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 tbb)
108 #:use-module (gnu packages tcl)
109 #:use-module (gnu packages tex)
110 #:use-module (gnu packages textutils)
111 #:use-module (gnu packages tls)
112 #:use-module (gnu packages uglifyjs)
113 #:use-module (gnu packages version-control)
114 #:use-module (gnu packages video)
115 #:use-module (gnu packages web)
116 #:use-module (gnu packages xml)
117 #:use-module (gnu packages xorg))
125 (uri (cran-uri "AER" version))
128 "1p6vxr0220lim5i4gwsvphqrfd65zbs8h3qydz4gipca9asmy2k5"))))
129 (properties `((upstream-name . "AER")))
130 (build-system r-build-system)
138 (home-page "https://cran.r-project.org/package=AER")
139 (synopsis "Applied econometrics with R")
141 "This package provides functions, data sets, examples, demos, and
142 vignettes for the book Christian Kleiber and Achim Zeileis (2008), Applied
143 Econometrics with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2. (See
144 the vignette \"AER\" for a package overview.)")
145 ;; Either version of the GPL
146 (license (list license:gpl2 license:gpl3))))
148 (define-public r-afpt
154 (uri (cran-uri "afpt" version))
157 "1z0r4r7prxbhadmkdg6345g0b5vq9dqyyw9hh3fpad9zkc7k6xbc"))))
158 (properties `((upstream-name . "afpt")))
159 (build-system r-build-system)
160 (native-inputs (list r-knitr))
161 (home-page "https://github.com/MarcoKlH/afpt-r/")
162 (synopsis "Tools for modelling of animal flight performance")
164 "This package allows estimation and modelling of flight costs in animal
165 (vertebrate) flight, implementing the aerodynamic power model. Flight
166 performance is estimated based on basic morphological measurements such as
167 body mass, wingspan and wing area. @code{Afpt} can be used to make
168 predictions on how animals should adjust their flight behaviour and wingbeat
169 kinematics to varying flight conditions.")
170 (license license:gpl3+)))
179 (uri (cran-uri "aod" version))
181 (base32 "0p2i536s0aa54rah1l465g77k2ldn6jm6s25y9vc06mk29xvx1cv"))))
182 (properties `((upstream-name . "aod")))
183 (build-system r-build-system)
184 (home-page "https://cran.r-project.org/package=aod")
185 (synopsis "Analysis of overdispersed data")
187 "This package provides a set of functions to analyze overdispersed counts
188 or proportions. Most of the methods are already available elsewhere but are
189 scattered in different packages. The proposed functions should be considered
190 as complements to more sophisticated methods such as @dfn{generalized
191 estimating equations} (GEE) or @dfn{generalized linear mixed effect
193 (license license:gpl2+)))
195 (define-public r-brio
202 (uri (cran-uri "brio" version))
205 "1inwzvlf6zj6gi47gd0byzqv02qajb3l475z8pjvx2b1hm0r1a7a"))))
206 (properties `((upstream-name . "brio")))
207 (build-system r-build-system)
208 (home-page "https://github.com/r-lib/brio")
209 (synopsis "Basic R input output")
211 "This package provides functions to handle basic input output. These
212 functions always read and write UTF-8 (8-bit Unicode Transformation Format)
213 files and provide more explicit control over line endings.")
214 (license license:expat)))
216 (define-public r-cachem
223 (uri (cran-uri "cachem" version))
226 "0r0q5w8lsxak46crnkbi739qzys90hlw7cqqqhv99xzkpkvm554s"))))
227 (properties `((upstream-name . "cachem")))
228 (build-system r-build-system)
230 (list r-fastmap r-rlang))
231 (home-page "https://cachem.r-lib.org/")
232 (synopsis "Cache R objects with automatic pruning")
234 "This package provides key-value stores with automatic pruning. Caches
235 can limit either their total size or the age of the oldest object (or both),
236 automatically pruning objects to maintain the constraints.")
237 (license license:expat)))
239 (define-public r-collections
241 (name "r-collections")
246 (uri (cran-uri "collections" version))
248 (base32 "053ig88pva78wxxwya3v7cz853k563dkpgxrf2xvd0l0d9fanxmz"))))
249 (properties `((upstream-name . "collections")))
250 (build-system r-build-system)
251 (home-page "https://github.com/randy3k/collections")
252 (synopsis "High performance container data types")
254 "This package provides high performance container data types such as
255 queues, stacks, deques, dicts and ordered dicts.")
256 (license license:expat)))
258 (define-public r-curry
265 (uri (cran-uri "curry" version))
268 "1ps9hvbnb02m0b8hlw4admwbziyjvswj08ldi2dk3ymnrpawcc29"))))
269 (properties `((upstream-name . "curry")))
270 (build-system r-build-system)
271 (home-page "https://github.com/thomasp85/curry")
272 (synopsis "Partial function application")
274 "Partial application is the process of reducing the arity of a function
275 by fixing one or more arguments, thus creating a new function lacking the
276 fixed arguments. The @code{curry} package provides three different ways of
277 performing partial function application by fixing arguments from either end of
278 the argument list (currying and tail currying) or by fixing multiple named
279 arguments (partial application). This package provides this functionality
280 through the @code{%<%}, @code{%-<%}, and @code{%><%} operators which allows
281 for a programming style comparable to modern functional languages. Compared
282 to other implementations such a @code{purrr::partial()} the operators in
283 @code{curry} composes functions with named arguments, aiding in autocomplete
285 (license license:gpl2+)))
287 (define-public r-datawizard
289 (name "r-datawizard")
294 (uri (cran-uri "datawizard" version))
297 "1r89h5npv8iwsvylkpazfpcadgh55zd336rz8hndbzp0w9dcmpli"))))
298 (properties `((upstream-name . "datawizard")))
299 (build-system r-build-system)
304 (home-page "https://easystats.github.io/datawizard/")
305 (synopsis "Easy data wrangling")
307 "This package provides a lightweight package to easily manipulate,
308 clean, transform, and prepare your data for analysis. It also forms the data
309 wrangling backend for the packages in the @code{easystats} ecosystem.")
310 (license license:gpl3)))
312 (define-public r-dbscan
319 (uri (cran-uri "dbscan" version))
321 (base32 "1h8x1v9kk5zmw5qd575cyr16yz8l226lsaq71n079l4i8crcrzg1"))))
322 (properties `((upstream-name . "dbscan")))
323 (build-system r-build-system)
324 (propagated-inputs (list r-rcpp))
325 (native-inputs (list r-knitr))
326 (home-page "https://github.com/mhahsler/dbscan")
327 (synopsis "Density-based spatial clustering of applications with noise")
329 "This package provides a fast reimplementation of several density-based
330 algorithms of the DBSCAN family. It includes the clustering algorithms DBSCAN
331 (density-based spatial clustering of applications with noise) and
332 @dfn{hierarchical DBSCAN} (HDBSCAN), the ordering algorithm @dfn{ordering
333 points to identify the clustering structure} (OPTICS), shared nearest neighbor
334 clustering, and the outlier detection algorithms @dfn{local outlier
335 factor} (LOF) and @dfn{global-local outlier score from hierarchies} (GLOSH).
336 The implementations use the kd-tree data structure for faster k-nearest
337 neighbor search. An R interface to fast kNN and fixed-radius NN search is
339 (license license:gpl2+)))
341 (define-public r-diffobj
348 (uri (cran-uri "diffobj" version))
351 "0q6gwd9pqh41f6j5p9jl92aji4p8kx9inffpha93d7jc3ndsfq6q"))))
352 (properties `((upstream-name . "diffobj")))
353 (build-system r-build-system)
354 (propagated-inputs (list r-crayon))
355 (native-inputs (list r-knitr))
356 (home-page "https://github.com/brodieG/diffobj")
357 (synopsis "Diffs for R objects")
359 "Generate a colorized diff of two R objects for an intuitive
360 visualization of their differences.")
361 (license license:gpl2+)))
363 (define-public r-dirichletreg
365 (name "r-dirichletreg")
370 (uri (cran-uri "DirichletReg" version))
372 (base32 "1ql5mwb7zb06y9j6inrlngq7c15as4j17wd8kc71fxs0a2jdj7xi"))))
373 (properties `((upstream-name . "DirichletReg")))
374 (build-system r-build-system)
375 (propagated-inputs (list r-formula r-maxlik))
376 (native-inputs (list r-knitr))
377 (home-page "https://cran.r-project.org/package=DirichletReg")
378 (synopsis "Dirichlet regression")
379 (description "This package implements Dirichlet regression models.")
380 (license license:gpl2+)))
382 (define-public r-dixontest
389 (uri (cran-uri "dixonTest" version))
391 (base32 "0gz39s1z987bg56vwrpcs14wzyf7p07s7l7z9napz0i38564wsdq"))))
392 (properties `((upstream-name . "dixonTest")))
393 (build-system r-build-system)
394 (native-inputs (list gfortran))
395 (home-page "https://cran.r-project.org/package=dixonTest")
396 (synopsis "Dixon's ratio test for outlier detection")
398 "For outlier detection in small and normally distributed samples the ratio
399 test of Dixon (Q-test) can be used. Density, distribution function, quantile
400 function and random generation for Dixon's ratio statistics are provided as
401 wrapper functions. The core applies McBane's Fortran functions that use
402 Gaussian quadrature for a numerical solution.")
403 (license license:gpl3)))
405 (define-public r-emdist
412 (uri (cran-uri "emdist" version))
415 "05mv6xhm15b0mq9kzyiblkb14bdqmjrwl64ghdk66il0w8i7p6nh"))))
416 (properties `((upstream-name . "emdist")))
417 (build-system r-build-system)
418 (home-page "http://www.rforge.net/emd")
419 (synopsis "Earth mover's distance")
421 "This package provides tools to calculate the Earth Mover's
423 (license license:expat)))
425 (define-public r-ggalt
431 (uri (cran-uri "ggalt" version))
434 "0ssa274d41vhd6crzjz7jqzbwgnjimxwxl23p2cx35aqs5wdfjpc"))))
435 (properties `((upstream-name . "ggalt")))
436 (build-system r-build-system)
451 (native-inputs (list r-knitr))
452 (home-page "https://github.com/hrbrmstr/ggalt")
454 "Geometries, coordinate systems, fonts and more for ggplot2")
456 "This package provides a compendium of new geometries, coordinate systems,
457 statistical transformations, scales and fonts for ggplot2, including splines,
458 1d and 2d densities, univariate average shifted histograms, a new map
459 coordinate system based on the PROJ.4-library along with
460 @code{geom_cartogram()} that mimics the original functionality of
461 @code{geom_map()}, formatters for \"bytes\", a @code{stat_stepribbon()}
462 function, increased @code{plotly} compatibility and the @code{StateFace} open
463 source font ProPublica. Further new functionality includes lollipop charts,
464 dumbbell charts, the ability to encircle points and coordinate-system-based
466 (license license:agpl3)))
468 (define-public r-glmpca
474 (uri (cran-uri "glmpca" version))
477 "02xjf0gg52925hw9nw2j0znfmzfzfwbv0fxjl9d2fy9j63drr2h4"))))
478 (properties `((upstream-name . "glmpca")))
479 (build-system r-build-system)
480 (propagated-inputs (list r-mass))
481 (native-inputs (list r-knitr))
482 (home-page "https://github.com/willtownes/glmpca")
483 (synopsis "Dimension Reduction of Non-Normally Distributed Data")
485 "This package implements a generalized version of principal components
486 analysis (GLM-PCA) for dimension reduction of non-normally distributed data
487 such as counts or binary matrices.")
488 (license license:lgpl3+)))
490 (define-public r-googledrive
492 (name "r-googledrive")
497 (uri (cran-uri "googledrive" version))
500 "09jsiknzyfgxd0nzdr3wrrjw24allch2x74h96qg8vh8dad4cp30"))))
501 (properties `((upstream-name . "googledrive")))
502 (build-system r-build-system)
520 (home-page "https://googledrive.tidyverse.org")
521 (synopsis "Interface to Google Drive")
522 (description "This package lets you manage Google Drive files from R.")
523 (license license:expat)))
525 (define-public r-googlevis
532 (uri (cran-uri "googleVis" version))
534 (base32 "1s82xcs6zrlmnhay764bspzwvabfyi35nq6fwdrrk3v79q13c5jz"))))
535 (properties `((upstream-name . "googleVis")))
536 (build-system r-build-system)
537 (propagated-inputs (list r-jsonlite))
538 (native-inputs (list r-knitr))
539 (home-page "https://mages.github.io/googleVis/")
540 (synopsis "R interface to Google Charts")
542 "The @code{googleVis} package provides an interface between R and the Google
543 Charts API. Google Charts offer interactive charts which can be embedded into
544 web pages. The functions of the @code{googleVis} package allow the user to
545 visualise data stored in R data frames with Google Charts without uploading
546 the data to Google. The output of a @code{googleVis} function is HTML code
547 that contains the data and references to JavaScript functions hosted by
548 Google. @code{googleVis} makes use of the internal R HTTP server to display
549 the output locally.")
550 (license license:gpl2+)))
552 (define-public r-guix-install
554 (name "r-guix-install")
559 (uri (cran-uri "guix.install" version))
561 (base32 "0s3wb5781yc43c9zwrn7i87zcbrlx7xr0ms0v9hvgs7qsv02id9j"))))
562 (properties `((upstream-name . "guix.install")))
563 (build-system r-build-system)
564 (propagated-inputs (list r-runit))
565 (home-page "https://github.com/BIMSBbioinfo/guix.install")
566 (synopsis "Install R packages with GNU Guix")
568 "This R package provides a single procedure @code{guix.install()}, which
569 allows users to install R packages via Guix right from within their running R
570 session. If the requested R package does not exist in Guix at this time, the
571 package and all its missing dependencies will be imported recursively and the
572 generated package definitions will be written to @file{~/.Rguix/packages.scm}.
573 This record of imported packages can be used later to reproduce the
574 environment, and to add the packages in question to a proper Guix channel (or
575 Guix itself). @code{guix.install()} not only supports installing packages
576 from CRAN, but also from Bioconductor or even arbitrary git or mercurial
577 repositories, replacing the need for installation via @code{devtools}.")
578 (license license:gpl3+)))
587 (uri (cran-uri "ids" version))
590 "1s6ga94gds5ydr9f8qbjfgfpg2dvbnkcrlybqlb33hk3c0c2l8dn"))))
591 (properties `((upstream-name . "ids")))
592 (build-system r-build-system)
594 (list r-openssl r-uuid))
595 (native-inputs (list r-knitr))
596 (home-page "https://github.com/richfitz/ids")
597 (synopsis "Generate random identifiers")
599 "This package lets you generate random or human readable and
600 pronounceable identifiers.")
601 (license license:expat)))
603 (define-public r-googlesheets4
605 (name "r-googlesheets4")
610 (uri (cran-uri "googlesheets4" version))
613 "14b5lzn6vjn72mw7vf3lzm2ppbjf0wr0n6sw0v5r6h4lk37cnki8"))))
614 (properties `((upstream-name . "googlesheets4")))
615 (build-system r-build-system)
631 (home-page "https://github.com/tidyverse/googlesheets4")
632 (synopsis "Access Google Sheets using the Sheets API V4")
634 "This package lets you interact with Google Sheets through the
635 @url{https://developers.google.com/sheets/api,Sheets API v4}. This package
636 can read and write both the metadata and the cell data in a Sheet.")
637 (license license:expat)))
639 (define-public r-proj4
645 (uri (cran-uri "proj4" version))
648 "07fil52jswbg2h807cd82m2wlm5j2fb891ifri9ms037099qdwf5"))))
649 (properties `((upstream-name . "proj4")))
650 (build-system r-build-system)
651 (inputs (list proj.4 zlib))
652 (native-inputs (list pkg-config))
653 (home-page "http://www.rforge.net/proj4/")
654 (synopsis "Simple interface to the PROJ.4 cartographic projections library")
656 "This package provides a simple interface to lat/long projection and
657 datum transformation of the PROJ.4 cartographic projections library. It
658 allows transformation of geographic coordinates from one projection and/or
660 (license license:gpl2)))
662 (define-public r-waldo
669 (uri (cran-uri "waldo" version))
672 "1aky28rn70l24s0sygl36267cf7hjzhchagsz26abfxwr7p8kvjp"))))
673 (properties `((upstream-name . "waldo")))
674 (build-system r-build-system)
683 (home-page "https://github.com/r-lib/waldo")
684 (synopsis "Find differences between R objects")
686 "Compare complex R objects and reveal the key differences. This package
687 was designed particularly for use in testing packages where being able to
688 quickly isolate key differences makes understanding test failures much
690 (license license:expat)))
692 (define-public r-rticles
699 (uri (cran-uri "rticles" version))
702 "05idvyfjfa4f244km4sxripg8gndvganx5s0ch00xbi4cqnlr2pq"))))
703 (properties `((upstream-name . "rticles")))
704 (build-system r-build-system)
706 (list r-knitr r-rmarkdown r-tinytex r-xfun r-yaml))
707 (home-page "https://github.com/rstudio/rticles")
708 (synopsis "Article formats for R Markdown")
710 "This package provides a suite of custom R Markdown formats and templates
711 for authoring journal articles and conference submissions.")
712 (license license:gpl3)))
714 (define-public r-babelwhale
716 (name "r-babelwhale")
721 (uri (cran-uri "babelwhale" version))
723 (base32 "01l8vwyz3bx0iks6cjs5y9ifdsnc1p1yqp4i0kzqd1gjhycizv6y"))))
724 (properties `((upstream-name . "babelwhale")))
725 (build-system r-build-system)
735 (home-page "https://github.com/dynverse/babelwhale")
736 (synopsis "Talking to Docker and Singularity containers")
738 "This package provides a unified interface to interact with Docker and
739 Singularity containers. You can execute a command inside a container, mount a
740 volume or copy a file.")
741 (license license:expat)))
743 (define-public r-benchmarkmedata
745 (name "r-benchmarkmedata")
749 (uri (cran-uri "benchmarkmeData" version))
752 "1n4vjkagqlm6kw2hilf4gjfcdjad0bcg652j9nl2ygbq3kdnh1vf"))))
753 (build-system r-build-system)
755 (list r-dplyr r-tibble))
756 (home-page "https://github.com/csgillespie/benchmarkme-data")
757 (synopsis "Data set for the @code{benchmarkme} package")
758 (description "This package contains the data set for the crowd-sourced
759 benchmarks from running the @code{benchmarkme} package.")
760 (license license:gpl2+)))
762 (define-public r-benchmarkme
764 (name "r-benchmarkme")
768 (uri (cran-uri "benchmarkme" version))
771 "0qaz8wy3n08k9lr8qljk5i8z8db18scbdc8m734aymd307h00w8x"))))
772 (build-system r-build-system)
776 (list r-benchmarkmedata
784 (home-page "https://csgillespie.github.io/benchmarkme/")
785 (synopsis "Crowd-sourced system benchmarks")
786 (description "This package provides functionality to benchmark your CPU
787 and compare against other CPUs. Also provides functions for obtaining system
788 specifications, such as RAM, CPU type, and R version.")
789 (license license:gpl2+)))
791 (define-public r-bezier
797 (uri (cran-uri "bezier" version))
800 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
801 (build-system r-build-system)
802 (home-page "https://cran.r-project.org/web/packages/bezier/")
803 (synopsis "Bezier curve and spline toolkit")
805 "This package is a toolkit for working with Bezier curves and splines.
806 The package provides functions for point generation, arc length estimation,
807 degree elevation and curve fitting.")
808 (license license:gpl2+)))
810 (define-public r-bwstest
817 (uri (cran-uri "BWStest" version))
819 (base32 "02amzlfprmw5pyis0dg0kg0x8xqh50a4vfdcxxmklrzik3b1vzzs"))))
820 (properties `((upstream-name . "BWStest")))
821 (build-system r-build-system)
822 (propagated-inputs (list r-memoise r-rcpp))
823 (home-page "https://github.com/shabbychef/BWStest")
824 (synopsis "Baumgartner Weiss Schindler Test of equal distributions")
826 "This package performs the Baumgartner-Weiss-Schindler two-sample test of
827 equal probability distributions (doi:10.2307/2533862). It also performs
828 similar rank-based tests for equal probability distributions due to Neuhauser
829 (doi:10.1080/10485250108832874) and Murakami
830 (doi:10.1080/00949655.2010.551516).")
831 (license license:lgpl3)))
840 (uri (cran-uri "V8" version))
843 "1w1zihmhrygn2i674wimbv7xqjnwlld4x3ndvh5dl4cdg7s1m24r"))))
844 (properties `((upstream-name . "V8")))
845 (build-system r-build-system)
848 (modify-phases %standard-phases
849 (add-after 'unpack 'find-v8
850 (lambda* (#:key inputs #:allow-other-keys)
851 (substitute* "configure"
853 (string-append "PKG_LIBS="
854 (assoc-ref inputs "libnode")
855 "/lib/libnode.so.64\n")))
856 (setenv "INCLUDE_DIR"
858 (assoc-ref inputs "libnode")
862 (assoc-ref inputs "libnode") "/lib")))))))
866 (list r-curl r-jsonlite r-rcpp))
869 (home-page "https://jeroen.cran.dev/V8")
870 (synopsis "Embedded JavaScript and WebAssembly engine for R")
872 "This package provides an R interface to V8: Google's JavaScript and
873 WebAssembly engine.")
874 (license license:expat)))
876 (define-public r-rvenn
883 (uri (cran-uri "RVenn" version))
886 "016m00xv59lkwm2is32v5nr4lw5a1ymdnz34r3ffflcv9bfrc6n4"))))
887 (properties `((upstream-name . "RVenn")))
888 (build-system r-build-system)
897 (native-inputs (list r-knitr))
898 (home-page "https://cran.r-project.org/package=RVenn")
899 (synopsis "Set operations for many sets")
901 "The base functions for set operations in @code{R} can be used for only two
902 sets. This package @code{RVenn} provides functions for dealing with multiple sets.
903 It uses @code{purr} to find the union, intersection and difference of three or
904 more sets. This package also provides functions for pairwise set operations among
905 several sets. Further, based on @code{ggplot2} and @code{ggforce}, a Venn diagram
906 can be drawn for two or three sets. For bigger data sets, a clustered heatmap
907 showing the presence or absence of the elements of the sets can be drawn based on
908 the @code{pheatmap} package. Finally, enrichment test can be applied to two sets
909 whether an overlap is statistically significant or not.")
910 (license license:gpl3)))
919 (uri (cran-uri "DOT" version))
922 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
923 (properties `((upstream-name . "DOT")))
924 (build-system r-build-system)
927 (home-page "http://haghish.com/dot")
928 (synopsis "Render and Export DOT Graphs in R")
930 "This package provides tools to render DOT diagram markup language in R
931 and also provides the possibility to export the graphs in PostScript and
932 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
933 programming packages such as @code{knitr} and @code{rmarkdown}.")
934 (license license:expat)))
936 (define-public r-carrier
943 (uri (cran-uri "carrier" version))
945 (base32 "0bqnwnnjqjk9q0lxq6kkz9s75ss10lfyyywyyi24m8wppxpw1vqc"))))
946 (properties `((upstream-name . "carrier")))
947 (build-system r-build-system)
949 (list r-pryr r-rlang))
950 (home-page "https://github.com/r-lib/carrier")
951 (synopsis "Isolate functions for remote execution")
953 "Sending functions to remote processes can be wasteful of resources
954 because they carry their environments with them. With this package, it is
955 easy to create functions that are isolated from their environment. These
956 isolated functions, also called crates, print to the console with their total
957 size and can be easily tested locally before being sent to a remote.")
958 (license license:gpl3)))
960 (define-public r-clipr
967 (uri (cran-uri "clipr" version))
970 "1s9vvv3cxnz8w11gsi8z9ddv9jzib5qf5qqxnwqrrv7vj8cr7hij"))))
971 (build-system r-build-system)
974 (home-page "https://github.com/mdlincoln/clipr")
975 (synopsis "Read and write from the system clipboard")
977 "This package provides simple utility functions to read from and write to
978 the system clipboards.")
979 (license license:gpl3)))
981 (define-public r-clvalid
987 (uri (cran-uri "clValid" version))
990 "18aiyjhnh5mfdxbzns4cy0r8bymfikhwkybpn4g04qhli5ls8z83"))))
991 (properties `((upstream-name . "clValid")))
992 (build-system r-build-system)
993 (propagated-inputs (list r-class r-cluster))
994 (home-page "https://cran.r-project.org/package=clValid")
995 (synopsis "Validation of clustering results")
997 "Statistical and biological validation of clustering results. This
998 package implements Dunn Index, Silhouette, Connectivity, Stability, BHI and
999 BSI. Further information can be found in Brock, G et al. (2008) <doi:
1000 10.18637/jss.v025.i04>.")
1001 (license license:lgpl3)))
1003 (define-public r-dlm
1010 (uri (cran-uri "dlm" version))
1012 (base32 "1aksm66sfa7ipl5xgs4j5giac7q2m744wjl40mva56xn6i674h4r"))))
1013 (properties `((upstream-name . "dlm")))
1014 (build-system r-build-system)
1015 (home-page "https://cran.r-project.org/package=dlm")
1016 (synopsis "Bayesian and Likelihood Analysis of Dynamic Linear Models")
1018 "This package provides routines for Maximum likelihood, Kalman filtering
1019 and smoothing, and Bayesian analysis of Normal linear State Space models, also
1020 known as Dynamic Linear Models.")
1021 (license license:gpl2+)))
1023 (define-public r-zoo
1029 (uri (cran-uri "zoo" version))
1032 "19cw09bhwj2qyd72765ym1cm2wmhh801ccif889nzq5gfpw513l4"))))
1033 (build-system r-build-system)
1036 (home-page "http://zoo.R-Forge.R-project.org/")
1037 (synopsis "S3 infrastructure for regular and irregular time series")
1038 (description "This package contains an S3 class with methods for totally
1039 ordered indexed observations. It is particularly aimed at irregular time
1040 series of numeric vectors/matrices and factors.")
1041 (license license:gpl2+)))
1043 (define-public r-fontawesome
1045 (name "r-fontawesome")
1050 (uri (cran-uri "fontawesome" version))
1052 (base32 "0c8sb8isiyn2gr3xfql75yyssf9wlb152cw67whq83aqsksgrvjd"))))
1053 (properties `((upstream-name . "fontawesome")))
1054 (build-system r-build-system)
1056 (list r-htmltools r-rlang))
1057 (home-page "https://github.com/rstudio/fontawesome")
1058 (synopsis "Easily work with Font Awesome icons")
1060 "Easily and flexibly insert Font Awesome icons into R Markdown documents
1061 and Shiny apps. These icons can be inserted into HTML content through inline
1062 SVG tags or @code{i} tags. There is also a utility function for exporting
1063 Font Awesome icons as PNG images for those situations where raster graphics
1065 (license license:expat)))
1067 (define-public r-fingerprint
1069 (name "r-fingerprint")
1074 (uri (cran-uri "fingerprint" version))
1076 (base32 "04jcwkydjrs31pia6kq8z2n9s54im950q08hs2ay15xjxxkmb8ic"))))
1077 (properties `((upstream-name . "fingerprint")))
1078 (build-system r-build-system)
1079 (home-page "https://cran.r-project.org/package=fingerprint")
1080 (synopsis "Functions to Operate on Binary Fingerprint Data")
1082 "This package provides functions to manipulate binary fingerprints of
1083 arbitrary length. A fingerprint is represented by an object of S4 class
1084 @code{fingerprint}. The bitwise logical functions in R are overridden so that
1085 they can be used directly with @code{fingerprint} objects. A number of
1086 distance metrics are also available. Fingerprints can be converted to
1087 Euclidean vectors (i.e., points on the unit hypersphere) and can also be
1088 folded. Arbitrary fingerprint formats can be handled via line handlers.
1089 Currently handlers are provided for CDK, MOE and BCI fingerprint data.")
1090 ;; Any version of the GPL
1091 (license (list license:gpl2+ license:gpl3+))))
1093 (define-public r-fpeek
1100 (uri (cran-uri "fpeek" version))
1102 (base32 "0kv46g21ndxchg3q8ynq7hjjkh6i2zlc21axn5y1jjzigrw047ii"))))
1103 (properties `((upstream-name . "fpeek")))
1104 (build-system r-build-system)
1105 (propagated-inputs (list r-rcpp))
1106 (home-page "https://github.com/davidgohel/fpeek")
1107 (synopsis "Check text files content at a glance")
1109 "This package provides tools to help working with text files. It can
1110 return the number of lines; print the first and last lines; convert encoding.
1111 Operations are made without reading the entire file before starting, resulting
1112 in good performances with large files.")
1113 (license license:expat)))
1115 (define-public r-ggalluvial
1117 (name "r-ggalluvial")
1121 (uri (cran-uri "ggalluvial" version))
1124 "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3"))))
1125 (properties `((upstream-name . "ggalluvial")))
1126 (build-system r-build-system)
1136 (home-page "http://corybrunson.github.io/ggalluvial/")
1137 (synopsis "Alluvial plots for ggplot2")
1138 (description "This package provides alluvial plots for @code{ggplot2}.
1139 Alluvial plots use variable-width ribbons and stacked bar plots to represent
1140 multi-dimensional or repeated-measures data with categorical or ordinal
1142 (license license:gpl3)))
1144 (define-public r-ggpp
1151 (uri (cran-uri "ggpp" version))
1154 "0wcaczxjav5yg8h2197cf288mqk13p3iq675q0x0di9g8lnblvk1"))))
1155 (properties `((upstream-name . "ggpp")))
1156 (build-system r-build-system)
1174 (home-page "https://docs.r4photobiology.info/ggpp/")
1175 (synopsis "Grammar extensions to ggplot2")
1177 "This package contains extensions to ggplot2.
1180 @item Geomas: @code{geom_table}, @code{geom_plot} and @code{geom_grob} add
1181 insets to plots using native data coordinates, while @code{geom_table_npc},
1182 @code{geom_plot_npc} and @code{geom_grob_npc} do the same using @code{npc}
1183 coordinates through new aesthetics @code{npcx} and @code{npcy}.
1184 @item Statistics: select observations based on 2D density.
1185 @item Positions: radial nudging away from a center point and nudging away from
1189 (license license:gpl2+)))
1191 (define-public r-ggprism
1197 (uri (cran-uri "ggprism" version))
1200 "09dh0r8r5s61i5dbk6rswajc2vm7k8wvlqyvzq8wr160676lycjp"))))
1201 (properties `((upstream-name . "ggprism")))
1202 (build-system r-build-system)
1211 (native-inputs (list r-knitr))
1212 (home-page "https://csdaw.github.io/ggprism/")
1213 (synopsis "ggplot2 extension inspired by GraphPad Prism")
1215 "This package provides various themes, palettes, and other functions that are
1216 used to customise ggplots to look like they were made in GraphPad Prism. The
1217 Prism-look is achieved with @code{theme_prism()} and
1218 @code{scale_fill|colour_prism()}, axes can be changed with custom guides like
1219 @code{guide_prism_minor()}, and significance indicators added with
1220 @code{add_pvalue()}.")
1221 (license license:gpl3+)))
1223 (define-public r-ggrastr
1229 (uri (cran-uri "ggrastr" version))
1232 "07sx5wlawfyb0zy5am2q1ajhkdym5r9ih47p57l8bv4dlc7ykml2"))))
1233 (properties `((upstream-name . "ggrastr")))
1234 (build-system r-build-system)
1235 (propagated-inputs (list r-cairo r-ggbeeswarm r-ggplot2 r-png r-ragg))
1236 (native-inputs (list r-knitr))
1237 (home-page "https://github.com/VPetukhov/ggrastr")
1238 (synopsis "Rasterize layers for ggplot2")
1240 "Rasterize only specific layers of a ggplot2 plot while simultaneously keeping
1241 all labels and text in vector format. This allows users to keep plots within
1242 the reasonable size limit without losing vector properties of the
1243 scale-sensitive information.")
1244 (license license:expat)))
1246 (define-public r-ggvenn
1252 (uri (cran-uri "ggvenn" version))
1255 "0bm52j3idchignp6nrw7c76jlbfkjf5zng258957vq019vx9qxrq"))))
1256 (properties `((upstream-name . "ggvenn")))
1257 (build-system r-build-system)
1258 (propagated-inputs (list r-dplyr r-ggplot2))
1259 (home-page "https://cran.r-project.org/package=ggvenn")
1260 (synopsis "Draw Venn diagram with ggplot2")
1262 "This package offers an easy to use way to draw a Venn diagram with
1264 (license license:expat)))
1266 (define-public r-ggvenndiagram
1268 (name "r-ggvenndiagram")
1273 (uri (cran-uri "ggVennDiagram" version))
1276 "1l4cincm7c2q9x3djiv1lm9bvivaqk7kincx19b8f760wz9hp74k"))))
1277 (properties `((upstream-name . "ggVennDiagram")))
1278 (build-system r-build-system)
1289 (native-inputs (list r-knitr))
1290 (home-page "https://github.com/gaospecial/ggVennDiagram")
1291 (synopsis "Implementention of the Venn diagram using ggplot2")
1293 "This package implements easy-to-use functions to generate 2-7 sets Venn
1294 plot in publication quality. @code{ggVennDiagram} plot Venn using
1295 well-defined geometry dataset and @code{ggplot2}. The shapes of 2-4 sets Venn
1296 use circles and ellipses, while the shapes of 4-7 sets Venn use irregular
1297 polygons (4 has both forms), which are developed and imported from another
1298 package @code{venn}. We provide internal functions to integrate shape data
1299 with user provided sets data, and calculated the geometry of every
1300 regions/intersections of them, then separately plot Venn in three components:
1301 set edges, set labels, and regions. From version 1.0, it is possible to
1302 customize these components as you demand in ordinary @code{ggplot2} grammar.")
1303 (license license:gpl3)))
1305 (define-public r-lmds
1312 (uri (cran-uri "lmds" version))
1314 (base32 "130azb0nc2wwxv0qi8v5s4rd02p9lc92zwn634pv7b8awbw81i65"))))
1315 (properties `((upstream-name . "lmds")))
1316 (build-system r-build-system)
1318 (list r-assertthat r-dynutils r-irlba r-matrix))
1319 (home-page "https://github.com/dynverse/lmds")
1320 (synopsis "Landmark multi-dimensional scaling")
1322 "This package provides a fast dimensionality reduction method scalable
1323 to large numbers of samples. @dfn{Landmark Multi-Dimensional Scaling} (LMDS)
1324 is an extension of classical Torgerson MDS, but rather than calculating a
1325 complete distance matrix between all pairs of samples, only the distances
1326 between a set of landmarks and the samples are calculated.")
1327 (license license:gpl3)))
1329 (define-public r-lmodel2
1336 (uri (cran-uri "lmodel2" version))
1338 (base32 "1fiin2nkffbihz1s8ixmw9lgf8mn3j9krr8iiflizk10mdv54hnb"))))
1339 (properties `((upstream-name . "lmodel2")))
1340 (build-system r-build-system)
1341 (home-page "https://cran.r-project.org/package=lmodel2")
1342 (synopsis "Model II regression")
1344 "This package computes model II simple linear regression using
1345 @dfn{ordinary least squares} (OLS), @dfn{major axis} (MA), @dfn{standard major
1346 axis} (SMA), and @dfn{ranged major axis} (RMA).")
1347 (license license:gpl2)))
1349 (define-public r-ggpmisc
1355 (uri (cran-uri "ggpmisc" version))
1358 "1i7cfmhmgih3hn0zr5yn33ziznfa3a4j8hkn237bv7jckwzpklxw"))))
1359 (build-system r-build-system)
1378 (home-page "https://www.r4photobiology.info/")
1379 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
1380 (description "This package provides extensions to @code{ggplot2},
1381 respecting the grammar of its graphics paradigm.")
1382 (license license:gpl2+)))
1384 (define-public r-ggside
1390 (uri (cran-uri "ggside" version))
1393 "1vl7kzgmi5xxxsqvyg4cm4xwd3lfjgysay1lw6hri5vj22mnga5h"))))
1394 (properties `((upstream-name . "ggside")))
1395 (build-system r-build-system)
1403 (native-inputs (list r-knitr))
1404 (home-page "https://cran.r-project.org/package=ggside")
1405 (synopsis "Side grammar graphics that extends @code{ggplot2}")
1407 "The grammar of graphics as shown in @code{ggplot2} has provided an
1408 expressive API for users to build plots. This package @{ggside} extends
1409 @code{ggplot2} by allowing users to add graphical information about one of the
1410 main panel's axis using a familiar @code{ggplot2} style API with tidy data.
1411 This package is particularly useful for visualizing metadata on a discrete
1412 axis, or summary graphics on a continuous axis such as a boxplot or a density
1414 (license license:expat)))
1416 (define-public r-gprofiler
1418 (name "r-gprofiler")
1423 (uri (cran-uri "gProfileR" version))
1426 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
1427 (properties `((upstream-name . "gProfileR")))
1428 (build-system r-build-system)
1430 (list r-plyr r-rcurl))
1431 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
1432 (synopsis "Interface to the g:Profiler toolkit")
1434 "This package provides tools for functional enrichment analysis,
1435 gene identifier conversion and mapping homologous genes across related
1436 organisms via the @code{g:Profiler} toolkit.")
1437 (license license:gpl2+)))
1439 (define-public r-gprofiler2
1441 (name "r-gprofiler2")
1446 (uri (cran-uri "gprofiler2" version))
1449 "0r0h34b35xzgd9rh55yndn0anxy0z45zdlqa6qfmpn91b6v1bb1g"))))
1450 (properties `((upstream-name . "gprofiler2")))
1451 (build-system r-build-system)
1462 (native-inputs (list r-knitr))
1463 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
1464 (synopsis "Interface to the g:Profiler toolset")
1466 "This package provides a toolset for functional enrichment analysis and
1467 visualization, gene/protein/SNP identifier conversion and mapping orthologous
1468 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
1472 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
1474 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
1476 @item @code{g:Orth}, orthology search across species;
1477 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
1478 genes and variant effects.
1481 This package is an R interface corresponding to the 2019 update of
1482 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
1484 (license license:gpl2+)))
1486 (define-public r-oenb
1493 (uri (cran-uri "oenb" version))
1496 "1jgxw7ycx2lcdzglg9nix8k08fs4r6i5jdsjzrd6w1dg6smsinl5"))))
1497 (properties `((upstream-name . "oenb")))
1498 (build-system r-build-system)
1500 (list r-dplyr r-xml))
1501 (native-inputs (list r-knitr))
1502 (home-page "https://github.com/franzmohr/oenb")
1503 (synopsis "Tools for the OeNB Data Web Service")
1505 "Tools to access data from the data web service of the
1506 @acronym{OeNB, Oesterreichische Nationalbank},
1507 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
1508 (license license:gpl2+)))
1510 (define-public r-orgmassspecr
1512 (name "r-orgmassspecr")
1516 (uri (cran-uri "OrgMassSpecR" version))
1519 "1dx9d8rb1dfqyhyc26zhfnxiv3rz2ikvs2mwqnsrq3lsjs9dvyc8"))))
1520 (properties `((upstream-name . "OrgMassSpecR")))
1521 (build-system r-build-system)
1522 (native-inputs (list r-knitr))
1523 (home-page "http://OrgMassSpec.github.io/")
1524 (synopsis "Organic or biological mass spectrometry data analysis")
1526 "This package @code{OrgMassSpecR} is an extension of the @code{R}
1527 statistical computing language. It contains functions to assist with organic
1528 or biological mass spectrometry data analysis. Mass spectral libraries are
1529 available as companion packages.")
1530 (license license:bsd-2)))
1532 (define-public r-scales
1539 (uri (cran-uri "scales" version))
1541 (base32 "027daznawr9dy0z9s99lh64i4am691hdir01n7gr7vmgpmnkwiar"))))
1542 (build-system r-build-system)
1552 (home-page "https://github.com/hadley/scales")
1553 (synopsis "Scale functions for visualization")
1555 "This package provides graphical scales that map data to aesthetics, and
1556 provides methods for automatically determining breaks and labels for axes and
1558 (license license:expat)))
1560 (define-public r-pacman
1566 (uri (cran-uri "pacman" version))
1569 "0z7gngd6h83cpjhq1vg75wvzhdjbgjh7gj5d4zvvi9gd2lmagjcy"))))
1570 (build-system r-build-system)
1573 (home-page "https://github.com/trinker/pacman")
1574 (synopsis "Package Management Tool")
1575 (description "This package provides tools to more conveniently perform
1576 tasks associated with add-on packages. @code{pacman} conveniently wraps
1577 library and package related functions and names them in an intuitive and
1578 consistent fashion. It seeks to combine functionality from lower level
1579 functions which can speed up workflow.")
1580 (license license:gpl2)))
1582 (define-public r-paralleldist
1584 (name "r-paralleldist")
1589 (uri (cran-uri "parallelDist" version))
1591 (base32 "01ly4hxwa64a0ya5gla8rvv72s9mcknsfznivjkh937pbjwb7iih"))))
1592 (properties `((upstream-name . "parallelDist")))
1593 (build-system r-build-system)
1594 (propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppparallel))
1595 (home-page "https://github.com/alexeckert/parallelDist")
1596 (synopsis "Parallel Distance Matrix Computation using multiple threads")
1598 "This package provides a fast parallelized alternative to R's native
1599 @code{dist} function to calculate distance matrices for continuous, binary,
1600 and multi-dimensional input matrices, which supports a broad variety of
1601 predefined distance functions from other R packages, as well as user- defined
1602 functions written in C++. For ease of use, the @code{parDist} function
1603 extends the signature of the @code{dist} function and uses the same parameter
1604 naming conventions as distance methods of existing R packages.")
1605 (license license:gpl2+)))
1607 (define-public r-pheatmap
1614 (uri (cran-uri "pheatmap" version))
1617 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
1618 (build-system r-build-system)
1620 (list r-gtable r-rcolorbrewer r-scales))
1621 (home-page "https://cran.r-project.org/web/packages/pheatmap")
1622 (synopsis "Pretty heatmaps")
1624 "This package provides an implementation of heatmaps that offers more
1625 control over dimensions and appearance.")
1626 (license license:gpl2+)))
1628 (define-public r-philentropy
1630 (name "r-philentropy")
1634 (uri (cran-uri "philentropy" version))
1637 "1dpf4hfflp4mcql4na46wzcq1flabkipiwyycz9wj5xbxlmcz2hk"))))
1638 (properties `((upstream-name . "philentropy")))
1639 (build-system r-build-system)
1640 (propagated-inputs (list r-kernsmooth r-poorman r-rcpp))
1641 (native-inputs (list r-knitr))
1642 (home-page "https://github.com/drostlab/philentropy")
1644 "Similarity and distance quantification between probability functions")
1646 "This package computes optimized distance and similarity measures for
1647 comparing probability functions (Drost (2018) <doi:10.21105/joss.00765>).
1648 These comparisons between probability functions have their foundations in a
1649 broad range of scientific disciplines from mathematics to ecology. The aim of
1650 this package is to provide a core framework for clustering, classification,
1651 statistical inference, goodness-of-fit, non-parametric statistics, information
1652 theory, and machine learning tasks that are based on comparing univariate or
1653 multivariate probability functions.")
1654 (license license:gpl2)))
1656 (define-public r-pnwcolors
1658 (name "r-pnwcolors")
1663 (uri (cran-uri "PNWColors" version))
1666 "1phplnclkficfv8s6wsyrckk4ixzbayiy5iix6dddg40485l9nyj"))))
1667 (properties `((upstream-name . "PNWColors")))
1668 (build-system r-build-system)
1669 (home-page "https://github.com/jakelawlor/PNWColors")
1670 (synopsis "Color palettes for data visualizations")
1672 "This package provides color palettes. They are checked for colorblind
1673 accessibility from hue, saturation, and lightness value scaling using the
1674 Chroma.js Color Palette Helper. See @url{https://gka.github.io/palettes}.")
1675 (license license:cc0)))
1677 (define-public r-plotfunctions
1679 (name "r-plotfunctions")
1684 (uri (cran-uri "plotfunctions" version))
1686 (base32 "0asmxw8283fpvl83h478j5nyg59xqifqaa8f2f6l199gvvswhhg2"))))
1687 (properties `((upstream-name . "plotfunctions")))
1688 (build-system r-build-system)
1689 (native-inputs (list r-knitr))
1690 (home-page "https://jacolienvanrij.com/tutorials.html")
1691 (synopsis "Various functions to facilitate visualization of data and analysis")
1693 "When analyzing data, plots are a helpful tool for visualizing data and
1694 interpreting statistical models. This package provides a set of simple tools
1695 for building plots incrementally, starting with an empty plot region, and
1696 adding bars, data points, regression lines, error bars, gradient legends,
1697 density distributions in the margins, and even pictures. The package builds
1698 further on R graphics by simply combining functions and settings in order to
1699 reduce the amount of code to produce for the user. As a result, the package
1700 does not use formula input or special syntax, but can be used in combination
1701 with default R plot functions.")
1702 (license license:gpl2+)))
1704 (define-public r-polychrome
1706 (name "r-polychrome")
1711 (uri (cran-uri "Polychrome" version))
1713 (base32 "0hyi02m2jpdhk1ky6ihz6dv5pwqwjwk4csjim2qr8ywx8midmrvg"))))
1714 (properties `((upstream-name . "Polychrome")))
1715 (build-system r-build-system)
1717 (list r-colorspace r-scatterplot3d))
1720 (home-page "http://oompa.r-forge.r-project.org/")
1721 (synopsis "Qualitative palettes with many colors")
1723 "This package provides tools for creating, viewing, and assessing
1724 qualitative palettes with many (20-30 or more) colors. See Coombes and
1725 colleagues (2019) @url{https://doi:10.18637/jss.v090.c01}.")
1726 (license license:asl2.0)))
1728 (define-public r-polylabelr
1730 (name "r-polylabelr")
1734 (uri (cran-uri "polylabelr" version))
1737 "01b2v0l5g8nxwbd6nwqv8ahypgh6gfhd4qabg75brlj7z1iyfzf2"))))
1738 (properties `((upstream-name . "polylabelr")))
1739 (build-system r-build-system)
1740 (propagated-inputs (list r-rcpp))
1741 (home-page "https://github.com/jolars/polylabelr")
1742 (synopsis "Finding pole of inaccessibility (visual center) of a polygon")
1744 "This package provides a wrapper around the @code{C++} library @code{
1745 polylabel} from @code{Mapbox}, providing an efficient routine for finding the
1746 approximate pole of inaccessibility of a polygon, which usually serves as an
1747 excellent candidate for labeling of a polygon.")
1748 (license license:expat)))
1750 (define-public r-poorman
1756 (uri (cran-uri "poorman" version))
1759 "0x1pk00ca7wjxnqfh1jphgsxcrq37s0c1nawv52yh5qgc4z0m3ij"))))
1760 (properties `((upstream-name . "poorman")))
1761 (build-system r-build-system)
1762 (native-inputs (list r-knitr))
1763 (home-page "https://nathaneastwood.github.io/poorman/")
1764 (synopsis "Dependency-free recreation of dplyr")
1766 "This package provides a replication of key functionality from
1767 @code{dplyr} and the wider @code{tidyverse} using only @code{base}.")
1768 (license license:expat)))
1770 (define-public r-ecp
1776 (uri (cran-uri "ecp" version))
1779 "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8"))))
1780 (build-system r-build-system)
1783 (home-page "https://cran.r-project.org/web/packages/ecp/")
1784 (synopsis "Multiple change-point analysis of multivariate data")
1786 "This package implements various procedures for finding multiple
1787 change-points. Two methods make use of dynamic programming and pruning, with
1788 no distributional assumptions other than the existence of certain absolute
1789 moments in one method. Hierarchical and exact search methods are included.
1790 All methods return the set of estimated change-points as well as other summary
1792 (license license:gpl2+)))
1794 (define-public r-ellipsis
1801 (uri (cran-uri "ellipsis" version))
1804 "0n0mm9jngklv7j9wa64jdji035z0smmnsp2dfwcz9isrxgjnc0m9"))))
1805 (build-system r-build-system)
1808 (home-page "https://github.com/hadley/ellipsis")
1809 (synopsis "Tools for working with additional arguments")
1811 "In S3 generics, it's useful to take @code{...} so that methods can have
1812 additional arguments. But this flexibility comes at a cost: misspelled
1813 arguments will be silently ignored. The @code{ellipsis} package is an
1814 experiment that allows a generic to warn if any arguments passed in @code{...}
1816 (license license:gpl3)))
1825 (uri (cran-uri "GA" version))
1827 (base32 "135z03lnbj44jihnk6dii5a684jmc666ncpdwyyi910vl4sccib2"))))
1828 (properties `((upstream-name . "GA")))
1829 (build-system r-build-system)
1839 (home-page "https://luca-scr.github.io/GA/")
1840 (synopsis "Genetic algorithms for stochastic optimisation")
1842 "Flexible general-purpose toolbox implementing genetic algorithms (GAs)
1843 for stochastic optimisation. Binary, real-valued, and permutation
1844 representations are available to optimize a fitness function, i.e., a function
1845 provided by users depending on their objective function. Several genetic
1846 operators are available and can be combined to explore the best settings for
1847 the current task. Furthermore, users can define new genetic operators and
1848 easily evaluate their performances. Local search using general-purpose
1849 optimisation algorithms can be applied stochastically to exploit interesting
1850 regions. GAs can be run sequentially or in parallel, using an explicit
1851 master-slave parallelisation or a coarse-grain islands approach.")
1852 (license license:gpl2+)))
1854 (define-public r-grr
1861 (uri (cran-uri "grr" version))
1864 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
1865 (build-system r-build-system)
1866 (home-page "https://cran.r-project.org/web/packages/grr")
1867 (synopsis "Alternative implementations of base R functions")
1869 "This package provides alternative implementations of some base R
1870 functions, including @code{sort}, @code{order}, and @code{match}. The
1871 functions are simplified but can be faster or have other advantages.")
1872 (license license:gpl3)))
1874 (define-public r-matrix-utils
1876 (name "r-matrix-utils")
1881 (uri (cran-uri "Matrix.utils" version))
1884 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
1885 (properties `((upstream-name . "Matrix.utils")))
1886 (build-system r-build-system)
1888 (list r-grr r-matrix))
1889 (home-page "https://github.com/cvarrichio/Matrix.utils")
1891 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
1893 "This package implements data manipulation methods such as @code{cast},
1894 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
1896 (license license:gpl3)))
1898 (define-public r-mboost
1904 (uri (cran-uri "mboost" version))
1907 "01ln0vxbbx1fq77q17sx61si82lhfibbchsnf2yw9032cn8wnhh2"))))
1908 (build-system r-build-system)
1917 (home-page "https://github.com/boost-R/mboost")
1918 (synopsis "Model-based boosting")
1920 "This package provides a functional gradient descent algorithm (boosting)
1921 for optimizing general risk functions utilizing component-wise (penalised)
1922 least squares estimates or regression trees as base-learners for fitting
1923 generalized linear, additive and interaction models to potentially
1924 high-dimensional data.")
1925 (license license:gpl2)))
1927 (define-public r-shadowtext
1929 (name "r-shadowtext")
1933 (uri (cran-uri "shadowtext" version))
1936 "0zdfidrcnmxmfhngv86ppxrjmpmz9kl78l4yfah2lc5vgmrlwg15"))))
1937 (properties `((upstream-name . "shadowtext")))
1938 (build-system r-build-system)
1940 (list r-ggplot2 r-scales))
1943 (home-page "https://github.com/GuangchuangYu/shadowtext/")
1944 (synopsis "Shadow text grob and layer")
1945 (description "This package implements @code{shadowtextGrob()} for
1946 @code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}.
1947 These functions draw text grob with background shadow.")
1948 (license license:artistic2.0)))
1950 (define-public r-sys
1957 (uri (cran-uri "sys" version))
1960 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p"))))
1961 (build-system r-build-system)
1962 (home-page "https://github.com/jeroen/sys")
1963 (synopsis "Powerful and reliable tools for running system commands in R")
1965 "This package provides drop-in replacements for the base @code{system2()}
1966 function with fine control and consistent behavior across platforms. It
1967 supports clean interruption, timeout, background tasks, and streaming STDIN /
1968 STDOUT / STDERR over binary or text connections. The package also provides
1969 functions for evaluating expressions inside a temporary fork. Such
1970 evaluations have no side effects on the main R process, and support reliable
1971 interrupts and timeouts. This provides the basis for a sandboxing
1973 (license license:expat)))
1975 (define-public r-ashr
1981 (uri (cran-uri "ashr" version))
1984 "177xs3apnc6yy6737qqv4z8snf0hkpbghab63hrplbyb9wfssfga"))))
1985 (properties `((upstream-name . "ashr")))
1986 (build-system r-build-system)
1997 (home-page "https://github.com/stephens999/ashr")
1998 (synopsis "Methods for adaptive shrinkage, using empirical bayes")
1999 (description "This package implements an empirical Bayes approach for
2000 large-scale hypothesis testing and false discovery rate estimation.")
2001 (license license:gpl3+)))
2003 (define-public r-askpass
2010 (uri (cran-uri "askpass" version))
2013 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
2014 (build-system r-build-system)
2015 (propagated-inputs (list r-sys))
2016 (home-page "https://github.com/jeroen/askpass")
2017 (synopsis "Safe password entry for R")
2019 "This package provides cross-platform utilities for prompting the user
2020 for credentials or a passphrase, for example to authenticate with a server or
2021 read a protected key.")
2022 (license license:expat)))
2024 (define-public r-astsa
2031 (uri (cran-uri "astsa" version))
2033 (base32 "09872vkqb180cwprdfr3cn85jhazlc4vjdj6pjc70s06bh834f3w"))))
2034 (properties `((upstream-name . "astsa")))
2035 (build-system r-build-system)
2036 (home-page "https://github.com/nickpoison/astsa/")
2037 (synopsis "Applied statistical time series analysis")
2039 "This package provides data sets and scripts to accompany Time Series
2040 Analysis and Its Applications: With R Examples (4th ed), by R.H. Shumway and
2041 D.S. Stoffer. Springer Texts in Statistics, 2017,
2042 @url{https://doi.org/10.1007/978-3-319-52452-8}, and Time Series: A Data
2043 Analysis Approach Using R. Chapman-Hall, 2019,
2044 @url{https://doi.org/10.1201/9780429273285}.")
2045 (license license:gpl3)))
2047 (define-public r-vegan
2054 (uri (cran-uri "vegan" version))
2057 "0nf0ny6jzfy135xiygzzkr0y55y8g27hrbk8c869plarr48d2xxb"))))
2058 (build-system r-build-system)
2060 (list r-knitr ; needed for vignettes
2063 (list r-cluster r-lattice r-mass r-mgcv r-permute))
2064 (home-page "https://cran.r-project.org/web/packages/vegan")
2065 (synopsis "Functions for community ecology")
2067 "The vegan package provides tools for descriptive community ecology. It
2068 has most basic functions of diversity analysis, community ordination and
2069 dissimilarity analysis. Most of its multivariate tools can be used for other
2070 data types as well.")
2071 (license license:gpl2+)))
2073 (define-public r-tidyverse
2075 (name "r-tidyverse")
2080 (uri (cran-uri "tidyverse" version))
2083 "0qfgq4p2aq95j39xd5kcing2cacy7rzy7f6zf0bnpsa95svziyrp"))))
2084 (build-system r-build-system)
2117 (home-page "https://tidyverse.tidyverse.org")
2118 (synopsis "Install and load packages from the \"Tidyverse\"")
2120 "The @code{tidyverse} is a set of packages that work in harmony because
2121 they share common data representations and API design. This package is
2122 designed to make it easy to install and load multiple tidyverse packages in a
2124 (license license:gpl3)))
2126 (define-public r-rvest
2133 (uri (cran-uri "rvest" version))
2135 (base32 "07hws9infwchy19smrcd9m6c0jii0bdn335yxqk3ramgj5ryyrd4"))))
2136 (build-system r-build-system)
2150 (home-page "https://github.com/hadley/rvest")
2151 (synopsis "Simple web scraping for R")
2153 "@code{r-rvest} helps you scrape information from web pages. It is
2154 designed to work with @code{magrittr} to make it easy to express common web
2155 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
2156 (license license:gpl3)))
2158 (define-public r-selectr
2165 (uri (cran-uri "selectr" version))
2167 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
2168 (build-system r-build-system)
2170 (list r-stringr r-r6))
2171 (home-page "https://sjp.co.nz/projects/selectr/")
2172 (synopsis "Translate CSS selectors to XPath expressions")
2174 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
2175 expression. This allows you to use CSS selectors when working with the XML
2176 package as it can only evaluate XPath expressions. Also provided are
2177 convenience functions useful for using CSS selectors on XML nodes. This
2178 package is a port of the Python package @code{cssselect}.")
2179 (license license:bsd-3)))
2181 (define-public r-reprex
2188 (uri (cran-uri "reprex" version))
2191 "14khx09yzn97xhags48lvym1g37h1l2ymvw6r1jlldhjc7i1cnx8"))))
2192 (build-system r-build-system)
2207 (home-page "https://github.com/tidyverse/reprex")
2208 (synopsis "Prepare reproducible R code examples for sharing")
2210 "This package provides a convenience wrapper that uses the
2211 @code{rmarkdown} package to render small snippets of code to target formats
2212 that include both code and output. The goal is to encourage the sharing of
2213 small, reproducible, and runnable examples on code-oriented websites or email.
2214 @code{reprex} also extracts clean, runnable R code from various common formats,
2215 such as copy/paste from an R session.")
2216 (license license:expat)))
2218 (define-public r-reordercluster
2220 (name "r-reordercluster")
2224 (uri (cran-uri "ReorderCluster" version))
2227 "0zq143xvv2br7016f9b1501ymcpkjqm3al1dn5qfm21axyi2p1iq"))))
2228 (build-system r-build-system)
2230 (list r-gplots r-gtools r-rcpp))
2231 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
2232 (synopsis "Reordering the dendrogram according to the class labels")
2233 (description "This package provides tools for performing the leaf reordering
2234 for the dendrogram that preserves the hierarchical clustering result and at the
2235 same time tries to group instances from the same class together.")
2236 (license license:gpl3+)))
2238 (define-public r-callr
2245 (uri (cran-uri "callr" version))
2248 "01q3b0w1cbrryvv1dwvnyd3j1f09xmhnwg1wskc51r3r4qhqmnhj"))))
2249 (build-system r-build-system)
2251 (list r-r6 r-processx))
2252 (home-page "https://github.com/r-lib/callr#readme")
2253 (synopsis "Call R from R")
2255 "It is sometimes useful to perform a computation in a separate R process,
2256 without affecting the current R process at all. This package does exactly
2258 (license license:expat)))
2260 (define-public r-depmixs4
2266 (uri (cran-uri "depmixS4" version))
2269 "1pacvhw5m4fsk3ysbal50fdqbvlaz8ywyqp6bn1wh42wipqbb2i8"))))
2271 (list r-nnet r-nlme r-mass r-rsolnp))
2272 (build-system r-build-system)
2273 (home-page "https://cran.r-project.org/web/packages/depmixS4/")
2274 (synopsis "Dependent Mixture Models")
2275 (description "This package fits latent (hidden) Markov models on mixed
2276 categorical and continuous (time series) data, otherwise known as dependent
2278 (license license:gpl2+)))
2280 (define-public r-readxl
2287 (uri (cran-uri "readxl" version))
2290 "1ym11mldwj31lgk5av264v8b2zn7fmq5nd30rnm1pchgjizvpgpn"))))
2291 (build-system r-build-system)
2293 (list r-cellranger r-cpp11 r-progress r-tibble))
2296 (home-page "https://readxl.tidyverse.org")
2297 (synopsis "Read Excel files")
2299 "This package lets you import Excel files into R. It supports
2300 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
2301 the embedded @code{RapidXML} C++ library.")
2302 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
2303 ;; 'rapidxml' which is Boost.
2304 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
2306 (define-public r-model4you
2308 (name "r-model4you")
2312 (uri (cran-uri "model4you" version))
2315 "0pni9v3nradvy8sp2m07903vc7z610xrh426lf19dxss12kgrfi8"))))
2316 (build-system r-build-system)
2324 (home-page "https://cran.r-project.org/web/packages/model4you/")
2325 (synopsis "Stratified and personalised models based on trees and forests")
2327 "This package provides procedures for model-based trees for subgroup
2328 analyses in clinical trials and model-based forests for the estimation and
2329 prediction of personalised treatment effects. Currently partitioning of linear
2330 models, @code{lm()}, generalised linear models, @code{glm()}, and
2331 Weibull models, @code{survreg()}, are supported. Advanced plotting functionality is
2332 supported for the trees and a test for parameter heterogeneity is provided for
2333 the personalised models.")
2334 (license license:gpl2+)))
2336 (define-public r-modelr
2343 (uri (cran-uri "modelr" version))
2346 "1jd9vxirj5ii4ac0ka07g0rcq1c8yqv06jg27nmvp5a6kvlgvs8h"))))
2347 (build-system r-build-system)
2357 (home-page "https://github.com/tidyverse/modelr")
2358 (synopsis "Helper functions for modelling in pipelines")
2360 "Functions for modelling that help you seamlessly integrate modelling
2361 into a pipeline of data manipulation and visualisation.")
2362 (license license:gpl3)))
2364 (define-public r-hmm
2370 (uri (cran-uri "HMM" version))
2373 "03b548bnwqpnd7zypb4gvy9chyi5li2hp99a9vrh4qszxg2ihas7"))))
2374 (properties `((upstream-name . "HMM")))
2375 (build-system r-build-system)
2376 (home-page "https://cran.r-project.org/web/packages/HMM/")
2377 (synopsis "Hidden Markov Models")
2378 (description "This package provides an easy to use library to setup, apply
2379 and make inference with discrete time and discrete space hidden Markov
2381 (license license:gpl2+)))
2383 (define-public r-hiddenmarkov
2385 (name "r-hiddenmarkov")
2389 (uri (cran-uri "HiddenMarkov" version))
2392 "05dm3nl0ffsz2ziw3bz5bivyxk7r5bxs8xhky3hz660qaqzd51ki"))))
2393 (build-system r-build-system)
2396 (home-page "https://cran.r-project.org/web/packages/HiddenMarkov/")
2397 (synopsis "Hidden markov models for R")
2398 (description "This package contains functions for the analysis of Discrete
2399 Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated
2400 Poisson Process. It includes functions for simulation, parameter estimation,
2401 and the Viterbi algorithm. The algorithms are based of those of Walter
2403 (license license:gpl2+)))
2405 (define-public r-httpuv
2411 (uri (cran-uri "httpuv" version))
2414 "14qjf7bpl7pay89b7vi2vccl342q8xs6101a9x6qijy54k9myfa1"))
2415 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
2416 ;; only contains fixes for building on Solaris.
2417 (patches (search-patches "r-httpuv-1.6.6-unvendor-libuv.patch"))
2418 (modules '((guix build utils)))
2419 ;; Cannot unbundle http-parser, because it contains local
2422 '(delete-file-recursively "src/libuv"))))
2423 (build-system r-build-system)
2426 (modify-phases %standard-phases
2427 (add-after 'unpack 'unbundle-libuv
2428 (lambda* (#:key outputs #:allow-other-keys)
2429 (substitute* (find-files "src" "\\.cpp$|\\.h$")
2430 (("\"libuv/include/uv\\.h\"")
2432 ;; Fix https://github.com/rstudio/httpuv/issues/282
2433 (substitute* "src/http.cpp"
2434 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
2435 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);")))))))
2439 (list r-later r-promises r-r6 r-rcpp))
2440 (home-page "https://github.com/rstudio/httpuv")
2441 (synopsis "HTTP and WebSocket server library for R")
2443 "The httpuv package provides low-level socket and protocol support for
2444 handling HTTP and WebSocket requests directly from within R. It is primarily
2445 intended as a building block for other packages, rather than making it
2446 particularly easy to create complete web applications using httpuv alone.")
2447 ;; This package includes third-party code that was originally released
2448 ;; under various non-copyleft licenses. Full licensing information can be
2449 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
2450 (license license:gpl3+)))
2452 (define-public r-jsonlite
2458 (uri (cran-uri "jsonlite" version))
2461 "0k6dal7gmm19jl5sjsry5gwbnhsbrnn00q3iixig8k6bxgpr463v"))))
2462 (build-system r-build-system)
2465 (home-page "https://arxiv.org/abs/1403.2805")
2466 (synopsis "Robust, high performance JSON parser and generator for R")
2468 "The jsonlite package provides a fast JSON parser and generator optimized
2469 for statistical data and the web. It offers flexible, robust, high
2470 performance tools for working with JSON in R and is particularly powerful for
2471 building pipelines and interacting with a web API. In addition to converting
2472 JSON data from/to R objects, jsonlite contains functions to stream, validate,
2473 and prettify JSON data. The unit tests included with the package verify that
2474 all edge cases are encoded and decoded consistently for use with dynamic data
2475 in systems and applications.")
2476 (license license:expat)))
2478 (define-public r-servr
2484 (uri (cran-uri "servr" version))
2487 "11x0857m3xzdbzr4z0vx4fcdk36arfagyf2qgamvprich0qisknr"))))
2488 (build-system r-build-system)
2490 (list r-httpuv r-jsonlite r-mime r-xfun))
2491 (home-page "https://github.com/yihui/servr")
2492 (synopsis "Simple HTTP server to serve static files or dynamic documents")
2494 "Servr provides an HTTP server in R to serve static files, or dynamic
2495 documents that can be converted to HTML files (e.g., R Markdown) under a given
2497 (license license:expat)))
2499 (define-public r-howmany
2505 (uri (cran-uri "howmany" version))
2508 "045ck8qahfg2swbgyf7dpl32ryq1m4sbalhr7m5qdgpm62vz8h7f"))))
2509 (build-system r-build-system)
2510 (home-page "https://cran.r-project.org/web/packages/howmany/")
2511 (synopsis "Lower bound for the number of correct rejections")
2512 (description "When testing multiple hypotheses simultaneously, this package
2513 provides functionality to calculate a lower bound for the number of correct
2514 rejections (as a function of the number of rejected hypotheses), which holds
2515 simultaneously -with high probability- for all possible number of rejections.
2516 As a special case, a lower bound for the total number of false null hypotheses
2517 can be inferred. Dependent test statistics can be handled for multiple tests
2518 of associations. For independent test statistics, it is sufficient to provide
2519 a list of p-values.")
2520 (license license:gpl2+)))
2522 (define-public r-htmltools
2524 (name "r-htmltools")
2528 (uri (cran-uri "htmltools" version))
2531 "0krjyz99q7zvdfg60b128c0zwr36h54gb05jw9c874d8kqv1ni9c"))))
2532 (build-system r-build-system)
2534 (list r-base64enc r-digest r-fastmap r-rlang))
2535 (home-page "https://cran.r-project.org/web/packages/htmltools")
2536 (synopsis "R tools for HTML")
2538 "This package provides tools for HTML generation and output in R.")
2539 (license license:expat)))
2541 (define-public r-htmlwidgets
2543 (name "r-htmlwidgets")
2547 (uri (cran-uri "htmlwidgets" version))
2550 "1hgz8sx8xrvfcdwa4q15k942w4qsqg8lyxbbf7qyfzbi807wcgqs"))))
2551 (build-system r-build-system)
2553 (list r-htmltools r-jsonlite r-yaml))
2556 (home-page "https://github.com/ramnathv/htmlwidgets")
2557 (synopsis "HTML Widgets for R")
2559 "HTML widgets is a framework for creating HTML widgets that render in
2560 various contexts including the R console, R Markdown documents, and Shiny web
2562 (license license:expat)))
2564 (define-public r-htmltable
2566 (name "r-htmltable")
2571 (uri (cran-uri "htmlTable" version))
2573 (base32 "14qg65nw0bpikqs1hb1x7apzdzrnnl3ykjnks67kkp46v1skwzrs"))))
2574 (properties `((upstream-name . "htmlTable")))
2575 (build-system r-build-system)
2586 (home-page "http://gforge.se/packages/")
2587 (synopsis "Advanced tables for Markdown/HTML")
2589 "This package provides functions to build tables with advanced layout
2590 elements such as row spanners, column spanners, table spanners, zebra
2591 striping, and more. While allowing advanced layout, the underlying
2592 CSS-structure is simple in order to maximize compatibility with word
2593 processors such as LibreOffice. The package also contains a few text
2594 formatting functions that help outputting text compatible with HTML or
2596 (license license:gpl3+)))
2598 (define-public r-curl
2604 (uri (cran-uri "curl" version))
2607 "0s55022hy8shjm1pzax1dqzrg20bv4nvlwnjnddk3dp89g5zmcch"))))
2608 (build-system r-build-system)
2611 (modify-phases %standard-phases
2612 ;; The environment variable CURL_CA_BUNDLE is only respected when
2613 ;; running Windows, so we disable the platform checks.
2614 ;; This can be removed once the libcurl has been patched.
2615 (add-after 'unpack 'allow-CURL_CA_BUNDLE
2617 (substitute* "R/onload.R"
2618 (("if \\(!grepl\\(\"mingw\".*")
2620 (substitute* "src/handle.c"
2621 (("/\\* Only set" m)
2623 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
2624 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
2629 (list pkg-config r-knitr))
2630 (home-page "https://github.com/jeroenooms/curl")
2631 (synopsis "HTTP client for R")
2633 "The @code{curl()} and @code{curl_download()} functions provide highly
2634 configurable drop-in replacements for base @code{url()} and
2635 @code{download.file()} with better performance, support for encryption, gzip
2636 compression, authentication, and other @code{libcurl} goodies. The core of
2637 the package implements a framework for performing fully customized requests
2638 where data can be processed either in memory, on disk, or streaming via the
2639 callback or connection interfaces.")
2640 (license license:expat)))
2642 (define-public r-hwriter
2649 (uri (cran-uri "hwriter" version))
2652 "1wxnv8h9cs65m3z01dpnnkgn2cpwfsck70g1jz9nbkr7mdaa4bzd"))))
2653 (build-system r-build-system)
2654 (home-page "https://cran.r-project.org/web/packages/hwriter")
2655 (synopsis "Output R objects in HTML format")
2657 "This package provides easy-to-use and versatile functions to output R
2658 objects in HTML format.")
2659 (license license:lgpl2.1+)))
2661 (define-public r-rjson
2668 (uri (cran-uri "rjson" version))
2671 "1qm27r1w677zg31gsiln60hcciszbymkw78cnaq7s36cbk9mcawq"))))
2672 (build-system r-build-system)
2673 (home-page "https://cran.r-project.org/web/packages/rjson")
2674 (synopsis "JSON library for R")
2676 "This package provides functions to convert R objects into JSON objects
2678 (license license:gpl2+)))
2680 (define-public r-fastmap
2687 (uri (cran-uri "fastmap" version))
2690 "0aw29hnq3ppn7bsnwg9d9sp84k1cvq30lrmfzqn315n0nhkfa4wi"))))
2691 (properties `((upstream-name . "fastmap")))
2692 (build-system r-build-system)
2693 (home-page "https://r-lib.github.io/fastmap/")
2694 (synopsis "Fast implementation of a key-value store")
2696 "This package provides a fast implementation of a key-value store.
2697 Environments are commonly used as key-value stores, but every time a new key
2698 is used, it is added to R's global symbol table, causing a small amount of
2699 memory leakage. This can be problematic in cases where many different keys
2700 are used. Fastmap avoids this memory leak issue by implementing the map using
2701 data structures in C++.")
2702 (license license:expat)))
2704 (define-public r-fastghquad
2706 (name "r-fastghquad")
2711 (uri (cran-uri "fastGHQuad" version))
2714 "1zj7nsbnx4g253m3dpz9vi3zk3jxwrixwjw1ks6n4shpb4dlkp2w"))))
2715 (properties `((upstream-name . "fastGHQuad")))
2716 (build-system r-build-system)
2719 (home-page "https://github.com/awblocker/fastGHQuad")
2720 (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature")
2722 "This package implements numerically-stable Gauss-Hermite quadrature
2723 rules and utility functions for adaptive GH quadrature.")
2724 (license license:expat)))
2726 (define-public r-rstpm2
2733 (uri (cran-uri "rstpm2" version))
2736 "1gsizffplj4m9x1ln82f76936psgxn9cii45m7658lpwf2nzwli2"))))
2737 (properties `((upstream-name . "rstpm2")))
2738 (build-system r-build-system)
2750 (home-page "https://github.com/mclements/rstpm2")
2751 (synopsis "Link-based survival models")
2753 "This package provides R implementations of @dfn{generalized survival
2754 models} (GSMs), smooth @dfn{accelerated failure time} (AFT) models and Markov
2755 multi-state models.")
2756 ;; One of these licenses
2757 (license (list license:gpl2 license:gpl3))))
2759 ;; This package includes minified JavaScript files. When upgrading please
2760 ;; check that there are no new minified JavaScript files.
2761 (define-public r-jquerylib
2763 (name "r-jquerylib")
2768 (uri (cran-uri "jquerylib" version))
2771 "04a40v4znpj98j7y6009d74a6g9dchj5rr3p08cgz9p3rlfw3g7h"))
2773 '(for-each delete-file
2774 '("inst/lib/1.12.4/jquery-1.12.4.min.js"
2775 "inst/lib/2.2.4/jquery-2.2.4.min.js"
2776 "inst/lib/3.6.0/jquery-3.6.0.min.js")))))
2777 (properties `((upstream-name . "jquerylib")))
2778 (build-system r-build-system)
2780 `(#:modules ((guix build utils)
2781 (guix build r-build-system)
2784 (modify-phases %standard-phases
2785 (add-after 'unpack 'process-javascript
2786 (lambda* (#:key inputs #:allow-other-keys)
2787 (with-directory-excursion "inst/lib/"
2791 `(("1.12.4/jquery-1.12.4.js"
2792 "1.12.4/jquery-1.12.4.min.js")
2793 ("2.2.4/jquery-2.2.4.js"
2794 "2.2.4/jquery-2.2.4.min.js")
2795 ("3.6.0/jquery-3.6.0.js"
2796 "3.6.0/jquery-3.6.0.min.js"))))
2797 (lambda (sources targets)
2798 (for-each (lambda (source target)
2799 (format #t "Processing ~a --> ~a~%"
2801 (invoke "esbuild" source "--minify"
2802 (string-append "--outfile=" target)))
2803 sources targets)))))))))
2808 (home-page "https://cran.r-project.org/package=jquerylib")
2809 (synopsis "Obtain jQuery as an HTML dependency object")
2811 "Obtain any major version of jQuery and use it in any webpage generated
2812 by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't
2813 need to use this package directly, but other R packages (e.g. shiny,
2814 rmarkdown, etc.) depend on this package to avoid bundling redundant copies of
2816 (license license:expat)))
2818 (define-public r-sass
2825 (uri (cran-uri "sass" version))
2828 "0iln5ky6k1ix0gddlyw4rr2953kc499x66bcyi9yiyp91nfh82dl"))))
2829 (properties `((upstream-name . "sass")))
2830 (build-system r-build-system)
2832 (list r-fs r-htmltools r-r6 r-rappdirs r-rlang))
2833 (native-inputs (list r-knitr))
2834 (home-page "https://github.com/rstudio/sass")
2835 (synopsis "Syntactically Awesome Style Sheets (SASS)")
2837 "This package provides an SCSS compiler, powered by the libsass library.
2838 With this, R developers can use variables, inheritance, and functions to
2839 generate dynamic style sheets. The package uses the Sass CSS extension
2840 language, which is stable, powerful, and CSS compatible.")
2841 (license license:expat)))
2843 (define-public r-saver
2849 (uri (cran-uri "SAVER" version))
2852 "1s1kw8idkaj7j90fw4qn9k0wd4vz0sblsk06ry6lm4afcar0p158"))))
2853 (properties `((upstream-name . "SAVER")))
2854 (build-system r-build-system)
2861 (native-inputs (list r-knitr))
2862 (home-page "https://github.com/mohuangx/SAVER")
2864 "Recovery of gene expression profile in noisy and sparse scRNA-seq data")
2866 "This package is an implementation of a regularized regression prediction
2867 and empirical Bayes method to recover the true gene expression profile in noisy
2868 and sparse single-cell RNA-seq data. In @dfn{single-cell RNA sequencing}
2869 (scRNA-seq) studies, only a small fraction of the transcripts present in each
2870 cell are sequenced. This leads to unreliable quantification of genes with low
2871 or moderate expression, which hinders downstream analysis. This package
2872 @dfn{single-cell analysis via expression recovery} (SAVER) implements an
2873 expression recovery method for unique molecule index (UMI)-based scRNA-seq
2874 data that borrows information across genes and cells to provide accurate
2875 expression estimates for all genes.")
2876 (license license:gpl2)))
2878 ;; This package includes minified JavaScript files. When upgrading please
2879 ;; check that there are no new minified JavaScript files.
2880 (define-public r-bslib
2887 (uri (cran-uri "bslib" version))
2890 "1hkmaj0mpygbf6qr1955biv9z4q3khflyqi5x0c3dwi6qz74xspv"))
2892 '(for-each delete-file
2893 '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js"
2894 "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js"
2895 "inst/lib/bs3/assets/javascripts/bootstrap.min.js"
2896 "inst/lib/bs4/dist/js/bootstrap.bundle.min.js"
2897 "inst/lib/bs5/dist/js/bootstrap.bundle.min.js")))))
2898 (properties `((upstream-name . "bslib")))
2899 (build-system r-build-system)
2901 `(#:modules ((guix build utils)
2902 (guix build r-build-system)
2905 (modify-phases %standard-phases
2906 (add-after 'unpack 'process-javascript
2907 (lambda* (#:key inputs #:allow-other-keys)
2908 (with-directory-excursion "inst/lib/"
2912 `(("bs-a11y-p/plugins/js/bootstrap-accessibility.js"
2913 "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js")
2914 ("bs-colorpicker/js/bootstrap-colorpicker.js"
2915 "bs-colorpicker/js/bootstrap-colorpicker.min.js")
2916 ("bs3/assets/javascripts/bootstrap.js"
2917 "bs3/assets/javascripts/bootstrap.min.js")
2918 (,(assoc-ref inputs "js-bootstrap4-bundle")
2919 "bs4/dist/js/bootstrap.bundle.min.js")
2920 (,(assoc-ref inputs "js-bootstrap5-bundle")
2921 "bs5/dist/js/bootstrap.bundle.min.js"))))
2922 (lambda (sources targets)
2923 (for-each (lambda (source target)
2924 (format #t "Processing ~a --> ~a~%"
2926 (invoke "esbuild" source "--minify"
2927 (string-append "--outfile=" target)))
2928 sources targets)))))))))
2938 `(("esbuild" ,esbuild)
2939 ("js-bootstrap4-bundle"
2942 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.6.0/dist/js/bootstrap.bundle.js")
2945 "04abvgp923w36qfqkkl2syim3bl119nwxbgials90z1jyb8jgss1"))))
2946 ("js-bootstrap5-bundle"
2949 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v5.1.3/dist/js/bootstrap.bundle.js")
2952 "116979i2vr1y9i6g7n5iir19p85xwr642scbl9jcqdr0w9801nw6"))))))
2953 (home-page "https://rstudio.github.io/bslib/")
2954 (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown")
2956 "This package simplifies custom CSS styling of both shiny and rmarkdown
2957 via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their
2958 various Bootswatch themes. An interactive widget is also provided for
2959 previewing themes in real time.")
2960 (license license:expat)))
2962 ;; This package includes minified JavaScript files. When upgrading please
2963 ;; check that there are no new minified JavaScript files.
2964 (define-public r-shiny
2972 (url "https://github.com/rstudio/shiny")
2973 (commit (string-append "v" version))))
2974 (file-name (git-file-name name version))
2977 "0wvc6jlgs41p05wbk8gahnl7sfnc4hpliyh9dbi5w52ngsg6wcr7"))
2979 '(for-each delete-file
2980 '("inst/www/shared/bootstrap/js/bootstrap.min.js"
2981 "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO
2982 "inst/www/shared/datatables/js/jquery.dataTables.min.js"
2983 "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js"
2984 "inst/www/shared/highlight/highlight.pack.js"
2985 "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js"
2986 "inst/www/shared/jquery.min.js"
2987 "inst/www/shared/jqueryui/jquery-ui.min.js"
2988 "inst/www/shared/legacy/jquery.min.js"
2989 "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js"
2990 "inst/www/shared/selectize/js/selectize.min.js"
2991 "inst/www/shared/shiny.min.js"
2992 "inst/www/shared/showdown/compressed/showdown.js"
2993 "inst/www/shared/strftime/strftime-min.js")))))
2994 (build-system r-build-system)
2996 `(#:modules ((guix build r-build-system)
2997 (guix build minify-build-system)
3000 #:imported-modules (,@%r-build-system-modules
3001 (guix build minify-build-system))
3003 (modify-phases (@ (guix build r-build-system) %standard-phases)
3004 (add-after 'unpack 'replace-bundled-minified-JavaScript
3005 (lambda* (#:key inputs #:allow-other-keys)
3006 (let ((replace-file (lambda (old new)
3007 (format #t "replacing ~a with ~a\n" old new)
3008 (symlink new old))))
3009 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
3010 ;; contain just data. They are not minified code, so we don't
3012 (with-directory-excursion "inst/www/shared"
3013 (replace-file "strftime/strftime-min.js"
3014 (search-input-file inputs
3015 "/share/javascript/strftime.min.js"))
3016 (replace-file "highlight/highlight.pack.js"
3017 (search-input-file inputs
3018 "/share/javascript/highlight.min.js"))
3019 (replace-file "datatables/js/jquery.dataTables.min.js"
3020 (search-input-file inputs
3021 "/share/javascript/jquery.dataTables.min.js"))
3022 (replace-file "selectize/js/selectize.min.js"
3023 (search-input-file inputs
3024 "/share/javascript/selectize.min.js"))
3025 (for-each (match-lambda
3027 (minify source #:target target)))
3028 `(("jqueryui/jquery-ui.js" .
3029 "jqueryui/jquery-ui.min.js")
3030 ("datepicker/js/bootstrap-datepicker.js" .
3031 "datepicker/js/bootstrap-datepicker.min.js")
3032 ("ionrangeslider/js/ion.rangeSlider.js" .
3033 "ionrangeslider/js/ion.rangeSlider.min.js")
3034 ("bootstrap/js/bootstrap.js" .
3035 "bootstrap/js/bootstrap.min.js")
3036 (,(assoc-ref inputs "js-bootstrap-accessibility") .
3037 "bootstrap/accessibility/js/bootstrap-accessibility.min.js")
3042 ("legacy/jquery.js" .
3043 "legacy/jquery.min.js")
3044 ("selectize/accessibility/js/selectize-plugin-a11y.js" .
3045 "selectize/accessibility/js/selectize-plugin-a11y.min.js")
3046 ("showdown/src/showdown.js" .
3047 "showdown/compressed/showdown.js"))))))))))
3070 (list js-datatables js-selectize js-strftime js-highlight))
3072 `(("uglifyjs" ,node-uglify-js)
3073 ("gfortran" ,gfortran)
3074 ("js-bootstrap-accessibility"
3077 (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\
3078 v1.0.7/_site/plugins/js/bootstrap-accessibility.js")
3081 "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8"))))))
3082 (home-page "https://shiny.rstudio.com")
3083 (synopsis "Easy interactive web applications with R")
3085 "Makes it incredibly easy to build interactive web applications
3086 with R. Automatic \"reactive\" binding between inputs and outputs and
3087 extensive prebuilt widgets make it possible to build beautiful,
3088 responsive, and powerful applications with minimal effort.")
3089 (license license:artistic2.0)))
3091 (define-public r-shinyhelper
3093 (name "r-shinyhelper")
3098 (uri (cran-uri "shinyhelper" version))
3100 (base32 "1c4hvf19j3yyh8r12nx85ldkxs89g98q74csnqs5ml5l79a65vgp"))))
3101 (properties `((upstream-name . "shinyhelper")))
3102 (build-system r-build-system)
3103 (propagated-inputs (list r-markdown r-shiny))
3104 (home-page "https://cran.r-project.org/package=shinyhelper")
3105 (synopsis "Easily add Markdown help files to shiny app elements")
3107 "This package creates a lightweight way to add markdown helpfiles to
3108 Shiny apps, using modal dialog boxes, with no need to observe each help button
3110 (license license:gpl3)))
3112 ;; This package includes minified JavaScript files. When upgrading please
3113 ;; check that there are no new minified JavaScript files.
3114 (define-public r-shinytree
3116 (name "r-shinytree")
3121 (uri (cran-uri "shinyTree" version))
3124 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
3125 (modules '((guix build utils)))
3128 ;; Delete minified JavaScript
3129 (for-each delete-file
3130 '("inst/www/jsTree-3.3.7/libs/require.js"
3131 "inst/www/jsTree-3.3.7/libs/jquery.js"
3132 "inst/www/jsTree-3.3.7/jstree.min.js"))
3134 (properties `((upstream-name . "shinyTree")))
3135 (build-system r-build-system)
3137 `(#:modules ((guix build utils)
3138 (guix build r-build-system)
3142 (modify-phases %standard-phases
3143 (add-after 'unpack 'replace-minified-javascript
3144 (lambda* (#:key inputs #:allow-other-keys)
3145 (with-directory-excursion "inst/www/jsTree-3.3.7/"
3146 (symlink (search-input-file inputs
3147 "/share/javascript/require.min.js")
3152 `((,(assoc-ref inputs "js-jquery")
3156 (lambda (sources targets)
3157 (for-each (lambda (source target)
3158 (format #t "Processing ~a --> ~a~%"
3160 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
3161 (call-with-output-file target
3163 (dump-port minified port)))))
3167 (list r-htmlwidgets r-jsonlite r-promises r-shiny r-stringr))
3169 (list js-requirejs))
3171 `(("uglifyjs" ,node-uglify-js)
3175 (uri "https://code.jquery.com/jquery-3.3.1.js")
3178 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
3179 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
3180 (synopsis "jsTree bindings for Shiny")
3182 "This package exposes R bindings to jsTree, a JavaScript library that
3183 supports interactive trees, to enable rich, editable trees in Shiny.")
3184 (license license:expat)))
3186 (define-public r-shinydashboard
3188 (name "r-shinydashboard")
3192 (uri (cran-uri "shinydashboard" version))
3195 "0hrqkwlpb8rnmp5j74p134g4c4cl16icmwc2ip6k1634fa2y8vm5"))))
3196 (build-system r-build-system)
3197 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
3198 ;; Regenerate it from the included sources.
3201 (modify-phases %standard-phases
3202 (add-after 'unpack 'generate-minified-javascript
3204 (with-directory-excursion "inst/AdminLTE"
3205 (let ((target "app.min.js")
3207 (format #t "Processing ~a --> ~a~%"
3209 (delete-file target)
3210 (invoke "esbuild" source "--minify"
3211 (string-append "--outfile=" target)))))))))
3213 (list r-htmltools r-promises r-shiny))
3216 (home-page "https://rstudio.github.io/shinydashboard/")
3217 (synopsis "Create dashboards with shiny")
3218 (description "This package provides an extension to the Shiny web
3219 application framework for R, making it easy to create attractive dashboards.")
3220 ;; This package includes software that was released under the Expat
3221 ;; license, but the whole package is released under GPL version 2 or
3223 (license license:gpl2+)))
3225 (define-public r-shinyfiles
3227 (name "r-shinyfiles")
3232 (uri (cran-uri "shinyFiles" version))
3234 (base32 "11kjq0vw5c98lzrg80m9w917lkgw5im2h9wgk1b84vlaxrjy2wja"))))
3235 (properties `((upstream-name . "shinyFiles")))
3236 (build-system r-build-system)
3238 (list r-fs r-htmltools r-jsonlite r-shiny r-tibble))
3239 (home-page "https://github.com/thomasp85/shinyFiles")
3240 (synopsis "Server-side file system viewer for Shiny")
3242 "This package provides functionality for client-side navigation of the
3243 server side file system in shiny apps. In case the app is running locally
3244 this gives the user direct access to the file system without the need to
3245 \"download\" files to a temporary location. Both file and folder selection as
3246 well as file saving is available.")
3247 (license license:gpl2+)))
3249 (define-public r-shinythemes
3251 (name "r-shinythemes")
3256 (uri (cran-uri "shinythemes" version))
3259 "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip"))))
3260 (properties `((upstream-name . "shinythemes")))
3261 (build-system r-build-system)
3262 (propagated-inputs (list r-shiny))
3263 (home-page "https://rstudio.github.io/shinythemes/")
3264 (synopsis "Themes for Shiny")
3266 "This package provides themes for use with Shiny. It includes several
3267 Bootstrap themes, which are packaged for use with Shiny applications.")
3268 ;; The package is released under version 3 of the GPL, but it includes
3269 ;; source files that are covered by the Expat license. It also includes
3270 ;; fonts under SIL or the ASL.
3271 (license (list license:gpl3 license:expat
3272 license:silofl1.1 license:asl2.0))))
3274 ;; The package sources include minified variants of d3.js and non-minified
3275 ;; source code of d3-jetpack.
3276 (define-public r-d3r
3283 (uri (cran-uri "d3r" version))
3286 "1qijkllfaaw0lb29j8mappm8jz9kg8gkihxq5wqhb4gabsazdwva"))))
3287 (build-system r-build-system)
3289 `(#:modules ((guix build utils)
3290 (guix build r-build-system)
3293 (modify-phases %standard-phases
3294 (add-after 'unpack 'process-javascript
3295 (lambda* (#:key inputs #:allow-other-keys)
3296 (with-directory-excursion "inst/www/d3/"
3300 `((,(assoc-ref inputs "d3.v3.js")
3301 "v3/dist/d3.min.js")
3302 (,(assoc-ref inputs "d3.v4.js")
3303 "v4/dist/d3.min.js")
3304 (,(assoc-ref inputs "d3.v5.js")
3305 "v5/dist/d3.min.js")
3306 (,(assoc-ref inputs "d3.v6.js")
3307 "v6/dist/d3.min.js")
3308 (,(assoc-ref inputs "d3.v7.js")
3309 "v7/dist/d3.min.js"))))
3310 (lambda (sources targets)
3311 (for-each (lambda (source target)
3312 (format #t "Processing ~a --> ~a~%"
3314 (delete-file target)
3315 (invoke "esbuild" source "--minify"
3316 (string-append "--outfile=" target)))
3317 sources targets)))))))))
3319 (list r-dplyr r-htmltools r-rlang r-tidyr))
3321 `(("esbuild" ,esbuild)
3325 (uri "https://d3js.org/d3.v3.js")
3328 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
3332 (uri "https://d3js.org/d3.v4.js")
3335 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
3339 (uri "https://d3js.org/d3.v5.js")
3342 "177ypw6mjrp2ch9lj6znibwacwrvm4ypjxflsxsnl2sigx5dcwic"))))
3346 (uri "https://d3js.org/d3.v6.js")
3349 "13hick3glizzm442b9swlwz584rzwwvhpq9qvfbh3m5jay10wxw0"))))
3353 (uri "https://d3js.org/d3.v7.js")
3356 "1hif1phswlkkpvcf1hbqmfsxdb5s5gr5g2frcwbh0rh8g6nbkyqi"))))))
3357 (home-page "https://github.com/timelyportfolio/d3r")
3358 (synopsis "d3.js utilities for R")
3360 "This package provides a suite of functions to help ease the use of the
3361 d3.js visualization library in R. These helpers include
3362 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
3363 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
3364 R objects into the JSON format that the d3.js library expects.")
3365 (license license:bsd-3)))
3367 ;; We use the latest commit here because the last release was in 2016 while
3368 ;; the latest commit was in 2018.
3369 (define-public r-sankeyd3
3370 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
3374 (version (git-version "0.3.2" revision commit))
3379 (url "https://github.com/fbreitwieser/sankeyD3")
3381 (file-name (git-file-name name version))
3384 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
3385 (build-system r-build-system)
3387 (list r-d3r r-htmlwidgets r-shiny r-magrittr))
3388 (home-page "https://github.com/fbreitwieser/sankeyD3")
3389 (synopsis "Sankey network graphs from R")
3391 "This package provides an R library to generate Sankey network graphs
3392 in R and Shiny via the D3 visualization library.")
3393 ;; The R code is licensed under GPLv3+. It includes the non-minified
3394 ;; JavaScript source code of d3-sankey, which is released under the
3395 ;; 3-clause BSD license.
3396 (license (list license:gpl3+ license:bsd-3)))))
3398 (define-public r-wesanderson
3400 (name "r-wesanderson")
3405 (uri (cran-uri "wesanderson" version))
3408 "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
3409 (properties `((upstream-name . "wesanderson")))
3410 (build-system r-build-system)
3411 (home-page "https://github.com/karthik/wesanderson")
3412 (synopsis "Wes Anderson color palette generator")
3414 "This package provides color palettes that have been generated mostly
3415 from Wes Anderson movies.")
3416 (license license:expat)))
3418 (define-public r-gg-gap
3425 (uri (cran-uri "gg.gap" version))
3428 "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h"))))
3429 (properties `((upstream-name . "gg.gap")))
3430 (build-system r-build-system)
3432 (list r-cowplot r-ggplot2))
3433 (home-page "https://github.com/ChrisLou-bioinfo/gg.gap")
3434 (synopsis "Define segments on the y-axis for ggplot2")
3436 "The @code{gg.gap} function enables you to define segments for the y-axis
3437 in a ggplot2 plot.")
3438 (license license:gpl3)))
3440 (define-public r-mbess
3447 (uri (cran-uri "MBESS" version))
3449 (base32 "18klyyjvmwggv4ma2x77jac3640yxbsbinl3s2rp1ik4n9phnjd0"))))
3450 (properties `((upstream-name . "MBESS")))
3451 (build-system r-build-system)
3453 (list r-boot r-lavaan r-mass r-mnormt r-nlme r-openmx r-sem r-semtools))
3454 (home-page "https://www3.nd.edu/~kkelley/site/MBESS.html")
3455 (synopsis "Methods for designing research studies")
3457 "This package implements methods that are useful in designing research
3458 studies and analyzing data, with particular emphasis on methods that are
3459 developed for or used within the behavioral, educational, and social
3460 sciences (broadly defined). That being said, many of the methods implemented
3461 within MBESS are applicable to a wide variety of disciplines. MBESS has a
3462 suite of functions for a variety of related topics, such as effect sizes,
3463 confidence intervals for effect sizes (including standardized effect sizes and
3464 noncentral effect sizes), sample size planning (from the @dfn{accuracy in
3465 parameter estimation} (AIPE), power analytic, equivalence, and minimum-risk
3466 point estimation perspectives), mediation analysis, various properties of
3467 distributions, and a variety of utility functions.")
3468 ;; Either version of the GPL.
3469 (license (list license:gpl2 license:gpl3))))
3471 (define-public r-homologene
3473 (name "r-homologene")
3474 (version "1.4.68.19.3.27")
3478 (uri (cran-uri "homologene" version))
3480 (base32 "0d7wxisk0vqk1n165v1i19bc02zv78h5r5d3jqai5y6nkmwn01sh"))))
3481 (properties `((upstream-name . "homologene")))
3482 (build-system r-build-system)
3484 (list r-dplyr r-magrittr r-purrr r-r-utils r-readr))
3485 (home-page "https://github.com/oganm/homologene")
3486 (synopsis "Quick access to homologene and gene annotation updates")
3488 "This package provides a wrapper for the homologene database by the
3489 National Center for Biotechnology Information (NCBI). It allows searching for
3490 gene homologs across species. The package also includes an updated version of
3491 the homologene database where gene identifiers and symbols are replaced with
3492 their latest (at the time of submission) version and functions to fetch latest
3493 annotation data to keep updated.")
3494 (license license:expat)))
3496 (define-public r-ggtern
3503 (uri (cran-uri "ggtern" version))
3505 (base32 "15hhn8msy0l8zbq8ms0zvg1iajn1c28gd77v3hp6dvwwsla8zzbd"))))
3506 (properties `((upstream-name . "ggtern")))
3507 (build-system r-build-system)
3509 (list r-compositions
3520 (home-page "http://www.ggtern.com")
3521 (synopsis "Extension to ggplot2 for ternary diagrams")
3523 "This package extends the functionality of ggplot2, providing the
3524 capability to plot ternary diagrams for (a subset of) the ggplot2 geometries.
3525 Additionally, ggtern has implemented several new geometries which are
3526 unavailable to the standard ggplot2 release.")
3527 (license license:gpl2)))
3529 (define-public r-tablerdash
3531 (name "r-tablerdash")
3536 (uri (cran-uri "tablerDash" version))
3539 "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm"))
3542 ;; Delete minified JavaScript
3543 (for-each delete-file
3544 '("inst/tablerDash-0.1.0/require.min.js"
3545 "inst/bootstrap-4.0.0/bootstrap.bundle.min.js"))
3547 (properties `((upstream-name . "tablerDash")))
3548 (build-system r-build-system)
3550 `(#:modules ((guix build utils)
3551 (guix build r-build-system)
3554 (modify-phases %standard-phases
3555 (add-after 'unpack 'process-javascript
3556 (lambda* (#:key inputs #:allow-other-keys)
3557 (with-directory-excursion "inst"
3561 `((,(assoc-ref inputs "js-requirejs")
3562 "tablerDash-0.1.0/require.min.js")
3563 (,(assoc-ref inputs "js-bootstrap")
3564 "bootstrap-4.0.0/bootstrap.bundle.min.js"))))
3565 (lambda (sources targets)
3566 (for-each (lambda (source target)
3567 (format #t "Processing ~a --> ~a~%"
3569 (invoke "esbuild" source "--minify"
3570 (string-append "--outfile=" target)))
3574 (list r-htmltools r-knitr r-shiny))
3576 `(("esbuild" ,esbuild)
3580 (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js")
3583 "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds"))))
3587 (uri "https://raw.githubusercontent.com/twbs/bootstrap/\
3588 v4.0.0/dist/js/bootstrap.bundle.js")
3591 "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj"))))))
3592 (home-page "https://rinterface.github.io/tablerDash/")
3593 (synopsis "Tabler API for Shiny")
3595 "This package provides an R interface to the
3596 @url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap
3597 4 dashboard template. There are different layouts available such as a one
3598 page dashboard or a multi-page template, where the navigation menu is
3599 contained in the navigation bar.")
3600 (license license:gpl2+)))
3602 (define-public r-spelling
3609 (uri (cran-uri "spelling" version))
3612 "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl"))))
3613 (properties `((upstream-name . "spelling")))
3614 (build-system r-build-system)
3616 (list r-commonmark r-hunspell r-knitr r-xml2))
3617 (home-page "https://docs.ropensci.org/spelling/")
3618 (synopsis "Tools for spell checking in R")
3620 "This is an R package for spell checking common document formats
3621 including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes
3622 utilities to automate checking of documentation and vignettes as a unit test
3623 during @code{R CMD check}. Both British and American English are supported
3624 out of the box and other languages can be added. In addition, packages may
3625 define a wordlist to allow custom terminology without having to abuse
3627 (license license:expat)))
3629 (define-public r-crosstalk
3631 (name "r-crosstalk")
3636 (uri (cran-uri "crosstalk" version))
3639 "180y7mhpj17axpadwhh7s0qvrpdnag7g977vk256l96d6nmvlds2"))))
3640 (build-system r-build-system)
3642 (list r-htmltools r-jsonlite r-lazyeval r-r6))
3643 (home-page "https://rstudio.github.io/crosstalk/")
3644 (synopsis "Inter-widget interactivity for HTML widgets")
3646 "This package provides building blocks for allowing HTML widgets to
3647 communicate with each other, with Shiny or without (i.e., static @code{.html}
3648 files). It currently supports linked brushing and filtering.")
3649 (license license:expat)))
3651 (define-public r-rook
3658 (uri (cran-uri "Rook" version))
3661 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
3662 (properties `((upstream-name . "Rook")))
3663 (build-system r-build-system)
3664 (propagated-inputs (list r-brew))
3665 (home-page "https://cran.r-project.org/web/packages/Rook")
3666 (synopsis "Web server interface for R")
3668 "This package contains the Rook specification and convenience software
3669 for building and running Rook applications. A Rook application is an R
3670 reference class object that implements a @code{call} method or an R closure
3671 that takes exactly one argument, an environment, and returns a list with three
3672 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
3673 (license license:gpl2)))
3675 (define-public r-miniui
3682 (uri (cran-uri "miniUI" version))
3685 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
3686 (properties `((upstream-name . "miniUI")))
3687 (build-system r-build-system)
3689 (list r-htmltools r-shiny))
3690 (home-page "https://cran.r-project.org/web/packages/miniUI/")
3691 (synopsis "Shiny UI widgets for small screens")
3693 "This package provides UI widget and layout functions for writing Shiny apps that
3694 work well on small screens.")
3695 (license license:gpl3)))
3697 (define-public r-feather
3704 (uri (cran-uri "feather" version))
3707 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
3708 (build-system r-build-system)
3710 (list r-hms r-rcpp r-tibble))
3711 (home-page "https://github.com/wesm/feather")
3712 (synopsis "R Bindings to the Feather API")
3713 (description "Read and write feather files, a lightweight binary columnar
3714 data store designed for maximum speed.")
3715 (license license:asl2.0)))
3717 (define-public r-maps
3724 (uri (cran-uri "maps" version))
3727 "0ispkx1szgwxhr0zzhdzgqqwcgc6psg7vry4sj4rb89w76rcq63r"))))
3728 (build-system r-build-system)
3729 (home-page "https://cran.r-project.org/web/packages/maps")
3730 (synopsis "Draw geographical maps")
3731 (description "This package provides an R module for display of maps.
3732 Projection code and larger maps are in separate packages (@code{mapproj} and
3734 (license license:gpl2)))
3736 (define-public r-mapproj
3743 (uri (cran-uri "mapproj" version))
3746 "10bpib827011fpgvzsmlv4j3i41s0r3cv1hvawwdlk753s7i0pw6"))))
3747 (build-system r-build-system)
3748 (propagated-inputs (list r-maps))
3749 (home-page "https://cran.r-project.org/web/packages/mapproj")
3750 (synopsis "Map projection in R")
3751 (description "This package converts latitude/longitude into projected
3753 (license (list license:gpl2 ; The R interface
3754 (license:non-copyleft ; The C code
3755 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
3756 "Lucent Public License Version 1.02")))))
3758 (define-public r-rgooglemaps
3760 (name "r-rgooglemaps")
3765 (uri (cran-uri "RgoogleMaps" version))
3768 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
3769 (properties `((upstream-name . "RgoogleMaps")))
3770 (build-system r-build-system)
3773 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
3774 (synopsis "Use Google Maps in R")
3775 (description "This package serves two purposes:
3777 @item Provide a comfortable R interface to query the Google server for static
3779 @item Use the map as a background image to overlay plots within R. This
3780 requires proper coordinate scaling.
3782 (license license:gpl2+)))
3784 (define-public r-gensa
3790 (uri (cran-uri "GenSA" version))
3793 "03xqwxm7v7rnihx730a4p65dfwhjh4345r3d78y0qxxplk8d76cx"))))
3794 (properties `((upstream-name . "GenSA")))
3795 (build-system r-build-system)
3796 (home-page "https://cran.r-project.org/package=GenSA")
3797 (synopsis "Generalized simulated annealing")
3798 (description "This package performs search for the global minimum of a very
3799 complex non-linear objective function with a very large number of optima.")
3800 (license license:gpl2)))
3802 (define-public r-geosphere
3804 (name "r-geosphere")
3809 (uri (cran-uri "geosphere" version))
3812 "0bg4vfmrw140j2ax0p6bflvb77w03ir39wa87l96rj473jpa9hzj"))))
3813 (build-system r-build-system)
3814 (propagated-inputs (list r-sp))
3815 (home-page "https://cran.r-project.org/web/packages/geosphere")
3816 (synopsis "Spherical trigonometry")
3817 (description "This package computes spherical trigonometry for geographic
3818 applications. That is, compute distances and related measures for angular
3819 (longitude/latitude) locations.")
3820 (license license:gpl3+)))
3822 (define-public r-jpeg
3829 (uri (cran-uri "jpeg" version))
3832 "0wihj538wdnr71wdldym83qadb4kh68a6rkallwbh2f25r27b881"))))
3833 (build-system r-build-system)
3834 (inputs (list libjpeg-turbo))
3835 (home-page "https://www.rforge.net/jpeg/")
3836 (synopsis "Read and write JPEG images with R")
3837 (description "This package provides a way to read, write and display
3838 bitmap images stored in the JPEG format with R. It can read and write both
3839 files and in-memory raw vectors.")
3840 (license license:gpl2+)))
3842 (define-public r-ggmap
3849 (uri (cran-uri "ggmap" version))
3852 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
3853 (build-system r-build-system)
3872 (home-page "https://github.com/dkahle/ggmap")
3873 (synopsis "Spatial visualization with ggplot2")
3874 (description "This package provides a collection of functions to visualize
3875 spatial data and models on top of static maps from various online sources (e.g
3876 Google Maps and Stamen Maps). It includes tools common to those tasks,
3877 including functions for geolocation and routing.")
3878 (license license:gpl2)))
3880 (define-public r-haven
3887 (uri (cran-uri "haven" version))
3890 "0w0aqm0z4h0rm1f7fylm1mbv79p43y2r795w64wczcd0jwh4ch4z"))
3891 (modules '((guix build utils)))
3893 ;; unvendor readstat
3894 '(delete-file-recursively "src/readstat"))))
3895 (build-system r-build-system)
3898 (modify-phases %standard-phases
3899 (add-after 'unpack 'unbundle-readstat
3901 ;; We’re not building readstat.
3902 (substitute* "configure"
3903 (("exit 1") "")) ;don't be so dramatic!
3904 (substitute* '("src/Makevars.in"
3906 (("^PKG_LIBS=.*") "PKG_LIBS=\"-lreadstat\"\n")))))))
3922 (home-page "https://haven.tidyverse.org")
3923 (synopsis "Import and export SPSS, Stata and SAS files")
3925 "This package lets you import foreign statistical formats into R via the
3926 @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
3927 (license license:expat)))
3929 (define-public r-amap
3935 (uri (cran-uri "amap" version))
3938 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
3939 (build-system r-build-system)
3942 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
3943 (synopsis "Another multidimensional analysis package")
3944 (description "This package provides tools for clustering and principal
3945 component analysis (with robust methods, and parallelized functions).")
3946 (license license:gpl2+)))
3948 (define-public r-ape
3955 (uri (cran-uri "ape" version))
3958 "0mqjsh7maczd02iwa4fb896q3kgd9jnlilq7y1yz18ch0c54aqlv"))))
3959 (build-system r-build-system)
3961 (list r-lattice r-nlme r-rcpp))
3962 (home-page "http://ape-package.ird.fr/")
3963 (synopsis "Analyses of phylogenetics and evolution")
3965 "This package provides functions for reading, writing, plotting, and
3966 manipulating phylogenetic trees, analyses of comparative data in a
3967 phylogenetic framework, ancestral character analyses, analyses of
3968 diversification and macroevolution, computing distances from DNA sequences,
3969 and several other tools.")
3970 (license license:gpl2+)))
3972 (define-public r-abbyyr
3979 (uri (cran-uri "abbyyR" version))
3982 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
3983 (properties `((upstream-name . "abbyyR")))
3984 (build-system r-build-system)
3992 (home-page "https://github.com/soodoku/abbyyR")
3993 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
3995 "This package provides tools to get text from images of text using Abbyy
3996 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
3997 OCR images, barcodes, forms, documents with machine readable zones, e.g.
3998 passports and get the results in a variety of formats including plain text and
3999 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
4000 (license license:expat)))
4002 (define-public r-colorspace
4004 (name "r-colorspace")
4009 (uri (cran-uri "colorspace" version))
4011 (base32 "0zw52s8g2gxp8i1ax96azxmxqrbhb7aad5px0c1vgr6n9p682mp7"))))
4012 (build-system r-build-system)
4015 (home-page "https://cran.r-project.org/web/packages/colorspace")
4016 (synopsis "Color space manipulation")
4018 "This package carries out a mapping between assorted color spaces
4019 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
4020 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
4021 colors are provided.")
4022 (license license:bsd-3)))
4024 (define-public r-glue
4031 (uri (cran-uri "glue" version))
4034 "1gzxk5jgdh2xq9r7z09xs306ygzf27vhg3pyfl7ck1755gqii9cx"))))
4035 (build-system r-build-system)
4036 ;; knitr depends on glue, so we can't add knitr here to build the
4040 `(("r-knitr" ,r-knitr)))
4041 (home-page "https://github.com/tidyverse/glue")
4042 (synopsis "Interpreted string literals")
4044 "This package provides an implementation of interpreted string literals,
4045 inspired by Python's Literal String Interpolation (PEP-0498) and
4046 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
4047 (license license:expat)))
4049 (define-public r-paletteer
4051 (name "r-paletteer")
4055 (uri (cran-uri "paletteer" version))
4058 "0vj945cgpfhmbd98mcj167mgshghv32dxh8m4ngxs6i4q4y5blm7"))))
4059 (properties `((upstream-name . "paletteer")))
4060 (build-system r-build-system)
4061 (propagated-inputs (list r-prismatic r-rematch2 r-rlang r-rstudioapi))
4062 (home-page "https://github.com/EmilHvitfeldt/paletteer")
4063 (synopsis "Comprehensive collection of color palettes")
4065 "The choices of color palettes in R can be quite overwhelming with palettes
4066 spread over many packages with many different API's. This package aims to
4067 collect all color palettes across the R ecosystem under the same package with
4068 a streamlined API.")
4069 (license license:gpl3)))
4071 (define-public r-palmerpenguins
4073 (name "r-palmerpenguins")
4078 (uri (cran-uri "palmerpenguins" version))
4081 "1d1h3bfx750is4qqj4w00rcigk9rrdy69bvd5bgqz5y7ls5x8h1a"))))
4083 `((upstream-name . "palmerpenguins")))
4084 (build-system r-build-system)
4085 (home-page "https://allisonhorst.github.io/palmerpenguins/")
4086 (synopsis "Palmer Archipelago (Antarctica) penguin data")
4088 "This package includes size measurements, clutch observations, and blood
4089 isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins
4090 observed on islands in the Palmer Archipelago near Palmer Station, Antarctica.
4091 Data were collected and made available by Dr. Kristen Gorman and the Palmer
4092 Station Long Term Ecological Research (LTER) Program.")
4093 (license license:cc0)))
4095 (define-public r-pastecs
4101 (uri (cran-uri "pastecs" version))
4104 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
4105 (build-system r-build-system)
4108 (home-page "https://github.com/phgrosjean/pastecs")
4109 (synopsis "Analysis of space-time ecological series")
4111 "This package provides functions for regulation, decomposition and analysis
4112 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
4113 initiative to bring PASSTEC 2000 functionalities to R.")
4114 (license license:gpl2+)))
4116 (define-public r-partykit
4122 (uri (cran-uri "partykit" version))
4125 "1cnx6qbw5svwh3nq40n5vr20179ihd3jgznm7mz4k50qkkid8hz6"))))
4126 (build-system r-build-system)
4134 (home-page "http://partykit.R-Forge.R-project.org/partykit")
4135 (synopsis "Toolkit for recursive partytioning")
4137 "This package provides a toolkit with infrastructure for representing,
4138 summarizing, and visualizing tree-structured regression and classification
4140 (license license:gpl2+)))
4142 (define-public r-plogr
4149 (uri (cran-uri "plogr" version))
4152 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
4153 (build-system r-build-system)
4154 (home-page "https://github.com/krlmlr/plogr")
4155 (synopsis "R bindings for the plog C++ logging library")
4157 "This package provides the header files for a stripped-down version of
4158 the plog header-only C++ logging library, and a method to log to R's standard
4160 (license license:expat)))
4162 (define-public r-pls
4169 (uri (cran-uri "pls" version))
4171 (base32 "137jg3x7aqwyki29i4kzp8d6imn17nq6wzzfjw5q19pixvmpybp2"))))
4172 (build-system r-build-system)
4173 (home-page "https://mevik.net/work/software/pls.html")
4174 (synopsis "Partial Least Squares and Principal Component Regression")
4176 "The pls package implements multivariate regression methods: Partial Least
4177 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
4178 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
4181 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
4182 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
4183 @item multi-response models (or @dfn{PLS2})
4184 @item flexible cross-validation
4185 @item Jackknife variance estimates of regression coefficients
4186 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
4187 (R)MSEP, R², and correlation loadings
4188 @item formula interface, modelled after @code{lm()}, with methods for predict,
4189 print, summary, plot, update, etc.
4190 @item extraction functions for coefficients, scores, and loadings
4191 @item MSEP, RMSEP, and R² estimates
4192 @item multiplicative scatter correction (@dfn{MSC})
4194 (license license:gpl2)))
4203 (uri (cran-uri "ps" version))
4205 (base32 "1waylmbrl23j62010r12c8xwzlvs1dys3cnh7hnrgk27glvqlicw"))))
4206 (build-system r-build-system)
4207 (home-page "https://ps.r-lib.org")
4208 (synopsis "List, query, and manipulate system processes")
4210 "The ps package implements an API to list, query, and manipulate system
4211 processes. Most of its code is based on the @code{psutil} Python package.")
4212 (license license:bsd-3)))
4214 (define-public r-pkgbuild
4221 (uri (cran-uri "pkgbuild" version))
4223 (base32 "0j6v5nbp8kg1m3j999gd1qsbdmqcqm1mf28ngmm177miwv8q4skw"))))
4224 (build-system r-build-system)
4234 (home-page "https://github.com/r-pkgs/pkgbuild")
4235 (synopsis "Find tools needed to build R packages")
4237 "This package provides functions used to build R packages. It locates
4238 compilers needed to build R packages on various platforms and ensures the PATH
4239 is configured appropriately so R can use them.")
4240 (license license:gpl3)))
4242 (define-public r-pkgload
4249 (uri (cran-uri "pkgload" version))
4252 "0a22kxgm9a8ax1dw2q9v3338qhjmhfbcqw8r4b6608k6074m7xjs"))))
4253 (build-system r-build-system)
4263 (home-page "https://github.com/r-lib/pkgload")
4264 (synopsis "Simulate package installation and attach")
4266 "This package simulates the process of installing a package and then
4267 attaching it. This is a key part of the @code{devtools} package as it allows
4268 you to rapidly iterate while developing a package.")
4269 (license license:gpl3)))
4271 (define-public r-pvclust
4277 (uri (cran-uri "pvclust" version))
4280 "0082icm54k2yq60k06qpr92a626k39j2jr0046lva4ylmhxqb4kq"))))
4281 (build-system r-build-system)
4282 (home-page "https://github.com/shimo-lab/pvclust")
4284 "Hierarchical clustering with P-values via multiscale bootstrap resampling")
4285 (description "This package provides an implementation of multiscale bootstrap
4286 resampling for assessing the uncertainty in hierarchical cluster analysis. It
4287 provides an AU (approximately unbiased) P-value as well as a BP (bootstrap probability)
4288 value for each cluster in a dendrogram.")
4289 (license license:gpl2+)))
4291 (define-public r-rcpp
4298 (uri (cran-uri "Rcpp" version))
4300 (base32 "0xli48y9nsj8x8p5vkhisiz4l23g8r2623rn0i4xb5javh3fqz40"))))
4301 (build-system r-build-system)
4302 (home-page "http://www.rcpp.org")
4303 (synopsis "Seamless R and C++ integration")
4305 "The Rcpp package provides R functions as well as C++ classes which offer
4306 a seamless integration of R and C++. Many R data types and objects can be
4307 mapped back and forth to C++ equivalents which facilitates both writing of new
4308 code as well as easier integration of third-party libraries. Documentation
4309 about Rcpp is provided by several vignettes included in this package, via the
4310 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
4311 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
4312 @code{citation(\"Rcpp\")} for details on these last two.")
4313 (license license:gpl2+)))
4315 (define-public r-rcppml
4322 (uri (cran-uri "RcppML" version))
4324 (base32 "1ih8i7i6m221iw227mnl3rvnaw2l53h8fpnc4f8yn9sm10anap1j"))))
4325 (properties `((upstream-name . "RcppML")))
4326 (build-system r-build-system)
4327 (propagated-inputs (list r-matrix r-rcpp r-rcppeigen))
4328 (native-inputs (list r-knitr))
4329 (home-page "https://github.com/zdebruine/RcppML")
4330 (synopsis "Rcpp machine learning library")
4332 "This package provides fast machine learning algorithms including matrix
4333 factorization and divisive clustering for large sparse and dense matrices.")
4334 (license license:gpl2+)))
4336 (define-public r-rcppthread
4338 (name "r-rcppthread")
4343 (uri (cran-uri "RcppThread" version))
4346 "0iprpidf7q1wlrgr9dwiikb6apqk80pyjcyni56k64nl7lrkszhj"))))
4347 (properties `((upstream-name . "RcppThread")))
4348 (build-system r-build-system)
4350 "https://github.com/tnagler/RcppThread")
4351 (synopsis "R threading in C++")
4353 "This package provides a C++11-style thread class and thread pool that can
4354 safely be interrupted from R.")
4355 (license license:expat)))
4357 (define-public r-rcppnumerical
4359 (name "r-rcppnumerical")
4363 (uri (cran-uri "RcppNumerical" version))
4366 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
4367 (build-system r-build-system)
4369 (list r-rcpp r-rcppeigen))
4370 (home-page "https://github.com/yixuan/RcppNumerical")
4371 (synopsis"Numerical computing libraries integration with @code{Rcpp}")
4372 (description "This package provides a collection of libraries for numerical
4373 computing (numerical integration, optimization, etc.) and their integration
4375 (license license:gpl2+)))
4377 (define-public r-rcppxptrutils
4379 (name "r-rcppxptrutils")
4384 (uri (cran-uri "RcppXPtrUtils" version))
4386 (base32 "0hm57nf4dzgsmg4hjj6wikwjx93fgfwkmybw6ly4b58wi6qwml1l"))))
4387 (properties `((upstream-name . "RcppXPtrUtils")))
4388 (build-system r-build-system)
4389 (propagated-inputs (list r-rcpp))
4390 (home-page "https://github.com/Enchufa2/RcppXPtrUtils")
4391 (synopsis "XPtr add-ons for Rcpp")
4393 "This package provides the means to compile user-supplied C++ functions
4394 with Rcpp and retrieve an @code{XPtr} that can be passed to other C++
4396 (license license:expat)))
4398 (define-public r-bindr
4405 (uri (cran-uri "bindr" version))
4408 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
4409 (build-system r-build-system)
4410 (home-page "https://github.com/krlmlr/bindr")
4411 (synopsis "Parametrized active bindings")
4413 "This package provides a simple interface for creating active bindings
4414 where the bound function accepts additional arguments.")
4415 (license license:expat)))
4417 (define-public r-bindrcpp
4424 (uri (cran-uri "bindrcpp" version))
4427 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
4428 (build-system r-build-system)
4430 (list r-bindr r-plogr r-rcpp))
4431 (home-page "https://github.com/krlmlr/bindrcpp")
4432 (synopsis "Rcpp interface to active bindings")
4434 "This package provides an easy way to fill an environment with active
4435 bindings that call a C++ function.")
4436 (license license:expat)))
4438 (define-public r-auc
4445 (uri (cran-uri "AUC" version))
4448 "07xf47kypqbsg2mixmq6mnh4s89aqan9bgl6kfv6lbx8ajv2asw3"))))
4449 (properties `((upstream-name . "AUC")))
4450 (build-system r-build-system)
4451 (home-page "https://cran.r-project.org/web/packages/AUC")
4452 (synopsis "Compute the area under the curve of selected measures")
4454 "This package includes functions to compute the area under the curve of
4455 selected measures: the area under the sensitivity curve (AUSEC), the area
4456 under the specificity curve (AUSPC), the area under the accuracy
4457 curve (AUACC), and the area under the receiver operating characteristic
4458 curve (AUROC). The curves can also be visualized. Support for partial areas
4460 (license license:gpl2+)))
4462 (define-public r-calibrate
4464 (name "r-calibrate")
4469 (uri (cran-uri "calibrate" version))
4471 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
4472 (build-system r-build-system)
4475 (home-page "https://cran.r-project.org/web/packages/calibrate")
4476 (synopsis "Calibration of scatterplot and biplot axes")
4478 "This is a package for drawing calibrated scales with tick marks
4479 on (non-orthogonal) variable vectors in scatterplots and biplots.")
4480 (license license:gpl2)))
4482 (define-public r-shape
4489 (uri (cran-uri "shape" version))
4492 "0yqbrrx2ywmfl99s6d1n6jblc63k1mxbiqyv8y0kq8jws1g3w45r"))))
4493 (build-system r-build-system)
4494 (home-page "https://cran.r-project.org/web/packages/shape")
4495 (synopsis "Functions for plotting graphical shapes")
4497 "This package provides functions for plotting graphical shapes such as
4498 ellipses, circles, cylinders, arrows, ...")
4499 (license license:gpl3+)))
4501 (define-public r-globaloptions
4503 (name "r-globaloptions")
4508 (uri (cran-uri "GlobalOptions" version))
4510 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
4511 (properties `((upstream-name . "GlobalOptions")))
4512 (build-system r-build-system)
4515 (home-page "https://github.com/jokergoo/GlobalOptions")
4516 (synopsis "Generate functions to get or set global options")
4518 "This package provides more controls on the option values such as
4519 validation and filtering on the values, making options invisible or private.")
4520 (license license:gpl2+)))
4522 (define-public r-circlize
4529 (uri (cran-uri "circlize" version))
4532 "1iswb7dy08as3pbzxvhx5qlsbnwvp79nwg8m158nfz7y2d9xa0nn"))))
4533 (build-system r-build-system)
4535 (list r-colorspace r-globaloptions r-shape))
4538 (home-page "https://github.com/jokergoo/circlize")
4539 (synopsis "Circular visualization")
4541 "Circular layout is an efficient way to visualise huge amounts of
4542 information. This package provides an implementation of circular layout
4543 generation in R as well as an enhancement of available software. Its
4544 flexibility is based on the usage of low-level graphics functions such that
4545 self-defined high-level graphics can be easily implemented by users for
4546 specific purposes. Together with the seamless connection between the powerful
4547 computational and visual environment in R, it gives users more convenience and
4548 freedom to design figures for better understanding complex patterns behind
4549 multi-dimensional data.")
4550 (license license:gpl2+)))
4552 (define-public r-powerlaw
4559 (uri (cran-uri "poweRlaw" version))
4561 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
4562 (properties `((upstream-name . "poweRlaw")))
4563 (build-system r-build-system)
4568 (home-page "https://github.com/csgillespie/poweRlaw")
4569 (synopsis "Tools for the analysis of heavy tailed distributions")
4571 "This package provides an implementation of maximum likelihood estimators
4572 for a variety of heavy tailed distributions, including both the discrete and
4573 continuous power law distributions. Additionally, a goodness-of-fit based
4574 approach is used to estimate the lower cut-off for the scaling region.")
4575 ;; Any of these GPL versions.
4576 (license (list license:gpl2 license:gpl3))))
4578 (define-public r-compare
4585 (uri (cran-uri "compare" version))
4588 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
4589 (build-system r-build-system)
4590 (home-page "https://cran.r-project.org/web/packages/compare")
4591 (synopsis "Comparing objects for differences")
4593 "This package provides functions to compare a model object to a
4594 comparison object. If the objects are not identical, the functions can be
4595 instructed to explore various modifications of the objects (e.g., sorting
4596 rows, dropping names) to see if the modified versions are identical.")
4597 (license license:gpl2+)))
4599 (define-public r-dendextend
4601 (name "r-dendextend")
4606 (uri (cran-uri "dendextend" version))
4609 "0rl4f0b73s1gdjfxgpnz87lhv131qazxb6vsv2935ad266fd0bzc"))))
4610 (build-system r-build-system)
4612 (list r-ggplot2 r-magrittr r-viridis))
4615 (home-page "https://cran.r-project.org/web/packages/dendextend")
4616 (synopsis "Extending 'dendrogram' functionality in R")
4618 "This package offers a set of functions for extending @code{dendrogram}
4619 objects in R, letting you visualize and compare trees of hierarchical
4620 clusterings. You can adjust a tree's graphical parameters (the color, size,
4621 type, etc of its branches, nodes and labels) and visually and statistically
4622 compare different dendrograms to one another.")
4623 ;; Any of these versions
4624 (license (list license:gpl2 license:gpl3))))
4626 (define-public r-getoptlong
4628 (name "r-getoptlong")
4633 (uri (cran-uri "GetoptLong" version))
4636 "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc"))))
4637 (properties `((upstream-name . "GetoptLong")))
4638 (build-system r-build-system)
4642 (list r-crayon r-globaloptions r-rjson))
4645 (home-page "https://github.com/jokergoo/GetoptLong")
4646 (synopsis "Parsing command-line arguments and variable interpolation")
4648 "This is yet another command-line argument parser which wraps the
4649 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
4650 use in R. It also provides a simple way for variable interpolation in R.")
4651 (license license:gpl2+)))
4653 (define-public r-fastmatch
4655 (name "r-fastmatch")
4660 (uri (cran-uri "fastmatch" version))
4663 "0qcq1gwl9pijgp34giyq5y9rk0ly3d7xza2b7r68xx63ifqa1vqx"))))
4664 (build-system r-build-system)
4665 (home-page "https://www.rforge.net/fastmatch")
4666 (synopsis "Fast match function")
4668 "This package provides a fast @code{match} replacement for cases that
4669 require repeated look-ups. It is slightly faster that R's built-in
4670 @code{match} function on first match against a table, but extremely fast on
4671 any subsequent lookup as it keeps the hash table in memory.")
4672 (license license:gpl2)))
4681 (uri (cran-uri "ff" version))
4684 "1yl3ipzz9bjkfy9bbna7xz5n7iz4lchnw5l7agww7by764yk6iqa"))))
4685 (build-system r-build-system)
4686 (propagated-inputs (list r-bit))
4687 (home-page "http://ff.r-forge.r-project.org/")
4688 (synopsis "Memory-efficient storage of large data on disk and access functions")
4690 "This package provides data structures that are stored on disk but
4691 behave (almost) as if they were in RAM by transparently mapping only a section
4693 ;; error Architecture not supported.
4694 (supported-systems (delete "aarch64-linux" %supported-systems))
4695 (license license:gpl2)))
4697 (define-public r-ffbase
4704 (uri (cran-uri "ffbase" version))
4707 "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk"))))
4708 (build-system r-build-system)
4710 (list r-bit r-fastmatch r-ff))
4711 (home-page "https://github.com/edwindj/ffbase")
4712 (synopsis "Basic statistical functions for package 'ff'")
4714 "This package extends the out of memory vectors of @code{ff} with
4715 statistical functions and other utilities to ease their usage.")
4716 (license license:gpl3)))
4718 (define-public r-prettyunits
4720 (name "r-prettyunits")
4725 (uri (cran-uri "prettyunits" version))
4728 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
4729 (build-system r-build-system)
4730 (home-page "https://github.com/gaborcsardi/prettyunits")
4731 (synopsis "Pretty, human readable formatting of quantities")
4733 "This package provides tools for pretty, human readable formatting of
4735 (license license:expat)))
4737 (define-public r-princurve
4739 (name "r-princurve")
4743 (uri (cran-uri "princurve" version))
4746 "0wzk329bxljkzz57y220lsfckpsn45w348m6dcxh29zbj0ik65h2"))))
4747 (build-system r-build-system)
4750 (home-page "https://github.com/rcannood/princurve")
4751 (synopsis "Fit a principal curve in arbitrary dimension")
4752 (description "This package provides procedures for fitting a principal
4753 curve to a data matrix in arbitrary dimensions.")
4754 (license license:gpl2)))
4756 (define-public r-prismatic
4758 (name "r-prismatic")
4762 (uri (cran-uri "prismatic" version))
4765 "013i0mq4n8s2zbzvfrz1vjcn2a6l98bamslkcv1a3cn70gpphja9"))))
4766 (properties `((upstream-name . "prismatic")))
4767 (build-system r-build-system)
4768 (propagated-inputs (list r-farver))
4769 (home-page "https://github.com/EmilHvitfeldt/prismatic")
4770 (synopsis "Color manipulation tools")
4772 "Manipulate and visualize colors in a intuitive, low-dependency and functional
4774 (license license:expat)))
4776 (define-public r-reshape
4783 (uri (cran-uri "reshape" version))
4786 "0j203qmc076x5lp6q2xi4dq4xdb73jmsa42rpxp1c37knnrph4br"))))
4787 (build-system r-build-system)
4790 (home-page "http://had.co.nz/reshape")
4791 (synopsis "Flexibly reshape data")
4793 "Flexibly restructure and aggregate data using just two functions:
4794 @code{melt} and @code{cast}. This package provides them.")
4795 (license license:expat)))
4797 (define-public r-restrserve
4799 (name "r-restrserve")
4804 (uri (cran-uri "RestRserve" version))
4806 (base32 "1xfcp0y9l31815g1jk33mnkb6z68qpjl0gb4fj7f4578kx3v1c8p"))))
4807 (build-system r-build-system)
4819 (home-page "https://restrserve.org")
4820 (synopsis "R web API framework")
4822 "RestRserve is an R web API framework for building high-performance AND
4823 robust microservices and app backends. With Rserve backend on UNIX-like
4824 systems it is parallel by design. It will handle incoming requests in
4825 parallel - each request in a separate fork.")
4826 (license license:gpl2+)))
4828 (define-public r-progress
4835 (uri (cran-uri "progress" version))
4838 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
4839 (build-system r-build-system)
4841 (list r-crayon r-hms r-prettyunits r-r6))
4842 (home-page "https://github.com/gaborcsardi/progress")
4843 (synopsis "Terminal progress bars")
4845 "This package provides configurable progress bars. They may include
4846 percentage, elapsed time, and/or the estimated completion time. They work in
4847 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
4848 package also provides a C++ API, that works with or without Rcpp.")
4849 (license license:expat)))
4851 (define-public r-ggally
4858 (uri (cran-uri "GGally" version))
4861 "1r98zgh2grn8330cf26r1c20gl131zm778szvn5wj6q6pwv2yd9h"))))
4862 (properties `((upstream-name . "GGally")))
4863 (build-system r-build-system)
4879 (home-page "https://ggobi.github.io/ggally")
4880 (synopsis "Extension to ggplot2")
4882 "The R package ggplot2 is a plotting system based on the grammar of
4883 graphics. GGally extends ggplot2 by adding several functions to reduce the
4884 complexity of combining geometric objects with transformed data. Some of
4885 these functions include a pairwise plot matrix, a two group pairwise plot
4886 matrix, a parallel coordinates plot, a survival plot, and several functions to
4888 (license license:gpl2+)))
4890 (define-public r-proxy
4897 (uri (cran-uri "proxy" version))
4900 "0gsng2aggnljl4z82la9hpnd26hngzhj8fizx4wx22npqjj93694"))))
4901 (build-system r-build-system)
4902 (home-page "https://cran.r-project.org/web/packages/proxy")
4903 (synopsis "Distance and similarity measures")
4905 "This package provides an extensible framework for the efficient
4906 calculation of auto- and cross-proximities, along with implementations of the
4907 most popular ones.")
4908 (license license:gpl2)))
4917 (uri (cran-uri "sp" version))
4919 (base32 "077q1wh9ihhcn1338xspnd90hy16ljxsav1xcrxdxj4fyynhd6lk"))))
4920 (build-system r-build-system)
4925 (home-page "https://cran.r-project.org/web/packages/sp")
4926 (synopsis "Classes and methods for spatial data")
4928 "This package provides classes and methods for spatial data; the classes
4929 document where the spatial location information resides, for 2D or 3D data.
4930 Utility functions are provided, e.g. for plotting data as maps, spatial
4931 selection, as well as methods for retrieving coordinates, for subsetting,
4932 print, summary, etc.")
4933 (license license:gpl2+)))
4935 (define-public r-laplacesdemon
4937 (name "r-laplacesdemon")
4942 (uri (cran-uri "LaplacesDemon" version))
4944 (base32 "1dsfp65cg06f25zjzd5ib4qyn1alfhbhpgyvpcw5n6bszn13idap"))))
4945 (properties `((upstream-name . "LaplacesDemon")))
4946 (build-system r-build-system)
4947 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
4948 (synopsis "Complete environment for Bayesian inference")
4950 "This package provides a complete environment for Bayesian inference using
4951 a variety of different samplers.")
4952 (license license:expat)))
4954 (define-public r-rmtstat
4961 (uri (cran-uri "RMTstat" version))
4964 "1r1a2sdqv64m9cpm2pz6r8abf7l810126ayd8iq3gx86c7bjfj5v"))))
4965 (properties `((upstream-name . "RMTstat")))
4966 (build-system r-build-system)
4967 (home-page "https://cran.r-project.org/web/packages/RMTstat")
4968 (synopsis "Distributions, statistics and tests derived from random matrix theory")
4970 "This package provides functions for working with the Tracy-Widom laws
4971 and other distributions related to the eigenvalues of large Wishart
4973 (license license:bsd-3)))
4975 (define-public r-rmpi
4981 (uri (cran-uri "Rmpi" version))
4984 "06mxqgrimhfsag5giv810c7ycdbaycqs4qcj41pnfbj0jypw32im"))))
4985 (properties `((upstream-name . "Rmpi")))
4986 (build-system r-build-system)
4988 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
4989 #:phases (modify-phases %standard-phases
4990 (add-before 'install 'mpi-setup
4996 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
4997 (synopsis "R interface to message-passing interface (MPI)")
4999 "This package provides an interface (wrapper) to MPI APIs. It also
5000 provides an interactive R manager and worker environment.")
5001 (license license:gpl2+)))
5003 (define-public r-lmoments
5010 (uri (cran-uri "Lmoments" version))
5013 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
5014 (properties `((upstream-name . "Lmoments")))
5015 (build-system r-build-system)
5017 (list r-rcpp r-rcpparmadillo))
5018 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
5019 (synopsis "L-moments and quantile mixtures")
5021 "This package contains functions to estimate L-moments and trimmed
5022 L-moments from the data. It also contains functions to estimate the
5023 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
5024 quantile mixture from L-moments and trimmed L-moments.")
5025 (license license:gpl2)))
5027 (define-public r-distillery
5029 (name "r-distillery")
5034 (uri (cran-uri "distillery" version))
5037 "1ymmxyamkq0zbz2m4gllln1ihks2hcib6gs0mls92as79srz122b"))))
5038 (build-system r-build-system)
5039 (home-page "https://ral.ucar.edu/staff/ericg/")
5040 (synopsis "Functions for confidence intervals and object information")
5042 "This package provides some very simple method functions for confidence
5043 interval calculation and to distill pertinent information from a potentially
5044 complex object; primarily used in common with the packages extRemes and
5046 (license license:gpl2+)))
5048 (define-public r-etrunct
5054 (uri (cran-uri "etrunct" version))
5057 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr"))))
5058 (properties `((upstream-name . "etrunct")))
5059 (build-system r-build-system)
5060 (home-page "https://cran.r-project.org/web/packages/etrunct")
5061 (synopsis "Computes moments of univariate truncated T distribution")
5062 (description "This package computes moments of univariate truncated
5063 T distribution. There is only one exported function, @code{e_trunct},
5064 which should be seen for details.")
5065 (license license:expat)))
5067 (define-public r-excelr
5074 (uri (cran-uri "excelR" version))
5076 (base32 "1pb4sy54zjv5vrh7gjjv7qlpab74km6mfsmfyl0yhmr0jx01hrw0"))
5078 '(delete-file "inst/htmlwidgets/lib/jexcel/js/jexcel.min.js"))))
5079 (properties `((upstream-name . "excelR")))
5080 (build-system r-build-system)
5083 (modify-phases %standard-phases
5084 (add-after 'unpack 'process-javascript
5085 (lambda* (#:key inputs #:allow-other-keys)
5086 (with-directory-excursion "inst/htmlwidgets/lib/jexcel/js/"
5087 (let ((source (assoc-ref inputs "js-jexcel"))
5088 (target "jexcel.min.js"))
5089 (format #true "Processing ~a --> ~a~%"
5091 (invoke "esbuild" source "--minify"
5092 (string-append "--outfile=" target)))))))))
5094 `(("esbuild" ,esbuild)
5095 ;; There is no tag for this particular commit, but comparison of the
5096 ;; contents of the JavaScript files point to this commit as the most
5101 (uri (string-append "https://raw.githubusercontent.com/jspreadsheet/ce/"
5102 "8af1960f76e6803bebc5750013d2ebe95354e88a/dist/jexcel.js"))
5105 "0y88hsr9d8cpnvdmbm17m328pc4kc5wbcv02kzmhm0bryzhviw7h"))))))
5106 (propagated-inputs (list r-htmlwidgets r-jsonlite))
5107 (home-page "https://github.com/Swechhya/excelR")
5108 (synopsis "Wrapper of the JavaScript library jExcel")
5110 "This package provides an R interface to the jExcel library to
5111 create web-based interactive tables and spreadsheets compatible with
5112 spreadsheet software.")
5113 (license license:expat)))
5115 (define-public r-extremes
5122 (uri (cran-uri "extRemes" version))
5125 "19q560prq02h3bwk01jb68693qb5bhsv8wiqhia7v5knm34qv8x7"))))
5126 (properties `((upstream-name . "extRemes")))
5127 (build-system r-build-system)
5129 (list r-distillery r-lmoments))
5130 (home-page "https://www.assessment.ucar.edu/toolkit/")
5131 (synopsis "Extreme value analysis")
5133 "ExtRemes is a suite of functions for carrying out analyses on the
5134 extreme values of a process of interest; be they block maxima over long blocks
5135 or excesses over a high threshold.")
5136 (license license:gpl2+)))
5138 (define-public r-lmtest
5145 (uri (cran-uri "lmtest" version))
5148 "15yr2kx08wy085bnziqmj1p6hf9mg3qp2a8465jk2df6di6hsh34"))))
5149 (build-system r-build-system)
5154 (home-page "https://cran.r-project.org/web/packages/lmtest")
5155 (synopsis "Testing linear regression models")
5157 "This package provides a collection of tests, data sets, and examples for
5158 diagnostic checking in linear regression models. Furthermore, some generic
5159 tools for inference in parametric models are provided.")
5160 ;; Either version is okay
5161 (license (list license:gpl2 license:gpl3))))
5163 (define-public r-idr
5169 (uri (cran-uri "idr" version))
5172 "1r6icxf0c0y9wvihwmkk5xqscr1qhacqk3w2076kjm2993f10fbb"))))
5173 (build-system r-build-system)
5174 (home-page "https://cran.r-project.org/web/packages/idr/")
5175 (synopsis "Irreproducible discovery rate")
5177 "This is a package for estimating the copula mixture model and plotting
5178 correspondence curves in \"Measuring reproducibility of high-throughput
5179 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
5180 by Li, Brown, Huang, and Bickel")
5181 (license license:gpl2+)))
5183 (define-public r-inline
5189 (uri (cran-uri "inline" version))
5192 "1mcr9hgq6kkq03n7pkcccxa7vg8jma0q7lfxc5vvkc6snydk1s8f"))))
5193 (build-system r-build-system)
5194 (home-page "https://cran.r-project.org/web/packages/inline")
5195 (synopsis "Functions to inline C, C++, Fortran function calls from R")
5197 "This package provides functionality to dynamically define R functions
5198 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
5199 @code{.Call} calling conventions.")
5200 ;; Any version of the LGPL.
5201 (license license:lgpl3+)))
5203 (define-public r-inum
5209 (uri (cran-uri "inum" version))
5212 "1khkzja8lwn9075864vbyajqina9m588ahf1fsrrajrsqilyzssz"))))
5213 (build-system r-build-system)
5216 (home-page "https://cran.r-project.org/web/packages/inum/")
5217 (synopsis "Interval and enum-type representation of vectors")
5219 "This package provides an enum-type representation of vectors and
5220 representation of intervals, including a method of coercing variables
5222 (license license:gpl2)))
5223 (define-public r-invgamma
5229 (uri (cran-uri "invgamma" version))
5232 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a"))))
5233 (properties `((upstream-name . "invgamma")))
5234 (build-system r-build-system)
5235 (home-page "https://github.com/dkahle/invgamma")
5236 (synopsis "Inverse gamma distribution")
5237 (description "This package provides a light weight implementation of the
5238 standard distribution functions for the inverse gamma distribution, wrapping
5239 those for the gamma distribution in the @code{stats} package.")
5240 (license license:gpl2)))
5242 (define-public r-bdsmatrix
5244 (name "r-bdsmatrix")
5249 (uri (cran-uri "bdsmatrix" version))
5252 "1g300x11rv56f826mbv7mbb67a5xz3dv74hpjc18jh3q8gap3j7r"))))
5253 (properties `((upstream-name . "bdsmatrix")))
5254 (build-system r-build-system)
5255 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
5256 (synopsis "Routines for block diagonal symmetric matrices")
5258 "This package provides procedures to work with block diagonal symmetric
5259 matrices, a special case of sparse matrices.")
5260 (license license:lgpl2.0)))
5262 (define-public r-bbmle
5269 (uri (cran-uri "bbmle" version))
5272 "0mdj21q7k0fp4cj7la14vmcjmp49zqm57g7r6zrwmxpv0acwda46"))))
5273 (build-system r-build-system)
5283 (home-page "https://cran.r-project.org/web/packages/bbmle")
5284 (synopsis "Tools for General Maximum Likelihood Estimation")
5286 "This package provides methods and functions for fitting maximum
5287 likelihood models in R. This package modifies and extends the @code{mle}
5288 classes in the @code{stats4} package.")
5289 ;; Any version of the GPL
5290 (license license:gpl2+)))
5292 (define-public r-emdbook
5299 (uri (cran-uri "emdbook" version))
5302 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
5303 (build-system r-build-system)
5305 (list r-bbmle r-coda r-lattice r-mass r-plyr))
5306 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
5307 (synopsis "Support functions and data for \"Ecological Models and Data\"")
5309 "This package provides auxiliary functions and data sets for \"Ecological
5310 Models and Data\", a book presenting maximum likelihood estimation and related
5311 topics for ecologists (ISBN 978-0-691-12522-0).")
5313 (license (list license:gpl2 license:gpl3))))
5315 (define-public r-lpsolve
5322 (uri (cran-uri "lpSolve" version))
5325 "0amvxki4l2sp60adcc6ra7kbqjrfv55gbn6kasq04klihi8ix88q"))))
5326 (properties `((upstream-name . "lpSolve")))
5327 (build-system r-build-system)
5328 (home-page "https://cran.r-project.org/web/packages/lpSolve")
5329 (synopsis "R interface to Lp_solve to solve linear/integer programs")
5331 "Lp_solve is software for solving linear, integer and mixed integer
5332 programs. This implementation supplies a \"wrapper\" function in C and some R
5333 functions that solve general linear/integer problems, assignment problems, and
5334 transportation problems.")
5335 (license license:lgpl2.0)))
5337 (define-public r-limsolve
5344 (uri (cran-uri "limSolve" version))
5347 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
5348 (properties `((upstream-name . "limSolve")))
5349 (build-system r-build-system)
5351 (list r-lpsolve r-mass r-quadprog))
5352 (native-inputs (list gfortran))
5353 (home-page "https://cran.r-project.org/web/packages/limSolve")
5354 (synopsis "Solving linear inverse models")
5356 "This package provides functions that:
5359 @item find the minimum/maximum of a linear or quadratic function,
5360 @item sample an underdetermined or overdetermined system,
5361 @item solve a linear system Ax=B for the unknown x.
5364 It includes banded and tridiagonal linear systems. The package calls Fortran
5365 functions from LINPACK.")
5367 (license (list license:gpl2+ license:gpl3+))))
5369 (define-public r-fitdistrplus
5371 (name "r-fitdistrplus")
5376 (uri (cran-uri "fitdistrplus" version))
5379 "0nhgjvwya95v6b9khbsgp44lw10xg35w61lmka1v6wq7yh827izk"))))
5380 (build-system r-build-system)
5382 (list r-mass r-survival))
5385 (home-page "http://riskassessment.r-forge.r-project.org")
5386 (synopsis "Fitting a parametric distribution from data")
5388 "This package extends the @code{fitdistr} function of the MASS package
5389 with several functions to help the fit of a parametric distribution to
5390 non-censored or censored data. Censored data may contain left-censored,
5391 right-censored and interval-censored values, with several lower and upper
5392 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
5393 provides moment matching (MME), quantile matching (QME) and maximum
5394 goodness-of-fit estimation (MGE) methods (available only for non-censored
5395 data). Weighted versions of MLE, MME and QME are available.")
5396 (license license:gpl2+)))
5398 (define-public r-energy
5405 (uri (cran-uri "energy" version))
5408 "19xyw5bkyzfk22gly2ca2nsznqnrhaq4a77727kr1k26bj3y8gal"))))
5409 (build-system r-build-system)
5411 (list r-boot r-gsl r-rcpp))
5412 (home-page "https://cran.r-project.org/web/packages/energy")
5413 (synopsis "Multivariate inference via the energy of data")
5415 "This package provides e-statistics (energy) tests and statistics for
5416 multivariate and univariate inference, including distance correlation,
5417 one-sample, two-sample, and multi-sample tests for comparing multivariate
5418 distributions, are implemented. Measuring and testing multivariate
5419 independence based on distance correlation, partial distance correlation,
5420 multivariate goodness-of-fit tests, clustering based on energy distance,
5421 testing for multivariate normality, distance components (disco) for
5422 non-parametric analysis of structured data, and other energy
5423 statistics/methods are implemented.")
5424 (license license:gpl2+)))
5426 (define-public r-suppdists
5428 (name "r-suppdists")
5433 (uri (cran-uri "SuppDists" version))
5436 "025b9nlxz62wk84295csyzbncpn80i3iby3sxdigf3swcgi2fmbb"))))
5437 (properties `((upstream-name . "SuppDists")))
5438 (build-system r-build-system)
5439 (home-page "https://cran.r-project.org/web/packages/SuppDists")
5440 (synopsis "Supplementary distributions")
5442 "This package provides ten distributions supplementing those built into
5443 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
5444 Spearman's rho, maximum F ratio, the Pearson product moment correlation
5445 coefficient, Johnson distributions, normal scores and generalized
5446 hypergeometric distributions. In addition two random number generators of
5447 George Marsaglia are included.")
5448 (license license:gpl2+)))
5450 (define-public r-ksamples
5457 (uri (cran-uri "kSamples" version))
5460 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
5461 (properties `((upstream-name . "kSamples")))
5462 (build-system r-build-system)
5465 (home-page "https://cran.r-project.org/web/packages/kSamples")
5466 (synopsis "K-Sample rank tests and their combinations")
5468 "This package provides tools to compares k samples using the
5469 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
5470 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
5471 test. It computes asymptotic, simulated or (limited) exact P-values, all
5472 valid under randomization, with or without ties, or conditionally under random
5473 sampling from populations, given the observed tie pattern. Except for Steel's
5474 test and the JT test it also combines these tests across several blocks of
5476 (license license:gpl2+)))
5478 (define-public r-cvst
5485 (uri (cran-uri "CVST" version))
5488 "0bgk0d6w3dyhb5s30idnp6jpb3m8wf3b79wqlg127wwm0cird8pg"))))
5489 (properties `((upstream-name . "CVST")))
5490 (build-system r-build-system)
5492 (list r-kernlab r-matrix))
5493 (home-page "https://cran.r-project.org/web/packages/CVST")
5494 (synopsis "Fast cross-validation via sequential testing")
5496 "This package implements the fast cross-validation via sequential
5497 testing (CVST) procedure. CVST is an improved cross-validation procedure
5498 which uses non-parametric testing coupled with sequential analysis to
5499 determine the best parameter set on linearly increasing subsets of the data.
5500 Additionally to the CVST the package contains an implementation of the
5501 ordinary k-fold cross-validation with a flexible and powerful set of helper
5502 objects and methods to handle the overall model selection process. The
5503 implementations of the Cochran's Q test with permutations and the sequential
5504 testing framework of Wald are generic and can therefore also be used in other
5506 (license license:gpl2+)))
5508 (define-public r-squarem
5515 (uri (cran-uri "SQUAREM" version))
5518 "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6"))))
5519 (properties `((upstream-name . "SQUAREM")))
5520 (build-system r-build-system)
5521 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
5522 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
5524 "This package provides algorithms for accelerating the convergence of
5525 slow, monotone sequences from smooth, contraction mapping such as the EM
5526 algorithm. It can be used to accelerate any smooth, linearly convergent
5527 acceleration scheme. A tutorial style introduction to this package is
5528 available in a vignette.")
5529 (license license:gpl2+)))
5531 (define-public r-progressr
5533 (name "r-progressr")
5538 (uri (cran-uri "progressr" version))
5540 (base32 "1nbc6vvsyqa1gvh1a1m4prnvng88wsa0r35i9fiwq84a6j18qrnq"))))
5541 (properties `((upstream-name . "progressr")))
5542 (build-system r-build-system)
5545 (home-page "https://progressr.futureverse.org")
5546 (synopsis "Inclusive, unifying API for progress updates")
5548 "This package provides a minimal, unifying API for scripts and packages
5549 to report progress updates from anywhere including when using parallel
5550 processing. The package is designed such that the developer can to focus on
5551 what progress should be reported on without having to worry about how to
5552 present it. The end user has full control of how, where, and when to render
5553 these progress updates.")
5554 (license license:gpl3+)))
5556 (define-public r-lava
5563 (uri (cran-uri "lava" version))
5566 "0bi3c1aqwlq7jbz4raz6vga4r264w7lldi0i62xjlbl7hnlgi23s"))))
5567 (build-system r-build-system)
5569 (list r-future-apply r-numderiv r-progressr r-squarem r-survival))
5572 (home-page "https://github.com/kkholst/lava")
5573 (synopsis "Latent variable models")
5575 "This package provides tools for the estimation and simulation of latent
5577 (license license:gpl3)))
5579 (define-public r-drr
5586 (uri (cran-uri "DRR" version))
5589 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
5590 (properties `((upstream-name . "DRR")))
5591 (build-system r-build-system)
5593 (list r-cvst r-kernlab r-matrix))
5594 (home-page "https://cran.r-project.org/web/packages/DRR")
5595 (synopsis "Dimensionality reduction via regression")
5597 "This package provides an implementation of dimensionality reduction via
5598 regression using Kernel Ridge Regression.")
5599 (license license:gpl3)))
5601 (define-public r-prodlim
5604 (version "2019.11.13")
5608 (uri (cran-uri "prodlim" version))
5611 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
5612 (build-system r-build-system)
5614 (list r-kernsmooth r-lava r-rcpp r-survival))
5615 (home-page "https://cran.r-project.org/web/packages/prodlim")
5616 (synopsis "Product-limit estimation for censored event history analysis")
5618 "This package provides a fast and user-friendly implementation of
5619 nonparametric estimators for censored event history (survival) analysis with
5620 the Kaplan-Meier and Aalen-Johansen methods.")
5621 (license license:gpl2+)))
5623 (define-public r-dimred
5630 (uri (cran-uri "dimRed" version))
5633 "05zlkf6hjdqqr1sgw7ww9f17vjnsiqfaj9kvdvi146phh53v2zls"))))
5634 (properties `((upstream-name . "dimRed")))
5635 (build-system r-build-system)
5637 (list r-drr r-magrittr))
5640 (home-page "https://github.com/gdkrmr/dimRed")
5641 (synopsis "Framework for dimensionality reduction")
5643 "This package provides a collection of dimensionality reduction
5644 techniques from R packages and provides a common interface for calling the
5646 (license license:gpl3)))
5648 (define-public r-timedate
5651 (version "4021.104")
5655 (uri (cran-uri "timeDate" version))
5658 "03ncgbc9igiwl4s8pa94nj2v7aw3gw8ay51pwvv9gkv2f7l7dvh3"))))
5659 (properties `((upstream-name . "timeDate")))
5660 (build-system r-build-system)
5661 (home-page "https://www.rmetrics.org")
5662 (synopsis "Chronological and calendar objects")
5664 "This package provides an environment for teaching \"Financial
5665 Engineering and Computational Finance\" and for managing chronological and
5667 (license license:gpl2+)))
5669 (define-public r-magic
5676 (uri (cran-uri "magic" version))
5679 "1gybia2aq80ldk1d845y5srncfzbbmpqhgl7vfaz7qqqjs6d85j5"))))
5680 (build-system r-build-system)
5683 (home-page "https://github.com/RobinHankin/magic.git")
5684 (synopsis "Create and investigate magic squares")
5686 "This package provides a collection of efficient, vectorized algorithms
5687 for the creation and investigation of magic squares and hypercubes, including
5688 a variety of functions for the manipulation and analysis of arbitrarily
5689 dimensioned arrays.")
5690 (license license:gpl2)))
5692 (define-public r-rmysql
5699 (uri (cran-uri "RMySQL" version))
5702 "05aavyggyjv46awa7ggbxlfcy9707vak5kh7kj0ljdx8zga7xb7l"))))
5703 (properties `((upstream-name . "RMySQL")))
5704 (build-system r-build-system)
5706 (list `(,mariadb "dev") zlib))
5709 (home-page "https://github.com/r-dbi/RMySQL")
5710 (synopsis "Database interface and MySQL driver for R")
5712 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
5713 package contains an old implementation based on legacy code from S-PLUS which
5714 is being phased out. A modern MySQL client based on Rcpp is available from
5715 the RMariaDB package.")
5716 (license license:gpl2)))
5718 (define-public r-rpostgresql
5720 (name "r-rpostgresql")
5725 (uri (cran-uri "RPostgreSQL" version))
5728 "1ijnsly8wgy6cfib4xvdaz2g9hk1gzg7q52r37zkvc7jjh0gdbdn"))))
5729 (properties `((upstream-name . "RPostgreSQL")))
5730 (build-system r-build-system)
5735 (home-page "https://github.com/tomoakin/RPostgreSQL")
5736 (synopsis "R interface to the PostgreSQL database system")
5738 "This package provides a Database Interface (DBI) compliant driver for R
5739 to access PostgreSQL database systems.")
5740 ;; The whole package is released under GPL version 2. It includes code
5741 ;; under the PostgreSQL license.
5742 (license license:gpl2)))
5744 (define-public r-linprog
5751 (uri (cran-uri "linprog" version))
5754 "1d34m2nyk7m6j2dci69bhy5mlw479xax1517j7f14pq7vhpsm9l1"))))
5755 (build-system r-build-system)
5756 (propagated-inputs (list r-lpsolve))
5757 (home-page "http://linprog.r-forge.r-project.org/")
5758 (synopsis "Linear programming and optimization")
5760 "This package can be used to solve Linear Programming / Linear
5761 Optimization problems by using the simplex algorithm.")
5762 (license license:gpl2+)))
5764 (define-public r-geometry
5771 (uri (cran-uri "geometry" version))
5774 "0wplszaxi6phxffp3zww5alwnfbh9521qi43h65w057lrm1pmj2j"))))
5775 (build-system r-build-system)
5777 (list r-magic r-linprog r-lpsolve r-rcpp r-rcppprogress))
5778 (home-page "http://geometry.r-forge.r-project.org/")
5779 (synopsis "Mesh generator and surface tessellator")
5781 "This package makes the qhull library available in R, in a similar manner
5782 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
5783 intersections about a point, Voronoi diagrams, furthest-site Delaunay
5784 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
5785 and higher dimensions. It implements the Quickhull algorithm for computing
5786 the convex hull. Qhull does not support constrained Delaunay triangulations,
5787 or mesh generation of non-convex objects, but the package does include some R
5788 functions that allow for this. Currently the package only gives access to
5789 Delaunay triangulation and convex hull computation.")
5790 ;; The Qhull sources are included and are distributed under a custom
5791 ;; non-copyleft license. The R sources are released under GPL version 2.
5792 (license (list license:gpl2
5793 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
5795 (define-public r-ddalpha
5802 (uri (cran-uri "ddalpha" version))
5805 "1bjfgb3lbzhjb5wx9hzp90jppq7vnj59bmd2n9ymi8sh1570m9p4"))))
5806 (build-system r-build-system)
5817 (home-page "https://cran.r-project.org/web/packages/ddalpha")
5818 (synopsis "Depth-Based classification and calculation of data depth")
5820 "This package contains procedures for depth-based supervised learning,
5821 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
5822 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
5823 statistical depth function to a compact low-dimensional space, where the final
5824 classification is done. It also offers an extension to functional data and
5825 routines for calculating certain notions of statistical depth functions. 50
5826 multivariate and 5 functional classification problems are included.")
5827 (license license:gpl2)))
5829 (define-public r-gower
5836 (uri (cran-uri "gower" version))
5839 "0p9qx9aafkdm7wibfwk59jzw6vspsff6zwp84bc40lg0myxbf737"))))
5840 (build-system r-build-system)
5841 (home-page "https://github.com/markvanderloo/gower")
5842 (synopsis "Gower's distance")
5844 "This package provides tools to compute Gower's distance (or similarity)
5845 coefficient between records, and to compute the top-n matches between records.
5846 Core algorithms are executed in parallel on systems supporting OpenMP.")
5847 (license license:gpl3)))
5849 (define-public r-rcpproll
5856 (uri (cran-uri "RcppRoll" version))
5859 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
5860 (properties `((upstream-name . "RcppRoll")))
5861 (build-system r-build-system)
5864 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
5865 (synopsis "Efficient rolling and windowed operations")
5867 "This package provides fast and efficient routines for common rolling /
5868 windowed operations. Routines for the efficient computation of windowed mean,
5869 median, sum, product, minimum, maximum, standard deviation and variance are
5871 (license license:gpl2+)))
5873 (define-public r-ipred
5880 (uri (cran-uri "ipred" version))
5883 "162ckhqn24l0l5ih7qi2k3lxw5iprm1g5a34q1ik0b9wv5ia0s31"))))
5884 (build-system r-build-system)
5892 (home-page "https://cran.r-project.org/web/packages/ipred")
5893 (synopsis "Improved predictors")
5895 "This package provides improved predictive models by indirect
5896 classification and bagging for classification, regression and survival
5897 problems as well as resampling based estimators of prediction error.")
5898 (license license:gpl2+)))
5900 (define-public r-psych
5907 (uri (cran-uri "psych" version))
5910 "08f3byqwabgkqcxwpjbsxdcjkdg012iraqinw0fzskfl1srzkhyw"))))
5911 (build-system r-build-system)
5913 (list r-lattice r-mnormt r-nlme))
5916 (home-page "https://cran.r-project.org/web/packages/psych/")
5917 (synopsis "Procedures for psychological, psychometric, and personality research")
5919 "This package provides a general purpose toolbox for personality,
5920 psychometric theory and experimental psychology. Functions are primarily for
5921 multivariate analysis and scale construction using factor analysis, principal
5922 component analysis, cluster analysis and reliability analysis, although others
5923 provide basic descriptive statistics. Item Response Theory is done using
5924 factor analysis of tetrachoric and polychoric correlations. Functions for
5925 analyzing data at multiple levels include within and between group statistics,
5926 including correlations and factor analysis. Functions for simulating and
5927 testing particular item and test structures are included. Several functions
5928 serve as a useful front end for structural equation modeling. Graphical
5929 displays of path diagrams, factor analysis and structural equation models are
5930 created using basic graphics.")
5931 (license license:gpl2+)))
5933 (define-public r-generics
5940 (uri (cran-uri "generics" version))
5943 "0lyhhwik0w7m5h3fbwl2f52gc1v2g6g6h6sc47sa9f58pxin213m"))))
5944 (build-system r-build-system)
5945 (home-page "https://github.com/r-lib/generics")
5946 (synopsis "Common S3 generics not provided by base R methods")
5948 "In order to reduce potential package dependencies and conflicts,
5949 generics provides a number of commonly used S3 generics that are not provided
5950 by base R methods related to model fitting.")
5951 (license license:gpl2)))
5953 (define-public r-broom
5960 (uri (cran-uri "broom" version))
5963 "14i8729m38nxf5q344isgq4006p3b50wi3q8jgckxqphhnj5lpjb"))))
5964 (build-system r-build-system)
5979 (home-page "https://github.com/tidyverse/broom")
5980 (synopsis "Convert statistical analysis objects into tidy data frames")
5982 "This package provides tools to convert statistical analysis objects from
5983 R into tidy data frames, so that they can more easily be combined, reshaped
5984 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
5985 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
5986 summarizes a model's statistical findings such as coefficients of a
5987 regression; @code{augment}, which adds columns to the original data such as
5988 predictions, residuals and cluster assignments; and @code{glance}, which
5989 provides a one-row summary of model-level statistics.")
5990 (license license:expat)))
5992 (define-public r-recipes
5999 (uri (cran-uri "recipes" version))
6002 "1jav29biq13xf0vg9kj3k6khqb71hqak26kxxi0vy29l849f4fly"))))
6003 (build-system r-build-system)
6027 (home-page "https://github.com/topepo/recipes")
6028 (synopsis "Preprocessing tools to create design matrices")
6030 "Recipes is an extensible framework to create and preprocess design
6031 matrices. Recipes consist of one or more data manipulation and analysis
6032 \"steps\". Statistical parameters for the steps can be estimated from an
6033 initial data set and then applied to other data sets. The resulting design
6034 matrices can then be used as inputs into statistical or machine learning
6036 (license license:gpl2)))
6038 (define-public r-pdist
6045 (uri (cran-uri "pdist" version))
6048 "0bvg8si81hs79v39d7svv4zbv2p0sk2r6m9vamibvkh9qvl4x406"))))
6049 (build-system r-build-system)
6050 (home-page "https://github.com/jeffwong/pdist")
6051 (synopsis "Partitioned distance function")
6053 "Pdist computes the euclidean distance between rows of a matrix X and
6054 rows of another matrix Y. Previously, this could be done by binding the two
6055 matrices together and calling @code{dist}, but this creates unnecessary
6056 computation by computing the distances between a row of X and another row of
6057 X, and likewise for Y. Pdist strictly computes distances across the two
6058 matrices, not within the same matrix, making computations significantly faster
6059 for certain use cases.")
6060 (license license:gpl3+)))
6062 (define-public r-ggrepel
6069 (uri (cran-uri "ggrepel" version))
6072 "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9"))))
6073 (build-system r-build-system)
6075 (list r-ggplot2 r-rcpp r-rlang r-scales))
6077 (list r-knitr)) ; for vignettes
6078 (home-page "https://github.com/slowkow/ggrepel")
6079 (synopsis "Repulsive text and label geometries for ggplot2")
6081 "This package provides text and label geometries for ggplot2 that help to
6082 avoid overlapping text labels. Labels repel away from each other and away
6083 from the data points.")
6084 (license license:gpl3)))
6086 (define-public r-coro
6093 (uri (cran-uri "coro" version))
6095 (base32 "0wvxdpdh3xrskz5s5wfkva856x849knx1jigbf0ff6s6n6qjjxsf"))))
6096 (properties `((upstream-name . "coro")))
6097 (build-system r-build-system)
6098 (propagated-inputs (list r-rlang))
6099 (native-inputs (list r-knitr))
6100 (home-page "https://github.com/r-lib/coro")
6101 (synopsis "Coroutines for R")
6103 "This package provides coroutines for R, a family of functions that can
6104 be suspended and resumed later on. This includes async functions (which
6105 await) and generators (which yield). Async functions are based on the
6106 concurrency framework of the @code{promises} package. Generators are based on
6107 a dependency free iteration protocol defined in @code{coro} and are compatible
6108 with iterators from the @code{reticulate} package.")
6109 (license license:expat)))
6111 (define-public r-corrplot
6118 (uri (cran-uri "corrplot" version))
6121 "1g98jk6xsl08z4n6sy5vriif99m31zhbz7j3dh1kfj4w7yb9zh78"))))
6122 (build-system r-build-system)
6125 (home-page "https://github.com/taiyun/corrplot")
6126 (synopsis "Visualization of a correlation matrix")
6128 "This package provides a graphical display of a correlation matrix or
6129 general matrix. It also contains some algorithms to do matrix reordering. In
6130 addition, corrplot is good at details, including choosing color, text labels,
6131 color labels, layout, etc.")
6132 ;; Any version of the GPL
6133 (license license:gpl2+)))
6135 (define-public r-stringdist
6137 (name "r-stringdist")
6142 (uri (cran-uri "stringdist" version))
6144 (base32 "1fv1hbdlm8qwx57b2aj50mw0say5k48awzavx65mfk67qp6ddk7g"))))
6145 (build-system r-build-system)
6146 (home-page "https://github.com/markvanderloo/stringdist")
6147 (synopsis "Approximate string matching and string distance functions")
6149 "This package implements an approximate string matching version of R's
6150 native @code{match} function. It can calculate various string distances based
6151 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment),
6152 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
6153 Jaro-Winkler). An implementation of soundex is provided as well. Distances
6154 can be computed between character vectors while taking proper care of encoding
6155 or between integer vectors representing generic sequences.")
6156 (license license:gpl3+)))
6158 (define-public r-ucminf
6165 (uri (cran-uri "ucminf" version))
6168 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
6169 (build-system r-build-system)
6170 (native-inputs (list gfortran))
6171 (home-page "https://cran.r-project.org/web/packages/ucminf/")
6172 (synopsis "General-purpose unconstrained non-linear optimization")
6174 "This package provides an implementation of an algorithm for
6175 general-purpose unconstrained non-linear optimization. The algorithm is of
6176 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
6177 search with a trust region type monitoring of the input to the line search
6178 algorithm. The interface of @code{ucminf} is designed for easy interchange
6179 with the package @code{optim}.")
6180 (license license:gpl2+)))
6182 (define-public r-usedist
6189 (uri (cran-uri "usedist" version))
6191 (base32 "0ddf1zcalbrn293qmr9kdzz3x16fzc4k1bwb1pjmwnspisqfi8kj"))))
6192 (properties `((upstream-name . "usedist")))
6193 (build-system r-build-system)
6194 (home-page "https://cran.r-project.org/package=usedist")
6195 (synopsis "Distance matrix utilities")
6197 "This package provides functions to re-arrange, extract, and work with
6199 (license license:gpl3)))
6201 (define-public r-useful
6207 (uri (cran-uri "useful" version))
6210 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
6211 (properties `((upstream-name . "useful")))
6212 (build-system r-build-system)
6222 (home-page "https://github.com/jaredlander/useful")
6223 (synopsis "Collection of handy, useful functions")
6224 (description "This package provides a set of little functions that have been
6225 found useful to do little odds and ends such as plotting the results of K-means
6226 clustering, substituting special text characters, viewing parts of a
6227 @code{data.frame}, constructing formulas from text and building design and
6228 response matrices.")
6229 (license license:bsd-3)))
6231 (define-public r-ordinal
6234 (version "2019.12-10")
6238 (uri (cran-uri "ordinal" version))
6241 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
6242 (build-system r-build-system)
6244 (list r-mass r-matrix r-numderiv r-ucminf))
6245 (home-page "https://github.com/runehaubo/ordinal")
6246 (synopsis "Regression models for ordinal data")
6248 "This package provides an implementation of cumulative link (mixed)
6249 models also known as ordered regression models, proportional odds models,
6250 proportional hazards models for grouped survival times and ordered models.
6251 Estimation is via maximum likelihood and mixed models are fitted with the
6252 Laplace approximation and adaptive Gauss-Hermite quadrature.")
6253 (license license:gpl2+)))
6255 (define-public r-jomo
6262 (uri (cran-uri "jomo" version))
6265 "1zck7p872k080hyfs0hibq7v13zmsry1jdlnq7k33ff1iljbq99d"))))
6266 (build-system r-build-system)
6268 (list r-lme4 r-mass r-ordinal r-survival r-tibble))
6269 (home-page "https://cran.r-project.org/web/packages/jomo/")
6270 (synopsis "Multilevel Joint Modelling Multiple Imputation")
6272 "Similarly to Schafer's package pan, jomo is a package for multilevel
6273 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
6274 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
6275 possibility of handling binary and categorical data through latent normal
6276 variables, the option to use cluster-specific covariance matrices and to
6277 impute compatibly with the substantive model.")
6278 (license license:gpl2)))
6280 (define-public r-pan
6287 (uri (cran-uri "pan" version))
6290 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
6291 (build-system r-build-system)
6292 (native-inputs (list gfortran))
6293 (home-page "https://cran.r-project.org/web/packages/pan/")
6294 (synopsis "Multiple imputation for multivariate panel or clustered data")
6296 "This package implements multiple imputation for multivariate panel or
6298 (license license:gpl3)))
6300 (define-public r-mitml
6307 (uri (cran-uri "mitml" version))
6310 "00i18nnvrdrg91crgcp2a431xs71cawaip3xkqk2myv0iav3xga9"))))
6311 (build-system r-build-system)
6313 (list r-haven r-jomo r-pan))
6316 (home-page "https://cran.r-project.org/web/packages/mitml/")
6317 (synopsis "Tools for multiple imputation in multilevel modeling")
6319 "This package provides tools for multiple imputation of missing data in
6320 multilevel modeling. It includes a user-friendly interface to the packages
6321 pan and jomo, and several functions for visualization, data management and the
6322 analysis of multiply imputed data sets.")
6323 (license license:gpl2+)))
6325 (define-public r-mice
6332 (uri (cran-uri "mice" version))
6335 "01fnfrr7adp29s5kic95r9q0rdznkz2pjmziyimnrqzyicyvfyzq"))))
6336 (build-system r-build-system)
6347 (home-page "https://cran.r-project.org/web/packages/mice/")
6348 (synopsis "Multivariate imputation by chained equations")
6350 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
6351 implemented by the MICE algorithm as described in @url{Van Buuren and
6352 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
6353 variable has its own imputation model. Built-in imputation models are
6354 provided for continuous data (predictive mean matching, normal), binary
6355 data (logistic regression), unordered categorical data (polytomous logistic
6356 regression) and ordered categorical data (proportional odds). MICE can also
6357 impute continuous two-level data (normal model, pan, second-level variables).
6358 Passive imputation can be used to maintain consistency between variables.
6359 Various diagnostic plots are available to inspect the quality of the
6361 ;; Any of these two versions.
6362 (license (list license:gpl2 license:gpl3))))
6364 (define-public r-truncnorm
6366 (name "r-truncnorm")
6371 (uri (cran-uri "truncnorm" version))
6374 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
6375 (build-system r-build-system)
6376 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
6377 (synopsis "Truncated normal distribution")
6378 (description "This package provides functions for the truncated normal
6379 distribution with mean equal to @code{mean} and standard deviation equal to
6380 @code{sd}. It includes density, distribution, quantile, and expected value
6381 functions, as well as a random generation function.")
6382 (license license:gpl2)))
6384 (define-public r-rsolnp
6391 (uri (cran-uri "Rsolnp" version))
6394 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
6395 (properties `((upstream-name . "Rsolnp")))
6396 (build-system r-build-system)
6399 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
6400 (synopsis "General non-linear optimization")
6401 (description "The Rsolnp package implements a general non-linear augmented
6402 Lagrange multiplier method solver, a @dfn{sequential quadratic
6403 programming} (SQP) based solver).")
6404 ;; Any version of the GPL.
6405 (license license:gpl2+)))
6407 (define-public r-hardyweinberg
6409 (name "r-hardyweinberg")
6414 (uri (cran-uri "HardyWeinberg" version))
6417 "0b3szw090dsc3bkas2kvx787ww2i6zzg2qmdyivmqc8amx5arn6g"))))
6418 (properties `((upstream-name . "HardyWeinberg")))
6419 (build-system r-build-system)
6421 (list r-mice r-nnet r-rcpp r-rsolnp))
6422 (home-page "https://cran.r-project.org/package=HardyWeinberg")
6423 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
6425 "This package contains tools for exploring Hardy-Weinberg equilibrium for
6426 diallelic genetic marker data. All classical tests (chi-square, exact,
6427 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
6428 included in the package, as well as functions for power computation and for
6429 the simulation of marker data under equilibrium and disequilibrium. Routines
6430 for dealing with markers on the X-chromosome are included. Functions for
6431 testing equilibrium in the presence of missing data by using multiple
6432 imputation are also provided. Implements several graphics for exploring the
6433 equilibrium status of a large set of diallelic markers: ternary plots with
6434 acceptance regions, log-ratio plots and Q-Q plots.")
6435 (license license:gpl2+)))
6440 (version "2.2-5.7.1")
6444 (uri (cran-uri "sm" version))
6447 "0mql7rlm8wkdwmx1lv7pscdk9ibvsdpfdv8bpaz1hv2gn4pc637a"))))
6448 (build-system r-build-system)
6449 (native-inputs (list gfortran))
6450 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
6451 (synopsis "Smoothing methods for nonparametric regression and density estimation")
6453 "This is software accompanying the book 'Applied Smoothing Techniques for
6454 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
6455 University Press. It provides smoothing methods for nonparametric regression
6456 and density estimation")
6457 (license license:gpl2+)))
6459 (define-public r-venndiagram
6461 (name "r-venndiagram")
6465 (uri (cran-uri "VennDiagram" version))
6468 "0ilcxcp8qskmb5cp7fyb7i0qizg42lrx0ny8ws3if90kfrglghp7"))))
6469 (properties `((upstream-name . "VennDiagram")))
6470 (build-system r-build-system)
6472 (list r-futile-logger))
6473 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
6474 (synopsis "Generate High-Resolution Venn and Euler Plots")
6476 "This package provides a set of functions to generate high-resolution
6477 Venn and Euler plots. It includes handling for several special cases,
6478 including two-case scaling, and extensive customization of plot shape and
6480 (license license:gpl2+)))
6482 (define-public r-vioplot
6489 (uri (cran-uri "vioplot" version))
6492 "1dmdasp3jldc41233z6r08w3j76vyyp9m3jrj7n4ahk48yd5siq6"))))
6493 (build-system r-build-system)
6498 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
6499 (synopsis "Violin plot")
6501 "This package provides a violin plot, which is a combination of a box
6502 plot and a kernel density plot.")
6503 (license license:bsd-3)))
6505 (define-public r-rsofia
6511 ;; This package has been removed from CRAN, so we can
6512 ;; only fetch it from the archives.
6513 (uri (string-append "https://cran.r-project.org/src/"
6514 "contrib/Archive/RSofia/RSofia_"
6518 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
6519 (properties `((upstream-name . "RSofia")))
6520 (build-system r-build-system)
6523 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
6524 (synopsis "Port of sofia-ml to R")
6525 (description "This package is a port of sofia-ml to R. Sofia-ml is a
6526 suite of fast incremental algorithms for machine learning that can be used for
6527 training models for classification or ranking.")
6528 (license license:asl2.0)))
6530 (define-public r-xts
6537 (uri (cran-uri "xts" version))
6540 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
6541 (build-system r-build-system)
6542 (propagated-inputs (list r-zoo))
6543 (home-page "https://github.com/joshuaulrich/xts")
6544 (synopsis "Extensible time series")
6546 "This package provides for uniform handling of R's different time-based
6547 data classes by extending @code{zoo}, maximizing native format information
6548 preservation and allowing for user-level customization and extension, while
6549 simplifying cross-class interoperability.")
6550 (license license:gpl2+)))
6552 (define-public r-performanceanalytics
6554 (name "r-performanceanalytics")
6559 (uri (cran-uri "PerformanceAnalytics" version))
6562 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
6564 `((upstream-name . "PerformanceAnalytics")))
6565 (build-system r-build-system)
6567 (list r-quadprog r-xts r-zoo))
6568 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
6569 (synopsis "Econometric tools for performance and risk analysis")
6570 (description "This is a collection of econometric functions for
6571 performance and risk analysis. This package aims to aid practitioners and
6572 researchers in utilizing the latest research in analysis of non-normal return
6573 streams. In general, it is most tested on return (rather than price) data on
6574 a regular scale, but most functions will work with irregular return data as
6575 well, and increasing numbers of functions will work with P&L or price data
6577 ;; Either version may be picked.
6578 (license (list license:gpl2 license:gpl3))))
6580 (define-public r-laeken
6587 (uri (cran-uri "laeken" version))
6590 "1p3ccbaydlr52p8qmgmm2l6kryvq6jjjx7mqn2vv0gpjaxqhyy92"))))
6591 (build-system r-build-system)
6593 (list r-boot r-mass))
6594 (home-page "https://cran.r-project.org/web/packages/laeken/")
6595 (synopsis "Estimation of indicators on social exclusion and poverty")
6596 (description "This package provides tools for the estimation of indicators
6597 on social exclusion and poverty, as well as an implementation of Pareto tail
6598 modeling for empirical income distributions.")
6599 (license license:gpl2+)))
6601 (define-public r-vcd
6608 (uri (cran-uri "vcd" version))
6611 "0nxkl1x39xf8l0apgvlbr30i8lasix7hyyc93g6514r8z8m1k23i"))))
6612 (build-system r-build-system)
6614 (list r-colorspace r-lmtest r-mass))
6615 (home-page "https://cran.r-project.org/web/packages/vcd/")
6616 (synopsis "Visualizing categorical data")
6617 (description "This package provides visualization techniques, data sets,
6618 summary and inference procedures aimed particularly at categorical data.
6619 Special emphasis is given to highly extensible grid graphics. The package was
6620 originally inspired by the book \"Visualizing Categorical Data\" by Michael
6621 Friendly and is now the main support package for a new book, \"Discrete Data
6622 Analysis with R\" by Michael Friendly and David Meyer (2015).")
6623 (license license:gpl2)))
6625 (define-public r-vcfr
6631 (uri (cran-uri "vcfR" version))
6634 "1g4y11vpr3wrvf5prj7y33c2bah6rn4xfb4a1y7n7niafd2yhg3l"))))
6635 (build-system r-build-system)
6651 (home-page "https://github.com/knausb/vcfR")
6652 (synopsis "Manipulate and visualize VCF data")
6653 (description "This package facilitates easy manipulation of variant call
6654 format (VCF) data. Functions are provided to rapidly read from and write to
6655 VCF files. Once VCF data is read into R, a parser function extracts matrices
6656 of data. This information can then be used for quality control or other
6657 purposes. Additional functions provide visualization of genomic data. Once
6658 processing is complete data may be written to a VCF file. It also may be
6659 converted into other popular R objects. This package provides a link between
6660 VCF data and familiar R software.")
6661 (license license:gpl3)))
6663 (define-public r-ica
6670 (uri (cran-uri "ica" version))
6673 "0rdqd3kz2cv3xvf6yz55bwhsg3k7j90d450i3azs2xkbn4q3aka7"))))
6674 (build-system r-build-system)
6675 (home-page "https://cran.r-project.org/web/packages/ica/")
6676 (synopsis "Independent component analysis")
6677 (description "This package provides tools for @dfn{Independent Component
6678 Analysis} (ICA) using various algorithms: FastICA,
6679 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
6680 of Eigenmatrices} (JADE).")
6681 (license license:gpl2+)))
6683 (define-public r-ips
6689 (uri (cran-uri "ips" version))
6692 "02jxanfhsjrabj33nwjv71vdc87hiyzikyqrfdj9ix6dky6lm199"))))
6693 (properties `((upstream-name . "ips")))
6694 (build-system r-build-system)
6695 (propagated-inputs (list r-ape r-phangorn r-plyr r-seqinr r-xml))
6696 (home-page "https://cran.r-project.org/package=ips")
6697 (synopsis "Interfaces to phylogenetic software in R")
6699 "This package provides functions that wrap popular phylogenetic software
6700 for sequence alignment, masking of sequence alignments, and estimation of
6701 phylogenies and ancestral character states.")
6702 (license license:gpl3)))
6704 (define-public r-dtw
6711 (uri (cran-uri "dtw" version))
6714 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z"))))
6715 (build-system r-build-system)
6716 (propagated-inputs (list r-proxy))
6717 (home-page "http://dtw.r-forge.r-project.org/")
6718 (synopsis "Dynamic Time Warping Algorithms")
6719 (description "This package provides a comprehensive implementation of
6720 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
6721 optimal (least cumulative distance) alignment between points of two time
6722 series. Common DTW variants covered include local (slope) and global (window)
6723 constraints, subsequence matches, arbitrary distance definitions,
6724 normalizations, minimum variance matching, and so on.")
6725 (license license:gpl2+)))
6727 (define-public r-sdmtools
6730 (version "1.1-221.2")
6734 (uri (cran-uri "SDMTools" version))
6737 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
6738 (properties `((upstream-name . "SDMTools")))
6739 (build-system r-build-system)
6740 (propagated-inputs (list r-r-utils))
6741 (home-page "https://www.rforge.net/SDMTools/")
6742 (synopsis "Species distribution modelling tools")
6743 (description "This package provides a set of tools for post processing
6744 the outcomes of species distribution modeling exercises. It includes novel
6745 methods for comparing models and tracking changes in distributions through
6746 time. It further includes methods for visualizing outcomes, selecting
6747 thresholds, calculating measures of accuracy and landscape fragmentation
6749 (license license:gpl3+)))
6751 (define-public r-scatterplot3d
6753 (name "r-scatterplot3d")
6758 (uri (cran-uri "scatterplot3d" version))
6761 "05jjdiam5w0znb114vc90zahclj22pqj1zzvr96nr10s1vkxvzm9"))))
6762 (build-system r-build-system)
6763 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
6764 (synopsis "3D scatter plot")
6765 (description "This package provides an implementation of scatter plots for
6766 plotting. a three dimensional point cloud.")
6767 (license license:gpl2)))
6769 (define-public r-ggridges
6776 (uri (cran-uri "ggridges" version))
6779 "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm"))))
6780 (build-system r-build-system)
6782 (list r-ggplot2 r-plyr r-scales r-withr))
6785 (home-page "https://github.com/clauswilke/ggridges")
6786 (synopsis "Ridgeline plots in ggplot2")
6788 "Ridgeline plots provide a convenient way of visualizing changes in
6789 distributions over time or space. This package enables the creation of such
6790 plots in @code{ggplot2}.")
6791 (license license:gpl2)))
6793 (define-public r-ggjoy
6800 (uri (cran-uri "ggjoy" version))
6803 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
6804 (build-system r-build-system)
6806 (list r-ggplot2 r-ggridges))
6807 (home-page "https://github.com/clauswilke/ggjoy")
6808 (synopsis "Joyplots in ggplot2")
6809 (description "Joyplots provide a convenient way of visualizing changes in
6810 distributions over time or space. This package enables the creation of such
6811 plots in @code{ggplot2}.")
6812 (license license:gpl2)))
6814 (define-public r-cli
6821 (uri (cran-uri "cli" version))
6824 "0mxsls49g8m5vrak64b9mpsgw3mh8hnb1xxn56skbn4qb1hppbff"))))
6825 (build-system r-build-system)
6826 (home-page "https://github.com/r-lib/cli#readme")
6827 (synopsis "Helpers for developing command line interfaces")
6828 (description "This package provides a suite of tools designed to build
6829 attractive command line interfaces (CLIs). It includes tools for drawing
6830 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
6831 (license license:expat)))
6833 (define-public r-argparser
6835 (name "r-argparser")
6840 (uri (cran-uri "argparser" version))
6843 "0xcl0ivsbc4iw8s7027q4cx68j6s5lihbby0xa9pmlv4wjmcvdr6"))))
6844 (build-system r-build-system)
6845 (home-page "https://bitbucket.org/djhshih/argparser")
6846 (synopsis "Command-line argument parser")
6848 "This package provides a cross-platform command-line argument parser
6849 written purely in R with no external dependencies. It is useful with the
6850 Rscript front-end and facilitates turning an R script into an executable
6852 (license license:gpl3+)))
6854 (define-public r-aricode
6860 (uri (cran-uri "aricode" version))
6863 "0772l9gyrih48l1kymih0mb7szjqqnwcm4lzj0yzp4cs8l2mdf4f"))))
6864 (properties `((upstream-name . "aricode")))
6865 (build-system r-build-system)
6866 (propagated-inputs (list r-matrix r-rcpp))
6867 (home-page "https://github.com/jchiquet/aricode")
6868 (synopsis "Efficient computations of standard clustering comparison measures")
6870 "This package implements an efficient O(n) algorithm based on
6871 bucket-sorting for fast computation of standard clustering comparison
6872 measures. Available measures include @dfn{adjusted Rand index} (ARI),
6873 @dfn{normalized information distance} (NID), @dfn{normalized mutual
6874 information} (NMI), @dfn{adjusted mutual information} (AMI), @dfn{normalized
6875 variation information} (NVI) and entropy.")
6876 (license license:gpl3+)))
6878 (define-public r-debugme
6885 (uri (cran-uri "debugme" version))
6888 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
6889 (build-system r-build-system)
6890 (propagated-inputs (list r-crayon))
6891 (home-page "https://github.com/r-lib/debugme#readme")
6892 (synopsis "Debug R packages")
6894 "This package allows the user to specify debug messages as special string
6895 constants, and control debugging of packages via environment variables.")
6896 (license license:expat)))
6898 (define-public r-processx
6905 (uri (cran-uri "processx" version))
6907 (base32 "1lsyspd3jak6g625sna5jdqrg5fw02qgdfiz0hsyqlzw6m0qssny"))))
6908 (build-system r-build-system)
6911 (home-page "https://github.com/r-lib/processx3")
6912 (synopsis "Execute and control system processes")
6914 "This package provides portable tools to run system processes in the
6915 background. It can check if a background process is running; wait on a
6916 background process to finish; get the exit status of finished processes; kill
6917 background processes and their children; restart processes. It can read the
6918 standard output and error of the processes, using non-blocking connections.
6919 @code{processx} can poll a process for standard output or error, with a
6920 timeout. It can also poll several processes at once.")
6921 (license license:expat)))
6923 (define-public r-tsp
6930 (uri (cran-uri "TSP" version))
6933 "1pa6pb4qrh2iybpjzjiny6hshj0shjdm0pxqnidcrg5hyfzzxd9b"))))
6934 (properties `((upstream-name . "TSP")))
6935 (build-system r-build-system)
6936 (propagated-inputs (list r-foreach))
6937 (home-page "https://cran.r-project.org/web/packages/TSP/")
6938 (synopsis "Traveling salesperson problem (TSP)")
6939 (description "This package provides basic infrastructure and some
6940 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
6941 traveling salesman problem).")
6942 (license license:gpl3)))
6944 (define-public r-qap
6951 (uri (cran-uri "qap" version))
6954 "19adb1bw46pcnmmhqz2jklr0vmma3llxajqp0j9mqfksmsisv927"))))
6955 (build-system r-build-system)
6956 (native-inputs (list gfortran))
6957 (home-page "https://cran.r-project.org/web/packages/qap/")
6958 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
6959 (description "This package implements heuristics for the @dfn{quadratic
6960 assignment problem} (QAP). Currently only a simulated annealing heuristic is
6962 (license license:gpl3)))
6964 (define-public r-gclus
6971 (uri (cran-uri "gclus" version))
6974 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
6975 (build-system r-build-system)
6976 (propagated-inputs (list r-cluster))
6977 (home-page "https://cran.r-project.org/web/packages/gclus/")
6978 (synopsis "Clustering graphics")
6979 (description "This package orders panels in scatterplot matrices and
6980 parallel coordinate displays by some merit index. It contains various indices
6981 of merit, ordering functions, and enhanced versions of @code{pairs} and
6982 @code{parcoord} which color panels according to their merit level.")
6983 (license license:gpl2+)))
6985 (define-public r-webshot
6992 (uri (cran-uri "webshot" version))
6995 "1h6v94zwq0ypgi4vf8xlhp5k13j7f9061hx908177i68c6zg5i5p"))))
6996 (build-system r-build-system)
6998 (list r-callr r-jsonlite r-magrittr))
6999 (home-page "https://github.com/wch/webshot/")
7000 (synopsis "Take screenshots of web pages")
7002 "Webshot makes it easy to take screenshots of web pages from within R.
7003 It can also run Shiny applications locally and take screenshots of the
7004 application; and it can render and screenshot static as well as interactive R
7005 Markdown documents.")
7006 (license license:gpl2)))
7008 (define-public r-seriation
7010 (name "r-seriation")
7015 (uri (cran-uri "seriation" version))
7018 "1i0bbfxbvzy2lwprliqrn97ww8lqr2s9klg0g3qqjyr8cdxs5fyc"))))
7019 (build-system r-build-system)
7028 (native-inputs (list gfortran))
7029 (home-page "https://s2.smu.edu/IDA/seriation/")
7030 (synopsis "Infrastructure for ordering objects using seriation")
7032 "This package provides infrastructure for seriation with an
7033 implementation of several seriation/sequencing techniques to reorder matrices,
7034 dissimilarity matrices, and dendrograms. It also provides (optimally)
7035 reordered heatmaps, color images and clustering visualizations like
7036 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
7038 (license license:gpl3)))
7040 (define-public r-xfun
7047 (uri (cran-uri "xfun" version))
7049 (base32 "0v7f84gqsb94zff4x64478fssjg0sbis9m34vsxnjyw6ab9c5ys5"))))
7050 (build-system r-build-system)
7051 ;; knitr itself depends on xfun
7054 `(("r-knitr" ,r-knitr)))
7055 (home-page "https://github.com/yihui/xfun")
7056 (synopsis "Miscellaneous functions")
7058 "This package provides miscellaneous functions commonly used in other
7059 packages maintained by Yihui Xie.")
7060 (license license:expat)))
7062 (define-public r-utf8
7069 (uri (cran-uri "utf8" version))
7072 "1x6qg19z4qih9lk3mvnmx0vailm1khp5lylw4hlwz6rssj3yw6m7"))))
7073 (build-system r-build-system)
7075 (list r-knitr r-rmarkdown)) ; for vignettes
7076 (home-page "https://github.com/patperry/r-utf8")
7077 (synopsis "Unicode text processing")
7079 "This package provides tools to process and print UTF-8 encoded
7080 international text (Unicode). Input, validate, normalize, encode, format, and
7082 (license license:asl2.0)))
7084 (define-public r-zeallot
7091 (uri (cran-uri "zeallot" version))
7094 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
7095 (build-system r-build-system)
7096 (home-page "https://github.com/nteetor/zeallot")
7097 (synopsis "Multiple, unpacking, and destructuring assignment")
7099 "This package provides a @code{%<-%} operator to perform multiple,
7100 unpacking, and destructuring assignment in R. The operator unpacks the
7101 right-hand side of an assignment into multiple values and assigns these values
7102 to variables on the left-hand side of the assignment.")
7103 (license license:expat)))
7105 (define-public r-zlog
7111 (uri (cran-uri "zlog" version))
7114 "1d5j31p0h3rrn230087h3ngpvwknlisjv0f1qdbicdj9m177spci"))))
7115 (properties `((upstream-name . "zlog")))
7116 (build-system r-build-system)
7117 (native-inputs (list r-knitr))
7118 (home-page "https://cran.r-project.org/package=zlog")
7119 (synopsis "Transformation for laboratory easurements")
7121 "The @code{zlog} package offers functions to transform laboratory
7122 measurements into standardised z or @math{z(log)-values}. Therefore the lower
7123 and upper reference limits are needed. If these are not known they could be
7124 estimated from a given sample.")
7125 (license license:gpl3+)))
7127 (define-public r-vctrs
7134 (uri (cran-uri "vctrs" version))
7137 "1pb0wjpwix29q8d8p3wi72a9mp9mif7369pk31w238cs00g8hxln"))))
7138 (build-system r-build-system)
7140 (list r-cli r-glue r-rlang))
7143 (home-page "https://github.com/r-lib/vctrs")
7144 (synopsis "Vector helpers")
7146 "There are three main goals to the @code{vctrs} package:
7149 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
7150 @code{length()} and @code{class()}. These definitions are paired with a
7151 framework for type-coercion and size-recycling.
7152 @item To define type- and size-stability as desirable function properties, use
7153 them to analyse existing base function, and to propose better alternatives.
7154 This work has been particularly motivated by thinking about the ideal
7155 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
7156 @item To provide a new @code{vctr} base class that makes it easy to create new
7157 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
7158 a few new @code{vctrs} generics, making implementation considerably simpler
7161 (license license:gpl3)))
7163 (define-public r-pillar
7170 (uri (cran-uri "pillar" version))
7173 "1v47dm2v4nlswd1gmgcx5c7yrgn1ksdfr9lqkc63jf2nkv6af1ig"))))
7174 (build-system r-build-system)
7185 (home-page "https://github.com/r-lib/pillar")
7186 (synopsis "Coloured formatting for columns")
7188 "This package provides a @code{pillar} generic designed for formatting
7189 columns of data using the full range of colours provided by modern
7191 (license license:gpl3)))
7193 (define-public r-pinfsc50
7199 (uri (cran-uri "pinfsc50" version))
7202 "1547xyxmfb7zi8h9bsm6k67dcw4hpp129xzvmgwfw7r6p4af47zd"))))
7203 (build-system r-build-system)
7204 (home-page "https://cran.r-project.org/web/packages/pinfsc50/")
7205 (synopsis "Genomic data for the plant pathogen Phytophthora infestans")
7206 (description "This package contains genomic data for the plant pathogen
7207 Phytophthora infestans. It includes a variant file, a sequence file and an
7208 annotation file. This package is intended to be used as example data for
7209 packages that work with genomic data.")
7210 (license license:gpl2+)))
7212 (define-public r-uuid
7219 (uri (cran-uri "uuid" version))
7222 "0bzlc2knmr338h4ykx8v8c2a1inizxafj8rh13kwii68gpp50nz7"))))
7223 (build-system r-build-system)
7224 (home-page "https://www.rforge.net/uuid")
7225 (synopsis "Tools for generating and handling of UUIDs")
7227 "This package provides tools for generating and handling of
7228 @dfn{Universally Unique Identifiers} (UUIDs).")
7229 (license license:expat)))
7231 (define-public r-tinytex
7238 (uri (cran-uri "tinytex" version))
7241 "1fhnh53fg8l4qyignvgz0nk5nqmljyykn8gpvq82nr7c051rfqaz"))))
7242 (build-system r-build-system)
7245 (home-page "https://github.com/yihui/tinytex")
7246 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
7248 "This package provides helper functions to install and maintain the LaTeX
7249 distribution named TinyTeX, a lightweight, cross-platform, portable, and
7250 easy-to-maintain version of TeX Live. This package also contains helper
7251 functions to compile LaTeX documents, and install missing LaTeX packages
7253 (license license:expat)))
7255 (define-public r-tinytest
7262 (uri (cran-uri "tinytest" version))
7265 "1mq31f7bzcz5bkgzl9khm1i80axfzra7gcjqxd2yqb4wrw1m3x4s"))))
7266 (properties `((upstream-name . "tinytest")))
7267 (build-system r-build-system)
7268 (home-page "https://github.com/markvanderloo/tinytest")
7269 (synopsis "Lightweight unit testing framework")
7271 "This package provides a lightweight unit testing framework. Main
7275 @item install tests with the package;
7276 @item test results are treated as data that can be stored and manipulated;
7277 @item test files are R scripts interspersed with test commands, that can be
7279 @item fully automated build-install-test sequence for packages;
7280 @item skip tests when not run locally (e.g. on CRAN);
7281 @item flexible and configurable output printing;
7282 @item compare computed output with output stored with the package;
7283 @item run tests in parallel;
7284 @item extensible by other packages;
7285 @item report side effects.
7288 (license license:gpl3)))
7290 (define-public r-network
7297 (uri (cran-uri "network" version))
7300 "1xrhzbci7ls4h05skdlirxl49jsvmylrqivz2kd6i33wh2ca324m"))))
7301 (build-system r-build-system)
7303 (list r-magrittr r-statnet-common r-tibble))
7304 (home-page "https://statnet.org/")
7305 (synopsis "Classes for relational data")
7307 "This package provides tools to create and modify network objects. The
7308 @code{network} class can represent a range of relational data types, and
7309 supports arbitrary vertex/edge/graph attributes.")
7310 (license license:gpl2+)))
7312 (define-public r-stabs
7319 (uri (cran-uri "stabs" version))
7322 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q"))))
7323 (build-system r-build-system)
7326 (home-page "https://github.com/hofnerb/stabs")
7327 (synopsis "Stability selection with error control")
7329 "This package provides resampling procedures to assess the stability of
7330 selected variables with additional finite sample error control for
7331 high-dimensional variable selection procedures such as Lasso or boosting.
7332 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
7333 complementary pairs stability selection with improved error bounds
7334 (Shah & Samworth, 2013) are implemented. The package can be combined with
7335 arbitrary user specified variable selection approaches.")
7336 (license license:gpl2)))
7338 (define-public r-rle
7345 (uri (cran-uri "rle" version))
7348 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40"))))
7349 (properties `((upstream-name . "rle")))
7350 (build-system r-build-system)
7351 (home-page "https://cran.r-project.org/web/packages/rle/")
7352 (synopsis "Common functions for run-length encoded vectors")
7354 "This package provides common @code{base} and @code{stats} methods for
7355 @code{rle} objects, aiming to make it possible to treat them transparently as
7357 (license license:gpl3)))
7359 (define-public r-statnet-common
7361 (name "r-statnet-common")
7366 (uri (cran-uri "statnet.common" version))
7369 "1cx1h1yzs8jjxk10y2h0wl69caspzgx5wdqp36dp4sxm0sk335xn"))))
7371 `((upstream-name . "statnet.common")))
7372 (build-system r-build-system)
7375 (home-page "https://statnet.org")
7376 (synopsis "R scripts and utilities used by the Statnet software")
7377 (description "This package provides non-statistical utilities used by the
7378 software developed by the Statnet Project.")
7379 (license license:gpl3)))
7381 (define-public r-statcheck
7383 (name "r-statcheck")
7388 (uri (cran-uri "statcheck" version))
7391 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
7392 (build-system r-build-system)
7394 (list r-ggplot2 r-plyr r-rmarkdown))
7395 (home-page "https://cran.r-project.org/web/packages/statcheck/")
7396 (synopsis "Extract statistics from articles and recompute p-values")
7397 (description "This package can automatically extract statistical
7398 null-hypothesis significant testing (NHST) results from articles and recompute
7399 the p-values based on the reported test statistic and degrees of freedom to
7400 detect possible inconsistencies.")
7401 (license license:gpl2)))
7403 (define-public r-sna
7410 (uri (cran-uri "sna" version))
7413 "0ka319s1w857fj28ja1i1ljgv2h6ji4d69riqy9pwhvvghsa83s4"))))
7414 (build-system r-build-system)
7416 (list r-network r-statnet-common))
7417 (home-page "https://statnet.org")
7418 (synopsis "Tools for social network analysis")
7420 "This package provides a range of tools for social network analysis,
7421 including node and graph-level indices, structural distance and covariance
7422 methods, structural equivalence detection, network regression, random graph
7423 generation, and 2D/3D network visualization.")
7424 (license license:gpl2+)))
7426 (define-public r-tfisher
7433 (uri (cran-uri "TFisher" version))
7436 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
7437 (properties `((upstream-name . "TFisher")))
7438 (build-system r-build-system)
7440 (list r-matrix r-mvtnorm r-sn))
7441 (home-page "https://cran.r-project.org/web/packages/TFisher/")
7442 (synopsis "Optimal thresholding Fisher's p-value combination method")
7444 "This package provides the @dfn{cumulative distribution function} (CDF),
7445 quantile, and statistical power calculator for a collection of thresholding
7446 Fisher's p-value combination methods, including Fisher's p-value combination
7447 method, truncated product method and, in particular, soft-thresholding
7448 Fisher's p-value combination method which is proven to be optimal in some
7449 context of signal detection. The p-value calculator for the omnibus version
7450 of these tests are also included.")
7451 (license license:gpl2)))
7453 (define-public r-ttr
7460 (uri (cran-uri "TTR" version))
7463 "11xsmbvmxq2j119j2z58bx1fkkb2xlhmzc35z5fbwr3nchrfz6jd"))))
7464 (properties `((upstream-name . "TTR")))
7465 (build-system r-build-system)
7467 (list r-curl r-xts r-zoo))
7468 (home-page "https://github.com/joshuaulrich/TTR")
7469 (synopsis "Technical trading rules")
7471 "This package provides functions and data to construct technical trading
7473 (license license:gpl2)))
7475 (define-public r-leaflet-providers
7477 (name "r-leaflet-providers")
7482 (uri (cran-uri "leaflet.providers" version))
7484 (base32 "0yynrwv4xd5cdh49cwvfxm4ranarah9iiry2cd3b4fiihdfcg3wy"))))
7485 (properties `((upstream-name . "leaflet.providers")))
7486 (build-system r-build-system)
7487 (home-page "https://github.com/rstudio/leaflet.providers")
7488 (synopsis "Leaflet map tile providers")
7490 "This package contains third-party map tile provider information from
7491 Leaflet.js, to be used with the @code{leaflet} R package. Additionally,
7492 @code{leaflet.providers} enables users to retrieve up-to-date provider
7493 information between package updates.")
7494 (license license:bsd-2)))
7496 ;; This package contains a lot of minified JavaScript with unclear provenance.
7497 ;; When upgrading please make sure that all minified JavaScript files are
7498 ;; removed in a snippet and that the replacement sources correspond to the
7499 ;; original minified scripts.
7500 (define-public r-leaflet
7507 (uri (cran-uri "leaflet" version))
7509 (base32 "0xsng9n08i1w7qj4hbi706m6d8jm9ixrnwq5xac2s3csfm1s1xij"))
7513 (list "inst/htmlwidgets/lib/leaflet/leaflet.js"
7514 "inst/htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js"
7515 "inst/htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js"
7516 "inst/htmlwidgets/lib/jquery/jquery.min.js"
7517 "inst/htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js"
7518 "inst/htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js"
7519 "inst/htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js"
7520 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js"
7521 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js"
7522 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js"
7523 "inst/legacy/www/leaflet.js")))))
7524 (properties `((upstream-name . "leaflet")))
7525 (build-system r-build-system)
7527 `(#:modules ((guix build utils)
7528 (guix build r-build-system)
7531 (modify-phases %standard-phases
7532 (add-after 'unpack 'process-javascript
7533 (lambda* (#:key inputs #:allow-other-keys)
7534 ;; The inst directory contains some minified JavaScript files.
7535 ;; Regenerate them from sources.
7536 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-leaflet"))
7537 (with-directory-excursion "inst/"
7541 `(("/tmp/leaflet-src.js"
7542 "htmlwidgets/lib/leaflet/leaflet.js")
7543 (,(assoc-ref inputs "js-leaflet-measure")
7544 "htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js")
7545 (,(assoc-ref inputs "js-leaflet-omnivore")
7546 "htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js")
7547 (,(assoc-ref inputs "js-jquery")
7548 "htmlwidgets/lib/jquery/jquery.min.js")
7549 ("htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.js"
7550 "htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js")
7551 (,(assoc-ref inputs "js-bootstrap3")
7552 "htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js")
7553 ("htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.js"
7554 "htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js")
7555 (,(string-append (assoc-ref inputs "js-leaflet-markercluster")
7556 "/dist/leaflet.markercluster-src.js")
7557 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js")
7558 (,(assoc-ref inputs "js-leaflet-markercluster-freezable")
7559 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js")
7560 (,(assoc-ref inputs "js-leaflet-markercluster-layersupport")
7561 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js")
7562 (,(assoc-ref inputs "js-proj4leaflet")
7563 "htmlwidgets/plugins/Proj4Leaflet/proj4.min.js")
7564 ("legacy/www/leaflet-src.js"
7565 "legacy/www/leaflet.js"))))
7566 (lambda (sources targets)
7567 (for-each (lambda (source target)
7568 (format #true "Processing ~a --> ~a~%"
7570 (invoke "esbuild" source "--minify"
7571 (string-append "--outfile=" target)))
7572 sources targets)))))))))
7574 `(("esbuild" ,esbuild)
7579 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v3.3.7/dist/js/bootstrap.js")
7582 "1j1qjagwj0m3q322z9wxxnpkd8zbk6g3kl047dsbmqad6gmqvgha"))))
7586 (uri "https://code.jquery.com/jquery-1.12.4.js")
7589 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
7593 (uri "http://cdn.leafletjs.com/leaflet/v1.3.1/leaflet.zip")
7596 "10phzd2vczy3zm1b64whp2nna69cf9hlj2bndc9yq47vf3ddqx8f"))))
7597 ("js-leaflet-omnivore"
7600 (uri (string-append "https://api.tiles.mapbox.com/mapbox.js/plugins/"
7601 "leaflet-omnivore/v0.3.1/leaflet-omnivore.js"))
7604 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
7605 ("js-leaflet-markercluster"
7609 (url "https://github.com/Leaflet/Leaflet.markercluster.git")
7611 (file-name (git-file-name "js-leaflet-markercluster" "1.1.0"))
7614 "0ds8c7picqjmc86bm5n6hm8k71fwsa2cpgib19sbdamzr9hm0rs1"))))
7615 ("js-leaflet-markercluster-freezable"
7619 "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.Freezable/"
7620 "9db80a3fba7dff4aee940e05d3d4dceaa1fffcf9/src/freezable.js"))
7621 (file-name "leaflet-markercluster-freezable.js")
7624 "1k6sn5n0z2x3an91vwvkzmqq4b8ppswgk5hi5qrr79klas1hbx1k"))))
7625 ("js-leaflet-markercluster-layersupport"
7629 "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.LayerSupport/"
7630 "87f3848b92e0516d9c98f6d4cd175f7b8a4e3805/src/layersupport.js"))
7631 (file-name "leaflet-markercluster-layersupport.js")
7634 "15qa21xif94y762c65yxxysxykz3mma6y6agw3nxpr3s7wbb75ff"))))
7635 ("js-leaflet-measure"
7638 (uri "https://unpkg.com/leaflet-measure@1.5.2/dist/leaflet-measure.js")
7639 (file-name "js-leaflet-measure-1.5.2.js")
7642 "0ggg3ffmm7pj9ry4gssrh0a17pnad3p6gwi0dg98y819pmpqa7y0"))))
7646 (uri "https://raw.githubusercontent.com/kartena/Proj4Leaflet/1.0.2/lib/proj4.js")
7647 (file-name "js-proj4leaflet-1.0.2.js")
7650 "0vyrbf6gv2lyh4c2bzp5349ivwvvg28gpn87y52a7jdb13rlkpab"))))))
7665 (home-page "https://rstudio.github.io/leaflet/")
7666 (synopsis "Create interactive web maps with the JavaScript Leaflet library")
7668 "Create and customize interactive maps using the Leaflet JavaScript
7669 library and the @code{htmlwidgets} package. These maps can be used directly
7670 from the R console, from RStudio, in Shiny applications and R Markdown
7672 (license license:gpl3)))
7674 (define-public r-leaps
7681 (uri (cran-uri "leaps" version))
7684 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
7685 (build-system r-build-system)
7686 (native-inputs (list gfortran))
7687 (home-page "https://cran.r-project.org/web/packages/leaps/")
7688 (synopsis "Regression subset selection")
7690 "This package provides tools for regression subset selection, including
7691 exhaustive search.")
7692 (license license:gpl2+)))
7694 (define-public r-splus2r
7701 (uri (cran-uri "splus2R" version))
7704 "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x"))))
7705 (properties `((upstream-name . "splus2R")))
7706 (build-system r-build-system)
7707 (home-page "https://cran.r-project.org/web/packages/splus2R/")
7708 (synopsis "Supplemental S-PLUS functionality in R")
7710 "Currently there are many functions in S-PLUS that are missing in R. To
7711 facilitate the conversion of S-PLUS packages to R packages, this package
7712 provides some missing S-PLUS functionality in R.")
7713 (license license:gpl2)))
7715 (define-public r-ifultools
7717 (name "r-ifultools")
7722 (uri (cran-uri "ifultools" version))
7725 "1lkmzrh65j6vdb8523axxk9gig5q4zxy08wiqsp16w482d2q2sl1"))))
7726 (build-system r-build-system)
7730 `(modify-phases %standard-phases
7731 (add-after 'unpack 'compatibility
7733 ;; These definitions are no longer part of R since 4.2.0. See
7734 ;; https://cran.r-project.org/doc/manuals/r-devel/NEWS.html for
7736 (substitute* "inst/include/ut_RS.h"
7737 (("#include \"R.h\"" m)
7739 #define R_PROBLEM_BUFSIZE 4096
7740 #define PROBLEM {char R_problem_buf[R_PROBLEM_BUFSIZE];(sprintf)(R_problem_buf,
7741 #define MESSAGE {char R_problem_buf[R_PROBLEM_BUFSIZE];(sprintf)(R_problem_buf,
7742 #define ERROR ),error(R_problem_buf);}
7743 #define WARNING(x) ),warning(R_problem_buf);}
7744 #define WARN WARNING(NULL)
7747 (list r-mass r-splus2r))
7748 (home-page "https://cran.r-project.org/web/packages/ifultools/")
7749 (synopsis "Insightful research tools")
7750 (description "This package provides C code used by the wmtsa, fractal, and
7752 (license license:gpl2)))
7754 (define-public r-sapa
7761 (uri (cran-uri "sapa" version))
7764 "0kj681rd4c2lvqr926lb6f4qwp281x5274dg6vbk8pf5y7s0qlpc"))))
7765 (build-system r-build-system)
7767 (list r-ifultools r-splus2r))
7768 (home-page "https://cran.r-project.org/web/packages/sapa/")
7769 (synopsis "Spectral analysis for physical applications")
7770 (description "This package provides software for the book Spectral
7771 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
7772 Cambridge University Press, 1993.")
7773 (license license:gpl2)))
7775 (define-public r-aggregation
7777 (name "r-aggregation")
7782 (uri (cran-uri "aggregation" version))
7785 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
7786 (build-system r-build-system)
7787 (home-page "https://cran.r-project.org/web/packages/aggregation/")
7788 (synopsis "Methods for p-value aggregation")
7790 "This package contains functionality for performing the following methods
7791 of p-value aggregation: Fisher's method, the Lancaster method (weighted
7792 Fisher's method), and Sidak correction.")
7793 (license license:gpl3)))
7795 (define-public r-quantmod
7802 (uri (cran-uri "quantmod" version))
7805 "154fqhw46kc7r08zsj5fsg97hg93phsli3z14xwmz22xb50xymzp"))))
7806 (build-system r-build-system)
7808 (list r-curl r-ttr r-xts r-zoo))
7809 (home-page "https://cran.r-project.org/web/packages/quantmod/")
7810 (synopsis "Quantitative financial modelling framework")
7811 (description "This package provides a quantitative financial modelling
7812 framework to allow users to specify, build, trade, and analyse quantitative
7813 financial trading strategies.")
7814 (license license:gpl3)))
7816 (define-public r-tseries
7823 (uri (cran-uri "tseries" version))
7826 "0zr09ikaz96djcvnjbr8ah6waqzjy06f4yd4isshlwc391q20px5"))))
7827 (build-system r-build-system)
7829 (list r-quadprog r-quantmod r-zoo))
7832 (home-page "https://cran.r-project.org/web/packages/tseries/")
7833 (synopsis "Time series analysis and computational finance")
7835 "This package provides functions relating to time series analysis and
7836 computational finance.")
7837 (license license:gpl2)))
7839 (define-public r-wmtsa
7846 (uri (cran-uri "wmtsa" version))
7849 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
7850 (build-system r-build-system)
7852 (list r-ifultools r-mass r-splus2r))
7853 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
7854 (synopsis "Wavelet methods for time series analysis")
7856 "This package provides software to accompany the book \"Wavelet Methods
7857 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
7858 University Press, 2000.")
7859 (license license:gpl2)))
7861 (define-public r-tsa
7868 (uri (cran-uri "TSA" version))
7871 "14g58s2w7wma1fgcg3b51267b3676zrv0w8v4hpypxygz023d9bx"))))
7872 (properties `((upstream-name . "TSA")))
7873 (build-system r-build-system)
7875 (list r-leaps r-locfit r-mgcv r-tseries))
7876 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
7877 (synopsis "Time series analysis")
7879 "This package contains R functions and datasets detailed in the book
7880 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
7881 Cryer and Kung-Sik Chan.")
7882 (license license:gpl2+)))
7884 (define-public r-extradistr
7886 (name "r-extradistr")
7891 (uri (cran-uri "extraDistr" version))
7894 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
7895 (properties `((upstream-name . "extraDistr")))
7896 (build-system r-build-system)
7899 (home-page "https://github.com/twolodzko/extraDistr")
7900 (synopsis "Additional univariate and multivariate distributions")
7902 "This package implements density, distribution functions, quantile
7903 functions and random generation functions for a large number of univariate and
7904 multivariate distributions.")
7905 (license license:gpl2)))
7907 (define-public r-fractal
7914 (uri (cran-uri "fractal" version))
7917 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
7918 (build-system r-build-system)
7926 (home-page "https://cran.r-project.org/web/packages/fractal/")
7927 (synopsis "Fractal time series modeling and analysis")
7929 "This package provides tools for stochastic fractal and deterministic
7930 chaotic time series analysis.")
7931 (license license:gpl2)))
7933 (define-public r-urca
7940 (uri (cran-uri "urca" version))
7943 "1wg9f691pif59xds43gnnw77mmzc9xpnhhvaksk2b0szffvaifj3"))))
7944 (build-system r-build-system)
7945 (propagated-inputs (list r-nlme))
7946 (native-inputs (list gfortran))
7947 (home-page "https://cran.r-project.org/web/packages/urca/")
7948 (synopsis "Unit root and cointegration tests for time series data")
7950 "This package provides unit root and cointegration tests encountered in
7951 applied econometric analysis.")
7952 (license license:gpl2+)))
7954 (define-public r-cubature
7961 (uri (cran-uri "cubature" version))
7964 "08whkhvn218089r930spn97m91vv1njgh2amksia8l3rbf7127x8"))))
7965 (build-system r-build-system)
7970 (home-page "https://github.com/bnaras/cubature")
7971 (synopsis "Adaptive multivariate integration over hypercubes")
7973 "This package is an R wrapper around the cubature C library for adaptive
7974 multivariate integration over hypercubes. This version provides both
7975 @code{hcubature} and @code{pcubature} routines in addition to a vector
7977 ;; The included cubature C library is released under GPLv2+, but the
7978 ;; wrapper declares the license to be GPLv3+.
7979 (license (list license:gpl2+ license:gpl3+))))
7981 (define-public r-trend
7988 (uri (cran-uri "trend" version))
7991 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
7992 (build-system r-build-system)
7994 (list r-extradistr))
7997 (home-page "https://cran.r-project.org/web/packages/trend/")
7998 (synopsis "Non-parametric trend tests and change-point detection")
8000 "The analysis of environmental data often requires the detection of
8001 trends and change-points. This package includes tests for trend
8002 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
8003 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
8004 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
8005 correlation trend test), change-point detection (Lanzante's test procedures,
8006 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
8007 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
8008 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
8009 sample Robust Rank-Order Distributional Test.")
8010 (license license:gpl3)))
8012 (define-public r-expm
8019 (uri (cran-uri "expm" version))
8022 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c"))))
8023 (build-system r-build-system)
8024 (propagated-inputs (list r-matrix))
8025 (native-inputs (list gfortran))
8026 (home-page "https://r-forge.r-project.org/projects/expm/")
8027 (synopsis "Tools for matrix exponentials and related quantities")
8029 "This package provides tools for the computation of the matrix
8030 exponential, logarithm, square root, and related quantities.")
8031 (license license:gpl2+)))
8033 (define-public r-exposition
8035 (name "r-exposition")
8039 (uri (cran-uri "ExPosition" version))
8042 "0x9400ggmgrnaish0cfgnyvw549g4ibfv9aj6vzq7j68n58vq405"))))
8043 (properties `((upstream-name . "ExPosition")))
8044 (build-system r-build-system)
8045 (propagated-inputs (list r-prettygraphs))
8046 (home-page "https://cran.r-project.org/package=ExPosition")
8047 (synopsis "Exploratory analysis with the singular value decomposition")
8049 "This package provides a variety of descriptive multivariate analyses
8050 with the singular value decomposition, such as principal components analysis,
8051 correspondence analysis, and multidimensional scaling. See An ExPosition of
8052 the Singular Value Decomposition in R (Beaton et al 2014)
8053 <doi:10.1016/j.csda.2013.11.006>.")
8054 (license license:gpl2)))
8056 (define-public r-complexplus
8058 (name "r-complexplus")
8063 (uri (cran-uri "complexplus" version))
8066 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
8067 (build-system r-build-system)
8069 (list r-expm r-matrix))
8070 (home-page "https://cran.r-project.org/web/packages/complexplus/")
8071 (synopsis "Functions of complex or real variables")
8073 "This package extends several functions to the complex domain, including
8074 the matrix exponential and logarithm, and the determinant.")
8075 (license license:gpl2)))
8077 (define-public r-phontools
8079 (name "r-phontools")
8084 (uri (cran-uri "phonTools" version))
8087 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
8088 (properties `((upstream-name . "phonTools")))
8089 (build-system r-build-system)
8090 (home-page "http://www.santiagobarreda.com/rscripts.html")
8091 (synopsis "Tools for phonetic and acoustic analyses")
8093 "This package contains tools for the organization, display, and analysis
8094 of the sorts of data frequently encountered in phonetics research and
8095 experimentation, including the easy creation of IPA vowel plots, and the
8096 creation and manipulation of WAVE audio files.")
8097 (license license:bsd-2)))
8106 (uri (cran-uri "np" version))
8109 "0v6mhcwdnqj5kjxwrzcqlff021ih2jdarwmikdm5bvjfwi8pyarl"))))
8110 (build-system r-build-system)
8112 (list r-boot r-cubature r-quadprog r-quantreg))
8113 (home-page "https://github.com/JeffreyRacine/R-Package-np")
8114 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
8115 (description "This package provides non-parametric (and semi-parametric)
8116 kernel methods that seamlessly handle a mix of continuous, unordered, and
8117 ordered factor data types.")
8118 ;; Any version of the GPL.
8119 (license license:gpl3+)))
8121 (define-public r-powerplus
8123 (name "r-powerplus")
8128 (uri (cran-uri "powerplus" version))
8131 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
8132 (build-system r-build-system)
8134 (list r-complexplus r-expm r-mass r-matrix r-phontools))
8135 (home-page "https://cran.r-project.org/web/packages/powerplus/")
8136 (synopsis "Exponentiation operations")
8138 "This package provides tools for the computation of matrix and scalar
8140 (license license:gpl2)))
8142 (define-public r-egg
8149 (uri (cran-uri "egg" version))
8152 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
8153 (properties `((upstream-name . "egg")))
8154 (build-system r-build-system)
8156 (list r-ggplot2 r-gridextra r-gtable))
8157 (home-page "https://cran.r-project.org/web/packages/egg")
8158 (synopsis "Extensions for ggplot2")
8160 "This package provides miscellaneous functions to help customize ggplot2
8161 objects. High-level functions are provided to post-process ggplot2 layouts
8162 and allow alignment between plot panels, as well as setting panel sizes to
8163 fixed values. Other functions include a custom @code{geom}, and helper
8164 functions to enforce symmetric scales or add tags to facetted plots.")
8165 (license license:gpl3)))
8167 (define-public r-heatmap3
8174 (uri (cran-uri "heatmap3" version))
8177 "0sfvizmmwfk1bjhn6zfx5a4qqfgj1ldg8x90b65crqibgfa36k2r"))))
8178 (build-system r-build-system)
8180 (list r-fastcluster))
8183 (home-page "https://cran.r-project.org/web/packages/heatmap3/")
8184 (synopsis "Improved heatmap package")
8186 "This package provides an improved heatmap package. It is completely
8187 compatible with the original R function @code{heatmap}, and provides more
8188 powerful and convenient features.")
8189 (license license:gpl2+)))
8191 (define-public r-heatmaply
8193 (name "r-heatmaply")
8198 (uri (cran-uri "heatmaply" version))
8201 "1w8yyzb68laxd4zxycvgmpqj5wnyidjgv1vbzbxndp9p92f2cp8a"))))
8202 (build-system r-build-system)
8220 (home-page "https://cran.r-project.org/package=heatmaply")
8221 (synopsis "Interactive cluster heat maps using plotly")
8223 "This package enables you to create interactive cluster heatmaps that can
8224 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
8225 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
8226 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
8227 a popular graphical method for visualizing high-dimensional data, in which a
8228 table of numbers is encoded as a grid of colored cells. The rows and columns
8229 of the matrix are ordered to highlight patterns and are often accompanied by
8231 ;; Either version of the license.
8232 (license (list license:gpl2 license:gpl3))))
8241 (uri (cran-uri "h5" version))
8244 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
8245 (build-system r-build-system)
8252 (home-page "https://github.com/mannau/h5")
8253 (synopsis "Interface to the HDF5 Library")
8255 "This package provides an S4 interface to the HDF5 library supporting
8256 fast storage and retrieval of R-objects like vectors, matrices and arrays to
8257 binary files in a language independent format. The HDF5 format can therefore
8258 be used as an alternative to R's save/load mechanism. Since h5 is able to
8259 access only subsets of stored data it can also handle data sets which do not
8261 (license license:bsd-2)))
8263 (define-public r-cgdsr
8270 (uri (cran-uri "cgdsr" version))
8273 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
8274 (build-system r-build-system)
8276 (list r-httr r-r-methodss3 r-r-oo))
8277 (home-page "https://github.com/cBioPortal/cgdsr")
8278 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
8280 "This package provides a basic set of R functions for querying the Cancer
8281 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
8282 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
8283 (license license:lgpl3)))
8285 (define-public r-import
8292 (uri (cran-uri "import" version))
8295 "19g4jnfg9pkvvsncw62yc15xlb97hfbdqxivpjd9jqi36i6mdjrg"))))
8296 (build-system r-build-system)
8299 (home-page "https://github.com/smbache/import")
8300 (synopsis "Import mechanism for R")
8302 "This is an alternative mechanism for importing objects from packages.
8303 The syntax allows for importing multiple objects from a package with a single
8304 command in an expressive way. The import package bridges some of the gap
8305 between using @code{library} (or @code{require}) and direct (single-object)
8306 imports. Furthermore the imported objects are not placed in the current
8307 environment. It is also possible to import objects from stand-alone @code{.R}
8309 (license license:expat)))
8311 (define-public r-shinyace
8318 (uri (cran-uri "shinyAce" version))
8321 "12mqvdh6rxsr61pc3pzla95r5f4l7xagjs2rcdr7c2lbqyxpx6aa"))))
8322 (properties `((upstream-name . "shinyAce")))
8323 (build-system r-build-system)
8325 (list r-shiny r-jsonlite))
8326 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
8327 (synopsis "Ace editor bindings for Shiny")
8329 "This package provides Ace editor bindings to enable a rich text editing
8330 environment within Shiny.")
8331 (license license:expat)))
8333 (define-public r-rafalib
8340 (uri (cran-uri "rafalib" version))
8342 (base32 "1dmxjl66bfdgrybhwyaa8d4i460liqcdw8b29a6w7shgksh29m0k"))))
8343 (properties `((upstream-name . "rafalib")))
8344 (build-system r-build-system)
8345 (propagated-inputs (list r-rcolorbrewer))
8346 (home-page "https://cran.r-project.org/package=rafalib")
8347 (synopsis "Convenience functions for routine data exploration")
8349 "This package provides a series of shortcuts for routine tasks to
8350 facilitate data exploration.")
8351 (license license:artistic2.0)))
8353 (define-public r-randomizr
8355 (name "r-randomizr")
8360 (uri (cran-uri "randomizr" version))
8363 "1grm0h3xkb0pdbbv0gd531g1kn6njp0gcy5fh153rrmajxgd8hhw"))))
8364 (properties `((upstream-name . "randomizr")))
8365 (build-system r-build-system)
8368 (home-page "https://declaredesign.org/r/randomizr/")
8369 (synopsis "Tools for common forms of random assignment and sampling")
8371 "This package provides tools for generating random assignments for common
8372 experimental designs and random samples for common sampling designs.")
8373 (license license:expat)))
8375 (define-public r-base64url
8377 (name "r-base64url")
8382 (uri (cran-uri "base64url" version))
8385 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
8386 (build-system r-build-system)
8389 (home-page "https://github.com/mllg/base64url")
8390 (synopsis "Fast and URL-safe base64 encoder and decoder")
8392 "This package provides a URL-safe base64 encoder and decoder. In
8393 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
8394 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
8395 encoder does not fill the string with trailing @code{=}. The resulting
8396 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
8397 and thus are safe to use in URLs or for file names. The package also comes
8398 with a simple base32 encoder/decoder suited for case insensitive file
8400 (license license:gpl3)))
8402 (define-public r-radiant-data
8404 (name "r-radiant-data")
8409 (uri (cran-uri "radiant.data" version))
8412 "1vas0bkpngwxybmpdcaimha2r008prnli4b3lgjbjfkzpgm966d1"))
8413 (modules '((guix build utils)))
8416 ;; Delete files that are under CC-NC-SA.
8417 (delete-file-recursively "inst/app/tools/help")
8419 (properties `((upstream-name . "radiant.data")))
8420 (build-system r-build-system)
8456 (home-page "https://github.com/radiant-rstats/radiant.data")
8457 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
8459 "The Radiant Data menu includes interfaces for loading, saving, viewing,
8460 visualizing, summarizing, transforming, and combining data. It also contains
8461 functionality to generate reproducible reports of the analyses conducted in
8463 (license license:agpl3)))
8465 (define-public r-algdesign
8467 (name "r-algdesign")
8472 (uri (cran-uri "AlgDesign" version))
8474 (base32 "01cx63wqr6yvgl5ml1lj6gh9p1sn42b6qcnsppcw7mvba9n652ar"))))
8475 (properties `((upstream-name . "AlgDesign")))
8476 (build-system r-build-system)
8477 (home-page "https://github.com/jvbraun/AlgDesign")
8478 (synopsis "Algorithmic experimental design")
8480 "This package provides tools to calculate exact and approximate theory
8481 experimental designs for D, A, and I criteria. Very large designs may be
8482 created. Experimental designs may be blocked or blocked designs created from
8483 a candidate list, using several criteria. The blocking can be done when whole
8484 and within plot factors interact.")
8485 (license license:gpl2+)))
8487 (define-public r-alluvial
8494 (uri (cran-uri "alluvial" version))
8496 (base32 "039frwrsxq1lb97s7vf2vbyyadimkigs628ymym06fxka53drdkp"))))
8497 (properties `((upstream-name . "alluvial")))
8498 (build-system r-build-system)
8499 (native-inputs (list r-knitr))
8500 (home-page "https://github.com/mbojan/alluvial")
8501 (synopsis "Create parallel sets plots (Alluvial Diagrams)")
8503 "This package creates alluvial diagrams (also known as parallel sets
8504 plots) for multivariate and time series-like data.")
8505 (license license:expat)))
8507 (define-public r-signal
8514 (uri (cran-uri "signal" version))
8517 "0qaf39vfmhn3d0bdjqd805ayfkaj48dkmf5dqd47bpk7dp21b837"))))
8518 (build-system r-build-system)
8519 (propagated-inputs (list r-mass))
8520 (native-inputs (list gfortran))
8521 (home-page "https://cran.r-project.org/web/packages/signal/")
8522 (synopsis "Signal processing")
8524 "This package provides a set of signal processing functions originally
8525 written for Matlab and GNU Octave. It includes filter generation utilities,
8526 filtering functions, resampling routines, and visualization of filter models.
8527 It also includes interpolation functions.")
8528 (license license:gpl2)))
8530 (define-public r-gsubfn
8537 (uri (cran-uri "gsubfn" version))
8540 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
8541 (build-system r-build-system)
8542 (propagated-inputs (list r-proto))
8543 (home-page "https://code.google.com/archive/p/gsubfn/")
8544 (synopsis "Utilities for strings and function arguments")
8546 "This package provides @code{gsubfn} which is like @code{gsub} but can
8547 take a replacement function or certain other objects instead of the
8548 replacement string. Matches and back references are input to the replacement
8549 function and replaced by the function output. @code{gsubfn} can be used to
8550 split strings based on content rather than delimiters and for quasi-perl-style
8551 string interpolation. The package also has facilities for translating
8552 formulas to functions and allowing such formulas in function calls instead of
8554 (license license:gpl2+)))
8556 (define-public r-sqldf
8563 (uri (cran-uri "sqldf" version))
8566 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
8567 (build-system r-build-system)
8569 (list r-chron r-dbi r-gsubfn r-proto r-rsqlite))
8570 (home-page "https://github.com/ggrothendieck/sqldf")
8571 (synopsis "Manipulate R data frames using SQL")
8573 "The @code{sqldf} function is typically passed a single argument which is
8574 an SQL select statement where the table names are ordinary R data frame names.
8575 @code{sqldf} transparently sets up a database, imports the data frames into
8576 that database, performs the SQL statement and returns the result using a
8577 heuristic to determine which class to assign to each column of the returned
8578 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
8579 used to read filtered files into R even if the original files are larger than
8580 R itself can handle.")
8581 (license license:gpl2)))
8583 (define-public r-abind
8590 (uri (cran-uri "abind" version))
8593 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
8594 (build-system r-build-system)
8595 (home-page "https://cran.r-project.org/web/packages/abind/")
8596 (synopsis "Combine multidimensional arrays")
8598 "This package provides tools to combine multidimensional arrays into a
8599 single array. This is a generalization of @code{cbind} and @code{rbind}. It
8600 works with vectors, matrices, and higher-dimensional arrays. It also provides
8601 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
8602 extracting and replacing data in arrays.")
8603 (license license:lgpl2.0+)))
8605 (define-public r-prroc
8612 (uri (cran-uri "PRROC" version))
8615 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
8616 (properties `((upstream-name . "PRROC")))
8617 (build-system r-build-system)
8618 (home-page "https://cran.r-project.org/web/packages/PRROC/")
8619 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
8621 "This package computes the areas under the @dfn{precision-recall} (PR)
8622 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
8623 contrast to other implementations, the interpolation between points of the PR
8624 curve is done by a non-linear piecewise function. In addition to the areas
8625 under the curves, the curves themselves can also be computed and plotted by a
8626 specific S3-method.")
8627 (license license:gpl3)))
8629 (define-public r-vim
8636 (uri (cran-uri "VIM" version))
8639 "1r0myxcx8y1a3fkf9ssk882f09snn2j6zilsygpld32hahn4k9xg"))))
8640 (properties `((upstream-name . "VIM")))
8641 (build-system r-build-system)
8658 (home-page "https://github.com/alexkowa/VIM")
8659 (synopsis "Visualization and imputation of missing values")
8661 "This package provides tools for the visualization of missing and/or
8662 imputed values are introduced, which can be used for exploring the data and
8663 the structure of the missing and/or imputed values. Depending on this
8664 structure of the missing values, the corresponding methods may help to
8665 identify the mechanism generating the missing values and explore the
8666 data including missing values. In addition, the quality of imputation can be
8667 visually explored using various univariate, bivariate, multiple and
8668 multivariate plot methods.")
8669 (license license:gpl2+)))
8671 (define-public r-fnn
8678 (uri (cran-uri "FNN" version))
8681 "0nmynpiy3d2dnd5ngjf4m79jy02byhk43gj0xny9a6j8243f5c2j"))))
8682 (properties `((upstream-name . "FNN")))
8683 (build-system r-build-system)
8684 (home-page "https://cran.r-project.org/web/packages/FNN")
8685 (synopsis "Fast nearest neighbor search algorithms and applications")
8687 "This package provides cover-tree and kd-tree fast k-nearest neighbor
8688 search algorithms. Related applications including KNN classification,
8689 regression and information measures are implemented.")
8690 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
8691 ;; later can be used.
8692 (license license:gpl2+)))
8694 (define-public r-smoother
8701 (uri (cran-uri "smoother" version))
8704 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
8705 (build-system r-build-system)
8708 (home-page "https://cran.r-project.org/web/packages/smoother")
8709 (synopsis "Functions relating to the smoothing of numerical data")
8711 "This package provides a collection of methods for smoothing numerical
8712 data, commencing with a port of the Matlab gaussian window smoothing function.
8713 In addition, several functions typically used in smoothing of financial data
8715 (license license:gpl2)))
8717 (define-public r-riverplot
8719 (name "r-riverplot")
8724 (uri (cran-uri "riverplot" version))
8727 "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj"))))
8728 (build-system r-build-system)
8730 (list r-rcolorbrewer))
8733 (home-page "https://logfc.wordpress.com")
8734 (synopsis "Sankey or ribbon plots")
8736 "Sankey plots are a type of diagram that is convenient to illustrate how
8737 flow of information, resources etc. separates and joins, much like observing
8738 how rivers split and merge. For example, they can be used to compare
8739 different clusterings. This package provides an implementation of Sankey
8741 (license license:gpl2+)))
8743 (define-public r-dyn
8750 (uri (cran-uri "dyn" version))
8753 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
8754 (build-system r-build-system)
8757 (home-page "https://cran.r-project.org/web/packages/dyn")
8758 (synopsis "Time series regression")
8760 "This package provides the dyn class interfaces @code{ts}, @code{irts},
8761 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
8762 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
8763 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
8764 @code{randomForest::randomForest()} and other regression functions, allowing
8765 those functions to be used with time series including specifications that may
8766 contain lags, diffs and missing values.")
8768 (license license:gpl2+)))
8770 (define-public r-dynutils
8777 (uri (cran-uri "dynutils" version))
8779 (base32 "1pcj4igaw1g898xb42kcpzfmqy80xai5ki5bpnkf8hg738wm00qz"))))
8780 (properties `((upstream-name . "dynutils")))
8781 (build-system r-build-system)
8795 (native-inputs (list r-knitr))
8796 (home-page "https://github.com/dynverse/dynutils")
8797 (synopsis "Common functionality for the dynverse packages")
8799 "This package provides common functionality for the
8800 @url{https://dynverse.org,dynverse} packages. dynverse is created to support
8801 the development, execution, and benchmarking of trajectory inference
8803 (license license:expat)))
8805 (define-public r-catdap
8812 (uri (cran-uri "catdap" version))
8815 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
8816 (build-system r-build-system)
8819 (home-page "https://cran.r-project.org/web/packages/catdap/")
8820 (synopsis "Tools for categorical data analysis")
8822 "This package provides functions for analyzing multivariate data.
8823 Dependencies of the distribution of the specified variable (response
8824 variable) to other variables (explanatory variables) are derived and
8825 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
8826 (license license:gpl2+)))
8828 (define-public r-arules
8835 (uri (cran-uri "arules" version))
8838 "0pmikfq1phs73lmvhb4j9rlxj3z7kbp9wb619q2gqxpi9948raij"))))
8839 (build-system r-build-system)
8841 (list r-generics r-matrix))
8842 (home-page "https://github.com/mhahsler/arules")
8843 (synopsis "Mining association rules and frequent itemsets")
8845 "This package provides an infrastructure for representing, manipulating
8846 and analyzing transaction data and patterns (frequent itemsets and association rules).
8847 It also provides C implementations of the association mining algorithms Apriori
8849 (license license:gpl3)))
8851 (define-public r-parsedate
8853 (name "r-parsedate")
8858 (uri (cran-uri "parsedate" version))
8861 "1c2cpsvma3fkx6zp191bpfvf5rmpsr13g8rzqk6ycyb0n7b9k4qy"))))
8862 (build-system r-build-system)
8863 (home-page "https://github.com/gaborcsardi/parsedate")
8865 "Recognize and parse dates in various formats")
8867 "This package provides three functions for dealing with dates:
8868 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
8869 time formats, @code{parse_date} parses dates in unspecified formats,
8870 and @code{format_iso_8601} formats a date in ISO 8601 format.")
8871 (license license:gpl2)))
8873 (define-public r-abc-data
8880 (uri (cran-uri "abc.data" version))
8883 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
8884 (properties `((upstream-name . "abc.data")))
8885 (build-system r-build-system)
8886 (home-page "https://cran.r-project.org/web/packages/abc.data/")
8887 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
8889 "This package contains data which are used by functions of the abc
8890 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
8891 algorithms for performing parameter estimation, model selection, and
8893 (license license:gpl3+)))
8895 (define-public r-abc
8902 (uri (cran-uri "abc" version))
8905 "16753lyzk2dfwgdjfyanwacqw3bvrwby52inq4709804labs6lnv"))))
8906 (build-system r-build-system)
8908 (list r-abc-data r-locfit r-mass r-nnet r-quantreg))
8909 (home-page "https://cran.r-project.org/web/packages/abc/")
8910 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
8912 "This package implements several @dfn{Approximate Bayesian
8913 Computation} (ABC) algorithms for performing parameter estimation, model
8914 selection, and goodness-of-fit. Cross-validation tools are also available for
8915 measuring the accuracy of ABC estimates, and to calculate the
8916 misclassification probabilities of different models.")
8917 (license license:gpl3+)))
8919 (define-public r-zip
8926 (uri (cran-uri "zip" version))
8929 "08hl0sqiwh9my9ivkvkig044w7ppk8h8n38j3i0kjcc1fh43v1ql"))))
8930 (build-system r-build-system)
8931 (home-page "https://github.com/gaborcsardi/zip")
8932 (synopsis "Cross-platform Zip compression")
8934 "This package provides a cross-platform Zip compression library for R.
8935 It is a replacement for the @code{zip} function, that does not require any
8936 additional external tools on any platform.")
8937 (license license:cc0)))
8939 (define-public r-openxlsx
8946 (uri (cran-uri "openxlsx" version))
8949 "0695b265g7jwiqk5c3vmmfkvagx82bkpwhvqzhqaqmmn34l6vl35"))))
8950 (build-system r-build-system)
8952 (list r-rcpp r-stringi r-zip))
8955 (home-page "https://github.com/awalker89/openxlsx")
8956 (synopsis "Read, write and edit XLSX files")
8958 "This package simplifies the creation of Excel @code{.xlsx} files by
8959 providing a high level interface to writing, styling and editing worksheets.
8960 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
8961 and @code{XLConnect} packages with the added benefit of removing the
8962 dependency on Java.")
8963 (license license:gpl3)))
8965 (define-public r-rio
8972 (uri (cran-uri "rio" version))
8975 "04jlrhyl0791yxwcpp1s8p1hhkljnijlc5iaxpk56h41w63k39lz"))))
8976 (build-system r-build-system)
8987 (home-page "https://github.com/leeper/rio")
8988 (synopsis "Swiss-army knife for data I/O")
8990 "This package provides streamlined data import and export infrastructure
8991 by making assumptions that the user is probably willing to make: @code{import}
8992 and @code{export} determine the data structure from the file extension,
8993 reasonable defaults are used for data import and export (e.g.,
8994 @code{stringsAsFactors=FALSE}), web-based import is natively
8995 supported (including from SSL/HTTPS), compressed files can be read directly
8996 without explicit decompression, and fast import packages are used where
8997 appropriate. An additional convenience function, @code{convert}, provides a
8998 simple method for converting between file types.")
8999 (license license:gpl2)))
9001 (define-public r-maptools
9008 (uri (cran-uri "maptools" version))
9011 "1jgx8iiirj8qhrmh19mkisa35jcql7352dmc7lvwi5vxg3wjbvpk"))))
9012 (build-system r-build-system)
9014 (list r-foreign r-lattice r-sp))
9015 (home-page "https://r-forge.r-project.org/projects/maptools/")
9016 (synopsis "Tools for reading and handling spatial objects")
9018 "This package provides a set of tools for manipulating and reading
9019 geographic data, in particular ESRI Shapefiles. It includes binary access to
9020 GSHHG shoreline files. The package also provides interface wrappers for
9021 exchanging spatial objects with other R packages.")
9022 ;; The C source files from shapelib are released under the Expat license.
9023 ;; The R code is released under GPL version 2 or later.
9024 (license (list license:gpl2+
9027 (define-public r-later
9034 (uri (cran-uri "later" version))
9037 "0acqg29hcm2iq1418b54np7zb5pnr3xzrwc3ijv2pz9wra10ix88"))))
9038 (build-system r-build-system)
9040 (list r-rcpp r-rlang))
9043 (home-page "https://github.com/r-lib/later")
9044 (synopsis "Utilities for delaying function execution")
9046 "This package provides tools to execute arbitrary R or C functions some
9047 time after the current time, after the R execution stack has emptied.")
9048 (license license:gpl2+)))
9050 (define-public r-promises
9057 (uri (cran-uri "promises" version))
9060 "1dy4cbqw17awh4q8m7cy3anaj0n9iynabfzflb1g94cyj0bq4fld"))))
9061 (build-system r-build-system)
9063 (list r-later r-magrittr r-r6 r-rcpp r-rlang))
9066 (home-page "https://rstudio.github.io/promises")
9067 (synopsis "Abstractions for promise-based asynchronous programming")
9069 "This package provides fundamental abstractions for doing asynchronous
9070 programming in R using promises. Asynchronous programming is useful for
9071 allowing a single R process to orchestrate multiple tasks in the background
9072 while also attending to something else. Semantics are similar to JavaScript
9073 promises, but with a syntax that is idiomatic R.")
9074 (license license:expat)))
9076 (define-public r-dosnow
9083 (uri (cran-uri "doSNOW" version))
9086 "1f5v0k2w0b2478p6iqa3hn2lwd1x3rzc348n57nd38ka2vnsnz4i"))))
9087 (properties `((upstream-name . "doSNOW")))
9088 (build-system r-build-system)
9090 (list r-foreach r-iterators r-snow))
9091 (home-page "https://cran.r-project.org/web/packages/doSNOW")
9092 (synopsis "Foreach parallel adaptor for the snow package")
9094 "This package provides a parallel backend for the @code{%dopar%} function
9095 using the @code{snow} package.")
9096 (license license:gpl2)))
9098 (define-public r-fstcore
9105 (uri (cran-uri "fstcore" version))
9107 (base32 "1a5m68n2dqhi3r8wf5jwg4vjvl550c7wypcf5j0xmkvl836yg1lg"))))
9108 (properties `((upstream-name . "fstcore")))
9109 (build-system r-build-system)
9110 (propagated-inputs (list r-rcpp))
9111 (inputs (list zlib))
9112 (native-inputs (list pkg-config))
9113 (home-page "https://www.fstpackage.org/fstcore/")
9114 (synopsis "R bindings to the fstlib library")
9116 "The fstlib library provides multithreaded serialization of compressed
9117 data frames using the fst format. The fst format allows for random access of
9118 stored data and compression with the LZ4 and ZSTD compressors.")
9119 (license license:mpl2.0)))
9121 (define-public r-fst
9128 (uri (cran-uri "fst" version))
9131 "0r96inwrr960m7wmc80603bw2vvvwab225bh9dq3lalwhy4yiis4"))))
9132 (properties `((upstream-name . "fst")))
9133 (build-system r-build-system)
9134 (propagated-inputs (list r-fstcore r-rcpp))
9135 (home-page "http://www.fstpackage.org")
9136 (synopsis "Fast serialization of data frames")
9138 "The fst package for R provides a fast, easy and flexible way to
9139 serialize data frames. With access speeds of multiple GB/s, fst is
9140 specifically designed to unlock the potential of high speed solid state disks.
9141 Data frames stored in the fst format have full random access, both in column
9142 and rows. The fst format allows for random access of stored data and
9143 compression with the LZ4 and ZSTD compressors.")
9144 (license license:agpl3)))
9146 (define-public r-snftool
9152 (uri (cran-uri "SNFtool" version))
9155 "05hz230aq5wbzhknxzr4iqv3nqjhbpf66n6bp1rc5h2jgz2yfbwq"))))
9156 (properties `((upstream-name . "SNFtool")))
9157 (build-system r-build-system)
9158 (propagated-inputs (list r-alluvial r-exposition))
9159 (home-page "https://cran.r-project.org/package=SNFtool")
9160 (synopsis "Similarity network fusion")
9162 "Similarity Network Fusion takes multiple views of a network and fuses
9163 them together to construct an overall status matrix. The input to our
9164 algorithm can be feature vectors, pairwise distances, or pairwise
9165 similarities. The learned status matrix can then be used for retrieval,
9166 clustering, and classification.")
9167 ;; Any version of the GPL
9168 (license license:gpl3+)))
9170 (define-public r-snowfall
9173 (version "1.84-6.2")
9176 (uri (cran-uri "snowfall" version))
9178 (base32 "0frmasv04wd47h04zbwaryhiyxllarf3ggpa39p5qicjp6r7lilv"))))
9179 (build-system r-build-system)
9182 (home-page "https://cran.r-project.org/web/packages/snowfall/")
9183 (synopsis "Easier cluster computing")
9184 (description "This package is a usability wrapper around snow for easier
9185 development of parallel R programs. This package offers e.g. extended error
9186 checks, and additional functions. All functions work in sequential mode, too,
9187 if no cluster is present or wished. The package is also designed as connector
9188 to the cluster management tool @code{sfCluster}, but can also used without
9190 (license license:gpl2+)))
9192 (define-public r-rgexf
9199 (uri (cran-uri "rgexf" version))
9202 "00c2zka1n3k7p1l0mlchr063s6x58p9r3fb64d4wgl4rvsq55q3f"))
9203 ;; Delete minified JavaScript files
9205 '(for-each delete-file
9206 '("inst/gexf-js/js/jquery-2.0.2.min.js"
9207 "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js"
9208 "inst/gexf-js/js/jquery.mousewheel.min.js")))))
9209 (properties `((upstream-name . "rgexf")))
9210 (build-system r-build-system)
9212 `(#:modules ((guix build utils)
9213 (guix build r-build-system)
9217 (modify-phases %standard-phases
9218 (add-after 'unpack 'process-javascript
9219 (lambda* (#:key inputs #:allow-other-keys)
9220 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-jquery-ui"))
9221 (with-directory-excursion "inst/gexf-js/js/"
9225 `((,(assoc-ref inputs "js-jquery")
9226 "jquery-2.0.2.min.js")
9227 ("/tmp/jquery-ui-1.10.3/ui/jquery-ui.js"
9228 "jquery-ui-1.10.3.custom.min.js")
9229 (,(assoc-ref inputs "js-jquery-mousewheel")
9230 "jquery.mousewheel.min.js"))))
9231 (lambda (sources targets)
9232 (for-each (lambda (source target)
9233 (format #true "Processing ~a --> ~a~%"
9235 (invoke "esbuild" source "--minify"
9236 (string-append "--outfile=" target)))
9237 sources targets)))))))))
9239 (list r-igraph r-servr r-xml))
9241 `(("r-knitr" ,r-knitr)
9242 ("esbuild" ,esbuild)
9247 (uri "https://code.jquery.com/jquery-2.0.2.js")
9250 "0v818bxpw48gdk8i95qqqij80r9jcgisi2r4ac6xnxca20h0gvfj"))))
9254 (uri "https://jqueryui.com/resources/download/jquery-ui-1.10.3.zip")
9257 "00xpfy0l69nj2yan4s8k65ldsrlfsjkmyw2dwcg93dc8mv454vxx"))))
9258 ("js-jquery-mousewheel"
9261 (uri "https://raw.githubusercontent.com/jquery/jquery-mousewheel/\
9262 3.0.6/jquery.mousewheel.js")
9265 "19lk5xy2s47bx8hsa7j6bg012f8yw6d770g230bcnm559kf4nc6v"))))))
9266 (home-page "https://gvegayon.github.io/rgexf")
9267 (synopsis "Build, import and export GEXF graph files")
9269 "Create, read and write GEXF (Graph Exchange XML Format) graph
9270 files (used in Gephi and others). It allows the user to easily build/read
9271 graph files including attributes, GEXF visual attributes (such as color, size,
9272 and position), network dynamics (for both edges and nodes) and edge weighting.
9273 Users can build/handle graphs element-by-element or massively through
9274 data-frames, visualize the graph on a web browser through gexf-js (a
9275 JavaScript library) and interact with the igraph package.")
9276 (license license:expat)))
9278 (define-public r-data-tree
9280 (name "r-data-tree")
9285 (uri (cran-uri "data.tree" version))
9288 "0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
9289 (properties `((upstream-name . "data.tree")))
9290 (build-system r-build-system)
9292 (list r-r6 r-stringi))
9295 (home-page "https://github.com/gluc/data.tree")
9296 (synopsis "General purpose hierarchical data structure")
9298 "Create tree structures from hierarchical data, and traverse the tree in
9299 various orders. Aggregate, cumulate, print, plot, convert to and from
9300 data.frame and more. This is useful for decision trees, machine learning,
9301 finance, conversion from and to JSON, and many other applications.")
9302 (license license:gpl2+)))
9304 (define-public r-dtplyr
9311 (uri (cran-uri "dtplyr" version))
9314 "1m72ac7461mlvanj1krpmfp2ljl3c2k5nw6zrahc66vhcgz2hngq"))))
9315 (properties `((upstream-name . "dtplyr")))
9316 (build-system r-build-system)
9330 (home-page "https://github.com/tidyverse/dtplyr")
9331 (synopsis "Data Table back-end for dplyr")
9333 "This package provides a @code{data.table} backend for @code{dplyr}. The
9334 goal of @code{dtplyr} is to allow you to write @code{dplyr} code that is
9335 automatically translated to the equivalent, but usually much faster,
9336 @code{data.table} code.")
9337 (license license:expat)))
9339 (define-public r-collapsibletree
9341 (name "r-collapsibletree")
9346 (uri (cran-uri "collapsibleTree" version))
9349 "0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
9352 ;; Delete minified JavaScript file
9353 (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js")
9356 `((upstream-name . "collapsibleTree")))
9357 (build-system r-build-system)
9360 (modify-phases %standard-phases
9361 (add-after 'unpack 'process-javascript
9362 (lambda* (#:key inputs #:allow-other-keys)
9363 (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/"
9364 (let ((source (assoc-ref inputs "d3.v4.js"))
9365 (target "d3.min.js"))
9366 (format #t "Processing ~a --> ~a~%"
9368 (invoke "esbuild" source "--minify"
9369 (string-append "--outfile=" target)))))))))
9371 (list r-data-tree r-htmlwidgets))
9373 `(("esbuild" ,esbuild)
9377 (uri "https://d3js.org/d3.v4.js")
9380 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
9381 (home-page "https://github.com/AdeelK93/collapsibleTree")
9382 (synopsis "Interactive collapsible tree diagrams using D3.js")
9384 "This is a package for interactive Reingold-Tilford tree diagrams created
9385 using D3.js, where every node can be expanded and collapsed by clicking on it.
9386 Tooltips and color gradients can be mapped to nodes using a numeric column in
9387 the source data frame.")
9388 (license license:gpl3+)))
9390 (define-public r-rappdirs
9397 (uri (cran-uri "rappdirs" version))
9400 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9"))))
9401 (build-system r-build-system)
9402 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
9403 (synopsis "Determine where to save data, caches, and logs")
9405 "This package provides an easy way to determine which directories on the
9406 user's computer should be used to save data, caches and logs. It is a port of
9407 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
9408 (license license:expat)))
9410 (define-public r-rastervis
9412 (name "r-rastervis")
9417 (uri (cran-uri "rasterVis" version))
9420 "0kgg6cm7xjqya2d46w0i1i1wjpkb8f99lyqy7rgwa7l9xmwzj5n1"))))
9421 (properties `((upstream-name . "rasterVis")))
9422 (build-system r-build-system)
9433 (home-page "https://oscarperpinan.github.io/rastervis/")
9434 (synopsis "Visualization methods for raster data")
9436 "This package provides methods for enhanced visualization and interaction
9437 with raster data. It implements visualization methods for quantitative data
9438 and categorical data, both for univariate and multivariate rasters. It also
9439 provides methods to display spatiotemporal rasters, and vector fields.")
9440 (license license:gpl3)))
9442 (define-public r-rentrez
9449 (uri (cran-uri "rentrez" version))
9452 "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv"))))
9453 (properties `((upstream-name . "rentrez")))
9454 (build-system r-build-system)
9456 (list r-httr r-jsonlite r-xml))
9459 (home-page "https://docs.ropensci.org/rentrez/")
9460 (synopsis "Entrez in R")
9462 "This package provides an R interface to the NCBI's EUtils API,
9463 allowing users to search databases like GenBank PubMed, process the results of
9464 those searches and pull data into their R sessions.")
9465 (license license:expat)))
9467 (define-public r-renv
9474 (uri (cran-uri "renv" version))
9477 "0bjq3ms5dg155clya62m462m93g90sxfxm7b4cqhqbx8vakskwdl"))))
9478 (properties `((upstream-name . "renv")))
9479 (build-system r-build-system)
9482 (home-page "https://rstudio.github.io/renv")
9483 (synopsis "Project environments")
9485 "This package provides a dependency management toolkit for R. Using
9486 renv, you can create and manage project-local R libraries, save the state of
9487 these libraries to a lockfile, and later restore your library as required.
9488 Together, these tools can help make your projects more isolated, portable, and
9490 (license license:expat)))
9492 (define-public r-learnr
9499 (uri (cran-uri "learnr" version))
9502 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
9503 (build-system r-build-system)
9519 (home-page "https://rstudio.github.io/learnr/")
9520 (synopsis "Interactive tutorials for R")
9522 "This package provides tools to create interactive tutorials using R
9523 Markdown. Use a combination of narrative, figures, videos, exercises, and
9524 quizzes to create self-paced tutorials for learning about R and R packages.")
9525 (license license:asl2.0)))
9527 (define-public r-analytics
9529 (name "r-analytics")
9534 (uri (cran-uri "analytics" version))
9537 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
9538 (build-system r-build-system)
9552 (home-page "https://cran.r-project.org/web/packages/analytics/")
9553 (synopsis "Collection of data analysis tools")
9555 "This package is a collection of data analysis tools. It includes tools
9556 for regression outlier detection in a fitted linear model, stationary
9557 bootstrap using a truncated geometric distribution, a comprehensive test for
9558 weak stationarity, column means by group, weighted biplots, and a heuristic to
9559 obtain a better initial configuration in non-metric MDS.")
9560 (license license:gpl2)))
9562 (define-public r-here
9569 (uri (cran-uri "here" version))
9571 (base32 "0srlr8h8qmr0wrmp7gs4g2ry5dni2hx8n947bik3s3a26f091v88"))))
9572 (properties `((upstream-name . "here")))
9573 (build-system r-build-system)
9574 (propagated-inputs (list r-rprojroot))
9575 (native-inputs (list r-knitr))
9576 (home-page "https://here.r-lib.org/")
9577 (synopsis "Simpler way to find files")
9579 "This package lets you construct paths to your project's files. Use the
9580 @code{here} function as a drop-in replacement for @code{file.path}, it will
9581 always locate the files relative to your project root.")
9582 (license license:expat)))
9584 (define-public r-reticulate
9586 (name "r-reticulate")
9591 (uri (cran-uri "reticulate" version))
9594 "1ibliic3qp597nskak2bfa6iyl721ssgcavwvfaf1c71plilimrz"))))
9595 (build-system r-build-system)
9599 '(modify-phases %standard-phases
9600 (add-after 'unpack 'build-reproducibly
9602 (setenv "PYTHONHASHSEED" "0")
9603 (setenv "PYTHONDONTWRITEBYTECODE" "1"))))))
9604 (inputs (list python))
9616 (home-page "https://github.com/rstudio/reticulate")
9617 (synopsis "R interface to Python")
9619 "This package provides an interface from R to Python modules, classes,
9620 and functions. When calling into Python, R data types are automatically
9621 converted to their equivalent Python types. When values are returned from
9622 Python to R they are converted back to R types.")
9623 (license license:asl2.0)))
9625 (define-public r-bibtex
9632 (uri (cran-uri "bibtex" version))
9635 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv"))))
9636 (build-system r-build-system)
9637 (propagated-inputs (list r-stringr))
9638 (home-page "https://github.com/romainfrancois/bibtex")
9639 (synopsis "Bibtex parser")
9640 (description "This package provides a utility for R to parse a bibtex
9642 (license license:gpl2+)))
9644 (define-public r-billboarder
9646 (name "r-billboarder")
9651 (uri (cran-uri "billboarder" version))
9653 (base32 "189ngvg84rcwhrivxskmjv3srhadvzr4p1v8pf11axyv2qn01b0x"))
9655 '(delete-file "inst/htmlwidgets/lib/billboard/billboard.pkgd.min.js"))))
9656 (properties `((upstream-name . "billboarder")))
9657 (build-system r-build-system)
9660 (modify-phases %standard-phases
9661 (add-after 'unpack 'process-javascript
9662 (lambda* (#:key inputs #:allow-other-keys)
9663 (with-directory-excursion "inst/htmlwidgets/lib/billboard/"
9664 (let ((source (assoc-ref inputs "js-billboard"))
9665 (target "billboard.pkgd.min.js"))
9666 (format #true "Processing ~a --> ~a~%"
9668 (invoke "esbuild" source "--minify"
9669 (string-append "--outfile=" target)))))))))
9680 `(("r-knitr" ,r-knitr)
9681 ("esbuild" ,esbuild)
9682 ;; It is not ideal to use this concatenated (but not minified)
9683 ;; JavaScript file, as the original source is written in TypeScript.
9684 ;; However, this can still be considered source code as it is readable
9685 ;; and can be modified.
9689 (uri "https://unpkg.com/billboard.js@3.2.0/dist/billboard.js")
9692 "1kx5rqmn87pgal2cwmcij2rrnwa0fgcsw6y99m4i0l2sdm0qffv2"))))))
9693 (home-page "https://github.com/dreamRs/billboarder")
9694 (synopsis "Create interactive charts with the JavaScript Billboard library")
9696 "This package provides an @code{htmlwidgets} interface to billboard.js,
9697 a re-usable easy interface JavaScript chart library, based on D3 v4+. Chart
9698 types include line charts, scatterplots, bar/lollipop charts,
9699 histogram/density plots, pie/donut charts and gauge charts. All charts are
9700 interactive, and a proxy method is implemented to smoothly update a chart
9701 without rendering it again in shiny apps.")
9702 (license license:expat)))
9704 (define-public r-ggseqlogo
9706 (name "r-ggseqlogo")
9711 (uri (cran-uri "ggseqlogo" version))
9714 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
9715 (build-system r-build-system)
9716 (propagated-inputs (list r-ggplot2))
9717 (home-page "https://github.com/omarwagih/ggseqlogo")
9718 (synopsis "ggplot2 extension for drawing genetic sequence logos")
9720 "The range of functions provided by this package makes it possible to
9721 draw highly versatile genomic sequence logos. Features include, but are not
9722 limited to, modifying colour schemes and fonts used to draw the logo,
9723 generating multiple logo plots, and aiding the visualisation with annotations.
9724 Sequence logos can easily be combined with other ggplot2 plots.")
9725 ;; Unspecified version of the LGPL.
9726 (license license:lgpl3+)))
9728 (define-public r-ggsci
9735 (uri (cran-uri "ggsci" version))
9738 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
9739 (build-system r-build-system)
9741 (list r-ggplot2 r-scales))
9742 (home-page "https://nanx.me/ggsci/")
9743 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
9745 "This package provides a collection of ggplot2 color palettes inspired by
9746 plots in scientific journals, data visualization libraries, science fiction
9747 movies, and TV shows.")
9748 (license license:gpl3)))
9750 (define-public r-ggsignif
9757 (uri (cran-uri "ggsignif" version))
9760 "1ad774c7s7y4i00xd89lfigr9aybl94q98ch598k3rchanr4b1fa"))))
9761 (build-system r-build-system)
9766 (home-page "https://github.com/const-ae/ggsignif")
9767 (synopsis "Significance brackets for ggplot2")
9769 "Enrich your ggplots with group-wise comparisons. This package provides
9770 an easy way to indicate if two groups are significantly different. Commonly
9771 this is shown by a bracket on top connecting the groups of interest which
9772 itself is annotated with the level of significance. The package provides a
9773 single layer that takes the groups for comparison and the test as arguments
9774 and adds the annotation to the plot.")
9775 (license license:gpl3)))
9777 (define-public r-rstatix
9784 (uri (cran-uri "rstatix" version))
9787 "0330y8iziffqg8j9j5h9zv4qcdyf8ybhmzxrr9fzq9nc6bf1gbm5"))))
9788 (properties `((upstream-name . "rstatix")))
9789 (build-system r-build-system)
9802 (home-page "https://rpkgs.datanovia.com/rstatix/")
9803 (synopsis "Pipe-friendly framework for basic statistical tests")
9805 "This package provides a simple and intuitive pipe-friendly framework,
9806 coherent with the @code{tidyverse} design philosophy, for performing basic
9807 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
9808 correlation analyses. The output of each test is automatically transformed
9809 into a tidy data frame to facilitate visualization. Additional functions are
9810 available for reshaping, reordering, manipulating and visualizing correlation
9812 (license license:gpl2)))
9814 (define-public r-ggpubr
9821 (uri (cran-uri "ggpubr" version))
9824 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
9825 (build-system r-build-system)
9843 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
9844 (synopsis "ggplot2-based publication-ready plots")
9846 "The ggplot2 package is an excellent and flexible package for elegant
9847 data visualization in R. However the default generated plots require some
9848 formatting before we can send them for publication. The ggpubr package
9849 provides some easy-to-use functions for creating and customizing ggplot2-based
9850 publication-ready plots.")
9851 (license license:gpl2)))
9853 (define-public r-ellipse
9860 (uri (cran-uri "ellipse" version))
9863 "0im9d36dixpksms52v6nsb3l0z2c7wc25r9j0f08naj6qc8jpvq2"))))
9864 (build-system r-build-system)
9865 (home-page "https://cran.r-project.org/web/packages/ellipse/")
9866 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
9868 "This package contains various routines for drawing ellipses and
9869 ellipse-like confidence regions, implementing the plots described in Murdoch
9870 and Chow (1996), A graphical display of large correlation matrices, The
9871 American Statistician 50, 178-180. There are also routines implementing the
9872 profile plots described in Bates and Watts (1988), Nonlinear Regression
9873 Analysis and its Applications.")
9874 (license license:gpl2+)))
9876 (define-public r-flashclust
9878 (name "r-flashclust")
9883 (uri (cran-uri "flashClust" version))
9886 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
9887 (properties `((upstream-name . "flashClust")))
9888 (build-system r-build-system)
9889 (native-inputs (list gfortran))
9890 (home-page "https://cran.r-project.org/web/packages/flashClust/")
9891 (synopsis "Implementation of optimal hierarchical clustering")
9893 "This package provides a fast implementation of hierarchical
9895 (license license:gpl2+)))
9897 (define-public r-factominer
9899 (name "r-factominer")
9904 (uri (cran-uri "FactoMineR" version))
9907 "0xcg4vjs5v9k28hhxhkfkks7nvpxpp2cvim00kh67f4pq041c9l1"))))
9908 (properties `((upstream-name . "FactoMineR")))
9909 (build-system r-build-system)
9926 (home-page "http://factominer.free.fr")
9927 (synopsis "Multivariate exploratory data analysis and data mining")
9929 "This package provides exploratory data analysis methods to summarize,
9930 visualize and describe datasets. The main principal component methods are
9931 available, those with the largest potential in terms of applications:
9932 principal component analysis (PCA) when variables are quantitative,
9933 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
9934 variables are categorical, Multiple Factor Analysis when variables are
9935 structured in groups, etc. and hierarchical cluster analysis.")
9936 (license license:gpl2+)))
9938 (define-public r-factoextra
9940 (name "r-factoextra")
9945 (uri (cran-uri "factoextra" version))
9948 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
9949 (build-system r-build-system)
9960 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
9961 (synopsis "Extract and visualize the results of multivariate data analyses")
9963 "This package provides some easy-to-use functions to extract and
9964 visualize the output of multivariate data analyses, including
9965 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
9966 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
9967 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
9968 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
9969 packages. It contains also functions for simplifying some clustering analysis
9970 steps and provides ggplot2-based elegant data visualization.")
9971 (license license:gpl2)))
9973 (define-public r-fansi
9980 (uri (cran-uri "fansi" version))
9983 "0sn0kflgcn2qrrv646pzqylm02cx8l5ws473ppmvla4xihyvi9w6"))))
9984 (build-system r-build-system)
9986 (list r-knitr)) ; for vignettes
9987 (home-page "https://github.com/brodieG/fansi")
9988 (synopsis "ANSI control sequence aware string functions")
9990 "This package provides counterparts to R string manipulation functions
9991 that account for the effects of ANSI text formatting control sequences.")
9992 (license license:gpl2+)))
9994 (define-public r-nbclust
10001 (uri (cran-uri "NbClust" version))
10004 "0k5hr4zgx4gp1n62xchgz2zvyl35ba2cnczhhvj8rfbg2n4hx6qs"))))
10005 (properties `((upstream-name . "NbClust")))
10006 (build-system r-build-system)
10007 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
10008 (synopsis "Determine the best number of clusters in a data set")
10010 "NbClust provides 30 indexes for determining the optimal number of
10011 clusters in a data set and offers the best clustering scheme from different
10012 results to the user.")
10013 (license license:gpl2)))
10015 (define-public r-hdf5r
10022 (uri (cran-uri "hdf5r" version))
10025 "16iin6krx2c50wm4d1id71v3kci6djvlari3ahic25vw1dg1k81l"))))
10026 (build-system r-build-system)
10030 (list r-bit64 r-r6))
10033 (home-page "https://hhoeflin.github.io/hdf5r")
10034 (synopsis "Interface to the HDF5 binary data format")
10036 "HDF5 is a data model, library and file format for storing and managing
10037 large amounts of data. This package provides a nearly feature complete,
10038 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
10039 functionality is added so that HDF5 objects behave very similar to their
10040 corresponding R counterparts.")
10041 (license license:asl2.0)))
10043 (define-public r-itertools
10045 (name "r-itertools")
10050 (uri (cran-uri "itertools" version))
10053 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
10054 (build-system r-build-system)
10056 (list r-iterators))
10057 (home-page "https://cran.r-project.org/web/packages/itertools/")
10058 (synopsis "Iterator tools")
10060 "This package provides various tools for creating iterators, many
10061 patterned after functions in the Python @code{itertools} module, and others
10062 patterned after functions in the snow package.")
10063 (license license:gpl2)))
10065 (define-public r-itsadug
10072 (uri (cran-uri "itsadug" version))
10074 (base32 "1sdqs279qxr3993hw08xg7b54yq03jw1597cqn6cf24sh9vpw9m1"))))
10075 (properties `((upstream-name . "itsadug")))
10076 (build-system r-build-system)
10077 (propagated-inputs (list r-mgcv r-plotfunctions))
10078 (native-inputs (list r-knitr))
10079 (home-page "https://cran.r-project.org/package=itsadug")
10080 (synopsis "Interpreting time series and autocorrelated data using GAMMs")
10082 "@dfn{Generalized Additive Mixed Modeling} (GAMM; Lin & Zhang, 1999) as
10083 implemented in the R package @code{mgcv} is a nonlinear regression analysis
10084 which is particularly useful for time course data such as EEG, pupil dilation,
10085 gaze data (eye tracking), and articulography recordings, but also for
10086 behavioral data such as reaction times and response data. As time course
10087 measures are sensitive to autocorrelation problems, GAMMs implements methods
10088 to reduce the autocorrelation problems. This package includes functions for
10089 the evaluation of GAMM models (e.g., model comparisons, determining regions of
10090 significance, inspection of autocorrelational structure in residuals) and
10091 interpreting of GAMMs (e.g., visualization of complex interactions, and
10093 (license license:gpl2+)))
10095 (define-public r-polynom
10102 (uri (cran-uri "polynom" version))
10105 "0y4j07syjwpnq5w6a1d90z6h1hjzijmm42pq0f8jk2vcn5xxn7mw"))))
10106 (build-system r-build-system)
10107 (native-inputs (list r-knitr))
10108 (home-page "https://cran.r-project.org/web/packages/polynom/")
10109 (synopsis "Functions for univariate polynomial manipulations")
10111 "This package provides a collection of functions to implement a class for
10112 univariate polynomial manipulations.")
10113 (license license:gpl2)))
10115 (define-public r-pupillometryr
10117 (name "r-pupillometryr")
10122 (uri (cran-uri "PupillometryR" version))
10124 (base32 "0yk30sgl2qqa6pva649swq523vh446ifmydildycfvfmlm1h4qza"))))
10125 (properties `((upstream-name . "PupillometryR")))
10126 (build-system r-build-system)
10139 (native-inputs (list r-knitr))
10140 (home-page "https://cran.r-project.org/package=PupillometryR")
10141 (synopsis "Unified pipeline for pupillometry data")
10143 "This package provides a unified pipeline to clean, prepare, plot, and
10144 run basic analyses on pupillometry experiments.")
10145 (license license:expat)))
10147 (define-public r-gbrd
10154 (uri (cran-uri "gbRd" version))
10157 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
10158 (properties `((upstream-name . "gbRd")))
10159 (build-system r-build-system)
10160 (home-page "https://cran.r-project.org/web/packages/gbRd/")
10161 (synopsis "Utilities for processing Rd objects and files")
10163 "This package provides utilities for processing Rd objects and files.
10164 Extract argument descriptions and other parts of the help pages of
10166 (license license:gpl2+)))
10168 (define-public r-rjags
10175 (uri (cran-uri "rjags" version))
10178 "0cibz6xhmh86fh7ynmdgpmlchizi57pi6dpslgc2if17a56c6p7q"))))
10179 (build-system r-build-system)
10186 (home-page "http://mcmc-jags.sourceforge.net")
10187 (synopsis "Bayesian graphical models using MCMC")
10189 "This package provides an R interface to the JAGS MCMC library. JAGS is
10190 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
10191 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
10192 (license license:gpl2)))
10194 (define-public r-rbibutils
10196 (name "r-rbibutils")
10201 (uri (cran-uri "rbibutils" version))
10204 "11pzbqykmn7m9gp5jspfcj6vij865wqf9ry6m3jkihvfj7zhfb5j"))))
10205 (properties `((upstream-name . "rbibutils")))
10206 (build-system r-build-system)
10207 (home-page "https://geobosh.github.io/rbibutils/")
10208 (synopsis "Convert between bibliography formats")
10210 "This package converts between a number of bibliography formats,
10211 including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils
10212 utilities and supports all bibliography formats and character encodings
10213 implemented in bibutils.")
10214 (license license:gpl2)))
10216 (define-public r-rdpack
10223 (uri (cran-uri "Rdpack" version))
10226 "109mylzmlncq5a09ayy4g2g0frj1k843lj8j78gvmz1h5g8sslkn"))))
10227 (properties `((upstream-name . "Rdpack")))
10228 (build-system r-build-system)
10230 (list r-rbibutils))
10231 (home-page "https://github.com/GeoBosh/Rdpack")
10232 (synopsis "Update and manipulate Rd documentation objects")
10234 "This package provides functions for manipulation of R documentation
10235 objects, including functions @code{reprompt()} and @code{ereprompt()} for
10236 updating Rd documentation for functions, methods and classes; it also includes
10237 Rd macros for citations and import of references from bibtex files for use in
10238 Rd files and roxygen2 comments, as well as many functions for manipulation of
10239 references and Rd files.")
10240 (license license:gpl2+)))
10242 (define-public r-officer
10249 (uri (cran-uri "officer" version))
10252 "1h6fcqw4bg644lwr5jggphyxp2d0ycya9q869z8099a50gc6h03f"))))
10253 (build-system r-build-system)
10255 (list r-r6 r-uuid r-xml2 r-zip))
10256 (home-page "https://davidgohel.github.io/officer")
10257 (synopsis "Manipulation of Word and PowerPoint documents")
10259 "This package provides tools to access and manipulate Word and PowerPoint
10260 documents from R. The package focuses on tabular and graphical reporting from
10261 R; it also provides two functions that let users get document content into
10262 data objects. A set of functions lets add and remove images, tables and
10263 paragraphs of text in new or existing documents. When working with PowerPoint
10264 presentations, slides can be added or removed; shapes inside slides can also
10265 be added or removed. When working with Word documents, a cursor can be used
10266 to help insert or delete content at a specific location in the document.")
10267 (license license:gpl3)))
10269 (define-public r-profilemodel
10271 (name "r-profilemodel")
10276 (uri (cran-uri "profileModel" version))
10279 "01m5nb8cmq0aq555pxk2a99182si65hhmn68yn9nal2j3zl2bp4i"))))
10280 (properties `((upstream-name . "profileModel")))
10281 (build-system r-build-system)
10282 (home-page "https://github.com/ikosmidis/profileModel")
10283 (synopsis "Profiling inference functions for various model classes")
10285 "This package provides tools that can be used to calculate, evaluate,
10286 plot and use for inference the profiles of *arbitrary* inference functions for
10287 arbitrary @code{glm}-like fitted models with linear predictors. More information
10288 on the methods that are implemented can be found in Kosmidis (2008)
10289 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
10290 (license license:gpl2+)))
10292 (define-public r-brglm
10299 (uri (cran-uri "brglm" version))
10302 "08shcz0j1npdn7xkhsvlzs3z4rdwq3g4rk6a4xx8wirqw8n8s2an"))))
10303 (properties `((upstream-name . "brglm")))
10304 (build-system r-build-system)
10306 (list r-profilemodel))
10307 (home-page "https://github.com/ikosmidis/brglm")
10308 (synopsis "Bias reduction in binomial-response generalized linear models")
10310 "Fit generalized linear models with binomial responses using either an
10311 adjusted-score approach to bias reduction or maximum penalized likelihood
10312 where penalization is by Jeffreys invariant prior. These procedures return
10313 estimates with improved frequentist properties (bias, mean squared error) that
10314 are always finite even in cases where the maximum likelihood estimates are
10315 infinite (data separation). Fitting takes place by fitting generalized linear
10316 models on iteratively updated pseudo-data. The interface is essentially the
10317 same as @code{glm}. More flexibility is provided by the fact that custom
10318 pseudo-data representations can be specified and used for model fitting.
10319 Functions are provided for the construction of confidence intervals for the
10320 reduced-bias estimates.")
10321 (license license:gpl2+)))
10323 (define-public r-entropy
10330 (uri (cran-uri "entropy" version))
10333 "1f0j8jsn6pzf4gi5g0akixx6x5vc69ci5f4m2vnwp40frvsqjnkg"))))
10334 (properties `((upstream-name . "entropy")))
10335 (build-system r-build-system)
10336 (home-page "https://www.strimmerlab.org/software/entropy/")
10337 (synopsis "Estimation of entropy, mutual information and related quantities")
10339 "This package implements various estimators of entropy, such as the
10340 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
10341 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
10342 estimator. It also offers an R interface to the NSB estimator. Furthermore,
10343 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
10344 mutual information, and chi-squared statistic of independence. In addition
10345 there are functions for discretizing continuous random variables.")
10346 (license license:gpl3+)))
10348 (define-public r-acd
10355 (uri (cran-uri "ACD" version))
10358 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
10359 (properties `((upstream-name . "ACD")))
10360 (build-system r-build-system)
10361 (home-page "https://cran.r-project.org/web/packages/ACD/")
10362 (synopsis "Categorical data analysis with complete or missing responses")
10364 "This package provides tools for categorical data analysis with complete
10365 or missing responses.")
10366 (license license:gpl2+)))
10368 (define-public r-acdm
10371 (version "1.0.4.1")
10375 (uri (cran-uri "ACDm" version))
10378 "129ykw0j8z30mr4c01qzx6qy6h4bl87zxvmps0vkh8cqb7akninq"))))
10379 (properties `((upstream-name . "ACDm")))
10380 (build-system r-build-system)
10382 (list r-dplyr r-ggplot2 r-plyr r-rsolnp r-zoo))
10383 (home-page "https://cran.r-project.org/web/packages/ACDm/")
10384 (synopsis "Tools for Autoregressive Conditional Duration Models")
10386 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
10387 and Russell, 1998) models. It creates trade, price or volume durations from
10388 transactions (tic) data, performs diurnal adjustments, fits various ACD models
10390 (license license:gpl2+)))
10392 (define-public r-overlap
10399 (uri (cran-uri "overlap" version))
10402 "1arxprhz035ab78ks88n6scwnlwmnb97mlac5gsx90ipb6gkgcyk"))))
10403 (build-system r-build-system)
10404 (home-page "https://cran.r-project.org/web/packages/overlap/")
10405 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
10407 "This package provides functions to fit kernel density functions to data
10408 on temporal activity patterns of animals; estimate coefficients of overlapping
10409 of densities for two species; and calculate bootstrap estimates of confidence
10411 (license license:gpl3+)))
10413 (define-public r-snakecase
10415 (name "r-snakecase")
10420 (uri (cran-uri "snakecase" version))
10423 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
10424 (build-system r-build-system)
10426 (list r-stringi r-stringr))
10427 (home-page "https://github.com/Tazinho/snakecase")
10428 (synopsis "Convert strings into any case")
10430 "This package provides a consistent, flexible and easy to use tool to
10431 parse and convert strings into cases like snake or camel among others.")
10432 (license license:gpl3)))
10434 (define-public r-prediction
10436 (name "r-prediction")
10441 (uri (cran-uri "prediction" version))
10444 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
10445 (build-system r-build-system)
10447 (list r-data-table))
10448 (home-page "https://github.com/leeper/prediction")
10449 (synopsis "Tidy, type-safe prediction methods")
10451 "This package provides the @code{prediction()} function, a type-safe
10452 alternative to @code{predict()} that always returns a data frame. The package
10453 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
10454 from the @code{stats} package, as well as numerous other model classes from
10455 other add-on packages.")
10456 (license license:expat)))
10458 (define-public r-prettygraphs
10460 (name "r-prettygraphs")
10464 (uri (cran-uri "prettyGraphs" version))
10467 "0yjpwxdy9mkj2k33zvd5klyv4ava46i19yls87n0bvf79y90ikpy"))))
10468 (properties `((upstream-name . "prettyGraphs")))
10469 (build-system r-build-system)
10470 (home-page "https://cran.r-project.org/package=prettyGraphs")
10471 (synopsis "Publication-quality graphics")
10473 "This package provides simple and crisp publication-quality graphics for
10474 the ExPosition family of packages. See An ExPosition of the Singular Value
10475 Decomposition in R (Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>.")
10476 (license license:gpl2)))
10478 (define-public r-insight
10485 (uri (cran-uri "insight" version))
10488 "1bj6dliin3draqb447zyy1w4z277n8rj5sdl3lnx468bq1yqc8h9"))))
10489 (build-system r-build-system)
10492 (home-page "https://easystats.github.io/insight/")
10493 (synopsis "Easy access to model information for various model objects")
10495 "This package provides a tool to provide an easy, intuitive and
10496 consistent access to information contained in various R models, like model
10497 formulas, model terms, information about random effects, data that was used to
10498 fit the model or data from response variables. The package mainly revolves
10499 around two types of functions: Functions that find (the names of) information,
10500 starting with @code{find_}, and functions that get the underlying data,
10501 starting with @code{get_}. The package has a consistent syntax and works with
10502 many different model objects, where otherwise functions to access these
10503 information are missing.")
10504 (license license:gpl3)))
10506 (define-public r-sjlabelled
10508 (name "r-sjlabelled")
10513 (uri (cran-uri "sjlabelled" version))
10516 "1va86q5wddyvqgdpy8d0an2c7v1qbb4hpn0ai6y1v5v1ff87w73k"))))
10517 (build-system r-build-system)
10519 (list r-datawizard r-insight))
10522 (home-page "https://github.com/strengejacke/sjlabelled")
10523 (synopsis "Labelled data utility functions")
10525 "This package provides a collection of functions dealing with labelled
10526 data, like reading and writing data between R and other statistical software
10527 packages. This includes easy ways to get, set or change value and variable
10528 label attributes, to convert labelled vectors into factors or numeric (and
10529 vice versa), or to deal with multiple declared missing values.")
10530 (license license:gpl3)))
10532 (define-public r-sjmisc
10539 (uri (cran-uri "sjmisc" version))
10542 "1gzkq95ckxr0vhrzggflzli9hs7zr8c0yym9zn1wf74yrr0mgc3q"))))
10543 (build-system r-build-system)
10554 (home-page "https://github.com/strengejacke/sjmisc")
10555 (synopsis "Data and variable transformation functions")
10557 "This package is a collection of miscellaneous utility functions,
10558 supporting data transformation tasks like recoding, dichotomizing or grouping
10559 variables, setting and replacing missing values. The data transformation
10560 functions also support labelled data, and all integrate seamlessly into a
10561 tidyverse workflow.")
10562 (license license:gpl3)))
10564 (define-public r-nortest
10571 (uri (cran-uri "nortest" version))
10574 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
10575 (build-system r-build-system)
10576 (home-page "https://cran.r-project.org/web/packages/nortest/")
10577 (synopsis "Tests for normality")
10579 "This package provides five omnibus tests for testing the composite
10580 hypothesis of normality.")
10581 (license license:gpl2+)))
10583 (define-public r-moonbook
10585 (name "r-moonbook")
10590 (uri (cran-uri "moonBook" version))
10593 "1ml4vvm0mvrprpyi0l50aw38brx18bk2qny4gybmkvlbakalz9bx"))))
10594 (properties `((upstream-name . "moonBook")))
10595 (build-system r-build-system)
10605 (home-page "https://github.com/cardiomoon/moonBook")
10606 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
10608 "This package provides several analysis-related functions for the book
10609 entitled \"R statistics and graph for medical articles\" (written in Korean),
10610 version 1, by Keon-Woong Moon with Korean demographic data with several plot
10612 (license license:gpl2)))
10614 (define-public r-flextable
10616 (name "r-flextable")
10621 (uri (cran-uri "flextable" version))
10624 "03l9wgsikg1n2i3hxkb850kprs49nlrawyrm46k1d95b83d2qq8s"))))
10625 (build-system r-build-system)
10639 (home-page "https://davidgohel.github.io/flextable")
10640 (synopsis "Functions for tabular reporting")
10642 "This package provides tools to create pretty tables for HTML documents
10643 and other formats. Functions are provided to let users create tables, modify
10644 and format their content. It extends the @code{officer} package and can be
10645 used within R markdown documents when rendering to HTML and to Word
10647 (license license:gpl3)))
10649 (define-public r-writexl
10656 (uri (cran-uri "writexl" version))
10659 "0mfzyn8n5x5x5gf382bqgq61zpw9dymrp5kzdm2sbszplmxf6xry"))))
10660 (build-system r-build-system)
10661 (inputs (list zlib))
10662 (home-page "https://github.com/ropensci/writexl")
10663 (synopsis "Export data frames to xlsx format")
10665 "This package provides a data frame to xlsx exporter based on
10667 (license license:bsd-2)))
10669 (define-public r-biasedurn
10671 (name "r-biasedurn")
10676 (uri (cran-uri "BiasedUrn" version))
10679 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
10680 (properties `((upstream-name . "BiasedUrn")))
10681 (build-system r-build-system)
10682 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
10683 (synopsis "Biased Urn model distributions")
10685 "This package provides statistical models of biased sampling in the form
10686 of univariate and multivariate noncentral hypergeometric distributions,
10687 including Wallenius' noncentral hypergeometric distribution and Fisher's
10688 noncentral hypergeometric distribution (also called extended hypergeometric
10690 (license license:gpl3)))
10692 (define-public r-goplot
10699 (uri (cran-uri "GOplot" version))
10702 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
10703 (properties `((upstream-name . "GOplot")))
10704 (build-system r-build-system)
10706 (list r-ggdendro r-ggplot2 r-gridextra r-rcolorbrewer))
10707 (home-page "https://github.com/wencke/wencke.github.io")
10708 (synopsis "Visualization of functional analysis data")
10710 "This package provides an implementation of multilayered visualizations
10711 for enhanced graphical representation of functional analysis data. It
10712 combines and integrates omics data derived from expression and functional
10713 annotation enrichment analyses. Its plotting functions have been developed
10714 with an hierarchical structure in mind: starting from a general overview to
10715 identify the most enriched categories (modified bar plot, bubble plot) to a
10716 more detailed one displaying different types of relevant information for the
10717 molecules in a given set of categories (circle plot, chord plot, cluster plot,
10718 Venn diagram, heatmap).")
10719 (license license:gpl2)))
10721 (define-public r-getopt
10728 (uri (cran-uri "getopt" version))
10731 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
10732 (build-system r-build-system)
10733 (home-page "https://github.com/trevorld/getopt")
10734 (synopsis "Command-line option processor for R")
10736 "This package is designed to be used with Rscript to write shebang
10737 scripts that accept short and long options. Many users will prefer to
10738 use the packages @code{optparse} or @code{argparse} which add extra
10739 features like automatically generated help options and usage texts,
10740 support for default values, positional argument support, etc.")
10741 (license license:gpl2+)))
10743 (define-public r-findpython
10745 (name "r-findpython")
10750 (uri (cran-uri "findpython" version))
10753 "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar"))))
10754 (build-system r-build-system)
10755 (home-page "https://github.com/trevorld/findpython")
10756 (synopsis "Functions to find an acceptable Python binary")
10758 "This package was designed to find an acceptable Python binary that
10759 matches version and feature constraints.")
10760 (license license:expat)))
10762 ;; This in not the same as "r-argparser"
10763 (define-public r-argparse
10765 (name "r-argparse")
10770 (uri (cran-uri "argparse" version))
10773 "14p57nm0w3siqd473snzhpmnvsgl72x92pdcd64vhy2qg6nzmmra"))))
10774 (build-system r-build-system)
10775 (inputs (list python))
10777 (list r-findpython r-jsonlite r-r6))
10780 (home-page "https://github.com/trevorld/argparse")
10781 (synopsis "Command line optional and positional argument parser")
10783 "This package provides a command line parser to be used with Rscript to
10784 write shebang scripts that gracefully accept positional and optional arguments
10785 and automatically generate usage notices.")
10786 (license license:gpl2+)))
10788 (define-public r-hash
10791 (version "2.2.6.2")
10795 (uri (cran-uri "hash" version))
10798 "17scs675a86c34hjbxmwi8kny4yyv97x3515s449zafj2i0ad8vm"))))
10799 (build-system r-build-system)
10800 (home-page "https://cran.r-project.org/web/packages/hash/")
10801 (synopsis "Implementation of hash/associated arrays/dictionaries")
10803 "This package implements a data structure similar to hashes in Perl and
10804 dictionaries in Python but with a purposefully R flavor. For objects of
10805 appreciable size, access using hashes outperforms native named lists and
10807 (license license:gpl2+)))
10809 (define-public r-orddom
10816 (uri (cran-uri "orddom" version))
10819 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
10820 (build-system r-build-system)
10821 (propagated-inputs (list r-psych))
10822 (home-page "https://cran.r-project.org/web/packages/orddom/")
10823 (synopsis "Ordinal dominance statistics")
10825 "This package provides tools to compute ordinal, statistics and effect
10826 sizes as an alternative to mean comparison: Cliff's delta or success rate
10827 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
10828 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
10829 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
10830 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
10831 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
10832 Group (Non-)Overlap considerations.")
10833 (license license:gpl2)))
10835 (define-public r-deriv
10842 (uri (cran-uri "Deriv" version))
10845 "130g3mv0z9sqs6y23a0a94512iiw05yr6fp378vhdxxbignzbnyv"))))
10846 (properties `((upstream-name . "Deriv")))
10847 (build-system r-build-system)
10848 (home-page "https://cran.r-project.org/web/packages/Deriv")
10849 (synopsis "Symbolic differentiation")
10851 "This package provides an R-based solution for symbolic differentiation.
10852 It admits user-defined functions as well as function substitution in arguments
10853 of functions to be differentiated. Some symbolic simplification is part of
10855 (license license:gpl3+)))
10857 (define-public r-doby
10864 (uri (cran-uri "doBy" version))
10867 "0qnfcw4rg5kd1mll3rq6vchz3lgdqfif9469p8x6ixsgrxxpivbz"))))
10868 (properties `((upstream-name . "doBy")))
10869 (build-system r-build-system)
10883 (home-page "https://people.math.aau.dk/~sorenh/software/doBy/")
10884 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
10886 "This package contains:
10889 @item facilities for working with grouped data: @code{do}
10890 something to data stratified @code{by} some variables.
10891 @item implementations of least-squares means, general linear contrasts, and
10892 @item miscellaneous other utilities.
10894 (license license:gpl2+)))
10896 (define-public r-refgenome
10898 (name "r-refgenome")
10903 (uri (cran-uri "refGenome" version))
10906 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
10907 (properties `((upstream-name . "refGenome")))
10908 (build-system r-build-system)
10910 (list r-dbi r-doby r-rsqlite))
10911 (home-page "https://cran.r-project.org/web/packages/refGenome/")
10913 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
10915 "This package contains functionality for importing and managing of
10916 downloaded genome annotation data from the Ensembl genome browser (European
10917 Bioinformatics Institute) and from the UCSC genome browser (University of
10918 California, Santa Cruz) and annotation routines for genomic positions and
10919 splice site positions.")
10920 (license license:gpl2)))
10922 (define-public r-basix
10929 (uri (cran-uri "BASIX" version))
10932 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
10933 (properties `((upstream-name . "BASIX")))
10934 (build-system r-build-system)
10935 (home-page "https://cran.r-project.org/web/packages/BASIX/")
10936 (synopsis "Efficient C/C++ toolset for R")
10938 "BASIX provides some efficient C/C++ implementations of native R
10939 procedures to speed up calculations in R.")
10940 (license license:gpl2)))
10942 (define-public r-blockfest
10944 (name "r-blockfest")
10949 (uri (cran-uri "BlockFeST" version))
10952 "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65"))))
10953 (properties `((upstream-name . "BlockFeST")))
10954 (build-system r-build-system)
10955 (propagated-inputs (list r-basix))
10956 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
10957 (synopsis "Bayesian calculation of region-specific fixation index")
10959 "This package provides an R implementation of an extension of the
10960 BayeScan software for codominant markers, adding the option to group
10961 individual SNPs into pre-defined blocks. A typical application of this new
10962 approach is the identification of genomic regions, genes, or gene sets
10963 containing one or more SNPs that evolved under directional selection.")
10964 (license license:gpl2)))
10966 (define-public r-proc
10973 (uri (cran-uri "pROC" version))
10976 "1abvbzdss12n64pp9vlgnn0q3abh0nj4n0a8cinwwvhphjrm9vym"))))
10977 (properties `((upstream-name . "pROC")))
10978 (build-system r-build-system)
10980 (list r-plyr r-rcpp))
10981 (home-page "https://web.expasy.org/pROC/")
10982 (synopsis "Display and analyze ROC curves")
10984 "This package provides tools for visualizing, smoothing and comparing
10985 receiver operating characteristic (ROC curves). The area under the
10986 curve (AUC) can be compared with statistical tests based on U-statistics or
10987 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
10988 (license license:gpl3+)))
10990 (define-public r-rootsolve
10992 (name "r-rootsolve")
10993 (version "1.8.2.3")
10997 (uri (cran-uri "rootSolve" version))
11000 "182bb727sgqi5f3pzmw8jnn328wdjrgj9lfvg49gv8s22rjd3cxm"))))
11001 (properties `((upstream-name . "rootSolve")))
11002 (build-system r-build-system)
11003 (native-inputs (list gfortran))
11004 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
11005 (synopsis "Tools for the analysis of ordinary differential equations")
11007 "This package provides routines to find the root of nonlinear functions,
11008 and to perform steady-state and equilibrium analysis of @dfn{ordinary
11009 differential equations} (ODE). It includes routines that:
11012 @item generate gradient and jacobian matrices (full and banded),
11013 @item find roots of non-linear equations by the Newton-Raphson method,
11014 @item estimate steady-state conditions of a system of (differential) equations
11015 in full, banded or sparse form, using the Newton-Raphson method, or by
11016 dynamically running,
11017 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
11018 and 3-D partial differential equations, that have been converted to ordinary
11019 differential equations by numerical differencing (using the method-of-lines
11022 (license license:gpl2+)))
11024 (define-public r-abcanalysis
11026 (name "r-abcanalysis")
11031 (uri (cran-uri "ABCanalysis" version))
11033 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
11034 (properties `((upstream-name . "ABCanalysis")))
11035 (build-system r-build-system)
11036 (propagated-inputs (list r-plotrix))
11037 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
11038 (synopsis "Computed ABC Analysis")
11040 "Multivariate data sets often differ in several factors or derived statistical
11041 parameters, which have to be selected for a valid interpretation. Basing this
11042 selection on traditional statistical limits leads occasionally to the perception
11043 of losing information from a data set. This package provides tools to calculate
11044 these limits on the basis of the mathematical properties of the distribution of
11045 the analyzed items.")
11046 (license license:gpl3)))
11048 (define-public r-slam
11055 (uri (cran-uri "slam" version))
11057 (base32 "1ggqcf8l1z2hpi7qy4mg0d2ps48bjjb8z1y1xz6fq162cqrbz6bq"))))
11058 (build-system r-build-system)
11059 (home-page "https://cran.r-project.org/web/packages/slam/")
11060 (synopsis "Sparse lightweight arrays and matrices")
11062 "This package contains data structures and algorithms for sparse arrays and matrices,
11063 based on index arrays and simple triplet representations, respectively.")
11064 (license license:gpl2)))
11066 (define-public r-manipulatewidget
11068 (name "r-manipulatewidget")
11073 (uri (cran-uri "manipulateWidget" version))
11075 (base32 "1dpgzmiv08afm57yxr017b014lfn9h3pa4w65prk5k3dgn6p4wsv"))))
11077 `((upstream-name . "manipulateWidget")))
11078 (build-system r-build-system)
11091 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
11092 (synopsis "Add even more interactivity to interactive charts")
11094 "This package lets you create in just a few lines of R code a nice user interface to
11095 modify the data or the graphical parameters of one or multiple interactive
11096 charts. It is useful to quickly explore visually some data or for package
11097 developers to generate user interfaces easy to maintain.")
11098 (license license:gpl2+)))
11100 (define-public r-a3
11107 (uri (cran-uri "A3" version))
11109 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
11110 (properties `((upstream-name . "A3")))
11111 (build-system r-build-system)
11113 (list r-pbapply r-xtable))
11114 (home-page "https://cran.r-project.org/web/packages/A3/")
11115 (synopsis "Error metrics for predictive models")
11117 "This package supplies tools for tabulating and analyzing the results of predictive
11118 models. The methods employed are applicable to virtually any predictive model
11119 and make comparisons between different methodologies straightforward.")
11120 (license license:gpl2+)))
11122 (define-public r-infotheo
11124 (name "r-infotheo")
11125 (version "1.2.0.1")
11129 (uri (cran-uri "infotheo" version))
11132 "1m1979vf8rvq3534mp1hihfadikhxrg3p6ac3hirz96kgb4qxyy0"))))
11133 (build-system r-build-system)
11134 (home-page "http://homepage.meyerp.com/software")
11135 (synopsis "Information-theoretic measures")
11137 "This package implements various measures of information theory based on
11138 several entropy estimators.")
11139 (license license:gpl3+)))
11141 (define-public r-nsprcomp
11143 (name "r-nsprcomp")
11144 (version "0.5.1-2")
11148 (uri (cran-uri "nsprcomp" version))
11151 "1zlc1ximx96f235c0l8qfs6vbp1kpnbf943wxsfahnnlnxvwi59f"))))
11152 (properties `((upstream-name . "nsprcomp")))
11153 (build-system r-build-system)
11154 (home-page "https://sigg-iten.ch/research/")
11155 (synopsis "Non-negative and sparse PCA")
11157 "This package implements two methods for performing a constrained
11158 principal component analysis (PCA), where non-negativity and/or sparsity
11159 constraints are enforced on the principal axes (PAs). The function
11160 @code{nsprcomp} computes one principal component (PC) after the other. Each
11161 PA is optimized such that the corresponding PC has maximum additional variance
11162 not explained by the previous components. In contrast, the function
11163 @code{nscumcomp} jointly computes all PCs such that the cumulative variance is
11164 maximal. Both functions have the same interface as the @code{prcomp} function
11165 from the @code{stats} package (plus some extra parameters).")
11166 (license license:gpl2+)))
11168 (define-public r-cmplot
11175 (uri (cran-uri "CMplot" version))
11178 "1h09prpiw7l32mr7jarp8ddrddg1431nfn4kw3bznfnv0sr78zfg"))))
11179 (properties `((upstream-name . "CMplot")))
11180 (build-system r-build-system)
11181 (home-page "https://github.com/YinLiLin/CMplot")
11182 (synopsis "Circle Manhattan plot")
11184 "Circle Manhattan Plot is an R package that can lay out genome-wide
11185 association study P-value results in both traditional rectangular patterns,
11186 QQ-plot and novel circular ones. United in only one bull's eye style plot,
11187 association results from multiple traits can be compared interactively,
11188 thereby to reveal both similarities and differences between signals.
11189 Additional functions include: highlight signals, a group of SNPs, chromosome
11190 visualization and candidate genes around SNPs.")
11191 (license license:gpl2+)))
11193 (define-public r-precrec
11200 (uri (cran-uri "precrec" version))
11203 "1dfz2rqx2ww2l5r40ahg0qdj3rjrwiwh427mw7j5ynhpcj21j2qm"))))
11204 (properties `((upstream-name . "precrec")))
11205 (build-system r-build-system)
11213 (native-inputs (list r-knitr))
11214 (home-page "https://evalclass.github.io/precrec/")
11215 (synopsis "Calculate accurate precision-recall and ROC curves")
11217 "This package provides tools for accurate calculations and visualization
11218 of precision-recall and ROC (Receiver Operator Characteristics) curves.")
11219 (license license:gpl3)))
11221 (define-public r-netrep
11228 (uri (cran-uri "NetRep" version))
11231 "1swlb2k9bc7whvslxbklz864j9ynvna73hvq5rhv61cv5vy05ksd"))))
11232 (properties `((upstream-name . "NetRep")))
11233 (build-system r-build-system)
11243 (native-inputs (list r-knitr))
11244 (home-page "https://cran.r-project.org/package=NetRep")
11245 (synopsis "Permutation testing network module preservation across datasets")
11247 "This package provides functions for assessing the
11248 replication/preservation of a network module's topology across datasets
11249 through permutation testing.")
11250 (license license:gpl2)))
11252 (define-public r-intergraph
11254 (name "r-intergraph")
11259 (uri (cran-uri "intergraph" version))
11262 "18a7xgb2rp0w9jl2rkh8nzyjprrs5w7h2iidvc8c38bzx3qpggkc"))))
11263 (properties `((upstream-name . "intergraph")))
11264 (build-system r-build-system)
11266 (list r-igraph r-network))
11269 (home-page "http://mbojan.github.io/intergraph")
11270 (synopsis "Coercion routines for network data objects")
11272 "Functions implemented in this package allow coercing (i.e. convert)
11273 network data between classes provided by other R packages. Currently
11274 supported classes are those defined in packages @code{network} and
11276 (license license:gpl3)))
11278 (define-public r-interp
11284 (uri (cran-uri "interp" version))
11287 "0gzsnlg8f7knb100n6vv6307c3v2jd8f9qzrq62jkc6g71mn0kmp"))))
11288 (properties `((upstream-name . "interp")))
11289 (build-system r-build-system)
11290 (propagated-inputs (list r-deldir r-rcpp r-rcppeigen))
11291 (native-inputs (list gfortran))
11292 (home-page "https://cran.r-project.org/package=interp")
11293 (synopsis "Interpolation methods")
11295 "Bivariate data interpolation on regular and irregular grids, either
11296 linear or using splines are the main part of this package. It is intended to
11297 provide replacement functions for the ACM licensed @code{akima::interp} and
11298 @code{tripack::tri.mesh} functions.")
11299 (license license:gpl2+)))
11301 (define-public r-abcoptim
11303 (name "r-abcoptim")
11308 (uri (cran-uri "ABCoptim" version))
11310 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
11311 (properties `((upstream-name . "ABCoptim")))
11312 (build-system r-build-system)
11313 (propagated-inputs (list r-rcpp))
11314 (home-page "https://github.com/gvegayon/ABCoptim/")
11315 (synopsis "Optimization of Artificial Bee Colony algorithm")
11317 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
11318 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
11319 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
11320 algorithms, and uses only common control parameters such as colony size and
11321 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
11322 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
11323 This version is a work-in-progress and is written in R code.")
11324 (license license:expat)))
11326 (define-public r-abcp2
11333 (uri (cran-uri "ABCp2" version))
11335 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
11336 (properties `((upstream-name . "ABCp2")))
11337 (build-system r-build-system)
11338 (propagated-inputs (list r-mass))
11339 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
11340 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
11342 "This package tests the goodness of fit of a distribution of offspring to the Normal,
11343 Poisson, and Gamma distribution and estimates the proportional paternity of the
11344 second male (P2) based on the best fit distribution.")
11345 (license license:gpl2)))
11347 (define-public r-abcrf
11354 (uri (cran-uri "abcrf" version))
11356 (base32 "08mh1a6gxp0mfx6qnp1qzcrfx7xp64qj9kad4ziyswfx22ykdsxi"))))
11357 (build-system r-build-system)
11368 (home-page "https://cran.r-project.org/web/packages/abcrf/")
11369 (synopsis "Approximate bayesian computation via random forests")
11371 "This package performs approximate bayesian computation (ABC) model choice and
11372 parameter inference via random forests. This machine learning tool named random
11373 forests (RF) can conduct selection among the highly complex models covered by
11375 (license license:gpl2+)))
11377 (define-public r-abctools
11379 (name "r-abctools")
11384 (uri (cran-uri "abctools" version))
11386 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
11387 (build-system r-build-system)
11389 (list r-abc r-abind r-hmisc r-plyr))
11390 (home-page "https://github.com/dennisprangle/abctools/")
11391 (synopsis "Tools for ABC analyses")
11393 "This @code{r-abctools} package provides tools for approximate Bayesian computation
11394 including summary statistic selection and assessing coverage. This includes
11395 recent dimension reduction algorithms to tune the choice of summary statistics,
11396 and coverage methods to tune the choice of threshold.")
11397 (license license:gpl2+)))
11399 (define-public r-ggstance
11401 (name "r-ggstance")
11406 (uri (cran-uri "ggstance" version))
11408 (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d"))))
11409 (build-system r-build-system)
11411 (list r-ggplot2 r-plyr r-rlang r-withr))
11412 (home-page "https://cran.r-project.org/web/packages/ggstance/")
11413 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
11415 "This package is a @code{r-ggplot2} extension that provides flipped components:
11417 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
11418 @item vertical versions of @code{r-ggplot2} positions.
11420 (license license:gpl3)))
11422 (define-public r-ggnetwork
11424 (name "r-ggnetwork")
11429 (uri (cran-uri "ggnetwork" version))
11432 "0gqdgy5yh700dg0f7xb80hczlnqfisn8l55j7amd1n7fp2x5sr8v"))))
11433 (properties `((upstream-name . "ggnetwork")))
11434 (build-system r-build-system)
11436 (list r-ggplot2 r-ggrepel r-igraph r-network r-sna))
11437 (native-inputs (list r-knitr))
11438 (home-page "https://github.com/briatte/ggnetwork")
11439 (synopsis "Geometries to plot networks with ggplot2")
11441 "This package provides geometries to plot network objects with the
11443 (license license:gpl3)))
11445 (define-public r-cvauc
11452 (uri (cran-uri "cvAUC" version))
11455 "1m2y50a1yapf1c74km9a4r47ds2z2bfp4wwwkqin7swv9v1s7d28"))))
11456 (properties `((upstream-name . "cvAUC")))
11457 (build-system r-build-system)
11459 (list r-data-table r-rocr))
11460 (home-page "https://github.com/ledell/cvAUC")
11461 (synopsis "Cross-validated area under the ROC curve confidence intervals")
11463 "This package contains various tools for working with and evaluating
11464 cross-validated area under the ROC curve (AUC) estimators. The primary
11465 functions of the package are @code{ci.cvAUC} and @code{ci.pooled.cvAUC}, which
11466 report cross-validated AUC and compute confidence intervals for
11467 cross-validated AUC estimates based on influence curves for i.i.d. and pooled
11468 repeated measures data, respectively.")
11469 (license license:asl2.0)))
11471 (define-public r-gam
11478 (uri (cran-uri "gam" version))
11481 "1ndgnaq5fk1w6l6z93w5gd22887yxkykrchbdbx366qmz8v8wcyg"))))
11482 (properties `((upstream-name . "gam")))
11483 (build-system r-build-system)
11488 (home-page "https://cran.r-project.org/package=gam")
11489 (synopsis "Generalized additive models")
11491 "This package provides functions for fitting and working with generalized
11492 additive models, as described in chapter 7 of \"Statistical Models in
11493 S\" (Chambers and Hastie (eds), 1991), and \"Generalized Additive
11494 Models\" (Hastie and Tibshirani, 1990).")
11495 (license license:gpl2)))
11497 (define-public r-superlearner
11499 (name "r-superlearner")
11504 (uri (cran-uri "SuperLearner" version))
11507 "00any24msgflyagy87nznpfjz5g9v15frqda6c679wa8plx26hjz"))))
11508 (properties `((upstream-name . "SuperLearner")))
11509 (build-system r-build-system)
11511 (list r-cvauc r-gam r-nnls))
11514 (home-page "https://github.com/ecpolley/SuperLearner")
11515 (synopsis "Super learner prediction")
11517 "This package implements the super learner prediction method and contains
11518 a library of prediction algorithms to be used in the super learner.")
11519 (license license:gpl3)))
11521 (define-public r-drtmle
11528 (uri (cran-uri "drtmle" version))
11531 "12vplpz9bg5444jy29mbdr70hqby073vb3iw76v2csrwy3ws3f21"))))
11532 (properties `((upstream-name . "drtmle")))
11533 (build-system r-build-system)
11535 (list r-future-apply r-np r-superlearner))
11538 (home-page "https://github.com/benkeser/drtmle")
11539 (synopsis "Doubly-robust nonparametric estimation and inference")
11541 "This package implements targeted minimum loss-based estimators of
11542 counterfactual means and causal effects that are doubly-robust with respect
11543 both to consistency and asymptotic normality.")
11544 (license license:expat)))
11546 (define-public r-dofuture
11548 (name "r-dofuture")
11553 (uri (cran-uri "doFuture" version))
11556 "0w07pmzpsfq4kvfc745s1i9b6dfn1df1wrfi4s9ys4ir3g2s8nk1"))))
11557 (properties `((upstream-name . "doFuture")))
11558 (build-system r-build-system)
11561 (modify-phases %standard-phases
11562 (add-after 'unpack 'set-HOME
11563 (lambda _ (setenv "HOME" "/tmp"))))))
11565 (list r-foreach r-future r-globals r-iterators))
11567 (list r-r-rsp)) ; vignette builder
11568 (home-page "https://github.com/HenrikBengtsson/doFuture")
11569 (synopsis "Foreach parallel adapter using the future API")
11571 "This package provides a @code{%dopar%} adapter such that any type of
11572 futures can be used as backends for the @code{foreach} framework.")
11573 (license license:lgpl2.1+)))
11575 (define-public r-superheat
11577 (name "r-superheat")
11582 (uri (cran-uri "superheat" version))
11585 "01v8s6px1k5fajlm6py3ksr1i853kwwlky1yryzhy3p1cxhwgg83"))))
11586 (properties `((upstream-name . "superheat")))
11587 (build-system r-build-system)
11596 (home-page "https://cran.r-project.org/package=superheat")
11597 (synopsis "Graphical tool for exploring complex datasets using heatmaps")
11599 "This package provides a system for generating extendable and
11600 customizable heatmaps for exploring complex datasets, including big data and
11601 data with multiple data types.")
11602 (license license:cc0)))
11604 (define-public r-qualv
11611 (uri (cran-uri "qualV" version))
11614 "0rkjzva2h158d5c631jmjjh7qjibbyisl0503san80rk9fgxl45b"))))
11615 (properties `((upstream-name . "qualV")))
11616 (build-system r-build-system)
11618 (list r-kernsmooth))
11619 (home-page "http://qualV.R-Forge.R-Project.org/")
11620 (synopsis "Qualitative Validation Methods")
11622 "This package provides qualitative methods for the validation of dynamic
11623 models. It contains
11626 @item an orthogonal set of deviance measures for absolute, relative and
11628 @item approaches accounting for time shifts.
11631 The first approach transforms time to take time delays and speed differences
11632 into account. The second divides the time series into interval units
11633 according to their main features and finds the @dfn{longest common
11634 subsequence} (LCS) using a dynamic programming algorithm.")
11635 (license license:gpl2+)))
11637 (define-public r-mosaiccore
11639 (name "r-mosaiccore")
11644 (uri (cran-uri "mosaicCore" version))
11646 (base32 "0mnizi1y7jn2z8v066b6kv08az7vss6avips740pjhgvi8frhsag"))))
11647 (properties `((upstream-name . "mosaicCore")))
11648 (build-system r-build-system)
11650 (list r-dplyr r-mass r-rlang r-tidyr))
11651 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
11652 (synopsis "Common utilities for mosaic family packages")
11654 "Common utilities used in other Mosaic family packages are collected here.")
11655 (license license:gpl2+)))
11657 (define-public r-labelled
11659 (name "r-labelled")
11664 (uri (cran-uri "labelled" version))
11667 "02n4r4bizsysnlmxpw86w7zkiqi6aill9dq2nmrn43xzrffy54sy"))))
11668 (properties `((upstream-name . "labelled")))
11669 (build-system r-build-system)
11680 (home-page "http://larmarange.github.io/labelled/")
11681 (synopsis "Manipulating labelled data")
11683 "This package provides useful functions to deal with the
11684 @code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the
11686 (license license:gpl3)))
11688 (define-public r-ggformula
11690 (name "r-ggformula")
11695 (uri (cran-uri "ggformula" version))
11697 (base32 "0xb39gjn6q7va1d1fhvf2dw9428s1q13wasx4y3cz2f0lls1r2wl"))))
11698 (build-system r-build-system)
11713 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
11714 (synopsis "Formula interface for the @code{r-ggplot2}")
11716 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
11717 gf_density(), and so on, bring the formula interface to ggplot(). This captures
11718 and extends the excellent simplicity of the lattice-graphics formula interface,
11719 while providing the intuitive capabilities of @code{r-ggplot2}.")
11720 (license license:expat)))
11722 (define-public r-mosaicdata
11724 (name "r-mosaicdata")
11729 (uri (cran-uri "mosaicData" version))
11731 (base32 "1s97yq24z7yhzmx0dpspfadpd8hndyhn7aiw0nslwrhvilhwa409"))))
11732 (properties `((upstream-name . "mosaicData")))
11733 (build-system r-build-system)
11734 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
11735 (synopsis "Data sets for project Mosaic")
11737 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
11738 used to teach mathematics, statistics, computation and modeling.")
11739 (license license:gpl2+)))
11741 (define-public r-raster
11748 (uri (cran-uri "raster" version))
11751 "1in3n0hqzcdhibjl3y82nwn6m6wcv4k3l6s2jw57jn32qgvy01lz"))))
11752 (build-system r-build-system)
11754 (list r-rcpp r-sp r-terra))
11755 (home-page "https://www.rspatial.org/")
11756 (synopsis "Geographic data analysis and modeling")
11758 "The package implements basic and high-level functions for reading,
11759 writing, manipulating, analyzing and modeling of gridded spatial data.
11760 Processing of very large files is supported.")
11761 (license license:gpl3+)))
11763 (define-public r-mosaic
11770 (uri (cran-uri "mosaic" version))
11772 (base32 "0ix9c4rpa1h7cya9mqzqph9ain1ng61px5v4wwvlaf76zdr51c0i"))))
11773 (build-system r-build-system)
11788 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
11789 (synopsis "Mathematics, statistics, and computation teaching utilities")
11791 "This package contain data sets and utilities from
11792 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
11793 statistics, computation and modeling. Project MOSAIC is a community of
11794 educators working to tie together aspects of quantitative work that students
11795 in science, technology, engineering and mathematics will need in their
11796 professional lives, but which are usually taught in isolation, if at all.")
11797 (license license:gpl2+)))
11799 (define-public r-abd
11806 (uri (cran-uri "abd" version))
11808 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
11809 (build-system r-build-system)
11811 (list r-lattice r-mosaic r-nlme))
11812 (home-page "https://cran.r-project.org/web/packages/abd/")
11813 (synopsis "Analysis of biological data")
11815 "The @code{r-abd} package contains data sets and sample code for the Analysis of
11816 biological data by Michael Whitlock and Dolph Schluter.")
11817 (license license:gpl2)))
11819 (define-public r-svgui
11826 (uri (cran-uri "svGUI" version))
11828 (base32 "0ch5gdfk834xj9w3vxpm3x4770fz3nnlyn8b0jsw9f3n2as7g979"))))
11829 (properties `((upstream-name . "svGUI")))
11830 (build-system r-build-system)
11833 (home-page "https://github.com/SciViews/svGUI/")
11834 (synopsis "Functions for managing GUI clients in R")
11836 "The SciViews @code{svGUI} package eases the management of Graphical User
11837 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
11838 centralizes info about GUI elements currently used, and it dispatches GUI
11839 calls to the particular toolkits in use in function of the context.")
11840 (license license:gpl2)))
11842 (define-public r-svdialogs
11844 (name "r-svdialogs")
11849 (uri (cran-uri "svDialogs" version))
11851 (base32 "0z3a5glsi0ab43mdk2yvslxyzg12nbqqqc35jvgzj475mpkbgjif"))))
11852 (properties `((upstream-name . "svDialogs")))
11853 (build-system r-build-system)
11857 (list r-rstudioapi r-svgui))
11860 (home-page "https://github.com/SciViews/svDialogs/")
11861 (synopsis "Portable dialog boxes")
11863 "This package helps to construct standard dialog boxes for your GUI, including
11864 message boxes, input boxes, list, file or directory selection, and others. In
11865 case R cannot display GUI dialog boxes, a simpler command line version of these
11866 interactive elements is also provided as a fallback solution.")
11867 (license license:gpl2)))
11869 (define-public r-abe
11876 (uri (cran-uri "abe" version))
11879 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
11880 (build-system r-build-system)
11881 (home-page "https://cran.r-project.org/web/packages/abe/")
11882 (synopsis "Augmented backward elimination")
11884 "This package performs augmented backward elimination and checks the
11885 stability of the obtained model. Augmented backward elimination combines
11886 significance or information based criteria with the change in estimate to
11887 either select the optimal model for prediction purposes or to serve as a tool
11888 to obtain a practically sound, highly interpretable model.")
11889 (license license:gpl2+)))
11891 (define-public r-abf2
11898 (uri (cran-uri "abf2" version))
11900 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
11901 (build-system r-build-system)
11902 (home-page "https://cran.r-project.org/web/packages/abf2/")
11903 (synopsis "Load gap-free axon @code{r-abf2} files")
11905 "This package loads electrophysiology data from ABF2 files, as created by
11906 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
11907 mode are currently supported.")
11908 (license license:artistic2.0)))
11910 (define-public r-abhgenotyper
11912 (name "r-abhgenotyper")
11917 (uri (cran-uri "ABHgenotypeR" version))
11919 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
11920 (properties `((upstream-name . "ABHgenotypeR")))
11921 (build-system r-build-system)
11923 (list r-ggplot2 r-reshape2))
11924 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
11925 (synopsis "Visualize and manipulate ABH genotypes")
11927 "The @code{r-abhgenotyper} package provides simple imputation,
11928 error-correction and plotting capacities for genotype data. The package is
11929 supposed to serve as an intermediate but independent analysis tool between the
11930 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
11931 not found in either TASSEL or @code{r-qtl} in addition to visualization of
11932 genotypes as \"graphical genotypes\".")
11933 (license license:gpl3)))
11935 (define-public r-furrr
11942 (uri (cran-uri "furrr" version))
11945 "12z4q0fn7asxis17hisi82bvfabl5if1338lmfqmkrwv5rg7748d"))))
11946 (build-system r-build-system)
11954 (home-page "https://github.com/DavisVaughan/furrr")
11955 (synopsis "Apply mapping functions in parallel using futures")
11957 "This package provides implementations of the family of @code{map()}
11958 functions from the @code{purrr} package that can be resolved using any
11959 @code{future}-supported backend, e.g. parallel on the local machine or
11960 distributed on a compute cluster.")
11961 (license license:lgpl2.1+)))
11963 (define-public r-abjutils
11965 (name "r-abjutils")
11970 (uri (cran-uri "abjutils" version))
11972 (base32 "0lmf4va8qnzwg698i2h4fcwvd6dhsgdkqsfh41aa3wg1flimhsr7"))))
11973 (build-system r-build-system)
11983 (home-page "https://github.com/abjur/abjutils/")
11984 (synopsis "Collection of tools for jurimetrical analysis")
11986 "This package implements general purpose tools, such as functions for
11987 sampling and basic manipulation of Brazilian lawsuits identification number.
11988 It also implements functions for text cleaning, such as accentuation
11990 (license license:expat)))
11992 (define-public r-abnormality
11994 (name "r-abnormality")
11999 (uri (cran-uri "abnormality" version))
12001 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
12002 (build-system r-build-system)
12004 (list r-mass r-matrix))
12005 (home-page "https://cran.r-project.org/web/packages/abnormality/")
12006 (synopsis "Measure a subject's abnormality with respect to a reference population")
12008 "This package contains functions to implement the methodology and
12009 considerations laid out by Marks et al. in the article \"Measuring abnormality
12010 in high dimensional spaces: applications in biomechanical gait analysis\".
12011 Using high-dimensional datasets to measure a subject's overall level of
12012 abnormality as compared to a reference population is often needed in outcomes
12014 (license license:expat)))
12016 (define-public r-abodoutlier
12018 (name "r-abodoutlier")
12023 (uri (cran-uri "abodOutlier" version))
12025 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
12026 (properties `((upstream-name . "abodOutlier")))
12027 (build-system r-build-system)
12030 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
12031 (synopsis "Angle-based outlier detection")
12033 "This package performs angle-based outlier detection on a given data
12034 frame. It offers three methods to process data:
12036 @item full but slow implementation using all the data that has cubic
12038 @item a fully randomized method;
12039 @item a method using k-nearest neighbours.
12041 These algorithms are well suited for high dimensional data outlier
12043 (license license:expat)))
12045 (define-public r-abps
12052 (uri (cran-uri "ABPS" version))
12054 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
12055 (properties `((upstream-name . "ABPS")))
12056 (build-system r-build-system)
12057 (propagated-inputs (list r-kernlab))
12058 (home-page "https://cran.r-project.org/web/packages/ABPS/")
12059 (synopsis "Abnormal blood profile score to detect blood doping")
12061 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
12062 The ABPS is a part of the Athlete biological passport program of the World
12063 anti-doping agency, which combines several blood parameters into a single
12064 score in order to detect blood doping. The package also contains functions to
12065 calculate other scores used in anti-doping programs, such as the ratio of
12066 hemoglobin to reticulocytes (OFF-score), as well as example data.")
12067 (license license:gpl2+)))
12069 (define-public r-parmigene
12071 (name "r-parmigene")
12076 (uri (cran-uri "parmigene" version))
12079 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
12080 (build-system r-build-system)
12081 (home-page "https://cran.r-project.org/web/packages/parmigene/")
12082 (synopsis "Mutual information estimation for gene network reconstruction")
12084 "This package provides a parallel estimation of the mutual information
12085 based on entropy estimates from k-nearest neighbors distances and algorithms
12086 for the reconstruction of gene regulatory networks.")
12087 (license license:agpl3+)))
12089 (define-public r-pscl
12096 (uri (cran-uri "pscl" version))
12098 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
12099 (build-system r-build-system)
12102 (home-page "https://github.com/atahk/pscl/")
12103 (synopsis "Political science computational laboratory")
12105 "The @code{pscl} is an R package providing classes and methods for:
12107 @item Bayesian analysis of roll call data (item-response models);
12108 @item elementary Bayesian statistics;
12109 @item maximum likelihood estimation of zero-inflated and hurdle models for count
12111 @item utility functions.
12113 (license license:gpl2)))
12115 (define-public r-accelmissing
12117 (name "r-accelmissing")
12122 (uri (cran-uri "accelmissing" version))
12124 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
12125 (build-system r-build-system)
12127 (list r-mice r-pscl))
12128 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
12129 (synopsis "Missing value imputation for accelerometer data")
12131 "This package provides a statistical method to impute the missing values in
12132 accelerometer data. The methodology includes both parametric and
12133 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
12134 model. It also provides multiple functions to preprocess the accelerometer data
12135 previous to the missing data imputation. These include detecting the wearing
12136 and the non-wearing time, selecting valid days and subjects, and creating plots.")
12137 (license license:gpl2+)))
12139 (define-public r-mhsmm
12146 (uri (cran-uri "mhsmm" version))
12148 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
12149 (build-system r-build-system)
12150 (propagated-inputs (list r-mvtnorm))
12151 (home-page "https://github.com/jaredo/mhsmm/")
12152 (synopsis "Inference for hidden Markov and semi-Markov models")
12154 "The @code{r-mhsmm} package implements estimation and prediction methods for
12155 hidden Markov and semi-Markov models for multiple observation sequences. Such
12156 techniques are of interest when observed data is thought to be dependent on some
12157 unobserved (or hidden) state. Also, this package is suitable for equidistant
12158 time series data, with multivariate and/or missing data. Allows user defined
12159 emission distributions.")
12160 (license license:gpl2+)))
12162 (define-public r-nleqslv
12169 (uri (cran-uri "nleqslv" version))
12171 (base32 "0cy65bqkmnnr8v0x1cag84caxwdxyr0yw4w443apxzfxjp7dyiif"))))
12172 (build-system r-build-system)
12173 (native-inputs (list gfortran))
12174 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
12175 (synopsis "Solve systems of nonlinear equations")
12177 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
12178 Broyden or a Newton method with a choice of global strategies such as line
12179 search and trust region. There are options for using a numerical or user
12180 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
12181 singular or ill-conditioned Jacobian.")
12182 (license license:gpl2+)))
12184 (define-public r-phyclust
12186 (name "r-phyclust")
12190 (uri (cran-uri "phyclust" version))
12193 "0fy9q95vmlm9idpax7alhpfwn30gflnc9md72g91jypyxkx5nr7p"))))
12194 (properties `((upstream-name . "phyclust")))
12195 (build-system r-build-system)
12196 (propagated-inputs (list r-ape))
12197 (home-page "https://snoweye.github.io/phyclust/")
12198 (synopsis "Studying phyloclustering and exploring DNA sequence data")
12200 "@dfn{Phylogenetic clustering} (phyloclustering) is an evolutionary continuous
12201 time Markov Chain model-based approach to identify population structure from
12202 molecular data without assuming linkage equilibrium. The package @code{phyclust}
12203 provides a convenient implementation of phyloclustering for DNA and SNP data,
12204 capable of clustering individuals into subpopulations and identifying molecular
12205 sequences representative of those subpopulations. It is designed in @code{C} for
12206 performance and interfaced with @code{R} for visualization.")
12207 (license license:gpl2+)))
12209 (define-public r-physicalactivity
12211 (name "r-physicalactivity")
12216 (uri (cran-uri "PhysicalActivity" version))
12218 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40"))))
12220 `((upstream-name . "PhysicalActivity")))
12221 (build-system r-build-system)
12222 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
12223 (synopsis "Processing accelerometer data for physical activity measurement")
12225 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
12226 for classification of monitored wear and nonwear time intervals in accelerometer
12227 data collected to assess physical activity. The package also contains functions
12228 for making plots of accelerometer data and obtaining the summary of various
12229 information including daily monitor wear time and the mean monitor wear time
12230 during valid days. The revised package version 0.2-1 improved the functions
12231 regarding speed, robustness and add better support for time zones and daylight
12232 saving. In addition, several functions were added:
12234 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
12235 @item the @code{markPAI} can categorize physical activity intensity level based
12236 on user-defined cut-points of accelerometer counts.
12238 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
12239 @code{queryActigraph} functions.")
12240 (license license:gpl3+)))
12242 (define-public r-acc
12249 (uri (cran-uri "acc" version))
12251 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
12252 (build-system r-build-system)
12267 (home-page "https://cran.r-project.org/web/packages/acc/")
12268 (synopsis "Exploring accelerometer data")
12270 "This package processes accelerometer data from uni-axial and tri-axial devices
12271 and generates data summaries. Also, includes functions to plot, analyze, and
12272 simulate accelerometer data.")
12273 (license license:gpl2+)))
12275 (define-public r-rbenchmark
12277 (name "r-rbenchmark")
12282 (uri (cran-uri "rbenchmark" version))
12284 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
12285 (build-system r-build-system)
12286 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
12287 (synopsis "Benchmarking routine for R")
12289 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
12290 and is intended to facilitate benchmarking of arbitrary R code. The library
12291 consists of just one function, benchmark, which is a simple wrapper around
12292 system.time. Given a specification of the benchmarking process (counts of
12293 replications, evaluation environment) and an arbitrary number of expressions,
12294 benchmark evaluates each of the expressions in the specified environment,
12295 replicating the evaluation as many times as specified, and returning the results
12296 conveniently wrapped into a data frame.")
12297 (license license:gpl2+)))
12299 (define-public r-mitools
12306 (uri (cran-uri "mitools" version))
12309 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
12310 (build-system r-build-system)
12311 (propagated-inputs (list r-dbi))
12312 (home-page "https://cran.r-project.org/web/packages/mitools/")
12313 (synopsis "Tools for multiple imputation of missing data")
12315 "This package provides tools to perform analyses and combine results from
12316 multiple-imputation datasets.")
12317 (license license:gpl2)))
12319 (define-public r-mixsqp
12325 (uri (cran-uri "mixsqp" version))
12328 "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q"))))
12329 (properties `((upstream-name . "mixsqp")))
12330 (build-system r-build-system)
12332 (list r-irlba r-rcpp r-rcpparmadillo))
12335 (home-page "https://github.com/stephenslab/mixsqp")
12337 "Sequential quadratic programming for maximum-likelihood estimation")
12339 "This package provides an optimization method based on sequential
12340 quadratic programming for maximum likelihood estimation of the mixture
12341 proportions in a finite mixture model where the component densities are
12342 known. The algorithm is expected to obtain solutions that are at least
12343 as accurate as the state-of-the-art MOSEK interior-point solver, and they
12344 are expected to arrive at solutions more quickly when the number of
12345 samples is large and the number of mixture components is not too large.")
12346 (license license:expat)))
12348 (define-public r-magick
12355 (uri (cran-uri "magick" version))
12358 "0h942bn7wfnzbbgq9hrs75c7igmg5r1c5sad2v0znhza4cp7p1w3"))))
12359 (build-system r-build-system)
12361 (list imagemagick zlib))
12363 (list r-curl r-magrittr r-rcpp))
12365 (list pkg-config r-knitr))
12366 (home-page "https://github.com/ropensci/magick")
12367 (synopsis "Advanced graphics and image-processing in R")
12369 "This package provides bindings to ImageMagick, a comprehensive image
12370 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
12371 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
12372 operations are vectorized via the Magick++ STL meaning they operate either on
12373 a single frame or a series of frames for working with layers, collages, or
12374 animation. In RStudio, images are automatically previewed when printed to the
12375 console, resulting in an interactive editing environment.")
12376 (license license:expat)))
12378 (define-public r-survey
12385 (uri (cran-uri "survey" version))
12388 "0ljsszybzri531q6xab04r6zq11vchfs7y0snjzk57m3g0b9ms05"))))
12389 (build-system r-build-system)
12397 (home-page "http://r-survey.r-forge.r-project.org/survey/")
12398 (synopsis "Analysis of complex survey samples")
12400 "This package provides tools for the analysis of complex survey samples.
12401 The provided features include: summary statistics, two-sample tests, rank
12402 tests, generalised linear models, cumulative link models, Cox models,
12403 loglinear models, and general maximum pseudolikelihood estimation for
12404 multistage stratified, cluster-sampled, unequally weighted survey samples;
12405 variances by Taylor series linearisation or replicate weights;
12406 post-stratification, calibration, and raking; two-phase subsampling designs;
12407 graphics; PPS sampling without replacement; principal components, and factor
12409 ;; Either version of the GPL.
12410 (license (list license:gpl2 license:gpl3))))
12412 (define-public r-gee
12415 (version "4.13-23")
12419 (uri (cran-uri "gee" version))
12422 "0v0fam678pqqkxmj95f1pwsi08y1rbz1wxnp1ig81jvpn0xpq8gq"))))
12423 (properties `((upstream-name . "gee")))
12424 (build-system r-build-system)
12427 (home-page "https://cran.r-project.org/web/packages/gee/")
12428 (synopsis "Generalized estimation equation solver")
12430 "This package provides a solver for generalized estimation equations.")
12431 (license license:gpl2)))
12433 (define-public r-tab
12440 (uri (cran-uri "tab" version))
12443 "1kg8c1safi9klkx2mdkmsf5dn9piy4jljwd4ma7g4jz2rwl4jzhv"))))
12444 (properties `((upstream-name . "tab")))
12445 (build-system r-build-system)
12447 (list r-dplyr r-kableextra r-knitr r-mass r-survey))
12450 (home-page "https://cran.r-project.org/web/packages/tab/")
12451 (synopsis "Create summary tables for statistical reports")
12453 "This package contains functions for creating various types of summary
12454 tables, e.g. comparing characteristics across levels of a categorical variable
12455 and summarizing fitted generalized linear models, generalized estimating
12456 equations, and Cox proportional hazards models. Functions are available to
12457 handle data from simple random samples as well as complex surveys.")
12458 (license license:gpl3+)))
12460 (define-public r-dvmisc
12467 (uri (cran-uri "dvmisc" version))
12469 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
12470 (build-system r-build-system)
12483 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
12484 (synopsis "Faster computation of common statistics and miscellaneous functions")
12486 "This package implements faster versions of base R functions (e.g. mean, standard
12487 deviation, covariance, weighted mean), mostly written in C++, along with
12488 miscellaneous functions for various purposes (e.g. create the histogram with
12489 fitted probability density function or probability mass function curve, create
12490 the body mass index groups, assess the linearity assumption in logistic
12492 (license license:gpl2)))
12494 (define-public r-accelerometry
12496 (name "r-accelerometry")
12501 (uri (cran-uri "accelerometry" version))
12503 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
12504 (build-system r-build-system)
12506 (list r-dvmisc r-rcpp))
12507 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
12508 (synopsis "Functions for processing accelerometer data")
12510 "This package provides a collection of functions that perform operations on
12511 time-series accelerometer data, such as identify the non-wear time, flag minutes
12512 that are part of an activity bout, and find the maximum 10-minute average count
12513 value. The functions are generally very flexible, allowing for a variety of
12514 algorithms to be implemented.")
12515 (license license:gpl3)))
12517 (define-public r-absim
12524 (uri (cran-uri "AbSim" version))
12526 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
12527 (properties `((upstream-name . "AbSim")))
12528 (build-system r-build-system)
12530 (list r-ape r-powerlaw))
12531 (home-page "https://cran.r-project.org/web/packages/AbSim/")
12532 (synopsis "Time resolved simulations of antibody repertoires")
12534 "This package provides simulation methods for the evolution of antibody repertoires.
12535 The heavy and light chain variable region of both human and C57BL/6 mice can
12536 be simulated in a time-dependent fashion. Both single lineages using one set of
12537 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
12538 with an initial V-D-J recombination event, starting the first phylogenetic tree.
12539 Upon completion, the main loop of the algorithm begins, with each iteration
12540 representing one simulated time step. Various mutation events are possible at
12541 each time step, contributing to a diverse final repertoire.")
12542 (license license:gpl2)))
12544 (define-public r-quic
12551 (uri (cran-uri "QUIC" version))
12553 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
12554 (properties `((upstream-name . "QUIC")))
12555 (build-system r-build-system)
12556 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
12557 (synopsis "Regularized sparse inverse covariance matrix estimation")
12559 "This package implements the regularized Gaussian maximum likelihood
12560 estimation of the inverse of a covariance matrix. It uses Newton's method and
12561 coordinate descent to solve the regularized inverse covariance matrix
12562 estimation problem.")
12563 ;; The project home page states that the release is under GPLv3 or later.
12564 ;; The CRAN page only says GPL-3.
12565 (license license:gpl3+)))
12567 (define-public r-abundant
12569 (name "r-abundant")
12574 (uri (cran-uri "abundant" version))
12576 (base32 "15m3ngj5aipjg961yy5kvdg9xlfcpliw30dq6gchzxabhnfzcipd"))))
12577 (build-system r-build-system)
12580 (home-page "https://cran.r-project.org/web/packages/abundant/")
12581 (synopsis "Abundant regression and high-dimensional principal fitted components")
12583 "This package provides tools to fit and predict with the high-dimensional
12584 principal fitted components model. This model is described by Cook, Forzani,
12585 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
12586 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
12587 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
12588 (license license:gpl2+)))
12590 (define-public r-ac3net
12597 (uri (cran-uri "Ac3net" version))
12599 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
12600 (properties `((upstream-name . "Ac3net")))
12601 (build-system r-build-system)
12603 (list r-data-table))
12604 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
12605 (synopsis "Inferring directional conservative causal core gene networks")
12606 (description "This package infers directional Conservative causal core
12607 (gene) networks (C3NET). This is a version of the algorithm C3NET with
12608 directional network.")
12609 (license license:gpl3+)))
12611 (define-public r-aca
12618 (uri (cran-uri "ACA" version))
12620 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
12621 (properties `((upstream-name . "ACA")))
12622 (build-system r-build-system)
12623 (home-page "https://cran.r-project.org/web/packages/ACA/")
12624 (synopsis "Abrupt change-point or aberration detection in point series")
12626 "This package offers an interactive function for the detection of breakpoints in
12628 ;; Any version of the GPL
12629 (license (list license:gpl2+ license:gpl3+))))
12631 (define-public r-acceptancesampling
12633 (name "r-acceptancesampling")
12638 (uri (cran-uri "AcceptanceSampling" version))
12640 (base32 "1ja1g0v8qvf7yj81x37wc6i7fkwpc573756jgvazazi8yf1gm12p"))))
12642 `((upstream-name . "AcceptanceSampling")))
12643 (build-system r-build-system)
12644 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
12645 (synopsis "Creation and evaluation of acceptance sampling plans")
12647 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
12648 acceptance sampling plans. Acceptance sampling is a methodology commonly used
12649 in quality control and improvement. International standards of acceptance
12650 sampling provide sampling plans for specific circumstances. The aim of this
12651 package is to provide an easy-to-use interface to visualize single, double or
12652 multiple sampling plans. In addition, methods have been provided to enable the
12653 user to assess sampling plans against pre-specified levels of performance, as
12654 measured by the probability of acceptance for a given level of quality in the
12656 (license license:gpl3+)))
12658 (define-public r-acclma
12665 (uri (cran-uri "ACCLMA" version))
12667 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
12668 (properties `((upstream-name . "ACCLMA")))
12669 (build-system r-build-system)
12670 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
12671 (synopsis "ACC & LMA graph plotting")
12673 "This package contains a function that imports data from a @acronym{CSV,
12674 Comma-Separated Values} file, or uses manually entered data from the format (x,
12675 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
12676 Curve} vs @acronym{LOI, Line of Independence} graph and
12677 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
12678 function is @code{plotLMA} (source file, header) that takes a data set and plots the
12679 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
12680 string) was passed, a manual data entry window is opened. The header parameter
12681 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
12682 a header row or not. The dataset should contain only one independent variable
12683 (x) and one dependent variable (y) and can contain a weight for each
12685 (license license:gpl2)))
12687 (define-public r-aspi
12694 (uri (cran-uri "aspi" version))
12696 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
12697 (build-system r-build-system)
12699 "https://cran.r-project.org/web/packages/aspi/")
12701 "Analysis of symmetry of parasitic infections")
12703 "This package provides tools for the analysis and visualization of bilateral
12704 asymmetry in parasitic infections.")
12705 (license license:gpl3+)))
12707 (define-public r-sandwich
12709 (name "r-sandwich")
12714 (uri (cran-uri "sandwich" version))
12717 "1d72vwxidsyac9mbyxrm06qds63rzcr82nn4c05466gbajsvcc3f"))
12718 (modules '((guix build utils)))
12720 '(with-directory-excursion "inst/doc"
12721 ;; These files are generated from Rnw files.
12722 (for-each delete-file
12723 (list "sandwich-OOP.pdf"
12733 (build-system r-build-system)
12736 (home-page "https://cran.r-project.org/web/packages/sandwich/")
12737 (synopsis "Robust Covariance Matrix Estimators")
12739 "This package provides model-robust standard error estimators for
12740 cross-sectional, time series, clustered, panel, and longitudinal data.")
12741 ;; Either version of the license.
12742 (license (list license:gpl2 license:gpl3))))
12744 (define-public r-th-data
12751 (uri (cran-uri "TH.data" version))
12754 "0ynxacnz002bjsp2ybql7rdqw4zd14af8r7w44nwbx22n4bapwzd"))))
12755 (properties `((upstream-name . "TH.data")))
12756 (build-system r-build-system)
12758 (list r-mass r-survival))
12761 (home-page "https://cran.r-project.org/web/packages/TH.data/")
12762 (synopsis "Shared data sets")
12764 "This package contains supporting data sets that are used in other
12765 packages maintained by Torsten Hothorn.")
12766 (license license:gpl3)))
12768 (define-public r-multcomp
12770 (name "r-multcomp")
12775 (uri (cran-uri "multcomp" version))
12778 "1z1cqklahnp4qi48r335xlqvw7h7xbjrlpb4pjky9gc987xf92rj"))))
12779 (build-system r-build-system)
12781 (list r-codetools r-mvtnorm r-sandwich r-survival r-th-data))
12782 (home-page "https://cran.r-project.org/web/packages/multcomp/")
12783 (synopsis "Simultaneous inference in general parametric models")
12785 "Simultaneous tests and confidence intervals for general linear
12786 hypotheses in parametric models, including linear, generalized linear, linear
12787 mixed effects, and survival models. The package includes demos reproducing
12788 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
12789 Hothorn, Westfall, 2010, CRC Press).")
12790 (license license:gpl2)))
12792 (define-public r-multcompview
12794 (name "r-multcompview")
12799 (uri (cran-uri "multcompView" version))
12801 (base32 "1rfq9wvvrghq0542ff40wy8vdmsyd8spzz6ihcywcvxdfa8m6g8j"))))
12802 (properties `((upstream-name . "multcompView")))
12803 (build-system r-build-system)
12804 (home-page "https://cran.r-project.org/package=multcompView")
12805 (synopsis "Visualizations of paired comparisons")
12807 "Convert a logical vector or a vector of p-values or a correlation,
12808 difference, or distance matrix into a display identifying the pairs for which
12809 the differences were not significantly different.")
12810 ;; Any version of the GPL.
12811 (license license:gpl3+)))
12813 (define-public r-emmeans
12816 (version "1.8.1-1")
12820 (uri (cran-uri "emmeans" version))
12823 "0xv55v50v3fdg289mfqirfm4p644gn4ckqnvs0wb09sl4m25xz3r"))))
12824 (build-system r-build-system)
12826 (list r-estimability r-mvtnorm r-numderiv r-xtable))
12829 (home-page "https://github.com/rvlenth/emmeans")
12830 (synopsis "Estimated marginal means, aka least-squares means")
12832 "This package provides tools to obtain @dfn{estimated marginal
12833 means} (EMMs) for many linear, generalized linear, and mixed models. It can
12834 be used to compute contrasts or linear functions of EMMs, trends, and
12835 comparisons of slopes.")
12836 ;; Either version of the license.
12837 (license (list license:gpl2 license:gpl3))))
12839 (define-public r-pwr
12846 (uri (cran-uri "pwr" version))
12849 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
12850 (build-system r-build-system)
12853 (home-page "https://github.com/heliosdrm/pwr")
12854 (synopsis "Basic functions for power analysis")
12856 "This package provides power analysis functions along the lines of
12858 (license license:gpl3+)))
12860 (define-public r-libcoin
12867 (uri (cran-uri "libcoin" version))
12869 (base32 "1syrcdj5qg5m3zd3dlxgpfklswbalfg42w058dr09hnzqsvx0z9d"))))
12870 (build-system r-build-system)
12871 (propagated-inputs (list r-mvtnorm))
12872 (home-page "https://cran.r-project.org/web/packages/libcoin")
12873 (synopsis "Linear test statistics for permutation inference")
12875 "This package provides basic infrastructure for linear test statistics
12876 and permutation inference in the framework of Strasser and Weber (1999).")
12877 (license license:gpl2)))
12879 (define-public r-coin
12886 (uri (cran-uri "coin" version))
12889 "1cpv7jx840inzg98bkhrb5yscx0gpag6br237r5qpnc2gbrd2ikm"))))
12890 (build-system r-build-system)
12898 (home-page "http://coin.r-forge.r-project.org")
12899 (synopsis "Conditional inference procedures in a permutation test framework")
12901 "This package provides conditional inference procedures for the general
12902 independence problem including two-sample, K-sample (non-parametric ANOVA),
12903 correlation, censored, ordered and multivariate problems.")
12904 (license license:gpl2)))
12906 (define-public r-bayesplot
12908 (name "r-bayesplot")
12913 (uri (cran-uri "bayesplot" version))
12916 "0hqy597ang53phxnl084hak35ffqz9lw9hygax7370gpkjws908a"))))
12917 (build-system r-build-system)
12932 (home-page "https://mc-stan.org/bayesplot")
12933 (synopsis "Plotting for Bayesian models")
12935 "This package provides plotting functions for posterior analysis, model
12936 checking, and MCMC diagnostics. The package is designed not only to provide
12937 convenient functionality for users, but also a common set of functions that
12938 can be easily used by developers working on a variety of R packages for
12939 Bayesian modeling.")
12940 (license license:gpl3+)))
12942 (define-public r-tmb
12949 (uri (cran-uri "TMB" version))
12952 "03zv38gig31ir5gdhgw5j6j8xn1f4y91j2r87fv31gywmg1bhzl9"))))
12953 (properties `((upstream-name . "TMB")))
12954 (build-system r-build-system)
12956 (list r-matrix r-rcppeigen))
12957 (home-page "http://tmb-project.org")
12958 (synopsis "Template model builder: a general random effect tool")
12960 "With this tool, a user should be able to quickly implement complex
12961 random effect models through simple C++ templates. The package combines
12962 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
12963 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
12964 from R) to obtain an efficient implementation of the applied Laplace
12965 approximation with exact derivatives. Key features are: Automatic sparseness
12966 detection, parallelism through BLAS and parallel user templates.")
12967 (license license:gpl2)))
12969 (define-public r-sjstats
12976 (uri (cran-uri "sjstats" version))
12978 (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka"))))
12979 (build-system r-build-system)
12998 (home-page "https://github.com/strengejacke/sjstats")
12999 (synopsis "Functions for common statistical computations")
13001 "This package provides a collection of convenient functions for common
13002 statistical computations, which are not directly provided by R's @code{base}
13003 or @code{stats} packages. This package aims at providing, first, shortcuts
13004 for statistical measures, which otherwise could only be calculated with
13005 additional effort. Second, these shortcut functions are generic, and can be
13006 applied not only to vectors, but also to other objects as well. The focus of
13007 most functions lies on summary statistics or fit measures for regression
13008 models, including generalized linear models, mixed effects models and Bayesian
13010 (license license:gpl3)))
13012 (define-public r-glmmtmb
13019 (uri (cran-uri "glmmTMB" version))
13022 "1ldly6qn8iwqr41ndqlwsdz4v2n36giavsmx33vybn9g7r2fq4m7"))))
13023 (properties `((upstream-name . "glmmTMB")))
13024 (build-system r-build-system)
13033 (list r-knitr r-rmarkdown)) ; for vignettes
13034 (home-page "https://github.com/glmmTMB")
13035 (synopsis "Generalized linear mixed models")
13037 "Fit linear and generalized linear mixed models with various extensions,
13038 including zero-inflation. The models are fitted using maximum likelihood
13039 estimation via the Template Model Builder. Random effects are assumed to be
13040 Gaussian on the scale of the linear predictor and are integrated out using the
13041 Laplace approximation. Gradients are calculated using automatic
13043 (license license:agpl3+)))
13045 (define-public r-bayestestr
13047 (name "r-bayestestr")
13052 (uri (cran-uri "bayestestR" version))
13055 "1951zm88qlbmr4ragrzfzgw72awm7mqhh464s6kck0mcx7shas90"))))
13056 (properties `((upstream-name . "bayestestR")))
13057 (build-system r-build-system)
13059 (list r-datawizard r-insight))
13062 (home-page "https://github.com/easystats/bayestestR")
13063 (synopsis "Describe Bayesian models and posterior distributions")
13065 "This package provides utilities to understand and describe posterior
13066 distributions and Bayesian models. It includes point-estimates such as
13067 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
13068 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
13069 ROPE percentage and pd).")
13070 (license license:gpl3)))
13072 (define-public r-performance
13074 (name "r-performance")
13079 (uri (cran-uri "performance" version))
13082 "0fdszf1dngqlbwcp7ynfdkzjgg0lang4d3b53ygjwsq7ph20xsw6"))))
13083 (build-system r-build-system)
13085 (list r-bayestestr r-datawizard r-insight))
13086 (home-page "https://easystats.github.io/performance/")
13087 (synopsis "Assessment of regression models performance")
13089 "This package provides utilities for computing measures to assess model
13090 quality, which are not directly provided by R's @code{base} or @code{stats}
13091 packages. These include e.g. measures like r-squared, intraclass correlation
13092 coefficient, root mean squared error or functions to check models for
13093 overdispersion, singularity or zero-inflation and more. Functions apply to a
13094 large variety of regression models, including generalized linear models, mixed
13095 effects models and Bayesian models.")
13096 (license license:gpl3)))
13098 (define-public r-ggeffects
13100 (name "r-ggeffects")
13105 (uri (cran-uri "ggeffects" version))
13108 "1h60s10b1b5ciqg125mfnhq7nf2paq9svs2lfgwpwdvs4f8l4aq7"))))
13109 (build-system r-build-system)
13111 (list r-insight r-mass r-sjlabelled))
13114 (home-page "https://github.com/strengejacke/ggeffects")
13115 (synopsis "Create tidy data frames of marginal effects for ggplot")
13117 "This package provides tools to compute marginal effects from statistical
13118 models and return the result as tidy data frames. These data frames are ready
13119 to use with the @code{ggplot2} package. Marginal effects can be calculated
13120 for many different models. Interaction terms, splines and polynomial terms
13121 are also supported. The two main functions are @code{ggpredict()} and
13122 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
13123 results using @code{ggplot2}.")
13124 (license license:gpl3)))
13126 (define-public r-effectsize
13128 (name "r-effectsize")
13129 (version "0.7.0.5")
13133 (uri (cran-uri "effectsize" version))
13136 "0y8ng4wsms25qx2wmyrm97rbv5dgm5xyhh5ys99f0clr9lrcxr91"))))
13137 (properties `((upstream-name . "effectsize")))
13138 (build-system r-build-system)
13140 (list r-bayestestr r-datawizard r-insight r-parameters
13144 (home-page "https://github.com/easystats/effectsize")
13145 (synopsis "Indices of effect size and standardized parameters")
13147 "This package provides utilities to work with indices of effect size and
13148 standardized parameters for a wide variety of models, allowing computation and
13149 conversion of indices such as Cohen's d, r, odds, etc.")
13150 (license license:gpl3)))
13152 (define-public r-sjplot
13159 (uri (cran-uri "sjPlot" version))
13161 (base32 "05iimcf1if1cx9bmsjb6f5gcq58hjiw10vx7kqd4nqnyhzcvy8yr"))))
13162 (properties `((upstream-name . "sjPlot")))
13163 (build-system r-build-system)
13185 (home-page "https://strengejacke.github.io/sjPlot/")
13186 (synopsis "Data visualization for statistics in social science")
13188 "This package represents a collection of plotting and table output
13189 functions for data visualization. Results of various statistical
13190 analyses (that are commonly used in social sciences) can be visualized using
13191 this package, including simple and cross tabulated frequencies, histograms,
13192 box plots, (generalized) linear models, mixed effects models, principal
13193 component analysis and correlation matrices, cluster analyses, scatter plots,
13194 stacked scales, effects plots of regression models (including interaction
13195 terms) and much more. This package supports labelled data.")
13196 (license license:gpl3)))
13198 (define-public r-ini
13205 (uri (cran-uri "ini" version))
13208 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
13209 (build-system r-build-system)
13210 (home-page "https://github.com/dvdscripter/ini")
13211 (synopsis "Read and write configuration files")
13213 "This package provides tools to parse simple @code{.ini} configuration
13214 files to an structured list. Users can manipulate this resulting list with
13215 @code{lapply()} functions. This same structured list can be used to write
13216 back to file after modifications.")
13217 (license license:gpl3)))
13219 (define-public r-gillespiessa2
13221 (name "r-gillespiessa2")
13226 (uri (cran-uri "GillespieSSA2" version))
13228 (base32 "03ym8qx5yc1a6j9l973lc0rjzs8hiax8fq13j7m1fcb1pvnbvar5"))))
13229 (properties `((upstream-name . "GillespieSSA2")))
13230 (build-system r-build-system)
13243 (native-inputs (list r-knitr))
13244 (home-page "https://github.com/rcannood/GillespieSSA2")
13245 (synopsis "Gillespie's stochastic simulation algorithm")
13247 "This package provides a fast, scalable, and versatile framework for
13248 simulating large systems with Gillespie's @dfn{Stochastic Simulation
13249 Algorithm} (SSA). This package is the spiritual successor to the GillespieSSA
13250 package. Benefits of this package include major speed improvements (>100x),
13251 easier to understand documentation, and many unit tests that try to ensure the
13252 package works as intended.")
13253 (license license:gpl3+)))
13255 (define-public r-gitcreds
13257 (name "r-gitcreds")
13262 (uri (cran-uri "gitcreds" version))
13265 "0pf70g4a2kxjcid5rc4ppmgcl3kpjhkszdgz4fqn4l33lp6apij1"))))
13266 (properties `((upstream-name . "gitcreds")))
13267 (build-system r-build-system)
13268 (inputs (list git-minimal))
13269 (native-inputs (list r-knitr))
13270 (home-page "https://github.com/r-lib/gitcreds")
13271 (synopsis "Query git credentials from R")
13273 "Query, set, and delete credentials from the git credential store.
13274 Manage GitHub tokens and other git credentials. This package is to be used by
13275 other packages that need to authenticate to GitHub and/or other git
13277 (license license:expat)))
13279 (define-public r-gh
13286 (uri (cran-uri "gh" version))
13289 "1vqjhqlhvvqq8w2cqbgrkqphj0ga5s6fbl4zhcl3vc6fvsms5bpv"))))
13290 (build-system r-build-system)
13292 (list r-cli r-gitcreds r-httr r-ini r-jsonlite))
13295 (home-page "https://github.com/r-lib/gh#readme")
13296 (synopsis "Access the GitHub API via R")
13298 "This package provides a minimal R client to access the GitHub API.")
13299 (license license:expat)))
13301 (define-public r-fs
13308 (uri (cran-uri "fs" version))
13311 "11qr3v0xn65vfhgcxl4l6yv48s4w0w3ldp3anpzc25vd3mwd3jim"))))
13312 (build-system r-build-system)
13315 (home-page "https://fs.r-lib.org")
13316 (synopsis "Cross-platform file system operations based on libuv")
13318 "This package provides a cross-platform interface to file system
13319 operations, built on top of the libuv C library.")
13320 (license license:gpl3)))
13322 (define-public r-clisymbols
13324 (name "r-clisymbols")
13329 (uri (cran-uri "clisymbols" version))
13332 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
13333 (build-system r-build-system)
13334 (home-page "https://github.com/gaborcsardi/clisymbols")
13335 (synopsis "Unicode symbols at the R prompt")
13337 "This package provides a small subset of Unicode symbols, that are useful
13338 when building command line applications. They fall back to alternatives on
13339 terminals that do not support Unicode.")
13340 (license license:expat)))
13342 (define-public r-credentials
13344 (name "r-credentials")
13349 (uri (cran-uri "credentials" version))
13352 "1f18j3zrq8c9kah57xwahmmljsjg5qphlgamvx507ynvpq8pryig"))))
13353 (properties `((upstream-name . "credentials")))
13354 (build-system r-build-system)
13357 (modify-phases %standard-phases
13358 (add-after 'unpack 'setenv-HOME
13360 ;; This is necessary because git looks for $HOME/.gitconfig
13361 (setenv "HOME" "/tmp"))))))
13363 (list git-minimal))
13365 (list r-askpass r-curl r-jsonlite r-openssl r-sys))
13368 (home-page "https://docs.ropensci.org/credentials/")
13369 (synopsis "Tools for managing SSH and Git credentials")
13371 "This package assists you in setting up and retrieving of HTTPS and SSH
13372 credentials for use with git and other services. For HTTPS remotes the
13373 package interfaces the @command{git-credential} utility which @command{git}
13374 uses to store HTTP usernames and passwords. For SSH remotes this package
13375 provides convenient functions to find or generate appropriate SSH keys. The
13376 package both helps the user to setup a local git installation, and also
13377 provides a back-end for git/ssh client libraries to authenticate with existing
13378 user credentials.")
13379 (license license:expat)))
13381 (define-public r-gert
13388 (uri (cran-uri "gert" version))
13391 "1lb9rf4c8ip8cll9mycx88x8q774bcmd01j4bwjx9h0kx1hgahkb"))))
13392 (properties `((upstream-name . "gert")))
13393 (build-system r-build-system)
13395 (list libgit2 zlib))
13404 (list pkg-config r-knitr))
13405 (home-page "https://docs.ropensci.org/gert/")
13406 (synopsis "Simple Git client for R")
13408 "This package provides a simple git client for R based on libgit2 with
13409 support for SSH and HTTPS remotes. All functions in gert use basic R data
13410 types (such as vectors and data-frames) for their arguments and return values.
13411 User credentials are shared with command line git through the
13412 @code{git-credential} store and SSH keys stored on disk or ssh-agent.")
13413 (license license:expat)))
13415 (define-public r-usethis
13422 (uri (cran-uri "usethis" version))
13425 "0638dzl4nm4c36990sf2biy74hjr2fzlqzfb98fsqrbhaw3ngp1i"))))
13426 (build-system r-build-system)
13447 (home-page "https://github.com/r-lib/usethis")
13448 (synopsis "Automate R package and project setup")
13450 "This package helps you to automate R package and project setup tasks
13451 that are otherwise performed manually. This includes setting up unit testing,
13452 test coverage, continuous integration, Git, GitHub integration, licenses,
13453 Rcpp, RStudio projects, and more.")
13454 (license license:gpl3)))
13456 (define-public r-sessioninfo
13458 (name "r-sessioninfo")
13463 (uri (cran-uri "sessioninfo" version))
13466 "1jy7n37qnrb4fgzmn8s8yf7kv29yw27x8zklwf8qdb2kgj2q6qpm"))))
13467 (build-system r-build-system)
13470 (home-page "https://github.com/r-lib/sessioninfo#readme")
13471 (synopsis "R session information")
13473 "This package provides tools to query and print information about the
13474 current R session. It is similar to @code{utils::sessionInfo()}, but includes
13475 more information about packages, and where they were installed from.")
13476 (license license:gpl2)))
13478 (define-public r-remotes
13485 (uri (cran-uri "remotes" version))
13488 "05m5dgv0nba5vhjbdkd8z5lbhpfxgkw31j58am7vz1d44igqgvzj"))))
13489 (build-system r-build-system)
13492 (home-page "https://github.com/r-lib/remotes#readme")
13493 (synopsis "R package installation from remote repositories")
13495 "Download and install R packages stored in GitHub, BitBucket, or plain
13496 subversion or git repositories. This package is a lightweight replacement of
13497 the @code{install_*} functions in the @code{devtools} package. Indeed most of
13498 the code was copied over from @code{devtools}.")
13499 (license license:gpl2+)))
13501 (define-public r-xopen
13508 (uri (cran-uri "xopen" version))
13511 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
13512 (build-system r-build-system)
13515 (home-page "https://github.com/r-lib/xopen#readme")
13516 (synopsis "Open system files, URLs, anything")
13518 "This package provides a cross-platform solution to open files,
13519 directories or URLs with their associated programs.")
13520 (license license:expat)))
13522 (define-public r-rcmdcheck
13524 (name "r-rcmdcheck")
13529 (uri (cran-uri "rcmdcheck" version))
13532 "1l696byn3kjq2xvz4wxybzaj6ink85h4lz3a35v2132ba5yyzm5v"))))
13533 (build-system r-build-system)
13547 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
13548 (synopsis "Run R CMD check from R and capture results")
13550 "Run @code{R CMD check} from R programmatically, and capture the results
13551 of the individual checks.")
13552 (license license:expat)))
13554 (define-public r-rapportools
13556 (name "r-rapportools")
13561 (uri (cran-uri "rapportools" version))
13564 "0qr86idng12g6hdd764j0wmli700v7rjhw7jdjxj0ka8xm5v7ymm"))))
13565 (build-system r-build-system)
13567 (list r-mass r-pander r-plyr r-reshape2))
13568 (home-page "https://cran.r-project.org/web/packages/rapportools/")
13569 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
13571 "This package provides helper functions that act as wrappers to more
13572 advanced statistical methods with the advantage of having sane defaults for
13574 (license license:agpl3+)))
13576 (define-public r-pander
13583 (uri (cran-uri "pander" version))
13586 "144zkq5w7v6fpzk3x40i0baybbp0y6x2ckh4b9qljryas9mhgp9a"))))
13587 (build-system r-build-system)
13589 (list r-digest r-rcpp))
13592 (home-page "https://rapporter.github.io/pander")
13593 (synopsis "Render R objects into Pandoc's markdown")
13595 "The main aim of the pander R package is to provide a minimal and easy
13596 tool for rendering R objects into Pandoc's markdown. The package is also
13597 capable of exporting/converting complex Pandoc documents (reports) in various
13599 ;; This package is licensed under either the AGPLv3+ or the very rarely
13601 (license license:agpl3+)))
13603 (define-public r-summarytools
13605 (name "r-summarytools")
13610 (uri (cran-uri "summarytools" version))
13613 "0gr95cd1ja8di6s0xghk6w7nj3bh3z4g7j7ixdy7f88q681aixgx"))))
13614 (build-system r-build-system)
13630 (home-page "https://github.com/dcomtois/summarytools")
13631 (synopsis "Tools to quickly and neatly summarize data")
13633 "This package provides tools for data frame summaries, cross-tabulations,
13634 weight-enabled frequency tables and common univariate statistics in concise
13635 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
13636 good point-of-entry for exploring data, both for experienced and new R
13638 (license license:gpl2)))
13640 (define-public r-lsei
13647 (uri (cran-uri "lsei" version))
13650 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2"))))
13651 (build-system r-build-system)
13654 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
13655 (synopsis "Solve regression problems under equality/inequality constraints")
13657 "It contains functions that solve least squares linear regression
13658 problems under linear equality/inequality constraints. Functions for solving
13659 quadratic programming problems are also available, which transform such
13660 problems into least squares ones first.")
13661 (license license:gpl2+)))
13663 (define-public r-npsurv
13670 (uri (cran-uri "npsurv" version))
13673 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw"))))
13674 (build-system r-build-system)
13677 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
13678 (synopsis "Nonparametric survival analysis")
13680 "This package contains functions for non-parametric survival analysis of
13681 exact and interval-censored observations.")
13682 (license license:gpl2+)))
13684 (define-public r-clusteval
13686 (name "r-clusteval")
13691 (uri (cran-uri "clusteval" version))
13694 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
13695 (build-system r-build-system)
13697 (list r-mvtnorm r-rcpp))
13698 (home-page "https://cran.r-project.org/web/packages/clusteval/")
13699 (synopsis "Evaluation of clustering algorithms")
13701 "This R package provides a suite of tools to evaluate clustering
13702 algorithms, clusterings, and individual clusters.")
13703 (license license:expat)))
13705 (define-public r-tweedie
13712 (uri (cran-uri "tweedie" version))
13715 "0ghwggdx6d391m7nay9n5li2xjqh3kmw416xx130sy2sxrgp8g4q"))))
13716 (build-system r-build-system)
13717 (native-inputs (list gfortran))
13718 (home-page "https://cran.r-project.org/web/packages/tweedie/")
13719 (synopsis "Evaluation of Tweedie exponential family models")
13721 "Maximum likelihood computations for Tweedie families, including the
13722 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
13723 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
13724 and related methods.")
13725 (license license:gpl2+)))
13727 (define-public r-rcppgsl
13734 (uri (cran-uri "RcppGSL" version))
13736 (base32 "1a5dms0axlzgpv1z2bhfrb77497h0ch1yslq0gidj14vr4kfm57h"))))
13737 (properties `((upstream-name . "RcppGSL")))
13738 (build-system r-build-system)
13741 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
13742 (synopsis "Rcpp integration for GSL vectors and matrices")
13744 "The GNU Scientific Library (or GSL) is a collection of numerical
13745 routines for scientific computing. It is particularly useful for C and C++
13746 programs as it provides a standard C interface to a wide range of mathematical
13747 routines. There are over 1000 functions in total with an extensive test
13748 suite. The RcppGSL package provides an easy-to-use interface between GSL data
13749 structures and R using concepts from Rcpp which is itself a package that eases
13750 the interfaces between R and C++.")
13751 (license license:gpl2+)))
13753 (define-public r-mvabund
13760 (uri (cran-uri "mvabund" version))
13763 "01kss9dx4an1ir5zs46jypvhj8sdc8wcs00i1223ai09av4lcsgd"))))
13764 (build-system r-build-system)
13766 (list r-mass r-rcpp r-rcppgsl r-statmod r-tweedie))
13767 (home-page "https://cran.r-project.org/web/packages/mvabund/")
13768 (synopsis "Statistical methods for analysing multivariate abundance data")
13770 "This package provides a set of tools for displaying, modeling and
13771 analysing multivariate abundance data in community ecology.")
13772 (license license:lgpl2.1+)))
13774 (define-public r-afex
13781 (uri (cran-uri "afex" version))
13784 "09q426s2zmzxx5ilxy0x5mflpb38pl075ss1s8xvpswkn6cia0b6"))))
13785 (build-system r-build-system)
13786 ;; This is needed for the vignette builder
13789 (modify-phases %standard-phases
13790 (add-after 'unpack 'set-HOME
13791 (lambda _ (setenv "HOME" "/tmp"))))))
13793 (list r-car r-lme4 r-lmertest r-pbkrtest r-reshape2))
13796 r-r-rsp)) ;vignette builder
13797 (home-page "https://afex.singmann.science/")
13798 (synopsis "Analysis of factorial experiments")
13800 "This package provides convenience functions for analyzing factorial
13801 experiments using ANOVA or mixed models.")
13802 (license license:gpl2+)))
13804 (define-public r-lmertest
13806 (name "r-lmertest")
13811 (uri (cran-uri "lmerTest" version))
13814 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim"))))
13815 (properties `((upstream-name . "lmerTest")))
13816 (build-system r-build-system)
13818 (list r-ggplot2 r-lme4 r-mass r-numderiv))
13819 (home-page "https://github.com/runehaubo/lmerTestR")
13820 (synopsis "Tests in linear mixed effects models")
13822 "This package provides p-values in type I, II or III anova and summary
13823 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
13824 method. A Kenward-Roger method is also available via the @code{pbkrtest}
13825 package. Model selection methods include step, drop1 and anova-like tables
13826 for random effects (ranova). Methods for Least-Square means (LS-means) and
13827 tests of linear contrasts of fixed effects are also available.")
13828 (license license:gpl2+)))
13830 (define-public r-r2glmm
13837 (uri (cran-uri "r2glmm" version))
13840 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
13841 (build-system r-build-system)
13853 (home-page "https://github.com/bcjaeger/r2glmm")
13854 (synopsis "Compute R squared for mixed (multilevel) models")
13856 "This package computes model and semi partial R squared with confidence
13857 limits for the linear and generalized linear mixed model (LMM and GLMM). The
13858 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
13859 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
13861 (license license:gpl2)))
13863 (define-public r-cmdfun
13870 (uri (cran-uri "cmdfun" version))
13873 "1pbcq7hi2lcmqnghmy3q2fsk0c9fy5m0637acyzmc096fxbx723j"))))
13874 (properties `((upstream-name . "cmdfun")))
13875 (build-system r-build-system)
13885 (home-page "https://snystrom.github.io/cmdfun/")
13886 (synopsis "Framework for building interfaces to shell commands")
13888 "Writing interfaces to command line software is cumbersome. The cmdfun
13889 package provides a framework for building function calls to seamlessly
13890 interface with shell commands by allowing lazy evaluation of command line
13891 arguments. It also provides methods for handling user-specific paths to tool
13892 installs or secrets like API keys. Its focus is to equally serve package
13893 builders who wish to wrap command line software, and to help analysts stay
13894 inside R when they might usually leave to execute non-R software.")
13895 (license license:expat)))
13897 (define-public r-rslurm
13904 (uri (cran-uri "rslurm" version))
13907 "19451icfh7snjbbmpzpr1hrdf52q8ijv0ag1di3y55r2la3jxxcf"))))
13908 (properties `((upstream-name . "rslurm")))
13909 (build-system r-build-system)
13910 (propagated-inputs (list r-whisker))
13911 (native-inputs (list r-knitr))
13912 (home-page "http://cyberhelp.sesync.org/rslurm/")
13913 (synopsis "Submit R calculations to a Slurm cluster")
13915 "This package provides functions that simplify submitting R scripts to a
13916 Slurm workload manager, in part by automating the division of embarrassingly
13917 parallel calculations across cluster nodes.")
13918 (license license:gpl3)))
13920 (define-public r-chk
13927 (uri (cran-uri "chk" version))
13930 "0nw3aj8sbd2x8rsvpglsiavk7kivd330mgx676k46m7lhhj7nmpw"))))
13931 (properties `((upstream-name . "chk")))
13932 (build-system r-build-system)
13934 (list r-lifecycle r-rlang))
13935 (native-inputs (list r-knitr))
13936 (home-page "https://github.com/poissonconsulting/chk")
13937 (synopsis "Check user-supplied function arguments")
13939 "This is a package for developers to check user-supplied function
13940 arguments. It is designed to be simple, fast and customizable. Error
13941 messages follow the tidyverse style guide.")
13942 (license license:expat)))
13944 (define-public r-weights
13951 (uri (cran-uri "weights" version))
13954 "1fnchf7f0hyl514bk8sc3l884kg25kb5xm4mc2l28n6hm7l6bgpg"))))
13955 (build-system r-build-system)
13957 (list r-gdata r-hmisc r-lme4 r-mice))
13958 (home-page "https://cran.r-project.org/web/packages/weights/")
13959 (synopsis "Weighting and weighted statistics")
13960 (description "This package Provides a variety of functions for producing
13961 simple weighted statistics, such as weighted Pearson's correlations, partial
13962 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
13963 includes some software for quickly recoding survey data and plotting point
13964 estimates from interaction terms in regressions (and multiply imputed
13965 regressions). NOTE: Weighted partial correlation calculations pulled to
13967 (license license:gpl2+)))
13969 (define-public r-rcppalgos
13971 (name "r-rcppalgos")
13975 (uri (cran-uri "RcppAlgos" version))
13978 "11dvh0ba3chsqf3vw8g9h1754arxgwqryayavx3n6vm5daz2krqa"))))
13979 (properties `((upstream-name . "RcppAlgos")))
13980 (build-system r-build-system)
13981 (inputs (list gmp))
13982 (propagated-inputs (list r-cpp11 r-gmp))
13983 (native-inputs (list r-knitr))
13984 (home-page "https://github.com/jwood000/RcppAlgos")
13986 "High performance tools for combinatorics and computational mathematics")
13988 "This package provides optimized functions and flexible combinatorial
13989 iterators implemented in C++ for solving problems in combinatorics and
13990 computational mathematics. It utilizes the @code{RMatrix} class from
13991 @code{RcppParallel} for thread safety. There are combination/permutation
13992 functions with constraint parameters that allow for generation of all results
13993 of a vector meeting specific criteria. It is capable of generating specific
13994 combinations/permutations which sets up nicely for parallelization as well as
13995 random sampling. Gmp support permits exploration where the total number of
13996 results is large. Additionally, there are several high performance number
13997 theoretic functions that are useful for problems common in computational
13999 (license license:gpl2+)))
14001 (define-public r-rcppannoy
14003 (name "r-rcppannoy")
14008 (uri (cran-uri "RcppAnnoy" version))
14011 "12k8ny981dmky5js8yl6bih5r5mq3w43f2f9admhkwqn0n80kcl9"))))
14012 (properties `((upstream-name . "RcppAnnoy")))
14013 (build-system r-build-system)
14016 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
14017 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
14019 "Annoy is a small C++ library for Approximate Nearest Neighbors written
14020 for efficient memory usage as well an ability to load from and save to disk.
14021 This package provides an R interface.")
14022 ;; Annoy is released under ASL 2.0, but this wrapper is released under
14024 (license (list license:gpl2+ license:asl2.0))))
14026 (define-public r-rcpphnsw
14028 (name "r-rcpphnsw")
14033 (uri (cran-uri "RcppHNSW" version))
14036 "0x3w14cz6hkrl8hi6217j0dl65l3yphbzka1dmsvgp3p9waq402g"))))
14037 (properties `((upstream-name . "RcppHNSW")))
14038 (build-system r-build-system)
14039 (propagated-inputs (list r-rcpp))
14040 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
14041 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
14043 "Hnswlib is a C++ library for approximate nearest neighbors. This
14044 package provides a minimal R interface by relying on the Rcpp package.")
14045 ;; hnswlib is released under Version 2.0 of the Apache License.
14046 (license (list license:gpl3 license:asl2.0))))
14048 (define-public r-rcppparallel
14050 (name "r-rcppparallel")
14055 (uri (cran-uri "RcppParallel" version))
14058 "1sn211ajlb1p12sglxqns175rg078yvww268m8cp0vvd7cmk55k3"))
14059 (modules '((guix build utils)))
14061 '(delete-file-recursively "src/tbb/"))))
14062 (properties `((upstream-name . "RcppParallel")))
14063 (build-system r-build-system)
14067 '(modify-phases %standard-phases
14068 (add-after 'unpack 'use-system-tbb
14069 (lambda* (#:key inputs #:allow-other-keys)
14070 (setenv "TBB_ROOT" (assoc-ref inputs "tbb")))))))
14071 (inputs (list tbb-2020))
14072 (home-page "https://rcppcore.github.io/RcppParallel/")
14073 (synopsis "Parallel programming tools for Rcpp")
14075 "This package provides high level functions for parallel programming with
14076 Rcpp. For example, the @code{parallelFor()} function can be used to convert
14077 the work of a standard serial @code{for} loop into a parallel one and the
14078 @code{parallelReduce()} function can be used for accumulating aggregates or
14080 (license license:gpl2)))
14082 (define-public r-ncdf4
14089 (uri (cran-uri "ncdf4" version))
14092 "0qzvin2fjzcb7h2knlnw14s6043pwi1nm7yf6p27ax7w269173fb"))))
14093 (build-system r-build-system)
14095 (list netcdf zlib))
14096 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
14097 (synopsis "R interface to Unidata netCDF format data files")
14099 "This package provides a high-level R interface to data files written
14100 using Unidata's netCDF library (version 4 or earlier), which are binary data
14101 files that are portable across platforms and include metadata information in
14102 addition to the data sets. Using this package, netCDF files can be opened and
14103 data sets read in easily. It is also easy to create new netCDF dimensions,
14104 variables, and files, in either version 3 or 4 format, and manipulate existing
14106 (license license:gpl3+)))
14108 (define-public r-biocmanager
14110 (name "r-biocmanager")
14111 (version "1.30.18")
14115 (uri (cran-uri "BiocManager" version))
14117 (base32 "0dawbd546rznllpw5wq282r0viga4cck398d4s1inkk18mmi4qzp"))))
14118 (properties `((upstream-name . "BiocManager")))
14119 (build-system r-build-system)
14122 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
14123 (synopsis "Access the Bioconductor project package repository")
14125 "This package provides a convenient tool to install and update
14126 Bioconductor packages.")
14127 (license license:artistic2.0)))
14129 (define-public r-rgl
14132 (version "0.109.6")
14136 (uri (cran-uri "rgl" version))
14139 "1jl89v2gwk1d4q3vn7kx8x7abjbgiisfiyrs4d40qixr6iil8hrz"))))
14140 (build-system r-build-system)
14144 r-rmarkdown)) ;for vignettes
14161 (home-page "https://r-forge.r-project.org/projects/rgl/")
14162 (synopsis "3D visualization using OpenGL")
14164 "This package provides medium to high level functions for 3D interactive graphics,
14165 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
14166 as functions for constructing representations of geometric
14167 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
14168 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
14169 image formats, including PNG, Postscript, SVG, PGF.")
14170 ;; Any version of the GPL.
14171 (license (list license:gpl2+ license:gpl3+))))
14173 (define-public r-multicool
14175 (name "r-multicool")
14180 (uri (cran-uri "multicool" version))
14183 "0djacq0irfqz4nlnx238kja73yvr1n5qybbfyl6bw1n6qgcjhza8"))))
14184 (build-system r-build-system)
14185 (propagated-inputs (list r-rcpp))
14186 (home-page "https://cran.r-project.org/web/packages/multicool/")
14187 (synopsis "Permutations of multisets in cool-lex order")
14189 "This package provides a set of tools to permute multisets without loops
14190 or hash tables and to generate integer partitions. Cool-lex order is similar
14191 to colexicographical order.")
14192 (license license:gpl2)))
14194 (define-public r-misc3d
14201 (uri (cran-uri "misc3d" version))
14204 "0r9x57s63kx9f6dgam2nhbziq8nrs9wd8pk7g76hds2kw46vnyx0"))))
14205 (build-system r-build-system)
14206 (home-page "https://cran.r-project.org/web/packages/misc3d/")
14207 (synopsis "Miscellaneous 3D Plots")
14209 "This package provides a collection of miscellaneous 3d plots, including
14211 ;; Any version of the GPL.
14212 (license (list license:gpl2+ license:gpl3+))))
14214 (define-public r-ks
14221 (uri (cran-uri "ks" version))
14223 (base32 "05bqrjkbx2kn5aax0hy3xd6pf7nxka9bm1sp8ll1cc2gf1nx1i6i"))))
14224 (build-system r-build-system)
14236 (home-page "https://www.mvstat.net/tduong/")
14237 (synopsis "Kernel smoothing")
14239 "This package provides kernel smoothers for univariate and multivariate
14240 data, including density functions, density derivatives, cumulative
14241 distributions, modal clustering, discriminant analysis, and two-sample
14242 hypothesis testing.")
14243 ;; Either version of the GPL.
14244 (license (list license:gpl2 license:gpl3))))
14246 (define-public r-feature
14253 (uri (cran-uri "feature" version))
14256 "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y"))))
14257 (build-system r-build-system)
14259 (list r-ks r-plot3d))
14262 (home-page "https://www.mvstat.net/tduong/")
14263 (synopsis "Inferential feature significance for kernel density estimation")
14265 "The feature package contains functions to display and compute kernel
14266 density estimates, significant gradient and significant curvature regions.
14267 Significant gradient and/or curvature regions often correspond to significant
14268 features (e.g. local modes).")
14269 ;; Either version of the GPL.
14270 (license (list license:gpl2 license:gpl3))))
14272 (define-public r-arm
14279 (uri (cran-uri "arm" version))
14282 "0dz9dnsky77da2mc198dr3600kz9vk75z1iihjarnsdrq68a4bf0"))))
14283 (build-system r-build-system)
14291 (home-page "https://cran.r-project.org/web/packages/arm/")
14292 (synopsis "Data analysis using regression and multilevel/hierarchical models")
14294 "This package provides functions to accompany A. Gelman and J. Hill,
14295 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
14296 University Press, 2007.")
14297 (license license:gpl3+)))
14299 (define-public r-circular
14301 (name "r-circular")
14306 (uri (cran-uri "circular" version))
14309 "1qmwj1pf37lc2s5r83y7nqckscznqhbsv66bdfgfbby7x4qkwga8"))))
14310 (build-system r-build-system)
14312 (list r-boot r-mvtnorm))
14315 (home-page "https://cran.r-project.org/web/packages/circular/")
14316 (synopsis "Circular statistics")
14318 "This package provides tools for circular statistics, from \"Topics in
14319 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
14321 (license license:gpl2+)))
14323 (define-public r-activity
14325 (name "r-activity")
14330 (uri (cran-uri "activity" version))
14333 "11n6wmqz7p3428rr615f92m61a5gb908xpn4l8q484h61bwg38c3"))))
14334 (build-system r-build-system)
14336 (list r-insol r-pbapply))
14337 (home-page "https://cran.r-project.org/web/packages/activity/")
14338 (synopsis "Animal activity statistics")
14340 "This package provides functions to fit kernel density functions to
14341 animal activity time data; plot activity distributions; quantify overall
14342 levels of activity; statistically compare activity metrics through
14343 bootstrapping; and evaluate variation in linear variables with time (or other
14344 circular variables).")
14345 (license license:gpl3)))
14347 (define-public r-ouch
14354 (uri (cran-uri "ouch" version))
14357 "119s9llpjy0b4q830xig2xr66fq6izp6mr2k4k79ggmf3gxww8as"))))
14358 (build-system r-build-system)
14359 (propagated-inputs (list r-subplex))
14360 (home-page "https://kingaa.github.io/ouch/")
14361 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
14363 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
14364 for evolution along a phylogenetic tree.")
14365 (license license:gpl2+)))
14367 (define-public r-fmri
14373 (uri (cran-uri "fmri" version))
14376 "1wh77xwpm8f9d9vky3r7vfmkik3hls008ifk8hkm2rq6i06jj53n"))))
14377 (properties `((upstream-name . "fmri")))
14378 (build-system r-build-system)
14379 (propagated-inputs (list r-aws r-metafor r-nlme))
14380 (native-inputs (list gfortran))
14381 (home-page "http://www.wias-berlin.de/software/imaging/")
14382 (synopsis "Analysis of fMRI experiments")
14384 "This package contains R-functions to perform an fMRI analysis as
14385 described in Polzehl and Tabelow (2019) <DOI:10.1007/978-3-030-29184-6>,
14386 Tabelow et al. (2006) <DOI:10.1016/j.neuroimage.2006.06.029>, Polzehl et
14387 al. (2010) <DOI:10.1016/j.neuroimage.2010.04.241>, Tabelow and Polzehl (2011)
14388 <DOI:10.18637/jss.v044.i11>.")
14389 (license license:gpl2+)))
14391 (define-public r-fmsb
14398 (uri (cran-uri "fmsb" version))
14401 "1gi94xr0b1yk9xzwfprfafxi25yic1lcivd66p73n6iqfzdaimbk"))))
14402 (build-system r-build-system)
14403 (home-page "http://minato.sip21c.org/msb/")
14404 (synopsis "Functions for medical statistics book with demographic data")
14406 "This package provides several utility functions for the book entitled
14407 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
14408 Japan, 2007) with Japanese demographic data and some demographic analysis
14409 related functions.")
14410 (license license:gpl2+)))
14412 (define-public r-stabledist
14414 (name "r-stabledist")
14419 (uri (cran-uri "stabledist" version))
14422 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
14423 (build-system r-build-system)
14424 (home-page "https://www.rmetrics.org")
14425 (synopsis "Stable distribution functions")
14427 "This package provides density, probability and quantile functions, and
14428 random number generation for (skew) stable distributions, using the
14429 parametrizations of Nolan.")
14430 (license license:gpl2+)))
14432 (define-public r-gsl
14435 (version "2.1-7.1")
14439 (uri (cran-uri "gsl" version))
14442 "118rj9kjx9rzlynvhrly19qz3yxg8jzws35971ssgzrp5lwd367f"))))
14443 (build-system r-build-system)
14446 (home-page "https://cran.r-project.org/web/packages/gsl")
14447 (synopsis "Wrapper for the GNU Scientific Library")
14449 "This package provides an R wrapper for the special functions and quasi
14450 random number generators of the GNU Scientific Library.")
14451 (license license:gpl2+)))
14453 (define-public r-adgoftest
14455 (name "r-adgoftest")
14460 (uri (cran-uri "ADGofTest" version))
14463 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
14464 (properties `((upstream-name . "ADGofTest")))
14465 (build-system r-build-system)
14466 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
14467 (synopsis "Anderson-Darling GoF test")
14469 "This package provides an implementation of the Anderson-Darling GoF test
14470 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
14471 Anderson-Darling Distribution\".")
14472 ;; Any version of the GPL.
14473 (license license:gpl3+)))
14475 (define-public r-adimpro
14481 (uri (cran-uri "adimpro" version))
14484 "0njw38vcdm02sni193nj10mpv7hiklpamrkjlz5bnhjxx9mvf4cl"))))
14485 (properties `((upstream-name . "adimpro")))
14486 (build-system r-build-system)
14490 (native-inputs (list gfortran))
14491 (home-page "https://www.wias-berlin.de/software/imaging/")
14492 (synopsis "Adaptive smoothing of digital images")
14494 "This package implements tools for manipulation of digital images and the
14495 Propagation Separation approach by Polzehl and Spokoiny (2006)
14496 <DOI:10.1007/s00440-005-0464-1> for smoothing digital images, see Polzehl and
14497 Tabelow (2007) <DOI:10.18637/jss.v019.i01>.")
14498 (license license:gpl2+)))
14500 (define-public r-admisc
14507 (uri (cran-uri "admisc" version))
14509 (base32 "01b2qjxz0qicqjm1swvm04qkiwhr7zjn7lhqv26l6rj4yb43y339"))))
14510 (properties `((upstream-name . "admisc")))
14511 (build-system r-build-system)
14512 (home-page "https://github.com/dusadrian/admisc")
14513 (synopsis "Adrian Dusa's miscellaneous")
14515 "This package contains miscellaneous functions used to interpret and
14516 translate, factorize and negate Sum of Products expressions, for both binary
14517 and multi-value crisp sets, and to extract information (set names, set values)
14518 from those expressions. Other functions perform various other checks if
14519 possibly numeric (even if all numbers reside in a character vector) and coerce
14520 to numeric, or check if the numbers are whole. It also offers, among many
14521 others, a highly flexible recoding routine and a more flexible alternative to
14522 the base function @code{with()}.")
14523 (license license:gpl3+)))
14525 (define-public r-oro-nifti
14527 (name "r-oro-nifti")
14531 (uri (cran-uri "oro.nifti" version))
14534 "01mn90qxb7i15zr83xrl2cn4akayfzpm83r5x71zczz3qb9gbr7g"))))
14535 (properties `((upstream-name . "oro.nifti")))
14536 (build-system r-build-system)
14537 (propagated-inputs (list r-abind r-bitops r-rnifti))
14538 (home-page "https://rigorousanalytics.blogspot.com")
14539 (synopsis "Vizualization of medical imaging data")
14541 "This package provides functions for the input/output and visualization
14542 of medical imaging data that follow either the ANALYZE, NIfTI or AFNI formats.
14543 This package is part of the Rigorous Analytics bundle.")
14544 (license license:bsd-3)))
14546 (define-public r-mritc
14552 (uri (cran-uri "mritc" version))
14555 "07b1b2k1ka43ikj2mhwnazw3ig7w10bf759fimxpksvk5k6wanx2"))))
14556 (properties `((upstream-name . "mritc")))
14557 (build-system r-build-system)
14558 (propagated-inputs (list r-lattice r-misc3d r-oro-nifti))
14559 (home-page "https://cran.r-project.org/package=mritc")
14560 (synopsis "MRI tissue classification")
14561 (description "This package provides various methods for MRI tissue
14563 ;; Any version of the GPL.
14564 (license license:gpl3+)))
14566 (define-public r-sodium
14573 (uri (cran-uri "sodium" version))
14576 "1a03z2asvmalnmsn89lapzp8a4fr0qvzdv3xgin8pbqhjyb9hvpp"))))
14577 (properties `((upstream-name . "sodium")))
14578 (build-system r-build-system)
14582 (list pkg-config r-knitr))
14583 (home-page "https://github.com/jeroen/sodium")
14584 (synopsis "R bindings to the libsodium crypto library")
14586 "This package provides bindings to libsodium: a library for encryption,
14587 decryption, signatures, password hashing and more. Sodium uses curve25519, a
14588 Diffie-Hellman function by Daniel Bernstein, which has become very popular
14589 after it was discovered that the NSA had backdoored Dual EC DRBG.")
14590 (license license:expat)))
14592 (define-public r-softimpute
14594 (name "r-softimpute")
14599 (uri (cran-uri "softImpute" version))
14602 "1v2a4d688ij5zcvkzpra9yx40xckdfnllnfnyq2450zf3n1kjk7a"))))
14603 (properties `((upstream-name . "softImpute")))
14604 (build-system r-build-system)
14608 (list gfortran r-knitr))
14609 (home-page "https://cran.r-project.org/web/packages/softImpute")
14610 (synopsis "Matrix completion via iterative soft-thresholded SVD")
14612 "This package provides iterative methods for matrix completion that use
14613 nuclear-norm regularization. The package includes procedures for centering
14614 and scaling rows, columns or both, and for computing low-rank @dfn{single
14615 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
14617 (license license:gpl2)))
14619 (define-public r-fftwtools
14621 (name "r-fftwtools")
14626 (uri (cran-uri "fftwtools" version))
14629 "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i"))))
14630 (build-system r-build-system)
14631 (inputs (list fftw))
14634 (home-page "https://github.com/krahim/fftwtools")
14635 (synopsis "Wrapper for FFTW3")
14637 "This package provides a wrapper for several FFTW functions. It provides
14638 access to the two-dimensional FFT, the multivariate FFT, and the
14639 one-dimensional real to complex FFT using the FFTW3 library. The package
14640 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
14641 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
14642 The FFT functions have a parameter that allows them to not return the
14643 redundant complex conjugate when the input is real data.")
14644 (license license:gpl2+)))
14646 (define-public r-tiff
14653 (uri (cran-uri "tiff" version))
14656 "0xgc7vyndxxahfhc2qqzmwi56bnfyl0pn72l820jz5sd24aymhxq"))))
14657 (build-system r-build-system)
14659 (list libtiff libjpeg-turbo zlib))
14662 (home-page "https://www.rforge.net/tiff/")
14663 (synopsis "Read and write TIFF images")
14665 "This package provides an easy and simple way to read, write and display
14666 bitmap images stored in the TIFF format. It can read and write both files and
14667 in-memory raw vectors.")
14668 ;; Either of these two license versions.
14669 (license (list license:gpl2 license:gpl3))))
14671 (define-public r-nlp
14678 (uri (cran-uri "NLP" version))
14681 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5"))))
14682 (properties `((upstream-name . "NLP")))
14683 (build-system r-build-system)
14684 (home-page "https://cran.r-project.org/web/packages/NLP/")
14685 (synopsis "Natural language processing infrastructure")
14687 "This package provides basic classes and methods for Natural Language
14689 (license license:gpl3)))
14691 (define-public r-tm
14698 (uri (cran-uri "tm" version))
14701 "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi"))))
14702 (properties `((upstream-name . "tm")))
14703 (build-system r-build-system)
14705 (list r-bh r-nlp r-rcpp r-slam r-xml2))
14706 (home-page "http://tm.r-forge.r-project.org/")
14707 (synopsis "Text mining package")
14709 "This package provides a framework for text mining applications within R.")
14710 (license license:gpl3)))
14712 (define-public r-waveslim
14714 (name "r-waveslim")
14719 (uri (cran-uri "waveslim" version))
14722 "1510xpkgrhdw394m5anxccdczjikcxazyd09ix2z73i15akyx3j0"))))
14723 (build-system r-build-system)
14726 (home-page "http://waveslim.blogspot.com")
14727 (synopsis "Basic wavelet routines for signal processing")
14729 "This package provides basic wavelet routines for time series (1D),
14730 image (2D) and array (3D) analysis. The code provided here is based on
14731 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
14732 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
14733 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
14734 pairs (Selesnick 2001, 2002).")
14735 (license license:bsd-3)))
14737 (define-public r-wordcloud
14739 (name "r-wordcloud")
14744 (uri (cran-uri "wordcloud" version))
14747 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
14748 (build-system r-build-system)
14750 (list r-rcolorbrewer r-rcpp
14751 ;; The "tm" package is only "suggested" according to CRAN, but the
14752 ;; wordcloud package cannot be loaded without it.
14754 (home-page "https://cran.r-project.org/web/packages/wordcloud")
14755 (synopsis "Word clouds")
14757 "This package provides functionality to create pretty word clouds,
14758 visualize differences and similarity between documents, and avoid
14759 over-plotting in scatter plots with text.")
14760 (license license:lgpl2.1)))
14762 (define-public r-colorramps
14764 (name "r-colorramps")
14769 (uri (cran-uri "colorRamps" version))
14772 "12jnkj50yh2hc5l7j56lrrrmn58akrj9dwj98vzf42iq4h42kwb1"))))
14773 (properties `((upstream-name . "colorRamps")))
14774 (build-system r-build-system)
14775 (home-page "https://cran.r-project.org/web/packages/colorRamps")
14776 (synopsis "Build color tables")
14777 (description "This package provides features to build gradient color
14779 ;; Any version of the GPL
14780 (license license:gpl3+)))
14782 (define-public r-tidytree
14784 (name "r-tidytree")
14789 (uri (cran-uri "tidytree" version))
14791 (base32 "0dm71zdrb1qwaja23jlzjpraa609b6yxl8bhksz8slgpfm1jgs00"))))
14792 (build-system r-build-system)
14806 (home-page "https://github.com/GuangchuangYu/tidytree")
14807 (synopsis "Tidy tool for phylogenetic tree data manipulation")
14809 "Phylogenetic trees generally contain multiple components including nodes,
14810 edges, branches and associated data. This package provides an approach to
14811 convert tree objects to tidy data frames. It also provides tidy interfaces to
14812 manipulate tree data.")
14813 (license license:artistic2.0)))
14815 (define-public r-rvcheck
14822 (uri (cran-uri "rvcheck" version))
14824 (base32 "09khjklvzbafd7r55496by01a9g3y291d87hpy43w44dmz9fzn9a"))))
14825 (build-system r-build-system)
14827 (list r-biocmanager r-yulab-utils))
14828 (home-page "https://cran.r-project.org/web/packages/rvcheck")
14829 (synopsis "R package version check")
14831 "This package provides tools to check the latest release version of R and
14832 R packages (on CRAN, Bioconductor or Github).")
14833 (license license:artistic2.0)))
14835 (define-public r-docopt
14842 (uri (cran-uri "docopt" version))
14845 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
14846 (build-system r-build-system)
14847 (home-page "https://github.com/docopt/docopt.R")
14848 (synopsis "Command-line interface specification language")
14850 "This package enables you to define a command-line interface by just
14851 giving it a description in the specific format.")
14852 (license license:expat)))
14854 (define-public r-sparsesvd
14856 (name "r-sparsesvd")
14861 (uri (cran-uri "sparsesvd" version))
14864 "0yz0mgayxriyrz6bbrd41cck0s56b916xvyh13hw86gydd6kpl5k"))))
14865 (build-system r-build-system)
14866 (propagated-inputs (list r-matrix))
14867 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
14868 (synopsis "Sparse truncated singular value decomposition")
14870 "This package provides a Wrapper around the SVDLIBC library
14871 for (truncated) singular value decomposition of a sparse matrix. Currently,
14872 only sparse real matrices in Matrix package format are supported.")
14873 ;; SVDLIBC is released under BSD-2. The R interface is released under
14875 (license (list license:bsd-3 license:bsd-2))))
14877 (define-public r-speedglm
14879 (name "r-speedglm")
14884 (uri (cran-uri "speedglm" version))
14887 "1kj662nfkfhvx37jrbvxd4dyjclz5cm3xh50z7s5rbzapiyxn4hs"))))
14888 (build-system r-build-system)
14890 (list r-mass r-matrix))
14891 (home-page "https://cran.r-project.org/web/packages/speedglm")
14892 (synopsis "Fit linear and generalized linear models to large data sets")
14894 "This package provides tools for fitting linear models and generalized
14895 linear models to large data sets by updating algorithms.")
14896 ;; Any version of the GPL
14897 (license license:gpl2+)))
14899 (define-public r-densityclust
14901 (name "r-densityclust")
14906 (uri (cran-uri "densityClust" version))
14909 "05x2fi1zdnkrg2nimf8k904j3lpyw0f7nmk6ax5p7x7a98wb2iqs"))))
14910 (properties `((upstream-name . "densityClust")))
14911 (build-system r-build-system)
14920 (home-page "https://cran.r-project.org/web/packages/densityClust")
14921 (synopsis "Clustering by fast search and find of density peaks")
14923 "This package provides an improved implementation (based on k-nearest
14924 neighbors) of the density peak clustering algorithm, originally described by
14925 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
14926 large datasets (> 100,000 samples) very efficiently.")
14927 (license license:gpl2+)))
14929 (define-public r-combinat
14931 (name "r-combinat")
14936 (uri (cran-uri "combinat" version))
14939 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
14940 (build-system r-build-system)
14941 (home-page "https://cran.r-project.org/web/packages/combinat")
14942 (synopsis "Combinatorics utilities")
14943 (description "This package provides assorted routines for combinatorics.")
14944 (license license:gpl2)))
14946 (define-public r-qlcmatrix
14948 (name "r-qlcmatrix")
14953 (uri (cran-uri "qlcMatrix" version))
14956 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
14957 (properties `((upstream-name . "qlcMatrix")))
14958 (build-system r-build-system)
14960 (list r-docopt r-matrix r-slam r-sparsesvd))
14961 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
14962 (synopsis "Sparse matrix functions for quantitative language comparison")
14964 "This package provides an extension of the functionality of the Matrix
14965 package for using sparse matrices. Some of the functions are very general,
14966 while other are highly specific for the special data format used for
14967 @dfn{quantitative language comparison} (QLC).")
14968 (license license:gpl3)))
14970 (define-public r-qmri
14976 (uri (cran-uri "qMRI" version))
14979 "10x59g8awxjib5j5mc1yd5wsibk3z6ki6zifxsg8azl0zblxbscf"))))
14980 (properties `((upstream-name . "qMRI")))
14981 (build-system r-build-system)
14982 (propagated-inputs (list r-adimpro r-aws r-awsmethods r-oro-nifti
14984 (native-inputs (list gfortran r-knitr))
14985 (home-page "http://www.wias-berlin.de/research/ats/imaging/")
14986 (synopsis "Methods for quantitative magnetic resonance imaging (qMRI)")
14988 "This package provides implementation of methods for estimation of
14989 quantitative maps from @dfn{Multi-Parameter Mapping} (MPM) acquisitions
14990 including adaptive smoothing methods in the framework of the ESTATICS model.
14991 The smoothing method is described in Mohammadi et
14992 al. (2017). <doi:10.20347/WIAS.PREPRINT.2432>. Usage of the package is also
14993 described in Polzehl and Tabelow (2019), Magnetic Resonance Brain Imaging,
14994 Chapter 6, Springer, Use R! Series. <doi:10.1007/978-3-030-29184-6_6>.")
14995 (license license:gpl2+)))
14997 (define-public r-ddrtree
15004 (uri (cran-uri "DDRTree" version))
15007 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
15008 (properties `((upstream-name . "DDRTree")))
15009 (build-system r-build-system)
15011 (list r-bh r-irlba r-rcpp r-rcppeigen))
15012 (home-page "https://cran.r-project.org/web/packages/DDRTree")
15013 (synopsis "Learning principal graphs with DDRTree")
15015 "This package provides an implementation of the framework of
15016 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
15017 dimensional space while constructs a principal tree which passes through the
15018 middle of the data simultaneously. DDRTree shows superiority to
15019 alternatives (Wishbone, DPT) for inferring the ordering as well as the
15020 intrinsic structure of single cell genomics data. In general, it could be
15021 used to reconstruct the temporal progression as well as the bifurcation
15022 structure of any data type.")
15023 (license license:asl2.0)))
15025 (define-public r-corpcor
15032 (uri (cran-uri "corpcor" version))
15035 "028fw61n61i79fhnaqx7gmdifdpbvp3yiaq9vvfrbv4k7i84r83i"))))
15036 (build-system r-build-system)
15037 (home-page "http://strimmerlab.org/software/corpcor/")
15038 (synopsis "Efficient estimation of covariance and (partial) correlation")
15040 "This package implements a James-Stein-type shrinkage estimator for the
15041 covariance matrix, with separate shrinkage for variances and correlations.
15042 Furthermore, functions are available for fast singular value decomposition,
15043 for computing the pseudoinverse, and for checking the rank and positive
15044 definiteness of a matrix.")
15045 (license license:gpl3+)))
15047 (define-public r-rspectra
15049 (name "r-rspectra")
15054 (uri (cran-uri "RSpectra" version))
15057 "16ij84wgpsmqmnxqiii8dgihy3bfxazry9znmckhwzba7m0d79fb"))))
15058 (properties `((upstream-name . "RSpectra")))
15059 (build-system r-build-system)
15061 (list r-matrix r-rcpp r-rcppeigen))
15064 (home-page "https://github.com/yixuan/RSpectra")
15065 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
15067 "This package provides an R interface to the Spectra library for
15068 large-scale eigenvalue and SVD problems. It is typically used to compute a
15069 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
15070 which is usually more efficient than @code{eigen()} if k << n.")
15072 (license license:mpl2.0)))
15074 (define-public r-vbsr
15081 (uri (cran-uri "vbsr" version))
15084 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
15085 (build-system r-build-system)
15086 (home-page "https://cran.r-project.org/web/packages/vbsr")
15087 (synopsis "Variational Bayes spike regression regularized linear models")
15089 "This package provides an efficient algorithm for solving ultra-sparse
15090 regularized regression models using a variational Bayes algorithm with a spike
15091 prior. The algorithm is solved on a path, with coordinate updates, and is
15092 capable of generating very sparse models. Very general model
15093 diagnostics for controlling type-1 errors are also provided.")
15094 (license license:gpl2)))
15096 (define-public r-flare
15099 (version "1.7.0.1")
15103 (uri (cran-uri "flare" version))
15106 "1xvrbvq2y7zfp98ijal3z8y1w2xbzfcdykzw4pqc3mnh0qrhq2d5"))))
15107 (build-system r-build-system)
15109 (list r-igraph r-lattice r-mass r-matrix))
15110 (home-page "https://cran.r-project.org/web/packages/flare")
15111 (synopsis "Family of Lasso regression implementations")
15113 "This package provides implementations of a family of Lasso variants
15114 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
15115 high dimensional sparse linear models.")
15116 (license license:gpl2)))
15118 (define-public r-lassopv
15125 (uri (cran-uri "lassopv" version))
15128 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
15129 (build-system r-build-system)
15130 (propagated-inputs (list r-lars))
15131 (home-page "https://github.com/lingfeiwang/lassopv")
15132 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
15134 "This package enables you to estimate the p-values for predictors x
15135 against target variable y in Lasso regression, using the regularization
15136 strength when each predictor enters the active set of regularization path for
15137 the first time as the statistic.")
15138 (license license:gpl3)))
15140 (define-public r-splitstackshape
15142 (name "r-splitstackshape")
15147 (uri (cran-uri "splitstackshape" version))
15150 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
15151 (build-system r-build-system)
15153 (list r-data-table))
15154 (home-page "https://github.com/mrdwab/splitstackshape")
15155 (synopsis "Stack and reshape datasets after splitting concatenated values")
15157 "Online data collection tools like Google Forms often export
15158 multiple-response questions with data concatenated in cells. The
15159 @code{concat.split} (cSplit) family of functions provided by this package
15160 splits such data into separate cells. This package also includes functions to
15161 stack groups of columns and to reshape wide data, even when the data are
15162 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
15163 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
15165 (license license:gpl3)))
15167 (define-public r-tfmpvalue
15169 (name "r-tfmpvalue")
15174 (uri (cran-uri "TFMPvalue" version))
15177 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
15178 (properties `((upstream-name . "TFMPvalue")))
15179 (build-system r-build-system)
15180 (propagated-inputs (list r-rcpp))
15181 (home-page "https://github.com/ge11232002/TFMPvalue")
15182 (synopsis "P-value computation for position weight matrices")
15184 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
15185 identification from sequence/alignments, we are interested in the significance
15186 of certain match scores. TFMPvalue provides the accurate calculation of a
15187 p-value with a score threshold for position weight matrices, or the score with
15188 a given p-value. It is an interface to code originally made available by
15189 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
15190 Touzet and Varre (2007).")
15191 (license license:gpl2)))
15193 (define-public r-rncl
15199 (uri (cran-uri "rncl" version))
15202 "1ywgwqn82z8h6zpcxxq4hgngdpfa6dj0lr7bfq4cwfml9z075jgw"))))
15203 (build-system r-build-system)
15205 (list r-progress r-rcpp))
15206 (home-page "https://github.com/fmichonneau/rncl")
15207 (synopsis "Interface to the Nexus class library")
15208 (description "This package provides an interface to the Nexus class
15209 library which allows parsing of NEXUS, Newick and other phylogenetic tree
15210 file formats. It provides elements of the file that can be used to build
15211 phylogenetic objects such as @code{ape}'s @code{phylo} or @code{phylobase}'s
15212 @code{phylo4(d)}. This functionality is demonstrated with
15213 @code{read_newick_phylo()} and @code{read_nexus_phylo()}.")
15214 (license license:bsd-2)))
15216 (define-public r-phylobase
15218 (name "r-phylobase")
15222 (uri (cran-uri "phylobase" version))
15225 "0jzr1gdvmi4l640hwwzh9bxqmpja69bn3ygnaqx37awvyh7khi2s"))))
15226 (build-system r-build-system)
15228 (list r-ade4 r-ape r-rcpp r-rncl r-rnexml))
15231 (home-page "https://github.com/fmichonneau/phylobase")
15232 (synopsis "Base package for phylogenetic structures and comparative data")
15233 (description "This package provides a base @code{S4} class for comparative
15234 methods, incorporating one or more trees and trait data.")
15235 (license license:gpl2+)))
15237 (define-public r-phylotools
15239 (name "r-phylotools")
15243 (uri (cran-uri "phylotools" version))
15246 "1dhk1ncp5zi4zl1xfnjz64v983dm7bq7iimfjin80j0bdcpps44w"))))
15247 (properties `((upstream-name . "phylotools")))
15248 (build-system r-build-system)
15249 (propagated-inputs (list r-ape))
15250 (home-page "https://github.com/helixcn/phylotools")
15251 (synopsis "Phylogenetic tools for eco-phylogenetics")
15253 "This package provides a collection of tools for building RAxML
15254 supermatrix using PHYLIP or aligned FASTA files. These functions will be
15255 useful for building large phylogenies using multiple markers.")
15256 (license license:gpl2)))
15258 (define-public r-rnexml
15264 (uri (cran-uri "RNeXML" version))
15267 "1zp6pijsc73jx8cmxb1hng36nvaf5wnhldnzlqhmba9kv9niscfb"))))
15268 (build-system r-build-system)
15285 (home-page "https://docs.ropensci.org/RNeXML/")
15286 (synopsis "Semantically rich I/O for the NeXML Format")
15287 (description "This package provides access to phyloinformatic data in
15288 NeXML format. The package should add new functionality to R such as the
15289 possibility to manipulate NeXML objects in more various and refined way
15290 and compatibility with @code{ape} objects.")
15291 (license license:bsd-3)))
15293 (define-public r-rnifti
15300 (uri (cran-uri "RNifti" version))
15303 "058jzhw91wd4hb9l06mn0ihf1yp2fapz1fyb32w9bjwxq7qxvii2"))))
15304 (properties `((upstream-name . "RNifti")))
15305 (build-system r-build-system)
15306 (inputs (list zlib))
15307 (propagated-inputs (list r-rcpp))
15308 (home-page "https://github.com/jonclayden/RNifti")
15309 (synopsis "Fast R and C++ access to NIfTI images")
15311 "This package provides very fast read and write access to images stored
15312 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
15313 compiled C and interpreted R code. It also provides a C/C++ API that can be
15314 used by other packages.")
15315 (license license:gpl2)))
15317 (define-public r-shades
15324 (uri (cran-uri "shades" version))
15327 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
15328 (build-system r-build-system)
15329 (home-page "https://github.com/jonclayden/shades")
15330 (synopsis "Simple color manipulation")
15332 "This package provides functions for easily manipulating colors,
15333 creating color scales and calculating color distances.")
15334 (license license:bsd-3)))
15336 (define-public r-ore
15339 (version "1.7.1.1")
15343 (uri (cran-uri "ore" version))
15345 (base32 "0rs5r5h11x4l4nsbl4xqzbl4ahajd5374fq05abcmfjnjr9j64w5"))))
15346 (build-system r-build-system)
15347 (home-page "https://github.com/jonclayden/ore")
15348 (synopsis "R interface to the Onigmo regular expression library")
15350 "This package provides an alternative to R's built-in functionality for
15351 handling regular expressions, based on the Onigmo library. It offers
15352 first-class compiled regex objects, partial matching and function-based
15353 substitutions, amongst other features.")
15354 (license license:bsd-3)))
15356 (define-public r-reportr
15363 (uri (cran-uri "reportr" version))
15366 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
15367 (build-system r-build-system)
15368 (propagated-inputs (list r-ore))
15369 (home-page "https://github.com/jonclayden/reportr")
15370 (synopsis "General message and error reporting system")
15372 "This package provides a system for reporting messages, which offers
15373 certain useful features over the standard R system, such as the incorporation
15374 of output consolidation, message filtering, assertions, expression
15375 substitution, automatic generation of stack traces for debugging, and
15376 conditional reporting based on the current \"output level\".")
15377 (license license:gpl2)))
15379 (define-public r-tractor-base
15381 (name "r-tractor-base")
15382 (version "3.3.5.1")
15386 (uri (cran-uri "tractor.base" version))
15389 "0fxbzbhpi6l55m14nmww8y3kdxgchzj4mw1yf4xkm2y6s68phvgc"))))
15390 (properties `((upstream-name . "tractor.base")))
15391 (build-system r-build-system)
15393 (list r-ore r-reportr r-rnifti r-shades))
15394 (home-page "https://www.tractor-mri.org.uk")
15395 (synopsis "Read, manipulate and visualize magnetic resonance images")
15397 "This package provides functions for working with magnetic resonance
15398 images. It supports reading and writing of popular file formats (DICOM,
15399 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
15400 visualization; flexible image manipulation; metadata and sparse image
15402 (license license:gpl2)))
15404 (define-public r-grimport
15406 (name "r-grimport")
15411 (uri (cran-uri "grImport" version))
15414 "0pbzc45wgp0cpycnw0bzn65ckdszzay0zrp7c7ssxdkifp8bai3a"))))
15415 (properties `((upstream-name . "grImport")))
15416 (build-system r-build-system)
15418 (list ghostscript))
15421 (home-page "https://cran.r-project.org/web/packages/grImport")
15422 (synopsis "Convert, import, and draw PostScript pictures")
15424 "This package provides functions for converting, importing, and drawing
15425 PostScript pictures in R plots.")
15426 (license license:gpl2+)))
15428 (define-public r-grimport2
15430 (name "r-grimport2")
15435 (uri (cran-uri "grImport2" version))
15438 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
15439 (properties `((upstream-name . "grImport2")))
15440 (build-system r-build-system)
15442 (list r-base64enc r-jpeg r-png r-xml))
15443 (home-page "https://cran.r-project.org/web/packages/grImport2/")
15444 (synopsis "Import SVG graphics")
15446 "This package provides functions for importing external vector images and
15447 drawing them as part of R plots. This package is different from the
15448 @code{grImport} package because, where that package imports PostScript format
15449 images, this package imports SVG format images. Furthermore, this package
15450 imports a specific subset of SVG, so external images must be preprocessed
15451 using a package like @code{rsvg} to produce SVG that this package can import.
15452 SVG features that are not supported by R graphics, such as gradient fills, can
15453 be imported and then exported via the @code{gridSVG} package.")
15454 (license license:gpl2+)))
15456 (define-public r-kohonen
15463 (uri (cran-uri "kohonen" version))
15466 "1bk3j0n8w4fhffv89rgyn4n21c0wcx6lr8jv4wbagpxprl585381"))))
15467 (build-system r-build-system)
15470 (home-page "https://cran.r-project.org/web/packages/kohonen")
15471 (synopsis "Supervised and unsupervised self-organising maps")
15473 "This package provides functions to train @dfn{self-organising
15474 maps} (SOMs). Also interrogation of the maps and prediction using trained
15475 maps are supported. The name of the package refers to Teuvo Kohonen, the
15476 inventor of the SOM.")
15477 (license license:gpl2+)))
15479 (define-public r-nnls
15486 (uri (cran-uri "nnls" version))
15489 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
15490 (build-system r-build-system)
15491 (native-inputs (list gfortran))
15492 (home-page "https://cran.r-project.org/web/packages/nnls")
15493 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
15495 "This package provides an R interface to the Lawson-Hanson implementation
15496 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
15497 the combination of non-negative and non-positive constraints.")
15498 (license license:gpl2+)))
15500 (define-public r-iso
15503 (version "0.0-18.1")
15507 (uri (cran-uri "Iso" version))
15510 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
15511 (properties `((upstream-name . "Iso")))
15512 (build-system r-build-system)
15513 (native-inputs (list gfortran))
15514 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
15515 (synopsis "Functions to perform isotonic regression")
15517 "This package provides support for linear order and unimodal
15518 order (univariate) isotonic regression and bivariate isotonic regression with
15519 linear order on both variables.")
15520 (license license:gpl2+)))
15522 (define-public r-chemometricswithr
15524 (name "r-chemometricswithr")
15529 (uri (cran-uri "ChemometricsWithR" version))
15532 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
15534 `((upstream-name . "ChemometricsWithR")))
15535 (build-system r-build-system)
15537 (list r-devtools r-kohonen r-mass r-pls))
15538 (home-page "https://github.com/rwehrens/CWR")
15539 (synopsis "Chemometrics with R")
15541 "This package provides functions and scripts used in the book
15542 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
15543 Life Sciences\" by Ron Wehrens, Springer (2011).")
15544 (license license:gpl2+)))
15546 (define-public r-als
15553 (uri (cran-uri "ALS" version))
15556 "184d6xr4mgs78jvi7xa4njrq6p625i9sx69wak6mdn53qpl9b8ap"))))
15557 (properties `((upstream-name . "ALS")))
15558 (build-system r-build-system)
15560 (list r-iso r-nnls))
15561 (home-page "https://cran.r-project.org/web/packages/ALS")
15562 (synopsis "Multivariate curve resolution alternating least squares")
15564 "Alternating least squares is often used to resolve components
15565 contributing to data with a bilinear structure; the basic technique may be
15566 extended to alternating constrained least squares. This package provides an
15567 implementation of @dfn{multivariate curve resolution alternating least
15568 squares} (MCR-ALS).
15570 Commonly applied constraints include unimodality, non-negativity, and
15571 normalization of components. Several data matrices may be decomposed
15572 simultaneously by assuming that one of the two matrices in the bilinear
15573 decomposition is shared between datasets.")
15574 (license license:gpl2+)))
15576 (define-public r-strucchange
15578 (name "r-strucchange")
15583 (uri (cran-uri "strucchange" version))
15586 "11hgz64snlwhfqsmqajmkciflwkz1wficxr340wqvk38iw1b9ina"))))
15587 (build-system r-build-system)
15589 (list r-sandwich r-zoo))
15590 (home-page "https://cran.r-project.org/web/packages/strucchange")
15591 (synopsis "Testing, monitoring, and dating structural changes")
15593 "This package provides tools for testing, monitoring and dating
15594 structural changes in (linear) regression models. It features tests/methods
15595 from the generalized fluctuation test framework as well as from the F
15596 test (Chow test) framework. This includes methods to fit, plot and test
15597 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
15598 statistics, respectively. It is possible to monitor incoming data online
15599 using fluctuation processes. Finally, the breakpoints in regression models
15600 with structural changes can be estimated together with confidence intervals.
15601 Emphasis is always given to methods for visualizing the data.")
15602 ;; Either of these two GPL versions
15603 (license (list license:gpl2 license:gpl3))))
15605 (define-public r-pixmap
15612 (uri (cran-uri "pixmap" version))
15615 "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9"))))
15616 (build-system r-build-system)
15617 (home-page "https://cran.r-project.org/web/packages/pixmap")
15618 (synopsis "Tools for bitmap images")
15620 "This package provides functions for importing, exporting, plotting and
15621 other manipulations of bitmapped images.")
15622 (license license:gpl2)))
15624 (define-public r-rapidjsonr
15626 (name "r-rapidjsonr")
15631 (uri (cran-uri "rapidjsonr" version))
15634 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
15635 (build-system r-build-system)
15636 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
15637 (synopsis "JSON parser")
15639 "This package provides JSON parsing capability through the Rapidjson
15641 (license license:expat)))
15643 (define-public r-ontologyindex
15645 (name "r-ontologyindex")
15650 (uri (cran-uri "ontologyIndex" version))
15653 "0hisb9scxyyqkxhxhvgsgwix54pkq0zma3xq3ywczyazvzcxd5f9"))))
15654 (properties `((upstream-name . "ontologyIndex")))
15655 (build-system r-build-system)
15658 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
15659 (synopsis "Functions for processing ontologies in R")
15661 "This package provides functions for reading ontologies into R as lists
15662 and manipulating sets of ontological terms.")
15663 (license license:gpl2+)))
15665 (define-public r-gargle
15672 (uri (cran-uri "gargle" version))
15675 "087hlbqpwjj7jnsg1ax2b12nc0h4zfj070q5hjp6fca05z4f4rzk"))))
15676 (build-system r-build-system)
15689 (home-page "https://gargle.r-lib.org")
15690 (synopsis "Utilities for working with Google APIs")
15692 "This package provides utilities for working with Google APIs. This
15693 includes functions and classes for handling common credential types and for
15694 preparing, executing, and processing HTTP requests.")
15695 (license license:expat)))
15697 (define-public r-bigrquery
15699 (name "r-bigrquery")
15704 (uri (cran-uri "bigrquery" version))
15707 "02msq61l7vamzpvbhvalh3qil1aa7pr68pwpsivbb6pvz6p4zyns"))))
15708 (build-system r-build-system)
15725 (home-page "https://github.com/rstats-db/bigrquery")
15726 (synopsis "R interface to Google's BigQuery API")
15728 "This package provides an R interface to Google's BigQuery database.")
15729 (license license:gpl3)))
15731 (define-public r-gmp
15738 (uri (cran-uri "gmp" version))
15741 "14r7xlxjrwww6l726sispq6jhxy2yfwbcqrqgc9x4ma812l9byl7"))))
15742 (build-system r-build-system)
15745 (modify-phases %standard-phases
15746 (add-after 'unpack 'set-CC
15747 (lambda _ (setenv "CC" "gcc") #t)))))
15748 (inputs (list gmp))
15749 (home-page "https://cran.r-project.org/web/packages/gmp")
15750 (synopsis "Multiple precision arithmetic")
15752 "This package supports multiple precision arithmetic (big integers and
15753 rationals, prime number tests, matrix computation), \"arithmetic without
15754 limitations\" using the GNU Multiple Precision library.")
15755 ;; Any version of the GPL.
15756 (license license:gpl3+)))
15758 (define-public r-rmpfr
15765 (uri (cran-uri "Rmpfr" version))
15768 "12mwvgyalzh4zf5d002fm1hpr3wwhiypy9ia6wy47ij9gns5mvng"))))
15769 (properties `((upstream-name . "Rmpfr")))
15770 (build-system r-build-system)
15777 (home-page "http://rmpfr.r-forge.r-project.org/")
15778 (synopsis "R bindings to the MPFR library")
15780 "This package supports arithmetic (via S4 classes and methods) for
15781 arbitrary precision floating point numbers, including transcendental
15782 functions. To this end, the package interfaces with the @dfn{Multiple
15783 Precision Floating-Point Reliable} (MPFR) library.")
15784 (license license:gpl2+)))
15786 (define-public r-assertive-base
15788 (name "r-assertive-base")
15793 (uri (cran-uri "assertive.base" version))
15796 "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b"))))
15798 `((upstream-name . "assertive.base")))
15799 (build-system r-build-system)
15800 (home-page "https://bitbucket.org/richierocks/assertive.base")
15801 (synopsis "Core of the assertive package")
15803 "This package provides a minimal set of predicates and assertions used by
15804 the assertive package. This is mainly for use by other package developers who
15805 want to include run-time testing features in their own packages.")
15806 (license license:gpl3+)))
15808 (define-public r-assertive-properties
15810 (name "r-assertive-properties")
15815 (uri (cran-uri "assertive.properties" version))
15818 "1pgljbwwbvbl4kc5c8mcv0qbzq3k6fzi29k88811yml263sm92dn"))))
15820 `((upstream-name . "assertive.properties")))
15821 (build-system r-build-system)
15823 (list r-assertive-base))
15824 (home-page "https://bitbucket.org/richierocks/assertive.properties")
15825 (synopsis "Assertions to check properties of variables")
15827 "This package provides a set of predicates and assertions for checking
15828 the properties of variables, such as length, names and attributes. This is
15829 mainly for use by other package developers who want to include run-time
15830 testing features in their own packages.")
15831 (license license:gpl3+)))
15833 (define-public r-assertive-numbers
15835 (name "r-assertive-numbers")
15840 (uri (cran-uri "assertive.numbers" version))
15843 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
15845 `((upstream-name . "assertive.numbers")))
15846 (build-system r-build-system)
15848 (list r-assertive-base))
15849 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
15850 (synopsis "Assertions to check properties of numbers")
15852 "This package provides a set of predicates and assertions for checking
15853 the properties of numbers. This is mainly for use by other package developers
15854 who want to include run-time testing features in their own packages.")
15855 (license license:gpl3+)))
15857 (define-public r-assertive-sets
15859 (name "r-assertive-sets")
15864 (uri (cran-uri "assertive.sets" version))
15867 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
15869 `((upstream-name . "assertive.sets")))
15870 (build-system r-build-system)
15872 (list r-assertive-base))
15873 (home-page "https://bitbucket.org/richierocks/assertive.sets")
15874 (synopsis "Assertions to check properties of sets")
15876 "This package provides a set of predicates and assertions for checking
15877 the properties of sets. This is mainly for use by other package developers
15878 who want to include run-time testing features in their own packages.")
15879 (license license:gpl3+)))
15881 (define-public r-assertive-matrices
15883 (name "r-assertive-matrices")
15888 (uri (cran-uri "assertive.matrices" version))
15891 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
15893 `((upstream-name . "assertive.matrices")))
15894 (build-system r-build-system)
15896 (list r-assertive-base))
15897 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
15898 (synopsis "Assertions to check properties of matrices")
15900 "This package provides a set of predicates and assertions for checking
15901 the properties of matrices. This is mainly for use by other package
15902 developers who want to include run-time testing features in their own
15904 (license license:gpl3+)))
15906 (define-public r-assertive-models
15908 (name "r-assertive-models")
15913 (uri (cran-uri "assertive.models" version))
15916 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
15918 `((upstream-name . "assertive.models")))
15919 (build-system r-build-system)
15921 (list r-assertive-base))
15922 (home-page "https://bitbucket.org/richierocks/assertive.models")
15923 (synopsis "Assertions to check properties of models")
15925 "This package provides a set of predicates and assertions for checking
15926 the properties of models. This is mainly for use by other package developers
15927 who want to include run-time testing features in their own packages.")
15928 (license license:gpl3+)))
15930 (define-public r-assertive-reflection
15932 (name "r-assertive-reflection")
15937 (uri (cran-uri "assertive.reflection" version))
15940 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
15942 `((upstream-name . "assertive.reflection")))
15943 (build-system r-build-system)
15945 (list r-assertive-base))
15946 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
15947 (synopsis "Assertions for checking the state of R")
15949 "This package provides a set of predicates and assertions for checking
15950 the state and capabilities of R, the operating system it is running on, and
15951 the IDE being used. This is mainly for use by other package developers who
15952 want to include run-time testing features in their own packages.")
15953 (license license:gpl3+)))
15955 (define-public r-assertive-types
15957 (name "r-assertive-types")
15962 (uri (cran-uri "assertive.types" version))
15965 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
15967 `((upstream-name . "assertive.types")))
15968 (build-system r-build-system)
15970 (list r-assertive-base r-assertive-properties r-codetools))
15971 (home-page "https://bitbucket.org/richierocks/assertive.types")
15972 (synopsis "Assertions to check types of variables")
15974 "This package provides a set of predicates and assertions for checking
15975 the types of variables. This is mainly for use by other package developers
15976 who want to include run-time testing features in their own packages.")
15977 (license license:gpl3+)))
15979 (define-public r-assertive-files
15981 (name "r-assertive-files")
15986 (uri (cran-uri "assertive.files" version))
15989 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
15991 `((upstream-name . "assertive.files")))
15992 (build-system r-build-system)
15994 (list r-assertive-base r-assertive-numbers))
15995 (home-page "https://bitbucket.org/richierocks/assertive.files")
15996 (synopsis "Assertions to check properties of files")
15998 "This package provides a set of predicates and assertions for checking
15999 the properties of files and connections. This is mainly for use by other
16000 package developers who want to include run-time testing features in their own
16002 (license license:gpl3+)))
16004 (define-public r-assertive-code
16006 (name "r-assertive-code")
16011 (uri (cran-uri "assertive.code" version))
16014 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
16016 `((upstream-name . "assertive.code")))
16017 (build-system r-build-system)
16019 (list r-assertive-base r-assertive-properties r-assertive-types))
16020 (home-page "https://bitbucket.org/richierocks/assertive.code")
16021 (synopsis "Assertions to check properties of code")
16023 "This package provides a set of predicates and assertions for checking
16024 the properties of code. This is mainly for use by other package developers
16025 who want to include run-time testing features in their own packages.")
16026 (license license:gpl3+)))
16028 (define-public r-assertive-datetimes
16030 (name "r-assertive-datetimes")
16035 (uri (cran-uri "assertive.datetimes" version))
16038 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
16040 `((upstream-name . "assertive.datetimes")))
16041 (build-system r-build-system)
16043 (list r-assertive-base r-assertive-types))
16044 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
16045 (synopsis "Assertions to check properties of dates and times")
16047 "This package provides a set of predicates and assertions for checking
16048 the properties of dates and times. This is mainly for use by other package
16049 developers who want to include run-time testing features in their own
16051 (license license:gpl3+)))
16053 (define-public r-assertive-strings
16055 (name "r-assertive-strings")
16060 (uri (cran-uri "assertive.strings" version))
16063 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
16065 `((upstream-name . "assertive.strings")))
16066 (build-system r-build-system)
16068 (list r-assertive-base r-assertive-types r-stringi))
16069 (home-page "https://bitbucket.org/richierocks/assertive.strings")
16070 (synopsis "Assertions to check properties of strings")
16072 "This package provides a set of predicates and assertions for checking
16073 the properties of strings. This is mainly for use by other package developers
16074 who want to include run-time testing features in their own packages.")
16075 (license license:gpl3+)))
16077 (define-public r-assertive-data-us
16079 (name "r-assertive-data-us")
16084 (uri (cran-uri "assertive.data.us" version))
16087 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
16089 `((upstream-name . "assertive.data.us")))
16090 (build-system r-build-system)
16092 (list r-assertive-base r-assertive-strings))
16093 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
16094 (synopsis "Assertions to check properties of strings")
16096 "This package provides a set of predicates and assertions for checking
16097 the properties of US-specific complex data types. This is mainly for use by
16098 other package developers who want to include run-time testing features in
16099 their own packages.")
16100 (license license:gpl3+)))
16102 (define-public r-assertive-data-uk
16104 (name "r-assertive-data-uk")
16109 (uri (cran-uri "assertive.data.uk" version))
16112 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
16114 `((upstream-name . "assertive.data.uk")))
16115 (build-system r-build-system)
16117 (list r-assertive-base r-assertive-strings))
16118 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
16119 (synopsis "Assertions to check properties of strings")
16121 "This package provides a set of predicates and assertions for checking
16122 the properties of UK-specific complex data types. This is mainly for use by
16123 other package developers who want to include run-time testing features in
16124 their own packages.")
16125 (license license:gpl3+)))
16127 (define-public r-assertive-data
16129 (name "r-assertive-data")
16134 (uri (cran-uri "assertive.data" version))
16137 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
16139 `((upstream-name . "assertive.data")))
16140 (build-system r-build-system)
16142 (list r-assertive-base r-assertive-strings))
16143 (home-page "https://bitbucket.org/richierocks/assertive.data")
16144 (synopsis "Assertions to check properties of data")
16146 "This package provides a set of predicates and assertions for checking
16147 the properties of (country independent) complex data types. This is mainly
16148 for use by other package developers who want to include run-time testing
16149 features in their own packages.")
16150 (license license:gpl3+)))
16152 (define-public r-assertive
16154 (name "r-assertive")
16159 (uri (cran-uri "assertive" version))
16162 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
16163 (build-system r-build-system)
16165 (list r-assertive-base
16168 r-assertive-data-uk
16169 r-assertive-data-us
16170 r-assertive-datetimes
16172 r-assertive-matrices
16174 r-assertive-numbers
16175 r-assertive-properties
16176 r-assertive-reflection
16178 r-assertive-strings
16183 (home-page "https://bitbucket.org/richierocks/assertive")
16184 (synopsis "Readable check functions to ensure code integrity")
16186 "This package provides lots of predicates (@code{is_*} functions) to
16187 check the state of your variables, and assertions (@code{assert_*} functions)
16188 to throw errors if they aren't in the right form.")
16189 (license license:gpl3+)))
16191 (define-public r-dotcall64
16193 (name "r-dotcall64")
16198 (uri (cran-uri "dotCall64" version))
16201 "1im5k8jbviwj2i42mq1kmjskh80isa7jr9w8i0fknidrzzy2h2zi"))))
16202 (properties `((upstream-name . "dotCall64")))
16203 (build-system r-build-system)
16204 (native-inputs (list gfortran))
16205 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
16206 (synopsis "Enhanced foreign function interface supporting long vectors")
16208 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
16209 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
16210 supports long vectors, arguments of type 64-bit integer, and provides a
16211 mechanism to avoid unnecessary copies of read-only and write-only arguments.
16212 This makes it a convenient and fast interface to C/C++ and Fortran code.")
16213 (license license:gpl2+)))
16215 (define-public r-spam
16222 (uri (cran-uri "spam" version))
16224 (base32 "1nvx965vxzs697k9m2l40a15bykflksn9bwa4py1p2wqg6922bn3"))))
16225 (build-system r-build-system)
16227 (list r-dotcall64))
16229 (list gfortran r-knitr))
16230 (home-page "https://www.math.uzh.ch/pages/spam/")
16231 (synopsis "Sparse matrix algebra")
16233 "This package provides a set of functions for sparse matrix algebra.
16234 Differences with other sparse matrix packages are:
16237 @item it only supports (essentially) one sparse matrix format;
16238 @item it is based on transparent and simple structure(s);
16239 @item it is tailored for MCMC calculations within G(M)RF;
16240 @item and it is fast and scalable (with the extension package @code{spam64}).
16242 ;; Either of these licenses
16243 (license (list license:bsd-3 license:lgpl2.0))))
16245 (define-public r-fields
16252 (uri (cran-uri "fields" version))
16254 (base32 "0d2lm4s9p3rv676z291fynpx3vdmi6cikcqlj23fxlj34icwbi2p"))))
16255 (build-system r-build-system)
16257 (list r-maps r-spam r-viridis))
16260 (home-page "https://www.image.ucar.edu/fields")
16261 (synopsis "Tools for spatial data")
16263 "This is a package for curve, surface and function fitting with an
16264 emphasis on splines, spatial data and spatial statistics. The major methods
16265 include cubic, and thin plate splines, Kriging, and compactly supported
16266 covariance functions for large data sets.")
16267 (license license:gpl2+)))
16269 (define-public r-spatialextremes
16271 (name "r-spatialextremes")
16276 (uri (cran-uri "SpatialExtremes" version))
16279 "0z1swxp1syz8hdskarjxx4sdd7wx835kcnb783bwqm235yh991j3"))))
16281 `((upstream-name . "SpatialExtremes")))
16282 (build-system r-build-system)
16284 (list r-fields r-maps))
16285 (home-page "http://spatialextremes.r-forge.r-project.org/")
16286 (synopsis "Modelling spatial extremes")
16288 "This package provides tools for the statistical modelling of spatial
16289 extremes using max-stable processes, copula or Bayesian hierarchical models.
16290 More precisely, this package allows (conditional) simulations from various
16291 parametric max-stable models, analysis of the extremal spatial dependence, the
16292 fitting of such processes using composite likelihoods or least square (simple
16293 max-stable processes only), model checking and selection and prediction.")
16294 (license license:gpl2+)))
16296 (define-public r-drc
16303 (uri (cran-uri "drc" version))
16306 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
16307 (build-system r-build-system)
16315 (home-page "https://cran.r-project.org/web/packages/drc")
16316 (synopsis "Analysis of dose-response curves")
16318 "This package provides a suite of flexible and versatile model fitting
16319 and after-fitting functions for the analysis of dose-response data.")
16320 (license license:gpl2+)))
16322 (define-public r-rmeta
16329 (uri (cran-uri "rmeta" version))
16332 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
16333 (build-system r-build-system)
16334 (home-page "https://cran.r-project.org/web/packages/rmeta")
16335 (synopsis "Tools for meta-analysis")
16337 "This package provides functions for simple fixed and random effects
16338 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
16339 draws standard summary plots, funnel plots, and computes summaries and tests
16340 for association and heterogeneity.")
16341 (license license:gpl2)))
16343 (define-public r-bootstrap
16345 (name "r-bootstrap")
16350 (uri (cran-uri "bootstrap" version))
16353 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
16354 (build-system r-build-system)
16355 (native-inputs (list gfortran))
16356 (home-page "https://cran.r-project.org/web/packages/bootstrap")
16357 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
16359 "This package provides software and data for the book \"An Introduction
16360 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
16361 This package is primarily provided for projects already based on it, and for
16362 support of the book. New projects should preferentially use the recommended
16363 package \"boot\".")
16364 (license license:bsd-3)))
16366 (define-public r-survivalroc
16368 (name "r-survivalroc")
16373 (uri (cran-uri "survivalROC" version))
16376 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
16377 (properties `((upstream-name . "survivalROC")))
16378 (build-system r-build-system)
16379 (home-page "https://cran.r-project.org/web/packages/survivalROC")
16380 (synopsis "Time-dependent ROC curve estimation from censored survival data")
16382 "Compute time-dependent ROC curve from censored survival data using
16383 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
16384 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
16385 (license license:gpl2+)))
16387 (define-public r-locfdr
16393 (uri (cran-uri "locfdr" version))
16396 "1falkbp2xz07am8jlhwlvyqvxnli4nwl188kd0g58vdfjcjy3mj2"))))
16397 (build-system r-build-system)
16398 (home-page "https://cran.r-project.org/web/packages/locfdr/")
16399 (synopsis "Computes local false discovery rates")
16400 (description "This package can be used to compute local false
16402 (license license:gpl2)))
16404 (define-public r-longitudinal
16406 (name "r-longitudinal")
16411 (uri (cran-uri "longitudinal" version))
16414 "046w3xbr535c5jyd68adv42a7limxp1mv57b5w6w673w707lmw2p"))))
16415 (build-system r-build-system)
16416 (propagated-inputs (list r-corpcor))
16417 (home-page "http://strimmerlab.org/software/longitudinal/")
16418 (synopsis "Analysis of multiple time course data")
16420 "This package contains general data structures and functions for
16421 longitudinal data with multiple variables, repeated measurements, and
16422 irregularly spaced time points. It also implements a shrinkage estimator of
16423 dynamical correlation and dynamical covariance.")
16424 (license license:gpl3+)))
16426 (define-public r-genenet
16433 (uri (cran-uri "GeneNet" version))
16436 "1r1khga3nxxjghs4vnbymzp0cwb1q17zw2v3a94qz8fsrirq1sf1"))))
16437 (properties `((upstream-name . "GeneNet")))
16438 (build-system r-build-system)
16440 (list r-corpcor r-fdrtool r-longitudinal))
16441 (home-page "http://strimmerlab.org/software/genenet/")
16442 (synopsis "Modeling and inferring gene networks")
16444 "This package analyzes gene expression (time series) data with focus on
16445 the inference of gene networks. In particular, GeneNet implements the methods
16446 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
16447 for learning large-scale gene association networks (including assignment of
16448 putative directions).")
16449 (license license:gpl3+)))
16451 (define-public r-rbamtools
16453 (name "r-rbamtools")
16454 (version "2.16.17")
16458 (uri (cran-uri "rbamtools" version))
16461 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
16462 (build-system r-build-system)
16463 (inputs (list zlib))
16465 (list r-refgenome))
16466 (home-page "https://cran.r-project.org/web/packages/rbamtools")
16467 (synopsis "Read and write BAM (binary alignment) files")
16469 "This package provides an R interface to functions of the SAMtools
16471 (license license:artistic2.0)))
16473 (define-public r-profvis
16479 (uri (cran-uri "profvis" version))
16482 "1f86m426pcf90l29hf4hkirzf8f38dihk52bxbdq2gvrrdili5s3"))
16483 (modules '((guix build utils)))
16485 '(with-directory-excursion "inst/htmlwidgets/lib"
16486 (for-each delete-file
16487 (list "highlight/highlight.js" ;from rmarkdown
16488 "jquery/jquery.min.js" ;version 1.12.4
16489 "d3/d3.min.js")))))) ;version 3.5.6
16490 (properties `((upstream-name . "profvis")))
16491 (build-system r-build-system)
16494 (modify-phases %standard-phases
16495 (add-after 'unpack 'process-javascript
16496 (lambda* (#:key inputs #:allow-other-keys)
16497 (with-directory-excursion "inst/htmlwidgets/lib/"
16500 inputs "/site-library/rmarkdown/rmd/h/highlightjs/highlight.js")
16501 "highlight/highlight.js")
16503 `((,(assoc-ref inputs "js-jquery")
16504 . "jquery/jquery.min.js")
16505 (,(assoc-ref inputs "js-d3")
16506 . "d3/d3.min.js"))))
16507 (for-each (lambda (source target)
16508 (format #true "Processing ~a --> ~a~%"
16510 (invoke "esbuild" source "--minify"
16511 (string-append "--outfile=" target)))
16513 (map cdr mapping)))))))))
16515 `(("esbuild" ,esbuild)
16516 ("r-rmarkdown" ,r-rmarkdown)
16520 (uri "https://raw.githubusercontent.com/d3/d3/v3.5.6/d3.js")
16523 "17qlbwn7vgx335gciq6zp2ib6zg1r9lfa6p1bd9g0ds0xbcsbvgd"))))
16527 (uri "https://code.jquery.com/jquery-1.12.4.js")
16530 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))))
16531 (propagated-inputs (list r-htmlwidgets r-stringr))
16532 (home-page "https://rstudio.github.io/profvis/")
16533 (synopsis "Interactive visualizations for profiling R code")
16534 (description "This package provides interactive visualizations for
16535 profiling R code.")
16536 (license license:gpl3)))
16538 (define-public r-protviz
16545 (uri (cran-uri "protViz" version))
16548 "0f6jwzcqi0w37hvg3i5dlk0c3anpkqh54ibf94vaf17r8sykr4nw"))))
16549 (properties `((upstream-name . "protViz")))
16550 (build-system r-build-system)
16551 (propagated-inputs (list r-rcpp))
16552 (home-page "https://github.com/protViz/protViz/")
16553 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
16555 "This package helps with quality checks, visualizations and analysis of
16556 mass spectrometry data, coming from proteomics experiments. The package is
16557 developed, tested and used at the Functional Genomics Center Zurich, where it
16558 is used mainly for prototyping, teaching, and having fun with proteomics data.
16559 But it can also be used to do data analysis for small scale data sets.")
16560 (license license:gpl3)))
16562 (define-public r-cmprsk
16569 (uri (cran-uri "cmprsk" version))
16571 (base32 "050f24l5ab1ds9824c7yjahimf6pg8ih2k83jzpzfb0n5k5jfh44"))))
16572 (build-system r-build-system)
16577 (home-page "https://cran.r-project.org/web/packages/cmprsk")
16578 (synopsis "Subdistribution analysis of competing risks")
16580 "This package provides tool for estimation, testing and regression
16581 modeling of subdistribution functions in competing risks, as described in
16582 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
16583 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
16584 A proportional hazards model for the subdistribution of a competing risk,
16585 JASA, 94:496-509.")
16586 (license license:gpl2+)))
16588 (define-public r-etm
16595 (uri (cran-uri "etm" version))
16598 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
16599 (build-system r-build-system)
16601 (list r-data-table r-lattice r-rcpp r-rcpparmadillo r-survival))
16602 (home-page "https://cran.r-project.org/web/packages/etm")
16603 (synopsis "Empirical transition matrix")
16605 "The @dfn{empirical transition matrix} (etm) package estimates
16606 the matrix of transition probabilities for any time-inhomogeneous multistate
16607 model with finite state space using the Aalen-Johansen estimator.")
16608 (license license:expat)))
16610 (define-public r-epi
16617 (uri (cran-uri "Epi" version))
16620 "1dkdx000cvy2rgxq3w6ppl3j9h7mwmcqg5xqsqh5hr3aks845pwx"))))
16621 (properties `((upstream-name . "Epi")))
16622 (build-system r-build-system)
16636 (home-page "https://BendixCarstensen.com/Epi/")
16637 (synopsis "Statistical analysis in epidemiology")
16639 "This package provides functions for demographic and epidemiological
16640 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
16641 particular representation, manipulation and simulation of multistate data -
16642 the Lexis suite of functions, which includes interfaces to the @code{mstate},
16643 @code{etm} and @code{cmprsk} packages. It also contains functions for
16644 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
16645 data and some useful functions for tabulation and plotting, as well as a
16646 number of epidemiological data sets.")
16647 (license license:gpl2)))
16649 (define-public r-ppls
16652 (version "1.6-1.1")
16656 (uri (cran-uri "ppls" version))
16659 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
16660 (build-system r-build-system)
16661 (propagated-inputs (list r-mass))
16662 (home-page "https://cran.r-project.org/web/packages/ppls")
16663 (synopsis "Penalized partial least squares")
16665 "This package contains linear and nonlinear regression methods based on
16666 partial least squares and penalization techniques. Model parameters are
16667 selected via cross-validation, and confidence intervals ans tests for the
16668 regression coefficients can be conducted via jackknifing.")
16669 (license license:gpl2+)))
16671 (define-public r-huge
16678 (uri (cran-uri "huge" version))
16680 (base32 "1sl457a1lndrx98y2j9a2smanawx2iqlhl82iand0g3p5xp8ch4j"))))
16681 (build-system r-build-system)
16683 (list r-igraph r-mass r-matrix r-rcpp r-rcppeigen))
16684 (home-page "https://cran.r-project.org/web/packages/huge")
16685 (synopsis "High-dimensional undirected graph estimation")
16687 "This package provides a general framework for high-dimensional
16688 undirected graph estimation. It integrates data preprocessing, neighborhood
16689 screening, graph estimation, and model selection techniques into a pipeline.")
16690 (license license:gpl2)))
16692 (define-public r-parcor
16699 (uri (cran-uri "parcor" version))
16702 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
16703 (build-system r-build-system)
16705 (list r-epi r-genenet r-glmnet r-mass r-ppls))
16706 (home-page "https://cran.r-project.org/web/packages/parcor")
16707 (synopsis "Regularized estimation of partial correlation matrices")
16709 "This package estimates the matrix of partial correlations based on
16710 different regularized regression methods: lasso, adaptive lasso, PLS, and
16711 Ridge Regression. In addition, the package provides model selection for
16712 lasso, adaptive lasso and Ridge regression based on cross-validation.")
16713 (license license:gpl2+)))
16715 (define-public r-mcmc
16722 (uri (cran-uri "mcmc" version))
16725 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
16726 (build-system r-build-system)
16727 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
16728 (synopsis "Markov chain Monte Carlo")
16730 "This package simulates continuous distributions of random vectors using
16731 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
16732 function that evaluates the log unnormalized density. Algorithms are random
16733 walk Metropolis algorithm (function @code{metrop}), simulated
16734 tempering (function @code{temper}), and morphometric random walk
16735 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
16736 by change of variable.")
16737 (license license:expat)))
16739 (define-public r-listenv
16746 (uri (cran-uri "listenv" version))
16749 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
16750 (build-system r-build-system)
16753 (modify-phases %standard-phases
16754 (add-after 'unpack 'set-HOME
16755 (lambda _ (setenv "HOME" "/tmp"))))))
16757 (list r-r-rsp)) ; vignette builder
16758 (home-page "https://github.com/HenrikBengtsson/listenv")
16759 (synopsis "Environments behaving (almost) as lists")
16761 "This package implements list environments. List environments are
16762 environments that have list-like properties. For instance, the elements of a
16763 list environment are ordered and can be accessed and iterated over using index
16765 (license license:lgpl2.1+)))
16767 (define-public r-globals
16774 (uri (cran-uri "globals" version))
16777 "158y39qv99f1kc2i7w8d4lm2ls96plb43fzamz31im9xb9bkmxpp"))))
16778 (build-system r-build-system)
16780 (list r-codetools))
16781 (home-page "https://github.com/HenrikBengtsson/globals")
16782 (synopsis "Identify global objects in R expressions")
16784 "This package provides tools to identify global (\"unknown\" or \"free\")
16785 objects in R expressions by code inspection using various strategies, e.g.
16786 conservative or liberal. The objective of this package is to make it as
16787 simple as possible to identify global objects for the purpose of exporting
16788 them in distributed compute environments.")
16789 (license license:lgpl2.1+)))
16791 (define-public r-parallelly
16793 (name "r-parallelly")
16798 (uri (cran-uri "parallelly" version))
16801 "146a9i999vrflr4g1fph1pgkl4bq0dw102bjw8pp1zy7kbsqbiii"))))
16802 (properties `((upstream-name . "parallelly")))
16803 (build-system r-build-system)
16804 (home-page "https://github.com/HenrikBengtsson/parallelly")
16805 (synopsis "Enhancements of the parallel package")
16807 "This package provides utility functions that enhance the @code{parallel}
16808 package and support the built-in parallel backends of the @code{future}
16809 package. For example, @code{availableCores} gives the number of CPU cores
16810 available to your R process as given by R options and environment variables,
16811 including those set by job schedulers on high-performance compute clusters.
16812 If none is set, it will fall back to @code{parallel::detectCores}. Another
16813 example is @code{makeClusterPSOCK}, which is backward compatible with
16814 @code{parallel::makePSOCKcluster} while doing a better job in setting up
16815 remote cluster workers without the need for configuring the firewall to do
16816 port-forwarding to your local computer.")
16817 (license license:lgpl2.1+)))
16819 (define-public r-future
16826 (uri (cran-uri "future" version))
16829 "1xhv0nf97yxxxsmxczyqqbnb4yn5sfn5vzvhm9dmw9csrmmadpbg"))))
16830 (build-system r-build-system)
16833 (modify-phases %standard-phases
16834 (add-after 'unpack 'set-HOME
16835 (lambda _ (setenv "HOME" "/tmp"))))))
16837 (list r-digest r-globals r-listenv r-parallelly))
16839 (list r-r-rsp)) ; vignette builder
16840 (home-page "https://github.com/HenrikBengtsson/future")
16841 (synopsis "Unified parallel and distributed processing in R")
16843 "The purpose of this package is to provide a lightweight and unified
16844 Future API for sequential and parallel processing of R expression via futures.
16845 This package implements sequential, multicore, multisession, and cluster
16846 futures. With these, R expressions can be evaluated on the local machine, in
16847 parallel a set of local machines, or distributed on a mix of local and remote
16848 machines. Extensions to this package implement additional backends for
16849 processing futures via compute cluster schedulers etc. Because of its unified
16850 API, there is no need to modify any code in order to switch from sequential on
16851 the local machine to, say, distributed processing on a remote compute cluster.")
16852 (license license:lgpl2.1+)))
16854 (define-public r-future-apply
16856 (name "r-future-apply")
16861 (uri (cran-uri "future.apply" version))
16864 "0cr141mamjxby79sww02493yal9lahslvp3a3ic7f856rbawq8jg"))))
16865 (properties `((upstream-name . "future.apply")))
16866 (build-system r-build-system)
16869 (modify-phases %standard-phases
16870 (add-after 'unpack 'set-HOME
16871 (lambda _ (setenv "HOME" "/tmp"))))))
16873 (list r-future r-globals))
16875 (list r-r-rsp)) ; vignette builder
16876 (home-page "https://github.com/HenrikBengtsson/future.apply")
16877 (synopsis "Apply function to elements in parallel using futures")
16879 "This package provides implementations of @code{apply()},
16880 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
16881 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
16882 can be resolved using any future-supported backend, e.g. parallel on the local
16883 machine or distributed on a compute cluster.")
16884 (license license:gpl2+)))
16886 (define-public r-rsvd
16893 (uri (cran-uri "rsvd" version))
16896 "07p2hjmpcwcsang8z9sjkpy94rydcin7m3hyvcgzgm5cd6w8c1p4"))))
16897 (build-system r-build-system)
16900 (home-page "https://github.com/erichson/rSVD")
16901 (synopsis "Randomized singular value decomposition")
16903 "Low-rank matrix decompositions are fundamental tools and widely used for
16904 data analysis, dimension reduction, and data compression. Classically, highly
16905 accurate deterministic matrix algorithms are used for this task. However, the
16906 emergence of large-scale data has severely challenged our computational
16907 ability to analyze big data. The concept of randomness has been demonstrated
16908 as an effective strategy to quickly produce approximate answers to familiar
16909 problems such as the @dfn{singular value decomposition} (SVD). This package
16910 provides several randomized matrix algorithms such as the randomized singular
16911 value decomposition (@code{rsvd}), randomized principal component
16912 analysis (@code{rpca}), randomized robust principal component
16913 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
16914 and the randomized CUR decomposition (@code{rcur}). In addition several plot
16915 functions are provided.")
16916 (license license:gpl3+)))
16918 (define-public r-sloop
16925 (uri (cran-uri "sloop" version))
16928 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
16929 (build-system r-build-system)
16931 (list r-codetools r-crayon r-purrr r-rlang r-tibble))
16932 (home-page "https://github.com/r-lib/sloop")
16933 (synopsis "Helpers for object-oriented programming in R")
16935 "This package provides a collection of helper functions designed to
16936 help you to better understand object oriented programming in R, particularly
16938 (license license:gpl3)))
16940 (define-public r-capushe
16947 (uri (cran-uri "capushe" version))
16950 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
16951 (build-system r-build-system)
16952 (propagated-inputs (list r-mass))
16953 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
16954 (synopsis "Calibrating penalties using slope heuristics")
16956 "This package provides tools for the calibration of penalized criteria
16957 for model selection. The calibration methods available are based on the slope
16959 (license license:gpl2+)))
16961 (define-public r-dorng
16968 (uri (cran-uri "doRNG" version))
16971 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
16972 (properties `((upstream-name . "doRNG")))
16973 (build-system r-build-system)
16975 (list r-foreach r-iterators r-rngtools))
16976 (home-page "https://renozao.github.io/doRNG/")
16977 (synopsis "Generic reproducible parallel backend for foreach loops")
16979 "This package provides functions to perform reproducible parallel
16980 @code{foreach} loops, using independent random streams as generated by
16981 L'Ecuyer's combined multiple-recursive generator. It enables to easily
16982 convert standard @code{%dopar%} loops into fully reproducible loops,
16983 independently of the number of workers, the task scheduling strategy, or the
16984 chosen parallel environment and associated foreach backend.")
16985 (license license:gpl2+)))
16987 (define-public r-blockmodeling
16989 (name "r-blockmodeling")
16994 (uri (cran-uri "blockmodeling" version))
16997 "19mxmxsnl6rrh85p0sak91vcaw4dz2cnm70hdzfwnvdrr695yw2z"))))
16998 (build-system r-build-system)
17001 (native-inputs (list gfortran))
17002 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
17003 (synopsis "Generalized and classical blockmodeling of valued networks")
17005 "This package is primarily meant as an implementation of generalized
17006 blockmodeling for valued networks. In addition, measures of similarity or
17007 dissimilarity based on structural equivalence and regular equivalence (REGE
17008 algorithms) can be computed and partitioned matrices can be plotted.")
17009 (license license:gpl2+)))
17011 (define-public r-upsetr
17018 (uri (cran-uri "UpSetR" version))
17021 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
17022 (properties `((upstream-name . "UpSetR")))
17023 (build-system r-build-system)
17025 (list r-ggplot2 r-gridextra r-plyr r-scales))
17026 (home-page "https://github.com/hms-dbmi/UpSetR")
17027 (synopsis "Visualize intersecting sets")
17029 "This package provides a more scalable alternative to Venn and Euler
17030 diagrams for visualizing intersecting sets. Create visualizations of
17031 intersecting sets using a novel matrix design, along with visualizations of
17032 several common set, element and attribute related tasks.")
17033 (license license:expat)))
17035 ;; This package includes a JavaScript file, which is not minified. When
17036 ;; upgrading please check that there are no new minified JavaScript files.
17037 (define-public r-shinybs
17044 (uri (cran-uri "shinyBS" version))
17047 "0h51685a9qll4agayldjyryi60ih969219ibg071slv0613p5v8a"))))
17048 (properties `((upstream-name . "shinyBS")))
17049 (build-system r-build-system)
17050 ;; The tests spawn Shiny browser apps. They cannot be run
17051 ;; non-interactively.
17052 (arguments '(#:tests? #f))
17054 (list r-htmltools r-shiny))
17055 (home-page "https://ebailey78.github.io/shinyBS/")
17056 (synopsis "Twitter Bootstrap components for Shiny")
17058 "This package adds additional Twitter Bootstrap components to Shiny.")
17059 (license license:gpl3)))
17061 (define-public r-shinyjqui
17063 (name "r-shinyjqui")
17068 (uri (cran-uri "shinyjqui" version))
17071 "135gwz7syyb6pbn0lkvmq0v1c6r1zivavnqhi1rnzbbzlysi27v1"))
17073 '(for-each delete-file
17074 (list "inst/www/shinyjqui.min.js"
17075 "inst/www/jquery.ui.touch-punch.min.js")))))
17076 (properties `((upstream-name . "shinyjqui")))
17077 (build-system r-build-system)
17080 (modify-phases %standard-phases
17081 (add-after 'unpack 'process-javascript
17082 (lambda* (#:key inputs #:allow-other-keys)
17083 (with-directory-excursion "inst/www"
17085 `((,(string-append (assoc-ref inputs "js-jquery.ui.touch-punch")
17086 "/jquery.ui.touch-punch.js")
17087 . "jquery.ui.touch-punch.min.js")
17089 . "shinyjqui.min.js"))))
17090 (for-each (lambda (source target)
17091 (format #true "Processing ~a --> ~a~%"
17093 (invoke "esbuild" source "--minify"
17094 (string-append "--outfile=" target)))
17096 (map cdr mapping)))))))))
17098 (list r-htmltools r-htmlwidgets r-jsonlite r-rlang r-shiny))
17100 `(("r-knitr" ,r-knitr)
17101 ("esbuild" ,esbuild)
17102 ("js-jquery.ui.touch-punch"
17105 (uri (git-reference
17106 (url "https://github.com/furf/jquery-ui-touch-punch")
17107 (commit "8f7559b6e65cdc3ee3648d5fe76d38c653f87ff5")))
17110 "1lzywp2q9hwx6d5fqjla95vp7ra2lahr5dam7lsqjmch9d98r48q"))))))
17111 (home-page "https://github.com/yang-tang/shinyjqui")
17112 (synopsis "jQuery UI interactions and effects for Shiny")
17114 "This is an extension to Shiny that brings interactions and animation
17115 effects from the jQuery UI library.")
17116 (license license:expat)))
17118 (define-public r-shinymanager
17120 (name "r-shinymanager")
17121 (version "1.0.400")
17125 (uri (cran-uri "shinymanager" version))
17127 (base32 "1np2yp5pn8g9i4jhysfgprmdn13cpw4vaaagrd72rnk2r4hpmyx4"))))
17128 (properties `((upstream-name . "shinymanager")))
17129 (build-system r-build-system)
17131 (list r-billboarder
17141 (native-inputs (list r-knitr))
17142 (home-page "https://github.com/datastorm-open/shinymanager")
17143 (synopsis "Authentication management for Shiny applications")
17145 "This package provides simple and secure authentication mechanism for
17146 single Shiny applications. Credentials are stored in an encrypted SQLite
17148 (license license:gpl3)))
17150 (define-public r-outliers
17152 (name "r-outliers")
17157 (uri (cran-uri "outliers" version))
17160 "1yrmwvjjb0a6sbx940k9svf23cykcxz8rrwcgyic7lpgzbrdfcfc"))))
17161 (build-system r-build-system)
17162 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
17163 (synopsis "Tests for outliers")
17165 "This package provides a collection of some tests commonly used for
17166 identifying outliers.")
17167 (license license:gpl2+)))
17169 (define-public r-bayesm
17176 (uri (cran-uri "bayesm" version))
17178 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
17179 (build-system r-build-system)
17181 (list r-rcpp r-rcpparmadillo))
17182 (home-page "http://www.perossi.org/home/bsm-1")
17183 (synopsis "Bayesian inference for marketing/micro-econometrics")
17185 "This package covers many important models used in marketing and
17186 micro-econometrics applications, including Bayes Regression (univariate or
17187 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
17188 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
17189 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
17190 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
17191 Estimation with normal base, Hierarchical Linear Models with normal prior and
17192 covariates, Hierarchical Linear Models with a mixture of normals prior and
17193 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
17194 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
17195 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
17196 analysis of choice-based conjoint data, Bayesian treatment of linear
17197 instrumental variables models, Analysis of Multivariate Ordinal survey data
17198 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
17199 Coefficient Logit Models.")
17200 (license license:gpl2+)))
17202 (define-public r-tensora
17209 (uri (cran-uri "tensorA" version))
17212 "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf"))))
17213 (properties `((upstream-name . "tensorA")))
17214 (build-system r-build-system)
17215 (home-page "http://www.stat.boogaart.de/tensorA")
17216 (synopsis "Advanced tensor arithmetic with named indices")
17218 "This package provides convenience functions for advanced linear algebra
17219 with tensors and computation with datasets of tensors on a higher level
17220 abstraction. It includes Einstein and Riemann summing conventions, dragging,
17221 co- and contravariate indices, and parallel computations on sequences of
17223 (license license:gpl2+)))
17225 (define-public r-rarpack
17232 (uri (cran-uri "rARPACK" version))
17235 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
17236 (properties `((upstream-name . "rARPACK")))
17237 (build-system r-build-system)
17238 (propagated-inputs (list r-rspectra))
17239 (home-page "https://github.com/yixuan/rARPACK")
17240 (synopsis "Solvers for large scale eigenvalue and SVD problems")
17242 "This package was previously an R wrapper of the ARPACK library, and now
17243 a shell of the R package RSpectra, an R interface to the Spectra library for
17244 solving large scale eigenvalue/vector problems. The current version of
17245 rARPACK simply imports and exports the functions provided by RSpectra. New
17246 users of rARPACK are advised to switch to the RSpectra package.")
17247 (license license:bsd-3)))
17249 (define-public r-compositions
17251 (name "r-compositions")
17256 (uri (cran-uri "compositions" version))
17259 "1bqg0qqzsf92q0jb7hdjycr54bwv8rk7ajhvxgch5yslyqxpm73v"))))
17260 (build-system r-build-system)
17262 (list r-bayesm r-mass r-robustbase r-tensora))
17265 (home-page "http://www.stat.boogaart.de/compositions")
17266 (synopsis "Compositional data analysis")
17268 "This package provides functions for the consistent analysis of
17269 compositional data (e.g. portions of substances) and positive
17270 numbers (e.g. concentrations).")
17271 (license license:gpl2+)))
17273 (define-public r-cobs
17280 (uri (cran-uri "cobs" version))
17283 "04f6a6gp11p93j2k35mbrfqgjx5qsgi3dj1085a5v5s0z6l7vbkz"))))
17284 (build-system r-build-system)
17286 (list r-quantreg r-sparsem))
17287 (home-page "https://cran.r-project.org/web/packages/cobs")
17288 (synopsis "Constrained B-Splines (sparse matrix based)")
17290 "This package provides qualitatively constrained (regression) smoothing
17291 splines via linear programming and sparse matrices.")
17292 (license license:gpl2+)))
17294 (define-public r-drimpute
17296 (name "r-drimpute")
17301 (uri (cran-uri "DrImpute" version))
17304 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
17305 (properties `((upstream-name . "DrImpute")))
17306 (build-system r-build-system)
17308 (list r-rcpp r-rcpparmadillo))
17309 (home-page "https://github.com/ikwak2/DrImpute")
17310 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
17312 "This is an R package for imputing dropout events. Many statistical
17313 methods in cell type identification, visualization and lineage reconstruction
17314 do not account for dropout events. DrImpute can improve the performance of
17315 such software by imputing dropout events.")
17316 (license license:gpl3)))
17318 (define-public r-gamlss-dist
17320 (name "r-gamlss-dist")
17325 (uri (cran-uri "gamlss.dist" version))
17327 (base32 "03m275qvrmpzmc10hs48277kxp503riz8sz6xk9pkpj8n7gsz20g"))))
17328 (properties `((upstream-name . "gamlss.dist")))
17329 (build-system r-build-system)
17330 (propagated-inputs (list r-mass))
17331 (home-page "http://www.gamlss.org/")
17332 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
17334 "This package provides a set of distributions which can be used for
17335 modelling the response variables in Generalized Additive Models for Location
17336 Scale and Shape. The distributions can be continuous, discrete or mixed
17337 distributions. Extra distributions can be created, by transforming, any
17338 continuous distribution defined on the real line, to a distribution defined on
17339 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
17340 transformation, respectively.")
17341 ;; Either version of the GPL.
17342 (license (list license:gpl2 license:gpl3))))
17344 ;; This package includes JavaScript files, which are not minified. When
17345 ;; upgrading please check that there are no new minified JavaScript files.
17346 (define-public r-shinyjs
17353 (uri (cran-uri "shinyjs" version))
17356 "1id9gsrkr28xl80a8794in17rxmmz06zqvd5hlns7mqz3fzhrhky"))))
17357 (build-system r-build-system)
17359 (list r-digest r-jsonlite r-shiny))
17362 (home-page "https://deanattali.com/shinyjs")
17363 (synopsis "Improve the user experience of your Shiny apps")
17365 "Perform common useful JavaScript operations in Shiny apps that will
17366 greatly improve your apps without having to know any JavaScript. Examples
17367 include: hiding an element, disabling an input, resetting an input back to its
17368 original value, delaying code execution by a few seconds, and many more useful
17369 functions for both the end user and the developer. Shinyjs can also be used
17370 to easily call your own custom JavaScript functions from R.")
17371 (license license:agpl3+)))
17373 ;; This package includes minified JavaScript files. When upgrading please
17374 ;; check that there are no new minified JavaScript files.
17375 (define-public r-colourpicker
17377 (name "r-colourpicker")
17382 (uri (cran-uri "colourpicker" version))
17385 "1q1wi3g403fbzp4ys3gsjbwdc86x770cx323qgi47ca8n219kl50"))))
17386 (build-system r-build-system)
17389 (modify-phases %standard-phases
17390 (add-after 'unpack 'process-javascript
17391 (lambda* (#:key inputs #:allow-other-keys)
17392 (with-directory-excursion "inst"
17394 `((,(assoc-ref inputs "js-salvattore")
17395 . "examples/colourInput/www/salvattore.min.js")
17396 (,(assoc-ref inputs "js-jquery")
17397 . "htmlwidgets/lib/jquery/jquery.min.js")
17398 ("www/shared/colourpicker/js/colourpicker.js"
17399 . "www/shared/colourpicker/js/colourpicker.min.js"))))
17400 (for-each (lambda (source target)
17401 (format #true "Processing ~a --> ~a~%"
17403 (delete-file target)
17404 (invoke "esbuild" source "--minify"
17405 (string-append "--outfile=" target)))
17407 (map cdr mapping)))))))))
17417 `(("esbuild" ,esbuild)
17421 (uri "https://code.jquery.com/jquery-1.11.3.js")
17424 "1v956yf5spw0156rni5z77hzqwmby7ajwdcd6mkhb6zvl36awr90"))))
17428 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
17431 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
17432 (home-page "https://github.com/daattali/colourpicker")
17433 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
17435 "This package provides a color picker that can be used as an input in
17436 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
17437 custom color palettes, and many more options. A plot color helper tool is
17438 available as an RStudio Addin, which helps you pick colors to use in your
17439 plots. A more generic color picker RStudio Addin is also provided to let you
17440 select colors to use in your R code.")
17441 (license license:expat)))
17443 (define-public r-ggextra
17450 (uri (cran-uri "ggExtra" version))
17453 "1rd3qv6ah3zphr1jicjhgxms73vi496mjnxnsrcgl7z8nyxmas6w"))))
17454 (properties `((upstream-name . "ggExtra")))
17455 (build-system r-build-system)
17457 (list r-colourpicker
17467 (home-page "https://github.com/daattali/ggExtra")
17468 (synopsis "Marginal histograms for ggplot2 and other enhancements")
17470 "This package is a collection of functions and layers to enhance ggplot2.
17471 The flagship function is @code{ggMarginal()}, which can be used to add
17472 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
17473 (license license:expat)))
17475 (define-public r-minpack-lm
17477 (name "r-minpack-lm")
17482 (uri (cran-uri "minpack.lm" version))
17485 "11yz6hk2r33571d16kq01cb1x6sgdzi6jmksqlrm8mr84l95c2f7"))))
17486 (properties `((upstream-name . "minpack.lm")))
17487 (build-system r-build-system)
17488 (native-inputs (list gfortran))
17489 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
17490 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
17492 "The @code{nls.lm} function provides an R interface to @code{lmder} and
17493 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
17494 problems by a modification of the Levenberg-Marquardt algorithm, with support
17495 for lower and upper parameter bounds. The implementation can be used via
17496 @code{nls}-like calls using the @code{nlsLM} function.")
17497 (license license:gpl3)))
17499 (define-public r-moments
17506 (uri (cran-uri "moments" version))
17509 "0r6qf3i1rzh2822bx1p0h8mh91gsbgg6asl2rzh2l4ys094bilif"))))
17510 (build-system r-build-system)
17511 (home-page "https://cran.r-project.org/web/packages/moments")
17512 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
17514 "This package provides functions to calculate: moments, Pearson's
17515 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
17516 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
17517 (license license:gpl2+)))
17519 (define-public r-msir
17526 (uri (cran-uri "msir" version))
17529 "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84"))))
17530 (build-system r-build-system)
17535 (home-page "https://cran.r-project.org/web/packages/msir")
17536 (synopsis "Model-based sliced inverse regression")
17538 "This is an R package for dimension reduction based on finite Gaussian
17539 mixture modeling of inverse regression.")
17540 (license license:gpl2+)))
17542 (define-public r-pbivnorm
17544 (name "r-pbivnorm")
17549 (uri (cran-uri "pbivnorm" version))
17552 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
17553 (build-system r-build-system)
17554 (native-inputs (list gfortran))
17555 (home-page "https://github.com/brentonk/pbivnorm")
17556 (synopsis "Vectorized bivariate normal CDF")
17558 "This package provides a vectorized R function for calculating
17559 probabilities from a standard bivariate normal CDF.")
17560 (license license:gpl2+)))
17562 (define-public r-lavaan
17569 (uri (cran-uri "lavaan" version))
17572 "17h79pnww1mihvlp6ap0r6d8wnly9bwszj13l5dkby0284z2fj40"))))
17573 (build-system r-build-system)
17575 (list r-mass r-mnormt r-numderiv r-pbivnorm))
17576 (home-page "https://lavaan.ugent.be")
17577 (synopsis "Latent variable analysis")
17579 "This package provides tools to fit a variety of latent variable models,
17580 including confirmatory factor analysis, structural equation modeling and
17581 latent growth curve models.")
17582 (license license:gpl2+)))
17584 (define-public r-nonnest2
17586 (name "r-nonnest2")
17591 (uri (cran-uri "nonnest2" version))
17594 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
17595 (build-system r-build-system)
17597 (list r-compquadform r-lavaan r-mvtnorm r-sandwich))
17600 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
17601 (synopsis "Tests of non-nested models")
17603 "This package allows for testing of non-nested models. It includes tests
17604 of model distinguishability and of model fit that can be applied to both
17605 nested and non-nested models. The package also includes functionality to
17606 obtain confidence intervals associated with AIC and BIC.")
17607 ;; Either version of the GPL.
17608 (license (list license:gpl2 license:gpl3))))
17610 (define-public r-penalized
17612 (name "r-penalized")
17617 (uri (cran-uri "penalized" version))
17620 "08badmgygppbqzay20qijyww028yw6s8dyd8ijcp8g4r9rn8xqyq"))))
17621 (build-system r-build-system)
17623 (list r-rcpp r-rcpparmadillo r-survival))
17624 (home-page "https://cran.r-project.org/web/packages/penalized/")
17625 (synopsis "Penalized estimation in GLMs and in the Cox model")
17627 "This package provides tools for fitting possibly high dimensional
17628 penalized regression models. The penalty structure can be any combination of
17629 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
17630 constraint on the regression coefficients. The supported regression models
17631 are linear, logistic and Poisson regression and the Cox Proportional Hazards
17632 model. Cross-validation routines allow optimization of the tuning
17634 (license license:gpl2+)))
17636 (define-public r-zim
17643 (uri (cran-uri "ZIM" version))
17646 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
17647 (properties `((upstream-name . "ZIM")))
17648 (build-system r-build-system)
17649 (propagated-inputs (list r-mass))
17650 (home-page "https://github.com/biostatstudio/ZIM")
17651 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
17653 "Analyze count time series with excess zeros. Two types of statistical
17654 models are supported: Markov regression and state-space models. They are also
17655 known as observation-driven and parameter-driven models respectively in the
17656 time series literature. The functions used for Markov regression or
17657 observation-driven models can also be used to fit ordinary regression models
17658 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
17659 negative binomial (ZINB) assumption. The package also contains miscellaneous
17660 functions to compute density, distribution, quantile, and generate random
17661 numbers from ZIP and ZINB distributions.")
17662 (license license:gpl3)))
17664 (define-public r-nor1mix
17671 (uri (cran-uri "nor1mix" version))
17674 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
17675 (build-system r-build-system)
17676 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
17677 (synopsis "Normal (1-d) mixture models")
17679 "This package provides S3 classes and methods for one-dimensional normal
17680 mixture models, for, e.g., density estimation or clustering algorithms
17681 research and teaching; it provides the widely used Marron-Wand densities. It
17682 also provides tools for efficient random number generation and graphics.")
17683 (license license:gpl2+)))
17685 (define-public r-beanplot
17687 (name "r-beanplot")
17692 (uri (cran-uri "beanplot" version))
17695 "1b8mvlcsv5l9g08ag92hndsvk8jmgxvznhzgazc8y4296kp8l5a9"))))
17696 (build-system r-build-system)
17697 (home-page "https://cran.r-project.org/web/packages/beanplot/")
17698 (synopsis "Visualization via beanplots")
17700 "This package provides beanplots, an alternative to
17701 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
17703 (license license:gpl2)))
17705 (define-public r-pbdzmq
17712 (uri (cran-uri "pbdZMQ" version))
17715 "020qy6fq8w8wq0j3bii14ahrlg8wzl0lrnndfr6scmrg9ghjnbfz"))))
17716 (properties `((upstream-name . "pbdZMQ")))
17717 (build-system r-build-system)
17719 (list zeromq zlib))
17722 (home-page "https://pbdr.org/")
17723 (synopsis "R interface to ZeroMQ")
17725 "ZeroMQ is a well-known library for high-performance asynchronous
17726 messaging in scalable, distributed applications. This package provides high
17727 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
17728 interactive client/server programming frameworks. A few wrapper functions
17729 compatible with @code{rzmq} are also provided.")
17730 (license license:gpl3)))
17732 (define-public r-repr
17739 (uri (cran-uri "repr" version))
17742 "0h3h14ybamcbwmm31ib66fx13v75vkzn4bn2v26n2h097sl9qybg"))))
17743 (build-system r-build-system)
17745 (list r-base64enc r-htmltools r-jsonlite r-pillar))
17746 (home-page "https://cran.r-project.org/web/packages/repr/")
17747 (synopsis "Serializable representations")
17749 "This package provides string and binary representations of objects for
17750 several formats and MIME types.")
17751 (license license:gpl3)))
17753 (define-public r-irdisplay
17755 (name "r-irdisplay")
17760 (uri (cran-uri "IRdisplay" version))
17763 "0awdiv4rr93y8jb1d64sm1iy37ywyniqm7w98yv6qm0zz47h7sw3"))))
17764 (properties `((upstream-name . "IRdisplay")))
17765 (build-system r-build-system)
17768 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
17769 (synopsis "Jupyter display machinery")
17771 "This package provides an interface to the rich display capabilities of
17772 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
17773 running IRkernel session.")
17774 (license license:expat)))
17776 (define-public r-irkernel
17778 (name "r-irkernel")
17783 (uri (cran-uri "IRkernel" version))
17786 "00qrmsywpzw2hfp88020zjaijma7q4hqm9h2cz53rywdjzywnzss"))))
17787 (properties `((upstream-name . "IRkernel")))
17788 (build-system r-build-system)
17791 (modify-phases %standard-phases
17792 (add-after 'install 'install-kernelspec
17793 (lambda* (#:key outputs #:allow-other-keys)
17794 (let ((out (assoc-ref outputs "out")))
17795 (setenv "HOME" "/tmp")
17796 (invoke "jupyter" "kernelspec" "install"
17799 (string-append out "/site-library/IRkernel/kernelspec"))
17800 ;; Record the absolute file name of the 'R' executable in
17802 (substitute* (string-append out "/share/jupyter"
17803 "/kernels/ir/kernel.json")
17805 (string-append "[\"" (which "R") "\",")))
17815 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
17820 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
17821 (synopsis "Native R kernel for Jupyter")
17823 "The R kernel for the Jupyter environment executes R code which the
17824 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
17826 (license license:expat)))
17828 (define-public r-gmodels
17831 (version "2.18.1.1")
17835 (uri (cran-uri "gmodels" version))
17838 "158y7yh4maawn9vki8cq4sil48xib2bbpl6qgj5gvlkw3c14hzfs"))))
17839 (build-system r-build-system)
17841 (list r-gdata r-mass))
17842 (home-page "https://cran.r-project.org/web/packages/gmodels/")
17843 (synopsis "Various R programming tools for model fitting")
17845 "This package provides various R programming tools for model fitting.")
17846 (license license:gpl2)))
17848 (define-public r-apcluster
17850 (name "r-apcluster")
17855 (uri (cran-uri "apcluster" version))
17858 "1820j1xjlbmw6j2fwwv2g806dqpk5qrbbaqsrbrn6igql8pzf552"))))
17859 (build-system r-build-system)
17861 (list r-matrix r-rcpp))
17862 (native-inputs (list r-knitr))
17863 (home-page "https://cran.r-project.org/web/packages/apcluster/")
17864 (synopsis "Affinity propagation clustering")
17866 "This package implements affinity propagation clustering introduced by
17867 Frey and Dueck (2007). The package further provides leveraged affinity
17868 propagation and an algorithm for exemplar-based agglomerative clustering that
17869 can also be used to join clusters obtained from affinity propagation. Various
17870 plotting functions are available for analyzing clustering results.")
17871 (license license:gpl2+)))
17873 (define-public r-rematch2
17875 (name "r-rematch2")
17880 (uri (cran-uri "rematch2" version))
17883 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
17884 (build-system r-build-system)
17887 (home-page "https://github.com/r-lib/rematch2")
17888 (synopsis "Tidy output from regular expression matching")
17890 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
17891 return the match results in tidy data frames.")
17892 (license license:expat)))
17894 (define-public r-picante
17901 (uri (cran-uri "picante" version))
17904 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
17905 (build-system r-build-system)
17907 (list r-ape r-nlme r-vegan))
17908 (home-page "https://cran.r-project.org/web/packages/picante/")
17909 (synopsis "Integrating phylogenies and ecology")
17911 "This package provides functions for phylocom integration, community
17912 analyses, null-models, traits and evolution. It implements numerous
17913 ecophylogenetic approaches including measures of community phylogenetic and
17914 trait diversity, phylogenetic signal, estimation of trait values for
17915 unobserved taxa, null models for community and phylogeny randomizations, and
17916 utility functions for data input/output and phylogeny plotting. A full
17917 description of package functionality and methods are provided by Kembel et
17919 (license license:gpl2)))
17921 (define-public r-reinforcelearn
17923 (name "r-reinforcelearn")
17928 (uri (cran-uri "reinforcelearn" version))
17931 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
17932 (build-system r-build-system)
17934 (list r-checkmate r-nnet r-purrr r-r6))
17935 (home-page "https://markusdumke.github.io/reinforcelearn")
17936 (synopsis "Reinforcement learning")
17938 "This package implements reinforcement learning environments and
17939 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
17940 can be used with function approximation, eligibility traces (Singh & Sutton,
17941 1996) and experience replay (Mnih et al., 2013).")
17942 (license license:expat)))
17944 (define-public r-lemon
17951 (uri (cran-uri "lemon" version))
17954 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
17955 (build-system r-build-system)
17967 (home-page "https://github.com/stefanedwards/lemon")
17968 (synopsis "Freshen up your ggplot2 plots")
17970 "This package provides functions for working with legends and axis lines
17971 of ggplot2, facets that repeat axis lines on all panels, and some knitr
17973 (license license:gpl3)))
17975 (define-public r-wgaim
17982 (uri (cran-uri "wgaim" version))
17984 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
17985 (build-system r-build-system)
17987 (list r-ggplot2 r-qtl))
17988 (home-page "https://cran.r-project.org/web/packages/wgaim")
17989 (synopsis "Whole genome average interval mapping for QTL detection")
17991 "This package integrates sophisticated mixed modelling methods with a
17992 whole genome approach to detecting significant QTL in linkage maps.")
17993 (license license:gpl2+)))
17995 (define-public r-bedr
18002 (uri (cran-uri "bedr" version))
18005 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
18006 (build-system r-build-system)
18015 htslib)) ; for tabix
18017 (list r-knitr)) ; for vignettes
18018 (home-page "https://cran.r-project.org/web/packages/bedr")
18019 (synopsis "Genomic region processing")
18021 "This package is for genomic regions processing using command line tools
18022 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
18023 utilities to perform genome arithmetic e.g indexing, formatting and merging.
18024 The bedr package's API enhances access to these tools as well as offers
18025 additional utilities for genomic regions processing.")
18026 (license license:gpl2)))
18028 (define-public r-sets
18035 (uri (cran-uri "sets" version))
18038 "1h1a03b1850kh5hd3gxbspx2nxqxvk2gb0wm0s60b70qb6zg0csp"))))
18039 (properties `((upstream-name . "sets")))
18040 (build-system r-build-system)
18041 (home-page "https://cran.r-project.org/web/packages/sets")
18042 (synopsis "Sets, generalized sets, customizable sets and intervals")
18044 "This package provides data structures and basic operations for ordinary
18045 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
18046 customizable sets, and intervals.")
18047 (license license:gpl2)))
18049 (define-public r-partitions
18051 (name "r-partitions")
18056 (uri (cran-uri "partitions" version))
18059 "1kxiy1wl7dr39kyfg2y9hd67s32knd83r2jsb7j9p3vg8iqq7yqb"))))
18060 (build-system r-build-system)
18062 (list r-gmp r-mathjaxr r-polynom r-rdpack r-sets))
18063 (home-page "https://cran.r-project.org/web/packages/partitions")
18064 (synopsis "Additive partitions of integers")
18066 "This package provides tools to enumerates the partitions, unequal
18067 partitions, and restricted partitions of an integer; the three corresponding
18068 partition functions are also given.")
18069 ;; Any version of the GPL
18070 (license license:gpl2+)))
18072 (define-public r-brobdingnag
18074 (name "r-brobdingnag")
18079 (uri (cran-uri "Brobdingnag" version))
18082 "0hnp5nrpnscykvgrrbgp7987660hcbv92zc2q8lmpnin4ws399vk"))))
18083 (properties `((upstream-name . "Brobdingnag")))
18084 (build-system r-build-system)
18085 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
18086 (synopsis "Very large numbers in R")
18088 "This package handles very large numbers in R. Real numbers are held
18089 using their natural logarithms, plus a logical flag indicating sign. The
18090 package includes a vignette that gives a step-by-step introduction to using S4
18092 ;; Any version of the GPL
18093 (license license:gpl2+)))
18095 (define-public r-untb
18102 (uri (cran-uri "untb" version))
18105 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
18106 (build-system r-build-system)
18108 (list r-brobdingnag r-partitions r-polynom))
18109 (home-page "https://github.com/RobinHankin/untb.git")
18110 (synopsis "Ecological drift under the UNTB")
18112 "This package provides numerical simulations, and visualizations, of
18113 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
18114 (license license:gpl2+)))
18116 (define-public r-stepwise
18118 (name "r-stepwise")
18123 (uri (cran-uri "stepwise" version))
18126 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
18127 (build-system r-build-system)
18128 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
18129 (synopsis "Stepwise detection of recombination breakpoints")
18131 "This package provides a stepwise approach to identifying recombination
18132 breakpoints in a genomic sequence alignment.")
18133 (license license:gpl2+)))
18135 (define-public r-snpmaxsel
18137 (name "r-snpmaxsel")
18142 (uri (cran-uri "SNPmaxsel" version))
18145 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
18146 (properties `((upstream-name . "SNPmaxsel")))
18147 (build-system r-build-system)
18149 (list r-combinat r-mvtnorm))
18150 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
18151 (synopsis "Maximally selected statistics for SNP data")
18153 "This package implements asymptotic methods related to maximally selected
18154 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
18156 (license license:gpl2+)))
18158 (define-public r-acsnminer
18160 (name "r-acsnminer")
18161 (version "0.16.8.25")
18164 (uri (cran-uri "ACSNMineR" version))
18167 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
18168 (properties `((upstream-name . "ACSNMineR")))
18169 (build-system r-build-system)
18171 (list r-ggplot2 r-gridextra))
18172 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
18173 (synopsis "Gene enrichment analysis")
18175 "This package provides tools to compute and represent gene set enrichment
18176 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
18177 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
18178 enrichment can be run with hypergeometric test or Fisher exact test, and can
18179 use multiple corrections. Visualization of data can be done either by
18180 barplots or heatmaps.")
18181 (license license:gpl2+)))
18183 (define-public r-seqinr
18190 (uri (cran-uri "seqinr" version))
18193 "0cj07b7km5mla63qhbkxg1mnqq6vh79lsyyfpnbm29gw68w2bwy4"))))
18194 (build-system r-build-system)
18196 (list r-ade4 r-segmented))
18199 (home-page "http://seqinr.r-forge.r-project.org/")
18200 (synopsis "Biological sequences retrieval and analysis")
18202 "This package provides tools for exploratory data analysis and data
18203 visualization of biological sequence (DNA and protein) data. It also includes
18204 utilities for sequence data management under the ACNUC system.")
18205 (license license:gpl2+)))
18207 (define-public r-units
18214 (uri (cran-uri "units" version))
18217 "06mjprqi06xprj6185k5cmrrdl025x0pd1r6a4x3s74ciq9zwilw"))))
18218 (build-system r-build-system)
18225 (home-page "https://github.com/r-quantities/units/")
18226 (synopsis "Measurement Units for R Vectors")
18228 "This package provides support for measurement units in R vectors,
18229 matrices and arrays: automatic propagation, conversion, derivation and
18230 simplification of units; raising errors in case of unit incompatibility. It
18231 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
18233 (license license:gpl2)))
18235 (define-public r-udunits2
18237 (name "r-udunits2")
18238 (version "0.13.2.1")
18242 (uri (cran-uri "udunits2" version))
18245 "00prsy8m41v1camcsz94d7gm8qab2mdnwl3x0dyhz4r49b02jm4z"))))
18246 (properties `((upstream-name . "udunits2")))
18247 (build-system r-build-system)
18250 (home-page "https://cran.r-project.org/package=udunits2")
18251 (synopsis "Udunits-2 bindings for R")
18253 "This package provides simple bindings to Unidata's udunits library.")
18254 (license license:gpl2)))
18256 (define-public r-classint
18258 (name "r-classint")
18263 (uri (cran-uri "classInt" version))
18266 "0vk06k10mxcm6wn4b74njzc1kc1ividsn03ii523j4yfhy4kl3m3"))))
18267 (properties `((upstream-name . "classInt")))
18268 (build-system r-build-system)
18270 (list r-class r-e1071 r-kernsmooth))
18272 (list gfortran r-knitr))
18273 (home-page "https://github.com/r-spatial/classInt/")
18274 (synopsis "Choose univariate class intervals")
18276 "This package provides selected commonly used methods for choosing
18277 univariate class intervals for mapping or other graphics purposes.")
18278 (license license:gpl2+)))
18280 (define-public r-spdata
18287 (uri (cran-uri "spData" version))
18290 "07whxr039cxvk2nn65jada3i8vqqw34lgca9j17ah8chy9r0m73f"))))
18291 (properties `((upstream-name . "spData")))
18292 (build-system r-build-system)
18295 (home-page "https://github.com/Nowosad/spData")
18296 (synopsis "Datasets for spatial analysis")
18298 "This a package containing diverse spatial datasets for demonstrating,
18299 benchmarking and teaching spatial data analysis. It includes R data of class
18300 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
18301 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
18302 of the datasets are designed to illustrate specific analysis techniques.
18303 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
18304 illustrate point pattern analysis techniques.")
18305 (license license:cc0)))
18307 (define-public r-learnbayes
18309 (name "r-learnbayes")
18314 (uri (cran-uri "LearnBayes" version))
18317 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
18318 (properties `((upstream-name . "LearnBayes")))
18319 (build-system r-build-system)
18320 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
18321 (synopsis "Functions for learning Bayesian inference")
18323 "This package provides a collection of functions helpful in learning the
18324 basic tenets of Bayesian statistical inference. It contains functions for
18325 summarizing basic one and two parameter posterior distributions and predictive
18326 distributions. It contains MCMC algorithms for summarizing posterior
18327 distributions defined by the user. It also contains functions for regression
18328 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
18330 (license license:gpl2+)))
18332 (define-public r-deldir
18339 (uri (cran-uri "deldir" version))
18342 "1igq0l2knsbhizncgydcsidgkvvlwwlkrifbcdyhnzk0bhrdixkd"))))
18343 (build-system r-build-system)
18344 (native-inputs (list gfortran))
18345 (home-page "https://cran.r-project.org/web/packages/deldir")
18346 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
18348 "This package provides tools for calculating the Delaunay triangulation
18349 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
18350 of a planar point set. It plots triangulations and tessellations in various
18351 ways, clips tessellations to sub-windows, calculates perimeters of
18352 tessellations, and summarizes information about the tiles of the
18354 (license license:gpl2+)))
18356 (define-public r-wk
18363 (uri (cran-uri "wk" version))
18366 "1xga4rrqsr190g55by39az4nimnn06bf5b6mcjgwqvba0lvjhb5g"))))
18367 (properties `((upstream-name . "wk")))
18368 (build-system r-build-system)
18369 (home-page "https://paleolimbot.github.io/wk/")
18370 (synopsis "Lightweight well-known geometry parsing")
18372 "This package provides a minimal R and C++ API for parsing well-known
18373 binary and well-known text representation of geometries to and from R-native
18374 formats. Well-known binary is compact and fast to parse; well-known text is
18375 human-readable and is useful for writing tests. These formats are only useful
18376 in R if the information they contain can be accessed in R, for which
18377 high-performance functions are provided here.")
18378 (license license:expat)))
18380 (define-public r-s2
18387 (uri (cran-uri "s2" version))
18390 "05n459rp5b1wk826sq3c5d2z1xwgkpfp8m1jnfshvs4gadlfkap3"))))
18391 (properties `((upstream-name . "s2")))
18392 (build-system r-build-system)
18396 `(modify-phases %standard-phases
18397 ;; We don't want to convert -lssl to -l:libssl.so.1.1; there is only
18398 ;; one libssl.so anyway and the -l:* thing breaks linking.
18399 (add-after 'unpack 'undo-library-versioning
18401 (substitute* "configure"
18402 (("PKG_LIBS_VERSIONED=.*")
18403 "PKG_LIBS_VERSIONED=\"${PKG_LIBS}\"\n")))))))
18405 (list r-rcpp r-wk))
18410 (home-page "https://r-spatial.github.io/s2/")
18411 (synopsis "Spherical geometry operators using the S2 geometry library")
18413 "This package provides R bindings for Google's s2 library for geometric
18414 calculations on the sphere. High-performance constructors and exporters
18415 provide high compatibility with existing spatial packages, transformers
18416 construct new geometries from existing geometries, predicates provide a means
18417 to select geometries based on spatial relationships, and accessors extract
18418 information about geometries.")
18419 (license license:asl2.0)))
18421 (define-public r-sf
18428 (uri (cran-uri "sf" version))
18431 "0cl7m47ar3iw95rpwpmjl23frdbscxa15q39mlzmwswxwy871p1x"))))
18432 (build-system r-build-system)
18434 (list gdal geos proj sqlite zlib))
18443 (list pkg-config r-knitr))
18444 (home-page "https://github.com/r-spatial/sf/")
18445 (synopsis "Simple features for R")
18447 "This package provides support for simple features, a standardized way to
18448 encode spatial vector data. It binds to GDAL for reading and writing data, to
18449 GEOS for geometrical operations, and to PROJ for projection conversions and
18450 datum transformations.")
18451 ;; Either of these licenses
18452 (license (list license:gpl2 license:expat))))
18454 (define-public r-spdep
18460 (uri (cran-uri "spdep" version))
18463 "1ib5jgahjgjpj2ajp5g71r4fw0q1zkddixgmywi1n73nqr39qwp2"))
18465 '(for-each delete-file '("inst/doc/CO69.html"
18469 "inst/doc/nb_sf.html"
18471 "inst/doc/nb_sf.Rmd"
18472 "inst/doc/sids.html"
18473 "inst/doc/sids.R")))))
18474 (build-system r-build-system)
18486 (home-page "https://github.com/r-spatial/spdep/")
18487 (synopsis "Spatial dependence: weighting schemes, statistics and models")
18489 "This package provides a collection of functions to create spatial
18490 weights matrix objects from polygon contiguities, from point patterns by
18491 distance and tessellations, for summarizing these objects, and for permitting
18492 their use in spatial data analysis, including regional aggregation by minimum
18494 (license license:gpl2+)))
18496 (define-public r-adegenet
18498 (name "r-adegenet")
18503 (uri (cran-uri "adegenet" version))
18506 "0zkbxw9w0fcb4s3zv2a8nxcsihzkfz49psaipxw99nwgm7l9jrh9"))))
18507 (build-system r-build-system)
18520 (home-page "https://github.com/thibautjombart/adegenet")
18521 (synopsis "Exploratory analysis of genetic and genomic data")
18523 "This package provides a toolset for the exploration of genetic and
18524 genomic data. Adegenet provides formal (S4) classes for storing and handling
18525 various genetic data, including genetic markers with varying ploidy and
18526 hierarchical population structure (@code{genind} class), alleles counts by
18527 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
18528 also implements original multivariate methods (DAPC, sPCA), graphics,
18529 statistical tests, simulation tools, distance and similarity measures, and
18530 several spatial methods. A range of both empirical and simulated datasets is
18531 also provided to illustrate various methods.")
18532 (license license:gpl2+)))
18534 (define-public r-pegas
18541 (uri (cran-uri "pegas" version))
18543 (base32 "0ngd0laqbs139ji9hm9kwsm9rm56agw2yyfcplxgqva936l93fl7"))))
18544 (build-system r-build-system)
18547 (home-page "http://ape-package.ird.fr/pegas.html")
18548 (synopsis "Population and evolutionary genetics analysis system")
18550 "This package provides functions for reading, writing, plotting,
18551 analysing, and manipulating allelic and haplotypic data, including from VCF
18552 files, and for the analysis of population nucleotide sequences and
18553 micro-satellites including coalescent analyses, linkage disequilibrium,
18554 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
18555 minimum spanning tree and network, and median-joining networks.")
18556 (license license:gpl2+)))
18558 (define-public r-rmetasim
18560 (name "r-rmetasim")
18565 (uri (cran-uri "rmetasim" version))
18568 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
18569 (build-system r-build-system)
18571 (list r-ade4 r-adegenet r-gtools r-pegas))
18572 (home-page "https://cran.r-project.org/web/packages/rmetasim")
18573 (synopsis "Individual-based population genetic simulation environment")
18575 "This package provides an interface between R and the metasim simulation
18576 engine. The simulation environment is documented in: Strand, A.(2002),
18577 Metasim 1.0: an individual-based environment for simulating population
18578 genetics of complex population dynamics.")
18580 (license license:gpl2+)))
18582 (define-public r-genetics
18584 (name "r-genetics")
18585 (version "1.3.8.1.3")
18589 (uri (cran-uri "genetics" version))
18592 "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy"))))
18593 (build-system r-build-system)
18595 (list r-combinat r-gdata r-gtools r-mass r-mvtnorm))
18596 (home-page "https://cran.r-project.org/web/packages/genetics/")
18597 (synopsis "Population genetics")
18599 "This package provides classes and methods for handling genetic data.
18600 It includes classes to represent genotypes and haplotypes at single markers up
18601 to multiple markers on multiple chromosomes. Function include allele
18602 frequencies, flagging homo/heterozygotes, flagging carriers of certain
18603 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
18604 and testing for linkage disequilibrium, ...")
18605 ;; Any GPL version.
18606 (license license:gpl2+)))
18608 (define-public r-snp-plotter
18610 (name "r-snp-plotter")
18615 (uri (cran-uri "snp.plotter" version))
18618 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
18619 (properties `((upstream-name . "snp.plotter")))
18620 (build-system r-build-system)
18621 (propagated-inputs (list r-genetics))
18622 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
18623 (synopsis "Plot p-values using single SNP and/or haplotype data")
18625 "This package helps you create plots of p-values using single SNP and/or
18626 haplotype data. Main features of the package include options to display a
18627 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
18628 datasets simultaneously. Plots can be created using global and/or individual
18629 haplotype p-values along with single SNP p-values. Images are created as
18630 either PDF/EPS files.")
18631 (license license:gpl2+)))
18633 (define-public r-polspline
18635 (name "r-polspline")
18640 (uri (cran-uri "polspline" version))
18642 (base32 "1dd1jwiaglkkhajzvqfkd1x5r3wzjlk5ww0yxzmns0s1kr74i4k9"))))
18643 (build-system r-build-system)
18644 (native-inputs (list gfortran))
18645 (home-page "https://cran.r-project.org/web/packages/polspline/")
18646 (synopsis "Polynomial spline routines")
18648 "This package provides routines for the polynomial spline fitting
18649 routines hazard regression, hazard estimation with flexible tails, logspline,
18650 lspec, polyclass, and polymars.")
18651 (license license:gpl2+)))
18653 (define-public r-rms
18660 (uri (cran-uri "rms" version))
18662 (base32 "1yfk800q4mgmrjkh0hqjkiv907sr1bi1jaigrj8l6pmg1mkynhbc"))))
18663 (build-system r-build-system)
18680 (native-inputs (list gfortran))
18681 (home-page "http://biostat.mc.vanderbilt.edu/rms")
18682 (synopsis "Regression modeling strategies")
18684 "This is a package for regression modeling, testing, estimation,
18685 validation, graphics, prediction, and typesetting by storing enhanced model
18686 design attributes in the fit. The rms package is a collection of functions
18687 that assist with and streamline modeling. It also contains functions for
18688 binary and ordinal logistic regression models, ordinal models for continuous Y
18689 with a variety of distribution families, and the Buckley-James multiple
18690 regression model for right-censored responses, and implements penalized
18691 maximum likelihood estimation for logistic and ordinary linear models. The
18692 package works with almost any regression model, but it was especially written
18693 to work with binary or ordinal regression models, Cox regression, accelerated
18694 failure time models, ordinary linear models, the Buckley-James model,
18695 generalized least squares for serially or spatially correlated observations,
18696 generalized linear models, and quantile regression.")
18697 (license license:gpl2+)))
18699 (define-public r-arsenal
18706 (uri (cran-uri "arsenal" version))
18709 "0qvs3ld28djnjnggdhqjwq8sbv8zz322qahlvf7dnx35yqf6xkms"))))
18710 (properties `((upstream-name . "arsenal")))
18711 (build-system r-build-system)
18712 (propagated-inputs (list r-knitr))
18713 (native-inputs (list r-knitr))
18714 (home-page "https://github.com/mayoverse/arsenal")
18715 (synopsis "Functions for large-scale statistical summaries")
18717 "This package provides an arsenal of R functions for large-scale
18718 statistical summaries, which are streamlined to work within the latest
18719 reporting tools in R and RStudio and which use formulas and versatile
18720 summary statistics for summary tables and models. The primary functions
18724 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
18725 levels of one or more categorical variables;
18726 @item @code{paired}, a Table-1-like summary of multiple variable types paired
18727 across two time points;
18728 @item @code{modelsum}, which performs simple model fits on one or more
18729 endpoints for many variables (univariate or adjusted for covariates);
18730 @item @code{freqlist}, a powerful frequency table across many categorical
18732 @item @code{comparedf}, a function for comparing @code{data.frames}; and
18733 @item @code{write2}, a function to output tables to a document.
18736 (license license:gpl2+)))
18738 (define-public r-haplo-stats
18740 (name "r-haplo-stats")
18745 (uri (cran-uri "haplo.stats" version))
18748 "0np9kw4f30xbvwr4f79g909ilis5n273ridmlwyzjxiskiry6mx0"))))
18749 (properties `((upstream-name . "haplo.stats")))
18750 (build-system r-build-system)
18752 (list r-arsenal r-rms))
18754 (list r-r-rsp)) ; for vignettes
18755 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
18756 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
18758 "This package provides routines for the analysis of indirectly measured
18759 haplotypes. The statistical methods assume that all subjects are unrelated
18760 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
18761 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
18762 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
18763 examples in the vignette.")
18764 (license license:gpl2+)))
18766 (define-public r-bqtl
18773 (uri (cran-uri "bqtl" version))
18776 "1sbzpi9z94f010lw2y1gmifjrvpmiqs4m26za7vr1xz72azrqvs9"))))
18777 (build-system r-build-system)
18778 (native-inputs (list gfortran))
18779 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
18780 (synopsis "Bayesian QTL mapping toolkit")
18782 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
18783 lines. It includes maximum likelihood and Bayesian tools.")
18784 (license license:gpl2+)))
18786 (define-public r-ibdreg
18793 (uri (cran-uri "ibdreg" version))
18796 "1x8z0vr2cmdks12hxfm0wwxskb0cr669w5j5rpa2ln8q704yy41g"))))
18797 (build-system r-build-system)
18798 (home-page "https://www.mayo.edu/research/labs/\
18799 statistical-genetics-genetic-epidemiology/software")
18800 (synopsis "Regression methods for IBD linkage with covariates")
18802 "This package provides a method to test genetic linkage with covariates
18803 by regression methods with response IBD sharing for relative pairs. Account
18804 for correlations of IBD statistics and covariates for relative pairs within
18805 the same pedigree.")
18806 (license license:gpl2+)))
18808 (define-public r-dlmap
18815 (uri (cran-uri "dlmap" version))
18818 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
18819 (build-system r-build-system)
18821 (list r-ibdreg r-mgcv r-nlme r-qtl r-wgaim))
18822 (home-page "https://cran.r-project.org/web/packages/dlmap/")
18823 (synopsis "Detection localization mapping for QTL")
18825 "This is package for QTL mapping in a mixed model framework with separate
18826 detection and localization stages. The first stage detects the number of QTL
18827 on each chromosome based on the genetic variation due to grouped markers on
18828 the chromosome; the second stage uses this information to determine the most
18829 likely QTL positions. The mixed model can accommodate general fixed and
18830 random effects, including spatial effects in field trials and pedigree
18831 effects. It is applicable to backcrosses, doubled haploids, recombinant
18832 inbred lines, F2 intercrosses, and association mapping populations.")
18833 (license license:gpl2)))
18835 (define-public r-hwde
18842 (uri (cran-uri "hwde" version))
18845 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
18846 (build-system r-build-system)
18847 (home-page "https://cran.r-project.org/web/packages/hwde/")
18848 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
18850 "This package fits models for genotypic disequilibria, as described in
18851 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
18852 terms are available that account for first order interactions between loci.
18853 It also implements, for a single locus in a single population, a conditional
18854 exact test for Hardy-Weinberg equilibrium.")
18855 (license license:gpl2+)))
18857 (define-public r-tdthap
18864 (uri (cran-uri "tdthap" version))
18867 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
18868 (build-system r-build-system)
18869 (home-page "https://cran.r-project.org/web/packages/tdthap/")
18870 (synopsis "TDT tests for extended haplotypes")
18872 "Functions and examples are provided for transmission/disequilibrium
18873 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
18874 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
18875 (license license:artistic2.0)))
18877 (define-public r-sparql
18883 (uri (cran-uri "SPARQL" version))
18886 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
18887 (properties `((upstream-name . "SPARQL")))
18888 (build-system r-build-system)
18890 (list r-rcurl r-xml))
18891 (home-page "https://cran.r-project.org/web/packages/SPARQL")
18892 (synopsis "SPARQL client for R")
18893 (description "This package provides an interface to use SPARQL to pose
18894 SELECT or UPDATE queries to an end-point.")
18895 ;; The only license indication is found in the DESCRIPTION file,
18896 ;; which states GPL-3. So we cannot assume GPLv3+.
18897 (license license:gpl3)))
18899 (define-public r-bookdown
18901 (name "r-bookdown")
18905 (uri (cran-uri "bookdown" version))
18908 "08zpky94bdbjsbhi90pymxpczpfkjxwbx7p1v7ip8raw9b23skjv"))))
18909 (build-system r-build-system)
18919 ;; We cannot add knitr because this package depends on xfun, which is an
18924 (home-page "https://github.com/rstudio/bookdown")
18925 (synopsis "Authoring books and technical documents with R markdown")
18926 (description "This package provides output formats and utilities for
18927 authoring books and technical documents with R Markdown.")
18928 (license license:gpl3)))
18930 (define-public r-optparse
18932 (name "r-optparse")
18937 (uri (cran-uri "optparse" version))
18940 "1v87db7fm494dwxvdsnl1m2kj84nplq7pkh0g41najhx0npy31v2"))))
18941 (build-system r-build-system)
18946 (home-page "https://github.com/trevorld/optparse")
18947 (synopsis "Command line option parser")
18949 "This package provides a command line parser inspired by Python's
18950 @code{optparse} library to be used with Rscript to write shebang scripts
18951 that accept short and long options.")
18952 (license license:gpl2+)))
18954 (define-public r-kernlab
18961 (uri (cran-uri "kernlab" version))
18963 (base32 "12i7ffc1aacyy7bpjc0w60wwivn88wri8jz43h77irn5q5jwcnbk"))))
18964 (build-system r-build-system)
18965 (home-page "https://cran.r-project.org/web/packages/kernlab")
18966 (synopsis "Kernel-based machine learning tools")
18968 "This package provides kernel-based machine learning methods for
18969 classification, regression, clustering, novelty detection, quantile regression
18970 and dimensionality reduction. Among other methods @code{kernlab} includes
18971 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
18973 (license license:gpl2)))
18975 (define-public r-hierfstat
18977 (name "r-hierfstat")
18982 (uri (cran-uri "hierfstat" version))
18985 "0nyb5091lr8ma9vydbssyx9503601rynlrbldv98mmrmh74h6v41"))))
18986 (build-system r-build-system)
18988 (list r-ade4 r-adegenet r-gaston r-gtools))
18991 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
18992 (synopsis "Estimation and tests of hierarchical F-statistics")
18994 "This package allows the estimation of hierarchical F-statistics from
18995 haploid or diploid genetic data with any numbers of levels in the hierarchy,
18996 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
18997 are also given to test via randomisations the significance of each F and
18998 variance components, using the likelihood-ratio statistics G.")
18999 (license license:gpl2+)))
19001 (define-public r-hapassoc
19003 (name "r-hapassoc")
19008 (uri (cran-uri "hapassoc" version))
19011 "09ijc4sbw743z74fzklmvig11ndkycg6j86k4214wfsj1yj6j9x6"))))
19012 (build-system r-build-system)
19013 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
19014 (synopsis "Inference of trait associations with SNP haplotypes")
19016 "Hapassoc performs likelihood inference of trait associations with
19017 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
19018 functions are developed primarily for data collected in cohort or
19019 cross-sectional studies. They can accommodate uncertain haplotype phase and
19020 handle missing genotypes at some SNPs.")
19021 (license license:gpl2)))
19023 (define-public r-sampling
19025 (name "r-sampling")
19030 (uri (cran-uri "sampling" version))
19033 "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz"))))
19034 (build-system r-build-system)
19036 (list r-lpsolve r-mass))
19037 (home-page "https://cran.r-project.org/web/packages/sampling/")
19038 (synopsis "Survey sampling")
19040 "This package provides functions for drawing and calibrating samples.")
19041 (license license:gpl2+)))
19043 (define-public r-r2html
19050 (uri (cran-uri "R2HTML" version))
19053 "12qg9rp1j26h2f48dfg5k9jds26ycacv3f3ymk686ks43hd1hzja"))))
19054 (properties `((upstream-name . "R2HTML")))
19055 (build-system r-build-system)
19056 (home-page "https://github.com/nalimilan/R2HTML")
19057 (synopsis "HTML export for R objects")
19059 "This package includes HTML functions and methods to write in an HTML
19060 file. Thus, making HTML reports is easy. It includes a function that allows
19061 redirection on the fly, which appears to be very useful for teaching purposes,
19062 as the student can keep a copy of the produced output to keep all that they
19063 did during the course. The package comes with a vignette describing how to
19064 write HTML reports for statistical analysis. Finally, a driver for Sweave
19065 parses HTML flat files containing R code and to automatically write
19066 the corresponding outputs (tables and graphs).")
19067 (license license:gpl2+)))
19069 (define-public r-rjava
19076 (uri (cran-uri "rJava" version))
19079 "1ijqhvnb8ab38cp9pwdf7zq7xqqlm6x94gkrab2dd98p6d4x1472"))))
19080 (properties `((upstream-name . "rJava")))
19081 (build-system r-build-system)
19083 `(#:modules ((guix build utils)
19084 (guix build r-build-system)
19087 (modify-phases %standard-phases
19088 (add-after 'unpack 'set-JAVA_HOME
19089 (lambda* (#:key inputs #:allow-other-keys)
19090 (let ((jdk (assoc-ref inputs "jdk")))
19091 (setenv "JAVA_HOME" jdk)
19092 (setenv "JAVA" (which "java"))
19093 (setenv "JAR" (which "jar"))
19094 (setenv "JAVAC" (which "javac"))
19095 (setenv "JAVAH" (which "javah"))
19096 (setenv "JAVA_CPPFLAGS"
19097 (string-append "-I" jdk "/include "
19098 "-I" jdk "/include/linux"))
19099 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
19100 ((lib) (setenv "JAVA_LIBS" lib))
19101 (_ (error "Could not find libjvm.so"))))
19105 ("jdk" ,icedtea-8 "jdk")
19107 (home-page "https://www.rforge.net/rJava/")
19108 (synopsis "Low-Level R to Java interface")
19110 "This package provides a low-level interface to the Java VM very much
19111 like .C/.Call and friends. It allows the creation of objects, calling methods
19112 and accessing fields.")
19113 (license license:gpl2)))
19115 (define-public r-svmisc
19122 (uri (cran-uri "svMisc" version))
19125 "1r3kih5bnr4plnzdn5f2gg3xl3krgyl7gkdlf58a2l8vk13j3m9d"))))
19126 (properties `((upstream-name . "svMisc")))
19127 (build-system r-build-system)
19130 (home-page "https://github.com/SciViews/svMisc")
19131 (synopsis "Miscellaneous functions for SciViews")
19133 "This package provides miscellaneous functions for SciViews or general
19134 use, including tools to manage a temporary environment attached to the search
19135 path for temporary variables you do not want to @code{save()} or
19136 @code{load()}; test the current platform; showing progress bars, etc.")
19137 (license license:gpl2)))
19139 (define-public r-xyz
19146 (uri (cran-uri "xyz" version))
19149 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
19150 (build-system r-build-system)
19153 (home-page "https://cran.r-project.org/web/packages/xyz/")
19154 (synopsis "Algorithm for fast interaction search in high-dimensional data")
19156 "High dimensional interaction search by brute force requires a quadratic
19157 computational cost in the number of variables. The xyz algorithm provably
19158 finds strong interactions in almost linear time. For details of the algorithm
19159 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
19160 interaction search in high-dimensional data.")
19161 ;; Any version of the GPL.
19162 (license license:gpl2+)))
19164 (define-public r-rttf2pt1
19166 (name "r-rttf2pt1")
19171 (uri (cran-uri "Rttf2pt1" version))
19174 "1fp1y0kxa5xg8w0dplm12wfm8h78az4k6ql1758wwhb3d17np241"))))
19175 (properties `((upstream-name . "Rttf2pt1")))
19176 (build-system r-build-system)
19177 (home-page "https://github.com/wch/Rttf2pt1")
19178 (synopsis "Font conversion utility")
19180 "This package contains the program @code{ttf2pt1}, for use with the
19181 @code{extrafont} package.")
19182 ;; Most of the files are covered under the Expat license. Some files are
19183 ;; covered under BSD-3. Deviations for individual files are recorded in
19184 ;; the LICENSE file.
19185 (license (list license:bsd-3 license:expat
19186 (license:non-copyleft "file://LICENSE")))))
19188 (define-public r-extrafontdb
19190 (name "r-extrafontdb")
19195 (uri (cran-uri "extrafontdb" version))
19198 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
19199 (build-system r-build-system)
19200 (home-page "https://github.com/wch/extrafontdb")
19201 (synopsis "Database for the extrafont package")
19203 "This package holds the database for the @code{extrafont} package.")
19204 (license license:gpl2)))
19206 (define-public r-extrafont
19208 (name "r-extrafont")
19213 (uri (cran-uri "extrafont" version))
19216 "0mx810mld67vb1w3wkl4fhpjmkq32lgpq5x1c0a9rf8li5wskrj4"))))
19217 (build-system r-build-system)
19219 (list r-extrafontdb r-rttf2pt1))
19220 (home-page "https://github.com/wch/extrafont")
19221 (synopsis "Tools for using fonts in R")
19223 "The extrafont package makes it easier to use fonts other than the basic
19224 PostScript fonts that R uses. Fonts that are imported into extrafont can be
19225 used with PDF or PostScript output files. There are two hurdles for using
19226 fonts in PDF (or Postscript) output files:
19229 @item Making R aware of the font and the dimensions of the characters.
19230 @item Embedding the fonts in the PDF file so that the PDF can be displayed
19231 properly on a device that doesn't have the font. This is usually needed if
19232 you want to print the PDF file or share it with others.
19235 The extrafont package makes both of these things easier.")
19236 (license license:gpl2)))
19238 (define-public r-xkcd
19245 (uri (cran-uri "xkcd" version))
19248 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
19249 (build-system r-build-system)
19251 (list r-extrafont r-ggplot2 r-hmisc))
19252 (home-page "https://cran.r-project.org/web/packages/xkcd/")
19253 (synopsis "Plot ggplot2 graphics in the XKCD style")
19255 "This package provides the means to plot ggplot2 graphs in the style of
19256 the XKCD web comic.")
19257 (license license:gpl3)))
19259 (define-public r-babelgene
19261 (name "r-babelgene")
19266 (uri (cran-uri "babelgene" version))
19269 "1735h4s2vahv55pmq65zkgxq8d5x71i1is03rf17dric8yynjjhg"))))
19270 (properties `((upstream-name . "babelgene")))
19271 (build-system r-build-system)
19273 (list r-dplyr r-rlang))
19277 "https://igordot.github.io/babelgene/")
19278 (synopsis "Gene orthologs for model organisms in a Tidy data format")
19280 "Genomic analysis of model organisms often requires the use of databases
19281 based on human data or making comparisons to patient-derived resources. This
19282 requires converting genes between human and non-human analogues. The
19283 babelgene R package provides predicted gene orthologs/homologs for frequently
19284 studied model organisms in an R-friendly tidy/long format. The package
19285 integrates orthology assertion predictions sourced from multiple databases as
19286 compiled by the HGNC Comparison of Orthology Predictions (HCOP).")
19287 (license license:expat)))
19289 (define-public r-msigdbr
19296 (uri (cran-uri "msigdbr" version))
19299 "1jna9bkq0a7r6f8nhxziyiw75kfhsyh1rv7sx5d4551mvxxlhc6w"))))
19300 (build-system r-build-system)
19310 (home-page "https://github.com/igordot/msigdbr")
19311 (synopsis "MSigDB gene sets for multiple organisms")
19313 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
19314 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
19315 software in a standard R data frame with key-value pairs. Included are the
19316 original human gene symbols and Entrez IDs as well as the equivalents for
19317 various frequently studied model organisms such as mouse, rat, pig, fly, and
19319 ;; The package is covered under the Expat license, but the upstream MSigDB
19320 ;; files are made available under the Creative Commons Attribution 4.0
19321 ;; International license.
19322 (license (list license:expat license:cc-by4.0))))
19324 (define-public r-gridgraphics
19326 (name "r-gridgraphics")
19331 (uri (cran-uri "gridGraphics" version))
19334 "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219"))))
19335 (properties `((upstream-name . "gridGraphics")))
19336 (build-system r-build-system)
19337 (home-page "https://github.com/pmur002/gridgraphics")
19338 (synopsis "Redraw base graphics using @code{grid} graphics")
19340 "This package provides functions to convert a page of plots drawn with
19341 the @code{graphics} package into identical output drawn with the @code{grid}
19342 package. The result looks like the original @code{graphics}-based plot, but
19343 consists of @code{grid} grobs and viewports that can then be manipulated with
19344 @code{grid} functions (e.g., edit grobs and revisit viewports).")
19345 (license license:gpl2+)))
19347 (define-public r-farver
19354 (uri (cran-uri "farver" version))
19357 "1klnr73fhm7n46q85in1v9gi99y6rcdzzg4h4wvnbx23lxndmkqd"))))
19358 (build-system r-build-system)
19359 (home-page "https://github.com/thomasp85/farver")
19360 (synopsis "Vectorized color conversion and comparison")
19362 "The encoding of color can be handled in many different ways, using
19363 different color spaces. As different color spaces have different uses,
19364 efficient conversion between these representations are important. This
19365 package provides a set of functions that gives access to very fast color space
19366 conversion and comparisons implemented in C++, and offers 100-fold speed
19367 improvements over the @code{convertColor} function in the @code{grDevices}
19369 (license license:expat)))
19371 (define-public r-yulab-utils
19373 (name "r-yulab-utils")
19378 (uri (cran-uri "yulab.utils" version))
19381 "0sq5wc0mp84h6fs4wa2smvf7dcn0p0xarzb2ljvqc3p4vb2lvkbf"))))
19382 (properties `((upstream-name . "yulab.utils")))
19383 (build-system r-build-system)
19384 (home-page "https://cran.r-project.org/package=yulab.utils")
19385 (synopsis "Supporting functions for packages maintained by YuLab-SMU")
19387 "Miscellaneous functions commonly used by YuLab-SMU, such as
19388 @code{install_zip_gh} to install R packages from Github ZIP files.")
19389 (license license:artistic2.0)))
19391 (define-public r-ggplotify
19393 (name "r-ggplotify")
19398 (uri (cran-uri "ggplotify" version))
19401 "12mk3fa8fdjxj7xxz21jkr7h91w5wdgwjqhszcz1qffwsgb773qp"))))
19402 (build-system r-build-system)
19404 (list r-ggplot2 r-gridgraphics r-yulab-utils))
19407 (home-page "https://github.com/GuangchuangYu/ggplotify")
19408 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
19410 "This package provides tools to convert plot function calls (using
19411 expression or formula) to @code{grob} or @code{ggplot} objects that are
19412 compatible with the @code{grid} and @code{ggplot2} environment. With this
19413 package, we are able to e.g. use @code{cowplot} to align plots produced by
19414 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
19415 converting them to @code{ggplot} objects.")
19416 (license license:artistic2.0)))
19418 (define-public r-triebeard
19420 (name "r-triebeard")
19425 (uri (cran-uri "triebeard" version))
19428 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
19429 (build-system r-build-system)
19430 (propagated-inputs (list r-rcpp))
19431 (home-page "https://github.com/Ironholds/triebeard/")
19432 (synopsis "Radix trees in Rcpp")
19434 "Radix trees, or tries, are key-value data structures optimized for
19435 efficient lookups, similar in purpose to hash tables. This package provides
19436 an implementation of radix trees for use in R programming and in developing
19437 packages with Rcpp.")
19438 (license license:expat)))
19440 (define-public r-tweenr
19447 (uri (cran-uri "tweenr" version))
19450 "1wqzcsxlz1isb1j0v5g6dgvd40q3q9qlahvgcgiq0j4d87nzvfv4"))))
19451 (build-system r-build-system)
19455 '(modify-phases %standard-phases
19456 (add-after 'unpack 'build-reproducibly
19458 (substitute* "R/aaa.R"
19459 (("BASEDATETIME <- Sys.time.*")
19460 "BASEDATETIME <- structure(0, class = c(\"POSIXct\", \"POSIXt\"))\n")))))))
19462 (list r-cpp11 r-farver r-magrittr r-rlang r-vctrs))
19463 (home-page "https://github.com/thomasp85/tweenr")
19464 (synopsis "Interpolate data for smooth animations")
19466 "In order to create smooth animation between states of data, tweening is
19467 necessary. This package provides a range of functions for creating tweened
19468 data that can be used as basis for animation. Furthermore it adds a number of
19469 vectorized interpolaters for common R data types such as numeric, date and
19471 (license license:expat)))
19473 (define-public r-polyclip
19475 (name "r-polyclip")
19480 (uri (cran-uri "polyclip" version))
19483 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
19484 (build-system r-build-system)
19485 (native-inputs (list pkg-config))
19486 (home-page "http://www.angusj.com/delphi/clipper.php")
19487 (synopsis "Polygon clipping")
19489 "This package provides an R port of the library Clipper. It performs
19490 polygon clipping operations (intersection, union, set minus, set difference)
19491 for polygonal regions of arbitrary complexity, including holes. It computes
19492 offset polygons (spatial buffer zones, morphological dilations, Minkowski
19493 dilations) for polygonal regions and polygonal lines. It computes the
19494 Minkowski Sum of general polygons. There is a function for removing
19495 self-intersections from polygon data.")
19496 (license license:boost1.0)))
19498 (define-public r-urlchecker
19500 (name "r-urlchecker")
19504 (uri (cran-uri "urlchecker" version))
19507 "06034lb94krbzawqg5xklwcksvyyzl3qy355f66baj5pw7dms5k2"))))
19508 (properties `((upstream-name . "urlchecker")))
19509 (build-system r-build-system)
19510 (propagated-inputs (list r-cli r-curl r-xml2))
19511 (home-page "https://github.com/r-lib/urlchecker")
19512 (synopsis "Run CRAN URL checks from older R versions")
19514 "This package provides the URL checking tools available in R 4.1+ as a
19515 package for earlier versions of R. It also uses concurrent requests so can be
19516 much faster than the serial versions.")
19517 (license license:gpl3)))
19519 (define-public r-urltools
19521 (name "r-urltools")
19526 (uri (cran-uri "urltools" version))
19529 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
19530 (build-system r-build-system)
19532 (list r-rcpp r-triebeard))
19533 (home-page "https://github.com/Ironholds/urltools/")
19534 (synopsis "Vectorized tools for URL handling and parsing")
19536 "This package provides a toolkit for all URL-handling needs, including
19537 encoding and decoding, parsing, parameter extraction and modification. All
19538 functions are designed to be both fast and entirely vectorized. It is
19539 intended to be useful for people dealing with web-related datasets, such as
19540 server-side logs, although may be useful for other situations involving large
19542 (license license:expat)))
19544 (define-public r-ggforce
19551 (uri (cran-uri "ggforce" version))
19554 "0lshvdb5kx0k5w36pc7fy653cs98w17spbw8f0jw36xb80sipiv2"))))
19555 (build-system r-build-system)
19569 (home-page "https://ggforce.data-imaginist.com")
19570 (synopsis "Accelerating ggplot2")
19572 "The aim of the ggplot2 package is to aid in visual data investigations.
19573 This focus has led to a lack of facilities for composing specialized plots.
19574 This package aims to be a collection of mainly new statistics and geometries
19575 that fills this gap.")
19576 (license license:expat)))
19578 (define-public r-europepmc
19580 (name "r-europepmc")
19585 (uri (cran-uri "europepmc" version))
19588 "16japbndid34shqg8n0bmjrxn84xmhrylvz832zclcllm6i93fn1"))))
19589 (build-system r-build-system)
19604 (home-page "https://github.com/ropensci/europepmc/")
19605 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
19607 "This package provides an R Client for the
19608 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
19609 Service}. It gives access to both metadata on life science literature and
19610 open access full texts. Europe PMC indexes all PubMed content and other
19611 literature sources including Agricola, a bibliographic database of citations
19612 to the agricultural literature, or Biological Patents. In addition to
19613 bibliographic metadata, the client allows users to fetch citations and
19614 reference lists. Links between life-science literature and other EBI
19615 databases, including ENA, PDB or ChEMBL are also accessible.")
19616 (license license:gpl3)))
19618 (define-public r-ggraph
19625 (uri (cran-uri "ggraph" version))
19628 "02nl92vgyp5pc61r14mmmbfhg5nhb6fibjjb3djfag2ahc6wj2kv"))))
19629 (build-system r-build-system)
19648 (home-page "https://cran.r-project.org/web/packages/ggraph/")
19649 (synopsis "Implementation of grammar of graphics for graphs and networks")
19651 "The grammar of graphics as implemented in ggplot2 is a poor fit for
19652 graph and network visualizations due to its reliance on tabular data input.
19653 The ggraph package is an extension of the ggplot2 API tailored to graph
19654 visualizations and provides the same flexible approach to building up plots
19656 (license license:gpl3)))
19658 (define-public r-gkmsvm
19665 (uri (cran-uri "gkmSVM" version))
19668 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
19669 (properties `((upstream-name . "gkmSVM")))
19670 (build-system r-build-system)
19672 (list r-kernlab r-rcpp r-rocr r-seqinr))
19673 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
19674 (synopsis "Gapped-kmer support vector machine")
19676 "This R package provides tools for training gapped-kmer SVM classifiers
19677 for DNA and protein sequences. This package supports several sequence
19678 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
19679 (license license:gpl2+)))
19681 (define-public r-varselrf
19683 (name "r-varselrf")
19688 (uri (cran-uri "varSelRF" version))
19691 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
19692 (properties `((upstream-name . "varSelRF")))
19693 (build-system r-build-system)
19695 (list r-randomforest))
19696 (home-page "https://www.ligarto.org/rdiaz/software/software")
19697 (synopsis "Variable selection using random forests")
19699 "This package provides tools for the variable selection from random
19700 forests using both backwards variable elimination (for the selection of small
19701 sets of non-redundant variables) and selection based on the importance
19702 spectrum (somewhat similar to scree plots; for the selection of large,
19703 potentially highly-correlated variables). The main applications are in
19704 high-dimensional data (e.g., microarray data, and other genomics and
19705 proteomics applications).")
19706 (license license:gpl2+)))
19708 (define-public r-pamr
19715 (uri (cran-uri "pamr" version))
19718 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
19719 (build-system r-build-system)
19721 (list r-cluster r-survival))
19722 (native-inputs (list gfortran))
19723 (home-page "https://cran.r-project.org/web/packages/pamr/")
19724 (synopsis "Prediction Analysis for Microarrays")
19726 "This package provides some functions for sample classification in
19728 (license license:gpl2)))
19730 (define-public r-rda
19733 (version "1.0.2-2.1")
19737 (uri (cran-uri "rda" version))
19740 "17ll0idnms4bcpbl65xnl8zfnwsk9ww0rg5z8qqh4ahk5qdab8zf"))))
19741 (build-system r-build-system)
19742 (home-page "https://cran.r-project.org/web/packages/rda/")
19743 (synopsis "Shrunken centroids regularized discriminant analysis")
19745 "This package provides tools for shrunken centroids regularized
19746 discriminant analysis for the purpose of classifying high dimensional data.")
19747 (license license:gpl2+)))
19749 (define-public r-ggvis
19756 (uri (cran-uri "ggvis" version))
19759 "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy"))))
19760 (build-system r-build-system)
19769 (home-page "https://ggvis.rstudio.com/")
19770 (synopsis "Interactive grammar of graphics")
19772 "This package is a data visualization package for R providing an
19773 implementation of an interactive grammar of graphics, taking the best parts of
19774 ggplot2, combining them with the reactive framework of Shiny and drawing web
19775 graphics using Vega.")
19776 (license license:gpl2)))
19778 (define-public r-gbm
19781 (version "2.1.8.1")
19785 (uri (cran-uri "gbm" version))
19788 "02z85d7zp3i5x8r8q005hyw2rx1ck7lw81q7a3lqwraj8l95c94d"))))
19789 (build-system r-build-system)
19791 (list r-lattice r-survival))
19794 (home-page "https://github.com/gbm-developers/gbm")
19795 (synopsis "Generalized boosted regression models")
19797 "This package is an implementation of extensions to Freund and Schapire's
19798 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
19799 regression methods for least squares, absolute loss, t-distribution loss,
19800 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
19801 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
19802 and Learning to Rank measures (LambdaMart).")
19803 (license license:gpl2+)))
19805 (define-public r-threejs
19812 (uri (cran-uri "threejs" version))
19815 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
19816 (build-system r-build-system)
19818 `(#:modules ((guix build utils)
19819 (guix build r-build-system)
19823 (modify-phases %standard-phases
19824 (add-after 'unpack 'process-javascript
19825 (lambda* (#:key inputs #:allow-other-keys)
19826 (with-directory-excursion "inst"
19830 `((,(assoc-ref inputs "js-jquery")
19831 "htmlwidgets/lib/jquery/jquery.min.js")
19832 (,(assoc-ref inputs "js-threejs-111")
19833 "htmlwidgets/lib/threejs-111/three.min.js"))))
19834 (lambda (sources targets)
19835 (for-each (lambda (source target)
19836 (format #t "Processing ~a --> ~a~%"
19838 (delete-file target)
19839 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
19840 (call-with-output-file target
19842 (dump-port minified port)))))
19843 sources targets))))
19846 (list r-base64enc r-crosstalk r-htmlwidgets r-igraph))
19848 `(("uglifyjs" ,node-uglify-js)
19852 (uri "https://code.jquery.com/jquery-1.12.4.js")
19855 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
19859 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
19862 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
19863 (home-page "https://bwlewis.github.io/rthreejs")
19864 (synopsis "Interactive 3D scatter plots, networks and globes")
19866 "Create interactive 3D scatter plots, network plots, and globes in R
19867 using the three.js visualization library.")
19868 (license license:expat)))
19870 (define-public r-mlbench
19877 (uri (cran-uri "mlbench" version))
19880 "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi"))))
19881 (build-system r-build-system)
19882 (home-page "https://cran.r-project.org/web/packages/mlbench/")
19883 (synopsis "Machine learning benchmark problems")
19885 "This package provides a collection of artificial and real-world machine
19886 learning benchmark problems, including, e.g., several data sets from the UCI
19888 (license license:gpl2)))
19890 (define-public r-mpm
19897 (uri (cran-uri "mpm" version))
19900 "1jpv2ddmw7aarqbbyfys1yb840arw33319wnny3v2hk84hldmayj"))))
19901 (build-system r-build-system)
19903 (list r-kernsmooth r-mass))
19904 (home-page "http://mpm.r-forge.r-project.org")
19905 (synopsis "Multivariate projection methods")
19907 "This is a package for exploratory graphical analysis of multivariate
19908 data, specifically gene expression data with different projection methods:
19909 principal component analysis, correspondence analysis, spectral map
19911 (license license:gpl2+)))
19913 (define-public r-png
19919 (uri (cran-uri "png" version))
19922 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
19923 (build-system r-build-system)
19925 (list libpng zlib))
19926 (home-page "https://www.rforge.net/png/")
19927 (synopsis "Read and write PNG images")
19929 "This package provides an easy and simple way to read, write and display
19930 bitmap images stored in the PNG format. It can read and write both files and
19931 in-memory raw vectors.")
19932 ;; Any of these GPL versions.
19933 (license (list license:gpl2 license:gpl3))))
19935 (define-public r-ggcorrplot
19937 (name "r-ggcorrplot")
19942 (uri (cran-uri "ggcorrplot" version))
19945 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
19946 (build-system r-build-system)
19948 (list r-ggplot2 r-reshape2))
19949 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
19950 (synopsis "Visualization of a correlation matrix using ggplot2")
19952 "The ggcorrplot package can be used to visualize easily a correlation
19953 matrix using ggplot2. It provides a solution for reordering the correlation
19954 matrix and displays the significance level on the plot. It also includes a
19955 function for computing a matrix of correlation p-values.")
19956 (license license:gpl2)))
19958 (define-public r-ggfun
19965 (uri (cran-uri "ggfun" version))
19968 "0x71p3mm0sw72hv92368wy2yiy7zv826p3kddpwndqv1bywmyfx8"))))
19969 (properties `((upstream-name . "ggfun")))
19970 (build-system r-build-system)
19972 (list r-ggplot2 r-rlang))
19973 (native-inputs (list r-knitr))
19974 (home-page "https://cran.r-project.org/package=ggfun")
19975 (synopsis "Miscellaneous functions for ggplot2")
19977 "This package provides useful functions to edit ggplot object (e.g.,
19978 setting fonts for theme and layers, adding rounded rectangle as background for
19979 each of the legends).")
19980 (license license:artistic2.0)))
19982 (define-public r-gridtext
19984 (name "r-gridtext")
19989 (uri (cran-uri "gridtext" version))
19992 "0f7i2qb8fawi8agy2iz2c173kfwj7cbb5ikjix64nmzqc5j7363d"))))
19993 (properties `((upstream-name . "gridtext")))
19994 (build-system r-build-system)
20004 (home-page "https://wilkelab.org/gridtext/")
20005 (synopsis "Improved text rendering support for Grid graphics")
20007 "This package provides support for rendering of formatted text using Grid
20008 graphics. Text can be formatted via a minimal subset of Markdown, HTML, and
20009 inline CSS directives, and it can be rendered both with and without word
20011 (license license:expat)))
20013 (define-public r-ggghost
20019 (uri (cran-uri "ggghost" version))
20022 "0kvsjadxxdf6yvzk4a6yqkg02q1ysslvf3m0a369bdim396z4hnv"))))
20023 (properties `((upstream-name . "ggghost")))
20024 (build-system r-build-system)
20025 (propagated-inputs (list r-animation r-ggplot2))
20026 (home-page "https://github.com/jonocarroll/ggghost")
20027 (synopsis "Capture the spirit of your ggplot2 calls")
20029 "This package lets you create a reproducible @code{ggplot2} object by
20030 storing the data and calls.")
20031 (license license:gpl3+)))
20033 (define-public r-ggtext
20040 (uri (cran-uri "ggtext" version))
20043 "10vrrxviv4yp9lqsanqvwsvbj64vn66hwm1w7860x1g58hf1g0l7"))))
20044 (properties `((upstream-name . "ggtext")))
20045 (build-system r-build-system)
20047 (list r-ggplot2 r-gridtext r-rlang r-scales))
20048 (native-inputs (list r-knitr))
20049 (home-page "https://wilkelab.org/ggtext/")
20050 (synopsis "Improved text rendering support for ggplot2")
20052 "This package provides a ggplot2 extension that enables the rendering of
20053 complex formatted plot labels (titles, subtitles, facet labels, axis labels,
20054 etc.). Text boxes with automatic word wrap are also supported.")
20055 (license license:gpl2)))
20057 (define-public r-ggthemeassist
20059 (name "r-ggthemeassist")
20063 (uri (cran-uri "ggThemeAssist" version))
20066 "1biw91a8p13h62v4w3yim6ghr98khmyhb3qd0h04asf91vvmpxbv"))))
20067 (properties `((upstream-name . "ggThemeAssist")))
20068 (build-system r-build-system)
20075 (home-page "https://github.com/calligross/ggthemeassist")
20076 (synopsis "Add-in to customize ggplot2 themes")
20078 "This package provides an Rstudio add-in that delivers a graphical
20079 interface for editing @code{ggplot2} theme elements.")
20080 (license license:gpl3)))
20082 ;; This package includes minified JavaScript files. When upgrading please
20083 ;; check that there are no new minified JavaScript files.
20084 (define-public r-flexdashboard
20086 (name "r-flexdashboard")
20091 (uri (cran-uri "flexdashboard" version))
20094 "0bvw2ca6xxscia4hvq505qvjf6zkgpsqv86f1s78aknzwr9jsikm"))
20095 (modules '((guix build utils)))
20098 ;; Delete bundled minified JavaScript files
20099 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
20100 (delete-file "inst/www/sly/sly.min.js")
20101 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
20102 (delete-file "inst/www/prism/prism.js")
20103 (delete-file "inst/www/featherlight/featherlight.min.js")))))
20104 (build-system r-build-system)
20106 `(#:modules ((guix build utils)
20107 (guix build r-build-system)
20111 (ice-9 textual-ports))
20113 (modify-phases %standard-phases
20114 (add-after 'unpack 'process-javascript
20115 (lambda* (#:key inputs #:allow-other-keys)
20116 (with-directory-excursion "inst"
20117 ;; Concatenate all components of prism.js
20118 (let ((contents (string-join
20119 (map (lambda (name)
20120 (call-with-input-file
20121 (assoc-ref inputs name)
20125 "js-prism-line-numbers"))
20127 (call-with-output-file "prism-src.js"
20128 (cut display contents <>)))
20132 `(("www/stickytableheaders/jquery.stickytableheaders.js"
20133 "www/stickytableheaders/jquery.stickytableheaders.min.js")
20135 "www/sly/sly.min.js")
20137 "www/prism/prism.js")
20138 (,(assoc-ref inputs "js-raphael")
20139 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
20140 (,(assoc-ref inputs "js-featherlight")
20141 "www/featherlight/featherlight.min.js"))))
20142 (lambda (sources targets)
20143 (for-each (lambda (source target)
20144 (format #t "Processing ~a --> ~a~%"
20146 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
20147 (call-with-output-file target
20149 (dump-port minified port)))))
20150 sources targets)))))))))
20162 `(("uglifyjs" ,node-uglify-js)
20166 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
20169 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
20173 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
20176 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
20180 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
20183 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
20184 ("js-prism-line-numbers"
20187 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
20190 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
20194 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
20197 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
20198 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
20199 (synopsis "R Markdown format for flexible dashboards")
20201 "This package provides an R Markdown format for converting an R Markdown
20202 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
20203 of its components to the containing web page.")
20204 (license license:expat)))
20206 (define-public r-preseqr
20213 (uri (cran-uri "preseqR" version))
20216 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
20217 (properties `((upstream-name . "preseqR")))
20218 (build-system r-build-system)
20221 (home-page "https://cran.r-project.org/web/packages/preseqR/")
20222 (synopsis "Predicting species accumulation curves")
20224 "This package can be used to predict the r-species accumulation
20225 curve (r-SAC), which is the number of species represented at least r times as
20226 a function of the sampling effort. When r = 1, the curve is known as the
20227 species accumulation curve, or the library complexity curve in high-throughput
20228 genomic sequencing. The package includes both parametric and nonparametric
20229 methods, as described by Deng C, et al. (2018).")
20230 (license license:gpl3)))
20232 (define-public r-mapplots
20234 (name "r-mapplots")
20239 (uri (cran-uri "mapplots" version))
20242 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
20243 (build-system r-build-system)
20244 (home-page "https://cran.r-project.org/web/packages/mapplots/")
20245 (synopsis "Data visualization on maps")
20247 "This package helps you create simple maps; add sub-plots like pie plots
20248 to a map or any other plot; format, plot and export gridded data. The package
20249 was developed for displaying fisheries data but most functions can be used for
20250 more generic data visualisation.")
20251 (license license:gpl2+)))
20253 (define-public r-pmcmr
20260 (uri (cran-uri "PMCMR" version))
20263 "05n13pp5yff6pzk4ry07crddfaj3jlglrd1vkcnacyd8jpaxkd77"))))
20264 (properties `((upstream-name . "PMCMR")))
20265 (build-system r-build-system)
20266 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
20267 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
20269 "This is a deprecated package for calculating pairwise multiple
20270 comparisons of mean rank sums. This package is superseded by the novel
20271 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
20272 compatibility of dependent packages for some time.")
20273 (license license:gpl3+)))
20275 (define-public r-downloader
20277 (name "r-downloader")
20282 (uri (cran-uri "downloader" version))
20285 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
20286 (build-system r-build-system)
20289 (home-page "https://github.com/wch/downloader")
20290 (synopsis "Download files over HTTP and HTTPS")
20292 "This package provides a wrapper for the @code{download.file} function,
20293 making it possible to download files over HTTPS across platforms. The
20294 @code{RCurl} package provides this functionality (and much more) but has
20295 external dependencies. This package has is implemented purely in R.")
20296 (license license:gpl2)))
20298 (define-public r-aplot
20305 (uri (cran-uri "aplot" version))
20308 "05l6pvhrl715xgdy7qmw6lyxigv9qn90ms3vf7awip8sdmghy9gn"))))
20309 (properties `((upstream-name . "aplot")))
20310 (build-system r-build-system)
20317 (home-page "https://github.com/YuLab-SMU/aplot")
20318 (synopsis "Decorate a ggplot with associated information")
20320 "Users may want to align plots with associated information that requires
20321 axes to be exactly matched in subplots, e.g. hierarchical clustering with a
20322 heatmap. This package provides utilities to align associated subplots to a
20323 main plot at different sides (left, right, top and bottom) with axes exactly
20325 (license license:artistic2.0)))
20327 (define-public r-ggnewscale
20329 (name "r-ggnewscale")
20334 (uri (cran-uri "ggnewscale" version))
20337 "108a7y6sqqvzyfk247lbmnacfpwdl405rf1b3fa62cgx8ycsq4kb"))))
20338 (properties `((upstream-name . "ggnewscale")))
20339 (build-system r-build-system)
20342 (home-page "https://cran.r-project.org/package=ggnewscale")
20343 (synopsis "Multiple fill and color scales in ggplot2")
20345 "This package lets you use multiple fill and color scales in ggplot2.")
20346 (license license:gpl3)))
20348 (define-public r-ggpointdensity
20350 (name "r-ggpointdensity")
20355 (uri (cran-uri "ggpointdensity" version))
20358 "0c9a14j3b0hvamqylhzldw2hjdxmfbllwahjkf3gg2rw337ld9iy"))))
20360 `((upstream-name . "ggpointdensity")))
20361 (build-system r-build-system)
20364 (home-page "https://github.com/LKremer/ggpointdensity")
20365 (synopsis "Cross between a 2D density plot and a scatter plot")
20367 "This package provides a cross between a 2D density plot and a scatter
20368 plot, implemented as a ggplot2 @code{geom}. Points in the scatter plot are
20369 colored by the number of neighboring points. This is useful to visualize the
20370 2D-distribution of points in case of overplotting.")
20371 (license license:gpl3)))
20373 (define-public r-arrow
20376 (version "9.0.0.1")
20380 (uri (cran-uri "arrow" version))
20383 "1vbjny6v1d4fdf01rphg4wg8ljs0bzrjyxlsjwjq58pd6g2qcdgc"))))
20384 (properties `((upstream-name . "arrow")))
20385 (build-system r-build-system)
20387 (list `(,apache-arrow "lib") zlib))
20398 (list pkg-config r-knitr))
20399 (home-page "https://github.com/apache/arrow/")
20400 (synopsis "R integration to Apache Arrow")
20402 "Apache Arrow is a cross-language development platform for in-memory
20403 data. It specifies a standardized language-independent columnar memory format
20404 for flat and hierarchical data, organized for efficient analytic operations on
20405 modern hardware. This package provides an R interface to the Arrow C++
20407 (license license:asl2.0)))
20409 (define-public r-rex
20416 (uri (cran-uri "rex" version))
20419 "1mmzlc3j7xa0rbjxa369f4sr0iw3gq58g8fmjjxbsjvfq14ychmg"))))
20420 (build-system r-build-system)
20425 (home-page "https://github.com/kevinushey/rex")
20426 (synopsis "Friendly regular expressions")
20428 "This package provides a friendly interface for the construction of
20429 regular expressions. Regular expressions are a very powerful feature, however
20430 they are often difficult to interpret. Rex allows you to build complex
20431 regular expressions from human readable expressions")
20432 (license license:expat)))
20434 (define-public r-mlapi
20441 (uri (cran-uri "mlapi" version))
20444 "1qyiii6x9b89i4pd4yi2zd23aabpmnpj18gqi5va0zy0l8r7kknr"))))
20445 (properties `((upstream-name . "mlapi")))
20446 (build-system r-build-system)
20448 (list r-matrix r-r6))
20451 (home-page "https://cran.r-project.org/package=mlapi")
20452 (synopsis "Abstract classes for building scikit-learn like API")
20454 "This package provides R6 abstract classes for building machine learning
20455 models with a scikit-learn like API. Scikit-learn is a popular module for the
20456 Python programming language whose design became a de facto standard in
20457 industry for machine learning tasks.")
20458 (license license:expat)))
20460 (define-public r-float
20467 (uri (cran-uri "float" version))
20470 "0m7bf3548vlgkk1c78jyrgj72ngwg0gsccap2iqinm3l3qrm4zbs"))))
20471 (properties `((upstream-name . "float")))
20472 (build-system r-build-system)
20475 (home-page "https://github.com/wrathematics/float")
20476 (synopsis "32-bit floats")
20478 "R comes with a suite of utilities for linear algebra with
20479 \"numeric\" (double precision) vectors/matrices. However, sometimes single
20480 precision (or less!) is more than enough for a particular task. This package
20481 extends R's linear algebra facilities to include 32-bit float (single
20482 precision) data. Float vectors/matrices have half the precision of their
20483 \"numeric\"-type counterparts but are generally faster to numerically operate
20484 on, for a performance vs accuracy trade-off.")
20485 (license license:bsd-2)))
20487 (define-public r-rsparse
20494 (uri (cran-uri "rsparse" version))
20497 "15kdllm2lh6xdlv4j0ljyj5pczhx26s9d8cac7953zbb0sd45chz"))))
20498 (properties `((upstream-name . "rsparse")))
20499 (build-system r-build-system)
20509 (home-page "https://github.com/rexyai/rsparse")
20510 (synopsis "Statistical learning on sparse matrices")
20512 "This package implements many algorithms for statistical learning on
20513 sparse matrices: matrix factorizations, matrix completion, elastic net
20514 regressions, factorization machines. The rsparse package also enhances the
20515 Matrix package by providing methods for multithreaded <sparse, dense> matrix
20516 products and native slicing of the sparse matrices in @dfn{Compressed Sparse
20517 Row} (CSR) format.")
20518 (license license:gpl2+)))
20520 (define-public r-text2vec
20522 (name "r-text2vec")
20527 (uri (cran-uri "text2vec" version))
20530 "1as58w1hb6h0hpncwcr2nx9a8bj5fy6bfllx2a8ck8hal764iach"))))
20531 (properties `((upstream-name . "text2vec")))
20532 (build-system r-build-system)
20545 (home-page "http://text2vec.org")
20546 (synopsis "Text mining framework for R")
20548 "This package provides fast and memory-friendly tools for text
20549 vectorization, topic modeling (LDA, LSA), word embeddings (GloVe),
20550 similarities. It provides a source-agnostic streaming API, which allows
20551 researchers to perform analysis of collections of documents which are larger
20552 than available RAM. All core functions are parallelized to benefit from
20553 multicore machines.")
20554 (license license:gpl2+)))
20556 (define-public r-mcmcpack
20558 (name "r-mcmcpack")
20563 (uri (cran-uri "MCMCpack" version))
20566 "1cwdjn43b9hxpxf9mnas583myhk6r2258mh57f0zsc8bd4hbl56b"))))
20567 (properties `((upstream-name . "MCMCpack")))
20568 (build-system r-build-system)
20570 (list r-coda r-lattice r-mass r-mcmc r-quantreg))
20571 (home-page "https://cran.r-project.org/package=MCMCpack")
20572 (synopsis "Markov Chain Monte Carlo (MCMC) package")
20574 "This package contains functions to perform Bayesian inference using
20575 posterior simulation for a number of statistical models. Most simulation is
20576 done in compiled C++ written in the Scythe Statistical Library. All models
20577 return @code{coda} @code{mcmc} objects that can then be summarized using the
20578 @code{coda} package. Some useful utility functions such as density functions,
20579 pseudo-random number generators for statistical distributions, a general
20580 purpose Metropolis sampling algorithm, and tools for visualization are
20582 (license license:gpl3)))
20584 (define-public r-xmlparsedata
20586 (name "r-xmlparsedata")
20591 (uri (cran-uri "xmlparsedata" version))
20594 "1c6bnz3ng1qw7sfip8wq3a4dn36a4d6rbja0sadn0a4pbsmk8q3n"))))
20595 (properties `((upstream-name . "xmlparsedata")))
20596 (build-system r-build-system)
20597 (home-page "https://github.com/r-lib/xmlparsedata#readme")
20598 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
20600 "This package provides tools to convert the output of
20601 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
20602 @code{XPath}, and is easier to manipulate in general.")
20603 (license license:expat)))
20605 (define-public r-cyclocomp
20607 (name "r-cyclocomp")
20612 (uri (cran-uri "cyclocomp" version))
20615 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
20616 (properties `((upstream-name . "cyclocomp")))
20617 (build-system r-build-system)
20619 (list r-callr r-crayon r-desc r-remotes r-withr))
20620 (home-page "https://github.com/MangoTheCat/cyclocomp")
20621 (synopsis "Cyclomatic complexity of R code")
20623 "Cyclomatic complexity is a software metric, used to indicate the
20624 complexity of a program. It is a quantitative measure of the number of
20625 linearly independent paths through a program's source code. This package
20626 provides tools to compute this metric.")
20627 (license license:expat)))
20629 (define-public r-lintr
20636 (uri (cran-uri "lintr" version))
20639 "18prww284sil98ck3gmkmfs6b4disn9nyfb00kfwwiwg7ay1df6g"))))
20640 (properties `((upstream-name . "lintr")))
20641 (build-system r-build-system)
20654 (native-inputs (list r-knitr))
20655 (home-page "https://github.com/jimhester/lintr")
20656 (synopsis "Linter for R code")
20657 (description "This package checks adherence to a given style, syntax
20658 errors and possible semantic issues. It supports on the fly checking of R
20659 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
20660 (license license:expat)))
20662 (define-public r-sctransform
20664 (name "r-sctransform")
20669 (uri (cran-uri "sctransform" version))
20672 "1nhmsbkrww74a55avln5zhd77g92f15p885j5q0khajw35iqnv0g"))))
20673 (build-system r-build-system)
20688 (home-page "https://github.com/ChristophH/sctransform")
20689 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
20691 "This package provides a normalization method for single-cell UMI count
20692 data using a variance stabilizing transformation. The transformation is based
20693 on a negative binomial regression model with regularized parameters. As part
20694 of the same regression framework, this package also provides functions for
20695 batch correction, and data correction.")
20696 (license license:gpl3)))
20698 (define-public r-styler
20705 (uri (cran-uri "styler" version))
20708 "1ki260ga0jrmayhdlx2sl788yp5kkmi4wyl32nmvvyb55sng6j9y"))))
20709 (build-system r-build-system)
20710 ;; This is needed by R.cache.
20713 (modify-phases %standard-phases
20714 (add-after 'unpack 'set-HOME
20715 (lambda _ (setenv "HOME" "/tmp"))))))
20728 (home-page "https://github.com/r-lib/styler")
20729 (synopsis "Non-invasive pretty printing of R code")
20731 "This is a package for pretty-printing R code without changing the user's
20732 formatting intent.")
20733 (license license:gpl3)))
20735 (define-public r-scrime
20742 (uri (cran-uri "scrime" version))
20745 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
20746 (build-system r-build-system)
20747 (home-page "https://cran.r-project.org/web/packages/scrime/")
20748 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
20750 "This package provides tools for the analysis of high-dimensional data
20751 developed/implemented at the group \"Statistical Complexity Reduction In
20752 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
20753 the functions can also be applied to other types of categorical data.")
20754 (license license:gpl2)))
20756 (define-public r-pbmcapply
20758 (name "r-pbmcapply")
20763 (uri (cran-uri "pbmcapply" version))
20766 "1p8jf7c4k45482w72sr0jw4jkz787krrxai3sl6jz5l4lda2iz3z"))))
20767 (build-system r-build-system)
20768 (home-page "https://github.com/kvnkuang/pbmcapply")
20769 (synopsis "Track the progress of apply procedures with a progress bar")
20771 "This light-weight package helps you track and visualize the progress of
20772 parallel versions of vectorized R functions of the @code{mc*apply} family.")
20773 (license license:expat)))
20775 (define-public r-blme
20782 (uri (cran-uri "blme" version))
20785 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7"))))
20786 (build-system r-build-system)
20787 (propagated-inputs (list r-lme4))
20788 (home-page "https://github.com/vdorie/blme")
20789 (synopsis "Bayesian linear mixed-effects models")
20791 "This package provides tools for maximum a posteriori estimation for
20792 linear and generalized linear mixed-effects models in a Bayesian setting. It
20793 extends the lme4 package.")
20794 (license license:gpl2+)))
20796 (define-public r-batchtools
20798 (name "r-batchtools")
20803 (uri (cran-uri "batchtools" version))
20806 "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52"))))
20807 (build-system r-build-system)
20823 (home-page "https://github.com/mllg/batchtools")
20824 (synopsis "Tools for computation on batch systems")
20826 "As a successor of the packages BatchJobs and BatchExperiments, this
20827 package provides a parallel implementation of the Map function for high
20828 performance computing systems managed by various schedulers. A multicore and
20829 socket mode allow the parallelization on a local machines, and multiple
20830 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
20831 the package provides an abstraction mechanism to define large-scale computer
20832 experiments in a well-organized and reproducible way.")
20833 (license license:lgpl3)))
20835 (define-public r-clue
20842 (uri (cran-uri "clue" version))
20845 "0cfw2k1kh4a8imdv7b5qw977xd6indampsabhfldj3rqrqb1ncbi"))))
20846 (build-system r-build-system)
20847 (propagated-inputs (list r-cluster))
20848 (home-page "https://cran.r-project.org/web/packages/clue/")
20849 (synopsis "Tools for analyzing cluster ensembles")
20850 (description "Cluster ensembles are collections of individual solutions to
20851 a given clustering problem which are useful or necessary to consider in a wide
20852 range of applications. This R package provides an extensible computational
20853 environment for creating and analyzing cluster ensembles, with basic data
20854 structures for representing partitions and hierarchies, and facilities for
20855 computing on them, including methods for measuring proximity and obtaining
20856 consensus and secondary clusterings.")
20857 (license license:gpl2)))
20859 (define-public r-sitmo
20866 (uri (cran-uri "sitmo" version))
20869 "1hm89zi38ldgbskyx1cn7gm87yqy7zrxli8q05a36y1ndvazi3j4"))))
20870 (build-system r-build-system)
20871 (propagated-inputs (list r-rcpp))
20874 (home-page "https://github.com/coatless/sitmo/")
20875 (synopsis "Parallel pseudo random number generator header files")
20877 "This package provides two high quality and fast PPRNGs that may be used
20878 in an OpenMP parallel environment. In addition, there is a generator for one
20879 dimensional low-discrepancy sequence.")
20880 (license license:expat)))
20882 (define-public r-dqrng
20889 (uri (cran-uri "dqrng" version))
20892 "1fwsldqcri2lccna4icbmmlqic3w4xyjm7rn0xmikrsw4kzapvjb"))))
20893 (build-system r-build-system)
20895 (list r-bh r-rcpp r-sitmo))
20898 (home-page "https://www.daqana.org/dqrng")
20899 (synopsis "Fast pseudo random number generators")
20901 "Several fast random number generators are provided as C++ header-only
20902 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
20903 Additionally, fast functions for generating random numbers according to a
20904 uniform, normal and exponential distribution are included. The latter two use
20905 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
20906 functions are exported to R and as a C++ interface and are enabled for use
20907 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
20908 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
20909 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
20910 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
20911 ;; whole is distributed under the terms of the AGPL 3.
20912 (license license:agpl3)))
20914 (define-public r-ingredients
20916 (name "r-ingredients")
20921 (uri (cran-uri "ingredients" version))
20924 "11bv4l4fn9kr7y2nfzrwnaya8fi9w3nwcm9vzlqb7dva83rkqbsc"))))
20925 (properties `((upstream-name . "ingredients")))
20926 (build-system r-build-system)
20928 (list r-ggplot2 r-gridextra r-scales))
20929 (native-inputs (list r-knitr))
20930 (home-page "https://ModelOriented.github.io/ingredients/")
20931 (synopsis "Effects and importances of model ingredients")
20933 "This is a collection of tools for assessment of feature importance and
20934 feature effects. Key functions are:
20937 @item @code{feature_importance()} for assessment of global level feature
20939 @item @code{ceteris_paribus()} for calculation of the what-if plots,
20940 @item @code{partial_dependence()} for partial dependence plots,
20941 @item @code{conditional_dependence()} for conditional dependence plots,
20942 @item @code{accumulated_dependence()} for accumulated local effects plots,
20943 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
20944 aggregation of ceteris paribus profiles,
20945 @item generic @code{print()} and @code{plot()} for better usability of
20946 selected explainers,
20947 @item generic @code{plotD3()} for interactive, D3 based explanations, and
20948 @item generic @code{describe()} for explanations in natural language.
20950 (license license:gpl3)))
20952 (define-public r-ibreakdown
20954 (name "r-ibreakdown")
20959 (uri (cran-uri "iBreakDown" version))
20962 "00jzrndb3ahsv6ihp2pvs732n9cc944m83vdinrl9v1pxd82prkh"))))
20963 (properties `((upstream-name . "iBreakDown")))
20964 (build-system r-build-system)
20965 (propagated-inputs (list r-ggplot2))
20966 (native-inputs (list r-knitr))
20967 (home-page "https://ModelOriented.github.io/iBreakDown/")
20968 (synopsis "Model agnostic instance level variable attributions")
20970 "This package provides a model agnostic tool for decomposition of
20971 predictions from black boxes. It supports additive attributions and
20972 attributions with interactions. The Break Down Table shows contributions of
20973 every variable to a final prediction. The Break Down Plot presents variable
20974 contributions in a concise graphical way. This package works for
20975 classification and regression models.")
20976 (license license:gpl3)))
20978 (define-public r-dae
20985 (uri (cran-uri "dae" version))
20988 "0mq94ah21p1glvsbvdmi2p7nlgz1bvq7w3rz2z3mdqq18kz6nkjw"))))
20989 (build-system r-build-system)
20991 (list r-ggplot2 r-plyr))
20993 (list r-r-rsp)) ; vignette builder
20994 (home-page "http://chris.brien.name")
20995 (synopsis "Functions useful in the design and ANOVA of experiments")
20997 "This package provides functions useful in the design and ANOVA of
20998 experiments. The content falls into the following groupings:
21002 @item factor manipulation functions,
21003 @item design functions,
21004 @item ANOVA functions,
21005 @item matrix functions,
21006 @item projector and canonical efficiency functions, and
21007 @item miscellaneous functions.
21010 There is a vignette called @code{DesignNotes} describing how to use the design
21011 functions for randomizing and assessing designs. The ANOVA functions
21012 facilitate the extraction of information when the @code{Error} function has
21013 been used in the call to @code{aov}.")
21014 (license license:gpl2)))
21016 (define-public r-dalex
21023 (uri (cran-uri "DALEX" version))
21026 "1m19ibv8rpghqm4vr8nrvarrjkm9rxw6jx8xl3hzrqnnmf2xifqr"))))
21027 (properties `((upstream-name . "DALEX")))
21028 (build-system r-build-system)
21030 (list r-ggplot2 r-ibreakdown r-ingredients))
21031 (home-page "https://pbiecek.github.io/DALEX/")
21032 (synopsis "Descriptive machine learning explanations")
21034 "Machine Learning models are widely used and have various applications in
21035 classification or regression. Models created with boosting, bagging, stacking
21036 or similar techniques are often used due to their high performance, but such
21037 black-box models usually lack interpretability. The DALEX package contains
21038 various explainers that help to understand the link between input variables
21039 and model output.")
21040 ;; Any version of the GPL
21041 (license license:gpl3+)))
21043 (define-public r-enrichr
21050 (uri (cran-uri "enrichR" version))
21053 "0ad7jp398prvmm2fym07268qhv40mg67dx55ml4ayqkwxwffr1i9"))))
21054 (properties `((upstream-name . "enrichR")))
21055 (build-system r-build-system)
21057 (list r-curl r-ggplot2 r-httr r-rjson))
21060 (home-page "https://cran.r-project.org/web/packages/enrichR/")
21061 (synopsis "R Interface to Enrichr database for analyzing gene sets")
21063 "This package provides an R interface to all Enrichr databases, a
21064 web-based tool for analyzing gene sets and returns any enrichment of common
21065 annotated biological functions.")
21066 (license license:gpl2+)))
21068 (define-public r-plot3d
21075 (uri (cran-uri "plot3D" version))
21078 "1h59zlsyzbjylaziwavppl9bjmnba4iiq34772y3dys6fqclajnh"))))
21079 (properties `((upstream-name . "plot3D")))
21080 (build-system r-build-system)
21081 (propagated-inputs (list r-misc3d))
21082 (home-page "https://cran.r-project.org/web/packages/plot3D")
21083 (synopsis "Plot multi-dimensional data")
21085 "This package provides functions for viewing 2D and 3D data, including
21086 perspective plots, slice plots, surface plots, scatter plots, etc. It
21087 includes data sets from oceanography.")
21088 (license license:gpl3+)))
21090 (define-public r-ggfortify
21092 (name "r-ggfortify")
21097 (uri (cran-uri "ggfortify" version))
21100 "038m74azpy43869ax1yi6wxbl1kr59iaxl8raiikjg749vcx6njw"))))
21101 (build-system r-build-system)
21112 (home-page "https://github.com/sinhrks/ggfortify")
21113 (synopsis "Data visualization tools for statistical analysis results")
21115 "This package provides unified plotting tools for statistics commonly
21116 used, such as GLM, time series, PCA families, clustering and survival
21117 analysis. The package offers a single plotting interface for these analysis
21118 results and plots in a unified style using the @code{ggplot2} package.")
21119 (license license:gpl2)))
21121 (define-public r-refmanager
21123 (name "r-refmanager")
21128 (uri (cran-uri "RefManageR" version))
21131 "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps"))))
21132 (properties `((upstream-name . "RefManageR")))
21133 (build-system r-build-system)
21143 (home-page "https://github.com/ropensci/RefManageR/")
21144 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
21146 "This package provides tools for importing and working with bibliographic
21147 references. It greatly enhances the @code{bibentry} class by providing a
21148 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
21149 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
21150 by various formats for name lists (author by last names, translator by full
21151 names, etc.). Entries can be updated, combined, sorted, printed in a number
21152 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
21153 into R and converted to @code{BibEntry} objects.")
21154 ;; Any of these licenses may be picked.
21155 (license (list license:gpl2 license:gpl3 license:bsd-3))))
21157 (define-public r-citr
21164 (uri (cran-uri "citr" version))
21167 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
21168 (build-system r-build-system)
21179 (home-page "https://github.com/crsh/citr")
21180 (synopsis "RStudio add-in to insert Markdown citations")
21182 "This package provides functions and an RStudio add-in that search a
21183 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
21184 the current document.")
21185 (license license:expat)))
21187 (define-public r-xgboost
21190 (version "1.6.0.1")
21194 (uri (cran-uri "xgboost" version))
21197 "1gafjv6vcpny03lqw8s68xszalsylniavaqwsbzh46vyk4h9mscs"))))
21198 (build-system r-build-system)
21200 (list r-data-table r-jsonlite r-matrix))
21203 (home-page "https://github.com/dmlc/xgboost")
21204 (synopsis "Extreme gradient boosting")
21206 "This package provides an R interface to Extreme Gradient Boosting, which
21207 is an efficient implementation of the gradient boosting framework from Chen
21208 and Guestrin (2016). The package includes efficient linear model solver and
21209 tree learning algorithms. The package can automatically do parallel
21210 computation on a single machine. It supports various objective functions,
21211 including regression, classification and ranking. The package is made to be
21212 extensible, so that users are also allowed to define their own objectives
21214 (license license:asl2.0)))
21216 (define-public r-umap
21219 (version "0.2.9.0")
21223 (uri (cran-uri "umap" version))
21226 "1282v09kpds83mlr7kz06k8a40ji15hw85p30vrnp1g6w64w26sm"))))
21227 (build-system r-build-system)
21229 (list r-matrix r-openssl r-rcpp r-reticulate r-rspectra))
21232 (home-page "https://github.com/tkonopka/umap")
21233 (synopsis "Uniform manifold approximation and projection")
21235 "Uniform manifold approximation and projection is a technique for
21236 dimension reduction. This package provides an interface to the UMAP algorithm
21237 in R, including a translation of the original algorithm into R.")
21238 (license license:expat)))
21240 (define-public r-uwot
21247 (uri (cran-uri "uwot" version))
21250 "1q4z98w3pkc51vrcpmwaibnwmlm17zjcnh0qlx660wky5ccyh5l0"))))
21251 (build-system r-build-system)
21260 (home-page "https://github.com/jlmelville/uwot")
21261 (synopsis "Uniform manifold approximation and projection")
21263 "This package provides an implementation of the Uniform Manifold
21264 Approximation and Projection dimensionality reduction by McInnes et
21265 al. (2018). It also provides means to transform new data and to carry out
21266 supervised dimensionality reduction. An implementation of the related
21267 LargeVis method of Tang et al. (2016) is also provided.")
21268 (license license:gpl3)))
21270 (define-public r-kableextra
21272 (name "r-kableextra")
21277 (uri (cran-uri "kableExtra" version))
21280 "1c5vzy95cbz36jwyssr927qicrayifinv861rvnmg4nghb1gl7q9"))))
21281 (properties `((upstream-name . "kableExtra")))
21282 (build-system r-build-system)
21300 (home-page "https://haozhu233.github.io/kableExtra/")
21301 (synopsis "Construct complex tables with pipe syntax")
21303 "Build complex HTML or LaTeX tables using @code{kable()} from
21304 @code{knitr} and the piping syntax from @code{magrittr}. The function
21305 @code{kable()} is a light weight table generator coming from @code{knitr}.
21306 This package simplifies the way to manipulate the HTML or LaTeX codes
21307 generated by @code{kable()} and allows users to construct complex tables and
21308 customize styles using a readable syntax.")
21309 (license license:expat)))
21311 (define-public r-glasso
21318 (uri (cran-uri "glasso" version))
21320 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
21321 (build-system r-build-system)
21322 (native-inputs (list gfortran))
21323 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
21324 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
21326 "This is a package for estimation of a sparse inverse covariance matrix
21327 using a lasso (L1) penalty. Facilities are provided for estimates along a
21328 path of values for the regularization parameter.")
21329 (license license:gpl2)))
21331 (define-public r-gldex
21334 (version "2.0.0.9")
21337 (uri (cran-uri "GLDEX" version))
21340 "1g0wg6z4ba1n6p2nw3kr734wlgmq0aw1a4spr6xw6djj7idsfi61"))))
21341 (properties `((upstream-name . "GLDEX")))
21342 (build-system r-build-system)
21343 (propagated-inputs (list r-cluster r-spacefillr))
21344 (home-page "https://cran.r-project.org/package=GLDEX")
21345 (synopsis "Fitting single and mixture of generalised lambda distributions")
21347 "@code{GLDEX} offers fitting algorithms corresponding to two major
21348 objectives. One is to provide a smoothing device to fit distributions to data
21349 using the weighted and unweighted discretised approach based on the bin width
21350 of the histogram. The other is to provide a definitive fit to the data set
21351 using the maximum likelihood and quantile matching estimation. Other methods
21352 such as moment matching, starship method, and L moment matching are also
21353 provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample
21354 tests and comparing mean, variance, skewness and kurtosis of the data with the
21355 fitted distribution.")
21356 (license license:gpl3+)))
21358 (define-public r-rhpcblasctl
21360 (name "r-rhpcblasctl")
21361 (version "0.21-247.1")
21365 (uri (cran-uri "RhpcBLASctl" version))
21368 "0scpr6jq25xx7wmqyc380ann4h536ll0g7wblikk25yqvpamzrav"))))
21369 (properties `((upstream-name . "RhpcBLASctl")))
21370 (build-system r-build-system)
21371 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
21372 (synopsis "Control the number of threads on BLAS")
21374 "This package allows you to control the number of threads the BLAS
21375 library uses. It is also possible to control the number of threads in
21377 (license license:agpl3+)))
21379 (define-public r-lda
21386 (uri (cran-uri "lda" version))
21389 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
21390 (build-system r-build-system)
21391 (home-page "https://cran.r-project.org/web/packages/lda/")
21392 (synopsis "Collapsed Gibbs sampling methods for topic models")
21394 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
21395 related models. This includes (but is not limited to) sLDA, corrLDA, and the
21396 mixed-membership stochastic blockmodel. Inference for all of these models is
21397 implemented via a fast collapsed Gibbs sampler written in C. Utility
21398 functions for reading/writing data typically used in topic models, as well as
21399 tools for examining posterior distributions are also included.")
21400 ;; Any version of the LGPL
21401 (license license:lgpl3+)))
21403 (define-public r-rann-l1
21410 (uri (cran-uri "RANN.L1" version))
21413 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
21414 (properties `((upstream-name . "RANN.L1")))
21415 (build-system r-build-system)
21416 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
21417 (synopsis "Fast nearest neighbour search using L1 metric")
21419 "This package provides tools to find the k nearest neighbours for every
21420 point in a given dataset in O(N log N) time using Arya and Mount's ANN
21421 library. There is support for approximate as well as exact searches, fixed
21422 radius searches and @code{bd} as well as @code{kd} trees. The distance is
21423 computed using the L1 (Manhattan, taxicab) metric.")
21424 (license license:gpl3+)))
21426 (define-public r-leiden
21433 (uri (cran-uri "leiden" version))
21436 "0f09k3mhb0di2cz1q95y6qd3rqh7xdybn0dpnd4ifqhfhr5lnika"))))
21437 (properties `((upstream-name . "leiden")))
21438 (build-system r-build-system)
21440 (list r-igraph r-matrix r-reticulate))
21443 (home-page "https://github.com/TomKellyGenetics/leiden")
21444 (synopsis "R implementation of Leiden clustering algorithm")
21446 "This package implements the Python @code{leidenalg} module to be called
21447 in R. It enables clustering using the Leiden algorithm for partitioning a
21448 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
21449 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
21450 (license license:gpl3)))
21452 (define-public r-patchwork
21454 (name "r-patchwork")
21459 (uri (cran-uri "patchwork" version))
21462 "0xw9mh1qakj131nw98icxrxwvdlwy2ngwvmagrqr3m84sz9dbffs"))))
21463 (build-system r-build-system)
21465 (list r-ggplot2 r-gtable))
21468 (home-page "https://github.com/thomasp85/patchwork")
21469 (synopsis "Compose ggplot2 plots")
21471 "The @code{ggplot2} package provides a strong API for sequentially
21472 building up a plot, but does not concern itself with composition of multiple
21473 plots. Patchwork is a package that expands the API to allow for arbitrarily
21474 complex composition of plots by providing mathematical operators for combining
21476 (license license:expat)))
21478 (define-public r-liger
21485 (uri (git-reference
21486 (url "https://github.com/MacoskoLab/liger")
21487 (commit (string-append "v" version))))
21488 (file-name (git-file-name name version))
21491 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
21492 (modules '((guix build utils)))
21495 (delete-file "inst/java/ModularityOptimizer.jar")
21497 (build-system r-build-system)
21500 (modify-phases %standard-phases
21501 (add-after 'unpack 'build-java-part
21502 (lambda* (#:key inputs #:allow-other-keys)
21503 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
21504 (for-each (lambda (file) (invoke "javac" file))
21505 (find-files "." "\\.java$"))
21506 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
21507 (find-files "." "\\.class$"))
21531 `(("jdk" ,icedtea "jdk")
21532 ;; See https://github.com/MacoskoLab/liger/issues/96
21533 ;; The optimizer is released under the Expat license.
21537 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
21540 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
21542 ("r-knitr" ,r-knitr))) ; for vignettes
21543 (home-page "https://github.com/MacoskoLab/liger")
21544 (synopsis "Integrate and analyze multiple single-cell datasets")
21546 "LIGER is a package for integrating and analyzing multiple single-cell
21547 datasets, developed and maintained by the Macosko lab. It relies on
21548 integrative non-negative matrix factorization to identify shared and
21549 dataset-specific factors.")
21550 (license license:gpl3)))
21552 (define-public r-harmony
21559 (uri (git-reference
21560 (url "https://github.com/immunogenomics/harmony")
21562 (file-name (git-file-name name version))
21565 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
21566 (modules '((guix build utils)))
21569 (for-each delete-file '("config.status" "configure"))
21571 (build-system r-build-system)
21586 (home-page "https://github.com/immunogenomics/harmony")
21587 (synopsis "Integration of single cell sequencing data")
21589 "This package provides an implementation of the Harmony algorithm for
21590 single cell integration, described in Korsunsky et al
21591 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
21592 function and interfaces to external frameworks.")
21593 (license license:gpl3)))
21595 (define-public r-covr
21602 (uri (cran-uri "covr" version))
21604 (base32 "0mqiqmbwq5f083lda208nqd4ya0f912bkkya2i62fkqsii1ibgpz"))))
21605 (properties `((upstream-name . "covr")))
21606 (build-system r-build-system)
21616 (list r-knitr)) ; for vignettes
21617 (home-page "https://github.com/r-lib/covr")
21618 (synopsis "Test coverage for R packages")
21620 "Thisp package enables you to track and report code coverage for your
21621 package and (optionally) upload the results to a coverage service. Code
21622 coverage is a measure of the amount of code being exercised by a set of tests.
21623 It is an indirect measure of test quality and completeness. This package is
21624 compatible with any testing methodology or framework and tracks coverage of
21625 both R code and compiled C/C++/FORTRAN code.")
21626 (license license:gpl3)))
21628 (define-public r-systemfonts
21630 (name "r-systemfonts")
21635 (uri (cran-uri "systemfonts" version))
21638 "1h44bal845jp7ya8i7ff1kz1n3wklkb00jk6hb9lgwa2p5snqxpg"))))
21639 (properties `((upstream-name . "systemfonts")))
21640 (build-system r-build-system)
21644 (list fontconfig freetype zlib))
21646 (list pkg-config r-knitr))
21647 (home-page "https://github.com/r-lib/systemfonts")
21648 (synopsis "System native font finding")
21650 "This package provides system native access to the font catalogue. As
21651 font handling varies between systems it is difficult to correctly locate
21652 installed fonts across different operating systems. The 'systemfonts' package
21653 provides bindings to the native libraries for finding font files that can then
21654 be used further by e.g. graphic devices.")
21655 (license license:expat)))
21657 (define-public r-graphlayouts
21659 (name "r-graphlayouts")
21664 (uri (cran-uri "graphlayouts" version))
21667 "0yhg42p3jlz78kd712jd5525zm1h3n5gmjplfscjkgn342r3w92v"))))
21668 (properties `((upstream-name . "graphlayouts")))
21669 (build-system r-build-system)
21671 (list r-igraph r-rcpp r-rcpparmadillo))
21672 (home-page "https://github.com/schochastics/graphlayouts")
21673 (synopsis "Additional layout algorithms for network visualizations")
21675 "This package provides several layout algorithms to visualize networks
21676 which are not part of the igraph library. Most are based on the concept of
21677 stress majorization by Gansner et al. (2004)
21678 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
21679 emphasize hidden group structures in networks or focus on specific nodes.")
21680 (license license:expat)))
21682 (define-public r-terra
21689 (uri (cran-uri "terra" version))
21692 "00mwigymvsqf7r3swbkdw8fwqzr05ddk84fhyhr16lfa4118z26v"))))
21693 (properties `((upstream-name . "terra")))
21694 (build-system r-build-system)
21699 sqlite ; needed for proj
21705 (home-page "https://rspatial.org/terra")
21706 (synopsis "Spatial data analysis")
21708 "This package provides methods for spatial data analysis, especially
21709 raster data. The included methods allow for low-level data manipulation as
21710 well as high-level global, local, zonal, and focal computation. The predict
21711 and interpolate methods facilitate the use of regression type (interpolation,
21712 machine learning) models for spatial prediction. Processing of very large
21713 files is supported.")
21714 (license license:gpl3+)))
21716 (define-public r-tidygraph
21718 (name "r-tidygraph")
21723 (uri (cran-uri "tidygraph" version))
21726 "0w34jfldjkynbkyinmi1vdrfjhjrs47hm599mbnx4sxmnpbclmfm"))))
21727 (properties `((upstream-name . "tidygraph")))
21728 (build-system r-build-system)
21740 (home-page "https://github.com/thomasp85/tidygraph")
21741 (synopsis "Tidy API for graph manipulation")
21743 "This package provides a graph implementation that can be thought of as
21744 two tidy data frames describing node and edge data respectively. It provides
21745 an approach to manipulate these two virtual data frames using the API defined
21746 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
21747 common graph algorithms.")
21748 (license license:expat)))
21750 (define-public r-soupx
21751 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
21755 (version (git-version "0.3.1" revision commit))
21759 (uri (git-reference
21760 (url "https://github.com/constantAmateur/SoupX")
21762 (file-name (git-file-name name version))
21765 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
21766 (properties `((upstream-name . "SoupX")))
21767 (build-system r-build-system)
21769 (list r-ggplot2 r-matrix r-seurat))
21770 (home-page "https://github.com/constantAmateur/SoupX")
21771 (synopsis "Single cell mRNA Soup eXterminator")
21773 "This package provides a package for quantifying, profiling and
21774 removing cell free mRNA contamination (the \"soup\") from droplet based single
21775 cell RNA-seq experiments.")
21776 (license license:gpl2))))
21778 (define-public r-assertr
21785 (uri (cran-uri "assertr" version))
21788 "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650"))))
21789 (build-system r-build-system)
21791 (list r-dplyr r-mass r-rlang))
21793 (list r-knitr)) ; needed for vignette
21794 (home-page "https://github.com/ropensci/assertr")
21795 (synopsis "Assertive programming for R analysis pipelines")
21797 "This package provides functionality to assert conditions that have to be
21798 met so that errors in data used in analysis pipelines can fail quickly. It is
21799 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
21801 (license license:expat)))
21803 (define-public r-parameters
21805 (name "r-parameters")
21810 (uri (cran-uri "parameters" version))
21813 "04swg19zb34y3nmclf94v19yskqlb2diqg93jflhgagrv9550az9"))))
21814 (properties `((upstream-name . "parameters")))
21815 (build-system r-build-system)
21817 (list r-bayestestr r-datawizard r-insight))
21820 (home-page "https://cran.r-project.org/web/packages/parameters")
21821 (synopsis "Processing of model parameters")
21823 "This package provides utilities for processing the parameters of various
21824 statistical models. Beyond computing p values, CIs, and other indices for a
21825 wide variety of models, this package implements features like standardization
21826 or bootstrapping of parameters and models, feature reduction (feature
21827 extraction and variable selection) as well as conversion between indices of
21829 (license license:gpl3)))
21831 (define-public r-rgdal
21838 (uri (cran-uri "rgdal" version))
21840 (base32 "1vbkyhw8nd7dw1r53qisphav31x6zvpbzilvnlvbjbj9hzhs90s5"))))
21841 (properties `((upstream-name . "rgdal")))
21842 (build-system r-build-system)
21844 (list gdal proj zlib))
21848 (list pkg-config r-knitr))
21849 (home-page "http://rgdal.r-forge.r-project.org")
21850 (synopsis "Bindings for the Geospatial Data Abstraction Library")
21852 "This package provides bindings to the Geospatial Data Abstraction
21853 Library (GDAL) and access to projection/transformation operations from the
21855 (license license:gpl2+)))
21857 (define-public r-insol
21864 (uri (cran-uri "insol" version))
21867 "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3"))))
21868 (properties `((upstream-name . "insol")))
21869 (build-system r-build-system)
21874 (home-page "https://meteoexploration.com/R/insol/index.html")
21875 (synopsis "Tools for calculating solar radiation")
21877 "This package provides functions to compute insolation on tilted
21878 surfaces, computes atmospheric transmittance and related parameters such as:
21879 Earth radius vector, declination, sunset and sunrise, daylength, equation of
21880 time, vector in the direction of the sun, vector normal to surface, and some
21881 atmospheric physics.")
21882 (license license:gpl2+)))
21884 (define-public r-lifecycle
21886 (name "r-lifecycle")
21891 (uri (cran-uri "lifecycle" version))
21894 "0qssl9lmfn94kmvcg1xpd4md17jx31i3sdbb77dwas60z673qgvv"))))
21895 (properties `((upstream-name . "lifecycle")))
21896 (build-system r-build-system)
21898 (list r-glue r-rlang))
21900 (list r-knitr)) ; for vignettes
21901 (home-page "https://github.com/r-lib/lifecycle")
21902 (synopsis "Manage the life cycle of your package functions")
21904 "Manage the life cycle of your exported functions with shared
21905 conventions, documentation badges, and non-invasive deprecation warnings. The
21906 lifecycle package defines four development stages (experimental, maturing,
21907 stable, and questioning) and three deprecation stages (soft-deprecated,
21908 deprecated, and defunct). It makes it easy to insert badges corresponding to
21909 these stages in your documentation. Usage of deprecated functions are
21910 signalled with increasing levels of non-invasive verbosity.")
21911 (license license:gpl3)))
21913 (define-public r-assertable
21915 (name "r-assertable")
21920 (uri (cran-uri "assertable" version))
21923 "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4"))))
21924 (build-system r-build-system)
21926 (list r-data-table))
21929 (home-page "https://cran.r-project.org/web/packages/assertable/")
21930 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
21931 (description "This package provides simple, flexible assertions on
21932 data.frame or data.table objects with verbose output for vetting. While other
21933 assertion packages apply towards more general use-cases, @code{assertable} is
21934 tailored towards tabular data. It includes functions to check variable names
21935 and values, whether the dataset contains all combinations of a given set of
21936 unique identifiers, and whether it is a certain length. In addition,
21937 @code{assertable} includes utility functions to check the existence of target
21938 files and to efficiently import multiple tabular data files into one
21940 (license license:gpl3)))
21942 (define-public r-quadprog
21944 (name "r-quadprog")
21949 (uri (cran-uri "quadprog" version))
21951 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
21952 (build-system r-build-system)
21955 (home-page "https://cran.r-project.org/web/packages/quadprog")
21956 (synopsis "Functions to solve quadratic programming problems")
21958 "This package contains routines and documentation for solving quadratic
21959 programming problems.")
21960 (license license:gpl3+)))
21962 (define-public r-desolve
21969 (uri (cran-uri "deSolve" version))
21971 (base32 "115nr3j1zp2016qpk9ab6r8n15zygvlihlmc10ilfznf0ng9gpki"))))
21972 (properties `((upstream-name . "deSolve")))
21973 (build-system r-build-system)
21976 (home-page "https://desolve.r-forge.r-project.org/")
21977 (synopsis "Solvers for initial value problems of differential equations")
21978 (description "This package provides functions that solve initial value
21979 problems of a system of first-order @dfn{ordinary differential
21980 equations} (ODE), of @dfn{partial differential equations} (PDE), of
21981 @dfn{differential algebraic equations} (DAE), and of delay differential
21982 equations. The functions provide an interface to the FORTRAN functions
21983 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
21984 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
21985 C-implementation of solvers of the Runge-Kutta family with fixed or variable
21986 time steps. The package contains routines designed for solving ODEs resulting
21987 from 1-D, 2-D and 3-D partial differential equations that have been converted
21988 to ODEs by numerical differencing.")
21989 (license license:gpl2+)))
21991 (define-public r-pmcmrplus
21993 (name "r-pmcmrplus")
21998 (uri (cran-uri "PMCMRplus" version))
22000 (base32 "1mvj3cwrdkl3frk7fvh6l7v7yya5p3xm4z0qhc4fvykxdmb92ivz"))))
22001 (properties `((upstream-name . "PMCMRplus")))
22002 (build-system r-build-system)
22003 (inputs (list gmp))
22013 (native-inputs (list gfortran r-knitr))
22014 (home-page "https://cran.r-project.org/package=PMCMRplus")
22015 (synopsis "Calculate pairwise multiple comparisons of mean rank sums extended")
22017 "This package provides multiple pairwise tests.")
22018 (license license:gpl3+)))
22020 (define-public r-pracma
22026 (uri (cran-uri "pracma" version))
22028 (base32 "0r17siivm37k4gp253v9mlg5m7cwqp85h9kk2hbp2wkf81ad80i3"))))
22029 (build-system r-build-system)
22030 (home-page "https://cran.r-project.org/web/packages/pracma/")
22031 (synopsis "Practical numerical math functions")
22032 (description "This package provides functions for numerical analysis and
22033 linear algebra, numerical optimization, differential equations, plus some
22034 special functions. It uses Matlab function names where appropriate to simplify
22036 (license license:gpl3+)))
22038 (define-public r-subplex
22045 (uri (cran-uri "subplex" version))
22048 "19g5bd39gmcn27xdsklkzxg99x1r5v5q8zcw1iwry31qj24ivhrv"))))
22049 (build-system r-build-system)
22052 (home-page "https://cran.r-project.org/web/packages/subplex")
22053 (synopsis "Unconstrained optimization using the subplex algorithm")
22055 "This package implements the Subplex optimization algorithm.
22056 It solves unconstrained optimization problems using a simplex method on
22057 subspaces. The method is well suited for optimizing objective functions that
22058 are noisy or are discontinuous at the solution.")
22059 (license license:gpl3+)))
22061 (define-public r-txtplot
22068 (uri (cran-uri "txtplot" version))
22071 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
22072 (build-system r-build-system)
22073 (home-page "https://cran.r-project.org/web/packages/txtplot/")
22074 (synopsis "Text-based plotting")
22075 (description "This package provides functions to produce rudimentary ASCII
22076 graphics directly in the terminal window. This package provides a basic
22077 plotting function (and equivalents of curve, density, acf and barplot) as well
22078 as a boxplot function.")
22079 (license license:lgpl3+)))
22081 (define-public r-bio3d
22088 (uri (cran-uri "bio3d" version))
22091 "0x3apqxbk4lvvcnvvdsyjd9f6qh9f9qgml3ih69hl9ikj06iy0y6"))))
22092 (properties `((upstream-name . "bio3d")))
22093 (build-system r-build-system)
22094 (inputs (list zlib))
22095 (propagated-inputs (list r-rcpp))
22098 (home-page "http://thegrantlab.org/bio3d/")
22099 (synopsis "Biological structure analysis")
22101 "This package provides utilities to process, organize and explore protein
22102 structure, sequence and dynamics data. Features include the ability to read
22103 and write structure, sequence and dynamic trajectory data, perform sequence
22104 and structure database searches, data summaries, atom selection, alignment,
22105 superposition, rigid core identification, clustering, torsion analysis,
22106 distance matrix analysis, structure and sequence conservation analysis, normal
22107 mode analysis, principal component analysis of heterogeneous structure data,
22108 and correlation network analysis from normal mode and molecular dynamics data.
22109 In addition, various utility functions are provided to enable the statistical
22110 and graphical power of the R environment to work with biological sequence and
22112 (license license:gpl2+)))
22114 (define-public r-bios2cor
22116 (name "r-bios2cor")
22121 (uri (cran-uri "Bios2cor" version))
22124 "0xj7ab9a463p4a67y0hlv6mfd08xf8didkn2mwrfa7gxjqqvix4z"))))
22125 (properties `((upstream-name . "Bios2cor")))
22126 (build-system r-build-system)
22128 (list r-bigmemory r-bio3d r-circular r-igraph))
22129 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
22130 (synopsis "From biological sequences and simulations to correlation analysis")
22132 "This package provides utilities for computation and analysis of
22133 correlation/covariation in multiple sequence alignments and in side chain
22134 motions during molecular dynamics simulations. Features include the
22135 computation of correlation/covariation scores using a variety of scoring
22136 functions between either sequence positions in alignments or side chain
22137 dihedral angles in molecular dynamics simulations and utilities to analyze the
22138 correlation/covariation matrix through a variety of tools including network
22139 representation and principal components analysis. In addition, several
22140 utility functions are based on the R graphical environment to provide friendly
22141 tools for help in data interpretation.")
22142 (license license:gpl2+)))
22144 ;; This package includes minified JavaScript files. When upgrading please
22145 ;; check that there are no new minified JavaScript files.
22146 (define-public r-networkd3
22148 (name "r-networkd3")
22153 (uri (cran-uri "networkD3" version))
22156 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
22159 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
22161 (properties `((upstream-name . "networkD3")))
22162 (build-system r-build-system)
22164 `(#:modules ((guix build utils)
22165 (guix build r-build-system)
22169 (modify-phases %standard-phases
22170 (add-after 'unpack 'process-javascript
22171 (lambda* (#:key inputs #:allow-other-keys)
22172 (with-directory-excursion "inst/htmlwidgets/lib/"
22176 `((,(assoc-ref inputs "d3.v4.js")
22177 "d3-4.5.0/d3.min.js"))))
22178 (lambda (sources targets)
22179 (for-each (lambda (source target)
22180 (format #t "Processing ~a --> ~a~%"
22182 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
22183 (call-with-output-file target
22185 (dump-port minified port)))))
22186 sources targets))))
22189 `(("uglifyjs" ,node-uglify-js)
22190 ;; NOTE: Make sure that this version of d3 is still valid when
22191 ;; upgrading the package.
22195 (uri "https://d3js.org/d3.v4.js")
22198 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
22200 (list r-htmlwidgets r-igraph r-magrittr))
22201 (home-page "https://cran.r-project.org/package=networkD3")
22202 (synopsis "D3 JavaScript network graphs from R")
22204 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
22206 (license license:gpl3+)))
22208 (define-public r-aasea
22215 (uri (cran-uri "aaSEA" version))
22218 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
22219 (properties `((upstream-name . "aaSEA")))
22220 (build-system r-build-system)
22231 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
22232 (synopsis "Amino acid substitution effect analyzer")
22234 "Given a protein multiple sequence alignment, it is a daunting task to
22235 assess the effects of substitutions along sequence length. The aaSEA package
22236 is intended to help researchers to rapidly analyze property changes caused by
22237 single, multiple and correlated amino acid substitutions in proteins.")
22238 (license license:gpl3)))
22240 (define-public r-abacus
22247 (uri (cran-uri "ABACUS" version))
22250 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
22251 (properties `((upstream-name . "ABACUS")))
22252 (build-system r-build-system)
22254 (list r-ggplot2 r-shiny))
22255 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
22256 (synopsis "Apps-based activities for communicating and understanding statistics")
22258 "This package provides a set of Shiny apps for effective communication
22259 and understanding in statistics. The current version includes properties of
22260 normal distribution, properties of sampling distribution, one-sample z and t
22261 tests, two samples independent (unpaired) t test and analysis of variance.")
22262 (license license:gpl3)))
22264 (define-public r-abc-rap
22271 (uri (cran-uri "ABC.RAP" version))
22274 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
22275 (properties `((upstream-name . "ABC.RAP")))
22276 (build-system r-build-system)
22277 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
22278 (synopsis "Array-based CpG region analysis pipeline")
22280 "This package aims to identify candidate genes that are differentially
22281 methylated between cases and controls. It applies Student's t-test and delta
22282 beta analysis to identify candidate genes containing multiple CpG sites.")
22283 (license license:gpl3)))
22285 (define-public r-abcadm
22292 (uri (cran-uri "abcADM" version))
22295 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
22296 (properties `((upstream-name . "abcADM")))
22297 (build-system r-build-system)
22299 (list r-bh r-rcpp))
22300 (home-page "https://cran.r-project.org/web/packages/abcADM/")
22301 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
22303 "This package provides tools to estimate parameters of accumulated
22304 damage (load duration) models based on failure time data under a Bayesian
22305 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
22306 long-term reliability under stochastic load profiles.")
22307 (license license:gpl3)))
22309 (define-public r-rglpk
22316 (uri (cran-uri "Rglpk" version))
22319 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
22320 (properties `((upstream-name . "Rglpk")))
22321 (build-system r-build-system)
22326 (home-page "https://r-forge.r-project.org/projects/rglp/")
22327 (synopsis "R interface to the GNU Linear Programming Kit")
22329 "This package provides an R interface to the GNU Linear Programming Kit,
22330 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
22331 integer linear programming} (MILP) and other related problems.")
22333 (license (list license:gpl2 license:gpl3))))
22335 (define-public r-abcdefba
22337 (name "r-abcdefba")
22342 (uri (cran-uri "abcdeFBA" version))
22345 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
22346 (properties `((upstream-name . "abcdeFBA")))
22347 (build-system r-build-system)
22349 (list r-corrplot r-lattice r-rgl r-rglpk))
22350 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
22351 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
22353 "This package provides functions for Constraint Based Simulation using
22354 Flux Balance Analysis and informative analysis of the data generated during
22356 (license license:gpl2)))
22358 (define-public r-abcrlda
22365 (uri (cran-uri "abcrlda" version))
22368 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
22369 (properties `((upstream-name . "abcrlda")))
22370 (build-system r-build-system)
22371 (home-page "https://ieeexplore.ieee.org/document/8720003/")
22372 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
22374 "This package offers methods to perform @dfn{asymptotically
22375 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
22376 cost-sensitive binary classification. The bias-correction is an estimate of
22377 the bias term added to regularized discriminant analysis that minimizes the
22379 (license license:gpl3)))
22381 (define-public r-abemus
22388 (uri (cran-uri "abemus" version))
22391 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
22392 (properties `((upstream-name . "abemus")))
22393 (build-system r-build-system)
22395 (list r-data-table))
22396 (home-page "https://cran.r-project.org/web/packages/abemus/")
22397 (synopsis "Adaptive base error model in ultra-deep sequencing data")
22399 "This package provides an implementation of @dfn{Adaptive Base Error
22400 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
22401 platform-specific genetic knowledge and empirical signal to readily detect and
22402 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
22403 cell free DNA} (cfDNA).")
22404 (license license:gpl3)))
22406 ;; This package includes minified JavaScript files. When upgrading please
22407 ;; check that there are no new minified JavaScript files.
22408 (define-public r-rintrojs
22410 (name "r-rintrojs")
22415 (uri (cran-uri "rintrojs" version))
22418 "19lpq421hrs1wc9bnimbwxx35p8bbzil3x1h9l28gjayn4djmjsh"))
22420 '(delete-file "inst/javascript/introjs/intro.min.js"))))
22421 (properties `((upstream-name . "rintrojs")))
22422 (build-system r-build-system)
22425 (modify-phases %standard-phases
22426 (add-after 'unpack 'process-javascript
22427 (lambda* (#:key inputs #:allow-other-keys)
22428 (with-directory-excursion "inst/javascript/introjs/"
22429 (let ((source (assoc-ref inputs "intro.js"))
22430 (target "intro.min.js"))
22431 (format #true "Processing ~a --> ~a~%"
22433 (invoke "esbuild" source "--minify"
22434 (string-append "--outfile=" target)))))))))
22436 `(("esbuild" ,esbuild)
22440 (uri "https://cdn.jsdelivr.net/npm/intro.js@3.2.1/intro.js")
22443 "0vh5n7hqqyx2pdvlqq6xadfqibcn78h5961rwhpf817kpxfzv8v7"))))))
22445 (list r-jsonlite r-shiny))
22446 (home-page "https://github.com/carlganz/rintrojs")
22447 (synopsis "Wrapper for the Intro.js library")
22449 "This package provides a wrapper for the @url{http://www.introjs.com,
22450 Intro.js} library. This package makes it easy to include step-by-step
22451 introductions, and clickable hints in a Shiny application. It supports both
22452 static introductions in the UI, and programmatic introductions from the
22454 ;; The intro.js library is licensed under Expat.
22455 (license (list license:agpl3+ license:expat))))
22457 (define-public r-sysfonts
22459 (name "r-sysfonts")
22464 (uri (cran-uri "sysfonts" version))
22467 "1fq5dn4l09sgrbznfz9cakf4vgc3761zwicvqaazh0s8mzbaicpn"))))
22468 (properties `((upstream-name . "sysfonts")))
22469 (build-system r-build-system)
22471 (list freetype libpng zlib))
22474 (home-page "https://github.com/yixuan/sysfonts")
22475 (synopsis "Loading fonts into R")
22477 "This is a package to simplify loading of system fonts and Google Fonts
22478 into R, in order to support other packages.")
22479 (license license:gpl2)))
22481 (define-public r-showtextdb
22483 (name "r-showtextdb")
22488 (uri (cran-uri "showtextdb" version))
22491 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
22492 (properties `((upstream-name . "showtextdb")))
22493 (build-system r-build-system)
22496 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
22497 (synopsis "Font files for the 'showtext' package")
22499 "This package provides font files that can be used by the @code{showtext}
22501 (license license:asl2.0)))
22503 (define-public r-showtext
22505 (name "r-showtext")
22510 (uri (cran-uri "showtext" version))
22513 "1larnqxn9nanbqiadm35ah5hh89xrzm4fdj9pfc93zzzhlfrvhb3"))))
22514 (properties `((upstream-name . "showtext")))
22515 (build-system r-build-system)
22517 (list freetype libpng zlib))
22519 (list r-showtextdb r-sysfonts))
22521 (list pkg-config r-knitr))
22522 (home-page "https://github.com/yixuan/showtext")
22523 (synopsis "Using fonts more easily in R graphs")
22525 "This package aims to make it easy to use various types of
22526 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
22527 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
22528 will be converted into polygons or raster images, hence after the plot has
22529 been created, it no longer relies on the font files. No external software
22530 such as Ghostscript is needed to use this package.")
22531 (license license:asl2.0)))
22533 (define-public r-emojifont
22535 (name "r-emojifont")
22540 (uri (cran-uri "emojifont" version))
22543 "1hhrwilv36hd9gs1kcl2zsi6519md0h9aixjrm6lfclxvz8r6k1i"))))
22544 (properties `((upstream-name . "emojifont")))
22545 (build-system r-build-system)
22547 (list r-ggplot2 r-proto r-showtext r-sysfonts))
22550 (home-page "https://guangchuangyu.github.io/emojifont")
22551 (synopsis "Emoji and Font Awesome in R graphics")
22553 "This package enables the use of emoji and the Font Awesome glyphs in
22554 both base and ggplot2 graphics.")
22555 (license license:artistic2.0)))
22557 (define-public r-abstractr
22559 (name "r-abstractr")
22564 (uri (cran-uri "abstractr" version))
22567 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
22568 (properties `((upstream-name . "abstractr")))
22569 (build-system r-build-system)
22571 (list r-colourpicker
22578 (home-page "https://matt-kumar.shinyapps.io/portfolio")
22579 (synopsis "R-Shiny application for creating visual abstracts")
22581 "This package provides an R Shiny application to create visual abstracts
22582 for original research. A variety of user defined options and formatting are
22584 (license license:gpl3)))
22586 (define-public r-qgam
22593 (uri (cran-uri "qgam" version))
22596 "1jyamamdffaks89rspyhmg18b4iik0nb1j0vgqzvfnm890514cvn"))))
22597 (properties `((upstream-name . "qgam")))
22598 (build-system r-build-system)
22600 (list r-doparallel r-mgcv r-plyr r-shiny))
22601 (native-inputs (list r-knitr))
22602 (home-page "https://cran.r-project.org/web/packages/qgam/")
22603 (synopsis "Smooth additive quantile regression models")
22605 "This package provides smooth additive quantile regression models, fitted
22606 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
22607 the smoothing parameters are estimated automatically by marginal loss
22608 minimization, while the regression coefficients are estimated using either
22609 PIRLS or Newton algorithm. The learning rate is determined so that the
22610 Bayesian credible intervals of the estimated effects have approximately the
22611 correct coverage. The main function is @code{qgam()} which is similar to
22612 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
22613 regression models.")
22614 (license license:gpl2+)))
22616 (define-public r-abtest
22623 (uri (cran-uri "abtest" version))
22626 "0jz2ry5364p8h8xlk5a5sycn8xlpxd1iasfg99bcr4jqzd92jfqg"))))
22627 (properties `((upstream-name . "abtest")))
22628 (build-system r-build-system)
22638 (home-page "https://cran.r-project.org/web/packages/abtest/")
22639 (synopsis "Bayesian A/B testing")
22641 "This package provides functions for Bayesian A/B testing including prior
22642 elicitation options based on Kass and Vaidyanathan (1992)
22643 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
22644 (license license:gpl2+)))
22646 (define-public r-reldist
22653 (uri (cran-uri "reldist" version))
22656 "17kbqqapqmckghv7jizibmicv3bzbycfr3mz4xg3yjp3c2bap4r6"))))
22657 (properties `((upstream-name . "reldist")))
22658 (build-system r-build-system)
22660 (list r-densestbayes r-mgcv))
22661 (home-page "http://www.stat.ucla.edu/~handcock/RelDist")
22662 (synopsis "Relative distribution methods")
22664 "This package provides tools for the comparison of distributions. This
22665 includes nonparametric estimation of the relative distribution PDF and CDF and
22666 numerical summaries as described in \"Relative Distribution Methods in the
22667 Social Sciences\" by Mark S. Handcock and Martina Morris, Springer-Verlag,
22668 1999, Springer-Verlag, ISBN 0387987789.")
22669 ;; See also https://cran.r-project.org/web/packages/reldist/LICENSE for
22670 ;; attribution requirements.
22671 (license license:gpl3)))
22673 (define-public r-accept
22680 (uri (cran-uri "accept" version))
22683 "0risdxw17jk3d56q40a78slb1rcj93b6kz71hn5hbwr0iih722gr"))))
22684 (properties `((upstream-name . "accept")))
22685 (build-system r-build-system)
22687 (list r-dplyr r-reldist))
22688 (home-page "https://cran.r-project.org/web/packages/accept/")
22689 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
22691 "This package allows clinicians to predict the rate and severity of
22692 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
22693 Disease} (COPD) patients, based on the clinical prediction model published in
22694 Adibi et al. (2019) @url{doi:10.1101/651901}.")
22695 (license license:gpl3)))
22697 (define-public r-smpracticals
22699 (name "r-smpracticals")
22704 (uri (cran-uri "SMPracticals" version))
22707 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
22708 (properties `((upstream-name . "SMPracticals")))
22709 (build-system r-build-system)
22711 (list r-ellipse r-mass r-nlme r-survival))
22712 (home-page "http://statwww.epfl.ch/davison/SM/")
22713 (synopsis "Practicals for use with Davison (2003) Statistical Models")
22715 "This package contains the datasets and a few functions for use with the
22716 practicals outlined in Appendix A of the book Statistical Models (Davison,
22717 2003, Cambridge University Press). The practicals themselves can be found at
22718 @url{http://statwww.epfl.ch/davison/SM/}.")
22719 (license license:gpl2+)))
22721 (define-public r-fgui
22728 (uri (cran-uri "fgui" version))
22731 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
22732 (properties `((upstream-name . "fgui")))
22733 (build-system r-build-system)
22735 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
22736 (synopsis "Create GUI for R functions")
22738 "Rapidly create a GUI for a function you created by automatically
22739 creating widgets for arguments of the function. This package automatically
22740 parses help routines for context-sensitive help to these arguments. The
22741 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
22742 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
22743 incorporated into the interface for greater customization for the more
22745 ;; Any version of the GPL.
22746 (license (list license:gpl2+ license:gpl3+))))
22748 (define-public r-tcltk2
22755 (uri (cran-uri "tcltk2" version))
22758 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
22759 (properties `((upstream-name . "tcltk2")))
22760 (build-system r-build-system)
22763 (home-page "https://www.sciviews.org/SciViews-R")
22764 (synopsis "Tcl/Tk additions")
22766 "This package provides a series of additional Tcl commands and Tk widgets
22767 with style and various functions to supplement the tcltk package")
22768 (license license:lgpl3)))
22770 (define-public r-accrual
22777 (uri (cran-uri "accrual" version))
22780 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
22781 (properties `((upstream-name . "accrual")))
22782 (build-system r-build-system)
22784 (list r-fgui r-smpracticals r-tcltk2))
22785 (home-page "https://cran.r-project.org/web/packages/accrual/")
22786 (synopsis "Bayesian accrual prediction")
22788 "Subject recruitment for medical research is challenging. Slow patient
22789 accrual leads to delay in research. Accrual monitoring during the process of
22790 recruitment is critical. Researchers need reliable tools to manage the
22791 accrual rate. This package provides an implementation of a Bayesian method
22792 that integrates researcher's experience on previous trials and data from the
22793 current study, providing reliable prediction on accrual rate for clinical
22794 studies. It provides functions for Bayesian accrual prediction which can be
22795 easily used by statisticians and clinical researchers.")
22796 (license license:gpl2)))
22798 (define-public r-accrued
22805 (uri (cran-uri "accrued" version))
22808 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
22809 (properties `((upstream-name . "accrued")))
22810 (build-system r-build-system)
22811 (home-page "https://cran.r-project.org/web/packages/accrued/")
22812 (synopsis "Data quality visualization tools for partially accruing data")
22814 "This is a package for visualizing data quality of partially accruing
22816 (license license:gpl3)))
22818 (define-public r-mda
22825 (uri (cran-uri "mda" version))
22828 "0qw4scc2w7jmnxssj5w2mdxb9rrl4dscqn54gplzm1gk2yf419mx"))))
22829 (properties `((upstream-name . "mda")))
22830 (build-system r-build-system)
22831 (propagated-inputs (list r-class))
22832 (native-inputs (list gfortran))
22833 (home-page "https://cran.r-project.org/web/packages/mda/")
22834 (synopsis "Mixture and flexible discriminant analysis")
22836 "This is a package for mixture and flexible discriminant analysis,
22837 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
22838 (license license:gpl2)))
22840 (define-public r-elasticnet
22842 (name "r-elasticnet")
22847 (uri (cran-uri "elasticnet" version))
22850 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
22851 (properties `((upstream-name . "elasticnet")))
22852 (build-system r-build-system)
22855 (home-page "http://users.stat.umn.edu/~zouxx019/")
22856 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
22858 "This package provides functions for fitting the entire solution path of
22859 the Elastic-Net and also provides functions for estimating sparse Principal
22860 Components. The Lasso solution paths can be computed by the same function.")
22861 (license license:gpl2+)))
22863 (define-public r-sparselda
22865 (name "r-sparselda")
22870 (uri (cran-uri "sparseLDA" version))
22873 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
22874 (properties `((upstream-name . "sparseLDA")))
22875 (build-system r-build-system)
22877 (list r-elasticnet r-mass r-mda))
22878 (home-page "https://www.imm.dtu.dk/~lkhc/")
22879 (synopsis "Sparse discriminant analysis")
22881 "This package performs sparse linear discriminant analysis for Gaussians
22882 and mixture of Gaussian models.")
22883 (license license:gpl2+)))
22885 (define-public r-accsda
22892 (uri (cran-uri "accSDA" version))
22895 "0jf4x5j9y7a3mvf2ghjp6bxdq1s5jh2sx3x3ar6f3lyzzvrnls4v"))))
22896 (properties `((upstream-name . "accSDA")))
22897 (build-system r-build-system)
22903 (home-page "https://github.com/gumeo/accSDA/wiki")
22904 (synopsis "Accelerated sparse discriminant analysis")
22906 "This package provides an implementation of sparse linear discriminant
22907 analysis, which is a supervised classification method for multiple classes.
22908 Various novel optimization approaches to this problem are implemented
22909 including @dfn{alternating direction method of multipliers} (ADMM),
22910 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
22911 Functions for performing cross validation are also supplied along with basic
22912 prediction and plotting functions. @dfn{Sparse zero variance
22913 discriminant} (SZVD) analysis is also included in the package.")
22914 (license license:gpl2+)))
22916 (define-public r-ace2fastq
22918 (name "r-ace2fastq")
22923 (uri (cran-uri "ace2fastq" version))
22926 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
22927 (properties `((upstream-name . "ace2fastq")))
22928 (build-system r-build-system)
22931 (home-page "https://github.com/c5sire/ace2fastq")
22932 (synopsis "ACE file to FASTQ converter")
22934 "The ACE file format is used in genomics to store contigs from sequencing
22935 machines. This tools converts it into FASTQ format. Both formats contain the
22936 sequence characters and their corresponding quality information. Unlike the
22937 FASTQ file, the ACE file stores the quality values numerically. The
22938 conversion algorithm uses the standard Sanger formula. The package
22939 facilitates insertion into pipelines, and content inspection.")
22940 (license license:gpl3)))
22942 (define-public r-rngwell
22949 (uri (cran-uri "rngWELL" version))
22952 "0f1dxxaimfb0fww8ym9ciqf6q760ai46wxldl37m5mfpd57ca00c"))))
22953 (properties `((upstream-name . "rngWELL")))
22954 (build-system r-build-system)
22955 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
22956 (synopsis "Toolbox for WELL random number generators")
22958 "This is a dedicated package to WELL pseudo random generators, which were
22959 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
22960 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
22961 (license license:bsd-3)))
22963 (define-public r-rnmf
22969 (uri (cran-uri "rNMF" version))
22972 "1nz6h0j5ywdh48m0swmhp34hbkycd7n13rclrxaw85qi9wc42597"))))
22973 (build-system r-build-system)
22975 (list r-knitr r-nnls))
22976 (home-page "https://cran.r-project.org/web/packages/rNMF/")
22977 (synopsis "Robust nonnegative matrix factorization")
22979 "This package provides an implementation of robust nonnegative matrix
22980 factorization (rNMF). The rNMF algorithm decomposes a nonnegative high
22981 dimension data matrix into the product of two low rank nonnegative matrices,
22982 while detecting and trimming outliers. The main function is @code{rnmf()}.
22983 The package also includes a visualization tool, @code{see()}, that arranges
22984 and prints vectorized images.")
22985 (license license:gpl2+)))
22987 (define-public r-randtoolbox
22989 (name "r-randtoolbox")
22994 (uri (cran-uri "randtoolbox" version))
22997 "0mvafd2gm1jpg19gdn6bw8668pqghi0xmcb56rl4fwamg8jg09xn"))))
22998 (properties `((upstream-name . "randtoolbox")))
22999 (build-system r-build-system)
23002 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
23003 (synopsis "Toolbox for pseudo and quasi random number generation")
23005 "This package provides
23008 @item pseudo random generators, such as general linear
23009 congruential generators, multiple recursive generators and generalized
23010 feedback shift register (SF-Mersenne Twister algorithm and WELL
23013 @item quasi random generators, such as the Torus algorithm, the Sobol
23014 sequence, the Halton sequence (including the Van der Corput sequence), and
23016 @item some generator tests: the gap test, the serial test, the poker test.
23019 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
23020 (license license:bsd-3)))
23022 (define-public r-lhs
23029 (uri (cran-uri "lhs" version))
23032 "0fb3bc3s5pbwg92qkjbg7v8ah36wm6qs05vf098hwjakr7f6yg3s"))))
23033 (properties `((upstream-name . "lhs")))
23034 (build-system r-build-system)
23035 (propagated-inputs (list r-rcpp))
23038 (home-page "https://github.com/bertcarnell/lhs")
23039 (synopsis "Latin Hypercube Samples")
23041 "This package provides a number of methods for creating and augmenting
23042 Latin Hypercube Samples.")
23043 (license license:gpl3)))
23045 (define-public r-acebayes
23047 (name "r-acebayes")
23052 (uri (cran-uri "acebayes" version))
23055 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73"))))
23056 (properties `((upstream-name . "acebayes")))
23057 (build-system r-build-system)
23059 (list r-compare r-lhs r-randtoolbox r-rcpp r-rcpparmadillo))
23060 (home-page "https://cran.r-project.org/web/packages/acebayes/")
23061 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
23063 "Finding an optimal Bayesian experimental design involves maximizing an
23064 objective function given by the expectation of some appropriately chosen
23065 utility function with respect to the joint distribution of unknown
23066 quantities (including responses). This objective function is usually not
23067 available in closed form and the design space can be continuous and of high
23068 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
23069 to maximise an approximation to the expectation of the utility function.")
23070 (license license:gpl2)))
23072 (define-public r-acet
23079 (uri (cran-uri "ACEt" version))
23082 "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4"))))
23083 (properties `((upstream-name . "ACEt")))
23084 (build-system r-build-system)
23086 (list r-bh r-mass r-rcpp r-rcpparmadillo))
23087 (home-page "https://cran.r-project.org/web/packages/ACEt/")
23088 (synopsis "Estimating dynamic heritability and twin model comparison")
23090 "This package supports twin models that are able to estimate the dynamic
23091 behaviour of the variance components in the classical twin models with respect
23092 to age using B-splines and P-splines.")
23093 (license license:gpl2+)))
23095 (define-public r-acfmperiod
23097 (name "r-acfmperiod")
23102 (uri (cran-uri "acfMPeriod" version))
23105 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
23106 (properties `((upstream-name . "acfMPeriod")))
23107 (build-system r-build-system)
23110 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
23111 (synopsis "Estimation of the ACF from the M-periodogram")
23113 "This package support non-robust and robust computations of the sample
23114 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
23115 univariate and multivariate processes. The methodology consists in reversing
23116 the diagonalization procedure involving the periodogram or the
23117 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
23118 ACOVF or the ACF as discussed in Fuller (1995)
23119 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
23120 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
23121 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
23122 (license license:gpl2+)))
23124 (define-public r-gamlss-data
23126 (name "r-gamlss-data")
23131 (uri (cran-uri "gamlss.data" version))
23134 "07mpdl4h9rwmnpl9jmsn6ig8ji11an6pyjfsvg62h2alapwbdcyv"))))
23135 (properties `((upstream-name . "gamlss.data")))
23136 (build-system r-build-system)
23137 (home-page "http://www.gamlss.org/")
23138 (synopsis "GAMLSS data")
23140 "This package provides data used as examples to demonstrate GAMLSS
23142 ;; Either version of the license
23143 (license (list license:gpl2 license:gpl3))))
23145 (define-public r-gamlss
23152 (uri (cran-uri "gamlss" version))
23155 "0xih19zqgpjl5qv5j38ana6x29y84shn2jfl2lk4kaw3q7yx86b6"))))
23156 (properties `((upstream-name . "gamlss")))
23157 (build-system r-build-system)
23159 (list r-gamlss-data r-gamlss-dist r-mass r-nlme r-survival))
23160 (home-page "http://www.gamlss.org/")
23161 (synopsis "Generalized additive models for location scale and shape")
23163 "This package provides functions for fitting the generalized additive
23164 models for location scale and shape introduced by Rigby and
23165 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
23166 use a distributional regression approach where all the parameters of the
23167 conditional distribution of the response variable are modelled using
23168 explanatory variables.")
23169 ;; Either version of the license
23170 (license (list license:gpl2 license:gpl3))))
23172 (define-public r-acid
23179 (uri (cran-uri "acid" version))
23182 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
23183 (properties `((upstream-name . "acid")))
23184 (build-system r-build-system)
23186 (list r-gamlss r-gamlss-dist r-hmisc))
23187 (home-page "https://cran.r-project.org/web/packages/acid/")
23188 (synopsis "Analysing conditional income distributions")
23190 "This package provides functions for the analysis of income distributions
23191 for subgroups of the population as defined by a set of variables like age,
23192 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
23193 distribution as well as functions for moments, inequality measures, entropy
23194 measures and polarisation measures of income distributions. This package thus
23195 aides the analysis of income inequality by offering tools for the exploratory
23196 analysis of income distributions at the disaggregated level.")
23197 (license license:gpl3)))
23199 (define-public r-acm4r
23206 (uri (cran-uri "acm4r" version))
23209 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
23210 (properties `((upstream-name . "acm4r")))
23211 (build-system r-build-system)
23212 (propagated-inputs (list r-mass))
23213 (home-page "https://cran.r-project.org/web/packages/acm4r/")
23214 (synopsis "Align-and-count method comparisons of RFLP data")
23216 "This is a package to compare sequence fragment lengths or molecular
23217 weights from pairs of lanes. The number of matching bands in the
23218 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
23219 the align-and-count method.")
23220 ;; Any version of the GPL
23221 (license (list license:gpl2+ license:gpl3+))))
23223 (define-public r-filelock
23225 (name "r-filelock")
23230 (uri (cran-uri "filelock" version))
23233 "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc"))))
23234 (properties `((upstream-name . "filelock")))
23235 (build-system r-build-system)
23236 (home-page "https://github.com/r-lib/filelock")
23237 (synopsis "Portable file locking")
23239 "This library lets you place an exclusive or shared lock on a file using
23240 the appropriate system call provided by the underlying operating system.")
23241 (license license:expat)))
23243 (define-public r-filematrix
23245 (name "r-filematrix")
23250 (uri (cran-uri "filematrix" version))
23253 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
23254 (properties `((upstream-name . "filematrix")))
23255 (build-system r-build-system)
23256 ;; These inputs are needed for vignettes
23258 (list r-knitr r-rmarkdown))
23259 (home-page "https://github.com/andreyshabalin/filematrix")
23260 (synopsis "File-backed matrix class with convenient read and write access")
23262 "This package provides an interface for working with large matrices
23263 stored in files, not in computer memory. It supports multiple non-character
23264 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
23265 byte real values). Access to parts of the matrix is done by indexing, exactly
23266 as with usual R matrices. It supports very large matrices; the package has
23267 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
23268 columns, ad allows for quick addition of extra columns to a filematrix.")
23269 (license license:lgpl3)))
23271 (define-public r-acmeeqtl
23273 (name "r-acmeeqtl")
23278 (uri (cran-uri "ACMEeqtl" version))
23281 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
23282 (properties `((upstream-name . "ACMEeqtl")))
23283 (build-system r-build-system)
23285 (list r-filematrix))
23286 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
23287 (synopsis "Estimation of interpretable eQTL effect sizes")
23289 "This package provides a non-linear model, termed ACME, that reflects a
23290 parsimonious biological model for allelic contributions of cis-acting eQTLs.
23291 With non-linear least-squares algorithm the maximum likelihood parameters can
23292 be estimated. The ACME model provides interpretable effect size estimates and
23293 p-values with well controlled Type-I error.")
23294 (license license:lgpl3)))
23296 (define-public r-acmer
23303 (uri (cran-uri "acmeR" version))
23306 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
23307 (properties `((upstream-name . "acmeR")))
23308 (build-system r-build-system)
23309 (propagated-inputs (list r-foreign))
23310 (home-page "https://cran.r-project.org/web/packages/acmeR/")
23311 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
23313 "This package provides an implementation of the ACME estimator, described
23314 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
23315 Mortality at Wind Turbines. Unlike most other models, this estimator supports
23316 decreasing-hazard Weibull model for persistence; decreasing search proficiency
23317 as carcasses age; variable bleed-through at successive searches; and interval
23318 mortality estimates. The package provides, based on search data, functions
23319 for estimating the mortality inflation factor in Frequentist and Bayesian
23321 (license license:expat)))
23323 (define-public r-r-huge
23330 (uri (cran-uri "R.huge" version))
23333 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
23334 (properties `((upstream-name . "R.huge")))
23335 (build-system r-build-system)
23337 (list r-r-methodss3 r-r-oo r-r-utils))
23338 (home-page "https://github.com/HenrikBengtsson/R.huge")
23339 (synopsis "Methods for accessing huge amounts of data")
23341 "This is a deprecated package for accessing huge amounts of data.
23342 Cross-platform alternatives are the following packages: bigmemory (CRAN),
23343 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
23344 the @code{aroma.affymetrix} package.")
23345 (license license:lgpl2.1+)))
23347 (define-public r-r-filesets
23349 (name "r-r-filesets")
23354 (uri (cran-uri "R.filesets" version))
23357 "14dngx6ffhfvlaixpvlq890nwgil6zyaw8wy3dlcrv001wynzmms"))))
23358 (properties `((upstream-name . "R.filesets")))
23359 (build-system r-build-system)
23362 (modify-phases %standard-phases
23363 (add-after 'unpack 'set-HOME
23364 (lambda _ (setenv "HOME" "/tmp"))))))
23366 (list r-digest r-r-cache r-r-methodss3 r-r-oo r-r-utils))
23367 (home-page "https://github.com/HenrikBengtsson/R.filesets")
23368 (synopsis "Easy handling of and access to files")
23370 "This package provides classes and methods to locate, setup, subset,
23371 navigate and iterate file sets, i.e. sets of files located in one or more
23372 directories on the file system. The API is designed such that these classes
23373 can be extended via inheritance to provide a richer API for special file
23374 formats. Moreover, a specific name format is defined such that filenames and
23375 directories can be considered to have full names which consists of a name
23376 followed by comma-separated tags. This adds additional flexibility to
23377 identify file sets and individual files.")
23378 (license license:lgpl2.1+)))
23380 (define-public r-r-devices
23382 (name "r-r-devices")
23387 (uri (cran-uri "R.devices" version))
23390 "02cwdhb9m97gxi4pki4kasc5j3a12r7yzsychzzk9h0ijc1mfziv"))))
23391 (properties `((upstream-name . "R.devices")))
23392 (build-system r-build-system)
23394 (list r-base64enc r-r-methodss3 r-r-oo r-r-utils))
23395 (home-page "https://github.com/HenrikBengtsson/R.devices")
23396 (synopsis "Unified handling of graphics devices")
23398 "This package provides functions for creating plots and image files in a
23399 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
23400 Default device options as well as scales and aspect ratios are controlled in a
23401 uniform way across all device types. Switching output format requires minimal
23402 changes in code. This package is ideal for large-scale batch processing,
23403 because it will never leave open graphics devices or incomplete image files
23404 behind, even on errors or user interrupts.")
23405 (license license:lgpl2.1+)))
23407 (define-public r-acnr
23414 (uri (cran-uri "acnr" version))
23417 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
23418 (properties `((upstream-name . "acnr")))
23419 (build-system r-build-system)
23420 (home-page "https://github.com/mpierrejean/acnr")
23421 (synopsis "Annotated copy-number regions")
23423 "This package provides SNP array data from different types of copy-number
23424 regions. These regions were identified manually by the authors of the package
23425 and may be used to generate realistic data sets with known truth.")
23426 (license license:lgpl2.1+)))
23428 (define-public r-acopula
23435 (uri (cran-uri "acopula" version))
23438 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
23439 (properties `((upstream-name . "acopula")))
23440 (build-system r-build-system)
23441 (home-page "https://cran.r-project.org/web/packages/acopula/")
23442 (synopsis "Modelling dependence with multivariate Archimax copulas")
23444 "Archimax copulas are a mixture of Archimedean and EV copulas. This
23445 package provides definitions of several parametric families of generator and
23446 dependence function, computes CDF and PDF, estimates parameters, tests for
23447 goodness of fit, generates random sample and checks copula properties for
23448 custom constructs. In the 2-dimensional case explicit formulas for density
23449 are used, contrary to higher dimensions when all derivatives are linearly
23450 approximated. Several non-archimax families (normal, FGM, Plackett) are
23451 provided as well.")
23452 (license license:gpl2)))
23454 (define-public r-tuner
23461 (uri (cran-uri "tuneR" version))
23464 "1sd0drxzbdy71bh35fccg9ajhpdhdpy0m9nja2lw82p1pzhyl7jn"))))
23465 (properties `((upstream-name . "tuneR")))
23466 (build-system r-build-system)
23467 (propagated-inputs (list r-signal))
23468 (home-page "https://cran.r-project.org/web/packages/tuneR/")
23469 (synopsis "Analysis of music and speech")
23471 "This is a package for the analysis of music and speech. Analyze music
23472 and speech, extract features like MFCCs, handle wave files and their
23473 representation in various ways, read MP3, read MIDI, perform steps of a
23474 transcription, ...")
23475 ;; Either of these versions.
23476 (license (list license:gpl2 license:gpl3))))
23478 (define-public r-seewave
23485 (uri (cran-uri "seewave" version))
23488 "0bi1l47l3846c18k6h2vrv0xp9xh00n544a578jrndahzrj1hfwl"))))
23489 (properties `((upstream-name . "seewave")))
23490 (build-system r-build-system)
23495 (home-page "http://rug.mnhn.fr/seewave")
23496 (synopsis "Sound analysis and synthesis")
23498 "This package provides functions for analysing, manipulating, displaying,
23499 editing and synthesizing time waves (particularly sound). This package
23500 processes time analysis (oscillograms and envelopes), spectral content,
23501 resonance quality factor, entropy, cross correlation and autocorrelation,
23502 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
23503 and 3D spectrograms and many other analyses.")
23504 (license license:gpl2+)))
23506 (define-public r-acousticndlcoder
23508 (name "r-acousticndlcoder")
23513 (uri (cran-uri "AcousticNDLCodeR" version))
23516 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
23518 `((upstream-name . "AcousticNDLCodeR")))
23519 (build-system r-build-system)
23521 (list r-seewave r-tuner r-zoo))
23522 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
23523 (synopsis "Coding sound files for use with NDL")
23525 "Make acoustic cues to use with the R package @code{ndl}.
23526 The package implements functions used in the PLoS ONE paper \"Words from
23527 spontaneous conversational speech can be recognized with human-like accuracy
23528 by an error-driven learning algorithm that discriminates between meanings
23529 straight from smart acoustic features, bypassing the phoneme as recognition
23530 unit.\" @url{doi:10.1371/journal.pone.0174623}")
23531 (license license:gpl2+)))
23533 (define-public r-acp
23540 (uri (cran-uri "acp" version))
23543 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
23544 (properties `((upstream-name . "acp")))
23545 (build-system r-build-system)
23547 (list r-quantmod r-tseries))
23548 (home-page "https://cran.r-project.org/web/packages/acp/")
23549 (synopsis "Autoregressive conditional Poisson")
23551 "This package supports the analysis of count data exhibiting
23552 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
23553 model (ACP(p,q)) proposed by Heinen (2003).")
23554 (license license:gpl2)))
23556 (define-public r-ada
23563 (uri (cran-uri "ada" version))
23566 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
23567 (properties `((upstream-name . "ada")))
23568 (build-system r-build-system)
23569 (propagated-inputs (list r-rpart))
23570 (home-page "https://cran.r-project.org/web/packages/ada/")
23571 (synopsis "Stochastic boosting")
23573 "This package provides a straightforward, well-documented, and broad
23574 boosting routine for classification, ideally suited for small to
23575 moderate-sized data sets. It performs discrete, real, and gentle boost under
23576 both exponential and logistic loss on a given data set.")
23577 ;; Any version of the GPL.
23578 (license (list license:gpl2+ license:gpl3+))))
23580 (define-public r-genalg
23587 (uri (cran-uri "genalg" version))
23590 "1y4qz1s85zpd1r3259gr542arssf2vpd4drhy0wnq5q47ignrvna"))))
23591 (properties `((upstream-name . "genalg")))
23592 (build-system r-build-system)
23593 (home-page "https://github.com/egonw/genalg")
23594 (synopsis "R based genetic algorithm")
23596 "This package provides an R based genetic algorithm for binary and
23597 floating point chromosomes.")
23598 (license license:gpl2)))
23600 (define-public r-kernelfactory
23602 (name "r-kernelfactory")
23607 (uri (cran-uri "kernelFactory" version))
23610 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
23611 (properties `((upstream-name . "kernelFactory")))
23612 (build-system r-build-system)
23614 (list r-auc r-genalg r-kernlab r-randomforest))
23615 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
23616 (synopsis "Ensemble of kernel machines")
23618 "Kernel factory is an ensemble method where each base classifier (random
23619 forest) is fit on the kernel matrix of a subset of the training data.")
23620 (license license:gpl2+)))
23622 (define-public r-dummies
23629 (uri (cran-uri "dummies" version))
23632 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
23633 (properties `((upstream-name . "dummies")))
23634 (build-system r-build-system)
23635 (home-page "https://decisionpatterns.com")
23636 (synopsis "Create dummy/indicator variables flexibly and efficiently")
23638 "This package lets you expand factors, characters and other eligible
23639 classes into dummy/indicator variables.")
23640 (license license:gpl2+)))
23642 (define-public r-acrm
23649 (uri (cran-uri "aCRM" version))
23652 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
23653 (properties `((upstream-name . "aCRM")))
23654 (build-system r-build-system)
23656 (list r-ada r-dummies r-kernelfactory r-randomforest))
23657 (home-page "https://cran.r-project.org/web/packages/aCRM/")
23658 (synopsis "Convenience functions for analytical customer relationship management")
23660 "This package provides convenience functions for data preparation and
23661 modeling often used in @dfn{analytical customer relationship
23662 management} (aCRM).")
23663 (license license:gpl2+)))
23665 (define-public r-tree
23671 (uri (cran-uri "tree" version))
23674 "1q3jgkhl5d4d8c396cyvkw60094p0z0a3x7xwhdbi8gl4c2c65ss"))))
23675 (build-system r-build-system)
23676 (home-page "https://cran.r-project.org/web/packages/tree/")
23677 (synopsis "Classification and regression trees")
23678 (description "This package provides procedures to work with classification
23679 and regression trees.")
23680 (license license:gpl2+)))
23682 (define-public r-treeclust
23684 (name "r-treeclust")
23689 (uri (cran-uri "treeClust" version))
23692 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
23693 (properties `((upstream-name . "treeClust")))
23694 (build-system r-build-system)
23696 (list r-cluster r-rpart))
23697 (home-page "https://cran.r-project.org/web/packages/treeClust/")
23698 (synopsis "Cluster distances through trees")
23700 "This package provides tools to create a measure of inter-point
23701 dissimilarity useful for clustering mixed data, and, optionally, perform the
23703 (license license:gpl2+)))
23705 (define-public r-acrosstic
23707 (name "r-acrosstic")
23712 (uri (cran-uri "AcrossTic" version))
23715 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
23716 (properties `((upstream-name . "AcrossTic")))
23717 (build-system r-build-system)
23719 (list r-lpsolve r-treeclust))
23720 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
23721 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
23723 "This is a package for constructing minimum-cost regular spanning
23724 subgraph as part of a non-parametric two-sample test for equality of
23726 (license license:gpl2+)))
23728 (define-public r-acrt
23735 (uri (cran-uri "acrt" version))
23738 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
23739 (properties `((upstream-name . "acrt")))
23740 (build-system r-build-system)
23742 (list r-rcpp r-rcppeigen r-sandwich))
23743 (home-page "https://cran.r-project.org/web/packages/acrt/")
23744 (synopsis "Autocorrelation robust testing")
23746 "This package provides functions for testing affine hypotheses on the
23747 regression coefficient vector in regression models with autocorrelated
23749 (license license:gpl2)))
23751 (define-public r-acs
23758 (uri (cran-uri "acs" version))
23761 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
23762 (properties `((upstream-name . "acs")))
23763 (build-system r-build-system)
23765 (list r-httr r-plyr r-rcpp r-stringr r-xml))
23766 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
23767 (synopsis "Work with data from the US Census")
23769 "This package provides a general toolkit for downloading, managing,
23770 analyzing, and presenting data from the
23771 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
23772 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
23773 American Community Survey (ACS). Confidence intervals provided with ACS data
23774 are converted to standard errors to be bundled with estimates in complex
23775 @code{acs} objects. The package provides new methods to conduct standard
23776 operations on @code{acs} objects and present/plot data in statistically
23777 appropriate ways.")
23778 (license license:gpl3)))
23780 (define-public r-acss-data
23782 (name "r-acss-data")
23787 (uri (cran-uri "acss.data" version))
23790 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
23791 (properties `((upstream-name . "acss.data")))
23792 (build-system r-build-system)
23793 (home-page "http://complexitycalculator.com/methodology.html")
23794 (synopsis "Data for algorithmic complexity of short strings")
23796 "This is a data only package providing the algorithmic complexity of
23797 short strings, computed using the coding theorem method. For a given set of
23798 symbols in a string, all possible or a large number of random samples of
23799 Turing machines with a given number of states (e.g., 5) and number of symbols
23800 corresponding to the number of symbols in the strings were simulated until
23801 they reached a halting state or failed to end. This package contains data on
23802 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
23803 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
23804 distribution of the halting states.")
23805 (license license:gpl2+)))
23807 (define-public r-acss
23814 (uri (cran-uri "acss" version))
23817 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
23818 (properties `((upstream-name . "acss")))
23819 (build-system r-build-system)
23821 (list r-acss-data r-zoo))
23822 (home-page "http://complexitycalculator.com/methodology.html")
23823 (synopsis "Algorithmic complexity for short strings")
23825 "The main purpose of this package is to provide the algorithmic
23826 complexity for short strings, an approximation of the Kolmogorov Complexity of
23827 a short string using the coding theorem method. While the database containing
23828 the complexity is provided in the data only package @code{acss.data}, this
23829 package provides functions accessing the data such as @code{prob_random}
23830 returning the posterior probability that a given string was produced by a
23831 random process. In addition, two traditional (but problematic) measures of
23832 complexity are also provided: entropy and change complexity.")
23833 (license license:gpl2+)))
23835 (define-public r-acswr
23842 (uri (cran-uri "ACSWR" version))
23845 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
23846 (properties `((upstream-name . "ACSWR")))
23847 (build-system r-build-system)
23850 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
23851 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
23853 "This is a companion package for the book \"A Course in Statistics with
23854 R\" (ISBN 978-1-119-15272-9.)")
23855 (license license:gpl2)))
23857 (define-public r-alabama
23860 (version "2022.4-1")
23864 (uri (cran-uri "alabama" version))
23867 "0v6kl6ndm8wvp9xzya3x4gj5kh03qgx13x5vyzn410wsndcjiim8"))))
23868 (properties `((upstream-name . "alabama")))
23869 (build-system r-build-system)
23870 (propagated-inputs (list r-numderiv))
23871 (home-page "https://cran.r-project.org/web/packages/alabama/")
23872 (synopsis "Constrained nonlinear optimization")
23874 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
23875 Algorithm; it is used for optimizing smooth nonlinear objective functions with
23876 constraints. Linear or nonlinear equality and inequality constraints are
23878 (license license:gpl2+)))
23880 (define-public r-gdina
23887 (uri (cran-uri "GDINA" version))
23890 "0bwg9sfsqs5nsqwhjnbb631fbhj0mx2dc4c185qkym9cjb5lfkm9"))))
23891 (properties `((upstream-name . "GDINA")))
23892 (build-system r-build-system)
23906 (home-page "https://github.com/Wenchao-Ma/GDINA")
23907 (synopsis "Generalized DINA model framework")
23909 "This package provides a set of psychometric tools for cognitive
23910 diagnosis modeling based on the generalized deterministic inputs, noisy and
23911 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
23912 and its extensions, including the sequential G-DINA model by Ma and de la
23913 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
23914 polytomous G-DINA model by Chen and de la Torre
23915 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
23916 distribution can be independent, saturated, higher-order, loglinear smoothed
23917 or structured. Q-matrix validation, item and model fit statistics, model
23918 comparison at test and item level and differential item functioning can also
23919 be conducted. A graphical user interface is also provided.")
23920 (license license:gpl3)))
23922 (define-public r-actcd
23929 (uri (cran-uri "ACTCD" version))
23932 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
23933 (properties `((upstream-name . "ACTCD")))
23934 (build-system r-build-system)
23936 (list r-gdina r-r-methodss3))
23939 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
23940 (synopsis "Asymptotic classification theory for cognitive diagnosis")
23942 "This is a package supporting cluster analysis for cognitive diagnosis
23943 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
23944 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
23945 sum-scores, cluster analysis techniques can be used to classify examinees into
23946 latent classes based on their attribute patterns. In addition to the
23947 algorithms used to classify data, three labeling approaches are proposed to
23948 label clusters so that examinees' attribute profiles can be obtained.")
23949 (license license:gpl2+)))
23951 (define-public r-ineq
23958 (uri (cran-uri "ineq" version))
23961 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
23962 (properties `((upstream-name . "ineq")))
23963 (build-system r-build-system)
23964 (home-page "https://cran.r-project.org/web/packages/ineq/")
23965 (synopsis "Measuring inequality, concentration, and poverty")
23967 "This package provides tools for measuring inequality, concentration, and
23968 poverty measures. It provides both empirical and theoretical Lorenz curves.")
23969 ;; Either of these two versions.
23970 (license (list license:gpl2 license:gpl3))))
23972 (define-public r-actfrag
23979 (uri (cran-uri "ActFrag" version))
23982 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
23983 (properties `((upstream-name . "ActFrag")))
23984 (build-system r-build-system)
23986 (list r-accelerometry r-dplyr r-ineq r-survival r-tidyr))
23987 (home-page "https://github.com/junruidi/ActFrag")
23988 (synopsis "Activity fragmentation metrics extraction")
23990 "This package provides functions to extract commonly used fragmentation
23991 metrics to quantify time accumulation strategies based on minute level
23992 actigraphy-measured activity counts data.")
23993 (license license:gpl3)))
23995 (define-public r-ash
24002 (uri (cran-uri "ash" version))
24005 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb"))))
24006 (properties `((upstream-name . "ash")))
24007 (build-system r-build-system)
24008 (native-inputs (list gfortran))
24009 (home-page "https://cran.r-project.org/web/packages/ash/")
24010 (synopsis "David Scott's ASH routines")
24012 "This package provides David Scott's ASH routines ported from S-PLUS to
24014 (license license:gpl2+)))
24016 (define-public r-hdrcde
24023 (uri (cran-uri "hdrcde" version))
24026 "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3"))))
24027 (properties `((upstream-name . "hdrcde")))
24028 (build-system r-build-system)
24036 (native-inputs (list gfortran))
24037 (home-page "http://pkg.robjhyndman.com/hdrcde")
24038 (synopsis "Highest density regions and conditional density estimation")
24040 "This is a package for the computation of highest density regions in one
24041 and two dimensions, kernel estimation of univariate density functions
24042 conditional on one covariate, and multimodal regression.")
24043 (license license:gpl3)))
24045 (define-public r-rainbow
24052 (uri (cran-uri "rainbow" version))
24055 "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3"))))
24056 (properties `((upstream-name . "rainbow")))
24057 (build-system r-build-system)
24065 (home-page "https://cran.r-project.org/web/packages/rainbow/")
24066 (synopsis "Bagplots, boxplots and rainbow plots for functional data")
24068 "This is a package for visualizing functional data and identifying
24069 functional outliers with bagplots, boxplots and rainbow plots.")
24070 (license license:gpl3)))
24072 (define-public r-fds
24079 (uri (cran-uri "fds" version))
24082 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0"))))
24083 (properties `((upstream-name . "fds")))
24084 (build-system r-build-system)
24086 (list r-rainbow r-rcurl))
24087 (home-page "https://cran.r-project.org/web/packages/fds/")
24088 (synopsis "Functional data sets")
24089 (description "This package contains a list of functional time series,
24090 sliced functional time series, and functional data sets. Functional time
24091 series is a special type of functional data observed over time. Sliced
24092 functional time series is a special type of functional time series with a time
24093 variable observed over time.")
24094 (license license:gpl2+)))
24096 (define-public r-fda
24103 (uri (cran-uri "fda" version))
24106 "1wdq35acxavarh7qrxxmdpcjc9jcs56mp3p9rbb4qa35ziv5fi0l"))))
24107 (properties `((upstream-name . "fda")))
24108 (build-system r-build-system)
24110 (list r-desolve r-fds))
24113 (home-page "https://www.functionaldata.org")
24114 (synopsis "Functional data analysis")
24116 "These functions were developed to support functional data analysis as
24117 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
24118 Analysis. The package includes data sets and script files working many
24120 (license license:gpl2+)))
24122 (define-public r-actigraphy
24124 (name "r-actigraphy")
24129 (uri (cran-uri "Actigraphy" version))
24132 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
24133 (properties `((upstream-name . "Actigraphy")))
24134 (build-system r-build-system)
24137 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
24138 (synopsis "Actigraphy data analysis")
24140 "This package provides tools for functional linear modeling and analysis
24141 of actigraphy data.")
24142 (license license:asl2.0)))
24144 (define-public r-activedriver
24146 (name "r-activedriver")
24151 (uri (cran-uri "ActiveDriver" version))
24154 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
24155 (properties `((upstream-name . "ActiveDriver")))
24156 (build-system r-build-system)
24159 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
24160 (synopsis "Tools for finding cancer driver proteins")
24162 "This package provides a mutation analysis tool that discovers cancer
24163 driver genes with frequent mutations in protein signalling sites such as
24164 post-translational modifications (phosphorylation, ubiquitination, etc). The
24165 Poisson generalized linear regression model identifies genes where cancer
24166 mutations in signalling sites are more frequent than expected from the
24167 sequence of the entire gene. Integration of mutations with signalling
24168 information helps find new driver genes and propose candidate mechanisms to
24170 (license license:gpl2+)))
24172 (define-public r-activitycounts
24174 (name "r-activitycounts")
24179 (uri (cran-uri "activityCounts" version))
24182 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
24184 `((upstream-name . "activityCounts")))
24185 (build-system r-build-system)
24187 (list r-lubridate r-magrittr r-seewave r-signal r-tibble))
24188 (home-page "https://github.com/walkabillylab/activityCounts")
24189 (synopsis "Generate ActiLife counts")
24191 "ActiLife generates activity counts from data collected by Actigraph
24192 accelerometers. Actigraph is one of the most common research-grade
24193 accelerometers. There is considerable research validating and developing
24194 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
24195 counts are proprietary and difficult to implement if researchers use different
24196 accelerometer brands. The code creates ActiLife counts from raw acceleration
24197 data for different accelerometer brands.")
24198 (license license:gpl3)))
24200 (define-public r-activityindex
24202 (name "r-activityindex")
24207 (uri (cran-uri "ActivityIndex" version))
24210 "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5"))))
24211 (properties `((upstream-name . "ActivityIndex")))
24212 (build-system r-build-system)
24214 (list r-data-table r-matrixstats r-r-utils))
24217 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
24218 (synopsis "Activity Index calculation using raw accelerometry data")
24220 "This is a package to read raw accelerometry from GT3X+ accelerometry
24221 data and plain table data to calculate the Activity Index from Bai et
24222 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
24223 (license license:gpl3)))
24225 (define-public r-activpal
24227 (name "r-activpal")
24232 (uri (cran-uri "activPAL" version))
24235 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
24236 (properties `((upstream-name . "activPAL")))
24237 (build-system r-build-system)
24245 (home-page "https://cran.r-project.org/web/packages/activPAL")
24246 (synopsis "Processing and chart generation from activPAL events files")
24248 "This package contains functions to generate pre-defined summary
24249 statistics from activPAL events files. The package also contains functions to
24250 produce informative graphics that visualize physical activity behaviour and
24251 trends. This includes generating graphs that align physical activity
24252 behaviour with additional time based observations described by other data
24253 sets, such as sleep diaries and continuous glucose monitoring data.")
24254 (license license:gpl3)))
24256 (define-public r-activpalprocessing
24258 (name "r-activpalprocessing")
24263 (uri (cran-uri "activpalProcessing" version))
24266 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
24268 `((upstream-name . "activpalProcessing")))
24269 (build-system r-build-system)
24272 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
24273 (synopsis "Process activPAL events files")
24275 "This package performs estimation of physical activity and sedentary
24276 behavior variables from activPAL events files.")
24277 ;; Either version of the GPL.
24278 (license (list license:gpl2 license:gpl3))))
24280 (define-public r-actogrammr
24282 (name "r-actogrammr")
24287 (uri (cran-uri "actogrammr" version))
24290 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
24291 (properties `((upstream-name . "actogrammr")))
24292 (build-system r-build-system)
24294 (list r-dplyr r-ggplot2 r-lubridate r-readr r-tidyr))
24295 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
24296 (synopsis "Read in activity data and plot actograms")
24298 "Read in activity measurements from standard file formats used by
24299 circadian rhythm researchers, currently only ClockLab format, and process and
24300 plot the data. The central type of plot is the actogram, as first described
24301 in \"Activity and distribution of certain wild mice in relation to biotic
24302 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
24303 (license license:gpl3)))
24305 (define-public r-expint
24312 (uri (cran-uri "expint" version))
24315 "01d0a7pc4qx7044a0cymnv5ld88r90vdvlqjbnzg9qlfbizdgyvw"))))
24316 (properties `((upstream-name . "expint")))
24317 (build-system r-build-system)
24318 (home-page "https://gitlab.com/vigou3/expint")
24319 (synopsis "Exponential integral and incomplete Gamma function")
24321 "This package provides the exponential integrals @code{E_1(x)},
24322 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
24323 function @code{G(a, x)} defined for negative values of its first argument.
24324 The package also gives easy access to the underlying C routines through an
24325 API; see the package vignette for details.")
24326 (license license:gpl2+)))
24328 (define-public r-actuar
24335 (uri (cran-uri "actuar" version))
24338 "1qi9y2x93pxxbynwl06rbiasm86vb0jh7sckw1dw3s21rsx1f5c5"))))
24339 (properties `((upstream-name . "actuar")))
24340 (build-system r-build-system)
24341 (propagated-inputs (list r-expint))
24342 (home-page "https://gitlab.com/vigou3/actuar")
24343 (synopsis "Actuarial functions and heavy tailed distributions")
24345 "This package provides functions and data sets for actuarial science:
24346 modeling of loss distributions; risk theory and ruin theory; simulation of
24347 compound models, discrete mixtures and compound hierarchical models;
24348 credibility theory. It boasts support for many additional probability
24349 distributions to model insurance loss amounts and loss frequency: 19
24350 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
24351 distribution; zero-truncated and zero-modified extensions of the standard
24352 discrete distributions. It also supports phase-type distributions commonly
24353 used to compute ruin probabilities.")
24354 (license license:gpl2+)))
24356 (define-public r-bmp
24363 (uri (cran-uri "bmp" version))
24366 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
24367 (properties `((upstream-name . "bmp")))
24368 (build-system r-build-system)
24369 (home-page "https://cran.r-project.org/web/packages/bmp/")
24370 (synopsis "Read Bitmap (BMP) images")
24372 "This package provides pure R tools to read BMP format images. It is
24373 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
24374 (license license:gpl2+)))
24376 (define-public r-readbitmap
24378 (name "r-readbitmap")
24383 (uri (cran-uri "readbitmap" version))
24386 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
24387 (properties `((upstream-name . "readbitmap")))
24388 (build-system r-build-system)
24390 (list libjpeg-turbo libpng))
24392 (list r-bmp r-jpeg r-png r-tiff))
24393 (home-page "https://github.com/jefferis/readbitmap")
24394 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
24396 "This package provides tools to identify and read BMP, JPEG, PNG, and
24397 TIFF format bitmap images. Identification defaults to the use of the magic
24398 number embedded in the file rather than the file extension.")
24399 (license license:gpl2+)))
24401 (define-public r-imager
24404 (version "0.42.13")
24408 (uri (cran-uri "imager" version))
24411 "0zygnmxwbbmj5i2l2affzdz90xvsa7b5pbkzkhjbm40is69rh2nr"))))
24412 (properties `((upstream-name . "imager")))
24413 (build-system r-build-system)
24415 (list fftw libtiff libx11 zlib))
24427 (list pkg-config r-knitr))
24428 (home-page "https://dahtah.github.io/imager/")
24429 (synopsis "Image processing library")
24431 "This is a package for fast image processing for images in up to 4
24432 dimensions (two spatial dimensions, one time/depth dimension, one color
24433 dimension). It provides most traditional image processing tools (filtering,
24434 morphology, transformations, etc.) as well as various functions for easily
24435 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
24436 simple, modern C++ library for image processing.")
24437 (license license:lgpl3)))
24439 (define-public r-acuityview
24441 (name "r-acuityview")
24446 (uri (cran-uri "AcuityView" version))
24449 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
24450 (properties `((upstream-name . "AcuityView")))
24451 (build-system r-build-system)
24453 (list r-fftwtools r-imager r-plotrix))
24454 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
24455 (synopsis "Display scenes as seen by an animal with less acute vision")
24457 "This package provides a simple method for representing a visual scene as
24458 it may be seen by an animal with less acute vision.")
24459 (license license:gpl2+)))
24461 (define-public r-caret
24468 (uri (cran-uri "caret" version))
24471 "01sa1h9pc3a062pwm0rxadvg9qxszwcylya7llv08fcxhy46n5ac"))))
24472 (build-system r-build-system)
24487 (home-page "https://github.com/topepo/caret")
24488 (synopsis "Classification and regression training")
24490 "This package provides miscellaneous functions for training and plotting
24491 classification and regression models.")
24492 (license license:gpl2+)))
24494 (define-public r-adabag
24501 (uri (cran-uri "adabag" version))
24504 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
24505 (properties `((upstream-name . "adabag")))
24506 (build-system r-build-system)
24508 (list r-caret r-doparallel r-foreach r-rpart))
24509 (home-page "https://cran.r-project.org/web/packages/adabag/")
24510 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
24512 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
24513 Breiman's Bagging algorithm using classification trees as individual
24514 classifiers. Once these classifiers have been trained, they can be used to
24515 predict on new data. Also, cross validation estimation of the error can be
24517 (license license:gpl2+)))
24519 (define-public r-adagio
24526 (uri (cran-uri "adagio" version))
24529 "0ihv05402iq003m0338f85pnqnlnrmx0pf1mg8cz9sgi5h98mbnl"))))
24530 (properties `((upstream-name . "adagio")))
24531 (build-system r-build-system)
24534 (home-page "https://cran.r-project.org/web/packages/adagio/")
24535 (synopsis "Discrete and global optimization routines")
24537 "This package provides methods and algorithms for discrete optimization,
24538 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
24539 Hooke-Jeeves minimization, and some (evolutionary) global optimization
24541 (license license:gpl3+)))
24543 (define-public r-univoutl
24545 (name "r-univoutl")
24550 (uri (cran-uri "univOutl" version))
24553 "1kp014bhs8v02fp7misrj4fpfp2na9lg45p5zqvlfaypnm5imsr9"))))
24554 (properties `((upstream-name . "univOutl")))
24555 (build-system r-build-system)
24557 (list r-hmisc r-robustbase))
24558 (home-page "https://github.com/marcellodo/univOutl")
24559 (synopsis "Detection of univariate outliers")
24561 "This package provides well-known outlier detection techniques in the
24562 univariate case. Methods to deal with skewed distribution are included too.
24563 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
24564 historical data is implemented as well. When available, survey weights can be
24565 used in outliers detection.")
24566 (license license:gpl2+)))
24568 (define-public r-tolerance
24570 (name "r-tolerance")
24575 (uri (cran-uri "tolerance" version))
24578 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
24579 (properties `((upstream-name . "tolerance")))
24580 (build-system r-build-system)
24582 (list r-mass r-rgl))
24583 (home-page "https://cran.r-project.org/web/packages/tolerance/")
24584 (synopsis "Statistical tolerance intervals and regions")
24586 "This package provides functions for estimating tolerance
24587 limits (intervals) for various univariate distributions (binomial, Cauchy,
24588 discrete Pareto, exponential, two-parameter exponential, extreme value,
24589 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
24590 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
24591 Bayesian normal tolerance limits, multivariate normal tolerance regions,
24592 nonparametric tolerance intervals, tolerance bands for regression
24593 settings (linear regression, nonlinear regression, nonparametric regression,
24594 and multivariate regression), and analysis of variance tolerance intervals.
24595 Visualizations are also available for most of these settings.")
24596 (license license:gpl2+)))
24598 ;; Keep this in sync with the liblantern package.
24599 (define-public r-torch
24606 (uri (cran-uri "torch" version))
24608 (base32 "1dncf5njdzw1hf98knlv94rxcxnc5gl3cmk2cvlbn1z8mri86rlc"))))
24609 (properties `((upstream-name . "torch")))
24610 (build-system r-build-system)
24614 (let ((python-version (version-major+minor (package-version python))))
24615 #~(modify-phases %standard-phases
24616 (add-after 'install 'link-libraries
24617 (lambda* (#:key inputs #:allow-other-keys)
24618 (let ((deps (string-append #$output "/site-library/torch/deps"))
24619 (site-packages (string-append "/lib/python"
24621 "/site-packages")))
24625 inputs (string-append site-packages "/torch/lib/libtorch.so"))
24626 (string-append deps "/libtorch.so"))
24629 inputs "/lib/liblantern.so")
24630 (string-append deps "/liblantern.so")))))))))
24632 (list python-pytorch-for-r-torch
24645 (native-inputs (list r-knitr))
24646 (home-page "https://torch.mlverse.org/docs")
24647 (synopsis "Tensors and neural networks with GPU acceleration")
24649 "This package provides functionality to define and train neural networks
24650 similar to PyTorch but written entirely in R using the libtorch library. It
24651 also supports low-level tensor operations and GPU acceleration.")
24652 (license license:expat)))
24654 (define-public r-additivitytests
24656 (name "r-additivitytests")
24657 (version "1.1-4.1")
24661 (uri (cran-uri "additivityTests" version))
24664 "00kzfv86z6kk0gvbz9mg3p6xi5fb8cn74rhslr17rdpd02md0884"))))
24666 `((upstream-name . "additivityTests")))
24667 (build-system r-build-system)
24668 (native-inputs (list r-knitr))
24669 (home-page "https://github.com/simecek/additivityTests")
24670 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
24672 "This package provides an implementation of the Tukey, Mandel,
24673 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
24674 (license license:gpl3)))
24676 (define-public r-flexclust
24678 (name "r-flexclust")
24683 (uri (cran-uri "flexclust" version))
24686 "13akk3w6a76jpws5v9108c3hdmb8i6gm0sc06lr2hqly0pgpfyfn"))))
24687 (properties `((upstream-name . "flexclust")))
24688 (build-system r-build-system)
24690 (list r-class r-lattice r-modeltools))
24691 (home-page "https://cran.r-project.org/web/packages/flexclust/")
24692 (synopsis "Flexible cluster algorithms")
24694 "The main function @code{kcca} implements a general framework for
24695 k-centroids cluster analysis supporting arbitrary distance measures and
24696 centroid computation. Further cluster methods include hard competitive
24697 learning, neural gas, and QT clustering. There are numerous visualization
24698 methods for cluster results (neighborhood graphs, convex cluster hulls,
24699 barcharts of centroids, ...), and bootstrap methods for the analysis of
24700 cluster stability.")
24701 (license license:gpl2)))
24703 (define-public r-biclust
24710 (uri (cran-uri "biclust" version))
24713 "0lgyc2f04dhr65cwga78pradxsdzgjrpp8vphchqn60ab1z95dlp"))))
24714 (properties `((upstream-name . "biclust")))
24715 (build-system r-build-system)
24717 (list r-additivitytests
24724 (home-page "https://cran.r-project.org/web/packages/biclust/")
24725 (synopsis "BiCluster algorithms")
24727 "The main function @code{biclust()} provides several algorithms to find
24728 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
24729 In addition, the package provides methods for data
24730 preprocessing (normalization and discretization), visualization, and
24731 validation of bicluster solutions.")
24732 (license license:gpl3)))
24734 (define-public r-icge
24741 (uri (cran-uri "ICGE" version))
24744 "0w6hbi3h98q6gsxqbb43p95v6xykgrasxcjivwm8hw9fly4avxyi"))))
24745 (properties `((upstream-name . "ICGE")))
24746 (build-system r-build-system)
24748 (list r-cluster r-fastcluster r-mass))
24749 (home-page "https://cran.r-project.org/web/packages/ICGE/")
24750 (synopsis "Cluster estimation and identification of atypical units")
24752 "ICGE is a package that helps to estimate the number of real clusters in
24753 data as well as to identify atypical units. The underlying methods are based
24754 on distances rather than on unit x variables.")
24755 (license license:gpl2+)))
24757 (define-public r-depth
24760 (version "2.1-1.1")
24764 (uri (cran-uri "depth" version))
24767 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
24768 (properties `((upstream-name . "depth")))
24769 (build-system r-build-system)
24771 (list r-abind r-circular r-rgl))
24774 (home-page "https://cran.r-project.org/web/packages/depth/")
24775 (synopsis "Nonparametric depth functions for multivariate analysis")
24777 "This package provides tools for depth functions methodology applied to
24778 multivariate analysis. Besides allowing calculation of depth values and
24779 depth-based location estimators, the package includes functions or drawing
24780 contour plots and perspective plots of depth functions. Euclidean and
24781 spherical depths are supported.")
24782 (license license:gpl2)))
24784 (define-public r-archetypes
24786 (name "r-archetypes")
24787 (version "2.2-0.1")
24791 (uri (cran-uri "archetypes" version))
24794 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
24795 (properties `((upstream-name . "archetypes")))
24796 (build-system r-build-system)
24798 (list r-modeltools r-nnls))
24799 (home-page "https://cran.r-project.org/web/packages/archetypes")
24800 (synopsis "Archetypal analysis")
24802 "The main function @code{archetypes} implements a framework for
24803 archetypal analysis supporting arbitrary problem solving mechanisms for the
24804 different conceptual parts of the algorithm.")
24805 (license license:gpl2+)))
24807 (define-public r-shapes
24814 (uri (cran-uri "shapes" version))
24817 "1p9fr95zk3q2v277c5ksb0nh26mcpzwjzjb2lmag51z6hck8cb66"))))
24818 (properties `((upstream-name . "shapes")))
24819 (build-system r-build-system)
24821 (list r-mass r-minpack-lm r-rgl r-scatterplot3d))
24822 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
24823 (synopsis "Statistical shape analysis")
24825 "This package provides routines for the statistical analysis of landmark
24826 shapes, including Procrustes analysis, graphical displays, principal
24827 components analysis, permutation and bootstrap tests, thin-plate spline
24828 transformation grids and comparing covariance matrices. See Dryden, I.L. and
24829 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
24830 Edition), John Wiley and Sons.")
24831 (license license:gpl2)))
24833 (define-public r-animation
24835 (name "r-animation")
24839 (uri (cran-uri "animation" version))
24842 "0sg4sz5lkn85yzpcg22xkr7921cbnh7g74nlp9imjy7c0hdqyhc8"))
24844 '(for-each delete-file
24845 '("inst/misc/scianimator/js/jquery.scianimator.min.js"
24846 "inst/misc/scianimator/js/jquery-1.4.4.min.js")))))
24847 (properties `((upstream-name . "animation")))
24848 (build-system r-build-system)
24852 '(modify-phases %standard-phases
24853 (add-after 'unpack 'process-javascript
24854 (lambda* (#:key inputs #:allow-other-keys)
24855 (with-directory-excursion "inst/misc/"
24856 (symlink (search-input-file
24858 "share/javascript/jquery.scianimator.min.js")
24859 "scianimator/js/jquery.scianimator.min.js")
24860 (invoke "esbuild" (assoc-ref inputs "js-jquery")
24862 (string-append "--outfile="
24863 "scianimator/js/jquery-1.4.4.min.js"))))))))
24864 (propagated-inputs (list r-magick))
24865 (inputs (list js-scianimator))
24867 `(("esbuild" ,esbuild)
24871 (uri "https://code.jquery.com/jquery-1.4.4.js")
24874 "10nl4smq63vrfb0c3n0fknm1zw7ss8gicy6wc6jb6l3rmyad075k"))))))
24875 (home-page "https://yihui.org/animation/")
24876 (synopsis "Gallery of animations and utilities to create animations")
24878 "This package provides functions for animations in statistics, covering
24879 topics in probability theory, mathematical statistics, multivariate
24880 statistics, non-parametric statistics, sampling survey, linear models, time
24881 series, computational statistics, data mining and machine learning. These
24882 functions may be helpful in teaching statistics and data analysis. Also
24883 provided in this package are a series of functions to save animations to
24884 various formats, e.g. GIF, HTML pages, PDF, and videos. PDF animations can be
24885 inserted into Sweave / @code{knitr} easily.")
24886 (license (list license:gpl2+ license:gpl3+))))
24888 (define-public r-anthropometry
24890 (name "r-anthropometry")
24895 (uri (cran-uri "Anthropometry" version))
24898 "0vxjlzxv16bygw8n57f25msq5bd1dydg41my92ximah0nzzvbg41"))))
24899 (properties `((upstream-name . "Anthropometry")))
24900 (build-system r-build-system)
24913 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
24914 (synopsis "Statistical methods for anthropometric data")
24916 "This package provides statistical methods especially developed to
24917 analyze anthropometric data. These methods are aimed at providing effective
24918 solutions to some commons problems related to Ergonomics and Anthropometry.
24919 They are based on clustering, the statistical concept of data depth,
24920 statistical shape analysis and archetypal analysis.")
24921 (license license:gpl2+)))
24923 (define-public r-anndata
24926 (version "0.7.5.4")
24930 (uri (cran-uri "anndata" version))
24932 (base32 "0vn64b0rpnwbznn0h03b810mp8hcqxjzw69nzyjmndwa8r9ial2y"))))
24933 (properties `((upstream-name . "anndata")))
24934 (build-system r-build-system)
24935 (propagated-inputs (list r-assertthat r-matrix r-r6 r-reticulate))
24936 (native-inputs (list r-knitr))
24937 (home-page "https://anndata.dynverse.org")
24938 (synopsis "Anndata for R")
24940 "This package provides a reticulate wrapper for the Python package
24941 @code{anndata}. It provides a scalable way of keeping track of data and
24942 learned annotations. It is used to read from and write to the h5ad file
24944 (license license:expat)))
24946 (define-public r-adamethods
24948 (name "r-adamethods")
24953 (uri (cran-uri "adamethods" version))
24956 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
24957 (properties `((upstream-name . "adamethods")))
24958 (build-system r-build-system)
24960 (list r-anthropometry
24967 (home-page "https://cran.r-project.org/web/packages/adamethods/")
24968 (synopsis "Archetypoid algorithms and anomaly detection")
24970 "This package is a collection of several algorithms to obtain
24971 archetypoids with small and large databases and with both classical
24972 multivariate data and functional data (univariate and multivariate). Some of
24973 these algorithms also detect anomalies (outliers).")
24974 (license license:gpl2+)))
24976 (define-public r-idpmisc
24983 (uri (cran-uri "IDPmisc" version))
24986 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
24987 (properties `((upstream-name . "IDPmisc")))
24988 (build-system r-build-system)
24991 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
24992 (synopsis "Functions for data analyses and visualization")
24994 "This package provides different high-level graphics functions for
24995 displaying large datasets, displaying circular data in a very flexible way,
24996 finding local maxima, brewing color ramps, drawing nice arrows, zooming
24997 2D-plots, creating figures with differently colored margin and plot region.
24998 In addition, the package contains auxiliary functions for data manipulation
24999 like omitting observations with irregular values or selecting data by logical
25000 vectors, which include NAs. Other functions are especially useful in
25001 spectroscopy and analyses of environmental data: robust baseline fitting,
25002 finding peaks in spectra, converting humidity measures.")
25003 (license license:gpl3+)))
25005 (define-public r-qqconf
25011 (uri (cran-uri "qqconf" version))
25014 "11sh0q5bwmqdygqd1gspx7xc5mysj18whz11afnz6s1m820snhhw"))))
25015 (properties `((upstream-name . "qqconf")))
25016 (build-system r-build-system)
25017 (inputs (list fftw))
25022 (native-inputs (list pkg-config r-knitr))
25023 (home-page "https://github.com/eweine/qqconf")
25024 (synopsis "Create simultaneous testing bands for QQ-plots")
25026 "This package provides functionality for creating Quantile-Quantile (QQ) and
25027 Probability-Probability (PP) plots with simultaneous testing bands to asses
25028 significance of sample deviation from a reference distribution.")
25029 (license license:gpl3)))
25031 (define-public r-qqman
25038 (uri (cran-uri "qqman" version))
25041 "1a6qp5wv9bvwjchfw8x4jh48hkynlnfr21a8vqgnswldvwbq7njq"))))
25042 (properties `((upstream-name . "qqman")))
25043 (build-system r-build-system)
25045 (list r-calibrate))
25048 (home-page "https://cran.r-project.org/web/packages/qqman/")
25049 (synopsis "Q-Q and Manhattan plots for GWAS data")
25051 "This package allows you to create Q-Q and Manhattan plots for GWAS data
25052 from PLINK results.")
25053 (license license:gpl3)))
25055 (define-public r-gghighlight
25057 (name "r-gghighlight")
25062 (uri (cran-uri "gghighlight" version))
25064 (base32 "0isfp5n0ijqpy3z5d7l75mlq15nbkjppv6812lcya6097ar2d381"))))
25065 (properties `((upstream-name . "gghighlight")))
25066 (build-system r-build-system)
25068 (list r-dplyr r-ggplot2 r-ggrepel r-lifecycle r-purrr r-rlang r-tibble))
25069 (native-inputs (list r-knitr))
25070 (home-page "https://github.com/yutannihilation/gghighlight/")
25071 (synopsis "Highlight lines and points in ggplot2")
25072 (description "Suppose we have data that has so many series that it is hard
25073 to identify them by their colors as the differences are so subtle. With
25074 gghighlight we can highlight those lines that match certain criteria. The
25075 result is a usual @code{ggplot} object, so it is fully customizable and can be
25076 used with custom themes and facets.")
25077 (license license:expat)))
25079 (define-public r-ggplot-multistats
25081 (name "r-ggplot-multistats")
25086 (uri (cran-uri "ggplot.multistats" version))
25089 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
25091 `((upstream-name . "ggplot.multistats")))
25092 (build-system r-build-system)
25094 (list r-ggplot2 r-hexbin r-rlang r-scales))
25095 (home-page "https://github.com/flying-sheep/ggplot.multistats")
25096 (synopsis "Multiple summary statistics for binned stats/geometries")
25098 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
25099 which functions similar to its singular form, but allows the use of multiple
25100 statistics per bin. Those statistics can be mapped to multiple bin
25102 (license license:gpl3)))
25104 (define-public r-knn-covertree
25106 (name "r-knn-covertree")
25111 (uri (cran-uri "knn.covertree" version))
25114 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
25115 (properties `((upstream-name . "knn.covertree")))
25116 (build-system r-build-system)
25118 (list r-matrix r-rcpp r-rcppeigen))
25119 (home-page "https://github.com/flying-sheep/knn.covertree")
25120 (synopsis "Accurate kNN Implementation with multiple distance measures")
25122 "Similarly to the FNN package, this package allows calculation of the k
25123 nearest neighbors (kNN) of a data matrix. The implementation is based on
25124 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
25125 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
25126 (license license:agpl3+)))
25128 (define-public r-poibin
25135 (uri (cran-uri "poibin" version))
25138 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
25139 (properties `((upstream-name . "poibin")))
25140 (build-system r-build-system)
25141 (home-page "https://cran.r-project.org/web/packages/poibin/")
25142 (synopsis "Poisson binomial distribution")
25144 "This package provides an implementation of both the exact and
25145 approximation methods for computing the @dfn{cumulative distribution
25146 function} (CDF) of the Poisson binomial distribution. It also provides the
25147 @dfn{probability mass function} (PMF), quantile function, and random number
25148 generation for the Poisson binomial distribution.")
25149 (license license:gpl2)))
25151 (define-public r-diagram
25158 (uri (cran-uri "diagram" version))
25161 "1r3lyl0h7mk9cfg8smr3jydfkjdawaphnxibkxfjqa7029vkxh79"))))
25162 (properties `((upstream-name . "diagram")))
25163 (build-system r-build-system)
25166 (home-page "https://cran.r-project.org/web/packages/diagram/")
25167 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
25169 "This package provides tools to visualize simple graphs (networks) based
25170 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
25171 electrical networks, etc. It also includes supporting material for the book
25172 \"A practical guide to ecological modelling - using R as a simulation
25173 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
25174 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
25175 Francesca Mazzia (2012).")
25176 (license license:gpl2+)))
25178 (define-public r-lim
25185 (uri (cran-uri "LIM" version))
25188 "0d9bgyd0mnag8wds993dsvlbpkhyakydlzwc3nghxzv2n8504hjj"))))
25189 (properties `((upstream-name . "LIM")))
25190 (build-system r-build-system)
25192 (list r-diagram r-limsolve))
25193 (home-page "https://cran.r-project.org/web/packages/LIM/")
25194 (synopsis "Linear inverse model examples and solution methods")
25196 "This package provides functions that read and solve linear inverse
25197 problems (food web problems, linear programming problems).")
25198 (license license:gpl2+)))
25200 (define-public r-shinycssloaders
25202 (name "r-shinycssloaders")
25207 (uri (cran-uri "shinycssloaders" version))
25210 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
25212 `((upstream-name . "shinycssloaders")))
25213 (build-system r-build-system)
25215 (list r-digest r-glue r-shiny))
25216 (home-page "https://github.com/andrewsali/shinycssloaders")
25217 (synopsis "Add CSS loading animations to Shiny outputs")
25219 "This package provides tools to create a lightweight Shiny wrapper for
25220 the css-loaders created by Luke Hass
25221 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
25222 automatically show a loader when the output is (re)calculating.")
25223 (license license:gpl3)))
25225 (define-public r-rsvg
25232 (uri (cran-uri "rsvg" version))
25235 "096w4d1gvfc65d4jg7ykp23k9f7cf7f8zvzfhvhd7qkfsbjpxqkj"))))
25236 (properties `((upstream-name . "rsvg")))
25237 (build-system r-build-system)
25239 (list librsvg zlib))
25241 (list pkg-config r-knitr))
25242 (home-page "https://github.com/jeroen/rsvg#readme")
25243 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
25245 "This package allows you to render vector-based SVG images into
25246 high-quality custom-size bitmap arrays using the librsvg2 library. The
25247 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
25248 addition, the package can convert images directly to various formats such as
25249 PDF or PostScript.")
25250 (license license:expat)))
25252 (define-public r-influencer
25254 (name "r-influencer")
25255 (version "0.1.0.1")
25259 (uri (cran-uri "influenceR" version))
25262 "0rj7rm236vn3v8302nwl12s0kvpv6xpdbm3q3gxk7vgwfl8nzi33"))))
25263 (properties `((upstream-name . "influenceR")))
25264 (build-system r-build-system)
25266 (list r-igraph r-matrix))
25267 (home-page "https://github.com/rcc-uchicago/influenceR")
25268 (synopsis "Tools to quantify structural importance of nodes in a network")
25270 "This package provides functionality to compute various node centrality
25271 measures on networks. Included are functions to compute betweenness
25272 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
25273 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
25274 algorithm to identify key players, and Valente's bridging metric. The
25275 betweenness, Key Players, and bridging implementations are parallelized with
25277 (license license:gpl2)))
25279 (define-public r-emplik
25286 (uri (cran-uri "emplik" version))
25289 "039kz7703ri91j2i93dr8ixap7i63sr72id9zp74cm7ws9pd1b27"))))
25290 (properties `((upstream-name . "emplik")))
25291 (build-system r-build-system)
25294 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
25295 (synopsis "Empirical likelihood ratio for censored/truncated data")
25297 "This package provides empirical likelihood ratio tests for
25298 means/quantiles/hazards from possibly censored and/or truncated data. It also
25300 (license license:gpl2+)))
25302 (define-public r-imputeyn
25304 (name "r-imputeyn")
25309 (uri (cran-uri "imputeYn" version))
25312 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
25313 (properties `((upstream-name . "imputeYn")))
25314 (build-system r-build-system)
25316 (list r-boot r-emplik r-mvtnorm r-quadprog r-survival))
25317 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
25318 (synopsis "Impute last largest censored observation under weighted least squares")
25320 "This package allows for the imputation of the last largest censored
25321 observantions. This method brings less bias and more efficient estimates for
25323 (license license:gpl2)))
25325 (define-public r-adapenetclass
25327 (name "r-adapenetclass")
25332 (uri (cran-uri "AdapEnetClass" version))
25335 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
25336 (properties `((upstream-name . "AdapEnetClass")))
25337 (build-system r-build-system)
25339 (list r-glmnet r-imputeyn r-lars r-quadprog))
25340 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
25341 (synopsis "Class of adaptive elastic net methods for censored data")
25343 "This package provides methods for variable selection for AFT models.")
25344 (license license:gpl2)))
25346 (define-public r-flock
25353 (uri (cran-uri "flock" version))
25356 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
25357 (properties `((upstream-name . "flock")))
25358 (build-system r-build-system)
25359 (propagated-inputs (list r-rcpp))
25360 (home-page "https://cran.r-project.org/web/packages/flock/")
25361 (synopsis "Process synchronization using file locks")
25363 "This package implements synchronization between R processes (spawned by
25364 using the @code{parallel} package for instance) using file locks. It supports
25365 both exclusive and shared locking.")
25366 (license license:asl2.0)))
25368 (define-public r-archivist
25370 (name "r-archivist")
25375 (uri (cran-uri "archivist" version))
25378 "0q1qysack30xzxdbvvi56rk7r85hsj4ghls9r70ki7bl3rqwr4c9"))))
25379 (properties `((upstream-name . "archivist")))
25380 (build-system r-build-system)
25392 (home-page "https://pbiecek.github.io/archivist/")
25393 (synopsis "Tools for storing, restoring and searching for R objects")
25395 "Data exploration and modelling is a process in which a lot of data
25396 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
25397 statistical models, different versions of data sets and different versions of
25398 results. Archivist helps to store and manage artifacts created in R. It
25399 allows you to store selected artifacts as binary files together with their
25400 metadata and relations. Archivist allows sharing artifacts with others. It
25401 can look for already created artifacts by using its class, name, date of the
25402 creation or other properties. It also makes it easy to restore such
25404 (license license:gpl2)))
25406 (define-public r-versions
25408 (name "r-versions")
25413 (uri (cran-uri "versions" version))
25416 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
25417 (properties `((upstream-name . "versions")))
25418 (build-system r-build-system)
25419 (home-page "https://cran.r-project.org/web/packages/versions/")
25420 (synopsis "Query and install specific versions of CRAN packages")
25422 "This package allows you to install specified versions of R packages
25423 hosted on CRAN and provides functions to list available versions and the
25424 versions of currently installed packages.")
25425 (license license:bsd-3)))
25427 (define-public r-adapr
25434 (uri (cran-uri "adapr" version))
25437 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
25438 (properties `((upstream-name . "adapr")))
25439 (build-system r-build-system)
25456 (home-page "https://cran.r-project.org/web/packages/adapr/")
25457 (synopsis "Implementation of an accountable data analysis process")
25459 "This package tracks reading and writing within R scripts that are
25460 organized into a directed acyclic graph. It contains an interactive Shiny
25461 application @code{adaprApp()}. It uses Git and file hashes to track version
25462 histories of inputs and outputs.")
25463 (license license:lgpl2.0)))
25465 (define-public r-adapsamp
25467 (name "r-adapsamp")
25472 (uri (cran-uri "AdapSamp" version))
25475 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
25476 (properties `((upstream-name . "AdapSamp")))
25477 (build-system r-build-system)
25478 (propagated-inputs (list r-pracma))
25479 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
25480 (synopsis "Adaptive sampling algorithms")
25482 "For distributions whose probability density functions are log-concave,
25483 the adaptive rejection sampling algorithm can be used to build envelope
25484 functions for sampling. For others, the modified adaptive rejection sampling
25485 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
25486 adaptive slice sampling algorithm can be used. This R package mainly includes
25487 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
25488 @code{rASS()}. These functions can realize sampling based on the algorithms
25490 (license license:gpl2)))
25492 (define-public r-adaptalint
25494 (name "r-adaptalint")
25499 (uri (cran-uri "adaptalint" version))
25502 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
25503 (properties `((upstream-name . "adaptalint")))
25504 (build-system r-build-system)
25506 (list r-dplyr r-lintr r-purrr))
25507 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
25508 (synopsis "Check R code style")
25510 "This package provides tools to infer the code style (which style rules
25511 are followed and which ones are not) from one package and use it to check
25512 another. This makes it easier to find and correct the most important problems
25514 (license license:gpl3)))
25516 (define-public r-fracdiff
25518 (name "r-fracdiff")
25523 (uri (cran-uri "fracdiff" version))
25526 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
25527 (properties `((upstream-name . "fracdiff")))
25528 (build-system r-build-system)
25529 (home-page "https://github.com/mmaechler/fracdiff")
25531 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
25533 "This package provides tools for the maximum likelihood estimation of the
25534 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
25535 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
25536 (license license:gpl2+)))
25538 (define-public r-forecast
25540 (name "r-forecast")
25545 (uri (cran-uri "forecast" version))
25548 "01633q2fg4cl8zg61dvsnrk8nk1iknk9jqk7p7xnkypxjckm7zl9"))))
25549 (properties `((upstream-name . "forecast")))
25550 (build-system r-build-system)
25566 (list r-knitr)) ; needed for vignettes
25567 (home-page "https://pkg.robjhyndman.com/forecast/")
25568 (synopsis "Forecasting functions for time series and linear models")
25570 "This package provides methods and tools for displaying and analysing
25571 univariate time series forecasts including exponential smoothing via state
25572 space models and automatic ARIMA modelling.")
25573 (license license:gpl3)))
25575 (define-public r-formattable
25577 (name "r-formattable")
25582 (uri (cran-uri "formattable" version))
25584 (base32 "1vdxi0xmg019qyzjrp8bkjxciz245jcxsrkhfzd44ynqcwi4s3ag"))))
25585 (properties `((upstream-name . "formattable")))
25586 (build-system r-build-system)
25588 (list r-htmltools r-htmlwidgets r-lifecycle r-rmarkdown))
25591 (home-page "https://github.com/renkun-ken/formattable")
25592 (synopsis "Print vectors and data frames with text fromatting")
25594 "This R package provides functions to create formattable vectors and data
25595 frames. @emph{Formattable} vectors are printed with text formatting, and
25596 formattable data frames are printed with multiple types of formatting in HTML
25597 to improve the readability of data presented in tabular form rendered in web
25599 (license license:expat)))
25601 (define-public r-xmisc
25608 (uri (cran-uri "Xmisc" version))
25611 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
25612 (properties `((upstream-name . "Xmisc")))
25613 (build-system r-build-system)
25614 (home-page "https://cran.r-project.org/package=Xmisc")
25616 "Xiaobei's miscellaneous classes and functions")
25618 "This package provides Xiaobei's miscellaneous classes and functions,
25619 which are useful when developing R packages for @dfn{object oriented
25620 programming} (OOP) using R Reference Class.")
25621 (license license:gpl2+)))
25623 (define-public r-proxyc
25630 (uri (cran-uri "proxyC" version))
25633 "1nfl6nrzw2h7argn6mh3cyl1s9ynf6516fx4vgqrjvychnd98mkb"))))
25634 (properties `((upstream-name . "proxyC")))
25635 (build-system r-build-system)
25637 (list r-matrix r-rcpp r-rcpparmadillo r-rcppparallel))
25638 (home-page "https://cran.r-project.org/package=proxyC")
25639 (synopsis "Compute proximity in large sparse matrices")
25641 "This package provides efficient tools to compute the proximity between
25642 rows or columns of large matrices. Functions are optimised for large sparse
25643 matrices using the Armadillo and Intel TBB libraries. Among several built-in
25644 similarity/distance measures, computation of correlation, cosine similarity
25645 and Euclidean distance is particularly fast.")
25646 (license license:gpl3)))
25648 (define-public r-isocodes
25650 (name "r-isocodes")
25651 (version "2022.01.10")
25655 (uri (cran-uri "ISOcodes" version))
25658 "0gy7n5bgxnl4rawry0pg078bkks9lzsbsrwjq8q5cvxl4k3dwpdj"))))
25659 (properties `((upstream-name . "ISOcodes")))
25660 (build-system r-build-system)
25661 (home-page "https://cran.r-project.org/package=ISOcodes")
25662 (synopsis "Selected ISO codes")
25664 "This package provides ISO language, territory, currency, script and
25665 character codes. It provides ISO 639 language codes, ISO 3166 territory
25666 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
25667 character codes as well as the UN M.49 area codes.")
25668 (license license:gpl2)))
25670 (define-public r-stopwords
25672 (name "r-stopwords")
25677 (uri (cran-uri "stopwords" version))
25680 "1ci1cgxrcvlhhplximsfv0plvjdbcd5kv0nphxnpildsn5m1rv65"))))
25681 (properties `((upstream-name . "stopwords")))
25682 (build-system r-build-system)
25685 (home-page "https://github.com/quanteda/stopwords")
25686 (synopsis "Multilingual stopword lists")
25688 "This package provides multiple sources of stopwords, for use in text
25689 analysis and natural language processing.")
25690 (license license:expat)))
25692 (define-public r-spacyr
25699 (uri (cran-uri "spacyr" version))
25702 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
25703 (properties `((upstream-name . "spacyr")))
25704 (build-system r-build-system)
25706 (list r-data-table r-reticulate))
25707 (home-page "https://spacyr.quanteda.io")
25708 (synopsis "R wrapper for the spaCy NLP library")
25710 "This package provides an R wrapper to the Python @dfn{natural language
25711 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
25712 (license license:gpl3)))
25714 (define-public r-snowballc
25716 (name "r-snowballc")
25721 (uri (cran-uri "SnowballC" version))
25724 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
25725 (properties `((upstream-name . "SnowballC")))
25726 (build-system r-build-system)
25727 (home-page "https://r-forge.r-project.org/projects/r-temis/")
25728 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
25730 "This package provides an R interface to the C @code{libstemmer} library
25731 that implements Porter's word stemming algorithm for collapsing words to a
25732 common root to aid comparison of vocabulary. Currently supported languages
25733 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
25734 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
25735 (license license:bsd-3)))
25737 (define-public r-quanteda
25739 (name "r-quanteda")
25744 (uri (cran-uri "quanteda" version))
25747 "1blk9nhydvqyyz0kzhph7nh7ahcjzflmgyr4sv8fx5bpmn4hwjzk"))))
25748 (properties `((upstream-name . "quanteda")))
25749 (build-system r-build-system)
25764 (home-page "https://quanteda.io")
25765 (synopsis "Quantitative analysis of textual data")
25767 "This package provides a fast, flexible, and comprehensive framework for
25768 quantitative text analysis in R. It provides functionality for corpus
25769 management, creating and manipulating tokens and ngrams, exploring keywords in
25770 context, forming and manipulating sparse matrices of documents by features and
25771 feature co-occurrences, analyzing keywords, computing feature similarities and
25772 distances, applying content dictionaries, applying supervised and unsupervised
25773 machine learning, visually representing text and text analyses, and more.")
25774 (license license:gpl3)))
25776 (define-public r-topicmodels
25778 (name "r-topicmodels")
25783 (uri (cran-uri "topicmodels" version))
25786 "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g"))))
25787 (properties `((upstream-name . "topicmodels")))
25788 (build-system r-build-system)
25792 (list r-modeltools r-slam r-tm))
25793 (home-page "https://cran.r-project.org/package=topicmodels")
25794 (synopsis "Topic models")
25796 "This package provides an interface to the C code for @dfn{Latent
25797 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
25798 David M. Blei and co-authors and the C++ code for fitting LDA models using
25799 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
25800 (license license:gpl2)))
25802 (define-public r-stm
25809 (uri (cran-uri "stm" version))
25812 "0qwq4nin2n9fjd06852r8k7arvcgh46kcfb3lm21swgx6j8bgrhb"))))
25813 (properties `((upstream-name . "stm")))
25814 (build-system r-build-system)
25827 (home-page "http://www.structuraltopicmodel.com/")
25828 (synopsis "Estimation of the Structural Topic Model")
25830 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
25831 topic models with document-level covariates. The package also includes tools
25832 for model selection, visualization, and estimation of topic-covariate
25834 (license license:expat)))
25836 (define-public r-polycor
25843 (uri (cran-uri "polycor" version))
25846 "0285rvx8238qp8dix0jq0cqq7ks8h6cjwsscbc7dx4n9nph56pzh"))))
25847 (properties `((upstream-name . "polycor")))
25848 (build-system r-build-system)
25850 (list r-admisc r-matrix r-mvtnorm))
25851 (home-page "https://r-forge.r-project.org/projects/polycor/")
25852 (synopsis "Polychoric and polyserial correlations")
25854 "This package provides tools to compute polychoric and polyserial
25855 correlations by quick \"two-step\" methods or ML, optionally with standard
25856 errors; tetrachoric and biserial correlations are special cases.")
25857 (license license:gpl2+)))
25859 (define-public r-msm
25866 (uri (cran-uri "msm" version))
25869 "08vhazswyxr3y1zb9y60mbg3bappzlizxml8s08p65mh82xxkz5f"))))
25870 (properties `((upstream-name . "msm")))
25871 (build-system r-build-system)
25873 (list r-expm r-mvtnorm r-survival))
25874 (home-page "https://github.com/chjackson/msm")
25875 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
25877 "This package provides functions for fitting continuous-time Markov and
25878 hidden Markov multi-state models to longitudinal data. It was designed for
25879 processes observed at arbitrary times in continuous time (panel data) but some
25880 other observation schemes are supported. Both Markov transition rates and the
25881 hidden Markov output process can be modelled in terms of covariates, which may
25882 be constant or piecewise-constant in time.")
25883 (license license:gpl2+)))
25885 (define-public r-ltm
25892 (uri (cran-uri "ltm" version))
25895 "0vhgbk6j0z3limsrbjkjkpfn2whiaij5j4jf1gg66mjs9dlylap1"))))
25896 (properties `((upstream-name . "ltm")))
25897 (build-system r-build-system)
25899 (list r-mass r-msm r-polycor))
25900 (home-page "https://github.com/drizopoulos/ltm")
25901 (synopsis "Latent trait models under IRT")
25903 "This is a package supporting the analysis of multivariate dichotomous
25904 and polytomous data using latent trait models under the Item Response Theory
25905 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
25906 Three-Parameter, the Graded Response, and the Generalized Partial Credit
25908 (license license:gpl2+)))
25910 (define-public r-mi
25917 (uri (cran-uri "mi" version))
25920 "11f75ivnax6p48mp2pasprws488cm2daym87sw2mcrywvf89fyjd"))))
25921 (properties `((upstream-name . "mi")))
25922 (build-system r-build-system)
25924 (list r-arm r-matrix))
25927 (home-page "http://www.stat.columbia.edu/~gelman/")
25928 (synopsis "Missing data imputation and model checking")
25930 "This package provides functions for data manipulation, imputing missing
25931 values in an approximate Bayesian framework, diagnostics of the models used to
25932 generate the imputations, confidence-building mechanisms to validate some of
25933 the assumptions of the imputation algorithm, and functions to analyze multiply
25934 imputed data sets with the appropriate degree of sampling uncertainty.")
25935 (license license:gpl2+)))
25937 (define-public r-matrixcalc
25939 (name "r-matrixcalc")
25944 (uri (cran-uri "matrixcalc" version))
25947 "09pk0ym6qzribxc6v18cpb6478i4r4kzxpkljjbb3n323zqx5iqb"))))
25948 (properties `((upstream-name . "matrixcalc")))
25949 (build-system r-build-system)
25950 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
25951 (synopsis "Collection of functions for matrix calculations")
25953 "This package provides a collection of functions to support matrix
25954 calculations for probability, econometric and numerical analysis. There are
25955 additional functions that are comparable to APL functions which are useful for
25956 actuarial models such as pension mathematics.")
25957 (license license:gpl2+)))
25959 (define-public r-matrixextra
25961 (name "r-matrixextra")
25966 (uri (cran-uri "MatrixExtra" version))
25968 (base32 "1s8y8zp9k7rsnyi1d8ghi4brjbbdwxijc9chhla24qm3fi6np33a"))))
25969 (properties `((upstream-name . "MatrixExtra")))
25970 (build-system r-build-system)
25972 (list r-float r-matrix r-rcpp r-rhpcblasctl))
25975 (home-page "https://github.com/david-cortes/MatrixExtra")
25976 (synopsis "Extra methods for sparse matrices")
25978 "This package extends sparse matrix and vector classes from the Matrix
25979 package by providing:
25982 @item Methods and operators that work natively on CSR formats (compressed
25983 sparse row, a.k.a. @code{RsparseMatrix}) such as slicing/sub-setting,
25984 assignment, @code{rbind()}, mathematical operators for CSR and COO such as
25985 addition or @code{sqrt()}, and methods such as @code{diag()};
25986 @item Multi-threaded matrix multiplication and cross-product for many
25987 @code{<sparse, dense>} types, including the @code{float32} type from
25989 @item Coercion methods between pairs of classes which are not present in
25990 @code{Matrix}, such as from @code{dgCMatrix} to @code{ngRMatrix}, as well as
25991 convenience conversion functions;
25992 @item Utility functions for sparse matrices such as sorting the indices or
25993 removing zero-valued entries;
25994 @item Fast transposes that work by outputting in the opposite storage format;
25995 @item Faster replacements for many @code{Matrix} methods for all sparse types,
25996 such as slicing and elementwise multiplication.
25997 @item Convenience functions for sparse objects, such as @code{mapSparse} or a
25998 shorter @code{show} method.
26001 (license license:gpl2+)))
26003 (define-public r-sem
26010 (uri (cran-uri "sem" version))
26013 "05hk72zxvyv6kkjhk5y6qw253c64108az7030z8j1sz8wq03n0md"))))
26014 (properties `((upstream-name . "sem")))
26015 (build-system r-build-system)
26017 (list r-boot r-mass r-mi))
26018 (home-page "https://cran.r-project.org/package=sem")
26019 (synopsis "Structural equation models")
26021 "This package provides functions for fitting general linear structural
26022 equation models (with observed and latent variables) using the RAM approach,
26023 and for fitting structural equations in observed-variable models by two-stage
26025 (license license:gpl2+)))
26027 (define-public r-semtools
26029 (name "r-semtools")
26034 (uri (cran-uri "semTools" version))
26037 "1wnakz76c4mgkwvx3iycmvgrzqys860jg9zpkba0ln5c08ycw8pm"))))
26038 (properties `((upstream-name . "semTools")))
26039 (build-system r-build-system)
26041 (list r-lavaan r-pbivnorm))
26042 (home-page "https://github.com/simsem/semTools/wiki")
26043 (synopsis "Useful tools for structural equation modeling")
26045 "This package provides useful tools for structural equation modeling.")
26046 (license license:gpl2+)))
26048 (define-public r-regsem
26055 (uri (cran-uri "regsem" version))
26058 "0vpizmdml55naxmhy9nfcm9ylhy15p9na7l0c6z3rvk29ck3g3sw"))))
26059 (properties `((upstream-name . "regsem")))
26060 (build-system r-build-system)
26062 (list r-lavaan r-rcpp r-rcpparmadillo r-rsolnp))
26065 (home-page "https://cran.r-project.org/package=regsem")
26066 (synopsis "Regularized structural equation modeling")
26068 "This package uses both ridge and lasso penalties (and extensions) to
26069 penalize specific parameters in structural equation models. The package
26070 offers additional cost functions, cross validation, and other extensions
26071 beyond traditional structural equation models. It also contains a function to
26072 perform @dfn{exploratory mediation} (XMed).")
26073 (license license:gpl2+)))
26075 (define-public r-stanheaders
26077 (name "r-stanheaders")
26078 (version "2.21.0-7")
26082 (uri (cran-uri "StanHeaders" version))
26085 "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17"))))
26086 (properties `((upstream-name . "StanHeaders")))
26087 (build-system r-build-system)
26088 (inputs (list pandoc))
26090 (list r-rcppeigen r-rcppparallel))
26092 (list gfortran r-knitr)) ; for vignettes
26093 (home-page "https://mc-stan.org/")
26094 (synopsis "C++ header files for Stan")
26096 "The C++ header files of the Stan project are provided by this package.
26097 There is a shared object containing part of the @code{CVODES} library, but it
26098 is not accessible from R. @code{r-stanheaders} is only useful for developers
26099 who want to utilize the @code{LinkingTo} directive of their package's
26100 DESCRIPTION file to build on the Stan library without incurring unnecessary
26103 The Stan project develops a probabilistic programming language that implements
26104 full or approximate Bayesian statistical inference via Markov Chain Monte
26105 Carlo or variational methods and implements (optionally penalized) maximum
26106 likelihood estimation via optimization. The Stan library includes an advanced
26107 automatic differentiation scheme, templated statistical and linear algebra
26108 functions that can handle the automatically differentiable scalar types (and
26109 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
26110 package provides user-facing R functions to parse, compile, test, estimate,
26111 and analyze Stan models.")
26112 (license license:bsd-3)))
26114 (define-public r-rpf
26121 (uri (cran-uri "rpf" version))
26124 "1yr1i7kswq57mcxv05lh7bvbicz1djqxcl6f13dlgsf3ww56gzg1"))))
26125 (properties `((upstream-name . "rpf")))
26126 (build-system r-build-system)
26128 (list r-lifecycle r-mvtnorm r-rcpp r-rcppeigen))
26131 (home-page "https://github.com/jpritikin/rpf")
26132 (synopsis "Response probability functions")
26134 "The purpose of this package is to factor out logic and math common to
26135 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
26136 core support code suitable for more specialized IRT packages to build upon.
26137 Complete access to optimized C functions is made available with
26138 @code{R_RegisterCCallable()}.")
26139 (license license:gpl3+)))
26141 (define-public r-openmx
26148 (uri (cran-uri "OpenMx" version))
26151 "1v969100hllh0lwlxd2gv0k7krrsp9gc07iinx0nn04wkzh0rib5"))))
26152 (properties `((upstream-name . "OpenMx")))
26153 (build-system r-build-system)
26165 (native-inputs (list r-knitr gfortran))
26166 (home-page "http://openmx.ssri.psu.edu")
26167 (synopsis "Extended structural equation modelling")
26169 "This package allows for the estimation of a wide variety of advanced
26170 multivariate statistical models. It consists of a library of functions and
26171 optimizers that allow you to quickly and flexibly define an SEM model and
26172 estimate parameters given observed data.")
26173 (license license:asl2.0)))
26175 (define-public r-kutils
26182 (uri (cran-uri "kutils" version))
26185 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
26186 (properties `((upstream-name . "kutils")))
26187 (build-system r-build-system)
26189 (list r-foreign r-openxlsx r-plyr r-runit r-xtable))
26190 (home-page "https://cran.r-project.org/package=kutils")
26191 (synopsis "Project management tools")
26193 "This package provides tools for data importation, recoding, and
26194 inspection. There are functions to create new project folders, R code
26195 templates, create uniquely named output directories, and to quickly obtain a
26196 visual summary for each variable in a data frame. The main feature here is
26197 the systematic implementation of the \"variable key\" framework for data
26198 importation and recoding.")
26199 (license license:gpl2)))
26201 (define-public r-rockchalk
26203 (name "r-rockchalk")
26204 (version "1.8.157")
26208 (uri (cran-uri "rockchalk" version))
26211 "13g2rdnxazqfgy653d7vj6w79b2vgnd7bbz0sqn9k4qiig59jh41"))))
26212 (properties `((upstream-name . "rockchalk")))
26213 (build-system r-build-system)
26215 (list r-cardata r-kutils r-lme4 r-mass))
26216 (home-page "https://cran.r-project.org/package=rockchalk")
26217 (synopsis "Regression estimation and presentation")
26219 "This package provides a collection of functions for interpretation and
26220 presentation of regression analysis. These functions are used to produce the
26221 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
26222 includes regression diagnostics, regression tables, and plots of interactions
26223 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
26224 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
26225 fairly comprehensive overview.")
26226 (license license:gpl3+)))
26228 (define-public r-lisreltor
26230 (name "r-lisreltor")
26235 (uri (cran-uri "lisrelToR" version))
26238 "0i51v0x87277ly0kggdd594w6q4zq62b4n7xs9r25j08bzs82nfk"))))
26239 (properties `((upstream-name . "lisrelToR")))
26240 (build-system r-build-system)
26241 (home-page "https://cran.r-project.org/package=lisrelToR")
26242 (synopsis "Import output from LISREL into R")
26244 "This is an unofficial package aimed at automating the import of LISREL
26246 (license license:gpl2)))
26248 (define-public r-bdgraph
26255 (uri (cran-uri "BDgraph" version))
26258 "1mixzkk8shcbyrxydhchq483j2jh2icgmdshmrl79a8vsnz9mmrm"))))
26259 (properties `((upstream-name . "BDgraph")))
26260 (build-system r-build-system)
26265 (home-page "https://www.uva.nl/profile/a.mohammadi")
26266 (synopsis "Bayesian structure learning in graphical models")
26268 "This package provides statistical tools for Bayesian structure learning
26269 in undirected graphical models for continuous, discrete, and mixed data. It
26270 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
26271 on a continuous-time birth-death process.")
26272 (license license:gpl2+)))
26274 (define-public r-bundesligr
26276 (name "r-bundesligr")
26280 (uri (cran-uri "bundesligR" version))
26283 "0dnhbh9jh7dfbk7mfh8msq4ys5kakalr0kwkycycrb2q8rd049vp"))))
26284 (properties `((upstream-name . "bundesligR")))
26285 (build-system r-build-system)
26286 (home-page "https://github.com/ottlngr/bundesligR")
26287 (synopsis "All final tables of the Bundesliga")
26289 "This package provides all final tables of Germany's highest football
26290 league, the Bundesliga. It contains data from 1964 to 2016.")
26291 (license license:gpl3)))
26293 (define-public r-d3network
26295 (name "r-d3network")
26296 (version "0.5.2.1")
26300 (uri (cran-uri "d3Network" version))
26303 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
26304 (properties `((upstream-name . "d3Network")))
26305 (build-system r-build-system)
26307 (list r-plyr r-rjson r-whisker))
26308 (home-page "http://christophergandrud.github.io/d3Network/")
26309 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
26311 "This package is intended to make it easy to create D3 JavaScript
26312 network, tree, dendrogram, and Sankey graphs from R using data frames.")
26313 (license license:gpl3+)))
26315 (define-public r-qgraph
26322 (uri (cran-uri "qgraph" version))
26325 "0r225b7rnsv6wz41ij0msmqr1xy0iqxh9dbsvjixbi1hvgv91wds"))))
26326 (properties `((upstream-name . "qgraph")))
26327 (build-system r-build-system)
26347 (home-page "http://sachaepskamp.com/qgraph/")
26348 (synopsis "Weighted network visualization and analysis")
26350 "This package implements tools for weighted network visualization and
26351 analysis, as well as Gaussian graphical model computation. It contains graph
26352 plotting methods, and tools for psychometric data visualization and graphical
26353 model estimation. See Epskamp et al. (2012)
26354 @url{doi:10.18637/jss.v048.i04}.")
26355 (license license:gpl2)))
26357 (define-public r-semplot
26364 (uri (cran-uri "semPlot" version))
26367 "0s9bp4pfsllg1k4x8a36yw82fw432dyz0xvmvi8dw9l12q3jkx8i"))))
26368 (properties `((upstream-name . "semPlot")))
26369 (build-system r-build-system)
26382 (home-page "https://github.com/SachaEpskamp/semPlot")
26383 (synopsis "Unified visualizations of structural equation models")
26385 "Structural equation modeling (SEM) has a long history of representing
26386 models graphically as path diagrams. The semPlot package for R fills the gap
26387 between advanced, but time-consuming, graphical software and the limited
26388 graphics produced automatically by SEM software. In addition, semPlot offers
26389 more functionality than drawing path diagrams: it can act as a common ground
26390 for importing SEM results into R. Any result usable as input to semPlot can
26391 also be represented in any of the three popular SEM frame-works, as well as
26392 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
26393 (license license:gpl2)))
26395 (define-public r-cdm
26402 (uri (cran-uri "CDM" version))
26405 "1lcq3i5rlyqkc12c26kj0x4fm2gh1jsisp6kbf59y3hjdkiqajhl"))))
26406 (properties `((upstream-name . "CDM")))
26407 (build-system r-build-system)
26409 (list r-mvtnorm r-polycor r-rcpp r-rcpparmadillo))
26411 "https://github.com/alexanderrobitzsch/CDM")
26412 (synopsis "Cognitive diagnosis modeling")
26414 "This package provides functions for cognitive diagnosis modeling and
26415 multidimensional item response modeling for dichotomous and polytomous item
26416 responses. It enables the estimation of the DINA and DINO model, the multiple
26417 group (polytomous) GDINA model, the multiple choice DINA model, the general
26418 diagnostic model (GDM), the structured latent class model (SLCA), and
26419 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
26420 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
26421 estimation and the package structure. For tutorials on how to use the CDM
26422 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
26423 well as Ravand and Robitzsch (2015).")
26424 (license license:gpl2+)))
26426 (define-public r-tam
26433 (uri (cran-uri "TAM" version))
26436 "0b81d0g4j94yrfzj019jffxrk1aw24iscddp60kjbkrl5p7qy38g"))))
26437 (properties `((upstream-name . "TAM")))
26438 (build-system r-build-system)
26440 (list r-cdm r-rcpp r-rcpparmadillo))
26441 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
26442 (synopsis "Test analysis modules")
26444 "This package includes tools for marginal maximum likelihood estimation
26445 and joint maximum likelihood estimation for unidimensional and
26446 multidimensional item response models. The package functionality covers the
26447 Rasch model, 2PL model, 3PL model, generalized partial credit model,
26448 multi-faceted Rasch model, nominal item response model, structured latent
26449 class model, mixture distribution IRT models, and located latent class models.
26450 Latent regression models and plausible value imputation are also supported.")
26451 (license license:gpl2+)))
26453 (define-public r-erm
26460 (uri (cran-uri "eRm" version))
26463 "0smym010kswc5vx90qr3x1vl16xj1x1i54rvrj006dc4agc1vmlk"))))
26464 (properties `((upstream-name . "eRm")))
26465 (build-system r-build-system)
26467 (list r-colorspace r-lattice r-mass r-matrix r-psych))
26468 (native-inputs (list gfortran))
26469 (home-page "https://cran.r-project.org/package=eRm")
26470 (synopsis "Extended Rasch modeling")
26472 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
26473 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
26474 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
26475 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
26476 data matrix. Additional features are the ML estimation of the person
26477 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
26478 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
26479 infit and outfit measures, ICC and other plots, automated stepwise item
26480 elimination, and a simulation module for various binary data matrices.")
26481 (license license:gpl3)))
26483 (define-public r-irtoys
26490 (uri (cran-uri "irtoys" version))
26493 "1qshz6czykgf53mq6xiswzv5xsjwrkrinpfkf1yavql4v08hs82b"))))
26494 (properties `((upstream-name . "irtoys")))
26495 (build-system r-build-system)
26500 (home-page "https://cran.r-project.org/package=irtoys")
26501 (synopsis "Collection of functions related to Item Response Theory (IRT)")
26503 "This package provides a collection of functions useful in learning and
26504 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
26505 programs. It provides basic CTT analysis, a simple common interface to the
26506 estimation of item parameters in IRT models for binary responses with three
26507 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
26508 EAP, WLE, plausible values), item and person fit statistics, scaling
26509 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
26510 array of parametric and non-parametric (kernel) plots. It estimates and plots
26511 Haberman's interaction model when all items are dichotomously scored.")
26512 (license license:gpl2+)))
26514 (define-public r-iheatmapr
26516 (name "r-iheatmapr")
26521 (uri (cran-uri "iheatmapr" version))
26524 "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx"))))
26525 (properties `((upstream-name . "iheatmapr")))
26526 (build-system r-build-system)
26528 (list r-fastcluster
26538 (home-page "https://docs.ropensci.org/iheatmapr")
26539 (synopsis "Interactive, Complex Heatmaps")
26541 "iheatmapr is an R package for building complex, interactive heatmaps
26542 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
26543 subplots along the rows or columns of the main heatmap add more information
26544 about each row or column. For example, a one column additional heatmap may
26545 indicate what group a particular row or column belongs to. Complex heatmaps
26546 may also include multiple side by side heatmaps which show different types of
26547 data for the same conditions. Interactivity can improve complex heatmaps by
26548 providing tooltips with information about each cell and enabling zooming into
26549 interesting features. iheatmapr uses the plotly library for interactivity.")
26550 (license license:expat)))
26552 (define-public r-packrat
26559 (uri (cran-uri "packrat" version))
26562 "1ni3xn51xifdb2bya5z54jn4nxgss6f23b3hn126j2kaz80h7ns5"))))
26563 (properties `((upstream-name . "packrat")))
26564 (build-system r-build-system)
26565 (home-page "https://github.com/rstudio/packrat/")
26566 (synopsis "Dependency management R projects")
26568 "This package provides a dependency manager for R projects that allows
26569 you to manage the R packages your project depends on in an isolated, portable,
26570 and reproducible way.")
26571 (license license:gpl2)))
26573 (define-public r-rsconnect
26575 (name "r-rsconnect")
26580 (uri (cran-uri "rsconnect" version))
26583 "170niwxcmyvad7qw8k115i5a48x3wiidcd82x9anikf7bxhdai0a"))))
26584 (properties `((upstream-name . "rsconnect")))
26585 (build-system r-build-system)
26594 (home-page "https://github.com/rstudio/rsconnect")
26595 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
26597 "This package provides a programmatic deployment interface for RPubs,
26598 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
26599 documents, Shiny applications, Plumber APIs, plots, and static web content.")
26600 (license license:gpl2)))
26602 ;; This package includes minified JavaScript files. When upgrading please
26603 ;; check that there are no new minified JavaScript files.
26604 (define-public r-dygraphs
26606 (name "r-dygraphs")
26607 (version "1.1.1.6")
26611 (uri (cran-uri "dygraphs" version))
26614 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
26615 (properties `((upstream-name . "dygraphs")))
26616 (build-system r-build-system)
26618 `(#:modules ((guix build utils)
26619 (guix build r-build-system)
26623 (modify-phases %standard-phases
26624 (add-after 'unpack 'process-javascript
26625 (lambda* (#:key inputs #:allow-other-keys)
26626 (with-directory-excursion "inst/htmlwidgets/lib/"
26630 `(("dygraphs/dygraph-combined-dev.js"
26631 "dygraph-combined.js")
26632 (,(assoc-ref inputs "js-jquery")
26633 "jquery/jquery.min.js")
26634 (,(assoc-ref inputs "js-fquarter")
26635 "fquarter/moment-fquarter.min.js"))))
26636 (lambda (sources targets)
26637 (for-each (lambda (source target)
26638 (format #t "Processing ~a --> ~a~%"
26640 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
26641 (call-with-output-file target
26643 (dump-port minified port)))))
26644 sources targets))))
26647 `(("uglifyjs" ,node-uglify-js)
26648 ;; They actually use version 1.11.1, but this more recent version
26649 ;; should be just fine.
26653 (uri "https://code.jquery.com/jquery-1.12.4.js")
26656 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
26660 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
26661 "moment-fquarter/1.0.1/moment-fquarter.js"))
26664 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
26666 (list r-htmltools r-htmlwidgets r-magrittr r-xts r-zoo))
26667 (home-page "https://github.com/rstudio/dygraphs")
26668 (synopsis "Interface to Dygraphs interactive time series charting library")
26670 "This package provides an R interface to the dygraphs JavaScript charting
26671 library (a copy of which is included in the package). It provides rich
26672 facilities for charting time-series data in R, including highly configurable
26673 series- and axis-display and interactive features like zoom/pan and
26674 series/point highlighting.")
26675 (license license:expat)))
26677 (define-public r-shinystan
26679 (name "r-shinystan")
26684 (uri (cran-uri "shinystan" version))
26687 "0afm703zriyqprz1zvypir80lq2ylfff3qvj5i7p9n365mm8b150"))))
26688 (properties `((upstream-name . "shinystan")))
26689 (build-system r-build-system)
26707 (home-page "https://mc-stan.org/")
26708 (synopsis "Interactive visual and numerical analysis for Bayesian models")
26710 "This package provides a graphical user interface for interactive
26711 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
26712 for analyzing a posterior sample. The interface is powered by the Shiny web
26713 application framework and works with the output of MCMC programs written in
26714 any programming language (and has extended functionality for Stan models fit
26715 using the @code{rstan} and @code{rstanarm} packages).")
26716 (license license:gpl3+)))
26718 (define-public r-rstantools
26720 (name "r-rstantools")
26725 (uri (cran-uri "rstantools" version))
26728 "1dsfgi02hps878n3vimfdbzpm4gr5n3ccrmnc61ncrqcp6p0p0fb"))))
26729 (properties `((upstream-name . "rstantools")))
26730 (build-system r-build-system)
26731 (inputs (list pandoc))
26733 (list r-desc r-rcpp r-rcppparallel))
26736 (home-page "https://mc-stan.org/rstantools/")
26737 (synopsis "Tools for developing R packages interfacing with Stan")
26739 "This package provides various tools for developers of R packages
26740 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
26741 up the required package structure, S3 generics and default methods to unify
26742 function naming across Stan-based R packages, and vignettes with
26743 recommendations for developers.")
26744 (license license:gpl3+)))
26746 (define-public r-loo
26753 (uri (cran-uri "loo" version))
26755 (base32 "1wa5hxk7lkr88mway6b7xd5arrkkl2ldl9rf0v1nqwp8lia2ysl6"))))
26756 (properties `((upstream-name . "loo")))
26757 (build-system r-build-system)
26761 (list r-checkmate r-matrixstats))
26764 (home-page "https://mc-stan.org/loo/")
26765 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
26767 "This package provides an implementation of efficient approximate
26768 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
26769 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
26770 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
26771 procedure for regularizing importance weights. As a byproduct of the
26772 calculations, we also obtain approximate standard errors for estimated
26773 predictive errors and for the comparison of predictive errors between models.
26774 The package also provides methods for using stacking and other model weighting
26775 techniques to average Bayesian predictive distributions.")
26776 (license license:gpl3+)))
26778 (define-public r-rstan
26785 (uri (cran-uri "rstan" version))
26788 "0ibd3pj2pvd7658sdg95fa2yhfmxz9gy0cjwcrdr546k209j55a4"))))
26789 (properties `((upstream-name . "rstan")))
26790 (build-system r-build-system)
26793 (modify-phases %standard-phases
26794 (add-before 'install 'set-timezone
26795 ;; This package is picky about timezones.
26796 (lambda* (#:key inputs #:allow-other-keys)
26797 (setenv "TZ" "UTC+1")
26799 (search-input-directory inputs
26800 "share/zoneinfo")))))))
26802 (list tzdata-for-tests pandoc r-knitr))
26814 (home-page "https://discourse.mc-stan.org/")
26815 (synopsis "R interface to Stan")
26817 "User-facing R functions are provided to parse, compile, test, estimate,
26818 and analyze Stan models by accessing the header-only Stan library provided by
26819 the StanHeaders package. The Stan project develops a probabilistic
26820 programming language that implements full Bayesian statistical inference via
26821 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
26822 approximation, and (optionally penalized) maximum likelihood estimation via
26823 optimization. In all three cases, automatic differentiation is used to
26824 quickly and accurately evaluate gradients without burdening the user with the
26825 need to derive the partial derivatives.")
26826 (license license:gpl3+)))
26828 (define-public r-rstanarm
26830 (name "r-rstanarm")
26835 (uri (cran-uri "rstanarm" version))
26838 "19rj396q84maxnd9d2xcd5rblg3310xn7sqbd6k18kwf3dvd7wp9"))))
26839 (properties `((upstream-name . "rstanarm")))
26840 (build-system r-build-system)
26861 (home-page "https://mc-stan.org/rstanarm/")
26862 (synopsis "Bayesian applied regression modeling via Stan")
26864 "This package estimates previously compiled regression models using the
26865 @code{rstan} package, which provides the R interface to the Stan C++ library
26866 for Bayesian estimation. Users specify models via the customary R syntax with
26867 a formula and @code{data.frame} plus some additional arguments for priors.")
26868 (license license:gpl3+)))
26870 (define-public r-kendall
26877 (uri (cran-uri "Kendall" version))
26880 "1xmk95l4i3kj9jn0xh1chi2rj322k29jq14ra5pa7316gwf9vx2m"))))
26881 (properties `((upstream-name . "Kendall")))
26882 (build-system r-build-system)
26887 (home-page "https://cran.r-project.org/web/packages/Kendall/")
26888 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
26890 "This package computes the Kendall rank correlation and Mann-Kendall
26892 (license license:gpl2+)))
26894 (define-public r-keyring
26901 (uri (cran-uri "keyring" version))
26904 "1j8l6nmh4dr70kwybiais8yh687fdwrj134xynq68igw1b1rm8ga"))))
26905 (properties `((upstream-name . "keyring")))
26906 (build-system r-build-system)
26916 (native-inputs (list pkg-config))
26917 (home-page "https://github.com/r-lib/keyring")
26918 (synopsis "Access the system credential store from R")
26920 "This package provides a platform-independent API to access the operating
26921 system's credential store. It currently supports Keychain on macOS,
26922 Credential Store on Windows, the Secret Service API on GNU/Linux, and a
26923 simple, platform independent store implemented with environment variables.
26924 Additional storage back-ends can be added easily.")
26925 (license license:expat)))
26927 (define-public r-zyp
26930 (version "0.10-1.1")
26934 (uri (cran-uri "zyp" version))
26937 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
26938 (properties `((upstream-name . "zyp")))
26939 (build-system r-build-system)
26942 (home-page "https://cran.r-project.org/web/packages/zyp/")
26943 (synopsis "Zhang + Yue-Pilon Trends Package")
26945 "This package contains an efficient implementation of Sen's slope
26946 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
26947 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
26949 (license license:lgpl2.1)))
26951 (define-public r-rlecuyer
26953 (name "r-rlecuyer")
26957 (uri (cran-uri "rlecuyer" version))
26960 "09mniai7v8gapr6hd3zm8sm3vi1zcyhgym389904ykb2yx7l68s7"))))
26961 (properties `((upstream-name . "rlecuyer")))
26962 (build-system r-build-system)
26964 "https://www.iro.umontreal.ca/~lecuyer/myftp/papers/streams00.pdf")
26965 (synopsis "R interface to RNG with multiple streams")
26967 "This package provides an interface to the C implementation of the random
26968 number generator with multiple independent streams developed by L'Ecuyer et
26969 al (2002). The main purpose of this package is to enable the use of this
26970 random number generator in parallel R applications.")
26971 (license license:gpl2+)))
26973 (define-public r-rlinsolve
26975 (name "r-rlinsolve")
26980 (uri (cran-uri "Rlinsolve" version))
26983 "1xv500n1480qyakw0isanw1s5ywykhc207hqja4804s5s2m8zfjw"))))
26984 (properties `((upstream-name . "Rlinsolve")))
26985 (build-system r-build-system)
26987 (list r-matrix r-rcpp r-rcpparmadillo r-rdpack))
26988 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
26989 (synopsis "Iterative solvers for (sparse) linear system of equations")
26991 "Solving a system of linear equations is one of the most fundamental
26992 computational problems for many fields of mathematical studies, such as
26993 regression problems from statistics or numerical partial differential
26994 equations. This package provides basic stationary iterative solvers such as
26995 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
26996 Nonstationary, also known as Krylov subspace methods are also provided.
26997 Sparse matrix computation is also supported in that solving large and sparse
26998 linear systems can be manageable using the @code{Matrix} package along with
26999 @code{RcppArmadillo}.")
27000 (license license:gpl3+)))
27002 (define-public r-zvcv
27009 (uri (cran-uri "ZVCV" version))
27012 "0gc76j9i8fkm2v638nyzzb1qxl4zmapbspkkaffb8gi5qyjja448"))))
27013 (properties `((upstream-name . "ZVCV")))
27014 (build-system r-build-system)
27025 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
27026 (synopsis "Zero-Variance Control Variates")
27028 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
27029 to reduce the variance of Monte Carlo estimators of expectations using the
27030 derivatives of the log target. Once the derivatives are available, the only
27031 additional computational effort is in solving a linear regression problem.
27032 This method has been extended to higher dimensions using regularisation. This
27033 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
27034 samples, derivatives and function evaluations are available. Additional
27035 functions for applying ZV-CV to two estimators for the normalising constant of
27036 the posterior distribution in Bayesian statistics are also supplied.")
27037 (license license:gpl2+)))
27039 (define-public r-ztype
27046 (uri (cran-uri "ztype" version))
27049 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
27050 (properties `((upstream-name . "ztype")))
27051 (build-system r-build-system)
27060 (home-page "https://cran.r-project.org/web/packages/ztype/")
27061 (synopsis "Run a Ztype game loaded with R functions")
27063 "How fast can you type R functions on your keyboard? Find out by running
27064 a @code{zty.pe} game: export R functions as instructions to type to destroy
27065 opponents' vessels.")
27066 (license license:gpl3)))
27068 (define-public r-zseq
27075 (uri (cran-uri "Zseq" version))
27078 "0xp7qi5kjg8xmci9wrfvmygjmz8gbhq60fl9bvk8rnka6s4ppkrc"))))
27079 (properties `((upstream-name . "Zseq")))
27080 (build-system r-build-system)
27083 (home-page "https://cran.r-project.org/web/packages/Zseq/")
27084 (synopsis "Integer sequence generator")
27086 "This package generates well-known integer sequences. The @code{gmp}
27087 package is adopted for computing with arbitrarily large numbers. Every
27088 function has a hyperlink to its corresponding item in the @dfn{On-Line
27089 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
27090 (license license:gpl3+)))
27092 (define-public r-isoband
27099 (uri (cran-uri "isoband" version))
27102 "19bbi0n0kz33xdgmdprcmc6raphd1hcm1w1brc16z5phcsh3zxa6"))))
27103 (properties `((upstream-name . "isoband")))
27104 (build-system r-build-system)
27107 (home-page "https://github.com/wilkelab/isoband")
27108 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
27110 "This package provides a fast C++ implementation to generate contour
27111 lines (isolines) and contour polygons (isobands) from regularly spaced grids
27112 containing elevation data.")
27113 (license license:expat)))
27115 (define-public r-ppcor
27122 (uri (cran-uri "ppcor" version))
27125 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
27126 (properties `((upstream-name . "ppcor")))
27127 (build-system r-build-system)
27130 (home-page "https://cran.r-project.org/web/packages/ppcor/")
27131 (synopsis "Partial and semi-partial correlation")
27133 "This package provides users not only with a function to readily
27134 calculate the higher-order partial and semi-partial correlations but also with
27135 statistics and p-values of the correlation coefficients.")
27136 (license license:gpl2)))
27138 (define-public r-hrbrthemes
27140 (name "r-hrbrthemes")
27145 (uri (cran-uri "hrbrthemes" version))
27147 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
27148 (properties `((upstream-name . "hrbrthemes")))
27149 (build-system r-build-system)
27161 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
27162 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
27164 "This package provides a compilation of extra @code{ggplot2} themes,
27165 scales and utilities, including a spell check function for plot label fields
27166 and an overall emphasis on typography.")
27167 (license license:expat)))
27169 (define-public r-crochet
27176 (uri (cran-uri "crochet" version))
27179 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
27180 (build-system r-build-system)
27183 (home-page "https://github.com/agrueneberg/crochet")
27184 (synopsis "Implementation Helper for Matrix-Like Types")
27186 "Functions to help implement the extraction / subsetting / indexing
27187 function @code{[} and replacement function @code{[<-} of custom matrix-like
27188 types (based on S3, S4, etc.), modeled as closely to the base matrix class
27189 as possible (with tests to prove it).")
27190 (license license:expat)))
27192 (define-public r-boa
27195 (version "1.1.8-2")
27199 (uri (cran-uri "boa" version))
27202 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
27203 (properties `((upstream-name . "boa")))
27204 (build-system r-build-system)
27205 (home-page "https://www.jstatsoft.org/v21/i11")
27206 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
27208 "This package provides a menu-driven program and library of functions for
27209 carrying out convergence diagnostics and statistical and graphical analysis of
27210 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
27211 (license license:gpl2+)))
27213 (define-public r-httpcode
27215 (name "r-httpcode")
27219 (uri (cran-uri "httpcode" version))
27222 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
27223 (build-system r-build-system)
27224 (home-page "https://github.com/sckott/httpcode")
27225 (synopsis "HTTP status code helper")
27226 (description "@code{httpcode} provides functionality for finding and
27227 explaining the meaning of @code{HTTP} status codes. Functions are included for
27228 searching for codes by full or partial number, by message, and to get
27229 appropriate dog and cat images for many status codes.")
27230 (license license:expat)))
27232 (define-public r-latex2exp
27234 (name "r-latex2exp")
27238 (uri (cran-uri "latex2exp" version))
27241 "153br3xflvnnxqhkhm1wgwb2664bw08alhslgdcgjdk73clafhla"))))
27242 (build-system r-build-system)
27244 (list r-stringr r-magrittr))
27247 (home-page "https://github.com/stefano-meschiari/latex2exp/")
27248 (synopsis "Use LaTeX expressions in plots")
27249 (description "@code{latex2exp} parses and converts LaTeX math formulas to
27250 R's plotmath expressions, used to enter mathematical formulas and symbols to be
27251 rendered as text, axis labels, etc. throughout R's plotting system.")
27252 (license license:expat)))
27254 (define-public r-oai
27260 (uri (cran-uri "oai" version))
27263 "1zcbcxhw692s0y6izvwazyzhgx0iwsxsbcan2nk0mb7n11p7bypb"))))
27264 (build-system r-build-system)
27266 (list r-xml2 r-httr r-plyr r-stringr r-tibble))
27269 (home-page "https://github.com/ropensci/oai/")
27270 (synopsis "General purpose OAI-PMH services client")
27271 (description "@code{oai} provides a general purpose client to work with
27272 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
27273 service. Functions are provided to work with the OAI-PMH verbs:
27274 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
27275 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
27276 (license license:expat)))
27278 (define-public r-argon2
27285 (uri (cran-uri "argon2" version))
27288 "09hzl0wz0lw2v7g64rdv0lij2hq36zl37a6rmxwvinmjdzijcsyw"))))
27289 (properties `((upstream-name . "argon2")))
27290 (build-system r-build-system)
27291 (home-page "https://github.com/wrathematics/argon2")
27292 (synopsis "Secure password hashing based on the argon2 algorithm")
27294 "This package provides utilities for secure password hashing via the
27295 argon2 algorithm.")
27296 (license license:bsd-2)))
27298 (define-public r-getpass
27305 (uri (cran-uri "getPass" version))
27308 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
27309 (properties `((upstream-name . "getPass")))
27310 (build-system r-build-system)
27312 (list r-rstudioapi))
27313 (home-page "https://github.com/wrathematics/getPass")
27314 (synopsis "Masked user input")
27316 "This package provides a micro-package for reading \"passwords\", i.e.
27317 reading user input with masking, so that the input is not displayed as it is
27318 typed. Currently, RStudio, the command line (every OS), and any platform
27319 where tcltk is present are supported.")
27320 (license license:bsd-2)))
27322 (define-public r-remoter
27329 (uri (cran-uri "remoter" version))
27332 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
27333 (properties `((upstream-name . "remoter")))
27334 (build-system r-build-system)
27336 (list r-argon2 r-getpass r-pbdzmq r-png))
27337 (home-page "https://github.com/RBigData/remoter")
27338 (synopsis "Control a remote R session from a local one")
27340 "This package provides a set of utilities for client/server computing
27341 with R, controlling a remote R session (the server) from a local one (the
27343 (license license:bsd-2)))
27345 (define-public r-asd
27352 (uri (cran-uri "asd" version))
27355 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
27356 (properties `((upstream-name . "asd")))
27357 (build-system r-build-system)
27360 (home-page "https://cran.r-project.org/web/packages/asd")
27361 (synopsis "Simulations for Adaptive Seamless Designs")
27363 "This package provdes means to run simulations for adaptive seamless
27364 designs with and without early outcomes for treatment selection and
27365 subpopulation type designs.")
27366 (license license:gpl3)))
27368 (define-public r-nbconvertr
27370 (name "r-nbconvertr")
27375 (uri (cran-uri "nbconvertR" version))
27378 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
27379 (properties `((upstream-name . "nbconvertR")))
27380 (build-system r-build-system)
27382 (list python-nbconvert pandoc))
27383 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
27384 (synopsis "Vignette engine wrapping Jupyter notebooks")
27386 "This package calls the Jupyter script @code{nbconvert} to create
27387 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
27388 containing rich text, code, and its output. Code cells can be edited and
27389 evaluated interactively.")
27390 (license license:gpl3)))
27392 (define-public r-bridgesampling
27394 (name "r-bridgesampling")
27399 (uri (cran-uri "bridgesampling" version))
27402 "0sry1xwiv4y52k44hq6z8y2kysp5kxgl4dix3m94svg3ladd7v2l"))))
27404 `((upstream-name . "bridgesampling")))
27405 (build-system r-build-system)
27407 (list r-brobdingnag
27415 (home-page "https://github.com/quentingronau/bridgesampling")
27416 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
27418 "This package provides functions for estimating marginal likelihoods,
27419 Bayes factors, posterior model probabilities, and normalizing constants in
27420 general, via different versions of bridge sampling.")
27421 (license license:gpl2+)))
27423 (define-public r-tea
27430 (uri (cran-uri "tea" version))
27433 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
27435 `((upstream-name . "tea")))
27436 (build-system r-build-system)
27439 (home-page "https://cran.r-project.org/web/packages/tea/")
27440 (synopsis "Threshold estimation approaches")
27442 "This package provides different approaches for selecting the threshold
27443 in generalized Pareto distributions. Most of them are based on minimizing the
27444 AMSE-criterion or at least by reducing the bias of the assumed GPD-model.
27445 Others are heuristically motivated by searching for stable sample paths, i.e.
27446 a nearly constant region of the tail index estimator with respect to k, which
27447 is the number of data in the tail. The third class is motivated by graphical
27448 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
27449 is also implemented here.")
27450 (license license:gpl3)))
27452 (define-public r-awsmethods
27454 (name "r-awsmethods")
27459 (uri (cran-uri "awsMethods" version))
27462 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
27464 `((upstream-name . "awsMethods")))
27465 (build-system r-build-system)
27466 (home-page "http://www.wias-berlin.de/software/imaging/")
27467 (synopsis "Class and methods definitions")
27469 "This package defines the generic method @code{extract} and provides
27470 @code{openMP} support as needed in several packages like
27471 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
27472 (license license:gpl2+)))
27474 (define-public r-aws
27481 (uri (cran-uri "aws" version))
27484 "1fhm87iax6bkvd4vszvjbcqw3b2drs11rjxr7zf2w4sgc72svaz8"))))
27486 `((upstream-name . "aws")))
27487 (build-system r-build-system)
27489 (list r-awsmethods r-gsl))
27492 (home-page "https://cran.r-project.org/web/packages/aws/")
27493 (synopsis "Adaptive weights smoothing")
27495 "This package provides a collection of R-functions implementing adaptive
27496 smoothing procedures in 1D, 2D and 3D. This includes the
27497 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
27498 Confidence Intervals} (ICI), variational approaches, and a non-local means
27500 (license license:gpl2+)))
27502 (define-public r-sgloptim
27504 (name "r-sgloptim")
27509 (uri (cran-uri "sglOptim" version))
27512 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
27514 `((upstream-name . "sglOptim")))
27515 (build-system r-build-system)
27526 (home-page "https://github.com/nielsrhansen/sglOptim")
27527 (synopsis "Generic sparse group Lasso solver")
27529 "This package provides a fast generic solver for sparse group lasso
27530 optimization problems. The loss (objective) function must be defined in a C++
27531 module. The optimization problem is solved using a coordinate gradient
27532 descent algorithm. Convergence of the algorithm is established and the
27533 algorithm is applicable to a broad class of loss functions. Use of parallel
27534 computing for cross validation and subsampling is supported through the
27535 @code{foreach} and @code{doParallel} packages.")
27536 (license license:gpl2+)))
27538 (define-public r-grouped
27545 (uri (cran-uri "grouped" version))
27548 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
27550 `((upstream-name . "grouped")))
27551 (build-system r-build-system)
27554 (home-page "https://cran.r-project.org/web/packages/grouped/")
27555 (synopsis "Regression analysis of grouped and coarse data")
27557 "This package provides regression models for grouped and coarse data,
27558 under the coarsened at random assumption.")
27559 (license license:gpl2+)))
27561 (define-public r-stam
27568 (uri (cran-uri "stam" version))
27571 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
27573 `((upstream-name . "stam")))
27574 (build-system r-build-system)
27577 (home-page "https://cran.r-project.org/web/packages/stam")
27578 (synopsis "Spatio-temporal analysis and modelling")
27580 "This package provides various methods to conduct Spatio-Temporal
27581 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
27582 Inferred Spatio-Temporal Modelling.")
27583 (license license:gpl2+)))
27585 (define-public r-dcv
27592 (uri (cran-uri "dcv" version))
27595 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
27597 `((upstream-name . "dcv")))
27598 (build-system r-build-system)
27601 (home-page "https://cran.r-project.org/web/packages/dcv/")
27602 (synopsis "Conventional cross-validation statistics for climate-growth model")
27604 "This package performs several conventional cross-validation statistical
27605 methods for climate-growth model in the climate reconstruction from tree
27606 rings, including Sign Test statistic, Reduction of Error statistic, Product
27607 Mean Test, Durbin-Watson statistic etc.")
27608 (license license:gpl2)))
27610 (define-public r-rcdd
27617 (uri (cran-uri "rcdd" version))
27620 "0zxx0qvv26ba30jkm8mvca4h59rqklay4jwazpcw7h9dzp4189jr"))))
27622 `((upstream-name . "rcdd")))
27623 (build-system r-build-system)
27626 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
27627 (synopsis "Computational geometry")
27629 "This package converts back and forth between two representations of a
27630 convex polytope: as solution of a set of linear equalities and inequalities
27631 and as convex hull of set of points and rays. Also does linear programming
27632 and redundant generator elimination. All functions can use exact
27633 infinite-precision rational arithmetic.")
27634 (license license:gpl2)))
27636 (define-public r-rxnat
27643 (uri (cran-uri "Rxnat" version))
27646 "0siylypjd8cgcmr2c443w8krg8sgr5gz4zapbinanp8vsfzivdv2"))))
27648 `((upstream-name . "Rxnat")))
27649 (build-system r-build-system)
27651 (list r-httr r-rcurl r-tibble))
27654 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
27655 (synopsis "Queries and extracts images from neuroimaging datasets")
27657 "This package allows communication with the Extensible Neuroimaging
27658 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
27660 (license license:gpl2)))
27662 (define-public r-rserve
27669 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
27670 version ".tar.gz"))
27673 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
27674 (build-system r-build-system)
27677 (modify-phases %standard-phases
27678 (add-before 'install 'install-server-binary
27679 ;; Makevars tries to install to R's store directory.
27680 (lambda* (#:key outputs #:allow-other-keys)
27681 (let* ((out (assoc-ref outputs "out"))
27682 (bin (string-append out "/bin")))
27683 (substitute* "src/Makevars.in"
27684 (("\\$\\(R_HOME\\)") out))
27685 (mkdir-p bin)))))))
27695 (list openssl zlib))
27696 (home-page "https://github.com/s-u/Rserve")
27698 "Server providing access to R from many languages and systems")
27700 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
27701 binary requests to be sent to R. Every connection has a separate workspace
27702 and working directory. Client-side implementations are available for popular
27703 languages such as C/C++ and Java, allowing any application to use facilities
27704 of R without the need of linking to R code. Rserve supports remote
27705 connection, user authentication and file transfer. A simple R client is
27706 included in this package as well.")
27707 (license license:gpl2)))
27709 (define-public r-gamm4
27716 (uri (cran-uri "gamm4" version))
27719 "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap"))))
27720 (properties `((upstream-name . "gamm4")))
27721 (build-system r-build-system)
27723 (list r-lme4 r-matrix r-mgcv))
27724 (home-page "https://cran.r-project.org/web/packages/gamm4/")
27725 (synopsis "Generalized additive mixed models using mgcv and lme4")
27727 "Estimate generalized additive mixed models via a version of function
27728 @code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor
27730 (license license:gpl2+)))
27732 (define-public r-optimx
27735 (version "2022-4.30")
27739 (uri (cran-uri "optimx" version))
27742 "045ls1vl1392ihwln6mngz0zg2w93ym1m607vfrg8v1949x8isgb"))))
27743 (properties `((upstream-name . "optimx")))
27744 (build-system r-build-system)
27745 (propagated-inputs (list r-numderiv))
27746 (native-inputs (list r-knitr))
27747 (home-page "https://cran.r-project.org/web/packages/optimx/")
27748 (synopsis "Expanded replacement and extension of the optim function")
27750 "This package provides a replacement and extension of the @code{optim}
27751 function to call to several function minimization codes in R in a single
27752 statement. These methods handle smooth, possibly box constrained functions of
27753 several or many parameters. Note that the function @code{optimr} was prepared
27754 to simplify the incorporation of minimization codes going forward. This
27755 package also implements some utility codes and some extra solvers, including
27756 safeguarded Newton methods. Many methods previously separate are now included
27758 (license license:gpl2)))
27760 (define-public r-projpred
27762 (name "r-projpred")
27767 (uri (cran-uri "projpred" version))
27770 "1a5hsqwcmn1w9lwjhsqw06av7cmqhwyxsil9zfrnv1396zfkpxhy"))))
27771 (properties `((upstream-name . "projpred")))
27772 (build-system r-build-system)
27786 (native-inputs (list r-knitr))
27787 (home-page "https://mc-stan.org/projpred/")
27788 (synopsis "Projection predictive feature selection")
27790 "This package performs projection predictive feature selection for
27791 generalized linear models and generalized linear and additive multilevel
27792 models. The package is compatible with the @code{rstanarm} and @code{brms}
27793 packages, but other reference models can also be used. See the package
27794 vignette for more information and examples.")
27795 (license license:gpl3)))
27797 (define-public r-distributional
27799 (name "r-distributional")
27804 (uri (cran-uri "distributional" version))
27807 "0pr34yq6igb7ciqss2ldwa7gc55xvla040x8rkd8m2hcrz5mczkj"))))
27809 `((upstream-name . "distributional")))
27810 (build-system r-build-system)
27821 (home-page "https://pkg.mitchelloharawild.com/distributional/")
27822 (synopsis "Vectorized probability distributions")
27824 "This package provides vectorized distribution objects with tools for
27825 manipulating, visualizing, and using probability distributions. It was
27826 designed to allow model prediction outputs to return distributions rather than
27827 their parameters, allowing users to directly interact with predictive
27828 distributions in a data-oriented workflow. In addition to providing generic
27829 replacements for p/d/q/r functions, other useful statistics can be computed
27830 including means, variances, intervals, and highest density regions.")
27831 (license license:gpl3)))
27833 (define-public r-posterior
27835 (name "r-posterior")
27840 (uri (cran-uri "posterior" version))
27843 "0yjdjdr4ifssnml1niqyxs6jsqpci8rx8va0pinyhjx2j017h03h"))))
27844 (properties `((upstream-name . "posterior")))
27845 (build-system r-build-system)
27858 (home-page "https://mc-stan.org/posterior/")
27859 (synopsis "Tools for working with posterior distributions")
27861 "This package provides useful tools for both users and developers of
27862 packages for fitting Bayesian models or working with output from Bayesian
27863 models. The primary goals of the package are to:
27866 @item Efficiently convert between many different useful formats of
27867 draws (samples) from posterior or prior distributions.
27869 @item Provide consistent methods for operations commonly performed on draws,
27870 for example, subsetting, binding, or mutating draws.
27872 @item Provide various summaries of draws in convenient formats.
27874 @item Provide lightweight implementations of state of the art posterior
27875 inference diagnostics.
27878 (license license:bsd-3)))
27880 (define-public r-brms
27887 (uri (cran-uri "brms" version))
27890 "0wff5rld4kgkk2nbllvm1h4c596igzgd0q7nx1cabgl11fja7r94"))))
27891 (properties `((upstream-name . "brms")))
27892 (build-system r-build-system)
27913 (native-inputs (list r-knitr))
27915 "https://github.com/paul-buerkner/brms")
27917 "Bayesian Regression Models using 'Stan'")
27919 "Fit Bayesian generalized (non-)linear multivariate multilevel models
27920 using 'Stan' for full Bayesian inference. A wide range of distributions and
27921 link functions are supported, allowing users to fit -- among others -- linear,
27922 robust linear, count data, survival, response times, ordinal, zero-inflated,
27923 hurdle, and even self-defined mixture models all in a multilevel context.
27924 Further modeling options include non-linear and smooth terms, auto-correlation
27925 structures, censored data, meta-analytic standard errors, and quite a few
27926 more. In addition, all parameters of the response distribution can be
27927 predicted in order to perform distributional regression. Prior specifications
27928 are flexible and explicitly encourage users to apply prior distributions that
27929 actually reflect their beliefs. Model fit can easily be assessed and compared
27930 with posterior predictive checks and leave-one-out cross-validation.")
27931 (license license:gpl2)))
27933 (define-public r-mstate
27940 (uri (cran-uri "mstate" version))
27943 "054dzrd5b0xjjjl7862q3aq1jwgrxbkqz7zpvbdirqsld3zksirw"))))
27944 (properties `((upstream-name . "mstate")))
27945 (build-system r-build-system)
27956 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
27958 "Data Preparation, Estimation and Prediction in Multi-State Models")
27960 "Contains functions for data preparation, descriptives, hazard estimation
27961 and prediction with Aalen-Johansen or simulation in competing risks and
27962 multi-state models.")
27963 (license license:gpl2+)))
27965 (define-public r-scatterpie
27967 (name "r-scatterpie")
27972 (uri (cran-uri "scatterpie" version))
27975 "183ji1q0wr8fswdrgaw161fvgh8y7j4x9xacf09s2gz6icxcdk56"))))
27976 (properties `((upstream-name . "scatterpie")))
27977 (build-system r-build-system)
27979 (list r-ggforce r-ggfun r-ggplot2 r-rlang r-tidyr))
27982 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
27983 (synopsis "Scatter pie plot")
27985 "This package creates scatterpie plots, especially useful for plotting
27987 (license license:artistic2.0)))
27989 (define-public r-scrypt
27996 (uri (cran-uri "scrypt" version))
27999 "12q9d4m7flbvlgssvjh1ga4jswkmqjfshf6pna6qk6v087gmzdsj"))))
28000 (properties `((upstream-name . "scrypt")))
28001 (build-system r-build-system)
28004 (home-page "https://github.com/rstudio/rscrypt")
28005 (synopsis "Key derivation functions for R based on Scrypt")
28007 "This package provides functions for working with the scrypt key
28008 derivation functions. Scrypt is a password-based key derivation function
28009 created by Colin Percival. The algorithm was specifically designed to make it
28010 costly to perform large-scale custom hardware attacks by requiring large
28011 amounts of memory.")
28012 (license license:bsd-2)))
28014 (define-public r-boruta
28021 (uri (cran-uri "Boruta" version))
28024 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
28025 (properties `((upstream-name . "Boruta")))
28026 (build-system r-build-system)
28027 (propagated-inputs (list r-ranger))
28028 (home-page "https://gitlab.com/mbq/Boruta/")
28029 (synopsis "Wrapper algorithm for all relevant feature selection")
28031 "This package provides an all relevant feature selection wrapper
28032 algorithm. It finds relevant features by comparing original attributes'
28033 importance with importance achievable at random, estimated using their
28034 permuted copies (shadows).")
28035 (license license:gpl2+)))
28037 (define-public r-directlabels
28039 (name "r-directlabels")
28040 (version "2021.1.13")
28044 (uri (cran-uri "directlabels" version))
28047 "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w"))))
28048 (build-system r-build-system)
28053 (home-page "http://directlabels.r-forge.r-project.org/")
28054 (synopsis "Direct labels for multicolor plots")
28056 "This package provides an extensible framework for automatically placing
28057 direct labels onto multicolor plots. Label positions are described using
28058 positioning methods that can be re-used across several different plots. There
28059 are heuristics for examining @code{trellis} and @code{ggplot} objects and
28060 inferring an appropriate positioning method.")
28061 (license license:gpl3)))
28063 (define-public r-lsd
28070 (uri (cran-uri "LSD" version))
28072 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
28073 (properties `((upstream-name . "LSD")))
28074 (build-system r-build-system)
28075 (home-page "https://cran.r-project.org/web/packages/LSD/")
28076 (synopsis "Lots of superior depictions tool creates colorful plots")
28078 "This package creates lots of colorful plots in a multitude of variations.
28079 Try a demo of the LSD by running @code{demotour()}.")
28081 (license (list license:gpl2 license:gpl3))))
28083 (define-public r-phylogram
28085 (name "r-phylogram")
28090 (uri (cran-uri "phylogram" version))
28092 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
28093 (properties `((upstream-name . "phylogram")))
28094 (build-system r-build-system)
28095 (propagated-inputs (list r-ape))
28096 (home-page "https://github.com/ropensci/phylogram/")
28097 (synopsis "Dendrograms for evolutionary analysis")
28099 "The @code{r-phylogram} package is a tool for for developing phylogenetic
28100 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
28101 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
28102 as well as several tools for command-line tree manipulation and import/export
28103 via Newick parenthetic text. This improves accessibility to the comprehensive
28104 range of object-specific analytical and tree-visualization functions found
28105 across a wide array of bioinformatic R packages.")
28106 (license license:gpl3)))
28108 (define-public r-kmer
28115 (uri (cran-uri "kmer" version))
28117 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
28118 (properties `((upstream-name . "kmer")))
28119 (build-system r-build-system)
28121 (list r-openssl r-phylogram r-rcpp))
28122 (home-page "https://github.com/shaunpwilkinson/kmer/")
28123 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
28125 "@code{r-kmer} is an R package for rapidly computing distance matrices
28126 and clustering large sequence datasets using fast alignment-free k-mer
28127 counting and recursive k-means partitioning.")
28128 (license license:gpl3)))
28130 (define-public r-hardhat
28137 (uri (cran-uri "hardhat" version))
28140 "0y5dxpd4gsrs365x1v4qf2vq7hq2qb6f6x50dyj29xmmn760wcpr"))))
28141 (properties `((upstream-name . "hardhat")))
28142 (build-system r-build-system)
28144 (list r-glue r-rlang r-tibble r-vctrs))
28147 (home-page "https://github.com/tidymodels/hardhat")
28148 (synopsis "Construct modeling packages")
28150 "Building modeling packages is hard. A large amount of effort generally
28151 goes into providing an implementation for a new method that is efficient,
28152 fast, and correct, but often less emphasis is put on the user interface. A
28153 good interface requires specialized knowledge about S3 methods and formulas,
28154 which the average package developer might not have. The goal of
28155 @code{hardhat} is to reduce the burden around building new modeling packages
28156 by providing functionality for preprocessing, predicting, and validating
28158 (license license:expat)))
28160 (define-public r-lightgbm
28162 (name "r-lightgbm")
28167 (uri (cran-uri "lightgbm" version))
28170 "12hbvm1va6sb5yny564jvhhzrkcq4j33rcdhqhwxaac2m08cpi8s"))))
28171 (properties `((upstream-name . "lightgbm")))
28172 (build-system r-build-system)
28174 (list r-data-table r-jsonlite r-matrix r-r6))
28175 (home-page "https://github.com/Microsoft/LightGBM")
28176 (synopsis "Light gradient boosting machine")
28178 "Tree based algorithms can be improved by introducing boosting
28179 frameworks. LightGBM is one such framework, based on Ke, Guolin et
28180 al. (2017). This package offers an R interface to work with it. It is
28181 designed to be distributed and efficient with the following goals:
28184 @item Faster training speed and higher efficiency;
28185 @item lower memory usage;
28186 @item better accuracy;
28187 @item parallel learning supported; and
28188 @item capable of handling large-scale data.
28191 (license license:expat)))
28193 (define-public r-shapforxgboost
28195 (name "r-shapforxgboost")
28200 (uri (cran-uri "SHAPforxgboost" version))
28203 "106nsf02b1w3yshb55lwnyw1rl1a60162v2wk8znjz3b4ln3mqj5"))))
28205 `((upstream-name . "SHAPforxgboost")))
28206 (build-system r-build-system)
28218 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
28219 (synopsis "SHAP Plots for XGBoost")
28221 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
28222 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
28223 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
28224 and force plot. It relies on the @code{XGBoost} package to produce SHAP
28226 (license license:expat)))
28228 (define-public r-rismed
28235 (uri (cran-uri "RISmed" version))
28238 "0vpi88gzi9r85v6nhjz9jbw671zkrmyazwna2z881346wfyr3l8b"))))
28239 (properties `((upstream-name . "RISmed")))
28240 (build-system r-build-system)
28242 (list r-httr r-xml2))
28243 (home-page "https://cran.r-project.org/web/packages/RISmed")
28244 (synopsis "Download content from NCBI databases")
28246 "This package provides a set of tools to extract bibliographic
28247 content from the National Center for Biotechnology Information (NCBI)
28248 databases, including PubMed. The name RISmed is a portmanteau of
28249 RIS (for Research Information Systems, a common tag format for
28250 bibliographic data) and PubMed.")
28251 (license license:gpl2+)))
28253 (define-public r-semver
28260 (uri (cran-uri "semver" version))
28263 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
28264 (properties `((upstream-name . "semver")))
28265 (build-system r-build-system)
28267 (list r-assertthat r-rcpp))
28268 (native-inputs (list r-knitr))
28269 (home-page "https://github.com/johndharrison/semver")
28270 (synopsis "Parser for Semantic Versioning 2.0.0")
28272 "This package provides tools and functions for parsing, rendering and
28273 operating on semantic version strings. Semantic versioning is a simple set of
28274 rules and requirements that dictate how version numbers are assigned and
28275 incremented as outlined at @url{http://semver.org}.")
28276 (license license:expat)))
28278 (define-public r-binman
28285 (uri (cran-uri "binman" version))
28288 "1xz9ky3axidm0fp518rj80ma6q14ybyvashil79hhkk3iqmx0lhw"))))
28289 (properties `((upstream-name . "binman")))
28290 (build-system r-build-system)
28299 (native-inputs (list r-knitr))
28300 (home-page "https://github.com/ropensci/binman")
28301 (synopsis "Binary download manager")
28303 "This package provides tools and functions for managing the download of
28304 binary files. Binary repositories are defined in the YAML format. Defining
28305 new pre-download, download and post-download templates allow additional
28306 repositories to be added.")
28307 (license license:expat)))
28309 (define-public r-wdman
28316 (uri (cran-uri "wdman" version))
28319 "0n0wwb9ip6qc8qzdxn4dsqfbc8b3f607n8l6jigryd7g83ibnbp6"))))
28320 (properties `((upstream-name . "wdman")))
28321 (build-system r-build-system)
28323 (list r-assertthat r-binman r-processx r-semver r-yaml))
28324 (native-inputs (list r-knitr))
28325 (home-page "https://docs.ropensci.org/wdman/")
28326 (synopsis "Webdriver/Selenium binary manager")
28328 "There are a number of binary files associated with the
28329 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
28330 @url{https://sites.google.com/a/chromium.org/chromedriver/},
28331 @url{https://github.com/mozilla/geckodriver},
28332 @url{http://phantomjs.org/download.html}, and
28333 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
28334 more information). This package provides functions to download these binaries
28335 and to manage processes involving them.")
28336 (license license:expat)))
28338 (define-public r-rselenium
28340 (name "r-rselenium")
28345 (uri (cran-uri "RSelenium" version))
28348 "18hd0gfpblg9ij99ik7ccc60q9dxha89n5rrwrrzx498c5sscjg2"))))
28349 (properties `((upstream-name . "RSelenium")))
28350 (build-system r-build-system)
28355 (native-inputs (list r-knitr))
28356 (home-page "https://docs.ropensci.org/RSelenium/")
28357 (synopsis "R bindings for Selenium WebDriver")
28359 "This package provides a set of R bindings for the Selenium 2.0
28360 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
28361 information) using the @code{JsonWireProtocol} (see
28362 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
28363 information). Selenium 2.0 WebDriver allows driving a web browser natively as
28364 a user would either locally or on a remote machine using the Selenium server
28365 it marks a leap forward in terms of web browser automation. Selenium
28366 automates web browsers (commonly referred to as browsers). Using RSelenium
28367 you can automate browsers locally or remotely.")
28368 (license license:agpl3+)))
28370 (define-public r-conquer
28377 (uri (cran-uri "conquer" version))
28380 "1mdwm0aanq4rx3042djvs0l2vkdx6zbzvrjfyfb9dhv0gfs8mhhl"))))
28381 (properties `((upstream-name . "conquer")))
28382 (build-system r-build-system)
28384 (list r-matrix r-matrixstats r-rcpp r-rcpparmadillo))
28385 (home-page "https://github.com/XiaoouPan/conquer")
28386 (synopsis "Convolution-type smoothed quantile regression")
28388 "This package provides fast and accurate convolution-type smoothed
28389 quantile regression, implemented using Barzilai-Borwein gradient descent with
28390 a Huber regression warm start. Confidence intervals for regression
28391 coefficients are constructed using multiplier bootstrap.")
28392 (license license:gpl3)))
28394 (define-public r-fastshap
28396 (name "r-fastshap")
28401 (uri (cran-uri "fastshap" version))
28404 "0gxch67i3bj6m8nb94m5hswq058w6n1q9war4dy2qnimlv7cmhdv"))))
28405 (properties `((upstream-name . "fastshap")))
28406 (build-system r-build-system)
28416 (home-page "https://github.com/bgreenwell/fastshap")
28417 (synopsis "Fast approximate Shapley values")
28419 "This package computes fast (relative to other implementations)
28420 approximate Shapley values for any supervised learning model. Shapley values
28421 help to explain the predictions from any black box model using ideas from game
28422 theory; see @url{Strumbel and Kononenko (2014),
28423 doi.org/10.1007/s10115-013-0679-x} for details.")
28424 (license license:gpl2+)))
28426 (define-public r-memuse
28432 (uri (cran-uri "memuse" version))
28435 "1wvwnjaaiv2647561z2b55dss35033ildx4kk8hzxfzgsjmdpsgm"))))
28436 (properties `((upstream-name . "memuse")))
28437 (build-system r-build-system)
28438 (home-page "https://github.com/shinra-dev/memuse")
28439 (synopsis "Memory Estimation Utilities")
28441 "This package provides procedures to answer the following questions:
28442 How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is
28443 your current R session using? How much ram do you even have?")
28444 (license license:bsd-2)))
28446 (define-public r-metrics
28453 (uri (cran-uri "Metrics" version))
28456 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
28457 (properties `((upstream-name . "Metrics")))
28458 (build-system r-build-system)
28459 (home-page "https://github.com/mfrasco/Metrics")
28460 (synopsis "Evaluation metrics for machine learning")
28462 "This package provides an implementation of evaluation metrics in R that
28463 are commonly used in supervised machine learning. It implements metrics for
28464 regression, time series, binary classification, classification, and
28465 information retrieval problems. It has zero dependencies and a consistent,
28466 simple interface for all functions.")
28467 (license license:bsd-3)))
28469 (define-public r-iml
28476 (uri (cran-uri "iml" version))
28479 "0fi37lv9czaxcc123f6r57607shqhs83ks96n2n0b93dl1qs0j52"))))
28480 (properties `((upstream-name . "iml")))
28481 (build-system r-build-system)
28492 (native-inputs (list r-knitr))
28493 (home-page "https://github.com/christophM/iml")
28494 (synopsis "Interpretable machine learning")
28496 "This package provides interpretability methods to analyze the behavior
28497 and predictions of any machine learning model. Implemented methods are:
28500 @item Feature importance described by Fisher et al. (2018),
28501 @item accumulated local effects plots described by Apley (2018),
28502 @item partial dependence plots described by Friedman (2001),
28503 @item individual conditional expectation ('ice') plots described by Goldstein
28504 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
28505 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
28506 @item the Shapley Value described by Strumbelj et. al (2014)
28507 @url{https://doi.org/10.1007/s10115-013-0679-x},
28508 @item feature interactions described by Friedman et. al
28509 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
28512 (license license:expat)))
28514 (define-public r-goftest
28521 (uri (cran-uri "goftest" version))
28524 "06bz6k7smr4jbvzmb73qc5fkf4my59w5gbl18wlmpkkymsv78prs"))))
28525 (properties `((upstream-name . "goftest")))
28526 (build-system r-build-system)
28527 (home-page "https://github.com/baddstats/goftest")
28528 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
28530 "This package provides Cramer-Von Mises and Anderson-Darling tests of
28531 goodness-of-fit for continuous univariate distributions, using efficient
28533 (license license:gpl2+)))
28535 (define-public r-tensor
28542 (uri (cran-uri "tensor" version))
28545 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
28546 (properties `((upstream-name . "tensor")))
28547 (build-system r-build-system)
28548 (home-page "https://cran.r-project.org/web/packages/tensor/")
28549 (synopsis "Tensor product of arrays")
28551 "The tensor product of two arrays is notionally an outer product of the
28552 arrays collapsed in specific extents by summing along the appropriate
28553 diagonals. This package allows you to compute the tensor product of arrays.")
28554 (license license:gpl2+)))
28556 (define-public r-spatstat-utils
28558 (name "r-spatstat-utils")
28563 (uri (cran-uri "spatstat.utils" version))
28566 "08pybliv4r3v4rcazmlfr4a07sjfhrkmksdmhhq9k185vw4474av"))))
28568 `((upstream-name . "spatstat.utils")))
28569 (build-system r-build-system)
28570 (home-page "http://www.spatstat.org")
28571 (synopsis "Utility functions for spatstat")
28573 "This package contains utility functions for the @code{spatstat} package
28574 which may also be useful for other purposes.")
28575 (license license:gpl2+)))
28577 (define-public r-spatstat-sparse
28579 (name "r-spatstat-sparse")
28584 (uri (cran-uri "spatstat.sparse" version))
28587 "00vkvv5pnm82gn7vqnzrrp68y46gbkhdq0hbwqx7nxjvf5lssdcs"))))
28589 `((upstream-name . "spatstat.sparse")))
28590 (build-system r-build-system)
28592 (list r-abind r-matrix r-spatstat-utils r-tensor))
28593 (home-page "http://spatstat.org/")
28594 (synopsis "Sparse three-dimensional arrays and linear algebra utilities")
28596 "This package defines sparse three-dimensional arrays and supports
28597 standard operations on them. The package also includes utility functions for
28598 matrix calculations that are common in statistics, such as quadratic forms.")
28599 (license license:gpl2+)))
28601 (define-public r-spatstat-data
28603 (name "r-spatstat-data")
28608 (uri (cran-uri "spatstat.data" version))
28611 "1rf36zy29h9qabpv19hx84gjdiay7i9y9777d2zn17ahyss3p56k"))))
28612 (properties `((upstream-name . "spatstat.data")))
28613 (build-system r-build-system)
28615 (list r-matrix r-spatstat-utils))
28616 (home-page "http://www.spatstat.org")
28617 (synopsis "Datasets for spatstat")
28619 "This package contains all the datasets for the @code{spatstat}
28621 (license license:gpl2+)))
28623 (define-public r-spatstat-geom
28625 (name "r-spatstat-geom")
28630 (uri (cran-uri "spatstat.geom" version))
28633 "0rwysq9a0ylbsr53q5kfh7wjk5mcdji211sc3s8gwzz8ki09mf1j"))))
28634 (properties `((upstream-name . "spatstat.geom")))
28635 (build-system r-build-system)
28637 (list r-deldir r-polyclip r-spatstat-data r-spatstat-utils))
28638 (home-page "http://spatstat.org/")
28639 (synopsis "Geometrical functionality of the spatstat package")
28641 "This is a subset of the original spatstat package, containing the
28642 user-level code from spatstat which performs geometrical operations, except
28643 for the geometry of linear networks.")
28644 (license license:gpl2+)))
28646 (define-public r-spatstat-core
28648 (name "r-spatstat-core")
28653 (uri (cran-uri "spatstat.core" version))
28656 "0fyi8y1z919nzn47kaviln7gflhcp5qdi3gfvf7nwkdix3pkk373"))))
28657 (properties `((upstream-name . "spatstat.core")))
28658 (build-system r-build-system)
28672 (home-page "http://spatstat.org/")
28673 (synopsis "Core functionality of the spatstat package")
28675 "This is a subset of the original spatstat package, containing all of the
28676 user-level code from spatstat, except for the code for linear networks.")
28677 (license license:gpl2+)))
28679 (define-public r-spatstat-linnet
28681 (name "r-spatstat-linnet")
28686 (uri (cran-uri "spatstat.linnet" version))
28689 "0y1py6x0xbw4ad3pjwcspi4ysgfh61f5fd79787zzgyyh2va8y4w"))))
28691 `((upstream-name . "spatstat.linnet")))
28692 (build-system r-build-system)
28701 (home-page "http://spatstat.org/")
28702 (synopsis "Linear networks functionality of the spatstat package")
28704 "This is a subset of the spatstat package, containing its functionality
28705 for spatial data on a linear network.")
28706 (license license:gpl2+)))
28708 (define-public r-spatstat-random
28710 (name "r-spatstat-random")
28715 (uri (cran-uri "spatstat.random" version))
28717 (base32 "0kb01s8k67ydcfqcnz3i55vpiksihh4xsg0w2p2bclxxkpdvpw25"))))
28718 (properties `((upstream-name . "spatstat.random")))
28719 (build-system r-build-system)
28720 (propagated-inputs (list r-spatstat-data r-spatstat-geom r-spatstat-utils))
28721 (home-page "http://spatstat.org/")
28722 (synopsis "Random Generation Functionality for the 'spatstat' Family")
28724 "This package provides functionality for random generation of spatial
28725 data in the spatstat family of packages. It generates random spatial patterns
28726 of points according to many simple rules (complete spatial randomness,
28727 Poisson, binomial, random grid, systematic, cell), randomised alteration of
28728 patterns (thinning, random shift, jittering), simulated realisations of random
28729 point processes (simple sequential inhibition, Matern inhibition models,
28730 Matern cluster process, Neyman-Scott cluster processes, log-Gaussian Cox
28731 processes, product shot noise cluster processes) and simulation of Gibbs point
28732 processes (Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs
28734 (license license:gpl2+)))
28736 (define-public r-spatstat
28738 (name "r-spatstat")
28743 (uri (cran-uri "spatstat" version))
28746 "1nlrp7660y68axlm4pczc5rxbdhbbac1ylh69azr4swj1gbzi82f"))))
28747 (properties `((upstream-name . "spatstat")))
28748 (build-system r-build-system)
28750 (list r-spatstat-core r-spatstat-data r-spatstat-geom
28751 r-spatstat-linnet r-spatstat-random r-spatstat-utils))
28752 (home-page "http://www.spatstat.org")
28753 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
28755 "This package provides a comprehensive toolbox for analysing Spatial
28756 Point Patterns. It is focused mainly on two-dimensional point patterns,
28757 including multitype/marked points, in any spatial region. It also supports
28758 three-dimensional point patterns, space-time point patterns in any number of
28759 dimensions, point patterns on a linear network, and patterns of other
28760 geometrical objects. It supports spatial covariate data such as pixel images
28761 and contains over 2000 functions for plotting spatial data, exploratory data
28762 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
28763 formal inference.")
28764 (license license:gpl2+)))
28766 (define-public r-gaston
28773 (uri (cran-uri "gaston" version))
28776 "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i"))))
28777 (properties `((upstream-name . "gaston")))
28778 (build-system r-build-system)
28779 (inputs (list zlib))
28781 (list r-rcpp r-rcppeigen r-rcppparallel))
28782 (native-inputs (list r-knitr))
28783 (home-page "https://cran.r-project.org/web/packages/gaston/")
28784 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
28786 "This is a package for the manipulation of genetic data (SNPs).
28787 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
28788 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
28789 for linear mixed models (AIREML).")
28790 (license license:gpl3)))
28792 (define-public r-cpp11
28799 (uri (cran-uri "cpp11" version))
28802 "16cvjfkbc7c0ymdmbcqg9px6pjsqx6qhyfq5frqj739mhazy0g20"))))
28803 (properties `((upstream-name . "cpp11")))
28804 (build-system r-build-system)
28805 (native-inputs (list r-knitr))
28806 (home-page "https://github.com/r-lib/cpp11")
28807 (synopsis "C++11 Interface for R's C Interface")
28809 "This package provides a header only, C++11 interface to R's C interface.
28810 Compared to other approaches @code{cpp11} strives to be safe against long
28811 jumps from the C API as well as C++ exceptions, conform to normal R function
28812 semantics and supports interaction with @code{ALTREP} vectors.")
28813 (license license:expat)))
28815 (define-public r-rcpptoml
28817 (name "r-rcpptoml")
28822 (uri (cran-uri "RcppTOML" version))
28824 (base32 "0h8517ipwqhqkhcfiyqmvsb585g01p0ra0azbpzyxip6pq6g029g"))))
28825 (properties `((upstream-name . "RcppTOML")))
28826 (build-system r-build-system)
28827 (propagated-inputs (list r-rcpp))
28828 (home-page "http://dirk.eddelbuettel.com/code/rcpp.toml.html")
28829 (synopsis "Rcpp bindings to TOML parser")
28831 "The TOML configuration format specifies an excellent format suitable for
28832 both human editing as well as the common uses of a machine-readable format.
28833 This package provides Rcpp bindings to a TOML parser.")
28834 (license license:gpl2+)))
28836 (define-public r-rcppziggurat
28838 (name "r-rcppziggurat")
28843 (uri (cran-uri "RcppZiggurat" version))
28846 "0wgd1v2p7zajnbrjf3hfi56p3pk3ld6iwkanbb04bjbnlif2ay4w"))))
28847 (properties `((upstream-name . "RcppZiggurat")))
28848 (build-system r-build-system)
28850 (list r-rcpp r-rcppgsl))
28851 (native-inputs (list r-knitr))
28852 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
28853 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
28855 "The Ziggurat generator for normally distributed random numbers,
28856 originally proposed by Marsaglia and Tsang (2000,
28857 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
28858 times starting with Leong et al (2005,
28859 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
28860 aggregation for comparing different implementations in order to provide a
28861 'faster but good enough' alternative for use with R and C++ code.")
28862 (license license:gpl2+)))
28864 (define-public r-rfast
28871 (uri (cran-uri "Rfast" version))
28874 "0zxykq021h57mq0n6giqbx8ncjsdly0arhmaj3fcp3yfcxf4ns9l"))))
28875 (properties `((upstream-name . "Rfast")))
28876 (build-system r-build-system)
28878 (list r-rcpp r-rcpparmadillo r-rcppziggurat))
28879 (home-page "https://github.com/RfastOfficial/Rfast")
28880 (synopsis "Collection of efficient and fast R functions")
28882 "This package provides a collection of fast (utility) functions for data
28883 analysis. Column- and row- wise means, medians, variances, minimums,
28884 maximums, many t, F and G-square tests, many regressions (normal, logistic,
28885 Poisson), are some of the many fast functions.")
28886 (license license:gpl2+)))
28888 (define-public r-rffc
28894 (uri (string-append
28895 "https://download.r-forge.r-project.org/src/contrib/"
28896 "rfFC_" version ".tar.gz"))
28899 "05x9wgzsmx4vb12lmcspymgmpb2xw8bwryb8ysg7vzg2nkh0ma3g"))))
28900 (build-system r-build-system)
28902 (list r-randomforest))
28903 (home-page "https://r-forge.r-project.org/projects/rffc/")
28904 (synopsis "Random Forest Feature Contributions")
28905 (description "This package provides functions for extracting feature
28906 contributions from a random forest model from package @code{randomForest}.
28907 Feature contributions provide detailed information about the relationship
28908 between data variables and the predicted value returned by random forest
28910 (license license:gpl2)))
28912 (define-public r-clusterr
28914 (name "r-clusterr")
28919 (uri (cran-uri "ClusterR" version))
28922 "00mha8madcba83ix4fc04rb7sagfm0lxlh1wvs7dvjdrngps41jr"))))
28923 (properties `((upstream-name . "ClusterR")))
28924 (build-system r-build-system)
28926 (list r-ggplot2 r-gmp r-gtools r-rcpp r-rcpparmadillo))
28927 (native-inputs (list r-knitr))
28928 (home-page "https://github.com/mlampros/ClusterR")
28929 (synopsis "Clustering")
28931 "This package provides Gaussian mixture models, k-means,
28932 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
28933 option to plot, validate, predict (new data) and estimate the optimal number
28934 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
28935 the computationally intensive parts of the functions. For more information,
28939 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
28940 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
28941 @url{https://doi.org/10.18637/jss.v001.i04};
28942 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
28943 Library, @url{https://doi.org/10.1145/1772690.1772862};
28944 @item \"Armadillo: a template-based C++ library
28945 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
28946 Software, @url{https://doi.org/10.21105/joss.00026};
28947 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
28948 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
28949 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
28952 (license license:gpl3)))
28954 (define-public r-spectrum
28956 (name "r-spectrum")
28961 (uri (cran-uri "Spectrum" version))
28964 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
28965 (properties `((upstream-name . "Spectrum")))
28966 (build-system r-build-system)
28968 (list r-clusterr r-diptest r-ggplot2 r-rfast))
28969 (native-inputs (list r-knitr))
28970 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
28971 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
28973 "This package provides a self-tuning spectral clustering method for
28974 single or multi-view data. Spectrum uses a new type of adaptive density aware
28975 kernel that strengthens connections in the graph based on common nearest
28976 neighbours. It uses a tensor product graph data integration and diffusion
28977 procedure to integrate different data sources and reduce noise. Spectrum uses
28978 either the eigengap or multimodality gap heuristics to determine the number of
28979 clusters. The method is sufficiently flexible so that a wide range of
28980 Gaussian and non-Gaussian structures can be clustered with automatic selection
28982 (license license:agpl3+)))
28984 (define-public r-nabor
28991 (uri (cran-uri "nabor" version))
28994 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
28995 (properties `((upstream-name . "nabor")))
28996 (build-system r-build-system)
28998 (list r-bh r-rcpp r-rcppeigen))
28999 (home-page "https://cran.r-project.org/web/packages/nabor/")
29000 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
29002 "This package provides an R wrapper for libnabo, an exact or approximate
29003 k nearest neighbour library which is optimised for low dimensional
29004 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
29005 designed as a drop-in replacement for the RANN function @code{nn2}. In
29006 addition, objects which include the k-d tree search structure can be returned
29007 to speed up repeated queries of the same set of target points.")
29008 (license license:bsd-3)))
29010 (define-public r-naturalsort
29012 (name "r-naturalsort")
29016 (uri (cran-uri "naturalsort" version))
29019 "0mz801y9mzld9ypp3xmsjw2d8l9q97sdnv09wrci9xi3yg2sjf6d"))))
29020 (build-system r-build-system)
29021 (home-page "https://cran.r-project.org/web/packages/naturalsort/")
29022 (synopsis "Natural ordering")
29023 (description "This package provides functions related to human natural
29024 ordering. It handles adjacent digits in a character sequence as a number
29025 so that natural sort function arranges a character vector by their numbers,
29026 not digit characters.")
29027 (license license:bsd-3)))
29029 (define-public r-visdat
29035 (uri (cran-uri "visdat" version))
29038 "1ikqp29nncbw1xlwyb9dqqgcdk9q0bs3wxhnhnjpb11vcjv7cz2j"))))
29039 (build-system r-build-system)
29051 (home-page "https://visdat.njtierney.com/")
29052 (synopsis "Preliminary Visualisation of Data")
29053 (description "This package provides procedures to create preliminary exploratory
29054 data visualisations of an entire dataset to identify problems or unexpected features
29055 using @code{ggplot2}.")
29056 (license license:expat)))
29058 (define-public r-muhaz
29061 (version "1.2.6.4")
29065 (uri (cran-uri "muhaz" version))
29068 "1ddy8ayr4rdhzcipdvxdwd7z5g9hfp0ppacl7xf6f2612cn1185g"))))
29069 (properties `((upstream-name . "muhaz")))
29070 (build-system r-build-system)
29075 (home-page "https://cran.r-project.org/web/packages/muhaz/")
29076 (synopsis "Hazard function estimation in survival analysis")
29078 "This package produces a smooth estimate of the hazard function for
29080 ;; Any version of the GPL.
29081 (license license:gpl3+)))
29083 (define-public r-flexsurv
29085 (name "r-flexsurv")
29090 (uri (cran-uri "flexsurv" version))
29093 "0244amsyf2izih6008n2535r3ddksgdnys8pyslrcb1c09spmjrw"))))
29094 (properties `((upstream-name . "flexsurv")))
29095 (build-system r-build-system)
29120 (home-page "https://github.com/chjackson/flexsurv-dev")
29121 (synopsis "Flexible parametric survival and multi-state models")
29123 "This package provides flexible parametric models for time-to-event data,
29124 including the Royston-Parmar spline model, generalized gamma and generalized F
29125 distributions. Any user-defined parametric distribution can be fitted, given
29126 at least an R function defining the probability density or hazard. There are
29127 also tools for fitting and predicting from fully parametric multi-state
29129 (license license:gpl2+)))
29131 (define-public r-transphylo
29133 (name "r-transphylo")
29138 (uri (cran-uri "TransPhylo" version))
29141 "0g92kwi1nlmpc8m4pc9kv9xhczryr2kn9icfr3js7da7vy8g50xy"))))
29142 (properties `((upstream-name . "TransPhylo")))
29143 (build-system r-build-system)
29145 (list r-ape r-rcpp))
29148 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
29149 (synopsis "Inference of transmission tree from a dated phylogeny")
29151 "This is a package to infer transmission trees from a dated phylogeny.
29152 It includes methods to simulate and analyze outbreaks. The methodology is
29153 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
29154 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
29155 (license license:gpl2+)))
29157 (define-public r-km-ci
29164 (uri (cran-uri "km.ci" version))
29167 "18sc9vhbdgks8lhk2nfxkkayh8j4j227hl63fm5p04f7z4wm6wc1"))))
29168 (properties `((upstream-name . "km.ci")))
29169 (build-system r-build-system)
29172 (home-page "https://cran.r-project.org/web/packages/km.ci/")
29173 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
29175 "This package computes various @dfn{confidence intervals} (CI) for the
29176 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
29177 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
29178 Nair and Hall and Wellner.")
29179 (license license:gpl2+)))
29181 (define-public r-kmsurv
29188 (uri (cran-uri "KMsurv" version))
29191 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
29192 (properties `((upstream-name . "KMsurv")))
29193 (build-system r-build-system)
29194 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
29195 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
29197 "This package provides data sets and functions for Klein and Moeschberger
29198 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
29200 (license license:gpl3+)))
29202 (define-public r-survmisc
29204 (name "r-survmisc")
29209 (uri (cran-uri "survMisc" version))
29212 "014cf7sfndmib9jmj0p3h67sr750k2pvw7m865zwdpvlqddi44fr"))))
29213 (properties `((upstream-name . "survMisc")))
29214 (build-system r-build-system)
29227 (home-page "https://cran.r-project.org/web/packages/survMisc/")
29228 (synopsis "Miscellaneous functions for survival data")
29230 "This package provides a collection of functions to help in the analysis
29231 of right-censored survival data. These extend the methods available in
29232 the @code{survival} package.")
29233 (license license:gpl2)))
29235 (define-public r-exactranktests
29237 (name "r-exactranktests")
29242 (uri (cran-uri "exactRankTests" version))
29245 "1qv9i57chhz8xiv0j8r47rbigyqs72fa7ssz99inyc0s8gzskd3y"))))
29247 `((upstream-name . "exactRankTests")))
29248 (build-system r-build-system)
29249 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
29250 (synopsis "Exact distributions for rank and permutation tests")
29252 "This package computes exact conditional p-values and quantiles using an
29253 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
29254 (license license:gpl2+)))
29256 (define-public r-maxstat
29263 (uri (cran-uri "maxstat" version))
29266 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
29267 (properties `((upstream-name . "maxstat")))
29268 (build-system r-build-system)
29270 (list r-exactranktests r-mvtnorm))
29271 (home-page "https://cran.r-project.org/web/packages/maxstat/")
29272 (synopsis "Maximally selected rank statistics")
29274 "This package provides maximally selected rank statistics with several
29275 p-value approximations.")
29276 (license license:gpl2+)))
29278 (define-public r-survminer
29280 (name "r-survminer")
29285 (uri (cran-uri "survminer" version))
29288 "0byh0wxdbjfwdrzsnqv4xlmnik6lj0vkkzfxy7lssk8dv5zmj7nz"))))
29289 (properties `((upstream-name . "survminer")))
29290 (build-system r-build-system)
29309 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
29310 (synopsis "Drawing survival curves using ggplot2")
29312 "This package contains the function @code{ggsurvplot()} for easily
29313 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
29314 risk' table and 'censoring count plot'. Other functions are also available to
29315 plot adjusted curves for Cox model and to visually examine Cox model
29317 (license license:gpl2)))
29319 (define-public r-forge
29326 (uri (cran-uri "forge" version))
29329 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
29330 (properties `((upstream-name . "forge")))
29331 (build-system r-build-system)
29333 (list r-magrittr r-rlang))
29334 (home-page "https://cran.r-project.org/web/packages/forge/")
29335 (synopsis "Cast values into shape")
29337 "This package provides helper functions with a consistent interface to
29338 coerce and verify the types and shapes of values for input checking.")
29339 (license license:asl2.0)))
29341 (define-public r-config
29348 (uri (cran-uri "config" version))
29351 "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l"))))
29352 (properties `((upstream-name . "config")))
29353 (build-system r-build-system)
29358 (home-page "https://github.com/rstudio/config")
29359 (synopsis "Manage environment specific configuration values")
29361 "This package lets you manage configuration values across multiple
29362 environments (e.g. development, test, production). It reads values using a
29363 function that determines the current environment and returns the appropriate
29365 (license license:gpl3)))
29367 (define-public r-confintr
29369 (name "r-confintr")
29373 (uri (cran-uri "confintr" version))
29376 "06c42jhqp7gp9062jf8f9py1lh34vx38q0g7b6l5kyf7a310ixr6"))))
29377 (properties `((upstream-name . "confintr")))
29378 (build-system r-build-system)
29379 (propagated-inputs (list r-boot))
29380 (native-inputs (list r-knitr))
29381 (home-page "https://github.com/mayer79/confintr")
29382 (synopsis "Confidence intervals")
29384 "This package calculates classic and/or bootstrap confidence intervals
29385 for many parameters such as the population mean, variance, @dfn{interquartile
29386 range} (IQR), @dfn{median absolute deviation} (MAD), skewness, kurtosis,
29387 Cramer's V, odds ratio, R-squared, quantiles (including median), proportions,
29388 different types of correlation measures, difference in means, quantiles and
29389 medians. Many of the classic confidence intervals are described in Smithson,
29390 M. (2003, ISBN: 978-0761924999). Bootstrap confidence intervals are
29391 calculated with the R package @code{boot}. Both one- and two-sided intervals
29393 (license license:gpl2+)))
29395 (define-public r-adaptivesparsity
29397 (name "r-adaptivesparsity")
29401 (uri (cran-uri "AdaptiveSparsity" version))
29404 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
29406 `((upstream-name . "AdaptiveSparsity")))
29407 (build-system r-build-system)
29410 (modify-phases %standard-phases
29411 (add-after 'unpack 'link-against-armadillo
29413 (substitute* "src/Makevars"
29414 (("PKG_LIBS=" prefix)
29415 (string-append prefix "-larmadillo")))
29418 (list r-mass r-matrix r-rcpp r-rcpparmadillo))
29421 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
29422 (synopsis "Adaptive sparsity models")
29424 "This package implements the Figueiredo machine learning algorithm for
29425 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
29426 geometric models.")
29427 (license license:lgpl3+)))
29429 (define-public r-add2ggplot
29431 (name "r-add2ggplot")
29436 (uri (cran-uri "add2ggplot" version))
29438 (base32 "0c94i1cfp2pvplvxmfvvz2fyj026r1jnax05mrzrc7ppnqzy25y0"))))
29439 (properties `((upstream-name . "add2ggplot")))
29440 (build-system r-build-system)
29442 (list r-ggplot2 r-magick r-magrittr r-rcolorbrewer r-zeallot))
29443 (native-inputs (list r-knitr))
29444 (home-page "https://github.com/JiaxiangBU/add2ggplot")
29445 (synopsis "Extension for ggplot2")
29446 (description "This package provides tools to create themes and color
29447 palettes for the package ggplot2.")
29448 (license license:expat)))
29450 (define-public r-diffusionmap
29452 (name "r-diffusionmap")
29457 (uri (cran-uri "diffusionMap" version))
29460 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
29461 (properties `((upstream-name . "diffusionMap")))
29462 (build-system r-build-system)
29464 (list r-igraph r-matrix r-scatterplot3d))
29465 (home-page "https://www.r-project.org")
29466 (synopsis "Diffusion map")
29467 (description "This package implements the diffusion map method of data
29468 parametrization, including creation and visualization of diffusion maps,
29469 clustering with diffusion K-means and regression using the adaptive regression
29471 (license license:gpl2)))
29473 (define-public r-igraph
29480 (uri (cran-uri "igraph" version))
29483 "1kyic5xmwgw5lm30rsvsf1x3m0yxysdlrnw63xn4fh8j4vcc66ms"))))
29484 (build-system r-build-system)
29488 (list gmp glpk libxml2 zlib))
29490 (list r-magrittr r-matrix r-pkgconfig r-rlang))
29491 (home-page "https://igraph.org")
29492 (synopsis "Network analysis and visualization")
29494 "This package provides routines for simple graphs and network analysis.
29495 It can handle large graphs very well and provides functions for generating
29496 random and regular graphs, graph visualization, centrality methods and much
29498 (license license:gpl2+)))
29500 (define-public r-workflows
29502 (name "r-workflows")
29507 (uri (cran-uri "workflows" version))
29510 "0bsizgqin5cya0xibs1nqzadrrxcph8n4bh5vlcfbqqzzkv7cx1b"))))
29511 (properties `((upstream-name . "workflows")))
29512 (build-system r-build-system)
29525 (home-page "https://github.com/tidymodels/workflows")
29526 (synopsis "Modeling workflows")
29528 "A workflow is an object that can bundle together your pre-processing,
29529 modeling, and post-processing requests. For example, if you have a
29530 @code{recipe} and @code{parsnip} model, these can be combined into a
29531 workflow. The advantages are:
29534 @item You don’t have to keep track of separate objects in your workspace.
29535 @item The recipe prepping and model fitting can be executed using a single
29536 call to @code{fit()}.
29537 @item If you have custom tuning parameter settings, these can be defined using
29538 a simpler interface when combined with @code{tune}.
29539 @item In the future, workflows will be able to add post-processing operations,
29540 such as modifying the probability cutoff for two-class models.
29543 (license license:expat)))
29545 (define-public r-lobstr
29552 (uri (cran-uri "lobstr" version))
29555 "060p7b7i2qx09d7nf0kdl85r9j886fivrkrsl2bn10cggvnk7icv"))))
29556 (properties `((upstream-name . "lobstr")))
29557 (build-system r-build-system)
29563 (home-page "https://github.com/r-lib/lobstr")
29564 (synopsis "Visualize R data structures with trees")
29566 "This package provides a set of tools for inspecting and understanding R
29567 data structures inspired by @code{str}. It includes @code{ast} for
29568 visualizing abstract syntax trees, @code{ref} for showing shared references,
29569 @code{cst} for showing call stack trees, and @code{obj_size} for computing
29571 (license license:gpl3)))
29573 (define-public r-gpfit
29580 (uri (cran-uri "GPfit" version))
29583 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
29584 (properties `((upstream-name . "GPfit")))
29585 (build-system r-build-system)
29587 (list r-lattice r-lhs))
29588 (home-page "https://cran.r-project.org/web/packages/GPfit/")
29589 (synopsis "Gaussian Processes modeling")
29591 "This package provides a computationally stable approach of fitting a
29592 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
29593 (license license:gpl2)))
29595 (define-public r-yardstick
29597 (name "r-yardstick")
29602 (uri (cran-uri "yardstick" version))
29605 "0bcirq9mp7c6kwx563nnsd4lk33xk0rfaakj1xj5r8pzmrcgbikj"))))
29606 (properties `((upstream-name . "yardstick")))
29607 (build-system r-build-system)
29617 (home-page "https://github.com/tidymodels/yardstick")
29618 (synopsis "Tidy characterizations of model performance")
29620 "This package provides tidy tools for quantifying how well a model fits
29621 to a data set such as confusion matrices, class probability curve summaries,
29622 and regression metrics (e.g., RMSE).")
29623 (license license:gpl2)))
29625 (define-public r-warp
29632 (uri (cran-uri "warp" version))
29635 "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
29636 (properties `((upstream-name . "warp")))
29637 (build-system r-build-system)
29638 (native-inputs (list r-knitr))
29639 (home-page "https://github.com/DavisVaughan/warp")
29640 (synopsis "Group dates")
29642 "This package provides tooling to group dates by a variety of periods
29643 including: yearly, monthly, by second, by week of the month, and more. The
29644 groups are defined in such a way that they also represent the distance between
29645 dates in terms of the period. This extracts valuable information that can be
29646 used in further calculations that rely on a specific temporal spacing between
29648 (license license:expat)))
29650 (define-public r-scico
29657 (uri (cran-uri "scico" version))
29659 (base32 "1f2czfhzdpi5dqjbxvbrrcnxjpylc5zzghj70ihlh2agq3n9hw5g"))))
29660 (properties `((upstream-name . "scico")))
29661 (build-system r-build-system)
29662 (propagated-inputs (list r-scales))
29663 (home-page "https://github.com/thomasp85/scico")
29664 (synopsis "Colour Palettes Based on the Scientific Colour-Maps")
29666 "This package provides colour choice in information visualisation. It
29667 important in order to avoid being mislead by inherent bias in the used colour
29668 palette. This package provides access to the perceptually uniform and
29669 colour-blindness friendly palettes developed by Fabio Crameri and released
29670 under the \"Scientific Colour-Maps\" moniker. The package contains 24
29671 different palettes and includes both diverging and sequential types.")
29672 (license license:expat)))
29674 (define-public r-slider
29681 (uri (cran-uri "slider" version))
29684 "1vxk2bc33svwcki2j8zr5jcxswh27i0fqgzjw2a5a1pp9dh3fmd3"))))
29685 (properties `((upstream-name . "slider")))
29686 (build-system r-build-system)
29688 (list r-ellipsis r-glue r-rlang r-vctrs r-warp))
29689 (native-inputs (list r-knitr))
29690 (home-page "https://github.com/DavisVaughan/slider")
29691 (synopsis "Sliding window functions")
29693 "This package provides type-stable rolling window functions over any R
29694 data type. Cumulative and expanding windows are also supported. For more
29695 advanced usage, an index can be used as a secondary vector that defines how
29696 sliding windows are to be created.")
29697 (license license:expat)))
29699 (define-public r-rlist
29702 (version "0.4.6.2")
29706 (uri (cran-uri "rlist" version))
29708 (base32 "15q99rhbbjq8zd976yjmfnny45dd5fg2p2dv1sljg2kwi66nbppb"))))
29709 (properties `((upstream-name . "rlist")))
29710 (build-system r-build-system)
29711 (propagated-inputs (list r-data-table r-jsonlite r-xml r-yaml))
29712 (home-page "https://renkun-ken.github.io/rlist/")
29713 (synopsis "A Toolbox for Non-Tabular Data Manipulation")
29715 "This package provides a set of functions for data manipulation with
29716 list objects, including mapping, filtering, grouping, sorting, updating,
29717 searching, and other useful functions. Most functions are designed to be
29718 pipeline friendly so that data processing with lists can be chained.")
29719 (license license:expat)))
29721 (define-public r-rsample
29728 (uri (cran-uri "rsample" version))
29731 "1iy61riwjch9z4m6k7whsrkl80sk9sww5lf1np4iq4vdfq6w01jb"))))
29732 (properties `((upstream-name . "rsample")))
29733 (build-system r-build-system)
29750 (home-page "https://rsample.tidymodels.org")
29751 (synopsis "General resampling infrastructure")
29753 "This package provides classes and functions to create and summarize
29754 different types of resampling objects (e.g. bootstrap, cross-validation).")
29755 (license license:gpl2)))
29757 (define-public r-dicedesign
29759 (name "r-dicedesign")
29764 (uri (cran-uri "DiceDesign" version))
29767 "1a8ixa65xgyfri03cviic8qi2plbhdyz8m02bwif8w94w0q3ghlk"))))
29768 (properties `((upstream-name . "DiceDesign")))
29769 (build-system r-build-system)
29770 (home-page "http://dice.emse.fr/")
29771 (synopsis "Designs of computer experiments")
29773 "This package provides tools to create some specific @code{Space-Filling
29774 Design} (SFD) and to test their quality.")
29775 (license license:gpl3)))
29777 (define-public r-dials
29784 (uri (cran-uri "dials" version))
29787 "0flpd7bxknsscv0gk6c7zz1aid9y3z6sibkvjp9zcyc5wnqldrvj"))))
29788 (properties `((upstream-name . "dials")))
29789 (build-system r-build-system)
29803 (native-inputs (list r-knitr))
29804 (home-page "https://dials.tidymodels.org/")
29805 (synopsis "Tools for creating tuning parameter values")
29807 "Many models contain tuning parameters (i.e. parameters that cannot be
29808 directly estimated from the data). These tools can be used to define objects
29809 for creating, simulating, or validating values for such parameters.")
29810 (license license:gpl2)))
29812 (define-public r-tune
29819 (uri (cran-uri "tune" version))
29822 "0jh29dy4gwa1fyi01fp1305hkxw1mpkx704j6kydplh8h09rv80p"))))
29823 (properties `((upstream-name . "tune")))
29824 (build-system r-build-system)
29848 (home-page "https://github.com/tidymodels/tune")
29849 (synopsis "Tidy tuning tools")
29851 "The ability to tune models is important. @code{tune} contains functions
29852 and classes to be used in conjunction with other @code{tidymodels} packages
29853 for finding reasonable values of hyper-parameters in models, pre-processing
29854 methods, and post-processing steps.")
29855 (license license:expat)))
29857 (define-public r-workflowsets
29859 (name "r-workflowsets")
29864 (uri (cran-uri "workflowsets" version))
29867 "12wj0m6kqnjh8k5k14kqh40wf14gzyg5l3shhbpr2lvk87l9ssqq"))))
29868 (properties `((upstream-name . "workflowsets")))
29869 (build-system r-build-system)
29892 (home-page "https://github.com/tidymodels/workflowsets")
29893 (synopsis "Create a collection of tidymodels workflows")
29895 "A workflow is a combination of a model and preprocessors (e.g, a
29896 formula, recipe, etc.). In order to try different combinations of these, an
29897 object can be created that contains many workflows. There are functions to
29898 create workflows en masse as well as training them and visualizing the
29900 (license license:expat)))
29902 (define-public r-tidyposterior
29904 (name "r-tidyposterior")
29909 (uri (cran-uri "tidyposterior" version))
29912 "19cyyhh417i5xcchb8kq3iycaf4y7aznr7y9r004h2k2vk3svc86"))))
29913 (properties `((upstream-name . "tidyposterior")))
29914 (build-system r-build-system)
29930 (home-page "https://tidyposterior.tidymodels.org")
29931 (synopsis "Bayesian analysis to compare models using resampling statistics")
29933 "This package can be used to conduct post hoc analyses of resampling
29934 results generated by models. For example, if two models are evaluated with
29935 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
29936 are 10 paired statistics. These can be used to make comparisons between
29937 models without involving a test set.")
29938 (license license:gpl2)))
29940 (define-public r-tidypredict
29942 (name "r-tidypredict")
29947 (uri (cran-uri "tidypredict" version))
29950 "0x0r36zvny4rqgndx7iqh39yhr53gl4d8wd8wpvdcgg35q6z02z2"))))
29951 (properties `((upstream-name . "tidypredict")))
29952 (build-system r-build-system)
29964 (home-page "https://tidypredict.tidymodels.org")
29965 (synopsis "Run predictions inside the database")
29967 "This package parses a fitted R model object, and returns a formula in
29968 Tidy Eval code that calculates the predictions. It works with several
29969 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
29970 final SQL translation of the algorithm. It currently supports @code{lm()},
29971 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
29972 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
29973 (license license:gpl3)))
29975 (define-public r-janeaustenr
29977 (name "r-janeaustenr")
29982 (uri (cran-uri "janeaustenr" version))
29985 "1ap8p1lpbj2wz90mpf1vbyzhv2spzv03bi8lwzpsir2y77hjxhxl"))))
29986 (properties `((upstream-name . "janeaustenr")))
29987 (build-system r-build-system)
29988 (home-page "https://github.com/juliasilge/janeaustenr")
29989 (synopsis "Jane Austen's complete novels")
29991 "This package provides the full texts for Jane Austen's six completed
29992 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
29993 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
29994 and \"Persuasion\".")
29995 (license license:expat)))
29997 (define-public r-janitor
30003 (uri (cran-uri "janitor" version))
30006 "09nqm957m2f54y2l30619b58x4i7gxwvr2lwg5kly5xy1ya1a1nn"))))
30007 (properties `((upstream-name . "janitor")))
30008 (build-system r-build-system)
30021 (native-inputs (list r-knitr))
30022 (home-page "https://github.com/sfirke/janitor")
30023 (synopsis "Simple tools for examining and cleaning dirty data")
30025 "The main janitor functions can: perfectly format @code{data.frame column}
30026 names; provide quick counts of variable combinations (i.e., frequency tables
30027 and crosstabs); and isolate duplicate records. Other janitor functions nicely
30028 format the tabulation results. These tabulate-and-report functions
30029 approximate popular features of SPSS and Excel. This package follows the
30030 principles of the \"tidyverse\" and works well with the pipe function
30031 @code{%>%}. janitor was built with beginning-to-intermediate R users in mind
30032 and is optimized for user-friendliness. Advanced R users can already do
30033 everything covered here, but with janitor they can do it faster and save their
30034 thinking for the fun stuff.")
30035 (license license:expat)))
30037 (define-public r-tokenizers
30039 (name "r-tokenizers")
30044 (uri (cran-uri "tokenizers" version))
30047 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
30048 (properties `((upstream-name . "tokenizers")))
30049 (build-system r-build-system)
30051 (list r-rcpp r-snowballc r-stringi))
30054 (home-page "https://lincolnmullen.com/software/tokenizers/")
30055 (synopsis "Fast, consistent tokenization of natural language text")
30057 "This is a package for converting natural language text into tokens.
30058 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
30059 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
30060 Treebank, regular expressions, as well as functions for counting characters,
30061 words, and sentences, and a function for splitting longer texts into separate
30062 documents, each with the same number of words. The tokenizers have a
30063 consistent interface, and the package is built on the @code{stringi} and
30064 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
30065 (license license:expat)))
30067 (define-public r-hunspell
30069 (name "r-hunspell")
30074 (uri (cran-uri "hunspell" version))
30077 "0kij39rhsx7s4lfddy6745f1zjyi003srj14ckjpbhkcyxamk8jy"))))
30078 (properties `((upstream-name . "hunspell")))
30079 (build-system r-build-system)
30081 (list r-digest r-rcpp))
30084 (home-page "https://github.com/ropensci/hunspell#readme")
30085 (synopsis "High-performance stemmer, tokenizer, and spell checker")
30087 "This package provides a low-level spell checker and morphological
30088 analyzer based on the famous @code{hunspell} library. The package can analyze
30089 or check individual words as well as parse text, LaTeX, HTML or XML documents.
30090 For a more user-friendly interface use the @code{spelling} package which
30091 builds on this package to automate checking of files, documentation and
30092 vignettes in all common formats.")
30093 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
30094 ;; MPL; in addition to these licenses the rest of the R wrapper is also
30095 ;; available under the Expat license.
30096 (license (list license:gpl2
30101 (define-public r-tidytext
30103 (name "r-tidytext")
30108 (uri (cran-uri "tidytext" version))
30111 "0mk75wdiy4mixj1xlksw9ns4ajlj8ak90sgchjcg1zb90qp7gg56"))))
30112 (properties `((upstream-name . "tidytext")))
30113 (build-system r-build-system)
30129 (home-page "https://github.com/juliasilge/tidytext")
30130 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
30132 "This is a package for text mining for word processing and sentiment
30133 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
30134 (license license:expat)))
30136 (define-public r-parsnip
30143 (uri (cran-uri "parsnip" version))
30146 "0pzr39jhlzjhm2nx1zcgd0mdxd4dxbdzhzc1qrvfsz05jwfb6xxy"))))
30147 (properties `((upstream-name . "parsnip")))
30148 (build-system r-build-system)
30169 (home-page "https://parsnip.tidymodels.org")
30170 (synopsis "Common API to modeling and analysis functions")
30172 "This package provides a common interface to allow users to specify a
30173 model without having to remember the different argument names across different
30174 functions or computational engines (e.g. R, Spark, Stan, etc).")
30175 (license license:gpl2)))
30177 (define-public r-infer
30184 (uri (cran-uri "infer" version))
30187 "1m5srhcmkh8wq12pvy57g3g703wilkl8r3gmm5s7lbj103iz7v8b"))))
30188 (properties `((upstream-name . "infer")))
30189 (build-system r-build-system)
30204 (home-page "https://github.com/tidymodels/infer")
30205 (synopsis "Tidy statistical inference")
30207 "The objective of this package is to perform inference using an
30208 expressive statistical grammar that coheres with the Tidy design framework.")
30209 (license license:cc0)))
30211 (define-public r-modeldata
30213 (name "r-modeldata")
30218 (uri (cran-uri "modeldata" version))
30221 "0ik4r25l69brkf0l248bln1kicy7dpi6mziwn19by8rq3f8fylhy"))))
30222 (properties `((upstream-name . "modeldata")))
30223 (build-system r-build-system)
30230 (home-page "https://modeldata.tidymodels.org")
30231 (synopsis "Data sets useful for modeling packages")
30233 "This package provides data sets used for demonstrating or testing
30234 model-related packages.")
30235 (license license:expat)))
30237 (define-public r-conflicted
30239 (name "r-conflicted")
30244 (uri (cran-uri "conflicted" version))
30247 "1qg9ar114r98wm0pnf65mss4v2ksq3924rlpm13mqp4s3p6j9yi4"))))
30248 (properties `((upstream-name . "conflicted")))
30249 (build-system r-build-system)
30251 (list r-memoise r-rlang))
30252 (home-page "https://github.com/r-lib/conflicted")
30253 (synopsis "Alternative conflict resolution strategy")
30255 "R's default conflict management system gives the most recently loaded
30256 package precedence. This can make it hard to detect conflicts, particularly
30257 when they arise because a package update creates ambiguity that did not
30258 previously exist. The @code{conflicted} package takes a different approach,
30259 making every conflict an error and forcing you to choose which function to
30261 (license license:gpl3)))
30263 (define-public r-tidymodels
30265 (name "r-tidymodels")
30270 (uri (cran-uri "tidymodels" version))
30273 "1zqdq7zwmhc19zs77x27l5ja01rhj01v8dw182j8jhy49h0alyz3"))))
30274 (properties `((upstream-name . "tidymodels")))
30275 (build-system r-build-system)
30300 (home-page "https://github.com/tidymodels/tidymodels")
30301 (synopsis "Tidy collection for modeling and statistical analysis")
30303 "The tidy modeling \"verse\" is a collection of packages for modeling and
30304 statistical analysis that share the underlying design philosophy, grammar, and
30305 data structures of the tidyverse.")
30306 (license license:gpl3)))
30308 (define-public r-lsa
30315 (uri (cran-uri "lsa" version))
30318 "16k1g0kh3yaw7azg76aqf3hn3b6jgqg92xx0syai8l0my9ci2zzh"))))
30319 (properties `((upstream-name . "lsa")))
30320 (build-system r-build-system)
30322 (list r-snowballc))
30323 (home-page "https://cran.r-project.org/package=lsa")
30324 (synopsis "Latent semantic analysis")
30326 "The basic idea of latent semantic analysis (LSA) is, that text do have a
30327 higher order (=latent semantic) structure which, however, is obscured by word
30328 usage (e.g. through the use of synonyms or polysemy). By using conceptual
30329 indices that are derived statistically via a truncated singular value
30330 decomposition (a two-mode factor analysis) over a given document-term matrix,
30331 this variability problem can be overcome.")
30332 (license license:gpl2+)))
30334 (define-public r-mlecens
30341 (uri (cran-uri "MLEcens" version))
30344 "0cdl0y44clds4sg8hikhk354a5xrfbyfg8lxrbh1bfg410rkj186"))))
30345 (properties `((upstream-name . "MLEcens")))
30346 (build-system r-build-system)
30347 (home-page "http://stat.ethz.ch/~maathuis/")
30348 (synopsis "Computation of the MLE for bivariate (interval) censored data")
30350 "This package contains functions to compute the nonparametric
30351 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
30352 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
30353 To be more precise, we consider the situation where we observe a set of
30354 rectangles that are known to contain the unobservable realizations of (X,Y).
30355 We compute the MLE based on such a set of rectangles. The methods can also be
30356 used for univariate censored data (see data set @code{cosmesis}), and for
30357 censored data with competing risks (see data set @code{menopause}). The
30358 package also provides functions to visualize the observed data and the MLE.")
30359 (license license:gpl2+)))
30361 (define-public r-metafor
30368 (uri (cran-uri "metafor" version))
30371 "05053cvk65fh2p4wrmygkvgqvrl73kz22rdbxsjxhi21jmzmg56n"))))
30372 (properties `((upstream-name . "metafor")))
30373 (build-system r-build-system)
30375 (list r-mathjaxr r-matrix r-metadat r-nlme r-pbapply))
30376 (home-page "https://cran.r-project.org/web/packages/metafor/")
30377 (synopsis "Meta-analysis package for R")
30379 "This package provides a comprehensive collection of functions for
30380 conducting meta-analyses in R. The package includes functions to calculate
30381 various effect sizes or outcome measures, fit fixed-, random-, and
30382 mixed-effects models to such data, carry out moderator and meta-regression
30383 analyses, and create various types of meta-analytical plots (e.g., forest,
30384 funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial
30385 and person-time data, the package also provides functions that implement
30386 specialized methods, including the Mantel-Haenszel method, Peto's method, and
30387 a variety of suitable generalized linear (mixed-effects) models (i.e.
30388 mixed-effects logistic and Poisson regression models). Finally, the package
30389 provides functionality for fitting meta-analytic multivariate/multilevel
30390 models that account for non-independent sampling errors and/or true
30391 effects (e.g. due to the inclusion of multiple treatment studies, multiple
30392 endpoints, or other forms of clustering). Network meta-analyses and
30393 meta-analyses accounting for known correlation structures (e.g. due to
30394 phylogenetic relatedness) can also be conducted.")
30395 (license license:gpl2+)))
30397 (define-public r-altmeta
30404 (uri (cran-uri "altmeta" version))
30407 "01v308389wqzp35icrp9ssb4y4gxwjzl600qw47c6rmm6s2mxzjh"))))
30408 (properties `((upstream-name . "altmeta")))
30409 (build-system r-build-system)
30411 (list r-coda r-lme4 r-matrix r-metafor r-rjags))
30412 (home-page "https://cran.r-project.org/web/packages/altmeta/")
30413 (synopsis "Alternative meta-analysis methods")
30415 "This package provides alternative statistical methods for meta-analysis,
30419 @item bivariate generalized linear mixed models for synthesizing odds ratios,
30420 relative risks, and risk differences
30421 @item heterogeneity tests and measures that are robust to outliers;
30422 @item measures, tests, and visualization tools for publication bias or
30423 small-study effects;
30424 @item meta-analysis of diagnostic tests for synthesizing sensitivities,
30425 specificities, etc.;
30426 @item meta-analysis methods for synthesizing proportions;
30427 @item models for multivariate meta-analysis.
30430 (license license:gpl2+)))
30432 (define-public r-perm
30435 (version "1.0-0.2")
30439 (uri (cran-uri "perm" version))
30442 "182ac1y91yzb34zwdcmx5fdfr5z0cha0gx2bgk36gwxhgfc994kj"))))
30443 (properties `((upstream-name . "perm")))
30444 (build-system r-build-system)
30445 (home-page "https://cran.r-project.org/web/packages/perm/")
30446 (synopsis "Exact or asymptotic permutation tests")
30448 "This package provides several methods for performing permutation tests.
30449 It has three main functions, to perform linear permutation tests. These tests
30450 are tests where the test statistic is the sum of the product of a
30451 covariate (usually group indicator) and the scores.")
30452 ;; Any version of the GPL
30453 (license license:gpl2+)))
30455 (define-public r-qtl
30462 (uri (cran-uri "qtl" version))
30465 "0q49g3ar1451whsl6ig7kz4mg8s9zxlcvgkj4ivyw4995wbwc2ij"))))
30466 (build-system r-build-system)
30467 (home-page "https://rqtl.org/")
30468 (synopsis "R package for analyzing QTL experiments in genetics")
30469 (description "R/qtl is an extension library for the R statistics system.
30470 It is used to analyze experimental crosses for identifying genes contributing
30471 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
30473 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
30474 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
30476 (license license:gpl3)))
30478 (define-public r-qtl2
30484 (uri (cran-uri "qtl2" version))
30486 (base32 "0ppc6dzlq77mppxc6bczai9gi40jrbxd1466y2cn2s8a4ah1jg9y"))))
30487 (build-system r-build-system)
30495 (home-page "https://kbroman.org/qtl2/")
30496 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
30498 "This package provides a set of tools to perform @dfn{Quantitative Trait
30499 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
30500 @code{R/qtl} package to better handle high-dimensional data and complex cross
30501 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
30502 (license license:gpl3)))
30504 (define-public r-seqminer
30506 (name "r-seqminer")
30511 (uri (cran-uri "seqminer" version))
30514 "1mbx1hw9dhgry7hhan43g6aiz2lyd5api7wxq3fwajyzjrc6p1g8"))))
30515 (build-system r-build-system)
30518 (home-page "http://seqminer.genomic.codes")
30519 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
30521 "This package provides tools to integrate nucleotide sequencing
30522 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
30523 ;; Any version of the GPL is acceptable
30524 (license (list license:gpl2+ license:gpl3+))))
30526 (define-public r-maldiquant
30528 (name "r-maldiquant")
30533 (uri (cran-uri "MALDIquant" version))
30536 "1y1g3819ss06dry70kfhg2syddw71682qmzkcyppfsma6hhghw87"))))
30537 (properties `((upstream-name . "MALDIquant")))
30538 (build-system r-build-system)
30541 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
30542 (synopsis "Quantitative analysis of mass spectrometry data")
30544 "This package provides a complete analysis pipeline for matrix-assisted
30545 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
30546 two-dimensional mass spectrometry data. In addition to commonly used plotting
30547 and processing methods it includes distinctive features, namely baseline
30548 subtraction methods such as morphological filters (TopHat) or the
30549 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
30550 alignment using warping functions, handling of replicated measurements as well
30551 as allowing spectra with different resolutions.")
30552 (license license:gpl3+)))
30554 (define-public r-scattermore
30556 (name "r-scattermore")
30561 (uri (cran-uri "scattermore" version))
30564 "1rgqm7r1k7j3h2y4i6d1a2y8fzivfcbmr7dj9d367c0w4vc77pfv"))))
30565 (properties `((upstream-name . "scattermore")))
30566 (build-system r-build-system)
30568 (list r-ggplot2 r-scales))
30569 (home-page "https://github.com/exaexa/scattermore")
30570 (synopsis "Scatterplots with more points")
30572 "This package provides C-based tools for converting large scatterplot
30573 data to rasters. It speeds up plotting of data with millions of points.")
30574 (license license:gpl3+)))
30576 (define-public r-seuratobject
30578 (name "r-seuratobject")
30583 (uri (cran-uri "SeuratObject" version))
30586 "03bd4fazcafaf5mp37cf9w6bxm9zwrlxkrqm9bjdnwxm07slanba"))))
30587 (properties `((upstream-name . "SeuratObject")))
30588 (build-system r-build-system)
30599 (home-page "https://satijalab.org/seurat")
30600 (synopsis "Data structures for single cell data")
30602 "This package defines S4 classes for single-cell genomic data and
30603 associated information, such as dimensionality reduction embeddings,
30604 nearest-neighbor graphs, and spatially-resolved coordinates. It provides data
30605 access methods and R-native hooks to ensure the Seurat object is familiar to
30607 (license license:gpl3)))
30609 (define-public r-seurat
30615 (uri (cran-uri "Seurat" version))
30618 "1klamxk6dj0jgpfwll5frcnj9h8lh8c5fxdn9ky7h8xk35lsj6i0"))))
30619 (properties `((upstream-name . "Seurat")))
30620 (build-system r-build-system)
30665 (home-page "http://www.satijalab.org/seurat")
30666 (synopsis "Seurat is an R toolkit for single cell genomics")
30668 "This package is an R package designed for QC, analysis, and
30669 exploration of single cell RNA-seq data. It easily enables widely-used
30670 analytical techniques, including the identification of highly variable genes,
30671 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
30672 algorithms; density clustering, hierarchical clustering, k-means, and the
30673 discovery of differentially expressed genes and markers.")
30674 (license license:gpl3)))
30676 (define-public r-seuratdisk
30677 (let ((commit "163f1aade5bac38ed1e9e9c912283a7e74781610")
30680 (name "r-seuratdisk")
30681 (version (git-version "0.0.0.9019" revision commit))
30685 (uri (git-reference
30686 (url "https://github.com/mojaveazure/seurat-disk")
30688 (file-name (git-file-name name version))
30690 (base32 "1d1v8qi6kknzy5fj6bl8akwy74h5h143i00lyidsnqjbwp9n4qnw"))))
30691 (properties `((upstream-name . "SeuratDisk")))
30692 (build-system r-build-system)
30706 (home-page "https://github.com/mojaveazure/seurat-disk")
30707 (synopsis "Interfaces for HDF5-based single cell file formats")
30709 "The h5Seurat file format is specifically designed for the storage and
30710 analysis of multi-modal single-cell and spatially-resolved expression
30711 experiments, for example, from CITE-seq or 10X Visium technologies. It holds
30712 all molecular information and associated metadata, including (for example)
30713 nearest-neighbor graphs, dimensional reduction information, spatial
30714 coordinates and image data, and cluster labels. This package also supports
30715 rapid and on-disk conversion between h5Seurat and AnnData objects, with the
30716 goal of enhancing interoperability between Seurat and Scanpy.")
30717 (license license:gpl3))))
30719 (define-public r-seuratdata
30720 (let ((commit "b59556b24d7d6728a5744c9c715dd5f7f32ed7a5")
30723 (name "r-seuratdata")
30724 (version (git-version "0.2.1" revision commit))
30728 (uri (git-reference
30729 (url "https://github.com/satijalab/seurat-data")
30731 (file-name (git-file-name name version))
30733 (base32 "1xfdmdmgn4r0z6w4cxa98ic6xk8i6qz054r215dvqbjs1vydsbf9"))))
30734 (properties `((upstream-name . "SeuratData")))
30735 (build-system r-build-system)
30738 (modify-phases %standard-phases
30739 ;; When there is no HOME directory, this package will fail to load
30740 ;; the included list of packages.
30741 (add-after 'unpack 'set-HOME
30742 (lambda _ (setenv "HOME" "/tmp"))))))
30744 (list r-cli r-crayon r-rappdirs))
30745 (home-page "https://github.com/satijalab/seurat-data")
30746 (synopsis "Install and manage Seurat datasets")
30748 "Single cell RNA sequencing datasets can be large, consisting of
30749 matrices that contain expression data for several thousand features across
30750 several thousand cells. This package is designed to easily install, manage,
30751 and learn about various single-cell datasets, provided Seurat objects and
30752 distributed as independent packages.")
30753 (license license:gpl3))))
30755 (define-public r-phangorn
30757 (name "r-phangorn")
30762 (uri (cran-uri "phangorn" version))
30765 "1kjxp352jdk1amxpk9jrql490d0qy79zm65y8szyxrm1adqghlyi"))))
30766 (build-system r-build-system)
30778 (home-page "https://github.com/KlausVigo/phangorn")
30779 (synopsis "Phylogenetic analysis in R")
30781 "Phangorn is a package for phylogenetic analysis in R. It supports
30782 estimation of phylogenetic trees and networks using Maximum Likelihood,
30783 Maximum Parsimony, distance methods and Hadamard conjugation.")
30784 (license license:gpl2+)))
30786 (define-public r-diversitree
30788 (name "r-diversitree")
30793 (uri (cran-uri "diversitree" version))
30796 "0rzrk7xsn4gy271pbcw3azndhx0c06bmsgrg6libjmlfnmq6j8sc"))))
30797 (build-system r-build-system)
30800 (inputs (list fftw gsl))
30802 (list r-ape r-desolve r-rcpp r-subplex))
30803 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
30804 (synopsis "Comparative 'phylogenetic' analyses of diversification")
30805 (description "This package contains a number of comparative \"phylogenetic\"
30806 methods, mostly focusing on analysing diversification and character evolution.
30807 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
30808 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
30809 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
30810 include Markov models of discrete and continuous trait evolution and constant
30811 rate speciation and extinction.")
30812 (license license:gpl2+)))
30814 (define-public r-calculus
30816 (name "r-calculus")
30821 (uri (cran-uri "calculus" version))
30824 "0hpibnbxl3ngfgzxq8cp9hxsn1yv03dnxyycm3gkr5iv5gkbbpw9"))))
30825 (properties `((upstream-name . "calculus")))
30826 (build-system r-build-system)
30831 (home-page "https://github.com/eguidotti/calculus")
30832 (synopsis "High dimensional numerical and symbolic calculus")
30834 "Efficient C++ optimized functions for numerical and symbolic calculus.
30835 It includes basic symbolic arithmetic, tensor calculus, Einstein summing
30836 convention, fast computation of the Levi-Civita symbol and generalized
30837 Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
30838 accurate high-order derivatives, differential operators (Gradient, Jacobian,
30839 Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
30840 orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
30841 parabolic or user defined by custom scale factors.")
30842 (license license:gpl3)))
30844 (define-public r-decon
30851 (uri (cran-uri "decon" version))
30854 "036cv56wf42q2p3d5h15hbrp5rc29xxy20qwv4k1qzhkq6hmw0qs"))))
30855 (properties `((upstream-name . "decon")))
30856 (build-system r-build-system)
30860 "https://cran.r-project.org/web/packages/decon/")
30861 (synopsis "Deconvolution Estimation in Measurement Error Models")
30863 "This package contains a collection of functions to deal with
30864 nonparametric measurement error problems using deconvolution
30865 kernel methods. We focus two measurement error models in the
30866 package: (1) an additive measurement error model, where the
30867 goal is to estimate the density or distribution function from
30868 contaminated data; (2) nonparametric regression model with
30869 errors-in-variables. The R functions allow the measurement errors
30870 to be either homoscedastic or heteroscedastic. To make the
30871 deconvolution estimators computationally more efficient in R,
30872 we adapt the \"Fast Fourier Transform\" (FFT) algorithm for
30873 density estimation with error-free data to the deconvolution
30874 kernel estimation. Several methods for the selection of the
30875 data-driven smoothing parameter are also provided in the package.
30876 See details in: Wang, X.F. and Wang, B. (2011). Deconvolution
30877 estimation in measurement error models: The R package decon.
30878 Journal of Statistical Software, 39(10), 1-24.")
30879 (license license:gpl3+)))
30881 (define-public r-densestbayes
30883 (name "r-densestbayes")
30884 (version "1.0-2.1")
30888 (uri (cran-uri "densEstBayes" version))
30890 (base32 "1pzmgn65lv91zg1588qhwczy9f2zgciknlc4l072mvh2i7hncw2b"))))
30891 (properties `((upstream-name . "densEstBayes")))
30892 (build-system r-build-system)
30904 (home-page "https://cran.r-project.org/package=densEstBayes")
30905 (synopsis "Density estimation via Bayesian inference engines")
30907 "Bayesian density estimates for univariate continuous random samples are
30908 provided using the Bayesian inference engine paradigm. The engine options
30909 are: Hamiltonian Monte Carlo, the no U-turn sampler, semiparametric mean field
30910 variational Bayes and slice sampling. The methodology is described in Wand
30911 and Yu (2020), arXiv:2009.06182.")
30912 (license license:gpl2+)))
30914 (define-public r-locpol
30921 (uri (cran-uri "locpol" version))
30924 "1p915n0l09kbwkly627074jslxl01yssp1rf0c7sygvsw6sgy5lm"))))
30925 (properties `((upstream-name . "locpol")))
30926 (build-system r-build-system)
30928 "https://cran.r-project.org/web/packages/locpol/")
30929 (synopsis "Kernel Local Polynomial Regression")
30931 "Computes local polynomial estimators for the regression and
30932 also density. It comprises several different utilities to handle
30933 kernel estimators.")
30934 (license license:gpl2+)))
30936 (define-public r-lpme
30943 (uri (cran-uri "lpme" version))
30946 "1ch11cwjci98m7952p9wdsh9fj5y1mjya6ayq0q4wmbm824qfpzb"))))
30947 (properties `((upstream-name . "lpme")))
30948 (build-system r-build-system)
30950 (list r-decon r-flexmix r-locpol r-rcpp r-rcpparmadillo))
30952 "https://cran.r-project.org/web/packages/lpme/")
30953 (synopsis "Nonparametric Estimation of Measurement Error Models")
30955 "Provide nonparametric methods for mean regression model,
30956 modal regression and conditional density estimation in the
30957 presence/absence of measurement error. Bandwidth selection is
30958 also provided for each method.")
30959 (license license:gpl2+)))
30961 (define-public r-aws-signature
30963 (name "r-aws-signature")
30968 (uri (cran-uri "aws.signature" version))
30971 "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp"))))
30972 (properties `((upstream-name . "aws.signature")))
30973 (build-system r-build-system)
30975 (list r-base64enc r-digest))
30976 (home-page "https://github.com/cloudyr/aws.signature")
30977 (synopsis "Amazon Web Services Request Signatures")
30979 "This package generates version 2 and 4 request signatures for Amazon Web
30980 Services (AWS) and provides a mechanism for retrieving credentials from
30981 environment variables, AWS credentials files, and EC2 instance metadata. For
30982 use on EC2 instances, the package 'aws.ec2metadata' is suggested.")
30983 (license license:gpl2+)))
30985 (define-public r-aws-s3
30992 (uri (cran-uri "aws.s3" version))
30995 "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx"))))
30996 (properties `((upstream-name . "aws.s3")))
30997 (build-system r-build-system)
30999 (list r-aws-signature
31005 (home-page "https://github.com/cloudyr/aws.s3")
31006 (synopsis "AWS S3 Client Package")
31008 "This package provides a simple client package for the Amazon Web
31009 Services (AWS) Simple Storage Service (S3) REST API.")
31010 (license license:gpl2+)))
31012 (define-public r-lgr
31018 (uri (cran-uri "lgr" version))
31021 "09x1vw6cnc1c0p0ylcz1q1vcxyaf1kljhh7ni3gl5jm19zii2h4c"))))
31022 (build-system r-build-system)
31027 (home-page "https://s-fleck.github.io/lgr/")
31028 (synopsis "Fully featured logging framework")
31029 (description "This package offers a flexible, feature-rich yet
31030 light-weight logging framework based on @code{R6} classes. It supports
31031 hierarchical loggers, custom log levels, arbitrary data fields in log events,
31032 logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as
31033 well as email and push notifications.")
31034 (license license:expat)))
31036 (define-public r-mhg
31043 (uri (cran-uri "mHG" version))
31046 "1rz5ncrvvv9h9grls15apa63v2nh9j87fmp4mwjjil37jx6a5zki"))))
31047 (properties `((upstream-name . "mHG")))
31048 (build-system r-build-system)
31049 (home-page "https://cran.r-project.org/package=mHG")
31050 (synopsis "Minimum-hypergeometric test")
31052 "This package runs a minimum-hypergeometric (mHG) test as described in
31053 \"Discovering Motifs in Ranked Lists of DNA Sequences\" by Eran Eden.")
31054 (license license:gpl2)))
31056 (define-public r-mlr3measures
31058 (name "r-mlr3measures")
31062 (uri (cran-uri "mlr3measures" version))
31065 "0k0i1xx63lds1870p2ljy1dlp2i376gdd0sq9s4xiqljqjb8va57"))))
31066 (build-system r-build-system)
31068 (list r-checkmate r-prroc))
31069 (home-page "https://mlr3measures.mlr-org.com/")
31070 (synopsis "Performance measures for mlr3")
31071 (description "This package implements multiple performance measures for
31072 supervised learning. It includes over 40 measures for regression and
31073 classification. Additionally, meta information about the performance measures
31074 can be queried, e.g. what the best and worst possible performances scores
31076 (license license:lgpl3)))
31078 (define-public r-mlr3misc
31080 (name "r-mlr3misc")
31084 (uri (cran-uri "mlr3misc" version))
31087 "1wnzyij1x67smkb3gjb9gpp7iy5andfl0s1c78xx4wylhycc6m11"))))
31088 (build-system r-build-system)
31090 (list r-backports r-checkmate r-data-table r-digest r-r6))
31091 (home-page "https://mlr3misc.mlr-org.com/")
31092 (synopsis "Helper functions for mlr3")
31093 (description "@code{mlr3misc} provides frequently used helper functions
31094 and assertions used in @code{mlr3} and its companion packages. It comes with
31095 helper functions for functional programming, for printing, to work with
31096 @code{data.table}, as well as some generally useful @code{R6} classes. This
31097 package also supersedes the package @code{BBmisc}.")
31098 (license license:lgpl3)))
31100 (define-public r-mlr3pipelines
31102 (name "r-mlr3pipelines")
31106 (uri (cran-uri "mlr3pipelines" version))
31109 "1zz55i8c08znxpcs6gp5inaw96c6la9wnsla0972ankvj1hsrcr2"))))
31110 (build-system r-build-system)
31122 (home-page "https://mlr3pipelines.mlr-org.com/")
31123 (synopsis "Preprocessing Operators and Pipelines for @code{mlr3}")
31124 (description "@code{mlr3pipelines} enriches @code{mlr3} with a diverse
31125 set of pipelining operators (PipeOps) that can be composed into graphs.
31126 Operations exist for data preprocessing, model fitting, and ensemble learning.
31127 Graphs can themselves be treated as @code{mlr3} Learners and can therefore be
31128 resampled, benchmarked, and tuned.")
31129 (license license:lgpl3)))
31131 (define-public r-mlr3ordinal
31132 (let ((commit "736e3a39be6b7088b650297cc6d90208ec58c0d7")
31135 (name "r-mlr3ordinal")
31136 (version (git-version "0.1.0-9000" revision commit))
31139 (uri (git-reference
31140 (url "https://github.com/mlr-org/mlr3ordinal")
31142 (file-name (git-file-name name version))
31145 "0ipf6n4m6giicn0x7f3lrfmbqkhw8zkz32hzq2xf209wndkqhqm1"))))
31146 (build-system r-build-system)
31157 (home-page "https://mlr3ordinal.mlr-org.com/")
31158 (synopsis "Ordinal Regression for mlr3")
31159 (description "This package extends @code{mlr3} with support for
31160 performing ordinal regression.")
31161 (license license:expat))))
31163 (define-public r-paradox
31169 (uri (cran-uri "paradox" version))
31172 "08h92wk8splf0w3rach9zbk3xz13phgcd1yybmgbs0sj4vx93whd"))))
31173 (build-system r-build-system)
31175 (list r-backports r-checkmate r-data-table r-mlr3misc r-r6))
31176 (home-page "https://paradox.mlr-org.com/")
31177 (synopsis "Define and work with parameter spaces for complex algorithms")
31178 (description "With this package it is possible to define parameter spaces,
31179 constraints and dependencies for arbitrary algorithms, and to program on such
31180 spaces. It also includes statistical designs and random samplers. Objects are
31181 implemented as @code{R6} classes.")
31182 (license license:lgpl3)))
31184 (define-public r-mlr3
31190 (uri (cran-uri "mlr3" version))
31193 "0cnyby4947g1w0h45nd3ld5zr4k19xrwp565mq1hnqkjwmyjsgdj"))))
31194 (build-system r-build-system)
31211 (home-page "https://mlr3.mlr-org.com/")
31212 (synopsis "Machine Learning in R - Next Generation")
31213 (description "@code{mlr3} enables efficient, object-oriented programming
31214 on the building blocks of machine learning. It provides @code{R6} objects for
31215 tasks, learners, resamplings, and measures. The package is geared towards
31216 scalability and larger datasets by supporting parallelization and out-of-memory
31217 data-backends like databases. While @code{mlr3} focuses on the core
31218 computational operations, add-on packages provide additional functionality.")
31219 (license license:lgpl3)))
31221 (define-public r-mlr3learners
31223 (name "r-mlr3learners")
31227 (uri (cran-uri "mlr3learners" version))
31230 "0sa2qjvhvjzsfssln9ah08zknzdcps1z28xzgkdfgi6dj25a0y3k"))))
31231 (build-system r-build-system)
31239 (home-page "https://mlr3learners.mlr-org.com/")
31240 (synopsis "Recommended Learners for @code{mlr3}")
31241 (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba}
31242 with interfaces to essential machine learning packages on CRAN. This includes,
31243 but is not limited to: (penalized) linear and logistic regression, linear and
31244 quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support
31245 vector machines, and gradient boosting.")
31246 (license license:lgpl3)))
31248 (define-public r-bbotk
31255 (uri (cran-uri "bbotk" version))
31258 "02dp0b62dv02rvxsgj63mkmmcdzrlf06vxjr5gqy9rhq5s2mg4fa"))))
31259 (properties `((upstream-name . "bbotk")))
31260 (build-system r-build-system)
31270 (home-page "https://bbotk.mlr-org.com")
31271 (synopsis "Black-Box Optimization Toolkit")
31272 (description "This package provides a common framework for optimization of
31273 black-box functions for other packages, e.g. @code{mlr3}. It offers various
31274 optimization methods e.g. grid search, random search and generalized simulated
31276 (license license:lgpl3)))
31278 (define-public r-mlr3tuning
31280 (name "r-mlr3tuning")
31284 (uri (cran-uri "mlr3tuning" version))
31287 "10q4m37sg79y1v0gwk7bjrnc5b0a6sb80ramnza93mx9gx3vl99m"))))
31288 (build-system r-build-system)
31298 (home-page "https://mlr3tuning.mlr-org.com/")
31299 (synopsis "Tuning for @code{mlr3}")
31300 (description "@code{mlr3tuning} implements methods for hyperparameter
31301 tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various
31302 termination criteria can be set and combined. The class @code{AutoTuner} provides a
31303 convenient way to perform nested resampling in combination with @code{mlr3}.")
31304 (license license:lgpl3)))
31306 (define-public r-fontliberation
31308 (name "r-fontliberation")
31313 (uri (cran-uri "fontLiberation" version))
31316 "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc"))))
31318 `((upstream-name . "fontLiberation")))
31319 (build-system r-build-system)
31320 (home-page "https://cran.r-project.org/package=fontLiberation")
31321 (synopsis "Liberation fonts")
31323 "This package provides a placeholder for the Liberation fontset intended
31324 for the fontquiver package. This fontset covers the 12 combinations of
31325 families (sans, serif, mono) and faces (plain, bold, italic, bold italic)
31326 supported in R graphics devices.")
31327 (license license:silofl1.1)))
31329 (define-public r-fontbitstreamvera
31331 (name "r-fontbitstreamvera")
31336 (uri (cran-uri "fontBitstreamVera" version))
31339 "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j"))))
31341 `((upstream-name . "fontBitstreamVera")))
31342 (build-system r-build-system)
31343 (home-page "https://cran.r-project.org/package=fontBitstreamVera")
31344 (synopsis "Fonts for fontquiver")
31346 "This package is a placeholder for the Bitstream Vera font. It is
31347 intended for the fontquiver package.")
31349 (license:fsdg-compatible
31350 "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts"
31351 "The Font Software may be sold as part of a larger software package but
31352 no copy of one or more of the Font Software typefaces may be sold by
31355 (define-public r-fontquiver
31357 (name "r-fontquiver")
31362 (uri (cran-uri "fontquiver" version))
31365 "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm"))))
31366 (properties `((upstream-name . "fontquiver")))
31367 (build-system r-build-system)
31369 (list r-fontbitstreamvera r-fontliberation))
31370 (home-page "https://cran.r-project.org/package=fontquiver")
31371 (synopsis "Set of installed fonts")
31373 "This package provides a set of fonts. This is useful when you want to
31374 avoid system fonts to make sure your outputs are reproducible.")
31375 (license license:gpl3)))
31377 (define-public r-freetypeharfbuzz
31379 (name "r-freetypeharfbuzz")
31384 (uri (cran-uri "freetypeharfbuzz" version))
31387 "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7"))))
31389 `((upstream-name . "freetypeharfbuzz")))
31390 (build-system r-build-system)
31393 (modify-phases %standard-phases
31394 (add-after 'unpack 'prepare-static-libraries
31395 (lambda* (#:key inputs #:allow-other-keys)
31396 (mkdir-p "src/target/include")
31397 (let ((freetype (assoc-ref inputs "static-freetype"))
31398 (harfbuzz (assoc-ref inputs "static-harfbuzz")))
31399 (substitute* "src/Makevars.in"
31400 (("include @MK_FILE@") "") ; do not build static libs
31401 (("^HB_STATIC_LIB =.*")
31402 (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n"))
31403 (("^FT_STATIC_LIB =.*")
31404 (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n")))
31405 (copy-recursively (string-append freetype "/include")
31406 "src/target/include")
31407 (copy-recursively (string-append harfbuzz "/include")
31408 "src/target/include")))))))
31410 (list r-fontquiver))
31411 ;; This may defeat the purpose of this package as our versions of freetype
31412 ;; and harfbuzz obviously differ from the tarballs offered by this
31413 ;; project. On the other hand, Guix arguably does a better job at
31414 ;; "ensur[ing] deterministic computation".
31416 `(("static-freetype"
31418 (inherit (static-package freetype))
31420 `(#:configure-flags
31421 (list "--enable-static=yes"
31426 "--without-harfbuzz")))))
31429 (inherit (static-package harfbuzz))
31431 `(#:tests? #false ; fail because shared library is disabled
31433 (list "--enable-static=yes"
31434 "--enable-shared=no"
31436 "--with-freetype=yes"
31439 "--without-fontconfig"
31440 "--without-glib")))))))
31443 (home-page "https://cran.r-project.org/package=freetypeharfbuzz")
31444 (synopsis "Deterministic computation of text box metrics")
31446 "Unlike other tools that dynamically link to the Cairo stack,
31447 freetypeharfbuzz is statically linked to specific versions of the FreeType and
31448 harfbuzz libraries. This ensures deterministic computation of text box
31449 extents for situations where reproducible results are crucial (for instance
31450 unit tests of graphics).")
31451 (license license:gpl3)))
31453 (define-public r-vdiffr
31460 (uri (cran-uri "vdiffr" version))
31463 "1z8nn8yh6jfzb9r7ylmigwh1p30lrclqm6khmp323qqphzmzfdwy"))))
31464 (properties `((upstream-name . "vdiffr")))
31465 (build-system r-build-system)
31467 (list libpng zlib))
31477 (home-page "https://github.com/r-lib/vdiffr")
31478 (synopsis "Visual regression testing and graphical diffing")
31480 "This package is an extension to the testthat package that makes it easy
31481 to add graphical unit tests. It provides a Shiny application to manage the
31483 (license license:gpl3)))
31485 (define-public r-highlight
31487 (name "r-highlight")
31492 (uri (cran-uri "highlight" version))
31495 "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf"))))
31496 (properties `((upstream-name . "highlight")))
31497 (build-system r-build-system)
31498 (home-page "https://github.com/hadley/highlight")
31499 (synopsis "Syntax highlighter for R code")
31501 "This package provides a syntax highlighter for R code based on the
31502 results of the R parser. It supports rendering in HTML and LaTeX markup. It
31503 includes a custom Sweave driver performing syntax highlighting of R code
31505 (license license:gpl3+)))
31507 (define-public r-clustree
31509 (name "r-clustree")
31514 (uri (cran-uri "clustree" version))
31517 "1haam13aifak8fladyxwa0gz56anj1zfczfjgs07gbw90kf6azx8"))))
31518 (properties `((upstream-name . "clustree")))
31519 (build-system r-build-system)
31532 (home-page "https://github.com/lazappi/clustree")
31533 (synopsis "Visualize clusterings at different resolutions")
31535 "Deciding what resolution to use can be a difficult question when
31536 approaching a clustering analysis. One way to approach this problem is to
31537 look at how samples move as the number of clusters increases. This package
31538 allows you to produce clustering trees, a visualization for interrogating
31539 clusterings as resolution increases.")
31540 (license license:gpl3)))
31542 (define-public r-textshaping
31544 (name "r-textshaping")
31549 (uri (cran-uri "textshaping" version))
31552 "1niaj1dh09rqrg9hrh98ddnc0f2nkyq9iizv24lcwm9gjs3w1ql0"))))
31553 (properties `((upstream-name . "textshaping")))
31554 (build-system r-build-system)
31556 (list freetype fribidi harfbuzz zlib))
31558 (list r-cpp11 r-systemfonts))
31560 (list pkg-config r-knitr))
31561 (home-page "https://github.com/r-lib/textshaping")
31562 (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping")
31564 "This package provides access to the text shaping functionality in the
31565 HarfBuzz library and the bidirectional algorithm in the Fribidi library. This
31566 is a low-level utility package mainly for graphic devices that expands upon
31567 the font tool-set provided by the @code{systemfonts} package.")
31568 (license license:expat)))
31570 (define-public r-ragg
31577 (uri (cran-uri "ragg" version))
31580 "1q43pwmljsqgrikkh2g1n7bpz9c8py5dnj44cfg3y2br7b4m2q9v"))))
31581 (properties `((upstream-name . "ragg")))
31582 (build-system r-build-system)
31584 (list freetype libjpeg-turbo libpng libtiff zlib))
31586 (list r-systemfonts r-textshaping))
31589 (home-page "https://ragg.r-lib.org")
31590 (synopsis "Graphic devices based on AGG")
31592 "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D
31593 drawing library. The ragg package provides a set of graphic devices based on
31594 AGG to use as alternative to the raster devices provided through the
31595 @code{grDevices} package.")
31596 (license license:expat)))
31598 (define-public r-downlit
31605 (uri (cran-uri "downlit" version))
31608 "0g3yncj3gmaqsc6cw7g9slgvd0kfk2414yz5m1dilk8h15lzdprk"))))
31609 (properties `((upstream-name . "downlit")))
31610 (build-system r-build-system)
31622 (home-page "https://downlit.r-lib.org/")
31623 (synopsis "Syntax highlighting and automatic linking")
31625 "This package provides syntax highlighting of R code, specifically
31626 designed for the needs of RMarkdown packages like @code{pkgdown},
31627 @code{hugodown}, and @code{bookdown}. It includes linking of function calls
31628 to their documentation on the web, and automatic translation of ANSI escapes
31629 in output to the equivalent HTML.")
31630 (license license:expat)))
31632 (define-public r-pkgdown
31639 (uri (cran-uri "pkgdown" version))
31642 "0sbz3kzd0hbdnszylsb281arldn2z1c9yxifhj4zv2dilp46b6nj"))))
31643 (properties `((upstream-name . "pkgdown")))
31644 (build-system r-build-system)
31645 (inputs (list pandoc))
31669 (home-page "https://pkgdown.r-lib.org")
31670 (synopsis "Make static HTML documentation for an R package")
31672 "The goal of this package is to generate an attractive and useful website
31673 from a source package. @code{pkgdown} converts your documentation, vignettes,
31674 README file, and more to HTML making it easy to share information about your
31676 (license license:expat)))
31678 (define-public r-prereg
31685 (uri (cran-uri "prereg" version))
31688 "039nrl5cirsx1ysh214dr6xnn1h6h3f90im6k9dgmzfksxdqigpw"))))
31689 (properties `((upstream-name . "prereg")))
31690 (build-system r-build-system)
31693 ;; The package provides a custom LaTex template in
31694 ;; inst/rmd/prereg_form.tex, which depends on these packages:
31698 texlive-generic-iftex
31699 texlive-latex-fancyhdr
31700 texlive-latex-fancyvrb
31701 texlive-latex-geometry
31702 texlive-latex-graphics
31703 texlive-latex-threeparttable
31704 texlive-latex-titlesec
31705 texlive-latex-upquote
31707 texlive-polyglossia
31711 (texlive-updmap.cfg (list texlive-amsfonts texlive-lm))))
31712 (home-page "https://github.com/crsh/prereg")
31714 "R Markdown Templates to preregister Scientific Studies")
31716 "This package provides a collection of templates to author
31717 preregistration documents for scientific studies in PDF format.")
31718 (license license:gpl3)))
31720 (define-public r-ez
31727 (uri (cran-uri "ez" version))
31730 "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq"))))
31731 (properties `((upstream-name . "ez")))
31732 (build-system r-build-system)
31744 (home-page "https://github.com/mike-lawrence/ez")
31745 (synopsis "Easy Analysis and Visualization of Factorial Experiments")
31747 "Facilitates easy analysis of factorial experiments, including purely
31748 within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss designs,
31749 and mixed within-and-between-Ss designs. The functions in this package aim to
31750 provide simple, intuitive and consistent specification of data analysis and
31751 visualization. Visualization functions also include design visualization for
31752 pre-analysis data auditing, and correlation matrix visualization. Finally,
31753 this package includes functions for non-parametric analysis, including
31754 permutation tests and bootstrap resampling. The bootstrap function obtains
31755 predictions either by cell means or by more advanced/powerful mixed effects
31756 models, yielding predictions and confidence intervals that may be easily
31757 visualized at any level of the experiment's design.")
31758 (license license:gpl2+)))
31760 (define-public r-qdapregex
31762 (name "r-qdapregex")
31767 (uri (cran-uri "qdapRegex" version))
31770 "1hdilycwrvi0q6cx7k8vg87bamm2xsafjkya5x4smxysm5k1r4qb"))))
31771 (properties `((upstream-name . "qdapRegex")))
31772 (build-system r-build-system)
31773 (propagated-inputs (list r-stringi))
31775 "https://trinker.github.com/qdapRegex/")
31777 "Regular Expression Removal, Extraction, and Replacement Tools")
31779 "This package provides a collection of regular expression tools
31780 associated with the @code{qdap} package that may be useful outside of the
31781 context of discourse analysis. Tools include removal/extraction/replacement of
31782 abbreviations, dates, dollar amounts, email addresses, hash tags, numbers,
31783 percentages, citations, person tags, phone numbers, times, and zip codes.")
31784 (license license:gpl2)))
31786 (define-public r-mgsub
31793 (uri (cran-uri "mgsub" version))
31796 "1mci6x65h94qiz9cwikx2inbrwkykv43zbs8abfbx416zrh2bbn9"))))
31797 (properties `((upstream-name . "mgsub")))
31798 (build-system r-build-system)
31799 (native-inputs (list r-knitr))
31801 "https://cran.r-project.org/package=mgsub")
31803 "Safe, Multiple, Simultaneous String Substitution")
31805 "Designed to enable simultaneous substitution in strings in a safe
31806 fashion. Safe means it does not rely on placeholders (which can cause errors
31807 in same length matches).")
31808 (license license:expat)))
31810 (define-public r-textshape
31812 (name "r-textshape")
31817 (uri (cran-uri "textshape" version))
31820 "0k9injxykgj2qprc7dygd7gafvcbh3r9x84qzaa1al21pk0dz7ds"))))
31821 (properties `((upstream-name . "textshape")))
31822 (build-system r-build-system)
31824 (list r-data-table r-slam r-stringi))
31825 (home-page "https://github.com/trinker/textshape")
31826 (synopsis "Tools for Reshaping Text")
31828 "Tools that can be used to reshape and restructure text data.")
31829 (license license:gpl2)))
31831 (define-public r-syuzhet
31838 (uri (cran-uri "syuzhet" version))
31841 "16iccqdbw02iw82nah6kwz3gwfghi864j2y698n4b9dyc386ijzv"))))
31842 (properties `((upstream-name . "syuzhet")))
31843 (build-system r-build-system)
31852 (native-inputs (list r-knitr))
31853 (home-page "https://github.com/mjockers/syuzhet")
31855 "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text")
31857 "Extracts sentiment and sentiment-derived plot arcs from text using a
31858 variety of sentiment dictionaries conveniently packaged for consumption by R
31859 users. Implemented dictionaries include @dfn{syuzhet} (default) developed in the
31860 Nebraska Literary Lab, @dfn{afinn} developed by Finn Arup Nielsen, @dfn{bing}
31861 developed by Minqing Hu and Bing Liu, and @dfn{nrc} developed by Mohammad, Saif
31862 M. and Turney, Peter D. Applicable references are available in
31863 @file{README.md} and in the documentation for the @code{get_sentiment}
31864 function. The package also provides a hack for implementing Stanford's coreNLP
31865 sentiment parser. The package provides several methods for plot arc
31867 (license license:gpl3)))
31869 (define-public r-lexicon
31876 (uri (cran-uri "lexicon" version))
31879 "0x7rscsh6par2lj11sby7bmz41cxn63iiw51lgh29z09cg8j606c"))))
31880 (properties `((upstream-name . "lexicon")))
31881 (build-system r-build-system)
31883 (list r-data-table r-syuzhet))
31884 (home-page "https://github.com/trinker/lexicon")
31885 (synopsis "Lexicons for Text Analysis")
31887 "This package provides a collection of lexical hash tables, dictionaries,
31889 (license license:gpl3)))
31891 (define-public r-english
31898 (uri (cran-uri "english" version))
31901 "1g3nmy5p8wj3ix1vp1qmkmy3dyqisrw0md8cjrx4klqkp0wqlms9"))))
31902 (properties `((upstream-name . "english")))
31903 (build-system r-build-system)
31904 (native-inputs (list r-knitr))
31906 "https://cran.r-project.org/package=english")
31907 (synopsis "Translate Integers into English")
31909 "Allow numbers to be presented in an English language version, one, two,
31910 three, ... Ordinals are also available, first, second, third, ... and
31911 indefinite article choice, \"a\" or \"an\".")
31912 (license license:gpl2)))
31914 (define-public r-textclean
31916 (name "r-textclean")
31921 (uri (cran-uri "textclean" version))
31924 "0kgjh6c4f14qkjc4fds7q7rpf4nkma3p0igm54fplmm3p853nvrz"))))
31925 (properties `((upstream-name . "textclean")))
31926 (build-system r-build-system)
31937 "https://github.com/trinker/textclean")
31938 (synopsis "Text Cleaning Tools")
31940 "Tools to clean and process text. Tools are geared at checking for
31941 substrings that are not optimal for analysis and replacing or removing them
31942 (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen,
31943 Kumar, Ostendorf, & Richards (2001) @url{doi:10.1006/csla.2001.0169}) or
31944 extracting them into new variables. For example, emoticons are often used in
31945 text but not always easily handled by analysis algorithms. The
31946 @code{replace_emoticon()} function replaces emoticons with word equivalents.")
31947 (license license:gpl2)))
31949 (define-public r-striprtf
31951 (name "r-striprtf")
31956 (uri (cran-uri "striprtf" version))
31959 "0dqcsh3fb8j0mmmxvxjl77rryhmrjm7a3scqvk2xkgxk4xq6q316"))))
31960 (properties `((upstream-name . "striprtf")))
31961 (build-system r-build-system)
31963 (list r-magrittr r-rcpp r-stringr))
31964 (home-page "https://github.com/kota7/striprtf")
31965 (synopsis "Extract Text from RTF File")
31967 "Extracts plain text from @dfn{Rich Text Format} (RTF) file.")
31968 (license license:expat)))
31970 (define-public r-ndjson
31977 (uri (cran-uri "ndjson" version))
31980 "0lvzbgfi1sg4kya1mvv67z14qk3vz9q57x22qh57xq8ampdkg812"))
31981 (modules '((guix build utils)))
31984 ;; unvendor gzstream
31985 (for-each delete-file '("src/gzstream.cpp" "src/gzstream.h"))
31987 (properties `((upstream-name . "ndjson")))
31988 (build-system r-build-system)
31991 (modify-phases %standard-phases
31992 (add-after 'unpack 'use-system-gzstream
31993 (lambda* (#:key inputs #:allow-other-keys)
31994 (substitute* "src/Makevars"
31995 (("PKG_LIBS = " all)
31996 (string-append all "-lgzstream ")))
31998 (inputs (list zlib gzstream))
32000 (list r-data-table r-rcpp r-tibble))
32001 (home-page "https://gitlab.com/hrbrmstr/ndjson")
32003 "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader")
32005 "@dfn{Streaming JSON} (ndjson) has one JSON record per-line and many
32006 modern ndjson files contain large numbers of records. These constructs may not
32007 be columnar in nature, but it is often useful to read in these files and
32008 \"flatten\" the structure out to enable working with the data in an R
32009 @code{data.frame}-like context. Functions are provided that make it possible
32010 to read in plain ndjson files or compressed (@code{gz}) ndjson files and either
32011 validate the format of the records or create \"flat\" @code{data.table}
32012 structures from them.")
32013 (license license:expat)))
32015 (define-public r-streamr
32022 (uri (cran-uri "streamR" version))
32025 "1clx3b0j2515r1nmnl6ki7qw5n54q3x2jvqv3zrc00kq71mlj7ix"))))
32026 (properties `((upstream-name . "streamR")))
32027 (build-system r-build-system)
32029 (list r-ndjson r-rcurl r-rjson))
32031 "https://cran.r-project.org/package=streamR")
32033 "Access to Twitter Streaming API via R")
32035 "This package provides functions to access Twitter's filter, sample, and
32036 user streams, and to parse the output into data frames.")
32037 (license license:gpl2)))
32039 (define-public r-readods
32046 (uri (cran-uri "readODS" version))
32049 "1hi217ab7hp15jsbzi5ak57cqf8jn2rv78bnn74q72gn9mrfra7n"))))
32050 (properties `((upstream-name . "readODS")))
32051 (build-system r-build-system)
32053 (list r-cellranger r-readr r-stringi r-xml2))
32054 (native-inputs (list r-knitr))
32056 "https://cran.r-project.org/package=readODS")
32057 (synopsis "Read and Write ODS Files")
32059 "Import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame.
32060 Also support writing data frame into ODS file.")
32061 (license license:gpl3)))
32063 (define-public r-qpdf
32070 (uri (cran-uri "qpdf" version))
32073 "1a1d7zad2l94z068mic6dg9wr9bq8mlmqszrj8vxps1441mb6gfh"))
32074 (modules '((guix build utils)))
32077 ;; unvendor libqpdf
32078 (delete-file-recursively "src/libqpdf")
32079 (delete-file-recursively "src/include/qpdf")))))
32080 (properties `((upstream-name . "qpdf")))
32081 (build-system r-build-system)
32084 (modify-phases %standard-phases
32085 (add-after 'unpack 'configure
32086 (lambda _ (setenv "EXTERNAL_QPDF" "1"))))))
32088 (list libjpeg-turbo qpdf zlib))
32090 (list r-askpass r-curl r-rcpp))
32091 (native-inputs (list pkg-config))
32092 (home-page "https://github.com/ropensci/qpdf")
32094 "Split, Combine and Compress PDF Files")
32096 "Content-preserving transformations transformations of PDF files such as
32097 split, combine, and compress. This package interfaces directly to the
32098 @code{qpdf} C++ API and does not require any command line utilities. Note that
32099 @code{qpdf} does not read actual content from PDF files: to extract text and
32100 data you need the @code{pdftools} package.")
32101 (license license:asl2.0)))
32103 (define-public r-pbdmpi
32109 (uri (cran-uri "pbdMPI" version))
32112 "006pm2yn4mdrpwhfflqcybzv41lz7zssrjrcpq5g98zf60p9c07a"))))
32113 (properties `((upstream-name . "pbdMPI")))
32114 (build-system r-build-system)
32117 (modify-phases %standard-phases
32118 (add-before 'install 'mpi-setup
32119 ,%openmpi-setup))))
32120 (inputs (list openmpi))
32121 (propagated-inputs (list r-float r-rlecuyer))
32122 (native-inputs (list pkg-config))
32123 (home-page "https://pbdr.org/")
32124 (synopsis "Programming with Big Data -- Interface to MPI")
32126 "This package provides an efficient interface to MPI by utilizing S4
32127 classes and methods with a focus on @dfn{Single Program/Multiple Data} (SPMD)
32128 parallel programming style, which is intended for batch parallel execution.")
32129 (license license:mpl2.0)))
32131 (define-public r-pdftools
32133 (name "r-pdftools")
32138 (uri (cran-uri "pdftools" version))
32141 "151f7vaznxigwka4qhp17v4gnahm245rfgcvb8j132vix7md44q9"))))
32142 (properties `((upstream-name . "pdftools")))
32143 (build-system r-build-system)
32144 (inputs (list zlib poppler))
32145 (propagated-inputs (list r-qpdf r-rcpp))
32146 (native-inputs (list pkg-config))
32147 (home-page "https://docs.ropensci.org/pdftools/")
32148 (synopsis "Text Extraction, Rendering and Converting of PDF Documents")
32150 "This package provides utilities based on @code{libpoppler} for
32151 extracting text, fonts, attachments and metadata from a PDF file. It also
32152 supports high quality rendering of PDF documents into PNG, JPEG, TIFF format,
32153 or into raw bitmap vectors for further processing in R.")
32154 (license license:expat)))
32156 (define-public r-antiword
32158 (name "r-antiword")
32163 (uri (cran-uri "antiword" version))
32166 "123v8zlczwh6fr1v3x7dl3885xlmddq1bqlcxih8zh07w0hlk1k2"))
32167 (modules '((guix build utils)))
32170 ;; unvendor libantiword
32171 (delete-file-recursively "src")
32173 (properties `((upstream-name . "antiword")))
32174 (build-system r-build-system)
32177 (modify-phases %standard-phases
32178 (add-after 'unpack 'use-system-antiword
32179 (lambda* (#:key inputs #:allow-other-keys)
32180 (substitute* "R/antiword.R"
32181 (("system.file\\(\"bin\", package = \"antiword\"\\)")
32182 (string-append "\"" (assoc-ref inputs "antiword") "/bin\"")))
32184 (inputs (list antiword))
32185 (propagated-inputs (list r-sys))
32187 "https://github.com/ropensci/antiword#readme")
32189 "Extract Text from Microsoft Word Documents")
32191 "Wraps the @code{AntiWord} utility to extract text from Microsoft Word
32192 documents. The utility only supports the old @code{doc} format, not the new
32193 xml based @code{docx} format. Use the @code{xml2} package to read the
32195 (license license:gpl2)))
32197 (define-public r-readtext
32199 (name "r-readtext")
32204 (uri (cran-uri "readtext" version))
32207 "0k782h5hns5v5h8a6qyfqck2hc15nq0awg8bsp196q4zviv5jw3c"))))
32208 (properties `((upstream-name . "readtext")))
32209 (build-system r-build-system)
32224 (native-inputs (list r-knitr))
32226 "https://github.com/quanteda/readtext")
32228 "Import and Handling for Plain and Formatted Text Files")
32230 "This package provides functions for importing and handling text files
32231 and formatted text files with additional meta-data, such including @code{.csv},
32232 @code{.tab}, @code{.json}, @code{.xml}, @code{.html}, @code{.pdf}, @code{.doc},
32233 @code{.docx}, @code{.rtf}, @code{.xls}, @code{.xlsx}, and others.")
32234 (license license:gpl3)))
32236 (define-public r-packcircles
32238 (name "r-packcircles")
32243 (uri (cran-uri "packcircles" version))
32246 "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk"))))
32247 (properties `((upstream-name . "packcircles")))
32248 (build-system r-build-system)
32249 (propagated-inputs (list r-rcpp))
32250 (native-inputs (list r-knitr))
32252 "https://github.com/mbedward/packcircles")
32253 (synopsis "Circle Packing")
32255 "Algorithms to find arrangements of non-overlapping circles.")
32256 (license license:expat)))
32258 ;; Cannot unbundle liblwgeom, because PostGIS does not support building it on
32260 (define-public r-lwgeom
32267 (uri (cran-uri "lwgeom" version))
32270 "0d4b1djwrzla91mmyya2m1250mb44fzmq3d36w5mk81d4bg952pl"))))
32271 (properties `((upstream-name . "lwgeom")))
32272 (build-system r-build-system)
32274 (list geos proj sqlite zlib))
32276 (list r-rcpp r-sf r-units))
32277 (native-inputs (list pkg-config))
32278 (home-page "https://github.com/r-spatial/lwgeom/")
32279 (synopsis "Bindings to Selected 'liblwgeom' Functions for Simple Features")
32281 "Access to selected functions found in
32282 @url{https://github.com/postgis/postgis/tree/master/liblwgeom,liblwgeom}, the
32283 light-weight geometry library used by @url{http://postgis.net/,PostGIS}.")
32284 (license license:gpl2)))
32286 (define-public r-stars
32293 (uri (cran-uri "stars" version))
32296 "0qcli9bangpym4yp96yfibd5f4li5qw1622jnbvzfd9n8aakqhg0"))))
32297 (properties `((upstream-name . "stars")))
32298 (build-system r-build-system)
32306 (native-inputs (list r-knitr))
32307 (home-page "https://r-spatial.github.io/stars/")
32309 "Spatiotemporal Arrays, Raster and Vector Data Cubes")
32311 "Reading, manipulating, writing and plotting spatiotemporal arrays
32312 (raster and vector data cubes) in @code{R}, using @code{GDAL} bindings provided
32313 by @code{sf}, and @code{NetCDF} bindings by @code{ncmeta} and @code{RNetCDF}.")
32314 (license license:asl2.0)))
32316 (define-public r-tmaptools
32318 (name "r-tmaptools")
32323 (uri (cran-uri "tmaptools" version))
32326 "0bal3czrdr93qig8s5cf5szld5vjbbks67rismfhlkmlgw6wp2gx"))))
32327 (properties `((upstream-name . "tmaptools")))
32328 (build-system r-build-system)
32340 "https://github.com/mtennekes/tmaptools")
32341 (synopsis "Thematic Map Tools")
32343 "Set of tools for reading and processing spatial data. The aim is to
32344 supply the workflow to create thematic maps. This package also facilitates
32345 @code{tmap}, the package for visualizing thematic maps.")
32346 (license license:gpl3)))
32348 (define-public r-rworldmap
32350 (name "r-rworldmap")
32355 (uri (cran-uri "rworldmap" version))
32358 "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk"))))
32359 (properties `((upstream-name . "rworldmap")))
32360 (build-system r-build-system)
32362 (list r-fields r-maptools r-sp))
32364 "https://github.com/AndySouth/rworldmap/")
32365 (synopsis "Mapping Global Data")
32367 "Enables mapping of country level and gridded user datasets.")
32368 (license license:gpl2+)))
32370 (define-public r-rtweet
32377 (uri (cran-uri "rtweet" version))
32380 "1dhdq2c2zl88h29caqpm7zh2i5970q7rfg98zf2xb7x4zak7bq9x"))))
32381 (properties `((upstream-name . "rtweet")))
32382 (build-system r-build-system)
32393 (native-inputs (list r-knitr))
32394 (home-page "https://docs.ropensci.org/rtweet/")
32395 (synopsis "Collect Twitter data")
32397 "This package implements tools designed to collect and organize Twitter
32398 data via @url{https://developer.twitter.com/en/docs,Twitter's REST and stream
32399 Application Program Interfaces (API)}.")
32400 (license license:expat)))
32402 (define-public r-intervals
32404 (name "r-intervals")
32409 (uri (cran-uri "intervals" version))
32412 "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb"))))
32413 (properties `((upstream-name . "intervals")))
32414 (build-system r-build-system)
32415 (home-page "https://github.com/edzer/intervals")
32417 "Tools for Working with Points and Intervals")
32419 "Tools for working with and comparing sets of points and intervals.")
32420 (license license:artistic2.0)))
32422 (define-public r-eyelinker
32424 (name "r-eyelinker")
32429 (uri (cran-uri "eyelinker" version))
32432 "0wijd45p6j2qal6wnj7zywks8p9v3m9cmyp7axmk44mrjdjx2i71"))))
32433 (properties `((upstream-name . "eyelinker")))
32434 (build-system r-build-system)
32436 (list r-intervals r-readr r-stringi r-stringr r-tibble))
32437 (native-inputs (list r-knitr))
32439 "https://github.com/a-hurst/eyelinker")
32441 "Import ASC Files from EyeLink Eye Trackers")
32443 "Imports plain-text ASC data files from EyeLink eye trackers into
32444 (relatively) tidy data frames for analysis and visualization.")
32445 (license license:gpl3)))
32447 (define-public r-btm
32454 (uri (cran-uri "BTM" version))
32457 "0ab0wr8nbwn1w1j9hpwfz52lm1sw0qk93713y9k0hpm3pw9dq4jr"))))
32458 (properties `((upstream-name . "BTM")))
32459 (build-system r-build-system)
32460 (propagated-inputs (list r-rcpp))
32461 (home-page "https://github.com/bnosac/BTM")
32462 (synopsis "Biterm Topic Models for Short Text")
32464 "Biterm Topic Models find topics in collections of short texts. It is a
32465 word co-occurrence based topic model that learns topics by modeling word-word
32466 co-occurrences patterns which are called biterms. This in contrast to
32467 traditional topic models like Latent Dirichlet Allocation and Probabilistic
32468 Latent Semantic Analysis which are word-document co-occurrence topic models. A
32469 biterm consists of two words co-occurring in the same short text window. This
32470 context window can for example be a twitter message, a short answer on a
32471 survey, a sentence of a text or a document identifier. The techniques are
32472 explained in detail in the paper 'A Biterm Topic Model For Short Text' by
32473 Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013)
32474 @url{https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/\
32476 (license license:asl2.0)))
32478 (define-public r-delaporte
32480 (name "r-delaporte")
32485 (uri (cran-uri "Delaporte" version))
32488 "1d1jkbxlwnqznh9pkjpkr7np2nmqzjvrdmlb210y1lb08mqmb73w"))))
32489 (properties `((upstream-name . "Delaporte")))
32490 (build-system r-build-system)
32491 (native-inputs (list gfortran))
32492 (home-page "https://github.com/aadler/Delaporte")
32493 (synopsis "Statistical functions for the Delaporte distribution")
32495 "This package provides probability mass, distribution, quantile,
32496 random-variate generation, and method-of-moments parameter-estimation
32497 functions for the Delaporte distribution with parameterization based on
32498 Vose (2008). The Delaporte is a discrete probability distribution which can
32499 be considered the convolution of a negative binomial distribution with a
32500 Poisson distribution. Alternatively, it can be considered a counting
32501 distribution with both Poisson and negative binomial components. It has been
32502 studied in actuarial science as a frequency distribution which has more
32503 variability than the Poisson, but less than the negative binomial.")
32504 (license license:bsd-2)))
32506 (define-public r-rjsonio
32509 (version "1.3-1.6")
32513 (uri (cran-uri "RJSONIO" version))
32516 "17x0ayk7daprbc8w2hvb2jl9mfnw4dic9yc3sr5adcjqfzmcklc2"))))
32517 (properties `((upstream-name . "RJSONIO")))
32518 (build-system r-build-system)
32519 (home-page "https://cran.r-project.org/package=RJSONIO")
32520 (synopsis "Serialize R objects to JSON")
32522 "This is a package that allows conversion to and from data in JavaScript
32523 Object Notation (JSON) format. This allows R objects to be inserted into
32524 Javascript/ECMAScript/ActionScript code and allows R programmers to read and
32525 convert JSON content to R objects. This is an alternative to the @code{rjson}
32527 (license license:bsd-3)))
32529 (define-public r-revgeo
32536 (uri (cran-uri "revgeo" version))
32539 "1ns7d1817475lriss6wwgvdm6lj760p40yxqaifla13c2xb73a55"))))
32540 (properties `((upstream-name . "revgeo")))
32541 (build-system r-build-system)
32543 (list r-rcurl r-rjsonio))
32544 (home-page "https://cran.r-project.org/package=revgeo")
32545 (synopsis "Reverse geocoding")
32547 "The @code{revgeo} procedure allows you to use the Photon geocoder for
32548 OpenStreetMap, Google Maps, and Bing to reverse geocode coordinate pairs with
32550 (license license:gpl3+)))
32552 (define-public r-qpcr
32559 (uri (cran-uri "qpcR" version))
32562 "1r01q7jv3w59yx1gc0qw91rq7rvdhqsi8y57sqqkmwyqfw2x2vsv"))))
32563 (properties `((upstream-name . "qpcR")))
32564 (build-system r-build-system)
32566 (list r-mass r-matrix r-minpack-lm r-rgl r-robustbase))
32567 (home-page "https://cran.r-project.org/package=qpcR")
32568 (synopsis "Modelling and analysis of real-time PCR data")
32570 "This is a package for model fitting, optimal model selection and
32571 calculation of various features that are essential in the analysis of
32572 quantitative real-time polymerase chain reaction (qPCR).")
32573 (license license:gpl2+)))
32575 (define-public r-textplot
32577 (name "r-textplot")
32582 (uri (cran-uri "textplot" version))
32585 "1ag2h365zsx0fxbl05s2yfhf1q13p40akvbqg4qwsb5ynh2a56bf"))))
32586 (properties `((upstream-name . "textplot")))
32587 (build-system r-build-system)
32589 (list r-data-table r-lattice r-matrix))
32590 (native-inputs (list r-knitr))
32591 (home-page "https://github.com/bnosac/textplot")
32592 (synopsis "Text Plots")
32594 "Visualise complex relations in texts. This is done by providing
32595 functionalities for displaying text co-occurrence networks, text correlation
32596 networks, dependency relationships as well as text clustering. Feel free to
32597 join the effort of providing interesting text visualisations.")
32598 (license license:gpl2)))
32600 (define-public r-gsa
32607 (uri (cran-uri "GSA" version))
32610 "1f1mrxxdbdlnibgav6nsvbpniz2x3km2svc0hf43spb4zicn0z8p"))))
32611 (properties `((upstream-name . "GSA")))
32612 (build-system r-build-system)
32613 (home-page "https://statweb.stanford.edu/~tibs/GSA/")
32614 (synopsis "Gene set analysis")
32615 (description "This package lets you determine the significance of
32616 pre-defined sets of genes with respect to an outcome variable, such as a group
32617 indicator, a quantitative variable or a survival time.")
32618 ;; Any version of the LGPL
32619 (license license:lgpl3+)))
32621 (define-public r-gsalib
32628 (uri (cran-uri "gsalib" version))
32631 "1k3zjdydzb0dfh1ihih08d4cw6rdamgb97cdqna9mf0qdjc3pcp1"))))
32632 (build-system r-build-system)
32633 (home-page "https://cran.r-project.org/web/packages/gsalib")
32634 (synopsis "Utility functions for GATK")
32635 (description "This package contains utility functions used by the Genome
32636 Analysis Toolkit (GATK) to load tables and plot data. The GATK is a toolkit
32637 for variant discovery in high-throughput sequencing data.")
32638 (license license:expat)))
32640 (define-public r-randomforestsrc
32642 (name "r-randomforestsrc")
32647 (uri (cran-uri "randomForestSRC" version))
32650 "05ifvj49jv0n5p6k46milpgj9r10sc5aw23fypyyibdgwpwvwixw"))))
32652 `((upstream-name . "randomForestSRC")))
32653 (build-system r-build-system)
32654 (home-page "https://cran.r-project.org/web/packages/randomForestSRC/")
32655 (synopsis "Random forests for survival, regression, and classification")
32657 "This package implements fast OpenMP parallel computing of Breiman's
32658 random forests for survival, competing risks, regression and classification
32659 based on Ishwaran and Kogalur's popular random survival forests (RSF) package.
32660 It handles missing data and now includes multivariate, unsupervised forests,
32661 quantile regression and solutions for class imbalanced data. It provides a
32662 fast interface using subsampling and confidence regions for variable
32664 (license license:gpl3+)))
32666 (define-public r-contfrac
32668 (name "r-contfrac")
32673 (uri (cran-uri "contfrac" version))
32676 "0sq5c7ny235yrkv2xc4insgxby6rvzc1qsj8h301cd2if3lwbgwm"))))
32677 (properties `((upstream-name . "contfrac")))
32678 (build-system r-build-system)
32680 "https://github.com/RobinHankin/contfrac")
32681 (synopsis "Continued Fractions")
32683 "Various utilities for evaluating continued fractions.")
32684 (license license:gpl2)))
32686 (define-public r-elliptic
32688 (name "r-elliptic")
32693 (uri (cran-uri "elliptic" version))
32696 "1dhba0yfxjd5rlqsxp5a7s2hclfkla9wigsr39dlma67l6qjjmxn"))))
32697 (properties `((upstream-name . "elliptic")))
32698 (build-system r-build-system)
32699 (inputs (list pari-gp))
32700 (propagated-inputs (list r-mass))
32702 "https://github.com/RobinHankin/elliptic")
32704 "Weierstrass and Jacobi Elliptic Functions")
32706 "A suite of elliptic and related functions including Weierstrass and
32707 Jacobi forms. Also includes various tools for manipulating and visualizing
32708 complex functions.")
32709 (license license:gpl2)))
32711 (define-public r-hypergeo
32713 (name "r-hypergeo")
32718 (uri (cran-uri "hypergeo" version))
32721 "13jdiy216znwhr91iqnh03mvkmyscw439syb3h4i67dd78sphnvd"))))
32722 (properties `((upstream-name . "hypergeo")))
32723 (build-system r-build-system)
32725 (list r-contfrac r-desolve r-elliptic))
32727 "https://cran.r-project.org/web/packages/hypergeo/")
32728 (synopsis "The Gauss Hypergeometric Function")
32730 "The Gaussian hypergeometric function for complex numbers.")
32731 (license license:gpl2)))
32733 (define-public r-gganimate
32735 (name "r-gganimate")
32740 (uri (cran-uri "gganimate" version))
32743 "1jabs9qr0319w508kdsk5nmzfhl6nzykpp1by7l639yfvrfqcbd1"))))
32744 (properties `((upstream-name . "gganimate")))
32745 (build-system r-build-system)
32748 (modify-phases %standard-phases
32749 (add-after 'unpack 'absolute-paths
32750 (lambda* (#:key inputs #:allow-other-keys)
32751 (substitute* "R/renderers.R"
32753 (string-append "'" (assoc-ref inputs "ffmpeg") "/bin/ffmpeg'"))))))))
32755 ;; For video output.
32765 ;; For GIF/SVG output. gifski is faster, but depends on Rust.
32767 ;; For HTML output.
32770 (native-inputs (list r-knitr))
32771 (home-page "https://gganimate.com")
32772 (synopsis "Grammar of Animated Graphics")
32774 "This package extends the grammar of graphics as implemented by
32775 @code{ggplot2} to include the description of animation. It does this by
32776 providing a range of new grammar classes that can be added to the plot object
32777 in order to customise how it should change with time.")
32778 (license license:expat)))
32780 ;; This library bundles ‘date’ from (gnu packages calendar). We cannot unbundle
32781 ;; it, because its C++ libtz.so is built with different compiler flags than
32783 (define-public r-tzdb
32790 (uri (cran-uri "tzdb" version))
32793 "0f3h4zaf9f4l371k6nc1mq6z2f9aj1vaf2inni8jnsds3zng16b0"))))
32794 (properties `((upstream-name . "tzdb")))
32795 (build-system r-build-system)
32796 (propagated-inputs (list r-cpp11))
32797 (home-page "https://github.com/r-lib/tzdb")
32798 (synopsis "Time Zone Database Information")
32800 "This package provides an up-to-date copy of the Internet Assigned
32801 Numbers Authority (IANA) Time Zone Database. It is updated periodically to
32802 reflect changes made by political bodies to time zone boundaries, UTC offsets,
32803 and daylight saving time rules. Additionally, this package provides a C++
32804 interface for working with the @code{date} library. @code{date} provides
32805 comprehensive support for working with dates and date-times, which this package
32806 exposes to make it easier for other R packages to utilize. Headers are
32807 provided for calendar specific calculations, along with a limited interface for
32808 time zone manipulations.")
32809 (license license:expat)))
32811 (define-public r-vroom
32818 (uri (cran-uri "vroom" version))
32821 "1plz20x6s01gkkcac51lhx4r2s024pgh778ri7y25hkiiwacp1yh"))))
32822 (properties `((upstream-name . "vroom")))
32823 (build-system r-build-system)
32839 (native-inputs (list r-knitr))
32840 (home-page "https://vroom.r-lib.org")
32842 "Read and Write Rectangular Text Data")
32844 "This package reads and writes data files like @acronym{CSV},
32845 @acronym{TSV} and @acronym{FWF}. When reading it uses a quick initial indexing
32846 step, then reads the values lazily, so only the data you actually use needs to
32847 be read. The writer formats the data in parallel and writes to disk
32848 asynchronously from formatting.")
32849 (license license:expat)))
32851 (define-public r-rmisc
32857 (uri (cran-uri "Rmisc" version))
32860 "1h6jb0xwkyhm9lwm7nj9bhrb5dhrsifvkpqkrd594j1lz74dar8x"))))
32861 (build-system r-build-system)
32863 (list r-plyr r-lattice))
32864 (home-page "https://cran.r-project.org/web/packages/Rmisc/")
32865 (synopsis "Ryan Miscellaneous")
32866 (description "The Rmisc library contains functions for data analysis and
32867 utility operations.")
32868 (license license:gpl3)))
32870 (define-public r-rsq
32876 (uri (cran-uri "rsq" version))
32879 "1r628srxhhf7b51lnj4qrzgbqajkm0ls47a9rzjkvmfq4ax5i73f"))))
32880 (properties `((upstream-name . "rsq")))
32881 (build-system r-build-system)
32888 (home-page "https://cran.r-project.org/package=rsq")
32889 (synopsis "R-squared and related measures")
32891 "Calculate generalized R-squared, partial R-squared, and partial correlation
32892 coefficients for generalized linear (mixed) models (including quasi models
32893 with well defined variance functions).")
32894 (license license:gpl2)))
32896 (define-public r-webutils
32898 (name "r-webutils")
32903 (uri (cran-uri "webutils" version))
32905 (base32 "16a6ds0fnb6y8i1r9ba1hf1ydb53am57s070b3hi5jmrs84b9qik"))))
32906 (properties `((upstream-name . "webutils")))
32907 (build-system r-build-system)
32909 (list r-curl r-jsonlite))
32910 (home-page "https://github.com/jeroen/webutils")
32911 (synopsis "Utility functions for developing web applications")
32913 "This package parses HTTP request data in @code{application/json},
32914 @code{multipart/form-data}, or @code{application/x-www-form-urlencoded}
32915 format. It includes an example of hosting and parsing HTML form data in R
32916 using either @code{httpuv} or @code{Rhttpd}.")
32917 (license license:expat)))
32919 (define-public r-protolite
32921 (name "r-protolite")
32926 (uri (cran-uri "protolite" version))
32928 (base32 "0g1r3lzmvx1w44qzqzdvxfn21zmz11srlp6cr76kd7pd5wzjv82p"))))
32929 (properties `((upstream-name . "protolite")))
32930 (build-system r-build-system)
32934 (list r-jsonlite r-rcpp))
32936 (list protobuf pkg-config))
32937 (home-page "https://github.com/jeroen/protolite")
32938 (synopsis "Highly optimized protocol buffer serializers")
32940 "This package provides pure C++ implementations for reading and writing
32941 several common data formats based on Google protocol-buffers. It currently
32942 supports @code{rexp.proto} for serialized R objects, @code{geobuf.proto} for
32943 binary geojson, and @code{mvt.proto} for vector tiles. This package uses the
32944 auto-generated C++ code by protobuf-compiler, hence the entire serialization
32945 is optimized at compile time. The @code{RProtoBuf} package on the other hand
32946 uses the protobuf runtime library to provide a general-purpose toolkit for
32947 reading and writing arbitrary protocol-buffer data in R.")
32948 (license license:expat)))
32950 (define-public r-opencpu
32957 (uri (cran-uri "opencpu" version))
32959 (base32 "1h0s7fbifyf4h1296sdk3amij0m6s12wq32mbky7xg4nz8wj29ni"))))
32960 (properties `((upstream-name . "opencpu")))
32961 (build-system r-build-system)
32981 (home-page "https://www.opencpu.org")
32982 (synopsis "API for embedded scientific computing")
32984 "This package provides a system for embedded scientific computing and
32985 reproducible research with R. The OpenCPU server exposes a simple but
32986 powerful HTTP API for RPC and data interchange with R. This provides a
32987 reliable and scalable foundation for statistical services or building R web
32988 applications. The OpenCPU server runs either as a single-user development
32989 server within the interactive R session, or as a multi-user stack based on
32991 (license license:asl2.0)))
32993 (define-public r-exactextractr
32995 (name "r-exactextractr")
33000 (uri (cran-uri "exactextractr" version))
33003 "13di9s0lv9kdv2p3hp9ksrr0rh98z6m998pj5a1xq9zl6iakankh"))))
33004 (properties `((upstream-name . "exactextractr")))
33005 (build-system r-build-system)
33006 (inputs (list geos))
33008 (list r-raster r-rcpp r-sf))
33011 (home-page "https://isciences.gitlab.io/exactextractr/")
33012 (synopsis "Fast extraction from raster datasets using polygons")
33014 "This package provides a replacement for the @code{extract} function from
33015 the @code{raster} package that is suitable for extracting raster values using
33016 @code{sf} polygons.")
33017 (license license:asl2.0)))
33019 (define-public r-stringfish
33021 (name "r-stringfish")
33026 (uri (cran-uri "stringfish" version))
33029 "0ddpsi7z0kzqgbq9y646pk9afclq0r7ak22zsdh0i93ni0x71c9l"))))
33030 (properties `((upstream-name . "stringfish")))
33031 (build-system r-build-system)
33033 (list r-rcpp r-rcppparallel))
33035 (list pkg-config r-knitr))
33036 (home-page "https://github.com/traversc/stringfish")
33037 (synopsis "Alternative string implementation")
33039 "This package provides an extendable, performant and multithreaded
33040 @code{alt-string} implementation backed by C++ vectors and strings.")
33041 (license license:gpl3)))
33043 (define-public r-rapiserialize
33045 (name "r-rapiserialize")
33050 (uri (cran-uri "RApiSerialize" version))
33053 "02k0l8bi849b2102ysb102xky4p84i9v2r4w6fab7bgf32wvph4w"))))
33054 (properties `((upstream-name . "RApiSerialize")))
33055 (build-system r-build-system)
33057 "https://cran.r-project.org/package=RApiSerialize")
33058 (synopsis "R API serialization")
33060 "This package provides other packages with access to the internal R
33061 serialization code. Access to this code is provided at the C function level
33062 by using the registration of native function mechanism. Client packages
33063 simply include a single header file RApiSerializeAPI.h provided by this
33065 (license license:gpl2+)))
33067 (define-public r-qs
33074 (uri (cran-uri "qs" version))
33077 "0cx5k0mzn6bm8ff58yrqz3hjidxcawxgqbpijnynvin1m4395i4j"))))
33078 (properties `((upstream-name . "qs")))
33079 (build-system r-build-system)
33080 (inputs (list zlib))
33082 (list r-rapiserialize r-rcpp r-stringfish))
33084 (list pkg-config r-knitr))
33085 (home-page "https://github.com/traversc/qs")
33086 (synopsis "Quick serialization of R objects")
33088 "This package provides functions for quickly writing and reading any R
33089 object to and from disk.")
33090 (license license:gpl3)))
33092 (define-public r-rgeos
33099 (uri (cran-uri "rgeos" version))
33102 "1m73y0nwrdwsjrl48c4fg1kdqnh79835brnmxv9ak01ndbzcp45b"))))
33103 (properties `((upstream-name . "rgeos")))
33104 (build-system r-build-system)
33109 (home-page "https://cran.r-project.org/package=rgeos")
33110 (synopsis "Interface to Geometry Engine (GEOS)")
33112 "This package provides an R interface to Geometry Engine (GEOS) using the
33113 C API for topology operations on geometries.")
33114 (license license:gpl2+)))
33116 (define-public r-tfruns
33123 (uri (cran-uri "tfruns" version))
33126 "1xk7dl51xd1h54798xwycvxmn77jv80in61hanm36zk0024wpxg8"))))
33127 (properties `((upstream-name . "tfruns")))
33128 (build-system r-build-system)
33140 (native-inputs (list r-knitr))
33141 (home-page "https://github.com/rstudio/tfruns")
33142 (synopsis "Training run tools for TensorFlow")
33144 "Create and manage unique directories for each TensorFlow training run.
33145 This package provides a unique, time stamped directory for each run along with
33146 functions to retrieve the directory of the latest run or latest several
33148 (license license:asl2.0)))
33150 (define-public r-tfautograph
33152 (name "r-tfautograph")
33157 (uri (cran-uri "tfautograph" version))
33160 "0fmaq1ggjyxgf2ss7qb8jk74sfwc3s1vc123pd5glclxcy1ib0j2"))))
33161 (properties `((upstream-name . "tfautograph")))
33162 (build-system r-build-system)
33163 (inputs (list tensorflow))
33165 (list r-backports r-reticulate))
33166 (home-page "https://t-kalinowski.github.io/tfautograph/")
33167 (synopsis "Autograph R for Tensorflow")
33169 "This package lets you translate R control flow expressions into
33170 Tensorflow graphs.")
33171 (license license:gpl3)))
33173 (define-public r-tensorflow
33175 (name "r-tensorflow")
33180 (uri (cran-uri "tensorflow" version))
33183 "12c6ndxx4g6fqjakpzp9pgl29ghswhqyr6q9jahpk0cawizh2znj"))))
33184 (properties `((upstream-name . "tensorflow")))
33185 (build-system r-build-system)
33186 (inputs (list tensorflow))
33195 (home-page "https://github.com/rstudio/tensorflow")
33196 (synopsis "R interface to TensorFlow")
33198 "R interface to TensorFlow a library for numerical computation using data
33199 flow graphs. Nodes in the graph represent mathematical operations, while the
33200 graph edges represent the multidimensional data arrays (tensors) communicated
33202 (license license:asl2.0)))
33204 (define-public r-keras
33211 (uri (cran-uri "keras" version))
33214 "06513d1fp7cxk4v03xm9lhgj6xmp9dqqvw3lnzwbzjwdkfj948yc"))))
33215 (properties `((upstream-name . "keras")))
33216 (build-system r-build-system)
33228 (native-inputs (list r-knitr))
33229 (home-page "https://keras.rstudio.com")
33230 (synopsis "R Interface to 'Keras'")
33232 "This package provides an interface to Keras, a high-level neural
33233 networks API. Keras was developed with a focus on enabling fast
33234 experimentation, supports both convolution based networks and recurrent
33235 networks (as well as combinations of the two), and runs seamlessly on both CPU
33237 (license license:expat)))
33239 (define-public r-zzlite
33246 (uri (cran-uri "zzlite" version))
33249 "0vi1slx2s4r5zf82lazqv0c3m12xq73wlgsbz6af4y00h0bkr3ps"))))
33250 (properties `((upstream-name . "zzlite")))
33251 (build-system r-build-system)
33253 (list r-httr r-jsonlite))
33256 (home-page "https://cran.r-project.org/package=zzlite")
33257 (synopsis "Wrapper for the Zamzar file conversion API")
33259 "This package provides a minor collection of HTTP wrappers for the Zamzar
33260 file conversion API. The wrappers makes it easy to utilize the API and thus
33261 convert between more than 100 different file formats (ranging from audio
33262 files, images, movie formats, etc., etc.) through an R session.")
33263 (license license:gpl3)))
33265 (define-public r-ztree
33272 (uri (cran-uri "zTree" version))
33275 "005zk6wpchpss6865ki35yawgf668pn70163ah97rnfkhfaswm6y"))))
33276 (properties `((upstream-name . "zTree")))
33277 (build-system r-build-system)
33280 (home-page "https://cran.r-project.org/package=zTree")
33281 (synopsis "Functions to import data from z-Tree into R")
33283 "This package provides tools for reading @code{.xls} and @code{.sbj}
33284 files which are written by the proprietary program z-Tree for developing and
33285 carrying out economic experiments.")
33286 (license license:gpl3)))
33288 (define-public r-distributionutils
33290 (name "r-distributionutils")
33295 (uri (cran-uri "DistributionUtils" version))
33298 "08vq54pyqxlqsj6q6gsg5ikqa0z3x842j52ld5dxaq272p6xchvl"))))
33300 `((upstream-name . "DistributionUtils")))
33301 (build-system r-build-system)
33304 (home-page "https://cran.r-project.org/package=DistributionUtils")
33305 (synopsis "Distribution utilities")
33307 "This package provides utilities for dealing with distributions.
33308 Functionality includes sample skewness and kurtosis, log-histogram, tail
33309 plots, moments by integration, changing the point about which a moment is
33310 calculated, functions for testing distributions using inversion tests and the
33311 Massart inequality. Also included is an implementation of the incomplete
33312 Bessel K function.")
33313 (license license:gpl2+)))
33315 (define-public r-ztpln
33322 (uri (cran-uri "ztpln" version))
33325 "1b22m72a8117yrgq5k1gzsrbx6yrsrj7bpd49lh7x3vbaz56c0wr"))))
33326 (properties `((upstream-name . "ztpln")))
33327 (build-system r-build-system)
33329 (list r-distributionutils r-mixtools r-rcpp r-rcppeigen
33333 (home-page "https://github.com/mattocci27/ztpln")
33334 (synopsis "Zero-truncated Poisson lognormal distribution")
33336 "This package provides functions for obtaining the density, random
33337 variates and maximum likelihood estimates of the Zero-truncated Poisson
33338 lognormal distribution and their mixture distribution.")
33339 (license license:expat)))
33341 (define-public r-zscorer
33348 (uri (cran-uri "zscorer" version))
33351 "0aijhs0fyird5gq68x4dxchb02mxa7ijk10k9zjhngghxbjj7iqn"))))
33352 (properties `((upstream-name . "zscorer")))
33353 (build-system r-build-system)
33358 (home-page "https://github.com/nutriverse/zscorer")
33359 (synopsis "Child Anthropometry z-Score Calculator")
33361 "This package provides a tool for calculating z-scores and centiles for
33362 weight-for-age, length/height-for-age, weight-for-length/height, BMI-for-age,
33363 head circumference-for-age, age circumference-for-age, subscapular
33364 skinfold-for-age, triceps skinfold-for-age based on the WHO Child Growth
33366 (license license:agpl3+)))
33368 (define-public r-zra
33375 (uri (cran-uri "ZRA" version))
33378 "1sx1q5yf68hhlb5j1hicpj594rmgajqr25llg7ax416j0m2rnagi"))))
33379 (properties `((upstream-name . "ZRA")))
33380 (build-system r-build-system)
33382 (list r-dygraphs r-forecast))
33383 (home-page "https://cran.r-project.org/package=ZRA")
33384 (synopsis "Dynamic plots for time series forecasting")
33386 "This package combines a forecast of a time series, using the function @code{forecast},
33387 with the dynamic plots from @code{dygraphs}.")
33388 (license license:gpl2+)))
33390 (define-public r-rfigshare
33392 (name "r-rfigshare")
33397 (uri (cran-uri "rfigshare" version))
33400 "10shwl1y9220m7ld5w9fjsjzy5yg8myrz9cz97ps9z2bw7bvka5j"))))
33401 (properties `((upstream-name . "rfigshare")))
33402 (build-system r-build-system)
33412 (home-page "https://github.com/ropensci/rfigshare")
33413 (synopsis "R Interface to figshare")
33415 "This package provides an interface to figshare, a scientific repository
33416 to archive and assign DOIs to data, software, figures, and more.")
33417 (license license:cc0)))
33419 (define-public r-dismo
33426 (uri (cran-uri "dismo" version))
33429 "17dwk4fv9l903fp38ab9arc4dfyrj1sbllfxlybkdwm9lpsn1qv6"))))
33430 (properties `((upstream-name . "dismo")))
33431 (build-system r-build-system)
33433 (list r-raster r-rcpp r-sp r-terra))
33434 (home-page "https://rspatial.org/raster/sdm/")
33435 (synopsis "Species distribution modeling")
33437 "This package provides methods for species distribution modeling, i.e.,
33438 predicting the environmental similarity of any site to that of the locations
33439 of known occurrences of a species.")
33440 (license license:gpl3+)))
33442 (define-public r-zoon
33449 (uri (cran-uri "zoon" version))
33452 "02y29vr2yn8al69km8faiqrwjrc1r3hsvw3dg8lwjr65cxw1krip"))))
33453 (properties `((upstream-name . "zoon")))
33454 (build-system r-build-system)
33469 (home-page "https://github.com/zoonproject/zoon")
33470 (synopsis "Reproducible, accessible and shareable species distribution modelling")
33472 "This package reads user submitted modules from an online repository,
33473 runs full species distribution modelling workflows and returns output that is
33474 fully reproducible.")
33475 (license license:bsd-3)))
33477 (define-public r-paws-common
33479 (name "r-paws-common")
33484 (uri (cran-uri "paws.common" version))
33487 "12dz3giv1xajdqq79s5gin9kw4x74w2iaw62ha6ssf8whrc3wmh5"))))
33488 (properties `((upstream-name . "paws.common")))
33489 (build-system r-build-system)
33498 (home-page "https://cran.r-project.org/package=paws.common")
33499 (synopsis "Paws low-level Amazon Web Services API")
33501 "This package provides functions for making low-level API requests to
33502 Amazon Web Services. The functions handle building, signing, and sending
33503 requests, and receiving responses. They are designed to help build
33504 higher-level interfaces to individual services, such as Simple Storage
33506 (license license:asl2.0)))
33508 (define-public r-paws-customer-engagement
33510 (name "r-paws-customer-engagement")
33515 (uri (cran-uri "paws.customer.engagement" version))
33518 "0ac6hzn4ilfjhzdmc9x80999fl18cz16mky31qd3y09m93w2xkdj"))))
33520 `((upstream-name . "paws.customer.engagement")))
33521 (build-system r-build-system)
33523 (list r-paws-common))
33524 (home-page "https://github.com/paws-r/paws")
33525 (synopsis "Amazon Web Services customer engagement services")
33527 "This package provides an interface to Amazon Web Services customer
33528 engagement services, including Simple Email Service, Connect contact center
33529 service, and more.")
33530 (license license:asl2.0)))
33532 (define-public r-paws-cost-management
33534 (name "r-paws-cost-management")
33539 (uri (cran-uri "paws.cost.management" version))
33542 "0in4f8ygw5g2v6vl3lz2y0v51llglh8b1ymbd04d54xxlgn83knh"))))
33544 `((upstream-name . "paws.cost.management")))
33545 (build-system r-build-system)
33547 (list r-paws-common))
33548 (home-page "https://github.com/paws-r/paws")
33549 (synopsis "Amazon Web Services cost management services")
33551 "This package provides an interface to Amazon Web Services cost
33552 management services, including cost and usage reports, budgets, pricing, and
33554 (license license:asl2.0)))
33556 (define-public r-paws-developer-tools
33558 (name "r-paws-developer-tools")
33563 (uri (cran-uri "paws.developer.tools" version))
33565 (base32 "16gb8g8s67al7qdd95fbigxqkih9a9p7slkyf3cga42wb6miiby2"))))
33566 (properties `((upstream-name . "paws.developer.tools")))
33567 (build-system r-build-system)
33569 (list r-paws-common))
33570 (home-page "https://github.com/paws-r/paws")
33571 (synopsis "Amazon Web Services developer tools services")
33573 "This package provides an interface to Amazon Web Services developer
33574 tools services, including version control, continuous integration and
33575 deployment, and more.")
33576 (license license:asl2.0)))
33578 (define-public r-paws-end-user-computing
33580 (name "r-paws-end-user-computing")
33585 (uri (cran-uri "paws.end.user.computing" version))
33587 (base32 "1xxsz86nx128sizym9np8vldzkbym0p3i6vcy94kq1y0cylaicv3"))))
33588 (properties `((upstream-name . "paws.end.user.computing")))
33589 (build-system r-build-system)
33591 (list r-paws-common))
33592 (home-page "https://github.com/paws-r/paws")
33593 (synopsis "Amazon Web Services end user computing services")
33595 "This package provides an interface to Amazon Web Services end user
33596 computing services, including collaborative document editing, mobile intranet,
33598 (license license:asl2.0)))
33600 (define-public r-paws-application-integration
33602 (name "r-paws-application-integration")
33607 (uri (cran-uri "paws.application.integration" version))
33610 "0llyd9hc679pad1ih0rcc38q5xxpzinhwrl8cvrkgsjgbc3agq42"))))
33612 `((upstream-name . "paws.application.integration")))
33613 (build-system r-build-system)
33615 (list r-paws-common))
33616 (home-page "https://github.com/paws-r/paws")
33617 (synopsis "Amazon Web Services application integration services")
33619 "This package provides an interface to Amazon Web Services application
33620 integration services, including Simple Queue Service (SQS) message queue,
33621 Simple Notification Service (SNS) publish/subscribe messaging, and more.")
33622 (license license:asl2.0)))
33624 (define-public r-paws-security-identity
33626 (name "r-paws-security-identity")
33631 (uri (cran-uri "paws.security.identity" version))
33634 "092lz2ipn5iqr593x7ra8c0bj64yf6315mdc3llgwrjyb4vfxif9"))))
33636 `((upstream-name . "paws.security.identity")))
33637 (build-system r-build-system)
33639 (list r-paws-common))
33640 (home-page "https://github.com/paws-r/paws")
33641 (synopsis "Amazon Web Services security, identity, and compliance services")
33643 "This package provides an interface to Amazon Web Services security,
33644 identity, and compliance services, including the Identity and Access
33645 Management (IAM) service for managing access to services and resources, and
33647 (license license:asl2.0)))
33649 (define-public r-paws-analytics
33651 (name "r-paws-analytics")
33656 (uri (cran-uri "paws.analytics" version))
33659 "04gnaxmj21l312xkrsd9bisi0bz9h6h5fyhwlqylcxi077z1yb2g"))))
33661 `((upstream-name . "paws.analytics")))
33662 (build-system r-build-system)
33664 (list r-paws-common))
33665 (home-page "https://github.com/paws-r/paws")
33666 (synopsis "Amazon Web Services analytics services")
33668 "This package provides an interface to Amazon Web Services analytics
33669 services, including Elastic MapReduce Hadoop and Spark big data service,
33670 Elasticsearch search engine, and more.")
33671 (license license:asl2.0)))
33673 (define-public r-paws-machine-learning
33675 (name "r-paws-machine-learning")
33680 (uri (cran-uri "paws.machine.learning" version))
33683 "01w2y5952pk50xjbzby2pc51xrkrzjpfxbmii1b10cl2xgzfkxsa"))))
33685 `((upstream-name . "paws.machine.learning")))
33686 (build-system r-build-system)
33688 (list r-paws-common))
33689 (home-page "https://github.com/paws-r/paws")
33690 (synopsis "Amazon Web Services machine learning services")
33692 "This package provides an interface to Amazon Web Services machine
33693 learning services, including SageMaker managed machine learning service,
33694 natural language processing, speech recognition, translation, and more.")
33695 (license license:asl2.0)))
33697 (define-public r-paws-management
33699 (name "r-paws-management")
33704 (uri (cran-uri "paws.management" version))
33707 "09k7wg0jlj40zs2yb3vldffpkdcjg7ap98n7c5lxr5plpca08swg"))))
33709 `((upstream-name . "paws.management")))
33710 (build-system r-build-system)
33712 (list r-paws-common))
33713 (home-page "https://github.com/paws-r/paws")
33714 (synopsis "Amazon Web Services management and governance services")
33716 "This package provides an interface to Amazon Web Services management and
33717 governance services, including CloudWatch application and infrastructure
33718 monitoring, Auto Scaling for automatically scaling resources, and more.")
33719 (license license:asl2.0)))
33721 (define-public r-paws-networking
33723 (name "r-paws-networking")
33728 (uri (cran-uri "paws.networking" version))
33731 "02hxaa5nlj70mdggh379ij3fn09xm8h5ldzsyf45c342prpl6zwj"))))
33733 `((upstream-name . "paws.networking")))
33734 (build-system r-build-system)
33736 (list r-paws-common))
33737 (home-page "https://github.com/paws-r/paws")
33738 (synopsis "Amazon Web Services networking and content delivery services")
33740 "This package provides an interface to Amazon Web Services networking and
33741 content delivery services, including Route 53 Domain Name System service,
33742 CloudFront content delivery, load balancing, and more.")
33743 (license license:asl2.0)))
33745 (define-public r-paws-database
33747 (name "r-paws-database")
33752 (uri (cran-uri "paws.database" version))
33755 "08jpwz95fw3f68j0wxh2lg57nn60khflldab0ryhkkbcw1iy0qyz"))))
33756 (properties `((upstream-name . "paws.database")))
33757 (build-system r-build-system)
33759 (list r-paws-common))
33760 (home-page "https://github.com/paws-r/paws")
33762 "Amazon Web Services Database Services")
33764 "This package provides an interface to Amazon Web Services database
33765 services, including Relational Database Service (RDS), DynamoDB NoSQL
33766 database, and more.")
33767 (license license:asl2.0)))
33769 (define-public r-paws-storage
33771 (name "r-paws-storage")
33776 (uri (cran-uri "paws.storage" version))
33779 "06m887vpqp5d6k3zxdlga599dsv8v3rladk7xqaxqnld1f17am04"))))
33780 (properties `((upstream-name . "paws.storage")))
33781 (build-system r-build-system)
33783 (list r-paws-common))
33784 (home-page "https://github.com/paws-r/paws")
33785 (synopsis "Amazon Web Services storage services")
33787 "This package provides an interface to Amazon Web Services storage
33788 services, including Simple Storage Service (S3).")
33789 (license license:asl2.0)))
33791 (define-public r-paws-compute
33793 (name "r-paws-compute")
33798 (uri (cran-uri "paws.compute" version))
33801 "1s7g4y2h763xf32p08drs3ygkfqb2zjikkgxb7yl91gk13zp7kjm"))))
33802 (properties `((upstream-name . "paws.compute")))
33803 (build-system r-build-system)
33805 (list r-paws-common))
33806 (home-page "https://github.com/paws-r/paws")
33807 (synopsis "Amazon Web Services compute services")
33809 "This package provides an interface to Amazon Web Services compute
33810 services, including Elastic Compute Cloud (EC2), Lambda
33811 functions-as-a-service, containers, batch processing, and more.")
33812 (license license:asl2.0)))
33814 (define-public r-paws
33821 (uri (cran-uri "paws" version))
33824 "0kn1z045r106fwqcaz52hb02bhrcblh479cajfjiq480s1iljcw6"))))
33825 (properties `((upstream-name . "paws")))
33826 (build-system r-build-system)
33828 (list r-paws-analytics
33829 r-paws-application-integration
33831 r-paws-cost-management
33832 r-paws-customer-engagement
33834 r-paws-developer-tools
33835 r-paws-end-user-computing
33836 r-paws-machine-learning
33839 r-paws-security-identity
33841 (home-page "https://github.com/paws-r/paws")
33842 (synopsis "Amazon Web Services software development kit")
33844 "This package provides an interface to Amazon Web Services, including
33845 storage, database, and compute services, such as Simple Storage Service (S3),
33846 DynamoDB NoSQL database, and Lambda functions-as-a-service.")
33847 (license license:asl2.0)))
33849 (define-public r-zoomgroupstats
33851 (name "r-zoomgroupstats")
33856 (uri (cran-uri "zoomGroupStats" version))
33859 "0gndiq92cy6gi7f833hdjvqii3cn83wz5rjvygcvjl3dw4pwv966"))))
33861 `((upstream-name . "zoomGroupStats")))
33862 (build-system r-build-system)
33873 (native-inputs (list r-knitr))
33874 (home-page "http://zoomgroupstats.org")
33875 (synopsis "Analyze text, audio, and video from Zoom meetings")
33877 "This package provides utilities for processing and analyzing the files
33878 that are exported from a recorded Zoom meeting. This includes analyzing data
33879 captured through video cameras and microphones, the text-based chat, and
33880 meta-data. You can analyze aspects of the conversation among meeting
33881 participants and their emotional expressions throughout the meeting.")
33882 (license license:expat)))
33884 (define-public r-zoom
33891 (uri (cran-uri "zoom" version))
33894 "05ikad4j1qi5y8mn77n9bw7d6ic3api9d7mbcn855w8xcc69ja4q"))))
33895 (properties `((upstream-name . "zoom")))
33896 (build-system r-build-system)
33897 (home-page "https://github.com/cbarbu/R-package-zoom")
33898 (synopsis "Spatial data visualization tool")
33900 "This package provides @code{zm}, a utility that allows you to
33901 zoom/navigate any plot when called with any active plot.")
33902 (license license:gpl3+)))
33904 (define-public r-zoolog
33911 (uri (cran-uri "zoolog" version))
33914 "06g44gjk9w73996n4h1a2q8kcd6q2mvm1vhx0iq0785gvrz18pj9"))))
33915 (properties `((upstream-name . "zoolog")))
33916 (build-system r-build-system)
33918 (list r-rdpack r-stringi))
33921 (home-page "https://josempozo.github.io/zoolog/")
33922 (synopsis "Zooarchaeological analysis with log-ratios")
33924 "This package includes functions and reference data to generate and
33925 manipulate log-ratios (also known as @dfn{log size index} (LSI) values) from
33926 measurements obtained on zooarchaeological material. Log ratios are used to
33927 compare the relative (rather than the absolute) dimensions of animals from
33928 archaeological contexts. The zoolog package is also able to seamlessly
33929 integrate data and references with heterogeneous nomenclature, which is
33930 internally managed by a zoolog thesaurus.")
33931 (license license:gpl3)))
33933 (define-public r-filehash
33935 (name "r-filehash")
33940 (uri (cran-uri "filehash" version))
33943 "1ga17smgjd4qsnf5a7qk0giwhpc5969ylqj520favs1k6b4y557k"))))
33944 (properties `((upstream-name . "filehash")))
33945 (build-system r-build-system)
33946 (home-page "http://github.com/rdpeng/filehash")
33947 (synopsis "Simple key-value database")
33949 "This package implements a simple key-value style database where
33950 character string keys are associated with data values that are stored on the
33951 disk. A simple interface is provided for inserting, retrieving, and deleting
33952 data from the database. Utilities are provided that allow filehash databases
33953 to be treated much like environments and lists are already used in R. These
33954 utilities are provided to encourage interactive and exploratory analysis on
33956 (license license:gpl2+)))
33958 (define-public r-mlearning
33960 (name "r-mlearning")
33965 (uri (cran-uri "mlearning" version))
33968 "1zjnh4gcw068li1bks60gazn3205xhmqz67hbkb1san33lmlxya3"))))
33969 (properties `((upstream-name . "mlearning")))
33970 (build-system r-build-system)
33978 (home-page "http://www.sciviews.org/zooimage")
33979 (synopsis "Machine learning algorithms with unified interface")
33981 "This package provides a unified interface to various machine learning
33982 algorithms. Confusion matrices are provided too.")
33983 (license license:gpl2+)))
33985 (define-public r-zooimage
33987 (name "r-zooimage")
33992 (uri (cran-uri "zooimage" version))
33995 "0ck8w0zb9l1n9xvjwqshq9q9l8pigy3yslq2hnfbgcwk17kk9mp8"))))
33996 (properties `((upstream-name . "zooimage")))
33997 (build-system r-build-system)
34011 (home-page "http://www.sciviews.org/zooimage")
34012 (synopsis "Analysis of numerical plankton images")
34014 "This package provides a solution for analyzing digital images of
34015 plankton. In combination with ImageJ, an image analysis system, it processes
34016 digital images, measures individuals, trains for automatic classification of
34017 taxa, and finally, measures plankton samples (abundances, total and partial
34018 size spectra or biomasses, etc.).")
34019 (license license:gpl2+)))
34021 (define-public r-zooarch
34028 (uri (cran-uri "zooaRch" version))
34031 "0grc378xppv0303sf4flfqz5002vq5a23nzbq4bsff41rww7dihc"))))
34032 (properties `((upstream-name . "zooaRch")))
34033 (build-system r-build-system)
34034 (propagated-inputs (list r-ggplot2))
34035 (native-inputs (list r-knitr))
34037 "https://cran.r-project.org/package=zooaRch")
34039 "Analytical Tools for Zooarchaeological Data")
34041 "The analysis and inference of faunal remains recovered from
34042 archaeological sites concerns the field of zooarchaeology. The zooaRch
34043 package provides analytical tools to make inferences on zooarchaeological
34044 data. Functions in this package allow users to read, manipulate, visualize,
34045 and analyze zooarchaeological data.")
34046 (license license:gpl2+)))
34048 (define-public r-zonebuilder
34050 (name "r-zonebuilder")
34055 (uri (cran-uri "zonebuilder" version))
34058 "0mxf3dz0d6bi5wwjilqivdxhy5ypnq5svky8zygha0clv45l4dmn"))))
34059 (properties `((upstream-name . "zonebuilder")))
34060 (build-system r-build-system)
34062 (list r-rcolorbrewer r-sf))
34065 (home-page "https://github.com/zonebuilders/zonebuilder")
34066 (synopsis "Create and explore geographic zoning systems")
34068 "This package provides functions, documentation and example data to help
34069 divide geographic space into discrete polygons (zones). The functions are
34070 motivated by research into the merits of different zoning systems. A flexible
34071 @code{ClockBoard} zoning system is provided, which breaks-up space by
34072 concentric rings and radial lines emanating from a central point.")
34073 (license license:gpl3)))
34075 (define-public r-zonator
34082 (uri (cran-uri "zonator" version))
34085 "1plxchpd4ypp36phl13pi9yvlrqi3lk83lv5rldrhdqynhcgfw2k"))))
34086 (properties `((upstream-name . "zonator")))
34087 (build-system r-build-system)
34089 (list r-ggplot2 r-raster r-rcolorbrewer r-reshape2 r-rgdal))
34090 (native-inputs (list r-knitr))
34091 (home-page "https://cbig.github.io/zonator/")
34092 (synopsis "Utilities for Zonation spatial conservation prioritization")
34094 "Create new analysis setups and deal with results of Zonation
34095 conservation prioritization software.")
34096 (license license:bsd-2)))
34098 (define-public r-mmwrweek
34100 (name "r-mmwrweek")
34105 (uri (cran-uri "MMWRweek" version))
34108 "1l1ks44v52iggw9nhs56lfj6804yab5b17k8fzrc6h1kvj3vda0s"))))
34109 (properties `((upstream-name . "MMWRweek")))
34110 (build-system r-build-system)
34111 (home-page "http://wwwn.cdc.gov/nndss/document/MMWR_Week_overview.pdf")
34112 (synopsis "Convert dates to MMWR day, week, and year")
34114 "The first day of any MMWR week is Sunday. MMWR week numbering is
34115 sequential beginning with 1 and incrementing with each week to a maximum of 52
34116 or 53. MMWR week #1 of an MMWR year is the first week of the year that has at
34117 least four days in the calendar year. This package provides functionality to
34118 convert dates to MMWR day, week, and year and the reverse.")
34119 (license license:gpl2+)))
34121 (define-public r-cccd
34128 (uri (cran-uri "cccd" version))
34130 (base32 "0cxh19jqappc6zq9nz3m40ybdmsp12mf7yvflsz96wks3ly2ld4y"))))
34131 (properties `((upstream-name . "cccd")))
34132 (build-system r-build-system)
34133 (propagated-inputs (list r-deldir r-fnn r-igraph r-proxy))
34134 (home-page "https://cran.r-project.org/package=cccd")
34135 (synopsis "Class cover catch digraphs")
34137 "This package provides tools to create Class Cover Catch Digraphs,
34138 neighborhood graphs, and relatives.")
34139 (license license:gpl2+)))
34141 (define-public r-crul
34148 (uri (cran-uri "crul" version))
34151 "0b8y12wb5kjylr8b4a2iarb5rpw1ydinw3lxp2ssq91pidyn2n40"))))
34152 (properties `((upstream-name . "crul")))
34153 (build-system r-build-system)
34161 (native-inputs (list r-knitr))
34162 (home-page "https://github.com/ropensci/crul")
34163 (synopsis "HTTP client")
34165 "This package provides a simple HTTP client, with tools for making HTTP
34166 requests, and mocking HTTP requests. The package is built on R6, and takes
34167 inspiration from Ruby's @code{faraday} gem.")
34168 (license license:expat)))
34170 (define-public r-gistr
34177 (uri (cran-uri "gistr" version))
34180 "0ac9ikrdg6i8xvlma0gizvsdva46408lk7hvsgkqirhy2ljy02hp"))))
34181 (properties `((upstream-name . "gistr")))
34182 (build-system r-build-system)
34192 (native-inputs (list r-knitr))
34193 (home-page "https://github.com/ropensci/gistr")
34194 (synopsis "Work with Gists in browser")
34196 "This package allows the user to create new Github gists, update gists
34197 with new files, rename files, delete files, get and delete gists, star and
34198 un-star them, fork them, open a gist in your default browser, get an embed
34199 code for a gist, list gist commits, and get rate limit information when
34201 (license license:expat)))
34203 (define-public r-rbokeh
34210 (uri (cran-uri "rbokeh" version))
34213 "1h2fpzqf17pw9d09r1g1iyxsj5qma4fsk8vnar7f1z4fjyypvi6q"))
34215 '(for-each delete-file '("inst/htmlwidgets/lib/bokehjs/bokeh-widgets.min.js"
34216 "inst/htmlwidgets/lib/bokehjs/bokeh.min.js")))))
34217 (properties `((upstream-name . "rbokeh")))
34218 (build-system r-build-system)
34221 (modify-phases %standard-phases
34222 (add-after 'unpack 'process-javascript
34223 (lambda* (#:key inputs #:allow-other-keys)
34224 (with-directory-excursion "inst/htmlwidgets/lib/bokehjs"
34226 `((,(assoc-ref inputs "js-bokeh-widgets")
34227 . "bokeh-widgets.min.js")
34228 (,(assoc-ref inputs "js-bokeh")
34229 . "bokeh.min.js"))))
34230 (for-each (lambda (source target)
34231 (format #true "Processing ~a --> ~a~%"
34233 (invoke "esbuild" source "--minify"
34234 (string-append "--outfile=" target)))
34236 (map cdr mapping)))))))))
34248 ;; Version 0.12.15 is mentioned in lib/htmlwidgets/rbokeh.yaml.
34250 `(("esbuild" ,esbuild)
34251 ("js-bokeh-widgets"
34254 (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh-widgets.js")
34257 "07v9lrkfcbdznpb10qqwi4m660zp65g85vlnfw7kn83zmkxkhhxy"))))
34261 (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh.js")
34264 "1pq0059aad7d2jv50nv9449p3w0gbkxkl0mhblc76m5d9qjqav2q"))))
34265 ("r-knitr" ,r-knitr)))
34266 (home-page "https://cran.r-project.org/web/packages/rbokeh/")
34267 (synopsis "R interface for the Bokeh visualization library")
34269 "This package provides a native R plotting library that provides a
34270 flexible declarative interface for creating interactive web-based graphics,
34271 backed by the @url{https://bokeh.pydata.org/, Bokeh visualization library}.")
34272 (license license:expat)))
34274 (define-public r-fauxpas
34281 (uri (cran-uri "fauxpas" version))
34284 "129fzqb7wsskbn50s8x0marr4wm8jrns6hiycqcsk166k3dnyyy8"))))
34285 (properties `((upstream-name . "fauxpas")))
34286 (build-system r-build-system)
34288 (list r-httpcode r-r6 r-whisker))
34291 (home-page "https://docs.ropensci.org/fauxpas")
34292 (synopsis "HTTP error helpers")
34294 "This package provides HTTP error helpers. Methods are included for
34295 general purpose HTTP error handling, as well as individual methods for every
34296 HTTP status code, both via status code numbers as well as their descriptive
34297 names. It supports the ability to adjust behavior to stop, message or
34298 warning. It includes the ability to use a custom whisker template to have any
34299 configuration of status code, short description, and verbose message.")
34300 (license license:expat)))
34302 (define-public r-webmockr
34304 (name "r-webmockr")
34309 (uri (cran-uri "webmockr" version))
34312 "06lqv3v095i51xsac8bvkjgd58l6a5azamchiip8m2y7q0nm4iw9"))))
34313 (properties `((upstream-name . "webmockr")))
34314 (build-system r-build-system)
34324 (home-page "https://github.com/ropensci/webmockr")
34325 (synopsis "Stubbing and setting expectations on HTTP Requests")
34327 "This is a package for stubbing and setting expectations on HTTP
34328 requests. It includes tools for stubbing HTTP requests, including expected
34329 request conditions and response conditions. You can match on HTTP method,
34330 query parameters, request body, headers and more. It can be used for unit
34331 tests or outside of a testing context.")
34332 (license license:expat)))
34334 (define-public r-iotools
34341 (uri (cran-uri "iotools" version))
34343 (base32 "07q0z0kszm1xx5hfhisfliyrcsxd8dc5mx0a2bwwnv5l1xzmix17"))))
34344 (properties `((upstream-name . "iotools")))
34345 (build-system r-build-system)
34346 (home-page "https://www.rforge.net/iotools")
34347 (synopsis "I/O tools for streaming")
34348 (description "This package provides basic I/O tools for streaming and data
34351 (license license:gpl3)))
34353 (define-public r-wordspace
34355 (name "r-wordspace")
34360 (uri (cran-uri "wordspace" version))
34362 (base32 "17fqd4zrsklv2ik3lg00x66yasfh1kyhs3k9ri6lrk56wwv6hzb2"))))
34363 (properties `((upstream-name . "wordspace")))
34364 (build-system r-build-system)
34366 (list r-cluster r-iotools r-mass r-matrix r-rcpp r-sparsesvd))
34367 (native-inputs (list r-knitr))
34368 (home-page "https://wordspace.r-forge.r-project.org/")
34369 (synopsis "Distributional semantic models in R")
34371 "The wordspace package turns R into an interactive laboratory for
34372 empirical research on @dfn{distributional semantic models} (DSM). It consists
34373 of a small set of carefully designed functions, most of which
34376 @item encapsulate non-trivial R operations in a user-friendly manner or
34377 @item provide efficient and memory-lean C implementations of key operations.
34380 (license license:gpl3)))
34382 (define-public r-maxlik
34389 (uri (cran-uri "maxLik" version))
34391 (base32 "0pdigfpyiqacj2ydhpn5w1h89dz1ydk0syzs25lsgdi40sz0bvkw"))))
34392 (properties `((upstream-name . "maxLik")))
34393 (build-system r-build-system)
34394 (propagated-inputs (list r-generics r-misctools r-sandwich))
34395 (home-page "https://cran.r-project.org/package=maxLik")
34396 (synopsis "Maximum Likelihood Estimation and related tools")
34398 "This package provides functions for @dfn{Maximum Likelihood} (ML) estimation,
34399 non-linear optimization, and related tools. It includes a unified way to call
34400 different optimizers, and classes and methods to handle the results from the
34401 Maximum Likelihood viewpoint. It also includes a number of convenience tools
34402 for testing and developing your own models.")
34403 (license license:gpl2+)))
34405 (define-public r-misctools
34407 (name "r-misctools")
34412 (uri (cran-uri "miscTools" version))
34414 (base32 "16pwfxpyl0zv3hjxx2kjchkg7p6kbj0s2rrpskj7rkhjr9imlg5y"))))
34415 (properties `((upstream-name . "miscTools")))
34416 (build-system r-build-system)
34417 (propagated-inputs (list r-digest))
34418 (home-page "http://www.micEcon.org")
34419 (synopsis "Miscellaneous tools and utilities")
34421 "This package provides miscellaneous small tools and utilities. Many of
34422 them facilitate the work with matrices, e.g. inserting rows or columns,
34423 creating symmetric matrices, or checking for semidefiniteness. Other tools
34424 facilitate the work with regression models, e.g. extracting the standard
34425 errors, obtaining the number of (estimated) parameters, or calculating
34426 R-squared values.")
34427 (license license:gpl2+)))
34429 (define-public r-mockery
34436 (uri (cran-uri "mockery" version))
34439 "0sj77m9vgn4bzb8c8nq93xb9lm8ih8rcb7sfccripraibibg3jcz"))))
34440 (properties `((upstream-name . "mockery")))
34441 (build-system r-build-system)
34446 (home-page "https://github.com/jfiksel/mockery")
34447 (synopsis "Mocking library for R")
34449 "The two main functionalities of this package are creating mock
34450 objects (functions) and selectively intercepting calls to a given function
34451 that originate in some other function. It can be used with any testing
34452 framework available for R. Mock objects can be injected with either this
34453 package's own @code{stub} function or a similar @code{with_mock} facility
34454 present in the @code{testthat} package.")
34455 (license license:expat)))
34457 (define-public r-zoltr
34464 (uri (cran-uri "zoltr" version))
34467 "12zh7y3pwidclscgvd0b0iaqq9j5y8mc8xd6pz4vs0jy5qs3ahar"))))
34468 (properties `((upstream-name . "zoltr")))
34469 (build-system r-build-system)
34481 (native-inputs (list r-knitr))
34482 (home-page "https://github.com/reichlab/zoltr")
34483 (synopsis "Interface to the Zoltar forecast repository API")
34485 "Zoltar is a website that provides a repository of model forecast results
34486 in a standardized format and a central location. It supports storing,
34487 retrieving, comparing, and analyzing time series forecasts for prediction
34488 challenges of interest to the modeling community. This package provides
34489 functions for working with the Zoltar API, including connecting and
34490 authenticating, getting information about projects, models, and forecasts,
34491 deleting and uploading forecast data, and downloading scores.")
34492 (license license:gpl3)))
34494 (define-public r-zoib
34501 (uri (cran-uri "zoib" version))
34504 "0inm7f2pc68ksqxvq12xp9jc99vj7ydylvs24ip12nksbj5k1n8f"))))
34505 (properties `((upstream-name . "zoib")))
34506 (build-system r-build-system)
34508 (list r-abind r-coda r-formula r-rjags))
34509 (home-page "https://www.r-project.org")
34510 (synopsis "Bayesian inference for beta regression")
34512 "This package lets you fit beta regression and zero-or-one inflated beta
34513 regression and obtain Bayesian inference of the model via the Markov Chain
34514 Monte Carlo approach implemented in JAGS.")
34515 (license license:gpl3+)))
34517 (define-public r-logger
34524 (uri (cran-uri "logger" version))
34526 (base32 "08kym5i5fvbf5xhh9qdszp4jdgyc7j7zpnwzy68wabqz73aff6sg"))))
34527 (properties `((upstream-name . "logger")))
34528 (build-system r-build-system)
34529 (native-inputs (list r-knitr))
34530 (home-page "https://daroczig.github.io/logger/")
34531 (synopsis "Lightweight and flexible logging utility")
34533 "Inspired by the the @code{futile.logger} R package and @code{logging}
34534 Python module, this utility provides a flexible and extensible way of
34535 formatting and delivering log messages with low overhead.")
34536 (license license:agpl3+)))
34538 (define-public r-fasterize
34540 (name "r-fasterize")
34545 (uri (cran-uri "fasterize" version))
34547 (base32 "10bzl77c1b9jhcn1xp467qzp2n8c7s3wpxn53qjh1nwvbri5kd32"))))
34548 (properties `((upstream-name . "fasterize")))
34549 (build-system r-build-system)
34551 (list r-raster r-rcpp r-rcpparmadillo r-sp))
34552 (native-inputs (list r-knitr))
34553 (home-page "https://github.com/ecohealthalliance/fasterize")
34554 (synopsis "Fast Polygon to Raster Conversion")
34556 "This package provides a drop-in replacement for @code{rasterize} from
34557 the @code{raster} package that takes sf-type objects, and is much faster.
34558 There is support for the main options provided by the @code{rasterize}
34559 function, including setting the field used and background value, and
34560 options for aggregating multi-layer rasters.")
34561 (license license:expat)))
34563 (define-public r-bien
34570 (uri (cran-uri "BIEN" version))
34572 (base32 "0s98n6zbf48vssd3h63k6kashcxv1kawcb026n0ngsfpc5dv6i48"))))
34573 (properties `((upstream-name . "BIEN")))
34574 (build-system r-build-system)
34589 (home-page "https://cran.r-project.org/package=BIEN")
34590 (synopsis "Tools for accessing the BIEN database")
34592 "This package provides tools for accessing the Botanical Information and
34593 Ecology Network (BIEN) database. The BIEN database contains cleaned and
34594 standardized botanical data including occurrence, trait, plot and taxonomic
34595 data. This package provides functions that query the BIEN database by
34596 constructing and executing optimized SQL queries.")
34597 (license license:expat)))
34599 (define-public r-varhandle
34601 (name "r-varhandle")
34606 (uri (cran-uri "varhandle" version))
34608 (base32 "1l42d0s6fbjjc9l28a2m3myxkrx2c0p0b9yj8wjjjgilw19yc3lv"))))
34609 (properties `((upstream-name . "varhandle")))
34610 (build-system r-build-system)
34611 (home-page "https://bitbucket.org/mehrad_mahmoudian/varhandle")
34612 (synopsis "Functions for robust variable handling")
34614 "This package contains some functions to help users (especially data
34615 explorers) to make more sense of their variables and take the most out of
34616 variables and hardware resources. Functions in this package are supposed to
34617 be efficient and easy to use.")
34618 (license license:gpl2+)))
34620 (define-public r-ggh4x
34627 (uri (cran-uri "ggh4x" version))
34630 "11mskrby3gyjhkvnkcwl2ar1bdh4h45y48dfnm4kzgc7nwvdl3ia"))))
34631 (properties `((upstream-name . "ggh4x")))
34632 (build-system r-build-system)
34643 (home-page "https://github.com/teunbrand/ggh4x")
34644 (synopsis "Extension for ggplot2")
34645 (description "This package is a @code{ggplot2} extension. It provides some
34646 utility functions that do not entirely fit within the grammar of graphics
34647 concept. The package extends @code{ggpplots} facets through customisation, by
34648 setting individual scales per panel, resizing panels and providing nested
34649 facets. It also allows multiple colour, fill scales per plot and hosts a
34650 smaller collection of stats, geoms and axis guides.")
34651 (license license:expat)))
34653 (define-public r-gghalves
34655 (name "r-gghalves")
34660 (uri (cran-uri "gghalves" version))
34663 "1lj4c38fzxwg8gy57ymf00lqjdplb7v2a0lnd262c1d5cavqiws4"))))
34664 (properties `((upstream-name . "gghalves")))
34665 (build-system r-build-system)
34667 (list r-ggplot2 r-gtable))
34670 (home-page "https://github.com/erocoar/gghalves")
34671 (synopsis "Compose half-half plots using your favourite geoms")
34672 (description "This package provides a @code{ggplot2} extension for easy
34673 plotting of half-half geom combinations. Think half boxplot and half
34674 jitterplot, or half violinplot and half dotplot.")
34675 (license license:expat)))
34677 (define-public r-zoeppritz
34679 (name "r-zoeppritz")
34683 (uri (cran-uri "zoeppritz" version))
34686 "1711szx9zz17q6pfinyzlyrw7m9772c8ywlixqar2l165bkjalgm"))))
34687 (properties `((upstream-name . "zoeppritz")))
34688 (build-system r-build-system)
34689 (home-page "https://cran.r-project.org/package=zoeppritz")
34690 (synopsis "Seismic reflection and scattering coefficients for waves")
34692 "The @code{r-zoeppritz} package calculates and plots scattering matrix
34693 coefficients or scattering amplitudes, for seismological P and S-waves at an
34695 (license license:gpl2+)))
34697 (define-public r-metadat
34703 (uri (cran-uri "metadat" version))
34706 "1f7mb3pw5d0akr09jjva06ay223izhpzbr21bapnw99x1kiybk7h"))))
34707 (properties `((upstream-name . "metadat")))
34708 (build-system r-build-system)
34709 (propagated-inputs (list r-mathjaxr))
34710 (home-page "https://github.com/wviechtb/metadat")
34711 (synopsis "Meta-Analysis Datasets")
34713 "This package provides a collection of meta-analysis datasets for teaching
34714 purposes, illustrating/testing meta-analytic methods, and validating published
34716 (license license:gpl2+)))
34718 (define-public r-mathjaxr
34720 (name "r-mathjaxr")
34724 (uri (cran-uri "mathjaxr" version))
34727 "0yf1sfkb2kjsplipl2v4k2gp20li9xzsynclg228sy0v243pdi7c"))
34728 (modules '((guix build utils)))
34731 (delete-file-recursively "src/mathjax/es5/input")
34732 (delete-file-recursively "src/mathjax/es5/output")
34733 (delete-file "src/mathjax/es5/tex-chtml-full.js")))))
34734 (properties `((upstream-name . "mathjaxr")))
34735 (build-system r-build-system)
34739 `(modify-phases %standard-phases
34740 (add-after 'unpack 'use-js-mathjax
34741 (lambda* (#:key inputs #:allow-other-keys)
34743 (search-input-directory
34744 inputs "/share/javascript/mathjax/es5/output")
34745 "src/mathjax/es5/output")
34747 (search-input-directory
34748 inputs "/share/javascript/mathjax/es5/input")
34749 "src/mathjax/es5/input")
34752 inputs "/share/javascript/mathjax/es5/tex-chtml-full.js")
34753 "src/mathjax/es5/tex-chtml-full.js"))))))
34755 (list js-mathjax-for-r-mathjaxr))
34756 (home-page "https://github.com/wviechtb/mathjaxr")
34757 (synopsis "Use Mathjax in Rd Files")
34759 "This package provides MathJax and macros to enable its use within Rd files
34760 for rendering equations in the HTML help files.")
34761 (license (list license:asl2.0 license:gpl3))))
34763 (define-public r-spacefillr
34765 (name "r-spacefillr")
34769 (uri (cran-uri "spacefillr" version))
34772 "0c4yasc1zizjmhd2ciyz86lg76fsrxvl19yjkb2fmkda9rmnc0bf"))))
34773 (properties `((upstream-name . "spacefillr")))
34774 (build-system r-build-system)
34775 (propagated-inputs (list r-rcpp))
34776 (home-page "https://github.com/tylermorganwall/spacefillr")
34777 (synopsis "Space-Filling Random and Quasi-Random Sequences")
34779 "@code{spacefillr} enables generation of random and quasi-random
34780 space-filling sequences. It supports the following sequences: Halton, Sobol,
34781 Owen-scrambled Sobol, Owen-scrambled Sobol with errors distributed as blue
34782 noise, progressive jittered, progressive multi-jittered (PMJ), PMJ with blue
34783 noise, PMJ02, and PMJ02 with blue noise. The package also includes a C++
34785 (license license:expat)))
34787 (define-public r-spacetime
34789 (name "r-spacetime")
34793 (uri (cran-uri "spacetime" version))
34796 "0nacy8a9mbxh22q248zxhnlcfrmgj9yslrgc3kj35zscmcks15s2"))))
34797 (properties `((upstream-name . "spacetime")))
34798 (build-system r-build-system)
34799 (propagated-inputs (list r-lattice r-sp r-zoo r-xts r-intervals))
34800 (native-inputs (list r-knitr))
34801 (home-page "https://github.com/edzer/spacetime/")
34802 (synopsis "Classes and methods for spatio-temporal data")
34804 "@command{spacetime} provides classes and methods for spatio-temporal
34805 data, including space-time regular lattices, sparse lattices, irregular data,
34806 and trajectories; utility functions for plotting data as map sequences (lattice
34807 or animation) or multiple time series; methods for spatial and temporal
34808 matching or aggregation, retrieving coordinates, print, summary, etc.")
34809 (license license:gpl2+)))
34811 (define-public r-gstat
34817 (uri (cran-uri "gstat" version))
34820 "19m4zcj1qvg6gs8yjr5ijvd6rrv4av5yp5rmhnb88f0m5qn06b0j"))))
34821 (properties `((upstream-name . "gstat")))
34822 (build-system r-build-system)
34823 (propagated-inputs (list r-lattice r-sp r-zoo r-spacetime r-fnn))
34824 (home-page "https://github.com/r-spatial/gstat/")
34825 (synopsis "Spatial and spatio-temporal geostatistical modelling,
34826 prediction and simulation")
34828 "This package enables variogram modelling, including: simple, ordinary and
34829 universal point or block (co)kriging; spatio-temporal kriging; and sequential
34830 Gaussian or indicator (co)simulation. It includes variogram and variogram map
34831 plotting utility functions, and supports @command{sf} and @command{stars}.")
34832 (license license:gpl2+)))
34834 (define-public r-automap
34840 (uri (cran-uri "automap" version))
34843 "0jz0p28gmx9cpzv4cz0xhbml3w1inf2nsd2ynbhmfxg5rm2f7dca"))))
34844 (properties `((upstream-name . "automap")))
34845 (build-system r-build-system)
34846 (propagated-inputs (list r-ggplot2
34852 (home-page "https://cran.r-project.org/package=automap")
34853 (synopsis "Automatic interpolation package")
34855 "@command{automap} performs an automatic interpolation by automatically
34856 estimating the variogram and then calling @command{gstat}.")
34857 (license (list license:gpl2+ license:gpl3+))))
34859 (define-public r-cartogram
34861 (name "r-cartogram")
34865 (uri (cran-uri "cartogram" version))
34868 "0kz8hwdr5n8llkylwaixnb66f4pzaxxniz57spxhqizmi6qay7yd"))))
34869 (properties `((upstream-name . "cartogram")))
34870 (build-system r-build-system)
34871 (propagated-inputs (list r-packcircles r-sf))
34872 (home-page "https://github.com/sjewo/cartogram/")
34873 (synopsis "Create cartograms with R")
34874 (description "This package enables construction of continuous and
34875 non-contiguous area cartograms.")
34876 (license license:gpl3)))
34878 (define-public r-measurements
34880 (name "r-measurements")
34884 (uri (cran-uri "measurements" version))
34887 "1kihavs9vgxwqjm9z1zjjngkmcwfsv8dg7nn9nrv5r06k5hv8bz6"))))
34888 (properties `((upstream-name . "measurements")))
34889 (build-system r-build-system)
34890 (home-page "https://cran.r-project.org/web/packages/measurements/")
34891 (synopsis "Tools for units of measurement")
34893 "This package provides a collection of tools to make working with physical
34894 measurements easier. One can convert between metric and imperial units, or
34895 calculate a dimension's unknown value from other dimensions' measurements.")
34896 (license license:gpl3)))
34898 (define-public r-sungeo
34901 (version "0.2.288")
34904 (uri (cran-uri "SUNGEO" version))
34907 "0c8y0ngx1020rw2v00rxmq8syd72f41ckik5sg7gigg7d80gi31w"))
34908 (modules '((guix build utils)))
34910 ;; Fortunately, the package does not actually use
34911 ;; rmapshaper, which has got a js/node dependency.
34912 ;; The only occurrence is in R/point2poly_tess.R,
34913 ;; where it is commented out.
34914 (substitute* "DESCRIPTION"
34915 (("rmapshaper,") ""))
34916 (substitute* "NAMESPACE"
34917 (("importFrom\\(rmapshaper,ms_dissolve\\)
34920 (properties `((upstream-name . "SUNGEO")))
34921 (build-system r-build-system)
34922 (propagated-inputs (list r-automap
34940 (home-page "https://github.com/zhukovyuri/SUNGEO/")
34941 (synopsis "Sub-National Geospatial Data Archive: Geoprocessing Toolkit")
34943 "Tools for integrating spatially-misaligned GIS datasets. Part of the
34944 Sub-National Geospatial Data Archive System.")
34945 (license license:gpl2)))
34948 ;;; Avoid adding new packages to the end of this file. To reduce the chances
34949 ;;; of a merge conflict, place them above by existing packages with similar
34950 ;;; functionality or similar names.