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 texinfo)
72 #:use-module (gnu packages time)
73 #:use-module (gnu packages tls)
74 #:use-module (gnu packages base)
75 #:use-module (gnu packages web)
76 #:use-module (gnu packages xml)
77 #:use-module (gnu packages xorg)
78 #:use-module (srfi srfi-1))
88 (uri (string-append "mirror://gnu/pspp/pspp-"
92 "07pp27zycrb5x927jwaj9r3q7hy915jh51xs85zxby6gfiwl63m5"))))
93 (build-system gnu-build-system)
96 ("gettext" ,gettext-minimal)
100 ("readline" ,readline)
102 ("gtksourceview" ,gtksourceview)
103 ("spread-sheet-widget" ,spread-sheet-widget)
106 `(("autoconf" ,autoconf) ;for tests
107 ("glib" ,glib "bin") ;for glib-genmarshal
109 ("pkg-config" ,pkg-config)
110 ("python" ,python-2) ;for tests
111 ("texinfo" ,texinfo)))
112 (home-page "https://www.gnu.org/software/pspp/")
113 (synopsis "Statistical analysis")
115 "GNU PSPP is a statistical analysis program. It can perform
116 descriptive statistics, T-tests, linear regression and non-parametric tests.
117 It features both a graphical interface as well as command-line input. PSPP
118 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
119 can be imported from spreadsheets, text files and database sources and it can
120 be output in text, PostScript, PDF or HTML.")
121 (license license:gpl3+)))
129 (uri (string-append "mirror://sourceforge/mcmc-jags/JAGS/"
130 (version-major version) ".x/Source/"
131 "JAGS-" version ".tar.gz"))
134 "1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica"))))
135 (build-system gnu-build-system)
136 (home-page "http://mcmc-jags.sourceforge.net/")
138 `(("gfortran" ,gfortran)
140 (synopsis "Gibbs sampler")
141 (description "JAGS is Just Another Gibbs Sampler. It is a program for
142 analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
143 simulation not wholly unlike BUGS. JAGS was written with three aims in mind:
146 @item To have a cross-platform engine for the BUGS language;
147 @item To be extensible, allowing users to write their own functions,
148 distributions and samplers;
149 @item To be a platform for experimentation with ideas in Bayesian modelling.
151 (license license:gpl2)))
153 (define-public libxls
160 (uri (string-append "https://github.com/libxls/libxls/releases/download/"
161 "v" version "/libxls-" version ".tar.gz"))
163 (base32 "00j2lrcvvhclmh3z9vy7myqq1br1jnnqkz2wzgk4a1gbg8c5afn5"))))
164 (build-system gnu-build-system)
165 (home-page "https://github.com/libxls/libxls")
166 (synopsis "Read binary (.xls) Excel spreadsheet files")
168 "libxls is a C library to read .xls spreadsheet files in the binary OLE
169 BIFF8 format as created by Excel 97 and later versions. It cannot write them.
171 This package also provides @command{xls2csv} to export Excel files to CSV.")
172 (license license:bsd-2)))
174 ;; Update this package together with the set of recommended packages: r-boot,
175 ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
176 ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
179 (name "r-with-tests")
183 (uri (string-append "mirror://cran/src/base/R-"
184 (version-major version) "/R-"
188 "1337irx9y0r3jm1rcq1dcwnxsgfhnvgjs5wadcyh17vhpnvkgyib"))))
189 (build-system gnu-build-system)
191 `(#:disallowed-references (,tzdata-for-tests)
193 (list (string-append "LDFLAGS=-Wl,-rpath="
194 (assoc-ref %outputs "out")
196 ;; This affects the embedded timestamp of only the core packages.
197 "PKG_BUILT_STAMP=1970-01-01")
199 (modify-phases %standard-phases
200 (add-before 'configure 'do-not-compress-serialized-files
201 (lambda* (#:key inputs #:allow-other-keys)
202 ;; This ensures that Guix can detect embedded store references;
203 ;; see bug #28157 for details.
204 (substitute* "src/library/base/makebasedb.R"
205 (("compress = TRUE") "compress = FALSE"))
207 (add-before 'configure 'patch-uname
208 (lambda* (#:key inputs #:allow-other-keys)
209 (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
211 (substitute* "src/scripts/R.sh.in"
212 (("uname") uname-bin)))
214 (add-after 'unpack 'build-reproducibly
216 ;; The documentation contains time stamps to demonstrate
217 ;; documentation generation in different phases.
218 (substitute* "src/library/tools/man/Rd2HTML.Rd"
219 (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
220 "(removed for reproducibility)"))
222 ;; Remove timestamp from tracing environment. This fixes
223 ;; reproducibility of "methods.rd{b,x}".
224 (substitute* "src/library/methods/R/trace.R"
225 (("dateCreated = Sys.time\\(\\)")
226 "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
228 ;; Ensure that gzipped files are reproducible.
229 (substitute* '("src/library/grDevices/Makefile.in"
230 "doc/manual/Makefile.in")
231 (("R_GZIPCMD\\)" line)
232 (string-append line " -n")))
234 ;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
235 ;; queries the mtime of a given file and records it in an object.
236 ;; This is acceptable at runtime to detect stale source files,
237 ;; but it destroys reproducibility at build time.
239 ;; Similarly, the "srcfilecopy" procedure records the current
240 ;; time. We change both of them to respect SOURCE_DATE_EPOCH.
241 (substitute* "src/library/base/R/srcfile.R"
242 (("timestamp <- (timestamp.*|file.mtime.*)" _ time)
243 (string-append "timestamp <- \
244 as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
245 as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
246 } else { " time "}, origin=\"1970-01-01\")\n")))
248 ;; This library is installed using "install_package_description",
249 ;; so we need to pass the "builtStamp" argument.
250 (substitute* "src/library/tools/Makefile.in"
251 (("(install_package_description\\(.*\"')\\)\"" line prefix)
252 (string-append prefix ", builtStamp='1970-01-01')\"")))
254 ;; R bundles an older version of help2man, which does not respect
255 ;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man,
256 ;; because that breaks a test.
257 (with-fluids ((%default-port-encoding "ISO-8859-1"))
258 (substitute* "tools/help2man.pl"
259 (("my \\$date = strftime \"%B %Y\", localtime" line)
260 (string-append line " 1"))))
262 (add-before 'configure 'set-default-pager
263 ;; Set default pager to "cat", because otherwise it is "false",
264 ;; making "help()" print nothing at all.
265 (lambda _ (setenv "PAGER" "cat") #t))
266 (add-before 'check 'set-timezone
267 ;; Some tests require the timezone to be set. However, the
268 ;; timezone may not just be "UTC", or else a brittle regression
269 ;; test in reg-tests-1d will fail.
270 (lambda* (#:key inputs #:allow-other-keys)
271 (setenv "TZ" "UTC+1")
273 (string-append (assoc-ref inputs "tzdata")
276 (add-after 'build 'make-info
277 (lambda _ (invoke "make" "info")))
278 (add-after 'build 'install-info
279 (lambda _ (invoke "make" "install-info"))))
281 `(;; We build the recommended packages here, because they are needed in
282 ;; order to run the test suite. We disable them in the r-minimal
285 "--with-blas=-lopenblas"
291 ,(string-append "--with-tcl-config="
292 (assoc-ref %build-inputs "tcl")
294 ,(string-append "--with-tk-config="
295 (assoc-ref %build-inputs "tk")
298 "--enable-BLAS-shlib"
299 "--with-system-tre")))
300 ;; R has some support for Java. When the JDK is available at configure
301 ;; time environment variables pointing to the JDK will be recorded under
302 ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
303 ;; CMD javareconf". "R CMD javareconf" appears to only be used to update
304 ;; the recorded environment variables in $R_HOME/etc. Refer to
305 ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
306 ;; for additional information.
308 ;; As the JDK is a rather large input with only very limited effects on R,
309 ;; we decided to drop it.
313 ("pkg-config" ,pkg-config)
314 ("texinfo" ,texinfo) ; for building HTML manuals
315 ("tzdata" ,tzdata-for-tests)
318 `(;; We need not only cairo here, but pango to ensure that tests for the
319 ;; "cairo" bitmapType plotting backend succeed.
321 ("coreutils" ,coreutils)
323 ("openblas" ,openblas)
324 ("gfortran" ,gfortran)
331 ("readline" ,readline)
332 ;; This avoids a reference to the ungraftable static bash. R uses the
333 ;; detected shell for the "system" procedure.
334 ("bash" ,bash-minimal)
340 (list (search-path-specification
341 (variable "R_LIBS_SITE")
342 (files (list "site-library/")))))
343 (home-page "https://www.r-project.org/")
344 (synopsis "Environment for statistical computing and graphics")
346 "R is a language and environment for statistical computing and graphics.
347 It provides a variety of statistical techniques, such as linear and nonlinear
348 modeling, classical statistical tests, time-series analysis, classification
349 and clustering. It also provides robust support for producing
350 publication-quality data plots. A large amount of 3rd-party packages are
351 available, greatly increasing its breadth and scope.")
352 (license license:gpl3+)))
354 (define-public r-minimal
355 (package (inherit r-with-tests)
359 ,@(substitute-keyword-arguments (package-arguments r-with-tests)
360 ((#:configure-flags flags)
361 ;; Do not build the recommended packages. The build system creates
362 ;; random temporary directories and embeds their names in some
363 ;; package files. We build these packages with the r-build-system
365 `(cons "--without-recommended-packages" ,flags)))))))
367 (define-public rmath-standalone
368 (package (inherit r-minimal)
369 (name "rmath-standalone")
372 (modify-phases %standard-phases
373 (add-after 'configure 'chdir
374 (lambda _ (chdir "src/nmath/standalone/") #t)))))
375 (synopsis "Standalone R math library")
377 "This package provides the R math library as an independent package.")))
379 (define-public r-boot
386 (uri (cran-uri "boot" version))
389 "0ai1qpm0p4z07xr0dvag8sdn9jrxcwanrsk9khzmww094jvr1jxd"))))
390 (build-system r-build-system)
391 (home-page "https://cran.r-project.org/web/packages/boot")
392 (synopsis "Bootstrap functions for R")
394 "This package provides functions and datasets for bootstrapping from the
395 book \"Bootstrap Methods and Their Application\" by A.C. Davison and
396 D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
397 ;; Unlimited distribution
398 (license (license:non-copyleft "file://R/bootfuns.q"))))
400 (define-public r-mass
407 (uri (cran-uri "MASS" version))
410 "1dh8cvvdsf9dx29x6va47qdkswmr03k3yjycinq98fnl0ivhw3jv"))))
411 (properties `((upstream-name . "MASS")))
412 (build-system r-build-system)
413 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
414 (synopsis "Support functions and datasets for Venables and Ripley's MASS")
416 "This package provides functions and datasets for the book \"Modern
417 Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
418 ;; Either version may be picked.
419 (license (list license:gpl2 license:gpl3))))
421 (define-public r-class
428 (uri (cran-uri "class" version))
431 "1x1hqz8xyhbpq4krsh02glqnlzcch25agkmn4a3da9n723b37gzn"))))
432 (build-system r-build-system)
434 `(("r-mass" ,r-mass)))
435 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
436 (synopsis "R functions for classification")
438 "This package provides various functions for classification, including
439 k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
440 ;; Either of the two versions can be picked.
441 (license (list license:gpl2 license:gpl3))))
443 (define-public r-cluster
450 (uri (cran-uri "cluster" version))
453 "0jkmlhjknndh0lmyvqz7s7j1hhnarixm6zb39np4ssw47flk0nfc"))))
454 (build-system r-build-system)
456 `(("gfortran" ,gfortran)))
457 (home-page "https://cran.r-project.org/web/packages/cluster")
458 (synopsis "Methods for cluster analysis")
460 "This package provides methods for cluster analysis. It is a much
461 extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
462 Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
463 (license license:gpl2+)))
465 (define-public r-codetools
472 (uri (cran-uri "codetools" version))
475 "00bmhzqprqfn3w6ghx7sakai6s7il8gbksfiawj8in5mbhbncypn"))))
476 (build-system r-build-system)
477 (home-page "https://cran.r-project.org/web/packages/codetools")
478 (synopsis "Code analysis tools for R")
479 (description "This package provides code analysis tools for R to check R
480 code for possible problems.")
481 ;; Any version of the GPL.
482 (license (list license:gpl2+ license:gpl3+))))
484 (define-public r-foreign
491 (uri (cran-uri "foreign" version))
494 "1mv04w3ycz0ymsszn8aa87k6k5sb8mg8lhf1b8w4zpfrphpkkliv"))))
495 (build-system r-build-system)
496 (home-page "https://cran.r-project.org/web/packages/foreign")
497 (synopsis "Read data stored by other statistics software")
499 "This package provides functions for reading and writing data stored by
500 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
501 for reading and writing some dBase files.")
502 (license license:gpl2+)))
504 (define-public r-kernsmooth
506 (name "r-kernsmooth")
511 (uri (cran-uri "KernSmooth" version))
514 "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb"))))
515 (properties `((upstream-name . "KernSmooth")))
516 (build-system r-build-system)
518 `(("gfortran" ,gfortran)))
519 (home-page "https://cran.r-project.org/web/packages/KernSmooth")
520 (synopsis "Functions for kernel smoothing")
522 "This package provides functions for kernel smoothing (and density
523 estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
524 \"Kernel Smoothing\".")
525 ;; Unlimited use and distribution
526 (license (license:non-copyleft "file://LICENCE.note"))))
528 (define-public r-lattice
534 (uri (cran-uri "lattice" version))
537 "0b8abkz7syscq883mrgv63pkwaqkcpwfx8rgbqy9vgfva0z5xszx"))))
538 (build-system r-build-system)
539 (home-page "http://lattice.r-forge.r-project.org/")
540 (synopsis "High-level data visualization system")
542 "The lattice package provides a powerful and elegant high-level data
543 visualization system inspired by Trellis graphics, with an emphasis on
544 multivariate data. Lattice is sufficient for typical graphics needs, and is
545 also flexible enough to handle most nonstandard requirements.")
546 (license license:gpl2+)))
548 (define-public r-matrix
555 (uri (cran-uri "Matrix" version))
558 "1k1zf92ycqr7fz44w7bp1p354ww7jg0wm23ybb8dzmbg37qfchyv"))))
559 (properties `((upstream-name . "Matrix")))
560 (build-system r-build-system)
562 `(("r-lattice" ,r-lattice)))
563 (home-page "http://Matrix.R-forge.R-project.org/")
564 (synopsis "Sparse and dense matrix classes and methods")
566 "This package provides classes and methods for dense and sparse matrices
567 and operations on them using LAPACK and SuiteSparse.")
568 (license license:gpl2+)))
570 (define-public r-nlme
577 (uri (cran-uri "nlme" version))
580 "11vyxxc0n36vb8d8g02zr0402ymicvbifwdsqm7gy9iqqnwrn101"))))
581 (build-system r-build-system)
583 `(("r-lattice" ,r-lattice)))
585 `(("gfortran" ,gfortran)))
586 (home-page "https://cran.r-project.org/web/packages/nlme")
587 (synopsis "Linear and nonlinear mixed effects models")
589 "This package provides tools to fit and compare Gaussian linear and
590 nonlinear mixed-effects models.")
591 (license license:gpl2+)))
593 (define-public r-mgcv
600 (uri (cran-uri "mgcv" version))
603 "1snkpnkkigwrj9zm31j1nlivv9ls56imz263cv167hnmghiahpmm"))))
604 (build-system r-build-system)
606 `(("r-matrix" ,r-matrix)
608 (home-page "https://cran.r-project.org/web/packages/mgcv")
609 (synopsis "Mixed generalised additive model computation")
611 "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
612 parameter estimation by GCV, REML or UBRE/AIC. The library includes a
613 @code{gam()} function, a wide variety of smoothers, JAGS support and
614 distributions beyond the exponential family.")
615 (license license:gpl2+)))
617 (define-public r-nnet
624 (uri (cran-uri "nnet" version))
627 "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7"))))
628 (build-system r-build-system)
629 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
630 (synopsis "Feed-forward neural networks and multinomial log-linear models")
632 "This package provides functions for feed-forward neural networks with a
633 single hidden layer, and for multinomial log-linear models.")
634 (license (list license:gpl2+ license:gpl3+))))
636 (define-public r-rpart
643 (uri (cran-uri "rpart" version))
646 "0k29qx3k3pj5sgrpg0p47yd8i811rmdakaw57bigpq1449asc4cf"))))
647 (build-system r-build-system)
648 (home-page "https://cran.r-project.org/web/packages/rpart")
649 (synopsis "Recursive partitioning and regression trees")
651 "This package provides recursive partitioning functions for
652 classification, regression and survival trees.")
653 (license (list license:gpl2+ license:gpl3+))))
655 (define-public r-spatial
662 (uri (cran-uri "spatial" version))
665 "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
666 (build-system r-build-system)
667 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
668 (synopsis "Functions for kriging and point pattern analysis")
670 "This package provides functions for kriging and point pattern
672 ;; Either version may be picked.
673 (license (list license:gpl2 license:gpl3))))
675 (define-public r-survival
682 (uri (cran-uri "survival" version))
685 "1faiwyg7x8y2kfzb66l4yc8br0mdlz4k20znmjrwq96dbzhm3cam"))))
686 (build-system r-build-system)
688 `(("r-matrix" ,r-matrix)))
689 (home-page "https://github.com/therneau/survival")
690 (synopsis "Survival analysis")
692 "This package contains the core survival analysis routines, including
693 definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
694 curves, Cox models, and parametric accelerated failure time models.")
695 (license license:lgpl2.0+)))
698 (package (inherit r-minimal)
701 (build-system trivial-build-system)
702 (arguments '(#:builder (begin (mkdir %output) #t)))
704 `(("r-minimal" ,r-minimal)
707 ("r-cluster" ,r-cluster)
708 ("r-codetools" ,r-codetools)
709 ("r-foreign" ,r-foreign)
710 ("r-kernsmooth" ,r-kernsmooth)
711 ("r-lattice" ,r-lattice)
713 ("r-matrix" ,r-matrix)
718 ("r-spatial" ,r-spatial)
719 ("r-survival" ,r-survival)))))
728 (uri (cran-uri "bit" version))
731 "0m7jrqzpa1pk8ixcl814x06jf96nlvvr16x6did6cfk4zghsrfjw"))))
732 (build-system r-build-system)
733 (home-page "http://ff.r-forge.r-project.org")
734 (synopsis "Class for vectors of 1-bit booleans")
736 "This package provides bitmapped vectors of booleans (no @code{NA}s),
737 coercion from and to logicals, integers and integer subscripts, fast boolean
738 operators and fast summary statistics. With @code{bit} class vectors of true
739 binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
740 (license license:gpl2)))
742 (define-public r-bit64
749 (uri (cran-uri "bit64" version))
752 "07znvz9vp1nz1y5ljng4qyskvm943cdbmy996s67560ijxzsm6kv"))))
753 (build-system r-build-system)
756 (home-page "http://ff.r-forge.r-project.org/")
757 (synopsis "S3 class for vectors of 64 bit integers")
759 "The bit64 package provides serializable S3 atomic 64 bit (signed)
760 integers that can be used in vectors, matrices, arrays and @code{data.frames}.
761 Methods are available for coercion from and to logicals, integers, doubles,
762 characters and factors as well as many elementwise and summary functions.
763 Many fast algorithmic operations such as @code{match} and @code{order} support
764 interactive data exploration and manipulation and optionally leverage
766 (license license:gpl2)))
768 (define-public r-dichromat
775 (uri (cran-uri "dichromat" version))
777 (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
778 (build-system r-build-system)
779 (home-page "https://cran.r-project.org/web/packages/dichromat")
780 (synopsis "Color schemes for dichromats")
782 "Dichromat collapses red-green or green-blue distinctions to simulate the
783 effects of different types of color-blindness.")
784 (license license:gpl2+)))
786 (define-public r-digest
793 (uri (cran-uri "digest" version))
795 (base32 "0k3iv0r8wy8w7zchmgrnrqv3bc149075j4817kf0q521vi4f6vbj"))))
796 (build-system r-build-system)
797 ;; Vignettes require r-knitr, which requires r-digest, so we have to
798 ;; disable them and the tests.
801 #:configure-flags (list "--no-build-vignettes")))
802 (home-page "http://dirk.eddelbuettel.com/code/digest.html")
803 (synopsis "Create cryptographic hash digests of R objects")
805 "This package contains an implementation of a function @code{digest()} for
806 the creation of hash digests of arbitrary R objects (using the md5, sha-1,
807 sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
808 of R language objects, as well as a function @code{hmac()} to create hash-based
809 message authentication code.
811 Please note that this package is not meant to be deployed for cryptographic
812 purposes for which more comprehensive (and widely tested) libraries such as
813 OpenSSL should be used.")
814 (license license:gpl2+)))
816 (define-public r-estimability
818 (name "r-estimability")
822 (uri (cran-uri "estimability" version))
825 "0cifdaa71spkcxl4db4z884jrya865sg3dhcv4isd8fnzg2pjcd3"))))
826 (build-system r-build-system)
827 (home-page "https://cran.r-project.org/web/packages/estimability")
828 (synopsis "Tools for assessing estimability of linear predictions")
829 (description "Provides tools for determining estimability of linear
830 functions of regression coefficients, and @code{epredict} methods that handle
831 non-estimable cases correctly.")
832 (license license:gpl2+)))
834 (define-public r-pheatmap
841 (uri (cran-uri "pheatmap" version))
844 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
845 (build-system r-build-system)
847 `(("r-gtable" ,r-gtable)
848 ("r-rcolorbrewer" ,r-rcolorbrewer)
849 ("r-scales" ,r-scales)))
851 "https://cran.r-project.org/web/packages/pheatmap")
852 (synopsis "Pretty heatmaps")
854 "This package provides an implementation of heatmaps that offers more
855 control over dimensions and appearance.")
856 (license license:gpl2+)))
858 (define-public r-labeling
865 (uri (cran-uri "labeling" version))
867 (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
868 (build-system r-build-system)
869 (home-page "https://cran.r-project.org/web/packages/labeling")
870 (synopsis "Axis labeling algorithms")
871 (description "The labeling package provides a range of axis labeling
873 (license license:expat)))
875 (define-public r-magrittr
882 (uri (cran-uri "magrittr" version))
884 (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
885 (build-system r-build-system)
886 (home-page "https://cran.r-project.org/web/packages/magrittr/index.html")
887 (synopsis "A forward-pipe operator for R")
889 "Magrittr provides a mechanism for chaining commands with a new
890 forward-pipe operator, %>%. This operator will forward a value, or the result
891 of an expression, into the next function call/expression. There is flexible
892 support for the type of right-hand side expressions. For more information,
893 see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
894 (license license:expat)))
896 (define-public r-munsell
903 (uri (cran-uri "munsell" version))
905 (base32 "16g1fzisbpqb15yh3pqf3iia4csppva5dnv1z88x9dg263xskwyh"))))
906 (build-system r-build-system)
908 `(("r-colorspace" ,r-colorspace)))
909 (home-page "https://cran.r-project.org/web/packages/munsell")
910 (synopsis "Munsell colour system")
912 "The Munsell package contains Functions for exploring and using the
913 Munsell colour system.")
914 (license license:expat)))
916 (define-public r-permute
923 (uri (cran-uri "permute" version))
926 "0ra8p5mf2590azrkas8z2ry7mif77xqxd29n4zgyi5vll225726j"))))
927 (build-system r-build-system)
928 ;; Tests do not run correctly, but running them properly would entail a
929 ;; circular dependency with vegan.
930 (home-page "https://github.com/gavinsimpson/permute")
931 (synopsis "Functions for Generating Restricted Permutations of Data")
933 "This package provides a set of restricted permutation designs for freely
934 exchangeable, line transects (time series), spatial grid designs and permutation
935 of blocks (groups of samples). @code{permute} also allows split-plot designs,
936 in which the whole-plots or split-plots or both can be freely exchangeable.")
937 (license license:gpl2+)))
939 (define-public r-plyr
946 (uri (cran-uri "plyr" version))
948 (base32 "1igar5pcjqh0jyxv0z3jah8rz617vfa86vw0r5c7c031b7bj5db0"))))
949 (build-system r-build-system)
950 (native-inputs `(("r-rcpp" ,r-rcpp)))
951 (home-page "http://had.co.nz/plyr")
952 (synopsis "Tools for Splitting, Applying and Combining Data")
954 "Plyr is a set of tools that solves a common set of problems: you need to
955 break a big problem down into manageable pieces, operate on each piece and
956 then put all the pieces back together. For example, you might want to fit a
957 model to each spatial location or time point in your study, summarise data by
958 panels or collapse high-dimensional arrays to simpler summary statistics.")
959 (license license:expat)))
961 (define-public r-proto
968 (uri (cran-uri "proto" version))
970 (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
971 (build-system r-build-system)
972 (home-page "https://github.com/hadley/proto")
973 (synopsis "Prototype object-based programming")
975 "Proto is an object oriented system using object-based, also called
976 prototype-based, rather than class-based object oriented ideas.")
977 (license license:gpl2+)))
979 (define-public r-rcolorbrewer
981 (name "r-rcolorbrewer")
986 (uri (cran-uri "RColorBrewer" version))
988 (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
989 (build-system r-build-system)
990 (home-page "https://cran.r-project.org/web/packages/RColorBrewer")
991 (synopsis "ColorBrewer palettes")
993 "This package provides color schemes for maps (and other graphics)
994 designed by Cynthia Brewer as described at http://colorbrewer2.org")
995 ;; Includes code licensed under bsd-4
996 (license license:asl2.0)))
998 (define-public r-sendmailr
1000 (name "r-sendmailr")
1005 (uri (cran-uri "sendmailR" version))
1008 "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
1009 (properties `((upstream-name . "sendmailR")))
1010 (build-system r-build-system)
1012 `(("r-base64enc" ,r-base64enc)))
1014 "https://cran.r-project.org/web/packages/sendmailR")
1015 (synopsis "Send email using R")
1017 "This package contains a simple SMTP client which provides a portable
1018 solution for sending email, including attachments, from within R.")
1019 (license license:gpl2+)))
1021 (define-public r-stringi
1028 (uri (cran-uri "stringi" version))
1031 "1vbr6g9p1iyzdj7wfw6afyizvnd1a2srfvkl72pq23vhdcwwpkhk"))))
1032 (build-system r-build-system)
1033 (inputs `(("icu4c" ,icu4c)))
1034 (native-inputs `(("pkg-config" ,pkg-config)))
1035 (home-page "http://stringi.rexamine.com/")
1036 (synopsis "Character string processing facilities")
1038 "This package allows for fast, correct, consistent, portable, as well as
1039 convenient character string/text processing in every locale and any native
1040 encoding. Owing to the use of the ICU library, the package provides R users
1041 with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
1042 programmers. Among available features there are: pattern searching
1043 (e.g. via regular expressions), random string generation, string collation,
1044 transliteration, concatenation, date-time formatting and parsing, etc.")
1045 (license license:bsd-3)))
1047 (define-public r-stringr
1054 (uri (cran-uri "stringr" version))
1056 (base32 "1p9ip7p87gbbg4s6d3d392svvzz2b5dqdq2c8ilgvn4s78nlsq47"))))
1057 (build-system r-build-system)
1059 `(("r-glue" ,r-glue)
1060 ("r-magrittr" ,r-magrittr)
1061 ("r-stringi" ,r-stringi)))
1062 (home-page "https://github.com/hadley/stringr")
1063 (synopsis "Simple, consistent wrappers for common string operations")
1065 "Stringr is a consistent, simple and easy to use set of wrappers around
1066 the fantastic @code{stringi} package. All function and argument names (and
1067 positions) are consistent, all functions deal with \"NA\"'s and zero length
1068 vectors in the same way, and the output from one function is easy to feed into
1069 the input of another.")
1070 (license license:gpl2+)))
1072 (define-public r-reshape2
1079 (uri (cran-uri "reshape2" version))
1081 (base32 "03ki5ka1dj208fc0dclbm0b4xp9d769pah2j9cs34l776p4r9zwa"))))
1082 (build-system r-build-system)
1084 `(("r-plyr" ,r-plyr)
1086 ("r-stringr" ,r-stringr)))
1087 (home-page "https://github.com/hadley/reshape")
1088 (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
1090 "Reshape2 is an R library to flexibly restructure and aggregate data
1091 using just two functions: melt and dcast (or acast).")
1092 (license license:expat)))
1094 (define-public r-scales
1101 (uri (cran-uri "scales" version))
1103 (base32 "0353dkh3d7x78463c6ds80hcml59lrqwr8rlv82a8dnkxla4l7qc"))))
1104 (build-system r-build-system)
1106 `(("r-labeling" ,r-labeling)
1107 ("r-munsell" ,r-munsell)
1108 ("r-rcolorbrewer" ,r-rcolorbrewer)
1111 ("r-viridislite" ,r-viridislite)))
1112 (home-page "https://github.com/hadley/scales")
1113 (synopsis "Scale functions for visualization")
1115 "This package provides graphical scales that map data to aesthetics, and
1116 provides methods for automatically determining breaks and labels for axes and
1118 (license license:expat)))
1120 (define-public r-ggplot2
1127 (uri (cran-uri "ggplot2" version))
1129 (base32 "1msy36r21nlmnpyaw2m9k0ykmnd19b9il01b65w457pfw75prrs9"))))
1130 (build-system r-build-system)
1132 `(("r-digest" ,r-digest)
1133 ("r-gtable" ,r-gtable)
1135 ("r-lazyeval" ,r-lazyeval)
1138 ("r-tibble" ,r-tibble)
1139 ("r-reshape2" ,r-reshape2)
1140 ("r-rlang" ,r-rlang)
1141 ("r-scales" ,r-scales)
1142 ("r-svglite" ,r-svglite) ; Needed for 'ggsave'
1143 ("r-viridislite" ,r-viridislite)
1144 ("r-withr" ,r-withr)))
1145 (home-page "https://ggplot2.tidyverse.org")
1146 (synopsis "An implementation of the grammar of graphics")
1148 "Ggplot2 is an implementation of the grammar of graphics in R. It
1149 combines the advantages of both base and lattice graphics: conditioning and
1150 shared axes are handled automatically, and you can still build up a plot step
1151 by step from multiple data sources. It also implements a sophisticated
1152 multidimensional conditioning system and a consistent interface to map data to
1153 aesthetic attributes.")
1154 (license license:gpl2+)))
1156 (define-public r-ggdendro
1162 (uri (cran-uri "ggdendro" version))
1165 "1zzq1hxd0d1qa5hrzwfkdw6fzscpcafbwbpkrb62dm559y8awp0j"))))
1166 (build-system r-build-system)
1168 `(("r-ggplot2" ,r-ggplot2)
1170 ("r-knitr" ,r-knitr)))
1171 (home-page "https://github.com/andrie/ggdendro")
1172 (synopsis "Create Dendrograms and Tree Diagrams Using ggplot2")
1173 (description "This is a set of tools for dendrograms and tree plots using
1174 ggplot2. The ggplot2 philosophy is to clearly separate data from the
1175 presentation. Unfortunately the plot method for dendrograms plots directly
1176 to a plot device with out exposing the data. The ggdendro package resolves
1177 this by making available functions that extract the dendrogram plot data.
1178 The package provides implementations for tree, rpart, as well as diana and
1179 agnes cluster diagrams.")
1180 (license license:gpl2+)))
1182 (define-public r-gdtools
1189 (uri (cran-uri "gdtools" version))
1192 "1ayy0s699ghaz34lklvcskfwman3x2n2772s5sa5x9k9xgsnxwcl"))))
1193 (build-system r-build-system)
1195 `(("pkg-config" ,pkg-config)))
1200 `(("r-rcpp" ,r-rcpp)
1201 ("r-withr" ,r-withr)))
1202 (home-page "https://cran.r-project.org/web/packages/gdtools")
1203 (synopsis "Utilities for graphical rendering")
1205 "The @code{gdtools} package provides functionalities to get font metrics
1206 and to generate base64 encoded string from raster matrix.")
1207 (license license:gpl3)))
1209 (define-public r-svglite
1216 (uri (cran-uri "svglite" version))
1219 "1bws3lc4hlhln11zd7lalhiyc43yk6c6vrzy41fkxk1dkjazfx51"))))
1220 (build-system r-build-system)
1221 (native-inputs `(("r-rcpp" ,r-rcpp)))
1224 ("r-gdtools" ,r-gdtools)))
1225 (home-page "https://github.com/hadley/svglite")
1226 (synopsis "SVG graphics device")
1228 "@code{svglite} is a graphics device that produces clean
1229 @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
1230 hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
1231 considerably faster, produces smaller files, and leaves text as is.")
1232 (license license:gpl2+)))
1234 (define-public r-assertthat
1236 (name "r-assertthat")
1240 (uri (cran-uri "assertthat" version))
1243 "17wy5bdfzg73sg2clisg1k3zyn1adkj59x56m5nwia2k8z67zkw5"))))
1244 (build-system r-build-system)
1245 (home-page "https://github.com/hadley/assertthat")
1246 (synopsis "Easy pre and post assertions")
1248 "Assertthat is an extension to stopifnot() that makes it easy to declare
1249 the pre and post conditions that your code should satisfy, while also
1250 producing friendly error messages so that your users know what they've done
1252 (license license:gpl3+)))
1254 (define-public r-lazyeval
1260 (uri (cran-uri "lazyeval" version))
1263 "1m10i059csrcqkcn59a8wspn784alxsq3symzhn24mhhl894346n"))))
1264 (build-system r-build-system)
1265 (home-page "https://github.com/hadley/lazyeval")
1266 (synopsis "Lazy (non-standard) evaluation in R")
1268 "This package provides the tools necessary to do non-standard
1269 evaluation (NSE) in R.")
1270 (license license:gpl3+)))
1272 (define-public r-dbi
1278 (uri (cran-uri "DBI" version))
1281 "1x8wy2vg2gcgd9bww04qmf0dsn3kp0rfjd8q8j1r2x9zxccg25pz"))))
1282 (build-system r-build-system)
1283 (home-page "https://github.com/rstats-db/DBI")
1284 (synopsis "R database interface")
1286 "The DBI package provides a database interface (DBI) definition for
1287 communication between R and relational database management systems. All
1288 classes in this package are virtual and need to be extended by the various
1289 R/DBMS implementations.")
1290 (license license:lgpl2.0+)))
1295 (version "1.69.0-1")
1298 (uri (cran-uri "BH" version))
1301 "18mckfwxxv8m8rzaz03mg2h6vhaj7y131h6yasfg0s73nxj47zd0"))))
1302 (build-system r-build-system)
1303 (home-page "https://github.com/eddelbuettel/bh")
1304 (synopsis "R package providing subset of Boost headers")
1306 "This package aims to provide the most useful subset of Boost libraries
1307 for template use among CRAN packages.")
1308 (license license:boost1.0)))
1310 (define-public r-evaluate
1316 (uri (cran-uri "evaluate" version))
1319 "0igvc27rsqxcswjb9slnpi5d509rffxn1y5d82hgqvv970nl3p2q"))))
1320 (build-system r-build-system)
1321 (home-page "https://github.com/hadley/evaluate")
1322 (synopsis "Parsing and evaluation tools for R")
1324 "This package provides tools that allow you to recreate the parsing,
1325 evaluation and display of R code, with enough information that you can
1326 accurately recreate what happens at the command line. The tools can easily be
1327 adapted for other output formats, such as HTML or LaTeX.")
1328 (license license:gpl3+)))
1330 (define-public r-formatr
1336 (uri (cran-uri "formatR" version))
1339 "0a9229rg3s9qga5v2fwfdqr0z3bk2yycv8kijrcm3jh66l68zjgm"))))
1340 (build-system r-build-system)
1341 (home-page "http://yihui.name/formatR")
1342 (synopsis "Format R code automatically")
1344 "This package provides a function to format R source code. Spaces and
1345 indent will be added to the code automatically, and comments will be preserved
1346 under certain conditions, so that R code will be more human-readable and tidy.
1347 There is also a Shiny app as a user interface in this package.")
1348 (license license:gpl3+)))
1350 (define-public r-highr
1356 (uri (cran-uri "highr" version))
1359 "0my6idnhmmgs4q1vs40y2lh56yij2p59mpwvm53wjs2zk6x1zl2b"))))
1360 (build-system r-build-system)
1361 (home-page "https://github.com/yihui/highr")
1362 (synopsis "Syntax highlighting for R source code")
1364 "This package provides syntax highlighting for R source code. Currently
1365 it supports LaTeX and HTML output. Source code of other languages is
1366 supported via Andre Simon's highlight package.")
1367 (license license:gpl3+)))
1369 (define-public r-mime
1375 (uri (cran-uri "mime" version))
1378 "00f4gw4sg1kn03s67gficxgb7a7fb6pwhlvrxrml05q1mc2vcxa7"))))
1379 (build-system r-build-system)
1380 (home-page "https://github.com/yihui/mime")
1381 (synopsis "R package to map filenames to MIME types")
1383 "This package guesses the MIME type from a filename extension using the
1384 data derived from /etc/mime.types in UNIX-type systems.")
1385 (license license:gpl2)))
1387 (define-public r-markdown
1393 (uri (cran-uri "markdown" version))
1396 "08xzs4bcf12jxp0276m6xqvq8kcgg5qp6fxrvsz6r9x73jjccs1h"))))
1397 (build-system r-build-system)
1398 ;; Skip check phase because the tests require the r-knitr package to be
1399 ;; installed. This prevents installation failures. Knitr normally
1400 ;; shouldn't be available since r-markdown is a dependency of the r-knitr
1402 (arguments `(#:tests? #f))
1404 `(("r-mime" ,r-mime)))
1405 (home-page "https://github.com/rstudio/markdown")
1406 (synopsis "Markdown rendering for R")
1408 "This package provides R bindings to the Sundown Markdown rendering
1409 library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
1410 syntax that can be converted to XHTML or other formats.")
1411 (license license:gpl2)))
1413 (define-public r-yaml
1419 (uri (cran-uri "yaml" version))
1422 "0in562nd0i23cg91a8kdbqgim656fgscykwi0icsnq53xj3srg2m"))))
1423 (build-system r-build-system)
1424 (home-page "https://cran.r-project.org/web/packages/yaml/")
1425 (synopsis "Methods to convert R data to YAML and back")
1427 "This package implements the libyaml YAML 1.1 parser and
1428 emitter (http://pyyaml.org/wiki/LibYAML) for R.")
1429 (license license:bsd-3)))
1431 (define-public r-knitr
1437 (uri (cran-uri "knitr" version))
1440 "1iks80g1cj25rvgyf0y2jc2pmfvsq4sbgdp788w9016bk71wzdcs"))))
1441 (build-system r-build-system)
1443 `(("r-evaluate" ,r-evaluate)
1444 ("r-highr" ,r-highr)
1445 ("r-markdown" ,r-markdown)
1446 ("r-stringr" ,r-stringr)
1448 ("r-yaml" ,r-yaml)))
1449 (home-page "http://yihui.name/knitr/")
1450 (synopsis "General-purpose package for dynamic report generation in R")
1452 "This package provides a general-purpose tool for dynamic report
1453 generation in R using Literate Programming techniques.")
1454 ;; The code is released under any version of the GPL. As it is used by
1455 ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
1457 (license license:gpl2+)))
1459 (define-public r-knitrbootstrap
1461 (name "r-knitrbootstrap")
1466 (uri (cran-uri "knitrBootstrap" version))
1469 "1aj60j7f0gcs120fdrnfbnb7vk7lfn1phil0mghg6a5zldz4cqs3"))))
1470 (properties `((upstream-name . "knitrBootstrap")))
1471 (build-system r-build-system)
1473 `(("r-knitr" ,r-knitr)
1474 ("r-rmarkdown" ,r-rmarkdown)
1475 ("r-markdown" ,r-markdown)))
1476 (home-page "https://github.com/jimhester/knitrBootstrap")
1477 (synopsis "Knitr bootstrap framework")
1479 "This package provides a framework to create Bootstrap 3 HTML reports
1480 from knitr Rmarkdown.")
1481 (license license:expat)))
1483 (define-public r-microbenchmark
1485 (name "r-microbenchmark")
1489 (uri (cran-uri "microbenchmark" version))
1492 "1sn1fxgzakm5iqbgc35g3k4yi0iqrkmwz33cvdrphrzh1lxnmi3s"))))
1493 (build-system r-build-system)
1494 (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
1495 (synopsis "Accurate timing functions for R")
1497 "This package provides infrastructure to accurately measure and compare
1498 the execution time of R expressions.")
1499 (license license:bsd-2)))
1501 (define-public r-pryr
1507 (uri (cran-uri "pryr" version))
1510 "06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k"))))
1511 (build-system r-build-system)
1513 `(("r-stringr" ,r-stringr)
1514 ("r-codetools" ,r-codetools)))
1516 `(("r-rcpp" ,r-rcpp)))
1517 (home-page "https://github.com/hadley/pryr")
1518 (synopsis "Tools for computing on the R language")
1520 "This package provides useful tools to pry back the covers of R and
1521 understand the language at a deeper level.")
1522 (license license:gpl2)))
1524 (define-public r-memoise
1530 (uri (cran-uri "memoise" version))
1533 "034qfc2xlh30x1q2vya239w34a3ir3y2fwnx2agbgbi6592zjxmj"))))
1534 (build-system r-build-system)
1536 `(("r-digest" ,r-digest)))
1537 (home-page "https://github.com/hadley/memoise")
1538 (synopsis "Memoise functions for R")
1540 "This R package allows to cache the results of a function so that when
1541 you call it again with the same arguments it returns the pre-computed value.")
1542 (license license:expat)))
1544 (define-public r-crayon
1550 (uri (cran-uri "crayon" version))
1553 "0s7s6vc3ww8pzanpjisym4jjvwcc5pi2qg8srx7jqlz9j3wrnvpw"))))
1554 (build-system r-build-system)
1556 `(("r-memoise" ,r-memoise)))
1557 (home-page "https://github.com/gaborcsardi/crayon")
1558 (synopsis "Colored terminal output for R")
1560 "Colored terminal output on terminals that support ANSI color and
1561 highlight codes. It also works in Emacs ESS. ANSI color support is
1562 automatically detected. Colors and highlighting can be combined and nested.
1563 New styles can also be created easily. This package was inspired by the
1564 \"chalk\" JavaScript project.")
1565 (license license:expat)))
1567 (define-public r-praise
1574 (uri (cran-uri "praise" version))
1577 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
1578 (build-system r-build-system)
1579 (home-page "https://github.com/gaborcsardi/praise")
1580 (synopsis "Functions to praise users")
1582 "This package provides template functions to assist in building friendly
1583 R packages that praise their users.")
1584 (license license:expat)))
1586 (define-public r-testthat
1592 (uri (cran-uri "testthat" version))
1595 "1cafy5xsjx6m08s45456mjsal7mfxzwpbrds0p4z3gwam948gpzy"))))
1596 (build-system r-build-system)
1599 ("r-crayon" ,r-crayon)
1600 ("r-digest" ,r-digest)
1601 ("r-magrittr" ,r-magrittr)
1602 ("r-praise" ,r-praise)
1604 ("r-rlang" ,r-rlang)
1605 ("r-withr" ,r-withr)))
1606 (home-page "https://github.com/hadley/testthat")
1607 (synopsis "Unit testing for R")
1609 "This package provides a unit testing system for R designed to be fun,
1610 flexible and easy to set up.")
1611 (license license:expat)))
1619 (uri (cran-uri "R6" version))
1622 "1kmbw2k5vvzwh3wwmn66mszpfny0z6k8dca980qgbxgvfh0i3gkh"))))
1623 (build-system r-build-system)
1624 (home-page "https://github.com/wch/R6/")
1625 (synopsis "Classes with reference semantics in R")
1627 "The R6 package allows the creation of classes with reference semantics,
1628 similar to R's built-in reference classes. Compared to reference classes, R6
1629 classes are simpler and lighter-weight, and they are not built on S4 classes
1630 so they do not require the methods package. These classes allow public and
1631 private members, and they support inheritance, even when the classes are
1632 defined in different packages.")
1633 (license license:expat)))
1635 (define-public r-rlang
1641 (uri (cran-uri "rlang" version))
1644 "1pdlafnijpd2vzy8jxcxwakfi66n4qzrqxvcxi1ja389m066cvbb"))))
1645 (build-system r-build-system)
1646 (home-page "http://rlang.tidyverse.org")
1647 (synopsis "Functions for base types, core R and Tidyverse features")
1648 (description "This package provides a toolbox for working with base types,
1649 core R features like the condition system, and core @code{Tidyverse} features
1650 like tidy evaluation.")
1651 (license license:gpl3)))
1653 (define-public r-tibble
1660 (uri (cran-uri "tibble" version))
1663 "111jl0hdjhh7hkydxvsr5l19gb0ylxq7xrkc28awnc9pzglpgis5"))))
1664 (build-system r-build-system)
1667 ("r-crayon" ,r-crayon)
1668 ("r-fansi" ,r-fansi)
1669 ("r-pkgconfig" ,r-pkgconfig)
1670 ("r-pillar" ,r-pillar)
1671 ("r-rlang" ,r-rlang)))
1672 (home-page "https://github.com/hadley/tibble")
1673 (synopsis "Simple data frames")
1675 "This package provides a @code{tbl_df} class that offers better checking
1676 and printing capabilities than traditional data frames.")
1677 (license license:expat)))
1679 (define-public r-dplyr
1685 (uri (cran-uri "dplyr" version))
1688 "0p6dbjrgqyklc67g53v1a5xdp9x2jpcsdcs6v3djf9d366fqh244"))))
1689 (build-system r-build-system)
1691 `(("r-assertthat" ,r-assertthat)
1694 ("r-magrittr" ,r-magrittr)
1695 ("r-pkgconfig" ,r-pkgconfig)
1696 ("r-plogr" ,r-plogr)
1699 ("r-rlang" ,r-rlang)
1700 ("r-tibble" ,r-tibble)
1701 ("r-tidyselect" ,r-tidyselect)))
1702 (home-page "https://github.com/hadley/dplyr")
1703 (synopsis "Tools for working with data frames in R")
1705 "dplyr is the next iteration of plyr. It is focussed on tools for
1706 working with data frames. It has three main goals: 1) identify the most
1707 important data manipulation tools needed for data analysis and make them easy
1708 to use in R; 2) provide fast performance for in-memory data by writing key
1709 pieces of code in C++; 3) use the same code interface to work with data no
1710 matter where it is stored, whether in a data frame, a data table or
1712 (license license:expat)))
1714 (define-public r-dbplyr
1721 (uri (cran-uri "dbplyr" version))
1724 "07p23vyvi7s4abldhkyir05kcf7xnfc18igfryq12j67xd0jql0m"))))
1725 (build-system r-build-system)
1727 `(("r-assertthat" ,r-assertthat)
1729 ("r-dplyr" ,r-dplyr)
1731 ("r-purrr" ,r-purrr)
1733 ("r-rlang" ,r-rlang)
1734 ("r-tibble" ,r-tibble)
1735 ("r-tidyselect" ,r-tidyselect)))
1736 (home-page "https://github.com/tidyverse/dbplyr")
1737 (synopsis "Dplyr back end for databases")
1739 "This package provides a dplyr back end for databases that allows you to
1740 work with remote database tables as if they are in-memory data frames. Basic
1741 features works with any database that has a @code{DBI} back end; more advanced
1742 features require SQL translation to be provided by the package author.")
1743 (license license:expat)))
1745 (define-public r-acepack
1752 (uri (cran-uri "acepack" version))
1755 "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
1756 (build-system r-build-system)
1758 `(("gfortran" ,gfortran)))
1759 (home-page "https://cran.r-project.org/web/packages/acepack")
1760 (synopsis "Functions for regression transformations")
1762 "This package provides ACE and AVAS methods for choosing regression
1764 (license license:expat)))
1766 (define-public r-formula
1773 (uri (cran-uri "Formula" version))
1776 "0wiqh8rr9d5ciy80wj8f5fnmiiw0ywanvvnhkwd622dx42dk848l"))))
1777 (properties `((upstream-name . "Formula")))
1778 (build-system r-build-system)
1779 (home-page "https://cran.r-project.org/web/packages/Formula")
1780 (synopsis "Extended model formulas")
1782 "This package provides a new class @code{Formula}, which extends the base
1783 class @code{formula}. It supports extended formulas with multiple parts of
1784 regressors on the right-hand side and/or multiple responses on the left-hand
1786 (license (list license:gpl2+ license:gpl3+))))
1788 (define-public r-locfit
1795 (uri (cran-uri "locfit" version))
1798 "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
1799 (build-system r-build-system)
1801 `(("r-lattice" ,r-lattice)))
1802 (home-page "https://cran.r-project.org/web/packages/locfit")
1803 (synopsis "Local regression, likelihood and density estimation")
1805 "This package provides functions used for local regression, likelihood
1806 and density estimation.")
1807 (license (list license:gpl2+ license:gpl3+))))
1809 (define-public r-chron
1815 (uri (cran-uri "chron" version))
1818 "02bkywwsxwrxc035hv51dxgdm1fjxdm7dn19ivifln59dfs1862j"))))
1819 (build-system r-build-system)
1820 (home-page "https://cran.r-project.org/web/packages/chron")
1821 (synopsis "Chronological R objects which can handle dates and times")
1823 "This package provides chronological R objects which can handle dates and
1825 (license license:gpl2)))
1827 (define-public r-data-table
1829 (name "r-data-table")
1833 (uri (cran-uri "data.table" version))
1836 "1xz388khklqqc39r1cmjvqm65azambgzqw0743aypm6v4chi26v1"))))
1837 (build-system r-build-system)
1838 (home-page "https://github.com/Rdatatable/data.table/wiki")
1839 (synopsis "Enhanced version of data.frame R object")
1841 "The R package @code{data.table} is an extension of @code{data.frame}
1842 providing functions for fast aggregation of large data (e.g. 100GB in RAM),
1843 fast ordered joins, fast add/modify/delete of columns by group, column listing
1844 and fast file reading.")
1845 (license license:gpl3+)))
1847 (define-public r-xtable
1854 (uri (cran-uri "xtable" version))
1857 "09f311gq9g7dzf8jdvcx72j11xb7p00jlg066jjbpa6pz3zv1cjk"))))
1858 (build-system r-build-system)
1860 `(("r-knitr" ,r-knitr))) ; for vignettes
1861 (home-page "http://xtable.r-forge.r-project.org/")
1862 (synopsis "Export R tables to LaTeX or HTML")
1864 "This package provides tools to export R data as LaTeX and HTML tables.")
1865 (license license:gpl2+)))
1867 (define-public python-patsy
1869 (name "python-patsy")
1873 (uri (pypi-uri "patsy" version ".zip"))
1876 "1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w"))))
1877 (build-system python-build-system)
1880 (modify-phases %standard-phases
1882 (lambda _ (invoke "nosetests" "-v"))))))
1884 `(("python-numpy" ,python-numpy)
1885 ("python-scipy" ,python-scipy)
1886 ("python-six" ,python-six)))
1888 `(("python-nose" ,python-nose)
1890 (home-page "https://github.com/pydata/patsy")
1891 (synopsis "Describe statistical models and build design matrices")
1893 "Patsy is a Python package for describing statistical models and for
1894 building design matrices.")
1895 ;; The majority of the code is distributed under BSD-2. The module
1896 ;; patsy.compat contains code derived from the Python standard library,
1897 ;; and is covered by the PSFL.
1898 (license (list license:bsd-2 license:psfl))))
1900 (define-public python2-patsy
1901 (package-with-python2 python-patsy))
1903 (define-public python-statsmodels
1905 (name "python-statsmodels")
1910 (uri (pypi-uri "statsmodels" version))
1913 "0fxs8a7sp4d7jvqlm36yi45i2d28kjfvraf9q8i9jr1chhxgjqb4"))))
1914 (build-system python-build-system)
1916 `(;; The test suite is very large and rather brittle. Tests often fail
1917 ;; because of minor changes in dependencies that upstream hasn't fixed
1918 ;; in a new release.
1921 (modify-phases %standard-phases
1922 (add-after 'unpack 'set-matplotlib-backend-to-agg
1924 ;; Set the matplotlib backend to Agg to avoid problems using the
1925 ;; GTK backend without a display.
1926 (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py")
1927 '("statsmodels/tsa/vector_ar/tests/test_var.py"
1928 "statsmodels/duration/tests/test_survfunc.py"))
1929 (("import matplotlib\\.pyplot as plt" line)
1930 (string-append "import matplotlib;matplotlib.use('Agg');"
1934 `(("python-numpy" ,python-numpy)
1935 ("python-scipy" ,python-scipy)
1936 ("python-pandas" ,python-pandas)
1937 ("python-patsy" ,python-patsy)
1938 ("python-matplotlib" ,python-matplotlib)))
1940 `(("python-cython" ,python-cython)
1941 ("python-nose" ,python-nose)
1942 ("python-sphinx" ,python-sphinx)))
1943 (home-page "http://statsmodels.sourceforge.net/")
1944 (synopsis "Statistical modeling and econometrics in Python")
1946 "Statsmodels is a Python package that provides a complement to scipy for
1947 statistical computations including descriptive statistics and estimation and
1948 inference for statistical models.")
1949 (license license:bsd-3)))
1951 (define-public python2-statsmodels
1952 (let ((stats (package-with-python2 python-statsmodels)))
1953 (package (inherit stats)
1955 `(("python2-pytz" ,python2-pytz)
1956 ("python2-numpy" ,python2-numpy)
1957 ("python2-scipy" ,python2-scipy)
1958 ("python2-pandas" ,python2-pandas)
1959 ("python2-patsy" ,python2-patsy)
1960 ("python2-matplotlib" ,python2-matplotlib))))))
1962 (define-public r-coda
1968 (uri (cran-uri "coda" version))
1971 "03fs3sdrrym3is92dgpa6ydk3m63gaihwy7bva4k0wm2hxm7x2k7"))))
1972 (build-system r-build-system)
1974 `(("r-lattice" ,r-lattice)))
1975 (home-page "https://cran.r-project.org/web/packages/coda")
1976 (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
1977 (description "This package provides functions for summarizing and plotting
1978 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
1979 diagnostic tests of convergence to the equilibrium distribution of the Markov
1981 (license license:gpl2+)))
1983 (define-public r-ade4
1990 (uri (cran-uri "ade4" version))
1993 "16z9jk4qj35ghsk4lwmq241dgc770y8a70dlmp9q4gz6d8ssgl7m"))))
1994 (build-system r-build-system)
1996 `(("r-mass" ,r-mass)))
1997 (home-page "http://pbil.univ-lyon1.fr/ADE-4")
1998 (synopsis "Multivariate data analysis and graphical display")
2000 "The ade4 package contains data analysis functions to analyze ecological
2001 and environmental data in the framework of Euclidean exploratory methods.")
2002 (license license:gpl2+)))
2004 (define-public r-xml2
2011 (uri (cran-uri "xml2" version))
2014 "154lmksfiwkhnlmryas25mjhfg6k4mmnnk7bbb29mnn5x5pr2yha"))))
2015 (build-system r-build-system)
2017 `(("libxml2" ,libxml2)
2020 `(("pkg-config" ,pkg-config)))
2022 `(("r-rcpp" ,r-rcpp)))
2023 (home-page "https://github.com/hadley/xml2")
2024 (synopsis "Parse XML with R")
2026 "This package provides a simple, consistent interface to working with XML
2027 files in R. It is built on top of the libxml2 C library.")
2028 (license license:gpl2+)))
2030 (define-public r-multitaper
2032 (name "r-multitaper")
2037 (uri (cran-uri "multitaper" version))
2040 "04wd9bbhyx7697pfy0fpj02v1csr48hkpqj62h9p8a6w84ji4k68"))))
2041 (build-system r-build-system)
2043 `(("gfortran" ,gfortran)))
2044 (home-page "https://github.com/wesleyburr/multitaper/")
2045 (synopsis "Multitaper spectral analysis tools")
2047 "This package implements multitaper spectral estimation
2048 techniques using prolate spheroidal sequences (Slepians) and sine
2049 tapers for time series analysis. It includes an adaptive weighted
2050 multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
2051 F-test, and complex demodulation. The Slepians sequences are
2052 generated efficiently using a tridiagonal matrix solution, and
2053 jackknifed confidence intervals are available for most estimates.")
2054 (license license:gpl2+)))
2056 (define-public r-rversions
2058 (name "r-rversions")
2062 (uri (cran-uri "rversions" version))
2065 "0i2gi05nrvknr7g89rbppkswyfcwwd4r9gp75fdfhpah8sgq1l11"))))
2066 (build-system r-build-system)
2068 `(("r-curl" ,r-curl)
2069 ("r-xml2" ,r-xml2)))
2070 (home-page "https://github.com/metacran/rversions")
2071 (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
2073 "This package provides functions to query the main R repository to find
2074 the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
2075 previous R versions and their release dates.")
2076 (license license:expat)))
2078 (define-public r-whisker
2084 (uri (cran-uri "whisker" version))
2087 "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28"))))
2088 (build-system r-build-system)
2089 (home-page "https://github.com/edwindj/whisker")
2090 (synopsis "Logicless mustache templating for R")
2092 "This package provides logicless templating, with a syntax that is not
2094 (license license:gpl3+)))
2096 (define-public r-backports
2098 (name "r-backports")
2103 (uri (cran-uri "backports" version))
2106 "1hac46xaawnqajlsfb5k7pfkc2ya9h76s5qv9ycj3jafh93d26z4"))))
2107 (build-system r-build-system)
2108 (home-page "https://cran.r-project.org/web/packages/backports")
2109 (synopsis "Reimplementations of functions introduced since R 3.0.0")
2111 "Provides implementations of functions which have been introduced in R
2112 since version 3.0.0. The backports are conditionally exported which results
2113 in R resolving the function names to the version shipped with R (if available)
2114 and uses the implemented backports as fallback. This way package developers
2115 can make use of the new functions without worrying about the minimum required
2117 (license license:gpl2+)))
2119 (define-public r-checkmate
2121 (name "r-checkmate")
2126 (uri (cran-uri "checkmate" version))
2129 "1y4ylzn55kpyfpzcx9rxb9413d3ck6hair36ldl0ak61ia5kc75p"))))
2130 (build-system r-build-system)
2132 `(("r-backports" ,r-backports)))
2133 (home-page "https://github.com/mllg/checkmate")
2134 (synopsis "Fast and versatile argument checks")
2136 "This package provides tests and assertions to perform frequent argument
2137 checks. A substantial part of the package was written in C to minimize any
2138 worries about execution time overhead.")
2139 (license license:bsd-3)))
2141 (define-public r-bbmisc
2148 (uri (cran-uri "BBmisc" version))
2151 "1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y"))))
2152 (properties `((upstream-name . "BBmisc")))
2153 (build-system r-build-system)
2155 `(("r-checkmate" ,r-checkmate)))
2156 (home-page "https://github.com/berndbischl/BBmisc")
2157 (synopsis "Miscellaneous functions for R package development")
2159 "This package provides miscellaneous helper functions for the development
2161 (license license:bsd-3)))
2163 (define-public r-fail
2170 (uri (cran-uri "fail" version))
2173 "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
2174 (build-system r-build-system)
2176 `(("r-bbmisc" ,r-bbmisc)
2177 ("r-checkmate" ,r-checkmate)))
2178 (home-page "https://github.com/mllg/fail")
2179 (synopsis "File abstraction interface layer (FAIL)")
2181 "This package provides a more comfortable interface to work with R data
2182 or source files in a key-value fashion.")
2183 (license license:bsd-3)))
2185 (define-public r-batchjobs
2187 (name "r-batchjobs")
2192 (uri (cran-uri "BatchJobs" version))
2195 "035658marnw57p4f38g99rwmvmb6hpbq0fhlxp3qbw22zfnnkvs9"))))
2196 (properties `((upstream-name . "BatchJobs")))
2197 (build-system r-build-system)
2199 `(("r-backports" ,r-backports)
2200 ("r-bbmisc" ,r-bbmisc)
2202 ("r-checkmate" ,r-checkmate)
2203 ("r-data-table" ,r-data-table)
2205 ("r-digest" ,r-digest)
2206 ("r-rsqlite" ,r-rsqlite)
2207 ("r-sendmailr" ,r-sendmailr)
2208 ("r-stringi" ,r-stringi)))
2209 (home-page "https://github.com/tudo-r/BatchJobs")
2210 (synopsis "Batch computing with R")
2212 "This package provides @code{Map}, @code{Reduce} and @code{Filter}
2213 variants to generate jobs on batch computing systems like PBS/Torque, LSF,
2214 SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
2215 (license license:bsd-2)))
2217 (define-public r-brew
2223 (uri (cran-uri "brew" version))
2226 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
2227 (build-system r-build-system)
2228 (home-page "https://cran.r-project.org/web/packages/brew")
2229 (synopsis "Templating framework for report generation")
2231 "The brew package implements a templating framework for mixing text and R
2232 code for report generation. The template syntax is similar to PHP, Ruby's erb
2233 module, Java Server Pages, and Python's psp module.")
2234 (license license:gpl2+)))
2236 (define-public r-desc
2243 (uri (cran-uri "desc" version))
2246 "1s6s13fk6sxwcj8wzkwxl9vr33153xx11p5wi9avqx3rzkabavz6"))))
2247 (build-system r-build-system)
2249 `(("r-assertthat" ,r-assertthat)
2250 ("r-crayon" ,r-crayon)
2252 ("r-rprojroot" ,r-rprojroot)))
2253 (home-page "https://github.com/r-pkgs/desc")
2254 (synopsis "Manipulate DESCRIPTION Files")
2256 "This package provides tools to read, write, create, and manipulate
2257 DESCRIPTION files. It is intended for packages that create or manipulate
2259 (license license:expat)))
2261 (define-public r-commonmark
2263 (name "r-commonmark")
2268 (uri (cran-uri "commonmark" version))
2271 "024iz1qp2kv6iz6y69ir0jk3qhjps86rhkzlcmhqsxx97rx7cjni"))))
2272 (build-system r-build-system)
2273 (home-page "https://cran.r-project.org/web/packages/commonmark")
2274 (synopsis "CommonMark and Github Markdown Rendering in R")
2276 "The CommonMark specification defines a rationalized version of markdown
2277 syntax. This package uses the @code{cmark} reference implementation for
2278 converting markdown text into various formats including HTML, LaTeX and groff
2279 man. In addition, it exposes the markdown parse tree in XML format. The latest
2280 version of this package also adds support for Github extensions including
2281 tables, autolinks and strikethrough text.")
2282 (license license:bsd-2)))
2284 (define-public r-roxygen2
2290 (uri (cran-uri "roxygen2" version))
2293 "0wq29ilqas8yn2z8v49fk0hbgchg29nmyyhwczgdipz0cbhbfipd"))))
2294 (build-system r-build-system)
2296 `(("r-brew" ,r-brew)
2297 ("r-commonmark" ,r-commonmark)
2299 ("r-digest" ,r-digest)
2300 ("r-pkgload" ,r-pkgload)
2301 ("r-purrr" ,r-purrr)
2304 ("r-stringi" ,r-stringi)
2305 ("r-stringr" ,r-stringr)
2306 ("r-xml2" ,r-xml2)))
2308 `(("r-knitr" ,r-knitr))) ; for vignettes
2309 (home-page "https://github.com/klutometis/roxygen")
2310 (synopsis "In-source documentation system for R")
2312 "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
2313 collation, and NAMESPACE files.")
2314 (license license:gpl2+)))
2316 (define-public r-openssl
2323 (uri (cran-uri "openssl" version))
2326 "1gx4mk7js1irzkql5rgk48ja9c6mm28ccxz483ngbhdd57az90qw"))))
2327 (build-system r-build-system)
2329 `(("libressl" ,libressl)))
2331 `(("pkg-config" ,pkg-config)))
2333 `(("r-askpass" ,r-askpass)))
2334 (home-page "https://github.com/jeroenooms/openssl")
2335 (synopsis "Toolkit for encryption, signatures and certificates")
2337 "This package provides R bindings to OpenSSL libssl and libcrypto, plus
2338 custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
2339 and P-521. Cryptographic signatures can either be created and verified
2340 manually or via x509 certificates. AES block cipher is used in CBC mode for
2341 symmetric encryption; RSA for asymmetric (public key) encryption. High-level
2342 envelope functions combine RSA and AES for encrypting arbitrary sized data.
2343 Other utilities include key generators, hash functions (md5, sha1, sha256,
2344 etc), base64 encoder, a secure random number generator, and @code{bignum} math
2345 methods for manually performing crypto calculations on large multibyte
2347 (license license:expat)))
2349 (define-public r-httr
2355 (uri (cran-uri "httr" version))
2358 "0j6vknwyvkjpjsxwch4q02aik4dnm3h4l0wc7dgzc555bm1g2cyn"))))
2359 (build-system r-build-system)
2361 `(("r-curl" ,r-curl)
2362 ("r-jsonlite" ,r-jsonlite)
2363 ("r-openssl" ,r-openssl)
2366 (home-page "https://github.com/hadley/httr")
2367 (synopsis "Tools for working with URLs and HTTP")
2369 "The aim of httr is to provide a wrapper for RCurl customised to the
2370 demands of modern web APIs. It provides useful tools for working with HTTP
2371 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
2372 functions make it easy to control additional request components.")
2373 (license license:expat)))
2375 (define-public r-git2r
2381 (uri (cran-uri "git2r" version))
2384 "15kpvz6ry2r8ii5hzinjwkggc5kgmkbcpsdwzahsf8gha52w80p0"))))
2385 (build-system r-build-system)
2386 ;; This R package contains modified sources of libgit2. This modified
2387 ;; version of libgit2 is built as the package is built. Hence libgit2 is
2388 ;; not among the inputs of this package.
2390 `(("libssh2" ,libssh2) ; for SSH transport
2391 ("openssl" ,openssl)
2394 `(("pkg-config" ,pkg-config)))
2395 (home-page "https://github.com/ropensci/git2r")
2396 (synopsis "Access Git repositories with R")
2398 "This package provides an R interface to the libgit2 library, which is a
2399 pure C implementation of the Git core methods.")
2400 ;; GPLv2 only with linking exception.
2401 (license license:gpl2)))
2403 (define-public r-rstudioapi
2405 (name "r-rstudioapi")
2409 (uri (cran-uri "rstudioapi" version))
2412 "15mbw607ncdf53mgga76n3va5zzdcjqz14nb0jcn9axwccqamic0"))))
2413 (build-system r-build-system)
2414 (home-page "https://cran.r-project.org/web/packages/rstudioapi")
2415 (synopsis "Safely access the RStudio API")
2417 "This package provides functions to access the RStudio API and provide
2418 informative error messages when it's not available.")
2419 (license license:expat)))
2421 (define-public r-devtools
2427 (uri (cran-uri "devtools" version))
2430 "1nyspqicn9zd1rgq3k07b3179i8w5ys6jbd65g9q8qczrb7z3x8f"))))
2431 (build-system r-build-system)
2433 `(("r-callr" ,r-callr)
2435 ("r-digest" ,r-digest)
2436 ("r-git2r" ,r-git2r)
2438 ("r-jsonlite" ,r-jsonlite)
2439 ("r-memoise" ,r-memoise)
2440 ("r-pkgbuild" ,r-pkgbuild)
2441 ("r-pkgload" ,r-pkgload)
2442 ("r-rcmdcheck" ,r-rcmdcheck)
2443 ("r-remotes" ,r-remotes)
2444 ("r-rstudioapi" ,r-rstudioapi)
2445 ("r-sessioninfo" ,r-sessioninfo)
2446 ("r-usethis" ,r-usethis)
2447 ("r-withr" ,r-withr)))
2448 (home-page "https://github.com/hadley/devtools")
2449 (synopsis "Tools to make developing R packages easier")
2450 (description "The devtools package is a collection of package development
2451 tools to simplify the devolpment of R packages.")
2452 (license license:gpl2+)))
2454 (define-public r-withr
2460 (uri (cran-uri "withr" version))
2463 "11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1"))))
2464 (build-system r-build-system)
2465 (home-page "https://github.com/jimhester/withr")
2466 (synopsis "Run code with temporarily modified global state")
2468 "This package provides a set of functions to run R code in an environment
2469 in which global state has been temporarily modified. Many of these functions
2470 were originally a part of the r-devtools package.")
2471 (license license:gpl2+)))
2473 (define-public r-hms
2480 (uri (cran-uri "hms" version))
2483 "1g6hslk3z0xga38r71irxq802wskg6nv804mp8y9f7i2wfrj0y55"))))
2484 (build-system r-build-system)
2486 `(("r-rlang" ,r-rlang)
2487 ("r-pkgconfig" ,r-pkgconfig)))
2488 (home-page "https://github.com/rstats-db/hms")
2489 (synopsis "Pretty time of day")
2491 "This package implements an S3 class for storing and formatting
2492 time-of-day values, based on the @code{difftime} class.")
2493 (license license:gpl3+)))
2495 (define-public r-readr
2501 (uri (cran-uri "readr" version))
2504 "1wz496rw0ah433p755n3xac8gh7yzid4xgdjzd1a7wmpkgilvy9k"))))
2505 (build-system r-build-system)
2507 `(("r-clipr" ,r-clipr)
2508 ("r-crayon" ,r-crayon)
2511 ("r-tibble" ,r-tibble)
2514 (home-page "https://github.com/hadley/readr")
2515 (synopsis "Read tabular data")
2517 "This package provides functions to read flat or tabular text files from
2518 disk (or a connection).")
2519 (license license:gpl2+)))
2521 (define-public r-plotrix
2527 (uri (cran-uri "plotrix" version))
2530 "1hs0zwaqs34559girinvysjfbvznyn8znp9cwvkqx6k2cqvcjinj"))))
2531 (build-system r-build-system)
2532 (home-page "https://cran.r-project.org/web/packages/plotrix")
2533 (synopsis "Various plotting functions")
2535 "This package provides lots of plotting, various labeling, axis and color
2536 scaling functions for R.")
2537 (license license:gpl2+)))
2539 (define-public r-gridbase
2545 (uri (cran-uri "gridBase" version))
2548 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
2549 (build-system r-build-system)
2550 (home-page "https://cran.r-project.org/web/packages/gridBase")
2551 (synopsis "Integration of base and grid graphics")
2553 "This package provides an integration of base and grid graphics for R.")
2554 (license license:gpl2+)))
2556 (define-public r-latticeextra
2558 (name "r-latticeextra")
2563 (uri (cran-uri "latticeExtra" version))
2566 "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq"))))
2567 (properties `((upstream-name . "latticeExtra")))
2568 (build-system r-build-system)
2570 `(("r-lattice" ,r-lattice)
2571 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2572 (home-page "http://latticeextra.r-forge.r-project.org/")
2573 (synopsis "Extra graphical utilities based on lattice")
2575 "Building on the infrastructure provided by the lattice package, this
2576 package provides several new high-level graphics functions and methods, as
2577 well as additional utilities such as panel and axis annotation functions.")
2578 (license license:gpl2+)))
2580 (define-public r-rcpparmadillo
2582 (name "r-rcpparmadillo")
2583 (version "0.9.300.2.0")
2586 (uri (cran-uri "RcppArmadillo" version))
2589 "02zha49v6s8g39dcmk5dz0pygx0jibgmcwsyzybp9wmlqxnmdvip"))))
2590 (properties `((upstream-name . "RcppArmadillo")))
2591 (build-system r-build-system)
2592 ;; All needed for vignettes
2594 `(("r-knitr" ,r-knitr)
2595 ("r-rmarkdown" ,r-rmarkdown)
2596 ("ghc-pandoc" ,ghc-pandoc)
2597 ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)))
2599 `(("r-rcpp" ,r-rcpp)))
2600 (home-page "https://github.com/RcppCore/RcppArmadillo")
2601 (synopsis "Rcpp integration for the Armadillo linear algebra library")
2603 "Armadillo is a templated C++ linear algebra library that aims towards a
2604 good balance between speed and ease of use. Integer, floating point and
2605 complex numbers are supported, as well as a subset of trigonometric and
2606 statistics functions. Various matrix decompositions are provided through
2607 optional integration with LAPACK and ATLAS libraries. This package includes
2608 the header files from the templated Armadillo library.")
2609 ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
2610 ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
2611 ;; later, as is the rest of 'Rcpp'.
2612 (license license:gpl2+)))
2614 (define-public r-bitops
2620 (uri (cran-uri "bitops" version))
2623 "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
2624 (build-system r-build-system)
2625 (home-page "https://cran.r-project.org/web/packages/bitops")
2626 (synopsis "Bitwise operations")
2628 "This package provides functions for bitwise operations on integer
2630 (license license:gpl2+)))
2632 (define-public r-catools
2635 (version "1.17.1.2")
2638 (uri (cran-uri "caTools" version))
2641 "0svj31y7h8vimvliygmmbl7pk850qk80k1vn38mlcxsnmcpm9k39"))))
2642 (properties `((upstream-name . "caTools")))
2643 (build-system r-build-system)
2645 `(("r-bitops" ,r-bitops)))
2646 (home-page "https://cran.r-project.org/web/packages/caTools")
2647 (synopsis "Various tools including functions for moving window statistics")
2649 "This package contains several basic utility functions including:
2650 moving (rolling, running) window statistic functions, read/write for GIF and
2651 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
2652 encoder/decoder, round-off-error-free sum and cumsum, etc.")
2653 (license license:gpl3+)))
2655 (define-public r-rprojroot
2657 (name "r-rprojroot")
2662 (uri (cran-uri "rprojroot" version))
2665 "12r3fdxmi2pmwn6ic3rhg0b20ll5z420m0d8fziv1n21961namnz"))))
2666 (build-system r-build-system)
2668 `(("r-backports" ,r-backports)))
2669 (home-page "https://github.com/krlmlr/rprojroot")
2670 (synopsis "Finding files in project subdirectories")
2672 "This package helps accessing files relative to a project root. It
2673 provides helpers for robust, reliable and flexible paths to files below a
2674 project root. The root of a project is defined as a directory that matches a
2675 certain criterion, e.g., it contains a certain regular file.")
2676 (license license:gpl3)))
2678 (define-public r-rmarkdown
2680 (name "r-rmarkdown")
2685 (uri (cran-uri "rmarkdown" version))
2688 "0milpdaf4nd36kq6sci9wc5dhwswl4w9c9fychfbppgjsgfp6kfv"))))
2689 (properties `((upstream-name . "rmarkdown")))
2690 (build-system r-build-system)
2692 `(("r-base64enc" ,r-base64enc)
2693 ("r-evaluate" ,r-evaluate)
2694 ("r-htmltools" ,r-htmltools)
2695 ("r-jsonlite" ,r-jsonlite)
2696 ("r-knitr" ,r-knitr)
2698 ("r-stringr" ,r-stringr)
2699 ("r-tinytex" ,r-tinytex)
2701 ("ghc-pandoc" ,ghc-pandoc)))
2702 (home-page "http://rmarkdown.rstudio.com")
2703 (synopsis "Convert R Markdown documents into a variety of formats")
2705 "This package provides tools to convert R Markdown documents into a
2706 variety of formats.")
2707 (license license:gpl3+)))
2709 (define-public r-gtable
2715 (uri (cran-uri "gtable" version))
2718 "1lyncxf2dqdjgw1071cn9c8zwzkz6sldnd5cgmicf70bc726qf7x"))))
2719 (properties `((upstream-name . "gtable")))
2720 (build-system r-build-system)
2721 (home-page "https://cran.r-project.org/web/packages/gtable")
2722 (synopsis "R library to arrange grobs in tables")
2724 "Gtable is a collection of tools to make it easier to work with
2725 \"tables\" of grobs.")
2726 (license license:gpl2+)))
2728 (define-public r-gridextra
2730 (name "r-gridextra")
2734 (uri (cran-uri "gridExtra" version))
2737 "0fwfk3cdwxxim7nd55pn7m31bcaqj48y06j7an2k1v1pybk0rdl1"))))
2738 (properties `((upstream-name . "gridExtra")))
2739 (build-system r-build-system)
2741 `(("r-gtable" ,r-gtable)))
2743 `(("r-knitr" ,r-knitr))) ;for building vignettes
2744 (home-page "https://github.com/baptiste/gridextra")
2745 (synopsis "Miscellaneous functions for \"Grid\" graphics")
2747 "This package provides a number of user-level functions to work with
2748 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
2750 (license license:gpl2+)))
2752 (define-public r-pkgconfig
2754 (name "r-pkgconfig")
2758 (uri (cran-uri "pkgconfig" version))
2761 "1jk9ip549xphb3anfixqv1yx5kidnndqgy9v3qjpmgmds5a7g695"))))
2762 (build-system r-build-system)
2763 (home-page "https://github.com/gaborcsardi/pkgconfig")
2764 (synopsis "Private configuration for R packages")
2765 (description "This package provides the functionality to set configuration
2766 options on a per-package basis. Options set by a given package only apply to
2767 that package, other packages are unaffected.")
2768 (license license:expat)))
2770 (define-public r-blob
2776 (uri (cran-uri "blob" version))
2779 "0lsg91hk508dd95ivig2lwg62qafwnarjw68110kx63cfk4zkjxc"))))
2780 (build-system r-build-system)
2782 `(("r-prettyunits" ,r-prettyunits)
2783 ("r-tibble" ,r-tibble)))
2784 (home-page "https://github.com/hadley/blob")
2785 (synopsis "Simple S3 Class for representing vectors of binary data")
2786 (description "Raw vectors in R are useful for storing a single binary
2787 object. What if you want to put a vector of them in a data frame? The blob
2788 package provides the blob object, a list of raw vectors, suitable for use as
2789 a column in data frame.")
2790 (license license:gpl3+)))
2792 (define-public r-rsqlite
2798 (uri (cran-uri "RSQLite" version))
2801 "1giwk4335sc6yhj3rs8h070g1mwy38kyqyqv6vcfxvskykj7vp6z"))))
2802 (properties `((upstream-name . "RSQLite")))
2803 (build-system r-build-system)
2807 ("r-memoise" ,r-memoise)
2808 ("r-plogr" ,r-plogr)
2810 ("r-bit64" ,r-bit64)
2812 ("r-pkgconfig" ,r-pkgconfig)))
2813 (home-page "https://github.com/rstats-db/RSQLite")
2814 (synopsis "SQLite interface for R")
2816 "This package embeds the SQLite database engine in R and provides an
2817 interface compliant with the DBI package. The source for the SQLite
2818 engine (version 3.8.8.2) is included.")
2819 (license license:lgpl2.0+)))
2821 (define-public r-rcurl
2824 (version "1.95-0.1.2")
2827 (uri (string-append "https://www.bioconductor.org/packages/"
2828 "release/extra/src/"
2829 "contrib/RCurl_" version ".tar.gz"))
2832 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
2833 (properties `((upstream-name . "RCurl")))
2834 (build-system r-build-system)
2837 (modify-phases %standard-phases
2838 (add-after 'unpack 'respect-CURL_CA_BUNDLE
2840 (substitute* "R/options.S"
2841 (("\\.els = rev\\(merge\\(list\\(\\.\\.\\.\\), \\.opts\\)\\)" m)
2843 certs = Sys.getenv(\"CURL_CA_BUNDLE\")
2844 if (certs != \"\") { .opts = merge.list(.opts, list(cainfo=certs)) }
2848 `(("libcurl" ,curl)))
2850 `(("r-bitops" ,r-bitops)))
2851 (home-page "http://www.omegahat.org/RCurl")
2852 (synopsis "General network client interface for R")
2854 "The package allows one to compose general HTTP requests and provides
2855 convenient functions to fetch URIs, GET and POST forms, etc. and process the
2856 results returned by the Web server. This provides a great deal of control
2857 over the HTTP/FTP/... connection and the form of the request while providing a
2858 higher-level interface than is available just using R socket connections.
2859 Additionally, the underlying implementation is robust and extensive,
2860 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
2861 ldap, and also supports cookies, redirects, authentication, etc.")
2862 (license license:bsd-3)))
2864 (define-public r-xml
2867 (version "3.98-1.19")
2870 (uri (cran-uri "XML" version))
2873 "1axyfa56q45x7z4zd56aasdn9hz9niv2vv5qm1zp9i94vyic9cc1"))))
2875 `((upstream-name . "XML")))
2876 (build-system r-build-system)
2878 `(("libxml2" ,libxml2)
2881 `(("pkg-config" ,pkg-config)))
2882 (home-page "http://www.omegahat.org/RSXML")
2883 (synopsis "Tools for parsing and generating XML within R")
2885 "Many approaches for both reading and creating XML (and HTML)
2886 documents (including DTDs), both local and accessible via HTTP or FTP. Also
2887 offers access to an XPath \"interpreter\".")
2888 (license license:bsd-2)))
2890 (define-public r-xnomial
2895 (origin (method url-fetch)
2896 (uri (cran-uri "XNomial" version))
2899 "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
2900 (properties (quasiquote ((upstream-name . "XNomial"))))
2901 (build-system r-build-system)
2902 (home-page "https://cran.r-project.org/web/packages/XNomial")
2903 (synopsis "Goodness-of-Fit test for multinomial data")
2905 "This package provides an exact Goodness-of-Fit test for
2906 multinomial data with fixed probabilities. It can be used to
2907 determine whether a set of counts fits a given expected ratio. To see
2908 whether a set of observed counts fits an expectation, one can examine
2909 all possible outcomes with @code{xmulti()} or a random sample of them
2910 with @code{xmonte()} and find the probability of an observation
2911 deviating from the expectation by at least as much as the observed.
2912 As a measure of deviation from the expected, one can use the
2913 log-likelihood ratio, the multinomial probability, or the classic
2914 chi-square statistic. A histogram of the test statistic can also be
2915 plotted and compared with the asymptotic curve.")
2916 (license (list license:gpl2+ license:gpl3+))))
2918 (define-public r-lambda-r
2924 (uri (cran-uri "lambda.r" version))
2927 "0cc6pszs6yccn0hgjpyn9gspv9aiva9d91ba0640i5m0l5xy7n0c"))))
2928 (properties `((upstream-name . "lambda.r")))
2929 (build-system r-build-system)
2931 `(("r-formatr" ,r-formatr)))
2932 (home-page "https://cran.r-project.org/web/packages/lambda.r")
2933 (synopsis "Functional programming extension for R")
2935 "This package provides a language extension to efficiently write
2936 functional programs in R. Syntax extensions include multi-part function
2937 definitions, pattern matching, guard statements, built-in (optional) type
2939 (license license:lgpl3+)))
2941 (define-public r-futile-options
2943 (name "r-futile-options")
2947 (uri (cran-uri "futile.options" version))
2950 "0w15agpi88y3qkv6fl72zy2pzyplzgvnj41a4ixhg64mw1sck73s"))))
2952 `((upstream-name . "futile.options")))
2953 (build-system r-build-system)
2954 (home-page "https://cran.r-project.org/web/packages/futile.options")
2955 (synopsis "Options management framework")
2957 "The futile.options subsystem provides an easy user-defined options
2958 management system that is properly scoped. This means that options created
2959 via @code{futile.options} are fully self-contained and will not collide with
2960 options defined in other packages.")
2961 (license license:lgpl3+)))
2963 (define-public r-futile-logger
2965 (name "r-futile-logger")
2969 (uri (cran-uri "futile.logger" version))
2972 "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
2973 (properties `((upstream-name . "futile.logger")))
2974 (build-system r-build-system)
2976 `(("r-futile-options" ,r-futile-options)
2977 ("r-lambda-r" ,r-lambda-r)))
2978 (home-page "https://cran.r-project.org/web/packages/futile.logger")
2979 (synopsis "Logging utility for R")
2981 "This package provides a simple yet powerful logging utility. Based
2982 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
2983 convenient and easy to use replacement for @code{cat} and @code{print}
2985 (license license:lgpl3+)))
2987 (define-public r-segmented
2989 (name "r-segmented")
2994 (uri (cran-uri "segmented" version))
2997 "0nrik5fyq59hwiwjcpbi4p5yfavgfjq6wyrynhkrbm4k6v1g1wlq"))))
2998 (build-system r-build-system)
2999 (home-page "https://cran.r-project.org/web/packages/segmented")
3000 (synopsis "Regression models with breakpoints estimation")
3002 "Given a regression model, segmented updates the model by adding one or
3003 more segmented (i.e., piecewise-linear) relationships. Several variables with
3004 multiple breakpoints are allowed.")
3005 (license (list license:gpl2+ license:gpl3+))))
3007 (define-public r-snow
3013 (uri (cran-uri "snow" version))
3016 "1n3n8pva9s34fvlw32yng0x416lmbv7q1fsd0ywa4kikmxym64l5"))))
3017 (build-system r-build-system)
3018 (home-page "https://cran.r-project.org/web/packages/snow")
3019 (synopsis "Support for simple parallel computing in R")
3021 "The snow package provides support for simple parallel computing on a
3022 network of workstations using R. A master R process calls @code{makeCluster}
3023 to start a cluster of worker processes; the master process then uses functions
3024 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
3025 worker processes and collect and return the results on the master.")
3026 (license (list license:gpl2+ license:gpl3+))))
3028 (define-public r-sparsem
3034 (uri (cran-uri "SparseM" version))
3037 "0p6ljma2h12cq1xmy0cxb48ih8dhxxbnwkqzvx3cckxf2kprycm9"))))
3039 `((upstream-name . "SparseM")))
3041 `(("gfortran" ,gfortran)))
3042 (build-system r-build-system)
3043 (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
3044 (synopsis "Sparse linear algebra")
3046 "This package provides some basic linear algebra functionality for sparse
3047 matrices. It includes Cholesky decomposition and backsolving as well as
3048 standard R subsetting and Kronecker products.")
3049 (license license:gpl2+)))
3051 (define-public r-iterators
3053 (name "r-iterators")
3058 (uri (cran-uri "iterators" version))
3061 "1s3iykfvccpnzs73z90rx18qvbvgw2dgl4nfcrvm5m1850qb5qd9"))))
3062 (build-system r-build-system)
3063 (home-page "https://cran.r-project.org/web/packages/iterators")
3064 (synopsis "Iterator construct for R")
3066 "This package provides support for iterators, which allow a programmer to
3067 traverse through all the elements of a vector, list, or other collection of
3069 (license license:asl2.0)))
3071 (define-public r-foreach
3078 (uri (cran-uri "foreach" version))
3081 "0j2yj0rn0d5nbzz9nq5rqqgnxhp9pbd92q4klsarl2xpsn8119y0"))))
3082 (build-system r-build-system)
3084 `(("r-codetools" ,r-codetools)
3085 ("r-iterators" ,r-iterators)))
3086 (home-page "https://cran.r-project.org/web/packages/foreach")
3087 (synopsis "Foreach looping construct for R")
3089 "This package provides support for the @code{foreach} looping construct.
3090 @code{foreach} is an idiom that allows for iterating over elements in a
3091 collection, without the use of an explicit loop counter. This package in
3092 particular is intended to be used for its return value, rather than for its
3093 side effects. In that sense, it is similar to the standard @code{lapply}
3094 function, but doesn't require the evaluation of a function. Using
3095 @code{foreach} without side effects also facilitates executing the loop in
3097 (license license:asl2.0)))
3099 (define-public r-doparallel
3101 (name "r-doparallel")
3106 (uri (cran-uri "doParallel" version))
3109 "01qjs4iw9f1kgymcypj0m2s4pvgqhxaycpli0fb8lq3dc0vpzfyb"))))
3110 (properties `((upstream-name . "doParallel")))
3111 (build-system r-build-system)
3113 `(("r-foreach" ,r-foreach)
3114 ("r-iterators" ,r-iterators)))
3115 (home-page "https://cran.r-project.org/web/packages/doParallel")
3116 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3118 "This package provides a parallel backend for the @code{%dopar%} function
3119 using the parallel package.")
3120 (license license:gpl2+)))
3122 (define-public r-domc
3129 (uri (cran-uri "doMC" version))
3132 "1vfrykvfvsyq12mypd266867ml1dcwc3rj5k9c3wrn5bddcm88kr"))))
3133 (properties `((upstream-name . "doMC")))
3134 (build-system r-build-system)
3136 `(("r-foreach" ,r-foreach)
3137 ("r-iterators" ,r-iterators)))
3138 (home-page "https://cran.r-project.org/web/packages/doMC")
3139 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3141 "This package provides a parallel backend for the @code{%dopar%} function
3142 using the multicore functionality of the parallel package.")
3143 (license license:gpl2+)))
3151 (uri (cran-uri "DT" version))
3154 "1s5d3sld4l8zygpkvprvlbqa0pm2cv1bm7h7p999wxlap28vnnqf"))))
3156 `((upstream-name . "DT")))
3157 (build-system r-build-system)
3159 `(("r-crosstalk" ,r-crosstalk)
3160 ("r-htmltools" ,r-htmltools)
3161 ("r-htmlwidgets" ,r-htmlwidgets)
3162 ("r-magrittr" ,r-magrittr)
3163 ("r-promises" ,r-promises)))
3164 (home-page "http://rstudio.github.io/DT")
3165 (synopsis "R wrapper of the DataTables JavaScript library")
3167 "This package allows for data objects in R to be rendered as HTML tables
3168 using the JavaScript library @code{DataTables} (typically via R Markdown or
3169 Shiny). The @code{DataTables} library has been included in this R package.")
3170 ;; The DT package as a whole is distributed under GPLv3. The DT package
3171 ;; inludes other software components under different licenses:
3173 ;; * Expat: jQuery, jquery.highlight.js, DataTables
3174 ;; * ASL2.0: selectize.js
3175 ;; * WTFPL: noUiSlider
3176 (license (list license:gpl3
3179 (license:non-copyleft "http://www.wtfpl.net/txt/copying/")))))
3181 (define-public r-base64enc
3183 (name "r-base64enc")
3187 (uri (cran-uri "base64enc" version))
3190 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
3191 (build-system r-build-system)
3192 (home-page "http://www.rforge.net/base64enc")
3193 (synopsis "Tools for Base64 encoding")
3195 "This package provides tools for handling Base64 encoding. It is more
3196 flexible than the orphaned \"base64\" package.")
3197 (license license:gpl2+)))
3199 (define-public r-irlba
3206 (uri (cran-uri "irlba" version))
3209 "1h7mzrqdjc41814cf6c93sbyl7nxwvsf3x8apl9rhmydgdlk7qkf"))))
3210 (build-system r-build-system)
3212 `(("r-matrix" ,r-matrix)))
3213 (home-page "https://cran.r-project.org/web/packages/irlba")
3214 (synopsis "Methods for eigendecomposition of large matrices")
3216 "This package provides fast and memory efficient methods for truncated
3217 singular and eigenvalue decompositions, as well as for principal component
3218 analysis of large sparse or dense matrices.")
3219 (license (list license:gpl2+ license:gpl3+))))
3221 (define-public r-glmnet
3228 (uri (cran-uri "glmnet" version))
3231 "1brr51z1fzbpyj6myyir4g6dhbp6xwl7nx4xnvrjarnf5y0csk55"))))
3232 (build-system r-build-system)
3234 `(("gfortran" ,gfortran)))
3236 `(("r-foreach" ,r-foreach)
3237 ("r-matrix" ,r-matrix)))
3238 (home-page "http://www.jstatsoft.org/v33/i01")
3239 (synopsis "Lasso and elastic-net regularized generalized linear models")
3241 "The glmnet package provides efficient procedures for fitting the entire
3242 lasso or elastic-net regularization path for linear and Poisson regression, as
3243 well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
3244 multinomial models. The algorithm uses cyclical coordinate descent in a
3245 path-wise fashion.")
3246 (license license:gpl2+)))
3248 (define-public r-pkgmaker
3255 (uri (cran-uri "pkgmaker" version))
3258 "0spcamjncj78kzjps2rw4v1a4494yazv6xvhn0vmdflnypc8k8hp"))))
3259 (build-system r-build-system)
3261 `(("r-bibtex" ,r-bibtex)
3262 ("r-codetools" ,r-codetools)
3263 ("r-digest" ,r-digest)
3264 ("r-magrittr" ,r-magrittr)
3265 ("r-registry" ,r-registry)
3266 ("r-stringi" ,r-stringi)
3267 ("r-stringr" ,r-stringr)
3268 ("r-withr" ,r-withr)
3269 ("r-xtable" ,r-xtable)))
3270 (home-page "https://renozao.github.io/pkgmaker")
3271 (synopsis "Package development utilities")
3273 "This package provides some low-level utilities to use for R package
3274 development. It currently provides managers for multiple package specific
3275 options and registries, vignette, unit test and bibtex related utilities.")
3276 (license license:gpl2+)))
3278 (define-public r-registry
3285 (uri (cran-uri "registry" version))
3288 "1k3j6dx350awamr0dwwgkhfs46vsnj4nf08iw5byq0x7n3nkdsnz"))))
3289 (build-system r-build-system)
3290 (home-page "https://cran.r-project.org/web/packages/registry")
3291 (synopsis "Infrastructure for R package registries")
3293 "This package provides a generic infrastructure for creating and using R
3294 package registries.")
3295 (license license:gpl2+)))
3297 (define-public r-rngtools
3304 (uri (cran-uri "rngtools" version))
3307 "097215qcfw6ybllpzmp1532r59h2srvch3aca4z4s6l2rf9w8gvn"))))
3308 (build-system r-build-system)
3310 `(("r-digest" ,r-digest)
3311 ("r-pkgmaker" ,r-pkgmaker)
3312 ("r-stringr" ,r-stringr)))
3313 (home-page "https://renozao.github.io/rngtools")
3314 (synopsis "Utility functions for working with random number generators")
3316 "This package contains a set of functions for working with Random Number
3317 Generators (RNGs). In particular, it defines a generic S4 framework for
3318 getting/setting the current RNG, or RNG data that are embedded into objects
3319 for reproducibility. Notably, convenient default methods greatly facilitate
3320 the way current RNG settings can be changed.")
3321 (license license:gpl3+)))
3323 (define-public r-rtsne
3330 (uri (cran-uri "Rtsne" version))
3333 "0v17vxizrs1msay24xl2bckfajr2c82wpqj07lyssbrq197nwdsn"))))
3334 (properties `((upstream-name . "Rtsne")))
3335 (build-system r-build-system)
3337 `(("r-rcpp" ,r-rcpp)))
3338 (home-page "https://github.com/jkrijthe/Rtsne")
3339 (synopsis "T-distributed stochastic neighbor embedding")
3341 "This package provides an R wrapper around the fast T-distributed
3342 Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
3343 ;; The declared license for this package is BSD-3, but it also includes
3344 ;; code licensed under BSD-4.
3345 (license (list license:bsd-3 license:bsd-4))))
3347 (define-public r-e1071
3354 (uri (cran-uri "e1071" version))
3357 "1zlxz3da216q6v6r4ff60il121xwz7g7m639vzdwglhw3jjh8psw"))))
3358 (build-system r-build-system)
3360 `(("r-class" ,r-class)))
3361 (home-page "https://cran.r-project.org/web/packages/e1071")
3362 (synopsis "Miscellaneous functions for probability theory")
3364 "This package provides functions for latent class analysis, short time
3365 Fourier transform, fuzzy clustering, support vector machines, shortest path
3366 computation, bagged clustering, naive Bayes classifier, and more.")
3367 (license license:gpl2+)))
3369 (define-public r-bigmemory-sri
3371 (name "r-bigmemory-sri")
3376 (uri (cran-uri "bigmemory.sri" version))
3378 (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
3380 `((upstream-name . "bigmemory.sri")))
3381 (build-system r-build-system)
3382 (home-page "https://cran.r-project.org/web/packages/bigmemory.sri")
3383 (synopsis "Shared resource interface for the bigmemory package")
3384 (description "This package provides a shared resource interface for the
3385 bigmemory and synchronicity packages.")
3386 ;; Users can choose either LGPLv3 or ASL2.0.
3387 (license (list license:lgpl3 license:asl2.0))))
3389 (define-public r-synchronicity
3391 (name "r-synchronicity")
3396 (uri (cran-uri "synchronicity" version))
3399 "1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx"))))
3400 (build-system r-build-system)
3403 ("r-bigmemory-sri" ,r-bigmemory-sri)
3405 ("r-uuid" ,r-uuid)))
3406 (home-page "http://www.bigmemory.org")
3407 (synopsis "Boost mutex functionality in R")
3408 (description "This package provides support for synchronization
3409 via mutexes and may eventually support interprocess communication and
3411 ;; Users can choose either LGPLv3 or ASL2.0.
3412 (license (list license:lgpl3 license:asl2.0))))
3414 (define-public r-bigmemory
3416 (name "r-bigmemory")
3421 (uri (cran-uri "bigmemory" version))
3424 "0ycl9dzm3drpyas625h34rir5bnbjlncxlvawfsfmqwcbmwdjdvj"))))
3425 (build-system r-build-system)
3429 ("r-bigmemory-sri" ,r-bigmemory-sri)))
3430 (home-page "http://www.bigmemory.org")
3431 (synopsis "Manage large matrices with shared memory or memory-mapped files")
3432 (description "This package provides methods to create, store, access, and
3433 manipulate large matrices. Matrices are allocated to shared memory and may use
3434 memory-mapped files.")
3435 ;; Users can choose either LGPLv3 or ASL2.0.
3436 (license (list license:lgpl3 license:asl2.0))))
3438 (define-public r-nmf
3445 (uri (cran-uri "NMF" version))
3448 "1qq25n3k5sgh3srlshb3ic6q92s12c1ilqf5cd5anvq6cqfchc1v"))))
3449 (properties `((upstream-name . "NMF")))
3450 (build-system r-build-system)
3452 `(("r-cluster" ,r-cluster)
3453 ("r-bigmemory" ,r-bigmemory) ; suggested
3454 ("r-synchronicity" ,r-synchronicity) ; suggested
3455 ("r-colorspace" ,r-colorspace)
3456 ("r-digest" ,r-digest)
3457 ("r-doparallel" ,r-doparallel)
3458 ("r-foreach" ,r-foreach)
3459 ("r-ggplot2" ,r-ggplot2)
3460 ("r-gridbase" ,r-gridbase)
3461 ("r-pkgmaker" ,r-pkgmaker)
3462 ("r-rcolorbrewer" ,r-rcolorbrewer)
3463 ("r-registry" ,r-registry)
3464 ("r-reshape2" ,r-reshape2)
3465 ("r-rngtools" ,r-rngtools)
3466 ("r-stringr" ,r-stringr)))
3467 (home-page "http://renozao.github.io/NMF")
3468 (synopsis "Algorithms and framework for nonnegative matrix factorization")
3470 "This package provides a framework to perform Non-negative Matrix
3471 Factorization (NMF). The package implements a set of already published
3472 algorithms and seeding methods, and provides a framework to test, develop and
3473 plug new or custom algorithms. Most of the built-in algorithms have been
3474 optimized in C++, and the main interface function provides an easy way of
3475 performing parallel computations on multicore machines.")
3476 (license license:gpl2+)))
3478 (define-public r-r-methodss3
3480 (name "r-r-methodss3")
3484 (uri (cran-uri "R.methodsS3" version))
3487 "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24"))))
3488 (properties `((upstream-name . "R.methodsS3")))
3489 (build-system r-build-system)
3490 (home-page "https://cran.r-project.org/web/packages/R.methodsS3")
3491 (synopsis "S3 methods simplified")
3493 "This package provides methods that simplify the setup of S3 generic
3494 functions and S3 methods. Major effort has been made in making definition of
3495 methods as simple as possible with a minimum of maintenance for package
3496 developers. For example, generic functions are created automatically, if
3497 missing, and naming conflict are automatically solved, if possible. The
3498 method @code{setMethodS3()} is a good start for those who in the future may
3499 want to migrate to S4.")
3500 (license license:lgpl2.1+)))
3502 (define-public r-r-oo
3508 (uri (cran-uri "R.oo" version))
3511 "0k6xwy93fpb2p7bs76lzk52br9rv5xnd9524xj8qyazv1132x1n0"))))
3512 (properties `((upstream-name . "R.oo")))
3513 (build-system r-build-system)
3515 `(("r-r-methodss3" ,r-r-methodss3)))
3516 (home-page "https://github.com/HenrikBengtsson/R.oo")
3517 (synopsis "R object-oriented programming with or without references")
3519 "This package provides methods and classes for object-oriented
3520 programming in R with or without references. Large effort has been made on
3521 making definition of methods as simple as possible with a minimum of
3522 maintenance for package developers.")
3523 (license license:lgpl2.1+)))
3525 (define-public r-r-utils
3531 (uri (cran-uri "R.utils" version))
3534 "1jaarld1jgpzh18kh9g3rlzcrk51vdgn2n1d1y28szzxlz94vifg"))))
3535 (properties `((upstream-name . "R.utils")))
3536 (build-system r-build-system)
3538 `(("r-r-methodss3" ,r-r-methodss3)
3539 ("r-r-oo" ,r-r-oo)))
3540 (home-page "https://github.com/HenrikBengtsson/R.utils")
3541 (synopsis "Various programming utilities")
3543 "This package provides utility functions useful when programming and
3544 developing R packages.")
3545 (license license:lgpl2.1+)))
3547 (define-public r-r-cache
3553 (uri (cran-uri "R.cache" version))
3556 "1hf5cb7xvnca5zlh9245b5g62sgsaxwdhiv7x59yld37cydakm6k"))))
3557 (properties `((upstream-name . "R.cache")))
3558 (build-system r-build-system)
3560 `(("r-digest" ,r-digest)
3561 ("r-r-methodss3" ,r-r-methodss3)
3563 ("r-r-utils" ,r-r-utils)))
3564 (home-page "https://github.com/HenrikBengtsson/R.cache")
3565 (synopsis "Light-weight caching of objects and results")
3567 "This package provides methods for caching or memoization of objects and
3568 results. With this package, any R object can be cached in a key-value storage
3569 where the key can be an arbitrary set of R objects. The cache memory is
3570 persistent (on the file system).")
3571 (license license:lgpl2.1+)))
3573 (define-public r-r-rsp
3579 (uri (cran-uri "R.rsp" version))
3582 "0i01p8jxc4j4zl2v2ykvvpfnm5hv650zj1wi1dh8hq0c98xi2yfr"))))
3583 (properties `((upstream-name . "R.rsp")))
3584 (build-system r-build-system)
3586 `(("r-digest" ,r-digest)
3587 ("r-r-cache" ,r-r-cache)
3588 ("r-r-methodss3" ,r-r-methodss3)
3590 ("r-r-utils" ,r-r-utils)))
3591 (home-page "https://github.com/HenrikBengtsson/R.rsp")
3592 (synopsis "Dynamic generation of scientific reports")
3594 "The RSP markup language provides a powerful markup for controlling the
3595 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
3596 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
3597 to many other literate programming languages, with RSP it is straightforward
3598 to loop over mixtures of code and text sections, e.g. in month-by-month
3599 summaries. RSP has also several preprocessing directives for incorporating
3600 static and dynamic contents of external files (local or online) among other
3601 things. RSP is ideal for self-contained scientific reports and R package
3603 (license license:lgpl2.1+)))
3605 (define-public r-mvtnorm
3611 (uri (cran-uri "mvtnorm" version))
3614 "04md0wmqgif24g0a4hx19ifn4kk8nx10986vf2d9vascig6ikpri"))))
3615 (build-system r-build-system)
3617 `(("gfortran" ,gfortran)))
3618 (home-page "http://mvtnorm.R-forge.R-project.org")
3619 (synopsis "Package for multivariate normal and t-distributions")
3620 (description "This package can compute multivariate normal and
3621 t-probabilities, quantiles, random deviates and densities.")
3622 (license license:gpl2)))
3624 (define-public r-matrixstats
3626 (name "r-matrixstats")
3630 (uri (cran-uri "matrixStats" version))
3633 "0vx00ldsg2zvdrjn49jxczk2c9iaabgvzgpdka5j02ihh7hv83cg"))))
3634 (properties `((upstream-name . "matrixStats")))
3635 (build-system r-build-system)
3637 `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
3638 (home-page "https://github.com/HenrikBengtsson/matrixStats")
3639 (synopsis "Methods applying to vectors and matrix rows and columns")
3641 "This package provides methods operating on rows and columns of matrices,
3642 e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
3643 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
3644 @code{weightedMedians()}. All methods have been optimized for speed and
3646 (license license:artistic2.0)))
3648 (define-public r-viridis
3654 (uri (cran-uri "viridis" version))
3657 "060rf1jn29dq53y3nhb0hykvcap6rqsk04rq544ypiiqb18ngwnx"))))
3658 (build-system r-build-system)
3660 `(("r-ggplot2" ,r-ggplot2)
3661 ("r-gridextra" ,r-gridextra)
3662 ("r-viridislite" ,r-viridislite)))
3663 (home-page "https://github.com/sjmgarnier/viridis")
3664 (synopsis "Matplotlib default color map")
3666 "This package is a port of the new @url{matplotlib,
3667 http://matplotlib.org/} color maps (@code{viridis}--the default--,
3668 @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
3669 designed in such a way that they will analytically be perfectly
3670 perceptually-uniform, both in regular form and also when converted to
3671 black-and-white. They are also designed to be perceived by readers with the
3672 most common form of color blindness.")
3673 (license license:x11)))
3675 (define-public r-viridislite
3677 (name "r-viridislite")
3682 (uri (cran-uri "viridisLite" version))
3685 "1by2l05f0yabwvv64lhnv7bbhx0w683s3wr9j2xda920ghpa23kq"))))
3686 (properties `((upstream-name . "viridisLite")))
3687 (build-system r-build-system)
3688 (home-page "https://github.com/sjmgarnier/viridisLite")
3689 (synopsis "Default color maps from matplotlib")
3691 "This package is a port of the new @code{matplotlib} color maps
3692 (@code{viridis}, @code{magma}, @code{plasma} and @code{inferno}) to R.
3693 matplotlib is a popular plotting library for Python. These color maps are
3694 designed in such a way that they will analytically be perfectly
3695 perceptually-uniform, both in regular form and also when converted to
3696 black-and-white. They are also designed to be perceived by readers with the
3697 most common form of color blindness. This is the @code{lite} version of the
3698 more complete @code{viridis} package.")
3699 (license license:expat)))
3701 (define-public r-tidyselect
3703 (name "r-tidyselect")
3708 (uri (cran-uri "tidyselect" version))
3711 "0x3cp36byhfjajikr1lwffjm85ayw3bcs7d7kb0cydgs61ifiqjw"))))
3712 (build-system r-build-system)
3714 `(("r-glue" ,r-glue)
3715 ("r-purrr" ,r-purrr)
3717 ("r-rlang" ,r-rlang)))
3718 (home-page "https://cran.r-project.org/web/packages/tidyselect")
3719 (synopsis "Select from a set of strings")
3721 "This package provides a backend for the selecting functions of the
3722 tidyverse. It makes it easy to implement select-like functions in your own
3723 packages in a way that is consistent with other tidyverse interfaces for
3725 (license license:gpl3)))
3727 (define-public r-tidyr
3734 (uri (cran-uri "tidyr" version))
3737 "0dyc4b03wi65bk7j0ma0y188syh37h57wgxji82i0h8j6pn593x1"))))
3738 (build-system r-build-system)
3740 `(("r-dplyr" ,r-dplyr)
3741 ("r-magrittr" ,r-magrittr)
3743 ("r-purrr" ,r-purrr)
3744 ("r-rlang" ,r-rlang)
3745 ("r-tidyselect" ,r-tidyselect)
3747 ("r-stringi" ,r-stringi)
3748 ("r-tibble" ,r-tibble)))
3749 (home-page "https://github.com/hadley/tidyr")
3750 (synopsis "Tidy data with `spread()` and `gather()` functions")
3752 "tidyr is a reframing of the reshape2 package designed to accompany the
3753 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
3754 a solid pipeline for data analysis. It is designed specifically for tidying
3755 data, not the general reshaping that reshape2 does, or the general aggregation
3756 that reshape did. In particular, built-in methods only work for data frames,
3757 and tidyr provides no margins or aggregation.")
3758 (license license:expat)))
3760 (define-public r-hexbin
3767 (uri (cran-uri "hexbin" version))
3770 "0lpfl0015lg5x7lvv9dr302bca22c7fs91pnd896ypgpzqg7pm26"))))
3771 (build-system r-build-system)
3773 `(("r-lattice" ,r-lattice)))
3775 `(("gfortran" ,gfortran)))
3776 (home-page "https://github.com/edzer/hexbin")
3777 (synopsis "Hexagonal binning routines")
3779 "This package provides binning and plotting functions for hexagonal bins.
3780 It uses and relies on grid graphics and formal (S4) classes and methods.")
3781 (license license:gpl2+)))
3783 (define-public r-purrr
3790 (uri (cran-uri "purrr" version))
3793 "0ccs78a2ylr60f3z0f7iywi8h1pwr8mz4ga78bs4pwgnwkclvir7"))))
3794 (build-system r-build-system)
3796 `(("r-magrittr" ,r-magrittr)
3797 ("r-rlang" ,r-rlang)))
3798 (home-page "https://github.com/hadley/purrr")
3799 (synopsis "Functional programming tools")
3801 "This package completes R's functional programming tools with missing
3802 features present in other programming languages.")
3803 (license license:gpl3+)))
3805 (define-public r-plotly
3811 (uri (cran-uri "plotly" version))
3814 "19p8pa03q9mw5vaan7r56xgd13d90ssiz0flbrkvpfrir2105ybq"))))
3815 (build-system r-build-system)
3817 `(("r-base64enc" ,r-base64enc)
3818 ("r-crosstalk" ,r-crosstalk)
3819 ("r-digest" ,r-digest)
3820 ("r-data-table" ,r-data-table)
3821 ("r-dplyr" ,r-dplyr)
3822 ("r-ggplot2" ,r-ggplot2)
3823 ("r-hexbin" ,r-hexbin)
3824 ("r-htmltools" ,r-htmltools)
3825 ("r-htmlwidgets" ,r-htmlwidgets)
3827 ("r-jsonlite" ,r-jsonlite)
3828 ("r-lazyeval" ,r-lazyeval)
3829 ("r-magrittr" ,r-magrittr)
3830 ("r-promises" ,r-promises)
3831 ("r-purrr" ,r-purrr)
3832 ("r-rcolorbrewer" ,r-rcolorbrewer)
3833 ("r-rlang" ,r-rlang)
3834 ("r-scales" ,r-scales)
3835 ("r-tibble" ,r-tibble)
3836 ("r-tidyr" ,r-tidyr)
3837 ("r-viridislite" ,r-viridislite)))
3838 (home-page "https://plot.ly/r")
3839 (synopsis "Create interactive web graphics")
3841 "This package enables the translation of ggplot2 graphs to an interactive
3842 web-based version and/or the creation of custom web-based visualizations
3843 directly from R. Once uploaded to a plotly account, plotly graphs (and the
3844 data behind them) can be viewed and modified in a web browser.")
3845 (license license:x11)))
3847 (define-public r-biased-urn
3849 (name "r-biased-urn")
3854 (uri (cran-uri "BiasedUrn" version))
3857 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
3858 (properties `((upstream-name . "BiasedUrn")))
3859 (build-system r-build-system)
3860 (home-page "http://www.agner.org/random/")
3861 (synopsis "Biased urn model distributions")
3863 "This package provides statistical models of biased sampling in the form
3864 of univariate and multivariate noncentral hypergeometric distributions,
3865 including Wallenius' noncentral hypergeometric distribution and Fisher's
3866 noncentral hypergeometric distribution (also called extended hypergeometric
3868 (license license:gpl3+)))
3870 (define-public r-rematch
3877 (uri (cran-uri "rematch" version))
3880 "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4"))))
3881 (build-system r-build-system)
3882 (home-page "https://github.com/MangoTheCat/rematch")
3883 (synopsis "Match regular expressions with a nicer API")
3885 "This package provides a small wrapper on @code{regexpr} to extract the
3886 matches and captured groups from the match of a regular expression to a
3888 (license license:expat)))
3890 (define-public r-cellranger
3892 (name "r-cellranger")
3897 (uri (cran-uri "cellranger" version))
3900 "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x"))))
3901 (build-system r-build-system)
3903 `(("r-rematch" ,r-rematch)
3904 ("r-tibble" ,r-tibble)))
3905 (home-page "https://github.com/rsheets/cellranger")
3906 (synopsis "Translate spreadsheet cell ranges to rows and columns")
3908 "This package provides helper functions to work with spreadsheets and the
3909 @code{A1:D10} style of cell range specification.")
3910 (license license:expat)))
3912 (define-public r-googlesheets
3914 (name "r-googlesheets")
3919 (uri (cran-uri "googlesheets" version))
3922 "11q07nxys72wkxx9mawmjyf20gvwvrb7h3gpa73h6lgh2vgrwnv8"))))
3923 (build-system r-build-system)
3925 `(("r-cellranger" ,r-cellranger)
3926 ("r-dplyr" ,r-dplyr)
3928 ("r-jsonlite" ,r-jsonlite)
3929 ("r-purrr" ,r-purrr)
3930 ("r-readr" ,r-readr)
3931 ("r-stringr" ,r-stringr)
3932 ("r-tibble" ,r-tibble)
3933 ("r-tidyr" ,r-tidyr)
3934 ("r-xml2" ,r-xml2)))
3935 (home-page "https://github.com/jennybc/googlesheets")
3936 (synopsis "Manage Google spreadsheets from R")
3937 (description "This package provides tools to interact with Google Sheets
3939 (license license:expat)))
3941 (define-public r-spams
3944 (version "2.6-2017-03-22")
3948 ;; Use the ‘Latest version’ link for a stable URI across releases.
3949 (uri (string-append "https://gforge.inria.fr/frs/download.php/"
3950 "latestfile/4531/spams-R-v" version ".tar.gz"))
3953 "13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx"))))
3954 (build-system r-build-system)
3957 (modify-phases %standard-phases
3958 (add-after 'unpack 'chdir
3959 (lambda _ (chdir "spams") #t))
3960 ;; Don't tune for the building machine.
3961 (add-after 'chdir 'no-mtune
3963 (substitute* "src/Makevars"
3964 (("-mtune=native") ""))
3967 `(("r-lattice" ,r-lattice)
3968 ("r-matrix" ,r-matrix)))
3969 (home-page "http://spams-devel.gforge.inria.fr")
3970 (synopsis "Toolbox for solving sparse estimation problems")
3971 (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
3972 for solving various sparse estimation problems. It includes tools for the
3976 @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
3977 component analysis} (PCA), ...)
3978 @item Solving sparse decomposition problems with LARS, coordinate descent,
3979 OMP, SOMP, proximal methods
3980 @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
3981 group lasso, tree-structured regularization, structured sparsity with
3982 overlapping groups,...).
3984 (license license:gpl3+)))
3986 (define-public r-base64
3993 (uri (cran-uri "base64" version))
3996 "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf"))))
3997 (build-system r-build-system)
3999 `(("r-openssl" ,r-openssl)))
4000 (home-page "https://cran.r-project.org/web/packages/base64")
4001 (synopsis "Base64 encoder and decoder")
4003 "This package is a compatibility wrapper to replace the orphaned package
4004 by Romain Francois. New applications should use the openssl or base64enc
4006 (license license:expat)))
4008 (define-public r-hmisc
4015 (uri (cran-uri "Hmisc" version))
4018 "1n8i2jhc308hd6bvys9cd7nrz7pwjszs03r5bwlh1pc869ki95ly"))))
4019 (properties `((upstream-name . "Hmisc")))
4020 (build-system r-build-system)
4022 `(("gfortran" ,gfortran)))
4024 `(("r-acepack" ,r-acepack)
4025 ("r-base64enc" ,r-base64enc)
4026 ("r-cluster" ,r-cluster)
4027 ("r-data-table" ,r-data-table)
4028 ("r-foreign" ,r-foreign)
4029 ("r-formula" ,r-formula)
4030 ("r-ggplot2" ,r-ggplot2)
4031 ("r-gridextra" ,r-gridextra)
4032 ("r-gtable" ,r-gtable)
4033 ("r-lattice" ,r-lattice)
4034 ("r-latticeextra" ,r-latticeextra)
4035 ("r-htmltable" ,r-htmltable)
4036 ("r-htmltools" ,r-htmltools)
4038 ("r-rpart" ,r-rpart)
4039 ("r-survival" ,r-survival)
4040 ("r-viridis" ,r-viridis)))
4041 (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
4042 (synopsis "Miscellaneous data analysis and graphics functions")
4044 "This package contains many functions useful for data analysis,
4045 high-level graphics, utility operations, functions for computing sample size
4046 and power, importing and annotating datasets, imputing missing values,
4047 advanced table making, variable clustering, character string manipulation,
4048 conversion of R objects to LaTeX code, and recoding variables.")
4049 (license license:gpl2+)))
4051 (define-public r-runit
4058 (uri (cran-uri "RUnit" version))
4061 "1wc1gwb7yw7phf8b0gkig6c23klya3ax11c6i4s0f049k42r78r3"))))
4062 (properties `((upstream-name . "RUnit")))
4063 (build-system r-build-system)
4064 (home-page "https://cran.r-project.org/web/packages/RUnit")
4065 (synopsis "R unit test framework")
4067 "This package provides R functions implementing a standard unit testing
4068 framework, with additional code inspection and report generation tools.")
4069 (license license:gpl2+)))
4071 (define-public r-dynamictreecut
4073 (name "r-dynamictreecut")
4078 (uri (cran-uri "dynamicTreeCut" version))
4081 "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"))))
4082 (properties `((upstream-name . "dynamicTreeCut")))
4083 (build-system r-build-system)
4085 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
4086 (synopsis "Detect clusters in hierarchical clustering dendrograms")
4088 "This package contains methods for the detection of clusters in
4089 hierarchical clustering dendrograms.")
4090 (license license:gpl2+)))
4092 (define-public r-preprocesscore
4094 (name "r-preprocesscore")
4099 (uri (bioconductor-uri "preprocessCore" version))
4102 "0ijyjqi8mxxf350dhvgp36swwww5ag7ac9a6r6ymihc5syjr4w4j"))))
4104 `((upstream-name . "preprocessCore")))
4105 (build-system r-build-system)
4106 (home-page "https://github.com/bmbolstad/preprocessCore")
4107 (synopsis "Collection of pre-processing functions")
4109 "This package provides a library of core pre-processing and normalization
4111 (license license:lgpl2.0+)))
4113 (define-public r-fastcluster
4115 (name "r-fastcluster")
4120 (uri (cran-uri "fastcluster" version))
4123 "01a2xnhhvv1swd4g8p4lzyn7ww7kg49jlnzc7kfz60jqjzpisrpk"))))
4124 (build-system r-build-system)
4125 (home-page "http://danifold.net/fastcluster.html")
4126 (synopsis "Fast hierarchical clustering routines")
4128 "This package implements fast hierarchical, agglomerative clustering
4129 routines. Part of the functionality is designed as drop-in replacement for
4130 existing routines: @code{linkage()} in the SciPy package
4131 @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package,
4132 and the @code{flashClust} package. It provides the same functionality with
4133 the benefit of a much faster implementation. Moreover, there are
4134 memory-saving routines for clustering of vector data, which go beyond what the
4135 existing packages provide.")
4136 (license license:bsd-2)))
4138 (define-public r-sfsmisc
4145 (uri (cran-uri "sfsmisc" version))
4148 "1y25nnw09qfm66523w1z4q766lv15a6ykvsq30r154n7m7aggvsq"))))
4149 (build-system r-build-system)
4150 (home-page "https://cran.r-project.org/web/packages/sfsmisc")
4151 (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
4153 "This package provides useful utilities from Seminar fuer Statistik ETH
4154 Zurich, including many that are related to graphics.")
4155 (license license:gpl2+)))
4157 (define-public r-gtools
4164 (uri (cran-uri "gtools" version))
4167 "0f5syk1qq6cjq6hwymvkiyhzwa389z94722v881ipbfqkd2q8505"))))
4168 (build-system r-build-system)
4171 (modify-phases %standard-phases
4172 (add-after 'unpack 'make-deterministic
4174 (substitute* "R/checkReverseDependencies.R"
4175 (("tempdir\\(\\)") "\"/tmp\""))
4177 (home-page "https://cran.r-project.org/web/packages/gtools")
4178 (synopsis "Various R programming tools")
4180 "This package contains a collection of various functions to assist in R
4181 programming, such as tools to assist in developing, updating, and maintaining
4182 R and R packages, calculating the logit and inverse logit transformations,
4183 tests for whether a value is missing, empty or contains only @code{NA} and
4184 @code{NULL} values, and many more.")
4185 (license license:gpl2)))
4187 (define-public r-gdata
4194 (uri (cran-uri "gdata" version))
4197 "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b"))))
4198 (build-system r-build-system)
4202 `(("r-gtools" ,r-gtools)))
4203 (home-page "https://cran.r-project.org/web/packages/gdata")
4204 (synopsis "Various R programming tools for data manipulation")
4206 "This package provides various R programming tools for data manipulation,
4210 @item medical unit conversions
4211 @item combining objects
4212 @item character vector operations
4213 @item factor manipulation
4214 @item obtaining information about R objects
4215 @item manipulating MS-Excel formatted files
4216 @item generating fixed-width format files
4217 @item extricating components of date and time objects
4218 @item operations on columns of data frames
4219 @item matrix operations
4220 @item operations on vectors and data frames
4221 @item value of last evaluated expression
4222 @item wrapper for @code{sample} that ensures consistent behavior for
4223 both scalar and vector arguments
4225 (license license:gpl2+)))
4227 (define-public r-gplots
4234 (uri (cran-uri "gplots" version))
4237 "033plcfs9w8pmn84n24mdhiixdirc2a7pz6dvm61fpd20gwh7cbx"))))
4238 (build-system r-build-system)
4240 `(("r-catools" ,r-catools)
4241 ("r-gdata" ,r-gdata)
4242 ("r-gtools" ,r-gtools)
4243 ("r-kernsmooth" ,r-kernsmooth)))
4244 (home-page "https://cran.r-project.org/web/packages/gplots")
4245 (synopsis "Various R programming tools for plotting data")
4247 "This package provides various R programming tools for plotting data,
4251 @item calculating and plotting locally smoothed summary function
4252 @item enhanced versions of standard plots
4253 @item manipulating colors
4254 @item calculating and plotting two-dimensional data summaries
4255 @item enhanced regression diagnostic plots
4256 @item formula-enabled interface to @code{stats::lowess} function
4257 @item displaying textual data in plots
4259 @item plotting \"Venn\" diagrams
4260 @item displaying Open-Office style plots
4261 @item plotting multiple data on same region, with separate axes
4262 @item plotting means and confidence intervals
4263 @item spacing points in an x-y plot so they don't overlap
4265 (license license:gpl2+)))
4267 (define-public r-rocr
4274 (uri (cran-uri "ROCR" version))
4277 "1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7"))))
4278 (properties `((upstream-name . "ROCR")))
4279 (build-system r-build-system)
4281 `(("r-gplots" ,r-gplots)))
4282 (home-page "http://rocr.bioinf.mpi-sb.mpg.de/")
4283 (synopsis "Visualizing the performance of scoring classifiers")
4285 "ROCR is a flexible tool for creating cutoff-parameterized 2D performance
4286 curves by freely combining two from over 25 performance measures (new
4287 performance measures can be added using a standard interface). Curves from
4288 different cross-validation or bootstrapping runs can be averaged by different
4289 methods, and standard deviations, standard errors or box plots can be used to
4290 visualize the variability across the runs. The parameterization can be
4291 visualized by printing cutoff values at the corresponding curve positions, or
4292 by coloring the curve according to cutoff. All components of a performance
4293 plot can be quickly adjusted using a flexible parameter dispatching
4295 (license license:gpl2+)))
4297 (define-public r-zoo
4303 (uri (cran-uri "zoo" version))
4306 "09p8gmd5ifz80ahnhiianarsr5xx3nz76jzp90d7v3fjffcrcww7"))))
4307 (build-system r-build-system)
4309 `(("r-lattice" ,r-lattice)))
4310 (home-page "http://zoo.R-Forge.R-project.org/")
4311 (synopsis "S3 infrastructure for regular and irregular time series")
4312 (description "This package contains an S3 class with methods for totally
4313 ordered indexed observations. It is particularly aimed at irregular time
4314 series of numeric vectors/matrices and factors.")
4315 (license license:gpl2+)))
4317 (define-public r-ztable
4323 (uri (cran-uri "ztable" version))
4326 "0g7khk5ifsdh9p31wlwh2l5mn1hzxzpv6qcn1wh34vsfjdmijjwy"))))
4327 (build-system r-build-system)
4329 `(("r-flextable" ,r-flextable)
4330 ("r-magrittr" ,r-magrittr)
4331 ("r-moonbook" ,r-moonbook)
4332 ("r-officer" ,r-officer)
4333 ("r-rcolorbrewer" ,r-rcolorbrewer)
4334 ("r-scales" ,r-scales)
4335 ("r-stringr" ,r-stringr)))
4336 (home-page "https://cran.r-project.org/web/packages/ztable")
4337 (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
4339 "This package provides functions to make zebra-striped tables (tables
4340 with alternating row colors) in LaTeX and HTML formats easily from
4341 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
4342 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
4343 @code{cbind.mytable} objects.")
4344 (license license:gpl2+)))
4346 (define-public r-vipor
4352 (uri (cran-uri "vipor" version))
4355 "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx"))))
4356 (build-system r-build-system)
4357 (home-page "https://cran.r-project.org/web/packages/vipor")
4358 (synopsis "Plot categorical data using noise and density estimates")
4360 "This package provides tools to generate a violin point plot, a
4361 combination of a violin/histogram plot and a scatter plot by offsetting points
4362 within a category based on their density using quasirandom noise.")
4363 (license license:gpl2+)))
4365 (define-public r-beeswarm
4371 (uri (cran-uri "beeswarm" version))
4374 "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
4375 (build-system r-build-system)
4376 (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/")
4377 (synopsis "Implementation of bee swarm plots")
4379 "This package provides an implementation of bee swarm plots. The bee
4380 swarm plot is a one-dimensional scatter plot like stripchart, but with
4381 closely-packed, non-overlapping points.")
4382 (license license:artistic2.0)))
4384 (define-public r-sourcetools
4386 (name "r-sourcetools")
4391 (uri (cran-uri "sourcetools" version))
4394 "1jnjir0q2dj724f1mjm6p5h77yzyx6xcqy9r2g7gmcxkxw349627"))))
4395 (build-system r-build-system)
4396 (home-page "https://cran.r-project.org/web/packages/sourcetools")
4397 (synopsis "Tools for reading, tokenizing and parsing R code")
4399 "The sourcetools package provides both an R and C++ interface for the
4400 tokenization of R code, and helpers for interacting with the tokenized
4401 representation of R code.")
4402 (license license:expat)))
4404 (define-public r-ggbeeswarm
4406 (name "r-ggbeeswarm")
4410 (uri (cran-uri "ggbeeswarm" version))
4413 "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v"))))
4414 (build-system r-build-system)
4416 `(("r-beeswarm" ,r-beeswarm)
4417 ("r-ggplot2" ,r-ggplot2)
4418 ("r-vipor" ,r-vipor)))
4419 (home-page "https://github.com/eclarke/ggbeeswarm")
4420 (synopsis "Categorical scatter (violin point) plots")
4422 "This package provides two methods of plotting categorical scatter plots
4423 such that the arrangement of points within a category reflects the density of
4424 data at that region, and avoids over-plotting.")
4425 (license license:gpl2+)))
4427 (define-public r-ggthemes
4433 (uri (cran-uri "ggthemes" version))
4436 "1a6r384v72hb91qkg9rz2m7s3qskbl9haxynf2vzz6v1ak9xd4c5"))))
4437 (build-system r-build-system)
4439 `(("r-ggplot2" ,r-ggplot2)
4440 ("r-purrr" ,r-purrr)
4441 ("r-scales" ,r-scales)
4442 ("r-stringr" ,r-stringr)
4443 ("r-tibble" ,r-tibble)))
4444 (home-page "https://cran.rstudio.com/web/packages/ggthemes")
4445 (synopsis "Extra themes, scales and geoms for @code{ggplot2}")
4446 (description "This package provides extra themes and scales for
4447 @code{ggplot2} that replicate the look of plots by Edward Tufte and
4448 Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The
4449 Wall Street Journal, among others. This package also provides
4450 @code{geoms} for Tufte's box plot and range frame.")
4451 (license license:gpl2)))
4453 (define-public r-statmod
4459 (uri (cran-uri "statmod" version))
4462 "07v4x8af60alcw6vbiwf5fp25bhra61kvxz9kqx64lszm0i1fb4x"))))
4463 (build-system r-build-system)
4464 (home-page "https://cran.r-project.org/web/packages/statmod")
4466 `(("gfortran" ,gfortran)))
4467 (synopsis "Statistical modeling")
4469 "This package provides a collection of algorithms and functions to aid
4470 statistical modeling. It includes growth curve comparisons, limiting dilution
4471 analysis (aka ELDA), mixed linear models, heteroscedastic regression,
4472 inverse-Gaussian probability calculations, Gauss quadrature and a secure
4473 convergence algorithm for nonlinear models. It also includes advanced
4474 generalized linear model functions that implement secure convergence,
4475 dispersion modeling and Tweedie power-law families.")
4476 ;; Statmod is distributed under either license
4477 (license (list license:gpl2 license:gpl3))))
4479 (define-public r-rann
4485 (uri (cran-uri "RANN" version))
4488 "10kid40w9w7vkz2hpcfkdpxr4afxzms5dzvfwr0sl5xynzgw76dj"))))
4490 `((upstream-name . "RANN")))
4491 (build-system r-build-system)
4492 (home-page "https://github.com/jefferis/RANN")
4493 (synopsis "Fast nearest neighbour search")
4495 "This package finds the k nearest neighbours for every point in a given
4496 dataset in O(N log N) time using Arya and Mount's ANN library. Provides
4497 approximate, exact searches, fixed radius searches, bd and kb trees.")
4498 (license license:gpl3+)))
4500 (define-public r-fivethirtyeight
4502 (name "r-fivethirtyeight")
4507 (uri (string-append "https://mran.microsoft.com/src/contrib/"
4508 "fivethirtyeight_" version ".tar.gz"))
4511 "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl"))))
4512 (build-system r-build-system)
4514 `(("r-knitr" ,r-knitr)
4515 ("r-rmarkdown" ,r-rmarkdown)
4516 ("r-dplyr" ,r-dplyr)
4517 ("r-readr" ,r-readr)
4518 ("r-ggplot2" ,r-ggplot2)
4519 ("r-magrittr" ,r-magrittr)
4520 ("r-stringr" ,r-stringr)))
4521 (home-page "https://mran.microsoft.com/package/fivethirtyeight/")
4522 (synopsis "Data and code behind the stories at FiveThirtyEight")
4523 (description "This R package provides access to the code and data sets
4524 published by the statistics blog FiveThirtyEight.")
4525 (license license:expat)))
4527 (define-public r-compquadform
4529 (name "r-compquadform")
4534 (uri (cran-uri "CompQuadForm" version))
4537 "1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4"))))
4538 (properties `((upstream-name . "CompQuadForm")))
4539 (build-system r-build-system)
4540 (home-page "https://cran.r-project.org/web/packages/CompQuadForm")
4541 (synopsis "Distribution function of quadratic forms in normal variables")
4543 "This package provides functions to compute the distribution function of
4544 quadratic forms in normal variables using Imhof's method, Davies's algorithm,
4545 Farebrother's algorithm or Liu et al.'s algorithm.")
4546 (license license:gpl2+)))
4548 (define-public r-cowplot
4555 (uri (cran-uri "cowplot" version))
4558 "0yvalwalvyddyqk0q66y8361nxlh2cvp3ssazax9g5q89lghjmzv"))))
4559 (build-system r-build-system)
4561 `(("r-ggplot2" ,r-ggplot2)
4562 ("r-gtable" ,r-gtable)
4564 ("r-scales" ,r-scales)))
4565 (home-page "https://github.com/wilkelab/cowplot")
4566 (synopsis "Streamlined plot theme and plot annotations for ggplot2")
4568 "This package provides some helpful extensions and modifications to the
4569 ggplot2 package to combine multiple ggplot2 plots into one and label them with
4570 letters, as is often required for scientific publications.")
4571 (license license:gpl2)))
4573 (define-public r-mixtools
4580 (uri (cran-uri "mixtools" version))
4583 "13wdm0xs5bakhpa8ypg6lvhjaqkxyabwz4glxdwn0jwdvkcdhgsl"))))
4584 (build-system r-build-system)
4586 `(("r-mass" ,r-mass)
4587 ("r-segmented" ,r-segmented)
4588 ("r-survival" ,r-survival)))
4589 (home-page "https://cran.r-project.org/web/packages/mixtools")
4590 (synopsis "Tools for analyzing finite mixture models")
4592 "This package provides a collection of R functions for analyzing finite
4594 (license license:gpl2+)))
4596 (define-public r-lars
4603 (uri (cran-uri "lars" version))
4606 "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
4607 (build-system r-build-system)
4609 `(("gfortran" ,gfortran)))
4610 (home-page "http://www-stat.stanford.edu/~hastie/Papers/#LARS")
4611 (synopsis "Least angle regression software")
4613 "Least Angle Regression (\"LAR\") is a model selection algorithm; a
4614 useful and less greedy version of traditional forward selection methods. A
4615 simple modification of the LAR algorithm implements Tibshirani's Lasso; the
4616 Lasso modification of LARS calculates the entire Lasso path of coefficients
4617 for a given problem at the cost of a single least squares fit. Another LARS
4618 modification efficiently implements epsilon Forward Stagewise linear
4620 (license license:gpl2)))
4622 (define-public r-fastica
4629 (uri (cran-uri "fastICA" version))
4632 "108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg"))))
4633 (properties `((upstream-name . "fastICA")))
4634 (build-system r-build-system)
4635 (home-page "https://cran.r-project.org/web/packages/fastICA")
4636 (synopsis "FastICA algorithms to perform ICA and projection pursuit")
4638 "This package provides an implementation of the FastICA algorithm to
4639 perform @dfn{independent component analysis} (ICA) and projection pursuit.")
4641 (license license:gpl3+)))
4643 (define-public r-randomforest
4645 (name "r-randomforest")
4650 (uri (cran-uri "randomForest" version))
4653 "0kbmm0l42fc2d1rdq0l7k09d34kd87q4lx651ffsic4y84h8kf7l"))))
4654 (properties `((upstream-name . "randomForest")))
4655 (build-system r-build-system)
4656 (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
4658 `(("gfortran" ,gfortran)))
4659 (synopsis "Breiman and Cutler's random forests for classification and regression")
4661 "This package provides the Breiman and Cutler's random forests algorithm, based on a
4662 forest of trees using random inputs, for classification and regression.")
4663 (license license:gpl2+)))
4665 (define-public r-diptest
4672 (uri (cran-uri "diptest" version))
4675 "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
4676 (build-system r-build-system)
4677 (home-page "https://cran.r-project.org/web/packages/diptest")
4678 (synopsis "Hartigan's dip test statistic for unimodality")
4680 "This package computes Hartigan's dip test statistic for unimodality,
4681 multimodality and provides a test with simulation based p-values, where the
4682 original public code has been corrected.")
4683 (license license:gpl2+)))
4685 (define-public r-modeltools
4687 (name "r-modeltools")
4692 (uri (cran-uri "modeltools" version))
4695 "1s9lmkac3rl0nknf4wizfhg7ryq7c8yvvyc4z619238br27hhsi5"))))
4696 (build-system r-build-system)
4697 (home-page "https://cran.r-project.org/web/packages/modeltools")
4698 (synopsis "Tools and classes for statistical models")
4700 "This package provides a collection of tools to deal with statistical
4701 models. The functionality is experimental and the user interface is likely
4702 to change in the future.")
4703 (license license:gpl2)))
4705 (define-public r-flexmix
4712 (uri (cran-uri "flexmix" version))
4715 "0hrz2axp2c9548b1r0bmrl57219nn030qndb83a8garkzq5lqi5s"))))
4716 (build-system r-build-system)
4718 `(("r-lattice" ,r-lattice)
4719 ("r-modeltools" ,r-modeltools)
4720 ("r-nnet" ,r-nnet)))
4721 (home-page "https://cran.r-project.org/web/packages/flexmix")
4722 (synopsis "Flexible mixture modeling")
4724 "This package implements a general framework for finite mixtures of
4725 regression models using the EM algorithm. FlexMix provides the E-step and
4726 all data handling, while the M-step can be supplied by the user to easily
4727 define new models. Existing drivers implement mixtures of standard linear
4728 models, generalized linear models and model-based clustering.")
4729 (license license:gpl2+)))
4731 (define-public r-mclust
4738 (uri (cran-uri "mclust" version))
4741 "18x5ych9zi3y87rxi4pf6f23sl2918dp9xxpw1pqa7p7drw817p6"))))
4742 (build-system r-build-system)
4744 `(("gfortran" ,gfortran)))
4745 (home-page "http://www.stat.washington.edu/mclust/")
4746 (synopsis "Gaussian mixture modelling for model-based clustering etc.")
4748 "This package provides Gaussian finite mixture models fitted via EM
4749 algorithm for model-based clustering, classification, and density estimation,
4750 including Bayesian regularization, dimension reduction for visualisation,
4751 and resampling-based inference.")
4752 (license license:gpl2+)))
4754 (define-public r-prabclus
4761 (uri (cran-uri "prabclus" version))
4764 "0h2nml8ri27mhfs2p6ngb6kfd6lyq30sc6813yybpskkrb6gs1pb"))))
4765 (build-system r-build-system)
4767 `(("r-mass" ,r-mass)
4768 ("r-mclust" ,r-mclust)))
4769 (home-page "https://cran.r-project.org/web/packages/prabclus")
4770 (synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
4772 "This package provides distance-based parametric bootstrap tests for
4773 clustering with spatial neighborhood information. It implements some distance
4774 measures, clustering of presence-absence, abundance and multilocus genetical
4775 data for species delimitation, nearest neighbor based noise detection.")
4776 (license license:gpl2+)))
4778 (define-public r-deoptimr
4785 (uri (cran-uri "DEoptimR" version))
4788 "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
4789 (properties `((upstream-name . "DEoptimR")))
4790 (build-system r-build-system)
4791 (home-page "https://cran.r-project.org/web/packages/DEoptimR")
4792 (synopsis "Differential evolution optimization in pure R")
4794 "This package provides a differential evolution (DE) stochastic
4795 algorithms for global optimization of problems with and without constraints.
4796 The aim is to curate a collection of its state-of-the-art variants that (1) do
4797 not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
4798 can be efficiently implemented directly in the R language.")
4799 (license license:gpl2+)))
4801 (define-public r-robustbase
4803 (name "r-robustbase")
4808 (uri (cran-uri "robustbase" version))
4811 "1q56y0iqp7qhavm4xnpzhs64q7l893y7yiq3b20fllpghka077pa"))))
4812 (build-system r-build-system)
4814 `(("gfortran" ,gfortran)))
4816 `(("r-deoptimr" ,r-deoptimr)))
4817 (home-page "http://robustbase.r-forge.r-project.org/")
4818 (synopsis "Basic robust statistics")
4820 "This packages allows to analyze data with robust methods such as
4821 regression methodology including model selections and multivariate statistics.")
4822 (license license:gpl2+)))
4824 (define-public r-pcapp
4831 (uri (cran-uri "pcaPP" version))
4834 "1z2kdf9gfp965xbcd4rg6vf20d1bl443na0qjkpq7gmzpaq6cifa"))))
4835 (properties `((upstream-name . "pcaPP")))
4836 (build-system r-build-system)
4838 `(("r-mvtnorm" ,r-mvtnorm)))
4839 (home-page "https://cran.r-project.org/web/packages/pcaPP")
4840 (synopsis "Robust PCA by projection pursuit")
4842 "This package provides functions for robust @dfn{principal component
4843 analysis} (PCA) by projection pursuit.")
4844 (license license:gpl3+)))
4846 (define-public r-rrcov
4853 (uri (cran-uri "rrcov" version))
4856 "14zjyqcdiqx6js99nx5s8hmyx564ixy2d8s6i7wa50xmx368rl6b"))))
4857 (build-system r-build-system)
4859 `(("r-cluster" ,r-cluster)
4860 ("r-lattice" ,r-lattice)
4861 ("r-mvtnorm" ,r-mvtnorm)
4862 ("r-pcapp" ,r-pcapp)
4863 ("r-robustbase" ,r-robustbase)))
4865 `(("gfortran" ,gfortran)))
4866 (home-page "https://cran.r-project.org/web/packages/rrcov")
4867 (synopsis "Scalable robust estimators with high breakdown Point")
4869 "This package provides an implementation of robust location and scatter
4870 estimation and robust multivariate analysis with high breakdown point.")
4871 (license license:gpl2+)))
4873 (define-public r-fit-models
4875 (name "r-fit-models")
4880 (uri (cran-uri "fit.models" version))
4883 "0vjbzmx0ambm6yzidb4vbgmhclwzwv2iz2cwl54ccdkvx4cx3fck"))))
4884 (properties `((upstream-name . "fit.models")))
4885 (build-system r-build-system)
4887 `(("r-lattice" ,r-lattice)))
4888 (home-page "https://cran.r-project.org/web/packages/fit.models")
4889 (synopsis "Compare fitted models")
4891 "The @code{fit.models} function and its associated methods (coefficients, print,
4892 summary, plot, etc.) were originally provided in the @code{robust} package to
4893 compare robustly and classically fitted model objects. The aim of the
4894 @code{fit.models} package is to separate this fitted model object comparison
4895 functionality from the robust package and to extend it to support fitting
4896 methods (e.g., classical, robust, Bayesian, regularized, etc.) more
4898 ;; Any version of the GPL
4899 (license (list license:gpl2+ license:gpl3+))))
4901 (define-public r-robust
4908 (uri (cran-uri "robust" version))
4911 "1b7qh1aff500nd6dh4y2ipmjgdiq8991shflb63pc39vpc0ny6g4"))))
4912 (build-system r-build-system)
4914 `(("r-fit-models" ,r-fit-models)
4915 ("r-lattice" ,r-lattice)
4917 ("r-robustbase" ,r-robustbase)
4918 ("r-rrcov" ,r-rrcov)))
4920 `(("gfortran" ,gfortran)))
4921 (home-page "https://cran.r-project.org/web/packages/robust")
4922 (synopsis "Port of the S+ \"Robust Library\"")
4924 "This package is a port of the S+ \"Robust Library\". It provides
4925 methods for robust statistics, notably for robust regression and robust
4926 multivariate analysis.")
4927 (license license:gpl2)))
4929 (define-public r-trimcluster
4931 (name "r-trimcluster")
4936 (uri (cran-uri "trimcluster" version))
4939 "0013bpyq6mkvjn38qsmwnsxfiwxgwngnqxycxvgpgmiadhm8fjmn"))))
4940 (build-system r-build-system)
4941 (home-page "https://cran.r-project.org/web/packages/trimcluster")
4942 (synopsis "Cluster analysis with trimming")
4944 "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
4945 Matran (1997). This optimizes the k-means criterion under trimming a portion
4948 (license (list license:gpl2+ license:gpl3+))))
4950 (define-public r-fpc
4953 (version "2.1-11.1")
4957 (uri (cran-uri "fpc" version))
4960 "1ari57hkgqsxh6khr6j52cfrzc0096cnn1q7ghxk2z4brdd4rznc"))))
4961 (build-system r-build-system)
4963 `(("r-class" ,r-class)
4964 ("r-cluster" ,r-cluster)
4965 ("r-diptest" ,r-diptest)
4966 ("r-flexmix" ,r-flexmix)
4967 ("r-kernlab" ,r-kernlab)
4969 ("r-mclust" ,r-mclust)
4970 ("r-mvtnorm" ,r-mvtnorm)
4971 ("r-prabclus" ,r-prabclus)
4972 ("r-robustbase" ,r-robustbase)
4973 ("r-trimcluster" ,r-trimcluster)))
4974 (home-page "https://cran.r-project.org/web/packages/fpc")
4975 (synopsis "Flexible procedures for clustering")
4977 "This package provides various methods for clustering and cluster validation.
4978 For example, it provides fixed point clustering, linear regression clustering,
4979 clustering by merging Gaussian mixture components, as well as symmetric and
4980 asymmetric discriminant projections for visualisation of the separation of
4982 (license license:gpl2+)))
4984 (define-public r-vgam
4991 (uri (cran-uri "VGAM" version))
4994 "0lnsqx3q3k0c7sj8gj0n6shn2fyxwrh8xph8h1r1i23ybbb2n6fy"))))
4995 (properties `((upstream-name . "VGAM")))
4996 (build-system r-build-system)
4998 `(("gfortran" ,gfortran)))
4999 (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
5000 (synopsis "Vector generalized linear and additive models")
5002 "This package is an implementation of about 6 major classes of statistical
5003 regression models. Currently only fixed-effects models are implemented, i.e.,
5004 no random-effects models. Many (150+) models and distributions are estimated
5005 by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
5006 VGLMs can be loosely thought of as multivariate generalised linear models.")
5007 (license license:gpl2+)))
5009 (define-public r-pbapply
5016 (uri (cran-uri "pbapply" version))
5019 "0bn7a9ni36xy5acnrl9ky3gd1k8jr5kxgazzh3pzd1q6bri1nx7k"))))
5020 (build-system r-build-system)
5021 (home-page "https://github.com/psolymos/pbapply")
5022 (synopsis "Adding progress bar to apply functions")
5024 "This lightweight package that adds progress bar to vectorized R
5025 functions apply. The implementation can easily be added to functions where
5026 showing the progress is useful e.g. bootstrap.")
5027 (license license:gpl2)))
5029 (define-public r-minqa
5036 (uri (cran-uri "minqa" version))
5039 "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
5040 (build-system r-build-system)
5042 `(("r-rcpp" ,r-rcpp)))
5044 `(("gfortran" ,gfortran)))
5045 (home-page "http://optimizer.r-forge.r-project.org")
5046 (synopsis "Derivative-free optimization algorithms by quadratic approximation")
5048 "This package provides a derivative-free optimization by quadratic approximation
5049 based on an interface to Fortran implementations by M. J. D. Powell.")
5050 (license license:gpl2)))
5052 (define-public r-rcppeigen
5054 (name "r-rcppeigen")
5055 (version "0.3.3.5.0")
5059 (uri (cran-uri "RcppEigen" version))
5062 "01bz41c29591ybzqn4z88ss036ai3anh9figryvmfpqcfwbszip5"))))
5063 (properties `((upstream-name . "RcppEigen")))
5064 (build-system r-build-system)
5066 `(("r-rcpp" ,r-rcpp)
5067 ("r-matrix" ,r-matrix)))
5068 (home-page "http://eigen.tuxfamily.org")
5069 (synopsis "Rcpp integration for the Eigen templated linear algebra library")
5071 "This package provides an integration of Eigen in R using a C++ template
5072 library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
5073 It supports dense and sparse matrices on integer, floating point and complex numbers,
5074 decompositions of such matrices, and solutions of linear systems.")
5075 (license license:gpl2+)))
5077 (define-public r-modelmetrics
5079 (name "r-modelmetrics")
5084 (uri (cran-uri "ModelMetrics" version))
5087 "158ddbw2snlyzd2q6mdaif5i67kq4qfvadylwjxgv1w2cmszrmk6"))))
5088 (properties `((upstream-name . "ModelMetrics")))
5089 (build-system r-build-system)
5091 `(("r-rcpp" ,r-rcpp)
5092 ("r-data-table" ,r-data-table)))
5093 (home-page "https://cran.r-project.org/web/packages/ModelMetrics")
5094 (synopsis "Rapid calculation of model metrics")
5096 "Written in C++ using @code{Rcpp}, this package provides a collection of
5097 metrics for evaluating models.")
5098 (license license:gpl2+)))
5100 (define-public r-matrixmodels
5102 (name "r-matrixmodels")
5107 (uri (cran-uri "MatrixModels" version))
5110 "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
5111 (properties `((upstream-name . "MatrixModels")))
5112 (build-system r-build-system)
5114 `(("r-matrix" ,r-matrix)))
5115 (home-page "https://cran.r-project.org/web/packages/MatrixModels")
5116 (synopsis "Modelling with sparse and dense matrices")
5118 "This package models with sparse and dense matrix matrices,
5119 using modular prediction and response module classes.")
5120 (license license:gpl2+)))
5122 (define-public r-quantreg
5129 (uri (cran-uri "quantreg" version))
5132 "1vvvnk291f0dccg04l3nsnk585gq75sk0b2vdbrqv3lczvv18nw1"))))
5133 (build-system r-build-system)
5135 `(("gfortran" ,gfortran)))
5137 `(("r-matrix" ,r-matrix)
5138 ("r-matrixmodels" ,r-matrixmodels)
5139 ("r-sparsem" ,r-sparsem)))
5140 (home-page "https://www.r-project.org")
5141 (synopsis "Quantile regression")
5143 "This package provides an estimation and inference methods for models
5144 of conditional quantiles: linear and nonlinear parametric and non-parametric
5145 models for conditional quantiles of a univariate response and several methods
5146 for handling censored survival data. Portfolio selection methods based on
5147 expected shortfall risk are also included.")
5148 (license license:gpl2+)))
5150 (define-public r-nloptr
5157 (uri (cran-uri "nloptr" version))
5160 "15yz60kljxwnhm2m3gryjzxl3ynhkhd5jiwc179b1hz6rlzf71hz"))))
5161 (build-system r-build-system)
5163 `(("r-knitr" ,r-knitr) ; for building vignettes
5164 ("pkg-config" ,pkg-config)
5165 ("gfortran" ,gfortran)))
5167 `(("nlopt" ,nlopt)))
5168 (home-page "https://cran.r-project.org/web/packages/nloptr")
5169 (synopsis "R interface to NLopt")
5171 "This package is interface to NLopt, a library for nonlinear
5172 optimization. NLopt is a library for nonlinear optimization, providing a
5173 common interface for a number of different free optimization routines
5174 available online as well as original implementations of various other
5176 (license license:lgpl3)))
5178 (define-public r-lme4
5185 (uri (cran-uri "lme4" version))
5188 "035j2hqkwv939xl07pm2vykvf3wlx8qj317846n9pkpqkyv58mbz"))))
5189 (build-system r-build-system)
5191 `(("r-boot" ,r-boot)
5192 ("r-lattice" ,r-lattice)
5194 ("r-matrix" ,r-matrix)
5195 ("r-minqa" ,r-minqa)
5196 ("r-nloptr" ,r-nloptr)
5199 ("r-rcppeigen" ,r-rcppeigen)))
5200 (home-page "https://cran.r-project.org/web/packages/lme4")
5201 (synopsis "Linear mixed-effects models using eigen and S4")
5203 "This package provides fit linear and generalized linear mixed-effects
5204 models. The models and their components are represented using S4 classes and
5205 methods. The core computational algorithms are implemented using the Eigen
5206 C++ library for numerical linear algebra and RcppEigen glue.")
5207 (license license:gpl2+)))
5209 (define-public r-pbkrtest
5216 (uri (cran-uri "pbkrtest" version))
5219 "1si3bhi59xc51a0pgjjglccq3h4aljyhw2k1b8574s145fnh7fsw"))))
5220 (build-system r-build-system)
5222 `(("r-lme4" ,r-lme4)
5224 ("r-matrix" ,r-matrix)))
5225 (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
5226 (synopsis "Methods for linear mixed model comparison")
5228 "This package implements a parametric bootstrap test and a Kenward Roger
5229 modification of F-tests for linear mixed effects models and a parametric
5230 bootstrap test for generalized linear mixed models.")
5231 (license license:gpl2+)))
5233 (define-public r-cardata
5240 (uri (cran-uri "carData" version))
5243 "152lfgaspgx6x2wzdb5p3zv6r87a0d2pg10h6fjmdr613kzlwp1v"))))
5244 (properties `((upstream-name . "carData")))
5245 (build-system r-build-system)
5246 (home-page "https://r-forge.r-project.org/projects/car/")
5247 (synopsis "Data Sets for the book Companion to Applied Regression")
5249 "This package provides datasets to accompany J. Fox and S. Weisberg, An R
5250 Companion to Applied Regression, Third Edition, Sage.")
5251 (license license:gpl2+)))
5253 (define-public r-car
5260 (uri (cran-uri "car" version))
5263 "0l3wyc9ia0ypcbap2p39slazfpbl84mjzydqvpsywrzdiyxajnfz"))))
5264 (build-system r-build-system)
5266 `(("r-abind" ,r-abind)
5267 ("r-cardata" ,r-cardata)
5269 ("r-maptools" ,r-maptools)
5274 ("r-pbkrtest" ,r-pbkrtest)
5275 ("r-quantreg" ,r-quantreg)
5277 (home-page "https://r-forge.r-project.org/projects/car/")
5278 (synopsis "Companion to applied regression")
5280 "This package provides functions and datasets from book Companion
5281 to Applied regression, Second Edition, Sage, 2011.")
5282 (license license:gpl2+)))
5284 (define-public r-caret
5291 (uri (cran-uri "caret" version))
5294 "0zgkmiiarl7ll2ffyciikah61jyps41fin5pjb5l8ja2b26lgrdg"))))
5295 (build-system r-build-system)
5297 `(("r-foreach" ,r-foreach)
5298 ("r-ggplot2" ,r-ggplot2)
5299 ("r-lattice" ,r-lattice)
5300 ("r-modelmetrics" ,r-modelmetrics)
5303 ("r-recipes" ,r-recipes)
5304 ("r-reshape2" ,r-reshape2)
5305 ("r-withr" ,r-withr)))
5306 (home-page "https://github.com/topepo/caret")
5307 (synopsis "Classification and regression training")
5309 "This package provides misc functions for training and plotting
5310 classification and regression models.")
5311 (license license:gpl2+)))
5313 (define-public r-rcppprogress
5315 (name "r-rcppprogress")
5320 (uri (cran-uri "RcppProgress" version))
5323 "0yk01hfv961zyp569682k9igvhnwqyg5j0n5fm63sxigj82l2xhi"))))
5324 (properties `((upstream-name . "RcppProgress")))
5325 (build-system r-build-system)
5327 `(("r-devtools" ,r-devtools)
5328 ("r-rcpp" ,r-rcpp)))
5329 (home-page "https://github.com/kforner/rcpp_progress")
5330 (synopsis "Interruptible progress bar for C++ in R packages")
5332 "This package allows to display a progress bar in the R console for long running
5333 computations taking place in C++ code, and support for interrupting those computations
5334 even in multithreaded code, typically using OpenMP.")
5335 (license license:gpl3+)))
5337 (define-public r-mnormt
5344 (uri (cran-uri "mnormt" version))
5347 "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z"))))
5348 (build-system r-build-system)
5350 `(("gfortran" ,gfortran)))
5351 (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
5352 (synopsis "Multivariate normal and \"t\" distributions")
5354 "This package provides functions for computing the density and the
5355 distribution function of multivariate normal and \"t\" random variables, and
5356 for generating random vectors sampled from these distributions. Probabilities
5357 are computed via non-Monte Carlo methods.")
5358 (license license:gpl2+)))
5360 (define-public r-numderiv
5363 (version "2016.8-1")
5367 (uri (cran-uri "numDeriv" version))
5370 "07ni52rwiap4wilfz94w5mrqaxr59axxmgn57857ip4p6qkiss0v"))))
5371 (properties `((upstream-name . "numDeriv")))
5372 (build-system r-build-system)
5373 (home-page "https://cran.r-project.org/web/packages/numDeriv")
5374 (synopsis "Accurate numerical derivatives")
5376 "This package provides methods for calculating accurate numerical
5377 first and second order derivatives.")
5378 (license license:gpl2)))
5387 (uri (cran-uri "sn" version))
5390 "10via4lg0vx9pzq350vwhz5wv1dhzxr2l3r6jq99nk37vmyvj8fc"))))
5391 (build-system r-build-system)
5393 `(("r-mnormt" ,r-mnormt)
5394 ("r-numderiv" ,r-numderiv)))
5395 (home-page "http://azzalini.stat.unipd.it/SN")
5396 (synopsis "The skew-normal and skew-t distributions")
5398 "This packages provides functionalities to build and manipulate
5399 probability distributions of the skew-normal family and some related
5400 ones, notably the skew-t family, and provides related statistical
5401 methods for data fitting and diagnostics, in the univariate and the
5402 multivariate case.")
5403 (license license:gpl2+)))
5405 (define-public r-tclust
5412 (uri (cran-uri "tclust" version))
5415 "17md6l9v9dl9b72l84df01b52h2xiynbcjm437mv9mzcr09fc2sb"))))
5416 (build-system r-build-system)
5417 ;; These are all suggested packages, not build dependencies.
5419 `(("r-cluster" ,r-cluster)
5420 ("r-mclust" ,r-mclust)
5421 ("r-mvtnorm" ,r-mvtnorm)
5423 (home-page "https://cran.r-project.org/web/packages/tclust")
5424 (synopsis "Robust trimmed clustering")
5426 "This package implements different robust clustering
5427 algorithms (@code{tclust}) based on trimming and including some graphical
5428 diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
5429 (license license:gpl3)))
5431 (define-public r-ranger
5438 (uri (cran-uri "ranger" version))
5441 "1sxyzxmjc6lm8wcmq15j6sscnza7aay4mr3dyri2zngx6fa8mb0k"))))
5442 (build-system r-build-system)
5444 `(("r-rcpp" ,r-rcpp)
5445 ("r-matrix" ,r-matrix)
5446 ("r-rcppeigen" ,r-rcppeigen)))
5447 (home-page "https://github.com/imbs-hl/ranger")
5448 (synopsis "Fast implementation of random forests")
5450 "This package provides a fast implementation of Random Forests,
5451 particularly suited for high dimensional data. Ensembles of classification,
5452 regression, survival and probability prediction trees are supported. Data from
5453 genome-wide association studies can be analyzed efficiently.")
5454 (license license:gpl3)))
5456 (define-public r-tsne
5463 (uri (cran-uri "tsne" version))
5466 "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
5467 (build-system r-build-system)
5468 (home-page "https://github.com/jdonaldson/rtsne/")
5469 (synopsis "t-Distributed Stochastic Neighbor Embedding for R")
5471 "This package provides a pure R implementation of the t-SNE algorithm.")
5472 (license license:gpl2+)))
5474 (define-public r-cairo
5481 (uri (cran-uri "Cairo" version))
5484 "1mdmd5zmjkh1b0x928zizgzh42x8swbajffb88rvnjfdhk1z0dvq"))))
5485 (properties `((upstream-name . "Cairo")))
5486 (build-system r-build-system)
5492 `(("pkg-config" ,pkg-config)))
5493 (home-page "http://www.rforge.net/Cairo/")
5494 (synopsis "R graphics device using Cairo graphics library")
5496 "This package provides a Cairo graphics device that can be use to
5497 create high-quality vector (PDF, PostScript and SVG) and bitmap
5498 output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11
5499 and Win32). Since it uses the same back-end for all output, copying
5500 across formats is WYSIWYG. Files are created without the dependence
5501 on X11 or other external programs. This device supports alpha
5502 channel (semi-transparent drawing) and resulting images can contain
5503 transparent and semi-transparent regions. It is ideal for use in
5504 server environments (file output) and as a replacement for other
5505 devices that don't have Cairo's capabilities such as alpha support or
5506 anti-aliasing. Backends are modular such that any subset of backends
5508 (license license:gpl2)))
5510 (define-public r-lubridate
5512 (name "r-lubridate")
5517 (uri (cran-uri "lubridate" version))
5520 "14a823il77w3wmmnzr89vwrqp50y56dh5raycnaw6c8nv5xsh32i"))))
5521 (build-system r-build-system)
5523 `(("r-rcpp" ,r-rcpp)
5524 ("r-stringr" ,r-stringr)))
5526 "https://cran.r-project.org/web/packages/lubridate")
5527 (synopsis "Make dealing with dates a little easier")
5529 "This package provides functions to work with date-times and time-spans:
5530 fast and user friendly parsing of date-time data, extraction and updating of
5531 components of a date-time (years, months, days, hours, minutes, and seconds),
5532 algebraic manipulation on date-time and time-span objects. The @code{lubridate}
5533 package has a consistent and memorable syntax that makes working with dates
5535 (license license:gpl2)))
5537 (define-public r-fdrtool
5544 (uri (cran-uri "fdrtool" version))
5547 "1h46frlk7d9f4qx0bg6p55nrm9wwwz2sv6d1nz7061wdfsm69yb5"))))
5548 (build-system r-build-system)
5549 (home-page "http://strimmerlab.org/software/fdrtool/")
5550 (synopsis "Estimation of false discovery rates and higher criticism")
5552 "This package provides tools to estimate tail area-based false discovery
5553 rates as well as local false discovery rates for a variety of null
5554 models (p-values, z-scores, correlation coefficients, t-scores). The
5555 proportion of null values and the parameters of the null distribution are
5556 adaptively estimated from the data. In addition, the package contains
5557 functions for non-parametric density estimation (Grenander estimator), for
5558 monotone regression (isotonic regression and antitonic regression with
5559 weights), for computing the @dfn{greatest convex minorant} (GCM) and the
5560 @dfn{least concave majorant} (LCM), for the half-normal and correlation
5561 distributions, and for computing empirical @dfn{higher criticism} (HC) scores
5562 and the corresponding decision threshold.")
5563 (license license:gpl3+)))
5565 (define-public r-forcats
5572 (uri (cran-uri "forcats" version))
5575 "1cnjh23z59fhbjmy7y95425hcq3m5wrwqvahsxwi7zm6d9bwp0vw"))))
5576 (build-system r-build-system)
5578 `(("r-ellipsis" ,r-ellipsis)
5579 ("r-magrittr" ,r-magrittr)
5580 ("r-tibble" ,r-tibble)
5581 ("r-rlang" ,r-rlang)))
5582 (home-page "http://forcats.tidyverse.org")
5583 (synopsis "Tools for working with factors")
5584 (description "This package provides helpers for reordering factor
5585 levels (including moving specified levels to front, ordering by first
5586 appearance, reversing, and randomly shuffling), and tools for modifying factor
5587 levels (including collapsing rare levels into other, \"anonymizing\", and
5588 manually \"recoding\").")
5589 (license license:gpl3)))
5591 (define-public r-tgstat
5592 (let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f")
5596 (version (string-append "1.0.2-" revision "." (string-take changeset 7)))
5601 (url "https://bitbucket.org/tanaylab/tgstat")
5602 (changeset changeset)))
5603 (file-name (string-append name "-" version "-checkout"))
5606 "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
5607 (build-system r-build-system)
5610 (modify-phases %standard-phases
5611 (add-after 'unpack 'fix-isnan
5613 (substitute* "src/tgstat.h"
5614 (("#define isnan ::isnan")
5615 "#define isnan std::isnan"))
5618 `(("r-rcpp" ,r-rcpp)))
5619 (home-page "https://bitbucket.org/tanaylab/tgstat/")
5620 (synopsis "Tanay's group statistical utilities")
5622 "The goal of tgstat is to provide fast and efficient statistical
5624 (license license:gpl2))))
5626 (define-public r-tgconfig
5627 (let ((changeset "1e02c7614713bd0866c46f0c679a058f8c6d627e")
5631 (version (string-append "0.0.0.9000-" revision "." (string-take changeset 7)))
5636 (url "https://bitbucket.org/tanaylab/tgconfig")
5637 (changeset changeset)))
5638 (file-name (string-append name "-" version "-checkout"))
5641 "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
5642 (build-system r-build-system)
5644 `(("r-yaml" ,r-yaml)))
5645 (home-page "https://bitbucket.org/tanaylab/tgconfig/")
5646 (synopsis "Infrastructure for managing package parameters")
5648 "The goal of tgconfig is to provide infrastructure for managing package
5650 (license license:gpl3))))
5652 (define-public r-directlabels
5654 (name "r-directlabels")
5655 (version "2018.05.22")
5659 (uri (cran-uri "directlabels" version))
5662 "0xcpc56ssb9430b0xcdhayk3qaak2qcakyss2pz14y5w2027hblv"))))
5663 (build-system r-build-system)
5665 `(("r-quadprog" ,r-quadprog)))
5666 (home-page "http://directlabels.r-forge.r-project.org/")
5667 (synopsis "Direct labels for multicolor plots")
5669 "This package provides an extensible framework for automatically placing
5670 direct labels onto multicolor plots. Label positions are described using
5671 positioning methods that can be re-used across several different plots. There
5672 are heuristics for examining @code{trellis} and @code{ggplot} objects and
5673 inferring an appropriate positioning method.")
5674 (license license:gpl3)))
5676 (define-public r-catterplots
5677 (let ((commit "40063ec57f9515d231508f135ca0ec769614efb9")
5680 (name "r-catterplots")
5681 (version (string-append "0-" revision "." (string-take commit 9)))
5685 (url "https://github.com/Gibbsdavidl/CatterPlots.git")
5687 (file-name (string-append name "-" version "-checkout"))
5690 "1wl80pgbz8d9kfpffvkh439hlgz2qldm9m75wqjfrgrg8lcjzrxg"))))
5691 (build-system r-build-system)
5693 `(("r-png" ,r-png)))
5694 (home-page "https://github.com/Gibbsdavidl/CatterPlots")
5695 (synopsis "Scatter plots with cat shaped points")
5696 (description "Did you ever wish you could make scatter plots with cat
5697 shaped points? Now you can!")
5698 (license license:asl2.0))))
5700 (define-public r-colorout
5707 (uri (string-append "https://github.com/jalvesaq/colorout/archive/"
5708 "v" version ".tar.gz"))
5709 (file-name (string-append name "-" version ".tar.gz"))
5712 "07vqx5ihgnq4dzn5jnfjfhdm3957v4prvf8vhnb3cwvlly4l7p9v"))))
5713 (build-system r-build-system)
5714 (home-page "https://github.com/jalvesaq/colorout")
5715 (synopsis "Colorize output in the R REPL")
5716 (description "@code{colorout} is an R package that colorizes R output when
5717 running in terminal emulator.
5719 R STDOUT is parsed and numbers, negative numbers, dates in the standard
5720 format, strings, and R constants are identified and wrapped by special ANSI
5721 scape codes that are interpreted by terminal emulators as commands to colorize
5722 the output. R STDERR is also parsed to identify the expressions warning and
5723 error and their translations to many languages. If these expressions are
5724 found, the output is colorized accordingly; otherwise, it is colorized as
5725 STDERROR (blue, by default).
5727 You can customize the colors according to your taste, guided by the color
5728 table made by the command @code{show256Colors()}. You can also set the colors
5729 to any arbitrary string. In this case, it is up to you to set valid values.")
5730 (license license:gpl3+)))
5732 (define-public r-txtplot
5739 (uri (cran-uri "txtplot" version))
5742 "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h"))))
5743 (build-system r-build-system)
5744 (home-page "https://cran.r-project.org/web/packages/txtplot/")
5745 (synopsis "Text-based plotting")
5746 (description "This package provides functions to produce rudimentary ASCII
5747 graphics directly in the terminal window. This package provides a basic
5748 plotting function (and equivalents of curve, density, acf and barplot) as well
5749 as a boxplot function.")
5750 (license license:lgpl3+)))
5752 (define-public python-rpy2
5754 (name "python-rpy2")
5759 (uri (pypi-uri "rpy2" version))
5762 "0bl1d2qhavmlrvalir9hmkjh74w21vzkvc2sg3cbb162s10zfmxy"))))
5763 (build-system python-build-system)
5765 '(#:modules ((ice-9 ftw)
5769 (guix build python-build-system))
5771 (modify-phases %standard-phases
5773 (lambda* (#:key outputs inputs #:allow-other-keys)
5774 (let ((cwd (getcwd)))
5775 (setenv "PYTHONPATH"
5776 (string-append cwd "/build/"
5777 (find (cut string-prefix? "lib" <>)
5778 (scandir (string-append cwd "/build")))
5780 (getenv "PYTHONPATH"))))
5781 (invoke "python" "-m" "rpy2.tests" "-v"))))))
5783 `(("python-six" ,python-six)
5784 ("python-jinja2" ,python-jinja2)
5785 ("python-pytz" ,python-pytz)))
5787 `(("readline" ,readline)
5790 ("r-minimal" ,r-minimal)
5791 ("r-survival" ,r-survival)
5792 ("r-ggplot2" ,r-ggplot2)
5793 ("r-rsqlite" ,r-rsqlite)
5794 ("r-dplyr" ,r-dplyr)
5795 ("r-dbplyr" ,r-dbplyr)
5796 ("python-numpy" ,python-numpy)))
5799 (home-page "https://rpy2.bitbucket.io/")
5800 (synopsis "Python interface to the R language")
5801 (description "rpy2 is a redesign and rewrite of rpy. It is providing a
5802 low-level interface to R from Python, a proposed high-level interface,
5803 including wrappers to graphical libraries, as well as R-like structures and
5805 ;; Any of these licenses can be picked for the R interface. The whole
5806 ;; project is released under GPLv2+ according to the license declaration
5808 (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+))))
5810 (define-public java-jdistlib
5812 (name "java-jdistlib")
5816 (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
5817 version "-src.jar"))
5820 "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
5821 (build-system ant-build-system)
5823 `(#:jar-name "jdistlib.jar"
5825 #:tests? #f ; no dedicated test directory
5827 (modify-phases %standard-phases
5828 (add-after 'unpack 'fix-broken-encoding
5830 (with-fluids ((%default-port-encoding "ISO-8859-1"))
5831 (substitute* "src/jdistlib/Beta.java"
5832 (("Scheff.+-Tukey") "Scheffe-Tukey")))
5835 `(("java-jtransforms" ,java-jtransforms)))
5837 `(("java-junit" ,java-junit)))
5838 (home-page "http://jdistlib.sourceforge.net/")
5839 (synopsis "Java library of statistical distributions")
5840 (description "JDistlib is the Java Statistical Distribution Library, a
5841 Java package that provides routines for various statistical distributions.")
5842 ;; The files that were translated from R code are under GPLv2+; some files
5843 ;; are under the GPLv3, which is a mistake. The author confirmed in an
5844 ;; email that this whole project should be under GPLv2+.
5845 (license license:gpl2+)))
5847 (define-public emacs-ess
5853 (uri (string-append "https://github.com/emacs-ess/ESS/archive/v"
5857 "0cbilbsiwvcyf6d5y24mymp57m3ana5dkzab3knfs83w4a3a4c5c"))
5858 (file-name (string-append name "-" version ".tar.gz"))
5859 (modules '((guix build utils)))
5862 ;; Stop ESS from trying to bundle an external julia-mode.el.
5863 (substitute* "lisp/Makefile"
5864 (("^\tjulia-mode.elc\\\\\n") "")
5865 (("^dist: all julia-mode.el")
5867 ;; No need to build docs in so many formats. Also, skipping
5868 ;; pdf lets us not pull in texlive.
5869 (substitute* "doc/Makefile"
5870 (("all : info text html pdf")
5872 (("install: install-info install-other-docs")
5873 "install: install-info"))
5874 ;; Test fails upstream
5875 (substitute* "test/ess-r-tests.el"
5876 (("ert-deftest ess-r-namespaced-eval-no-srcref-in-errors ()")
5877 "ert-deftest ess-r-namespaced-eval-no-srcref-in-errors () :expected-result :failed"))
5879 (build-system gnu-build-system)
5881 (let ((base-directory "/share/emacs/site-lisp/guix.d/ess"))
5882 `(#:make-flags (list (string-append "PREFIX=" %output)
5883 (string-append "ETCDIR=" %output "/"
5884 ,base-directory "/etc")
5885 (string-append "LISPDIR=" %output "/"
5888 (modify-phases %standard-phases
5890 (add-before 'build 'more-shebang-patching
5891 (lambda* (#:key inputs #:allow-other-keys)
5892 (substitute* "Makeconf"
5893 (("SHELL = /bin/sh")
5894 (string-append "SHELL = " (which "sh"))))
5898 (invoke "make" "test")))))))
5900 `(("emacs" ,emacs-minimal)
5901 ("r-minimal" ,r-minimal)))
5904 ("texinfo" ,texinfo)))
5906 `(("emacs-julia-mode" ,emacs-julia-mode)))
5907 (home-page "https://ess.r-project.org/")
5908 (synopsis "Emacs mode for statistical analysis programs")
5909 (description "Emacs Speaks Statistics (ESS) is an add-on package for GNU
5910 Emacs. It is designed to support editing of scripts and interaction with
5911 various statistical analysis programs such as R, Julia, and JAGS.")
5912 (license license:gpl2+)))