1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com>
4 ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
5 ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
6 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
7 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
8 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
9 ;;; Copyright © 2016, 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
10 ;;; Copyright © 2017 Kyle Meyer <kyle@kyleam.com>
11 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
13 ;;; This file is part of GNU Guix.
15 ;;; GNU Guix is free software; you can redistribute it and/or modify it
16 ;;; under the terms of the GNU General Public License as published by
17 ;;; the Free Software Foundation; either version 3 of the License, or (at
18 ;;; your option) any later version.
20 ;;; GNU Guix is distributed in the hope that it will be useful, but
21 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
22 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
23 ;;; GNU General Public License for more details.
25 ;;; You should have received a copy of the GNU General Public License
26 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
28 (define-module (gnu packages statistics)
29 #:use-module ((guix licenses) #:prefix license:)
30 #:use-module (guix packages)
31 #:use-module (guix download)
32 #:use-module (guix hg-download)
33 #:use-module (guix git-download)
34 #:use-module (guix utils)
35 #:use-module (guix build-system ant)
36 #:use-module (guix build-system gnu)
37 #:use-module (guix build-system r)
38 #:use-module (guix build-system python)
39 #:use-module (guix build-system trivial)
40 #:use-module (gnu packages)
41 #:use-module (gnu packages algebra)
42 #:use-module (gnu packages bash)
43 #:use-module (gnu packages check)
44 #:use-module (gnu packages compression)
45 #:use-module (gnu packages cran)
46 #:use-module (gnu packages curl)
47 #:use-module (gnu packages gcc)
48 #:use-module (gnu packages gtk)
49 #:use-module (gnu packages gettext)
50 #:use-module (gnu packages glib)
51 #:use-module (gnu packages haskell)
52 #:use-module (gnu packages icu4c)
53 #:use-module (gnu packages image)
54 #:use-module (gnu packages java)
55 #:use-module (gnu packages machine-learning)
56 #:use-module (gnu packages maths)
57 #:use-module (gnu packages multiprecision)
58 #:use-module (gnu packages pcre)
59 #:use-module (gnu packages perl)
60 #:use-module (gnu packages pkg-config)
61 #:use-module (gnu packages python)
62 #:use-module (gnu packages readline)
63 #:use-module (gnu packages ssh)
64 #:use-module (gnu packages texinfo)
65 #:use-module (gnu packages time)
66 #:use-module (gnu packages tls)
67 #:use-module (gnu packages base)
68 #:use-module (gnu packages web)
69 #:use-module (gnu packages xml)
70 #:use-module (gnu packages xorg)
71 #:use-module (srfi srfi-1))
81 (uri (string-append "mirror://gnu/pspp/pspp-"
85 "1r8smr5057993h90nx0mdnff8nxw9x546zzh6qpy4h3xblp1la5s"))))
86 (build-system gnu-build-system)
89 ("gettext" ,gettext-minimal)
93 ("readline" ,readline)
95 ("gtksourceview" ,gtksourceview)
98 `(("glib" ,glib "bin") ;for glib-genmarshal
100 ("pkg-config" ,pkg-config)))
101 (home-page "https://www.gnu.org/software/pspp/")
102 (synopsis "Statistical analysis")
104 "GNU PSPP is a statistical analysis program. It can perform
105 descriptive statistics, T-tests, linear regression and non-parametric tests.
106 It features both a graphical interface as well as command-line input. PSPP
107 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
108 can be imported from spreadsheets, text files and database sources and it can
109 be output in text, PostScript, PDF or HTML.")
110 (license license:gpl3+)))
112 ;; Update this package together with the set of recommended packages: r-boot,
113 ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
114 ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
115 (define-public r-minimal
121 (uri (string-append "mirror://cran/src/base/R-"
122 (version-major version) "/R-"
126 "0dq3jsnwsb5j3fhl0wi3p5ycv8avf8s5j1y4ap3d2mkjmcppvsdk"))))
127 (build-system gnu-build-system)
129 `(#:disallowed-references (,tzdata-for-tests)
131 (list (string-append "LDFLAGS=-Wl,-rpath="
132 (assoc-ref %outputs "out")
134 ;; This affects the embedded timestamp of only the core packages.
135 "PKG_BUILT_STAMP=1970-01-01")
137 (modify-phases %standard-phases
138 (add-before 'configure 'do-not-compress-serialized-files
139 (lambda* (#:key inputs #:allow-other-keys)
140 ;; This ensures that Guix can detect embedded store references;
141 ;; see bug #28157 for details.
142 (substitute* "src/library/base/makebasedb.R"
143 (("compress = TRUE") "compress = FALSE"))
145 (add-before 'configure 'patch-uname
146 (lambda* (#:key inputs #:allow-other-keys)
147 (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
149 (substitute* "src/scripts/R.sh.in"
150 (("uname") uname-bin)))
152 (add-after 'unpack 'build-reproducibly
154 ;; The documentation contains time stamps to demonstrate
155 ;; documentation generation in different phases.
156 (substitute* "src/library/tools/man/Rd2HTML.Rd"
157 (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
158 "(removed for reproducibility)"))
160 ;; Remove timestamp from tracing environment. This fixes
161 ;; reproducibility of "methods.rd{b,x}".
162 (substitute* "src/library/methods/R/trace.R"
163 (("dateCreated = Sys.time\\(\\)")
164 "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
166 ;; Ensure that gzipped files are reproducible.
167 (substitute* '("src/library/grDevices/Makefile.in"
168 "doc/manual/Makefile.in")
169 (("R_GZIPCMD\\)" line)
170 (string-append line " -n")))
172 ;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
173 ;; queries the mtime of a given file and records it in an object.
174 ;; This is acceptable at runtime to detect stale source files,
175 ;; but it destroys reproducibility at build time.
177 ;; Similarly, the "srcfilecopy" procedure records the current
178 ;; time. We change both of them to respect SOURCE_DATE_EPOCH.
179 (substitute* "src/library/base/R/srcfile.R"
180 (("timestamp <- (timestamp.*|file.mtime.*)" _ time)
181 (string-append "timestamp <- \
182 as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
183 as.numeric(Sys.getenv(\"SOURCE_DATE_EPOCH\"))\
184 } else { " time "}, origin=\"1970-01-01\")\n")))
186 ;; This library is installed using "install_package_description",
187 ;; so we need to pass the "builtStamp" argument.
188 (substitute* "src/library/tools/Makefile.in"
189 (("(install_package_description\\(.*\"')\\)\"" line prefix)
190 (string-append prefix ", builtStamp='1970-01-01')\"")))
192 ;; R bundles an older version of help2man, which does not respect
193 ;; SOURCE_DATE_EPOCH. We cannot just use the latest help2man,
194 ;; because that breaks a test.
195 (with-fluids ((%default-port-encoding "ISO-8859-1"))
196 (substitute* "tools/help2man.pl"
197 (("my \\$date = strftime \"%B %Y\", localtime" line)
198 (string-append line " 1"))))
200 (add-before 'configure 'set-default-pager
201 ;; Set default pager to "cat", because otherwise it is "false",
202 ;; making "help()" print nothing at all.
203 (lambda _ (setenv "PAGER" "cat") #t))
204 (add-before 'check 'set-timezone
205 ;; Some tests require the timezone to be set. However, the
206 ;; timezone may not just be "UTC", or else a brittle regression
207 ;; test in reg-tests-1d will fail.
208 (lambda* (#:key inputs #:allow-other-keys)
209 (setenv "TZ" "UTC+1")
211 (string-append (assoc-ref inputs "tzdata")
214 (add-after 'build 'make-info
215 (lambda _ (zero? (system* "make" "info"))))
216 (add-after 'build 'install-info
217 (lambda _ (zero? (system* "make" "install-info")))))
219 '(;; Do not build the recommended packages. The build system creates
220 ;; random temporary directories and embeds their names in some
221 ;; package files. We build these packages with the r-build-system
223 "--without-recommended-packages"
225 "--with-blas=-lopenblas"
231 "--enable-BLAS-shlib"
232 "--with-system-tre")))
233 ;; R has some support for Java. When the JDK is available at configure
234 ;; time environment variables pointing to the JDK will be recorded under
235 ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
236 ;; CMD javareconf". "R CMD javareconf" appears to only be used to update
237 ;; the recorded environment variables in $R_HOME/etc. Refer to
238 ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
239 ;; for additional information.
241 ;; As the JDK is a rather large input with only very limited effects on R,
242 ;; we decided to drop it.
246 ("pkg-config" ,pkg-config)
247 ("texinfo" ,texinfo) ; for building HTML manuals
248 ("tzdata" ,tzdata-for-tests)
251 `(;; We need not only cairo here, but pango to ensure that tests for the
252 ;; "cairo" bitmapType plotting backend succeed.
254 ("coreutils" ,coreutils)
256 ("openblas" ,openblas)
257 ("gfortran" ,gfortran)
264 ("readline" ,readline)
265 ;; This avoids a reference to the ungraftable static bash. R uses the
266 ;; detected shell for the "system" procedure.
267 ("bash" ,bash-minimal)
271 (list (search-path-specification
272 (variable "R_LIBS_SITE")
273 (files (list "site-library/")))))
274 (home-page "https://www.r-project.org/")
275 (synopsis "Environment for statistical computing and graphics")
277 "R is a language and environment for statistical computing and graphics.
278 It provides a variety of statistical techniques, such as linear and nonlinear
279 modeling, classical statistical tests, time-series analysis, classification
280 and clustering. It also provides robust support for producing
281 publication-quality data plots. A large amount of 3rd-party packages are
282 available, greatly increasing its breadth and scope.")
283 (license license:gpl3+)))
285 (define-public rmath-standalone
286 (package (inherit r-minimal)
287 (name "rmath-standalone")
290 (modify-phases %standard-phases
291 (add-after 'configure 'chdir
292 (lambda _ (chdir "src/nmath/standalone/") #t)))))
293 (synopsis "Standalone R math library")
295 "This package provides the R math library as an independent package.")))
297 (define-public r-boot
304 (uri (cran-uri "boot" version))
307 "0ai1qpm0p4z07xr0dvag8sdn9jrxcwanrsk9khzmww094jvr1jxd"))))
308 (build-system r-build-system)
309 (home-page "https://cran.r-project.org/web/packages/boot")
310 (synopsis "Bootstrap functions for R")
312 "This package provides functions and datasets for bootstrapping from the
313 book \"Bootstrap Methods and Their Application\" by A.C. Davison and
314 D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
315 ;; Unlimited distribution
316 (license (license:non-copyleft "file://R/bootfuns.q"))))
318 (define-public r-mass
325 (uri (cran-uri "MASS" version))
328 "1yjbnj1p4z0vw84wga8q5fyqiw4n6r7pc6rdwam7vsbiamyzfcqs"))))
329 (properties `((upstream-name . "MASS")))
330 (build-system r-build-system)
331 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
332 (synopsis "Support functions and datasets for Venables and Ripley's MASS")
334 "This package provides functions and datasets for the book \"Modern
335 Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
336 ;; Either version may be picked.
337 (license (list license:gpl2 license:gpl3))))
339 (define-public r-class
346 (uri (cran-uri "class" version))
349 "173b8a16lh1i0zjmr784l0xr0azp9v8bgslh12hfdswbq7dpdf0q"))))
350 (build-system r-build-system)
352 `(("r-mass" ,r-mass)))
353 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
354 (synopsis "R functions for classification")
356 "This package provides various functions for classification, including
357 k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
358 ;; Either of the two versions can be picked.
359 (license (list license:gpl2 license:gpl3))))
361 (define-public r-cluster
368 (uri (cran-uri "cluster" version))
371 "1z4gbz7chxxi4ly6c0yjlikwgf8aa8dlg05cn5cd6pjr21zvh97l"))))
372 (build-system r-build-system)
374 `(("gfortran" ,gfortran)))
375 (home-page "https://cran.r-project.org/web/packages/cluster")
376 (synopsis "Methods for cluster analysis")
378 "This package provides methods for cluster analysis. It is a much
379 extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
380 Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
381 (license license:gpl2+)))
383 (define-public r-codetools
390 (uri (cran-uri "codetools" version))
393 "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf"))))
394 (build-system r-build-system)
395 (home-page "https://cran.r-project.org/web/packages/codetools")
396 (synopsis "Code analysis tools for R")
397 (description "This package provides code analysis tools for R to check R
398 code for possible problems.")
399 ;; Any version of the GPL.
400 (license (list license:gpl2+ license:gpl3+))))
402 (define-public r-foreign
409 (uri (cran-uri "foreign" version))
412 "0s1lxmd85dd0kxx8hwk02w9l7pmpk4bpy7787fbyh2dbq5g9ys0k"))))
413 (build-system r-build-system)
414 (home-page "https://cran.r-project.org/web/packages/foreign")
415 (synopsis "Read data stored by other statistics software")
417 "This package provides functions for reading and writing data stored by
418 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
419 for reading and writing some dBase files.")
420 (license license:gpl2+)))
422 (define-public r-kernsmooth
424 (name "r-kernsmooth")
429 (uri (cran-uri "KernSmooth" version))
432 "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb"))))
433 (properties `((upstream-name . "KernSmooth")))
434 (build-system r-build-system)
436 `(("gfortran" ,gfortran)))
437 (home-page "https://cran.r-project.org/web/packages/KernSmooth")
438 (synopsis "Functions for kernel smoothing")
440 "This package provides functions for kernel smoothing (and density
441 estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
442 \"Kernel Smoothing\".")
443 ;; Unlimited use and distribution
444 (license (license:non-copyleft "file://LICENCE.note"))))
446 (define-public r-lattice
452 (uri (cran-uri "lattice" version))
455 "0pcnmaz3lr62ly0dcy5hnnqxshc4yqd43hrvlz3almgc9l7sna88"))))
456 (build-system r-build-system)
457 (home-page "http://lattice.r-forge.r-project.org/")
458 (synopsis "High-level data visualization system")
460 "The lattice package provides a powerful and elegant high-level data
461 visualization system inspired by Trellis graphics, with an emphasis on
462 multivariate data. Lattice is sufficient for typical graphics needs, and is
463 also flexible enough to handle most nonstandard requirements.")
464 (license license:gpl2+)))
466 (define-public r-matrix
473 (uri (cran-uri "Matrix" version))
476 "1wm45hg4x5ay15y03k6rmgkd1n9r01da72mszk24vafwd7pimr8n"))))
477 (properties `((upstream-name . "Matrix")))
478 (build-system r-build-system)
480 `(("r-lattice" ,r-lattice)))
481 (home-page "http://Matrix.R-forge.R-project.org/")
482 (synopsis "Sparse and dense matrix classes and methods")
484 "This package provides classes and methods for dense and sparse matrices
485 and operations on them using LAPACK and SuiteSparse.")
486 (license license:gpl2+)))
488 (define-public r-nlme
491 (version "3.1-131.1")
495 (uri (cran-uri "nlme" version))
498 "1xafi670a9jzb52kqxkacxfmy0viac3aql5byfq86kgkgla2sg0y"))))
499 (build-system r-build-system)
501 `(("r-lattice" ,r-lattice)))
503 `(("gfortran" ,gfortran)))
504 (home-page "https://cran.r-project.org/web/packages/nlme")
505 (synopsis "Linear and nonlinear mixed effects models")
507 "This package provides tools to fit and compare Gaussian linear and
508 nonlinear mixed-effects models.")
509 (license license:gpl2+)))
511 (define-public r-mgcv
518 (uri (cran-uri "mgcv" version))
521 "1lsrhf1yzn25pfn3f5x8yxjqnfryim4jx3iqd7ah8aalh5asqwbp"))))
522 (build-system r-build-system)
524 `(("r-matrix" ,r-matrix)
526 (home-page "https://cran.r-project.org/web/packages/mgcv")
527 (synopsis "Mixed generalised additive model computation")
529 "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
530 parameter estimation by GCV, REML or UBRE/AIC. The library includes a
531 @code{gam()} function, a wide variety of smoothers, JAGS support and
532 distributions beyond the exponential family.")
533 (license license:gpl2+)))
535 (define-public r-nnet
542 (uri (cran-uri "nnet" version))
545 "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7"))))
546 (build-system r-build-system)
547 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
548 (synopsis "Feed-forward neural networks and multinomial log-linear models")
550 "This package provides functions for feed-forward neural networks with a
551 single hidden layer, and for multinomial log-linear models.")
552 (license (list license:gpl2+ license:gpl3+))))
554 (define-public r-rpart
561 (uri (cran-uri "rpart" version))
564 "0k29qx3k3pj5sgrpg0p47yd8i811rmdakaw57bigpq1449asc4cf"))))
565 (build-system r-build-system)
566 (home-page "https://cran.r-project.org/web/packages/rpart")
567 (synopsis "Recursive partitioning and regression trees")
569 "This package provides recursive partitioning functions for
570 classification, regression and survival trees.")
571 (license (list license:gpl2+ license:gpl3+))))
573 (define-public r-spatial
580 (uri (cran-uri "spatial" version))
583 "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
584 (build-system r-build-system)
585 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
586 (synopsis "Functions for kriging and point pattern analysis")
588 "This package provides functions for kriging and point pattern
590 ;; Either version may be picked.
591 (license (list license:gpl2 license:gpl3))))
593 (define-public r-survival
600 (uri (cran-uri "survival" version))
603 "07cnr0hnki6ybbjll54l4s5lllhk19vni5f8m0mvsfp99ls7qygk"))))
604 (build-system r-build-system)
606 `(("r-matrix" ,r-matrix)))
607 (home-page "https://github.com/therneau/survival")
608 (synopsis "Survival analysis")
610 "This package contains the core survival analysis routines, including
611 definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
612 curves, Cox models, and parametric accelerated failure time models.")
613 (license license:lgpl2.0+)))
616 (package (inherit r-minimal)
619 (build-system trivial-build-system)
620 (arguments '(#:builder (mkdir %output)))
622 `(("r-minimal" ,r-minimal)
625 ("r-cluster" ,r-cluster)
626 ("r-codetools" ,r-codetools)
627 ("r-foreign" ,r-foreign)
628 ("r-kernsmooth" ,r-kernsmooth)
629 ("r-lattice" ,r-lattice)
631 ("r-matrix" ,r-matrix)
636 ("r-spatial" ,r-spatial)
637 ("r-survival" ,r-survival)))))
646 (uri (cran-uri "bit" version))
649 "0a6ig6nnjzq80r2ll4hc74za3xwzbzig6wlyb4dby0knzf3iqa6f"))))
650 (build-system r-build-system)
651 (home-page "http://ff.r-forge.r-project.org")
652 (synopsis "Class for vectors of 1-bit booleans")
654 "This package provides bitmapped vectors of booleans (no @code{NA}s),
655 coercion from and to logicals, integers and integer subscripts, fast boolean
656 operators and fast summary statistics. With @code{bit} class vectors of true
657 binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
658 (license license:gpl2)))
660 (define-public r-bit64
667 (uri (cran-uri "bit64" version))
670 "07znvz9vp1nz1y5ljng4qyskvm943cdbmy996s67560ijxzsm6kv"))))
671 (build-system r-build-system)
674 (home-page "http://ff.r-forge.r-project.org/")
675 (synopsis "S3 class for vectors of 64 bit integers")
677 "The bit64 package provides serializable S3 atomic 64 bit (signed)
678 integers that can be used in vectors, matrices, arrays and @code{data.frames}.
679 Methods are available for coercion from and to logicals, integers, doubles,
680 characters and factors as well as many elementwise and summary functions.
681 Many fast algorithmic operations such as @code{match} and @code{order} support
682 interactive data exploration and manipulation and optionally leverage
684 (license license:gpl2)))
686 (define-public r-dichromat
693 (uri (cran-uri "dichromat" version))
695 (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
696 (build-system r-build-system)
697 (home-page "https://cran.r-project.org/web/packages/dichromat")
698 (synopsis "Color schemes for dichromats")
700 "Dichromat collapses red-green or green-blue distinctions to simulate the
701 effects of different types of color-blindness.")
702 (license license:gpl2+)))
704 (define-public r-digest
711 (uri (cran-uri "digest" version))
713 (base32 "1ia4ak956gnn0f5aqhwgam6g9z6f1y57zz8jv45jc8h79yxp8bl8"))))
714 (build-system r-build-system)
715 ;; Vignettes require r-knitr, which requires r-digest, so we have to
716 ;; disable them and the tests.
719 #:configure-flags (list "--no-build-vignettes")))
720 (home-page "http://dirk.eddelbuettel.com/code/digest.html")
721 (synopsis "Create cryptographic hash digests of R objects")
723 "This package contains an implementation of a function 'digest()' for the
724 creation of hash digests of arbitrary R objects (using the md5, sha-1,
725 sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
726 of R language objects, as well as a function 'hmac()' to create hash-based
727 message authentication code.
729 Please note that this package is not meant to be deployed for cryptographic
730 purposes for which more comprehensive (and widely tested) libraries such as
731 OpenSSL should be used.")
732 (license license:gpl2+)))
734 (define-public r-estimability
736 (name "r-estimability")
740 (uri (cran-uri "estimability" version))
743 "0cifdaa71spkcxl4db4z884jrya865sg3dhcv4isd8fnzg2pjcd3"))))
744 (build-system r-build-system)
745 (home-page "https://cran.r-project.org/web/packages/estimability")
746 (synopsis "Tools for assessing estimability of linear predictions")
747 (description "Provides tools for determining estimability of linear
748 functions of regression coefficients, and 'epredict' methods that handle
749 non-estimable cases correctly.")
750 (license license:gpl2+)))
752 (define-public r-pheatmap
759 (uri (cran-uri "pheatmap" version))
762 "1ik0k69kb4n7xl3bkx4p09kw08ri93855zcsxq1c668171jqfiji"))))
763 (build-system r-build-system)
765 `(("r-gtable" ,r-gtable)
766 ("r-rcolorbrewer" ,r-rcolorbrewer)
767 ("r-scales" ,r-scales)))
769 "https://cran.r-project.org/web/packages/pheatmap")
770 (synopsis "Pretty heatmaps")
772 "This package provides an implementation of heatmaps that offers more
773 control over dimensions and appearance.")
774 (license license:gpl2+)))
776 (define-public r-labeling
783 (uri (cran-uri "labeling" version))
785 (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
786 (build-system r-build-system)
787 (home-page "https://cran.r-project.org/web/packages/labeling")
788 (synopsis "Axis labeling algorithms")
789 (description "The labeling package provides a range of axis labeling
791 (license license:expat)))
793 (define-public r-magrittr
800 (uri (cran-uri "magrittr" version))
802 (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
803 (build-system r-build-system)
804 (home-page "https://cran.r-project.org/web/packages/magrittr/index.html")
805 (synopsis "A forward-pipe operator for R")
807 "Magrittr provides a mechanism for chaining commands with a new
808 forward-pipe operator, %>%. This operator will forward a value, or the result
809 of an expression, into the next function call/expression. There is flexible
810 support for the type of right-hand side expressions. For more information,
811 see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
812 (license license:expat)))
814 (define-public r-munsell
821 (uri (cran-uri "munsell" version))
823 (base32 "0jdxlbjslkzaqgp058da1cgm85qvqi09wpcgpvp4hvwnmy83qz1r"))))
824 (build-system r-build-system)
826 `(("r-colorspace" ,r-colorspace)))
827 (home-page "https://cran.r-project.org/web/packages/munsell")
828 (synopsis "Munsell colour system")
830 "The Munsell package contains Functions for exploring and using the
831 Munsell colour system.")
832 (license license:expat)))
834 (define-public r-permute
841 (uri (cran-uri "permute" version))
844 "1w8wzk1fg9q7wvisnfp2js70dg0m9wi12gkdhpyngpbdcgssahd5"))))
845 (build-system r-build-system)
846 ;; Tests do not run correctly, but running them properly would entail a
847 ;; circular dependency with vegan.
848 (home-page "https://github.com/gavinsimpson/permute")
849 (synopsis "Functions for Generating Restricted Permutations of Data")
851 "This package provides a set of restricted permutation designs for freely
852 exchangeable, line transects (time series), spatial grid designs and permutation
853 of blocks (groups of samples). @code{permute} also allows split-plot designs,
854 in which the whole-plots or split-plots or both can be freely exchangeable.")
855 (license license:gpl2+)))
857 (define-public r-plyr
864 (uri (cran-uri "plyr" version))
866 (base32 "1igar5pcjqh0jyxv0z3jah8rz617vfa86vw0r5c7c031b7bj5db0"))))
867 (build-system r-build-system)
868 (native-inputs `(("r-rcpp" ,r-rcpp)))
869 (home-page "http://had.co.nz/plyr")
870 (synopsis "Tools for Splitting, Applying and Combining Data")
872 "Plyr is a set of tools that solves a common set of problems: you need to
873 break a big problem down into manageable pieces, operate on each piece and
874 then put all the pieces back together. For example, you might want to fit a
875 model to each spatial location or time point in your study, summarise data by
876 panels or collapse high-dimensional arrays to simpler summary statistics.")
877 (license license:expat)))
879 (define-public r-proto
886 (uri (cran-uri "proto" version))
888 (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
889 (build-system r-build-system)
890 (home-page "https://github.com/hadley/proto")
891 (synopsis "Prototype object-based programming")
893 "Proto is an object oriented system using object-based, also called
894 prototype-based, rather than class-based object oriented ideas.")
895 (license license:gpl2+)))
897 (define-public r-rcolorbrewer
899 (name "r-rcolorbrewer")
904 (uri (cran-uri "RColorBrewer" version))
906 (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
907 (build-system r-build-system)
908 (home-page "https://cran.r-project.org/web/packages/RColorBrewer")
909 (synopsis "ColorBrewer palettes")
911 "This package provides color schemes for maps (and other graphics)
912 designed by Cynthia Brewer as described at http://colorbrewer2.org")
913 ;; Includes code licensed under bsd-4
914 (license license:asl2.0)))
916 (define-public r-sendmailr
923 (uri (cran-uri "sendmailR" version))
926 "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
927 (properties `((upstream-name . "sendmailR")))
928 (build-system r-build-system)
930 `(("r-base64enc" ,r-base64enc)))
932 "https://cran.r-project.org/web/packages/sendmailR")
933 (synopsis "Send email using R")
935 "This package contains a simple SMTP client which provides a portable
936 solution for sending email, including attachments, from within R.")
937 (license license:gpl2+)))
939 (define-public r-stringi
946 (uri (cran-uri "stringi" version))
949 "0nck1s2iglmkrn15ay2chrrwsy5lngcylz2sc87fxy5skxaahxdl"))))
950 (build-system r-build-system)
951 (inputs `(("icu4c" ,icu4c)))
952 (native-inputs `(("pkg-config" ,pkg-config)))
953 (home-page "http://stringi.rexamine.com/")
954 (synopsis "Character string processing facilities")
956 "This package allows for fast, correct, consistent, portable, as well as
957 convenient character string/text processing in every locale and any native
958 encoding. Owing to the use of the ICU library, the package provides R users
959 with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
960 programmers. Among available features there are: pattern searching
961 (e.g. via regular expressions), random string generation, string collation,
962 transliteration, concatenation, date-time formatting and parsing, etc.")
963 (license license:bsd-3)))
965 (define-public r-stringr
972 (uri (cran-uri "stringr" version))
974 (base32 "07dvfbkhv8gk6l32j43jvxpmqlhqp0mdby406h5a3bsc6k94ic13"))))
975 (build-system r-build-system)
978 ("r-magrittr" ,r-magrittr)
979 ("r-stringi" ,r-stringi)))
980 (home-page "https://github.com/hadley/stringr")
981 (synopsis "Simple, consistent wrappers for common string operations")
983 "Stringr is a consistent, simple and easy to use set of wrappers around
984 the fantastic 'stringi' package. All function and argument names (and
985 positions) are consistent, all functions deal with \"NA\"'s and zero length
986 vectors in the same way, and the output from one function is easy to feed into
987 the input of another.")
988 (license license:gpl2+)))
990 (define-public r-reshape2
997 (uri (cran-uri "reshape2" version))
999 (base32 "03ki5ka1dj208fc0dclbm0b4xp9d769pah2j9cs34l776p4r9zwa"))))
1000 (build-system r-build-system)
1002 `(("r-plyr" ,r-plyr)
1004 ("r-stringr" ,r-stringr)))
1005 (home-page "https://github.com/hadley/reshape")
1006 (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
1008 "Reshape2 is an R library to flexibly restructure and aggregate data
1009 using just two functions: melt and dcast (or acast).")
1010 (license license:expat)))
1012 (define-public r-scales
1019 (uri (cran-uri "scales" version))
1021 (base32 "0zg9wfzmsdjxpbld0nzv7hcpq5r0wazqxmn7grvvif2agj0w1z6v"))))
1022 (build-system r-build-system)
1024 `(("r-dichromat" ,r-dichromat)
1025 ("r-labeling" ,r-labeling)
1026 ("r-munsell" ,r-munsell)
1028 ("r-rcolorbrewer" ,r-rcolorbrewer)
1031 ("r-viridislite" ,r-viridislite)))
1032 (home-page "https://github.com/hadley/scales")
1033 (synopsis "Scale functions for visualization")
1035 "This package provides graphical scales that map data to aesthetics, and
1036 provides methods for automatically determining breaks and labels for axes and
1038 (license license:expat)))
1040 (define-public r-ggplot2
1047 (uri (cran-uri "ggplot2" version))
1049 (base32 "0543782ddv2hp6s0l702mnxfg8n7a6qlbm8bm55x22hnqgz8kg2z"))))
1050 (build-system r-build-system)
1052 `(("r-digest" ,r-digest)
1053 ("r-gtable" ,r-gtable)
1055 ("r-lazyeval" ,r-lazyeval)
1057 ("r-tibble" ,r-tibble)
1058 ("r-reshape2" ,r-reshape2)
1059 ("r-scales" ,r-scales)
1060 ("r-svglite" ,r-svglite))) ; Needed for 'ggsave'
1061 (home-page "http://ggplot2.org")
1062 (synopsis "An implementation of the grammar of graphics")
1064 "Ggplot2 is an implementation of the grammar of graphics in R. It
1065 combines the advantages of both base and lattice graphics: conditioning and
1066 shared axes are handled automatically, and you can still build up a plot step
1067 by step from multiple data sources. It also implements a sophisticated
1068 multidimensional conditioning system and a consistent interface to map data to
1069 aesthetic attributes.")
1070 (license license:gpl2+)))
1072 (define-public r-ggdendro
1078 (uri (cran-uri "ggdendro" version))
1081 "1zzq1hxd0d1qa5hrzwfkdw6fzscpcafbwbpkrb62dm559y8awp0j"))))
1082 (build-system r-build-system)
1084 `(("r-ggplot2" ,r-ggplot2)
1086 ("r-knitr" ,r-knitr)))
1087 (home-page "https://github.com/andrie/ggdendro")
1088 (synopsis "Create Dendrograms and Tree Diagrams Using ggplot2")
1089 (description "This is a set of tools for dendrograms and tree plots using
1090 ggplot2. The ggplot2 philosophy is to clearly separate data from the
1091 presentation. Unfortunately the plot method for dendrograms plots directly
1092 to a plot device with out exposing the data. The ggdendro package resolves
1093 this by making available functions that extract the dendrogram plot data.
1094 The package provides implementations for tree, rpart, as well as diana and
1095 agnes cluster diagrams.")
1096 (license license:gpl2+)))
1098 (define-public r-gdtools
1105 (uri (cran-uri "gdtools" version))
1108 "122k9spymawfnfyksxyapwq9cigydy5nrjwhrwrhy3qkax3aycf6"))))
1109 (build-system r-build-system)
1111 `(("r-rcpp" ,r-rcpp)
1112 ("pkg-config" ,pkg-config)))
1117 `(("r-withr" ,r-withr)))
1118 (home-page "https://cran.r-project.org/web/packages/gdtools")
1119 (synopsis "Utilities for graphical rendering")
1121 "The @code{gdtools} package provides functionalities to get font metrics
1122 and to generate base64 encoded string from raster matrix.")
1123 (license license:gpl3)))
1125 (define-public r-svglite
1132 (uri (cran-uri "svglite" version))
1135 "1bws3lc4hlhln11zd7lalhiyc43yk6c6vrzy41fkxk1dkjazfx51"))))
1136 (build-system r-build-system)
1137 (native-inputs `(("r-rcpp" ,r-rcpp)))
1140 ("r-gdtools" ,r-gdtools)))
1141 (home-page "https://github.com/hadley/svglite")
1142 (synopsis "SVG graphics device")
1144 "@code{svglite} is a graphics device that produces clean
1145 @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
1146 hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
1147 considerably faster, produces smaller files, and leaves text as is.")
1148 (license license:gpl2+)))
1150 (define-public r-assertthat
1152 (name "r-assertthat")
1156 (uri (cran-uri "assertthat" version))
1159 "1wp5znk3xy338x6hknppk702jn596yr735d9i7c3wabm3sdzfgnp"))))
1160 (build-system r-build-system)
1161 (home-page "https://github.com/hadley/assertthat")
1162 (synopsis "Easy pre and post assertions")
1164 "Assertthat is an extension to stopifnot() that makes it easy to declare
1165 the pre and post conditions that your code should satisfy, while also
1166 producing friendly error messages so that your users know what they've done
1168 (license license:gpl3+)))
1170 (define-public r-lazyeval
1176 (uri (cran-uri "lazyeval" version))
1179 "0q9zx78ncy2ffzrf9sh053069kd3w1xn1ss3gsbyf3y4jhza9cw3"))))
1180 (build-system r-build-system)
1181 (home-page "https://github.com/hadley/lazyeval")
1182 (synopsis "Lazy (non-standard) evaluation in R")
1184 "This package provides the tools necessary to do non-standard
1185 evaluation (NSE) in R.")
1186 (license license:gpl3+)))
1188 (define-public r-dbi
1194 (uri (cran-uri "DBI" version))
1197 "16nf8flxr5vdz8yrpprfbzydy3ajixkp9hc8ibd9n7r9nc29waym"))))
1198 (build-system r-build-system)
1199 (home-page "https://github.com/rstats-db/DBI")
1200 (synopsis "R database interface")
1202 "The DBI package provides a database interface (DBI) definition for
1203 communication between R and relational database management systems. All
1204 classes in this package are virtual and need to be extended by the various
1205 R/DBMS implementations.")
1206 (license license:lgpl2.0+)))
1211 (version "1.66.0-1")
1214 (uri (cran-uri "BH" version))
1217 "14kab6wp0c27d8x4jqyf065p4bj210s9b67c0bfsfjnp29aypn8p"))))
1218 (build-system r-build-system)
1219 (home-page "https://github.com/eddelbuettel/bh")
1220 (synopsis "R package providing subset of Boost headers")
1222 "This package aims to provide the most useful subset of Boost libraries
1223 for template use among CRAN packages.")
1224 (license license:boost1.0)))
1226 (define-public r-evaluate
1232 (uri (cran-uri "evaluate" version))
1235 "070vvmnbdlp7sz2zhza7fhd2a6mlwiln8fn4hyzhsiizbn4n79y9"))))
1236 (build-system r-build-system)
1238 `(("r-stringr" ,r-stringr)))
1239 (home-page "https://github.com/hadley/evaluate")
1240 (synopsis "Parsing and evaluation tools for R")
1242 "This package provides tools that allow you to recreate the parsing,
1243 evaluation and display of R code, with enough information that you can
1244 accurately recreate what happens at the command line. The tools can easily be
1245 adapted for other output formats, such as HTML or LaTeX.")
1246 (license license:gpl3+)))
1248 (define-public r-formatr
1254 (uri (cran-uri "formatR" version))
1257 "19sd23vgs4ac0fwlw40j3676k6mramb0ajlq8hdw23kjwdx1jk47"))))
1258 (build-system r-build-system)
1259 (home-page "http://yihui.name/formatR")
1260 (synopsis "Format R code automatically")
1262 "This package provides a function to format R source code. Spaces and
1263 indent will be added to the code automatically, and comments will be preserved
1264 under certain conditions, so that R code will be more human-readable and tidy.
1265 There is also a Shiny app as a user interface in this package.")
1266 (license license:gpl3+)))
1268 (define-public r-highr
1274 (uri (cran-uri "highr" version))
1277 "0n9v44dxdy5fhkdmpbpa2p78whyd9z3rhhy42ipdz5m5vsr55qa3"))))
1278 (build-system r-build-system)
1279 (home-page "https://github.com/yihui/highr")
1280 (synopsis "Syntax highlighting for R source code")
1282 "This package provides syntax highlighting for R source code. Currently
1283 it supports LaTeX and HTML output. Source code of other languages is
1284 supported via Andre Simon's highlight package.")
1285 (license license:gpl3+)))
1287 (define-public r-mime
1293 (uri (cran-uri "mime" version))
1296 "0i91m3ivaja1k33jwcvz16pfjypkci27awm8glil7sxhmwaj3izw"))))
1297 (build-system r-build-system)
1298 (home-page "https://github.com/yihui/mime")
1299 (synopsis "R package to map filenames to MIME types")
1301 "This package guesses the MIME type from a filename extension using the
1302 data derived from /etc/mime.types in UNIX-type systems.")
1303 (license license:gpl2)))
1305 (define-public r-markdown
1311 (uri (cran-uri "markdown" version))
1314 "1vcgsh2m2f5kfgappgg71nbf04ff0j1sbk668krjs3r2n89dk3sk"))))
1315 (build-system r-build-system)
1316 ;; Skip check phase because the tests require the r-knitr package to be
1317 ;; installed. This prevents installation failures. Knitr normally
1318 ;; shouldn't be available since r-markdown is a dependency of the r-knitr
1320 (arguments `(#:tests? #f))
1322 `(("r-mime" ,r-mime)))
1323 (home-page "https://github.com/rstudio/markdown")
1324 (synopsis "Markdown rendering for R")
1326 "This package provides R bindings to the Sundown Markdown rendering
1327 library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
1328 syntax that can be converted to XHTML or other formats.")
1329 (license license:gpl2)))
1331 (define-public r-yaml
1337 (uri (cran-uri "yaml" version))
1340 "10y6wnv2v8k396far29haqv2s82p4zm04rrsxk183wg19gb51was"))))
1341 (build-system r-build-system)
1342 (home-page "https://cran.r-project.org/web/packages/yaml/")
1343 (synopsis "Methods to convert R data to YAML and back")
1345 "This package implements the libyaml YAML 1.1 parser and
1346 emitter (http://pyyaml.org/wiki/LibYAML) for R.")
1347 (license license:bsd-3)))
1349 (define-public r-knitr
1355 (uri (cran-uri "knitr" version))
1358 "1408dm25cxahk2clff8hlajaqdj5v1gs40nm3q6rf0ghd82hj93v"))))
1359 (build-system r-build-system)
1361 `(("r-evaluate" ,r-evaluate)
1362 ("r-highr" ,r-highr)
1363 ("r-markdown" ,r-markdown)
1364 ("r-stringr" ,r-stringr)
1365 ("r-yaml" ,r-yaml)))
1366 (home-page "http://yihui.name/knitr/")
1367 (synopsis "General-purpose package for dynamic report generation in R")
1369 "This package provides a general-purpose tool for dynamic report
1370 generation in R using Literate Programming techniques.")
1371 ;; The code is released under any version of the GPL. As it is used by
1372 ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
1374 (license license:gpl2+)))
1376 (define-public r-knitrbootstrap
1378 (name "r-knitrbootstrap")
1383 (uri (cran-uri "knitrBootstrap" version))
1386 "089147g7nqp99rwdxxsfmklsrwc8aia09sr8ndmrc335r33v6r6p"))))
1387 (properties `((upstream-name . "knitrBootstrap")))
1388 (build-system r-build-system)
1390 `(("r-knitr" ,r-knitr)
1391 ("r-rmarkdown" ,r-rmarkdown)))
1392 (home-page "https://github.com/jimhester/knitrBootstrap")
1393 (synopsis "Knitr bootstrap framework")
1395 "This package provides a framework to create Bootstrap 3 HTML reports
1396 from knitr Rmarkdown.")
1397 (license license:expat)))
1399 (define-public r-microbenchmark
1401 (name "r-microbenchmark")
1405 (uri (cran-uri "microbenchmark" version))
1408 "0fv2w2vsiz18imf4115nd9chhmf275w2mb49pn7pkxi6z3bamc9c"))))
1409 (build-system r-build-system)
1410 (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
1411 (synopsis "Accurate timing functions for R")
1413 "This package provides infrastructure to accurately measure and compare
1414 the execution time of R expressions.")
1415 (license license:bsd-2)))
1417 (define-public r-pryr
1423 (uri (cran-uri "pryr" version))
1426 "06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k"))))
1427 (build-system r-build-system)
1429 `(("r-stringr" ,r-stringr)
1430 ("r-codetools" ,r-codetools)))
1432 `(("r-rcpp" ,r-rcpp)))
1433 (home-page "https://github.com/hadley/pryr")
1434 (synopsis "Tools for computing on the R language")
1436 "This package provides useful tools to pry back the covers of R and
1437 understand the language at a deeper level.")
1438 (license license:gpl2)))
1440 (define-public r-memoise
1446 (uri (cran-uri "memoise" version))
1449 "034qfc2xlh30x1q2vya239w34a3ir3y2fwnx2agbgbi6592zjxmj"))))
1450 (build-system r-build-system)
1452 `(("r-digest" ,r-digest)))
1453 (home-page "https://github.com/hadley/memoise")
1454 (synopsis "Memoise functions for R")
1456 "This R package allows to cache the results of a function so that when
1457 you call it again with the same arguments it returns the pre-computed value.")
1458 (license license:expat)))
1460 (define-public r-crayon
1466 (uri (cran-uri "crayon" version))
1469 "0s7s6vc3ww8pzanpjisym4jjvwcc5pi2qg8srx7jqlz9j3wrnvpw"))))
1470 (build-system r-build-system)
1472 `(("r-memoise" ,r-memoise)))
1473 (home-page "https://github.com/gaborcsardi/crayon")
1474 (synopsis "Colored terminal output for R")
1476 "Colored terminal output on terminals that support ANSI color and
1477 highlight codes. It also works in Emacs ESS. ANSI color support is
1478 automatically detected. Colors and highlighting can be combined and nested.
1479 New styles can also be created easily. This package was inspired by the
1480 \"chalk\" JavaScript project.")
1481 (license license:expat)))
1483 (define-public r-praise
1490 (uri (cran-uri "praise" version))
1493 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
1494 (build-system r-build-system)
1495 (home-page "https://github.com/gaborcsardi/praise")
1496 (synopsis "Functions to praise users")
1498 "This package provides template functions to assist in building friendly
1499 R packages that praise their users.")
1500 (license license:expat)))
1502 (define-public r-testthat
1508 (uri (cran-uri "testthat" version))
1511 "155l53kb69jga5d8c5nvdwqlvlgfmk4vzyyl4d0108j53jnlgh1v"))))
1512 (build-system r-build-system)
1515 ("r-crayon" ,r-crayon)
1516 ("r-digest" ,r-digest)
1517 ("r-magrittr" ,r-magrittr)
1518 ("r-praise" ,r-praise)
1520 ("r-rlang" ,r-rlang)
1521 ("r-withr" ,r-withr)))
1522 (home-page "https://github.com/hadley/testthat")
1523 (synopsis "Unit testing for R")
1525 "This package provides a unit testing system for R designed to be fun,
1526 flexible and easy to set up.")
1527 (license license:expat)))
1535 (uri (cran-uri "R6" version))
1538 "13xfdr19ca7ymisidsanm6w7hsk3qmy5l8c0mlz3nk48f7s5cxq8"))))
1539 (build-system r-build-system)
1540 (home-page "https://github.com/wch/R6/")
1541 (synopsis "Classes with reference semantics in R")
1543 "The R6 package allows the creation of classes with reference semantics,
1544 similar to R's built-in reference classes. Compared to reference classes, R6
1545 classes are simpler and lighter-weight, and they are not built on S4 classes
1546 so they do not require the methods package. These classes allow public and
1547 private members, and they support inheritance, even when the classes are
1548 defined in different packages.")
1549 (license license:expat)))
1551 (define-public r-rlang
1557 (uri (cran-uri "rlang" version))
1560 "0f87fhw5pj6s2zjdxnpnd7pwn78czdz71b0xhm5adqg1p38sfwj8"))))
1561 (build-system r-build-system)
1562 (home-page "http://rlang.tidyverse.org")
1563 (synopsis "Functions for base types, core R and Tidyverse features")
1564 (description "This package provides a toolbox for working with base types,
1565 core R features like the condition system, and core @code{Tidyverse} features
1566 like tidy evaluation.")
1567 (license license:gpl3)))
1569 (define-public r-tibble
1576 (uri (cran-uri "tibble" version))
1579 "05svbjkm1xqv56ybjgsqqg2pp8nn6hams1yxcr8aanbhzx9h6rqi"))))
1580 (build-system r-build-system)
1582 `(("r-rlang" ,r-rlang)
1584 ("r-crayon" ,r-crayon)
1585 ("r-pillar" ,r-pillar)))
1586 (home-page "https://github.com/hadley/tibble")
1587 (synopsis "Simple data frames")
1589 "This package provides a @code{tbl_df} class that offers better checking
1590 and printing capabilities than traditional data frames.")
1591 (license license:expat)))
1593 (define-public r-dplyr
1599 (uri (cran-uri "dplyr" version))
1602 "1hm8ml7yaraag1ak6kvz2mxx6if568c759ix8a1n9d7va03wj7vv"))))
1603 (build-system r-build-system)
1605 `(("r-assertthat" ,r-assertthat)
1607 ("r-magrittr" ,r-magrittr)
1608 ("r-rlang" ,r-rlang)
1609 ("r-plogr" ,r-plogr)
1611 ("r-pkgconfig" ,r-pkgconfig)
1612 ("r-bindrcpp" ,r-bindrcpp)
1613 ("r-tibble" ,r-tibble)))
1615 `(("r-rcpp" ,r-rcpp)
1617 (home-page "https://github.com/hadley/dplyr")
1618 (synopsis "Tools for working with data frames in R")
1620 "dplyr is the next iteration of plyr. It is focussed on tools for
1621 working with data frames. It has three main goals: 1) identify the most
1622 important data manipulation tools needed for data analysis and make them easy
1623 to use in R; 2) provide fast performance for in-memory data by writing key
1624 pieces of code in C++; 3) use the same code interface to work with data no
1625 matter where it is stored, whether in a data frame, a data table or
1627 (license license:expat)))
1629 (define-public r-dbplyr
1636 (uri (cran-uri "dbplyr" version))
1639 "1nwrls9c3kc9q7405jp6b9sh23642sz13yw55iikgw134shffj5k"))))
1640 (build-system r-build-system)
1642 `(("r-assertthat" ,r-assertthat)
1644 ("r-dplyr" ,r-dplyr)
1646 ("r-purrr" ,r-purrr)
1648 ("r-rlang" ,r-rlang)
1649 ("r-tibble" ,r-tibble)
1650 ("r-tidyselect" ,r-tidyselect)))
1651 (home-page "https://github.com/tidyverse/dbplyr")
1652 (synopsis "Dplyr back end for databases")
1654 "This package provides a dplyr back end for databases that allows you to
1655 work with remote database tables as if they are in-memory data frames. Basic
1656 features works with any database that has a @code{DBI} back end; more advanced
1657 features require SQL translation to be provided by the package author.")
1658 (license license:expat)))
1660 (define-public r-acepack
1667 (uri (cran-uri "acepack" version))
1670 "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
1671 (build-system r-build-system)
1673 `(("gfortran" ,gfortran)))
1674 (home-page "https://cran.r-project.org/web/packages/acepack")
1675 (synopsis "Functions for regression transformations")
1677 "This package provides ACE and AVAS methods for choosing regression
1679 (license license:expat)))
1681 (define-public r-formula
1688 (uri (cran-uri "Formula" version))
1691 "0ad49bzip1zqmpj1d8jajwl4bd81fm3k6dq8p26x6mvlzc04dvwd"))))
1692 (properties `((upstream-name . "Formula")))
1693 (build-system r-build-system)
1694 (home-page "https://cran.r-project.org/web/packages/Formula")
1695 (synopsis "Extended model formulas")
1697 "This package provides a new class @code{Formula}, which extends the base
1698 class @code{formula}. It supports extended formulas with multiple parts of
1699 regressors on the right-hand side and/or multiple responses on the left-hand
1701 (license (list license:gpl2+ license:gpl3+))))
1703 (define-public r-locfit
1710 (uri (cran-uri "locfit" version))
1713 "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
1714 (build-system r-build-system)
1716 `(("r-lattice" ,r-lattice)))
1717 (home-page "https://cran.r-project.org/web/packages/locfit")
1718 (synopsis "Local regression, likelihood and density estimation")
1720 "This package provides functions used for local regression, likelihood
1721 and density estimation.")
1722 (license (list license:gpl2+ license:gpl3+))))
1724 (define-public r-chron
1730 (uri (cran-uri "chron" version))
1733 "185lfp75cv3l4cavg64sccj8lgc5sivch13n6gkannv3pd5cyzy4"))))
1734 (build-system r-build-system)
1735 (home-page "https://cran.r-project.org/web/packages/chron")
1736 (synopsis "Chronological R objects which can handle dates and times")
1738 "This package provides chronological R objects which can handle dates and
1740 (license license:gpl2)))
1742 (define-public r-data-table
1744 (name "r-data-table")
1745 (version "1.10.4-3")
1748 (uri (cran-uri "data.table" version))
1751 "12caklgr19vy9wprdks6zh825vr1iw1cajgwcnbpyvmijqdlz2xs"))))
1752 (build-system r-build-system)
1753 (home-page "https://github.com/Rdatatable/data.table/wiki")
1754 (synopsis "Enhanced version of data.frame R object")
1756 "The R package @code{data.table} is an extension of @code{data.frame}
1757 providing functions for fast aggregation of large data (e.g. 100GB in RAM),
1758 fast ordered joins, fast add/modify/delete of columns by group, column listing
1759 and fast file reading.")
1760 (license license:gpl3+)))
1762 (define-public r-xtable
1769 (uri (cran-uri "xtable" version))
1772 "0398qkpvlw3dv0myz4mjcyqwpwc2m31l127r8vdzwc71wb6s28qn"))))
1773 (build-system r-build-system)
1775 `(("r-knitr" ,r-knitr)))
1776 (home-page "http://xtable.r-forge.r-project.org/")
1777 (synopsis "Export R tables to LaTeX or HTML")
1779 "This package provides tools to export R data as LaTeX and HTML tables.")
1780 (license license:gpl2+)))
1782 (define-public python-patsy
1784 (name "python-patsy")
1788 (uri (pypi-uri "patsy" version ".zip"))
1791 "1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w"))))
1792 (build-system python-build-system)
1795 (modify-phases %standard-phases
1796 (replace 'check (lambda _ (zero? (system* "nosetests" "-v")))))))
1798 `(("python-numpy" ,python-numpy)
1799 ("python-scipy" ,python-scipy)
1800 ("python-six" ,python-six)))
1802 `(("python-nose" ,python-nose)
1804 (home-page "https://github.com/pydata/patsy")
1805 (synopsis "Describe statistical models and build design matrices")
1807 "Patsy is a Python package for describing statistical models and for
1808 building design matrices.")
1809 ;; The majority of the code is distributed under BSD-2. The module
1810 ;; patsy.compat contains code derived from the Python standard library,
1811 ;; and is covered by the PSFL.
1812 (license (list license:bsd-2 license:psfl))))
1814 (define-public python2-patsy
1815 (package-with-python2 python-patsy))
1817 (define-public python-statsmodels
1819 (name "python-statsmodels")
1824 (uri (pypi-uri "statsmodels" version))
1827 "0j30v3932shnj9368c9jr3svkyrvfj90h2l7nxnqkbpv0svilhr6"))
1828 (patches (search-patches "python-statsmodels-fix-tests.patch"))))
1829 (build-system python-build-system)
1832 (modify-phases %standard-phases
1833 ;; tests must be run after installation
1835 (add-after 'unpack 'set-matplotlib-backend-to-agg
1837 ;; Set the matplotlib backend to Agg to avoid problems using the
1838 ;; GTK backend without a display.
1839 (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py")
1840 '("statsmodels/tsa/vector_ar/tests/test_var.py"
1841 "statsmodels/duration/tests/test_survfunc.py"))
1842 (("import matplotlib\\.pyplot as plt" line)
1843 (string-append "import matplotlib;matplotlib.use('Agg');"
1846 (add-after 'install 'check
1847 (lambda* (#:key inputs outputs #:allow-other-keys)
1848 ;; Make installed package available for running the tests
1849 (add-installed-pythonpath inputs outputs)
1850 (with-directory-excursion "/tmp"
1851 (zero? (system* "nosetests"
1853 "-v" "statsmodels"))))))))
1855 `(("python-numpy" ,python-numpy)
1856 ("python-scipy" ,python-scipy)
1857 ("python-pandas" ,python-pandas)
1858 ("python-patsy" ,python-patsy)
1859 ("python-matplotlib" ,python-matplotlib)))
1861 `(("python-cython" ,python-cython)
1862 ("python-nose" ,python-nose)
1863 ("python-sphinx" ,python-sphinx)))
1864 (home-page "http://statsmodels.sourceforge.net/")
1865 (synopsis "Statistical modeling and econometrics in Python")
1867 "Statsmodels is a Python package that provides a complement to scipy for
1868 statistical computations including descriptive statistics and estimation and
1869 inference for statistical models.")
1870 (license license:bsd-3)))
1872 (define-public python2-statsmodels
1873 (let ((stats (package-with-python2 python-statsmodels)))
1874 (package (inherit stats)
1876 `(("python2-pytz" ,python2-pytz)
1877 ("python2-numpy" ,python2-numpy)
1878 ("python2-scipy" ,python2-scipy)
1879 ("python2-pandas" ,python2-pandas)
1880 ("python2-patsy" ,python2-patsy)
1881 ("python2-matplotlib" ,python2-matplotlib))))))
1883 (define-public r-coda
1889 (uri (cran-uri "coda" version))
1892 "14a4a8df4ygj05h37chmdn8kzcqs07fpbflxfrq530563mrza7yl"))))
1893 (build-system r-build-system)
1895 `(("r-lattice" ,r-lattice)))
1896 (home-page "https://cran.r-project.org/web/packages/coda")
1897 (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
1898 (description "This package provides functions for summarizing and plotting
1899 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
1900 diagnostic tests of convergence to the equilibrium distribution of the Markov
1902 (license license:gpl2+)))
1904 (define-public r-ade4
1911 (uri (cran-uri "ade4" version))
1914 "0zk81x0yn30gbyc0jpzyw1nxd08ccihl6vyk0ijvj3aw3nr5flc6"))))
1915 (build-system r-build-system)
1917 `(("r-mass" ,r-mass)))
1918 (home-page "http://pbil.univ-lyon1.fr/ADE-4")
1919 (synopsis "Multivariate data analysis and graphical display")
1921 "The ade4 package contains data analysis functions to analyze ecological
1922 and environmental data in the framework of Euclidean exploratory methods.")
1923 (license license:gpl2+)))
1925 (define-public r-xml2
1932 (uri (cran-uri "xml2" version))
1935 "154lmksfiwkhnlmryas25mjhfg6k4mmnnk7bbb29mnn5x5pr2yha"))))
1936 (build-system r-build-system)
1938 `(("libxml2" ,libxml2)
1941 `(("pkg-config" ,pkg-config)))
1943 `(("r-rcpp" ,r-rcpp)))
1944 (home-page "https://github.com/hadley/xml2")
1945 (synopsis "Parse XML with R")
1947 "This package provides a simple, consistent interface to working with XML
1948 files in R. It is built on top of the libxml2 C library.")
1949 (license license:gpl2+)))
1951 (define-public r-multitaper
1953 (name "r-multitaper")
1958 (uri (cran-uri "multitaper" version))
1961 "04wd9bbhyx7697pfy0fpj02v1csr48hkpqj62h9p8a6w84ji4k68"))))
1962 (build-system r-build-system)
1964 `(("gfortran" ,gfortran)))
1965 (home-page "https://github.com/wesleyburr/multitaper/")
1966 (synopsis "Multitaper spectral analysis tools")
1968 "This package implements multitaper spectral estimation
1969 techniques using prolate spheroidal sequences (Slepians) and sine
1970 tapers for time series analysis. It includes an adaptive weighted
1971 multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
1972 F-test, and complex demodulation. The Slepians sequences are
1973 generated efficiently using a tridiagonal matrix solution, and
1974 jackknifed confidence intervals are available for most estimates.")
1975 (license license:gpl2+)))
1977 (define-public r-rversions
1979 (name "r-rversions")
1983 (uri (cran-uri "rversions" version))
1986 "0i2gi05nrvknr7g89rbppkswyfcwwd4r9gp75fdfhpah8sgq1l11"))))
1987 (build-system r-build-system)
1989 `(("r-curl" ,r-curl)
1990 ("r-xml2" ,r-xml2)))
1991 (home-page "https://github.com/metacran/rversions")
1992 (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
1994 "This package provides functions to query the main R repository to find
1995 the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
1996 previous R versions and their release dates.")
1997 (license license:expat)))
1999 (define-public r-whisker
2005 (uri (cran-uri "whisker" version))
2008 "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28"))))
2009 (build-system r-build-system)
2010 (home-page "https://github.com/edwindj/whisker")
2011 (synopsis "Logicless mustache templating for R")
2013 "This package provides logicless templating, with a syntax that is not
2015 (license license:gpl3+)))
2017 (define-public r-backports
2019 (name "r-backports")
2024 (uri (cran-uri "backports" version))
2027 "0mml9h3xagi7144pyb3jj9zbh9qzns7izkhdg7df20v7bikr6nz8"))))
2028 (build-system r-build-system)
2029 (home-page "https://cran.r-project.org/web/packages/backports")
2030 (synopsis "Reimplementations of functions introduced since R 3.0.0")
2032 "Provides implementations of functions which have been introduced in R
2033 since version 3.0.0. The backports are conditionally exported which results
2034 in R resolving the function names to the version shipped with R (if available)
2035 and uses the implemented backports as fallback. This way package developers
2036 can make use of the new functions without worrying about the minimum required
2038 (license license:gpl2+)))
2040 (define-public r-checkmate
2042 (name "r-checkmate")
2047 (uri (cran-uri "checkmate" version))
2050 "1q6igk50lq4fp5d3imgcn1j063h3gsp214ra4nlf534hf4wjlkg9"))))
2051 (build-system r-build-system)
2053 `(("r-backports" ,r-backports)))
2054 (home-page "https://github.com/mllg/checkmate")
2055 (synopsis "Fast and versatile argument checks")
2057 "This package provides tests and assertions to perform frequent argument
2058 checks. A substantial part of the package was written in C to minimize any
2059 worries about execution time overhead.")
2060 (license license:bsd-3)))
2062 (define-public r-bbmisc
2069 (uri (cran-uri "BBmisc" version))
2072 "1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y"))))
2073 (properties `((upstream-name . "BBmisc")))
2074 (build-system r-build-system)
2076 `(("r-checkmate" ,r-checkmate)))
2077 (home-page "https://github.com/berndbischl/BBmisc")
2078 (synopsis "Miscellaneous functions for R package development")
2080 "This package provides miscellaneous helper functions for the development
2082 (license license:bsd-3)))
2084 (define-public r-fail
2091 (uri (cran-uri "fail" version))
2094 "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
2095 (build-system r-build-system)
2097 `(("r-bbmisc" ,r-bbmisc)
2098 ("r-checkmate" ,r-checkmate)))
2099 (home-page "https://github.com/mllg/fail")
2100 (synopsis "File abstraction interface layer (FAIL)")
2102 "This package provides a more comfortable interface to work with R data
2103 or source files in a key-value fashion.")
2104 (license license:bsd-3)))
2106 (define-public r-batchjobs
2108 (name "r-batchjobs")
2113 (uri (cran-uri "BatchJobs" version))
2116 "035658marnw57p4f38g99rwmvmb6hpbq0fhlxp3qbw22zfnnkvs9"))))
2117 (properties `((upstream-name . "BatchJobs")))
2118 (build-system r-build-system)
2120 `(("r-backports" ,r-backports)
2121 ("r-bbmisc" ,r-bbmisc)
2123 ("r-checkmate" ,r-checkmate)
2124 ("r-data-table" ,r-data-table)
2126 ("r-digest" ,r-digest)
2127 ("r-rsqlite" ,r-rsqlite)
2128 ("r-sendmailr" ,r-sendmailr)
2129 ("r-stringi" ,r-stringi)))
2130 (home-page "https://github.com/tudo-r/BatchJobs")
2131 (synopsis "Batch computing with R")
2133 "This package provides @code{Map}, @code{Reduce} and @code{Filter}
2134 variants to generate jobs on batch computing systems like PBS/Torque, LSF,
2135 SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
2136 (license license:bsd-2)))
2138 (define-public r-brew
2144 (uri (cran-uri "brew" version))
2147 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
2148 (build-system r-build-system)
2149 (home-page "https://cran.r-project.org/web/packages/brew")
2150 (synopsis "Templating framework for report generation")
2152 "The brew package implements a templating framework for mixing text and R
2153 code for report generation. The template syntax is similar to PHP, Ruby's erb
2154 module, Java Server Pages, and Python's psp module.")
2155 (license license:gpl2+)))
2157 (define-public r-desc
2164 (uri (cran-uri "desc" version))
2167 "0k07qighac1xzmm8k988zi7i88a0yfvia3gk5hbz0fyvb2v9kzrj"))))
2168 (build-system r-build-system)
2170 `(("r-assertthat" ,r-assertthat)
2171 ("r-crayon" ,r-crayon)
2173 ("r-rprojroot" ,r-rprojroot)))
2174 (home-page "https://github.com/r-pkgs/desc")
2175 (synopsis "Manipulate DESCRIPTION Files")
2177 "This package provides tools to read, write, create, and manipulate
2178 DESCRIPTION files. It is intended for packages that create or manipulate
2180 (license license:expat)))
2182 (define-public r-commonmark
2184 (name "r-commonmark")
2189 (uri (cran-uri "commonmark" version))
2192 "1vb8r9khpvcf0q7acv8rsplfjjwcll302bg5kp596cvn6aacypl6"))))
2193 (build-system r-build-system)
2194 (home-page "https://cran.r-project.org/web/packages/commonmark")
2195 (synopsis "CommonMark and Github Markdown Rendering in R")
2197 "The CommonMark specification defines a rationalized version of markdown
2198 syntax. This package uses the 'cmark' reference implementation for converting
2199 markdown text into various formats including HTML, LaTeX and groff man. In
2200 addition, it exposes the markdown parse tree in XML format. The latest
2201 version of this package also adds support for Github extensions including
2202 tables, autolinks and strikethrough text.")
2203 (license license:bsd-2)))
2205 (define-public r-roxygen2
2211 (uri (cran-uri "roxygen2" version))
2214 "0xpzziminf225kjwhyl51kgkzhplyzhk5farhf5s822krl2xqbfj"))))
2215 (build-system r-build-system)
2217 `(("r-brew" ,r-brew)
2218 ("r-commonmark" ,r-commonmark)
2220 ("r-digest" ,r-digest)
2223 ("r-stringi" ,r-stringi)
2224 ("r-stringr" ,r-stringr)
2225 ("r-xml2" ,r-xml2)))
2226 (home-page "https://github.com/klutometis/roxygen")
2227 (synopsis "In-source documentation system for R")
2229 "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
2230 collation, and NAMESPACE files.")
2231 (license license:gpl2+)))
2233 (define-public r-openssl
2240 (uri (cran-uri "openssl" version))
2243 "1qyql5gpwf88bkm1qarjhbqbq4hn6w0d8j4pxb5x7i96is30ap30"))))
2244 (build-system r-build-system)
2246 `(("libressl" ,libressl)))
2247 (home-page "https://github.com/jeroenooms/openssl")
2248 (synopsis "Toolkit for encryption, signatures and certificates")
2250 "This package provides R bindings to OpenSSL libssl and libcrypto, plus
2251 custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
2252 and P-521. Cryptographic signatures can either be created and verified
2253 manually or via x509 certificates. AES block cipher is used in CBC mode for
2254 symmetric encryption; RSA for asymmetric (public key) encryption. High-level
2255 envelope functions combine RSA and AES for encrypting arbitrary sized data.
2256 Other utilities include key generators, hash functions (md5, sha1, sha256,
2257 etc), base64 encoder, a secure random number generator, and @code{bignum} math
2258 methods for manually performing crypto calculations on large multibyte
2260 (license license:expat)))
2262 (define-public r-httr
2268 (uri (cran-uri "httr" version))
2271 "0n7jz2digbgv48rbr9vmzv4vmf4rahl9jjy31izs7sxj4rs4s4r2"))))
2272 (build-system r-build-system)
2274 `(("r-curl" ,r-curl)
2275 ("r-jsonlite" ,r-jsonlite)
2276 ("r-openssl" ,r-openssl)
2279 (home-page "https://github.com/hadley/httr")
2280 (synopsis "Tools for working with URLs and HTTP")
2282 "The aim of httr is to provide a wrapper for RCurl customised to the
2283 demands of modern web APIs. It provides useful tools for working with HTTP
2284 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
2285 functions make it easy to control additional request components.")
2286 (license license:expat)))
2288 (define-public r-git2r
2294 (uri (cran-uri "git2r" version))
2297 "11xgddmxzh9cy85k8fb90il43qswpvryz0h9r0j1gbclfg2f9004"))))
2298 (build-system r-build-system)
2299 ;; This R package contains modified sources of libgit2. This modified
2300 ;; version of libgit2 is built as the package is built. Hence libgit2 is
2301 ;; not among the inputs of this package.
2303 `(("libssh2" ,libssh2)
2304 ("openssl" ,openssl)
2306 (home-page "https://github.com/ropensci/git2r")
2307 (synopsis "Access Git repositories with R")
2309 "This package provides an R interface to the libgit2 library, which is a
2310 pure C implementation of the Git core methods.")
2311 ;; GPLv2 only with linking exception.
2312 (license license:gpl2)))
2314 (define-public r-rstudioapi
2316 (name "r-rstudioapi")
2320 (uri (cran-uri "rstudioapi" version))
2323 "133s75q2hr6jg28m1wvs96qrbc9c4vw87migwhkjqb88xxvbqhd5"))))
2324 (build-system r-build-system)
2325 (home-page "https://cran.r-project.org/web/packages/rstudioapi")
2326 (synopsis "Safely access the RStudio API")
2328 "This package provides functions to access the RStudio API and provide
2329 informative error messages when it's not available.")
2330 (license license:expat)))
2332 (define-public r-devtools
2338 (uri (cran-uri "devtools" version))
2341 "1x3wsk7dh3yakii61kbfvafx9yz66h40ixiwfkf03dnp2n24hngs"))))
2342 (build-system r-build-system)
2344 `(("r-digest" ,r-digest)
2345 ("r-git2r" ,r-git2r)
2347 ("r-jsonlite" ,r-jsonlite)
2348 ("r-memoise" ,r-memoise)
2349 ("r-rstudioapi" ,r-rstudioapi)
2350 ("r-whisker" ,r-whisker)
2351 ("r-withr" ,r-withr)))
2352 (home-page "https://github.com/hadley/devtools")
2353 (synopsis "Tools to make developing R packages easier")
2354 (description "The devtools package is a collection of package development
2355 tools to simplify the devolpment of R packages.")
2356 (license license:gpl2+)))
2358 (define-public r-withr
2364 (uri (cran-uri "withr" version))
2367 "11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1"))))
2368 (build-system r-build-system)
2369 (home-page "https://github.com/jimhester/withr")
2370 (synopsis "Run code with temporarily modified global state")
2372 "This package provides a set of functions to run R code in an environment
2373 in which global state has been temporarily modified. Many of these functions
2374 were originally a part of the r-devtools package.")
2375 (license license:gpl2+)))
2377 (define-public r-hms
2384 (uri (cran-uri "hms" version))
2387 "0vr7k3a7k52a5yf67bwzl88lkjz09v1avw5axdk1y9v3nz33zl2h"))))
2388 (build-system r-build-system)
2390 `(("r-rlang" ,r-rlang)
2391 ("r-pkgconfig" ,r-pkgconfig)))
2392 (home-page "https://github.com/rstats-db/hms")
2393 (synopsis "Pretty time of day")
2395 "This package implements an S3 class for storing and formatting
2396 time-of-day values, based on the @code{difftime} class.")
2397 (license license:gpl3+)))
2399 (define-public r-readr
2405 (uri (cran-uri "readr" version))
2408 "1cvw5wdcqk88cp5fyv678mnmp66l3whcd2yh33p2qvx0168bja8s"))))
2409 (build-system r-build-system)
2411 `(("r-rcpp" ,r-rcpp)
2413 ("r-tibble" ,r-tibble)
2416 (home-page "https://github.com/hadley/readr")
2417 (synopsis "Read tabular data")
2419 "This package provides functions to read flat or tabular text files from
2420 disk (or a connection).")
2421 (license license:gpl2+)))
2423 (define-public r-plotrix
2429 (uri (cran-uri "plotrix" version))
2432 "0rw81n9p3d2i03b4pgcfj5blryc94f29bm9a4j9bnp5h8qjj6pry"))))
2433 (build-system r-build-system)
2434 (home-page "https://cran.r-project.org/web/packages/plotrix")
2435 (synopsis "Various plotting functions")
2437 "This package provides lots of plotting, various labeling, axis and color
2438 scaling functions for R.")
2439 (license license:gpl2+)))
2441 (define-public r-gridbase
2447 (uri (cran-uri "gridBase" version))
2450 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
2451 (build-system r-build-system)
2452 (home-page "https://cran.r-project.org/web/packages/gridBase")
2453 (synopsis "Integration of base and grid graphics")
2455 "This package provides an integration of base and grid graphics for R.")
2456 (license license:gpl2+)))
2458 (define-public r-latticeextra
2460 (name "r-latticeextra")
2465 (uri (cran-uri "latticeExtra" version))
2468 "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq"))))
2469 (properties `((upstream-name . "latticeExtra")))
2470 (build-system r-build-system)
2472 `(("r-lattice" ,r-lattice)
2473 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2474 (home-page "http://latticeextra.r-forge.r-project.org/")
2475 (synopsis "Extra graphical utilities based on lattice")
2477 "Building on the infrastructure provided by the lattice package, this
2478 package provides several new high-level graphics functions and methods, as
2479 well as additional utilities such as panel and axis annotation functions.")
2480 (license license:gpl2+)))
2482 (define-public r-rcpparmadillo
2484 (name "r-rcpparmadillo")
2485 (version "0.8.400.0.0")
2488 (uri (cran-uri "RcppArmadillo" version))
2491 "11y2ksf46zw6fcz0kk70szyfn7qqxwwd33xylrxvnyb7ldmbc5yr"))))
2492 (properties `((upstream-name . "RcppArmadillo")))
2493 (build-system r-build-system)
2495 `(("r-knitr" ,r-knitr))) ; needed for vignettes
2497 `(("r-rcpp" ,r-rcpp)))
2498 (home-page "https://github.com/RcppCore/RcppArmadillo")
2499 (synopsis "Rcpp integration for the Armadillo linear algebra library")
2501 "Armadillo is a templated C++ linear algebra library that aims towards a
2502 good balance between speed and ease of use. Integer, floating point and
2503 complex numbers are supported, as well as a subset of trigonometric and
2504 statistics functions. Various matrix decompositions are provided through
2505 optional integration with LAPACK and ATLAS libraries. This package includes
2506 the header files from the templated Armadillo library.")
2507 ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
2508 ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
2509 ;; later, as is the rest of 'Rcpp'.
2510 (license license:gpl2+)))
2512 (define-public r-bitops
2518 (uri (cran-uri "bitops" version))
2521 "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
2522 (build-system r-build-system)
2523 (home-page "https://cran.r-project.org/web/packages/bitops")
2524 (synopsis "Bitwise operations")
2526 "This package provides functions for bitwise operations on integer
2528 (license license:gpl2+)))
2530 (define-public r-catools
2536 (uri (cran-uri "caTools" version))
2539 "1x4szsn2qmbzpyjfdaiz2q7jwhap2gky9wq0riah74q0pzz76ank"))))
2540 (properties `((upstream-name . "caTools")))
2541 (build-system r-build-system)
2543 `(("r-bitops" ,r-bitops)))
2544 (home-page "https://cran.r-project.org/web/packages/caTools")
2545 (synopsis "Various tools including functions for moving window statistics")
2547 "This package contains several basic utility functions including:
2548 moving (rolling, running) window statistic functions, read/write for GIF and
2549 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
2550 encoder/decoder, round-off-error-free sum and cumsum, etc.")
2551 (license license:gpl3+)))
2553 (define-public r-rprojroot
2555 (name "r-rprojroot")
2560 (uri (cran-uri "rprojroot" version))
2563 "12r3fdxmi2pmwn6ic3rhg0b20ll5z420m0d8fziv1n21961namnz"))))
2564 (build-system r-build-system)
2566 `(("r-backports" ,r-backports)))
2567 (home-page "https://github.com/krlmlr/rprojroot")
2568 (synopsis "Finding files in project subdirectories")
2570 "This package helps accessing files relative to a project root. It
2571 provides helpers for robust, reliable and flexible paths to files below a
2572 project root. The root of a project is defined as a directory that matches a
2573 certain criterion, e.g., it contains a certain regular file.")
2574 (license license:gpl3)))
2576 (define-public r-rmarkdown
2578 (name "r-rmarkdown")
2583 (uri (cran-uri "rmarkdown" version))
2586 "0wq6kbhrkv3fhcy4hg5yyv9gdvf8gr4nsjwdifs4ih8lnn0dmdyb"))))
2587 (properties `((upstream-name . "rmarkdown")))
2588 (build-system r-build-system)
2590 `(("r-base64enc" ,r-base64enc)
2591 ("r-evaluate" ,r-evaluate)
2592 ("r-htmltools" ,r-htmltools)
2593 ("r-jsonlite" ,r-jsonlite)
2594 ("r-knitr" ,r-knitr)
2596 ("r-rprojroot" ,r-rprojroot)
2597 ("r-stringr" ,r-stringr)
2599 ;; rmarkdown works with the 2.x release of Pandoc, but with degraded
2600 ;; functionality. For example, tabbed plots do not currently work with
2601 ;; Pandoc 2. The authors of rmarkdown recommend the use of Pandoc 1
2602 ;; for the time being.
2603 ("ghc-pandoc" ,ghc-pandoc-1)))
2604 (home-page "http://rmarkdown.rstudio.com")
2605 (synopsis "Convert R Markdown documents into a variety of formats")
2607 "This package provides tools to convert R Markdown documents into a
2608 variety of formats.")
2609 (license license:gpl3+)))
2611 (define-public r-gtable
2617 (uri (cran-uri "gtable" version))
2620 "0vz7073m0a2q12qzzihrfh5c2kx5jqi5l7z470fxmwqghdllh7l0"))))
2621 (properties `((upstream-name . "gtable")))
2622 (build-system r-build-system)
2623 (home-page "https://cran.r-project.org/web/packages/gtable")
2624 (synopsis "R library to arrange grobs in tables")
2626 "Gtable is a collection of tools to make it easier to work with
2627 \"tables\" of grobs.")
2628 (license license:gpl2+)))
2630 (define-public r-gridextra
2632 (name "r-gridextra")
2636 (uri (cran-uri "gridExtra" version))
2639 "0fwfk3cdwxxim7nd55pn7m31bcaqj48y06j7an2k1v1pybk0rdl1"))))
2640 (properties `((upstream-name . "gridExtra")))
2641 (build-system r-build-system)
2643 `(("r-gtable" ,r-gtable)))
2645 `(("r-knitr" ,r-knitr))) ;for building vignettes
2646 (home-page "https://github.com/baptiste/gridextra")
2647 (synopsis "Miscellaneous functions for \"Grid\" graphics")
2649 "This package provides a number of user-level functions to work with
2650 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
2652 (license license:gpl2+)))
2654 (define-public r-pkgconfig
2656 (name "r-pkgconfig")
2660 (uri (cran-uri "pkgconfig" version))
2663 "0h2sp93fqqjbfqgq82a3i94ybnndx6ghaal8pbf99firnsjb40mb"))))
2664 (build-system r-build-system)
2665 (home-page "https://github.com/gaborcsardi/pkgconfig")
2666 (synopsis "Private configuration for R packages")
2667 (description "This package provides the functionality to set configuration
2668 options on a per-package basis. Options set by a given package only apply to
2669 that package, other packages are unaffected.")
2670 (license license:expat)))
2672 (define-public r-blob
2678 (uri (cran-uri "blob" version))
2681 "05pazzcyz3c3vd2l70zq9cf172cgjff4dnf419zigfnxycyn1mhn"))))
2682 (build-system r-build-system)
2684 `(("r-tibble" ,r-tibble)))
2685 (home-page "https://github.com/hadley/blob")
2686 (synopsis "Simple S3 Class for representing vectors of binary data")
2687 (description "Raw vectors in R are useful for storing a single binary
2688 object. What if you want to put a vector of them in a data frame? The blob
2689 package provides the blob object, a list of raw vectors, suitable for use as
2690 a column in data frame.")
2691 (license license:gpl3+)))
2693 (define-public r-rsqlite
2699 (uri (cran-uri "RSQLite" version))
2702 "1xpg1i1jkzkzv44k512k90c2vvl960pl2d4a3spwcha6yclyc3vz"))))
2703 (properties `((upstream-name . "RSQLite")))
2704 (build-system r-build-system)
2708 ("r-memoise" ,r-memoise)
2709 ("r-plogr" ,r-plogr)
2711 ("r-bit64" ,r-bit64)
2713 ("r-pkgconfig" ,r-pkgconfig)))
2714 (home-page "https://github.com/rstats-db/RSQLite")
2715 (synopsis "SQLite interface for R")
2717 "This package embeds the SQLite database engine in R and provides an
2718 interface compliant with the DBI package. The source for the SQLite
2719 engine (version 3.8.8.2) is included.")
2720 (license license:lgpl2.0+)))
2722 (define-public r-rcurl
2725 (version "1.95-0.1.2")
2728 (uri (string-append "https://www.bioconductor.org/packages/"
2729 "release/extra/src/"
2730 "contrib/RCurl_" version ".tar.gz"))
2733 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
2734 (properties `((upstream-name . "RCurl")))
2735 (build-system r-build-system)
2737 `(("libcurl" ,curl)))
2739 `(("r-bitops" ,r-bitops)))
2740 (home-page "http://www.omegahat.org/RCurl")
2741 (synopsis "General network client interface for R")
2743 "The package allows one to compose general HTTP requests and provides
2744 convenient functions to fetch URIs, GET and POST forms, etc. and process the
2745 results returned by the Web server. This provides a great deal of control
2746 over the HTTP/FTP/... connection and the form of the request while providing a
2747 higher-level interface than is available just using R socket connections.
2748 Additionally, the underlying implementation is robust and extensive,
2749 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
2750 ldap, and also supports cookies, redirects, authentication, etc.")
2751 (license license:bsd-3)))
2753 (define-public r-xml
2756 (version "3.98-1.10")
2759 (uri (cran-uri "XML" version))
2762 "1faza9bbllp67lf1yv1sllxc3iv8llz52m9diazhq322iqbh97m1"))))
2764 `((upstream-name . "XML")))
2765 (build-system r-build-system)
2767 `(("libxml2" ,libxml2)
2770 `(("pkg-config" ,pkg-config)))
2771 (home-page "http://www.omegahat.org/RSXML")
2772 (synopsis "Tools for parsing and generating XML within R")
2774 "Many approaches for both reading and creating XML (and HTML)
2775 documents (including DTDs), both local and accessible via HTTP or FTP. Also
2776 offers access to an XPath \"interpreter\".")
2777 (license license:bsd-2)))
2779 (define-public r-xnomial
2784 (origin (method url-fetch)
2785 (uri (cran-uri "XNomial" version))
2788 "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
2789 (properties (quasiquote ((upstream-name . "XNomial"))))
2790 (build-system r-build-system)
2791 (home-page "https://cran.r-project.org/web/packages/XNomial")
2792 (synopsis "Goodness-of-Fit test for multinomial data")
2794 "This package provides an exact Goodness-of-Fit test for
2795 multinomial data with fixed probabilities. It can be used to
2796 determine whether a set of counts fits a given expected ratio. To see
2797 whether a set of observed counts fits an expectation, one can examine
2798 all possible outcomes with @code{xmulti()} or a random sample of them
2799 with @code{xmonte()} and find the probability of an observation
2800 deviating from the expectation by at least as much as the observed.
2801 As a measure of deviation from the expected, one can use the
2802 log-likelihood ratio, the multinomial probability, or the classic
2803 chi-square statistic. A histogram of the test statistic can also be
2804 plotted and compared with the asymptotic curve.")
2805 (license (list license:gpl2+ license:gpl3+))))
2807 (define-public r-lambda-r
2813 (uri (cran-uri "lambda.r" version))
2816 "0vql32np716dpd0kjn7s7wgawd02ysgp2a5il4kb19nlw661ii3x"))))
2817 (properties `((upstream-name . "lambda.r")))
2818 (build-system r-build-system)
2821 (modify-phases %standard-phases
2822 (add-after 'check 'delete-test-log
2823 ;; The test report contains time stamps and is not important for
2824 ;; the installed package.
2825 (lambda* (#:key outputs #:allow-other-keys)
2826 (delete-file-recursively
2827 (string-append (assoc-ref outputs "out")
2828 "/site-library/lambda.r/unitTests"))
2831 `(("r-runit" ,r-runit)))
2832 (home-page "https://cran.r-project.org/web/packages/lambda.r")
2833 (synopsis "Functional programming extension for R")
2835 "This package provides a language extension to efficiently write
2836 functional programs in R. Syntax extensions include multi-part function
2837 definitions, pattern matching, guard statements, built-in (optional) type
2839 (license license:lgpl3+)))
2841 (define-public r-futile-options
2843 (name "r-futile-options")
2847 (uri (cran-uri "futile.options" version))
2850 "1hp82h6xqq5cck67h7lpf22n3j7mg3v1mla5y5ivnzrrb7iyr17f"))))
2852 `((upstream-name . "futile.options")))
2853 (build-system r-build-system)
2854 (home-page "https://cran.r-project.org/web/packages/futile.options")
2855 (synopsis "Options management framework")
2857 "The futile.options subsystem provides an easy user-defined options
2858 management system that is properly scoped. This means that options created
2859 via @code{futile.options} are fully self-contained and will not collide with
2860 options defined in other packages.")
2861 (license license:lgpl3+)))
2863 (define-public r-futile-logger
2865 (name "r-futile-logger")
2869 (uri (cran-uri "futile.logger" version))
2872 "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
2873 (properties `((upstream-name . "futile.logger")))
2874 (build-system r-build-system)
2876 `(("r-futile-options" ,r-futile-options)
2877 ("r-lambda-r" ,r-lambda-r)))
2878 (home-page "https://cran.r-project.org/web/packages/futile.logger")
2879 (synopsis "Logging utility for R")
2881 "This package provides a simple yet powerful logging utility. Based
2882 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
2883 convenient and easy to use replacement for @code{cat} and @code{print}
2885 (license license:lgpl3+)))
2887 (define-public r-segmented
2889 (name "r-segmented")
2894 (uri (cran-uri "segmented" version))
2897 "0nrik5fyq59hwiwjcpbi4p5yfavgfjq6wyrynhkrbm4k6v1g1wlq"))))
2898 (build-system r-build-system)
2899 (home-page "https://cran.r-project.org/web/packages/segmented")
2900 (synopsis "Regression models with breakpoints estimation")
2902 "Given a regression model, segmented updates the model by adding one or
2903 more segmented (i.e., piecewise-linear) relationships. Several variables with
2904 multiple breakpoints are allowed.")
2905 (license (list license:gpl2+ license:gpl3+))))
2907 (define-public r-snow
2913 (uri (cran-uri "snow" version))
2916 "1mxbrkpnmq32x4wd0194d541661yvfrrjlr3lsf7qq53ms3h21zf"))))
2917 (build-system r-build-system)
2918 (home-page "https://cran.r-project.org/web/packages/snow")
2919 (synopsis "Support for simple parallel computing in R")
2921 "The snow package provides support for simple parallel computing on a
2922 network of workstations using R. A master R process calls @code{makeCluster}
2923 to start a cluster of worker processes; the master process then uses functions
2924 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
2925 worker processes and collect and return the results on the master.")
2926 (license (list license:gpl2+ license:gpl3+))))
2928 (define-public r-sparsem
2934 (uri (cran-uri "SparseM" version))
2937 "0p6ljma2h12cq1xmy0cxb48ih8dhxxbnwkqzvx3cckxf2kprycm9"))))
2939 `((upstream-name . "SparseM")))
2941 `(("gfortran" ,gfortran)))
2942 (build-system r-build-system)
2943 (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
2944 (synopsis "Sparse linear algebra")
2946 "This package provides some basic linear algebra functionality for sparse
2947 matrices. It includes Cholesky decomposition and backsolving as well as
2948 standard R subsetting and Kronecker products.")
2949 (license license:gpl2+)))
2951 (define-public r-iterators
2953 (name "r-iterators")
2958 (uri (cran-uri "iterators" version))
2961 "16sycjq912ix52fjxjhcwiaqr0yj1v5iqmrvjljd3z857031w06y"))))
2962 (build-system r-build-system)
2963 (home-page "https://cran.r-project.org/web/packages/iterators")
2964 (synopsis "Iterator construct for R")
2966 "This package provides support for iterators, which allow a programmer to
2967 traverse through all the elements of a vector, list, or other collection of
2969 (license license:asl2.0)))
2971 (define-public r-foreach
2978 (uri (cran-uri "foreach" version))
2981 "0j2yj0rn0d5nbzz9nq5rqqgnxhp9pbd92q4klsarl2xpsn8119y0"))))
2982 (build-system r-build-system)
2984 `(("r-codetools" ,r-codetools)
2985 ("r-iterators" ,r-iterators)))
2986 (home-page "https://cran.r-project.org/web/packages/foreach")
2987 (synopsis "Foreach looping construct for R")
2989 "This package provides support for the @code{foreach} looping construct.
2990 @code{foreach} is an idiom that allows for iterating over elements in a
2991 collection, without the use of an explicit loop counter. This package in
2992 particular is intended to be used for its return value, rather than for its
2993 side effects. In that sense, it is similar to the standard @code{lapply}
2994 function, but doesn't require the evaluation of a function. Using
2995 @code{foreach} without side effects also facilitates executing the loop in
2997 (license license:asl2.0)))
2999 (define-public r-doparallel
3001 (name "r-doparallel")
3006 (uri (cran-uri "doParallel" version))
3009 "0sppgxk3d8mfsrb3cjdyn0mv0s4i7pcy8g8c3cjzbr6k8vmx5jsc"))))
3010 (properties `((upstream-name . "doParallel")))
3011 (build-system r-build-system)
3013 `(("r-foreach" ,r-foreach)
3014 ("r-iterators" ,r-iterators)))
3015 (home-page "https://cran.r-project.org/web/packages/doParallel")
3016 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3018 "This package provides a parallel backend for the @code{%dopar%} function
3019 using the parallel package.")
3020 (license license:gpl2+)))
3022 (define-public r-domc
3029 (uri (cran-uri "doMC" version))
3032 "1vfrykvfvsyq12mypd266867ml1dcwc3rj5k9c3wrn5bddcm88kr"))))
3033 (properties `((upstream-name . "doMC")))
3034 (build-system r-build-system)
3036 `(("r-foreach" ,r-foreach)
3037 ("r-iterators" ,r-iterators)))
3038 (home-page "https://cran.r-project.org/web/packages/doMC")
3039 (synopsis "Foreach parallel adaptor for the 'parallel' package")
3041 "This package provides a parallel backend for the @code{%dopar%} function
3042 using the multicore functionality of the parallel package.")
3043 (license license:gpl2+)))
3051 (uri (cran-uri "DT" version))
3054 "06gsqz7p2fv6hc3fm3759gaa50krcfrqrmy7qbxyam6a36w9daix"))))
3056 `((upstream-name . "DT")))
3057 (build-system r-build-system)
3059 `(("r-crosstalk" ,r-crosstalk)
3060 ("r-htmltools" ,r-htmltools)
3061 ("r-htmlwidgets" ,r-htmlwidgets)
3062 ("r-magrittr" ,r-magrittr)))
3063 (home-page "http://rstudio.github.io/DT")
3064 (synopsis "R wrapper of the DataTables JavaScript library")
3066 "This package allows for data objects in R to be rendered as HTML tables
3067 using the JavaScript library 'DataTables' (typically via R Markdown or Shiny).
3068 The 'DataTables' library has been included in this R package.")
3069 ;; The DT package as a whole is distributed under GPLv3. The DT package
3070 ;; inludes other software components under different licenses:
3072 ;; * Expat: jQuery, jquery.highlight.js, DataTables
3073 ;; * ASL2.0: selectize.js
3074 ;; * WTFPL: noUiSlider
3075 (license (list license:gpl3
3078 (license:non-copyleft "http://www.wtfpl.net/txt/copying/")))))
3080 (define-public r-base64enc
3082 (name "r-base64enc")
3086 (uri (cran-uri "base64enc" version))
3089 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
3090 (build-system r-build-system)
3091 (home-page "http://www.rforge.net/base64enc")
3092 (synopsis "Tools for Base64 encoding")
3094 "This package provides tools for handling Base64 encoding. It is more
3095 flexible than the orphaned \"base64\" package.")
3096 (license license:gpl2+)))
3098 (define-public r-irlba
3105 (uri (cran-uri "irlba" version))
3108 "0f7wb12wa0zbyllk5adcf4f517wgjpkhsx4j176i9ax6xy7jvprz"))))
3109 (build-system r-build-system)
3111 `(("r-matrix" ,r-matrix)))
3112 (home-page "https://cran.r-project.org/web/packages/irlba")
3113 (synopsis "Methods for eigendecomposition of large matrices")
3115 "This package provides fast and memory efficient methods for truncated
3116 singular and eigenvalue decompositions, as well as for principal component
3117 analysis of large sparse or dense matrices.")
3118 (license (list license:gpl2+ license:gpl3+))))
3120 (define-public r-glmnet
3127 (uri (cran-uri "glmnet" version))
3130 "1zdqp6wnqxzp5qn2ky47phbkrxv3cpgbwmdp896h3xxjvp58sa7k"))))
3131 (build-system r-build-system)
3133 `(("gfortran" ,gfortran)))
3135 `(("r-foreach" ,r-foreach)
3136 ("r-matrix" ,r-matrix)))
3137 (home-page "http://www.jstatsoft.org/v33/i01")
3138 (synopsis "Lasso and elastic-net regularized generalized linear models")
3140 "The glmnet package provides efficient procedures for fitting the entire
3141 lasso or elastic-net regularization path for linear and Poisson regression, as
3142 well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
3143 multinomial models. The algorithm uses cyclical coordinate descent in a
3144 path-wise fashion.")
3145 (license license:gpl2+)))
3147 (define-public r-pkgmaker
3154 (uri (cran-uri "pkgmaker" version))
3157 "0vrqnd3kg6liqvpbd969jjsdx0f0rvmmxgdbwwrp6xfmdg0pib8r"))))
3158 (build-system r-build-system)
3160 `(("r-codetools" ,r-codetools)
3161 ("r-digest" ,r-digest)
3162 ("r-registry" ,r-registry)
3163 ("r-stringr" ,r-stringr)
3164 ("r-xtable" ,r-xtable)))
3165 (home-page "https://renozao.github.io/pkgmaker")
3166 (synopsis "Package development utilities")
3168 "This package provides some low-level utilities to use for R package
3169 development. It currently provides managers for multiple package specific
3170 options and registries, vignette, unit test and bibtex related utilities.")
3171 (license license:gpl2+)))
3173 (define-public r-registry
3180 (uri (cran-uri "registry" version))
3183 "1yqfl1g6vsl28zn8brzc39659k8lqsmfms7900j7p64ilydyb2sx"))))
3184 (build-system r-build-system)
3185 (home-page "https://cran.r-project.org/web/packages/registry")
3186 (synopsis "Infrastructure for R package registries")
3188 "This package provides a generic infrastructure for creating and using R
3189 package registries.")
3190 (license license:gpl2+)))
3192 (define-public r-rngtools
3199 (uri (cran-uri "rngtools" version))
3202 "1fcgfqrrb48z37xgy8sffx91p9irp39yqzxv7nqp1x2hnwsrh097"))))
3203 (build-system r-build-system)
3205 `(("r-digest" ,r-digest)
3206 ("r-pkgmaker" ,r-pkgmaker)
3207 ("r-stringr" ,r-stringr)))
3208 (home-page "https://renozao.github.io/rngtools")
3209 (synopsis "Utility functions for working with random number generators")
3211 "This package contains a set of functions for working with Random Number
3212 Generators (RNGs). In particular, it defines a generic S4 framework for
3213 getting/setting the current RNG, or RNG data that are embedded into objects
3214 for reproducibility. Notably, convenient default methods greatly facilitate
3215 the way current RNG settings can be changed.")
3216 (license license:gpl3+)))
3218 (define-public r-rtsne
3225 (uri (cran-uri "Rtsne" version))
3228 "17crbdi80q4g2pwp9v7j3bdaznk96qlrqx01zvj3wwqippizyfqw"))))
3229 (properties `((upstream-name . "Rtsne")))
3230 (build-system r-build-system)
3232 `(("r-rcpp" ,r-rcpp)))
3233 (home-page "https://github.com/jkrijthe/Rtsne")
3234 (synopsis "T-distributed stochastic neighbor embedding")
3236 "This package provides an R wrapper around the fast T-distributed
3237 Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
3238 ;; The declared license for this package is BSD-3, but it also includes
3239 ;; code licensed under BSD-4.
3240 (license (list license:bsd-3 license:bsd-4))))
3242 (define-public r-e1071
3249 (uri (cran-uri "e1071" version))
3252 "08n6i26nfckjpxjkzi8phhanc3ahsrirkv5rz38y2jcv7ds031pn"))))
3253 (build-system r-build-system)
3255 `(("r-class" ,r-class)))
3256 (home-page "https://cran.r-project.org/web/packages/e1071")
3257 (synopsis "Miscellaneous functions for probability theory")
3259 "This package provides functions for latent class analysis, short time
3260 Fourier transform, fuzzy clustering, support vector machines, shortest path
3261 computation, bagged clustering, naive Bayes classifier, and more.")
3262 (license license:gpl2+)))
3264 (define-public r-bigmemory-sri
3266 (name "r-bigmemory-sri")
3271 (uri (cran-uri "bigmemory.sri" version))
3273 (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
3275 `((upstream-name . "bigmemory.sri")))
3276 (build-system r-build-system)
3277 (home-page "https://cran.r-project.org/web/packages/bigmemory.sri")
3278 (synopsis "Shared resource interface for the bigmemory package")
3279 (description "This package provides a shared resource interface for the
3280 bigmemory and synchronicity packages.")
3281 ;; Users can choose either LGPLv3 or ASL2.0.
3282 (license (list license:lgpl3 license:asl2.0))))
3284 (define-public r-synchronicity
3286 (name "r-synchronicity")
3291 (uri (cran-uri "synchronicity" version))
3294 "1idrjzl7nkamf1ip55s6qcf64s63xs9j8z9jv3r89p6r5lw7k5mv"))))
3295 (build-system r-build-system)
3298 ("r-bigmemory-sri" ,r-bigmemory-sri)
3300 ("r-uuid" ,r-uuid)))
3301 (home-page "http://www.bigmemory.org")
3302 (synopsis "Boost mutex functionality in R")
3303 (description "This package provides support for synchronization
3304 via mutexes and may eventually support interprocess communication and
3306 ;; Users can choose either LGPLv3 or ASL2.0.
3307 (license (list license:lgpl3 license:asl2.0))))
3309 (define-public r-bigmemory
3311 (name "r-bigmemory")
3316 (uri (cran-uri "bigmemory" version))
3319 "0ycl9dzm3drpyas625h34rir5bnbjlncxlvawfsfmqwcbmwdjdvj"))))
3320 (build-system r-build-system)
3324 ("r-bigmemory-sri" ,r-bigmemory-sri)))
3325 (home-page "http://www.bigmemory.org")
3326 (synopsis "Manage large matrices with shared memory or memory-mapped files")
3327 (description "This package provides methods to create, store, access, and
3328 manipulate large matrices. Matrices are allocated to shared memory and may use
3329 memory-mapped files.")
3330 ;; Users can choose either LGPLv3 or ASL2.0.
3331 (license (list license:lgpl3 license:asl2.0))))
3333 (define-public r-nmf
3340 (uri (cran-uri "NMF" version))
3343 "1qq25n3k5sgh3srlshb3ic6q92s12c1ilqf5cd5anvq6cqfchc1v"))))
3344 (properties `((upstream-name . "NMF")))
3345 (build-system r-build-system)
3347 `(("r-cluster" ,r-cluster)
3348 ("r-bigmemory" ,r-bigmemory) ; suggested
3349 ("r-synchronicity" ,r-synchronicity) ; suggested
3350 ("r-colorspace" ,r-colorspace)
3351 ("r-digest" ,r-digest)
3352 ("r-doparallel" ,r-doparallel)
3353 ("r-foreach" ,r-foreach)
3354 ("r-ggplot2" ,r-ggplot2)
3355 ("r-gridbase" ,r-gridbase)
3356 ("r-pkgmaker" ,r-pkgmaker)
3357 ("r-rcolorbrewer" ,r-rcolorbrewer)
3358 ("r-registry" ,r-registry)
3359 ("r-reshape2" ,r-reshape2)
3360 ("r-rngtools" ,r-rngtools)
3361 ("r-stringr" ,r-stringr)))
3362 (home-page "http://renozao.github.io/NMF")
3363 (synopsis "Algorithms and framework for nonnegative matrix factorization")
3365 "This package provides a framework to perform Non-negative Matrix
3366 Factorization (NMF). The package implements a set of already published
3367 algorithms and seeding methods, and provides a framework to test, develop and
3368 plug new or custom algorithms. Most of the built-in algorithms have been
3369 optimized in C++, and the main interface function provides an easy way of
3370 performing parallel computations on multicore machines.")
3371 (license license:gpl2+)))
3373 (define-public r-r-methodss3
3375 (name "r-r-methodss3")
3379 (uri (cran-uri "R.methodsS3" version))
3382 "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24"))))
3383 (properties `((upstream-name . "R.methodsS3")))
3384 (build-system r-build-system)
3385 (home-page "https://cran.r-project.org/web/packages/R.methodsS3")
3386 (synopsis "S3 methods simplified")
3388 "This package provides methods that simplify the setup of S3 generic
3389 functions and S3 methods. Major effort has been made in making definition of
3390 methods as simple as possible with a minimum of maintenance for package
3391 developers. For example, generic functions are created automatically, if
3392 missing, and naming conflict are automatically solved, if possible. The
3393 method @code{setMethodS3()} is a good start for those who in the future may
3394 want to migrate to S4.")
3395 (license license:lgpl2.1+)))
3397 (define-public r-r-oo
3403 (uri (cran-uri "R.oo" version))
3406 "0723gxjazgqq7v3lwnl7axw3brzcnizvhbd71ijkkv8mz31fwp34"))))
3407 (properties `((upstream-name . "R.oo")))
3408 (build-system r-build-system)
3410 `(("r-r-methodss3" ,r-r-methodss3)))
3411 (home-page "https://github.com/HenrikBengtsson/R.oo")
3412 (synopsis "R object-oriented programming with or without references")
3414 "This package provides methods and classes for object-oriented
3415 programming in R with or without references. Large effort has been made on
3416 making definition of methods as simple as possible with a minimum of
3417 maintenance for package developers.")
3418 (license license:lgpl2.1+)))
3420 (define-public r-r-utils
3426 (uri (cran-uri "R.utils" version))
3429 "03j7hrs03kyj9qrjxyp5kqv4lpqqpk6xwbkzx6j15d8928yrjr2x"))))
3430 (properties `((upstream-name . "R.utils")))
3431 (build-system r-build-system)
3433 `(("r-r-methodss3" ,r-r-methodss3)
3434 ("r-r-oo" ,r-r-oo)))
3435 (home-page "https://github.com/HenrikBengtsson/R.utils")
3436 (synopsis "Various programming utilities")
3438 "This package provides utility functions useful when programming and
3439 developing R packages.")
3440 (license license:lgpl2.1+)))
3442 (define-public r-r-cache
3448 (uri (cran-uri "R.cache" version))
3451 "1hf5cb7xvnca5zlh9245b5g62sgsaxwdhiv7x59yld37cydakm6k"))))
3452 (properties `((upstream-name . "R.cache")))
3453 (build-system r-build-system)
3455 `(("r-digest" ,r-digest)
3456 ("r-r-methodss3" ,r-r-methodss3)
3458 ("r-r-utils" ,r-r-utils)))
3459 (home-page "https://github.com/HenrikBengtsson/R.cache")
3460 (synopsis "Light-weight caching of objects and results")
3462 "This package provides methods for caching or memoization of objects and
3463 results. With this package, any R object can be cached in a key-value storage
3464 where the key can be an arbitrary set of R objects. The cache memory is
3465 persistent (on the file system).")
3466 (license license:lgpl2.1+)))
3468 (define-public r-r-rsp
3474 (uri (cran-uri "R.rsp" version))
3477 "1zcq0hzi0j7fvj2rs796a1i120wbr0387vck17rrd644awwbsbm0"))))
3478 (properties `((upstream-name . "R.rsp")))
3479 (build-system r-build-system)
3481 `(("r-digest" ,r-digest)
3482 ("r-r-cache" ,r-r-cache)
3483 ("r-r-methodss3" ,r-r-methodss3)
3485 ("r-r-utils" ,r-r-utils)))
3486 (home-page "https://github.com/HenrikBengtsson/R.rsp")
3487 (synopsis "Dynamic generation of scientific reports")
3489 "The RSP markup language provides a powerful markup for controlling the
3490 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
3491 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
3492 to many other literate programming languages, with RSP it is straightforward
3493 to loop over mixtures of code and text sections, e.g. in month-by-month
3494 summaries. RSP has also several preprocessing directives for incorporating
3495 static and dynamic contents of external files (local or online) among other
3496 things. RSP is ideal for self-contained scientific reports and R package
3498 (license license:lgpl2.1+)))
3500 (define-public r-mvtnorm
3506 (uri (cran-uri "mvtnorm" version))
3509 "0f7hzflygdnbwvzadr3knhybhanwg7agqddclj6mhbvwqpgb0qyh"))))
3510 (build-system r-build-system)
3512 `(("gfortran" ,gfortran)))
3513 (home-page "http://mvtnorm.R-forge.R-project.org")
3514 (synopsis "Package for multivariate normal and t-distributions")
3515 (description "This package can compute multivariate normal and
3516 t-probabilities, quantiles, random deviates and densities.")
3517 (license license:gpl2)))
3519 (define-public r-matrixstats
3521 (name "r-matrixstats")
3525 (uri (cran-uri "matrixStats" version))
3528 "0bkiz5fm09d3512mfr2ymj9qsb1b8aic5l5m6fkaf5j7nsgvqw6z"))))
3529 (properties `((upstream-name . "matrixStats")))
3530 (build-system r-build-system)
3532 `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
3533 (home-page "https://github.com/HenrikBengtsson/matrixStats")
3534 (synopsis "Methods applying to vectors and matrix rows and columns")
3536 "This package provides methods operating on rows and columns of matrices,
3537 e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
3538 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
3539 @code{weightedMedians()}. All methods have been optimized for speed and
3541 (license license:artistic2.0)))
3543 (define-public r-viridis
3549 (uri (cran-uri "viridis" version))
3552 "1ka6amybgzqkg3cbwfxwwqzzzpfn6q5jcia5am0bw48y5hbpg97y"))))
3553 (build-system r-build-system)
3555 `(("r-ggplot2" ,r-ggplot2)
3556 ("r-gridextra" ,r-gridextra)
3557 ("r-viridislite" ,r-viridislite)))
3558 (home-page "https://github.com/sjmgarnier/viridis")
3559 (synopsis "Matplotlib default color map")
3561 "This package is a port of the new @url{matplotlib,
3562 http://matplotlib.org/} color maps (@code{viridis}--the default--,
3563 @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
3564 designed in such a way that they will analytically be perfectly
3565 perceptually-uniform, both in regular form and also when converted to
3566 black-and-white. They are also designed to be perceived by readers with the
3567 most common form of color blindness.")
3568 (license license:x11)))
3570 (define-public r-viridislite
3572 (name "r-viridislite")
3577 (uri (cran-uri "viridisLite" version))
3580 "1by2l05f0yabwvv64lhnv7bbhx0w683s3wr9j2xda920ghpa23kq"))))
3581 (properties `((upstream-name . "viridisLite")))
3582 (build-system r-build-system)
3583 (home-page "https://github.com/sjmgarnier/viridisLite")
3584 (synopsis "Default color maps from matplotlib")
3586 "This package is a port of the new @code{matplotlib} color maps ('viridis',
3587 'magma', 'plasma' and 'inferno') to R. matplotlib is a popular plotting
3588 library for Python. These color maps are designed in such a way that they
3589 will analytically be perfectly perceptually-uniform, both in regular form and
3590 also when converted to black-and-white. They are also designed to be
3591 perceived by readers with the most common form of color blindness. This is
3592 the 'lite' version of the more complete @code{viridis} package.")
3593 (license license:expat)))
3595 (define-public r-tidyselect
3597 (name "r-tidyselect")
3602 (uri (cran-uri "tidyselect" version))
3605 "1592dbzawhd1hpsp9919l4sifyiaaj6xr7lnhsbwa6jwmmb0xcsw"))))
3606 (build-system r-build-system)
3608 `(("r-glue" ,r-glue)
3609 ("r-purrr" ,r-purrr)
3611 ("r-rlang" ,r-rlang)))
3612 (home-page "https://cran.r-project.org/web/packages/tidyselect")
3613 (synopsis "Select from a set of strings")
3615 "This package provides a backend for the selecting functions of the
3616 tidyverse. It makes it easy to implement select-like functions in your own
3617 packages in a way that is consistent with other tidyverse interfaces for
3619 (license license:gpl3)))
3621 (define-public r-tidyr
3628 (uri (cran-uri "tidyr" version))
3631 "1qjpbj1a2vw6nw4hdb6fgassnrxrdpqwf9a8i6wqnv3wxvjb6zqb"))))
3632 (build-system r-build-system)
3634 `(("r-dplyr" ,r-dplyr)
3635 ("r-magrittr" ,r-magrittr)
3637 ("r-purrr" ,r-purrr)
3638 ("r-rlang" ,r-rlang)
3639 ("r-tidyselect" ,r-tidyselect)
3641 ("r-stringi" ,r-stringi)
3642 ("r-tibble" ,r-tibble)))
3643 (home-page "https://github.com/hadley/tidyr")
3644 (synopsis "Tidy data with `spread()` and `gather()` functions")
3646 "tidyr is a reframing of the reshape2 package designed to accompany the
3647 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
3648 a solid pipeline for data analysis. It is designed specifically for tidying
3649 data, not the general reshaping that reshape2 does, or the general aggregation
3650 that reshape did. In particular, built-in methods only work for data frames,
3651 and tidyr provides no margins or aggregation.")
3652 (license license:expat)))
3654 (define-public r-hexbin
3661 (uri (cran-uri "hexbin" version))
3664 "0lpfl0015lg5x7lvv9dr302bca22c7fs91pnd896ypgpzqg7pm26"))))
3665 (build-system r-build-system)
3667 `(("r-lattice" ,r-lattice)))
3669 `(("gfortran" ,gfortran)))
3670 (home-page "https://github.com/edzer/hexbin")
3671 (synopsis "Hexagonal binning routines")
3673 "This package provides binning and plotting functions for hexagonal bins.
3674 It uses and relies on grid graphics and formal (S4) classes and methods.")
3675 (license license:gpl2+)))
3677 (define-public r-purrr
3684 (uri (cran-uri "purrr" version))
3687 "0wgbnbrqncjpggg8f9bdpcd1gy351s5f0az5k8lc55cvs9lhz3gd"))))
3688 (build-system r-build-system)
3690 `(("r-tibble" ,r-tibble)
3691 ("r-magrittr" ,r-magrittr)
3692 ("r-rlang" ,r-rlang)))
3693 (home-page "https://github.com/hadley/purrr")
3694 (synopsis "Functional programming tools")
3696 "This package completes R's functional programming tools with missing
3697 features present in other programming languages.")
3698 (license license:gpl3+)))
3700 (define-public r-plotly
3706 (uri (cran-uri "plotly" version))
3709 "0wj9lw7w28z8w9ip9vadv6sydjhqyg65kfiai9m3bndzz50b1m3w"))))
3710 (build-system r-build-system)
3712 `(("r-base64enc" ,r-base64enc)
3713 ("r-crosstalk" ,r-crosstalk)
3714 ("r-digest" ,r-digest)
3715 ("r-data-table" ,r-data-table)
3716 ("r-dplyr" ,r-dplyr)
3717 ("r-ggplot2" ,r-ggplot2)
3718 ("r-hexbin" ,r-hexbin)
3719 ("r-htmltools" ,r-htmltools)
3720 ("r-htmlwidgets" ,r-htmlwidgets)
3722 ("r-jsonlite" ,r-jsonlite)
3723 ("r-lazyeval" ,r-lazyeval)
3724 ("r-magrittr" ,r-magrittr)
3725 ("r-purrr" ,r-purrr)
3726 ("r-rcolorbrewer" ,r-rcolorbrewer)
3727 ("r-scales" ,r-scales)
3728 ("r-tibble" ,r-tibble)
3729 ("r-tidyr" ,r-tidyr)
3730 ("r-viridislite" ,r-viridislite)))
3731 (home-page "https://plot.ly/r")
3732 (synopsis "Create interactive web graphics")
3734 "This package enables the translation of ggplot2 graphs to an interactive
3735 web-based version and/or the creation of custom web-based visualizations
3736 directly from R. Once uploaded to a plotly account, plotly graphs (and the
3737 data behind them) can be viewed and modified in a web browser.")
3738 (license license:x11)))
3740 (define-public r-biased-urn
3742 (name "r-biased-urn")
3747 (uri (cran-uri "BiasedUrn" version))
3750 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
3751 (properties `((upstream-name . "BiasedUrn")))
3752 (build-system r-build-system)
3753 (home-page "http://www.agner.org/random/")
3754 (synopsis "Biased urn model distributions")
3756 "This package provides statistical models of biased sampling in the form
3757 of univariate and multivariate noncentral hypergeometric distributions,
3758 including Wallenius' noncentral hypergeometric distribution and Fisher's
3759 noncentral hypergeometric distribution (also called extended hypergeometric
3761 (license license:gpl3+)))
3763 (define-public r-rematch
3770 (uri (cran-uri "rematch" version))
3773 "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4"))))
3774 (build-system r-build-system)
3775 (home-page "https://github.com/MangoTheCat/rematch")
3776 (synopsis "Match regular expressions with a nicer API")
3778 "This package provides a small wrapper on @code{regexpr} to extract the
3779 matches and captured groups from the match of a regular expression to a
3781 (license license:expat)))
3783 (define-public r-cellranger
3785 (name "r-cellranger")
3790 (uri (cran-uri "cellranger" version))
3793 "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x"))))
3794 (build-system r-build-system)
3796 `(("r-rematch" ,r-rematch)
3797 ("r-tibble" ,r-tibble)))
3798 (home-page "https://github.com/rsheets/cellranger")
3799 (synopsis "Translate spreadsheet cell ranges to rows and columns")
3801 "This package provides helper functions to work with spreadsheets and the
3802 @code{A1:D10} style of cell range specification.")
3803 (license license:expat)))
3805 (define-public r-googlesheets
3807 (name "r-googlesheets")
3812 (uri (cran-uri "googlesheets" version))
3815 "18q0xmxn09b52rmky7gr5flp0awndcnsgb7zcvkzvkrkvmwad52b"))))
3816 (build-system r-build-system)
3818 `(("r-cellranger" ,r-cellranger)
3819 ("r-dplyr" ,r-dplyr)
3821 ("r-jsonlite" ,r-jsonlite)
3822 ("r-purrr" ,r-purrr)
3823 ("r-readr" ,r-readr)
3824 ("r-stringr" ,r-stringr)
3825 ("r-tidyr" ,r-tidyr)
3826 ("r-xml2" ,r-xml2)))
3827 (home-page "https://github.com/jennybc/googlesheets")
3828 (synopsis "Manage Google spreadsheets from R")
3829 (description "This package provides tools to interact with Google Sheets
3831 (license license:expat)))
3833 (define-public r-spams
3836 (version "2.6-2017-03-22")
3840 (uri (string-append "https://gforge.inria.fr/frs/download.php/36615/"
3841 "spams-R-v" version ".tar.gz"))
3844 "13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx"))))
3845 (build-system r-build-system)
3848 (modify-phases %standard-phases
3849 (add-after 'unpack 'chdir
3850 (lambda _ (chdir "spams") #t))
3851 ;; Don't tune for the building machine
3852 (add-after 'chdir 'no-mtune
3854 (substitute* "src/Makevars"
3855 (("-mtune=native") ""))
3858 `(("r-lattice" ,r-lattice)
3859 ("r-matrix" ,r-matrix)))
3860 (home-page "http://spams-devel.gforge.inria.fr")
3861 (synopsis "Toolbox for solving sparse estimation problems")
3862 (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
3863 for solving various sparse estimation problems. It includes tools for the
3867 @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
3868 component analysis} (PCA), ...)
3869 @item Solving sparse decomposition problems with LARS, coordinate descent,
3870 OMP, SOMP, proximal methods
3871 @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
3872 group lasso, tree-structured regularization, structured sparsity with
3873 overlapping groups,...).
3875 (license license:gpl3+)))
3877 (define-public r-base64
3884 (uri (cran-uri "base64" version))
3887 "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf"))))
3888 (build-system r-build-system)
3890 `(("r-openssl" ,r-openssl)))
3891 (home-page "https://cran.r-project.org/web/packages/base64")
3892 (synopsis "Base64 encoder and decoder")
3894 "This package is a compatibility wrapper to replace the orphaned package
3895 by Romain Francois. New applications should use the openssl or base64enc
3897 (license license:expat)))
3899 (define-public r-hmisc
3906 (uri (cran-uri "Hmisc" version))
3909 "160l50ppjs69ipcaya1mlcz29zbn5rmqg91r09dvzzvkvwfb47cr"))))
3910 (properties `((upstream-name . "Hmisc")))
3911 (build-system r-build-system)
3913 `(("gfortran" ,gfortran)))
3915 `(("r-acepack" ,r-acepack)
3916 ("r-base64enc" ,r-base64enc)
3917 ("r-cluster" ,r-cluster)
3918 ("r-data-table" ,r-data-table)
3919 ("r-foreign" ,r-foreign)
3920 ("r-formula" ,r-formula)
3921 ("r-ggplot2" ,r-ggplot2)
3922 ("r-gridextra" ,r-gridextra)
3923 ("r-gtable" ,r-gtable)
3924 ("r-lattice" ,r-lattice)
3925 ("r-latticeextra" ,r-latticeextra)
3926 ("r-htmltable" ,r-htmltable)
3927 ("r-htmltools" ,r-htmltools)
3929 ("r-rpart" ,r-rpart)
3930 ("r-survival" ,r-survival)
3931 ("r-viridis" ,r-viridis)))
3932 (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
3933 (synopsis "Miscellaneous data analysis and graphics functions")
3935 "This package contains many functions useful for data analysis,
3936 high-level graphics, utility operations, functions for computing sample size
3937 and power, importing and annotating datasets, imputing missing values,
3938 advanced table making, variable clustering, character string manipulation,
3939 conversion of R objects to LaTeX code, and recoding variables.")
3940 (license license:gpl2+)))
3942 (define-public r-runit
3949 (uri (cran-uri "RUnit" version))
3952 "1jqr871jkll2xmk7wk5hv1z3a36hyn2ibgivw7bwk4b346940xlx"))))
3953 (properties `((upstream-name . "RUnit")))
3954 (build-system r-build-system)
3955 (home-page "https://cran.r-project.org/web/packages/RUnit")
3956 (synopsis "R unit test framework")
3958 "This package provides R functions implementing a standard unit testing
3959 framework, with additional code inspection and report generation tools.")
3960 (license license:gpl2+)))
3962 (define-public r-dynamictreecut
3964 (name "r-dynamictreecut")
3969 (uri (cran-uri "dynamicTreeCut" version))
3972 "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"))))
3973 (properties `((upstream-name . "dynamicTreeCut")))
3974 (build-system r-build-system)
3976 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
3977 (synopsis "Detect clusters in hierarchical clustering dendrograms")
3979 "This package contains methods for the detection of clusters in
3980 hierarchical clustering dendrograms.")
3981 (license license:gpl2+)))
3983 (define-public r-preprocesscore
3985 (name "r-preprocesscore")
3990 (uri (bioconductor-uri "preprocessCore" version))
3993 "0mrdgbkb9dcfr9gsqyxfpshnxx60mq97pl98b8yl00l2gfwz48ph"))))
3995 `((upstream-name . "preprocessCore")))
3996 (build-system r-build-system)
3997 (home-page "https://github.com/bmbolstad/preprocessCore")
3998 (synopsis "Collection of pre-processing functions")
4000 "This package provides a library of core pre-processing and normalization
4002 (license license:lgpl2.0+)))
4004 (define-public r-fastcluster
4006 (name "r-fastcluster")
4011 (uri (cran-uri "fastcluster" version))
4014 "15drhl22wm8whsy6b3vv754skfddiydb068zn1whrw5sknvkkjc2"))))
4015 (build-system r-build-system)
4016 (home-page "http://danifold.net/fastcluster.html")
4017 (synopsis "Fast hierarchical clustering routines")
4019 "This package implements fast hierarchical, agglomerative clustering
4020 routines. Part of the functionality is designed as drop-in replacement for
4021 existing routines: @code{linkage()} in the SciPy package
4022 @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package,
4023 and the @code{flashClust} package. It provides the same functionality with
4024 the benefit of a much faster implementation. Moreover, there are
4025 memory-saving routines for clustering of vector data, which go beyond what the
4026 existing packages provide.")
4027 (license license:bsd-2)))
4029 (define-public r-sfsmisc
4036 (uri (cran-uri "sfsmisc" version))
4039 "0cgq2h11ngkzd6p34k6mqjnvlvc5vj4lnqrl64k05lb391j391w0"))))
4040 (build-system r-build-system)
4041 (home-page "https://cran.r-project.org/web/packages/sfsmisc")
4042 (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
4044 "This package provides useful utilities from Seminar fuer Statistik ETH
4045 Zurich, including many that are related to graphics.")
4046 (license license:gpl2+)))
4048 (define-public r-gtools
4055 (uri (cran-uri "gtools" version))
4058 "1xknwk9xlsj027pg0nwiizigcrsc84hdrig0jn0cgcyxj8dabdl6"))))
4059 (build-system r-build-system)
4062 (modify-phases %standard-phases
4063 (add-after 'unpack 'make-deterministic
4065 (substitute* "R/checkReverseDependencies.R"
4066 (("tempdir\\(\\)") "\"/tmp\""))
4068 (home-page "https://cran.r-project.org/web/packages/gtools")
4069 (synopsis "Various R programming tools")
4071 "This package contains a collection of various functions to assist in R
4072 programming, such as tools to assist in developing, updating, and maintaining
4073 R and R packages, calculating the logit and inverse logit transformations,
4074 tests for whether a value is missing, empty or contains only @code{NA} and
4075 @code{NULL} values, and many more.")
4076 (license license:gpl2)))
4078 (define-public r-gdata
4085 (uri (cran-uri "gdata" version))
4088 "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b"))))
4089 (build-system r-build-system)
4093 `(("r-gtools" ,r-gtools)))
4094 (home-page "https://cran.r-project.org/web/packages/gdata")
4095 (synopsis "Various R programming tools for data manipulation")
4097 "This package provides various R programming tools for data manipulation,
4101 @item medical unit conversions
4102 @item combining objects
4103 @item character vector operations
4104 @item factor manipulation
4105 @item obtaining information about R objects
4106 @item manipulating MS-Excel formatted files
4107 @item generating fixed-width format files
4108 @item extricating components of date and time objects
4109 @item operations on columns of data frames
4110 @item matrix operations
4111 @item operations on vectors and data frames
4112 @item value of last evaluated expression
4113 @item wrapper for @code{sample} that ensures consistent behavior for
4114 both scalar and vector arguments
4116 (license license:gpl2+)))
4118 (define-public r-gplots
4125 (uri (cran-uri "gplots" version))
4128 "02nb8n3s7c1zxq2s7ycaq2ys72y7mzirxrwj954h6gdc4x1zhg9l"))))
4129 (build-system r-build-system)
4131 `(("r-catools" ,r-catools)
4132 ("r-gdata" ,r-gdata)
4133 ("r-gtools" ,r-gtools)
4134 ("r-kernsmooth" ,r-kernsmooth)))
4135 (home-page "https://cran.r-project.org/web/packages/gplots")
4136 (synopsis "Various R programming tools for plotting data")
4138 "This package provides various R programming tools for plotting data,
4142 @item calculating and plotting locally smoothed summary function
4143 @item enhanced versions of standard plots
4144 @item manipulating colors
4145 @item calculating and plotting two-dimensional data summaries
4146 @item enhanced regression diagnostic plots
4147 @item formula-enabled interface to @code{stats::lowess} function
4148 @item displaying textual data in plots
4150 @item plotting \"Venn\" diagrams
4151 @item displaying Open-Office style plots
4152 @item plotting multiple data on same region, with separate axes
4153 @item plotting means and confidence intervals
4154 @item spacing points in an x-y plot so they don't overlap
4156 (license license:gpl2+)))
4158 (define-public r-rocr
4165 (uri (cran-uri "ROCR" version))
4168 "1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7"))))
4169 (properties `((upstream-name . "ROCR")))
4170 (build-system r-build-system)
4172 `(("r-gplots" ,r-gplots)))
4173 (home-page "http://rocr.bioinf.mpi-sb.mpg.de/")
4174 (synopsis "Visualizing the performance of scoring classifiers")
4176 "ROCR is a flexible tool for creating cutoff-parameterized 2D performance
4177 curves by freely combining two from over 25 performance measures (new
4178 performance measures can be added using a standard interface). Curves from
4179 different cross-validation or bootstrapping runs can be averaged by different
4180 methods, and standard deviations, standard errors or box plots can be used to
4181 visualize the variability across the runs. The parameterization can be
4182 visualized by printing cutoff values at the corresponding curve positions, or
4183 by coloring the curve according to cutoff. All components of a performance
4184 plot can be quickly adjusted using a flexible parameter dispatching
4186 (license license:gpl2+)))
4188 (define-public r-zoo
4194 (uri (cran-uri "zoo" version))
4197 "16nc5jnpkf5j9vgq3pzssv7knj30mi055wj7q3sygz3l0d88hgfr"))))
4198 (build-system r-build-system)
4200 `(("r-lattice" ,r-lattice)))
4201 (home-page "http://zoo.R-Forge.R-project.org/")
4202 (synopsis "S3 infrastructure for regular and irregular time series")
4203 (description "This package contains an S3 class with methods for totally
4204 ordered indexed observations. It is particularly aimed at irregular time
4205 series of numeric vectors/matrices and factors.")
4206 (license license:gpl2+)))
4208 (define-public r-ztable
4214 (uri (cran-uri "ztable" version))
4217 "1jfqnqy9544gfvz3bsb48v4177nwp4b4n9l2743asq8sbq305b5r"))))
4218 (build-system r-build-system)
4219 (home-page "https://cran.r-project.org/web/packages/ztable")
4220 (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
4222 "This package provides functions to make zebra-striped tables (tables
4223 with alternating row colors) in LaTeX and HTML formats easily from
4224 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
4225 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
4226 @code{cbind.mytable} objects.")
4227 (license license:gpl2+)))
4229 (define-public r-vipor
4235 (uri (cran-uri "vipor" version))
4238 "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx"))))
4239 (build-system r-build-system)
4240 (home-page "https://cran.r-project.org/web/packages/vipor")
4241 (synopsis "Plot categorical data using noise and density estimates")
4243 "This package provides tools to generate a violin point plot, a
4244 combination of a violin/histogram plot and a scatter plot by offsetting points
4245 within a category based on their density using quasirandom noise.")
4246 (license license:gpl2+)))
4248 (define-public r-beeswarm
4254 (uri (cran-uri "beeswarm" version))
4257 "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
4258 (build-system r-build-system)
4259 (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/")
4260 (synopsis "Implementation of bee swarm plots")
4262 "This package provides an implementation of bee swarm plots. The bee
4263 swarm plot is a one-dimensional scatter plot like stripchart, but with
4264 closely-packed, non-overlapping points.")
4265 (license license:artistic2.0)))
4267 (define-public r-sourcetools
4269 (name "r-sourcetools")
4274 (uri (cran-uri "sourcetools" version))
4277 "0l8c6fql82cb246qh7hfgxb4s35qn0qfgy6dzvkx0zkz1cpqvx69"))))
4278 (build-system r-build-system)
4279 (home-page "https://cran.r-project.org/web/packages/sourcetools")
4280 (synopsis "Tools for reading, tokenizing and parsing R code")
4282 "The sourcetools package provides both an R and C++ interface for the
4283 tokenization of R code, and helpers for interacting with the tokenized
4284 representation of R code.")
4285 (license license:expat)))
4287 (define-public r-ggbeeswarm
4289 (name "r-ggbeeswarm")
4293 (uri (cran-uri "ggbeeswarm" version))
4296 "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v"))))
4297 (build-system r-build-system)
4299 `(("r-beeswarm" ,r-beeswarm)
4300 ("r-ggplot2" ,r-ggplot2)
4301 ("r-vipor" ,r-vipor)))
4302 (home-page "https://github.com/eclarke/ggbeeswarm")
4303 (synopsis "Categorical scatter (violin point) plots")
4305 "This package provides two methods of plotting categorical scatter plots
4306 such that the arrangement of points within a category reflects the density of
4307 data at that region, and avoids over-plotting.")
4308 (license license:gpl2+)))
4310 (define-public r-ggthemes
4316 (uri (cran-uri "ggthemes" version))
4319 "1jj8lp7jbk3489kpgbw4b5phpn01gkfmksc21c6sn3x6wmzyn6hs"))))
4320 (build-system r-build-system)
4322 `(("r-assertthat" ,r-assertthat)
4323 ("r-colorspace" ,r-colorspace)
4324 ("r-ggplot2" ,r-ggplot2)
4325 ("r-scales" ,r-scales)))
4326 (home-page "https://cran.rstudio.com/web/packages/ggthemes")
4327 (synopsis "Extra themes, scales and geoms for @code{ggplot2}")
4328 (description "This package provides extra themes and scales for
4329 @code{ggplot2} that replicate the look of plots by Edward Tufte and
4330 Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The
4331 Wall Street Journal, among others. This package also provides
4332 @code{geoms} for Tufte's box plot and range frame.")
4333 (license license:gpl2)))
4335 (define-public r-statmod
4341 (uri (cran-uri "statmod" version))
4344 "07v4x8af60alcw6vbiwf5fp25bhra61kvxz9kqx64lszm0i1fb4x"))))
4345 (build-system r-build-system)
4346 (home-page "https://cran.r-project.org/web/packages/statmod")
4348 `(("gfortran" ,gfortran)))
4349 (synopsis "Statistical modeling")
4351 "This package provides a collection of algorithms and functions to aid
4352 statistical modeling. It includes growth curve comparisons, limiting dilution
4353 analysis (aka ELDA), mixed linear models, heteroscedastic regression,
4354 inverse-Gaussian probability calculations, Gauss quadrature and a secure
4355 convergence algorithm for nonlinear models. It also includes advanced
4356 generalized linear model functions that implement secure convergence,
4357 dispersion modeling and Tweedie power-law families.")
4358 ;; Statmod is distributed under either license
4359 (license (list license:gpl2 license:gpl3))))
4361 (define-public r-rann
4367 (uri (cran-uri "RANN" version))
4370 "0il5i99vbcagnxvb15af5n37g04a4q1x96bz73zh3jhki9fpw9vm"))))
4372 `((upstream-name . "RANN")))
4373 (build-system r-build-system)
4374 (home-page "https://github.com/jefferis/RANN")
4375 (synopsis "Fast nearest neighbour search")
4377 "This package finds the k nearest neighbours for every point in a given
4378 dataset in O(N log N) time using Arya and Mount's ANN library. Provides
4379 approximate, exact searches, fixed radius searches, bd and kb trees.")
4380 (license license:gpl3+)))
4382 (define-public r-fivethirtyeight
4384 (name "r-fivethirtyeight")
4389 (uri (string-append "https://mran.microsoft.com/src/contrib/"
4390 "fivethirtyeight_" version ".tar.gz"))
4393 "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl"))))
4394 (build-system r-build-system)
4396 `(("r-knitr" ,r-knitr)
4397 ("r-rmarkdown" ,r-rmarkdown)
4398 ("r-dplyr" ,r-dplyr)
4399 ("r-readr" ,r-readr)
4400 ("r-ggplot2" ,r-ggplot2)
4401 ("r-magrittr" ,r-magrittr)
4402 ("r-stringr" ,r-stringr)))
4403 (home-page "https://mran.microsoft.com/package/fivethirtyeight/")
4404 (synopsis "Data and code behind the stories at FiveThirtyEight")
4405 (description "This R package provides access to the code and data sets
4406 published by the statistics blog FiveThirtyEight.")
4407 (license license:expat)))
4409 (define-public r-compquadform
4411 (name "r-compquadform")
4416 (uri (cran-uri "CompQuadForm" version))
4419 "1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4"))))
4420 (properties `((upstream-name . "CompQuadForm")))
4421 (build-system r-build-system)
4422 (home-page "https://cran.r-project.org/web/packages/CompQuadForm")
4423 (synopsis "Distribution function of quadratic forms in normal variables")
4425 "This package provides functions to compute the distribution function of
4426 quadratic forms in normal variables using Imhof's method, Davies's algorithm,
4427 Farebrother's algorithm or Liu et al.'s algorithm.")
4428 (license license:gpl2+)))
4430 (define-public r-cowplot
4437 (uri (cran-uri "cowplot" version))
4440 "13yjw7yv7imyqiawqqp304hkp6x36iv6rf6gn03dwzwkj9zwx4lb"))))
4441 (build-system r-build-system)
4443 `(("r-ggplot2" ,r-ggplot2)
4444 ("r-gtable" ,r-gtable)
4446 ("r-scales" ,r-scales)))
4447 (home-page "https://github.com/wilkelab/cowplot")
4448 (synopsis "Streamlined plot theme and plot annotations for ggplot2")
4450 "This package provides some helpful extensions and modifications to the
4451 ggplot2 package to combine multiple ggplot2 plots into one and label them with
4452 letters, as is often required for scientific publications.")
4453 (license license:gpl2)))
4455 (define-public r-mixtools
4462 (uri (cran-uri "mixtools" version))
4465 "13wdm0xs5bakhpa8ypg6lvhjaqkxyabwz4glxdwn0jwdvkcdhgsl"))))
4466 (build-system r-build-system)
4468 `(("r-mass" ,r-mass)
4469 ("r-segmented" ,r-segmented)
4470 ("r-survival" ,r-survival)))
4471 (home-page "https://cran.r-project.org/web/packages/mixtools")
4472 (synopsis "Tools for analyzing finite mixture models")
4474 "This package provides a collection of R functions for analyzing finite
4476 (license license:gpl2+)))
4478 (define-public r-lars
4485 (uri (cran-uri "lars" version))
4488 "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
4489 (build-system r-build-system)
4491 `(("gfortran" ,gfortran)))
4492 (home-page "http://www-stat.stanford.edu/~hastie/Papers/#LARS")
4493 (synopsis "Least angle regression software")
4495 "Least Angle Regression (\"LAR\") is a model selection algorithm; a
4496 useful and less greedy version of traditional forward selection methods. A
4497 simple modification of the LAR algorithm implements Tibshirani's Lasso; the
4498 Lasso modification of LARS calculates the entire Lasso path of coefficients
4499 for a given problem at the cost of a single least squares fit. Another LARS
4500 modification efficiently implements epsilon Forward Stagewise linear
4502 (license license:gpl2)))
4504 (define-public r-fastica
4511 (uri (cran-uri "fastICA" version))
4514 "108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg"))))
4515 (properties `((upstream-name . "fastICA")))
4516 (build-system r-build-system)
4517 (home-page "https://cran.r-project.org/web/packages/fastICA")
4518 (synopsis "FastICA algorithms to perform ICA and projection pursuit")
4520 "This package provides an implementation of the FastICA algorithm to
4521 perform @dfn{independent component analysis} (ICA) and projection pursuit.")
4523 (license license:gpl3+)))
4525 (define-public r-randomforest
4527 (name "r-randomforest")
4532 (uri (cran-uri "randomForest" version))
4535 "1i43idaihhl6nwqw42v9dqpl6f8z3ykcn2in32lh2755i27jylbf"))))
4536 (properties `((upstream-name . "randomForest")))
4537 (build-system r-build-system)
4538 (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
4540 `(("gfortran" ,gfortran)))
4541 (synopsis "Breiman and Cutler's random forests for classification and regression")
4543 "This package provides the Breiman and Cutler's random forests algorithm, based on a
4544 forest of trees using random inputs, for classification and regression.")
4545 (license license:gpl2+)))
4547 (define-public r-diptest
4554 (uri (cran-uri "diptest" version))
4557 "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
4558 (build-system r-build-system)
4559 (home-page "https://cran.r-project.org/web/packages/diptest")
4560 (synopsis "Hartigan's dip test statistic for unimodality")
4562 "This package computes Hartigan's dip test statistic for unimodality,
4563 multimodality and provides a test with simulation based p-values, where the
4564 original public code has been corrected.")
4565 (license license:gpl2+)))
4567 (define-public r-modeltools
4569 (name "r-modeltools")
4574 (uri (cran-uri "modeltools" version))
4577 "0ynds453xprxv0jqqzi3blnv5w6vrdww9pvd1sq4lrr5ar3k3cq7"))))
4578 (build-system r-build-system)
4579 (home-page "https://cran.r-project.org/web/packages/modeltools")
4580 (synopsis "Tools and classes for statistical models")
4582 "This package provides a collection of tools to deal with statistical
4583 models. The functionality is experimental and the user interface is likely
4584 to change in the future.")
4585 (license license:gpl2)))
4587 (define-public r-flexmix
4594 (uri (cran-uri "flexmix" version))
4597 "0sl4zxh1sb2sr5q7svjw9ihrm219jzn82yrc9d43q6r1b8bpyz43"))))
4598 (build-system r-build-system)
4600 `(("r-lattice" ,r-lattice)
4601 ("r-modeltools" ,r-modeltools)
4602 ("r-nnet" ,r-nnet)))
4603 (home-page "https://cran.r-project.org/web/packages/flexmix")
4604 (synopsis "Flexible mixture modeling")
4606 "This package implements a general framework for finite mixtures of
4607 regression models using the EM algorithm. FlexMix provides the E-step and
4608 all data handling, while the M-step can be supplied by the user to easily
4609 define new models. Existing drivers implement mixtures of standard linear
4610 models, generalized linear models and model-based clustering.")
4611 (license license:gpl2+)))
4613 (define-public r-mclust
4620 (uri (cran-uri "mclust" version))
4623 "1i3v1q8qq0al3ifvjhcvxfsg68cx9mq8jz67jwmiqai78mw0aqvk"))))
4624 (build-system r-build-system)
4626 `(("gfortran" ,gfortran)))
4627 (home-page "http://www.stat.washington.edu/mclust/")
4628 (synopsis "Gaussian mixture modelling for model-based clustering etc.")
4630 "This package provides Gaussian finite mixture models fitted via EM
4631 algorithm for model-based clustering, classification, and density estimation,
4632 including Bayesian regularization, dimension reduction for visualisation,
4633 and resampling-based inference.")
4634 (license license:gpl2+)))
4636 (define-public r-prabclus
4643 (uri (cran-uri "prabclus" version))
4646 "0qjsxrx6yv338bxm4ki0w9h8hind1l98abdrz828588bwj02jya1"))))
4647 (build-system r-build-system)
4649 `(("r-mass" ,r-mass)
4650 ("r-mclust" ,r-mclust)))
4651 (home-page "https://cran.r-project.org/web/packages/prabclus")
4652 (synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
4654 "This package provides distance-based parametric bootstrap tests for
4655 clustering with spatial neighborhood information. It implements some distance
4656 measures, clustering of presence-absence, abundance and multilocus genetical
4657 data for species delimitation, nearest neighbor based noise detection.")
4658 (license license:gpl2+)))
4660 (define-public r-deoptimr
4667 (uri (cran-uri "DEoptimR" version))
4670 "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
4671 (properties `((upstream-name . "DEoptimR")))
4672 (build-system r-build-system)
4673 (home-page "https://cran.r-project.org/web/packages/DEoptimR")
4674 (synopsis "Differential evolution optimization in pure R")
4676 "This package provides a differential evolution (DE) stochastic
4677 algorithms for global optimization of problems with and without constraints.
4678 The aim is to curate a collection of its state-of-the-art variants that (1) do
4679 not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
4680 can be efficiently implemented directly in the R language.")
4681 (license license:gpl2+)))
4683 (define-public r-robustbase
4685 (name "r-robustbase")
4690 (uri (cran-uri "robustbase" version))
4693 "080ynchq8pvhnmbivj4fp74n0x9lyr9923sg0s9gq5irgm68kgxw"))))
4694 (build-system r-build-system)
4696 `(("gfortran" ,gfortran)))
4698 `(("r-deoptimr" ,r-deoptimr)))
4699 (home-page "http://robustbase.r-forge.r-project.org/")
4700 (synopsis "Basic robust statistics")
4702 "This packages allows to analyze data with robust methods such as
4703 regression methodology including model selections and multivariate statistics.")
4704 (license license:gpl2+)))
4706 (define-public r-pcapp
4713 (uri (cran-uri "pcaPP" version))
4716 "1z2kdf9gfp965xbcd4rg6vf20d1bl443na0qjkpq7gmzpaq6cifa"))))
4717 (properties `((upstream-name . "pcaPP")))
4718 (build-system r-build-system)
4720 `(("r-mvtnorm" ,r-mvtnorm)))
4721 (home-page "https://cran.r-project.org/web/packages/pcaPP")
4722 (synopsis "Robust PCA by projection pursuit")
4724 "This package provides functions for robust @dfn{principal component
4725 analysis} (PCA) by projection pursuit.")
4726 (license license:gpl3+)))
4728 (define-public r-rrcov
4735 (uri (cran-uri "rrcov" version))
4738 "0kagqggi634mvrhd67ia7mpjrj5v6w2wq0z3kyppg5xkvzh335nq"))))
4739 (build-system r-build-system)
4741 `(("r-cluster" ,r-cluster)
4742 ("r-lattice" ,r-lattice)
4743 ("r-mvtnorm" ,r-mvtnorm)
4744 ("r-pcapp" ,r-pcapp)
4745 ("r-robustbase" ,r-robustbase)))
4747 `(("gfortran" ,gfortran)))
4748 (home-page "https://cran.r-project.org/web/packages/rrcov")
4749 (synopsis "Scalable robust estimators with high breakdown Point")
4751 "This package provides an implementation of robust location and scatter
4752 estimation and robust multivariate analysis with high breakdown point.")
4753 (license license:gpl2+)))
4755 (define-public r-fit-models
4757 (name "r-fit-models")
4762 (uri (cran-uri "fit.models" version))
4765 "0vjbzmx0ambm6yzidb4vbgmhclwzwv2iz2cwl54ccdkvx4cx3fck"))))
4766 (properties `((upstream-name . "fit.models")))
4767 (build-system r-build-system)
4769 `(("r-lattice" ,r-lattice)))
4770 (home-page "https://cran.r-project.org/web/packages/fit.models")
4771 (synopsis "Compare fitted models")
4773 "The @code{fit.models} function and its associated methods (coefficients, print,
4774 summary, plot, etc.) were originally provided in the @code{robust} package to
4775 compare robustly and classically fitted model objects. The aim of the
4776 @code{fit.models} package is to separate this fitted model object comparison
4777 functionality from the robust package and to extend it to support fitting
4778 methods (e.g., classical, robust, Bayesian, regularized, etc.) more
4780 ;; Any version of the GPL
4781 (license (list license:gpl2+ license:gpl3+))))
4783 (define-public r-robust
4790 (uri (cran-uri "robust" version))
4793 "1b7qh1aff500nd6dh4y2ipmjgdiq8991shflb63pc39vpc0ny6g4"))))
4794 (build-system r-build-system)
4796 `(("r-fit-models" ,r-fit-models)
4797 ("r-lattice" ,r-lattice)
4799 ("r-robustbase" ,r-robustbase)
4800 ("r-rrcov" ,r-rrcov)))
4802 `(("gfortran" ,gfortran)))
4803 (home-page "https://cran.r-project.org/web/packages/robust")
4804 (synopsis "Port of the S+ \"Robust Library\"")
4806 "This package is a port of the S+ \"Robust Library\". It provides
4807 methods for robust statistics, notably for robust regression and robust
4808 multivariate analysis.")
4809 (license license:gpl2)))
4811 (define-public r-trimcluster
4813 (name "r-trimcluster")
4818 (uri (cran-uri "trimcluster" version))
4821 "0lsgbg93hm0w1rdb813ry0ks2l0jfpyqzqkf3h3bj6fch0avcbv2"))))
4822 (build-system r-build-system)
4823 (home-page "https://cran.r-project.org/web/packages/trimcluster")
4824 (synopsis "Cluster analysis with trimming")
4826 "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
4827 Matran (1997). This optimizes the k-means criterion under trimming a portion
4830 (license (list license:gpl2+ license:gpl3+))))
4832 (define-public r-fpc
4839 (uri (cran-uri "fpc" version))
4842 "04alsqb5gbhsjg1000d8w52pmpnlwca29r0s12f7n7mdccdv6xar"))))
4843 (build-system r-build-system)
4845 `(("r-class" ,r-class)
4846 ("r-cluster" ,r-cluster)
4847 ("r-diptest" ,r-diptest)
4848 ("r-flexmix" ,r-flexmix)
4849 ("r-kernlab" ,r-kernlab)
4851 ("r-mclust" ,r-mclust)
4852 ("r-mvtnorm" ,r-mvtnorm)
4853 ("r-prabclus" ,r-prabclus)
4854 ("r-robustbase" ,r-robustbase)
4855 ("r-trimcluster" ,r-trimcluster)))
4856 (home-page "https://cran.r-project.org/web/packages/fpc")
4857 (synopsis "Flexible procedures for clustering")
4859 "This package provides various methods for clustering and cluster validation.
4860 For example, it provides fixed point clustering, linear regression clustering,
4861 clustering by merging Gaussian mixture components, as well as symmetric and
4862 asymmetric discriminant projections for visualisation of the separation of
4864 (license license:gpl2+)))
4866 (define-public r-vgam
4873 (uri (cran-uri "VGAM" version))
4876 "0ik3wyv6jj54bg34z0fzzk4xg0h6x98jqx4q2r7g1f0in0qgbb01"))))
4877 (properties `((upstream-name . "VGAM")))
4878 (build-system r-build-system)
4880 `(("gfortran" ,gfortran)))
4881 (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
4882 (synopsis "Vector generalized linear and additive models")
4884 "This package is an implementation of about 6 major classes of statistical
4885 regression models. Currently only fixed-effects models are implemented, i.e.,
4886 no random-effects models. Many (150+) models and distributions are estimated
4887 by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
4888 VGLMs can be loosely thought of as multivariate generalised linear models.")
4889 (license license:gpl2+)))
4891 (define-public r-pbapply
4898 (uri (cran-uri "pbapply" version))
4901 "0lk5kxac09xzdv6vf7ix6r5bfrm7cnpyr2l5mkd4igpciadszzfd"))))
4902 (build-system r-build-system)
4903 (home-page "https://github.com/psolymos/pbapply")
4904 (synopsis "Adding progress bar to apply functions")
4906 "This lightweight package that adds progress bar to vectorized R
4907 functions apply. The implementation can easily be added to functions where
4908 showing the progress is useful e.g. bootstrap.")
4909 (license license:gpl2)))
4911 (define-public r-minqa
4918 (uri (cran-uri "minqa" version))
4921 "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
4922 (build-system r-build-system)
4924 `(("r-rcpp" ,r-rcpp)))
4926 `(("gfortran" ,gfortran)))
4927 (home-page "http://optimizer.r-forge.r-project.org")
4928 (synopsis "Derivative-free optimization algorithms by quadratic approximation")
4930 "This package provides a derivative-free optimization by quadratic approximation
4931 based on an interface to Fortran implementations by M. J. D. Powell.")
4932 (license license:gpl2)))
4934 (define-public r-rcppeigen
4936 (name "r-rcppeigen")
4937 (version "0.3.3.4.0")
4941 (uri (cran-uri "RcppEigen" version))
4944 "1m6ssq6lvi36ggf26y4hhq996583pxxdb978jnn1x6r9gdb0q0hi"))))
4945 (properties `((upstream-name . "RcppEigen")))
4946 (build-system r-build-system)
4948 `(("r-rcpp" ,r-rcpp)
4949 ("r-matrix" ,r-matrix)))
4950 (home-page "http://eigen.tuxfamily.org")
4951 (synopsis "Rcpp integration for the Eigen templated linear algebra library")
4953 "This package provides an integration of Eigen in R using a C++ template
4954 library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
4955 It supports dense and sparse matrices on integer, floating point and complex numbers,
4956 decompositions of such matrices, and solutions of linear systems.")
4957 (license license:gpl2+)))
4959 (define-public r-modelmetrics
4961 (name "r-modelmetrics")
4966 (uri (cran-uri "ModelMetrics" version))
4969 "119xxmzb5biq7k1yxqsf0jmmarmfn6lds9x9hfgv593xlpym6za8"))))
4970 (properties `((upstream-name . "ModelMetrics")))
4971 (build-system r-build-system)
4973 `(("r-rcpp" ,r-rcpp)))
4974 (home-page "https://cran.r-project.org/web/packages/ModelMetrics")
4975 (synopsis "Rapid calculation of model metrics")
4977 "Written in C++ using @code{Rcpp}, this package provides a collection of
4978 metrics for evaluating models.")
4979 (license license:gpl2+)))
4981 (define-public r-matrixmodels
4983 (name "r-matrixmodels")
4988 (uri (cran-uri "MatrixModels" version))
4991 "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
4992 (properties `((upstream-name . "MatrixModels")))
4993 (build-system r-build-system)
4995 `(("r-matrix" ,r-matrix)))
4996 (home-page "https://cran.r-project.org/web/packages/MatrixModels")
4997 (synopsis "Modelling with sparse and dense matrices")
4999 "This package models with sparse and dense matrix matrices,
5000 using modular prediction and response module classes.")
5001 (license license:gpl2+)))
5003 (define-public r-quantreg
5010 (uri (cran-uri "quantreg" version))
5013 "18f3qxv1j1bqmq55hzssz8mnp5ww4flhy80rm2v1rk0mmg9paz7m"))))
5014 (build-system r-build-system)
5016 `(("gfortran" ,gfortran)))
5018 `(("r-matrix" ,r-matrix)
5019 ("r-matrixmodels" ,r-matrixmodels)
5020 ("r-sparsem" ,r-sparsem)))
5021 (home-page "https://www.r-project.org")
5022 (synopsis "Quantile regression")
5024 "This package provides an estimation and inference methods for models
5025 of conditional quantiles: linear and nonlinear parametric and non-parametric
5026 models for conditional quantiles of a univariate response and several methods
5027 for handling censored survival data. Portfolio selection methods based on
5028 expected shortfall risk are also included.")
5029 (license license:gpl2+)))
5031 (define-public r-nloptr
5038 (uri (cran-uri "nloptr" version))
5041 "1sz1xj3785x4vsm4nd6in298bk32hs2jk5nsxma7ivxi7jcmn8l4"))))
5042 (build-system r-build-system)
5044 `(("pkg-config" ,pkg-config)))
5046 `(("nlopt" ,nlopt)))
5047 (home-page "https://cran.r-project.org/web/packages/nloptr")
5048 (synopsis "R interface to NLopt")
5050 "This package is interface to NLopt, a library for nonlinear
5051 optimization. NLopt is a library for nonlinear optimization, providing a
5052 common interface for a number of different free optimization routines
5053 available online as well as original implementations of various other
5055 (license license:lgpl3)))
5057 (define-public r-lme4
5064 (uri (cran-uri "lme4" version))
5067 "0sc6rvhiizxxpkdc3wps200wg3pqc0d89crn29lzm75fk8qdd7vx"))))
5068 (build-system r-build-system)
5070 `(("r-rcpp" ,r-rcpp)
5071 ("r-rcppeigen" ,r-rcppeigen)))
5073 `(("r-lattice" ,r-lattice)
5074 ("r-matrix" ,r-matrix)
5075 ("r-minqa" ,r-minqa)
5076 ("r-nloptr" ,r-nloptr)
5078 ("r-nlme" ,r-nlme)))
5079 (home-page "https://cran.r-project.org/web/packages/lme4")
5080 (synopsis "Linear mixed-effects models using eigen and S4")
5082 "This package provides fit linear and generalized linear mixed-effects
5083 models. The models and their components are represented using S4 classes and
5084 methods. The core computational algorithms are implemented using the Eigen
5085 C++ library for numerical linear algebra and RcppEigen glue.")
5086 (license license:gpl2+)))
5088 (define-public r-pbkrtest
5095 (uri (cran-uri "pbkrtest" version))
5098 "1si3bhi59xc51a0pgjjglccq3h4aljyhw2k1b8574s145fnh7fsw"))))
5099 (build-system r-build-system)
5101 `(("r-lme4" ,r-lme4)
5103 ("r-matrix" ,r-matrix)))
5104 (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
5105 (synopsis "Methods for linear mixed model comparison")
5107 "This package implements a parametric bootstrap test and a Kenward Roger
5108 modification of F-tests for linear mixed effects models and a parametric
5109 bootstrap test for generalized linear mixed models.")
5110 (license license:gpl2+)))
5112 (define-public r-car
5119 (uri (cran-uri "car" version))
5122 "14l4d9j87xnb0bz2wgqqbxnlnbcdfb5vx2fw6kdxj91kyrk6lhnj"))))
5123 (build-system r-build-system)
5125 `(("r-mass" ,r-mass)
5128 ("r-pbkrtest" ,r-pbkrtest)
5129 ("r-quantreg" ,r-quantreg)))
5130 (home-page "https://r-forge.r-project.org/projects/car/")
5131 (synopsis "Companion to applied regression")
5133 "This package provides functions and datasets from book Companion
5134 to Applied regression, Second Edition, Sage, 2011.")
5135 (license license:gpl2+)))
5137 (define-public r-caret
5144 (uri (cran-uri "caret" version))
5147 "0h1nxzii2h80aslp1zsjczrlfmaks44sskabk4yq9c5rafc7ka6y"))))
5148 (build-system r-build-system)
5150 `(("r-foreach" ,r-foreach)
5151 ("r-ggplot2" ,r-ggplot2)
5152 ("r-lattice" ,r-lattice)
5153 ("r-modelmetrics" ,r-modelmetrics)
5156 ("r-recipes" ,r-recipes)
5157 ("r-reshape2" ,r-reshape2)
5158 ("r-withr" ,r-withr)))
5159 (home-page "https://github.com/topepo/caret")
5160 (synopsis "Classification and regression training")
5162 "This package provides misc functions for training and plotting
5163 classification and regression models.")
5164 (license license:gpl2+)))
5166 (define-public r-rcppprogress
5168 (name "r-rcppprogress")
5173 (uri (cran-uri "RcppProgress" version))
5176 "09ayw6d69i0lplmaj5md25p5hn1nmiyp6a4sh60v93nrrs1cq7iv"))))
5177 (properties `((upstream-name . "RcppProgress")))
5178 (build-system r-build-system)
5180 `(("r-devtools" ,r-devtools)
5181 ("r-rcpp" ,r-rcpp)))
5182 (home-page "https://github.com/kforner/rcpp_progress")
5183 (synopsis "Interruptible progress bar for C++ in R packages")
5185 "This package allows to display a progress bar in the R console for long running
5186 computations taking place in C++ code, and support for interrupting those computations
5187 even in multithreaded code, typically using OpenMP.")
5188 (license license:gpl3+)))
5190 (define-public r-mnormt
5197 (uri (cran-uri "mnormt" version))
5200 "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z"))))
5201 (build-system r-build-system)
5203 `(("gfortran" ,gfortran)))
5204 (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
5205 (synopsis "Multivariate normal and \"t\" distributions")
5207 "This package provides functions for computing the density and the
5208 distribution function of multivariate normal and \"t\" random variables, and
5209 for generating random vectors sampled from these distributions. Probabilities
5210 are computed via non-Monte Carlo methods.")
5211 (license license:gpl2+)))
5213 (define-public r-numderiv
5216 (version "2016.8-1")
5220 (uri (cran-uri "numDeriv" version))
5223 "07ni52rwiap4wilfz94w5mrqaxr59axxmgn57857ip4p6qkiss0v"))))
5224 (properties `((upstream-name . "numDeriv")))
5225 (build-system r-build-system)
5226 (home-page "https://cran.r-project.org/web/packages/numDeriv")
5227 (synopsis "Accurate numerical derivatives")
5229 "This package provides methods for calculating accurate numerical
5230 first and second order derivatives.")
5231 (license license:gpl2)))
5240 (uri (cran-uri "sn" version))
5243 "0l7qlah6dwkp8jswnr2mn3phlm15naba5zkmv0g5pcqy5ix0gz7w"))))
5244 (build-system r-build-system)
5246 `(("r-mnormt" ,r-mnormt)
5247 ("r-numderiv" ,r-numderiv)))
5248 (home-page "http://azzalini.stat.unipd.it/SN")
5249 (synopsis "The skew-normal and skew-t distributions")
5251 "This packages provides functionalities to build and manipulate
5252 probability distributions of the skew-normal family and some related
5253 ones, notably the skew-t family, and provides related statistical
5254 methods for data fitting and diagnostics, in the univariate and the
5255 multivariate case.")
5256 (license license:gpl2+)))
5258 (define-public r-tclust
5265 (uri (cran-uri "tclust" version))
5268 "1li62wynv81kb17fx7nk63a26qlb78l8fdf63in8yzcl7fkpji7y"))))
5269 (build-system r-build-system)
5271 `(("r-cluster" ,r-cluster)
5272 ("r-mclust" ,r-mclust)
5273 ("r-mvtnorm" ,r-mvtnorm)
5275 (home-page "https://cran.r-project.org/web/packages/tclust")
5276 (synopsis "Robust trimmed clustering")
5278 "This package implements different robust clustering
5279 algorithms (@code{tclust}) based on trimming and including some graphical
5280 diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
5281 (license license:gpl3)))
5283 (define-public r-ranger
5290 (uri (cran-uri "ranger" version))
5293 "1pilj5pxl8jl0gsy9vsyqxqdqfcxzvphbgvrlp4hf7r9mrfw9v0p"))))
5294 (build-system r-build-system)
5296 `(("r-rcpp" ,r-rcpp)
5297 ("r-matrix" ,r-matrix)
5298 ("r-rcppeigen" ,r-rcppeigen)))
5299 (home-page "https://github.com/imbs-hl/ranger")
5300 (synopsis "Fast implementation of random forests")
5302 "This package provides a fast implementation of Random Forests,
5303 particularly suited for high dimensional data. Ensembles of classification,
5304 regression, survival and probability prediction trees are supported. Data from
5305 genome-wide association studies can be analyzed efficiently.")
5306 (license license:gpl3)))
5308 (define-public r-tsne
5315 (uri (cran-uri "tsne" version))
5318 "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
5319 (build-system r-build-system)
5320 (home-page "https://github.com/jdonaldson/rtsne/")
5321 (synopsis "t-Distributed Stochastic Neighbor Embedding for R")
5323 "This package provides a pure R implementation of the t-SNE algorithm.")
5324 (license license:gpl2+)))
5326 (define-public r-cairo
5333 (uri (cran-uri "Cairo" version))
5336 "1x1q99r3r978rlkkm5gixkv03p0mcr6k7ydcqdmisrwnmrn7p1ia"))))
5337 (properties `((upstream-name . "Cairo")))
5338 (build-system r-build-system)
5343 `(("pkg-config" ,pkg-config)))
5344 (home-page "http://www.rforge.net/Cairo/")
5345 (synopsis "R graphics device using Cairo graphics library")
5347 "This package provides a Cairo graphics device that can be use to
5348 create high-quality vector (PDF, PostScript and SVG) and bitmap
5349 output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11
5350 and Win32). Since it uses the same back-end for all output, copying
5351 across formats is WYSIWYG. Files are created without the dependence
5352 on X11 or other external programs. This device supports alpha
5353 channel (semi-transparent drawing) and resulting images can contain
5354 transparent and semi-transparent regions. It is ideal for use in
5355 server environments (file output) and as a replacement for other
5356 devices that don't have Cairo's capabilities such as alpha support or
5357 anti-aliasing. Backends are modular such that any subset of backends
5359 (license license:gpl2)))
5361 (define-public r-lubridate
5363 (name "r-lubridate")
5368 (uri (cran-uri "lubridate" version))
5371 "1pzkqfiahnsdm3zx46asgn8fw43vlxvbh7r4cn70c7ffmxabzzrc"))))
5372 (build-system r-build-system)
5374 `(("r-rcpp" ,r-rcpp)
5375 ("r-stringr" ,r-stringr)))
5377 "https://cran.r-project.org/web/packages/lubridate")
5378 (synopsis "Make dealing with dates a little easier")
5380 "This package provides functions to work with date-times and time-spans:
5381 fast and user friendly parsing of date-time data, extraction and updating of
5382 components of a date-time (years, months, days, hours, minutes, and seconds),
5383 algebraic manipulation on date-time and time-span objects. The 'lubridate'
5384 package has a consistent and memorable syntax that makes working with dates
5386 (license license:gpl2)))
5388 (define-public r-fdrtool
5395 (uri (cran-uri "fdrtool" version))
5398 "1h46frlk7d9f4qx0bg6p55nrm9wwwz2sv6d1nz7061wdfsm69yb5"))))
5399 (build-system r-build-system)
5400 (home-page "http://strimmerlab.org/software/fdrtool/")
5401 (synopsis "Estimation of false discovery rates and higher criticism")
5403 "This package provides tools to estimate tail area-based false discovery
5404 rates as well as local false discovery rates for a variety of null
5405 models (p-values, z-scores, correlation coefficients, t-scores). The
5406 proportion of null values and the parameters of the null distribution are
5407 adaptively estimated from the data. In addition, the package contains
5408 functions for non-parametric density estimation (Grenander estimator), for
5409 monotone regression (isotonic regression and antitonic regression with
5410 weights), for computing the @dfn{greatest convex minorant} (GCM) and the
5411 @dfn{least concave majorant} (LCM), for the half-normal and correlation
5412 distributions, and for computing empirical @dfn{higher criticism} (HC) scores
5413 and the corresponding decision threshold.")
5414 (license license:gpl3+)))
5416 (define-public r-forcats
5423 (uri (cran-uri "forcats" version))
5426 "0mxn1hng43zdjh1v8shd80hrszrqahcpaqxs1s1sif0qxh84d0cm"))))
5427 (build-system r-build-system)
5429 `(("r-magrittr" ,r-magrittr)
5430 ("r-tibble" ,r-tibble)
5431 ("r-rlang" ,r-rlang)))
5432 (home-page "http://forcats.tidyverse.org")
5433 (synopsis "Tools for working with factors")
5434 (description "This package provides helpers for reordering factor
5435 levels (including moving specified levels to front, ordering by first
5436 appearance, reversing, and randomly shuffling), and tools for modifying factor
5437 levels (including collapsing rare levels into other, \"anonymizing\", and
5438 manually \"recoding\").")
5439 (license license:gpl3)))
5441 (define-public r-tgstat
5442 (let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f")
5446 (version (string-append "1.0.2-" revision "." (string-take changeset 7)))
5451 (url "https://bitbucket.org/tanaylab/tgstat")
5452 (changeset changeset)))
5453 (file-name (string-append name "-" version "-checkout"))
5456 "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn"))))
5457 (build-system r-build-system)
5460 (modify-phases %standard-phases
5461 (add-after 'unpack 'fix-isnan
5463 (substitute* "src/tgstat.h"
5464 (("#define isnan ::isnan")
5465 "#define isnan std::isnan"))
5468 `(("r-rcpp" ,r-rcpp)))
5469 (home-page "https://bitbucket.org/tanaylab/tgstat/")
5470 (synopsis "Tanay's group statistical utilities")
5472 "The goal of tgstat is to provide fast and efficient statistical
5474 (license license:gpl2))))
5476 (define-public r-tgconfig
5477 (let ((changeset "1e02c7614713bd0866c46f0c679a058f8c6d627e")
5481 (version (string-append "0.0.0.9000-" revision "." (string-take changeset 7)))
5486 (url "https://bitbucket.org/tanaylab/tgconfig")
5487 (changeset changeset)))
5488 (file-name (string-append name "-" version "-checkout"))
5491 "0xy6c7s7mn1yx191154bwbv1bl424bnvc80syqpl1vdl28ba46rj"))))
5492 (build-system r-build-system)
5494 `(("r-yaml" ,r-yaml)))
5495 (home-page "https://bitbucket.org/tanaylab/tgconfig/")
5496 (synopsis "Infrastructure for managing package parameters")
5498 "The goal of tgconfig is to provide infrastructure for managing package
5500 (license license:gpl3))))
5502 (define-public r-directlabels
5504 (name "r-directlabels")
5505 (version "2017.03.31")
5509 (uri (cran-uri "directlabels" version))
5512 "01ahw0c56mnzwl611s8hnghicww4c4dgf5v2wv6bl1s1pramw9pr"))))
5513 (build-system r-build-system)
5515 `(("r-quadprog" ,r-quadprog)))
5516 (home-page "http://directlabels.r-forge.r-project.org/")
5517 (synopsis "Direct labels for multicolor plots")
5519 "This package provides an extensible framework for automatically placing
5520 direct labels onto multicolor plots. Label positions are described using
5521 positioning methods that can be re-used across several different plots. There
5522 are heuristics for examining @code{trellis} and @code{ggplot} objects and
5523 inferring an appropriate positioning method.")
5524 (license license:gpl3)))
5526 (define-public r-catterplots
5527 (let ((commit "40063ec57f9515d231508f135ca0ec769614efb9")
5530 (name "r-catterplots")
5531 (version (string-append "0-" revision "." (string-take commit 9)))
5535 (url "https://github.com/Gibbsdavidl/CatterPlots.git")
5537 (file-name (string-append name "-" version "-checkout"))
5540 "1wl80pgbz8d9kfpffvkh439hlgz2qldm9m75wqjfrgrg8lcjzrxg"))))
5541 (build-system r-build-system)
5543 `(("r-png" ,r-png)))
5544 (home-page "https://github.com/Gibbsdavidl/CatterPlots")
5545 (synopsis "Scatter plots with cat shaped points")
5546 (description "Did you ever wish you could make scatter plots with cat
5547 shaped points? Now you can!")
5548 (license license:asl2.0))))
5550 (define-public r-colorout
5557 (uri (string-append "https://github.com/jalvesaq/colorout/archive/"
5558 "v" version ".tar.gz"))
5559 (file-name (string-append name "-" version ".tar.gz"))
5562 "07vqx5ihgnq4dzn5jnfjfhdm3957v4prvf8vhnb3cwvlly4l7p9v"))))
5563 (build-system r-build-system)
5564 (home-page "https://github.com/jalvesaq/colorout")
5565 (synopsis "Colorize output in the R REPL")
5566 (description "@code{colorout} is an R package that colorizes R output when
5567 running in terminal emulator.
5569 R STDOUT is parsed and numbers, negative numbers, dates in the standard
5570 format, strings, and R constants are identified and wrapped by special ANSI
5571 scape codes that are interpreted by terminal emulators as commands to colorize
5572 the output. R STDERR is also parsed to identify the expressions warning and
5573 error and their translations to many languages. If these expressions are
5574 found, the output is colorized accordingly; otherwise, it is colorized as
5575 STDERROR (blue, by default).
5577 You can customize the colors according to your taste, guided by the color
5578 table made by the command @code{show256Colors()}. You can also set the colors
5579 to any arbitrary string. In this case, it is up to you to set valid values.")
5580 (license license:gpl3+)))
5582 (define-public java-jdistlib
5584 (name "java-jdistlib")
5588 (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-"
5589 version "-src.jar"))
5592 "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11"))))
5593 (build-system ant-build-system)
5595 `(#:jar-name "jdistlib.jar"
5597 #:tests? #f ; no dedicated test directory
5599 (modify-phases %standard-phases
5600 (add-after 'unpack 'fix-broken-encoding
5602 (with-fluids ((%default-port-encoding "ISO-8859-1"))
5603 (substitute* "src/jdistlib/Beta.java"
5604 (("Scheff.+-Tukey") "Scheffe-Tukey")))
5607 `(("java-jtransforms" ,java-jtransforms)))
5609 `(("java-junit" ,java-junit)))
5610 (home-page "http://jdistlib.sourceforge.net/")
5611 (synopsis "Java library of statistical distributions")
5612 (description "JDistlib is the Java Statistical Distribution Library, a
5613 Java package that provides routines for various statistical distributions.")
5614 ;; The files that were translated from R code are under GPLv2+; some files
5615 ;; are under the GPLv3, which is a mistake. The author confirmed in an
5616 ;; email that this whole project should be under GPLv2+.
5617 (license license:gpl2+)))