1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com>
4 ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
5 ;;; Copyright © 2016, 2017, 2019 Efraim Flashner <efraim@flashner.co.il>
6 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
7 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
8 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
9 ;;; Copyright © 2016, 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
10 ;;; Copyright © 2017 Kyle Meyer <kyle@kyleam.com>
11 ;;; Copyright © 2017, 2018, 2019 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 sphinx)
70 #:use-module (gnu packages ssh)
71 #:use-module (gnu packages tcl)
72 #:use-module (gnu packages tex)
73 #:use-module (gnu packages texinfo)
74 #:use-module (gnu packages time)
75 #:use-module (gnu packages tls)
76 #:use-module (gnu packages base)
77 #:use-module (gnu packages web)
78 #:use-module (gnu packages xml)
79 #:use-module (gnu packages xorg)
80 #:use-module (srfi srfi-1))
90 (uri (string-append "mirror://gnu/pspp/pspp-"
94 "07pp27zycrb5x927jwaj9r3q7hy915jh51xs85zxby6gfiwl63m5"))))
95 (build-system gnu-build-system)
98 ("gettext" ,gettext-minimal)
102 ("readline" ,readline)
104 ("gtksourceview" ,gtksourceview)
105 ("spread-sheet-widget" ,spread-sheet-widget)
108 `(("autoconf" ,autoconf) ;for tests
109 ("glib" ,glib "bin") ;for glib-genmarshal
111 ("pkg-config" ,pkg-config)
112 ("python" ,python-2) ;for tests
113 ("texinfo" ,texinfo)))
114 (home-page "https://www.gnu.org/software/pspp/")
115 (synopsis "Statistical analysis")
117 "GNU PSPP is a statistical analysis program. It can perform
118 descriptive statistics, T-tests, linear regression and non-parametric tests.
119 It features both a graphical interface as well as command-line input. PSPP
120 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
121 can be imported from spreadsheets, text files and database sources and it can
122 be output in text, PostScript, PDF or HTML.")
123 (license license:gpl3+)))
131 (uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/"
132 (version-major version) ".x/Source/"
133 "JAGS-" version ".tar.gz"))
136 "1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica"))))
137 (build-system gnu-build-system)
138 (home-page "http://mcmc-jags.sourceforge.net/")
140 `(("gfortran" ,gfortran)
142 (synopsis "Gibbs sampler")
143 (description "JAGS is Just Another Gibbs Sampler. It is a program for
144 analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
145 simulation not wholly unlike BUGS. JAGS was written with three aims in mind:
148 @item To have a cross-platform engine for the BUGS language;
149 @item To be extensible, allowing users to write their own functions,
150 distributions and samplers;
151 @item To be a platform for experimentation with ideas in Bayesian modelling.
153 (license license:gpl2)))
155 (define-public libxls
162 (uri (string-append "https://github.com/libxls/libxls/releases/download/"
163 "v" version "/libxls-" version ".tar.gz"))
165 (base32 "00j2lrcvvhclmh3z9vy7myqq1br1jnnqkz2wzgk4a1gbg8c5afn5"))))
166 (build-system gnu-build-system)
167 (home-page "https://github.com/libxls/libxls")
168 (synopsis "Read binary (.xls) Excel spreadsheet files")
170 "libxls is a C library to read .xls spreadsheet files in the binary OLE
171 BIFF8 format as created by Excel 97 and later versions. It cannot write them.
173 This package also provides @command{xls2csv} to export Excel files to CSV.")
174 (license license:bsd-2)))
176 ;; Update this package together with the set of recommended packages: r-boot,
177 ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
178 ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
181 (name "r-with-tests")
185 (uri (string-append "mirror://cran/src/base/R-"
186 (version-major version) "/R-"
190 "02bmylmzrm9sdidirmwy233lghmd2346z725ca71ari68lzarz1n"))))
191 (build-system gnu-build-system)
193 `(#:disallowed-references (,tzdata-for-tests)
195 (list (string-append "LDFLAGS=-Wl,-rpath="
196 (assoc-ref %outputs "out")
198 ;; This affects the embedded timestamp of only the core packages.
199 "PKG_BUILT_STAMP=1970-01-01")
201 (modify-phases %standard-phases
202 (add-before 'configure 'do-not-compress-serialized-files
203 (lambda* (#:key inputs #:allow-other-keys)
204 ;; This ensures that Guix can detect embedded store references;
205 ;; see bug #28157 for details.
206 (substitute* "src/library/base/makebasedb.R"
207 (("compress = TRUE") "compress = FALSE"))
209 (add-before 'configure 'patch-uname
210 (lambda* (#:key inputs #:allow-other-keys)
211 (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
213 (substitute* "src/scripts/R.sh.in"
214 (("uname") uname-bin)))
216 (add-after 'unpack 'build-reproducibly
218 ;; The documentation contains time stamps to demonstrate
219 ;; documentation generation in different phases.
220 (substitute* "src/library/tools/man/Rd2HTML.Rd"
221 (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
222 "(removed for reproducibility)"))
224 ;; Remove timestamp from tracing environment. This fixes
225 ;; reproducibility of "methods.rd{b,x}".
226 (substitute* "src/library/methods/R/trace.R"
227 (("dateCreated = Sys.time\\(\\)")
228 "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
230 ;; Ensure that gzipped files are reproducible.
231 (substitute* '("src/library/grDevices/Makefile.in"
232 "doc/manual/Makefile.in")
233 (("R_GZIPCMD\\)" line)
234 (string-append line " -n")))
236 ;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
237 ;; queries the mtime of a given file and records it in an object.
238 ;; This is acceptable at runtime to detect stale source files,
239 ;; but it destroys reproducibility at build time.
241 ;; Similarly, the "srcfilecopy" procedure records the current
242 ;; time. We change both of them to respect SOURCE_DATE_EPOCH.
243 (substitute* "src/library/base/R/srcfile.R"
244 (("timestamp <- (timestamp.*|file.mtime.*)" _ time)
245 (string-append "timestamp <- \
246 as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
247 as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
248 } else { " time "}, origin=\"1970-01-01\")\n")))
250 ;; This library is installed using "install_package_description",
251 ;; so we need to pass the "builtStamp" argument.
252 (substitute* "src/library/tools/Makefile.in"
253 (("(install_package_description\\(.*\"')\\)\"" line prefix)
254 (string-append prefix ", builtStamp='1970-01-01')\"")))
256 (substitute* "src/library/Recommended/Makefile.in"
257 (("INSTALL_OPTS =" m)
258 (string-append m " --built-timestamp=1970-01-01" m)))
260 ;; R bundles an older version of help2man, which does not respect
261 ;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man,
262 ;; because that breaks a test.
263 (with-fluids ((%default-port-encoding "ISO-8859-1"))
264 (substitute* "tools/help2man.pl"
265 (("my \\$date = strftime \"%B %Y\", localtime" line)
266 (string-append line " 1"))))
268 (add-before 'configure 'set-default-pager
269 ;; Set default pager to "cat", because otherwise it is "false",
270 ;; making "help()" print nothing at all.
271 (lambda _ (setenv "PAGER" "cat") #t))
272 (add-before 'check 'set-timezone
273 ;; Some tests require the timezone to be set. However, the
274 ;; timezone may not just be "UTC", or else a brittle regression
275 ;; test in reg-tests-1d will fail.
276 (lambda* (#:key inputs #:allow-other-keys)
277 (setenv "TZ" "UTC+1")
279 (string-append (assoc-ref inputs "tzdata")
282 (add-after 'build 'make-info
283 (lambda _ (invoke "make" "info")))
284 (add-after 'build 'install-info
285 (lambda _ (invoke "make" "install-info"))))
287 `(;; We build the recommended packages here, because they are needed in
288 ;; order to run the test suite. We disable them in the r-minimal
291 "--with-blas=-lopenblas"
297 ,(string-append "--with-tcl-config="
298 (assoc-ref %build-inputs "tcl")
300 ,(string-append "--with-tk-config="
301 (assoc-ref %build-inputs "tk")
304 "--enable-BLAS-shlib"
305 "--with-system-tre")))
306 ;; R has some support for Java. When the JDK is available at configure
307 ;; time environment variables pointing to the JDK will be recorded under
308 ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
309 ;; CMD javareconf". "R CMD javareconf" appears to only be used to update
310 ;; the recorded environment variables in $R_HOME/etc. Refer to
311 ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
312 ;; for additional information.
314 ;; As the JDK is a rather large input with only very limited effects on R,
315 ;; we decided to drop it.
319 ("pkg-config" ,pkg-config)
320 ("texinfo" ,texinfo) ; for building HTML manuals
321 ("texlive" ,(texlive-union (list texlive-fonts-amsfonts
323 texlive-latex-amsfonts
325 texlive-latex-fancyvrb
326 texlive-latex-graphics
327 texlive-latex-hyperref
328 texlive-latex-oberdiek
330 texlive-latex-upquote
332 ("tzdata" ,tzdata-for-tests)
335 `(;; We need not only cairo here, but pango to ensure that tests for the
336 ;; "cairo" bitmapType plotting backend succeed.
338 ("coreutils" ,coreutils)
340 ("openblas" ,openblas)
341 ("gfortran" ,gfortran)
348 ("readline" ,readline)
349 ;; This avoids a reference to the ungraftable static bash. R uses the
350 ;; detected shell for the "system" procedure.
351 ("bash" ,bash-minimal)
357 (list (search-path-specification
358 (variable "R_LIBS_SITE")
359 (files (list "site-library/")))))
360 (home-page "https://www.r-project.org/")
361 (synopsis "Environment for statistical computing and graphics")
363 "R is a language and environment for statistical computing and graphics.
364 It provides a variety of statistical techniques, such as linear and nonlinear
365 modeling, classical statistical tests, time-series analysis, classification
366 and clustering. It also provides robust support for producing
367 publication-quality data plots. A large amount of 3rd-party packages are
368 available, greatly increasing its breadth and scope.")
369 (license license:gpl3+)))
371 (define-public r-minimal
372 (package (inherit r-with-tests)
376 ,@(substitute-keyword-arguments (package-arguments r-with-tests)
377 ((#:configure-flags flags)
378 ;; Do not build the recommended packages. The build system creates
379 ;; random temporary directories and embeds their names in some
380 ;; package files. We build these packages with the r-build-system
382 `(cons "--without-recommended-packages" ,flags)))))))
384 (define-public rmath-standalone
385 (package (inherit r-minimal)
386 (name "rmath-standalone")
389 (modify-phases %standard-phases
390 (add-after 'configure 'chdir
391 (lambda _ (chdir "src/nmath/standalone/") #t)))))
392 (synopsis "Standalone R math library")
394 "This package provides the R math library as an independent package.")))
396 (define-public r-boot
403 (uri (cran-uri "boot" version))
406 "1z2dig1mi76b3b9ck6qlkh07l3hs478gaf70db5nv8x7w2qhq7yg"))))
407 (build-system r-build-system)
408 (home-page "https://cran.r-project.org/web/packages/boot")
409 (synopsis "Bootstrap functions for R")
411 "This package provides functions and datasets for bootstrapping from the
412 book \"Bootstrap Methods and Their Application\" by A.C. Davison and
413 D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
414 ;; Unlimited distribution
415 (license (license:non-copyleft "file://R/bootfuns.q"))))
417 (define-public r-mass
424 (uri (cran-uri "MASS" version))
427 "0x1ckf51y851g0kvbhsgdxb26vfpmbw3xdbcnh3ck7fjm13da4cr"))))
428 (properties `((upstream-name . "MASS")))
429 (build-system r-build-system)
430 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
431 (synopsis "Support functions and datasets for Venables and Ripley's MASS")
433 "This package provides functions and datasets for the book \"Modern
434 Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
435 ;; Either version may be picked.
436 (license (list license:gpl2 license:gpl3))))
438 (define-public r-class
445 (uri (cran-uri "class" version))
448 "1x1hqz8xyhbpq4krsh02glqnlzcch25agkmn4a3da9n723b37gzn"))))
449 (build-system r-build-system)
451 `(("r-mass" ,r-mass)))
452 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
453 (synopsis "R functions for classification")
455 "This package provides various functions for classification, including
456 k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
457 ;; Either of the two versions can be picked.
458 (license (list license:gpl2 license:gpl3))))
460 (define-public r-cluster
467 (uri (cran-uri "cluster" version))
470 "1bg5dvs4bzj0rp75jpxaklz12rvyh5w99h7zkvfgpgn86ljg1rlf"))))
471 (build-system r-build-system)
473 `(("gfortran" ,gfortran)))
474 (home-page "https://cran.r-project.org/web/packages/cluster")
475 (synopsis "Methods for cluster analysis")
477 "This package provides methods for cluster analysis. It is a much
478 extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
479 Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
480 (license license:gpl2+)))
482 (define-public r-codetools
489 (uri (cran-uri "codetools" version))
492 "00bmhzqprqfn3w6ghx7sakai6s7il8gbksfiawj8in5mbhbncypn"))))
493 (build-system r-build-system)
494 (home-page "https://cran.r-project.org/web/packages/codetools")
495 (synopsis "Code analysis tools for R")
496 (description "This package provides code analysis tools for R to check R
497 code for possible problems.")
498 ;; Any version of the GPL.
499 (license (list license:gpl2+ license:gpl3+))))
501 (define-public r-foreign
508 (uri (cran-uri "foreign" version))
511 "1mv04w3ycz0ymsszn8aa87k6k5sb8mg8lhf1b8w4zpfrphpkkliv"))))
512 (build-system r-build-system)
513 (home-page "https://cran.r-project.org/web/packages/foreign")
514 (synopsis "Read data stored by other statistics software")
516 "This package provides functions for reading and writing data stored by
517 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
518 for reading and writing some dBase files.")
519 (license license:gpl2+)))
521 (define-public r-kernsmooth
523 (name "r-kernsmooth")
528 (uri (cran-uri "KernSmooth" version))
531 "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb"))))
532 (properties `((upstream-name . "KernSmooth")))
533 (build-system r-build-system)
535 `(("gfortran" ,gfortran)))
536 (home-page "https://cran.r-project.org/web/packages/KernSmooth")
537 (synopsis "Functions for kernel smoothing")
539 "This package provides functions for kernel smoothing (and density
540 estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
541 \"Kernel Smoothing\".")
542 ;; Unlimited use and distribution
543 (license (license:non-copyleft "file://LICENCE.note"))))
545 (define-public r-lattice
551 (uri (cran-uri "lattice" version))
554 "0b8abkz7syscq883mrgv63pkwaqkcpwfx8rgbqy9vgfva0z5xszx"))))
555 (build-system r-build-system)
556 (home-page "http://lattice.r-forge.r-project.org/")
557 (synopsis "High-level data visualization system")
559 "The lattice package provides a powerful and elegant high-level data
560 visualization system inspired by Trellis graphics, with an emphasis on
561 multivariate data. Lattice is sufficient for typical graphics needs, and is
562 also flexible enough to handle most nonstandard requirements.")
563 (license license:gpl2+)))
565 (define-public r-matrix
572 (uri (cran-uri "Matrix" version))
575 "1k1zf92ycqr7fz44w7bp1p354ww7jg0wm23ybb8dzmbg37qfchyv"))))
576 (properties `((upstream-name . "Matrix")))
577 (build-system r-build-system)
579 `(("r-lattice" ,r-lattice)))
580 (home-page "http://Matrix.R-forge.R-project.org/")
581 (synopsis "Sparse and dense matrix classes and methods")
583 "This package provides classes and methods for dense and sparse matrices
584 and operations on them using LAPACK and SuiteSparse.")
585 (license license:gpl2+)))
587 (define-public r-nlme
594 (uri (cran-uri "nlme" version))
597 "0k9x5j34fx093a023da9ny3b3101lbwpmfm27mkvfj950l22z88x"))))
598 (build-system r-build-system)
600 `(("r-lattice" ,r-lattice)))
602 `(("gfortran" ,gfortran)))
603 (home-page "https://cran.r-project.org/web/packages/nlme")
604 (synopsis "Linear and nonlinear mixed effects models")
606 "This package provides tools to fit and compare Gaussian linear and
607 nonlinear mixed-effects models.")
608 (license license:gpl2+)))
610 (define-public r-mgcv
617 (uri (cran-uri "mgcv" version))
620 "1snkpnkkigwrj9zm31j1nlivv9ls56imz263cv167hnmghiahpmm"))))
621 (build-system r-build-system)
623 `(("r-matrix" ,r-matrix)
625 (home-page "https://cran.r-project.org/web/packages/mgcv")
626 (synopsis "Mixed generalised additive model computation")
628 "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
629 parameter estimation by GCV, REML or UBRE/AIC. The library includes a
630 @code{gam()} function, a wide variety of smoothers, JAGS support and
631 distributions beyond the exponential family.")
632 (license license:gpl2+)))
634 (define-public r-nnet
641 (uri (cran-uri "nnet" version))
644 "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7"))))
645 (build-system r-build-system)
646 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
647 (synopsis "Feed-forward neural networks and multinomial log-linear models")
649 "This package provides functions for feed-forward neural networks with a
650 single hidden layer, and for multinomial log-linear models.")
651 (license (list license:gpl2+ license:gpl3+))))
653 (define-public r-rpart
660 (uri (cran-uri "rpart" version))
663 "0p5frya963ppn476p5dxs2mnarsalksr6gw9zzmjsn8ikq7bx3ib"))))
664 (build-system r-build-system)
665 (home-page "https://cran.r-project.org/web/packages/rpart")
666 (synopsis "Recursive partitioning and regression trees")
668 "This package provides recursive partitioning functions for
669 classification, regression and survival trees.")
670 (license (list license:gpl2+ license:gpl3+))))
672 (define-public r-spatial
679 (uri (cran-uri "spatial" version))
682 "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
683 (build-system r-build-system)
684 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
685 (synopsis "Functions for kriging and point pattern analysis")
687 "This package provides functions for kriging and point pattern
689 ;; Either version may be picked.
690 (license (list license:gpl2 license:gpl3))))
692 (define-public r-survival
699 (uri (cran-uri "survival" version))
702 "1faiwyg7x8y2kfzb66l4yc8br0mdlz4k20znmjrwq96dbzhm3cam"))))
703 (build-system r-build-system)
705 `(("r-matrix" ,r-matrix)))
706 (home-page "https://github.com/therneau/survival")
707 (synopsis "Survival analysis")
709 "This package contains the core survival analysis routines, including
710 definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
711 curves, Cox models, and parametric accelerated failure time models.")
712 (license license:lgpl2.0+)))
715 (package (inherit r-minimal)
718 (build-system trivial-build-system)
719 (arguments '(#:builder (begin (mkdir %output) #t)))
721 `(("r-minimal" ,r-minimal)
724 ("r-cluster" ,r-cluster)
725 ("r-codetools" ,r-codetools)
726 ("r-foreign" ,r-foreign)
727 ("r-kernsmooth" ,r-kernsmooth)
728 ("r-lattice" ,r-lattice)
730 ("r-matrix" ,r-matrix)
735 ("r-spatial" ,r-spatial)
736 ("r-survival" ,r-survival)))))
745 (uri (cran-uri "bit" version))
748 "0m7jrqzpa1pk8ixcl814x06jf96nlvvr16x6did6cfk4zghsrfjw"))))
749 (build-system r-build-system)
750 (home-page "http://ff.r-forge.r-project.org")
751 (synopsis "Class for vectors of 1-bit booleans")
753 "This package provides bitmapped vectors of booleans (no @code{NA}s),
754 coercion from and to logicals, integers and integer subscripts, fast boolean
755 operators and fast summary statistics. With @code{bit} class vectors of true
756 binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
757 (license license:gpl2)))
759 (define-public r-bit64
766 (uri (cran-uri "bit64" version))
769 "07znvz9vp1nz1y5ljng4qyskvm943cdbmy996s67560ijxzsm6kv"))))
770 (build-system r-build-system)
773 (home-page "http://ff.r-forge.r-project.org/")
774 (synopsis "S3 class for vectors of 64 bit integers")
776 "The bit64 package provides serializable S3 atomic 64 bit (signed)
777 integers that can be used in vectors, matrices, arrays and @code{data.frames}.
778 Methods are available for coercion from and to logicals, integers, doubles,
779 characters and factors as well as many elementwise and summary functions.
780 Many fast algorithmic operations such as @code{match} and @code{order} support
781 interactive data exploration and manipulation and optionally leverage
783 (license license:gpl2)))
785 (define-public r-dichromat
792 (uri (cran-uri "dichromat" version))
794 (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
795 (build-system r-build-system)
796 (home-page "https://cran.r-project.org/web/packages/dichromat")
797 (synopsis "Color schemes for dichromats")
799 "Dichromat collapses red-green or green-blue distinctions to simulate the
800 effects of different types of color-blindness.")
801 (license license:gpl2+)))
803 (define-public r-digest
810 (uri (cran-uri "digest" version))
812 (base32 "1x6cbj9qvkk7pxv9xdqibazw3x8psjp6x0m0ildx1jwyb2ymkl98"))))
813 (build-system r-build-system)
814 ;; Vignettes require r-knitr, which requires r-digest, so we have to
815 ;; disable them and the tests.
818 #:configure-flags (list "--no-build-vignettes")))
819 (home-page "http://dirk.eddelbuettel.com/code/digest.html")
820 (synopsis "Create cryptographic hash digests of R objects")
822 "This package contains an implementation of a function @code{digest()} for
823 the creation of hash digests of arbitrary R objects (using the md5, sha-1,
824 sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
825 of R language objects, as well as a function @code{hmac()} to create hash-based
826 message authentication code.
828 Please note that this package is not meant to be deployed for cryptographic
829 purposes for which more comprehensive (and widely tested) libraries such as
830 OpenSSL should be used.")
831 (license license:gpl2+)))
833 (define-public r-estimability
835 (name "r-estimability")
839 (uri (cran-uri "estimability" version))
842 "0cifdaa71spkcxl4db4z884jrya865sg3dhcv4isd8fnzg2pjcd3"))))
843 (build-system r-build-system)
844 (home-page "https://cran.r-project.org/web/packages/estimability")
845 (synopsis "Tools for assessing estimability of linear predictions")
846 (description "Provides tools for determining estimability of linear
847 functions of regression coefficients, and @code{epredict} methods that handle
848 non-estimable cases correctly.")
849 (license license:gpl2+)))
851 (define-public r-pheatmap
858 (uri (cran-uri "pheatmap" version))
861 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
862 (build-system r-build-system)
864 `(("r-gtable" ,r-gtable)
865 ("r-rcolorbrewer" ,r-rcolorbrewer)
866 ("r-scales" ,r-scales)))
868 "https://cran.r-project.org/web/packages/pheatmap")
869 (synopsis "Pretty heatmaps")
871 "This package provides an implementation of heatmaps that offers more
872 control over dimensions and appearance.")
873 (license license:gpl2+)))
875 (define-public r-labeling
882 (uri (cran-uri "labeling" version))
884 (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
885 (build-system r-build-system)
886 (home-page "https://cran.r-project.org/web/packages/labeling")
887 (synopsis "Axis labeling algorithms")
888 (description "The labeling package provides a range of axis labeling
890 (license license:expat)))
892 (define-public r-magrittr
899 (uri (cran-uri "magrittr" version))
901 (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
902 (build-system r-build-system)
903 (home-page "https://cran.r-project.org/web/packages/magrittr/index.html")
904 (synopsis "A forward-pipe operator for R")
906 "Magrittr provides a mechanism for chaining commands with a new
907 forward-pipe operator, %>%. This operator will forward a value, or the result
908 of an expression, into the next function call/expression. There is flexible
909 support for the type of right-hand side expressions. For more information,
910 see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
911 (license license:expat)))
913 (define-public r-munsell
920 (uri (cran-uri "munsell" version))
922 (base32 "16g1fzisbpqb15yh3pqf3iia4csppva5dnv1z88x9dg263xskwyh"))))
923 (build-system r-build-system)
925 `(("r-colorspace" ,r-colorspace)))
926 (home-page "https://cran.r-project.org/web/packages/munsell")
927 (synopsis "Munsell colour system")
929 "The Munsell package contains Functions for exploring and using the
930 Munsell colour system.")
931 (license license:expat)))
933 (define-public r-permute
940 (uri (cran-uri "permute" version))
943 "0ra8p5mf2590azrkas8z2ry7mif77xqxd29n4zgyi5vll225726j"))))
944 (build-system r-build-system)
945 ;; Tests do not run correctly, but running them properly would entail a
946 ;; circular dependency with vegan.
947 (home-page "https://github.com/gavinsimpson/permute")
948 (synopsis "Functions for Generating Restricted Permutations of Data")
950 "This package provides a set of restricted permutation designs for freely
951 exchangeable, line transects (time series), spatial grid designs and permutation
952 of blocks (groups of samples). @code{permute} also allows split-plot designs,
953 in which the whole-plots or split-plots or both can be freely exchangeable.")
954 (license license:gpl2+)))
956 (define-public r-plyr
963 (uri (cran-uri "plyr" version))
965 (base32 "1igar5pcjqh0jyxv0z3jah8rz617vfa86vw0r5c7c031b7bj5db0"))))
966 (build-system r-build-system)
967 (native-inputs `(("r-rcpp" ,r-rcpp)))
968 (home-page "http://had.co.nz/plyr")
969 (synopsis "Tools for Splitting, Applying and Combining Data")
971 "Plyr is a set of tools that solves a common set of problems: you need to
972 break a big problem down into manageable pieces, operate on each piece and
973 then put all the pieces back together. For example, you might want to fit a
974 model to each spatial location or time point in your study, summarise data by
975 panels or collapse high-dimensional arrays to simpler summary statistics.")
976 (license license:expat)))
978 (define-public r-proto
985 (uri (cran-uri "proto" version))
987 (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
988 (build-system r-build-system)
989 (home-page "https://github.com/hadley/proto")
990 (synopsis "Prototype object-based programming")
992 "Proto is an object oriented system using object-based, also called
993 prototype-based, rather than class-based object oriented ideas.")
994 (license license:gpl2+)))
996 (define-public r-rcolorbrewer
998 (name "r-rcolorbrewer")
1003 (uri (cran-uri "RColorBrewer" version))
1005 (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
1006 (build-system r-build-system)
1007 (home-page "https://cran.r-project.org/web/packages/RColorBrewer")
1008 (synopsis "ColorBrewer palettes")
1010 "This package provides color schemes for maps (and other graphics)
1011 designed by Cynthia Brewer as described at http://colorbrewer2.org")
1012 ;; Includes code licensed under bsd-4
1013 (license license:asl2.0)))
1015 (define-public r-sendmailr
1017 (name "r-sendmailr")
1022 (uri (cran-uri "sendmailR" version))
1025 "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
1026 (properties `((upstream-name . "sendmailR")))
1027 (build-system r-build-system)
1029 `(("r-base64enc" ,r-base64enc)))
1031 "https://cran.r-project.org/web/packages/sendmailR")
1032 (synopsis "Send email using R")
1034 "This package contains a simple SMTP client which provides a portable
1035 solution for sending email, including attachments, from within R.")
1036 (license license:gpl2+)))
1038 (define-public r-stringi
1045 (uri (cran-uri "stringi" version))
1048 "1vbr6g9p1iyzdj7wfw6afyizvnd1a2srfvkl72pq23vhdcwwpkhk"))))
1049 (build-system r-build-system)
1050 (inputs `(("icu4c" ,icu4c)))
1051 (native-inputs `(("pkg-config" ,pkg-config)))
1052 (home-page "http://stringi.rexamine.com/")
1053 (synopsis "Character string processing facilities")
1055 "This package allows for fast, correct, consistent, portable, as well as
1056 convenient character string/text processing in every locale and any native
1057 encoding. Owing to the use of the ICU library, the package provides R users
1058 with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
1059 programmers. Among available features there are: pattern searching
1060 (e.g. via regular expressions), random string generation, string collation,
1061 transliteration, concatenation, date-time formatting and parsing, etc.")
1062 (license license:bsd-3)))
1064 (define-public r-stringr
1071 (uri (cran-uri "stringr" version))
1073 (base32 "1p9ip7p87gbbg4s6d3d392svvzz2b5dqdq2c8ilgvn4s78nlsq47"))))
1074 (build-system r-build-system)
1076 `(("r-glue" ,r-glue)
1077 ("r-magrittr" ,r-magrittr)
1078 ("r-stringi" ,r-stringi)))
1079 (home-page "https://github.com/hadley/stringr")
1080 (synopsis "Simple, consistent wrappers for common string operations")
1082 "Stringr is a consistent, simple and easy to use set of wrappers around
1083 the fantastic @code{stringi} package. All function and argument names (and
1084 positions) are consistent, all functions deal with \"NA\"'s and zero length
1085 vectors in the same way, and the output from one function is easy to feed into
1086 the input of another.")
1087 (license license:gpl2+)))
1089 (define-public r-reshape2
1096 (uri (cran-uri "reshape2" version))
1098 (base32 "03ki5ka1dj208fc0dclbm0b4xp9d769pah2j9cs34l776p4r9zwa"))))
1099 (build-system r-build-system)
1101 `(("r-plyr" ,r-plyr)
1103 ("r-stringr" ,r-stringr)))
1104 (home-page "https://github.com/hadley/reshape")
1105 (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
1107 "Reshape2 is an R library to flexibly restructure and aggregate data
1108 using just two functions: melt and dcast (or acast).")
1109 (license license:expat)))
1111 (define-public r-scales
1118 (uri (cran-uri "scales" version))
1120 (base32 "0353dkh3d7x78463c6ds80hcml59lrqwr8rlv82a8dnkxla4l7qc"))))
1121 (build-system r-build-system)
1123 `(("r-labeling" ,r-labeling)
1124 ("r-munsell" ,r-munsell)
1125 ("r-rcolorbrewer" ,r-rcolorbrewer)
1128 ("r-viridislite" ,r-viridislite)))
1129 (home-page "https://github.com/hadley/scales")
1130 (synopsis "Scale functions for visualization")
1132 "This package provides graphical scales that map data to aesthetics, and
1133 provides methods for automatically determining breaks and labels for axes and
1135 (license license:expat)))
1137 (define-public r-ggplot2
1144 (uri (cran-uri "ggplot2" version))
1146 (base32 "0y8cks9r9hvjlx0isnvbgs3p0al167hlr3q7c3syfcj77dzjkpmz"))))
1147 (build-system r-build-system)
1149 `(("r-digest" ,r-digest)
1150 ("r-gtable" ,r-gtable)
1152 ("r-lazyeval" ,r-lazyeval)
1155 ("r-tibble" ,r-tibble)
1156 ("r-reshape2" ,r-reshape2)
1157 ("r-rlang" ,r-rlang)
1158 ("r-scales" ,r-scales)
1159 ("r-svglite" ,r-svglite) ; Needed for 'ggsave'
1160 ("r-viridislite" ,r-viridislite)
1161 ("r-withr" ,r-withr)))
1162 (home-page "https://ggplot2.tidyverse.org")
1163 (synopsis "An implementation of the grammar of graphics")
1165 "Ggplot2 is an implementation of the grammar of graphics in R. It
1166 combines the advantages of both base and lattice graphics: conditioning and
1167 shared axes are handled automatically, and you can still build up a plot step
1168 by step from multiple data sources. It also implements a sophisticated
1169 multidimensional conditioning system and a consistent interface to map data to
1170 aesthetic attributes.")
1171 (license license:gpl2+)))
1173 (define-public r-ggdendro
1179 (uri (cran-uri "ggdendro" version))
1182 "1zzq1hxd0d1qa5hrzwfkdw6fzscpcafbwbpkrb62dm559y8awp0j"))))
1183 (build-system r-build-system)
1185 `(("r-ggplot2" ,r-ggplot2)
1187 ("r-knitr" ,r-knitr)))
1188 (home-page "https://github.com/andrie/ggdendro")
1189 (synopsis "Create Dendrograms and Tree Diagrams Using ggplot2")
1190 (description "This is a set of tools for dendrograms and tree plots using
1191 ggplot2. The ggplot2 philosophy is to clearly separate data from the
1192 presentation. Unfortunately the plot method for dendrograms plots directly
1193 to a plot device with out exposing the data. The ggdendro package resolves
1194 this by making available functions that extract the dendrogram plot data.
1195 The package provides implementations for tree, rpart, as well as diana and
1196 agnes cluster diagrams.")
1197 (license license:gpl2+)))
1199 (define-public r-gdtools
1206 (uri (cran-uri "gdtools" version))
1209 "1ayy0s699ghaz34lklvcskfwman3x2n2772s5sa5x9k9xgsnxwcl"))))
1210 (build-system r-build-system)
1212 `(("pkg-config" ,pkg-config)))
1217 `(("r-rcpp" ,r-rcpp)
1218 ("r-withr" ,r-withr)))
1219 (home-page "https://cran.r-project.org/web/packages/gdtools")
1220 (synopsis "Utilities for graphical rendering")
1222 "The @code{gdtools} package provides functionalities to get font metrics
1223 and to generate base64 encoded string from raster matrix.")
1224 (license license:gpl3)))
1226 (define-public r-svglite
1233 (uri (cran-uri "svglite" version))
1236 "1gwv51wqp6pgm2f9gavsiq65njs77fr49n8y6y9ax60k3a4vvg14"))))
1237 (build-system r-build-system)
1240 ("r-gdtools" ,r-gdtools)
1241 ("r-rcpp" ,r-rcpp)))
1242 (home-page "https://github.com/hadley/svglite")
1243 (synopsis "SVG graphics device")
1245 "@code{svglite} is a graphics device that produces clean
1246 @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
1247 hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
1248 considerably faster, produces smaller files, and leaves text as is.")
1249 (license license:gpl2+)))
1251 (define-public r-assertthat
1253 (name "r-assertthat")
1257 (uri (cran-uri "assertthat" version))
1260 "17wy5bdfzg73sg2clisg1k3zyn1adkj59x56m5nwia2k8z67zkw5"))))
1261 (build-system r-build-system)
1262 (home-page "https://github.com/hadley/assertthat")
1263 (synopsis "Easy pre and post assertions")
1265 "Assertthat is an extension to stopifnot() that makes it easy to declare
1266 the pre and post conditions that your code should satisfy, while also
1267 producing friendly error messages so that your users know what they've done
1269 (license license:gpl3+)))
1271 (define-public r-lazyeval
1277 (uri (cran-uri "lazyeval" version))
1280 "1m10i059csrcqkcn59a8wspn784alxsq3symzhn24mhhl894346n"))))
1281 (build-system r-build-system)
1282 (home-page "https://github.com/hadley/lazyeval")
1283 (synopsis "Lazy (non-standard) evaluation in R")
1285 "This package provides the tools necessary to do non-standard
1286 evaluation (NSE) in R.")
1287 (license license:gpl3+)))
1289 (define-public r-dbi
1295 (uri (cran-uri "DBI" version))
1298 "1x8wy2vg2gcgd9bww04qmf0dsn3kp0rfjd8q8j1r2x9zxccg25pz"))))
1299 (build-system r-build-system)
1300 (home-page "https://github.com/rstats-db/DBI")
1301 (synopsis "R database interface")
1303 "The DBI package provides a database interface (DBI) definition for
1304 communication between R and relational database management systems. All
1305 classes in this package are virtual and need to be extended by the various
1306 R/DBMS implementations.")
1307 (license license:lgpl2.0+)))
1312 (version "1.69.0-1")
1315 (uri (cran-uri "BH" version))
1318 "18mckfwxxv8m8rzaz03mg2h6vhaj7y131h6yasfg0s73nxj47zd0"))))
1319 (build-system r-build-system)
1320 (home-page "https://github.com/eddelbuettel/bh")
1321 (synopsis "R package providing subset of Boost headers")
1323 "This package aims to provide the most useful subset of Boost libraries
1324 for template use among CRAN packages.")
1325 (license license:boost1.0)))
1327 (define-public r-evaluate
1333 (uri (cran-uri "evaluate" version))
1336 "0a2y7j534gbgixkwj9r1z76l2vssw4g1hznzbpclc076wkdqpj58"))))
1337 (build-system r-build-system)
1338 (home-page "https://github.com/hadley/evaluate")
1339 (synopsis "Parsing and evaluation tools for R")
1341 "This package provides tools that allow you to recreate the parsing,
1342 evaluation and display of R code, with enough information that you can
1343 accurately recreate what happens at the command line. The tools can easily be
1344 adapted for other output formats, such as HTML or LaTeX.")
1345 (license license:gpl3+)))
1347 (define-public r-formatr
1353 (uri (cran-uri "formatR" version))
1356 "0a9229rg3s9qga5v2fwfdqr0z3bk2yycv8kijrcm3jh66l68zjgm"))))
1357 (build-system r-build-system)
1358 (home-page "http://yihui.name/formatR")
1359 (synopsis "Format R code automatically")
1361 "This package provides a function to format R source code. Spaces and
1362 indent will be added to the code automatically, and comments will be preserved
1363 under certain conditions, so that R code will be more human-readable and tidy.
1364 There is also a Shiny app as a user interface in this package.")
1365 (license license:gpl3+)))
1367 (define-public r-highr
1373 (uri (cran-uri "highr" version))
1376 "0my6idnhmmgs4q1vs40y2lh56yij2p59mpwvm53wjs2zk6x1zl2b"))))
1377 (build-system r-build-system)
1378 (home-page "https://github.com/yihui/highr")
1379 (synopsis "Syntax highlighting for R source code")
1381 "This package provides syntax highlighting for R source code. Currently
1382 it supports LaTeX and HTML output. Source code of other languages is
1383 supported via Andre Simon's highlight package.")
1384 (license license:gpl3+)))
1386 (define-public r-mime
1392 (uri (cran-uri "mime" version))
1395 "00f4gw4sg1kn03s67gficxgb7a7fb6pwhlvrxrml05q1mc2vcxa7"))))
1396 (build-system r-build-system)
1397 (home-page "https://github.com/yihui/mime")
1398 (synopsis "R package to map filenames to MIME types")
1400 "This package guesses the MIME type from a filename extension using the
1401 data derived from /etc/mime.types in UNIX-type systems.")
1402 (license license:gpl2)))
1404 (define-public r-markdown
1410 (uri (cran-uri "markdown" version))
1413 "08xzs4bcf12jxp0276m6xqvq8kcgg5qp6fxrvsz6r9x73jjccs1h"))))
1414 (build-system r-build-system)
1415 ;; Skip check phase because the tests require the r-knitr package to be
1416 ;; installed. This prevents installation failures. Knitr normally
1417 ;; shouldn't be available since r-markdown is a dependency of the r-knitr
1419 (arguments `(#:tests? #f))
1421 `(("r-mime" ,r-mime)))
1422 (home-page "https://github.com/rstudio/markdown")
1423 (synopsis "Markdown rendering for R")
1425 "This package provides R bindings to the Sundown Markdown rendering
1426 library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
1427 syntax that can be converted to XHTML or other formats.")
1428 (license license:gpl2)))
1430 (define-public r-yaml
1436 (uri (cran-uri "yaml" version))
1439 "0in562nd0i23cg91a8kdbqgim656fgscykwi0icsnq53xj3srg2m"))))
1440 (build-system r-build-system)
1441 (home-page "https://cran.r-project.org/web/packages/yaml/")
1442 (synopsis "Methods to convert R data to YAML and back")
1444 "This package implements the libyaml YAML 1.1 parser and
1445 emitter (http://pyyaml.org/wiki/LibYAML) for R.")
1446 (license license:bsd-3)))
1448 (define-public r-knitr
1454 (uri (cran-uri "knitr" version))
1457 "16ba4258c915xydhniw4cw7fvv1vp4cnwd1w49ykx7zw00rznfq6"))))
1458 (build-system r-build-system)
1460 `(("r-evaluate" ,r-evaluate)
1461 ("r-highr" ,r-highr)
1462 ("r-markdown" ,r-markdown)
1463 ("r-stringr" ,r-stringr)
1465 ("r-yaml" ,r-yaml)))
1466 (home-page "http://yihui.name/knitr/")
1467 (synopsis "General-purpose package for dynamic report generation in R")
1469 "This package provides a general-purpose tool for dynamic report
1470 generation in R using Literate Programming techniques.")
1471 ;; The code is released under any version of the GPL. As it is used by
1472 ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
1474 (license license:gpl2+)))
1476 (define-public r-knitrbootstrap
1478 (name "r-knitrbootstrap")
1483 (uri (cran-uri "knitrBootstrap" version))
1486 "1aj60j7f0gcs120fdrnfbnb7vk7lfn1phil0mghg6a5zldz4cqs3"))))
1487 (properties `((upstream-name . "knitrBootstrap")))
1488 (build-system r-build-system)
1490 `(("r-knitr" ,r-knitr)
1491 ("r-rmarkdown" ,r-rmarkdown)
1492 ("r-markdown" ,r-markdown)))
1493 (home-page "https://github.com/jimhester/knitrBootstrap")
1494 (synopsis "Knitr bootstrap framework")
1496 "This package provides a framework to create Bootstrap 3 HTML reports
1497 from knitr Rmarkdown.")
1498 (license license:expat)))
1500 (define-public r-microbenchmark
1502 (name "r-microbenchmark")
1506 (uri (cran-uri "microbenchmark" version))
1509 "1sn1fxgzakm5iqbgc35g3k4yi0iqrkmwz33cvdrphrzh1lxnmi3s"))))
1510 (build-system r-build-system)
1511 (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
1512 (synopsis "Accurate timing functions for R")
1514 "This package provides infrastructure to accurately measure and compare
1515 the execution time of R expressions.")
1516 (license license:bsd-2)))
1518 (define-public r-pryr
1524 (uri (cran-uri "pryr" version))
1527 "06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k"))))
1528 (build-system r-build-system)
1530 `(("r-stringr" ,r-stringr)
1531 ("r-codetools" ,r-codetools)))
1533 `(("r-rcpp" ,r-rcpp)))
1534 (home-page "https://github.com/hadley/pryr")
1535 (synopsis "Tools for computing on the R language")
1537 "This package provides useful tools to pry back the covers of R and
1538 understand the language at a deeper level.")
1539 (license license:gpl2)))
1541 (define-public r-memoise
1547 (uri (cran-uri "memoise" version))
1550 "034qfc2xlh30x1q2vya239w34a3ir3y2fwnx2agbgbi6592zjxmj"))))
1551 (build-system r-build-system)
1553 `(("r-digest" ,r-digest)))
1554 (home-page "https://github.com/hadley/memoise")
1555 (synopsis "Memoise functions for R")
1557 "This R package allows to cache the results of a function so that when
1558 you call it again with the same arguments it returns the pre-computed value.")
1559 (license license:expat)))
1561 (define-public r-crayon
1567 (uri (cran-uri "crayon" version))
1570 "0s7s6vc3ww8pzanpjisym4jjvwcc5pi2qg8srx7jqlz9j3wrnvpw"))))
1571 (build-system r-build-system)
1573 `(("r-memoise" ,r-memoise)))
1574 (home-page "https://github.com/gaborcsardi/crayon")
1575 (synopsis "Colored terminal output for R")
1577 "Colored terminal output on terminals that support ANSI color and
1578 highlight codes. It also works in Emacs ESS. ANSI color support is
1579 automatically detected. Colors and highlighting can be combined and nested.
1580 New styles can also be created easily. This package was inspired by the
1581 \"chalk\" JavaScript project.")
1582 (license license:expat)))
1584 (define-public r-praise
1591 (uri (cran-uri "praise" version))
1594 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
1595 (build-system r-build-system)
1596 (home-page "https://github.com/gaborcsardi/praise")
1597 (synopsis "Functions to praise users")
1599 "This package provides template functions to assist in building friendly
1600 R packages that praise their users.")
1601 (license license:expat)))
1603 (define-public r-testthat
1609 (uri (cran-uri "testthat" version))
1612 "03jgr0hlr77yp0aib4v30yjyjrjsa8dczr02yk21m93vl25vqvkp"))))
1613 (build-system r-build-system)
1616 ("r-crayon" ,r-crayon)
1617 ("r-digest" ,r-digest)
1618 ("r-magrittr" ,r-magrittr)
1619 ("r-praise" ,r-praise)
1621 ("r-rlang" ,r-rlang)
1622 ("r-withr" ,r-withr)))
1623 (home-page "https://github.com/hadley/testthat")
1624 (synopsis "Unit testing for R")
1626 "This package provides a unit testing system for R designed to be fun,
1627 flexible and easy to set up.")
1628 (license license:expat)))
1636 (uri (cran-uri "R6" version))
1639 "1kmbw2k5vvzwh3wwmn66mszpfny0z6k8dca980qgbxgvfh0i3gkh"))))
1640 (build-system r-build-system)
1641 (home-page "https://github.com/wch/R6/")
1642 (synopsis "Classes with reference semantics in R")
1644 "The R6 package allows the creation of classes with reference semantics,
1645 similar to R's built-in reference classes. Compared to reference classes, R6
1646 classes are simpler and lighter-weight, and they are not built on S4 classes
1647 so they do not require the methods package. These classes allow public and
1648 private members, and they support inheritance, even when the classes are
1649 defined in different packages.")
1650 (license license:expat)))
1652 (define-public r-rlang
1658 (uri (cran-uri "rlang" version))
1661 "1pks7d2xavzgaxqrnk3f79qsmv4wqv93f8991jv93pnb1mxpyijf"))))
1662 (build-system r-build-system)
1663 (home-page "http://rlang.tidyverse.org")
1664 (synopsis "Functions for base types, core R and Tidyverse features")
1665 (description "This package provides a toolbox for working with base types,
1666 core R features like the condition system, and core @code{Tidyverse} features
1667 like tidy evaluation.")
1668 (license license:gpl3)))
1670 (define-public r-tibble
1677 (uri (cran-uri "tibble" version))
1680 "111jl0hdjhh7hkydxvsr5l19gb0ylxq7xrkc28awnc9pzglpgis5"))))
1681 (build-system r-build-system)
1684 ("r-crayon" ,r-crayon)
1685 ("r-fansi" ,r-fansi)
1686 ("r-pkgconfig" ,r-pkgconfig)
1687 ("r-pillar" ,r-pillar)
1688 ("r-rlang" ,r-rlang)))
1689 (home-page "https://github.com/hadley/tibble")
1690 (synopsis "Simple data frames")
1692 "This package provides a @code{tbl_df} class that offers better checking
1693 and printing capabilities than traditional data frames.")
1694 (license license:expat)))
1696 (define-public r-dplyr
1702 (uri (cran-uri "dplyr" version))
1705 "1nw12hzk1jcac5879nfmf1yp98jpb3i59qkb8sfpk2cd6zqgfgjz"))))
1706 (build-system r-build-system)
1708 `(("r-assertthat" ,r-assertthat)
1711 ("r-magrittr" ,r-magrittr)
1712 ("r-pkgconfig" ,r-pkgconfig)
1713 ("r-plogr" ,r-plogr)
1716 ("r-rlang" ,r-rlang)
1717 ("r-tibble" ,r-tibble)
1718 ("r-tidyselect" ,r-tidyselect)))
1719 (home-page "https://github.com/hadley/dplyr")
1720 (synopsis "Tools for working with data frames in R")
1722 "dplyr is the next iteration of plyr. It is focussed on tools for
1723 working with data frames. It has three main goals: 1) identify the most
1724 important data manipulation tools needed for data analysis and make them easy
1725 to use in R; 2) provide fast performance for in-memory data by writing key
1726 pieces of code in C++; 3) use the same code interface to work with data no
1727 matter where it is stored, whether in a data frame, a data table or
1729 (license license:expat)))
1731 (define-public r-dbplyr
1738 (uri (cran-uri "dbplyr" version))
1741 "0f4gfkzl07gfwihyc747kdnzxahaw2g28wli4jmikrvczldvjqjx"))))
1742 (build-system r-build-system)
1744 `(("r-assertthat" ,r-assertthat)
1746 ("r-dplyr" ,r-dplyr)
1748 ("r-purrr" ,r-purrr)
1750 ("r-rlang" ,r-rlang)
1751 ("r-tibble" ,r-tibble)
1752 ("r-tidyselect" ,r-tidyselect)))
1753 (home-page "https://github.com/tidyverse/dbplyr")
1754 (synopsis "Dplyr back end for databases")
1756 "This package provides a dplyr back end for databases that allows you to
1757 work with remote database tables as if they are in-memory data frames. Basic
1758 features works with any database that has a @code{DBI} back end; more advanced
1759 features require SQL translation to be provided by the package author.")
1760 (license license:expat)))
1762 (define-public r-acepack
1769 (uri (cran-uri "acepack" version))
1772 "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
1773 (build-system r-build-system)
1775 `(("gfortran" ,gfortran)))
1776 (home-page "https://cran.r-project.org/web/packages/acepack")
1777 (synopsis "Functions for regression transformations")
1779 "This package provides ACE and AVAS methods for choosing regression
1781 (license license:expat)))
1783 (define-public r-formula
1790 (uri (cran-uri "Formula" version))
1793 "0wiqh8rr9d5ciy80wj8f5fnmiiw0ywanvvnhkwd622dx42dk848l"))))
1794 (properties `((upstream-name . "Formula")))
1795 (build-system r-build-system)
1796 (home-page "https://cran.r-project.org/web/packages/Formula")
1797 (synopsis "Extended model formulas")
1799 "This package provides a new class @code{Formula}, which extends the base
1800 class @code{formula}. It supports extended formulas with multiple parts of
1801 regressors on the right-hand side and/or multiple responses on the left-hand
1803 (license (list license:gpl2+ license:gpl3+))))
1805 (define-public r-locfit
1812 (uri (cran-uri "locfit" version))
1815 "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
1816 (build-system r-build-system)
1818 `(("r-lattice" ,r-lattice)))
1819 (home-page "https://cran.r-project.org/web/packages/locfit")
1820 (synopsis "Local regression, likelihood and density estimation")
1822 "This package provides functions used for local regression, likelihood
1823 and density estimation.")
1824 (license (list license:gpl2+ license:gpl3+))))
1826 (define-public r-chron
1832 (uri (cran-uri "chron" version))
1835 "02bkywwsxwrxc035hv51dxgdm1fjxdm7dn19ivifln59dfs1862j"))))
1836 (build-system r-build-system)
1837 (home-page "https://cran.r-project.org/web/packages/chron")
1838 (synopsis "Chronological R objects which can handle dates and times")
1840 "This package provides chronological R objects which can handle dates and
1842 (license license:gpl2)))
1844 (define-public r-data-table
1846 (name "r-data-table")
1850 (uri (cran-uri "data.table" version))
1853 "1x929lwhai6nkppm4zvicyw5qh5va5sizp86r30qnfkh1n7w2mfv"))))
1854 (build-system r-build-system)
1855 (home-page "https://github.com/Rdatatable/data.table/wiki")
1856 (synopsis "Enhanced version of data.frame R object")
1858 "The R package @code{data.table} is an extension of @code{data.frame}
1859 providing functions for fast aggregation of large data (e.g. 100GB in RAM),
1860 fast ordered joins, fast add/modify/delete of columns by group, column listing
1861 and fast file reading.")
1862 (license license:gpl3+)))
1864 (define-public r-xtable
1871 (uri (cran-uri "xtable" version))
1874 "077xfm0gphvhsay75amd9v90zk57kjgrrlgih04fyrbqqblc1gjs"))))
1875 (build-system r-build-system)
1877 `(("r-knitr" ,r-knitr))) ; for vignettes
1878 (home-page "http://xtable.r-forge.r-project.org/")
1879 (synopsis "Export R tables to LaTeX or HTML")
1881 "This package provides tools to export R data as LaTeX and HTML tables.")
1882 (license license:gpl2+)))
1884 (define-public python-patsy
1886 (name "python-patsy")
1890 (uri (pypi-uri "patsy" version ".zip"))
1893 "1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w"))))
1894 (build-system python-build-system)
1897 (modify-phases %standard-phases
1899 (lambda _ (invoke "nosetests" "-v"))))))
1901 `(("python-numpy" ,python-numpy)
1902 ("python-scipy" ,python-scipy)
1903 ("python-six" ,python-six)))
1905 `(("python-nose" ,python-nose)
1907 (home-page "https://github.com/pydata/patsy")
1908 (synopsis "Describe statistical models and build design matrices")
1910 "Patsy is a Python package for describing statistical models and for
1911 building design matrices.")
1912 ;; The majority of the code is distributed under BSD-2. The module
1913 ;; patsy.compat contains code derived from the Python standard library,
1914 ;; and is covered by the PSFL.
1915 (license (list license:bsd-2 license:psfl))))
1917 (define-public python2-patsy
1918 (package-with-python2 python-patsy))
1920 (define-public python-statsmodels
1922 (name "python-statsmodels")
1927 (uri (pypi-uri "statsmodels" version))
1930 "0fxs8a7sp4d7jvqlm36yi45i2d28kjfvraf9q8i9jr1chhxgjqb4"))))
1931 (build-system python-build-system)
1933 `(;; The test suite is very large and rather brittle. Tests often fail
1934 ;; because of minor changes in dependencies that upstream hasn't fixed
1935 ;; in a new release.
1938 (modify-phases %standard-phases
1939 (add-after 'unpack 'set-matplotlib-backend-to-agg
1941 ;; Set the matplotlib backend to Agg to avoid problems using the
1942 ;; GTK backend without a display.
1943 (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py")
1944 '("statsmodels/tsa/vector_ar/tests/test_var.py"
1945 "statsmodels/duration/tests/test_survfunc.py"))
1946 (("import matplotlib\\.pyplot as plt" line)
1947 (string-append "import matplotlib;matplotlib.use('Agg');"
1951 `(("python-numpy" ,python-numpy)
1952 ("python-scipy" ,python-scipy)
1953 ("python-pandas" ,python-pandas)
1954 ("python-patsy" ,python-patsy)
1955 ("python-matplotlib" ,python-matplotlib)))
1957 `(("python-cython" ,python-cython)
1958 ("python-nose" ,python-nose)
1959 ("python-sphinx" ,python-sphinx)))
1960 (home-page "http://statsmodels.sourceforge.net/")
1961 (synopsis "Statistical modeling and econometrics in Python")
1963 "Statsmodels is a Python package that provides a complement to scipy for
1964 statistical computations including descriptive statistics and estimation and
1965 inference for statistical models.")
1966 (license license:bsd-3)))
1968 (define-public python2-statsmodels
1969 (let ((stats (package-with-python2 python-statsmodels)))
1970 (package (inherit stats)
1972 `(("python2-pytz" ,python2-pytz)
1973 ("python2-numpy" ,python2-numpy)
1974 ("python2-scipy" ,python2-scipy)
1975 ("python2-pandas" ,python2-pandas)
1976 ("python2-patsy" ,python2-patsy)
1977 ("python2-matplotlib" ,python2-matplotlib))))))
1979 (define-public r-coda
1985 (uri (cran-uri "coda" version))
1988 "03fs3sdrrym3is92dgpa6ydk3m63gaihwy7bva4k0wm2hxm7x2k7"))))
1989 (build-system r-build-system)
1991 `(("r-lattice" ,r-lattice)))
1992 (home-page "https://cran.r-project.org/web/packages/coda")
1993 (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
1994 (description "This package provides functions for summarizing and plotting
1995 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
1996 diagnostic tests of convergence to the equilibrium distribution of the Markov
1998 (license license:gpl2+)))
2000 (define-public r-ade4
2007 (uri (cran-uri "ade4" version))
2010 "16z9jk4qj35ghsk4lwmq241dgc770y8a70dlmp9q4gz6d8ssgl7m"))))
2011 (build-system r-build-system)
2013 `(("r-mass" ,r-mass)))
2014 (home-page "http://pbil.univ-lyon1.fr/ADE-4")
2015 (synopsis "Multivariate data analysis and graphical display")
2017 "The ade4 package contains data analysis functions to analyze ecological
2018 and environmental data in the framework of Euclidean exploratory methods.")
2019 (license license:gpl2+)))
2021 (define-public r-xml2
2028 (uri (cran-uri "xml2" version))
2031 "154lmksfiwkhnlmryas25mjhfg6k4mmnnk7bbb29mnn5x5pr2yha"))))
2032 (build-system r-build-system)
2034 `(("libxml2" ,libxml2)
2037 `(("pkg-config" ,pkg-config)))
2039 `(("r-rcpp" ,r-rcpp)))
2040 (home-page "https://github.com/hadley/xml2")
2041 (synopsis "Parse XML with R")
2043 "This package provides a simple, consistent interface to working with XML
2044 files in R. It is built on top of the libxml2 C library.")
2045 (license license:gpl2+)))
2047 (define-public r-multitaper
2049 (name "r-multitaper")
2054 (uri (cran-uri "multitaper" version))
2057 "04wd9bbhyx7697pfy0fpj02v1csr48hkpqj62h9p8a6w84ji4k68"))))
2058 (build-system r-build-system)
2060 `(("gfortran" ,gfortran)))
2061 (home-page "https://github.com/wesleyburr/multitaper/")
2062 (synopsis "Multitaper spectral analysis tools")
2064 "This package implements multitaper spectral estimation
2065 techniques using prolate spheroidal sequences (Slepians) and sine
2066 tapers for time series analysis. It includes an adaptive weighted
2067 multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
2068 F-test, and complex demodulation. The Slepians sequences are
2069 generated efficiently using a tridiagonal matrix solution, and
2070 jackknifed confidence intervals are available for most estimates.")
2071 (license license:gpl2+)))
2073 (define-public r-rversions
2075 (name "r-rversions")
2079 (uri (cran-uri "rversions" version))
2082 "0mkg9zrjxlbwqzijiysivrs523x48syqj30xdfp88clpkqfk435m"))))
2083 (build-system r-build-system)
2085 `(("r-curl" ,r-curl)
2086 ("r-xml2" ,r-xml2)))
2087 (home-page "https://github.com/metacran/rversions")
2088 (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
2090 "This package provides functions to query the main R repository to find
2091 the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
2092 previous R versions and their release dates.")
2093 (license license:expat)))
2095 (define-public r-whisker
2101 (uri (cran-uri "whisker" version))
2104 "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28"))))
2105 (build-system r-build-system)
2106 (home-page "https://github.com/edwindj/whisker")
2107 (synopsis "Logicless mustache templating for R")
2109 "This package provides logicless templating, with a syntax that is not
2111 (license license:gpl3+)))
2113 (define-public r-backports
2115 (name "r-backports")
2120 (uri (cran-uri "backports" version))
2123 "00zz969vc2gfi5p9q65pzghq2bxm3p9zqgwqswkyz9rgybz5wjzf"))))
2124 (build-system r-build-system)
2125 (home-page "https://cran.r-project.org/web/packages/backports")
2126 (synopsis "Reimplementations of functions introduced since R 3.0.0")
2128 "Provides implementations of functions which have been introduced in R
2129 since version 3.0.0. The backports are conditionally exported which results
2130 in R resolving the function names to the version shipped with R (if available)
2131 and uses the implemented backports as fallback. This way package developers
2132 can make use of the new functions without worrying about the minimum required
2134 (license license:gpl2+)))
2136 (define-public r-checkmate
2138 (name "r-checkmate")
2143 (uri (cran-uri "checkmate" version))
2146 "15ccwvmw73c2zz1k10k5zdn8px0rrbnvs1b4nzvlb0iwj7cimhp4"))))
2147 (build-system r-build-system)
2149 `(("r-backports" ,r-backports)))
2150 (home-page "https://github.com/mllg/checkmate")
2151 (synopsis "Fast and versatile argument checks")
2153 "This package provides tests and assertions to perform frequent argument
2154 checks. A substantial part of the package was written in C to minimize any
2155 worries about execution time overhead.")
2156 (license license:bsd-3)))
2158 (define-public r-bbmisc
2165 (uri (cran-uri "BBmisc" version))
2168 "1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y"))))
2169 (properties `((upstream-name . "BBmisc")))
2170 (build-system r-build-system)
2172 `(("r-checkmate" ,r-checkmate)))
2173 (home-page "https://github.com/berndbischl/BBmisc")
2174 (synopsis "Miscellaneous functions for R package development")
2176 "This package provides miscellaneous helper functions for the development
2178 (license license:bsd-3)))
2180 (define-public r-fail
2187 (uri (cran-uri "fail" version))
2190 "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
2191 (build-system r-build-system)
2193 `(("r-bbmisc" ,r-bbmisc)
2194 ("r-checkmate" ,r-checkmate)))
2195 (home-page "https://github.com/mllg/fail")
2196 (synopsis "File abstraction interface layer (FAIL)")
2198 "This package provides a more comfortable interface to work with R data
2199 or source files in a key-value fashion.")
2200 (license license:bsd-3)))
2202 (define-public r-batchjobs
2204 (name "r-batchjobs")
2209 (uri (cran-uri "BatchJobs" version))
2212 "1zz4sspj596pijxlz321g0jy2rg9ki83j6fihbwisjwr66p2vk1m"))))
2213 (properties `((upstream-name . "BatchJobs")))
2214 (build-system r-build-system)
2216 `(("r-backports" ,r-backports)
2217 ("r-bbmisc" ,r-bbmisc)
2219 ("r-checkmate" ,r-checkmate)
2220 ("r-data-table" ,r-data-table)
2222 ("r-digest" ,r-digest)
2223 ("r-rsqlite" ,r-rsqlite)
2224 ("r-sendmailr" ,r-sendmailr)
2225 ("r-stringi" ,r-stringi)))
2226 (home-page "https://github.com/tudo-r/BatchJobs")
2227 (synopsis "Batch computing with R")
2229 "This package provides @code{Map}, @code{Reduce} and @code{Filter}
2230 variants to generate jobs on batch computing systems like PBS/Torque, LSF,
2231 SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
2232 (license license:bsd-2)))
2234 (define-public r-brew
2240 (uri (cran-uri "brew" version))
2243 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
2244 (build-system r-build-system)
2245 (home-page "https://cran.r-project.org/web/packages/brew")
2246 (synopsis "Templating framework for report generation")
2248 "The brew package implements a templating framework for mixing text and R
2249 code for report generation. The template syntax is similar to PHP, Ruby's erb
2250 module, Java Server Pages, and Python's psp module.")
2251 (license license:gpl2+)))
2253 (define-public r-desc
2260 (uri (cran-uri "desc" version))
2263 "1s6s13fk6sxwcj8wzkwxl9vr33153xx11p5wi9avqx3rzkabavz6"))))
2264 (build-system r-build-system)
2266 `(("r-assertthat" ,r-assertthat)
2267 ("r-crayon" ,r-crayon)
2269 ("r-rprojroot" ,r-rprojroot)))
2270 (home-page "https://github.com/r-pkgs/desc")
2271 (synopsis "Manipulate DESCRIPTION Files")
2273 "This package provides tools to read, write, create, and manipulate
2274 DESCRIPTION files. It is intended for packages that create or manipulate
2276 (license license:expat)))
2278 (define-public r-commonmark
2280 (name "r-commonmark")
2285 (uri (cran-uri "commonmark" version))
2288 "024iz1qp2kv6iz6y69ir0jk3qhjps86rhkzlcmhqsxx97rx7cjni"))))
2289 (build-system r-build-system)
2290 (home-page "https://cran.r-project.org/web/packages/commonmark")
2291 (synopsis "CommonMark and Github Markdown Rendering in R")
2293 "The CommonMark specification defines a rationalized version of markdown
2294 syntax. This package uses the @code{cmark} reference implementation for
2295 converting markdown text into various formats including HTML, LaTeX and groff
2296 man. In addition, it exposes the markdown parse tree in XML format. The latest
2297 version of this package also adds support for Github extensions including
2298 tables, autolinks and strikethrough text.")
2299 (license license:bsd-2)))
2301 (define-public r-roxygen2
2307 (uri (cran-uri "roxygen2" version))
2310 "0wq29ilqas8yn2z8v49fk0hbgchg29nmyyhwczgdipz0cbhbfipd"))))
2311 (build-system r-build-system)
2313 `(("r-brew" ,r-brew)
2314 ("r-commonmark" ,r-commonmark)
2316 ("r-digest" ,r-digest)
2317 ("r-pkgload" ,r-pkgload)
2318 ("r-purrr" ,r-purrr)
2321 ("r-stringi" ,r-stringi)
2322 ("r-stringr" ,r-stringr)
2323 ("r-xml2" ,r-xml2)))
2325 `(("r-knitr" ,r-knitr))) ; for vignettes
2326 (home-page "https://github.com/klutometis/roxygen")
2327 (synopsis "In-source documentation system for R")
2329 "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
2330 collation, and NAMESPACE files.")
2331 (license license:gpl2+)))
2333 (define-public r-openssl
2340 (uri (cran-uri "openssl" version))
2343 "1gx4mk7js1irzkql5rgk48ja9c6mm28ccxz483ngbhdd57az90qw"))))
2344 (build-system r-build-system)
2346 `(("libressl" ,libressl)))
2348 `(("pkg-config" ,pkg-config)))
2350 `(("r-askpass" ,r-askpass)))
2351 (home-page "https://github.com/jeroenooms/openssl")
2352 (synopsis "Toolkit for encryption, signatures and certificates")
2354 "This package provides R bindings to OpenSSL libssl and libcrypto, plus
2355 custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
2356 and P-521. Cryptographic signatures can either be created and verified
2357 manually or via x509 certificates. AES block cipher is used in CBC mode for
2358 symmetric encryption; RSA for asymmetric (public key) encryption. High-level
2359 envelope functions combine RSA and AES for encrypting arbitrary sized data.
2360 Other utilities include key generators, hash functions (md5, sha1, sha256,
2361 etc), base64 encoder, a secure random number generator, and @code{bignum} math
2362 methods for manually performing crypto calculations on large multibyte
2364 (license license:expat)))
2366 (define-public r-httr
2372 (uri (cran-uri "httr" version))
2375 "0j6vknwyvkjpjsxwch4q02aik4dnm3h4l0wc7dgzc555bm1g2cyn"))))
2376 (build-system r-build-system)
2378 `(("r-curl" ,r-curl)
2379 ("r-jsonlite" ,r-jsonlite)
2380 ("r-openssl" ,r-openssl)
2383 (home-page "https://github.com/hadley/httr")
2384 (synopsis "Tools for working with URLs and HTTP")
2386 "The aim of httr is to provide a wrapper for RCurl customised to the
2387 demands of modern web APIs. It provides useful tools for working with HTTP
2388 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
2389 functions make it easy to control additional request components.")
2390 (license license:expat)))
2392 (define-public r-git2r
2398 (uri (cran-uri "git2r" version))
2401 "15kpvz6ry2r8ii5hzinjwkggc5kgmkbcpsdwzahsf8gha52w80p0"))))
2402 (build-system r-build-system)
2403 ;; This R package contains modified sources of libgit2. This modified
2404 ;; version of libgit2 is built as the package is built. Hence libgit2 is
2405 ;; not among the inputs of this package.
2407 `(("libssh2" ,libssh2) ; for SSH transport
2408 ("openssl" ,openssl)
2411 `(("pkg-config" ,pkg-config)))
2412 (home-page "https://github.com/ropensci/git2r")
2413 (synopsis "Access Git repositories with R")
2415 "This package provides an R interface to the libgit2 library, which is a
2416 pure C implementation of the Git core methods.")
2417 ;; GPLv2 only with linking exception.
2418 (license license:gpl2)))
2420 (define-public r-rstudioapi
2422 (name "r-rstudioapi")
2426 (uri (cran-uri "rstudioapi" version))
2429 "15mbw607ncdf53mgga76n3va5zzdcjqz14nb0jcn9axwccqamic0"))))
2430 (build-system r-build-system)
2431 (home-page "https://cran.r-project.org/web/packages/rstudioapi")
2432 (synopsis "Safely access the RStudio API")
2434 "This package provides functions to access the RStudio API and provide
2435 informative error messages when it's not available.")
2436 (license license:expat)))
2438 (define-public r-devtools
2444 (uri (cran-uri "devtools" version))
2447 "028pppj39ng7q17k27531s8k00lmw982vz5krn74n9b8f2azm8lr"))))
2448 (build-system r-build-system)
2450 `(("r-callr" ,r-callr)
2452 ("r-digest" ,r-digest)
2453 ("r-git2r" ,r-git2r)
2455 ("r-jsonlite" ,r-jsonlite)
2456 ("r-memoise" ,r-memoise)
2457 ("r-pkgbuild" ,r-pkgbuild)
2458 ("r-pkgload" ,r-pkgload)
2459 ("r-rcmdcheck" ,r-rcmdcheck)
2460 ("r-remotes" ,r-remotes)
2461 ("r-rstudioapi" ,r-rstudioapi)
2462 ("r-sessioninfo" ,r-sessioninfo)
2463 ("r-usethis" ,r-usethis)
2464 ("r-withr" ,r-withr)))
2465 (home-page "https://github.com/hadley/devtools")
2466 (synopsis "Tools to make developing R packages easier")
2467 (description "The devtools package is a collection of package development
2468 tools to simplify the devolpment of R packages.")
2469 (license license:gpl2+)))
2471 (define-public r-withr
2477 (uri (cran-uri "withr" version))
2480 "11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1"))))
2481 (build-system r-build-system)
2482 (home-page "https://github.com/jimhester/withr")
2483 (synopsis "Run code with temporarily modified global state")
2485 "This package provides a set of functions to run R code in an environment
2486 in which global state has been temporarily modified. Many of these functions
2487 were originally a part of the r-devtools package.")
2488 (license license:gpl2+)))
2490 (define-public r-hms
2497 (uri (cran-uri "hms" version))
2500 "1g6hslk3z0xga38r71irxq802wskg6nv804mp8y9f7i2wfrj0y55"))))
2501 (build-system r-build-system)
2503 `(("r-rlang" ,r-rlang)
2504 ("r-pkgconfig" ,r-pkgconfig)))
2505 (home-page "https://github.com/rstats-db/hms")
2506 (synopsis "Pretty time of day")
2508 "This package implements an S3 class for storing and formatting
2509 time-of-day values, based on the @code{difftime} class.")
2510 (license license:gpl3+)))
2512 (define-public r-readr
2518 (uri (cran-uri "readr" version))
2521 "1wz496rw0ah433p755n3xac8gh7yzid4xgdjzd1a7wmpkgilvy9k"))))
2522 (build-system r-build-system)
2524 `(("r-clipr" ,r-clipr)
2525 ("r-crayon" ,r-crayon)
2528 ("r-tibble" ,r-tibble)
2531 (home-page "https://github.com/hadley/readr")
2532 (synopsis "Read tabular data")
2534 "This package provides functions to read flat or tabular text files from
2535 disk (or a connection).")
2536 (license license:gpl2+)))
2538 (define-public r-plotrix
2544 (uri (cran-uri "plotrix" version))
2547 "0k6ivryac1k81z2dijjds376a9jxwk8rf5g48snj67cnjffkybxj"))))
2548 (build-system r-build-system)
2549 (home-page "https://cran.r-project.org/web/packages/plotrix")
2550 (synopsis "Various plotting functions")
2552 "This package provides lots of plotting, various labeling, axis and color
2553 scaling functions for R.")
2554 (license license:gpl2+)))
2556 (define-public r-gridbase
2562 (uri (cran-uri "gridBase" version))
2565 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
2566 (build-system r-build-system)
2567 (home-page "https://cran.r-project.org/web/packages/gridBase")
2568 (synopsis "Integration of base and grid graphics")
2570 "This package provides an integration of base and grid graphics for R.")
2571 (license license:gpl2+)))
2573 (define-public r-latticeextra
2575 (name "r-latticeextra")
2580 (uri (cran-uri "latticeExtra" version))
2583 "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq"))))
2584 (properties `((upstream-name . "latticeExtra")))
2585 (build-system r-build-system)
2587 `(("r-lattice" ,r-lattice)
2588 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2589 (home-page "http://latticeextra.r-forge.r-project.org/")
2590 (synopsis "Extra graphical utilities based on lattice")
2592 "Building on the infrastructure provided by the lattice package, this
2593 package provides several new high-level graphics functions and methods, as
2594 well as additional utilities such as panel and axis annotation functions.")
2595 (license license:gpl2+)))
2597 (define-public r-rcpparmadillo
2599 (name "r-rcpparmadillo")
2600 (version "0.9.400.3.0")
2603 (uri (cran-uri "RcppArmadillo" version))
2606 "1c0kmp54xgg67hxpqm8bibcxmmwljbdvm9p1d9wzirp83x86v4sn"))))
2607 (properties `((upstream-name . "RcppArmadillo")))
2608 (build-system r-build-system)
2609 ;; All needed for vignettes
2611 `(("r-knitr" ,r-knitr)
2612 ("r-rmarkdown" ,r-rmarkdown)
2613 ("ghc-pandoc" ,ghc-pandoc)
2614 ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)))
2616 `(("r-rcpp" ,r-rcpp)))
2617 (home-page "https://github.com/RcppCore/RcppArmadillo")
2618 (synopsis "Rcpp integration for the Armadillo linear algebra library")
2620 "Armadillo is a templated C++ linear algebra library that aims towards a
2621 good balance between speed and ease of use. Integer, floating point and
2622 complex numbers are supported, as well as a subset of trigonometric and
2623 statistics functions. Various matrix decompositions are provided through
2624 optional integration with LAPACK and ATLAS libraries. This package includes
2625 the header files from the templated Armadillo library.")
2626 ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
2627 ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
2628 ;; later, as is the rest of 'Rcpp'.
2629 (license license:gpl2+)))
2631 (define-public r-bitops
2637 (uri (cran-uri "bitops" version))
2640 "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
2641 (build-system r-build-system)
2642 (home-page "https://cran.r-project.org/web/packages/bitops")
2643 (synopsis "Bitwise operations")
2645 "This package provides functions for bitwise operations on integer
2647 (license license:gpl2+)))
2649 (define-public r-catools
2652 (version "1.17.1.2")
2655 (uri (cran-uri "caTools" version))
2658 "0svj31y7h8vimvliygmmbl7pk850qk80k1vn38mlcxsnmcpm9k39"))))
2659 (properties `((upstream-name . "caTools")))
2660 (build-system r-build-system)
2662 `(("r-bitops" ,r-bitops)))
2663 (home-page "https://cran.r-project.org/web/packages/caTools")
2664 (synopsis "Various tools including functions for moving window statistics")
2666 "This package contains several basic utility functions including:
2667 moving (rolling, running) window statistic functions, read/write for GIF and
2668 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
2669 encoder/decoder, round-off-error-free sum and cumsum, etc.")
2670 (license license:gpl3+)))
2672 (define-public r-rprojroot
2674 (name "r-rprojroot")
2679 (uri (cran-uri "rprojroot" version))
2682 "12r3fdxmi2pmwn6ic3rhg0b20ll5z420m0d8fziv1n21961namnz"))))
2683 (build-system r-build-system)
2685 `(("r-backports" ,r-backports)))
2686 (home-page "https://github.com/krlmlr/rprojroot")
2687 (synopsis "Finding files in project subdirectories")
2689 "This package helps accessing files relative to a project root. It
2690 provides helpers for robust, reliable and flexible paths to files below a
2691 project root. The root of a project is defined as a directory that matches a
2692 certain criterion, e.g., it contains a certain regular file.")
2693 (license license:gpl3)))
2695 (define-public r-rmarkdown
2697 (name "r-rmarkdown")
2702 (uri (cran-uri "rmarkdown" version))
2705 "1vv3b8nlw8ra19492rjg3na42lwh3xr5a2jy2ia81fvvs846pywn"))))
2706 (properties `((upstream-name . "rmarkdown")))
2707 (build-system r-build-system)
2709 `(("r-base64enc" ,r-base64enc)
2710 ("r-evaluate" ,r-evaluate)
2711 ("r-htmltools" ,r-htmltools)
2712 ("r-jsonlite" ,r-jsonlite)
2713 ("r-knitr" ,r-knitr)
2715 ("r-stringr" ,r-stringr)
2716 ("r-tinytex" ,r-tinytex)
2719 ("ghc-pandoc" ,ghc-pandoc)))
2720 (home-page "http://rmarkdown.rstudio.com")
2721 (synopsis "Convert R Markdown documents into a variety of formats")
2723 "This package provides tools to convert R Markdown documents into a
2724 variety of formats.")
2725 (license license:gpl3+)))
2727 (define-public r-gtable
2733 (uri (cran-uri "gtable" version))
2736 "1lyncxf2dqdjgw1071cn9c8zwzkz6sldnd5cgmicf70bc726qf7x"))))
2737 (properties `((upstream-name . "gtable")))
2738 (build-system r-build-system)
2739 (home-page "https://cran.r-project.org/web/packages/gtable")
2740 (synopsis "R library to arrange grobs in tables")
2742 "Gtable is a collection of tools to make it easier to work with
2743 \"tables\" of grobs.")
2744 (license license:gpl2+)))
2746 (define-public r-gridextra
2748 (name "r-gridextra")
2752 (uri (cran-uri "gridExtra" version))
2755 "0fwfk3cdwxxim7nd55pn7m31bcaqj48y06j7an2k1v1pybk0rdl1"))))
2756 (properties `((upstream-name . "gridExtra")))
2757 (build-system r-build-system)
2759 `(("r-gtable" ,r-gtable)))
2761 `(("r-knitr" ,r-knitr))) ;for building vignettes
2762 (home-page "https://github.com/baptiste/gridextra")
2763 (synopsis "Miscellaneous functions for \"Grid\" graphics")
2765 "This package provides a number of user-level functions to work with
2766 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
2768 (license license:gpl2+)))
2770 (define-public r-pkgconfig
2772 (name "r-pkgconfig")
2776 (uri (cran-uri "pkgconfig" version))
2779 "1jk9ip549xphb3anfixqv1yx5kidnndqgy9v3qjpmgmds5a7g695"))))
2780 (build-system r-build-system)
2781 (home-page "https://github.com/gaborcsardi/pkgconfig")
2782 (synopsis "Private configuration for R packages")
2783 (description "This package provides the functionality to set configuration
2784 options on a per-package basis. Options set by a given package only apply to
2785 that package, other packages are unaffected.")
2786 (license license:expat)))
2788 (define-public r-blob
2794 (uri (cran-uri "blob" version))
2797 "0lsg91hk508dd95ivig2lwg62qafwnarjw68110kx63cfk4zkjxc"))))
2798 (build-system r-build-system)
2800 `(("r-prettyunits" ,r-prettyunits)
2801 ("r-tibble" ,r-tibble)))
2802 (home-page "https://github.com/hadley/blob")
2803 (synopsis "Simple S3 Class for representing vectors of binary data")
2804 (description "Raw vectors in R are useful for storing a single binary
2805 object. What if you want to put a vector of them in a data frame? The blob
2806 package provides the blob object, a list of raw vectors, suitable for use as
2807 a column in data frame.")
2808 (license license:gpl3+)))
2810 (define-public r-rsqlite
2816 (uri (cran-uri "RSQLite" version))
2819 "1giwk4335sc6yhj3rs8h070g1mwy38kyqyqv6vcfxvskykj7vp6z"))))
2820 (properties `((upstream-name . "RSQLite")))
2821 (build-system r-build-system)
2825 ("r-memoise" ,r-memoise)
2826 ("r-plogr" ,r-plogr)
2828 ("r-bit64" ,r-bit64)
2830 ("r-pkgconfig" ,r-pkgconfig)))
2831 (home-page "https://github.com/rstats-db/RSQLite")
2832 (synopsis "SQLite interface for R")
2834 "This package embeds the SQLite database engine in R and provides an
2835 interface compliant with the DBI package. The source for the SQLite
2836 engine (version 3.8.8.2) is included.")
2837 (license license:lgpl2.0+)))
2839 (define-public r-rcurl
2842 (version "1.95-0.1.2")
2845 (uri (string-append "https://www.bioconductor.org/packages/"
2846 "release/extra/src/"
2847 "contrib/RCurl_" version ".tar.gz"))
2850 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
2851 (properties `((upstream-name . "RCurl")))
2852 (build-system r-build-system)
2855 (modify-phases %standard-phases
2856 (add-after 'unpack 'respect-CURL_CA_BUNDLE
2858 (substitute* "R/options.S"
2859 (("\\.els = rev\\(merge\\(list\\(\\.\\.\\.\\), \\.opts\\)\\)" m)
2861 certs = Sys.getenv(\"CURL_CA_BUNDLE\")
2862 if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) }
2866 `(("libcurl" ,curl)))
2868 `(("r-bitops" ,r-bitops)))
2869 (home-page "http://www.omegahat.org/RCurl")
2870 (synopsis "General network client interface for R")
2872 "The package allows one to compose general HTTP requests and provides
2873 convenient functions to fetch URIs, GET and POST forms, etc. and process the
2874 results returned by the Web server. This provides a great deal of control
2875 over the HTTP/FTP/... connection and the form of the request while providing a
2876 higher-level interface than is available just using R socket connections.
2877 Additionally, the underlying implementation is robust and extensive,
2878 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
2879 ldap, and also supports cookies, redirects, authentication, etc.")
2880 (license license:bsd-3)))
2882 (define-public r-xml
2885 (version "3.98-1.19")
2888 (uri (cran-uri "XML" version))
2891 "1axyfa56q45x7z4zd56aasdn9hz9niv2vv5qm1zp9i94vyic9cc1"))))
2893 `((upstream-name . "XML")))
2894 (build-system r-build-system)
2896 `(("libxml2" ,libxml2)
2899 `(("pkg-config" ,pkg-config)))
2900 (home-page "http://www.omegahat.org/RSXML")
2901 (synopsis "Tools for parsing and generating XML within R")
2903 "Many approaches for both reading and creating XML (and HTML)
2904 documents (including DTDs), both local and accessible via HTTP or FTP. Also
2905 offers access to an XPath \"interpreter\".")
2906 (license license:bsd-2)))
2908 (define-public r-xnomial
2913 (origin (method url-fetch)
2914 (uri (cran-uri "XNomial" version))
2917 "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
2918 (properties (quasiquote ((upstream-name . "XNomial"))))
2919 (build-system r-build-system)
2920 (home-page "https://cran.r-project.org/web/packages/XNomial")
2921 (synopsis "Goodness-of-Fit test for multinomial data")
2923 "This package provides an exact Goodness-of-Fit test for
2924 multinomial data with fixed probabilities. It can be used to
2925 determine whether a set of counts fits a given expected ratio. To see
2926 whether a set of observed counts fits an expectation, one can examine
2927 all possible outcomes with @code{xmulti()} or a random sample of them
2928 with @code{xmonte()} and find the probability of an observation
2929 deviating from the expectation by at least as much as the observed.
2930 As a measure of deviation from the expected, one can use the
2931 log-likelihood ratio, the multinomial probability, or the classic
2932 chi-square statistic. A histogram of the test statistic can also be
2933 plotted and compared with the asymptotic curve.")
2934 (license (list license:gpl2+ license:gpl3+))))
2936 (define-public r-lambda-r
2942 (uri (cran-uri "lambda.r" version))
2945 "0cc6pszs6yccn0hgjpyn9gspv9aiva9d91ba0640i5m0l5xy7n0c"))))
2946 (properties `((upstream-name . "lambda.r")))
2947 (build-system r-build-system)
2949 `(("r-formatr" ,r-formatr)))
2950 (home-page "https://cran.r-project.org/web/packages/lambda.r")
2951 (synopsis "Functional programming extension for R")
2953 "This package provides a language extension to efficiently write
2954 functional programs in R. Syntax extensions include multi-part function
2955 definitions, pattern matching, guard statements, built-in (optional) type
2957 (license license:lgpl3+)))
2959 (define-public r-futile-options
2961 (name "r-futile-options")
2965 (uri (cran-uri "futile.options" version))
2968 "0w15agpi88y3qkv6fl72zy2pzyplzgvnj41a4ixhg64mw1sck73s"))))
2970 `((upstream-name . "futile.options")))
2971 (build-system r-build-system)
2972 (home-page "https://cran.r-project.org/web/packages/futile.options")
2973 (synopsis "Options management framework")
2975 "The futile.options subsystem provides an easy user-defined options
2976 management system that is properly scoped. This means that options created
2977 via @code{futile.options} are fully self-contained and will not collide with
2978 options defined in other packages.")
2979 (license license:lgpl3+)))
2981 (define-public r-futile-logger
2983 (name "r-futile-logger")
2987 (uri (cran-uri "futile.logger" version))
2990 "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
2991 (properties `((upstream-name . "futile.logger")))
2992 (build-system r-build-system)
2994 `(("r-futile-options" ,r-futile-options)
2995 ("r-lambda-r" ,r-lambda-r)))
2996 (home-page "https://cran.r-project.org/web/packages/futile.logger")
2997 (synopsis "Logging utility for R")
2999 "This package provides a simple yet powerful logging utility. Based
3000 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
3001 convenient and easy to use replacement for @code{cat} and @code{print}
3003 (license license:lgpl3+)))
3005 (define-public r-segmented
3007 (name "r-segmented")
3012 (uri (cran-uri "segmented" version))
3015 "0wa0xjda2j33284jkp5hj1wdjysc5f4paj1s1lcixgawj4ckmxkz"))))
3016 (build-system r-build-system)
3017 (home-page "https://cran.r-project.org/web/packages/segmented")
3018 (synopsis "Regression models with breakpoints estimation")
3020 "Given a regression model, segmented updates the model by adding one or
3021 more segmented (i.e., piecewise-linear) relationships. Several variables with
3022 multiple breakpoints are allowed.")
3023 (license (list license:gpl2+ license:gpl3+))))
3025 (define-public r-snow
3031 (uri (cran-uri "snow" version))
3034 "1n3n8pva9s34fvlw32yng0x416lmbv7q1fsd0ywa4kikmxym64l5"))))
3035 (build-system r-build-system)
3036 (home-page "https://cran.r-project.org/web/packages/snow")
3037 (synopsis "Support for simple parallel computing in R")
3039 "The snow package provides support for simple parallel computing on a
3040 network of workstations using R. A master R process calls @code{makeCluster}
3041 to start a cluster of worker processes; the master process then uses functions
3042 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
3043 worker processes and collect and return the results on the master.")
3044 (license (list license:gpl2+ license:gpl3+))))
3046 (define-public r-sparsem
3052 (uri (cran-uri "SparseM" version))
3055 "0p6ljma2h12cq1xmy0cxb48ih8dhxxbnwkqzvx3cckxf2kprycm9"))))
3057 `((upstream-name . "SparseM")))
3059 `(("gfortran" ,gfortran)))
3060 (build-system r-build-system)
3061 (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
3062 (synopsis "Sparse linear algebra")
3064 "This package provides some basic linear algebra functionality for sparse
3065 matrices. It includes Cholesky decomposition and backsolving as well as
3066 standard R subsetting and Kronecker products.")
3067 (license license:gpl2+)))
3069 (define-public r-iterators
3071 (name "r-iterators")
3076 (uri (cran-uri "iterators" version))
3079 "1s3iykfvccpnzs73z90rx18qvbvgw2dgl4nfcrvm5m1850qb5qd9"))))
3080 (build-system r-build-system)
3081 (home-page "https://cran.r-project.org/web/packages/iterators")
3082 (synopsis "Iterator construct for R")
3084 "This package provides support for iterators, which allow a programmer to
3085 traverse through all the elements of a vector, list, or other collection of
3087 (license license:asl2.0)))
3089 (define-public r-foreach
3096 (uri (cran-uri "foreach" version))
3099 "0j2yj0rn0d5nbzz9nq5rqqgnxhp9pbd92q4klsarl2xpsn8119y0"))))
3100 (build-system r-build-system)
3102 `(("r-codetools" ,r-codetools)
3103 ("r-iterators" ,r-iterators)))
3104 (home-page "https://cran.r-project.org/web/packages/foreach")
3105 (synopsis "Foreach looping construct for R")
3107 "This package provides support for the @code{foreach} looping construct.
3108 @code{foreach} is an idiom that allows for iterating over elements in a
3109 collection, without the use of an explicit loop counter. This package in
3110 particular is intended to be used for its return value, rather than for its
3111 side effects. In that sense, it is similar to the standard @code{lapply}
3112 function, but doesn't require the evaluation of a function. Using
3113 @code{foreach} without side effects also facilitates executing the loop in
3115 (license license:asl2.0)))
3117 (define-public r-doparallel
3119 (name "r-doparallel")
3124 (uri (cran-uri "doParallel" version))
3127 "01qjs4iw9f1kgymcypj0m2s4pvgqhxaycpli0fb8lq3dc0vpzfyb"))))
3128 (properties `((upstream-name . "doParallel")))
3129 (build-system r-build-system)
3131 `(("r-foreach" ,r-foreach)
3132 ("r-iterators" ,r-iterators)))
3133 (home-page "https://cran.r-project.org/web/packages/doParallel")
3134 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3136 "This package provides a parallel backend for the @code{%dopar%} function
3137 using the parallel package.")
3138 (license license:gpl2+)))
3140 (define-public r-domc
3147 (uri (cran-uri "doMC" version))
3150 "1vfrykvfvsyq12mypd266867ml1dcwc3rj5k9c3wrn5bddcm88kr"))))
3151 (properties `((upstream-name . "doMC")))
3152 (build-system r-build-system)
3154 `(("r-foreach" ,r-foreach)
3155 ("r-iterators" ,r-iterators)))
3156 (home-page "https://cran.r-project.org/web/packages/doMC")
3157 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3159 "This package provides a parallel backend for the @code{%dopar%} function
3160 using the multicore functionality of the parallel package.")
3161 (license license:gpl2+)))
3169 (uri (cran-uri "DT" version))
3172 "05kr88yshq6siarp5q7aapvsr63vx3p0aqablwgifn8m2sfqxmif"))))
3174 `((upstream-name . "DT")))
3175 (build-system r-build-system)
3177 `(("r-crosstalk" ,r-crosstalk)
3178 ("r-htmltools" ,r-htmltools)
3179 ("r-htmlwidgets" ,r-htmlwidgets)
3180 ("r-magrittr" ,r-magrittr)
3181 ("r-promises" ,r-promises)))
3182 (home-page "http://rstudio.github.io/DT")
3183 (synopsis "R wrapper of the DataTables JavaScript library")
3185 "This package allows for data objects in R to be rendered as HTML tables
3186 using the JavaScript library @code{DataTables} (typically via R Markdown or
3187 Shiny). The @code{DataTables} library has been included in this R package.")
3188 ;; The DT package as a whole is distributed under GPLv3. The DT package
3189 ;; inludes other software components under different licenses:
3191 ;; * Expat: jQuery, jquery.highlight.js, DataTables
3192 ;; * ASL2.0: selectize.js
3193 ;; * WTFPL: noUiSlider
3194 (license (list license:gpl3
3197 (license:non-copyleft "http://www.wtfpl.net/txt/copying/")))))
3199 (define-public r-base64enc
3201 (name "r-base64enc")
3205 (uri (cran-uri "base64enc" version))
3208 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
3209 (build-system r-build-system)
3210 (home-page "http://www.rforge.net/base64enc")
3211 (synopsis "Tools for Base64 encoding")
3213 "This package provides tools for handling Base64 encoding. It is more
3214 flexible than the orphaned \"base64\" package.")
3215 (license license:gpl2+)))
3217 (define-public r-irlba
3224 (uri (cran-uri "irlba" version))
3227 "1h7mzrqdjc41814cf6c93sbyl7nxwvsf3x8apl9rhmydgdlk7qkf"))))
3228 (build-system r-build-system)
3230 `(("r-matrix" ,r-matrix)))
3231 (home-page "https://cran.r-project.org/web/packages/irlba")
3232 (synopsis "Methods for eigendecomposition of large matrices")
3234 "This package provides fast and memory efficient methods for truncated
3235 singular and eigenvalue decompositions, as well as for principal component
3236 analysis of large sparse or dense matrices.")
3237 (license (list license:gpl2+ license:gpl3+))))
3239 (define-public r-glmnet
3246 (uri (cran-uri "glmnet" version))
3249 "0sr5akaiaab1sdh9c8gfmc4kp9b4vqhd90d9ig0rqpqhp3bykp78"))))
3250 (build-system r-build-system)
3252 `(("gfortran" ,gfortran)))
3254 `(("r-foreach" ,r-foreach)
3255 ("r-matrix" ,r-matrix)))
3256 (home-page "http://www.jstatsoft.org/v33/i01")
3257 (synopsis "Lasso and elastic-net regularized generalized linear models")
3259 "The glmnet package provides efficient procedures for fitting the entire
3260 lasso or elastic-net regularization path for linear and Poisson regression, as
3261 well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
3262 multinomial models. The algorithm uses cyclical coordinate descent in a
3263 path-wise fashion.")
3264 (license license:gpl2+)))
3266 (define-public r-pkgmaker
3273 (uri (cran-uri "pkgmaker" version))
3276 "0spcamjncj78kzjps2rw4v1a4494yazv6xvhn0vmdflnypc8k8hp"))))
3277 (build-system r-build-system)
3279 `(("r-bibtex" ,r-bibtex)
3280 ("r-codetools" ,r-codetools)
3281 ("r-digest" ,r-digest)
3282 ("r-magrittr" ,r-magrittr)
3283 ("r-registry" ,r-registry)
3284 ("r-stringi" ,r-stringi)
3285 ("r-stringr" ,r-stringr)
3286 ("r-withr" ,r-withr)
3287 ("r-xtable" ,r-xtable)))
3288 (home-page "https://renozao.github.io/pkgmaker")
3289 (synopsis "Package development utilities")
3291 "This package provides some low-level utilities to use for R package
3292 development. It currently provides managers for multiple package specific
3293 options and registries, vignette, unit test and bibtex related utilities.")
3294 (license license:gpl2+)))
3296 (define-public r-registry
3303 (uri (cran-uri "registry" version))
3306 "1k3j6dx350awamr0dwwgkhfs46vsnj4nf08iw5byq0x7n3nkdsnz"))))
3307 (build-system r-build-system)
3308 (home-page "https://cran.r-project.org/web/packages/registry")
3309 (synopsis "Infrastructure for R package registries")
3311 "This package provides a generic infrastructure for creating and using R
3312 package registries.")
3313 (license license:gpl2+)))
3315 (define-public r-rngtools
3322 (uri (cran-uri "rngtools" version))
3325 "0k1nlcxggflq0043m15dfclnqnzchkpw2ik7jk82h4dqwvysiqcr"))))
3326 (build-system r-build-system)
3328 `(("r-digest" ,r-digest)
3329 ("r-pkgmaker" ,r-pkgmaker)
3330 ("r-stringr" ,r-stringr)))
3331 (home-page "https://renozao.github.io/rngtools")
3332 (synopsis "Utility functions for working with random number generators")
3334 "This package contains a set of functions for working with Random Number
3335 Generators (RNGs). In particular, it defines a generic S4 framework for
3336 getting/setting the current RNG, or RNG data that are embedded into objects
3337 for reproducibility. Notably, convenient default methods greatly facilitate
3338 the way current RNG settings can be changed.")
3339 (license license:gpl3+)))
3341 (define-public r-rtsne
3348 (uri (cran-uri "Rtsne" version))
3351 "0v17vxizrs1msay24xl2bckfajr2c82wpqj07lyssbrq197nwdsn"))))
3352 (properties `((upstream-name . "Rtsne")))
3353 (build-system r-build-system)
3355 `(("r-rcpp" ,r-rcpp)))
3356 (home-page "https://github.com/jkrijthe/Rtsne")
3357 (synopsis "T-distributed stochastic neighbor embedding")
3359 "This package provides an R wrapper around the fast T-distributed
3360 Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
3361 ;; The declared license for this package is BSD-3, but it also includes
3362 ;; code licensed under BSD-4.
3363 (license (list license:bsd-3 license:bsd-4))))
3365 (define-public r-e1071
3372 (uri (cran-uri "e1071" version))
3375 "1zlxz3da216q6v6r4ff60il121xwz7g7m639vzdwglhw3jjh8psw"))))
3376 (build-system r-build-system)
3378 `(("r-class" ,r-class)))
3379 (home-page "https://cran.r-project.org/web/packages/e1071")
3380 (synopsis "Miscellaneous functions for probability theory")
3382 "This package provides functions for latent class analysis, short time
3383 Fourier transform, fuzzy clustering, support vector machines, shortest path
3384 computation, bagged clustering, naive Bayes classifier, and more.")
3385 (license license:gpl2+)))
3387 (define-public r-bigmemory-sri
3389 (name "r-bigmemory-sri")
3394 (uri (cran-uri "bigmemory.sri" version))
3396 (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
3398 `((upstream-name . "bigmemory.sri")))
3399 (build-system r-build-system)
3400 (home-page "https://cran.r-project.org/web/packages/bigmemory.sri")
3401 (synopsis "Shared resource interface for the bigmemory package")
3402 (description "This package provides a shared resource interface for the
3403 bigmemory and synchronicity packages.")
3404 ;; Users can choose either LGPLv3 or ASL2.0.
3405 (license (list license:lgpl3 license:asl2.0))))
3407 (define-public r-synchronicity
3409 (name "r-synchronicity")
3414 (uri (cran-uri "synchronicity" version))
3417 "1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx"))))
3418 (build-system r-build-system)
3421 ("r-bigmemory-sri" ,r-bigmemory-sri)
3423 ("r-uuid" ,r-uuid)))
3424 (home-page "http://www.bigmemory.org")
3425 (synopsis "Boost mutex functionality in R")
3426 (description "This package provides support for synchronization
3427 via mutexes and may eventually support interprocess communication and
3429 ;; Users can choose either LGPLv3 or ASL2.0.
3430 (license (list license:lgpl3 license:asl2.0))))
3432 (define-public r-bigmemory
3434 (name "r-bigmemory")
3439 (uri (cran-uri "bigmemory" version))
3442 "0ycl9dzm3drpyas625h34rir5bnbjlncxlvawfsfmqwcbmwdjdvj"))))
3443 (build-system r-build-system)
3447 ("r-bigmemory-sri" ,r-bigmemory-sri)))
3448 (home-page "http://www.bigmemory.org")
3449 (synopsis "Manage large matrices with shared memory or memory-mapped files")
3450 (description "This package provides methods to create, store, access, and
3451 manipulate large matrices. Matrices are allocated to shared memory and may use
3452 memory-mapped files.")
3453 ;; Users can choose either LGPLv3 or ASL2.0.
3454 (license (list license:lgpl3 license:asl2.0))))
3456 (define-public r-nmf
3463 (uri (cran-uri "NMF" version))
3466 "1qq25n3k5sgh3srlshb3ic6q92s12c1ilqf5cd5anvq6cqfchc1v"))))
3467 (properties `((upstream-name . "NMF")))
3468 (build-system r-build-system)
3470 `(("r-cluster" ,r-cluster)
3471 ("r-bigmemory" ,r-bigmemory) ; suggested
3472 ("r-synchronicity" ,r-synchronicity) ; suggested
3473 ("r-colorspace" ,r-colorspace)
3474 ("r-digest" ,r-digest)
3475 ("r-doparallel" ,r-doparallel)
3476 ("r-foreach" ,r-foreach)
3477 ("r-ggplot2" ,r-ggplot2)
3478 ("r-gridbase" ,r-gridbase)
3479 ("r-pkgmaker" ,r-pkgmaker)
3480 ("r-rcolorbrewer" ,r-rcolorbrewer)
3481 ("r-registry" ,r-registry)
3482 ("r-reshape2" ,r-reshape2)
3483 ("r-rngtools" ,r-rngtools)
3484 ("r-stringr" ,r-stringr)))
3485 (home-page "http://renozao.github.io/NMF")
3486 (synopsis "Algorithms and framework for nonnegative matrix factorization")
3488 "This package provides a framework to perform Non-negative Matrix
3489 Factorization (NMF). The package implements a set of already published
3490 algorithms and seeding methods, and provides a framework to test, develop and
3491 plug new or custom algorithms. Most of the built-in algorithms have been
3492 optimized in C++, and the main interface function provides an easy way of
3493 performing parallel computations on multicore machines.")
3494 (license license:gpl2+)))
3496 (define-public r-r-methodss3
3498 (name "r-r-methodss3")
3502 (uri (cran-uri "R.methodsS3" version))
3505 "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24"))))
3506 (properties `((upstream-name . "R.methodsS3")))
3507 (build-system r-build-system)
3508 (home-page "https://cran.r-project.org/web/packages/R.methodsS3")
3509 (synopsis "S3 methods simplified")
3511 "This package provides methods that simplify the setup of S3 generic
3512 functions and S3 methods. Major effort has been made in making definition of
3513 methods as simple as possible with a minimum of maintenance for package
3514 developers. For example, generic functions are created automatically, if
3515 missing, and naming conflict are automatically solved, if possible. The
3516 method @code{setMethodS3()} is a good start for those who in the future may
3517 want to migrate to S4.")
3518 (license license:lgpl2.1+)))
3520 (define-public r-r-oo
3526 (uri (cran-uri "R.oo" version))
3529 "0k6xwy93fpb2p7bs76lzk52br9rv5xnd9524xj8qyazv1132x1n0"))))
3530 (properties `((upstream-name . "R.oo")))
3531 (build-system r-build-system)
3533 `(("r-r-methodss3" ,r-r-methodss3)))
3534 (home-page "https://github.com/HenrikBengtsson/R.oo")
3535 (synopsis "R object-oriented programming with or without references")
3537 "This package provides methods and classes for object-oriented
3538 programming in R with or without references. Large effort has been made on
3539 making definition of methods as simple as possible with a minimum of
3540 maintenance for package developers.")
3541 (license license:lgpl2.1+)))
3543 (define-public r-r-utils
3549 (uri (cran-uri "R.utils" version))
3552 "1jaarld1jgpzh18kh9g3rlzcrk51vdgn2n1d1y28szzxlz94vifg"))))
3553 (properties `((upstream-name . "R.utils")))
3554 (build-system r-build-system)
3556 `(("r-r-methodss3" ,r-r-methodss3)
3557 ("r-r-oo" ,r-r-oo)))
3558 (home-page "https://github.com/HenrikBengtsson/R.utils")
3559 (synopsis "Various programming utilities")
3561 "This package provides utility functions useful when programming and
3562 developing R packages.")
3563 (license license:lgpl2.1+)))
3565 (define-public r-r-cache
3571 (uri (cran-uri "R.cache" version))
3574 "1hf5cb7xvnca5zlh9245b5g62sgsaxwdhiv7x59yld37cydakm6k"))))
3575 (properties `((upstream-name . "R.cache")))
3576 (build-system r-build-system)
3578 `(("r-digest" ,r-digest)
3579 ("r-r-methodss3" ,r-r-methodss3)
3581 ("r-r-utils" ,r-r-utils)))
3582 (home-page "https://github.com/HenrikBengtsson/R.cache")
3583 (synopsis "Light-weight caching of objects and results")
3585 "This package provides methods for caching or memoization of objects and
3586 results. With this package, any R object can be cached in a key-value storage
3587 where the key can be an arbitrary set of R objects. The cache memory is
3588 persistent (on the file system).")
3589 (license license:lgpl2.1+)))
3591 (define-public r-r-rsp
3597 (uri (cran-uri "R.rsp" version))
3600 "0i01p8jxc4j4zl2v2ykvvpfnm5hv650zj1wi1dh8hq0c98xi2yfr"))))
3601 (properties `((upstream-name . "R.rsp")))
3602 (build-system r-build-system)
3604 `(("r-digest" ,r-digest)
3605 ("r-r-cache" ,r-r-cache)
3606 ("r-r-methodss3" ,r-r-methodss3)
3608 ("r-r-utils" ,r-r-utils)))
3609 (home-page "https://github.com/HenrikBengtsson/R.rsp")
3610 (synopsis "Dynamic generation of scientific reports")
3612 "The RSP markup language provides a powerful markup for controlling the
3613 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
3614 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
3615 to many other literate programming languages, with RSP it is straightforward
3616 to loop over mixtures of code and text sections, e.g. in month-by-month
3617 summaries. RSP has also several preprocessing directives for incorporating
3618 static and dynamic contents of external files (local or online) among other
3619 things. RSP is ideal for self-contained scientific reports and R package
3621 (license license:lgpl2.1+)))
3623 (define-public r-mvtnorm
3629 (uri (cran-uri "mvtnorm" version))
3632 "04md0wmqgif24g0a4hx19ifn4kk8nx10986vf2d9vascig6ikpri"))))
3633 (build-system r-build-system)
3635 `(("gfortran" ,gfortran)))
3636 (home-page "http://mvtnorm.R-forge.R-project.org")
3637 (synopsis "Package for multivariate normal and t-distributions")
3638 (description "This package can compute multivariate normal and
3639 t-probabilities, quantiles, random deviates and densities.")
3640 (license license:gpl2)))
3642 (define-public r-matrixstats
3644 (name "r-matrixstats")
3648 (uri (cran-uri "matrixStats" version))
3651 "0vx00ldsg2zvdrjn49jxczk2c9iaabgvzgpdka5j02ihh7hv83cg"))))
3652 (properties `((upstream-name . "matrixStats")))
3653 (build-system r-build-system)
3655 `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
3656 (home-page "https://github.com/HenrikBengtsson/matrixStats")
3657 (synopsis "Methods applying to vectors and matrix rows and columns")
3659 "This package provides methods operating on rows and columns of matrices,
3660 e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
3661 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
3662 @code{weightedMedians()}. All methods have been optimized for speed and
3664 (license license:artistic2.0)))
3666 (define-public r-viridis
3672 (uri (cran-uri "viridis" version))
3675 "060rf1jn29dq53y3nhb0hykvcap6rqsk04rq544ypiiqb18ngwnx"))))
3676 (build-system r-build-system)
3678 `(("r-ggplot2" ,r-ggplot2)
3679 ("r-gridextra" ,r-gridextra)
3680 ("r-viridislite" ,r-viridislite)))
3681 (home-page "https://github.com/sjmgarnier/viridis")
3682 (synopsis "Matplotlib default color map")
3684 "This package is a port of the new @url{matplotlib,
3685 http://matplotlib.org/} color maps (@code{viridis}--the default--,
3686 @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
3687 designed in such a way that they will analytically be perfectly
3688 perceptually-uniform, both in regular form and also when converted to
3689 black-and-white. They are also designed to be perceived by readers with the
3690 most common form of color blindness.")
3691 (license license:x11)))
3693 (define-public r-viridislite
3695 (name "r-viridislite")
3700 (uri (cran-uri "viridisLite" version))
3703 "1by2l05f0yabwvv64lhnv7bbhx0w683s3wr9j2xda920ghpa23kq"))))
3704 (properties `((upstream-name . "viridisLite")))
3705 (build-system r-build-system)
3706 (home-page "https://github.com/sjmgarnier/viridisLite")
3707 (synopsis "Default color maps from matplotlib")
3709 "This package is a port of the new @code{matplotlib} color maps
3710 (@code{viridis}, @code{magma}, @code{plasma} and @code{inferno}) to R.
3711 matplotlib is a popular plotting library for Python. These color maps are
3712 designed in such a way that they will analytically be perfectly
3713 perceptually-uniform, both in regular form and also when converted to
3714 black-and-white. They are also designed to be perceived by readers with the
3715 most common form of color blindness. This is the @code{lite} version of the
3716 more complete @code{viridis} package.")
3717 (license license:expat)))
3719 (define-public r-tidyselect
3721 (name "r-tidyselect")
3726 (uri (cran-uri "tidyselect" version))
3729 "0x3cp36byhfjajikr1lwffjm85ayw3bcs7d7kb0cydgs61ifiqjw"))))
3730 (build-system r-build-system)
3732 `(("r-glue" ,r-glue)
3733 ("r-purrr" ,r-purrr)
3735 ("r-rlang" ,r-rlang)))
3736 (home-page "https://cran.r-project.org/web/packages/tidyselect")
3737 (synopsis "Select from a set of strings")
3739 "This package provides a backend for the selecting functions of the
3740 tidyverse. It makes it easy to implement select-like functions in your own
3741 packages in a way that is consistent with other tidyverse interfaces for
3743 (license license:gpl3)))
3745 (define-public r-tidyr
3752 (uri (cran-uri "tidyr" version))
3755 "0dyc4b03wi65bk7j0ma0y188syh37h57wgxji82i0h8j6pn593x1"))))
3756 (build-system r-build-system)
3758 `(("r-dplyr" ,r-dplyr)
3759 ("r-magrittr" ,r-magrittr)
3761 ("r-purrr" ,r-purrr)
3762 ("r-rlang" ,r-rlang)
3763 ("r-tidyselect" ,r-tidyselect)
3765 ("r-stringi" ,r-stringi)
3766 ("r-tibble" ,r-tibble)))
3767 (home-page "https://github.com/hadley/tidyr")
3768 (synopsis "Tidy data with `spread()` and `gather()` functions")
3770 "tidyr is a reframing of the reshape2 package designed to accompany the
3771 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
3772 a solid pipeline for data analysis. It is designed specifically for tidying
3773 data, not the general reshaping that reshape2 does, or the general aggregation
3774 that reshape did. In particular, built-in methods only work for data frames,
3775 and tidyr provides no margins or aggregation.")
3776 (license license:expat)))
3778 (define-public r-hexbin
3785 (uri (cran-uri "hexbin" version))
3788 "14f181lw6sj5xhfxbrpyyinsjfl0nzqilq6z80lgrhj2cnkj593y"))))
3789 (build-system r-build-system)
3791 `(("r-lattice" ,r-lattice)))
3793 `(("gfortran" ,gfortran)))
3794 (home-page "https://github.com/edzer/hexbin")
3795 (synopsis "Hexagonal binning routines")
3797 "This package provides binning and plotting functions for hexagonal bins.
3798 It uses and relies on grid graphics and formal (S4) classes and methods.")
3799 (license license:gpl2+)))
3801 (define-public r-purrr
3808 (uri (cran-uri "purrr" version))
3811 "0ccs78a2ylr60f3z0f7iywi8h1pwr8mz4ga78bs4pwgnwkclvir7"))))
3812 (build-system r-build-system)
3814 `(("r-magrittr" ,r-magrittr)
3815 ("r-rlang" ,r-rlang)))
3816 (home-page "https://github.com/hadley/purrr")
3817 (synopsis "Functional programming tools")
3819 "This package completes R's functional programming tools with missing
3820 features present in other programming languages.")
3821 (license license:gpl3+)))
3823 (define-public r-plotly
3829 (uri (cran-uri "plotly" version))
3832 "1kz2hm7vnkn4clxr6yyxxnmdmkz9zwjq6bzysw7j27r3721i8qgp"))))
3833 (build-system r-build-system)
3835 `(("r-base64enc" ,r-base64enc)
3836 ("r-crosstalk" ,r-crosstalk)
3837 ("r-digest" ,r-digest)
3838 ("r-data-table" ,r-data-table)
3839 ("r-dplyr" ,r-dplyr)
3840 ("r-ggplot2" ,r-ggplot2)
3841 ("r-hexbin" ,r-hexbin)
3842 ("r-htmltools" ,r-htmltools)
3843 ("r-htmlwidgets" ,r-htmlwidgets)
3845 ("r-jsonlite" ,r-jsonlite)
3846 ("r-lazyeval" ,r-lazyeval)
3847 ("r-magrittr" ,r-magrittr)
3848 ("r-promises" ,r-promises)
3849 ("r-purrr" ,r-purrr)
3850 ("r-rcolorbrewer" ,r-rcolorbrewer)
3851 ("r-rlang" ,r-rlang)
3852 ("r-scales" ,r-scales)
3853 ("r-tibble" ,r-tibble)
3854 ("r-tidyr" ,r-tidyr)
3855 ("r-viridislite" ,r-viridislite)))
3856 (home-page "https://plot.ly/r")
3857 (synopsis "Create interactive web graphics")
3859 "This package enables the translation of ggplot2 graphs to an interactive
3860 web-based version and/or the creation of custom web-based visualizations
3861 directly from R. Once uploaded to a plotly account, plotly graphs (and the
3862 data behind them) can be viewed and modified in a web browser.")
3863 (license license:x11)))
3865 (define-public r-biased-urn
3867 (name "r-biased-urn")
3872 (uri (cran-uri "BiasedUrn" version))
3875 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
3876 (properties `((upstream-name . "BiasedUrn")))
3877 (build-system r-build-system)
3878 (home-page "http://www.agner.org/random/")
3879 (synopsis "Biased urn model distributions")
3881 "This package provides statistical models of biased sampling in the form
3882 of univariate and multivariate noncentral hypergeometric distributions,
3883 including Wallenius' noncentral hypergeometric distribution and Fisher's
3884 noncentral hypergeometric distribution (also called extended hypergeometric
3886 (license license:gpl3+)))
3888 (define-public r-rematch
3895 (uri (cran-uri "rematch" version))
3898 "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4"))))
3899 (build-system r-build-system)
3900 (home-page "https://github.com/MangoTheCat/rematch")
3901 (synopsis "Match regular expressions with a nicer API")
3903 "This package provides a small wrapper on @code{regexpr} to extract the
3904 matches and captured groups from the match of a regular expression to a
3906 (license license:expat)))
3908 (define-public r-cellranger
3910 (name "r-cellranger")
3915 (uri (cran-uri "cellranger" version))
3918 "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x"))))
3919 (build-system r-build-system)
3921 `(("r-rematch" ,r-rematch)
3922 ("r-tibble" ,r-tibble)))
3923 (home-page "https://github.com/rsheets/cellranger")
3924 (synopsis "Translate spreadsheet cell ranges to rows and columns")
3926 "This package provides helper functions to work with spreadsheets and the
3927 @code{A1:D10} style of cell range specification.")
3928 (license license:expat)))
3930 (define-public r-googlesheets
3932 (name "r-googlesheets")
3937 (uri (cran-uri "googlesheets" version))
3940 "11q07nxys72wkxx9mawmjyf20gvwvrb7h3gpa73h6lgh2vgrwnv8"))))
3941 (build-system r-build-system)
3943 `(("r-cellranger" ,r-cellranger)
3944 ("r-dplyr" ,r-dplyr)
3946 ("r-jsonlite" ,r-jsonlite)
3947 ("r-purrr" ,r-purrr)
3948 ("r-readr" ,r-readr)
3949 ("r-stringr" ,r-stringr)
3950 ("r-tibble" ,r-tibble)
3951 ("r-tidyr" ,r-tidyr)
3952 ("r-xml2" ,r-xml2)))
3953 (home-page "https://github.com/jennybc/googlesheets")
3954 (synopsis "Manage Google spreadsheets from R")
3955 (description "This package provides tools to interact with Google Sheets
3957 (license license:expat)))
3959 (define-public r-spams
3962 (version "2.6-2017-03-22")
3966 ;; Use the ‘Latest version’ link for a stable URI across releases.
3967 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
3968 "latestfile/4531/spams-R-v" version ".tar.gz"))
3971 "13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx"))))
3972 (build-system r-build-system)
3975 (modify-phases %standard-phases
3976 (add-after 'unpack 'chdir
3977 (lambda _ (chdir "spams") #t))
3978 ;; Don't tune for the building machine.
3979 (add-after 'chdir 'no-mtune
3981 (substitute* "src/Makevars"
3982 (("-mtune=native") ""))
3985 `(("r-lattice" ,r-lattice)
3986 ("r-matrix" ,r-matrix)))
3987 (home-page "http://spams-devel.gforge.inria.fr")
3988 (synopsis "Toolbox for solving sparse estimation problems")
3989 (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
3990 for solving various sparse estimation problems. It includes tools for the
3994 @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
3995 component analysis} (PCA), ...)
3996 @item Solving sparse decomposition problems with LARS, coordinate descent,
3997 OMP, SOMP, proximal methods
3998 @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
3999 group lasso, tree-structured regularization, structured sparsity with
4000 overlapping groups,...).
4002 (license license:gpl3+)))
4004 (define-public r-base64
4011 (uri (cran-uri "base64" version))
4014 "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf"))))
4015 (build-system r-build-system)
4017 `(("r-openssl" ,r-openssl)))
4018 (home-page "https://cran.r-project.org/web/packages/base64")
4019 (synopsis "Base64 encoder and decoder")
4021 "This package is a compatibility wrapper to replace the orphaned package
4022 by Romain Francois. New applications should use the openssl or base64enc
4024 (license license:expat)))
4026 (define-public r-hmisc
4033 (uri (cran-uri "Hmisc" version))
4036 "1n8i2jhc308hd6bvys9cd7nrz7pwjszs03r5bwlh1pc869ki95ly"))))
4037 (properties `((upstream-name . "Hmisc")))
4038 (build-system r-build-system)
4040 `(("gfortran" ,gfortran)))
4042 `(("r-acepack" ,r-acepack)
4043 ("r-base64enc" ,r-base64enc)
4044 ("r-cluster" ,r-cluster)
4045 ("r-data-table" ,r-data-table)
4046 ("r-foreign" ,r-foreign)
4047 ("r-formula" ,r-formula)
4048 ("r-ggplot2" ,r-ggplot2)
4049 ("r-gridextra" ,r-gridextra)
4050 ("r-gtable" ,r-gtable)
4051 ("r-lattice" ,r-lattice)
4052 ("r-latticeextra" ,r-latticeextra)
4053 ("r-htmltable" ,r-htmltable)
4054 ("r-htmltools" ,r-htmltools)
4056 ("r-rpart" ,r-rpart)
4057 ("r-survival" ,r-survival)
4058 ("r-viridis" ,r-viridis)))
4059 (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
4060 (synopsis "Miscellaneous data analysis and graphics functions")
4062 "This package contains many functions useful for data analysis,
4063 high-level graphics, utility operations, functions for computing sample size
4064 and power, importing and annotating datasets, imputing missing values,
4065 advanced table making, variable clustering, character string manipulation,
4066 conversion of R objects to LaTeX code, and recoding variables.")
4067 (license license:gpl2+)))
4069 (define-public r-runit
4076 (uri (cran-uri "RUnit" version))
4079 "1wc1gwb7yw7phf8b0gkig6c23klya3ax11c6i4s0f049k42r78r3"))))
4080 (properties `((upstream-name . "RUnit")))
4081 (build-system r-build-system)
4082 (home-page "https://cran.r-project.org/web/packages/RUnit")
4083 (synopsis "R unit test framework")
4085 "This package provides R functions implementing a standard unit testing
4086 framework, with additional code inspection and report generation tools.")
4087 (license license:gpl2+)))
4089 (define-public r-dynamictreecut
4091 (name "r-dynamictreecut")
4096 (uri (cran-uri "dynamicTreeCut" version))
4099 "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"))))
4100 (properties `((upstream-name . "dynamicTreeCut")))
4101 (build-system r-build-system)
4103 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
4104 (synopsis "Detect clusters in hierarchical clustering dendrograms")
4106 "This package contains methods for the detection of clusters in
4107 hierarchical clustering dendrograms.")
4108 (license license:gpl2+)))
4110 (define-public r-preprocesscore
4112 (name "r-preprocesscore")
4117 (uri (bioconductor-uri "preprocessCore" version))
4120 "0iiyn42hlvmc5vabg5x15mls11124i23sh4qijwk0narh438cqm0"))))
4122 `((upstream-name . "preprocessCore")))
4123 (build-system r-build-system)
4124 (home-page "https://github.com/bmbolstad/preprocessCore")
4125 (synopsis "Collection of pre-processing functions")
4127 "This package provides a library of core pre-processing and normalization
4129 (license license:lgpl2.0+)))
4131 (define-public r-fastcluster
4133 (name "r-fastcluster")
4138 (uri (cran-uri "fastcluster" version))
4141 "01a2xnhhvv1swd4g8p4lzyn7ww7kg49jlnzc7kfz60jqjzpisrpk"))))
4142 (build-system r-build-system)
4143 (home-page "http://danifold.net/fastcluster.html")
4144 (synopsis "Fast hierarchical clustering routines")
4146 "This package implements fast hierarchical, agglomerative clustering
4147 routines. Part of the functionality is designed as drop-in replacement for
4148 existing routines: @code{linkage()} in the SciPy package
4149 @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package,
4150 and the @code{flashClust} package. It provides the same functionality with
4151 the benefit of a much faster implementation. Moreover, there are
4152 memory-saving routines for clustering of vector data, which go beyond what the
4153 existing packages provide.")
4154 (license license:bsd-2)))
4156 (define-public r-sfsmisc
4163 (uri (cran-uri "sfsmisc" version))
4166 "0zaw617zarmwir8l60riky0z6r1j3mwfnm1f32vqcbljb74akdj4"))))
4167 (build-system r-build-system)
4168 (home-page "https://cran.r-project.org/web/packages/sfsmisc")
4169 (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
4171 "This package provides useful utilities from Seminar fuer Statistik ETH
4172 Zurich, including many that are related to graphics.")
4173 (license license:gpl2+)))
4175 (define-public r-gtools
4182 (uri (cran-uri "gtools" version))
4185 "0f5syk1qq6cjq6hwymvkiyhzwa389z94722v881ipbfqkd2q8505"))))
4186 (build-system r-build-system)
4189 (modify-phases %standard-phases
4190 (add-after 'unpack 'make-deterministic
4192 (substitute* "R/checkReverseDependencies.R"
4193 (("tempdir\\(\\)") "\"/tmp\""))
4195 (home-page "https://cran.r-project.org/web/packages/gtools")
4196 (synopsis "Various R programming tools")
4198 "This package contains a collection of various functions to assist in R
4199 programming, such as tools to assist in developing, updating, and maintaining
4200 R and R packages, calculating the logit and inverse logit transformations,
4201 tests for whether a value is missing, empty or contains only @code{NA} and
4202 @code{NULL} values, and many more.")
4203 (license license:gpl2)))
4205 (define-public r-gdata
4212 (uri (cran-uri "gdata" version))
4215 "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b"))))
4216 (build-system r-build-system)
4220 `(("r-gtools" ,r-gtools)))
4221 (home-page "https://cran.r-project.org/web/packages/gdata")
4222 (synopsis "Various R programming tools for data manipulation")
4224 "This package provides various R programming tools for data manipulation,
4228 @item medical unit conversions
4229 @item combining objects
4230 @item character vector operations
4231 @item factor manipulation
4232 @item obtaining information about R objects
4233 @item manipulating MS-Excel formatted files
4234 @item generating fixed-width format files
4235 @item extricating components of date and time objects
4236 @item operations on columns of data frames
4237 @item matrix operations
4238 @item operations on vectors and data frames
4239 @item value of last evaluated expression
4240 @item wrapper for @code{sample} that ensures consistent behavior for
4241 both scalar and vector arguments
4243 (license license:gpl2+)))
4245 (define-public r-gplots
4252 (uri (cran-uri "gplots" version))
4255 "033plcfs9w8pmn84n24mdhiixdirc2a7pz6dvm61fpd20gwh7cbx"))))
4256 (build-system r-build-system)
4258 `(("r-catools" ,r-catools)
4259 ("r-gdata" ,r-gdata)
4260 ("r-gtools" ,r-gtools)
4261 ("r-kernsmooth" ,r-kernsmooth)))
4262 (home-page "https://cran.r-project.org/web/packages/gplots")
4263 (synopsis "Various R programming tools for plotting data")
4265 "This package provides various R programming tools for plotting data,
4269 @item calculating and plotting locally smoothed summary function
4270 @item enhanced versions of standard plots
4271 @item manipulating colors
4272 @item calculating and plotting two-dimensional data summaries
4273 @item enhanced regression diagnostic plots
4274 @item formula-enabled interface to @code{stats::lowess} function
4275 @item displaying textual data in plots
4277 @item plotting \"Venn\" diagrams
4278 @item displaying Open-Office style plots
4279 @item plotting multiple data on same region, with separate axes
4280 @item plotting means and confidence intervals
4281 @item spacing points in an x-y plot so they don't overlap
4283 (license license:gpl2+)))
4285 (define-public r-rocr
4292 (uri (cran-uri "ROCR" version))
4295 "1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7"))))
4296 (properties `((upstream-name . "ROCR")))
4297 (build-system r-build-system)
4299 `(("r-gplots" ,r-gplots)))
4300 (home-page "http://rocr.bioinf.mpi-sb.mpg.de/")
4301 (synopsis "Visualizing the performance of scoring classifiers")
4303 "ROCR is a flexible tool for creating cutoff-parameterized 2D performance
4304 curves by freely combining two from over 25 performance measures (new
4305 performance measures can be added using a standard interface). Curves from
4306 different cross-validation or bootstrapping runs can be averaged by different
4307 methods, and standard deviations, standard errors or box plots can be used to
4308 visualize the variability across the runs. The parameterization can be
4309 visualized by printing cutoff values at the corresponding curve positions, or
4310 by coloring the curve according to cutoff. All components of a performance
4311 plot can be quickly adjusted using a flexible parameter dispatching
4313 (license license:gpl2+)))
4315 (define-public r-zoo
4321 (uri (cran-uri "zoo" version))
4324 "09p8gmd5ifz80ahnhiianarsr5xx3nz76jzp90d7v3fjffcrcww7"))))
4325 (build-system r-build-system)
4327 `(("r-lattice" ,r-lattice)))
4328 (home-page "http://zoo.R-Forge.R-project.org/")
4329 (synopsis "S3 infrastructure for regular and irregular time series")
4330 (description "This package contains an S3 class with methods for totally
4331 ordered indexed observations. It is particularly aimed at irregular time
4332 series of numeric vectors/matrices and factors.")
4333 (license license:gpl2+)))
4335 (define-public r-ztable
4341 (uri (cran-uri "ztable" version))
4344 "0g7khk5ifsdh9p31wlwh2l5mn1hzxzpv6qcn1wh34vsfjdmijjwy"))))
4345 (build-system r-build-system)
4347 `(("r-flextable" ,r-flextable)
4348 ("r-magrittr" ,r-magrittr)
4349 ("r-moonbook" ,r-moonbook)
4350 ("r-officer" ,r-officer)
4351 ("r-rcolorbrewer" ,r-rcolorbrewer)
4352 ("r-scales" ,r-scales)
4353 ("r-stringr" ,r-stringr)))
4354 (home-page "https://cran.r-project.org/web/packages/ztable")
4355 (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
4357 "This package provides functions to make zebra-striped tables (tables
4358 with alternating row colors) in LaTeX and HTML formats easily from
4359 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
4360 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
4361 @code{cbind.mytable} objects.")
4362 (license license:gpl2+)))
4364 (define-public r-vipor
4370 (uri (cran-uri "vipor" version))
4373 "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx"))))
4374 (build-system r-build-system)
4375 (home-page "https://cran.r-project.org/web/packages/vipor")
4376 (synopsis "Plot categorical data using noise and density estimates")
4378 "This package provides tools to generate a violin point plot, a
4379 combination of a violin/histogram plot and a scatter plot by offsetting points
4380 within a category based on their density using quasirandom noise.")
4381 (license license:gpl2+)))
4383 (define-public r-beeswarm
4389 (uri (cran-uri "beeswarm" version))
4392 "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
4393 (build-system r-build-system)
4394 (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/")
4395 (synopsis "Implementation of bee swarm plots")
4397 "This package provides an implementation of bee swarm plots. The bee
4398 swarm plot is a one-dimensional scatter plot like stripchart, but with
4399 closely-packed, non-overlapping points.")
4400 (license license:artistic2.0)))
4402 (define-public r-sourcetools
4404 (name "r-sourcetools")
4409 (uri (cran-uri "sourcetools" version))
4412 "1jnjir0q2dj724f1mjm6p5h77yzyx6xcqy9r2g7gmcxkxw349627"))))
4413 (build-system r-build-system)
4414 (home-page "https://cran.r-project.org/web/packages/sourcetools")
4415 (synopsis "Tools for reading, tokenizing and parsing R code")
4417 "The sourcetools package provides both an R and C++ interface for the
4418 tokenization of R code, and helpers for interacting with the tokenized
4419 representation of R code.")
4420 (license license:expat)))
4422 (define-public r-ggbeeswarm
4424 (name "r-ggbeeswarm")
4428 (uri (cran-uri "ggbeeswarm" version))
4431 "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v"))))
4432 (build-system r-build-system)
4434 `(("r-beeswarm" ,r-beeswarm)
4435 ("r-ggplot2" ,r-ggplot2)
4436 ("r-vipor" ,r-vipor)))
4437 (home-page "https://github.com/eclarke/ggbeeswarm")
4438 (synopsis "Categorical scatter (violin point) plots")
4440 "This package provides two methods of plotting categorical scatter plots
4441 such that the arrangement of points within a category reflects the density of
4442 data at that region, and avoids over-plotting.")
4443 (license license:gpl2+)))
4445 (define-public r-ggthemes
4451 (uri (cran-uri "ggthemes" version))
4454 "0rrkzfggc1nlda1w1lbqdycx6nawxbkac1szhvkwrqlzh6agxcsv"))))
4455 (build-system r-build-system)
4457 `(("r-ggplot2" ,r-ggplot2)
4458 ("r-purrr" ,r-purrr)
4459 ("r-scales" ,r-scales)
4460 ("r-stringr" ,r-stringr)
4461 ("r-tibble" ,r-tibble)))
4462 (home-page "https://cran.rstudio.com/web/packages/ggthemes")
4463 (synopsis "Extra themes, scales and geoms for @code{ggplot2}")
4464 (description "This package provides extra themes and scales for
4465 @code{ggplot2} that replicate the look of plots by Edward Tufte and
4466 Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The
4467 Wall Street Journal, among others. This package also provides
4468 @code{geoms} for Tufte's box plot and range frame.")
4469 (license license:gpl2)))
4471 (define-public r-statmod
4477 (uri (cran-uri "statmod" version))
4480 "07v4x8af60alcw6vbiwf5fp25bhra61kvxz9kqx64lszm0i1fb4x"))))
4481 (build-system r-build-system)
4482 (home-page "https://cran.r-project.org/web/packages/statmod")
4484 `(("gfortran" ,gfortran)))
4485 (synopsis "Statistical modeling")
4487 "This package provides a collection of algorithms and functions to aid
4488 statistical modeling. It includes growth curve comparisons, limiting dilution
4489 analysis (aka ELDA), mixed linear models, heteroscedastic regression,
4490 inverse-Gaussian probability calculations, Gauss quadrature and a secure
4491 convergence algorithm for nonlinear models. It also includes advanced
4492 generalized linear model functions that implement secure convergence,
4493 dispersion modeling and Tweedie power-law families.")
4494 ;; Statmod is distributed under either license
4495 (license (list license:gpl2 license:gpl3))))
4497 (define-public r-rann
4503 (uri (cran-uri "RANN" version))
4506 "10kid40w9w7vkz2hpcfkdpxr4afxzms5dzvfwr0sl5xynzgw76dj"))))
4508 `((upstream-name . "RANN")))
4509 (build-system r-build-system)
4510 (home-page "https://github.com/jefferis/RANN")
4511 (synopsis "Fast nearest neighbour search")
4513 "This package finds the k nearest neighbours for every point in a given
4514 dataset in O(N log N) time using Arya and Mount's ANN library. Provides
4515 approximate, exact searches, fixed radius searches, bd and kb trees.")
4516 (license license:gpl3+)))
4518 (define-public r-fivethirtyeight
4520 (name "r-fivethirtyeight")
4525 (uri (string-append "https://mran.microsoft.com/src/contrib/"
4526 "fivethirtyeight_" version ".tar.gz"))
4529 "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl"))))
4530 (build-system r-build-system)
4532 `(("r-knitr" ,r-knitr)
4533 ("r-rmarkdown" ,r-rmarkdown)
4534 ("r-dplyr" ,r-dplyr)
4535 ("r-readr" ,r-readr)
4536 ("r-ggplot2" ,r-ggplot2)
4537 ("r-magrittr" ,r-magrittr)
4538 ("r-stringr" ,r-stringr)))
4539 (home-page "https://mran.microsoft.com/package/fivethirtyeight/")
4540 (synopsis "Data and code behind the stories at FiveThirtyEight")
4541 (description "This R package provides access to the code and data sets
4542 published by the statistics blog FiveThirtyEight.")
4543 (license license:expat)))
4545 (define-public r-compquadform
4547 (name "r-compquadform")
4552 (uri (cran-uri "CompQuadForm" version))
4555 "1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4"))))
4556 (properties `((upstream-name . "CompQuadForm")))
4557 (build-system r-build-system)
4558 (home-page "https://cran.r-project.org/web/packages/CompQuadForm")
4559 (synopsis "Distribution function of quadratic forms in normal variables")
4561 "This package provides functions to compute the distribution function of
4562 quadratic forms in normal variables using Imhof's method, Davies's algorithm,
4563 Farebrother's algorithm or Liu et al.'s algorithm.")
4564 (license license:gpl2+)))
4566 (define-public r-cowplot
4573 (uri (cran-uri "cowplot" version))
4576 "0yvalwalvyddyqk0q66y8361nxlh2cvp3ssazax9g5q89lghjmzv"))))
4577 (build-system r-build-system)
4579 `(("r-ggplot2" ,r-ggplot2)
4580 ("r-gtable" ,r-gtable)
4582 ("r-scales" ,r-scales)))
4583 (home-page "https://github.com/wilkelab/cowplot")
4584 (synopsis "Streamlined plot theme and plot annotations for ggplot2")
4586 "This package provides some helpful extensions and modifications to the
4587 ggplot2 package to combine multiple ggplot2 plots into one and label them with
4588 letters, as is often required for scientific publications.")
4589 (license license:gpl2)))
4591 (define-public r-mixtools
4598 (uri (cran-uri "mixtools" version))
4601 "13wdm0xs5bakhpa8ypg6lvhjaqkxyabwz4glxdwn0jwdvkcdhgsl"))))
4602 (build-system r-build-system)
4604 `(("r-mass" ,r-mass)
4605 ("r-segmented" ,r-segmented)
4606 ("r-survival" ,r-survival)))
4607 (home-page "https://cran.r-project.org/web/packages/mixtools")
4608 (synopsis "Tools for analyzing finite mixture models")
4610 "This package provides a collection of R functions for analyzing finite
4612 (license license:gpl2+)))
4614 (define-public r-lars
4621 (uri (cran-uri "lars" version))
4624 "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
4625 (build-system r-build-system)
4627 `(("gfortran" ,gfortran)))
4628 (home-page "http://www-stat.stanford.edu/~hastie/Papers/#LARS")
4629 (synopsis "Least angle regression software")
4631 "Least Angle Regression (\"LAR\") is a model selection algorithm; a
4632 useful and less greedy version of traditional forward selection methods. A
4633 simple modification of the LAR algorithm implements Tibshirani's Lasso; the
4634 Lasso modification of LARS calculates the entire Lasso path of coefficients
4635 for a given problem at the cost of a single least squares fit. Another LARS
4636 modification efficiently implements epsilon Forward Stagewise linear
4638 (license license:gpl2)))
4640 (define-public r-fastica
4647 (uri (cran-uri "fastICA" version))
4650 "108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg"))))
4651 (properties `((upstream-name . "fastICA")))
4652 (build-system r-build-system)
4653 (home-page "https://cran.r-project.org/web/packages/fastICA")
4654 (synopsis "FastICA algorithms to perform ICA and projection pursuit")
4656 "This package provides an implementation of the FastICA algorithm to
4657 perform @dfn{independent component analysis} (ICA) and projection pursuit.")
4659 (license license:gpl3+)))
4661 (define-public r-randomforest
4663 (name "r-randomforest")
4668 (uri (cran-uri "randomForest" version))
4671 "0kbmm0l42fc2d1rdq0l7k09d34kd87q4lx651ffsic4y84h8kf7l"))))
4672 (properties `((upstream-name . "randomForest")))
4673 (build-system r-build-system)
4674 (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
4676 `(("gfortran" ,gfortran)))
4677 (synopsis "Breiman and Cutler's random forests for classification and regression")
4679 "This package provides the Breiman and Cutler's random forests algorithm, based on a
4680 forest of trees using random inputs, for classification and regression.")
4681 (license license:gpl2+)))
4683 (define-public r-diptest
4690 (uri (cran-uri "diptest" version))
4693 "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
4694 (build-system r-build-system)
4695 (home-page "https://cran.r-project.org/web/packages/diptest")
4696 (synopsis "Hartigan's dip test statistic for unimodality")
4698 "This package computes Hartigan's dip test statistic for unimodality,
4699 multimodality and provides a test with simulation based p-values, where the
4700 original public code has been corrected.")
4701 (license license:gpl2+)))
4703 (define-public r-modeltools
4705 (name "r-modeltools")
4710 (uri (cran-uri "modeltools" version))
4713 "1s9lmkac3rl0nknf4wizfhg7ryq7c8yvvyc4z619238br27hhsi5"))))
4714 (build-system r-build-system)
4715 (home-page "https://cran.r-project.org/web/packages/modeltools")
4716 (synopsis "Tools and classes for statistical models")
4718 "This package provides a collection of tools to deal with statistical
4719 models. The functionality is experimental and the user interface is likely
4720 to change in the future.")
4721 (license license:gpl2)))
4723 (define-public r-flexmix
4730 (uri (cran-uri "flexmix" version))
4733 "0hrz2axp2c9548b1r0bmrl57219nn030qndb83a8garkzq5lqi5s"))))
4734 (build-system r-build-system)
4736 `(("r-lattice" ,r-lattice)
4737 ("r-modeltools" ,r-modeltools)
4738 ("r-nnet" ,r-nnet)))
4739 (home-page "https://cran.r-project.org/web/packages/flexmix")
4740 (synopsis "Flexible mixture modeling")
4742 "This package implements a general framework for finite mixtures of
4743 regression models using the EM algorithm. FlexMix provides the E-step and
4744 all data handling, while the M-step can be supplied by the user to easily
4745 define new models. Existing drivers implement mixtures of standard linear
4746 models, generalized linear models and model-based clustering.")
4747 (license license:gpl2+)))
4749 (define-public r-mclust
4756 (uri (cran-uri "mclust" version))
4759 "18x5ych9zi3y87rxi4pf6f23sl2918dp9xxpw1pqa7p7drw817p6"))))
4760 (build-system r-build-system)
4762 `(("gfortran" ,gfortran)))
4763 (home-page "http://www.stat.washington.edu/mclust/")
4764 (synopsis "Gaussian mixture modelling for model-based clustering etc.")
4766 "This package provides Gaussian finite mixture models fitted via EM
4767 algorithm for model-based clustering, classification, and density estimation,
4768 including Bayesian regularization, dimension reduction for visualisation,
4769 and resampling-based inference.")
4770 (license license:gpl2+)))
4772 (define-public r-prabclus
4779 (uri (cran-uri "prabclus" version))
4782 "0h2nml8ri27mhfs2p6ngb6kfd6lyq30sc6813yybpskkrb6gs1pb"))))
4783 (build-system r-build-system)
4785 `(("r-mass" ,r-mass)
4786 ("r-mclust" ,r-mclust)))
4787 (home-page "https://cran.r-project.org/web/packages/prabclus")
4788 (synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
4790 "This package provides distance-based parametric bootstrap tests for
4791 clustering with spatial neighborhood information. It implements some distance
4792 measures, clustering of presence-absence, abundance and multilocus genetical
4793 data for species delimitation, nearest neighbor based noise detection.")
4794 (license license:gpl2+)))
4796 (define-public r-deoptimr
4803 (uri (cran-uri "DEoptimR" version))
4806 "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
4807 (properties `((upstream-name . "DEoptimR")))
4808 (build-system r-build-system)
4809 (home-page "https://cran.r-project.org/web/packages/DEoptimR")
4810 (synopsis "Differential evolution optimization in pure R")
4812 "This package provides a differential evolution (DE) stochastic
4813 algorithms for global optimization of problems with and without constraints.
4814 The aim is to curate a collection of its state-of-the-art variants that (1) do
4815 not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
4816 can be efficiently implemented directly in the R language.")
4817 (license license:gpl2+)))
4819 (define-public r-robustbase
4821 (name "r-robustbase")
4826 (uri (cran-uri "robustbase" version))
4829 "0mkzbsjl5nihyj7mzks14p6kr3spp44xvygjz4ran11gspdn9rdx"))))
4830 (build-system r-build-system)
4832 `(("gfortran" ,gfortran)))
4834 `(("r-deoptimr" ,r-deoptimr)))
4835 (home-page "http://robustbase.r-forge.r-project.org/")
4836 (synopsis "Basic robust statistics")
4838 "This package allows to analyze data with robust methods such as
4839 regression methodology including model selections and multivariate statistics.")
4840 (license license:gpl2+)))
4842 (define-public r-pcapp
4849 (uri (cran-uri "pcaPP" version))
4852 "1z2kdf9gfp965xbcd4rg6vf20d1bl443na0qjkpq7gmzpaq6cifa"))))
4853 (properties `((upstream-name . "pcaPP")))
4854 (build-system r-build-system)
4856 `(("r-mvtnorm" ,r-mvtnorm)))
4857 (home-page "https://cran.r-project.org/web/packages/pcaPP")
4858 (synopsis "Robust PCA by projection pursuit")
4860 "This package provides functions for robust @dfn{principal component
4861 analysis} (PCA) by projection pursuit.")
4862 (license license:gpl3+)))
4864 (define-public r-rrcov
4871 (uri (cran-uri "rrcov" version))
4874 "14zjyqcdiqx6js99nx5s8hmyx564ixy2d8s6i7wa50xmx368rl6b"))))
4875 (build-system r-build-system)
4877 `(("r-cluster" ,r-cluster)
4878 ("r-lattice" ,r-lattice)
4879 ("r-mvtnorm" ,r-mvtnorm)
4880 ("r-pcapp" ,r-pcapp)
4881 ("r-robustbase" ,r-robustbase)))
4883 `(("gfortran" ,gfortran)))
4884 (home-page "https://cran.r-project.org/web/packages/rrcov")
4885 (synopsis "Scalable robust estimators with high breakdown Point")
4887 "This package provides an implementation of robust location and scatter
4888 estimation and robust multivariate analysis with high breakdown point.")
4889 (license license:gpl2+)))
4891 (define-public r-fit-models
4893 (name "r-fit-models")
4898 (uri (cran-uri "fit.models" version))
4901 "0vjbzmx0ambm6yzidb4vbgmhclwzwv2iz2cwl54ccdkvx4cx3fck"))))
4902 (properties `((upstream-name . "fit.models")))
4903 (build-system r-build-system)
4905 `(("r-lattice" ,r-lattice)))
4906 (home-page "https://cran.r-project.org/web/packages/fit.models")
4907 (synopsis "Compare fitted models")
4909 "The @code{fit.models} function and its associated methods (coefficients, print,
4910 summary, plot, etc.) were originally provided in the @code{robust} package to
4911 compare robustly and classically fitted model objects. The aim of the
4912 @code{fit.models} package is to separate this fitted model object comparison
4913 functionality from the robust package and to extend it to support fitting
4914 methods (e.g., classical, robust, Bayesian, regularized, etc.) more
4916 ;; Any version of the GPL
4917 (license (list license:gpl2+ license:gpl3+))))
4919 (define-public r-robust
4926 (uri (cran-uri "robust" version))
4929 "1b7qh1aff500nd6dh4y2ipmjgdiq8991shflb63pc39vpc0ny6g4"))))
4930 (build-system r-build-system)
4932 `(("r-fit-models" ,r-fit-models)
4933 ("r-lattice" ,r-lattice)
4935 ("r-robustbase" ,r-robustbase)
4936 ("r-rrcov" ,r-rrcov)))
4938 `(("gfortran" ,gfortran)))
4939 (home-page "https://cran.r-project.org/web/packages/robust")
4940 (synopsis "Port of the S+ \"Robust Library\"")
4942 "This package is a port of the S+ \"Robust Library\". It provides
4943 methods for robust statistics, notably for robust regression and robust
4944 multivariate analysis.")
4945 (license license:gpl2)))
4947 (define-public r-trimcluster
4949 (name "r-trimcluster")
4954 (uri (cran-uri "trimcluster" version))
4957 "0013bpyq6mkvjn38qsmwnsxfiwxgwngnqxycxvgpgmiadhm8fjmn"))))
4958 (build-system r-build-system)
4959 (home-page "https://cran.r-project.org/web/packages/trimcluster")
4960 (synopsis "Cluster analysis with trimming")
4962 "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
4963 Matran (1997). This optimizes the k-means criterion under trimming a portion
4966 (license (list license:gpl2+ license:gpl3+))))
4968 (define-public r-fpc
4971 (version "2.1-11.2")
4975 (uri (cran-uri "fpc" version))
4978 "0wjjp9xn283acfg6cm1wa6fsi7pf0z97227hrnlpmprks3mbj8kr"))))
4979 (build-system r-build-system)
4981 `(("r-class" ,r-class)
4982 ("r-cluster" ,r-cluster)
4983 ("r-diptest" ,r-diptest)
4984 ("r-flexmix" ,r-flexmix)
4985 ("r-kernlab" ,r-kernlab)
4987 ("r-mclust" ,r-mclust)
4988 ("r-mvtnorm" ,r-mvtnorm)
4989 ("r-prabclus" ,r-prabclus)
4990 ("r-robustbase" ,r-robustbase)
4991 ("r-trimcluster" ,r-trimcluster)))
4992 (home-page "https://cran.r-project.org/web/packages/fpc")
4993 (synopsis "Flexible procedures for clustering")
4995 "This package provides various methods for clustering and cluster validation.
4996 For example, it provides fixed point clustering, linear regression clustering,
4997 clustering by merging Gaussian mixture components, as well as symmetric and
4998 asymmetric discriminant projections for visualisation of the separation of
5000 (license license:gpl2+)))
5002 (define-public r-vgam
5009 (uri (cran-uri "VGAM" version))
5012 "0lnsqx3q3k0c7sj8gj0n6shn2fyxwrh8xph8h1r1i23ybbb2n6fy"))))
5013 (properties `((upstream-name . "VGAM")))
5014 (build-system r-build-system)
5016 `(("gfortran" ,gfortran)))
5017 (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
5018 (synopsis "Vector generalized linear and additive models")
5020 "This package is an implementation of about 6 major classes of statistical
5021 regression models. Currently only fixed-effects models are implemented, i.e.,
5022 no random-effects models. Many (150+) models and distributions are estimated
5023 by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
5024 VGLMs can be loosely thought of as multivariate generalised linear models.")
5025 (license license:gpl2+)))
5027 (define-public r-pbapply
5034 (uri (cran-uri "pbapply" version))
5037 "0bn7a9ni36xy5acnrl9ky3gd1k8jr5kxgazzh3pzd1q6bri1nx7k"))))
5038 (build-system r-build-system)
5039 (home-page "https://github.com/psolymos/pbapply")
5040 (synopsis "Adding progress bar to apply functions")
5042 "This lightweight package that adds progress bar to vectorized R
5043 functions apply. The implementation can easily be added to functions where
5044 showing the progress is useful e.g. bootstrap.")
5045 (license license:gpl2)))
5047 (define-public r-minqa
5054 (uri (cran-uri "minqa" version))
5057 "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
5058 (build-system r-build-system)
5060 `(("r-rcpp" ,r-rcpp)))
5062 `(("gfortran" ,gfortran)))
5063 (home-page "http://optimizer.r-forge.r-project.org")
5064 (synopsis "Derivative-free optimization algorithms by quadratic approximation")
5066 "This package provides a derivative-free optimization by quadratic approximation
5067 based on an interface to Fortran implementations by M. J. D. Powell.")
5068 (license license:gpl2)))
5070 (define-public r-rcppeigen
5072 (name "r-rcppeigen")
5073 (version "0.3.3.5.0")
5077 (uri (cran-uri "RcppEigen" version))
5080 "01bz41c29591ybzqn4z88ss036ai3anh9figryvmfpqcfwbszip5"))))
5081 (properties `((upstream-name . "RcppEigen")))
5082 (build-system r-build-system)
5084 `(("r-rcpp" ,r-rcpp)
5085 ("r-matrix" ,r-matrix)))
5086 (home-page "http://eigen.tuxfamily.org")
5087 (synopsis "Rcpp integration for the Eigen templated linear algebra library")
5089 "This package provides an integration of Eigen in R using a C++ template
5090 library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
5091 It supports dense and sparse matrices on integer, floating point and complex numbers,
5092 decompositions of such matrices, and solutions of linear systems.")
5093 (license license:gpl2+)))
5095 (define-public r-modelmetrics
5097 (name "r-modelmetrics")
5102 (uri (cran-uri "ModelMetrics" version))
5105 "158ddbw2snlyzd2q6mdaif5i67kq4qfvadylwjxgv1w2cmszrmk6"))))
5106 (properties `((upstream-name . "ModelMetrics")))
5107 (build-system r-build-system)
5109 `(("r-rcpp" ,r-rcpp)
5110 ("r-data-table" ,r-data-table)))
5111 (home-page "https://cran.r-project.org/web/packages/ModelMetrics")
5112 (synopsis "Rapid calculation of model metrics")
5114 "Written in C++ using @code{Rcpp}, this package provides a collection of
5115 metrics for evaluating models.")
5116 (license license:gpl2+)))
5118 (define-public r-matrixmodels
5120 (name "r-matrixmodels")
5125 (uri (cran-uri "MatrixModels" version))
5128 "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
5129 (properties `((upstream-name . "MatrixModels")))
5130 (build-system r-build-system)
5132 `(("r-matrix" ,r-matrix)))
5133 (home-page "https://cran.r-project.org/web/packages/MatrixModels")
5134 (synopsis "Modelling with sparse and dense matrices")
5136 "This package models with sparse and dense matrix matrices,
5137 using modular prediction and response module classes.")
5138 (license license:gpl2+)))
5140 (define-public r-quantreg
5147 (uri (cran-uri "quantreg" version))
5150 "1vvvnk291f0dccg04l3nsnk585gq75sk0b2vdbrqv3lczvv18nw1"))))
5151 (build-system r-build-system)
5153 `(("gfortran" ,gfortran)))
5155 `(("r-matrix" ,r-matrix)
5156 ("r-matrixmodels" ,r-matrixmodels)
5157 ("r-sparsem" ,r-sparsem)))
5158 (home-page "https://www.r-project.org")
5159 (synopsis "Quantile regression")
5161 "This package provides an estimation and inference methods for models
5162 of conditional quantiles: linear and nonlinear parametric and non-parametric
5163 models for conditional quantiles of a univariate response and several methods
5164 for handling censored survival data. Portfolio selection methods based on
5165 expected shortfall risk are also included.")
5166 (license license:gpl2+)))
5168 (define-public r-nloptr
5175 (uri (cran-uri "nloptr" version))
5178 "15yz60kljxwnhm2m3gryjzxl3ynhkhd5jiwc179b1hz6rlzf71hz"))))
5179 (build-system r-build-system)
5181 `(("r-knitr" ,r-knitr) ; for building vignettes
5182 ("pkg-config" ,pkg-config)
5183 ("gfortran" ,gfortran)))
5185 `(("nlopt" ,nlopt)))
5186 (home-page "https://cran.r-project.org/web/packages/nloptr")
5187 (synopsis "R interface to NLopt")
5189 "This package is interface to NLopt, a library for nonlinear
5190 optimization. NLopt is a library for nonlinear optimization, providing a
5191 common interface for a number of different free optimization routines
5192 available online as well as original implementations of various other
5194 (license license:lgpl3)))
5196 (define-public r-lme4
5203 (uri (cran-uri "lme4" version))
5206 "035j2hqkwv939xl07pm2vykvf3wlx8qj317846n9pkpqkyv58mbz"))))
5207 (build-system r-build-system)
5209 `(("r-boot" ,r-boot)
5210 ("r-lattice" ,r-lattice)
5212 ("r-matrix" ,r-matrix)
5213 ("r-minqa" ,r-minqa)
5214 ("r-nloptr" ,r-nloptr)
5217 ("r-rcppeigen" ,r-rcppeigen)))
5218 (home-page "https://cran.r-project.org/web/packages/lme4")
5219 (synopsis "Linear mixed-effects models using eigen and S4")
5221 "This package provides fit linear and generalized linear mixed-effects
5222 models. The models and their components are represented using S4 classes and
5223 methods. The core computational algorithms are implemented using the Eigen
5224 C++ library for numerical linear algebra and RcppEigen glue.")
5225 (license license:gpl2+)))
5227 (define-public r-pbkrtest
5234 (uri (cran-uri "pbkrtest" version))
5237 "1si3bhi59xc51a0pgjjglccq3h4aljyhw2k1b8574s145fnh7fsw"))))
5238 (build-system r-build-system)
5240 `(("r-lme4" ,r-lme4)
5242 ("r-matrix" ,r-matrix)))
5243 (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
5244 (synopsis "Methods for linear mixed model comparison")
5246 "This package implements a parametric bootstrap test and a Kenward Roger
5247 modification of F-tests for linear mixed effects models and a parametric
5248 bootstrap test for generalized linear mixed models.")
5249 (license license:gpl2+)))
5251 (define-public r-cardata
5258 (uri (cran-uri "carData" version))
5261 "152lfgaspgx6x2wzdb5p3zv6r87a0d2pg10h6fjmdr613kzlwp1v"))))
5262 (properties `((upstream-name . "carData")))
5263 (build-system r-build-system)
5264 (home-page "https://r-forge.r-project.org/projects/car/")
5265 (synopsis "Data Sets for the book Companion to Applied Regression")
5267 "This package provides datasets to accompany J. Fox and S. Weisberg, An R
5268 Companion to Applied Regression, Third Edition, Sage.")
5269 (license license:gpl2+)))
5271 (define-public r-car
5278 (uri (cran-uri "car" version))
5281 "0l3wyc9ia0ypcbap2p39slazfpbl84mjzydqvpsywrzdiyxajnfz"))))
5282 (build-system r-build-system)
5284 `(("r-abind" ,r-abind)
5285 ("r-cardata" ,r-cardata)
5287 ("r-maptools" ,r-maptools)
5292 ("r-pbkrtest" ,r-pbkrtest)
5293 ("r-quantreg" ,r-quantreg)
5295 (home-page "https://r-forge.r-project.org/projects/car/")
5296 (synopsis "Companion to applied regression")
5298 "This package provides functions and datasets from book Companion
5299 to Applied regression, Second Edition, Sage, 2011.")
5300 (license license:gpl2+)))
5302 (define-public r-caret
5309 (uri (cran-uri "caret" version))
5312 "03898irgb70q0p01kq99yb6q6xji0jx4jmj0yxlv8wcwd841r0x1"))))
5313 (build-system r-build-system)
5315 `(("r-foreach" ,r-foreach)
5316 ("r-ggplot2" ,r-ggplot2)
5317 ("r-lattice" ,r-lattice)
5318 ("r-modelmetrics" ,r-modelmetrics)
5321 ("r-recipes" ,r-recipes)
5322 ("r-reshape2" ,r-reshape2)
5323 ("r-withr" ,r-withr)))
5324 (home-page "https://github.com/topepo/caret")
5325 (synopsis "Classification and regression training")
5327 "This package provides misc functions for training and plotting
5328 classification and regression models.")
5329 (license license:gpl2+)))
5331 (define-public r-rcppprogress
5333 (name "r-rcppprogress")
5338 (uri (cran-uri "RcppProgress" version))
5341 "0yk01hfv961zyp569682k9igvhnwqyg5j0n5fm63sxigj82l2xhi"))))
5342 (properties `((upstream-name . "RcppProgress")))
5343 (build-system r-build-system)
5345 `(("r-devtools" ,r-devtools)
5346 ("r-rcpp" ,r-rcpp)))
5347 (home-page "https://github.com/kforner/rcpp_progress")
5348 (synopsis "Interruptible progress bar for C++ in R packages")
5350 "This package allows to display a progress bar in the R console for long running
5351 computations taking place in C++ code, and support for interrupting those computations
5352 even in multithreaded code, typically using OpenMP.")
5353 (license license:gpl3+)))
5355 (define-public r-mnormt
5362 (uri (cran-uri "mnormt" version))
5365 "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z"))))
5366 (build-system r-build-system)
5368 `(("gfortran" ,gfortran)))
5369 (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
5370 (synopsis "Multivariate normal and \"t\" distributions")
5372 "This package provides functions for computing the density and the
5373 distribution function of multivariate normal and \"t\" random variables, and
5374 for generating random vectors sampled from these distributions. Probabilities
5375 are computed via non-Monte Carlo methods.")
5376 (license license:gpl2+)))
5378 (define-public r-numderiv
5381 (version "2016.8-1")
5385 (uri (cran-uri "numDeriv" version))
5388 "07ni52rwiap4wilfz94w5mrqaxr59axxmgn57857ip4p6qkiss0v"))))
5389 (properties `((upstream-name . "numDeriv")))
5390 (build-system r-build-system)
5391 (home-page "https://cran.r-project.org/web/packages/numDeriv")
5392 (synopsis "Accurate numerical derivatives")
5394 "This package provides methods for calculating accurate numerical
5395 first and second order derivatives.")
5396 (license license:gpl2)))
5405 (uri (cran-uri "sn" version))
5408 "0x46gxkplxbnhaqbpiav1r4xlv4ib7n57kxmca7scqwj22y7wrs6"))))
5409 (build-system r-build-system)
5411 `(("r-mnormt" ,r-mnormt)
5412 ("r-numderiv" ,r-numderiv)))
5413 (home-page "http://azzalini.stat.unipd.it/SN")
5414 (synopsis "The skew-normal and skew-t distributions")
5416 "This package provides functionalities to build and manipulate
5417 probability distributions of the skew-normal family and some related
5418 ones, notably the skew-t family, and provides related statistical
5419 methods for data fitting and diagnostics, in the univariate and the
5420 multivariate case.")
5421 (license license:gpl2+)))
5423 (define-public r-tclust
5430 (uri (cran-uri "tclust" version))
5433 "17md6l9v9dl9b72l84df01b52h2xiynbcjm437mv9mzcr09fc2sb"))))
5434 (build-system r-build-system)
5435 ;; These are all suggested packages, not build dependencies.
5437 `(("r-cluster" ,r-cluster)
5438 ("r-mclust" ,r-mclust)
5439 ("r-mvtnorm" ,r-mvtnorm)
5441 (home-page "https://cran.r-project.org/web/packages/tclust")
5442 (synopsis "Robust trimmed clustering")
5444 "This package implements different robust clustering
5445 algorithms (@code{tclust}) based on trimming and including some graphical
5446 diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
5447 (license license:gpl3)))
5449 (define-public r-ranger
5456 (uri (cran-uri "ranger" version))
5459 "1sxyzxmjc6lm8wcmq15j6sscnza7aay4mr3dyri2zngx6fa8mb0k"))))
5460 (build-system r-build-system)
5462 `(("r-rcpp" ,r-rcpp)
5463 ("r-matrix" ,r-matrix)
5464 ("r-rcppeigen" ,r-rcppeigen)))
5465 (home-page "https://github.com/imbs-hl/ranger")
5466 (synopsis "Fast implementation of random forests")
5468 "This package provides a fast implementation of Random Forests,
5469 particularly suited for high dimensional data. Ensembles of classification,
5470 regression, survival and probability prediction trees are supported. Data from
5471 genome-wide association studies can be analyzed efficiently.")
5472 (license license:gpl3)))
5474 (define-public r-tsne
5481 (uri (cran-uri "tsne" version))
5484 "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
5485 (build-system r-build-system)
5486 (home-page "https://github.com/jdonaldson/rtsne/")
5487 (synopsis "t-Distributed Stochastic Neighbor Embedding for R")
5489 "This package provides a pure R implementation of the t-SNE algorithm.")
5490 (license license:gpl2+)))
5492 (define-public r-cairo
5499 (uri (cran-uri "Cairo" version))
5502 "1mdmd5zmjkh1b0x928zizgzh42x8swbajffb88rvnjfdhk1z0dvq"))))
5503 (properties `((upstream-name . "Cairo")))
5504 (build-system r-build-system)
5510 `(("pkg-config" ,pkg-config)))
5511 (home-page "http://www.rforge.net/Cairo/")
5512 (synopsis "R graphics device using Cairo graphics library")
5514 "This package provides a Cairo graphics device that can be use to
5515 create high-quality vector (PDF, PostScript and SVG) and bitmap
5516 output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11
5517 and Win32). Since it uses the same back-end for all output, copying
5518 across formats is WYSIWYG. Files are created without the dependence
5519 on X11 or other external programs. This device supports alpha
5520 channel (semi-transparent drawing) and resulting images can contain
5521 transparent and semi-transparent regions. It is ideal for use in
5522 server environments (file output) and as a replacement for other
5523 devices that don't have Cairo's capabilities such as alpha support or
5524 anti-aliasing. Backends are modular such that any subset of backends
5526 (license license:gpl2)))
5528 (define-public r-lubridate
5530 (name "r-lubridate")
5535 (uri (cran-uri "lubridate" version))
5538 "14a823il77w3wmmnzr89vwrqp50y56dh5raycnaw6c8nv5xsh32i"))))
5539 (build-system r-build-system)
5541 `(("r-rcpp" ,r-rcpp)
5542 ("r-stringr" ,r-stringr)))
5544 "https://cran.r-project.org/web/packages/lubridate")
5545 (synopsis "Make dealing with dates a little easier")
5547 "This package provides functions to work with date-times and time-spans:
5548 fast and user friendly parsing of date-time data, extraction and updating of
5549 components of a date-time (years, months, days, hours, minutes, and seconds),
5550 algebraic manipulation on date-time and time-span objects. The @code{lubridate}
5551 package has a consistent and memorable syntax that makes working with dates
5553 (license license:gpl2)))
5555 (define-public r-fdrtool
5562 (uri (cran-uri "fdrtool" version))
5565 "1h46frlk7d9f4qx0bg6p55nrm9wwwz2sv6d1nz7061wdfsm69yb5"))))
5566 (build-system r-build-system)
5567 (home-page "http://strimmerlab.org/software/fdrtool/")
5568 (synopsis "Estimation of false discovery rates and higher criticism")
5570 "This package provides tools to estimate tail area-based false discovery
5571 rates as well as local false discovery rates for a variety of null
5572 models (p-values, z-scores, correlation coefficients, t-scores). The
5573 proportion of null values and the parameters of the null distribution are
5574 adaptively estimated from the data. In addition, the package contains
5575 functions for non-parametric density estimation (Grenander estimator), for
5576 monotone regression (isotonic regression and antitonic regression with
5577 weights), for computing the @dfn{greatest convex minorant} (GCM) and the
5578 @dfn{least concave majorant} (LCM), for the half-normal and correlation
5579 distributions, and for computing empirical @dfn{higher criticism} (HC) scores
5580 and the corresponding decision threshold.")
5581 (license license:gpl3+)))
5583 (define-public r-forcats
5590 (uri (cran-uri "forcats" version))
5593 "1cnjh23z59fhbjmy7y95425hcq3m5wrwqvahsxwi7zm6d9bwp0vw"))))
5594 (build-system r-build-system)
5596 `(("r-ellipsis" ,r-ellipsis)
5597 ("r-magrittr" ,r-magrittr)
5598 ("r-tibble" ,r-tibble)
5599 ("r-rlang" ,r-rlang)))
5600 (home-page "http://forcats.tidyverse.org")
5601 (synopsis "Tools for working with factors")
5602 (description "This package provides helpers for reordering factor
5603 levels (including moving specified levels to front, ordering by first
5604 appearance, reversing, and randomly shuffling), and tools for modifying factor
5605 levels (including collapsing rare levels into other, \"anonymizing\", and
5606 manually \"recoding\").")
5607 (license license:gpl3)))
5609 (define-public r-tgstat
5610 (let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f")
5614 (version (string-append "1.0.2-" revision "." (string-take changeset 7)))
5619 (url "https://bitbucket.org/tanaylab/tgstat")
5620 (changeset changeset)))
5621 (file-name (string-append name "-" version "-checkout"))
5624 "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
5625 (build-system r-build-system)
5628 (modify-phases %standard-phases
5629 (add-after 'unpack 'fix-isnan
5631 (substitute* "src/tgstat.h"
5632 (("#define isnan ::isnan")
5633 "#define isnan std::isnan"))
5636 `(("r-rcpp" ,r-rcpp)))
5637 (home-page "https://bitbucket.org/tanaylab/tgstat/")
5638 (synopsis "Tanay's group statistical utilities")
5640 "The goal of tgstat is to provide fast and efficient statistical
5642 (license license:gpl2))))
5644 (define-public r-tgconfig
5645 (let ((changeset "1e02c7614713bd0866c46f0c679a058f8c6d627e")
5649 (version (string-append "0.0.0.9000-" revision "." (string-take changeset 7)))
5654 (url "https://bitbucket.org/tanaylab/tgconfig")
5655 (changeset changeset)))
5656 (file-name (string-append name "-" version "-checkout"))
5659 "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
5660 (build-system r-build-system)
5662 `(("r-yaml" ,r-yaml)))
5663 (home-page "https://bitbucket.org/tanaylab/tgconfig/")
5664 (synopsis "Infrastructure for managing package parameters")
5666 "The goal of tgconfig is to provide infrastructure for managing package
5668 (license license:gpl3))))
5670 (define-public r-directlabels
5672 (name "r-directlabels")
5673 (version "2018.05.22")
5677 (uri (cran-uri "directlabels" version))
5680 "0xcpc56ssb9430b0xcdhayk3qaak2qcakyss2pz14y5w2027hblv"))))
5681 (build-system r-build-system)
5683 `(("r-quadprog" ,r-quadprog)))
5684 (home-page "http://directlabels.r-forge.r-project.org/")
5685 (synopsis "Direct labels for multicolor plots")
5687 "This package provides an extensible framework for automatically placing
5688 direct labels onto multicolor plots. Label positions are described using
5689 positioning methods that can be re-used across several different plots. There
5690 are heuristics for examining @code{trellis} and @code{ggplot} objects and
5691 inferring an appropriate positioning method.")
5692 (license license:gpl3)))
5694 (define-public r-catterplots
5695 (let ((commit "40063ec57f9515d231508f135ca0ec769614efb9")
5698 (name "r-catterplots")
5699 (version (string-append "0-" revision "." (string-take commit 9)))
5703 (url "https://github.com/Gibbsdavidl/CatterPlots.git")
5705 (file-name (string-append name "-" version "-checkout"))
5708 "1wl80pgbz8d9kfpffvkh439hlgz2qldm9m75wqjfrgrg8lcjzrxg"))))
5709 (build-system r-build-system)
5711 `(("r-png" ,r-png)))
5712 (home-page "https://github.com/Gibbsdavidl/CatterPlots")
5713 (synopsis "Scatter plots with cat shaped points")
5714 (description "Did you ever wish you could make scatter plots with cat
5715 shaped points? Now you can!")
5716 (license license:asl2.0))))
5718 (define-public r-colorout
5725 (uri (string-append "https://github.com/jalvesaq/colorout/archive/"
5726 "v" version ".tar.gz"))
5727 (file-name (string-append name "-" version ".tar.gz"))
5730 "07vqx5ihgnq4dzn5jnfjfhdm3957v4prvf8vhnb3cwvlly4l7p9v"))))
5731 (build-system r-build-system)
5732 (home-page "https://github.com/jalvesaq/colorout")
5733 (synopsis "Colorize output in the R REPL")
5734 (description "@code{colorout} is an R package that colorizes R output when
5735 running in terminal emulator.
5737 R STDOUT is parsed and numbers, negative numbers, dates in the standard
5738 format, strings, and R constants are identified and wrapped by special ANSI
5739 scape codes that are interpreted by terminal emulators as commands to colorize
5740 the output. R STDERR is also parsed to identify the expressions warning and
5741 error and their translations to many languages. If these expressions are
5742 found, the output is colorized accordingly; otherwise, it is colorized as
5743 STDERROR (blue, by default).
5745 You can customize the colors according to your taste, guided by the color
5746 table made by the command @code{show256Colors()}. You can also set the colors
5747 to any arbitrary string. In this case, it is up to you to set valid values.")
5748 (license license:gpl3+)))
5750 (define-public r-txtplot
5757 (uri (cran-uri "txtplot" version))
5760 "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h"))))
5761 (build-system r-build-system)
5762 (home-page "https://cran.r-project.org/web/packages/txtplot/")
5763 (synopsis "Text-based plotting")
5764 (description "This package provides functions to produce rudimentary ASCII
5765 graphics directly in the terminal window. This package provides a basic
5766 plotting function (and equivalents of curve, density, acf and barplot) as well
5767 as a boxplot function.")
5768 (license license:lgpl3+)))
5770 (define-public python-rpy2
5772 (name "python-rpy2")
5777 (uri (pypi-uri "rpy2" version))
5780 "0bl1d2qhavmlrvalir9hmkjh74w21vzkvc2sg3cbb162s10zfmxy"))))
5781 (build-system python-build-system)
5783 '(#:modules ((ice-9 ftw)
5787 (guix build python-build-system))
5789 (modify-phases %standard-phases
5791 (lambda* (#:key outputs inputs #:allow-other-keys)
5792 (let ((cwd (getcwd)))
5793 (setenv "PYTHONPATH"
5794 (string-append cwd "/build/"
5795 (find (cut string-prefix? "lib" <>)
5796 (scandir (string-append cwd "/build")))
5798 (getenv "PYTHONPATH"))))
5799 (invoke "python" "-m" "rpy2.tests" "-v"))))))
5801 `(("python-six" ,python-six)
5802 ("python-jinja2" ,python-jinja2)
5803 ("python-pytz" ,python-pytz)))
5805 `(("readline" ,readline)
5808 ("r-minimal" ,r-minimal)
5809 ("r-survival" ,r-survival)
5810 ("r-ggplot2" ,r-ggplot2)
5811 ("r-rsqlite" ,r-rsqlite)
5812 ("r-dplyr" ,r-dplyr)
5813 ("r-dbplyr" ,r-dbplyr)
5814 ("python-numpy" ,python-numpy)))
5817 (home-page "https://rpy2.bitbucket.io/")
5818 (synopsis "Python interface to the R language")
5819 (description "rpy2 is a redesign and rewrite of rpy. It is providing a
5820 low-level interface to R from Python, a proposed high-level interface,
5821 including wrappers to graphical libraries, as well as R-like structures and
5823 ;; Any of these licenses can be picked for the R interface. The whole
5824 ;; project is released under GPLv2+ according to the license declaration
5826 (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+))))
5828 (define-public java-jdistlib
5830 (name "java-jdistlib")
5834 (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
5835 version "-src.jar"))
5838 "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
5839 (build-system ant-build-system)
5841 `(#:jar-name "jdistlib.jar"
5843 #:tests? #f ; no dedicated test directory
5845 (modify-phases %standard-phases
5846 (add-after 'unpack 'fix-broken-encoding
5848 (with-fluids ((%default-port-encoding "ISO-8859-1"))
5849 (substitute* "src/jdistlib/Beta.java"
5850 (("Scheff.+-Tukey") "Scheffe-Tukey")))
5853 `(("java-jtransforms" ,java-jtransforms)))
5855 `(("java-junit" ,java-junit)))
5856 (home-page "http://jdistlib.sourceforge.net/")
5857 (synopsis "Java library of statistical distributions")
5858 (description "JDistlib is the Java Statistical Distribution Library, a
5859 Java package that provides routines for various statistical distributions.")
5860 ;; The files that were translated from R code are under GPLv2+; some files
5861 ;; are under the GPLv3, which is a mistake. The author confirmed in an
5862 ;; email that this whole project should be under GPLv2+.
5863 (license license:gpl2+)))
5865 (define-public emacs-ess
5871 (uri (string-append "https://github.com/emacs-ess/ESS/archive/v"
5875 "0cbilbsiwvcyf6d5y24mymp57m3ana5dkzab3knfs83w4a3a4c5c"))
5876 (file-name (string-append name "-" version ".tar.gz"))
5877 (modules '((guix build utils)))
5880 ;; Stop ESS from trying to bundle an external julia-mode.el.
5881 (substitute* "lisp/Makefile"
5882 (("^\tjulia-mode.elc\\\\\n") "")
5883 (("^dist: all julia-mode.el")
5885 ;; No need to build docs in so many formats. Also, skipping
5886 ;; pdf lets us not pull in texlive.
5887 (substitute* "doc/Makefile"
5888 (("all : info text html pdf")
5890 (("install: install-info install-other-docs")
5891 "install: install-info"))
5892 ;; Test fails upstream
5893 (substitute* "test/ess-r-tests.el"
5894 (("ert-deftest ess-r-namespaced-eval-no-srcref-in-errors ()")
5895 "ert-deftest ess-r-namespaced-eval-no-srcref-in-errors () :expected-result :failed"))
5897 (build-system gnu-build-system)
5899 (let ((base-directory "/share/emacs/site-lisp/guix.d/ess"))
5900 `(#:make-flags (list (string-append "PREFIX=" %output)
5901 (string-append "ETCDIR=" %output "/"
5902 ,base-directory "/etc")
5903 (string-append "LISPDIR=" %output "/"
5906 (modify-phases %standard-phases
5908 (add-before 'build 'more-shebang-patching
5909 (lambda* (#:key inputs #:allow-other-keys)
5910 (substitute* "Makeconf"
5911 (("SHELL = /bin/sh")
5912 (string-append "SHELL = " (which "sh"))))
5916 (invoke "make" "test")))))))
5918 `(("emacs" ,emacs-minimal)
5919 ("r-minimal" ,r-minimal)))
5922 ("texinfo" ,texinfo)))
5924 `(("emacs-julia-mode" ,emacs-julia-mode)))
5925 (home-page "https://ess.r-project.org/")
5926 (synopsis "Emacs mode for statistical analysis programs")
5927 (description "Emacs Speaks Statistics (ESS) is an add-on package for GNU
5928 Emacs. It is designed to support editing of scripts and interaction with
5929 various statistical analysis programs such as R, Julia, and JAGS.")
5930 (license license:gpl2+)))