1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017 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>
11 ;;; This file is part of GNU Guix.
13 ;;; GNU Guix is free software; you can redistribute it and/or modify it
14 ;;; under the terms of the GNU General Public License as published by
15 ;;; the Free Software Foundation; either version 3 of the License, or (at
16 ;;; your option) any later version.
18 ;;; GNU Guix is distributed in the hope that it will be useful, but
19 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
20 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21 ;;; GNU General Public License for more details.
23 ;;; You should have received a copy of the GNU General Public License
24 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
26 (define-module (gnu packages statistics)
27 #:use-module ((guix licenses) #:prefix license:)
28 #:use-module (guix packages)
29 #:use-module (guix download)
30 #:use-module (guix utils)
31 #:use-module (guix build-system gnu)
32 #:use-module (guix build-system r)
33 #:use-module (guix build-system python)
34 #:use-module (guix build-system trivial)
35 #:use-module (gnu packages)
36 #:use-module (gnu packages compression)
37 #:use-module (gnu packages cran)
38 #:use-module (gnu packages curl)
39 #:use-module (gnu packages gcc)
40 #:use-module (gnu packages gtk)
41 #:use-module (gnu packages gettext)
42 #:use-module (gnu packages glib)
43 #:use-module (gnu packages haskell)
44 #:use-module (gnu packages icu4c)
45 #:use-module (gnu packages image)
46 #:use-module (gnu packages java)
47 #:use-module (gnu packages machine-learning)
48 #:use-module (gnu packages maths)
49 #:use-module (gnu packages multiprecision)
50 #:use-module (gnu packages pcre)
51 #:use-module (gnu packages perl)
52 #:use-module (gnu packages pkg-config)
53 #:use-module (gnu packages python)
54 #:use-module (gnu packages readline)
55 #:use-module (gnu packages ssh)
56 #:use-module (gnu packages texinfo)
57 #:use-module (gnu packages tls)
58 #:use-module (gnu packages base)
59 #:use-module (gnu packages web)
60 #:use-module (gnu packages xml)
61 #:use-module (gnu packages xorg)
62 #:use-module (srfi srfi-1))
72 (uri (string-append "mirror://gnu/pspp/pspp-"
76 "1afsq0a3iij64qacczvwhk81qg0q5rfqm055y5h9ls28d6paqz7p"))))
77 (build-system gnu-build-system)
80 ("gettext" ,gettext-minimal)
84 ("readline" ,readline)
86 ("gtksourceview" ,gtksourceview)
89 `(("glib" ,glib "bin") ;for glib-genmarshal
91 ("pkg-config" ,pkg-config)))
92 (home-page "https://www.gnu.org/software/pspp/")
93 (synopsis "Statistical analysis")
95 "GNU PSPP is a statistical analysis program. It can perform
96 descriptive statistics, T-tests, linear regression and non-parametric tests.
97 It features both a graphical interface as well as command-line input. PSPP
98 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data
99 can be imported from spreadsheets, text files and database sources and it can
100 be output in text, PostScript, PDF or HTML.")
101 (license license:gpl3+)))
103 ;; Update this package together with the set of recommended packages: r-boot,
104 ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
105 ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
106 (define-public r-minimal
112 (uri (string-append "mirror://cran/src/base/R-"
113 (version-prefix version 1) "/R-"
117 "14cb8bwi3akvdb6934kqic2862f2qgav6cq4g0h7gi2p4ka9x3i8"))))
118 (build-system gnu-build-system)
120 `(#:disallowed-references (,tzdata-2017a)
122 (list (string-append "LDFLAGS=-Wl,-rpath="
123 (assoc-ref %outputs "out")
125 ;; This affects the embedded timestamp of only the core packages.
126 "PKG_BUILT_STAMP=1970-01-01")
128 (modify-phases %standard-phases
129 (add-before 'configure 'patch-uname
130 (lambda* (#:key inputs #:allow-other-keys)
131 (let ((uname-bin (string-append (assoc-ref inputs "coreutils")
133 (substitute* "src/scripts/R.sh.in"
134 (("uname") uname-bin)))
136 (add-after 'unpack 'build-reproducibly
138 ;; The documentation contains time stamps to demonstrate
139 ;; documentation generation in different phases.
140 (substitute* "src/library/tools/man/Rd2HTML.Rd"
141 (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
142 "(removed for reproducibility)"))
144 ;; Remove timestamp from tracing environment. This fixes
145 ;; reproducibility of "methods.rd{b,x}".
146 (substitute* "src/library/methods/R/trace.R"
147 (("dateCreated = Sys.time\\(\\)")
148 "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
150 ;; Ensure that gzipped files are reproducible.
151 (substitute* '("src/library/grDevices/Makefile.in"
152 "doc/manual/Makefile.in")
153 (("R_GZIPCMD\\)" line)
154 (string-append line " -n")))
156 ;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
157 ;; queries the mtime of a given file and records it in an object.
158 ;; This is acceptable at runtime to detect stale source files,
159 ;; but it destroys reproducibility at build time.
161 ;; Instead of disabling this feature, which may have unexpected
162 ;; consequences, we reset the mtime of generated files before
163 ;; passing them to the "srcfile" procedure.
164 (substitute* "src/library/Makefile.in"
165 (("@\\(cd base && \\$\\(MAKE\\) mkdesc\\)" line)
166 (string-append line "\n find $(top_builddir)/library/tools | xargs touch -d '1970-01-01'; \n"))
167 (("@\\$\\(MAKE\\) Rdobjects" line)
168 (string-append "@find $(srcdir)/tools | xargs touch -d '1970-01-01'; \n "
170 (substitute* "src/library/tools/Makefile.in"
171 (("@\\$\\(INSTALL_DATA\\) all.R \\$\\(top_builddir\\)/library/\\$\\(pkg\\)/R/\\$\\(pkg\\)" line)
174 "\n find $(srcdir)/$(pkg) $(top_builddir)/library/$(pkg) | xargs touch -d \"1970-01-01\"; \n")))
176 ;; This library is installed using "install_package_description",
177 ;; so we need to pass the "builtStamp" argument.
178 (substitute* "src/library/tools/Makefile.in"
179 (("(install_package_description\\(.*\"')\\)\"" line prefix)
180 (string-append prefix ", builtStamp='1970-01-01')\"")))
182 (add-before 'configure 'set-default-pager
183 ;; Set default pager to "cat", because otherwise it is "false",
184 ;; making "help()" print nothing at all.
185 (lambda _ (setenv "PAGER" "cat") #t))
186 (add-before 'check 'set-timezone
187 ;; Some tests require the timezone to be set. However, the
188 ;; timezone may not just be "UTC", or else a brittle regression
189 ;; test in reg-tests-1d will fail.
190 (lambda* (#:key inputs #:allow-other-keys)
191 (setenv "TZ" "UTC+1")
193 (string-append (assoc-ref inputs "tzdata")
196 (add-after 'build 'make-info
197 (lambda _ (zero? (system* "make" "info"))))
198 (add-after 'build 'install-info
199 (lambda _ (zero? (system* "make" "install-info")))))
201 '(;; Do not build the recommended packages. The build system creates
202 ;; random temporary directories and embeds their names in some
203 ;; package files. We build these packages with the r-build-system
205 "--without-recommended-packages"
207 "--with-blas=-lopenblas"
213 "--enable-BLAS-shlib"
214 "--with-system-tre")))
215 ;; R has some support for Java. When the JDK is available at configure
216 ;; time environment variables pointing to the JDK will be recorded under
217 ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
218 ;; CMD javareconf". "R CMD javareconf" appears to only be used to update
219 ;; the recorded environment variables in $R_HOME/etc. Refer to
220 ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
221 ;; for additional information.
223 ;; As the JDK is a rather large input with only very limited effects on R,
224 ;; we decided to drop it.
228 ("pkg-config" ,pkg-config)
229 ("texinfo" ,texinfo) ; for building HTML manuals
230 ("which" ,which) ; for tests/Examples/base-Ex.R
231 ("tzdata" ,tzdata-2017a)
234 `(;; We need not only cairo here, but pango to ensure that tests for the
235 ;; "cairo" bitmapType plotting backend succeed.
237 ("coreutils" ,coreutils)
239 ("openblas" ,openblas)
240 ("gfortran" ,gfortran)
247 ("readline" ,readline)
250 (list (search-path-specification
251 (variable "R_LIBS_SITE")
252 (files (list "site-library/")))))
253 (home-page "http://www.r-project.org/")
254 (synopsis "Environment for statistical computing and graphics")
256 "R is a language and environment for statistical computing and graphics.
257 It provides a variety of statistical techniques, such as linear and nonlinear
258 modeling, classical statistical tests, time-series analysis, classification
259 and clustering. It also provides robust support for producing
260 publication-quality data plots. A large amount of 3rd-party packages are
261 available, greatly increasing its breadth and scope.")
262 (license license:gpl3+)))
264 (define-public r-boot
271 (uri (cran-uri "boot" version))
274 "0ai1qpm0p4z07xr0dvag8sdn9jrxcwanrsk9khzmww094jvr1jxd"))))
275 (build-system r-build-system)
276 (home-page "http://cran.r-project.org/web/packages/boot")
277 (synopsis "Bootstrap functions for R")
279 "This package provides functions and datasets for bootstrapping from the
280 book \"Bootstrap Methods and Their Application\" by A.C. Davison and
281 D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
282 ;; Unlimited distribution
283 (license (license:non-copyleft "file://R/bootfuns.q"))))
285 (define-public r-mass
292 (uri (cran-uri "MASS" version))
295 "1gy6z7ly9wn86rfn9xrmqiqq1ijw3pkasrr2299kbzsgx2mwsi7d"))))
296 (properties `((upstream-name . "MASS")))
297 (build-system r-build-system)
298 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
299 (synopsis "Support functions and datasets for Venables and Ripley's MASS")
301 "This package provides functions and datasets for the book \"Modern
302 Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
303 ;; Either version may be picked.
304 (license (list license:gpl2 license:gpl3))))
306 (define-public r-class
313 (uri (cran-uri "class" version))
316 "173b8a16lh1i0zjmr784l0xr0azp9v8bgslh12hfdswbq7dpdf0q"))))
317 (build-system r-build-system)
319 `(("r-mass" ,r-mass)))
320 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
321 (synopsis "R functions for classification")
323 "This package provides various functions for classification, including
324 k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
325 ;; Either of the two versions can be picked.
326 (license (list license:gpl2 license:gpl3))))
328 (define-public r-cluster
335 (uri (cran-uri "cluster" version))
338 "1bkvqmv8h2c423q9ag2afb6s9j2vcdlxsf559zzbimraphrr2c2b"))))
339 (build-system r-build-system)
340 (home-page "http://cran.r-project.org/web/packages/cluster")
341 (synopsis "Methods for cluster analysis")
343 "This package provides methods for cluster analysis. It is a much
344 extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
345 Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
346 (license license:gpl2+)))
348 (define-public r-codetools
355 (uri (cran-uri "codetools" version))
358 "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf"))))
359 (build-system r-build-system)
360 (home-page "http://cran.r-project.org/web/packages/codetools")
361 (synopsis "Code analysis tools for R")
362 (description "This package provides code analysis tools for R.")
363 ;; Any version of the GPL.
364 (license (list license:gpl2+ license:gpl3+))))
366 (define-public r-foreign
373 (uri (cran-uri "foreign" version))
376 "0s1lxmd85dd0kxx8hwk02w9l7pmpk4bpy7787fbyh2dbq5g9ys0k"))))
377 (build-system r-build-system)
378 (home-page "http://cran.r-project.org/web/packages/foreign")
379 (synopsis "Read data stored by other statistics software")
381 "This package provides functions for reading and writing data stored by
382 some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
383 for reading and writing some dBase files.")
384 (license license:gpl2+)))
386 (define-public r-kernsmooth
388 (name "r-kernsmooth")
393 (uri (cran-uri "KernSmooth" version))
396 "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb"))))
397 (properties `((upstream-name . "KernSmooth")))
398 (build-system r-build-system)
399 (home-page "http://cran.r-project.org/web/packages/KernSmooth")
400 (synopsis "Functions for kernel smoothing")
402 "This package provides functions for kernel smoothing (and density
403 estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
404 \"Kernel Smoothing\".")
405 ;; Unlimited distribution
406 (license (license:non-copyleft "file://LICENCE.note"))))
408 (define-public r-lattice
414 (uri (cran-uri "lattice" version))
417 "0pcnmaz3lr62ly0dcy5hnnqxshc4yqd43hrvlz3almgc9l7sna88"))))
418 (build-system r-build-system)
419 (home-page "http://lattice.r-forge.r-project.org/")
420 (synopsis "High-level data visualization system")
422 "The lattice package provides a powerful and elegant high-level data
423 visualization system inspired by Trellis graphics, with an emphasis on
424 multivariate data. Lattice is sufficient for typical graphics needs, and is
425 also flexible enough to handle most nonstandard requirements.")
426 (license license:gpl2+)))
428 (define-public r-matrix
435 (uri (cran-uri "Matrix" version))
438 "0r3qjcz92xwgdzrfz444mqzwnja5sv9abaf252fh6k48qbyahahh"))))
439 (properties `((upstream-name . "Matrix")))
440 (build-system r-build-system)
442 `(("r-lattice" ,r-lattice)))
443 (home-page "http://Matrix.R-forge.R-project.org/")
444 (synopsis "Sparse and dense matrix classes and methods")
446 "This package provides classes and methods for dense and sparse matrices
447 and operations on them using LAPACK and SuiteSparse.")
448 (license license:gpl2+)))
450 (define-public r-nlme
457 (uri (cran-uri "nlme" version))
460 "0k2nvdzhic6bzhfsbq6la6q6a1i5nlj4pnh6lpdxiiwvxdks3nkr"))))
461 (build-system r-build-system)
463 `(("r-lattice" ,r-lattice)))
465 `(("gfortran" ,gfortran)))
466 (home-page "http://cran.r-project.org/web/packages/nlme")
467 (synopsis "Linear and nonlinear mixed effects models")
469 "This package provides tools to fit and compare Gaussian linear and
470 nonlinear mixed-effects models.")
471 (license license:gpl2+)))
473 (define-public r-mgcv
480 (uri (cran-uri "mgcv" version))
483 "011mgcypr56xvm9nizsfsb2285kzql93x0d3lzg849g39vbpp4s2"))))
484 (build-system r-build-system)
486 `(("r-matrix" ,r-matrix)
488 (home-page "http://cran.r-project.org/web/packages/mgcv")
489 (synopsis "Mixed generalised additive model computation")
491 "GAMs, GAMMs and other generalized ridge regression with multiple smoothing
492 parameter estimation by GCV, REML or UBRE/AIC. The library includes a
493 @code{gam()} function, a wide variety of smoothers, JAGS support and
494 distributions beyond the exponential family.")
495 (license license:gpl2+)))
497 (define-public r-nnet
504 (uri (cran-uri "nnet" version))
507 "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7"))))
508 (build-system r-build-system)
509 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
510 (synopsis "Feed-forward neural networks and multinomial log-linear models")
512 "This package provides functions for feed-forward neural networks with a
513 single hidden layer, and for multinomial log-linear models.")
514 (license (list license:gpl2+ license:gpl3+))))
516 (define-public r-rpart
523 (uri (cran-uri "rpart" version))
526 "165djqj7lk81jr7z5fwccq3h7ayys26hx1kj9hndvg2rkyaq1arq"))))
527 (build-system r-build-system)
528 (home-page "http://cran.r-project.org/web/packages/rpart")
529 (synopsis "Recursive partitioning and regression trees")
531 "This package provides recursive partitioning functions for
532 classification, regression and survival trees.")
533 (license (list license:gpl2+ license:gpl3+))))
535 (define-public r-spatial
542 (uri (cran-uri "spatial" version))
545 "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
546 (build-system r-build-system)
547 (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
548 (synopsis "Functions for kriging and point pattern analysis")
550 "This package provides functions for kriging and point pattern
552 ;; Either version may be picked.
553 (license (list license:gpl2 license:gpl3))))
555 (define-public r-survival
562 (uri (cran-uri "survival" version))
565 "07cnr0hnki6ybbjll54l4s5lllhk19vni5f8m0mvsfp99ls7qygk"))))
566 (build-system r-build-system)
568 `(("r-matrix" ,r-matrix)))
569 (home-page "https://github.com/therneau/survival")
570 (synopsis "Survival analysis")
572 "This package contains the core survival analysis routines, including
573 definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
574 curves, Cox models, and parametric accelerated failure time models.")
575 (license license:lgpl2.0+)))
578 (package (inherit r-minimal)
581 (build-system trivial-build-system)
582 (arguments '(#:builder (mkdir %output)))
584 `(("r-minimal" ,r-minimal)
587 ("r-cluster" ,r-cluster)
588 ("r-codetools" ,r-codetools)
589 ("r-foreign" ,r-foreign)
590 ("r-kernsmooth" ,r-kernsmooth)
591 ("r-lattice" ,r-lattice)
593 ("r-matrix" ,r-matrix)
598 ("r-spatial" ,r-spatial)
599 ("r-survival" ,r-survival)))))
608 (uri (cran-uri "bit" version))
611 "0a6ig6nnjzq80r2ll4hc74za3xwzbzig6wlyb4dby0knzf3iqa6f"))))
612 (build-system r-build-system)
613 (home-page "http://ff.r-forge.r-project.org")
614 (synopsis "Class for vectors of 1-bit booleans")
616 "This package provides bitmapped vectors of booleans (no @code{NA}s),
617 coercion from and to logicals, integers and integer subscripts, fast boolean
618 operators and fast summary statistics. With @code{bit} class vectors of true
619 binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
620 (license license:gpl2)))
622 (define-public r-bit64
629 (uri (cran-uri "bit64" version))
632 "07znvz9vp1nz1y5ljng4qyskvm943cdbmy996s67560ijxzsm6kv"))))
633 (build-system r-build-system)
636 (home-page "http://ff.r-forge.r-project.org/")
637 (synopsis "S3 class for vectors of 64 bit integers")
639 "The bit64 package provides serializable S3 atomic 64 bit (signed)
640 integers that can be used in vectors, matrices, arrays and @code{data.frames}.
641 Methods are available for coercion from and to logicals, integers, doubles,
642 characters and factors as well as many elementwise and summary functions.
643 Many fast algorithmic operations such as @code{match} and @code{order} support
644 interactive data exploration and manipulation and optionally leverage
646 (license license:gpl2)))
648 (define-public r-dichromat
655 (uri (cran-uri "dichromat" version))
657 (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
658 (build-system r-build-system)
659 (home-page "http://cran.r-project.org/web/packages/dichromat")
660 (synopsis "Color schemes for dichromats")
662 "Dichromat collapses red-green or green-blue distinctions to simulate the
663 effects of different types of color-blindness.")
664 (license license:gpl2+)))
666 (define-public r-digest
673 (uri (cran-uri "digest" version))
675 (base32 "1awy9phxdvqnadby7rvwy2hkbrj210bqf4xvi27asdq028zlcyd4"))))
676 (build-system r-build-system)
677 ;; Vignettes require r-knitr, which requires r-digest, so we have to
678 ;; disable them and the tests.
681 #:configure-flags (list "--no-build-vignettes")))
682 (home-page "http://dirk.eddelbuettel.com/code/digest.html")
683 (synopsis "Create cryptographic hash digests of R objects")
685 "This package contains an implementation of a function 'digest()' for the
686 creation of hash digests of arbitrary R objects (using the md5, sha-1,
687 sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
688 of R language objects, as well as a function 'hmac()' to create hash-based
689 message authentication code.
691 Please note that this package is not meant to be deployed for cryptographic
692 purposes for which more comprehensive (and widely tested) libraries such as
693 OpenSSL should be used.")
694 (license license:gpl2+)))
696 (define-public r-estimability
698 (name "r-estimability")
702 (uri (cran-uri "estimability" version))
705 "13b80bpnbrarazjvnpnk91ljjsqgfm2fm3gy66aj09cmmsmv199h"))))
706 (build-system r-build-system)
707 (home-page "http://cran.r-project.org/web/packages/estimability")
708 (synopsis "Tools for assessing estimability of linear predictions")
709 (description "Provides tools for determining estimability of linear
710 functions of regression coefficients, and 'epredict' methods that handle
711 non-estimable cases correctly.")
712 (license license:gpl2+)))
714 (define-public r-pheatmap
721 (uri (cran-uri "pheatmap" version))
724 "1ik0k69kb4n7xl3bkx4p09kw08ri93855zcsxq1c668171jqfiji"))))
725 (build-system r-build-system)
727 `(("r-gtable" ,r-gtable)
728 ("r-rcolorbrewer" ,r-rcolorbrewer)
729 ("r-scales" ,r-scales)))
731 "http://cran.r-project.org/web/packages/pheatmap")
732 (synopsis "Pretty heatmaps")
734 "This package provides an implementation of heatmaps that offers more
735 control over dimensions and appearance.")
736 (license license:gpl2+)))
738 (define-public r-labeling
745 (uri (cran-uri "labeling" version))
747 (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
748 (build-system r-build-system)
749 (home-page "http://cran.r-project.org/web/packages/labeling")
750 (synopsis "Axis labeling algorithms")
751 (description "The labeling package provides a range of axis labeling
753 (license license:expat)))
755 (define-public r-magrittr
762 (uri (cran-uri "magrittr" version))
764 (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
765 (build-system r-build-system)
766 (home-page "http://cran.r-project.org/web/packages/magrittr/index.html")
767 (synopsis "A forward-pipe operator for R")
769 "Magrittr provides a mechanism for chaining commands with a new
770 forward-pipe operator, %>%. This operator will forward a value, or the result
771 of an expression, into the next function call/expression. There is flexible
772 support for the type of right-hand side expressions. For more information,
773 see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
774 (license license:expat)))
776 (define-public r-munsell
783 (uri (cran-uri "munsell" version))
785 (base32 "0jdxlbjslkzaqgp058da1cgm85qvqi09wpcgpvp4hvwnmy83qz1r"))))
786 (build-system r-build-system)
788 `(("r-colorspace" ,r-colorspace)))
789 (home-page "http://cran.r-project.org/web/packages/munsell")
790 (synopsis "Munsell colour system")
792 "The Munsell package contains Functions for exploring and using the
793 Munsell colour system.")
794 (license license:expat)))
796 (define-public r-permute
803 (uri (cran-uri "permute" version))
806 "1w8wzk1fg9q7wvisnfp2js70dg0m9wi12gkdhpyngpbdcgssahd5"))))
807 (build-system r-build-system)
808 ;; Tests do not run correctly, but running them properly would entail a
809 ;; circular dependency with vegan.
810 (home-page "https://github.com/gavinsimpson/permute")
811 (synopsis "Functions for Generating Restricted Permutations of Data")
813 "This package provides a set of restricted permutation designs for freely
814 exchangeable, line transects (time series), spatial grid designs and permutation
815 of blocks (groups of samples). @code{permute} also allows split-plot designs,
816 in which the whole-plots or split-plots or both can be freely exchangeable.")
817 (license license:gpl2+)))
819 (define-public r-plyr
826 (uri (cran-uri "plyr" version))
828 (base32 "1igar5pcjqh0jyxv0z3jah8rz617vfa86vw0r5c7c031b7bj5db0"))))
829 (build-system r-build-system)
830 (native-inputs `(("r-rcpp" ,r-rcpp)))
831 (home-page "http://had.co.nz/plyr")
832 (synopsis "Tools for Splitting, Applying and Combining Data")
834 "Plyr is a set of tools that solves a common set of problems: you need to
835 break a big problem down into manageable pieces, operate on each piece and
836 then put all the pieces back together. For example, you might want to fit a
837 model to each spatial location or time point in your study, summarise data by
838 panels or collapse high-dimensional arrays to simpler summary statistics.")
839 (license license:expat)))
841 (define-public r-proto
848 (uri (cran-uri "proto" version))
850 (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
851 (build-system r-build-system)
852 (home-page "https://github.com/hadley/proto")
853 (synopsis "Prototype object-based programming")
855 "Proto is an object oriented system using object-based, also called
856 prototype-based, rather than class-based object oriented ideas.")
857 (license license:gpl2+)))
859 (define-public r-rcolorbrewer
861 (name "r-rcolorbrewer")
866 (uri (cran-uri "RColorBrewer" version))
868 (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
869 (build-system r-build-system)
870 (home-page "http://cran.r-project.org/web/packages/RColorBrewer")
871 (synopsis "ColorBrewer palettes")
873 "This package provides color schemes for maps (and other graphics)
874 designed by Cynthia Brewer as described at http://colorbrewer2.org")
875 ;; Includes code licensed under bsd-4
876 (license license:asl2.0)))
878 (define-public r-sendmailr
885 (uri (cran-uri "sendmailR" version))
888 "0z7ipywnzgkhfvl4zb2fjwl1xq7b5wib296vn9c9qgbndj6b1zh4"))))
889 (properties `((upstream-name . "sendmailR")))
890 (build-system r-build-system)
892 `(("r-base64enc" ,r-base64enc)))
894 "http://cran.r-project.org/web/packages/sendmailR")
895 (synopsis "Send email using R")
897 "This package contains a simple SMTP client which provides a portable
898 solution for sending email, including attachments, from within R.")
899 (license license:gpl2+)))
901 (define-public r-stringi
908 (uri (cran-uri "stringi" version))
911 "1wh20is24lmzhcd9487ckv7r19009fyz4is3ianp3ky69vy8a7k5"))))
912 (build-system r-build-system)
913 (inputs `(("icu4c" ,icu4c)))
914 (native-inputs `(("pkg-config" ,pkg-config)))
915 (home-page "http://stringi.rexamine.com/")
916 (synopsis "Character string processing facilities")
918 "This package allows for fast, correct, consistent, portable, as well as
919 convenient character string/text processing in every locale and any native
920 encoding. Owing to the use of the ICU library, the package provides R users
921 with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
922 programmers. Among available features there are: pattern searching
923 (e.g. via regular expressions), random string generation, string collation,
924 transliteration, concatenation, date-time formatting and parsing, etc.")
925 (license license:bsd-3)))
927 (define-public r-stringr
934 (uri (cran-uri "stringr" version))
936 (base32 "16hj2rmv8x03lp6cp2jk0k2plibvbggf444kp05przdvd03v7l31"))))
937 (build-system r-build-system)
939 `(("r-magrittr" ,r-magrittr)
940 ("r-stringi" ,r-stringi)))
941 (home-page "https://github.com/hadley/stringr")
942 (synopsis "Simple, consistent wrappers for common string operations")
944 "Stringr is a consistent, simple and easy to use set of wrappers around
945 the fantastic 'stringi' package. All function and argument names (and
946 positions) are consistent, all functions deal with \"NA\"'s and zero length
947 vectors in the same way, and the output from one function is easy to feed into
948 the input of another.")
949 (license license:gpl2+)))
951 (define-public r-reshape2
958 (uri (cran-uri "reshape2" version))
960 (base32 "0swvjmc9f8cvkrsz463cp6snd8bncbv6q8yrfrb4rgkr0dhq6dvd"))))
961 (build-system r-build-system)
965 ("r-stringr" ,r-stringr)))
966 (home-page "https://github.com/hadley/reshape")
967 (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
969 "Reshape2 is an R library to flexibly restructure and aggregate data
970 using just two functions: melt and dcast (or acast).")
971 (license license:expat)))
973 (define-public r-scales
980 (uri (cran-uri "scales" version))
982 (base32 "1lqccfmqdwrw0cjyqvw2zvgpk2jvnqrfb303l1raqyyf3zxqhav4"))))
983 (build-system r-build-system)
985 `(("r-dichromat" ,r-dichromat)
986 ("r-labeling" ,r-labeling)
987 ("r-munsell" ,r-munsell)
989 ("r-rcolorbrewer" ,r-rcolorbrewer)
991 (home-page "https://github.com/hadley/scales")
992 (synopsis "Scale functions for visualization")
994 "This package provides graphical scales that map data to aesthetics, and
995 provides methods for automatically determining breaks and labels for axes and
997 (license license:expat)))
999 (define-public r-ggplot2
1006 (uri (cran-uri "ggplot2" version))
1008 (base32 "0543782ddv2hp6s0l702mnxfg8n7a6qlbm8bm55x22hnqgz8kg2z"))))
1009 (build-system r-build-system)
1011 `(("r-digest" ,r-digest)
1012 ("r-gtable" ,r-gtable)
1014 ("r-lazyeval" ,r-lazyeval)
1016 ("r-tibble" ,r-tibble)
1017 ("r-reshape2" ,r-reshape2)
1018 ("r-scales" ,r-scales)
1019 ("r-svglite" ,r-svglite))) ; Needed for 'ggsave'
1020 (home-page "http://ggplot2.org")
1021 (synopsis "An implementation of the grammar of graphics")
1023 "Ggplot2 is an implementation of the grammar of graphics in R. It
1024 combines the advantages of both base and lattice graphics: conditioning and
1025 shared axes are handled automatically, and you can still build up a plot step
1026 by step from multiple data sources. It also implements a sophisticated
1027 multidimensional conditioning system and a consistent interface to map data to
1028 aesthetic attributes.")
1029 (license license:gpl2+)))
1031 (define-public r-gdtools
1038 (uri (cran-uri "gdtools" version))
1041 "09y9x09gri33ghhrvjjnj5k5rk0kdpsk3wq02cln8gmywd6728vk"))))
1042 (build-system r-build-system)
1044 `(("r-rcpp" ,r-rcpp)
1045 ("pkg-config" ,pkg-config)))
1047 `(("cairo" ,cairo)))
1049 `(("r-withr" ,r-withr)))
1050 (home-page "http://cran.r-project.org/web/packages/gdtools")
1051 (synopsis "Utilities for graphical rendering")
1053 "The @code{gdtools} package provides functionalities to get font metrics
1054 and to generate base64 encoded string from raster matrix.")
1055 (license license:gpl3)))
1057 (define-public r-svglite
1064 (uri (cran-uri "svglite" version))
1067 "1s1gvmlmmna5y4jsn9h6438pg5b86fl4nwfvkgm6n4h6ljfgqyx3"))))
1068 (build-system r-build-system)
1069 (native-inputs `(("r-rcpp" ,r-rcpp)))
1072 ("r-gdtools" ,r-gdtools)))
1073 (home-page "https://github.com/hadley/svglite")
1074 (synopsis "SVG graphics device")
1076 "@code{svglite} is a graphics device that produces clean
1077 @dfn{SVG} (Scalable Vector Graphics) output, suitable for use on the web, or
1078 hand editing. Compared to the built-in @code{svg()}, @code{svglite} is
1079 considerably faster, produces smaller files, and leaves text as is.")
1080 (license license:gpl2+)))
1082 (define-public r-assertthat
1084 (name "r-assertthat")
1088 (uri (cran-uri "assertthat" version))
1091 "1wp5znk3xy338x6hknppk702jn596yr735d9i7c3wabm3sdzfgnp"))))
1092 (build-system r-build-system)
1093 (home-page "https://github.com/hadley/assertthat")
1094 (synopsis "Easy pre and post assertions")
1096 "Assertthat is an extension to stopifnot() that makes it easy to declare
1097 the pre and post conditions that your code should satisfy, while also
1098 producing friendly error messages so that your users know what they've done
1100 (license license:gpl3+)))
1102 (define-public r-lazyeval
1108 (uri (cran-uri "lazyeval" version))
1111 "1jwdz40nznlc44hpjli7h98gnpa4d98ifggmj7z88h84n9aqywqk"))))
1112 (build-system r-build-system)
1113 (home-page "https://github.com/hadley/lazyeval")
1114 (synopsis "Lazy (non-standard) evaluation in R")
1116 "This package provides the tools necessary to do non-standard
1117 evaluation (NSE) in R.")
1118 (license license:gpl3+)))
1120 (define-public r-dbi
1126 (uri (cran-uri "DBI" version))
1129 "04fyrxdpqcygg5wviy637y6lgk64xqjjq31lvv4hwqj5kbaxamr5"))))
1130 (build-system r-build-system)
1131 (home-page "https://github.com/rstats-db/DBI")
1132 (synopsis "R database interface")
1134 "The DBI package provides a database interface (DBI) definition for
1135 communication between R and relational database management systems. All
1136 classes in this package are virtual and need to be extended by the various
1137 R/DBMS implementations.")
1138 (license license:lgpl2.0+)))
1143 (version "1.62.0-1")
1146 (uri (cran-uri "BH" version))
1149 "01vfdpfznd4ynqql33z238xr262mvy3i80lyi8l3a3p3hi0a262p"))))
1150 (build-system r-build-system)
1151 (home-page "https://github.com/eddelbuettel/bh")
1152 (synopsis "R package providing subset of Boost headers")
1154 "This package aims to provide the most useful subset of Boost libraries
1155 for template use among CRAN packages.")
1156 (license license:boost1.0)))
1158 (define-public r-evaluate
1164 (uri (cran-uri "evaluate" version))
1167 "070vvmnbdlp7sz2zhza7fhd2a6mlwiln8fn4hyzhsiizbn4n79y9"))))
1168 (build-system r-build-system)
1170 `(("r-stringr" ,r-stringr)))
1171 (home-page "https://github.com/hadley/evaluate")
1172 (synopsis "Parsing and evaluation tools for R")
1174 "This package provides tools that allow you to recreate the parsing,
1175 evaluation and display of R code, with enough information that you can
1176 accurately recreate what happens at the command line. The tools can easily be
1177 adapted for other output formats, such as HTML or LaTeX.")
1178 (license license:gpl3+)))
1180 (define-public r-formatr
1186 (uri (cran-uri "formatR" version))
1189 "19sd23vgs4ac0fwlw40j3676k6mramb0ajlq8hdw23kjwdx1jk47"))))
1190 (build-system r-build-system)
1191 (home-page "http://yihui.name/formatR")
1192 (synopsis "Format R code automatically")
1194 "This package provides a function to format R source code. Spaces and
1195 indent will be added to the code automatically, and comments will be preserved
1196 under certain conditions, so that R code will be more human-readable and tidy.
1197 There is also a Shiny app as a user interface in this package.")
1198 (license license:gpl3+)))
1200 (define-public r-highr
1206 (uri (cran-uri "highr" version))
1209 "0n9v44dxdy5fhkdmpbpa2p78whyd9z3rhhy42ipdz5m5vsr55qa3"))))
1210 (build-system r-build-system)
1211 (home-page "https://github.com/yihui/highr")
1212 (synopsis "Syntax highlighting for R source code")
1214 "This package provides syntax highlighting for R source code. Currently
1215 it supports LaTeX and HTML output. Source code of other languages is
1216 supported via Andre Simon's highlight package.")
1217 (license license:gpl3+)))
1219 (define-public r-mime
1225 (uri (cran-uri "mime" version))
1228 "0i91m3ivaja1k33jwcvz16pfjypkci27awm8glil7sxhmwaj3izw"))))
1229 (build-system r-build-system)
1230 (home-page "https://github.com/yihui/mime")
1231 (synopsis "R package to map filenames to MIME types")
1233 "This package guesses the MIME type from a filename extension using the
1234 data derived from /etc/mime.types in UNIX-type systems.")
1235 (license license:gpl2)))
1237 (define-public r-markdown
1243 (uri (cran-uri "markdown" version))
1246 "1vcgsh2m2f5kfgappgg71nbf04ff0j1sbk668krjs3r2n89dk3sk"))))
1247 (build-system r-build-system)
1248 ;; Skip check phase because the tests require the r-knitr package to be
1249 ;; installed. This prevents installation failures. Knitr normally
1250 ;; shouldn't be available since r-markdown is a dependency of the r-knitr
1252 (arguments `(#:tests? #f))
1254 `(("r-mime" ,r-mime)))
1255 (home-page "https://github.com/rstudio/markdown")
1256 (synopsis "Markdown rendering for R")
1258 "This package provides R bindings to the Sundown Markdown rendering
1259 library (https://github.com/vmg/sundown). Markdown is a plain-text formatting
1260 syntax that can be converted to XHTML or other formats.")
1261 (license license:gpl2)))
1263 (define-public r-yaml
1269 (uri (cran-uri "yaml" version))
1272 "0x88xicrf7vwp77xgan27mnpdljhpkn0pz5kphnwqi3ddy25k9a1"))))
1273 (build-system r-build-system)
1274 (home-page "https://cran.r-project.org/web/packages/yaml/")
1275 (synopsis "Methods to convert R data to YAML and back")
1277 "This package implements the libyaml YAML 1.1 parser and
1278 emitter (http://pyyaml.org/wiki/LibYAML) for R.")
1279 (license license:bsd-3)))
1281 (define-public r-knitr
1287 (uri (cran-uri "knitr" version))
1290 "02balmhvc955rkqv4v0wkxbw4vjphydajgcpy4ml0s3b4sziyj0h"))))
1291 (build-system r-build-system)
1293 `(("r-evaluate" ,r-evaluate)
1294 ("r-digest" ,r-digest)
1295 ("r-highr" ,r-highr)
1296 ("r-markdown" ,r-markdown)
1297 ("r-stringr" ,r-stringr)
1298 ("r-yaml" ,r-yaml)))
1299 (home-page "http://yihui.name/knitr/")
1300 (synopsis "General-purpose package for dynamic report generation in R")
1302 "This package provides a general-purpose tool for dynamic report
1303 generation in R using Literate Programming techniques.")
1304 ;; The code is released under any version of the GPL. As it is used by
1305 ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
1307 (license license:gpl2+)))
1309 (define-public r-knitrbootstrap
1311 (name "r-knitrbootstrap")
1316 (uri (cran-uri "knitrBootstrap" version))
1319 "089147g7nqp99rwdxxsfmklsrwc8aia09sr8ndmrc335r33v6r6p"))))
1320 (properties `((upstream-name . "knitrBootstrap")))
1321 (build-system r-build-system)
1323 `(("r-knitr" ,r-knitr)
1324 ("r-rmarkdown" ,r-rmarkdown)))
1325 (home-page "https://github.com/jimhester/knitrBootstrap")
1326 (synopsis "Knitr bootstrap framework")
1328 "This package provides a framework to create Bootstrap 3 HTML reports
1329 from knitr Rmarkdown.")
1330 (license license:expat)))
1332 (define-public r-microbenchmark
1334 (name "r-microbenchmark")
1338 (uri (cran-uri "microbenchmark" version))
1341 "0qn5r1a6qidghcisc2hpbdmj62pnixc3zz6p4ipk8mvakf0hdsvg"))))
1342 (build-system r-build-system)
1344 `(("r-ggplot2" ,r-ggplot2)))
1345 (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
1346 (synopsis "Accurate timing functions for R")
1348 "This package provides infrastructure to accurately measure and compare
1349 the execution time of R expressions.")
1350 (license license:bsd-2)))
1352 (define-public r-pryr
1358 (uri (cran-uri "pryr" version))
1361 "1in350a8hxwf580afavasvn3jc7x2p1b7nlwmj1scakfz74vghk5"))))
1362 (build-system r-build-system)
1364 `(("r-stringr" ,r-stringr)
1365 ("r-codetools" ,r-codetools)))
1367 `(("r-rcpp" ,r-rcpp)))
1368 (home-page "https://github.com/hadley/pryr")
1369 (synopsis "Tools for computing on the R language")
1371 "This package provides useful tools to pry back the covers of R and
1372 understand the language at a deeper level.")
1373 (license license:gpl2)))
1375 (define-public r-memoise
1381 (uri (cran-uri "memoise" version))
1384 "034qfc2xlh30x1q2vya239w34a3ir3y2fwnx2agbgbi6592zjxmj"))))
1385 (build-system r-build-system)
1387 `(("r-digest" ,r-digest)))
1388 (home-page "https://github.com/hadley/memoise")
1389 (synopsis "Memoise functions for R")
1391 "This R package allows to cache the results of a function so that when
1392 you call it again with the same arguments it returns the pre-computed value.")
1393 (license license:expat)))
1395 (define-public r-crayon
1401 (uri (cran-uri "crayon" version))
1404 "0s2yam18slph7xsw4pyc9f92gdyf609r5w92yax69zh57kb7asws"))))
1405 (build-system r-build-system)
1407 `(("r-memoise" ,r-memoise)))
1408 (home-page "https://github.com/gaborcsardi/crayon")
1409 (synopsis "Colored terminal output for R")
1411 "Colored terminal output on terminals that support ANSI color and
1412 highlight codes. It also works in Emacs ESS. ANSI color support is
1413 automatically detected. Colors and highlighting can be combined and nested.
1414 New styles can also be created easily. This package was inspired by the
1415 \"chalk\" JavaScript project.")
1416 (license license:expat)))
1418 (define-public r-praise
1425 (uri (cran-uri "praise" version))
1428 "1gfyypnvmih97p2r0php9qa39grzqpsdbq5g0fdsbpq5zms5w0sw"))))
1429 (build-system r-build-system)
1430 (home-page "https://github.com/gaborcsardi/praise")
1431 (synopsis "Functions to praise users")
1433 "This package provides template functions to assist in building friendly
1434 R packages that praise their users.")
1435 (license license:expat)))
1437 (define-public r-testthat
1443 (uri (cran-uri "testthat" version))
1446 "0pj1r01x4ny4capr83dfa19hi5i2sjjxky99schzip8zrq5dzxqf"))))
1447 (build-system r-build-system)
1449 `(("r-digest" ,r-digest)
1450 ("r-crayon" ,r-crayon)
1451 ("r-magrittr" ,r-magrittr)
1452 ("r-praise" ,r-praise)
1454 (home-page "https://github.com/hadley/testthat")
1455 (synopsis "Unit testing for R")
1457 "This package provides a unit testing system for R designed to be fun,
1458 flexible and easy to set up.")
1459 (license license:expat)))
1467 (uri (cran-uri "R6" version))
1470 "13xfdr19ca7ymisidsanm6w7hsk3qmy5l8c0mlz3nk48f7s5cxq8"))))
1471 (build-system r-build-system)
1472 (home-page "https://github.com/wch/R6/")
1473 (synopsis "Classes with reference semantics in R")
1475 "The R6 package allows the creation of classes with reference semantics,
1476 similar to R's built-in reference classes. Compared to reference classes, R6
1477 classes are simpler and lighter-weight, and they are not built on S4 classes
1478 so they do not require the methods package. These classes allow public and
1479 private members, and they support inheritance, even when the classes are
1480 defined in different packages.")
1481 (license license:expat)))
1483 (define-public r-rlang
1489 (uri (cran-uri "rlang" version))
1492 "0grwqy3zkvz96mvpwfbfyqid4jkfrqh3ldy2n6dpv2kjd1fzj0ar"))))
1493 (build-system r-build-system)
1494 (home-page "http://rlang.tidyverse.org")
1495 (synopsis "Functions for base types, core R and Tidyverse features")
1496 (description "This package provides a toolbox for working with base types,
1497 core R features like the condition system, and core @code{Tidyverse} features
1498 like tidy evaluation.")
1499 (license license:gpl3)))
1501 (define-public r-tibble
1508 (uri (cran-uri "tibble" version))
1511 "1bhq4pm56l7l6s1k44ajrcr7hz56h37m9ck4zji9f8xfdqschbl0"))))
1512 (build-system r-build-system)
1514 `(("r-rlang" ,r-rlang)
1515 ("r-rcpp" ,r-rcpp)))
1516 (home-page "https://github.com/hadley/tibble")
1517 (synopsis "Simple data frames")
1519 "This package provides a @code{tbl_df} class that offers better checking
1520 and printing capabilities than traditional data frames.")
1521 (license license:expat)))
1523 (define-public r-dplyr
1529 (uri (cran-uri "dplyr" version))
1532 "0jpb32ca1c0mr660igna4yw4fmzydzfhxshd0g8wgmggkynx2qi2"))))
1533 (build-system r-build-system)
1535 `(("r-assertthat" ,r-assertthat)
1537 ("r-magrittr" ,r-magrittr)
1538 ("r-rlang" ,r-rlang)
1539 ("r-plogr" ,r-plogr)
1541 ("r-pkgconfig" ,r-pkgconfig)
1542 ("r-bindrcpp" ,r-bindrcpp)
1543 ("r-tibble" ,r-tibble)))
1545 `(("r-rcpp" ,r-rcpp)
1547 (home-page "https://github.com/hadley/dplyr")
1548 (synopsis "Tools for working with data frames in R")
1550 "dplyr is the next iteration of plyr. It is focussed on tools for
1551 working with data frames. It has three main goals: 1) identify the most
1552 important data manipulation tools needed for data analysis and make them easy
1553 to use in R; 2) provide fast performance for in-memory data by writing key
1554 pieces of code in C++; 3) use the same code interface to work with data no
1555 matter where it is stored, whether in a data frame, a data table or
1557 (license license:expat)))
1559 (define-public r-acepack
1566 (uri (cran-uri "acepack" version))
1569 "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
1570 (build-system r-build-system)
1572 `(("gfortran" ,gfortran)))
1573 (home-page "http://cran.r-project.org/web/packages/acepack")
1574 (synopsis "Functions for regression transformations")
1576 "This package provides ACE and AVAS methods for choosing regression
1578 (license license:expat)))
1580 (define-public r-cluster
1587 (uri (cran-uri "cluster" version))
1590 "1z4gbz7chxxi4ly6c0yjlikwgf8aa8dlg05cn5cd6pjr21zvh97l"))))
1591 (build-system r-build-system)
1593 `(("gfortran" ,gfortran)))
1594 (home-page "http://cran.r-project.org/web/packages/cluster")
1595 (synopsis "Methods for data cluster analysis")
1597 "This package provides tools that are useful in finding groups in data.
1598 It is based on the methods described in Kaufman and Rousseeuw (1990) \"Finding
1600 (license license:gpl2+)))
1602 (define-public r-formula
1609 (uri (cran-uri "Formula" version))
1612 "0ad49bzip1zqmpj1d8jajwl4bd81fm3k6dq8p26x6mvlzc04dvwd"))))
1613 (properties `((upstream-name . "Formula")))
1614 (build-system r-build-system)
1615 (home-page "http://cran.r-project.org/web/packages/Formula")
1616 (synopsis "Extended model formulas")
1618 "This package provides a new class @code{Formula}, which extends the base
1619 class @code{formula}. It supports extended formulas with multiple parts of
1620 regressors on the right-hand side and/or multiple responses on the left-hand
1622 (license (list license:gpl2+ license:gpl3+))))
1624 (define-public r-locfit
1631 (uri (cran-uri "locfit" version))
1634 "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
1635 (build-system r-build-system)
1637 `(("r-lattice" ,r-lattice)))
1638 (home-page "http://cran.r-project.org/web/packages/locfit")
1639 (synopsis "Local regression, likelihood and density estimation")
1641 "This package provides functions used for local regression, likelihood
1642 and density estimation.")
1643 (license (list license:gpl2+ license:gpl3+))))
1645 (define-public r-chron
1651 (uri (cran-uri "chron" version))
1654 "1w3sl60gsirniqslb3pa75caiqbzbvc44phpd4czvwkb62xx1vx9"))))
1655 (build-system r-build-system)
1656 (home-page "http://cran.r-project.org/web/packages/chron")
1657 (synopsis "Chronological R objects which can handle dates and times")
1659 "This package provides chronological R objects which can handle dates and
1661 (license license:gpl2)))
1663 (define-public r-data-table
1665 (name "r-data-table")
1669 (uri (cran-uri "data.table" version))
1672 "0ykbjr1x50ajxbri385vi3mnxj7zg1dcgh9y0snp341qmmmdypw6"))))
1673 (build-system r-build-system)
1674 (home-page "https://github.com/Rdatatable/data.table/wiki")
1675 (synopsis "Enhanced version of data.frame R object")
1677 "The R package @code{data.table} is an extension of @code{data.frame}
1678 providing functions for fast aggregation of large data (e.g. 100GB in RAM),
1679 fast ordered joins, fast add/modify/delete of columns by group, column listing
1680 and fast file reading.")
1681 (license license:gpl3+)))
1683 (define-public r-xtable
1690 (uri (cran-uri "xtable" version))
1693 "0398qkpvlw3dv0myz4mjcyqwpwc2m31l127r8vdzwc71wb6s28qn"))))
1694 (build-system r-build-system)
1696 `(("r-knitr" ,r-knitr)))
1697 (home-page "http://xtable.r-forge.r-project.org/")
1698 (synopsis "Export R tables to LaTeX or HTML")
1700 "This package provides tools to export R data as LaTeX and HTML tables.")
1701 (license license:gpl2+)))
1703 (define-public python-patsy
1705 (name "python-patsy")
1709 (uri (pypi-uri "patsy" version ".zip"))
1712 "1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w"))))
1713 (build-system python-build-system)
1716 (modify-phases %standard-phases
1717 (replace 'check (lambda _ (zero? (system* "nosetests" "-v")))))))
1719 `(("python-numpy" ,python-numpy)
1720 ("python-scipy" ,python-scipy)
1721 ("python-six" ,python-six)))
1723 `(("python-nose" ,python-nose)
1725 (home-page "https://github.com/pydata/patsy")
1726 (synopsis "Describe statistical models and build design matrices")
1728 "Patsy is a Python package for describing statistical models and for
1729 building design matrices.")
1730 ;; The majority of the code is distributed under BSD-2. The module
1731 ;; patsy.compat contains code derived from the Python standard library,
1732 ;; and is covered by the PSFL.
1733 (license (list license:bsd-2 license:psfl))))
1735 (define-public python2-patsy
1736 (package-with-python2 python-patsy))
1738 (define-public python-statsmodels
1740 (name "python-statsmodels")
1745 (uri (pypi-uri "statsmodels" version))
1748 "0j30v3932shnj9368c9jr3svkyrvfj90h2l7nxnqkbpv0svilhr6"))
1749 (patches (search-patches "python-statsmodels-fix-tests.patch"))))
1750 (build-system python-build-system)
1753 (modify-phases %standard-phases
1754 ;; tests must be run after installation
1756 (add-after 'unpack 'set-matplotlib-backend-to-agg
1758 ;; Set the matplotlib backend to Agg to avoid problems using the
1759 ;; GTK backend without a display.
1760 (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py")
1761 '("statsmodels/tsa/vector_ar/tests/test_var.py"
1762 "statsmodels/duration/tests/test_survfunc.py"))
1763 (("import matplotlib\\.pyplot as plt" line)
1764 (string-append "import matplotlib;matplotlib.use('Agg');"
1767 (add-after 'install 'check
1768 (lambda* (#:key inputs outputs #:allow-other-keys)
1769 ;; Make installed package available for running the tests
1770 (add-installed-pythonpath inputs outputs)
1771 (with-directory-excursion "/tmp"
1772 (zero? (system* "nosetests"
1774 "-v" "statsmodels"))))))))
1776 `(("python-numpy" ,python-numpy)
1777 ("python-scipy" ,python-scipy)
1778 ("python-pandas" ,python-pandas)
1779 ("python-patsy" ,python-patsy)
1780 ("python-matplotlib" ,python-matplotlib)))
1782 `(("python-cython" ,python-cython)
1783 ("python-nose" ,python-nose)
1784 ("python-sphinx" ,python-sphinx)))
1785 (home-page "http://statsmodels.sourceforge.net/")
1786 (synopsis "Statistical modeling and econometrics in Python")
1788 "Statsmodels is a Python package that provides a complement to scipy for
1789 statistical computations including descriptive statistics and estimation and
1790 inference for statistical models.")
1791 (license license:bsd-3)))
1793 (define-public python2-statsmodels
1794 (let ((stats (package-with-python2 python-statsmodels)))
1795 (package (inherit stats)
1797 `(("python2-pytz" ,python2-pytz)
1798 ("python2-numpy" ,python2-numpy)
1799 ("python2-scipy" ,python2-scipy)
1800 ("python2-pandas" ,python2-pandas)
1801 ("python2-patsy" ,python2-patsy)
1802 ("python2-matplotlib" ,python2-matplotlib))))))
1804 (define-public r-coda
1810 (uri (cran-uri "coda" version))
1813 "14a4a8df4ygj05h37chmdn8kzcqs07fpbflxfrq530563mrza7yl"))))
1814 (build-system r-build-system)
1816 `(("r-lattice" ,r-lattice)))
1817 (home-page "http://cran.r-project.org/web/packages/coda")
1818 (synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
1819 (description "This package provides functions for summarizing and plotting
1820 the output from Markov Chain Monte Carlo (MCMC) simulations, as well as
1821 diagnostic tests of convergence to the equilibrium distribution of the Markov
1823 (license license:gpl2+)))
1825 (define-public r-ade4
1832 (uri (cran-uri "ade4" version))
1835 "0lnc37d6waajmagy8qvw206pyc4vgrpzl3hk3j9frh6wa0b8x140"))))
1836 (build-system r-build-system)
1837 (home-page "http://pbil.univ-lyon1.fr/ADE-4")
1838 (synopsis "Multivariate data analysis and graphical display")
1840 "The ade4 package contains data analysis functions to analyze ecological
1841 and environmental data in the framework of Euclidean exploratory methods.")
1842 (license license:gpl2+)))
1844 (define-public r-xml2
1851 (uri (cran-uri "xml2" version))
1854 "05iifrcgzx53w5ciw8bbm4vdwc3giv4xsvazv8chqxkndfvf7wq0"))))
1855 (build-system r-build-system)
1857 `(("libxml2" ,libxml2)))
1859 `(("r-rcpp" ,r-rcpp)
1861 (home-page "https://github.com/hadley/xml2")
1862 (synopsis "Parse XML with R")
1864 "This package provides a simple, consistent interface to working with XML
1865 files in R. It is built on top of the libxml2 C library.")
1866 (license license:gpl2+)))
1868 (define-public r-multitaper
1870 (name "r-multitaper")
1875 (uri (cran-uri "multitaper" version))
1878 "1ckf9bhvd5k7ypaw2viqh3cyj9jij0ygcp4q9pxwqs508s6yx3a5"))))
1879 (build-system r-build-system)
1881 `(("gfortran" ,gfortran)))
1882 (home-page "https://github.com/wesleyburr/multitaper/")
1883 (synopsis "Multitaper spectral analysis tools")
1885 "This package implements multitaper spectral estimation
1886 techniques using prolate spheroidal sequences (Slepians) and sine
1887 tapers for time series analysis. It includes an adaptive weighted
1888 multitaper spectral estimate, a coherence estimate, Thomson's Harmonic
1889 F-test, and complex demodulation. The Slepians sequences are
1890 generated efficiently using a tridiagonal matrix solution, and
1891 jackknifed confidence intervals are available for most estimates.")
1892 (license license:gpl2+)))
1894 (define-public r-rversions
1896 (name "r-rversions")
1900 (uri (cran-uri "rversions" version))
1903 "0i2gi05nrvknr7g89rbppkswyfcwwd4r9gp75fdfhpah8sgq1l11"))))
1904 (build-system r-build-system)
1906 `(("r-curl" ,r-curl)
1907 ("r-xml2" ,r-xml2)))
1908 (home-page "https://github.com/metacran/rversions")
1909 (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
1911 "This package provides functions to query the main R repository to find
1912 the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
1913 previous R versions and their release dates.")
1914 (license license:expat)))
1916 (define-public r-whisker
1922 (uri (cran-uri "whisker" version))
1925 "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28"))))
1926 (build-system r-build-system)
1927 (home-page "https://github.com/edwindj/whisker")
1928 (synopsis "Logicless mustache templating for R")
1930 "This package provides logicless templating, with a syntax that is not
1932 (license license:gpl3+)))
1934 (define-public r-backports
1936 (name "r-backports")
1941 (uri (cran-uri "backports" version))
1944 "1kcz6j82by28cjk5wi2j6dfqdin1kib4y7d2r4h3zabcxmk6jly5"))))
1945 (build-system r-build-system)
1946 (home-page "http://cran.r-project.org/web/packages/backports")
1947 (synopsis "Reimplementations of functions introduced since R 3.0.0")
1949 "Provides implementations of functions which have been introduced in R
1950 since version 3.0.0. The backports are conditionally exported which results
1951 in R resolving the function names to the version shipped with R (if available)
1952 and uses the implemented backports as fallback. This way package developers
1953 can make use of the new functions without worrying about the minimum required
1955 (license license:gpl2+)))
1957 (define-public r-checkmate
1959 (name "r-checkmate")
1964 (uri (cran-uri "checkmate" version))
1967 "04rxabzamhv6ybynx627sxk02qvq8znkv0y10vmq67xx6pxhqvla"))))
1968 (build-system r-build-system)
1970 `(("r-backports" ,r-backports)))
1971 (home-page "https://github.com/mllg/checkmate")
1972 (synopsis "Fast and versatile argument checks")
1974 "This package provides tests and assertions to perform frequent argument
1975 checks. A substantial part of the package was written in C to minimize any
1976 worries about execution time overhead.")
1977 (license license:bsd-3)))
1979 (define-public r-bbmisc
1986 (uri (cran-uri "BBmisc" version))
1989 "1lh1n4bvxzivb5rbz69mvd8xdgr3gr2bnqd68a39sd1530l8r90y"))))
1990 (properties `((upstream-name . "BBmisc")))
1991 (build-system r-build-system)
1993 `(("r-checkmate" ,r-checkmate)))
1994 (home-page "https://github.com/berndbischl/BBmisc")
1995 (synopsis "Miscellaneous functions for R package development")
1997 "This package provides miscellaneous helper functions for the development
1999 (license license:bsd-3)))
2001 (define-public r-fail
2008 (uri (cran-uri "fail" version))
2011 "0vfm6kmpmgsamda5p0sl771kbnsscan31l2chzssyw93kwmams7d"))))
2012 (build-system r-build-system)
2014 `(("r-bbmisc" ,r-bbmisc)
2015 ("r-checkmate" ,r-checkmate)))
2016 (home-page "https://github.com/mllg/fail")
2017 (synopsis "File abstraction interface layer (FAIL)")
2019 "This package provides a more comfortable interface to work with R data
2020 or source files in a key-value fashion.")
2021 (license license:bsd-3)))
2023 (define-public r-batchjobs
2025 (name "r-batchjobs")
2030 (uri (cran-uri "BatchJobs" version))
2033 "1kb99024jih5bycc226bl4jyvbbl1sg72q3m2wnlshl7s8p6vva0"))))
2034 (properties `((upstream-name . "BatchJobs")))
2035 (build-system r-build-system)
2037 `(("r-bbmisc" ,r-bbmisc)
2039 ("r-checkmate" ,r-checkmate)
2041 ("r-digest" ,r-digest)
2043 ("r-rsqlite" ,r-rsqlite)
2044 ("r-sendmailr" ,r-sendmailr)
2045 ("r-stringr" ,r-stringr)))
2046 (home-page "https://github.com/tudo-r/BatchJobs")
2047 (synopsis "Batch computing with R")
2049 "This package provides @code{Map}, @code{Reduce} and @code{Filter}
2050 variants to generate jobs on batch computing systems like PBS/Torque, LSF,
2051 SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.")
2052 (license license:bsd-2)))
2054 (define-public r-brew
2060 (uri (cran-uri "brew" version))
2063 "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
2064 (build-system r-build-system)
2065 (home-page "http://cran.r-project.org/web/packages/brew")
2066 (synopsis "Templating framework for report generation")
2068 "The brew package implements a templating framework for mixing text and R
2069 code for report generation. The template syntax is similar to PHP, Ruby's erb
2070 module, Java Server Pages, and Python's psp module.")
2071 (license license:gpl2+)))
2073 (define-public r-desc
2080 (uri (cran-uri "desc" version))
2083 "0k07qighac1xzmm8k988zi7i88a0yfvia3gk5hbz0fyvb2v9kzrj"))))
2084 (build-system r-build-system)
2086 `(("r-assertthat" ,r-assertthat)
2087 ("r-crayon" ,r-crayon)
2089 ("r-rprojroot" ,r-rprojroot)))
2090 (home-page "https://github.com/r-pkgs/desc")
2091 (synopsis "Manipulate DESCRIPTION Files")
2093 "This package provides tools to read, write, create, and manipulate
2094 DESCRIPTION files. It is intended for packages that create or manipulate
2096 (license license:expat)))
2098 (define-public r-commonmark
2100 (name "r-commonmark")
2105 (uri (cran-uri "commonmark" version))
2108 "12q5mncxvkwdxc35is6y5idx8a1h99hyz5x6ri0arni6k25krchk"))))
2109 (build-system r-build-system)
2110 ;;(inputs `(("zlib" ,zlib)))
2111 (home-page "http://cran.r-project.org/web/packages/commonmark")
2112 (synopsis "CommonMark and Github Markdown Rendering in R")
2114 "The CommonMark specification defines a rationalized version of markdown
2115 syntax. This package uses the 'cmark' reference implementation for converting
2116 markdown text into various formats including HTML, LaTeX and groff man. In
2117 addition, it exposes the markdown parse tree in XML format. The latest
2118 version of this package also adds support for Github extensions including
2119 tables, autolinks and strikethrough text.")
2120 (license license:bsd-2)))
2122 (define-public r-roxygen2
2128 (uri (cran-uri "roxygen2" version))
2131 "0xpzziminf225kjwhyl51kgkzhplyzhk5farhf5s822krl2xqbfj"))))
2132 (build-system r-build-system)
2134 `(("r-brew" ,r-brew)
2135 ("r-commonmark" ,r-commonmark)
2137 ("r-digest" ,r-digest)
2140 ("r-stringi" ,r-stringi)
2141 ("r-stringr" ,r-stringr)
2142 ("r-xml2" ,r-xml2)))
2143 (home-page "https://github.com/klutometis/roxygen")
2144 (synopsis "In-source documentation system for R")
2146 "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
2147 collation, and NAMESPACE files.")
2148 (license license:gpl2+)))
2150 (define-public r-openssl
2157 (uri (cran-uri "openssl" version))
2160 "0ffwllii8xl6sa2v66134g0fwaw1y3zn3mvaa4nrc120vv5d3mkd"))))
2161 (build-system r-build-system)
2163 `(("openssl" ,openssl)))
2164 (home-page "https://github.com/jeroenooms/openssl")
2165 (synopsis "Toolkit for encryption, signatures and certificates")
2167 "This package provides R bindings to OpenSSL libssl and libcrypto, plus
2168 custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384
2169 and P-521. Cryptographic signatures can either be created and verified
2170 manually or via x509 certificates. AES block cipher is used in CBC mode for
2171 symmetric encryption; RSA for asymmetric (public key) encryption. High-level
2172 envelope functions combine RSA and AES for encrypting arbitrary sized data.
2173 Other utilities include key generators, hash functions (md5, sha1, sha256,
2174 etc), base64 encoder, a secure random number generator, and @code{bignum} math
2175 methods for manually performing crypto calculations on large multibyte
2177 (license license:expat)))
2179 (define-public r-httr
2185 (uri (cran-uri "httr" version))
2188 "03kkjlhyvvi5znwaxfm6cmdsg3q7ivwsvkzgabhjdj2jxs80pfg7"))))
2189 (build-system r-build-system)
2191 `(("r-curl" ,r-curl)
2192 ("r-digest" ,r-digest)
2193 ("r-jsonlite" ,r-jsonlite)
2194 ("r-openssl" ,r-openssl)
2197 ("r-stringr" ,r-stringr)))
2198 (home-page "https://github.com/hadley/httr")
2199 (synopsis "Tools for working with URLs and HTTP")
2201 "The aim of httr is to provide a wrapper for RCurl customised to the
2202 demands of modern web APIs. It provides useful tools for working with HTTP
2203 organised by HTTP verbs (@code{GET()}, @code{POST()}, etc). Configuration
2204 functions make it easy to control additional request components.")
2205 (license license:expat)))
2207 (define-public r-git2r
2213 (uri (cran-uri "git2r" version))
2216 "0ws6fbndmaafk2am4dwnz24qizxhld0yh54hgx0z6lzv3p1j209q"))))
2217 (build-system r-build-system)
2218 ;; This R package contains modified sources of libgit2. This modified
2219 ;; version of libgit2 is built as the package is built. Hence libgit2 is
2220 ;; not among the inputs of this package.
2222 `(("libssh2" ,libssh2)
2223 ("openssl" ,openssl)
2225 (home-page "https://github.com/ropensci/git2r")
2226 (synopsis "Access Git repositories with R")
2228 "This package provides an R interface to the libgit2 library, which is a
2229 pure C implementation of the Git core methods.")
2230 ;; GPLv2 only with linking exception.
2231 (license license:gpl2)))
2233 (define-public r-rstudioapi
2235 (name "r-rstudioapi")
2239 (uri (cran-uri "rstudioapi" version))
2242 "1zkvz72z6nw0xc8bhb21y5x1nk6avijs0w8n4vsbvw9sn76wc96s"))))
2243 (build-system r-build-system)
2244 (home-page "http://cran.r-project.org/web/packages/rstudioapi")
2245 (synopsis "Safely access the RStudio API")
2247 "This package provides functions to access the RStudio API and provide
2248 informative error messages when it's not available.")
2249 (license license:expat)))
2251 (define-public r-devtools
2257 (uri (cran-uri "devtools" version))
2260 "146wb09cmfh10vhn1ps2nmzx104zldb3nj9qv2ic0gbcikbbryp6"))))
2261 (build-system r-build-system)
2263 `(("r-digest" ,r-digest)
2264 ("r-git2r" ,r-git2r)
2266 ("r-jsonlite" ,r-jsonlite)
2267 ("r-memoise" ,r-memoise)
2268 ("r-rstudioapi" ,r-rstudioapi)
2269 ("r-whisker" ,r-whisker)
2270 ("r-withr" ,r-withr)))
2271 (home-page "https://github.com/hadley/devtools")
2272 (synopsis "Tools to make developing R packages easier")
2273 (description "The devtools package is a collection of package development
2274 tools to simplify the devolpment of R packages.")
2275 (license license:gpl2+)))
2277 (define-public r-withr
2283 (uri (cran-uri "withr" version))
2286 "0ncq9ygx33rx7aazn53p0a0vbr5xv0r6wbkzcwbhbwyd8k55bgin"))))
2287 (build-system r-build-system)
2288 (home-page "https://github.com/jimhester/withr")
2289 (synopsis "Run code with temporarily modified global state")
2291 "This package provides a set of functions to run R code in an environment
2292 in which global state has been temporarily modified. Many of these functions
2293 were originally a part of the r-devtools package.")
2294 (license license:gpl2+)))
2296 (define-public r-hms
2303 (uri (cran-uri "hms" version))
2306 "127znf522r5mn3k6frhdd7pqh063bs3l85gn9h7cx50hpjf2as4k"))))
2307 (build-system r-build-system)
2308 (home-page "https://github.com/rstats-db/hms")
2309 (synopsis "Pretty time of day")
2311 "This package implements an S3 class for storing and formatting
2312 time-of-day values, based on the @code{difftime} class.")
2313 (license license:gpl3+)))
2315 (define-public r-readr
2321 (uri (cran-uri "readr" version))
2324 "1cvw5wdcqk88cp5fyv678mnmp66l3whcd2yh33p2qvx0168bja8s"))))
2325 (build-system r-build-system)
2327 `(("r-rcpp" ,r-rcpp)
2329 ("r-tibble" ,r-tibble)
2332 (home-page "https://github.com/hadley/readr")
2333 (synopsis "Read tabular data")
2335 "This package provides functions to read flat or tabular text files from
2336 disk (or a connection).")
2337 (license license:gpl2+)))
2339 (define-public r-plotrix
2345 (uri (cran-uri "plotrix" version))
2348 "01655y3qzy0283ppc85bi0g42g20zrqzcl0qb30cl6rcbflhymlb"))))
2349 (build-system r-build-system)
2350 (home-page "http://cran.r-project.org/web/packages/plotrix")
2351 (synopsis "Various plotting functions")
2353 "This package provides lots of plotting, various labeling, axis and color
2354 scaling functions for R.")
2355 (license license:gpl2+)))
2357 (define-public r-gridbase
2363 (uri (cran-uri "gridBase" version))
2366 "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
2367 (build-system r-build-system)
2368 (home-page "http://cran.r-project.org/web/packages/gridBase")
2369 (synopsis "Integration of base and grid graphics")
2371 "This package provides an integration of base and grid graphics for R.")
2372 (license license:gpl2+)))
2374 (define-public r-latticeextra
2376 (name "r-latticeextra")
2381 (uri (cran-uri "latticeExtra" version))
2384 "1hkyqsa7klk5glj9y1hg3rxr5qilqw8h0017zc4c3nps7lr9a1kq"))))
2385 (properties `((upstream-name . "latticeExtra")))
2386 (build-system r-build-system)
2388 `(("r-lattice" ,r-lattice)
2389 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2390 (home-page "http://latticeextra.r-forge.r-project.org/")
2391 (synopsis "Extra graphical utilities based on lattice")
2393 "Building on the infrastructure provided by the lattice package, this
2394 package provides several new high-level graphics functions and methods, as
2395 well as additional utilities such as panel and axis annotation functions.")
2396 (license license:gpl2+)))
2398 (define-public r-rcpparmadillo
2400 (name "r-rcpparmadillo")
2401 (version "0.7.900.2.0")
2404 (uri (cran-uri "RcppArmadillo" version))
2407 "01qsff2p1fp5i9lq7rsykrskgr6smz24ddspbl5ad9a8rkmczwyv"))))
2408 (properties `((upstream-name . "RcppArmadillo")))
2409 (build-system r-build-system)
2411 `(("r-rcpp" ,r-rcpp)))
2412 (home-page "https://github.com/RcppCore/RcppArmadillo")
2413 (synopsis "Rcpp integration for the Armadillo linear algebra library")
2415 "Armadillo is a templated C++ linear algebra library that aims towards a
2416 good balance between speed and ease of use. Integer, floating point and
2417 complex numbers are supported, as well as a subset of trigonometric and
2418 statistics functions. Various matrix decompositions are provided through
2419 optional integration with LAPACK and ATLAS libraries. This package includes
2420 the header files from the templated Armadillo library.")
2421 ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
2422 ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
2423 ;; later, as is the rest of 'Rcpp'.
2424 (license license:gpl2+)))
2426 (define-public r-bitops
2432 (uri (cran-uri "bitops" version))
2435 "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
2436 (build-system r-build-system)
2437 (home-page "http://cran.r-project.org/web/packages/bitops")
2438 (synopsis "Bitwise operations")
2440 "This package provides functions for bitwise operations on integer
2442 (license license:gpl2+)))
2444 (define-public r-catools
2450 (uri (cran-uri "caTools" version))
2453 "1x4szsn2qmbzpyjfdaiz2q7jwhap2gky9wq0riah74q0pzz76ank"))))
2454 (properties `((upstream-name . "caTools")))
2455 (build-system r-build-system)
2457 `(("r-bitops" ,r-bitops)))
2458 (home-page "http://cran.r-project.org/web/packages/caTools")
2459 (synopsis "Various tools including functions for moving window statistics")
2461 "This package contains several basic utility functions including:
2462 moving (rolling, running) window statistic functions, read/write for GIF and
2463 ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
2464 encoder/decoder, round-off-error-free sum and cumsum, etc.")
2465 (license license:gpl3+)))
2467 (define-public r-rprojroot
2469 (name "r-rprojroot")
2474 (uri (cran-uri "rprojroot" version))
2477 "1fgyxv1zv04sllcclzz089xl6hpdzac7xk61l0l4acb7rqsx5d18"))))
2478 (build-system r-build-system)
2480 `(("r-backports" ,r-backports)))
2481 (home-page "https://github.com/krlmlr/rprojroot")
2482 (synopsis "Finding files in project subdirectories")
2484 "This package helps accessing files relative to a project root. It
2485 provides helpers for robust, reliable and flexible paths to files below a
2486 project root. The root of a project is defined as a directory that matches a
2487 certain criterion, e.g., it contains a certain regular file.")
2488 (license license:gpl3)))
2490 (define-public r-rmarkdown
2492 (name "r-rmarkdown")
2497 (uri (cran-uri "rmarkdown" version))
2500 "0p8ph5z5pifk1nxc1bppkfs1ir5gjc6ap9n64b4255m2fdaqfrc7"))))
2501 (properties `((upstream-name . "rmarkdown")))
2502 (build-system r-build-system)
2504 `(("r-catools" ,r-catools)
2505 ("r-evaluate" ,r-evaluate)
2506 ("r-htmltools" ,r-htmltools)
2507 ("r-jsonlite" ,r-jsonlite)
2508 ("r-base64enc" ,r-base64enc)
2509 ("r-knitr" ,r-knitr)
2510 ("r-rprojroot" ,r-rprojroot)
2512 ("ghc-pandoc" ,ghc-pandoc)))
2513 (home-page "http://rmarkdown.rstudio.com")
2514 (synopsis "Convert R Markdown documents into a variety of formats")
2516 "This package provides tools to convert R Markdown documents into a
2517 variety of formats.")
2518 (license license:gpl3+)))
2520 (define-public r-gtable
2526 (uri (cran-uri "gtable" version))
2529 "0vz7073m0a2q12qzzihrfh5c2kx5jqi5l7z470fxmwqghdllh7l0"))))
2530 (properties `((upstream-name . "gtable")))
2531 (build-system r-build-system)
2532 (home-page "https://cran.r-project.org/web/packages/gtable")
2533 (synopsis "R library to arrange grobs in tables")
2535 "Gtable is a collection of tools to make it easier to work with
2536 \"tables\" of grobs.")
2537 (license license:gpl2+)))
2539 (define-public r-gridextra
2541 (name "r-gridextra")
2545 (uri (cran-uri "gridExtra" version))
2548 "0638ihwl00j76ivaxxhxvi8z573lwy1jym3srr78mx6dbdd4bzj4"))))
2549 (properties `((upstream-name . "gridExtra")))
2550 (build-system r-build-system)
2552 `(("r-gtable" ,r-gtable)))
2554 `(("r-knitr" ,r-knitr))) ;for building vignettes
2555 (home-page "https://github.com/baptiste/gridextra")
2556 (synopsis "Miscellaneous functions for \"Grid\" graphics")
2558 "This package provides a number of user-level functions to work with
2559 @code{grid} graphics, notably to arrange multiple grid-based plots on a page,
2561 (license license:gpl2+)))
2563 (define-public r-pkgconfig
2565 (name "r-pkgconfig")
2569 (uri (cran-uri "pkgconfig" version))
2572 "0h2sp93fqqjbfqgq82a3i94ybnndx6ghaal8pbf99firnsjb40mb"))))
2573 (build-system r-build-system)
2574 (home-page "https://github.com/gaborcsardi/pkgconfig")
2575 (synopsis "Private configuration for R packages")
2576 (description "This package provides the functionality to set configuration
2577 options on a per-package basis. Options set by a given package only apply to
2578 that package, other packages are unaffected.")
2579 (license license:expat)))
2581 (define-public r-blob
2587 (uri (cran-uri "blob" version))
2590 "05pazzcyz3c3vd2l70zq9cf172cgjff4dnf419zigfnxycyn1mhn"))))
2591 (build-system r-build-system)
2593 `(("r-tibble" ,r-tibble)))
2594 (home-page "https://github.com/hadley/blob")
2595 (synopsis "Simple S3 Class for representing vectors of binary data")
2596 (description "Raw vectors in R are useful for storing a single binary
2597 object. What if you want to put a vector of them in a data frame? The blob
2598 package provides the blob object, a list of raw vectors, suitable for use as
2599 a column in data frame.")
2600 (license license:gpl3+)))
2602 (define-public r-rsqlite
2608 (uri (cran-uri "RSQLite" version))
2611 "1xpg1i1jkzkzv44k512k90c2vvl960pl2d4a3spwcha6yclyc3vz"))))
2612 (properties `((upstream-name . "RSQLite")))
2613 (build-system r-build-system)
2617 ("r-memoise" ,r-memoise)
2618 ("r-plogr" ,r-plogr)
2620 ("r-bit64" ,r-bit64)
2622 ("r-pkgconfig" ,r-pkgconfig)))
2623 (home-page "https://github.com/rstats-db/RSQLite")
2624 (synopsis "SQLite interface for R")
2626 "This package embeds the SQLite database engine in R and provides an
2627 interface compliant with the DBI package. The source for the SQLite
2628 engine (version 3.8.8.2) is included.")
2629 (license license:lgpl2.0+)))
2631 (define-public r-rcurl
2634 (version "1.95-0.1.2")
2637 (uri (string-append "http://www.bioconductor.org/packages/"
2638 "release/extra/src/"
2639 "contrib/RCurl_" version ".tar.gz"))
2642 "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
2643 (properties `((upstream-name . "RCurl")))
2644 (build-system r-build-system)
2646 `(("libcurl" ,curl)))
2648 `(("r-bitops" ,r-bitops)))
2649 (home-page "http://www.omegahat.org/RCurl")
2650 (synopsis "General network client interface for R")
2652 "The package allows one to compose general HTTP requests and provides
2653 convenient functions to fetch URIs, GET and POST forms, etc. and process the
2654 results returned by the Web server. This provides a great deal of control
2655 over the HTTP/FTP/... connection and the form of the request while providing a
2656 higher-level interface than is available just using R socket connections.
2657 Additionally, the underlying implementation is robust and extensive,
2658 supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
2659 ldap, and also supports cookies, redirects, authentication, etc.")
2660 (license license:bsd-3)))
2662 (define-public r-xml
2665 (version "3.98-1.9")
2668 (uri (cran-uri "XML" version))
2671 "1hzkdkgs0nzmfg9wm7kyh1j9i0i2g7925whzlihqvg9grdlh3dx3"))))
2673 `((upstream-name . "XML")))
2674 (build-system r-build-system)
2676 `(("libxml2" ,libxml2)))
2677 (home-page "http://www.omegahat.org/RSXML")
2678 (synopsis "Tools for parsing and generating XML within R")
2680 "Many approaches for both reading and creating XML (and HTML)
2681 documents (including DTDs), both local and accessible via HTTP or FTP. Also
2682 offers access to an XPath \"interpreter\".")
2683 (license license:bsd-2)))
2685 (define-public r-xnomial
2690 (origin (method url-fetch)
2691 (uri (cran-uri "XNomial" version))
2694 "1mwx302576rmsjllbq2clfxilm3hkyp5bw0wmwqbn0kgv5wpy8z6"))))
2695 (properties (quasiquote ((upstream-name . "XNomial"))))
2696 (build-system r-build-system)
2697 (home-page "http://cran.r-project.org/web/packages/XNomial")
2698 (synopsis "Goodness-of-Fit test for multinomial data")
2700 "This package provides an exact Goodness-of-Fit test for
2701 multinomial data with fixed probabilities. It can be used to
2702 determine whether a set of counts fits a given expected ratio. To see
2703 whether a set of observed counts fits an expectation, one can examine
2704 all possible outcomes with @code{xmulti()} or a random sample of them
2705 with @code{xmonte()} and find the probability of an observation
2706 deviating from the expectation by at least as much as the observed.
2707 As a measure of deviation from the expected, one can use the
2708 log-likelihood ratio, the multinomial probability, or the classic
2709 chi-square statistic. A histogram of the test statistic can also be
2710 plotted and compared with the asymptotic curve.")
2711 (license (list license:gpl2+ license:gpl3+))))
2713 (define-public r-lambda-r
2719 (uri (cran-uri "lambda.r" version))
2722 "1j6287iqvs3ill6r5g6ksf5809qp0l0nf20ib8266m1r09lc9j14"))))
2723 (properties `((upstream-name . "lambda.r")))
2724 (build-system r-build-system)
2725 (home-page "http://cran.r-project.org/web/packages/lambda.r")
2726 (synopsis "Functional programming extension for R")
2728 "This package provides a language extension to efficiently write
2729 functional programs in R. Syntax extensions include multi-part function
2730 definitions, pattern matching, guard statements, built-in (optional) type
2732 (license license:lgpl3+)))
2734 (define-public r-futile-options
2736 (name "r-futile-options")
2740 (uri (cran-uri "futile.options" version))
2743 "1hp82h6xqq5cck67h7lpf22n3j7mg3v1mla5y5ivnzrrb7iyr17f"))))
2745 `((upstream-name . "futile.options")))
2746 (build-system r-build-system)
2747 (home-page "http://cran.r-project.org/web/packages/futile.options")
2748 (synopsis "Options management framework")
2750 "The futile.options subsystem provides an easy user-defined options
2751 management system that is properly scoped. This means that options created
2752 via @code{futile.options} are fully self-contained and will not collide with
2753 options defined in other packages.")
2754 (license license:lgpl3+)))
2756 (define-public r-futile-logger
2758 (name "r-futile-logger")
2762 (uri (cran-uri "futile.logger" version))
2765 "1r3nayk0z9n1svbf8640vw90dal5q07nkn0gv4bnva3pbzb352sy"))))
2766 (properties `((upstream-name . "futile.logger")))
2767 (build-system r-build-system)
2769 `(("r-futile-options" ,r-futile-options)
2770 ("r-lambda-r" ,r-lambda-r)))
2771 (home-page "http://cran.r-project.org/web/packages/futile.logger")
2772 (synopsis "Logging utility for R")
2774 "This package provides a simple yet powerful logging utility. Based
2775 loosely on log4j, futile.logger takes advantage of R idioms to make logging a
2776 convenient and easy to use replacement for @code{cat} and @code{print}
2778 (license license:lgpl3+)))
2780 (define-public r-segmented
2782 (name "r-segmented")
2787 (uri (cran-uri "segmented" version))
2790 "1i576xksc761nyv2dmq86nwbgqvp0plz6bjcn69nkdwq2wbizmw8"))))
2791 (build-system r-build-system)
2792 (home-page "http://cran.r-project.org/web/packages/segmented")
2793 (synopsis "Regression models with breakpoints estimation")
2795 "Given a regression model, segmented updates the model by adding one or
2796 more segmented (i.e., piecewise-linear) relationships. Several variables with
2797 multiple breakpoints are allowed.")
2798 (license (list license:gpl2+ license:gpl3+))))
2800 (define-public r-snow
2806 (uri (cran-uri "snow" version))
2809 "1mxbrkpnmq32x4wd0194d541661yvfrrjlr3lsf7qq53ms3h21zf"))))
2810 (build-system r-build-system)
2811 (home-page "http://cran.r-project.org/web/packages/snow")
2812 (synopsis "Support for simple parallel computing in R")
2814 "The snow package provides support for simple parallel computing on a
2815 network of workstations using R. A master R process calls @code{makeCluster}
2816 to start a cluster of worker processes; the master process then uses functions
2817 such as @code{clusterCall} and @code{clusterApply} to execute R code on the
2818 worker processes and collect and return the results on the master.")
2819 (license (list license:gpl2+ license:gpl3+))))
2821 (define-public r-sparsem
2827 (uri (cran-uri "SparseM" version))
2830 "0p6ljma2h12cq1xmy0cxb48ih8dhxxbnwkqzvx3cckxf2kprycm9"))))
2832 `((upstream-name . "SparseM")))
2834 `(("gfortran" ,gfortran)))
2835 (build-system r-build-system)
2836 (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
2837 (synopsis "Sparse linear algebra")
2839 "This package provides some basic linear algebra functionality for sparse
2840 matrices. It includes Cholesky decomposition and backsolving as well as
2841 standard R subsetting and Kronecker products.")
2842 (license license:gpl2+)))
2844 (define-public r-iterators
2846 (name "r-iterators")
2851 (uri (cran-uri "iterators" version))
2854 "1f057pabs7ss9h1n244can26qsi5n2k3salrdk0b0vkphlrs4kmf"))))
2855 (build-system r-build-system)
2856 (home-page "http://cran.r-project.org/web/packages/iterators")
2857 (synopsis "Iterator construct for R")
2859 "This package provides support for iterators, which allow a programmer to
2860 traverse through all the elements of a vector, list, or other collection of
2862 (license license:asl2.0)))
2864 (define-public r-codetools
2866 (name "r-codetools")
2871 (uri (cran-uri "codetools" version))
2874 "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf"))))
2875 (build-system r-build-system)
2876 (home-page "https://cran.r-project.org/web/packages/codetools")
2877 (synopsis "Code analysis tools for R")
2878 (description "This package provides code analysis tools for R to check R
2879 code for possible problems.")
2880 (license (list license:gpl2+ license:gpl3+))))
2882 (define-public r-foreach
2889 (uri (cran-uri "foreach" version))
2892 "10aqsd3rxz03s1qdb6gsb1cj89mj4vmh491zfpin4skj1xvkzw0y"))))
2893 (build-system r-build-system)
2895 `(("r-codetools" ,r-codetools)
2896 ("r-iterators" ,r-iterators)))
2897 (home-page "http://cran.r-project.org/web/packages/foreach")
2898 (synopsis "Foreach looping construct for R")
2900 "This package provides support for the @code{foreach} looping construct.
2901 @code{foreach} is an idiom that allows for iterating over elements in a
2902 collection, without the use of an explicit loop counter. This package in
2903 particular is intended to be used for its return value, rather than for its
2904 side effects. In that sense, it is similar to the standard @code{lapply}
2905 function, but doesn't require the evaluation of a function. Using
2906 @code{foreach} without side effects also facilitates executing the loop in
2908 (license license:asl2.0)))
2910 (define-public r-doparallel
2912 (name "r-doparallel")
2917 (uri (cran-uri "doParallel" version))
2920 "1mddx25l25pw9d0csnx2q203dbg5hbrhkr1f08kw0p02a1lln0kh"))))
2921 (properties `((upstream-name . "doParallel")))
2922 (build-system r-build-system)
2924 `(("r-foreach" ,r-foreach)
2925 ("r-iterators" ,r-iterators)))
2926 (home-page "http://cran.r-project.org/web/packages/doParallel")
2927 (synopsis "Foreach parallel adaptor for the 'parallel' package")
2929 "This package provides a parallel backend for the @code{%dopar%} function
2930 using the parallel package.")
2931 (license license:gpl2+)))
2933 (define-public r-domc
2940 (uri (cran-uri "doMC" version))
2943 "0y47jl6g4f83r14pj8bafdzq1phj7bxy5dwyz3k43d2rr8phk8bn"))))
2944 (properties `((upstream-name . "doMC")))
2945 (build-system r-build-system)
2947 `(("r-foreach" ,r-foreach)
2948 ("r-iterators" ,r-iterators)))
2949 (home-page "http://cran.r-project.org/web/packages/doMC")
2950 (synopsis "Foreach parallel adaptor for the 'parallel' package")
2952 "This package provides a parallel backend for the @code{%dopar%} function
2953 using the multicore functionality of the parallel package.")
2954 (license license:gpl2+)))
2962 (uri (cran-uri "DT" version))
2965 "1g86p0jcjqi2ph5rhm45jkzibsa6yfcj8n5cg3giy90sqgjzkdx1"))))
2967 `((upstream-name . "DT")))
2968 (build-system r-build-system)
2970 `(("r-htmltools" ,r-htmltools)
2971 ("r-htmlwidgets" ,r-htmlwidgets)
2972 ("r-magrittr" ,r-magrittr)))
2973 (home-page "http://rstudio.github.io/DT")
2974 (synopsis "R wrapper of the DataTables JavaScript library")
2976 "This package allows for data objects in R to be rendered as HTML tables
2977 using the JavaScript library 'DataTables' (typically via R Markdown or Shiny).
2978 The 'DataTables' library has been included in this R package.")
2979 ;; The DT package as a whole is distributed under GPLv3. The DT package
2980 ;; inludes other software components under different licenses:
2982 ;; * Expat: jQuery, jquery.highlight.js, DataTables
2983 ;; * ASL2.0: selectize.js
2984 ;; * WTFPL: noUiSlider
2985 (license (list license:gpl3
2988 (license:non-copyleft "http://www.wtfpl.net/txt/copying/")))))
2990 (define-public r-base64enc
2992 (name "r-base64enc")
2996 (uri (cran-uri "base64enc" version))
2999 "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
3000 (build-system r-build-system)
3001 (home-page "http://www.rforge.net/base64enc")
3002 (synopsis "Tools for Base64 encoding")
3004 "This package provides tools for handling Base64 encoding. It is more
3005 flexible than the orphaned \"base64\" package.")
3006 (license license:gpl2+)))
3008 (define-public r-irlba
3015 (uri (cran-uri "irlba" version))
3018 "0zfb7x1701n6gask0f8y2yq0vmb82xkxf6limp43ivx551hx600s"))))
3019 (build-system r-build-system)
3021 `(("r-matrix" ,r-matrix)))
3022 (home-page "http://cran.r-project.org/web/packages/irlba")
3023 (synopsis "Methods for eigendecomposition of large matrices")
3025 "This package provides fast and memory efficient methods for truncated
3026 singular and eigenvalue decompositions, as well as for principal component
3027 analysis of large sparse or dense matrices.")
3028 (license (list license:gpl2+ license:gpl3+))))
3030 (define-public r-glmnet
3037 (uri (cran-uri "glmnet" version))
3040 "07n2hz4fvjyv0siai8z8wqwfj8d58i8n1vzf1ckdfzp4kxa3z08d"))))
3041 (build-system r-build-system)
3043 `(("gfortran" ,gfortran)))
3045 `(("r-foreach" ,r-foreach)
3046 ("r-matrix" ,r-matrix)))
3047 (home-page "http://www.jstatsoft.org/v33/i01")
3048 (synopsis "Lasso and elastic-net regularized generalized linear models")
3050 "The glmnet package provides efficient procedures for fitting the entire
3051 lasso or elastic-net regularization path for linear and Poisson regression, as
3052 well as logistic, multinomial, Cox, multiple-response Gaussian and grouped
3053 multinomial models. The algorithm uses cyclical coordinate descent in a
3054 path-wise fashion.")
3055 (license license:gpl2+)))
3057 (define-public r-pkgmaker
3064 (uri (cran-uri "pkgmaker" version))
3067 "0vrqnd3kg6liqvpbd969jjsdx0f0rvmmxgdbwwrp6xfmdg0pib8r"))))
3068 (build-system r-build-system)
3070 `(("r-codetools" ,r-codetools)
3071 ("r-digest" ,r-digest)
3072 ("r-registry" ,r-registry)
3073 ("r-stringr" ,r-stringr)
3074 ("r-xtable" ,r-xtable)))
3075 (home-page "https://renozao.github.io/pkgmaker")
3076 (synopsis "Package development utilities")
3078 "This package provides some low-level utilities to use for R package
3079 development. It currently provides managers for multiple package specific
3080 options and registries, vignette, unit test and bibtex related utilities.")
3081 (license license:gpl2+)))
3083 (define-public r-registry
3090 (uri (cran-uri "registry" version))
3093 "0c7lscfxncwwd8zp46h2xfw9gw14dypqv6m2kx85xjhjh0xw99aq"))))
3094 (build-system r-build-system)
3095 (home-page "http://cran.r-project.org/web/packages/registry")
3096 (synopsis "Infrastructure for R package registries")
3098 "This package provides a generic infrastructure for creating and using R
3099 package registries.")
3100 (license license:gpl2+)))
3102 (define-public r-rngtools
3109 (uri (cran-uri "rngtools" version))
3112 "1fcgfqrrb48z37xgy8sffx91p9irp39yqzxv7nqp1x2hnwsrh097"))))
3113 (build-system r-build-system)
3115 `(("r-digest" ,r-digest)
3116 ("r-pkgmaker" ,r-pkgmaker)
3117 ("r-stringr" ,r-stringr)))
3118 (home-page "https://renozao.github.io/rngtools")
3119 (synopsis "Utility functions for working with random number generators")
3121 "This package contains a set of functions for working with Random Number
3122 Generators (RNGs). In particular, it defines a generic S4 framework for
3123 getting/setting the current RNG, or RNG data that are embedded into objects
3124 for reproducibility. Notably, convenient default methods greatly facilitate
3125 the way current RNG settings can be changed.")
3126 (license license:gpl3+)))
3128 (define-public r-rtsne
3135 (uri (cran-uri "Rtsne" version))
3138 "17crbdi80q4g2pwp9v7j3bdaznk96qlrqx01zvj3wwqippizyfqw"))))
3139 (properties `((upstream-name . "Rtsne")))
3140 (build-system r-build-system)
3142 `(("r-rcpp" ,r-rcpp)))
3143 (home-page "https://github.com/jkrijthe/Rtsne")
3144 (synopsis "T-distributed stochastic neighbor embedding")
3146 "This package provides an R wrapper around the fast T-distributed
3147 Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
3148 ;; The declared license for this package is BSD-3, but it also includes
3149 ;; code licensed under BSD-4.
3150 (license (list license:bsd-3 license:bsd-4))))
3152 (define-public r-e1071
3159 (uri (cran-uri "e1071" version))
3162 "08n6i26nfckjpxjkzi8phhanc3ahsrirkv5rz38y2jcv7ds031pn"))))
3163 (build-system r-build-system)
3165 `(("r-class" ,r-class)))
3166 (home-page "http://cran.r-project.org/web/packages/e1071")
3167 (synopsis "Miscellaneous functions for probability theory")
3169 "This package provides functions for latent class analysis, short time
3170 Fourier transform, fuzzy clustering, support vector machines, shortest path
3171 computation, bagged clustering, naive Bayes classifier, and more.")
3172 (license license:gpl2+)))
3174 (define-public r-bigmemory-sri
3176 (name "r-bigmemory-sri")
3181 (uri (cran-uri "bigmemory.sri" version))
3183 (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
3185 `((upstream-name . "bigmemory.sri")))
3186 (build-system r-build-system)
3187 (home-page "http://cran.r-project.org/web/packages/bigmemory.sri")
3188 (synopsis "Shared resource interface for the bigmemory package")
3189 (description "This package provides a shared resource interface for the
3190 bigmemory and synchronicity packages.")
3191 ;; Users can choose either LGPLv3 or ASL2.0.
3192 (license (list license:lgpl3 license:asl2.0))))
3194 (define-public r-synchronicity
3196 (name "r-synchronicity")
3201 (uri (cran-uri "synchronicity" version))
3204 "0d9skpwmsnkn4xb3f2kgyyv8bhdi0r9p1kj3cvi0s92fjjnpi00c"))))
3205 (build-system r-build-system)
3208 ("r-bigmemory-sri" ,r-bigmemory-sri)
3209 ("r-rcpp" ,r-rcpp)))
3210 (home-page "http://www.bigmemory.org")
3211 (synopsis "Boost mutex functionality in R")
3212 (description "This package provides support for synchronization
3213 via mutexes and may eventually support interprocess communication and
3215 ;; Users can choose either LGPLv3 or ASL2.0.
3216 (license (list license:lgpl3 license:asl2.0))))
3218 (define-public r-bigmemory
3220 (name "r-bigmemory")
3225 (uri (cran-uri "bigmemory" version))
3228 "191gbzca557kpk7mdsg716vfyqpr7j5din6qb8hin4g1nkzzwmg6"))))
3229 (build-system r-build-system)
3233 ("r-bigmemory-sri" ,r-bigmemory-sri)
3234 ("r-r-utils" ,r-r-utils)))
3235 (home-page "http://www.bigmemory.org")
3236 (synopsis "Manage large matrices with shared memory or memory-mapped files")
3237 (description "This package provides methods to create, store, access, and
3238 manipulate large matrices. Matrices are allocated to shared memory and may use
3239 memory-mapped files.")
3240 ;; Users can choose either LGPLv3 or ASL2.0.
3241 (license (list license:lgpl3 license:asl2.0))))
3243 (define-public r-nmf
3250 (uri (cran-uri "NMF" version))
3253 "0mmh9bz0zjwd8h9jplz4rq3g94npaqj8s4px51vcv47csssd9k6z"))))
3254 (properties `((upstream-name . "NMF")))
3255 (build-system r-build-system)
3257 `(("r-cluster" ,r-cluster)
3258 ("r-bigmemory" ,r-bigmemory)
3259 ("r-synchronicity" ,r-synchronicity)
3260 ("r-colorspace" ,r-colorspace)
3261 ("r-digest" ,r-digest)
3262 ("r-doparallel" ,r-doparallel)
3263 ("r-foreach" ,r-foreach)
3264 ("r-ggplot2" ,r-ggplot2)
3265 ("r-gridbase" ,r-gridbase)
3266 ("r-pkgmaker" ,r-pkgmaker)
3267 ("r-rcolorbrewer" ,r-rcolorbrewer)
3268 ("r-registry" ,r-registry)
3269 ("r-reshape2" ,r-reshape2)
3270 ("r-rngtools" ,r-rngtools)
3271 ("r-stringr" ,r-stringr)))
3272 (home-page "http://renozao.github.io/NMF")
3273 (synopsis "Algorithms and framework for nonnegative matrix factorization")
3275 "This package provides a framework to perform Non-negative Matrix
3276 Factorization (NMF). The package implements a set of already published
3277 algorithms and seeding methods, and provides a framework to test, develop and
3278 plug new or custom algorithms. Most of the built-in algorithms have been
3279 optimized in C++, and the main interface function provides an easy way of
3280 performing parallel computations on multicore machines.")
3281 (license license:gpl2+)))
3283 (define-public r-r-methodss3
3285 (name "r-r-methodss3")
3289 (uri (cran-uri "R.methodsS3" version))
3292 "11z6v2i7jl647wxi9p5z66yvfnnqv6s7fxqmz7w2gkb6j8wl1f24"))))
3293 (properties `((upstream-name . "R.methodsS3")))
3294 (build-system r-build-system)
3295 (home-page "http://cran.r-project.org/web/packages/R.methodsS3")
3296 (synopsis "S3 methods simplified")
3298 "This package provides methods that simplify the setup of S3 generic
3299 functions and S3 methods. Major effort has been made in making definition of
3300 methods as simple as possible with a minimum of maintenance for package
3301 developers. For example, generic functions are created automatically, if
3302 missing, and naming conflict are automatically solved, if possible. The
3303 method @code{setMethodS3()} is a good start for those who in the future may
3304 want to migrate to S4.")
3305 (license license:lgpl2.1+)))
3307 (define-public r-r-oo
3313 (uri (cran-uri "R.oo" version))
3316 "0723gxjazgqq7v3lwnl7axw3brzcnizvhbd71ijkkv8mz31fwp34"))))
3317 (properties `((upstream-name . "R.oo")))
3318 (build-system r-build-system)
3320 `(("r-r-methodss3" ,r-r-methodss3)))
3321 (home-page "https://github.com/HenrikBengtsson/R.oo")
3322 (synopsis "R object-oriented programming with or without references")
3324 "This package provides methods and classes for object-oriented
3325 programming in R with or without references. Large effort has been made on
3326 making definition of methods as simple as possible with a minimum of
3327 maintenance for package developers.")
3328 (license license:lgpl2.1+)))
3330 (define-public r-r-utils
3336 (uri (cran-uri "R.utils" version))
3339 "17q3w5dlly5xl2srrzsmf9s7vs5d576vqbcs6sr2p5x4qvqa1q8s"))))
3340 (properties `((upstream-name . "R.utils")))
3341 (build-system r-build-system)
3343 `(("r-r-methodss3" ,r-r-methodss3)
3344 ("r-r-oo" ,r-r-oo)))
3345 (home-page "https://github.com/HenrikBengtsson/R.utils")
3346 (synopsis "Various programming utilities")
3348 "This package provides utility functions useful when programming and
3349 developing R packages.")
3350 (license license:lgpl2.1+)))
3352 (define-public r-r-cache
3358 (uri (cran-uri "R.cache" version))
3361 "006x52w9r8phw5hgqmyp0bz8z42vn8p5yibibnzi1sfa1xlw8iyx"))))
3362 (properties `((upstream-name . "R.cache")))
3363 (build-system r-build-system)
3365 `(("r-digest" ,r-digest)
3366 ("r-r-methodss3" ,r-r-methodss3)
3368 ("r-r-utils" ,r-r-utils)))
3369 (home-page "https://github.com/HenrikBengtsson/R.cache")
3370 (synopsis "Light-weight caching of objects and results")
3372 "This package provides methods for caching or memoization of objects and
3373 results. With this package, any R object can be cached in a key-value storage
3374 where the key can be an arbitrary set of R objects. The cache memory is
3375 persistent (on the file system).")
3376 (license license:lgpl2.1+)))
3378 (define-public r-r-rsp
3384 (uri (cran-uri "R.rsp" version))
3387 "01l430avj5ggmdsla2kiriix72g0dlzx9klniq321bs0za808v3c"))))
3388 (properties `((upstream-name . "R.rsp")))
3389 (build-system r-build-system)
3391 `(("r-r-cache" ,r-r-cache)
3392 ("r-r-methodss3" ,r-r-methodss3)
3394 ("r-r-utils" ,r-r-utils)))
3395 (home-page "https://github.com/HenrikBengtsson/R.rsp")
3396 (synopsis "Dynamic generation of scientific reports")
3398 "The RSP markup language provides a powerful markup for controlling the
3399 content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
3400 documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}. Contrary
3401 to many other literate programming languages, with RSP it is straightforward
3402 to loop over mixtures of code and text sections, e.g. in month-by-month
3403 summaries. RSP has also several preprocessing directives for incorporating
3404 static and dynamic contents of external files (local or online) among other
3405 things. RSP is ideal for self-contained scientific reports and R package
3407 (license license:lgpl2.1+)))
3409 (define-public r-mvtnorm
3415 (uri (cran-uri "mvtnorm" version))
3418 "0i74s9dl4jf1gln6agra8h38qn9ifd5v0gi13caj1da5nrbmn0aa"))))
3419 (build-system r-build-system)
3421 `(("gfortran" ,gfortran)))
3422 (home-page "http://mvtnorm.R-forge.R-project.org")
3423 (synopsis "Package for multivariate normal and t-distributions")
3424 (description "This package can compute multivariate normal and
3425 t-probabilities, quantiles, random deviates and densities.")
3426 (license license:gpl2)))
3428 (define-public r-matrixstats
3430 (name "r-matrixstats")
3434 (uri (cran-uri "matrixStats" version))
3437 "19fjf19cr0p3j9pj17myz39zpi5bh7ci72db3la9my09n6k6mnir"))))
3438 (properties `((upstream-name . "matrixStats")))
3439 (build-system r-build-system)
3441 `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
3442 (home-page "https://github.com/HenrikBengtsson/matrixStats")
3443 (synopsis "Methods applying to vectors and matrix rows and columns")
3445 "This package provides methods operating on rows and columns of matrices,
3446 e.g. @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}. There are
3447 also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
3448 @code{weightedMedians()}. All methods have been optimized for speed and
3450 (license license:artistic2.0)))
3452 (define-public r-viridis
3458 (uri (cran-uri "viridis" version))
3461 "03mha2935k1mw7mjjkq7mrx185hl0m3vq3967iiwbknpivbdxllk"))))
3462 (build-system r-build-system)
3464 `(("r-ggplot2" ,r-ggplot2)
3465 ("r-gridextra" ,r-gridextra)
3466 ("r-viridislite" ,r-viridislite)))
3467 (home-page "https://github.com/sjmgarnier/viridis")
3468 (synopsis "Matplotlib default color map")
3470 "This package is a port of the new @url{matplotlib,
3471 http://matplotlib.org/} color maps (@code{viridis}--the default--,
3472 @code{magma}, @code{plasma}, and @code{inferno}) to R. These color maps are
3473 designed in such a way that they will analytically be perfectly
3474 perceptually-uniform, both in regular form and also when converted to
3475 black-and-white. They are also designed to be perceived by readers with the
3476 most common form of color blindness.")
3477 (license license:x11)))
3479 (define-public r-viridislite
3481 (name "r-viridislite")
3486 (uri (cran-uri "viridisLite" version))
3489 "1546h44ng4dxs130jkh6lkh990hmp90m1w45sq5p47n546gr0k9d"))))
3490 (properties `((upstream-name . "viridisLite")))
3491 (build-system r-build-system)
3492 (home-page "https://github.com/sjmgarnier/viridisLite")
3493 (synopsis "Default color maps from matplotlib")
3495 "This package is a port of the new @code{matplotlib} color maps ('viridis',
3496 'magma', 'plasma' and 'inferno') to R. matplotlib is a popular plotting
3497 library for Python. These color maps are designed in such a way that they
3498 will analytically be perfectly perceptually-uniform, both in regular form and
3499 also when converted to black-and-white. They are also designed to be
3500 perceived by readers with the most common form of color blindness. This is
3501 the 'lite' version of the more complete @code{viridis} package.")
3502 (license license:expat)))
3504 (define-public r-tidyr
3511 (uri (cran-uri "tidyr" version))
3514 "14s57zrjm2phiy600z9ivq4az71z0ggmp6nj0js7yrybxf0dlah6"))))
3515 (build-system r-build-system)
3517 `(("r-dplyr" ,r-dplyr)
3518 ("r-lazyeval" ,r-lazyeval)
3519 ("r-magrittr" ,r-magrittr)
3521 ("r-stringi" ,r-stringi)
3522 ("r-tibble" ,r-tibble)))
3523 (home-page "https://github.com/hadley/tidyr")
3524 (synopsis "Tidy data with `spread()` and `gather()` functions")
3526 "tidyr is a reframing of the reshape2 package designed to accompany the
3527 tidy data framework, and to work hand-in-hand with magrittr and dplyr to build
3528 a solid pipeline for data analysis. It is designed specifically for tidying
3529 data, not the general reshaping that reshape2 does, or the general aggregation
3530 that reshape did. In particular, built-in methods only work for data frames,
3531 and tidyr provides no margins or aggregation.")
3532 (license license:expat)))
3534 (define-public r-hexbin
3537 ;; The package tarball was updated in place, resulting in a change in the
3538 ;; hash value. We decided to bump the version to 1.27.1-1 instead of
3539 ;; keeping the version at upstream's 1.27.1.
3540 (version "1.27.1-1")
3544 (uri (cran-uri "hexbin" "1.27.1"))
3547 "025d609z1nyy684hwvp34b9mjzkgvild7fvfr95f941dmsikan87"))))
3548 (build-system r-build-system)
3550 `(("r-lattice" ,r-lattice)))
3552 `(("gfortran" ,gfortran)))
3553 (home-page "https://github.com/edzer/hexbin")
3554 (synopsis "Hexagonal binning routines")
3556 "This package provides binning and plotting functions for hexagonal bins.
3557 It uses and relies on grid graphics and formal (S4) classes and methods.")
3558 (license license:gpl2+)))
3560 (define-public r-purrr
3567 (uri (cran-uri "purrr" version))
3570 "0j1y0nbvljcis9hgic4wbbzslcsidhpw0wzs7d2hx7a2ygi6mkma"))))
3571 (build-system r-build-system)
3573 `(("r-tibble" ,r-tibble)
3574 ("r-magrittr" ,r-magrittr)
3575 ("r-rlang" ,r-rlang)))
3576 (home-page "https://github.com/hadley/purrr")
3577 (synopsis "Functional programming tools")
3579 "This package completes R's functional programming tools with missing
3580 features present in other programming languages.")
3581 (license license:gpl3+)))
3583 (define-public r-plotly
3589 (uri (cran-uri "plotly" version))
3592 "0wj9lw7w28z8w9ip9vadv6sydjhqyg65kfiai9m3bndzz50b1m3w"))))
3593 (build-system r-build-system)
3595 `(("r-base64enc" ,r-base64enc)
3596 ("r-crosstalk" ,r-crosstalk)
3597 ("r-digest" ,r-digest)
3598 ("r-data-table" ,r-data-table)
3599 ("r-dplyr" ,r-dplyr)
3600 ("r-ggplot2" ,r-ggplot2)
3601 ("r-hexbin" ,r-hexbin)
3602 ("r-htmltools" ,r-htmltools)
3603 ("r-htmlwidgets" ,r-htmlwidgets)
3605 ("r-jsonlite" ,r-jsonlite)
3606 ("r-lazyeval" ,r-lazyeval)
3607 ("r-magrittr" ,r-magrittr)
3608 ("r-purrr" ,r-purrr)
3609 ("r-rcolorbrewer" ,r-rcolorbrewer)
3610 ("r-scales" ,r-scales)
3611 ("r-tibble" ,r-tibble)
3612 ("r-tidyr" ,r-tidyr)
3613 ("r-viridislite" ,r-viridislite)))
3614 (home-page "https://plot.ly/r")
3615 (synopsis "Create interactive web graphics")
3617 "This package enables the translation of ggplot2 graphs to an interactive
3618 web-based version and/or the creation of custom web-based visualizations
3619 directly from R. Once uploaded to a plotly account, plotly graphs (and the
3620 data behind them) can be viewed and modified in a web browser.")
3621 (license license:x11)))
3623 (define-public r-biased-urn
3625 (name "r-biased-urn")
3630 (uri (cran-uri "BiasedUrn" version))
3633 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
3634 (properties `((upstream-name . "BiasedUrn")))
3635 (build-system r-build-system)
3636 (home-page "http://www.agner.org/random/")
3637 (synopsis "Biased urn model distributions")
3639 "This package provides statistical models of biased sampling in the form
3640 of univariate and multivariate noncentral hypergeometric distributions,
3641 including Wallenius' noncentral hypergeometric distribution and Fisher's
3642 noncentral hypergeometric distribution (also called extended hypergeometric
3644 (license license:gpl3+)))
3646 (define-public r-rematch
3653 (uri (cran-uri "rematch" version))
3656 "0y3mshvpvz9csmq8hk8jbabx4nxlv5sckvfzvm6920ndg34xw2d4"))))
3657 (build-system r-build-system)
3658 (home-page "https://github.com/MangoTheCat/rematch")
3659 (synopsis "Match regular expressions with a nicer API")
3661 "This package provides a small wrapper on @code{regexpr} to extract the
3662 matches and captured groups from the match of a regular expression to a
3664 (license license:expat)))
3666 (define-public r-cellranger
3668 (name "r-cellranger")
3673 (uri (cran-uri "cellranger" version))
3676 "16fgi3annn34c3cxi0pxf62mmmmxi21hp0zzlv7bkfsjqy4g4f2x"))))
3677 (build-system r-build-system)
3679 `(("r-rematch" ,r-rematch)
3680 ("r-tibble" ,r-tibble)))
3681 (home-page "https://github.com/rsheets/cellranger")
3682 (synopsis "Translate spreadsheet cell ranges to rows and columns")
3684 "This package provides helper functions to work with spreadsheets and the
3685 @code{A1:D10} style of cell range specification.")
3686 (license license:expat)))
3688 (define-public r-googlesheets
3690 (name "r-googlesheets")
3695 (uri (cran-uri "googlesheets" version))
3698 "18q0xmxn09b52rmky7gr5flp0awndcnsgb7zcvkzvkrkvmwad52b"))))
3699 (build-system r-build-system)
3701 `(("r-cellranger" ,r-cellranger)
3702 ("r-dplyr" ,r-dplyr)
3704 ("r-jsonlite" ,r-jsonlite)
3705 ("r-purrr" ,r-purrr)
3706 ("r-readr" ,r-readr)
3707 ("r-stringr" ,r-stringr)
3708 ("r-tidyr" ,r-tidyr)
3709 ("r-xml2" ,r-xml2)))
3710 (home-page "https://github.com/jennybc/googlesheets")
3711 (synopsis "Manage Google spreadsheets from R")
3712 (description "This package provides tools to interact with Google Sheets
3714 (license license:expat)))
3716 (define-public r-spams
3719 (version "2.6-2017-03-22")
3723 (uri (string-append "https://gforge.inria.fr/frs/download.php/36615/"
3724 "spams-R-v" version ".tar.gz"))
3727 "13z2293jixf1r9g8dyy856xrhvpjr2ln2n9smn6644126r9hmhkx"))))
3728 (build-system r-build-system)
3731 (modify-phases %standard-phases
3732 (add-after 'unpack 'chdir
3733 (lambda _ (chdir "spams") #t))
3734 ;; Don't tune for the building machine
3735 (add-after 'chdir 'no-mtune
3737 (substitute* "src/Makevars"
3738 (("-mtune=native") ""))
3741 `(("r-lattice" ,r-lattice)
3742 ("r-matrix" ,r-matrix)))
3743 (home-page "http://spams-devel.gforge.inria.fr")
3744 (synopsis "Toolbox for solving sparse estimation problems")
3745 (description "SPAMS (SPArse Modeling Software) is an optimization toolbox
3746 for solving various sparse estimation problems. It includes tools for the
3750 @item Dictionary learning and matrix factorization (NMF, sparse @dfn{principle
3751 component analysis} (PCA), ...)
3752 @item Solving sparse decomposition problems with LARS, coordinate descent,
3753 OMP, SOMP, proximal methods
3754 @item Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse
3755 group lasso, tree-structured regularization, structured sparsity with
3756 overlapping groups,...).
3758 (license license:gpl3+)))
3760 (define-public r-base64
3767 (uri (cran-uri "base64" version))
3770 "1labh0ycdm2xcjssj8bhnyjvbk44mcdsi0rb2p8rfqa428mrq9cf"))))
3771 (build-system r-build-system)
3773 `(("r-openssl" ,r-openssl)))
3774 (home-page "http://cran.r-project.org/web/packages/base64")
3775 (synopsis "Base64 encoder and decoder")
3777 "This package is a compatibility wrapper to replace the orphaned package
3778 by Romain Francois. New applications should use the openssl or base64enc
3780 (license license:expat)))
3782 (define-public r-hmisc
3789 (uri (cran-uri "Hmisc" version))
3792 "1a7i7azag6pldgala85d8hh7wnx1shamyiriy4jfc65nxrr2lq8w"))))
3793 (properties `((upstream-name . "Hmisc")))
3794 (build-system r-build-system)
3796 `(("gfortran" ,gfortran)))
3798 `(("r-acepack" ,r-acepack)
3799 ("r-base64enc" ,r-base64enc)
3800 ("r-cluster" ,r-cluster)
3801 ("r-data-table" ,r-data-table)
3802 ("r-foreign" ,r-foreign)
3803 ("r-formula" ,r-formula)
3804 ("r-ggplot2" ,r-ggplot2)
3805 ("r-gridextra" ,r-gridextra)
3806 ("r-gtable" ,r-gtable)
3807 ("r-lattice" ,r-lattice)
3808 ("r-latticeextra" ,r-latticeextra)
3809 ("r-htmltable" ,r-htmltable)
3810 ("r-htmltools" ,r-htmltools)
3812 ("r-rpart" ,r-rpart)
3813 ("r-survival" ,r-survival)
3814 ("r-viridis" ,r-viridis)))
3815 (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
3816 (synopsis "Miscellaneous data analysis and graphics functions")
3818 "This package contains many functions useful for data analysis,
3819 high-level graphics, utility operations, functions for computing sample size
3820 and power, importing and annotating datasets, imputing missing values,
3821 advanced table making, variable clustering, character string manipulation,
3822 conversion of R objects to LaTeX code, and recoding variables.")
3823 (license license:gpl2+)))
3825 (define-public r-runit
3832 (uri (cran-uri "RUnit" version))
3835 "1jqr871jkll2xmk7wk5hv1z3a36hyn2ibgivw7bwk4b346940xlx"))))
3836 (properties `((upstream-name . "RUnit")))
3837 (build-system r-build-system)
3838 (home-page "http://cran.r-project.org/web/packages/RUnit")
3839 (synopsis "R unit test framework")
3841 "This package provides R functions implementing a standard unit testing
3842 framework, with additional code inspection and report generation tools.")
3843 (license license:gpl2+)))
3845 (define-public r-dynamictreecut
3847 (name "r-dynamictreecut")
3852 (uri (cran-uri "dynamicTreeCut" version))
3855 "1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"))))
3856 (properties `((upstream-name . "dynamicTreeCut")))
3857 (build-system r-build-system)
3859 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/")
3860 (synopsis "Detect clusters in hierarchical clustering dendrograms")
3862 "This package contains methods for the detection of clusters in
3863 hierarchical clustering dendrograms.")
3864 (license license:gpl2+)))
3866 (define-public r-preprocesscore
3868 (name "r-preprocesscore")
3873 (uri (bioconductor-uri "preprocessCore" version))
3876 "1ggvmak13rhxc4ghf16ncjfvgszc8yvza93s2l9kn8yiwr96vp2h"))))
3878 `((upstream-name . "preprocessCore")))
3879 (build-system r-build-system)
3880 (home-page "https://github.com/bmbolstad/preprocessCore")
3881 (synopsis "Collection of pre-processing functions")
3883 "This package provides a library of core pre-processing and normalization
3885 (license license:lgpl2.0+)))
3887 (define-public r-fastcluster
3889 (name "r-fastcluster")
3894 (uri (cran-uri "fastcluster" version))
3897 "006k9isra5biyavqwci61avladw19mhp6kmkjj3777rl1r4r8b9z"))))
3898 (build-system r-build-system)
3899 (home-page "http://danifold.net/fastcluster.html")
3900 (synopsis "Fast hierarchical clustering routines")
3902 "This package implements fast hierarchical, agglomerative clustering
3903 routines. Part of the functionality is designed as drop-in replacement for
3904 existing routines: @code{linkage()} in the SciPy package
3905 @code{scipy.cluster.hierarchy}, @code{hclust()} in R's @code{stats} package,
3906 and the @code{flashClust} package. It provides the same functionality with
3907 the benefit of a much faster implementation. Moreover, there are
3908 memory-saving routines for clustering of vector data, which go beyond what the
3909 existing packages provide.")
3910 (license license:bsd-2)))
3912 (define-public r-sfsmisc
3919 (uri (cran-uri "sfsmisc" version))
3922 "0jzmbywlyzfxs7hlmyd0iynghfc9qp5sa5lnhr73y8r360yv1ahf"))))
3923 (build-system r-build-system)
3924 (home-page "http://cran.r-project.org/web/packages/sfsmisc")
3925 (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich")
3927 "This package provides useful utilities from Seminar fuer Statistik ETH
3928 Zurich, including many that are related to graphics.")
3929 (license license:gpl2+)))
3931 (define-public r-gtools
3938 (uri (cran-uri "gtools" version))
3941 "1xknwk9xlsj027pg0nwiizigcrsc84hdrig0jn0cgcyxj8dabdl6"))))
3942 (build-system r-build-system)
3943 (home-page "http://cran.r-project.org/web/packages/gtools")
3944 (synopsis "Various R programming tools")
3946 "This package contains a collection of various functions to assist in R
3947 programming, such as tools to assist in developing, updating, and maintaining
3948 R and R packages, calculating the logit and inverse logit transformations,
3949 tests for whether a value is missing, empty or contains only @code{NA} and
3950 @code{NULL} values, and many more.")
3951 (license license:gpl2)))
3953 (define-public r-gdata
3960 (uri (cran-uri "gdata" version))
3963 "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b"))))
3964 (build-system r-build-system)
3968 `(("r-gtools" ,r-gtools)))
3969 (home-page "http://cran.r-project.org/web/packages/gdata")
3970 (synopsis "Various R programming tools for data manipulation")
3972 "This package provides various R programming tools for data manipulation,
3976 @item medical unit conversions
3977 @item combining objects
3978 @item character vector operations
3979 @item factor manipulation
3980 @item obtaining information about R objects
3981 @item manipulating MS-Excel formatted files
3982 @item generating fixed-width format files
3983 @item extricating components of date and time objects
3984 @item operations on columns of data frames
3985 @item matrix operations
3986 @item operations on vectors and data frames
3987 @item value of last evaluated expression
3988 @item wrapper for @code{sample} that ensures consistent behavior for
3989 both scalar and vector arguments
3991 (license license:gpl2+)))
3993 (define-public r-gplots
4000 (uri (cran-uri "gplots" version))
4003 "02nb8n3s7c1zxq2s7ycaq2ys72y7mzirxrwj954h6gdc4x1zhg9l"))))
4004 (build-system r-build-system)
4006 `(("r-catools" ,r-catools)
4007 ("r-gdata" ,r-gdata)
4008 ("r-gtools" ,r-gtools)
4009 ("r-kernsmooth" ,r-kernsmooth)))
4010 (home-page "http://cran.r-project.org/web/packages/gplots")
4011 (synopsis "Various R programming tools for plotting data")
4013 "This package provides various R programming tools for plotting data,
4017 @item calculating and plotting locally smoothed summary function
4018 @item enhanced versions of standard plots
4019 @item manipulating colors
4020 @item calculating and plotting two-dimensional data summaries
4021 @item enhanced regression diagnostic plots
4022 @item formula-enabled interface to @code{stats::lowess} function
4023 @item displaying textual data in plots
4025 @item plotting \"Venn\" diagrams
4026 @item displaying Open-Office style plots
4027 @item plotting multiple data on same region, with separate axes
4028 @item plotting means and confidence intervals
4029 @item spacing points in an x-y plot so they don't overlap
4031 (license license:gpl2+)))
4033 (define-public r-rocr
4040 (uri (cran-uri "ROCR" version))
4043 "1jay8cm7lgq56i967vm5c2hgaxqkphfpip0gn941li3yhh7p3vz7"))))
4044 (properties `((upstream-name . "ROCR")))
4045 (build-system r-build-system)
4047 `(("r-gplots" ,r-gplots)))
4048 (home-page "http://rocr.bioinf.mpi-sb.mpg.de/")
4049 (synopsis "Visualizing the performance of scoring classifiers")
4051 "ROCR is a flexible tool for creating cutoff-parameterized 2D performance
4052 curves by freely combining two from over 25 performance measures (new
4053 performance measures can be added using a standard interface). Curves from
4054 different cross-validation or bootstrapping runs can be averaged by different
4055 methods, and standard deviations, standard errors or box plots can be used to
4056 visualize the variability across the runs. The parameterization can be
4057 visualized by printing cutoff values at the corresponding curve positions, or
4058 by coloring the curve according to cutoff. All components of a performance
4059 plot can be quickly adjusted using a flexible parameter dispatching
4061 (license license:gpl2+)))
4063 (define-public r-kernsmooth
4065 (name "r-kernsmooth")
4070 (uri (cran-uri "KernSmooth" version))
4073 "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb"))))
4074 (properties `((upstream-name . "KernSmooth")))
4075 (build-system r-build-system)
4077 `(("gfortran" ,gfortran)))
4078 (home-page "http://cran.r-project.org/web/packages/KernSmooth")
4079 (synopsis "Functions for kernel smoothing")
4081 "This package provides functions for kernel smoothing (and density
4082 estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
4083 \"Kernel Smoothing\".")
4084 ;; Unlimited use and distribution
4085 (license (license:non-copyleft "file://LICENSE.note"))))
4087 (define-public r-zoo
4093 (uri (cran-uri "zoo" version))
4096 "0mqklbx92ifwa0awm7gpm4r9dvwa09p55zjxjnypiqsxy532r4h9"))))
4097 (build-system r-build-system)
4099 `(("r-lattice" ,r-lattice)))
4100 (home-page "http://zoo.R-Forge.R-project.org/")
4101 (synopsis "S3 infrastructure for regular and irregular time series")
4102 (description "This package contains an S3 class with methods for totally
4103 ordered indexed observations. It is particularly aimed at irregular time
4104 series of numeric vectors/matrices and factors.")
4105 (license license:gpl2+)))
4107 (define-public r-ztable
4113 (uri (cran-uri "ztable" version))
4116 "1jfqnqy9544gfvz3bsb48v4177nwp4b4n9l2743asq8sbq305b5r"))))
4117 (build-system r-build-system)
4118 (home-page "http://cran.r-project.org/web/packages/ztable")
4119 (synopsis "Zebra-striped tables in LaTeX and HTML formats for R")
4121 "This package provides functions to make zebra-striped tables (tables
4122 with alternating row colors) in LaTeX and HTML formats easily from
4123 @code{data.frame}, @code{matrix}, @code{lm}, @code{aov}, @code{anova},
4124 @code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
4125 @code{cbind.mytable} objects.")
4126 (license license:gpl2+)))
4128 (define-public r-vipor
4134 (uri (cran-uri "vipor" version))
4137 "112gc0d7f8iavgf56pnzfxb7hy75yhd0zlyjzshdcfbnqcd2a6bx"))))
4138 (build-system r-build-system)
4139 (home-page "http://cran.r-project.org/web/packages/vipor")
4140 (synopsis "Plot categorical data using noise and density estimates")
4142 "This package provides tools to generate a violin point plot, a
4143 combination of a violin/histogram plot and a scatter plot by offsetting points
4144 within a category based on their density using quasirandom noise.")
4145 (license license:gpl2+)))
4147 (define-public r-beeswarm
4153 (uri (cran-uri "beeswarm" version))
4156 "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
4157 (build-system r-build-system)
4158 (home-page "http://www.cbs.dtu.dk/~eklund/beeswarm/")
4159 (synopsis "Implementation of bee swarm plots")
4161 "This package provides an implementation of bee swarm plots. The bee
4162 swarm plot is a one-dimensional scatter plot like stripchart, but with
4163 closely-packed, non-overlapping points.")
4164 (license license:artistic2.0)))
4166 (define-public r-sourcetools
4168 (name "r-sourcetools")
4173 (uri (cran-uri "sourcetools" version))
4176 "0l8c6fql82cb246qh7hfgxb4s35qn0qfgy6dzvkx0zkz1cpqvx69"))))
4177 (build-system r-build-system)
4178 (home-page "http://cran.r-project.org/web/packages/sourcetools")
4179 (synopsis "Tools for reading, tokenizing and parsing R code")
4181 "The sourcetools package provides both an R and C++ interface for the
4182 tokenization of R code, and helpers for interacting with the tokenized
4183 representation of R code.")
4184 (license license:expat)))
4186 (define-public r-ggbeeswarm
4188 (name "r-ggbeeswarm")
4192 (uri (cran-uri "ggbeeswarm" version))
4195 "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v"))))
4196 (build-system r-build-system)
4198 `(("r-beeswarm" ,r-beeswarm)
4199 ("r-ggplot2" ,r-ggplot2)
4200 ("r-vipor" ,r-vipor)))
4201 (home-page "https://github.com/eclarke/ggbeeswarm")
4202 (synopsis "Categorical scatter (violin point) plots")
4204 "This package provides two methods of plotting categorical scatter plots
4205 such that the arrangement of points within a category reflects the density of
4206 data at that region, and avoids over-plotting.")
4207 (license license:gpl2+)))
4209 (define-public r-ggthemes
4215 (uri (cran-uri "ggthemes" version))
4218 "1jj8lp7jbk3489kpgbw4b5phpn01gkfmksc21c6sn3x6wmzyn6hs"))))
4219 (build-system r-build-system)
4221 `(("r-assertthat" ,r-assertthat)
4222 ("r-colorspace" ,r-colorspace)
4223 ("r-ggplot2" ,r-ggplot2)
4224 ("r-scales" ,r-scales)))
4225 (home-page "https://cran.rstudio.com/web/packages/ggthemes")
4226 (synopsis "Extra themes, scales and geoms for @code{ggplot2}")
4227 (description "This package provides extra themes and scales for
4228 @code{ggplot2} that replicate the look of plots by Edward Tufte and
4229 Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The
4230 Wall Street Journal, among others. This package also provides
4231 @code{geoms} for Tufte's box plot and range frame.")
4232 (license license:gpl2)))
4234 (define-public r-statmod
4240 (uri (cran-uri "statmod" version))
4243 "07v4x8af60alcw6vbiwf5fp25bhra61kvxz9kqx64lszm0i1fb4x"))))
4244 (build-system r-build-system)
4245 (home-page "http://cran.r-project.org/web/packages/statmod")
4247 `(("gfortran" ,gfortran)))
4248 (synopsis "Statistical modeling")
4250 "This package provides a collection of algorithms and functions to aid
4251 statistical modeling. It includes growth curve comparisons, limiting dilution
4252 analysis (aka ELDA), mixed linear models, heteroscedastic regression,
4253 inverse-Gaussian probability calculations, Gauss quadrature and a secure
4254 convergence algorithm for nonlinear models. It also includes advanced
4255 generalized linear model functions that implement secure convergence,
4256 dispersion modeling and Tweedie power-law families.")
4257 ;; Statmod is distributed under either license
4258 (license (list license:gpl2 license:gpl3))))
4260 (define-public r-rann
4266 (uri (cran-uri "RANN" version))
4269 "0il5i99vbcagnxvb15af5n37g04a4q1x96bz73zh3jhki9fpw9vm"))))
4271 `((upstream-name . "RANN")))
4272 (build-system r-build-system)
4273 (home-page "https://github.com/jefferis/RANN")
4274 (synopsis "Fast nearest neighbour search")
4276 "This package finds the k nearest neighbours for every point in a given
4277 dataset in O(N log N) time using Arya and Mount's ANN library. Provides
4278 approximate, exact searches, fixed radius searches, bd and kb trees.")
4279 (license license:gpl3+)))
4281 (define-public r-fivethirtyeight
4283 (name "r-fivethirtyeight")
4288 (uri (string-append "https://mran.microsoft.com/src/contrib/"
4289 "fivethirtyeight_" version ".tar.gz"))
4292 "0fcc8rq745nsghp27dk0lgih90y4zx8hrzcvsn6ih786yv7qxhvl"))))
4293 (build-system r-build-system)
4295 `(("r-knitr" ,r-knitr)
4296 ("r-rmarkdown" ,r-rmarkdown)
4297 ("r-dplyr" ,r-dplyr)
4298 ("r-readr" ,r-readr)
4299 ("r-ggplot2" ,r-ggplot2)
4300 ("r-magrittr" ,r-magrittr)
4301 ("r-stringr" ,r-stringr)))
4302 (home-page "https://mran.microsoft.com/package/fivethirtyeight/")
4303 (synopsis "Data and code behind the stories at FiveThirtyEight")
4304 (description "This R package provides access to the code and data sets
4305 published by the statistics blog FiveThirtyEight.")
4306 (license license:expat)))
4308 (define-public r-compquadform
4310 (name "r-compquadform")
4315 (uri (cran-uri "CompQuadForm" version))
4318 "1i30hrqdk64q17vsn918c3q79brchgx2wzh1gbsgbn0dh1ncabq4"))))
4319 (properties `((upstream-name . "CompQuadForm")))
4320 (build-system r-build-system)
4321 (home-page "http://cran.r-project.org/web/packages/CompQuadForm")
4322 (synopsis "Distribution function of quadratic forms in normal variables")
4324 "This package provides functions to compute the distribution function of
4325 quadratic forms in normal variables using Imhof's method, Davies's algorithm,
4326 Farebrother's algorithm or Liu et al.'s algorithm.")
4327 (license license:gpl2+)))
4329 (define-public r-cowplot
4336 (uri (cran-uri "cowplot" version))
4339 "03bh0r6ynr95gk4lc8asfi3kpmskm59vfzwn417pdziha3igs5x6"))))
4340 (build-system r-build-system)
4342 `(("r-ggplot2" ,r-ggplot2)
4343 ("r-gtable" ,r-gtable)
4344 ("r-plyr" ,r-plyr)))
4345 (home-page "https://github.com/wilkelab/cowplot")
4346 (synopsis "Streamlined plot theme and plot annotations for ggplot2")
4348 "This package provides some helpful extensions and modifications to the
4349 ggplot2 package to combine multiple ggplot2 plots into one and label them with
4350 letters, as is often required for scientific publications.")
4351 (license license:gpl2)))
4353 (define-public r-mixtools
4360 (uri (cran-uri "mixtools" version))
4363 "13wdm0xs5bakhpa8ypg6lvhjaqkxyabwz4glxdwn0jwdvkcdhgsl"))))
4364 (build-system r-build-system)
4366 `(("r-mass" ,r-mass)
4367 ("r-segmented" ,r-segmented)
4368 ("r-survival" ,r-survival)))
4369 (home-page "http://cran.r-project.org/web/packages/mixtools")
4370 (synopsis "Tools for analyzing finite mixture models")
4372 "This package provides a collection of R functions for analyzing finite
4374 (license license:gpl2+)))
4376 (define-public r-lars
4383 (uri (cran-uri "lars" version))
4386 "0blj44wqrx6lmym1m9v6wkz8zxzbjax2zl6swgdczci0ixb5nx34"))))
4387 (build-system r-build-system)
4389 `(("gfortran" ,gfortran)))
4390 (home-page "http://www-stat.stanford.edu/~hastie/Papers/#LARS")
4391 (synopsis "Least angle regression software")
4393 "Least Angle Regression (\"LAR\") is a model selection algorithm; a
4394 useful and less greedy version of traditional forward selection methods. A
4395 simple modification of the LAR algorithm implements Tibshirani's Lasso; the
4396 Lasso modification of LARS calculates the entire Lasso path of coefficients
4397 for a given problem at the cost of a single least squares fit. Another LARS
4398 modification efficiently implements epsilon Forward Stagewise linear
4400 (license license:gpl2)))
4402 (define-public r-fastica
4409 (uri (cran-uri "fastICA" version))
4412 "108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg"))))
4413 (properties `((upstream-name . "fastICA")))
4414 (build-system r-build-system)
4415 (home-page "http://cran.r-project.org/web/packages/fastICA")
4416 (synopsis "FastICA algorithms to perform ICA and projection pursuit")
4418 "This package provides an implementation of the FastICA algorithm to
4419 perform @dfn{independent component analysis} (ICA) and projection pursuit.")
4421 (license license:gpl3+)))
4423 (define-public r-randomforest
4425 (name "r-randomforest")
4430 (uri (cran-uri "randomForest" version))
4433 "1i43idaihhl6nwqw42v9dqpl6f8z3ykcn2in32lh2755i27jylbf"))))
4434 (properties `((upstream-name . "randomForest")))
4435 (build-system r-build-system)
4436 (home-page "https://www.stat.berkeley.edu/~breiman/RandomForests/")
4438 `(("gfortran" ,gfortran)))
4439 (synopsis "Breiman and Cutler's random forests for classification and regression")
4441 "This package provides the Breiman and Cutler's random forests algorithm, based on a
4442 forest of trees using random inputs, for classification and regression.")
4443 (license license:gpl2+)))
4445 (define-public r-diptest
4452 (uri (cran-uri "diptest" version))
4455 "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
4456 (build-system r-build-system)
4457 (home-page "http://cran.r-project.org/web/packages/diptest")
4458 (synopsis "Hartigan's dip test statistic for unimodality")
4460 "This package computes Hartigan's dip test statistic for unimodality,
4461 multimodality and provides a test with simulation based p-values, where the
4462 original public code has been corrected.")
4463 (license license:gpl2+)))
4465 (define-public r-modeltools
4467 (name "r-modeltools")
4472 (uri (cran-uri "modeltools" version))
4475 "0ynds453xprxv0jqqzi3blnv5w6vrdww9pvd1sq4lrr5ar3k3cq7"))))
4476 (build-system r-build-system)
4477 (home-page "http://cran.r-project.org/web/packages/modeltools")
4478 (synopsis "Tools and classes for statistical models")
4480 "This package provides a collection of tools to deal with statistical
4481 models. The functionality is experimental and the user interface is likely
4482 to change in the future.")
4483 (license license:gpl2)))
4485 (define-public r-flexmix
4492 (uri (cran-uri "flexmix" version))
4495 "0sl4zxh1sb2sr5q7svjw9ihrm219jzn82yrc9d43q6r1b8bpyz43"))))
4496 (build-system r-build-system)
4498 `(("r-lattice" ,r-lattice)
4499 ("r-modeltools" ,r-modeltools)
4500 ("r-nnet" ,r-nnet)))
4501 (home-page "http://cran.r-project.org/web/packages/flexmix")
4502 (synopsis "Flexible mixture modeling")
4504 "This package implements a general framework for finite mixtures of
4505 regression models using the EM algorithm. FlexMix provides the E-step and
4506 all data handling, while the M-step can be supplied by the user to easily
4507 define new models. Existing drivers implement mixtures of standard linear
4508 models, generalized linear models and model-based clustering.")
4509 (license license:gpl2+)))
4511 (define-public r-mclust
4518 (uri (cran-uri "mclust" version))
4521 "0h5syvpg3azrz5d10z2afilaa27jb4azi38idzlv05mfcs16s6rb"))))
4522 (build-system r-build-system)
4524 `(("gfortran" ,gfortran)))
4525 (home-page "http://www.stat.washington.edu/mclust/")
4526 (synopsis "Gaussian mixture modelling for model-based clustering etc.")
4528 "This package provides Gaussian finite mixture models fitted via EM
4529 algorithm for model-based clustering, classification, and density estimation,
4530 including Bayesian regularization, dimension reduction for visualisation,
4531 and resampling-based inference.")
4532 (license license:gpl2+)))
4534 (define-public r-prabclus
4541 (uri (cran-uri "prabclus" version))
4544 "0qjsxrx6yv338bxm4ki0w9h8hind1l98abdrz828588bwj02jya1"))))
4545 (build-system r-build-system)
4547 `(("r-mass" ,r-mass)
4548 ("r-mclust" ,r-mclust)))
4549 (home-page "https://cran.r-project.org/web/packages/prabclus")
4550 (synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
4552 "This package provides a distance-based parametric bootstrap tests
4553 for clustering with spatial neighborhood information. Some distance measures,
4554 clustering of presence-absence, abundance and multilocus genetical data for
4555 species delimitation, nearest neighbor based noise detection.")
4556 (license license:gpl2+)))
4558 (define-public r-deoptimr
4565 (uri (cran-uri "DEoptimR" version))
4568 "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
4569 (properties `((upstream-name . "DEoptimR")))
4570 (build-system r-build-system)
4571 (home-page "http://cran.r-project.org/web/packages/DEoptimR")
4572 (synopsis "Differential evolution optimization in pure R")
4574 "This package provides a differential evolution (DE) stochastic
4575 algorithms for global optimization of problems with and without constraints.
4576 The aim is to curate a collection of its state-of-the-art variants that (1) do
4577 not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
4578 can be efficiently implemented directly in the R language.")
4579 (license license:gpl2+)))
4581 (define-public r-robustbase
4583 (name "r-robustbase")
4588 (uri (cran-uri "robustbase" version))
4591 "13xz4am7y0s0kl5bmbcw3dlhl7ji8h9sjx56wsgmj6r9n35nrggw"))))
4592 (build-system r-build-system)
4594 `(("gfortran" ,gfortran)))
4596 `(("r-deoptimr" ,r-deoptimr)))
4597 (home-page "http://robustbase.r-forge.r-project.org/")
4598 (synopsis "Basic robust statistics")
4600 "This packages allows to analyze data with robust methods such as
4601 regression methodology including model selections and multivariate statistics.")
4602 (license license:gpl2+)))
4604 (define-public r-trimcluster
4606 (name "r-trimcluster")
4611 (uri (cran-uri "trimcluster" version))
4614 "0lsgbg93hm0w1rdb813ry0ks2l0jfpyqzqkf3h3bj6fch0avcbv2"))))
4615 (build-system r-build-system)
4616 (home-page "http://cran.r-project.org/web/packages/trimcluster")
4617 (synopsis "Cluster analysis with trimming")
4619 "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
4620 Matran (1997). This optimizes the k-means criterion under trimming a portion
4622 (license license:gpl2+)))
4624 (define-public r-fpc
4631 (uri (cran-uri "fpc" version))
4634 "15m0p9l9w2v7sl0cnzyg81i2fmx3hrhvr3371544mwn3fpsca5sx"))))
4635 (build-system r-build-system)
4637 `(("r-class" ,r-class)
4638 ("r-cluster" ,r-cluster)
4639 ("r-diptest" ,r-diptest)
4640 ("r-flexmix" ,r-flexmix)
4641 ("r-kernlab" ,r-kernlab)
4643 ("r-mclust" ,r-mclust)
4644 ("r-mvtnorm" ,r-mvtnorm)
4645 ("r-prabclus" ,r-prabclus)
4646 ("r-robustbase" ,r-robustbase)
4647 ("r-trimcluster" ,r-trimcluster)))
4648 (home-page "http://cran.r-project.org/web/packages/fpc")
4649 (synopsis "Flexible procedures for clustering")
4651 "This package provides various methods for clustering and cluster validation.
4652 For example, it provides fixed point clustering, linear regression clustering,
4653 clustering by merging Gaussian mixture components, as well as symmetric and
4654 asymmetric discriminant projections for visualisation of the separation of
4656 (license license:gpl2+)))
4658 (define-public r-vgam
4665 (uri (cran-uri "VGAM" version))
4668 "0r59hyp3afmvms890b3v2yyckf8v0qkjf2w11rnqd2zgg1gri0g5"))))
4669 (properties `((upstream-name . "VGAM")))
4670 (build-system r-build-system)
4672 `(("gfortran" ,gfortran)))
4673 (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
4674 (synopsis "Vector generalized linear and additive models")
4676 "This package is an implementation of about 6 major classes of statistical
4677 regression models. Currently only fixed-effects models are implemented, i.e.,
4678 no random-effects models. Many (150+) models and distributions are estimated
4679 by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
4680 VGLMs can be loosely thought of as multivariate generalised linear models.")
4681 (license license:gpl2+)))
4683 (define-public r-pbapply
4690 (uri (cran-uri "pbapply" version))
4693 "0iqhymf65jffh00qf056h1p76xf92bfmij6aymlmgnvn24fv4ybk"))))
4694 (build-system r-build-system)
4695 (home-page "https://github.com/psolymos/pbapply")
4696 (synopsis "Adding progress bar to apply functions")
4698 "This lightweight package that adds progress bar to vectorized R
4699 functions apply. The implementation can easily be added to functions where
4700 showing the progress is useful e.g. bootstrap.")
4701 (license license:gpl2)))
4703 (define-public r-fnn
4710 (uri (cran-uri "FNN" version))
4713 "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj"))))
4714 (properties `((upstream-name . "FNN")))
4715 (build-system r-build-system)
4716 (home-page "http://cran.r-project.org/web/packages/FNN")
4717 (synopsis "Fast nearest neighbor search algorithms and applications")
4719 "This package provides cover-tree and kd-tree fast k-nearest neighbor
4720 search algorithms and related applications including KNN classification,
4721 regression and information measures.")
4722 (license license:gpl2+)))
4724 (define-public r-minqa
4731 (uri (cran-uri "minqa" version))
4734 "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
4735 (build-system r-build-system)
4737 `(("r-rcpp" ,r-rcpp)))
4739 `(("gfortran" ,gfortran)))
4740 (home-page "http://optimizer.r-forge.r-project.org")
4741 (synopsis "Derivative-free optimization algorithms by quadratic approximation")
4743 "This package provides a derivative-free optimization by quadratic approximation
4744 based on an interface to Fortran implementations by M. J. D. Powell.")
4745 (license license:gpl2)))
4747 (define-public r-rcppeigen
4749 (name "r-rcppeigen")
4750 (version "0.3.3.3.0")
4754 (uri (cran-uri "RcppEigen" version))
4757 "0zz9v0f8nnlvhhqv91lkyfblvjnmav84l89mr6vmbqjc2hzqd3n8"))))
4758 (properties `((upstream-name . "RcppEigen")))
4759 (build-system r-build-system)
4761 `(("r-rcpp" ,r-rcpp)
4762 ("r-matrix" ,r-matrix)))
4763 (home-page "http://eigen.tuxfamily.org")
4764 (synopsis "Rcpp integration for the Eigen templated linear algebra library")
4766 "This package provides an integration of Eigen in R using a C++ template
4767 library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
4768 It supports dense and sparse matrices on integer, floating point and complex numbers,
4769 decompositions of such matrices, and solutions of linear systems.")
4770 (license license:gpl2+)))
4772 (define-public r-modelmetrics
4774 (name "r-modelmetrics")
4779 (uri (cran-uri "ModelMetrics" version))
4782 "119xxmzb5biq7k1yxqsf0jmmarmfn6lds9x9hfgv593xlpym6za8"))))
4783 (properties `((upstream-name . "ModelMetrics")))
4784 (build-system r-build-system)
4786 `(("r-rcpp" ,r-rcpp)))
4787 (home-page "http://cran.r-project.org/web/packages/ModelMetrics")
4788 (synopsis "Rapid calculation of model metrics")
4790 "Written in C++ using @code{Rcpp}, this package provides a collection of
4791 metrics for evaluating models.")
4792 (license license:gpl2+)))
4794 (define-public r-matrixmodels
4796 (name "r-matrixmodels")
4801 (uri (cran-uri "MatrixModels" version))
4804 "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
4805 (properties `((upstream-name . "MatrixModels")))
4806 (build-system r-build-system)
4808 `(("r-matrix" ,r-matrix)))
4809 (home-page "https://cran.r-project.org/web/packages/MatrixModels")
4810 (synopsis "Modelling with sparse and dense matrices")
4812 "This package models with sparse and dense matrix matrices,
4813 using modular prediction and response module classes.")
4814 (license license:gpl2+)))
4816 (define-public r-quantreg
4823 (uri (cran-uri "quantreg" version))
4826 "1dirmxa4cd05nb0yv0ga6ivw5hkr2zr2cb2lixl1nb6amqn024is"))))
4827 (build-system r-build-system)
4829 `(("gfortran" ,gfortran)))
4831 `(("r-matrix" ,r-matrix)
4832 ("r-matrixmodels" ,r-matrixmodels)
4833 ("r-sparsem" ,r-sparsem)))
4834 (home-page "http://www.r-project.org")
4835 (synopsis "Quantile regression")
4837 "This package provides an estimation and inference methods for models
4838 of conditional quantiles: linear and nonlinear parametric and non-parametric
4839 models for conditional quantiles of a univariate response and several methods
4840 for handling censored survival data. Portfolio selection methods based on
4841 expected shortfall risk are also included.")
4842 (license license:gpl2+)))
4844 (define-public r-nloptr
4851 (uri (cran-uri "nloptr" version))
4854 "1cypz91z28vhvwq2rzqjrbdc6a2lvfr2g16vid2sax618q6ai089"))))
4855 (build-system r-build-system)
4857 `(("pkg-config" ,pkg-config)))
4859 `(("nlopt" ,nlopt)))
4860 (home-page "http://cran.r-project.org/web/packages/nloptr")
4861 (synopsis "R interface to NLopt")
4863 "This package is interface to NLopt, a library for nonlinear
4864 optimization. NLopt is a library for nonlinear optimization, providing a
4865 common interface for a number of different free optimization routines
4866 available online as well as original implementations of various other
4868 (license license:lgpl3)))
4870 (define-public r-lme4
4877 (uri (cran-uri "lme4" version))
4880 "13j4a721rx0272pdxrz6nabjv56xb6srklq5w4z1abc82lyvda2z"))))
4881 (build-system r-build-system)
4883 `(("r-rcpp" ,r-rcpp)
4884 ("r-rcppeigen" ,r-rcppeigen)))
4886 `(("r-lattice" ,r-lattice)
4887 ("r-matrix" ,r-matrix)
4888 ("r-minqa" ,r-minqa)
4889 ("r-nloptr" ,r-nloptr)
4891 ("r-nlme" ,r-nlme)))
4892 (home-page "http://cran.r-project.org/web/packages/lme4")
4893 (synopsis "Linear mixed-effects models using eigen and S4")
4895 "This package provides fit linear and generalized linear mixed-effects
4896 models. The models and their components are represented using S4 classes and
4897 methods. The core computational algorithms are implemented using the Eigen
4898 C++ library for numerical linear algebra and RcppEigen glue.")
4899 (license license:gpl2+)))
4901 (define-public r-pbkrtest
4908 (uri (cran-uri "pbkrtest" version))
4911 "1si3bhi59xc51a0pgjjglccq3h4aljyhw2k1b8574s145fnh7fsw"))))
4912 (build-system r-build-system)
4914 `(("r-lme4" ,r-lme4)
4916 ("r-matrix" ,r-matrix)))
4917 (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
4918 (synopsis "Methods for linear mixed model comparison")
4920 "This package implements a parametric bootstrap test and a Kenward Roger
4921 modification of F-tests for linear mixed effects models and a parametric
4922 bootstrap test for generalized linear mixed models.")
4923 (license license:gpl2+)))
4925 (define-public r-car
4932 (uri (cran-uri "car" version))
4935 "1bm0ks9ga60z3izgq0d4kvirr9v4yf1820d1wznkihnbb55bc3m6"))))
4936 (build-system r-build-system)
4938 `(("r-mass" ,r-mass)
4941 ("r-pbkrtest" ,r-pbkrtest)
4942 ("r-quantreg" ,r-quantreg)))
4943 (home-page "https://r-forge.r-project.org/projects/car/")
4944 (synopsis "Companion to applied regression")
4946 "This package provides functions and datasets from book Companion
4947 to Applied regression, Second Edition, Sage, 2011.")
4948 (license license:gpl2+)))
4950 (define-public r-caret
4957 (uri (cran-uri "caret" version))
4960 "1w31xzpmj8p6r6s7s1vwnjxainq54bbh4cqm177ba0myv69hh8cc"))))
4961 (build-system r-build-system)
4964 ("r-foreach" ,r-foreach)
4965 ("r-ggplot2" ,r-ggplot2)
4966 ("r-lattice" ,r-lattice)
4967 ("r-modelmetrics" ,r-modelmetrics)
4970 ("r-reshape2" ,r-reshape2)))
4971 (home-page "https://github.com/topepo/caret")
4972 (synopsis "Classification and regression training")
4974 "This package provides misc functions for training and plotting
4975 classification and regression models.")
4976 (license license:gpl2+)))
4978 (define-public r-rcppprogress
4980 (name "r-rcppprogress")
4985 (uri (cran-uri "RcppProgress" version))
4988 "0796g11w7iv3ix1wfm3fh09qq7jki4r4cp1mjagq77igri3xrr9x"))))
4989 (properties `((upstream-name . "RcppProgress")))
4990 (build-system r-build-system)
4992 `(("r-rcpp" ,r-rcpp)))
4993 (home-page "https://github.com/kforner/rcpp_progress")
4994 (synopsis "Interruptible progress bar for C++ in R packages")
4996 "This package allows to display a progress bar in the R console for long running
4997 computations taking place in C++ code, and support for interrupting those computations
4998 even in multithreaded code, typically using OpenMP.")
4999 (license license:gpl3+)))
5001 (define-public r-mnormt
5008 (uri (cran-uri "mnormt" version))
5011 "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z"))))
5012 (build-system r-build-system)
5014 `(("gfortran" ,gfortran)))
5015 (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
5016 (synopsis "Multivariate normal and \"t\" distributions")
5018 "This package provides functions for computing the density and the
5019 distribution function of multivariate normal and \"t\" random variables, and
5020 for generating random vectors sampled from these distributions. Probabilities
5021 are computed via non-Monte Carlo methods.")
5022 (license license:gpl2+)))
5024 (define-public r-numderiv
5027 (version "2016.8-1")
5031 (uri (cran-uri "numDeriv" version))
5034 "07ni52rwiap4wilfz94w5mrqaxr59axxmgn57857ip4p6qkiss0v"))))
5035 (properties `((upstream-name . "numDeriv")))
5036 (build-system r-build-system)
5037 (home-page "https://cran.r-project.org/web/packages/numDeriv")
5038 (synopsis "Accurate numerical derivatives")
5040 "This package provides methods for calculating accurate numerical
5041 first and second order derivatives.")
5042 (license license:gpl2)))
5051 (uri (cran-uri "sn" version))
5054 "0fh7xjsfd2x8d9lbnss7raldh24b72b3pvcv7zqa1qprzg7zfr01"))))
5055 (build-system r-build-system)
5057 `(("r-mnormt" ,r-mnormt)
5058 ("r-numderiv" ,r-numderiv)))
5059 (home-page "http://azzalini.stat.unipd.it/SN")
5060 (synopsis "The skew-normal and skew-t distributions")
5062 "This packages provides functionalities to build and manipulate
5063 probability distributions of the skew-normal family and some related
5064 ones, notably the skew-t family, and provides related statistical
5065 methods for data fitting and diagnostics, in the univariate and the
5066 multivariate case.")
5067 (license license:gpl2+)))
5069 (define-public r-tclust
5076 (uri (cran-uri "tclust" version))
5079 "1mvqr280c6kwpg98byd0r1y0qf238xn2x15y8npqch6lpcszlb3x"))))
5080 (build-system r-build-system)
5082 `(("r-cluster" ,r-cluster)
5083 ("r-mclust" ,r-mclust)
5084 ("r-mvtnorm" ,r-mvtnorm)
5086 (home-page "http://cran.r-project.org/web/packages/tclust")
5087 (synopsis "Robust trimmed clustering")
5089 "This package implements different robust clustering
5090 algorithms (@code{tclust}) based on trimming and including some graphical
5091 diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
5092 (license license:gpl3)))
5094 (define-public r-ranger
5101 (uri (cran-uri "ranger" version))
5104 "1fdbm879wx3hlng8s4c4f8f2x5yxz57llakcqnpa0lymybidw3vz"))))
5105 (build-system r-build-system)
5107 `(("r-rcpp" ,r-rcpp)
5108 ("r-matrix" ,r-matrix)
5109 ("r-rcppeigen" ,r-rcppeigen)))
5110 (home-page "https://github.com/imbs-hl/ranger")
5111 (synopsis "Fast implementation of random forests")
5113 "This package provides a fast implementation of Random Forests,
5114 particularly suited for high dimensional data. Ensembles of classification,
5115 regression, survival and probability prediction trees are supported. Data from
5116 genome-wide association studies can be analyzed efficiently.")
5117 (license license:gpl3)))
5119 (define-public r-tsne
5126 (uri (cran-uri "tsne" version))
5129 "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
5130 (build-system r-build-system)
5131 (home-page "https://github.com/jdonaldson/rtsne/")
5132 (synopsis "t-Distributed Stochastic Neighbor Embedding for R")
5134 "This package provides a pure R implementation of the t-SNE algorithm.")
5135 (license license:gpl2+)))
5137 (define-public r-cairo
5144 (uri (cran-uri "Cairo" version))
5147 "1x1q99r3r978rlkkm5gixkv03p0mcr6k7ydcqdmisrwnmrn7p1ia"))))
5148 (properties `((upstream-name . "Cairo")))
5149 (build-system r-build-system)
5154 `(("pkg-config" ,pkg-config)))
5155 (home-page "http://www.rforge.net/Cairo/")
5156 (synopsis "R graphics device using Cairo graphics library")
5158 "This package provides a Cairo graphics device that can be use to
5159 create high-quality vector (PDF, PostScript and SVG) and bitmap
5160 output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11
5161 and Win32). Since it uses the same back-end for all output, copying
5162 across formats is WYSIWYG. Files are created without the dependence
5163 on X11 or other external programs. This device supports alpha
5164 channel (semi-transparent drawing) and resulting images can contain
5165 transparent and semi-transparent regions. It is ideal for use in
5166 server environments (file output) and as a replacement for other
5167 devices that don't have Cairo's capabilities such as alpha support or
5168 anti-aliasing. Backends are modular such that any subset of backends
5170 (license license:gpl2)))
5172 (define-public r-lubridate
5174 (name "r-lubridate")
5179 (uri (cran-uri "lubridate" version))
5182 "0ci6rwij9i1inn840m0mlh1nqgh6vm2lada9kdnjpcjp5kyfv1qs"))))
5183 (build-system r-build-system)
5185 `(("r-stringr" ,r-stringr)))
5187 "http://cran.r-project.org/web/packages/lubridate")
5188 (synopsis "Make dealing with dates a little easier")
5190 "This package provides functions to work with date-times and time-spans:
5191 fast and user friendly parsing of date-time data, extraction and updating of
5192 components of a date-time (years, months, days, hours, minutes, and seconds),
5193 algebraic manipulation on date-time and time-span objects. The 'lubridate'
5194 package has a consistent and memorable syntax that makes working with dates
5196 (license license:gpl2)))
5198 (define-public r-fdrtool
5205 (uri (cran-uri "fdrtool" version))
5208 "1h46frlk7d9f4qx0bg6p55nrm9wwwz2sv6d1nz7061wdfsm69yb5"))))
5209 (build-system r-build-system)
5210 (home-page "http://strimmerlab.org/software/fdrtool/")
5211 (synopsis "Estimation of false discovery rates and higher criticism")
5213 "This package provides tools to estimate both tail area-based false
5214 discovery rates (Fdr) as well as local false discovery rates (fdr) for a
5215 variety of null models (p-values, z-scores, correlation coefficients,
5216 t-scores). The proportion of null values and the parameters of the null
5217 distribution are adaptively estimated from the data. In addition, the package
5218 contains functions for non-parametric density estimation (Grenander
5219 estimator), for monotone regression (isotonic regression and antitonic
5220 regression with weights), for computing the greatest convex minorant (GCM) and
5221 the least concave majorant (LCM), for the half-normal and correlation
5222 distributions, and for computing empirical higher criticism (HC) scores and
5223 the corresponding decision threshold.")
5224 (license license:gpl3+)))