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 ssh)
70 #:use-module (gnu packages tcl)
71 #:use-module (gnu packages tex)
72 #:use-module (gnu packages texinfo)
73 #:use-module (gnu packages time)
74 #:use-module (gnu packages tls)
75 #:use-module (gnu packages base)
76 #:use-module (gnu packages web)
77 #:use-module (gnu packages xml)
78 #:use-module (gnu packages xorg)
79 #:use-module (srfi srfi-1))
89 (uri (string-append "mirror://gnu/pspp/pspp-"
93 "07pp27zycrb5x927jwaj9r3q7hy915jh51xs85zxby6gfiwl63m5"))))
94 (build-system gnu-build-system)
97 ("gettext" ,gettext-minimal)
101 ("readline" ,readline)
103 ("gtksourceview" ,gtksourceview)
104 ("spread-sheet-widget" ,spread-sheet-widget)
107 `(("autoconf" ,autoconf) ;for tests
108 ("glib" ,glib "bin") ;for glib-genmarshal
110 ("pkg-config" ,pkg-config)
111 ("python" ,python-2) ;for tests
112 ("texinfo" ,texinfo)))
113 (home-page "https://www.gnu.org/software/pspp/")
114 (synopsis "Statistical analysis")
116 "GNU PSPP is a statistical analysis program. It can perform
117 descriptive statistics, T-tests, linear regression and non-parametric tests.
118 It features both a graphical interface as well as command-line input. PSPP
119 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
120 can be imported from spreadsheets, text files and database sources and it can
121 be output in text, PostScript, PDF or HTML.")
122 (license license:gpl3+)))
130 (uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/"
131 (version-major version) ".x/Source/"
132 "JAGS-" version ".tar.gz"))
135 "1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica"))))
136 (build-system gnu-build-system)
137 (home-page "http://mcmc-jags.sourceforge.net/")
139 `(("gfortran" ,gfortran)
141 (synopsis "Gibbs sampler")
142 (description "JAGS is Just Another Gibbs Sampler. It is a program for
143 analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
144 simulation not wholly unlike BUGS. JAGS was written with three aims in mind:
147 @item To have a cross-platform engine for the BUGS language;
148 @item To be extensible, allowing users to write their own functions,
149 distributions and samplers;
150 @item To be a platform for experimentation with ideas in Bayesian modelling.
152 (license license:gpl2)))
154 (define-public libxls
161 (uri (string-append "https://github.com/libxls/libxls/releases/download/"
162 "v" version "/libxls-" version ".tar.gz"))
164 (base32 "00j2lrcvvhclmh3z9vy7myqq1br1jnnqkz2wzgk4a1gbg8c5afn5"))))
165 (build-system gnu-build-system)
166 (home-page "https://github.com/libxls/libxls")
167 (synopsis "Read binary (.xls) Excel spreadsheet files")
169 "libxls is a C library to read .xls spreadsheet files in the binary OLE
170 BIFF8 format as created by Excel 97 and later versions. It cannot write them.
172 This package also provides @command{xls2csv} to export Excel files to CSV.")
173 (license license:bsd-2)))
175 ;; Update this package together with the set of recommended packages: r-boot,
176 ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
177 ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
180 (name "r-with-tests")
184 (uri (string-append "mirror://cran/src/base/R-"
185 (version-major version) "/R-"
189 "02bmylmzrm9sdidirmwy233lghmd2346z725ca71ari68lzarz1n"))))
190 (build-system gnu-build-system)
192 `(#:disallowed-references (,tzdata-for-tests)
194 (list (string-append "LDFLAGS=-Wl,-rpath="
195 (assoc-ref %outputs "out")
197 ;; This affects the embedded timestamp of only the core packages.
198 "PKG_BUILT_STAMP=1970-01-01")
200 (modify-phases %standard-phases
201 (add-before 'configure 'do-not-compress-serialized-files
202 (lambda* (#:key inputs #:allow-other-keys)
203 ;; This ensures that Guix can detect embedded store references;
204 ;; see bug #28157 for details.
205 (substitute* "src/library/base/makebasedb.R"
206 (("compress = TRUE") "compress = FALSE"))
208 (add-before 'configure 'patch-uname
209 (lambda* (#:key inputs #:allow-other-keys)
210 (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
212 (substitute* "src/scripts/R.sh.in"
213 (("uname") uname-bin)))
215 (add-after 'unpack 'build-reproducibly
217 ;; The documentation contains time stamps to demonstrate
218 ;; documentation generation in different phases.
219 (substitute* "src/library/tools/man/Rd2HTML.Rd"
220 (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
221 "(removed for reproducibility)"))
223 ;; Remove timestamp from tracing environment. This fixes
224 ;; reproducibility of "methods.rd{b,x}".
225 (substitute* "src/library/methods/R/trace.R"
226 (("dateCreated = Sys.time\\(\\)")
227 "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
229 ;; Ensure that gzipped files are reproducible.
230 (substitute* '("src/library/grDevices/Makefile.in"
231 "doc/manual/Makefile.in")
232 (("R_GZIPCMD\\)" line)
233 (string-append line " -n")))
235 ;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
236 ;; queries the mtime of a given file and records it in an object.
237 ;; This is acceptable at runtime to detect stale source files,
238 ;; but it destroys reproducibility at build time.
240 ;; Similarly, the "srcfilecopy" procedure records the current
241 ;; time. We change both of them to respect SOURCE_DATE_EPOCH.
242 (substitute* "src/library/base/R/srcfile.R"
243 (("timestamp <- (timestamp.*|file.mtime.*)" _ time)
244 (string-append "timestamp <- \
245 as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
246 as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
247 } else { " time "}, origin=\"1970-01-01\")\n")))
249 ;; This library is installed using "install_package_description",
250 ;; so we need to pass the "builtStamp" argument.
251 (substitute* "src/library/tools/Makefile.in"
252 (("(install_package_description\\(.*\"')\\)\"" line prefix)
253 (string-append prefix ", builtStamp='1970-01-01')\"")))
255 (substitute* "src/library/Recommended/Makefile.in"
256 (("INSTALL_OPTS =" m)
257 (string-append m " --built-timestamp=1970-01-01" m)))
259 ;; R bundles an older version of help2man, which does not respect
260 ;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man,
261 ;; because that breaks a test.
262 (with-fluids ((%default-port-encoding "ISO-8859-1"))
263 (substitute* "tools/help2man.pl"
264 (("my \\$date = strftime \"%B %Y\", localtime" line)
265 (string-append line " 1"))))
267 (add-before 'configure 'set-default-pager
268 ;; Set default pager to "cat", because otherwise it is "false",
269 ;; making "help()" print nothing at all.
270 (lambda _ (setenv "PAGER" "cat") #t))
271 (add-before 'check 'set-timezone
272 ;; Some tests require the timezone to be set. However, the
273 ;; timezone may not just be "UTC", or else a brittle regression
274 ;; test in reg-tests-1d will fail.
275 (lambda* (#:key inputs #:allow-other-keys)
276 (setenv "TZ" "UTC+1")
278 (string-append (assoc-ref inputs "tzdata")
281 (add-after 'build 'make-info
282 (lambda _ (invoke "make" "info")))
283 (add-after 'build 'install-info
284 (lambda _ (invoke "make" "install-info"))))
286 `(;; We build the recommended packages here, because they are needed in
287 ;; order to run the test suite. We disable them in the r-minimal
290 "--with-blas=-lopenblas"
296 ,(string-append "--with-tcl-config="
297 (assoc-ref %build-inputs "tcl")
299 ,(string-append "--with-tk-config="
300 (assoc-ref %build-inputs "tk")
303 "--enable-BLAS-shlib"
304 "--with-system-tre")))
305 ;; R has some support for Java. When the JDK is available at configure
306 ;; time environment variables pointing to the JDK will be recorded under
307 ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
308 ;; CMD javareconf". "R CMD javareconf" appears to only be used to update
309 ;; the recorded environment variables in $R_HOME/etc. Refer to
310 ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
311 ;; for additional information.
313 ;; As the JDK is a rather large input with only very limited effects on R,
314 ;; we decided to drop it.
318 ("pkg-config" ,pkg-config)
319 ("texinfo" ,texinfo) ; for building HTML manuals
320 ("texlive" ,(texlive-union (list texlive-fonts-amsfonts
322 texlive-latex-amsfonts
324 texlive-latex-fancyvrb
325 texlive-latex-graphics
326 texlive-latex-hyperref
327 texlive-latex-oberdiek
329 texlive-latex-upquote
331 ("tzdata" ,tzdata-for-tests)
334 `(;; We need not only cairo here, but pango to ensure that tests for the
335 ;; "cairo" bitmapType plotting backend succeed.
337 ("coreutils" ,coreutils)
339 ("openblas" ,openblas)
340 ("gfortran" ,gfortran)
347 ("readline" ,readline)
348 ;; This avoids a reference to the ungraftable static bash. R uses the
349 ;; detected shell for the "system" procedure.
350 ("bash" ,bash-minimal)
356 (list (search-path-specification
357 (variable "R_LIBS_SITE")
358 (files (list "site-library/")))))
359 (home-page "https://www.r-project.org/")
360 (synopsis "Environment for statistical computing and graphics")
362 "R is a language and environment for statistical computing and graphics.
363 It provides a variety of statistical techniques, such as linear and nonlinear
364 modeling, classical statistical tests, time-series analysis, classification
365 and clustering. It also provides robust support for producing
366 publication-quality data plots. A large amount of 3rd-party packages are
367 available, greatly increasing its breadth and scope.")
368 (license license:gpl3+)))
370 (define-public r-minimal
371 (package (inherit r-with-tests)
375 ,@(substitute-keyword-arguments (package-arguments r-with-tests)
376 ((#:configure-flags flags)
377 ;; Do not build the recommended packages. The build system creates
378 ;; random temporary directories and embeds their names in some
379 ;; package files. We build these packages with the r-build-system
381 `(cons "--without-recommended-packages" ,flags)))))))
383 (define-public rmath-standalone
384 (package (inherit r-minimal)
385 (name "rmath-standalone")
388 (modify-phases %standard-phases
389 (add-after 'configure 'chdir
390 (lambda _ (chdir "src/nmath/standalone/") #t)))))
391 (synopsis "Standalone R math library")
393 "This package provides the R math library as an independent package.")))
395 (define-public r-boot
402 (uri (cran-uri "boot" version))
405 "1z2dig1mi76b3b9ck6qlkh07l3hs478gaf70db5nv8x7w2qhq7yg"))))
406 (build-system r-build-system)
407 (home-page "https://cran.r-project.org/web/packages/boot")
408 (synopsis "Bootstrap functions for R")
410 "This package provides functions and datasets for bootstrapping from the
411 book \"Bootstrap Methods and Their Application\" by A.C. Davison and
412 D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
413 ;; Unlimited distribution
414 (license (license:non-copyleft "file://R/bootfuns.q"))))
416 (define-public r-mass
423 (uri (cran-uri "MASS" version))
426 "0x1ckf51y851g0kvbhsgdxb26vfpmbw3xdbcnh3ck7fjm13da4cr"))))
427 (properties `((upstream-name . "MASS")))
428 (build-system r-build-system)
429 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
430 (synopsis "Support functions and datasets for Venables and Ripley's MASS")
432 "This package provides functions and datasets for the book \"Modern
433 Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
434 ;; Either version may be picked.
435 (license (list license:gpl2 license:gpl3))))
437 (define-public r-class
444 (uri (cran-uri "class" version))
447 "1x1hqz8xyhbpq4krsh02glqnlzcch25agkmn4a3da9n723b37gzn"))))
448 (build-system r-build-system)
450 `(("r-mass" ,r-mass)))
451 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
452 (synopsis "R functions for classification")
454 "This package provides various functions for classification, including
455 k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
456 ;; Either of the two versions can be picked.
457 (license (list license:gpl2 license:gpl3))))
459 (define-public r-cluster
466 (uri (cran-uri "cluster" version))
469 "1bg5dvs4bzj0rp75jpxaklz12rvyh5w99h7zkvfgpgn86ljg1rlf"))))
470 (build-system r-build-system)
472 `(("gfortran" ,gfortran)))
473 (home-page "https://cran.r-project.org/web/packages/cluster")
474 (synopsis "Methods for cluster analysis")
476 "This package provides methods for cluster analysis. It is a much
477 extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
478 Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
479 (license license:gpl2+)))
481 (define-public r-codetools
488 (uri (cran-uri "codetools" version))
491 "00bmhzqprqfn3w6ghx7sakai6s7il8gbksfiawj8in5mbhbncypn"))))
492 (build-system r-build-system)
493 (home-page "https://cran.r-project.org/web/packages/codetools")
494 (synopsis "Code analysis tools for R")
495 (description "This package provides code analysis tools for R to check R
496 code for possible problems.")
497 ;; Any version of the GPL.
498 (license (list license:gpl2+ license:gpl3+))))
500 (define-public r-foreign
507 (uri (cran-uri "foreign" version))
510 "1mv04w3ycz0ymsszn8aa87k6k5sb8mg8lhf1b8w4zpfrphpkkliv"))))
511 (build-system r-build-system)
512 (home-page "https://cran.r-project.org/web/packages/foreign")
513 (synopsis "Read data stored by other statistics software")
515 "This package provides functions for reading and writing data stored by
516 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
517 for reading and writing some dBase files.")
518 (license license:gpl2+)))
520 (define-public r-kernsmooth
522 (name "r-kernsmooth")
527 (uri (cran-uri "KernSmooth" version))
530 "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb"))))
531 (properties `((upstream-name . "KernSmooth")))
532 (build-system r-build-system)
534 `(("gfortran" ,gfortran)))
535 (home-page "https://cran.r-project.org/web/packages/KernSmooth")
536 (synopsis "Functions for kernel smoothing")
538 "This package provides functions for kernel smoothing (and density
539 estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
540 \"Kernel Smoothing\".")
541 ;; Unlimited use and distribution
542 (license (license:non-copyleft "file://LICENCE.note"))))
544 (define-public r-lattice
550 (uri (cran-uri "lattice" version))
553 "0b8abkz7syscq883mrgv63pkwaqkcpwfx8rgbqy9vgfva0z5xszx"))))
554 (build-system r-build-system)
555 (home-page "http://lattice.r-forge.r-project.org/")
556 (synopsis "High-level data visualization system")
558 "The lattice package provides a powerful and elegant high-level data
559 visualization system inspired by Trellis graphics, with an emphasis on
560 multivariate data. Lattice is sufficient for typical graphics needs, and is
561 also flexible enough to handle most nonstandard requirements.")
562 (license license:gpl2+)))
564 (define-public r-matrix
571 (uri (cran-uri "Matrix" version))
574 "1k1zf92ycqr7fz44w7bp1p354ww7jg0wm23ybb8dzmbg37qfchyv"))))
575 (properties `((upstream-name . "Matrix")))
576 (build-system r-build-system)
578 `(("r-lattice" ,r-lattice)))
579 (home-page "http://Matrix.R-forge.R-project.org/")
580 (synopsis "Sparse and dense matrix classes and methods")
582 "This package provides classes and methods for dense and sparse matrices
583 and operations on them using LAPACK and SuiteSparse.")
584 (license license:gpl2+)))
586 (define-public r-nlme
593 (uri (cran-uri "nlme" version))
596 "0k9x5j34fx093a023da9ny3b3101lbwpmfm27mkvfj950l22z88x"))))
597 (build-system r-build-system)
599 `(("r-lattice" ,r-lattice)))
601 `(("gfortran" ,gfortran)))
602 (home-page "https://cran.r-project.org/web/packages/nlme")
603 (synopsis "Linear and nonlinear mixed effects models")
605 "This package provides tools to fit and compare Gaussian linear and
606 nonlinear mixed-effects models.")
607 (license license:gpl2+)))
609 (define-public r-mgcv
616 (uri (cran-uri "mgcv" version))
619 "1snkpnkkigwrj9zm31j1nlivv9ls56imz263cv167hnmghiahpmm"))))
620 (build-system r-build-system)
622 `(("r-matrix" ,r-matrix)
624 (home-page "https://cran.r-project.org/web/packages/mgcv")
625 (synopsis "Mixed generalised additive model computation")
627 "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
628 parameter estimation by GCV, REML or UBRE/AIC. The library includes a
629 @code{gam()} function, a wide variety of smoothers, JAGS support and
630 distributions beyond the exponential family.")
631 (license license:gpl2+)))
633 (define-public r-nnet
640 (uri (cran-uri "nnet" version))
643 "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7"))))
644 (build-system r-build-system)
645 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
646 (synopsis "Feed-forward neural networks and multinomial log-linear models")
648 "This package provides functions for feed-forward neural networks with a
649 single hidden layer, and for multinomial log-linear models.")
650 (license (list license:gpl2+ license:gpl3+))))
652 (define-public r-rpart
659 (uri (cran-uri "rpart" version))
662 "0p5frya963ppn476p5dxs2mnarsalksr6gw9zzmjsn8ikq7bx3ib"))))
663 (build-system r-build-system)
664 (home-page "https://cran.r-project.org/web/packages/rpart")
665 (synopsis "Recursive partitioning and regression trees")
667 "This package provides recursive partitioning functions for
668 classification, regression and survival trees.")
669 (license (list license:gpl2+ license:gpl3+))))
671 (define-public r-spatial
678 (uri (cran-uri "spatial" version))
681 "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
682 (build-system r-build-system)
683 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
684 (synopsis "Functions for kriging and point pattern analysis")
686 "This package provides functions for kriging and point pattern
688 ;; Either version may be picked.
689 (license (list license:gpl2 license:gpl3))))
691 (define-public r-survival
698 (uri (cran-uri "survival" version))
701 "1faiwyg7x8y2kfzb66l4yc8br0mdlz4k20znmjrwq96dbzhm3cam"))))
702 (build-system r-build-system)
704 `(("r-matrix" ,r-matrix)))
705 (home-page "https://github.com/therneau/survival")
706 (synopsis "Survival analysis")
708 "This package contains the core survival analysis routines, including
709 definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
710 curves, Cox models, and parametric accelerated failure time models.")
711 (license license:lgpl2.0+)))
714 (package (inherit r-minimal)
717 (build-system trivial-build-system)
718 (arguments '(#:builder (begin (mkdir %output) #t)))
720 `(("r-minimal" ,r-minimal)
723 ("r-cluster" ,r-cluster)
724 ("r-codetools" ,r-codetools)
725 ("r-foreign" ,r-foreign)
726 ("r-kernsmooth" ,r-kernsmooth)
727 ("r-lattice" ,r-lattice)
729 ("r-matrix" ,r-matrix)
734 ("r-spatial" ,r-spatial)
735 ("r-survival" ,r-survival)))))
744 (uri (cran-uri "bit" version))
747 "0m7jrqzpa1pk8ixcl814x06jf96nlvvr16x6did6cfk4zghsrfjw"))))
748 (build-system r-build-system)
749 (home-page "http://ff.r-forge.r-project.org")
750 (synopsis "Class for vectors of 1-bit booleans")
752 "This package provides bitmapped vectors of booleans (no @code{NA}s),
753 coercion from and to logicals, integers and integer subscripts, fast boolean
754 operators and fast summary statistics. With @code{bit} class vectors of true
755 binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
756 (license license:gpl2)))
758 (define-public r-bit64
765 (uri (cran-uri "bit64" version))
768 "07znvz9vp1nz1y5ljng4qyskvm943cdbmy996s67560ijxzsm6kv"))))
769 (build-system r-build-system)
772 (home-page "http://ff.r-forge.r-project.org/")
773 (synopsis "S3 class for vectors of 64 bit integers")
775 "The bit64 package provides serializable S3 atomic 64 bit (signed)
776 integers that can be used in vectors, matrices, arrays and @code{data.frames}.
777 Methods are available for coercion from and to logicals, integers, doubles,
778 characters and factors as well as many elementwise and summary functions.
779 Many fast algorithmic operations such as @code{match} and @code{order} support
780 interactive data exploration and manipulation and optionally leverage
782 (license license:gpl2)))
784 (define-public r-dichromat
791 (uri (cran-uri "dichromat" version))
793 (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
794 (build-system r-build-system)
795 (home-page "https://cran.r-project.org/web/packages/dichromat")
796 (synopsis "Color schemes for dichromats")
798 "Dichromat collapses red-green or green-blue distinctions to simulate the
799 effects of different types of color-blindness.")
800 (license license:gpl2+)))
802 (define-public r-digest
809 (uri (cran-uri "digest" version))
811 (base32 "0k3iv0r8wy8w7zchmgrnrqv3bc149075j4817kf0q521vi4f6vbj"))))
812 (build-system r-build-system)
813 ;; Vignettes require r-knitr, which requires r-digest, so we have to
814 ;; disable them and the tests.
817 #:configure-flags (list "--no-build-vignettes")))
818 (home-page "http://dirk.eddelbuettel.com/code/digest.html")
819 (synopsis "Create cryptographic hash digests of R objects")
821 "This package contains an implementation of a function @code{digest()} for
822 the creation of hash digests of arbitrary R objects (using the md5, sha-1,
823 sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
824 of R language objects, as well as a function @code{hmac()} to create hash-based
825 message authentication code.
827 Please note that this package is not meant to be deployed for cryptographic
828 purposes for which more comprehensive (and widely tested) libraries such as
829 OpenSSL should be used.")
830 (license license:gpl2+)))
832 (define-public r-estimability
834 (name "r-estimability")
838 (uri (cran-uri "estimability" version))
841 "0cifdaa71spkcxl4db4z884jrya865sg3dhcv4isd8fnzg2pjcd3"))))
842 (build-system r-build-system)
843 (home-page "https://cran.r-project.org/web/packages/estimability")
844 (synopsis "Tools for assessing estimability of linear predictions")
845 (description "Provides tools for determining estimability of linear
846 functions of regression coefficients, and @code{epredict} methods that handle
847 non-estimable cases correctly.")
848 (license license:gpl2+)))
850 (define-public r-pheatmap
857 (uri (cran-uri "pheatmap" version))
860 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
861 (build-system r-build-system)
863 `(("r-gtable" ,r-gtable)
864 ("r-rcolorbrewer" ,r-rcolorbrewer)
865 ("r-scales" ,r-scales)))
867 "https://cran.r-project.org/web/packages/pheatmap")
868 (synopsis "Pretty heatmaps")
870 "This package provides an implementation of heatmaps that offers more
871 control over dimensions and appearance.")
872 (license license:gpl2+)))
874 (define-public r-labeling
881 (uri (cran-uri "labeling" version))
883 (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
884 (build-system r-build-system)
885 (home-page "https://cran.r-project.org/web/packages/labeling")
886 (synopsis "Axis labeling algorithms")
887 (description "The labeling package provides a range of axis labeling
889 (license license:expat)))
891 (define-public r-magrittr
898 (uri (cran-uri "magrittr" version))
900 (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
901 (build-system r-build-system)
902 (home-page "https://cran.r-project.org/web/packages/magrittr/index.html")
903 (synopsis "A forward-pipe operator for R")
905 "Magrittr provides a mechanism for chaining commands with a new
906 forward-pipe operator, %>%. This operator will forward a value, or the result
907 of an expression, into the next function call/expression. There is flexible
908 support for the type of right-hand side expressions. For more information,
909 see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
910 (license license:expat)))
912 (define-public r-munsell
919 (uri (cran-uri "munsell" version))
921 (base32 "16g1fzisbpqb15yh3pqf3iia4csppva5dnv1z88x9dg263xskwyh"))))
922 (build-system r-build-system)
924 `(("r-colorspace" ,r-colorspace)))
925 (home-page "https://cran.r-project.org/web/packages/munsell")
926 (synopsis "Munsell colour system")
928 "The Munsell package contains Functions for exploring and using the
929 Munsell colour system.")
930 (license license:expat)))
932 (define-public r-permute
939 (uri (cran-uri "permute" version))
942 "0ra8p5mf2590azrkas8z2ry7mif77xqxd29n4zgyi5vll225726j"))))
943 (build-system r-build-system)
944 ;; Tests do not run correctly, but running them properly would entail a
945 ;; circular dependency with vegan.
946 (home-page "https://github.com/gavinsimpson/permute")
947 (synopsis "Functions for Generating Restricted Permutations of Data")
949 "This package provides a set of restricted permutation designs for freely
950 exchangeable, line transects (time series), spatial grid designs and permutation
951 of blocks (groups of samples). @code{permute} also allows split-plot designs,
952 in which the whole-plots or split-plots or both can be freely exchangeable.")
953 (license license:gpl2+)))
955 (define-public r-plyr
962 (uri (cran-uri "plyr" version))
964 (base32 "1igar5pcjqh0jyxv0z3jah8rz617vfa86vw0r5c7c031b7bj5db0"))))
965 (build-system r-build-system)
966 (native-inputs `(("r-rcpp" ,r-rcpp)))
967 (home-page "http://had.co.nz/plyr")
968 (synopsis "Tools for Splitting, Applying and Combining Data")
970 "Plyr is a set of tools that solves a common set of problems: you need to
971 break a big problem down into manageable pieces, operate on each piece and
972 then put all the pieces back together. For example, you might want to fit a
973 model to each spatial location or time point in your study, summarise data by
974 panels or collapse high-dimensional arrays to simpler summary statistics.")
975 (license license:expat)))
977 (define-public r-proto
984 (uri (cran-uri "proto" version))
986 (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
987 (build-system r-build-system)
988 (home-page "https://github.com/hadley/proto")
989 (synopsis "Prototype object-based programming")
991 "Proto is an object oriented system using object-based, also called
992 prototype-based, rather than class-based object oriented ideas.")
993 (license license:gpl2+)))
995 (define-public r-rcolorbrewer
997 (name "r-rcolorbrewer")
1002 (uri (cran-uri "RColorBrewer" version))
1004 (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
1005 (build-system r-build-system)
1006 (home-page "https://cran.r-project.org/web/packages/RColorBrewer")
1007 (synopsis "ColorBrewer palettes")
1009 "This package provides color schemes for maps (and other graphics)
1010 designed by Cynthia Brewer as described at http://colorbrewer2.org")
1011 ;; Includes code licensed under bsd-4
1012 (license license:asl2.0)))
1014 (define-public r-sendmailr
1016 (name "r-sendmailr")
1021 (uri (cran-uri "sendmailR" version))
1024 "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
1025 (properties `((upstream-name . "sendmailR")))
1026 (build-system r-build-system)
1028 `(("r-base64enc" ,r-base64enc)))
1030 "https://cran.r-project.org/web/packages/sendmailR")
1031 (synopsis "Send email using R")
1033 "This package contains a simple SMTP client which provides a portable
1034 solution for sending email, including attachments, from within R.")
1035 (license license:gpl2+)))
1037 (define-public r-stringi
1044 (uri (cran-uri "stringi" version))
1047 "1vbr6g9p1iyzdj7wfw6afyizvnd1a2srfvkl72pq23vhdcwwpkhk"))))
1048 (build-system r-build-system)
1049 (inputs `(("icu4c" ,icu4c)))
1050 (native-inputs `(("pkg-config" ,pkg-config)))
1051 (home-page "http://stringi.rexamine.com/")
1052 (synopsis "Character string processing facilities")
1054 "This package allows for fast, correct, consistent, portable, as well as
1055 convenient character string/text processing in every locale and any native
1056 encoding. Owing to the use of the ICU library, the package provides R users
1057 with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
1058 programmers. Among available features there are: pattern searching
1059 (e.g. via regular expressions), random string generation, string collation,
1060 transliteration, concatenation, date-time formatting and parsing, etc.")
1061 (license license:bsd-3)))
1063 (define-public r-stringr
1070 (uri (cran-uri "stringr" version))
1072 (base32 "1p9ip7p87gbbg4s6d3d392svvzz2b5dqdq2c8ilgvn4s78nlsq47"))))
1073 (build-system r-build-system)
1075 `(("r-glue" ,r-glue)
1076 ("r-magrittr" ,r-magrittr)
1077 ("r-stringi" ,r-stringi)))
1078 (home-page "https://github.com/hadley/stringr")
1079 (synopsis "Simple, consistent wrappers for common string operations")
1081 "Stringr is a consistent, simple and easy to use set of wrappers around
1082 the fantastic @code{stringi} package. All function and argument names (and
1083 positions) are consistent, all functions deal with \"NA\"'s and zero length
1084 vectors in the same way, and the output from one function is easy to feed into
1085 the input of another.")
1086 (license license:gpl2+)))
1088 (define-public r-reshape2
1095 (uri (cran-uri "reshape2" version))
1097 (base32 "03ki5ka1dj208fc0dclbm0b4xp9d769pah2j9cs34l776p4r9zwa"))))
1098 (build-system r-build-system)
1100 `(("r-plyr" ,r-plyr)
1102 ("r-stringr" ,r-stringr)))
1103 (home-page "https://github.com/hadley/reshape")
1104 (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
1106 "Reshape2 is an R library to flexibly restructure and aggregate data
1107 using just two functions: melt and dcast (or acast).")
1108 (license license:expat)))
1110 (define-public r-scales
1117 (uri (cran-uri "scales" version))
1119 (base32 "0353dkh3d7x78463c6ds80hcml59lrqwr8rlv82a8dnkxla4l7qc"))))
1120 (build-system r-build-system)
1122 `(("r-labeling" ,r-labeling)
1123 ("r-munsell" ,r-munsell)
1124 ("r-rcolorbrewer" ,r-rcolorbrewer)
1127 ("r-viridislite" ,r-viridislite)))
1128 (home-page "https://github.com/hadley/scales")
1129 (synopsis "Scale functions for visualization")
1131 "This package provides graphical scales that map data to aesthetics, and
1132 provides methods for automatically determining breaks and labels for axes and
1134 (license license:expat)))
1136 (define-public r-ggplot2
1143 (uri (cran-uri "ggplot2" version))
1145 (base32 "0y8cks9r9hvjlx0isnvbgs3p0al167hlr3q7c3syfcj77dzjkpmz"))))
1146 (build-system r-build-system)
1148 `(("r-digest" ,r-digest)
1149 ("r-gtable" ,r-gtable)
1151 ("r-lazyeval" ,r-lazyeval)
1154 ("r-tibble" ,r-tibble)
1155 ("r-reshape2" ,r-reshape2)
1156 ("r-rlang" ,r-rlang)
1157 ("r-scales" ,r-scales)
1158 ("r-svglite" ,r-svglite) ; Needed for 'ggsave'
1159 ("r-viridislite" ,r-viridislite)
1160 ("r-withr" ,r-withr)))
1161 (home-page "https://ggplot2.tidyverse.org")
1162 (synopsis "An implementation of the grammar of graphics")
1164 "Ggplot2 is an implementation of the grammar of graphics in R. It
1165 combines the advantages of both base and lattice graphics: conditioning and
1166 shared axes are handled automatically, and you can still build up a plot step
1167 by step from multiple data sources. It also implements a sophisticated
1168 multidimensional conditioning system and a consistent interface to map data to
1169 aesthetic attributes.")
1170 (license license:gpl2+)))
1172 (define-public r-ggdendro
1178 (uri (cran-uri "ggdendro" version))
1181 "1zzq1hxd0d1qa5hrzwfkdw6fzscpcafbwbpkrb62dm559y8awp0j"))))
1182 (build-system r-build-system)
1184 `(("r-ggplot2" ,r-ggplot2)
1186 ("r-knitr" ,r-knitr)))
1187 (home-page "https://github.com/andrie/ggdendro")
1188 (synopsis "Create Dendrograms and Tree Diagrams Using ggplot2")
1189 (description "This is a set of tools for dendrograms and tree plots using
1190 ggplot2. The ggplot2 philosophy is to clearly separate data from the
1191 presentation. Unfortunately the plot method for dendrograms plots directly
1192 to a plot device with out exposing the data. The ggdendro package resolves
1193 this by making available functions that extract the dendrogram plot data.
1194 The package provides implementations for tree, rpart, as well as diana and
1195 agnes cluster diagrams.")
1196 (license license:gpl2+)))
1198 (define-public r-gdtools
1205 (uri (cran-uri "gdtools" version))
1208 "1ayy0s699ghaz34lklvcskfwman3x2n2772s5sa5x9k9xgsnxwcl"))))
1209 (build-system r-build-system)
1211 `(("pkg-config" ,pkg-config)))
1216 `(("r-rcpp" ,r-rcpp)
1217 ("r-withr" ,r-withr)))
1218 (home-page "https://cran.r-project.org/web/packages/gdtools")
1219 (synopsis "Utilities for graphical rendering")
1221 "The @code{gdtools} package provides functionalities to get font metrics
1222 and to generate base64 encoded string from raster matrix.")
1223 (license license:gpl3)))
1225 (define-public r-svglite
1232 (uri (cran-uri "svglite" version))
1235 "1gwv51wqp6pgm2f9gavsiq65njs77fr49n8y6y9ax60k3a4vvg14"))))
1236 (build-system r-build-system)
1239 ("r-gdtools" ,r-gdtools)
1240 ("r-rcpp" ,r-rcpp)))
1241 (home-page "https://github.com/hadley/svglite")
1242 (synopsis "SVG graphics device")
1244 "@code{svglite} is a graphics device that produces clean
1245 @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
1246 hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
1247 considerably faster, produces smaller files, and leaves text as is.")
1248 (license license:gpl2+)))
1250 (define-public r-assertthat
1252 (name "r-assertthat")
1256 (uri (cran-uri "assertthat" version))
1259 "17wy5bdfzg73sg2clisg1k3zyn1adkj59x56m5nwia2k8z67zkw5"))))
1260 (build-system r-build-system)
1261 (home-page "https://github.com/hadley/assertthat")
1262 (synopsis "Easy pre and post assertions")
1264 "Assertthat is an extension to stopifnot() that makes it easy to declare
1265 the pre and post conditions that your code should satisfy, while also
1266 producing friendly error messages so that your users know what they've done
1268 (license license:gpl3+)))
1270 (define-public r-lazyeval
1276 (uri (cran-uri "lazyeval" version))
1279 "1m10i059csrcqkcn59a8wspn784alxsq3symzhn24mhhl894346n"))))
1280 (build-system r-build-system)
1281 (home-page "https://github.com/hadley/lazyeval")
1282 (synopsis "Lazy (non-standard) evaluation in R")
1284 "This package provides the tools necessary to do non-standard
1285 evaluation (NSE) in R.")
1286 (license license:gpl3+)))
1288 (define-public r-dbi
1294 (uri (cran-uri "DBI" version))
1297 "1x8wy2vg2gcgd9bww04qmf0dsn3kp0rfjd8q8j1r2x9zxccg25pz"))))
1298 (build-system r-build-system)
1299 (home-page "https://github.com/rstats-db/DBI")
1300 (synopsis "R database interface")
1302 "The DBI package provides a database interface (DBI) definition for
1303 communication between R and relational database management systems. All
1304 classes in this package are virtual and need to be extended by the various
1305 R/DBMS implementations.")
1306 (license license:lgpl2.0+)))
1311 (version "1.69.0-1")
1314 (uri (cran-uri "BH" version))
1317 "18mckfwxxv8m8rzaz03mg2h6vhaj7y131h6yasfg0s73nxj47zd0"))))
1318 (build-system r-build-system)
1319 (home-page "https://github.com/eddelbuettel/bh")
1320 (synopsis "R package providing subset of Boost headers")
1322 "This package aims to provide the most useful subset of Boost libraries
1323 for template use among CRAN packages.")
1324 (license license:boost1.0)))
1326 (define-public r-evaluate
1332 (uri (cran-uri "evaluate" version))
1335 "0igvc27rsqxcswjb9slnpi5d509rffxn1y5d82hgqvv970nl3p2q"))))
1336 (build-system r-build-system)
1337 (home-page "https://github.com/hadley/evaluate")
1338 (synopsis "Parsing and evaluation tools for R")
1340 "This package provides tools that allow you to recreate the parsing,
1341 evaluation and display of R code, with enough information that you can
1342 accurately recreate what happens at the command line. The tools can easily be
1343 adapted for other output formats, such as HTML or LaTeX.")
1344 (license license:gpl3+)))
1346 (define-public r-formatr
1352 (uri (cran-uri "formatR" version))
1355 "0a9229rg3s9qga5v2fwfdqr0z3bk2yycv8kijrcm3jh66l68zjgm"))))
1356 (build-system r-build-system)
1357 (home-page "http://yihui.name/formatR")
1358 (synopsis "Format R code automatically")
1360 "This package provides a function to format R source code. Spaces and
1361 indent will be added to the code automatically, and comments will be preserved
1362 under certain conditions, so that R code will be more human-readable and tidy.
1363 There is also a Shiny app as a user interface in this package.")
1364 (license license:gpl3+)))
1366 (define-public r-highr
1372 (uri (cran-uri "highr" version))
1375 "0my6idnhmmgs4q1vs40y2lh56yij2p59mpwvm53wjs2zk6x1zl2b"))))
1376 (build-system r-build-system)
1377 (home-page "https://github.com/yihui/highr")
1378 (synopsis "Syntax highlighting for R source code")
1380 "This package provides syntax highlighting for R source code. Currently
1381 it supports LaTeX and HTML output. Source code of other languages is
1382 supported via Andre Simon's highlight package.")
1383 (license license:gpl3+)))
1385 (define-public r-mime
1391 (uri (cran-uri "mime" version))
1394 "00f4gw4sg1kn03s67gficxgb7a7fb6pwhlvrxrml05q1mc2vcxa7"))))
1395 (build-system r-build-system)
1396 (home-page "https://github.com/yihui/mime")
1397 (synopsis "R package to map filenames to MIME types")
1399 "This package guesses the MIME type from a filename extension using the
1400 data derived from /etc/mime.types in UNIX-type systems.")
1401 (license license:gpl2)))
1403 (define-public r-markdown
1409 (uri (cran-uri "markdown" version))
1412 "08xzs4bcf12jxp0276m6xqvq8kcgg5qp6fxrvsz6r9x73jjccs1h"))))
1413 (build-system r-build-system)
1414 ;; Skip check phase because the tests require the r-knitr package to be
1415 ;; installed. This prevents installation failures. Knitr normally
1416 ;; shouldn't be available since r-markdown is a dependency of the r-knitr
1418 (arguments `(#:tests? #f))
1420 `(("r-mime" ,r-mime)))
1421 (home-page "https://github.com/rstudio/markdown")
1422 (synopsis "Markdown rendering for R")
1424 "This package provides R bindings to the Sundown Markdown rendering
1425 library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
1426 syntax that can be converted to XHTML or other formats.")
1427 (license license:gpl2)))
1429 (define-public r-yaml
1435 (uri (cran-uri "yaml" version))
1438 "0in562nd0i23cg91a8kdbqgim656fgscykwi0icsnq53xj3srg2m"))))
1439 (build-system r-build-system)
1440 (home-page "https://cran.r-project.org/web/packages/yaml/")
1441 (synopsis "Methods to convert R data to YAML and back")
1443 "This package implements the libyaml YAML 1.1 parser and
1444 emitter (http://pyyaml.org/wiki/LibYAML) for R.")
1445 (license license:bsd-3)))
1447 (define-public r-knitr
1453 (uri (cran-uri "knitr" version))
1456 "1iks80g1cj25rvgyf0y2jc2pmfvsq4sbgdp788w9016bk71wzdcs"))))
1457 (build-system r-build-system)
1459 `(("r-evaluate" ,r-evaluate)
1460 ("r-highr" ,r-highr)
1461 ("r-markdown" ,r-markdown)
1462 ("r-stringr" ,r-stringr)
1464 ("r-yaml" ,r-yaml)))
1465 (home-page "http://yihui.name/knitr/")
1466 (synopsis "General-purpose package for dynamic report generation in R")
1468 "This package provides a general-purpose tool for dynamic report
1469 generation in R using Literate Programming techniques.")
1470 ;; The code is released under any version of the GPL. As it is used by
1471 ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
1473 (license license:gpl2+)))
1475 (define-public r-knitrbootstrap
1477 (name "r-knitrbootstrap")
1482 (uri (cran-uri "knitrBootstrap" version))
1485 "1aj60j7f0gcs120fdrnfbnb7vk7lfn1phil0mghg6a5zldz4cqs3"))))
1486 (properties `((upstream-name . "knitrBootstrap")))
1487 (build-system r-build-system)
1489 `(("r-knitr" ,r-knitr)
1490 ("r-rmarkdown" ,r-rmarkdown)
1491 ("r-markdown" ,r-markdown)))
1492 (home-page "https://github.com/jimhester/knitrBootstrap")
1493 (synopsis "Knitr bootstrap framework")
1495 "This package provides a framework to create Bootstrap 3 HTML reports
1496 from knitr Rmarkdown.")
1497 (license license:expat)))
1499 (define-public r-microbenchmark
1501 (name "r-microbenchmark")
1505 (uri (cran-uri "microbenchmark" version))
1508 "1sn1fxgzakm5iqbgc35g3k4yi0iqrkmwz33cvdrphrzh1lxnmi3s"))))
1509 (build-system r-build-system)
1510 (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
1511 (synopsis "Accurate timing functions for R")
1513 "This package provides infrastructure to accurately measure and compare
1514 the execution time of R expressions.")
1515 (license license:bsd-2)))
1517 (define-public r-pryr
1523 (uri (cran-uri "pryr" version))
1526 "06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k"))))
1527 (build-system r-build-system)
1529 `(("r-stringr" ,r-stringr)
1530 ("r-codetools" ,r-codetools)))
1532 `(("r-rcpp" ,r-rcpp)))
1533 (home-page "https://github.com/hadley/pryr")
1534 (synopsis "Tools for computing on the R language")
1536 "This package provides useful tools to pry back the covers of R and
1537 understand the language at a deeper level.")
1538 (license license:gpl2)))
1540 (define-public r-memoise
1546 (uri (cran-uri "memoise" version))
1549 "034qfc2xlh30x1q2vya239w34a3ir3y2fwnx2agbgbi6592zjxmj"))))
1550 (build-system r-build-system)
1552 `(("r-digest" ,r-digest)))
1553 (home-page "https://github.com/hadley/memoise")
1554 (synopsis "Memoise functions for R")
1556 "This R package allows to cache the results of a function so that when
1557 you call it again with the same arguments it returns the pre-computed value.")
1558 (license license:expat)))
1560 (define-public r-crayon
1566 (uri (cran-uri "crayon" version))
1569 "0s7s6vc3ww8pzanpjisym4jjvwcc5pi2qg8srx7jqlz9j3wrnvpw"))))
1570 (build-system r-build-system)
1572 `(("r-memoise" ,r-memoise)))
1573 (home-page "https://github.com/gaborcsardi/crayon")
1574 (synopsis "Colored terminal output for R")
1576 "Colored terminal output on terminals that support ANSI color and
1577 highlight codes. It also works in Emacs ESS. ANSI color support is
1578 automatically detected. Colors and highlighting can be combined and nested.
1579 New styles can also be created easily. This package was inspired by the
1580 \"chalk\" JavaScript project.")
1581 (license license:expat)))
1583 (define-public r-praise
1590 (uri (cran-uri "praise" version))
1593 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
1594 (build-system r-build-system)
1595 (home-page "https://github.com/gaborcsardi/praise")
1596 (synopsis "Functions to praise users")
1598 "This package provides template functions to assist in building friendly
1599 R packages that praise their users.")
1600 (license license:expat)))
1602 (define-public r-testthat
1608 (uri (cran-uri "testthat" version))
1611 "03jgr0hlr77yp0aib4v30yjyjrjsa8dczr02yk21m93vl25vqvkp"))))
1612 (build-system r-build-system)
1615 ("r-crayon" ,r-crayon)
1616 ("r-digest" ,r-digest)
1617 ("r-magrittr" ,r-magrittr)
1618 ("r-praise" ,r-praise)
1620 ("r-rlang" ,r-rlang)
1621 ("r-withr" ,r-withr)))
1622 (home-page "https://github.com/hadley/testthat")
1623 (synopsis "Unit testing for R")
1625 "This package provides a unit testing system for R designed to be fun,
1626 flexible and easy to set up.")
1627 (license license:expat)))
1635 (uri (cran-uri "R6" version))
1638 "1kmbw2k5vvzwh3wwmn66mszpfny0z6k8dca980qgbxgvfh0i3gkh"))))
1639 (build-system r-build-system)
1640 (home-page "https://github.com/wch/R6/")
1641 (synopsis "Classes with reference semantics in R")
1643 "The R6 package allows the creation of classes with reference semantics,
1644 similar to R's built-in reference classes. Compared to reference classes, R6
1645 classes are simpler and lighter-weight, and they are not built on S4 classes
1646 so they do not require the methods package. These classes allow public and
1647 private members, and they support inheritance, even when the classes are
1648 defined in different packages.")
1649 (license license:expat)))
1651 (define-public r-rlang
1657 (uri (cran-uri "rlang" version))
1660 "1pks7d2xavzgaxqrnk3f79qsmv4wqv93f8991jv93pnb1mxpyijf"))))
1661 (build-system r-build-system)
1662 (home-page "http://rlang.tidyverse.org")
1663 (synopsis "Functions for base types, core R and Tidyverse features")
1664 (description "This package provides a toolbox for working with base types,
1665 core R features like the condition system, and core @code{Tidyverse} features
1666 like tidy evaluation.")
1667 (license license:gpl3)))
1669 (define-public r-tibble
1676 (uri (cran-uri "tibble" version))
1679 "111jl0hdjhh7hkydxvsr5l19gb0ylxq7xrkc28awnc9pzglpgis5"))))
1680 (build-system r-build-system)
1683 ("r-crayon" ,r-crayon)
1684 ("r-fansi" ,r-fansi)
1685 ("r-pkgconfig" ,r-pkgconfig)
1686 ("r-pillar" ,r-pillar)
1687 ("r-rlang" ,r-rlang)))
1688 (home-page "https://github.com/hadley/tibble")
1689 (synopsis "Simple data frames")
1691 "This package provides a @code{tbl_df} class that offers better checking
1692 and printing capabilities than traditional data frames.")
1693 (license license:expat)))
1695 (define-public r-dplyr
1701 (uri (cran-uri "dplyr" version))
1704 "1nw12hzk1jcac5879nfmf1yp98jpb3i59qkb8sfpk2cd6zqgfgjz"))))
1705 (build-system r-build-system)
1707 `(("r-assertthat" ,r-assertthat)
1710 ("r-magrittr" ,r-magrittr)
1711 ("r-pkgconfig" ,r-pkgconfig)
1712 ("r-plogr" ,r-plogr)
1715 ("r-rlang" ,r-rlang)
1716 ("r-tibble" ,r-tibble)
1717 ("r-tidyselect" ,r-tidyselect)))
1718 (home-page "https://github.com/hadley/dplyr")
1719 (synopsis "Tools for working with data frames in R")
1721 "dplyr is the next iteration of plyr. It is focussed on tools for
1722 working with data frames. It has three main goals: 1) identify the most
1723 important data manipulation tools needed for data analysis and make them easy
1724 to use in R; 2) provide fast performance for in-memory data by writing key
1725 pieces of code in C++; 3) use the same code interface to work with data no
1726 matter where it is stored, whether in a data frame, a data table or
1728 (license license:expat)))
1730 (define-public r-dbplyr
1737 (uri (cran-uri "dbplyr" version))
1740 "0f4gfkzl07gfwihyc747kdnzxahaw2g28wli4jmikrvczldvjqjx"))))
1741 (build-system r-build-system)
1743 `(("r-assertthat" ,r-assertthat)
1745 ("r-dplyr" ,r-dplyr)
1747 ("r-purrr" ,r-purrr)
1749 ("r-rlang" ,r-rlang)
1750 ("r-tibble" ,r-tibble)
1751 ("r-tidyselect" ,r-tidyselect)))
1752 (home-page "https://github.com/tidyverse/dbplyr")
1753 (synopsis "Dplyr back end for databases")
1755 "This package provides a dplyr back end for databases that allows you to
1756 work with remote database tables as if they are in-memory data frames. Basic
1757 features works with any database that has a @code{DBI} back end; more advanced
1758 features require SQL translation to be provided by the package author.")
1759 (license license:expat)))
1761 (define-public r-acepack
1768 (uri (cran-uri "acepack" version))
1771 "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
1772 (build-system r-build-system)
1774 `(("gfortran" ,gfortran)))
1775 (home-page "https://cran.r-project.org/web/packages/acepack")
1776 (synopsis "Functions for regression transformations")
1778 "This package provides ACE and AVAS methods for choosing regression
1780 (license license:expat)))
1782 (define-public r-formula
1789 (uri (cran-uri "Formula" version))
1792 "0wiqh8rr9d5ciy80wj8f5fnmiiw0ywanvvnhkwd622dx42dk848l"))))
1793 (properties `((upstream-name . "Formula")))
1794 (build-system r-build-system)
1795 (home-page "https://cran.r-project.org/web/packages/Formula")
1796 (synopsis "Extended model formulas")
1798 "This package provides a new class @code{Formula}, which extends the base
1799 class @code{formula}. It supports extended formulas with multiple parts of
1800 regressors on the right-hand side and/or multiple responses on the left-hand
1802 (license (list license:gpl2+ license:gpl3+))))
1804 (define-public r-locfit
1811 (uri (cran-uri "locfit" version))
1814 "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
1815 (build-system r-build-system)
1817 `(("r-lattice" ,r-lattice)))
1818 (home-page "https://cran.r-project.org/web/packages/locfit")
1819 (synopsis "Local regression, likelihood and density estimation")
1821 "This package provides functions used for local regression, likelihood
1822 and density estimation.")
1823 (license (list license:gpl2+ license:gpl3+))))
1825 (define-public r-chron
1831 (uri (cran-uri "chron" version))
1834 "02bkywwsxwrxc035hv51dxgdm1fjxdm7dn19ivifln59dfs1862j"))))
1835 (build-system r-build-system)
1836 (home-page "https://cran.r-project.org/web/packages/chron")
1837 (synopsis "Chronological R objects which can handle dates and times")
1839 "This package provides chronological R objects which can handle dates and
1841 (license license:gpl2)))
1843 (define-public r-data-table
1845 (name "r-data-table")
1849 (uri (cran-uri "data.table" version))
1852 "1x929lwhai6nkppm4zvicyw5qh5va5sizp86r30qnfkh1n7w2mfv"))))
1853 (build-system r-build-system)
1854 (home-page "https://github.com/Rdatatable/data.table/wiki")
1855 (synopsis "Enhanced version of data.frame R object")
1857 "The R package @code{data.table} is an extension of @code{data.frame}
1858 providing functions for fast aggregation of large data (e.g. 100GB in RAM),
1859 fast ordered joins, fast add/modify/delete of columns by group, column listing
1860 and fast file reading.")
1861 (license license:gpl3+)))
1863 (define-public r-xtable
1870 (uri (cran-uri "xtable" version))
1873 "077xfm0gphvhsay75amd9v90zk57kjgrrlgih04fyrbqqblc1gjs"))))
1874 (build-system r-build-system)
1876 `(("r-knitr" ,r-knitr))) ; for vignettes
1877 (home-page "http://xtable.r-forge.r-project.org/")
1878 (synopsis "Export R tables to LaTeX or HTML")
1880 "This package provides tools to export R data as LaTeX and HTML tables.")
1881 (license license:gpl2+)))
1883 (define-public python-patsy
1885 (name "python-patsy")
1889 (uri (pypi-uri "patsy" version ".zip"))
1892 "1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w"))))
1893 (build-system python-build-system)
1896 (modify-phases %standard-phases
1898 (lambda _ (invoke "nosetests" "-v"))))))
1900 `(("python-numpy" ,python-numpy)
1901 ("python-scipy" ,python-scipy)
1902 ("python-six" ,python-six)))
1904 `(("python-nose" ,python-nose)
1906 (home-page "https://github.com/pydata/patsy")
1907 (synopsis "Describe statistical models and build design matrices")
1909 "Patsy is a Python package for describing statistical models and for
1910 building design matrices.")
1911 ;; The majority of the code is distributed under BSD-2. The module
1912 ;; patsy.compat contains code derived from the Python standard library,
1913 ;; and is covered by the PSFL.
1914 (license (list license:bsd-2 license:psfl))))
1916 (define-public python2-patsy
1917 (package-with-python2 python-patsy))
1919 (define-public python-statsmodels
1921 (name "python-statsmodels")
1926 (uri (pypi-uri "statsmodels" version))
1929 "0fxs8a7sp4d7jvqlm36yi45i2d28kjfvraf9q8i9jr1chhxgjqb4"))))
1930 (build-system python-build-system)
1932 `(;; The test suite is very large and rather brittle. Tests often fail
1933 ;; because of minor changes in dependencies that upstream hasn't fixed
1934 ;; in a new release.
1937 (modify-phases %standard-phases
1938 (add-after 'unpack 'set-matplotlib-backend-to-agg
1940 ;; Set the matplotlib backend to Agg to avoid problems using the
1941 ;; GTK backend without a display.
1942 (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py")
1943 '("statsmodels/tsa/vector_ar/tests/test_var.py"
1944 "statsmodels/duration/tests/test_survfunc.py"))
1945 (("import matplotlib\\.pyplot as plt" line)
1946 (string-append "import matplotlib;matplotlib.use('Agg');"
1950 `(("python-numpy" ,python-numpy)
1951 ("python-scipy" ,python-scipy)
1952 ("python-pandas" ,python-pandas)
1953 ("python-patsy" ,python-patsy)
1954 ("python-matplotlib" ,python-matplotlib)))
1956 `(("python-cython" ,python-cython)
1957 ("python-nose" ,python-nose)
1958 ("python-sphinx" ,python-sphinx)))
1959 (home-page "http://statsmodels.sourceforge.net/")
1960 (synopsis "Statistical modeling and econometrics in Python")
1962 "Statsmodels is a Python package that provides a complement to scipy for
1963 statistical computations including descriptive statistics and estimation and
1964 inference for statistical models.")
1965 (license license:bsd-3)))
1967 (define-public python2-statsmodels
1968 (let ((stats (package-with-python2 python-statsmodels)))
1969 (package (inherit stats)
1971 `(("python2-pytz" ,python2-pytz)
1972 ("python2-numpy" ,python2-numpy)
1973 ("python2-scipy" ,python2-scipy)
1974 ("python2-pandas" ,python2-pandas)
1975 ("python2-patsy" ,python2-patsy)
1976 ("python2-matplotlib" ,python2-matplotlib))))))
1978 (define-public r-coda
1984 (uri (cran-uri "coda" version))
1987 "03fs3sdrrym3is92dgpa6ydk3m63gaihwy7bva4k0wm2hxm7x2k7"))))
1988 (build-system r-build-system)
1990 `(("r-lattice" ,r-lattice)))
1991 (home-page "https://cran.r-project.org/web/packages/coda")
1992 (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
1993 (description "This package provides functions for summarizing and plotting
1994 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
1995 diagnostic tests of convergence to the equilibrium distribution of the Markov
1997 (license license:gpl2+)))
1999 (define-public r-ade4
2006 (uri (cran-uri "ade4" version))
2009 "16z9jk4qj35ghsk4lwmq241dgc770y8a70dlmp9q4gz6d8ssgl7m"))))
2010 (build-system r-build-system)
2012 `(("r-mass" ,r-mass)))
2013 (home-page "http://pbil.univ-lyon1.fr/ADE-4")
2014 (synopsis "Multivariate data analysis and graphical display")
2016 "The ade4 package contains data analysis functions to analyze ecological
2017 and environmental data in the framework of Euclidean exploratory methods.")
2018 (license license:gpl2+)))
2020 (define-public r-xml2
2027 (uri (cran-uri "xml2" version))
2030 "154lmksfiwkhnlmryas25mjhfg6k4mmnnk7bbb29mnn5x5pr2yha"))))
2031 (build-system r-build-system)
2033 `(("libxml2" ,libxml2)
2036 `(("pkg-config" ,pkg-config)))
2038 `(("r-rcpp" ,r-rcpp)))
2039 (home-page "https://github.com/hadley/xml2")
2040 (synopsis "Parse XML with R")
2042 "This package provides a simple, consistent interface to working with XML
2043 files in R. It is built on top of the libxml2 C library.")
2044 (license license:gpl2+)))
2046 (define-public r-multitaper
2048 (name "r-multitaper")
2053 (uri (cran-uri "multitaper" version))
2056 "04wd9bbhyx7697pfy0fpj02v1csr48hkpqj62h9p8a6w84ji4k68"))))
2057 (build-system r-build-system)
2059 `(("gfortran" ,gfortran)))
2060 (home-page "https://github.com/wesleyburr/multitaper/")
2061 (synopsis "Multitaper spectral analysis tools")
2063 "This package implements multitaper spectral estimation
2064 techniques using prolate spheroidal sequences (Slepians) and sine
2065 tapers for time series analysis. It includes an adaptive weighted
2066 multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
2067 F-test, and complex demodulation. The Slepians sequences are
2068 generated efficiently using a tridiagonal matrix solution, and
2069 jackknifed confidence intervals are available for most estimates.")
2070 (license license:gpl2+)))
2072 (define-public r-rversions
2074 (name "r-rversions")
2078 (uri (cran-uri "rversions" version))
2081 "0mkg9zrjxlbwqzijiysivrs523x48syqj30xdfp88clpkqfk435m"))))
2082 (build-system r-build-system)
2084 `(("r-curl" ,r-curl)
2085 ("r-xml2" ,r-xml2)))
2086 (home-page "https://github.com/metacran/rversions")
2087 (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
2089 "This package provides functions to query the main R repository to find
2090 the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
2091 previous R versions and their release dates.")
2092 (license license:expat)))
2094 (define-public r-whisker
2100 (uri (cran-uri "whisker" version))
2103 "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28"))))
2104 (build-system r-build-system)
2105 (home-page "https://github.com/edwindj/whisker")
2106 (synopsis "Logicless mustache templating for R")
2108 "This package provides logicless templating, with a syntax that is not
2110 (license license:gpl3+)))
2112 (define-public r-backports
2114 (name "r-backports")
2119 (uri (cran-uri "backports" version))
2122 "00zz969vc2gfi5p9q65pzghq2bxm3p9zqgwqswkyz9rgybz5wjzf"))))
2123 (build-system r-build-system)
2124 (home-page "https://cran.r-project.org/web/packages/backports")
2125 (synopsis "Reimplementations of functions introduced since R 3.0.0")
2127 "Provides implementations of functions which have been introduced in R
2128 since version 3.0.0. The backports are conditionally exported which results
2129 in R resolving the function names to the version shipped with R (if available)
2130 and uses the implemented backports as fallback. This way package developers
2131 can make use of the new functions without worrying about the minimum required
2133 (license license:gpl2+)))
2135 (define-public r-checkmate
2137 (name "r-checkmate")
2142 (uri (cran-uri "checkmate" version))
2145 "15ccwvmw73c2zz1k10k5zdn8px0rrbnvs1b4nzvlb0iwj7cimhp4"))))
2146 (build-system r-build-system)
2148 `(("r-backports" ,r-backports)))
2149 (home-page "https://github.com/mllg/checkmate")
2150 (synopsis "Fast and versatile argument checks")
2152 "This package provides tests and assertions to perform frequent argument
2153 checks. A substantial part of the package was written in C to minimize any
2154 worries about execution time overhead.")
2155 (license license:bsd-3)))
2157 (define-public r-bbmisc
2164 (uri (cran-uri "BBmisc" version))
2167 "1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y"))))
2168 (properties `((upstream-name . "BBmisc")))
2169 (build-system r-build-system)
2171 `(("r-checkmate" ,r-checkmate)))
2172 (home-page "https://github.com/berndbischl/BBmisc")
2173 (synopsis "Miscellaneous functions for R package development")
2175 "This package provides miscellaneous helper functions for the development
2177 (license license:bsd-3)))
2179 (define-public r-fail
2186 (uri (cran-uri "fail" version))
2189 "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
2190 (build-system r-build-system)
2192 `(("r-bbmisc" ,r-bbmisc)
2193 ("r-checkmate" ,r-checkmate)))
2194 (home-page "https://github.com/mllg/fail")
2195 (synopsis "File abstraction interface layer (FAIL)")
2197 "This package provides a more comfortable interface to work with R data
2198 or source files in a key-value fashion.")
2199 (license license:bsd-3)))
2201 (define-public r-batchjobs
2203 (name "r-batchjobs")
2208 (uri (cran-uri "BatchJobs" version))
2211 "1zz4sspj596pijxlz321g0jy2rg9ki83j6fihbwisjwr66p2vk1m"))))
2212 (properties `((upstream-name . "BatchJobs")))
2213 (build-system r-build-system)
2215 `(("r-backports" ,r-backports)
2216 ("r-bbmisc" ,r-bbmisc)
2218 ("r-checkmate" ,r-checkmate)
2219 ("r-data-table" ,r-data-table)
2221 ("r-digest" ,r-digest)
2222 ("r-rsqlite" ,r-rsqlite)
2223 ("r-sendmailr" ,r-sendmailr)
2224 ("r-stringi" ,r-stringi)))
2225 (home-page "https://github.com/tudo-r/BatchJobs")
2226 (synopsis "Batch computing with R")
2228 "This package provides @code{Map}, @code{Reduce} and @code{Filter}
2229 variants to generate jobs on batch computing systems like PBS/Torque, LSF,
2230 SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
2231 (license license:bsd-2)))
2233 (define-public r-brew
2239 (uri (cran-uri "brew" version))
2242 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
2243 (build-system r-build-system)
2244 (home-page "https://cran.r-project.org/web/packages/brew")
2245 (synopsis "Templating framework for report generation")
2247 "The brew package implements a templating framework for mixing text and R
2248 code for report generation. The template syntax is similar to PHP, Ruby's erb
2249 module, Java Server Pages, and Python's psp module.")
2250 (license license:gpl2+)))
2252 (define-public r-desc
2259 (uri (cran-uri "desc" version))
2262 "1s6s13fk6sxwcj8wzkwxl9vr33153xx11p5wi9avqx3rzkabavz6"))))
2263 (build-system r-build-system)
2265 `(("r-assertthat" ,r-assertthat)
2266 ("r-crayon" ,r-crayon)
2268 ("r-rprojroot" ,r-rprojroot)))
2269 (home-page "https://github.com/r-pkgs/desc")
2270 (synopsis "Manipulate DESCRIPTION Files")
2272 "This package provides tools to read, write, create, and manipulate
2273 DESCRIPTION files. It is intended for packages that create or manipulate
2275 (license license:expat)))
2277 (define-public r-commonmark
2279 (name "r-commonmark")
2284 (uri (cran-uri "commonmark" version))
2287 "024iz1qp2kv6iz6y69ir0jk3qhjps86rhkzlcmhqsxx97rx7cjni"))))
2288 (build-system r-build-system)
2289 (home-page "https://cran.r-project.org/web/packages/commonmark")
2290 (synopsis "CommonMark and Github Markdown Rendering in R")
2292 "The CommonMark specification defines a rationalized version of markdown
2293 syntax. This package uses the @code{cmark} reference implementation for
2294 converting markdown text into various formats including HTML, LaTeX and groff
2295 man. In addition, it exposes the markdown parse tree in XML format. The latest
2296 version of this package also adds support for Github extensions including
2297 tables, autolinks and strikethrough text.")
2298 (license license:bsd-2)))
2300 (define-public r-roxygen2
2306 (uri (cran-uri "roxygen2" version))
2309 "0wq29ilqas8yn2z8v49fk0hbgchg29nmyyhwczgdipz0cbhbfipd"))))
2310 (build-system r-build-system)
2312 `(("r-brew" ,r-brew)
2313 ("r-commonmark" ,r-commonmark)
2315 ("r-digest" ,r-digest)
2316 ("r-pkgload" ,r-pkgload)
2317 ("r-purrr" ,r-purrr)
2320 ("r-stringi" ,r-stringi)
2321 ("r-stringr" ,r-stringr)
2322 ("r-xml2" ,r-xml2)))
2324 `(("r-knitr" ,r-knitr))) ; for vignettes
2325 (home-page "https://github.com/klutometis/roxygen")
2326 (synopsis "In-source documentation system for R")
2328 "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
2329 collation, and NAMESPACE files.")
2330 (license license:gpl2+)))
2332 (define-public r-openssl
2339 (uri (cran-uri "openssl" version))
2342 "1gx4mk7js1irzkql5rgk48ja9c6mm28ccxz483ngbhdd57az90qw"))))
2343 (build-system r-build-system)
2345 `(("libressl" ,libressl)))
2347 `(("pkg-config" ,pkg-config)))
2349 `(("r-askpass" ,r-askpass)))
2350 (home-page "https://github.com/jeroenooms/openssl")
2351 (synopsis "Toolkit for encryption, signatures and certificates")
2353 "This package provides R bindings to OpenSSL libssl and libcrypto, plus
2354 custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
2355 and P-521. Cryptographic signatures can either be created and verified
2356 manually or via x509 certificates. AES block cipher is used in CBC mode for
2357 symmetric encryption; RSA for asymmetric (public key) encryption. High-level
2358 envelope functions combine RSA and AES for encrypting arbitrary sized data.
2359 Other utilities include key generators, hash functions (md5, sha1, sha256,
2360 etc), base64 encoder, a secure random number generator, and @code{bignum} math
2361 methods for manually performing crypto calculations on large multibyte
2363 (license license:expat)))
2365 (define-public r-httr
2371 (uri (cran-uri "httr" version))
2374 "0j6vknwyvkjpjsxwch4q02aik4dnm3h4l0wc7dgzc555bm1g2cyn"))))
2375 (build-system r-build-system)
2377 `(("r-curl" ,r-curl)
2378 ("r-jsonlite" ,r-jsonlite)
2379 ("r-openssl" ,r-openssl)
2382 (home-page "https://github.com/hadley/httr")
2383 (synopsis "Tools for working with URLs and HTTP")
2385 "The aim of httr is to provide a wrapper for RCurl customised to the
2386 demands of modern web APIs. It provides useful tools for working with HTTP
2387 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
2388 functions make it easy to control additional request components.")
2389 (license license:expat)))
2391 (define-public r-git2r
2397 (uri (cran-uri "git2r" version))
2400 "15kpvz6ry2r8ii5hzinjwkggc5kgmkbcpsdwzahsf8gha52w80p0"))))
2401 (build-system r-build-system)
2402 ;; This R package contains modified sources of libgit2. This modified
2403 ;; version of libgit2 is built as the package is built. Hence libgit2 is
2404 ;; not among the inputs of this package.
2406 `(("libssh2" ,libssh2) ; for SSH transport
2407 ("openssl" ,openssl)
2410 `(("pkg-config" ,pkg-config)))
2411 (home-page "https://github.com/ropensci/git2r")
2412 (synopsis "Access Git repositories with R")
2414 "This package provides an R interface to the libgit2 library, which is a
2415 pure C implementation of the Git core methods.")
2416 ;; GPLv2 only with linking exception.
2417 (license license:gpl2)))
2419 (define-public r-rstudioapi
2421 (name "r-rstudioapi")
2425 (uri (cran-uri "rstudioapi" version))
2428 "15mbw607ncdf53mgga76n3va5zzdcjqz14nb0jcn9axwccqamic0"))))
2429 (build-system r-build-system)
2430 (home-page "https://cran.r-project.org/web/packages/rstudioapi")
2431 (synopsis "Safely access the RStudio API")
2433 "This package provides functions to access the RStudio API and provide
2434 informative error messages when it's not available.")
2435 (license license:expat)))
2437 (define-public r-devtools
2443 (uri (cran-uri "devtools" version))
2446 "028pppj39ng7q17k27531s8k00lmw982vz5krn74n9b8f2azm8lr"))))
2447 (build-system r-build-system)
2449 `(("r-callr" ,r-callr)
2451 ("r-digest" ,r-digest)
2452 ("r-git2r" ,r-git2r)
2454 ("r-jsonlite" ,r-jsonlite)
2455 ("r-memoise" ,r-memoise)
2456 ("r-pkgbuild" ,r-pkgbuild)
2457 ("r-pkgload" ,r-pkgload)
2458 ("r-rcmdcheck" ,r-rcmdcheck)
2459 ("r-remotes" ,r-remotes)
2460 ("r-rstudioapi" ,r-rstudioapi)
2461 ("r-sessioninfo" ,r-sessioninfo)
2462 ("r-usethis" ,r-usethis)
2463 ("r-withr" ,r-withr)))
2464 (home-page "https://github.com/hadley/devtools")
2465 (synopsis "Tools to make developing R packages easier")
2466 (description "The devtools package is a collection of package development
2467 tools to simplify the devolpment of R packages.")
2468 (license license:gpl2+)))
2470 (define-public r-withr
2476 (uri (cran-uri "withr" version))
2479 "11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1"))))
2480 (build-system r-build-system)
2481 (home-page "https://github.com/jimhester/withr")
2482 (synopsis "Run code with temporarily modified global state")
2484 "This package provides a set of functions to run R code in an environment
2485 in which global state has been temporarily modified. Many of these functions
2486 were originally a part of the r-devtools package.")
2487 (license license:gpl2+)))
2489 (define-public r-hms
2496 (uri (cran-uri "hms" version))
2499 "1g6hslk3z0xga38r71irxq802wskg6nv804mp8y9f7i2wfrj0y55"))))
2500 (build-system r-build-system)
2502 `(("r-rlang" ,r-rlang)
2503 ("r-pkgconfig" ,r-pkgconfig)))
2504 (home-page "https://github.com/rstats-db/hms")
2505 (synopsis "Pretty time of day")
2507 "This package implements an S3 class for storing and formatting
2508 time-of-day values, based on the @code{difftime} class.")
2509 (license license:gpl3+)))
2511 (define-public r-readr
2517 (uri (cran-uri "readr" version))
2520 "1wz496rw0ah433p755n3xac8gh7yzid4xgdjzd1a7wmpkgilvy9k"))))
2521 (build-system r-build-system)
2523 `(("r-clipr" ,r-clipr)
2524 ("r-crayon" ,r-crayon)
2527 ("r-tibble" ,r-tibble)
2530 (home-page "https://github.com/hadley/readr")
2531 (synopsis "Read tabular data")
2533 "This package provides functions to read flat or tabular text files from
2534 disk (or a connection).")
2535 (license license:gpl2+)))
2537 (define-public r-plotrix
2543 (uri (cran-uri "plotrix" version))
2546 "0k6ivryac1k81z2dijjds376a9jxwk8rf5g48snj67cnjffkybxj"))))
2547 (build-system r-build-system)
2548 (home-page "https://cran.r-project.org/web/packages/plotrix")
2549 (synopsis "Various plotting functions")
2551 "This package provides lots of plotting, various labeling, axis and color
2552 scaling functions for R.")
2553 (license license:gpl2+)))
2555 (define-public r-gridbase
2561 (uri (cran-uri "gridBase" version))
2564 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
2565 (build-system r-build-system)
2566 (home-page "https://cran.r-project.org/web/packages/gridBase")
2567 (synopsis "Integration of base and grid graphics")
2569 "This package provides an integration of base and grid graphics for R.")
2570 (license license:gpl2+)))
2572 (define-public r-latticeextra
2574 (name "r-latticeextra")
2579 (uri (cran-uri "latticeExtra" version))
2582 "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq"))))
2583 (properties `((upstream-name . "latticeExtra")))
2584 (build-system r-build-system)
2586 `(("r-lattice" ,r-lattice)
2587 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2588 (home-page "http://latticeextra.r-forge.r-project.org/")
2589 (synopsis "Extra graphical utilities based on lattice")
2591 "Building on the infrastructure provided by the lattice package, this
2592 package provides several new high-level graphics functions and methods, as
2593 well as additional utilities such as panel and axis annotation functions.")
2594 (license license:gpl2+)))
2596 (define-public r-rcpparmadillo
2598 (name "r-rcpparmadillo")
2599 (version "0.9.400.3.0")
2602 (uri (cran-uri "RcppArmadillo" version))
2605 "1c0kmp54xgg67hxpqm8bibcxmmwljbdvm9p1d9wzirp83x86v4sn"))))
2606 (properties `((upstream-name . "RcppArmadillo")))
2607 (build-system r-build-system)
2608 ;; All needed for vignettes
2610 `(("r-knitr" ,r-knitr)
2611 ("r-rmarkdown" ,r-rmarkdown)
2612 ("ghc-pandoc" ,ghc-pandoc)
2613 ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)))
2615 `(("r-rcpp" ,r-rcpp)))
2616 (home-page "https://github.com/RcppCore/RcppArmadillo")
2617 (synopsis "Rcpp integration for the Armadillo linear algebra library")
2619 "Armadillo is a templated C++ linear algebra library that aims towards a
2620 good balance between speed and ease of use. Integer, floating point and
2621 complex numbers are supported, as well as a subset of trigonometric and
2622 statistics functions. Various matrix decompositions are provided through
2623 optional integration with LAPACK and ATLAS libraries. This package includes
2624 the header files from the templated Armadillo library.")
2625 ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
2626 ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
2627 ;; later, as is the rest of 'Rcpp'.
2628 (license license:gpl2+)))
2630 (define-public r-bitops
2636 (uri (cran-uri "bitops" version))
2639 "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
2640 (build-system r-build-system)
2641 (home-page "https://cran.r-project.org/web/packages/bitops")
2642 (synopsis "Bitwise operations")
2644 "This package provides functions for bitwise operations on integer
2646 (license license:gpl2+)))
2648 (define-public r-catools
2651 (version "1.17.1.2")
2654 (uri (cran-uri "caTools" version))
2657 "0svj31y7h8vimvliygmmbl7pk850qk80k1vn38mlcxsnmcpm9k39"))))
2658 (properties `((upstream-name . "caTools")))
2659 (build-system r-build-system)
2661 `(("r-bitops" ,r-bitops)))
2662 (home-page "https://cran.r-project.org/web/packages/caTools")
2663 (synopsis "Various tools including functions for moving window statistics")
2665 "This package contains several basic utility functions including:
2666 moving (rolling, running) window statistic functions, read/write for GIF and
2667 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
2668 encoder/decoder, round-off-error-free sum and cumsum, etc.")
2669 (license license:gpl3+)))
2671 (define-public r-rprojroot
2673 (name "r-rprojroot")
2678 (uri (cran-uri "rprojroot" version))
2681 "12r3fdxmi2pmwn6ic3rhg0b20ll5z420m0d8fziv1n21961namnz"))))
2682 (build-system r-build-system)
2684 `(("r-backports" ,r-backports)))
2685 (home-page "https://github.com/krlmlr/rprojroot")
2686 (synopsis "Finding files in project subdirectories")
2688 "This package helps accessing files relative to a project root. It
2689 provides helpers for robust, reliable and flexible paths to files below a
2690 project root. The root of a project is defined as a directory that matches a
2691 certain criterion, e.g., it contains a certain regular file.")
2692 (license license:gpl3)))
2694 (define-public r-rmarkdown
2696 (name "r-rmarkdown")
2701 (uri (cran-uri "rmarkdown" version))
2704 "0milpdaf4nd36kq6sci9wc5dhwswl4w9c9fychfbppgjsgfp6kfv"))))
2705 (properties `((upstream-name . "rmarkdown")))
2706 (build-system r-build-system)
2708 `(("r-base64enc" ,r-base64enc)
2709 ("r-evaluate" ,r-evaluate)
2710 ("r-htmltools" ,r-htmltools)
2711 ("r-jsonlite" ,r-jsonlite)
2712 ("r-knitr" ,r-knitr)
2714 ("r-stringr" ,r-stringr)
2715 ("r-tinytex" ,r-tinytex)
2717 ("ghc-pandoc" ,ghc-pandoc)))
2718 (home-page "http://rmarkdown.rstudio.com")
2719 (synopsis "Convert R Markdown documents into a variety of formats")
2721 "This package provides tools to convert R Markdown documents into a
2722 variety of formats.")
2723 (license license:gpl3+)))
2725 (define-public r-gtable
2731 (uri (cran-uri "gtable" version))
2734 "1lyncxf2dqdjgw1071cn9c8zwzkz6sldnd5cgmicf70bc726qf7x"))))
2735 (properties `((upstream-name . "gtable")))
2736 (build-system r-build-system)
2737 (home-page "https://cran.r-project.org/web/packages/gtable")
2738 (synopsis "R library to arrange grobs in tables")
2740 "Gtable is a collection of tools to make it easier to work with
2741 \"tables\" of grobs.")
2742 (license license:gpl2+)))
2744 (define-public r-gridextra
2746 (name "r-gridextra")
2750 (uri (cran-uri "gridExtra" version))
2753 "0fwfk3cdwxxim7nd55pn7m31bcaqj48y06j7an2k1v1pybk0rdl1"))))
2754 (properties `((upstream-name . "gridExtra")))
2755 (build-system r-build-system)
2757 `(("r-gtable" ,r-gtable)))
2759 `(("r-knitr" ,r-knitr))) ;for building vignettes
2760 (home-page "https://github.com/baptiste/gridextra")
2761 (synopsis "Miscellaneous functions for \"Grid\" graphics")
2763 "This package provides a number of user-level functions to work with
2764 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
2766 (license license:gpl2+)))
2768 (define-public r-pkgconfig
2770 (name "r-pkgconfig")
2774 (uri (cran-uri "pkgconfig" version))
2777 "1jk9ip549xphb3anfixqv1yx5kidnndqgy9v3qjpmgmds5a7g695"))))
2778 (build-system r-build-system)
2779 (home-page "https://github.com/gaborcsardi/pkgconfig")
2780 (synopsis "Private configuration for R packages")
2781 (description "This package provides the functionality to set configuration
2782 options on a per-package basis. Options set by a given package only apply to
2783 that package, other packages are unaffected.")
2784 (license license:expat)))
2786 (define-public r-blob
2792 (uri (cran-uri "blob" version))
2795 "0lsg91hk508dd95ivig2lwg62qafwnarjw68110kx63cfk4zkjxc"))))
2796 (build-system r-build-system)
2798 `(("r-prettyunits" ,r-prettyunits)
2799 ("r-tibble" ,r-tibble)))
2800 (home-page "https://github.com/hadley/blob")
2801 (synopsis "Simple S3 Class for representing vectors of binary data")
2802 (description "Raw vectors in R are useful for storing a single binary
2803 object. What if you want to put a vector of them in a data frame? The blob
2804 package provides the blob object, a list of raw vectors, suitable for use as
2805 a column in data frame.")
2806 (license license:gpl3+)))
2808 (define-public r-rsqlite
2814 (uri (cran-uri "RSQLite" version))
2817 "1giwk4335sc6yhj3rs8h070g1mwy38kyqyqv6vcfxvskykj7vp6z"))))
2818 (properties `((upstream-name . "RSQLite")))
2819 (build-system r-build-system)
2823 ("r-memoise" ,r-memoise)
2824 ("r-plogr" ,r-plogr)
2826 ("r-bit64" ,r-bit64)
2828 ("r-pkgconfig" ,r-pkgconfig)))
2829 (home-page "https://github.com/rstats-db/RSQLite")
2830 (synopsis "SQLite interface for R")
2832 "This package embeds the SQLite database engine in R and provides an
2833 interface compliant with the DBI package. The source for the SQLite
2834 engine (version 3.8.8.2) is included.")
2835 (license license:lgpl2.0+)))
2837 (define-public r-rcurl
2840 (version "1.95-0.1.2")
2843 (uri (string-append "https://www.bioconductor.org/packages/"
2844 "release/extra/src/"
2845 "contrib/RCurl_" version ".tar.gz"))
2848 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
2849 (properties `((upstream-name . "RCurl")))
2850 (build-system r-build-system)
2853 (modify-phases %standard-phases
2854 (add-after 'unpack 'respect-CURL_CA_BUNDLE
2856 (substitute* "R/options.S"
2857 (("\\.els = rev\\(merge\\(list\\(\\.\\.\\.\\), \\.opts\\)\\)" m)
2859 certs = Sys.getenv(\"CURL_CA_BUNDLE\")
2860 if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) }
2864 `(("libcurl" ,curl)))
2866 `(("r-bitops" ,r-bitops)))
2867 (home-page "http://www.omegahat.org/RCurl")
2868 (synopsis "General network client interface for R")
2870 "The package allows one to compose general HTTP requests and provides
2871 convenient functions to fetch URIs, GET and POST forms, etc. and process the
2872 results returned by the Web server. This provides a great deal of control
2873 over the HTTP/FTP/... connection and the form of the request while providing a
2874 higher-level interface than is available just using R socket connections.
2875 Additionally, the underlying implementation is robust and extensive,
2876 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
2877 ldap, and also supports cookies, redirects, authentication, etc.")
2878 (license license:bsd-3)))
2880 (define-public r-xml
2883 (version "3.98-1.19")
2886 (uri (cran-uri "XML" version))
2889 "1axyfa56q45x7z4zd56aasdn9hz9niv2vv5qm1zp9i94vyic9cc1"))))
2891 `((upstream-name . "XML")))
2892 (build-system r-build-system)
2894 `(("libxml2" ,libxml2)
2897 `(("pkg-config" ,pkg-config)))
2898 (home-page "http://www.omegahat.org/RSXML")
2899 (synopsis "Tools for parsing and generating XML within R")
2901 "Many approaches for both reading and creating XML (and HTML)
2902 documents (including DTDs), both local and accessible via HTTP or FTP. Also
2903 offers access to an XPath \"interpreter\".")
2904 (license license:bsd-2)))
2906 (define-public r-xnomial
2911 (origin (method url-fetch)
2912 (uri (cran-uri "XNomial" version))
2915 "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
2916 (properties (quasiquote ((upstream-name . "XNomial"))))
2917 (build-system r-build-system)
2918 (home-page "https://cran.r-project.org/web/packages/XNomial")
2919 (synopsis "Goodness-of-Fit test for multinomial data")
2921 "This package provides an exact Goodness-of-Fit test for
2922 multinomial data with fixed probabilities. It can be used to
2923 determine whether a set of counts fits a given expected ratio. To see
2924 whether a set of observed counts fits an expectation, one can examine
2925 all possible outcomes with @code{xmulti()} or a random sample of them
2926 with @code{xmonte()} and find the probability of an observation
2927 deviating from the expectation by at least as much as the observed.
2928 As a measure of deviation from the expected, one can use the
2929 log-likelihood ratio, the multinomial probability, or the classic
2930 chi-square statistic. A histogram of the test statistic can also be
2931 plotted and compared with the asymptotic curve.")
2932 (license (list license:gpl2+ license:gpl3+))))
2934 (define-public r-lambda-r
2940 (uri (cran-uri "lambda.r" version))
2943 "0cc6pszs6yccn0hgjpyn9gspv9aiva9d91ba0640i5m0l5xy7n0c"))))
2944 (properties `((upstream-name . "lambda.r")))
2945 (build-system r-build-system)
2947 `(("r-formatr" ,r-formatr)))
2948 (home-page "https://cran.r-project.org/web/packages/lambda.r")
2949 (synopsis "Functional programming extension for R")
2951 "This package provides a language extension to efficiently write
2952 functional programs in R. Syntax extensions include multi-part function
2953 definitions, pattern matching, guard statements, built-in (optional) type
2955 (license license:lgpl3+)))
2957 (define-public r-futile-options
2959 (name "r-futile-options")
2963 (uri (cran-uri "futile.options" version))
2966 "0w15agpi88y3qkv6fl72zy2pzyplzgvnj41a4ixhg64mw1sck73s"))))
2968 `((upstream-name . "futile.options")))
2969 (build-system r-build-system)
2970 (home-page "https://cran.r-project.org/web/packages/futile.options")
2971 (synopsis "Options management framework")
2973 "The futile.options subsystem provides an easy user-defined options
2974 management system that is properly scoped. This means that options created
2975 via @code{futile.options} are fully self-contained and will not collide with
2976 options defined in other packages.")
2977 (license license:lgpl3+)))
2979 (define-public r-futile-logger
2981 (name "r-futile-logger")
2985 (uri (cran-uri "futile.logger" version))
2988 "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
2989 (properties `((upstream-name . "futile.logger")))
2990 (build-system r-build-system)
2992 `(("r-futile-options" ,r-futile-options)
2993 ("r-lambda-r" ,r-lambda-r)))
2994 (home-page "https://cran.r-project.org/web/packages/futile.logger")
2995 (synopsis "Logging utility for R")
2997 "This package provides a simple yet powerful logging utility. Based
2998 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
2999 convenient and easy to use replacement for @code{cat} and @code{print}
3001 (license license:lgpl3+)))
3003 (define-public r-segmented
3005 (name "r-segmented")
3010 (uri (cran-uri "segmented" version))
3013 "0nrik5fyq59hwiwjcpbi4p5yfavgfjq6wyrynhkrbm4k6v1g1wlq"))))
3014 (build-system r-build-system)
3015 (home-page "https://cran.r-project.org/web/packages/segmented")
3016 (synopsis "Regression models with breakpoints estimation")
3018 "Given a regression model, segmented updates the model by adding one or
3019 more segmented (i.e., piecewise-linear) relationships. Several variables with
3020 multiple breakpoints are allowed.")
3021 (license (list license:gpl2+ license:gpl3+))))
3023 (define-public r-snow
3029 (uri (cran-uri "snow" version))
3032 "1n3n8pva9s34fvlw32yng0x416lmbv7q1fsd0ywa4kikmxym64l5"))))
3033 (build-system r-build-system)
3034 (home-page "https://cran.r-project.org/web/packages/snow")
3035 (synopsis "Support for simple parallel computing in R")
3037 "The snow package provides support for simple parallel computing on a
3038 network of workstations using R. A master R process calls @code{makeCluster}
3039 to start a cluster of worker processes; the master process then uses functions
3040 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
3041 worker processes and collect and return the results on the master.")
3042 (license (list license:gpl2+ license:gpl3+))))
3044 (define-public r-sparsem
3050 (uri (cran-uri "SparseM" version))
3053 "0p6ljma2h12cq1xmy0cxb48ih8dhxxbnwkqzvx3cckxf2kprycm9"))))
3055 `((upstream-name . "SparseM")))
3057 `(("gfortran" ,gfortran)))
3058 (build-system r-build-system)
3059 (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
3060 (synopsis "Sparse linear algebra")
3062 "This package provides some basic linear algebra functionality for sparse
3063 matrices. It includes Cholesky decomposition and backsolving as well as
3064 standard R subsetting and Kronecker products.")
3065 (license license:gpl2+)))
3067 (define-public r-iterators
3069 (name "r-iterators")
3074 (uri (cran-uri "iterators" version))
3077 "1s3iykfvccpnzs73z90rx18qvbvgw2dgl4nfcrvm5m1850qb5qd9"))))
3078 (build-system r-build-system)
3079 (home-page "https://cran.r-project.org/web/packages/iterators")
3080 (synopsis "Iterator construct for R")
3082 "This package provides support for iterators, which allow a programmer to
3083 traverse through all the elements of a vector, list, or other collection of
3085 (license license:asl2.0)))
3087 (define-public r-foreach
3094 (uri (cran-uri "foreach" version))
3097 "0j2yj0rn0d5nbzz9nq5rqqgnxhp9pbd92q4klsarl2xpsn8119y0"))))
3098 (build-system r-build-system)
3100 `(("r-codetools" ,r-codetools)
3101 ("r-iterators" ,r-iterators)))
3102 (home-page "https://cran.r-project.org/web/packages/foreach")
3103 (synopsis "Foreach looping construct for R")
3105 "This package provides support for the @code{foreach} looping construct.
3106 @code{foreach} is an idiom that allows for iterating over elements in a
3107 collection, without the use of an explicit loop counter. This package in
3108 particular is intended to be used for its return value, rather than for its
3109 side effects. In that sense, it is similar to the standard @code{lapply}
3110 function, but doesn't require the evaluation of a function. Using
3111 @code{foreach} without side effects also facilitates executing the loop in
3113 (license license:asl2.0)))
3115 (define-public r-doparallel
3117 (name "r-doparallel")
3122 (uri (cran-uri "doParallel" version))
3125 "01qjs4iw9f1kgymcypj0m2s4pvgqhxaycpli0fb8lq3dc0vpzfyb"))))
3126 (properties `((upstream-name . "doParallel")))
3127 (build-system r-build-system)
3129 `(("r-foreach" ,r-foreach)
3130 ("r-iterators" ,r-iterators)))
3131 (home-page "https://cran.r-project.org/web/packages/doParallel")
3132 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3134 "This package provides a parallel backend for the @code{%dopar%} function
3135 using the parallel package.")
3136 (license license:gpl2+)))
3138 (define-public r-domc
3145 (uri (cran-uri "doMC" version))
3148 "1vfrykvfvsyq12mypd266867ml1dcwc3rj5k9c3wrn5bddcm88kr"))))
3149 (properties `((upstream-name . "doMC")))
3150 (build-system r-build-system)
3152 `(("r-foreach" ,r-foreach)
3153 ("r-iterators" ,r-iterators)))
3154 (home-page "https://cran.r-project.org/web/packages/doMC")
3155 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3157 "This package provides a parallel backend for the @code{%dopar%} function
3158 using the multicore functionality of the parallel package.")
3159 (license license:gpl2+)))
3167 (uri (cran-uri "DT" version))
3170 "05kr88yshq6siarp5q7aapvsr63vx3p0aqablwgifn8m2sfqxmif"))))
3172 `((upstream-name . "DT")))
3173 (build-system r-build-system)
3175 `(("r-crosstalk" ,r-crosstalk)
3176 ("r-htmltools" ,r-htmltools)
3177 ("r-htmlwidgets" ,r-htmlwidgets)
3178 ("r-magrittr" ,r-magrittr)
3179 ("r-promises" ,r-promises)))
3180 (home-page "http://rstudio.github.io/DT")
3181 (synopsis "R wrapper of the DataTables JavaScript library")
3183 "This package allows for data objects in R to be rendered as HTML tables
3184 using the JavaScript library @code{DataTables} (typically via R Markdown or
3185 Shiny). The @code{DataTables} library has been included in this R package.")
3186 ;; The DT package as a whole is distributed under GPLv3. The DT package
3187 ;; inludes other software components under different licenses:
3189 ;; * Expat: jQuery, jquery.highlight.js, DataTables
3190 ;; * ASL2.0: selectize.js
3191 ;; * WTFPL: noUiSlider
3192 (license (list license:gpl3
3195 (license:non-copyleft "http://www.wtfpl.net/txt/copying/")))))
3197 (define-public r-base64enc
3199 (name "r-base64enc")
3203 (uri (cran-uri "base64enc" version))
3206 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
3207 (build-system r-build-system)
3208 (home-page "http://www.rforge.net/base64enc")
3209 (synopsis "Tools for Base64 encoding")
3211 "This package provides tools for handling Base64 encoding. It is more
3212 flexible than the orphaned \"base64\" package.")
3213 (license license:gpl2+)))
3215 (define-public r-irlba
3222 (uri (cran-uri "irlba" version))
3225 "1h7mzrqdjc41814cf6c93sbyl7nxwvsf3x8apl9rhmydgdlk7qkf"))))
3226 (build-system r-build-system)
3228 `(("r-matrix" ,r-matrix)))
3229 (home-page "https://cran.r-project.org/web/packages/irlba")
3230 (synopsis "Methods for eigendecomposition of large matrices")
3232 "This package provides fast and memory efficient methods for truncated
3233 singular and eigenvalue decompositions, as well as for principal component
3234 analysis of large sparse or dense matrices.")
3235 (license (list license:gpl2+ license:gpl3+))))
3237 (define-public r-glmnet
3244 (uri (cran-uri "glmnet" version))
3247 "1brr51z1fzbpyj6myyir4g6dhbp6xwl7nx4xnvrjarnf5y0csk55"))))
3248 (build-system r-build-system)
3250 `(("gfortran" ,gfortran)))
3252 `(("r-foreach" ,r-foreach)
3253 ("r-matrix" ,r-matrix)))
3254 (home-page "http://www.jstatsoft.org/v33/i01")
3255 (synopsis "Lasso and elastic-net regularized generalized linear models")
3257 "The glmnet package provides efficient procedures for fitting the entire
3258 lasso or elastic-net regularization path for linear and Poisson regression, as
3259 well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
3260 multinomial models. The algorithm uses cyclical coordinate descent in a
3261 path-wise fashion.")
3262 (license license:gpl2+)))
3264 (define-public r-pkgmaker
3271 (uri (cran-uri "pkgmaker" version))
3274 "0spcamjncj78kzjps2rw4v1a4494yazv6xvhn0vmdflnypc8k8hp"))))
3275 (build-system r-build-system)
3277 `(("r-bibtex" ,r-bibtex)
3278 ("r-codetools" ,r-codetools)
3279 ("r-digest" ,r-digest)
3280 ("r-magrittr" ,r-magrittr)
3281 ("r-registry" ,r-registry)
3282 ("r-stringi" ,r-stringi)
3283 ("r-stringr" ,r-stringr)
3284 ("r-withr" ,r-withr)
3285 ("r-xtable" ,r-xtable)))
3286 (home-page "https://renozao.github.io/pkgmaker")
3287 (synopsis "Package development utilities")
3289 "This package provides some low-level utilities to use for R package
3290 development. It currently provides managers for multiple package specific
3291 options and registries, vignette, unit test and bibtex related utilities.")
3292 (license license:gpl2+)))
3294 (define-public r-registry
3301 (uri (cran-uri "registry" version))
3304 "1k3j6dx350awamr0dwwgkhfs46vsnj4nf08iw5byq0x7n3nkdsnz"))))
3305 (build-system r-build-system)
3306 (home-page "https://cran.r-project.org/web/packages/registry")
3307 (synopsis "Infrastructure for R package registries")
3309 "This package provides a generic infrastructure for creating and using R
3310 package registries.")
3311 (license license:gpl2+)))
3313 (define-public r-rngtools
3320 (uri (cran-uri "rngtools" version))
3323 "0k1nlcxggflq0043m15dfclnqnzchkpw2ik7jk82h4dqwvysiqcr"))))
3324 (build-system r-build-system)
3326 `(("r-digest" ,r-digest)
3327 ("r-pkgmaker" ,r-pkgmaker)
3328 ("r-stringr" ,r-stringr)))
3329 (home-page "https://renozao.github.io/rngtools")
3330 (synopsis "Utility functions for working with random number generators")
3332 "This package contains a set of functions for working with Random Number
3333 Generators (RNGs). In particular, it defines a generic S4 framework for
3334 getting/setting the current RNG, or RNG data that are embedded into objects
3335 for reproducibility. Notably, convenient default methods greatly facilitate
3336 the way current RNG settings can be changed.")
3337 (license license:gpl3+)))
3339 (define-public r-rtsne
3346 (uri (cran-uri "Rtsne" version))
3349 "0v17vxizrs1msay24xl2bckfajr2c82wpqj07lyssbrq197nwdsn"))))
3350 (properties `((upstream-name . "Rtsne")))
3351 (build-system r-build-system)
3353 `(("r-rcpp" ,r-rcpp)))
3354 (home-page "https://github.com/jkrijthe/Rtsne")
3355 (synopsis "T-distributed stochastic neighbor embedding")
3357 "This package provides an R wrapper around the fast T-distributed
3358 Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
3359 ;; The declared license for this package is BSD-3, but it also includes
3360 ;; code licensed under BSD-4.
3361 (license (list license:bsd-3 license:bsd-4))))
3363 (define-public r-e1071
3370 (uri (cran-uri "e1071" version))
3373 "1zlxz3da216q6v6r4ff60il121xwz7g7m639vzdwglhw3jjh8psw"))))
3374 (build-system r-build-system)
3376 `(("r-class" ,r-class)))
3377 (home-page "https://cran.r-project.org/web/packages/e1071")
3378 (synopsis "Miscellaneous functions for probability theory")
3380 "This package provides functions for latent class analysis, short time
3381 Fourier transform, fuzzy clustering, support vector machines, shortest path
3382 computation, bagged clustering, naive Bayes classifier, and more.")
3383 (license license:gpl2+)))
3385 (define-public r-bigmemory-sri
3387 (name "r-bigmemory-sri")
3392 (uri (cran-uri "bigmemory.sri" version))
3394 (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
3396 `((upstream-name . "bigmemory.sri")))
3397 (build-system r-build-system)
3398 (home-page "https://cran.r-project.org/web/packages/bigmemory.sri")
3399 (synopsis "Shared resource interface for the bigmemory package")
3400 (description "This package provides a shared resource interface for the
3401 bigmemory and synchronicity packages.")
3402 ;; Users can choose either LGPLv3 or ASL2.0.
3403 (license (list license:lgpl3 license:asl2.0))))
3405 (define-public r-synchronicity
3407 (name "r-synchronicity")
3412 (uri (cran-uri "synchronicity" version))
3415 "1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx"))))
3416 (build-system r-build-system)
3419 ("r-bigmemory-sri" ,r-bigmemory-sri)
3421 ("r-uuid" ,r-uuid)))
3422 (home-page "http://www.bigmemory.org")
3423 (synopsis "Boost mutex functionality in R")
3424 (description "This package provides support for synchronization
3425 via mutexes and may eventually support interprocess communication and
3427 ;; Users can choose either LGPLv3 or ASL2.0.
3428 (license (list license:lgpl3 license:asl2.0))))
3430 (define-public r-bigmemory
3432 (name "r-bigmemory")
3437 (uri (cran-uri "bigmemory" version))
3440 "0ycl9dzm3drpyas625h34rir5bnbjlncxlvawfsfmqwcbmwdjdvj"))))
3441 (build-system r-build-system)
3445 ("r-bigmemory-sri" ,r-bigmemory-sri)))
3446 (home-page "http://www.bigmemory.org")
3447 (synopsis "Manage large matrices with shared memory or memory-mapped files")
3448 (description "This package provides methods to create, store, access, and
3449 manipulate large matrices. Matrices are allocated to shared memory and may use
3450 memory-mapped files.")
3451 ;; Users can choose either LGPLv3 or ASL2.0.
3452 (license (list license:lgpl3 license:asl2.0))))
3454 (define-public r-nmf
3461 (uri (cran-uri "NMF" version))
3464 "1qq25n3k5sgh3srlshb3ic6q92s12c1ilqf5cd5anvq6cqfchc1v"))))
3465 (properties `((upstream-name . "NMF")))
3466 (build-system r-build-system)
3468 `(("r-cluster" ,r-cluster)
3469 ("r-bigmemory" ,r-bigmemory) ; suggested
3470 ("r-synchronicity" ,r-synchronicity) ; suggested
3471 ("r-colorspace" ,r-colorspace)
3472 ("r-digest" ,r-digest)
3473 ("r-doparallel" ,r-doparallel)
3474 ("r-foreach" ,r-foreach)
3475 ("r-ggplot2" ,r-ggplot2)
3476 ("r-gridbase" ,r-gridbase)
3477 ("r-pkgmaker" ,r-pkgmaker)
3478 ("r-rcolorbrewer" ,r-rcolorbrewer)
3479 ("r-registry" ,r-registry)
3480 ("r-reshape2" ,r-reshape2)
3481 ("r-rngtools" ,r-rngtools)
3482 ("r-stringr" ,r-stringr)))
3483 (home-page "http://renozao.github.io/NMF")
3484 (synopsis "Algorithms and framework for nonnegative matrix factorization")
3486 "This package provides a framework to perform Non-negative Matrix
3487 Factorization (NMF). The package implements a set of already published
3488 algorithms and seeding methods, and provides a framework to test, develop and
3489 plug new or custom algorithms. Most of the built-in algorithms have been
3490 optimized in C++, and the main interface function provides an easy way of
3491 performing parallel computations on multicore machines.")
3492 (license license:gpl2+)))
3494 (define-public r-r-methodss3
3496 (name "r-r-methodss3")
3500 (uri (cran-uri "R.methodsS3" version))
3503 "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24"))))
3504 (properties `((upstream-name . "R.methodsS3")))
3505 (build-system r-build-system)
3506 (home-page "https://cran.r-project.org/web/packages/R.methodsS3")
3507 (synopsis "S3 methods simplified")
3509 "This package provides methods that simplify the setup of S3 generic
3510 functions and S3 methods. Major effort has been made in making definition of
3511 methods as simple as possible with a minimum of maintenance for package
3512 developers. For example, generic functions are created automatically, if
3513 missing, and naming conflict are automatically solved, if possible. The
3514 method @code{setMethodS3()} is a good start for those who in the future may
3515 want to migrate to S4.")
3516 (license license:lgpl2.1+)))
3518 (define-public r-r-oo
3524 (uri (cran-uri "R.oo" version))
3527 "0k6xwy93fpb2p7bs76lzk52br9rv5xnd9524xj8qyazv1132x1n0"))))
3528 (properties `((upstream-name . "R.oo")))
3529 (build-system r-build-system)
3531 `(("r-r-methodss3" ,r-r-methodss3)))
3532 (home-page "https://github.com/HenrikBengtsson/R.oo")
3533 (synopsis "R object-oriented programming with or without references")
3535 "This package provides methods and classes for object-oriented
3536 programming in R with or without references. Large effort has been made on
3537 making definition of methods as simple as possible with a minimum of
3538 maintenance for package developers.")
3539 (license license:lgpl2.1+)))
3541 (define-public r-r-utils
3547 (uri (cran-uri "R.utils" version))
3550 "1jaarld1jgpzh18kh9g3rlzcrk51vdgn2n1d1y28szzxlz94vifg"))))
3551 (properties `((upstream-name . "R.utils")))
3552 (build-system r-build-system)
3554 `(("r-r-methodss3" ,r-r-methodss3)
3555 ("r-r-oo" ,r-r-oo)))
3556 (home-page "https://github.com/HenrikBengtsson/R.utils")
3557 (synopsis "Various programming utilities")
3559 "This package provides utility functions useful when programming and
3560 developing R packages.")
3561 (license license:lgpl2.1+)))
3563 (define-public r-r-cache
3569 (uri (cran-uri "R.cache" version))
3572 "1hf5cb7xvnca5zlh9245b5g62sgsaxwdhiv7x59yld37cydakm6k"))))
3573 (properties `((upstream-name . "R.cache")))
3574 (build-system r-build-system)
3576 `(("r-digest" ,r-digest)
3577 ("r-r-methodss3" ,r-r-methodss3)
3579 ("r-r-utils" ,r-r-utils)))
3580 (home-page "https://github.com/HenrikBengtsson/R.cache")
3581 (synopsis "Light-weight caching of objects and results")
3583 "This package provides methods for caching or memoization of objects and
3584 results. With this package, any R object can be cached in a key-value storage
3585 where the key can be an arbitrary set of R objects. The cache memory is
3586 persistent (on the file system).")
3587 (license license:lgpl2.1+)))
3589 (define-public r-r-rsp
3595 (uri (cran-uri "R.rsp" version))
3598 "0i01p8jxc4j4zl2v2ykvvpfnm5hv650zj1wi1dh8hq0c98xi2yfr"))))
3599 (properties `((upstream-name . "R.rsp")))
3600 (build-system r-build-system)
3602 `(("r-digest" ,r-digest)
3603 ("r-r-cache" ,r-r-cache)
3604 ("r-r-methodss3" ,r-r-methodss3)
3606 ("r-r-utils" ,r-r-utils)))
3607 (home-page "https://github.com/HenrikBengtsson/R.rsp")
3608 (synopsis "Dynamic generation of scientific reports")
3610 "The RSP markup language provides a powerful markup for controlling the
3611 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
3612 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
3613 to many other literate programming languages, with RSP it is straightforward
3614 to loop over mixtures of code and text sections, e.g. in month-by-month
3615 summaries. RSP has also several preprocessing directives for incorporating
3616 static and dynamic contents of external files (local or online) among other
3617 things. RSP is ideal for self-contained scientific reports and R package
3619 (license license:lgpl2.1+)))
3621 (define-public r-mvtnorm
3627 (uri (cran-uri "mvtnorm" version))
3630 "04md0wmqgif24g0a4hx19ifn4kk8nx10986vf2d9vascig6ikpri"))))
3631 (build-system r-build-system)
3633 `(("gfortran" ,gfortran)))
3634 (home-page "http://mvtnorm.R-forge.R-project.org")
3635 (synopsis "Package for multivariate normal and t-distributions")
3636 (description "This package can compute multivariate normal and
3637 t-probabilities, quantiles, random deviates and densities.")
3638 (license license:gpl2)))
3640 (define-public r-matrixstats
3642 (name "r-matrixstats")
3646 (uri (cran-uri "matrixStats" version))
3649 "0vx00ldsg2zvdrjn49jxczk2c9iaabgvzgpdka5j02ihh7hv83cg"))))
3650 (properties `((upstream-name . "matrixStats")))
3651 (build-system r-build-system)
3653 `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
3654 (home-page "https://github.com/HenrikBengtsson/matrixStats")
3655 (synopsis "Methods applying to vectors and matrix rows and columns")
3657 "This package provides methods operating on rows and columns of matrices,
3658 e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
3659 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
3660 @code{weightedMedians()}. All methods have been optimized for speed and
3662 (license license:artistic2.0)))
3664 (define-public r-viridis
3670 (uri (cran-uri "viridis" version))
3673 "060rf1jn29dq53y3nhb0hykvcap6rqsk04rq544ypiiqb18ngwnx"))))
3674 (build-system r-build-system)
3676 `(("r-ggplot2" ,r-ggplot2)
3677 ("r-gridextra" ,r-gridextra)
3678 ("r-viridislite" ,r-viridislite)))
3679 (home-page "https://github.com/sjmgarnier/viridis")
3680 (synopsis "Matplotlib default color map")
3682 "This package is a port of the new @url{matplotlib,
3683 http://matplotlib.org/} color maps (@code{viridis}--the default--,
3684 @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
3685 designed in such a way that they will analytically be perfectly
3686 perceptually-uniform, both in regular form and also when converted to
3687 black-and-white. They are also designed to be perceived by readers with the
3688 most common form of color blindness.")
3689 (license license:x11)))
3691 (define-public r-viridislite
3693 (name "r-viridislite")
3698 (uri (cran-uri "viridisLite" version))
3701 "1by2l05f0yabwvv64lhnv7bbhx0w683s3wr9j2xda920ghpa23kq"))))
3702 (properties `((upstream-name . "viridisLite")))
3703 (build-system r-build-system)
3704 (home-page "https://github.com/sjmgarnier/viridisLite")
3705 (synopsis "Default color maps from matplotlib")
3707 "This package is a port of the new @code{matplotlib} color maps
3708 (@code{viridis}, @code{magma}, @code{plasma} and @code{inferno}) to R.
3709 matplotlib is a popular plotting library for Python. These color maps are
3710 designed in such a way that they will analytically be perfectly
3711 perceptually-uniform, both in regular form and also when converted to
3712 black-and-white. They are also designed to be perceived by readers with the
3713 most common form of color blindness. This is the @code{lite} version of the
3714 more complete @code{viridis} package.")
3715 (license license:expat)))
3717 (define-public r-tidyselect
3719 (name "r-tidyselect")
3724 (uri (cran-uri "tidyselect" version))
3727 "0x3cp36byhfjajikr1lwffjm85ayw3bcs7d7kb0cydgs61ifiqjw"))))
3728 (build-system r-build-system)
3730 `(("r-glue" ,r-glue)
3731 ("r-purrr" ,r-purrr)
3733 ("r-rlang" ,r-rlang)))
3734 (home-page "https://cran.r-project.org/web/packages/tidyselect")
3735 (synopsis "Select from a set of strings")
3737 "This package provides a backend for the selecting functions of the
3738 tidyverse. It makes it easy to implement select-like functions in your own
3739 packages in a way that is consistent with other tidyverse interfaces for
3741 (license license:gpl3)))
3743 (define-public r-tidyr
3750 (uri (cran-uri "tidyr" version))
3753 "0dyc4b03wi65bk7j0ma0y188syh37h57wgxji82i0h8j6pn593x1"))))
3754 (build-system r-build-system)
3756 `(("r-dplyr" ,r-dplyr)
3757 ("r-magrittr" ,r-magrittr)
3759 ("r-purrr" ,r-purrr)
3760 ("r-rlang" ,r-rlang)
3761 ("r-tidyselect" ,r-tidyselect)
3763 ("r-stringi" ,r-stringi)
3764 ("r-tibble" ,r-tibble)))
3765 (home-page "https://github.com/hadley/tidyr")
3766 (synopsis "Tidy data with `spread()` and `gather()` functions")
3768 "tidyr is a reframing of the reshape2 package designed to accompany the
3769 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
3770 a solid pipeline for data analysis. It is designed specifically for tidying
3771 data, not the general reshaping that reshape2 does, or the general aggregation
3772 that reshape did. In particular, built-in methods only work for data frames,
3773 and tidyr provides no margins or aggregation.")
3774 (license license:expat)))
3776 (define-public r-hexbin
3783 (uri (cran-uri "hexbin" version))
3786 "0lpfl0015lg5x7lvv9dr302bca22c7fs91pnd896ypgpzqg7pm26"))))
3787 (build-system r-build-system)
3789 `(("r-lattice" ,r-lattice)))
3791 `(("gfortran" ,gfortran)))
3792 (home-page "https://github.com/edzer/hexbin")
3793 (synopsis "Hexagonal binning routines")
3795 "This package provides binning and plotting functions for hexagonal bins.
3796 It uses and relies on grid graphics and formal (S4) classes and methods.")
3797 (license license:gpl2+)))
3799 (define-public r-purrr
3806 (uri (cran-uri "purrr" version))
3809 "0ccs78a2ylr60f3z0f7iywi8h1pwr8mz4ga78bs4pwgnwkclvir7"))))
3810 (build-system r-build-system)
3812 `(("r-magrittr" ,r-magrittr)
3813 ("r-rlang" ,r-rlang)))
3814 (home-page "https://github.com/hadley/purrr")
3815 (synopsis "Functional programming tools")
3817 "This package completes R's functional programming tools with missing
3818 features present in other programming languages.")
3819 (license license:gpl3+)))
3821 (define-public r-plotly
3827 (uri (cran-uri "plotly" version))
3830 "1kz2hm7vnkn4clxr6yyxxnmdmkz9zwjq6bzysw7j27r3721i8qgp"))))
3831 (build-system r-build-system)
3833 `(("r-base64enc" ,r-base64enc)
3834 ("r-crosstalk" ,r-crosstalk)
3835 ("r-digest" ,r-digest)
3836 ("r-data-table" ,r-data-table)
3837 ("r-dplyr" ,r-dplyr)
3838 ("r-ggplot2" ,r-ggplot2)
3839 ("r-hexbin" ,r-hexbin)
3840 ("r-htmltools" ,r-htmltools)
3841 ("r-htmlwidgets" ,r-htmlwidgets)
3843 ("r-jsonlite" ,r-jsonlite)
3844 ("r-lazyeval" ,r-lazyeval)
3845 ("r-magrittr" ,r-magrittr)
3846 ("r-promises" ,r-promises)
3847 ("r-purrr" ,r-purrr)
3848 ("r-rcolorbrewer" ,r-rcolorbrewer)
3849 ("r-rlang" ,r-rlang)
3850 ("r-scales" ,r-scales)
3851 ("r-tibble" ,r-tibble)
3852 ("r-tidyr" ,r-tidyr)
3853 ("r-viridislite" ,r-viridislite)))
3854 (home-page "https://plot.ly/r")
3855 (synopsis "Create interactive web graphics")
3857 "This package enables the translation of ggplot2 graphs to an interactive
3858 web-based version and/or the creation of custom web-based visualizations
3859 directly from R. Once uploaded to a plotly account, plotly graphs (and the
3860 data behind them) can be viewed and modified in a web browser.")
3861 (license license:x11)))
3863 (define-public r-biased-urn
3865 (name "r-biased-urn")
3870 (uri (cran-uri "BiasedUrn" version))
3873 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
3874 (properties `((upstream-name . "BiasedUrn")))
3875 (build-system r-build-system)
3876 (home-page "http://www.agner.org/random/")
3877 (synopsis "Biased urn model distributions")
3879 "This package provides statistical models of biased sampling in the form
3880 of univariate and multivariate noncentral hypergeometric distributions,
3881 including Wallenius' noncentral hypergeometric distribution and Fisher's
3882 noncentral hypergeometric distribution (also called extended hypergeometric
3884 (license license:gpl3+)))
3886 (define-public r-rematch
3893 (uri (cran-uri "rematch" version))
3896 "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4"))))
3897 (build-system r-build-system)
3898 (home-page "https://github.com/MangoTheCat/rematch")
3899 (synopsis "Match regular expressions with a nicer API")
3901 "This package provides a small wrapper on @code{regexpr} to extract the
3902 matches and captured groups from the match of a regular expression to a
3904 (license license:expat)))
3906 (define-public r-cellranger
3908 (name "r-cellranger")
3913 (uri (cran-uri "cellranger" version))
3916 "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x"))))
3917 (build-system r-build-system)
3919 `(("r-rematch" ,r-rematch)
3920 ("r-tibble" ,r-tibble)))
3921 (home-page "https://github.com/rsheets/cellranger")
3922 (synopsis "Translate spreadsheet cell ranges to rows and columns")
3924 "This package provides helper functions to work with spreadsheets and the
3925 @code{A1:D10} style of cell range specification.")
3926 (license license:expat)))
3928 (define-public r-googlesheets
3930 (name "r-googlesheets")
3935 (uri (cran-uri "googlesheets" version))
3938 "11q07nxys72wkxx9mawmjyf20gvwvrb7h3gpa73h6lgh2vgrwnv8"))))
3939 (build-system r-build-system)
3941 `(("r-cellranger" ,r-cellranger)
3942 ("r-dplyr" ,r-dplyr)
3944 ("r-jsonlite" ,r-jsonlite)
3945 ("r-purrr" ,r-purrr)
3946 ("r-readr" ,r-readr)
3947 ("r-stringr" ,r-stringr)
3948 ("r-tibble" ,r-tibble)
3949 ("r-tidyr" ,r-tidyr)
3950 ("r-xml2" ,r-xml2)))
3951 (home-page "https://github.com/jennybc/googlesheets")
3952 (synopsis "Manage Google spreadsheets from R")
3953 (description "This package provides tools to interact with Google Sheets
3955 (license license:expat)))
3957 (define-public r-spams
3960 (version "2.6-2017-03-22")
3964 ;; Use the ‘Latest version’ link for a stable URI across releases.
3965 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
3966 "latestfile/4531/spams-R-v" version ".tar.gz"))
3969 "13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx"))))
3970 (build-system r-build-system)
3973 (modify-phases %standard-phases
3974 (add-after 'unpack 'chdir
3975 (lambda _ (chdir "spams") #t))
3976 ;; Don't tune for the building machine.
3977 (add-after 'chdir 'no-mtune
3979 (substitute* "src/Makevars"
3980 (("-mtune=native") ""))
3983 `(("r-lattice" ,r-lattice)
3984 ("r-matrix" ,r-matrix)))
3985 (home-page "http://spams-devel.gforge.inria.fr")
3986 (synopsis "Toolbox for solving sparse estimation problems")
3987 (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
3988 for solving various sparse estimation problems. It includes tools for the
3992 @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
3993 component analysis} (PCA), ...)
3994 @item Solving sparse decomposition problems with LARS, coordinate descent,
3995 OMP, SOMP, proximal methods
3996 @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
3997 group lasso, tree-structured regularization, structured sparsity with
3998 overlapping groups,...).
4000 (license license:gpl3+)))
4002 (define-public r-base64
4009 (uri (cran-uri "base64" version))
4012 "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf"))))
4013 (build-system r-build-system)
4015 `(("r-openssl" ,r-openssl)))
4016 (home-page "https://cran.r-project.org/web/packages/base64")
4017 (synopsis "Base64 encoder and decoder")
4019 "This package is a compatibility wrapper to replace the orphaned package
4020 by Romain Francois. New applications should use the openssl or base64enc
4022 (license license:expat)))
4024 (define-public r-hmisc
4031 (uri (cran-uri "Hmisc" version))
4034 "1n8i2jhc308hd6bvys9cd7nrz7pwjszs03r5bwlh1pc869ki95ly"))))
4035 (properties `((upstream-name . "Hmisc")))
4036 (build-system r-build-system)
4038 `(("gfortran" ,gfortran)))
4040 `(("r-acepack" ,r-acepack)
4041 ("r-base64enc" ,r-base64enc)
4042 ("r-cluster" ,r-cluster)
4043 ("r-data-table" ,r-data-table)
4044 ("r-foreign" ,r-foreign)
4045 ("r-formula" ,r-formula)
4046 ("r-ggplot2" ,r-ggplot2)
4047 ("r-gridextra" ,r-gridextra)
4048 ("r-gtable" ,r-gtable)
4049 ("r-lattice" ,r-lattice)
4050 ("r-latticeextra" ,r-latticeextra)
4051 ("r-htmltable" ,r-htmltable)
4052 ("r-htmltools" ,r-htmltools)
4054 ("r-rpart" ,r-rpart)
4055 ("r-survival" ,r-survival)
4056 ("r-viridis" ,r-viridis)))
4057 (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
4058 (synopsis "Miscellaneous data analysis and graphics functions")
4060 "This package contains many functions useful for data analysis,
4061 high-level graphics, utility operations, functions for computing sample size
4062 and power, importing and annotating datasets, imputing missing values,
4063 advanced table making, variable clustering, character string manipulation,
4064 conversion of R objects to LaTeX code, and recoding variables.")
4065 (license license:gpl2+)))
4067 (define-public r-runit
4074 (uri (cran-uri "RUnit" version))
4077 "1wc1gwb7yw7phf8b0gkig6c23klya3ax11c6i4s0f049k42r78r3"))))
4078 (properties `((upstream-name . "RUnit")))
4079 (build-system r-build-system)
4080 (home-page "https://cran.r-project.org/web/packages/RUnit")
4081 (synopsis "R unit test framework")
4083 "This package provides R functions implementing a standard unit testing
4084 framework, with additional code inspection and report generation tools.")
4085 (license license:gpl2+)))
4087 (define-public r-dynamictreecut
4089 (name "r-dynamictreecut")
4094 (uri (cran-uri "dynamicTreeCut" version))
4097 "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"))))
4098 (properties `((upstream-name . "dynamicTreeCut")))
4099 (build-system r-build-system)
4101 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
4102 (synopsis "Detect clusters in hierarchical clustering dendrograms")
4104 "This package contains methods for the detection of clusters in
4105 hierarchical clustering dendrograms.")
4106 (license license:gpl2+)))
4108 (define-public r-preprocesscore
4110 (name "r-preprocesscore")
4115 (uri (bioconductor-uri "preprocessCore" version))
4118 "0iiyn42hlvmc5vabg5x15mls11124i23sh4qijwk0narh438cqm0"))))
4120 `((upstream-name . "preprocessCore")))
4121 (build-system r-build-system)
4122 (home-page "https://github.com/bmbolstad/preprocessCore")
4123 (synopsis "Collection of pre-processing functions")
4125 "This package provides a library of core pre-processing and normalization
4127 (license license:lgpl2.0+)))
4129 (define-public r-fastcluster
4131 (name "r-fastcluster")
4136 (uri (cran-uri "fastcluster" version))
4139 "01a2xnhhvv1swd4g8p4lzyn7ww7kg49jlnzc7kfz60jqjzpisrpk"))))
4140 (build-system r-build-system)
4141 (home-page "http://danifold.net/fastcluster.html")
4142 (synopsis "Fast hierarchical clustering routines")
4144 "This package implements fast hierarchical, agglomerative clustering
4145 routines. Part of the functionality is designed as drop-in replacement for
4146 existing routines: @code{linkage()} in the SciPy package
4147 @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package,
4148 and the @code{flashClust} package. It provides the same functionality with
4149 the benefit of a much faster implementation. Moreover, there are
4150 memory-saving routines for clustering of vector data, which go beyond what the
4151 existing packages provide.")
4152 (license license:bsd-2)))
4154 (define-public r-sfsmisc
4161 (uri (cran-uri "sfsmisc" version))
4164 "0zaw617zarmwir8l60riky0z6r1j3mwfnm1f32vqcbljb74akdj4"))))
4165 (build-system r-build-system)
4166 (home-page "https://cran.r-project.org/web/packages/sfsmisc")
4167 (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
4169 "This package provides useful utilities from Seminar fuer Statistik ETH
4170 Zurich, including many that are related to graphics.")
4171 (license license:gpl2+)))
4173 (define-public r-gtools
4180 (uri (cran-uri "gtools" version))
4183 "0f5syk1qq6cjq6hwymvkiyhzwa389z94722v881ipbfqkd2q8505"))))
4184 (build-system r-build-system)
4187 (modify-phases %standard-phases
4188 (add-after 'unpack 'make-deterministic
4190 (substitute* "R/checkReverseDependencies.R"
4191 (("tempdir\\(\\)") "\"/tmp\""))
4193 (home-page "https://cran.r-project.org/web/packages/gtools")
4194 (synopsis "Various R programming tools")
4196 "This package contains a collection of various functions to assist in R
4197 programming, such as tools to assist in developing, updating, and maintaining
4198 R and R packages, calculating the logit and inverse logit transformations,
4199 tests for whether a value is missing, empty or contains only @code{NA} and
4200 @code{NULL} values, and many more.")
4201 (license license:gpl2)))
4203 (define-public r-gdata
4210 (uri (cran-uri "gdata" version))
4213 "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b"))))
4214 (build-system r-build-system)
4218 `(("r-gtools" ,r-gtools)))
4219 (home-page "https://cran.r-project.org/web/packages/gdata")
4220 (synopsis "Various R programming tools for data manipulation")
4222 "This package provides various R programming tools for data manipulation,
4226 @item medical unit conversions
4227 @item combining objects
4228 @item character vector operations
4229 @item factor manipulation
4230 @item obtaining information about R objects
4231 @item manipulating MS-Excel formatted files
4232 @item generating fixed-width format files
4233 @item extricating components of date and time objects
4234 @item operations on columns of data frames
4235 @item matrix operations
4236 @item operations on vectors and data frames
4237 @item value of last evaluated expression
4238 @item wrapper for @code{sample} that ensures consistent behavior for
4239 both scalar and vector arguments
4241 (license license:gpl2+)))
4243 (define-public r-gplots
4250 (uri (cran-uri "gplots" version))
4253 "033plcfs9w8pmn84n24mdhiixdirc2a7pz6dvm61fpd20gwh7cbx"))))
4254 (build-system r-build-system)
4256 `(("r-catools" ,r-catools)
4257 ("r-gdata" ,r-gdata)
4258 ("r-gtools" ,r-gtools)
4259 ("r-kernsmooth" ,r-kernsmooth)))
4260 (home-page "https://cran.r-project.org/web/packages/gplots")
4261 (synopsis "Various R programming tools for plotting data")
4263 "This package provides various R programming tools for plotting data,
4267 @item calculating and plotting locally smoothed summary function
4268 @item enhanced versions of standard plots
4269 @item manipulating colors
4270 @item calculating and plotting two-dimensional data summaries
4271 @item enhanced regression diagnostic plots
4272 @item formula-enabled interface to @code{stats::lowess} function
4273 @item displaying textual data in plots
4275 @item plotting \"Venn\" diagrams
4276 @item displaying Open-Office style plots
4277 @item plotting multiple data on same region, with separate axes
4278 @item plotting means and confidence intervals
4279 @item spacing points in an x-y plot so they don't overlap
4281 (license license:gpl2+)))
4283 (define-public r-rocr
4290 (uri (cran-uri "ROCR" version))
4293 "1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7"))))
4294 (properties `((upstream-name . "ROCR")))
4295 (build-system r-build-system)
4297 `(("r-gplots" ,r-gplots)))
4298 (home-page "http://rocr.bioinf.mpi-sb.mpg.de/")
4299 (synopsis "Visualizing the performance of scoring classifiers")
4301 "ROCR is a flexible tool for creating cutoff-parameterized 2D performance
4302 curves by freely combining two from over 25 performance measures (new
4303 performance measures can be added using a standard interface). Curves from
4304 different cross-validation or bootstrapping runs can be averaged by different
4305 methods, and standard deviations, standard errors or box plots can be used to
4306 visualize the variability across the runs. The parameterization can be
4307 visualized by printing cutoff values at the corresponding curve positions, or
4308 by coloring the curve according to cutoff. All components of a performance
4309 plot can be quickly adjusted using a flexible parameter dispatching
4311 (license license:gpl2+)))
4313 (define-public r-zoo
4319 (uri (cran-uri "zoo" version))
4322 "09p8gmd5ifz80ahnhiianarsr5xx3nz76jzp90d7v3fjffcrcww7"))))
4323 (build-system r-build-system)
4325 `(("r-lattice" ,r-lattice)))
4326 (home-page "http://zoo.R-Forge.R-project.org/")
4327 (synopsis "S3 infrastructure for regular and irregular time series")
4328 (description "This package contains an S3 class with methods for totally
4329 ordered indexed observations. It is particularly aimed at irregular time
4330 series of numeric vectors/matrices and factors.")
4331 (license license:gpl2+)))
4333 (define-public r-ztable
4339 (uri (cran-uri "ztable" version))
4342 "0g7khk5ifsdh9p31wlwh2l5mn1hzxzpv6qcn1wh34vsfjdmijjwy"))))
4343 (build-system r-build-system)
4345 `(("r-flextable" ,r-flextable)
4346 ("r-magrittr" ,r-magrittr)
4347 ("r-moonbook" ,r-moonbook)
4348 ("r-officer" ,r-officer)
4349 ("r-rcolorbrewer" ,r-rcolorbrewer)
4350 ("r-scales" ,r-scales)
4351 ("r-stringr" ,r-stringr)))
4352 (home-page "https://cran.r-project.org/web/packages/ztable")
4353 (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
4355 "This package provides functions to make zebra-striped tables (tables
4356 with alternating row colors) in LaTeX and HTML formats easily from
4357 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
4358 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
4359 @code{cbind.mytable} objects.")
4360 (license license:gpl2+)))
4362 (define-public r-vipor
4368 (uri (cran-uri "vipor" version))
4371 "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx"))))
4372 (build-system r-build-system)
4373 (home-page "https://cran.r-project.org/web/packages/vipor")
4374 (synopsis "Plot categorical data using noise and density estimates")
4376 "This package provides tools to generate a violin point plot, a
4377 combination of a violin/histogram plot and a scatter plot by offsetting points
4378 within a category based on their density using quasirandom noise.")
4379 (license license:gpl2+)))
4381 (define-public r-beeswarm
4387 (uri (cran-uri "beeswarm" version))
4390 "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
4391 (build-system r-build-system)
4392 (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/")
4393 (synopsis "Implementation of bee swarm plots")
4395 "This package provides an implementation of bee swarm plots. The bee
4396 swarm plot is a one-dimensional scatter plot like stripchart, but with
4397 closely-packed, non-overlapping points.")
4398 (license license:artistic2.0)))
4400 (define-public r-sourcetools
4402 (name "r-sourcetools")
4407 (uri (cran-uri "sourcetools" version))
4410 "1jnjir0q2dj724f1mjm6p5h77yzyx6xcqy9r2g7gmcxkxw349627"))))
4411 (build-system r-build-system)
4412 (home-page "https://cran.r-project.org/web/packages/sourcetools")
4413 (synopsis "Tools for reading, tokenizing and parsing R code")
4415 "The sourcetools package provides both an R and C++ interface for the
4416 tokenization of R code, and helpers for interacting with the tokenized
4417 representation of R code.")
4418 (license license:expat)))
4420 (define-public r-ggbeeswarm
4422 (name "r-ggbeeswarm")
4426 (uri (cran-uri "ggbeeswarm" version))
4429 "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v"))))
4430 (build-system r-build-system)
4432 `(("r-beeswarm" ,r-beeswarm)
4433 ("r-ggplot2" ,r-ggplot2)
4434 ("r-vipor" ,r-vipor)))
4435 (home-page "https://github.com/eclarke/ggbeeswarm")
4436 (synopsis "Categorical scatter (violin point) plots")
4438 "This package provides two methods of plotting categorical scatter plots
4439 such that the arrangement of points within a category reflects the density of
4440 data at that region, and avoids over-plotting.")
4441 (license license:gpl2+)))
4443 (define-public r-ggthemes
4449 (uri (cran-uri "ggthemes" version))
4452 "092hks6bxi6al8nclgswnzfmx5wp6n3qf63aqiajca7dx8w8n0m2"))))
4453 (build-system r-build-system)
4455 `(("r-ggplot2" ,r-ggplot2)
4456 ("r-purrr" ,r-purrr)
4457 ("r-scales" ,r-scales)
4458 ("r-stringr" ,r-stringr)
4459 ("r-tibble" ,r-tibble)))
4460 (home-page "https://cran.rstudio.com/web/packages/ggthemes")
4461 (synopsis "Extra themes, scales and geoms for @code{ggplot2}")
4462 (description "This package provides extra themes and scales for
4463 @code{ggplot2} that replicate the look of plots by Edward Tufte and
4464 Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The
4465 Wall Street Journal, among others. This package also provides
4466 @code{geoms} for Tufte's box plot and range frame.")
4467 (license license:gpl2)))
4469 (define-public r-statmod
4475 (uri (cran-uri "statmod" version))
4478 "07v4x8af60alcw6vbiwf5fp25bhra61kvxz9kqx64lszm0i1fb4x"))))
4479 (build-system r-build-system)
4480 (home-page "https://cran.r-project.org/web/packages/statmod")
4482 `(("gfortran" ,gfortran)))
4483 (synopsis "Statistical modeling")
4485 "This package provides a collection of algorithms and functions to aid
4486 statistical modeling. It includes growth curve comparisons, limiting dilution
4487 analysis (aka ELDA), mixed linear models, heteroscedastic regression,
4488 inverse-Gaussian probability calculations, Gauss quadrature and a secure
4489 convergence algorithm for nonlinear models. It also includes advanced
4490 generalized linear model functions that implement secure convergence,
4491 dispersion modeling and Tweedie power-law families.")
4492 ;; Statmod is distributed under either license
4493 (license (list license:gpl2 license:gpl3))))
4495 (define-public r-rann
4501 (uri (cran-uri "RANN" version))
4504 "10kid40w9w7vkz2hpcfkdpxr4afxzms5dzvfwr0sl5xynzgw76dj"))))
4506 `((upstream-name . "RANN")))
4507 (build-system r-build-system)
4508 (home-page "https://github.com/jefferis/RANN")
4509 (synopsis "Fast nearest neighbour search")
4511 "This package finds the k nearest neighbours for every point in a given
4512 dataset in O(N log N) time using Arya and Mount's ANN library. Provides
4513 approximate, exact searches, fixed radius searches, bd and kb trees.")
4514 (license license:gpl3+)))
4516 (define-public r-fivethirtyeight
4518 (name "r-fivethirtyeight")
4523 (uri (string-append "https://mran.microsoft.com/src/contrib/"
4524 "fivethirtyeight_" version ".tar.gz"))
4527 "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl"))))
4528 (build-system r-build-system)
4530 `(("r-knitr" ,r-knitr)
4531 ("r-rmarkdown" ,r-rmarkdown)
4532 ("r-dplyr" ,r-dplyr)
4533 ("r-readr" ,r-readr)
4534 ("r-ggplot2" ,r-ggplot2)
4535 ("r-magrittr" ,r-magrittr)
4536 ("r-stringr" ,r-stringr)))
4537 (home-page "https://mran.microsoft.com/package/fivethirtyeight/")
4538 (synopsis "Data and code behind the stories at FiveThirtyEight")
4539 (description "This R package provides access to the code and data sets
4540 published by the statistics blog FiveThirtyEight.")
4541 (license license:expat)))
4543 (define-public r-compquadform
4545 (name "r-compquadform")
4550 (uri (cran-uri "CompQuadForm" version))
4553 "1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4"))))
4554 (properties `((upstream-name . "CompQuadForm")))
4555 (build-system r-build-system)
4556 (home-page "https://cran.r-project.org/web/packages/CompQuadForm")
4557 (synopsis "Distribution function of quadratic forms in normal variables")
4559 "This package provides functions to compute the distribution function of
4560 quadratic forms in normal variables using Imhof's method, Davies's algorithm,
4561 Farebrother's algorithm or Liu et al.'s algorithm.")
4562 (license license:gpl2+)))
4564 (define-public r-cowplot
4571 (uri (cran-uri "cowplot" version))
4574 "0yvalwalvyddyqk0q66y8361nxlh2cvp3ssazax9g5q89lghjmzv"))))
4575 (build-system r-build-system)
4577 `(("r-ggplot2" ,r-ggplot2)
4578 ("r-gtable" ,r-gtable)
4580 ("r-scales" ,r-scales)))
4581 (home-page "https://github.com/wilkelab/cowplot")
4582 (synopsis "Streamlined plot theme and plot annotations for ggplot2")
4584 "This package provides some helpful extensions and modifications to the
4585 ggplot2 package to combine multiple ggplot2 plots into one and label them with
4586 letters, as is often required for scientific publications.")
4587 (license license:gpl2)))
4589 (define-public r-mixtools
4596 (uri (cran-uri "mixtools" version))
4599 "13wdm0xs5bakhpa8ypg6lvhjaqkxyabwz4glxdwn0jwdvkcdhgsl"))))
4600 (build-system r-build-system)
4602 `(("r-mass" ,r-mass)
4603 ("r-segmented" ,r-segmented)
4604 ("r-survival" ,r-survival)))
4605 (home-page "https://cran.r-project.org/web/packages/mixtools")
4606 (synopsis "Tools for analyzing finite mixture models")
4608 "This package provides a collection of R functions for analyzing finite
4610 (license license:gpl2+)))
4612 (define-public r-lars
4619 (uri (cran-uri "lars" version))
4622 "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
4623 (build-system r-build-system)
4625 `(("gfortran" ,gfortran)))
4626 (home-page "http://www-stat.stanford.edu/~hastie/Papers/#LARS")
4627 (synopsis "Least angle regression software")
4629 "Least Angle Regression (\"LAR\") is a model selection algorithm; a
4630 useful and less greedy version of traditional forward selection methods. A
4631 simple modification of the LAR algorithm implements Tibshirani's Lasso; the
4632 Lasso modification of LARS calculates the entire Lasso path of coefficients
4633 for a given problem at the cost of a single least squares fit. Another LARS
4634 modification efficiently implements epsilon Forward Stagewise linear
4636 (license license:gpl2)))
4638 (define-public r-fastica
4645 (uri (cran-uri "fastICA" version))
4648 "108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg"))))
4649 (properties `((upstream-name . "fastICA")))
4650 (build-system r-build-system)
4651 (home-page "https://cran.r-project.org/web/packages/fastICA")
4652 (synopsis "FastICA algorithms to perform ICA and projection pursuit")
4654 "This package provides an implementation of the FastICA algorithm to
4655 perform @dfn{independent component analysis} (ICA) and projection pursuit.")
4657 (license license:gpl3+)))
4659 (define-public r-randomforest
4661 (name "r-randomforest")
4666 (uri (cran-uri "randomForest" version))
4669 "0kbmm0l42fc2d1rdq0l7k09d34kd87q4lx651ffsic4y84h8kf7l"))))
4670 (properties `((upstream-name . "randomForest")))
4671 (build-system r-build-system)
4672 (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
4674 `(("gfortran" ,gfortran)))
4675 (synopsis "Breiman and Cutler's random forests for classification and regression")
4677 "This package provides the Breiman and Cutler's random forests algorithm, based on a
4678 forest of trees using random inputs, for classification and regression.")
4679 (license license:gpl2+)))
4681 (define-public r-diptest
4688 (uri (cran-uri "diptest" version))
4691 "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
4692 (build-system r-build-system)
4693 (home-page "https://cran.r-project.org/web/packages/diptest")
4694 (synopsis "Hartigan's dip test statistic for unimodality")
4696 "This package computes Hartigan's dip test statistic for unimodality,
4697 multimodality and provides a test with simulation based p-values, where the
4698 original public code has been corrected.")
4699 (license license:gpl2+)))
4701 (define-public r-modeltools
4703 (name "r-modeltools")
4708 (uri (cran-uri "modeltools" version))
4711 "1s9lmkac3rl0nknf4wizfhg7ryq7c8yvvyc4z619238br27hhsi5"))))
4712 (build-system r-build-system)
4713 (home-page "https://cran.r-project.org/web/packages/modeltools")
4714 (synopsis "Tools and classes for statistical models")
4716 "This package provides a collection of tools to deal with statistical
4717 models. The functionality is experimental and the user interface is likely
4718 to change in the future.")
4719 (license license:gpl2)))
4721 (define-public r-flexmix
4728 (uri (cran-uri "flexmix" version))
4731 "0hrz2axp2c9548b1r0bmrl57219nn030qndb83a8garkzq5lqi5s"))))
4732 (build-system r-build-system)
4734 `(("r-lattice" ,r-lattice)
4735 ("r-modeltools" ,r-modeltools)
4736 ("r-nnet" ,r-nnet)))
4737 (home-page "https://cran.r-project.org/web/packages/flexmix")
4738 (synopsis "Flexible mixture modeling")
4740 "This package implements a general framework for finite mixtures of
4741 regression models using the EM algorithm. FlexMix provides the E-step and
4742 all data handling, while the M-step can be supplied by the user to easily
4743 define new models. Existing drivers implement mixtures of standard linear
4744 models, generalized linear models and model-based clustering.")
4745 (license license:gpl2+)))
4747 (define-public r-mclust
4754 (uri (cran-uri "mclust" version))
4757 "18x5ych9zi3y87rxi4pf6f23sl2918dp9xxpw1pqa7p7drw817p6"))))
4758 (build-system r-build-system)
4760 `(("gfortran" ,gfortran)))
4761 (home-page "http://www.stat.washington.edu/mclust/")
4762 (synopsis "Gaussian mixture modelling for model-based clustering etc.")
4764 "This package provides Gaussian finite mixture models fitted via EM
4765 algorithm for model-based clustering, classification, and density estimation,
4766 including Bayesian regularization, dimension reduction for visualisation,
4767 and resampling-based inference.")
4768 (license license:gpl2+)))
4770 (define-public r-prabclus
4777 (uri (cran-uri "prabclus" version))
4780 "0h2nml8ri27mhfs2p6ngb6kfd6lyq30sc6813yybpskkrb6gs1pb"))))
4781 (build-system r-build-system)
4783 `(("r-mass" ,r-mass)
4784 ("r-mclust" ,r-mclust)))
4785 (home-page "https://cran.r-project.org/web/packages/prabclus")
4786 (synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
4788 "This package provides distance-based parametric bootstrap tests for
4789 clustering with spatial neighborhood information. It implements some distance
4790 measures, clustering of presence-absence, abundance and multilocus genetical
4791 data for species delimitation, nearest neighbor based noise detection.")
4792 (license license:gpl2+)))
4794 (define-public r-deoptimr
4801 (uri (cran-uri "DEoptimR" version))
4804 "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
4805 (properties `((upstream-name . "DEoptimR")))
4806 (build-system r-build-system)
4807 (home-page "https://cran.r-project.org/web/packages/DEoptimR")
4808 (synopsis "Differential evolution optimization in pure R")
4810 "This package provides a differential evolution (DE) stochastic
4811 algorithms for global optimization of problems with and without constraints.
4812 The aim is to curate a collection of its state-of-the-art variants that (1) do
4813 not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
4814 can be efficiently implemented directly in the R language.")
4815 (license license:gpl2+)))
4817 (define-public r-robustbase
4819 (name "r-robustbase")
4824 (uri (cran-uri "robustbase" version))
4827 "1q56y0iqp7qhavm4xnpzhs64q7l893y7yiq3b20fllpghka077pa"))))
4828 (build-system r-build-system)
4830 `(("gfortran" ,gfortran)))
4832 `(("r-deoptimr" ,r-deoptimr)))
4833 (home-page "http://robustbase.r-forge.r-project.org/")
4834 (synopsis "Basic robust statistics")
4836 "This packages allows to analyze data with robust methods such as
4837 regression methodology including model selections and multivariate statistics.")
4838 (license license:gpl2+)))
4840 (define-public r-pcapp
4847 (uri (cran-uri "pcaPP" version))
4850 "1z2kdf9gfp965xbcd4rg6vf20d1bl443na0qjkpq7gmzpaq6cifa"))))
4851 (properties `((upstream-name . "pcaPP")))
4852 (build-system r-build-system)
4854 `(("r-mvtnorm" ,r-mvtnorm)))
4855 (home-page "https://cran.r-project.org/web/packages/pcaPP")
4856 (synopsis "Robust PCA by projection pursuit")
4858 "This package provides functions for robust @dfn{principal component
4859 analysis} (PCA) by projection pursuit.")
4860 (license license:gpl3+)))
4862 (define-public r-rrcov
4869 (uri (cran-uri "rrcov" version))
4872 "14zjyqcdiqx6js99nx5s8hmyx564ixy2d8s6i7wa50xmx368rl6b"))))
4873 (build-system r-build-system)
4875 `(("r-cluster" ,r-cluster)
4876 ("r-lattice" ,r-lattice)
4877 ("r-mvtnorm" ,r-mvtnorm)
4878 ("r-pcapp" ,r-pcapp)
4879 ("r-robustbase" ,r-robustbase)))
4881 `(("gfortran" ,gfortran)))
4882 (home-page "https://cran.r-project.org/web/packages/rrcov")
4883 (synopsis "Scalable robust estimators with high breakdown Point")
4885 "This package provides an implementation of robust location and scatter
4886 estimation and robust multivariate analysis with high breakdown point.")
4887 (license license:gpl2+)))
4889 (define-public r-fit-models
4891 (name "r-fit-models")
4896 (uri (cran-uri "fit.models" version))
4899 "0vjbzmx0ambm6yzidb4vbgmhclwzwv2iz2cwl54ccdkvx4cx3fck"))))
4900 (properties `((upstream-name . "fit.models")))
4901 (build-system r-build-system)
4903 `(("r-lattice" ,r-lattice)))
4904 (home-page "https://cran.r-project.org/web/packages/fit.models")
4905 (synopsis "Compare fitted models")
4907 "The @code{fit.models} function and its associated methods (coefficients, print,
4908 summary, plot, etc.) were originally provided in the @code{robust} package to
4909 compare robustly and classically fitted model objects. The aim of the
4910 @code{fit.models} package is to separate this fitted model object comparison
4911 functionality from the robust package and to extend it to support fitting
4912 methods (e.g., classical, robust, Bayesian, regularized, etc.) more
4914 ;; Any version of the GPL
4915 (license (list license:gpl2+ license:gpl3+))))
4917 (define-public r-robust
4924 (uri (cran-uri "robust" version))
4927 "1b7qh1aff500nd6dh4y2ipmjgdiq8991shflb63pc39vpc0ny6g4"))))
4928 (build-system r-build-system)
4930 `(("r-fit-models" ,r-fit-models)
4931 ("r-lattice" ,r-lattice)
4933 ("r-robustbase" ,r-robustbase)
4934 ("r-rrcov" ,r-rrcov)))
4936 `(("gfortran" ,gfortran)))
4937 (home-page "https://cran.r-project.org/web/packages/robust")
4938 (synopsis "Port of the S+ \"Robust Library\"")
4940 "This package is a port of the S+ \"Robust Library\". It provides
4941 methods for robust statistics, notably for robust regression and robust
4942 multivariate analysis.")
4943 (license license:gpl2)))
4945 (define-public r-trimcluster
4947 (name "r-trimcluster")
4952 (uri (cran-uri "trimcluster" version))
4955 "0013bpyq6mkvjn38qsmwnsxfiwxgwngnqxycxvgpgmiadhm8fjmn"))))
4956 (build-system r-build-system)
4957 (home-page "https://cran.r-project.org/web/packages/trimcluster")
4958 (synopsis "Cluster analysis with trimming")
4960 "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
4961 Matran (1997). This optimizes the k-means criterion under trimming a portion
4964 (license (list license:gpl2+ license:gpl3+))))
4966 (define-public r-fpc
4969 (version "2.1-11.2")
4973 (uri (cran-uri "fpc" version))
4976 "0wjjp9xn283acfg6cm1wa6fsi7pf0z97227hrnlpmprks3mbj8kr"))))
4977 (build-system r-build-system)
4979 `(("r-class" ,r-class)
4980 ("r-cluster" ,r-cluster)
4981 ("r-diptest" ,r-diptest)
4982 ("r-flexmix" ,r-flexmix)
4983 ("r-kernlab" ,r-kernlab)
4985 ("r-mclust" ,r-mclust)
4986 ("r-mvtnorm" ,r-mvtnorm)
4987 ("r-prabclus" ,r-prabclus)
4988 ("r-robustbase" ,r-robustbase)
4989 ("r-trimcluster" ,r-trimcluster)))
4990 (home-page "https://cran.r-project.org/web/packages/fpc")
4991 (synopsis "Flexible procedures for clustering")
4993 "This package provides various methods for clustering and cluster validation.
4994 For example, it provides fixed point clustering, linear regression clustering,
4995 clustering by merging Gaussian mixture components, as well as symmetric and
4996 asymmetric discriminant projections for visualisation of the separation of
4998 (license license:gpl2+)))
5000 (define-public r-vgam
5007 (uri (cran-uri "VGAM" version))
5010 "0lnsqx3q3k0c7sj8gj0n6shn2fyxwrh8xph8h1r1i23ybbb2n6fy"))))
5011 (properties `((upstream-name . "VGAM")))
5012 (build-system r-build-system)
5014 `(("gfortran" ,gfortran)))
5015 (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
5016 (synopsis "Vector generalized linear and additive models")
5018 "This package is an implementation of about 6 major classes of statistical
5019 regression models. Currently only fixed-effects models are implemented, i.e.,
5020 no random-effects models. Many (150+) models and distributions are estimated
5021 by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
5022 VGLMs can be loosely thought of as multivariate generalised linear models.")
5023 (license license:gpl2+)))
5025 (define-public r-pbapply
5032 (uri (cran-uri "pbapply" version))
5035 "0bn7a9ni36xy5acnrl9ky3gd1k8jr5kxgazzh3pzd1q6bri1nx7k"))))
5036 (build-system r-build-system)
5037 (home-page "https://github.com/psolymos/pbapply")
5038 (synopsis "Adding progress bar to apply functions")
5040 "This lightweight package that adds progress bar to vectorized R
5041 functions apply. The implementation can easily be added to functions where
5042 showing the progress is useful e.g. bootstrap.")
5043 (license license:gpl2)))
5045 (define-public r-minqa
5052 (uri (cran-uri "minqa" version))
5055 "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
5056 (build-system r-build-system)
5058 `(("r-rcpp" ,r-rcpp)))
5060 `(("gfortran" ,gfortran)))
5061 (home-page "http://optimizer.r-forge.r-project.org")
5062 (synopsis "Derivative-free optimization algorithms by quadratic approximation")
5064 "This package provides a derivative-free optimization by quadratic approximation
5065 based on an interface to Fortran implementations by M. J. D. Powell.")
5066 (license license:gpl2)))
5068 (define-public r-rcppeigen
5070 (name "r-rcppeigen")
5071 (version "0.3.3.5.0")
5075 (uri (cran-uri "RcppEigen" version))
5078 "01bz41c29591ybzqn4z88ss036ai3anh9figryvmfpqcfwbszip5"))))
5079 (properties `((upstream-name . "RcppEigen")))
5080 (build-system r-build-system)
5082 `(("r-rcpp" ,r-rcpp)
5083 ("r-matrix" ,r-matrix)))
5084 (home-page "http://eigen.tuxfamily.org")
5085 (synopsis "Rcpp integration for the Eigen templated linear algebra library")
5087 "This package provides an integration of Eigen in R using a C++ template
5088 library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
5089 It supports dense and sparse matrices on integer, floating point and complex numbers,
5090 decompositions of such matrices, and solutions of linear systems.")
5091 (license license:gpl2+)))
5093 (define-public r-modelmetrics
5095 (name "r-modelmetrics")
5100 (uri (cran-uri "ModelMetrics" version))
5103 "158ddbw2snlyzd2q6mdaif5i67kq4qfvadylwjxgv1w2cmszrmk6"))))
5104 (properties `((upstream-name . "ModelMetrics")))
5105 (build-system r-build-system)
5107 `(("r-rcpp" ,r-rcpp)
5108 ("r-data-table" ,r-data-table)))
5109 (home-page "https://cran.r-project.org/web/packages/ModelMetrics")
5110 (synopsis "Rapid calculation of model metrics")
5112 "Written in C++ using @code{Rcpp}, this package provides a collection of
5113 metrics for evaluating models.")
5114 (license license:gpl2+)))
5116 (define-public r-matrixmodels
5118 (name "r-matrixmodels")
5123 (uri (cran-uri "MatrixModels" version))
5126 "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
5127 (properties `((upstream-name . "MatrixModels")))
5128 (build-system r-build-system)
5130 `(("r-matrix" ,r-matrix)))
5131 (home-page "https://cran.r-project.org/web/packages/MatrixModels")
5132 (synopsis "Modelling with sparse and dense matrices")
5134 "This package models with sparse and dense matrix matrices,
5135 using modular prediction and response module classes.")
5136 (license license:gpl2+)))
5138 (define-public r-quantreg
5145 (uri (cran-uri "quantreg" version))
5148 "1vvvnk291f0dccg04l3nsnk585gq75sk0b2vdbrqv3lczvv18nw1"))))
5149 (build-system r-build-system)
5151 `(("gfortran" ,gfortran)))
5153 `(("r-matrix" ,r-matrix)
5154 ("r-matrixmodels" ,r-matrixmodels)
5155 ("r-sparsem" ,r-sparsem)))
5156 (home-page "https://www.r-project.org")
5157 (synopsis "Quantile regression")
5159 "This package provides an estimation and inference methods for models
5160 of conditional quantiles: linear and nonlinear parametric and non-parametric
5161 models for conditional quantiles of a univariate response and several methods
5162 for handling censored survival data. Portfolio selection methods based on
5163 expected shortfall risk are also included.")
5164 (license license:gpl2+)))
5166 (define-public r-nloptr
5173 (uri (cran-uri "nloptr" version))
5176 "15yz60kljxwnhm2m3gryjzxl3ynhkhd5jiwc179b1hz6rlzf71hz"))))
5177 (build-system r-build-system)
5179 `(("r-knitr" ,r-knitr) ; for building vignettes
5180 ("pkg-config" ,pkg-config)
5181 ("gfortran" ,gfortran)))
5183 `(("nlopt" ,nlopt)))
5184 (home-page "https://cran.r-project.org/web/packages/nloptr")
5185 (synopsis "R interface to NLopt")
5187 "This package is interface to NLopt, a library for nonlinear
5188 optimization. NLopt is a library for nonlinear optimization, providing a
5189 common interface for a number of different free optimization routines
5190 available online as well as original implementations of various other
5192 (license license:lgpl3)))
5194 (define-public r-lme4
5201 (uri (cran-uri "lme4" version))
5204 "035j2hqkwv939xl07pm2vykvf3wlx8qj317846n9pkpqkyv58mbz"))))
5205 (build-system r-build-system)
5207 `(("r-boot" ,r-boot)
5208 ("r-lattice" ,r-lattice)
5210 ("r-matrix" ,r-matrix)
5211 ("r-minqa" ,r-minqa)
5212 ("r-nloptr" ,r-nloptr)
5215 ("r-rcppeigen" ,r-rcppeigen)))
5216 (home-page "https://cran.r-project.org/web/packages/lme4")
5217 (synopsis "Linear mixed-effects models using eigen and S4")
5219 "This package provides fit linear and generalized linear mixed-effects
5220 models. The models and their components are represented using S4 classes and
5221 methods. The core computational algorithms are implemented using the Eigen
5222 C++ library for numerical linear algebra and RcppEigen glue.")
5223 (license license:gpl2+)))
5225 (define-public r-pbkrtest
5232 (uri (cran-uri "pbkrtest" version))
5235 "1si3bhi59xc51a0pgjjglccq3h4aljyhw2k1b8574s145fnh7fsw"))))
5236 (build-system r-build-system)
5238 `(("r-lme4" ,r-lme4)
5240 ("r-matrix" ,r-matrix)))
5241 (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
5242 (synopsis "Methods for linear mixed model comparison")
5244 "This package implements a parametric bootstrap test and a Kenward Roger
5245 modification of F-tests for linear mixed effects models and a parametric
5246 bootstrap test for generalized linear mixed models.")
5247 (license license:gpl2+)))
5249 (define-public r-cardata
5256 (uri (cran-uri "carData" version))
5259 "152lfgaspgx6x2wzdb5p3zv6r87a0d2pg10h6fjmdr613kzlwp1v"))))
5260 (properties `((upstream-name . "carData")))
5261 (build-system r-build-system)
5262 (home-page "https://r-forge.r-project.org/projects/car/")
5263 (synopsis "Data Sets for the book Companion to Applied Regression")
5265 "This package provides datasets to accompany J. Fox and S. Weisberg, An R
5266 Companion to Applied Regression, Third Edition, Sage.")
5267 (license license:gpl2+)))
5269 (define-public r-car
5276 (uri (cran-uri "car" version))
5279 "0l3wyc9ia0ypcbap2p39slazfpbl84mjzydqvpsywrzdiyxajnfz"))))
5280 (build-system r-build-system)
5282 `(("r-abind" ,r-abind)
5283 ("r-cardata" ,r-cardata)
5285 ("r-maptools" ,r-maptools)
5290 ("r-pbkrtest" ,r-pbkrtest)
5291 ("r-quantreg" ,r-quantreg)
5293 (home-page "https://r-forge.r-project.org/projects/car/")
5294 (synopsis "Companion to applied regression")
5296 "This package provides functions and datasets from book Companion
5297 to Applied regression, Second Edition, Sage, 2011.")
5298 (license license:gpl2+)))
5300 (define-public r-caret
5307 (uri (cran-uri "caret" version))
5310 "03898irgb70q0p01kq99yb6q6xji0jx4jmj0yxlv8wcwd841r0x1"))))
5311 (build-system r-build-system)
5313 `(("r-foreach" ,r-foreach)
5314 ("r-ggplot2" ,r-ggplot2)
5315 ("r-lattice" ,r-lattice)
5316 ("r-modelmetrics" ,r-modelmetrics)
5319 ("r-recipes" ,r-recipes)
5320 ("r-reshape2" ,r-reshape2)
5321 ("r-withr" ,r-withr)))
5322 (home-page "https://github.com/topepo/caret")
5323 (synopsis "Classification and regression training")
5325 "This package provides misc functions for training and plotting
5326 classification and regression models.")
5327 (license license:gpl2+)))
5329 (define-public r-rcppprogress
5331 (name "r-rcppprogress")
5336 (uri (cran-uri "RcppProgress" version))
5339 "0yk01hfv961zyp569682k9igvhnwqyg5j0n5fm63sxigj82l2xhi"))))
5340 (properties `((upstream-name . "RcppProgress")))
5341 (build-system r-build-system)
5343 `(("r-devtools" ,r-devtools)
5344 ("r-rcpp" ,r-rcpp)))
5345 (home-page "https://github.com/kforner/rcpp_progress")
5346 (synopsis "Interruptible progress bar for C++ in R packages")
5348 "This package allows to display a progress bar in the R console for long running
5349 computations taking place in C++ code, and support for interrupting those computations
5350 even in multithreaded code, typically using OpenMP.")
5351 (license license:gpl3+)))
5353 (define-public r-mnormt
5360 (uri (cran-uri "mnormt" version))
5363 "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z"))))
5364 (build-system r-build-system)
5366 `(("gfortran" ,gfortran)))
5367 (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
5368 (synopsis "Multivariate normal and \"t\" distributions")
5370 "This package provides functions for computing the density and the
5371 distribution function of multivariate normal and \"t\" random variables, and
5372 for generating random vectors sampled from these distributions. Probabilities
5373 are computed via non-Monte Carlo methods.")
5374 (license license:gpl2+)))
5376 (define-public r-numderiv
5379 (version "2016.8-1")
5383 (uri (cran-uri "numDeriv" version))
5386 "07ni52rwiap4wilfz94w5mrqaxr59axxmgn57857ip4p6qkiss0v"))))
5387 (properties `((upstream-name . "numDeriv")))
5388 (build-system r-build-system)
5389 (home-page "https://cran.r-project.org/web/packages/numDeriv")
5390 (synopsis "Accurate numerical derivatives")
5392 "This package provides methods for calculating accurate numerical
5393 first and second order derivatives.")
5394 (license license:gpl2)))
5403 (uri (cran-uri "sn" version))
5406 "10via4lg0vx9pzq350vwhz5wv1dhzxr2l3r6jq99nk37vmyvj8fc"))))
5407 (build-system r-build-system)
5409 `(("r-mnormt" ,r-mnormt)
5410 ("r-numderiv" ,r-numderiv)))
5411 (home-page "http://azzalini.stat.unipd.it/SN")
5412 (synopsis "The skew-normal and skew-t distributions")
5414 "This packages provides functionalities to build and manipulate
5415 probability distributions of the skew-normal family and some related
5416 ones, notably the skew-t family, and provides related statistical
5417 methods for data fitting and diagnostics, in the univariate and the
5418 multivariate case.")
5419 (license license:gpl2+)))
5421 (define-public r-tclust
5428 (uri (cran-uri "tclust" version))
5431 "17md6l9v9dl9b72l84df01b52h2xiynbcjm437mv9mzcr09fc2sb"))))
5432 (build-system r-build-system)
5433 ;; These are all suggested packages, not build dependencies.
5435 `(("r-cluster" ,r-cluster)
5436 ("r-mclust" ,r-mclust)
5437 ("r-mvtnorm" ,r-mvtnorm)
5439 (home-page "https://cran.r-project.org/web/packages/tclust")
5440 (synopsis "Robust trimmed clustering")
5442 "This package implements different robust clustering
5443 algorithms (@code{tclust}) based on trimming and including some graphical
5444 diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
5445 (license license:gpl3)))
5447 (define-public r-ranger
5454 (uri (cran-uri "ranger" version))
5457 "1sxyzxmjc6lm8wcmq15j6sscnza7aay4mr3dyri2zngx6fa8mb0k"))))
5458 (build-system r-build-system)
5460 `(("r-rcpp" ,r-rcpp)
5461 ("r-matrix" ,r-matrix)
5462 ("r-rcppeigen" ,r-rcppeigen)))
5463 (home-page "https://github.com/imbs-hl/ranger")
5464 (synopsis "Fast implementation of random forests")
5466 "This package provides a fast implementation of Random Forests,
5467 particularly suited for high dimensional data. Ensembles of classification,
5468 regression, survival and probability prediction trees are supported. Data from
5469 genome-wide association studies can be analyzed efficiently.")
5470 (license license:gpl3)))
5472 (define-public r-tsne
5479 (uri (cran-uri "tsne" version))
5482 "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
5483 (build-system r-build-system)
5484 (home-page "https://github.com/jdonaldson/rtsne/")
5485 (synopsis "t-Distributed Stochastic Neighbor Embedding for R")
5487 "This package provides a pure R implementation of the t-SNE algorithm.")
5488 (license license:gpl2+)))
5490 (define-public r-cairo
5497 (uri (cran-uri "Cairo" version))
5500 "1mdmd5zmjkh1b0x928zizgzh42x8swbajffb88rvnjfdhk1z0dvq"))))
5501 (properties `((upstream-name . "Cairo")))
5502 (build-system r-build-system)
5508 `(("pkg-config" ,pkg-config)))
5509 (home-page "http://www.rforge.net/Cairo/")
5510 (synopsis "R graphics device using Cairo graphics library")
5512 "This package provides a Cairo graphics device that can be use to
5513 create high-quality vector (PDF, PostScript and SVG) and bitmap
5514 output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11
5515 and Win32). Since it uses the same back-end for all output, copying
5516 across formats is WYSIWYG. Files are created without the dependence
5517 on X11 or other external programs. This device supports alpha
5518 channel (semi-transparent drawing) and resulting images can contain
5519 transparent and semi-transparent regions. It is ideal for use in
5520 server environments (file output) and as a replacement for other
5521 devices that don't have Cairo's capabilities such as alpha support or
5522 anti-aliasing. Backends are modular such that any subset of backends
5524 (license license:gpl2)))
5526 (define-public r-lubridate
5528 (name "r-lubridate")
5533 (uri (cran-uri "lubridate" version))
5536 "14a823il77w3wmmnzr89vwrqp50y56dh5raycnaw6c8nv5xsh32i"))))
5537 (build-system r-build-system)
5539 `(("r-rcpp" ,r-rcpp)
5540 ("r-stringr" ,r-stringr)))
5542 "https://cran.r-project.org/web/packages/lubridate")
5543 (synopsis "Make dealing with dates a little easier")
5545 "This package provides functions to work with date-times and time-spans:
5546 fast and user friendly parsing of date-time data, extraction and updating of
5547 components of a date-time (years, months, days, hours, minutes, and seconds),
5548 algebraic manipulation on date-time and time-span objects. The @code{lubridate}
5549 package has a consistent and memorable syntax that makes working with dates
5551 (license license:gpl2)))
5553 (define-public r-fdrtool
5560 (uri (cran-uri "fdrtool" version))
5563 "1h46frlk7d9f4qx0bg6p55nrm9wwwz2sv6d1nz7061wdfsm69yb5"))))
5564 (build-system r-build-system)
5565 (home-page "http://strimmerlab.org/software/fdrtool/")
5566 (synopsis "Estimation of false discovery rates and higher criticism")
5568 "This package provides tools to estimate tail area-based false discovery
5569 rates as well as local false discovery rates for a variety of null
5570 models (p-values, z-scores, correlation coefficients, t-scores). The
5571 proportion of null values and the parameters of the null distribution are
5572 adaptively estimated from the data. In addition, the package contains
5573 functions for non-parametric density estimation (Grenander estimator), for
5574 monotone regression (isotonic regression and antitonic regression with
5575 weights), for computing the @dfn{greatest convex minorant} (GCM) and the
5576 @dfn{least concave majorant} (LCM), for the half-normal and correlation
5577 distributions, and for computing empirical @dfn{higher criticism} (HC) scores
5578 and the corresponding decision threshold.")
5579 (license license:gpl3+)))
5581 (define-public r-forcats
5588 (uri (cran-uri "forcats" version))
5591 "1cnjh23z59fhbjmy7y95425hcq3m5wrwqvahsxwi7zm6d9bwp0vw"))))
5592 (build-system r-build-system)
5594 `(("r-ellipsis" ,r-ellipsis)
5595 ("r-magrittr" ,r-magrittr)
5596 ("r-tibble" ,r-tibble)
5597 ("r-rlang" ,r-rlang)))
5598 (home-page "http://forcats.tidyverse.org")
5599 (synopsis "Tools for working with factors")
5600 (description "This package provides helpers for reordering factor
5601 levels (including moving specified levels to front, ordering by first
5602 appearance, reversing, and randomly shuffling), and tools for modifying factor
5603 levels (including collapsing rare levels into other, \"anonymizing\", and
5604 manually \"recoding\").")
5605 (license license:gpl3)))
5607 (define-public r-tgstat
5608 (let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f")
5612 (version (string-append "1.0.2-" revision "." (string-take changeset 7)))
5617 (url "https://bitbucket.org/tanaylab/tgstat")
5618 (changeset changeset)))
5619 (file-name (string-append name "-" version "-checkout"))
5622 "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
5623 (build-system r-build-system)
5626 (modify-phases %standard-phases
5627 (add-after 'unpack 'fix-isnan
5629 (substitute* "src/tgstat.h"
5630 (("#define isnan ::isnan")
5631 "#define isnan std::isnan"))
5634 `(("r-rcpp" ,r-rcpp)))
5635 (home-page "https://bitbucket.org/tanaylab/tgstat/")
5636 (synopsis "Tanay's group statistical utilities")
5638 "The goal of tgstat is to provide fast and efficient statistical
5640 (license license:gpl2))))
5642 (define-public r-tgconfig
5643 (let ((changeset "1e02c7614713bd0866c46f0c679a058f8c6d627e")
5647 (version (string-append "0.0.0.9000-" revision "." (string-take changeset 7)))
5652 (url "https://bitbucket.org/tanaylab/tgconfig")
5653 (changeset changeset)))
5654 (file-name (string-append name "-" version "-checkout"))
5657 "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
5658 (build-system r-build-system)
5660 `(("r-yaml" ,r-yaml)))
5661 (home-page "https://bitbucket.org/tanaylab/tgconfig/")
5662 (synopsis "Infrastructure for managing package parameters")
5664 "The goal of tgconfig is to provide infrastructure for managing package
5666 (license license:gpl3))))
5668 (define-public r-directlabels
5670 (name "r-directlabels")
5671 (version "2018.05.22")
5675 (uri (cran-uri "directlabels" version))
5678 "0xcpc56ssb9430b0xcdhayk3qaak2qcakyss2pz14y5w2027hblv"))))
5679 (build-system r-build-system)
5681 `(("r-quadprog" ,r-quadprog)))
5682 (home-page "http://directlabels.r-forge.r-project.org/")
5683 (synopsis "Direct labels for multicolor plots")
5685 "This package provides an extensible framework for automatically placing
5686 direct labels onto multicolor plots. Label positions are described using
5687 positioning methods that can be re-used across several different plots. There
5688 are heuristics for examining @code{trellis} and @code{ggplot} objects and
5689 inferring an appropriate positioning method.")
5690 (license license:gpl3)))
5692 (define-public r-catterplots
5693 (let ((commit "40063ec57f9515d231508f135ca0ec769614efb9")
5696 (name "r-catterplots")
5697 (version (string-append "0-" revision "." (string-take commit 9)))
5701 (url "https://github.com/Gibbsdavidl/CatterPlots.git")
5703 (file-name (string-append name "-" version "-checkout"))
5706 "1wl80pgbz8d9kfpffvkh439hlgz2qldm9m75wqjfrgrg8lcjzrxg"))))
5707 (build-system r-build-system)
5709 `(("r-png" ,r-png)))
5710 (home-page "https://github.com/Gibbsdavidl/CatterPlots")
5711 (synopsis "Scatter plots with cat shaped points")
5712 (description "Did you ever wish you could make scatter plots with cat
5713 shaped points? Now you can!")
5714 (license license:asl2.0))))
5716 (define-public r-colorout
5723 (uri (string-append "https://github.com/jalvesaq/colorout/archive/"
5724 "v" version ".tar.gz"))
5725 (file-name (string-append name "-" version ".tar.gz"))
5728 "07vqx5ihgnq4dzn5jnfjfhdm3957v4prvf8vhnb3cwvlly4l7p9v"))))
5729 (build-system r-build-system)
5730 (home-page "https://github.com/jalvesaq/colorout")
5731 (synopsis "Colorize output in the R REPL")
5732 (description "@code{colorout} is an R package that colorizes R output when
5733 running in terminal emulator.
5735 R STDOUT is parsed and numbers, negative numbers, dates in the standard
5736 format, strings, and R constants are identified and wrapped by special ANSI
5737 scape codes that are interpreted by terminal emulators as commands to colorize
5738 the output. R STDERR is also parsed to identify the expressions warning and
5739 error and their translations to many languages. If these expressions are
5740 found, the output is colorized accordingly; otherwise, it is colorized as
5741 STDERROR (blue, by default).
5743 You can customize the colors according to your taste, guided by the color
5744 table made by the command @code{show256Colors()}. You can also set the colors
5745 to any arbitrary string. In this case, it is up to you to set valid values.")
5746 (license license:gpl3+)))
5748 (define-public r-txtplot
5755 (uri (cran-uri "txtplot" version))
5758 "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h"))))
5759 (build-system r-build-system)
5760 (home-page "https://cran.r-project.org/web/packages/txtplot/")
5761 (synopsis "Text-based plotting")
5762 (description "This package provides functions to produce rudimentary ASCII
5763 graphics directly in the terminal window. This package provides a basic
5764 plotting function (and equivalents of curve, density, acf and barplot) as well
5765 as a boxplot function.")
5766 (license license:lgpl3+)))
5768 (define-public python-rpy2
5770 (name "python-rpy2")
5775 (uri (pypi-uri "rpy2" version))
5778 "0bl1d2qhavmlrvalir9hmkjh74w21vzkvc2sg3cbb162s10zfmxy"))))
5779 (build-system python-build-system)
5781 '(#:modules ((ice-9 ftw)
5785 (guix build python-build-system))
5787 (modify-phases %standard-phases
5789 (lambda* (#:key outputs inputs #:allow-other-keys)
5790 (let ((cwd (getcwd)))
5791 (setenv "PYTHONPATH"
5792 (string-append cwd "/build/"
5793 (find (cut string-prefix? "lib" <>)
5794 (scandir (string-append cwd "/build")))
5796 (getenv "PYTHONPATH"))))
5797 (invoke "python" "-m" "rpy2.tests" "-v"))))))
5799 `(("python-six" ,python-six)
5800 ("python-jinja2" ,python-jinja2)
5801 ("python-pytz" ,python-pytz)))
5803 `(("readline" ,readline)
5806 ("r-minimal" ,r-minimal)
5807 ("r-survival" ,r-survival)
5808 ("r-ggplot2" ,r-ggplot2)
5809 ("r-rsqlite" ,r-rsqlite)
5810 ("r-dplyr" ,r-dplyr)
5811 ("r-dbplyr" ,r-dbplyr)
5812 ("python-numpy" ,python-numpy)))
5815 (home-page "https://rpy2.bitbucket.io/")
5816 (synopsis "Python interface to the R language")
5817 (description "rpy2 is a redesign and rewrite of rpy. It is providing a
5818 low-level interface to R from Python, a proposed high-level interface,
5819 including wrappers to graphical libraries, as well as R-like structures and
5821 ;; Any of these licenses can be picked for the R interface. The whole
5822 ;; project is released under GPLv2+ according to the license declaration
5824 (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+))))
5826 (define-public java-jdistlib
5828 (name "java-jdistlib")
5832 (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
5833 version "-src.jar"))
5836 "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
5837 (build-system ant-build-system)
5839 `(#:jar-name "jdistlib.jar"
5841 #:tests? #f ; no dedicated test directory
5843 (modify-phases %standard-phases
5844 (add-after 'unpack 'fix-broken-encoding
5846 (with-fluids ((%default-port-encoding "ISO-8859-1"))
5847 (substitute* "src/jdistlib/Beta.java"
5848 (("Scheff.+-Tukey") "Scheffe-Tukey")))
5851 `(("java-jtransforms" ,java-jtransforms)))
5853 `(("java-junit" ,java-junit)))
5854 (home-page "http://jdistlib.sourceforge.net/")
5855 (synopsis "Java library of statistical distributions")
5856 (description "JDistlib is the Java Statistical Distribution Library, a
5857 Java package that provides routines for various statistical distributions.")
5858 ;; The files that were translated from R code are under GPLv2+; some files
5859 ;; are under the GPLv3, which is a mistake. The author confirmed in an
5860 ;; email that this whole project should be under GPLv2+.
5861 (license license:gpl2+)))
5863 (define-public emacs-ess
5869 (uri (string-append "https://github.com/emacs-ess/ESS/archive/v"
5873 "0cbilbsiwvcyf6d5y24mymp57m3ana5dkzab3knfs83w4a3a4c5c"))
5874 (file-name (string-append name "-" version ".tar.gz"))
5875 (modules '((guix build utils)))
5878 ;; Stop ESS from trying to bundle an external julia-mode.el.
5879 (substitute* "lisp/Makefile"
5880 (("^\tjulia-mode.elc\\\\\n") "")
5881 (("^dist: all julia-mode.el")
5883 ;; No need to build docs in so many formats. Also, skipping
5884 ;; pdf lets us not pull in texlive.
5885 (substitute* "doc/Makefile"
5886 (("all : info text html pdf")
5888 (("install: install-info install-other-docs")
5889 "install: install-info"))
5890 ;; Test fails upstream
5891 (substitute* "test/ess-r-tests.el"
5892 (("ert-deftest ess-r-namespaced-eval-no-srcref-in-errors ()")
5893 "ert-deftest ess-r-namespaced-eval-no-srcref-in-errors () :expected-result :failed"))
5895 (build-system gnu-build-system)
5897 (let ((base-directory "/share/emacs/site-lisp/guix.d/ess"))
5898 `(#:make-flags (list (string-append "PREFIX=" %output)
5899 (string-append "ETCDIR=" %output "/"
5900 ,base-directory "/etc")
5901 (string-append "LISPDIR=" %output "/"
5904 (modify-phases %standard-phases
5906 (add-before 'build 'more-shebang-patching
5907 (lambda* (#:key inputs #:allow-other-keys)
5908 (substitute* "Makeconf"
5909 (("SHELL = /bin/sh")
5910 (string-append "SHELL = " (which "sh"))))
5914 (invoke "make" "test")))))))
5916 `(("emacs" ,emacs-minimal)
5917 ("r-minimal" ,r-minimal)))
5920 ("texinfo" ,texinfo)))
5922 `(("emacs-julia-mode" ,emacs-julia-mode)))
5923 (home-page "https://ess.r-project.org/")
5924 (synopsis "Emacs mode for statistical analysis programs")
5925 (description "Emacs Speaks Statistics (ESS) is an add-on package for GNU
5926 Emacs. It is designed to support editing of scripts and interaction with
5927 various statistical analysis programs such as R, Julia, and JAGS.")
5928 (license license:gpl2+)))