1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
4 ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
5 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
6 ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org>
7 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
8 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
9 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
10 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
11 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
12 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
13 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
14 ;;; Copyright © 2018, 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
15 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
16 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
17 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
18 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
19 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
20 ;;; Copyright © 2019, 2020, 2021 Wiktor Żelazny <wzelazny@vurv.cz>
21 ;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de>
22 ;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
23 ;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
24 ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
25 ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
26 ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
27 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
28 ;;; Copyright © 2020 Rafael Luque Leiva <rafael.luque@osoco.es>
29 ;;; Copyright © 2020, 2021 Lars-Dominik Braun <ldb@leibniz-psychology.org>
30 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
31 ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net>
32 ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
33 ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com>
34 ;;; Copyright © 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
35 ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com>
36 ;;; Copyright © 2021 Marcel Schilling <marcel.schilling@uni-luebeck.de>
37 ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
38 ;;; Copyright © 2022 Navid Afkhami <navid.afkhami@mdc-berlin.de>
39 ;;; Copyright © 2022 Greg Hogan <code@greghogan.com>
41 ;;; This file is part of GNU Guix.
43 ;;; GNU Guix is free software; you can redistribute it and/or modify it
44 ;;; under the terms of the GNU General Public License as published by
45 ;;; the Free Software Foundation; either version 3 of the License, or (at
46 ;;; your option) any later version.
48 ;;; GNU Guix is distributed in the hope that it will be useful, but
49 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
50 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
51 ;;; GNU General Public License for more details.
53 ;;; You should have received a copy of the GNU General Public License
54 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
56 (define-module (gnu packages cran)
57 #:use-module ((guix licenses) #:prefix license:)
58 #:use-module (guix packages)
59 #:use-module (guix download)
60 #:use-module (guix gexp)
61 #:use-module (guix git-download)
62 #:use-module (guix utils)
63 #:use-module (guix build-system gnu)
64 #:use-module (guix build-system r)
65 #:use-module (gnu packages)
66 #:use-module (gnu packages algebra)
67 #:use-module (gnu packages autotools)
68 #:use-module (gnu packages base)
69 #:use-module (gnu packages bioinformatics)
70 #:use-module (gnu packages c)
71 #:use-module (gnu packages compression)
72 #:use-module (gnu packages crypto)
73 #:use-module (gnu packages curl)
74 #:use-module (gnu packages databases)
75 #:use-module (gnu packages fontutils)
76 #:use-module (gnu packages fribidi)
77 #:use-module (gnu packages gcc)
78 #:use-module (gnu packages geo)
79 #:use-module (gnu packages ghostscript)
80 #:use-module (gnu packages gl)
81 #:use-module (gnu packages gnome)
82 #:use-module (gnu packages graph)
83 #:use-module (gnu packages gtk)
84 #:use-module (gnu packages haskell-xyz)
85 #:use-module (gnu packages icu4c)
86 #:use-module (gnu packages image)
87 #:use-module (gnu packages imagemagick)
88 #:use-module (gnu packages java)
89 #:use-module (gnu packages javascript)
90 #:use-module (gnu packages libevent)
91 #:use-module (gnu packages machine-learning)
92 #:use-module (gnu packages maths)
93 #:use-module (gnu packages mpi)
94 #:use-module (gnu packages multiprecision)
95 #:use-module (gnu packages networking)
96 #:use-module (gnu packages node)
97 #:use-module (gnu packages pcre)
98 #:use-module (gnu packages pdf)
99 #:use-module (gnu packages perl)
100 #:use-module (gnu packages pkg-config)
101 #:use-module (gnu packages pulseaudio) ;libsndfile
102 #:use-module (gnu packages protobuf)
103 #:use-module (gnu packages python)
104 #:use-module (gnu packages python-xyz)
105 #:use-module (gnu packages sqlite)
106 #:use-module (gnu packages statistics)
107 #:use-module (gnu packages tcl)
108 #:use-module (gnu packages tex)
109 #:use-module (gnu packages textutils)
110 #:use-module (gnu packages tls)
111 #:use-module (gnu packages uglifyjs)
112 #:use-module (gnu packages version-control)
113 #:use-module (gnu packages video)
114 #:use-module (gnu packages web)
115 #:use-module (gnu packages xml)
116 #:use-module (gnu packages xorg))
118 (define-public r-afpt
124 (uri (cran-uri "afpt" version))
127 "1z0r4r7prxbhadmkdg6345g0b5vq9dqyyw9hh3fpad9zkc7k6xbc"))))
128 (properties `((upstream-name . "afpt")))
129 (build-system r-build-system)
130 (native-inputs (list r-knitr))
131 (home-page "https://github.com/MarcoKlH/afpt-r/")
132 (synopsis "Tools for modelling of animal flight performance")
134 "This package allows estimation and modelling of flight costs in animal
135 (vertebrate) flight, implementing the aerodynamic power model. Flight
136 performance is estimated based on basic morphological measurements such as
137 body mass, wingspan and wing area. @code{Afpt} can be used to make
138 predictions on how animals should adjust their flight behaviour and wingbeat
139 kinematics to varying flight conditions.")
140 (license license:gpl3+)))
149 (uri (cran-uri "aod" version))
151 (base32 "0p2i536s0aa54rah1l465g77k2ldn6jm6s25y9vc06mk29xvx1cv"))))
152 (properties `((upstream-name . "aod")))
153 (build-system r-build-system)
154 (home-page "https://cran.r-project.org/package=aod")
155 (synopsis "Analysis of overdispersed data")
157 "This package provides a set of functions to analyze overdispersed counts
158 or proportions. Most of the methods are already available elsewhere but are
159 scattered in different packages. The proposed functions should be considered
160 as complements to more sophisticated methods such as @dfn{generalized
161 estimating equations} (GEE) or @dfn{generalized linear mixed effect
163 (license license:gpl2+)))
165 (define-public r-brio
172 (uri (cran-uri "brio" version))
175 "1inwzvlf6zj6gi47gd0byzqv02qajb3l475z8pjvx2b1hm0r1a7a"))))
176 (properties `((upstream-name . "brio")))
177 (build-system r-build-system)
178 (home-page "https://github.com/r-lib/brio")
179 (synopsis "Basic R input output")
181 "This package provides functions to handle basic input output. These
182 functions always read and write UTF-8 (8-bit Unicode Transformation Format)
183 files and provide more explicit control over line endings.")
184 (license license:expat)))
186 (define-public r-cachem
193 (uri (cran-uri "cachem" version))
196 "0r0q5w8lsxak46crnkbi739qzys90hlw7cqqqhv99xzkpkvm554s"))))
197 (properties `((upstream-name . "cachem")))
198 (build-system r-build-system)
200 (list r-fastmap r-rlang))
201 (home-page "https://cachem.r-lib.org/")
202 (synopsis "Cache R objects with automatic pruning")
204 "This package provides key-value stores with automatic pruning. Caches
205 can limit either their total size or the age of the oldest object (or both),
206 automatically pruning objects to maintain the constraints.")
207 (license license:expat)))
209 (define-public r-collections
211 (name "r-collections")
216 (uri (cran-uri "collections" version))
218 (base32 "053ig88pva78wxxwya3v7cz853k563dkpgxrf2xvd0l0d9fanxmz"))))
219 (properties `((upstream-name . "collections")))
220 (build-system r-build-system)
221 (home-page "https://github.com/randy3k/collections")
222 (synopsis "High performance container data types")
224 "This package provides high performance container data types such as
225 queues, stacks, deques, dicts and ordered dicts.")
226 (license license:expat)))
228 (define-public r-curry
235 (uri (cran-uri "curry" version))
238 "1ps9hvbnb02m0b8hlw4admwbziyjvswj08ldi2dk3ymnrpawcc29"))))
239 (properties `((upstream-name . "curry")))
240 (build-system r-build-system)
241 (home-page "https://github.com/thomasp85/curry")
242 (synopsis "Partial function application")
244 "Partial application is the process of reducing the arity of a function
245 by fixing one or more arguments, thus creating a new function lacking the
246 fixed arguments. The @code{curry} package provides three different ways of
247 performing partial function application by fixing arguments from either end of
248 the argument list (currying and tail currying) or by fixing multiple named
249 arguments (partial application). This package provides this functionality
250 through the @code{%<%}, @code{%-<%}, and @code{%><%} operators which allows
251 for a programming style comparable to modern functional languages. Compared
252 to other implementations such a @code{purrr::partial()} the operators in
253 @code{curry} composes functions with named arguments, aiding in autocomplete
255 (license license:gpl2+)))
257 (define-public r-datawizard
259 (name "r-datawizard")
264 (uri (cran-uri "datawizard" version))
267 "09lyh1awm2rplfzgwbdw4iy76mbaqwjd4hwlrsgvxj9pwdnjs4cx"))))
268 (properties `((upstream-name . "datawizard")))
269 (build-system r-build-system)
274 (home-page "https://easystats.github.io/datawizard/")
275 (synopsis "Easy data wrangling")
277 "This package provides a lightweight package to easily manipulate,
278 clean, transform, and prepare your data for analysis. It also forms the data
279 wrangling backend for the packages in the @code{easystats} ecosystem.")
280 (license license:gpl3)))
282 (define-public r-dbscan
289 (uri (cran-uri "dbscan" version))
291 (base32 "1h8x1v9kk5zmw5qd575cyr16yz8l226lsaq71n079l4i8crcrzg1"))))
292 (properties `((upstream-name . "dbscan")))
293 (build-system r-build-system)
294 (propagated-inputs (list r-rcpp))
295 (native-inputs (list r-knitr))
296 (home-page "https://github.com/mhahsler/dbscan")
297 (synopsis "Density-based spatial clustering of applications with noise")
299 "This package provides a fast reimplementation of several density-based
300 algorithms of the DBSCAN family. It includes the clustering algorithms DBSCAN
301 (density-based spatial clustering of applications with noise) and
302 @dfn{hierarchical DBSCAN} (HDBSCAN), the ordering algorithm @dfn{ordering
303 points to identify the clustering structure} (OPTICS), shared nearest neighbor
304 clustering, and the outlier detection algorithms @dfn{local outlier
305 factor} (LOF) and @dfn{global-local outlier score from hierarchies} (GLOSH).
306 The implementations use the kd-tree data structure for faster k-nearest
307 neighbor search. An R interface to fast kNN and fixed-radius NN search is
309 (license license:gpl2+)))
311 (define-public r-diffobj
318 (uri (cran-uri "diffobj" version))
321 "0q6gwd9pqh41f6j5p9jl92aji4p8kx9inffpha93d7jc3ndsfq6q"))))
322 (properties `((upstream-name . "diffobj")))
323 (build-system r-build-system)
324 (propagated-inputs (list r-crayon))
325 (native-inputs (list r-knitr))
326 (home-page "https://github.com/brodieG/diffobj")
327 (synopsis "Diffs for R objects")
329 "Generate a colorized diff of two R objects for an intuitive
330 visualization of their differences.")
331 (license license:gpl2+)))
333 (define-public r-dirichletreg
335 (name "r-dirichletreg")
340 (uri (cran-uri "DirichletReg" version))
342 (base32 "1ql5mwb7zb06y9j6inrlngq7c15as4j17wd8kc71fxs0a2jdj7xi"))))
343 (properties `((upstream-name . "DirichletReg")))
344 (build-system r-build-system)
345 (propagated-inputs (list r-formula r-maxlik))
346 (native-inputs (list r-knitr))
347 (home-page "https://cran.r-project.org/package=DirichletReg")
348 (synopsis "Dirichlet regression")
349 (description "This package implements Dirichlet regression models.")
350 (license license:gpl2+)))
352 (define-public r-dixontest
359 (uri (cran-uri "dixonTest" version))
361 (base32 "1a3yc30g5rbb0jhm2b0iir5i1dy4jyl67spkhx4yysg4snz131wv"))))
362 (properties `((upstream-name . "dixonTest")))
363 (build-system r-build-system)
364 (native-inputs (list gfortran))
365 (home-page "https://cran.r-project.org/package=dixonTest")
366 (synopsis "Dixon's ratio test for outlier detection")
368 "For outlier detection in small and normally distributed samples the ratio
369 test of Dixon (Q-test) can be used. Density, distribution function, quantile
370 function and random generation for Dixon's ratio statistics are provided as
371 wrapper functions. The core applies McBane's Fortran functions that use
372 Gaussian quadrature for a numerical solution.")
373 (license license:gpl3)))
375 (define-public r-emdist
382 (uri (cran-uri "emdist" version))
385 "05mv6xhm15b0mq9kzyiblkb14bdqmjrwl64ghdk66il0w8i7p6nh"))))
386 (properties `((upstream-name . "emdist")))
387 (build-system r-build-system)
388 (home-page "http://www.rforge.net/emd")
389 (synopsis "Earth mover's distance")
391 "This package provides tools to calculate the Earth Mover's
393 (license license:expat)))
395 (define-public r-googledrive
397 (name "r-googledrive")
402 (uri (cran-uri "googledrive" version))
405 "09jsiknzyfgxd0nzdr3wrrjw24allch2x74h96qg8vh8dad4cp30"))))
406 (properties `((upstream-name . "googledrive")))
407 (build-system r-build-system)
425 (home-page "https://googledrive.tidyverse.org")
426 (synopsis "Interface to Google Drive")
427 (description "This package lets you manage Google Drive files from R.")
428 (license license:expat)))
430 (define-public r-googlevis
437 (uri (cran-uri "googleVis" version))
439 (base32 "1s82xcs6zrlmnhay764bspzwvabfyi35nq6fwdrrk3v79q13c5jz"))))
440 (properties `((upstream-name . "googleVis")))
441 (build-system r-build-system)
442 (propagated-inputs (list r-jsonlite))
443 (native-inputs (list r-knitr))
444 (home-page "https://mages.github.io/googleVis/")
445 (synopsis "R interface to Google Charts")
447 "The @code{googleVis} package provides an interface between R and the Google
448 Charts API. Google Charts offer interactive charts which can be embedded into
449 web pages. The functions of the @code{googleVis} package allow the user to
450 visualise data stored in R data frames with Google Charts without uploading
451 the data to Google. The output of a @code{googleVis} function is HTML code
452 that contains the data and references to JavaScript functions hosted by
453 Google. @code{googleVis} makes use of the internal R HTTP server to display
454 the output locally.")
455 (license license:gpl2+)))
457 (define-public r-guix-install
459 (name "r-guix-install")
464 (uri (cran-uri "guix.install" version))
466 (base32 "0s3wb5781yc43c9zwrn7i87zcbrlx7xr0ms0v9hvgs7qsv02id9j"))))
467 (properties `((upstream-name . "guix.install")))
468 (build-system r-build-system)
469 (propagated-inputs (list r-runit))
470 (home-page "https://github.com/BIMSBbioinfo/guix.install")
471 (synopsis "Install R packages with GNU Guix")
473 "This R package provides a single procedure @code{guix.install()}, which
474 allows users to install R packages via Guix right from within their running R
475 session. If the requested R package does not exist in Guix at this time, the
476 package and all its missing dependencies will be imported recursively and the
477 generated package definitions will be written to @file{~/.Rguix/packages.scm}.
478 This record of imported packages can be used later to reproduce the
479 environment, and to add the packages in question to a proper Guix channel (or
480 Guix itself). @code{guix.install()} not only supports installing packages
481 from CRAN, but also from Bioconductor or even arbitrary git or mercurial
482 repositories, replacing the need for installation via @code{devtools}.")
483 (license license:gpl3+)))
492 (uri (cran-uri "ids" version))
495 "1s6ga94gds5ydr9f8qbjfgfpg2dvbnkcrlybqlb33hk3c0c2l8dn"))))
496 (properties `((upstream-name . "ids")))
497 (build-system r-build-system)
499 (list r-openssl r-uuid))
500 (native-inputs (list r-knitr))
501 (home-page "https://github.com/richfitz/ids")
502 (synopsis "Generate random identifiers")
504 "This package lets you generate random or human readable and
505 pronounceable identifiers.")
506 (license license:expat)))
508 (define-public r-googlesheets4
510 (name "r-googlesheets4")
515 (uri (cran-uri "googlesheets4" version))
518 "0yncqwv9l5knyrv88ys5gwcv44hl1j0mbklpins6v7f9m9v7s40a"))))
519 (properties `((upstream-name . "googlesheets4")))
520 (build-system r-build-system)
536 (home-page "https://github.com/tidyverse/googlesheets4")
537 (synopsis "Access Google Sheets using the Sheets API V4")
539 "This package lets you interact with Google Sheets through the
540 @url{https://developers.google.com/sheets/api,Sheets API v4}. This package
541 can read and write both the metadata and the cell data in a Sheet.")
542 (license license:expat)))
544 (define-public r-waldo
551 (uri (cran-uri "waldo" version))
554 "1aky28rn70l24s0sygl36267cf7hjzhchagsz26abfxwr7p8kvjp"))))
555 (properties `((upstream-name . "waldo")))
556 (build-system r-build-system)
565 (home-page "https://github.com/r-lib/waldo")
566 (synopsis "Find differences between R objects")
568 "Compare complex R objects and reveal the key differences. This package
569 was designed particularly for use in testing packages where being able to
570 quickly isolate key differences makes understanding test failures much
572 (license license:expat)))
574 (define-public r-rticles
581 (uri (cran-uri "rticles" version))
584 "1ipblw3rmkma22jl2hf1pyfm6l8k31zcmm3swmwii6k0x7khiav1"))))
585 (properties `((upstream-name . "rticles")))
586 (build-system r-build-system)
588 (list r-knitr r-rmarkdown r-tinytex r-xfun r-yaml))
589 (home-page "https://github.com/rstudio/rticles")
590 (synopsis "Article formats for R Markdown")
592 "This package provides a suite of custom R Markdown formats and templates
593 for authoring journal articles and conference submissions.")
594 (license license:gpl3)))
596 (define-public r-babelwhale
598 (name "r-babelwhale")
603 (uri (cran-uri "babelwhale" version))
605 (base32 "0ph825dwvr48fhamy1l5564linz7cj7b9sj511as77f1yqycv4a2"))))
606 (properties `((upstream-name . "babelwhale")))
607 (build-system r-build-system)
609 (list r-crayon r-dplyr r-dynutils r-processx r-purrr))
610 (home-page "https://github.com/dynverse/babelwhale")
611 (synopsis "Talking to Docker and Singularity containers")
613 "This package provides a unified interface to interact with Docker and
614 Singularity containers. You can execute a command inside a container, mount a
615 volume or copy a file.")
616 (license license:expat)))
618 (define-public r-benchmarkmedata
620 (name "r-benchmarkmedata")
624 (uri (cran-uri "benchmarkmeData" version))
627 "1n4vjkagqlm6kw2hilf4gjfcdjad0bcg652j9nl2ygbq3kdnh1vf"))))
628 (build-system r-build-system)
630 (list r-dplyr r-tibble))
631 (home-page "https://github.com/csgillespie/benchmarkme-data")
632 (synopsis "Data set for the @code{benchmarkme} package")
633 (description "This package contains the data set for the crowd-sourced
634 benchmarks from running the @code{benchmarkme} package.")
635 (license license:gpl2+)))
637 (define-public r-benchmarkme
639 (name "r-benchmarkme")
643 (uri (cran-uri "benchmarkme" version))
646 "0qaz8wy3n08k9lr8qljk5i8z8db18scbdc8m734aymd307h00w8x"))))
647 (build-system r-build-system)
651 (list r-benchmarkmedata
659 (home-page "https://csgillespie.github.io/benchmarkme/")
660 (synopsis "Crowd-sourced system benchmarks")
661 (description "This package provides functionality to benchmark your CPU
662 and compare against other CPUs. Also provides functions for obtaining system
663 specifications, such as RAM, CPU type, and R version.")
664 (license license:gpl2+)))
666 (define-public r-bezier
672 (uri (cran-uri "bezier" version))
675 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
676 (build-system r-build-system)
677 (home-page "https://cran.r-project.org/web/packages/bezier/")
678 (synopsis "Bezier curve and spline toolkit")
680 "This package is a toolkit for working with Bezier curves and splines.
681 The package provides functions for point generation, arc length estimation,
682 degree elevation and curve fitting.")
683 (license license:gpl2+)))
685 (define-public r-bwstest
692 (uri (cran-uri "BWStest" version))
694 (base32 "02amzlfprmw5pyis0dg0kg0x8xqh50a4vfdcxxmklrzik3b1vzzs"))))
695 (properties `((upstream-name . "BWStest")))
696 (build-system r-build-system)
697 (propagated-inputs (list r-memoise r-rcpp))
698 (home-page "https://github.com/shabbychef/BWStest")
699 (synopsis "Baumgartner Weiss Schindler Test of equal distributions")
701 "This package performs the Baumgartner-Weiss-Schindler two-sample test of
702 equal probability distributions (doi:10.2307/2533862). It also performs
703 similar rank-based tests for equal probability distributions due to Neuhauser
704 (doi:10.1080/10485250108832874) and Murakami
705 (doi:10.1080/00949655.2010.551516).")
706 (license license:lgpl3)))
715 (uri (cran-uri "V8" version))
718 "0hs7ajjw6y3q7mp7z00a9712y4cn6wgcnk5dbjbzlc6cfk4zsqkc"))))
719 (properties `((upstream-name . "V8")))
720 (build-system r-build-system)
723 (modify-phases %standard-phases
724 (add-after 'unpack 'find-v8
725 (lambda* (#:key inputs #:allow-other-keys)
726 (substitute* "configure"
728 (string-append "PKG_LIBS="
729 (assoc-ref inputs "libnode")
730 "/lib/libnode.so.64\n")))
731 (setenv "INCLUDE_DIR"
733 (assoc-ref inputs "libnode")
737 (assoc-ref inputs "libnode") "/lib")))))))
741 (list r-curl r-jsonlite r-rcpp))
744 (home-page "https://jeroen.cran.dev/V8")
745 (synopsis "Embedded JavaScript and WebAssembly engine for R")
747 "This package provides an R interface to V8: Google's JavaScript and
748 WebAssembly engine.")
749 (license license:expat)))
758 (uri (cran-uri "DOT" version))
761 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
762 (properties `((upstream-name . "DOT")))
763 (build-system r-build-system)
766 (home-page "http://haghish.com/dot")
767 (synopsis "Render and Export DOT Graphs in R")
769 "This package provides tools to render DOT diagram markup language in R
770 and also provides the possibility to export the graphs in PostScript and
771 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
772 programming packages such as @code{knitr} and @code{rmarkdown}.")
773 (license license:expat)))
775 (define-public r-carrier
782 (uri (cran-uri "carrier" version))
784 (base32 "0bqnwnnjqjk9q0lxq6kkz9s75ss10lfyyywyyi24m8wppxpw1vqc"))))
785 (properties `((upstream-name . "carrier")))
786 (build-system r-build-system)
788 (list r-pryr r-rlang))
789 (home-page "https://github.com/r-lib/carrier")
790 (synopsis "Isolate functions for remote execution")
792 "Sending functions to remote processes can be wasteful of resources
793 because they carry their environments with them. With this package, it is
794 easy to create functions that are isolated from their environment. These
795 isolated functions, also called crates, print to the console with their total
796 size and can be easily tested locally before being sent to a remote.")
797 (license license:gpl3)))
799 (define-public r-clipr
806 (uri (cran-uri "clipr" version))
809 "1s9vvv3cxnz8w11gsi8z9ddv9jzib5qf5qqxnwqrrv7vj8cr7hij"))))
810 (build-system r-build-system)
813 (home-page "https://github.com/mdlincoln/clipr")
814 (synopsis "Read and write from the system clipboard")
816 "This package provides simple utility functions to read from and write to
817 the system clipboards.")
818 (license license:gpl3)))
827 (uri (cran-uri "dlm" version))
829 (base32 "1aksm66sfa7ipl5xgs4j5giac7q2m744wjl40mva56xn6i674h4r"))))
830 (properties `((upstream-name . "dlm")))
831 (build-system r-build-system)
832 (home-page "https://cran.r-project.org/package=dlm")
833 (synopsis "Bayesian and Likelihood Analysis of Dynamic Linear Models")
835 "This package provides routines for Maximum likelihood, Kalman filtering
836 and smoothing, and Bayesian analysis of Normal linear State Space models, also
837 known as Dynamic Linear Models.")
838 (license license:gpl2+)))
846 (uri (cran-uri "zoo" version))
849 "0izd66dywq6qd62hdp64apncainrrb9mgmm19wf6a8jc03c858n9"))))
850 (build-system r-build-system)
853 (home-page "http://zoo.R-Forge.R-project.org/")
854 (synopsis "S3 infrastructure for regular and irregular time series")
855 (description "This package contains an S3 class with methods for totally
856 ordered indexed observations. It is particularly aimed at irregular time
857 series of numeric vectors/matrices and factors.")
858 (license license:gpl2+)))
860 (define-public r-fontawesome
862 (name "r-fontawesome")
867 (uri (cran-uri "fontawesome" version))
869 (base32 "0r6zb5175cr4ybqj6bl0mbhadwv9xjxaf32yjc0y76rw3d6vcbap"))))
870 (properties `((upstream-name . "fontawesome")))
871 (build-system r-build-system)
873 (list r-htmltools r-rlang))
874 (home-page "https://github.com/rstudio/fontawesome")
875 (synopsis "Easily work with Font Awesome icons")
877 "Easily and flexibly insert Font Awesome icons into R Markdown documents
878 and Shiny apps. These icons can be inserted into HTML content through inline
879 SVG tags or @code{i} tags. There is also a utility function for exporting
880 Font Awesome icons as PNG images for those situations where raster graphics
882 (license license:expat)))
884 (define-public r-fingerprint
886 (name "r-fingerprint")
891 (uri (cran-uri "fingerprint" version))
893 (base32 "04jcwkydjrs31pia6kq8z2n9s54im950q08hs2ay15xjxxkmb8ic"))))
894 (properties `((upstream-name . "fingerprint")))
895 (build-system r-build-system)
896 (home-page "https://cran.r-project.org/package=fingerprint")
897 (synopsis "Functions to Operate on Binary Fingerprint Data")
899 "This package provides functions to manipulate binary fingerprints of
900 arbitrary length. A fingerprint is represented by an object of S4 class
901 @code{fingerprint}. The bitwise logical functions in R are overridden so that
902 they can be used directly with @code{fingerprint} objects. A number of
903 distance metrics are also available. Fingerprints can be converted to
904 Euclidean vectors (i.e., points on the unit hypersphere) and can also be
905 folded. Arbitrary fingerprint formats can be handled via line handlers.
906 Currently handlers are provided for CDK, MOE and BCI fingerprint data.")
907 ;; Any version of the GPL
908 (license (list license:gpl2+ license:gpl3+))))
910 (define-public r-fpeek
917 (uri (cran-uri "fpeek" version))
919 (base32 "0kv46g21ndxchg3q8ynq7hjjkh6i2zlc21axn5y1jjzigrw047ii"))))
920 (properties `((upstream-name . "fpeek")))
921 (build-system r-build-system)
922 (propagated-inputs (list r-rcpp))
923 (home-page "https://github.com/davidgohel/fpeek")
924 (synopsis "Check text files content at a glance")
926 "This package provides tools to help working with text files. It can
927 return the number of lines; print the first and last lines; convert encoding.
928 Operations are made without reading the entire file before starting, resulting
929 in good performances with large files.")
930 (license license:expat)))
932 (define-public r-ggalluvial
934 (name "r-ggalluvial")
938 (uri (cran-uri "ggalluvial" version))
941 "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3"))))
942 (properties `((upstream-name . "ggalluvial")))
943 (build-system r-build-system)
953 (home-page "http://corybrunson.github.io/ggalluvial/")
954 (synopsis "Alluvial plots for ggplot2")
955 (description "This package provides alluvial plots for @code{ggplot2}.
956 Alluvial plots use variable-width ribbons and stacked bar plots to represent
957 multi-dimensional or repeated-measures data with categorical or ordinal
959 (license license:gpl3)))
961 (define-public r-ggpp
968 (uri (cran-uri "ggpp" version))
971 "0wcaczxjav5yg8h2197cf288mqk13p3iq675q0x0di9g8lnblvk1"))))
972 (properties `((upstream-name . "ggpp")))
973 (build-system r-build-system)
991 (home-page "https://docs.r4photobiology.info/ggpp/")
992 (synopsis "Grammar extensions to ggplot2")
994 "This package contains extensions to ggplot2.
997 @item Geomas: @code{geom_table}, @code{geom_plot} and @code{geom_grob} add
998 insets to plots using native data coordinates, while @code{geom_table_npc},
999 @code{geom_plot_npc} and @code{geom_grob_npc} do the same using @code{npc}
1000 coordinates through new aesthetics @code{npcx} and @code{npcy}.
1001 @item Statistics: select observations based on 2D density.
1002 @item Positions: radial nudging away from a center point and nudging away from
1006 (license license:gpl2+)))
1008 (define-public r-lmds
1015 (uri (cran-uri "lmds" version))
1017 (base32 "130azb0nc2wwxv0qi8v5s4rd02p9lc92zwn634pv7b8awbw81i65"))))
1018 (properties `((upstream-name . "lmds")))
1019 (build-system r-build-system)
1021 (list r-assertthat r-dynutils r-irlba r-matrix))
1022 (home-page "https://github.com/dynverse/lmds")
1023 (synopsis "Landmark multi-dimensional scaling")
1025 "This package provides a fast dimensionality reduction method scalable
1026 to large numbers of samples. @dfn{Landmark Multi-Dimensional Scaling} (LMDS)
1027 is an extension of classical Torgerson MDS, but rather than calculating a
1028 complete distance matrix between all pairs of samples, only the distances
1029 between a set of landmarks and the samples are calculated.")
1030 (license license:gpl3)))
1032 (define-public r-lmodel2
1039 (uri (cran-uri "lmodel2" version))
1041 (base32 "1fiin2nkffbihz1s8ixmw9lgf8mn3j9krr8iiflizk10mdv54hnb"))))
1042 (properties `((upstream-name . "lmodel2")))
1043 (build-system r-build-system)
1044 (home-page "https://cran.r-project.org/package=lmodel2")
1045 (synopsis "Model II regression")
1047 "This package computes model II simple linear regression using
1048 @dfn{ordinary least squares} (OLS), @dfn{major axis} (MA), @dfn{standard major
1049 axis} (SMA), and @dfn{ranged major axis} (RMA).")
1050 (license license:gpl2)))
1052 (define-public r-ggpmisc
1058 (uri (cran-uri "ggpmisc" version))
1061 "1iq39rx4nj1lf37hnj4df0c7gbk9374d0mzcnhdr7aqpxaxgs3ys"))))
1062 (build-system r-build-system)
1080 (home-page "https://www.r4photobiology.info/")
1081 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
1082 (description "This package provides extensions to @code{ggplot2},
1083 respecting the grammar of its graphics paradigm.")
1084 (license license:gpl2+)))
1086 (define-public r-ggside
1092 (uri (cran-uri "ggside" version))
1095 "1x505zizv7hf65pxp9j5v92c3bchhxh9dsrkk1m55kwqqnsl5nza"))))
1096 (properties `((upstream-name . "ggside")))
1097 (build-system r-build-system)
1098 (propagated-inputs (list r-ggplot2 r-glue r-gtable r-rlang r-scales))
1099 (native-inputs (list r-knitr))
1100 (home-page "https://cran.r-project.org/package=ggside")
1101 (synopsis "Side grammar graphics that extends @code{ggplot2}")
1103 "The grammar of graphics as shown in @code{ggplot2} has provided an
1104 expressive API for users to build plots. This package @{ggside} extends
1105 @code{ggplot2} by allowing users to add graphical information about one of the
1106 main panel's axis using a familiar @code{ggplot2} style API with tidy data.
1107 This package is particularly useful for visualizing metadata on a discrete
1108 axis, or summary graphics on a continuous axis such as a boxplot or a density
1110 (license license:expat)))
1112 (define-public r-gprofiler
1114 (name "r-gprofiler")
1119 (uri (cran-uri "gProfileR" version))
1122 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
1123 (properties `((upstream-name . "gProfileR")))
1124 (build-system r-build-system)
1126 (list r-plyr r-rcurl))
1127 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
1128 (synopsis "Interface to the g:Profiler toolkit")
1130 "This package provides tools for functional enrichment analysis,
1131 gene identifier conversion and mapping homologous genes across related
1132 organisms via the @code{g:Profiler} toolkit.")
1133 (license license:gpl2+)))
1135 (define-public r-gprofiler2
1137 (name "r-gprofiler2")
1142 (uri (cran-uri "gprofiler2" version))
1145 "0r0h34b35xzgd9rh55yndn0anxy0z45zdlqa6qfmpn91b6v1bb1g"))))
1146 (properties `((upstream-name . "gprofiler2")))
1147 (build-system r-build-system)
1158 (native-inputs (list r-knitr))
1159 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
1160 (synopsis "Interface to the g:Profiler toolset")
1162 "This package provides a toolset for functional enrichment analysis and
1163 visualization, gene/protein/SNP identifier conversion and mapping orthologous
1164 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
1168 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
1170 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
1172 @item @code{g:Orth}, orthology search across species;
1173 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
1174 genes and variant effects.
1177 This package is an R interface corresponding to the 2019 update of
1178 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
1180 (license license:gpl2+)))
1182 (define-public r-oenb
1189 (uri (cran-uri "oenb" version))
1192 "1jgxw7ycx2lcdzglg9nix8k08fs4r6i5jdsjzrd6w1dg6smsinl5"))))
1193 (properties `((upstream-name . "oenb")))
1194 (build-system r-build-system)
1196 (list r-dplyr r-xml))
1197 (native-inputs (list r-knitr))
1198 (home-page "https://github.com/franzmohr/oenb")
1199 (synopsis "Tools for the OeNB Data Web Service")
1201 "Tools to access data from the data web service of the
1202 @acronym{OeNB, Oesterreichische Nationalbank},
1203 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
1204 (license license:gpl2+)))
1206 (define-public r-orgmassspecr
1208 (name "r-orgmassspecr")
1212 (uri (cran-uri "OrgMassSpecR" version))
1215 "1dx9d8rb1dfqyhyc26zhfnxiv3rz2ikvs2mwqnsrq3lsjs9dvyc8"))))
1216 (properties `((upstream-name . "OrgMassSpecR")))
1217 (build-system r-build-system)
1218 (native-inputs (list r-knitr))
1219 (home-page "http://OrgMassSpec.github.io/")
1220 (synopsis "Organic or biological mass spectrometry data analysis")
1222 "This package @code{OrgMassSpecR} is an extension of the @code{R}
1223 statistical computing language. It contains functions to assist with organic
1224 or biological mass spectrometry data analysis. Mass spectral libraries are
1225 available as companion packages.")
1226 (license license:bsd-2)))
1228 (define-public r-scales
1235 (uri (cran-uri "scales" version))
1237 (base32 "1pq2rrix6a5gsi8xw38viiydp1bsxxmcmyy7dv9q8gkb1qj50p8q"))))
1238 (build-system r-build-system)
1248 (home-page "https://github.com/hadley/scales")
1249 (synopsis "Scale functions for visualization")
1251 "This package provides graphical scales that map data to aesthetics, and
1252 provides methods for automatically determining breaks and labels for axes and
1254 (license license:expat)))
1256 (define-public r-pacman
1262 (uri (cran-uri "pacman" version))
1265 "0z7gngd6h83cpjhq1vg75wvzhdjbgjh7gj5d4zvvi9gd2lmagjcy"))))
1266 (build-system r-build-system)
1269 (home-page "https://github.com/trinker/pacman")
1270 (synopsis "Package Management Tool")
1271 (description "This package provides tools to more conveniently perform
1272 tasks associated with add-on packages. @code{pacman} conveniently wraps
1273 library and package related functions and names them in an intuitive and
1274 consistent fashion. It seeks to combine functionality from lower level
1275 functions which can speed up workflow.")
1276 (license license:gpl2)))
1278 (define-public r-paralleldist
1280 (name "r-paralleldist")
1285 (uri (cran-uri "parallelDist" version))
1287 (base32 "01ly4hxwa64a0ya5gla8rvv72s9mcknsfznivjkh937pbjwb7iih"))))
1288 (properties `((upstream-name . "parallelDist")))
1289 (build-system r-build-system)
1290 (propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppparallel))
1291 (home-page "https://github.com/alexeckert/parallelDist")
1292 (synopsis "Parallel Distance Matrix Computation using multiple threads")
1294 "This package provides a fast parallelized alternative to R's native
1295 @code{dist} function to calculate distance matrices for continuous, binary,
1296 and multi-dimensional input matrices, which supports a broad variety of
1297 predefined distance functions from other R packages, as well as user- defined
1298 functions written in C++. For ease of use, the @code{parDist} function
1299 extends the signature of the @code{dist} function and uses the same parameter
1300 naming conventions as distance methods of existing R packages.")
1301 (license license:gpl2+)))
1303 (define-public r-pheatmap
1310 (uri (cran-uri "pheatmap" version))
1313 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
1314 (build-system r-build-system)
1316 (list r-gtable r-rcolorbrewer r-scales))
1317 (home-page "https://cran.r-project.org/web/packages/pheatmap")
1318 (synopsis "Pretty heatmaps")
1320 "This package provides an implementation of heatmaps that offers more
1321 control over dimensions and appearance.")
1322 (license license:gpl2+)))
1324 (define-public r-pnwcolors
1326 (name "r-pnwcolors")
1331 (uri (cran-uri "PNWColors" version))
1334 "1phplnclkficfv8s6wsyrckk4ixzbayiy5iix6dddg40485l9nyj"))))
1335 (properties `((upstream-name . "PNWColors")))
1336 (build-system r-build-system)
1337 (home-page "https://github.com/jakelawlor/PNWColors")
1338 (synopsis "Color palettes for data visualizations")
1340 "This package provides color palettes. They are checked for colorblind
1341 accessibility from hue, saturation, and lightness value scaling using the
1342 Chroma.js Color Palette Helper. See @url{https://gka.github.io/palettes}.")
1343 (license license:cc0)))
1345 (define-public r-plotfunctions
1347 (name "r-plotfunctions")
1352 (uri (cran-uri "plotfunctions" version))
1354 (base32 "0asmxw8283fpvl83h478j5nyg59xqifqaa8f2f6l199gvvswhhg2"))))
1355 (properties `((upstream-name . "plotfunctions")))
1356 (build-system r-build-system)
1357 (native-inputs (list r-knitr))
1358 (home-page "https://jacolienvanrij.com/tutorials.html")
1359 (synopsis "Various functions to facilitate visualization of data and analysis")
1361 "When analyzing data, plots are a helpful tool for visualizing data and
1362 interpreting statistical models. This package provides a set of simple tools
1363 for building plots incrementally, starting with an empty plot region, and
1364 adding bars, data points, regression lines, error bars, gradient legends,
1365 density distributions in the margins, and even pictures. The package builds
1366 further on R graphics by simply combining functions and settings in order to
1367 reduce the amount of code to produce for the user. As a result, the package
1368 does not use formula input or special syntax, but can be used in combination
1369 with default R plot functions.")
1370 (license license:gpl2+)))
1372 (define-public r-polychrome
1374 (name "r-polychrome")
1379 (uri (cran-uri "Polychrome" version))
1381 (base32 "0hyi02m2jpdhk1ky6ihz6dv5pwqwjwk4csjim2qr8ywx8midmrvg"))))
1382 (properties `((upstream-name . "Polychrome")))
1383 (build-system r-build-system)
1385 (list r-colorspace r-scatterplot3d))
1388 (home-page "http://oompa.r-forge.r-project.org/")
1389 (synopsis "Qualitative palettes with many colors")
1391 "This package provides tools for creating, viewing, and assessing
1392 qualitative palettes with many (20-30 or more) colors. See Coombes and
1393 colleagues (2019) @url{https://doi:10.18637/jss.v090.c01}.")
1394 (license license:asl2.0)))
1396 (define-public r-ecp
1402 (uri (cran-uri "ecp" version))
1405 "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8"))))
1406 (build-system r-build-system)
1409 (home-page "https://cran.r-project.org/web/packages/ecp/")
1410 (synopsis "Multiple change-point analysis of multivariate data")
1412 "This package implements various procedures for finding multiple
1413 change-points. Two methods make use of dynamic programming and pruning, with
1414 no distributional assumptions other than the existence of certain absolute
1415 moments in one method. Hierarchical and exact search methods are included.
1416 All methods return the set of estimated change-points as well as other summary
1418 (license license:gpl2+)))
1420 (define-public r-ellipsis
1427 (uri (cran-uri "ellipsis" version))
1430 "0n0mm9jngklv7j9wa64jdji035z0smmnsp2dfwcz9isrxgjnc0m9"))))
1431 (build-system r-build-system)
1434 (home-page "https://github.com/hadley/ellipsis")
1435 (synopsis "Tools for working with additional arguments")
1437 "In S3 generics, it's useful to take @code{...} so that methods can have
1438 additional arguments. But this flexibility comes at a cost: misspelled
1439 arguments will be silently ignored. The @code{ellipsis} package is an
1440 experiment that allows a generic to warn if any arguments passed in @code{...}
1442 (license license:gpl3)))
1451 (uri (cran-uri "GA" version))
1453 (base32 "135z03lnbj44jihnk6dii5a684jmc666ncpdwyyi910vl4sccib2"))))
1454 (properties `((upstream-name . "GA")))
1455 (build-system r-build-system)
1465 (home-page "https://luca-scr.github.io/GA/")
1466 (synopsis "Genetic algorithms for stochastic optimisation")
1468 "Flexible general-purpose toolbox implementing genetic algorithms (GAs)
1469 for stochastic optimisation. Binary, real-valued, and permutation
1470 representations are available to optimize a fitness function, i.e., a function
1471 provided by users depending on their objective function. Several genetic
1472 operators are available and can be combined to explore the best settings for
1473 the current task. Furthermore, users can define new genetic operators and
1474 easily evaluate their performances. Local search using general-purpose
1475 optimisation algorithms can be applied stochastically to exploit interesting
1476 regions. GAs can be run sequentially or in parallel, using an explicit
1477 master-slave parallelisation or a coarse-grain islands approach.")
1478 (license license:gpl2+)))
1480 (define-public r-grr
1487 (uri (cran-uri "grr" version))
1490 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
1491 (build-system r-build-system)
1492 (home-page "https://cran.r-project.org/web/packages/grr")
1493 (synopsis "Alternative implementations of base R functions")
1495 "This package provides alternative implementations of some base R
1496 functions, including @code{sort}, @code{order}, and @code{match}. The
1497 functions are simplified but can be faster or have other advantages.")
1498 (license license:gpl3)))
1500 (define-public r-matrix-utils
1502 (name "r-matrix-utils")
1507 (uri (cran-uri "Matrix.utils" version))
1510 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
1511 (properties `((upstream-name . "Matrix.utils")))
1512 (build-system r-build-system)
1514 (list r-grr r-matrix))
1515 (home-page "https://github.com/cvarrichio/Matrix.utils")
1517 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
1519 "This package implements data manipulation methods such as @code{cast},
1520 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
1522 (license license:gpl3)))
1524 (define-public r-mboost
1530 (uri (cran-uri "mboost" version))
1533 "01ln0vxbbx1fq77q17sx61si82lhfibbchsnf2yw9032cn8wnhh2"))))
1534 (build-system r-build-system)
1543 (home-page "https://github.com/boost-R/mboost")
1544 (synopsis "Model-based boosting")
1546 "This package provides a functional gradient descent algorithm (boosting)
1547 for optimizing general risk functions utilizing component-wise (penalised)
1548 least squares estimates or regression trees as base-learners for fitting
1549 generalized linear, additive and interaction models to potentially
1550 high-dimensional data.")
1551 (license license:gpl2)))
1553 (define-public r-shadowtext
1555 (name "r-shadowtext")
1559 (uri (cran-uri "shadowtext" version))
1562 "0zdfidrcnmxmfhngv86ppxrjmpmz9kl78l4yfah2lc5vgmrlwg15"))))
1563 (properties `((upstream-name . "shadowtext")))
1564 (build-system r-build-system)
1566 (list r-ggplot2 r-scales))
1569 (home-page "https://github.com/GuangchuangYu/shadowtext/")
1570 (synopsis "Shadow text grob and layer")
1571 (description "This package implements @code{shadowtextGrob()} for
1572 @code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}.
1573 These functions draw text grob with background shadow.")
1574 (license license:artistic2.0)))
1576 (define-public r-sys
1583 (uri (cran-uri "sys" version))
1586 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p"))))
1587 (build-system r-build-system)
1588 (home-page "https://github.com/jeroen/sys")
1589 (synopsis "Powerful and reliable tools for running system commands in R")
1591 "This package provides drop-in replacements for the base @code{system2()}
1592 function with fine control and consistent behavior across platforms. It
1593 supports clean interruption, timeout, background tasks, and streaming STDIN /
1594 STDOUT / STDERR over binary or text connections. The package also provides
1595 functions for evaluating expressions inside a temporary fork. Such
1596 evaluations have no side effects on the main R process, and support reliable
1597 interrupts and timeouts. This provides the basis for a sandboxing
1599 (license license:expat)))
1601 (define-public r-ashr
1607 (uri (cran-uri "ashr" version))
1610 "177xs3apnc6yy6737qqv4z8snf0hkpbghab63hrplbyb9wfssfga"))))
1611 (properties `((upstream-name . "ashr")))
1612 (build-system r-build-system)
1623 (home-page "https://github.com/stephens999/ashr")
1624 (synopsis "Methods for adaptive shrinkage, using empirical bayes")
1625 (description "This package implements an empirical Bayes approach for
1626 large-scale hypothesis testing and false discovery rate estimation.")
1627 (license license:gpl3+)))
1629 (define-public r-askpass
1636 (uri (cran-uri "askpass" version))
1639 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
1640 (build-system r-build-system)
1641 (propagated-inputs (list r-sys))
1642 (home-page "https://github.com/jeroen/askpass")
1643 (synopsis "Safe password entry for R")
1645 "This package provides cross-platform utilities for prompting the user
1646 for credentials or a passphrase, for example to authenticate with a server or
1647 read a protected key.")
1648 (license license:expat)))
1650 (define-public r-astsa
1657 (uri (cran-uri "astsa" version))
1659 (base32 "0mllsq0xdqkviyvs77lq565r1vznsj1qp9cnlj5p48k9v76d7arp"))))
1660 (properties `((upstream-name . "astsa")))
1661 (build-system r-build-system)
1662 (home-page "https://github.com/nickpoison/astsa/")
1663 (synopsis "Applied statistical time series analysis")
1665 "This package provides data sets and scripts to accompany Time Series
1666 Analysis and Its Applications: With R Examples (4th ed), by R.H. Shumway and
1667 D.S. Stoffer. Springer Texts in Statistics, 2017,
1668 @url{https://doi.org/10.1007/978-3-319-52452-8}, and Time Series: A Data
1669 Analysis Approach Using R. Chapman-Hall, 2019,
1670 @url{https://doi.org/10.1201/9780429273285}.")
1671 (license license:gpl3)))
1673 (define-public r-vegan
1680 (uri (cran-uri "vegan" version))
1683 "0nf0ny6jzfy135xiygzzkr0y55y8g27hrbk8c869plarr48d2xxb"))))
1684 (build-system r-build-system)
1686 (list r-knitr ; needed for vignettes
1689 (list r-cluster r-lattice r-mass r-mgcv r-permute))
1690 (home-page "https://cran.r-project.org/web/packages/vegan")
1691 (synopsis "Functions for community ecology")
1693 "The vegan package provides tools for descriptive community ecology. It
1694 has most basic functions of diversity analysis, community ordination and
1695 dissimilarity analysis. Most of its multivariate tools can be used for other
1696 data types as well.")
1697 (license license:gpl2+)))
1699 (define-public r-tidyverse
1701 (name "r-tidyverse")
1706 (uri (cran-uri "tidyverse" version))
1709 "0ck6xmsw5p168jmw2fqv79fzfnw5jckfra7mfii261j6kl89bkw3"))))
1710 (build-system r-build-system)
1743 (home-page "https://tidyverse.tidyverse.org")
1744 (synopsis "Install and load packages from the \"Tidyverse\"")
1746 "The @code{tidyverse} is a set of packages that work in harmony because
1747 they share common data representations and API design. This package is
1748 designed to make it easy to install and load multiple tidyverse packages in a
1750 (license license:gpl3)))
1752 (define-public r-rvest
1759 (uri (cran-uri "rvest" version))
1761 (base32 "1905vxgnj3q09l1wf6rwxpbpydznp06nbkrclnc05j2415z4gfw9"))))
1762 (build-system r-build-system)
1773 (home-page "https://github.com/hadley/rvest")
1774 (synopsis "Simple web scraping for R")
1776 "@code{r-rvest} helps you scrape information from web pages. It is
1777 designed to work with @code{magrittr} to make it easy to express common web
1778 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
1779 (license license:gpl3)))
1781 (define-public r-selectr
1788 (uri (cran-uri "selectr" version))
1790 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
1791 (build-system r-build-system)
1793 (list r-stringr r-r6))
1794 (home-page "https://sjp.co.nz/projects/selectr/")
1795 (synopsis "Translate CSS selectors to XPath expressions")
1797 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
1798 expression. This allows you to use CSS selectors when working with the XML
1799 package as it can only evaluate XPath expressions. Also provided are
1800 convenience functions useful for using CSS selectors on XML nodes. This
1801 package is a port of the Python package @code{cssselect}.")
1802 (license license:bsd-3)))
1804 (define-public r-reprex
1811 (uri (cran-uri "reprex" version))
1814 "09k4rasp7mz6n796dsklcbc5l7prljiznrm7fra16qybr9kqcv8f"))))
1815 (build-system r-build-system)
1829 (home-page "https://github.com/tidyverse/reprex")
1830 (synopsis "Prepare reproducible R code examples for sharing")
1832 "This package provides a convenience wrapper that uses the
1833 @code{rmarkdown} package to render small snippets of code to target formats
1834 that include both code and output. The goal is to encourage the sharing of
1835 small, reproducible, and runnable examples on code-oriented websites or email.
1836 @code{reprex} also extracts clean, runnable R code from various common formats,
1837 such as copy/paste from an R session.")
1838 (license license:expat)))
1840 (define-public r-reordercluster
1842 (name "r-reordercluster")
1846 (uri (cran-uri "ReorderCluster" version))
1849 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
1850 (build-system r-build-system)
1852 (list r-gplots r-rcpp))
1853 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
1854 (synopsis "Reordering the dendrogram according to the class labels")
1855 (description "This package provides tools for performing the leaf reordering
1856 for the dendrogram that preserves the hierarchical clustering result and at the
1857 same time tries to group instances from the same class together.")
1858 (license license:gpl3+)))
1860 (define-public r-callr
1867 (uri (cran-uri "callr" version))
1870 "02inaf3c7b0hikii7p2zwaphrq5myv4in92d9jxd1ilmhla5awnn"))))
1871 (build-system r-build-system)
1873 (list r-r6 r-processx))
1874 (home-page "https://github.com/r-lib/callr#readme")
1875 (synopsis "Call R from R")
1877 "It is sometimes useful to perform a computation in a separate R process,
1878 without affecting the current R process at all. This package does exactly
1880 (license license:expat)))
1882 (define-public r-depmixs4
1888 (uri (cran-uri "depmixS4" version))
1891 "1pacvhw5m4fsk3ysbal50fdqbvlaz8ywyqp6bn1wh42wipqbb2i8"))))
1893 (list r-nnet r-nlme r-mass r-rsolnp))
1894 (build-system r-build-system)
1895 (home-page "https://cran.r-project.org/web/packages/depmixS4/")
1896 (synopsis "Dependent Mixture Models")
1897 (description "This package fits latent (hidden) Markov models on mixed
1898 categorical and continuous (time series) data, otherwise known as dependent
1900 (license license:gpl2+)))
1902 (define-public r-readxl
1909 (uri (cran-uri "readxl" version))
1912 "1xwi4k5si48hwkgfc59icfmp9dzlvfri59k5fsgn96zp9713k4mb"))))
1913 (build-system r-build-system)
1915 (list r-cellranger r-cpp11 r-progress r-tibble))
1918 (home-page "https://readxl.tidyverse.org")
1919 (synopsis "Read Excel files")
1921 "This package lets you import Excel files into R. It supports
1922 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
1923 the embedded @code{RapidXML} C++ library.")
1924 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
1925 ;; 'rapidxml' which is Boost.
1926 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
1928 (define-public r-model4you
1930 (name "r-model4you")
1934 (uri (cran-uri "model4you" version))
1937 "0pni9v3nradvy8sp2m07903vc7z610xrh426lf19dxss12kgrfi8"))))
1938 (build-system r-build-system)
1946 (home-page "https://cran.r-project.org/web/packages/model4you/")
1947 (synopsis "Stratified and personalised models based on trees and forests")
1949 "This package provides procedures for model-based trees for subgroup
1950 analyses in clinical trials and model-based forests for the estimation and
1951 prediction of personalised treatment effects. Currently partitioning of linear
1952 models, @code{lm()}, generalised linear models, @code{glm()}, and
1953 Weibull models, @code{survreg()}, are supported. Advanced plotting functionality is
1954 supported for the trees and a test for parameter heterogeneity is provided for
1955 the personalised models.")
1956 (license license:gpl2+)))
1958 (define-public r-modelr
1965 (uri (cran-uri "modelr" version))
1968 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
1969 (build-system r-build-system)
1979 (home-page "https://github.com/tidyverse/modelr")
1980 (synopsis "Helper functions for modelling in pipelines")
1982 "Functions for modelling that help you seamlessly integrate modelling
1983 into a pipeline of data manipulation and visualisation.")
1984 (license license:gpl3)))
1986 (define-public r-hmm
1992 (uri (cran-uri "HMM" version))
1995 "03b548bnwqpnd7zypb4gvy9chyi5li2hp99a9vrh4qszxg2ihas7"))))
1996 (properties `((upstream-name . "HMM")))
1997 (build-system r-build-system)
1998 (home-page "https://cran.r-project.org/web/packages/HMM/")
1999 (synopsis "Hidden Markov Models")
2000 (description "This package provides an easy to use library to setup, apply
2001 and make inference with discrete time and discrete space hidden Markov
2003 (license license:gpl2+)))
2005 (define-public r-hiddenmarkov
2007 (name "r-hiddenmarkov")
2011 (uri (cran-uri "HiddenMarkov" version))
2014 "05dm3nl0ffsz2ziw3bz5bivyxk7r5bxs8xhky3hz660qaqzd51ki"))))
2015 (build-system r-build-system)
2018 (home-page "https://cran.r-project.org/web/packages/HiddenMarkov/")
2019 (synopsis "Hidden markov models for R")
2020 (description "This package contains functions for the analysis of Discrete
2021 Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated
2022 Poisson Process. It includes functions for simulation, parameter estimation,
2023 and the Viterbi algorithm. The algorithms are based of those of Walter
2025 (license license:gpl2+)))
2027 (define-public r-httpuv
2033 (uri (cran-uri "httpuv" version))
2036 "0mlilxh2mlrsbbrncla2rg02crr8nnajv649d8whx7ayr8lkdxpm"))
2037 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
2038 ;; only contains fixes for building on Solaris.
2039 (patches (search-patches "r-httpuv-1.5.5-unvendor-libuv.patch"))
2040 (modules '((guix build utils)))
2041 ;; Cannot unbundle http-parser, because it contains local
2044 '(delete-file-recursively "src/libuv"))))
2045 (build-system r-build-system)
2048 (modify-phases %standard-phases
2049 (add-after 'unpack 'unbundle-libuv
2050 (lambda* (#:key outputs #:allow-other-keys)
2051 (substitute* (find-files "src" "\\.cpp$|\\.h$")
2052 (("\"libuv/include/uv\\.h\"")
2054 ;; Fix https://github.com/rstudio/httpuv/issues/282
2055 (substitute* "src/http.cpp"
2056 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
2057 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);")))))))
2061 (list r-later r-promises r-r6 r-rcpp))
2062 (home-page "https://github.com/rstudio/httpuv")
2063 (synopsis "HTTP and WebSocket server library for R")
2065 "The httpuv package provides low-level socket and protocol support for
2066 handling HTTP and WebSocket requests directly from within R. It is primarily
2067 intended as a building block for other packages, rather than making it
2068 particularly easy to create complete web applications using httpuv alone.")
2069 ;; This package includes third-party code that was originally released
2070 ;; under various non-copyleft licenses. Full licensing information can be
2071 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
2072 (license license:gpl3+)))
2074 (define-public r-jsonlite
2080 (uri (cran-uri "jsonlite" version))
2083 "0k6dal7gmm19jl5sjsry5gwbnhsbrnn00q3iixig8k6bxgpr463v"))))
2084 (build-system r-build-system)
2087 (home-page "https://arxiv.org/abs/1403.2805")
2088 (synopsis "Robust, high performance JSON parser and generator for R")
2090 "The jsonlite package provides a fast JSON parser and generator optimized
2091 for statistical data and the web. It offers flexible, robust, high
2092 performance tools for working with JSON in R and is particularly powerful for
2093 building pipelines and interacting with a web API. In addition to converting
2094 JSON data from/to R objects, jsonlite contains functions to stream, validate,
2095 and prettify JSON data. The unit tests included with the package verify that
2096 all edge cases are encoded and decoded consistently for use with dynamic data
2097 in systems and applications.")
2098 (license license:expat)))
2100 (define-public r-servr
2106 (uri (cran-uri "servr" version))
2109 "11x0857m3xzdbzr4z0vx4fcdk36arfagyf2qgamvprich0qisknr"))))
2110 (build-system r-build-system)
2112 (list r-httpuv r-jsonlite r-mime r-xfun))
2113 (home-page "https://github.com/yihui/servr")
2114 (synopsis "Simple HTTP server to serve static files or dynamic documents")
2116 "Servr provides an HTTP server in R to serve static files, or dynamic
2117 documents that can be converted to HTML files (e.g., R Markdown) under a given
2119 (license license:expat)))
2121 (define-public r-howmany
2127 (uri (cran-uri "howmany" version))
2130 "045ck8qahfg2swbgyf7dpl32ryq1m4sbalhr7m5qdgpm62vz8h7f"))))
2131 (build-system r-build-system)
2132 (home-page "https://cran.r-project.org/web/packages/howmany/")
2133 (synopsis "Lower bound for the number of correct rejections")
2134 (description "When testing multiple hypotheses simultaneously, this package
2135 provides functionality to calculate a lower bound for the number of correct
2136 rejections (as a function of the number of rejected hypotheses), which holds
2137 simultaneously -with high probability- for all possible number of rejections.
2138 As a special case, a lower bound for the total number of false null hypotheses
2139 can be inferred. Dependent test statistics can be handled for multiple tests
2140 of associations. For independent test statistics, it is sufficient to provide
2141 a list of p-values.")
2142 (license license:gpl2+)))
2144 (define-public r-htmltools
2146 (name "r-htmltools")
2150 (uri (cran-uri "htmltools" version))
2153 "1yv74ydyqm28gfhimmr7825sj1iaawpwsnzq05c2ma756q2dbivx"))))
2154 (build-system r-build-system)
2156 (list r-base64enc r-digest r-fastmap r-rlang))
2157 (home-page "https://cran.r-project.org/web/packages/htmltools")
2158 (synopsis "R tools for HTML")
2160 "This package provides tools for HTML generation and output in R.")
2161 (license license:expat)))
2163 (define-public r-htmlwidgets
2165 (name "r-htmlwidgets")
2169 (uri (cran-uri "htmlwidgets" version))
2172 "1hgz8sx8xrvfcdwa4q15k942w4qsqg8lyxbbf7qyfzbi807wcgqs"))))
2173 (build-system r-build-system)
2175 (list r-htmltools r-jsonlite r-yaml))
2178 (home-page "https://github.com/ramnathv/htmlwidgets")
2179 (synopsis "HTML Widgets for R")
2181 "HTML widgets is a framework for creating HTML widgets that render in
2182 various contexts including the R console, R Markdown documents, and Shiny web
2184 (license license:expat)))
2186 (define-public r-htmltable
2188 (name "r-htmltable")
2193 (uri (cran-uri "htmlTable" version))
2195 (base32 "17csp0ry4iy4m5xy271dn5wd81v4p03l79swmvlfxkvpdmhvb8jc"))))
2196 (properties `((upstream-name . "htmlTable")))
2197 (build-system r-build-system)
2208 (home-page "http://gforge.se/packages/")
2209 (synopsis "Advanced tables for Markdown/HTML")
2211 "This package provides functions to build tables with advanced layout
2212 elements such as row spanners, column spanners, table spanners, zebra
2213 striping, and more. While allowing advanced layout, the underlying
2214 CSS-structure is simple in order to maximize compatibility with word
2215 processors such as LibreOffice. The package also contains a few text
2216 formatting functions that help outputting text compatible with HTML or
2218 (license license:gpl3+)))
2220 (define-public r-curl
2226 (uri (cran-uri "curl" version))
2229 "0s55022hy8shjm1pzax1dqzrg20bv4nvlwnjnddk3dp89g5zmcch"))))
2230 (build-system r-build-system)
2233 (modify-phases %standard-phases
2234 ;; The environment variable CURL_CA_BUNDLE is only respected when
2235 ;; running Windows, so we disable the platform checks.
2236 ;; This can be removed once the libcurl has been patched.
2237 (add-after 'unpack 'allow-CURL_CA_BUNDLE
2239 (substitute* "R/onload.R"
2240 (("if \\(!grepl\\(\"mingw\".*")
2242 (substitute* "src/handle.c"
2243 (("/\\* Only set" m)
2245 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
2246 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
2251 (list pkg-config r-knitr))
2252 (home-page "https://github.com/jeroenooms/curl")
2253 (synopsis "HTTP client for R")
2255 "The @code{curl()} and @code{curl_download()} functions provide highly
2256 configurable drop-in replacements for base @code{url()} and
2257 @code{download.file()} with better performance, support for encryption, gzip
2258 compression, authentication, and other @code{libcurl} goodies. The core of
2259 the package implements a framework for performing fully customized requests
2260 where data can be processed either in memory, on disk, or streaming via the
2261 callback or connection interfaces.")
2262 (license license:expat)))
2264 (define-public r-hwriter
2271 (uri (cran-uri "hwriter" version))
2274 "1wxnv8h9cs65m3z01dpnnkgn2cpwfsck70g1jz9nbkr7mdaa4bzd"))))
2275 (build-system r-build-system)
2276 (home-page "https://cran.r-project.org/web/packages/hwriter")
2277 (synopsis "Output R objects in HTML format")
2279 "This package provides easy-to-use and versatile functions to output R
2280 objects in HTML format.")
2281 (license license:lgpl2.1+)))
2283 (define-public r-rjson
2290 (uri (cran-uri "rjson" version))
2293 "1qm27r1w677zg31gsiln60hcciszbymkw78cnaq7s36cbk9mcawq"))))
2294 (build-system r-build-system)
2295 (home-page "https://cran.r-project.org/web/packages/rjson")
2296 (synopsis "JSON library for R")
2298 "This package provides functions to convert R objects into JSON objects
2300 (license license:gpl2+)))
2302 (define-public r-fastmap
2309 (uri (cran-uri "fastmap" version))
2312 "0aw29hnq3ppn7bsnwg9d9sp84k1cvq30lrmfzqn315n0nhkfa4wi"))))
2313 (properties `((upstream-name . "fastmap")))
2314 (build-system r-build-system)
2315 (home-page "https://r-lib.github.io/fastmap/")
2316 (synopsis "Fast implementation of a key-value store")
2318 "This package provides a fast implementation of a key-value store.
2319 Environments are commonly used as key-value stores, but every time a new key
2320 is used, it is added to R's global symbol table, causing a small amount of
2321 memory leakage. This can be problematic in cases where many different keys
2322 are used. Fastmap avoids this memory leak issue by implementing the map using
2323 data structures in C++.")
2324 (license license:expat)))
2326 (define-public r-fastghquad
2328 (name "r-fastghquad")
2333 (uri (cran-uri "fastGHQuad" version))
2336 "1zj7nsbnx4g253m3dpz9vi3zk3jxwrixwjw1ks6n4shpb4dlkp2w"))))
2337 (properties `((upstream-name . "fastGHQuad")))
2338 (build-system r-build-system)
2341 (home-page "https://github.com/awblocker/fastGHQuad")
2342 (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature")
2344 "This package implements numerically-stable Gauss-Hermite quadrature
2345 rules and utility functions for adaptive GH quadrature.")
2346 (license license:expat)))
2348 (define-public r-rstpm2
2355 (uri (cran-uri "rstpm2" version))
2358 "17mhzfxh761vl64ar6pynpj3k2jkhjgbacxsjhkrfkbmy3aiv0d1"))))
2359 (properties `((upstream-name . "rstpm2")))
2360 (build-system r-build-system)
2372 (home-page "https://github.com/mclements/rstpm2")
2373 (synopsis "Link-based survival models")
2375 "This package provides R implementations of @dfn{generalized survival
2376 models} (GSMs), smooth @dfn{accelerated failure time} (AFT) models and Markov
2377 multi-state models.")
2378 ;; One of these licenses
2379 (license (list license:gpl2 license:gpl3))))
2381 ;; This package includes minified JavaScript files. When upgrading please
2382 ;; check that there are no new minified JavaScript files.
2383 (define-public r-jquerylib
2385 (name "r-jquerylib")
2390 (uri (cran-uri "jquerylib" version))
2393 "04a40v4znpj98j7y6009d74a6g9dchj5rr3p08cgz9p3rlfw3g7h"))
2395 '(for-each delete-file
2396 '("inst/lib/1.12.4/jquery-1.12.4.min.js"
2397 "inst/lib/2.2.4/jquery-2.2.4.min.js"
2398 "inst/lib/3.6.0/jquery-3.6.0.min.js")))))
2399 (properties `((upstream-name . "jquerylib")))
2400 (build-system r-build-system)
2402 `(#:modules ((guix build utils)
2403 (guix build r-build-system)
2406 (modify-phases %standard-phases
2407 (add-after 'unpack 'process-javascript
2408 (lambda* (#:key inputs #:allow-other-keys)
2409 (with-directory-excursion "inst/lib/"
2413 `(("1.12.4/jquery-1.12.4.js"
2414 "1.12.4/jquery-1.12.4.min.js")
2415 ("2.2.4/jquery-2.2.4.js"
2416 "2.2.4/jquery-2.2.4.min.js")
2417 ("3.6.0/jquery-3.6.0.js"
2418 "3.6.0/jquery-3.6.0.min.js"))))
2419 (lambda (sources targets)
2420 (for-each (lambda (source target)
2421 (format #t "Processing ~a --> ~a~%"
2423 (invoke "esbuild" source "--minify"
2424 (string-append "--outfile=" target)))
2425 sources targets)))))))))
2430 (home-page "https://cran.r-project.org/package=jquerylib")
2431 (synopsis "Obtain jQuery as an HTML dependency object")
2433 "Obtain any major version of jQuery and use it in any webpage generated
2434 by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't
2435 need to use this package directly, but other R packages (e.g. shiny,
2436 rmarkdown, etc.) depend on this package to avoid bundling redundant copies of
2438 (license license:expat)))
2440 (define-public r-sass
2447 (uri (cran-uri "sass" version))
2450 "1fq8wqnxmx10lg0dh4qzmxdkhd22fjh8vhassapxb1chsimwn3w5"))))
2451 (properties `((upstream-name . "sass")))
2452 (build-system r-build-system)
2454 (list r-fs r-htmltools r-r6 r-rappdirs r-rlang))
2455 (native-inputs (list r-knitr))
2456 (home-page "https://github.com/rstudio/sass")
2457 (synopsis "Syntactically Awesome Style Sheets (SASS)")
2459 "This package provides an SCSS compiler, powered by the libsass library.
2460 With this, R developers can use variables, inheritance, and functions to
2461 generate dynamic style sheets. The package uses the Sass CSS extension
2462 language, which is stable, powerful, and CSS compatible.")
2463 (license license:expat)))
2465 (define-public r-saver
2471 (uri (cran-uri "SAVER" version))
2474 "1s1kw8idkaj7j90fw4qn9k0wd4vz0sblsk06ry6lm4afcar0p158"))))
2475 (properties `((upstream-name . "SAVER")))
2476 (build-system r-build-system)
2483 (native-inputs (list r-knitr))
2484 (home-page "https://github.com/mohuangx/SAVER")
2486 "Recovery of gene expression profile in noisy and sparse scRNA-seq data")
2488 "This package is an implementation of a regularized regression prediction
2489 and empirical Bayes method to recover the true gene expression profile in noisy
2490 and sparse single-cell RNA-seq data. In @dfn{single-cell RNA sequencing}
2491 (scRNA-seq) studies, only a small fraction of the transcripts present in each
2492 cell are sequenced. This leads to unreliable quantification of genes with low
2493 or moderate expression, which hinders downstream analysis. This package
2494 @dfn{single-cell analysis via expression recovery} (SAVER) implements an
2495 expression recovery method for unique molecule index (UMI)-based scRNA-seq
2496 data that borrows information across genes and cells to provide accurate
2497 expression estimates for all genes.")
2498 (license license:gpl2)))
2500 ;; This package includes minified JavaScript files. When upgrading please
2501 ;; check that there are no new minified JavaScript files.
2502 (define-public r-bslib
2509 (uri (cran-uri "bslib" version))
2512 "0jcqklry1nkibz0sydsz5xdsnb4wnrrhvmyr9ji3k45bbipbap2z"))
2514 '(for-each delete-file
2515 '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js"
2516 "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js"
2517 "inst/lib/bs3/assets/javascripts/bootstrap.min.js"
2518 "inst/lib/bs4/dist/js/bootstrap.bundle.min.js"
2519 "inst/lib/bs5/dist/js/bootstrap.bundle.min.js")))))
2520 (properties `((upstream-name . "bslib")))
2521 (build-system r-build-system)
2523 `(#:modules ((guix build utils)
2524 (guix build r-build-system)
2527 (modify-phases %standard-phases
2528 (add-after 'unpack 'process-javascript
2529 (lambda* (#:key inputs #:allow-other-keys)
2530 (with-directory-excursion "inst/lib/"
2534 `(("bs-a11y-p/plugins/js/bootstrap-accessibility.js"
2535 "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js")
2536 ("bs-colorpicker/js/bootstrap-colorpicker.js"
2537 "bs-colorpicker/js/bootstrap-colorpicker.min.js")
2538 ("bs3/assets/javascripts/bootstrap.js"
2539 "bs3/assets/javascripts/bootstrap.min.js")
2540 (,(assoc-ref inputs "js-bootstrap4-bundle")
2541 "bs4/dist/js/bootstrap.bundle.min.js")
2542 (,(assoc-ref inputs "js-bootstrap5-bundle")
2543 "bs5/dist/js/bootstrap.bundle.min.js"))))
2544 (lambda (sources targets)
2545 (for-each (lambda (source target)
2546 (format #t "Processing ~a --> ~a~%"
2548 (invoke "esbuild" source "--minify"
2549 (string-append "--outfile=" target)))
2550 sources targets)))))))))
2552 (list r-htmltools r-jquerylib r-jsonlite r-rlang r-sass))
2554 `(("esbuild" ,esbuild)
2555 ("js-bootstrap4-bundle"
2558 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.6.0/dist/js/bootstrap.bundle.js")
2561 "04abvgp923w36qfqkkl2syim3bl119nwxbgials90z1jyb8jgss1"))))
2562 ("js-bootstrap5-bundle"
2565 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v5.0.2/dist/js/bootstrap.bundle.js")
2568 "06vin94nqw1vzs4zrqcms8z9js9fckbj8gwyx07awm8jkjhnqfhl"))))))
2569 (home-page "https://rstudio.github.io/bslib/")
2570 (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown")
2572 "This package simplifies custom CSS styling of both shiny and rmarkdown
2573 via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their
2574 various Bootswatch themes. An interactive widget is also provided for
2575 previewing themes in real time.")
2576 (license license:expat)))
2578 ;; This package includes minified JavaScript files. When upgrading please
2579 ;; check that there are no new minified JavaScript files.
2580 (define-public r-shiny
2588 (url "https://github.com/rstudio/shiny")
2589 (commit (string-append "v" version))))
2590 (file-name (git-file-name name version))
2593 "0wvc6jlgs41p05wbk8gahnl7sfnc4hpliyh9dbi5w52ngsg6wcr7"))
2595 '(for-each delete-file
2596 '("inst/www/shared/bootstrap/js/bootstrap.min.js"
2597 "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO
2598 "inst/www/shared/datatables/js/jquery.dataTables.min.js"
2599 "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js"
2600 "inst/www/shared/highlight/highlight.pack.js"
2601 "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js"
2602 "inst/www/shared/jquery.min.js"
2603 "inst/www/shared/jqueryui/jquery-ui.min.js"
2604 "inst/www/shared/legacy/jquery.min.js"
2605 "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js"
2606 "inst/www/shared/selectize/js/selectize.min.js"
2607 "inst/www/shared/shiny.min.js"
2608 "inst/www/shared/showdown/compressed/showdown.js"
2609 "inst/www/shared/strftime/strftime-min.js")))))
2610 (build-system r-build-system)
2612 `(#:modules ((guix build r-build-system)
2613 (guix build minify-build-system)
2616 #:imported-modules (,@%r-build-system-modules
2617 (guix build minify-build-system))
2619 (modify-phases (@ (guix build r-build-system) %standard-phases)
2620 (add-after 'unpack 'replace-bundled-minified-JavaScript
2621 (lambda* (#:key inputs #:allow-other-keys)
2622 (let ((replace-file (lambda (old new)
2623 (format #t "replacing ~a with ~a\n" old new)
2624 (symlink new old))))
2625 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
2626 ;; contain just data. They are not minified code, so we don't
2628 (with-directory-excursion "inst/www/shared"
2629 (replace-file "strftime/strftime-min.js"
2630 (search-input-file inputs
2631 "/share/javascript/strftime.min.js"))
2632 (replace-file "highlight/highlight.pack.js"
2633 (search-input-file inputs
2634 "/share/javascript/highlight.min.js"))
2635 (replace-file "datatables/js/jquery.dataTables.min.js"
2636 (search-input-file inputs
2637 "/share/javascript/jquery.dataTables.min.js"))
2638 (replace-file "selectize/js/selectize.min.js"
2639 (search-input-file inputs
2640 "/share/javascript/selectize.min.js"))
2641 (for-each (match-lambda
2643 (minify source #:target target)))
2644 `(("jqueryui/jquery-ui.js" .
2645 "jqueryui/jquery-ui.min.js")
2646 ("datepicker/js/bootstrap-datepicker.js" .
2647 "datepicker/js/bootstrap-datepicker.min.js")
2648 ("ionrangeslider/js/ion.rangeSlider.js" .
2649 "ionrangeslider/js/ion.rangeSlider.min.js")
2650 ("bootstrap/js/bootstrap.js" .
2651 "bootstrap/js/bootstrap.min.js")
2652 (,(assoc-ref inputs "js-bootstrap-accessibility") .
2653 "bootstrap/accessibility/js/bootstrap-accessibility.min.js")
2658 ("legacy/jquery.js" .
2659 "legacy/jquery.min.js")
2660 ("selectize/accessibility/js/selectize-plugin-a11y.js" .
2661 "selectize/accessibility/js/selectize-plugin-a11y.min.js")
2662 ("showdown/src/showdown.js" .
2663 "showdown/compressed/showdown.js"))))))))))
2686 (list js-datatables js-selectize js-strftime js-highlight))
2688 `(("uglifyjs" ,node-uglify-js)
2689 ("gfortran" ,gfortran)
2690 ("js-bootstrap-accessibility"
2693 (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\
2694 v1.0.7/_site/plugins/js/bootstrap-accessibility.js")
2697 "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8"))))))
2698 (home-page "https://shiny.rstudio.com")
2699 (synopsis "Easy interactive web applications with R")
2701 "Makes it incredibly easy to build interactive web applications
2702 with R. Automatic \"reactive\" binding between inputs and outputs and
2703 extensive prebuilt widgets make it possible to build beautiful,
2704 responsive, and powerful applications with minimal effort.")
2705 (license license:artistic2.0)))
2707 (define-public r-shinyhelper
2709 (name "r-shinyhelper")
2714 (uri (cran-uri "shinyhelper" version))
2716 (base32 "1c4hvf19j3yyh8r12nx85ldkxs89g98q74csnqs5ml5l79a65vgp"))))
2717 (properties `((upstream-name . "shinyhelper")))
2718 (build-system r-build-system)
2719 (propagated-inputs (list r-markdown r-shiny))
2720 (home-page "https://cran.r-project.org/package=shinyhelper")
2721 (synopsis "Easily add Markdown help files to shiny app elements")
2723 "This package creates a lightweight way to add markdown helpfiles to
2724 Shiny apps, using modal dialog boxes, with no need to observe each help button
2726 (license license:gpl3)))
2728 ;; This package includes minified JavaScript files. When upgrading please
2729 ;; check that there are no new minified JavaScript files.
2730 (define-public r-shinytree
2732 (name "r-shinytree")
2737 (uri (cran-uri "shinyTree" version))
2740 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
2741 (modules '((guix build utils)))
2744 ;; Delete minified JavaScript
2745 (for-each delete-file
2746 '("inst/www/jsTree-3.3.7/libs/require.js"
2747 "inst/www/jsTree-3.3.7/libs/jquery.js"
2748 "inst/www/jsTree-3.3.7/jstree.min.js"))
2750 (properties `((upstream-name . "shinyTree")))
2751 (build-system r-build-system)
2753 `(#:modules ((guix build utils)
2754 (guix build r-build-system)
2758 (modify-phases %standard-phases
2759 (add-after 'unpack 'replace-minified-javascript
2760 (lambda* (#:key inputs #:allow-other-keys)
2761 (with-directory-excursion "inst/www/jsTree-3.3.7/"
2762 (symlink (search-input-file inputs
2763 "/share/javascript/require.min.js")
2768 `((,(assoc-ref inputs "js-jquery")
2772 (lambda (sources targets)
2773 (for-each (lambda (source target)
2774 (format #t "Processing ~a --> ~a~%"
2776 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
2777 (call-with-output-file target
2779 (dump-port minified port)))))
2783 (list r-htmlwidgets r-jsonlite r-promises r-shiny r-stringr))
2785 (list js-requirejs))
2787 `(("uglifyjs" ,node-uglify-js)
2791 (uri "https://code.jquery.com/jquery-3.3.1.js")
2794 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
2795 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
2796 (synopsis "jsTree bindings for Shiny")
2798 "This package exposes R bindings to jsTree, a JavaScript library that
2799 supports interactive trees, to enable rich, editable trees in Shiny.")
2800 (license license:expat)))
2802 (define-public r-shinydashboard
2804 (name "r-shinydashboard")
2808 (uri (cran-uri "shinydashboard" version))
2811 "0hrqkwlpb8rnmp5j74p134g4c4cl16icmwc2ip6k1634fa2y8vm5"))))
2812 (build-system r-build-system)
2813 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
2814 ;; Regenerate it from the included sources.
2817 (modify-phases %standard-phases
2818 (add-after 'unpack 'generate-minified-javascript
2820 (with-directory-excursion "inst/AdminLTE"
2821 (let ((target "app.min.js")
2823 (format #t "Processing ~a --> ~a~%"
2825 (delete-file target)
2826 (invoke "esbuild" source "--minify"
2827 (string-append "--outfile=" target)))))))))
2829 (list r-htmltools r-promises r-shiny))
2832 (home-page "https://rstudio.github.io/shinydashboard/")
2833 (synopsis "Create dashboards with shiny")
2834 (description "This package provides an extension to the Shiny web
2835 application framework for R, making it easy to create attractive dashboards.")
2836 ;; This package includes software that was released under the Expat
2837 ;; license, but the whole package is released under GPL version 2 or
2839 (license license:gpl2+)))
2841 (define-public r-shinyfiles
2843 (name "r-shinyfiles")
2848 (uri (cran-uri "shinyFiles" version))
2850 (base32 "1l4a4v9ivxkj2vx6xw4z3pk7a8px23icppcgvgpybibq2j74pglg"))))
2851 (properties `((upstream-name . "shinyFiles")))
2852 (build-system r-build-system)
2854 (list r-fs r-htmltools r-jsonlite r-shiny r-tibble))
2855 (home-page "https://github.com/thomasp85/shinyFiles")
2856 (synopsis "Server-side file system viewer for Shiny")
2858 "This package provides functionality for client-side navigation of the
2859 server side file system in shiny apps. In case the app is running locally
2860 this gives the user direct access to the file system without the need to
2861 \"download\" files to a temporary location. Both file and folder selection as
2862 well as file saving is available.")
2863 (license license:gpl2+)))
2865 (define-public r-shinythemes
2867 (name "r-shinythemes")
2872 (uri (cran-uri "shinythemes" version))
2875 "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip"))))
2876 (properties `((upstream-name . "shinythemes")))
2877 (build-system r-build-system)
2878 (propagated-inputs (list r-shiny))
2879 (home-page "https://rstudio.github.io/shinythemes/")
2880 (synopsis "Themes for Shiny")
2882 "This package provides themes for use with Shiny. It includes several
2883 Bootstrap themes, which are packaged for use with Shiny applications.")
2884 ;; The package is released under version 3 of the GPL, but it includes
2885 ;; source files that are covered by the Expat license. It also includes
2886 ;; fonts under SIL or the ASL.
2887 (license (list license:gpl3 license:expat
2888 license:silofl1.1 license:asl2.0))))
2890 ;; The package sources include minified variants of d3.js and non-minified
2891 ;; source code of d3-jetpack.
2892 (define-public r-d3r
2899 (uri (cran-uri "d3r" version))
2902 "1qijkllfaaw0lb29j8mappm8jz9kg8gkihxq5wqhb4gabsazdwva"))))
2903 (build-system r-build-system)
2905 `(#:modules ((guix build utils)
2906 (guix build r-build-system)
2909 (modify-phases %standard-phases
2910 (add-after 'unpack 'process-javascript
2911 (lambda* (#:key inputs #:allow-other-keys)
2912 (with-directory-excursion "inst/www/d3/"
2916 `((,(assoc-ref inputs "d3.v3.js")
2917 "v3/dist/d3.min.js")
2918 (,(assoc-ref inputs "d3.v4.js")
2919 "v4/dist/d3.min.js")
2920 (,(assoc-ref inputs "d3.v5.js")
2921 "v5/dist/d3.min.js")
2922 (,(assoc-ref inputs "d3.v6.js")
2923 "v6/dist/d3.min.js")
2924 (,(assoc-ref inputs "d3.v7.js")
2925 "v7/dist/d3.min.js"))))
2926 (lambda (sources targets)
2927 (for-each (lambda (source target)
2928 (format #t "Processing ~a --> ~a~%"
2930 (delete-file target)
2931 (invoke "esbuild" source "--minify"
2932 (string-append "--outfile=" target)))
2933 sources targets)))))))))
2935 (list r-dplyr r-htmltools r-rlang r-tidyr))
2937 `(("esbuild" ,esbuild)
2941 (uri "https://d3js.org/d3.v3.js")
2944 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
2948 (uri "https://d3js.org/d3.v4.js")
2951 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
2955 (uri "https://d3js.org/d3.v5.js")
2958 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))
2962 (uri "https://d3js.org/d3.v6.js")
2965 "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9"))))
2969 (uri "https://d3js.org/d3.v7.js")
2972 "0sd6vavxs8mx5xyb8xahlqghdiczqd284a7d5wravhqnrj0bw097"))))))
2973 (home-page "https://github.com/timelyportfolio/d3r")
2974 (synopsis "d3.js utilities for R")
2976 "This package provides a suite of functions to help ease the use of the
2977 d3.js visualization library in R. These helpers include
2978 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
2979 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
2980 R objects into the JSON format that the d3.js library expects.")
2981 (license license:bsd-3)))
2983 ;; We use the latest commit here because the last release was in 2016 while
2984 ;; the latest commit was in 2018.
2985 (define-public r-sankeyd3
2986 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
2990 (version (git-version "0.3.2" revision commit))
2995 (url "https://github.com/fbreitwieser/sankeyD3")
2997 (file-name (git-file-name name version))
3000 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
3001 (build-system r-build-system)
3003 (list r-d3r r-htmlwidgets r-shiny r-magrittr))
3004 (home-page "https://github.com/fbreitwieser/sankeyD3")
3005 (synopsis "Sankey network graphs from R")
3007 "This package provides an R library to generate Sankey network graphs
3008 in R and Shiny via the D3 visualization library.")
3009 ;; The R code is licensed under GPLv3+. It includes the non-minified
3010 ;; JavaScript source code of d3-sankey, which is released under the
3011 ;; 3-clause BSD license.
3012 (license (list license:gpl3+ license:bsd-3)))))
3014 (define-public r-wesanderson
3016 (name "r-wesanderson")
3021 (uri (cran-uri "wesanderson" version))
3024 "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
3025 (properties `((upstream-name . "wesanderson")))
3026 (build-system r-build-system)
3027 (home-page "https://github.com/karthik/wesanderson")
3028 (synopsis "Wes Anderson color palette generator")
3030 "This package provides color palettes that have been generated mostly
3031 from Wes Anderson movies.")
3032 (license license:expat)))
3034 (define-public r-gg-gap
3041 (uri (cran-uri "gg.gap" version))
3044 "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h"))))
3045 (properties `((upstream-name . "gg.gap")))
3046 (build-system r-build-system)
3048 (list r-cowplot r-ggplot2))
3049 (home-page "https://github.com/ChrisLou-bioinfo/gg.gap")
3050 (synopsis "Define segments on the y-axis for ggplot2")
3052 "The @code{gg.gap} function enables you to define segments for the y-axis
3053 in a ggplot2 plot.")
3054 (license license:gpl3)))
3056 (define-public r-mbess
3063 (uri (cran-uri "MBESS" version))
3065 (base32 "0qmyvjx2zn5hlzdbz8c94g8l4707swhn7sq9mxkdqiydmflzv0b5"))))
3066 (properties `((upstream-name . "MBESS")))
3067 (build-system r-build-system)
3069 (list r-boot r-lavaan r-mass r-mnormt r-nlme r-openmx r-sem r-semtools))
3070 (home-page "https://www3.nd.edu/~kkelley/site/MBESS.html")
3071 (synopsis "Methods for designing research studies")
3073 "This package implements methods that are useful in designing research
3074 studies and analyzing data, with particular emphasis on methods that are
3075 developed for or used within the behavioral, educational, and social
3076 sciences (broadly defined). That being said, many of the methods implemented
3077 within MBESS are applicable to a wide variety of disciplines. MBESS has a
3078 suite of functions for a variety of related topics, such as effect sizes,
3079 confidence intervals for effect sizes (including standardized effect sizes and
3080 noncentral effect sizes), sample size planning (from the @dfn{accuracy in
3081 parameter estimation} (AIPE), power analytic, equivalence, and minimum-risk
3082 point estimation perspectives), mediation analysis, various properties of
3083 distributions, and a variety of utility functions.")
3084 ;; Either version of the GPL.
3085 (license (list license:gpl2 license:gpl3))))
3087 (define-public r-homologene
3089 (name "r-homologene")
3090 (version "1.4.68.19.3.27")
3094 (uri (cran-uri "homologene" version))
3096 (base32 "0d7wxisk0vqk1n165v1i19bc02zv78h5r5d3jqai5y6nkmwn01sh"))))
3097 (properties `((upstream-name . "homologene")))
3098 (build-system r-build-system)
3100 (list r-dplyr r-magrittr r-purrr r-r-utils r-readr))
3101 (home-page "https://github.com/oganm/homologene")
3102 (synopsis "Quick access to homologene and gene annotation updates")
3104 "This package provides a wrapper for the homologene database by the
3105 National Center for Biotechnology Information (NCBI). It allows searching for
3106 gene homologs across species. The package also includes an updated version of
3107 the homologene database where gene identifiers and symbols are replaced with
3108 their latest (at the time of submission) version and functions to fetch latest
3109 annotation data to keep updated.")
3110 (license license:expat)))
3112 (define-public r-ggtern
3119 (uri (cran-uri "ggtern" version))
3121 (base32 "15hhn8msy0l8zbq8ms0zvg1iajn1c28gd77v3hp6dvwwsla8zzbd"))))
3122 (properties `((upstream-name . "ggtern")))
3123 (build-system r-build-system)
3125 (list r-compositions
3136 (home-page "http://www.ggtern.com")
3137 (synopsis "Extension to ggplot2 for ternary diagrams")
3139 "This package extends the functionality of ggplot2, providing the
3140 capability to plot ternary diagrams for (a subset of) the ggplot2 geometries.
3141 Additionally, ggtern has implemented several new geometries which are
3142 unavailable to the standard ggplot2 release.")
3143 (license license:gpl2)))
3145 (define-public r-tablerdash
3147 (name "r-tablerdash")
3152 (uri (cran-uri "tablerDash" version))
3155 "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm"))
3158 ;; Delete minified JavaScript
3159 (for-each delete-file
3160 '("inst/tablerDash-0.1.0/require.min.js"
3161 "inst/bootstrap-4.0.0/bootstrap.bundle.min.js"))
3163 (properties `((upstream-name . "tablerDash")))
3164 (build-system r-build-system)
3166 `(#:modules ((guix build utils)
3167 (guix build r-build-system)
3170 (modify-phases %standard-phases
3171 (add-after 'unpack 'process-javascript
3172 (lambda* (#:key inputs #:allow-other-keys)
3173 (with-directory-excursion "inst"
3177 `((,(assoc-ref inputs "js-requirejs")
3178 "tablerDash-0.1.0/require.min.js")
3179 (,(assoc-ref inputs "js-bootstrap")
3180 "bootstrap-4.0.0/bootstrap.bundle.min.js"))))
3181 (lambda (sources targets)
3182 (for-each (lambda (source target)
3183 (format #t "Processing ~a --> ~a~%"
3185 (invoke "esbuild" source "--minify"
3186 (string-append "--outfile=" target)))
3190 (list r-htmltools r-knitr r-shiny))
3192 `(("esbuild" ,esbuild)
3196 (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js")
3199 "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds"))))
3203 (uri "https://raw.githubusercontent.com/twbs/bootstrap/\
3204 v4.0.0/dist/js/bootstrap.bundle.js")
3207 "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj"))))))
3208 (home-page "https://rinterface.github.io/tablerDash/")
3209 (synopsis "Tabler API for Shiny")
3211 "This package provides an R interface to the
3212 @url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap
3213 4 dashboard template. There are different layouts available such as a one
3214 page dashboard or a multi-page template, where the navigation menu is
3215 contained in the navigation bar.")
3216 (license license:gpl2+)))
3218 (define-public r-spelling
3225 (uri (cran-uri "spelling" version))
3228 "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl"))))
3229 (properties `((upstream-name . "spelling")))
3230 (build-system r-build-system)
3232 (list r-commonmark r-hunspell r-knitr r-xml2))
3233 (home-page "https://docs.ropensci.org/spelling/")
3234 (synopsis "Tools for spell checking in R")
3236 "This is an R package for spell checking common document formats
3237 including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes
3238 utilities to automate checking of documentation and vignettes as a unit test
3239 during @code{R CMD check}. Both British and American English are supported
3240 out of the box and other languages can be added. In addition, packages may
3241 define a wordlist to allow custom terminology without having to abuse
3243 (license license:expat)))
3245 (define-public r-crosstalk
3247 (name "r-crosstalk")
3252 (uri (cran-uri "crosstalk" version))
3255 "180y7mhpj17axpadwhh7s0qvrpdnag7g977vk256l96d6nmvlds2"))))
3256 (build-system r-build-system)
3258 (list r-htmltools r-jsonlite r-lazyeval r-r6))
3259 (home-page "https://rstudio.github.io/crosstalk/")
3260 (synopsis "Inter-widget interactivity for HTML widgets")
3262 "This package provides building blocks for allowing HTML widgets to
3263 communicate with each other, with Shiny or without (i.e. static @code{.html}
3264 files). It currently supports linked brushing and filtering.")
3265 (license license:expat)))
3267 (define-public r-rook
3274 (uri (cran-uri "Rook" version))
3277 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
3278 (properties `((upstream-name . "Rook")))
3279 (build-system r-build-system)
3280 (propagated-inputs (list r-brew))
3281 (home-page "https://cran.r-project.org/web/packages/Rook")
3282 (synopsis "Web server interface for R")
3284 "This package contains the Rook specification and convenience software
3285 for building and running Rook applications. A Rook application is an R
3286 reference class object that implements a @code{call} method or an R closure
3287 that takes exactly one argument, an environment, and returns a list with three
3288 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
3289 (license license:gpl2)))
3291 (define-public r-miniui
3298 (uri (cran-uri "miniUI" version))
3301 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
3302 (properties `((upstream-name . "miniUI")))
3303 (build-system r-build-system)
3305 (list r-htmltools r-shiny))
3306 (home-page "https://cran.r-project.org/web/packages/miniUI/")
3307 (synopsis "Shiny UI widgets for small screens")
3309 "This package provides UI widget and layout functions for writing Shiny apps that
3310 work well on small screens.")
3311 (license license:gpl3)))
3313 (define-public r-feather
3320 (uri (cran-uri "feather" version))
3323 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
3324 (build-system r-build-system)
3326 (list r-hms r-rcpp r-tibble))
3327 (home-page "https://github.com/wesm/feather")
3328 (synopsis "R Bindings to the Feather API")
3329 (description "Read and write feather files, a lightweight binary columnar
3330 data store designed for maximum speed.")
3331 (license license:asl2.0)))
3333 (define-public r-maps
3340 (uri (cran-uri "maps" version))
3343 "0ispkx1szgwxhr0zzhdzgqqwcgc6psg7vry4sj4rb89w76rcq63r"))))
3344 (build-system r-build-system)
3345 (home-page "https://cran.r-project.org/web/packages/maps")
3346 (synopsis "Draw geographical maps")
3347 (description "This package provides an R module for display of maps.
3348 Projection code and larger maps are in separate packages (@code{mapproj} and
3350 (license license:gpl2)))
3352 (define-public r-mapproj
3359 (uri (cran-uri "mapproj" version))
3362 "10bpib827011fpgvzsmlv4j3i41s0r3cv1hvawwdlk753s7i0pw6"))))
3363 (build-system r-build-system)
3364 (propagated-inputs (list r-maps))
3365 (home-page "https://cran.r-project.org/web/packages/mapproj")
3366 (synopsis "Map projection in R")
3367 (description "This package converts latitude/longitude into projected
3369 (license (list license:gpl2 ; The R interface
3370 (license:non-copyleft ; The C code
3371 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
3372 "Lucent Public License Version 1.02")))))
3374 (define-public r-rgooglemaps
3376 (name "r-rgooglemaps")
3381 (uri (cran-uri "RgoogleMaps" version))
3384 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
3385 (properties `((upstream-name . "RgoogleMaps")))
3386 (build-system r-build-system)
3389 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
3390 (synopsis "Use Google Maps in R")
3391 (description "This package serves two purposes:
3393 @item Provide a comfortable R interface to query the Google server for static
3395 @item Use the map as a background image to overlay plots within R. This
3396 requires proper coordinate scaling.
3398 (license license:gpl2+)))
3400 (define-public r-geosphere
3402 (name "r-geosphere")
3407 (uri (cran-uri "geosphere" version))
3410 "0bg4vfmrw140j2ax0p6bflvb77w03ir39wa87l96rj473jpa9hzj"))))
3411 (build-system r-build-system)
3412 (propagated-inputs (list r-sp))
3413 (home-page "https://cran.r-project.org/web/packages/geosphere")
3414 (synopsis "Spherical trigonometry")
3415 (description "This package computes spherical trigonometry for geographic
3416 applications. That is, compute distances and related measures for angular
3417 (longitude/latitude) locations.")
3418 (license license:gpl3+)))
3420 (define-public r-jpeg
3427 (uri (cran-uri "jpeg" version))
3430 "0wihj538wdnr71wdldym83qadb4kh68a6rkallwbh2f25r27b881"))))
3431 (build-system r-build-system)
3432 (inputs (list libjpeg-turbo))
3433 (home-page "https://www.rforge.net/jpeg/")
3434 (synopsis "Read and write JPEG images with R")
3435 (description "This package provides a way to read, write and display
3436 bitmap images stored in the JPEG format with R. It can read and write both
3437 files and in-memory raw vectors.")
3438 (license license:gpl2+)))
3440 (define-public r-ggmap
3447 (uri (cran-uri "ggmap" version))
3450 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
3451 (build-system r-build-system)
3470 (home-page "https://github.com/dkahle/ggmap")
3471 (synopsis "Spatial visualization with ggplot2")
3472 (description "This package provides a collection of functions to visualize
3473 spatial data and models on top of static maps from various online sources (e.g
3474 Google Maps and Stamen Maps). It includes tools common to those tasks,
3475 including functions for geolocation and routing.")
3476 (license license:gpl2)))
3478 (define-public r-haven
3485 (uri (cran-uri "haven" version))
3488 "1x5g6kjrzcyarbjz91f4aaspx7rb50qs6a9y29mzr3mjq4dk305m"))
3489 (modules '((guix build utils)))
3491 ;; unvendor readstat
3492 '(delete-file-recursively "src/readstat"))))
3493 (build-system r-build-system)
3496 (modify-phases %standard-phases
3497 (add-after 'unpack 'unbundle-readstat
3499 ;; We’re not building readstat.
3500 (substitute* "configure"
3501 (("exit 1") "")) ;don't be so dramatic!
3502 (substitute* '("src/Makevars.in"
3504 (("^PKG_LIBS=.*") "PKG_LIBS=\"-lreadstat\"\n")))))))
3520 (home-page "https://haven.tidyverse.org")
3521 (synopsis "Import and export SPSS, Stata and SAS files")
3523 "This package lets you import foreign statistical formats into R via the
3524 @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
3525 (license license:expat)))
3527 (define-public r-amap
3533 (uri (cran-uri "amap" version))
3536 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
3537 (build-system r-build-system)
3540 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
3541 (synopsis "Another multidimensional analysis package")
3542 (description "This package provides tools for clustering and principal
3543 component analysis (with robust methods, and parallelized functions).")
3544 (license license:gpl2+)))
3546 (define-public r-ape
3553 (uri (cran-uri "ape" version))
3556 "0mqjsh7maczd02iwa4fb896q3kgd9jnlilq7y1yz18ch0c54aqlv"))))
3557 (build-system r-build-system)
3559 (list r-lattice r-nlme r-rcpp))
3560 (home-page "http://ape-package.ird.fr/")
3561 (synopsis "Analyses of phylogenetics and evolution")
3563 "This package provides functions for reading, writing, plotting, and
3564 manipulating phylogenetic trees, analyses of comparative data in a
3565 phylogenetic framework, ancestral character analyses, analyses of
3566 diversification and macroevolution, computing distances from DNA sequences,
3567 and several other tools.")
3568 (license license:gpl2+)))
3570 (define-public r-abbyyr
3577 (uri (cran-uri "abbyyR" version))
3580 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
3581 (properties `((upstream-name . "abbyyR")))
3582 (build-system r-build-system)
3590 (home-page "https://github.com/soodoku/abbyyR")
3591 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
3593 "This package provides tools to get text from images of text using Abbyy
3594 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
3595 OCR images, barcodes, forms, documents with machine readable zones, e.g.
3596 passports and get the results in a variety of formats including plain text and
3597 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
3598 (license license:expat)))
3600 (define-public r-colorspace
3602 (name "r-colorspace")
3607 (uri (cran-uri "colorspace" version))
3609 (base32 "0zw52s8g2gxp8i1ax96azxmxqrbhb7aad5px0c1vgr6n9p682mp7"))))
3610 (build-system r-build-system)
3613 (home-page "https://cran.r-project.org/web/packages/colorspace")
3614 (synopsis "Color space manipulation")
3616 "This package carries out a mapping between assorted color spaces
3617 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
3618 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
3619 colors are provided.")
3620 (license license:bsd-3)))
3622 (define-public r-glue
3629 (uri (cran-uri "glue" version))
3632 "1gzxk5jgdh2xq9r7z09xs306ygzf27vhg3pyfl7ck1755gqii9cx"))))
3633 (build-system r-build-system)
3634 ;; knitr depends on glue, so we can't add knitr here to build the
3638 `(("r-knitr" ,r-knitr)))
3639 (home-page "https://github.com/tidyverse/glue")
3640 (synopsis "Interpreted string literals")
3642 "This package provides an implementation of interpreted string literals,
3643 inspired by Python's Literal String Interpolation (PEP-0498) and
3644 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
3645 (license license:expat)))
3647 (define-public r-palmerpenguins
3649 (name "r-palmerpenguins")
3654 (uri (cran-uri "palmerpenguins" version))
3657 "0q1k3cdkliq7kwrg1n0vs9b6cjwyfarhlgdijhp9c6riy6y5ik7x"))))
3659 `((upstream-name . "palmerpenguins")))
3660 (build-system r-build-system)
3661 (home-page "https://allisonhorst.github.io/palmerpenguins/")
3662 (synopsis "Palmer Archipelago (Antarctica) penguin data")
3664 "This package includes size measurements, clutch observations, and blood
3665 isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins
3666 observed on islands in the Palmer Archipelago near Palmer Station, Antarctica.
3667 Data were collected and made available by Dr. Kristen Gorman and the Palmer
3668 Station Long Term Ecological Research (LTER) Program.")
3669 (license license:cc0)))
3671 (define-public r-pastecs
3677 (uri (cran-uri "pastecs" version))
3680 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
3681 (build-system r-build-system)
3684 (home-page "https://github.com/phgrosjean/pastecs")
3685 (synopsis "Analysis of space-time ecological series")
3687 "This package provides functions for regulation, decomposition and analysis
3688 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
3689 initiative to bring PASSTEC 2000 functionalities to R.")
3690 (license license:gpl2+)))
3692 (define-public r-partykit
3698 (uri (cran-uri "partykit" version))
3701 "1b73s5l19yicwginqsg5xr7fzb005x372n0wb34kk6jb5x5lbsdj"))))
3702 (build-system r-build-system)
3710 (home-page "http://partykit.R-Forge.R-project.org/partykit")
3711 (synopsis "Toolkit for recursive partytioning")
3713 "This package provides a toolkit with infrastructure for representing,
3714 summarizing, and visualizing tree-structured regression and classification
3716 (license license:gpl2+)))
3718 (define-public r-plogr
3725 (uri (cran-uri "plogr" version))
3728 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
3729 (build-system r-build-system)
3730 (home-page "https://github.com/krlmlr/plogr")
3731 (synopsis "R bindings for the plog C++ logging library")
3733 "This package provides the header files for a stripped-down version of
3734 the plog header-only C++ logging library, and a method to log to R's standard
3736 (license license:expat)))
3738 (define-public r-pls
3745 (uri (cran-uri "pls" version))
3747 (base32 "1gqq8rcq6p0hs2gfzwfj690rz3pwywmnv8qzcv0wsd6aaqkskwzg"))))
3748 (build-system r-build-system)
3749 (home-page "https://mevik.net/work/software/pls.html")
3750 (synopsis "Partial Least Squares and Principal Component Regression")
3752 "The pls package implements multivariate regression methods: Partial Least
3753 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
3754 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
3757 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
3758 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
3759 @item multi-response models (or @dfn{PLS2})
3760 @item flexible cross-validation
3761 @item Jackknife variance estimates of regression coefficients
3762 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
3763 (R)MSEP, R², and correlation loadings
3764 @item formula interface, modelled after @code{lm()}, with methods for predict,
3765 print, summary, plot, update, etc.
3766 @item extraction functions for coefficients, scores, and loadings
3767 @item MSEP, RMSEP, and R² estimates
3768 @item multiplicative scatter correction (@dfn{MSC})
3770 (license license:gpl2)))
3779 (uri (cran-uri "ps" version))
3781 (base32 "1qaj9gyz7q09aadlnj5al53k2pa4axmzjsbndf5r0b51qqrcy842"))))
3782 (build-system r-build-system)
3783 (home-page "https://ps.r-lib.org")
3784 (synopsis "List, query, and manipulate system processes")
3786 "The ps package implements an API to list, query, and manipulate system
3787 processes. Most of its code is based on the @code{psutil} Python package.")
3788 (license license:bsd-3)))
3790 (define-public r-pkgbuild
3797 (uri (cran-uri "pkgbuild" version))
3799 (base32 "0j6v5nbp8kg1m3j999gd1qsbdmqcqm1mf28ngmm177miwv8q4skw"))))
3800 (build-system r-build-system)
3810 (home-page "https://github.com/r-pkgs/pkgbuild")
3811 (synopsis "Find tools needed to build R packages")
3813 "This package provides functions used to build R packages. It locates
3814 compilers needed to build R packages on various platforms and ensures the PATH
3815 is configured appropriately so R can use them.")
3816 (license license:gpl3)))
3818 (define-public r-pkgload
3825 (uri (cran-uri "pkgload" version))
3828 "03yr9mswx9nij27bp21q6c533zx310xwzhwm52dwr7554k42p4fn"))))
3829 (build-system r-build-system)
3838 (home-page "https://github.com/r-lib/pkgload")
3839 (synopsis "Simulate package installation and attach")
3841 "This package simulates the process of installing a package and then
3842 attaching it. This is a key part of the @code{devtools} package as it allows
3843 you to rapidly iterate while developing a package.")
3844 (license license:gpl3)))
3846 (define-public r-pvclust
3852 (uri (cran-uri "pvclust" version))
3855 "0082icm54k2yq60k06qpr92a626k39j2jr0046lva4ylmhxqb4kq"))))
3856 (build-system r-build-system)
3857 (home-page "https://github.com/shimo-lab/pvclust")
3859 "Hierarchical clustering with P-values via multiscale bootstrap resampling")
3860 (description "This package provides an implementation of multiscale bootstrap
3861 resampling for assessing the uncertainty in hierarchical cluster analysis. It
3862 provides an AU (approximately unbiased) P-value as well as a BP (bootstrap probability)
3863 value for each cluster in a dendrogram.")
3864 (license license:gpl2+)))
3866 (define-public r-rcpp
3873 (uri (cran-uri "Rcpp" version))
3875 (base32 "1gzqfn1xjawzig30ama3rldykqpcn6bd8sg684mrfvpmv96bi9cx"))))
3876 (build-system r-build-system)
3877 (home-page "http://www.rcpp.org")
3878 (synopsis "Seamless R and C++ integration")
3880 "The Rcpp package provides R functions as well as C++ classes which offer
3881 a seamless integration of R and C++. Many R data types and objects can be
3882 mapped back and forth to C++ equivalents which facilitates both writing of new
3883 code as well as easier integration of third-party libraries. Documentation
3884 about Rcpp is provided by several vignettes included in this package, via the
3885 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
3886 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
3887 @code{citation(\"Rcpp\")} for details on these last two.")
3888 (license license:gpl2+)))
3890 (define-public r-rcppml
3897 (uri (cran-uri "RcppML" version))
3899 (base32 "1ih8i7i6m221iw227mnl3rvnaw2l53h8fpnc4f8yn9sm10anap1j"))))
3900 (properties `((upstream-name . "RcppML")))
3901 (build-system r-build-system)
3902 (propagated-inputs (list r-matrix r-rcpp r-rcppeigen))
3903 (native-inputs (list r-knitr))
3904 (home-page "https://github.com/zdebruine/RcppML")
3905 (synopsis "Rcpp machine learning library")
3907 "This package provides fast machine learning algorithms including matrix
3908 factorization and divisive clustering for large sparse and dense matrices.")
3909 (license license:gpl2+)))
3911 (define-public r-rcppthread
3913 (name "r-rcppthread")
3918 (uri (cran-uri "RcppThread" version))
3921 "0iprpidf7q1wlrgr9dwiikb6apqk80pyjcyni56k64nl7lrkszhj"))))
3922 (properties `((upstream-name . "RcppThread")))
3923 (build-system r-build-system)
3925 "https://github.com/tnagler/RcppThread")
3926 (synopsis "R threading in C++")
3928 "This package provides a C++11-style thread class and thread pool that can
3929 safely be interrupted from R.")
3930 (license license:expat)))
3932 (define-public r-rcppnumerical
3934 (name "r-rcppnumerical")
3938 (uri (cran-uri "RcppNumerical" version))
3941 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
3942 (build-system r-build-system)
3944 (list r-rcpp r-rcppeigen))
3945 (home-page "https://github.com/yixuan/RcppNumerical")
3946 (synopsis"Numerical computing libraries integration with @code{Rcpp}")
3947 (description "This package provides a collection of libraries for numerical
3948 computing (numerical integration, optimization, etc.) and their integration
3950 (license license:gpl2+)))
3952 (define-public r-rcppxptrutils
3954 (name "r-rcppxptrutils")
3959 (uri (cran-uri "RcppXPtrUtils" version))
3961 (base32 "0hm57nf4dzgsmg4hjj6wikwjx93fgfwkmybw6ly4b58wi6qwml1l"))))
3962 (properties `((upstream-name . "RcppXPtrUtils")))
3963 (build-system r-build-system)
3964 (propagated-inputs (list r-rcpp))
3965 (home-page "https://github.com/Enchufa2/RcppXPtrUtils")
3966 (synopsis "XPtr add-ons for Rcpp")
3968 "This package provides the means to compile user-supplied C++ functions
3969 with Rcpp and retrieve an @code{XPtr} that can be passed to other C++
3971 (license license:expat)))
3973 (define-public r-bindr
3980 (uri (cran-uri "bindr" version))
3983 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
3984 (build-system r-build-system)
3985 (home-page "https://github.com/krlmlr/bindr")
3986 (synopsis "Parametrized active bindings")
3988 "This package provides a simple interface for creating active bindings
3989 where the bound function accepts additional arguments.")
3990 (license license:expat)))
3992 (define-public r-bindrcpp
3999 (uri (cran-uri "bindrcpp" version))
4002 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
4003 (build-system r-build-system)
4005 (list r-bindr r-plogr r-rcpp))
4006 (home-page "https://github.com/krlmlr/bindrcpp")
4007 (synopsis "Rcpp interface to active bindings")
4009 "This package provides an easy way to fill an environment with active
4010 bindings that call a C++ function.")
4011 (license license:expat)))
4013 (define-public r-auc
4020 (uri (cran-uri "AUC" version))
4023 "07xf47kypqbsg2mixmq6mnh4s89aqan9bgl6kfv6lbx8ajv2asw3"))))
4024 (properties `((upstream-name . "AUC")))
4025 (build-system r-build-system)
4026 (home-page "https://cran.r-project.org/web/packages/AUC")
4027 (synopsis "Compute the area under the curve of selected measures")
4029 "This package includes functions to compute the area under the curve of
4030 selected measures: the area under the sensitivity curve (AUSEC), the area
4031 under the specificity curve (AUSPC), the area under the accuracy
4032 curve (AUACC), and the area under the receiver operating characteristic
4033 curve (AUROC). The curves can also be visualized. Support for partial areas
4035 (license license:gpl2+)))
4037 (define-public r-calibrate
4039 (name "r-calibrate")
4044 (uri (cran-uri "calibrate" version))
4046 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
4047 (build-system r-build-system)
4050 (home-page "https://cran.r-project.org/web/packages/calibrate")
4051 (synopsis "Calibration of scatterplot and biplot axes")
4053 "This is a package for drawing calibrated scales with tick marks
4054 on (non-orthogonal) variable vectors in scatterplots and biplots.")
4055 (license license:gpl2)))
4057 (define-public r-shape
4064 (uri (cran-uri "shape" version))
4067 "0yqbrrx2ywmfl99s6d1n6jblc63k1mxbiqyv8y0kq8jws1g3w45r"))))
4068 (build-system r-build-system)
4069 (home-page "https://cran.r-project.org/web/packages/shape")
4070 (synopsis "Functions for plotting graphical shapes")
4072 "This package provides functions for plotting graphical shapes such as
4073 ellipses, circles, cylinders, arrows, ...")
4074 (license license:gpl3+)))
4076 (define-public r-globaloptions
4078 (name "r-globaloptions")
4083 (uri (cran-uri "GlobalOptions" version))
4085 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
4086 (properties `((upstream-name . "GlobalOptions")))
4087 (build-system r-build-system)
4090 (home-page "https://github.com/jokergoo/GlobalOptions")
4091 (synopsis "Generate functions to get or set global options")
4093 "This package provides more controls on the option values such as
4094 validation and filtering on the values, making options invisible or private.")
4095 (license license:gpl2+)))
4097 (define-public r-circlize
4104 (uri (cran-uri "circlize" version))
4107 "1iswb7dy08as3pbzxvhx5qlsbnwvp79nwg8m158nfz7y2d9xa0nn"))))
4108 (build-system r-build-system)
4110 (list r-colorspace r-globaloptions r-shape))
4113 (home-page "https://github.com/jokergoo/circlize")
4114 (synopsis "Circular visualization")
4116 "Circular layout is an efficient way to visualise huge amounts of
4117 information. This package provides an implementation of circular layout
4118 generation in R as well as an enhancement of available software. Its
4119 flexibility is based on the usage of low-level graphics functions such that
4120 self-defined high-level graphics can be easily implemented by users for
4121 specific purposes. Together with the seamless connection between the powerful
4122 computational and visual environment in R, it gives users more convenience and
4123 freedom to design figures for better understanding complex patterns behind
4124 multi-dimensional data.")
4125 (license license:gpl2+)))
4127 (define-public r-powerlaw
4134 (uri (cran-uri "poweRlaw" version))
4136 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
4137 (properties `((upstream-name . "poweRlaw")))
4138 (build-system r-build-system)
4143 (home-page "https://github.com/csgillespie/poweRlaw")
4144 (synopsis "Tools for the analysis of heavy tailed distributions")
4146 "This package provides an implementation of maximum likelihood estimators
4147 for a variety of heavy tailed distributions, including both the discrete and
4148 continuous power law distributions. Additionally, a goodness-of-fit based
4149 approach is used to estimate the lower cut-off for the scaling region.")
4150 ;; Any of these GPL versions.
4151 (license (list license:gpl2 license:gpl3))))
4153 (define-public r-compare
4160 (uri (cran-uri "compare" version))
4163 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
4164 (build-system r-build-system)
4165 (home-page "https://cran.r-project.org/web/packages/compare")
4166 (synopsis "Comparing objects for differences")
4168 "This package provides functions to compare a model object to a
4169 comparison object. If the objects are not identical, the functions can be
4170 instructed to explore various modifications of the objects (e.g., sorting
4171 rows, dropping names) to see if the modified versions are identical.")
4172 (license license:gpl2+)))
4174 (define-public r-dendextend
4176 (name "r-dendextend")
4181 (uri (cran-uri "dendextend" version))
4184 "06wjs8451hmnimzgngpzbai3yrgy33133vzzapa8jib9crdqi8sb"))))
4185 (build-system r-build-system)
4187 (list r-ggplot2 r-magrittr r-viridis))
4190 (home-page "https://cran.r-project.org/web/packages/dendextend")
4191 (synopsis "Extending 'dendrogram' functionality in R")
4193 "This package offers a set of functions for extending @code{dendrogram}
4194 objects in R, letting you visualize and compare trees of hierarchical
4195 clusterings. You can adjust a tree's graphical parameters (the color, size,
4196 type, etc of its branches, nodes and labels) and visually and statistically
4197 compare different dendrograms to one another.")
4198 ;; Any of these versions
4199 (license (list license:gpl2 license:gpl3))))
4201 (define-public r-getoptlong
4203 (name "r-getoptlong")
4208 (uri (cran-uri "GetoptLong" version))
4211 "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc"))))
4212 (properties `((upstream-name . "GetoptLong")))
4213 (build-system r-build-system)
4217 (list r-crayon r-globaloptions r-rjson))
4220 (home-page "https://github.com/jokergoo/GetoptLong")
4221 (synopsis "Parsing command-line arguments and variable interpolation")
4223 "This is yet another command-line argument parser which wraps the
4224 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
4225 use in R. It also provides a simple way for variable interpolation in R.")
4226 (license license:gpl2+)))
4228 (define-public r-fastmatch
4230 (name "r-fastmatch")
4235 (uri (cran-uri "fastmatch" version))
4238 "0qcq1gwl9pijgp34giyq5y9rk0ly3d7xza2b7r68xx63ifqa1vqx"))))
4239 (build-system r-build-system)
4240 (home-page "https://www.rforge.net/fastmatch")
4241 (synopsis "Fast match function")
4243 "This package provides a fast @code{match} replacement for cases that
4244 require repeated look-ups. It is slightly faster that R's built-in
4245 @code{match} function on first match against a table, but extremely fast on
4246 any subsequent lookup as it keeps the hash table in memory.")
4247 (license license:gpl2)))
4256 (uri (cran-uri "ff" version))
4259 "1yl3ipzz9bjkfy9bbna7xz5n7iz4lchnw5l7agww7by764yk6iqa"))))
4260 (build-system r-build-system)
4261 (propagated-inputs (list r-bit))
4262 (home-page "http://ff.r-forge.r-project.org/")
4263 (synopsis "Memory-efficient storage of large data on disk and access functions")
4265 "This package provides data structures that are stored on disk but
4266 behave (almost) as if they were in RAM by transparently mapping only a section
4268 ;; error Architecture not supported.
4269 (supported-systems (delete "aarch64-linux" %supported-systems))
4270 (license license:gpl2)))
4272 (define-public r-ffbase
4279 (uri (cran-uri "ffbase" version))
4282 "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk"))))
4283 (build-system r-build-system)
4285 (list r-bit r-fastmatch r-ff))
4286 (home-page "https://github.com/edwindj/ffbase")
4287 (synopsis "Basic statistical functions for package 'ff'")
4289 "This package extends the out of memory vectors of @code{ff} with
4290 statistical functions and other utilities to ease their usage.")
4291 (license license:gpl3)))
4293 (define-public r-prettyunits
4295 (name "r-prettyunits")
4300 (uri (cran-uri "prettyunits" version))
4303 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
4304 (build-system r-build-system)
4305 (home-page "https://github.com/gaborcsardi/prettyunits")
4306 (synopsis "Pretty, human readable formatting of quantities")
4308 "This package provides tools for pretty, human readable formatting of
4310 (license license:expat)))
4312 (define-public r-princurve
4314 (name "r-princurve")
4318 (uri (cran-uri "princurve" version))
4321 "0wzk329bxljkzz57y220lsfckpsn45w348m6dcxh29zbj0ik65h2"))))
4322 (build-system r-build-system)
4325 (home-page "https://github.com/rcannood/princurve")
4326 (synopsis "Fit a principal curve in arbitrary dimension")
4327 (description "This package provides procedures for fitting a principal
4328 curve to a data matrix in arbitrary dimensions.")
4329 (license license:gpl2)))
4331 (define-public r-reshape
4338 (uri (cran-uri "reshape" version))
4341 "0j203qmc076x5lp6q2xi4dq4xdb73jmsa42rpxp1c37knnrph4br"))))
4342 (build-system r-build-system)
4345 (home-page "http://had.co.nz/reshape")
4346 (synopsis "Flexibly reshape data")
4348 "Flexibly restructure and aggregate data using just two functions:
4349 @code{melt} and @code{cast}. This package provides them.")
4350 (license license:expat)))
4352 (define-public r-restrserve
4354 (name "r-restrserve")
4359 (uri (cran-uri "RestRserve" version))
4361 (base32 "03mlzhs2k728kwy6csp60m7qy8n9ma5dd37j87rzh07fcdlx8wim"))))
4362 (build-system r-build-system)
4374 (home-page "https://restrserve.org")
4375 (synopsis "R web API framework")
4377 "RestRserve is an R web API framework for building high-performance AND
4378 robust microservices and app backends. With Rserve backend on UNIX-like
4379 systems it is parallel by design. It will handle incoming requests in
4380 parallel - each request in a separate fork.")
4381 (license license:gpl2+)))
4383 (define-public r-progress
4390 (uri (cran-uri "progress" version))
4393 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
4394 (build-system r-build-system)
4396 (list r-crayon r-hms r-prettyunits r-r6))
4397 (home-page "https://github.com/gaborcsardi/progress")
4398 (synopsis "Terminal progress bars")
4400 "This package provides configurable progress bars. They may include
4401 percentage, elapsed time, and/or the estimated completion time. They work in
4402 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
4403 package also provides a C++ API, that works with or without Rcpp.")
4404 (license license:expat)))
4406 (define-public r-ggally
4413 (uri (cran-uri "GGally" version))
4416 "1r98zgh2grn8330cf26r1c20gl131zm778szvn5wj6q6pwv2yd9h"))))
4417 (properties `((upstream-name . "GGally")))
4418 (build-system r-build-system)
4434 (home-page "https://ggobi.github.io/ggally")
4435 (synopsis "Extension to ggplot2")
4437 "The R package ggplot2 is a plotting system based on the grammar of
4438 graphics. GGally extends ggplot2 by adding several functions to reduce the
4439 complexity of combining geometric objects with transformed data. Some of
4440 these functions include a pairwise plot matrix, a two group pairwise plot
4441 matrix, a parallel coordinates plot, a survival plot, and several functions to
4443 (license license:gpl2+)))
4445 (define-public r-proxy
4452 (uri (cran-uri "proxy" version))
4455 "0gsng2aggnljl4z82la9hpnd26hngzhj8fizx4wx22npqjj93694"))))
4456 (build-system r-build-system)
4457 (home-page "https://cran.r-project.org/web/packages/proxy")
4458 (synopsis "Distance and similarity measures")
4460 "This package provides an extensible framework for the efficient
4461 calculation of auto- and cross-proximities, along with implementations of the
4462 most popular ones.")
4463 (license license:gpl2)))
4472 (uri (cran-uri "sp" version))
4474 (base32 "077q1wh9ihhcn1338xspnd90hy16ljxsav1xcrxdxj4fyynhd6lk"))))
4475 (build-system r-build-system)
4480 (home-page "https://cran.r-project.org/web/packages/sp")
4481 (synopsis "Classes and methods for spatial data")
4483 "This package provides classes and methods for spatial data; the classes
4484 document where the spatial location information resides, for 2D or 3D data.
4485 Utility functions are provided, e.g. for plotting data as maps, spatial
4486 selection, as well as methods for retrieving coordinates, for subsetting,
4487 print, summary, etc.")
4488 (license license:gpl2+)))
4490 (define-public r-laplacesdemon
4492 (name "r-laplacesdemon")
4497 (uri (cran-uri "LaplacesDemon" version))
4499 (base32 "1dsfp65cg06f25zjzd5ib4qyn1alfhbhpgyvpcw5n6bszn13idap"))))
4500 (properties `((upstream-name . "LaplacesDemon")))
4501 (build-system r-build-system)
4502 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
4503 (synopsis "Complete environment for Bayesian inference")
4505 "This package provides a complete environment for Bayesian inference using
4506 a variety of different samplers.")
4507 (license license:expat)))
4509 (define-public r-rmtstat
4516 (uri (cran-uri "RMTstat" version))
4519 "1r1a2sdqv64m9cpm2pz6r8abf7l810126ayd8iq3gx86c7bjfj5v"))))
4520 (properties `((upstream-name . "RMTstat")))
4521 (build-system r-build-system)
4522 (home-page "https://cran.r-project.org/web/packages/RMTstat")
4523 (synopsis "Distributions, statistics and tests derived from random matrix theory")
4525 "This package provides functions for working with the Tracy-Widom laws
4526 and other distributions related to the eigenvalues of large Wishart
4528 (license license:bsd-3)))
4530 (define-public r-rmpi
4536 (uri (cran-uri "Rmpi" version))
4539 "06mxqgrimhfsag5giv810c7ycdbaycqs4qcj41pnfbj0jypw32im"))))
4540 (properties `((upstream-name . "Rmpi")))
4541 (build-system r-build-system)
4543 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
4544 #:phases (modify-phases %standard-phases
4545 (add-before 'install 'mpi-setup
4551 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
4552 (synopsis "R interface to message-passing interface (MPI)")
4554 "This package provides an interface (wrapper) to MPI APIs. It also
4555 provides an interactive R manager and worker environment.")
4556 (license license:gpl2+)))
4558 (define-public r-lmoments
4565 (uri (cran-uri "Lmoments" version))
4568 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
4569 (properties `((upstream-name . "Lmoments")))
4570 (build-system r-build-system)
4572 (list r-rcpp r-rcpparmadillo))
4573 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
4574 (synopsis "L-moments and quantile mixtures")
4576 "This package contains functions to estimate L-moments and trimmed
4577 L-moments from the data. It also contains functions to estimate the
4578 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
4579 quantile mixture from L-moments and trimmed L-moments.")
4580 (license license:gpl2)))
4582 (define-public r-distillery
4584 (name "r-distillery")
4589 (uri (cran-uri "distillery" version))
4592 "1ymmxyamkq0zbz2m4gllln1ihks2hcib6gs0mls92as79srz122b"))))
4593 (build-system r-build-system)
4594 (home-page "https://ral.ucar.edu/staff/ericg/")
4595 (synopsis "Functions for confidence intervals and object information")
4597 "This package provides some very simple method functions for confidence
4598 interval calculation and to distill pertinent information from a potentially
4599 complex object; primarily used in common with the packages extRemes and
4601 (license license:gpl2+)))
4603 (define-public r-etrunct
4609 (uri (cran-uri "etrunct" version))
4612 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr"))))
4613 (properties `((upstream-name . "etrunct")))
4614 (build-system r-build-system)
4615 (home-page "https://cran.r-project.org/web/packages/etrunct")
4616 (synopsis "Computes moments of univariate truncated T distribution")
4617 (description "This package computes moments of univariate truncated
4618 T distribution. There is only one exported function, @code{e_trunct},
4619 which should be seen for details.")
4620 (license license:expat)))
4622 (define-public r-excelr
4629 (uri (cran-uri "excelR" version))
4631 (base32 "1pb4sy54zjv5vrh7gjjv7qlpab74km6mfsmfyl0yhmr0jx01hrw0"))
4633 '(delete-file "inst/htmlwidgets/lib/jexcel/js/jexcel.min.js"))))
4634 (properties `((upstream-name . "excelR")))
4635 (build-system r-build-system)
4638 (modify-phases %standard-phases
4639 (add-after 'unpack 'process-javascript
4640 (lambda* (#:key inputs #:allow-other-keys)
4641 (with-directory-excursion "inst/htmlwidgets/lib/jexcel/js/"
4642 (let ((source (assoc-ref inputs "js-jexcel"))
4643 (target "jexcel.min.js"))
4644 (format #true "Processing ~a --> ~a~%"
4646 (invoke "esbuild" source "--minify"
4647 (string-append "--outfile=" target)))))))))
4649 `(("esbuild" ,esbuild)
4650 ;; There is no tag for this particular commit, but comparison of the
4651 ;; contents of the JavaScript files point to this commit as the most
4656 (uri (string-append "https://raw.githubusercontent.com/jspreadsheet/ce/"
4657 "8af1960f76e6803bebc5750013d2ebe95354e88a/dist/jexcel.js"))
4660 "0y88hsr9d8cpnvdmbm17m328pc4kc5wbcv02kzmhm0bryzhviw7h"))))))
4661 (propagated-inputs (list r-htmlwidgets r-jsonlite))
4662 (home-page "https://github.com/Swechhya/excelR")
4663 (synopsis "Wrapper of the JavaScript library jExcel")
4665 "This package provides an R interface to the jExcel library to
4666 create web-based interactive tables and spreadsheets compatible with
4667 spreadsheet software.")
4668 (license license:expat)))
4670 (define-public r-extremes
4677 (uri (cran-uri "extRemes" version))
4680 "19q560prq02h3bwk01jb68693qb5bhsv8wiqhia7v5knm34qv8x7"))))
4681 (properties `((upstream-name . "extRemes")))
4682 (build-system r-build-system)
4684 (list r-distillery r-lmoments))
4685 (home-page "https://www.assessment.ucar.edu/toolkit/")
4686 (synopsis "Extreme value analysis")
4688 "ExtRemes is a suite of functions for carrying out analyses on the
4689 extreme values of a process of interest; be they block maxima over long blocks
4690 or excesses over a high threshold.")
4691 (license license:gpl2+)))
4693 (define-public r-lmtest
4700 (uri (cran-uri "lmtest" version))
4703 "15yr2kx08wy085bnziqmj1p6hf9mg3qp2a8465jk2df6di6hsh34"))))
4704 (build-system r-build-system)
4709 (home-page "https://cran.r-project.org/web/packages/lmtest")
4710 (synopsis "Testing linear regression models")
4712 "This package provides a collection of tests, data sets, and examples for
4713 diagnostic checking in linear regression models. Furthermore, some generic
4714 tools for inference in parametric models are provided.")
4715 ;; Either version is okay
4716 (license (list license:gpl2 license:gpl3))))
4718 (define-public r-idr
4724 (uri (cran-uri "idr" version))
4727 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
4728 (build-system r-build-system)
4729 (home-page "https://cran.r-project.org/web/packages/idr/")
4730 (synopsis "Irreproducible discovery rate")
4732 "This is a package for estimating the copula mixture model and plotting
4733 correspondence curves in \"Measuring reproducibility of high-throughput
4734 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
4735 by Li, Brown, Huang, and Bickel")
4736 (license license:gpl2+)))
4738 (define-public r-inline
4744 (uri (cran-uri "inline" version))
4747 "1mcr9hgq6kkq03n7pkcccxa7vg8jma0q7lfxc5vvkc6snydk1s8f"))))
4748 (build-system r-build-system)
4749 (home-page "https://cran.r-project.org/web/packages/inline")
4750 (synopsis "Functions to inline C, C++, Fortran function calls from R")
4752 "This package provides functionality to dynamically define R functions
4753 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
4754 @code{.Call} calling conventions.")
4755 ;; Any version of the LGPL.
4756 (license license:lgpl3+)))
4758 (define-public r-inum
4764 (uri (cran-uri "inum" version))
4767 "1khkzja8lwn9075864vbyajqina9m588ahf1fsrrajrsqilyzssz"))))
4768 (build-system r-build-system)
4771 (home-page "https://cran.r-project.org/web/packages/inum/")
4772 (synopsis "Interval and enum-type representation of vectors")
4774 "This package provides an enum-type representation of vectors and
4775 representation of intervals, including a method of coercing variables
4777 (license license:gpl2)))
4778 (define-public r-invgamma
4784 (uri (cran-uri "invgamma" version))
4787 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a"))))
4788 (properties `((upstream-name . "invgamma")))
4789 (build-system r-build-system)
4790 (home-page "https://github.com/dkahle/invgamma")
4791 (synopsis "Inverse gamma distribution")
4792 (description "This package provides a light weight implementation of the
4793 standard distribution functions for the inverse gamma distribution, wrapping
4794 those for the gamma distribution in the @code{stats} package.")
4795 (license license:gpl2)))
4797 (define-public r-bdsmatrix
4799 (name "r-bdsmatrix")
4804 (uri (cran-uri "bdsmatrix" version))
4807 "1g300x11rv56f826mbv7mbb67a5xz3dv74hpjc18jh3q8gap3j7r"))))
4808 (properties `((upstream-name . "bdsmatrix")))
4809 (build-system r-build-system)
4810 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
4811 (synopsis "Routines for block diagonal symmetric matrices")
4813 "This package provides procedures to work with block diagonal symmetric
4814 matrices, a special case of sparse matrices.")
4815 (license license:lgpl2.0)))
4817 (define-public r-bbmle
4824 (uri (cran-uri "bbmle" version))
4827 "0mdj21q7k0fp4cj7la14vmcjmp49zqm57g7r6zrwmxpv0acwda46"))))
4828 (build-system r-build-system)
4838 (home-page "https://cran.r-project.org/web/packages/bbmle")
4839 (synopsis "Tools for General Maximum Likelihood Estimation")
4841 "This package provides methods and functions for fitting maximum
4842 likelihood models in R. This package modifies and extends the @code{mle}
4843 classes in the @code{stats4} package.")
4844 ;; Any version of the GPL
4845 (license license:gpl2+)))
4847 (define-public r-emdbook
4854 (uri (cran-uri "emdbook" version))
4857 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
4858 (build-system r-build-system)
4860 (list r-bbmle r-coda r-lattice r-mass r-plyr))
4861 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
4862 (synopsis "Support functions and data for \"Ecological Models and Data\"")
4864 "This package provides auxiliary functions and data sets for \"Ecological
4865 Models and Data\", a book presenting maximum likelihood estimation and related
4866 topics for ecologists (ISBN 978-0-691-12522-0).")
4868 (license (list license:gpl2 license:gpl3))))
4870 (define-public r-lpsolve
4877 (uri (cran-uri "lpSolve" version))
4880 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
4881 (properties `((upstream-name . "lpSolve")))
4882 (build-system r-build-system)
4883 (home-page "https://cran.r-project.org/web/packages/lpSolve")
4884 (synopsis "R interface to Lp_solve to solve linear/integer programs")
4886 "Lp_solve is software for solving linear, integer and mixed integer
4887 programs. This implementation supplies a \"wrapper\" function in C and some R
4888 functions that solve general linear/integer problems, assignment problems, and
4889 transportation problems.")
4890 (license license:lgpl2.0)))
4892 (define-public r-limsolve
4899 (uri (cran-uri "limSolve" version))
4902 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
4903 (properties `((upstream-name . "limSolve")))
4904 (build-system r-build-system)
4906 (list r-lpsolve r-mass r-quadprog))
4907 (native-inputs (list gfortran))
4908 (home-page "https://cran.r-project.org/web/packages/limSolve")
4909 (synopsis "Solving linear inverse models")
4911 "This package provides functions that:
4914 @item find the minimum/maximum of a linear or quadratic function,
4915 @item sample an underdetermined or overdetermined system,
4916 @item solve a linear system Ax=B for the unknown x.
4919 It includes banded and tridiagonal linear systems. The package calls Fortran
4920 functions from LINPACK.")
4922 (license (list license:gpl2+ license:gpl3+))))
4924 (define-public r-fitdistrplus
4926 (name "r-fitdistrplus")
4931 (uri (cran-uri "fitdistrplus" version))
4934 "0nhgjvwya95v6b9khbsgp44lw10xg35w61lmka1v6wq7yh827izk"))))
4935 (build-system r-build-system)
4937 (list r-mass r-survival))
4940 (home-page "http://riskassessment.r-forge.r-project.org")
4941 (synopsis "Fitting a parametric distribution from data")
4943 "This package extends the @code{fitdistr} function of the MASS package
4944 with several functions to help the fit of a parametric distribution to
4945 non-censored or censored data. Censored data may contain left-censored,
4946 right-censored and interval-censored values, with several lower and upper
4947 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
4948 provides moment matching (MME), quantile matching (QME) and maximum
4949 goodness-of-fit estimation (MGE) methods (available only for non-censored
4950 data). Weighted versions of MLE, MME and QME are available.")
4951 (license license:gpl2+)))
4953 (define-public r-energy
4960 (uri (cran-uri "energy" version))
4963 "19xyw5bkyzfk22gly2ca2nsznqnrhaq4a77727kr1k26bj3y8gal"))))
4964 (build-system r-build-system)
4966 (list r-boot r-gsl r-rcpp))
4967 (home-page "https://cran.r-project.org/web/packages/energy")
4968 (synopsis "Multivariate inference via the energy of data")
4970 "This package provides e-statistics (energy) tests and statistics for
4971 multivariate and univariate inference, including distance correlation,
4972 one-sample, two-sample, and multi-sample tests for comparing multivariate
4973 distributions, are implemented. Measuring and testing multivariate
4974 independence based on distance correlation, partial distance correlation,
4975 multivariate goodness-of-fit tests, clustering based on energy distance,
4976 testing for multivariate normality, distance components (disco) for
4977 non-parametric analysis of structured data, and other energy
4978 statistics/methods are implemented.")
4979 (license license:gpl2+)))
4981 (define-public r-suppdists
4983 (name "r-suppdists")
4988 (uri (cran-uri "SuppDists" version))
4991 "025b9nlxz62wk84295csyzbncpn80i3iby3sxdigf3swcgi2fmbb"))))
4992 (properties `((upstream-name . "SuppDists")))
4993 (build-system r-build-system)
4994 (home-page "https://cran.r-project.org/web/packages/SuppDists")
4995 (synopsis "Supplementary distributions")
4997 "This package provides ten distributions supplementing those built into
4998 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
4999 Spearman's rho, maximum F ratio, the Pearson product moment correlation
5000 coefficient, Johnson distributions, normal scores and generalized
5001 hypergeometric distributions. In addition two random number generators of
5002 George Marsaglia are included.")
5003 (license license:gpl2+)))
5005 (define-public r-ksamples
5012 (uri (cran-uri "kSamples" version))
5015 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
5016 (properties `((upstream-name . "kSamples")))
5017 (build-system r-build-system)
5020 (home-page "https://cran.r-project.org/web/packages/kSamples")
5021 (synopsis "K-Sample rank tests and their combinations")
5023 "This package provides tools to compares k samples using the
5024 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
5025 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
5026 test. It computes asymptotic, simulated or (limited) exact P-values, all
5027 valid under randomization, with or without ties, or conditionally under random
5028 sampling from populations, given the observed tie pattern. Except for Steel's
5029 test and the JT test it also combines these tests across several blocks of
5031 (license license:gpl2+)))
5033 (define-public r-cvst
5040 (uri (cran-uri "CVST" version))
5043 "0bgk0d6w3dyhb5s30idnp6jpb3m8wf3b79wqlg127wwm0cird8pg"))))
5044 (properties `((upstream-name . "CVST")))
5045 (build-system r-build-system)
5047 (list r-kernlab r-matrix))
5048 (home-page "https://cran.r-project.org/web/packages/CVST")
5049 (synopsis "Fast cross-validation via sequential testing")
5051 "This package implements the fast cross-validation via sequential
5052 testing (CVST) procedure. CVST is an improved cross-validation procedure
5053 which uses non-parametric testing coupled with sequential analysis to
5054 determine the best parameter set on linearly increasing subsets of the data.
5055 Additionally to the CVST the package contains an implementation of the
5056 ordinary k-fold cross-validation with a flexible and powerful set of helper
5057 objects and methods to handle the overall model selection process. The
5058 implementations of the Cochran's Q test with permutations and the sequential
5059 testing framework of Wald are generic and can therefore also be used in other
5061 (license license:gpl2+)))
5063 (define-public r-squarem
5070 (uri (cran-uri "SQUAREM" version))
5073 "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6"))))
5074 (properties `((upstream-name . "SQUAREM")))
5075 (build-system r-build-system)
5076 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
5077 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
5079 "This package provides algorithms for accelerating the convergence of
5080 slow, monotone sequences from smooth, contraction mapping such as the EM
5081 algorithm. It can be used to accelerate any smooth, linearly convergent
5082 acceleration scheme. A tutorial style introduction to this package is
5083 available in a vignette.")
5084 (license license:gpl2+)))
5086 (define-public r-progressr
5088 (name "r-progressr")
5093 (uri (cran-uri "progressr" version))
5095 (base32 "1ldf7hqsz8vbjggz31990sqqyhrbiilzcnyla1krjlkg595h50wg"))))
5096 (properties `((upstream-name . "progressr")))
5097 (build-system r-build-system)
5100 (home-page "https://progressr.futureverse.org")
5101 (synopsis "Inclusive, unifying API for progress updates")
5103 "This package provides a minimal, unifying API for scripts and packages
5104 to report progress updates from anywhere including when using parallel
5105 processing. The package is designed such that the developer can to focus on
5106 what progress should be reported on without having to worry about how to
5107 present it. The end user has full control of how, where, and when to render
5108 these progress updates.")
5109 (license license:gpl3+)))
5111 (define-public r-lava
5118 (uri (cran-uri "lava" version))
5121 "0bi3c1aqwlq7jbz4raz6vga4r264w7lldi0i62xjlbl7hnlgi23s"))))
5122 (build-system r-build-system)
5124 (list r-future-apply r-numderiv r-progressr r-squarem r-survival))
5127 (home-page "https://github.com/kkholst/lava")
5128 (synopsis "Latent variable models")
5130 "This package provides tools for the estimation and simulation of latent
5132 (license license:gpl3)))
5134 (define-public r-drr
5141 (uri (cran-uri "DRR" version))
5144 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
5145 (properties `((upstream-name . "DRR")))
5146 (build-system r-build-system)
5148 (list r-cvst r-kernlab r-matrix))
5149 (home-page "https://cran.r-project.org/web/packages/DRR")
5150 (synopsis "Dimensionality reduction via regression")
5152 "This package provides an implementation of dimensionality reduction via
5153 regression using Kernel Ridge Regression.")
5154 (license license:gpl3)))
5156 (define-public r-prodlim
5159 (version "2019.11.13")
5163 (uri (cran-uri "prodlim" version))
5166 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
5167 (build-system r-build-system)
5169 (list r-kernsmooth r-lava r-rcpp r-survival))
5170 (home-page "https://cran.r-project.org/web/packages/prodlim")
5171 (synopsis "Product-limit estimation for censored event history analysis")
5173 "This package provides a fast and user-friendly implementation of
5174 nonparametric estimators for censored event history (survival) analysis with
5175 the Kaplan-Meier and Aalen-Johansen methods.")
5176 (license license:gpl2+)))
5178 (define-public r-dimred
5185 (uri (cran-uri "dimRed" version))
5188 "1z8fqdc8mslvfix8ngxs1y2yrvlanp5581hwp2nzldj6mk5kn15b"))))
5189 (properties `((upstream-name . "dimRed")))
5190 (build-system r-build-system)
5192 (list r-drr r-magrittr))
5195 (home-page "https://github.com/gdkrmr/dimRed")
5196 (synopsis "Framework for dimensionality reduction")
5198 "This package provides a collection of dimensionality reduction
5199 techniques from R packages and provides a common interface for calling the
5201 (license license:gpl3)))
5203 (define-public r-timedate
5206 (version "3043.102")
5210 (uri (cran-uri "timeDate" version))
5213 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
5214 (properties `((upstream-name . "timeDate")))
5215 (build-system r-build-system)
5216 (home-page "https://www.rmetrics.org")
5217 (synopsis "Chronological and calendar objects")
5219 "This package provides an environment for teaching \"Financial
5220 Engineering and Computational Finance\" and for managing chronological and
5222 (license license:gpl2+)))
5224 (define-public r-magic
5231 (uri (cran-uri "magic" version))
5234 "1gybia2aq80ldk1d845y5srncfzbbmpqhgl7vfaz7qqqjs6d85j5"))))
5235 (build-system r-build-system)
5238 (home-page "https://github.com/RobinHankin/magic.git")
5239 (synopsis "Create and investigate magic squares")
5241 "This package provides a collection of efficient, vectorized algorithms
5242 for the creation and investigation of magic squares and hypercubes, including
5243 a variety of functions for the manipulation and analysis of arbitrarily
5244 dimensioned arrays.")
5245 (license license:gpl2)))
5247 (define-public r-rmysql
5254 (uri (cran-uri "RMySQL" version))
5257 "05aavyggyjv46awa7ggbxlfcy9707vak5kh7kj0ljdx8zga7xb7l"))))
5258 (properties `((upstream-name . "RMySQL")))
5259 (build-system r-build-system)
5261 (list `(,mariadb "dev") zlib))
5264 (home-page "https://github.com/r-dbi/RMySQL")
5265 (synopsis "Database interface and MySQL driver for R")
5267 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
5268 package contains an old implementation based on legacy code from S-PLUS which
5269 is being phased out. A modern MySQL client based on Rcpp is available from
5270 the RMariaDB package.")
5271 (license license:gpl2)))
5273 (define-public r-rpostgresql
5275 (name "r-rpostgresql")
5280 (uri (cran-uri "RPostgreSQL" version))
5283 "1fbixmnjp1kh6yiv8zhg8zi5ryvdf5j2jxv4agq5gcxf541s3g5x"))))
5284 (properties `((upstream-name . "RPostgreSQL")))
5285 (build-system r-build-system)
5290 (home-page "https://github.com/tomoakin/RPostgreSQL")
5291 (synopsis "R interface to the PostgreSQL database system")
5293 "This package provides a Database Interface (DBI) compliant driver for R
5294 to access PostgreSQL database systems.")
5295 ;; The whole package is released under GPL version 2. It includes code
5296 ;; under the PostgreSQL license.
5297 (license license:gpl2)))
5299 (define-public r-linprog
5306 (uri (cran-uri "linprog" version))
5309 "1d34m2nyk7m6j2dci69bhy5mlw479xax1517j7f14pq7vhpsm9l1"))))
5310 (build-system r-build-system)
5311 (propagated-inputs (list r-lpsolve))
5312 (home-page "http://linprog.r-forge.r-project.org/")
5313 (synopsis "Linear programming and optimization")
5315 "This package can be used to solve Linear Programming / Linear
5316 Optimization problems by using the simplex algorithm.")
5317 (license license:gpl2+)))
5319 (define-public r-geometry
5326 (uri (cran-uri "geometry" version))
5329 "1n7m0djqlhrv01l98r76grkki6cv4k4q2z6c7fksqgq4r2l6a14i"))))
5330 (build-system r-build-system)
5332 (list r-magic r-linprog r-lpsolve r-rcpp r-rcppprogress))
5333 (home-page "http://geometry.r-forge.r-project.org/")
5334 (synopsis "Mesh generator and surface tessellator")
5336 "This package makes the qhull library available in R, in a similar manner
5337 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
5338 intersections about a point, Voronoi diagrams, furthest-site Delaunay
5339 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
5340 and higher dimensions. It implements the Quickhull algorithm for computing
5341 the convex hull. Qhull does not support constrained Delaunay triangulations,
5342 or mesh generation of non-convex objects, but the package does include some R
5343 functions that allow for this. Currently the package only gives access to
5344 Delaunay triangulation and convex hull computation.")
5345 ;; The Qhull sources are included and are distributed under a custom
5346 ;; non-copyleft license. The R sources are released under GPL version 2.
5347 (license (list license:gpl2
5348 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
5350 (define-public r-ddalpha
5357 (uri (cran-uri "ddalpha" version))
5360 "1bjfgb3lbzhjb5wx9hzp90jppq7vnj59bmd2n9ymi8sh1570m9p4"))))
5361 (build-system r-build-system)
5372 (home-page "https://cran.r-project.org/web/packages/ddalpha")
5373 (synopsis "Depth-Based classification and calculation of data depth")
5375 "This package contains procedures for depth-based supervised learning,
5376 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
5377 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
5378 statistical depth function to a compact low-dimensional space, where the final
5379 classification is done. It also offers an extension to functional data and
5380 routines for calculating certain notions of statistical depth functions. 50
5381 multivariate and 5 functional classification problems are included.")
5382 (license license:gpl2)))
5384 (define-public r-gower
5391 (uri (cran-uri "gower" version))
5394 "0p9qx9aafkdm7wibfwk59jzw6vspsff6zwp84bc40lg0myxbf737"))))
5395 (build-system r-build-system)
5396 (home-page "https://github.com/markvanderloo/gower")
5397 (synopsis "Gower's distance")
5399 "This package provides tools to compute Gower's distance (or similarity)
5400 coefficient between records, and to compute the top-n matches between records.
5401 Core algorithms are executed in parallel on systems supporting OpenMP.")
5402 (license license:gpl3)))
5404 (define-public r-rcpproll
5411 (uri (cran-uri "RcppRoll" version))
5414 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
5415 (properties `((upstream-name . "RcppRoll")))
5416 (build-system r-build-system)
5419 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
5420 (synopsis "Efficient rolling and windowed operations")
5422 "This package provides fast and efficient routines for common rolling /
5423 windowed operations. Routines for the efficient computation of windowed mean,
5424 median, sum, product, minimum, maximum, standard deviation and variance are
5426 (license license:gpl2+)))
5428 (define-public r-ipred
5435 (uri (cran-uri "ipred" version))
5438 "162ckhqn24l0l5ih7qi2k3lxw5iprm1g5a34q1ik0b9wv5ia0s31"))))
5439 (build-system r-build-system)
5447 (home-page "https://cran.r-project.org/web/packages/ipred")
5448 (synopsis "Improved predictors")
5450 "This package provides improved predictive models by indirect
5451 classification and bagging for classification, regression and survival
5452 problems as well as resampling based estimators of prediction error.")
5453 (license license:gpl2+)))
5455 (define-public r-psych
5462 (uri (cran-uri "psych" version))
5465 "08f3byqwabgkqcxwpjbsxdcjkdg012iraqinw0fzskfl1srzkhyw"))))
5466 (build-system r-build-system)
5468 (list r-lattice r-mnormt r-nlme))
5471 (home-page "https://cran.r-project.org/web/packages/psych/")
5472 (synopsis "Procedures for psychological, psychometric, and personality research")
5474 "This package provides a general purpose toolbox for personality,
5475 psychometric theory and experimental psychology. Functions are primarily for
5476 multivariate analysis and scale construction using factor analysis, principal
5477 component analysis, cluster analysis and reliability analysis, although others
5478 provide basic descriptive statistics. Item Response Theory is done using
5479 factor analysis of tetrachoric and polychoric correlations. Functions for
5480 analyzing data at multiple levels include within and between group statistics,
5481 including correlations and factor analysis. Functions for simulating and
5482 testing particular item and test structures are included. Several functions
5483 serve as a useful front end for structural equation modeling. Graphical
5484 displays of path diagrams, factor analysis and structural equation models are
5485 created using basic graphics.")
5486 (license license:gpl2+)))
5488 (define-public r-generics
5495 (uri (cran-uri "generics" version))
5498 "162q9hdsnfcwjj255ahbi6v9vnyynvda7gb75p721y28j5xb7sk3"))))
5499 (build-system r-build-system)
5500 (home-page "https://github.com/r-lib/generics")
5501 (synopsis "Common S3 generics not provided by base R methods")
5503 "In order to reduce potential package dependencies and conflicts,
5504 generics provides a number of commonly used S3 generics that are not provided
5505 by base R methods related to model fitting.")
5506 (license license:gpl2)))
5508 (define-public r-broom
5515 (uri (cran-uri "broom" version))
5518 "16grzja9hz5mqpfzbp1r6zif1gp7swfadkm52340si9h8ifhk8b6"))))
5519 (build-system r-build-system)
5534 (home-page "https://github.com/tidyverse/broom")
5535 (synopsis "Convert statistical analysis objects into tidy data frames")
5537 "This package provides tools to convert statistical analysis objects from
5538 R into tidy data frames, so that they can more easily be combined, reshaped
5539 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
5540 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
5541 summarizes a model's statistical findings such as coefficients of a
5542 regression; @code{augment}, which adds columns to the original data such as
5543 predictions, residuals and cluster assignments; and @code{glance}, which
5544 provides a one-row summary of model-level statistics.")
5545 (license license:expat)))
5547 (define-public r-recipes
5554 (uri (cran-uri "recipes" version))
5557 "1950rvva19ms6xy9d3jx94gzy589qprk115zjjd0ib4qxgip601x"))))
5558 (build-system r-build-system)
5581 (home-page "https://github.com/topepo/recipes")
5582 (synopsis "Preprocessing tools to create design matrices")
5584 "Recipes is an extensible framework to create and preprocess design
5585 matrices. Recipes consist of one or more data manipulation and analysis
5586 \"steps\". Statistical parameters for the steps can be estimated from an
5587 initial data set and then applied to other data sets. The resulting design
5588 matrices can then be used as inputs into statistical or machine learning
5590 (license license:gpl2)))
5592 (define-public r-pdist
5599 (uri (cran-uri "pdist" version))
5602 "0bvg8si81hs79v39d7svv4zbv2p0sk2r6m9vamibvkh9qvl4x406"))))
5603 (build-system r-build-system)
5604 (home-page "https://github.com/jeffwong/pdist")
5605 (synopsis "Partitioned distance function")
5607 "Pdist computes the euclidean distance between rows of a matrix X and
5608 rows of another matrix Y. Previously, this could be done by binding the two
5609 matrices together and calling @code{dist}, but this creates unnecessary
5610 computation by computing the distances between a row of X and another row of
5611 X, and likewise for Y. Pdist strictly computes distances across the two
5612 matrices, not within the same matrix, making computations significantly faster
5613 for certain use cases.")
5614 (license license:gpl3+)))
5616 (define-public r-ggrepel
5623 (uri (cran-uri "ggrepel" version))
5626 "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9"))))
5627 (build-system r-build-system)
5629 (list r-ggplot2 r-rcpp r-rlang r-scales))
5631 (list r-knitr)) ; for vignettes
5632 (home-page "https://github.com/slowkow/ggrepel")
5633 (synopsis "Repulsive text and label geometries for ggplot2")
5635 "This package provides text and label geometries for ggplot2 that help to
5636 avoid overlapping text labels. Labels repel away from each other and away
5637 from the data points.")
5638 (license license:gpl3)))
5640 (define-public r-coro
5647 (uri (cran-uri "coro" version))
5649 (base32 "14irld29dipgfd34y0k351daqg9vqpnpdx8m3pxmqr1aiyj5f5cv"))))
5650 (properties `((upstream-name . "coro")))
5651 (build-system r-build-system)
5652 (propagated-inputs (list r-rlang))
5653 (native-inputs (list r-knitr))
5654 (home-page "https://github.com/r-lib/coro")
5655 (synopsis "Coroutines for R")
5657 "This package provides coroutines for R, a family of functions that can
5658 be suspended and resumed later on. This includes async functions (which
5659 await) and generators (which yield). Async functions are based on the
5660 concurrency framework of the @code{promises} package. Generators are based on
5661 a dependency free iteration protocol defined in @code{coro} and are compatible
5662 with iterators from the @code{reticulate} package.")
5663 (license license:expat)))
5665 (define-public r-corrplot
5672 (uri (cran-uri "corrplot" version))
5675 "1g98jk6xsl08z4n6sy5vriif99m31zhbz7j3dh1kfj4w7yb9zh78"))))
5676 (build-system r-build-system)
5679 (home-page "https://github.com/taiyun/corrplot")
5680 (synopsis "Visualization of a correlation matrix")
5682 "This package provides a graphical display of a correlation matrix or
5683 general matrix. It also contains some algorithms to do matrix reordering. In
5684 addition, corrplot is good at details, including choosing color, text labels,
5685 color labels, layout, etc.")
5686 ;; Any version of the GPL
5687 (license license:gpl2+)))
5689 (define-public r-stringdist
5691 (name "r-stringdist")
5696 (uri (cran-uri "stringdist" version))
5698 (base32 "1fv1hbdlm8qwx57b2aj50mw0say5k48awzavx65mfk67qp6ddk7g"))))
5699 (build-system r-build-system)
5700 (home-page "https://github.com/markvanderloo/stringdist")
5701 (synopsis "Approximate string matching and string distance functions")
5703 "This package implements an approximate string matching version of R's
5704 native @code{match} function. It can calculate various string distances based
5705 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment),
5706 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
5707 Jaro-Winkler). An implementation of soundex is provided as well. Distances
5708 can be computed between character vectors while taking proper care of encoding
5709 or between integer vectors representing generic sequences.")
5710 (license license:gpl3+)))
5712 (define-public r-ucminf
5719 (uri (cran-uri "ucminf" version))
5722 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
5723 (build-system r-build-system)
5724 (native-inputs (list gfortran))
5725 (home-page "https://cran.r-project.org/web/packages/ucminf/")
5726 (synopsis "General-purpose unconstrained non-linear optimization")
5728 "This package provides an implementation of an algorithm for
5729 general-purpose unconstrained non-linear optimization. The algorithm is of
5730 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
5731 search with a trust region type monitoring of the input to the line search
5732 algorithm. The interface of @code{ucminf} is designed for easy interchange
5733 with the package @code{optim}.")
5734 (license license:gpl2+)))
5736 (define-public r-usedist
5743 (uri (cran-uri "usedist" version))
5745 (base32 "0ddf1zcalbrn293qmr9kdzz3x16fzc4k1bwb1pjmwnspisqfi8kj"))))
5746 (properties `((upstream-name . "usedist")))
5747 (build-system r-build-system)
5748 (home-page "https://cran.r-project.org/package=usedist")
5749 (synopsis "Distance matrix utilities")
5751 "This package provides functions to re-arrange, extract, and work with
5753 (license license:gpl3)))
5755 (define-public r-useful
5761 (uri (cran-uri "useful" version))
5764 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
5765 (properties `((upstream-name . "useful")))
5766 (build-system r-build-system)
5776 (home-page "https://github.com/jaredlander/useful")
5777 (synopsis "Collection of handy, useful functions")
5778 (description "This package provides a set of little functions that have been
5779 found useful to do little odds and ends such as plotting the results of K-means
5780 clustering, substituting special text characters, viewing parts of a
5781 @code{data.frame}, constructing formulas from text and building design and
5782 response matrices.")
5783 (license license:bsd-3)))
5785 (define-public r-ordinal
5788 (version "2019.12-10")
5792 (uri (cran-uri "ordinal" version))
5795 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
5796 (build-system r-build-system)
5798 (list r-mass r-matrix r-numderiv r-ucminf))
5799 (home-page "https://github.com/runehaubo/ordinal")
5800 (synopsis "Regression models for ordinal data")
5802 "This package provides an implementation of cumulative link (mixed)
5803 models also known as ordered regression models, proportional odds models,
5804 proportional hazards models for grouped survival times and ordered models.
5805 Estimation is via maximum likelihood and mixed models are fitted with the
5806 Laplace approximation and adaptive Gauss-Hermite quadrature.")
5807 (license license:gpl2+)))
5809 (define-public r-jomo
5816 (uri (cran-uri "jomo" version))
5819 "0qq03zspmh8x2c8w882ynsw7wshr9b0fyrpwnqx5yc1xlzrqffcx"))))
5820 (build-system r-build-system)
5822 (list r-lme4 r-mass r-ordinal r-survival r-tibble))
5823 (home-page "https://cran.r-project.org/web/packages/jomo/")
5824 (synopsis "Multilevel Joint Modelling Multiple Imputation")
5826 "Similarly to Schafer's package pan, jomo is a package for multilevel
5827 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
5828 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
5829 possibility of handling binary and categorical data through latent normal
5830 variables, the option to use cluster-specific covariance matrices and to
5831 impute compatibly with the substantive model.")
5832 (license license:gpl2)))
5834 (define-public r-pan
5841 (uri (cran-uri "pan" version))
5844 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
5845 (build-system r-build-system)
5846 (native-inputs (list gfortran))
5847 (home-page "https://cran.r-project.org/web/packages/pan/")
5848 (synopsis "Multiple imputation for multivariate panel or clustered data")
5850 "This package implements multiple imputation for multivariate panel or
5852 (license license:gpl3)))
5854 (define-public r-mitml
5861 (uri (cran-uri "mitml" version))
5864 "00i18nnvrdrg91crgcp2a431xs71cawaip3xkqk2myv0iav3xga9"))))
5865 (build-system r-build-system)
5867 (list r-haven r-jomo r-pan))
5870 (home-page "https://cran.r-project.org/web/packages/mitml/")
5871 (synopsis "Tools for multiple imputation in multilevel modeling")
5873 "This package provides tools for multiple imputation of missing data in
5874 multilevel modeling. It includes a user-friendly interface to the packages
5875 pan and jomo, and several functions for visualization, data management and the
5876 analysis of multiply imputed data sets.")
5877 (license license:gpl2+)))
5879 (define-public r-mice
5886 (uri (cran-uri "mice" version))
5889 "01fnfrr7adp29s5kic95r9q0rdznkz2pjmziyimnrqzyicyvfyzq"))))
5890 (build-system r-build-system)
5901 (home-page "https://cran.r-project.org/web/packages/mice/")
5902 (synopsis "Multivariate imputation by chained equations")
5904 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
5905 implemented by the MICE algorithm as described in @url{Van Buuren and
5906 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
5907 variable has its own imputation model. Built-in imputation models are
5908 provided for continuous data (predictive mean matching, normal), binary
5909 data (logistic regression), unordered categorical data (polytomous logistic
5910 regression) and ordered categorical data (proportional odds). MICE can also
5911 impute continuous two-level data (normal model, pan, second-level variables).
5912 Passive imputation can be used to maintain consistency between variables.
5913 Various diagnostic plots are available to inspect the quality of the
5915 ;; Any of these two versions.
5916 (license (list license:gpl2 license:gpl3))))
5918 (define-public r-truncnorm
5920 (name "r-truncnorm")
5925 (uri (cran-uri "truncnorm" version))
5928 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
5929 (build-system r-build-system)
5930 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
5931 (synopsis "Truncated normal distribution")
5932 (description "This package provides functions for the truncated normal
5933 distribution with mean equal to @code{mean} and standard deviation equal to
5934 @code{sd}. It includes density, distribution, quantile, and expected value
5935 functions, as well as a random generation function.")
5936 (license license:gpl2)))
5938 (define-public r-rsolnp
5945 (uri (cran-uri "Rsolnp" version))
5948 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
5949 (properties `((upstream-name . "Rsolnp")))
5950 (build-system r-build-system)
5953 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
5954 (synopsis "General non-linear optimization")
5955 (description "The Rsolnp package implements a general non-linear augmented
5956 Lagrange multiplier method solver, a @dfn{sequential quadratic
5957 programming} (SQP) based solver).")
5958 ;; Any version of the GPL.
5959 (license license:gpl2+)))
5961 (define-public r-hardyweinberg
5963 (name "r-hardyweinberg")
5968 (uri (cran-uri "HardyWeinberg" version))
5971 "0b3szw090dsc3bkas2kvx787ww2i6zzg2qmdyivmqc8amx5arn6g"))))
5972 (properties `((upstream-name . "HardyWeinberg")))
5973 (build-system r-build-system)
5975 (list r-mice r-nnet r-rcpp r-rsolnp))
5976 (home-page "https://cran.r-project.org/package=HardyWeinberg")
5977 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
5979 "This package contains tools for exploring Hardy-Weinberg equilibrium for
5980 diallelic genetic marker data. All classical tests (chi-square, exact,
5981 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
5982 included in the package, as well as functions for power computation and for
5983 the simulation of marker data under equilibrium and disequilibrium. Routines
5984 for dealing with markers on the X-chromosome are included. Functions for
5985 testing equilibrium in the presence of missing data by using multiple
5986 imputation are also provided. Implements several graphics for exploring the
5987 equilibrium status of a large set of diallelic markers: ternary plots with
5988 acceptance regions, log-ratio plots and Q-Q plots.")
5989 (license license:gpl2+)))
5998 (uri (cran-uri "sm" version))
6001 "03z8igsjqr32x407asxvkrbayvm6yhv9xyfs0n8fkmv8zk5a41r6"))))
6002 (build-system r-build-system)
6003 (native-inputs (list gfortran))
6004 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
6005 (synopsis "Smoothing methods for nonparametric regression and density estimation")
6007 "This is software accompanying the book 'Applied Smoothing Techniques for
6008 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
6009 University Press. It provides smoothing methods for nonparametric regression
6010 and density estimation")
6011 (license license:gpl2+)))
6013 (define-public r-venndiagram
6015 (name "r-venndiagram")
6019 (uri (cran-uri "VennDiagram" version))
6022 "0ilcxcp8qskmb5cp7fyb7i0qizg42lrx0ny8ws3if90kfrglghp7"))))
6023 (properties `((upstream-name . "VennDiagram")))
6024 (build-system r-build-system)
6026 (list r-futile-logger))
6027 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
6028 (synopsis "Generate High-Resolution Venn and Euler Plots")
6030 "This package provides a set of functions to generate high-resolution
6031 Venn and Euler plots. It includes handling for several special cases,
6032 including two-case scaling, and extensive customization of plot shape and
6034 (license license:gpl2+)))
6036 (define-public r-vioplot
6043 (uri (cran-uri "vioplot" version))
6046 "1dmdasp3jldc41233z6r08w3j76vyyp9m3jrj7n4ahk48yd5siq6"))))
6047 (build-system r-build-system)
6052 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
6053 (synopsis "Violin plot")
6055 "This package provides a violin plot, which is a combination of a box
6056 plot and a kernel density plot.")
6057 (license license:bsd-3)))
6059 (define-public r-rsofia
6065 ;; This package has been removed from CRAN, so we can
6066 ;; only fetch it from the archives.
6067 (uri (string-append "https://cran.r-project.org/src/"
6068 "contrib/Archive/RSofia/RSofia_"
6072 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
6073 (properties `((upstream-name . "RSofia")))
6074 (build-system r-build-system)
6077 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
6078 (synopsis "Port of sofia-ml to R")
6079 (description "This package is a port of sofia-ml to R. Sofia-ml is a
6080 suite of fast incremental algorithms for machine learning that can be used for
6081 training models for classification or ranking.")
6082 (license license:asl2.0)))
6084 (define-public r-xts
6091 (uri (cran-uri "xts" version))
6094 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
6095 (build-system r-build-system)
6096 (propagated-inputs (list r-zoo))
6097 (home-page "https://github.com/joshuaulrich/xts")
6098 (synopsis "Extensible time series")
6100 "This package provides for uniform handling of R's different time-based
6101 data classes by extending @code{zoo}, maximizing native format information
6102 preservation and allowing for user-level customization and extension, while
6103 simplifying cross-class interoperability.")
6104 (license license:gpl2+)))
6106 (define-public r-performanceanalytics
6108 (name "r-performanceanalytics")
6113 (uri (cran-uri "PerformanceAnalytics" version))
6116 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
6118 `((upstream-name . "PerformanceAnalytics")))
6119 (build-system r-build-system)
6121 (list r-quadprog r-xts r-zoo))
6122 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
6123 (synopsis "Econometric tools for performance and risk analysis")
6124 (description "This is a collection of econometric functions for
6125 performance and risk analysis. This package aims to aid practitioners and
6126 researchers in utilizing the latest research in analysis of non-normal return
6127 streams. In general, it is most tested on return (rather than price) data on
6128 a regular scale, but most functions will work with irregular return data as
6129 well, and increasing numbers of functions will work with P&L or price data
6131 ;; Either version may be picked.
6132 (license (list license:gpl2 license:gpl3))))
6134 (define-public r-laeken
6141 (uri (cran-uri "laeken" version))
6144 "1p3ccbaydlr52p8qmgmm2l6kryvq6jjjx7mqn2vv0gpjaxqhyy92"))))
6145 (build-system r-build-system)
6147 (list r-boot r-mass))
6148 (home-page "https://cran.r-project.org/web/packages/laeken/")
6149 (synopsis "Estimation of indicators on social exclusion and poverty")
6150 (description "This package provides tools for the estimation of indicators
6151 on social exclusion and poverty, as well as an implementation of Pareto tail
6152 modeling for empirical income distributions.")
6153 (license license:gpl2+)))
6155 (define-public r-vcd
6162 (uri (cran-uri "vcd" version))
6165 "0nxkl1x39xf8l0apgvlbr30i8lasix7hyyc93g6514r8z8m1k23i"))))
6166 (build-system r-build-system)
6168 (list r-colorspace r-lmtest r-mass))
6169 (home-page "https://cran.r-project.org/web/packages/vcd/")
6170 (synopsis "Visualizing categorical data")
6171 (description "This package provides visualization techniques, data sets,
6172 summary and inference procedures aimed particularly at categorical data.
6173 Special emphasis is given to highly extensible grid graphics. The package was
6174 originally inspired by the book \"Visualizing Categorical Data\" by Michael
6175 Friendly and is now the main support package for a new book, \"Discrete Data
6176 Analysis with R\" by Michael Friendly and David Meyer (2015).")
6177 (license license:gpl2)))
6179 (define-public r-vcfr
6185 (uri (cran-uri "vcfR" version))
6188 "0lhxb3ac4fafwik9q3cds46svzf0hyca8k54chw3dpk50c0zz1yx"))))
6189 (build-system r-build-system)
6205 (home-page "https://github.com/knausb/vcfR")
6206 (synopsis "Manipulate and visualize VCF data")
6207 (description "This package facilitates easy manipulation of variant call
6208 format (VCF) data. Functions are provided to rapidly read from and write to
6209 VCF files. Once VCF data is read into R, a parser function extracts matrices
6210 of data. This information can then be used for quality control or other
6211 purposes. Additional functions provide visualization of genomic data. Once
6212 processing is complete data may be written to a VCF file. It also may be
6213 converted into other popular R objects. This package provides a link between
6214 VCF data and familiar R software.")
6215 (license license:gpl3)))
6217 (define-public r-ica
6224 (uri (cran-uri "ica" version))
6227 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
6228 (build-system r-build-system)
6229 (home-page "https://cran.r-project.org/web/packages/ica/")
6230 (synopsis "Independent component analysis")
6231 (description "This package provides tools for @dfn{Independent Component
6232 Analysis} (ICA) using various algorithms: FastICA,
6233 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
6234 of Eigenmatrices} (JADE).")
6235 (license license:gpl2+)))
6237 (define-public r-dtw
6244 (uri (cran-uri "dtw" version))
6247 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z"))))
6248 (build-system r-build-system)
6249 (propagated-inputs (list r-proxy))
6250 (home-page "http://dtw.r-forge.r-project.org/")
6251 (synopsis "Dynamic Time Warping Algorithms")
6252 (description "This package provides a comprehensive implementation of
6253 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
6254 optimal (least cumulative distance) alignment between points of two time
6255 series. Common DTW variants covered include local (slope) and global (window)
6256 constraints, subsequence matches, arbitrary distance definitions,
6257 normalizations, minimum variance matching, and so on.")
6258 (license license:gpl2+)))
6260 (define-public r-sdmtools
6263 (version "1.1-221.2")
6267 (uri (cran-uri "SDMTools" version))
6270 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
6271 (properties `((upstream-name . "SDMTools")))
6272 (build-system r-build-system)
6273 (propagated-inputs (list r-r-utils))
6274 (home-page "https://www.rforge.net/SDMTools/")
6275 (synopsis "Species distribution modelling tools")
6276 (description "This package provides a set of tools for post processing
6277 the outcomes of species distribution modeling exercises. It includes novel
6278 methods for comparing models and tracking changes in distributions through
6279 time. It further includes methods for visualizing outcomes, selecting
6280 thresholds, calculating measures of accuracy and landscape fragmentation
6282 (license license:gpl3+)))
6284 (define-public r-scatterplot3d
6286 (name "r-scatterplot3d")
6291 (uri (cran-uri "scatterplot3d" version))
6294 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
6295 (build-system r-build-system)
6296 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
6297 (synopsis "3D scatter plot")
6298 (description "This package provides an implementation of scatter plots for
6299 plotting. a three dimensional point cloud.")
6300 (license license:gpl2)))
6302 (define-public r-ggridges
6309 (uri (cran-uri "ggridges" version))
6312 "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm"))))
6313 (build-system r-build-system)
6315 (list r-ggplot2 r-plyr r-scales r-withr))
6318 (home-page "https://github.com/clauswilke/ggridges")
6319 (synopsis "Ridgeline plots in ggplot2")
6321 "Ridgeline plots provide a convenient way of visualizing changes in
6322 distributions over time or space. This package enables the creation of such
6323 plots in @code{ggplot2}.")
6324 (license license:gpl2)))
6326 (define-public r-ggjoy
6333 (uri (cran-uri "ggjoy" version))
6336 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
6337 (build-system r-build-system)
6339 (list r-ggplot2 r-ggridges))
6340 (home-page "https://github.com/clauswilke/ggjoy")
6341 (synopsis "Joyplots in ggplot2")
6342 (description "Joyplots provide a convenient way of visualizing changes in
6343 distributions over time or space. This package enables the creation of such
6344 plots in @code{ggplot2}.")
6345 (license license:gpl2)))
6347 (define-public r-cli
6354 (uri (cran-uri "cli" version))
6357 "0qqd4mscv8ndjbji7knprdlv2hhyk35gazagvapbjzq1p6yfpaf3"))))
6358 (build-system r-build-system)
6361 (home-page "https://github.com/r-lib/cli#readme")
6362 (synopsis "Helpers for developing command line interfaces")
6363 (description "This package provides a suite of tools designed to build
6364 attractive command line interfaces (CLIs). It includes tools for drawing
6365 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
6366 (license license:expat)))
6368 (define-public r-argparser
6370 (name "r-argparser")
6375 (uri (cran-uri "argparser" version))
6378 "0xcl0ivsbc4iw8s7027q4cx68j6s5lihbby0xa9pmlv4wjmcvdr6"))))
6379 (build-system r-build-system)
6380 (home-page "https://bitbucket.org/djhshih/argparser")
6381 (synopsis "Command-line argument parser")
6383 "This package provides a cross-platform command-line argument parser
6384 written purely in R with no external dependencies. It is useful with the
6385 Rscript front-end and facilitates turning an R script into an executable
6387 (license license:gpl3+)))
6389 (define-public r-debugme
6396 (uri (cran-uri "debugme" version))
6399 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
6400 (build-system r-build-system)
6401 (propagated-inputs (list r-crayon))
6402 (home-page "https://github.com/r-lib/debugme#readme")
6403 (synopsis "Debug R packages")
6405 "This package allows the user to specify debug messages as special string
6406 constants, and control debugging of packages via environment variables.")
6407 (license license:expat)))
6409 (define-public r-processx
6416 (uri (cran-uri "processx" version))
6418 (base32 "0kx6hvkkj6lh8lrdh819hvkx8nyq5aac53mkvpqyskwkmmlnf63m"))))
6419 (build-system r-build-system)
6422 (home-page "https://github.com/r-lib/processx3")
6423 (synopsis "Execute and control system processes")
6425 "This package provides portable tools to run system processes in the
6426 background. It can check if a background process is running; wait on a
6427 background process to finish; get the exit status of finished processes; kill
6428 background processes and their children; restart processes. It can read the
6429 standard output and error of the processes, using non-blocking connections.
6430 @code{processx} can poll a process for standard output or error, with a
6431 timeout. It can also poll several processes at once.")
6432 (license license:expat)))
6434 (define-public r-tsp
6441 (uri (cran-uri "TSP" version))
6444 "022k0972kcxb0w6qhx09l9cif8fmpkpvwddvgxiy60bx343ywzia"))))
6445 (properties `((upstream-name . "TSP")))
6446 (build-system r-build-system)
6447 (propagated-inputs (list r-foreach))
6448 (home-page "https://cran.r-project.org/web/packages/TSP/")
6449 (synopsis "Traveling salesperson problem (TSP)")
6450 (description "This package provides basic infrastructure and some
6451 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
6452 traveling salesman problem).")
6453 (license license:gpl3)))
6455 (define-public r-qap
6462 (uri (cran-uri "qap" version))
6465 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
6466 (build-system r-build-system)
6467 (native-inputs (list gfortran))
6468 (home-page "https://cran.r-project.org/web/packages/qap/")
6469 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
6470 (description "This package implements heuristics for the @dfn{quadratic
6471 assignment problem} (QAP). Currently only a simulated annealing heuristic is
6473 (license license:gpl3)))
6475 (define-public r-gclus
6482 (uri (cran-uri "gclus" version))
6485 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
6486 (build-system r-build-system)
6487 (propagated-inputs (list r-cluster))
6488 (home-page "https://cran.r-project.org/web/packages/gclus/")
6489 (synopsis "Clustering graphics")
6490 (description "This package orders panels in scatterplot matrices and
6491 parallel coordinate displays by some merit index. It contains various indices
6492 of merit, ordering functions, and enhanced versions of @code{pairs} and
6493 @code{parcoord} which color panels according to their merit level.")
6494 (license license:gpl2+)))
6496 (define-public r-webshot
6503 (uri (cran-uri "webshot" version))
6506 "1h6v94zwq0ypgi4vf8xlhp5k13j7f9061hx908177i68c6zg5i5p"))))
6507 (build-system r-build-system)
6509 (list r-callr r-jsonlite r-magrittr))
6510 (home-page "https://github.com/wch/webshot/")
6511 (synopsis "Take screenshots of web pages")
6513 "Webshot makes it easy to take screenshots of web pages from within R.
6514 It can also run Shiny applications locally and take screenshots of the
6515 application; and it can render and screenshot static as well as interactive R
6516 Markdown documents.")
6517 (license license:gpl2)))
6519 (define-public r-seriation
6521 (name "r-seriation")
6526 (uri (cran-uri "seriation" version))
6529 "0dlj0mqpg585m6i7yn0h878i8ag6pyqph98xkk42i2nvghpy01gr"))))
6530 (build-system r-build-system)
6539 (native-inputs (list gfortran))
6540 (home-page "https://s2.smu.edu/IDA/seriation/")
6541 (synopsis "Infrastructure for ordering objects using seriation")
6543 "This package provides infrastructure for seriation with an
6544 implementation of several seriation/sequencing techniques to reorder matrices,
6545 dissimilarity matrices, and dendrograms. It also provides (optimally)
6546 reordered heatmaps, color images and clustering visualizations like
6547 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
6549 (license license:gpl3)))
6551 (define-public r-xfun
6558 (uri (cran-uri "xfun" version))
6560 (base32 "0dgjkrlwl6rxmvdn6s1xrbiaa53hkfx2s7rqrbrc7c6shbkg6sfi"))))
6561 (build-system r-build-system)
6562 ;; knitr itself depends on xfun
6565 `(("r-knitr" ,r-knitr)))
6566 (home-page "https://github.com/yihui/xfun")
6567 (synopsis "Miscellaneous functions")
6569 "This package provides miscellaneous functions commonly used in other
6570 packages maintained by Yihui Xie.")
6571 (license license:expat)))
6573 (define-public r-utf8
6580 (uri (cran-uri "utf8" version))
6583 "1x6qg19z4qih9lk3mvnmx0vailm1khp5lylw4hlwz6rssj3yw6m7"))))
6584 (build-system r-build-system)
6586 (list r-knitr r-rmarkdown)) ; for vignettes
6587 (home-page "https://github.com/patperry/r-utf8")
6588 (synopsis "Unicode text processing")
6590 "This package provides tools to process and print UTF-8 encoded
6591 international text (Unicode). Input, validate, normalize, encode, format, and
6593 (license license:asl2.0)))
6595 (define-public r-zeallot
6602 (uri (cran-uri "zeallot" version))
6605 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
6606 (build-system r-build-system)
6607 (home-page "https://github.com/nteetor/zeallot")
6608 (synopsis "Multiple, unpacking, and destructuring assignment")
6610 "This package provides a @code{%<-%} operator to perform multiple,
6611 unpacking, and destructuring assignment in R. The operator unpacks the
6612 right-hand side of an assignment into multiple values and assigns these values
6613 to variables on the left-hand side of the assignment.")
6614 (license license:expat)))
6616 (define-public r-zlog
6622 (uri (cran-uri "zlog" version))
6625 "1d5j31p0h3rrn230087h3ngpvwknlisjv0f1qdbicdj9m177spci"))))
6626 (properties `((upstream-name . "zlog")))
6627 (build-system r-build-system)
6628 (native-inputs (list r-knitr))
6629 (home-page "https://cran.r-project.org/package=zlog")
6630 (synopsis "Transformation for laboratory easurements")
6632 "The @code{zlog} package offers functions to transform laboratory
6633 measurements into standardised z or @math{z(log)-values}. Therefore the lower
6634 and upper reference limits are needed. If these are not known they could be
6635 estimated from a given sample.")
6636 (license license:gpl3+)))
6638 (define-public r-vctrs
6645 (uri (cran-uri "vctrs" version))
6648 "1pb0wjpwix29q8d8p3wi72a9mp9mif7369pk31w238cs00g8hxln"))))
6649 (build-system r-build-system)
6651 (list r-cli r-glue r-rlang))
6654 (home-page "https://github.com/r-lib/vctrs")
6655 (synopsis "Vector helpers")
6657 "There are three main goals to the @code{vctrs} package:
6660 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
6661 @code{length()} and @code{class()}. These definitions are paired with a
6662 framework for type-coercion and size-recycling.
6663 @item To define type- and size-stability as desirable function properties, use
6664 them to analyse existing base function, and to propose better alternatives.
6665 This work has been particularly motivated by thinking about the ideal
6666 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
6667 @item To provide a new @code{vctr} base class that makes it easy to create new
6668 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
6669 a few new @code{vctrs} generics, making implementation considerably simpler
6672 (license license:gpl3)))
6674 (define-public r-pillar
6681 (uri (cran-uri "pillar" version))
6684 "1fqk18vc9ashf12gdqkdi6n1nj5lh324vwhgiib3b2fcb2bghhbq"))))
6685 (build-system r-build-system)
6698 (home-page "https://github.com/r-lib/pillar")
6699 (synopsis "Coloured formatting for columns")
6701 "This package provides a @code{pillar} generic designed for formatting
6702 columns of data using the full range of colours provided by modern
6704 (license license:gpl3)))
6706 (define-public r-pinfsc50
6712 (uri (cran-uri "pinfsc50" version))
6715 "1547xyxmfb7zi8h9bsm6k67dcw4hpp129xzvmgwfw7r6p4af47zd"))))
6716 (build-system r-build-system)
6717 (home-page "https://cran.r-project.org/web/packages/pinfsc50/")
6718 (synopsis "Genomic data for the plant pathogen Phytophthora infestans")
6719 (description "This package contains genomic data for the plant pathogen
6720 Phytophthora infestans. It includes a variant file, a sequence file and an
6721 annotation file. This package is intended to be used as example data for
6722 packages that work with genomic data.")
6723 (license license:gpl2+)))
6725 (define-public r-uuid
6732 (uri (cran-uri "uuid" version))
6735 "0bzlc2knmr338h4ykx8v8c2a1inizxafj8rh13kwii68gpp50nz7"))))
6736 (build-system r-build-system)
6737 (home-page "https://www.rforge.net/uuid")
6738 (synopsis "Tools for generating and handling of UUIDs")
6740 "This package provides tools for generating and handling of
6741 @dfn{Universally Unique Identifiers} (UUIDs).")
6742 (license license:expat)))
6744 (define-public r-tinytex
6751 (uri (cran-uri "tinytex" version))
6754 "1v95pjxdq0ma90jji5yqh8ihlcf35cmrqx9v0z649zh0q9vrnbpj"))))
6755 (build-system r-build-system)
6758 (home-page "https://github.com/yihui/tinytex")
6759 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
6761 "This package provides helper functions to install and maintain the LaTeX
6762 distribution named TinyTeX, a lightweight, cross-platform, portable, and
6763 easy-to-maintain version of TeX Live. This package also contains helper
6764 functions to compile LaTeX documents, and install missing LaTeX packages
6766 (license license:expat)))
6768 (define-public r-tinytest
6775 (uri (cran-uri "tinytest" version))
6778 "1mq31f7bzcz5bkgzl9khm1i80axfzra7gcjqxd2yqb4wrw1m3x4s"))))
6779 (properties `((upstream-name . "tinytest")))
6780 (build-system r-build-system)
6781 (home-page "https://github.com/markvanderloo/tinytest")
6782 (synopsis "Lightweight unit testing framework")
6784 "This package provides a lightweight unit testing framework. Main
6788 @item install tests with the package;
6789 @item test results are treated as data that can be stored and manipulated;
6790 @item test files are R scripts interspersed with test commands, that can be
6792 @item fully automated build-install-test sequence for packages;
6793 @item skip tests when not run locally (e.g. on CRAN);
6794 @item flexible and configurable output printing;
6795 @item compare computed output with output stored with the package;
6796 @item run tests in parallel;
6797 @item extensible by other packages;
6798 @item report side effects.
6801 (license license:gpl3)))
6803 (define-public r-network
6810 (uri (cran-uri "network" version))
6813 "1xrhzbci7ls4h05skdlirxl49jsvmylrqivz2kd6i33wh2ca324m"))))
6814 (build-system r-build-system)
6816 (list r-magrittr r-statnet-common r-tibble))
6817 (home-page "https://statnet.org/")
6818 (synopsis "Classes for relational data")
6820 "This package provides tools to create and modify network objects. The
6821 @code{network} class can represent a range of relational data types, and
6822 supports arbitrary vertex/edge/graph attributes.")
6823 (license license:gpl2+)))
6825 (define-public r-stabs
6832 (uri (cran-uri "stabs" version))
6835 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q"))))
6836 (build-system r-build-system)
6839 (home-page "https://github.com/hofnerb/stabs")
6840 (synopsis "Stability selection with error control")
6842 "This package provides resampling procedures to assess the stability of
6843 selected variables with additional finite sample error control for
6844 high-dimensional variable selection procedures such as Lasso or boosting.
6845 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
6846 complementary pairs stability selection with improved error bounds
6847 (Shah & Samworth, 2013) are implemented. The package can be combined with
6848 arbitrary user specified variable selection approaches.")
6849 (license license:gpl2)))
6851 (define-public r-rle
6858 (uri (cran-uri "rle" version))
6861 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40"))))
6862 (properties `((upstream-name . "rle")))
6863 (build-system r-build-system)
6864 (home-page "https://cran.r-project.org/web/packages/rle/")
6865 (synopsis "Common functions for run-length encoded vectors")
6867 "This package provides common @code{base} and @code{stats} methods for
6868 @code{rle} objects, aiming to make it possible to treat them transparently as
6870 (license license:gpl3)))
6872 (define-public r-statnet-common
6874 (name "r-statnet-common")
6879 (uri (cran-uri "statnet.common" version))
6882 "07djgc6qbxahiy5v15lfayxbj4188lxsb8xcs7hnbm2hic953bfx"))))
6884 `((upstream-name . "statnet.common")))
6885 (build-system r-build-system)
6888 (home-page "https://statnet.org")
6889 (synopsis "R scripts and utilities used by the Statnet software")
6890 (description "This package provides non-statistical utilities used by the
6891 software developed by the Statnet Project.")
6892 (license license:gpl3)))
6894 (define-public r-statcheck
6896 (name "r-statcheck")
6901 (uri (cran-uri "statcheck" version))
6904 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
6905 (build-system r-build-system)
6907 (list r-ggplot2 r-plyr r-rmarkdown))
6908 (home-page "https://cran.r-project.org/web/packages/statcheck/")
6909 (synopsis "Extract statistics from articles and recompute p-values")
6910 (description "This package can automatically extract statistical
6911 null-hypothesis significant testing (NHST) results from articles and recompute
6912 the p-values based on the reported test statistic and degrees of freedom to
6913 detect possible inconsistencies.")
6914 (license license:gpl2)))
6916 (define-public r-sna
6923 (uri (cran-uri "sna" version))
6926 "0ka319s1w857fj28ja1i1ljgv2h6ji4d69riqy9pwhvvghsa83s4"))))
6927 (build-system r-build-system)
6929 (list r-network r-statnet-common))
6930 (home-page "https://statnet.org")
6931 (synopsis "Tools for social network analysis")
6933 "This package provides a range of tools for social network analysis,
6934 including node and graph-level indices, structural distance and covariance
6935 methods, structural equivalence detection, network regression, random graph
6936 generation, and 2D/3D network visualization.")
6937 (license license:gpl2+)))
6939 (define-public r-tfisher
6946 (uri (cran-uri "TFisher" version))
6949 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
6950 (properties `((upstream-name . "TFisher")))
6951 (build-system r-build-system)
6953 (list r-matrix r-mvtnorm r-sn))
6954 (home-page "https://cran.r-project.org/web/packages/TFisher/")
6955 (synopsis "Optimal thresholding Fisher's p-value combination method")
6957 "This package provides the @dfn{cumulative distribution function} (CDF),
6958 quantile, and statistical power calculator for a collection of thresholding
6959 Fisher's p-value combination methods, including Fisher's p-value combination
6960 method, truncated product method and, in particular, soft-thresholding
6961 Fisher's p-value combination method which is proven to be optimal in some
6962 context of signal detection. The p-value calculator for the omnibus version
6963 of these tests are also included.")
6964 (license license:gpl2)))
6966 (define-public r-ttr
6973 (uri (cran-uri "TTR" version))
6976 "11xsmbvmxq2j119j2z58bx1fkkb2xlhmzc35z5fbwr3nchrfz6jd"))))
6977 (properties `((upstream-name . "TTR")))
6978 (build-system r-build-system)
6980 (list r-curl r-xts r-zoo))
6981 (home-page "https://github.com/joshuaulrich/TTR")
6982 (synopsis "Technical trading rules")
6984 "This package provides functions and data to construct technical trading
6986 (license license:gpl2)))
6988 (define-public r-leaflet-providers
6990 (name "r-leaflet-providers")
6995 (uri (cran-uri "leaflet.providers" version))
6997 (base32 "0yynrwv4xd5cdh49cwvfxm4ranarah9iiry2cd3b4fiihdfcg3wy"))))
6998 (properties `((upstream-name . "leaflet.providers")))
6999 (build-system r-build-system)
7000 (home-page "https://github.com/rstudio/leaflet.providers")
7001 (synopsis "Leaflet map tile providers")
7003 "This package contains third-party map tile provider information from
7004 Leaflet.js, to be used with the @code{leaflet} R package. Additionally,
7005 @code{leaflet.providers} enables users to retrieve up-to-date provider
7006 information between package updates.")
7007 (license license:bsd-2)))
7009 ;; This package contains a lot of minified JavaScript with unclear provenance.
7010 ;; When upgrading please make sure that all minified JavaScript files are
7011 ;; removed in a snippet and that the replacement sources correspond to the
7012 ;; original minified scripts.
7013 (define-public r-leaflet
7020 (uri (cran-uri "leaflet" version))
7022 (base32 "0xsng9n08i1w7qj4hbi706m6d8jm9ixrnwq5xac2s3csfm1s1xij"))
7026 (list "inst/htmlwidgets/lib/leaflet/leaflet.js"
7027 "inst/htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js"
7028 "inst/htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js"
7029 "inst/htmlwidgets/lib/jquery/jquery.min.js"
7030 "inst/htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js"
7031 "inst/htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js"
7032 "inst/htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js"
7033 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js"
7034 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js"
7035 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js"
7036 "inst/legacy/www/leaflet.js")))))
7037 (properties `((upstream-name . "leaflet")))
7038 (build-system r-build-system)
7040 `(#:modules ((guix build utils)
7041 (guix build r-build-system)
7044 (modify-phases %standard-phases
7045 (add-after 'unpack 'process-javascript
7046 (lambda* (#:key inputs #:allow-other-keys)
7047 ;; The inst directory contains some minified JavaScript files.
7048 ;; Regenerate them from sources.
7049 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-leaflet"))
7050 (with-directory-excursion "inst/"
7054 `(("/tmp/leaflet-src.js"
7055 "htmlwidgets/lib/leaflet/leaflet.js")
7056 (,(assoc-ref inputs "js-leaflet-measure")
7057 "htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js")
7058 (,(assoc-ref inputs "js-leaflet-omnivore")
7059 "htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js")
7060 (,(assoc-ref inputs "js-jquery")
7061 "htmlwidgets/lib/jquery/jquery.min.js")
7062 ("htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.js"
7063 "htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js")
7064 (,(assoc-ref inputs "js-bootstrap3")
7065 "htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js")
7066 ("htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.js"
7067 "htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js")
7068 (,(string-append (assoc-ref inputs "js-leaflet-markercluster")
7069 "/dist/leaflet.markercluster-src.js")
7070 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js")
7071 (,(assoc-ref inputs "js-leaflet-markercluster-freezable")
7072 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js")
7073 (,(assoc-ref inputs "js-leaflet-markercluster-layersupport")
7074 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js")
7075 (,(assoc-ref inputs "js-proj4leaflet")
7076 "htmlwidgets/plugins/Proj4Leaflet/proj4.min.js")
7077 ("legacy/www/leaflet-src.js"
7078 "legacy/www/leaflet.js"))))
7079 (lambda (sources targets)
7080 (for-each (lambda (source target)
7081 (format #true "Processing ~a --> ~a~%"
7083 (invoke "esbuild" source "--minify"
7084 (string-append "--outfile=" target)))
7085 sources targets)))))))))
7087 `(("esbuild" ,esbuild)
7092 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v3.3.7/dist/js/bootstrap.js")
7095 "1j1qjagwj0m3q322z9wxxnpkd8zbk6g3kl047dsbmqad6gmqvgha"))))
7099 (uri "https://code.jquery.com/jquery-1.12.4.js")
7102 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
7106 (uri "http://cdn.leafletjs.com/leaflet/v1.3.1/leaflet.zip")
7109 "10phzd2vczy3zm1b64whp2nna69cf9hlj2bndc9yq47vf3ddqx8f"))))
7110 ("js-leaflet-omnivore"
7113 (uri (string-append "https://api.tiles.mapbox.com/mapbox.js/plugins/"
7114 "leaflet-omnivore/v0.3.1/leaflet-omnivore.js"))
7117 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
7118 ("js-leaflet-markercluster"
7122 (url "https://github.com/Leaflet/Leaflet.markercluster.git")
7124 (file-name (git-file-name "js-leaflet-markercluster" "1.1.0"))
7127 "0ds8c7picqjmc86bm5n6hm8k71fwsa2cpgib19sbdamzr9hm0rs1"))))
7128 ("js-leaflet-markercluster-freezable"
7132 "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.Freezable/"
7133 "9db80a3fba7dff4aee940e05d3d4dceaa1fffcf9/src/freezable.js"))
7134 (file-name "leaflet-markercluster-freezable.js")
7137 "1k6sn5n0z2x3an91vwvkzmqq4b8ppswgk5hi5qrr79klas1hbx1k"))))
7138 ("js-leaflet-markercluster-layersupport"
7142 "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.LayerSupport/"
7143 "87f3848b92e0516d9c98f6d4cd175f7b8a4e3805/src/layersupport.js"))
7144 (file-name "leaflet-markercluster-layersupport.js")
7147 "15qa21xif94y762c65yxxysxykz3mma6y6agw3nxpr3s7wbb75ff"))))
7148 ("js-leaflet-measure"
7151 (uri "https://unpkg.com/leaflet-measure@1.5.2/dist/leaflet-measure.js")
7152 (file-name "js-leaflet-measure-1.5.2.js")
7155 "0ggg3ffmm7pj9ry4gssrh0a17pnad3p6gwi0dg98y819pmpqa7y0"))))
7159 (uri "https://raw.githubusercontent.com/kartena/Proj4Leaflet/1.0.2/lib/proj4.js")
7160 (file-name "js-proj4leaflet-1.0.2.js")
7163 "0vyrbf6gv2lyh4c2bzp5349ivwvvg28gpn87y52a7jdb13rlkpab"))))))
7178 (home-page "https://rstudio.github.io/leaflet/")
7179 (synopsis "Create interactive web maps with the JavaScript Leaflet library")
7181 "Create and customize interactive maps using the Leaflet JavaScript
7182 library and the @code{htmlwidgets} package. These maps can be used directly
7183 from the R console, from RStudio, in Shiny applications and R Markdown
7185 (license license:gpl3)))
7187 (define-public r-leaps
7194 (uri (cran-uri "leaps" version))
7197 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
7198 (build-system r-build-system)
7199 (native-inputs (list gfortran))
7200 (home-page "https://cran.r-project.org/web/packages/leaps/")
7201 (synopsis "Regression subset selection")
7203 "This package provides tools for regression subset selection, including
7204 exhaustive search.")
7205 (license license:gpl2+)))
7207 (define-public r-splus2r
7214 (uri (cran-uri "splus2R" version))
7217 "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x"))))
7218 (properties `((upstream-name . "splus2R")))
7219 (build-system r-build-system)
7220 (home-page "https://cran.r-project.org/web/packages/splus2R/")
7221 (synopsis "Supplemental S-PLUS functionality in R")
7223 "Currently there are many functions in S-PLUS that are missing in R. To
7224 facilitate the conversion of S-PLUS packages to R packages, this package
7225 provides some missing S-PLUS functionality in R.")
7226 (license license:gpl2)))
7228 (define-public r-ifultools
7230 (name "r-ifultools")
7235 (uri (cran-uri "ifultools" version))
7238 "16a7rbvlym3bnfm93ikr5kl0l86ppk0s41fva6idvcx765g3fqkk"))))
7239 (build-system r-build-system)
7241 (list r-mass r-splus2r))
7242 (home-page "https://cran.r-project.org/web/packages/ifultools/")
7243 (synopsis "Insightful research tools")
7244 (description "This package provides C code used by the wmtsa, fractal, and
7246 (license license:gpl2)))
7248 (define-public r-sapa
7255 (uri (cran-uri "sapa" version))
7258 "0kj681rd4c2lvqr926lb6f4qwp281x5274dg6vbk8pf5y7s0qlpc"))))
7259 (build-system r-build-system)
7261 (list r-ifultools r-splus2r))
7262 (home-page "https://cran.r-project.org/web/packages/sapa/")
7263 (synopsis "Spectral analysis for physical applications")
7264 (description "This package provides software for the book Spectral
7265 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
7266 Cambridge University Press, 1993.")
7267 (license license:gpl2)))
7269 (define-public r-aggregation
7271 (name "r-aggregation")
7276 (uri (cran-uri "aggregation" version))
7279 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
7280 (build-system r-build-system)
7281 (home-page "https://cran.r-project.org/web/packages/aggregation/")
7282 (synopsis "Methods for p-value aggregation")
7284 "This package contains functionality for performing the following methods
7285 of p-value aggregation: Fisher's method, the Lancaster method (weighted
7286 Fisher's method), and Sidak correction.")
7287 (license license:gpl3)))
7289 (define-public r-quantmod
7296 (uri (cran-uri "quantmod" version))
7299 "154fqhw46kc7r08zsj5fsg97hg93phsli3z14xwmz22xb50xymzp"))))
7300 (build-system r-build-system)
7302 (list r-curl r-ttr r-xts r-zoo))
7303 (home-page "https://cran.r-project.org/web/packages/quantmod/")
7304 (synopsis "Quantitative financial modelling framework")
7305 (description "This package provides a quantitative financial modelling
7306 framework to allow users to specify, build, trade, and analyse quantitative
7307 financial trading strategies.")
7308 (license license:gpl3)))
7310 (define-public r-tseries
7317 (uri (cran-uri "tseries" version))
7320 "0zr09ikaz96djcvnjbr8ah6waqzjy06f4yd4isshlwc391q20px5"))))
7321 (build-system r-build-system)
7323 (list r-quadprog r-quantmod r-zoo))
7326 (home-page "https://cran.r-project.org/web/packages/tseries/")
7327 (synopsis "Time series analysis and computational finance")
7329 "This package provides functions relating to time series analysis and
7330 computational finance.")
7331 (license license:gpl2)))
7333 (define-public r-wmtsa
7340 (uri (cran-uri "wmtsa" version))
7343 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
7344 (build-system r-build-system)
7346 (list r-ifultools r-mass r-splus2r))
7347 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
7348 (synopsis "Wavelet methods for time series analysis")
7350 "This package provides software to accompany the book \"Wavelet Methods
7351 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
7352 University Press, 2000.")
7353 (license license:gpl2)))
7355 (define-public r-tsa
7362 (uri (cran-uri "TSA" version))
7365 "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb"))))
7366 (properties `((upstream-name . "TSA")))
7367 (build-system r-build-system)
7369 (list r-leaps r-locfit r-mgcv r-tseries))
7370 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
7371 (synopsis "Time series analysis")
7373 "This package contains R functions and datasets detailed in the book
7374 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
7375 Cryer and Kung-Sik Chan.")
7376 (license license:gpl2+)))
7378 (define-public r-extradistr
7380 (name "r-extradistr")
7385 (uri (cran-uri "extraDistr" version))
7388 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
7389 (properties `((upstream-name . "extraDistr")))
7390 (build-system r-build-system)
7393 (home-page "https://github.com/twolodzko/extraDistr")
7394 (synopsis "Additional univariate and multivariate distributions")
7396 "This package implements density, distribution functions, quantile
7397 functions and random generation functions for a large number of univariate and
7398 multivariate distributions.")
7399 (license license:gpl2)))
7401 (define-public r-fractal
7408 (uri (cran-uri "fractal" version))
7411 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
7412 (build-system r-build-system)
7420 (home-page "https://cran.r-project.org/web/packages/fractal/")
7421 (synopsis "Fractal time series modeling and analysis")
7423 "This package provides tools for stochastic fractal and deterministic
7424 chaotic time series analysis.")
7425 (license license:gpl2)))
7427 (define-public r-urca
7434 (uri (cran-uri "urca" version))
7437 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
7438 (build-system r-build-system)
7439 (propagated-inputs (list r-nlme))
7440 (native-inputs (list gfortran))
7441 (home-page "https://cran.r-project.org/web/packages/urca/")
7442 (synopsis "Unit root and cointegration tests for time series data")
7444 "This package provides unit root and cointegration tests encountered in
7445 applied econometric analysis.")
7446 (license license:gpl2+)))
7448 (define-public r-cubature
7455 (uri (cran-uri "cubature" version))
7458 "0sfmcy5xpa40w3qn0jbg7b802wksl5k8glz9jpx77n159wn3nyq8"))))
7459 (build-system r-build-system)
7464 (home-page "https://github.com/bnaras/cubature")
7465 (synopsis "Adaptive multivariate integration over hypercubes")
7467 "This package is an R wrapper around the cubature C library for adaptive
7468 multivariate integration over hypercubes. This version provides both
7469 @code{hcubature} and @code{pcubature} routines in addition to a vector
7471 ;; The included cubature C library is released under GPLv2+, but the
7472 ;; wrapper declares the license to be GPLv3+.
7473 (license (list license:gpl2+ license:gpl3+))))
7475 (define-public r-trend
7482 (uri (cran-uri "trend" version))
7485 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
7486 (build-system r-build-system)
7488 (list r-extradistr))
7491 (home-page "https://cran.r-project.org/web/packages/trend/")
7492 (synopsis "Non-parametric trend tests and change-point detection")
7494 "The analysis of environmental data often requires the detection of
7495 trends and change-points. This package includes tests for trend
7496 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
7497 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
7498 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
7499 correlation trend test), change-point detection (Lanzante's test procedures,
7500 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
7501 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
7502 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
7503 sample Robust Rank-Order Distributional Test.")
7504 (license license:gpl3)))
7506 (define-public r-expm
7513 (uri (cran-uri "expm" version))
7516 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c"))))
7517 (build-system r-build-system)
7518 (propagated-inputs (list r-matrix))
7519 (native-inputs (list gfortran))
7520 (home-page "https://r-forge.r-project.org/projects/expm/")
7521 (synopsis "Tools for matrix exponentials and related quantities")
7523 "This package provides tools for the computation of the matrix
7524 exponential, logarithm, square root, and related quantities.")
7525 (license license:gpl2+)))
7527 (define-public r-complexplus
7529 (name "r-complexplus")
7534 (uri (cran-uri "complexplus" version))
7537 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
7538 (build-system r-build-system)
7540 (list r-expm r-matrix))
7541 (home-page "https://cran.r-project.org/web/packages/complexplus/")
7542 (synopsis "Functions of complex or real variables")
7544 "This package extends several functions to the complex domain, including
7545 the matrix exponential and logarithm, and the determinant.")
7546 (license license:gpl2)))
7548 (define-public r-phontools
7550 (name "r-phontools")
7555 (uri (cran-uri "phonTools" version))
7558 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
7559 (properties `((upstream-name . "phonTools")))
7560 (build-system r-build-system)
7561 (home-page "http://www.santiagobarreda.com/rscripts.html")
7562 (synopsis "Tools for phonetic and acoustic analyses")
7564 "This package contains tools for the organization, display, and analysis
7565 of the sorts of data frequently encountered in phonetics research and
7566 experimentation, including the easy creation of IPA vowel plots, and the
7567 creation and manipulation of WAVE audio files.")
7568 (license license:bsd-2)))
7577 (uri (cran-uri "np" version))
7580 "1a9kzn37cddwfdki5zjmzanxp75pccdjnsvqfrh84hhcsy51pcx3"))))
7581 (build-system r-build-system)
7583 (list r-boot r-cubature r-quadprog r-quantreg))
7584 (home-page "https://github.com/JeffreyRacine/R-Package-np")
7585 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
7586 (description "This package provides non-parametric (and semi-parametric)
7587 kernel methods that seamlessly handle a mix of continuous, unordered, and
7588 ordered factor data types.")
7589 ;; Any version of the GPL.
7590 (license license:gpl3+)))
7592 (define-public r-powerplus
7594 (name "r-powerplus")
7599 (uri (cran-uri "powerplus" version))
7602 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
7603 (build-system r-build-system)
7605 (list r-complexplus r-expm r-mass r-matrix r-phontools))
7606 (home-page "https://cran.r-project.org/web/packages/powerplus/")
7607 (synopsis "Exponentiation operations")
7609 "This package provides tools for the computation of matrix and scalar
7611 (license license:gpl2)))
7613 (define-public r-egg
7620 (uri (cran-uri "egg" version))
7623 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
7624 (properties `((upstream-name . "egg")))
7625 (build-system r-build-system)
7627 (list r-ggplot2 r-gridextra r-gtable))
7628 (home-page "https://cran.r-project.org/web/packages/egg")
7629 (synopsis "Extensions for ggplot2")
7631 "This package provides miscellaneous functions to help customize ggplot2
7632 objects. High-level functions are provided to post-process ggplot2 layouts
7633 and allow alignment between plot panels, as well as setting panel sizes to
7634 fixed values. Other functions include a custom @code{geom}, and helper
7635 functions to enforce symmetric scales or add tags to facetted plots.")
7636 (license license:gpl3)))
7638 (define-public r-heatmap3
7645 (uri (cran-uri "heatmap3" version))
7648 "0sfvizmmwfk1bjhn6zfx5a4qqfgj1ldg8x90b65crqibgfa36k2r"))))
7649 (build-system r-build-system)
7651 (list r-fastcluster))
7654 (home-page "https://cran.r-project.org/web/packages/heatmap3/")
7655 (synopsis "Improved heatmap package")
7657 "This package provides an improved heatmap package. It is completely
7658 compatible with the original R function @code{heatmap}, and provides more
7659 powerful and convenient features.")
7660 (license license:gpl2+)))
7662 (define-public r-heatmaply
7664 (name "r-heatmaply")
7669 (uri (cran-uri "heatmaply" version))
7672 "1w8yyzb68laxd4zxycvgmpqj5wnyidjgv1vbzbxndp9p92f2cp8a"))))
7673 (build-system r-build-system)
7691 (home-page "https://cran.r-project.org/package=heatmaply")
7692 (synopsis "Interactive cluster heat maps using plotly")
7694 "This package enables you to create interactive cluster heatmaps that can
7695 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
7696 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
7697 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
7698 a popular graphical method for visualizing high-dimensional data, in which a
7699 table of numbers is encoded as a grid of colored cells. The rows and columns
7700 of the matrix are ordered to highlight patterns and are often accompanied by
7702 ;; Either version of the license.
7703 (license (list license:gpl2 license:gpl3))))
7712 (uri (cran-uri "h5" version))
7715 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
7716 (build-system r-build-system)
7723 (home-page "https://github.com/mannau/h5")
7724 (synopsis "Interface to the HDF5 Library")
7726 "This package provides an S4 interface to the HDF5 library supporting
7727 fast storage and retrieval of R-objects like vectors, matrices and arrays to
7728 binary files in a language independent format. The HDF5 format can therefore
7729 be used as an alternative to R's save/load mechanism. Since h5 is able to
7730 access only subsets of stored data it can also handle data sets which do not
7732 (license license:bsd-2)))
7734 (define-public r-cgdsr
7741 (uri (cran-uri "cgdsr" version))
7744 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
7745 (build-system r-build-system)
7747 (list r-httr r-r-methodss3 r-r-oo))
7748 (home-page "https://github.com/cBioPortal/cgdsr")
7749 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
7751 "This package provides a basic set of R functions for querying the Cancer
7752 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
7753 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
7754 (license license:lgpl3)))
7756 (define-public r-import
7763 (uri (cran-uri "import" version))
7766 "19g4jnfg9pkvvsncw62yc15xlb97hfbdqxivpjd9jqi36i6mdjrg"))))
7767 (build-system r-build-system)
7770 (home-page "https://github.com/smbache/import")
7771 (synopsis "Import mechanism for R")
7773 "This is an alternative mechanism for importing objects from packages.
7774 The syntax allows for importing multiple objects from a package with a single
7775 command in an expressive way. The import package bridges some of the gap
7776 between using @code{library} (or @code{require}) and direct (single-object)
7777 imports. Furthermore the imported objects are not placed in the current
7778 environment. It is also possible to import objects from stand-alone @code{.R}
7780 (license license:expat)))
7782 (define-public r-shinyace
7789 (uri (cran-uri "shinyAce" version))
7792 "12mqvdh6rxsr61pc3pzla95r5f4l7xagjs2rcdr7c2lbqyxpx6aa"))))
7793 (properties `((upstream-name . "shinyAce")))
7794 (build-system r-build-system)
7796 (list r-shiny r-jsonlite))
7797 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
7798 (synopsis "Ace editor bindings for Shiny")
7800 "This package provides Ace editor bindings to enable a rich text editing
7801 environment within Shiny.")
7802 (license license:expat)))
7804 (define-public r-rafalib
7811 (uri (cran-uri "rafalib" version))
7813 (base32 "1dmxjl66bfdgrybhwyaa8d4i460liqcdw8b29a6w7shgksh29m0k"))))
7814 (properties `((upstream-name . "rafalib")))
7815 (build-system r-build-system)
7816 (propagated-inputs (list r-rcolorbrewer))
7817 (home-page "https://cran.r-project.org/package=rafalib")
7818 (synopsis "Convenience functions for routine data exploration")
7820 "This package provides a series of shortcuts for routine tasks to
7821 facilitate data exploration.")
7822 (license license:artistic2.0)))
7824 (define-public r-randomizr
7826 (name "r-randomizr")
7831 (uri (cran-uri "randomizr" version))
7834 "1grm0h3xkb0pdbbv0gd531g1kn6njp0gcy5fh153rrmajxgd8hhw"))))
7835 (properties `((upstream-name . "randomizr")))
7836 (build-system r-build-system)
7839 (home-page "https://declaredesign.org/r/randomizr/")
7840 (synopsis "Tools for common forms of random assignment and sampling")
7842 "This package provides tools for generating random assignments for common
7843 experimental designs and random samples for common sampling designs.")
7844 (license license:expat)))
7846 (define-public r-base64url
7848 (name "r-base64url")
7853 (uri (cran-uri "base64url" version))
7856 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
7857 (build-system r-build-system)
7860 (home-page "https://github.com/mllg/base64url")
7861 (synopsis "Fast and URL-safe base64 encoder and decoder")
7863 "This package provides a URL-safe base64 encoder and decoder. In
7864 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
7865 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
7866 encoder does not fill the string with trailing @code{=}. The resulting
7867 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
7868 and thus are safe to use in URLs or for file names. The package also comes
7869 with a simple base32 encoder/decoder suited for case insensitive file
7871 (license license:gpl3)))
7873 (define-public r-radiant-data
7875 (name "r-radiant-data")
7880 (uri (cran-uri "radiant.data" version))
7883 "0c5c99q13pwv6k0b07x3r2bxmh0h2w15h02xb1pincgs61qwi15k"))
7884 (modules '((guix build utils)))
7887 ;; Delete files that are under CC-NC-SA.
7888 (delete-file-recursively "inst/app/tools/help")
7890 (properties `((upstream-name . "radiant.data")))
7891 (build-system r-build-system)
7925 (home-page "https://github.com/radiant-rstats/radiant.data")
7926 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
7928 "The Radiant Data menu includes interfaces for loading, saving, viewing,
7929 visualizing, summarizing, transforming, and combining data. It also contains
7930 functionality to generate reproducible reports of the analyses conducted in
7932 (license license:agpl3)))
7934 (define-public r-algdesign
7936 (name "r-algdesign")
7941 (uri (cran-uri "AlgDesign" version))
7943 (base32 "01cx63wqr6yvgl5ml1lj6gh9p1sn42b6qcnsppcw7mvba9n652ar"))))
7944 (properties `((upstream-name . "AlgDesign")))
7945 (build-system r-build-system)
7946 (home-page "https://github.com/jvbraun/AlgDesign")
7947 (synopsis "Algorithmic experimental design")
7949 "This package provides tools to calculate exact and approximate theory
7950 experimental designs for D, A, and I criteria. Very large designs may be
7951 created. Experimental designs may be blocked or blocked designs created from
7952 a candidate list, using several criteria. The blocking can be done when whole
7953 and within plot factors interact.")
7954 (license license:gpl2+)))
7956 (define-public r-alluvial
7963 (uri (cran-uri "alluvial" version))
7965 (base32 "039frwrsxq1lb97s7vf2vbyyadimkigs628ymym06fxka53drdkp"))))
7966 (properties `((upstream-name . "alluvial")))
7967 (build-system r-build-system)
7968 (native-inputs (list r-knitr))
7969 (home-page "https://github.com/mbojan/alluvial")
7970 (synopsis "Create parallel sets plots (Alluvial Diagrams)")
7972 "This package creates alluvial diagrams (also known as parallel sets
7973 plots) for multivariate and time series-like data.")
7974 (license license:expat)))
7976 (define-public r-signal
7983 (uri (cran-uri "signal" version))
7986 "0qaf39vfmhn3d0bdjqd805ayfkaj48dkmf5dqd47bpk7dp21b837"))))
7987 (build-system r-build-system)
7988 (propagated-inputs (list r-mass))
7989 (native-inputs (list gfortran))
7990 (home-page "https://cran.r-project.org/web/packages/signal/")
7991 (synopsis "Signal processing")
7993 "This package provides a set of signal processing functions originally
7994 written for Matlab and GNU Octave. It includes filter generation utilities,
7995 filtering functions, resampling routines, and visualization of filter models.
7996 It also includes interpolation functions.")
7997 (license license:gpl2)))
7999 (define-public r-gsubfn
8006 (uri (cran-uri "gsubfn" version))
8009 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
8010 (build-system r-build-system)
8011 (propagated-inputs (list r-proto))
8012 (home-page "https://code.google.com/archive/p/gsubfn/")
8013 (synopsis "Utilities for strings and function arguments")
8015 "This package provides @code{gsubfn} which is like @code{gsub} but can
8016 take a replacement function or certain other objects instead of the
8017 replacement string. Matches and back references are input to the replacement
8018 function and replaced by the function output. @code{gsubfn} can be used to
8019 split strings based on content rather than delimiters and for quasi-perl-style
8020 string interpolation. The package also has facilities for translating
8021 formulas to functions and allowing such formulas in function calls instead of
8023 (license license:gpl2+)))
8025 (define-public r-sqldf
8032 (uri (cran-uri "sqldf" version))
8035 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
8036 (build-system r-build-system)
8038 (list r-chron r-dbi r-gsubfn r-proto r-rsqlite))
8039 (home-page "https://github.com/ggrothendieck/sqldf")
8040 (synopsis "Manipulate R data frames using SQL")
8042 "The @code{sqldf} function is typically passed a single argument which is
8043 an SQL select statement where the table names are ordinary R data frame names.
8044 @code{sqldf} transparently sets up a database, imports the data frames into
8045 that database, performs the SQL statement and returns the result using a
8046 heuristic to determine which class to assign to each column of the returned
8047 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
8048 used to read filtered files into R even if the original files are larger than
8049 R itself can handle.")
8050 (license license:gpl2)))
8052 (define-public r-abind
8059 (uri (cran-uri "abind" version))
8062 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
8063 (build-system r-build-system)
8064 (home-page "https://cran.r-project.org/web/packages/abind/")
8065 (synopsis "Combine multidimensional arrays")
8067 "This package provides tools to combine multidimensional arrays into a
8068 single array. This is a generalization of @code{cbind} and @code{rbind}. It
8069 works with vectors, matrices, and higher-dimensional arrays. It also provides
8070 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
8071 extracting and replacing data in arrays.")
8072 (license license:lgpl2.0+)))
8074 (define-public r-prroc
8081 (uri (cran-uri "PRROC" version))
8084 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
8085 (properties `((upstream-name . "PRROC")))
8086 (build-system r-build-system)
8087 (home-page "https://cran.r-project.org/web/packages/PRROC/")
8088 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
8090 "This package computes the areas under the @dfn{precision-recall} (PR)
8091 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
8092 contrast to other implementations, the interpolation between points of the PR
8093 curve is done by a non-linear piecewise function. In addition to the areas
8094 under the curves, the curves themselves can also be computed and plotted by a
8095 specific S3-method.")
8096 (license license:gpl3)))
8098 (define-public r-vim
8105 (uri (cran-uri "VIM" version))
8108 "0fbpm6y3hhiw8srnbc38k19b859jcqzsh78ib8yvj86gck5av0bm"))))
8109 (properties `((upstream-name . "VIM")))
8110 (build-system r-build-system)
8127 (home-page "https://github.com/alexkowa/VIM")
8128 (synopsis "Visualization and imputation of missing values")
8130 "This package provides tools for the visualization of missing and/or
8131 imputed values are introduced, which can be used for exploring the data and
8132 the structure of the missing and/or imputed values. Depending on this
8133 structure of the missing values, the corresponding methods may help to
8134 identify the mechanism generating the missing values and explore the
8135 data including missing values. In addition, the quality of imputation can be
8136 visually explored using various univariate, bivariate, multiple and
8137 multivariate plot methods.")
8138 (license license:gpl2+)))
8140 (define-public r-fnn
8147 (uri (cran-uri "FNN" version))
8150 "0nmynpiy3d2dnd5ngjf4m79jy02byhk43gj0xny9a6j8243f5c2j"))))
8151 (properties `((upstream-name . "FNN")))
8152 (build-system r-build-system)
8153 (home-page "https://cran.r-project.org/web/packages/FNN")
8154 (synopsis "Fast nearest neighbor search algorithms and applications")
8156 "This package provides cover-tree and kd-tree fast k-nearest neighbor
8157 search algorithms. Related applications including KNN classification,
8158 regression and information measures are implemented.")
8159 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
8160 ;; later can be used.
8161 (license license:gpl2+)))
8163 (define-public r-smoother
8170 (uri (cran-uri "smoother" version))
8173 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
8174 (build-system r-build-system)
8177 (home-page "https://cran.r-project.org/web/packages/smoother")
8178 (synopsis "Functions relating to the smoothing of numerical data")
8180 "This package provides a collection of methods for smoothing numerical
8181 data, commencing with a port of the Matlab gaussian window smoothing function.
8182 In addition, several functions typically used in smoothing of financial data
8184 (license license:gpl2)))
8186 (define-public r-riverplot
8188 (name "r-riverplot")
8193 (uri (cran-uri "riverplot" version))
8196 "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj"))))
8197 (build-system r-build-system)
8199 (list r-rcolorbrewer))
8202 (home-page "https://logfc.wordpress.com")
8203 (synopsis "Sankey or ribbon plots")
8205 "Sankey plots are a type of diagram that is convenient to illustrate how
8206 flow of information, resources etc. separates and joins, much like observing
8207 how rivers split and merge. For example, they can be used to compare
8208 different clusterings. This package provides an implementation of Sankey
8210 (license license:gpl2+)))
8212 (define-public r-dyn
8219 (uri (cran-uri "dyn" version))
8222 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
8223 (build-system r-build-system)
8226 (home-page "https://cran.r-project.org/web/packages/dyn")
8227 (synopsis "Time series regression")
8229 "This package provides the dyn class interfaces @code{ts}, @code{irts},
8230 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
8231 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
8232 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
8233 @code{randomForest::randomForest()} and other regression functions, allowing
8234 those functions to be used with time series including specifications that may
8235 contain lags, diffs and missing values.")
8237 (license license:gpl2+)))
8239 (define-public r-dynutils
8246 (uri (cran-uri "dynutils" version))
8248 (base32 "1pcj4igaw1g898xb42kcpzfmqy80xai5ki5bpnkf8hg738wm00qz"))))
8249 (properties `((upstream-name . "dynutils")))
8250 (build-system r-build-system)
8264 (native-inputs (list r-knitr))
8265 (home-page "https://github.com/dynverse/dynutils")
8266 (synopsis "Common functionality for the dynverse packages")
8268 "This package provides common functionality for the
8269 @url{https://dynverse.org,dynverse} packages. dynverse is created to support
8270 the development, execution, and benchmarking of trajectory inference
8272 (license license:expat)))
8274 (define-public r-catdap
8281 (uri (cran-uri "catdap" version))
8284 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
8285 (build-system r-build-system)
8288 (home-page "https://cran.r-project.org/web/packages/catdap/")
8289 (synopsis "Tools for categorical data analysis")
8291 "This package provides functions for analyzing multivariate data.
8292 Dependencies of the distribution of the specified variable (response
8293 variable) to other variables (explanatory variables) are derived and
8294 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
8295 (license license:gpl2+)))
8297 (define-public r-arules
8304 (uri (cran-uri "arules" version))
8307 "05g6ik4z87g83nlicmb380331f84sqchvv1vch49zb7rq6v8gw6r"))))
8308 (build-system r-build-system)
8310 (list r-generics r-matrix))
8311 (home-page "https://github.com/mhahsler/arules")
8312 (synopsis "Mining association rules and frequent itemsets")
8314 "This package provides an infrastructure for representing, manipulating
8315 and analyzing transaction data and patterns (frequent itemsets and association rules).
8316 It also provides C implementations of the association mining algorithms Apriori
8318 (license license:gpl3)))
8320 (define-public r-parsedate
8322 (name "r-parsedate")
8327 (uri (cran-uri "parsedate" version))
8330 "1c2cpsvma3fkx6zp191bpfvf5rmpsr13g8rzqk6ycyb0n7b9k4qy"))))
8331 (build-system r-build-system)
8332 (home-page "https://github.com/gaborcsardi/parsedate")
8334 "Recognize and parse dates in various formats")
8336 "This package provides three functions for dealing with dates:
8337 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
8338 time formats, @code{parse_date} parses dates in unspecified formats,
8339 and @code{format_iso_8601} formats a date in ISO 8601 format.")
8340 (license license:gpl2)))
8342 (define-public r-abc-data
8349 (uri (cran-uri "abc.data" version))
8352 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
8353 (properties `((upstream-name . "abc.data")))
8354 (build-system r-build-system)
8355 (home-page "https://cran.r-project.org/web/packages/abc.data/")
8356 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
8358 "This package contains data which are used by functions of the abc
8359 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
8360 algorithms for performing parameter estimation, model selection, and
8362 (license license:gpl3+)))
8364 (define-public r-abc
8371 (uri (cran-uri "abc" version))
8374 "16753lyzk2dfwgdjfyanwacqw3bvrwby52inq4709804labs6lnv"))))
8375 (build-system r-build-system)
8377 (list r-abc-data r-locfit r-mass r-nnet r-quantreg))
8378 (home-page "https://cran.r-project.org/web/packages/abc/")
8379 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
8381 "This package implements several @dfn{Approximate Bayesian
8382 Computation} (ABC) algorithms for performing parameter estimation, model
8383 selection, and goodness-of-fit. Cross-validation tools are also available for
8384 measuring the accuracy of ABC estimates, and to calculate the
8385 misclassification probabilities of different models.")
8386 (license license:gpl3+)))
8388 (define-public r-zip
8395 (uri (cran-uri "zip" version))
8398 "1n5ryjdj3i16b4mdp29wapgaklz3yzas5k8ffx7q6fa0jry9i5cz"))))
8399 (build-system r-build-system)
8400 (home-page "https://github.com/gaborcsardi/zip")
8401 (synopsis "Cross-platform Zip compression")
8403 "This package provides a cross-platform Zip compression library for R.
8404 It is a replacement for the @code{zip} function, that does not require any
8405 additional external tools on any platform.")
8406 (license license:cc0)))
8408 (define-public r-openxlsx
8415 (uri (cran-uri "openxlsx" version))
8418 "0695b265g7jwiqk5c3vmmfkvagx82bkpwhvqzhqaqmmn34l6vl35"))))
8419 (build-system r-build-system)
8421 (list r-rcpp r-stringi r-zip))
8424 (home-page "https://github.com/awalker89/openxlsx")
8425 (synopsis "Read, write and edit XLSX files")
8427 "This package simplifies the creation of Excel @code{.xlsx} files by
8428 providing a high level interface to writing, styling and editing worksheets.
8429 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
8430 and @code{XLConnect} packages with the added benefit of removing the
8431 dependency on Java.")
8432 (license license:gpl3)))
8434 (define-public r-rio
8441 (uri (cran-uri "rio" version))
8444 "04jlrhyl0791yxwcpp1s8p1hhkljnijlc5iaxpk56h41w63k39lz"))))
8445 (build-system r-build-system)
8456 (home-page "https://github.com/leeper/rio")
8457 (synopsis "Swiss-army knife for data I/O")
8459 "This package provides streamlined data import and export infrastructure
8460 by making assumptions that the user is probably willing to make: @code{import}
8461 and @code{export} determine the data structure from the file extension,
8462 reasonable defaults are used for data import and export (e.g.,
8463 @code{stringsAsFactors=FALSE}), web-based import is natively
8464 supported (including from SSL/HTTPS), compressed files can be read directly
8465 without explicit decompression, and fast import packages are used where
8466 appropriate. An additional convenience function, @code{convert}, provides a
8467 simple method for converting between file types.")
8468 (license license:gpl2)))
8470 (define-public r-maptools
8477 (uri (cran-uri "maptools" version))
8480 "1jgx8iiirj8qhrmh19mkisa35jcql7352dmc7lvwi5vxg3wjbvpk"))))
8481 (build-system r-build-system)
8483 (list r-foreign r-lattice r-sp))
8484 (home-page "https://r-forge.r-project.org/projects/maptools/")
8485 (synopsis "Tools for reading and handling spatial objects")
8487 "This package provides a set of tools for manipulating and reading
8488 geographic data, in particular ESRI Shapefiles. It includes binary access to
8489 GSHHG shoreline files. The package also provides interface wrappers for
8490 exchanging spatial objects with other R packages.")
8491 ;; The C source files from shapelib are released under the Expat license.
8492 ;; The R code is released under GPL version 2 or later.
8493 (license (list license:gpl2+
8496 (define-public r-later
8503 (uri (cran-uri "later" version))
8506 "0acqg29hcm2iq1418b54np7zb5pnr3xzrwc3ijv2pz9wra10ix88"))))
8507 (build-system r-build-system)
8509 (list r-rcpp r-rlang))
8512 (home-page "https://github.com/r-lib/later")
8513 (synopsis "Utilities for delaying function execution")
8515 "This package provides tools to execute arbitrary R or C functions some
8516 time after the current time, after the R execution stack has emptied.")
8517 (license license:gpl2+)))
8519 (define-public r-promises
8526 (uri (cran-uri "promises" version))
8529 "1dy4cbqw17awh4q8m7cy3anaj0n9iynabfzflb1g94cyj0bq4fld"))))
8530 (build-system r-build-system)
8532 (list r-later r-magrittr r-r6 r-rcpp r-rlang))
8535 (home-page "https://rstudio.github.io/promises")
8536 (synopsis "Abstractions for promise-based asynchronous programming")
8538 "This package provides fundamental abstractions for doing asynchronous
8539 programming in R using promises. Asynchronous programming is useful for
8540 allowing a single R process to orchestrate multiple tasks in the background
8541 while also attending to something else. Semantics are similar to JavaScript
8542 promises, but with a syntax that is idiomatic R.")
8543 (license license:expat)))
8545 (define-public r-dosnow
8552 (uri (cran-uri "doSNOW" version))
8555 "1f5v0k2w0b2478p6iqa3hn2lwd1x3rzc348n57nd38ka2vnsnz4i"))))
8556 (properties `((upstream-name . "doSNOW")))
8557 (build-system r-build-system)
8559 (list r-foreach r-iterators r-snow))
8560 (home-page "https://cran.r-project.org/web/packages/doSNOW")
8561 (synopsis "Foreach parallel adaptor for the snow package")
8563 "This package provides a parallel backend for the @code{%dopar%} function
8564 using the @code{snow} package.")
8565 (license license:gpl2)))
8567 (define-public r-fstcore
8574 (uri (cran-uri "fstcore" version))
8576 (base32 "1a5m68n2dqhi3r8wf5jwg4vjvl550c7wypcf5j0xmkvl836yg1lg"))))
8577 (properties `((upstream-name . "fstcore")))
8578 (build-system r-build-system)
8579 (propagated-inputs (list r-rcpp))
8580 (inputs (list zlib))
8581 (native-inputs (list pkg-config))
8582 (home-page "https://www.fstpackage.org/fstcore/")
8583 (synopsis "R bindings to the fstlib library")
8585 "The fstlib library provides multithreaded serialization of compressed
8586 data frames using the fst format. The fst format allows for random access of
8587 stored data and compression with the LZ4 and ZSTD compressors.")
8588 (license license:mpl2.0)))
8590 (define-public r-fst
8597 (uri (cran-uri "fst" version))
8600 "0r96inwrr960m7wmc80603bw2vvvwab225bh9dq3lalwhy4yiis4"))))
8601 (properties `((upstream-name . "fst")))
8602 (build-system r-build-system)
8603 (propagated-inputs (list r-fstcore r-rcpp))
8604 (home-page "http://www.fstpackage.org")
8605 (synopsis "Fast serialization of data frames")
8607 "The fst package for R provides a fast, easy and flexible way to
8608 serialize data frames. With access speeds of multiple GB/s, fst is
8609 specifically designed to unlock the potential of high speed solid state disks.
8610 Data frames stored in the fst format have full random access, both in column
8611 and rows. The fst format allows for random access of stored data and
8612 compression with the LZ4 and ZSTD compressors.")
8613 (license license:agpl3)))
8615 (define-public r-snowfall
8618 (version "1.84-6.1")
8621 (uri (cran-uri "snowfall" version))
8623 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
8624 (build-system r-build-system)
8627 (home-page "https://cran.r-project.org/web/packages/snowfall/")
8628 (synopsis "Easier cluster computing")
8629 (description "This package is a usability wrapper around snow for easier
8630 development of parallel R programs. This package offers e.g. extended error
8631 checks, and additional functions. All functions work in sequential mode, too,
8632 if no cluster is present or wished. The package is also designed as connector
8633 to the cluster management tool @code{sfCluster}, but can also used without
8635 (license license:gpl2+)))
8637 (define-public r-rgexf
8644 (uri (cran-uri "rgexf" version))
8647 "00c2zka1n3k7p1l0mlchr063s6x58p9r3fb64d4wgl4rvsq55q3f"))
8648 ;; Delete minified JavaScript files
8650 '(for-each delete-file
8651 '("inst/gexf-js/js/jquery-2.0.2.min.js"
8652 "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js"
8653 "inst/gexf-js/js/jquery.mousewheel.min.js")))))
8654 (properties `((upstream-name . "rgexf")))
8655 (build-system r-build-system)
8657 `(#:modules ((guix build utils)
8658 (guix build r-build-system)
8662 (modify-phases %standard-phases
8663 (add-after 'unpack 'process-javascript
8664 (lambda* (#:key inputs #:allow-other-keys)
8665 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-jquery-ui"))
8666 (with-directory-excursion "inst/gexf-js/js/"
8670 `((,(assoc-ref inputs "js-jquery")
8671 "jquery-2.0.2.min.js")
8672 ("/tmp/jquery-ui-1.10.3/ui/jquery-ui.js"
8673 "jquery-ui-1.10.3.custom.min.js")
8674 (,(assoc-ref inputs "js-jquery-mousewheel")
8675 "jquery.mousewheel.min.js"))))
8676 (lambda (sources targets)
8677 (for-each (lambda (source target)
8678 (format #true "Processing ~a --> ~a~%"
8680 (invoke "esbuild" source "--minify"
8681 (string-append "--outfile=" target)))
8682 sources targets)))))))))
8684 (list r-igraph r-servr r-xml))
8686 `(("r-knitr" ,r-knitr)
8687 ("esbuild" ,esbuild)
8692 (uri "https://code.jquery.com/jquery-2.0.2.js")
8695 "0v818bxpw48gdk8i95qqqij80r9jcgisi2r4ac6xnxca20h0gvfj"))))
8699 (uri "https://jqueryui.com/resources/download/jquery-ui-1.10.3.zip")
8702 "00xpfy0l69nj2yan4s8k65ldsrlfsjkmyw2dwcg93dc8mv454vxx"))))
8703 ("js-jquery-mousewheel"
8706 (uri "https://raw.githubusercontent.com/jquery/jquery-mousewheel/\
8707 3.0.6/jquery.mousewheel.js")
8710 "19lk5xy2s47bx8hsa7j6bg012f8yw6d770g230bcnm559kf4nc6v"))))))
8711 (home-page "https://gvegayon.github.io/rgexf")
8712 (synopsis "Build, import and export GEXF graph files")
8714 "Create, read and write GEXF (Graph Exchange XML Format) graph
8715 files (used in Gephi and others). It allows the user to easily build/read
8716 graph files including attributes, GEXF visual attributes (such as color, size,
8717 and position), network dynamics (for both edges and nodes) and edge weighting.
8718 Users can build/handle graphs element-by-element or massively through
8719 data-frames, visualize the graph on a web browser through gexf-js (a
8720 JavaScript library) and interact with the igraph package.")
8721 (license license:expat)))
8723 (define-public r-data-tree
8725 (name "r-data-tree")
8730 (uri (cran-uri "data.tree" version))
8733 "0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
8734 (properties `((upstream-name . "data.tree")))
8735 (build-system r-build-system)
8737 (list r-r6 r-stringi))
8740 (home-page "https://github.com/gluc/data.tree")
8741 (synopsis "General purpose hierarchical data structure")
8743 "Create tree structures from hierarchical data, and traverse the tree in
8744 various orders. Aggregate, cumulate, print, plot, convert to and from
8745 data.frame and more. This is useful for decision trees, machine learning,
8746 finance, conversion from and to JSON, and many other applications.")
8747 (license license:gpl2+)))
8749 (define-public r-dtplyr
8756 (uri (cran-uri "dtplyr" version))
8759 "1wyhhn16mvdj55k2xsh7vy489l7xk4mkz7pjrw16z87awk6yjh16"))))
8760 (properties `((upstream-name . "dtplyr")))
8761 (build-system r-build-system)
8775 (home-page "https://github.com/tidyverse/dtplyr")
8776 (synopsis "Data Table back-end for dplyr")
8778 "This package provides a @code{data.table} backend for @code{dplyr}. The
8779 goal of @code{dtplyr} is to allow you to write @code{dplyr} code that is
8780 automatically translated to the equivalent, but usually much faster,
8781 @code{data.table} code.")
8782 (license license:expat)))
8784 (define-public r-collapsibletree
8786 (name "r-collapsibletree")
8791 (uri (cran-uri "collapsibleTree" version))
8794 "0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
8797 ;; Delete minified JavaScript file
8798 (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js")
8801 `((upstream-name . "collapsibleTree")))
8802 (build-system r-build-system)
8805 (modify-phases %standard-phases
8806 (add-after 'unpack 'process-javascript
8807 (lambda* (#:key inputs #:allow-other-keys)
8808 (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/"
8809 (let ((source (assoc-ref inputs "d3.v4.js"))
8810 (target "d3.min.js"))
8811 (format #t "Processing ~a --> ~a~%"
8813 (invoke "esbuild" source "--minify"
8814 (string-append "--outfile=" target)))))))))
8816 (list r-data-tree r-htmlwidgets))
8818 `(("esbuild" ,esbuild)
8822 (uri "https://d3js.org/d3.v4.js")
8825 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
8826 (home-page "https://github.com/AdeelK93/collapsibleTree")
8827 (synopsis "Interactive collapsible tree diagrams using D3.js")
8829 "This is a package for interactive Reingold-Tilford tree diagrams created
8830 using D3.js, where every node can be expanded and collapsed by clicking on it.
8831 Tooltips and color gradients can be mapped to nodes using a numeric column in
8832 the source data frame.")
8833 (license license:gpl3+)))
8835 (define-public r-rappdirs
8842 (uri (cran-uri "rappdirs" version))
8845 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9"))))
8846 (build-system r-build-system)
8847 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
8848 (synopsis "Determine where to save data, caches, and logs")
8850 "This package provides an easy way to determine which directories on the
8851 user's computer should be used to save data, caches and logs. It is a port of
8852 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
8853 (license license:expat)))
8855 (define-public r-rastervis
8857 (name "r-rastervis")
8862 (uri (cran-uri "rasterVis" version))
8865 "0kgg6cm7xjqya2d46w0i1i1wjpkb8f99lyqy7rgwa7l9xmwzj5n1"))))
8866 (properties `((upstream-name . "rasterVis")))
8867 (build-system r-build-system)
8878 (home-page "https://oscarperpinan.github.io/rastervis/")
8879 (synopsis "Visualization methods for raster data")
8881 "This package provides methods for enhanced visualization and interaction
8882 with raster data. It implements visualization methods for quantitative data
8883 and categorical data, both for univariate and multivariate rasters. It also
8884 provides methods to display spatiotemporal rasters, and vector fields.")
8885 (license license:gpl3)))
8887 (define-public r-rentrez
8894 (uri (cran-uri "rentrez" version))
8897 "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv"))))
8898 (properties `((upstream-name . "rentrez")))
8899 (build-system r-build-system)
8901 (list r-httr r-jsonlite r-xml))
8904 (home-page "https://docs.ropensci.org/rentrez/")
8905 (synopsis "Entrez in R")
8907 "This package provides an R interface to the NCBI's EUtils API,
8908 allowing users to search databases like GenBank PubMed, process the results of
8909 those searches and pull data into their R sessions.")
8910 (license license:expat)))
8912 (define-public r-renv
8919 (uri (cran-uri "renv" version))
8922 "0bjq3ms5dg155clya62m462m93g90sxfxm7b4cqhqbx8vakskwdl"))))
8923 (properties `((upstream-name . "renv")))
8924 (build-system r-build-system)
8927 (home-page "https://rstudio.github.io/renv")
8928 (synopsis "Project environments")
8930 "This package provides a dependency management toolkit for R. Using
8931 renv, you can create and manage project-local R libraries, save the state of
8932 these libraries to a lockfile, and later restore your library as required.
8933 Together, these tools can help make your projects more isolated, portable, and
8935 (license license:expat)))
8937 (define-public r-learnr
8944 (uri (cran-uri "learnr" version))
8947 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
8948 (build-system r-build-system)
8964 (home-page "https://rstudio.github.io/learnr/")
8965 (synopsis "Interactive tutorials for R")
8967 "This package provides tools to create interactive tutorials using R
8968 Markdown. Use a combination of narrative, figures, videos, exercises, and
8969 quizzes to create self-paced tutorials for learning about R and R packages.")
8970 (license license:asl2.0)))
8972 (define-public r-analytics
8974 (name "r-analytics")
8979 (uri (cran-uri "analytics" version))
8982 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
8983 (build-system r-build-system)
8997 (home-page "https://cran.r-project.org/web/packages/analytics/")
8998 (synopsis "Collection of data analysis tools")
9000 "This package is a collection of data analysis tools. It includes tools
9001 for regression outlier detection in a fitted linear model, stationary
9002 bootstrap using a truncated geometric distribution, a comprehensive test for
9003 weak stationarity, column means by group, weighted biplots, and a heuristic to
9004 obtain a better initial configuration in non-metric MDS.")
9005 (license license:gpl2)))
9007 (define-public r-here
9014 (uri (cran-uri "here" version))
9016 (base32 "0srlr8h8qmr0wrmp7gs4g2ry5dni2hx8n947bik3s3a26f091v88"))))
9017 (properties `((upstream-name . "here")))
9018 (build-system r-build-system)
9019 (propagated-inputs (list r-rprojroot))
9020 (native-inputs (list r-knitr))
9021 (home-page "https://here.r-lib.org/")
9022 (synopsis "Simpler way to find files")
9024 "This package lets you construct paths to your project's files. Use the
9025 @code{here} function as a drop-in replacement for @code{file.path}, it will
9026 always locate the files relative to your project root.")
9027 (license license:expat)))
9029 (define-public r-reticulate
9031 (name "r-reticulate")
9036 (uri (cran-uri "reticulate" version))
9039 "0b1szzsqyc8wcfpkn5517bb1ds064vs2hky71my3p74kfngay991"))))
9040 (build-system r-build-system)
9041 (inputs (list python))
9053 (home-page "https://github.com/rstudio/reticulate")
9054 (synopsis "R interface to Python")
9056 "This package provides an interface from R to Python modules, classes,
9057 and functions. When calling into Python, R data types are automatically
9058 converted to their equivalent Python types. When values are returned from
9059 Python to R they are converted back to R types.")
9060 (license license:asl2.0)))
9062 (define-public r-bibtex
9069 (uri (cran-uri "bibtex" version))
9072 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv"))))
9073 (build-system r-build-system)
9074 (propagated-inputs (list r-stringr))
9075 (home-page "https://github.com/romainfrancois/bibtex")
9076 (synopsis "Bibtex parser")
9077 (description "This package provides a utility for R to parse a bibtex
9079 (license license:gpl2+)))
9081 (define-public r-billboarder
9083 (name "r-billboarder")
9088 (uri (cran-uri "billboarder" version))
9090 (base32 "189ngvg84rcwhrivxskmjv3srhadvzr4p1v8pf11axyv2qn01b0x"))
9092 '(delete-file "inst/htmlwidgets/lib/billboard/billboard.pkgd.min.js"))))
9093 (properties `((upstream-name . "billboarder")))
9094 (build-system r-build-system)
9097 (modify-phases %standard-phases
9098 (add-after 'unpack 'process-javascript
9099 (lambda* (#:key inputs #:allow-other-keys)
9100 (with-directory-excursion "inst/htmlwidgets/lib/billboard/"
9101 (let ((source (assoc-ref inputs "js-billboard"))
9102 (target "billboard.pkgd.min.js"))
9103 (format #true "Processing ~a --> ~a~%"
9105 (invoke "esbuild" source "--minify"
9106 (string-append "--outfile=" target)))))))))
9117 `(("r-knitr" ,r-knitr)
9118 ("esbuild" ,esbuild)
9119 ;; It is not ideal to use this concatenated (but not minified)
9120 ;; JavaScript file, as the original source is written in TypeScript.
9121 ;; However, this can still be considered source code as it is readable
9122 ;; and can be modified.
9126 (uri "https://unpkg.com/billboard.js@3.2.0/dist/billboard.js")
9129 "1kx5rqmn87pgal2cwmcij2rrnwa0fgcsw6y99m4i0l2sdm0qffv2"))))))
9130 (home-page "https://github.com/dreamRs/billboarder")
9131 (synopsis "Create interactive charts with the JavaScript Billboard library")
9133 "This package provides an @code{htmlwidgets} interface to billboard.js,
9134 a re-usable easy interface JavaScript chart library, based on D3 v4+. Chart
9135 types include line charts, scatterplots, bar/lollipop charts,
9136 histogram/density plots, pie/donut charts and gauge charts. All charts are
9137 interactive, and a proxy method is implemented to smoothly update a chart
9138 without rendering it again in shiny apps.")
9139 (license license:expat)))
9141 (define-public r-ggseqlogo
9143 (name "r-ggseqlogo")
9148 (uri (cran-uri "ggseqlogo" version))
9151 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
9152 (build-system r-build-system)
9153 (propagated-inputs (list r-ggplot2))
9154 (home-page "https://github.com/omarwagih/ggseqlogo")
9155 (synopsis "ggplot2 extension for drawing genetic sequence logos")
9157 "The range of functions provided by this package makes it possible to
9158 draw highly versatile genomic sequence logos. Features include, but are not
9159 limited to, modifying colour schemes and fonts used to draw the logo,
9160 generating multiple logo plots, and aiding the visualisation with annotations.
9161 Sequence logos can easily be combined with other ggplot2 plots.")
9162 ;; Unspecified version of the LGPL.
9163 (license license:lgpl3+)))
9165 (define-public r-ggsci
9172 (uri (cran-uri "ggsci" version))
9175 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
9176 (build-system r-build-system)
9178 (list r-ggplot2 r-scales))
9179 (home-page "https://nanx.me/ggsci/")
9180 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
9182 "This package provides a collection of ggplot2 color palettes inspired by
9183 plots in scientific journals, data visualization libraries, science fiction
9184 movies, and TV shows.")
9185 (license license:gpl3)))
9187 (define-public r-ggsignif
9194 (uri (cran-uri "ggsignif" version))
9197 "1ad774c7s7y4i00xd89lfigr9aybl94q98ch598k3rchanr4b1fa"))))
9198 (build-system r-build-system)
9203 (home-page "https://github.com/const-ae/ggsignif")
9204 (synopsis "Significance brackets for ggplot2")
9206 "Enrich your ggplots with group-wise comparisons. This package provides
9207 an easy way to indicate if two groups are significantly different. Commonly
9208 this is shown by a bracket on top connecting the groups of interest which
9209 itself is annotated with the level of significance. The package provides a
9210 single layer that takes the groups for comparison and the test as arguments
9211 and adds the annotation to the plot.")
9212 (license license:gpl3)))
9214 (define-public r-rstatix
9221 (uri (cran-uri "rstatix" version))
9224 "0330y8iziffqg8j9j5h9zv4qcdyf8ybhmzxrr9fzq9nc6bf1gbm5"))))
9225 (properties `((upstream-name . "rstatix")))
9226 (build-system r-build-system)
9239 (home-page "https://rpkgs.datanovia.com/rstatix/")
9240 (synopsis "Pipe-friendly framework for basic statistical tests")
9242 "This package provides a simple and intuitive pipe-friendly framework,
9243 coherent with the @code{tidyverse} design philosophy, for performing basic
9244 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
9245 correlation analyses. The output of each test is automatically transformed
9246 into a tidy data frame to facilitate visualization. Additional functions are
9247 available for reshaping, reordering, manipulating and visualizing correlation
9249 (license license:gpl2)))
9251 (define-public r-ggpubr
9258 (uri (cran-uri "ggpubr" version))
9261 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
9262 (build-system r-build-system)
9280 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
9281 (synopsis "ggplot2-based publication-ready plots")
9283 "The ggplot2 package is an excellent and flexible package for elegant
9284 data visualization in R. However the default generated plots require some
9285 formatting before we can send them for publication. The ggpubr package
9286 provides some easy-to-use functions for creating and customizing ggplot2-based
9287 publication-ready plots.")
9288 (license license:gpl2)))
9290 (define-public r-ellipse
9297 (uri (cran-uri "ellipse" version))
9300 "0im9d36dixpksms52v6nsb3l0z2c7wc25r9j0f08naj6qc8jpvq2"))))
9301 (build-system r-build-system)
9302 (home-page "https://cran.r-project.org/web/packages/ellipse/")
9303 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
9305 "This package contains various routines for drawing ellipses and
9306 ellipse-like confidence regions, implementing the plots described in Murdoch
9307 and Chow (1996), A graphical display of large correlation matrices, The
9308 American Statistician 50, 178-180. There are also routines implementing the
9309 profile plots described in Bates and Watts (1988), Nonlinear Regression
9310 Analysis and its Applications.")
9311 (license license:gpl2+)))
9313 (define-public r-flashclust
9315 (name "r-flashclust")
9320 (uri (cran-uri "flashClust" version))
9323 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
9324 (properties `((upstream-name . "flashClust")))
9325 (build-system r-build-system)
9326 (native-inputs (list gfortran))
9327 (home-page "https://cran.r-project.org/web/packages/flashClust/")
9328 (synopsis "Implementation of optimal hierarchical clustering")
9330 "This package provides a fast implementation of hierarchical
9332 (license license:gpl2+)))
9334 (define-public r-factominer
9336 (name "r-factominer")
9341 (uri (cran-uri "FactoMineR" version))
9344 "0lg8n9fxxk46nchnj4pbpqqf4swxfsq7r9jzr36dmd36kb7avqxr"))))
9345 (properties `((upstream-name . "FactoMineR")))
9346 (build-system r-build-system)
9361 (home-page "http://factominer.free.fr")
9362 (synopsis "Multivariate exploratory data analysis and data mining")
9364 "This package provides exploratory data analysis methods to summarize,
9365 visualize and describe datasets. The main principal component methods are
9366 available, those with the largest potential in terms of applications:
9367 principal component analysis (PCA) when variables are quantitative,
9368 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
9369 variables are categorical, Multiple Factor Analysis when variables are
9370 structured in groups, etc. and hierarchical cluster analysis.")
9371 (license license:gpl2+)))
9373 (define-public r-factoextra
9375 (name "r-factoextra")
9380 (uri (cran-uri "factoextra" version))
9383 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
9384 (build-system r-build-system)
9395 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
9396 (synopsis "Extract and visualize the results of multivariate data analyses")
9398 "This package provides some easy-to-use functions to extract and
9399 visualize the output of multivariate data analyses, including
9400 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
9401 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
9402 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
9403 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
9404 packages. It contains also functions for simplifying some clustering analysis
9405 steps and provides ggplot2-based elegant data visualization.")
9406 (license license:gpl2)))
9408 (define-public r-fansi
9415 (uri (cran-uri "fansi" version))
9418 "0sn0kflgcn2qrrv646pzqylm02cx8l5ws473ppmvla4xihyvi9w6"))))
9419 (build-system r-build-system)
9421 (list r-knitr)) ; for vignettes
9422 (home-page "https://github.com/brodieG/fansi")
9423 (synopsis "ANSI control sequence aware string functions")
9425 "This package provides counterparts to R string manipulation functions
9426 that account for the effects of ANSI text formatting control sequences.")
9427 (license license:gpl2+)))
9429 (define-public r-nbclust
9436 (uri (cran-uri "NbClust" version))
9439 "0k5hr4zgx4gp1n62xchgz2zvyl35ba2cnczhhvj8rfbg2n4hx6qs"))))
9440 (properties `((upstream-name . "NbClust")))
9441 (build-system r-build-system)
9442 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
9443 (synopsis "Determine the best number of clusters in a data set")
9445 "NbClust provides 30 indexes for determining the optimal number of
9446 clusters in a data set and offers the best clustering scheme from different
9447 results to the user.")
9448 (license license:gpl2)))
9450 (define-public r-hdf5r
9457 (uri (cran-uri "hdf5r" version))
9460 "0bv2q4ir73sbk5ra2q4mc8wbcmiwkws8k0mjlnx9ysi2mdrm3dw7"))))
9461 (build-system r-build-system)
9465 (list r-bit64 r-r6))
9468 (home-page "https://hhoeflin.github.io/hdf5r")
9469 (synopsis "Interface to the HDF5 binary data format")
9471 "HDF5 is a data model, library and file format for storing and managing
9472 large amounts of data. This package provides a nearly feature complete,
9473 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
9474 functionality is added so that HDF5 objects behave very similar to their
9475 corresponding R counterparts.")
9476 (license license:asl2.0)))
9478 (define-public r-itertools
9480 (name "r-itertools")
9485 (uri (cran-uri "itertools" version))
9488 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
9489 (build-system r-build-system)
9492 (home-page "https://cran.r-project.org/web/packages/itertools/")
9493 (synopsis "Iterator tools")
9495 "This package provides various tools for creating iterators, many
9496 patterned after functions in the Python @code{itertools} module, and others
9497 patterned after functions in the snow package.")
9498 (license license:gpl2)))
9500 (define-public r-itsadug
9507 (uri (cran-uri "itsadug" version))
9509 (base32 "0759l7hhvj05dp92pz59xwrxjm9s1iwkwrdhs68l0fq57550j70l"))))
9510 (properties `((upstream-name . "itsadug")))
9511 (build-system r-build-system)
9512 (propagated-inputs (list r-mgcv r-plotfunctions))
9513 (native-inputs (list r-knitr))
9514 (home-page "https://cran.r-project.org/package=itsadug")
9515 (synopsis "Interpreting time series and autocorrelated data using GAMMs")
9517 "@dfn{Generalized Additive Mixed Modeling} (GAMM; Lin & Zhang, 1999) as
9518 implemented in the R package @code{mgcv} is a nonlinear regression analysis
9519 which is particularly useful for time course data such as EEG, pupil dilation,
9520 gaze data (eye tracking), and articulography recordings, but also for
9521 behavioral data such as reaction times and response data. As time course
9522 measures are sensitive to autocorrelation problems, GAMMs implements methods
9523 to reduce the autocorrelation problems. This package includes functions for
9524 the evaluation of GAMM models (e.g., model comparisons, determining regions of
9525 significance, inspection of autocorrelational structure in residuals) and
9526 interpreting of GAMMs (e.g., visualization of complex interactions, and
9528 (license license:gpl2+)))
9530 (define-public r-polynom
9537 (uri (cran-uri "polynom" version))
9540 "0y4j07syjwpnq5w6a1d90z6h1hjzijmm42pq0f8jk2vcn5xxn7mw"))))
9541 (build-system r-build-system)
9542 (native-inputs (list r-knitr))
9543 (home-page "https://cran.r-project.org/web/packages/polynom/")
9544 (synopsis "Functions for univariate polynomial manipulations")
9546 "This package provides a collection of functions to implement a class for
9547 univariate polynomial manipulations.")
9548 (license license:gpl2)))
9550 (define-public r-pupillometryr
9552 (name "r-pupillometryr")
9557 (uri (cran-uri "PupillometryR" version))
9559 (base32 "0yk30sgl2qqa6pva649swq523vh446ifmydildycfvfmlm1h4qza"))))
9560 (properties `((upstream-name . "PupillometryR")))
9561 (build-system r-build-system)
9574 (native-inputs (list r-knitr))
9575 (home-page "https://cran.r-project.org/package=PupillometryR")
9576 (synopsis "Unified pipeline for pupillometry data")
9578 "This package provides a unified pipeline to clean, prepare, plot, and
9579 run basic analyses on pupillometry experiments.")
9580 (license license:expat)))
9582 (define-public r-gbrd
9589 (uri (cran-uri "gbRd" version))
9592 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
9593 (properties `((upstream-name . "gbRd")))
9594 (build-system r-build-system)
9595 (home-page "https://cran.r-project.org/web/packages/gbRd/")
9596 (synopsis "Utilities for processing Rd objects and files")
9598 "This package provides utilities for processing Rd objects and files.
9599 Extract argument descriptions and other parts of the help pages of
9601 (license license:gpl2+)))
9603 (define-public r-rjags
9610 (uri (cran-uri "rjags" version))
9613 "0cibz6xhmh86fh7ynmdgpmlchizi57pi6dpslgc2if17a56c6p7q"))))
9614 (build-system r-build-system)
9621 (home-page "http://mcmc-jags.sourceforge.net")
9622 (synopsis "Bayesian graphical models using MCMC")
9624 "This package provides an R interface to the JAGS MCMC library. JAGS is
9625 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
9626 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
9627 (license license:gpl2)))
9629 (define-public r-rbibutils
9631 (name "r-rbibutils")
9636 (uri (cran-uri "rbibutils" version))
9639 "0lnia2fk8zlvkkgnl7r7dyi1ip5vqlw448qrvqs2s14rpbpcvbpi"))))
9640 (properties `((upstream-name . "rbibutils")))
9641 (build-system r-build-system)
9642 (home-page "https://geobosh.github.io/rbibutils/")
9643 (synopsis "Convert between bibliography formats")
9645 "This package converts between a number of bibliography formats,
9646 including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils
9647 utilities and supports all bibliography formats and character encodings
9648 implemented in bibutils.")
9649 (license license:gpl2)))
9651 (define-public r-rdpack
9658 (uri (cran-uri "Rdpack" version))
9661 "12j45n4srs987s9mqvp3524cviqbl2pnpx7yw8agac9ynnfmwgmm"))))
9662 (properties `((upstream-name . "Rdpack")))
9663 (build-system r-build-system)
9666 (home-page "https://github.com/GeoBosh/Rdpack")
9667 (synopsis "Update and manipulate Rd documentation objects")
9669 "This package provides functions for manipulation of R documentation
9670 objects, including functions @code{reprompt()} and @code{ereprompt()} for
9671 updating Rd documentation for functions, methods and classes; it also includes
9672 Rd macros for citations and import of references from bibtex files for use in
9673 Rd files and roxygen2 comments, as well as many functions for manipulation of
9674 references and Rd files.")
9675 (license license:gpl2+)))
9677 (define-public r-officer
9684 (uri (cran-uri "officer" version))
9687 "1ksfmwqb91j8n8x4vchpqr848scvf817mgiknwac7n8lfz79synk"))))
9688 (build-system r-build-system)
9690 (list r-r6 r-uuid r-xml2 r-zip))
9691 (home-page "https://davidgohel.github.io/officer")
9692 (synopsis "Manipulation of Word and PowerPoint documents")
9694 "This package provides tools to access and manipulate Word and PowerPoint
9695 documents from R. The package focuses on tabular and graphical reporting from
9696 R; it also provides two functions that let users get document content into
9697 data objects. A set of functions lets add and remove images, tables and
9698 paragraphs of text in new or existing documents. When working with PowerPoint
9699 presentations, slides can be added or removed; shapes inside slides can also
9700 be added or removed. When working with Word documents, a cursor can be used
9701 to help insert or delete content at a specific location in the document.")
9702 (license license:gpl3)))
9704 (define-public r-profilemodel
9706 (name "r-profilemodel")
9711 (uri (cran-uri "profileModel" version))
9714 "01m5nb8cmq0aq555pxk2a99182si65hhmn68yn9nal2j3zl2bp4i"))))
9715 (properties `((upstream-name . "profileModel")))
9716 (build-system r-build-system)
9717 (home-page "https://github.com/ikosmidis/profileModel")
9718 (synopsis "Profiling inference functions for various model classes")
9720 "This package provides tools that can be used to calculate, evaluate,
9721 plot and use for inference the profiles of *arbitrary* inference functions for
9722 arbitrary @code{glm}-like fitted models with linear predictors. More information
9723 on the methods that are implemented can be found in Kosmidis (2008)
9724 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
9725 (license license:gpl2+)))
9727 (define-public r-brglm
9734 (uri (cran-uri "brglm" version))
9737 "08shcz0j1npdn7xkhsvlzs3z4rdwq3g4rk6a4xx8wirqw8n8s2an"))))
9738 (properties `((upstream-name . "brglm")))
9739 (build-system r-build-system)
9741 (list r-profilemodel))
9742 (home-page "https://github.com/ikosmidis/brglm")
9743 (synopsis "Bias reduction in binomial-response generalized linear models")
9745 "Fit generalized linear models with binomial responses using either an
9746 adjusted-score approach to bias reduction or maximum penalized likelihood
9747 where penalization is by Jeffreys invariant prior. These procedures return
9748 estimates with improved frequentist properties (bias, mean squared error) that
9749 are always finite even in cases where the maximum likelihood estimates are
9750 infinite (data separation). Fitting takes place by fitting generalized linear
9751 models on iteratively updated pseudo-data. The interface is essentially the
9752 same as @code{glm}. More flexibility is provided by the fact that custom
9753 pseudo-data representations can be specified and used for model fitting.
9754 Functions are provided for the construction of confidence intervals for the
9755 reduced-bias estimates.")
9756 (license license:gpl2+)))
9758 (define-public r-entropy
9765 (uri (cran-uri "entropy" version))
9768 "1f0j8jsn6pzf4gi5g0akixx6x5vc69ci5f4m2vnwp40frvsqjnkg"))))
9769 (properties `((upstream-name . "entropy")))
9770 (build-system r-build-system)
9771 (home-page "https://www.strimmerlab.org/software/entropy/")
9772 (synopsis "Estimation of entropy, mutual information and related quantities")
9774 "This package implements various estimators of entropy, such as the
9775 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
9776 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
9777 estimator. It also offers an R interface to the NSB estimator. Furthermore,
9778 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
9779 mutual information, and chi-squared statistic of independence. In addition
9780 there are functions for discretizing continuous random variables.")
9781 (license license:gpl3+)))
9783 (define-public r-acd
9790 (uri (cran-uri "ACD" version))
9793 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
9794 (properties `((upstream-name . "ACD")))
9795 (build-system r-build-system)
9796 (home-page "https://cran.r-project.org/web/packages/ACD/")
9797 (synopsis "Categorical data analysis with complete or missing responses")
9799 "This package provides tools for categorical data analysis with complete
9800 or missing responses.")
9801 (license license:gpl2+)))
9803 (define-public r-acdm
9810 (uri (cran-uri "ACDm" version))
9813 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
9814 (properties `((upstream-name . "ACDm")))
9815 (build-system r-build-system)
9817 (list r-dplyr r-ggplot2 r-plyr r-rsolnp r-zoo))
9818 (home-page "https://cran.r-project.org/web/packages/ACDm/")
9819 (synopsis "Tools for Autoregressive Conditional Duration Models")
9821 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
9822 and Russell, 1998) models. It creates trade, price or volume durations from
9823 transactions (tic) data, performs diurnal adjustments, fits various ACD models
9825 (license license:gpl2+)))
9827 (define-public r-overlap
9834 (uri (cran-uri "overlap" version))
9837 "1arxprhz035ab78ks88n6scwnlwmnb97mlac5gsx90ipb6gkgcyk"))))
9838 (build-system r-build-system)
9839 (home-page "https://cran.r-project.org/web/packages/overlap/")
9840 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
9842 "This package provides functions to fit kernel density functions to data
9843 on temporal activity patterns of animals; estimate coefficients of overlapping
9844 of densities for two species; and calculate bootstrap estimates of confidence
9846 (license license:gpl3+)))
9848 (define-public r-snakecase
9850 (name "r-snakecase")
9855 (uri (cran-uri "snakecase" version))
9858 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
9859 (build-system r-build-system)
9861 (list r-stringi r-stringr))
9862 (home-page "https://github.com/Tazinho/snakecase")
9863 (synopsis "Convert strings into any case")
9865 "This package provides a consistent, flexible and easy to use tool to
9866 parse and convert strings into cases like snake or camel among others.")
9867 (license license:gpl3)))
9869 (define-public r-prediction
9871 (name "r-prediction")
9876 (uri (cran-uri "prediction" version))
9879 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
9880 (build-system r-build-system)
9882 (list r-data-table))
9883 (home-page "https://github.com/leeper/prediction")
9884 (synopsis "Tidy, type-safe prediction methods")
9886 "This package provides the @code{prediction()} function, a type-safe
9887 alternative to @code{predict()} that always returns a data frame. The package
9888 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
9889 from the @code{stats} package, as well as numerous other model classes from
9890 other add-on packages.")
9891 (license license:expat)))
9893 (define-public r-insight
9900 (uri (cran-uri "insight" version))
9903 "0dffrsimgijdqsgvr9cad4g4w97d5ssjl3l0fm5ssly9l115ag35"))))
9904 (build-system r-build-system)
9907 (home-page "https://easystats.github.io/insight/")
9908 (synopsis "Easy access to model information for various model objects")
9910 "This package provides a tool to provide an easy, intuitive and
9911 consistent access to information contained in various R models, like model
9912 formulas, model terms, information about random effects, data that was used to
9913 fit the model or data from response variables. The package mainly revolves
9914 around two types of functions: Functions that find (the names of) information,
9915 starting with @code{find_}, and functions that get the underlying data,
9916 starting with @code{get_}. The package has a consistent syntax and works with
9917 many different model objects, where otherwise functions to access these
9918 information are missing.")
9919 (license license:gpl3)))
9921 (define-public r-sjlabelled
9923 (name "r-sjlabelled")
9928 (uri (cran-uri "sjlabelled" version))
9931 "1va86q5wddyvqgdpy8d0an2c7v1qbb4hpn0ai6y1v5v1ff87w73k"))))
9932 (build-system r-build-system)
9934 (list r-datawizard r-insight))
9937 (home-page "https://github.com/strengejacke/sjlabelled")
9938 (synopsis "Labelled data utility functions")
9940 "This package provides a collection of functions dealing with labelled
9941 data, like reading and writing data between R and other statistical software
9942 packages. This includes easy ways to get, set or change value and variable
9943 label attributes, to convert labelled vectors into factors or numeric (and
9944 vice versa), or to deal with multiple declared missing values.")
9945 (license license:gpl3)))
9947 (define-public r-sjmisc
9954 (uri (cran-uri "sjmisc" version))
9957 "1gzkq95ckxr0vhrzggflzli9hs7zr8c0yym9zn1wf74yrr0mgc3q"))))
9958 (build-system r-build-system)
9969 (home-page "https://github.com/strengejacke/sjmisc")
9970 (synopsis "Data and variable transformation functions")
9972 "This package is a collection of miscellaneous utility functions,
9973 supporting data transformation tasks like recoding, dichotomizing or grouping
9974 variables, setting and replacing missing values. The data transformation
9975 functions also support labelled data, and all integrate seamlessly into a
9976 tidyverse workflow.")
9977 (license license:gpl3)))
9979 (define-public r-nortest
9986 (uri (cran-uri "nortest" version))
9989 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
9990 (build-system r-build-system)
9991 (home-page "https://cran.r-project.org/web/packages/nortest/")
9992 (synopsis "Tests for normality")
9994 "This package provides five omnibus tests for testing the composite
9995 hypothesis of normality.")
9996 (license license:gpl2+)))
9998 (define-public r-moonbook
10000 (name "r-moonbook")
10005 (uri (cran-uri "moonBook" version))
10008 "1ml4vvm0mvrprpyi0l50aw38brx18bk2qny4gybmkvlbakalz9bx"))))
10009 (properties `((upstream-name . "moonBook")))
10010 (build-system r-build-system)
10020 (home-page "https://github.com/cardiomoon/moonBook")
10021 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
10023 "This package provides several analysis-related functions for the book
10024 entitled \"R statistics and graph for medical articles\" (written in Korean),
10025 version 1, by Keon-Woong Moon with Korean demographic data with several plot
10027 (license license:gpl2)))
10029 (define-public r-flextable
10031 (name "r-flextable")
10036 (uri (cran-uri "flextable" version))
10039 "03nxh9a9q0jgqz05i7kgp8zjncpq9m4f54dx3bvqgpds4hcqxli9"))))
10040 (build-system r-build-system)
10054 (home-page "https://davidgohel.github.io/flextable")
10055 (synopsis "Functions for tabular reporting")
10057 "This package provides tools to create pretty tables for HTML documents
10058 and other formats. Functions are provided to let users create tables, modify
10059 and format their content. It extends the @code{officer} package and can be
10060 used within R markdown documents when rendering to HTML and to Word
10062 (license license:gpl3)))
10064 (define-public r-writexl
10071 (uri (cran-uri "writexl" version))
10074 "0mfzyn8n5x5x5gf382bqgq61zpw9dymrp5kzdm2sbszplmxf6xry"))))
10075 (build-system r-build-system)
10076 (inputs (list zlib))
10077 (home-page "https://github.com/ropensci/writexl")
10078 (synopsis "Export data frames to xlsx format")
10080 "This package provides a data frame to xlsx exporter based on
10082 (license license:bsd-2)))
10084 (define-public r-biasedurn
10086 (name "r-biasedurn")
10091 (uri (cran-uri "BiasedUrn" version))
10094 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
10095 (properties `((upstream-name . "BiasedUrn")))
10096 (build-system r-build-system)
10097 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
10098 (synopsis "Biased Urn model distributions")
10100 "This package provides statistical models of biased sampling in the form
10101 of univariate and multivariate noncentral hypergeometric distributions,
10102 including Wallenius' noncentral hypergeometric distribution and Fisher's
10103 noncentral hypergeometric distribution (also called extended hypergeometric
10105 (license license:gpl3)))
10107 (define-public r-goplot
10114 (uri (cran-uri "GOplot" version))
10117 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
10118 (properties `((upstream-name . "GOplot")))
10119 (build-system r-build-system)
10121 (list r-ggdendro r-ggplot2 r-gridextra r-rcolorbrewer))
10122 (home-page "https://github.com/wencke/wencke.github.io")
10123 (synopsis "Visualization of functional analysis data")
10125 "This package provides an implementation of multilayered visualizations
10126 for enhanced graphical representation of functional analysis data. It
10127 combines and integrates omics data derived from expression and functional
10128 annotation enrichment analyses. Its plotting functions have been developed
10129 with an hierarchical structure in mind: starting from a general overview to
10130 identify the most enriched categories (modified bar plot, bubble plot) to a
10131 more detailed one displaying different types of relevant information for the
10132 molecules in a given set of categories (circle plot, chord plot, cluster plot,
10133 Venn diagram, heatmap).")
10134 (license license:gpl2)))
10136 (define-public r-getopt
10143 (uri (cran-uri "getopt" version))
10146 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
10147 (build-system r-build-system)
10148 (home-page "https://github.com/trevorld/getopt")
10149 (synopsis "Command-line option processor for R")
10151 "This package is designed to be used with Rscript to write shebang
10152 scripts that accept short and long options. Many users will prefer to
10153 use the packages @code{optparse} or @code{argparse} which add extra
10154 features like automatically generated help options and usage texts,
10155 support for default values, positional argument support, etc.")
10156 (license license:gpl2+)))
10158 (define-public r-findpython
10160 (name "r-findpython")
10165 (uri (cran-uri "findpython" version))
10168 "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar"))))
10169 (build-system r-build-system)
10170 (home-page "https://github.com/trevorld/findpython")
10171 (synopsis "Functions to find an acceptable Python binary")
10173 "This package was designed to find an acceptable Python binary that
10174 matches version and feature constraints.")
10175 (license license:expat)))
10177 ;; This in not the same as "r-argparser"
10178 (define-public r-argparse
10180 (name "r-argparse")
10185 (uri (cran-uri "argparse" version))
10188 "13b5halfxc7nr57vkz3qmkkcpw1hr4xdk1mjh2cq8cvpnjz15qc3"))))
10189 (build-system r-build-system)
10190 (inputs (list python))
10192 (list r-findpython r-jsonlite r-r6))
10195 (home-page "https://github.com/trevorld/argparse")
10196 (synopsis "Command line optional and positional argument parser")
10198 "This package provides a command line parser to be used with Rscript to
10199 write shebang scripts that gracefully accept positional and optional arguments
10200 and automatically generate usage notices.")
10201 (license license:gpl2+)))
10203 (define-public r-hash
10206 (version "2.2.6.2")
10210 (uri (cran-uri "hash" version))
10213 "17scs675a86c34hjbxmwi8kny4yyv97x3515s449zafj2i0ad8vm"))))
10214 (build-system r-build-system)
10215 (home-page "https://cran.r-project.org/web/packages/hash/")
10216 (synopsis "Implementation of hash/associated arrays/dictionaries")
10218 "This package implements a data structure similar to hashes in Perl and
10219 dictionaries in Python but with a purposefully R flavor. For objects of
10220 appreciable size, access using hashes outperforms native named lists and
10222 (license license:gpl2+)))
10224 (define-public r-orddom
10231 (uri (cran-uri "orddom" version))
10234 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
10235 (build-system r-build-system)
10236 (propagated-inputs (list r-psych))
10237 (home-page "https://cran.r-project.org/web/packages/orddom/")
10238 (synopsis "Ordinal dominance statistics")
10240 "This package provides tools to compute ordinal, statistics and effect
10241 sizes as an alternative to mean comparison: Cliff's delta or success rate
10242 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
10243 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
10244 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
10245 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
10246 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
10247 Group (Non-)Overlap considerations.")
10248 (license license:gpl2)))
10250 (define-public r-deriv
10257 (uri (cran-uri "Deriv" version))
10260 "130g3mv0z9sqs6y23a0a94512iiw05yr6fp378vhdxxbignzbnyv"))))
10261 (properties `((upstream-name . "Deriv")))
10262 (build-system r-build-system)
10263 (home-page "https://cran.r-project.org/web/packages/Deriv")
10264 (synopsis "Symbolic differentiation")
10266 "This package provides an R-based solution for symbolic differentiation.
10267 It admits user-defined functions as well as function substitution in arguments
10268 of functions to be differentiated. Some symbolic simplification is part of
10270 (license license:gpl3+)))
10272 (define-public r-doby
10279 (uri (cran-uri "doBy" version))
10282 "0qnfcw4rg5kd1mll3rq6vchz3lgdqfif9469p8x6ixsgrxxpivbz"))))
10283 (properties `((upstream-name . "doBy")))
10284 (build-system r-build-system)
10298 (home-page "https://people.math.aau.dk/~sorenh/software/doBy/")
10299 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
10301 "This package contains:
10304 @item facilities for working with grouped data: @code{do}
10305 something to data stratified @code{by} some variables.
10306 @item implementations of least-squares means, general linear contrasts, and
10307 @item miscellaneous other utilities.
10309 (license license:gpl2+)))
10311 (define-public r-refgenome
10313 (name "r-refgenome")
10318 (uri (cran-uri "refGenome" version))
10321 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
10322 (properties `((upstream-name . "refGenome")))
10323 (build-system r-build-system)
10325 (list r-dbi r-doby r-rsqlite))
10326 (home-page "https://cran.r-project.org/web/packages/refGenome/")
10328 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
10330 "This package contains functionality for importing and managing of
10331 downloaded genome annotation data from the Ensembl genome browser (European
10332 Bioinformatics Institute) and from the UCSC genome browser (University of
10333 California, Santa Cruz) and annotation routines for genomic positions and
10334 splice site positions.")
10335 (license license:gpl2)))
10337 (define-public r-basix
10344 (uri (cran-uri "BASIX" version))
10347 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
10348 (properties `((upstream-name . "BASIX")))
10349 (build-system r-build-system)
10350 (home-page "https://cran.r-project.org/web/packages/BASIX/")
10351 (synopsis "Efficient C/C++ toolset for R")
10353 "BASIX provides some efficient C/C++ implementations of native R
10354 procedures to speed up calculations in R.")
10355 (license license:gpl2)))
10357 (define-public r-blockfest
10359 (name "r-blockfest")
10364 (uri (cran-uri "BlockFeST" version))
10367 "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65"))))
10368 (properties `((upstream-name . "BlockFeST")))
10369 (build-system r-build-system)
10370 (propagated-inputs (list r-basix))
10371 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
10372 (synopsis "Bayesian calculation of region-specific fixation index")
10374 "This package provides an R implementation of an extension of the
10375 BayeScan software for codominant markers, adding the option to group
10376 individual SNPs into pre-defined blocks. A typical application of this new
10377 approach is the identification of genomic regions, genes, or gene sets
10378 containing one or more SNPs that evolved under directional selection.")
10379 (license license:gpl2)))
10381 (define-public r-proc
10388 (uri (cran-uri "pROC" version))
10391 "1abvbzdss12n64pp9vlgnn0q3abh0nj4n0a8cinwwvhphjrm9vym"))))
10392 (properties `((upstream-name . "pROC")))
10393 (build-system r-build-system)
10395 (list r-plyr r-rcpp))
10396 (home-page "https://web.expasy.org/pROC/")
10397 (synopsis "Display and analyze ROC curves")
10399 "This package provides tools for visualizing, smoothing and comparing
10400 receiver operating characteristic (ROC curves). The area under the
10401 curve (AUC) can be compared with statistical tests based on U-statistics or
10402 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
10403 (license license:gpl3+)))
10405 (define-public r-rootsolve
10407 (name "r-rootsolve")
10408 (version "1.8.2.3")
10412 (uri (cran-uri "rootSolve" version))
10415 "182bb727sgqi5f3pzmw8jnn328wdjrgj9lfvg49gv8s22rjd3cxm"))))
10416 (properties `((upstream-name . "rootSolve")))
10417 (build-system r-build-system)
10418 (native-inputs (list gfortran))
10419 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
10420 (synopsis "Tools for the analysis of ordinary differential equations")
10422 "This package provides routines to find the root of nonlinear functions,
10423 and to perform steady-state and equilibrium analysis of @dfn{ordinary
10424 differential equations} (ODE). It includes routines that:
10427 @item generate gradient and jacobian matrices (full and banded),
10428 @item find roots of non-linear equations by the Newton-Raphson method,
10429 @item estimate steady-state conditions of a system of (differential) equations
10430 in full, banded or sparse form, using the Newton-Raphson method, or by
10431 dynamically running,
10432 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
10433 and 3-D partial differential equations, that have been converted to ordinary
10434 differential equations by numerical differencing (using the method-of-lines
10437 (license license:gpl2+)))
10439 (define-public r-abcanalysis
10441 (name "r-abcanalysis")
10446 (uri (cran-uri "ABCanalysis" version))
10448 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
10449 (properties `((upstream-name . "ABCanalysis")))
10450 (build-system r-build-system)
10451 (propagated-inputs (list r-plotrix))
10452 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
10453 (synopsis "Computed ABC Analysis")
10455 "Multivariate data sets often differ in several factors or derived statistical
10456 parameters, which have to be selected for a valid interpretation. Basing this
10457 selection on traditional statistical limits leads occasionally to the perception
10458 of losing information from a data set. This package provides tools to calculate
10459 these limits on the basis of the mathematical properties of the distribution of
10460 the analyzed items.")
10461 (license license:gpl3)))
10463 (define-public r-slam
10470 (uri (cran-uri "slam" version))
10472 (base32 "1ggqcf8l1z2hpi7qy4mg0d2ps48bjjb8z1y1xz6fq162cqrbz6bq"))))
10473 (build-system r-build-system)
10474 (home-page "https://cran.r-project.org/web/packages/slam/")
10475 (synopsis "Sparse lightweight arrays and matrices")
10477 "This package contains data structures and algorithms for sparse arrays and matrices,
10478 based on index arrays and simple triplet representations, respectively.")
10479 (license license:gpl2)))
10481 (define-public r-manipulatewidget
10483 (name "r-manipulatewidget")
10488 (uri (cran-uri "manipulateWidget" version))
10490 (base32 "1dpgzmiv08afm57yxr017b014lfn9h3pa4w65prk5k3dgn6p4wsv"))))
10492 `((upstream-name . "manipulateWidget")))
10493 (build-system r-build-system)
10506 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
10507 (synopsis "Add even more interactivity to interactive charts")
10509 "This package lets you create in just a few lines of R code a nice user interface to
10510 modify the data or the graphical parameters of one or multiple interactive
10511 charts. It is useful to quickly explore visually some data or for package
10512 developers to generate user interfaces easy to maintain.")
10513 (license license:gpl2+)))
10515 (define-public r-a3
10522 (uri (cran-uri "A3" version))
10524 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
10525 (properties `((upstream-name . "A3")))
10526 (build-system r-build-system)
10528 (list r-pbapply r-xtable))
10529 (home-page "https://cran.r-project.org/web/packages/A3/")
10530 (synopsis "Error metrics for predictive models")
10532 "This package supplies tools for tabulating and analyzing the results of predictive
10533 models. The methods employed are applicable to virtually any predictive model
10534 and make comparisons between different methodologies straightforward.")
10535 (license license:gpl2+)))
10537 (define-public r-infotheo
10539 (name "r-infotheo")
10540 (version "1.2.0.1")
10544 (uri (cran-uri "infotheo" version))
10547 "1m1979vf8rvq3534mp1hihfadikhxrg3p6ac3hirz96kgb4qxyy0"))))
10548 (build-system r-build-system)
10549 (home-page "http://homepage.meyerp.com/software")
10550 (synopsis "Information-theoretic measures")
10552 "This package implements various measures of information theory based on
10553 several entropy estimators.")
10554 (license license:gpl3+)))
10556 (define-public r-nsprcomp
10558 (name "r-nsprcomp")
10559 (version "0.5.1-2")
10563 (uri (cran-uri "nsprcomp" version))
10566 "1zlc1ximx96f235c0l8qfs6vbp1kpnbf943wxsfahnnlnxvwi59f"))))
10567 (properties `((upstream-name . "nsprcomp")))
10568 (build-system r-build-system)
10569 (home-page "https://sigg-iten.ch/research/")
10570 (synopsis "Non-negative and sparse PCA")
10572 "This package implements two methods for performing a constrained
10573 principal component analysis (PCA), where non-negativity and/or sparsity
10574 constraints are enforced on the principal axes (PAs). The function
10575 @code{nsprcomp} computes one principal component (PC) after the other. Each
10576 PA is optimized such that the corresponding PC has maximum additional variance
10577 not explained by the previous components. In contrast, the function
10578 @code{nscumcomp} jointly computes all PCs such that the cumulative variance is
10579 maximal. Both functions have the same interface as the @code{prcomp} function
10580 from the @code{stats} package (plus some extra parameters).")
10581 (license license:gpl2+)))
10583 (define-public r-cmplot
10590 (uri (cran-uri "CMplot" version))
10593 "1h09prpiw7l32mr7jarp8ddrddg1431nfn4kw3bznfnv0sr78zfg"))))
10594 (properties `((upstream-name . "CMplot")))
10595 (build-system r-build-system)
10596 (home-page "https://github.com/YinLiLin/CMplot")
10597 (synopsis "Circle Manhattan plot")
10599 "Circle Manhattan Plot is an R package that can lay out genome-wide
10600 association study P-value results in both traditional rectangular patterns,
10601 QQ-plot and novel circular ones. United in only one bull's eye style plot,
10602 association results from multiple traits can be compared interactively,
10603 thereby to reveal both similarities and differences between signals.
10604 Additional functions include: highlight signals, a group of SNPs, chromosome
10605 visualization and candidate genes around SNPs.")
10606 (license license:gpl2+)))
10608 (define-public r-precrec
10615 (uri (cran-uri "precrec" version))
10618 "1dfz2rqx2ww2l5r40ahg0qdj3rjrwiwh427mw7j5ynhpcj21j2qm"))))
10619 (properties `((upstream-name . "precrec")))
10620 (build-system r-build-system)
10628 (native-inputs (list r-knitr))
10629 (home-page "https://evalclass.github.io/precrec/")
10630 (synopsis "Calculate accurate precision-recall and ROC curves")
10632 "This package provides tools for accurate calculations and visualization
10633 of precision-recall and ROC (Receiver Operator Characteristics) curves.")
10634 (license license:gpl3)))
10636 (define-public r-netrep
10643 (uri (cran-uri "NetRep" version))
10646 "1swlb2k9bc7whvslxbklz864j9ynvna73hvq5rhv61cv5vy05ksd"))))
10647 (properties `((upstream-name . "NetRep")))
10648 (build-system r-build-system)
10658 (native-inputs (list r-knitr))
10659 (home-page "https://cran.r-project.org/package=NetRep")
10660 (synopsis "Permutation testing network module preservation across datasets")
10662 "This package provides functions for assessing the
10663 replication/preservation of a network module's topology across datasets
10664 through permutation testing.")
10665 (license license:gpl2)))
10667 (define-public r-intergraph
10669 (name "r-intergraph")
10674 (uri (cran-uri "intergraph" version))
10677 "18a7xgb2rp0w9jl2rkh8nzyjprrs5w7h2iidvc8c38bzx3qpggkc"))))
10678 (properties `((upstream-name . "intergraph")))
10679 (build-system r-build-system)
10681 (list r-igraph r-network))
10684 (home-page "http://mbojan.github.io/intergraph")
10685 (synopsis "Coercion routines for network data objects")
10687 "Functions implemented in this package allow coercing (i.e. convert)
10688 network data between classes provided by other R packages. Currently
10689 supported classes are those defined in packages @code{network} and
10691 (license license:gpl3)))
10693 (define-public r-abcoptim
10695 (name "r-abcoptim")
10700 (uri (cran-uri "ABCoptim" version))
10702 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
10703 (properties `((upstream-name . "ABCoptim")))
10704 (build-system r-build-system)
10705 (propagated-inputs (list r-rcpp))
10706 (home-page "https://github.com/gvegayon/ABCoptim/")
10707 (synopsis "Optimization of Artificial Bee Colony algorithm")
10709 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
10710 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
10711 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
10712 algorithms, and uses only common control parameters such as colony size and
10713 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
10714 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
10715 This version is a work-in-progress and is written in R code.")
10716 (license license:expat)))
10718 (define-public r-abcp2
10725 (uri (cran-uri "ABCp2" version))
10727 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
10728 (properties `((upstream-name . "ABCp2")))
10729 (build-system r-build-system)
10730 (propagated-inputs (list r-mass))
10731 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
10732 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
10734 "This package tests the goodness of fit of a distribution of offspring to the Normal,
10735 Poisson, and Gamma distribution and estimates the proportional paternity of the
10736 second male (P2) based on the best fit distribution.")
10737 (license license:gpl2)))
10739 (define-public r-abcrf
10746 (uri (cran-uri "abcrf" version))
10748 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
10749 (build-system r-build-system)
10760 (home-page "https://cran.r-project.org/web/packages/abcrf/")
10761 (synopsis "Approximate bayesian computation via random forests")
10763 "This package performs approximate bayesian computation (ABC) model choice and
10764 parameter inference via random forests. This machine learning tool named random
10765 forests (RF) can conduct selection among the highly complex models covered by
10767 (license license:gpl2+)))
10769 (define-public r-abctools
10771 (name "r-abctools")
10776 (uri (cran-uri "abctools" version))
10778 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
10779 (build-system r-build-system)
10781 (list r-abc r-abind r-hmisc r-plyr))
10782 (home-page "https://github.com/dennisprangle/abctools/")
10783 (synopsis "Tools for ABC analyses")
10785 "This @code{r-abctools} package provides tools for approximate Bayesian computation
10786 including summary statistic selection and assessing coverage. This includes
10787 recent dimension reduction algorithms to tune the choice of summary statistics,
10788 and coverage methods to tune the choice of threshold.")
10789 (license license:gpl2+)))
10791 (define-public r-ggstance
10793 (name "r-ggstance")
10798 (uri (cran-uri "ggstance" version))
10800 (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d"))))
10801 (build-system r-build-system)
10803 (list r-ggplot2 r-plyr r-rlang r-withr))
10804 (home-page "https://cran.r-project.org/web/packages/ggstance/")
10805 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
10807 "This package is a @code{r-ggplot2} extension that provides flipped components:
10809 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
10810 @item vertical versions of @code{r-ggplot2} positions.
10812 (license license:gpl3)))
10814 (define-public r-ggnetwork
10816 (name "r-ggnetwork")
10821 (uri (cran-uri "ggnetwork" version))
10824 "0gqdgy5yh700dg0f7xb80hczlnqfisn8l55j7amd1n7fp2x5sr8v"))))
10825 (properties `((upstream-name . "ggnetwork")))
10826 (build-system r-build-system)
10828 (list r-ggplot2 r-ggrepel r-igraph r-network r-sna))
10829 (native-inputs (list r-knitr))
10830 (home-page "https://github.com/briatte/ggnetwork")
10831 (synopsis "Geometries to plot networks with ggplot2")
10833 "This package provides geometries to plot network objects with the
10835 (license license:gpl3)))
10837 (define-public r-cvauc
10844 (uri (cran-uri "cvAUC" version))
10847 "1m2y50a1yapf1c74km9a4r47ds2z2bfp4wwwkqin7swv9v1s7d28"))))
10848 (properties `((upstream-name . "cvAUC")))
10849 (build-system r-build-system)
10851 (list r-data-table r-rocr))
10852 (home-page "https://github.com/ledell/cvAUC")
10853 (synopsis "Cross-validated area under the ROC curve confidence intervals")
10855 "This package contains various tools for working with and evaluating
10856 cross-validated area under the ROC curve (AUC) estimators. The primary
10857 functions of the package are @code{ci.cvAUC} and @code{ci.pooled.cvAUC}, which
10858 report cross-validated AUC and compute confidence intervals for
10859 cross-validated AUC estimates based on influence curves for i.i.d. and pooled
10860 repeated measures data, respectively.")
10861 (license license:asl2.0)))
10863 (define-public r-gam
10870 (uri (cran-uri "gam" version))
10873 "1bbxiqfgi7jc9vw1hspw5q41d69nlw2v6k91zqlvmam5pvxcd1sp"))))
10874 (properties `((upstream-name . "gam")))
10875 (build-system r-build-system)
10880 (home-page "https://cran.r-project.org/package=gam")
10881 (synopsis "Generalized additive models")
10883 "This package provides functions for fitting and working with generalized
10884 additive models, as described in chapter 7 of \"Statistical Models in
10885 S\" (Chambers and Hastie (eds), 1991), and \"Generalized Additive
10886 Models\" (Hastie and Tibshirani, 1990).")
10887 (license license:gpl2)))
10889 (define-public r-superlearner
10891 (name "r-superlearner")
10896 (uri (cran-uri "SuperLearner" version))
10899 "00any24msgflyagy87nznpfjz5g9v15frqda6c679wa8plx26hjz"))))
10900 (properties `((upstream-name . "SuperLearner")))
10901 (build-system r-build-system)
10903 (list r-cvauc r-gam r-nnls))
10906 (home-page "https://github.com/ecpolley/SuperLearner")
10907 (synopsis "Super learner prediction")
10909 "This package implements the super learner prediction method and contains
10910 a library of prediction algorithms to be used in the super learner.")
10911 (license license:gpl3)))
10913 (define-public r-drtmle
10920 (uri (cran-uri "drtmle" version))
10923 "12vplpz9bg5444jy29mbdr70hqby073vb3iw76v2csrwy3ws3f21"))))
10924 (properties `((upstream-name . "drtmle")))
10925 (build-system r-build-system)
10927 (list r-future-apply r-np r-superlearner))
10930 (home-page "https://github.com/benkeser/drtmle")
10931 (synopsis "Doubly-robust nonparametric estimation and inference")
10933 "This package implements targeted minimum loss-based estimators of
10934 counterfactual means and causal effects that are doubly-robust with respect
10935 both to consistency and asymptotic normality.")
10936 (license license:expat)))
10938 (define-public r-dofuture
10940 (name "r-dofuture")
10945 (uri (cran-uri "doFuture" version))
10948 "0w07pmzpsfq4kvfc745s1i9b6dfn1df1wrfi4s9ys4ir3g2s8nk1"))))
10949 (properties `((upstream-name . "doFuture")))
10950 (build-system r-build-system)
10953 (modify-phases %standard-phases
10954 (add-after 'unpack 'set-HOME
10955 (lambda _ (setenv "HOME" "/tmp"))))))
10957 (list r-foreach r-future r-globals r-iterators))
10959 (list r-r-rsp)) ; vignette builder
10960 (home-page "https://github.com/HenrikBengtsson/doFuture")
10961 (synopsis "Foreach parallel adapter using the future API")
10963 "This package provides a @code{%dopar%} adapter such that any type of
10964 futures can be used as backends for the @code{foreach} framework.")
10965 (license license:lgpl2.1+)))
10967 (define-public r-superheat
10969 (name "r-superheat")
10974 (uri (cran-uri "superheat" version))
10977 "01v8s6px1k5fajlm6py3ksr1i853kwwlky1yryzhy3p1cxhwgg83"))))
10978 (properties `((upstream-name . "superheat")))
10979 (build-system r-build-system)
10988 (home-page "https://cran.r-project.org/package=superheat")
10989 (synopsis "Graphical tool for exploring complex datasets using heatmaps")
10991 "This package provides a system for generating extendable and
10992 customizable heatmaps for exploring complex datasets, including big data and
10993 data with multiple data types.")
10994 (license license:cc0)))
10996 (define-public r-qualv
11003 (uri (cran-uri "qualV" version))
11006 "0rkjzva2h158d5c631jmjjh7qjibbyisl0503san80rk9fgxl45b"))))
11007 (properties `((upstream-name . "qualV")))
11008 (build-system r-build-system)
11010 (list r-kernsmooth))
11011 (home-page "http://qualV.R-Forge.R-Project.org/")
11012 (synopsis "Qualitative Validation Methods")
11014 "This package provides qualitative methods for the validation of dynamic
11015 models. It contains
11018 @item an orthogonal set of deviance measures for absolute, relative and
11020 @item approaches accounting for time shifts.
11023 The first approach transforms time to take time delays and speed differences
11024 into account. The second divides the time series into interval units
11025 according to their main features and finds the @dfn{longest common
11026 subsequence} (LCS) using a dynamic programming algorithm.")
11027 (license license:gpl2+)))
11029 (define-public r-mosaiccore
11031 (name "r-mosaiccore")
11036 (uri (cran-uri "mosaicCore" version))
11038 (base32 "1h3ixzna4xy42rdnd89jj0v9q0riy3fnkd33z6l5c0zaidzm58fz"))))
11039 (properties `((upstream-name . "mosaicCore")))
11040 (build-system r-build-system)
11042 (list r-dplyr r-mass r-rlang r-tidyr))
11043 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
11044 (synopsis "Common utilities for mosaic family packages")
11046 "Common utilities used in other Mosaic family packages are collected here.")
11047 (license license:gpl2+)))
11049 (define-public r-labelled
11051 (name "r-labelled")
11056 (uri (cran-uri "labelled" version))
11059 "0h7scbyzh7kr51gds222rkhld2b3k36s86hj8rrzpwv4bwj0pccy"))))
11060 (properties `((upstream-name . "labelled")))
11061 (build-system r-build-system)
11072 (home-page "http://larmarange.github.io/labelled/")
11073 (synopsis "Manipulating labelled data")
11075 "This package provides useful functions to deal with the
11076 @code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the
11078 (license license:gpl3)))
11080 (define-public r-ggformula
11082 (name "r-ggformula")
11087 (uri (cran-uri "ggformula" version))
11089 (base32 "1ph5jd8svk8hmshi894vmmpq3zwgdmf4yn3gmdlkad68z8jynhsp"))))
11090 (build-system r-build-system)
11105 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
11106 (synopsis "Formula interface for the @code{r-ggplot2}")
11108 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
11109 gf_density(), and so on, bring the formula interface to ggplot(). This captures
11110 and extends the excellent simplicity of the lattice-graphics formula interface,
11111 while providing the intuitive capabilities of @code{r-ggplot2}.")
11112 (license license:expat)))
11114 (define-public r-mosaicdata
11116 (name "r-mosaicdata")
11121 (uri (cran-uri "mosaicData" version))
11123 (base32 "0h3f5fgzkzjfgf3ml0qa5j52921y6wy6jgggxmhs31bs8fd4srg4"))))
11124 (properties `((upstream-name . "mosaicData")))
11125 (build-system r-build-system)
11126 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
11127 (synopsis "Data sets for project Mosaic")
11129 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
11130 used to teach mathematics, statistics, computation and modeling.")
11131 (license license:gpl2+)))
11133 (define-public r-raster
11140 (uri (cran-uri "raster" version))
11143 "11fnznymwavpph733dayklhcx4phpjgrijfxlaszi122sg2x7ir9"))))
11144 (build-system r-build-system)
11146 (list r-rcpp r-sp r-terra))
11147 (home-page "https://www.rspatial.org/")
11148 (synopsis "Geographic data analysis and modeling")
11150 "The package implements basic and high-level functions for reading,
11151 writing, manipulating, analyzing and modeling of gridded spatial data.
11152 Processing of very large files is supported.")
11153 (license license:gpl3+)))
11155 (define-public r-mosaic
11162 (uri (cran-uri "mosaic" version))
11164 (base32 "1y0isqbva0vi5zlx1xvixbq87n4xp66ljh43qnd0cpzaz0mn21cg"))))
11165 (build-system r-build-system)
11189 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
11190 (synopsis "Mathematics, statistics, and computation teaching utilities")
11192 "This package contain data sets and utilities from
11193 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
11194 statistics, computation and modeling. Project MOSAIC is a community of
11195 educators working to tie together aspects of quantitative work that students
11196 in science, technology, engineering and mathematics will need in their
11197 professional lives, but which are usually taught in isolation, if at all.")
11198 (license license:gpl2+)))
11200 (define-public r-abd
11207 (uri (cran-uri "abd" version))
11209 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
11210 (build-system r-build-system)
11212 (list r-lattice r-mosaic r-nlme))
11213 (home-page "https://cran.r-project.org/web/packages/abd/")
11214 (synopsis "Analysis of biological data")
11216 "The @code{r-abd} package contains data sets and sample code for the Analysis of
11217 biological data by Michael Whitlock and Dolph Schluter.")
11218 (license license:gpl2)))
11220 (define-public r-svgui
11227 (uri (cran-uri "svGUI" version))
11229 (base32 "0ch5gdfk834xj9w3vxpm3x4770fz3nnlyn8b0jsw9f3n2as7g979"))))
11230 (properties `((upstream-name . "svGUI")))
11231 (build-system r-build-system)
11234 (home-page "https://github.com/SciViews/svGUI/")
11235 (synopsis "Functions for managing GUI clients in R")
11237 "The SciViews @code{svGUI} package eases the management of Graphical User
11238 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
11239 centralizes info about GUI elements currently used, and it dispatches GUI
11240 calls to the particular toolkits in use in function of the context.")
11241 (license license:gpl2)))
11243 (define-public r-svdialogs
11245 (name "r-svdialogs")
11250 (uri (cran-uri "svDialogs" version))
11252 (base32 "0z3a5glsi0ab43mdk2yvslxyzg12nbqqqc35jvgzj475mpkbgjif"))))
11253 (properties `((upstream-name . "svDialogs")))
11254 (build-system r-build-system)
11258 (list r-rstudioapi r-svgui))
11261 (home-page "https://github.com/SciViews/svDialogs/")
11262 (synopsis "Portable dialog boxes")
11264 "This package helps to construct standard dialog boxes for your GUI, including
11265 message boxes, input boxes, list, file or directory selection, and others. In
11266 case R cannot display GUI dialog boxes, a simpler command line version of these
11267 interactive elements is also provided as a fallback solution.")
11268 (license license:gpl2)))
11270 (define-public r-abe
11277 (uri (cran-uri "abe" version))
11280 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
11281 (build-system r-build-system)
11282 (home-page "https://cran.r-project.org/web/packages/abe/")
11283 (synopsis "Augmented backward elimination")
11285 "This package performs augmented backward elimination and checks the
11286 stability of the obtained model. Augmented backward elimination combines
11287 significance or information based criteria with the change in estimate to
11288 either select the optimal model for prediction purposes or to serve as a tool
11289 to obtain a practically sound, highly interpretable model.")
11290 (license license:gpl2+)))
11292 (define-public r-abf2
11299 (uri (cran-uri "abf2" version))
11301 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
11302 (build-system r-build-system)
11303 (home-page "https://cran.r-project.org/web/packages/abf2/")
11304 (synopsis "Load gap-free axon @code{r-abf2} files")
11306 "This package loads electrophysiology data from ABF2 files, as created by
11307 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
11308 mode are currently supported.")
11309 (license license:artistic2.0)))
11311 (define-public r-abhgenotyper
11313 (name "r-abhgenotyper")
11318 (uri (cran-uri "ABHgenotypeR" version))
11320 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
11321 (properties `((upstream-name . "ABHgenotypeR")))
11322 (build-system r-build-system)
11324 (list r-ggplot2 r-reshape2))
11325 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
11326 (synopsis "Visualize and manipulate ABH genotypes")
11328 "The @code{r-abhgenotyper} package provides simple imputation,
11329 error-correction and plotting capacities for genotype data. The package is
11330 supposed to serve as an intermediate but independent analysis tool between the
11331 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
11332 not found in either TASSEL or @code{r-qtl} in addition to visualization of
11333 genotypes as \"graphical genotypes\".")
11334 (license license:gpl3)))
11336 (define-public r-furrr
11343 (uri (cran-uri "furrr" version))
11346 "117xj66l14r08macwghgyibzm282ljv1afpa133h952gc70irs9z"))))
11347 (build-system r-build-system)
11355 (home-page "https://github.com/DavisVaughan/furrr")
11356 (synopsis "Apply mapping functions in parallel using futures")
11358 "This package provides implementations of the family of @code{map()}
11359 functions from the @code{purrr} package that can be resolved using any
11360 @code{future}-supported backend, e.g. parallel on the local machine or
11361 distributed on a compute cluster.")
11362 (license license:lgpl2.1+)))
11364 (define-public r-abjutils
11366 (name "r-abjutils")
11371 (uri (cran-uri "abjutils" version))
11373 (base32 "0lmf4va8qnzwg698i2h4fcwvd6dhsgdkqsfh41aa3wg1flimhsr7"))))
11374 (build-system r-build-system)
11384 (home-page "https://github.com/abjur/abjutils/")
11385 (synopsis "Collection of tools for jurimetrical analysis")
11387 "This package implements general purpose tools, such as functions for
11388 sampling and basic manipulation of Brazilian lawsuits identification number.
11389 It also implements functions for text cleaning, such as accentuation
11391 (license license:expat)))
11393 (define-public r-abnormality
11395 (name "r-abnormality")
11400 (uri (cran-uri "abnormality" version))
11402 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
11403 (build-system r-build-system)
11405 (list r-mass r-matrix))
11406 (home-page "https://cran.r-project.org/web/packages/abnormality/")
11407 (synopsis "Measure a subject's abnormality with respect to a reference population")
11409 "This package contains functions to implement the methodology and
11410 considerations laid out by Marks et al. in the article \"Measuring abnormality
11411 in high dimensional spaces: applications in biomechanical gait analysis\".
11412 Using high-dimensional datasets to measure a subject's overall level of
11413 abnormality as compared to a reference population is often needed in outcomes
11415 (license license:expat)))
11417 (define-public r-abodoutlier
11419 (name "r-abodoutlier")
11424 (uri (cran-uri "abodOutlier" version))
11426 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
11427 (properties `((upstream-name . "abodOutlier")))
11428 (build-system r-build-system)
11431 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
11432 (synopsis "Angle-based outlier detection")
11434 "This package performs angle-based outlier detection on a given data
11435 frame. It offers three methods to process data:
11437 @item full but slow implementation using all the data that has cubic
11439 @item a fully randomized method;
11440 @item a method using k-nearest neighbours.
11442 These algorithms are well suited for high dimensional data outlier
11444 (license license:expat)))
11446 (define-public r-abps
11453 (uri (cran-uri "ABPS" version))
11455 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
11456 (properties `((upstream-name . "ABPS")))
11457 (build-system r-build-system)
11458 (propagated-inputs (list r-kernlab))
11459 (home-page "https://cran.r-project.org/web/packages/ABPS/")
11460 (synopsis "Abnormal blood profile score to detect blood doping")
11462 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
11463 The ABPS is a part of the Athlete biological passport program of the World
11464 anti-doping agency, which combines several blood parameters into a single
11465 score in order to detect blood doping. The package also contains functions to
11466 calculate other scores used in anti-doping programs, such as the ratio of
11467 hemoglobin to reticulocytes (OFF-score), as well as example data.")
11468 (license license:gpl2+)))
11470 (define-public r-parmigene
11472 (name "r-parmigene")
11477 (uri (cran-uri "parmigene" version))
11480 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
11481 (build-system r-build-system)
11482 (home-page "https://cran.r-project.org/web/packages/parmigene/")
11483 (synopsis "Mutual information estimation for gene network reconstruction")
11485 "This package provides a parallel estimation of the mutual information
11486 based on entropy estimates from k-nearest neighbors distances and algorithms
11487 for the reconstruction of gene regulatory networks.")
11488 (license license:agpl3+)))
11490 (define-public r-pscl
11497 (uri (cran-uri "pscl" version))
11499 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
11500 (build-system r-build-system)
11503 (home-page "https://github.com/atahk/pscl/")
11504 (synopsis "Political science computational laboratory")
11506 "The @code{pscl} is an R package providing classes and methods for:
11508 @item Bayesian analysis of roll call data (item-response models);
11509 @item elementary Bayesian statistics;
11510 @item maximum likelihood estimation of zero-inflated and hurdle models for count
11512 @item utility functions.
11514 (license license:gpl2)))
11516 (define-public r-accelmissing
11518 (name "r-accelmissing")
11523 (uri (cran-uri "accelmissing" version))
11525 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
11526 (build-system r-build-system)
11528 (list r-mice r-pscl))
11529 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
11530 (synopsis "Missing value imputation for accelerometer data")
11532 "This package provides a statistical method to impute the missing values in
11533 accelerometer data. The methodology includes both parametric and
11534 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
11535 model. It also provides multiple functions to preprocess the accelerometer data
11536 previous to the missing data imputation. These include detecting the wearing
11537 and the non-wearing time, selecting valid days and subjects, and creating plots.")
11538 (license license:gpl2+)))
11540 (define-public r-mhsmm
11547 (uri (cran-uri "mhsmm" version))
11549 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
11550 (build-system r-build-system)
11551 (propagated-inputs (list r-mvtnorm))
11552 (home-page "https://github.com/jaredo/mhsmm/")
11553 (synopsis "Inference for hidden Markov and semi-Markov models")
11555 "The @code{r-mhsmm} package implements estimation and prediction methods for
11556 hidden Markov and semi-Markov models for multiple observation sequences. Such
11557 techniques are of interest when observed data is thought to be dependent on some
11558 unobserved (or hidden) state. Also, this package is suitable for equidistant
11559 time series data, with multivariate and/or missing data. Allows user defined
11560 emission distributions.")
11561 (license license:gpl2+)))
11563 (define-public r-nleqslv
11570 (uri (cran-uri "nleqslv" version))
11572 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
11573 (build-system r-build-system)
11574 (native-inputs (list gfortran))
11575 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
11576 (synopsis "Solve systems of nonlinear equations")
11578 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
11579 Broyden or a Newton method with a choice of global strategies such as line
11580 search and trust region. There are options for using a numerical or user
11581 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
11582 singular or ill-conditioned Jacobian.")
11583 (license license:gpl2+)))
11585 (define-public r-physicalactivity
11587 (name "r-physicalactivity")
11592 (uri (cran-uri "PhysicalActivity" version))
11594 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40"))))
11596 `((upstream-name . "PhysicalActivity")))
11597 (build-system r-build-system)
11598 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
11599 (synopsis "Processing accelerometer data for physical activity measurement")
11601 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
11602 for classification of monitored wear and nonwear time intervals in accelerometer
11603 data collected to assess physical activity. The package also contains functions
11604 for making plots of accelerometer data and obtaining the summary of various
11605 information including daily monitor wear time and the mean monitor wear time
11606 during valid days. The revised package version 0.2-1 improved the functions
11607 regarding speed, robustness and add better support for time zones and daylight
11608 saving. In addition, several functions were added:
11610 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
11611 @item the @code{markPAI} can categorize physical activity intensity level based
11612 on user-defined cut-points of accelerometer counts.
11614 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
11615 @code{queryActigraph} functions.")
11616 (license license:gpl3+)))
11618 (define-public r-acc
11625 (uri (cran-uri "acc" version))
11627 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
11628 (build-system r-build-system)
11643 (home-page "https://cran.r-project.org/web/packages/acc/")
11644 (synopsis "Exploring accelerometer data")
11646 "This package processes accelerometer data from uni-axial and tri-axial devices
11647 and generates data summaries. Also, includes functions to plot, analyze, and
11648 simulate accelerometer data.")
11649 (license license:gpl2+)))
11651 (define-public r-rbenchmark
11653 (name "r-rbenchmark")
11658 (uri (cran-uri "rbenchmark" version))
11660 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
11661 (build-system r-build-system)
11662 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
11663 (synopsis "Benchmarking routine for R")
11665 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
11666 and is intended to facilitate benchmarking of arbitrary R code. The library
11667 consists of just one function, benchmark, which is a simple wrapper around
11668 system.time. Given a specification of the benchmarking process (counts of
11669 replications, evaluation environment) and an arbitrary number of expressions,
11670 benchmark evaluates each of the expressions in the specified environment,
11671 replicating the evaluation as many times as specified, and returning the results
11672 conveniently wrapped into a data frame.")
11673 (license license:gpl2+)))
11675 (define-public r-mitools
11682 (uri (cran-uri "mitools" version))
11685 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
11686 (build-system r-build-system)
11687 (propagated-inputs (list r-dbi))
11688 (home-page "https://cran.r-project.org/web/packages/mitools/")
11689 (synopsis "Tools for multiple imputation of missing data")
11691 "This package provides tools to perform analyses and combine results from
11692 multiple-imputation datasets.")
11693 (license license:gpl2)))
11695 (define-public r-mixsqp
11701 (uri (cran-uri "mixsqp" version))
11704 "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q"))))
11705 (properties `((upstream-name . "mixsqp")))
11706 (build-system r-build-system)
11708 (list r-irlba r-rcpp r-rcpparmadillo))
11711 (home-page "https://github.com/stephenslab/mixsqp")
11713 "Sequential quadratic programming for maximum-likelihood estimation")
11715 "This package provides an optimization method based on sequential
11716 quadratic programming for maximum likelihood estimation of the mixture
11717 proportions in a finite mixture model where the component densities are
11718 known. The algorithm is expected to obtain solutions that are at least
11719 as accurate as the state-of-the-art MOSEK interior-point solver, and they
11720 are expected to arrive at solutions more quickly when the number of
11721 samples is large and the number of mixture components is not too large.")
11722 (license license:expat)))
11724 (define-public r-magick
11731 (uri (cran-uri "magick" version))
11734 "0h942bn7wfnzbbgq9hrs75c7igmg5r1c5sad2v0znhza4cp7p1w3"))))
11735 (build-system r-build-system)
11737 (list imagemagick zlib))
11739 (list r-curl r-magrittr r-rcpp))
11741 (list pkg-config r-knitr))
11742 (home-page "https://github.com/ropensci/magick")
11743 (synopsis "Advanced graphics and image-processing in R")
11745 "This package provides bindings to ImageMagick, a comprehensive image
11746 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
11747 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
11748 operations are vectorized via the Magick++ STL meaning they operate either on
11749 a single frame or a series of frames for working with layers, collages, or
11750 animation. In RStudio, images are automatically previewed when printed to the
11751 console, resulting in an interactive editing environment.")
11752 (license license:expat)))
11754 (define-public r-survey
11761 (uri (cran-uri "survey" version))
11764 "0ljsszybzri531q6xab04r6zq11vchfs7y0snjzk57m3g0b9ms05"))))
11765 (build-system r-build-system)
11773 (home-page "http://r-survey.r-forge.r-project.org/survey/")
11774 (synopsis "Analysis of complex survey samples")
11776 "This package provides tools for the analysis of complex survey samples.
11777 The provided features include: summary statistics, two-sample tests, rank
11778 tests, generalised linear models, cumulative link models, Cox models,
11779 loglinear models, and general maximum pseudolikelihood estimation for
11780 multistage stratified, cluster-sampled, unequally weighted survey samples;
11781 variances by Taylor series linearisation or replicate weights;
11782 post-stratification, calibration, and raking; two-phase subsampling designs;
11783 graphics; PPS sampling without replacement; principal components, and factor
11785 ;; Either version of the GPL.
11786 (license (list license:gpl2 license:gpl3))))
11788 (define-public r-gee
11791 (version "4.13-23")
11795 (uri (cran-uri "gee" version))
11798 "0v0fam678pqqkxmj95f1pwsi08y1rbz1wxnp1ig81jvpn0xpq8gq"))))
11799 (properties `((upstream-name . "gee")))
11800 (build-system r-build-system)
11803 (home-page "https://cran.r-project.org/web/packages/gee/")
11804 (synopsis "Generalized estimation equation solver")
11806 "This package provides a solver for generalized estimation equations.")
11807 (license license:gpl2)))
11809 (define-public r-tab
11816 (uri (cran-uri "tab" version))
11819 "1kg8c1safi9klkx2mdkmsf5dn9piy4jljwd4ma7g4jz2rwl4jzhv"))))
11820 (properties `((upstream-name . "tab")))
11821 (build-system r-build-system)
11823 (list r-dplyr r-kableextra r-knitr r-mass r-survey))
11826 (home-page "https://cran.r-project.org/web/packages/tab/")
11827 (synopsis "Create summary tables for statistical reports")
11829 "This package contains functions for creating various types of summary
11830 tables, e.g. comparing characteristics across levels of a categorical variable
11831 and summarizing fitted generalized linear models, generalized estimating
11832 equations, and Cox proportional hazards models. Functions are available to
11833 handle data from simple random samples as well as complex surveys.")
11834 (license license:gpl3+)))
11836 (define-public r-dvmisc
11843 (uri (cran-uri "dvmisc" version))
11845 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
11846 (build-system r-build-system)
11859 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
11860 (synopsis "Faster computation of common statistics and miscellaneous functions")
11862 "This package implements faster versions of base R functions (e.g. mean, standard
11863 deviation, covariance, weighted mean), mostly written in C++, along with
11864 miscellaneous functions for various purposes (e.g. create the histogram with
11865 fitted probability density function or probability mass function curve, create
11866 the body mass index groups, assess the linearity assumption in logistic
11868 (license license:gpl2)))
11870 (define-public r-accelerometry
11872 (name "r-accelerometry")
11877 (uri (cran-uri "accelerometry" version))
11879 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
11880 (build-system r-build-system)
11882 (list r-dvmisc r-rcpp))
11883 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
11884 (synopsis "Functions for processing accelerometer data")
11886 "This package provides a collection of functions that perform operations on
11887 time-series accelerometer data, such as identify the non-wear time, flag minutes
11888 that are part of an activity bout, and find the maximum 10-minute average count
11889 value. The functions are generally very flexible, allowing for a variety of
11890 algorithms to be implemented.")
11891 (license license:gpl3)))
11893 (define-public r-absim
11900 (uri (cran-uri "AbSim" version))
11902 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
11903 (properties `((upstream-name . "AbSim")))
11904 (build-system r-build-system)
11906 (list r-ape r-powerlaw))
11907 (home-page "https://cran.r-project.org/web/packages/AbSim/")
11908 (synopsis "Time resolved simulations of antibody repertoires")
11910 "This package provides simulation methods for the evolution of antibody repertoires.
11911 The heavy and light chain variable region of both human and C57BL/6 mice can
11912 be simulated in a time-dependent fashion. Both single lineages using one set of
11913 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
11914 with an initial V-D-J recombination event, starting the first phylogenetic tree.
11915 Upon completion, the main loop of the algorithm begins, with each iteration
11916 representing one simulated time step. Various mutation events are possible at
11917 each time step, contributing to a diverse final repertoire.")
11918 (license license:gpl2)))
11920 (define-public r-quic
11927 (uri (cran-uri "QUIC" version))
11929 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
11930 (properties `((upstream-name . "QUIC")))
11931 (build-system r-build-system)
11932 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
11933 (synopsis "Regularized sparse inverse covariance matrix estimation")
11935 "This package implements the regularized Gaussian maximum likelihood
11936 estimation of the inverse of a covariance matrix. It uses Newton's method and
11937 coordinate descent to solve the regularized inverse covariance matrix
11938 estimation problem.")
11939 ;; The project home page states that the release is under GPLv3 or later.
11940 ;; The CRAN page only says GPL-3.
11941 (license license:gpl3+)))
11943 (define-public r-abundant
11945 (name "r-abundant")
11950 (uri (cran-uri "abundant" version))
11952 (base32 "15m3ngj5aipjg961yy5kvdg9xlfcpliw30dq6gchzxabhnfzcipd"))))
11953 (build-system r-build-system)
11956 (home-page "https://cran.r-project.org/web/packages/abundant/")
11957 (synopsis "Abundant regression and high-dimensional principal fitted components")
11959 "This package provides tools to fit and predict with the high-dimensional
11960 principal fitted components model. This model is described by Cook, Forzani,
11961 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
11962 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
11963 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
11964 (license license:gpl2+)))
11966 (define-public r-ac3net
11973 (uri (cran-uri "Ac3net" version))
11975 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
11976 (properties `((upstream-name . "Ac3net")))
11977 (build-system r-build-system)
11979 (list r-data-table))
11980 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
11981 (synopsis "Inferring directional conservative causal core gene networks")
11982 (description "This package infers directional Conservative causal core
11983 (gene) networks (C3NET). This is a version of the algorithm C3NET with
11984 directional network.")
11985 (license license:gpl3+)))
11987 (define-public r-aca
11994 (uri (cran-uri "ACA" version))
11996 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
11997 (properties `((upstream-name . "ACA")))
11998 (build-system r-build-system)
11999 (home-page "https://cran.r-project.org/web/packages/ACA/")
12000 (synopsis "Abrupt change-point or aberration detection in point series")
12002 "This package offers an interactive function for the detection of breakpoints in
12004 ;; Any version of the GPL
12005 (license (list license:gpl2+ license:gpl3+))))
12007 (define-public r-acceptancesampling
12009 (name "r-acceptancesampling")
12014 (uri (cran-uri "AcceptanceSampling" version))
12016 (base32 "1ja1g0v8qvf7yj81x37wc6i7fkwpc573756jgvazazi8yf1gm12p"))))
12018 `((upstream-name . "AcceptanceSampling")))
12019 (build-system r-build-system)
12020 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
12021 (synopsis "Creation and evaluation of acceptance sampling plans")
12023 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
12024 acceptance sampling plans. Acceptance sampling is a methodology commonly used
12025 in quality control and improvement. International standards of acceptance
12026 sampling provide sampling plans for specific circumstances. The aim of this
12027 package is to provide an easy-to-use interface to visualize single, double or
12028 multiple sampling plans. In addition, methods have been provided to enable the
12029 user to assess sampling plans against pre-specified levels of performance, as
12030 measured by the probability of acceptance for a given level of quality in the
12032 (license license:gpl3+)))
12034 (define-public r-acclma
12041 (uri (cran-uri "ACCLMA" version))
12043 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
12044 (properties `((upstream-name . "ACCLMA")))
12045 (build-system r-build-system)
12046 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
12047 (synopsis "ACC & LMA graph plotting")
12049 "This package contains a function that imports data from a @acronym{CSV,
12050 Comma-Separated Values} file, or uses manually entered data from the format (x,
12051 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
12052 Curve} vs @acronym{LOI, Line of Independence} graph and
12053 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
12054 function is @code{plotLMA} (source file, header) that takes a data set and plots the
12055 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
12056 string) was passed, a manual data entry window is opened. The header parameter
12057 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
12058 a header row or not. The dataset should contain only one independent variable
12059 (x) and one dependent variable (y) and can contain a weight for each
12061 (license license:gpl2)))
12063 (define-public r-aspi
12070 (uri (cran-uri "aspi" version))
12072 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
12073 (build-system r-build-system)
12075 "https://cran.r-project.org/web/packages/aspi/")
12077 "Analysis of symmetry of parasitic infections")
12079 "This package provides tools for the analysis and visualization of bilateral
12080 asymmetry in parasitic infections.")
12081 (license license:gpl3+)))
12083 (define-public r-sandwich
12085 (name "r-sandwich")
12090 (uri (cran-uri "sandwich" version))
12093 "12aa5083k3sfrfq1jy3l94wffss9h0rga8j71jy3n8pkhiq4nn7n"))))
12094 (build-system r-build-system)
12097 (home-page "https://cran.r-project.org/web/packages/sandwich/")
12098 (synopsis "Robust Covariance Matrix Estimators")
12100 "This package provides model-robust standard error estimators for
12101 cross-sectional, time series, clustered, panel, and longitudinal data.")
12102 ;; Either version of the license.
12103 (license (list license:gpl2 license:gpl3))))
12105 (define-public r-th-data
12112 (uri (cran-uri "TH.data" version))
12115 "0ynxacnz002bjsp2ybql7rdqw4zd14af8r7w44nwbx22n4bapwzd"))))
12116 (properties `((upstream-name . "TH.data")))
12117 (build-system r-build-system)
12119 (list r-mass r-survival))
12122 (home-page "https://cran.r-project.org/web/packages/TH.data/")
12123 (synopsis "Shared data sets")
12125 "This package contains supporting data sets that are used in other
12126 packages maintained by Torsten Hothorn.")
12127 (license license:gpl3)))
12129 (define-public r-multcomp
12131 (name "r-multcomp")
12136 (uri (cran-uri "multcomp" version))
12139 "0mz5wdqrqpp2gqijfpp9rgfbq8yvxki4is8fbbc4qwdwryqp6d7h"))))
12140 (build-system r-build-system)
12142 (list r-codetools r-mvtnorm r-sandwich r-survival r-th-data))
12143 (home-page "https://cran.r-project.org/web/packages/multcomp/")
12144 (synopsis "Simultaneous inference in general parametric models")
12146 "Simultaneous tests and confidence intervals for general linear
12147 hypotheses in parametric models, including linear, generalized linear, linear
12148 mixed effects, and survival models. The package includes demos reproducing
12149 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
12150 Hothorn, Westfall, 2010, CRC Press).")
12151 (license license:gpl2)))
12153 (define-public r-multcompview
12155 (name "r-multcompview")
12160 (uri (cran-uri "multcompView" version))
12162 (base32 "1rfq9wvvrghq0542ff40wy8vdmsyd8spzz6ihcywcvxdfa8m6g8j"))))
12163 (properties `((upstream-name . "multcompView")))
12164 (build-system r-build-system)
12165 (home-page "https://cran.r-project.org/package=multcompView")
12166 (synopsis "Visualizations of paired comparisons")
12168 "Convert a logical vector or a vector of p-values or a correlation,
12169 difference, or distance matrix into a display identifying the pairs for which
12170 the differences were not significantly different.")
12171 ;; Any version of the GPL.
12172 (license license:gpl3+)))
12174 (define-public r-emmeans
12177 (version "1.7.4-1")
12181 (uri (cran-uri "emmeans" version))
12184 "08g7ifqhwqa00hc850nwx03dp7isz0281ig6kvixc4xdahmkm8zp"))))
12185 (build-system r-build-system)
12187 (list r-estimability r-mvtnorm r-numderiv r-xtable))
12190 (home-page "https://github.com/rvlenth/emmeans")
12191 (synopsis "Estimated marginal means, aka least-squares means")
12193 "This package provides tools to obtain @dfn{estimated marginal
12194 means} (EMMs) for many linear, generalized linear, and mixed models. It can
12195 be used to compute contrasts or linear functions of EMMs, trends, and
12196 comparisons of slopes.")
12197 ;; Either version of the license.
12198 (license (list license:gpl2 license:gpl3))))
12200 (define-public r-pwr
12207 (uri (cran-uri "pwr" version))
12210 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
12211 (build-system r-build-system)
12214 (home-page "https://github.com/heliosdrm/pwr")
12215 (synopsis "Basic functions for power analysis")
12217 "This package provides power analysis functions along the lines of
12219 (license license:gpl3+)))
12221 (define-public r-libcoin
12228 (uri (cran-uri "libcoin" version))
12230 (base32 "1syrcdj5qg5m3zd3dlxgpfklswbalfg42w058dr09hnzqsvx0z9d"))))
12231 (build-system r-build-system)
12232 (propagated-inputs (list r-mvtnorm))
12233 (home-page "https://cran.r-project.org/web/packages/libcoin")
12234 (synopsis "Linear test statistics for permutation inference")
12236 "This package provides basic infrastructure for linear test statistics
12237 and permutation inference in the framework of Strasser and Weber (1999).")
12238 (license license:gpl2)))
12240 (define-public r-coin
12247 (uri (cran-uri "coin" version))
12250 "1cpv7jx840inzg98bkhrb5yscx0gpag6br237r5qpnc2gbrd2ikm"))))
12251 (build-system r-build-system)
12259 (home-page "http://coin.r-forge.r-project.org")
12260 (synopsis "Conditional inference procedures in a permutation test framework")
12262 "This package provides conditional inference procedures for the general
12263 independence problem including two-sample, K-sample (non-parametric ANOVA),
12264 correlation, censored, ordered and multivariate problems.")
12265 (license license:gpl2)))
12267 (define-public r-bayesplot
12269 (name "r-bayesplot")
12274 (uri (cran-uri "bayesplot" version))
12277 "0hqy597ang53phxnl084hak35ffqz9lw9hygax7370gpkjws908a"))))
12278 (build-system r-build-system)
12293 (home-page "https://mc-stan.org/bayesplot")
12294 (synopsis "Plotting for Bayesian models")
12296 "This package provides plotting functions for posterior analysis, model
12297 checking, and MCMC diagnostics. The package is designed not only to provide
12298 convenient functionality for users, but also a common set of functions that
12299 can be easily used by developers working on a variety of R packages for
12300 Bayesian modeling.")
12301 (license license:gpl3+)))
12303 (define-public r-tmb
12310 (uri (cran-uri "TMB" version))
12313 "1mr5vwamw6ag1fhd83jyy6015296908qwshwq0fcphhiv60x579c"))))
12314 (properties `((upstream-name . "TMB")))
12315 (build-system r-build-system)
12317 (list r-matrix r-rcppeigen))
12318 (home-page "http://tmb-project.org")
12319 (synopsis "Template model builder: a general random effect tool")
12321 "With this tool, a user should be able to quickly implement complex
12322 random effect models through simple C++ templates. The package combines
12323 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
12324 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
12325 from R) to obtain an efficient implementation of the applied Laplace
12326 approximation with exact derivatives. Key features are: Automatic sparseness
12327 detection, parallelism through BLAS and parallel user templates.")
12328 (license license:gpl2)))
12330 (define-public r-sjstats
12337 (uri (cran-uri "sjstats" version))
12339 (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka"))))
12340 (build-system r-build-system)
12359 (home-page "https://github.com/strengejacke/sjstats")
12360 (synopsis "Functions for common statistical computations")
12362 "This package provides a collection of convenient functions for common
12363 statistical computations, which are not directly provided by R's @code{base}
12364 or @code{stats} packages. This package aims at providing, first, shortcuts
12365 for statistical measures, which otherwise could only be calculated with
12366 additional effort. Second, these shortcut functions are generic, and can be
12367 applied not only to vectors, but also to other objects as well. The focus of
12368 most functions lies on summary statistics or fit measures for regression
12369 models, including generalized linear models, mixed effects models and Bayesian
12371 (license license:gpl3)))
12373 (define-public r-glmmtmb
12380 (uri (cran-uri "glmmTMB" version))
12383 "0xdjc3gx0cj098rrjzlsy9cccxzfvn029xh4ycpya4xjhxsykldr"))))
12384 (properties `((upstream-name . "glmmTMB")))
12385 (build-system r-build-system)
12394 (list r-knitr r-rmarkdown)) ; for vignettes
12395 (home-page "https://github.com/glmmTMB")
12396 (synopsis "Generalized linear mixed models")
12398 "Fit linear and generalized linear mixed models with various extensions,
12399 including zero-inflation. The models are fitted using maximum likelihood
12400 estimation via the Template Model Builder. Random effects are assumed to be
12401 Gaussian on the scale of the linear predictor and are integrated out using the
12402 Laplace approximation. Gradients are calculated using automatic
12404 (license license:agpl3+)))
12406 (define-public r-bayestestr
12408 (name "r-bayestestr")
12413 (uri (cran-uri "bayestestR" version))
12416 "1fbkpagc5zznrafy7h68nhx43a1yg4v7242pbqjkd0h2481c101z"))))
12417 (properties `((upstream-name . "bayestestR")))
12418 (build-system r-build-system)
12420 (list r-datawizard r-insight))
12423 (home-page "https://github.com/easystats/bayestestR")
12424 (synopsis "Describe Bayesian models and posterior distributions")
12426 "This package provides utilities to understand and describe posterior
12427 distributions and Bayesian models. It includes point-estimates such as
12428 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
12429 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
12430 ROPE percentage and pd).")
12431 (license license:gpl3)))
12433 (define-public r-performance
12435 (name "r-performance")
12440 (uri (cran-uri "performance" version))
12443 "1znr4i1pjv6z3lj6qrma2i3l94rz1z29w92mrxxfy3ch0s71crww"))))
12444 (build-system r-build-system)
12446 (list r-bayestestr r-datawizard r-insight))
12447 (home-page "https://easystats.github.io/performance/")
12448 (synopsis "Assessment of regression models performance")
12450 "This package provides utilities for computing measures to assess model
12451 quality, which are not directly provided by R's @code{base} or @code{stats}
12452 packages. These include e.g. measures like r-squared, intraclass correlation
12453 coefficient, root mean squared error or functions to check models for
12454 overdispersion, singularity or zero-inflation and more. Functions apply to a
12455 large variety of regression models, including generalized linear models, mixed
12456 effects models and Bayesian models.")
12457 (license license:gpl3)))
12459 (define-public r-ggeffects
12461 (name "r-ggeffects")
12466 (uri (cran-uri "ggeffects" version))
12469 "01yyfw7fkbxrp0gpwni5y8m4w9l3xckwc3crnvy1fqs1d6gwx3xx"))))
12470 (build-system r-build-system)
12472 (list r-insight r-mass r-sjlabelled))
12475 (home-page "https://github.com/strengejacke/ggeffects")
12476 (synopsis "Create tidy data frames of marginal effects for ggplot")
12478 "This package provides tools to compute marginal effects from statistical
12479 models and return the result as tidy data frames. These data frames are ready
12480 to use with the @code{ggplot2} package. Marginal effects can be calculated
12481 for many different models. Interaction terms, splines and polynomial terms
12482 are also supported. The two main functions are @code{ggpredict()} and
12483 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
12484 results using @code{ggplot2}.")
12485 (license license:gpl3)))
12487 (define-public r-effectsize
12489 (name "r-effectsize")
12494 (uri (cran-uri "effectsize" version))
12497 "07dbj7n9vwjkb7xrdj224lzc3ppr3jjdgyyilkj7gpkvgjgfrqhz"))))
12498 (properties `((upstream-name . "effectsize")))
12499 (build-system r-build-system)
12501 (list r-bayestestr r-datawizard r-insight r-parameters
12505 (home-page "https://github.com/easystats/effectsize")
12506 (synopsis "Indices of effect size and standardized parameters")
12508 "This package provides utilities to work with indices of effect size and
12509 standardized parameters for a wide variety of models, allowing computation and
12510 conversion of indices such as Cohen's d, r, odds, etc.")
12511 (license license:gpl3)))
12513 (define-public r-sjplot
12520 (uri (cran-uri "sjPlot" version))
12522 (base32 "1rnwhh271xj8xgvvlpqw9ain56mfz37fvl7f6jq9nzx9jxx95bjd"))))
12523 (properties `((upstream-name . "sjPlot")))
12524 (build-system r-build-system)
12546 (home-page "https://strengejacke.github.io/sjPlot/")
12547 (synopsis "Data visualization for statistics in social science")
12549 "This package represents a collection of plotting and table output
12550 functions for data visualization. Results of various statistical
12551 analyses (that are commonly used in social sciences) can be visualized using
12552 this package, including simple and cross tabulated frequencies, histograms,
12553 box plots, (generalized) linear models, mixed effects models, principal
12554 component analysis and correlation matrices, cluster analyses, scatter plots,
12555 stacked scales, effects plots of regression models (including interaction
12556 terms) and much more. This package supports labelled data.")
12557 (license license:gpl3)))
12559 (define-public r-ini
12566 (uri (cran-uri "ini" version))
12569 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
12570 (build-system r-build-system)
12571 (home-page "https://github.com/dvdscripter/ini")
12572 (synopsis "Read and write configuration files")
12574 "This package provides tools to parse simple @code{.ini} configuration
12575 files to an structured list. Users can manipulate this resulting list with
12576 @code{lapply()} functions. This same structured list can be used to write
12577 back to file after modifications.")
12578 (license license:gpl3)))
12580 (define-public r-gillespiessa2
12582 (name "r-gillespiessa2")
12587 (uri (cran-uri "GillespieSSA2" version))
12589 (base32 "03ym8qx5yc1a6j9l973lc0rjzs8hiax8fq13j7m1fcb1pvnbvar5"))))
12590 (properties `((upstream-name . "GillespieSSA2")))
12591 (build-system r-build-system)
12604 (native-inputs (list r-knitr))
12605 (home-page "https://github.com/rcannood/GillespieSSA2")
12606 (synopsis "Gillespie's stochastic simulation algorithm")
12608 "This package provides a fast, scalable, and versatile framework for
12609 simulating large systems with Gillespie's @dfn{Stochastic Simulation
12610 Algorithm} (SSA). This package is the spiritual successor to the GillespieSSA
12611 package. Benefits of this package include major speed improvements (>100x),
12612 easier to understand documentation, and many unit tests that try to ensure the
12613 package works as intended.")
12614 (license license:gpl3+)))
12616 (define-public r-gitcreds
12618 (name "r-gitcreds")
12623 (uri (cran-uri "gitcreds" version))
12626 "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi"))))
12627 (properties `((upstream-name . "gitcreds")))
12628 (build-system r-build-system)
12629 (inputs (list git-minimal))
12630 (native-inputs (list r-knitr))
12631 (home-page "https://github.com/r-lib/gitcreds")
12632 (synopsis "Query git credentials from R")
12634 "Query, set, and delete credentials from the git credential store.
12635 Manage GitHub tokens and other git credentials. This package is to be used by
12636 other packages that need to authenticate to GitHub and/or other git
12638 (license license:expat)))
12640 (define-public r-gh
12647 (uri (cran-uri "gh" version))
12650 "077drbxz3rx7idv6w24ipj1p6jnzv86a3iyryab699cc9q2kjh54"))))
12651 (build-system r-build-system)
12653 (list r-cli r-gitcreds r-httr r-ini r-jsonlite))
12656 (home-page "https://github.com/r-lib/gh#readme")
12657 (synopsis "Access the GitHub API via R")
12659 "This package provides a minimal R client to access the GitHub API.")
12660 (license license:expat)))
12662 (define-public r-fs
12669 (uri (cran-uri "fs" version))
12672 "11qr3v0xn65vfhgcxl4l6yv48s4w0w3ldp3anpzc25vd3mwd3jim"))))
12673 (build-system r-build-system)
12676 (home-page "https://fs.r-lib.org")
12677 (synopsis "Cross-platform file system operations based on libuv")
12679 "This package provides a cross-platform interface to file system
12680 operations, built on top of the libuv C library.")
12681 (license license:gpl3)))
12683 (define-public r-clisymbols
12685 (name "r-clisymbols")
12690 (uri (cran-uri "clisymbols" version))
12693 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
12694 (build-system r-build-system)
12695 (home-page "https://github.com/gaborcsardi/clisymbols")
12696 (synopsis "Unicode symbols at the R prompt")
12698 "This package provides a small subset of Unicode symbols, that are useful
12699 when building command line applications. They fall back to alternatives on
12700 terminals that do not support Unicode.")
12701 (license license:expat)))
12703 (define-public r-credentials
12705 (name "r-credentials")
12710 (uri (cran-uri "credentials" version))
12713 "1f18j3zrq8c9kah57xwahmmljsjg5qphlgamvx507ynvpq8pryig"))))
12714 (properties `((upstream-name . "credentials")))
12715 (build-system r-build-system)
12718 (modify-phases %standard-phases
12719 (add-after 'unpack 'setenv-HOME
12721 ;; This is necessary because git looks for $HOME/.gitconfig
12722 (setenv "HOME" "/tmp"))))))
12724 (list git-minimal))
12726 (list r-askpass r-curl r-jsonlite r-openssl r-sys))
12729 (home-page "https://docs.ropensci.org/credentials/")
12730 (synopsis "Tools for managing SSH and Git credentials")
12732 "This package assists you in setting up and retrieving of HTTPS and SSH
12733 credentials for use with git and other services. For HTTPS remotes the
12734 package interfaces the @command{git-credential} utility which @command{git}
12735 uses to store HTTP usernames and passwords. For SSH remotes this package
12736 provides convenient functions to find or generate appropriate SSH keys. The
12737 package both helps the user to setup a local git installation, and also
12738 provides a back-end for git/ssh client libraries to authenticate with existing
12739 user credentials.")
12740 (license license:expat)))
12742 (define-public r-gert
12749 (uri (cran-uri "gert" version))
12752 "0r19vi77yyjw5gbhgjibdysjlszlw2095v14f6sv675zpbp0li4c"))))
12753 (properties `((upstream-name . "gert")))
12754 (build-system r-build-system)
12756 (list libgit2 zlib))
12765 (list pkg-config r-knitr))
12766 (home-page "https://docs.ropensci.org/gert/")
12767 (synopsis "Simple Git client for R")
12769 "This package provides a simple git client for R based on libgit2 with
12770 support for SSH and HTTPS remotes. All functions in gert use basic R data
12771 types (such as vectors and data-frames) for their arguments and return values.
12772 User credentials are shared with command line git through the
12773 @code{git-credential} store and SSH keys stored on disk or ssh-agent.")
12774 (license license:expat)))
12776 (define-public r-usethis
12783 (uri (cran-uri "usethis" version))
12786 "0638dzl4nm4c36990sf2biy74hjr2fzlqzfb98fsqrbhaw3ngp1i"))))
12787 (build-system r-build-system)
12808 (home-page "https://github.com/r-lib/usethis")
12809 (synopsis "Automate R package and project setup")
12811 "This package helps you to automate R package and project setup tasks
12812 that are otherwise performed manually. This includes setting up unit testing,
12813 test coverage, continuous integration, Git, GitHub integration, licenses,
12814 Rcpp, RStudio projects, and more.")
12815 (license license:gpl3)))
12817 (define-public r-sessioninfo
12819 (name "r-sessioninfo")
12824 (uri (cran-uri "sessioninfo" version))
12827 "1jy7n37qnrb4fgzmn8s8yf7kv29yw27x8zklwf8qdb2kgj2q6qpm"))))
12828 (build-system r-build-system)
12831 (home-page "https://github.com/r-lib/sessioninfo#readme")
12832 (synopsis "R session information")
12834 "This package provides tools to query and print information about the
12835 current R session. It is similar to @code{utils::sessionInfo()}, but includes
12836 more information about packages, and where they were installed from.")
12837 (license license:gpl2)))
12839 (define-public r-remotes
12846 (uri (cran-uri "remotes" version))
12849 "05m5dgv0nba5vhjbdkd8z5lbhpfxgkw31j58am7vz1d44igqgvzj"))))
12850 (build-system r-build-system)
12853 (home-page "https://github.com/r-lib/remotes#readme")
12854 (synopsis "R package installation from remote repositories")
12856 "Download and install R packages stored in GitHub, BitBucket, or plain
12857 subversion or git repositories. This package is a lightweight replacement of
12858 the @code{install_*} functions in the @code{devtools} package. Indeed most of
12859 the code was copied over from @code{devtools}.")
12860 (license license:gpl2+)))
12862 (define-public r-xopen
12869 (uri (cran-uri "xopen" version))
12872 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
12873 (build-system r-build-system)
12876 (home-page "https://github.com/r-lib/xopen#readme")
12877 (synopsis "Open system files, URLs, anything")
12879 "This package provides a cross-platform solution to open files,
12880 directories or URLs with their associated programs.")
12881 (license license:expat)))
12883 (define-public r-rcmdcheck
12885 (name "r-rcmdcheck")
12890 (uri (cran-uri "rcmdcheck" version))
12893 "1l696byn3kjq2xvz4wxybzaj6ink85h4lz3a35v2132ba5yyzm5v"))))
12894 (build-system r-build-system)
12908 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
12909 (synopsis "Run R CMD check from R and capture results")
12911 "Run @code{R CMD check} from R programmatically, and capture the results
12912 of the individual checks.")
12913 (license license:expat)))
12915 (define-public r-rapportools
12917 (name "r-rapportools")
12922 (uri (cran-uri "rapportools" version))
12925 "0qr86idng12g6hdd764j0wmli700v7rjhw7jdjxj0ka8xm5v7ymm"))))
12926 (build-system r-build-system)
12928 (list r-mass r-pander r-plyr r-reshape2))
12929 (home-page "https://cran.r-project.org/web/packages/rapportools/")
12930 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
12932 "This package provides helper functions that act as wrappers to more
12933 advanced statistical methods with the advantage of having sane defaults for
12935 (license license:agpl3+)))
12937 (define-public r-pander
12944 (uri (cran-uri "pander" version))
12947 "144zkq5w7v6fpzk3x40i0baybbp0y6x2ckh4b9qljryas9mhgp9a"))))
12948 (build-system r-build-system)
12950 (list r-digest r-rcpp))
12953 (home-page "https://rapporter.github.io/pander")
12954 (synopsis "Render R objects into Pandoc's markdown")
12956 "The main aim of the pander R package is to provide a minimal and easy
12957 tool for rendering R objects into Pandoc's markdown. The package is also
12958 capable of exporting/converting complex Pandoc documents (reports) in various
12960 ;; This package is licensed under either the AGPLv3+ or the very rarely
12962 (license license:agpl3+)))
12964 (define-public r-summarytools
12966 (name "r-summarytools")
12971 (uri (cran-uri "summarytools" version))
12974 "0gr95cd1ja8di6s0xghk6w7nj3bh3z4g7j7ixdy7f88q681aixgx"))))
12975 (build-system r-build-system)
12991 (home-page "https://github.com/dcomtois/summarytools")
12992 (synopsis "Tools to quickly and neatly summarize data")
12994 "This package provides tools for data frame summaries, cross-tabulations,
12995 weight-enabled frequency tables and common univariate statistics in concise
12996 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
12997 good point-of-entry for exploring data, both for experienced and new R
12999 (license license:gpl2)))
13001 (define-public r-lsei
13008 (uri (cran-uri "lsei" version))
13011 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2"))))
13012 (build-system r-build-system)
13015 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
13016 (synopsis "Solve regression problems under equality/inequality constraints")
13018 "It contains functions that solve least squares linear regression
13019 problems under linear equality/inequality constraints. Functions for solving
13020 quadratic programming problems are also available, which transform such
13021 problems into least squares ones first.")
13022 (license license:gpl2+)))
13024 (define-public r-npsurv
13031 (uri (cran-uri "npsurv" version))
13034 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw"))))
13035 (build-system r-build-system)
13038 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
13039 (synopsis "Nonparametric survival analysis")
13041 "This package contains functions for non-parametric survival analysis of
13042 exact and interval-censored observations.")
13043 (license license:gpl2+)))
13045 (define-public r-clusteval
13047 (name "r-clusteval")
13052 (uri (cran-uri "clusteval" version))
13055 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
13056 (build-system r-build-system)
13058 (list r-mvtnorm r-rcpp))
13059 (home-page "https://cran.r-project.org/web/packages/clusteval/")
13060 (synopsis "Evaluation of clustering algorithms")
13062 "This R package provides a suite of tools to evaluate clustering
13063 algorithms, clusterings, and individual clusters.")
13064 (license license:expat)))
13066 (define-public r-tweedie
13073 (uri (cran-uri "tweedie" version))
13076 "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0"))))
13077 (build-system r-build-system)
13078 (native-inputs (list gfortran))
13079 (home-page "https://cran.r-project.org/web/packages/tweedie/")
13080 (synopsis "Evaluation of Tweedie exponential family models")
13082 "Maximum likelihood computations for Tweedie families, including the
13083 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
13084 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
13085 and related methods.")
13086 (license license:gpl2+)))
13088 (define-public r-rcppgsl
13095 (uri (cran-uri "RcppGSL" version))
13097 (base32 "1a5dms0axlzgpv1z2bhfrb77497h0ch1yslq0gidj14vr4kfm57h"))))
13098 (properties `((upstream-name . "RcppGSL")))
13099 (build-system r-build-system)
13102 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
13103 (synopsis "Rcpp integration for GSL vectors and matrices")
13105 "The GNU Scientific Library (or GSL) is a collection of numerical
13106 routines for scientific computing. It is particularly useful for C and C++
13107 programs as it provides a standard C interface to a wide range of mathematical
13108 routines. There are over 1000 functions in total with an extensive test
13109 suite. The RcppGSL package provides an easy-to-use interface between GSL data
13110 structures and R using concepts from Rcpp which is itself a package that eases
13111 the interfaces between R and C++.")
13112 (license license:gpl2+)))
13114 (define-public r-mvabund
13121 (uri (cran-uri "mvabund" version))
13124 "01kss9dx4an1ir5zs46jypvhj8sdc8wcs00i1223ai09av4lcsgd"))))
13125 (build-system r-build-system)
13127 (list r-mass r-rcpp r-rcppgsl r-statmod r-tweedie))
13128 (home-page "https://cran.r-project.org/web/packages/mvabund/")
13129 (synopsis "Statistical methods for analysing multivariate abundance data")
13131 "This package provides a set of tools for displaying, modeling and
13132 analysing multivariate abundance data in community ecology.")
13133 (license license:lgpl2.1+)))
13135 (define-public r-afex
13142 (uri (cran-uri "afex" version))
13145 "09q426s2zmzxx5ilxy0x5mflpb38pl075ss1s8xvpswkn6cia0b6"))))
13146 (build-system r-build-system)
13147 ;; This is needed for the vignette builder
13150 (modify-phases %standard-phases
13151 (add-after 'unpack 'set-HOME
13152 (lambda _ (setenv "HOME" "/tmp"))))))
13154 (list r-car r-lme4 r-lmertest r-pbkrtest r-reshape2))
13157 r-r-rsp)) ;vignette builder
13158 (home-page "https://afex.singmann.science/")
13159 (synopsis "Analysis of factorial experiments")
13161 "This package provides convenience functions for analyzing factorial
13162 experiments using ANOVA or mixed models.")
13163 (license license:gpl2+)))
13165 (define-public r-lmertest
13167 (name "r-lmertest")
13172 (uri (cran-uri "lmerTest" version))
13175 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim"))))
13176 (properties `((upstream-name . "lmerTest")))
13177 (build-system r-build-system)
13179 (list r-ggplot2 r-lme4 r-mass r-numderiv))
13180 (home-page "https://github.com/runehaubo/lmerTestR")
13181 (synopsis "Tests in linear mixed effects models")
13183 "This package provides p-values in type I, II or III anova and summary
13184 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
13185 method. A Kenward-Roger method is also available via the @code{pbkrtest}
13186 package. Model selection methods include step, drop1 and anova-like tables
13187 for random effects (ranova). Methods for Least-Square means (LS-means) and
13188 tests of linear contrasts of fixed effects are also available.")
13189 (license license:gpl2+)))
13191 (define-public r-r2glmm
13198 (uri (cran-uri "r2glmm" version))
13201 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
13202 (build-system r-build-system)
13214 (home-page "https://github.com/bcjaeger/r2glmm")
13215 (synopsis "Compute R squared for mixed (multilevel) models")
13217 "This package computes model and semi partial R squared with confidence
13218 limits for the linear and generalized linear mixed model (LMM and GLMM). The
13219 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
13220 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
13222 (license license:gpl2)))
13224 (define-public r-cmdfun
13231 (uri (cran-uri "cmdfun" version))
13234 "1pbcq7hi2lcmqnghmy3q2fsk0c9fy5m0637acyzmc096fxbx723j"))))
13235 (properties `((upstream-name . "cmdfun")))
13236 (build-system r-build-system)
13246 (home-page "https://snystrom.github.io/cmdfun/")
13247 (synopsis "Framework for building interfaces to shell commands")
13249 "Writing interfaces to command line software is cumbersome. The cmdfun
13250 package provides a framework for building function calls to seamlessly
13251 interface with shell commands by allowing lazy evaluation of command line
13252 arguments. It also provides methods for handling user-specific paths to tool
13253 installs or secrets like API keys. Its focus is to equally serve package
13254 builders who wish to wrap command line software, and to help analysts stay
13255 inside R when they might usually leave to execute non-R software.")
13256 (license license:expat)))
13258 (define-public r-rslurm
13265 (uri (cran-uri "rslurm" version))
13268 "19451icfh7snjbbmpzpr1hrdf52q8ijv0ag1di3y55r2la3jxxcf"))))
13269 (properties `((upstream-name . "rslurm")))
13270 (build-system r-build-system)
13271 (propagated-inputs (list r-whisker))
13272 (native-inputs (list r-knitr))
13273 (home-page "http://cyberhelp.sesync.org/rslurm/")
13274 (synopsis "Submit R calculations to a Slurm cluster")
13276 "This package provides functions that simplify submitting R scripts to a
13277 Slurm workload manager, in part by automating the division of embarrassingly
13278 parallel calculations across cluster nodes.")
13279 (license license:gpl3)))
13281 (define-public r-chk
13288 (uri (cran-uri "chk" version))
13291 "10gcv00mgi88vgxr9jrs0ar67crmdcdi4m9g86cm6pg3ly0v097y"))))
13292 (properties `((upstream-name . "chk")))
13293 (build-system r-build-system)
13295 (list r-lifecycle r-rlang))
13296 (native-inputs (list r-knitr))
13297 (home-page "https://github.com/poissonconsulting/chk")
13298 (synopsis "Check user-supplied function arguments")
13300 "This is a package for developers to check user-supplied function
13301 arguments. It is designed to be simple, fast and customizable. Error
13302 messages follow the tidyverse style guide.")
13303 (license license:expat)))
13305 (define-public r-weights
13312 (uri (cran-uri "weights" version))
13315 "1fnchf7f0hyl514bk8sc3l884kg25kb5xm4mc2l28n6hm7l6bgpg"))))
13316 (build-system r-build-system)
13318 (list r-gdata r-hmisc r-lme4 r-mice))
13319 (home-page "https://cran.r-project.org/web/packages/weights/")
13320 (synopsis "Weighting and weighted statistics")
13321 (description "This package Provides a variety of functions for producing
13322 simple weighted statistics, such as weighted Pearson's correlations, partial
13323 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
13324 includes some software for quickly recoding survey data and plotting point
13325 estimates from interaction terms in regressions (and multiply imputed
13326 regressions). NOTE: Weighted partial correlation calculations pulled to
13328 (license license:gpl2+)))
13330 (define-public r-rcppannoy
13332 (name "r-rcppannoy")
13337 (uri (cran-uri "RcppAnnoy" version))
13340 "12k8ny981dmky5js8yl6bih5r5mq3w43f2f9admhkwqn0n80kcl9"))))
13341 (properties `((upstream-name . "RcppAnnoy")))
13342 (build-system r-build-system)
13345 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
13346 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
13348 "Annoy is a small C++ library for Approximate Nearest Neighbors written
13349 for efficient memory usage as well an ability to load from and save to disk.
13350 This package provides an R interface.")
13351 ;; Annoy is released under ASL 2.0, but this wrapper is released under
13353 (license (list license:gpl2+ license:asl2.0))))
13355 (define-public r-rcpphnsw
13357 (name "r-rcpphnsw")
13362 (uri (cran-uri "RcppHNSW" version))
13365 "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
13366 (properties `((upstream-name . "RcppHNSW")))
13367 (build-system r-build-system)
13368 (propagated-inputs (list r-rcpp))
13369 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
13370 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
13372 "Hnswlib is a C++ library for approximate nearest neighbors. This
13373 package provides a minimal R interface by relying on the Rcpp package.")
13374 ;; hnswlib is released under Version 2.0 of the Apache License.
13375 (license (list license:gpl3 license:asl2.0))))
13377 (define-public r-rcppparallel
13379 (name "r-rcppparallel")
13384 (uri (cran-uri "RcppParallel" version))
13387 "1sn211ajlb1p12sglxqns175rg078yvww268m8cp0vvd7cmk55k3"))))
13388 (properties `((upstream-name . "RcppParallel")))
13389 (build-system r-build-system)
13390 (home-page "https://rcppcore.github.io/RcppParallel/")
13391 (synopsis "Parallel programming tools for Rcpp")
13393 "This package provides high level functions for parallel programming with
13394 Rcpp. For example, the @code{parallelFor()} function can be used to convert
13395 the work of a standard serial @code{for} loop into a parallel one and the
13396 @code{parallelReduce()} function can be used for accumulating aggregates or
13398 (license license:gpl2)))
13400 (define-public r-ncdf4
13407 (uri (cran-uri "ncdf4" version))
13410 "0qzvin2fjzcb7h2knlnw14s6043pwi1nm7yf6p27ax7w269173fb"))))
13411 (build-system r-build-system)
13413 (list netcdf zlib))
13414 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
13415 (synopsis "R interface to Unidata netCDF format data files")
13417 "This package provides a high-level R interface to data files written
13418 using Unidata's netCDF library (version 4 or earlier), which are binary data
13419 files that are portable across platforms and include metadata information in
13420 addition to the data sets. Using this package, netCDF files can be opened and
13421 data sets read in easily. It is also easy to create new netCDF dimensions,
13422 variables, and files, in either version 3 or 4 format, and manipulate existing
13424 (license license:gpl3+)))
13426 (define-public r-biocmanager
13428 (name "r-biocmanager")
13429 (version "1.30.18")
13433 (uri (cran-uri "BiocManager" version))
13435 (base32 "0dawbd546rznllpw5wq282r0viga4cck398d4s1inkk18mmi4qzp"))))
13436 (properties `((upstream-name . "BiocManager")))
13437 (build-system r-build-system)
13440 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
13441 (synopsis "Access the Bioconductor project package repository")
13443 "This package provides a convenient tool to install and update
13444 Bioconductor packages.")
13445 (license license:artistic2.0)))
13447 (define-public r-rgl
13450 (version "0.109.2")
13454 (uri (cran-uri "rgl" version))
13457 "15rckpi2vzjc45glqk1mibxw1vja9y08hj9id2qd1si2bb708x8i"))))
13458 (build-system r-build-system)
13462 r-rmarkdown)) ;for vignettes
13479 (home-page "https://r-forge.r-project.org/projects/rgl/")
13480 (synopsis "3D visualization using OpenGL")
13482 "This package provides medium to high level functions for 3D interactive graphics,
13483 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
13484 as functions for constructing representations of geometric
13485 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
13486 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
13487 image formats, including PNG, Postscript, SVG, PGF.")
13488 ;; Any version of the GPL.
13489 (license (list license:gpl2+ license:gpl3+))))
13491 (define-public r-multicool
13493 (name "r-multicool")
13498 (uri (cran-uri "multicool" version))
13501 "0djacq0irfqz4nlnx238kja73yvr1n5qybbfyl6bw1n6qgcjhza8"))))
13502 (build-system r-build-system)
13503 (propagated-inputs (list r-rcpp))
13504 (home-page "https://cran.r-project.org/web/packages/multicool/")
13505 (synopsis "Permutations of multisets in cool-lex order")
13507 "This package provides a set of tools to permute multisets without loops
13508 or hash tables and to generate integer partitions. Cool-lex order is similar
13509 to colexicographical order.")
13510 (license license:gpl2)))
13512 (define-public r-misc3d
13519 (uri (cran-uri "misc3d" version))
13522 "0r9x57s63kx9f6dgam2nhbziq8nrs9wd8pk7g76hds2kw46vnyx0"))))
13523 (build-system r-build-system)
13524 (home-page "https://cran.r-project.org/web/packages/misc3d/")
13525 (synopsis "Miscellaneous 3D Plots")
13527 "This package provides a collection of miscellaneous 3d plots, including
13529 ;; Any version of the GPL.
13530 (license (list license:gpl2+ license:gpl3+))))
13532 (define-public r-ks
13539 (uri (cran-uri "ks" version))
13541 (base32 "05bqrjkbx2kn5aax0hy3xd6pf7nxka9bm1sp8ll1cc2gf1nx1i6i"))))
13542 (build-system r-build-system)
13554 (home-page "https://www.mvstat.net/tduong/")
13555 (synopsis "Kernel smoothing")
13557 "This package provides kernel smoothers for univariate and multivariate
13558 data, including density functions, density derivatives, cumulative
13559 distributions, modal clustering, discriminant analysis, and two-sample
13560 hypothesis testing.")
13561 ;; Either version of the GPL.
13562 (license (list license:gpl2 license:gpl3))))
13564 (define-public r-feature
13571 (uri (cran-uri "feature" version))
13574 "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y"))))
13575 (build-system r-build-system)
13577 (list r-ks r-plot3d))
13580 (home-page "https://www.mvstat.net/tduong/")
13581 (synopsis "Inferential feature significance for kernel density estimation")
13583 "The feature package contains functions to display and compute kernel
13584 density estimates, significant gradient and significant curvature regions.
13585 Significant gradient and/or curvature regions often correspond to significant
13586 features (e.g. local modes).")
13587 ;; Either version of the GPL.
13588 (license (list license:gpl2 license:gpl3))))
13590 (define-public r-arm
13597 (uri (cran-uri "arm" version))
13600 "0pagrc1vkaz460d0lvrgb4xj6gcd920f4mrc8zpzw07c3v1s2sw1"))))
13601 (build-system r-build-system)
13609 (home-page "https://cran.r-project.org/web/packages/arm/")
13610 (synopsis "Data analysis using regression and multilevel/hierarchical models")
13612 "This package provides functions to accompany A. Gelman and J. Hill,
13613 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
13614 University Press, 2007.")
13615 (license license:gpl3+)))
13617 (define-public r-circular
13619 (name "r-circular")
13624 (uri (cran-uri "circular" version))
13627 "1qmwj1pf37lc2s5r83y7nqckscznqhbsv66bdfgfbby7x4qkwga8"))))
13628 (build-system r-build-system)
13630 (list r-boot r-mvtnorm))
13633 (home-page "https://cran.r-project.org/web/packages/circular/")
13634 (synopsis "Circular statistics")
13636 "This package provides tools for circular statistics, from \"Topics in
13637 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
13639 (license license:gpl2+)))
13641 (define-public r-activity
13643 (name "r-activity")
13648 (uri (cran-uri "activity" version))
13651 "11n6wmqz7p3428rr615f92m61a5gb908xpn4l8q484h61bwg38c3"))))
13652 (build-system r-build-system)
13654 (list r-insol r-pbapply))
13655 (home-page "https://cran.r-project.org/web/packages/activity/")
13656 (synopsis "Animal activity statistics")
13658 "This package provides functions to fit kernel density functions to
13659 animal activity time data; plot activity distributions; quantify overall
13660 levels of activity; statistically compare activity metrics through
13661 bootstrapping; and evaluate variation in linear variables with time (or other
13662 circular variables).")
13663 (license license:gpl3)))
13665 (define-public r-ouch
13672 (uri (cran-uri "ouch" version))
13675 "119s9llpjy0b4q830xig2xr66fq6izp6mr2k4k79ggmf3gxww8as"))))
13676 (build-system r-build-system)
13677 (propagated-inputs (list r-subplex))
13678 (home-page "https://kingaa.github.io/ouch/")
13679 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
13681 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
13682 for evolution along a phylogenetic tree.")
13683 (license license:gpl2+)))
13685 (define-public r-fmsb
13692 (uri (cran-uri "fmsb" version))
13695 "1gi94xr0b1yk9xzwfprfafxi25yic1lcivd66p73n6iqfzdaimbk"))))
13696 (build-system r-build-system)
13697 (home-page "http://minato.sip21c.org/msb/")
13698 (synopsis "Functions for medical statistics book with demographic data")
13700 "This package provides several utility functions for the book entitled
13701 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
13702 Japan, 2007) with Japanese demographic data and some demographic analysis
13703 related functions.")
13704 (license license:gpl2+)))
13706 (define-public r-stabledist
13708 (name "r-stabledist")
13713 (uri (cran-uri "stabledist" version))
13716 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
13717 (build-system r-build-system)
13718 (home-page "https://www.rmetrics.org")
13719 (synopsis "Stable distribution functions")
13721 "This package provides density, probability and quantile functions, and
13722 random number generation for (skew) stable distributions, using the
13723 parametrizations of Nolan.")
13724 (license license:gpl2+)))
13726 (define-public r-gsl
13729 (version "2.1-7.1")
13733 (uri (cran-uri "gsl" version))
13736 "118rj9kjx9rzlynvhrly19qz3yxg8jzws35971ssgzrp5lwd367f"))))
13737 (build-system r-build-system)
13740 (home-page "https://cran.r-project.org/web/packages/gsl")
13741 (synopsis "Wrapper for the GNU Scientific Library")
13743 "This package provides an R wrapper for the special functions and quasi
13744 random number generators of the GNU Scientific Library.")
13745 (license license:gpl2+)))
13747 (define-public r-adgoftest
13749 (name "r-adgoftest")
13754 (uri (cran-uri "ADGofTest" version))
13757 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
13758 (properties `((upstream-name . "ADGofTest")))
13759 (build-system r-build-system)
13760 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
13761 (synopsis "Anderson-Darling GoF test")
13763 "This package provides an implementation of the Anderson-Darling GoF test
13764 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
13765 Anderson-Darling Distribution\".")
13766 ;; Any version of the GPL.
13767 (license license:gpl3+)))
13769 (define-public r-admisc
13776 (uri (cran-uri "admisc" version))
13778 (base32 "0cfx4g64mybd69xm595zzv79j4fbzn7vihpvzcvicggs3immppha"))))
13779 (properties `((upstream-name . "admisc")))
13780 (build-system r-build-system)
13781 (home-page "https://github.com/dusadrian/admisc")
13782 (synopsis "Adrian Dusa's miscellaneous")
13784 "This package contains miscellaneous functions used to interpret and
13785 translate, factorize and negate Sum of Products expressions, for both binary
13786 and multi-value crisp sets, and to extract information (set names, set values)
13787 from those expressions. Other functions perform various other checks if
13788 possibly numeric (even if all numbers reside in a character vector) and coerce
13789 to numeric, or check if the numbers are whole. It also offers, among many
13790 others, a highly flexible recoding routine and a more flexible alternative to
13791 the base function @code{with()}.")
13792 (license license:gpl3+)))
13794 (define-public r-sodium
13801 (uri (cran-uri "sodium" version))
13804 "1a03z2asvmalnmsn89lapzp8a4fr0qvzdv3xgin8pbqhjyb9hvpp"))))
13805 (properties `((upstream-name . "sodium")))
13806 (build-system r-build-system)
13810 (list pkg-config r-knitr))
13811 (home-page "https://github.com/jeroen/sodium")
13812 (synopsis "R bindings to the libsodium crypto library")
13814 "This package provides bindings to libsodium: a library for encryption,
13815 decryption, signatures, password hashing and more. Sodium uses curve25519, a
13816 Diffie-Hellman function by Daniel Bernstein, which has become very popular
13817 after it was discovered that the NSA had backdoored Dual EC DRBG.")
13818 (license license:expat)))
13820 (define-public r-softimpute
13822 (name "r-softimpute")
13827 (uri (cran-uri "softImpute" version))
13830 "1v2a4d688ij5zcvkzpra9yx40xckdfnllnfnyq2450zf3n1kjk7a"))))
13831 (properties `((upstream-name . "softImpute")))
13832 (build-system r-build-system)
13836 (list gfortran r-knitr))
13837 (home-page "https://cran.r-project.org/web/packages/softImpute")
13838 (synopsis "Matrix completion via iterative soft-thresholded SVD")
13840 "This package provides iterative methods for matrix completion that use
13841 nuclear-norm regularization. The package includes procedures for centering
13842 and scaling rows, columns or both, and for computing low-rank @dfn{single
13843 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
13845 (license license:gpl2)))
13847 (define-public r-fftwtools
13849 (name "r-fftwtools")
13854 (uri (cran-uri "fftwtools" version))
13857 "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i"))))
13858 (build-system r-build-system)
13859 (inputs (list fftw))
13862 (home-page "https://github.com/krahim/fftwtools")
13863 (synopsis "Wrapper for FFTW3")
13865 "This package provides a wrapper for several FFTW functions. It provides
13866 access to the two-dimensional FFT, the multivariate FFT, and the
13867 one-dimensional real to complex FFT using the FFTW3 library. The package
13868 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
13869 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
13870 The FFT functions have a parameter that allows them to not return the
13871 redundant complex conjugate when the input is real data.")
13872 (license license:gpl2+)))
13874 (define-public r-tiff
13881 (uri (cran-uri "tiff" version))
13884 "0xgc7vyndxxahfhc2qqzmwi56bnfyl0pn72l820jz5sd24aymhxq"))))
13885 (build-system r-build-system)
13887 (list libtiff libjpeg-turbo zlib))
13890 (home-page "https://www.rforge.net/tiff/")
13891 (synopsis "Read and write TIFF images")
13893 "This package provides an easy and simple way to read, write and display
13894 bitmap images stored in the TIFF format. It can read and write both files and
13895 in-memory raw vectors.")
13896 ;; Either of these two license versions.
13897 (license (list license:gpl2 license:gpl3))))
13899 (define-public r-nlp
13906 (uri (cran-uri "NLP" version))
13909 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5"))))
13910 (properties `((upstream-name . "NLP")))
13911 (build-system r-build-system)
13912 (home-page "https://cran.r-project.org/web/packages/NLP/")
13913 (synopsis "Natural language processing infrastructure")
13915 "This package provides basic classes and methods for Natural Language
13917 (license license:gpl3)))
13919 (define-public r-tm
13926 (uri (cran-uri "tm" version))
13929 "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi"))))
13930 (properties `((upstream-name . "tm")))
13931 (build-system r-build-system)
13933 (list r-bh r-nlp r-rcpp r-slam r-xml2))
13934 (home-page "http://tm.r-forge.r-project.org/")
13935 (synopsis "Text mining package")
13937 "This package provides a framework for text mining applications within R.")
13938 (license license:gpl3)))
13940 (define-public r-waveslim
13942 (name "r-waveslim")
13947 (uri (cran-uri "waveslim" version))
13950 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
13951 (build-system r-build-system)
13954 (home-page "http://waveslim.blogspot.com")
13955 (synopsis "Basic wavelet routines for signal processing")
13957 "This package provides basic wavelet routines for time series (1D),
13958 image (2D) and array (3D) analysis. The code provided here is based on
13959 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
13960 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
13961 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
13962 pairs (Selesnick 2001, 2002).")
13963 (license license:bsd-3)))
13965 (define-public r-wordcloud
13967 (name "r-wordcloud")
13972 (uri (cran-uri "wordcloud" version))
13975 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
13976 (build-system r-build-system)
13978 (list r-rcolorbrewer r-rcpp
13979 ;; The "tm" package is only "suggested" according to CRAN, but the
13980 ;; wordcloud package cannot be loaded without it.
13982 (home-page "https://cran.r-project.org/web/packages/wordcloud")
13983 (synopsis "Word clouds")
13985 "This package provides functionality to create pretty word clouds,
13986 visualize differences and similarity between documents, and avoid
13987 over-plotting in scatter plots with text.")
13988 (license license:lgpl2.1)))
13990 (define-public r-colorramps
13992 (name "r-colorramps")
13997 (uri (cran-uri "colorRamps" version))
14000 "12jnkj50yh2hc5l7j56lrrrmn58akrj9dwj98vzf42iq4h42kwb1"))))
14001 (properties `((upstream-name . "colorRamps")))
14002 (build-system r-build-system)
14003 (home-page "https://cran.r-project.org/web/packages/colorRamps")
14004 (synopsis "Build color tables")
14005 (description "This package provides features to build gradient color
14007 ;; Any version of the GPL
14008 (license license:gpl3+)))
14010 (define-public r-tidytree
14012 (name "r-tidytree")
14017 (uri (cran-uri "tidytree" version))
14019 (base32 "1prfv2jy6z4zp4gyi9krzbysipsbnjrkxcccflm4nwsd9i7mshqj"))))
14020 (build-system r-build-system)
14034 (home-page "https://github.com/GuangchuangYu/tidytree")
14035 (synopsis "Tidy tool for phylogenetic tree data manipulation")
14037 "Phylogenetic trees generally contain multiple components including nodes,
14038 edges, branches and associated data. This package provides an approach to
14039 convert tree objects to tidy data frames. It also provides tidy interfaces to
14040 manipulate tree data.")
14041 (license license:artistic2.0)))
14043 (define-public r-rvcheck
14050 (uri (cran-uri "rvcheck" version))
14052 (base32 "09khjklvzbafd7r55496by01a9g3y291d87hpy43w44dmz9fzn9a"))))
14053 (build-system r-build-system)
14055 (list r-biocmanager r-yulab-utils))
14056 (home-page "https://cran.r-project.org/web/packages/rvcheck")
14057 (synopsis "R package version check")
14059 "This package provides tools to check the latest release version of R and
14060 R packages (on CRAN, Bioconductor or Github).")
14061 (license license:artistic2.0)))
14063 (define-public r-docopt
14070 (uri (cran-uri "docopt" version))
14073 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
14074 (build-system r-build-system)
14075 (home-page "https://github.com/docopt/docopt.R")
14076 (synopsis "Command-line interface specification language")
14078 "This package enables you to define a command-line interface by just
14079 giving it a description in the specific format.")
14080 (license license:expat)))
14082 (define-public r-sparsesvd
14084 (name "r-sparsesvd")
14089 (uri (cran-uri "sparsesvd" version))
14092 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
14093 (build-system r-build-system)
14094 (propagated-inputs (list r-matrix))
14095 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
14096 (synopsis "Sparse truncated singular value decomposition")
14098 "This package provides a Wrapper around the SVDLIBC library
14099 for (truncated) singular value decomposition of a sparse matrix. Currently,
14100 only sparse real matrices in Matrix package format are supported.")
14101 ;; SVDLIBC is released under BSD-2. The R interface is released under
14103 (license (list license:bsd-3 license:bsd-2))))
14105 (define-public r-speedglm
14107 (name "r-speedglm")
14112 (uri (cran-uri "speedglm" version))
14115 "1kj662nfkfhvx37jrbvxd4dyjclz5cm3xh50z7s5rbzapiyxn4hs"))))
14116 (build-system r-build-system)
14118 (list r-mass r-matrix))
14119 (home-page "https://cran.r-project.org/web/packages/speedglm")
14120 (synopsis "Fit linear and generalized linear models to large data sets")
14122 "This package provides tools for fitting linear models and generalized
14123 linear models to large data sets by updating algorithms.")
14124 ;; Any version of the GPL
14125 (license license:gpl2+)))
14127 (define-public r-densityclust
14129 (name "r-densityclust")
14134 (uri (cran-uri "densityClust" version))
14137 "05x2fi1zdnkrg2nimf8k904j3lpyw0f7nmk6ax5p7x7a98wb2iqs"))))
14138 (properties `((upstream-name . "densityClust")))
14139 (build-system r-build-system)
14148 (home-page "https://cran.r-project.org/web/packages/densityClust")
14149 (synopsis "Clustering by fast search and find of density peaks")
14151 "This package provides an improved implementation (based on k-nearest
14152 neighbors) of the density peak clustering algorithm, originally described by
14153 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
14154 large datasets (> 100,000 samples) very efficiently.")
14155 (license license:gpl2+)))
14157 (define-public r-combinat
14159 (name "r-combinat")
14164 (uri (cran-uri "combinat" version))
14167 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
14168 (build-system r-build-system)
14169 (home-page "https://cran.r-project.org/web/packages/combinat")
14170 (synopsis "Combinatorics utilities")
14171 (description "This package provides assorted routines for combinatorics.")
14172 (license license:gpl2)))
14174 (define-public r-qlcmatrix
14176 (name "r-qlcmatrix")
14181 (uri (cran-uri "qlcMatrix" version))
14184 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
14185 (properties `((upstream-name . "qlcMatrix")))
14186 (build-system r-build-system)
14188 (list r-docopt r-matrix r-slam r-sparsesvd))
14189 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
14190 (synopsis "Sparse matrix functions for quantitative language comparison")
14192 "This package provides an extension of the functionality of the Matrix
14193 package for using sparse matrices. Some of the functions are very general,
14194 while other are highly specific for the special data format used for
14195 @dfn{quantitative language comparison} (QLC).")
14196 (license license:gpl3)))
14198 (define-public r-ddrtree
14205 (uri (cran-uri "DDRTree" version))
14208 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
14209 (properties `((upstream-name . "DDRTree")))
14210 (build-system r-build-system)
14212 (list r-bh r-irlba r-rcpp r-rcppeigen))
14213 (home-page "https://cran.r-project.org/web/packages/DDRTree")
14214 (synopsis "Learning principal graphs with DDRTree")
14216 "This package provides an implementation of the framework of
14217 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
14218 dimensional space while constructs a principal tree which passes through the
14219 middle of the data simultaneously. DDRTree shows superiority to
14220 alternatives (Wishbone, DPT) for inferring the ordering as well as the
14221 intrinsic structure of single cell genomics data. In general, it could be
14222 used to reconstruct the temporal progression as well as the bifurcation
14223 structure of any data type.")
14224 (license license:asl2.0)))
14226 (define-public r-corpcor
14233 (uri (cran-uri "corpcor" version))
14236 "028fw61n61i79fhnaqx7gmdifdpbvp3yiaq9vvfrbv4k7i84r83i"))))
14237 (build-system r-build-system)
14238 (home-page "http://strimmerlab.org/software/corpcor/")
14239 (synopsis "Efficient estimation of covariance and (partial) correlation")
14241 "This package implements a James-Stein-type shrinkage estimator for the
14242 covariance matrix, with separate shrinkage for variances and correlations.
14243 Furthermore, functions are available for fast singular value decomposition,
14244 for computing the pseudoinverse, and for checking the rank and positive
14245 definiteness of a matrix.")
14246 (license license:gpl3+)))
14248 (define-public r-rspectra
14250 (name "r-rspectra")
14255 (uri (cran-uri "RSpectra" version))
14258 "16ij84wgpsmqmnxqiii8dgihy3bfxazry9znmckhwzba7m0d79fb"))))
14259 (properties `((upstream-name . "RSpectra")))
14260 (build-system r-build-system)
14262 (list r-matrix r-rcpp r-rcppeigen))
14265 (home-page "https://github.com/yixuan/RSpectra")
14266 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
14268 "This package provides an R interface to the Spectra library for
14269 large-scale eigenvalue and SVD problems. It is typically used to compute a
14270 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
14271 which is usually more efficient than @code{eigen()} if k << n.")
14273 (license license:mpl2.0)))
14275 (define-public r-vbsr
14282 (uri (cran-uri "vbsr" version))
14285 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
14286 (build-system r-build-system)
14287 (home-page "https://cran.r-project.org/web/packages/vbsr")
14288 (synopsis "Variational Bayes spike regression regularized linear models")
14290 "This package provides an efficient algorithm for solving ultra-sparse
14291 regularized regression models using a variational Bayes algorithm with a spike
14292 prior. The algorithm is solved on a path, with coordinate updates, and is
14293 capable of generating very sparse models. Very general model
14294 diagnostics for controlling type-1 errors are also provided.")
14295 (license license:gpl2)))
14297 (define-public r-flare
14300 (version "1.7.0.1")
14304 (uri (cran-uri "flare" version))
14307 "1xvrbvq2y7zfp98ijal3z8y1w2xbzfcdykzw4pqc3mnh0qrhq2d5"))))
14308 (build-system r-build-system)
14310 (list r-igraph r-lattice r-mass r-matrix))
14311 (home-page "https://cran.r-project.org/web/packages/flare")
14312 (synopsis "Family of Lasso regression implementations")
14314 "This package provides implementations of a family of Lasso variants
14315 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
14316 high dimensional sparse linear models.")
14317 (license license:gpl2)))
14319 (define-public r-lassopv
14326 (uri (cran-uri "lassopv" version))
14329 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
14330 (build-system r-build-system)
14331 (propagated-inputs (list r-lars))
14332 (home-page "https://github.com/lingfeiwang/lassopv")
14333 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
14335 "This package enables you to estimate the p-values for predictors x
14336 against target variable y in Lasso regression, using the regularization
14337 strength when each predictor enters the active set of regularization path for
14338 the first time as the statistic.")
14339 (license license:gpl3)))
14341 (define-public r-splitstackshape
14343 (name "r-splitstackshape")
14348 (uri (cran-uri "splitstackshape" version))
14351 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
14352 (build-system r-build-system)
14354 (list r-data-table))
14355 (home-page "https://github.com/mrdwab/splitstackshape")
14356 (synopsis "Stack and reshape datasets after splitting concatenated values")
14358 "Online data collection tools like Google Forms often export
14359 multiple-response questions with data concatenated in cells. The
14360 @code{concat.split} (cSplit) family of functions provided by this package
14361 splits such data into separate cells. This package also includes functions to
14362 stack groups of columns and to reshape wide data, even when the data are
14363 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
14364 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
14366 (license license:gpl3)))
14368 (define-public r-tfmpvalue
14370 (name "r-tfmpvalue")
14375 (uri (cran-uri "TFMPvalue" version))
14378 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
14379 (properties `((upstream-name . "TFMPvalue")))
14380 (build-system r-build-system)
14381 (propagated-inputs (list r-rcpp))
14382 (home-page "https://github.com/ge11232002/TFMPvalue")
14383 (synopsis "P-value computation for position weight matrices")
14385 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
14386 identification from sequence/alignments, we are interested in the significance
14387 of certain match scores. TFMPvalue provides the accurate calculation of a
14388 p-value with a score threshold for position weight matrices, or the score with
14389 a given p-value. It is an interface to code originally made available by
14390 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
14391 Touzet and Varre (2007).")
14392 (license license:gpl2)))
14394 (define-public r-rncl
14400 (uri (cran-uri "rncl" version))
14403 "1ywgwqn82z8h6zpcxxq4hgngdpfa6dj0lr7bfq4cwfml9z075jgw"))))
14404 (build-system r-build-system)
14406 (list r-progress r-rcpp))
14407 (home-page "https://github.com/fmichonneau/rncl")
14408 (synopsis "Interface to the Nexus class library")
14409 (description "This package provides an interface to the Nexus class
14410 library which allows parsing of NEXUS, Newick and other phylogenetic tree
14411 file formats. It provides elements of the file that can be used to build
14412 phylogenetic objects such as @code{ape}'s @code{phylo} or @code{phylobase}'s
14413 @code{phylo4(d)}. This functionality is demonstrated with
14414 @code{read_newick_phylo()} and @code{read_nexus_phylo()}.")
14415 (license license:bsd-2)))
14417 (define-public r-phylobase
14419 (name "r-phylobase")
14423 (uri (cran-uri "phylobase" version))
14426 "0jzr1gdvmi4l640hwwzh9bxqmpja69bn3ygnaqx37awvyh7khi2s"))))
14427 (build-system r-build-system)
14429 (list r-ade4 r-ape r-rcpp r-rncl r-rnexml))
14432 (home-page "https://github.com/fmichonneau/phylobase")
14433 (synopsis "Base package for phylogenetic structures and comparative data")
14434 (description "This package provides a base @code{S4} class for comparative
14435 methods, incorporating one or more trees and trait data.")
14436 (license license:gpl2+)))
14438 (define-public r-rnexml
14444 (uri (cran-uri "RNeXML" version))
14447 "1zp6pijsc73jx8cmxb1hng36nvaf5wnhldnzlqhmba9kv9niscfb"))))
14448 (build-system r-build-system)
14465 (home-page "https://docs.ropensci.org/RNeXML/")
14466 (synopsis "Semantically rich I/O for the NeXML Format")
14467 (description "This package provides access to phyloinformatic data in
14468 NeXML format. The package should add new functionality to R such as the
14469 possibility to manipulate NeXML objects in more various and refined way
14470 and compatibility with @code{ape} objects.")
14471 (license license:bsd-3)))
14473 (define-public r-rnifti
14480 (uri (cran-uri "RNifti" version))
14483 "0kkj9dby85iwnlqb7zwrh1xidlvqip7i1mbgckb5qg4b0a3zgibc"))))
14484 (properties `((upstream-name . "RNifti")))
14485 (build-system r-build-system)
14486 (inputs (list zlib))
14487 (propagated-inputs (list r-rcpp))
14488 (home-page "https://github.com/jonclayden/RNifti")
14489 (synopsis "Fast R and C++ access to NIfTI images")
14491 "This package provides very fast read and write access to images stored
14492 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
14493 compiled C and interpreted R code. It also provides a C/C++ API that can be
14494 used by other packages.")
14495 (license license:gpl2)))
14497 (define-public r-shades
14504 (uri (cran-uri "shades" version))
14507 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
14508 (build-system r-build-system)
14509 (home-page "https://github.com/jonclayden/shades")
14510 (synopsis "Simple color manipulation")
14512 "This package provides functions for easily manipulating colors,
14513 creating color scales and calculating color distances.")
14514 (license license:bsd-3)))
14516 (define-public r-ore
14519 (version "1.7.1.1")
14523 (uri (cran-uri "ore" version))
14525 (base32 "0rs5r5h11x4l4nsbl4xqzbl4ahajd5374fq05abcmfjnjr9j64w5"))))
14526 (build-system r-build-system)
14527 (home-page "https://github.com/jonclayden/ore")
14528 (synopsis "R interface to the Onigmo regular expression library")
14530 "This package provides an alternative to R's built-in functionality for
14531 handling regular expressions, based on the Onigmo library. It offers
14532 first-class compiled regex objects, partial matching and function-based
14533 substitutions, amongst other features.")
14534 (license license:bsd-3)))
14536 (define-public r-reportr
14543 (uri (cran-uri "reportr" version))
14546 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
14547 (build-system r-build-system)
14548 (propagated-inputs (list r-ore))
14549 (home-page "https://github.com/jonclayden/reportr")
14550 (synopsis "General message and error reporting system")
14552 "This package provides a system for reporting messages, which offers
14553 certain useful features over the standard R system, such as the incorporation
14554 of output consolidation, message filtering, assertions, expression
14555 substitution, automatic generation of stack traces for debugging, and
14556 conditional reporting based on the current \"output level\".")
14557 (license license:gpl2)))
14559 (define-public r-tractor-base
14561 (name "r-tractor-base")
14562 (version "3.3.3.1")
14566 (uri (cran-uri "tractor.base" version))
14569 "0w5jw7pf77npkgig7667yikpbwv4dfk1dcq63qm88l409ga2f95p"))))
14570 (properties `((upstream-name . "tractor.base")))
14571 (build-system r-build-system)
14573 (list r-ore r-reportr r-rnifti r-shades))
14574 (home-page "https://www.tractor-mri.org.uk")
14575 (synopsis "Read, manipulate and visualize magnetic resonance images")
14577 "This package provides functions for working with magnetic resonance
14578 images. It supports reading and writing of popular file formats (DICOM,
14579 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
14580 visualization; flexible image manipulation; metadata and sparse image
14582 (license license:gpl2)))
14584 (define-public r-grimport
14586 (name "r-grimport")
14591 (uri (cran-uri "grImport" version))
14594 "0pbzc45wgp0cpycnw0bzn65ckdszzay0zrp7c7ssxdkifp8bai3a"))))
14595 (properties `((upstream-name . "grImport")))
14596 (build-system r-build-system)
14598 (list ghostscript))
14601 (home-page "https://cran.r-project.org/web/packages/grImport")
14602 (synopsis "Convert, import, and draw PostScript pictures")
14604 "This package provides functions for converting, importing, and drawing
14605 PostScript pictures in R plots.")
14606 (license license:gpl2+)))
14608 (define-public r-grimport2
14610 (name "r-grimport2")
14615 (uri (cran-uri "grImport2" version))
14618 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
14619 (properties `((upstream-name . "grImport2")))
14620 (build-system r-build-system)
14622 (list r-base64enc r-jpeg r-png r-xml))
14623 (home-page "https://cran.r-project.org/web/packages/grImport2/")
14624 (synopsis "Import SVG graphics")
14626 "This package provides functions for importing external vector images and
14627 drawing them as part of R plots. This package is different from the
14628 @code{grImport} package because, where that package imports PostScript format
14629 images, this package imports SVG format images. Furthermore, this package
14630 imports a specific subset of SVG, so external images must be preprocessed
14631 using a package like @code{rsvg} to produce SVG that this package can import.
14632 SVG features that are not supported by R graphics, such as gradient fills, can
14633 be imported and then exported via the @code{gridSVG} package.")
14634 (license license:gpl2+)))
14636 (define-public r-kohonen
14643 (uri (cran-uri "kohonen" version))
14646 "1bk3j0n8w4fhffv89rgyn4n21c0wcx6lr8jv4wbagpxprl585381"))))
14647 (build-system r-build-system)
14650 (home-page "https://cran.r-project.org/web/packages/kohonen")
14651 (synopsis "Supervised and unsupervised self-organising maps")
14653 "This package provides functions to train @dfn{self-organising
14654 maps} (SOMs). Also interrogation of the maps and prediction using trained
14655 maps are supported. The name of the package refers to Teuvo Kohonen, the
14656 inventor of the SOM.")
14657 (license license:gpl2+)))
14659 (define-public r-nnls
14666 (uri (cran-uri "nnls" version))
14669 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
14670 (build-system r-build-system)
14671 (native-inputs (list gfortran))
14672 (home-page "https://cran.r-project.org/web/packages/nnls")
14673 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
14675 "This package provides an R interface to the Lawson-Hanson implementation
14676 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
14677 the combination of non-negative and non-positive constraints.")
14678 (license license:gpl2+)))
14680 (define-public r-iso
14683 (version "0.0-18.1")
14687 (uri (cran-uri "Iso" version))
14690 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
14691 (properties `((upstream-name . "Iso")))
14692 (build-system r-build-system)
14693 (native-inputs (list gfortran))
14694 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
14695 (synopsis "Functions to perform isotonic regression")
14697 "This package provides support for linear order and unimodal
14698 order (univariate) isotonic regression and bivariate isotonic regression with
14699 linear order on both variables.")
14700 (license license:gpl2+)))
14702 (define-public r-chemometricswithr
14704 (name "r-chemometricswithr")
14709 (uri (cran-uri "ChemometricsWithR" version))
14712 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
14714 `((upstream-name . "ChemometricsWithR")))
14715 (build-system r-build-system)
14717 (list r-devtools r-kohonen r-mass r-pls))
14718 (home-page "https://github.com/rwehrens/CWR")
14719 (synopsis "Chemometrics with R")
14721 "This package provides functions and scripts used in the book
14722 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
14723 Life Sciences\" by Ron Wehrens, Springer (2011).")
14724 (license license:gpl2+)))
14726 (define-public r-als
14733 (uri (cran-uri "ALS" version))
14736 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
14737 (properties `((upstream-name . "ALS")))
14738 (build-system r-build-system)
14740 (list r-iso r-nnls))
14741 (home-page "https://cran.r-project.org/web/packages/ALS")
14742 (synopsis "Multivariate curve resolution alternating least squares")
14744 "Alternating least squares is often used to resolve components
14745 contributing to data with a bilinear structure; the basic technique may be
14746 extended to alternating constrained least squares. This package provides an
14747 implementation of @dfn{multivariate curve resolution alternating least
14748 squares} (MCR-ALS).
14750 Commonly applied constraints include unimodality, non-negativity, and
14751 normalization of components. Several data matrices may be decomposed
14752 simultaneously by assuming that one of the two matrices in the bilinear
14753 decomposition is shared between datasets.")
14754 (license license:gpl2+)))
14756 (define-public r-strucchange
14758 (name "r-strucchange")
14763 (uri (cran-uri "strucchange" version))
14766 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
14767 (build-system r-build-system)
14769 (list r-sandwich r-zoo))
14770 (home-page "https://cran.r-project.org/web/packages/strucchange")
14771 (synopsis "Testing, monitoring, and dating structural changes")
14773 "This package provides tools for testing, monitoring and dating
14774 structural changes in (linear) regression models. It features tests/methods
14775 from the generalized fluctuation test framework as well as from the F
14776 test (Chow test) framework. This includes methods to fit, plot and test
14777 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
14778 statistics, respectively. It is possible to monitor incoming data online
14779 using fluctuation processes. Finally, the breakpoints in regression models
14780 with structural changes can be estimated together with confidence intervals.
14781 Emphasis is always given to methods for visualizing the data.")
14782 ;; Either of these two GPL versions
14783 (license (list license:gpl2 license:gpl3))))
14785 (define-public r-pixmap
14792 (uri (cran-uri "pixmap" version))
14795 "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9"))))
14796 (build-system r-build-system)
14797 (home-page "https://cran.r-project.org/web/packages/pixmap")
14798 (synopsis "Tools for bitmap images")
14800 "This package provides functions for importing, exporting, plotting and
14801 other manipulations of bitmapped images.")
14802 (license license:gpl2)))
14804 (define-public r-rapidjsonr
14806 (name "r-rapidjsonr")
14811 (uri (cran-uri "rapidjsonr" version))
14814 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
14815 (build-system r-build-system)
14816 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
14817 (synopsis "JSON parser")
14819 "This package provides JSON parsing capability through the Rapidjson
14821 (license license:expat)))
14823 (define-public r-ontologyindex
14825 (name "r-ontologyindex")
14830 (uri (cran-uri "ontologyIndex" version))
14833 "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k"))))
14834 (properties `((upstream-name . "ontologyIndex")))
14835 (build-system r-build-system)
14838 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
14839 (synopsis "Functions for processing ontologies in R")
14841 "This package provides functions for reading ontologies into R as lists
14842 and manipulating sets of ontological terms.")
14843 (license license:gpl2+)))
14845 (define-public r-gargle
14852 (uri (cran-uri "gargle" version))
14855 "0fypj70c1fjmvs57birik76wfx8a2fs4gzicbb52k57i6clwlijd"))))
14856 (build-system r-build-system)
14869 (home-page "https://gargle.r-lib.org")
14870 (synopsis "Utilities for working with Google APIs")
14872 "This package provides utilities for working with Google APIs. This
14873 includes functions and classes for handling common credential types and for
14874 preparing, executing, and processing HTTP requests.")
14875 (license license:expat)))
14877 (define-public r-bigrquery
14879 (name "r-bigrquery")
14884 (uri (cran-uri "bigrquery" version))
14887 "02msq61l7vamzpvbhvalh3qil1aa7pr68pwpsivbb6pvz6p4zyns"))))
14888 (build-system r-build-system)
14905 (home-page "https://github.com/rstats-db/bigrquery")
14906 (synopsis "R interface to Google's BigQuery API")
14908 "This package provides an R interface to Google's BigQuery database.")
14909 (license license:gpl3)))
14911 (define-public r-gmp
14918 (uri (cran-uri "gmp" version))
14921 "0llyd1wx606vpgvv7d61m0fv2a5yxsmisd38fhzanbjl2wynzrwa"))))
14922 (build-system r-build-system)
14925 (modify-phases %standard-phases
14926 (add-after 'unpack 'set-CC
14927 (lambda _ (setenv "CC" "gcc") #t)))))
14928 (inputs (list gmp))
14929 (home-page "https://cran.r-project.org/web/packages/gmp")
14930 (synopsis "Multiple precision arithmetic")
14932 "This package supports multiple precision arithmetic (big integers and
14933 rationals, prime number tests, matrix computation), \"arithmetic without
14934 limitations\" using the GNU Multiple Precision library.")
14935 ;; Any version of the GPL.
14936 (license license:gpl3+)))
14938 (define-public r-rmpfr
14945 (uri (cran-uri "Rmpfr" version))
14948 "12mwvgyalzh4zf5d002fm1hpr3wwhiypy9ia6wy47ij9gns5mvng"))))
14949 (properties `((upstream-name . "Rmpfr")))
14950 (build-system r-build-system)
14957 (home-page "http://rmpfr.r-forge.r-project.org/")
14958 (synopsis "R bindings to the MPFR library")
14960 "This package supports arithmetic (via S4 classes and methods) for
14961 arbitrary precision floating point numbers, including transcendental
14962 functions. To this end, the package interfaces with the @dfn{Multiple
14963 Precision Floating-Point Reliable} (MPFR) library.")
14964 (license license:gpl2+)))
14966 (define-public r-assertive-base
14968 (name "r-assertive-base")
14973 (uri (cran-uri "assertive.base" version))
14976 "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b"))))
14978 `((upstream-name . "assertive.base")))
14979 (build-system r-build-system)
14980 (home-page "https://bitbucket.org/richierocks/assertive.base")
14981 (synopsis "Core of the assertive package")
14983 "This package provides a minimal set of predicates and assertions used by
14984 the assertive package. This is mainly for use by other package developers who
14985 want to include run-time testing features in their own packages.")
14986 (license license:gpl3+)))
14988 (define-public r-assertive-properties
14990 (name "r-assertive-properties")
14995 (uri (cran-uri "assertive.properties" version))
14998 "1pgljbwwbvbl4kc5c8mcv0qbzq3k6fzi29k88811yml263sm92dn"))))
15000 `((upstream-name . "assertive.properties")))
15001 (build-system r-build-system)
15003 (list r-assertive-base))
15004 (home-page "https://bitbucket.org/richierocks/assertive.properties")
15005 (synopsis "Assertions to check properties of variables")
15007 "This package provides a set of predicates and assertions for checking
15008 the properties of variables, such as length, names and attributes. This is
15009 mainly for use by other package developers who want to include run-time
15010 testing features in their own packages.")
15011 (license license:gpl3+)))
15013 (define-public r-assertive-numbers
15015 (name "r-assertive-numbers")
15020 (uri (cran-uri "assertive.numbers" version))
15023 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
15025 `((upstream-name . "assertive.numbers")))
15026 (build-system r-build-system)
15028 (list r-assertive-base))
15029 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
15030 (synopsis "Assertions to check properties of numbers")
15032 "This package provides a set of predicates and assertions for checking
15033 the properties of numbers. This is mainly for use by other package developers
15034 who want to include run-time testing features in their own packages.")
15035 (license license:gpl3+)))
15037 (define-public r-assertive-sets
15039 (name "r-assertive-sets")
15044 (uri (cran-uri "assertive.sets" version))
15047 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
15049 `((upstream-name . "assertive.sets")))
15050 (build-system r-build-system)
15052 (list r-assertive-base))
15053 (home-page "https://bitbucket.org/richierocks/assertive.sets")
15054 (synopsis "Assertions to check properties of sets")
15056 "This package provides a set of predicates and assertions for checking
15057 the properties of sets. This is mainly for use by other package developers
15058 who want to include run-time testing features in their own packages.")
15059 (license license:gpl3+)))
15061 (define-public r-assertive-matrices
15063 (name "r-assertive-matrices")
15068 (uri (cran-uri "assertive.matrices" version))
15071 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
15073 `((upstream-name . "assertive.matrices")))
15074 (build-system r-build-system)
15076 (list r-assertive-base))
15077 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
15078 (synopsis "Assertions to check properties of matrices")
15080 "This package provides a set of predicates and assertions for checking
15081 the properties of matrices. This is mainly for use by other package
15082 developers who want to include run-time testing features in their own
15084 (license license:gpl3+)))
15086 (define-public r-assertive-models
15088 (name "r-assertive-models")
15093 (uri (cran-uri "assertive.models" version))
15096 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
15098 `((upstream-name . "assertive.models")))
15099 (build-system r-build-system)
15101 (list r-assertive-base))
15102 (home-page "https://bitbucket.org/richierocks/assertive.models")
15103 (synopsis "Assertions to check properties of models")
15105 "This package provides a set of predicates and assertions for checking
15106 the properties of models. This is mainly for use by other package developers
15107 who want to include run-time testing features in their own packages.")
15108 (license license:gpl3+)))
15110 (define-public r-assertive-reflection
15112 (name "r-assertive-reflection")
15117 (uri (cran-uri "assertive.reflection" version))
15120 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
15122 `((upstream-name . "assertive.reflection")))
15123 (build-system r-build-system)
15125 (list r-assertive-base))
15126 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
15127 (synopsis "Assertions for checking the state of R")
15129 "This package provides a set of predicates and assertions for checking
15130 the state and capabilities of R, the operating system it is running on, and
15131 the IDE being used. This is mainly for use by other package developers who
15132 want to include run-time testing features in their own packages.")
15133 (license license:gpl3+)))
15135 (define-public r-assertive-types
15137 (name "r-assertive-types")
15142 (uri (cran-uri "assertive.types" version))
15145 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
15147 `((upstream-name . "assertive.types")))
15148 (build-system r-build-system)
15150 (list r-assertive-base r-assertive-properties r-codetools))
15151 (home-page "https://bitbucket.org/richierocks/assertive.types")
15152 (synopsis "Assertions to check types of variables")
15154 "This package provides a set of predicates and assertions for checking
15155 the types of variables. This is mainly for use by other package developers
15156 who want to include run-time testing features in their own packages.")
15157 (license license:gpl3+)))
15159 (define-public r-assertive-files
15161 (name "r-assertive-files")
15166 (uri (cran-uri "assertive.files" version))
15169 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
15171 `((upstream-name . "assertive.files")))
15172 (build-system r-build-system)
15174 (list r-assertive-base r-assertive-numbers))
15175 (home-page "https://bitbucket.org/richierocks/assertive.files")
15176 (synopsis "Assertions to check properties of files")
15178 "This package provides a set of predicates and assertions for checking
15179 the properties of files and connections. This is mainly for use by other
15180 package developers who want to include run-time testing features in their own
15182 (license license:gpl3+)))
15184 (define-public r-assertive-code
15186 (name "r-assertive-code")
15191 (uri (cran-uri "assertive.code" version))
15194 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
15196 `((upstream-name . "assertive.code")))
15197 (build-system r-build-system)
15199 (list r-assertive-base r-assertive-properties r-assertive-types))
15200 (home-page "https://bitbucket.org/richierocks/assertive.code")
15201 (synopsis "Assertions to check properties of code")
15203 "This package provides a set of predicates and assertions for checking
15204 the properties of code. This is mainly for use by other package developers
15205 who want to include run-time testing features in their own packages.")
15206 (license license:gpl3+)))
15208 (define-public r-assertive-datetimes
15210 (name "r-assertive-datetimes")
15215 (uri (cran-uri "assertive.datetimes" version))
15218 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
15220 `((upstream-name . "assertive.datetimes")))
15221 (build-system r-build-system)
15223 (list r-assertive-base r-assertive-types))
15224 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
15225 (synopsis "Assertions to check properties of dates and times")
15227 "This package provides a set of predicates and assertions for checking
15228 the properties of dates and times. This is mainly for use by other package
15229 developers who want to include run-time testing features in their own
15231 (license license:gpl3+)))
15233 (define-public r-assertive-strings
15235 (name "r-assertive-strings")
15240 (uri (cran-uri "assertive.strings" version))
15243 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
15245 `((upstream-name . "assertive.strings")))
15246 (build-system r-build-system)
15248 (list r-assertive-base r-assertive-types r-stringi))
15249 (home-page "https://bitbucket.org/richierocks/assertive.strings")
15250 (synopsis "Assertions to check properties of strings")
15252 "This package provides a set of predicates and assertions for checking
15253 the properties of strings. This is mainly for use by other package developers
15254 who want to include run-time testing features in their own packages.")
15255 (license license:gpl3+)))
15257 (define-public r-assertive-data-us
15259 (name "r-assertive-data-us")
15264 (uri (cran-uri "assertive.data.us" version))
15267 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
15269 `((upstream-name . "assertive.data.us")))
15270 (build-system r-build-system)
15272 (list r-assertive-base r-assertive-strings))
15273 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
15274 (synopsis "Assertions to check properties of strings")
15276 "This package provides a set of predicates and assertions for checking
15277 the properties of US-specific complex data types. This is mainly for use by
15278 other package developers who want to include run-time testing features in
15279 their own packages.")
15280 (license license:gpl3+)))
15282 (define-public r-assertive-data-uk
15284 (name "r-assertive-data-uk")
15289 (uri (cran-uri "assertive.data.uk" version))
15292 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
15294 `((upstream-name . "assertive.data.uk")))
15295 (build-system r-build-system)
15297 (list r-assertive-base r-assertive-strings))
15298 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
15299 (synopsis "Assertions to check properties of strings")
15301 "This package provides a set of predicates and assertions for checking
15302 the properties of UK-specific complex data types. This is mainly for use by
15303 other package developers who want to include run-time testing features in
15304 their own packages.")
15305 (license license:gpl3+)))
15307 (define-public r-assertive-data
15309 (name "r-assertive-data")
15314 (uri (cran-uri "assertive.data" version))
15317 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
15319 `((upstream-name . "assertive.data")))
15320 (build-system r-build-system)
15322 (list r-assertive-base r-assertive-strings))
15323 (home-page "https://bitbucket.org/richierocks/assertive.data")
15324 (synopsis "Assertions to check properties of data")
15326 "This package provides a set of predicates and assertions for checking
15327 the properties of (country independent) complex data types. This is mainly
15328 for use by other package developers who want to include run-time testing
15329 features in their own packages.")
15330 (license license:gpl3+)))
15332 (define-public r-assertive
15334 (name "r-assertive")
15339 (uri (cran-uri "assertive" version))
15342 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
15343 (build-system r-build-system)
15345 (list r-assertive-base
15348 r-assertive-data-uk
15349 r-assertive-data-us
15350 r-assertive-datetimes
15352 r-assertive-matrices
15354 r-assertive-numbers
15355 r-assertive-properties
15356 r-assertive-reflection
15358 r-assertive-strings
15363 (home-page "https://bitbucket.org/richierocks/assertive")
15364 (synopsis "Readable check functions to ensure code integrity")
15366 "This package provides lots of predicates (@code{is_*} functions) to
15367 check the state of your variables, and assertions (@code{assert_*} functions)
15368 to throw errors if they aren't in the right form.")
15369 (license license:gpl3+)))
15371 (define-public r-dotcall64
15373 (name "r-dotcall64")
15378 (uri (cran-uri "dotCall64" version))
15381 "1im5k8jbviwj2i42mq1kmjskh80isa7jr9w8i0fknidrzzy2h2zi"))))
15382 (properties `((upstream-name . "dotCall64")))
15383 (build-system r-build-system)
15384 (native-inputs (list gfortran))
15385 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
15386 (synopsis "Enhanced foreign function interface supporting long vectors")
15388 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
15389 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
15390 supports long vectors, arguments of type 64-bit integer, and provides a
15391 mechanism to avoid unnecessary copies of read-only and write-only arguments.
15392 This makes it a convenient and fast interface to C/C++ and Fortran code.")
15393 (license license:gpl2+)))
15395 (define-public r-spam
15402 (uri (cran-uri "spam" version))
15404 (base32 "1ann2a2ifr3z983fcg1c0pkgmbxz6a0ym5q1dmq1r382bd1pg0fr"))))
15405 (build-system r-build-system)
15407 (list r-dotcall64))
15409 (list gfortran r-knitr))
15410 (home-page "https://www.math.uzh.ch/pages/spam/")
15411 (synopsis "Sparse matrix algebra")
15413 "This package provides a set of functions for sparse matrix algebra.
15414 Differences with other sparse matrix packages are:
15417 @item it only supports (essentially) one sparse matrix format;
15418 @item it is based on transparent and simple structure(s);
15419 @item it is tailored for MCMC calculations within G(M)RF;
15420 @item and it is fast and scalable (with the extension package @code{spam64}).
15422 ;; Either of these licenses
15423 (license (list license:bsd-3 license:lgpl2.0))))
15425 (define-public r-fields
15432 (uri (cran-uri "fields" version))
15434 (base32 "1hs4k5a9hh0r5fsrnpnvs6wvf78xpjzj8a2j6643dsz73a5q6ln6"))))
15435 (build-system r-build-system)
15437 (list r-maps r-spam r-viridis))
15440 (home-page "https://www.image.ucar.edu/fields")
15441 (synopsis "Tools for spatial data")
15443 "This is a package for curve, surface and function fitting with an
15444 emphasis on splines, spatial data and spatial statistics. The major methods
15445 include cubic, and thin plate splines, Kriging, and compactly supported
15446 covariance functions for large data sets.")
15447 (license license:gpl2+)))
15449 (define-public r-spatialextremes
15451 (name "r-spatialextremes")
15456 (uri (cran-uri "SpatialExtremes" version))
15459 "0z1swxp1syz8hdskarjxx4sdd7wx835kcnb783bwqm235yh991j3"))))
15461 `((upstream-name . "SpatialExtremes")))
15462 (build-system r-build-system)
15464 (list r-fields r-maps))
15465 (home-page "http://spatialextremes.r-forge.r-project.org/")
15466 (synopsis "Modelling spatial extremes")
15468 "This package provides tools for the statistical modelling of spatial
15469 extremes using max-stable processes, copula or Bayesian hierarchical models.
15470 More precisely, this package allows (conditional) simulations from various
15471 parametric max-stable models, analysis of the extremal spatial dependence, the
15472 fitting of such processes using composite likelihoods or least square (simple
15473 max-stable processes only), model checking and selection and prediction.")
15474 (license license:gpl2+)))
15476 (define-public r-drc
15483 (uri (cran-uri "drc" version))
15486 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
15487 (build-system r-build-system)
15495 (home-page "https://cran.r-project.org/web/packages/drc")
15496 (synopsis "Analysis of dose-response curves")
15498 "This package provides a suite of flexible and versatile model fitting
15499 and after-fitting functions for the analysis of dose-response data.")
15500 (license license:gpl2+)))
15502 (define-public r-rmeta
15509 (uri (cran-uri "rmeta" version))
15512 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
15513 (build-system r-build-system)
15514 (home-page "https://cran.r-project.org/web/packages/rmeta")
15515 (synopsis "Tools for meta-analysis")
15517 "This package provides functions for simple fixed and random effects
15518 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
15519 draws standard summary plots, funnel plots, and computes summaries and tests
15520 for association and heterogeneity.")
15521 (license license:gpl2)))
15523 (define-public r-bootstrap
15525 (name "r-bootstrap")
15530 (uri (cran-uri "bootstrap" version))
15533 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
15534 (build-system r-build-system)
15535 (native-inputs (list gfortran))
15536 (home-page "https://cran.r-project.org/web/packages/bootstrap")
15537 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
15539 "This package provides software and data for the book \"An Introduction
15540 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
15541 This package is primarily provided for projects already based on it, and for
15542 support of the book. New projects should preferentially use the recommended
15543 package \"boot\".")
15544 (license license:bsd-3)))
15546 (define-public r-survivalroc
15548 (name "r-survivalroc")
15553 (uri (cran-uri "survivalROC" version))
15556 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
15557 (properties `((upstream-name . "survivalROC")))
15558 (build-system r-build-system)
15559 (home-page "https://cran.r-project.org/web/packages/survivalROC")
15560 (synopsis "Time-dependent ROC curve estimation from censored survival data")
15562 "Compute time-dependent ROC curve from censored survival data using
15563 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
15564 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
15565 (license license:gpl2+)))
15567 (define-public r-locfdr
15573 (uri (cran-uri "locfdr" version))
15576 "1falkbp2xz07am8jlhwlvyqvxnli4nwl188kd0g58vdfjcjy3mj2"))))
15577 (build-system r-build-system)
15578 (home-page "https://cran.r-project.org/web/packages/locfdr/")
15579 (synopsis "Computes local false discovery rates")
15580 (description "This package can be used to compute local false
15582 (license license:gpl2)))
15584 (define-public r-longitudinal
15586 (name "r-longitudinal")
15591 (uri (cran-uri "longitudinal" version))
15594 "046w3xbr535c5jyd68adv42a7limxp1mv57b5w6w673w707lmw2p"))))
15595 (build-system r-build-system)
15596 (propagated-inputs (list r-corpcor))
15597 (home-page "http://strimmerlab.org/software/longitudinal/")
15598 (synopsis "Analysis of multiple time course data")
15600 "This package contains general data structures and functions for
15601 longitudinal data with multiple variables, repeated measurements, and
15602 irregularly spaced time points. It also implements a shrinkage estimator of
15603 dynamical correlation and dynamical covariance.")
15604 (license license:gpl3+)))
15606 (define-public r-genenet
15613 (uri (cran-uri "GeneNet" version))
15616 "1r1khga3nxxjghs4vnbymzp0cwb1q17zw2v3a94qz8fsrirq1sf1"))))
15617 (properties `((upstream-name . "GeneNet")))
15618 (build-system r-build-system)
15620 (list r-corpcor r-fdrtool r-longitudinal))
15621 (home-page "http://strimmerlab.org/software/genenet/")
15622 (synopsis "Modeling and inferring gene networks")
15624 "This package analyzes gene expression (time series) data with focus on
15625 the inference of gene networks. In particular, GeneNet implements the methods
15626 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
15627 for learning large-scale gene association networks (including assignment of
15628 putative directions).")
15629 (license license:gpl3+)))
15631 (define-public r-rbamtools
15633 (name "r-rbamtools")
15634 (version "2.16.17")
15638 (uri (cran-uri "rbamtools" version))
15641 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
15642 (build-system r-build-system)
15643 (inputs (list zlib))
15645 (list r-refgenome))
15646 (home-page "https://cran.r-project.org/web/packages/rbamtools")
15647 (synopsis "Read and write BAM (binary alignment) files")
15649 "This package provides an R interface to functions of the SAMtools
15651 (license license:artistic2.0)))
15653 (define-public r-protviz
15660 (uri (cran-uri "protViz" version))
15663 "0f6jwzcqi0w37hvg3i5dlk0c3anpkqh54ibf94vaf17r8sykr4nw"))))
15664 (properties `((upstream-name . "protViz")))
15665 (build-system r-build-system)
15666 (propagated-inputs (list r-rcpp))
15667 (home-page "https://github.com/protViz/protViz/")
15668 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
15670 "This package helps with quality checks, visualizations and analysis of
15671 mass spectrometry data, coming from proteomics experiments. The package is
15672 developed, tested and used at the Functional Genomics Center Zurich, where it
15673 is used mainly for prototyping, teaching, and having fun with proteomics data.
15674 But it can also be used to do data analysis for small scale data sets.")
15675 (license license:gpl3)))
15677 (define-public r-cmprsk
15684 (uri (cran-uri "cmprsk" version))
15686 (base32 "050f24l5ab1ds9824c7yjahimf6pg8ih2k83jzpzfb0n5k5jfh44"))))
15687 (build-system r-build-system)
15692 (home-page "https://cran.r-project.org/web/packages/cmprsk")
15693 (synopsis "Subdistribution analysis of competing risks")
15695 "This package provides tool for estimation, testing and regression
15696 modeling of subdistribution functions in competing risks, as described in
15697 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
15698 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
15699 A proportional hazards model for the subdistribution of a competing risk,
15700 JASA, 94:496-509.")
15701 (license license:gpl2+)))
15703 (define-public r-etm
15710 (uri (cran-uri "etm" version))
15713 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
15714 (build-system r-build-system)
15716 (list r-data-table r-lattice r-rcpp r-rcpparmadillo r-survival))
15717 (home-page "https://cran.r-project.org/web/packages/etm")
15718 (synopsis "Empirical transition matrix")
15720 "The @dfn{empirical transition matrix} (etm) package estimates
15721 the matrix of transition probabilities for any time-inhomogeneous multistate
15722 model with finite state space using the Aalen-Johansen estimator.")
15723 (license license:expat)))
15725 (define-public r-epi
15732 (uri (cran-uri "Epi" version))
15735 "0s3ij0rya4wd7k97kc4s3pwj1d1ypaxl1s7zqr6sa07hp4a8fzz0"))))
15736 (properties `((upstream-name . "Epi")))
15737 (build-system r-build-system)
15751 (home-page "https://BendixCarstensen.com/Epi/")
15752 (synopsis "Statistical analysis in epidemiology")
15754 "This package provides functions for demographic and epidemiological
15755 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
15756 particular representation, manipulation and simulation of multistate data -
15757 the Lexis suite of functions, which includes interfaces to the @code{mstate},
15758 @code{etm} and @code{cmprsk} packages. It also contains functions for
15759 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
15760 data and some useful functions for tabulation and plotting, as well as a
15761 number of epidemiological data sets.")
15762 (license license:gpl2)))
15764 (define-public r-ppls
15767 (version "1.6-1.1")
15771 (uri (cran-uri "ppls" version))
15774 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
15775 (build-system r-build-system)
15776 (propagated-inputs (list r-mass))
15777 (home-page "https://cran.r-project.org/web/packages/ppls")
15778 (synopsis "Penalized partial least squares")
15780 "This package contains linear and nonlinear regression methods based on
15781 partial least squares and penalization techniques. Model parameters are
15782 selected via cross-validation, and confidence intervals ans tests for the
15783 regression coefficients can be conducted via jackknifing.")
15784 (license license:gpl2+)))
15786 (define-public r-huge
15793 (uri (cran-uri "huge" version))
15795 (base32 "1sl457a1lndrx98y2j9a2smanawx2iqlhl82iand0g3p5xp8ch4j"))))
15796 (build-system r-build-system)
15798 (list r-igraph r-mass r-matrix r-rcpp r-rcppeigen))
15799 (home-page "https://cran.r-project.org/web/packages/huge")
15800 (synopsis "High-dimensional undirected graph estimation")
15802 "This package provides a general framework for high-dimensional
15803 undirected graph estimation. It integrates data preprocessing, neighborhood
15804 screening, graph estimation, and model selection techniques into a pipeline.")
15805 (license license:gpl2)))
15807 (define-public r-parcor
15814 (uri (cran-uri "parcor" version))
15817 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
15818 (build-system r-build-system)
15820 (list r-epi r-genenet r-glmnet r-mass r-ppls))
15821 (home-page "https://cran.r-project.org/web/packages/parcor")
15822 (synopsis "Regularized estimation of partial correlation matrices")
15824 "This package estimates the matrix of partial correlations based on
15825 different regularized regression methods: lasso, adaptive lasso, PLS, and
15826 Ridge Regression. In addition, the package provides model selection for
15827 lasso, adaptive lasso and Ridge regression based on cross-validation.")
15828 (license license:gpl2+)))
15830 (define-public r-mcmc
15837 (uri (cran-uri "mcmc" version))
15840 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
15841 (build-system r-build-system)
15842 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
15843 (synopsis "Markov chain Monte Carlo")
15845 "This package simulates continuous distributions of random vectors using
15846 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
15847 function that evaluates the log unnormalized density. Algorithms are random
15848 walk Metropolis algorithm (function @code{metrop}), simulated
15849 tempering (function @code{temper}), and morphometric random walk
15850 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
15851 by change of variable.")
15852 (license license:expat)))
15854 (define-public r-listenv
15861 (uri (cran-uri "listenv" version))
15864 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
15865 (build-system r-build-system)
15868 (modify-phases %standard-phases
15869 (add-after 'unpack 'set-HOME
15870 (lambda _ (setenv "HOME" "/tmp"))))))
15872 (list r-r-rsp)) ; vignette builder
15873 (home-page "https://github.com/HenrikBengtsson/listenv")
15874 (synopsis "Environments behaving (almost) as lists")
15876 "This package implements list environments. List environments are
15877 environments that have list-like properties. For instance, the elements of a
15878 list environment are ordered and can be accessed and iterated over using index
15880 (license license:lgpl2.1+)))
15882 (define-public r-globals
15889 (uri (cran-uri "globals" version))
15892 "15llx4233ihj4w815k7inc17530w9ja0mi29n1i0s2sr42j8jdpq"))))
15893 (build-system r-build-system)
15895 (list r-codetools))
15896 (home-page "https://github.com/HenrikBengtsson/globals")
15897 (synopsis "Identify global objects in R expressions")
15899 "This package provides tools to identify global (\"unknown\" or \"free\")
15900 objects in R expressions by code inspection using various strategies, e.g.
15901 conservative or liberal. The objective of this package is to make it as
15902 simple as possible to identify global objects for the purpose of exporting
15903 them in distributed compute environments.")
15904 (license license:lgpl2.1+)))
15906 (define-public r-parallelly
15908 (name "r-parallelly")
15913 (uri (cran-uri "parallelly" version))
15916 "0yg1hmgkp81ihgwqaynqh0jgki2mkdy78j4fgjmqvc1ig5ga774h"))))
15917 (properties `((upstream-name . "parallelly")))
15918 (build-system r-build-system)
15919 (home-page "https://github.com/HenrikBengtsson/parallelly")
15920 (synopsis "Enhancements of the parallel package")
15922 "This package provides utility functions that enhance the @code{parallel}
15923 package and support the built-in parallel backends of the @code{future}
15924 package. For example, @code{availableCores} gives the number of CPU cores
15925 available to your R process as given by R options and environment variables,
15926 including those set by job schedulers on high-performance compute clusters.
15927 If none is set, it will fall back to @code{parallel::detectCores}. Another
15928 example is @code{makeClusterPSOCK}, which is backward compatible with
15929 @code{parallel::makePSOCKcluster} while doing a better job in setting up
15930 remote cluster workers without the need for configuring the firewall to do
15931 port-forwarding to your local computer.")
15932 (license license:lgpl2.1+)))
15934 (define-public r-future
15941 (uri (cran-uri "future" version))
15944 "1mchjdvvwgs8v0iv8z5m6gav3xzvnq11h8qrc7lfnrb2x3d0np53"))))
15945 (build-system r-build-system)
15948 (modify-phases %standard-phases
15949 (add-after 'unpack 'set-HOME
15950 (lambda _ (setenv "HOME" "/tmp"))))))
15952 (list r-digest r-globals r-listenv r-parallelly))
15954 (list r-r-rsp)) ; vignette builder
15955 (home-page "https://github.com/HenrikBengtsson/future")
15956 (synopsis "Unified parallel and distributed processing in R")
15958 "The purpose of this package is to provide a lightweight and unified
15959 Future API for sequential and parallel processing of R expression via futures.
15960 This package implements sequential, multicore, multisession, and cluster
15961 futures. With these, R expressions can be evaluated on the local machine, in
15962 parallel a set of local machines, or distributed on a mix of local and remote
15963 machines. Extensions to this package implement additional backends for
15964 processing futures via compute cluster schedulers etc. Because of its unified
15965 API, there is no need to modify any code in order to switch from sequential on
15966 the local machine to, say, distributed processing on a remote compute cluster.")
15967 (license license:lgpl2.1+)))
15969 (define-public r-future-apply
15971 (name "r-future-apply")
15976 (uri (cran-uri "future.apply" version))
15979 "1xb7qj8izjwmy4aa92p5f4cdbhgp220hrly3b5879f9hrv2w2rk1"))))
15980 (properties `((upstream-name . "future.apply")))
15981 (build-system r-build-system)
15984 (modify-phases %standard-phases
15985 (add-after 'unpack 'set-HOME
15986 (lambda _ (setenv "HOME" "/tmp"))))))
15988 (list r-future r-globals))
15990 (list r-r-rsp)) ; vignette builder
15991 (home-page "https://github.com/HenrikBengtsson/future.apply")
15992 (synopsis "Apply function to elements in parallel using futures")
15994 "This package provides implementations of @code{apply()},
15995 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
15996 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
15997 can be resolved using any future-supported backend, e.g. parallel on the local
15998 machine or distributed on a compute cluster.")
15999 (license license:gpl2+)))
16001 (define-public r-rsvd
16008 (uri (cran-uri "rsvd" version))
16011 "07p2hjmpcwcsang8z9sjkpy94rydcin7m3hyvcgzgm5cd6w8c1p4"))))
16012 (build-system r-build-system)
16015 (home-page "https://github.com/erichson/rSVD")
16016 (synopsis "Randomized singular value decomposition")
16018 "Low-rank matrix decompositions are fundamental tools and widely used for
16019 data analysis, dimension reduction, and data compression. Classically, highly
16020 accurate deterministic matrix algorithms are used for this task. However, the
16021 emergence of large-scale data has severely challenged our computational
16022 ability to analyze big data. The concept of randomness has been demonstrated
16023 as an effective strategy to quickly produce approximate answers to familiar
16024 problems such as the @dfn{singular value decomposition} (SVD). This package
16025 provides several randomized matrix algorithms such as the randomized singular
16026 value decomposition (@code{rsvd}), randomized principal component
16027 analysis (@code{rpca}), randomized robust principal component
16028 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
16029 and the randomized CUR decomposition (@code{rcur}). In addition several plot
16030 functions are provided.")
16031 (license license:gpl3+)))
16033 (define-public r-sloop
16040 (uri (cran-uri "sloop" version))
16043 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
16044 (build-system r-build-system)
16046 (list r-codetools r-crayon r-purrr r-rlang r-tibble))
16047 (home-page "https://github.com/r-lib/sloop")
16048 (synopsis "Helpers for object-oriented programming in R")
16050 "This package provides a collection of helper functions designed to
16051 help you to better understand object oriented programming in R, particularly
16053 (license license:gpl3)))
16055 (define-public r-capushe
16062 (uri (cran-uri "capushe" version))
16065 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
16066 (build-system r-build-system)
16067 (propagated-inputs (list r-mass))
16068 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
16069 (synopsis "Calibrating penalties using slope heuristics")
16071 "This package provides tools for the calibration of penalized criteria
16072 for model selection. The calibration methods available are based on the slope
16074 (license license:gpl2+)))
16076 (define-public r-dorng
16083 (uri (cran-uri "doRNG" version))
16086 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
16087 (properties `((upstream-name . "doRNG")))
16088 (build-system r-build-system)
16090 (list r-foreach r-iterators r-rngtools))
16091 (home-page "https://renozao.github.io/doRNG/")
16092 (synopsis "Generic reproducible parallel backend for foreach loops")
16094 "This package provides functions to perform reproducible parallel
16095 @code{foreach} loops, using independent random streams as generated by
16096 L'Ecuyer's combined multiple-recursive generator. It enables to easily
16097 convert standard @code{%dopar%} loops into fully reproducible loops,
16098 independently of the number of workers, the task scheduling strategy, or the
16099 chosen parallel environment and associated foreach backend.")
16100 (license license:gpl2+)))
16102 (define-public r-blockmodeling
16104 (name "r-blockmodeling")
16109 (uri (cran-uri "blockmodeling" version))
16112 "1vc8gy4slsywcwxq532373i0dq73fhs5cac9mr6zz2pjaaxjghhq"))))
16113 (build-system r-build-system)
16116 (native-inputs (list gfortran))
16117 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
16118 (synopsis "Generalized and classical blockmodeling of valued networks")
16120 "This package is primarily meant as an implementation of generalized
16121 blockmodeling for valued networks. In addition, measures of similarity or
16122 dissimilarity based on structural equivalence and regular equivalence (REGE
16123 algorithms) can be computed and partitioned matrices can be plotted.")
16124 (license license:gpl2+)))
16126 (define-public r-upsetr
16133 (uri (cran-uri "UpSetR" version))
16136 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
16137 (properties `((upstream-name . "UpSetR")))
16138 (build-system r-build-system)
16140 (list r-ggplot2 r-gridextra r-plyr r-scales))
16141 (home-page "https://github.com/hms-dbmi/UpSetR")
16142 (synopsis "Visualize intersecting sets")
16144 "This package provides a more scalable alternative to Venn and Euler
16145 diagrams for visualizing intersecting sets. Create visualizations of
16146 intersecting sets using a novel matrix design, along with visualizations of
16147 several common set, element and attribute related tasks.")
16148 (license license:expat)))
16150 ;; This package includes a JavaScript file, which is not minified. When
16151 ;; upgrading please check that there are no new minified JavaScript files.
16152 (define-public r-shinybs
16159 (uri (cran-uri "shinyBS" version))
16162 "0h51685a9qll4agayldjyryi60ih969219ibg071slv0613p5v8a"))))
16163 (properties `((upstream-name . "shinyBS")))
16164 (build-system r-build-system)
16165 ;; The tests spawn Shiny browser apps. They cannot be run
16166 ;; non-interactively.
16167 (arguments '(#:tests? #f))
16169 (list r-htmltools r-shiny))
16170 (home-page "https://ebailey78.github.io/shinyBS/")
16171 (synopsis "Twitter Bootstrap components for Shiny")
16173 "This package adds additional Twitter Bootstrap components to Shiny.")
16174 (license license:gpl3)))
16176 (define-public r-shinyjqui
16178 (name "r-shinyjqui")
16183 (uri (cran-uri "shinyjqui" version))
16186 "135gwz7syyb6pbn0lkvmq0v1c6r1zivavnqhi1rnzbbzlysi27v1"))
16188 '(for-each delete-file
16189 (list "inst/www/shinyjqui.min.js"
16190 "inst/www/jquery.ui.touch-punch.min.js")))))
16191 (properties `((upstream-name . "shinyjqui")))
16192 (build-system r-build-system)
16195 (modify-phases %standard-phases
16196 (add-after 'unpack 'process-javascript
16197 (lambda* (#:key inputs #:allow-other-keys)
16198 (with-directory-excursion "inst/www"
16200 `((,(string-append (assoc-ref inputs "js-jquery.ui.touch-punch")
16201 "/jquery.ui.touch-punch.js")
16202 . "jquery.ui.touch-punch.min.js")
16204 . "shinyjqui.min.js"))))
16205 (for-each (lambda (source target)
16206 (format #true "Processing ~a --> ~a~%"
16208 (invoke "esbuild" source "--minify"
16209 (string-append "--outfile=" target)))
16211 (map cdr mapping)))))))))
16213 (list r-htmltools r-htmlwidgets r-jsonlite r-rlang r-shiny))
16215 `(("r-knitr" ,r-knitr)
16216 ("esbuild" ,esbuild)
16217 ("js-jquery.ui.touch-punch"
16220 (uri (git-reference
16221 (url "https://github.com/furf/jquery-ui-touch-punch")
16222 (commit "8f7559b6e65cdc3ee3648d5fe76d38c653f87ff5")))
16225 "1lzywp2q9hwx6d5fqjla95vp7ra2lahr5dam7lsqjmch9d98r48q"))))))
16226 (home-page "https://github.com/yang-tang/shinyjqui")
16227 (synopsis "jQuery UI interactions and effects for Shiny")
16229 "This is an extension to Shiny that brings interactions and animation
16230 effects from the jQuery UI library.")
16231 (license license:expat)))
16233 (define-public r-shinymanager
16235 (name "r-shinymanager")
16236 (version "1.0.400")
16240 (uri (cran-uri "shinymanager" version))
16242 (base32 "1np2yp5pn8g9i4jhysfgprmdn13cpw4vaaagrd72rnk2r4hpmyx4"))))
16243 (properties `((upstream-name . "shinymanager")))
16244 (build-system r-build-system)
16246 (list r-billboarder
16256 (native-inputs (list r-knitr))
16257 (home-page "https://github.com/datastorm-open/shinymanager")
16258 (synopsis "Authentication management for Shiny applications")
16260 "This package provides simple and secure authentification mechanism for
16261 single Shiny applications. Credentials are stored in an encrypted SQLite
16263 (license license:gpl3)))
16265 (define-public r-outliers
16267 (name "r-outliers")
16272 (uri (cran-uri "outliers" version))
16275 "1yrmwvjjb0a6sbx940k9svf23cykcxz8rrwcgyic7lpgzbrdfcfc"))))
16276 (build-system r-build-system)
16277 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
16278 (synopsis "Tests for outliers")
16280 "This package provides a collection of some tests commonly used for
16281 identifying outliers.")
16282 (license license:gpl2+)))
16284 (define-public r-bayesm
16291 (uri (cran-uri "bayesm" version))
16293 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
16294 (build-system r-build-system)
16296 (list r-rcpp r-rcpparmadillo))
16297 (home-page "http://www.perossi.org/home/bsm-1")
16298 (synopsis "Bayesian inference for marketing/micro-econometrics")
16300 "This package covers many important models used in marketing and
16301 micro-econometrics applications, including Bayes Regression (univariate or
16302 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
16303 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
16304 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
16305 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
16306 Estimation with normal base, Hierarchical Linear Models with normal prior and
16307 covariates, Hierarchical Linear Models with a mixture of normals prior and
16308 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
16309 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
16310 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
16311 analysis of choice-based conjoint data, Bayesian treatment of linear
16312 instrumental variables models, Analysis of Multivariate Ordinal survey data
16313 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
16314 Coefficient Logit Models.")
16315 (license license:gpl2+)))
16317 (define-public r-tensora
16324 (uri (cran-uri "tensorA" version))
16327 "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf"))))
16328 (properties `((upstream-name . "tensorA")))
16329 (build-system r-build-system)
16330 (home-page "http://www.stat.boogaart.de/tensorA")
16331 (synopsis "Advanced tensor arithmetic with named indices")
16333 "This package provides convenience functions for advanced linear algebra
16334 with tensors and computation with datasets of tensors on a higher level
16335 abstraction. It includes Einstein and Riemann summing conventions, dragging,
16336 co- and contravariate indices, and parallel computations on sequences of
16338 (license license:gpl2+)))
16340 (define-public r-rarpack
16347 (uri (cran-uri "rARPACK" version))
16350 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
16351 (properties `((upstream-name . "rARPACK")))
16352 (build-system r-build-system)
16353 (propagated-inputs (list r-rspectra))
16354 (home-page "https://github.com/yixuan/rARPACK")
16355 (synopsis "Solvers for large scale eigenvalue and SVD problems")
16357 "This package was previously an R wrapper of the ARPACK library, and now
16358 a shell of the R package RSpectra, an R interface to the Spectra library for
16359 solving large scale eigenvalue/vector problems. The current version of
16360 rARPACK simply imports and exports the functions provided by RSpectra. New
16361 users of rARPACK are advised to switch to the RSpectra package.")
16362 (license license:bsd-3)))
16364 (define-public r-compositions
16366 (name "r-compositions")
16371 (uri (cran-uri "compositions" version))
16374 "1bqg0qqzsf92q0jb7hdjycr54bwv8rk7ajhvxgch5yslyqxpm73v"))))
16375 (build-system r-build-system)
16377 (list r-bayesm r-mass r-robustbase r-tensora))
16380 (home-page "http://www.stat.boogaart.de/compositions")
16381 (synopsis "Compositional data analysis")
16383 "This package provides functions for the consistent analysis of
16384 compositional data (e.g. portions of substances) and positive
16385 numbers (e.g. concentrations).")
16386 (license license:gpl2+)))
16388 (define-public r-cobs
16395 (uri (cran-uri "cobs" version))
16398 "04f6a6gp11p93j2k35mbrfqgjx5qsgi3dj1085a5v5s0z6l7vbkz"))))
16399 (build-system r-build-system)
16401 (list r-quantreg r-sparsem))
16402 (home-page "https://cran.r-project.org/web/packages/cobs")
16403 (synopsis "Constrained B-Splines (sparse matrix based)")
16405 "This package provides qualitatively constrained (regression) smoothing
16406 splines via linear programming and sparse matrices.")
16407 (license license:gpl2+)))
16409 (define-public r-drimpute
16411 (name "r-drimpute")
16416 (uri (cran-uri "DrImpute" version))
16419 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
16420 (properties `((upstream-name . "DrImpute")))
16421 (build-system r-build-system)
16423 (list r-rcpp r-rcpparmadillo))
16424 (home-page "https://github.com/ikwak2/DrImpute")
16425 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
16427 "This is an R package for imputing dropout events. Many statistical
16428 methods in cell type identification, visualization and lineage reconstruction
16429 do not account for dropout events. DrImpute can improve the performance of
16430 such software by imputing dropout events.")
16431 (license license:gpl3)))
16433 (define-public r-gamlss-dist
16435 (name "r-gamlss-dist")
16440 (uri (cran-uri "gamlss.dist" version))
16442 (base32 "1gqjr419v8z2ygh0h1xz7bipnsbp820njzwq7z3r9f41rn1ym47c"))))
16443 (properties `((upstream-name . "gamlss.dist")))
16444 (build-system r-build-system)
16445 (propagated-inputs (list r-mass))
16446 (home-page "http://www.gamlss.org/")
16447 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
16449 "This package provides a set of distributions which can be used for
16450 modelling the response variables in Generalized Additive Models for Location
16451 Scale and Shape. The distributions can be continuous, discrete or mixed
16452 distributions. Extra distributions can be created, by transforming, any
16453 continuous distribution defined on the real line, to a distribution defined on
16454 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
16455 transformation, respectively.")
16456 ;; Either version of the GPL.
16457 (license (list license:gpl2 license:gpl3))))
16459 ;; This package includes JavaScript files, which are not minified. When
16460 ;; upgrading please check that there are no new minified JavaScript files.
16461 (define-public r-shinyjs
16468 (uri (cran-uri "shinyjs" version))
16471 "1id9gsrkr28xl80a8794in17rxmmz06zqvd5hlns7mqz3fzhrhky"))))
16472 (build-system r-build-system)
16474 (list r-digest r-jsonlite r-shiny))
16477 (home-page "https://deanattali.com/shinyjs")
16478 (synopsis "Improve the user experience of your Shiny apps")
16480 "Perform common useful JavaScript operations in Shiny apps that will
16481 greatly improve your apps without having to know any JavaScript. Examples
16482 include: hiding an element, disabling an input, resetting an input back to its
16483 original value, delaying code execution by a few seconds, and many more useful
16484 functions for both the end user and the developer. Shinyjs can also be used
16485 to easily call your own custom JavaScript functions from R.")
16486 (license license:agpl3+)))
16488 ;; This package includes minified JavaScript files. When upgrading please
16489 ;; check that there are no new minified JavaScript files.
16490 (define-public r-colourpicker
16492 (name "r-colourpicker")
16497 (uri (cran-uri "colourpicker" version))
16500 "1q1wi3g403fbzp4ys3gsjbwdc86x770cx323qgi47ca8n219kl50"))))
16501 (build-system r-build-system)
16504 (modify-phases %standard-phases
16505 (add-after 'unpack 'process-javascript
16506 (lambda* (#:key inputs #:allow-other-keys)
16507 (with-directory-excursion "inst"
16509 `((,(assoc-ref inputs "js-salvattore")
16510 . "examples/colourInput/www/salvattore.min.js")
16511 (,(assoc-ref inputs "js-jquery")
16512 . "htmlwidgets/lib/jquery/jquery.min.js")
16513 ("www/shared/colourpicker/js/colourpicker.js"
16514 . "www/shared/colourpicker/js/colourpicker.min.js"))))
16515 (for-each (lambda (source target)
16516 (format #true "Processing ~a --> ~a~%"
16518 (delete-file target)
16519 (invoke "esbuild" source "--minify"
16520 (string-append "--outfile=" target)))
16522 (map cdr mapping)))))))))
16532 `(("esbuild" ,esbuild)
16536 (uri "https://code.jquery.com/jquery-1.11.3.js")
16539 "1v956yf5spw0156rni5z77hzqwmby7ajwdcd6mkhb6zvl36awr90"))))
16543 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
16546 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
16547 (home-page "https://github.com/daattali/colourpicker")
16548 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
16550 "This package provides a color picker that can be used as an input in
16551 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
16552 custom color palettes, and many more options. A plot color helper tool is
16553 available as an RStudio Addin, which helps you pick colors to use in your
16554 plots. A more generic color picker RStudio Addin is also provided to let you
16555 select colors to use in your R code.")
16556 (license license:expat)))
16558 (define-public r-ggextra
16565 (uri (cran-uri "ggExtra" version))
16568 "1rd3qv6ah3zphr1jicjhgxms73vi496mjnxnsrcgl7z8nyxmas6w"))))
16569 (properties `((upstream-name . "ggExtra")))
16570 (build-system r-build-system)
16572 (list r-colourpicker
16582 (home-page "https://github.com/daattali/ggExtra")
16583 (synopsis "Marginal histograms for ggplot2 and other enhancements")
16585 "This package is a collection of functions and layers to enhance ggplot2.
16586 The flagship function is @code{ggMarginal()}, which can be used to add
16587 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
16588 (license license:expat)))
16590 (define-public r-minpack-lm
16592 (name "r-minpack-lm")
16597 (uri (cran-uri "minpack.lm" version))
16600 "11yz6hk2r33571d16kq01cb1x6sgdzi6jmksqlrm8mr84l95c2f7"))))
16601 (properties `((upstream-name . "minpack.lm")))
16602 (build-system r-build-system)
16603 (native-inputs (list gfortran))
16604 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
16605 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
16607 "The @code{nls.lm} function provides an R interface to @code{lmder} and
16608 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
16609 problems by a modification of the Levenberg-Marquardt algorithm, with support
16610 for lower and upper parameter bounds. The implementation can be used via
16611 @code{nls}-like calls using the @code{nlsLM} function.")
16612 (license license:gpl3)))
16614 (define-public r-moments
16621 (uri (cran-uri "moments" version))
16624 "0r6qf3i1rzh2822bx1p0h8mh91gsbgg6asl2rzh2l4ys094bilif"))))
16625 (build-system r-build-system)
16626 (home-page "https://cran.r-project.org/web/packages/moments")
16627 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
16629 "This package provides functions to calculate: moments, Pearson's
16630 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
16631 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
16632 (license license:gpl2+)))
16634 (define-public r-msir
16641 (uri (cran-uri "msir" version))
16644 "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84"))))
16645 (build-system r-build-system)
16650 (home-page "https://cran.r-project.org/web/packages/msir")
16651 (synopsis "Model-based sliced inverse regression")
16653 "This is an R package for dimension reduction based on finite Gaussian
16654 mixture modeling of inverse regression.")
16655 (license license:gpl2+)))
16657 (define-public r-pbivnorm
16659 (name "r-pbivnorm")
16664 (uri (cran-uri "pbivnorm" version))
16667 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
16668 (build-system r-build-system)
16669 (native-inputs (list gfortran))
16670 (home-page "https://github.com/brentonk/pbivnorm")
16671 (synopsis "Vectorized bivariate normal CDF")
16673 "This package provides a vectorized R function for calculating
16674 probabilities from a standard bivariate normal CDF.")
16675 (license license:gpl2+)))
16677 (define-public r-lavaan
16684 (uri (cran-uri "lavaan" version))
16687 "026k32paf51lpy6zxm9m81zg9szx14j37dxdip6nba334jw97h9c"))))
16688 (build-system r-build-system)
16690 (list r-mass r-mnormt r-numderiv r-pbivnorm))
16691 (home-page "https://lavaan.ugent.be")
16692 (synopsis "Latent variable analysis")
16694 "This package provides tools to fit a variety of latent variable models,
16695 including confirmatory factor analysis, structural equation modeling and
16696 latent growth curve models.")
16697 (license license:gpl2+)))
16699 (define-public r-nonnest2
16701 (name "r-nonnest2")
16706 (uri (cran-uri "nonnest2" version))
16709 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
16710 (build-system r-build-system)
16712 (list r-compquadform r-lavaan r-mvtnorm r-sandwich))
16715 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
16716 (synopsis "Tests of non-nested models")
16718 "This package allows for testing of non-nested models. It includes tests
16719 of model distinguishability and of model fit that can be applied to both
16720 nested and non-nested models. The package also includes functionality to
16721 obtain confidence intervals associated with AIC and BIC.")
16722 ;; Either version of the GPL.
16723 (license (list license:gpl2 license:gpl3))))
16725 (define-public r-penalized
16727 (name "r-penalized")
16732 (uri (cran-uri "penalized" version))
16735 "08badmgygppbqzay20qijyww028yw6s8dyd8ijcp8g4r9rn8xqyq"))))
16736 (build-system r-build-system)
16738 (list r-rcpp r-rcpparmadillo r-survival))
16739 (home-page "https://cran.r-project.org/web/packages/penalized/")
16740 (synopsis "Penalized estimation in GLMs and in the Cox model")
16742 "This package provides tools for fitting possibly high dimensional
16743 penalized regression models. The penalty structure can be any combination of
16744 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
16745 constraint on the regression coefficients. The supported regression models
16746 are linear, logistic and Poisson regression and the Cox Proportional Hazards
16747 model. Cross-validation routines allow optimization of the tuning
16749 (license license:gpl2+)))
16751 (define-public r-zim
16758 (uri (cran-uri "ZIM" version))
16761 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
16762 (properties `((upstream-name . "ZIM")))
16763 (build-system r-build-system)
16764 (propagated-inputs (list r-mass))
16765 (home-page "https://github.com/biostatstudio/ZIM")
16766 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
16768 "Analyze count time series with excess zeros. Two types of statistical
16769 models are supported: Markov regression and state-space models. They are also
16770 known as observation-driven and parameter-driven models respectively in the
16771 time series literature. The functions used for Markov regression or
16772 observation-driven models can also be used to fit ordinary regression models
16773 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
16774 negative binomial (ZINB) assumption. The package also contains miscellaneous
16775 functions to compute density, distribution, quantile, and generate random
16776 numbers from ZIP and ZINB distributions.")
16777 (license license:gpl3)))
16779 (define-public r-nor1mix
16786 (uri (cran-uri "nor1mix" version))
16789 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
16790 (build-system r-build-system)
16791 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
16792 (synopsis "Normal (1-d) mixture models")
16794 "This package provides S3 classes and methods for one-dimensional normal
16795 mixture models, for, e.g., density estimation or clustering algorithms
16796 research and teaching; it provides the widely used Marron-Wand densities. It
16797 also provides tools for efficient random number generation and graphics.")
16798 (license license:gpl2+)))
16800 (define-public r-beanplot
16802 (name "r-beanplot")
16807 (uri (cran-uri "beanplot" version))
16810 "1b8mvlcsv5l9g08ag92hndsvk8jmgxvznhzgazc8y4296kp8l5a9"))))
16811 (build-system r-build-system)
16812 (home-page "https://cran.r-project.org/web/packages/beanplot/")
16813 (synopsis "Visualization via beanplots")
16815 "This package provides beanplots, an alternative to
16816 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
16818 (license license:gpl2)))
16820 (define-public r-pbdzmq
16827 (uri (cran-uri "pbdZMQ" version))
16830 "020qy6fq8w8wq0j3bii14ahrlg8wzl0lrnndfr6scmrg9ghjnbfz"))))
16831 (properties `((upstream-name . "pbdZMQ")))
16832 (build-system r-build-system)
16834 (list zeromq zlib))
16837 (home-page "https://pbdr.org/")
16838 (synopsis "R interface to ZeroMQ")
16840 "ZeroMQ is a well-known library for high-performance asynchronous
16841 messaging in scalable, distributed applications. This package provides high
16842 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
16843 interactive client/server programming frameworks. A few wrapper functions
16844 compatible with @code{rzmq} are also provided.")
16845 (license license:gpl3)))
16847 (define-public r-repr
16854 (uri (cran-uri "repr" version))
16857 "0h3h14ybamcbwmm31ib66fx13v75vkzn4bn2v26n2h097sl9qybg"))))
16858 (build-system r-build-system)
16860 (list r-base64enc r-htmltools r-jsonlite r-pillar))
16861 (home-page "https://cran.r-project.org/web/packages/repr/")
16862 (synopsis "Serializable representations")
16864 "This package provides string and binary representations of objects for
16865 several formats and MIME types.")
16866 (license license:gpl3)))
16868 (define-public r-irdisplay
16870 (name "r-irdisplay")
16875 (uri (cran-uri "IRdisplay" version))
16878 "0awdiv4rr93y8jb1d64sm1iy37ywyniqm7w98yv6qm0zz47h7sw3"))))
16879 (properties `((upstream-name . "IRdisplay")))
16880 (build-system r-build-system)
16883 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
16884 (synopsis "Jupyter display machinery")
16886 "This package provides an interface to the rich display capabilities of
16887 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
16888 running IRkernel session.")
16889 (license license:expat)))
16891 (define-public r-irkernel
16893 (name "r-irkernel")
16898 (uri (cran-uri "IRkernel" version))
16901 "00qrmsywpzw2hfp88020zjaijma7q4hqm9h2cz53rywdjzywnzss"))))
16902 (properties `((upstream-name . "IRkernel")))
16903 (build-system r-build-system)
16906 (modify-phases %standard-phases
16907 (add-after 'install 'install-kernelspec
16908 (lambda* (#:key outputs #:allow-other-keys)
16909 (let ((out (assoc-ref outputs "out")))
16910 (setenv "HOME" "/tmp")
16911 (invoke "jupyter" "kernelspec" "install"
16914 (string-append out "/site-library/IRkernel/kernelspec"))
16915 ;; Record the absolute file name of the 'R' executable in
16917 (substitute* (string-append out "/share/jupyter"
16918 "/kernels/ir/kernel.json")
16920 (string-append "[\"" (which "R") "\",")))
16930 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
16935 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
16936 (synopsis "Native R kernel for Jupyter")
16938 "The R kernel for the Jupyter environment executes R code which the
16939 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
16941 (license license:expat)))
16943 (define-public r-gmodels
16946 (version "2.18.1.1")
16950 (uri (cran-uri "gmodels" version))
16953 "158y7yh4maawn9vki8cq4sil48xib2bbpl6qgj5gvlkw3c14hzfs"))))
16954 (build-system r-build-system)
16956 (list r-gdata r-mass))
16957 (home-page "https://cran.r-project.org/web/packages/gmodels/")
16958 (synopsis "Various R programming tools for model fitting")
16960 "This package provides various R programming tools for model fitting.")
16961 (license license:gpl2)))
16963 (define-public r-apcluster
16965 (name "r-apcluster")
16970 (uri (cran-uri "apcluster" version))
16973 "1820j1xjlbmw6j2fwwv2g806dqpk5qrbbaqsrbrn6igql8pzf552"))))
16974 (build-system r-build-system)
16976 (list r-matrix r-rcpp))
16977 (native-inputs (list r-knitr))
16978 (home-page "https://cran.r-project.org/web/packages/apcluster/")
16979 (synopsis "Affinity propagation clustering")
16981 "This package implements affinity propagation clustering introduced by
16982 Frey and Dueck (2007). The package further provides leveraged affinity
16983 propagation and an algorithm for exemplar-based agglomerative clustering that
16984 can also be used to join clusters obtained from affinity propagation. Various
16985 plotting functions are available for analyzing clustering results.")
16986 (license license:gpl2+)))
16988 (define-public r-rematch2
16990 (name "r-rematch2")
16995 (uri (cran-uri "rematch2" version))
16998 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
16999 (build-system r-build-system)
17002 (home-page "https://github.com/r-lib/rematch2")
17003 (synopsis "Tidy output from regular expression matching")
17005 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
17006 return the match results in tidy data frames.")
17007 (license license:expat)))
17009 (define-public r-picante
17016 (uri (cran-uri "picante" version))
17019 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
17020 (build-system r-build-system)
17022 (list r-ape r-nlme r-vegan))
17023 (home-page "https://cran.r-project.org/web/packages/picante/")
17024 (synopsis "Integrating phylogenies and ecology")
17026 "This package provides functions for phylocom integration, community
17027 analyses, null-models, traits and evolution. It implements numerous
17028 ecophylogenetic approaches including measures of community phylogenetic and
17029 trait diversity, phylogenetic signal, estimation of trait values for
17030 unobserved taxa, null models for community and phylogeny randomizations, and
17031 utility functions for data input/output and phylogeny plotting. A full
17032 description of package functionality and methods are provided by Kembel et
17034 (license license:gpl2)))
17036 (define-public r-reinforcelearn
17038 (name "r-reinforcelearn")
17043 (uri (cran-uri "reinforcelearn" version))
17046 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
17047 (build-system r-build-system)
17049 (list r-checkmate r-nnet r-purrr r-r6))
17050 (home-page "https://markusdumke.github.io/reinforcelearn")
17051 (synopsis "Reinforcement learning")
17053 "This package implements reinforcement learning environments and
17054 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
17055 can be used with function approximation, eligibility traces (Singh & Sutton,
17056 1996) and experience replay (Mnih et al., 2013).")
17057 (license license:expat)))
17059 (define-public r-lemon
17066 (uri (cran-uri "lemon" version))
17069 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
17070 (build-system r-build-system)
17082 (home-page "https://github.com/stefanedwards/lemon")
17083 (synopsis "Freshen up your ggplot2 plots")
17085 "This package provides functions for working with legends and axis lines
17086 of ggplot2, facets that repeat axis lines on all panels, and some knitr
17088 (license license:gpl3)))
17090 (define-public r-wgaim
17097 (uri (cran-uri "wgaim" version))
17099 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
17100 (build-system r-build-system)
17102 (list r-ggplot2 r-qtl))
17103 (home-page "https://cran.r-project.org/web/packages/wgaim")
17104 (synopsis "Whole genome average interval mapping for QTL detection")
17106 "This package integrates sophisticated mixed modelling methods with a
17107 whole genome approach to detecting significant QTL in linkage maps.")
17108 (license license:gpl2+)))
17110 (define-public r-bedr
17117 (uri (cran-uri "bedr" version))
17120 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
17121 (build-system r-build-system)
17130 htslib)) ; for tabix
17132 (list r-knitr)) ; for vignettes
17133 (home-page "https://cran.r-project.org/web/packages/bedr")
17134 (synopsis "Genomic region processing")
17136 "This package is for genomic regions processing using command line tools
17137 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
17138 utilities to perform genome arithmetic e.g indexing, formatting and merging.
17139 The bedr package's API enhances access to these tools as well as offers
17140 additional utilities for genomic regions processing.")
17141 (license license:gpl2)))
17143 (define-public r-sets
17150 (uri (cran-uri "sets" version))
17153 "1h1a03b1850kh5hd3gxbspx2nxqxvk2gb0wm0s60b70qb6zg0csp"))))
17154 (properties `((upstream-name . "sets")))
17155 (build-system r-build-system)
17156 (home-page "https://cran.r-project.org/web/packages/sets")
17157 (synopsis "Sets, generalized sets, customizable sets and intervals")
17159 "This package provides data structures and basic operations for ordinary
17160 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
17161 customizable sets, and intervals.")
17162 (license license:gpl2)))
17164 (define-public r-partitions
17166 (name "r-partitions")
17171 (uri (cran-uri "partitions" version))
17174 "1ik7cj2yfybx4v847nvnjrbkd0k66pfqqv6lkygfnlrldi0r205i"))))
17175 (build-system r-build-system)
17177 (list r-gmp r-mathjaxr r-polynom r-sets))
17178 (home-page "https://cran.r-project.org/web/packages/partitions")
17179 (synopsis "Additive partitions of integers")
17181 "This package provides tools to enumerates the partitions, unequal
17182 partitions, and restricted partitions of an integer; the three corresponding
17183 partition functions are also given.")
17184 ;; Any version of the GPL
17185 (license license:gpl2+)))
17187 (define-public r-brobdingnag
17189 (name "r-brobdingnag")
17194 (uri (cran-uri "Brobdingnag" version))
17197 "0hnp5nrpnscykvgrrbgp7987660hcbv92zc2q8lmpnin4ws399vk"))))
17198 (properties `((upstream-name . "Brobdingnag")))
17199 (build-system r-build-system)
17200 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
17201 (synopsis "Very large numbers in R")
17203 "This package handles very large numbers in R. Real numbers are held
17204 using their natural logarithms, plus a logical flag indicating sign. The
17205 package includes a vignette that gives a step-by-step introduction to using S4
17207 ;; Any version of the GPL
17208 (license license:gpl2+)))
17210 (define-public r-untb
17217 (uri (cran-uri "untb" version))
17220 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
17221 (build-system r-build-system)
17223 (list r-brobdingnag r-partitions r-polynom))
17224 (home-page "https://github.com/RobinHankin/untb.git")
17225 (synopsis "Ecological drift under the UNTB")
17227 "This package provides numerical simulations, and visualizations, of
17228 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
17229 (license license:gpl2+)))
17231 (define-public r-stepwise
17233 (name "r-stepwise")
17238 (uri (cran-uri "stepwise" version))
17241 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
17242 (build-system r-build-system)
17243 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
17244 (synopsis "Stepwise detection of recombination breakpoints")
17246 "This package provides a stepwise approach to identifying recombination
17247 breakpoints in a genomic sequence alignment.")
17248 (license license:gpl2+)))
17250 (define-public r-snpmaxsel
17252 (name "r-snpmaxsel")
17257 (uri (cran-uri "SNPmaxsel" version))
17260 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
17261 (properties `((upstream-name . "SNPmaxsel")))
17262 (build-system r-build-system)
17264 (list r-combinat r-mvtnorm))
17265 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
17266 (synopsis "Maximally selected statistics for SNP data")
17268 "This package implements asymptotic methods related to maximally selected
17269 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
17271 (license license:gpl2+)))
17273 (define-public r-acsnminer
17275 (name "r-acsnminer")
17276 (version "0.16.8.25")
17279 (uri (cran-uri "ACSNMineR" version))
17282 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
17283 (properties `((upstream-name . "ACSNMineR")))
17284 (build-system r-build-system)
17286 (list r-ggplot2 r-gridextra))
17287 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
17288 (synopsis "Gene enrichment analysis")
17290 "This package provides tools to compute and represent gene set enrichment
17291 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
17292 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
17293 enrichment can be run with hypergeometric test or Fisher exact test, and can
17294 use multiple corrections. Visualization of data can be done either by
17295 barplots or heatmaps.")
17296 (license license:gpl2+)))
17298 (define-public r-seqinr
17305 (uri (cran-uri "seqinr" version))
17308 "0cj07b7km5mla63qhbkxg1mnqq6vh79lsyyfpnbm29gw68w2bwy4"))))
17309 (build-system r-build-system)
17311 (list r-ade4 r-segmented))
17314 (home-page "http://seqinr.r-forge.r-project.org/")
17315 (synopsis "Biological sequences retrieval and analysis")
17317 "This package provides tools for exploratory data analysis and data
17318 visualization of biological sequence (DNA and protein) data. It also includes
17319 utilities for sequence data management under the ACNUC system.")
17320 (license license:gpl2+)))
17322 (define-public r-units
17329 (uri (cran-uri "units" version))
17332 "06mjprqi06xprj6185k5cmrrdl025x0pd1r6a4x3s74ciq9zwilw"))))
17333 (build-system r-build-system)
17340 (home-page "https://github.com/r-quantities/units/")
17341 (synopsis "Measurement Units for R Vectors")
17343 "This package provides support for measurement units in R vectors,
17344 matrices and arrays: automatic propagation, conversion, derivation and
17345 simplification of units; raising errors in case of unit incompatibility. It
17346 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
17348 (license license:gpl2)))
17350 (define-public r-udunits2
17352 (name "r-udunits2")
17353 (version "0.13.2.1")
17357 (uri (cran-uri "udunits2" version))
17360 "00prsy8m41v1camcsz94d7gm8qab2mdnwl3x0dyhz4r49b02jm4z"))))
17361 (properties `((upstream-name . "udunits2")))
17362 (build-system r-build-system)
17365 (home-page "https://cran.r-project.org/package=udunits2")
17366 (synopsis "Udunits-2 bindings for R")
17368 "This package provides simple bindings to Unidata's udunits library.")
17369 (license license:gpl2)))
17371 (define-public r-classint
17373 (name "r-classint")
17378 (uri (cran-uri "classInt" version))
17381 "0vk06k10mxcm6wn4b74njzc1kc1ividsn03ii523j4yfhy4kl3m3"))))
17382 (properties `((upstream-name . "classInt")))
17383 (build-system r-build-system)
17385 (list r-class r-e1071 r-kernsmooth))
17387 (list gfortran r-knitr))
17388 (home-page "https://github.com/r-spatial/classInt/")
17389 (synopsis "Choose univariate class intervals")
17391 "This package provides selected commonly used methods for choosing
17392 univariate class intervals for mapping or other graphics purposes.")
17393 (license license:gpl2+)))
17395 (define-public r-spdata
17402 (uri (cran-uri "spData" version))
17405 "1z4hp5ivwzyvl8mkp98j2ng1cl1xksqbjxv85vdlqfqjwpia6df6"))))
17406 (properties `((upstream-name . "spData")))
17407 (build-system r-build-system)
17409 (list r-raster r-sp))
17410 (home-page "https://github.com/Nowosad/spData")
17411 (synopsis "Datasets for spatial analysis")
17413 "This a package containing diverse spatial datasets for demonstrating,
17414 benchmarking and teaching spatial data analysis. It includes R data of class
17415 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
17416 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
17417 of the datasets are designed to illustrate specific analysis techniques.
17418 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
17419 illustrate point pattern analysis techniques.")
17420 (license license:cc0)))
17422 (define-public r-learnbayes
17424 (name "r-learnbayes")
17429 (uri (cran-uri "LearnBayes" version))
17432 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
17433 (properties `((upstream-name . "LearnBayes")))
17434 (build-system r-build-system)
17435 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
17436 (synopsis "Functions for learning Bayesian inference")
17438 "This package provides a collection of functions helpful in learning the
17439 basic tenets of Bayesian statistical inference. It contains functions for
17440 summarizing basic one and two parameter posterior distributions and predictive
17441 distributions. It contains MCMC algorithms for summarizing posterior
17442 distributions defined by the user. It also contains functions for regression
17443 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
17445 (license license:gpl2+)))
17447 (define-public r-deldir
17454 (uri (cran-uri "deldir" version))
17457 "1igq0l2knsbhizncgydcsidgkvvlwwlkrifbcdyhnzk0bhrdixkd"))))
17458 (build-system r-build-system)
17459 (native-inputs (list gfortran))
17460 (home-page "https://cran.r-project.org/web/packages/deldir")
17461 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
17463 "This package provides tools for calculating the Delaunay triangulation
17464 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
17465 of a planar point set. It plots triangulations and tessellations in various
17466 ways, clips tessellations to sub-windows, calculates perimeters of
17467 tessellations, and summarizes information about the tiles of the
17469 (license license:gpl2+)))
17471 (define-public r-wk
17478 (uri (cran-uri "wk" version))
17481 "1xga4rrqsr190g55by39az4nimnn06bf5b6mcjgwqvba0lvjhb5g"))))
17482 (properties `((upstream-name . "wk")))
17483 (build-system r-build-system)
17484 (home-page "https://paleolimbot.github.io/wk/")
17485 (synopsis "Lightweight well-known geometry parsing")
17487 "This package provides a minimal R and C++ API for parsing well-known
17488 binary and well-known text representation of geometries to and from R-native
17489 formats. Well-known binary is compact and fast to parse; well-known text is
17490 human-readable and is useful for writing tests. These formats are only useful
17491 in R if the information they contain can be accessed in R, for which
17492 high-performance functions are provided here.")
17493 (license license:expat)))
17495 (define-public r-s2
17502 (uri (cran-uri "s2" version))
17505 "0gwydn6wdl675ydkcckrci6ylcx30qn8nfhmrp4qx4r9mv3c2410"))))
17506 (properties `((upstream-name . "s2")))
17507 (build-system r-build-system)
17509 (list r-rcpp r-wk))
17514 (home-page "https://r-spatial.github.io/s2/")
17515 (synopsis "Spherical geometry operators using the S2 geometry library")
17517 "This package provides R bindings for Google's s2 library for geometric
17518 calculations on the sphere. High-performance constructors and exporters
17519 provide high compatibility with existing spatial packages, transformers
17520 construct new geometries from existing geometries, predicates provide a means
17521 to select geometries based on spatial relationships, and accessors extract
17522 information about geometries.")
17523 (license license:asl2.0)))
17525 (define-public r-sf
17532 (uri (cran-uri "sf" version))
17535 "0lsl4rh4lbv386hxlsnnwsjb5x1n9d3z0ckjmxakmmrqjjmiywyh"))))
17536 (build-system r-build-system)
17538 (list gdal geos proj sqlite zlib))
17547 (list pkg-config r-knitr))
17548 (home-page "https://github.com/r-spatial/sf/")
17549 (synopsis "Simple features for R")
17551 "This package provides support for simple features, a standardized way to
17552 encode spatial vector data. It binds to GDAL for reading and writing data, to
17553 GEOS for geometrical operations, and to PROJ for projection conversions and
17554 datum transformations.")
17555 ;; Either of these licenses
17556 (license (list license:gpl2 license:expat))))
17558 (define-public r-spdep
17564 (uri (cran-uri "spdep" version))
17567 "0xx6k3rsvsz1hwj0ny8aqfi9ca54x38f8pz8sfya5cggaspxbx59"))
17569 '(for-each delete-file '("inst/doc/CO69.html"
17573 "inst/doc/nb_sf.html"
17575 "inst/doc/nb_sf.Rmd"
17576 "inst/doc/sids.html"
17577 "inst/doc/sids.R")))))
17578 (build-system r-build-system)
17590 (home-page "https://github.com/r-spatial/spdep/")
17591 (synopsis "Spatial dependence: weighting schemes, statistics and models")
17593 "This package provides a collection of functions to create spatial
17594 weights matrix objects from polygon contiguities, from point patterns by
17595 distance and tessellations, for summarizing these objects, and for permitting
17596 their use in spatial data analysis, including regional aggregation by minimum
17598 (license license:gpl2+)))
17600 (define-public r-adegenet
17602 (name "r-adegenet")
17607 (uri (cran-uri "adegenet" version))
17610 "0zkbxw9w0fcb4s3zv2a8nxcsihzkfz49psaipxw99nwgm7l9jrh9"))))
17611 (build-system r-build-system)
17624 (home-page "https://github.com/thibautjombart/adegenet")
17625 (synopsis "Exploratory analysis of genetic and genomic data")
17627 "This package provides a toolset for the exploration of genetic and
17628 genomic data. Adegenet provides formal (S4) classes for storing and handling
17629 various genetic data, including genetic markers with varying ploidy and
17630 hierarchical population structure (@code{genind} class), alleles counts by
17631 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
17632 also implements original multivariate methods (DAPC, sPCA), graphics,
17633 statistical tests, simulation tools, distance and similarity measures, and
17634 several spatial methods. A range of both empirical and simulated datasets is
17635 also provided to illustrate various methods.")
17636 (license license:gpl2+)))
17638 (define-public r-pegas
17645 (uri (cran-uri "pegas" version))
17647 (base32 "0ngd0laqbs139ji9hm9kwsm9rm56agw2yyfcplxgqva936l93fl7"))))
17648 (build-system r-build-system)
17651 (home-page "http://ape-package.ird.fr/pegas.html")
17652 (synopsis "Population and evolutionary genetics analysis system")
17654 "This package provides functions for reading, writing, plotting,
17655 analysing, and manipulating allelic and haplotypic data, including from VCF
17656 files, and for the analysis of population nucleotide sequences and
17657 micro-satellites including coalescent analyses, linkage disequilibrium,
17658 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
17659 minimum spanning tree and network, and median-joining networks.")
17660 (license license:gpl2+)))
17662 (define-public r-rmetasim
17664 (name "r-rmetasim")
17669 (uri (cran-uri "rmetasim" version))
17672 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
17673 (build-system r-build-system)
17675 (list r-ade4 r-adegenet r-gtools r-pegas))
17676 (home-page "https://cran.r-project.org/web/packages/rmetasim")
17677 (synopsis "Individual-based population genetic simulation environment")
17679 "This package provides an interface between R and the metasim simulation
17680 engine. The simulation environment is documented in: Strand, A.(2002),
17681 Metasim 1.0: an individual-based environment for simulating population
17682 genetics of complex population dynamics.")
17684 (license license:gpl2+)))
17686 (define-public r-genetics
17688 (name "r-genetics")
17689 (version "1.3.8.1.3")
17693 (uri (cran-uri "genetics" version))
17696 "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy"))))
17697 (build-system r-build-system)
17699 (list r-combinat r-gdata r-gtools r-mass r-mvtnorm))
17700 (home-page "https://cran.r-project.org/web/packages/genetics/")
17701 (synopsis "Population genetics")
17703 "This package provides classes and methods for handling genetic data.
17704 It includes classes to represent genotypes and haplotypes at single markers up
17705 to multiple markers on multiple chromosomes. Function include allele
17706 frequencies, flagging homo/heterozygotes, flagging carriers of certain
17707 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
17708 and testing for linkage disequilibrium, ...")
17709 ;; Any GPL version.
17710 (license license:gpl2+)))
17712 (define-public r-snp-plotter
17714 (name "r-snp-plotter")
17719 (uri (cran-uri "snp.plotter" version))
17722 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
17723 (properties `((upstream-name . "snp.plotter")))
17724 (build-system r-build-system)
17725 (propagated-inputs (list r-genetics))
17726 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
17727 (synopsis "Plot p-values using single SNP and/or haplotype data")
17729 "This package helps you create plots of p-values using single SNP and/or
17730 haplotype data. Main features of the package include options to display a
17731 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
17732 datasets simultaneously. Plots can be created using global and/or individual
17733 haplotype p-values along with single SNP p-values. Images are created as
17734 either PDF/EPS files.")
17735 (license license:gpl2+)))
17737 (define-public r-polspline
17739 (name "r-polspline")
17744 (uri (cran-uri "polspline" version))
17746 (base32 "1dd1jwiaglkkhajzvqfkd1x5r3wzjlk5ww0yxzmns0s1kr74i4k9"))))
17747 (build-system r-build-system)
17748 (native-inputs (list gfortran))
17749 (home-page "https://cran.r-project.org/web/packages/polspline/")
17750 (synopsis "Polynomial spline routines")
17752 "This package provides routines for the polynomial spline fitting
17753 routines hazard regression, hazard estimation with flexible tails, logspline,
17754 lspec, polyclass, and polymars.")
17755 (license license:gpl2+)))
17757 (define-public r-rms
17764 (uri (cran-uri "rms" version))
17766 (base32 "1yfk800q4mgmrjkh0hqjkiv907sr1bi1jaigrj8l6pmg1mkynhbc"))))
17767 (build-system r-build-system)
17784 (native-inputs (list gfortran))
17785 (home-page "http://biostat.mc.vanderbilt.edu/rms")
17786 (synopsis "Regression modeling strategies")
17788 "This is a package for regression modeling, testing, estimation,
17789 validation, graphics, prediction, and typesetting by storing enhanced model
17790 design attributes in the fit. The rms package is a collection of functions
17791 that assist with and streamline modeling. It also contains functions for
17792 binary and ordinal logistic regression models, ordinal models for continuous Y
17793 with a variety of distribution families, and the Buckley-James multiple
17794 regression model for right-censored responses, and implements penalized
17795 maximum likelihood estimation for logistic and ordinary linear models. The
17796 package works with almost any regression model, but it was especially written
17797 to work with binary or ordinal regression models, Cox regression, accelerated
17798 failure time models, ordinary linear models, the Buckley-James model,
17799 generalized least squares for serially or spatially correlated observations,
17800 generalized linear models, and quantile regression.")
17801 (license license:gpl2+)))
17803 (define-public r-arsenal
17810 (uri (cran-uri "arsenal" version))
17813 "0qvs3ld28djnjnggdhqjwq8sbv8zz322qahlvf7dnx35yqf6xkms"))))
17814 (properties `((upstream-name . "arsenal")))
17815 (build-system r-build-system)
17816 (propagated-inputs (list r-knitr))
17817 (native-inputs (list r-knitr))
17818 (home-page "https://github.com/mayoverse/arsenal")
17819 (synopsis "Functions for large-scale statistical summaries")
17821 "This package provides an arsenal of R functions for large-scale
17822 statistical summaries, which are streamlined to work within the latest
17823 reporting tools in R and RStudio and which use formulas and versatile
17824 summary statistics for summary tables and models. The primary functions
17828 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
17829 levels of one or more categorical variables;
17830 @item @code{paired}, a Table-1-like summary of multiple variable types paired
17831 across two time points;
17832 @item @code{modelsum}, which performs simple model fits on one or more
17833 endpoints for many variables (univariate or adjusted for covariates);
17834 @item @code{freqlist}, a powerful frequency table across many categorical
17836 @item @code{comparedf}, a function for comparing @code{data.frames}; and
17837 @item @code{write2}, a function to output tables to a document.
17840 (license license:gpl2+)))
17842 (define-public r-haplo-stats
17844 (name "r-haplo-stats")
17849 (uri (cran-uri "haplo.stats" version))
17852 "0np9kw4f30xbvwr4f79g909ilis5n273ridmlwyzjxiskiry6mx0"))))
17853 (properties `((upstream-name . "haplo.stats")))
17854 (build-system r-build-system)
17856 (list r-arsenal r-rms))
17858 (list r-r-rsp)) ; for vignettes
17859 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
17860 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
17862 "This package provides routines for the analysis of indirectly measured
17863 haplotypes. The statistical methods assume that all subjects are unrelated
17864 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
17865 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
17866 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
17867 examples in the vignette.")
17868 (license license:gpl2+)))
17870 (define-public r-bqtl
17877 (uri (cran-uri "bqtl" version))
17880 "1sbzpi9z94f010lw2y1gmifjrvpmiqs4m26za7vr1xz72azrqvs9"))))
17881 (build-system r-build-system)
17882 (native-inputs (list gfortran))
17883 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
17884 (synopsis "Bayesian QTL mapping toolkit")
17886 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
17887 lines. It includes maximum likelihood and Bayesian tools.")
17888 (license license:gpl2+)))
17890 (define-public r-ibdreg
17897 (uri (cran-uri "ibdreg" version))
17900 "1x8z0vr2cmdks12hxfm0wwxskb0cr669w5j5rpa2ln8q704yy41g"))))
17901 (build-system r-build-system)
17902 (home-page "https://www.mayo.edu/research/labs/\
17903 statistical-genetics-genetic-epidemiology/software")
17904 (synopsis "Regression methods for IBD linkage with covariates")
17906 "This package provides a method to test genetic linkage with covariates
17907 by regression methods with response IBD sharing for relative pairs. Account
17908 for correlations of IBD statistics and covariates for relative pairs within
17909 the same pedigree.")
17910 (license license:gpl2+)))
17912 (define-public r-dlmap
17919 (uri (cran-uri "dlmap" version))
17922 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
17923 (build-system r-build-system)
17925 (list r-ibdreg r-mgcv r-nlme r-qtl r-wgaim))
17926 (home-page "https://cran.r-project.org/web/packages/dlmap/")
17927 (synopsis "Detection localization mapping for QTL")
17929 "This is package for QTL mapping in a mixed model framework with separate
17930 detection and localization stages. The first stage detects the number of QTL
17931 on each chromosome based on the genetic variation due to grouped markers on
17932 the chromosome; the second stage uses this information to determine the most
17933 likely QTL positions. The mixed model can accommodate general fixed and
17934 random effects, including spatial effects in field trials and pedigree
17935 effects. It is applicable to backcrosses, doubled haploids, recombinant
17936 inbred lines, F2 intercrosses, and association mapping populations.")
17937 (license license:gpl2)))
17939 (define-public r-hwde
17946 (uri (cran-uri "hwde" version))
17949 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
17950 (build-system r-build-system)
17951 (home-page "https://cran.r-project.org/web/packages/hwde/")
17952 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
17954 "This package fits models for genotypic disequilibria, as described in
17955 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
17956 terms are available that account for first order interactions between loci.
17957 It also implements, for a single locus in a single population, a conditional
17958 exact test for Hardy-Weinberg equilibrium.")
17959 (license license:gpl2+)))
17961 (define-public r-tdthap
17968 (uri (cran-uri "tdthap" version))
17971 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
17972 (build-system r-build-system)
17973 (home-page "https://cran.r-project.org/web/packages/tdthap/")
17974 (synopsis "TDT tests for extended haplotypes")
17976 "Functions and examples are provided for transmission/disequilibrium
17977 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
17978 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
17979 (license license:artistic2.0)))
17981 (define-public r-sparql
17987 (uri (cran-uri "SPARQL" version))
17990 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
17991 (properties `((upstream-name . "SPARQL")))
17992 (build-system r-build-system)
17994 (list r-rcurl r-xml))
17995 (home-page "https://cran.r-project.org/web/packages/SPARQL")
17996 (synopsis "SPARQL client for R")
17997 (description "This package provides an interface to use SPARQL to pose
17998 SELECT or UPDATE queries to an end-point.")
17999 ;; The only license indication is found in the DESCRIPTION file,
18000 ;; which states GPL-3. So we cannot assume GPLv3+.
18001 (license license:gpl3)))
18003 (define-public r-bookdown
18005 (name "r-bookdown")
18009 (uri (cran-uri "bookdown" version))
18012 "11din9h2sgzvg44627xc5is4psbq2b34km5sbiaprskjrf474866"))))
18013 (build-system r-build-system)
18023 ;; We cannot add knitr because this package depends on xfun, which is an
18028 (home-page "https://github.com/rstudio/bookdown")
18029 (synopsis "Authoring books and technical documents with R markdown")
18030 (description "This package provides output formats and utilities for
18031 authoring books and technical documents with R Markdown.")
18032 (license license:gpl3)))
18034 (define-public r-optparse
18036 (name "r-optparse")
18041 (uri (cran-uri "optparse" version))
18044 "1rqz0y4r94y3mwbb9kyz97cjqpnprka96qbncvbnbmgg2d630kij"))))
18045 (build-system r-build-system)
18050 (home-page "https://github.com/trevorld/optparse")
18051 (synopsis "Command line option parser")
18053 "This package provides a command line parser inspired by Python's
18054 @code{optparse} library to be used with Rscript to write shebang scripts
18055 that accept short and long options.")
18056 (license license:gpl2+)))
18058 (define-public r-kernlab
18065 (uri (cran-uri "kernlab" version))
18067 (base32 "12i7ffc1aacyy7bpjc0w60wwivn88wri8jz43h77irn5q5jwcnbk"))))
18068 (build-system r-build-system)
18069 (home-page "https://cran.r-project.org/web/packages/kernlab")
18070 (synopsis "Kernel-based machine learning tools")
18072 "This package provides kernel-based machine learning methods for
18073 classification, regression, clustering, novelty detection, quantile regression
18074 and dimensionality reduction. Among other methods @code{kernlab} includes
18075 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
18077 (license license:gpl2)))
18079 (define-public r-hierfstat
18081 (name "r-hierfstat")
18086 (uri (cran-uri "hierfstat" version))
18089 "0nyb5091lr8ma9vydbssyx9503601rynlrbldv98mmrmh74h6v41"))))
18090 (build-system r-build-system)
18092 (list r-ade4 r-adegenet r-gaston r-gtools))
18095 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
18096 (synopsis "Estimation and tests of hierarchical F-statistics")
18098 "This package allows the estimation of hierarchical F-statistics from
18099 haploid or diploid genetic data with any numbers of levels in the hierarchy,
18100 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
18101 are also given to test via randomisations the significance of each F and
18102 variance components, using the likelihood-ratio statistics G.")
18103 (license license:gpl2+)))
18105 (define-public r-hapassoc
18107 (name "r-hapassoc")
18112 (uri (cran-uri "hapassoc" version))
18115 "09ijc4sbw743z74fzklmvig11ndkycg6j86k4214wfsj1yj6j9x6"))))
18116 (build-system r-build-system)
18117 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
18118 (synopsis "Inference of trait associations with SNP haplotypes")
18120 "Hapassoc performs likelihood inference of trait associations with
18121 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
18122 functions are developed primarily for data collected in cohort or
18123 cross-sectional studies. They can accommodate uncertain haplotype phase and
18124 handle missing genotypes at some SNPs.")
18125 (license license:gpl2)))
18127 (define-public r-sampling
18129 (name "r-sampling")
18134 (uri (cran-uri "sampling" version))
18137 "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz"))))
18138 (build-system r-build-system)
18140 (list r-lpsolve r-mass))
18141 (home-page "https://cran.r-project.org/web/packages/sampling/")
18142 (synopsis "Survey sampling")
18144 "This package provides functions for drawing and calibrating samples.")
18145 (license license:gpl2+)))
18147 (define-public r-r2html
18154 (uri (cran-uri "R2HTML" version))
18157 "12qg9rp1j26h2f48dfg5k9jds26ycacv3f3ymk686ks43hd1hzja"))))
18158 (properties `((upstream-name . "R2HTML")))
18159 (build-system r-build-system)
18160 (home-page "https://github.com/nalimilan/R2HTML")
18161 (synopsis "HTML export for R objects")
18163 "This package includes HTML functions and methods to write in an HTML
18164 file. Thus, making HTML reports is easy. It includes a function that allows
18165 redirection on the fly, which appears to be very useful for teaching purposes,
18166 as the student can keep a copy of the produced output to keep all that they
18167 did during the course. The package comes with a vignette describing how to
18168 write HTML reports for statistical analysis. Finally, a driver for Sweave
18169 parses HTML flat files containing R code and to automatically write
18170 the corresponding outputs (tables and graphs).")
18171 (license license:gpl2+)))
18173 (define-public r-rjava
18180 (uri (cran-uri "rJava" version))
18183 "1ijqhvnb8ab38cp9pwdf7zq7xqqlm6x94gkrab2dd98p6d4x1472"))))
18184 (properties `((upstream-name . "rJava")))
18185 (build-system r-build-system)
18187 `(#:modules ((guix build utils)
18188 (guix build r-build-system)
18191 (modify-phases %standard-phases
18192 (add-after 'unpack 'set-JAVA_HOME
18193 (lambda* (#:key inputs #:allow-other-keys)
18194 (let ((jdk (assoc-ref inputs "jdk")))
18195 (setenv "JAVA_HOME" jdk)
18196 (setenv "JAVA" (which "java"))
18197 (setenv "JAR" (which "jar"))
18198 (setenv "JAVAC" (which "javac"))
18199 (setenv "JAVAH" (which "javah"))
18200 (setenv "JAVA_CPPFLAGS"
18201 (string-append "-I" jdk "/include "
18202 "-I" jdk "/include/linux"))
18203 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
18204 ((lib) (setenv "JAVA_LIBS" lib))
18205 (_ (error "Could not find libjvm.so"))))
18209 ("jdk" ,icedtea-8 "jdk")
18211 (home-page "https://www.rforge.net/rJava/")
18212 (synopsis "Low-Level R to Java interface")
18214 "This package provides a low-level interface to the Java VM very much
18215 like .C/.Call and friends. It allows the creation of objects, calling methods
18216 and accessing fields.")
18217 (license license:gpl2)))
18219 (define-public r-svmisc
18226 (uri (cran-uri "svMisc" version))
18229 "1r3kih5bnr4plnzdn5f2gg3xl3krgyl7gkdlf58a2l8vk13j3m9d"))))
18230 (properties `((upstream-name . "svMisc")))
18231 (build-system r-build-system)
18234 (home-page "https://github.com/SciViews/svMisc")
18235 (synopsis "Miscellaneous functions for SciViews")
18237 "This package provides miscellaneous functions for SciViews or general
18238 use, including tools to manage a temporary environment attached to the search
18239 path for temporary variables you do not want to @code{save()} or
18240 @code{load()}; test the current platform; showing progress bars, etc.")
18241 (license license:gpl2)))
18243 (define-public r-xyz
18250 (uri (cran-uri "xyz" version))
18253 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
18254 (build-system r-build-system)
18257 (home-page "https://cran.r-project.org/web/packages/xyz/")
18258 (synopsis "Algorithm for fast interaction search in high-dimensional data")
18260 "High dimensional interaction search by brute force requires a quadratic
18261 computational cost in the number of variables. The xyz algorithm provably
18262 finds strong interactions in almost linear time. For details of the algorithm
18263 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
18264 interaction search in high-dimensional data.")
18265 ;; Any version of the GPL.
18266 (license license:gpl2+)))
18268 (define-public r-rttf2pt1
18270 (name "r-rttf2pt1")
18275 (uri (cran-uri "Rttf2pt1" version))
18278 "1fp1y0kxa5xg8w0dplm12wfm8h78az4k6ql1758wwhb3d17np241"))))
18279 (properties `((upstream-name . "Rttf2pt1")))
18280 (build-system r-build-system)
18281 (home-page "https://github.com/wch/Rttf2pt1")
18282 (synopsis "Font conversion utility")
18284 "This package contains the program @code{ttf2pt1}, for use with the
18285 @code{extrafont} package.")
18286 ;; Most of the files are covered under the Expat license. Some files are
18287 ;; covered under BSD-3. Deviations for individual files are recorded in
18288 ;; the LICENSE file.
18289 (license (list license:bsd-3 license:expat
18290 (license:non-copyleft "file://LICENSE")))))
18292 (define-public r-extrafontdb
18294 (name "r-extrafontdb")
18299 (uri (cran-uri "extrafontdb" version))
18302 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
18303 (build-system r-build-system)
18304 (home-page "https://github.com/wch/extrafontdb")
18305 (synopsis "Database for the extrafont package")
18307 "This package holds the database for the @code{extrafont} package.")
18308 (license license:gpl2)))
18310 (define-public r-extrafont
18312 (name "r-extrafont")
18317 (uri (cran-uri "extrafont" version))
18320 "0mx810mld67vb1w3wkl4fhpjmkq32lgpq5x1c0a9rf8li5wskrj4"))))
18321 (build-system r-build-system)
18323 (list r-extrafontdb r-rttf2pt1))
18324 (home-page "https://github.com/wch/extrafont")
18325 (synopsis "Tools for using fonts in R")
18327 "The extrafont package makes it easier to use fonts other than the basic
18328 PostScript fonts that R uses. Fonts that are imported into extrafont can be
18329 used with PDF or PostScript output files. There are two hurdles for using
18330 fonts in PDF (or Postscript) output files:
18333 @item Making R aware of the font and the dimensions of the characters.
18334 @item Embedding the fonts in the PDF file so that the PDF can be displayed
18335 properly on a device that doesn't have the font. This is usually needed if
18336 you want to print the PDF file or share it with others.
18339 The extrafont package makes both of these things easier.")
18340 (license license:gpl2)))
18342 (define-public r-xkcd
18349 (uri (cran-uri "xkcd" version))
18352 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
18353 (build-system r-build-system)
18355 (list r-extrafont r-ggplot2 r-hmisc))
18356 (home-page "https://cran.r-project.org/web/packages/xkcd/")
18357 (synopsis "Plot ggplot2 graphics in the XKCD style")
18359 "This package provides the means to plot ggplot2 graphs in the style of
18360 the XKCD web comic.")
18361 (license license:gpl3)))
18363 (define-public r-babelgene
18365 (name "r-babelgene")
18370 (uri (cran-uri "babelgene" version))
18373 "1735h4s2vahv55pmq65zkgxq8d5x71i1is03rf17dric8yynjjhg"))))
18374 (properties `((upstream-name . "babelgene")))
18375 (build-system r-build-system)
18377 (list r-dplyr r-rlang))
18381 "https://igordot.github.io/babelgene/")
18382 (synopsis "Gene orthologs for model organisms in a Tidy data format")
18384 "Genomic analysis of model organisms often requires the use of databases
18385 based on human data or making comparisons to patient-derived resources. This
18386 requires converting genes between human and non-human analogues. The
18387 babelgene R package provides predicted gene orthologs/homologs for frequently
18388 studied model organisms in an R-friendly tidy/long format. The package
18389 integrates orthology assertion predictions sourced from multiple databases as
18390 compiled by the HGNC Comparison of Orthology Predictions (HCOP).")
18391 (license license:expat)))
18393 (define-public r-msigdbr
18400 (uri (cran-uri "msigdbr" version))
18403 "1jna9bkq0a7r6f8nhxziyiw75kfhsyh1rv7sx5d4551mvxxlhc6w"))))
18404 (build-system r-build-system)
18414 (home-page "https://github.com/igordot/msigdbr")
18415 (synopsis "MSigDB gene sets for multiple organisms")
18417 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
18418 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
18419 software in a standard R data frame with key-value pairs. Included are the
18420 original human gene symbols and Entrez IDs as well as the equivalents for
18421 various frequently studied model organisms such as mouse, rat, pig, fly, and
18423 ;; The package is covered under the Expat license, but the upstream MSigDB
18424 ;; files are made available under the Creative Commons Attribution 4.0
18425 ;; International license.
18426 (license (list license:expat license:cc-by4.0))))
18428 (define-public r-gridgraphics
18430 (name "r-gridgraphics")
18435 (uri (cran-uri "gridGraphics" version))
18438 "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219"))))
18439 (properties `((upstream-name . "gridGraphics")))
18440 (build-system r-build-system)
18441 (home-page "https://github.com/pmur002/gridgraphics")
18442 (synopsis "Redraw base graphics using @code{grid} graphics")
18444 "This package provides functions to convert a page of plots drawn with
18445 the @code{graphics} package into identical output drawn with the @code{grid}
18446 package. The result looks like the original @code{graphics}-based plot, but
18447 consists of @code{grid} grobs and viewports that can then be manipulated with
18448 @code{grid} functions (e.g., edit grobs and revisit viewports).")
18449 (license license:gpl2+)))
18451 (define-public r-farver
18458 (uri (cran-uri "farver" version))
18461 "1x6ffwxqbrwlylnk995jz2a6nz2y9z59jaq0ncpni7q40w367j75"))))
18462 (build-system r-build-system)
18463 (home-page "https://github.com/thomasp85/farver")
18464 (synopsis "Vectorized color conversion and comparison")
18466 "The encoding of color can be handled in many different ways, using
18467 different color spaces. As different color spaces have different uses,
18468 efficient conversion between these representations are important. This
18469 package provides a set of functions that gives access to very fast color space
18470 conversion and comparisons implemented in C++, and offers 100-fold speed
18471 improvements over the @code{convertColor} function in the @code{grDevices}
18473 (license license:expat)))
18475 (define-public r-yulab-utils
18477 (name "r-yulab-utils")
18482 (uri (cran-uri "yulab.utils" version))
18485 "1bj93gnj7j4b7dgkbr5v22rsbwfcw5dvipl5irmidaakvrihd19q"))))
18486 (properties `((upstream-name . "yulab.utils")))
18487 (build-system r-build-system)
18488 (home-page "https://cran.r-project.org/package=yulab.utils")
18489 (synopsis "Supporting functions for packages maintained by YuLab-SMU")
18491 "Miscellaneous functions commonly used by YuLab-SMU, such as
18492 @code{install_zip_gh} to install R packages from Github ZIP files.")
18493 (license license:artistic2.0)))
18495 (define-public r-ggplotify
18497 (name "r-ggplotify")
18502 (uri (cran-uri "ggplotify" version))
18505 "12mk3fa8fdjxj7xxz21jkr7h91w5wdgwjqhszcz1qffwsgb773qp"))))
18506 (build-system r-build-system)
18508 (list r-ggplot2 r-gridgraphics r-yulab-utils))
18511 (home-page "https://github.com/GuangchuangYu/ggplotify")
18512 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
18514 "This package provides tools to convert plot function calls (using
18515 expression or formula) to @code{grob} or @code{ggplot} objects that are
18516 compatible with the @code{grid} and @code{ggplot2} environment. With this
18517 package, we are able to e.g. use @code{cowplot} to align plots produced by
18518 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
18519 converting them to @code{ggplot} objects.")
18520 (license license:artistic2.0)))
18522 (define-public r-triebeard
18524 (name "r-triebeard")
18529 (uri (cran-uri "triebeard" version))
18532 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
18533 (build-system r-build-system)
18534 (propagated-inputs (list r-rcpp))
18535 (home-page "https://github.com/Ironholds/triebeard/")
18536 (synopsis "Radix trees in Rcpp")
18538 "Radix trees, or tries, are key-value data structures optimized for
18539 efficient lookups, similar in purpose to hash tables. This package provides
18540 an implementation of radix trees for use in R programming and in developing
18541 packages with Rcpp.")
18542 (license license:expat)))
18544 (define-public r-tweenr
18551 (uri (cran-uri "tweenr" version))
18554 "17znizh4yabh2zs9mzyr0sl6p0pw49961i61br7cl1b7v9sza18q"))))
18555 (build-system r-build-system)
18557 (list r-farver r-magrittr r-rcpp r-rlang))
18558 (home-page "https://github.com/thomasp85/tweenr")
18559 (synopsis "Interpolate data for smooth animations")
18561 "In order to create smooth animation between states of data, tweening is
18562 necessary. This package provides a range of functions for creating tweened
18563 data that can be used as basis for animation. Furthermore it adds a number of
18564 vectorized interpolaters for common R data types such as numeric, date and
18566 (license license:expat)))
18568 (define-public r-polyclip
18570 (name "r-polyclip")
18575 (uri (cran-uri "polyclip" version))
18578 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
18579 (build-system r-build-system)
18580 (native-inputs (list pkg-config))
18581 (home-page "http://www.angusj.com/delphi/clipper.php")
18582 (synopsis "Polygon clipping")
18584 "This package provides an R port of the library Clipper. It performs
18585 polygon clipping operations (intersection, union, set minus, set difference)
18586 for polygonal regions of arbitrary complexity, including holes. It computes
18587 offset polygons (spatial buffer zones, morphological dilations, Minkowski
18588 dilations) for polygonal regions and polygonal lines. It computes the
18589 Minkowski Sum of general polygons. There is a function for removing
18590 self-intersections from polygon data.")
18591 (license license:boost1.0)))
18593 (define-public r-urltools
18595 (name "r-urltools")
18600 (uri (cran-uri "urltools" version))
18603 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
18604 (build-system r-build-system)
18606 (list r-rcpp r-triebeard))
18607 (home-page "https://github.com/Ironholds/urltools/")
18608 (synopsis "Vectorized tools for URL handling and parsing")
18610 "This package provides a toolkit for all URL-handling needs, including
18611 encoding and decoding, parsing, parameter extraction and modification. All
18612 functions are designed to be both fast and entirely vectorized. It is
18613 intended to be useful for people dealing with web-related datasets, such as
18614 server-side logs, although may be useful for other situations involving large
18616 (license license:expat)))
18618 (define-public r-ggforce
18625 (uri (cran-uri "ggforce" version))
18628 "0bwzjbjl678xvc2ihm80dwn9pidwafqjdab3k299csys16s3na1a"))))
18629 (build-system r-build-system)
18642 (home-page "https://ggforce.data-imaginist.com")
18643 (synopsis "Accelerating ggplot2")
18645 "The aim of the ggplot2 package is to aid in visual data investigations.
18646 This focus has led to a lack of facilities for composing specialized plots.
18647 This package aims to be a collection of mainly new statistics and geometries
18648 that fills this gap.")
18649 (license license:expat)))
18651 (define-public r-europepmc
18653 (name "r-europepmc")
18658 (uri (cran-uri "europepmc" version))
18661 "16japbndid34shqg8n0bmjrxn84xmhrylvz832zclcllm6i93fn1"))))
18662 (build-system r-build-system)
18677 (home-page "https://github.com/ropensci/europepmc/")
18678 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
18680 "This package provides an R Client for the
18681 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
18682 Service}. It gives access to both metadata on life science literature and
18683 open access full texts. Europe PMC indexes all PubMed content and other
18684 literature sources including Agricola, a bibliographic database of citations
18685 to the agricultural literature, or Biological Patents. In addition to
18686 bibliographic metadata, the client allows users to fetch citations and
18687 reference lists. Links between life-science literature and other EBI
18688 databases, including ENA, PDB or ChEMBL are also accessible.")
18689 (license license:gpl3)))
18691 (define-public r-ggraph
18698 (uri (cran-uri "ggraph" version))
18701 "0m4n8iw2b9jk8hcy5blg5w59zsqcpsbv27wbw598dvljpafx8sp3"))))
18702 (build-system r-build-system)
18721 (home-page "https://cran.r-project.org/web/packages/ggraph/")
18722 (synopsis "Implementation of grammar of graphics for graphs and networks")
18724 "The grammar of graphics as implemented in ggplot2 is a poor fit for
18725 graph and network visualizations due to its reliance on tabular data input.
18726 The ggraph package is an extension of the ggplot2 API tailored to graph
18727 visualizations and provides the same flexible approach to building up plots
18729 (license license:gpl3)))
18731 (define-public r-gkmsvm
18738 (uri (cran-uri "gkmSVM" version))
18741 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
18742 (properties `((upstream-name . "gkmSVM")))
18743 (build-system r-build-system)
18745 (list r-kernlab r-rcpp r-rocr r-seqinr))
18746 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
18747 (synopsis "Gapped-kmer support vector machine")
18749 "This R package provides tools for training gapped-kmer SVM classifiers
18750 for DNA and protein sequences. This package supports several sequence
18751 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
18752 (license license:gpl2+)))
18754 (define-public r-varselrf
18756 (name "r-varselrf")
18761 (uri (cran-uri "varSelRF" version))
18764 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
18765 (properties `((upstream-name . "varSelRF")))
18766 (build-system r-build-system)
18768 (list r-randomforest))
18769 (home-page "https://www.ligarto.org/rdiaz/software/software")
18770 (synopsis "Variable selection using random forests")
18772 "This package provides tools for the variable selection from random
18773 forests using both backwards variable elimination (for the selection of small
18774 sets of non-redundant variables) and selection based on the importance
18775 spectrum (somewhat similar to scree plots; for the selection of large,
18776 potentially highly-correlated variables). The main applications are in
18777 high-dimensional data (e.g., microarray data, and other genomics and
18778 proteomics applications).")
18779 (license license:gpl2+)))
18781 (define-public r-pamr
18788 (uri (cran-uri "pamr" version))
18791 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
18792 (build-system r-build-system)
18794 (list r-cluster r-survival))
18795 (native-inputs (list gfortran))
18796 (home-page "https://cran.r-project.org/web/packages/pamr/")
18797 (synopsis "Prediction Analysis for Microarrays")
18799 "This package provides some functions for sample classification in
18801 (license license:gpl2)))
18803 (define-public r-rda
18806 (version "1.0.2-2.1")
18810 (uri (cran-uri "rda" version))
18813 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
18814 (build-system r-build-system)
18815 (home-page "https://cran.r-project.org/web/packages/rda/")
18816 (synopsis "Shrunken centroids regularized discriminant analysis")
18818 "This package provides tools for shrunken centroids regularized
18819 discriminant analysis for the purpose of classifying high dimensional data.")
18820 (license license:gpl2+)))
18822 (define-public r-ggvis
18829 (uri (cran-uri "ggvis" version))
18832 "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy"))))
18833 (build-system r-build-system)
18842 (home-page "https://ggvis.rstudio.com/")
18843 (synopsis "Interactive grammar of graphics")
18845 "This package is a data visualization package for R providing an
18846 implementation of an interactive grammar of graphics, taking the best parts of
18847 ggplot2, combining them with the reactive framework of Shiny and drawing web
18848 graphics using Vega.")
18849 (license license:gpl2)))
18851 (define-public r-gbm
18858 (uri (cran-uri "gbm" version))
18861 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
18862 (build-system r-build-system)
18864 (list r-lattice r-survival))
18867 (home-page "https://github.com/gbm-developers/gbm")
18868 (synopsis "Generalized boosted regression models")
18870 "This package is an implementation of extensions to Freund and Schapire's
18871 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
18872 regression methods for least squares, absolute loss, t-distribution loss,
18873 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
18874 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
18875 and Learning to Rank measures (LambdaMart).")
18876 (license license:gpl2+)))
18878 (define-public r-threejs
18885 (uri (cran-uri "threejs" version))
18888 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
18889 (build-system r-build-system)
18891 `(#:modules ((guix build utils)
18892 (guix build r-build-system)
18896 (modify-phases %standard-phases
18897 (add-after 'unpack 'process-javascript
18898 (lambda* (#:key inputs #:allow-other-keys)
18899 (with-directory-excursion "inst"
18903 `((,(assoc-ref inputs "js-jquery")
18904 "htmlwidgets/lib/jquery/jquery.min.js")
18905 (,(assoc-ref inputs "js-threejs-111")
18906 "htmlwidgets/lib/threejs-111/three.min.js"))))
18907 (lambda (sources targets)
18908 (for-each (lambda (source target)
18909 (format #t "Processing ~a --> ~a~%"
18911 (delete-file target)
18912 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
18913 (call-with-output-file target
18915 (dump-port minified port)))))
18916 sources targets))))
18919 (list r-base64enc r-crosstalk r-htmlwidgets r-igraph))
18921 `(("uglifyjs" ,node-uglify-js)
18925 (uri "https://code.jquery.com/jquery-1.12.4.js")
18928 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
18932 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
18935 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
18936 (home-page "https://bwlewis.github.io/rthreejs")
18937 (synopsis "Interactive 3D scatter plots, networks and globes")
18939 "Create interactive 3D scatter plots, network plots, and globes in R
18940 using the three.js visualization library.")
18941 (license license:expat)))
18943 (define-public r-mlbench
18950 (uri (cran-uri "mlbench" version))
18953 "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi"))))
18954 (build-system r-build-system)
18955 (home-page "https://cran.r-project.org/web/packages/mlbench/")
18956 (synopsis "Machine learning benchmark problems")
18958 "This package provides a collection of artificial and real-world machine
18959 learning benchmark problems, including, e.g., several data sets from the UCI
18961 (license license:gpl2)))
18963 (define-public r-mpm
18970 (uri (cran-uri "mpm" version))
18973 "1jpv2ddmw7aarqbbyfys1yb840arw33319wnny3v2hk84hldmayj"))))
18974 (build-system r-build-system)
18976 (list r-kernsmooth r-mass))
18977 (home-page "http://mpm.r-forge.r-project.org")
18978 (synopsis "Multivariate projection methods")
18980 "This is a package for exploratory graphical analysis of multivariate
18981 data, specifically gene expression data with different projection methods:
18982 principal component analysis, correspondence analysis, spectral map
18984 (license license:gpl2+)))
18986 (define-public r-png
18992 (uri (cran-uri "png" version))
18995 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
18996 (build-system r-build-system)
18998 (list libpng zlib))
18999 (home-page "https://www.rforge.net/png/")
19000 (synopsis "Read and write PNG images")
19002 "This package provides an easy and simple way to read, write and display
19003 bitmap images stored in the PNG format. It can read and write both files and
19004 in-memory raw vectors.")
19005 ;; Any of these GPL versions.
19006 (license (list license:gpl2 license:gpl3))))
19008 (define-public r-ggcorrplot
19010 (name "r-ggcorrplot")
19015 (uri (cran-uri "ggcorrplot" version))
19018 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
19019 (build-system r-build-system)
19021 (list r-ggplot2 r-reshape2))
19022 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
19023 (synopsis "Visualization of a correlation matrix using ggplot2")
19025 "The ggcorrplot package can be used to visualize easily a correlation
19026 matrix using ggplot2. It provides a solution for reordering the correlation
19027 matrix and displays the significance level on the plot. It also includes a
19028 function for computing a matrix of correlation p-values.")
19029 (license license:gpl2)))
19031 (define-public r-ggfun
19038 (uri (cran-uri "ggfun" version))
19041 "06si42b60hp8wprs5nbks93qlb9s269k9kw7akcirizwc399x62r"))))
19042 (properties `((upstream-name . "ggfun")))
19043 (build-system r-build-system)
19045 (list r-ggplot2 r-rlang))
19046 (native-inputs (list r-knitr))
19047 (home-page "https://cran.r-project.org/package=ggfun")
19048 (synopsis "Miscellaneous functions for ggplot2")
19050 "This package provides useful functions to edit ggplot object (e.g.,
19051 setting fonts for theme and layers, adding rounded rectangle as background for
19052 each of the legends).")
19053 (license license:artistic2.0)))
19055 (define-public r-gridtext
19057 (name "r-gridtext")
19062 (uri (cran-uri "gridtext" version))
19065 "131kw7nkfwksviwfifd2kk7lyvhxzzzv1nnj8rahkr3dik3akk61"))))
19066 (properties `((upstream-name . "gridtext")))
19067 (build-system r-build-system)
19077 (home-page "https://wilkelab.org/gridtext/")
19078 (synopsis "Improved text rendering support for Grid graphics")
19080 "This package provides support for rendering of formatted text using Grid
19081 graphics. Text can be formatted via a minimal subset of Markdown, HTML, and
19082 inline CSS directives, and it can be rendered both with and without word
19084 (license license:expat)))
19086 (define-public r-ggtext
19093 (uri (cran-uri "ggtext" version))
19096 "0n19dlcys8v7myfyckr6dnq0kx79k3sbh8nwx1jsx8pgzfbi8a2b"))))
19097 (properties `((upstream-name . "ggtext")))
19098 (build-system r-build-system)
19100 (list r-ggplot2 r-gridtext r-rlang r-scales))
19101 (native-inputs (list r-knitr))
19102 (home-page "https://wilkelab.org/ggtext/")
19103 (synopsis "Improved text rendering support for ggplot2")
19105 "This package provides a ggplot2 extension that enables the rendering of
19106 complex formatted plot labels (titles, subtitles, facet labels, axis labels,
19107 etc.). Text boxes with automatic word wrap are also supported.")
19108 (license license:gpl2)))
19110 ;; This package includes minified JavaScript files. When upgrading please
19111 ;; check that there are no new minified JavaScript files.
19112 (define-public r-flexdashboard
19114 (name "r-flexdashboard")
19119 (uri (cran-uri "flexdashboard" version))
19122 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
19123 (modules '((guix build utils)))
19126 ;; Delete bundled minified JavaScript files
19127 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
19128 (delete-file "inst/www/sly/sly.min.js")
19129 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
19130 (delete-file "inst/www/prism/prism.js")
19132 (build-system r-build-system)
19134 `(#:modules ((guix build utils)
19135 (guix build r-build-system)
19139 (ice-9 textual-ports))
19141 (modify-phases %standard-phases
19142 (add-after 'unpack 'process-javascript
19143 (lambda* (#:key inputs #:allow-other-keys)
19144 (with-directory-excursion "inst"
19145 ;; Concatenate all components of prism.js
19146 (let ((contents (string-join
19147 (map (lambda (name)
19148 (call-with-input-file
19149 (assoc-ref inputs name)
19153 "js-prism-line-numbers"))
19155 (call-with-output-file "prism-src.js"
19156 (cut display contents <>)))
19160 `(("www/stickytableheaders/jquery.stickytableheaders.js"
19161 "www/stickytableheaders/jquery.stickytableheaders.min.js")
19163 "www/sly/sly.min.js")
19165 "www/prism/prism.js")
19166 (,(assoc-ref inputs "js-raphael")
19167 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
19168 (,(assoc-ref inputs "js-featherlight")
19169 "www/featherlight/featherlight.min.js"))))
19170 (lambda (sources targets)
19171 (for-each (lambda (source target)
19172 (format #t "Processing ~a --> ~a~%"
19174 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
19175 (call-with-output-file target
19177 (dump-port minified port)))))
19178 sources targets))))
19188 `(("uglifyjs" ,node-uglify-js)
19192 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
19195 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
19199 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
19202 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
19206 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
19209 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
19210 ("js-prism-line-numbers"
19213 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
19216 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
19220 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
19223 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
19224 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
19225 (synopsis "R Markdown format for flexible dashboards")
19227 "This package provides an R Markdown format for converting an R Markdown
19228 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
19229 of its components to the containing web page.")
19230 (license license:expat)))
19232 (define-public r-preseqr
19239 (uri (cran-uri "preseqR" version))
19242 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
19243 (properties `((upstream-name . "preseqR")))
19244 (build-system r-build-system)
19247 (home-page "https://cran.r-project.org/web/packages/preseqR/")
19248 (synopsis "Predicting species accumulation curves")
19250 "This package can be used to predict the r-species accumulation
19251 curve (r-SAC), which is the number of species represented at least r times as
19252 a function of the sampling effort. When r = 1, the curve is known as the
19253 species accumulation curve, or the library complexity curve in high-throughput
19254 genomic sequencing. The package includes both parametric and nonparametric
19255 methods, as described by Deng C, et al. (2018).")
19256 (license license:gpl3)))
19258 (define-public r-mapplots
19260 (name "r-mapplots")
19265 (uri (cran-uri "mapplots" version))
19268 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
19269 (build-system r-build-system)
19270 (home-page "https://cran.r-project.org/web/packages/mapplots/")
19271 (synopsis "Data visualization on maps")
19273 "This package helps you create simple maps; add sub-plots like pie plots
19274 to a map or any other plot; format, plot and export gridded data. The package
19275 was developed for displaying fisheries data but most functions can be used for
19276 more generic data visualisation.")
19277 (license license:gpl2+)))
19279 (define-public r-pmcmr
19286 (uri (cran-uri "PMCMR" version))
19289 "05n13pp5yff6pzk4ry07crddfaj3jlglrd1vkcnacyd8jpaxkd77"))))
19290 (properties `((upstream-name . "PMCMR")))
19291 (build-system r-build-system)
19292 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
19293 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
19295 "This is a deprecated package for calculating pairwise multiple
19296 comparisons of mean rank sums. This package is superseded by the novel
19297 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
19298 compatibility of dependent packages for some time.")
19299 (license license:gpl3+)))
19301 (define-public r-downloader
19303 (name "r-downloader")
19308 (uri (cran-uri "downloader" version))
19311 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
19312 (build-system r-build-system)
19315 (home-page "https://github.com/wch/downloader")
19316 (synopsis "Download files over HTTP and HTTPS")
19318 "This package provides a wrapper for the @code{download.file} function,
19319 making it possible to download files over HTTPS across platforms. The
19320 @code{RCurl} package provides this functionality (and much more) but has
19321 external dependencies. This package has is implemented purely in R.")
19322 (license license:gpl2)))
19324 (define-public r-aplot
19331 (uri (cran-uri "aplot" version))
19334 "0310z9db2r8vr4053vy6w4rbcqhg5cv56p60rk7dh4y6ifbd2sbx"))))
19335 (properties `((upstream-name . "aplot")))
19336 (build-system r-build-system)
19343 (home-page "https://github.com/YuLab-SMU/aplot")
19344 (synopsis "Decorate a ggplot with associated information")
19346 "Users may want to align plots with associated information that requires
19347 axes to be exactly matched in subplots, e.g. hierarchical clustering with a
19348 heatmap. This package provides utilities to align associated subplots to a
19349 main plot at different sides (left, right, top and bottom) with axes exactly
19351 (license license:artistic2.0)))
19353 (define-public r-ggnewscale
19355 (name "r-ggnewscale")
19360 (uri (cran-uri "ggnewscale" version))
19363 "108a7y6sqqvzyfk247lbmnacfpwdl405rf1b3fa62cgx8ycsq4kb"))))
19364 (properties `((upstream-name . "ggnewscale")))
19365 (build-system r-build-system)
19368 (home-page "https://cran.r-project.org/package=ggnewscale")
19369 (synopsis "Multiple fill and color scales in ggplot2")
19371 "This package lets you use multiple fill and color scales in ggplot2.")
19372 (license license:gpl3)))
19374 (define-public r-ggpointdensity
19376 (name "r-ggpointdensity")
19381 (uri (cran-uri "ggpointdensity" version))
19384 "0c9a14j3b0hvamqylhzldw2hjdxmfbllwahjkf3gg2rw337ld9iy"))))
19386 `((upstream-name . "ggpointdensity")))
19387 (build-system r-build-system)
19390 (home-page "https://github.com/LKremer/ggpointdensity")
19391 (synopsis "Cross between a 2D density plot and a scatter plot")
19393 "This package provides a cross between a 2D density plot and a scatter
19394 plot, implemented as a ggplot2 @code{geom}. Points in the scatter plot are
19395 colored by the number of neighboring points. This is useful to visualize the
19396 2D-distribution of points in case of overplotting.")
19397 (license license:gpl3)))
19399 (define-public r-arrow
19406 (uri (cran-uri "arrow" version))
19409 "1b85vc5ld7nibqgsdkl5kbzc0rm5jh5lqfdrssvrrcxpd26a16kc"))))
19410 (properties `((upstream-name . "arrow")))
19411 (build-system r-build-system)
19413 (list `(,apache-arrow "lib") zlib))
19424 (list pkg-config r-knitr))
19425 (home-page "https://github.com/apache/arrow/")
19426 (synopsis "R integration to Apache Arrow")
19428 "Apache Arrow is a cross-language development platform for in-memory
19429 data. It specifies a standardized language-independent columnar memory format
19430 for flat and hierarchical data, organized for efficient analytic operations on
19431 modern hardware. This package provides an R interface to the Arrow C++
19433 (license license:asl2.0)))
19435 (define-public r-rex
19442 (uri (cran-uri "rex" version))
19445 "1mmzlc3j7xa0rbjxa369f4sr0iw3gq58g8fmjjxbsjvfq14ychmg"))))
19446 (build-system r-build-system)
19451 (home-page "https://github.com/kevinushey/rex")
19452 (synopsis "Friendly regular expressions")
19454 "This package provides a friendly interface for the construction of
19455 regular expressions. Regular expressions are a very powerful feature, however
19456 they are often difficult to interpret. Rex allows you to build complex
19457 regular expressions from human readable expressions")
19458 (license license:expat)))
19460 (define-public r-mlapi
19467 (uri (cran-uri "mlapi" version))
19470 "1qyiii6x9b89i4pd4yi2zd23aabpmnpj18gqi5va0zy0l8r7kknr"))))
19471 (properties `((upstream-name . "mlapi")))
19472 (build-system r-build-system)
19474 (list r-matrix r-r6))
19477 (home-page "https://cran.r-project.org/package=mlapi")
19478 (synopsis "Abstract classes for building scikit-learn like API")
19480 "This package provides R6 abstract classes for building machine learning
19481 models with a scikit-learn like API. Scikit-learn is a popular module for the
19482 Python programming language whose design became a de facto standard in
19483 industry for machine learning tasks.")
19484 (license license:expat)))
19486 (define-public r-float
19493 (uri (cran-uri "float" version))
19496 "0m7bf3548vlgkk1c78jyrgj72ngwg0gsccap2iqinm3l3qrm4zbs"))))
19497 (properties `((upstream-name . "float")))
19498 (build-system r-build-system)
19501 (home-page "https://github.com/wrathematics/float")
19502 (synopsis "32-bit floats")
19504 "R comes with a suite of utilities for linear algebra with
19505 \"numeric\" (double precision) vectors/matrices. However, sometimes single
19506 precision (or less!) is more than enough for a particular task. This package
19507 extends R's linear algebra facilities to include 32-bit float (single
19508 precision) data. Float vectors/matrices have half the precision of their
19509 \"numeric\"-type counterparts but are generally faster to numerically operate
19510 on, for a performance vs accuracy trade-off.")
19511 (license license:bsd-2)))
19513 (define-public r-rsparse
19520 (uri (cran-uri "rsparse" version))
19523 "0d05h47j29zipyxbkv9cwzv2dzj894z6hh9dqfhwswwjbv6ciwpq"))))
19524 (properties `((upstream-name . "rsparse")))
19525 (build-system r-build-system)
19535 (home-page "https://github.com/rexyai/rsparse")
19536 (synopsis "Statistical learning on sparse matrices")
19538 "This package implements many algorithms for statistical learning on
19539 sparse matrices: matrix factorizations, matrix completion, elastic net
19540 regressions, factorization machines. The rsparse package also enhances the
19541 Matrix package by providing methods for multithreaded <sparse, dense> matrix
19542 products and native slicing of the sparse matrices in @dfn{Compressed Sparse
19543 Row} (CSR) format.")
19544 (license license:gpl2+)))
19546 (define-public r-text2vec
19548 (name "r-text2vec")
19553 (uri (cran-uri "text2vec" version))
19556 "0bisr31051hnshw26rp9r4bm8ksr977dl9k1d3fb1x79pq5aa2pi"))))
19557 (properties `((upstream-name . "text2vec")))
19558 (build-system r-build-system)
19571 (home-page "http://text2vec.org")
19572 (synopsis "Text mining framework for R")
19574 "This package provides fast and memory-friendly tools for text
19575 vectorization, topic modeling (LDA, LSA), word embeddings (GloVe),
19576 similarities. It provides a source-agnostic streaming API, which allows
19577 researchers to perform analysis of collections of documents which are larger
19578 than available RAM. All core functions are parallelized to benefit from
19579 multicore machines.")
19580 (license license:gpl2+)))
19582 (define-public r-mcmcpack
19584 (name "r-mcmcpack")
19589 (uri (cran-uri "MCMCpack" version))
19592 "1cwdjn43b9hxpxf9mnas583myhk6r2258mh57f0zsc8bd4hbl56b"))))
19593 (properties `((upstream-name . "MCMCpack")))
19594 (build-system r-build-system)
19596 (list r-coda r-lattice r-mass r-mcmc r-quantreg))
19597 (home-page "https://cran.r-project.org/package=MCMCpack")
19598 (synopsis "Markov Chain Monte Carlo (MCMC) package")
19600 "This package contains functions to perform Bayesian inference using
19601 posterior simulation for a number of statistical models. Most simulation is
19602 done in compiled C++ written in the Scythe Statistical Library. All models
19603 return @code{coda} @code{mcmc} objects that can then be summarized using the
19604 @code{coda} package. Some useful utility functions such as density functions,
19605 pseudo-random number generators for statistical distributions, a general
19606 purpose Metropolis sampling algorithm, and tools for visualization are
19608 (license license:gpl3)))
19610 (define-public r-xmlparsedata
19612 (name "r-xmlparsedata")
19617 (uri (cran-uri "xmlparsedata" version))
19620 "1c6bnz3ng1qw7sfip8wq3a4dn36a4d6rbja0sadn0a4pbsmk8q3n"))))
19621 (properties `((upstream-name . "xmlparsedata")))
19622 (build-system r-build-system)
19623 (home-page "https://github.com/r-lib/xmlparsedata#readme")
19624 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
19626 "This package provides tools to convert the output of
19627 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
19628 @code{XPath}, and is easier to manipulate in general.")
19629 (license license:expat)))
19631 (define-public r-cyclocomp
19633 (name "r-cyclocomp")
19638 (uri (cran-uri "cyclocomp" version))
19641 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
19642 (properties `((upstream-name . "cyclocomp")))
19643 (build-system r-build-system)
19645 (list r-callr r-crayon r-desc r-remotes r-withr))
19646 (home-page "https://github.com/MangoTheCat/cyclocomp")
19647 (synopsis "Cyclomatic complexity of R code")
19649 "Cyclomatic complexity is a software metric, used to indicate the
19650 complexity of a program. It is a quantitative measure of the number of
19651 linearly independent paths through a program's source code. This package
19652 provides tools to compute this metric.")
19653 (license license:expat)))
19655 (define-public r-lintr
19662 (uri (cran-uri "lintr" version))
19665 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
19666 (properties `((upstream-name . "lintr")))
19667 (build-system r-build-system)
19681 (home-page "https://github.com/jimhester/lintr")
19682 (synopsis "Linter for R code")
19683 (description "This package checks adherence to a given style, syntax
19684 errors and possible semantic issues. It supports on the fly checking of R
19685 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
19686 (license license:expat)))
19688 (define-public r-sctransform
19690 (name "r-sctransform")
19695 (uri (cran-uri "sctransform" version))
19698 "0aqbcarsvvzkh5h4i65f08y4b8dfcs3zi62hmvfy24gj81f15bw3"))))
19699 (build-system r-build-system)
19714 (home-page "https://github.com/ChristophH/sctransform")
19715 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
19717 "This package provides a normalization method for single-cell UMI count
19718 data using a variance stabilizing transformation. The transformation is based
19719 on a negative binomial regression model with regularized parameters. As part
19720 of the same regression framework, this package also provides functions for
19721 batch correction, and data correction.")
19722 (license license:gpl3)))
19724 (define-public r-styler
19731 (uri (cran-uri "styler" version))
19734 "1ki260ga0jrmayhdlx2sl788yp5kkmi4wyl32nmvvyb55sng6j9y"))))
19735 (build-system r-build-system)
19736 ;; This is needed by R.cache.
19739 (modify-phases %standard-phases
19740 (add-after 'unpack 'set-HOME
19741 (lambda _ (setenv "HOME" "/tmp"))))))
19754 (home-page "https://github.com/r-lib/styler")
19755 (synopsis "Non-invasive pretty printing of R code")
19757 "This is a package for pretty-printing R code without changing the user's
19758 formatting intent.")
19759 (license license:gpl3)))
19761 (define-public r-scrime
19768 (uri (cran-uri "scrime" version))
19771 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
19772 (build-system r-build-system)
19773 (home-page "https://cran.r-project.org/web/packages/scrime/")
19774 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
19776 "This package provides tools for the analysis of high-dimensional data
19777 developed/implemented at the group \"Statistical Complexity Reduction In
19778 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
19779 the functions can also be applied to other types of categorical data.")
19780 (license license:gpl2)))
19782 (define-public r-pbmcapply
19784 (name "r-pbmcapply")
19789 (uri (cran-uri "pbmcapply" version))
19792 "1p8jf7c4k45482w72sr0jw4jkz787krrxai3sl6jz5l4lda2iz3z"))))
19793 (build-system r-build-system)
19794 (home-page "https://github.com/kvnkuang/pbmcapply")
19795 (synopsis "Track the progress of apply procedures with a progress bar")
19797 "This light-weight package helps you track and visualize the progress of
19798 parallel versions of vectorized R functions of the @code{mc*apply} family.")
19799 (license license:expat)))
19801 (define-public r-blme
19808 (uri (cran-uri "blme" version))
19811 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7"))))
19812 (build-system r-build-system)
19813 (propagated-inputs (list r-lme4))
19814 (home-page "https://github.com/vdorie/blme")
19815 (synopsis "Bayesian linear mixed-effects models")
19817 "This package provides tools for maximum a posteriori estimation for
19818 linear and generalized linear mixed-effects models in a Bayesian setting. It
19819 extends the lme4 package.")
19820 (license license:gpl2+)))
19822 (define-public r-batchtools
19824 (name "r-batchtools")
19829 (uri (cran-uri "batchtools" version))
19832 "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52"))))
19833 (build-system r-build-system)
19849 (home-page "https://github.com/mllg/batchtools")
19850 (synopsis "Tools for computation on batch systems")
19852 "As a successor of the packages BatchJobs and BatchExperiments, this
19853 package provides a parallel implementation of the Map function for high
19854 performance computing systems managed by various schedulers. A multicore and
19855 socket mode allow the parallelization on a local machines, and multiple
19856 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
19857 the package provides an abstraction mechanism to define large-scale computer
19858 experiments in a well-organized and reproducible way.")
19859 (license license:lgpl3)))
19861 (define-public r-clue
19868 (uri (cran-uri "clue" version))
19871 "0cfw2k1kh4a8imdv7b5qw977xd6indampsabhfldj3rqrqb1ncbi"))))
19872 (build-system r-build-system)
19873 (propagated-inputs (list r-cluster))
19874 (home-page "https://cran.r-project.org/web/packages/clue/")
19875 (synopsis "Tools for analyzing cluster ensembles")
19876 (description "Cluster ensembles are collections of individual solutions to
19877 a given clustering problem which are useful or necessary to consider in a wide
19878 range of applications. This R package provides an extensible computational
19879 environment for creating and analyzing cluster ensembles, with basic data
19880 structures for representing partitions and hierarchies, and facilities for
19881 computing on them, including methods for measuring proximity and obtaining
19882 consensus and secondary clusterings.")
19883 (license license:gpl2)))
19885 (define-public r-sitmo
19892 (uri (cran-uri "sitmo" version))
19895 "1hm89zi38ldgbskyx1cn7gm87yqy7zrxli8q05a36y1ndvazi3j4"))))
19896 (build-system r-build-system)
19897 (propagated-inputs (list r-rcpp))
19900 (home-page "https://github.com/coatless/sitmo/")
19901 (synopsis "Parallel pseudo random number generator header files")
19903 "This package provides two high quality and fast PPRNGs that may be used
19904 in an OpenMP parallel environment. In addition, there is a generator for one
19905 dimensional low-discrepancy sequence.")
19906 (license license:expat)))
19908 (define-public r-dqrng
19915 (uri (cran-uri "dqrng" version))
19918 "1fwsldqcri2lccna4icbmmlqic3w4xyjm7rn0xmikrsw4kzapvjb"))))
19919 (build-system r-build-system)
19921 (list r-bh r-rcpp r-sitmo))
19924 (home-page "https://www.daqana.org/dqrng")
19925 (synopsis "Fast pseudo random number generators")
19927 "Several fast random number generators are provided as C++ header-only
19928 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
19929 Additionally, fast functions for generating random numbers according to a
19930 uniform, normal and exponential distribution are included. The latter two use
19931 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
19932 functions are exported to R and as a C++ interface and are enabled for use
19933 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
19934 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
19935 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
19936 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
19937 ;; whole is distributed under the terms of the AGPL 3.
19938 (license license:agpl3)))
19940 (define-public r-ingredients
19942 (name "r-ingredients")
19947 (uri (cran-uri "ingredients" version))
19950 "11bv4l4fn9kr7y2nfzrwnaya8fi9w3nwcm9vzlqb7dva83rkqbsc"))))
19951 (properties `((upstream-name . "ingredients")))
19952 (build-system r-build-system)
19954 (list r-ggplot2 r-gridextra r-scales))
19955 (native-inputs (list r-knitr))
19956 (home-page "https://ModelOriented.github.io/ingredients/")
19957 (synopsis "Effects and importances of model ingredients")
19959 "This is a collection of tools for assessment of feature importance and
19960 feature effects. Key functions are:
19963 @item @code{feature_importance()} for assessment of global level feature
19965 @item @code{ceteris_paribus()} for calculation of the what-if plots,
19966 @item @code{partial_dependence()} for partial dependence plots,
19967 @item @code{conditional_dependence()} for conditional dependence plots,
19968 @item @code{accumulated_dependence()} for accumulated local effects plots,
19969 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
19970 aggregation of ceteris paribus profiles,
19971 @item generic @code{print()} and @code{plot()} for better usability of
19972 selected explainers,
19973 @item generic @code{plotD3()} for interactive, D3 based explanations, and
19974 @item generic @code{describe()} for explanations in natural language.
19976 (license license:gpl3)))
19978 (define-public r-ibreakdown
19980 (name "r-ibreakdown")
19985 (uri (cran-uri "iBreakDown" version))
19988 "00jzrndb3ahsv6ihp2pvs732n9cc944m83vdinrl9v1pxd82prkh"))))
19989 (properties `((upstream-name . "iBreakDown")))
19990 (build-system r-build-system)
19991 (propagated-inputs (list r-ggplot2))
19992 (native-inputs (list r-knitr))
19993 (home-page "https://ModelOriented.github.io/iBreakDown/")
19994 (synopsis "Model agnostic instance level variable attributions")
19996 "This package provides a model agnostic tool for decomposition of
19997 predictions from black boxes. It supports additive attributions and
19998 attributions with interactions. The Break Down Table shows contributions of
19999 every variable to a final prediction. The Break Down Plot presents variable
20000 contributions in a concise graphical way. This package works for
20001 classification and regression models.")
20002 (license license:gpl3)))
20004 (define-public r-dae
20011 (uri (cran-uri "dae" version))
20014 "0mq94ah21p1glvsbvdmi2p7nlgz1bvq7w3rz2z3mdqq18kz6nkjw"))))
20015 (build-system r-build-system)
20017 (list r-ggplot2 r-plyr))
20019 (list r-r-rsp)) ; vignette builder
20020 (home-page "http://chris.brien.name")
20021 (synopsis "Functions useful in the design and ANOVA of experiments")
20023 "This package provides functions useful in the design and ANOVA of
20024 experiments. The content falls into the following groupings:
20028 @item factor manipulation functions,
20029 @item design functions,
20030 @item ANOVA functions,
20031 @item matrix functions,
20032 @item projector and canonical efficiency functions, and
20033 @item miscellaneous functions.
20036 There is a vignette called @code{DesignNotes} describing how to use the design
20037 functions for randomizing and assessing designs. The ANOVA functions
20038 facilitate the extraction of information when the @code{Error} function has
20039 been used in the call to @code{aov}.")
20040 (license license:gpl2)))
20042 (define-public r-dalex
20049 (uri (cran-uri "DALEX" version))
20052 "0mcdd2bd8zlsz7x174g87dp8vy4wc06w58dyr27f6lgv9shzya8j"))))
20053 (properties `((upstream-name . "DALEX")))
20054 (build-system r-build-system)
20056 (list r-ggplot2 r-ibreakdown r-ingredients))
20057 (home-page "https://pbiecek.github.io/DALEX/")
20058 (synopsis "Descriptive machine learning explanations")
20060 "Machine Learning models are widely used and have various applications in
20061 classification or regression. Models created with boosting, bagging, stacking
20062 or similar techniques are often used due to their high performance, but such
20063 black-box models usually lack interpretability. The DALEX package contains
20064 various explainers that help to understand the link between input variables
20065 and model output.")
20066 ;; Any version of the GPL
20067 (license license:gpl3+)))
20069 (define-public r-enrichr
20076 (uri (cran-uri "enrichR" version))
20079 "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3"))))
20080 (properties `((upstream-name . "enrichR")))
20081 (build-system r-build-system)
20083 (list r-ggplot2 r-httr r-rjson))
20086 (home-page "https://cran.r-project.org/web/packages/enrichR/")
20087 (synopsis "R Interface to Enrichr database for analyzing gene sets")
20089 "This package provides an R interface to all Enrichr databases, a
20090 web-based tool for analyzing gene sets and returns any enrichment of common
20091 annotated biological functions.")
20092 (license license:gpl2+)))
20094 (define-public r-plot3d
20101 (uri (cran-uri "plot3D" version))
20104 "1h59zlsyzbjylaziwavppl9bjmnba4iiq34772y3dys6fqclajnh"))))
20105 (properties `((upstream-name . "plot3D")))
20106 (build-system r-build-system)
20107 (propagated-inputs (list r-misc3d))
20108 (home-page "https://cran.r-project.org/web/packages/plot3D")
20109 (synopsis "Plot multi-dimensional data")
20111 "This package provides functions for viewing 2D and 3D data, including
20112 perspective plots, slice plots, surface plots, scatter plots, etc. It
20113 includes data sets from oceanography.")
20114 (license license:gpl3+)))
20116 (define-public r-ggfortify
20118 (name "r-ggfortify")
20123 (uri (cran-uri "ggfortify" version))
20126 "038m74azpy43869ax1yi6wxbl1kr59iaxl8raiikjg749vcx6njw"))))
20127 (build-system r-build-system)
20138 (home-page "https://github.com/sinhrks/ggfortify")
20139 (synopsis "Data visualization tools for statistical analysis results")
20141 "This package provides unified plotting tools for statistics commonly
20142 used, such as GLM, time series, PCA families, clustering and survival
20143 analysis. The package offers a single plotting interface for these analysis
20144 results and plots in a unified style using the @code{ggplot2} package.")
20145 (license license:gpl2)))
20147 (define-public r-refmanager
20149 (name "r-refmanager")
20154 (uri (cran-uri "RefManageR" version))
20157 "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps"))))
20158 (properties `((upstream-name . "RefManageR")))
20159 (build-system r-build-system)
20169 (home-page "https://github.com/ropensci/RefManageR/")
20170 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
20172 "This package provides tools for importing and working with bibliographic
20173 references. It greatly enhances the @code{bibentry} class by providing a
20174 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
20175 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
20176 by various formats for name lists (author by last names, translator by full
20177 names, etc.). Entries can be updated, combined, sorted, printed in a number
20178 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
20179 into R and converted to @code{BibEntry} objects.")
20180 ;; Any of these licenses may be picked.
20181 (license (list license:gpl2 license:gpl3 license:bsd-3))))
20183 (define-public r-citr
20190 (uri (cran-uri "citr" version))
20193 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
20194 (build-system r-build-system)
20205 (home-page "https://github.com/crsh/citr")
20206 (synopsis "RStudio add-in to insert Markdown citations")
20208 "This package provides functions and an RStudio add-in that search a
20209 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
20210 the current document.")
20211 (license license:expat)))
20213 (define-public r-xgboost
20216 (version "1.6.0.1")
20220 (uri (cran-uri "xgboost" version))
20223 "1gafjv6vcpny03lqw8s68xszalsylniavaqwsbzh46vyk4h9mscs"))))
20224 (build-system r-build-system)
20226 (list r-data-table r-jsonlite r-matrix))
20229 (home-page "https://github.com/dmlc/xgboost")
20230 (synopsis "Extreme gradient boosting")
20232 "This package provides an R interface to Extreme Gradient Boosting, which
20233 is an efficient implementation of the gradient boosting framework from Chen
20234 and Guestrin (2016). The package includes efficient linear model solver and
20235 tree learning algorithms. The package can automatically do parallel
20236 computation on a single machine. It supports various objective functions,
20237 including regression, classification and ranking. The package is made to be
20238 extensible, so that users are also allowed to define their own objectives
20240 (license license:asl2.0)))
20242 (define-public r-umap
20245 (version "0.2.8.0")
20249 (uri (cran-uri "umap" version))
20252 "0aiarnzc8gl932gi8fxd9f9rshaiwh9vj570l135fkiaja3q2wap"))))
20253 (build-system r-build-system)
20255 (list r-matrix r-openssl r-rcpp r-reticulate r-rspectra))
20258 (home-page "https://github.com/tkonopka/umap")
20259 (synopsis "Uniform manifold approximation and projection")
20261 "Uniform manifold approximation and projection is a technique for
20262 dimension reduction. This package provides an interface to the UMAP algorithm
20263 in R, including a translation of the original algorithm into R.")
20264 (license license:expat)))
20266 (define-public r-uwot
20273 (uri (cran-uri "uwot" version))
20276 "06ylzxmdh8jipbrzgqaiivd2lnqmbcva41cyvc0iyals6vqr1ksg"))))
20277 (build-system r-build-system)
20287 (home-page "https://github.com/jlmelville/uwot")
20288 (synopsis "Uniform manifold approximation and projection")
20290 "This package provides an implementation of the Uniform Manifold
20291 Approximation and Projection dimensionality reduction by McInnes et
20292 al. (2018). It also provides means to transform new data and to carry out
20293 supervised dimensionality reduction. An implementation of the related
20294 LargeVis method of Tang et al. (2016) is also provided.")
20295 (license license:gpl3)))
20297 (define-public r-kableextra
20299 (name "r-kableextra")
20304 (uri (cran-uri "kableExtra" version))
20307 "1c5vzy95cbz36jwyssr927qicrayifinv861rvnmg4nghb1gl7q9"))))
20308 (properties `((upstream-name . "kableExtra")))
20309 (build-system r-build-system)
20327 (home-page "https://haozhu233.github.io/kableExtra/")
20328 (synopsis "Construct complex tables with pipe syntax")
20330 "Build complex HTML or LaTeX tables using @code{kable()} from
20331 @code{knitr} and the piping syntax from @code{magrittr}. The function
20332 @code{kable()} is a light weight table generator coming from @code{knitr}.
20333 This package simplifies the way to manipulate the HTML or LaTeX codes
20334 generated by @code{kable()} and allows users to construct complex tables and
20335 customize styles using a readable syntax.")
20336 (license license:expat)))
20338 (define-public r-glasso
20345 (uri (cran-uri "glasso" version))
20347 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
20348 (build-system r-build-system)
20349 (native-inputs (list gfortran))
20350 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
20351 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
20353 "This is a package for estimation of a sparse inverse covariance matrix
20354 using a lasso (L1) penalty. Facilities are provided for estimates along a
20355 path of values for the regularization parameter.")
20356 (license license:gpl2)))
20358 (define-public r-rhpcblasctl
20360 (name "r-rhpcblasctl")
20361 (version "0.21-247.1")
20365 (uri (cran-uri "RhpcBLASctl" version))
20368 "0scpr6jq25xx7wmqyc380ann4h536ll0g7wblikk25yqvpamzrav"))))
20369 (properties `((upstream-name . "RhpcBLASctl")))
20370 (build-system r-build-system)
20371 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
20372 (synopsis "Control the number of threads on BLAS")
20374 "This package allows you to control the number of threads the BLAS
20375 library uses. It is also possible to control the number of threads in
20377 (license license:agpl3+)))
20379 (define-public r-lda
20386 (uri (cran-uri "lda" version))
20389 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
20390 (build-system r-build-system)
20391 (home-page "https://cran.r-project.org/web/packages/lda/")
20392 (synopsis "Collapsed Gibbs sampling methods for topic models")
20394 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
20395 related models. This includes (but is not limited to) sLDA, corrLDA, and the
20396 mixed-membership stochastic blockmodel. Inference for all of these models is
20397 implemented via a fast collapsed Gibbs sampler written in C. Utility
20398 functions for reading/writing data typically used in topic models, as well as
20399 tools for examining posterior distributions are also included.")
20400 ;; Any version of the LGPL
20401 (license license:lgpl3+)))
20403 (define-public r-rann-l1
20410 (uri (cran-uri "RANN.L1" version))
20413 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
20414 (properties `((upstream-name . "RANN.L1")))
20415 (build-system r-build-system)
20416 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
20417 (synopsis "Fast nearest neighbour search using L1 metric")
20419 "This package provides tools to find the k nearest neighbours for every
20420 point in a given dataset in O(N log N) time using Arya and Mount's ANN
20421 library. There is support for approximate as well as exact searches, fixed
20422 radius searches and @code{bd} as well as @code{kd} trees. The distance is
20423 computed using the L1 (Manhattan, taxicab) metric.")
20424 (license license:gpl3+)))
20426 (define-public r-leiden
20433 (uri (cran-uri "leiden" version))
20436 "1gg24afwbz818041bhmswmdqgxv35zp5h1i1102p58aaiis8dkna"))))
20437 (properties `((upstream-name . "leiden")))
20438 (build-system r-build-system)
20440 (list r-igraph r-matrix r-reticulate))
20443 (home-page "https://github.com/TomKellyGenetics/leiden")
20444 (synopsis "R implementation of Leiden clustering algorithm")
20446 "This package implements the Python @code{leidenalg} module to be called
20447 in R. It enables clustering using the Leiden algorithm for partitioning a
20448 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
20449 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
20450 (license license:gpl3)))
20452 (define-public r-patchwork
20454 (name "r-patchwork")
20459 (uri (cran-uri "patchwork" version))
20462 "10glgkf58lcykcwda1hj6xdps02m3i247qynk6s2jmwljagps3fg"))))
20463 (build-system r-build-system)
20465 (list r-ggplot2 r-gtable))
20468 (home-page "https://github.com/thomasp85/patchwork")
20469 (synopsis "Compose ggplot2 plots")
20471 "The @code{ggplot2} package provides a strong API for sequentially
20472 building up a plot, but does not concern itself with composition of multiple
20473 plots. Patchwork is a package that expands the API to allow for arbitrarily
20474 complex composition of plots by providing mathematical operators for combining
20476 (license license:expat)))
20478 (define-public r-liger
20485 (uri (git-reference
20486 (url "https://github.com/MacoskoLab/liger")
20487 (commit (string-append "v" version))))
20488 (file-name (git-file-name name version))
20491 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
20492 (modules '((guix build utils)))
20495 (delete-file "inst/java/ModularityOptimizer.jar")
20497 (build-system r-build-system)
20500 (modify-phases %standard-phases
20501 (add-after 'unpack 'build-java-part
20502 (lambda* (#:key inputs #:allow-other-keys)
20503 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
20504 (for-each (lambda (file) (invoke "javac" file))
20505 (find-files "." "\\.java$"))
20506 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
20507 (find-files "." "\\.class$"))
20531 `(("jdk" ,icedtea "jdk")
20532 ;; See https://github.com/MacoskoLab/liger/issues/96
20533 ;; The optimizer is released under the Expat license.
20537 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
20540 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
20542 ("r-knitr" ,r-knitr))) ; for vignettes
20543 (home-page "https://github.com/MacoskoLab/liger")
20544 (synopsis "Integrate and analyze multiple single-cell datasets")
20546 "LIGER is a package for integrating and analyzing multiple single-cell
20547 datasets, developed and maintained by the Macosko lab. It relies on
20548 integrative non-negative matrix factorization to identify shared and
20549 dataset-specific factors.")
20550 (license license:gpl3)))
20552 (define-public r-harmony
20559 (uri (git-reference
20560 (url "https://github.com/immunogenomics/harmony")
20562 (file-name (git-file-name name version))
20565 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
20566 (modules '((guix build utils)))
20569 (for-each delete-file '("config.status" "configure"))
20571 (build-system r-build-system)
20586 (home-page "https://github.com/immunogenomics/harmony")
20587 (synopsis "Integration of single cell sequencing data")
20589 "This package provides an implementation of the Harmony algorithm for
20590 single cell integration, described in Korsunsky et al
20591 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
20592 function and interfaces to external frameworks.")
20593 (license license:gpl3)))
20595 (define-public r-covr
20602 (uri (cran-uri "covr" version))
20604 (base32 "0v5cv3cw2kpdr6wxmkbd3wclavr17zipypdcb10hhmpa4cvgqk55"))))
20605 (properties `((upstream-name . "covr")))
20606 (build-system r-build-system)
20616 (list r-knitr)) ; for vignettes
20617 (home-page "https://github.com/r-lib/covr")
20618 (synopsis "Test coverage for R packages")
20620 "Thisp package enables you to track and report code coverage for your
20621 package and (optionally) upload the results to a coverage service. Code
20622 coverage is a measure of the amount of code being exercised by a set of tests.
20623 It is an indirect measure of test quality and completeness. This package is
20624 compatible with any testing methodology or framework and tracks coverage of
20625 both R code and compiled C/C++/FORTRAN code.")
20626 (license license:gpl3)))
20628 (define-public r-systemfonts
20630 (name "r-systemfonts")
20635 (uri (cran-uri "systemfonts" version))
20638 "1h44bal845jp7ya8i7ff1kz1n3wklkb00jk6hb9lgwa2p5snqxpg"))))
20639 (properties `((upstream-name . "systemfonts")))
20640 (build-system r-build-system)
20644 (list fontconfig freetype zlib))
20646 (list pkg-config r-knitr))
20647 (home-page "https://github.com/r-lib/systemfonts")
20648 (synopsis "System native font finding")
20650 "This package provides system native access to the font catalogue. As
20651 font handling varies between systems it is difficult to correctly locate
20652 installed fonts across different operating systems. The 'systemfonts' package
20653 provides bindings to the native libraries for finding font files that can then
20654 be used further by e.g. graphic devices.")
20655 (license license:expat)))
20657 (define-public r-graphlayouts
20659 (name "r-graphlayouts")
20664 (uri (cran-uri "graphlayouts" version))
20667 "1l7gkn0r1ijllv3w7cbwcbi0jggs7wlkq9b2lykprng4g1kjc96p"))))
20668 (properties `((upstream-name . "graphlayouts")))
20669 (build-system r-build-system)
20671 (list r-igraph r-rcpp r-rcpparmadillo))
20672 (home-page "https://github.com/schochastics/graphlayouts")
20673 (synopsis "Additional layout algorithms for network visualizations")
20675 "This package provides several layout algorithms to visualize networks
20676 which are not part of the igraph library. Most are based on the concept of
20677 stress majorization by Gansner et al. (2004)
20678 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
20679 emphasize hidden group structures in networks or focus on specific nodes.")
20680 (license license:expat)))
20682 (define-public r-terra
20689 (uri (cran-uri "terra" version))
20692 "075azi23gi1b1jxm3s1f1hpc6in7qz4fp38shq9pflfnzbs8ib9w"))))
20693 (properties `((upstream-name . "terra")))
20694 (build-system r-build-system)
20699 sqlite ; needed for proj
20705 (home-page "https://rspatial.org/terra")
20706 (synopsis "Spatial data analysis")
20708 "This package provides methods for spatial data analysis, especially
20709 raster data. The included methods allow for low-level data manipulation as
20710 well as high-level global, local, zonal, and focal computation. The predict
20711 and interpolate methods facilitate the use of regression type (interpolation,
20712 machine learning) models for spatial prediction. Processing of very large
20713 files is supported.")
20714 (license license:gpl3+)))
20716 (define-public r-tidygraph
20718 (name "r-tidygraph")
20723 (uri (cran-uri "tidygraph" version))
20726 "0dmdff3bkg53xn0c51xd6k2d9c7l250x1lhl5z3libf533dw5g9g"))))
20727 (properties `((upstream-name . "tidygraph")))
20728 (build-system r-build-system)
20740 (home-page "https://github.com/thomasp85/tidygraph")
20741 (synopsis "Tidy API for graph manipulation")
20743 "This package provides a graph implementation that can be thought of as
20744 two tidy data frames describing node and edge data respectively. It provides
20745 an approach to manipulate these two virtual data frames using the API defined
20746 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
20747 common graph algorithms.")
20748 (license license:expat)))
20750 (define-public r-soupx
20751 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
20755 (version (git-version "0.3.1" revision commit))
20759 (uri (git-reference
20760 (url "https://github.com/constantAmateur/SoupX")
20762 (file-name (git-file-name name version))
20765 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
20766 (properties `((upstream-name . "SoupX")))
20767 (build-system r-build-system)
20769 (list r-ggplot2 r-matrix r-seurat))
20770 (home-page "https://github.com/constantAmateur/SoupX")
20771 (synopsis "Single cell mRNA Soup eXterminator")
20773 "This package provides a package for quantifying, profiling and
20774 removing cell free mRNA contamination (the \"soup\") from droplet based single
20775 cell RNA-seq experiments.")
20776 (license license:gpl2))))
20778 (define-public r-assertr
20785 (uri (cran-uri "assertr" version))
20788 "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650"))))
20789 (build-system r-build-system)
20791 (list r-dplyr r-mass r-rlang))
20793 (list r-knitr)) ; needed for vignette
20794 (home-page "https://github.com/ropensci/assertr")
20795 (synopsis "Assertive programming for R analysis pipelines")
20797 "This package provides functionality to assert conditions that have to be
20798 met so that errors in data used in analysis pipelines can fail quickly. It is
20799 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
20801 (license license:expat)))
20803 (define-public r-parameters
20805 (name "r-parameters")
20810 (uri (cran-uri "parameters" version))
20813 "0zcypf3fi745pa18vpqgx3q9izhkkmpcvcv1gv8pxawyq9mw8ag9"))))
20814 (properties `((upstream-name . "parameters")))
20815 (build-system r-build-system)
20817 (list r-bayestestr r-datawizard r-insight))
20820 (home-page "https://cran.r-project.org/web/packages/parameters")
20821 (synopsis "Processing of model parameters")
20823 "This package provides utilities for processing the parameters of various
20824 statistical models. Beyond computing p values, CIs, and other indices for a
20825 wide variety of models, this package implements features like standardization
20826 or bootstrapping of parameters and models, feature reduction (feature
20827 extraction and variable selection) as well as conversion between indices of
20829 (license license:gpl3)))
20831 (define-public r-rgdal
20838 (uri (cran-uri "rgdal" version))
20840 (base32 "1vbkyhw8nd7dw1r53qisphav31x6zvpbzilvnlvbjbj9hzhs90s5"))))
20841 (properties `((upstream-name . "rgdal")))
20842 (build-system r-build-system)
20844 (list gdal proj zlib))
20848 (list pkg-config r-knitr))
20849 (home-page "http://rgdal.r-forge.r-project.org")
20850 (synopsis "Bindings for the Geospatial Data Abstraction Library")
20852 "This package provides bindings to the Geospatial Data Abstraction
20853 Library (GDAL) and access to projection/transformation operations from the
20855 (license license:gpl2+)))
20857 (define-public r-insol
20864 (uri (cran-uri "insol" version))
20867 "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3"))))
20868 (properties `((upstream-name . "insol")))
20869 (build-system r-build-system)
20874 (home-page "https://meteoexploration.com/R/insol/index.html")
20875 (synopsis "Tools for calculating solar radiation")
20877 "This package provides functions to compute insolation on tilted
20878 surfaces, computes atmospheric transmittance and related parameters such as:
20879 Earth radius vector, declination, sunset and sunrise, daylength, equation of
20880 time, vector in the direction of the sun, vector normal to surface, and some
20881 atmospheric physics.")
20882 (license license:gpl2+)))
20884 (define-public r-lifecycle
20886 (name "r-lifecycle")
20891 (uri (cran-uri "lifecycle" version))
20894 "183v1z1h037pvsgrj6vakpwhnhsr29hsw8p16k59dgpi00f6x9qx"))))
20895 (properties `((upstream-name . "lifecycle")))
20896 (build-system r-build-system)
20898 (list r-glue r-rlang))
20900 (list r-knitr)) ; for vignettes
20901 (home-page "https://github.com/r-lib/lifecycle")
20902 (synopsis "Manage the life cycle of your package functions")
20904 "Manage the life cycle of your exported functions with shared
20905 conventions, documentation badges, and non-invasive deprecation warnings. The
20906 lifecycle package defines four development stages (experimental, maturing,
20907 stable, and questioning) and three deprecation stages (soft-deprecated,
20908 deprecated, and defunct). It makes it easy to insert badges corresponding to
20909 these stages in your documentation. Usage of deprecated functions are
20910 signalled with increasing levels of non-invasive verbosity.")
20911 (license license:gpl3)))
20913 (define-public r-assertable
20915 (name "r-assertable")
20920 (uri (cran-uri "assertable" version))
20923 "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4"))))
20924 (build-system r-build-system)
20926 (list r-data-table))
20929 (home-page "https://cran.r-project.org/web/packages/assertable/")
20930 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
20931 (description "This package provides simple, flexible assertions on
20932 data.frame or data.table objects with verbose output for vetting. While other
20933 assertion packages apply towards more general use-cases, @code{assertable} is
20934 tailored towards tabular data. It includes functions to check variable names
20935 and values, whether the dataset contains all combinations of a given set of
20936 unique identifiers, and whether it is a certain length. In addition,
20937 @code{assertable} includes utility functions to check the existence of target
20938 files and to efficiently import multiple tabular data files into one
20940 (license license:gpl3)))
20942 (define-public r-quadprog
20944 (name "r-quadprog")
20949 (uri (cran-uri "quadprog" version))
20951 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
20952 (build-system r-build-system)
20955 (home-page "https://cran.r-project.org/web/packages/quadprog")
20956 (synopsis "Functions to solve quadratic programming problems")
20958 "This package contains routines and documentation for solving quadratic
20959 programming problems.")
20960 (license license:gpl3+)))
20962 (define-public r-desolve
20969 (uri (cran-uri "deSolve" version))
20971 (base32 "1bfr4w760nr7mjhpmf32z39swr6isnn1665cld2d1pdgx8b0yrvl"))))
20972 (properties `((upstream-name . "deSolve")))
20973 (build-system r-build-system)
20976 (home-page "https://desolve.r-forge.r-project.org/")
20977 (synopsis "Solvers for initial value problems of differential equations")
20978 (description "This package provides functions that solve initial value
20979 problems of a system of first-order @dfn{ordinary differential
20980 equations} (ODE), of @dfn{partial differential equations} (PDE), of
20981 @dfn{differential algebraic equations} (DAE), and of delay differential
20982 equations. The functions provide an interface to the FORTRAN functions
20983 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
20984 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
20985 C-implementation of solvers of the Runge-Kutta family with fixed or variable
20986 time steps. The package contains routines designed for solving ODEs resulting
20987 from 1-D, 2-D and 3-D partial differential equations that have been converted
20988 to ODEs by numerical differencing.")
20989 (license license:gpl2+)))
20991 (define-public r-pmcmrplus
20993 (name "r-pmcmrplus")
20998 (uri (cran-uri "PMCMRplus" version))
21000 (base32 "16m1pdrzjq9vnx5v7zv56mz9r1205rkw92883cxaqbvdpds6dhqy"))))
21001 (properties `((upstream-name . "PMCMRplus")))
21002 (build-system r-build-system)
21003 (inputs (list gmp))
21013 (native-inputs (list gfortran r-knitr))
21014 (home-page "https://cran.r-project.org/package=PMCMRplus")
21015 (synopsis "Calculate pairwise multiple comparisons of mean rank sums extended")
21017 "This package provides multiple pairwise tests.")
21018 (license license:gpl3+)))
21020 (define-public r-pracma
21026 (uri (cran-uri "pracma" version))
21028 (base32 "0r17siivm37k4gp253v9mlg5m7cwqp85h9kk2hbp2wkf81ad80i3"))))
21029 (build-system r-build-system)
21030 (home-page "https://cran.r-project.org/web/packages/pracma/")
21031 (synopsis "Practical numerical math functions")
21032 (description "This package provides functions for numerical analysis and
21033 linear algebra, numerical optimization, differential equations, plus some
21034 special functions. It uses Matlab function names where appropriate to simplify
21036 (license license:gpl3+)))
21038 (define-public r-subplex
21045 (uri (cran-uri "subplex" version))
21048 "19g5bd39gmcn27xdsklkzxg99x1r5v5q8zcw1iwry31qj24ivhrv"))))
21049 (build-system r-build-system)
21052 (home-page "https://cran.r-project.org/web/packages/subplex")
21053 (synopsis "Unconstrained optimization using the subplex algorithm")
21055 "This package implements the Subplex optimization algorithm.
21056 It solves unconstrained optimization problems using a simplex method on
21057 subspaces. The method is well suited for optimizing objective functions that
21058 are noisy or are discontinuous at the solution.")
21059 (license license:gpl3+)))
21061 (define-public r-txtplot
21068 (uri (cran-uri "txtplot" version))
21071 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
21072 (build-system r-build-system)
21073 (home-page "https://cran.r-project.org/web/packages/txtplot/")
21074 (synopsis "Text-based plotting")
21075 (description "This package provides functions to produce rudimentary ASCII
21076 graphics directly in the terminal window. This package provides a basic
21077 plotting function (and equivalents of curve, density, acf and barplot) as well
21078 as a boxplot function.")
21079 (license license:lgpl3+)))
21081 (define-public r-bio3d
21088 (uri (cran-uri "bio3d" version))
21091 "0x3apqxbk4lvvcnvvdsyjd9f6qh9f9qgml3ih69hl9ikj06iy0y6"))))
21092 (properties `((upstream-name . "bio3d")))
21093 (build-system r-build-system)
21094 (inputs (list zlib))
21095 (propagated-inputs (list r-rcpp))
21098 (home-page "http://thegrantlab.org/bio3d/")
21099 (synopsis "Biological structure analysis")
21101 "This package provides utilities to process, organize and explore protein
21102 structure, sequence and dynamics data. Features include the ability to read
21103 and write structure, sequence and dynamic trajectory data, perform sequence
21104 and structure database searches, data summaries, atom selection, alignment,
21105 superposition, rigid core identification, clustering, torsion analysis,
21106 distance matrix analysis, structure and sequence conservation analysis, normal
21107 mode analysis, principal component analysis of heterogeneous structure data,
21108 and correlation network analysis from normal mode and molecular dynamics data.
21109 In addition, various utility functions are provided to enable the statistical
21110 and graphical power of the R environment to work with biological sequence and
21112 (license license:gpl2+)))
21114 (define-public r-bios2cor
21116 (name "r-bios2cor")
21121 (uri (cran-uri "Bios2cor" version))
21124 "1wkj9vr33m9jilidil9jpw5rzr3pf7gkimxdvch22ks4bgkx7l1w"))))
21125 (properties `((upstream-name . "Bios2cor")))
21126 (build-system r-build-system)
21128 (list r-bigmemory r-bio3d r-circular r-igraph))
21129 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
21130 (synopsis "From biological sequences and simulations to correlation analysis")
21132 "This package provides utilities for computation and analysis of
21133 correlation/covariation in multiple sequence alignments and in side chain
21134 motions during molecular dynamics simulations. Features include the
21135 computation of correlation/covariation scores using a variety of scoring
21136 functions between either sequence positions in alignments or side chain
21137 dihedral angles in molecular dynamics simulations and utilities to analyze the
21138 correlation/covariation matrix through a variety of tools including network
21139 representation and principal components analysis. In addition, several
21140 utility functions are based on the R graphical environment to provide friendly
21141 tools for help in data interpretation.")
21142 (license license:gpl2+)))
21144 ;; This package includes minified JavaScript files. When upgrading please
21145 ;; check that there are no new minified JavaScript files.
21146 (define-public r-networkd3
21148 (name "r-networkd3")
21153 (uri (cran-uri "networkD3" version))
21156 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
21159 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
21161 (properties `((upstream-name . "networkD3")))
21162 (build-system r-build-system)
21164 `(#:modules ((guix build utils)
21165 (guix build r-build-system)
21169 (modify-phases %standard-phases
21170 (add-after 'unpack 'process-javascript
21171 (lambda* (#:key inputs #:allow-other-keys)
21172 (with-directory-excursion "inst/htmlwidgets/lib/"
21176 `((,(assoc-ref inputs "d3.v4.js")
21177 "d3-4.5.0/d3.min.js"))))
21178 (lambda (sources targets)
21179 (for-each (lambda (source target)
21180 (format #t "Processing ~a --> ~a~%"
21182 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
21183 (call-with-output-file target
21185 (dump-port minified port)))))
21186 sources targets))))
21189 `(("uglifyjs" ,node-uglify-js)
21190 ;; NOTE: Make sure that this version of d3 is still valid when
21191 ;; upgrading the package.
21195 (uri "https://d3js.org/d3.v4.js")
21198 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
21200 (list r-htmlwidgets r-igraph r-magrittr))
21201 (home-page "https://cran.r-project.org/package=networkD3")
21202 (synopsis "D3 JavaScript network graphs from R")
21204 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
21206 (license license:gpl3+)))
21208 (define-public r-aasea
21215 (uri (cran-uri "aaSEA" version))
21218 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
21219 (properties `((upstream-name . "aaSEA")))
21220 (build-system r-build-system)
21231 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
21232 (synopsis "Amino acid substitution effect analyzer")
21234 "Given a protein multiple sequence alignment, it is a daunting task to
21235 assess the effects of substitutions along sequence length. The aaSEA package
21236 is intended to help researchers to rapidly analyze property changes caused by
21237 single, multiple and correlated amino acid substitutions in proteins.")
21238 (license license:gpl3)))
21240 (define-public r-abacus
21247 (uri (cran-uri "ABACUS" version))
21250 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
21251 (properties `((upstream-name . "ABACUS")))
21252 (build-system r-build-system)
21254 (list r-ggplot2 r-shiny))
21255 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
21256 (synopsis "Apps-based activities for communicating and understanding statistics")
21258 "This package provides a set of Shiny apps for effective communication
21259 and understanding in statistics. The current version includes properties of
21260 normal distribution, properties of sampling distribution, one-sample z and t
21261 tests, two samples independent (unpaired) t test and analysis of variance.")
21262 (license license:gpl3)))
21264 (define-public r-abc-rap
21271 (uri (cran-uri "ABC.RAP" version))
21274 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
21275 (properties `((upstream-name . "ABC.RAP")))
21276 (build-system r-build-system)
21277 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
21278 (synopsis "Array-based CpG region analysis pipeline")
21280 "This package aims to identify candidate genes that are differentially
21281 methylated between cases and controls. It applies Student's t-test and delta
21282 beta analysis to identify candidate genes containing multiple CpG sites.")
21283 (license license:gpl3)))
21285 (define-public r-abcadm
21292 (uri (cran-uri "abcADM" version))
21295 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
21296 (properties `((upstream-name . "abcADM")))
21297 (build-system r-build-system)
21299 (list r-bh r-rcpp))
21300 (home-page "https://cran.r-project.org/web/packages/abcADM/")
21301 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
21303 "This package provides tools to estimate parameters of accumulated
21304 damage (load duration) models based on failure time data under a Bayesian
21305 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
21306 long-term reliability under stochastic load profiles.")
21307 (license license:gpl3)))
21309 (define-public r-rglpk
21316 (uri (cran-uri "Rglpk" version))
21319 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
21320 (properties `((upstream-name . "Rglpk")))
21321 (build-system r-build-system)
21326 (home-page "https://r-forge.r-project.org/projects/rglp/")
21327 (synopsis "R interface to the GNU Linear Programming Kit")
21329 "This package provides an R interface to the GNU Linear Programming Kit,
21330 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
21331 integer linear programming} (MILP) and other related problems.")
21333 (license (list license:gpl2 license:gpl3))))
21335 (define-public r-abcdefba
21337 (name "r-abcdefba")
21342 (uri (cran-uri "abcdeFBA" version))
21345 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
21346 (properties `((upstream-name . "abcdeFBA")))
21347 (build-system r-build-system)
21349 (list r-corrplot r-lattice r-rgl r-rglpk))
21350 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
21351 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
21353 "This package provides functions for Constraint Based Simulation using
21354 Flux Balance Analysis and informative analysis of the data generated during
21356 (license license:gpl2)))
21358 (define-public r-abcrlda
21365 (uri (cran-uri "abcrlda" version))
21368 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
21369 (properties `((upstream-name . "abcrlda")))
21370 (build-system r-build-system)
21371 (home-page "https://ieeexplore.ieee.org/document/8720003/")
21372 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
21374 "This package offers methods to perform @dfn{asymptotically
21375 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
21376 cost-sensitive binary classification. The bias-correction is an estimate of
21377 the bias term added to regularized discriminant analysis that minimizes the
21379 (license license:gpl3)))
21381 (define-public r-abemus
21388 (uri (cran-uri "abemus" version))
21391 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
21392 (properties `((upstream-name . "abemus")))
21393 (build-system r-build-system)
21395 (list r-data-table))
21396 (home-page "https://cran.r-project.org/web/packages/abemus/")
21397 (synopsis "Adaptive base error model in ultra-deep sequencing data")
21399 "This package provides an implementation of @dfn{Adaptive Base Error
21400 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
21401 platform-specific genetic knowledge and empirical signal to readily detect and
21402 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
21403 cell free DNA} (cfDNA).")
21404 (license license:gpl3)))
21406 ;; This package includes minified JavaScript files. When upgrading please
21407 ;; check that there are no new minified JavaScript files.
21408 (define-public r-rintrojs
21410 (name "r-rintrojs")
21415 (uri (cran-uri "rintrojs" version))
21418 "00l5mk80gj3xkbf3m1kip566ic98bhd88lh0bg69ybkpk4gifpyw"))
21420 '(delete-file "inst/javascript/introjs/intro.min.js"))))
21421 (properties `((upstream-name . "rintrojs")))
21422 (build-system r-build-system)
21425 (modify-phases %standard-phases
21426 (add-after 'unpack 'process-javascript
21427 (lambda* (#:key inputs #:allow-other-keys)
21428 (with-directory-excursion "inst/javascript/introjs/"
21429 (let ((source (assoc-ref inputs "intro.js"))
21430 (target "intro.min.js"))
21431 (format #true "Processing ~a --> ~a~%"
21433 (invoke "esbuild" source "--minify"
21434 (string-append "--outfile=" target)))))))))
21436 `(("esbuild" ,esbuild)
21440 (uri "https://cdn.jsdelivr.net/npm/intro.js@3.2.1/intro.js")
21443 "0vh5n7hqqyx2pdvlqq6xadfqibcn78h5961rwhpf817kpxfzv8v7"))))))
21445 (list r-jsonlite r-shiny))
21446 (home-page "https://github.com/carlganz/rintrojs")
21447 (synopsis "Wrapper for the Intro.js library")
21449 "This package provides a wrapper for the @url{http://www.introjs.com,
21450 Intro.js} library. This package makes it easy to include step-by-step
21451 introductions, and clickable hints in a Shiny application. It supports both
21452 static introductions in the UI, and programmatic introductions from the
21454 ;; The intro.js library is licensed under Expat.
21455 (license (list license:agpl3+ license:expat))))
21457 (define-public r-sysfonts
21459 (name "r-sysfonts")
21464 (uri (cran-uri "sysfonts" version))
21467 "1fq5dn4l09sgrbznfz9cakf4vgc3761zwicvqaazh0s8mzbaicpn"))))
21468 (properties `((upstream-name . "sysfonts")))
21469 (build-system r-build-system)
21471 (list freetype libpng zlib))
21474 (home-page "https://github.com/yixuan/sysfonts")
21475 (synopsis "Loading fonts into R")
21477 "This is a package to simplify loading of system fonts and Google Fonts
21478 into R, in order to support other packages.")
21479 (license license:gpl2)))
21481 (define-public r-showtextdb
21483 (name "r-showtextdb")
21488 (uri (cran-uri "showtextdb" version))
21491 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
21492 (properties `((upstream-name . "showtextdb")))
21493 (build-system r-build-system)
21496 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
21497 (synopsis "Font files for the 'showtext' package")
21499 "This package provides font files that can be used by the @code{showtext}
21501 (license license:asl2.0)))
21503 (define-public r-showtext
21505 (name "r-showtext")
21510 (uri (cran-uri "showtext" version))
21513 "1larnqxn9nanbqiadm35ah5hh89xrzm4fdj9pfc93zzzhlfrvhb3"))))
21514 (properties `((upstream-name . "showtext")))
21515 (build-system r-build-system)
21517 (list freetype libpng zlib))
21519 (list r-showtextdb r-sysfonts))
21521 (list pkg-config r-knitr))
21522 (home-page "https://github.com/yixuan/showtext")
21523 (synopsis "Using fonts more easily in R graphs")
21525 "This package aims to make it easy to use various types of
21526 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
21527 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
21528 will be converted into polygons or raster images, hence after the plot has
21529 been created, it no longer relies on the font files. No external software
21530 such as Ghostscript is needed to use this package.")
21531 (license license:asl2.0)))
21533 (define-public r-emojifont
21535 (name "r-emojifont")
21540 (uri (cran-uri "emojifont" version))
21543 "1hhrwilv36hd9gs1kcl2zsi6519md0h9aixjrm6lfclxvz8r6k1i"))))
21544 (properties `((upstream-name . "emojifont")))
21545 (build-system r-build-system)
21547 (list r-ggplot2 r-proto r-showtext r-sysfonts))
21550 (home-page "https://guangchuangyu.github.io/emojifont")
21551 (synopsis "Emoji and Font Awesome in R graphics")
21553 "This package enables the use of emoji and the Font Awesome glyphs in
21554 both base and ggplot2 graphics.")
21555 (license license:artistic2.0)))
21557 (define-public r-abstractr
21559 (name "r-abstractr")
21564 (uri (cran-uri "abstractr" version))
21567 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
21568 (properties `((upstream-name . "abstractr")))
21569 (build-system r-build-system)
21571 (list r-colourpicker
21578 (home-page "https://matt-kumar.shinyapps.io/portfolio")
21579 (synopsis "R-Shiny application for creating visual abstracts")
21581 "This package provides an R Shiny application to create visual abstracts
21582 for original research. A variety of user defined options and formatting are
21584 (license license:gpl3)))
21586 (define-public r-qgam
21593 (uri (cran-uri "qgam" version))
21596 "1jyamamdffaks89rspyhmg18b4iik0nb1j0vgqzvfnm890514cvn"))))
21597 (properties `((upstream-name . "qgam")))
21598 (build-system r-build-system)
21600 (list r-doparallel r-mgcv r-plyr r-shiny))
21601 (native-inputs (list r-knitr))
21602 (home-page "https://cran.r-project.org/web/packages/qgam/")
21603 (synopsis "Smooth additive quantile regression models")
21605 "This package provides smooth additive quantile regression models, fitted
21606 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
21607 the smoothing parameters are estimated automatically by marginal loss
21608 minimization, while the regression coefficients are estimated using either
21609 PIRLS or Newton algorithm. The learning rate is determined so that the
21610 Bayesian credible intervals of the estimated effects have approximately the
21611 correct coverage. The main function is @code{qgam()} which is similar to
21612 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
21613 regression models.")
21614 (license license:gpl2+)))
21616 (define-public r-abtest
21623 (uri (cran-uri "abtest" version))
21626 "0jz2ry5364p8h8xlk5a5sycn8xlpxd1iasfg99bcr4jqzd92jfqg"))))
21627 (properties `((upstream-name . "abtest")))
21628 (build-system r-build-system)
21638 (home-page "https://cran.r-project.org/web/packages/abtest/")
21639 (synopsis "Bayesian A/B testing")
21641 "This package provides functions for Bayesian A/B testing including prior
21642 elicitation options based on Kass and Vaidyanathan (1992)
21643 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
21644 (license license:gpl2+)))
21646 (define-public r-reldist
21653 (uri (cran-uri "reldist" version))
21656 "17kbqqapqmckghv7jizibmicv3bzbycfr3mz4xg3yjp3c2bap4r6"))))
21657 (properties `((upstream-name . "reldist")))
21658 (build-system r-build-system)
21660 (list r-densestbayes r-mgcv))
21661 (home-page "http://www.stat.ucla.edu/~handcock/RelDist")
21662 (synopsis "Relative distribution methods")
21664 "This package provides tools for the comparison of distributions. This
21665 includes nonparametric estimation of the relative distribution PDF and CDF and
21666 numerical summaries as described in \"Relative Distribution Methods in the
21667 Social Sciences\" by Mark S. Handcock and Martina Morris, Springer-Verlag,
21668 1999, Springer-Verlag, ISBN 0387987789.")
21669 ;; See also https://cran.r-project.org/web/packages/reldist/LICENSE for
21670 ;; attribution requirements.
21671 (license license:gpl3)))
21673 (define-public r-accept
21680 (uri (cran-uri "accept" version))
21683 "13kx8fbnbpasjklgbq2rf4n73j2s8rvy5v77ywqhfzln24937qgh"))))
21684 (properties `((upstream-name . "accept")))
21685 (build-system r-build-system)
21687 (list r-dplyr r-reldist))
21688 (home-page "https://cran.r-project.org/web/packages/accept/")
21689 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
21691 "This package allows clinicians to predict the rate and severity of
21692 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
21693 Disease} (COPD) patients, based on the clinical prediction model published in
21694 Adibi et al. (2019) @url{doi:10.1101/651901}.")
21695 (license license:gpl3)))
21697 (define-public r-smpracticals
21699 (name "r-smpracticals")
21704 (uri (cran-uri "SMPracticals" version))
21707 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
21708 (properties `((upstream-name . "SMPracticals")))
21709 (build-system r-build-system)
21711 (list r-ellipse r-mass r-nlme r-survival))
21712 (home-page "http://statwww.epfl.ch/davison/SM/")
21713 (synopsis "Practicals for use with Davison (2003) Statistical Models")
21715 "This package contains the datasets and a few functions for use with the
21716 practicals outlined in Appendix A of the book Statistical Models (Davison,
21717 2003, Cambridge University Press). The practicals themselves can be found at
21718 @url{http://statwww.epfl.ch/davison/SM/}.")
21719 (license license:gpl2+)))
21721 (define-public r-fgui
21728 (uri (cran-uri "fgui" version))
21731 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
21732 (properties `((upstream-name . "fgui")))
21733 (build-system r-build-system)
21735 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
21736 (synopsis "Create GUI for R functions")
21738 "Rapidly create a GUI for a function you created by automatically
21739 creating widgets for arguments of the function. This package automatically
21740 parses help routines for context-sensitive help to these arguments. The
21741 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
21742 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
21743 incorporated into the interface for greater customization for the more
21745 ;; Any version of the GPL.
21746 (license (list license:gpl2+ license:gpl3+))))
21748 (define-public r-tcltk2
21755 (uri (cran-uri "tcltk2" version))
21758 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
21759 (properties `((upstream-name . "tcltk2")))
21760 (build-system r-build-system)
21763 (home-page "https://www.sciviews.org/SciViews-R")
21764 (synopsis "Tcl/Tk additions")
21766 "This package provides a series of additional Tcl commands and Tk widgets
21767 with style and various functions to supplement the tcltk package")
21768 (license license:lgpl3)))
21770 (define-public r-accrual
21777 (uri (cran-uri "accrual" version))
21780 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
21781 (properties `((upstream-name . "accrual")))
21782 (build-system r-build-system)
21784 (list r-fgui r-smpracticals r-tcltk2))
21785 (home-page "https://cran.r-project.org/web/packages/accrual/")
21786 (synopsis "Bayesian accrual prediction")
21788 "Subject recruitment for medical research is challenging. Slow patient
21789 accrual leads to delay in research. Accrual monitoring during the process of
21790 recruitment is critical. Researchers need reliable tools to manage the
21791 accrual rate. This package provides an implementation of a Bayesian method
21792 that integrates researcher's experience on previous trials and data from the
21793 current study, providing reliable prediction on accrual rate for clinical
21794 studies. It provides functions for Bayesian accrual prediction which can be
21795 easily used by statisticians and clinical researchers.")
21796 (license license:gpl2)))
21798 (define-public r-accrued
21805 (uri (cran-uri "accrued" version))
21808 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
21809 (properties `((upstream-name . "accrued")))
21810 (build-system r-build-system)
21811 (home-page "https://cran.r-project.org/web/packages/accrued/")
21812 (synopsis "Data quality visualization tools for partially accruing data")
21814 "This is a package for visualizing data quality of partially accruing
21816 (license license:gpl3)))
21818 (define-public r-mda
21825 (uri (cran-uri "mda" version))
21828 "0qw4scc2w7jmnxssj5w2mdxb9rrl4dscqn54gplzm1gk2yf419mx"))))
21829 (properties `((upstream-name . "mda")))
21830 (build-system r-build-system)
21831 (propagated-inputs (list r-class))
21832 (native-inputs (list gfortran))
21833 (home-page "https://cran.r-project.org/web/packages/mda/")
21834 (synopsis "Mixture and flexible discriminant analysis")
21836 "This is a package for mixture and flexible discriminant analysis,
21837 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
21838 (license license:gpl2)))
21840 (define-public r-elasticnet
21842 (name "r-elasticnet")
21847 (uri (cran-uri "elasticnet" version))
21850 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
21851 (properties `((upstream-name . "elasticnet")))
21852 (build-system r-build-system)
21855 (home-page "http://users.stat.umn.edu/~zouxx019/")
21856 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
21858 "This package provides functions for fitting the entire solution path of
21859 the Elastic-Net and also provides functions for estimating sparse Principal
21860 Components. The Lasso solution paths can be computed by the same function.")
21861 (license license:gpl2+)))
21863 (define-public r-sparselda
21865 (name "r-sparselda")
21870 (uri (cran-uri "sparseLDA" version))
21873 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
21874 (properties `((upstream-name . "sparseLDA")))
21875 (build-system r-build-system)
21877 (list r-elasticnet r-mass r-mda))
21878 (home-page "https://www.imm.dtu.dk/~lkhc/")
21879 (synopsis "Sparse discriminant analysis")
21881 "This package performs sparse linear discriminant analysis for Gaussians
21882 and mixture of Gaussian models.")
21883 (license license:gpl2+)))
21885 (define-public r-accsda
21892 (uri (cran-uri "accSDA" version))
21895 "104xdz63mnibh6827xm0pfr9zbhbi2a7iw4m1x27xjqi7zqvbky6"))))
21896 (properties `((upstream-name . "accSDA")))
21897 (build-system r-build-system)
21903 (home-page "https://github.com/gumeo/accSDA/wiki")
21904 (synopsis "Accelerated sparse discriminant analysis")
21906 "This package provides an implementation of sparse linear discriminant
21907 analysis, which is a supervised classification method for multiple classes.
21908 Various novel optimization approaches to this problem are implemented
21909 including @dfn{alternating direction method of multipliers} (ADMM),
21910 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
21911 Functions for performing cross validation are also supplied along with basic
21912 prediction and plotting functions. @dfn{Sparse zero variance
21913 discriminant} (SZVD) analysis is also included in the package.")
21914 (license license:gpl2+)))
21916 (define-public r-ace2fastq
21918 (name "r-ace2fastq")
21923 (uri (cran-uri "ace2fastq" version))
21926 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
21927 (properties `((upstream-name . "ace2fastq")))
21928 (build-system r-build-system)
21931 (home-page "https://github.com/c5sire/ace2fastq")
21932 (synopsis "ACE file to FASTQ converter")
21934 "The ACE file format is used in genomics to store contigs from sequencing
21935 machines. This tools converts it into FASTQ format. Both formats contain the
21936 sequence characters and their corresponding quality information. Unlike the
21937 FASTQ file, the ACE file stores the quality values numerically. The
21938 conversion algorithm uses the standard Sanger formula. The package
21939 facilitates insertion into pipelines, and content inspection.")
21940 (license license:gpl3)))
21942 (define-public r-rngwell
21949 (uri (cran-uri "rngWELL" version))
21952 "0f1dxxaimfb0fww8ym9ciqf6q760ai46wxldl37m5mfpd57ca00c"))))
21953 (properties `((upstream-name . "rngWELL")))
21954 (build-system r-build-system)
21955 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
21956 (synopsis "Toolbox for WELL random number generators")
21958 "This is a dedicated package to WELL pseudo random generators, which were
21959 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
21960 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
21961 (license license:bsd-3)))
21963 (define-public r-rnmf
21969 (uri (cran-uri "rNMF" version))
21972 "1nz6h0j5ywdh48m0swmhp34hbkycd7n13rclrxaw85qi9wc42597"))))
21973 (build-system r-build-system)
21975 (list r-knitr r-nnls))
21976 (home-page "https://cran.r-project.org/web/packages/rNMF/")
21977 (synopsis "Robust nonnegative matrix factorization")
21979 "This package provides an implementation of robust nonnegative matrix
21980 factorization (rNMF). The rNMF algorithm decomposes a nonnegative high
21981 dimension data matrix into the product of two low rank nonnegative matrices,
21982 while detecting and trimming outliers. The main function is @code{rnmf()}.
21983 The package also includes a visualization tool, @code{see()}, that arranges
21984 and prints vectorized images.")
21985 (license license:gpl2+)))
21987 (define-public r-randtoolbox
21989 (name "r-randtoolbox")
21994 (uri (cran-uri "randtoolbox" version))
21997 "1p2jsn0hpihc49zk605z82mhhvma0ji2f5b94wa85g2xzriqkwn4"))))
21998 (properties `((upstream-name . "randtoolbox")))
21999 (build-system r-build-system)
22002 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
22003 (synopsis "Toolbox for pseudo and quasi random number generation")
22005 "This package provides
22008 @item pseudo random generators, such as general linear
22009 congruential generators, multiple recursive generators and generalized
22010 feedback shift register (SF-Mersenne Twister algorithm and WELL
22013 @item quasi random generators, such as the Torus algorithm, the Sobol
22014 sequence, the Halton sequence (including the Van der Corput sequence), and
22016 @item some generator tests: the gap test, the serial test, the poker test.
22019 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
22020 (license license:bsd-3)))
22022 (define-public r-lhs
22029 (uri (cran-uri "lhs" version))
22032 "0fb3bc3s5pbwg92qkjbg7v8ah36wm6qs05vf098hwjakr7f6yg3s"))))
22033 (properties `((upstream-name . "lhs")))
22034 (build-system r-build-system)
22035 (propagated-inputs (list r-rcpp))
22038 (home-page "https://github.com/bertcarnell/lhs")
22039 (synopsis "Latin Hypercube Samples")
22041 "This package provides a number of methods for creating and augmenting
22042 Latin Hypercube Samples.")
22043 (license license:gpl3)))
22045 (define-public r-acebayes
22047 (name "r-acebayes")
22052 (uri (cran-uri "acebayes" version))
22055 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73"))))
22056 (properties `((upstream-name . "acebayes")))
22057 (build-system r-build-system)
22059 (list r-compare r-lhs r-randtoolbox r-rcpp r-rcpparmadillo))
22060 (home-page "https://cran.r-project.org/web/packages/acebayes/")
22061 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
22063 "Finding an optimal Bayesian experimental design involves maximizing an
22064 objective function given by the expectation of some appropriately chosen
22065 utility function with respect to the joint distribution of unknown
22066 quantities (including responses). This objective function is usually not
22067 available in closed form and the design space can be continuous and of high
22068 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
22069 to maximise an approximation to the expectation of the utility function.")
22070 (license license:gpl2)))
22072 (define-public r-acet
22079 (uri (cran-uri "ACEt" version))
22082 "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4"))))
22083 (properties `((upstream-name . "ACEt")))
22084 (build-system r-build-system)
22086 (list r-bh r-mass r-rcpp r-rcpparmadillo))
22087 (home-page "https://cran.r-project.org/web/packages/ACEt/")
22088 (synopsis "Estimating dynamic heritability and twin model comparison")
22090 "This package supports twin models that are able to estimate the dynamic
22091 behaviour of the variance components in the classical twin models with respect
22092 to age using B-splines and P-splines.")
22093 (license license:gpl2+)))
22095 (define-public r-acfmperiod
22097 (name "r-acfmperiod")
22102 (uri (cran-uri "acfMPeriod" version))
22105 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
22106 (properties `((upstream-name . "acfMPeriod")))
22107 (build-system r-build-system)
22110 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
22111 (synopsis "Estimation of the ACF from the M-periodogram")
22113 "This package support non-robust and robust computations of the sample
22114 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
22115 univariate and multivariate processes. The methodology consists in reversing
22116 the diagonalization procedure involving the periodogram or the
22117 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
22118 ACOVF or the ACF as discussed in Fuller (1995)
22119 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
22120 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
22121 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
22122 (license license:gpl2+)))
22124 (define-public r-gamlss-data
22126 (name "r-gamlss-data")
22131 (uri (cran-uri "gamlss.data" version))
22134 "07mpdl4h9rwmnpl9jmsn6ig8ji11an6pyjfsvg62h2alapwbdcyv"))))
22135 (properties `((upstream-name . "gamlss.data")))
22136 (build-system r-build-system)
22137 (home-page "http://www.gamlss.org/")
22138 (synopsis "GAMLSS data")
22140 "This package provides data used as examples to demonstrate GAMLSS
22142 ;; Either version of the license
22143 (license (list license:gpl2 license:gpl3))))
22145 (define-public r-gamlss
22152 (uri (cran-uri "gamlss" version))
22155 "0xih19zqgpjl5qv5j38ana6x29y84shn2jfl2lk4kaw3q7yx86b6"))))
22156 (properties `((upstream-name . "gamlss")))
22157 (build-system r-build-system)
22159 (list r-gamlss-data r-gamlss-dist r-mass r-nlme r-survival))
22160 (home-page "http://www.gamlss.org/")
22161 (synopsis "Generalized additive models for location scale and shape")
22163 "This package provides functions for fitting the generalized additive
22164 models for location scale and shape introduced by Rigby and
22165 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
22166 use a distributional regression approach where all the parameters of the
22167 conditional distribution of the response variable are modelled using
22168 explanatory variables.")
22169 ;; Either version of the license
22170 (license (list license:gpl2 license:gpl3))))
22172 (define-public r-acid
22179 (uri (cran-uri "acid" version))
22182 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
22183 (properties `((upstream-name . "acid")))
22184 (build-system r-build-system)
22186 (list r-gamlss r-gamlss-dist r-hmisc))
22187 (home-page "https://cran.r-project.org/web/packages/acid/")
22188 (synopsis "Analysing conditional income distributions")
22190 "This package provides functions for the analysis of income distributions
22191 for subgroups of the population as defined by a set of variables like age,
22192 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
22193 distribution as well as functions for moments, inequality measures, entropy
22194 measures and polarisation measures of income distributions. This package thus
22195 aides the analysis of income inequality by offering tools for the exploratory
22196 analysis of income distributions at the disaggregated level.")
22197 (license license:gpl3)))
22199 (define-public r-acm4r
22206 (uri (cran-uri "acm4r" version))
22209 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
22210 (properties `((upstream-name . "acm4r")))
22211 (build-system r-build-system)
22212 (propagated-inputs (list r-mass))
22213 (home-page "https://cran.r-project.org/web/packages/acm4r/")
22214 (synopsis "Align-and-count method comparisons of RFLP data")
22216 "This is a package to compare sequence fragment lengths or molecular
22217 weights from pairs of lanes. The number of matching bands in the
22218 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
22219 the align-and-count method.")
22220 ;; Any version of the GPL
22221 (license (list license:gpl2+ license:gpl3+))))
22223 (define-public r-filelock
22225 (name "r-filelock")
22230 (uri (cran-uri "filelock" version))
22233 "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc"))))
22234 (properties `((upstream-name . "filelock")))
22235 (build-system r-build-system)
22236 (home-page "https://github.com/r-lib/filelock")
22237 (synopsis "Portable file locking")
22239 "This library lets you place an exclusive or shared lock on a file using
22240 the appropriate system call provided by the underlying operating system.")
22241 (license license:expat)))
22243 (define-public r-filematrix
22245 (name "r-filematrix")
22250 (uri (cran-uri "filematrix" version))
22253 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
22254 (properties `((upstream-name . "filematrix")))
22255 (build-system r-build-system)
22256 ;; These inputs are needed for vignettes
22258 (list r-knitr r-rmarkdown))
22259 (home-page "https://github.com/andreyshabalin/filematrix")
22260 (synopsis "File-backed matrix class with convenient read and write access")
22262 "This package provides an interface for working with large matrices
22263 stored in files, not in computer memory. It supports multiple non-character
22264 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
22265 byte real values). Access to parts of the matrix is done by indexing, exactly
22266 as with usual R matrices. It supports very large matrices; the package has
22267 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
22268 columns, ad allows for quick addition of extra columns to a filematrix.")
22269 (license license:lgpl3)))
22271 (define-public r-acmeeqtl
22273 (name "r-acmeeqtl")
22278 (uri (cran-uri "ACMEeqtl" version))
22281 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
22282 (properties `((upstream-name . "ACMEeqtl")))
22283 (build-system r-build-system)
22285 (list r-filematrix))
22286 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
22287 (synopsis "Estimation of interpretable eQTL effect sizes")
22289 "This package provides a non-linear model, termed ACME, that reflects a
22290 parsimonious biological model for allelic contributions of cis-acting eQTLs.
22291 With non-linear least-squares algorithm the maximum likelihood parameters can
22292 be estimated. The ACME model provides interpretable effect size estimates and
22293 p-values with well controlled Type-I error.")
22294 (license license:lgpl3)))
22296 (define-public r-acmer
22303 (uri (cran-uri "acmeR" version))
22306 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
22307 (properties `((upstream-name . "acmeR")))
22308 (build-system r-build-system)
22309 (propagated-inputs (list r-foreign))
22310 (home-page "https://cran.r-project.org/web/packages/acmeR/")
22311 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
22313 "This package provides an implementation of the ACME estimator, described
22314 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
22315 Mortality at Wind Turbines. Unlike most other models, this estimator supports
22316 decreasing-hazard Weibull model for persistence; decreasing search proficiency
22317 as carcasses age; variable bleed-through at successive searches; and interval
22318 mortality estimates. The package provides, based on search data, functions
22319 for estimating the mortality inflation factor in Frequentist and Bayesian
22321 (license license:expat)))
22323 (define-public r-r-huge
22330 (uri (cran-uri "R.huge" version))
22333 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
22334 (properties `((upstream-name . "R.huge")))
22335 (build-system r-build-system)
22337 (list r-r-methodss3 r-r-oo r-r-utils))
22338 (home-page "https://github.com/HenrikBengtsson/R.huge")
22339 (synopsis "Methods for accessing huge amounts of data")
22341 "This is a deprecated package for accessing huge amounts of data.
22342 Cross-platform alternatives are the following packages: bigmemory (CRAN),
22343 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
22344 the @code{aroma.affymetrix} package.")
22345 (license license:lgpl2.1+)))
22347 (define-public r-r-filesets
22349 (name "r-r-filesets")
22354 (uri (cran-uri "R.filesets" version))
22357 "08xv8b3c81nf54viyr3w912al18483k5gfnjpg7bxbdfk70dfzbh"))))
22358 (properties `((upstream-name . "R.filesets")))
22359 (build-system r-build-system)
22362 (modify-phases %standard-phases
22363 (add-after 'unpack 'set-HOME
22364 (lambda _ (setenv "HOME" "/tmp"))))))
22366 (list r-digest r-r-cache r-r-methodss3 r-r-oo r-r-utils))
22367 (home-page "https://github.com/HenrikBengtsson/R.filesets")
22368 (synopsis "Easy handling of and access to files")
22370 "This package provides classes and methods to locate, setup, subset,
22371 navigate and iterate file sets, i.e. sets of files located in one or more
22372 directories on the file system. The API is designed such that these classes
22373 can be extended via inheritance to provide a richer API for special file
22374 formats. Moreover, a specific name format is defined such that filenames and
22375 directories can be considered to have full names which consists of a name
22376 followed by comma-separated tags. This adds additional flexibility to
22377 identify file sets and individual files.")
22378 (license license:lgpl2.1+)))
22380 (define-public r-r-devices
22382 (name "r-r-devices")
22387 (uri (cran-uri "R.devices" version))
22390 "1djz6vm1b7sjvx1q319dl47gbnz9kvipaxcz9i0spyp094lv3m62"))))
22391 (properties `((upstream-name . "R.devices")))
22392 (build-system r-build-system)
22394 (list r-base64enc r-r-methodss3 r-r-oo r-r-utils))
22395 (home-page "https://github.com/HenrikBengtsson/R.devices")
22396 (synopsis "Unified handling of graphics devices")
22398 "This package provides functions for creating plots and image files in a
22399 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
22400 Default device options as well as scales and aspect ratios are controlled in a
22401 uniform way across all device types. Switching output format requires minimal
22402 changes in code. This package is ideal for large-scale batch processing,
22403 because it will never leave open graphics devices or incomplete image files
22404 behind, even on errors or user interrupts.")
22405 (license license:lgpl2.1+)))
22407 (define-public r-acnr
22414 (uri (cran-uri "acnr" version))
22417 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
22418 (properties `((upstream-name . "acnr")))
22419 (build-system r-build-system)
22420 (home-page "https://github.com/mpierrejean/acnr")
22421 (synopsis "Annotated copy-number regions")
22423 "This package provides SNP array data from different types of copy-number
22424 regions. These regions were identified manually by the authors of the package
22425 and may be used to generate realistic data sets with known truth.")
22426 (license license:lgpl2.1+)))
22428 (define-public r-acopula
22435 (uri (cran-uri "acopula" version))
22438 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
22439 (properties `((upstream-name . "acopula")))
22440 (build-system r-build-system)
22441 (home-page "https://cran.r-project.org/web/packages/acopula/")
22442 (synopsis "Modelling dependence with multivariate Archimax copulas")
22444 "Archimax copulas are a mixture of Archimedean and EV copulas. This
22445 package provides definitions of several parametric families of generator and
22446 dependence function, computes CDF and PDF, estimates parameters, tests for
22447 goodness of fit, generates random sample and checks copula properties for
22448 custom constructs. In the 2-dimensional case explicit formulas for density
22449 are used, contrary to higher dimensions when all derivatives are linearly
22450 approximated. Several non-archimax families (normal, FGM, Plackett) are
22451 provided as well.")
22452 (license license:gpl2)))
22454 (define-public r-tuner
22461 (uri (cran-uri "tuneR" version))
22464 "1sd0drxzbdy71bh35fccg9ajhpdhdpy0m9nja2lw82p1pzhyl7jn"))))
22465 (properties `((upstream-name . "tuneR")))
22466 (build-system r-build-system)
22467 (propagated-inputs (list r-signal))
22468 (home-page "https://cran.r-project.org/web/packages/tuneR/")
22469 (synopsis "Analysis of music and speech")
22471 "This is a package for the analysis of music and speech. Analyze music
22472 and speech, extract features like MFCCs, handle wave files and their
22473 representation in various ways, read MP3, read MIDI, perform steps of a
22474 transcription, ...")
22475 ;; Either of these versions.
22476 (license (list license:gpl2 license:gpl3))))
22478 (define-public r-seewave
22485 (uri (cran-uri "seewave" version))
22488 "0bi1l47l3846c18k6h2vrv0xp9xh00n544a578jrndahzrj1hfwl"))))
22489 (properties `((upstream-name . "seewave")))
22490 (build-system r-build-system)
22495 (home-page "http://rug.mnhn.fr/seewave")
22496 (synopsis "Sound analysis and synthesis")
22498 "This package provides functions for analysing, manipulating, displaying,
22499 editing and synthesizing time waves (particularly sound). This package
22500 processes time analysis (oscillograms and envelopes), spectral content,
22501 resonance quality factor, entropy, cross correlation and autocorrelation,
22502 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
22503 and 3D spectrograms and many other analyses.")
22504 (license license:gpl2+)))
22506 (define-public r-acousticndlcoder
22508 (name "r-acousticndlcoder")
22513 (uri (cran-uri "AcousticNDLCodeR" version))
22516 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
22518 `((upstream-name . "AcousticNDLCodeR")))
22519 (build-system r-build-system)
22521 (list r-seewave r-tuner r-zoo))
22522 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
22523 (synopsis "Coding sound files for use with NDL")
22525 "Make acoustic cues to use with the R package @code{ndl}.
22526 The package implements functions used in the PLoS ONE paper \"Words from
22527 spontaneous conversational speech can be recognized with human-like accuracy
22528 by an error-driven learning algorithm that discriminates between meanings
22529 straight from smart acoustic features, bypassing the phoneme as recognition
22530 unit.\" @url{doi:10.1371/journal.pone.0174623}")
22531 (license license:gpl2+)))
22533 (define-public r-acp
22540 (uri (cran-uri "acp" version))
22543 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
22544 (properties `((upstream-name . "acp")))
22545 (build-system r-build-system)
22547 (list r-quantmod r-tseries))
22548 (home-page "https://cran.r-project.org/web/packages/acp/")
22549 (synopsis "Autoregressive conditional Poisson")
22551 "This package supports the analysis of count data exhibiting
22552 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
22553 model (ACP(p,q)) proposed by Heinen (2003).")
22554 (license license:gpl2)))
22556 (define-public r-ada
22563 (uri (cran-uri "ada" version))
22566 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
22567 (properties `((upstream-name . "ada")))
22568 (build-system r-build-system)
22569 (propagated-inputs (list r-rpart))
22570 (home-page "https://cran.r-project.org/web/packages/ada/")
22571 (synopsis "Stochastic boosting")
22573 "This package provides a straightforward, well-documented, and broad
22574 boosting routine for classification, ideally suited for small to
22575 moderate-sized data sets. It performs discrete, real, and gentle boost under
22576 both exponential and logistic loss on a given data set.")
22577 ;; Any version of the GPL.
22578 (license (list license:gpl2+ license:gpl3+))))
22580 (define-public r-genalg
22587 (uri (cran-uri "genalg" version))
22590 "1y4qz1s85zpd1r3259gr542arssf2vpd4drhy0wnq5q47ignrvna"))))
22591 (properties `((upstream-name . "genalg")))
22592 (build-system r-build-system)
22593 (home-page "https://github.com/egonw/genalg")
22594 (synopsis "R based genetic algorithm")
22596 "This package provides an R based genetic algorithm for binary and
22597 floating point chromosomes.")
22598 (license license:gpl2)))
22600 (define-public r-kernelfactory
22602 (name "r-kernelfactory")
22607 (uri (cran-uri "kernelFactory" version))
22610 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
22611 (properties `((upstream-name . "kernelFactory")))
22612 (build-system r-build-system)
22614 (list r-auc r-genalg r-kernlab r-randomforest))
22615 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
22616 (synopsis "Ensemble of kernel machines")
22618 "Kernel factory is an ensemble method where each base classifier (random
22619 forest) is fit on the kernel matrix of a subset of the training data.")
22620 (license license:gpl2+)))
22622 (define-public r-dummies
22629 (uri (cran-uri "dummies" version))
22632 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
22633 (properties `((upstream-name . "dummies")))
22634 (build-system r-build-system)
22635 (home-page "https://decisionpatterns.com")
22636 (synopsis "Create dummy/indicator variables flexibly and efficiently")
22638 "This package lets you expand factors, characters and other eligible
22639 classes into dummy/indicator variables.")
22640 (license license:gpl2+)))
22642 (define-public r-acrm
22649 (uri (cran-uri "aCRM" version))
22652 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
22653 (properties `((upstream-name . "aCRM")))
22654 (build-system r-build-system)
22656 (list r-ada r-dummies r-kernelfactory r-randomforest))
22657 (home-page "https://cran.r-project.org/web/packages/aCRM/")
22658 (synopsis "Convenience functions for analytical customer relationship management")
22660 "This package provides convenience functions for data preparation and
22661 modeling often used in @dfn{analytical customer relationship
22662 management} (aCRM).")
22663 (license license:gpl2+)))
22665 (define-public r-tree
22671 (uri (cran-uri "tree" version))
22674 "1q3jgkhl5d4d8c396cyvkw60094p0z0a3x7xwhdbi8gl4c2c65ss"))))
22675 (build-system r-build-system)
22676 (home-page "https://cran.r-project.org/web/packages/tree/")
22677 (synopsis "Classification and regression trees")
22678 (description "This package provides procedures to work with classification
22679 and regression trees.")
22680 (license license:gpl2+)))
22682 (define-public r-treeclust
22684 (name "r-treeclust")
22689 (uri (cran-uri "treeClust" version))
22692 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
22693 (properties `((upstream-name . "treeClust")))
22694 (build-system r-build-system)
22696 (list r-cluster r-rpart))
22697 (home-page "https://cran.r-project.org/web/packages/treeClust/")
22698 (synopsis "Cluster distances through trees")
22700 "This package provides tools to create a measure of inter-point
22701 dissimilarity useful for clustering mixed data, and, optionally, perform the
22703 (license license:gpl2+)))
22705 (define-public r-acrosstic
22707 (name "r-acrosstic")
22712 (uri (cran-uri "AcrossTic" version))
22715 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
22716 (properties `((upstream-name . "AcrossTic")))
22717 (build-system r-build-system)
22719 (list r-lpsolve r-treeclust))
22720 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
22721 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
22723 "This is a package for constructing minimum-cost regular spanning
22724 subgraph as part of a non-parametric two-sample test for equality of
22726 (license license:gpl2+)))
22728 (define-public r-acrt
22735 (uri (cran-uri "acrt" version))
22738 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
22739 (properties `((upstream-name . "acrt")))
22740 (build-system r-build-system)
22742 (list r-rcpp r-rcppeigen r-sandwich))
22743 (home-page "https://cran.r-project.org/web/packages/acrt/")
22744 (synopsis "Autocorrelation robust testing")
22746 "This package provides functions for testing affine hypotheses on the
22747 regression coefficient vector in regression models with autocorrelated
22749 (license license:gpl2)))
22751 (define-public r-acs
22758 (uri (cran-uri "acs" version))
22761 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
22762 (properties `((upstream-name . "acs")))
22763 (build-system r-build-system)
22765 (list r-httr r-plyr r-rcpp r-stringr r-xml))
22766 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
22767 (synopsis "Work with data from the US Census")
22769 "This package provides a general toolkit for downloading, managing,
22770 analyzing, and presenting data from the
22771 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
22772 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
22773 American Community Survey (ACS). Confidence intervals provided with ACS data
22774 are converted to standard errors to be bundled with estimates in complex
22775 @code{acs} objects. The package provides new methods to conduct standard
22776 operations on @code{acs} objects and present/plot data in statistically
22777 appropriate ways.")
22778 (license license:gpl3)))
22780 (define-public r-acss-data
22782 (name "r-acss-data")
22787 (uri (cran-uri "acss.data" version))
22790 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
22791 (properties `((upstream-name . "acss.data")))
22792 (build-system r-build-system)
22793 (home-page "http://complexitycalculator.com/methodology.html")
22794 (synopsis "Data for algorithmic complexity of short strings")
22796 "This is a data only package providing the algorithmic complexity of
22797 short strings, computed using the coding theorem method. For a given set of
22798 symbols in a string, all possible or a large number of random samples of
22799 Turing machines with a given number of states (e.g., 5) and number of symbols
22800 corresponding to the number of symbols in the strings were simulated until
22801 they reached a halting state or failed to end. This package contains data on
22802 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
22803 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
22804 distribution of the halting states.")
22805 (license license:gpl2+)))
22807 (define-public r-acss
22814 (uri (cran-uri "acss" version))
22817 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
22818 (properties `((upstream-name . "acss")))
22819 (build-system r-build-system)
22821 (list r-acss-data r-zoo))
22822 (home-page "http://complexitycalculator.com/methodology.html")
22823 (synopsis "Algorithmic complexity for short strings")
22825 "The main purpose of this package is to provide the algorithmic
22826 complexity for short strings, an approximation of the Kolmogorov Complexity of
22827 a short string using the coding theorem method. While the database containing
22828 the complexity is provided in the data only package @code{acss.data}, this
22829 package provides functions accessing the data such as @code{prob_random}
22830 returning the posterior probability that a given string was produced by a
22831 random process. In addition, two traditional (but problematic) measures of
22832 complexity are also provided: entropy and change complexity.")
22833 (license license:gpl2+)))
22835 (define-public r-acswr
22842 (uri (cran-uri "ACSWR" version))
22845 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
22846 (properties `((upstream-name . "ACSWR")))
22847 (build-system r-build-system)
22850 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
22851 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
22853 "This is a companion package for the book \"A Course in Statistics with
22854 R\" (ISBN 978-1-119-15272-9.)")
22855 (license license:gpl2)))
22857 (define-public r-alabama
22860 (version "2022.4-1")
22864 (uri (cran-uri "alabama" version))
22867 "0v6kl6ndm8wvp9xzya3x4gj5kh03qgx13x5vyzn410wsndcjiim8"))))
22868 (properties `((upstream-name . "alabama")))
22869 (build-system r-build-system)
22870 (propagated-inputs (list r-numderiv))
22871 (home-page "https://cran.r-project.org/web/packages/alabama/")
22872 (synopsis "Constrained nonlinear optimization")
22874 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
22875 Algorithm; it is used for optimizing smooth nonlinear objective functions with
22876 constraints. Linear or nonlinear equality and inequality constraints are
22878 (license license:gpl2+)))
22880 (define-public r-gdina
22887 (uri (cran-uri "GDINA" version))
22890 "1slq1npsq8s8aghnrpm6vvc6kxj4svz0kr2x0akblndrcr25wxjr"))))
22891 (properties `((upstream-name . "GDINA")))
22892 (build-system r-build-system)
22905 (home-page "https://github.com/Wenchao-Ma/GDINA")
22906 (synopsis "Generalized DINA model framework")
22908 "This package provides a set of psychometric tools for cognitive
22909 diagnosis modeling based on the generalized deterministic inputs, noisy and
22910 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
22911 and its extensions, including the sequential G-DINA model by Ma and de la
22912 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
22913 polytomous G-DINA model by Chen and de la Torre
22914 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
22915 distribution can be independent, saturated, higher-order, loglinear smoothed
22916 or structured. Q-matrix validation, item and model fit statistics, model
22917 comparison at test and item level and differential item functioning can also
22918 be conducted. A graphical user interface is also provided.")
22919 (license license:gpl3)))
22921 (define-public r-actcd
22928 (uri (cran-uri "ACTCD" version))
22931 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
22932 (properties `((upstream-name . "ACTCD")))
22933 (build-system r-build-system)
22935 (list r-gdina r-r-methodss3))
22938 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
22939 (synopsis "Asymptotic classification theory for cognitive diagnosis")
22941 "This is a package supporting cluster analysis for cognitive diagnosis
22942 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
22943 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
22944 sum-scores, cluster analysis techniques can be used to classify examinees into
22945 latent classes based on their attribute patterns. In addition to the
22946 algorithms used to classify data, three labeling approaches are proposed to
22947 label clusters so that examinees' attribute profiles can be obtained.")
22948 (license license:gpl2+)))
22950 (define-public r-ineq
22957 (uri (cran-uri "ineq" version))
22960 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
22961 (properties `((upstream-name . "ineq")))
22962 (build-system r-build-system)
22963 (home-page "https://cran.r-project.org/web/packages/ineq/")
22964 (synopsis "Measuring inequality, concentration, and poverty")
22966 "This package provides tools for measuring inequality, concentration, and
22967 poverty measures. It provides both empirical and theoretical Lorenz curves.")
22968 ;; Either of these two versions.
22969 (license (list license:gpl2 license:gpl3))))
22971 (define-public r-actfrag
22978 (uri (cran-uri "ActFrag" version))
22981 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
22982 (properties `((upstream-name . "ActFrag")))
22983 (build-system r-build-system)
22985 (list r-accelerometry r-dplyr r-ineq r-survival r-tidyr))
22986 (home-page "https://github.com/junruidi/ActFrag")
22987 (synopsis "Activity fragmentation metrics extraction")
22989 "This package provides functions to extract commonly used fragmentation
22990 metrics to quantify time accumulation strategies based on minute level
22991 actigraphy-measured activity counts data.")
22992 (license license:gpl3)))
22994 (define-public r-ash
23001 (uri (cran-uri "ash" version))
23004 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb"))))
23005 (properties `((upstream-name . "ash")))
23006 (build-system r-build-system)
23007 (native-inputs (list gfortran))
23008 (home-page "https://cran.r-project.org/web/packages/ash/")
23009 (synopsis "David Scott's ASH routines")
23011 "This package provides David Scott's ASH routines ported from S-PLUS to
23013 (license license:gpl2+)))
23015 (define-public r-hdrcde
23022 (uri (cran-uri "hdrcde" version))
23025 "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3"))))
23026 (properties `((upstream-name . "hdrcde")))
23027 (build-system r-build-system)
23035 (native-inputs (list gfortran))
23036 (home-page "http://pkg.robjhyndman.com/hdrcde")
23037 (synopsis "Highest density regions and conditional density estimation")
23039 "This is a package for the computation of highest density regions in one
23040 and two dimensions, kernel estimation of univariate density functions
23041 conditional on one covariate, and multimodal regression.")
23042 (license license:gpl3)))
23044 (define-public r-rainbow
23051 (uri (cran-uri "rainbow" version))
23054 "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3"))))
23055 (properties `((upstream-name . "rainbow")))
23056 (build-system r-build-system)
23064 (home-page "https://cran.r-project.org/web/packages/rainbow/")
23065 (synopsis "Bagplots, boxplots and rainbow plots for functional data")
23067 "This is a package for visualizing functional data and identifying
23068 functional outliers with bagplots, boxplots and rainbow plots.")
23069 (license license:gpl3)))
23071 (define-public r-fds
23078 (uri (cran-uri "fds" version))
23081 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0"))))
23082 (properties `((upstream-name . "fds")))
23083 (build-system r-build-system)
23085 (list r-rainbow r-rcurl))
23086 (home-page "https://cran.r-project.org/web/packages/fds/")
23087 (synopsis "Functional data sets")
23088 (description "This package contains a list of functional time series,
23089 sliced functional time series, and functional data sets. Functional time
23090 series is a special type of functional data observed over time. Sliced
23091 functional time series is a special type of functional time series with a time
23092 variable observed over time.")
23093 (license license:gpl2+)))
23095 (define-public r-fda
23102 (uri (cran-uri "fda" version))
23105 "1lvp4i4hqz650k27sa5flbdlkalihc79xy9128hfhr16h6wi8n10"))))
23106 (properties `((upstream-name . "fda")))
23107 (build-system r-build-system)
23109 (list r-desolve r-fds))
23112 (home-page "https://www.functionaldata.org")
23113 (synopsis "Functional data analysis")
23115 "These functions were developed to support functional data analysis as
23116 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
23117 Analysis. The package includes data sets and script files working many
23119 (license license:gpl2+)))
23121 (define-public r-actigraphy
23123 (name "r-actigraphy")
23128 (uri (cran-uri "Actigraphy" version))
23131 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
23132 (properties `((upstream-name . "Actigraphy")))
23133 (build-system r-build-system)
23136 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
23137 (synopsis "Actigraphy data analysis")
23139 "This package provides tools for functional linear modeling and analysis
23140 of actigraphy data.")
23141 (license license:asl2.0)))
23143 (define-public r-activedriver
23145 (name "r-activedriver")
23150 (uri (cran-uri "ActiveDriver" version))
23153 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
23154 (properties `((upstream-name . "ActiveDriver")))
23155 (build-system r-build-system)
23158 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
23159 (synopsis "Tools for finding cancer driver proteins")
23161 "This package provides a mutation analysis tool that discovers cancer
23162 driver genes with frequent mutations in protein signalling sites such as
23163 post-translational modifications (phosphorylation, ubiquitination, etc). The
23164 Poisson generalized linear regression model identifies genes where cancer
23165 mutations in signalling sites are more frequent than expected from the
23166 sequence of the entire gene. Integration of mutations with signalling
23167 information helps find new driver genes and propose candidate mechanisms to
23169 (license license:gpl2+)))
23171 (define-public r-activitycounts
23173 (name "r-activitycounts")
23178 (uri (cran-uri "activityCounts" version))
23181 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
23183 `((upstream-name . "activityCounts")))
23184 (build-system r-build-system)
23186 (list r-lubridate r-magrittr r-seewave r-signal r-tibble))
23187 (home-page "https://github.com/walkabillylab/activityCounts")
23188 (synopsis "Generate ActiLife counts")
23190 "ActiLife generates activity counts from data collected by Actigraph
23191 accelerometers. Actigraph is one of the most common research-grade
23192 accelerometers. There is considerable research validating and developing
23193 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
23194 counts are proprietary and difficult to implement if researchers use different
23195 accelerometer brands. The code creates ActiLife counts from raw acceleration
23196 data for different accelerometer brands.")
23197 (license license:gpl3)))
23199 (define-public r-activityindex
23201 (name "r-activityindex")
23206 (uri (cran-uri "ActivityIndex" version))
23209 "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5"))))
23210 (properties `((upstream-name . "ActivityIndex")))
23211 (build-system r-build-system)
23213 (list r-data-table r-matrixstats r-r-utils))
23216 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
23217 (synopsis "Activity Index calculation using raw accelerometry data")
23219 "This is a package to read raw accelerometry from GT3X+ accelerometry
23220 data and plain table data to calculate the Activity Index from Bai et
23221 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
23222 (license license:gpl3)))
23224 (define-public r-activpal
23226 (name "r-activpal")
23231 (uri (cran-uri "activPAL" version))
23234 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
23235 (properties `((upstream-name . "activPAL")))
23236 (build-system r-build-system)
23244 (home-page "https://cran.r-project.org/web/packages/activPAL")
23245 (synopsis "Processing and chart generation from activPAL events files")
23247 "This package contains functions to generate pre-defined summary
23248 statistics from activPAL events files. The package also contains functions to
23249 produce informative graphics that visualize physical activity behaviour and
23250 trends. This includes generating graphs that align physical activity
23251 behaviour with additional time based observations described by other data
23252 sets, such as sleep diaries and continuous glucose monitoring data.")
23253 (license license:gpl3)))
23255 (define-public r-activpalprocessing
23257 (name "r-activpalprocessing")
23262 (uri (cran-uri "activpalProcessing" version))
23265 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
23267 `((upstream-name . "activpalProcessing")))
23268 (build-system r-build-system)
23271 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
23272 (synopsis "Process activPAL events files")
23274 "This package performs estimation of physical activity and sedentary
23275 behavior variables from activPAL events files.")
23276 ;; Either version of the GPL.
23277 (license (list license:gpl2 license:gpl3))))
23279 (define-public r-actogrammr
23281 (name "r-actogrammr")
23286 (uri (cran-uri "actogrammr" version))
23289 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
23290 (properties `((upstream-name . "actogrammr")))
23291 (build-system r-build-system)
23293 (list r-dplyr r-ggplot2 r-lubridate r-readr r-tidyr))
23294 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
23295 (synopsis "Read in activity data and plot actograms")
23297 "Read in activity measurements from standard file formats used by
23298 circadian rhythm researchers, currently only ClockLab format, and process and
23299 plot the data. The central type of plot is the actogram, as first described
23300 in \"Activity and distribution of certain wild mice in relation to biotic
23301 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
23302 (license license:gpl3)))
23304 (define-public r-expint
23311 (uri (cran-uri "expint" version))
23314 "01d0a7pc4qx7044a0cymnv5ld88r90vdvlqjbnzg9qlfbizdgyvw"))))
23315 (properties `((upstream-name . "expint")))
23316 (build-system r-build-system)
23317 (home-page "https://gitlab.com/vigou3/expint")
23318 (synopsis "Exponential integral and incomplete Gamma function")
23320 "This package provides the exponential integrals @code{E_1(x)},
23321 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
23322 function @code{G(a, x)} defined for negative values of its first argument.
23323 The package also gives easy access to the underlying C routines through an
23324 API; see the package vignette for details.")
23325 (license license:gpl2+)))
23327 (define-public r-actuar
23334 (uri (cran-uri "actuar" version))
23337 "0dhpaivyga0jwvw1csagbx74biy9jfkw4a8sa871579njxl1x7p1"))))
23338 (properties `((upstream-name . "actuar")))
23339 (build-system r-build-system)
23340 (propagated-inputs (list r-expint))
23341 (home-page "https://gitlab.com/vigou3/actuar")
23342 (synopsis "Actuarial functions and heavy tailed distributions")
23344 "This package provides functions and data sets for actuarial science:
23345 modeling of loss distributions; risk theory and ruin theory; simulation of
23346 compound models, discrete mixtures and compound hierarchical models;
23347 credibility theory. It boasts support for many additional probability
23348 distributions to model insurance loss amounts and loss frequency: 19
23349 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
23350 distribution; zero-truncated and zero-modified extensions of the standard
23351 discrete distributions. It also supports phase-type distributions commonly
23352 used to compute ruin probabilities.")
23353 (license license:gpl2+)))
23355 (define-public r-bmp
23362 (uri (cran-uri "bmp" version))
23365 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
23366 (properties `((upstream-name . "bmp")))
23367 (build-system r-build-system)
23368 (home-page "https://cran.r-project.org/web/packages/bmp/")
23369 (synopsis "Read Bitmap (BMP) images")
23371 "This package provides pure R tools to read BMP format images. It is
23372 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
23373 (license license:gpl2+)))
23375 (define-public r-readbitmap
23377 (name "r-readbitmap")
23382 (uri (cran-uri "readbitmap" version))
23385 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
23386 (properties `((upstream-name . "readbitmap")))
23387 (build-system r-build-system)
23389 (list libjpeg-turbo libpng))
23391 (list r-bmp r-jpeg r-png r-tiff))
23392 (home-page "https://github.com/jefferis/readbitmap")
23393 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
23395 "This package provides tools to identify and read BMP, JPEG, PNG, and
23396 TIFF format bitmap images. Identification defaults to the use of the magic
23397 number embedded in the file rather than the file extension.")
23398 (license license:gpl2+)))
23400 (define-public r-imager
23403 (version "0.42.13")
23407 (uri (cran-uri "imager" version))
23410 "0zygnmxwbbmj5i2l2affzdz90xvsa7b5pbkzkhjbm40is69rh2nr"))))
23411 (properties `((upstream-name . "imager")))
23412 (build-system r-build-system)
23414 (list fftw libtiff libx11 zlib))
23426 (list pkg-config r-knitr))
23427 (home-page "https://dahtah.github.io/imager/")
23428 (synopsis "Image processing library")
23430 "This is a package for fast image processing for images in up to 4
23431 dimensions (two spatial dimensions, one time/depth dimension, one color
23432 dimension). It provides most traditional image processing tools (filtering,
23433 morphology, transformations, etc.) as well as various functions for easily
23434 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
23435 simple, modern C++ library for image processing.")
23436 (license license:lgpl3)))
23438 (define-public r-acuityview
23440 (name "r-acuityview")
23445 (uri (cran-uri "AcuityView" version))
23448 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
23449 (properties `((upstream-name . "AcuityView")))
23450 (build-system r-build-system)
23452 (list r-fftwtools r-imager r-plotrix))
23453 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
23454 (synopsis "Display scenes as seen by an animal with less acute vision")
23456 "This package provides a simple method for representing a visual scene as
23457 it may be seen by an animal with less acute vision.")
23458 (license license:gpl2+)))
23460 (define-public r-caret
23467 (uri (cran-uri "caret" version))
23470 "048mp325ndfl83a8p4dkd1b6zh5bws4gg9kxka5ss8qsj8m4m08x"))))
23471 (build-system r-build-system)
23486 (home-page "https://github.com/topepo/caret")
23487 (synopsis "Classification and regression training")
23489 "This package provides miscellaneous functions for training and plotting
23490 classification and regression models.")
23491 (license license:gpl2+)))
23493 (define-public r-adabag
23500 (uri (cran-uri "adabag" version))
23503 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
23504 (properties `((upstream-name . "adabag")))
23505 (build-system r-build-system)
23507 (list r-caret r-doparallel r-foreach r-rpart))
23508 (home-page "https://cran.r-project.org/web/packages/adabag/")
23509 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
23511 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
23512 Breiman's Bagging algorithm using classification trees as individual
23513 classifiers. Once these classifiers have been trained, they can be used to
23514 predict on new data. Also, cross validation estimation of the error can be
23516 (license license:gpl2+)))
23518 (define-public r-adagio
23525 (uri (cran-uri "adagio" version))
23528 "0ihv05402iq003m0338f85pnqnlnrmx0pf1mg8cz9sgi5h98mbnl"))))
23529 (properties `((upstream-name . "adagio")))
23530 (build-system r-build-system)
23533 (home-page "https://cran.r-project.org/web/packages/adagio/")
23534 (synopsis "Discrete and global optimization routines")
23536 "This package provides methods and algorithms for discrete optimization,
23537 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
23538 Hooke-Jeeves minimization, and some (evolutionary) global optimization
23540 (license license:gpl3+)))
23542 (define-public r-univoutl
23544 (name "r-univoutl")
23549 (uri (cran-uri "univOutl" version))
23552 "1kp014bhs8v02fp7misrj4fpfp2na9lg45p5zqvlfaypnm5imsr9"))))
23553 (properties `((upstream-name . "univOutl")))
23554 (build-system r-build-system)
23556 (list r-hmisc r-robustbase))
23557 (home-page "https://github.com/marcellodo/univOutl")
23558 (synopsis "Detection of univariate outliers")
23560 "This package provides well-known outlier detection techniques in the
23561 univariate case. Methods to deal with skewed distribution are included too.
23562 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
23563 historical data is implemented as well. When available, survey weights can be
23564 used in outliers detection.")
23565 (license license:gpl2+)))
23567 (define-public r-tolerance
23569 (name "r-tolerance")
23574 (uri (cran-uri "tolerance" version))
23577 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
23578 (properties `((upstream-name . "tolerance")))
23579 (build-system r-build-system)
23581 (list r-mass r-rgl))
23582 (home-page "https://cran.r-project.org/web/packages/tolerance/")
23583 (synopsis "Statistical tolerance intervals and regions")
23585 "This package provides functions for estimating tolerance
23586 limits (intervals) for various univariate distributions (binomial, Cauchy,
23587 discrete Pareto, exponential, two-parameter exponential, extreme value,
23588 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
23589 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
23590 Bayesian normal tolerance limits, multivariate normal tolerance regions,
23591 nonparametric tolerance intervals, tolerance bands for regression
23592 settings (linear regression, nonlinear regression, nonparametric regression,
23593 and multivariate regression), and analysis of variance tolerance intervals.
23594 Visualizations are also available for most of these settings.")
23595 (license license:gpl2+)))
23597 ;; Keep this in sync with the liblantern package.
23598 (define-public r-torch
23605 (uri (cran-uri "torch" version))
23607 (base32 "0n2rmv2mwfp4y002x46fd278kssmhi54zcyj37558k4r1kazzfxp"))))
23608 (properties `((upstream-name . "torch")))
23609 (build-system r-build-system)
23613 #~(modify-phases %standard-phases
23614 (add-after 'install 'link-libraries
23615 (lambda* (#:key inputs #:allow-other-keys)
23616 (let ((deps (string-append #$output "/site-library/torch/deps")))
23620 inputs "/lib/python3.9/site-packages/torch/lib/libtorch.so")
23621 (string-append deps "/libtorch.so"))
23624 inputs "/lib/liblantern.so")
23625 (string-append deps "/liblantern.so"))))))))
23627 (list python-pytorch-for-r-torch
23640 (native-inputs (list r-knitr))
23641 (home-page "https://torch.mlverse.org/docs")
23642 (synopsis "Tensors and neural networks with GPU acceleration")
23644 "This package provides functionality to define and train neural networks
23645 similar to PyTorch but written entirely in R using the libtorch library. It
23646 also supports low-level tensor operations and GPU acceleration.")
23647 (license license:expat)))
23649 (define-public r-additivitytests
23651 (name "r-additivitytests")
23656 (uri (cran-uri "additivityTests" version))
23659 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
23661 `((upstream-name . "additivityTests")))
23662 (build-system r-build-system)
23663 (home-page "https://github.com/simecek/additivityTests")
23664 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
23666 "This package provides an implementation of the Tukey, Mandel,
23667 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
23668 (license license:gpl3)))
23670 (define-public r-flexclust
23672 (name "r-flexclust")
23677 (uri (cran-uri "flexclust" version))
23680 "13akk3w6a76jpws5v9108c3hdmb8i6gm0sc06lr2hqly0pgpfyfn"))))
23681 (properties `((upstream-name . "flexclust")))
23682 (build-system r-build-system)
23684 (list r-class r-lattice r-modeltools))
23685 (home-page "https://cran.r-project.org/web/packages/flexclust/")
23686 (synopsis "Flexible cluster algorithms")
23688 "The main function @code{kcca} implements a general framework for
23689 k-centroids cluster analysis supporting arbitrary distance measures and
23690 centroid computation. Further cluster methods include hard competitive
23691 learning, neural gas, and QT clustering. There are numerous visualization
23692 methods for cluster results (neighborhood graphs, convex cluster hulls,
23693 barcharts of centroids, ...), and bootstrap methods for the analysis of
23694 cluster stability.")
23695 (license license:gpl2)))
23697 (define-public r-biclust
23704 (uri (cran-uri "biclust" version))
23707 "0lgyc2f04dhr65cwga78pradxsdzgjrpp8vphchqn60ab1z95dlp"))))
23708 (properties `((upstream-name . "biclust")))
23709 (build-system r-build-system)
23711 (list r-additivitytests
23718 (home-page "https://cran.r-project.org/web/packages/biclust/")
23719 (synopsis "BiCluster algorithms")
23721 "The main function @code{biclust()} provides several algorithms to find
23722 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
23723 In addition, the package provides methods for data
23724 preprocessing (normalization and discretization), visualization, and
23725 validation of bicluster solutions.")
23726 (license license:gpl3)))
23728 (define-public r-icge
23735 (uri (cran-uri "ICGE" version))
23738 "0w6hbi3h98q6gsxqbb43p95v6xykgrasxcjivwm8hw9fly4avxyi"))))
23739 (properties `((upstream-name . "ICGE")))
23740 (build-system r-build-system)
23742 (list r-cluster r-fastcluster r-mass))
23743 (home-page "https://cran.r-project.org/web/packages/ICGE/")
23744 (synopsis "Cluster estimation and identification of atypical units")
23746 "ICGE is a package that helps to estimate the number of real clusters in
23747 data as well as to identify atypical units. The underlying methods are based
23748 on distances rather than on unit x variables.")
23749 (license license:gpl2+)))
23751 (define-public r-depth
23754 (version "2.1-1.1")
23758 (uri (cran-uri "depth" version))
23761 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
23762 (properties `((upstream-name . "depth")))
23763 (build-system r-build-system)
23765 (list r-abind r-circular r-rgl))
23768 (home-page "https://cran.r-project.org/web/packages/depth/")
23769 (synopsis "Nonparametric depth functions for multivariate analysis")
23771 "This package provides tools for depth functions methodology applied to
23772 multivariate analysis. Besides allowing calculation of depth values and
23773 depth-based location estimators, the package includes functions or drawing
23774 contour plots and perspective plots of depth functions. Euclidean and
23775 spherical depths are supported.")
23776 (license license:gpl2)))
23778 (define-public r-archetypes
23780 (name "r-archetypes")
23781 (version "2.2-0.1")
23785 (uri (cran-uri "archetypes" version))
23788 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
23789 (properties `((upstream-name . "archetypes")))
23790 (build-system r-build-system)
23792 (list r-modeltools r-nnls))
23793 (home-page "https://cran.r-project.org/web/packages/archetypes")
23794 (synopsis "Archetypal analysis")
23796 "The main function @code{archetypes} implements a framework for
23797 archetypal analysis supporting arbitrary problem solving mechanisms for the
23798 different conceptual parts of the algorithm.")
23799 (license license:gpl2+)))
23801 (define-public r-shapes
23808 (uri (cran-uri "shapes" version))
23811 "1p9fr95zk3q2v277c5ksb0nh26mcpzwjzjb2lmag51z6hck8cb66"))))
23812 (properties `((upstream-name . "shapes")))
23813 (build-system r-build-system)
23815 (list r-mass r-minpack-lm r-rgl r-scatterplot3d))
23816 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
23817 (synopsis "Statistical shape analysis")
23819 "This package provides routines for the statistical analysis of landmark
23820 shapes, including Procrustes analysis, graphical displays, principal
23821 components analysis, permutation and bootstrap tests, thin-plate spline
23822 transformation grids and comparing covariance matrices. See Dryden, I.L. and
23823 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
23824 Edition), John Wiley and Sons.")
23825 (license license:gpl2)))
23827 (define-public r-anthropometry
23829 (name "r-anthropometry")
23834 (uri (cran-uri "Anthropometry" version))
23837 "0vxjlzxv16bygw8n57f25msq5bd1dydg41my92ximah0nzzvbg41"))))
23838 (properties `((upstream-name . "Anthropometry")))
23839 (build-system r-build-system)
23852 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
23853 (synopsis "Statistical methods for anthropometric data")
23855 "This package provides statistical methods especially developed to
23856 analyze anthropometric data. These methods are aimed at providing effective
23857 solutions to some commons problems related to Ergonomics and Anthropometry.
23858 They are based on clustering, the statistical concept of data depth,
23859 statistical shape analysis and archetypal analysis.")
23860 (license license:gpl2+)))
23862 (define-public r-anndata
23865 (version "0.7.5.3")
23869 (uri (cran-uri "anndata" version))
23871 (base32 "115v7gdilayd18hd519vzkixp2s6rvvrd1inc1i6amn7d0spy8r1"))))
23872 (properties `((upstream-name . "anndata")))
23873 (build-system r-build-system)
23874 (propagated-inputs (list r-assertthat r-matrix r-r6 r-reticulate))
23875 (native-inputs (list r-knitr))
23876 (home-page "https://anndata.dynverse.org")
23877 (synopsis "Anndata for R")
23879 "This package provides a reticulate wrapper for the Python package
23880 @code{anndata}. It provides a scalable way of keeping track of data and
23881 learned annotations. It is used to read from and write to the h5ad file
23883 (license license:expat)))
23885 (define-public r-adamethods
23887 (name "r-adamethods")
23892 (uri (cran-uri "adamethods" version))
23895 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
23896 (properties `((upstream-name . "adamethods")))
23897 (build-system r-build-system)
23899 (list r-anthropometry
23906 (home-page "https://cran.r-project.org/web/packages/adamethods/")
23907 (synopsis "Archetypoid algorithms and anomaly detection")
23909 "This package is a collection of several algorithms to obtain
23910 archetypoids with small and large databases and with both classical
23911 multivariate data and functional data (univariate and multivariate). Some of
23912 these algorithms also detect anomalies (outliers).")
23913 (license license:gpl2+)))
23915 (define-public r-idpmisc
23922 (uri (cran-uri "IDPmisc" version))
23925 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
23926 (properties `((upstream-name . "IDPmisc")))
23927 (build-system r-build-system)
23930 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
23931 (synopsis "Functions for data analyses and visualization")
23933 "This package provides different high-level graphics functions for
23934 displaying large datasets, displaying circular data in a very flexible way,
23935 finding local maxima, brewing color ramps, drawing nice arrows, zooming
23936 2D-plots, creating figures with differently colored margin and plot region.
23937 In addition, the package contains auxiliary functions for data manipulation
23938 like omitting observations with irregular values or selecting data by logical
23939 vectors, which include NAs. Other functions are especially useful in
23940 spectroscopy and analyses of environmental data: robust baseline fitting,
23941 finding peaks in spectra, converting humidity measures.")
23942 (license license:gpl3+)))
23944 (define-public r-qqconf
23950 (uri (cran-uri "qqconf" version))
23953 "0qnfzq2zb776kmvbwmyj9di4nlzx7dg0nz4097hfcllfx9160nwv"))))
23954 (properties `((upstream-name . "qqconf")))
23955 (build-system r-build-system)
23956 (inputs (list fftw))
23964 (native-inputs (list pkg-config r-knitr))
23965 (home-page "https://github.com/eweine/qqconf")
23966 (synopsis "Create simultaneous testing bands for QQ-plots")
23968 "This package provides functionality for creating Quantile-Quantile (QQ) and
23969 Probability-Probability (PP) plots with simultaneous testing bands to asses
23970 significance of sample deviation from a reference distribution.")
23971 (license license:gpl3)))
23973 (define-public r-qqman
23980 (uri (cran-uri "qqman" version))
23983 "1a6qp5wv9bvwjchfw8x4jh48hkynlnfr21a8vqgnswldvwbq7njq"))))
23984 (properties `((upstream-name . "qqman")))
23985 (build-system r-build-system)
23987 (list r-calibrate))
23990 (home-page "https://cran.r-project.org/web/packages/qqman/")
23991 (synopsis "Q-Q and Manhattan plots for GWAS data")
23993 "This package allows you to create Q-Q and Manhattan plots for GWAS data
23994 from PLINK results.")
23995 (license license:gpl3)))
23997 (define-public r-gghighlight
23999 (name "r-gghighlight")
24004 (uri (cran-uri "gghighlight" version))
24006 (base32 "0isfp5n0ijqpy3z5d7l75mlq15nbkjppv6812lcya6097ar2d381"))))
24007 (properties `((upstream-name . "gghighlight")))
24008 (build-system r-build-system)
24010 (list r-dplyr r-ggplot2 r-ggrepel r-lifecycle r-purrr r-rlang r-tibble))
24011 (native-inputs (list r-knitr))
24012 (home-page "https://github.com/yutannihilation/gghighlight/")
24013 (synopsis "Highlight lines and points in ggplot2")
24014 (description "Suppose we have data that has so many series that it is hard
24015 to identify them by their colors as the differences are so subtle. With
24016 gghighlight we can highlight those lines that match certain criteria. The
24017 result is a usual @code{ggplot} object, so it is fully customizable and can be
24018 used with custom themes and facets.")
24019 (license license:expat)))
24021 (define-public r-ggplot-multistats
24023 (name "r-ggplot-multistats")
24028 (uri (cran-uri "ggplot.multistats" version))
24031 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
24033 `((upstream-name . "ggplot.multistats")))
24034 (build-system r-build-system)
24036 (list r-ggplot2 r-hexbin r-rlang r-scales))
24037 (home-page "https://github.com/flying-sheep/ggplot.multistats")
24038 (synopsis "Multiple summary statistics for binned stats/geometries")
24040 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
24041 which functions similar to its singular form, but allows the use of multiple
24042 statistics per bin. Those statistics can be mapped to multiple bin
24044 (license license:gpl3)))
24046 (define-public r-knn-covertree
24048 (name "r-knn-covertree")
24053 (uri (cran-uri "knn.covertree" version))
24056 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
24057 (properties `((upstream-name . "knn.covertree")))
24058 (build-system r-build-system)
24060 (list r-matrix r-rcpp r-rcppeigen))
24061 (home-page "https://github.com/flying-sheep/knn.covertree")
24062 (synopsis "Accurate kNN Implementation with multiple distance measures")
24064 "Similarly to the FNN package, this package allows calculation of the k
24065 nearest neighbors (kNN) of a data matrix. The implementation is based on
24066 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
24067 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
24068 (license license:agpl3+)))
24070 (define-public r-poibin
24077 (uri (cran-uri "poibin" version))
24080 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
24081 (properties `((upstream-name . "poibin")))
24082 (build-system r-build-system)
24083 (home-page "https://cran.r-project.org/web/packages/poibin/")
24084 (synopsis "Poisson binomial distribution")
24086 "This package provides an implementation of both the exact and
24087 approximation methods for computing the @dfn{cumulative distribution
24088 function} (CDF) of the Poisson binomial distribution. It also provides the
24089 @dfn{probability mass function} (PMF), quantile function, and random number
24090 generation for the Poisson binomial distribution.")
24091 (license license:gpl2)))
24093 (define-public r-diagram
24100 (uri (cran-uri "diagram" version))
24103 "1r3lyl0h7mk9cfg8smr3jydfkjdawaphnxibkxfjqa7029vkxh79"))))
24104 (properties `((upstream-name . "diagram")))
24105 (build-system r-build-system)
24108 (home-page "https://cran.r-project.org/web/packages/diagram/")
24109 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
24111 "This package provides tools to visualize simple graphs (networks) based
24112 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
24113 electrical networks, etc. It also includes supporting material for the book
24114 \"A practical guide to ecological modelling - using R as a simulation
24115 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
24116 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
24117 Francesca Mazzia (2012).")
24118 (license license:gpl2+)))
24120 (define-public r-lim
24127 (uri (cran-uri "LIM" version))
24130 "0d9bgyd0mnag8wds993dsvlbpkhyakydlzwc3nghxzv2n8504hjj"))))
24131 (properties `((upstream-name . "LIM")))
24132 (build-system r-build-system)
24134 (list r-diagram r-limsolve))
24135 (home-page "https://cran.r-project.org/web/packages/LIM/")
24136 (synopsis "Linear inverse model examples and solution methods")
24138 "This package provides functions that read and solve linear inverse
24139 problems (food web problems, linear programming problems).")
24140 (license license:gpl2+)))
24142 (define-public r-shinycssloaders
24144 (name "r-shinycssloaders")
24149 (uri (cran-uri "shinycssloaders" version))
24152 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
24154 `((upstream-name . "shinycssloaders")))
24155 (build-system r-build-system)
24157 (list r-digest r-glue r-shiny))
24158 (home-page "https://github.com/andrewsali/shinycssloaders")
24159 (synopsis "Add CSS loading animations to Shiny outputs")
24161 "This package provides tools to create a lightweight Shiny wrapper for
24162 the css-loaders created by Luke Hass
24163 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
24164 automatically show a loader when the output is (re)calculating.")
24165 (license license:gpl3)))
24167 (define-public r-rsvg
24174 (uri (cran-uri "rsvg" version))
24177 "096w4d1gvfc65d4jg7ykp23k9f7cf7f8zvzfhvhd7qkfsbjpxqkj"))))
24178 (properties `((upstream-name . "rsvg")))
24179 (build-system r-build-system)
24181 (list librsvg zlib))
24183 (list pkg-config r-knitr))
24184 (home-page "https://github.com/jeroen/rsvg#readme")
24185 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
24187 "This package allows you to render vector-based SVG images into
24188 high-quality custom-size bitmap arrays using the librsvg2 library. The
24189 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
24190 addition, the package can convert images directly to various formats such as
24191 PDF or PostScript.")
24192 (license license:expat)))
24194 (define-public r-influencer
24196 (name "r-influencer")
24197 (version "0.1.0.1")
24201 (uri (cran-uri "influenceR" version))
24204 "0rj7rm236vn3v8302nwl12s0kvpv6xpdbm3q3gxk7vgwfl8nzi33"))))
24205 (properties `((upstream-name . "influenceR")))
24206 (build-system r-build-system)
24208 (list r-igraph r-matrix))
24209 (home-page "https://github.com/rcc-uchicago/influenceR")
24210 (synopsis "Tools to quantify structural importance of nodes in a network")
24212 "This package provides functionality to compute various node centrality
24213 measures on networks. Included are functions to compute betweenness
24214 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
24215 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
24216 algorithm to identify key players, and Valente's bridging metric. The
24217 betweenness, Key Players, and bridging implementations are parallelized with
24219 (license license:gpl2)))
24221 (define-public r-emplik
24228 (uri (cran-uri "emplik" version))
24231 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
24232 (properties `((upstream-name . "emplik")))
24233 (build-system r-build-system)
24236 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
24237 (synopsis "Empirical likelihood ratio for censored/truncated data")
24239 "This package provides empirical likelihood ratio tests for
24240 means/quantiles/hazards from possibly censored and/or truncated data. It also
24242 (license license:gpl2+)))
24244 (define-public r-imputeyn
24246 (name "r-imputeyn")
24251 (uri (cran-uri "imputeYn" version))
24254 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
24255 (properties `((upstream-name . "imputeYn")))
24256 (build-system r-build-system)
24258 (list r-boot r-emplik r-mvtnorm r-quadprog r-survival))
24259 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
24260 (synopsis "Impute last largest censored observation under weighted least squares")
24262 "This package allows for the imputation of the last largest censored
24263 observantions. This method brings less bias and more efficient estimates for
24265 (license license:gpl2)))
24267 (define-public r-adapenetclass
24269 (name "r-adapenetclass")
24274 (uri (cran-uri "AdapEnetClass" version))
24277 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
24278 (properties `((upstream-name . "AdapEnetClass")))
24279 (build-system r-build-system)
24281 (list r-glmnet r-imputeyn r-lars r-quadprog))
24282 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
24283 (synopsis "Class of adaptive elastic net methods for censored data")
24285 "This package provides methods for variable selection for AFT models.")
24286 (license license:gpl2)))
24288 (define-public r-flock
24295 (uri (cran-uri "flock" version))
24298 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
24299 (properties `((upstream-name . "flock")))
24300 (build-system r-build-system)
24301 (propagated-inputs (list r-rcpp))
24302 (home-page "https://cran.r-project.org/web/packages/flock/")
24303 (synopsis "Process synchronization using file locks")
24305 "This package implements synchronization between R processes (spawned by
24306 using the @code{parallel} package for instance) using file locks. It supports
24307 both exclusive and shared locking.")
24308 (license license:asl2.0)))
24310 (define-public r-archivist
24312 (name "r-archivist")
24317 (uri (cran-uri "archivist" version))
24320 "0q1qysack30xzxdbvvi56rk7r85hsj4ghls9r70ki7bl3rqwr4c9"))))
24321 (properties `((upstream-name . "archivist")))
24322 (build-system r-build-system)
24334 (home-page "https://pbiecek.github.io/archivist/")
24335 (synopsis "Tools for storing, restoring and searching for R objects")
24337 "Data exploration and modelling is a process in which a lot of data
24338 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
24339 statistical models, different versions of data sets and different versions of
24340 results. Archivist helps to store and manage artifacts created in R. It
24341 allows you to store selected artifacts as binary files together with their
24342 metadata and relations. Archivist allows sharing artifacts with others. It
24343 can look for already created artifacts by using its class, name, date of the
24344 creation or other properties. It also makes it easy to restore such
24346 (license license:gpl2)))
24348 (define-public r-versions
24350 (name "r-versions")
24355 (uri (cran-uri "versions" version))
24358 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
24359 (properties `((upstream-name . "versions")))
24360 (build-system r-build-system)
24361 (home-page "https://cran.r-project.org/web/packages/versions/")
24362 (synopsis "Query and install specific versions of CRAN packages")
24364 "This package allows you to install specified versions of R packages
24365 hosted on CRAN and provides functions to list available versions and the
24366 versions of currently installed packages.")
24367 (license license:bsd-3)))
24369 (define-public r-adapr
24376 (uri (cran-uri "adapr" version))
24379 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
24380 (properties `((upstream-name . "adapr")))
24381 (build-system r-build-system)
24398 (home-page "https://cran.r-project.org/web/packages/adapr/")
24399 (synopsis "Implementation of an accountable data analysis process")
24401 "This package tracks reading and writing within R scripts that are
24402 organized into a directed acyclic graph. It contains an interactive Shiny
24403 application @code{adaprApp()}. It uses Git and file hashes to track version
24404 histories of inputs and outputs.")
24405 (license license:lgpl2.0)))
24407 (define-public r-adapsamp
24409 (name "r-adapsamp")
24414 (uri (cran-uri "AdapSamp" version))
24417 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
24418 (properties `((upstream-name . "AdapSamp")))
24419 (build-system r-build-system)
24420 (propagated-inputs (list r-pracma))
24421 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
24422 (synopsis "Adaptive sampling algorithms")
24424 "For distributions whose probability density functions are log-concave,
24425 the adaptive rejection sampling algorithm can be used to build envelope
24426 functions for sampling. For others, the modified adaptive rejection sampling
24427 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
24428 adaptive slice sampling algorithm can be used. This R package mainly includes
24429 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
24430 @code{rASS()}. These functions can realize sampling based on the algorithms
24432 (license license:gpl2)))
24434 (define-public r-adaptalint
24436 (name "r-adaptalint")
24441 (uri (cran-uri "adaptalint" version))
24444 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
24445 (properties `((upstream-name . "adaptalint")))
24446 (build-system r-build-system)
24448 (list r-dplyr r-lintr r-purrr))
24449 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
24450 (synopsis "Check R code style")
24452 "This package provides tools to infer the code style (which style rules
24453 are followed and which ones are not) from one package and use it to check
24454 another. This makes it easier to find and correct the most important problems
24456 (license license:gpl3)))
24458 (define-public r-fracdiff
24460 (name "r-fracdiff")
24465 (uri (cran-uri "fracdiff" version))
24468 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
24469 (properties `((upstream-name . "fracdiff")))
24470 (build-system r-build-system)
24471 (home-page "https://github.com/mmaechler/fracdiff")
24473 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
24475 "This package provides tools for the maximum likelihood estimation of the
24476 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
24477 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
24478 (license license:gpl2+)))
24480 (define-public r-forecast
24482 (name "r-forecast")
24487 (uri (cran-uri "forecast" version))
24490 "0zvn44k7npxai8kj0hgxaaqv1hgd8rxicnvj4cg7wfl8ba4yn0cz"))))
24491 (properties `((upstream-name . "forecast")))
24492 (build-system r-build-system)
24507 (list r-knitr)) ; needed for vignettes
24508 (home-page "https://pkg.robjhyndman.com/forecast/")
24509 (synopsis "Forecasting functions for time series and linear models")
24511 "This package provides methods and tools for displaying and analysing
24512 univariate time series forecasts including exponential smoothing via state
24513 space models and automatic ARIMA modelling.")
24514 (license license:gpl3)))
24516 (define-public r-formattable
24518 (name "r-formattable")
24523 (uri (cran-uri "formattable" version))
24525 (base32 "1vdxi0xmg019qyzjrp8bkjxciz245jcxsrkhfzd44ynqcwi4s3ag"))))
24526 (properties `((upstream-name . "formattable")))
24527 (build-system r-build-system)
24529 (list r-htmltools r-htmlwidgets r-lifecycle r-rmarkdown))
24532 (home-page "https://github.com/renkun-ken/formattable")
24533 (synopsis "Print vectors and data frames with text fromatting")
24535 "This R package provides functions to create formattable vectors and data
24536 frames. @emph{Formattable} vectors are printed with text formatting, and
24537 formattable data frames are printed with multiple types of formatting in HTML
24538 to improve the readability of data presented in tabular form rendered in web
24540 (license license:expat)))
24542 (define-public r-xmisc
24549 (uri (cran-uri "Xmisc" version))
24552 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
24553 (properties `((upstream-name . "Xmisc")))
24554 (build-system r-build-system)
24555 (home-page "https://cran.r-project.org/package=Xmisc")
24557 "Xiaobei's miscellaneous classes and functions")
24559 "This package provides Xiaobei's miscellaneous classes and functions,
24560 which are useful when developing R packages for @dfn{object oriented
24561 programming} (OOP) using R Reference Class.")
24562 (license license:gpl2+)))
24564 (define-public r-proxyc
24571 (uri (cran-uri "proxyC" version))
24574 "1mcimswrx1cjjm7wsgkzfrgh3jpf4sncwfvdvg2f14fzfzy7afd6"))))
24575 (properties `((upstream-name . "proxyC")))
24576 (build-system r-build-system)
24578 (list r-matrix r-rcpp r-rcpparmadillo r-rcppparallel))
24579 (home-page "https://cran.r-project.org/package=proxyC")
24580 (synopsis "Compute proximity in large sparse matrices")
24582 "This package provides efficient tools to compute the proximity between
24583 rows or columns of large matrices. Functions are optimised for large sparse
24584 matrices using the Armadillo and Intel TBB libraries. Among several built-in
24585 similarity/distance measures, computation of correlation, cosine similarity
24586 and Euclidean distance is particularly fast.")
24587 (license license:gpl3)))
24589 (define-public r-isocodes
24591 (name "r-isocodes")
24592 (version "2022.01.10")
24596 (uri (cran-uri "ISOcodes" version))
24599 "0gy7n5bgxnl4rawry0pg078bkks9lzsbsrwjq8q5cvxl4k3dwpdj"))))
24600 (properties `((upstream-name . "ISOcodes")))
24601 (build-system r-build-system)
24602 (home-page "https://cran.r-project.org/package=ISOcodes")
24603 (synopsis "Selected ISO codes")
24605 "This package provides ISO language, territory, currency, script and
24606 character codes. It provides ISO 639 language codes, ISO 3166 territory
24607 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
24608 character codes as well as the UN M.49 area codes.")
24609 (license license:gpl2)))
24611 (define-public r-stopwords
24613 (name "r-stopwords")
24618 (uri (cran-uri "stopwords" version))
24621 "1ci1cgxrcvlhhplximsfv0plvjdbcd5kv0nphxnpildsn5m1rv65"))))
24622 (properties `((upstream-name . "stopwords")))
24623 (build-system r-build-system)
24626 (home-page "https://github.com/quanteda/stopwords")
24627 (synopsis "Multilingual stopword lists")
24629 "This package provides multiple sources of stopwords, for use in text
24630 analysis and natural language processing.")
24631 (license license:expat)))
24633 (define-public r-spacyr
24640 (uri (cran-uri "spacyr" version))
24643 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
24644 (properties `((upstream-name . "spacyr")))
24645 (build-system r-build-system)
24647 (list r-data-table r-reticulate))
24648 (home-page "https://spacyr.quanteda.io")
24649 (synopsis "R wrapper for the spaCy NLP library")
24651 "This package provides an R wrapper to the Python @dfn{natural language
24652 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
24653 (license license:gpl3)))
24655 (define-public r-snowballc
24657 (name "r-snowballc")
24662 (uri (cran-uri "SnowballC" version))
24665 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
24666 (properties `((upstream-name . "SnowballC")))
24667 (build-system r-build-system)
24668 (home-page "https://r-forge.r-project.org/projects/r-temis/")
24669 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
24671 "This package provides an R interface to the C @code{libstemmer} library
24672 that implements Porter's word stemming algorithm for collapsing words to a
24673 common root to aid comparison of vocabulary. Currently supported languages
24674 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
24675 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
24676 (license license:bsd-3)))
24678 (define-public r-quanteda
24680 (name "r-quanteda")
24685 (uri (cran-uri "quanteda" version))
24688 "102wlx6481fskgdr5wv467n29f666q0qg9kjm0ivqfg9xsbvza12"))))
24689 (properties `((upstream-name . "quanteda")))
24690 (build-system r-build-system)
24705 (home-page "https://quanteda.io")
24706 (synopsis "Quantitative analysis of textual data")
24708 "This package provides a fast, flexible, and comprehensive framework for
24709 quantitative text analysis in R. It provides functionality for corpus
24710 management, creating and manipulating tokens and ngrams, exploring keywords in
24711 context, forming and manipulating sparse matrices of documents by features and
24712 feature co-occurrences, analyzing keywords, computing feature similarities and
24713 distances, applying content dictionaries, applying supervised and unsupervised
24714 machine learning, visually representing text and text analyses, and more.")
24715 (license license:gpl3)))
24717 (define-public r-topicmodels
24719 (name "r-topicmodels")
24724 (uri (cran-uri "topicmodels" version))
24727 "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g"))))
24728 (properties `((upstream-name . "topicmodels")))
24729 (build-system r-build-system)
24733 (list r-modeltools r-slam r-tm))
24734 (home-page "https://cran.r-project.org/package=topicmodels")
24735 (synopsis "Topic models")
24737 "This package provides an interface to the C code for @dfn{Latent
24738 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
24739 David M. Blei and co-authors and the C++ code for fitting LDA models using
24740 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
24741 (license license:gpl2)))
24743 (define-public r-stm
24750 (uri (cran-uri "stm" version))
24753 "0qwq4nin2n9fjd06852r8k7arvcgh46kcfb3lm21swgx6j8bgrhb"))))
24754 (properties `((upstream-name . "stm")))
24755 (build-system r-build-system)
24768 (home-page "http://www.structuraltopicmodel.com/")
24769 (synopsis "Estimation of the Structural Topic Model")
24771 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
24772 topic models with document-level covariates. The package also includes tools
24773 for model selection, visualization, and estimation of topic-covariate
24775 (license license:expat)))
24777 (define-public r-polycor
24784 (uri (cran-uri "polycor" version))
24787 "0285rvx8238qp8dix0jq0cqq7ks8h6cjwsscbc7dx4n9nph56pzh"))))
24788 (properties `((upstream-name . "polycor")))
24789 (build-system r-build-system)
24791 (list r-admisc r-matrix r-mvtnorm))
24792 (home-page "https://r-forge.r-project.org/projects/polycor/")
24793 (synopsis "Polychoric and polyserial correlations")
24795 "This package provides tools to compute polychoric and polyserial
24796 correlations by quick \"two-step\" methods or ML, optionally with standard
24797 errors; tetrachoric and biserial correlations are special cases.")
24798 (license license:gpl2+)))
24800 (define-public r-msm
24807 (uri (cran-uri "msm" version))
24810 "08vhazswyxr3y1zb9y60mbg3bappzlizxml8s08p65mh82xxkz5f"))))
24811 (properties `((upstream-name . "msm")))
24812 (build-system r-build-system)
24814 (list r-expm r-mvtnorm r-survival))
24815 (home-page "https://github.com/chjackson/msm")
24816 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
24818 "This package provides functions for fitting continuous-time Markov and
24819 hidden Markov multi-state models to longitudinal data. It was designed for
24820 processes observed at arbitrary times in continuous time (panel data) but some
24821 other observation schemes are supported. Both Markov transition rates and the
24822 hidden Markov output process can be modelled in terms of covariates, which may
24823 be constant or piecewise-constant in time.")
24824 (license license:gpl2+)))
24826 (define-public r-ltm
24833 (uri (cran-uri "ltm" version))
24836 "0vhgbk6j0z3limsrbjkjkpfn2whiaij5j4jf1gg66mjs9dlylap1"))))
24837 (properties `((upstream-name . "ltm")))
24838 (build-system r-build-system)
24840 (list r-mass r-msm r-polycor))
24841 (home-page "https://github.com/drizopoulos/ltm")
24842 (synopsis "Latent trait models under IRT")
24844 "This is a package supporting the analysis of multivariate dichotomous
24845 and polytomous data using latent trait models under the Item Response Theory
24846 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
24847 Three-Parameter, the Graded Response, and the Generalized Partial Credit
24849 (license license:gpl2+)))
24851 (define-public r-mi
24858 (uri (cran-uri "mi" version))
24861 "11f75ivnax6p48mp2pasprws488cm2daym87sw2mcrywvf89fyjd"))))
24862 (properties `((upstream-name . "mi")))
24863 (build-system r-build-system)
24865 (list r-arm r-matrix))
24868 (home-page "http://www.stat.columbia.edu/~gelman/")
24869 (synopsis "Missing data imputation and model checking")
24871 "This package provides functions for data manipulation, imputing missing
24872 values in an approximate Bayesian framework, diagnostics of the models used to
24873 generate the imputations, confidence-building mechanisms to validate some of
24874 the assumptions of the imputation algorithm, and functions to analyze multiply
24875 imputed data sets with the appropriate degree of sampling uncertainty.")
24876 (license license:gpl2+)))
24878 (define-public r-matrixcalc
24880 (name "r-matrixcalc")
24885 (uri (cran-uri "matrixcalc" version))
24888 "1jkgl1v1q7cqpl1rf49qahdr9y0f33f0ldsbgby8xhfv0vpy21jr"))))
24889 (properties `((upstream-name . "matrixcalc")))
24890 (build-system r-build-system)
24891 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
24892 (synopsis "Collection of functions for matrix calculations")
24894 "This package provides a collection of functions to support matrix
24895 calculations for probability, econometric and numerical analysis. There are
24896 additional functions that are comparable to APL functions which are useful for
24897 actuarial models such as pension mathematics.")
24898 (license license:gpl2+)))
24900 (define-public r-matrixextra
24902 (name "r-matrixextra")
24907 (uri (cran-uri "MatrixExtra" version))
24909 (base32 "00f6sgw6p2709gs3df68yr59nvsr429pk9xql71id3kachjzh618"))))
24910 (properties `((upstream-name . "MatrixExtra")))
24911 (build-system r-build-system)
24913 (list r-float r-matrix r-rcpp r-rhpcblasctl))
24916 (home-page "https://github.com/david-cortes/MatrixExtra")
24917 (synopsis "Extra methods for sparse matrices")
24919 "This package extends sparse matrix and vector classes from the Matrix
24920 package by providing:
24923 @item Methods and operators that work natively on CSR formats (compressed
24924 sparse row, a.k.a. @code{RsparseMatrix}) such as slicing/sub-setting,
24925 assignment, @code{rbind()}, mathematical operators for CSR and COO such as
24926 addition or @code{sqrt()}, and methods such as @code{diag()};
24927 @item Multi-threaded matrix multiplication and cross-product for many
24928 @code{<sparse, dense>} types, including the @code{float32} type from
24930 @item Coercion methods between pairs of classes which are not present in
24931 @code{Matrix}, such as from @code{dgCMatrix} to @code{ngRMatrix}, as well as
24932 convenience conversion functions;
24933 @item Utility functions for sparse matrices such as sorting the indices or
24934 removing zero-valued entries;
24935 @item Fast transposes that work by outputting in the opposite storage format;
24936 @item Faster replacements for many @code{Matrix} methods for all sparse types,
24937 such as slicing and elementwise multiplication.
24938 @item Convenience functions for sparse objects, such as @code{mapSparse} or a
24939 shorter @code{show} method.
24942 (license license:gpl2+)))
24944 (define-public r-sem
24951 (uri (cran-uri "sem" version))
24954 "05hk72zxvyv6kkjhk5y6qw253c64108az7030z8j1sz8wq03n0md"))))
24955 (properties `((upstream-name . "sem")))
24956 (build-system r-build-system)
24958 (list r-boot r-mass r-mi))
24959 (home-page "https://cran.r-project.org/package=sem")
24960 (synopsis "Structural equation models")
24962 "This package provides functions for fitting general linear structural
24963 equation models (with observed and latent variables) using the RAM approach,
24964 and for fitting structural equations in observed-variable models by two-stage
24966 (license license:gpl2+)))
24968 (define-public r-semtools
24970 (name "r-semtools")
24975 (uri (cran-uri "semTools" version))
24978 "1wnakz76c4mgkwvx3iycmvgrzqys860jg9zpkba0ln5c08ycw8pm"))))
24979 (properties `((upstream-name . "semTools")))
24980 (build-system r-build-system)
24982 (list r-lavaan r-pbivnorm))
24983 (home-page "https://github.com/simsem/semTools/wiki")
24984 (synopsis "Useful tools for structural equation modeling")
24986 "This package provides useful tools for structural equation modeling.")
24987 (license license:gpl2+)))
24989 (define-public r-regsem
24996 (uri (cran-uri "regsem" version))
24999 "1v33wkrsawcvaa06cijp8ybwi82a0x34y59hdknwdbywplnirzr8"))))
25000 (properties `((upstream-name . "regsem")))
25001 (build-system r-build-system)
25003 (list r-lavaan r-rcpp r-rcpparmadillo r-rsolnp))
25006 (home-page "https://cran.r-project.org/package=regsem")
25007 (synopsis "Regularized structural equation modeling")
25009 "This package uses both ridge and lasso penalties (and extensions) to
25010 penalize specific parameters in structural equation models. The package
25011 offers additional cost functions, cross validation, and other extensions
25012 beyond traditional structural equation models. It also contains a function to
25013 perform @dfn{exploratory mediation} (XMed).")
25014 (license license:gpl2+)))
25016 (define-public r-stanheaders
25018 (name "r-stanheaders")
25019 (version "2.21.0-7")
25023 (uri (cran-uri "StanHeaders" version))
25026 "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17"))))
25027 (properties `((upstream-name . "StanHeaders")))
25028 (build-system r-build-system)
25029 (inputs (list pandoc))
25031 (list r-rcppeigen r-rcppparallel))
25033 (list gfortran r-knitr)) ; for vignettes
25034 (home-page "https://mc-stan.org/")
25035 (synopsis "C++ header files for Stan")
25037 "The C++ header files of the Stan project are provided by this package.
25038 There is a shared object containing part of the @code{CVODES} library, but it
25039 is not accessible from R. @code{r-stanheaders} is only useful for developers
25040 who want to utilize the @code{LinkingTo} directive of their package's
25041 DESCRIPTION file to build on the Stan library without incurring unnecessary
25044 The Stan project develops a probabilistic programming language that implements
25045 full or approximate Bayesian statistical inference via Markov Chain Monte
25046 Carlo or variational methods and implements (optionally penalized) maximum
25047 likelihood estimation via optimization. The Stan library includes an advanced
25048 automatic differentiation scheme, templated statistical and linear algebra
25049 functions that can handle the automatically differentiable scalar types (and
25050 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
25051 package provides user-facing R functions to parse, compile, test, estimate,
25052 and analyze Stan models.")
25053 (license license:bsd-3)))
25055 (define-public r-rpf
25062 (uri (cran-uri "rpf" version))
25065 "1yr1i7kswq57mcxv05lh7bvbicz1djqxcl6f13dlgsf3ww56gzg1"))))
25066 (properties `((upstream-name . "rpf")))
25067 (build-system r-build-system)
25069 (list r-lifecycle r-mvtnorm r-rcpp r-rcppeigen))
25072 (home-page "https://github.com/jpritikin/rpf")
25073 (synopsis "Response probability functions")
25075 "The purpose of this package is to factor out logic and math common to
25076 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
25077 core support code suitable for more specialized IRT packages to build upon.
25078 Complete access to optimized C functions is made available with
25079 @code{R_RegisterCCallable()}.")
25080 (license license:gpl3+)))
25082 (define-public r-openmx
25089 (uri (cran-uri "OpenMx" version))
25092 "1v969100hllh0lwlxd2gv0k7krrsp9gc07iinx0nn04wkzh0rib5"))))
25093 (properties `((upstream-name . "OpenMx")))
25094 (build-system r-build-system)
25106 (native-inputs (list r-knitr gfortran))
25107 (home-page "http://openmx.ssri.psu.edu")
25108 (synopsis "Extended structural equation modelling")
25110 "This package allows for the estimation of a wide variety of advanced
25111 multivariate statistical models. It consists of a library of functions and
25112 optimizers that allow you to quickly and flexibly define an SEM model and
25113 estimate parameters given observed data.")
25114 (license license:asl2.0)))
25116 (define-public r-kutils
25123 (uri (cran-uri "kutils" version))
25126 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
25127 (properties `((upstream-name . "kutils")))
25128 (build-system r-build-system)
25130 (list r-foreign r-openxlsx r-plyr r-runit r-xtable))
25131 (home-page "https://cran.r-project.org/package=kutils")
25132 (synopsis "Project management tools")
25134 "This package provides tools for data importation, recoding, and
25135 inspection. There are functions to create new project folders, R code
25136 templates, create uniquely named output directories, and to quickly obtain a
25137 visual summary for each variable in a data frame. The main feature here is
25138 the systematic implementation of the \"variable key\" framework for data
25139 importation and recoding.")
25140 (license license:gpl2)))
25142 (define-public r-rockchalk
25144 (name "r-rockchalk")
25145 (version "1.8.152")
25149 (uri (cran-uri "rockchalk" version))
25152 "1d15jlgcy35pvaicaddd4zrhwm5ajb9yc3jk6dyxm99gc5wcn6h3"))))
25153 (properties `((upstream-name . "rockchalk")))
25154 (build-system r-build-system)
25156 (list r-cardata r-kutils r-lme4 r-mass))
25157 (home-page "https://cran.r-project.org/package=rockchalk")
25158 (synopsis "Regression estimation and presentation")
25160 "This package provides a collection of functions for interpretation and
25161 presentation of regression analysis. These functions are used to produce the
25162 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
25163 includes regression diagnostics, regression tables, and plots of interactions
25164 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
25165 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
25166 fairly comprehensive overview.")
25167 (license license:gpl3+)))
25169 (define-public r-lisreltor
25171 (name "r-lisreltor")
25176 (uri (cran-uri "lisrelToR" version))
25179 "0i51v0x87277ly0kggdd594w6q4zq62b4n7xs9r25j08bzs82nfk"))))
25180 (properties `((upstream-name . "lisrelToR")))
25181 (build-system r-build-system)
25182 (home-page "https://cran.r-project.org/package=lisrelToR")
25183 (synopsis "Import output from LISREL into R")
25185 "This is an unofficial package aimed at automating the import of LISREL
25187 (license license:gpl2)))
25189 (define-public r-bdgraph
25196 (uri (cran-uri "BDgraph" version))
25199 "0s2j4462zlgyjnqvvvxg4lynhmwwnjaw1cr1chzmagfvaj94qhhz"))))
25200 (properties `((upstream-name . "BDgraph")))
25201 (build-system r-build-system)
25206 (home-page "https://www.uva.nl/profile/a.mohammadi")
25207 (synopsis "Bayesian structure learning in graphical models")
25209 "This package provides statistical tools for Bayesian structure learning
25210 in undirected graphical models for continuous, discrete, and mixed data. It
25211 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
25212 on a continuous-time birth-death process.")
25213 (license license:gpl2+)))
25215 (define-public r-d3network
25217 (name "r-d3network")
25218 (version "0.5.2.1")
25222 (uri (cran-uri "d3Network" version))
25225 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
25226 (properties `((upstream-name . "d3Network")))
25227 (build-system r-build-system)
25229 (list r-plyr r-rjson r-whisker))
25230 (home-page "http://christophergandrud.github.io/d3Network/")
25231 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
25233 "This package is intended to make it easy to create D3 JavaScript
25234 network, tree, dendrogram, and Sankey graphs from R using data frames.")
25235 (license license:gpl3+)))
25237 (define-public r-qgraph
25244 (uri (cran-uri "qgraph" version))
25247 "0r225b7rnsv6wz41ij0msmqr1xy0iqxh9dbsvjixbi1hvgv91wds"))))
25248 (properties `((upstream-name . "qgraph")))
25249 (build-system r-build-system)
25269 (home-page "http://sachaepskamp.com/qgraph/")
25270 (synopsis "Weighted network visualization and analysis")
25272 "This package implements tools for weighted network visualization and
25273 analysis, as well as Gaussian graphical model computation. It contains graph
25274 plotting methods, and tools for psychometric data visualization and graphical
25275 model estimation. See Epskamp et al. (2012)
25276 @url{doi:10.18637/jss.v048.i04}.")
25277 (license license:gpl2)))
25279 (define-public r-semplot
25286 (uri (cran-uri "semPlot" version))
25289 "0d7v9yqc9nhx3hdrp444w1ah66zai3lg5y778m85r7ngh1prxlvc"))))
25290 (properties `((upstream-name . "semPlot")))
25291 (build-system r-build-system)
25304 (home-page "https://github.com/SachaEpskamp/semPlot")
25305 (synopsis "Unified visualizations of structural equation models")
25307 "Structural equation modeling (SEM) has a long history of representing
25308 models graphically as path diagrams. The semPlot package for R fills the gap
25309 between advanced, but time-consuming, graphical software and the limited
25310 graphics produced automatically by SEM software. In addition, semPlot offers
25311 more functionality than drawing path diagrams: it can act as a common ground
25312 for importing SEM results into R. Any result usable as input to semPlot can
25313 also be represented in any of the three popular SEM frame-works, as well as
25314 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
25315 (license license:gpl2)))
25317 (define-public r-cdm
25324 (uri (cran-uri "CDM" version))
25327 "1cnk19k09cj81ic43rwbvcalvczfca4ncdyy8r1gyc8fzf2glb0i"))))
25328 (properties `((upstream-name . "CDM")))
25329 (build-system r-build-system)
25331 (list r-mvtnorm r-polycor r-rcpp r-rcpparmadillo))
25333 "https://github.com/alexanderrobitzsch/CDM")
25334 (synopsis "Cognitive diagnosis modeling")
25336 "This package provides functions for cognitive diagnosis modeling and
25337 multidimensional item response modeling for dichotomous and polytomous item
25338 responses. It enables the estimation of the DINA and DINO model, the multiple
25339 group (polytomous) GDINA model, the multiple choice DINA model, the general
25340 diagnostic model (GDM), the structured latent class model (SLCA), and
25341 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
25342 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
25343 estimation and the package structure. For tutorials on how to use the CDM
25344 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
25345 well as Ravand and Robitzsch (2015).")
25346 (license license:gpl2+)))
25348 (define-public r-tam
25355 (uri (cran-uri "TAM" version))
25358 "00ww277hsyci5rph4gb155h0y95dmjhqgn9amz6g8zbrjb2748dw"))))
25359 (properties `((upstream-name . "TAM")))
25360 (build-system r-build-system)
25362 (list r-cdm r-rcpp r-rcpparmadillo))
25363 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
25364 (synopsis "Test analysis modules")
25366 "This package includes tools for marginal maximum likelihood estimation
25367 and joint maximum likelihood estimation for unidimensional and
25368 multidimensional item response models. The package functionality covers the
25369 Rasch model, 2PL model, 3PL model, generalized partial credit model,
25370 multi-faceted Rasch model, nominal item response model, structured latent
25371 class model, mixture distribution IRT models, and located latent class models.
25372 Latent regression models and plausible value imputation are also supported.")
25373 (license license:gpl2+)))
25375 (define-public r-erm
25382 (uri (cran-uri "eRm" version))
25385 "0smym010kswc5vx90qr3x1vl16xj1x1i54rvrj006dc4agc1vmlk"))))
25386 (properties `((upstream-name . "eRm")))
25387 (build-system r-build-system)
25389 (list r-colorspace r-lattice r-mass r-matrix r-psych))
25390 (native-inputs (list gfortran))
25391 (home-page "https://cran.r-project.org/package=eRm")
25392 (synopsis "Extended Rasch modeling")
25394 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
25395 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
25396 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
25397 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
25398 data matrix. Additional features are the ML estimation of the person
25399 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
25400 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
25401 infit and outfit measures, ICC and other plots, automated stepwise item
25402 elimination, and a simulation module for various binary data matrices.")
25403 (license license:gpl3)))
25405 (define-public r-irtoys
25412 (uri (cran-uri "irtoys" version))
25415 "1qshz6czykgf53mq6xiswzv5xsjwrkrinpfkf1yavql4v08hs82b"))))
25416 (properties `((upstream-name . "irtoys")))
25417 (build-system r-build-system)
25422 (home-page "https://cran.r-project.org/package=irtoys")
25423 (synopsis "Collection of functions related to Item Response Theory (IRT)")
25425 "This package provides a collection of functions useful in learning and
25426 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
25427 programs. It provides basic CTT analysis, a simple common interface to the
25428 estimation of item parameters in IRT models for binary responses with three
25429 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
25430 EAP, WLE, plausible values), item and person fit statistics, scaling
25431 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
25432 array of parametric and non-parametric (kernel) plots. It estimates and plots
25433 Haberman's interaction model when all items are dichotomously scored.")
25434 (license license:gpl2+)))
25436 (define-public r-iheatmapr
25438 (name "r-iheatmapr")
25443 (uri (cran-uri "iheatmapr" version))
25446 "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx"))))
25447 (properties `((upstream-name . "iheatmapr")))
25448 (build-system r-build-system)
25450 (list r-fastcluster
25460 (home-page "https://docs.ropensci.org/iheatmapr")
25461 (synopsis "Interactive, Complex Heatmaps")
25463 "iheatmapr is an R package for building complex, interactive heatmaps
25464 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
25465 subplots along the rows or columns of the main heatmap add more information
25466 about each row or column. For example, a one column additional heatmap may
25467 indicate what group a particular row or column belongs to. Complex heatmaps
25468 may also include multiple side by side heatmaps which show different types of
25469 data for the same conditions. Interactivity can improve complex heatmaps by
25470 providing tooltips with information about each cell and enabling zooming into
25471 interesting features. iheatmapr uses the plotly library for interactivity.")
25472 (license license:expat)))
25474 (define-public r-packrat
25481 (uri (cran-uri "packrat" version))
25484 "1vs4i19x6jdwl3jnanp127k4hk80h1mj56cjn07w1gkl542vj99h"))))
25485 (properties `((upstream-name . "packrat")))
25486 (build-system r-build-system)
25487 (home-page "https://github.com/rstudio/packrat/")
25488 (synopsis "Dependency management R projects")
25490 "This package provides a dependency manager for R projects that allows
25491 you to manage the R packages your project depends on in an isolated, portable,
25492 and reproducible way.")
25493 (license license:gpl2)))
25495 (define-public r-rsconnect
25497 (name "r-rsconnect")
25502 (uri (cran-uri "rsconnect" version))
25505 "1vazdgpha7545h4riz11njbl8azg38i1y1a5nfckfx03v2zapbzs"))))
25506 (properties `((upstream-name . "rsconnect")))
25507 (build-system r-build-system)
25516 (home-page "https://github.com/rstudio/rsconnect")
25517 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
25519 "This package provides a programmatic deployment interface for RPubs,
25520 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
25521 documents, Shiny applications, Plumber APIs, plots, and static web content.")
25522 (license license:gpl2)))
25524 ;; This package includes minified JavaScript files. When upgrading please
25525 ;; check that there are no new minified JavaScript files.
25526 (define-public r-dygraphs
25528 (name "r-dygraphs")
25529 (version "1.1.1.6")
25533 (uri (cran-uri "dygraphs" version))
25536 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
25537 (properties `((upstream-name . "dygraphs")))
25538 (build-system r-build-system)
25540 `(#:modules ((guix build utils)
25541 (guix build r-build-system)
25545 (modify-phases %standard-phases
25546 (add-after 'unpack 'process-javascript
25547 (lambda* (#:key inputs #:allow-other-keys)
25548 (with-directory-excursion "inst/htmlwidgets/lib/"
25552 `(("dygraphs/dygraph-combined-dev.js"
25553 "dygraph-combined.js")
25554 (,(assoc-ref inputs "js-jquery")
25555 "jquery/jquery.min.js")
25556 (,(assoc-ref inputs "js-fquarter")
25557 "fquarter/moment-fquarter.min.js"))))
25558 (lambda (sources targets)
25559 (for-each (lambda (source target)
25560 (format #t "Processing ~a --> ~a~%"
25562 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
25563 (call-with-output-file target
25565 (dump-port minified port)))))
25566 sources targets))))
25569 `(("uglifyjs" ,node-uglify-js)
25570 ;; They actually use version 1.11.1, but this more recent version
25571 ;; should be just fine.
25575 (uri "https://code.jquery.com/jquery-1.12.4.js")
25578 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
25582 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
25583 "moment-fquarter/1.0.1/moment-fquarter.js"))
25586 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
25588 (list r-htmltools r-htmlwidgets r-magrittr r-xts r-zoo))
25589 (home-page "https://github.com/rstudio/dygraphs")
25590 (synopsis "Interface to Dygraphs interactive time series charting library")
25592 "This package provides an R interface to the dygraphs JavaScript charting
25593 library (a copy of which is included in the package). It provides rich
25594 facilities for charting time-series data in R, including highly configurable
25595 series- and axis-display and interactive features like zoom/pan and
25596 series/point highlighting.")
25597 (license license:expat)))
25599 (define-public r-shinystan
25601 (name "r-shinystan")
25606 (uri (cran-uri "shinystan" version))
25609 "0afm703zriyqprz1zvypir80lq2ylfff3qvj5i7p9n365mm8b150"))))
25610 (properties `((upstream-name . "shinystan")))
25611 (build-system r-build-system)
25629 (home-page "https://mc-stan.org/")
25630 (synopsis "Interactive visual and numerical analysis for Bayesian models")
25632 "This package provides a graphical user interface for interactive
25633 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
25634 for analyzing a posterior sample. The interface is powered by the Shiny web
25635 application framework and works with the output of MCMC programs written in
25636 any programming language (and has extended functionality for Stan models fit
25637 using the @code{rstan} and @code{rstanarm} packages).")
25638 (license license:gpl3+)))
25640 (define-public r-rstantools
25642 (name "r-rstantools")
25647 (uri (cran-uri "rstantools" version))
25650 "1dsfgi02hps878n3vimfdbzpm4gr5n3ccrmnc61ncrqcp6p0p0fb"))))
25651 (properties `((upstream-name . "rstantools")))
25652 (build-system r-build-system)
25653 (inputs (list pandoc))
25655 (list r-desc r-rcpp r-rcppparallel))
25658 (home-page "https://mc-stan.org/rstantools/")
25659 (synopsis "Tools for developing R packages interfacing with Stan")
25661 "This package provides various tools for developers of R packages
25662 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
25663 up the required package structure, S3 generics and default methods to unify
25664 function naming across Stan-based R packages, and vignettes with
25665 recommendations for developers.")
25666 (license license:gpl3+)))
25668 (define-public r-loo
25675 (uri (cran-uri "loo" version))
25677 (base32 "1wa5hxk7lkr88mway6b7xd5arrkkl2ldl9rf0v1nqwp8lia2ysl6"))))
25678 (properties `((upstream-name . "loo")))
25679 (build-system r-build-system)
25683 (list r-checkmate r-matrixstats))
25686 (home-page "https://mc-stan.org/loo/")
25687 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
25689 "This package provides an implementation of efficient approximate
25690 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
25691 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
25692 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
25693 procedure for regularizing importance weights. As a byproduct of the
25694 calculations, we also obtain approximate standard errors for estimated
25695 predictive errors and for the comparison of predictive errors between models.
25696 The package also provides methods for using stacking and other model weighting
25697 techniques to average Bayesian predictive distributions.")
25698 (license license:gpl3+)))
25700 (define-public r-rstan
25707 (uri (cran-uri "rstan" version))
25710 "1smr5cjrqvpdnkmjpjp73p96sy581x15mwrn4fqd1p4d5mbgxr46"))))
25711 (properties `((upstream-name . "rstan")))
25712 (build-system r-build-system)
25715 (modify-phases %standard-phases
25716 (add-before 'install 'set-timezone
25717 ;; This package is picky about timezones.
25718 (lambda* (#:key inputs #:allow-other-keys)
25719 (setenv "TZ" "UTC+1")
25721 (search-input-directory inputs
25722 "share/zoneinfo")))))))
25724 (list tzdata-for-tests pandoc r-knitr))
25736 (home-page "https://discourse.mc-stan.org/")
25737 (synopsis "R interface to Stan")
25739 "User-facing R functions are provided to parse, compile, test, estimate,
25740 and analyze Stan models by accessing the header-only Stan library provided by
25741 the StanHeaders package. The Stan project develops a probabilistic
25742 programming language that implements full Bayesian statistical inference via
25743 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
25744 approximation, and (optionally penalized) maximum likelihood estimation via
25745 optimization. In all three cases, automatic differentiation is used to
25746 quickly and accurately evaluate gradients without burdening the user with the
25747 need to derive the partial derivatives.")
25748 (license license:gpl3+)))
25750 (define-public r-rstanarm
25752 (name "r-rstanarm")
25757 (uri (cran-uri "rstanarm" version))
25760 "19rj396q84maxnd9d2xcd5rblg3310xn7sqbd6k18kwf3dvd7wp9"))))
25761 (properties `((upstream-name . "rstanarm")))
25762 (build-system r-build-system)
25783 (home-page "https://mc-stan.org/rstanarm/")
25784 (synopsis "Bayesian applied regression modeling via Stan")
25786 "This package estimates previously compiled regression models using the
25787 @code{rstan} package, which provides the R interface to the Stan C++ library
25788 for Bayesian estimation. Users specify models via the customary R syntax with
25789 a formula and @code{data.frame} plus some additional arguments for priors.")
25790 (license license:gpl3+)))
25792 (define-public r-kendall
25799 (uri (cran-uri "Kendall" version))
25802 "1xmk95l4i3kj9jn0xh1chi2rj322k29jq14ra5pa7316gwf9vx2m"))))
25803 (properties `((upstream-name . "Kendall")))
25804 (build-system r-build-system)
25809 (home-page "https://cran.r-project.org/web/packages/Kendall/")
25810 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
25812 "This package computes the Kendall rank correlation and Mann-Kendall
25814 (license license:gpl2+)))
25816 (define-public r-keyring
25823 (uri (cran-uri "keyring" version))
25826 "1j8l6nmh4dr70kwybiais8yh687fdwrj134xynq68igw1b1rm8ga"))))
25827 (properties `((upstream-name . "keyring")))
25828 (build-system r-build-system)
25838 (native-inputs (list pkg-config))
25839 (home-page "https://github.com/r-lib/keyring")
25840 (synopsis "Access the system credential store from R")
25842 "This package provides a platform-independent API to access the operating
25843 system's credential store. It currently supports Keychain on macOS,
25844 Credential Store on Windows, the Secret Service API on GNU/Linux, and a
25845 simple, platform independent store implemented with environment variables.
25846 Additional storage back-ends can be added easily.")
25847 (license license:expat)))
25849 (define-public r-zyp
25852 (version "0.10-1.1")
25856 (uri (cran-uri "zyp" version))
25859 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
25860 (properties `((upstream-name . "zyp")))
25861 (build-system r-build-system)
25864 (home-page "https://cran.r-project.org/web/packages/zyp/")
25865 (synopsis "Zhang + Yue-Pilon Trends Package")
25867 "This package contains an efficient implementation of Sen's slope
25868 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
25869 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
25871 (license license:lgpl2.1)))
25873 (define-public r-rlinsolve
25875 (name "r-rlinsolve")
25880 (uri (cran-uri "Rlinsolve" version))
25883 "1xv500n1480qyakw0isanw1s5ywykhc207hqja4804s5s2m8zfjw"))))
25884 (properties `((upstream-name . "Rlinsolve")))
25885 (build-system r-build-system)
25887 (list r-matrix r-rcpp r-rcpparmadillo r-rdpack))
25888 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
25889 (synopsis "Iterative solvers for (sparse) linear system of equations")
25891 "Solving a system of linear equations is one of the most fundamental
25892 computational problems for many fields of mathematical studies, such as
25893 regression problems from statistics or numerical partial differential
25894 equations. This package provides basic stationary iterative solvers such as
25895 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
25896 Nonstationary, also known as Krylov subspace methods are also provided.
25897 Sparse matrix computation is also supported in that solving large and sparse
25898 linear systems can be manageable using the @code{Matrix} package along with
25899 @code{RcppArmadillo}.")
25900 (license license:gpl3+)))
25902 (define-public r-zvcv
25909 (uri (cran-uri "ZVCV" version))
25912 "0gc76j9i8fkm2v638nyzzb1qxl4zmapbspkkaffb8gi5qyjja448"))))
25913 (properties `((upstream-name . "ZVCV")))
25914 (build-system r-build-system)
25925 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
25926 (synopsis "Zero-Variance Control Variates")
25928 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
25929 to reduce the variance of Monte Carlo estimators of expectations using the
25930 derivatives of the log target. Once the derivatives are available, the only
25931 additional computational effort is in solving a linear regression problem.
25932 This method has been extended to higher dimensions using regularisation. This
25933 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
25934 samples, derivatives and function evaluations are available. Additional
25935 functions for applying ZV-CV to two estimators for the normalising constant of
25936 the posterior distribution in Bayesian statistics are also supplied.")
25937 (license license:gpl2+)))
25939 (define-public r-ztype
25946 (uri (cran-uri "ztype" version))
25949 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
25950 (properties `((upstream-name . "ztype")))
25951 (build-system r-build-system)
25960 (home-page "https://cran.r-project.org/web/packages/ztype/")
25961 (synopsis "Run a Ztype game loaded with R functions")
25963 "How fast can you type R functions on your keyboard? Find out by running
25964 a @code{zty.pe} game: export R functions as instructions to type to destroy
25965 opponents' vessels.")
25966 (license license:gpl3)))
25968 (define-public r-zseq
25975 (uri (cran-uri "Zseq" version))
25978 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
25979 (properties `((upstream-name . "Zseq")))
25980 (build-system r-build-system)
25983 (home-page "https://cran.r-project.org/web/packages/Zseq/")
25984 (synopsis "Integer sequence generator")
25986 "This package generates well-known integer sequences. The @code{gmp}
25987 package is adopted for computing with arbitrarily large numbers. Every
25988 function has a hyperlink to its corresponding item in the @dfn{On-Line
25989 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
25990 (license license:gpl3+)))
25992 (define-public r-isoband
25999 (uri (cran-uri "isoband" version))
26002 "19bbi0n0kz33xdgmdprcmc6raphd1hcm1w1brc16z5phcsh3zxa6"))))
26003 (properties `((upstream-name . "isoband")))
26004 (build-system r-build-system)
26007 (home-page "https://github.com/wilkelab/isoband")
26008 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
26010 "This package provides a fast C++ implementation to generate contour
26011 lines (isolines) and contour polygons (isobands) from regularly spaced grids
26012 containing elevation data.")
26013 (license license:expat)))
26015 (define-public r-ppcor
26022 (uri (cran-uri "ppcor" version))
26025 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
26026 (properties `((upstream-name . "ppcor")))
26027 (build-system r-build-system)
26030 (home-page "https://cran.r-project.org/web/packages/ppcor/")
26031 (synopsis "Partial and semi-partial correlation")
26033 "This package provides users not only with a function to readily
26034 calculate the higher-order partial and semi-partial correlations but also with
26035 statistics and p-values of the correlation coefficients.")
26036 (license license:gpl2)))
26038 (define-public r-hrbrthemes
26040 (name "r-hrbrthemes")
26045 (uri (cran-uri "hrbrthemes" version))
26047 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
26048 (properties `((upstream-name . "hrbrthemes")))
26049 (build-system r-build-system)
26061 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
26062 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
26064 "This package provides a compilation of extra @code{ggplot2} themes,
26065 scales and utilities, including a spell check function for plot label fields
26066 and an overall emphasis on typography.")
26067 (license license:expat)))
26069 (define-public r-crochet
26076 (uri (cran-uri "crochet" version))
26079 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
26080 (build-system r-build-system)
26083 (home-page "https://github.com/agrueneberg/crochet")
26084 (synopsis "Implementation Helper for Matrix-Like Types")
26086 "Functions to help implement the extraction / subsetting / indexing
26087 function @code{[} and replacement function @code{[<-} of custom matrix-like
26088 types (based on S3, S4, etc.), modeled as closely to the base matrix class
26089 as possible (with tests to prove it).")
26090 (license license:expat)))
26092 (define-public r-boa
26095 (version "1.1.8-2")
26099 (uri (cran-uri "boa" version))
26102 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
26103 (properties `((upstream-name . "boa")))
26104 (build-system r-build-system)
26105 (home-page "https://www.jstatsoft.org/v21/i11")
26106 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
26108 "This package provides a menu-driven program and library of functions for
26109 carrying out convergence diagnostics and statistical and graphical analysis of
26110 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
26111 (license license:gpl2+)))
26113 (define-public r-httpcode
26115 (name "r-httpcode")
26119 (uri (cran-uri "httpcode" version))
26122 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
26123 (build-system r-build-system)
26124 (home-page "https://github.com/sckott/httpcode")
26125 (synopsis "HTTP status code helper")
26126 (description "@code{httpcode} provides functionality for finding and
26127 explaining the meaning of @code{HTTP} status codes. Functions are included for
26128 searching for codes by full or partial number, by message, and to get
26129 appropriate dog and cat images for many status codes.")
26130 (license license:expat)))
26132 (define-public r-latex2exp
26134 (name "r-latex2exp")
26138 (uri (cran-uri "latex2exp" version))
26141 "0zbbrbgg524lpm733j8qsqk5ssg75c51s6dgzb18c6fk8byrx945"))))
26142 (build-system r-build-system)
26144 (list r-stringr r-magrittr))
26147 (home-page "https://github.com/stefano-meschiari/latex2exp/")
26148 (synopsis "Use LaTeX expressions in plots")
26149 (description "@code{latex2exp} parses and converts LaTeX math formulas to
26150 R's plotmath expressions, used to enter mathematical formulas and symbols to be
26151 rendered as text, axis labels, etc. throughout R's plotting system.")
26152 (license license:expat)))
26154 (define-public r-oai
26160 (uri (cran-uri "oai" version))
26163 "1zcbcxhw692s0y6izvwazyzhgx0iwsxsbcan2nk0mb7n11p7bypb"))))
26164 (build-system r-build-system)
26166 (list r-xml2 r-httr r-plyr r-stringr r-tibble))
26169 (home-page "https://github.com/ropensci/oai/")
26170 (synopsis "General purpose OAI-PMH services client")
26171 (description "@code{oai} provides a general purpose client to work with
26172 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
26173 service. Functions are provided to work with the OAI-PMH verbs:
26174 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
26175 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
26176 (license license:expat)))
26178 (define-public r-argon2
26185 (uri (cran-uri "argon2" version))
26188 "09hzl0wz0lw2v7g64rdv0lij2hq36zl37a6rmxwvinmjdzijcsyw"))))
26189 (properties `((upstream-name . "argon2")))
26190 (build-system r-build-system)
26191 (home-page "https://github.com/wrathematics/argon2")
26192 (synopsis "Secure password hashing based on the argon2 algorithm")
26194 "This package provides utilities for secure password hashing via the
26195 argon2 algorithm.")
26196 (license license:bsd-2)))
26198 (define-public r-getpass
26205 (uri (cran-uri "getPass" version))
26208 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
26209 (properties `((upstream-name . "getPass")))
26210 (build-system r-build-system)
26212 (list r-rstudioapi))
26213 (home-page "https://github.com/wrathematics/getPass")
26214 (synopsis "Masked user input")
26216 "This package provides a micro-package for reading \"passwords\", i.e.
26217 reading user input with masking, so that the input is not displayed as it is
26218 typed. Currently, RStudio, the command line (every OS), and any platform
26219 where tcltk is present are supported.")
26220 (license license:bsd-2)))
26222 (define-public r-remoter
26229 (uri (cran-uri "remoter" version))
26232 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
26233 (properties `((upstream-name . "remoter")))
26234 (build-system r-build-system)
26236 (list r-argon2 r-getpass r-pbdzmq r-png))
26237 (home-page "https://github.com/RBigData/remoter")
26238 (synopsis "Control a remote R session from a local one")
26240 "This package provides a set of utilities for client/server computing
26241 with R, controlling a remote R session (the server) from a local one (the
26243 (license license:bsd-2)))
26245 (define-public r-asd
26252 (uri (cran-uri "asd" version))
26255 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
26256 (properties `((upstream-name . "asd")))
26257 (build-system r-build-system)
26260 (home-page "https://cran.r-project.org/web/packages/asd")
26261 (synopsis "Simulations for Adaptive Seamless Designs")
26263 "This package provdes means to run simulations for adaptive seamless
26264 designs with and without early outcomes for treatment selection and
26265 subpopulation type designs.")
26266 (license license:gpl3)))
26268 (define-public r-nbconvertr
26270 (name "r-nbconvertr")
26275 (uri (cran-uri "nbconvertR" version))
26278 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
26279 (properties `((upstream-name . "nbconvertR")))
26280 (build-system r-build-system)
26282 (list python-nbconvert pandoc))
26283 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
26284 (synopsis "Vignette engine wrapping Jupyter notebooks")
26286 "This package calls the Jupyter script @code{nbconvert} to create
26287 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
26288 containing rich text, code, and its output. Code cells can be edited and
26289 evaluated interactively.")
26290 (license license:gpl3)))
26292 (define-public r-bridgesampling
26294 (name "r-bridgesampling")
26299 (uri (cran-uri "bridgesampling" version))
26302 "0sry1xwiv4y52k44hq6z8y2kysp5kxgl4dix3m94svg3ladd7v2l"))))
26304 `((upstream-name . "bridgesampling")))
26305 (build-system r-build-system)
26307 (list r-brobdingnag
26315 (home-page "https://github.com/quentingronau/bridgesampling")
26316 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
26318 "This package provides functions for estimating marginal likelihoods,
26319 Bayes factors, posterior model probabilities, and normalizing constants in
26320 general, via different versions of bridge sampling.")
26321 (license license:gpl2+)))
26323 (define-public r-tea
26330 (uri (cran-uri "tea" version))
26333 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
26335 `((upstream-name . "tea")))
26336 (build-system r-build-system)
26339 (home-page "https://cran.r-project.org/web/packages/tea/")
26340 (synopsis "Threshold estimation approaches")
26342 "This package provides different approaches for selecting the threshold
26343 in generalized Pareto distributions. Most of them are based on minimizing the
26344 AMSE-criterion or at least by reducing the bias of the assumed GPD-model.
26345 Others are heuristically motivated by searching for stable sample paths, i.e.
26346 a nearly constant region of the tail index estimator with respect to k, which
26347 is the number of data in the tail. The third class is motivated by graphical
26348 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
26349 is also implemented here.")
26350 (license license:gpl3)))
26352 (define-public r-awsmethods
26354 (name "r-awsmethods")
26359 (uri (cran-uri "awsMethods" version))
26362 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
26364 `((upstream-name . "awsMethods")))
26365 (build-system r-build-system)
26366 (home-page "http://www.wias-berlin.de/software/imaging/")
26367 (synopsis "Class and methods definitions")
26369 "This package defines the generic method @code{extract} and provides
26370 @code{openMP} support as needed in several packages like
26371 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
26372 (license license:gpl2+)))
26374 (define-public r-aws
26381 (uri (cran-uri "aws" version))
26384 "1fhm87iax6bkvd4vszvjbcqw3b2drs11rjxr7zf2w4sgc72svaz8"))))
26386 `((upstream-name . "aws")))
26387 (build-system r-build-system)
26389 (list r-awsmethods r-gsl))
26392 (home-page "https://cran.r-project.org/web/packages/aws/")
26393 (synopsis "Adaptive weights smoothing")
26395 "This package provides a collection of R-functions implementing adaptive
26396 smoothing procedures in 1D, 2D and 3D. This includes the
26397 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
26398 Confidence Intervals} (ICI), variational approaches, and a non-local means
26400 (license license:gpl2+)))
26402 (define-public r-sgloptim
26404 (name "r-sgloptim")
26409 (uri (cran-uri "sglOptim" version))
26412 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
26414 `((upstream-name . "sglOptim")))
26415 (build-system r-build-system)
26426 (home-page "https://github.com/nielsrhansen/sglOptim")
26427 (synopsis "Generic sparse group Lasso solver")
26429 "This package provides a fast generic solver for sparse group lasso
26430 optimization problems. The loss (objective) function must be defined in a C++
26431 module. The optimization problem is solved using a coordinate gradient
26432 descent algorithm. Convergence of the algorithm is established and the
26433 algorithm is applicable to a broad class of loss functions. Use of parallel
26434 computing for cross validation and subsampling is supported through the
26435 @code{foreach} and @code{doParallel} packages.")
26436 (license license:gpl2+)))
26438 (define-public r-grouped
26445 (uri (cran-uri "grouped" version))
26448 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
26450 `((upstream-name . "grouped")))
26451 (build-system r-build-system)
26454 (home-page "https://cran.r-project.org/web/packages/grouped/")
26455 (synopsis "Regression analysis of grouped and coarse data")
26457 "This package provides regression models for grouped and coarse data,
26458 under the coarsened at random assumption.")
26459 (license license:gpl2+)))
26461 (define-public r-stam
26468 (uri (cran-uri "stam" version))
26471 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
26473 `((upstream-name . "stam")))
26474 (build-system r-build-system)
26477 (home-page "https://cran.r-project.org/web/packages/stam")
26478 (synopsis "Spatio-temporal analysis and modelling")
26480 "This package provides various methods to conduct Spatio-Temporal
26481 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
26482 Inferred Spatio-Temporal Modelling.")
26483 (license license:gpl2+)))
26485 (define-public r-dcv
26492 (uri (cran-uri "dcv" version))
26495 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
26497 `((upstream-name . "dcv")))
26498 (build-system r-build-system)
26501 (home-page "https://cran.r-project.org/web/packages/dcv/")
26502 (synopsis "Conventional cross-validation statistics for climate-growth model")
26504 "This package performs several conventional cross-validation statistical
26505 methods for climate-growth model in the climate reconstruction from tree
26506 rings, including Sign Test statistic, Reduction of Error statistic, Product
26507 Mean Test, Durbin-Watson statistic etc.")
26508 (license license:gpl2)))
26510 (define-public r-rcdd
26517 (uri (cran-uri "rcdd" version))
26520 "0zxx0qvv26ba30jkm8mvca4h59rqklay4jwazpcw7h9dzp4189jr"))))
26522 `((upstream-name . "rcdd")))
26523 (build-system r-build-system)
26526 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
26527 (synopsis "Computational geometry")
26529 "This package converts back and forth between two representations of a
26530 convex polytope: as solution of a set of linear equalities and inequalities
26531 and as convex hull of set of points and rays. Also does linear programming
26532 and redundant generator elimination. All functions can use exact
26533 infinite-precision rational arithmetic.")
26534 (license license:gpl2)))
26536 (define-public r-rxnat
26543 (uri (cran-uri "Rxnat" version))
26546 "0siylypjd8cgcmr2c443w8krg8sgr5gz4zapbinanp8vsfzivdv2"))))
26548 `((upstream-name . "Rxnat")))
26549 (build-system r-build-system)
26551 (list r-httr r-rcurl r-tibble))
26554 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
26555 (synopsis "Queries and extracts images from neuroimaging datasets")
26557 "This package allows communication with the Extensible Neuroimaging
26558 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
26560 (license license:gpl2)))
26562 (define-public r-rserve
26569 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
26570 version ".tar.gz"))
26573 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
26574 (build-system r-build-system)
26577 (modify-phases %standard-phases
26578 (add-before 'install 'install-server-binary
26579 ;; Makevars tries to install to R's store directory.
26580 (lambda* (#:key outputs #:allow-other-keys)
26581 (let* ((out (assoc-ref outputs "out"))
26582 (bin (string-append out "/bin")))
26583 (substitute* "src/Makevars.in"
26584 (("\\$\\(R_HOME\\)") out))
26585 (mkdir-p bin)))))))
26595 (list openssl zlib))
26596 (home-page "https://github.com/s-u/Rserve")
26598 "Server providing access to R from many languages and systems")
26600 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
26601 binary requests to be sent to R. Every connection has a separate workspace
26602 and working directory. Client-side implementations are available for popular
26603 languages such as C/C++ and Java, allowing any application to use facilities
26604 of R without the need of linking to R code. Rserve supports remote
26605 connection, user authentication and file transfer. A simple R client is
26606 included in this package as well.")
26607 (license license:gpl2)))
26609 (define-public r-gamm4
26616 (uri (cran-uri "gamm4" version))
26619 "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap"))))
26620 (properties `((upstream-name . "gamm4")))
26621 (build-system r-build-system)
26623 (list r-lme4 r-matrix r-mgcv))
26624 (home-page "https://cran.r-project.org/web/packages/gamm4/")
26625 (synopsis "Generalized additive mixed models using mgcv and lme4")
26627 "Estimate generalized additive mixed models via a version of function
26628 @code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor
26630 (license license:gpl2+)))
26632 (define-public r-optimx
26635 (version "2022-4.30")
26639 (uri (cran-uri "optimx" version))
26642 "045ls1vl1392ihwln6mngz0zg2w93ym1m607vfrg8v1949x8isgb"))))
26643 (properties `((upstream-name . "optimx")))
26644 (build-system r-build-system)
26645 (propagated-inputs (list r-numderiv))
26646 (native-inputs (list r-knitr))
26647 (home-page "https://cran.r-project.org/web/packages/optimx/")
26648 (synopsis "Expanded replacement and extension of the optim function")
26650 "This package provides a replacement and extension of the @code{optim}
26651 function to call to several function minimization codes in R in a single
26652 statement. These methods handle smooth, possibly box constrained functions of
26653 several or many parameters. Note that the function @code{optimr} was prepared
26654 to simplify the incorporation of minimization codes going forward. This
26655 package also implements some utility codes and some extra solvers, including
26656 safeguarded Newton methods. Many methods previously separate are now included
26658 (license license:gpl2)))
26660 (define-public r-projpred
26662 (name "r-projpred")
26667 (uri (cran-uri "projpred" version))
26670 "1c6gnmknd3vb0fb5h6gd372dk27nzif90b4c1snql49wacg6b2m8"))))
26671 (properties `((upstream-name . "projpred")))
26672 (build-system r-build-system)
26686 (native-inputs (list r-knitr))
26687 (home-page "https://mc-stan.org/projpred/")
26688 (synopsis "Projection predictive feature selection")
26690 "This package performs projection predictive feature selection for
26691 generalized linear models and generalized linear and additive multilevel
26692 models. The package is compatible with the @code{rstanarm} and @code{brms}
26693 packages, but other reference models can also be used. See the package
26694 vignette for more information and examples.")
26695 (license license:gpl3)))
26697 (define-public r-distributional
26699 (name "r-distributional")
26704 (uri (cran-uri "distributional" version))
26707 "1mji8xlhwrw8msih5wdpbzwv4g59kly0xkdklhn8yzb18rrnrczs"))))
26709 `((upstream-name . "distributional")))
26710 (build-system r-build-system)
26722 (home-page "https://pkg.mitchelloharawild.com/distributional/")
26723 (synopsis "Vectorized probability distributions")
26725 "This package provides vectorized distribution objects with tools for
26726 manipulating, visualizing, and using probability distributions. It was
26727 designed to allow model prediction outputs to return distributions rather than
26728 their parameters, allowing users to directly interact with predictive
26729 distributions in a data-oriented workflow. In addition to providing generic
26730 replacements for p/d/q/r functions, other useful statistics can be computed
26731 including means, variances, intervals, and highest density regions.")
26732 (license license:gpl3)))
26734 (define-public r-posterior
26736 (name "r-posterior")
26741 (uri (cran-uri "posterior" version))
26744 "0frm7p6cjkjfl4gviixaa7448qaac8n9ilkr5c02fa9vnisys5fn"))))
26745 (properties `((upstream-name . "posterior")))
26746 (build-system r-build-system)
26759 (home-page "https://mc-stan.org/posterior/")
26760 (synopsis "Tools for working with posterior distributions")
26762 "This package provides useful tools for both users and developers of
26763 packages for fitting Bayesian models or working with output from Bayesian
26764 models. The primary goals of the package are to:
26767 @item Efficiently convert between many different useful formats of
26768 draws (samples) from posterior or prior distributions.
26770 @item Provide consistent methods for operations commonly performed on draws,
26771 for example, subsetting, binding, or mutating draws.
26773 @item Provide various summaries of draws in convenient formats.
26775 @item Provide lightweight implementations of state of the art posterior
26776 inference diagnostics.
26779 (license license:bsd-3)))
26781 (define-public r-brms
26788 (uri (cran-uri "brms" version))
26791 "0wff5rld4kgkk2nbllvm1h4c596igzgd0q7nx1cabgl11fja7r94"))))
26792 (properties `((upstream-name . "brms")))
26793 (build-system r-build-system)
26814 (native-inputs (list r-knitr))
26816 "https://github.com/paul-buerkner/brms")
26818 "Bayesian Regression Models using 'Stan'")
26820 "Fit Bayesian generalized (non-)linear multivariate multilevel models
26821 using 'Stan' for full Bayesian inference. A wide range of distributions and
26822 link functions are supported, allowing users to fit -- among others -- linear,
26823 robust linear, count data, survival, response times, ordinal, zero-inflated,
26824 hurdle, and even self-defined mixture models all in a multilevel context.
26825 Further modeling options include non-linear and smooth terms, auto-correlation
26826 structures, censored data, meta-analytic standard errors, and quite a few
26827 more. In addition, all parameters of the response distribution can be
26828 predicted in order to perform distributional regression. Prior specifications
26829 are flexible and explicitly encourage users to apply prior distributions that
26830 actually reflect their beliefs. Model fit can easily be assessed and compared
26831 with posterior predictive checks and leave-one-out cross-validation.")
26832 (license license:gpl2)))
26834 (define-public r-mstate
26841 (uri (cran-uri "mstate" version))
26844 "054dzrd5b0xjjjl7862q3aq1jwgrxbkqz7zpvbdirqsld3zksirw"))))
26845 (properties `((upstream-name . "mstate")))
26846 (build-system r-build-system)
26857 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
26859 "Data Preparation, Estimation and Prediction in Multi-State Models")
26861 "Contains functions for data preparation, descriptives, hazard estimation
26862 and prediction with Aalen-Johansen or simulation in competing risks and
26863 multi-state models.")
26864 (license license:gpl2+)))
26866 (define-public r-scatterpie
26868 (name "r-scatterpie")
26873 (uri (cran-uri "scatterpie" version))
26876 "1pmspv8a7k20zyd5xvmav2k9mnjrkfhdij3rr9k504zyki8hfy1z"))))
26877 (properties `((upstream-name . "scatterpie")))
26878 (build-system r-build-system)
26880 (list r-ggforce r-ggfun r-ggplot2 r-rlang r-tidyr))
26883 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
26884 (synopsis "Scatter pie plot")
26886 "This package creates scatterpie plots, especially useful for plotting
26888 (license license:artistic2.0)))
26890 (define-public r-scrypt
26897 (uri (cran-uri "scrypt" version))
26900 "12q9d4m7flbvlgssvjh1ga4jswkmqjfshf6pna6qk6v087gmzdsj"))))
26901 (properties `((upstream-name . "scrypt")))
26902 (build-system r-build-system)
26905 (home-page "https://github.com/rstudio/rscrypt")
26906 (synopsis "Key derivation functions for R based on Scrypt")
26908 "This package provides functions for working with the scrypt key
26909 derivation functions. Scrypt is a password-based key derivation function
26910 created by Colin Percival. The algorithm was specifically designed to make it
26911 costly to perform large-scale custom hardware attacks by requiring large
26912 amounts of memory.")
26913 (license license:bsd-2)))
26915 (define-public r-boruta
26922 (uri (cran-uri "Boruta" version))
26925 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
26926 (properties `((upstream-name . "Boruta")))
26927 (build-system r-build-system)
26928 (propagated-inputs (list r-ranger))
26929 (home-page "https://gitlab.com/mbq/Boruta/")
26930 (synopsis "Wrapper algorithm for all relevant feature selection")
26932 "This package provides an all relevant feature selection wrapper
26933 algorithm. It finds relevant features by comparing original attributes'
26934 importance with importance achievable at random, estimated using their
26935 permuted copies (shadows).")
26936 (license license:gpl2+)))
26938 (define-public r-directlabels
26940 (name "r-directlabels")
26941 (version "2021.1.13")
26945 (uri (cran-uri "directlabels" version))
26948 "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w"))))
26949 (build-system r-build-system)
26954 (home-page "http://directlabels.r-forge.r-project.org/")
26955 (synopsis "Direct labels for multicolor plots")
26957 "This package provides an extensible framework for automatically placing
26958 direct labels onto multicolor plots. Label positions are described using
26959 positioning methods that can be re-used across several different plots. There
26960 are heuristics for examining @code{trellis} and @code{ggplot} objects and
26961 inferring an appropriate positioning method.")
26962 (license license:gpl3)))
26964 (define-public r-lsd
26971 (uri (cran-uri "LSD" version))
26973 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
26974 (properties `((upstream-name . "LSD")))
26975 (build-system r-build-system)
26976 (home-page "https://cran.r-project.org/web/packages/LSD/")
26977 (synopsis "Lots of superior depictions tool creates colorful plots")
26979 "This package creates lots of colorful plots in a multitude of variations.
26980 Try a demo of the LSD by running @code{demotour()}.")
26982 (license (list license:gpl2 license:gpl3))))
26984 (define-public r-phylogram
26986 (name "r-phylogram")
26991 (uri (cran-uri "phylogram" version))
26993 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
26994 (properties `((upstream-name . "phylogram")))
26995 (build-system r-build-system)
26996 (propagated-inputs (list r-ape))
26997 (home-page "https://github.com/ropensci/phylogram/")
26998 (synopsis "Dendrograms for evolutionary analysis")
27000 "The @code{r-phylogram} package is a tool for for developing phylogenetic
27001 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
27002 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
27003 as well as several tools for command-line tree manipulation and import/export
27004 via Newick parenthetic text. This improves accessibility to the comprehensive
27005 range of object-specific analytical and tree-visualization functions found
27006 across a wide array of bioinformatic R packages.")
27007 (license license:gpl3)))
27009 (define-public r-kmer
27016 (uri (cran-uri "kmer" version))
27018 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
27019 (properties `((upstream-name . "kmer")))
27020 (build-system r-build-system)
27022 (list r-openssl r-phylogram r-rcpp))
27023 (home-page "https://github.com/shaunpwilkinson/kmer/")
27024 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
27026 "@code{r-kmer} is an R package for rapidly computing distance matrices
27027 and clustering large sequence datasets using fast alignment-free k-mer
27028 counting and recursive k-means partitioning.")
27029 (license license:gpl3)))
27031 (define-public r-hardhat
27038 (uri (cran-uri "hardhat" version))
27041 "1cdl52lzv3wffq8fzrb6sk85i4i8lm8skgad1c8az3ifmzssjx03"))))
27042 (properties `((upstream-name . "hardhat")))
27043 (build-system r-build-system)
27045 (list r-glue r-rlang r-tibble r-vctrs))
27048 (home-page "https://github.com/tidymodels/hardhat")
27049 (synopsis "Construct modeling packages")
27051 "Building modeling packages is hard. A large amount of effort generally
27052 goes into providing an implementation for a new method that is efficient,
27053 fast, and correct, but often less emphasis is put on the user interface. A
27054 good interface requires specialized knowledge about S3 methods and formulas,
27055 which the average package developer might not have. The goal of
27056 @code{hardhat} is to reduce the burden around building new modeling packages
27057 by providing functionality for preprocessing, predicting, and validating
27059 (license license:expat)))
27061 (define-public r-lightgbm
27063 (name "r-lightgbm")
27068 (uri (cran-uri "lightgbm" version))
27071 "12hbvm1va6sb5yny564jvhhzrkcq4j33rcdhqhwxaac2m08cpi8s"))))
27072 (properties `((upstream-name . "lightgbm")))
27073 (build-system r-build-system)
27075 (list r-data-table r-jsonlite r-matrix r-r6))
27076 (home-page "https://github.com/Microsoft/LightGBM")
27077 (synopsis "Light gradient boosting machine")
27079 "Tree based algorithms can be improved by introducing boosting
27080 frameworks. LightGBM is one such framework, based on Ke, Guolin et
27081 al. (2017). This package offers an R interface to work with it. It is
27082 designed to be distributed and efficient with the following goals:
27085 @item Faster training speed and higher efficiency;
27086 @item lower memory usage;
27087 @item better accuracy;
27088 @item parallel learning supported; and
27089 @item capable of handling large-scale data.
27092 (license license:expat)))
27094 (define-public r-shapforxgboost
27096 (name "r-shapforxgboost")
27101 (uri (cran-uri "SHAPforxgboost" version))
27104 "106nsf02b1w3yshb55lwnyw1rl1a60162v2wk8znjz3b4ln3mqj5"))))
27106 `((upstream-name . "SHAPforxgboost")))
27107 (build-system r-build-system)
27119 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
27120 (synopsis "SHAP Plots for XGBoost")
27122 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
27123 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
27124 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
27125 and force plot. It relies on the @code{XGBoost} package to produce SHAP
27127 (license license:expat)))
27129 (define-public r-rismed
27136 (uri (cran-uri "RISmed" version))
27139 "0vpi88gzi9r85v6nhjz9jbw671zkrmyazwna2z881346wfyr3l8b"))))
27140 (properties `((upstream-name . "RISmed")))
27141 (build-system r-build-system)
27143 (list r-httr r-xml2))
27144 (home-page "https://cran.r-project.org/web/packages/RISmed")
27145 (synopsis "Download content from NCBI databases")
27147 "This package provides a set of tools to extract bibliographic
27148 content from the National Center for Biotechnology Information (NCBI)
27149 databases, including PubMed. The name RISmed is a portmanteau of
27150 RIS (for Research Information Systems, a common tag format for
27151 bibliographic data) and PubMed.")
27152 (license license:gpl2+)))
27154 (define-public r-semver
27161 (uri (cran-uri "semver" version))
27164 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
27165 (properties `((upstream-name . "semver")))
27166 (build-system r-build-system)
27168 (list r-assertthat r-rcpp))
27169 (native-inputs (list r-knitr))
27170 (home-page "https://github.com/johndharrison/semver")
27171 (synopsis "Parser for Semantic Versioning 2.0.0")
27173 "This package provides tools and functions for parsing, rendering and
27174 operating on semantic version strings. Semantic versioning is a simple set of
27175 rules and requirements that dictate how version numbers are assigned and
27176 incremented as outlined at @url{http://semver.org}.")
27177 (license license:expat)))
27179 (define-public r-binman
27186 (uri (cran-uri "binman" version))
27189 "00l7m98h41r67gf0qxqis3vx63j7wylnk9vlgcyk41szkrz8ikkc"))))
27190 (properties `((upstream-name . "binman")))
27191 (build-system r-build-system)
27200 (native-inputs (list r-knitr))
27201 (home-page "https://github.com/ropensci/binman")
27202 (synopsis "Binary download manager")
27204 "This package provides tools and functions for managing the download of
27205 binary files. Binary repositories are defined in the YAML format. Defining
27206 new pre-download, download and post-download templates allow additional
27207 repositories to be added.")
27208 (license license:expat)))
27210 (define-public r-wdman
27217 (uri (cran-uri "wdman" version))
27220 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
27221 (properties `((upstream-name . "wdman")))
27222 (build-system r-build-system)
27224 (list r-assertthat r-binman r-processx r-semver r-yaml))
27225 (native-inputs (list r-knitr))
27226 (home-page "https://docs.ropensci.org/wdman/")
27227 (synopsis "Webdriver/Selenium binary manager")
27229 "There are a number of binary files associated with the
27230 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
27231 @url{https://sites.google.com/a/chromium.org/chromedriver/},
27232 @url{https://github.com/mozilla/geckodriver},
27233 @url{http://phantomjs.org/download.html}, and
27234 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
27235 more information). This package provides functions to download these binaries
27236 and to manage processes involving them.")
27237 (license license:expat)))
27239 (define-public r-rselenium
27241 (name "r-rselenium")
27246 (uri (cran-uri "RSelenium" version))
27249 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
27250 (properties `((upstream-name . "RSelenium")))
27251 (build-system r-build-system)
27259 (native-inputs (list r-knitr))
27260 (home-page "https://docs.ropensci.org/RSelenium/")
27261 (synopsis "R bindings for Selenium WebDriver")
27263 "This package provides a set of R bindings for the Selenium 2.0
27264 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
27265 information) using the @code{JsonWireProtocol} (see
27266 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
27267 information). Selenium 2.0 WebDriver allows driving a web browser natively as
27268 a user would either locally or on a remote machine using the Selenium server
27269 it marks a leap forward in terms of web browser automation. Selenium
27270 automates web browsers (commonly referred to as browsers). Using RSelenium
27271 you can automate browsers locally or remotely.")
27272 (license license:agpl3+)))
27274 (define-public r-conquer
27281 (uri (cran-uri "conquer" version))
27284 "1ynmaf7lgqjb8grsifx5dzy29cd5kz4x3yh0abnl2vxdr4c4wddc"))))
27285 (properties `((upstream-name . "conquer")))
27286 (build-system r-build-system)
27288 (list r-matrix r-matrixstats r-rcpp r-rcpparmadillo))
27289 (home-page "https://github.com/XiaoouPan/conquer")
27290 (synopsis "Convolution-type smoothed quantile regression")
27292 "This package provides fast and accurate convolution-type smoothed
27293 quantile regression, implemented using Barzilai-Borwein gradient descent with
27294 a Huber regression warm start. Confidence intervals for regression
27295 coefficients are constructed using multiplier bootstrap.")
27296 (license license:gpl3)))
27298 (define-public r-fastshap
27300 (name "r-fastshap")
27305 (uri (cran-uri "fastshap" version))
27308 "0gxch67i3bj6m8nb94m5hswq058w6n1q9war4dy2qnimlv7cmhdv"))))
27309 (properties `((upstream-name . "fastshap")))
27310 (build-system r-build-system)
27320 (home-page "https://github.com/bgreenwell/fastshap")
27321 (synopsis "Fast approximate Shapley values")
27323 "This package computes fast (relative to other implementations)
27324 approximate Shapley values for any supervised learning model. Shapley values
27325 help to explain the predictions from any black box model using ideas from game
27326 theory; see @url{Strumbel and Kononenko (2014),
27327 doi.org/10.1007/s10115-013-0679-x} for details.")
27328 (license license:gpl2+)))
27330 (define-public r-memuse
27336 (uri (cran-uri "memuse" version))
27339 "1wvwnjaaiv2647561z2b55dss35033ildx4kk8hzxfzgsjmdpsgm"))))
27340 (properties `((upstream-name . "memuse")))
27341 (build-system r-build-system)
27342 (home-page "https://github.com/shinra-dev/memuse")
27343 (synopsis "Memory Estimation Utilities")
27345 "This package provides procedures to answer the following questions:
27346 How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is
27347 your current R session using? How much ram do you even have?")
27348 (license license:bsd-2)))
27350 (define-public r-metrics
27357 (uri (cran-uri "Metrics" version))
27360 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
27361 (properties `((upstream-name . "Metrics")))
27362 (build-system r-build-system)
27363 (home-page "https://github.com/mfrasco/Metrics")
27364 (synopsis "Evaluation metrics for machine learning")
27366 "This package provides an implementation of evaluation metrics in R that
27367 are commonly used in supervised machine learning. It implements metrics for
27368 regression, time series, binary classification, classification, and
27369 information retrieval problems. It has zero dependencies and a consistent,
27370 simple interface for all functions.")
27371 (license license:bsd-3)))
27373 (define-public r-iml
27380 (uri (cran-uri "iml" version))
27383 "1za7bjnp07i20vyb6vxz2ya5cr8g4p076w61n8m38wnz04lz5yz5"))))
27384 (properties `((upstream-name . "iml")))
27385 (build-system r-build-system)
27396 (native-inputs (list r-knitr))
27397 (home-page "https://github.com/christophM/iml")
27398 (synopsis "Interpretable machine learning")
27400 "This package provides interpretability methods to analyze the behavior
27401 and predictions of any machine learning model. Implemented methods are:
27404 @item Feature importance described by Fisher et al. (2018),
27405 @item accumulated local effects plots described by Apley (2018),
27406 @item partial dependence plots described by Friedman (2001),
27407 @item individual conditional expectation ('ice') plots described by Goldstein
27408 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
27409 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
27410 @item the Shapley Value described by Strumbelj et. al (2014)
27411 @url{https://doi.org/10.1007/s10115-013-0679-x},
27412 @item feature interactions described by Friedman et. al
27413 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
27416 (license license:expat)))
27418 (define-public r-goftest
27425 (uri (cran-uri "goftest" version))
27428 "06bz6k7smr4jbvzmb73qc5fkf4my59w5gbl18wlmpkkymsv78prs"))))
27429 (properties `((upstream-name . "goftest")))
27430 (build-system r-build-system)
27431 (home-page "https://github.com/baddstats/goftest")
27432 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
27434 "This package provides Cramer-Von Mises and Anderson-Darling tests of
27435 goodness-of-fit for continuous univariate distributions, using efficient
27437 (license license:gpl2+)))
27439 (define-public r-tensor
27446 (uri (cran-uri "tensor" version))
27449 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
27450 (properties `((upstream-name . "tensor")))
27451 (build-system r-build-system)
27452 (home-page "https://cran.r-project.org/web/packages/tensor/")
27453 (synopsis "Tensor product of arrays")
27455 "The tensor product of two arrays is notionally an outer product of the
27456 arrays collapsed in specific extents by summing along the appropriate
27457 diagonals. This package allows you to compute the tensor product of arrays.")
27458 (license license:gpl2+)))
27460 (define-public r-spatstat-utils
27462 (name "r-spatstat-utils")
27467 (uri (cran-uri "spatstat.utils" version))
27470 "08pybliv4r3v4rcazmlfr4a07sjfhrkmksdmhhq9k185vw4474av"))))
27472 `((upstream-name . "spatstat.utils")))
27473 (build-system r-build-system)
27474 (home-page "http://www.spatstat.org")
27475 (synopsis "Utility functions for spatstat")
27477 "This package contains utility functions for the @code{spatstat} package
27478 which may also be useful for other purposes.")
27479 (license license:gpl2+)))
27481 (define-public r-spatstat-sparse
27483 (name "r-spatstat-sparse")
27488 (uri (cran-uri "spatstat.sparse" version))
27491 "00vkvv5pnm82gn7vqnzrrp68y46gbkhdq0hbwqx7nxjvf5lssdcs"))))
27493 `((upstream-name . "spatstat.sparse")))
27494 (build-system r-build-system)
27496 (list r-abind r-matrix r-spatstat-utils r-tensor))
27497 (home-page "http://spatstat.org/")
27498 (synopsis "Sparse three-dimensional arrays and linear algebra utilities")
27500 "This package defines sparse three-dimensional arrays and supports
27501 standard operations on them. The package also includes utility functions for
27502 matrix calculations that are common in statistics, such as quadratic forms.")
27503 (license license:gpl2+)))
27505 (define-public r-spatstat-data
27507 (name "r-spatstat-data")
27512 (uri (cran-uri "spatstat.data" version))
27515 "1rf36zy29h9qabpv19hx84gjdiay7i9y9777d2zn17ahyss3p56k"))))
27516 (properties `((upstream-name . "spatstat.data")))
27517 (build-system r-build-system)
27519 (list r-matrix r-spatstat-utils))
27520 (home-page "http://www.spatstat.org")
27521 (synopsis "Datasets for spatstat")
27523 "This package contains all the datasets for the @code{spatstat}
27525 (license license:gpl2+)))
27527 (define-public r-spatstat-geom
27529 (name "r-spatstat-geom")
27534 (uri (cran-uri "spatstat.geom" version))
27537 "0rwysq9a0ylbsr53q5kfh7wjk5mcdji211sc3s8gwzz8ki09mf1j"))))
27538 (properties `((upstream-name . "spatstat.geom")))
27539 (build-system r-build-system)
27541 (list r-deldir r-polyclip r-spatstat-data r-spatstat-utils))
27542 (home-page "http://spatstat.org/")
27543 (synopsis "Geometrical functionality of the spatstat package")
27545 "This is a subset of the original spatstat package, containing the
27546 user-level code from spatstat which performs geometrical operations, except
27547 for the geometry of linear networks.")
27548 (license license:gpl2+)))
27550 (define-public r-spatstat-core
27552 (name "r-spatstat-core")
27557 (uri (cran-uri "spatstat.core" version))
27560 "0fyi8y1z919nzn47kaviln7gflhcp5qdi3gfvf7nwkdix3pkk373"))))
27561 (properties `((upstream-name . "spatstat.core")))
27562 (build-system r-build-system)
27576 (home-page "http://spatstat.org/")
27577 (synopsis "Core functionality of the spatstat package")
27579 "This is a subset of the original spatstat package, containing all of the
27580 user-level code from spatstat, except for the code for linear networks.")
27581 (license license:gpl2+)))
27583 (define-public r-spatstat-linnet
27585 (name "r-spatstat-linnet")
27590 (uri (cran-uri "spatstat.linnet" version))
27593 "0y1py6x0xbw4ad3pjwcspi4ysgfh61f5fd79787zzgyyh2va8y4w"))))
27595 `((upstream-name . "spatstat.linnet")))
27596 (build-system r-build-system)
27605 (home-page "http://spatstat.org/")
27606 (synopsis "Linear networks functionality of the spatstat package")
27608 "This is a subset of the spatstat package, containing its functionality
27609 for spatial data on a linear network.")
27610 (license license:gpl2+)))
27612 (define-public r-spatstat-random
27614 (name "r-spatstat-random")
27619 (uri (cran-uri "spatstat.random" version))
27621 (base32 "0kb01s8k67ydcfqcnz3i55vpiksihh4xsg0w2p2bclxxkpdvpw25"))))
27622 (properties `((upstream-name . "spatstat.random")))
27623 (build-system r-build-system)
27624 (propagated-inputs (list r-spatstat-data r-spatstat-geom r-spatstat-utils))
27625 (home-page "http://spatstat.org/")
27626 (synopsis "Random Generation Functionality for the 'spatstat' Family")
27628 "This package provides functionality for random generation of spatial
27629 data in the spatstat family of packages. It generates random spatial patterns
27630 of points according to many simple rules (complete spatial randomness,
27631 Poisson, binomial, random grid, systematic, cell), randomised alteration of
27632 patterns (thinning, random shift, jittering), simulated realisations of random
27633 point processes (simple sequential inhibition, Matern inhibition models,
27634 Matern cluster process, Neyman-Scott cluster processes, log-Gaussian Cox
27635 processes, product shot noise cluster processes) and simulation of Gibbs point
27636 processes (Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs
27638 (license license:gpl2+)))
27640 (define-public r-spatstat
27642 (name "r-spatstat")
27647 (uri (cran-uri "spatstat" version))
27650 "1nlrp7660y68axlm4pczc5rxbdhbbac1ylh69azr4swj1gbzi82f"))))
27651 (properties `((upstream-name . "spatstat")))
27652 (build-system r-build-system)
27654 (list r-spatstat-core r-spatstat-data r-spatstat-geom
27655 r-spatstat-linnet r-spatstat-random r-spatstat-utils))
27656 (home-page "http://www.spatstat.org")
27657 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
27659 "This package provides a comprehensive toolbox for analysing Spatial
27660 Point Patterns. It is focused mainly on two-dimensional point patterns,
27661 including multitype/marked points, in any spatial region. It also supports
27662 three-dimensional point patterns, space-time point patterns in any number of
27663 dimensions, point patterns on a linear network, and patterns of other
27664 geometrical objects. It supports spatial covariate data such as pixel images
27665 and contains over 2000 functions for plotting spatial data, exploratory data
27666 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
27667 formal inference.")
27668 (license license:gpl2+)))
27670 (define-public r-gaston
27677 (uri (cran-uri "gaston" version))
27680 "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i"))))
27681 (properties `((upstream-name . "gaston")))
27682 (build-system r-build-system)
27683 (inputs (list zlib))
27685 (list r-rcpp r-rcppeigen r-rcppparallel))
27686 (native-inputs (list r-knitr))
27687 (home-page "https://cran.r-project.org/web/packages/gaston/")
27688 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
27690 "This is a package for the manipulation of genetic data (SNPs).
27691 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
27692 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
27693 for linear mixed models (AIREML).")
27694 (license license:gpl3)))
27696 (define-public r-cpp11
27703 (uri (cran-uri "cpp11" version))
27706 "16cvjfkbc7c0ymdmbcqg9px6pjsqx6qhyfq5frqj739mhazy0g20"))))
27707 (properties `((upstream-name . "cpp11")))
27708 (build-system r-build-system)
27709 (native-inputs (list r-knitr))
27710 (home-page "https://github.com/r-lib/cpp11")
27711 (synopsis "C++11 Interface for R's C Interface")
27713 "This package provides a header only, C++11 interface to R's C interface.
27714 Compared to other approaches @code{cpp11} strives to be safe against long
27715 jumps from the C API as well as C++ exceptions, conform to normal R function
27716 semantics and supports interaction with @code{ALTREP} vectors.")
27717 (license license:expat)))
27719 (define-public r-rcpptoml
27721 (name "r-rcpptoml")
27726 (uri (cran-uri "RcppTOML" version))
27728 (base32 "0h8517ipwqhqkhcfiyqmvsb585g01p0ra0azbpzyxip6pq6g029g"))))
27729 (properties `((upstream-name . "RcppTOML")))
27730 (build-system r-build-system)
27731 (propagated-inputs (list r-rcpp))
27732 (home-page "http://dirk.eddelbuettel.com/code/rcpp.toml.html")
27733 (synopsis "Rcpp bindings to TOML parser")
27735 "The TOML configuration format specifies an excellent format suitable for
27736 both human editing as well as the common uses of a machine-readable format.
27737 This package provides Rcpp bindings to a TOML parser.")
27738 (license license:gpl2+)))
27740 (define-public r-rcppziggurat
27742 (name "r-rcppziggurat")
27747 (uri (cran-uri "RcppZiggurat" version))
27750 "0wgd1v2p7zajnbrjf3hfi56p3pk3ld6iwkanbb04bjbnlif2ay4w"))))
27751 (properties `((upstream-name . "RcppZiggurat")))
27752 (build-system r-build-system)
27754 (list r-rcpp r-rcppgsl))
27755 (native-inputs (list r-knitr))
27756 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
27757 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
27759 "The Ziggurat generator for normally distributed random numbers,
27760 originally proposed by Marsaglia and Tsang (2000,
27761 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
27762 times starting with Leong et al (2005,
27763 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
27764 aggregation for comparing different implementations in order to provide a
27765 'faster but good enough' alternative for use with R and C++ code.")
27766 (license license:gpl2+)))
27768 (define-public r-rfast
27775 (uri (cran-uri "Rfast" version))
27778 "0zxykq021h57mq0n6giqbx8ncjsdly0arhmaj3fcp3yfcxf4ns9l"))))
27779 (properties `((upstream-name . "Rfast")))
27780 (build-system r-build-system)
27782 (list r-rcpp r-rcpparmadillo r-rcppziggurat))
27783 (home-page "https://github.com/RfastOfficial/Rfast")
27784 (synopsis "Collection of efficient and fast R functions")
27786 "This package provides a collection of fast (utility) functions for data
27787 analysis. Column- and row- wise means, medians, variances, minimums,
27788 maximums, many t, F and G-square tests, many regressions (normal, logistic,
27789 Poisson), are some of the many fast functions.")
27790 (license license:gpl2+)))
27792 (define-public r-rffc
27798 (uri (string-append
27799 "https://download.r-forge.r-project.org/src/contrib/"
27800 "rfFC_" version ".tar.gz"))
27803 "05x9wgzsmx4vb12lmcspymgmpb2xw8bwryb8ysg7vzg2nkh0ma3g"))))
27804 (build-system r-build-system)
27806 (list r-randomforest))
27807 (home-page "https://r-forge.r-project.org/projects/rffc/")
27808 (synopsis "Random Forest Feature Contributions")
27809 (description "This package provides functions for extracting feature
27810 contributions from a random forest model from package @code{randomForest}.
27811 Feature contributions provide detailed information about the relationship
27812 between data variables and the predicted value returned by random forest
27814 (license license:gpl2)))
27816 (define-public r-clusterr
27818 (name "r-clusterr")
27823 (uri (cran-uri "ClusterR" version))
27826 "00mha8madcba83ix4fc04rb7sagfm0lxlh1wvs7dvjdrngps41jr"))))
27827 (properties `((upstream-name . "ClusterR")))
27828 (build-system r-build-system)
27830 (list r-ggplot2 r-gmp r-gtools r-rcpp r-rcpparmadillo))
27831 (native-inputs (list r-knitr))
27832 (home-page "https://github.com/mlampros/ClusterR")
27833 (synopsis "Clustering")
27835 "This package provides Gaussian mixture models, k-means,
27836 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
27837 option to plot, validate, predict (new data) and estimate the optimal number
27838 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
27839 the computationally intensive parts of the functions. For more information,
27843 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
27844 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
27845 @url{https://doi.org/10.18637/jss.v001.i04};
27846 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
27847 Library, @url{https://doi.org/10.1145/1772690.1772862};
27848 @item \"Armadillo: a template-based C++ library
27849 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
27850 Software, @url{https://doi.org/10.21105/joss.00026};
27851 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
27852 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
27853 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
27856 (license license:gpl3)))
27858 (define-public r-spectrum
27860 (name "r-spectrum")
27865 (uri (cran-uri "Spectrum" version))
27868 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
27869 (properties `((upstream-name . "Spectrum")))
27870 (build-system r-build-system)
27872 (list r-clusterr r-diptest r-ggplot2 r-rfast))
27873 (native-inputs (list r-knitr))
27874 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
27875 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
27877 "This package provides a self-tuning spectral clustering method for
27878 single or multi-view data. Spectrum uses a new type of adaptive density aware
27879 kernel that strengthens connections in the graph based on common nearest
27880 neighbours. It uses a tensor product graph data integration and diffusion
27881 procedure to integrate different data sources and reduce noise. Spectrum uses
27882 either the eigengap or multimodality gap heuristics to determine the number of
27883 clusters. The method is sufficiently flexible so that a wide range of
27884 Gaussian and non-Gaussian structures can be clustered with automatic selection
27886 (license license:agpl3+)))
27888 (define-public r-nabor
27895 (uri (cran-uri "nabor" version))
27898 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
27899 (properties `((upstream-name . "nabor")))
27900 (build-system r-build-system)
27902 (list r-bh r-rcpp r-rcppeigen))
27903 (home-page "https://cran.r-project.org/web/packages/nabor/")
27904 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
27906 "This package provides an R wrapper for libnabo, an exact or approximate
27907 k nearest neighbour library which is optimised for low dimensional
27908 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
27909 designed as a drop-in replacement for the RANN function @code{nn2}. In
27910 addition, objects which include the k-d tree search structure can be returned
27911 to speed up repeated queries of the same set of target points.")
27912 (license license:bsd-3)))
27914 (define-public r-naturalsort
27916 (name "r-naturalsort")
27920 (uri (cran-uri "naturalsort" version))
27923 "0mz801y9mzld9ypp3xmsjw2d8l9q97sdnv09wrci9xi3yg2sjf6d"))))
27924 (build-system r-build-system)
27925 (home-page "https://cran.r-project.org/web/packages/naturalsort/")
27926 (synopsis "Natural ordering")
27927 (description "This package provides functions related to human natural
27928 ordering. It handles adjacent digits in a character sequence as a number
27929 so that natural sort function arranges a character vector by their numbers,
27930 not digit characters.")
27931 (license license:bsd-3)))
27933 (define-public r-visdat
27939 (uri (cran-uri "visdat" version))
27942 "1ikqp29nncbw1xlwyb9dqqgcdk9q0bs3wxhnhnjpb11vcjv7cz2j"))))
27943 (build-system r-build-system)
27955 (home-page "https://visdat.njtierney.com/")
27956 (synopsis "Preliminary Visualisation of Data")
27957 (description "This package provides procedures to create preliminary exploratory
27958 data visualisations of an entire dataset to identify problems or unexpected features
27959 using @code{ggplot2}.")
27960 (license license:expat)))
27962 (define-public r-muhaz
27965 (version "1.2.6.4")
27969 (uri (cran-uri "muhaz" version))
27972 "1ddy8ayr4rdhzcipdvxdwd7z5g9hfp0ppacl7xf6f2612cn1185g"))))
27973 (properties `((upstream-name . "muhaz")))
27974 (build-system r-build-system)
27979 (home-page "https://cran.r-project.org/web/packages/muhaz/")
27980 (synopsis "Hazard function estimation in survival analysis")
27982 "This package produces a smooth estimate of the hazard function for
27984 ;; Any version of the GPL.
27985 (license license:gpl3+)))
27987 (define-public r-flexsurv
27989 (name "r-flexsurv")
27994 (uri (cran-uri "flexsurv" version))
27997 "0kwij9nkdvnsn1kn12fj3hjkd2qpgw7bdda4qad7basq5p6divlp"))))
27998 (properties `((upstream-name . "flexsurv")))
27999 (build-system r-build-system)
28022 (home-page "https://github.com/chjackson/flexsurv-dev")
28023 (synopsis "Flexible parametric survival and multi-state models")
28025 "This package provides flexible parametric models for time-to-event data,
28026 including the Royston-Parmar spline model, generalized gamma and generalized F
28027 distributions. Any user-defined parametric distribution can be fitted, given
28028 at least an R function defining the probability density or hazard. There are
28029 also tools for fitting and predicting from fully parametric multi-state
28031 (license license:gpl2+)))
28033 (define-public r-transphylo
28035 (name "r-transphylo")
28040 (uri (cran-uri "TransPhylo" version))
28043 "0g92kwi1nlmpc8m4pc9kv9xhczryr2kn9icfr3js7da7vy8g50xy"))))
28044 (properties `((upstream-name . "TransPhylo")))
28045 (build-system r-build-system)
28047 (list r-ape r-rcpp))
28050 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
28051 (synopsis "Inference of transmission tree from a dated phylogeny")
28053 "This is a package to infer transmission trees from a dated phylogeny.
28054 It includes methods to simulate and analyze outbreaks. The methodology is
28055 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
28056 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
28057 (license license:gpl2+)))
28059 (define-public r-km-ci
28066 (uri (cran-uri "km.ci" version))
28069 "18sc9vhbdgks8lhk2nfxkkayh8j4j227hl63fm5p04f7z4wm6wc1"))))
28070 (properties `((upstream-name . "km.ci")))
28071 (build-system r-build-system)
28074 (home-page "https://cran.r-project.org/web/packages/km.ci/")
28075 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
28077 "This package computes various @dfn{confidence intervals} (CI) for the
28078 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
28079 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
28080 Nair and Hall and Wellner.")
28081 (license license:gpl2+)))
28083 (define-public r-kmsurv
28090 (uri (cran-uri "KMsurv" version))
28093 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
28094 (properties `((upstream-name . "KMsurv")))
28095 (build-system r-build-system)
28096 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
28097 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
28099 "This package provides data sets and functions for Klein and Moeschberger
28100 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
28102 (license license:gpl3+)))
28104 (define-public r-survmisc
28106 (name "r-survmisc")
28111 (uri (cran-uri "survMisc" version))
28114 "014cf7sfndmib9jmj0p3h67sr750k2pvw7m865zwdpvlqddi44fr"))))
28115 (properties `((upstream-name . "survMisc")))
28116 (build-system r-build-system)
28129 (home-page "https://cran.r-project.org/web/packages/survMisc/")
28130 (synopsis "Miscellaneous functions for survival data")
28132 "This package provides a collection of functions to help in the analysis
28133 of right-censored survival data. These extend the methods available in
28134 the @code{survival} package.")
28135 (license license:gpl2)))
28137 (define-public r-exactranktests
28139 (name "r-exactranktests")
28144 (uri (cran-uri "exactRankTests" version))
28147 "1qv9i57chhz8xiv0j8r47rbigyqs72fa7ssz99inyc0s8gzskd3y"))))
28149 `((upstream-name . "exactRankTests")))
28150 (build-system r-build-system)
28151 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
28152 (synopsis "Exact distributions for rank and permutation tests")
28154 "This package computes exact conditional p-values and quantiles using an
28155 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
28156 (license license:gpl2+)))
28158 (define-public r-maxstat
28165 (uri (cran-uri "maxstat" version))
28168 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
28169 (properties `((upstream-name . "maxstat")))
28170 (build-system r-build-system)
28172 (list r-exactranktests r-mvtnorm))
28173 (home-page "https://cran.r-project.org/web/packages/maxstat/")
28174 (synopsis "Maximally selected rank statistics")
28176 "This package provides maximally selected rank statistics with several
28177 p-value approximations.")
28178 (license license:gpl2+)))
28180 (define-public r-survminer
28182 (name "r-survminer")
28187 (uri (cran-uri "survminer" version))
28190 "0byh0wxdbjfwdrzsnqv4xlmnik6lj0vkkzfxy7lssk8dv5zmj7nz"))))
28191 (properties `((upstream-name . "survminer")))
28192 (build-system r-build-system)
28211 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
28212 (synopsis "Drawing survival curves using ggplot2")
28214 "This package contains the function @code{ggsurvplot()} for easily
28215 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
28216 risk' table and 'censoring count plot'. Other functions are also available to
28217 plot adjusted curves for Cox model and to visually examine Cox model
28219 (license license:gpl2)))
28221 (define-public r-forge
28228 (uri (cran-uri "forge" version))
28231 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
28232 (properties `((upstream-name . "forge")))
28233 (build-system r-build-system)
28235 (list r-magrittr r-rlang))
28236 (home-page "https://cran.r-project.org/web/packages/forge/")
28237 (synopsis "Cast values into shape")
28239 "This package provides helper functions with a consistent interface to
28240 coerce and verify the types and shapes of values for input checking.")
28241 (license license:asl2.0)))
28243 (define-public r-config
28250 (uri (cran-uri "config" version))
28253 "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l"))))
28254 (properties `((upstream-name . "config")))
28255 (build-system r-build-system)
28260 (home-page "https://github.com/rstudio/config")
28261 (synopsis "Manage environment specific configuration values")
28263 "This package lets you manage configuration values across multiple
28264 environments (e.g. development, test, production). It reads values using a
28265 function that determines the current environment and returns the appropriate
28267 (license license:gpl3)))
28269 (define-public r-adaptivesparsity
28271 (name "r-adaptivesparsity")
28275 (uri (cran-uri "AdaptiveSparsity" version))
28278 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
28280 `((upstream-name . "AdaptiveSparsity")))
28281 (build-system r-build-system)
28284 (modify-phases %standard-phases
28285 (add-after 'unpack 'link-against-armadillo
28287 (substitute* "src/Makevars"
28288 (("PKG_LIBS=" prefix)
28289 (string-append prefix "-larmadillo")))
28292 (list r-mass r-matrix r-rcpp r-rcpparmadillo))
28295 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
28296 (synopsis "Adaptive sparsity models")
28298 "This package implements the Figueiredo machine learning algorithm for
28299 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
28300 geometric models.")
28301 (license license:lgpl3+)))
28303 (define-public r-add2ggplot
28305 (name "r-add2ggplot")
28310 (uri (cran-uri "add2ggplot" version))
28312 (base32 "0c94i1cfp2pvplvxmfvvz2fyj026r1jnax05mrzrc7ppnqzy25y0"))))
28313 (properties `((upstream-name . "add2ggplot")))
28314 (build-system r-build-system)
28316 (list r-ggplot2 r-magick r-magrittr r-rcolorbrewer r-zeallot))
28317 (native-inputs (list r-knitr))
28318 (home-page "https://github.com/JiaxiangBU/add2ggplot")
28319 (synopsis "Extension for ggplot2")
28320 (description "This package provides tools to create themes and color
28321 palettes for the package ggplot2.")
28322 (license license:expat)))
28324 (define-public r-diffusionmap
28326 (name "r-diffusionmap")
28331 (uri (cran-uri "diffusionMap" version))
28334 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
28335 (properties `((upstream-name . "diffusionMap")))
28336 (build-system r-build-system)
28338 (list r-igraph r-matrix r-scatterplot3d))
28339 (home-page "https://www.r-project.org")
28340 (synopsis "Diffusion map")
28341 (description "This package implements the diffusion map method of data
28342 parametrization, including creation and visualization of diffusion maps,
28343 clustering with diffusion K-means and regression using the adaptive regression
28345 (license license:gpl2)))
28347 (define-public r-igraph
28354 (uri (cran-uri "igraph" version))
28357 "0khl87ncc9hkvx4f1kyzv7w7bg9zbyd1rk20ja3azkhpqjkjnnjh"))))
28358 (build-system r-build-system)
28362 (list gmp glpk libxml2 zlib))
28364 (list r-magrittr r-matrix r-pkgconfig))
28365 (home-page "https://igraph.org")
28366 (synopsis "Network analysis and visualization")
28368 "This package provides routines for simple graphs and network analysis.
28369 It can handle large graphs very well and provides functions for generating
28370 random and regular graphs, graph visualization, centrality methods and much
28372 (license license:gpl2+)))
28374 (define-public r-workflows
28376 (name "r-workflows")
28381 (uri (cran-uri "workflows" version))
28384 "0xhc1j25fjipw8hvcpdbvfm640kp0flwvifj5f7g4n6b3wb8cm6a"))))
28385 (properties `((upstream-name . "workflows")))
28386 (build-system r-build-system)
28399 (home-page "https://github.com/tidymodels/workflows")
28400 (synopsis "Modeling workflows")
28402 "A workflow is an object that can bundle together your pre-processing,
28403 modeling, and post-processing requests. For example, if you have a
28404 @code{recipe} and @code{parsnip} model, these can be combined into a
28405 workflow. The advantages are:
28408 @item You don’t have to keep track of separate objects in your workspace.
28409 @item The recipe prepping and model fitting can be executed using a single
28410 call to @code{fit()}.
28411 @item If you have custom tuning parameter settings, these can be defined using
28412 a simpler interface when combined with @code{tune}.
28413 @item In the future, workflows will be able to add post-processing operations,
28414 such as modifying the probability cutoff for two-class models.
28417 (license license:expat)))
28419 (define-public r-lobstr
28426 (uri (cran-uri "lobstr" version))
28429 "0vkif17825x33cz8r89j0qph4wj5l8fzfgl8nh2g7m2v140cxjdq"))))
28430 (properties `((upstream-name . "lobstr")))
28431 (build-system r-build-system)
28433 (list r-crayon r-rcpp r-rlang))
28434 (home-page "https://github.com/r-lib/lobstr")
28435 (synopsis "Visualize R data structures with trees")
28437 "This package provides a set of tools for inspecting and understanding R
28438 data structures inspired by @code{str}. It includes @code{ast} for
28439 visualizing abstract syntax trees, @code{ref} for showing shared references,
28440 @code{cst} for showing call stack trees, and @code{obj_size} for computing
28442 (license license:gpl3)))
28444 (define-public r-gpfit
28451 (uri (cran-uri "GPfit" version))
28454 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
28455 (properties `((upstream-name . "GPfit")))
28456 (build-system r-build-system)
28458 (list r-lattice r-lhs))
28459 (home-page "https://cran.r-project.org/web/packages/GPfit/")
28460 (synopsis "Gaussian Processes modeling")
28462 "This package provides a computationally stable approach of fitting a
28463 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
28464 (license license:gpl2)))
28466 (define-public r-yardstick
28468 (name "r-yardstick")
28473 (uri (cran-uri "yardstick" version))
28476 "0mnpvwbzybxp47w4yibmjb7xppwinbjcqcyqfn8qn38l5liwy8yd"))))
28477 (properties `((upstream-name . "yardstick")))
28478 (build-system r-build-system)
28488 (home-page "https://github.com/tidymodels/yardstick")
28489 (synopsis "Tidy characterizations of model performance")
28491 "This package provides tidy tools for quantifying how well a model fits
28492 to a data set such as confusion matrices, class probability curve summaries,
28493 and regression metrics (e.g., RMSE).")
28494 (license license:gpl2)))
28496 (define-public r-warp
28503 (uri (cran-uri "warp" version))
28506 "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
28507 (properties `((upstream-name . "warp")))
28508 (build-system r-build-system)
28509 (native-inputs (list r-knitr))
28510 (home-page "https://github.com/DavisVaughan/warp")
28511 (synopsis "Group dates")
28513 "This package provides tooling to group dates by a variety of periods
28514 including: yearly, monthly, by second, by week of the month, and more. The
28515 groups are defined in such a way that they also represent the distance between
28516 dates in terms of the period. This extracts valuable information that can be
28517 used in further calculations that rely on a specific temporal spacing between
28519 (license license:expat)))
28521 (define-public r-scico
28528 (uri (cran-uri "scico" version))
28530 (base32 "08grfbjd5s0vdw76ni37yjl2242rr8i2jy72sgpwgra282hpnji3"))))
28531 (properties `((upstream-name . "scico")))
28532 (build-system r-build-system)
28533 (propagated-inputs (list r-scales))
28534 (home-page "https://github.com/thomasp85/scico")
28535 (synopsis "Colour Palettes Based on the Scientific Colour-Maps")
28537 "This package provides colour choice in information visualisation. It
28538 important in order to avoid being mislead by inherent bias in the used colour
28539 palette. This package provides access to the perceptually uniform and
28540 colour-blindness friendly palettes developed by Fabio Crameri and released
28541 under the \"Scientific Colour-Maps\" moniker. The package contains 24
28542 different palettes and includes both diverging and sequential types.")
28543 (license license:expat)))
28545 (define-public r-slider
28552 (uri (cran-uri "slider" version))
28555 "1vxk2bc33svwcki2j8zr5jcxswh27i0fqgzjw2a5a1pp9dh3fmd3"))))
28556 (properties `((upstream-name . "slider")))
28557 (build-system r-build-system)
28559 (list r-ellipsis r-glue r-rlang r-vctrs r-warp))
28560 (native-inputs (list r-knitr))
28561 (home-page "https://github.com/DavisVaughan/slider")
28562 (synopsis "Sliding window functions")
28564 "This package provides type-stable rolling window functions over any R
28565 data type. Cumulative and expanding windows are also supported. For more
28566 advanced usage, an index can be used as a secondary vector that defines how
28567 sliding windows are to be created.")
28568 (license license:expat)))
28570 (define-public r-rlist
28573 (version "0.4.6.2")
28577 (uri (cran-uri "rlist" version))
28579 (base32 "15q99rhbbjq8zd976yjmfnny45dd5fg2p2dv1sljg2kwi66nbppb"))))
28580 (properties `((upstream-name . "rlist")))
28581 (build-system r-build-system)
28582 (propagated-inputs (list r-data-table r-jsonlite r-xml r-yaml))
28583 (home-page "https://renkun-ken.github.io/rlist/")
28584 (synopsis "A Toolbox for Non-Tabular Data Manipulation")
28586 "This package provides a set of functions for data manipulation with
28587 list objects, including mapping, filtering, grouping, sorting, updating,
28588 searching, and other useful functions. Most functions are designed to be
28589 pipeline friendly so that data processing with lists can be chained.")
28590 (license license:expat)))
28592 (define-public r-rsample
28599 (uri (cran-uri "rsample" version))
28602 "01xwhj4zfvxbv9cjb6mbz3aphxqc3cnjjx1xy2yx2wd94fbka42z"))))
28603 (properties `((upstream-name . "rsample")))
28604 (build-system r-build-system)
28620 (home-page "https://rsample.tidymodels.org")
28621 (synopsis "General resampling infrastructure")
28623 "This package provides classes and functions to create and summarize
28624 different types of resampling objects (e.g. bootstrap, cross-validation).")
28625 (license license:gpl2)))
28627 (define-public r-dicedesign
28629 (name "r-dicedesign")
28634 (uri (cran-uri "DiceDesign" version))
28637 "1a8ixa65xgyfri03cviic8qi2plbhdyz8m02bwif8w94w0q3ghlk"))))
28638 (properties `((upstream-name . "DiceDesign")))
28639 (build-system r-build-system)
28640 (home-page "http://dice.emse.fr/")
28641 (synopsis "Designs of computer experiments")
28643 "This package provides tools to create some specific @code{Space-Filling
28644 Design} (SFD) and to test their quality.")
28645 (license license:gpl3)))
28647 (define-public r-dials
28654 (uri (cran-uri "dials" version))
28657 "1h695g9vklqn0vd53j9k03s0989xjpjr11h5qhz3a0v6465fwm8a"))))
28658 (properties `((upstream-name . "dials")))
28659 (build-system r-build-system)
28672 (native-inputs (list r-knitr))
28673 (home-page "https://dials.tidymodels.org/")
28674 (synopsis "Tools for creating tuning parameter values")
28676 "Many models contain tuning parameters (i.e. parameters that cannot be
28677 directly estimated from the data). These tools can be used to define objects
28678 for creating, simulating, or validating values for such parameters.")
28679 (license license:gpl2)))
28681 (define-public r-tune
28688 (uri (cran-uri "tune" version))
28691 "05gxlsaqv6sjk11r5g4nkdd6hlb3bnfmc29cx4vln1blha37jx4i"))))
28692 (properties `((upstream-name . "tune")))
28693 (build-system r-build-system)
28716 (home-page "https://github.com/tidymodels/tune")
28717 (synopsis "Tidy tuning tools")
28719 "The ability to tune models is important. @code{tune} contains functions
28720 and classes to be used in conjunction with other @code{tidymodels} packages
28721 for finding reasonable values of hyper-parameters in models, pre-processing
28722 methods, and post-processing steps.")
28723 (license license:expat)))
28725 (define-public r-workflowsets
28727 (name "r-workflowsets")
28732 (uri (cran-uri "workflowsets" version))
28735 "0q42nhnw0mbivadcfb07v71fp39x8fcnjipvn5l5yhjzc56cfxi8"))))
28736 (properties `((upstream-name . "workflowsets")))
28737 (build-system r-build-system)
28757 (home-page "https://github.com/tidymodels/workflowsets")
28758 (synopsis "Create a collection of tidymodels workflows")
28760 "A workflow is a combination of a model and preprocessors (e.g, a
28761 formula, recipe, etc.). In order to try different combinations of these, an
28762 object can be created that contains many workflows. There are functions to
28763 create workflows en masse as well as training them and visualizing the
28765 (license license:expat)))
28767 (define-public r-tidyposterior
28769 (name "r-tidyposterior")
28774 (uri (cran-uri "tidyposterior" version))
28777 "1h1664sjrg6akph6nrk8ynn2kjiswv6gshy35gamam1h4axf6wah"))))
28778 (properties `((upstream-name . "tidyposterior")))
28779 (build-system r-build-system)
28795 (home-page "https://tidyposterior.tidymodels.org")
28796 (synopsis "Bayesian analysis to compare models using resampling statistics")
28798 "This package can be used to conduct post hoc analyses of resampling
28799 results generated by models. For example, if two models are evaluated with
28800 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
28801 are 10 paired statistics. These can be used to make comparisons between
28802 models without involving a test set.")
28803 (license license:gpl2)))
28805 (define-public r-tidypredict
28807 (name "r-tidypredict")
28812 (uri (cran-uri "tidypredict" version))
28815 "0x0r36zvny4rqgndx7iqh39yhr53gl4d8wd8wpvdcgg35q6z02z2"))))
28816 (properties `((upstream-name . "tidypredict")))
28817 (build-system r-build-system)
28829 (home-page "https://tidypredict.tidymodels.org")
28830 (synopsis "Run predictions inside the database")
28832 "This package parses a fitted R model object, and returns a formula in
28833 Tidy Eval code that calculates the predictions. It works with several
28834 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
28835 final SQL translation of the algorithm. It currently supports @code{lm()},
28836 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
28837 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
28838 (license license:gpl3)))
28840 (define-public r-janeaustenr
28842 (name "r-janeaustenr")
28847 (uri (cran-uri "janeaustenr" version))
28850 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
28851 (properties `((upstream-name . "janeaustenr")))
28852 (build-system r-build-system)
28853 (home-page "https://github.com/juliasilge/janeaustenr")
28854 (synopsis "Jane Austen's complete novels")
28856 "This package provides the full texts for Jane Austen's six completed
28857 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
28858 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
28859 and \"Persuasion\".")
28860 (license license:expat)))
28862 (define-public r-tokenizers
28864 (name "r-tokenizers")
28869 (uri (cran-uri "tokenizers" version))
28872 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
28873 (properties `((upstream-name . "tokenizers")))
28874 (build-system r-build-system)
28876 (list r-rcpp r-snowballc r-stringi))
28879 (home-page "https://lincolnmullen.com/software/tokenizers/")
28880 (synopsis "Fast, consistent tokenization of natural language text")
28882 "This is a package for converting natural language text into tokens.
28883 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
28884 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
28885 Treebank, regular expressions, as well as functions for counting characters,
28886 words, and sentences, and a function for splitting longer texts into separate
28887 documents, each with the same number of words. The tokenizers have a
28888 consistent interface, and the package is built on the @code{stringi} and
28889 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
28890 (license license:expat)))
28892 (define-public r-hunspell
28894 (name "r-hunspell")
28899 (uri (cran-uri "hunspell" version))
28902 "0ql6y05d4xxpm468rslb0wxdp1x9l3flxzmb5w6pjg617f8vpv8z"))))
28903 (properties `((upstream-name . "hunspell")))
28904 (build-system r-build-system)
28906 (list r-digest r-rcpp))
28909 (home-page "https://github.com/ropensci/hunspell#readme")
28910 (synopsis "High-performance stemmer, tokenizer, and spell checker")
28912 "This package provides a low-level spell checker and morphological
28913 analyzer based on the famous @code{hunspell} library. The package can analyze
28914 or check individual words as well as parse text, LaTeX, HTML or XML documents.
28915 For a more user-friendly interface use the @code{spelling} package which
28916 builds on this package to automate checking of files, documentation and
28917 vignettes in all common formats.")
28918 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
28919 ;; MPL; in addition to these licenses the rest of the R wrapper is also
28920 ;; available under the Expat license.
28921 (license (list license:gpl2
28926 (define-public r-tidytext
28928 (name "r-tidytext")
28933 (uri (cran-uri "tidytext" version))
28936 "0kljaxyhhzbcv9jkjdy0wn6gkamh25y2xfb9k11sqhz3lv72nfvm"))))
28937 (properties `((upstream-name . "tidytext")))
28938 (build-system r-build-system)
28954 (home-page "https://github.com/juliasilge/tidytext")
28955 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
28957 "This is a package for text mining for word processing and sentiment
28958 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
28959 (license license:expat)))
28961 (define-public r-parsnip
28968 (uri (cran-uri "parsnip" version))
28971 "195i4j38mljv9193yx8lmh65h85yhc52y9vc1mk8zvxi52ks1yln"))))
28972 (properties `((upstream-name . "parsnip")))
28973 (build-system r-build-system)
28993 (home-page "https://parsnip.tidymodels.org")
28994 (synopsis "Common API to modeling and analysis functions")
28996 "This package provides a common interface to allow users to specify a
28997 model without having to remember the different argument names across different
28998 functions or computational engines (e.g. R, Spark, Stan, etc).")
28999 (license license:gpl2)))
29001 (define-public r-infer
29008 (uri (cran-uri "infer" version))
29011 "0qfrxljvwpa8d1k66ii80irarlv593wr6rmcsmi4flc7adgydrnp"))))
29012 (properties `((upstream-name . "infer")))
29013 (build-system r-build-system)
29028 (home-page "https://github.com/tidymodels/infer")
29029 (synopsis "Tidy statistical inference")
29031 "The objective of this package is to perform inference using an
29032 expressive statistical grammar that coheres with the Tidy design framework.")
29033 (license license:cc0)))
29035 (define-public r-modeldata
29037 (name "r-modeldata")
29042 (uri (cran-uri "modeldata" version))
29045 "0jgrwf9k8p9j3ywg3yv2wzwsx3snlwm3dd9vfqwhlr7j63jg3cm4"))))
29046 (properties `((upstream-name . "modeldata")))
29047 (build-system r-build-system)
29048 (home-page "https://modeldata.tidymodels.org")
29049 (synopsis "Data sets useful for modeling packages")
29051 "This package provides data sets used for demonstrating or testing
29052 model-related packages.")
29053 (license license:expat)))
29055 (define-public r-conflicted
29057 (name "r-conflicted")
29062 (uri (cran-uri "conflicted" version))
29065 "1qg9ar114r98wm0pnf65mss4v2ksq3924rlpm13mqp4s3p6j9yi4"))))
29066 (properties `((upstream-name . "conflicted")))
29067 (build-system r-build-system)
29069 (list r-memoise r-rlang))
29070 (home-page "https://github.com/r-lib/conflicted")
29071 (synopsis "Alternative conflict resolution strategy")
29073 "R's default conflict management system gives the most recently loaded
29074 package precedence. This can make it hard to detect conflicts, particularly
29075 when they arise because a package update creates ambiguity that did not
29076 previously exist. The @code{conflicted} package takes a different approach,
29077 making every conflict an error and forcing you to choose which function to
29079 (license license:gpl3)))
29081 (define-public r-tidymodels
29083 (name "r-tidymodels")
29088 (uri (cran-uri "tidymodels" version))
29091 "1xkv4s4kn7k9137svb39zrm5302gxpxyp1jv5bb6z0xrvj5wwa4i"))))
29092 (properties `((upstream-name . "tidymodels")))
29093 (build-system r-build-system)
29118 (home-page "https://github.com/tidymodels/tidymodels")
29119 (synopsis "Tidy collection for modeling and statistical analysis")
29121 "The tidy modeling \"verse\" is a collection of packages for modeling and
29122 statistical analysis that share the underlying design philosophy, grammar, and
29123 data structures of the tidyverse.")
29124 (license license:gpl3)))
29126 (define-public r-lsa
29133 (uri (cran-uri "lsa" version))
29136 "16k1g0kh3yaw7azg76aqf3hn3b6jgqg92xx0syai8l0my9ci2zzh"))))
29137 (properties `((upstream-name . "lsa")))
29138 (build-system r-build-system)
29140 (list r-snowballc))
29141 (home-page "https://cran.r-project.org/package=lsa")
29142 (synopsis "Latent semantic analysis")
29144 "The basic idea of latent semantic analysis (LSA) is, that text do have a
29145 higher order (=latent semantic) structure which, however, is obscured by word
29146 usage (e.g. through the use of synonyms or polysemy). By using conceptual
29147 indices that are derived statistically via a truncated singular value
29148 decomposition (a two-mode factor analysis) over a given document-term matrix,
29149 this variability problem can be overcome.")
29150 (license license:gpl2+)))
29152 (define-public r-mlecens
29159 (uri (cran-uri "MLEcens" version))
29162 "0cdl0y44clds4sg8hikhk354a5xrfbyfg8lxrbh1bfg410rkj186"))))
29163 (properties `((upstream-name . "MLEcens")))
29164 (build-system r-build-system)
29165 (home-page "http://stat.ethz.ch/~maathuis/")
29166 (synopsis "Computation of the MLE for bivariate (interval) censored data")
29168 "This package contains functions to compute the nonparametric
29169 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
29170 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
29171 To be more precise, we consider the situation where we observe a set of
29172 rectangles that are known to contain the unobservable realizations of (X,Y).
29173 We compute the MLE based on such a set of rectangles. The methods can also be
29174 used for univariate censored data (see data set @code{cosmesis}), and for
29175 censored data with competing risks (see data set @code{menopause}). The
29176 package also provides functions to visualize the observed data and the MLE.")
29177 (license license:gpl2+)))
29179 (define-public r-metafor
29186 (uri (cran-uri "metafor" version))
29189 "0vn244xfgq7yxwl6ykvadb305z360ssc9vzva7kbcdfiqhhvrqcj"))))
29190 (properties `((upstream-name . "metafor")))
29191 (build-system r-build-system)
29193 (list r-mathjaxr r-matrix r-metadat r-nlme r-pbapply))
29194 (home-page "https://cran.r-project.org/web/packages/metafor/")
29195 (synopsis "Meta-analysis package for R")
29197 "This package provides a comprehensive collection of functions for
29198 conducting meta-analyses in R. The package includes functions to calculate
29199 various effect sizes or outcome measures, fit fixed-, random-, and
29200 mixed-effects models to such data, carry out moderator and meta-regression
29201 analyses, and create various types of meta-analytical plots (e.g., forest,
29202 funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial
29203 and person-time data, the package also provides functions that implement
29204 specialized methods, including the Mantel-Haenszel method, Peto's method, and
29205 a variety of suitable generalized linear (mixed-effects) models (i.e.
29206 mixed-effects logistic and Poisson regression models). Finally, the package
29207 provides functionality for fitting meta-analytic multivariate/multilevel
29208 models that account for non-independent sampling errors and/or true
29209 effects (e.g. due to the inclusion of multiple treatment studies, multiple
29210 endpoints, or other forms of clustering). Network meta-analyses and
29211 meta-analyses accounting for known correlation structures (e.g. due to
29212 phylogenetic relatedness) can also be conducted.")
29213 (license license:gpl2+)))
29215 (define-public r-altmeta
29222 (uri (cran-uri "altmeta" version))
29225 "17cyiydf4n5j64izj7jph2v43h4x9kfd5b0x6m0ik5ci2aw8xzr5"))))
29226 (properties `((upstream-name . "altmeta")))
29227 (build-system r-build-system)
29229 (list r-coda r-lme4 r-matrix r-metafor r-rjags))
29230 (home-page "https://cran.r-project.org/web/packages/altmeta/")
29231 (synopsis "Alternative meta-analysis methods")
29233 "This package provides alternative statistical methods for meta-analysis,
29237 @item bivariate generalized linear mixed models for synthesizing odds ratios,
29238 relative risks, and risk differences
29239 @item heterogeneity tests and measures that are robust to outliers;
29240 @item measures, tests, and visualization tools for publication bias or
29241 small-study effects;
29242 @item meta-analysis of diagnostic tests for synthesizing sensitivities,
29243 specificities, etc.;
29244 @item meta-analysis methods for synthesizing proportions;
29245 @item models for multivariate meta-analysis.
29248 (license license:gpl2+)))
29250 (define-public r-perm
29253 (version "1.0-0.2")
29257 (uri (cran-uri "perm" version))
29260 "182ac1y91yzb34zwdcmx5fdfr5z0cha0gx2bgk36gwxhgfc994kj"))))
29261 (properties `((upstream-name . "perm")))
29262 (build-system r-build-system)
29263 (home-page "https://cran.r-project.org/web/packages/perm/")
29264 (synopsis "Exact or asymptotic permutation tests")
29266 "This package provides several methods for performing permutation tests.
29267 It has three main functions, to perform linear permutation tests. These tests
29268 are tests where the test statistic is the sum of the product of a
29269 covariate (usually group indicator) and the scores.")
29270 ;; Any version of the GPL
29271 (license license:gpl2+)))
29273 (define-public r-qtl
29280 (uri (cran-uri "qtl" version))
29283 "1mcy9wlp5lj5f3z4mf3n5li7x32vj67rmhjnzsp8fhfw0ipnaf1d"))))
29284 (build-system r-build-system)
29285 (home-page "https://rqtl.org/")
29286 (synopsis "R package for analyzing QTL experiments in genetics")
29287 (description "R/qtl is an extension library for the R statistics system.
29288 It is used to analyze experimental crosses for identifying genes contributing
29289 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
29291 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
29292 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
29294 (license license:gpl3)))
29296 (define-public r-qtl2
29302 (uri (cran-uri "qtl2" version))
29304 (base32 "0ppc6dzlq77mppxc6bczai9gi40jrbxd1466y2cn2s8a4ah1jg9y"))))
29305 (build-system r-build-system)
29313 (home-page "https://kbroman.org/qtl2/")
29314 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
29316 "This package provides a set of tools to perform @dfn{Quantitative Trait
29317 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
29318 @code{R/qtl} package to better handle high-dimensional data and complex cross
29319 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
29320 (license license:gpl3)))
29322 (define-public r-seqminer
29324 (name "r-seqminer")
29329 (uri (cran-uri "seqminer" version))
29332 "1mbx1hw9dhgry7hhan43g6aiz2lyd5api7wxq3fwajyzjrc6p1g8"))))
29333 (build-system r-build-system)
29336 (home-page "http://seqminer.genomic.codes")
29337 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
29339 "This package provides tools to integrate nucleotide sequencing
29340 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
29341 ;; Any version of the GPL is acceptable
29342 (license (list license:gpl2+ license:gpl3+))))
29344 (define-public r-maldiquant
29346 (name "r-maldiquant")
29351 (uri (cran-uri "MALDIquant" version))
29354 "1y1g3819ss06dry70kfhg2syddw71682qmzkcyppfsma6hhghw87"))))
29355 (properties `((upstream-name . "MALDIquant")))
29356 (build-system r-build-system)
29359 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
29360 (synopsis "Quantitative analysis of mass spectrometry data")
29362 "This package provides a complete analysis pipeline for matrix-assisted
29363 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
29364 two-dimensional mass spectrometry data. In addition to commonly used plotting
29365 and processing methods it includes distinctive features, namely baseline
29366 subtraction methods such as morphological filters (TopHat) or the
29367 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
29368 alignment using warping functions, handling of replicated measurements as well
29369 as allowing spectra with different resolutions.")
29370 (license license:gpl3+)))
29372 (define-public r-scattermore
29374 (name "r-scattermore")
29379 (uri (cran-uri "scattermore" version))
29382 "1rgqm7r1k7j3h2y4i6d1a2y8fzivfcbmr7dj9d367c0w4vc77pfv"))))
29383 (properties `((upstream-name . "scattermore")))
29384 (build-system r-build-system)
29386 (list r-ggplot2 r-scales))
29387 (home-page "https://github.com/exaexa/scattermore")
29388 (synopsis "Scatterplots with more points")
29390 "This package provides C-based tools for converting large scatterplot
29391 data to rasters. It speeds up plotting of data with millions of points.")
29392 (license license:gpl3+)))
29394 (define-public r-seuratobject
29396 (name "r-seuratobject")
29401 (uri (cran-uri "SeuratObject" version))
29404 "018anas8a9m3kh9jn5370v64d93k64z3iic13a75hp6r7g5hd94w"))))
29405 (properties `((upstream-name . "SeuratObject")))
29406 (build-system r-build-system)
29417 (home-page "https://satijalab.org/seurat")
29418 (synopsis "Data structures for single cell data")
29420 "This package defines S4 classes for single-cell genomic data and
29421 associated information, such as dimensionality reduction embeddings,
29422 nearest-neighbor graphs, and spatially-resolved coordinates. It provides data
29423 access methods and R-native hooks to ensure the Seurat object is familiar to
29425 (license license:gpl3)))
29427 (define-public r-seurat
29433 (uri (cran-uri "Seurat" version))
29436 "1klamxk6dj0jgpfwll5frcnj9h8lh8c5fxdn9ky7h8xk35lsj6i0"))))
29437 (properties `((upstream-name . "Seurat")))
29438 (build-system r-build-system)
29483 (home-page "http://www.satijalab.org/seurat")
29484 (synopsis "Seurat is an R toolkit for single cell genomics")
29486 "This package is an R package designed for QC, analysis, and
29487 exploration of single cell RNA-seq data. It easily enables widely-used
29488 analytical techniques, including the identification of highly variable genes,
29489 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
29490 algorithms; density clustering, hierarchical clustering, k-means, and the
29491 discovery of differentially expressed genes and markers.")
29492 (license license:gpl3)))
29494 (define-public r-seuratdisk
29495 (let ((commit "163f1aade5bac38ed1e9e9c912283a7e74781610")
29498 (name "r-seuratdisk")
29499 (version (git-version "0.0.0.9019" revision commit))
29503 (uri (git-reference
29504 (url "https://github.com/mojaveazure/seurat-disk")
29506 (file-name (git-file-name name version))
29508 (base32 "1d1v8qi6kknzy5fj6bl8akwy74h5h143i00lyidsnqjbwp9n4qnw"))))
29509 (properties `((upstream-name . "SeuratDisk")))
29510 (build-system r-build-system)
29524 (home-page "https://github.com/mojaveazure/seurat-disk")
29525 (synopsis "Interfaces for HDF5-based single cell file formats")
29527 "The h5Seurat file format is specifically designed for the storage and
29528 analysis of multi-modal single-cell and spatially-resolved expression
29529 experiments, for example, from CITE-seq or 10X Visium technologies. It holds
29530 all molecular information and associated metadata, including (for example)
29531 nearest-neighbor graphs, dimensional reduction information, spatial
29532 coordinates and image data, and cluster labels. This package also supports
29533 rapid and on-disk conversion between h5Seurat and AnnData objects, with the
29534 goal of enhancing interoperability between Seurat and Scanpy.")
29535 (license license:gpl3))))
29537 (define-public r-seuratdata
29538 (let ((commit "b59556b24d7d6728a5744c9c715dd5f7f32ed7a5")
29541 (name "r-seuratdata")
29542 (version (git-version "0.2.1" revision commit))
29546 (uri (git-reference
29547 (url "https://github.com/satijalab/seurat-data")
29549 (file-name (git-file-name name version))
29551 (base32 "1xfdmdmgn4r0z6w4cxa98ic6xk8i6qz054r215dvqbjs1vydsbf9"))))
29552 (properties `((upstream-name . "SeuratData")))
29553 (build-system r-build-system)
29556 (modify-phases %standard-phases
29557 ;; When there is no HOME directory, this package will fail to load
29558 ;; the included list of packages.
29559 (add-after 'unpack 'set-HOME
29560 (lambda _ (setenv "HOME" "/tmp"))))))
29562 (list r-cli r-crayon r-rappdirs))
29563 (home-page "https://github.com/satijalab/seurat-data")
29564 (synopsis "Install and manage Seurat datasets")
29566 "Single cell RNA sequencing datasets can be large, consisting of
29567 matrices that contain expression data for several thousand features across
29568 several thousand cells. This package is designed to easily install, manage,
29569 and learn about various single-cell datasets, provided Seurat objects and
29570 distributed as independent packages.")
29571 (license license:gpl3))))
29573 (define-public r-phangorn
29575 (name "r-phangorn")
29580 (uri (cran-uri "phangorn" version))
29583 "0xfwi7adl1pcfcwk72fj7lkwfm0wiip96ij7m4252xr9mq818ivd"))))
29584 (build-system r-build-system)
29594 (home-page "https://github.com/KlausVigo/phangorn")
29595 (synopsis "Phylogenetic analysis in R")
29597 "Phangorn is a package for phylogenetic analysis in R. It supports
29598 estimation of phylogenetic trees and networks using Maximum Likelihood,
29599 Maximum Parsimony, distance methods and Hadamard conjugation.")
29600 (license license:gpl2+)))
29602 (define-public r-diversitree
29604 (name "r-diversitree")
29609 (uri (cran-uri "diversitree" version))
29612 "0rzrk7xsn4gy271pbcw3azndhx0c06bmsgrg6libjmlfnmq6j8sc"))))
29613 (build-system r-build-system)
29616 (inputs (list fftw gsl))
29618 (list r-ape r-desolve r-rcpp r-subplex))
29619 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
29620 (synopsis "Comparative 'phylogenetic' analyses of diversification")
29621 (description "This package contains a number of comparative \"phylogenetic\"
29622 methods, mostly focusing on analysing diversification and character evolution.
29623 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
29624 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
29625 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
29626 include Markov models of discrete and continuous trait evolution and constant
29627 rate speciation and extinction.")
29628 (license license:gpl2+)))
29630 (define-public r-calculus
29632 (name "r-calculus")
29637 (uri (cran-uri "calculus" version))
29640 "1fhvr0l2mqik3d95v0vanafxmiab147g5a87q956g2i945wc5f22"))))
29641 (properties `((upstream-name . "calculus")))
29642 (build-system r-build-system)
29647 (home-page "https://github.com/eguidotti/calculus")
29648 (synopsis "High dimensional numerical and symbolic calculus")
29650 "Efficient C++ optimized functions for numerical and symbolic calculus.
29651 It includes basic symbolic arithmetic, tensor calculus, Einstein summing
29652 convention, fast computation of the Levi-Civita symbol and generalized
29653 Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
29654 accurate high-order derivatives, differential operators (Gradient, Jacobian,
29655 Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
29656 orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
29657 parabolic or user defined by custom scale factors.")
29658 (license license:gpl3)))
29660 (define-public r-decon
29667 (uri (cran-uri "decon" version))
29670 "036cv56wf42q2p3d5h15hbrp5rc29xxy20qwv4k1qzhkq6hmw0qs"))))
29671 (properties `((upstream-name . "decon")))
29672 (build-system r-build-system)
29676 "https://cran.r-project.org/web/packages/decon/")
29677 (synopsis "Deconvolution Estimation in Measurement Error Models")
29679 "This package contains a collection of functions to deal with
29680 nonparametric measurement error problems using deconvolution
29681 kernel methods. We focus two measurement error models in the
29682 package: (1) an additive measurement error model, where the
29683 goal is to estimate the density or distribution function from
29684 contaminated data; (2) nonparametric regression model with
29685 errors-in-variables. The R functions allow the measurement errors
29686 to be either homoscedastic or heteroscedastic. To make the
29687 deconvolution estimators computationally more efficient in R,
29688 we adapt the \"Fast Fourier Transform\" (FFT) algorithm for
29689 density estimation with error-free data to the deconvolution
29690 kernel estimation. Several methods for the selection of the
29691 data-driven smoothing parameter are also provided in the package.
29692 See details in: Wang, X.F. and Wang, B. (2011). Deconvolution
29693 estimation in measurement error models: The R package decon.
29694 Journal of Statistical Software, 39(10), 1-24.")
29695 (license license:gpl3+)))
29697 (define-public r-densestbayes
29699 (name "r-densestbayes")
29700 (version "1.0-2.1")
29704 (uri (cran-uri "densEstBayes" version))
29706 (base32 "1pzmgn65lv91zg1588qhwczy9f2zgciknlc4l072mvh2i7hncw2b"))))
29707 (properties `((upstream-name . "densEstBayes")))
29708 (build-system r-build-system)
29720 (home-page "https://cran.r-project.org/package=densEstBayes")
29721 (synopsis "Density estimation via Bayesian inference engines")
29723 "Bayesian density estimates for univariate continuous random samples are
29724 provided using the Bayesian inference engine paradigm. The engine options
29725 are: Hamiltonian Monte Carlo, the no U-turn sampler, semiparametric mean field
29726 variational Bayes and slice sampling. The methodology is described in Wand
29727 and Yu (2020), arXiv:2009.06182.")
29728 (license license:gpl2+)))
29730 (define-public r-locpol
29737 (uri (cran-uri "locpol" version))
29740 "1p915n0l09kbwkly627074jslxl01yssp1rf0c7sygvsw6sgy5lm"))))
29741 (properties `((upstream-name . "locpol")))
29742 (build-system r-build-system)
29744 "https://cran.r-project.org/web/packages/locpol/")
29745 (synopsis "Kernel Local Polynomial Regression")
29747 "Computes local polynomial estimators for the regression and
29748 also density. It comprises several different utilities to handle
29749 kernel estimators.")
29750 (license license:gpl2+)))
29752 (define-public r-lpme
29759 (uri (cran-uri "lpme" version))
29762 "1ch11cwjci98m7952p9wdsh9fj5y1mjya6ayq0q4wmbm824qfpzb"))))
29763 (properties `((upstream-name . "lpme")))
29764 (build-system r-build-system)
29766 (list r-decon r-flexmix r-locpol r-rcpp r-rcpparmadillo))
29768 "https://cran.r-project.org/web/packages/lpme/")
29769 (synopsis "Nonparametric Estimation of Measurement Error Models")
29771 "Provide nonparametric methods for mean regression model,
29772 modal regression and conditional density estimation in the
29773 presence/absence of measurement error. Bandwidth selection is
29774 also provided for each method.")
29775 (license license:gpl2+)))
29777 (define-public r-aws-signature
29779 (name "r-aws-signature")
29784 (uri (cran-uri "aws.signature" version))
29787 "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp"))))
29788 (properties `((upstream-name . "aws.signature")))
29789 (build-system r-build-system)
29791 (list r-base64enc r-digest))
29792 (home-page "https://github.com/cloudyr/aws.signature")
29793 (synopsis "Amazon Web Services Request Signatures")
29795 "This package generates version 2 and 4 request signatures for Amazon Web
29796 Services (AWS) and provides a mechanism for retrieving credentials from
29797 environment variables, AWS credentials files, and EC2 instance metadata. For
29798 use on EC2 instances, the package 'aws.ec2metadata' is suggested.")
29799 (license license:gpl2+)))
29801 (define-public r-aws-s3
29808 (uri (cran-uri "aws.s3" version))
29811 "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx"))))
29812 (properties `((upstream-name . "aws.s3")))
29813 (build-system r-build-system)
29815 (list r-aws-signature
29821 (home-page "https://github.com/cloudyr/aws.s3")
29822 (synopsis "AWS S3 Client Package")
29824 "This package provides a simple client package for the Amazon Web
29825 Services (AWS) Simple Storage Service (S3) REST API.")
29826 (license license:gpl2+)))
29828 (define-public r-lgr
29834 (uri (cran-uri "lgr" version))
29837 "18s92qyakhvp336kk2777ydypwfrfwfz6a1gqkq812zy3kcb4mcc"))))
29838 (build-system r-build-system)
29843 (home-page "https://s-fleck.github.io/lgr/")
29844 (synopsis "Fully featured logging framework")
29845 (description "This package offers a flexible, feature-rich yet
29846 light-weight logging framework based on @code{R6} classes. It supports
29847 hierarchical loggers, custom log levels, arbitrary data fields in log events,
29848 logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as
29849 well as email and push notifications.")
29850 (license license:expat)))
29852 (define-public r-mhg
29859 (uri (cran-uri "mHG" version))
29862 "1rz5ncrvvv9h9grls15apa63v2nh9j87fmp4mwjjil37jx6a5zki"))))
29863 (properties `((upstream-name . "mHG")))
29864 (build-system r-build-system)
29865 (home-page "https://cran.r-project.org/package=mHG")
29866 (synopsis "Minimum-hypergeometric test")
29868 "This package runs a minimum-hypergeometric (mHG) test as described in
29869 \"Discovering Motifs in Ranked Lists of DNA Sequences\" by Eran Eden.")
29870 (license license:gpl2)))
29872 (define-public r-mlr3measures
29874 (name "r-mlr3measures")
29878 (uri (cran-uri "mlr3measures" version))
29881 "1kbw3xd7c9x65v9zzs8i5skmrvl0mf2wsbyssmiif0lvrbzfhcmb"))))
29882 (build-system r-build-system)
29884 (list r-checkmate r-prroc))
29885 (home-page "https://mlr3measures.mlr-org.com/")
29886 (synopsis "Performance measures for mlr3")
29887 (description "This package implements multiple performance measures for
29888 supervised learning. It includes over 40 measures for regression and
29889 classification. Additionally, meta information about the performance measures
29890 can be queried, e.g. what the best and worst possible performances scores
29892 (license license:lgpl3)))
29894 (define-public r-mlr3misc
29896 (name "r-mlr3misc")
29900 (uri (cran-uri "mlr3misc" version))
29903 "1wnzyij1x67smkb3gjb9gpp7iy5andfl0s1c78xx4wylhycc6m11"))))
29904 (build-system r-build-system)
29906 (list r-backports r-checkmate r-data-table r-digest r-r6))
29907 (home-page "https://mlr3misc.mlr-org.com/")
29908 (synopsis "Helper functions for mlr3")
29909 (description "@code{mlr3misc} provides frequently used helper functions
29910 and assertions used in @code{mlr3} and its companion packages. It comes with
29911 helper functions for functional programming, for printing, to work with
29912 @code{data.table}, as well as some generally useful @code{R6} classes. This
29913 package also supersedes the package @code{BBmisc}.")
29914 (license license:lgpl3)))
29916 (define-public r-mlr3pipelines
29918 (name "r-mlr3pipelines")
29922 (uri (cran-uri "mlr3pipelines" version))
29925 "1zz55i8c08znxpcs6gp5inaw96c6la9wnsla0972ankvj1hsrcr2"))))
29926 (build-system r-build-system)
29938 (home-page "https://mlr3pipelines.mlr-org.com/")
29939 (synopsis "Preprocessing Operators and Pipelines for @code{mlr3}")
29940 (description "@code{mlr3pipelines} enriches @code{mlr3} with a diverse
29941 set of pipelining operators (PipeOps) that can be composed into graphs.
29942 Operations exist for data preprocessing, model fitting, and ensemble learning.
29943 Graphs can themselves be treated as @code{mlr3} Learners and can therefore be
29944 resampled, benchmarked, and tuned.")
29945 (license license:lgpl3)))
29947 (define-public r-mlr3ordinal
29948 (let ((commit "9febac983b11b7b1f477e5cf0212e5999cd2ed44")
29951 (name "r-mlr3ordinal")
29952 (version (git-version "0.1.0-9000" revision commit))
29955 (uri (git-reference
29956 (url "https://github.com/mlr-org/mlr3ordinal")
29958 (file-name (git-file-name name version))
29961 "1icfhz1pjm0mlsn2y60gsrbk31b2p7xmpx3xsg7639rcgdb5f9gl"))))
29962 (build-system r-build-system)
29973 (home-page "https://mlr3ordinal.mlr-org.com/")
29974 (synopsis "Ordinal Regression for mlr3")
29975 (description "This package extends @code{mlr3} with support for
29976 performing ordinal regression.")
29977 (license license:expat))))
29979 (define-public r-paradox
29985 (uri (cran-uri "paradox" version))
29988 "0fzq59903fklgj3kblnpzasy13a82s72c1qjsy7d1m0fyj28ahdw"))))
29989 (build-system r-build-system)
29991 (list r-backports r-checkmate r-data-table r-mlr3misc r-r6))
29992 (home-page "https://paradox.mlr-org.com/")
29993 (synopsis "Define and work with parameter spaces for complex algorithms")
29994 (description "With this package it is possible to define parameter spaces,
29995 constraints and dependencies for arbitrary algorithms, and to program on such
29996 spaces. It also includes statistical designs and random samplers. Objects are
29997 implemented as @code{R6} classes.")
29998 (license license:lgpl3)))
30000 (define-public r-mlr3
30006 (uri (cran-uri "mlr3" version))
30009 "010kl51zsgpc0qv63g1fg9kiw9m0wzqskcr14f1j8b9zi1lwi0bf"))))
30010 (build-system r-build-system)
30027 (home-page "https://mlr3.mlr-org.com/")
30028 (synopsis "Machine Learning in R - Next Generation")
30029 (description "@code{mlr3} enables efficient, object-oriented programming
30030 on the building blocks of machine learning. It provides @code{R6} objects for
30031 tasks, learners, resamplings, and measures. The package is geared towards
30032 scalability and larger datasets by supporting parallelization and out-of-memory
30033 data-backends like databases. While @code{mlr3} focuses on the core
30034 computational operations, add-on packages provide additional functionality.")
30035 (license license:lgpl3)))
30037 (define-public r-mlr3learners
30039 (name "r-mlr3learners")
30043 (uri (cran-uri "mlr3learners" version))
30046 "088i2piv7sgxsvc7jyr6mq53vqf8yjdlrysgqphsryq6k50i00zd"))))
30047 (build-system r-build-system)
30055 (home-page "https://mlr3learners.mlr-org.com/")
30056 (synopsis "Recommended Learners for @code{mlr3}")
30057 (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba}
30058 with interfaces to essential machine learning packages on CRAN. This includes,
30059 but is not limited to: (penalized) linear and logistic regression, linear and
30060 quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support
30061 vector machines, and gradient boosting.")
30062 (license license:lgpl3)))
30064 (define-public r-bbotk
30071 (uri (cran-uri "bbotk" version))
30074 "13qj8qysqismv9k9rfw770r7w8jdaw82n71k7sp3wsrlhxjxw734"))))
30075 (properties `((upstream-name . "bbotk")))
30076 (build-system r-build-system)
30086 (home-page "https://bbotk.mlr-org.com")
30087 (synopsis "Black-Box Optimization Toolkit")
30088 (description "This package provides a common framework for optimization of
30089 black-box functions for other packages, e.g. @code{mlr3}. It offers various
30090 optimization methods e.g. grid search, random search and generalized simulated
30092 (license license:lgpl3)))
30094 (define-public r-mlr3tuning
30096 (name "r-mlr3tuning")
30100 (uri (cran-uri "mlr3tuning" version))
30103 "0jfslx6pwk408ydn69grrvsp22jd7gsjmwvss0a1j0zav3q1pvks"))))
30104 (build-system r-build-system)
30114 (home-page "https://mlr3tuning.mlr-org.com/")
30115 (synopsis "Tuning for @code{mlr3}")
30116 (description "@code{mlr3tuning} implements methods for hyperparameter
30117 tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various
30118 termination criteria can be set and combined. The class @code{AutoTuner} provides a
30119 convenient way to perform nested resampling in combination with @code{mlr3}.")
30120 (license license:lgpl3)))
30122 (define-public r-fontliberation
30124 (name "r-fontliberation")
30129 (uri (cran-uri "fontLiberation" version))
30132 "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc"))))
30134 `((upstream-name . "fontLiberation")))
30135 (build-system r-build-system)
30136 (home-page "https://cran.r-project.org/package=fontLiberation")
30137 (synopsis "Liberation fonts")
30139 "This package provides a placeholder for the Liberation fontset intended
30140 for the fontquiver package. This fontset covers the 12 combinations of
30141 families (sans, serif, mono) and faces (plain, bold, italic, bold italic)
30142 supported in R graphics devices.")
30143 (license license:silofl1.1)))
30145 (define-public r-fontbitstreamvera
30147 (name "r-fontbitstreamvera")
30152 (uri (cran-uri "fontBitstreamVera" version))
30155 "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j"))))
30157 `((upstream-name . "fontBitstreamVera")))
30158 (build-system r-build-system)
30159 (home-page "https://cran.r-project.org/package=fontBitstreamVera")
30160 (synopsis "Fonts for fontquiver")
30162 "This package is a placeholder for the Bitstream Vera font. It is
30163 intended for the fontquiver package.")
30165 (license:fsdg-compatible
30166 "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts"
30167 "The Font Software may be sold as part of a larger software package but
30168 no copy of one or more of the Font Software typefaces may be sold by
30171 (define-public r-fontquiver
30173 (name "r-fontquiver")
30178 (uri (cran-uri "fontquiver" version))
30181 "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm"))))
30182 (properties `((upstream-name . "fontquiver")))
30183 (build-system r-build-system)
30185 (list r-fontbitstreamvera r-fontliberation))
30186 (home-page "https://cran.r-project.org/package=fontquiver")
30187 (synopsis "Set of installed fonts")
30189 "This package provides a set of fonts. This is useful when you want to
30190 avoid system fonts to make sure your outputs are reproducible.")
30191 (license license:gpl3)))
30193 (define-public r-freetypeharfbuzz
30195 (name "r-freetypeharfbuzz")
30200 (uri (cran-uri "freetypeharfbuzz" version))
30203 "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7"))))
30205 `((upstream-name . "freetypeharfbuzz")))
30206 (build-system r-build-system)
30209 (modify-phases %standard-phases
30210 (add-after 'unpack 'prepare-static-libraries
30211 (lambda* (#:key inputs #:allow-other-keys)
30212 (mkdir-p "src/target/include")
30213 (let ((freetype (assoc-ref inputs "static-freetype"))
30214 (harfbuzz (assoc-ref inputs "static-harfbuzz")))
30215 (substitute* "src/Makevars.in"
30216 (("include @MK_FILE@") "") ; do not build static libs
30217 (("^HB_STATIC_LIB =.*")
30218 (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n"))
30219 (("^FT_STATIC_LIB =.*")
30220 (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n")))
30221 (copy-recursively (string-append freetype "/include")
30222 "src/target/include")
30223 (copy-recursively (string-append harfbuzz "/include")
30224 "src/target/include")))))))
30226 (list r-fontquiver))
30227 ;; This may defeat the purpose of this package as our versions of freetype
30228 ;; and harfbuzz obviously differ from the tarballs offered by this
30229 ;; project. On the other hand, Guix arguably does a better job at
30230 ;; "ensur[ing] deterministic computation".
30232 `(("static-freetype"
30234 (inherit (static-package freetype))
30236 `(#:configure-flags
30237 (list "--enable-static=yes"
30242 "--without-harfbuzz")))))
30245 (inherit (static-package harfbuzz))
30247 `(#:tests? #false ; fail because shared library is disabled
30249 (list "--enable-static=yes"
30250 "--enable-shared=no"
30252 "--with-freetype=yes"
30255 "--without-fontconfig"
30256 "--without-glib")))))))
30259 (home-page "https://cran.r-project.org/package=freetypeharfbuzz")
30260 (synopsis "Deterministic computation of text box metrics")
30262 "Unlike other tools that dynamically link to the Cairo stack,
30263 freetypeharfbuzz is statically linked to specific versions of the FreeType and
30264 harfbuzz libraries. This ensures deterministic computation of text box
30265 extents for situations where reproducible results are crucial (for instance
30266 unit tests of graphics).")
30267 (license license:gpl3)))
30269 (define-public r-vdiffr
30276 (uri (cran-uri "vdiffr" version))
30279 "1z8nn8yh6jfzb9r7ylmigwh1p30lrclqm6khmp323qqphzmzfdwy"))))
30280 (properties `((upstream-name . "vdiffr")))
30281 (build-system r-build-system)
30283 (list libpng zlib))
30293 (home-page "https://github.com/r-lib/vdiffr")
30294 (synopsis "Visual regression testing and graphical diffing")
30296 "This package is an extension to the testthat package that makes it easy
30297 to add graphical unit tests. It provides a Shiny application to manage the
30299 (license license:gpl3)))
30301 (define-public r-highlight
30303 (name "r-highlight")
30308 (uri (cran-uri "highlight" version))
30311 "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf"))))
30312 (properties `((upstream-name . "highlight")))
30313 (build-system r-build-system)
30314 (home-page "https://github.com/hadley/highlight")
30315 (synopsis "Syntax highlighter for R code")
30317 "This package provides a syntax highlighter for R code based on the
30318 results of the R parser. It supports rendering in HTML and LaTeX markup. It
30319 includes a custom Sweave driver performing syntax highlighting of R code
30321 (license license:gpl3+)))
30323 (define-public r-clustree
30325 (name "r-clustree")
30330 (uri (cran-uri "clustree" version))
30333 "0vwmicajl7c0rmjdmf4f857fii0xrxz25vjkn888svlsikw00qbs"))))
30334 (properties `((upstream-name . "clustree")))
30335 (build-system r-build-system)
30348 (home-page "https://github.com/lazappi/clustree")
30349 (synopsis "Visualize clusterings at different resolutions")
30351 "Deciding what resolution to use can be a difficult question when
30352 approaching a clustering analysis. One way to approach this problem is to
30353 look at how samples move as the number of clusters increases. This package
30354 allows you to produce clustering trees, a visualization for interrogating
30355 clusterings as resolution increases.")
30356 (license license:gpl3)))
30358 (define-public r-textshaping
30360 (name "r-textshaping")
30365 (uri (cran-uri "textshaping" version))
30368 "1niaj1dh09rqrg9hrh98ddnc0f2nkyq9iizv24lcwm9gjs3w1ql0"))))
30369 (properties `((upstream-name . "textshaping")))
30370 (build-system r-build-system)
30372 (list freetype fribidi harfbuzz zlib))
30374 (list r-cpp11 r-systemfonts))
30376 (list pkg-config r-knitr))
30377 (home-page "https://github.com/r-lib/textshaping")
30378 (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping")
30380 "This package provides access to the text shaping functionality in the
30381 HarfBuzz library and the bidirectional algorithm in the Fribidi library. This
30382 is a low-level utility package mainly for graphic devices that expands upon
30383 the font tool-set provided by the @code{systemfonts} package.")
30384 (license license:expat)))
30386 (define-public r-ragg
30393 (uri (cran-uri "ragg" version))
30396 "1q43pwmljsqgrikkh2g1n7bpz9c8py5dnj44cfg3y2br7b4m2q9v"))))
30397 (properties `((upstream-name . "ragg")))
30398 (build-system r-build-system)
30400 (list freetype libjpeg-turbo libpng libtiff zlib))
30402 (list r-systemfonts r-textshaping))
30405 (home-page "https://ragg.r-lib.org")
30406 (synopsis "Graphic devices based on AGG")
30408 "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D
30409 drawing library. The ragg package provides a set of graphic devices based on
30410 AGG to use as alternative to the raster devices provided through the
30411 @code{grDevices} package.")
30412 (license license:expat)))
30414 (define-public r-downlit
30421 (uri (cran-uri "downlit" version))
30424 "10zvrqdpwavdy97h3q26bqh3k63z61fmc04w9vwsnvmnv8hnh3vl"))))
30425 (properties `((upstream-name . "downlit")))
30426 (build-system r-build-system)
30437 (home-page "https://downlit.r-lib.org/")
30438 (synopsis "Syntax highlighting and automatic linking")
30440 "This package provides syntax highlighting of R code, specifically
30441 designed for the needs of RMarkdown packages like @code{pkgdown},
30442 @code{hugodown}, and @code{bookdown}. It includes linking of function calls
30443 to their documentation on the web, and automatic translation of ANSI escapes
30444 in output to the equivalent HTML.")
30445 (license license:expat)))
30447 (define-public r-pkgdown
30454 (uri (cran-uri "pkgdown" version))
30457 "02lwr53xvxybcsg8md8qbq1wq833ap7ssn5v92cd4qqay5iya374"))))
30458 (properties `((upstream-name . "pkgdown")))
30459 (build-system r-build-system)
30460 (inputs (list pandoc))
30484 (home-page "https://pkgdown.r-lib.org")
30485 (synopsis "Make static HTML documentation for an R package")
30487 "The goal of this package is to generate an attractive and useful website
30488 from a source package. @code{pkgdown} converts your documentation, vignettes,
30489 README file, and more to HTML making it easy to share information about your
30491 (license license:expat)))
30493 (define-public r-prereg
30500 (uri (cran-uri "prereg" version))
30503 "039nrl5cirsx1ysh214dr6xnn1h6h3f90im6k9dgmzfksxdqigpw"))))
30504 (properties `((upstream-name . "prereg")))
30505 (build-system r-build-system)
30508 ;; The package provides a custom LaTex template in
30509 ;; inst/rmd/prereg_form.tex, which depends on these packages:
30513 texlive-generic-iftex
30514 texlive-latex-fancyhdr
30515 texlive-latex-fancyvrb
30516 texlive-latex-geometry
30517 texlive-latex-graphics
30518 texlive-latex-threeparttable
30519 texlive-latex-titlesec
30520 texlive-latex-upquote
30522 texlive-polyglossia
30526 (texlive-updmap.cfg (list texlive-amsfonts texlive-lm))))
30527 (home-page "https://github.com/crsh/prereg")
30529 "R Markdown Templates to preregister Scientific Studies")
30531 "This package provides a collection of templates to author
30532 preregistration documents for scientific studies in PDF format.")
30533 (license license:gpl3)))
30535 (define-public r-ez
30542 (uri (cran-uri "ez" version))
30545 "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq"))))
30546 (properties `((upstream-name . "ez")))
30547 (build-system r-build-system)
30559 (home-page "https://github.com/mike-lawrence/ez")
30560 (synopsis "Easy Analysis and Visualization of Factorial Experiments")
30562 "Facilitates easy analysis of factorial experiments, including purely
30563 within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss designs,
30564 and mixed within-and-between-Ss designs. The functions in this package aim to
30565 provide simple, intuitive and consistent specification of data analysis and
30566 visualization. Visualization functions also include design visualization for
30567 pre-analysis data auditing, and correlation matrix visualization. Finally,
30568 this package includes functions for non-parametric analysis, including
30569 permutation tests and bootstrap resampling. The bootstrap function obtains
30570 predictions either by cell means or by more advanced/powerful mixed effects
30571 models, yielding predictions and confidence intervals that may be easily
30572 visualized at any level of the experiment's design.")
30573 (license license:gpl2+)))
30575 (define-public r-qdapregex
30577 (name "r-qdapregex")
30582 (uri (cran-uri "qdapRegex" version))
30585 "1hdilycwrvi0q6cx7k8vg87bamm2xsafjkya5x4smxysm5k1r4qb"))))
30586 (properties `((upstream-name . "qdapRegex")))
30587 (build-system r-build-system)
30588 (propagated-inputs (list r-stringi))
30590 "https://trinker.github.com/qdapRegex/")
30592 "Regular Expression Removal, Extraction, and Replacement Tools")
30594 "This package provides a collection of regular expression tools
30595 associated with the @code{qdap} package that may be useful outside of the
30596 context of discourse analysis. Tools include removal/extraction/replacement of
30597 abbreviations, dates, dollar amounts, email addresses, hash tags, numbers,
30598 percentages, citations, person tags, phone numbers, times, and zip codes.")
30599 (license license:gpl2)))
30601 (define-public r-mgsub
30608 (uri (cran-uri "mgsub" version))
30611 "1mci6x65h94qiz9cwikx2inbrwkykv43zbs8abfbx416zrh2bbn9"))))
30612 (properties `((upstream-name . "mgsub")))
30613 (build-system r-build-system)
30614 (native-inputs (list r-knitr))
30616 "https://cran.r-project.org/package=mgsub")
30618 "Safe, Multiple, Simultaneous String Substitution")
30620 "Designed to enable simultaneous substitution in strings in a safe
30621 fashion. Safe means it does not rely on placeholders (which can cause errors
30622 in same length matches).")
30623 (license license:expat)))
30625 (define-public r-textshape
30627 (name "r-textshape")
30632 (uri (cran-uri "textshape" version))
30635 "0k9injxykgj2qprc7dygd7gafvcbh3r9x84qzaa1al21pk0dz7ds"))))
30636 (properties `((upstream-name . "textshape")))
30637 (build-system r-build-system)
30639 (list r-data-table r-slam r-stringi))
30640 (home-page "https://github.com/trinker/textshape")
30641 (synopsis "Tools for Reshaping Text")
30643 "Tools that can be used to reshape and restructure text data.")
30644 (license license:gpl2)))
30646 (define-public r-syuzhet
30653 (uri (cran-uri "syuzhet" version))
30656 "16iccqdbw02iw82nah6kwz3gwfghi864j2y698n4b9dyc386ijzv"))))
30657 (properties `((upstream-name . "syuzhet")))
30658 (build-system r-build-system)
30667 (native-inputs (list r-knitr))
30668 (home-page "https://github.com/mjockers/syuzhet")
30670 "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text")
30672 "Extracts sentiment and sentiment-derived plot arcs from text using a
30673 variety of sentiment dictionaries conveniently packaged for consumption by R
30674 users. Implemented dictionaries include @dfn{syuzhet} (default) developed in the
30675 Nebraska Literary Lab, @dfn{afinn} developed by Finn Arup Nielsen, @dfn{bing}
30676 developed by Minqing Hu and Bing Liu, and @dfn{nrc} developed by Mohammad, Saif
30677 M. and Turney, Peter D. Applicable references are available in
30678 @file{README.md} and in the documentation for the @code{get_sentiment}
30679 function. The package also provides a hack for implementing Stanford's coreNLP
30680 sentiment parser. The package provides several methods for plot arc
30682 (license license:gpl3)))
30684 (define-public r-lexicon
30691 (uri (cran-uri "lexicon" version))
30694 "0x7rscsh6par2lj11sby7bmz41cxn63iiw51lgh29z09cg8j606c"))))
30695 (properties `((upstream-name . "lexicon")))
30696 (build-system r-build-system)
30698 (list r-data-table r-syuzhet))
30699 (home-page "https://github.com/trinker/lexicon")
30700 (synopsis "Lexicons for Text Analysis")
30702 "This package provides a collection of lexical hash tables, dictionaries,
30704 (license license:gpl3)))
30706 (define-public r-english
30713 (uri (cran-uri "english" version))
30716 "1g3nmy5p8wj3ix1vp1qmkmy3dyqisrw0md8cjrx4klqkp0wqlms9"))))
30717 (properties `((upstream-name . "english")))
30718 (build-system r-build-system)
30719 (native-inputs (list r-knitr))
30721 "https://cran.r-project.org/package=english")
30722 (synopsis "Translate Integers into English")
30724 "Allow numbers to be presented in an English language version, one, two,
30725 three, ... Ordinals are also available, first, second, third, ... and
30726 indefinite article choice, \"a\" or \"an\".")
30727 (license license:gpl2)))
30729 (define-public r-textclean
30731 (name "r-textclean")
30736 (uri (cran-uri "textclean" version))
30739 "0kgjh6c4f14qkjc4fds7q7rpf4nkma3p0igm54fplmm3p853nvrz"))))
30740 (properties `((upstream-name . "textclean")))
30741 (build-system r-build-system)
30752 "https://github.com/trinker/textclean")
30753 (synopsis "Text Cleaning Tools")
30755 "Tools to clean and process text. Tools are geared at checking for
30756 substrings that are not optimal for analysis and replacing or removing them
30757 (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen,
30758 Kumar, Ostendorf, & Richards (2001) @url{doi:10.1006/csla.2001.0169}) or
30759 extracting them into new variables. For example, emoticons are often used in
30760 text but not always easily handled by analysis algorithms. The
30761 @code{replace_emoticon()} function replaces emoticons with word equivalents.")
30762 (license license:gpl2)))
30764 (define-public r-striprtf
30766 (name "r-striprtf")
30771 (uri (cran-uri "striprtf" version))
30774 "0dqcsh3fb8j0mmmxvxjl77rryhmrjm7a3scqvk2xkgxk4xq6q316"))))
30775 (properties `((upstream-name . "striprtf")))
30776 (build-system r-build-system)
30778 (list r-magrittr r-rcpp r-stringr))
30779 (home-page "https://github.com/kota7/striprtf")
30780 (synopsis "Extract Text from RTF File")
30782 "Extracts plain text from @dfn{Rich Text Format} (RTF) file.")
30783 (license license:expat)))
30785 (define-public r-ndjson
30792 (uri (cran-uri "ndjson" version))
30795 "0lvzbgfi1sg4kya1mvv67z14qk3vz9q57x22qh57xq8ampdkg812"))
30796 (modules '((guix build utils)))
30799 ;; unvendor gzstream
30800 (for-each delete-file '("src/gzstream.cpp" "src/gzstream.h"))
30802 (properties `((upstream-name . "ndjson")))
30803 (build-system r-build-system)
30806 (modify-phases %standard-phases
30807 (add-after 'unpack 'use-system-gzstream
30808 (lambda* (#:key inputs #:allow-other-keys)
30809 (substitute* "src/Makevars"
30810 (("PKG_LIBS = " all)
30811 (string-append all "-lgzstream ")))
30813 (inputs (list zlib gzstream))
30815 (list r-data-table r-rcpp r-tibble))
30816 (home-page "https://gitlab.com/hrbrmstr/ndjson")
30818 "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader")
30820 "@dfn{Streaming JSON} (ndjson) has one JSON record per-line and many
30821 modern ndjson files contain large numbers of records. These constructs may not
30822 be columnar in nature, but it is often useful to read in these files and
30823 \"flatten\" the structure out to enable working with the data in an R
30824 @code{data.frame}-like context. Functions are provided that make it possible
30825 to read in plain ndjson files or compressed (@code{gz}) ndjson files and either
30826 validate the format of the records or create \"flat\" @code{data.table}
30827 structures from them.")
30828 (license license:expat)))
30830 (define-public r-streamr
30837 (uri (cran-uri "streamR" version))
30840 "1clx3b0j2515r1nmnl6ki7qw5n54q3x2jvqv3zrc00kq71mlj7ix"))))
30841 (properties `((upstream-name . "streamR")))
30842 (build-system r-build-system)
30844 (list r-ndjson r-rcurl r-rjson))
30846 "https://cran.r-project.org/package=streamR")
30848 "Access to Twitter Streaming API via R")
30850 "This package provides functions to access Twitter's filter, sample, and
30851 user streams, and to parse the output into data frames.")
30852 (license license:gpl2)))
30854 (define-public r-readods
30861 (uri (cran-uri "readODS" version))
30864 "1hi217ab7hp15jsbzi5ak57cqf8jn2rv78bnn74q72gn9mrfra7n"))))
30865 (properties `((upstream-name . "readODS")))
30866 (build-system r-build-system)
30868 (list r-cellranger r-readr r-stringi r-xml2))
30869 (native-inputs (list r-knitr))
30871 "https://cran.r-project.org/package=readODS")
30872 (synopsis "Read and Write ODS Files")
30874 "Import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame.
30875 Also support writing data frame into ODS file.")
30876 (license license:gpl3)))
30878 (define-public r-qpdf
30885 (uri (cran-uri "qpdf" version))
30888 "1a1d7zad2l94z068mic6dg9wr9bq8mlmqszrj8vxps1441mb6gfh"))
30889 (modules '((guix build utils)))
30892 ;; unvendor libqpdf
30893 (delete-file-recursively "src/libqpdf")
30894 (delete-file-recursively "src/include/qpdf")))))
30895 (properties `((upstream-name . "qpdf")))
30896 (build-system r-build-system)
30899 (modify-phases %standard-phases
30900 (add-after 'unpack 'configure
30901 (lambda _ (setenv "EXTERNAL_QPDF" "1"))))))
30903 (list libjpeg-turbo qpdf zlib))
30905 (list r-askpass r-curl r-rcpp))
30906 (native-inputs (list pkg-config))
30907 (home-page "https://github.com/ropensci/qpdf")
30909 "Split, Combine and Compress PDF Files")
30911 "Content-preserving transformations transformations of PDF files such as
30912 split, combine, and compress. This package interfaces directly to the
30913 @code{qpdf} C++ API and does not require any command line utilities. Note that
30914 @code{qpdf} does not read actual content from PDF files: to extract text and
30915 data you need the @code{pdftools} package.")
30916 (license license:asl2.0)))
30918 (define-public r-pdftools
30920 (name "r-pdftools")
30925 (uri (cran-uri "pdftools" version))
30928 "1b9ppdndvlf8nl0i3xy1rx4f9j0j8ic6q9n0c4zn3rv6jdy8zqfi"))))
30929 (properties `((upstream-name . "pdftools")))
30930 (build-system r-build-system)
30931 (inputs (list zlib poppler))
30932 (propagated-inputs (list r-qpdf r-rcpp))
30933 (native-inputs (list pkg-config))
30934 (home-page "https://docs.ropensci.org/pdftools/")
30935 (synopsis "Text Extraction, Rendering and Converting of PDF Documents")
30937 "This package provides utilities based on @code{libpoppler} for
30938 extracting text, fonts, attachments and metadata from a PDF file. It also
30939 supports high quality rendering of PDF documents into PNG, JPEG, TIFF format,
30940 or into raw bitmap vectors for further processing in R.")
30941 (license license:expat)))
30943 (define-public r-antiword
30945 (name "r-antiword")
30950 (uri (cran-uri "antiword" version))
30953 "123v8zlczwh6fr1v3x7dl3885xlmddq1bqlcxih8zh07w0hlk1k2"))
30954 (modules '((guix build utils)))
30957 ;; unvendor libantiword
30958 (delete-file-recursively "src")
30960 (properties `((upstream-name . "antiword")))
30961 (build-system r-build-system)
30964 (modify-phases %standard-phases
30965 (add-after 'unpack 'use-system-antiword
30966 (lambda* (#:key inputs #:allow-other-keys)
30967 (substitute* "R/antiword.R"
30968 (("system.file\\(\"bin\", package = \"antiword\"\\)")
30969 (string-append "\"" (assoc-ref inputs "antiword") "/bin\"")))
30971 (inputs (list antiword))
30972 (propagated-inputs (list r-sys))
30974 "https://github.com/ropensci/antiword#readme")
30976 "Extract Text from Microsoft Word Documents")
30978 "Wraps the @code{AntiWord} utility to extract text from Microsoft Word
30979 documents. The utility only supports the old @code{doc} format, not the new
30980 xml based @code{docx} format. Use the @code{xml2} package to read the
30982 (license license:gpl2)))
30984 (define-public r-readtext
30986 (name "r-readtext")
30991 (uri (cran-uri "readtext" version))
30994 "0k782h5hns5v5h8a6qyfqck2hc15nq0awg8bsp196q4zviv5jw3c"))))
30995 (properties `((upstream-name . "readtext")))
30996 (build-system r-build-system)
31011 (native-inputs (list r-knitr))
31013 "https://github.com/quanteda/readtext")
31015 "Import and Handling for Plain and Formatted Text Files")
31017 "This package provides functions for importing and handling text files
31018 and formatted text files with additional meta-data, such including @code{.csv},
31019 @code{.tab}, @code{.json}, @code{.xml}, @code{.html}, @code{.pdf}, @code{.doc},
31020 @code{.docx}, @code{.rtf}, @code{.xls}, @code{.xlsx}, and others.")
31021 (license license:gpl3)))
31023 (define-public r-packcircles
31025 (name "r-packcircles")
31030 (uri (cran-uri "packcircles" version))
31033 "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk"))))
31034 (properties `((upstream-name . "packcircles")))
31035 (build-system r-build-system)
31036 (propagated-inputs (list r-rcpp))
31037 (native-inputs (list r-knitr))
31039 "https://github.com/mbedward/packcircles")
31040 (synopsis "Circle Packing")
31042 "Algorithms to find arrangements of non-overlapping circles.")
31043 (license license:expat)))
31045 ;; Cannot unbundle liblwgeom, because PostGIS does not support building it on
31047 (define-public r-lwgeom
31054 (uri (cran-uri "lwgeom" version))
31057 "0d4b1djwrzla91mmyya2m1250mb44fzmq3d36w5mk81d4bg952pl"))))
31058 (properties `((upstream-name . "lwgeom")))
31059 (build-system r-build-system)
31061 (list geos proj sqlite zlib))
31063 (list r-rcpp r-sf r-units))
31064 (native-inputs (list pkg-config))
31065 (home-page "https://github.com/r-spatial/lwgeom/")
31066 (synopsis "Bindings to Selected 'liblwgeom' Functions for Simple Features")
31068 "Access to selected functions found in
31069 @url{https://github.com/postgis/postgis/tree/master/liblwgeom,liblwgeom}, the
31070 light-weight geometry library used by @url{http://postgis.net/,PostGIS}.")
31071 (license license:gpl2)))
31073 (define-public r-stars
31080 (uri (cran-uri "stars" version))
31083 "0hcbzr8c7wk30qjwrvx6bflzwkjpms79pavaxawnq1h8kry5fngk"))))
31084 (properties `((upstream-name . "stars")))
31085 (build-system r-build-system)
31093 (native-inputs (list r-knitr))
31094 (home-page "https://r-spatial.github.io/stars/")
31096 "Spatiotemporal Arrays, Raster and Vector Data Cubes")
31098 "Reading, manipulating, writing and plotting spatiotemporal arrays
31099 (raster and vector data cubes) in @code{R}, using @code{GDAL} bindings provided
31100 by @code{sf}, and @code{NetCDF} bindings by @code{ncmeta} and @code{RNetCDF}.")
31101 (license license:asl2.0)))
31103 (define-public r-tmaptools
31105 (name "r-tmaptools")
31110 (uri (cran-uri "tmaptools" version))
31113 "0bal3czrdr93qig8s5cf5szld5vjbbks67rismfhlkmlgw6wp2gx"))))
31114 (properties `((upstream-name . "tmaptools")))
31115 (build-system r-build-system)
31127 "https://github.com/mtennekes/tmaptools")
31128 (synopsis "Thematic Map Tools")
31130 "Set of tools for reading and processing spatial data. The aim is to
31131 supply the workflow to create thematic maps. This package also facilitates
31132 @code{tmap}, the package for visualizing thematic maps.")
31133 (license license:gpl3)))
31135 (define-public r-rworldmap
31137 (name "r-rworldmap")
31142 (uri (cran-uri "rworldmap" version))
31145 "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk"))))
31146 (properties `((upstream-name . "rworldmap")))
31147 (build-system r-build-system)
31149 (list r-fields r-maptools r-sp))
31151 "https://github.com/AndySouth/rworldmap/")
31152 (synopsis "Mapping Global Data")
31154 "Enables mapping of country level and gridded user datasets.")
31155 (license license:gpl2+)))
31157 (define-public r-rtweet
31164 (uri (cran-uri "rtweet" version))
31167 "05pbvxm2vmf6935b9s6663k3aifnkr3m52wh2jvnplmrwyrfpn9n"))))
31168 (properties `((upstream-name . "rtweet")))
31169 (build-system r-build-system)
31178 (native-inputs (list r-knitr))
31180 "https://docs.ropensci.org/rtweet/")
31181 (synopsis "Collecting Twitter Data")
31183 "An implementation of calls designed to collect and organize Twitter data
31184 via @url{https://developer.twitter.com/en/docs,Twitter's REST and stream
31185 Application Program Interfaces (API)}.")
31186 (license license:expat)))
31188 (define-public r-intervals
31190 (name "r-intervals")
31195 (uri (cran-uri "intervals" version))
31198 "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb"))))
31199 (properties `((upstream-name . "intervals")))
31200 (build-system r-build-system)
31201 (home-page "https://github.com/edzer/intervals")
31203 "Tools for Working with Points and Intervals")
31205 "Tools for working with and comparing sets of points and intervals.")
31206 (license license:artistic2.0)))
31208 (define-public r-eyelinker
31210 (name "r-eyelinker")
31215 (uri (cran-uri "eyelinker" version))
31218 "0wijd45p6j2qal6wnj7zywks8p9v3m9cmyp7axmk44mrjdjx2i71"))))
31219 (properties `((upstream-name . "eyelinker")))
31220 (build-system r-build-system)
31222 (list r-intervals r-readr r-stringi r-stringr r-tibble))
31223 (native-inputs (list r-knitr))
31225 "https://github.com/a-hurst/eyelinker")
31227 "Import ASC Files from EyeLink Eye Trackers")
31229 "Imports plain-text ASC data files from EyeLink eye trackers into
31230 (relatively) tidy data frames for analysis and visualization.")
31231 (license license:gpl3)))
31233 (define-public r-btm
31240 (uri (cran-uri "BTM" version))
31243 "0ab0wr8nbwn1w1j9hpwfz52lm1sw0qk93713y9k0hpm3pw9dq4jr"))))
31244 (properties `((upstream-name . "BTM")))
31245 (build-system r-build-system)
31246 (propagated-inputs (list r-rcpp))
31247 (home-page "https://github.com/bnosac/BTM")
31248 (synopsis "Biterm Topic Models for Short Text")
31250 "Biterm Topic Models find topics in collections of short texts. It is a
31251 word co-occurrence based topic model that learns topics by modeling word-word
31252 co-occurrences patterns which are called biterms. This in contrast to
31253 traditional topic models like Latent Dirichlet Allocation and Probabilistic
31254 Latent Semantic Analysis which are word-document co-occurrence topic models. A
31255 biterm consists of two words co-occurring in the same short text window. This
31256 context window can for example be a twitter message, a short answer on a
31257 survey, a sentence of a text or a document identifier. The techniques are
31258 explained in detail in the paper 'A Biterm Topic Model For Short Text' by
31259 Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013)
31260 @url{https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/\
31262 (license license:asl2.0)))
31264 (define-public r-delaporte
31266 (name "r-delaporte")
31271 (uri (cran-uri "Delaporte" version))
31274 "10xsmms2jfw7x4hmgpd35dv4n4azpjzmfid6585kg6qfh2zg23g5"))))
31275 (properties `((upstream-name . "Delaporte")))
31276 (build-system r-build-system)
31277 (native-inputs (list gfortran))
31278 (home-page "https://github.com/aadler/Delaporte")
31279 (synopsis "Statistical functions for the Delaporte distribution")
31281 "This package provides probability mass, distribution, quantile,
31282 random-variate generation, and method-of-moments parameter-estimation
31283 functions for the Delaporte distribution with parameterization based on
31284 Vose (2008). The Delaporte is a discrete probability distribution which can
31285 be considered the convolution of a negative binomial distribution with a
31286 Poisson distribution. Alternatively, it can be considered a counting
31287 distribution with both Poisson and negative binomial components. It has been
31288 studied in actuarial science as a frequency distribution which has more
31289 variability than the Poisson, but less than the negative binomial.")
31290 (license license:bsd-2)))
31292 (define-public r-rjsonio
31295 (version "1.3-1.6")
31299 (uri (cran-uri "RJSONIO" version))
31302 "17x0ayk7daprbc8w2hvb2jl9mfnw4dic9yc3sr5adcjqfzmcklc2"))))
31303 (properties `((upstream-name . "RJSONIO")))
31304 (build-system r-build-system)
31305 (home-page "https://cran.r-project.org/package=RJSONIO")
31306 (synopsis "Serialize R objects to JSON")
31308 "This is a package that allows conversion to and from data in JavaScript
31309 Object Notation (JSON) format. This allows R objects to be inserted into
31310 Javascript/ECMAScript/ActionScript code and allows R programmers to read and
31311 convert JSON content to R objects. This is an alternative to the @code{rjson}
31313 (license license:bsd-3)))
31315 (define-public r-revgeo
31322 (uri (cran-uri "revgeo" version))
31325 "1ns7d1817475lriss6wwgvdm6lj760p40yxqaifla13c2xb73a55"))))
31326 (properties `((upstream-name . "revgeo")))
31327 (build-system r-build-system)
31329 (list r-rcurl r-rjsonio))
31330 (home-page "https://cran.r-project.org/package=revgeo")
31331 (synopsis "Reverse geocoding")
31333 "The @code{revgeo} procedure allows you to use the Photon geocoder for
31334 OpenStreetMap, Google Maps, and Bing to reverse geocode coordinate pairs with
31336 (license license:gpl3+)))
31338 (define-public r-qpcr
31345 (uri (cran-uri "qpcR" version))
31348 "1r01q7jv3w59yx1gc0qw91rq7rvdhqsi8y57sqqkmwyqfw2x2vsv"))))
31349 (properties `((upstream-name . "qpcR")))
31350 (build-system r-build-system)
31352 (list r-mass r-matrix r-minpack-lm r-rgl r-robustbase))
31353 (home-page "https://cran.r-project.org/package=qpcR")
31354 (synopsis "Modelling and analysis of real-time PCR data")
31356 "This is a package for model fitting, optimal model selection and
31357 calculation of various features that are essential in the analysis of
31358 quantitative real-time polymerase chain reaction (qPCR).")
31359 (license license:gpl2+)))
31361 (define-public r-textplot
31363 (name "r-textplot")
31368 (uri (cran-uri "textplot" version))
31371 "10nxh9axhy6kyp6f3rz7smq08yl35ydx9jx47bs7i0bmcl2kwxvl"))))
31372 (properties `((upstream-name . "textplot")))
31373 (build-system r-build-system)
31375 (list r-data-table r-lattice r-matrix))
31376 (native-inputs (list r-knitr))
31377 (home-page "https://github.com/bnosac/textplot")
31378 (synopsis "Text Plots")
31380 "Visualise complex relations in texts. This is done by providing
31381 functionalities for displaying text co-occurrence networks, text correlation
31382 networks, dependency relationships as well as text clustering. Feel free to
31383 join the effort of providing interesting text visualisations.")
31384 (license license:gpl2)))
31386 (define-public r-gsa
31393 (uri (cran-uri "GSA" version))
31396 "1f1mrxxdbdlnibgav6nsvbpniz2x3km2svc0hf43spb4zicn0z8p"))))
31397 (properties `((upstream-name . "GSA")))
31398 (build-system r-build-system)
31399 (home-page "https://statweb.stanford.edu/~tibs/GSA/")
31400 (synopsis "Gene set analysis")
31401 (description "This package lets you determine the significance of
31402 pre-defined sets of genes with respect to an outcome variable, such as a group
31403 indicator, a quantitative variable or a survival time.")
31404 ;; Any version of the LGPL
31405 (license license:lgpl3+)))
31407 (define-public r-gsalib
31414 (uri (cran-uri "gsalib" version))
31417 "1k3zjdydzb0dfh1ihih08d4cw6rdamgb97cdqna9mf0qdjc3pcp1"))))
31418 (build-system r-build-system)
31419 (home-page "https://cran.r-project.org/web/packages/gsalib")
31420 (synopsis "Utility functions for GATK")
31421 (description "This package contains utility functions used by the Genome
31422 Analysis Toolkit (GATK) to load tables and plot data. The GATK is a toolkit
31423 for variant discovery in high-throughput sequencing data.")
31424 (license license:expat)))
31426 (define-public r-randomforestsrc
31428 (name "r-randomforestsrc")
31433 (uri (cran-uri "randomForestSRC" version))
31436 "05ifvj49jv0n5p6k46milpgj9r10sc5aw23fypyyibdgwpwvwixw"))))
31438 `((upstream-name . "randomForestSRC")))
31439 (build-system r-build-system)
31440 (home-page "https://cran.r-project.org/web/packages/randomForestSRC/")
31441 (synopsis "Random forests for survival, regression, and classification")
31443 "This package implements fast OpenMP parallel computing of Breiman's
31444 random forests for survival, competing risks, regression and classification
31445 based on Ishwaran and Kogalur's popular random survival forests (RSF) package.
31446 It handles missing data and now includes multivariate, unsupervised forests,
31447 quantile regression and solutions for class imbalanced data. It provides a
31448 fast interface using subsampling and confidence regions for variable
31450 (license license:gpl3+)))
31452 (define-public r-contfrac
31454 (name "r-contfrac")
31459 (uri (cran-uri "contfrac" version))
31462 "0sq5c7ny235yrkv2xc4insgxby6rvzc1qsj8h301cd2if3lwbgwm"))))
31463 (properties `((upstream-name . "contfrac")))
31464 (build-system r-build-system)
31466 "https://github.com/RobinHankin/contfrac")
31467 (synopsis "Continued Fractions")
31469 "Various utilities for evaluating continued fractions.")
31470 (license license:gpl2)))
31472 (define-public r-elliptic
31474 (name "r-elliptic")
31479 (uri (cran-uri "elliptic" version))
31482 "1dhba0yfxjd5rlqsxp5a7s2hclfkla9wigsr39dlma67l6qjjmxn"))))
31483 (properties `((upstream-name . "elliptic")))
31484 (build-system r-build-system)
31485 (inputs (list pari-gp))
31486 (propagated-inputs (list r-mass))
31488 "https://github.com/RobinHankin/elliptic")
31490 "Weierstrass and Jacobi Elliptic Functions")
31492 "A suite of elliptic and related functions including Weierstrass and
31493 Jacobi forms. Also includes various tools for manipulating and visualizing
31494 complex functions.")
31495 (license license:gpl2)))
31497 (define-public r-hypergeo
31499 (name "r-hypergeo")
31504 (uri (cran-uri "hypergeo" version))
31507 "13jdiy216znwhr91iqnh03mvkmyscw439syb3h4i67dd78sphnvd"))))
31508 (properties `((upstream-name . "hypergeo")))
31509 (build-system r-build-system)
31511 (list r-contfrac r-desolve r-elliptic))
31513 "https://cran.r-project.org/web/packages/hypergeo/")
31514 (synopsis "The Gauss Hypergeometric Function")
31516 "The Gaussian hypergeometric function for complex numbers.")
31517 (license license:gpl2)))
31519 (define-public r-gganimate
31521 (name "r-gganimate")
31526 (uri (cran-uri "gganimate" version))
31529 "046v6j92xxgaghsnh88dy5h8x040qsfa8csvhp4dmsfmrrf0dz0f"))))
31530 (properties `((upstream-name . "gganimate")))
31531 (build-system r-build-system)
31534 (modify-phases %standard-phases
31535 (add-after 'unpack 'absolute-paths
31536 (lambda* (#:key inputs #:allow-other-keys)
31537 (substitute* "R/renderers.R"
31539 (string-append "'" (assoc-ref inputs "ffmpeg") "/bin/ffmpeg'"))))))))
31541 ;; For video output.
31552 ;; For GIF/SVG output. gifski is faster, but depends on Rust.
31554 ;; For HTML output.
31557 (native-inputs (list r-knitr))
31558 (home-page "https://gganimate.com")
31559 (synopsis "Grammar of Animated Graphics")
31561 "This package extends the grammar of graphics as implemented by
31562 @code{ggplot2} to include the description of animation. It does this by
31563 providing a range of new grammar classes that can be added to the plot object
31564 in order to customise how it should change with time.")
31565 (license license:expat)))
31567 ;; This library bundles ‘date’ from (gnu packages calendar). We cannot unbundle
31568 ;; it, because its C++ libtz.so is built with different compiler flags than
31570 (define-public r-tzdb
31577 (uri (cran-uri "tzdb" version))
31580 "0f3h4zaf9f4l371k6nc1mq6z2f9aj1vaf2inni8jnsds3zng16b0"))))
31581 (properties `((upstream-name . "tzdb")))
31582 (build-system r-build-system)
31583 (propagated-inputs (list r-cpp11))
31584 (home-page "https://github.com/r-lib/tzdb")
31585 (synopsis "Time Zone Database Information")
31587 "This package provides an up-to-date copy of the Internet Assigned
31588 Numbers Authority (IANA) Time Zone Database. It is updated periodically to
31589 reflect changes made by political bodies to time zone boundaries, UTC offsets,
31590 and daylight saving time rules. Additionally, this package provides a C++
31591 interface for working with the @code{date} library. @code{date} provides
31592 comprehensive support for working with dates and date-times, which this package
31593 exposes to make it easier for other R packages to utilize. Headers are
31594 provided for calendar specific calculations, along with a limited interface for
31595 time zone manipulations.")
31596 (license license:expat)))
31598 (define-public r-vroom
31605 (uri (cran-uri "vroom" version))
31608 "1plz20x6s01gkkcac51lhx4r2s024pgh778ri7y25hkiiwacp1yh"))))
31609 (properties `((upstream-name . "vroom")))
31610 (build-system r-build-system)
31626 (native-inputs (list r-knitr))
31627 (home-page "https://vroom.r-lib.org")
31629 "Read and Write Rectangular Text Data")
31631 "This package reads and writes data files like @acronym{CSV},
31632 @acronym{TSV} and @acronym{FWF}. When reading it uses a quick initial indexing
31633 step, then reads the values lazily, so only the data you actually use needs to
31634 be read. The writer formats the data in parallel and writes to disk
31635 asynchronously from formatting.")
31636 (license license:expat)))
31638 (define-public r-rmisc
31644 (uri (cran-uri "Rmisc" version))
31647 "1h6jb0xwkyhm9lwm7nj9bhrb5dhrsifvkpqkrd594j1lz74dar8x"))))
31648 (build-system r-build-system)
31650 (list r-plyr r-lattice))
31651 (home-page "https://cran.r-project.org/web/packages/Rmisc/")
31652 (synopsis "Ryan Miscellaneous")
31653 (description "The Rmisc library contains functions for data analysis and
31654 utility operations.")
31655 (license license:gpl3)))
31657 (define-public r-rsq
31663 (uri (cran-uri "rsq" version))
31666 "1r628srxhhf7b51lnj4qrzgbqajkm0ls47a9rzjkvmfq4ax5i73f"))))
31667 (properties `((upstream-name . "rsq")))
31668 (build-system r-build-system)
31675 (home-page "https://cran.r-project.org/package=rsq")
31676 (synopsis "R-squared and related measures")
31678 "Calculate generalized R-squared, partial R-squared, and partial correlation
31679 coefficients for generalized linear (mixed) models (including quasi models
31680 with well defined variance functions).")
31681 (license license:gpl2)))
31683 (define-public r-webutils
31685 (name "r-webutils")
31690 (uri (cran-uri "webutils" version))
31692 (base32 "16a6ds0fnb6y8i1r9ba1hf1ydb53am57s070b3hi5jmrs84b9qik"))))
31693 (properties `((upstream-name . "webutils")))
31694 (build-system r-build-system)
31696 (list r-curl r-jsonlite))
31697 (home-page "https://github.com/jeroen/webutils")
31698 (synopsis "Utility functions for developing web applications")
31700 "This package parses HTTP request data in @code{application/json},
31701 @code{multipart/form-data}, or @code{application/x-www-form-urlencoded}
31702 format. It includes an example of hosting and parsing HTML form data in R
31703 using either @code{httpuv} or @code{Rhttpd}.")
31704 (license license:expat)))
31706 (define-public r-protolite
31708 (name "r-protolite")
31713 (uri (cran-uri "protolite" version))
31715 (base32 "0g1r3lzmvx1w44qzqzdvxfn21zmz11srlp6cr76kd7pd5wzjv82p"))))
31716 (properties `((upstream-name . "protolite")))
31717 (build-system r-build-system)
31721 (list r-jsonlite r-rcpp))
31723 (list protobuf pkg-config))
31724 (home-page "https://github.com/jeroen/protolite")
31725 (synopsis "Highly optimized protocol buffer serializers")
31727 "This package provides pure C++ implementations for reading and writing
31728 several common data formats based on Google protocol-buffers. It currently
31729 supports @code{rexp.proto} for serialized R objects, @code{geobuf.proto} for
31730 binary geojson, and @code{mvt.proto} for vector tiles. This package uses the
31731 auto-generated C++ code by protobuf-compiler, hence the entire serialization
31732 is optimized at compile time. The @code{RProtoBuf} package on the other hand
31733 uses the protobuf runtime library to provide a general-purpose toolkit for
31734 reading and writing arbitrary protocol-buffer data in R.")
31735 (license license:expat)))
31737 (define-public r-opencpu
31744 (uri (cran-uri "opencpu" version))
31746 (base32 "1h0s7fbifyf4h1296sdk3amij0m6s12wq32mbky7xg4nz8wj29ni"))))
31747 (properties `((upstream-name . "opencpu")))
31748 (build-system r-build-system)
31768 (home-page "https://www.opencpu.org")
31769 (synopsis "API for embedded scientific computing")
31771 "This package provides a system for embedded scientific computing and
31772 reproducible research with R. The OpenCPU server exposes a simple but
31773 powerful HTTP API for RPC and data interchange with R. This provides a
31774 reliable and scalable foundation for statistical services or building R web
31775 applications. The OpenCPU server runs either as a single-user development
31776 server within the interactive R session, or as a multi-user stack based on
31778 (license license:asl2.0)))
31780 (define-public r-exactextractr
31782 (name "r-exactextractr")
31787 (uri (cran-uri "exactextractr" version))
31790 "0x4axrq9iznvajqy07gcfcrvzniz5yj6wabchgksg0fqz0xancnc"))))
31791 (properties `((upstream-name . "exactextractr")))
31792 (build-system r-build-system)
31793 (inputs (list geos))
31795 (list r-raster r-rcpp r-sf))
31798 (home-page "https://isciences.gitlab.io/exactextractr/")
31799 (synopsis "Fast extraction from raster datasets using polygons")
31801 "This package provides a replacement for the @code{extract} function from
31802 the @code{raster} package that is suitable for extracting raster values using
31803 @code{sf} polygons.")
31804 (license license:asl2.0)))
31806 (define-public r-stringfish
31808 (name "r-stringfish")
31813 (uri (cran-uri "stringfish" version))
31816 "0ddpsi7z0kzqgbq9y646pk9afclq0r7ak22zsdh0i93ni0x71c9l"))))
31817 (properties `((upstream-name . "stringfish")))
31818 (build-system r-build-system)
31820 (list r-rcpp r-rcppparallel))
31822 (list pkg-config r-knitr))
31823 (home-page "https://github.com/traversc/stringfish")
31824 (synopsis "Alternative string implementation")
31826 "This package provides an extendable, performant and multithreaded
31827 @code{alt-string} implementation backed by C++ vectors and strings.")
31828 (license license:gpl3)))
31830 (define-public r-rapiserialize
31832 (name "r-rapiserialize")
31837 (uri (cran-uri "RApiSerialize" version))
31840 "0gm2j8kh40imhncwwx1sx9kmraaxcxycvgwls53lcyy2ap344k9j"))))
31841 (properties `((upstream-name . "RApiSerialize")))
31842 (build-system r-build-system)
31844 "https://cran.r-project.org/package=RApiSerialize")
31845 (synopsis "R API serialization")
31847 "This package provides other packages with access to the internal R
31848 serialization code. Access to this code is provided at the C function level
31849 by using the registration of native function mechanism. Client packages
31850 simply include a single header file RApiSerializeAPI.h provided by this
31852 (license license:gpl2+)))
31854 (define-public r-qs
31861 (uri (cran-uri "qs" version))
31864 "0sxy497v5arjv6lwxng7chkbzrn703waqmgsxv77i7y12ahzdbai"))))
31865 (properties `((upstream-name . "qs")))
31866 (build-system r-build-system)
31867 (inputs (list zlib))
31869 (list r-rapiserialize r-rcpp r-stringfish))
31871 (list pkg-config r-knitr))
31872 (home-page "https://github.com/traversc/qs")
31873 (synopsis "Quick serialization of R objects")
31875 "This package provides functions for quickly writing and reading any R
31876 object to and from disk.")
31877 (license license:gpl3)))
31879 (define-public r-rgeos
31886 (uri (cran-uri "rgeos" version))
31889 "1m73y0nwrdwsjrl48c4fg1kdqnh79835brnmxv9ak01ndbzcp45b"))))
31890 (properties `((upstream-name . "rgeos")))
31891 (build-system r-build-system)
31896 (home-page "https://cran.r-project.org/package=rgeos")
31897 (synopsis "Interface to Geometry Engine (GEOS)")
31899 "This package provides an R interface to Geometry Engine (GEOS) using the
31900 C API for topology operations on geometries.")
31901 (license license:gpl2+)))
31903 (define-public r-tfruns
31910 (uri (cran-uri "tfruns" version))
31913 "04lfckg1if3kfwcl4s4fcc9aw04crwk4m1qr55ag22j2x2jlb2l9"))))
31914 (properties `((upstream-name . "tfruns")))
31915 (build-system r-build-system)
31927 (native-inputs (list r-knitr))
31928 (home-page "https://github.com/rstudio/tfruns")
31929 (synopsis "Training run tools for TensorFlow")
31931 "Create and manage unique directories for each TensorFlow training run.
31932 This package provides a unique, time stamped directory for each run along with
31933 functions to retrieve the directory of the latest run or latest several
31935 (license license:asl2.0)))
31937 (define-public r-tfautograph
31939 (name "r-tfautograph")
31944 (uri (cran-uri "tfautograph" version))
31947 "0fmaq1ggjyxgf2ss7qb8jk74sfwc3s1vc123pd5glclxcy1ib0j2"))))
31948 (properties `((upstream-name . "tfautograph")))
31949 (build-system r-build-system)
31950 (inputs (list tensorflow))
31952 (list r-backports r-reticulate))
31953 (home-page "https://t-kalinowski.github.io/tfautograph/")
31954 (synopsis "Autograph R for Tensorflow")
31956 "This package lets you translate R control flow expressions into
31957 Tensorflow graphs.")
31958 (license license:gpl3)))
31960 (define-public r-tensorflow
31962 (name "r-tensorflow")
31967 (uri (cran-uri "tensorflow" version))
31970 "12c6ndxx4g6fqjakpzp9pgl29ghswhqyr6q9jahpk0cawizh2znj"))))
31971 (properties `((upstream-name . "tensorflow")))
31972 (build-system r-build-system)
31973 (inputs (list tensorflow))
31982 (home-page "https://github.com/rstudio/tensorflow")
31983 (synopsis "R interface to TensorFlow")
31985 "R interface to TensorFlow a library for numerical computation using data
31986 flow graphs. Nodes in the graph represent mathematical operations, while the
31987 graph edges represent the multidimensional data arrays (tensors) communicated
31989 (license license:asl2.0)))
31991 (define-public r-keras
31998 (uri (cran-uri "keras" version))
32001 "06513d1fp7cxk4v03xm9lhgj6xmp9dqqvw3lnzwbzjwdkfj948yc"))))
32002 (properties `((upstream-name . "keras")))
32003 (build-system r-build-system)
32015 (native-inputs (list r-knitr))
32016 (home-page "https://keras.rstudio.com")
32017 (synopsis "R Interface to 'Keras'")
32019 "This package provides an interface to Keras, a high-level neural
32020 networks API. Keras was developed with a focus on enabling fast
32021 experimentation, supports both convolution based networks and recurrent
32022 networks (as well as combinations of the two), and runs seamlessly on both CPU
32024 (license license:expat)))
32026 (define-public r-zzlite
32033 (uri (cran-uri "zzlite" version))
32036 "0vi1slx2s4r5zf82lazqv0c3m12xq73wlgsbz6af4y00h0bkr3ps"))))
32037 (properties `((upstream-name . "zzlite")))
32038 (build-system r-build-system)
32040 (list r-httr r-jsonlite))
32043 (home-page "https://cran.r-project.org/package=zzlite")
32044 (synopsis "Wrapper for the Zamzar file conversion API")
32046 "This package provides a minor collection of HTTP wrappers for the Zamzar
32047 file conversion API. The wrappers makes it easy to utilize the API and thus
32048 convert between more than 100 different file formats (ranging from audio
32049 files, images, movie formats, etc., etc.) through an R session.")
32050 (license license:gpl3)))
32052 (define-public r-ztree
32059 (uri (cran-uri "zTree" version))
32062 "005zk6wpchpss6865ki35yawgf668pn70163ah97rnfkhfaswm6y"))))
32063 (properties `((upstream-name . "zTree")))
32064 (build-system r-build-system)
32067 (home-page "https://cran.r-project.org/package=zTree")
32068 (synopsis "Functions to import data from z-Tree into R")
32070 "This package provides tools for reading @code{.xls} and @code{.sbj}
32071 files which are written by the proprietary program z-Tree for developing and
32072 carrying out economic experiments.")
32073 (license license:gpl3)))
32075 (define-public r-distributionutils
32077 (name "r-distributionutils")
32082 (uri (cran-uri "DistributionUtils" version))
32085 "08vq54pyqxlqsj6q6gsg5ikqa0z3x842j52ld5dxaq272p6xchvl"))))
32087 `((upstream-name . "DistributionUtils")))
32088 (build-system r-build-system)
32091 (home-page "https://cran.r-project.org/package=DistributionUtils")
32092 (synopsis "Distribution utilities")
32094 "This package provides utilities for dealing with distributions.
32095 Functionality includes sample skewness and kurtosis, log-histogram, tail
32096 plots, moments by integration, changing the point about which a moment is
32097 calculated, functions for testing distributions using inversion tests and the
32098 Massart inequality. Also included is an implementation of the incomplete
32099 Bessel K function.")
32100 (license license:gpl2+)))
32102 (define-public r-ztpln
32109 (uri (cran-uri "ztpln" version))
32112 "1b22m72a8117yrgq5k1gzsrbx6yrsrj7bpd49lh7x3vbaz56c0wr"))))
32113 (properties `((upstream-name . "ztpln")))
32114 (build-system r-build-system)
32116 (list r-distributionutils r-mixtools r-rcpp r-rcppeigen
32120 (home-page "https://github.com/mattocci27/ztpln")
32121 (synopsis "Zero-truncated Poisson lognormal distribution")
32123 "This package provides functions for obtaining the density, random
32124 variates and maximum likelihood estimates of the Zero-truncated Poisson
32125 lognormal distribution and their mixture distribution.")
32126 (license license:expat)))
32128 (define-public r-zscorer
32135 (uri (cran-uri "zscorer" version))
32138 "0aijhs0fyird5gq68x4dxchb02mxa7ijk10k9zjhngghxbjj7iqn"))))
32139 (properties `((upstream-name . "zscorer")))
32140 (build-system r-build-system)
32145 (home-page "https://github.com/nutriverse/zscorer")
32146 (synopsis "Child Anthropometry z-Score Calculator")
32148 "This package provides a tool for calculating z-scores and centiles for
32149 weight-for-age, length/height-for-age, weight-for-length/height, BMI-for-age,
32150 head circumference-for-age, age circumference-for-age, subscapular
32151 skinfold-for-age, triceps skinfold-for-age based on the WHO Child Growth
32153 (license license:agpl3+)))
32155 (define-public r-zra
32162 (uri (cran-uri "ZRA" version))
32165 "1sx1q5yf68hhlb5j1hicpj594rmgajqr25llg7ax416j0m2rnagi"))))
32166 (properties `((upstream-name . "ZRA")))
32167 (build-system r-build-system)
32169 (list r-dygraphs r-forecast))
32170 (home-page "https://cran.r-project.org/package=ZRA")
32171 (synopsis "Dynamic plots for time series forecasting")
32173 "This package combines a forecast of a time series, using the function @code{forecast},
32174 with the dynamic plots from @code{dygraphs}.")
32175 (license license:gpl2+)))
32177 (define-public r-rfigshare
32179 (name "r-rfigshare")
32184 (uri (cran-uri "rfigshare" version))
32187 "10shwl1y9220m7ld5w9fjsjzy5yg8myrz9cz97ps9z2bw7bvka5j"))))
32188 (properties `((upstream-name . "rfigshare")))
32189 (build-system r-build-system)
32199 (home-page "https://github.com/ropensci/rfigshare")
32200 (synopsis "R Interface to figshare")
32202 "This package provides an interface to figshare, a scientific repository
32203 to archive and assign DOIs to data, software, figures, and more.")
32204 (license license:cc0)))
32206 (define-public r-dismo
32213 (uri (cran-uri "dismo" version))
32216 "1rqf6h4imbqvs7hjd1k4my6154wg0qnmnp5byan403rcshr1jbl1"))))
32217 (properties `((upstream-name . "dismo")))
32218 (build-system r-build-system)
32220 (list r-raster r-rcpp r-sp r-terra))
32221 (home-page "https://rspatial.org/raster/sdm/")
32222 (synopsis "Species distribution modeling")
32224 "This package provides methods for species distribution modeling, i.e.,
32225 predicting the environmental similarity of any site to that of the locations
32226 of known occurrences of a species.")
32227 (license license:gpl3+)))
32229 (define-public r-zoon
32236 (uri (cran-uri "zoon" version))
32239 "02y29vr2yn8al69km8faiqrwjrc1r3hsvw3dg8lwjr65cxw1krip"))))
32240 (properties `((upstream-name . "zoon")))
32241 (build-system r-build-system)
32256 (home-page "https://github.com/zoonproject/zoon")
32257 (synopsis "Reproducible, accessible and shareable species distribution modelling")
32259 "This package reads user submitted modules from an online repository,
32260 runs full species distribution modelling workflows and returns output that is
32261 fully reproducible.")
32262 (license license:bsd-3)))
32264 (define-public r-paws-common
32266 (name "r-paws-common")
32271 (uri (cran-uri "paws.common" version))
32274 "1dg18hwnrjd6m1vjcxfs2vm1zxciivf4vzhq0z76dmmiqz2yjm28"))))
32275 (properties `((upstream-name . "paws.common")))
32276 (build-system r-build-system)
32278 (list r-base64enc r-digest r-httr r-jsonlite r-xml2))
32279 (home-page "https://cran.r-project.org/package=paws.common")
32280 (synopsis "Paws low-level Amazon Web Services API")
32282 "This package provides functions for making low-level API requests to
32283 Amazon Web Services. The functions handle building, signing, and sending
32284 requests, and receiving responses. They are designed to help build
32285 higher-level interfaces to individual services, such as Simple Storage
32287 (license license:asl2.0)))
32289 (define-public r-paws-customer-engagement
32291 (name "r-paws-customer-engagement")
32296 (uri (cran-uri "paws.customer.engagement" version))
32299 "0ac6hzn4ilfjhzdmc9x80999fl18cz16mky31qd3y09m93w2xkdj"))))
32301 `((upstream-name . "paws.customer.engagement")))
32302 (build-system r-build-system)
32304 (list r-paws-common))
32305 (home-page "https://github.com/paws-r/paws")
32306 (synopsis "Amazon Web Services customer engagement services")
32308 "This package provides an interface to Amazon Web Services customer
32309 engagement services, including Simple Email Service, Connect contact center
32310 service, and more.")
32311 (license license:asl2.0)))
32313 (define-public r-paws-cost-management
32315 (name "r-paws-cost-management")
32320 (uri (cran-uri "paws.cost.management" version))
32323 "0in4f8ygw5g2v6vl3lz2y0v51llglh8b1ymbd04d54xxlgn83knh"))))
32325 `((upstream-name . "paws.cost.management")))
32326 (build-system r-build-system)
32328 (list r-paws-common))
32329 (home-page "https://github.com/paws-r/paws")
32330 (synopsis "Amazon Web Services cost management services")
32332 "This package provides an interface to Amazon Web Services cost
32333 management services, including cost and usage reports, budgets, pricing, and
32335 (license license:asl2.0)))
32337 (define-public r-paws-developer-tools
32339 (name "r-paws-developer-tools")
32344 (uri (cran-uri "paws.developer.tools" version))
32346 (base32 "16gb8g8s67al7qdd95fbigxqkih9a9p7slkyf3cga42wb6miiby2"))))
32347 (properties `((upstream-name . "paws.developer.tools")))
32348 (build-system r-build-system)
32350 (list r-paws-common))
32351 (home-page "https://github.com/paws-r/paws")
32352 (synopsis "Amazon Web Services developer tools services")
32354 "This package provides an interface to Amazon Web Services developer
32355 tools services, including version control, continuous integration and
32356 deployment, and more.")
32357 (license license:asl2.0)))
32359 (define-public r-paws-end-user-computing
32361 (name "r-paws-end-user-computing")
32366 (uri (cran-uri "paws.end.user.computing" version))
32368 (base32 "1xxsz86nx128sizym9np8vldzkbym0p3i6vcy94kq1y0cylaicv3"))))
32369 (properties `((upstream-name . "paws.end.user.computing")))
32370 (build-system r-build-system)
32372 (list r-paws-common))
32373 (home-page "https://github.com/paws-r/paws")
32374 (synopsis "Amazon Web Services end user computing services")
32376 "This package provides an interface to Amazon Web Services end user
32377 computing services, including collaborative document editing, mobile intranet,
32379 (license license:asl2.0)))
32381 (define-public r-paws-application-integration
32383 (name "r-paws-application-integration")
32388 (uri (cran-uri "paws.application.integration" version))
32391 "0llyd9hc679pad1ih0rcc38q5xxpzinhwrl8cvrkgsjgbc3agq42"))))
32393 `((upstream-name . "paws.application.integration")))
32394 (build-system r-build-system)
32396 (list r-paws-common))
32397 (home-page "https://github.com/paws-r/paws")
32398 (synopsis "Amazon Web Services application integration services")
32400 "This package provides an interface to Amazon Web Services application
32401 integration services, including Simple Queue Service (SQS) message queue,
32402 Simple Notification Service (SNS) publish/subscribe messaging, and more.")
32403 (license license:asl2.0)))
32405 (define-public r-paws-security-identity
32407 (name "r-paws-security-identity")
32412 (uri (cran-uri "paws.security.identity" version))
32415 "092lz2ipn5iqr593x7ra8c0bj64yf6315mdc3llgwrjyb4vfxif9"))))
32417 `((upstream-name . "paws.security.identity")))
32418 (build-system r-build-system)
32420 (list r-paws-common))
32421 (home-page "https://github.com/paws-r/paws")
32422 (synopsis "Amazon Web Services security, identity, and compliance services")
32424 "This package provides an interface to Amazon Web Services security,
32425 identity, and compliance services, including the Identity and Access
32426 Management (IAM) service for managing access to services and resources, and
32428 (license license:asl2.0)))
32430 (define-public r-paws-analytics
32432 (name "r-paws-analytics")
32437 (uri (cran-uri "paws.analytics" version))
32440 "04gnaxmj21l312xkrsd9bisi0bz9h6h5fyhwlqylcxi077z1yb2g"))))
32442 `((upstream-name . "paws.analytics")))
32443 (build-system r-build-system)
32445 (list r-paws-common))
32446 (home-page "https://github.com/paws-r/paws")
32447 (synopsis "Amazon Web Services analytics services")
32449 "This package provides an interface to Amazon Web Services analytics
32450 services, including Elastic MapReduce Hadoop and Spark big data service,
32451 Elasticsearch search engine, and more.")
32452 (license license:asl2.0)))
32454 (define-public r-paws-machine-learning
32456 (name "r-paws-machine-learning")
32461 (uri (cran-uri "paws.machine.learning" version))
32464 "01w2y5952pk50xjbzby2pc51xrkrzjpfxbmii1b10cl2xgzfkxsa"))))
32466 `((upstream-name . "paws.machine.learning")))
32467 (build-system r-build-system)
32469 (list r-paws-common))
32470 (home-page "https://github.com/paws-r/paws")
32471 (synopsis "Amazon Web Services machine learning services")
32473 "This package provides an interface to Amazon Web Services machine
32474 learning services, including SageMaker managed machine learning service,
32475 natural language processing, speech recognition, translation, and more.")
32476 (license license:asl2.0)))
32478 (define-public r-paws-management
32480 (name "r-paws-management")
32485 (uri (cran-uri "paws.management" version))
32488 "09k7wg0jlj40zs2yb3vldffpkdcjg7ap98n7c5lxr5plpca08swg"))))
32490 `((upstream-name . "paws.management")))
32491 (build-system r-build-system)
32493 (list r-paws-common))
32494 (home-page "https://github.com/paws-r/paws")
32495 (synopsis "Amazon Web Services management and governance services")
32497 "This package provides an interface to Amazon Web Services management and
32498 governance services, including CloudWatch application and infrastructure
32499 monitoring, Auto Scaling for automatically scaling resources, and more.")
32500 (license license:asl2.0)))
32502 (define-public r-paws-networking
32504 (name "r-paws-networking")
32509 (uri (cran-uri "paws.networking" version))
32512 "02hxaa5nlj70mdggh379ij3fn09xm8h5ldzsyf45c342prpl6zwj"))))
32514 `((upstream-name . "paws.networking")))
32515 (build-system r-build-system)
32517 (list r-paws-common))
32518 (home-page "https://github.com/paws-r/paws")
32519 (synopsis "Amazon Web Services networking and content delivery services")
32521 "This package provides an interface to Amazon Web Services networking and
32522 content delivery services, including Route 53 Domain Name System service,
32523 CloudFront content delivery, load balancing, and more.")
32524 (license license:asl2.0)))
32526 (define-public r-paws-database
32528 (name "r-paws-database")
32533 (uri (cran-uri "paws.database" version))
32536 "08jpwz95fw3f68j0wxh2lg57nn60khflldab0ryhkkbcw1iy0qyz"))))
32537 (properties `((upstream-name . "paws.database")))
32538 (build-system r-build-system)
32540 (list r-paws-common))
32541 (home-page "https://github.com/paws-r/paws")
32543 "Amazon Web Services Database Services")
32545 "This package provides an interface to Amazon Web Services database
32546 services, including Relational Database Service (RDS), DynamoDB NoSQL
32547 database, and more.")
32548 (license license:asl2.0)))
32550 (define-public r-paws-storage
32552 (name "r-paws-storage")
32557 (uri (cran-uri "paws.storage" version))
32560 "06m887vpqp5d6k3zxdlga599dsv8v3rladk7xqaxqnld1f17am04"))))
32561 (properties `((upstream-name . "paws.storage")))
32562 (build-system r-build-system)
32564 (list r-paws-common))
32565 (home-page "https://github.com/paws-r/paws")
32566 (synopsis "Amazon Web Services storage services")
32568 "This package provides an interface to Amazon Web Services storage
32569 services, including Simple Storage Service (S3).")
32570 (license license:asl2.0)))
32572 (define-public r-paws-compute
32574 (name "r-paws-compute")
32579 (uri (cran-uri "paws.compute" version))
32582 "1km6fng6il5fcjlrbbndahsw2dr2ql83hwac9wlpd67zm3wy9lky"))))
32583 (properties `((upstream-name . "paws.compute")))
32584 (build-system r-build-system)
32586 (list r-paws-common))
32587 (home-page "https://github.com/paws-r/paws")
32588 (synopsis "Amazon Web Services compute services")
32590 "This package provides an interface to Amazon Web Services compute
32591 services, including Elastic Compute Cloud (EC2), Lambda
32592 functions-as-a-service, containers, batch processing, and more.")
32593 (license license:asl2.0)))
32595 (define-public r-paws
32602 (uri (cran-uri "paws" version))
32605 "0kn1z045r106fwqcaz52hb02bhrcblh479cajfjiq480s1iljcw6"))))
32606 (properties `((upstream-name . "paws")))
32607 (build-system r-build-system)
32609 (list r-paws-analytics
32610 r-paws-application-integration
32612 r-paws-cost-management
32613 r-paws-customer-engagement
32615 r-paws-developer-tools
32616 r-paws-end-user-computing
32617 r-paws-machine-learning
32620 r-paws-security-identity
32622 (home-page "https://github.com/paws-r/paws")
32623 (synopsis "Amazon Web Services software development kit")
32625 "This package provides an interface to Amazon Web Services, including
32626 storage, database, and compute services, such as Simple Storage Service (S3),
32627 DynamoDB NoSQL database, and Lambda functions-as-a-service.")
32628 (license license:asl2.0)))
32630 (define-public r-zoomgroupstats
32632 (name "r-zoomgroupstats")
32637 (uri (cran-uri "zoomGroupStats" version))
32640 "0gndiq92cy6gi7f833hdjvqii3cn83wz5rjvygcvjl3dw4pwv966"))))
32642 `((upstream-name . "zoomGroupStats")))
32643 (build-system r-build-system)
32654 (native-inputs (list r-knitr))
32655 (home-page "http://zoomgroupstats.org")
32656 (synopsis "Analyze text, audio, and video from Zoom meetings")
32658 "This package provides utilities for processing and analyzing the files
32659 that are exported from a recorded Zoom meeting. This includes analyzing data
32660 captured through video cameras and microphones, the text-based chat, and
32661 meta-data. You can analyze aspects of the conversation among meeting
32662 participants and their emotional expressions throughout the meeting.")
32663 (license license:expat)))
32665 (define-public r-zoom
32672 (uri (cran-uri "zoom" version))
32675 "05ikad4j1qi5y8mn77n9bw7d6ic3api9d7mbcn855w8xcc69ja4q"))))
32676 (properties `((upstream-name . "zoom")))
32677 (build-system r-build-system)
32678 (home-page "https://github.com/cbarbu/R-package-zoom")
32679 (synopsis "Spatial data visualization tool")
32681 "This package provides @code{zm}, a utility that allows you to
32682 zoom/navigate any plot when called with any active plot.")
32683 (license license:gpl3+)))
32685 (define-public r-zoolog
32692 (uri (cran-uri "zoolog" version))
32695 "00fi7czfwr0ll9070w3ijskd0xvilj02gy8wkgqzzrlilij8ah7p"))))
32696 (properties `((upstream-name . "zoolog")))
32697 (build-system r-build-system)
32699 (list r-rdpack r-stringi))
32702 (home-page "https://josempozo.github.io/zoolog/")
32703 (synopsis "Zooarchaeological analysis with log-ratios")
32705 "This package includes functions and reference data to generate and
32706 manipulate log-ratios (also known as @dfn{log size index} (LSI) values) from
32707 measurements obtained on zooarchaeological material. Log ratios are used to
32708 compare the relative (rather than the absolute) dimensions of animals from
32709 archaeological contexts. The zoolog package is also able to seamlessly
32710 integrate data and references with heterogeneous nomenclature, which is
32711 internally managed by a zoolog thesaurus.")
32712 (license license:gpl3)))
32714 (define-public r-filehash
32716 (name "r-filehash")
32721 (uri (cran-uri "filehash" version))
32724 "1ga17smgjd4qsnf5a7qk0giwhpc5969ylqj520favs1k6b4y557k"))))
32725 (properties `((upstream-name . "filehash")))
32726 (build-system r-build-system)
32727 (home-page "http://github.com/rdpeng/filehash")
32728 (synopsis "Simple key-value database")
32730 "This package implements a simple key-value style database where
32731 character string keys are associated with data values that are stored on the
32732 disk. A simple interface is provided for inserting, retrieving, and deleting
32733 data from the database. Utilities are provided that allow filehash databases
32734 to be treated much like environments and lists are already used in R. These
32735 utilities are provided to encourage interactive and exploratory analysis on
32737 (license license:gpl2+)))
32739 (define-public r-mlearning
32741 (name "r-mlearning")
32746 (uri (cran-uri "mlearning" version))
32749 "1zjnh4gcw068li1bks60gazn3205xhmqz67hbkb1san33lmlxya3"))))
32750 (properties `((upstream-name . "mlearning")))
32751 (build-system r-build-system)
32759 (home-page "http://www.sciviews.org/zooimage")
32760 (synopsis "Machine learning algorithms with unified interface")
32762 "This package provides a unified interface to various machine learning
32763 algorithms. Confusion matrices are provided too.")
32764 (license license:gpl2+)))
32766 (define-public r-zooimage
32768 (name "r-zooimage")
32773 (uri (cran-uri "zooimage" version))
32776 "0ck8w0zb9l1n9xvjwqshq9q9l8pigy3yslq2hnfbgcwk17kk9mp8"))))
32777 (properties `((upstream-name . "zooimage")))
32778 (build-system r-build-system)
32792 (home-page "http://www.sciviews.org/zooimage")
32793 (synopsis "Analysis of numerical plankton images")
32795 "This package provides a solution for analyzing digital images of
32796 plankton. In combination with ImageJ, an image analysis system, it processes
32797 digital images, measures individuals, trains for automatic classification of
32798 taxa, and finally, measures plankton samples (abundances, total and partial
32799 size spectra or biomasses, etc.).")
32800 (license license:gpl2+)))
32802 (define-public r-zooarch
32809 (uri (cran-uri "zooaRch" version))
32812 "0grc378xppv0303sf4flfqz5002vq5a23nzbq4bsff41rww7dihc"))))
32813 (properties `((upstream-name . "zooaRch")))
32814 (build-system r-build-system)
32815 (propagated-inputs (list r-ggplot2))
32816 (native-inputs (list r-knitr))
32818 "https://cran.r-project.org/package=zooaRch")
32820 "Analytical Tools for Zooarchaeological Data")
32822 "The analysis and inference of faunal remains recovered from
32823 archaeological sites concerns the field of zooarchaeology. The zooaRch
32824 package provides analytical tools to make inferences on zooarchaeological
32825 data. Functions in this package allow users to read, manipulate, visualize,
32826 and analyze zooarchaeological data.")
32827 (license license:gpl2+)))
32829 (define-public r-zonebuilder
32831 (name "r-zonebuilder")
32836 (uri (cran-uri "zonebuilder" version))
32839 "0mxf3dz0d6bi5wwjilqivdxhy5ypnq5svky8zygha0clv45l4dmn"))))
32840 (properties `((upstream-name . "zonebuilder")))
32841 (build-system r-build-system)
32843 (list r-rcolorbrewer r-sf))
32846 (home-page "https://github.com/zonebuilders/zonebuilder")
32847 (synopsis "Create and explore geographic zoning systems")
32849 "This package provides functions, documentation and example data to help
32850 divide geographic space into discrete polygons (zones). The functions are
32851 motivated by research into the merits of different zoning systems. A flexible
32852 @code{ClockBoard} zoning system is provided, which breaks-up space by
32853 concentric rings and radial lines emanating from a central point.")
32854 (license license:gpl3)))
32856 (define-public r-zonator
32863 (uri (cran-uri "zonator" version))
32866 "1plxchpd4ypp36phl13pi9yvlrqi3lk83lv5rldrhdqynhcgfw2k"))))
32867 (properties `((upstream-name . "zonator")))
32868 (build-system r-build-system)
32870 (list r-ggplot2 r-raster r-rcolorbrewer r-reshape2 r-rgdal))
32871 (native-inputs (list r-knitr))
32872 (home-page "https://cbig.github.io/zonator/")
32873 (synopsis "Utilities for Zonation spatial conservation prioritization")
32875 "Create new analysis setups and deal with results of Zonation
32876 conservation prioritization software.")
32877 (license license:bsd-2)))
32879 (define-public r-mmwrweek
32881 (name "r-mmwrweek")
32886 (uri (cran-uri "MMWRweek" version))
32889 "1l1ks44v52iggw9nhs56lfj6804yab5b17k8fzrc6h1kvj3vda0s"))))
32890 (properties `((upstream-name . "MMWRweek")))
32891 (build-system r-build-system)
32892 (home-page "http://wwwn.cdc.gov/nndss/document/MMWR_Week_overview.pdf")
32893 (synopsis "Convert dates to MMWR day, week, and year")
32895 "The first day of any MMWR week is Sunday. MMWR week numbering is
32896 sequential beginning with 1 and incrementing with each week to a maximum of 52
32897 or 53. MMWR week #1 of an MMWR year is the first week of the year that has at
32898 least four days in the calendar year. This package provides functionality to
32899 convert dates to MMWR day, week, and year and the reverse.")
32900 (license license:gpl2+)))
32902 (define-public r-cccd
32909 (uri (cran-uri "cccd" version))
32911 (base32 "0cxh19jqappc6zq9nz3m40ybdmsp12mf7yvflsz96wks3ly2ld4y"))))
32912 (properties `((upstream-name . "cccd")))
32913 (build-system r-build-system)
32914 (propagated-inputs (list r-deldir r-fnn r-igraph r-proxy))
32915 (home-page "https://cran.r-project.org/package=cccd")
32916 (synopsis "Class cover catch digraphs")
32918 "This package provides tools to create Class Cover Catch Digraphs,
32919 neighborhood graphs, and relatives.")
32920 (license license:gpl2+)))
32922 (define-public r-crul
32929 (uri (cran-uri "crul" version))
32932 "133g0skz4lifl8hm8pqdryd2m2drbrm6mdfzbbsrw8fg46di86my"))))
32933 (properties `((upstream-name . "crul")))
32934 (build-system r-build-system)
32942 (native-inputs (list r-knitr))
32943 (home-page "https://github.com/ropensci/crul")
32944 (synopsis "HTTP client")
32946 "This package provides a simple HTTP client, with tools for making HTTP
32947 requests, and mocking HTTP requests. The package is built on R6, and takes
32948 inspiration from Ruby's @code{faraday} gem.")
32949 (license license:expat)))
32951 (define-public r-gistr
32958 (uri (cran-uri "gistr" version))
32961 "0ac9ikrdg6i8xvlma0gizvsdva46408lk7hvsgkqirhy2ljy02hp"))))
32962 (properties `((upstream-name . "gistr")))
32963 (build-system r-build-system)
32973 (native-inputs (list r-knitr))
32974 (home-page "https://github.com/ropensci/gistr")
32975 (synopsis "Work with Gists in browser")
32977 "This package allows the user to create new Github gists, update gists
32978 with new files, rename files, delete files, get and delete gists, star and
32979 un-star them, fork them, open a gist in your default browser, get an embed
32980 code for a gist, list gist commits, and get rate limit information when
32982 (license license:expat)))
32984 (define-public r-rbokeh
32991 (uri (cran-uri "rbokeh" version))
32994 "1h2fpzqf17pw9d09r1g1iyxsj5qma4fsk8vnar7f1z4fjyypvi6q"))
32996 '(for-each delete-file '("inst/htmlwidgets/lib/bokehjs/bokeh-widgets.min.js"
32997 "inst/htmlwidgets/lib/bokehjs/bokeh.min.js")))))
32998 (properties `((upstream-name . "rbokeh")))
32999 (build-system r-build-system)
33002 (modify-phases %standard-phases
33003 (add-after 'unpack 'process-javascript
33004 (lambda* (#:key inputs #:allow-other-keys)
33005 (with-directory-excursion "inst/htmlwidgets/lib/bokehjs"
33007 `((,(assoc-ref inputs "js-bokeh-widgets")
33008 . "bokeh-widgets.min.js")
33009 (,(assoc-ref inputs "js-bokeh")
33010 . "bokeh.min.js"))))
33011 (for-each (lambda (source target)
33012 (format #true "Processing ~a --> ~a~%"
33014 (invoke "esbuild" source "--minify"
33015 (string-append "--outfile=" target)))
33017 (map cdr mapping)))))))))
33029 ;; Version 0.12.15 is mentioned in lib/htmlwidgets/rbokeh.yaml.
33031 `(("esbuild" ,esbuild)
33032 ("js-bokeh-widgets"
33035 (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh-widgets.js")
33038 "07v9lrkfcbdznpb10qqwi4m660zp65g85vlnfw7kn83zmkxkhhxy"))))
33042 (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh.js")
33045 "1pq0059aad7d2jv50nv9449p3w0gbkxkl0mhblc76m5d9qjqav2q"))))
33046 ("r-knitr" ,r-knitr)))
33047 (home-page "https://cran.r-project.org/web/packages/rbokeh/")
33048 (synopsis "R interface for the Bokeh visualization library")
33050 "This package provides a native R plotting library that provides a
33051 flexible declarative interface for creating interactive web-based graphics,
33052 backed by the @url{https://bokeh.pydata.org/, Bokeh visualization library}.")
33053 (license license:expat)))
33055 (define-public r-fauxpas
33062 (uri (cran-uri "fauxpas" version))
33065 "129fzqb7wsskbn50s8x0marr4wm8jrns6hiycqcsk166k3dnyyy8"))))
33066 (properties `((upstream-name . "fauxpas")))
33067 (build-system r-build-system)
33069 (list r-httpcode r-r6 r-whisker))
33072 (home-page "https://docs.ropensci.org/fauxpas")
33073 (synopsis "HTTP error helpers")
33075 "This package provides HTTP error helpers. Methods are included for
33076 general purpose HTTP error handling, as well as individual methods for every
33077 HTTP status code, both via status code numbers as well as their descriptive
33078 names. It supports the ability to adjust behavior to stop, message or
33079 warning. It includes the ability to use a custom whisker template to have any
33080 configuration of status code, short description, and verbose message.")
33081 (license license:expat)))
33083 (define-public r-webmockr
33085 (name "r-webmockr")
33090 (uri (cran-uri "webmockr" version))
33093 "0j40srwi0yasmllb9wsww4m6zkiyzqd549cis4dxd7c7p24hak8j"))))
33094 (properties `((upstream-name . "webmockr")))
33095 (build-system r-build-system)
33105 (home-page "https://github.com/ropensci/webmockr")
33106 (synopsis "Stubbing and setting expectations on HTTP Requests")
33108 "This is a package for stubbing and setting expectations on HTTP
33109 requests. It includes tools for stubbing HTTP requests, including expected
33110 request conditions and response conditions. You can match on HTTP method,
33111 query parameters, request body, headers and more. It can be used for unit
33112 tests or outside of a testing context.")
33113 (license license:expat)))
33115 (define-public r-iotools
33122 (uri (cran-uri "iotools" version))
33124 (base32 "07q0z0kszm1xx5hfhisfliyrcsxd8dc5mx0a2bwwnv5l1xzmix17"))))
33125 (properties `((upstream-name . "iotools")))
33126 (build-system r-build-system)
33127 (home-page "https://www.rforge.net/iotools")
33128 (synopsis "I/O tools for streaming")
33129 (description "This package provides basic I/O tools for streaming and data
33132 (license license:gpl3)))
33134 (define-public r-wordspace
33136 (name "r-wordspace")
33141 (uri (cran-uri "wordspace" version))
33143 (base32 "0hrjv5mag7gwl4wj7np248sdyns5i623wl37b11hlgalhbmlypyf"))))
33144 (properties `((upstream-name . "wordspace")))
33145 (build-system r-build-system)
33147 (list r-cluster r-iotools r-mass r-matrix r-rcpp r-sparsesvd))
33148 (native-inputs (list r-knitr))
33149 (home-page "https://wordspace.r-forge.r-project.org/")
33150 (synopsis "Distributional semantic models in R")
33152 "The wordspace package turns R into an interactive laboratory for
33153 empirical research on @dfn{distributional semantic models} (DSM). It consists
33154 of a small set of carefully designed functions, most of which
33157 @item encapsulate non-trivial R operations in a user-friendly manner or
33158 @item provide efficient and memory-lean C implementations of key operations.
33161 (license license:gpl3)))
33163 (define-public r-maxlik
33170 (uri (cran-uri "maxLik" version))
33172 (base32 "0pdigfpyiqacj2ydhpn5w1h89dz1ydk0syzs25lsgdi40sz0bvkw"))))
33173 (properties `((upstream-name . "maxLik")))
33174 (build-system r-build-system)
33175 (propagated-inputs (list r-generics r-misctools r-sandwich))
33176 (home-page "https://cran.r-project.org/package=maxLik")
33177 (synopsis "Maximum Likelihood Estimation and related tools")
33179 "This package provides functions for @dfn{Maximum Likelihood} (ML) estimation,
33180 non-linear optimization, and related tools. It includes a unified way to call
33181 different optimizers, and classes and methods to handle the results from the
33182 Maximum Likelihood viewpoint. It also includes a number of convenience tools
33183 for testing and developing your own models.")
33184 (license license:gpl2+)))
33186 (define-public r-misctools
33188 (name "r-misctools")
33193 (uri (cran-uri "miscTools" version))
33195 (base32 "16pwfxpyl0zv3hjxx2kjchkg7p6kbj0s2rrpskj7rkhjr9imlg5y"))))
33196 (properties `((upstream-name . "miscTools")))
33197 (build-system r-build-system)
33198 (propagated-inputs (list r-digest))
33199 (home-page "http://www.micEcon.org")
33200 (synopsis "Miscellaneous tools and utilities")
33202 "This package provides miscellaneous small tools and utilities. Many of
33203 them facilitate the work with matrices, e.g. inserting rows or columns,
33204 creating symmetric matrices, or checking for semidefiniteness. Other tools
33205 facilitate the work with regression models, e.g. extracting the standard
33206 errors, obtaining the number of (estimated) parameters, or calculating
33207 R-squared values.")
33208 (license license:gpl2+)))
33210 (define-public r-mockery
33217 (uri (cran-uri "mockery" version))
33220 "0sj77m9vgn4bzb8c8nq93xb9lm8ih8rcb7sfccripraibibg3jcz"))))
33221 (properties `((upstream-name . "mockery")))
33222 (build-system r-build-system)
33227 (home-page "https://github.com/jfiksel/mockery")
33228 (synopsis "Mocking library for R")
33230 "The two main functionalities of this package are creating mock
33231 objects (functions) and selectively intercepting calls to a given function
33232 that originate in some other function. It can be used with any testing
33233 framework available for R. Mock objects can be injected with either this
33234 package's own @code{stub} function or a similar @code{with_mock} facility
33235 present in the @code{testthat} package.")
33236 (license license:expat)))
33238 (define-public r-zoltr
33245 (uri (cran-uri "zoltr" version))
33248 "12zh7y3pwidclscgvd0b0iaqq9j5y8mc8xd6pz4vs0jy5qs3ahar"))))
33249 (properties `((upstream-name . "zoltr")))
33250 (build-system r-build-system)
33262 (native-inputs (list r-knitr))
33263 (home-page "https://github.com/reichlab/zoltr")
33264 (synopsis "Interface to the Zoltar forecast repository API")
33266 "Zoltar is a website that provides a repository of model forecast results
33267 in a standardized format and a central location. It supports storing,
33268 retrieving, comparing, and analyzing time series forecasts for prediction
33269 challenges of interest to the modeling community. This package provides
33270 functions for working with the Zoltar API, including connecting and
33271 authenticating, getting information about projects, models, and forecasts,
33272 deleting and uploading forecast data, and downloading scores.")
33273 (license license:gpl3)))
33275 (define-public r-zoib
33282 (uri (cran-uri "zoib" version))
33285 "0inm7f2pc68ksqxvq12xp9jc99vj7ydylvs24ip12nksbj5k1n8f"))))
33286 (properties `((upstream-name . "zoib")))
33287 (build-system r-build-system)
33289 (list r-abind r-coda r-formula r-rjags))
33290 (home-page "https://www.r-project.org")
33291 (synopsis "Bayesian inference for beta regression")
33293 "This package lets you fit beta regression and zero-or-one inflated beta
33294 regression and obtain Bayesian inference of the model via the Markov Chain
33295 Monte Carlo approach implemented in JAGS.")
33296 (license license:gpl3+)))
33298 (define-public r-logger
33305 (uri (cran-uri "logger" version))
33307 (base32 "08kym5i5fvbf5xhh9qdszp4jdgyc7j7zpnwzy68wabqz73aff6sg"))))
33308 (properties `((upstream-name . "logger")))
33309 (build-system r-build-system)
33310 (native-inputs (list r-knitr))
33311 (home-page "https://daroczig.github.io/logger/")
33312 (synopsis "Lightweight and flexible logging utility")
33314 "Inspired by the the @code{futile.logger} R package and @code{logging}
33315 Python module, this utility provides a flexible and extensible way of
33316 formatting and delivering log messages with low overhead.")
33317 (license license:agpl3+)))
33319 (define-public r-fasterize
33321 (name "r-fasterize")
33326 (uri (cran-uri "fasterize" version))
33328 (base32 "10bzl77c1b9jhcn1xp467qzp2n8c7s3wpxn53qjh1nwvbri5kd32"))))
33329 (properties `((upstream-name . "fasterize")))
33330 (build-system r-build-system)
33332 (list r-raster r-rcpp r-rcpparmadillo r-sp))
33333 (native-inputs (list r-knitr))
33334 (home-page "https://github.com/ecohealthalliance/fasterize")
33335 (synopsis "Fast Polygon to Raster Conversion")
33337 "This package provides a drop-in replacement for @code{rasterize} from
33338 the @code{raster} package that takes sf-type objects, and is much faster.
33339 There is support for the main options provided by the @code{rasterize}
33340 function, including setting the field used and background value, and
33341 options for aggregating multi-layer rasters.")
33342 (license license:expat)))
33344 (define-public r-bien
33351 (uri (cran-uri "BIEN" version))
33353 (base32 "0s98n6zbf48vssd3h63k6kashcxv1kawcb026n0ngsfpc5dv6i48"))))
33354 (properties `((upstream-name . "BIEN")))
33355 (build-system r-build-system)
33370 (home-page "https://cran.r-project.org/package=BIEN")
33371 (synopsis "Tools for accessing the BIEN database")
33373 "This package provides tools for accessing the Botanical Information and
33374 Ecology Network (BIEN) database. The BIEN database contains cleaned and
33375 standardized botanical data including occurrence, trait, plot and taxonomic
33376 data. This package provides functions that query the BIEN database by
33377 constructing and executing optimized SQL queries.")
33378 (license license:expat)))
33380 (define-public r-varhandle
33382 (name "r-varhandle")
33387 (uri (cran-uri "varhandle" version))
33389 (base32 "1l42d0s6fbjjc9l28a2m3myxkrx2c0p0b9yj8wjjjgilw19yc3lv"))))
33390 (properties `((upstream-name . "varhandle")))
33391 (build-system r-build-system)
33392 (home-page "https://bitbucket.org/mehrad_mahmoudian/varhandle")
33393 (synopsis "Functions for robust variable handling")
33395 "This package contains some functions to help users (especially data
33396 explorers) to make more sense of their variables and take the most out of
33397 variables and hardware resources. Functions in this package are supposed to
33398 be efficient and easy to use.")
33399 (license license:gpl2+)))
33401 (define-public r-ggh4x
33408 (uri (cran-uri "ggh4x" version))
33411 "1r49yfm5fqv5s7jb92ad6rf8hd9plcry6f500czjhnhhrp16cqfp"))))
33412 (properties `((upstream-name . "ggh4x")))
33413 (build-system r-build-system)
33415 (list r-ggplot2 r-gtable r-rlang r-scales r-vctrs))
33418 (home-page "https://github.com/teunbrand/ggh4x")
33419 (synopsis "Extension for ggplot2")
33420 (description "This package is a @code{ggplot2} extension. It provides some
33421 utility functions that do not entirely fit within the grammar of graphics
33422 concept. The package extends @code{ggpplots} facets through customisation, by
33423 setting individual scales per panel, resizing panels and providing nested
33424 facets. It also allows multiple colour, fill scales per plot and hosts a
33425 smaller collection of stats, geoms and axis guides.")
33426 (license license:expat)))
33428 (define-public r-gghalves
33430 (name "r-gghalves")
33435 (uri (cran-uri "gghalves" version))
33438 "1lj4c38fzxwg8gy57ymf00lqjdplb7v2a0lnd262c1d5cavqiws4"))))
33439 (properties `((upstream-name . "gghalves")))
33440 (build-system r-build-system)
33442 (list r-ggplot2 r-gtable))
33445 (home-page "https://github.com/erocoar/gghalves")
33446 (synopsis "Compose half-half plots using your favourite geoms")
33447 (description "This package provides a @code{ggplot2} extension for easy
33448 plotting of half-half geom combinations. Think half boxplot and half
33449 jitterplot, or half violinplot and half dotplot.")
33450 (license license:expat)))
33452 (define-public r-zoeppritz
33454 (name "r-zoeppritz")
33458 (uri (cran-uri "zoeppritz" version))
33461 "1711szx9zz17q6pfinyzlyrw7m9772c8ywlixqar2l165bkjalgm"))))
33462 (properties `((upstream-name . "zoeppritz")))
33463 (build-system r-build-system)
33464 (home-page "https://cran.r-project.org/package=zoeppritz")
33465 (synopsis "Seismic reflection and scattering coefficients for waves")
33467 "The @code{r-zoeppritz} package calculates and plots scattering matrix
33468 coefficients or scattering amplitudes, for seismological P and S-waves at an
33470 (license license:gpl2+)))
33472 (define-public r-metadat
33478 (uri (cran-uri "metadat" version))
33481 "1f7mb3pw5d0akr09jjva06ay223izhpzbr21bapnw99x1kiybk7h"))))
33482 (properties `((upstream-name . "metadat")))
33483 (build-system r-build-system)
33484 (propagated-inputs (list r-mathjaxr))
33485 (home-page "https://github.com/wviechtb/metadat")
33486 (synopsis "Meta-Analysis Datasets")
33488 "This package provides a collection of meta-analysis datasets for teaching
33489 purposes, illustrating/testing meta-analytic methods, and validating published
33491 (license license:gpl2+)))
33493 (define-public r-mathjaxr
33495 (name "r-mathjaxr")
33499 (uri (cran-uri "mathjaxr" version))
33502 "0yf1sfkb2kjsplipl2v4k2gp20li9xzsynclg228sy0v243pdi7c"))
33503 (modules '((guix build utils)))
33506 (delete-file-recursively "src/mathjax/es5/input")
33507 (delete-file-recursively "src/mathjax/es5/output")
33508 (delete-file "src/mathjax/es5/tex-chtml-full.js")))))
33509 (properties `((upstream-name . "mathjaxr")))
33510 (build-system r-build-system)
33514 `(modify-phases %standard-phases
33515 (add-after 'unpack 'use-js-mathjax
33516 (lambda* (#:key inputs #:allow-other-keys)
33518 (search-input-directory
33519 inputs "/share/javascript/mathjax/es5/output")
33520 "src/mathjax/es5/output")
33522 (search-input-directory
33523 inputs "/share/javascript/mathjax/es5/input")
33524 "src/mathjax/es5/input")
33527 inputs "/share/javascript/mathjax/es5/tex-chtml-full.js")
33528 "src/mathjax/es5/tex-chtml-full.js"))))))
33530 (list js-mathjax-for-r-mathjaxr))
33531 (home-page "https://github.com/wviechtb/mathjaxr")
33532 (synopsis "Use Mathjax in Rd Files")
33534 "This package provides MathJax and macros to enable its use within Rd files
33535 for rendering equations in the HTML help files.")
33536 (license (list license:asl2.0 license:gpl3))))
33538 (define-public r-spacetime
33540 (name "r-spacetime")
33544 (uri (cran-uri "spacetime" version))
33547 "0zpaib69dbdvgj36x807ci3m5jkyc0hp2j5722xkwvl1faynjlhf"))))
33548 (properties `((upstream-name . "spacetime")))
33549 (build-system r-build-system)
33550 (propagated-inputs (list r-lattice r-sp r-zoo r-xts r-intervals))
33551 (home-page "https://github.com/edzer/spacetime/")
33552 (synopsis "Classes and methods for spatio-temporal data")
33554 "@command{spacetime} provides classes and methods for spatio-temporal
33555 data, including space-time regular lattices, sparse lattices, irregular data,
33556 and trajectories; utility functions for plotting data as map sequences (lattice
33557 or animation) or multiple time series; methods for spatial and temporal
33558 matching or aggregation, retrieving coordinates, print, summary, etc.")
33559 (license license:gpl2+)))
33561 (define-public r-gstat
33567 (uri (cran-uri "gstat" version))
33570 "19m4zcj1qvg6gs8yjr5ijvd6rrv4av5yp5rmhnb88f0m5qn06b0j"))))
33571 (properties `((upstream-name . "gstat")))
33572 (build-system r-build-system)
33573 (propagated-inputs (list r-lattice r-sp r-zoo r-spacetime r-fnn))
33574 (home-page "https://github.com/r-spatial/gstat/")
33575 (synopsis "Spatial and spatio-temporal geostatistical modelling,
33576 prediction and simulation")
33578 "This package enables variogram modelling, including: simple, ordinary and
33579 universal point or block (co)kriging; spatio-temporal kriging; and sequential
33580 Gaussian or indicator (co)simulation. It includes variogram and variogram map
33581 plotting utility functions, and supports @command{sf} and @command{stars}.")
33582 (license license:gpl2+)))