output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11
5474 and Win32). Since it uses the same back-end for all output, copying
5475 across formats is WYSIWYG. Files are created without the dependence
5476 on X11 or other external programs. This device supports alpha
5477 channel (semi-transparent drawing) and resulting images can contain
5478 transparent and semi-transparent regions. It is ideal for use in
5479 server environments (file output) and as a replacement for other
5480 devices that don't have Cairo's capabilities such as alpha support or
5481 anti-aliasing. Backends are modular such that any subset of backends
5483 (license license:gpl2)))
5485 (define-public r-lubridate
5487 (name "r-lubridate")
5492 (uri (cran-uri "lubridate" version))
5495 "14a823il77w3wmmnzr89vwrqp50y56dh5raycnaw6c8nv5xsh32i"))))
5496 (build-system r-build-system)
5498 `(("r-rcpp" ,r-rcpp)
5499 ("r-stringr" ,r-stringr)))
5501 "https://cran.r-project.org/web/packages/lubridate")
5502 (synopsis "Make dealing with dates a little easier")
5504 "This package provides functions to work with date-times and time-spans:
5505 fast and user friendly parsing of date-time data, extraction and updating of
5506 components of a date-time (years, months, days, hours, minutes, and seconds),
5507 algebraic manipulation on date-time and time-span objects. The 'lubridate'
5508 package has a consistent and memorable syntax that makes working with dates
5510 (license license:gpl2)))
5512 (define-public r-fdrtool
5519 (uri (cran-uri "fdrtool" version))
5522 "1h46frlk7d9f4qx0bg6p55nrm9wwwz2sv6d1nz7061wdfsm69yb5"))))
5523 (build-system r-build-system)
5524 (home-page "http://strimmerlab.org/software/fdrtool/")
5525 (synopsis "Estimation of false discovery rates and higher criticism")
5527 "This package provides tools to estimate tail area-based false discovery
5528 rates as well as local false discovery rates for a variety of null
5529 models (p-values, z-scores, correlation coefficients, t-scores). The
5530 proportion of null values and the parameters of the null distribution are
5531 adaptively estimated from the data. In addition, the package contains
5532 functions for non-parametric density estimation (Grenander estimator), for
5533 monotone regression (isotonic regression and antitonic regression with
5534 weights), for computing the @dfn{greatest convex minorant} (GCM) and the
5535 @dfn{least concave majorant} (LCM), for the half-normal and correlation
5536 distributions, and for computing empirical @dfn{higher criticism} (HC) scores
5537 and the corresponding decision threshold.")
5538 (license license:gpl3+)))
5540 (define-public r-forcats
5547 (uri (cran-uri "forcats" version))
5550 "0mxn1hng43zdjh1v8shd80hrszrqahcpaqxs1s1sif0qxh84d0cm"))))
5551 (build-system r-build-system)
5553 `(("r-magrittr" ,r-magrittr)
5554 ("r-tibble" ,r-tibble)
5555 ("r-rlang" ,r-rlang)))
5556 (home-page "http://forcats.tidyverse.org")
5557 (synopsis "Tools for working with factors")
5558 (description "This package provides helpers for reordering factor
5559 levels (including moving specified levels to front, ordering by first
5560 appearance, reversing, and randomly shuffling), and tools for modifying factor
5561 levels (including collapsing rare levels into other, \"anonymizing\", and
5562 manually \"recoding\").")
5563 (license license:gpl3)))
5565 (define-public r-tgstat
5566 (let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f")
5570 (version (string-append "1.0.2-" revision "." (string-take changeset 7)))
5575 (url "https://bitbucket.org/tanaylab/tgstat")
5576 (changeset changeset)))
5577 (file-name (string-append name "-" version "-checkout"))
5580 "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
5581 (build-system r-build-system)
5584 (modify-phases %standard-phases
5585 (add-after 'unpack 'fix-isnan
5587 (substitute* "src/tgstat.h"
5588 (("#define isnan ::isnan")
5589 "#define isnan std::isnan"))
5592 `(("r-rcpp" ,r-rcpp)))
5593 (home-page "https://bitbucket.org/tanaylab/tgstat/")
5594 (synopsis "Tanay's group statistical utilities")
5596 "The goal of tgstat is to provide fast and efficient statistical
5598 (license license:gpl2))))
5600 (define-public r-tgconfig
5601 (let ((changeset "1e02c7614713bd0866c46f0c679a058f8c6d627e")
5605 (version (string-append "0.0.0.9000-" revision "." (string-take changeset 7)))
5610 (url "https://bitbucket.org/tanaylab/tgconfig")
5611 (changeset changeset)))
5612 (file-name (string-append name "-" version "-checkout"))
5615 "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
5616 (build-system r-build-system)
5618 `(("r-yaml" ,r-yaml)))
5619 (home-page "https://bitbucket.org/tanaylab/tgconfig/")
5620 (synopsis "Infrastructure for managing package parameters")
5622 "The goal of tgconfig is to provide infrastructure for managing package
5624 (license license:gpl3))))
5626 (define-public r-directlabels
5628 (name "r-directlabels")
5629 (version "2018.05.22")
5633 (uri (cran-uri "directlabels" version))
5636 "0xcpc56ssb9430b0xcdhayk3qaak2qcakyss2pz14y5w2027hblv"))))
5637 (build-system r-build-system)
5639 `(("r-quadprog" ,r-quadprog)))
5640 (home-page "http://directlabels.r-forge.r-project.org/")
5641 (synopsis "Direct labels for multicolor plots")
5643 "This package provides an extensible framework for automatically placing
5644 direct labels onto multicolor plots. Label positions are described using
5645 positioning methods that can be re-used across several different plots. There
5646 are heuristics for examining @code{trellis} and @code{ggplot} objects and
5647 inferring an appropriate positioning method.")
5648 (license license:gpl3)))
5650 (define-public r-catterplots
5651 (let ((commit "40063ec57f9515d231508f135ca0ec769614efb9")
5654 (name "r-catterplots")
5655 (version (string-append "0-" revision "." (string-take commit 9)))
5659 (url "https://github.com/Gibbsdavidl/CatterPlots.git")
5661 (file-name (string-append name "-" version "-checkout"))
5664 "1wl80pgbz8d9kfpffvkh439hlgz2qldm9m75wqjfrgrg8lcjzrxg"))))
5665 (build-system r-build-system)
5667 `(("r-png" ,r-png)))
5668 (home-page "https://github.com/Gibbsdavidl/CatterPlots")
5669 (synopsis "Scatter plots with cat shaped points")
5670 (description "Did you ever wish you could make scatter plots with cat
5671 shaped points? Now you can!")
5672 (license license:asl2.0))))
5674 (define-public r-colorout
5681 (uri (string-append "https://github.com/jalvesaq/colorout/archive/"
5682 "v" version ".tar.gz"))
5683 (file-name (string-append name "-" version ".tar.gz"))
5686 "07vqx5ihgnq4dzn5jnfjfhdm3957v4prvf8vhnb3cwvlly4l7p9v"))))
5687 (build-system r-build-system)
5688 (home-page "https://github.com/jalvesaq/colorout")
5689 (synopsis "Colorize output in the R REPL")
5690 (description "@code{colorout} is an R package that colorizes R output when
5691 running in terminal emulator.
5693 R STDOUT is parsed and numbers, negative numbers, dates in the standard
5694 format, strings, and R constants are identified and wrapped by special ANSI
5695 scape codes that are interpreted by terminal emulators as commands to colorize
5696 the output. R STDERR is also parsed to identify the expressions warning and
5697 error and their translations to many languages. If these expressions are
5698 found, the output is colorized accordingly; otherwise, it is colorized as
5699 STDERROR (blue, by default).
5701 You can customize the colors according to your taste, guided by the color
5702 table made by the command @code{show256Colors()}. You can also set the colors
5703 to any arbitrary string. In this case, it is up to you to set valid values.")
5704 (license license:gpl3+)))
5706 (define-public r-txtplot
5713 (uri (cran-uri "txtplot" version))
5716 "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h"))))
5717 (build-system r-build-system)
5718 (home-page "https://cran.r-project.org/web/packages/txtplot/")
5719 (synopsis "Text-based plotting")
5720 (description "This package provides functions to produce rudimentary ASCII
5721 graphics directly in the terminal window. This package provides a basic
5722 plotting function (and equivalents of curve, density, acf and barplot) as well
5723 as a boxplot function.")
5724 (license license:lgpl3+)))
5726 (define-public python-rpy2
5728 (name "python-rpy2")
5733 (uri (pypi-uri "rpy2" version))
5736 "0bl1d2qhavmlrvalir9hmkjh74w21vzkvc2sg3cbb162s10zfmxy"))))
5737 (build-system python-build-system)
5739 '(#:modules ((ice-9 ftw)
5743 (guix build python-build-system))
5745 (modify-phases %standard-phases
5747 (lambda* (#:key outputs inputs #:allow-other-keys)
5748 (let ((cwd (getcwd)))
5749 (setenv "PYTHONPATH"
5750 (string-append cwd "/build/"
5751 (find (cut string-prefix? "lib" <>)
5752 (scandir (string-append cwd "/build")))
5754 (getenv "PYTHONPATH"))))
5755 (invoke "python" "-m" "rpy2.tests" "-v"))))))
5757 `(("python-six" ,python-six)
5758 ("python-jinja2" ,python-jinja2)
5759 ("python-pytz" ,python-pytz)))
5761 `(("readline" ,readline)
5764 ("r-minimal" ,r-minimal)
5765 ("r-survival" ,r-survival)
5766 ("r-ggplot2" ,r-ggplot2)
5767 ("r-rsqlite" ,r-rsqlite)
5768 ("r-dplyr" ,r-dplyr)
5769 ("r-dbplyr" ,r-dbplyr)
5770 ("python-numpy" ,python-numpy)))
5773 (home-page "https://rpy2.bitbucket.io/")
5774 (synopsis "Python interface to the R language")
5775 (description "rpy2 is a redesign and rewrite of rpy. It is providing a
5776 low-level interface to R from Python, a proposed high-level interface,
5777 including wrappers to graphical libraries, as well as R-like structures and
5779 ;; Any of these licenses can be picked for the R interface. The whole
5780 ;; project is released under GPLv2+ according to the license declaration
5782 (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+))))
5784 (define-public java-jdistlib
5786 (name "java-jdistlib")
5790 (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
5791 version "-src.jar"))
5794 "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
5795 (build-system ant-build-system)
5797 `(#:jar-name "jdistlib.jar"
5799 #:tests? #f ; no dedicated test directory
5801 (modify-phases %standard-phases
5802 (add-after 'unpack 'fix-broken-encoding
5804 (with-fluids ((%default-port-encoding "ISO-8859-1"))
5805 (substitute* "src/jdistlib/Beta.java"
5806 (("Scheff.+-Tukey") "Scheffe-Tukey")))
5809 `(("java-jtransforms" ,java-jtransforms)))
5811 `(("java-junit" ,java-junit)))
5812 (home-page "http://jdistlib.sourceforge.net/")
5813 (synopsis "Java library of statistical distributions")
5814 (description "JDistlib is the Java Statistical Distribution Library, a
5815 Java package that provides routines for various statistical distributions.")
5816 ;; The files that were translated from R code are under GPLv2+; some files
5817 ;; are under the GPLv3, which is a mistake. The author confirmed in an
5818 ;; email that this whole project should be under GPLv2+.
5819 (license license:gpl2+)))
5821 (define-public emacs-ess
5827 (uri (string-append "https://github.com/emacs-ess/ESS/archive/v"
5831 "0cbilbsiwvcyf6d5y24mymp57m3ana5dkzab3knfs83w4a3a4c5c"))
5832 (file-name (string-append name "-" version ".tar.gz"))
5833 (modules '((guix build utils)))
5836 ;; Stop ESS from trying to bundle an external julia-mode.el.
5837 (substitute* "lisp/Makefile"
5838 (("^\tjulia-mode.elc\\\\\n") "")
5839 (("^dist: all julia-mode.el")
5841 ;; No need to build docs in so many formats. Also, skipping
5842 ;; pdf lets us not pull in texlive.
5843 (substitute* "doc/Makefile"
5844 (("all : info text html pdf")
5846 (("install: install-info install-other-docs")
5847 "install: install-info"))
5848 ;; Test fails upstream
5849 (substitute* "test/ess-r-tests.el"
5850 (("ert-deftest ess-r-namespaced-eval-no-srcref-in-errors ()")
5851 "ert-deftest ess-r-namespaced-eval-no-srcref-in-errors () :expected-result :failed"))
5853 (build-system gnu-build-system)
5855 (let ((base-directory "/share/emacs/site-lisp/guix.d/ess"))
5856 `(#:make-flags (list (string-append "PREFIX=" %output)
5857 (string-append "ETCDIR=" %output "/"
5858 ,base-directory "/etc")
5859 (string-append "LISPDIR=" %output "/"
5862 (modify-phases %standard-phases
5864 (add-before 'build 'more-shebang-patching
5865 (lambda* (#:key inputs #:allow-other-keys)
5866 (substitute* "Makeconf"
5867 (("SHELL = /bin/sh")
5868 (string-append "SHELL = " (which "sh"))))
5872 (invoke "make" "test")))))))
5874 `(("emacs" ,emacs-minimal)
5875 ("r-minimal" ,r-minimal)))
5878 ("texinfo" ,texinfo)))
5880 `(("emacs-julia-mode" ,emacs-julia-mode)))
5881 (home-page "https://ess.r-project.org/")
5882 (synopsis "Emacs mode for statistical analysis programs")
5883 (description "Emacs Speaks Statistics (ESS) is an add-on package for GNU
5884 Emacs. It is designed to support editing of scripts and interaction with
5885 various statistical analysis programs such as R, Julia, and JAGS.")
5886 (license license:gpl2+)))