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)))
222 (uri (cran-uri "ca" version))
225 "095lk7p2b9835hc3a03c4019wg0baf0dhz6c2vqpaq1m9k4jy304"))))
226 (properties `((upstream-name . "ca")))
227 (build-system r-build-system)
228 (home-page "http://www.carme-n.org/")
229 (synopsis "Simple, multiple and joint correspondence analysis")
231 "This is a package for computation and visualization of simple,
232 multiple and joint correspondence analysis.")
233 ;; Any version of the GPL
234 (license license:gpl3+)))
236 (define-public r-cachem
243 (uri (cran-uri "cachem" version))
246 "0r0q5w8lsxak46crnkbi739qzys90hlw7cqqqhv99xzkpkvm554s"))))
247 (properties `((upstream-name . "cachem")))
248 (build-system r-build-system)
250 (list r-fastmap r-rlang))
251 (home-page "https://cachem.r-lib.org/")
252 (synopsis "Cache R objects with automatic pruning")
254 "This package provides key-value stores with automatic pruning. Caches
255 can limit either their total size or the age of the oldest object (or both),
256 automatically pruning objects to maintain the constraints.")
257 (license license:expat)))
259 (define-public r-collections
261 (name "r-collections")
266 (uri (cran-uri "collections" version))
268 (base32 "19y7nds67700zy6354s1i0aglgjylzv65psccz5x3ih8f48sakr3"))))
269 (properties `((upstream-name . "collections")))
270 (build-system r-build-system)
271 (home-page "https://github.com/randy3k/collections")
272 (synopsis "High performance container data types")
274 "This package provides high performance container data types such as
275 queues, stacks, deques, dicts and ordered dicts.")
276 (license license:expat)))
278 (define-public r-curry
285 (uri (cran-uri "curry" version))
288 "1ps9hvbnb02m0b8hlw4admwbziyjvswj08ldi2dk3ymnrpawcc29"))))
289 (properties `((upstream-name . "curry")))
290 (build-system r-build-system)
291 (home-page "https://github.com/thomasp85/curry")
292 (synopsis "Partial function application")
294 "Partial application is the process of reducing the arity of a function
295 by fixing one or more arguments, thus creating a new function lacking the
296 fixed arguments. The @code{curry} package provides three different ways of
297 performing partial function application by fixing arguments from either end of
298 the argument list (currying and tail currying) or by fixing multiple named
299 arguments (partial application). This package provides this functionality
300 through the @code{%<%}, @code{%-<%}, and @code{%><%} operators which allows
301 for a programming style comparable to modern functional languages. Compared
302 to other implementations such a @code{purrr::partial()} the operators in
303 @code{curry} composes functions with named arguments, aiding in autocomplete
305 (license license:gpl2+)))
307 (define-public r-datawizard
309 (name "r-datawizard")
314 (uri (cran-uri "datawizard" version))
317 "0cn9ixljf4l333d401pz5rcwqkzpl6d90as153j1wrkz9rjzm6i7"))))
318 (properties `((upstream-name . "datawizard")))
319 (build-system r-build-system)
324 (home-page "https://easystats.github.io/datawizard/")
325 (synopsis "Easy data wrangling")
327 "This package provides a lightweight package to easily manipulate,
328 clean, transform, and prepare your data for analysis. It also forms the data
329 wrangling backend for the packages in the @code{easystats} ecosystem.")
330 (license license:gpl3)))
332 (define-public r-dbscan
339 (uri (cran-uri "dbscan" version))
341 (base32 "0bz66lvvg7290c5260ph92k4r7adgisbx3vml9096qhjwrkqwjgh"))))
342 (properties `((upstream-name . "dbscan")))
343 (build-system r-build-system)
344 (propagated-inputs (list r-rcpp))
345 (native-inputs (list r-knitr))
346 (home-page "https://github.com/mhahsler/dbscan")
347 (synopsis "Density-based spatial clustering of applications with noise")
349 "This package provides a fast reimplementation of several density-based
350 algorithms of the DBSCAN family. It includes the clustering algorithms DBSCAN
351 (density-based spatial clustering of applications with noise) and
352 @dfn{hierarchical DBSCAN} (HDBSCAN), the ordering algorithm @dfn{ordering
353 points to identify the clustering structure} (OPTICS), shared nearest neighbor
354 clustering, and the outlier detection algorithms @dfn{local outlier
355 factor} (LOF) and @dfn{global-local outlier score from hierarchies} (GLOSH).
356 The implementations use the kd-tree data structure for faster k-nearest
357 neighbor search. An R interface to fast kNN and fixed-radius NN search is
359 (license license:gpl2+)))
361 (define-public r-diffobj
368 (uri (cran-uri "diffobj" version))
371 "0q6gwd9pqh41f6j5p9jl92aji4p8kx9inffpha93d7jc3ndsfq6q"))))
372 (properties `((upstream-name . "diffobj")))
373 (build-system r-build-system)
374 (propagated-inputs (list r-crayon))
375 (native-inputs (list r-knitr))
376 (home-page "https://github.com/brodieG/diffobj")
377 (synopsis "Diffs for R objects")
379 "Generate a colorized diff of two R objects for an intuitive
380 visualization of their differences.")
381 (license license:gpl2+)))
383 (define-public r-dirichletreg
385 (name "r-dirichletreg")
390 (uri (cran-uri "DirichletReg" version))
392 (base32 "1ql5mwb7zb06y9j6inrlngq7c15as4j17wd8kc71fxs0a2jdj7xi"))))
393 (properties `((upstream-name . "DirichletReg")))
394 (build-system r-build-system)
395 (propagated-inputs (list r-formula r-maxlik))
396 (native-inputs (list r-knitr))
397 (home-page "https://cran.r-project.org/package=DirichletReg")
398 (synopsis "Dirichlet regression")
399 (description "This package implements Dirichlet regression models.")
400 (license license:gpl2+)))
402 (define-public r-dixontest
409 (uri (cran-uri "dixonTest" version))
411 (base32 "0gz39s1z987bg56vwrpcs14wzyf7p07s7l7z9napz0i38564wsdq"))))
412 (properties `((upstream-name . "dixonTest")))
413 (build-system r-build-system)
414 (native-inputs (list gfortran))
415 (home-page "https://cran.r-project.org/package=dixonTest")
416 (synopsis "Dixon's ratio test for outlier detection")
418 "For outlier detection in small and normally distributed samples the ratio
419 test of Dixon (Q-test) can be used. Density, distribution function, quantile
420 function and random generation for Dixon's ratio statistics are provided as
421 wrapper functions. The core applies McBane's Fortran functions that use
422 Gaussian quadrature for a numerical solution.")
423 (license license:gpl3)))
425 (define-public r-dmwr2
431 (uri (cran-uri "DMwR2" version))
434 "1vzfbz2k05j8r2hpig3d2grb99rnnh2s1sviii3prcyqicxfh0i9"))))
435 (properties `((upstream-name . "DMwR2")))
436 (build-system r-build-system)
446 (home-page "https://github.com/ltorgo/DMwR2")
448 "Functions and data for the second edition of \"Data Mining with R\"")
450 "This package provides functions and data accompanying the second
451 edition of the book \"Data Mining with R, learning with case studies\"
452 by Luis Torgo, published by CRC Press.")
453 (license license:gpl2+)))
455 (define-public r-emdist
462 (uri (cran-uri "emdist" version))
465 "05mv6xhm15b0mq9kzyiblkb14bdqmjrwl64ghdk66il0w8i7p6nh"))))
466 (properties `((upstream-name . "emdist")))
467 (build-system r-build-system)
468 (home-page "http://www.rforge.net/emd")
469 (synopsis "Earth mover's distance")
471 "This package provides tools to calculate the Earth Mover's
473 (license license:expat)))
475 (define-public r-ggalt
481 (uri (cran-uri "ggalt" version))
484 "0ssa274d41vhd6crzjz7jqzbwgnjimxwxl23p2cx35aqs5wdfjpc"))))
485 (properties `((upstream-name . "ggalt")))
486 (build-system r-build-system)
501 (native-inputs (list r-knitr))
502 (home-page "https://github.com/hrbrmstr/ggalt")
504 "Geometries, coordinate systems, fonts and more for ggplot2")
506 "This package provides a compendium of new geometries, coordinate systems,
507 statistical transformations, scales and fonts for ggplot2, including splines,
508 1d and 2d densities, univariate average shifted histograms, a new map
509 coordinate system based on the PROJ.4-library along with
510 @code{geom_cartogram()} that mimics the original functionality of
511 @code{geom_map()}, formatters for \"bytes\", a @code{stat_stepribbon()}
512 function, increased @code{plotly} compatibility and the @code{StateFace} open
513 source font ProPublica. Further new functionality includes lollipop charts,
514 dumbbell charts, the ability to encircle points and coordinate-system-based
516 (license license:agpl3)))
518 (define-public r-glmpca
524 (uri (cran-uri "glmpca" version))
527 "02xjf0gg52925hw9nw2j0znfmzfzfwbv0fxjl9d2fy9j63drr2h4"))))
528 (properties `((upstream-name . "glmpca")))
529 (build-system r-build-system)
530 (propagated-inputs (list r-mass))
531 (native-inputs (list r-knitr))
532 (home-page "https://github.com/willtownes/glmpca")
533 (synopsis "Dimension Reduction of Non-Normally Distributed Data")
535 "This package implements a generalized version of principal components
536 analysis (GLM-PCA) for dimension reduction of non-normally distributed data
537 such as counts or binary matrices.")
538 (license license:lgpl3+)))
540 (define-public r-googledrive
542 (name "r-googledrive")
547 (uri (cran-uri "googledrive" version))
550 "09jsiknzyfgxd0nzdr3wrrjw24allch2x74h96qg8vh8dad4cp30"))))
551 (properties `((upstream-name . "googledrive")))
552 (build-system r-build-system)
570 (home-page "https://googledrive.tidyverse.org")
571 (synopsis "Interface to Google Drive")
572 (description "This package lets you manage Google Drive files from R.")
573 (license license:expat)))
575 (define-public r-googlevis
582 (uri (cran-uri "googleVis" version))
584 (base32 "1s82xcs6zrlmnhay764bspzwvabfyi35nq6fwdrrk3v79q13c5jz"))))
585 (properties `((upstream-name . "googleVis")))
586 (build-system r-build-system)
587 (propagated-inputs (list r-jsonlite))
588 (native-inputs (list r-knitr))
589 (home-page "https://mages.github.io/googleVis/")
590 (synopsis "R interface to Google Charts")
592 "The @code{googleVis} package provides an interface between R and the Google
593 Charts API. Google Charts offer interactive charts which can be embedded into
594 web pages. The functions of the @code{googleVis} package allow the user to
595 visualise data stored in R data frames with Google Charts without uploading
596 the data to Google. The output of a @code{googleVis} function is HTML code
597 that contains the data and references to JavaScript functions hosted by
598 Google. @code{googleVis} makes use of the internal R HTTP server to display
599 the output locally.")
600 (license license:gpl2+)))
602 (define-public r-guix-install
604 (name "r-guix-install")
609 (uri (cran-uri "guix.install" version))
611 (base32 "0s3wb5781yc43c9zwrn7i87zcbrlx7xr0ms0v9hvgs7qsv02id9j"))))
612 (properties `((upstream-name . "guix.install")))
613 (build-system r-build-system)
614 (propagated-inputs (list r-runit))
615 (home-page "https://github.com/BIMSBbioinfo/guix.install")
616 (synopsis "Install R packages with GNU Guix")
618 "This R package provides a single procedure @code{guix.install()}, which
619 allows users to install R packages via Guix right from within their running R
620 session. If the requested R package does not exist in Guix at this time, the
621 package and all its missing dependencies will be imported recursively and the
622 generated package definitions will be written to @file{~/.Rguix/packages.scm}.
623 This record of imported packages can be used later to reproduce the
624 environment, and to add the packages in question to a proper Guix channel (or
625 Guix itself). @code{guix.install()} not only supports installing packages
626 from CRAN, but also from Bioconductor or even arbitrary git or mercurial
627 repositories, replacing the need for installation via @code{devtools}.")
628 (license license:gpl3+)))
637 (uri (cran-uri "ids" version))
640 "1s6ga94gds5ydr9f8qbjfgfpg2dvbnkcrlybqlb33hk3c0c2l8dn"))))
641 (properties `((upstream-name . "ids")))
642 (build-system r-build-system)
644 (list r-openssl r-uuid))
645 (native-inputs (list r-knitr))
646 (home-page "https://github.com/richfitz/ids")
647 (synopsis "Generate random identifiers")
649 "This package lets you generate random or human readable and
650 pronounceable identifiers.")
651 (license license:expat)))
653 (define-public r-googlesheets4
655 (name "r-googlesheets4")
660 (uri (cran-uri "googlesheets4" version))
663 "14b5lzn6vjn72mw7vf3lzm2ppbjf0wr0n6sw0v5r6h4lk37cnki8"))))
664 (properties `((upstream-name . "googlesheets4")))
665 (build-system r-build-system)
681 (home-page "https://github.com/tidyverse/googlesheets4")
682 (synopsis "Access Google Sheets using the Sheets API V4")
684 "This package lets you interact with Google Sheets through the
685 @url{https://developers.google.com/sheets/api,Sheets API v4}. This package
686 can read and write both the metadata and the cell data in a Sheet.")
687 (license license:expat)))
689 (define-public r-proj4
695 (uri (cran-uri "proj4" version))
698 "07fil52jswbg2h807cd82m2wlm5j2fb891ifri9ms037099qdwf5"))))
699 (properties `((upstream-name . "proj4")))
700 (build-system r-build-system)
701 (inputs (list proj.4 zlib))
702 (native-inputs (list pkg-config))
703 (home-page "http://www.rforge.net/proj4/")
704 (synopsis "Simple interface to the PROJ.4 cartographic projections library")
706 "This package provides a simple interface to lat/long projection and
707 datum transformation of the PROJ.4 cartographic projections library. It
708 allows transformation of geographic coordinates from one projection and/or
710 (license license:gpl2)))
712 (define-public r-waldo
719 (uri (cran-uri "waldo" version))
722 "1aky28rn70l24s0sygl36267cf7hjzhchagsz26abfxwr7p8kvjp"))))
723 (properties `((upstream-name . "waldo")))
724 (build-system r-build-system)
733 (home-page "https://github.com/r-lib/waldo")
734 (synopsis "Find differences between R objects")
736 "Compare complex R objects and reveal the key differences. This package
737 was designed particularly for use in testing packages where being able to
738 quickly isolate key differences makes understanding test failures much
740 (license license:expat)))
742 (define-public r-rticles
749 (uri (cran-uri "rticles" version))
752 "05idvyfjfa4f244km4sxripg8gndvganx5s0ch00xbi4cqnlr2pq"))))
753 (properties `((upstream-name . "rticles")))
754 (build-system r-build-system)
756 (list r-knitr r-rmarkdown r-tinytex r-xfun r-yaml))
757 (home-page "https://github.com/rstudio/rticles")
758 (synopsis "Article formats for R Markdown")
760 "This package provides a suite of custom R Markdown formats and templates
761 for authoring journal articles and conference submissions.")
762 (license license:gpl3)))
764 (define-public r-babelwhale
766 (name "r-babelwhale")
771 (uri (cran-uri "babelwhale" version))
773 (base32 "01l8vwyz3bx0iks6cjs5y9ifdsnc1p1yqp4i0kzqd1gjhycizv6y"))))
774 (properties `((upstream-name . "babelwhale")))
775 (build-system r-build-system)
785 (home-page "https://github.com/dynverse/babelwhale")
786 (synopsis "Talking to Docker and Singularity containers")
788 "This package provides a unified interface to interact with Docker and
789 Singularity containers. You can execute a command inside a container, mount a
790 volume or copy a file.")
791 (license license:expat)))
793 (define-public r-benchmarkmedata
795 (name "r-benchmarkmedata")
799 (uri (cran-uri "benchmarkmeData" version))
802 "1n4vjkagqlm6kw2hilf4gjfcdjad0bcg652j9nl2ygbq3kdnh1vf"))))
803 (build-system r-build-system)
805 (list r-dplyr r-tibble))
806 (home-page "https://github.com/csgillespie/benchmarkme-data")
807 (synopsis "Data set for the @code{benchmarkme} package")
808 (description "This package contains the data set for the crowd-sourced
809 benchmarks from running the @code{benchmarkme} package.")
810 (license license:gpl2+)))
812 (define-public r-benchmarkme
814 (name "r-benchmarkme")
818 (uri (cran-uri "benchmarkme" version))
821 "0qaz8wy3n08k9lr8qljk5i8z8db18scbdc8m734aymd307h00w8x"))))
822 (build-system r-build-system)
826 (list r-benchmarkmedata
834 (home-page "https://csgillespie.github.io/benchmarkme/")
835 (synopsis "Crowd-sourced system benchmarks")
836 (description "This package provides functionality to benchmark your CPU
837 and compare against other CPUs. Also provides functions for obtaining system
838 specifications, such as RAM, CPU type, and R version.")
839 (license license:gpl2+)))
841 (define-public r-bezier
847 (uri (cran-uri "bezier" version))
850 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
851 (build-system r-build-system)
852 (home-page "https://cran.r-project.org/web/packages/bezier/")
853 (synopsis "Bezier curve and spline toolkit")
855 "This package is a toolkit for working with Bezier curves and splines.
856 The package provides functions for point generation, arc length estimation,
857 degree elevation and curve fitting.")
858 (license license:gpl2+)))
860 (define-public r-bwstest
867 (uri (cran-uri "BWStest" version))
869 (base32 "02amzlfprmw5pyis0dg0kg0x8xqh50a4vfdcxxmklrzik3b1vzzs"))))
870 (properties `((upstream-name . "BWStest")))
871 (build-system r-build-system)
872 (propagated-inputs (list r-memoise r-rcpp))
873 (home-page "https://github.com/shabbychef/BWStest")
874 (synopsis "Baumgartner Weiss Schindler Test of equal distributions")
876 "This package performs the Baumgartner-Weiss-Schindler two-sample test of
877 equal probability distributions (doi:10.2307/2533862). It also performs
878 similar rank-based tests for equal probability distributions due to Neuhauser
879 (doi:10.1080/10485250108832874) and Murakami
880 (doi:10.1080/00949655.2010.551516).")
881 (license license:lgpl3)))
890 (uri (cran-uri "V8" version))
893 "1w1zihmhrygn2i674wimbv7xqjnwlld4x3ndvh5dl4cdg7s1m24r"))))
894 (properties `((upstream-name . "V8")))
895 (build-system r-build-system)
898 (modify-phases %standard-phases
899 (add-after 'unpack 'find-v8
900 (lambda* (#:key inputs #:allow-other-keys)
901 (substitute* "configure"
903 (string-append "PKG_LIBS="
904 (assoc-ref inputs "libnode")
905 "/lib/libnode.so.64\n")))
906 (setenv "INCLUDE_DIR"
908 (assoc-ref inputs "libnode")
912 (assoc-ref inputs "libnode") "/lib")))))))
916 (list r-curl r-jsonlite r-rcpp))
919 (home-page "https://jeroen.cran.dev/V8")
920 (synopsis "Embedded JavaScript and WebAssembly engine for R")
922 "This package provides an R interface to V8: Google's JavaScript and
923 WebAssembly engine.")
924 (license license:expat)))
926 (define-public r-rvenn
933 (uri (cran-uri "RVenn" version))
936 "016m00xv59lkwm2is32v5nr4lw5a1ymdnz34r3ffflcv9bfrc6n4"))))
937 (properties `((upstream-name . "RVenn")))
938 (build-system r-build-system)
947 (native-inputs (list r-knitr))
948 (home-page "https://cran.r-project.org/package=RVenn")
949 (synopsis "Set operations for many sets")
951 "The base functions for set operations in @code{R} can be used for only two
952 sets. This package @code{RVenn} provides functions for dealing with multiple sets.
953 It uses @code{purr} to find the union, intersection and difference of three or
954 more sets. This package also provides functions for pairwise set operations among
955 several sets. Further, based on @code{ggplot2} and @code{ggforce}, a Venn diagram
956 can be drawn for two or three sets. For bigger data sets, a clustered heatmap
957 showing the presence or absence of the elements of the sets can be drawn based on
958 the @code{pheatmap} package. Finally, enrichment test can be applied to two sets
959 whether an overlap is statistically significant or not.")
960 (license license:gpl3)))
969 (uri (cran-uri "DOT" version))
972 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
973 (properties `((upstream-name . "DOT")))
974 (build-system r-build-system)
977 (home-page "http://haghish.com/dot")
978 (synopsis "Render and Export DOT Graphs in R")
980 "This package provides tools to render DOT diagram markup language in R
981 and also provides the possibility to export the graphs in PostScript and
982 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
983 programming packages such as @code{knitr} and @code{rmarkdown}.")
984 (license license:expat)))
986 (define-public r-carrier
993 (uri (cran-uri "carrier" version))
995 (base32 "0bqnwnnjqjk9q0lxq6kkz9s75ss10lfyyywyyi24m8wppxpw1vqc"))))
996 (properties `((upstream-name . "carrier")))
997 (build-system r-build-system)
999 (list r-pryr r-rlang))
1000 (home-page "https://github.com/r-lib/carrier")
1001 (synopsis "Isolate functions for remote execution")
1003 "Sending functions to remote processes can be wasteful of resources
1004 because they carry their environments with them. With this package, it is
1005 easy to create functions that are isolated from their environment. These
1006 isolated functions, also called crates, print to the console with their total
1007 size and can be easily tested locally before being sent to a remote.")
1008 (license license:gpl3)))
1010 (define-public r-clipr
1017 (uri (cran-uri "clipr" version))
1020 "1s9vvv3cxnz8w11gsi8z9ddv9jzib5qf5qqxnwqrrv7vj8cr7hij"))))
1021 (build-system r-build-system)
1024 (home-page "https://github.com/mdlincoln/clipr")
1025 (synopsis "Read and write from the system clipboard")
1027 "This package provides simple utility functions to read from and write to
1028 the system clipboards.")
1029 (license license:gpl3)))
1031 (define-public r-clvalid
1037 (uri (cran-uri "clValid" version))
1040 "18aiyjhnh5mfdxbzns4cy0r8bymfikhwkybpn4g04qhli5ls8z83"))))
1041 (properties `((upstream-name . "clValid")))
1042 (build-system r-build-system)
1043 (propagated-inputs (list r-class r-cluster))
1044 (home-page "https://cran.r-project.org/package=clValid")
1045 (synopsis "Validation of clustering results")
1047 "Statistical and biological validation of clustering results. This
1048 package implements Dunn Index, Silhouette, Connectivity, Stability, BHI and
1049 BSI. Further information can be found in Brock, G et al. (2008) <doi:
1050 10.18637/jss.v025.i04>.")
1051 (license license:lgpl3)))
1053 (define-public r-dlm
1060 (uri (cran-uri "dlm" version))
1062 (base32 "1aksm66sfa7ipl5xgs4j5giac7q2m744wjl40mva56xn6i674h4r"))))
1063 (properties `((upstream-name . "dlm")))
1064 (build-system r-build-system)
1065 (home-page "https://cran.r-project.org/package=dlm")
1066 (synopsis "Bayesian and Likelihood Analysis of Dynamic Linear Models")
1068 "This package provides routines for Maximum likelihood, Kalman filtering
1069 and smoothing, and Bayesian analysis of Normal linear State Space models, also
1070 known as Dynamic Linear Models.")
1071 (license license:gpl2+)))
1073 (define-public r-zoo
1079 (uri (cran-uri "zoo" version))
1082 "19cw09bhwj2qyd72765ym1cm2wmhh801ccif889nzq5gfpw513l4"))))
1083 (build-system r-build-system)
1086 (home-page "http://zoo.R-Forge.R-project.org/")
1087 (synopsis "S3 infrastructure for regular and irregular time series")
1088 (description "This package contains an S3 class with methods for totally
1089 ordered indexed observations. It is particularly aimed at irregular time
1090 series of numeric vectors/matrices and factors.")
1091 (license license:gpl2+)))
1093 (define-public r-fontawesome
1095 (name "r-fontawesome")
1100 (uri (cran-uri "fontawesome" version))
1102 (base32 "0br4sjl2z5av5kf42mnp35sichk3syrz68xic08wxnqdnp2hn2kn"))))
1103 (properties `((upstream-name . "fontawesome")))
1104 (build-system r-build-system)
1106 (list r-htmltools r-rlang))
1107 (home-page "https://github.com/rstudio/fontawesome")
1108 (synopsis "Easily work with Font Awesome icons")
1110 "Easily and flexibly insert Font Awesome icons into R Markdown documents
1111 and Shiny apps. These icons can be inserted into HTML content through inline
1112 SVG tags or @code{i} tags. There is also a utility function for exporting
1113 Font Awesome icons as PNG images for those situations where raster graphics
1115 (license license:expat)))
1117 (define-public r-fingerprint
1119 (name "r-fingerprint")
1124 (uri (cran-uri "fingerprint" version))
1126 (base32 "04jcwkydjrs31pia6kq8z2n9s54im950q08hs2ay15xjxxkmb8ic"))))
1127 (properties `((upstream-name . "fingerprint")))
1128 (build-system r-build-system)
1129 (home-page "https://cran.r-project.org/package=fingerprint")
1130 (synopsis "Functions to Operate on Binary Fingerprint Data")
1132 "This package provides functions to manipulate binary fingerprints of
1133 arbitrary length. A fingerprint is represented by an object of S4 class
1134 @code{fingerprint}. The bitwise logical functions in R are overridden so that
1135 they can be used directly with @code{fingerprint} objects. A number of
1136 distance metrics are also available. Fingerprints can be converted to
1137 Euclidean vectors (i.e., points on the unit hypersphere) and can also be
1138 folded. Arbitrary fingerprint formats can be handled via line handlers.
1139 Currently handlers are provided for CDK, MOE and BCI fingerprint data.")
1140 ;; Any version of the GPL
1141 (license (list license:gpl2+ license:gpl3+))))
1143 (define-public r-fpeek
1150 (uri (cran-uri "fpeek" version))
1152 (base32 "0kv46g21ndxchg3q8ynq7hjjkh6i2zlc21axn5y1jjzigrw047ii"))))
1153 (properties `((upstream-name . "fpeek")))
1154 (build-system r-build-system)
1155 (propagated-inputs (list r-rcpp))
1156 (home-page "https://github.com/davidgohel/fpeek")
1157 (synopsis "Check text files content at a glance")
1159 "This package provides tools to help working with text files. It can
1160 return the number of lines; print the first and last lines; convert encoding.
1161 Operations are made without reading the entire file before starting, resulting
1162 in good performances with large files.")
1163 (license license:expat)))
1165 (define-public r-ggalluvial
1167 (name "r-ggalluvial")
1171 (uri (cran-uri "ggalluvial" version))
1174 "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3"))))
1175 (properties `((upstream-name . "ggalluvial")))
1176 (build-system r-build-system)
1186 (home-page "http://corybrunson.github.io/ggalluvial/")
1187 (synopsis "Alluvial plots for ggplot2")
1188 (description "This package provides alluvial plots for @code{ggplot2}.
1189 Alluvial plots use variable-width ribbons and stacked bar plots to represent
1190 multi-dimensional or repeated-measures data with categorical or ordinal
1192 (license license:gpl3)))
1194 (define-public r-ggpp
1201 (uri (cran-uri "ggpp" version))
1204 "02inwvfz2zxsj7bq0nz11c5spnyaf8zhjnlfllpwfjfy46qrx2p9"))))
1205 (properties `((upstream-name . "ggpp")))
1206 (build-system r-build-system)
1224 (home-page "https://docs.r4photobiology.info/ggpp/")
1225 (synopsis "Grammar extensions to ggplot2")
1227 "This package contains extensions to ggplot2.
1230 @item Geomas: @code{geom_table}, @code{geom_plot} and @code{geom_grob} add
1231 insets to plots using native data coordinates, while @code{geom_table_npc},
1232 @code{geom_plot_npc} and @code{geom_grob_npc} do the same using @code{npc}
1233 coordinates through new aesthetics @code{npcx} and @code{npcy}.
1234 @item Statistics: select observations based on 2D density.
1235 @item Positions: radial nudging away from a center point and nudging away from
1239 (license license:gpl2+)))
1241 (define-public r-ggprism
1247 (uri (cran-uri "ggprism" version))
1250 "09dh0r8r5s61i5dbk6rswajc2vm7k8wvlqyvzq8wr160676lycjp"))))
1251 (properties `((upstream-name . "ggprism")))
1252 (build-system r-build-system)
1261 (native-inputs (list r-knitr))
1262 (home-page "https://csdaw.github.io/ggprism/")
1263 (synopsis "ggplot2 extension inspired by GraphPad Prism")
1265 "This package provides various themes, palettes, and other functions that are
1266 used to customise ggplots to look like they were made in GraphPad Prism. The
1267 Prism-look is achieved with @code{theme_prism()} and
1268 @code{scale_fill|colour_prism()}, axes can be changed with custom guides like
1269 @code{guide_prism_minor()}, and significance indicators added with
1270 @code{add_pvalue()}.")
1271 (license license:gpl3+)))
1273 (define-public r-ggrastr
1279 (uri (cran-uri "ggrastr" version))
1282 "07sx5wlawfyb0zy5am2q1ajhkdym5r9ih47p57l8bv4dlc7ykml2"))))
1283 (properties `((upstream-name . "ggrastr")))
1284 (build-system r-build-system)
1285 (propagated-inputs (list r-cairo r-ggbeeswarm r-ggplot2 r-png r-ragg))
1286 (native-inputs (list r-knitr))
1287 (home-page "https://github.com/VPetukhov/ggrastr")
1288 (synopsis "Rasterize layers for ggplot2")
1290 "Rasterize only specific layers of a ggplot2 plot while simultaneously keeping
1291 all labels and text in vector format. This allows users to keep plots within
1292 the reasonable size limit without losing vector properties of the
1293 scale-sensitive information.")
1294 (license license:expat)))
1296 (define-public r-ggvenn
1302 (uri (cran-uri "ggvenn" version))
1305 "0bm52j3idchignp6nrw7c76jlbfkjf5zng258957vq019vx9qxrq"))))
1306 (properties `((upstream-name . "ggvenn")))
1307 (build-system r-build-system)
1308 (propagated-inputs (list r-dplyr r-ggplot2))
1309 (home-page "https://cran.r-project.org/package=ggvenn")
1310 (synopsis "Draw Venn diagram with ggplot2")
1312 "This package offers an easy to use way to draw a Venn diagram with
1314 (license license:expat)))
1316 (define-public r-ggvenndiagram
1318 (name "r-ggvenndiagram")
1323 (uri (cran-uri "ggVennDiagram" version))
1326 "1l4cincm7c2q9x3djiv1lm9bvivaqk7kincx19b8f760wz9hp74k"))))
1327 (properties `((upstream-name . "ggVennDiagram")))
1328 (build-system r-build-system)
1339 (native-inputs (list r-knitr))
1340 (home-page "https://github.com/gaospecial/ggVennDiagram")
1341 (synopsis "Implementention of the Venn diagram using ggplot2")
1343 "This package implements easy-to-use functions to generate 2-7 sets Venn
1344 plot in publication quality. @code{ggVennDiagram} plot Venn using
1345 well-defined geometry dataset and @code{ggplot2}. The shapes of 2-4 sets Venn
1346 use circles and ellipses, while the shapes of 4-7 sets Venn use irregular
1347 polygons (4 has both forms), which are developed and imported from another
1348 package @code{venn}. We provide internal functions to integrate shape data
1349 with user provided sets data, and calculated the geometry of every
1350 regions/intersections of them, then separately plot Venn in three components:
1351 set edges, set labels, and regions. From version 1.0, it is possible to
1352 customize these components as you demand in ordinary @code{ggplot2} grammar.")
1353 (license license:gpl3)))
1355 (define-public r-lmds
1362 (uri (cran-uri "lmds" version))
1364 (base32 "130azb0nc2wwxv0qi8v5s4rd02p9lc92zwn634pv7b8awbw81i65"))))
1365 (properties `((upstream-name . "lmds")))
1366 (build-system r-build-system)
1368 (list r-assertthat r-dynutils r-irlba r-matrix))
1369 (home-page "https://github.com/dynverse/lmds")
1370 (synopsis "Landmark multi-dimensional scaling")
1372 "This package provides a fast dimensionality reduction method scalable
1373 to large numbers of samples. @dfn{Landmark Multi-Dimensional Scaling} (LMDS)
1374 is an extension of classical Torgerson MDS, but rather than calculating a
1375 complete distance matrix between all pairs of samples, only the distances
1376 between a set of landmarks and the samples are calculated.")
1377 (license license:gpl3)))
1379 (define-public r-lmodel2
1386 (uri (cran-uri "lmodel2" version))
1388 (base32 "1fiin2nkffbihz1s8ixmw9lgf8mn3j9krr8iiflizk10mdv54hnb"))))
1389 (properties `((upstream-name . "lmodel2")))
1390 (build-system r-build-system)
1391 (home-page "https://cran.r-project.org/package=lmodel2")
1392 (synopsis "Model II regression")
1394 "This package computes model II simple linear regression using
1395 @dfn{ordinary least squares} (OLS), @dfn{major axis} (MA), @dfn{standard major
1396 axis} (SMA), and @dfn{ranged major axis} (RMA).")
1397 (license license:gpl2)))
1399 (define-public r-ggpmisc
1405 (uri (cran-uri "ggpmisc" version))
1408 "18085n6id5v3g3w1z1010im85i4yii4wib2cmcxwqk7qvk9rsrqi"))))
1409 (build-system r-build-system)
1428 (home-page "https://www.r4photobiology.info/")
1429 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
1430 (description "This package provides extensions to @code{ggplot2},
1431 respecting the grammar of its graphics paradigm.")
1432 (license license:gpl2+)))
1434 (define-public r-ggside
1440 (uri (cran-uri "ggside" version))
1443 "1vl7kzgmi5xxxsqvyg4cm4xwd3lfjgysay1lw6hri5vj22mnga5h"))))
1444 (properties `((upstream-name . "ggside")))
1445 (build-system r-build-system)
1453 (native-inputs (list r-knitr))
1454 (home-page "https://cran.r-project.org/package=ggside")
1455 (synopsis "Side grammar graphics that extends @code{ggplot2}")
1457 "The grammar of graphics as shown in @code{ggplot2} has provided an
1458 expressive API for users to build plots. This package @{ggside} extends
1459 @code{ggplot2} by allowing users to add graphical information about one of the
1460 main panel's axis using a familiar @code{ggplot2} style API with tidy data.
1461 This package is particularly useful for visualizing metadata on a discrete
1462 axis, or summary graphics on a continuous axis such as a boxplot or a density
1464 (license license:expat)))
1466 (define-public r-gprofiler
1468 (name "r-gprofiler")
1473 (uri (cran-uri "gProfileR" version))
1476 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
1477 (properties `((upstream-name . "gProfileR")))
1478 (build-system r-build-system)
1480 (list r-plyr r-rcurl))
1481 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
1482 (synopsis "Interface to the g:Profiler toolkit")
1484 "This package provides tools for functional enrichment analysis,
1485 gene identifier conversion and mapping homologous genes across related
1486 organisms via the @code{g:Profiler} toolkit.")
1487 (license license:gpl2+)))
1489 (define-public r-gprofiler2
1491 (name "r-gprofiler2")
1496 (uri (cran-uri "gprofiler2" version))
1499 "0r0h34b35xzgd9rh55yndn0anxy0z45zdlqa6qfmpn91b6v1bb1g"))))
1500 (properties `((upstream-name . "gprofiler2")))
1501 (build-system r-build-system)
1512 (native-inputs (list r-knitr))
1513 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
1514 (synopsis "Interface to the g:Profiler toolset")
1516 "This package provides a toolset for functional enrichment analysis and
1517 visualization, gene/protein/SNP identifier conversion and mapping orthologous
1518 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
1522 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
1524 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
1526 @item @code{g:Orth}, orthology search across species;
1527 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
1528 genes and variant effects.
1531 This package is an R interface corresponding to the 2019 update of
1532 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
1534 (license license:gpl2+)))
1536 (define-public r-oenb
1543 (uri (cran-uri "oenb" version))
1546 "1jgxw7ycx2lcdzglg9nix8k08fs4r6i5jdsjzrd6w1dg6smsinl5"))))
1547 (properties `((upstream-name . "oenb")))
1548 (build-system r-build-system)
1550 (list r-dplyr r-xml))
1551 (native-inputs (list r-knitr))
1552 (home-page "https://github.com/franzmohr/oenb")
1553 (synopsis "Tools for the OeNB Data Web Service")
1555 "Tools to access data from the data web service of the
1556 @acronym{OeNB, Oesterreichische Nationalbank},
1557 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
1558 (license license:gpl2+)))
1560 (define-public r-orgmassspecr
1562 (name "r-orgmassspecr")
1566 (uri (cran-uri "OrgMassSpecR" version))
1569 "1dx9d8rb1dfqyhyc26zhfnxiv3rz2ikvs2mwqnsrq3lsjs9dvyc8"))))
1570 (properties `((upstream-name . "OrgMassSpecR")))
1571 (build-system r-build-system)
1572 (native-inputs (list r-knitr))
1573 (home-page "http://OrgMassSpec.github.io/")
1574 (synopsis "Organic or biological mass spectrometry data analysis")
1576 "This package @code{OrgMassSpecR} is an extension of the @code{R}
1577 statistical computing language. It contains functions to assist with organic
1578 or biological mass spectrometry data analysis. Mass spectral libraries are
1579 available as companion packages.")
1580 (license license:bsd-2)))
1582 (define-public r-scales
1589 (uri (cran-uri "scales" version))
1591 (base32 "027daznawr9dy0z9s99lh64i4am691hdir01n7gr7vmgpmnkwiar"))))
1592 (build-system r-build-system)
1602 (home-page "https://github.com/hadley/scales")
1603 (synopsis "Scale functions for visualization")
1605 "This package provides graphical scales that map data to aesthetics, and
1606 provides methods for automatically determining breaks and labels for axes and
1608 (license license:expat)))
1610 (define-public r-pacman
1616 (uri (cran-uri "pacman" version))
1619 "0z7gngd6h83cpjhq1vg75wvzhdjbgjh7gj5d4zvvi9gd2lmagjcy"))))
1620 (build-system r-build-system)
1623 (home-page "https://github.com/trinker/pacman")
1624 (synopsis "Package Management Tool")
1625 (description "This package provides tools to more conveniently perform
1626 tasks associated with add-on packages. @code{pacman} conveniently wraps
1627 library and package related functions and names them in an intuitive and
1628 consistent fashion. It seeks to combine functionality from lower level
1629 functions which can speed up workflow.")
1630 (license license:gpl2)))
1632 (define-public r-paralleldist
1634 (name "r-paralleldist")
1639 (uri (cran-uri "parallelDist" version))
1641 (base32 "01ly4hxwa64a0ya5gla8rvv72s9mcknsfznivjkh937pbjwb7iih"))))
1642 (properties `((upstream-name . "parallelDist")))
1643 (build-system r-build-system)
1644 (propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppparallel))
1645 (home-page "https://github.com/alexeckert/parallelDist")
1646 (synopsis "Parallel Distance Matrix Computation using multiple threads")
1648 "This package provides a fast parallelized alternative to R's native
1649 @code{dist} function to calculate distance matrices for continuous, binary,
1650 and multi-dimensional input matrices, which supports a broad variety of
1651 predefined distance functions from other R packages, as well as user- defined
1652 functions written in C++. For ease of use, the @code{parDist} function
1653 extends the signature of the @code{dist} function and uses the same parameter
1654 naming conventions as distance methods of existing R packages.")
1655 (license license:gpl2+)))
1657 (define-public r-pheatmap
1664 (uri (cran-uri "pheatmap" version))
1667 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
1668 (build-system r-build-system)
1670 (list r-gtable r-rcolorbrewer r-scales))
1671 (home-page "https://cran.r-project.org/web/packages/pheatmap")
1672 (synopsis "Pretty heatmaps")
1674 "This package provides an implementation of heatmaps that offers more
1675 control over dimensions and appearance.")
1676 (license license:gpl2+)))
1678 (define-public r-philentropy
1680 (name "r-philentropy")
1684 (uri (cran-uri "philentropy" version))
1687 "1dpf4hfflp4mcql4na46wzcq1flabkipiwyycz9wj5xbxlmcz2hk"))))
1688 (properties `((upstream-name . "philentropy")))
1689 (build-system r-build-system)
1690 (propagated-inputs (list r-kernsmooth r-poorman r-rcpp))
1691 (native-inputs (list r-knitr))
1692 (home-page "https://github.com/drostlab/philentropy")
1694 "Similarity and distance quantification between probability functions")
1696 "This package computes optimized distance and similarity measures for
1697 comparing probability functions (Drost (2018) <doi:10.21105/joss.00765>).
1698 These comparisons between probability functions have their foundations in a
1699 broad range of scientific disciplines from mathematics to ecology. The aim of
1700 this package is to provide a core framework for clustering, classification,
1701 statistical inference, goodness-of-fit, non-parametric statistics, information
1702 theory, and machine learning tasks that are based on comparing univariate or
1703 multivariate probability functions.")
1704 (license license:gpl2)))
1706 (define-public r-pnwcolors
1708 (name "r-pnwcolors")
1713 (uri (cran-uri "PNWColors" version))
1716 "1phplnclkficfv8s6wsyrckk4ixzbayiy5iix6dddg40485l9nyj"))))
1717 (properties `((upstream-name . "PNWColors")))
1718 (build-system r-build-system)
1719 (home-page "https://github.com/jakelawlor/PNWColors")
1720 (synopsis "Color palettes for data visualizations")
1722 "This package provides color palettes. They are checked for colorblind
1723 accessibility from hue, saturation, and lightness value scaling using the
1724 Chroma.js Color Palette Helper. See @url{https://gka.github.io/palettes}.")
1725 (license license:cc0)))
1727 (define-public r-plotfunctions
1729 (name "r-plotfunctions")
1734 (uri (cran-uri "plotfunctions" version))
1736 (base32 "0asmxw8283fpvl83h478j5nyg59xqifqaa8f2f6l199gvvswhhg2"))))
1737 (properties `((upstream-name . "plotfunctions")))
1738 (build-system r-build-system)
1739 (native-inputs (list r-knitr))
1740 (home-page "https://jacolienvanrij.com/tutorials.html")
1741 (synopsis "Various functions to facilitate visualization of data and analysis")
1743 "When analyzing data, plots are a helpful tool for visualizing data and
1744 interpreting statistical models. This package provides a set of simple tools
1745 for building plots incrementally, starting with an empty plot region, and
1746 adding bars, data points, regression lines, error bars, gradient legends,
1747 density distributions in the margins, and even pictures. The package builds
1748 further on R graphics by simply combining functions and settings in order to
1749 reduce the amount of code to produce for the user. As a result, the package
1750 does not use formula input or special syntax, but can be used in combination
1751 with default R plot functions.")
1752 (license license:gpl2+)))
1754 (define-public r-polychrome
1756 (name "r-polychrome")
1761 (uri (cran-uri "Polychrome" version))
1763 (base32 "0hyi02m2jpdhk1ky6ihz6dv5pwqwjwk4csjim2qr8ywx8midmrvg"))))
1764 (properties `((upstream-name . "Polychrome")))
1765 (build-system r-build-system)
1767 (list r-colorspace r-scatterplot3d))
1770 (home-page "http://oompa.r-forge.r-project.org/")
1771 (synopsis "Qualitative palettes with many colors")
1773 "This package provides tools for creating, viewing, and assessing
1774 qualitative palettes with many (20-30 or more) colors. See Coombes and
1775 colleagues (2019) @url{https://doi:10.18637/jss.v090.c01}.")
1776 (license license:asl2.0)))
1778 (define-public r-polylabelr
1780 (name "r-polylabelr")
1784 (uri (cran-uri "polylabelr" version))
1787 "01b2v0l5g8nxwbd6nwqv8ahypgh6gfhd4qabg75brlj7z1iyfzf2"))))
1788 (properties `((upstream-name . "polylabelr")))
1789 (build-system r-build-system)
1790 (propagated-inputs (list r-rcpp))
1791 (home-page "https://github.com/jolars/polylabelr")
1792 (synopsis "Finding pole of inaccessibility (visual center) of a polygon")
1794 "This package provides a wrapper around the @code{C++} library @code{
1795 polylabel} from @code{Mapbox}, providing an efficient routine for finding the
1796 approximate pole of inaccessibility of a polygon, which usually serves as an
1797 excellent candidate for labeling of a polygon.")
1798 (license license:expat)))
1800 (define-public r-poorman
1806 (uri (cran-uri "poorman" version))
1809 "0x1pk00ca7wjxnqfh1jphgsxcrq37s0c1nawv52yh5qgc4z0m3ij"))))
1810 (properties `((upstream-name . "poorman")))
1811 (build-system r-build-system)
1812 (native-inputs (list r-knitr))
1813 (home-page "https://nathaneastwood.github.io/poorman/")
1814 (synopsis "Dependency-free recreation of dplyr")
1816 "This package provides a replication of key functionality from
1817 @code{dplyr} and the wider @code{tidyverse} using only @code{base}.")
1818 (license license:expat)))
1820 (define-public r-ecp
1826 (uri (cran-uri "ecp" version))
1829 "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8"))))
1830 (build-system r-build-system)
1833 (home-page "https://cran.r-project.org/web/packages/ecp/")
1834 (synopsis "Multiple change-point analysis of multivariate data")
1836 "This package implements various procedures for finding multiple
1837 change-points. Two methods make use of dynamic programming and pruning, with
1838 no distributional assumptions other than the existence of certain absolute
1839 moments in one method. Hierarchical and exact search methods are included.
1840 All methods return the set of estimated change-points as well as other summary
1842 (license license:gpl2+)))
1844 (define-public r-ellipsis
1851 (uri (cran-uri "ellipsis" version))
1854 "0n0mm9jngklv7j9wa64jdji035z0smmnsp2dfwcz9isrxgjnc0m9"))))
1855 (build-system r-build-system)
1858 (home-page "https://github.com/hadley/ellipsis")
1859 (synopsis "Tools for working with additional arguments")
1861 "In S3 generics, it's useful to take @code{...} so that methods can have
1862 additional arguments. But this flexibility comes at a cost: misspelled
1863 arguments will be silently ignored. The @code{ellipsis} package is an
1864 experiment that allows a generic to warn if any arguments passed in @code{...}
1866 (license license:gpl3)))
1875 (uri (cran-uri "GA" version))
1877 (base32 "0q0br75zklnp0g3j98x6lll5fhyayxqzaqs3hc2z39s2imwi2fpb"))))
1878 (properties `((upstream-name . "GA")))
1879 (build-system r-build-system)
1889 (home-page "https://luca-scr.github.io/GA/")
1890 (synopsis "Genetic algorithms for stochastic optimisation")
1892 "Flexible general-purpose toolbox implementing genetic algorithms (GAs)
1893 for stochastic optimisation. Binary, real-valued, and permutation
1894 representations are available to optimize a fitness function, i.e., a function
1895 provided by users depending on their objective function. Several genetic
1896 operators are available and can be combined to explore the best settings for
1897 the current task. Furthermore, users can define new genetic operators and
1898 easily evaluate their performances. Local search using general-purpose
1899 optimisation algorithms can be applied stochastically to exploit interesting
1900 regions. GAs can be run sequentially or in parallel, using an explicit
1901 master-slave parallelisation or a coarse-grain islands approach.")
1902 (license license:gpl2+)))
1904 (define-public r-grr
1911 (uri (cran-uri "grr" version))
1914 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
1915 (build-system r-build-system)
1916 (home-page "https://cran.r-project.org/web/packages/grr")
1917 (synopsis "Alternative implementations of base R functions")
1919 "This package provides alternative implementations of some base R
1920 functions, including @code{sort}, @code{order}, and @code{match}. The
1921 functions are simplified but can be faster or have other advantages.")
1922 (license license:gpl3)))
1924 (define-public r-matrix-utils
1926 (name "r-matrix-utils")
1931 (uri (cran-uri "Matrix.utils" version))
1934 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
1935 (properties `((upstream-name . "Matrix.utils")))
1936 (build-system r-build-system)
1938 (list r-grr r-matrix))
1939 (home-page "https://github.com/cvarrichio/Matrix.utils")
1941 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
1943 "This package implements data manipulation methods such as @code{cast},
1944 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
1946 (license license:gpl3)))
1948 (define-public r-mboost
1954 (uri (cran-uri "mboost" version))
1957 "01ln0vxbbx1fq77q17sx61si82lhfibbchsnf2yw9032cn8wnhh2"))))
1958 (build-system r-build-system)
1967 (home-page "https://github.com/boost-R/mboost")
1968 (synopsis "Model-based boosting")
1970 "This package provides a functional gradient descent algorithm (boosting)
1971 for optimizing general risk functions utilizing component-wise (penalised)
1972 least squares estimates or regression trees as base-learners for fitting
1973 generalized linear, additive and interaction models to potentially
1974 high-dimensional data.")
1975 (license license:gpl2)))
1977 (define-public r-shadowtext
1979 (name "r-shadowtext")
1983 (uri (cran-uri "shadowtext" version))
1986 "0zdfidrcnmxmfhngv86ppxrjmpmz9kl78l4yfah2lc5vgmrlwg15"))))
1987 (properties `((upstream-name . "shadowtext")))
1988 (build-system r-build-system)
1990 (list r-ggplot2 r-scales))
1993 (home-page "https://github.com/GuangchuangYu/shadowtext/")
1994 (synopsis "Shadow text grob and layer")
1995 (description "This package implements @code{shadowtextGrob()} for
1996 @code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}.
1997 These functions draw text grob with background shadow.")
1998 (license license:artistic2.0)))
2000 (define-public r-sys
2007 (uri (cran-uri "sys" version))
2010 "0lng3ri17jxq06c6hhhmvsb65lazkiqpp1h4pii4w9jqvs7nskij"))))
2011 (build-system r-build-system)
2012 (home-page "https://github.com/jeroen/sys")
2013 (synopsis "Powerful and reliable tools for running system commands in R")
2015 "This package provides drop-in replacements for the base @code{system2()}
2016 function with fine control and consistent behavior across platforms. It
2017 supports clean interruption, timeout, background tasks, and streaming STDIN /
2018 STDOUT / STDERR over binary or text connections. The package also provides
2019 functions for evaluating expressions inside a temporary fork. Such
2020 evaluations have no side effects on the main R process, and support reliable
2021 interrupts and timeouts. This provides the basis for a sandboxing
2023 (license license:expat)))
2025 (define-public r-ashr
2031 (uri (cran-uri "ashr" version))
2034 "177xs3apnc6yy6737qqv4z8snf0hkpbghab63hrplbyb9wfssfga"))))
2035 (properties `((upstream-name . "ashr")))
2036 (build-system r-build-system)
2047 (home-page "https://github.com/stephens999/ashr")
2048 (synopsis "Methods for adaptive shrinkage, using empirical bayes")
2049 (description "This package implements an empirical Bayes approach for
2050 large-scale hypothesis testing and false discovery rate estimation.")
2051 (license license:gpl3+)))
2053 (define-public r-askpass
2060 (uri (cran-uri "askpass" version))
2063 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
2064 (build-system r-build-system)
2065 (propagated-inputs (list r-sys))
2066 (home-page "https://github.com/jeroen/askpass")
2067 (synopsis "Safe password entry for R")
2069 "This package provides cross-platform utilities for prompting the user
2070 for credentials or a passphrase, for example to authenticate with a server or
2071 read a protected key.")
2072 (license license:expat)))
2074 (define-public r-astsa
2081 (uri (cran-uri "astsa" version))
2083 (base32 "09872vkqb180cwprdfr3cn85jhazlc4vjdj6pjc70s06bh834f3w"))))
2084 (properties `((upstream-name . "astsa")))
2085 (build-system r-build-system)
2086 (home-page "https://github.com/nickpoison/astsa/")
2087 (synopsis "Applied statistical time series analysis")
2089 "This package provides data sets and scripts to accompany Time Series
2090 Analysis and Its Applications: With R Examples (4th ed), by R.H. Shumway and
2091 D.S. Stoffer. Springer Texts in Statistics, 2017,
2092 @url{https://doi.org/10.1007/978-3-319-52452-8}, and Time Series: A Data
2093 Analysis Approach Using R. Chapman-Hall, 2019,
2094 @url{https://doi.org/10.1201/9780429273285}.")
2095 (license license:gpl3)))
2097 (define-public r-vegan
2104 (uri (cran-uri "vegan" version))
2107 "01hxlb5sy0d28ajq993fqs4z0qjcyl610d0ahjyjpbkrpszd92jx"))))
2108 (build-system r-build-system)
2110 (list r-knitr ; needed for vignettes
2113 (list r-cluster r-lattice r-mass r-mgcv r-permute))
2114 (home-page "https://cran.r-project.org/web/packages/vegan")
2115 (synopsis "Functions for community ecology")
2117 "The vegan package provides tools for descriptive community ecology. It
2118 has most basic functions of diversity analysis, community ordination and
2119 dissimilarity analysis. Most of its multivariate tools can be used for other
2120 data types as well.")
2121 (license license:gpl2+)))
2123 (define-public r-tidyverse
2125 (name "r-tidyverse")
2130 (uri (cran-uri "tidyverse" version))
2133 "0qfgq4p2aq95j39xd5kcing2cacy7rzy7f6zf0bnpsa95svziyrp"))))
2134 (build-system r-build-system)
2167 (home-page "https://tidyverse.tidyverse.org")
2168 (synopsis "Install and load packages from the \"Tidyverse\"")
2170 "The @code{tidyverse} is a set of packages that work in harmony because
2171 they share common data representations and API design. This package is
2172 designed to make it easy to install and load multiple tidyverse packages in a
2174 (license license:gpl3)))
2176 (define-public r-rvest
2183 (uri (cran-uri "rvest" version))
2185 (base32 "07hws9infwchy19smrcd9m6c0jii0bdn335yxqk3ramgj5ryyrd4"))))
2186 (build-system r-build-system)
2200 (home-page "https://github.com/hadley/rvest")
2201 (synopsis "Simple web scraping for R")
2203 "@code{r-rvest} helps you scrape information from web pages. It is
2204 designed to work with @code{magrittr} to make it easy to express common web
2205 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
2206 (license license:gpl3)))
2208 (define-public r-selectr
2215 (uri (cran-uri "selectr" version))
2217 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
2218 (build-system r-build-system)
2220 (list r-stringr r-r6))
2221 (home-page "https://sjp.co.nz/projects/selectr/")
2222 (synopsis "Translate CSS selectors to XPath expressions")
2224 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
2225 expression. This allows you to use CSS selectors when working with the XML
2226 package as it can only evaluate XPath expressions. Also provided are
2227 convenience functions useful for using CSS selectors on XML nodes. This
2228 package is a port of the Python package @code{cssselect}.")
2229 (license license:bsd-3)))
2231 (define-public r-reprex
2238 (uri (cran-uri "reprex" version))
2241 "14khx09yzn97xhags48lvym1g37h1l2ymvw6r1jlldhjc7i1cnx8"))))
2242 (build-system r-build-system)
2257 (home-page "https://github.com/tidyverse/reprex")
2258 (synopsis "Prepare reproducible R code examples for sharing")
2260 "This package provides a convenience wrapper that uses the
2261 @code{rmarkdown} package to render small snippets of code to target formats
2262 that include both code and output. The goal is to encourage the sharing of
2263 small, reproducible, and runnable examples on code-oriented websites or email.
2264 @code{reprex} also extracts clean, runnable R code from various common formats,
2265 such as copy/paste from an R session.")
2266 (license license:expat)))
2268 (define-public r-reordercluster
2270 (name "r-reordercluster")
2274 (uri (cran-uri "ReorderCluster" version))
2277 "0zq143xvv2br7016f9b1501ymcpkjqm3al1dn5qfm21axyi2p1iq"))))
2278 (build-system r-build-system)
2280 (list r-gplots r-gtools r-rcpp))
2281 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
2282 (synopsis "Reordering the dendrogram according to the class labels")
2283 (description "This package provides tools for performing the leaf reordering
2284 for the dendrogram that preserves the hierarchical clustering result and at the
2285 same time tries to group instances from the same class together.")
2286 (license license:gpl3+)))
2288 (define-public r-callr
2295 (uri (cran-uri "callr" version))
2298 "01q3b0w1cbrryvv1dwvnyd3j1f09xmhnwg1wskc51r3r4qhqmnhj"))))
2299 (build-system r-build-system)
2301 (list r-r6 r-processx))
2302 (home-page "https://github.com/r-lib/callr#readme")
2303 (synopsis "Call R from R")
2305 "It is sometimes useful to perform a computation in a separate R process,
2306 without affecting the current R process at all. This package does exactly
2308 (license license:expat)))
2310 (define-public r-depmixs4
2316 (uri (cran-uri "depmixS4" version))
2319 "1pacvhw5m4fsk3ysbal50fdqbvlaz8ywyqp6bn1wh42wipqbb2i8"))))
2321 (list r-nnet r-nlme r-mass r-rsolnp))
2322 (build-system r-build-system)
2323 (home-page "https://cran.r-project.org/web/packages/depmixS4/")
2324 (synopsis "Dependent Mixture Models")
2325 (description "This package fits latent (hidden) Markov models on mixed
2326 categorical and continuous (time series) data, otherwise known as dependent
2328 (license license:gpl2+)))
2330 (define-public r-readxl
2337 (uri (cran-uri "readxl" version))
2340 "1ym11mldwj31lgk5av264v8b2zn7fmq5nd30rnm1pchgjizvpgpn"))))
2341 (build-system r-build-system)
2343 (list r-cellranger r-cpp11 r-progress r-tibble))
2346 (home-page "https://readxl.tidyverse.org")
2347 (synopsis "Read Excel files")
2349 "This package lets you import Excel files into R. It supports
2350 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
2351 the embedded @code{RapidXML} C++ library.")
2352 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
2353 ;; 'rapidxml' which is Boost.
2354 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
2356 (define-public r-model4you
2358 (name "r-model4you")
2362 (uri (cran-uri "model4you" version))
2365 "0pni9v3nradvy8sp2m07903vc7z610xrh426lf19dxss12kgrfi8"))))
2366 (build-system r-build-system)
2374 (home-page "https://cran.r-project.org/web/packages/model4you/")
2375 (synopsis "Stratified and personalised models based on trees and forests")
2377 "This package provides procedures for model-based trees for subgroup
2378 analyses in clinical trials and model-based forests for the estimation and
2379 prediction of personalised treatment effects. Currently partitioning of linear
2380 models, @code{lm()}, generalised linear models, @code{glm()}, and
2381 Weibull models, @code{survreg()}, are supported. Advanced plotting functionality is
2382 supported for the trees and a test for parameter heterogeneity is provided for
2383 the personalised models.")
2384 (license license:gpl2+)))
2386 (define-public r-modelr
2393 (uri (cran-uri "modelr" version))
2396 "1jd9vxirj5ii4ac0ka07g0rcq1c8yqv06jg27nmvp5a6kvlgvs8h"))))
2397 (build-system r-build-system)
2407 (home-page "https://github.com/tidyverse/modelr")
2408 (synopsis "Helper functions for modelling in pipelines")
2410 "Functions for modelling that help you seamlessly integrate modelling
2411 into a pipeline of data manipulation and visualisation.")
2412 (license license:gpl3)))
2414 (define-public r-hmm
2420 (uri (cran-uri "HMM" version))
2423 "03b548bnwqpnd7zypb4gvy9chyi5li2hp99a9vrh4qszxg2ihas7"))))
2424 (properties `((upstream-name . "HMM")))
2425 (build-system r-build-system)
2426 (home-page "https://cran.r-project.org/web/packages/HMM/")
2427 (synopsis "Hidden Markov Models")
2428 (description "This package provides an easy to use library to setup, apply
2429 and make inference with discrete time and discrete space hidden Markov
2431 (license license:gpl2+)))
2433 (define-public r-hiddenmarkov
2435 (name "r-hiddenmarkov")
2439 (uri (cran-uri "HiddenMarkov" version))
2442 "05dm3nl0ffsz2ziw3bz5bivyxk7r5bxs8xhky3hz660qaqzd51ki"))))
2443 (build-system r-build-system)
2446 (home-page "https://cran.r-project.org/web/packages/HiddenMarkov/")
2447 (synopsis "Hidden markov models for R")
2448 (description "This package contains functions for the analysis of Discrete
2449 Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated
2450 Poisson Process. It includes functions for simulation, parameter estimation,
2451 and the Viterbi algorithm. The algorithms are based of those of Walter
2453 (license license:gpl2+)))
2455 (define-public r-httpuv
2461 (uri (cran-uri "httpuv" version))
2464 "14qjf7bpl7pay89b7vi2vccl342q8xs6101a9x6qijy54k9myfa1"))
2465 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
2466 ;; only contains fixes for building on Solaris.
2467 (patches (search-patches "r-httpuv-1.6.6-unvendor-libuv.patch"))
2468 (modules '((guix build utils)))
2469 ;; Cannot unbundle http-parser, because it contains local
2472 '(delete-file-recursively "src/libuv"))))
2473 (build-system r-build-system)
2476 (modify-phases %standard-phases
2477 (add-after 'unpack 'unbundle-libuv
2478 (lambda* (#:key outputs #:allow-other-keys)
2479 (substitute* (find-files "src" "\\.cpp$|\\.h$")
2480 (("\"libuv/include/uv\\.h\"")
2482 ;; Fix https://github.com/rstudio/httpuv/issues/282
2483 (substitute* "src/http.cpp"
2484 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
2485 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);")))))))
2489 (list r-later r-promises r-r6 r-rcpp))
2490 (home-page "https://github.com/rstudio/httpuv")
2491 (synopsis "HTTP and WebSocket server library for R")
2493 "The httpuv package provides low-level socket and protocol support for
2494 handling HTTP and WebSocket requests directly from within R. It is primarily
2495 intended as a building block for other packages, rather than making it
2496 particularly easy to create complete web applications using httpuv alone.")
2497 ;; This package includes third-party code that was originally released
2498 ;; under various non-copyleft licenses. Full licensing information can be
2499 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
2500 (license license:gpl3+)))
2502 (define-public r-jsonlite
2508 (uri (cran-uri "jsonlite" version))
2511 "1w685bwhvqxh8y3b4rmzmbbxsj0sqrdad4rni7dxbiqzd2piszy5"))))
2512 (build-system r-build-system)
2515 (home-page "https://arxiv.org/abs/1403.2805")
2516 (synopsis "Robust, high performance JSON parser and generator for R")
2518 "The jsonlite package provides a fast JSON parser and generator optimized
2519 for statistical data and the web. It offers flexible, robust, high
2520 performance tools for working with JSON in R and is particularly powerful for
2521 building pipelines and interacting with a web API. In addition to converting
2522 JSON data from/to R objects, jsonlite contains functions to stream, validate,
2523 and prettify JSON data. The unit tests included with the package verify that
2524 all edge cases are encoded and decoded consistently for use with dynamic data
2525 in systems and applications.")
2526 (license license:expat)))
2528 (define-public r-servr
2534 (uri (cran-uri "servr" version))
2537 "11x0857m3xzdbzr4z0vx4fcdk36arfagyf2qgamvprich0qisknr"))))
2538 (build-system r-build-system)
2540 (list r-httpuv r-jsonlite r-mime r-xfun))
2541 (home-page "https://github.com/yihui/servr")
2542 (synopsis "Simple HTTP server to serve static files or dynamic documents")
2544 "Servr provides an HTTP server in R to serve static files, or dynamic
2545 documents that can be converted to HTML files (e.g., R Markdown) under a given
2547 (license license:expat)))
2549 (define-public r-howmany
2555 (uri (cran-uri "howmany" version))
2558 "045ck8qahfg2swbgyf7dpl32ryq1m4sbalhr7m5qdgpm62vz8h7f"))))
2559 (build-system r-build-system)
2560 (home-page "https://cran.r-project.org/web/packages/howmany/")
2561 (synopsis "Lower bound for the number of correct rejections")
2562 (description "When testing multiple hypotheses simultaneously, this package
2563 provides functionality to calculate a lower bound for the number of correct
2564 rejections (as a function of the number of rejected hypotheses), which holds
2565 simultaneously -with high probability- for all possible number of rejections.
2566 As a special case, a lower bound for the total number of false null hypotheses
2567 can be inferred. Dependent test statistics can be handled for multiple tests
2568 of associations. For independent test statistics, it is sufficient to provide
2569 a list of p-values.")
2570 (license license:gpl2+)))
2572 (define-public r-htmltools
2574 (name "r-htmltools")
2578 (uri (cran-uri "htmltools" version))
2581 "0krjyz99q7zvdfg60b128c0zwr36h54gb05jw9c874d8kqv1ni9c"))))
2582 (build-system r-build-system)
2584 (list r-base64enc r-digest r-fastmap r-rlang))
2585 (home-page "https://cran.r-project.org/web/packages/htmltools")
2586 (synopsis "R tools for HTML")
2588 "This package provides tools for HTML generation and output in R.")
2589 (license license:expat)))
2591 (define-public r-htmlwidgets
2593 (name "r-htmlwidgets")
2597 (uri (cran-uri "htmlwidgets" version))
2600 "1hgz8sx8xrvfcdwa4q15k942w4qsqg8lyxbbf7qyfzbi807wcgqs"))))
2601 (build-system r-build-system)
2603 (list r-htmltools r-jsonlite r-yaml))
2606 (home-page "https://github.com/ramnathv/htmlwidgets")
2607 (synopsis "HTML Widgets for R")
2609 "HTML widgets is a framework for creating HTML widgets that render in
2610 various contexts including the R console, R Markdown documents, and Shiny web
2612 (license license:expat)))
2614 (define-public r-htmltable
2616 (name "r-htmltable")
2621 (uri (cran-uri "htmlTable" version))
2623 (base32 "14qg65nw0bpikqs1hb1x7apzdzrnnl3ykjnks67kkp46v1skwzrs"))))
2624 (properties `((upstream-name . "htmlTable")))
2625 (build-system r-build-system)
2636 (home-page "http://gforge.se/packages/")
2637 (synopsis "Advanced tables for Markdown/HTML")
2639 "This package provides functions to build tables with advanced layout
2640 elements such as row spanners, column spanners, table spanners, zebra
2641 striping, and more. While allowing advanced layout, the underlying
2642 CSS-structure is simple in order to maximize compatibility with word
2643 processors such as LibreOffice. The package also contains a few text
2644 formatting functions that help outputting text compatible with HTML or
2646 (license license:gpl3+)))
2648 (define-public r-curl
2654 (uri (cran-uri "curl" version))
2657 "17kwc7njblfndnlij0m5a7a3jj42ag412xg0ry5ddnj0mnnbcrrm"))))
2658 (build-system r-build-system)
2661 (modify-phases %standard-phases
2662 ;; The environment variable CURL_CA_BUNDLE is only respected when
2663 ;; running Windows, so we disable the platform checks.
2664 ;; This can be removed once the libcurl has been patched.
2665 (add-after 'unpack 'allow-CURL_CA_BUNDLE
2667 (substitute* "R/onload.R"
2668 (("if \\(!grepl\\(\"mingw\".*")
2670 (substitute* "src/handle.c"
2671 (("/\\* Only set" m)
2673 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
2674 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
2679 (list pkg-config r-knitr))
2680 (home-page "https://github.com/jeroenooms/curl")
2681 (synopsis "HTTP client for R")
2683 "The @code{curl()} and @code{curl_download()} functions provide highly
2684 configurable drop-in replacements for base @code{url()} and
2685 @code{download.file()} with better performance, support for encryption, gzip
2686 compression, authentication, and other @code{libcurl} goodies. The core of
2687 the package implements a framework for performing fully customized requests
2688 where data can be processed either in memory, on disk, or streaming via the
2689 callback or connection interfaces.")
2690 (license license:expat)))
2692 (define-public r-hwriter
2699 (uri (cran-uri "hwriter" version))
2702 "1wxnv8h9cs65m3z01dpnnkgn2cpwfsck70g1jz9nbkr7mdaa4bzd"))))
2703 (build-system r-build-system)
2704 (home-page "https://cran.r-project.org/web/packages/hwriter")
2705 (synopsis "Output R objects in HTML format")
2707 "This package provides easy-to-use and versatile functions to output R
2708 objects in HTML format.")
2709 (license license:lgpl2.1+)))
2711 (define-public r-rjson
2718 (uri (cran-uri "rjson" version))
2721 "1qm27r1w677zg31gsiln60hcciszbymkw78cnaq7s36cbk9mcawq"))))
2722 (build-system r-build-system)
2723 (home-page "https://cran.r-project.org/web/packages/rjson")
2724 (synopsis "JSON library for R")
2726 "This package provides functions to convert R objects into JSON objects
2728 (license license:gpl2+)))
2730 (define-public r-fastmap
2737 (uri (cran-uri "fastmap" version))
2740 "0aw29hnq3ppn7bsnwg9d9sp84k1cvq30lrmfzqn315n0nhkfa4wi"))))
2741 (properties `((upstream-name . "fastmap")))
2742 (build-system r-build-system)
2743 (home-page "https://r-lib.github.io/fastmap/")
2744 (synopsis "Fast implementation of a key-value store")
2746 "This package provides a fast implementation of a key-value store.
2747 Environments are commonly used as key-value stores, but every time a new key
2748 is used, it is added to R's global symbol table, causing a small amount of
2749 memory leakage. This can be problematic in cases where many different keys
2750 are used. Fastmap avoids this memory leak issue by implementing the map using
2751 data structures in C++.")
2752 (license license:expat)))
2754 (define-public r-fastghquad
2756 (name "r-fastghquad")
2761 (uri (cran-uri "fastGHQuad" version))
2764 "1zj7nsbnx4g253m3dpz9vi3zk3jxwrixwjw1ks6n4shpb4dlkp2w"))))
2765 (properties `((upstream-name . "fastGHQuad")))
2766 (build-system r-build-system)
2769 (home-page "https://github.com/awblocker/fastGHQuad")
2770 (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature")
2772 "This package implements numerically-stable Gauss-Hermite quadrature
2773 rules and utility functions for adaptive GH quadrature.")
2774 (license license:expat)))
2776 (define-public r-rstpm2
2783 (uri (cran-uri "rstpm2" version))
2786 "038qq5kar9f5ygd18aicwfqrr7fl37p0r9shgpc6wf2vmj564crn"))))
2787 (properties `((upstream-name . "rstpm2")))
2788 (build-system r-build-system)
2800 (home-page "https://github.com/mclements/rstpm2")
2801 (synopsis "Link-based survival models")
2803 "This package provides R implementations of @dfn{generalized survival
2804 models} (GSMs), smooth @dfn{accelerated failure time} (AFT) models and Markov
2805 multi-state models.")
2806 ;; One of these licenses
2807 (license (list license:gpl2 license:gpl3))))
2809 ;; This package includes minified JavaScript files. When upgrading please
2810 ;; check that there are no new minified JavaScript files.
2811 (define-public r-jquerylib
2813 (name "r-jquerylib")
2818 (uri (cran-uri "jquerylib" version))
2821 "04a40v4znpj98j7y6009d74a6g9dchj5rr3p08cgz9p3rlfw3g7h"))
2823 '(for-each delete-file
2824 '("inst/lib/1.12.4/jquery-1.12.4.min.js"
2825 "inst/lib/2.2.4/jquery-2.2.4.min.js"
2826 "inst/lib/3.6.0/jquery-3.6.0.min.js")))))
2827 (properties `((upstream-name . "jquerylib")))
2828 (build-system r-build-system)
2830 `(#:modules ((guix build utils)
2831 (guix build r-build-system)
2834 (modify-phases %standard-phases
2835 (add-after 'unpack 'process-javascript
2836 (lambda* (#:key inputs #:allow-other-keys)
2837 (with-directory-excursion "inst/lib/"
2841 `(("1.12.4/jquery-1.12.4.js"
2842 "1.12.4/jquery-1.12.4.min.js")
2843 ("2.2.4/jquery-2.2.4.js"
2844 "2.2.4/jquery-2.2.4.min.js")
2845 ("3.6.0/jquery-3.6.0.js"
2846 "3.6.0/jquery-3.6.0.min.js"))))
2847 (lambda (sources targets)
2848 (for-each (lambda (source target)
2849 (format #t "Processing ~a --> ~a~%"
2851 (invoke "esbuild" source "--minify"
2852 (string-append "--outfile=" target)))
2853 sources targets)))))))))
2858 (home-page "https://cran.r-project.org/package=jquerylib")
2859 (synopsis "Obtain jQuery as an HTML dependency object")
2861 "Obtain any major version of jQuery and use it in any webpage generated
2862 by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't
2863 need to use this package directly, but other R packages (e.g. shiny,
2864 rmarkdown, etc.) depend on this package to avoid bundling redundant copies of
2866 (license license:expat)))
2868 (define-public r-sass
2875 (uri (cran-uri "sass" version))
2878 "0iln5ky6k1ix0gddlyw4rr2953kc499x66bcyi9yiyp91nfh82dl"))))
2879 (properties `((upstream-name . "sass")))
2880 (build-system r-build-system)
2882 (list r-fs r-htmltools r-r6 r-rappdirs r-rlang))
2883 (native-inputs (list r-knitr))
2884 (home-page "https://github.com/rstudio/sass")
2885 (synopsis "Syntactically Awesome Style Sheets (SASS)")
2887 "This package provides an SCSS compiler, powered by the libsass library.
2888 With this, R developers can use variables, inheritance, and functions to
2889 generate dynamic style sheets. The package uses the Sass CSS extension
2890 language, which is stable, powerful, and CSS compatible.")
2891 (license license:expat)))
2893 (define-public r-saver
2899 (uri (cran-uri "SAVER" version))
2902 "1s1kw8idkaj7j90fw4qn9k0wd4vz0sblsk06ry6lm4afcar0p158"))))
2903 (properties `((upstream-name . "SAVER")))
2904 (build-system r-build-system)
2911 (native-inputs (list r-knitr))
2912 (home-page "https://github.com/mohuangx/SAVER")
2914 "Recovery of gene expression profile in noisy and sparse scRNA-seq data")
2916 "This package is an implementation of a regularized regression prediction
2917 and empirical Bayes method to recover the true gene expression profile in noisy
2918 and sparse single-cell RNA-seq data. In @dfn{single-cell RNA sequencing}
2919 (scRNA-seq) studies, only a small fraction of the transcripts present in each
2920 cell are sequenced. This leads to unreliable quantification of genes with low
2921 or moderate expression, which hinders downstream analysis. This package
2922 @dfn{single-cell analysis via expression recovery} (SAVER) implements an
2923 expression recovery method for unique molecule index (UMI)-based scRNA-seq
2924 data that borrows information across genes and cells to provide accurate
2925 expression estimates for all genes.")
2926 (license license:gpl2)))
2928 ;; This package includes minified JavaScript files. When upgrading please
2929 ;; check that there are no new minified JavaScript files.
2930 (define-public r-bslib
2937 (uri (cran-uri "bslib" version))
2940 "1hkmaj0mpygbf6qr1955biv9z4q3khflyqi5x0c3dwi6qz74xspv"))
2942 '(for-each delete-file
2943 '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js"
2944 "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js"
2945 "inst/lib/bs3/assets/javascripts/bootstrap.min.js"
2946 "inst/lib/bs4/dist/js/bootstrap.bundle.min.js"
2947 "inst/lib/bs5/dist/js/bootstrap.bundle.min.js")))))
2948 (properties `((upstream-name . "bslib")))
2949 (build-system r-build-system)
2951 `(#:modules ((guix build utils)
2952 (guix build r-build-system)
2955 (modify-phases %standard-phases
2956 (add-after 'unpack 'process-javascript
2957 (lambda* (#:key inputs #:allow-other-keys)
2958 (with-directory-excursion "inst/lib/"
2962 `(("bs-a11y-p/plugins/js/bootstrap-accessibility.js"
2963 "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js")
2964 ("bs-colorpicker/js/bootstrap-colorpicker.js"
2965 "bs-colorpicker/js/bootstrap-colorpicker.min.js")
2966 ("bs3/assets/javascripts/bootstrap.js"
2967 "bs3/assets/javascripts/bootstrap.min.js")
2968 (,(assoc-ref inputs "js-bootstrap4-bundle")
2969 "bs4/dist/js/bootstrap.bundle.min.js")
2970 (,(assoc-ref inputs "js-bootstrap5-bundle")
2971 "bs5/dist/js/bootstrap.bundle.min.js"))))
2972 (lambda (sources targets)
2973 (for-each (lambda (source target)
2974 (format #t "Processing ~a --> ~a~%"
2976 (invoke "esbuild" source "--minify"
2977 (string-append "--outfile=" target)))
2978 sources targets)))))))))
2988 `(("esbuild" ,esbuild)
2989 ("js-bootstrap4-bundle"
2992 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.6.0/dist/js/bootstrap.bundle.js")
2995 "04abvgp923w36qfqkkl2syim3bl119nwxbgials90z1jyb8jgss1"))))
2996 ("js-bootstrap5-bundle"
2999 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v5.1.3/dist/js/bootstrap.bundle.js")
3002 "116979i2vr1y9i6g7n5iir19p85xwr642scbl9jcqdr0w9801nw6"))))))
3003 (home-page "https://rstudio.github.io/bslib/")
3004 (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown")
3006 "This package simplifies custom CSS styling of both shiny and rmarkdown
3007 via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their
3008 various Bootswatch themes. An interactive widget is also provided for
3009 previewing themes in real time.")
3010 (license license:expat)))
3012 ;; This package includes minified JavaScript files. When upgrading please
3013 ;; check that there are no new minified JavaScript files.
3014 (define-public r-shiny
3022 (url "https://github.com/rstudio/shiny")
3023 (commit (string-append "v" version))))
3024 (file-name (git-file-name name version))
3027 "0wvc6jlgs41p05wbk8gahnl7sfnc4hpliyh9dbi5w52ngsg6wcr7"))
3029 '(for-each delete-file
3030 '("inst/www/shared/bootstrap/js/bootstrap.min.js"
3031 "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO
3032 "inst/www/shared/datatables/js/jquery.dataTables.min.js"
3033 "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js"
3034 "inst/www/shared/highlight/highlight.pack.js"
3035 "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js"
3036 "inst/www/shared/jquery.min.js"
3037 "inst/www/shared/jqueryui/jquery-ui.min.js"
3038 "inst/www/shared/legacy/jquery.min.js"
3039 "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js"
3040 "inst/www/shared/selectize/js/selectize.min.js"
3041 "inst/www/shared/shiny.min.js"
3042 "inst/www/shared/showdown/compressed/showdown.js"
3043 "inst/www/shared/strftime/strftime-min.js")))))
3044 (build-system r-build-system)
3046 `(#:modules ((guix build r-build-system)
3047 (guix build minify-build-system)
3050 #:imported-modules (,@%r-build-system-modules
3051 (guix build minify-build-system))
3053 (modify-phases (@ (guix build r-build-system) %standard-phases)
3054 (add-after 'unpack 'replace-bundled-minified-JavaScript
3055 (lambda* (#:key inputs #:allow-other-keys)
3056 (let ((replace-file (lambda (old new)
3057 (format #t "replacing ~a with ~a\n" old new)
3058 (symlink new old))))
3059 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
3060 ;; contain just data. They are not minified code, so we don't
3062 (with-directory-excursion "inst/www/shared"
3063 (replace-file "strftime/strftime-min.js"
3064 (search-input-file inputs
3065 "/share/javascript/strftime.min.js"))
3066 (replace-file "highlight/highlight.pack.js"
3067 (search-input-file inputs
3068 "/share/javascript/highlight.min.js"))
3069 (replace-file "datatables/js/jquery.dataTables.min.js"
3070 (search-input-file inputs
3071 "/share/javascript/jquery.dataTables.min.js"))
3072 (replace-file "selectize/js/selectize.min.js"
3073 (search-input-file inputs
3074 "/share/javascript/selectize.min.js"))
3075 (for-each (match-lambda
3077 (minify source #:target target)))
3078 `(("jqueryui/jquery-ui.js" .
3079 "jqueryui/jquery-ui.min.js")
3080 ("datepicker/js/bootstrap-datepicker.js" .
3081 "datepicker/js/bootstrap-datepicker.min.js")
3082 ("ionrangeslider/js/ion.rangeSlider.js" .
3083 "ionrangeslider/js/ion.rangeSlider.min.js")
3084 ("bootstrap/js/bootstrap.js" .
3085 "bootstrap/js/bootstrap.min.js")
3086 (,(assoc-ref inputs "js-bootstrap-accessibility") .
3087 "bootstrap/accessibility/js/bootstrap-accessibility.min.js")
3092 ("legacy/jquery.js" .
3093 "legacy/jquery.min.js")
3094 ("selectize/accessibility/js/selectize-plugin-a11y.js" .
3095 "selectize/accessibility/js/selectize-plugin-a11y.min.js")
3096 ("showdown/src/showdown.js" .
3097 "showdown/compressed/showdown.js"))))))))))
3120 (list js-datatables js-selectize js-strftime js-highlight))
3122 `(("uglifyjs" ,node-uglify-js)
3123 ("gfortran" ,gfortran)
3124 ("js-bootstrap-accessibility"
3127 (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\
3128 v1.0.7/_site/plugins/js/bootstrap-accessibility.js")
3131 "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8"))))))
3132 (home-page "https://shiny.rstudio.com")
3133 (synopsis "Easy interactive web applications with R")
3135 "Makes it incredibly easy to build interactive web applications
3136 with R. Automatic \"reactive\" binding between inputs and outputs and
3137 extensive prebuilt widgets make it possible to build beautiful,
3138 responsive, and powerful applications with minimal effort.")
3139 (license license:artistic2.0)))
3141 (define-public r-shinyhelper
3143 (name "r-shinyhelper")
3148 (uri (cran-uri "shinyhelper" version))
3150 (base32 "1c4hvf19j3yyh8r12nx85ldkxs89g98q74csnqs5ml5l79a65vgp"))))
3151 (properties `((upstream-name . "shinyhelper")))
3152 (build-system r-build-system)
3153 (propagated-inputs (list r-markdown r-shiny))
3154 (home-page "https://cran.r-project.org/package=shinyhelper")
3155 (synopsis "Easily add Markdown help files to shiny app elements")
3157 "This package creates a lightweight way to add markdown helpfiles to
3158 Shiny apps, using modal dialog boxes, with no need to observe each help button
3160 (license license:gpl3)))
3162 ;; This package includes minified JavaScript files. When upgrading please
3163 ;; check that there are no new minified JavaScript files.
3164 (define-public r-shinytree
3166 (name "r-shinytree")
3171 (uri (cran-uri "shinyTree" version))
3174 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
3175 (modules '((guix build utils)))
3178 ;; Delete minified JavaScript
3179 (for-each delete-file
3180 '("inst/www/jsTree-3.3.7/libs/require.js"
3181 "inst/www/jsTree-3.3.7/libs/jquery.js"
3182 "inst/www/jsTree-3.3.7/jstree.min.js"))
3184 (properties `((upstream-name . "shinyTree")))
3185 (build-system r-build-system)
3187 `(#:modules ((guix build utils)
3188 (guix build r-build-system)
3192 (modify-phases %standard-phases
3193 (add-after 'unpack 'replace-minified-javascript
3194 (lambda* (#:key inputs #:allow-other-keys)
3195 (with-directory-excursion "inst/www/jsTree-3.3.7/"
3196 (symlink (search-input-file inputs
3197 "/share/javascript/require.min.js")
3202 `((,(assoc-ref inputs "js-jquery")
3206 (lambda (sources targets)
3207 (for-each (lambda (source target)
3208 (format #t "Processing ~a --> ~a~%"
3210 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
3211 (call-with-output-file target
3213 (dump-port minified port)))))
3217 (list r-htmlwidgets r-jsonlite r-promises r-shiny r-stringr))
3219 (list js-requirejs))
3221 `(("uglifyjs" ,node-uglify-js)
3225 (uri "https://code.jquery.com/jquery-3.3.1.js")
3228 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
3229 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
3230 (synopsis "jsTree bindings for Shiny")
3232 "This package exposes R bindings to jsTree, a JavaScript library that
3233 supports interactive trees, to enable rich, editable trees in Shiny.")
3234 (license license:expat)))
3236 (define-public r-shinydashboard
3238 (name "r-shinydashboard")
3242 (uri (cran-uri "shinydashboard" version))
3245 "0hrqkwlpb8rnmp5j74p134g4c4cl16icmwc2ip6k1634fa2y8vm5"))))
3246 (build-system r-build-system)
3247 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
3248 ;; Regenerate it from the included sources.
3251 (modify-phases %standard-phases
3252 (add-after 'unpack 'generate-minified-javascript
3254 (with-directory-excursion "inst/AdminLTE"
3255 (let ((target "app.min.js")
3257 (format #t "Processing ~a --> ~a~%"
3259 (delete-file target)
3260 (invoke "esbuild" source "--minify"
3261 (string-append "--outfile=" target)))))))))
3263 (list r-htmltools r-promises r-shiny))
3266 (home-page "https://rstudio.github.io/shinydashboard/")
3267 (synopsis "Create dashboards with shiny")
3268 (description "This package provides an extension to the Shiny web
3269 application framework for R, making it easy to create attractive dashboards.")
3270 ;; This package includes software that was released under the Expat
3271 ;; license, but the whole package is released under GPL version 2 or
3273 (license license:gpl2+)))
3275 (define-public r-shinyfiles
3277 (name "r-shinyfiles")
3282 (uri (cran-uri "shinyFiles" version))
3284 (base32 "11kjq0vw5c98lzrg80m9w917lkgw5im2h9wgk1b84vlaxrjy2wja"))))
3285 (properties `((upstream-name . "shinyFiles")))
3286 (build-system r-build-system)
3288 (list r-fs r-htmltools r-jsonlite r-shiny r-tibble))
3289 (home-page "https://github.com/thomasp85/shinyFiles")
3290 (synopsis "Server-side file system viewer for Shiny")
3292 "This package provides functionality for client-side navigation of the
3293 server side file system in shiny apps. In case the app is running locally
3294 this gives the user direct access to the file system without the need to
3295 \"download\" files to a temporary location. Both file and folder selection as
3296 well as file saving is available.")
3297 (license license:gpl2+)))
3299 (define-public r-shinythemes
3301 (name "r-shinythemes")
3306 (uri (cran-uri "shinythemes" version))
3309 "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip"))))
3310 (properties `((upstream-name . "shinythemes")))
3311 (build-system r-build-system)
3312 (propagated-inputs (list r-shiny))
3313 (home-page "https://rstudio.github.io/shinythemes/")
3314 (synopsis "Themes for Shiny")
3316 "This package provides themes for use with Shiny. It includes several
3317 Bootstrap themes, which are packaged for use with Shiny applications.")
3318 ;; The package is released under version 3 of the GPL, but it includes
3319 ;; source files that are covered by the Expat license. It also includes
3320 ;; fonts under SIL or the ASL.
3321 (license (list license:gpl3 license:expat
3322 license:silofl1.1 license:asl2.0))))
3324 ;; The package sources include minified variants of d3.js and non-minified
3325 ;; source code of d3-jetpack.
3326 (define-public r-d3r
3333 (uri (cran-uri "d3r" version))
3336 "1qijkllfaaw0lb29j8mappm8jz9kg8gkihxq5wqhb4gabsazdwva"))))
3337 (build-system r-build-system)
3339 `(#:modules ((guix build utils)
3340 (guix build r-build-system)
3343 (modify-phases %standard-phases
3344 (add-after 'unpack 'process-javascript
3345 (lambda* (#:key inputs #:allow-other-keys)
3346 (with-directory-excursion "inst/www/d3/"
3350 `((,(assoc-ref inputs "d3.v3.js")
3351 "v3/dist/d3.min.js")
3352 (,(assoc-ref inputs "d3.v4.js")
3353 "v4/dist/d3.min.js")
3354 (,(assoc-ref inputs "d3.v5.js")
3355 "v5/dist/d3.min.js")
3356 (,(assoc-ref inputs "d3.v6.js")
3357 "v6/dist/d3.min.js")
3358 (,(assoc-ref inputs "d3.v7.js")
3359 "v7/dist/d3.min.js"))))
3360 (lambda (sources targets)
3361 (for-each (lambda (source target)
3362 (format #t "Processing ~a --> ~a~%"
3364 (delete-file target)
3365 (invoke "esbuild" source "--minify"
3366 (string-append "--outfile=" target)))
3367 sources targets)))))))))
3369 (list r-dplyr r-htmltools r-rlang r-tidyr))
3371 `(("esbuild" ,esbuild)
3375 (uri "https://d3js.org/d3.v3.js")
3378 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
3382 (uri "https://d3js.org/d3.v4.js")
3385 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
3389 (uri "https://d3js.org/d3.v5.js")
3392 "177ypw6mjrp2ch9lj6znibwacwrvm4ypjxflsxsnl2sigx5dcwic"))))
3396 (uri "https://d3js.org/d3.v6.js")
3399 "13hick3glizzm442b9swlwz584rzwwvhpq9qvfbh3m5jay10wxw0"))))
3403 (uri "https://d3js.org/d3.v7.js")
3406 "1hif1phswlkkpvcf1hbqmfsxdb5s5gr5g2frcwbh0rh8g6nbkyqi"))))))
3407 (home-page "https://github.com/timelyportfolio/d3r")
3408 (synopsis "d3.js utilities for R")
3410 "This package provides a suite of functions to help ease the use of the
3411 d3.js visualization library in R. These helpers include
3412 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
3413 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
3414 R objects into the JSON format that the d3.js library expects.")
3415 (license license:bsd-3)))
3417 ;; We use the latest commit here because the last release was in 2016 while
3418 ;; the latest commit was in 2018.
3419 (define-public r-sankeyd3
3420 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
3424 (version (git-version "0.3.2" revision commit))
3429 (url "https://github.com/fbreitwieser/sankeyD3")
3431 (file-name (git-file-name name version))
3434 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
3435 (build-system r-build-system)
3437 (list r-d3r r-htmlwidgets r-shiny r-magrittr))
3438 (home-page "https://github.com/fbreitwieser/sankeyD3")
3439 (synopsis "Sankey network graphs from R")
3441 "This package provides an R library to generate Sankey network graphs
3442 in R and Shiny via the D3 visualization library.")
3443 ;; The R code is licensed under GPLv3+. It includes the non-minified
3444 ;; JavaScript source code of d3-sankey, which is released under the
3445 ;; 3-clause BSD license.
3446 (license (list license:gpl3+ license:bsd-3)))))
3448 (define-public r-wesanderson
3450 (name "r-wesanderson")
3455 (uri (cran-uri "wesanderson" version))
3458 "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
3459 (properties `((upstream-name . "wesanderson")))
3460 (build-system r-build-system)
3461 (home-page "https://github.com/karthik/wesanderson")
3462 (synopsis "Wes Anderson color palette generator")
3464 "This package provides color palettes that have been generated mostly
3465 from Wes Anderson movies.")
3466 (license license:expat)))
3468 (define-public r-gg-gap
3475 (uri (cran-uri "gg.gap" version))
3478 "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h"))))
3479 (properties `((upstream-name . "gg.gap")))
3480 (build-system r-build-system)
3482 (list r-cowplot r-ggplot2))
3483 (home-page "https://github.com/ChrisLou-bioinfo/gg.gap")
3484 (synopsis "Define segments on the y-axis for ggplot2")
3486 "The @code{gg.gap} function enables you to define segments for the y-axis
3487 in a ggplot2 plot.")
3488 (license license:gpl3)))
3490 (define-public r-mbess
3497 (uri (cran-uri "MBESS" version))
3499 (base32 "0cq4z7nx361rcw42jflrrdjbqs2q5973dlvhcr7i2wbkj3gzkwla"))))
3500 (properties `((upstream-name . "MBESS")))
3501 (build-system r-build-system)
3503 (list r-boot r-lavaan r-mass r-mnormt r-nlme r-openmx r-sem r-semtools))
3504 (home-page "https://www3.nd.edu/~kkelley/site/MBESS.html")
3505 (synopsis "Methods for designing research studies")
3507 "This package implements methods that are useful in designing research
3508 studies and analyzing data, with particular emphasis on methods that are
3509 developed for or used within the behavioral, educational, and social
3510 sciences (broadly defined). That being said, many of the methods implemented
3511 within MBESS are applicable to a wide variety of disciplines. MBESS has a
3512 suite of functions for a variety of related topics, such as effect sizes,
3513 confidence intervals for effect sizes (including standardized effect sizes and
3514 noncentral effect sizes), sample size planning (from the @dfn{accuracy in
3515 parameter estimation} (AIPE), power analytic, equivalence, and minimum-risk
3516 point estimation perspectives), mediation analysis, various properties of
3517 distributions, and a variety of utility functions.")
3518 ;; Either version of the GPL.
3519 (license (list license:gpl2 license:gpl3))))
3521 (define-public r-homologene
3523 (name "r-homologene")
3524 (version "1.4.68.19.3.27")
3528 (uri (cran-uri "homologene" version))
3530 (base32 "0d7wxisk0vqk1n165v1i19bc02zv78h5r5d3jqai5y6nkmwn01sh"))))
3531 (properties `((upstream-name . "homologene")))
3532 (build-system r-build-system)
3534 (list r-dplyr r-magrittr r-purrr r-r-utils r-readr))
3535 (home-page "https://github.com/oganm/homologene")
3536 (synopsis "Quick access to homologene and gene annotation updates")
3538 "This package provides a wrapper for the homologene database by the
3539 National Center for Biotechnology Information (NCBI). It allows searching for
3540 gene homologs across species. The package also includes an updated version of
3541 the homologene database where gene identifiers and symbols are replaced with
3542 their latest (at the time of submission) version and functions to fetch latest
3543 annotation data to keep updated.")
3544 (license license:expat)))
3546 (define-public r-ggtern
3553 (uri (cran-uri "ggtern" version))
3555 (base32 "15hhn8msy0l8zbq8ms0zvg1iajn1c28gd77v3hp6dvwwsla8zzbd"))))
3556 (properties `((upstream-name . "ggtern")))
3557 (build-system r-build-system)
3559 (list r-compositions
3570 (home-page "http://www.ggtern.com")
3571 (synopsis "Extension to ggplot2 for ternary diagrams")
3573 "This package extends the functionality of ggplot2, providing the
3574 capability to plot ternary diagrams for (a subset of) the ggplot2 geometries.
3575 Additionally, ggtern has implemented several new geometries which are
3576 unavailable to the standard ggplot2 release.")
3577 (license license:gpl2)))
3579 (define-public r-tablerdash
3581 (name "r-tablerdash")
3586 (uri (cran-uri "tablerDash" version))
3589 "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm"))
3592 ;; Delete minified JavaScript
3593 (for-each delete-file
3594 '("inst/tablerDash-0.1.0/require.min.js"
3595 "inst/bootstrap-4.0.0/bootstrap.bundle.min.js"))
3597 (properties `((upstream-name . "tablerDash")))
3598 (build-system r-build-system)
3600 `(#:modules ((guix build utils)
3601 (guix build r-build-system)
3604 (modify-phases %standard-phases
3605 (add-after 'unpack 'process-javascript
3606 (lambda* (#:key inputs #:allow-other-keys)
3607 (with-directory-excursion "inst"
3611 `((,(assoc-ref inputs "js-requirejs")
3612 "tablerDash-0.1.0/require.min.js")
3613 (,(assoc-ref inputs "js-bootstrap")
3614 "bootstrap-4.0.0/bootstrap.bundle.min.js"))))
3615 (lambda (sources targets)
3616 (for-each (lambda (source target)
3617 (format #t "Processing ~a --> ~a~%"
3619 (invoke "esbuild" source "--minify"
3620 (string-append "--outfile=" target)))
3624 (list r-htmltools r-knitr r-shiny))
3626 `(("esbuild" ,esbuild)
3630 (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js")
3633 "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds"))))
3637 (uri "https://raw.githubusercontent.com/twbs/bootstrap/\
3638 v4.0.0/dist/js/bootstrap.bundle.js")
3641 "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj"))))))
3642 (home-page "https://rinterface.github.io/tablerDash/")
3643 (synopsis "Tabler API for Shiny")
3645 "This package provides an R interface to the
3646 @url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap
3647 4 dashboard template. There are different layouts available such as a one
3648 page dashboard or a multi-page template, where the navigation menu is
3649 contained in the navigation bar.")
3650 (license license:gpl2+)))
3652 (define-public r-spelling
3659 (uri (cran-uri "spelling" version))
3662 "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl"))))
3663 (properties `((upstream-name . "spelling")))
3664 (build-system r-build-system)
3666 (list r-commonmark r-hunspell r-knitr r-xml2))
3667 (home-page "https://docs.ropensci.org/spelling/")
3668 (synopsis "Tools for spell checking in R")
3670 "This is an R package for spell checking common document formats
3671 including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes
3672 utilities to automate checking of documentation and vignettes as a unit test
3673 during @code{R CMD check}. Both British and American English are supported
3674 out of the box and other languages can be added. In addition, packages may
3675 define a wordlist to allow custom terminology without having to abuse
3677 (license license:expat)))
3679 (define-public r-crosstalk
3681 (name "r-crosstalk")
3686 (uri (cran-uri "crosstalk" version))
3689 "180y7mhpj17axpadwhh7s0qvrpdnag7g977vk256l96d6nmvlds2"))))
3690 (build-system r-build-system)
3692 (list r-htmltools r-jsonlite r-lazyeval r-r6))
3693 (home-page "https://rstudio.github.io/crosstalk/")
3694 (synopsis "Inter-widget interactivity for HTML widgets")
3696 "This package provides building blocks for allowing HTML widgets to
3697 communicate with each other, with Shiny or without (i.e., static @code{.html}
3698 files). It currently supports linked brushing and filtering.")
3699 (license license:expat)))
3701 (define-public r-rook
3708 (uri (cran-uri "Rook" version))
3711 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
3712 (properties `((upstream-name . "Rook")))
3713 (build-system r-build-system)
3714 (propagated-inputs (list r-brew))
3715 (home-page "https://cran.r-project.org/web/packages/Rook")
3716 (synopsis "Web server interface for R")
3718 "This package contains the Rook specification and convenience software
3719 for building and running Rook applications. A Rook application is an R
3720 reference class object that implements a @code{call} method or an R closure
3721 that takes exactly one argument, an environment, and returns a list with three
3722 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
3723 (license license:gpl2)))
3725 (define-public r-miniui
3732 (uri (cran-uri "miniUI" version))
3735 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
3736 (properties `((upstream-name . "miniUI")))
3737 (build-system r-build-system)
3739 (list r-htmltools r-shiny))
3740 (home-page "https://cran.r-project.org/web/packages/miniUI/")
3741 (synopsis "Shiny UI widgets for small screens")
3743 "This package provides UI widget and layout functions for writing Shiny apps that
3744 work well on small screens.")
3745 (license license:gpl3)))
3747 (define-public r-feather
3754 (uri (cran-uri "feather" version))
3757 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
3758 (build-system r-build-system)
3760 (list r-hms r-rcpp r-tibble))
3761 (home-page "https://github.com/wesm/feather")
3762 (synopsis "R Bindings to the Feather API")
3763 (description "Read and write feather files, a lightweight binary columnar
3764 data store designed for maximum speed.")
3765 (license license:asl2.0)))
3767 (define-public r-maps
3774 (uri (cran-uri "maps" version))
3777 "0034114pdakxcx480b45qy9j4vq1v5ss961ssy92w4nqiqhsb4z6"))))
3778 (build-system r-build-system)
3779 (home-page "https://cran.r-project.org/web/packages/maps")
3780 (synopsis "Draw geographical maps")
3781 (description "This package provides an R module for display of maps.
3782 Projection code and larger maps are in separate packages (@code{mapproj} and
3784 (license license:gpl2)))
3786 (define-public r-mapproj
3793 (uri (cran-uri "mapproj" version))
3796 "10nzfbyfkc545qxf51i33g0f8iiidcnhj971ylphnbh7j2sgla6s"))))
3797 (build-system r-build-system)
3798 (propagated-inputs (list r-maps))
3799 (home-page "https://cran.r-project.org/web/packages/mapproj")
3800 (synopsis "Map projection in R")
3801 (description "This package converts latitude/longitude into projected
3803 (license (list license:gpl2 ; The R interface
3804 (license:non-copyleft ; The C code
3805 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
3806 "Lucent Public License Version 1.02")))))
3808 (define-public r-rgooglemaps
3810 (name "r-rgooglemaps")
3815 (uri (cran-uri "RgoogleMaps" version))
3818 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
3819 (properties `((upstream-name . "RgoogleMaps")))
3820 (build-system r-build-system)
3823 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
3824 (synopsis "Use Google Maps in R")
3825 (description "This package serves two purposes:
3827 @item Provide a comfortable R interface to query the Google server for static
3829 @item Use the map as a background image to overlay plots within R. This
3830 requires proper coordinate scaling.
3832 (license license:gpl2+)))
3834 (define-public r-gensa
3840 (uri (cran-uri "GenSA" version))
3843 "03xqwxm7v7rnihx730a4p65dfwhjh4345r3d78y0qxxplk8d76cx"))))
3844 (properties `((upstream-name . "GenSA")))
3845 (build-system r-build-system)
3846 (home-page "https://cran.r-project.org/package=GenSA")
3847 (synopsis "Generalized simulated annealing")
3848 (description "This package performs search for the global minimum of a very
3849 complex non-linear objective function with a very large number of optima.")
3850 (license license:gpl2)))
3852 (define-public r-geosphere
3854 (name "r-geosphere")
3859 (uri (cran-uri "geosphere" version))
3862 "0bg4vfmrw140j2ax0p6bflvb77w03ir39wa87l96rj473jpa9hzj"))))
3863 (build-system r-build-system)
3864 (propagated-inputs (list r-sp))
3865 (home-page "https://cran.r-project.org/web/packages/geosphere")
3866 (synopsis "Spherical trigonometry")
3867 (description "This package computes spherical trigonometry for geographic
3868 applications. That is, compute distances and related measures for angular
3869 (longitude/latitude) locations.")
3870 (license license:gpl3+)))
3872 (define-public r-jpeg
3879 (uri (cran-uri "jpeg" version))
3882 "0wihj538wdnr71wdldym83qadb4kh68a6rkallwbh2f25r27b881"))))
3883 (build-system r-build-system)
3884 (inputs (list libjpeg-turbo))
3885 (home-page "https://www.rforge.net/jpeg/")
3886 (synopsis "Read and write JPEG images with R")
3887 (description "This package provides a way to read, write and display
3888 bitmap images stored in the JPEG format with R. It can read and write both
3889 files and in-memory raw vectors.")
3890 (license license:gpl2+)))
3892 (define-public r-ggmap
3899 (uri (cran-uri "ggmap" version))
3902 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
3903 (build-system r-build-system)
3922 (home-page "https://github.com/dkahle/ggmap")
3923 (synopsis "Spatial visualization with ggplot2")
3924 (description "This package provides a collection of functions to visualize
3925 spatial data and models on top of static maps from various online sources (e.g
3926 Google Maps and Stamen Maps). It includes tools common to those tasks,
3927 including functions for geolocation and routing.")
3928 (license license:gpl2)))
3930 (define-public r-haven
3937 (uri (cran-uri "haven" version))
3940 "0w0aqm0z4h0rm1f7fylm1mbv79p43y2r795w64wczcd0jwh4ch4z"))
3941 (modules '((guix build utils)))
3943 ;; unvendor readstat
3944 '(delete-file-recursively "src/readstat"))))
3945 (build-system r-build-system)
3948 (modify-phases %standard-phases
3949 (add-after 'unpack 'unbundle-readstat
3951 ;; We’re not building readstat.
3952 (substitute* "configure"
3953 (("exit 1") "")) ;don't be so dramatic!
3954 (substitute* '("src/Makevars.in"
3956 (("^PKG_LIBS=.*") "PKG_LIBS=\"-lreadstat\"\n")))))))
3972 (home-page "https://haven.tidyverse.org")
3973 (synopsis "Import and export SPSS, Stata and SAS files")
3975 "This package lets you import foreign statistical formats into R via the
3976 @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
3977 (license license:expat)))
3979 (define-public r-amap
3985 (uri (cran-uri "amap" version))
3988 "000r5705lq2mc15skin07dfxjf5816nbfy4gqkya1sv99dlfljbk"))))
3989 (build-system r-build-system)
3992 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
3993 (synopsis "Another multidimensional analysis package")
3994 (description "This package provides tools for clustering and principal
3995 component analysis (with robust methods, and parallelized functions).")
3996 (license license:gpl2+)))
3998 (define-public r-ape
4005 (uri (cran-uri "ape" version))
4008 "0mqjsh7maczd02iwa4fb896q3kgd9jnlilq7y1yz18ch0c54aqlv"))))
4009 (build-system r-build-system)
4011 (list r-lattice r-nlme r-rcpp))
4012 (home-page "http://ape-package.ird.fr/")
4013 (synopsis "Analyses of phylogenetics and evolution")
4015 "This package provides functions for reading, writing, plotting, and
4016 manipulating phylogenetic trees, analyses of comparative data in a
4017 phylogenetic framework, ancestral character analyses, analyses of
4018 diversification and macroevolution, computing distances from DNA sequences,
4019 and several other tools.")
4020 (license license:gpl2+)))
4022 (define-public r-abbyyr
4029 (uri (cran-uri "abbyyR" version))
4032 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
4033 (properties `((upstream-name . "abbyyR")))
4034 (build-system r-build-system)
4042 (home-page "https://github.com/soodoku/abbyyR")
4043 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
4045 "This package provides tools to get text from images of text using Abbyy
4046 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
4047 OCR images, barcodes, forms, documents with machine readable zones, e.g.
4048 passports and get the results in a variety of formats including plain text and
4049 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
4050 (license license:expat)))
4052 (define-public r-colorspace
4054 (name "r-colorspace")
4059 (uri (cran-uri "colorspace" version))
4061 (base32 "0zw52s8g2gxp8i1ax96azxmxqrbhb7aad5px0c1vgr6n9p682mp7"))))
4062 (build-system r-build-system)
4065 (home-page "https://cran.r-project.org/web/packages/colorspace")
4066 (synopsis "Color space manipulation")
4068 "This package carries out a mapping between assorted color spaces
4069 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
4070 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
4071 colors are provided.")
4072 (license license:bsd-3)))
4074 (define-public r-glue
4081 (uri (cran-uri "glue" version))
4084 "1gzxk5jgdh2xq9r7z09xs306ygzf27vhg3pyfl7ck1755gqii9cx"))))
4085 (build-system r-build-system)
4086 ;; knitr depends on glue, so we can't add knitr here to build the
4090 `(("r-knitr" ,r-knitr)))
4091 (home-page "https://github.com/tidyverse/glue")
4092 (synopsis "Interpreted string literals")
4094 "This package provides an implementation of interpreted string literals,
4095 inspired by Python's Literal String Interpolation (PEP-0498) and
4096 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
4097 (license license:expat)))
4099 (define-public r-paletteer
4101 (name "r-paletteer")
4105 (uri (cran-uri "paletteer" version))
4108 "1mm0k651356cjasv7wibscw82m1k8mwpp4xafpv66dsq24h28ikl"))))
4109 (properties `((upstream-name . "paletteer")))
4110 (build-system r-build-system)
4111 (propagated-inputs (list r-prismatic r-rematch2 r-rlang r-rstudioapi))
4112 (home-page "https://github.com/EmilHvitfeldt/paletteer")
4113 (synopsis "Comprehensive collection of color palettes")
4115 "The choices of color palettes in R can be quite overwhelming with palettes
4116 spread over many packages with many different API's. This package aims to
4117 collect all color palettes across the R ecosystem under the same package with
4118 a streamlined API.")
4119 (license license:gpl3)))
4121 (define-public r-palmerpenguins
4123 (name "r-palmerpenguins")
4128 (uri (cran-uri "palmerpenguins" version))
4131 "1d1h3bfx750is4qqj4w00rcigk9rrdy69bvd5bgqz5y7ls5x8h1a"))))
4133 `((upstream-name . "palmerpenguins")))
4134 (build-system r-build-system)
4135 (home-page "https://allisonhorst.github.io/palmerpenguins/")
4136 (synopsis "Palmer Archipelago (Antarctica) penguin data")
4138 "This package includes size measurements, clutch observations, and blood
4139 isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins
4140 observed on islands in the Palmer Archipelago near Palmer Station, Antarctica.
4141 Data were collected and made available by Dr. Kristen Gorman and the Palmer
4142 Station Long Term Ecological Research (LTER) Program.")
4143 (license license:cc0)))
4145 (define-public r-pastecs
4151 (uri (cran-uri "pastecs" version))
4154 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
4155 (build-system r-build-system)
4158 (home-page "https://github.com/phgrosjean/pastecs")
4159 (synopsis "Analysis of space-time ecological series")
4161 "This package provides functions for regulation, decomposition and analysis
4162 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
4163 initiative to bring PASSTEC 2000 functionalities to R.")
4164 (license license:gpl2+)))
4166 (define-public r-partykit
4172 (uri (cran-uri "partykit" version))
4175 "1cnx6qbw5svwh3nq40n5vr20179ihd3jgznm7mz4k50qkkid8hz6"))))
4176 (build-system r-build-system)
4184 (home-page "http://partykit.R-Forge.R-project.org/partykit")
4185 (synopsis "Toolkit for recursive partytioning")
4187 "This package provides a toolkit with infrastructure for representing,
4188 summarizing, and visualizing tree-structured regression and classification
4190 (license license:gpl2+)))
4192 (define-public r-plogr
4199 (uri (cran-uri "plogr" version))
4202 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
4203 (build-system r-build-system)
4204 (home-page "https://github.com/krlmlr/plogr")
4205 (synopsis "R bindings for the plog C++ logging library")
4207 "This package provides the header files for a stripped-down version of
4208 the plog header-only C++ logging library, and a method to log to R's standard
4210 (license license:expat)))
4212 (define-public r-pls
4219 (uri (cran-uri "pls" version))
4221 (base32 "137jg3x7aqwyki29i4kzp8d6imn17nq6wzzfjw5q19pixvmpybp2"))))
4222 (build-system r-build-system)
4223 (home-page "https://mevik.net/work/software/pls.html")
4224 (synopsis "Partial Least Squares and Principal Component Regression")
4226 "The pls package implements multivariate regression methods: Partial Least
4227 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
4228 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
4231 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
4232 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
4233 @item multi-response models (or @dfn{PLS2})
4234 @item flexible cross-validation
4235 @item Jackknife variance estimates of regression coefficients
4236 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
4237 (R)MSEP, R², and correlation loadings
4238 @item formula interface, modelled after @code{lm()}, with methods for predict,
4239 print, summary, plot, update, etc.
4240 @item extraction functions for coefficients, scores, and loadings
4241 @item MSEP, RMSEP, and R² estimates
4242 @item multiplicative scatter correction (@dfn{MSC})
4244 (license license:gpl2)))
4253 (uri (cran-uri "ps" version))
4255 (base32 "06mjwsn074195vd4yv7zzkmcf3sc124cw0cbnddj86swvggfn9cj"))))
4256 (build-system r-build-system)
4257 (home-page "https://ps.r-lib.org")
4258 (synopsis "List, query, and manipulate system processes")
4260 "The ps package implements an API to list, query, and manipulate system
4261 processes. Most of its code is based on the @code{psutil} Python package.")
4262 (license license:bsd-3)))
4264 (define-public r-pkgbuild
4271 (uri (cran-uri "pkgbuild" version))
4273 (base32 "0j6v5nbp8kg1m3j999gd1qsbdmqcqm1mf28ngmm177miwv8q4skw"))))
4274 (build-system r-build-system)
4284 (home-page "https://github.com/r-pkgs/pkgbuild")
4285 (synopsis "Find tools needed to build R packages")
4287 "This package provides functions used to build R packages. It locates
4288 compilers needed to build R packages on various platforms and ensures the PATH
4289 is configured appropriately so R can use them.")
4290 (license license:gpl3)))
4292 (define-public r-pkgload
4299 (uri (cran-uri "pkgload" version))
4302 "16k7n5hrwkzdwm54qyf5p6d1v5rf6vq688x48iylw6bygc6vgf66"))))
4303 (build-system r-build-system)
4313 (home-page "https://github.com/r-lib/pkgload")
4314 (synopsis "Simulate package installation and attach")
4316 "This package simulates the process of installing a package and then
4317 attaching it. This is a key part of the @code{devtools} package as it allows
4318 you to rapidly iterate while developing a package.")
4319 (license license:gpl3)))
4321 (define-public r-pvclust
4327 (uri (cran-uri "pvclust" version))
4330 "0082icm54k2yq60k06qpr92a626k39j2jr0046lva4ylmhxqb4kq"))))
4331 (build-system r-build-system)
4332 (home-page "https://github.com/shimo-lab/pvclust")
4334 "Hierarchical clustering with P-values via multiscale bootstrap resampling")
4335 (description "This package provides an implementation of multiscale bootstrap
4336 resampling for assessing the uncertainty in hierarchical cluster analysis. It
4337 provides an AU (approximately unbiased) P-value as well as a BP (bootstrap probability)
4338 value for each cluster in a dendrogram.")
4339 (license license:gpl2+)))
4341 (define-public r-rcpp
4348 (uri (cran-uri "Rcpp" version))
4350 (base32 "0xli48y9nsj8x8p5vkhisiz4l23g8r2623rn0i4xb5javh3fqz40"))))
4351 (build-system r-build-system)
4352 (home-page "http://www.rcpp.org")
4353 (synopsis "Seamless R and C++ integration")
4355 "The Rcpp package provides R functions as well as C++ classes which offer
4356 a seamless integration of R and C++. Many R data types and objects can be
4357 mapped back and forth to C++ equivalents which facilitates both writing of new
4358 code as well as easier integration of third-party libraries. Documentation
4359 about Rcpp is provided by several vignettes included in this package, via the
4360 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
4361 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
4362 @code{citation(\"Rcpp\")} for details on these last two.")
4363 (license license:gpl2+)))
4365 (define-public r-rcppml
4372 (uri (cran-uri "RcppML" version))
4374 (base32 "1ih8i7i6m221iw227mnl3rvnaw2l53h8fpnc4f8yn9sm10anap1j"))))
4375 (properties `((upstream-name . "RcppML")))
4376 (build-system r-build-system)
4377 (propagated-inputs (list r-matrix r-rcpp r-rcppeigen))
4378 (native-inputs (list r-knitr))
4379 (home-page "https://github.com/zdebruine/RcppML")
4380 (synopsis "Rcpp machine learning library")
4382 "This package provides fast machine learning algorithms including matrix
4383 factorization and divisive clustering for large sparse and dense matrices.")
4384 (license license:gpl2+)))
4386 (define-public r-rcppthread
4388 (name "r-rcppthread")
4393 (uri (cran-uri "RcppThread" version))
4396 "0iprpidf7q1wlrgr9dwiikb6apqk80pyjcyni56k64nl7lrkszhj"))))
4397 (properties `((upstream-name . "RcppThread")))
4398 (build-system r-build-system)
4400 "https://github.com/tnagler/RcppThread")
4401 (synopsis "R threading in C++")
4403 "This package provides a C++11-style thread class and thread pool that can
4404 safely be interrupted from R.")
4405 (license license:expat)))
4407 (define-public r-rcppnumerical
4409 (name "r-rcppnumerical")
4413 (uri (cran-uri "RcppNumerical" version))
4416 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
4417 (build-system r-build-system)
4419 (list r-rcpp r-rcppeigen))
4420 (home-page "https://github.com/yixuan/RcppNumerical")
4421 (synopsis"Numerical computing libraries integration with @code{Rcpp}")
4422 (description "This package provides a collection of libraries for numerical
4423 computing (numerical integration, optimization, etc.) and their integration
4425 (license license:gpl2+)))
4427 (define-public r-rcppxptrutils
4429 (name "r-rcppxptrutils")
4434 (uri (cran-uri "RcppXPtrUtils" version))
4436 (base32 "0hm57nf4dzgsmg4hjj6wikwjx93fgfwkmybw6ly4b58wi6qwml1l"))))
4437 (properties `((upstream-name . "RcppXPtrUtils")))
4438 (build-system r-build-system)
4439 (propagated-inputs (list r-rcpp))
4440 (home-page "https://github.com/Enchufa2/RcppXPtrUtils")
4441 (synopsis "XPtr add-ons for Rcpp")
4443 "This package provides the means to compile user-supplied C++ functions
4444 with Rcpp and retrieve an @code{XPtr} that can be passed to other C++
4446 (license license:expat)))
4448 (define-public r-bindr
4455 (uri (cran-uri "bindr" version))
4458 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
4459 (build-system r-build-system)
4460 (home-page "https://github.com/krlmlr/bindr")
4461 (synopsis "Parametrized active bindings")
4463 "This package provides a simple interface for creating active bindings
4464 where the bound function accepts additional arguments.")
4465 (license license:expat)))
4467 (define-public r-bindrcpp
4474 (uri (cran-uri "bindrcpp" version))
4477 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
4478 (build-system r-build-system)
4480 (list r-bindr r-plogr r-rcpp))
4481 (home-page "https://github.com/krlmlr/bindrcpp")
4482 (synopsis "Rcpp interface to active bindings")
4484 "This package provides an easy way to fill an environment with active
4485 bindings that call a C++ function.")
4486 (license license:expat)))
4488 (define-public r-auc
4495 (uri (cran-uri "AUC" version))
4498 "07xf47kypqbsg2mixmq6mnh4s89aqan9bgl6kfv6lbx8ajv2asw3"))))
4499 (properties `((upstream-name . "AUC")))
4500 (build-system r-build-system)
4501 (home-page "https://cran.r-project.org/web/packages/AUC")
4502 (synopsis "Compute the area under the curve of selected measures")
4504 "This package includes functions to compute the area under the curve of
4505 selected measures: the area under the sensitivity curve (AUSEC), the area
4506 under the specificity curve (AUSPC), the area under the accuracy
4507 curve (AUACC), and the area under the receiver operating characteristic
4508 curve (AUROC). The curves can also be visualized. Support for partial areas
4510 (license license:gpl2+)))
4512 (define-public r-calibrate
4514 (name "r-calibrate")
4519 (uri (cran-uri "calibrate" version))
4521 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
4522 (build-system r-build-system)
4525 (home-page "https://cran.r-project.org/web/packages/calibrate")
4526 (synopsis "Calibration of scatterplot and biplot axes")
4528 "This is a package for drawing calibrated scales with tick marks
4529 on (non-orthogonal) variable vectors in scatterplots and biplots.")
4530 (license license:gpl2)))
4532 (define-public r-shape
4539 (uri (cran-uri "shape" version))
4542 "0yqbrrx2ywmfl99s6d1n6jblc63k1mxbiqyv8y0kq8jws1g3w45r"))))
4543 (build-system r-build-system)
4544 (home-page "https://cran.r-project.org/web/packages/shape")
4545 (synopsis "Functions for plotting graphical shapes")
4547 "This package provides functions for plotting graphical shapes such as
4548 ellipses, circles, cylinders, arrows, ...")
4549 (license license:gpl3+)))
4551 (define-public r-globaloptions
4553 (name "r-globaloptions")
4558 (uri (cran-uri "GlobalOptions" version))
4560 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
4561 (properties `((upstream-name . "GlobalOptions")))
4562 (build-system r-build-system)
4565 (home-page "https://github.com/jokergoo/GlobalOptions")
4566 (synopsis "Generate functions to get or set global options")
4568 "This package provides more controls on the option values such as
4569 validation and filtering on the values, making options invisible or private.")
4570 (license license:gpl2+)))
4572 (define-public r-circlize
4579 (uri (cran-uri "circlize" version))
4582 "1iswb7dy08as3pbzxvhx5qlsbnwvp79nwg8m158nfz7y2d9xa0nn"))))
4583 (build-system r-build-system)
4585 (list r-colorspace r-globaloptions r-shape))
4588 (home-page "https://github.com/jokergoo/circlize")
4589 (synopsis "Circular visualization")
4591 "Circular layout is an efficient way to visualise huge amounts of
4592 information. This package provides an implementation of circular layout
4593 generation in R as well as an enhancement of available software. Its
4594 flexibility is based on the usage of low-level graphics functions such that
4595 self-defined high-level graphics can be easily implemented by users for
4596 specific purposes. Together with the seamless connection between the powerful
4597 computational and visual environment in R, it gives users more convenience and
4598 freedom to design figures for better understanding complex patterns behind
4599 multi-dimensional data.")
4600 (license license:gpl2+)))
4602 (define-public r-powerlaw
4609 (uri (cran-uri "poweRlaw" version))
4611 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
4612 (properties `((upstream-name . "poweRlaw")))
4613 (build-system r-build-system)
4618 (home-page "https://github.com/csgillespie/poweRlaw")
4619 (synopsis "Tools for the analysis of heavy tailed distributions")
4621 "This package provides an implementation of maximum likelihood estimators
4622 for a variety of heavy tailed distributions, including both the discrete and
4623 continuous power law distributions. Additionally, a goodness-of-fit based
4624 approach is used to estimate the lower cut-off for the scaling region.")
4625 ;; Any of these GPL versions.
4626 (license (list license:gpl2 license:gpl3))))
4628 (define-public r-compare
4635 (uri (cran-uri "compare" version))
4638 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
4639 (build-system r-build-system)
4640 (home-page "https://cran.r-project.org/web/packages/compare")
4641 (synopsis "Comparing objects for differences")
4643 "This package provides functions to compare a model object to a
4644 comparison object. If the objects are not identical, the functions can be
4645 instructed to explore various modifications of the objects (e.g., sorting
4646 rows, dropping names) to see if the modified versions are identical.")
4647 (license license:gpl2+)))
4649 (define-public r-dendextend
4651 (name "r-dendextend")
4656 (uri (cran-uri "dendextend" version))
4659 "0rl4f0b73s1gdjfxgpnz87lhv131qazxb6vsv2935ad266fd0bzc"))))
4660 (build-system r-build-system)
4662 (list r-ggplot2 r-magrittr r-viridis))
4665 (home-page "https://cran.r-project.org/web/packages/dendextend")
4666 (synopsis "Extending 'dendrogram' functionality in R")
4668 "This package offers a set of functions for extending @code{dendrogram}
4669 objects in R, letting you visualize and compare trees of hierarchical
4670 clusterings. You can adjust a tree's graphical parameters (the color, size,
4671 type, etc of its branches, nodes and labels) and visually and statistically
4672 compare different dendrograms to one another.")
4673 ;; Any of these versions
4674 (license (list license:gpl2 license:gpl3))))
4676 (define-public r-getoptlong
4678 (name "r-getoptlong")
4683 (uri (cran-uri "GetoptLong" version))
4686 "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc"))))
4687 (properties `((upstream-name . "GetoptLong")))
4688 (build-system r-build-system)
4692 (list r-crayon r-globaloptions r-rjson))
4695 (home-page "https://github.com/jokergoo/GetoptLong")
4696 (synopsis "Parsing command-line arguments and variable interpolation")
4698 "This is yet another command-line argument parser which wraps the
4699 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
4700 use in R. It also provides a simple way for variable interpolation in R.")
4701 (license license:gpl2+)))
4703 (define-public r-fastmatch
4705 (name "r-fastmatch")
4710 (uri (cran-uri "fastmatch" version))
4713 "0qcq1gwl9pijgp34giyq5y9rk0ly3d7xza2b7r68xx63ifqa1vqx"))))
4714 (build-system r-build-system)
4715 (home-page "https://www.rforge.net/fastmatch")
4716 (synopsis "Fast match function")
4718 "This package provides a fast @code{match} replacement for cases that
4719 require repeated look-ups. It is slightly faster that R's built-in
4720 @code{match} function on first match against a table, but extremely fast on
4721 any subsequent lookup as it keeps the hash table in memory.")
4722 (license license:gpl2)))
4731 (uri (cran-uri "ff" version))
4734 "1yl3ipzz9bjkfy9bbna7xz5n7iz4lchnw5l7agww7by764yk6iqa"))))
4735 (build-system r-build-system)
4736 (propagated-inputs (list r-bit))
4737 (home-page "http://ff.r-forge.r-project.org/")
4738 (synopsis "Memory-efficient storage of large data on disk and access functions")
4740 "This package provides data structures that are stored on disk but
4741 behave (almost) as if they were in RAM by transparently mapping only a section
4743 ;; error Architecture not supported.
4744 (supported-systems (delete "aarch64-linux" %supported-systems))
4745 (license license:gpl2)))
4747 (define-public r-ffbase
4754 (uri (cran-uri "ffbase" version))
4757 "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk"))))
4758 (build-system r-build-system)
4760 (list r-bit r-fastmatch r-ff))
4761 (home-page "https://github.com/edwindj/ffbase")
4762 (synopsis "Basic statistical functions for package 'ff'")
4764 "This package extends the out of memory vectors of @code{ff} with
4765 statistical functions and other utilities to ease their usage.")
4766 (license license:gpl3)))
4768 (define-public r-prettyunits
4770 (name "r-prettyunits")
4775 (uri (cran-uri "prettyunits" version))
4778 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
4779 (build-system r-build-system)
4780 (home-page "https://github.com/gaborcsardi/prettyunits")
4781 (synopsis "Pretty, human readable formatting of quantities")
4783 "This package provides tools for pretty, human readable formatting of
4785 (license license:expat)))
4787 (define-public r-princurve
4789 (name "r-princurve")
4793 (uri (cran-uri "princurve" version))
4796 "0wzk329bxljkzz57y220lsfckpsn45w348m6dcxh29zbj0ik65h2"))))
4797 (build-system r-build-system)
4800 (home-page "https://github.com/rcannood/princurve")
4801 (synopsis "Fit a principal curve in arbitrary dimension")
4802 (description "This package provides procedures for fitting a principal
4803 curve to a data matrix in arbitrary dimensions.")
4804 (license license:gpl2)))
4806 (define-public r-prismatic
4808 (name "r-prismatic")
4812 (uri (cran-uri "prismatic" version))
4815 "013i0mq4n8s2zbzvfrz1vjcn2a6l98bamslkcv1a3cn70gpphja9"))))
4816 (properties `((upstream-name . "prismatic")))
4817 (build-system r-build-system)
4818 (propagated-inputs (list r-farver))
4819 (home-page "https://github.com/EmilHvitfeldt/prismatic")
4820 (synopsis "Color manipulation tools")
4822 "Manipulate and visualize colors in a intuitive, low-dependency and functional
4824 (license license:expat)))
4826 (define-public r-reshape
4833 (uri (cran-uri "reshape" version))
4836 "0j203qmc076x5lp6q2xi4dq4xdb73jmsa42rpxp1c37knnrph4br"))))
4837 (build-system r-build-system)
4840 (home-page "http://had.co.nz/reshape")
4841 (synopsis "Flexibly reshape data")
4843 "Flexibly restructure and aggregate data using just two functions:
4844 @code{melt} and @code{cast}. This package provides them.")
4845 (license license:expat)))
4847 (define-public r-restrserve
4849 (name "r-restrserve")
4854 (uri (cran-uri "RestRserve" version))
4856 (base32 "1xfcp0y9l31815g1jk33mnkb6z68qpjl0gb4fj7f4578kx3v1c8p"))))
4857 (build-system r-build-system)
4869 (home-page "https://restrserve.org")
4870 (synopsis "R web API framework")
4872 "RestRserve is an R web API framework for building high-performance AND
4873 robust microservices and app backends. With Rserve backend on UNIX-like
4874 systems it is parallel by design. It will handle incoming requests in
4875 parallel - each request in a separate fork.")
4876 (license license:gpl2+)))
4878 (define-public r-progress
4885 (uri (cran-uri "progress" version))
4888 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
4889 (build-system r-build-system)
4891 (list r-crayon r-hms r-prettyunits r-r6))
4892 (home-page "https://github.com/gaborcsardi/progress")
4893 (synopsis "Terminal progress bars")
4895 "This package provides configurable progress bars. They may include
4896 percentage, elapsed time, and/or the estimated completion time. They work in
4897 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
4898 package also provides a C++ API, that works with or without Rcpp.")
4899 (license license:expat)))
4901 (define-public r-ggally
4908 (uri (cran-uri "GGally" version))
4911 "1r98zgh2grn8330cf26r1c20gl131zm778szvn5wj6q6pwv2yd9h"))))
4912 (properties `((upstream-name . "GGally")))
4913 (build-system r-build-system)
4929 (home-page "https://ggobi.github.io/ggally")
4930 (synopsis "Extension to ggplot2")
4932 "The R package ggplot2 is a plotting system based on the grammar of
4933 graphics. GGally extends ggplot2 by adding several functions to reduce the
4934 complexity of combining geometric objects with transformed data. Some of
4935 these functions include a pairwise plot matrix, a two group pairwise plot
4936 matrix, a parallel coordinates plot, a survival plot, and several functions to
4938 (license license:gpl2+)))
4940 (define-public r-proxy
4947 (uri (cran-uri "proxy" version))
4950 "0gsng2aggnljl4z82la9hpnd26hngzhj8fizx4wx22npqjj93694"))))
4951 (build-system r-build-system)
4952 (home-page "https://cran.r-project.org/web/packages/proxy")
4953 (synopsis "Distance and similarity measures")
4955 "This package provides an extensible framework for the efficient
4956 calculation of auto- and cross-proximities, along with implementations of the
4957 most popular ones.")
4958 (license license:gpl2)))
4967 (uri (cran-uri "sp" version))
4969 (base32 "077q1wh9ihhcn1338xspnd90hy16ljxsav1xcrxdxj4fyynhd6lk"))))
4970 (build-system r-build-system)
4975 (home-page "https://cran.r-project.org/web/packages/sp")
4976 (synopsis "Classes and methods for spatial data")
4978 "This package provides classes and methods for spatial data; the classes
4979 document where the spatial location information resides, for 2D or 3D data.
4980 Utility functions are provided, e.g. for plotting data as maps, spatial
4981 selection, as well as methods for retrieving coordinates, for subsetting,
4982 print, summary, etc.")
4983 (license license:gpl2+)))
4985 (define-public r-laplacesdemon
4987 (name "r-laplacesdemon")
4992 (uri (cran-uri "LaplacesDemon" version))
4994 (base32 "1dsfp65cg06f25zjzd5ib4qyn1alfhbhpgyvpcw5n6bszn13idap"))))
4995 (properties `((upstream-name . "LaplacesDemon")))
4996 (build-system r-build-system)
4997 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
4998 (synopsis "Complete environment for Bayesian inference")
5000 "This package provides a complete environment for Bayesian inference using
5001 a variety of different samplers.")
5002 (license license:expat)))
5004 (define-public r-rmtstat
5011 (uri (cran-uri "RMTstat" version))
5014 "1r1a2sdqv64m9cpm2pz6r8abf7l810126ayd8iq3gx86c7bjfj5v"))))
5015 (properties `((upstream-name . "RMTstat")))
5016 (build-system r-build-system)
5017 (home-page "https://cran.r-project.org/web/packages/RMTstat")
5018 (synopsis "Distributions, statistics and tests derived from random matrix theory")
5020 "This package provides functions for working with the Tracy-Widom laws
5021 and other distributions related to the eigenvalues of large Wishart
5023 (license license:bsd-3)))
5025 (define-public r-rmpi
5031 (uri (cran-uri "Rmpi" version))
5034 "06mxqgrimhfsag5giv810c7ycdbaycqs4qcj41pnfbj0jypw32im"))))
5035 (properties `((upstream-name . "Rmpi")))
5036 (build-system r-build-system)
5038 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
5039 #:phases (modify-phases %standard-phases
5040 (add-before 'install 'mpi-setup
5046 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
5047 (synopsis "R interface to message-passing interface (MPI)")
5049 "This package provides an interface (wrapper) to MPI APIs. It also
5050 provides an interactive R manager and worker environment.")
5051 (license license:gpl2+)))
5053 (define-public r-lmoments
5060 (uri (cran-uri "Lmoments" version))
5063 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
5064 (properties `((upstream-name . "Lmoments")))
5065 (build-system r-build-system)
5067 (list r-rcpp r-rcpparmadillo))
5068 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
5069 (synopsis "L-moments and quantile mixtures")
5071 "This package contains functions to estimate L-moments and trimmed
5072 L-moments from the data. It also contains functions to estimate the
5073 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
5074 quantile mixture from L-moments and trimmed L-moments.")
5075 (license license:gpl2)))
5077 (define-public r-distillery
5079 (name "r-distillery")
5084 (uri (cran-uri "distillery" version))
5087 "1ymmxyamkq0zbz2m4gllln1ihks2hcib6gs0mls92as79srz122b"))))
5088 (build-system r-build-system)
5089 (home-page "https://ral.ucar.edu/staff/ericg/")
5090 (synopsis "Functions for confidence intervals and object information")
5092 "This package provides some very simple method functions for confidence
5093 interval calculation and to distill pertinent information from a potentially
5094 complex object; primarily used in common with the packages extRemes and
5096 (license license:gpl2+)))
5098 (define-public r-etrunct
5104 (uri (cran-uri "etrunct" version))
5107 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr"))))
5108 (properties `((upstream-name . "etrunct")))
5109 (build-system r-build-system)
5110 (home-page "https://cran.r-project.org/web/packages/etrunct")
5111 (synopsis "Computes moments of univariate truncated T distribution")
5112 (description "This package computes moments of univariate truncated
5113 T distribution. There is only one exported function, @code{e_trunct},
5114 which should be seen for details.")
5115 (license license:expat)))
5117 (define-public r-excelr
5124 (uri (cran-uri "excelR" version))
5126 (base32 "1pb4sy54zjv5vrh7gjjv7qlpab74km6mfsmfyl0yhmr0jx01hrw0"))
5128 '(delete-file "inst/htmlwidgets/lib/jexcel/js/jexcel.min.js"))))
5129 (properties `((upstream-name . "excelR")))
5130 (build-system r-build-system)
5133 (modify-phases %standard-phases
5134 (add-after 'unpack 'process-javascript
5135 (lambda* (#:key inputs #:allow-other-keys)
5136 (with-directory-excursion "inst/htmlwidgets/lib/jexcel/js/"
5137 (let ((source (assoc-ref inputs "js-jexcel"))
5138 (target "jexcel.min.js"))
5139 (format #true "Processing ~a --> ~a~%"
5141 (invoke "esbuild" source "--minify"
5142 (string-append "--outfile=" target)))))))))
5144 `(("esbuild" ,esbuild)
5145 ;; There is no tag for this particular commit, but comparison of the
5146 ;; contents of the JavaScript files point to this commit as the most
5151 (uri (string-append "https://raw.githubusercontent.com/jspreadsheet/ce/"
5152 "8af1960f76e6803bebc5750013d2ebe95354e88a/dist/jexcel.js"))
5155 "0y88hsr9d8cpnvdmbm17m328pc4kc5wbcv02kzmhm0bryzhviw7h"))))))
5156 (propagated-inputs (list r-htmlwidgets r-jsonlite))
5157 (home-page "https://github.com/Swechhya/excelR")
5158 (synopsis "Wrapper of the JavaScript library jExcel")
5160 "This package provides an R interface to the jExcel library to
5161 create web-based interactive tables and spreadsheets compatible with
5162 spreadsheet software.")
5163 (license license:expat)))
5165 (define-public r-extremes
5172 (uri (cran-uri "extRemes" version))
5175 "19q560prq02h3bwk01jb68693qb5bhsv8wiqhia7v5knm34qv8x7"))))
5176 (properties `((upstream-name . "extRemes")))
5177 (build-system r-build-system)
5179 (list r-distillery r-lmoments))
5180 (home-page "https://www.assessment.ucar.edu/toolkit/")
5181 (synopsis "Extreme value analysis")
5183 "ExtRemes is a suite of functions for carrying out analyses on the
5184 extreme values of a process of interest; be they block maxima over long blocks
5185 or excesses over a high threshold.")
5186 (license license:gpl2+)))
5188 (define-public r-lmtest
5195 (uri (cran-uri "lmtest" version))
5198 "15yr2kx08wy085bnziqmj1p6hf9mg3qp2a8465jk2df6di6hsh34"))))
5199 (build-system r-build-system)
5204 (home-page "https://cran.r-project.org/web/packages/lmtest")
5205 (synopsis "Testing linear regression models")
5207 "This package provides a collection of tests, data sets, and examples for
5208 diagnostic checking in linear regression models. Furthermore, some generic
5209 tools for inference in parametric models are provided.")
5210 ;; Either version is okay
5211 (license (list license:gpl2 license:gpl3))))
5213 (define-public r-idr
5219 (uri (cran-uri "idr" version))
5222 "1r6icxf0c0y9wvihwmkk5xqscr1qhacqk3w2076kjm2993f10fbb"))))
5223 (build-system r-build-system)
5224 (home-page "https://cran.r-project.org/web/packages/idr/")
5225 (synopsis "Irreproducible discovery rate")
5227 "This is a package for estimating the copula mixture model and plotting
5228 correspondence curves in \"Measuring reproducibility of high-throughput
5229 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
5230 by Li, Brown, Huang, and Bickel")
5231 (license license:gpl2+)))
5233 (define-public r-inline
5239 (uri (cran-uri "inline" version))
5242 "1mcr9hgq6kkq03n7pkcccxa7vg8jma0q7lfxc5vvkc6snydk1s8f"))))
5243 (build-system r-build-system)
5244 (home-page "https://cran.r-project.org/web/packages/inline")
5245 (synopsis "Functions to inline C, C++, Fortran function calls from R")
5247 "This package provides functionality to dynamically define R functions
5248 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
5249 @code{.Call} calling conventions.")
5250 ;; Any version of the LGPL.
5251 (license license:lgpl3+)))
5253 (define-public r-inum
5259 (uri (cran-uri "inum" version))
5262 "1khkzja8lwn9075864vbyajqina9m588ahf1fsrrajrsqilyzssz"))))
5263 (build-system r-build-system)
5266 (home-page "https://cran.r-project.org/web/packages/inum/")
5267 (synopsis "Interval and enum-type representation of vectors")
5269 "This package provides an enum-type representation of vectors and
5270 representation of intervals, including a method of coercing variables
5272 (license license:gpl2)))
5273 (define-public r-invgamma
5279 (uri (cran-uri "invgamma" version))
5282 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a"))))
5283 (properties `((upstream-name . "invgamma")))
5284 (build-system r-build-system)
5285 (home-page "https://github.com/dkahle/invgamma")
5286 (synopsis "Inverse gamma distribution")
5287 (description "This package provides a light weight implementation of the
5288 standard distribution functions for the inverse gamma distribution, wrapping
5289 those for the gamma distribution in the @code{stats} package.")
5290 (license license:gpl2)))
5292 (define-public r-bdsmatrix
5294 (name "r-bdsmatrix")
5299 (uri (cran-uri "bdsmatrix" version))
5302 "1g300x11rv56f826mbv7mbb67a5xz3dv74hpjc18jh3q8gap3j7r"))))
5303 (properties `((upstream-name . "bdsmatrix")))
5304 (build-system r-build-system)
5305 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
5306 (synopsis "Routines for block diagonal symmetric matrices")
5308 "This package provides procedures to work with block diagonal symmetric
5309 matrices, a special case of sparse matrices.")
5310 (license license:lgpl2.0)))
5312 (define-public r-bbmle
5319 (uri (cran-uri "bbmle" version))
5322 "0mdj21q7k0fp4cj7la14vmcjmp49zqm57g7r6zrwmxpv0acwda46"))))
5323 (build-system r-build-system)
5333 (home-page "https://cran.r-project.org/web/packages/bbmle")
5334 (synopsis "Tools for General Maximum Likelihood Estimation")
5336 "This package provides methods and functions for fitting maximum
5337 likelihood models in R. This package modifies and extends the @code{mle}
5338 classes in the @code{stats4} package.")
5339 ;; Any version of the GPL
5340 (license license:gpl2+)))
5342 (define-public r-emdbook
5349 (uri (cran-uri "emdbook" version))
5352 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
5353 (build-system r-build-system)
5355 (list r-bbmle r-coda r-lattice r-mass r-plyr))
5356 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
5357 (synopsis "Support functions and data for \"Ecological Models and Data\"")
5359 "This package provides auxiliary functions and data sets for \"Ecological
5360 Models and Data\", a book presenting maximum likelihood estimation and related
5361 topics for ecologists (ISBN 978-0-691-12522-0).")
5363 (license (list license:gpl2 license:gpl3))))
5365 (define-public r-lpsolve
5372 (uri (cran-uri "lpSolve" version))
5375 "124jdjvxi1kqfd10jv85jqllvba1hi2z4j5g7n8wc1fwv4mq09gp"))))
5376 (properties `((upstream-name . "lpSolve")))
5377 (build-system r-build-system)
5378 (home-page "https://cran.r-project.org/web/packages/lpSolve")
5379 (synopsis "R interface to Lp_solve to solve linear/integer programs")
5381 "Lp_solve is software for solving linear, integer and mixed integer
5382 programs. This implementation supplies a \"wrapper\" function in C and some R
5383 functions that solve general linear/integer problems, assignment problems, and
5384 transportation problems.")
5385 (license license:lgpl2.0)))
5387 (define-public r-limsolve
5394 (uri (cran-uri "limSolve" version))
5397 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
5398 (properties `((upstream-name . "limSolve")))
5399 (build-system r-build-system)
5401 (list r-lpsolve r-mass r-quadprog))
5402 (native-inputs (list gfortran))
5403 (home-page "https://cran.r-project.org/web/packages/limSolve")
5404 (synopsis "Solving linear inverse models")
5406 "This package provides functions that:
5409 @item find the minimum/maximum of a linear or quadratic function,
5410 @item sample an underdetermined or overdetermined system,
5411 @item solve a linear system Ax=B for the unknown x.
5414 It includes banded and tridiagonal linear systems. The package calls Fortran
5415 functions from LINPACK.")
5417 (license (list license:gpl2+ license:gpl3+))))
5419 (define-public r-fitdistrplus
5421 (name "r-fitdistrplus")
5426 (uri (cran-uri "fitdistrplus" version))
5429 "0nhgjvwya95v6b9khbsgp44lw10xg35w61lmka1v6wq7yh827izk"))))
5430 (build-system r-build-system)
5432 (list r-mass r-survival))
5435 (home-page "http://riskassessment.r-forge.r-project.org")
5436 (synopsis "Fitting a parametric distribution from data")
5438 "This package extends the @code{fitdistr} function of the MASS package
5439 with several functions to help the fit of a parametric distribution to
5440 non-censored or censored data. Censored data may contain left-censored,
5441 right-censored and interval-censored values, with several lower and upper
5442 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
5443 provides moment matching (MME), quantile matching (QME) and maximum
5444 goodness-of-fit estimation (MGE) methods (available only for non-censored
5445 data). Weighted versions of MLE, MME and QME are available.")
5446 (license license:gpl2+)))
5448 (define-public r-energy
5455 (uri (cran-uri "energy" version))
5458 "19xyw5bkyzfk22gly2ca2nsznqnrhaq4a77727kr1k26bj3y8gal"))))
5459 (build-system r-build-system)
5461 (list r-boot r-gsl r-rcpp))
5462 (home-page "https://cran.r-project.org/web/packages/energy")
5463 (synopsis "Multivariate inference via the energy of data")
5465 "This package provides e-statistics (energy) tests and statistics for
5466 multivariate and univariate inference, including distance correlation,
5467 one-sample, two-sample, and multi-sample tests for comparing multivariate
5468 distributions, are implemented. Measuring and testing multivariate
5469 independence based on distance correlation, partial distance correlation,
5470 multivariate goodness-of-fit tests, clustering based on energy distance,
5471 testing for multivariate normality, distance components (disco) for
5472 non-parametric analysis of structured data, and other energy
5473 statistics/methods are implemented.")
5474 (license license:gpl2+)))
5476 (define-public r-suppdists
5478 (name "r-suppdists")
5483 (uri (cran-uri "SuppDists" version))
5486 "025b9nlxz62wk84295csyzbncpn80i3iby3sxdigf3swcgi2fmbb"))))
5487 (properties `((upstream-name . "SuppDists")))
5488 (build-system r-build-system)
5489 (home-page "https://cran.r-project.org/web/packages/SuppDists")
5490 (synopsis "Supplementary distributions")
5492 "This package provides ten distributions supplementing those built into
5493 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
5494 Spearman's rho, maximum F ratio, the Pearson product moment correlation
5495 coefficient, Johnson distributions, normal scores and generalized
5496 hypergeometric distributions. In addition two random number generators of
5497 George Marsaglia are included.")
5498 (license license:gpl2+)))
5500 (define-public r-ksamples
5507 (uri (cran-uri "kSamples" version))
5510 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
5511 (properties `((upstream-name . "kSamples")))
5512 (build-system r-build-system)
5515 (home-page "https://cran.r-project.org/web/packages/kSamples")
5516 (synopsis "K-Sample rank tests and their combinations")
5518 "This package provides tools to compares k samples using the
5519 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
5520 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
5521 test. It computes asymptotic, simulated or (limited) exact P-values, all
5522 valid under randomization, with or without ties, or conditionally under random
5523 sampling from populations, given the observed tie pattern. Except for Steel's
5524 test and the JT test it also combines these tests across several blocks of
5526 (license license:gpl2+)))
5528 (define-public r-cvst
5535 (uri (cran-uri "CVST" version))
5538 "0bgk0d6w3dyhb5s30idnp6jpb3m8wf3b79wqlg127wwm0cird8pg"))))
5539 (properties `((upstream-name . "CVST")))
5540 (build-system r-build-system)
5542 (list r-kernlab r-matrix))
5543 (home-page "https://cran.r-project.org/web/packages/CVST")
5544 (synopsis "Fast cross-validation via sequential testing")
5546 "This package implements the fast cross-validation via sequential
5547 testing (CVST) procedure. CVST is an improved cross-validation procedure
5548 which uses non-parametric testing coupled with sequential analysis to
5549 determine the best parameter set on linearly increasing subsets of the data.
5550 Additionally to the CVST the package contains an implementation of the
5551 ordinary k-fold cross-validation with a flexible and powerful set of helper
5552 objects and methods to handle the overall model selection process. The
5553 implementations of the Cochran's Q test with permutations and the sequential
5554 testing framework of Wald are generic and can therefore also be used in other
5556 (license license:gpl2+)))
5558 (define-public r-squarem
5565 (uri (cran-uri "SQUAREM" version))
5568 "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6"))))
5569 (properties `((upstream-name . "SQUAREM")))
5570 (build-system r-build-system)
5571 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
5572 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
5574 "This package provides algorithms for accelerating the convergence of
5575 slow, monotone sequences from smooth, contraction mapping such as the EM
5576 algorithm. It can be used to accelerate any smooth, linearly convergent
5577 acceleration scheme. A tutorial style introduction to this package is
5578 available in a vignette.")
5579 (license license:gpl2+)))
5581 (define-public r-progressr
5583 (name "r-progressr")
5588 (uri (cran-uri "progressr" version))
5590 (base32 "1nbc6vvsyqa1gvh1a1m4prnvng88wsa0r35i9fiwq84a6j18qrnq"))))
5591 (properties `((upstream-name . "progressr")))
5592 (build-system r-build-system)
5595 (home-page "https://progressr.futureverse.org")
5596 (synopsis "Inclusive, unifying API for progress updates")
5598 "This package provides a minimal, unifying API for scripts and packages
5599 to report progress updates from anywhere including when using parallel
5600 processing. The package is designed such that the developer can to focus on
5601 what progress should be reported on without having to worry about how to
5602 present it. The end user has full control of how, where, and when to render
5603 these progress updates.")
5604 (license license:gpl3+)))
5606 (define-public r-lava
5613 (uri (cran-uri "lava" version))
5616 "092y5v5mp9a9mqia47fqh22br31crp8w5b4ks2y15242ydlxly1h"))))
5617 (build-system r-build-system)
5619 (list r-future-apply r-numderiv r-progressr r-squarem r-survival))
5622 (home-page "https://github.com/kkholst/lava")
5623 (synopsis "Latent variable models")
5625 "This package provides tools for the estimation and simulation of latent
5627 (license license:gpl3)))
5629 (define-public r-drr
5636 (uri (cran-uri "DRR" version))
5639 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
5640 (properties `((upstream-name . "DRR")))
5641 (build-system r-build-system)
5643 (list r-cvst r-kernlab r-matrix))
5644 (home-page "https://cran.r-project.org/web/packages/DRR")
5645 (synopsis "Dimensionality reduction via regression")
5647 "This package provides an implementation of dimensionality reduction via
5648 regression using Kernel Ridge Regression.")
5649 (license license:gpl3)))
5651 (define-public r-prodlim
5654 (version "2019.11.13")
5658 (uri (cran-uri "prodlim" version))
5661 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
5662 (build-system r-build-system)
5664 (list r-kernsmooth r-lava r-rcpp r-survival))
5665 (home-page "https://cran.r-project.org/web/packages/prodlim")
5666 (synopsis "Product-limit estimation for censored event history analysis")
5668 "This package provides a fast and user-friendly implementation of
5669 nonparametric estimators for censored event history (survival) analysis with
5670 the Kaplan-Meier and Aalen-Johansen methods.")
5671 (license license:gpl2+)))
5673 (define-public r-dimred
5680 (uri (cran-uri "dimRed" version))
5683 "05zlkf6hjdqqr1sgw7ww9f17vjnsiqfaj9kvdvi146phh53v2zls"))))
5684 (properties `((upstream-name . "dimRed")))
5685 (build-system r-build-system)
5687 (list r-drr r-magrittr))
5690 (home-page "https://github.com/gdkrmr/dimRed")
5691 (synopsis "Framework for dimensionality reduction")
5693 "This package provides a collection of dimensionality reduction
5694 techniques from R packages and provides a common interface for calling the
5696 (license license:gpl3)))
5698 (define-public r-timedate
5701 (version "4021.106")
5705 (uri (cran-uri "timeDate" version))
5708 "1qhh1d85s8r4wkcf4fljfm67lnkj8flnx9iz4hdg305xdkng3b8l"))))
5709 (properties `((upstream-name . "timeDate")))
5710 (build-system r-build-system)
5711 (home-page "https://www.rmetrics.org")
5712 (synopsis "Chronological and calendar objects")
5714 "This package provides an environment for teaching \"Financial
5715 Engineering and Computational Finance\" and for managing chronological and
5717 (license license:gpl2+)))
5719 (define-public r-magic
5726 (uri (cran-uri "magic" version))
5729 "1gybia2aq80ldk1d845y5srncfzbbmpqhgl7vfaz7qqqjs6d85j5"))))
5730 (build-system r-build-system)
5733 (home-page "https://github.com/RobinHankin/magic.git")
5734 (synopsis "Create and investigate magic squares")
5736 "This package provides a collection of efficient, vectorized algorithms
5737 for the creation and investigation of magic squares and hypercubes, including
5738 a variety of functions for the manipulation and analysis of arbitrarily
5739 dimensioned arrays.")
5740 (license license:gpl2)))
5742 (define-public r-rmysql
5749 (uri (cran-uri "RMySQL" version))
5752 "0hbjcf0gzkkg8h50msj4a6ymax9s3j4aw44jl1mqcxkdmfn9l6ya"))))
5753 (properties `((upstream-name . "RMySQL")))
5754 (build-system r-build-system)
5756 (list `(,mariadb "dev") zlib))
5759 (home-page "https://github.com/r-dbi/RMySQL")
5760 (synopsis "Database interface and MySQL driver for R")
5762 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
5763 package contains an old implementation based on legacy code from S-PLUS which
5764 is being phased out. A modern MySQL client based on Rcpp is available from
5765 the RMariaDB package.")
5766 (license license:gpl2)))
5768 (define-public r-rpostgresql
5770 (name "r-rpostgresql")
5775 (uri (cran-uri "RPostgreSQL" version))
5778 "1ijnsly8wgy6cfib4xvdaz2g9hk1gzg7q52r37zkvc7jjh0gdbdn"))))
5779 (properties `((upstream-name . "RPostgreSQL")))
5780 (build-system r-build-system)
5785 (home-page "https://github.com/tomoakin/RPostgreSQL")
5786 (synopsis "R interface to the PostgreSQL database system")
5788 "This package provides a Database Interface (DBI) compliant driver for R
5789 to access PostgreSQL database systems.")
5790 ;; The whole package is released under GPL version 2. It includes code
5791 ;; under the PostgreSQL license.
5792 (license license:gpl2)))
5794 (define-public r-linprog
5801 (uri (cran-uri "linprog" version))
5804 "1d34m2nyk7m6j2dci69bhy5mlw479xax1517j7f14pq7vhpsm9l1"))))
5805 (build-system r-build-system)
5806 (propagated-inputs (list r-lpsolve))
5807 (home-page "http://linprog.r-forge.r-project.org/")
5808 (synopsis "Linear programming and optimization")
5810 "This package can be used to solve Linear Programming / Linear
5811 Optimization problems by using the simplex algorithm.")
5812 (license license:gpl2+)))
5814 (define-public r-geometry
5821 (uri (cran-uri "geometry" version))
5824 "0wplszaxi6phxffp3zww5alwnfbh9521qi43h65w057lrm1pmj2j"))))
5825 (build-system r-build-system)
5827 (list r-magic r-linprog r-lpsolve r-rcpp r-rcppprogress))
5828 (home-page "http://geometry.r-forge.r-project.org/")
5829 (synopsis "Mesh generator and surface tessellator")
5831 "This package makes the qhull library available in R, in a similar manner
5832 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
5833 intersections about a point, Voronoi diagrams, furthest-site Delaunay
5834 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
5835 and higher dimensions. It implements the Quickhull algorithm for computing
5836 the convex hull. Qhull does not support constrained Delaunay triangulations,
5837 or mesh generation of non-convex objects, but the package does include some R
5838 functions that allow for this. Currently the package only gives access to
5839 Delaunay triangulation and convex hull computation.")
5840 ;; The Qhull sources are included and are distributed under a custom
5841 ;; non-copyleft license. The R sources are released under GPL version 2.
5842 (license (list license:gpl2
5843 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
5845 (define-public r-ddalpha
5852 (uri (cran-uri "ddalpha" version))
5855 "1bjfgb3lbzhjb5wx9hzp90jppq7vnj59bmd2n9ymi8sh1570m9p4"))))
5856 (build-system r-build-system)
5867 (home-page "https://cran.r-project.org/web/packages/ddalpha")
5868 (synopsis "Depth-Based classification and calculation of data depth")
5870 "This package contains procedures for depth-based supervised learning,
5871 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
5872 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
5873 statistical depth function to a compact low-dimensional space, where the final
5874 classification is done. It also offers an extension to functional data and
5875 routines for calculating certain notions of statistical depth functions. 50
5876 multivariate and 5 functional classification problems are included.")
5877 (license license:gpl2)))
5879 (define-public r-gower
5886 (uri (cran-uri "gower" version))
5889 "0p9qx9aafkdm7wibfwk59jzw6vspsff6zwp84bc40lg0myxbf737"))))
5890 (build-system r-build-system)
5891 (home-page "https://github.com/markvanderloo/gower")
5892 (synopsis "Gower's distance")
5894 "This package provides tools to compute Gower's distance (or similarity)
5895 coefficient between records, and to compute the top-n matches between records.
5896 Core algorithms are executed in parallel on systems supporting OpenMP.")
5897 (license license:gpl3)))
5899 (define-public r-rcpproll
5906 (uri (cran-uri "RcppRoll" version))
5909 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
5910 (properties `((upstream-name . "RcppRoll")))
5911 (build-system r-build-system)
5914 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
5915 (synopsis "Efficient rolling and windowed operations")
5917 "This package provides fast and efficient routines for common rolling /
5918 windowed operations. Routines for the efficient computation of windowed mean,
5919 median, sum, product, minimum, maximum, standard deviation and variance are
5921 (license license:gpl2+)))
5923 (define-public r-ipred
5930 (uri (cran-uri "ipred" version))
5933 "162ckhqn24l0l5ih7qi2k3lxw5iprm1g5a34q1ik0b9wv5ia0s31"))))
5934 (build-system r-build-system)
5942 (home-page "https://cran.r-project.org/web/packages/ipred")
5943 (synopsis "Improved predictors")
5945 "This package provides improved predictive models by indirect
5946 classification and bagging for classification, regression and survival
5947 problems as well as resampling based estimators of prediction error.")
5948 (license license:gpl2+)))
5950 (define-public r-psych
5957 (uri (cran-uri "psych" version))
5960 "0wamcwbwn2x5y91d5hv3l3sfc41k685hlsv9cx8gkzl7yfziimac"))))
5961 (build-system r-build-system)
5963 (list r-lattice r-mnormt r-nlme))
5966 (home-page "https://cran.r-project.org/web/packages/psych/")
5967 (synopsis "Procedures for psychological, psychometric, and personality research")
5969 "This package provides a general purpose toolbox for personality,
5970 psychometric theory and experimental psychology. Functions are primarily for
5971 multivariate analysis and scale construction using factor analysis, principal
5972 component analysis, cluster analysis and reliability analysis, although others
5973 provide basic descriptive statistics. Item Response Theory is done using
5974 factor analysis of tetrachoric and polychoric correlations. Functions for
5975 analyzing data at multiple levels include within and between group statistics,
5976 including correlations and factor analysis. Functions for simulating and
5977 testing particular item and test structures are included. Several functions
5978 serve as a useful front end for structural equation modeling. Graphical
5979 displays of path diagrams, factor analysis and structural equation models are
5980 created using basic graphics.")
5981 (license license:gpl2+)))
5983 (define-public r-generics
5990 (uri (cran-uri "generics" version))
5993 "0lyhhwik0w7m5h3fbwl2f52gc1v2g6g6h6sc47sa9f58pxin213m"))))
5994 (build-system r-build-system)
5995 (home-page "https://github.com/r-lib/generics")
5996 (synopsis "Common S3 generics not provided by base R methods")
5998 "In order to reduce potential package dependencies and conflicts,
5999 generics provides a number of commonly used S3 generics that are not provided
6000 by base R methods related to model fitting.")
6001 (license license:gpl2)))
6003 (define-public r-broom
6010 (uri (cran-uri "broom" version))
6013 "14i8729m38nxf5q344isgq4006p3b50wi3q8jgckxqphhnj5lpjb"))))
6014 (build-system r-build-system)
6029 (home-page "https://github.com/tidyverse/broom")
6030 (synopsis "Convert statistical analysis objects into tidy data frames")
6032 "This package provides tools to convert statistical analysis objects from
6033 R into tidy data frames, so that they can more easily be combined, reshaped
6034 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
6035 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
6036 summarizes a model's statistical findings such as coefficients of a
6037 regression; @code{augment}, which adds columns to the original data such as
6038 predictions, residuals and cluster assignments; and @code{glance}, which
6039 provides a one-row summary of model-level statistics.")
6040 (license license:expat)))
6042 (define-public r-recipes
6049 (uri (cran-uri "recipes" version))
6052 "03k7spw5vivj35lwqj8xj259smgc04qxkdimk5ck9yj656d5lyqs"))))
6053 (build-system r-build-system)
6077 (home-page "https://github.com/topepo/recipes")
6078 (synopsis "Preprocessing tools to create design matrices")
6080 "Recipes is an extensible framework to create and preprocess design
6081 matrices. Recipes consist of one or more data manipulation and analysis
6082 \"steps\". Statistical parameters for the steps can be estimated from an
6083 initial data set and then applied to other data sets. The resulting design
6084 matrices can then be used as inputs into statistical or machine learning
6086 (license license:gpl2)))
6088 (define-public r-pdist
6095 (uri (cran-uri "pdist" version))
6098 "0bvg8si81hs79v39d7svv4zbv2p0sk2r6m9vamibvkh9qvl4x406"))))
6099 (build-system r-build-system)
6100 (home-page "https://github.com/jeffwong/pdist")
6101 (synopsis "Partitioned distance function")
6103 "Pdist computes the euclidean distance between rows of a matrix X and
6104 rows of another matrix Y. Previously, this could be done by binding the two
6105 matrices together and calling @code{dist}, but this creates unnecessary
6106 computation by computing the distances between a row of X and another row of
6107 X, and likewise for Y. Pdist strictly computes distances across the two
6108 matrices, not within the same matrix, making computations significantly faster
6109 for certain use cases.")
6110 (license license:gpl3+)))
6112 (define-public r-ggrepel
6119 (uri (cran-uri "ggrepel" version))
6122 "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9"))))
6123 (build-system r-build-system)
6125 (list r-ggplot2 r-rcpp r-rlang r-scales))
6127 (list r-knitr)) ; for vignettes
6128 (home-page "https://github.com/slowkow/ggrepel")
6129 (synopsis "Repulsive text and label geometries for ggplot2")
6131 "This package provides text and label geometries for ggplot2 that help to
6132 avoid overlapping text labels. Labels repel away from each other and away
6133 from the data points.")
6134 (license license:gpl3)))
6136 (define-public r-coro
6143 (uri (cran-uri "coro" version))
6145 (base32 "0wvxdpdh3xrskz5s5wfkva856x849knx1jigbf0ff6s6n6qjjxsf"))))
6146 (properties `((upstream-name . "coro")))
6147 (build-system r-build-system)
6148 (propagated-inputs (list r-rlang))
6149 (native-inputs (list r-knitr))
6150 (home-page "https://github.com/r-lib/coro")
6151 (synopsis "Coroutines for R")
6153 "This package provides coroutines for R, a family of functions that can
6154 be suspended and resumed later on. This includes async functions (which
6155 await) and generators (which yield). Async functions are based on the
6156 concurrency framework of the @code{promises} package. Generators are based on
6157 a dependency free iteration protocol defined in @code{coro} and are compatible
6158 with iterators from the @code{reticulate} package.")
6159 (license license:expat)))
6161 (define-public r-corrplot
6168 (uri (cran-uri "corrplot" version))
6171 "1g98jk6xsl08z4n6sy5vriif99m31zhbz7j3dh1kfj4w7yb9zh78"))))
6172 (build-system r-build-system)
6175 (home-page "https://github.com/taiyun/corrplot")
6176 (synopsis "Visualization of a correlation matrix")
6178 "This package provides a graphical display of a correlation matrix or
6179 general matrix. It also contains some algorithms to do matrix reordering. In
6180 addition, corrplot is good at details, including choosing color, text labels,
6181 color labels, layout, etc.")
6182 ;; Any version of the GPL
6183 (license license:gpl2+)))
6185 (define-public r-stringdist
6187 (name "r-stringdist")
6192 (uri (cran-uri "stringdist" version))
6194 (base32 "0pkggr25azadczhnsxc9wh1753wigf3wijyvwfc2ip5a42c1f55x"))))
6195 (build-system r-build-system)
6196 (home-page "https://github.com/markvanderloo/stringdist")
6197 (synopsis "Approximate string matching and string distance functions")
6199 "This package implements an approximate string matching version of R's
6200 native @code{match} function. It can calculate various string distances based
6201 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment),
6202 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
6203 Jaro-Winkler). An implementation of soundex is provided as well. Distances
6204 can be computed between character vectors while taking proper care of encoding
6205 or between integer vectors representing generic sequences.")
6206 (license license:gpl3+)))
6208 (define-public r-ucminf
6215 (uri (cran-uri "ucminf" version))
6218 "1cknk42allcflgk16i4gwi4a389idrxqz6y2w8i7s9mdfgrvd981"))))
6219 (build-system r-build-system)
6220 (native-inputs (list gfortran))
6221 (home-page "https://cran.r-project.org/web/packages/ucminf/")
6222 (synopsis "General-purpose unconstrained non-linear optimization")
6224 "This package provides an implementation of an algorithm for
6225 general-purpose unconstrained non-linear optimization. The algorithm is of
6226 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
6227 search with a trust region type monitoring of the input to the line search
6228 algorithm. The interface of @code{ucminf} is designed for easy interchange
6229 with the package @code{optim}.")
6230 (license license:gpl2+)))
6232 (define-public r-usedist
6239 (uri (cran-uri "usedist" version))
6241 (base32 "0ddf1zcalbrn293qmr9kdzz3x16fzc4k1bwb1pjmwnspisqfi8kj"))))
6242 (properties `((upstream-name . "usedist")))
6243 (build-system r-build-system)
6244 (home-page "https://cran.r-project.org/package=usedist")
6245 (synopsis "Distance matrix utilities")
6247 "This package provides functions to re-arrange, extract, and work with
6249 (license license:gpl3)))
6251 (define-public r-useful
6257 (uri (cran-uri "useful" version))
6260 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
6261 (properties `((upstream-name . "useful")))
6262 (build-system r-build-system)
6272 (home-page "https://github.com/jaredlander/useful")
6273 (synopsis "Collection of handy, useful functions")
6274 (description "This package provides a set of little functions that have been
6275 found useful to do little odds and ends such as plotting the results of K-means
6276 clustering, substituting special text characters, viewing parts of a
6277 @code{data.frame}, constructing formulas from text and building design and
6278 response matrices.")
6279 (license license:bsd-3)))
6281 (define-public r-ordinal
6284 (version "2019.12-10")
6288 (uri (cran-uri "ordinal" version))
6291 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
6292 (build-system r-build-system)
6294 (list r-mass r-matrix r-numderiv r-ucminf))
6295 (home-page "https://github.com/runehaubo/ordinal")
6296 (synopsis "Regression models for ordinal data")
6298 "This package provides an implementation of cumulative link (mixed)
6299 models also known as ordered regression models, proportional odds models,
6300 proportional hazards models for grouped survival times and ordered models.
6301 Estimation is via maximum likelihood and mixed models are fitted with the
6302 Laplace approximation and adaptive Gauss-Hermite quadrature.")
6303 (license license:gpl2+)))
6305 (define-public r-jomo
6312 (uri (cran-uri "jomo" version))
6315 "1zck7p872k080hyfs0hibq7v13zmsry1jdlnq7k33ff1iljbq99d"))))
6316 (build-system r-build-system)
6318 (list r-lme4 r-mass r-ordinal r-survival r-tibble))
6319 (home-page "https://cran.r-project.org/web/packages/jomo/")
6320 (synopsis "Multilevel Joint Modelling Multiple Imputation")
6322 "Similarly to Schafer's package pan, jomo is a package for multilevel
6323 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
6324 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
6325 possibility of handling binary and categorical data through latent normal
6326 variables, the option to use cluster-specific covariance matrices and to
6327 impute compatibly with the substantive model.")
6328 (license license:gpl2)))
6330 (define-public r-pan
6337 (uri (cran-uri "pan" version))
6340 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
6341 (build-system r-build-system)
6342 (native-inputs (list gfortran))
6343 (home-page "https://cran.r-project.org/web/packages/pan/")
6344 (synopsis "Multiple imputation for multivariate panel or clustered data")
6346 "This package implements multiple imputation for multivariate panel or
6348 (license license:gpl3)))
6350 (define-public r-mitml
6357 (uri (cran-uri "mitml" version))
6360 "00i18nnvrdrg91crgcp2a431xs71cawaip3xkqk2myv0iav3xga9"))))
6361 (build-system r-build-system)
6363 (list r-haven r-jomo r-pan))
6366 (home-page "https://cran.r-project.org/web/packages/mitml/")
6367 (synopsis "Tools for multiple imputation in multilevel modeling")
6369 "This package provides tools for multiple imputation of missing data in
6370 multilevel modeling. It includes a user-friendly interface to the packages
6371 pan and jomo, and several functions for visualization, data management and the
6372 analysis of multiply imputed data sets.")
6373 (license license:gpl2+)))
6375 (define-public r-mice
6382 (uri (cran-uri "mice" version))
6385 "01fnfrr7adp29s5kic95r9q0rdznkz2pjmziyimnrqzyicyvfyzq"))))
6386 (build-system r-build-system)
6397 (home-page "https://cran.r-project.org/web/packages/mice/")
6398 (synopsis "Multivariate imputation by chained equations")
6400 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
6401 implemented by the MICE algorithm as described in @url{Van Buuren and
6402 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
6403 variable has its own imputation model. Built-in imputation models are
6404 provided for continuous data (predictive mean matching, normal), binary
6405 data (logistic regression), unordered categorical data (polytomous logistic
6406 regression) and ordered categorical data (proportional odds). MICE can also
6407 impute continuous two-level data (normal model, pan, second-level variables).
6408 Passive imputation can be used to maintain consistency between variables.
6409 Various diagnostic plots are available to inspect the quality of the
6411 ;; Any of these two versions.
6412 (license (list license:gpl2 license:gpl3))))
6414 (define-public r-truncnorm
6416 (name "r-truncnorm")
6421 (uri (cran-uri "truncnorm" version))
6424 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
6425 (build-system r-build-system)
6426 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
6427 (synopsis "Truncated normal distribution")
6428 (description "This package provides functions for the truncated normal
6429 distribution with mean equal to @code{mean} and standard deviation equal to
6430 @code{sd}. It includes density, distribution, quantile, and expected value
6431 functions, as well as a random generation function.")
6432 (license license:gpl2)))
6434 (define-public r-rsolnp
6441 (uri (cran-uri "Rsolnp" version))
6444 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
6445 (properties `((upstream-name . "Rsolnp")))
6446 (build-system r-build-system)
6449 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
6450 (synopsis "General non-linear optimization")
6451 (description "The Rsolnp package implements a general non-linear augmented
6452 Lagrange multiplier method solver, a @dfn{sequential quadratic
6453 programming} (SQP) based solver).")
6454 ;; Any version of the GPL.
6455 (license license:gpl2+)))
6457 (define-public r-hardyweinberg
6459 (name "r-hardyweinberg")
6464 (uri (cran-uri "HardyWeinberg" version))
6467 "0b3szw090dsc3bkas2kvx787ww2i6zzg2qmdyivmqc8amx5arn6g"))))
6468 (properties `((upstream-name . "HardyWeinberg")))
6469 (build-system r-build-system)
6471 (list r-mice r-nnet r-rcpp r-rsolnp))
6472 (home-page "https://cran.r-project.org/package=HardyWeinberg")
6473 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
6475 "This package contains tools for exploring Hardy-Weinberg equilibrium for
6476 diallelic genetic marker data. All classical tests (chi-square, exact,
6477 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
6478 included in the package, as well as functions for power computation and for
6479 the simulation of marker data under equilibrium and disequilibrium. Routines
6480 for dealing with markers on the X-chromosome are included. Functions for
6481 testing equilibrium in the presence of missing data by using multiple
6482 imputation are also provided. Implements several graphics for exploring the
6483 equilibrium status of a large set of diallelic markers: ternary plots with
6484 acceptance regions, log-ratio plots and Q-Q plots.")
6485 (license license:gpl2+)))
6490 (version "2.2-5.7.1")
6494 (uri (cran-uri "sm" version))
6497 "0mql7rlm8wkdwmx1lv7pscdk9ibvsdpfdv8bpaz1hv2gn4pc637a"))))
6498 (build-system r-build-system)
6499 (native-inputs (list gfortran))
6500 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
6501 (synopsis "Smoothing methods for nonparametric regression and density estimation")
6503 "This is software accompanying the book 'Applied Smoothing Techniques for
6504 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
6505 University Press. It provides smoothing methods for nonparametric regression
6506 and density estimation")
6507 (license license:gpl2+)))
6509 (define-public r-smurf
6515 (uri (cran-uri "smurf" version))
6518 "0n99dzsb17r0a6d8nkijfg6rdvvc2g4pard2dnmyjq0p69j3f3gb"))))
6519 (properties `((upstream-name . "smurf")))
6520 (build-system r-build-system)
6531 (native-inputs (list r-knitr))
6532 (home-page "https://gitlab.com/TReynkens/smurf")
6533 (synopsis "Sparse multi-type regularized feature modeling")
6535 "The @code{smurf} package contains the implementation of the
6536 @dfn{Sparse Multi-type Regularized Feature} (SMuRF) modeling algorithm
6537 to fit @dfn{generalized linear models} (GLMs) with multiple types of
6538 predictors via regularized maximum likelihood. Next to the fitting
6539 procedure, following functionality is available:
6542 @item Selection of the regularization tuning parameter lambda using
6543 three different approaches: in-sample, out-of-sample or using
6545 @item S3 methods to handle the fitted object including visualization
6546 of the coefficients and a model summary.
6548 (license license:gpl2+)))
6550 (define-public r-venndiagram
6552 (name "r-venndiagram")
6556 (uri (cran-uri "VennDiagram" version))
6559 "0ilcxcp8qskmb5cp7fyb7i0qizg42lrx0ny8ws3if90kfrglghp7"))))
6560 (properties `((upstream-name . "VennDiagram")))
6561 (build-system r-build-system)
6563 (list r-futile-logger))
6564 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
6565 (synopsis "Generate High-Resolution Venn and Euler Plots")
6567 "This package provides a set of functions to generate high-resolution
6568 Venn and Euler plots. It includes handling for several special cases,
6569 including two-case scaling, and extensive customization of plot shape and
6571 (license license:gpl2+)))
6573 (define-public r-vioplot
6580 (uri (cran-uri "vioplot" version))
6583 "1dmdasp3jldc41233z6r08w3j76vyyp9m3jrj7n4ahk48yd5siq6"))))
6584 (build-system r-build-system)
6589 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
6590 (synopsis "Violin plot")
6592 "This package provides a violin plot, which is a combination of a box
6593 plot and a kernel density plot.")
6594 (license license:bsd-3)))
6596 (define-public r-rsofia
6602 ;; This package has been removed from CRAN, so we can
6603 ;; only fetch it from the archives.
6604 (uri (string-append "https://cran.r-project.org/src/"
6605 "contrib/Archive/RSofia/RSofia_"
6609 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
6610 (properties `((upstream-name . "RSofia")))
6611 (build-system r-build-system)
6614 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
6615 (synopsis "Port of sofia-ml to R")
6616 (description "This package is a port of sofia-ml to R. Sofia-ml is a
6617 suite of fast incremental algorithms for machine learning that can be used for
6618 training models for classification or ranking.")
6619 (license license:asl2.0)))
6621 (define-public r-xts
6628 (uri (cran-uri "xts" version))
6631 "0hx7vh8cm4c80rnhwqg78l5xb0snvf4adrkbb74z93vmxgm7qa4w"))))
6632 (build-system r-build-system)
6633 (propagated-inputs (list r-zoo))
6634 (home-page "https://github.com/joshuaulrich/xts")
6635 (synopsis "Extensible time series")
6637 "This package provides for uniform handling of R's different time-based
6638 data classes by extending @code{zoo}, maximizing native format information
6639 preservation and allowing for user-level customization and extension, while
6640 simplifying cross-class interoperability.")
6641 (license license:gpl2+)))
6643 (define-public r-performanceanalytics
6645 (name "r-performanceanalytics")
6650 (uri (cran-uri "PerformanceAnalytics" version))
6653 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
6655 `((upstream-name . "PerformanceAnalytics")))
6656 (build-system r-build-system)
6658 (list r-quadprog r-xts r-zoo))
6659 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
6660 (synopsis "Econometric tools for performance and risk analysis")
6661 (description "This is a collection of econometric functions for
6662 performance and risk analysis. This package aims to aid practitioners and
6663 researchers in utilizing the latest research in analysis of non-normal return
6664 streams. In general, it is most tested on return (rather than price) data on
6665 a regular scale, but most functions will work with irregular return data as
6666 well, and increasing numbers of functions will work with P&L or price data
6668 ;; Either version may be picked.
6669 (license (list license:gpl2 license:gpl3))))
6671 (define-public r-laeken
6678 (uri (cran-uri "laeken" version))
6681 "1p3ccbaydlr52p8qmgmm2l6kryvq6jjjx7mqn2vv0gpjaxqhyy92"))))
6682 (build-system r-build-system)
6684 (list r-boot r-mass))
6685 (home-page "https://cran.r-project.org/web/packages/laeken/")
6686 (synopsis "Estimation of indicators on social exclusion and poverty")
6687 (description "This package provides tools for the estimation of indicators
6688 on social exclusion and poverty, as well as an implementation of Pareto tail
6689 modeling for empirical income distributions.")
6690 (license license:gpl2+)))
6692 (define-public r-vcd
6699 (uri (cran-uri "vcd" version))
6702 "0nxkl1x39xf8l0apgvlbr30i8lasix7hyyc93g6514r8z8m1k23i"))))
6703 (build-system r-build-system)
6705 (list r-colorspace r-lmtest r-mass))
6706 (home-page "https://cran.r-project.org/web/packages/vcd/")
6707 (synopsis "Visualizing categorical data")
6708 (description "This package provides visualization techniques, data sets,
6709 summary and inference procedures aimed particularly at categorical data.
6710 Special emphasis is given to highly extensible grid graphics. The package was
6711 originally inspired by the book \"Visualizing Categorical Data\" by Michael
6712 Friendly and is now the main support package for a new book, \"Discrete Data
6713 Analysis with R\" by Michael Friendly and David Meyer (2015).")
6714 (license license:gpl2)))
6716 (define-public r-vcfr
6722 (uri (cran-uri "vcfR" version))
6725 "1g4y11vpr3wrvf5prj7y33c2bah6rn4xfb4a1y7n7niafd2yhg3l"))))
6726 (build-system r-build-system)
6742 (home-page "https://github.com/knausb/vcfR")
6743 (synopsis "Manipulate and visualize VCF data")
6744 (description "This package facilitates easy manipulation of variant call
6745 format (VCF) data. Functions are provided to rapidly read from and write to
6746 VCF files. Once VCF data is read into R, a parser function extracts matrices
6747 of data. This information can then be used for quality control or other
6748 purposes. Additional functions provide visualization of genomic data. Once
6749 processing is complete data may be written to a VCF file. It also may be
6750 converted into other popular R objects. This package provides a link between
6751 VCF data and familiar R software.")
6752 (license license:gpl3)))
6754 (define-public r-ica
6761 (uri (cran-uri "ica" version))
6764 "0rdqd3kz2cv3xvf6yz55bwhsg3k7j90d450i3azs2xkbn4q3aka7"))))
6765 (build-system r-build-system)
6766 (home-page "https://cran.r-project.org/web/packages/ica/")
6767 (synopsis "Independent component analysis")
6768 (description "This package provides tools for @dfn{Independent Component
6769 Analysis} (ICA) using various algorithms: FastICA,
6770 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
6771 of Eigenmatrices} (JADE).")
6772 (license license:gpl2+)))
6774 (define-public r-ips
6780 (uri (cran-uri "ips" version))
6783 "02jxanfhsjrabj33nwjv71vdc87hiyzikyqrfdj9ix6dky6lm199"))))
6784 (properties `((upstream-name . "ips")))
6785 (build-system r-build-system)
6786 (propagated-inputs (list r-ape r-phangorn r-plyr r-seqinr r-xml))
6787 (home-page "https://cran.r-project.org/package=ips")
6788 (synopsis "Interfaces to phylogenetic software in R")
6790 "This package provides functions that wrap popular phylogenetic software
6791 for sequence alignment, masking of sequence alignments, and estimation of
6792 phylogenies and ancestral character states.")
6793 (license license:gpl3)))
6795 (define-public r-dtw
6802 (uri (cran-uri "dtw" version))
6805 "0vc2is1hf1g0sw92kzl8mddck264qwiqgm5q2wkcwwz65fss7mkf"))))
6806 (build-system r-build-system)
6807 (propagated-inputs (list r-proxy))
6808 (home-page "http://dtw.r-forge.r-project.org/")
6809 (synopsis "Dynamic Time Warping Algorithms")
6810 (description "This package provides a comprehensive implementation of
6811 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
6812 optimal (least cumulative distance) alignment between points of two time
6813 series. Common DTW variants covered include local (slope) and global (window)
6814 constraints, subsequence matches, arbitrary distance definitions,
6815 normalizations, minimum variance matching, and so on.")
6816 (license license:gpl2+)))
6818 (define-public r-sdmtools
6821 (version "1.1-221.2")
6825 (uri (cran-uri "SDMTools" version))
6828 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
6829 (properties `((upstream-name . "SDMTools")))
6830 (build-system r-build-system)
6831 (propagated-inputs (list r-r-utils))
6832 (home-page "https://www.rforge.net/SDMTools/")
6833 (synopsis "Species distribution modelling tools")
6834 (description "This package provides a set of tools for post processing
6835 the outcomes of species distribution modeling exercises. It includes novel
6836 methods for comparing models and tracking changes in distributions through
6837 time. It further includes methods for visualizing outcomes, selecting
6838 thresholds, calculating measures of accuracy and landscape fragmentation
6840 (license license:gpl3+)))
6842 (define-public r-scatterplot3d
6844 (name "r-scatterplot3d")
6849 (uri (cran-uri "scatterplot3d" version))
6852 "05jjdiam5w0znb114vc90zahclj22pqj1zzvr96nr10s1vkxvzm9"))))
6853 (build-system r-build-system)
6854 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
6855 (synopsis "3D scatter plot")
6856 (description "This package provides an implementation of scatter plots for
6857 plotting. a three dimensional point cloud.")
6858 (license license:gpl2)))
6860 (define-public r-ggridges
6867 (uri (cran-uri "ggridges" version))
6870 "0lfqx21g09s3fp74mld47qfx1nnav18xqj37griyqk406hh1rxrb"))))
6871 (build-system r-build-system)
6873 (list r-ggplot2 r-scales r-withr))
6876 (home-page "https://github.com/clauswilke/ggridges")
6877 (synopsis "Ridgeline plots in ggplot2")
6879 "Ridgeline plots provide a convenient way of visualizing changes in
6880 distributions over time or space. This package enables the creation of such
6881 plots in @code{ggplot2}.")
6882 (license license:gpl2)))
6884 (define-public r-ggjoy
6891 (uri (cran-uri "ggjoy" version))
6894 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
6895 (build-system r-build-system)
6897 (list r-ggplot2 r-ggridges))
6898 (home-page "https://github.com/clauswilke/ggjoy")
6899 (synopsis "Joyplots in ggplot2")
6900 (description "Joyplots provide a convenient way of visualizing changes in
6901 distributions over time or space. This package enables the creation of such
6902 plots in @code{ggplot2}.")
6903 (license license:gpl2)))
6905 (define-public r-cli
6912 (uri (cran-uri "cli" version))
6915 "0kklv5zy9rhly8fr7fdl3dlm3hr81yvbqd5cdz38b1lbzpxmwn0w"))))
6916 (build-system r-build-system)
6917 (home-page "https://github.com/r-lib/cli#readme")
6918 (synopsis "Helpers for developing command line interfaces")
6919 (description "This package provides a suite of tools designed to build
6920 attractive command line interfaces (CLIs). It includes tools for drawing
6921 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
6922 (license license:expat)))
6924 (define-public r-argparser
6926 (name "r-argparser")
6931 (uri (cran-uri "argparser" version))
6934 "0xcl0ivsbc4iw8s7027q4cx68j6s5lihbby0xa9pmlv4wjmcvdr6"))))
6935 (build-system r-build-system)
6936 (home-page "https://bitbucket.org/djhshih/argparser")
6937 (synopsis "Command-line argument parser")
6939 "This package provides a cross-platform command-line argument parser
6940 written purely in R with no external dependencies. It is useful with the
6941 Rscript front-end and facilitates turning an R script into an executable
6943 (license license:gpl3+)))
6945 (define-public r-aricode
6951 (uri (cran-uri "aricode" version))
6954 "0772l9gyrih48l1kymih0mb7szjqqnwcm4lzj0yzp4cs8l2mdf4f"))))
6955 (properties `((upstream-name . "aricode")))
6956 (build-system r-build-system)
6957 (propagated-inputs (list r-matrix r-rcpp))
6958 (home-page "https://github.com/jchiquet/aricode")
6959 (synopsis "Efficient computations of standard clustering comparison measures")
6961 "This package implements an efficient O(n) algorithm based on
6962 bucket-sorting for fast computation of standard clustering comparison
6963 measures. Available measures include @dfn{adjusted Rand index} (ARI),
6964 @dfn{normalized information distance} (NID), @dfn{normalized mutual
6965 information} (NMI), @dfn{adjusted mutual information} (AMI), @dfn{normalized
6966 variation information} (NVI) and entropy.")
6967 (license license:gpl3+)))
6969 (define-public r-debugme
6976 (uri (cran-uri "debugme" version))
6979 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
6980 (build-system r-build-system)
6981 (propagated-inputs (list r-crayon))
6982 (home-page "https://github.com/r-lib/debugme#readme")
6983 (synopsis "Debug R packages")
6985 "This package allows the user to specify debug messages as special string
6986 constants, and control debugging of packages via environment variables.")
6987 (license license:expat)))
6989 (define-public r-processx
6996 (uri (cran-uri "processx" version))
6998 (base32 "02zviyqk1ljvrdc3bgqxnkyb8mkmqlgmq6l0c881a523dk9djw4j"))))
6999 (build-system r-build-system)
7002 (home-page "https://github.com/r-lib/processx3")
7003 (synopsis "Execute and control system processes")
7005 "This package provides portable tools to run system processes in the
7006 background. It can check if a background process is running; wait on a
7007 background process to finish; get the exit status of finished processes; kill
7008 background processes and their children; restart processes. It can read the
7009 standard output and error of the processes, using non-blocking connections.
7010 @code{processx} can poll a process for standard output or error, with a
7011 timeout. It can also poll several processes at once.")
7012 (license license:expat)))
7014 (define-public r-tsp
7021 (uri (cran-uri "TSP" version))
7024 "1pa6pb4qrh2iybpjzjiny6hshj0shjdm0pxqnidcrg5hyfzzxd9b"))))
7025 (properties `((upstream-name . "TSP")))
7026 (build-system r-build-system)
7027 (propagated-inputs (list r-foreach))
7028 (home-page "https://cran.r-project.org/web/packages/TSP/")
7029 (synopsis "Traveling salesperson problem (TSP)")
7030 (description "This package provides basic infrastructure and some
7031 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
7032 traveling salesman problem).")
7033 (license license:gpl3)))
7035 (define-public r-qap
7042 (uri (cran-uri "qap" version))
7045 "19adb1bw46pcnmmhqz2jklr0vmma3llxajqp0j9mqfksmsisv927"))))
7046 (build-system r-build-system)
7047 (native-inputs (list gfortran))
7048 (home-page "https://cran.r-project.org/web/packages/qap/")
7049 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
7050 (description "This package implements heuristics for the @dfn{quadratic
7051 assignment problem} (QAP). Currently only a simulated annealing heuristic is
7053 (license license:gpl3)))
7055 (define-public r-gclus
7062 (uri (cran-uri "gclus" version))
7065 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
7066 (build-system r-build-system)
7067 (propagated-inputs (list r-cluster))
7068 (home-page "https://cran.r-project.org/web/packages/gclus/")
7069 (synopsis "Clustering graphics")
7070 (description "This package orders panels in scatterplot matrices and
7071 parallel coordinate displays by some merit index. It contains various indices
7072 of merit, ordering functions, and enhanced versions of @code{pairs} and
7073 @code{parcoord} which color panels according to their merit level.")
7074 (license license:gpl2+)))
7076 (define-public r-webshot
7083 (uri (cran-uri "webshot" version))
7086 "094ggb6yby5irf3hj45p6vp5wdy6rjwpc0h6xbgf2mbqxyxbkhix"))))
7087 (build-system r-build-system)
7089 (list r-callr r-jsonlite r-magrittr))
7090 (home-page "https://github.com/wch/webshot/")
7091 (synopsis "Take screenshots of web pages")
7093 "Webshot makes it easy to take screenshots of web pages from within R.
7094 It can also run Shiny applications locally and take screenshots of the
7095 application; and it can render and screenshot static as well as interactive R
7096 Markdown documents.")
7097 (license license:gpl2)))
7099 (define-public r-seriation
7101 (name "r-seriation")
7106 (uri (cran-uri "seriation" version))
7109 "1bcd559wsjjdmpc1892vsf8wrkh4ijgn1y71h3y3v5clmd21ycmx"))))
7110 (build-system r-build-system)
7120 (native-inputs (list gfortran))
7121 (home-page "https://s2.smu.edu/IDA/seriation/")
7122 (synopsis "Infrastructure for ordering objects using seriation")
7124 "This package provides infrastructure for seriation with an
7125 implementation of several seriation/sequencing techniques to reorder matrices,
7126 dissimilarity matrices, and dendrograms. It also provides (optimally)
7127 reordered heatmaps, color images and clustering visualizations like
7128 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
7130 (license license:gpl3)))
7132 (define-public r-xfun
7139 (uri (cran-uri "xfun" version))
7141 (base32 "0gc5lbk73bf0yhvc7wwz7hbq39hvphd8xdsgwi2c125rxcgnrrsh"))))
7142 (build-system r-build-system)
7143 ;; knitr itself depends on xfun
7146 `(("r-knitr" ,r-knitr)))
7147 (home-page "https://github.com/yihui/xfun")
7148 (synopsis "Miscellaneous functions")
7150 "This package provides miscellaneous functions commonly used in other
7151 packages maintained by Yihui Xie.")
7152 (license license:expat)))
7154 (define-public r-utf8
7161 (uri (cran-uri "utf8" version))
7164 "1x6qg19z4qih9lk3mvnmx0vailm1khp5lylw4hlwz6rssj3yw6m7"))))
7165 (build-system r-build-system)
7167 (list r-knitr r-rmarkdown)) ; for vignettes
7168 (home-page "https://github.com/patperry/r-utf8")
7169 (synopsis "Unicode text processing")
7171 "This package provides tools to process and print UTF-8 encoded
7172 international text (Unicode). Input, validate, normalize, encode, format, and
7174 (license license:asl2.0)))
7176 (define-public r-zeallot
7183 (uri (cran-uri "zeallot" version))
7186 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
7187 (build-system r-build-system)
7188 (home-page "https://github.com/nteetor/zeallot")
7189 (synopsis "Multiple, unpacking, and destructuring assignment")
7191 "This package provides a @code{%<-%} operator to perform multiple,
7192 unpacking, and destructuring assignment in R. The operator unpacks the
7193 right-hand side of an assignment into multiple values and assigns these values
7194 to variables on the left-hand side of the assignment.")
7195 (license license:expat)))
7197 (define-public r-zlog
7203 (uri (cran-uri "zlog" version))
7206 "1d5j31p0h3rrn230087h3ngpvwknlisjv0f1qdbicdj9m177spci"))))
7207 (properties `((upstream-name . "zlog")))
7208 (build-system r-build-system)
7209 (native-inputs (list r-knitr))
7210 (home-page "https://cran.r-project.org/package=zlog")
7211 (synopsis "Transformation for laboratory easurements")
7213 "The @code{zlog} package offers functions to transform laboratory
7214 measurements into standardised z or @math{z(log)-values}. Therefore the lower
7215 and upper reference limits are needed. If these are not known they could be
7216 estimated from a given sample.")
7217 (license license:gpl3+)))
7219 (define-public r-vctrs
7226 (uri (cran-uri "vctrs" version))
7229 "11pnblg2fpa3lr5hbiyw6w7wvlkdvqw35wxrkffcxnlxqc9jwdvw"))))
7230 (build-system r-build-system)
7232 (list r-cli r-glue r-lifecycle r-rlang))
7235 (home-page "https://github.com/r-lib/vctrs")
7236 (synopsis "Vector helpers")
7238 "There are three main goals to the @code{vctrs} package:
7241 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
7242 @code{length()} and @code{class()}. These definitions are paired with a
7243 framework for type-coercion and size-recycling.
7244 @item To define type- and size-stability as desirable function properties, use
7245 them to analyse existing base function, and to propose better alternatives.
7246 This work has been particularly motivated by thinking about the ideal
7247 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
7248 @item To provide a new @code{vctr} base class that makes it easy to create new
7249 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
7250 a few new @code{vctrs} generics, making implementation considerably simpler
7253 (license license:gpl3)))
7255 (define-public r-pillar
7262 (uri (cran-uri "pillar" version))
7265 "1v47dm2v4nlswd1gmgcx5c7yrgn1ksdfr9lqkc63jf2nkv6af1ig"))))
7266 (build-system r-build-system)
7277 (home-page "https://github.com/r-lib/pillar")
7278 (synopsis "Coloured formatting for columns")
7280 "This package provides a @code{pillar} generic designed for formatting
7281 columns of data using the full range of colours provided by modern
7283 (license license:gpl3)))
7285 (define-public r-pinfsc50
7291 (uri (cran-uri "pinfsc50" version))
7294 "1547xyxmfb7zi8h9bsm6k67dcw4hpp129xzvmgwfw7r6p4af47zd"))))
7295 (build-system r-build-system)
7296 (home-page "https://cran.r-project.org/web/packages/pinfsc50/")
7297 (synopsis "Genomic data for the plant pathogen Phytophthora infestans")
7298 (description "This package contains genomic data for the plant pathogen
7299 Phytophthora infestans. It includes a variant file, a sequence file and an
7300 annotation file. This package is intended to be used as example data for
7301 packages that work with genomic data.")
7302 (license license:gpl2+)))
7304 (define-public r-uuid
7311 (uri (cran-uri "uuid" version))
7314 "0bzlc2knmr338h4ykx8v8c2a1inizxafj8rh13kwii68gpp50nz7"))))
7315 (build-system r-build-system)
7316 (home-page "https://www.rforge.net/uuid")
7317 (synopsis "Tools for generating and handling of UUIDs")
7319 "This package provides tools for generating and handling of
7320 @dfn{Universally Unique Identifiers} (UUIDs).")
7321 (license license:expat)))
7323 (define-public r-tinytex
7330 (uri (cran-uri "tinytex" version))
7333 "1c925r62h84mhwd7v5j35ckdldf6cwb3wzczdn5s72hig0cplpr0"))))
7334 (build-system r-build-system)
7337 (home-page "https://github.com/yihui/tinytex")
7338 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
7340 "This package provides helper functions to install and maintain the LaTeX
7341 distribution named TinyTeX, a lightweight, cross-platform, portable, and
7342 easy-to-maintain version of TeX Live. This package also contains helper
7343 functions to compile LaTeX documents, and install missing LaTeX packages
7345 (license license:expat)))
7347 (define-public r-tinytest
7354 (uri (cran-uri "tinytest" version))
7357 "1mq31f7bzcz5bkgzl9khm1i80axfzra7gcjqxd2yqb4wrw1m3x4s"))))
7358 (properties `((upstream-name . "tinytest")))
7359 (build-system r-build-system)
7360 (home-page "https://github.com/markvanderloo/tinytest")
7361 (synopsis "Lightweight unit testing framework")
7363 "This package provides a lightweight unit testing framework. Main
7367 @item install tests with the package;
7368 @item test results are treated as data that can be stored and manipulated;
7369 @item test files are R scripts interspersed with test commands, that can be
7371 @item fully automated build-install-test sequence for packages;
7372 @item skip tests when not run locally (e.g. on CRAN);
7373 @item flexible and configurable output printing;
7374 @item compare computed output with output stored with the package;
7375 @item run tests in parallel;
7376 @item extensible by other packages;
7377 @item report side effects.
7380 (license license:gpl3)))
7382 (define-public r-network
7389 (uri (cran-uri "network" version))
7392 "0nyf8i94lnqm4gfjz1szbwvl4c438xg3rjdkqr18fz68fh0v3x2r"))))
7393 (build-system r-build-system)
7395 (list r-magrittr r-statnet-common r-tibble))
7396 (home-page "https://statnet.org/")
7397 (synopsis "Classes for relational data")
7399 "This package provides tools to create and modify network objects. The
7400 @code{network} class can represent a range of relational data types, and
7401 supports arbitrary vertex/edge/graph attributes.")
7402 (license license:gpl2+)))
7404 (define-public r-stabs
7411 (uri (cran-uri "stabs" version))
7414 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q"))))
7415 (build-system r-build-system)
7418 (home-page "https://github.com/hofnerb/stabs")
7419 (synopsis "Stability selection with error control")
7421 "This package provides resampling procedures to assess the stability of
7422 selected variables with additional finite sample error control for
7423 high-dimensional variable selection procedures such as Lasso or boosting.
7424 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
7425 complementary pairs stability selection with improved error bounds
7426 (Shah & Samworth, 2013) are implemented. The package can be combined with
7427 arbitrary user specified variable selection approaches.")
7428 (license license:gpl2)))
7430 (define-public r-rle
7437 (uri (cran-uri "rle" version))
7440 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40"))))
7441 (properties `((upstream-name . "rle")))
7442 (build-system r-build-system)
7443 (home-page "https://cran.r-project.org/web/packages/rle/")
7444 (synopsis "Common functions for run-length encoded vectors")
7446 "This package provides common @code{base} and @code{stats} methods for
7447 @code{rle} objects, aiming to make it possible to treat them transparently as
7449 (license license:gpl3)))
7451 (define-public r-statnet-common
7453 (name "r-statnet-common")
7458 (uri (cran-uri "statnet.common" version))
7461 "1cx1h1yzs8jjxk10y2h0wl69caspzgx5wdqp36dp4sxm0sk335xn"))))
7463 `((upstream-name . "statnet.common")))
7464 (build-system r-build-system)
7467 (home-page "https://statnet.org")
7468 (synopsis "R scripts and utilities used by the Statnet software")
7469 (description "This package provides non-statistical utilities used by the
7470 software developed by the Statnet Project.")
7471 (license license:gpl3)))
7473 (define-public r-statcheck
7475 (name "r-statcheck")
7480 (uri (cran-uri "statcheck" version))
7483 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
7484 (build-system r-build-system)
7486 (list r-ggplot2 r-plyr r-rmarkdown))
7487 (home-page "https://cran.r-project.org/web/packages/statcheck/")
7488 (synopsis "Extract statistics from articles and recompute p-values")
7489 (description "This package can automatically extract statistical
7490 null-hypothesis significant testing (NHST) results from articles and recompute
7491 the p-values based on the reported test statistic and degrees of freedom to
7492 detect possible inconsistencies.")
7493 (license license:gpl2)))
7495 (define-public r-sna
7502 (uri (cran-uri "sna" version))
7505 "0ka319s1w857fj28ja1i1ljgv2h6ji4d69riqy9pwhvvghsa83s4"))))
7506 (build-system r-build-system)
7508 (list r-network r-statnet-common))
7509 (home-page "https://statnet.org")
7510 (synopsis "Tools for social network analysis")
7512 "This package provides a range of tools for social network analysis,
7513 including node and graph-level indices, structural distance and covariance
7514 methods, structural equivalence detection, network regression, random graph
7515 generation, and 2D/3D network visualization.")
7516 (license license:gpl2+)))
7518 (define-public r-tfisher
7525 (uri (cran-uri "TFisher" version))
7528 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
7529 (properties `((upstream-name . "TFisher")))
7530 (build-system r-build-system)
7532 (list r-matrix r-mvtnorm r-sn))
7533 (home-page "https://cran.r-project.org/web/packages/TFisher/")
7534 (synopsis "Optimal thresholding Fisher's p-value combination method")
7536 "This package provides the @dfn{cumulative distribution function} (CDF),
7537 quantile, and statistical power calculator for a collection of thresholding
7538 Fisher's p-value combination methods, including Fisher's p-value combination
7539 method, truncated product method and, in particular, soft-thresholding
7540 Fisher's p-value combination method which is proven to be optimal in some
7541 context of signal detection. The p-value calculator for the omnibus version
7542 of these tests are also included.")
7543 (license license:gpl2)))
7545 (define-public r-ttr
7552 (uri (cran-uri "TTR" version))
7555 "11xsmbvmxq2j119j2z58bx1fkkb2xlhmzc35z5fbwr3nchrfz6jd"))))
7556 (properties `((upstream-name . "TTR")))
7557 (build-system r-build-system)
7559 (list r-curl r-xts r-zoo))
7560 (home-page "https://github.com/joshuaulrich/TTR")
7561 (synopsis "Technical trading rules")
7563 "This package provides functions and data to construct technical trading
7565 (license license:gpl2)))
7567 (define-public r-leaflet-providers
7569 (name "r-leaflet-providers")
7574 (uri (cran-uri "leaflet.providers" version))
7576 (base32 "0yynrwv4xd5cdh49cwvfxm4ranarah9iiry2cd3b4fiihdfcg3wy"))))
7577 (properties `((upstream-name . "leaflet.providers")))
7578 (build-system r-build-system)
7579 (home-page "https://github.com/rstudio/leaflet.providers")
7580 (synopsis "Leaflet map tile providers")
7582 "This package contains third-party map tile provider information from
7583 Leaflet.js, to be used with the @code{leaflet} R package. Additionally,
7584 @code{leaflet.providers} enables users to retrieve up-to-date provider
7585 information between package updates.")
7586 (license license:bsd-2)))
7588 ;; This package contains a lot of minified JavaScript with unclear provenance.
7589 ;; When upgrading please make sure that all minified JavaScript files are
7590 ;; removed in a snippet and that the replacement sources correspond to the
7591 ;; original minified scripts.
7592 (define-public r-leaflet
7599 (uri (cran-uri "leaflet" version))
7601 (base32 "0xsng9n08i1w7qj4hbi706m6d8jm9ixrnwq5xac2s3csfm1s1xij"))
7605 (list "inst/htmlwidgets/lib/leaflet/leaflet.js"
7606 "inst/htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js"
7607 "inst/htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js"
7608 "inst/htmlwidgets/lib/jquery/jquery.min.js"
7609 "inst/htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js"
7610 "inst/htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js"
7611 "inst/htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js"
7612 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js"
7613 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js"
7614 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js"
7615 "inst/legacy/www/leaflet.js")))))
7616 (properties `((upstream-name . "leaflet")))
7617 (build-system r-build-system)
7619 `(#:modules ((guix build utils)
7620 (guix build r-build-system)
7623 (modify-phases %standard-phases
7624 (add-after 'unpack 'process-javascript
7625 (lambda* (#:key inputs #:allow-other-keys)
7626 ;; The inst directory contains some minified JavaScript files.
7627 ;; Regenerate them from sources.
7628 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-leaflet"))
7629 (with-directory-excursion "inst/"
7633 `(("/tmp/leaflet-src.js"
7634 "htmlwidgets/lib/leaflet/leaflet.js")
7635 (,(assoc-ref inputs "js-leaflet-measure")
7636 "htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js")
7637 (,(assoc-ref inputs "js-leaflet-omnivore")
7638 "htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js")
7639 (,(assoc-ref inputs "js-jquery")
7640 "htmlwidgets/lib/jquery/jquery.min.js")
7641 ("htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.js"
7642 "htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js")
7643 (,(assoc-ref inputs "js-bootstrap3")
7644 "htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js")
7645 ("htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.js"
7646 "htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js")
7647 (,(string-append (assoc-ref inputs "js-leaflet-markercluster")
7648 "/dist/leaflet.markercluster-src.js")
7649 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js")
7650 (,(assoc-ref inputs "js-leaflet-markercluster-freezable")
7651 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js")
7652 (,(assoc-ref inputs "js-leaflet-markercluster-layersupport")
7653 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js")
7654 (,(assoc-ref inputs "js-proj4leaflet")
7655 "htmlwidgets/plugins/Proj4Leaflet/proj4.min.js")
7656 ("legacy/www/leaflet-src.js"
7657 "legacy/www/leaflet.js"))))
7658 (lambda (sources targets)
7659 (for-each (lambda (source target)
7660 (format #true "Processing ~a --> ~a~%"
7662 (invoke "esbuild" source "--minify"
7663 (string-append "--outfile=" target)))
7664 sources targets)))))))))
7666 `(("esbuild" ,esbuild)
7671 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v3.3.7/dist/js/bootstrap.js")
7674 "1j1qjagwj0m3q322z9wxxnpkd8zbk6g3kl047dsbmqad6gmqvgha"))))
7678 (uri "https://code.jquery.com/jquery-1.12.4.js")
7681 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
7685 (uri "http://cdn.leafletjs.com/leaflet/v1.3.1/leaflet.zip")
7688 "10phzd2vczy3zm1b64whp2nna69cf9hlj2bndc9yq47vf3ddqx8f"))))
7689 ("js-leaflet-omnivore"
7692 (uri (string-append "https://api.tiles.mapbox.com/mapbox.js/plugins/"
7693 "leaflet-omnivore/v0.3.1/leaflet-omnivore.js"))
7696 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
7697 ("js-leaflet-markercluster"
7701 (url "https://github.com/Leaflet/Leaflet.markercluster.git")
7703 (file-name (git-file-name "js-leaflet-markercluster" "1.1.0"))
7706 "0ds8c7picqjmc86bm5n6hm8k71fwsa2cpgib19sbdamzr9hm0rs1"))))
7707 ("js-leaflet-markercluster-freezable"
7711 "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.Freezable/"
7712 "9db80a3fba7dff4aee940e05d3d4dceaa1fffcf9/src/freezable.js"))
7713 (file-name "leaflet-markercluster-freezable.js")
7716 "1k6sn5n0z2x3an91vwvkzmqq4b8ppswgk5hi5qrr79klas1hbx1k"))))
7717 ("js-leaflet-markercluster-layersupport"
7721 "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.LayerSupport/"
7722 "87f3848b92e0516d9c98f6d4cd175f7b8a4e3805/src/layersupport.js"))
7723 (file-name "leaflet-markercluster-layersupport.js")
7726 "15qa21xif94y762c65yxxysxykz3mma6y6agw3nxpr3s7wbb75ff"))))
7727 ("js-leaflet-measure"
7730 (uri "https://unpkg.com/leaflet-measure@1.5.2/dist/leaflet-measure.js")
7731 (file-name "js-leaflet-measure-1.5.2.js")
7734 "0ggg3ffmm7pj9ry4gssrh0a17pnad3p6gwi0dg98y819pmpqa7y0"))))
7738 (uri "https://raw.githubusercontent.com/kartena/Proj4Leaflet/1.0.2/lib/proj4.js")
7739 (file-name "js-proj4leaflet-1.0.2.js")
7742 "0vyrbf6gv2lyh4c2bzp5349ivwvvg28gpn87y52a7jdb13rlkpab"))))))
7757 (home-page "https://rstudio.github.io/leaflet/")
7758 (synopsis "Create interactive web maps with the JavaScript Leaflet library")
7760 "Create and customize interactive maps using the Leaflet JavaScript
7761 library and the @code{htmlwidgets} package. These maps can be used directly
7762 from the R console, from RStudio, in Shiny applications and R Markdown
7764 (license license:gpl3)))
7766 (define-public r-leaps
7773 (uri (cran-uri "leaps" version))
7776 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
7777 (build-system r-build-system)
7778 (native-inputs (list gfortran))
7779 (home-page "https://cran.r-project.org/web/packages/leaps/")
7780 (synopsis "Regression subset selection")
7782 "This package provides tools for regression subset selection, including
7783 exhaustive search.")
7784 (license license:gpl2+)))
7786 (define-public r-splus2r
7793 (uri (cran-uri "splus2R" version))
7796 "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x"))))
7797 (properties `((upstream-name . "splus2R")))
7798 (build-system r-build-system)
7799 (home-page "https://cran.r-project.org/web/packages/splus2R/")
7800 (synopsis "Supplemental S-PLUS functionality in R")
7802 "Currently there are many functions in S-PLUS that are missing in R. To
7803 facilitate the conversion of S-PLUS packages to R packages, this package
7804 provides some missing S-PLUS functionality in R.")
7805 (license license:gpl2)))
7807 (define-public r-ifultools
7809 (name "r-ifultools")
7814 (uri (cran-uri "ifultools" version))
7817 "1lkmzrh65j6vdb8523axxk9gig5q4zxy08wiqsp16w482d2q2sl1"))))
7818 (build-system r-build-system)
7822 `(modify-phases %standard-phases
7823 (add-after 'unpack 'compatibility
7825 ;; These definitions are no longer part of R since 4.2.0. See
7826 ;; https://cran.r-project.org/doc/manuals/r-devel/NEWS.html for
7828 (substitute* "inst/include/ut_RS.h"
7829 (("#include \"R.h\"" m)
7831 #define R_PROBLEM_BUFSIZE 4096
7832 #define PROBLEM {char R_problem_buf[R_PROBLEM_BUFSIZE];(sprintf)(R_problem_buf,
7833 #define MESSAGE {char R_problem_buf[R_PROBLEM_BUFSIZE];(sprintf)(R_problem_buf,
7834 #define ERROR ),error(R_problem_buf);}
7835 #define WARNING(x) ),warning(R_problem_buf);}
7836 #define WARN WARNING(NULL)
7839 (list r-mass r-splus2r))
7840 (home-page "https://cran.r-project.org/web/packages/ifultools/")
7841 (synopsis "Insightful research tools")
7842 (description "This package provides C code used by the wmtsa, fractal, and
7844 (license license:gpl2)))
7846 (define-public r-sapa
7853 (uri (cran-uri "sapa" version))
7856 "0kj681rd4c2lvqr926lb6f4qwp281x5274dg6vbk8pf5y7s0qlpc"))))
7857 (build-system r-build-system)
7859 (list r-ifultools r-splus2r))
7860 (home-page "https://cran.r-project.org/web/packages/sapa/")
7861 (synopsis "Spectral analysis for physical applications")
7862 (description "This package provides software for the book Spectral
7863 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
7864 Cambridge University Press, 1993.")
7865 (license license:gpl2)))
7867 (define-public r-aggregation
7869 (name "r-aggregation")
7874 (uri (cran-uri "aggregation" version))
7877 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
7878 (build-system r-build-system)
7879 (home-page "https://cran.r-project.org/web/packages/aggregation/")
7880 (synopsis "Methods for p-value aggregation")
7882 "This package contains functionality for performing the following methods
7883 of p-value aggregation: Fisher's method, the Lancaster method (weighted
7884 Fisher's method), and Sidak correction.")
7885 (license license:gpl3)))
7887 (define-public r-quantmod
7894 (uri (cran-uri "quantmod" version))
7897 "154fqhw46kc7r08zsj5fsg97hg93phsli3z14xwmz22xb50xymzp"))))
7898 (build-system r-build-system)
7900 (list r-curl r-ttr r-xts r-zoo))
7901 (home-page "https://cran.r-project.org/web/packages/quantmod/")
7902 (synopsis "Quantitative financial modelling framework")
7903 (description "This package provides a quantitative financial modelling
7904 framework to allow users to specify, build, trade, and analyse quantitative
7905 financial trading strategies.")
7906 (license license:gpl3)))
7908 (define-public r-tseries
7915 (uri (cran-uri "tseries" version))
7918 "0icgmng0dzvfkkn6dam74wvlz8g0cy46wkw57f5lpd5kxpdwi6ck"))))
7919 (build-system r-build-system)
7921 (list r-quadprog r-quantmod r-zoo))
7924 (home-page "https://cran.r-project.org/web/packages/tseries/")
7925 (synopsis "Time series analysis and computational finance")
7927 "This package provides functions relating to time series analysis and
7928 computational finance.")
7929 (license license:gpl2)))
7931 (define-public r-wmtsa
7938 (uri (cran-uri "wmtsa" version))
7941 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
7942 (build-system r-build-system)
7944 (list r-ifultools r-mass r-splus2r))
7945 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
7946 (synopsis "Wavelet methods for time series analysis")
7948 "This package provides software to accompany the book \"Wavelet Methods
7949 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
7950 University Press, 2000.")
7951 (license license:gpl2)))
7953 (define-public r-tsa
7960 (uri (cran-uri "TSA" version))
7963 "14g58s2w7wma1fgcg3b51267b3676zrv0w8v4hpypxygz023d9bx"))))
7964 (properties `((upstream-name . "TSA")))
7965 (build-system r-build-system)
7967 (list r-leaps r-locfit r-mgcv r-tseries))
7968 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
7969 (synopsis "Time series analysis")
7971 "This package contains R functions and datasets detailed in the book
7972 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
7973 Cryer and Kung-Sik Chan.")
7974 (license license:gpl2+)))
7976 (define-public r-extradistr
7978 (name "r-extradistr")
7983 (uri (cran-uri "extraDistr" version))
7986 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
7987 (properties `((upstream-name . "extraDistr")))
7988 (build-system r-build-system)
7991 (home-page "https://github.com/twolodzko/extraDistr")
7992 (synopsis "Additional univariate and multivariate distributions")
7994 "This package implements density, distribution functions, quantile
7995 functions and random generation functions for a large number of univariate and
7996 multivariate distributions.")
7997 (license license:gpl2)))
7999 (define-public r-fractal
8006 (uri (cran-uri "fractal" version))
8009 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
8010 (build-system r-build-system)
8018 (home-page "https://cran.r-project.org/web/packages/fractal/")
8019 (synopsis "Fractal time series modeling and analysis")
8021 "This package provides tools for stochastic fractal and deterministic
8022 chaotic time series analysis.")
8023 (license license:gpl2)))
8025 (define-public r-urca
8032 (uri (cran-uri "urca" version))
8035 "1wg9f691pif59xds43gnnw77mmzc9xpnhhvaksk2b0szffvaifj3"))))
8036 (build-system r-build-system)
8037 (propagated-inputs (list r-nlme))
8038 (native-inputs (list gfortran))
8039 (home-page "https://cran.r-project.org/web/packages/urca/")
8040 (synopsis "Unit root and cointegration tests for time series data")
8042 "This package provides unit root and cointegration tests encountered in
8043 applied econometric analysis.")
8044 (license license:gpl2+)))
8046 (define-public r-cubature
8053 (uri (cran-uri "cubature" version))
8056 "08whkhvn218089r930spn97m91vv1njgh2amksia8l3rbf7127x8"))))
8057 (build-system r-build-system)
8062 (home-page "https://github.com/bnaras/cubature")
8063 (synopsis "Adaptive multivariate integration over hypercubes")
8065 "This package is an R wrapper around the cubature C library for adaptive
8066 multivariate integration over hypercubes. This version provides both
8067 @code{hcubature} and @code{pcubature} routines in addition to a vector
8069 ;; The included cubature C library is released under GPLv2+, but the
8070 ;; wrapper declares the license to be GPLv3+.
8071 (license (list license:gpl2+ license:gpl3+))))
8073 (define-public r-trend
8080 (uri (cran-uri "trend" version))
8083 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
8084 (build-system r-build-system)
8086 (list r-extradistr))
8089 (home-page "https://cran.r-project.org/web/packages/trend/")
8090 (synopsis "Non-parametric trend tests and change-point detection")
8092 "The analysis of environmental data often requires the detection of
8093 trends and change-points. This package includes tests for trend
8094 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
8095 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
8096 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
8097 correlation trend test), change-point detection (Lanzante's test procedures,
8098 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
8099 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
8100 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
8101 sample Robust Rank-Order Distributional Test.")
8102 (license license:gpl3)))
8104 (define-public r-expm
8111 (uri (cran-uri "expm" version))
8114 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c"))))
8115 (build-system r-build-system)
8116 (propagated-inputs (list r-matrix))
8117 (native-inputs (list gfortran))
8118 (home-page "https://r-forge.r-project.org/projects/expm/")
8119 (synopsis "Tools for matrix exponentials and related quantities")
8121 "This package provides tools for the computation of the matrix
8122 exponential, logarithm, square root, and related quantities.")
8123 (license license:gpl2+)))
8125 (define-public r-exposition
8127 (name "r-exposition")
8131 (uri (cran-uri "ExPosition" version))
8134 "0x9400ggmgrnaish0cfgnyvw549g4ibfv9aj6vzq7j68n58vq405"))))
8135 (properties `((upstream-name . "ExPosition")))
8136 (build-system r-build-system)
8137 (propagated-inputs (list r-prettygraphs))
8138 (home-page "https://cran.r-project.org/package=ExPosition")
8139 (synopsis "Exploratory analysis with the singular value decomposition")
8141 "This package provides a variety of descriptive multivariate analyses
8142 with the singular value decomposition, such as principal components analysis,
8143 correspondence analysis, and multidimensional scaling. See An ExPosition of
8144 the Singular Value Decomposition in R (Beaton et al 2014)
8145 <doi:10.1016/j.csda.2013.11.006>.")
8146 (license license:gpl2)))
8148 (define-public r-complexplus
8150 (name "r-complexplus")
8155 (uri (cran-uri "complexplus" version))
8158 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
8159 (build-system r-build-system)
8161 (list r-expm r-matrix))
8162 (home-page "https://cran.r-project.org/web/packages/complexplus/")
8163 (synopsis "Functions of complex or real variables")
8165 "This package extends several functions to the complex domain, including
8166 the matrix exponential and logarithm, and the determinant.")
8167 (license license:gpl2)))
8169 (define-public r-phontools
8171 (name "r-phontools")
8176 (uri (cran-uri "phonTools" version))
8179 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
8180 (properties `((upstream-name . "phonTools")))
8181 (build-system r-build-system)
8182 (home-page "http://www.santiagobarreda.com/rscripts.html")
8183 (synopsis "Tools for phonetic and acoustic analyses")
8185 "This package contains tools for the organization, display, and analysis
8186 of the sorts of data frequently encountered in phonetics research and
8187 experimentation, including the easy creation of IPA vowel plots, and the
8188 creation and manipulation of WAVE audio files.")
8189 (license license:bsd-2)))
8198 (uri (cran-uri "np" version))
8201 "1c01drwvh2jj0s40q19ghdf429s6px07akg6d0yfanah3706gydy"))))
8202 (build-system r-build-system)
8204 (list r-boot r-cubature r-quadprog r-quantreg))
8205 (home-page "https://github.com/JeffreyRacine/R-Package-np")
8206 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
8207 (description "This package provides non-parametric (and semi-parametric)
8208 kernel methods that seamlessly handle a mix of continuous, unordered, and
8209 ordered factor data types.")
8210 ;; Any version of the GPL.
8211 (license license:gpl3+)))
8213 (define-public r-powerplus
8215 (name "r-powerplus")
8220 (uri (cran-uri "powerplus" version))
8223 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
8224 (build-system r-build-system)
8226 (list r-complexplus r-expm r-mass r-matrix r-phontools))
8227 (home-page "https://cran.r-project.org/web/packages/powerplus/")
8228 (synopsis "Exponentiation operations")
8230 "This package provides tools for the computation of matrix and scalar
8232 (license license:gpl2)))
8234 (define-public r-egg
8241 (uri (cran-uri "egg" version))
8244 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
8245 (properties `((upstream-name . "egg")))
8246 (build-system r-build-system)
8248 (list r-ggplot2 r-gridextra r-gtable))
8249 (home-page "https://cran.r-project.org/web/packages/egg")
8250 (synopsis "Extensions for ggplot2")
8252 "This package provides miscellaneous functions to help customize ggplot2
8253 objects. High-level functions are provided to post-process ggplot2 layouts
8254 and allow alignment between plot panels, as well as setting panel sizes to
8255 fixed values. Other functions include a custom @code{geom}, and helper
8256 functions to enforce symmetric scales or add tags to facetted plots.")
8257 (license license:gpl3)))
8259 (define-public r-heatmap3
8266 (uri (cran-uri "heatmap3" version))
8269 "0sfvizmmwfk1bjhn6zfx5a4qqfgj1ldg8x90b65crqibgfa36k2r"))))
8270 (build-system r-build-system)
8272 (list r-fastcluster))
8275 (home-page "https://cran.r-project.org/web/packages/heatmap3/")
8276 (synopsis "Improved heatmap package")
8278 "This package provides an improved heatmap package. It is completely
8279 compatible with the original R function @code{heatmap}, and provides more
8280 powerful and convenient features.")
8281 (license license:gpl2+)))
8283 (define-public r-heatmaply
8285 (name "r-heatmaply")
8290 (uri (cran-uri "heatmaply" version))
8293 "0q1vkf55a5r0ssybdbi2fyhn13p29kw04yp46c34n7apm0k2ymgi"))))
8294 (build-system r-build-system)
8312 (home-page "https://cran.r-project.org/package=heatmaply")
8313 (synopsis "Interactive cluster heat maps using plotly")
8315 "This package enables you to create interactive cluster heatmaps that can
8316 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
8317 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
8318 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
8319 a popular graphical method for visualizing high-dimensional data, in which a
8320 table of numbers is encoded as a grid of colored cells. The rows and columns
8321 of the matrix are ordered to highlight patterns and are often accompanied by
8323 ;; Either version of the license.
8324 (license (list license:gpl2 license:gpl3))))
8333 (uri (cran-uri "h5" version))
8336 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
8337 (build-system r-build-system)
8344 (home-page "https://github.com/mannau/h5")
8345 (synopsis "Interface to the HDF5 Library")
8347 "This package provides an S4 interface to the HDF5 library supporting
8348 fast storage and retrieval of R-objects like vectors, matrices and arrays to
8349 binary files in a language independent format. The HDF5 format can therefore
8350 be used as an alternative to R's save/load mechanism. Since h5 is able to
8351 access only subsets of stored data it can also handle data sets which do not
8353 (license license:bsd-2)))
8355 (define-public r-cgdsr
8362 (uri (cran-uri "cgdsr" version))
8365 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
8366 (build-system r-build-system)
8368 (list r-httr r-r-methodss3 r-r-oo))
8369 (home-page "https://github.com/cBioPortal/cgdsr")
8370 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
8372 "This package provides a basic set of R functions for querying the Cancer
8373 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
8374 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
8375 (license license:lgpl3)))
8377 (define-public r-import
8384 (uri (cran-uri "import" version))
8387 "19g4jnfg9pkvvsncw62yc15xlb97hfbdqxivpjd9jqi36i6mdjrg"))))
8388 (build-system r-build-system)
8391 (home-page "https://github.com/smbache/import")
8392 (synopsis "Import mechanism for R")
8394 "This is an alternative mechanism for importing objects from packages.
8395 The syntax allows for importing multiple objects from a package with a single
8396 command in an expressive way. The import package bridges some of the gap
8397 between using @code{library} (or @code{require}) and direct (single-object)
8398 imports. Furthermore the imported objects are not placed in the current
8399 environment. It is also possible to import objects from stand-alone @code{.R}
8401 (license license:expat)))
8403 (define-public r-shinyace
8410 (uri (cran-uri "shinyAce" version))
8413 "12mqvdh6rxsr61pc3pzla95r5f4l7xagjs2rcdr7c2lbqyxpx6aa"))))
8414 (properties `((upstream-name . "shinyAce")))
8415 (build-system r-build-system)
8417 (list r-shiny r-jsonlite))
8418 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
8419 (synopsis "Ace editor bindings for Shiny")
8421 "This package provides Ace editor bindings to enable a rich text editing
8422 environment within Shiny.")
8423 (license license:expat)))
8425 (define-public r-rafalib
8432 (uri (cran-uri "rafalib" version))
8434 (base32 "1dmxjl66bfdgrybhwyaa8d4i460liqcdw8b29a6w7shgksh29m0k"))))
8435 (properties `((upstream-name . "rafalib")))
8436 (build-system r-build-system)
8437 (propagated-inputs (list r-rcolorbrewer))
8438 (home-page "https://cran.r-project.org/package=rafalib")
8439 (synopsis "Convenience functions for routine data exploration")
8441 "This package provides a series of shortcuts for routine tasks to
8442 facilitate data exploration.")
8443 (license license:artistic2.0)))
8445 (define-public r-randomizr
8447 (name "r-randomizr")
8452 (uri (cran-uri "randomizr" version))
8455 "1grm0h3xkb0pdbbv0gd531g1kn6njp0gcy5fh153rrmajxgd8hhw"))))
8456 (properties `((upstream-name . "randomizr")))
8457 (build-system r-build-system)
8460 (home-page "https://declaredesign.org/r/randomizr/")
8461 (synopsis "Tools for common forms of random assignment and sampling")
8463 "This package provides tools for generating random assignments for common
8464 experimental designs and random samples for common sampling designs.")
8465 (license license:expat)))
8467 (define-public r-base64url
8469 (name "r-base64url")
8474 (uri (cran-uri "base64url" version))
8477 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
8478 (build-system r-build-system)
8481 (home-page "https://github.com/mllg/base64url")
8482 (synopsis "Fast and URL-safe base64 encoder and decoder")
8484 "This package provides a URL-safe base64 encoder and decoder. In
8485 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
8486 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
8487 encoder does not fill the string with trailing @code{=}. The resulting
8488 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
8489 and thus are safe to use in URLs or for file names. The package also comes
8490 with a simple base32 encoder/decoder suited for case insensitive file
8492 (license license:gpl3)))
8494 (define-public r-radiant-data
8496 (name "r-radiant-data")
8501 (uri (cran-uri "radiant.data" version))
8504 "1vas0bkpngwxybmpdcaimha2r008prnli4b3lgjbjfkzpgm966d1"))
8505 (modules '((guix build utils)))
8508 ;; Delete files that are under CC-NC-SA.
8509 (delete-file-recursively "inst/app/tools/help")
8511 (properties `((upstream-name . "radiant.data")))
8512 (build-system r-build-system)
8548 (home-page "https://github.com/radiant-rstats/radiant.data")
8549 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
8551 "The Radiant Data menu includes interfaces for loading, saving, viewing,
8552 visualizing, summarizing, transforming, and combining data. It also contains
8553 functionality to generate reproducible reports of the analyses conducted in
8555 (license license:agpl3)))
8557 (define-public r-algdesign
8559 (name "r-algdesign")
8564 (uri (cran-uri "AlgDesign" version))
8566 (base32 "01cx63wqr6yvgl5ml1lj6gh9p1sn42b6qcnsppcw7mvba9n652ar"))))
8567 (properties `((upstream-name . "AlgDesign")))
8568 (build-system r-build-system)
8569 (home-page "https://github.com/jvbraun/AlgDesign")
8570 (synopsis "Algorithmic experimental design")
8572 "This package provides tools to calculate exact and approximate theory
8573 experimental designs for D, A, and I criteria. Very large designs may be
8574 created. Experimental designs may be blocked or blocked designs created from
8575 a candidate list, using several criteria. The blocking can be done when whole
8576 and within plot factors interact.")
8577 (license license:gpl2+)))
8579 (define-public r-alluvial
8586 (uri (cran-uri "alluvial" version))
8588 (base32 "039frwrsxq1lb97s7vf2vbyyadimkigs628ymym06fxka53drdkp"))))
8589 (properties `((upstream-name . "alluvial")))
8590 (build-system r-build-system)
8591 (native-inputs (list r-knitr))
8592 (home-page "https://github.com/mbojan/alluvial")
8593 (synopsis "Create parallel sets plots (Alluvial Diagrams)")
8595 "This package creates alluvial diagrams (also known as parallel sets
8596 plots) for multivariate and time series-like data.")
8597 (license license:expat)))
8599 (define-public r-signal
8606 (uri (cran-uri "signal" version))
8609 "0qaf39vfmhn3d0bdjqd805ayfkaj48dkmf5dqd47bpk7dp21b837"))))
8610 (build-system r-build-system)
8611 (propagated-inputs (list r-mass))
8612 (native-inputs (list gfortran))
8613 (home-page "https://cran.r-project.org/web/packages/signal/")
8614 (synopsis "Signal processing")
8616 "This package provides a set of signal processing functions originally
8617 written for Matlab and GNU Octave. It includes filter generation utilities,
8618 filtering functions, resampling routines, and visualization of filter models.
8619 It also includes interpolation functions.")
8620 (license license:gpl2)))
8622 (define-public r-gsubfn
8629 (uri (cran-uri "gsubfn" version))
8632 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
8633 (build-system r-build-system)
8634 (propagated-inputs (list r-proto))
8635 (home-page "https://code.google.com/archive/p/gsubfn/")
8636 (synopsis "Utilities for strings and function arguments")
8638 "This package provides @code{gsubfn} which is like @code{gsub} but can
8639 take a replacement function or certain other objects instead of the
8640 replacement string. Matches and back references are input to the replacement
8641 function and replaced by the function output. @code{gsubfn} can be used to
8642 split strings based on content rather than delimiters and for quasi-perl-style
8643 string interpolation. The package also has facilities for translating
8644 formulas to functions and allowing such formulas in function calls instead of
8646 (license license:gpl2+)))
8648 (define-public r-sqldf
8655 (uri (cran-uri "sqldf" version))
8658 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
8659 (build-system r-build-system)
8661 (list r-chron r-dbi r-gsubfn r-proto r-rsqlite))
8662 (home-page "https://github.com/ggrothendieck/sqldf")
8663 (synopsis "Manipulate R data frames using SQL")
8665 "The @code{sqldf} function is typically passed a single argument which is
8666 an SQL select statement where the table names are ordinary R data frame names.
8667 @code{sqldf} transparently sets up a database, imports the data frames into
8668 that database, performs the SQL statement and returns the result using a
8669 heuristic to determine which class to assign to each column of the returned
8670 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
8671 used to read filtered files into R even if the original files are larger than
8672 R itself can handle.")
8673 (license license:gpl2)))
8675 (define-public r-abind
8682 (uri (cran-uri "abind" version))
8685 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
8686 (build-system r-build-system)
8687 (home-page "https://cran.r-project.org/web/packages/abind/")
8688 (synopsis "Combine multidimensional arrays")
8690 "This package provides tools to combine multidimensional arrays into a
8691 single array. This is a generalization of @code{cbind} and @code{rbind}. It
8692 works with vectors, matrices, and higher-dimensional arrays. It also provides
8693 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
8694 extracting and replacing data in arrays.")
8695 (license license:lgpl2.0+)))
8697 (define-public r-prroc
8704 (uri (cran-uri "PRROC" version))
8707 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
8708 (properties `((upstream-name . "PRROC")))
8709 (build-system r-build-system)
8710 (home-page "https://cran.r-project.org/web/packages/PRROC/")
8711 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
8713 "This package computes the areas under the @dfn{precision-recall} (PR)
8714 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
8715 contrast to other implementations, the interpolation between points of the PR
8716 curve is done by a non-linear piecewise function. In addition to the areas
8717 under the curves, the curves themselves can also be computed and plotted by a
8718 specific S3-method.")
8719 (license license:gpl3)))
8721 (define-public r-vim
8728 (uri (cran-uri "VIM" version))
8731 "1r0myxcx8y1a3fkf9ssk882f09snn2j6zilsygpld32hahn4k9xg"))))
8732 (properties `((upstream-name . "VIM")))
8733 (build-system r-build-system)
8750 (home-page "https://github.com/alexkowa/VIM")
8751 (synopsis "Visualization and imputation of missing values")
8753 "This package provides tools for the visualization of missing and/or
8754 imputed values are introduced, which can be used for exploring the data and
8755 the structure of the missing and/or imputed values. Depending on this
8756 structure of the missing values, the corresponding methods may help to
8757 identify the mechanism generating the missing values and explore the
8758 data including missing values. In addition, the quality of imputation can be
8759 visually explored using various univariate, bivariate, multiple and
8760 multivariate plot methods.")
8761 (license license:gpl2+)))
8763 (define-public r-fnn
8770 (uri (cran-uri "FNN" version))
8773 "0nmynpiy3d2dnd5ngjf4m79jy02byhk43gj0xny9a6j8243f5c2j"))))
8774 (properties `((upstream-name . "FNN")))
8775 (build-system r-build-system)
8776 (home-page "https://cran.r-project.org/web/packages/FNN")
8777 (synopsis "Fast nearest neighbor search algorithms and applications")
8779 "This package provides cover-tree and kd-tree fast k-nearest neighbor
8780 search algorithms. Related applications including KNN classification,
8781 regression and information measures are implemented.")
8782 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
8783 ;; later can be used.
8784 (license license:gpl2+)))
8786 (define-public r-smoother
8793 (uri (cran-uri "smoother" version))
8796 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
8797 (build-system r-build-system)
8800 (home-page "https://cran.r-project.org/web/packages/smoother")
8801 (synopsis "Functions relating to the smoothing of numerical data")
8803 "This package provides a collection of methods for smoothing numerical
8804 data, commencing with a port of the Matlab gaussian window smoothing function.
8805 In addition, several functions typically used in smoothing of financial data
8807 (license license:gpl2)))
8809 (define-public r-riverplot
8811 (name "r-riverplot")
8816 (uri (cran-uri "riverplot" version))
8819 "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj"))))
8820 (build-system r-build-system)
8822 (list r-rcolorbrewer))
8825 (home-page "https://logfc.wordpress.com")
8826 (synopsis "Sankey or ribbon plots")
8828 "Sankey plots are a type of diagram that is convenient to illustrate how
8829 flow of information, resources etc. separates and joins, much like observing
8830 how rivers split and merge. For example, they can be used to compare
8831 different clusterings. This package provides an implementation of Sankey
8833 (license license:gpl2+)))
8835 (define-public r-dyn
8842 (uri (cran-uri "dyn" version))
8845 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
8846 (build-system r-build-system)
8849 (home-page "https://cran.r-project.org/web/packages/dyn")
8850 (synopsis "Time series regression")
8852 "This package provides the dyn class interfaces @code{ts}, @code{irts},
8853 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
8854 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
8855 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
8856 @code{randomForest::randomForest()} and other regression functions, allowing
8857 those functions to be used with time series including specifications that may
8858 contain lags, diffs and missing values.")
8860 (license license:gpl2+)))
8862 (define-public r-dynutils
8869 (uri (cran-uri "dynutils" version))
8871 (base32 "06an2bm1d131v28m240vii2wisbz3zs32wbamm2w7r8rl3yrxkh9"))))
8872 (properties `((upstream-name . "dynutils")))
8873 (build-system r-build-system)
8887 (native-inputs (list r-knitr))
8888 (home-page "https://github.com/dynverse/dynutils")
8889 (synopsis "Common functionality for the dynverse packages")
8891 "This package provides common functionality for the
8892 @url{https://dynverse.org,dynverse} packages. dynverse is created to support
8893 the development, execution, and benchmarking of trajectory inference
8895 (license license:expat)))
8897 (define-public r-catdap
8904 (uri (cran-uri "catdap" version))
8907 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
8908 (build-system r-build-system)
8911 (home-page "https://cran.r-project.org/web/packages/catdap/")
8912 (synopsis "Tools for categorical data analysis")
8914 "This package provides functions for analyzing multivariate data.
8915 Dependencies of the distribution of the specified variable (response
8916 variable) to other variables (explanatory variables) are derived and
8917 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
8918 (license license:gpl2+)))
8920 (define-public r-catdata
8926 (uri (cran-uri "catdata" version))
8929 "14kx7yi0cv6dyh9wjasb8gn6cp1bhglgwql7dc2a7lqvdcp0d5vj"))))
8930 (properties `((upstream-name . "catdata")))
8931 (build-system r-build-system)
8932 (propagated-inputs (list r-mass))
8933 (home-page "https://cran.r-project.org/package=catdata")
8935 "Datasets and examples used in the book @emph{Regression for Categorical Data}")
8937 "This R package contains examples from the book @emph{Regression
8938 for Categorical Data}, Tutz 2012, Cambridge University Press. The
8939 names of the examples refer to the chapter and the data set that is
8941 (license license:gpl2)))
8943 (define-public r-arules
8950 (uri (cran-uri "arules" version))
8953 "0d04w28hl9gcrvkj0v0q77x4a89jhvzf1imw58xfgncap8mc6555"))))
8954 (build-system r-build-system)
8956 (list r-generics r-matrix))
8957 (home-page "https://github.com/mhahsler/arules")
8958 (synopsis "Mining association rules and frequent itemsets")
8960 "This package provides an infrastructure for representing, manipulating
8961 and analyzing transaction data and patterns (frequent itemsets and association rules).
8962 It also provides C implementations of the association mining algorithms Apriori
8964 (license license:gpl3)))
8966 (define-public r-parsedate
8968 (name "r-parsedate")
8973 (uri (cran-uri "parsedate" version))
8976 "1cfinqlbchmkhkgmdwiy3mnxb17lp02jfk2gpw56hq9vh6wimhqz"))))
8977 (build-system r-build-system)
8978 (home-page "https://github.com/gaborcsardi/parsedate")
8980 "Recognize and parse dates in various formats")
8982 "This package provides three functions for dealing with dates:
8983 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
8984 time formats, @code{parse_date} parses dates in unspecified formats,
8985 and @code{format_iso_8601} formats a date in ISO 8601 format.")
8986 (license license:gpl2)))
8988 (define-public r-abc-data
8995 (uri (cran-uri "abc.data" version))
8998 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
8999 (properties `((upstream-name . "abc.data")))
9000 (build-system r-build-system)
9001 (home-page "https://cran.r-project.org/web/packages/abc.data/")
9002 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
9004 "This package contains data which are used by functions of the abc
9005 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
9006 algorithms for performing parameter estimation, model selection, and
9008 (license license:gpl3+)))
9010 (define-public r-abc
9017 (uri (cran-uri "abc" version))
9020 "16753lyzk2dfwgdjfyanwacqw3bvrwby52inq4709804labs6lnv"))))
9021 (build-system r-build-system)
9023 (list r-abc-data r-locfit r-mass r-nnet r-quantreg))
9024 (home-page "https://cran.r-project.org/web/packages/abc/")
9025 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
9027 "This package implements several @dfn{Approximate Bayesian
9028 Computation} (ABC) algorithms for performing parameter estimation, model
9029 selection, and goodness-of-fit. Cross-validation tools are also available for
9030 measuring the accuracy of ABC estimates, and to calculate the
9031 misclassification probabilities of different models.")
9032 (license license:gpl3+)))
9034 (define-public r-zip
9041 (uri (cran-uri "zip" version))
9044 "194f19649jqw8wa2bd1kj3873hqnqxsrbqdwnvlzngi8pcixwv71"))))
9045 (build-system r-build-system)
9046 (home-page "https://github.com/gaborcsardi/zip")
9047 (synopsis "Cross-platform Zip compression")
9049 "This package provides a cross-platform Zip compression library for R.
9050 It is a replacement for the @code{zip} function, that does not require any
9051 additional external tools on any platform.")
9052 (license license:cc0)))
9054 (define-public r-openxlsx
9061 (uri (cran-uri "openxlsx" version))
9064 "1j2516plvlrp7l0mw7xqjhjjcidfdnfsybdhi2bx3n0910w29lk4"))))
9065 (build-system r-build-system)
9067 (list r-rcpp r-stringi r-zip))
9070 (home-page "https://github.com/awalker89/openxlsx")
9071 (synopsis "Read, write and edit XLSX files")
9073 "This package simplifies the creation of Excel @code{.xlsx} files by
9074 providing a high level interface to writing, styling and editing worksheets.
9075 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
9076 and @code{XLConnect} packages with the added benefit of removing the
9077 dependency on Java.")
9078 (license license:gpl3)))
9080 (define-public r-rio
9087 (uri (cran-uri "rio" version))
9090 "04jlrhyl0791yxwcpp1s8p1hhkljnijlc5iaxpk56h41w63k39lz"))))
9091 (build-system r-build-system)
9102 (home-page "https://github.com/leeper/rio")
9103 (synopsis "Swiss-army knife for data I/O")
9105 "This package provides streamlined data import and export infrastructure
9106 by making assumptions that the user is probably willing to make: @code{import}
9107 and @code{export} determine the data structure from the file extension,
9108 reasonable defaults are used for data import and export (e.g.,
9109 @code{stringsAsFactors=FALSE}), web-based import is natively
9110 supported (including from SSL/HTTPS), compressed files can be read directly
9111 without explicit decompression, and fast import packages are used where
9112 appropriate. An additional convenience function, @code{convert}, provides a
9113 simple method for converting between file types.")
9114 (license license:gpl2)))
9116 (define-public r-maptools
9123 (uri (cran-uri "maptools" version))
9126 "1p155w26hpmqc589kxha0xgw5b4x6610a3im7ap4mjx1sfavvn9w"))))
9127 (build-system r-build-system)
9129 (list r-foreign r-lattice r-sp))
9130 (home-page "https://r-forge.r-project.org/projects/maptools/")
9131 (synopsis "Tools for reading and handling spatial objects")
9133 "This package provides a set of tools for manipulating and reading
9134 geographic data, in particular ESRI Shapefiles. It includes binary access to
9135 GSHHG shoreline files. The package also provides interface wrappers for
9136 exchanging spatial objects with other R packages.")
9137 ;; The C source files from shapelib are released under the Expat license.
9138 ;; The R code is released under GPL version 2 or later.
9139 (license (list license:gpl2+
9142 (define-public r-later
9149 (uri (cran-uri "later" version))
9152 "0acqg29hcm2iq1418b54np7zb5pnr3xzrwc3ijv2pz9wra10ix88"))))
9153 (build-system r-build-system)
9155 (list r-rcpp r-rlang))
9158 (home-page "https://github.com/r-lib/later")
9159 (synopsis "Utilities for delaying function execution")
9161 "This package provides tools to execute arbitrary R or C functions some
9162 time after the current time, after the R execution stack has emptied.")
9163 (license license:gpl2+)))
9165 (define-public r-promises
9172 (uri (cran-uri "promises" version))
9175 "1dy4cbqw17awh4q8m7cy3anaj0n9iynabfzflb1g94cyj0bq4fld"))))
9176 (build-system r-build-system)
9178 (list r-later r-magrittr r-r6 r-rcpp r-rlang))
9181 (home-page "https://rstudio.github.io/promises")
9182 (synopsis "Abstractions for promise-based asynchronous programming")
9184 "This package provides fundamental abstractions for doing asynchronous
9185 programming in R using promises. Asynchronous programming is useful for
9186 allowing a single R process to orchestrate multiple tasks in the background
9187 while also attending to something else. Semantics are similar to JavaScript
9188 promises, but with a syntax that is idiomatic R.")
9189 (license license:expat)))
9191 (define-public r-dosnow
9198 (uri (cran-uri "doSNOW" version))
9201 "1f5v0k2w0b2478p6iqa3hn2lwd1x3rzc348n57nd38ka2vnsnz4i"))))
9202 (properties `((upstream-name . "doSNOW")))
9203 (build-system r-build-system)
9205 (list r-foreach r-iterators r-snow))
9206 (home-page "https://cran.r-project.org/web/packages/doSNOW")
9207 (synopsis "Foreach parallel adaptor for the snow package")
9209 "This package provides a parallel backend for the @code{%dopar%} function
9210 using the @code{snow} package.")
9211 (license license:gpl2)))
9213 (define-public r-fstcore
9220 (uri (cran-uri "fstcore" version))
9222 (base32 "1a5m68n2dqhi3r8wf5jwg4vjvl550c7wypcf5j0xmkvl836yg1lg"))))
9223 (properties `((upstream-name . "fstcore")))
9224 (build-system r-build-system)
9225 (propagated-inputs (list r-rcpp))
9226 (inputs (list zlib))
9227 (native-inputs (list pkg-config))
9228 (home-page "https://www.fstpackage.org/fstcore/")
9229 (synopsis "R bindings to the fstlib library")
9231 "The fstlib library provides multithreaded serialization of compressed
9232 data frames using the fst format. The fst format allows for random access of
9233 stored data and compression with the LZ4 and ZSTD compressors.")
9234 (license license:mpl2.0)))
9236 (define-public r-fst
9243 (uri (cran-uri "fst" version))
9246 "0r96inwrr960m7wmc80603bw2vvvwab225bh9dq3lalwhy4yiis4"))))
9247 (properties `((upstream-name . "fst")))
9248 (build-system r-build-system)
9249 (propagated-inputs (list r-fstcore r-rcpp))
9250 (home-page "http://www.fstpackage.org")
9251 (synopsis "Fast serialization of data frames")
9253 "The fst package for R provides a fast, easy and flexible way to
9254 serialize data frames. With access speeds of multiple GB/s, fst is
9255 specifically designed to unlock the potential of high speed solid state disks.
9256 Data frames stored in the fst format have full random access, both in column
9257 and rows. The fst format allows for random access of stored data and
9258 compression with the LZ4 and ZSTD compressors.")
9259 (license license:agpl3)))
9261 (define-public r-snftool
9267 (uri (cran-uri "SNFtool" version))
9270 "05hz230aq5wbzhknxzr4iqv3nqjhbpf66n6bp1rc5h2jgz2yfbwq"))))
9271 (properties `((upstream-name . "SNFtool")))
9272 (build-system r-build-system)
9273 (propagated-inputs (list r-alluvial r-exposition))
9274 (home-page "https://cran.r-project.org/package=SNFtool")
9275 (synopsis "Similarity network fusion")
9277 "Similarity Network Fusion takes multiple views of a network and fuses
9278 them together to construct an overall status matrix. The input to our
9279 algorithm can be feature vectors, pairwise distances, or pairwise
9280 similarities. The learned status matrix can then be used for retrieval,
9281 clustering, and classification.")
9282 ;; Any version of the GPL
9283 (license license:gpl3+)))
9285 (define-public r-snowfall
9288 (version "1.84-6.2")
9291 (uri (cran-uri "snowfall" version))
9293 (base32 "0frmasv04wd47h04zbwaryhiyxllarf3ggpa39p5qicjp6r7lilv"))))
9294 (build-system r-build-system)
9297 (home-page "https://cran.r-project.org/web/packages/snowfall/")
9298 (synopsis "Easier cluster computing")
9299 (description "This package is a usability wrapper around snow for easier
9300 development of parallel R programs. This package offers e.g. extended error
9301 checks, and additional functions. All functions work in sequential mode, too,
9302 if no cluster is present or wished. The package is also designed as connector
9303 to the cluster management tool @code{sfCluster}, but can also used without
9305 (license license:gpl2+)))
9307 (define-public r-rgexf
9314 (uri (cran-uri "rgexf" version))
9317 "00c2zka1n3k7p1l0mlchr063s6x58p9r3fb64d4wgl4rvsq55q3f"))
9318 ;; Delete minified JavaScript files
9320 '(for-each delete-file
9321 '("inst/gexf-js/js/jquery-2.0.2.min.js"
9322 "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js"
9323 "inst/gexf-js/js/jquery.mousewheel.min.js")))))
9324 (properties `((upstream-name . "rgexf")))
9325 (build-system r-build-system)
9327 `(#:modules ((guix build utils)
9328 (guix build r-build-system)
9332 (modify-phases %standard-phases
9333 (add-after 'unpack 'process-javascript
9334 (lambda* (#:key inputs #:allow-other-keys)
9335 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-jquery-ui"))
9336 (with-directory-excursion "inst/gexf-js/js/"
9340 `((,(assoc-ref inputs "js-jquery")
9341 "jquery-2.0.2.min.js")
9342 ("/tmp/jquery-ui-1.10.3/ui/jquery-ui.js"
9343 "jquery-ui-1.10.3.custom.min.js")
9344 (,(assoc-ref inputs "js-jquery-mousewheel")
9345 "jquery.mousewheel.min.js"))))
9346 (lambda (sources targets)
9347 (for-each (lambda (source target)
9348 (format #true "Processing ~a --> ~a~%"
9350 (invoke "esbuild" source "--minify"
9351 (string-append "--outfile=" target)))
9352 sources targets)))))))))
9354 (list r-igraph r-servr r-xml))
9356 `(("r-knitr" ,r-knitr)
9357 ("esbuild" ,esbuild)
9362 (uri "https://code.jquery.com/jquery-2.0.2.js")
9365 "0v818bxpw48gdk8i95qqqij80r9jcgisi2r4ac6xnxca20h0gvfj"))))
9369 (uri "https://jqueryui.com/resources/download/jquery-ui-1.10.3.zip")
9372 "00xpfy0l69nj2yan4s8k65ldsrlfsjkmyw2dwcg93dc8mv454vxx"))))
9373 ("js-jquery-mousewheel"
9376 (uri "https://raw.githubusercontent.com/jquery/jquery-mousewheel/\
9377 3.0.6/jquery.mousewheel.js")
9380 "19lk5xy2s47bx8hsa7j6bg012f8yw6d770g230bcnm559kf4nc6v"))))))
9381 (home-page "https://gvegayon.github.io/rgexf")
9382 (synopsis "Build, import and export GEXF graph files")
9384 "Create, read and write GEXF (Graph Exchange XML Format) graph
9385 files (used in Gephi and others). It allows the user to easily build/read
9386 graph files including attributes, GEXF visual attributes (such as color, size,
9387 and position), network dynamics (for both edges and nodes) and edge weighting.
9388 Users can build/handle graphs element-by-element or massively through
9389 data-frames, visualize the graph on a web browser through gexf-js (a
9390 JavaScript library) and interact with the igraph package.")
9391 (license license:expat)))
9393 (define-public r-data-tree
9395 (name "r-data-tree")
9400 (uri (cran-uri "data.tree" version))
9403 "0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
9404 (properties `((upstream-name . "data.tree")))
9405 (build-system r-build-system)
9407 (list r-r6 r-stringi))
9410 (home-page "https://github.com/gluc/data.tree")
9411 (synopsis "General purpose hierarchical data structure")
9413 "Create tree structures from hierarchical data, and traverse the tree in
9414 various orders. Aggregate, cumulate, print, plot, convert to and from
9415 data.frame and more. This is useful for decision trees, machine learning,
9416 finance, conversion from and to JSON, and many other applications.")
9417 (license license:gpl2+)))
9419 (define-public r-dtplyr
9426 (uri (cran-uri "dtplyr" version))
9429 "1m72ac7461mlvanj1krpmfp2ljl3c2k5nw6zrahc66vhcgz2hngq"))))
9430 (properties `((upstream-name . "dtplyr")))
9431 (build-system r-build-system)
9445 (home-page "https://github.com/tidyverse/dtplyr")
9446 (synopsis "Data Table back-end for dplyr")
9448 "This package provides a @code{data.table} backend for @code{dplyr}. The
9449 goal of @code{dtplyr} is to allow you to write @code{dplyr} code that is
9450 automatically translated to the equivalent, but usually much faster,
9451 @code{data.table} code.")
9452 (license license:expat)))
9454 (define-public r-collapsibletree
9456 (name "r-collapsibletree")
9461 (uri (cran-uri "collapsibleTree" version))
9464 "0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
9467 ;; Delete minified JavaScript file
9468 (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js")
9471 `((upstream-name . "collapsibleTree")))
9472 (build-system r-build-system)
9475 (modify-phases %standard-phases
9476 (add-after 'unpack 'process-javascript
9477 (lambda* (#:key inputs #:allow-other-keys)
9478 (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/"
9479 (let ((source (assoc-ref inputs "d3.v4.js"))
9480 (target "d3.min.js"))
9481 (format #t "Processing ~a --> ~a~%"
9483 (invoke "esbuild" source "--minify"
9484 (string-append "--outfile=" target)))))))))
9486 (list r-data-tree r-htmlwidgets))
9488 `(("esbuild" ,esbuild)
9492 (uri "https://d3js.org/d3.v4.js")
9495 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
9496 (home-page "https://github.com/AdeelK93/collapsibleTree")
9497 (synopsis "Interactive collapsible tree diagrams using D3.js")
9499 "This is a package for interactive Reingold-Tilford tree diagrams created
9500 using D3.js, where every node can be expanded and collapsed by clicking on it.
9501 Tooltips and color gradients can be mapped to nodes using a numeric column in
9502 the source data frame.")
9503 (license license:gpl3+)))
9505 (define-public r-rappdirs
9512 (uri (cran-uri "rappdirs" version))
9515 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9"))))
9516 (build-system r-build-system)
9517 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
9518 (synopsis "Determine where to save data, caches, and logs")
9520 "This package provides an easy way to determine which directories on the
9521 user's computer should be used to save data, caches and logs. It is a port of
9522 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
9523 (license license:expat)))
9525 (define-public r-rastervis
9527 (name "r-rastervis")
9532 (uri (cran-uri "rasterVis" version))
9535 "0kgg6cm7xjqya2d46w0i1i1wjpkb8f99lyqy7rgwa7l9xmwzj5n1"))))
9536 (properties `((upstream-name . "rasterVis")))
9537 (build-system r-build-system)
9548 (home-page "https://oscarperpinan.github.io/rastervis/")
9549 (synopsis "Visualization methods for raster data")
9551 "This package provides methods for enhanced visualization and interaction
9552 with raster data. It implements visualization methods for quantitative data
9553 and categorical data, both for univariate and multivariate rasters. It also
9554 provides methods to display spatiotemporal rasters, and vector fields.")
9555 (license license:gpl3)))
9557 (define-public r-rentrez
9564 (uri (cran-uri "rentrez" version))
9567 "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv"))))
9568 (properties `((upstream-name . "rentrez")))
9569 (build-system r-build-system)
9571 (list r-httr r-jsonlite r-xml))
9574 (home-page "https://docs.ropensci.org/rentrez/")
9575 (synopsis "Entrez in R")
9577 "This package provides an R interface to the NCBI's EUtils API,
9578 allowing users to search databases like GenBank PubMed, process the results of
9579 those searches and pull data into their R sessions.")
9580 (license license:expat)))
9582 (define-public r-renv
9589 (uri (cran-uri "renv" version))
9592 "05m0idzjmg3wjlip9dy60nydk8dq7hdf3n9vnw6ldgp9f5mkx8gk"))))
9593 (properties `((upstream-name . "renv")))
9594 (build-system r-build-system)
9597 (home-page "https://rstudio.github.io/renv")
9598 (synopsis "Project environments")
9600 "This package provides a dependency management toolkit for R. Using
9601 renv, you can create and manage project-local R libraries, save the state of
9602 these libraries to a lockfile, and later restore your library as required.
9603 Together, these tools can help make your projects more isolated, portable, and
9605 (license license:expat)))
9607 (define-public r-learnr
9614 (uri (cran-uri "learnr" version))
9617 "1p3943hv3ybmbcyfbxidd55dripi0570pf5l51hwz9r3635cx3zs"))))
9618 (build-system r-build-system)
9619 (native-inputs (list r-knitr))
9640 (home-page "https://rstudio.github.io/learnr/")
9641 (synopsis "Interactive tutorials for R")
9643 "This package provides tools to create interactive tutorials using R
9644 Markdown. Use a combination of narrative, figures, videos, exercises, and
9645 quizzes to create self-paced tutorials for learning about R and R packages.")
9646 (license license:asl2.0)))
9648 (define-public r-analytics
9650 (name "r-analytics")
9655 (uri (cran-uri "analytics" version))
9658 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
9659 (build-system r-build-system)
9673 (home-page "https://cran.r-project.org/web/packages/analytics/")
9674 (synopsis "Collection of data analysis tools")
9676 "This package is a collection of data analysis tools. It includes tools
9677 for regression outlier detection in a fitted linear model, stationary
9678 bootstrap using a truncated geometric distribution, a comprehensive test for
9679 weak stationarity, column means by group, weighted biplots, and a heuristic to
9680 obtain a better initial configuration in non-metric MDS.")
9681 (license license:gpl2)))
9683 (define-public r-here
9690 (uri (cran-uri "here" version))
9692 (base32 "0srlr8h8qmr0wrmp7gs4g2ry5dni2hx8n947bik3s3a26f091v88"))))
9693 (properties `((upstream-name . "here")))
9694 (build-system r-build-system)
9695 (propagated-inputs (list r-rprojroot))
9696 (native-inputs (list r-knitr))
9697 (home-page "https://here.r-lib.org/")
9698 (synopsis "Simpler way to find files")
9700 "This package lets you construct paths to your project's files. Use the
9701 @code{here} function as a drop-in replacement for @code{file.path}, it will
9702 always locate the files relative to your project root.")
9703 (license license:expat)))
9705 (define-public r-reticulate
9707 (name "r-reticulate")
9712 (uri (cran-uri "reticulate" version))
9715 "1ibliic3qp597nskak2bfa6iyl721ssgcavwvfaf1c71plilimrz"))))
9716 (build-system r-build-system)
9720 '(modify-phases %standard-phases
9721 (add-after 'unpack 'build-reproducibly
9723 (setenv "PYTHONHASHSEED" "0")
9724 (setenv "PYTHONDONTWRITEBYTECODE" "1"))))))
9725 (inputs (list python))
9737 (home-page "https://github.com/rstudio/reticulate")
9738 (synopsis "R interface to Python")
9740 "This package provides an interface from R to Python modules, classes,
9741 and functions. When calling into Python, R data types are automatically
9742 converted to their equivalent Python types. When values are returned from
9743 Python to R they are converted back to R types.")
9744 (license license:asl2.0)))
9746 (define-public r-bibtex
9753 (uri (cran-uri "bibtex" version))
9756 "0rwinwj0kw2872q2whhk03ianl9lcgs6dlhqzm513wj3bgpb90gc"))))
9757 (build-system r-build-system)
9758 (propagated-inputs (list r-backports))
9759 (home-page "https://github.com/romainfrancois/bibtex")
9760 (synopsis "Bibtex parser")
9761 (description "This package provides a utility for R to parse a bibtex
9763 (license license:gpl2+)))
9765 (define-public r-billboarder
9767 (name "r-billboarder")
9772 (uri (cran-uri "billboarder" version))
9774 (base32 "189ngvg84rcwhrivxskmjv3srhadvzr4p1v8pf11axyv2qn01b0x"))
9776 '(delete-file "inst/htmlwidgets/lib/billboard/billboard.pkgd.min.js"))))
9777 (properties `((upstream-name . "billboarder")))
9778 (build-system r-build-system)
9781 (modify-phases %standard-phases
9782 (add-after 'unpack 'process-javascript
9783 (lambda* (#:key inputs #:allow-other-keys)
9784 (with-directory-excursion "inst/htmlwidgets/lib/billboard/"
9785 (let ((source (assoc-ref inputs "js-billboard"))
9786 (target "billboard.pkgd.min.js"))
9787 (format #true "Processing ~a --> ~a~%"
9789 (invoke "esbuild" source "--minify"
9790 (string-append "--outfile=" target)))))))))
9801 `(("r-knitr" ,r-knitr)
9802 ("esbuild" ,esbuild)
9803 ;; It is not ideal to use this concatenated (but not minified)
9804 ;; JavaScript file, as the original source is written in TypeScript.
9805 ;; However, this can still be considered source code as it is readable
9806 ;; and can be modified.
9810 (uri "https://unpkg.com/billboard.js@3.2.0/dist/billboard.js")
9813 "1kx5rqmn87pgal2cwmcij2rrnwa0fgcsw6y99m4i0l2sdm0qffv2"))))))
9814 (home-page "https://github.com/dreamRs/billboarder")
9815 (synopsis "Create interactive charts with the JavaScript Billboard library")
9817 "This package provides an @code{htmlwidgets} interface to billboard.js,
9818 a re-usable easy interface JavaScript chart library, based on D3 v4+. Chart
9819 types include line charts, scatterplots, bar/lollipop charts,
9820 histogram/density plots, pie/donut charts and gauge charts. All charts are
9821 interactive, and a proxy method is implemented to smoothly update a chart
9822 without rendering it again in shiny apps.")
9823 (license license:expat)))
9825 (define-public r-ggseqlogo
9827 (name "r-ggseqlogo")
9832 (uri (cran-uri "ggseqlogo" version))
9835 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
9836 (build-system r-build-system)
9837 (propagated-inputs (list r-ggplot2))
9838 (home-page "https://github.com/omarwagih/ggseqlogo")
9839 (synopsis "ggplot2 extension for drawing genetic sequence logos")
9841 "The range of functions provided by this package makes it possible to
9842 draw highly versatile genomic sequence logos. Features include, but are not
9843 limited to, modifying colour schemes and fonts used to draw the logo,
9844 generating multiple logo plots, and aiding the visualisation with annotations.
9845 Sequence logos can easily be combined with other ggplot2 plots.")
9846 ;; Unspecified version of the LGPL.
9847 (license license:lgpl3+)))
9849 (define-public r-ggsci
9856 (uri (cran-uri "ggsci" version))
9859 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
9860 (build-system r-build-system)
9862 (list r-ggplot2 r-scales))
9863 (home-page "https://nanx.me/ggsci/")
9864 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
9866 "This package provides a collection of ggplot2 color palettes inspired by
9867 plots in scientific journals, data visualization libraries, science fiction
9868 movies, and TV shows.")
9869 (license license:gpl3)))
9871 (define-public r-ggsignif
9878 (uri (cran-uri "ggsignif" version))
9881 "02mjailzyqkdnzky60dgampw2sq6mnn7s66fk0lhy32s8apm280i"))))
9882 (build-system r-build-system)
9887 (home-page "https://github.com/const-ae/ggsignif")
9888 (synopsis "Significance brackets for ggplot2")
9890 "Enrich your ggplots with group-wise comparisons. This package provides
9891 an easy way to indicate if two groups are significantly different. Commonly
9892 this is shown by a bracket on top connecting the groups of interest which
9893 itself is annotated with the level of significance. The package provides a
9894 single layer that takes the groups for comparison and the test as arguments
9895 and adds the annotation to the plot.")
9896 (license license:gpl3)))
9898 (define-public r-rstatix
9905 (uri (cran-uri "rstatix" version))
9908 "0330y8iziffqg8j9j5h9zv4qcdyf8ybhmzxrr9fzq9nc6bf1gbm5"))))
9909 (properties `((upstream-name . "rstatix")))
9910 (build-system r-build-system)
9923 (home-page "https://rpkgs.datanovia.com/rstatix/")
9924 (synopsis "Pipe-friendly framework for basic statistical tests")
9926 "This package provides a simple and intuitive pipe-friendly framework,
9927 coherent with the @code{tidyverse} design philosophy, for performing basic
9928 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
9929 correlation analyses. The output of each test is automatically transformed
9930 into a tidy data frame to facilitate visualization. Additional functions are
9931 available for reshaping, reordering, manipulating and visualizing correlation
9933 (license license:gpl2)))
9935 (define-public r-ggpubr
9942 (uri (cran-uri "ggpubr" version))
9945 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
9946 (build-system r-build-system)
9964 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
9965 (synopsis "ggplot2-based publication-ready plots")
9967 "The ggplot2 package is an excellent and flexible package for elegant
9968 data visualization in R. However the default generated plots require some
9969 formatting before we can send them for publication. The ggpubr package
9970 provides some easy-to-use functions for creating and customizing ggplot2-based
9971 publication-ready plots.")
9972 (license license:gpl2)))
9974 (define-public r-ellipse
9981 (uri (cran-uri "ellipse" version))
9984 "0im9d36dixpksms52v6nsb3l0z2c7wc25r9j0f08naj6qc8jpvq2"))))
9985 (build-system r-build-system)
9986 (home-page "https://cran.r-project.org/web/packages/ellipse/")
9987 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
9989 "This package contains various routines for drawing ellipses and
9990 ellipse-like confidence regions, implementing the plots described in Murdoch
9991 and Chow (1996), A graphical display of large correlation matrices, The
9992 American Statistician 50, 178-180. There are also routines implementing the
9993 profile plots described in Bates and Watts (1988), Nonlinear Regression
9994 Analysis and its Applications.")
9995 (license license:gpl2+)))
9997 (define-public r-flashclust
9999 (name "r-flashclust")
10004 (uri (cran-uri "flashClust" version))
10007 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
10008 (properties `((upstream-name . "flashClust")))
10009 (build-system r-build-system)
10010 (native-inputs (list gfortran))
10011 (home-page "https://cran.r-project.org/web/packages/flashClust/")
10012 (synopsis "Implementation of optimal hierarchical clustering")
10014 "This package provides a fast implementation of hierarchical
10016 (license license:gpl2+)))
10018 (define-public r-factominer
10020 (name "r-factominer")
10025 (uri (cran-uri "FactoMineR" version))
10028 "0xcg4vjs5v9k28hhxhkfkks7nvpxpp2cvim00kh67f4pq041c9l1"))))
10029 (properties `((upstream-name . "FactoMineR")))
10030 (build-system r-build-system)
10047 (home-page "http://factominer.free.fr")
10048 (synopsis "Multivariate exploratory data analysis and data mining")
10050 "This package provides exploratory data analysis methods to summarize,
10051 visualize and describe datasets. The main principal component methods are
10052 available, those with the largest potential in terms of applications:
10053 principal component analysis (PCA) when variables are quantitative,
10054 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
10055 variables are categorical, Multiple Factor Analysis when variables are
10056 structured in groups, etc. and hierarchical cluster analysis.")
10057 (license license:gpl2+)))
10059 (define-public r-factoextra
10061 (name "r-factoextra")
10066 (uri (cran-uri "factoextra" version))
10069 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
10070 (build-system r-build-system)
10081 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
10082 (synopsis "Extract and visualize the results of multivariate data analyses")
10084 "This package provides some easy-to-use functions to extract and
10085 visualize the output of multivariate data analyses, including
10086 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
10087 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
10088 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
10089 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
10090 packages. It contains also functions for simplifying some clustering analysis
10091 steps and provides ggplot2-based elegant data visualization.")
10092 (license license:gpl2)))
10094 (define-public r-fansi
10101 (uri (cran-uri "fansi" version))
10104 "0sn0kflgcn2qrrv646pzqylm02cx8l5ws473ppmvla4xihyvi9w6"))))
10105 (build-system r-build-system)
10107 (list r-knitr)) ; for vignettes
10108 (home-page "https://github.com/brodieG/fansi")
10109 (synopsis "ANSI control sequence aware string functions")
10111 "This package provides counterparts to R string manipulation functions
10112 that account for the effects of ANSI text formatting control sequences.")
10113 (license license:gpl2+)))
10115 (define-public r-nbclust
10122 (uri (cran-uri "NbClust" version))
10125 "0k5hr4zgx4gp1n62xchgz2zvyl35ba2cnczhhvj8rfbg2n4hx6qs"))))
10126 (properties `((upstream-name . "NbClust")))
10127 (build-system r-build-system)
10128 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
10129 (synopsis "Determine the best number of clusters in a data set")
10131 "NbClust provides 30 indexes for determining the optimal number of
10132 clusters in a data set and offers the best clustering scheme from different
10133 results to the user.")
10134 (license license:gpl2)))
10136 (define-public r-hdf5r
10143 (uri (cran-uri "hdf5r" version))
10146 "0nr9iywl2z7hrydvq5z61jvx6ls8wg72lzpr875p1jfi7s2052kf"))))
10147 (build-system r-build-system)
10151 (list r-bit64 r-r6))
10154 (home-page "https://hhoeflin.github.io/hdf5r")
10155 (synopsis "Interface to the HDF5 binary data format")
10157 "HDF5 is a data model, library and file format for storing and managing
10158 large amounts of data. This package provides a nearly feature complete,
10159 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
10160 functionality is added so that HDF5 objects behave very similar to their
10161 corresponding R counterparts.")
10162 (license license:asl2.0)))
10164 (define-public r-itertools
10166 (name "r-itertools")
10171 (uri (cran-uri "itertools" version))
10174 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
10175 (build-system r-build-system)
10177 (list r-iterators))
10178 (home-page "https://cran.r-project.org/web/packages/itertools/")
10179 (synopsis "Iterator tools")
10181 "This package provides various tools for creating iterators, many
10182 patterned after functions in the Python @code{itertools} module, and others
10183 patterned after functions in the snow package.")
10184 (license license:gpl2)))
10186 (define-public r-itsadug
10193 (uri (cran-uri "itsadug" version))
10195 (base32 "1sdqs279qxr3993hw08xg7b54yq03jw1597cqn6cf24sh9vpw9m1"))))
10196 (properties `((upstream-name . "itsadug")))
10197 (build-system r-build-system)
10198 (propagated-inputs (list r-mgcv r-plotfunctions))
10199 (native-inputs (list r-knitr))
10200 (home-page "https://cran.r-project.org/package=itsadug")
10201 (synopsis "Interpreting time series and autocorrelated data using GAMMs")
10203 "@dfn{Generalized Additive Mixed Modeling} (GAMM; Lin & Zhang, 1999) as
10204 implemented in the R package @code{mgcv} is a nonlinear regression analysis
10205 which is particularly useful for time course data such as EEG, pupil dilation,
10206 gaze data (eye tracking), and articulography recordings, but also for
10207 behavioral data such as reaction times and response data. As time course
10208 measures are sensitive to autocorrelation problems, GAMMs implements methods
10209 to reduce the autocorrelation problems. This package includes functions for
10210 the evaluation of GAMM models (e.g., model comparisons, determining regions of
10211 significance, inspection of autocorrelational structure in residuals) and
10212 interpreting of GAMMs (e.g., visualization of complex interactions, and
10214 (license license:gpl2+)))
10216 (define-public r-polynom
10223 (uri (cran-uri "polynom" version))
10226 "0y4j07syjwpnq5w6a1d90z6h1hjzijmm42pq0f8jk2vcn5xxn7mw"))))
10227 (build-system r-build-system)
10228 (native-inputs (list r-knitr))
10229 (home-page "https://cran.r-project.org/web/packages/polynom/")
10230 (synopsis "Functions for univariate polynomial manipulations")
10232 "This package provides a collection of functions to implement a class for
10233 univariate polynomial manipulations.")
10234 (license license:gpl2)))
10236 (define-public r-pupillometryr
10238 (name "r-pupillometryr")
10243 (uri (cran-uri "PupillometryR" version))
10245 (base32 "0yk30sgl2qqa6pva649swq523vh446ifmydildycfvfmlm1h4qza"))))
10246 (properties `((upstream-name . "PupillometryR")))
10247 (build-system r-build-system)
10260 (native-inputs (list r-knitr))
10261 (home-page "https://cran.r-project.org/package=PupillometryR")
10262 (synopsis "Unified pipeline for pupillometry data")
10264 "This package provides a unified pipeline to clean, prepare, plot, and
10265 run basic analyses on pupillometry experiments.")
10266 (license license:expat)))
10268 (define-public r-gbrd
10275 (uri (cran-uri "gbRd" version))
10278 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
10279 (properties `((upstream-name . "gbRd")))
10280 (build-system r-build-system)
10281 (home-page "https://cran.r-project.org/web/packages/gbRd/")
10282 (synopsis "Utilities for processing Rd objects and files")
10284 "This package provides utilities for processing Rd objects and files.
10285 Extract argument descriptions and other parts of the help pages of
10287 (license license:gpl2+)))
10289 (define-public r-rjags
10296 (uri (cran-uri "rjags" version))
10299 "0cibz6xhmh86fh7ynmdgpmlchizi57pi6dpslgc2if17a56c6p7q"))))
10300 (build-system r-build-system)
10307 (home-page "http://mcmc-jags.sourceforge.net")
10308 (synopsis "Bayesian graphical models using MCMC")
10310 "This package provides an R interface to the JAGS MCMC library. JAGS is
10311 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
10312 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
10313 (license license:gpl2)))
10315 (define-public r-rbibutils
10317 (name "r-rbibutils")
10322 (uri (cran-uri "rbibutils" version))
10325 "11pzbqykmn7m9gp5jspfcj6vij865wqf9ry6m3jkihvfj7zhfb5j"))))
10326 (properties `((upstream-name . "rbibutils")))
10327 (build-system r-build-system)
10328 (home-page "https://geobosh.github.io/rbibutils/")
10329 (synopsis "Convert between bibliography formats")
10331 "This package converts between a number of bibliography formats,
10332 including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils
10333 utilities and supports all bibliography formats and character encodings
10334 implemented in bibutils.")
10335 (license license:gpl2)))
10337 (define-public r-rdpack
10344 (uri (cran-uri "Rdpack" version))
10347 "109mylzmlncq5a09ayy4g2g0frj1k843lj8j78gvmz1h5g8sslkn"))))
10348 (properties `((upstream-name . "Rdpack")))
10349 (build-system r-build-system)
10351 (list r-rbibutils))
10352 (home-page "https://github.com/GeoBosh/Rdpack")
10353 (synopsis "Update and manipulate Rd documentation objects")
10355 "This package provides functions for manipulation of R documentation
10356 objects, including functions @code{reprompt()} and @code{ereprompt()} for
10357 updating Rd documentation for functions, methods and classes; it also includes
10358 Rd macros for citations and import of references from bibtex files for use in
10359 Rd files and roxygen2 comments, as well as many functions for manipulation of
10360 references and Rd files.")
10361 (license license:gpl2+)))
10363 (define-public r-officer
10370 (uri (cran-uri "officer" version))
10373 "1h6fcqw4bg644lwr5jggphyxp2d0ycya9q869z8099a50gc6h03f"))))
10374 (build-system r-build-system)
10376 (list r-r6 r-uuid r-xml2 r-zip))
10377 (home-page "https://davidgohel.github.io/officer")
10378 (synopsis "Manipulation of Word and PowerPoint documents")
10380 "This package provides tools to access and manipulate Word and PowerPoint
10381 documents from R. The package focuses on tabular and graphical reporting from
10382 R; it also provides two functions that let users get document content into
10383 data objects. A set of functions lets add and remove images, tables and
10384 paragraphs of text in new or existing documents. When working with PowerPoint
10385 presentations, slides can be added or removed; shapes inside slides can also
10386 be added or removed. When working with Word documents, a cursor can be used
10387 to help insert or delete content at a specific location in the document.")
10388 (license license:gpl3)))
10390 (define-public r-profilemodel
10392 (name "r-profilemodel")
10397 (uri (cran-uri "profileModel" version))
10400 "01m5nb8cmq0aq555pxk2a99182si65hhmn68yn9nal2j3zl2bp4i"))))
10401 (properties `((upstream-name . "profileModel")))
10402 (build-system r-build-system)
10403 (home-page "https://github.com/ikosmidis/profileModel")
10404 (synopsis "Profiling inference functions for various model classes")
10406 "This package provides tools that can be used to calculate, evaluate,
10407 plot and use for inference the profiles of *arbitrary* inference functions for
10408 arbitrary @code{glm}-like fitted models with linear predictors. More information
10409 on the methods that are implemented can be found in Kosmidis (2008)
10410 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
10411 (license license:gpl2+)))
10413 (define-public r-brglm
10420 (uri (cran-uri "brglm" version))
10423 "08shcz0j1npdn7xkhsvlzs3z4rdwq3g4rk6a4xx8wirqw8n8s2an"))))
10424 (properties `((upstream-name . "brglm")))
10425 (build-system r-build-system)
10427 (list r-profilemodel))
10428 (home-page "https://github.com/ikosmidis/brglm")
10429 (synopsis "Bias reduction in binomial-response generalized linear models")
10431 "Fit generalized linear models with binomial responses using either an
10432 adjusted-score approach to bias reduction or maximum penalized likelihood
10433 where penalization is by Jeffreys invariant prior. These procedures return
10434 estimates with improved frequentist properties (bias, mean squared error) that
10435 are always finite even in cases where the maximum likelihood estimates are
10436 infinite (data separation). Fitting takes place by fitting generalized linear
10437 models on iteratively updated pseudo-data. The interface is essentially the
10438 same as @code{glm}. More flexibility is provided by the fact that custom
10439 pseudo-data representations can be specified and used for model fitting.
10440 Functions are provided for the construction of confidence intervals for the
10441 reduced-bias estimates.")
10442 (license license:gpl2+)))
10444 (define-public r-entropy
10451 (uri (cran-uri "entropy" version))
10454 "1f0j8jsn6pzf4gi5g0akixx6x5vc69ci5f4m2vnwp40frvsqjnkg"))))
10455 (properties `((upstream-name . "entropy")))
10456 (build-system r-build-system)
10457 (home-page "https://www.strimmerlab.org/software/entropy/")
10458 (synopsis "Estimation of entropy, mutual information and related quantities")
10460 "This package implements various estimators of entropy, such as the
10461 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
10462 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
10463 estimator. It also offers an R interface to the NSB estimator. Furthermore,
10464 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
10465 mutual information, and chi-squared statistic of independence. In addition
10466 there are functions for discretizing continuous random variables.")
10467 (license license:gpl3+)))
10469 (define-public r-acd
10476 (uri (cran-uri "ACD" version))
10479 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
10480 (properties `((upstream-name . "ACD")))
10481 (build-system r-build-system)
10482 (home-page "https://cran.r-project.org/web/packages/ACD/")
10483 (synopsis "Categorical data analysis with complete or missing responses")
10485 "This package provides tools for categorical data analysis with complete
10486 or missing responses.")
10487 (license license:gpl2+)))
10489 (define-public r-acdm
10492 (version "1.0.4.1")
10496 (uri (cran-uri "ACDm" version))
10499 "129ykw0j8z30mr4c01qzx6qy6h4bl87zxvmps0vkh8cqb7akninq"))))
10500 (properties `((upstream-name . "ACDm")))
10501 (build-system r-build-system)
10503 (list r-dplyr r-ggplot2 r-plyr r-rsolnp r-zoo))
10504 (home-page "https://cran.r-project.org/web/packages/ACDm/")
10505 (synopsis "Tools for Autoregressive Conditional Duration Models")
10507 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
10508 and Russell, 1998) models. It creates trade, price or volume durations from
10509 transactions (tic) data, performs diurnal adjustments, fits various ACD models
10511 (license license:gpl2+)))
10513 (define-public r-overlap
10520 (uri (cran-uri "overlap" version))
10523 "1arxprhz035ab78ks88n6scwnlwmnb97mlac5gsx90ipb6gkgcyk"))))
10524 (build-system r-build-system)
10525 (home-page "https://cran.r-project.org/web/packages/overlap/")
10526 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
10528 "This package provides functions to fit kernel density functions to data
10529 on temporal activity patterns of animals; estimate coefficients of overlapping
10530 of densities for two species; and calculate bootstrap estimates of confidence
10532 (license license:gpl3+)))
10534 (define-public r-snakecase
10536 (name "r-snakecase")
10541 (uri (cran-uri "snakecase" version))
10544 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
10545 (build-system r-build-system)
10547 (list r-stringi r-stringr))
10548 (home-page "https://github.com/Tazinho/snakecase")
10549 (synopsis "Convert strings into any case")
10551 "This package provides a consistent, flexible and easy to use tool to
10552 parse and convert strings into cases like snake or camel among others.")
10553 (license license:gpl3)))
10555 (define-public r-prediction
10557 (name "r-prediction")
10562 (uri (cran-uri "prediction" version))
10565 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
10566 (build-system r-build-system)
10568 (list r-data-table))
10569 (home-page "https://github.com/leeper/prediction")
10570 (synopsis "Tidy, type-safe prediction methods")
10572 "This package provides the @code{prediction()} function, a type-safe
10573 alternative to @code{predict()} that always returns a data frame. The package
10574 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
10575 from the @code{stats} package, as well as numerous other model classes from
10576 other add-on packages.")
10577 (license license:expat)))
10579 (define-public r-prettygraphs
10581 (name "r-prettygraphs")
10585 (uri (cran-uri "prettyGraphs" version))
10588 "0yjpwxdy9mkj2k33zvd5klyv4ava46i19yls87n0bvf79y90ikpy"))))
10589 (properties `((upstream-name . "prettyGraphs")))
10590 (build-system r-build-system)
10591 (home-page "https://cran.r-project.org/package=prettyGraphs")
10592 (synopsis "Publication-quality graphics")
10594 "This package provides simple and crisp publication-quality graphics for
10595 the ExPosition family of packages. See An ExPosition of the Singular Value
10596 Decomposition in R (Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>.")
10597 (license license:gpl2)))
10599 (define-public r-insight
10606 (uri (cran-uri "insight" version))
10609 "1bhwfx75lnjrvn6byl2dn8fzfh2in2msghxwyy9jwpvnxk4c63db"))))
10610 (build-system r-build-system)
10613 (home-page "https://easystats.github.io/insight/")
10614 (synopsis "Easy access to model information for various model objects")
10616 "This package provides a tool to provide an easy, intuitive and
10617 consistent access to information contained in various R models, like model
10618 formulas, model terms, information about random effects, data that was used to
10619 fit the model or data from response variables. The package mainly revolves
10620 around two types of functions: Functions that find (the names of) information,
10621 starting with @code{find_}, and functions that get the underlying data,
10622 starting with @code{get_}. The package has a consistent syntax and works with
10623 many different model objects, where otherwise functions to access these
10624 information are missing.")
10625 (license license:gpl3)))
10627 (define-public r-sjlabelled
10629 (name "r-sjlabelled")
10634 (uri (cran-uri "sjlabelled" version))
10637 "1va86q5wddyvqgdpy8d0an2c7v1qbb4hpn0ai6y1v5v1ff87w73k"))))
10638 (build-system r-build-system)
10640 (list r-datawizard r-insight))
10643 (home-page "https://github.com/strengejacke/sjlabelled")
10644 (synopsis "Labelled data utility functions")
10646 "This package provides a collection of functions dealing with labelled
10647 data, like reading and writing data between R and other statistical software
10648 packages. This includes easy ways to get, set or change value and variable
10649 label attributes, to convert labelled vectors into factors or numeric (and
10650 vice versa), or to deal with multiple declared missing values.")
10651 (license license:gpl3)))
10653 (define-public r-sjmisc
10660 (uri (cran-uri "sjmisc" version))
10663 "1gzkq95ckxr0vhrzggflzli9hs7zr8c0yym9zn1wf74yrr0mgc3q"))))
10664 (build-system r-build-system)
10675 (home-page "https://github.com/strengejacke/sjmisc")
10676 (synopsis "Data and variable transformation functions")
10678 "This package is a collection of miscellaneous utility functions,
10679 supporting data transformation tasks like recoding, dichotomizing or grouping
10680 variables, setting and replacing missing values. The data transformation
10681 functions also support labelled data, and all integrate seamlessly into a
10682 tidyverse workflow.")
10683 (license license:gpl3)))
10685 (define-public r-nortest
10692 (uri (cran-uri "nortest" version))
10695 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
10696 (build-system r-build-system)
10697 (home-page "https://cran.r-project.org/web/packages/nortest/")
10698 (synopsis "Tests for normality")
10700 "This package provides five omnibus tests for testing the composite
10701 hypothesis of normality.")
10702 (license license:gpl2+)))
10704 (define-public r-moonbook
10706 (name "r-moonbook")
10711 (uri (cran-uri "moonBook" version))
10714 "1ml4vvm0mvrprpyi0l50aw38brx18bk2qny4gybmkvlbakalz9bx"))))
10715 (properties `((upstream-name . "moonBook")))
10716 (build-system r-build-system)
10726 (home-page "https://github.com/cardiomoon/moonBook")
10727 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
10729 "This package provides several analysis-related functions for the book
10730 entitled \"R statistics and graph for medical articles\" (written in Korean),
10731 version 1, by Keon-Woong Moon with Korean demographic data with several plot
10733 (license license:gpl2)))
10735 (define-public r-flextable
10737 (name "r-flextable")
10742 (uri (cran-uri "flextable" version))
10745 "054rkx98qhwp8i4fj9jkv5297sc4g193wfs6b537q62iyqmcjlx3"))))
10746 (build-system r-build-system)
10760 (home-page "https://davidgohel.github.io/flextable")
10761 (synopsis "Functions for tabular reporting")
10763 "This package provides tools to create pretty tables for HTML documents
10764 and other formats. Functions are provided to let users create tables, modify
10765 and format their content. It extends the @code{officer} package and can be
10766 used within R markdown documents when rendering to HTML and to Word
10768 (license license:gpl3)))
10770 (define-public r-writexl
10777 (uri (cran-uri "writexl" version))
10780 "1qhf7p14mijdyl5i40gfpzgvdflcs6s8xnwrabsnjxpa17xbamkn"))))
10781 (build-system r-build-system)
10782 (inputs (list zlib))
10783 (home-page "https://github.com/ropensci/writexl")
10784 (synopsis "Export data frames to xlsx format")
10786 "This package provides a data frame to xlsx exporter based on
10788 (license license:bsd-2)))
10790 (define-public r-biasedurn
10792 (name "r-biasedurn")
10797 (uri (cran-uri "BiasedUrn" version))
10800 "0mmq8zf52p6y76nqm0fcvvg8bdlrfl12mlfr9fznz9zvm26pypi0"))))
10801 (properties `((upstream-name . "BiasedUrn")))
10802 (build-system r-build-system)
10803 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
10804 (synopsis "Biased Urn model distributions")
10806 "This package provides statistical models of biased sampling in the form
10807 of univariate and multivariate noncentral hypergeometric distributions,
10808 including Wallenius' noncentral hypergeometric distribution and Fisher's
10809 noncentral hypergeometric distribution (also called extended hypergeometric
10811 (license license:gpl3)))
10813 (define-public r-goplot
10820 (uri (cran-uri "GOplot" version))
10823 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
10824 (properties `((upstream-name . "GOplot")))
10825 (build-system r-build-system)
10827 (list r-ggdendro r-ggplot2 r-gridextra r-rcolorbrewer))
10828 (home-page "https://github.com/wencke/wencke.github.io")
10829 (synopsis "Visualization of functional analysis data")
10831 "This package provides an implementation of multilayered visualizations
10832 for enhanced graphical representation of functional analysis data. It
10833 combines and integrates omics data derived from expression and functional
10834 annotation enrichment analyses. Its plotting functions have been developed
10835 with an hierarchical structure in mind: starting from a general overview to
10836 identify the most enriched categories (modified bar plot, bubble plot) to a
10837 more detailed one displaying different types of relevant information for the
10838 molecules in a given set of categories (circle plot, chord plot, cluster plot,
10839 Venn diagram, heatmap).")
10840 (license license:gpl2)))
10842 (define-public r-getopt
10849 (uri (cran-uri "getopt" version))
10852 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
10853 (build-system r-build-system)
10854 (home-page "https://github.com/trevorld/getopt")
10855 (synopsis "Command-line option processor for R")
10857 "This package is designed to be used with Rscript to write shebang
10858 scripts that accept short and long options. Many users will prefer to
10859 use the packages @code{optparse} or @code{argparse} which add extra
10860 features like automatically generated help options and usage texts,
10861 support for default values, positional argument support, etc.")
10862 (license license:gpl2+)))
10864 (define-public r-findpython
10866 (name "r-findpython")
10871 (uri (cran-uri "findpython" version))
10874 "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar"))))
10875 (build-system r-build-system)
10876 (home-page "https://github.com/trevorld/findpython")
10877 (synopsis "Functions to find an acceptable Python binary")
10879 "This package was designed to find an acceptable Python binary that
10880 matches version and feature constraints.")
10881 (license license:expat)))
10883 ;; This in not the same as "r-argparser"
10884 (define-public r-argparse
10886 (name "r-argparse")
10891 (uri (cran-uri "argparse" version))
10894 "14p57nm0w3siqd473snzhpmnvsgl72x92pdcd64vhy2qg6nzmmra"))))
10895 (build-system r-build-system)
10896 (inputs (list python))
10898 (list r-findpython r-jsonlite r-r6))
10901 (home-page "https://github.com/trevorld/argparse")
10902 (synopsis "Command line optional and positional argument parser")
10904 "This package provides a command line parser to be used with Rscript to
10905 write shebang scripts that gracefully accept positional and optional arguments
10906 and automatically generate usage notices.")
10907 (license license:gpl2+)))
10909 (define-public r-hash
10912 (version "2.2.6.2")
10916 (uri (cran-uri "hash" version))
10919 "17scs675a86c34hjbxmwi8kny4yyv97x3515s449zafj2i0ad8vm"))))
10920 (build-system r-build-system)
10921 (home-page "https://cran.r-project.org/web/packages/hash/")
10922 (synopsis "Implementation of hash/associated arrays/dictionaries")
10924 "This package implements a data structure similar to hashes in Perl and
10925 dictionaries in Python but with a purposefully R flavor. For objects of
10926 appreciable size, access using hashes outperforms native named lists and
10928 (license license:gpl2+)))
10930 (define-public r-orddom
10937 (uri (cran-uri "orddom" version))
10940 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
10941 (build-system r-build-system)
10942 (propagated-inputs (list r-psych))
10943 (home-page "https://cran.r-project.org/web/packages/orddom/")
10944 (synopsis "Ordinal dominance statistics")
10946 "This package provides tools to compute ordinal, statistics and effect
10947 sizes as an alternative to mean comparison: Cliff's delta or success rate
10948 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
10949 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
10950 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
10951 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
10952 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
10953 Group (Non-)Overlap considerations.")
10954 (license license:gpl2)))
10956 (define-public r-deriv
10963 (uri (cran-uri "Deriv" version))
10966 "130g3mv0z9sqs6y23a0a94512iiw05yr6fp378vhdxxbignzbnyv"))))
10967 (properties `((upstream-name . "Deriv")))
10968 (build-system r-build-system)
10969 (home-page "https://cran.r-project.org/web/packages/Deriv")
10970 (synopsis "Symbolic differentiation")
10972 "This package provides an R-based solution for symbolic differentiation.
10973 It admits user-defined functions as well as function substitution in arguments
10974 of functions to be differentiated. Some symbolic simplification is part of
10976 (license license:gpl3+)))
10978 (define-public r-doby
10985 (uri (cran-uri "doBy" version))
10988 "1ps6r7yxs0a6rpfi2yzrb9j41862za3gdl1aq9vw3j5cmgrk8w1n"))))
10989 (properties `((upstream-name . "doBy")))
10990 (build-system r-build-system)
11004 (home-page "https://people.math.aau.dk/~sorenh/software/doBy/")
11005 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
11007 "This package contains:
11010 @item facilities for working with grouped data: @code{do}
11011 something to data stratified @code{by} some variables.
11012 @item implementations of least-squares means, general linear contrasts, and
11013 @item miscellaneous other utilities.
11015 (license license:gpl2+)))
11017 (define-public r-refgenome
11019 (name "r-refgenome")
11024 (uri (cran-uri "refGenome" version))
11027 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
11028 (properties `((upstream-name . "refGenome")))
11029 (build-system r-build-system)
11031 (list r-dbi r-doby r-rsqlite))
11032 (home-page "https://cran.r-project.org/web/packages/refGenome/")
11034 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
11036 "This package contains functionality for importing and managing of
11037 downloaded genome annotation data from the Ensembl genome browser (European
11038 Bioinformatics Institute) and from the UCSC genome browser (University of
11039 California, Santa Cruz) and annotation routines for genomic positions and
11040 splice site positions.")
11041 (license license:gpl2)))
11043 (define-public r-basix
11050 (uri (cran-uri "BASIX" version))
11053 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
11054 (properties `((upstream-name . "BASIX")))
11055 (build-system r-build-system)
11056 (home-page "https://cran.r-project.org/web/packages/BASIX/")
11057 (synopsis "Efficient C/C++ toolset for R")
11059 "BASIX provides some efficient C/C++ implementations of native R
11060 procedures to speed up calculations in R.")
11061 (license license:gpl2)))
11063 (define-public r-blockfest
11065 (name "r-blockfest")
11070 (uri (cran-uri "BlockFeST" version))
11073 "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65"))))
11074 (properties `((upstream-name . "BlockFeST")))
11075 (build-system r-build-system)
11076 (propagated-inputs (list r-basix))
11077 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
11078 (synopsis "Bayesian calculation of region-specific fixation index")
11080 "This package provides an R implementation of an extension of the
11081 BayeScan software for codominant markers, adding the option to group
11082 individual SNPs into pre-defined blocks. A typical application of this new
11083 approach is the identification of genomic regions, genes, or gene sets
11084 containing one or more SNPs that evolved under directional selection.")
11085 (license license:gpl2)))
11087 (define-public r-proc
11094 (uri (cran-uri "pROC" version))
11097 "1abvbzdss12n64pp9vlgnn0q3abh0nj4n0a8cinwwvhphjrm9vym"))))
11098 (properties `((upstream-name . "pROC")))
11099 (build-system r-build-system)
11101 (list r-plyr r-rcpp))
11102 (home-page "https://web.expasy.org/pROC/")
11103 (synopsis "Display and analyze ROC curves")
11105 "This package provides tools for visualizing, smoothing and comparing
11106 receiver operating characteristic (ROC curves). The area under the
11107 curve (AUC) can be compared with statistical tests based on U-statistics or
11108 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
11109 (license license:gpl3+)))
11111 (define-public r-rootsolve
11113 (name "r-rootsolve")
11114 (version "1.8.2.3")
11118 (uri (cran-uri "rootSolve" version))
11121 "182bb727sgqi5f3pzmw8jnn328wdjrgj9lfvg49gv8s22rjd3cxm"))))
11122 (properties `((upstream-name . "rootSolve")))
11123 (build-system r-build-system)
11124 (native-inputs (list gfortran))
11125 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
11126 (synopsis "Tools for the analysis of ordinary differential equations")
11128 "This package provides routines to find the root of nonlinear functions,
11129 and to perform steady-state and equilibrium analysis of @dfn{ordinary
11130 differential equations} (ODE). It includes routines that:
11133 @item generate gradient and jacobian matrices (full and banded),
11134 @item find roots of non-linear equations by the Newton-Raphson method,
11135 @item estimate steady-state conditions of a system of (differential) equations
11136 in full, banded or sparse form, using the Newton-Raphson method, or by
11137 dynamically running,
11138 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
11139 and 3-D partial differential equations, that have been converted to ordinary
11140 differential equations by numerical differencing (using the method-of-lines
11143 (license license:gpl2+)))
11145 (define-public r-abcanalysis
11147 (name "r-abcanalysis")
11152 (uri (cran-uri "ABCanalysis" version))
11154 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
11155 (properties `((upstream-name . "ABCanalysis")))
11156 (build-system r-build-system)
11157 (propagated-inputs (list r-plotrix))
11158 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
11159 (synopsis "Computed ABC Analysis")
11161 "Multivariate data sets often differ in several factors or derived statistical
11162 parameters, which have to be selected for a valid interpretation. Basing this
11163 selection on traditional statistical limits leads occasionally to the perception
11164 of losing information from a data set. This package provides tools to calculate
11165 these limits on the basis of the mathematical properties of the distribution of
11166 the analyzed items.")
11167 (license license:gpl3)))
11169 (define-public r-slam
11176 (uri (cran-uri "slam" version))
11178 (base32 "1ggqcf8l1z2hpi7qy4mg0d2ps48bjjb8z1y1xz6fq162cqrbz6bq"))))
11179 (build-system r-build-system)
11180 (home-page "https://cran.r-project.org/web/packages/slam/")
11181 (synopsis "Sparse lightweight arrays and matrices")
11183 "This package contains data structures and algorithms for sparse arrays and matrices,
11184 based on index arrays and simple triplet representations, respectively.")
11185 (license license:gpl2)))
11187 (define-public r-manipulatewidget
11189 (name "r-manipulatewidget")
11194 (uri (cran-uri "manipulateWidget" version))
11196 (base32 "1dpgzmiv08afm57yxr017b014lfn9h3pa4w65prk5k3dgn6p4wsv"))))
11198 `((upstream-name . "manipulateWidget")))
11199 (build-system r-build-system)
11212 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
11213 (synopsis "Add even more interactivity to interactive charts")
11215 "This package lets you create in just a few lines of R code a nice user interface to
11216 modify the data or the graphical parameters of one or multiple interactive
11217 charts. It is useful to quickly explore visually some data or for package
11218 developers to generate user interfaces easy to maintain.")
11219 (license license:gpl2+)))
11221 (define-public r-a3
11228 (uri (cran-uri "A3" version))
11230 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
11231 (properties `((upstream-name . "A3")))
11232 (build-system r-build-system)
11234 (list r-pbapply r-xtable))
11235 (home-page "https://cran.r-project.org/web/packages/A3/")
11236 (synopsis "Error metrics for predictive models")
11238 "This package supplies tools for tabulating and analyzing the results of predictive
11239 models. The methods employed are applicable to virtually any predictive model
11240 and make comparisons between different methodologies straightforward.")
11241 (license license:gpl2+)))
11243 (define-public r-infotheo
11245 (name "r-infotheo")
11246 (version "1.2.0.1")
11250 (uri (cran-uri "infotheo" version))
11253 "1m1979vf8rvq3534mp1hihfadikhxrg3p6ac3hirz96kgb4qxyy0"))))
11254 (build-system r-build-system)
11255 (home-page "http://homepage.meyerp.com/software")
11256 (synopsis "Information-theoretic measures")
11258 "This package implements various measures of information theory based on
11259 several entropy estimators.")
11260 (license license:gpl3+)))
11262 (define-public r-nsprcomp
11264 (name "r-nsprcomp")
11265 (version "0.5.1-2")
11269 (uri (cran-uri "nsprcomp" version))
11272 "1zlc1ximx96f235c0l8qfs6vbp1kpnbf943wxsfahnnlnxvwi59f"))))
11273 (properties `((upstream-name . "nsprcomp")))
11274 (build-system r-build-system)
11275 (home-page "https://sigg-iten.ch/research/")
11276 (synopsis "Non-negative and sparse PCA")
11278 "This package implements two methods for performing a constrained
11279 principal component analysis (PCA), where non-negativity and/or sparsity
11280 constraints are enforced on the principal axes (PAs). The function
11281 @code{nsprcomp} computes one principal component (PC) after the other. Each
11282 PA is optimized such that the corresponding PC has maximum additional variance
11283 not explained by the previous components. In contrast, the function
11284 @code{nscumcomp} jointly computes all PCs such that the cumulative variance is
11285 maximal. Both functions have the same interface as the @code{prcomp} function
11286 from the @code{stats} package (plus some extra parameters).")
11287 (license license:gpl2+)))
11289 (define-public r-cmplot
11296 (uri (cran-uri "CMplot" version))
11299 "1icb7r8wj7x9vgcysr9qi28nvgxb9j3dhqw090smpp6d7b39zrjd"))))
11300 (properties `((upstream-name . "CMplot")))
11301 (build-system r-build-system)
11302 (home-page "https://github.com/YinLiLin/CMplot")
11303 (synopsis "Circle Manhattan plot")
11305 "Circle Manhattan Plot is an R package that can lay out genome-wide
11306 association study P-value results in both traditional rectangular patterns,
11307 QQ-plot and novel circular ones. United in only one bull's eye style plot,
11308 association results from multiple traits can be compared interactively,
11309 thereby to reveal both similarities and differences between signals.
11310 Additional functions include: highlight signals, a group of SNPs, chromosome
11311 visualization and candidate genes around SNPs.")
11312 (license license:gpl2+)))
11314 (define-public r-precrec
11321 (uri (cran-uri "precrec" version))
11324 "1dfz2rqx2ww2l5r40ahg0qdj3rjrwiwh427mw7j5ynhpcj21j2qm"))))
11325 (properties `((upstream-name . "precrec")))
11326 (build-system r-build-system)
11334 (native-inputs (list r-knitr))
11335 (home-page "https://evalclass.github.io/precrec/")
11336 (synopsis "Calculate accurate precision-recall and ROC curves")
11338 "This package provides tools for accurate calculations and visualization
11339 of precision-recall and ROC (Receiver Operator Characteristics) curves.")
11340 (license license:gpl3)))
11342 (define-public r-netrep
11349 (uri (cran-uri "NetRep" version))
11352 "1swlb2k9bc7whvslxbklz864j9ynvna73hvq5rhv61cv5vy05ksd"))))
11353 (properties `((upstream-name . "NetRep")))
11354 (build-system r-build-system)
11364 (native-inputs (list r-knitr))
11365 (home-page "https://cran.r-project.org/package=NetRep")
11366 (synopsis "Permutation testing network module preservation across datasets")
11368 "This package provides functions for assessing the
11369 replication/preservation of a network module's topology across datasets
11370 through permutation testing.")
11371 (license license:gpl2)))
11373 (define-public r-intergraph
11375 (name "r-intergraph")
11380 (uri (cran-uri "intergraph" version))
11383 "18a7xgb2rp0w9jl2rkh8nzyjprrs5w7h2iidvc8c38bzx3qpggkc"))))
11384 (properties `((upstream-name . "intergraph")))
11385 (build-system r-build-system)
11387 (list r-igraph r-network))
11390 (home-page "http://mbojan.github.io/intergraph")
11391 (synopsis "Coercion routines for network data objects")
11393 "Functions implemented in this package allow coercing (i.e. convert)
11394 network data between classes provided by other R packages. Currently
11395 supported classes are those defined in packages @code{network} and
11397 (license license:gpl3)))
11399 (define-public r-interp
11405 (uri (cran-uri "interp" version))
11408 "0gzsnlg8f7knb100n6vv6307c3v2jd8f9qzrq62jkc6g71mn0kmp"))))
11409 (properties `((upstream-name . "interp")))
11410 (build-system r-build-system)
11411 (propagated-inputs (list r-deldir r-rcpp r-rcppeigen))
11412 (native-inputs (list gfortran))
11413 (home-page "https://cran.r-project.org/package=interp")
11414 (synopsis "Interpolation methods")
11416 "Bivariate data interpolation on regular and irregular grids, either
11417 linear or using splines are the main part of this package. It is intended to
11418 provide replacement functions for the ACM licensed @code{akima::interp} and
11419 @code{tripack::tri.mesh} functions.")
11420 (license license:gpl2+)))
11422 (define-public r-abcoptim
11424 (name "r-abcoptim")
11429 (uri (cran-uri "ABCoptim" version))
11431 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
11432 (properties `((upstream-name . "ABCoptim")))
11433 (build-system r-build-system)
11434 (propagated-inputs (list r-rcpp))
11435 (home-page "https://github.com/gvegayon/ABCoptim/")
11436 (synopsis "Optimization of Artificial Bee Colony algorithm")
11438 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
11439 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
11440 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
11441 algorithms, and uses only common control parameters such as colony size and
11442 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
11443 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
11444 This version is a work-in-progress and is written in R code.")
11445 (license license:expat)))
11447 (define-public r-abcp2
11454 (uri (cran-uri "ABCp2" version))
11456 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
11457 (properties `((upstream-name . "ABCp2")))
11458 (build-system r-build-system)
11459 (propagated-inputs (list r-mass))
11460 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
11461 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
11463 "This package tests the goodness of fit of a distribution of offspring to the Normal,
11464 Poisson, and Gamma distribution and estimates the proportional paternity of the
11465 second male (P2) based on the best fit distribution.")
11466 (license license:gpl2)))
11468 (define-public r-abcrf
11475 (uri (cran-uri "abcrf" version))
11477 (base32 "08mh1a6gxp0mfx6qnp1qzcrfx7xp64qj9kad4ziyswfx22ykdsxi"))))
11478 (build-system r-build-system)
11489 (home-page "https://cran.r-project.org/web/packages/abcrf/")
11490 (synopsis "Approximate bayesian computation via random forests")
11492 "This package performs approximate bayesian computation (ABC) model choice and
11493 parameter inference via random forests. This machine learning tool named random
11494 forests (RF) can conduct selection among the highly complex models covered by
11496 (license license:gpl2+)))
11498 (define-public r-abctools
11500 (name "r-abctools")
11505 (uri (cran-uri "abctools" version))
11507 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
11508 (build-system r-build-system)
11510 (list r-abc r-abind r-hmisc r-plyr))
11511 (home-page "https://github.com/dennisprangle/abctools/")
11512 (synopsis "Tools for ABC analyses")
11514 "This @code{r-abctools} package provides tools for approximate Bayesian computation
11515 including summary statistic selection and assessing coverage. This includes
11516 recent dimension reduction algorithms to tune the choice of summary statistics,
11517 and coverage methods to tune the choice of threshold.")
11518 (license license:gpl2+)))
11520 (define-public r-ggstance
11522 (name "r-ggstance")
11527 (uri (cran-uri "ggstance" version))
11529 (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d"))))
11530 (build-system r-build-system)
11532 (list r-ggplot2 r-plyr r-rlang r-withr))
11533 (home-page "https://cran.r-project.org/web/packages/ggstance/")
11534 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
11536 "This package is a @code{r-ggplot2} extension that provides flipped components:
11538 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
11539 @item vertical versions of @code{r-ggplot2} positions.
11541 (license license:gpl3)))
11543 (define-public r-ggnetwork
11545 (name "r-ggnetwork")
11550 (uri (cran-uri "ggnetwork" version))
11553 "0gqdgy5yh700dg0f7xb80hczlnqfisn8l55j7amd1n7fp2x5sr8v"))))
11554 (properties `((upstream-name . "ggnetwork")))
11555 (build-system r-build-system)
11557 (list r-ggplot2 r-ggrepel r-igraph r-network r-sna))
11558 (native-inputs (list r-knitr))
11559 (home-page "https://github.com/briatte/ggnetwork")
11560 (synopsis "Geometries to plot networks with ggplot2")
11562 "This package provides geometries to plot network objects with the
11564 (license license:gpl3)))
11566 (define-public r-cvauc
11573 (uri (cran-uri "cvAUC" version))
11576 "1m2y50a1yapf1c74km9a4r47ds2z2bfp4wwwkqin7swv9v1s7d28"))))
11577 (properties `((upstream-name . "cvAUC")))
11578 (build-system r-build-system)
11580 (list r-data-table r-rocr))
11581 (home-page "https://github.com/ledell/cvAUC")
11582 (synopsis "Cross-validated area under the ROC curve confidence intervals")
11584 "This package contains various tools for working with and evaluating
11585 cross-validated area under the ROC curve (AUC) estimators. The primary
11586 functions of the package are @code{ci.cvAUC} and @code{ci.pooled.cvAUC}, which
11587 report cross-validated AUC and compute confidence intervals for
11588 cross-validated AUC estimates based on influence curves for i.i.d. and pooled
11589 repeated measures data, respectively.")
11590 (license license:asl2.0)))
11592 (define-public r-gam
11599 (uri (cran-uri "gam" version))
11602 "1ndgnaq5fk1w6l6z93w5gd22887yxkykrchbdbx366qmz8v8wcyg"))))
11603 (properties `((upstream-name . "gam")))
11604 (build-system r-build-system)
11609 (home-page "https://cran.r-project.org/package=gam")
11610 (synopsis "Generalized additive models")
11612 "This package provides functions for fitting and working with generalized
11613 additive models, as described in chapter 7 of \"Statistical Models in
11614 S\" (Chambers and Hastie (eds), 1991), and \"Generalized Additive
11615 Models\" (Hastie and Tibshirani, 1990).")
11616 (license license:gpl2)))
11618 (define-public r-superlearner
11620 (name "r-superlearner")
11625 (uri (cran-uri "SuperLearner" version))
11628 "00any24msgflyagy87nznpfjz5g9v15frqda6c679wa8plx26hjz"))))
11629 (properties `((upstream-name . "SuperLearner")))
11630 (build-system r-build-system)
11632 (list r-cvauc r-gam r-nnls))
11635 (home-page "https://github.com/ecpolley/SuperLearner")
11636 (synopsis "Super learner prediction")
11638 "This package implements the super learner prediction method and contains
11639 a library of prediction algorithms to be used in the super learner.")
11640 (license license:gpl3)))
11642 (define-public r-drtmle
11649 (uri (cran-uri "drtmle" version))
11652 "12vplpz9bg5444jy29mbdr70hqby073vb3iw76v2csrwy3ws3f21"))))
11653 (properties `((upstream-name . "drtmle")))
11654 (build-system r-build-system)
11656 (list r-future-apply r-np r-superlearner))
11659 (home-page "https://github.com/benkeser/drtmle")
11660 (synopsis "Doubly-robust nonparametric estimation and inference")
11662 "This package implements targeted minimum loss-based estimators of
11663 counterfactual means and causal effects that are doubly-robust with respect
11664 both to consistency and asymptotic normality.")
11665 (license license:expat)))
11667 (define-public r-dofuture
11669 (name "r-dofuture")
11674 (uri (cran-uri "doFuture" version))
11677 "0w07pmzpsfq4kvfc745s1i9b6dfn1df1wrfi4s9ys4ir3g2s8nk1"))))
11678 (properties `((upstream-name . "doFuture")))
11679 (build-system r-build-system)
11682 (modify-phases %standard-phases
11683 (add-after 'unpack 'set-HOME
11684 (lambda _ (setenv "HOME" "/tmp"))))))
11686 (list r-foreach r-future r-globals r-iterators))
11688 (list r-r-rsp)) ; vignette builder
11689 (home-page "https://github.com/HenrikBengtsson/doFuture")
11690 (synopsis "Foreach parallel adapter using the future API")
11692 "This package provides a @code{%dopar%} adapter such that any type of
11693 futures can be used as backends for the @code{foreach} framework.")
11694 (license license:lgpl2.1+)))
11696 (define-public r-superheat
11698 (name "r-superheat")
11703 (uri (cran-uri "superheat" version))
11706 "01v8s6px1k5fajlm6py3ksr1i853kwwlky1yryzhy3p1cxhwgg83"))))
11707 (properties `((upstream-name . "superheat")))
11708 (build-system r-build-system)
11717 (home-page "https://cran.r-project.org/package=superheat")
11718 (synopsis "Graphical tool for exploring complex datasets using heatmaps")
11720 "This package provides a system for generating extendable and
11721 customizable heatmaps for exploring complex datasets, including big data and
11722 data with multiple data types.")
11723 (license license:cc0)))
11725 (define-public r-qualv
11732 (uri (cran-uri "qualV" version))
11735 "0rkjzva2h158d5c631jmjjh7qjibbyisl0503san80rk9fgxl45b"))))
11736 (properties `((upstream-name . "qualV")))
11737 (build-system r-build-system)
11739 (list r-kernsmooth))
11740 (home-page "http://qualV.R-Forge.R-Project.org/")
11741 (synopsis "Qualitative Validation Methods")
11743 "This package provides qualitative methods for the validation of dynamic
11744 models. It contains
11747 @item an orthogonal set of deviance measures for absolute, relative and
11749 @item approaches accounting for time shifts.
11752 The first approach transforms time to take time delays and speed differences
11753 into account. The second divides the time series into interval units
11754 according to their main features and finds the @dfn{longest common
11755 subsequence} (LCS) using a dynamic programming algorithm.")
11756 (license license:gpl2+)))
11758 (define-public r-mosaiccore
11760 (name "r-mosaiccore")
11761 (version "0.9.2.1")
11765 (uri (cran-uri "mosaicCore" version))
11767 (base32 "1yns15yxr6215xf9qsxfvl24a9zvh1chw49n31dql7fy1zr1dkmp"))))
11768 (properties `((upstream-name . "mosaicCore")))
11769 (build-system r-build-system)
11771 (list r-dplyr r-mass r-rlang r-tidyr))
11772 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
11773 (synopsis "Common utilities for mosaic family packages")
11775 "Common utilities used in other Mosaic family packages are collected here.")
11776 (license license:gpl2+)))
11778 (define-public r-labelled
11780 (name "r-labelled")
11785 (uri (cran-uri "labelled" version))
11788 "02n4r4bizsysnlmxpw86w7zkiqi6aill9dq2nmrn43xzrffy54sy"))))
11789 (properties `((upstream-name . "labelled")))
11790 (build-system r-build-system)
11801 (home-page "http://larmarange.github.io/labelled/")
11802 (synopsis "Manipulating labelled data")
11804 "This package provides useful functions to deal with the
11805 @code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the
11807 (license license:gpl3)))
11809 (define-public r-ggformula
11811 (name "r-ggformula")
11816 (uri (cran-uri "ggformula" version))
11818 (base32 "0xb39gjn6q7va1d1fhvf2dw9428s1q13wasx4y3cz2f0lls1r2wl"))))
11819 (build-system r-build-system)
11834 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
11835 (synopsis "Formula interface for the @code{r-ggplot2}")
11837 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
11838 gf_density(), and so on, bring the formula interface to ggplot(). This captures
11839 and extends the excellent simplicity of the lattice-graphics formula interface,
11840 while providing the intuitive capabilities of @code{r-ggplot2}.")
11841 (license license:expat)))
11843 (define-public r-mosaicdata
11845 (name "r-mosaicdata")
11850 (uri (cran-uri "mosaicData" version))
11852 (base32 "1s97yq24z7yhzmx0dpspfadpd8hndyhn7aiw0nslwrhvilhwa409"))))
11853 (properties `((upstream-name . "mosaicData")))
11854 (build-system r-build-system)
11855 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
11856 (synopsis "Data sets for project Mosaic")
11858 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
11859 used to teach mathematics, statistics, computation and modeling.")
11860 (license license:gpl2+)))
11862 (define-public r-raster
11869 (uri (cran-uri "raster" version))
11872 "1in3n0hqzcdhibjl3y82nwn6m6wcv4k3l6s2jw57jn32qgvy01lz"))))
11873 (build-system r-build-system)
11875 (list r-rcpp r-sp r-terra))
11876 (home-page "https://www.rspatial.org/")
11877 (synopsis "Geographic data analysis and modeling")
11879 "The package implements basic and high-level functions for reading,
11880 writing, manipulating, analyzing and modeling of gridded spatial data.
11881 Processing of very large files is supported.")
11882 (license license:gpl3+)))
11884 (define-public r-mosaic
11887 (version "1.8.4.2")
11891 (uri (cran-uri "mosaic" version))
11893 (base32 "12kpkb7vm54na9hjjkvzw6gm5plx0m6i0l9kihz2r30zanfx5jca"))))
11894 (build-system r-build-system)
11909 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
11910 (synopsis "Mathematics, statistics, and computation teaching utilities")
11912 "This package contain data sets and utilities from
11913 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
11914 statistics, computation and modeling. Project MOSAIC is a community of
11915 educators working to tie together aspects of quantitative work that students
11916 in science, technology, engineering and mathematics will need in their
11917 professional lives, but which are usually taught in isolation, if at all.")
11918 (license license:gpl2+)))
11920 (define-public r-abd
11927 (uri (cran-uri "abd" version))
11929 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
11930 (build-system r-build-system)
11932 (list r-lattice r-mosaic r-nlme))
11933 (home-page "https://cran.r-project.org/web/packages/abd/")
11934 (synopsis "Analysis of biological data")
11936 "The @code{r-abd} package contains data sets and sample code for the Analysis of
11937 biological data by Michael Whitlock and Dolph Schluter.")
11938 (license license:gpl2)))
11940 (define-public r-svgui
11947 (uri (cran-uri "svGUI" version))
11949 (base32 "0ch5gdfk834xj9w3vxpm3x4770fz3nnlyn8b0jsw9f3n2as7g979"))))
11950 (properties `((upstream-name . "svGUI")))
11951 (build-system r-build-system)
11954 (home-page "https://github.com/SciViews/svGUI/")
11955 (synopsis "Functions for managing GUI clients in R")
11957 "The SciViews @code{svGUI} package eases the management of Graphical User
11958 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
11959 centralizes info about GUI elements currently used, and it dispatches GUI
11960 calls to the particular toolkits in use in function of the context.")
11961 (license license:gpl2)))
11963 (define-public r-svdialogs
11965 (name "r-svdialogs")
11970 (uri (cran-uri "svDialogs" version))
11972 (base32 "0z3a5glsi0ab43mdk2yvslxyzg12nbqqqc35jvgzj475mpkbgjif"))))
11973 (properties `((upstream-name . "svDialogs")))
11974 (build-system r-build-system)
11978 (list r-rstudioapi r-svgui))
11981 (home-page "https://github.com/SciViews/svDialogs/")
11982 (synopsis "Portable dialog boxes")
11984 "This package helps to construct standard dialog boxes for your GUI, including
11985 message boxes, input boxes, list, file or directory selection, and others. In
11986 case R cannot display GUI dialog boxes, a simpler command line version of these
11987 interactive elements is also provided as a fallback solution.")
11988 (license license:gpl2)))
11990 (define-public r-abe
11997 (uri (cran-uri "abe" version))
12000 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
12001 (build-system r-build-system)
12002 (home-page "https://cran.r-project.org/web/packages/abe/")
12003 (synopsis "Augmented backward elimination")
12005 "This package performs augmented backward elimination and checks the
12006 stability of the obtained model. Augmented backward elimination combines
12007 significance or information based criteria with the change in estimate to
12008 either select the optimal model for prediction purposes or to serve as a tool
12009 to obtain a practically sound, highly interpretable model.")
12010 (license license:gpl2+)))
12012 (define-public r-abf2
12019 (uri (cran-uri "abf2" version))
12021 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
12022 (build-system r-build-system)
12023 (home-page "https://cran.r-project.org/web/packages/abf2/")
12024 (synopsis "Load gap-free axon @code{r-abf2} files")
12026 "This package loads electrophysiology data from ABF2 files, as created by
12027 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
12028 mode are currently supported.")
12029 (license license:artistic2.0)))
12031 (define-public r-abhgenotyper
12033 (name "r-abhgenotyper")
12038 (uri (cran-uri "ABHgenotypeR" version))
12040 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
12041 (properties `((upstream-name . "ABHgenotypeR")))
12042 (build-system r-build-system)
12044 (list r-ggplot2 r-reshape2))
12045 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
12046 (synopsis "Visualize and manipulate ABH genotypes")
12048 "The @code{r-abhgenotyper} package provides simple imputation,
12049 error-correction and plotting capacities for genotype data. The package is
12050 supposed to serve as an intermediate but independent analysis tool between the
12051 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
12052 not found in either TASSEL or @code{r-qtl} in addition to visualization of
12053 genotypes as \"graphical genotypes\".")
12054 (license license:gpl3)))
12056 (define-public r-furrr
12063 (uri (cran-uri "furrr" version))
12066 "12z4q0fn7asxis17hisi82bvfabl5if1338lmfqmkrwv5rg7748d"))))
12067 (build-system r-build-system)
12075 (home-page "https://github.com/DavisVaughan/furrr")
12076 (synopsis "Apply mapping functions in parallel using futures")
12078 "This package provides implementations of the family of @code{map()}
12079 functions from the @code{purrr} package that can be resolved using any
12080 @code{future}-supported backend, e.g. parallel on the local machine or
12081 distributed on a compute cluster.")
12082 (license license:lgpl2.1+)))
12084 (define-public r-abjutils
12086 (name "r-abjutils")
12091 (uri (cran-uri "abjutils" version))
12093 (base32 "0lmf4va8qnzwg698i2h4fcwvd6dhsgdkqsfh41aa3wg1flimhsr7"))))
12094 (build-system r-build-system)
12104 (home-page "https://github.com/abjur/abjutils/")
12105 (synopsis "Collection of tools for jurimetrical analysis")
12107 "This package implements general purpose tools, such as functions for
12108 sampling and basic manipulation of Brazilian lawsuits identification number.
12109 It also implements functions for text cleaning, such as accentuation
12111 (license license:expat)))
12113 (define-public r-abnormality
12115 (name "r-abnormality")
12120 (uri (cran-uri "abnormality" version))
12122 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
12123 (build-system r-build-system)
12125 (list r-mass r-matrix))
12126 (home-page "https://cran.r-project.org/web/packages/abnormality/")
12127 (synopsis "Measure a subject's abnormality with respect to a reference population")
12129 "This package contains functions to implement the methodology and
12130 considerations laid out by Marks et al. in the article \"Measuring abnormality
12131 in high dimensional spaces: applications in biomechanical gait analysis\".
12132 Using high-dimensional datasets to measure a subject's overall level of
12133 abnormality as compared to a reference population is often needed in outcomes
12135 (license license:expat)))
12137 (define-public r-abodoutlier
12139 (name "r-abodoutlier")
12144 (uri (cran-uri "abodOutlier" version))
12146 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
12147 (properties `((upstream-name . "abodOutlier")))
12148 (build-system r-build-system)
12151 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
12152 (synopsis "Angle-based outlier detection")
12154 "This package performs angle-based outlier detection on a given data
12155 frame. It offers three methods to process data:
12157 @item full but slow implementation using all the data that has cubic
12159 @item a fully randomized method;
12160 @item a method using k-nearest neighbours.
12162 These algorithms are well suited for high dimensional data outlier
12164 (license license:expat)))
12166 (define-public r-abps
12173 (uri (cran-uri "ABPS" version))
12175 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
12176 (properties `((upstream-name . "ABPS")))
12177 (build-system r-build-system)
12178 (propagated-inputs (list r-kernlab))
12179 (home-page "https://cran.r-project.org/web/packages/ABPS/")
12180 (synopsis "Abnormal blood profile score to detect blood doping")
12182 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
12183 The ABPS is a part of the Athlete biological passport program of the World
12184 anti-doping agency, which combines several blood parameters into a single
12185 score in order to detect blood doping. The package also contains functions to
12186 calculate other scores used in anti-doping programs, such as the ratio of
12187 hemoglobin to reticulocytes (OFF-score), as well as example data.")
12188 (license license:gpl2+)))
12190 (define-public r-parmigene
12192 (name "r-parmigene")
12197 (uri (cran-uri "parmigene" version))
12200 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
12201 (build-system r-build-system)
12202 (home-page "https://cran.r-project.org/web/packages/parmigene/")
12203 (synopsis "Mutual information estimation for gene network reconstruction")
12205 "This package provides a parallel estimation of the mutual information
12206 based on entropy estimates from k-nearest neighbors distances and algorithms
12207 for the reconstruction of gene regulatory networks.")
12208 (license license:agpl3+)))
12210 (define-public r-pscl
12217 (uri (cran-uri "pscl" version))
12219 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
12220 (build-system r-build-system)
12223 (home-page "https://github.com/atahk/pscl/")
12224 (synopsis "Political science computational laboratory")
12226 "The @code{pscl} is an R package providing classes and methods for:
12228 @item Bayesian analysis of roll call data (item-response models);
12229 @item elementary Bayesian statistics;
12230 @item maximum likelihood estimation of zero-inflated and hurdle models for count
12232 @item utility functions.
12234 (license license:gpl2)))
12236 (define-public r-accelmissing
12238 (name "r-accelmissing")
12243 (uri (cran-uri "accelmissing" version))
12245 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
12246 (build-system r-build-system)
12248 (list r-mice r-pscl))
12249 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
12250 (synopsis "Missing value imputation for accelerometer data")
12252 "This package provides a statistical method to impute the missing values in
12253 accelerometer data. The methodology includes both parametric and
12254 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
12255 model. It also provides multiple functions to preprocess the accelerometer data
12256 previous to the missing data imputation. These include detecting the wearing
12257 and the non-wearing time, selecting valid days and subjects, and creating plots.")
12258 (license license:gpl2+)))
12260 (define-public r-mhsmm
12267 (uri (cran-uri "mhsmm" version))
12269 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
12270 (build-system r-build-system)
12271 (propagated-inputs (list r-mvtnorm))
12272 (home-page "https://github.com/jaredo/mhsmm/")
12273 (synopsis "Inference for hidden Markov and semi-Markov models")
12275 "The @code{r-mhsmm} package implements estimation and prediction methods for
12276 hidden Markov and semi-Markov models for multiple observation sequences. Such
12277 techniques are of interest when observed data is thought to be dependent on some
12278 unobserved (or hidden) state. Also, this package is suitable for equidistant
12279 time series data, with multivariate and/or missing data. Allows user defined
12280 emission distributions.")
12281 (license license:gpl2+)))
12283 (define-public r-nleqslv
12290 (uri (cran-uri "nleqslv" version))
12292 (base32 "0cy65bqkmnnr8v0x1cag84caxwdxyr0yw4w443apxzfxjp7dyiif"))))
12293 (build-system r-build-system)
12294 (native-inputs (list gfortran))
12295 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
12296 (synopsis "Solve systems of nonlinear equations")
12298 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
12299 Broyden or a Newton method with a choice of global strategies such as line
12300 search and trust region. There are options for using a numerical or user
12301 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
12302 singular or ill-conditioned Jacobian.")
12303 (license license:gpl2+)))
12305 (define-public r-phyclust
12307 (name "r-phyclust")
12311 (uri (cran-uri "phyclust" version))
12314 "1ga2pzksp97psqbl484fikfnr4bl3bgyys86wb3ya904xxwghy6c"))))
12315 (properties `((upstream-name . "phyclust")))
12316 (build-system r-build-system)
12317 (propagated-inputs (list r-ape))
12318 (home-page "https://snoweye.github.io/phyclust/")
12319 (synopsis "Studying phyloclustering and exploring DNA sequence data")
12321 "@dfn{Phylogenetic clustering} (phyloclustering) is an evolutionary continuous
12322 time Markov Chain model-based approach to identify population structure from
12323 molecular data without assuming linkage equilibrium. The package @code{phyclust}
12324 provides a convenient implementation of phyloclustering for DNA and SNP data,
12325 capable of clustering individuals into subpopulations and identifying molecular
12326 sequences representative of those subpopulations. It is designed in @code{C} for
12327 performance and interfaced with @code{R} for visualization.")
12328 (license license:gpl2+)))
12330 (define-public r-physicalactivity
12332 (name "r-physicalactivity")
12337 (uri (cran-uri "PhysicalActivity" version))
12339 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40"))))
12341 `((upstream-name . "PhysicalActivity")))
12342 (build-system r-build-system)
12343 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
12344 (synopsis "Processing accelerometer data for physical activity measurement")
12346 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
12347 for classification of monitored wear and nonwear time intervals in accelerometer
12348 data collected to assess physical activity. The package also contains functions
12349 for making plots of accelerometer data and obtaining the summary of various
12350 information including daily monitor wear time and the mean monitor wear time
12351 during valid days. The revised package version 0.2-1 improved the functions
12352 regarding speed, robustness and add better support for time zones and daylight
12353 saving. In addition, several functions were added:
12355 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
12356 @item the @code{markPAI} can categorize physical activity intensity level based
12357 on user-defined cut-points of accelerometer counts.
12359 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
12360 @code{queryActigraph} functions.")
12361 (license license:gpl3+)))
12363 (define-public r-acc
12370 (uri (cran-uri "acc" version))
12372 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
12373 (build-system r-build-system)
12388 (home-page "https://cran.r-project.org/web/packages/acc/")
12389 (synopsis "Exploring accelerometer data")
12391 "This package processes accelerometer data from uni-axial and tri-axial devices
12392 and generates data summaries. Also, includes functions to plot, analyze, and
12393 simulate accelerometer data.")
12394 (license license:gpl2+)))
12396 (define-public r-rbenchmark
12398 (name "r-rbenchmark")
12403 (uri (cran-uri "rbenchmark" version))
12405 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
12406 (build-system r-build-system)
12407 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
12408 (synopsis "Benchmarking routine for R")
12410 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
12411 and is intended to facilitate benchmarking of arbitrary R code. The library
12412 consists of just one function, benchmark, which is a simple wrapper around
12413 system.time. Given a specification of the benchmarking process (counts of
12414 replications, evaluation environment) and an arbitrary number of expressions,
12415 benchmark evaluates each of the expressions in the specified environment,
12416 replicating the evaluation as many times as specified, and returning the results
12417 conveniently wrapped into a data frame.")
12418 (license license:gpl2+)))
12420 (define-public r-mitools
12427 (uri (cran-uri "mitools" version))
12430 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
12431 (build-system r-build-system)
12432 (propagated-inputs (list r-dbi))
12433 (home-page "https://cran.r-project.org/web/packages/mitools/")
12434 (synopsis "Tools for multiple imputation of missing data")
12436 "This package provides tools to perform analyses and combine results from
12437 multiple-imputation datasets.")
12438 (license license:gpl2)))
12440 (define-public r-mixsqp
12446 (uri (cran-uri "mixsqp" version))
12449 "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q"))))
12450 (properties `((upstream-name . "mixsqp")))
12451 (build-system r-build-system)
12453 (list r-irlba r-rcpp r-rcpparmadillo))
12456 (home-page "https://github.com/stephenslab/mixsqp")
12458 "Sequential quadratic programming for maximum-likelihood estimation")
12460 "This package provides an optimization method based on sequential
12461 quadratic programming for maximum likelihood estimation of the mixture
12462 proportions in a finite mixture model where the component densities are
12463 known. The algorithm is expected to obtain solutions that are at least
12464 as accurate as the state-of-the-art MOSEK interior-point solver, and they
12465 are expected to arrive at solutions more quickly when the number of
12466 samples is large and the number of mixture components is not too large.")
12467 (license license:expat)))
12469 (define-public r-magick
12476 (uri (cran-uri "magick" version))
12479 "0h942bn7wfnzbbgq9hrs75c7igmg5r1c5sad2v0znhza4cp7p1w3"))))
12480 (build-system r-build-system)
12482 (list imagemagick zlib))
12484 (list r-curl r-magrittr r-rcpp))
12486 (list pkg-config r-knitr))
12487 (home-page "https://github.com/ropensci/magick")
12488 (synopsis "Advanced graphics and image-processing in R")
12490 "This package provides bindings to ImageMagick, a comprehensive image
12491 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
12492 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
12493 operations are vectorized via the Magick++ STL meaning they operate either on
12494 a single frame or a series of frames for working with layers, collages, or
12495 animation. In RStudio, images are automatically previewed when printed to the
12496 console, resulting in an interactive editing environment.")
12497 (license license:expat)))
12499 (define-public r-survey
12506 (uri (cran-uri "survey" version))
12509 "0ljsszybzri531q6xab04r6zq11vchfs7y0snjzk57m3g0b9ms05"))))
12510 (build-system r-build-system)
12518 (home-page "http://r-survey.r-forge.r-project.org/survey/")
12519 (synopsis "Analysis of complex survey samples")
12521 "This package provides tools for the analysis of complex survey samples.
12522 The provided features include: summary statistics, two-sample tests, rank
12523 tests, generalised linear models, cumulative link models, Cox models,
12524 loglinear models, and general maximum pseudolikelihood estimation for
12525 multistage stratified, cluster-sampled, unequally weighted survey samples;
12526 variances by Taylor series linearisation or replicate weights;
12527 post-stratification, calibration, and raking; two-phase subsampling designs;
12528 graphics; PPS sampling without replacement; principal components, and factor
12530 ;; Either version of the GPL.
12531 (license (list license:gpl2 license:gpl3))))
12533 (define-public r-gee
12536 (version "4.13-25")
12540 (uri (cran-uri "gee" version))
12543 "128f810h88jxz1wdcmqjj3drb69b0rwx38l682i97rzb5wg8hh71"))))
12544 (properties `((upstream-name . "gee")))
12545 (build-system r-build-system)
12548 (home-page "https://cran.r-project.org/web/packages/gee/")
12549 (synopsis "Generalized estimation equation solver")
12551 "This package provides a solver for generalized estimation equations.")
12552 (license license:gpl2)))
12554 (define-public r-tab
12561 (uri (cran-uri "tab" version))
12564 "1kg8c1safi9klkx2mdkmsf5dn9piy4jljwd4ma7g4jz2rwl4jzhv"))))
12565 (properties `((upstream-name . "tab")))
12566 (build-system r-build-system)
12568 (list r-dplyr r-kableextra r-knitr r-mass r-survey))
12571 (home-page "https://cran.r-project.org/web/packages/tab/")
12572 (synopsis "Create summary tables for statistical reports")
12574 "This package contains functions for creating various types of summary
12575 tables, e.g. comparing characteristics across levels of a categorical variable
12576 and summarizing fitted generalized linear models, generalized estimating
12577 equations, and Cox proportional hazards models. Functions are available to
12578 handle data from simple random samples as well as complex surveys.")
12579 (license license:gpl3+)))
12581 (define-public r-dvmisc
12588 (uri (cran-uri "dvmisc" version))
12590 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
12591 (build-system r-build-system)
12604 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
12605 (synopsis "Faster computation of common statistics and miscellaneous functions")
12607 "This package implements faster versions of base R functions (e.g. mean, standard
12608 deviation, covariance, weighted mean), mostly written in C++, along with
12609 miscellaneous functions for various purposes (e.g. create the histogram with
12610 fitted probability density function or probability mass function curve, create
12611 the body mass index groups, assess the linearity assumption in logistic
12613 (license license:gpl2)))
12615 (define-public r-accelerometry
12617 (name "r-accelerometry")
12622 (uri (cran-uri "accelerometry" version))
12624 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
12625 (build-system r-build-system)
12627 (list r-dvmisc r-rcpp))
12628 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
12629 (synopsis "Functions for processing accelerometer data")
12631 "This package provides a collection of functions that perform operations on
12632 time-series accelerometer data, such as identify the non-wear time, flag minutes
12633 that are part of an activity bout, and find the maximum 10-minute average count
12634 value. The functions are generally very flexible, allowing for a variety of
12635 algorithms to be implemented.")
12636 (license license:gpl3)))
12638 (define-public r-absim
12645 (uri (cran-uri "AbSim" version))
12647 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
12648 (properties `((upstream-name . "AbSim")))
12649 (build-system r-build-system)
12651 (list r-ape r-powerlaw))
12652 (home-page "https://cran.r-project.org/web/packages/AbSim/")
12653 (synopsis "Time resolved simulations of antibody repertoires")
12655 "This package provides simulation methods for the evolution of antibody repertoires.
12656 The heavy and light chain variable region of both human and C57BL/6 mice can
12657 be simulated in a time-dependent fashion. Both single lineages using one set of
12658 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
12659 with an initial V-D-J recombination event, starting the first phylogenetic tree.
12660 Upon completion, the main loop of the algorithm begins, with each iteration
12661 representing one simulated time step. Various mutation events are possible at
12662 each time step, contributing to a diverse final repertoire.")
12663 (license license:gpl2)))
12665 (define-public r-quic
12672 (uri (cran-uri "QUIC" version))
12674 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
12675 (properties `((upstream-name . "QUIC")))
12676 (build-system r-build-system)
12677 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
12678 (synopsis "Regularized sparse inverse covariance matrix estimation")
12680 "This package implements the regularized Gaussian maximum likelihood
12681 estimation of the inverse of a covariance matrix. It uses Newton's method and
12682 coordinate descent to solve the regularized inverse covariance matrix
12683 estimation problem.")
12684 ;; The project home page states that the release is under GPLv3 or later.
12685 ;; The CRAN page only says GPL-3.
12686 (license license:gpl3+)))
12688 (define-public r-abundant
12690 (name "r-abundant")
12695 (uri (cran-uri "abundant" version))
12697 (base32 "15m3ngj5aipjg961yy5kvdg9xlfcpliw30dq6gchzxabhnfzcipd"))))
12698 (build-system r-build-system)
12701 (home-page "https://cran.r-project.org/web/packages/abundant/")
12702 (synopsis "Abundant regression and high-dimensional principal fitted components")
12704 "This package provides tools to fit and predict with the high-dimensional
12705 principal fitted components model. This model is described by Cook, Forzani,
12706 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
12707 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
12708 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
12709 (license license:gpl2+)))
12711 (define-public r-ac3net
12718 (uri (cran-uri "Ac3net" version))
12720 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
12721 (properties `((upstream-name . "Ac3net")))
12722 (build-system r-build-system)
12724 (list r-data-table))
12725 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
12726 (synopsis "Inferring directional conservative causal core gene networks")
12727 (description "This package infers directional Conservative causal core
12728 (gene) networks (C3NET). This is a version of the algorithm C3NET with
12729 directional network.")
12730 (license license:gpl3+)))
12732 (define-public r-aca
12739 (uri (cran-uri "ACA" version))
12741 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
12742 (properties `((upstream-name . "ACA")))
12743 (build-system r-build-system)
12744 (home-page "https://cran.r-project.org/web/packages/ACA/")
12745 (synopsis "Abrupt change-point or aberration detection in point series")
12747 "This package offers an interactive function for the detection of breakpoints in
12749 ;; Any version of the GPL
12750 (license (list license:gpl2+ license:gpl3+))))
12752 (define-public r-acceptancesampling
12754 (name "r-acceptancesampling")
12759 (uri (cran-uri "AcceptanceSampling" version))
12761 (base32 "1ja1g0v8qvf7yj81x37wc6i7fkwpc573756jgvazazi8yf1gm12p"))))
12763 `((upstream-name . "AcceptanceSampling")))
12764 (build-system r-build-system)
12765 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
12766 (synopsis "Creation and evaluation of acceptance sampling plans")
12768 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
12769 acceptance sampling plans. Acceptance sampling is a methodology commonly used
12770 in quality control and improvement. International standards of acceptance
12771 sampling provide sampling plans for specific circumstances. The aim of this
12772 package is to provide an easy-to-use interface to visualize single, double or
12773 multiple sampling plans. In addition, methods have been provided to enable the
12774 user to assess sampling plans against pre-specified levels of performance, as
12775 measured by the probability of acceptance for a given level of quality in the
12777 (license license:gpl3+)))
12779 (define-public r-acclma
12786 (uri (cran-uri "ACCLMA" version))
12788 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
12789 (properties `((upstream-name . "ACCLMA")))
12790 (build-system r-build-system)
12791 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
12792 (synopsis "ACC & LMA graph plotting")
12794 "This package contains a function that imports data from a @acronym{CSV,
12795 Comma-Separated Values} file, or uses manually entered data from the format (x,
12796 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
12797 Curve} vs @acronym{LOI, Line of Independence} graph and
12798 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
12799 function is @code{plotLMA} (source file, header) that takes a data set and plots the
12800 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
12801 string) was passed, a manual data entry window is opened. The header parameter
12802 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
12803 a header row or not. The dataset should contain only one independent variable
12804 (x) and one dependent variable (y) and can contain a weight for each
12806 (license license:gpl2)))
12808 (define-public r-aspi
12815 (uri (cran-uri "aspi" version))
12817 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
12818 (build-system r-build-system)
12820 "https://cran.r-project.org/web/packages/aspi/")
12822 "Analysis of symmetry of parasitic infections")
12824 "This package provides tools for the analysis and visualization of bilateral
12825 asymmetry in parasitic infections.")
12826 (license license:gpl3+)))
12828 (define-public r-sandwich
12830 (name "r-sandwich")
12835 (uri (cran-uri "sandwich" version))
12838 "1d72vwxidsyac9mbyxrm06qds63rzcr82nn4c05466gbajsvcc3f"))
12839 (modules '((guix build utils)))
12841 '(with-directory-excursion "inst/doc"
12842 ;; These files are generated from Rnw files.
12843 (for-each delete-file
12844 (list "sandwich-OOP.pdf"
12854 (build-system r-build-system)
12857 (home-page "https://cran.r-project.org/web/packages/sandwich/")
12858 (synopsis "Robust Covariance Matrix Estimators")
12860 "This package provides model-robust standard error estimators for
12861 cross-sectional, time series, clustered, panel, and longitudinal data.")
12862 ;; Either version of the license.
12863 (license (list license:gpl2 license:gpl3))))
12865 (define-public r-th-data
12872 (uri (cran-uri "TH.data" version))
12875 "0ynxacnz002bjsp2ybql7rdqw4zd14af8r7w44nwbx22n4bapwzd"))))
12876 (properties `((upstream-name . "TH.data")))
12877 (build-system r-build-system)
12879 (list r-mass r-survival))
12882 (home-page "https://cran.r-project.org/web/packages/TH.data/")
12883 (synopsis "Shared data sets")
12885 "This package contains supporting data sets that are used in other
12886 packages maintained by Torsten Hothorn.")
12887 (license license:gpl3)))
12889 (define-public r-multcomp
12891 (name "r-multcomp")
12896 (uri (cran-uri "multcomp" version))
12899 "1z1cqklahnp4qi48r335xlqvw7h7xbjrlpb4pjky9gc987xf92rj"))))
12900 (build-system r-build-system)
12902 (list r-codetools r-mvtnorm r-sandwich r-survival r-th-data))
12903 (home-page "https://cran.r-project.org/web/packages/multcomp/")
12904 (synopsis "Simultaneous inference in general parametric models")
12906 "Simultaneous tests and confidence intervals for general linear
12907 hypotheses in parametric models, including linear, generalized linear, linear
12908 mixed effects, and survival models. The package includes demos reproducing
12909 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
12910 Hothorn, Westfall, 2010, CRC Press).")
12911 (license license:gpl2)))
12913 (define-public r-multcompview
12915 (name "r-multcompview")
12920 (uri (cran-uri "multcompView" version))
12922 (base32 "1rfq9wvvrghq0542ff40wy8vdmsyd8spzz6ihcywcvxdfa8m6g8j"))))
12923 (properties `((upstream-name . "multcompView")))
12924 (build-system r-build-system)
12925 (home-page "https://cran.r-project.org/package=multcompView")
12926 (synopsis "Visualizations of paired comparisons")
12928 "Convert a logical vector or a vector of p-values or a correlation,
12929 difference, or distance matrix into a display identifying the pairs for which
12930 the differences were not significantly different.")
12931 ;; Any version of the GPL.
12932 (license license:gpl3+)))
12934 (define-public r-emmeans
12941 (uri (cran-uri "emmeans" version))
12944 "02fj957f67m1ik9n31h1p726hjnlhwlvd1wz93glfrcagm2p6nbq"))))
12945 (build-system r-build-system)
12947 (list r-estimability r-mvtnorm r-numderiv r-xtable))
12950 (home-page "https://github.com/rvlenth/emmeans")
12951 (synopsis "Estimated marginal means, aka least-squares means")
12953 "This package provides tools to obtain @dfn{estimated marginal
12954 means} (EMMs) for many linear, generalized linear, and mixed models. It can
12955 be used to compute contrasts or linear functions of EMMs, trends, and
12956 comparisons of slopes.")
12957 ;; Either version of the license.
12958 (license (list license:gpl2 license:gpl3))))
12960 (define-public r-pwr
12967 (uri (cran-uri "pwr" version))
12970 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
12971 (build-system r-build-system)
12974 (home-page "https://github.com/heliosdrm/pwr")
12975 (synopsis "Basic functions for power analysis")
12977 "This package provides power analysis functions along the lines of
12979 (license license:gpl3+)))
12981 (define-public r-libcoin
12988 (uri (cran-uri "libcoin" version))
12990 (base32 "1syrcdj5qg5m3zd3dlxgpfklswbalfg42w058dr09hnzqsvx0z9d"))))
12991 (build-system r-build-system)
12992 (propagated-inputs (list r-mvtnorm))
12993 (home-page "https://cran.r-project.org/web/packages/libcoin")
12994 (synopsis "Linear test statistics for permutation inference")
12996 "This package provides basic infrastructure for linear test statistics
12997 and permutation inference in the framework of Strasser and Weber (1999).")
12998 (license license:gpl2)))
13000 (define-public r-coin
13007 (uri (cran-uri "coin" version))
13010 "1cpv7jx840inzg98bkhrb5yscx0gpag6br237r5qpnc2gbrd2ikm"))))
13011 (build-system r-build-system)
13019 (home-page "http://coin.r-forge.r-project.org")
13020 (synopsis "Conditional inference procedures in a permutation test framework")
13022 "This package provides conditional inference procedures for the general
13023 independence problem including two-sample, K-sample (non-parametric ANOVA),
13024 correlation, censored, ordered and multivariate problems.")
13025 (license license:gpl2)))
13027 (define-public r-bayesplot
13029 (name "r-bayesplot")
13034 (uri (cran-uri "bayesplot" version))
13037 "0hqy597ang53phxnl084hak35ffqz9lw9hygax7370gpkjws908a"))))
13038 (build-system r-build-system)
13053 (home-page "https://mc-stan.org/bayesplot")
13054 (synopsis "Plotting for Bayesian models")
13056 "This package provides plotting functions for posterior analysis, model
13057 checking, and MCMC diagnostics. The package is designed not only to provide
13058 convenient functionality for users, but also a common set of functions that
13059 can be easily used by developers working on a variety of R packages for
13060 Bayesian modeling.")
13061 (license license:gpl3+)))
13063 (define-public r-tmb
13070 (uri (cran-uri "TMB" version))
13073 "03zv38gig31ir5gdhgw5j6j8xn1f4y91j2r87fv31gywmg1bhzl9"))))
13074 (properties `((upstream-name . "TMB")))
13075 (build-system r-build-system)
13077 (list r-matrix r-rcppeigen))
13078 (home-page "http://tmb-project.org")
13079 (synopsis "Template model builder: a general random effect tool")
13081 "With this tool, a user should be able to quickly implement complex
13082 random effect models through simple C++ templates. The package combines
13083 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
13084 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
13085 from R) to obtain an efficient implementation of the applied Laplace
13086 approximation with exact derivatives. Key features are: Automatic sparseness
13087 detection, parallelism through BLAS and parallel user templates.")
13088 (license license:gpl2)))
13090 (define-public r-sjstats
13097 (uri (cran-uri "sjstats" version))
13099 (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka"))))
13100 (build-system r-build-system)
13119 (home-page "https://github.com/strengejacke/sjstats")
13120 (synopsis "Functions for common statistical computations")
13122 "This package provides a collection of convenient functions for common
13123 statistical computations, which are not directly provided by R's @code{base}
13124 or @code{stats} packages. This package aims at providing, first, shortcuts
13125 for statistical measures, which otherwise could only be calculated with
13126 additional effort. Second, these shortcut functions are generic, and can be
13127 applied not only to vectors, but also to other objects as well. The focus of
13128 most functions lies on summary statistics or fit measures for regression
13129 models, including generalized linear models, mixed effects models and Bayesian
13131 (license license:gpl3)))
13133 (define-public r-glmmtmb
13140 (uri (cran-uri "glmmTMB" version))
13143 "1ldly6qn8iwqr41ndqlwsdz4v2n36giavsmx33vybn9g7r2fq4m7"))))
13144 (properties `((upstream-name . "glmmTMB")))
13145 (build-system r-build-system)
13154 (list r-knitr r-rmarkdown)) ; for vignettes
13155 (home-page "https://github.com/glmmTMB")
13156 (synopsis "Generalized linear mixed models")
13158 "Fit linear and generalized linear mixed models with various extensions,
13159 including zero-inflation. The models are fitted using maximum likelihood
13160 estimation via the Template Model Builder. Random effects are assumed to be
13161 Gaussian on the scale of the linear predictor and are integrated out using the
13162 Laplace approximation. Gradients are calculated using automatic
13164 (license license:agpl3+)))
13166 (define-public r-bayestestr
13168 (name "r-bayestestr")
13173 (uri (cran-uri "bayestestR" version))
13176 "1951zm88qlbmr4ragrzfzgw72awm7mqhh464s6kck0mcx7shas90"))))
13177 (properties `((upstream-name . "bayestestR")))
13178 (build-system r-build-system)
13180 (list r-datawizard r-insight))
13183 (home-page "https://github.com/easystats/bayestestR")
13184 (synopsis "Describe Bayesian models and posterior distributions")
13186 "This package provides utilities to understand and describe posterior
13187 distributions and Bayesian models. It includes point-estimates such as
13188 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
13189 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
13190 ROPE percentage and pd).")
13191 (license license:gpl3)))
13193 (define-public r-performance
13195 (name "r-performance")
13200 (uri (cran-uri "performance" version))
13203 "15yx75y17h3l1v7jpp8zbygy64lz7kds5yrgd7wrzw56564d2rhb"))))
13204 (build-system r-build-system)
13206 (list r-bayestestr r-datawizard r-insight))
13207 (home-page "https://easystats.github.io/performance/")
13208 (synopsis "Assessment of regression models performance")
13210 "This package provides utilities for computing measures to assess model
13211 quality, which are not directly provided by R's @code{base} or @code{stats}
13212 packages. These include e.g. measures like r-squared, intraclass correlation
13213 coefficient, root mean squared error or functions to check models for
13214 overdispersion, singularity or zero-inflation and more. Functions apply to a
13215 large variety of regression models, including generalized linear models, mixed
13216 effects models and Bayesian models.")
13217 (license license:gpl3)))
13219 (define-public r-ggeffects
13221 (name "r-ggeffects")
13226 (uri (cran-uri "ggeffects" version))
13229 "1j3l5v00f3xx2pwwfg1z9y31h8qja88nx7lycwj1y55ry5i6drr1"))))
13230 (build-system r-build-system)
13235 (home-page "https://github.com/strengejacke/ggeffects")
13236 (synopsis "Create tidy data frames of marginal effects for ggplot")
13238 "This package provides tools to compute marginal effects from statistical
13239 models and return the result as tidy data frames. These data frames are ready
13240 to use with the @code{ggplot2} package. Marginal effects can be calculated
13241 for many different models. Interaction terms, splines and polynomial terms
13242 are also supported. The two main functions are @code{ggpredict()} and
13243 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
13244 results using @code{ggplot2}.")
13245 (license license:gpl3)))
13247 (define-public r-effectsize
13249 (name "r-effectsize")
13254 (uri (cran-uri "effectsize" version))
13257 "1ibkvvpkd4md73d53823wnwzk3iqi1k4vr99jkyiiybcn6mv5qkc"))))
13258 (properties `((upstream-name . "effectsize")))
13259 (build-system r-build-system)
13261 (list r-bayestestr r-datawizard r-insight r-parameters
13265 (home-page "https://github.com/easystats/effectsize")
13266 (synopsis "Indices of effect size and standardized parameters")
13268 "This package provides utilities to work with indices of effect size and
13269 standardized parameters for a wide variety of models, allowing computation and
13270 conversion of indices such as Cohen's d, r, odds, etc.")
13271 (license license:gpl3)))
13273 (define-public r-sjplot
13280 (uri (cran-uri "sjPlot" version))
13282 (base32 "05iimcf1if1cx9bmsjb6f5gcq58hjiw10vx7kqd4nqnyhzcvy8yr"))))
13283 (properties `((upstream-name . "sjPlot")))
13284 (build-system r-build-system)
13306 (home-page "https://strengejacke.github.io/sjPlot/")
13307 (synopsis "Data visualization for statistics in social science")
13309 "This package represents a collection of plotting and table output
13310 functions for data visualization. Results of various statistical
13311 analyses (that are commonly used in social sciences) can be visualized using
13312 this package, including simple and cross tabulated frequencies, histograms,
13313 box plots, (generalized) linear models, mixed effects models, principal
13314 component analysis and correlation matrices, cluster analyses, scatter plots,
13315 stacked scales, effects plots of regression models (including interaction
13316 terms) and much more. This package supports labelled data.")
13317 (license license:gpl3)))
13319 (define-public r-ini
13326 (uri (cran-uri "ini" version))
13329 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
13330 (build-system r-build-system)
13331 (home-page "https://github.com/dvdscripter/ini")
13332 (synopsis "Read and write configuration files")
13334 "This package provides tools to parse simple @code{.ini} configuration
13335 files to an structured list. Users can manipulate this resulting list with
13336 @code{lapply()} functions. This same structured list can be used to write
13337 back to file after modifications.")
13338 (license license:gpl3)))
13340 (define-public r-gillespiessa2
13342 (name "r-gillespiessa2")
13347 (uri (cran-uri "GillespieSSA2" version))
13349 (base32 "0mvsjkjkm27j1y6mfipmxjmki4hpxw0cnmcmls7i5pacnrxc1gcb"))))
13350 (properties `((upstream-name . "GillespieSSA2")))
13351 (build-system r-build-system)
13364 (native-inputs (list r-knitr))
13365 (home-page "https://github.com/rcannood/GillespieSSA2")
13366 (synopsis "Gillespie's stochastic simulation algorithm")
13368 "This package provides a fast, scalable, and versatile framework for
13369 simulating large systems with Gillespie's @dfn{Stochastic Simulation
13370 Algorithm} (SSA). This package is the spiritual successor to the GillespieSSA
13371 package. Benefits of this package include major speed improvements (>100x),
13372 easier to understand documentation, and many unit tests that try to ensure the
13373 package works as intended.")
13374 (license license:gpl3+)))
13376 (define-public r-gitcreds
13378 (name "r-gitcreds")
13383 (uri (cran-uri "gitcreds" version))
13386 "0pf70g4a2kxjcid5rc4ppmgcl3kpjhkszdgz4fqn4l33lp6apij1"))))
13387 (properties `((upstream-name . "gitcreds")))
13388 (build-system r-build-system)
13389 (inputs (list git-minimal))
13390 (native-inputs (list r-knitr))
13391 (home-page "https://github.com/r-lib/gitcreds")
13392 (synopsis "Query git credentials from R")
13394 "Query, set, and delete credentials from the git credential store.
13395 Manage GitHub tokens and other git credentials. This package is to be used by
13396 other packages that need to authenticate to GitHub and/or other git
13398 (license license:expat)))
13400 (define-public r-gh
13407 (uri (cran-uri "gh" version))
13410 "1vqjhqlhvvqq8w2cqbgrkqphj0ga5s6fbl4zhcl3vc6fvsms5bpv"))))
13411 (build-system r-build-system)
13413 (list r-cli r-gitcreds r-httr r-ini r-jsonlite))
13416 (home-page "https://github.com/r-lib/gh#readme")
13417 (synopsis "Access the GitHub API via R")
13419 "This package provides a minimal R client to access the GitHub API.")
13420 (license license:expat)))
13422 (define-public r-fs
13429 (uri (cran-uri "fs" version))
13432 "11qr3v0xn65vfhgcxl4l6yv48s4w0w3ldp3anpzc25vd3mwd3jim"))))
13433 (build-system r-build-system)
13436 (home-page "https://fs.r-lib.org")
13437 (synopsis "Cross-platform file system operations based on libuv")
13439 "This package provides a cross-platform interface to file system
13440 operations, built on top of the libuv C library.")
13441 (license license:gpl3)))
13443 (define-public r-clisymbols
13445 (name "r-clisymbols")
13450 (uri (cran-uri "clisymbols" version))
13453 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
13454 (build-system r-build-system)
13455 (home-page "https://github.com/gaborcsardi/clisymbols")
13456 (synopsis "Unicode symbols at the R prompt")
13458 "This package provides a small subset of Unicode symbols, that are useful
13459 when building command line applications. They fall back to alternatives on
13460 terminals that do not support Unicode.")
13461 (license license:expat)))
13463 (define-public r-credentials
13465 (name "r-credentials")
13470 (uri (cran-uri "credentials" version))
13473 "1f18j3zrq8c9kah57xwahmmljsjg5qphlgamvx507ynvpq8pryig"))))
13474 (properties `((upstream-name . "credentials")))
13475 (build-system r-build-system)
13478 (modify-phases %standard-phases
13479 (add-after 'unpack 'setenv-HOME
13481 ;; This is necessary because git looks for $HOME/.gitconfig
13482 (setenv "HOME" "/tmp"))))))
13484 (list git-minimal))
13486 (list r-askpass r-curl r-jsonlite r-openssl r-sys))
13489 (home-page "https://docs.ropensci.org/credentials/")
13490 (synopsis "Tools for managing SSH and Git credentials")
13492 "This package assists you in setting up and retrieving of HTTPS and SSH
13493 credentials for use with git and other services. For HTTPS remotes the
13494 package interfaces the @command{git-credential} utility which @command{git}
13495 uses to store HTTP usernames and passwords. For SSH remotes this package
13496 provides convenient functions to find or generate appropriate SSH keys. The
13497 package both helps the user to setup a local git installation, and also
13498 provides a back-end for git/ssh client libraries to authenticate with existing
13499 user credentials.")
13500 (license license:expat)))
13502 (define-public r-gert
13509 (uri (cran-uri "gert" version))
13512 "1p8z5qap06qf680r25y78wgnprzl9ib3xp3kvsw01bh819v1h7bm"))))
13513 (properties `((upstream-name . "gert")))
13514 (build-system r-build-system)
13516 (list libgit2 zlib))
13525 (list pkg-config r-knitr))
13526 (home-page "https://docs.ropensci.org/gert/")
13527 (synopsis "Simple Git client for R")
13529 "This package provides a simple git client for R based on libgit2 with
13530 support for SSH and HTTPS remotes. All functions in gert use basic R data
13531 types (such as vectors and data-frames) for their arguments and return values.
13532 User credentials are shared with command line git through the
13533 @code{git-credential} store and SSH keys stored on disk or ssh-agent.")
13534 (license license:expat)))
13536 (define-public r-usethis
13543 (uri (cran-uri "usethis" version))
13546 "0638dzl4nm4c36990sf2biy74hjr2fzlqzfb98fsqrbhaw3ngp1i"))))
13547 (build-system r-build-system)
13568 (home-page "https://github.com/r-lib/usethis")
13569 (synopsis "Automate R package and project setup")
13571 "This package helps you to automate R package and project setup tasks
13572 that are otherwise performed manually. This includes setting up unit testing,
13573 test coverage, continuous integration, Git, GitHub integration, licenses,
13574 Rcpp, RStudio projects, and more.")
13575 (license license:gpl3)))
13577 (define-public r-sessioninfo
13579 (name "r-sessioninfo")
13584 (uri (cran-uri "sessioninfo" version))
13587 "1jy7n37qnrb4fgzmn8s8yf7kv29yw27x8zklwf8qdb2kgj2q6qpm"))))
13588 (build-system r-build-system)
13591 (home-page "https://github.com/r-lib/sessioninfo#readme")
13592 (synopsis "R session information")
13594 "This package provides tools to query and print information about the
13595 current R session. It is similar to @code{utils::sessionInfo()}, but includes
13596 more information about packages, and where they were installed from.")
13597 (license license:gpl2)))
13599 (define-public r-remotes
13606 (uri (cran-uri "remotes" version))
13609 "05m5dgv0nba5vhjbdkd8z5lbhpfxgkw31j58am7vz1d44igqgvzj"))))
13610 (build-system r-build-system)
13613 (home-page "https://github.com/r-lib/remotes#readme")
13614 (synopsis "R package installation from remote repositories")
13616 "Download and install R packages stored in GitHub, BitBucket, or plain
13617 subversion or git repositories. This package is a lightweight replacement of
13618 the @code{install_*} functions in the @code{devtools} package. Indeed most of
13619 the code was copied over from @code{devtools}.")
13620 (license license:gpl2+)))
13622 (define-public r-xopen
13629 (uri (cran-uri "xopen" version))
13632 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
13633 (build-system r-build-system)
13636 (home-page "https://github.com/r-lib/xopen#readme")
13637 (synopsis "Open system files, URLs, anything")
13639 "This package provides a cross-platform solution to open files,
13640 directories or URLs with their associated programs.")
13641 (license license:expat)))
13643 (define-public r-rcmdcheck
13645 (name "r-rcmdcheck")
13650 (uri (cran-uri "rcmdcheck" version))
13653 "1l696byn3kjq2xvz4wxybzaj6ink85h4lz3a35v2132ba5yyzm5v"))))
13654 (build-system r-build-system)
13668 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
13669 (synopsis "Run R CMD check from R and capture results")
13671 "Run @code{R CMD check} from R programmatically, and capture the results
13672 of the individual checks.")
13673 (license license:expat)))
13675 (define-public r-rapportools
13677 (name "r-rapportools")
13682 (uri (cran-uri "rapportools" version))
13685 "0qr86idng12g6hdd764j0wmli700v7rjhw7jdjxj0ka8xm5v7ymm"))))
13686 (build-system r-build-system)
13688 (list r-mass r-pander r-plyr r-reshape2))
13689 (home-page "https://cran.r-project.org/web/packages/rapportools/")
13690 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
13692 "This package provides helper functions that act as wrappers to more
13693 advanced statistical methods with the advantage of having sane defaults for
13695 (license license:agpl3+)))
13697 (define-public r-pander
13704 (uri (cran-uri "pander" version))
13707 "144zkq5w7v6fpzk3x40i0baybbp0y6x2ckh4b9qljryas9mhgp9a"))))
13708 (build-system r-build-system)
13710 (list r-digest r-rcpp))
13713 (home-page "https://rapporter.github.io/pander")
13714 (synopsis "Render R objects into Pandoc's markdown")
13716 "The main aim of the pander R package is to provide a minimal and easy
13717 tool for rendering R objects into Pandoc's markdown. The package is also
13718 capable of exporting/converting complex Pandoc documents (reports) in various
13720 ;; This package is licensed under either the AGPLv3+ or the very rarely
13722 (license license:agpl3+)))
13724 (define-public r-summarytools
13726 (name "r-summarytools")
13731 (uri (cran-uri "summarytools" version))
13734 "0gr95cd1ja8di6s0xghk6w7nj3bh3z4g7j7ixdy7f88q681aixgx"))))
13735 (build-system r-build-system)
13751 (home-page "https://github.com/dcomtois/summarytools")
13752 (synopsis "Tools to quickly and neatly summarize data")
13754 "This package provides tools for data frame summaries, cross-tabulations,
13755 weight-enabled frequency tables and common univariate statistics in concise
13756 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
13757 good point-of-entry for exploring data, both for experienced and new R
13759 (license license:gpl2)))
13761 (define-public r-lsei
13768 (uri (cran-uri "lsei" version))
13771 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2"))))
13772 (build-system r-build-system)
13775 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
13776 (synopsis "Solve regression problems under equality/inequality constraints")
13778 "It contains functions that solve least squares linear regression
13779 problems under linear equality/inequality constraints. Functions for solving
13780 quadratic programming problems are also available, which transform such
13781 problems into least squares ones first.")
13782 (license license:gpl2+)))
13784 (define-public r-npsurv
13791 (uri (cran-uri "npsurv" version))
13794 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw"))))
13795 (build-system r-build-system)
13798 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
13799 (synopsis "Nonparametric survival analysis")
13801 "This package contains functions for non-parametric survival analysis of
13802 exact and interval-censored observations.")
13803 (license license:gpl2+)))
13805 (define-public r-clusteval
13807 (name "r-clusteval")
13812 (uri (cran-uri "clusteval" version))
13815 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
13816 (build-system r-build-system)
13818 (list r-mvtnorm r-rcpp))
13819 (home-page "https://cran.r-project.org/web/packages/clusteval/")
13820 (synopsis "Evaluation of clustering algorithms")
13822 "This R package provides a suite of tools to evaluate clustering
13823 algorithms, clusterings, and individual clusters.")
13824 (license license:expat)))
13826 (define-public r-tweedie
13833 (uri (cran-uri "tweedie" version))
13836 "0ghwggdx6d391m7nay9n5li2xjqh3kmw416xx130sy2sxrgp8g4q"))))
13837 (build-system r-build-system)
13838 (native-inputs (list gfortran))
13839 (home-page "https://cran.r-project.org/web/packages/tweedie/")
13840 (synopsis "Evaluation of Tweedie exponential family models")
13842 "Maximum likelihood computations for Tweedie families, including the
13843 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
13844 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
13845 and related methods.")
13846 (license license:gpl2+)))
13848 (define-public r-rcppgsl
13855 (uri (cran-uri "RcppGSL" version))
13857 (base32 "1qmrwd0zc0kwbhpwxg5s5fxp0pmfh0hwcli8vqh1q41997yyy14m"))))
13858 (properties `((upstream-name . "RcppGSL")))
13859 (build-system r-build-system)
13862 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
13863 (synopsis "Rcpp integration for GSL vectors and matrices")
13865 "The GNU Scientific Library (or GSL) is a collection of numerical
13866 routines for scientific computing. It is particularly useful for C and C++
13867 programs as it provides a standard C interface to a wide range of mathematical
13868 routines. There are over 1000 functions in total with an extensive test
13869 suite. The RcppGSL package provides an easy-to-use interface between GSL data
13870 structures and R using concepts from Rcpp which is itself a package that eases
13871 the interfaces between R and C++.")
13872 (license license:gpl2+)))
13874 (define-public r-mvabund
13881 (uri (cran-uri "mvabund" version))
13884 "01kss9dx4an1ir5zs46jypvhj8sdc8wcs00i1223ai09av4lcsgd"))))
13885 (build-system r-build-system)
13887 (list r-mass r-rcpp r-rcppgsl r-statmod r-tweedie))
13888 (home-page "https://cran.r-project.org/web/packages/mvabund/")
13889 (synopsis "Statistical methods for analysing multivariate abundance data")
13891 "This package provides a set of tools for displaying, modeling and
13892 analysing multivariate abundance data in community ecology.")
13893 (license license:lgpl2.1+)))
13895 (define-public r-afex
13902 (uri (cran-uri "afex" version))
13905 "1hii6mx4qbmv4m1hy44sp19xf0r7mc68p767bwc58qrgpawgymwb"))))
13906 (build-system r-build-system)
13907 ;; This is needed for the vignette builder
13910 (modify-phases %standard-phases
13911 (add-after 'unpack 'set-HOME
13912 (lambda _ (setenv "HOME" "/tmp"))))))
13914 (list r-car r-lme4 r-lmertest r-pbkrtest r-reshape2))
13917 r-r-rsp)) ;vignette builder
13918 (home-page "https://afex.singmann.science/")
13919 (synopsis "Analysis of factorial experiments")
13921 "This package provides convenience functions for analyzing factorial
13922 experiments using ANOVA or mixed models.")
13923 (license license:gpl2+)))
13925 (define-public r-lmertest
13927 (name "r-lmertest")
13932 (uri (cran-uri "lmerTest" version))
13935 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim"))))
13936 (properties `((upstream-name . "lmerTest")))
13937 (build-system r-build-system)
13939 (list r-ggplot2 r-lme4 r-mass r-numderiv))
13940 (home-page "https://github.com/runehaubo/lmerTestR")
13941 (synopsis "Tests in linear mixed effects models")
13943 "This package provides p-values in type I, II or III anova and summary
13944 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
13945 method. A Kenward-Roger method is also available via the @code{pbkrtest}
13946 package. Model selection methods include step, drop1 and anova-like tables
13947 for random effects (ranova). Methods for Least-Square means (LS-means) and
13948 tests of linear contrasts of fixed effects are also available.")
13949 (license license:gpl2+)))
13951 (define-public r-r2glmm
13958 (uri (cran-uri "r2glmm" version))
13961 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
13962 (build-system r-build-system)
13974 (home-page "https://github.com/bcjaeger/r2glmm")
13975 (synopsis "Compute R squared for mixed (multilevel) models")
13977 "This package computes model and semi partial R squared with confidence
13978 limits for the linear and generalized linear mixed model (LMM and GLMM). The
13979 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
13980 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
13982 (license license:gpl2)))
13984 (define-public r-cmdfun
13991 (uri (cran-uri "cmdfun" version))
13994 "1pbcq7hi2lcmqnghmy3q2fsk0c9fy5m0637acyzmc096fxbx723j"))))
13995 (properties `((upstream-name . "cmdfun")))
13996 (build-system r-build-system)
14006 (home-page "https://snystrom.github.io/cmdfun/")
14007 (synopsis "Framework for building interfaces to shell commands")
14009 "Writing interfaces to command line software is cumbersome. The cmdfun
14010 package provides a framework for building function calls to seamlessly
14011 interface with shell commands by allowing lazy evaluation of command line
14012 arguments. It also provides methods for handling user-specific paths to tool
14013 installs or secrets like API keys. Its focus is to equally serve package
14014 builders who wish to wrap command line software, and to help analysts stay
14015 inside R when they might usually leave to execute non-R software.")
14016 (license license:expat)))
14018 (define-public r-rslurm
14025 (uri (cran-uri "rslurm" version))
14028 "19451icfh7snjbbmpzpr1hrdf52q8ijv0ag1di3y55r2la3jxxcf"))))
14029 (properties `((upstream-name . "rslurm")))
14030 (build-system r-build-system)
14031 (propagated-inputs (list r-whisker))
14032 (native-inputs (list r-knitr))
14033 (home-page "http://cyberhelp.sesync.org/rslurm/")
14034 (synopsis "Submit R calculations to a Slurm cluster")
14036 "This package provides functions that simplify submitting R scripts to a
14037 Slurm workload manager, in part by automating the division of embarrassingly
14038 parallel calculations across cluster nodes.")
14039 (license license:gpl3)))
14041 (define-public r-chk
14048 (uri (cran-uri "chk" version))
14051 "0nw3aj8sbd2x8rsvpglsiavk7kivd330mgx676k46m7lhhj7nmpw"))))
14052 (properties `((upstream-name . "chk")))
14053 (build-system r-build-system)
14055 (list r-lifecycle r-rlang))
14056 (native-inputs (list r-knitr))
14057 (home-page "https://github.com/poissonconsulting/chk")
14058 (synopsis "Check user-supplied function arguments")
14060 "This is a package for developers to check user-supplied function
14061 arguments. It is designed to be simple, fast and customizable. Error
14062 messages follow the tidyverse style guide.")
14063 (license license:expat)))
14065 (define-public r-weights
14072 (uri (cran-uri "weights" version))
14075 "1fnchf7f0hyl514bk8sc3l884kg25kb5xm4mc2l28n6hm7l6bgpg"))))
14076 (build-system r-build-system)
14078 (list r-gdata r-hmisc r-lme4 r-mice))
14079 (home-page "https://cran.r-project.org/web/packages/weights/")
14080 (synopsis "Weighting and weighted statistics")
14081 (description "This package Provides a variety of functions for producing
14082 simple weighted statistics, such as weighted Pearson's correlations, partial
14083 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
14084 includes some software for quickly recoding survey data and plotting point
14085 estimates from interaction terms in regressions (and multiply imputed
14086 regressions). NOTE: Weighted partial correlation calculations pulled to
14088 (license license:gpl2+)))
14090 (define-public r-rcppalgos
14092 (name "r-rcppalgos")
14096 (uri (cran-uri "RcppAlgos" version))
14099 "11dvh0ba3chsqf3vw8g9h1754arxgwqryayavx3n6vm5daz2krqa"))))
14100 (properties `((upstream-name . "RcppAlgos")))
14101 (build-system r-build-system)
14102 (inputs (list gmp))
14103 (propagated-inputs (list r-cpp11 r-gmp))
14104 (native-inputs (list r-knitr))
14105 (home-page "https://github.com/jwood000/RcppAlgos")
14107 "High performance tools for combinatorics and computational mathematics")
14109 "This package provides optimized functions and flexible combinatorial
14110 iterators implemented in C++ for solving problems in combinatorics and
14111 computational mathematics. It utilizes the @code{RMatrix} class from
14112 @code{RcppParallel} for thread safety. There are combination/permutation
14113 functions with constraint parameters that allow for generation of all results
14114 of a vector meeting specific criteria. It is capable of generating specific
14115 combinations/permutations which sets up nicely for parallelization as well as
14116 random sampling. Gmp support permits exploration where the total number of
14117 results is large. Additionally, there are several high performance number
14118 theoretic functions that are useful for problems common in computational
14120 (license license:gpl2+)))
14122 (define-public r-rcppannoy
14124 (name "r-rcppannoy")
14129 (uri (cran-uri "RcppAnnoy" version))
14132 "11fgxbx3w36937h22v9pqx0nk5vpxp3hybj7k1b0lk8mj7hcginw"))))
14133 (properties `((upstream-name . "RcppAnnoy")))
14134 (build-system r-build-system)
14137 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
14138 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
14140 "Annoy is a small C++ library for Approximate Nearest Neighbors written
14141 for efficient memory usage as well an ability to load from and save to disk.
14142 This package provides an R interface.")
14143 ;; Annoy is released under ASL 2.0, but this wrapper is released under
14145 (license (list license:gpl2+ license:asl2.0))))
14147 (define-public r-rcpphnsw
14149 (name "r-rcpphnsw")
14154 (uri (cran-uri "RcppHNSW" version))
14157 "0x3w14cz6hkrl8hi6217j0dl65l3yphbzka1dmsvgp3p9waq402g"))))
14158 (properties `((upstream-name . "RcppHNSW")))
14159 (build-system r-build-system)
14160 (propagated-inputs (list r-rcpp))
14161 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
14162 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
14164 "Hnswlib is a C++ library for approximate nearest neighbors. This
14165 package provides a minimal R interface by relying on the Rcpp package.")
14166 ;; hnswlib is released under Version 2.0 of the Apache License.
14167 (license (list license:gpl3 license:asl2.0))))
14169 (define-public r-rcppparallel
14171 (name "r-rcppparallel")
14176 (uri (cran-uri "RcppParallel" version))
14179 "1sn211ajlb1p12sglxqns175rg078yvww268m8cp0vvd7cmk55k3"))
14180 (modules '((guix build utils)))
14182 '(delete-file-recursively "src/tbb/"))))
14183 (properties `((upstream-name . "RcppParallel")))
14184 (build-system r-build-system)
14188 '(modify-phases %standard-phases
14189 (add-after 'unpack 'use-system-tbb
14190 (lambda* (#:key inputs #:allow-other-keys)
14191 (setenv "TBB_ROOT" (assoc-ref inputs "tbb")))))))
14192 (inputs (list tbb-2020))
14193 (home-page "https://rcppcore.github.io/RcppParallel/")
14194 (synopsis "Parallel programming tools for Rcpp")
14196 "This package provides high level functions for parallel programming with
14197 Rcpp. For example, the @code{parallelFor()} function can be used to convert
14198 the work of a standard serial @code{for} loop into a parallel one and the
14199 @code{parallelReduce()} function can be used for accumulating aggregates or
14201 (license license:gpl2)))
14203 (define-public r-ncdf4
14210 (uri (cran-uri "ncdf4" version))
14213 "0qzvin2fjzcb7h2knlnw14s6043pwi1nm7yf6p27ax7w269173fb"))))
14214 (build-system r-build-system)
14216 (list netcdf zlib))
14217 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
14218 (synopsis "R interface to Unidata netCDF format data files")
14220 "This package provides a high-level R interface to data files written
14221 using Unidata's netCDF library (version 4 or earlier), which are binary data
14222 files that are portable across platforms and include metadata information in
14223 addition to the data sets. Using this package, netCDF files can be opened and
14224 data sets read in easily. It is also easy to create new netCDF dimensions,
14225 variables, and files, in either version 3 or 4 format, and manipulate existing
14227 (license license:gpl3+)))
14229 (define-public r-biocmanager
14231 (name "r-biocmanager")
14232 (version "1.30.19")
14236 (uri (cran-uri "BiocManager" version))
14238 (base32 "1qhq1k1sr23bi2kmnd99mjs3ns0c2p20pmr2iq8a6bxbb0fap5v8"))))
14239 (properties `((upstream-name . "BiocManager")))
14240 (build-system r-build-system)
14243 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
14244 (synopsis "Access the Bioconductor project package repository")
14246 "This package provides a convenient tool to install and update
14247 Bioconductor packages.")
14248 (license license:artistic2.0)))
14250 (define-public r-rgl
14253 (version "0.110.2")
14257 (uri (cran-uri "rgl" version))
14260 "0v9lrsdmhw0wqfbrrjirgppd40cn00ignq3rg2jn3q8ak70ih4fs"))))
14261 (build-system r-build-system)
14265 r-rmarkdown)) ;for vignettes
14282 (home-page "https://r-forge.r-project.org/projects/rgl/")
14283 (synopsis "3D visualization using OpenGL")
14285 "This package provides medium to high level functions for 3D interactive graphics,
14286 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
14287 as functions for constructing representations of geometric
14288 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
14289 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
14290 image formats, including PNG, Postscript, SVG, PGF.")
14291 ;; Any version of the GPL.
14292 (license (list license:gpl2+ license:gpl3+))))
14294 (define-public r-multicool
14296 (name "r-multicool")
14301 (uri (cran-uri "multicool" version))
14304 "0djacq0irfqz4nlnx238kja73yvr1n5qybbfyl6bw1n6qgcjhza8"))))
14305 (build-system r-build-system)
14306 (propagated-inputs (list r-rcpp))
14307 (home-page "https://cran.r-project.org/web/packages/multicool/")
14308 (synopsis "Permutations of multisets in cool-lex order")
14310 "This package provides a set of tools to permute multisets without loops
14311 or hash tables and to generate integer partitions. Cool-lex order is similar
14312 to colexicographical order.")
14313 (license license:gpl2)))
14315 (define-public r-misc3d
14322 (uri (cran-uri "misc3d" version))
14325 "0r9x57s63kx9f6dgam2nhbziq8nrs9wd8pk7g76hds2kw46vnyx0"))))
14326 (build-system r-build-system)
14327 (home-page "https://cran.r-project.org/web/packages/misc3d/")
14328 (synopsis "Miscellaneous 3D Plots")
14330 "This package provides a collection of miscellaneous 3d plots, including
14332 ;; Any version of the GPL.
14333 (license (list license:gpl2+ license:gpl3+))))
14335 (define-public r-ks
14342 (uri (cran-uri "ks" version))
14344 (base32 "05bqrjkbx2kn5aax0hy3xd6pf7nxka9bm1sp8ll1cc2gf1nx1i6i"))))
14345 (build-system r-build-system)
14357 (home-page "https://www.mvstat.net/tduong/")
14358 (synopsis "Kernel smoothing")
14360 "This package provides kernel smoothers for univariate and multivariate
14361 data, including density functions, density derivatives, cumulative
14362 distributions, modal clustering, discriminant analysis, and two-sample
14363 hypothesis testing.")
14364 ;; Either version of the GPL.
14365 (license (list license:gpl2 license:gpl3))))
14367 (define-public r-feature
14374 (uri (cran-uri "feature" version))
14377 "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y"))))
14378 (build-system r-build-system)
14380 (list r-ks r-plot3d))
14383 (home-page "https://www.mvstat.net/tduong/")
14384 (synopsis "Inferential feature significance for kernel density estimation")
14386 "The feature package contains functions to display and compute kernel
14387 density estimates, significant gradient and significant curvature regions.
14388 Significant gradient and/or curvature regions often correspond to significant
14389 features (e.g. local modes).")
14390 ;; Either version of the GPL.
14391 (license (list license:gpl2 license:gpl3))))
14393 (define-public r-arm
14400 (uri (cran-uri "arm" version))
14403 "0dz9dnsky77da2mc198dr3600kz9vk75z1iihjarnsdrq68a4bf0"))))
14404 (build-system r-build-system)
14412 (home-page "https://cran.r-project.org/web/packages/arm/")
14413 (synopsis "Data analysis using regression and multilevel/hierarchical models")
14415 "This package provides functions to accompany A. Gelman and J. Hill,
14416 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
14417 University Press, 2007.")
14418 (license license:gpl3+)))
14420 (define-public r-circular
14422 (name "r-circular")
14427 (uri (cran-uri "circular" version))
14430 "1qmwj1pf37lc2s5r83y7nqckscznqhbsv66bdfgfbby7x4qkwga8"))))
14431 (build-system r-build-system)
14433 (list r-boot r-mvtnorm))
14436 (home-page "https://cran.r-project.org/web/packages/circular/")
14437 (synopsis "Circular statistics")
14439 "This package provides tools for circular statistics, from \"Topics in
14440 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
14442 (license license:gpl2+)))
14444 (define-public r-activity
14446 (name "r-activity")
14451 (uri (cran-uri "activity" version))
14454 "11n6wmqz7p3428rr615f92m61a5gb908xpn4l8q484h61bwg38c3"))))
14455 (build-system r-build-system)
14457 (list r-insol r-pbapply))
14458 (home-page "https://cran.r-project.org/web/packages/activity/")
14459 (synopsis "Animal activity statistics")
14461 "This package provides functions to fit kernel density functions to
14462 animal activity time data; plot activity distributions; quantify overall
14463 levels of activity; statistically compare activity metrics through
14464 bootstrapping; and evaluate variation in linear variables with time (or other
14465 circular variables).")
14466 (license license:gpl3)))
14468 (define-public r-ouch
14475 (uri (cran-uri "ouch" version))
14478 "119s9llpjy0b4q830xig2xr66fq6izp6mr2k4k79ggmf3gxww8as"))))
14479 (build-system r-build-system)
14480 (propagated-inputs (list r-subplex))
14481 (home-page "https://kingaa.github.io/ouch/")
14482 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
14484 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
14485 for evolution along a phylogenetic tree.")
14486 (license license:gpl2+)))
14488 (define-public r-fmri
14494 (uri (cran-uri "fmri" version))
14497 "1wh77xwpm8f9d9vky3r7vfmkik3hls008ifk8hkm2rq6i06jj53n"))))
14498 (properties `((upstream-name . "fmri")))
14499 (build-system r-build-system)
14500 (propagated-inputs (list r-aws r-metafor r-nlme))
14501 (native-inputs (list gfortran))
14502 (home-page "http://www.wias-berlin.de/software/imaging/")
14503 (synopsis "Analysis of fMRI experiments")
14505 "This package contains R-functions to perform an fMRI analysis as
14506 described in Polzehl and Tabelow (2019) <DOI:10.1007/978-3-030-29184-6>,
14507 Tabelow et al. (2006) <DOI:10.1016/j.neuroimage.2006.06.029>, Polzehl et
14508 al. (2010) <DOI:10.1016/j.neuroimage.2010.04.241>, Tabelow and Polzehl (2011)
14509 <DOI:10.18637/jss.v044.i11>.")
14510 (license license:gpl2+)))
14512 (define-public r-fmsb
14519 (uri (cran-uri "fmsb" version))
14522 "1gi94xr0b1yk9xzwfprfafxi25yic1lcivd66p73n6iqfzdaimbk"))))
14523 (build-system r-build-system)
14524 (home-page "http://minato.sip21c.org/msb/")
14525 (synopsis "Functions for medical statistics book with demographic data")
14527 "This package provides several utility functions for the book entitled
14528 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
14529 Japan, 2007) with Japanese demographic data and some demographic analysis
14530 related functions.")
14531 (license license:gpl2+)))
14533 (define-public r-stabledist
14535 (name "r-stabledist")
14540 (uri (cran-uri "stabledist" version))
14543 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
14544 (build-system r-build-system)
14545 (home-page "https://www.rmetrics.org")
14546 (synopsis "Stable distribution functions")
14548 "This package provides density, probability and quantile functions, and
14549 random number generation for (skew) stable distributions, using the
14550 parametrizations of Nolan.")
14551 (license license:gpl2+)))
14553 (define-public r-gsl
14556 (version "2.1-7.1")
14560 (uri (cran-uri "gsl" version))
14563 "118rj9kjx9rzlynvhrly19qz3yxg8jzws35971ssgzrp5lwd367f"))))
14564 (build-system r-build-system)
14567 (home-page "https://cran.r-project.org/web/packages/gsl")
14568 (synopsis "Wrapper for the GNU Scientific Library")
14570 "This package provides an R wrapper for the special functions and quasi
14571 random number generators of the GNU Scientific Library.")
14572 (license license:gpl2+)))
14574 (define-public r-adgoftest
14576 (name "r-adgoftest")
14581 (uri (cran-uri "ADGofTest" version))
14584 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
14585 (properties `((upstream-name . "ADGofTest")))
14586 (build-system r-build-system)
14587 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
14588 (synopsis "Anderson-Darling GoF test")
14590 "This package provides an implementation of the Anderson-Darling GoF test
14591 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
14592 Anderson-Darling Distribution\".")
14593 ;; Any version of the GPL.
14594 (license license:gpl3+)))
14596 (define-public r-adimpro
14602 (uri (cran-uri "adimpro" version))
14605 "0njw38vcdm02sni193nj10mpv7hiklpamrkjlz5bnhjxx9mvf4cl"))))
14606 (properties `((upstream-name . "adimpro")))
14607 (build-system r-build-system)
14611 (native-inputs (list gfortran))
14612 (home-page "https://www.wias-berlin.de/software/imaging/")
14613 (synopsis "Adaptive smoothing of digital images")
14615 "This package implements tools for manipulation of digital images and the
14616 Propagation Separation approach by Polzehl and Spokoiny (2006)
14617 <DOI:10.1007/s00440-005-0464-1> for smoothing digital images, see Polzehl and
14618 Tabelow (2007) <DOI:10.18637/jss.v019.i01>.")
14619 (license license:gpl2+)))
14621 (define-public r-admisc
14628 (uri (cran-uri "admisc" version))
14630 (base32 "01b2qjxz0qicqjm1swvm04qkiwhr7zjn7lhqv26l6rj4yb43y339"))))
14631 (properties `((upstream-name . "admisc")))
14632 (build-system r-build-system)
14633 (home-page "https://github.com/dusadrian/admisc")
14634 (synopsis "Adrian Dusa's miscellaneous")
14636 "This package contains miscellaneous functions used to interpret and
14637 translate, factorize and negate Sum of Products expressions, for both binary
14638 and multi-value crisp sets, and to extract information (set names, set values)
14639 from those expressions. Other functions perform various other checks if
14640 possibly numeric (even if all numbers reside in a character vector) and coerce
14641 to numeric, or check if the numbers are whole. It also offers, among many
14642 others, a highly flexible recoding routine and a more flexible alternative to
14643 the base function @code{with()}.")
14644 (license license:gpl3+)))
14646 (define-public r-oro-nifti
14648 (name "r-oro-nifti")
14652 (uri (cran-uri "oro.nifti" version))
14655 "01mn90qxb7i15zr83xrl2cn4akayfzpm83r5x71zczz3qb9gbr7g"))))
14656 (properties `((upstream-name . "oro.nifti")))
14657 (build-system r-build-system)
14658 (propagated-inputs (list r-abind r-bitops r-rnifti))
14659 (home-page "https://rigorousanalytics.blogspot.com")
14660 (synopsis "Vizualization of medical imaging data")
14662 "This package provides functions for the input/output and visualization
14663 of medical imaging data that follow either the ANALYZE, NIfTI or AFNI formats.
14664 This package is part of the Rigorous Analytics bundle.")
14665 (license license:bsd-3)))
14667 (define-public r-mritc
14673 (uri (cran-uri "mritc" version))
14676 "07b1b2k1ka43ikj2mhwnazw3ig7w10bf759fimxpksvk5k6wanx2"))))
14677 (properties `((upstream-name . "mritc")))
14678 (build-system r-build-system)
14679 (propagated-inputs (list r-lattice r-misc3d r-oro-nifti))
14680 (home-page "https://cran.r-project.org/package=mritc")
14681 (synopsis "MRI tissue classification")
14682 (description "This package provides various methods for MRI tissue
14684 ;; Any version of the GPL.
14685 (license license:gpl3+)))
14687 (define-public r-sodium
14694 (uri (cran-uri "sodium" version))
14697 "1a03z2asvmalnmsn89lapzp8a4fr0qvzdv3xgin8pbqhjyb9hvpp"))))
14698 (properties `((upstream-name . "sodium")))
14699 (build-system r-build-system)
14703 (list pkg-config r-knitr))
14704 (home-page "https://github.com/jeroen/sodium")
14705 (synopsis "R bindings to the libsodium crypto library")
14707 "This package provides bindings to libsodium: a library for encryption,
14708 decryption, signatures, password hashing and more. Sodium uses curve25519, a
14709 Diffie-Hellman function by Daniel Bernstein, which has become very popular
14710 after it was discovered that the NSA had backdoored Dual EC DRBG.")
14711 (license license:expat)))
14713 (define-public r-softimpute
14715 (name "r-softimpute")
14720 (uri (cran-uri "softImpute" version))
14723 "1v2a4d688ij5zcvkzpra9yx40xckdfnllnfnyq2450zf3n1kjk7a"))))
14724 (properties `((upstream-name . "softImpute")))
14725 (build-system r-build-system)
14729 (list gfortran r-knitr))
14730 (home-page "https://cran.r-project.org/web/packages/softImpute")
14731 (synopsis "Matrix completion via iterative soft-thresholded SVD")
14733 "This package provides iterative methods for matrix completion that use
14734 nuclear-norm regularization. The package includes procedures for centering
14735 and scaling rows, columns or both, and for computing low-rank @dfn{single
14736 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
14738 (license license:gpl2)))
14740 (define-public r-fftwtools
14742 (name "r-fftwtools")
14747 (uri (cran-uri "fftwtools" version))
14750 "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i"))))
14751 (build-system r-build-system)
14752 (inputs (list fftw))
14755 (home-page "https://github.com/krahim/fftwtools")
14756 (synopsis "Wrapper for FFTW3")
14758 "This package provides a wrapper for several FFTW functions. It provides
14759 access to the two-dimensional FFT, the multivariate FFT, and the
14760 one-dimensional real to complex FFT using the FFTW3 library. The package
14761 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
14762 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
14763 The FFT functions have a parameter that allows them to not return the
14764 redundant complex conjugate when the input is real data.")
14765 (license license:gpl2+)))
14767 (define-public r-tiff
14774 (uri (cran-uri "tiff" version))
14777 "0xgc7vyndxxahfhc2qqzmwi56bnfyl0pn72l820jz5sd24aymhxq"))))
14778 (build-system r-build-system)
14780 (list libtiff libjpeg-turbo zlib))
14783 (home-page "https://www.rforge.net/tiff/")
14784 (synopsis "Read and write TIFF images")
14786 "This package provides an easy and simple way to read, write and display
14787 bitmap images stored in the TIFF format. It can read and write both files and
14788 in-memory raw vectors.")
14789 ;; Either of these two license versions.
14790 (license (list license:gpl2 license:gpl3))))
14792 (define-public r-nlp
14799 (uri (cran-uri "NLP" version))
14802 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5"))))
14803 (properties `((upstream-name . "NLP")))
14804 (build-system r-build-system)
14805 (home-page "https://cran.r-project.org/web/packages/NLP/")
14806 (synopsis "Natural language processing infrastructure")
14808 "This package provides basic classes and methods for Natural Language
14810 (license license:gpl3)))
14812 (define-public r-tm
14819 (uri (cran-uri "tm" version))
14822 "0a3ylj9735i21fh6iz63fkh1pnf2hs8ipp8wjdj25dahl18yhlyv"))))
14823 (properties `((upstream-name . "tm")))
14824 (build-system r-build-system)
14826 (list r-bh r-nlp r-rcpp r-slam r-xml2))
14827 (home-page "http://tm.r-forge.r-project.org/")
14828 (synopsis "Text mining package")
14830 "This package provides a framework for text mining applications within R.")
14831 (license license:gpl3)))
14833 (define-public r-waveslim
14835 (name "r-waveslim")
14840 (uri (cran-uri "waveslim" version))
14843 "1510xpkgrhdw394m5anxccdczjikcxazyd09ix2z73i15akyx3j0"))))
14844 (build-system r-build-system)
14847 (home-page "http://waveslim.blogspot.com")
14848 (synopsis "Basic wavelet routines for signal processing")
14850 "This package provides basic wavelet routines for time series (1D),
14851 image (2D) and array (3D) analysis. The code provided here is based on
14852 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
14853 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
14854 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
14855 pairs (Selesnick 2001, 2002).")
14856 (license license:bsd-3)))
14858 (define-public r-wordcloud
14860 (name "r-wordcloud")
14865 (uri (cran-uri "wordcloud" version))
14868 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
14869 (build-system r-build-system)
14871 (list r-rcolorbrewer r-rcpp
14872 ;; The "tm" package is only "suggested" according to CRAN, but the
14873 ;; wordcloud package cannot be loaded without it.
14875 (home-page "https://cran.r-project.org/web/packages/wordcloud")
14876 (synopsis "Word clouds")
14878 "This package provides functionality to create pretty word clouds,
14879 visualize differences and similarity between documents, and avoid
14880 over-plotting in scatter plots with text.")
14881 (license license:lgpl2.1)))
14883 (define-public r-colorramps
14885 (name "r-colorramps")
14890 (uri (cran-uri "colorRamps" version))
14893 "12jnkj50yh2hc5l7j56lrrrmn58akrj9dwj98vzf42iq4h42kwb1"))))
14894 (properties `((upstream-name . "colorRamps")))
14895 (build-system r-build-system)
14896 (home-page "https://cran.r-project.org/web/packages/colorRamps")
14897 (synopsis "Build color tables")
14898 (description "This package provides features to build gradient color
14900 ;; Any version of the GPL
14901 (license license:gpl3+)))
14903 (define-public r-tidytree
14905 (name "r-tidytree")
14910 (uri (cran-uri "tidytree" version))
14912 (base32 "1sq982x0pqvrn4d77m6v5xbbr9c8dkrwvw3as1pc5cg12x6kdi7v"))))
14913 (build-system r-build-system)
14927 (home-page "https://github.com/GuangchuangYu/tidytree")
14928 (synopsis "Tidy tool for phylogenetic tree data manipulation")
14930 "Phylogenetic trees generally contain multiple components including nodes,
14931 edges, branches and associated data. This package provides an approach to
14932 convert tree objects to tidy data frames. It also provides tidy interfaces to
14933 manipulate tree data.")
14934 (license license:artistic2.0)))
14936 (define-public r-rvcheck
14943 (uri (cran-uri "rvcheck" version))
14945 (base32 "09khjklvzbafd7r55496by01a9g3y291d87hpy43w44dmz9fzn9a"))))
14946 (build-system r-build-system)
14948 (list r-biocmanager r-yulab-utils))
14949 (home-page "https://cran.r-project.org/web/packages/rvcheck")
14950 (synopsis "R package version check")
14952 "This package provides tools to check the latest release version of R and
14953 R packages (on CRAN, Bioconductor or Github).")
14954 (license license:artistic2.0)))
14956 (define-public r-docopt
14963 (uri (cran-uri "docopt" version))
14966 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
14967 (build-system r-build-system)
14968 (home-page "https://github.com/docopt/docopt.R")
14969 (synopsis "Command-line interface specification language")
14971 "This package enables you to define a command-line interface by just
14972 giving it a description in the specific format.")
14973 (license license:expat)))
14975 (define-public r-sparsesvd
14977 (name "r-sparsesvd")
14982 (uri (cran-uri "sparsesvd" version))
14985 "0yz0mgayxriyrz6bbrd41cck0s56b916xvyh13hw86gydd6kpl5k"))))
14986 (build-system r-build-system)
14987 (propagated-inputs (list r-matrix))
14988 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
14989 (synopsis "Sparse truncated singular value decomposition")
14991 "This package provides a Wrapper around the SVDLIBC library
14992 for (truncated) singular value decomposition of a sparse matrix. Currently,
14993 only sparse real matrices in Matrix package format are supported.")
14994 ;; SVDLIBC is released under BSD-2. The R interface is released under
14996 (license (list license:bsd-3 license:bsd-2))))
14998 (define-public r-speedglm
15000 (name "r-speedglm")
15005 (uri (cran-uri "speedglm" version))
15008 "1kj662nfkfhvx37jrbvxd4dyjclz5cm3xh50z7s5rbzapiyxn4hs"))))
15009 (build-system r-build-system)
15011 (list r-mass r-matrix))
15012 (home-page "https://cran.r-project.org/web/packages/speedglm")
15013 (synopsis "Fit linear and generalized linear models to large data sets")
15015 "This package provides tools for fitting linear models and generalized
15016 linear models to large data sets by updating algorithms.")
15017 ;; Any version of the GPL
15018 (license license:gpl2+)))
15020 (define-public r-densityclust
15022 (name "r-densityclust")
15027 (uri (cran-uri "densityClust" version))
15030 "05x2fi1zdnkrg2nimf8k904j3lpyw0f7nmk6ax5p7x7a98wb2iqs"))))
15031 (properties `((upstream-name . "densityClust")))
15032 (build-system r-build-system)
15041 (home-page "https://cran.r-project.org/web/packages/densityClust")
15042 (synopsis "Clustering by fast search and find of density peaks")
15044 "This package provides an improved implementation (based on k-nearest
15045 neighbors) of the density peak clustering algorithm, originally described by
15046 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
15047 large datasets (> 100,000 samples) very efficiently.")
15048 (license license:gpl2+)))
15050 (define-public r-combinat
15052 (name "r-combinat")
15057 (uri (cran-uri "combinat" version))
15060 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
15061 (build-system r-build-system)
15062 (home-page "https://cran.r-project.org/web/packages/combinat")
15063 (synopsis "Combinatorics utilities")
15064 (description "This package provides assorted routines for combinatorics.")
15065 (license license:gpl2)))
15067 (define-public r-qlcmatrix
15069 (name "r-qlcmatrix")
15074 (uri (cran-uri "qlcMatrix" version))
15077 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
15078 (properties `((upstream-name . "qlcMatrix")))
15079 (build-system r-build-system)
15081 (list r-docopt r-matrix r-slam r-sparsesvd))
15082 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
15083 (synopsis "Sparse matrix functions for quantitative language comparison")
15085 "This package provides an extension of the functionality of the Matrix
15086 package for using sparse matrices. Some of the functions are very general,
15087 while other are highly specific for the special data format used for
15088 @dfn{quantitative language comparison} (QLC).")
15089 (license license:gpl3)))
15091 (define-public r-qmri
15097 (uri (cran-uri "qMRI" version))
15100 "10x59g8awxjib5j5mc1yd5wsibk3z6ki6zifxsg8azl0zblxbscf"))))
15101 (properties `((upstream-name . "qMRI")))
15102 (build-system r-build-system)
15103 (propagated-inputs (list r-adimpro r-aws r-awsmethods r-oro-nifti
15105 (native-inputs (list gfortran r-knitr))
15106 (home-page "http://www.wias-berlin.de/research/ats/imaging/")
15107 (synopsis "Methods for quantitative magnetic resonance imaging (qMRI)")
15109 "This package provides implementation of methods for estimation of
15110 quantitative maps from @dfn{Multi-Parameter Mapping} (MPM) acquisitions
15111 including adaptive smoothing methods in the framework of the ESTATICS model.
15112 The smoothing method is described in Mohammadi et
15113 al. (2017). <doi:10.20347/WIAS.PREPRINT.2432>. Usage of the package is also
15114 described in Polzehl and Tabelow (2019), Magnetic Resonance Brain Imaging,
15115 Chapter 6, Springer, Use R! Series. <doi:10.1007/978-3-030-29184-6_6>.")
15116 (license license:gpl2+)))
15118 (define-public r-ddrtree
15125 (uri (cran-uri "DDRTree" version))
15128 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
15129 (properties `((upstream-name . "DDRTree")))
15130 (build-system r-build-system)
15132 (list r-bh r-irlba r-rcpp r-rcppeigen))
15133 (home-page "https://cran.r-project.org/web/packages/DDRTree")
15134 (synopsis "Learning principal graphs with DDRTree")
15136 "This package provides an implementation of the framework of
15137 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
15138 dimensional space while constructs a principal tree which passes through the
15139 middle of the data simultaneously. DDRTree shows superiority to
15140 alternatives (Wishbone, DPT) for inferring the ordering as well as the
15141 intrinsic structure of single cell genomics data. In general, it could be
15142 used to reconstruct the temporal progression as well as the bifurcation
15143 structure of any data type.")
15144 (license license:asl2.0)))
15146 (define-public r-corpcor
15153 (uri (cran-uri "corpcor" version))
15156 "028fw61n61i79fhnaqx7gmdifdpbvp3yiaq9vvfrbv4k7i84r83i"))))
15157 (build-system r-build-system)
15158 (home-page "http://strimmerlab.org/software/corpcor/")
15159 (synopsis "Efficient estimation of covariance and (partial) correlation")
15161 "This package implements a James-Stein-type shrinkage estimator for the
15162 covariance matrix, with separate shrinkage for variances and correlations.
15163 Furthermore, functions are available for fast singular value decomposition,
15164 for computing the pseudoinverse, and for checking the rank and positive
15165 definiteness of a matrix.")
15166 (license license:gpl3+)))
15168 (define-public r-rspectra
15170 (name "r-rspectra")
15175 (uri (cran-uri "RSpectra" version))
15178 "16ij84wgpsmqmnxqiii8dgihy3bfxazry9znmckhwzba7m0d79fb"))))
15179 (properties `((upstream-name . "RSpectra")))
15180 (build-system r-build-system)
15182 (list r-matrix r-rcpp r-rcppeigen))
15185 (home-page "https://github.com/yixuan/RSpectra")
15186 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
15188 "This package provides an R interface to the Spectra library for
15189 large-scale eigenvalue and SVD problems. It is typically used to compute a
15190 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
15191 which is usually more efficient than @code{eigen()} if k << n.")
15193 (license license:mpl2.0)))
15195 (define-public r-vbsr
15202 (uri (cran-uri "vbsr" version))
15205 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
15206 (build-system r-build-system)
15207 (home-page "https://cran.r-project.org/web/packages/vbsr")
15208 (synopsis "Variational Bayes spike regression regularized linear models")
15210 "This package provides an efficient algorithm for solving ultra-sparse
15211 regularized regression models using a variational Bayes algorithm with a spike
15212 prior. The algorithm is solved on a path, with coordinate updates, and is
15213 capable of generating very sparse models. Very general model
15214 diagnostics for controlling type-1 errors are also provided.")
15215 (license license:gpl2)))
15217 (define-public r-flare
15220 (version "1.7.0.1")
15224 (uri (cran-uri "flare" version))
15227 "1xvrbvq2y7zfp98ijal3z8y1w2xbzfcdykzw4pqc3mnh0qrhq2d5"))))
15228 (build-system r-build-system)
15230 (list r-igraph r-lattice r-mass r-matrix))
15231 (home-page "https://cran.r-project.org/web/packages/flare")
15232 (synopsis "Family of Lasso regression implementations")
15234 "This package provides implementations of a family of Lasso variants
15235 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
15236 high dimensional sparse linear models.")
15237 (license license:gpl2)))
15239 (define-public r-lassopv
15246 (uri (cran-uri "lassopv" version))
15249 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
15250 (build-system r-build-system)
15251 (propagated-inputs (list r-lars))
15252 (home-page "https://github.com/lingfeiwang/lassopv")
15253 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
15255 "This package enables you to estimate the p-values for predictors x
15256 against target variable y in Lasso regression, using the regularization
15257 strength when each predictor enters the active set of regularization path for
15258 the first time as the statistic.")
15259 (license license:gpl3)))
15261 (define-public r-splitstackshape
15263 (name "r-splitstackshape")
15268 (uri (cran-uri "splitstackshape" version))
15271 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
15272 (build-system r-build-system)
15274 (list r-data-table))
15275 (home-page "https://github.com/mrdwab/splitstackshape")
15276 (synopsis "Stack and reshape datasets after splitting concatenated values")
15278 "Online data collection tools like Google Forms often export
15279 multiple-response questions with data concatenated in cells. The
15280 @code{concat.split} (cSplit) family of functions provided by this package
15281 splits such data into separate cells. This package also includes functions to
15282 stack groups of columns and to reshape wide data, even when the data are
15283 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
15284 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
15286 (license license:gpl3)))
15288 (define-public r-tfmpvalue
15290 (name "r-tfmpvalue")
15295 (uri (cran-uri "TFMPvalue" version))
15298 "1rsxqvq1nkyhwmhm7mf7rd02rvh7xinnhqbqic6q9vicbvkmdnxr"))))
15299 (properties `((upstream-name . "TFMPvalue")))
15300 (build-system r-build-system)
15301 (propagated-inputs (list r-rcpp))
15302 (home-page "https://github.com/ge11232002/TFMPvalue")
15303 (synopsis "P-value computation for position weight matrices")
15305 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
15306 identification from sequence/alignments, we are interested in the significance
15307 of certain match scores. TFMPvalue provides the accurate calculation of a
15308 p-value with a score threshold for position weight matrices, or the score with
15309 a given p-value. It is an interface to code originally made available by
15310 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
15311 Touzet and Varre (2007).")
15312 (license license:gpl2)))
15314 (define-public r-rncl
15320 (uri (cran-uri "rncl" version))
15323 "1ywgwqn82z8h6zpcxxq4hgngdpfa6dj0lr7bfq4cwfml9z075jgw"))))
15324 (build-system r-build-system)
15326 (list r-progress r-rcpp))
15327 (home-page "https://github.com/fmichonneau/rncl")
15328 (synopsis "Interface to the Nexus class library")
15329 (description "This package provides an interface to the Nexus class
15330 library which allows parsing of NEXUS, Newick and other phylogenetic tree
15331 file formats. It provides elements of the file that can be used to build
15332 phylogenetic objects such as @code{ape}'s @code{phylo} or @code{phylobase}'s
15333 @code{phylo4(d)}. This functionality is demonstrated with
15334 @code{read_newick_phylo()} and @code{read_nexus_phylo()}.")
15335 (license license:bsd-2)))
15337 (define-public r-phylobase
15339 (name "r-phylobase")
15343 (uri (cran-uri "phylobase" version))
15346 "0jzr1gdvmi4l640hwwzh9bxqmpja69bn3ygnaqx37awvyh7khi2s"))))
15347 (build-system r-build-system)
15349 (list r-ade4 r-ape r-rcpp r-rncl r-rnexml))
15352 (home-page "https://github.com/fmichonneau/phylobase")
15353 (synopsis "Base package for phylogenetic structures and comparative data")
15354 (description "This package provides a base @code{S4} class for comparative
15355 methods, incorporating one or more trees and trait data.")
15356 (license license:gpl2+)))
15358 (define-public r-phylotools
15360 (name "r-phylotools")
15364 (uri (cran-uri "phylotools" version))
15367 "1dhk1ncp5zi4zl1xfnjz64v983dm7bq7iimfjin80j0bdcpps44w"))))
15368 (properties `((upstream-name . "phylotools")))
15369 (build-system r-build-system)
15370 (propagated-inputs (list r-ape))
15371 (home-page "https://github.com/helixcn/phylotools")
15372 (synopsis "Phylogenetic tools for eco-phylogenetics")
15374 "This package provides a collection of tools for building RAxML
15375 supermatrix using PHYLIP or aligned FASTA files. These functions will be
15376 useful for building large phylogenies using multiple markers.")
15377 (license license:gpl2)))
15379 (define-public r-rnexml
15385 (uri (cran-uri "RNeXML" version))
15388 "0l5qpg6f107k927vnnki7g9yfs20xkpd7c5pkvbj8bpybbwjkm16"))))
15389 (build-system r-build-system)
15405 (home-page "https://docs.ropensci.org/RNeXML/")
15406 (synopsis "Semantically rich I/O for the NeXML Format")
15407 (description "This package provides access to phyloinformatic data in
15408 NeXML format. The package should add new functionality to R such as the
15409 possibility to manipulate NeXML objects in more various and refined way
15410 and compatibility with @code{ape} objects.")
15411 (license license:bsd-3)))
15413 (define-public r-rnifti
15420 (uri (cran-uri "RNifti" version))
15423 "1zr9g102zhb1h6a06p141g1jq0ik94kah8r3z3q2zharj30y2waz"))))
15424 (properties `((upstream-name . "RNifti")))
15425 (build-system r-build-system)
15426 (inputs (list zlib))
15427 (propagated-inputs (list r-rcpp))
15428 (home-page "https://github.com/jonclayden/RNifti")
15429 (synopsis "Fast R and C++ access to NIfTI images")
15431 "This package provides very fast read and write access to images stored
15432 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
15433 compiled C and interpreted R code. It also provides a C/C++ API that can be
15434 used by other packages.")
15435 (license license:gpl2)))
15437 (define-public r-shades
15444 (uri (cran-uri "shades" version))
15447 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
15448 (build-system r-build-system)
15449 (home-page "https://github.com/jonclayden/shades")
15450 (synopsis "Simple color manipulation")
15452 "This package provides functions for easily manipulating colors,
15453 creating color scales and calculating color distances.")
15454 (license license:bsd-3)))
15456 (define-public r-ore
15459 (version "1.7.1.1")
15463 (uri (cran-uri "ore" version))
15465 (base32 "0rs5r5h11x4l4nsbl4xqzbl4ahajd5374fq05abcmfjnjr9j64w5"))))
15466 (build-system r-build-system)
15467 (home-page "https://github.com/jonclayden/ore")
15468 (synopsis "R interface to the Onigmo regular expression library")
15470 "This package provides an alternative to R's built-in functionality for
15471 handling regular expressions, based on the Onigmo library. It offers
15472 first-class compiled regex objects, partial matching and function-based
15473 substitutions, amongst other features.")
15474 (license license:bsd-3)))
15476 (define-public r-reportr
15483 (uri (cran-uri "reportr" version))
15486 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
15487 (build-system r-build-system)
15488 (propagated-inputs (list r-ore))
15489 (home-page "https://github.com/jonclayden/reportr")
15490 (synopsis "General message and error reporting system")
15492 "This package provides a system for reporting messages, which offers
15493 certain useful features over the standard R system, such as the incorporation
15494 of output consolidation, message filtering, assertions, expression
15495 substitution, automatic generation of stack traces for debugging, and
15496 conditional reporting based on the current \"output level\".")
15497 (license license:gpl2)))
15499 (define-public r-tractor-base
15501 (name "r-tractor-base")
15502 (version "3.3.5.1")
15506 (uri (cran-uri "tractor.base" version))
15509 "0fxbzbhpi6l55m14nmww8y3kdxgchzj4mw1yf4xkm2y6s68phvgc"))))
15510 (properties `((upstream-name . "tractor.base")))
15511 (build-system r-build-system)
15513 (list r-ore r-reportr r-rnifti r-shades))
15514 (home-page "https://www.tractor-mri.org.uk")
15515 (synopsis "Read, manipulate and visualize magnetic resonance images")
15517 "This package provides functions for working with magnetic resonance
15518 images. It supports reading and writing of popular file formats (DICOM,
15519 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
15520 visualization; flexible image manipulation; metadata and sparse image
15522 (license license:gpl2)))
15524 (define-public r-grimport
15526 (name "r-grimport")
15531 (uri (cran-uri "grImport" version))
15534 "0pbzc45wgp0cpycnw0bzn65ckdszzay0zrp7c7ssxdkifp8bai3a"))))
15535 (properties `((upstream-name . "grImport")))
15536 (build-system r-build-system)
15538 (list ghostscript))
15541 (home-page "https://cran.r-project.org/web/packages/grImport")
15542 (synopsis "Convert, import, and draw PostScript pictures")
15544 "This package provides functions for converting, importing, and drawing
15545 PostScript pictures in R plots.")
15546 (license license:gpl2+)))
15548 (define-public r-grimport2
15550 (name "r-grimport2")
15555 (uri (cran-uri "grImport2" version))
15558 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
15559 (properties `((upstream-name . "grImport2")))
15560 (build-system r-build-system)
15562 (list r-base64enc r-jpeg r-png r-xml))
15563 (home-page "https://cran.r-project.org/web/packages/grImport2/")
15564 (synopsis "Import SVG graphics")
15566 "This package provides functions for importing external vector images and
15567 drawing them as part of R plots. This package is different from the
15568 @code{grImport} package because, where that package imports PostScript format
15569 images, this package imports SVG format images. Furthermore, this package
15570 imports a specific subset of SVG, so external images must be preprocessed
15571 using a package like @code{rsvg} to produce SVG that this package can import.
15572 SVG features that are not supported by R graphics, such as gradient fills, can
15573 be imported and then exported via the @code{gridSVG} package.")
15574 (license license:gpl2+)))
15576 (define-public r-kohonen
15583 (uri (cran-uri "kohonen" version))
15586 "1bk3j0n8w4fhffv89rgyn4n21c0wcx6lr8jv4wbagpxprl585381"))))
15587 (build-system r-build-system)
15590 (home-page "https://cran.r-project.org/web/packages/kohonen")
15591 (synopsis "Supervised and unsupervised self-organising maps")
15593 "This package provides functions to train @dfn{self-organising
15594 maps} (SOMs). Also interrogation of the maps and prediction using trained
15595 maps are supported. The name of the package refers to Teuvo Kohonen, the
15596 inventor of the SOM.")
15597 (license license:gpl2+)))
15599 (define-public r-nnls
15606 (uri (cran-uri "nnls" version))
15609 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
15610 (build-system r-build-system)
15611 (native-inputs (list gfortran))
15612 (home-page "https://cran.r-project.org/web/packages/nnls")
15613 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
15615 "This package provides an R interface to the Lawson-Hanson implementation
15616 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
15617 the combination of non-negative and non-positive constraints.")
15618 (license license:gpl2+)))
15620 (define-public r-iso
15623 (version "0.0-18.1")
15627 (uri (cran-uri "Iso" version))
15630 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
15631 (properties `((upstream-name . "Iso")))
15632 (build-system r-build-system)
15633 (native-inputs (list gfortran))
15634 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
15635 (synopsis "Functions to perform isotonic regression")
15637 "This package provides support for linear order and unimodal
15638 order (univariate) isotonic regression and bivariate isotonic regression with
15639 linear order on both variables.")
15640 (license license:gpl2+)))
15642 (define-public r-chemometricswithr
15644 (name "r-chemometricswithr")
15649 (uri (cran-uri "ChemometricsWithR" version))
15652 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
15654 `((upstream-name . "ChemometricsWithR")))
15655 (build-system r-build-system)
15657 (list r-devtools r-kohonen r-mass r-pls))
15658 (home-page "https://github.com/rwehrens/CWR")
15659 (synopsis "Chemometrics with R")
15661 "This package provides functions and scripts used in the book
15662 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
15663 Life Sciences\" by Ron Wehrens, Springer (2011).")
15664 (license license:gpl2+)))
15666 (define-public r-als
15673 (uri (cran-uri "ALS" version))
15676 "184d6xr4mgs78jvi7xa4njrq6p625i9sx69wak6mdn53qpl9b8ap"))))
15677 (properties `((upstream-name . "ALS")))
15678 (build-system r-build-system)
15680 (list r-iso r-nnls))
15681 (home-page "https://cran.r-project.org/web/packages/ALS")
15682 (synopsis "Multivariate curve resolution alternating least squares")
15684 "Alternating least squares is often used to resolve components
15685 contributing to data with a bilinear structure; the basic technique may be
15686 extended to alternating constrained least squares. This package provides an
15687 implementation of @dfn{multivariate curve resolution alternating least
15688 squares} (MCR-ALS).
15690 Commonly applied constraints include unimodality, non-negativity, and
15691 normalization of components. Several data matrices may be decomposed
15692 simultaneously by assuming that one of the two matrices in the bilinear
15693 decomposition is shared between datasets.")
15694 (license license:gpl2+)))
15696 (define-public r-strucchange
15698 (name "r-strucchange")
15703 (uri (cran-uri "strucchange" version))
15706 "11hgz64snlwhfqsmqajmkciflwkz1wficxr340wqvk38iw1b9ina"))))
15707 (build-system r-build-system)
15709 (list r-sandwich r-zoo))
15710 (home-page "https://cran.r-project.org/web/packages/strucchange")
15711 (synopsis "Testing, monitoring, and dating structural changes")
15713 "This package provides tools for testing, monitoring and dating
15714 structural changes in (linear) regression models. It features tests/methods
15715 from the generalized fluctuation test framework as well as from the F
15716 test (Chow test) framework. This includes methods to fit, plot and test
15717 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
15718 statistics, respectively. It is possible to monitor incoming data online
15719 using fluctuation processes. Finally, the breakpoints in regression models
15720 with structural changes can be estimated together with confidence intervals.
15721 Emphasis is always given to methods for visualizing the data.")
15722 ;; Either of these two GPL versions
15723 (license (list license:gpl2 license:gpl3))))
15725 (define-public r-pixmap
15732 (uri (cran-uri "pixmap" version))
15735 "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9"))))
15736 (build-system r-build-system)
15737 (home-page "https://cran.r-project.org/web/packages/pixmap")
15738 (synopsis "Tools for bitmap images")
15740 "This package provides functions for importing, exporting, plotting and
15741 other manipulations of bitmapped images.")
15742 (license license:gpl2)))
15744 (define-public r-rapidjsonr
15746 (name "r-rapidjsonr")
15751 (uri (cran-uri "rapidjsonr" version))
15754 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
15755 (build-system r-build-system)
15756 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
15757 (synopsis "JSON parser")
15759 "This package provides JSON parsing capability through the Rapidjson
15761 (license license:expat)))
15763 (define-public r-ontologyindex
15765 (name "r-ontologyindex")
15770 (uri (cran-uri "ontologyIndex" version))
15773 "0hisb9scxyyqkxhxhvgsgwix54pkq0zma3xq3ywczyazvzcxd5f9"))))
15774 (properties `((upstream-name . "ontologyIndex")))
15775 (build-system r-build-system)
15778 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
15779 (synopsis "Functions for processing ontologies in R")
15781 "This package provides functions for reading ontologies into R as lists
15782 and manipulating sets of ontological terms.")
15783 (license license:gpl2+)))
15785 (define-public r-gargle
15792 (uri (cran-uri "gargle" version))
15795 "087hlbqpwjj7jnsg1ax2b12nc0h4zfj070q5hjp6fca05z4f4rzk"))))
15796 (build-system r-build-system)
15809 (home-page "https://gargle.r-lib.org")
15810 (synopsis "Utilities for working with Google APIs")
15812 "This package provides utilities for working with Google APIs. This
15813 includes functions and classes for handling common credential types and for
15814 preparing, executing, and processing HTTP requests.")
15815 (license license:expat)))
15817 (define-public r-bigrquery
15819 (name "r-bigrquery")
15824 (uri (cran-uri "bigrquery" version))
15827 "1rcz1zq0azrrchhxz4b0g4m9c3ymp4pasi7ji1nvx25w5x41sdmv"))))
15828 (build-system r-build-system)
15846 (home-page "https://github.com/rstats-db/bigrquery")
15847 (synopsis "R interface to Google's BigQuery API")
15849 "This package provides an R interface to Google's BigQuery database.")
15850 (license license:gpl3)))
15852 (define-public r-gmp
15859 (uri (cran-uri "gmp" version))
15862 "119z6q3xca1ysdpjfmq3crplj355vlwggxvqh2gs4yi63xlzwcv3"))))
15863 (build-system r-build-system)
15866 (modify-phases %standard-phases
15867 (add-after 'unpack 'set-CC
15868 (lambda _ (setenv "CC" "gcc") #t)))))
15869 (inputs (list gmp))
15870 (home-page "https://cran.r-project.org/web/packages/gmp")
15871 (synopsis "Multiple precision arithmetic")
15873 "This package supports multiple precision arithmetic (big integers and
15874 rationals, prime number tests, matrix computation), \"arithmetic without
15875 limitations\" using the GNU Multiple Precision library.")
15876 ;; Any version of the GPL.
15877 (license license:gpl3+)))
15879 (define-public r-rmpfr
15886 (uri (cran-uri "Rmpfr" version))
15889 "12mwvgyalzh4zf5d002fm1hpr3wwhiypy9ia6wy47ij9gns5mvng"))))
15890 (properties `((upstream-name . "Rmpfr")))
15891 (build-system r-build-system)
15898 (home-page "http://rmpfr.r-forge.r-project.org/")
15899 (synopsis "R bindings to the MPFR library")
15901 "This package supports arithmetic (via S4 classes and methods) for
15902 arbitrary precision floating point numbers, including transcendental
15903 functions. To this end, the package interfaces with the @dfn{Multiple
15904 Precision Floating-Point Reliable} (MPFR) library.")
15905 (license license:gpl2+)))
15907 (define-public r-assertive-base
15909 (name "r-assertive-base")
15914 (uri (cran-uri "assertive.base" version))
15917 "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b"))))
15919 `((upstream-name . "assertive.base")))
15920 (build-system r-build-system)
15921 (home-page "https://bitbucket.org/richierocks/assertive.base")
15922 (synopsis "Core of the assertive package")
15924 "This package provides a minimal set of predicates and assertions used by
15925 the assertive package. This is mainly for use by other package developers who
15926 want to include run-time testing features in their own packages.")
15927 (license license:gpl3+)))
15929 (define-public r-assertive-properties
15931 (name "r-assertive-properties")
15936 (uri (cran-uri "assertive.properties" version))
15939 "1pgljbwwbvbl4kc5c8mcv0qbzq3k6fzi29k88811yml263sm92dn"))))
15941 `((upstream-name . "assertive.properties")))
15942 (build-system r-build-system)
15944 (list r-assertive-base))
15945 (home-page "https://bitbucket.org/richierocks/assertive.properties")
15946 (synopsis "Assertions to check properties of variables")
15948 "This package provides a set of predicates and assertions for checking
15949 the properties of variables, such as length, names and attributes. This is
15950 mainly for use by other package developers who want to include run-time
15951 testing features in their own packages.")
15952 (license license:gpl3+)))
15954 (define-public r-assertive-numbers
15956 (name "r-assertive-numbers")
15961 (uri (cran-uri "assertive.numbers" version))
15964 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
15966 `((upstream-name . "assertive.numbers")))
15967 (build-system r-build-system)
15969 (list r-assertive-base))
15970 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
15971 (synopsis "Assertions to check properties of numbers")
15973 "This package provides a set of predicates and assertions for checking
15974 the properties of numbers. This is mainly for use by other package developers
15975 who want to include run-time testing features in their own packages.")
15976 (license license:gpl3+)))
15978 (define-public r-assertive-sets
15980 (name "r-assertive-sets")
15985 (uri (cran-uri "assertive.sets" version))
15988 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
15990 `((upstream-name . "assertive.sets")))
15991 (build-system r-build-system)
15993 (list r-assertive-base))
15994 (home-page "https://bitbucket.org/richierocks/assertive.sets")
15995 (synopsis "Assertions to check properties of sets")
15997 "This package provides a set of predicates and assertions for checking
15998 the properties of sets. This is mainly for use by other package developers
15999 who want to include run-time testing features in their own packages.")
16000 (license license:gpl3+)))
16002 (define-public r-assertive-matrices
16004 (name "r-assertive-matrices")
16009 (uri (cran-uri "assertive.matrices" version))
16012 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
16014 `((upstream-name . "assertive.matrices")))
16015 (build-system r-build-system)
16017 (list r-assertive-base))
16018 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
16019 (synopsis "Assertions to check properties of matrices")
16021 "This package provides a set of predicates and assertions for checking
16022 the properties of matrices. This is mainly for use by other package
16023 developers who want to include run-time testing features in their own
16025 (license license:gpl3+)))
16027 (define-public r-assertive-models
16029 (name "r-assertive-models")
16034 (uri (cran-uri "assertive.models" version))
16037 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
16039 `((upstream-name . "assertive.models")))
16040 (build-system r-build-system)
16042 (list r-assertive-base))
16043 (home-page "https://bitbucket.org/richierocks/assertive.models")
16044 (synopsis "Assertions to check properties of models")
16046 "This package provides a set of predicates and assertions for checking
16047 the properties of models. This is mainly for use by other package developers
16048 who want to include run-time testing features in their own packages.")
16049 (license license:gpl3+)))
16051 (define-public r-assertive-reflection
16053 (name "r-assertive-reflection")
16058 (uri (cran-uri "assertive.reflection" version))
16061 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
16063 `((upstream-name . "assertive.reflection")))
16064 (build-system r-build-system)
16066 (list r-assertive-base))
16067 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
16068 (synopsis "Assertions for checking the state of R")
16070 "This package provides a set of predicates and assertions for checking
16071 the state and capabilities of R, the operating system it is running on, and
16072 the IDE being used. This is mainly for use by other package developers who
16073 want to include run-time testing features in their own packages.")
16074 (license license:gpl3+)))
16076 (define-public r-assertive-types
16078 (name "r-assertive-types")
16083 (uri (cran-uri "assertive.types" version))
16086 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
16088 `((upstream-name . "assertive.types")))
16089 (build-system r-build-system)
16091 (list r-assertive-base r-assertive-properties r-codetools))
16092 (home-page "https://bitbucket.org/richierocks/assertive.types")
16093 (synopsis "Assertions to check types of variables")
16095 "This package provides a set of predicates and assertions for checking
16096 the types of variables. This is mainly for use by other package developers
16097 who want to include run-time testing features in their own packages.")
16098 (license license:gpl3+)))
16100 (define-public r-assertive-files
16102 (name "r-assertive-files")
16107 (uri (cran-uri "assertive.files" version))
16110 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
16112 `((upstream-name . "assertive.files")))
16113 (build-system r-build-system)
16115 (list r-assertive-base r-assertive-numbers))
16116 (home-page "https://bitbucket.org/richierocks/assertive.files")
16117 (synopsis "Assertions to check properties of files")
16119 "This package provides a set of predicates and assertions for checking
16120 the properties of files and connections. This is mainly for use by other
16121 package developers who want to include run-time testing features in their own
16123 (license license:gpl3+)))
16125 (define-public r-assertive-code
16127 (name "r-assertive-code")
16132 (uri (cran-uri "assertive.code" version))
16135 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
16137 `((upstream-name . "assertive.code")))
16138 (build-system r-build-system)
16140 (list r-assertive-base r-assertive-properties r-assertive-types))
16141 (home-page "https://bitbucket.org/richierocks/assertive.code")
16142 (synopsis "Assertions to check properties of code")
16144 "This package provides a set of predicates and assertions for checking
16145 the properties of code. This is mainly for use by other package developers
16146 who want to include run-time testing features in their own packages.")
16147 (license license:gpl3+)))
16149 (define-public r-assertive-datetimes
16151 (name "r-assertive-datetimes")
16156 (uri (cran-uri "assertive.datetimes" version))
16159 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
16161 `((upstream-name . "assertive.datetimes")))
16162 (build-system r-build-system)
16164 (list r-assertive-base r-assertive-types))
16165 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
16166 (synopsis "Assertions to check properties of dates and times")
16168 "This package provides a set of predicates and assertions for checking
16169 the properties of dates and times. This is mainly for use by other package
16170 developers who want to include run-time testing features in their own
16172 (license license:gpl3+)))
16174 (define-public r-assertive-strings
16176 (name "r-assertive-strings")
16181 (uri (cran-uri "assertive.strings" version))
16184 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
16186 `((upstream-name . "assertive.strings")))
16187 (build-system r-build-system)
16189 (list r-assertive-base r-assertive-types r-stringi))
16190 (home-page "https://bitbucket.org/richierocks/assertive.strings")
16191 (synopsis "Assertions to check properties of strings")
16193 "This package provides a set of predicates and assertions for checking
16194 the properties of strings. This is mainly for use by other package developers
16195 who want to include run-time testing features in their own packages.")
16196 (license license:gpl3+)))
16198 (define-public r-assertive-data-us
16200 (name "r-assertive-data-us")
16205 (uri (cran-uri "assertive.data.us" version))
16208 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
16210 `((upstream-name . "assertive.data.us")))
16211 (build-system r-build-system)
16213 (list r-assertive-base r-assertive-strings))
16214 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
16215 (synopsis "Assertions to check properties of strings")
16217 "This package provides a set of predicates and assertions for checking
16218 the properties of US-specific complex data types. This is mainly for use by
16219 other package developers who want to include run-time testing features in
16220 their own packages.")
16221 (license license:gpl3+)))
16223 (define-public r-assertive-data-uk
16225 (name "r-assertive-data-uk")
16230 (uri (cran-uri "assertive.data.uk" version))
16233 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
16235 `((upstream-name . "assertive.data.uk")))
16236 (build-system r-build-system)
16238 (list r-assertive-base r-assertive-strings))
16239 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
16240 (synopsis "Assertions to check properties of strings")
16242 "This package provides a set of predicates and assertions for checking
16243 the properties of UK-specific complex data types. This is mainly for use by
16244 other package developers who want to include run-time testing features in
16245 their own packages.")
16246 (license license:gpl3+)))
16248 (define-public r-assertive-data
16250 (name "r-assertive-data")
16255 (uri (cran-uri "assertive.data" version))
16258 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
16260 `((upstream-name . "assertive.data")))
16261 (build-system r-build-system)
16263 (list r-assertive-base r-assertive-strings))
16264 (home-page "https://bitbucket.org/richierocks/assertive.data")
16265 (synopsis "Assertions to check properties of data")
16267 "This package provides a set of predicates and assertions for checking
16268 the properties of (country independent) complex data types. This is mainly
16269 for use by other package developers who want to include run-time testing
16270 features in their own packages.")
16271 (license license:gpl3+)))
16273 (define-public r-assertive
16275 (name "r-assertive")
16280 (uri (cran-uri "assertive" version))
16283 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
16284 (build-system r-build-system)
16286 (list r-assertive-base
16289 r-assertive-data-uk
16290 r-assertive-data-us
16291 r-assertive-datetimes
16293 r-assertive-matrices
16295 r-assertive-numbers
16296 r-assertive-properties
16297 r-assertive-reflection
16299 r-assertive-strings
16304 (home-page "https://bitbucket.org/richierocks/assertive")
16305 (synopsis "Readable check functions to ensure code integrity")
16307 "This package provides lots of predicates (@code{is_*} functions) to
16308 check the state of your variables, and assertions (@code{assert_*} functions)
16309 to throw errors if they aren't in the right form.")
16310 (license license:gpl3+)))
16312 (define-public r-dotcall64
16314 (name "r-dotcall64")
16319 (uri (cran-uri "dotCall64" version))
16322 "1b546z9r26q4xpr17gy2wzfych52q17sxvzydpqfp9dyxf575iz0"))))
16323 (properties `((upstream-name . "dotCall64")))
16324 (build-system r-build-system)
16325 (native-inputs (list gfortran))
16326 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
16327 (synopsis "Enhanced foreign function interface supporting long vectors")
16329 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
16330 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
16331 supports long vectors, arguments of type 64-bit integer, and provides a
16332 mechanism to avoid unnecessary copies of read-only and write-only arguments.
16333 This makes it a convenient and fast interface to C/C++ and Fortran code.")
16334 (license license:gpl2+)))
16336 (define-public r-spam
16343 (uri (cran-uri "spam" version))
16345 (base32 "1nvx965vxzs697k9m2l40a15bykflksn9bwa4py1p2wqg6922bn3"))))
16346 (build-system r-build-system)
16348 (list r-dotcall64))
16350 (list gfortran r-knitr))
16351 (home-page "https://www.math.uzh.ch/pages/spam/")
16352 (synopsis "Sparse matrix algebra")
16354 "This package provides a set of functions for sparse matrix algebra.
16355 Differences with other sparse matrix packages are:
16358 @item it only supports (essentially) one sparse matrix format;
16359 @item it is based on transparent and simple structure(s);
16360 @item it is tailored for MCMC calculations within G(M)RF;
16361 @item and it is fast and scalable (with the extension package @code{spam64}).
16363 ;; Either of these licenses
16364 (license (list license:bsd-3 license:lgpl2.0))))
16366 (define-public r-fields
16373 (uri (cran-uri "fields" version))
16375 (base32 "0d2lm4s9p3rv676z291fynpx3vdmi6cikcqlj23fxlj34icwbi2p"))))
16376 (build-system r-build-system)
16378 (list r-maps r-spam r-viridis))
16381 (home-page "https://www.image.ucar.edu/fields")
16382 (synopsis "Tools for spatial data")
16384 "This is a package for curve, surface and function fitting with an
16385 emphasis on splines, spatial data and spatial statistics. The major methods
16386 include cubic, and thin plate splines, Kriging, and compactly supported
16387 covariance functions for large data sets.")
16388 (license license:gpl2+)))
16390 (define-public r-spatialextremes
16392 (name "r-spatialextremes")
16397 (uri (cran-uri "SpatialExtremes" version))
16400 "0z1swxp1syz8hdskarjxx4sdd7wx835kcnb783bwqm235yh991j3"))))
16402 `((upstream-name . "SpatialExtremes")))
16403 (build-system r-build-system)
16405 (list r-fields r-maps))
16406 (home-page "http://spatialextremes.r-forge.r-project.org/")
16407 (synopsis "Modelling spatial extremes")
16409 "This package provides tools for the statistical modelling of spatial
16410 extremes using max-stable processes, copula or Bayesian hierarchical models.
16411 More precisely, this package allows (conditional) simulations from various
16412 parametric max-stable models, analysis of the extremal spatial dependence, the
16413 fitting of such processes using composite likelihoods or least square (simple
16414 max-stable processes only), model checking and selection and prediction.")
16415 (license license:gpl2+)))
16417 (define-public r-drc
16424 (uri (cran-uri "drc" version))
16427 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
16428 (build-system r-build-system)
16436 (home-page "https://cran.r-project.org/web/packages/drc")
16437 (synopsis "Analysis of dose-response curves")
16439 "This package provides a suite of flexible and versatile model fitting
16440 and after-fitting functions for the analysis of dose-response data.")
16441 (license license:gpl2+)))
16443 (define-public r-rmeta
16450 (uri (cran-uri "rmeta" version))
16453 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
16454 (build-system r-build-system)
16455 (home-page "https://cran.r-project.org/web/packages/rmeta")
16456 (synopsis "Tools for meta-analysis")
16458 "This package provides functions for simple fixed and random effects
16459 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
16460 draws standard summary plots, funnel plots, and computes summaries and tests
16461 for association and heterogeneity.")
16462 (license license:gpl2)))
16464 (define-public r-bootstrap
16466 (name "r-bootstrap")
16471 (uri (cran-uri "bootstrap" version))
16474 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
16475 (build-system r-build-system)
16476 (native-inputs (list gfortran))
16477 (home-page "https://cran.r-project.org/web/packages/bootstrap")
16478 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
16480 "This package provides software and data for the book \"An Introduction
16481 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
16482 This package is primarily provided for projects already based on it, and for
16483 support of the book. New projects should preferentially use the recommended
16484 package \"boot\".")
16485 (license license:bsd-3)))
16487 (define-public r-survivalroc
16489 (name "r-survivalroc")
16494 (uri (cran-uri "survivalROC" version))
16497 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
16498 (properties `((upstream-name . "survivalROC")))
16499 (build-system r-build-system)
16500 (home-page "https://cran.r-project.org/web/packages/survivalROC")
16501 (synopsis "Time-dependent ROC curve estimation from censored survival data")
16503 "Compute time-dependent ROC curve from censored survival data using
16504 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
16505 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
16506 (license license:gpl2+)))
16508 (define-public r-locfdr
16514 (uri (cran-uri "locfdr" version))
16517 "1falkbp2xz07am8jlhwlvyqvxnli4nwl188kd0g58vdfjcjy3mj2"))))
16518 (build-system r-build-system)
16519 (home-page "https://cran.r-project.org/web/packages/locfdr/")
16520 (synopsis "Computes local false discovery rates")
16521 (description "This package can be used to compute local false
16523 (license license:gpl2)))
16525 (define-public r-longitudinal
16527 (name "r-longitudinal")
16532 (uri (cran-uri "longitudinal" version))
16535 "046w3xbr535c5jyd68adv42a7limxp1mv57b5w6w673w707lmw2p"))))
16536 (build-system r-build-system)
16537 (propagated-inputs (list r-corpcor))
16538 (home-page "http://strimmerlab.org/software/longitudinal/")
16539 (synopsis "Analysis of multiple time course data")
16541 "This package contains general data structures and functions for
16542 longitudinal data with multiple variables, repeated measurements, and
16543 irregularly spaced time points. It also implements a shrinkage estimator of
16544 dynamical correlation and dynamical covariance.")
16545 (license license:gpl3+)))
16547 (define-public r-genenet
16554 (uri (cran-uri "GeneNet" version))
16557 "1r1khga3nxxjghs4vnbymzp0cwb1q17zw2v3a94qz8fsrirq1sf1"))))
16558 (properties `((upstream-name . "GeneNet")))
16559 (build-system r-build-system)
16561 (list r-corpcor r-fdrtool r-longitudinal))
16562 (home-page "http://strimmerlab.org/software/genenet/")
16563 (synopsis "Modeling and inferring gene networks")
16565 "This package analyzes gene expression (time series) data with focus on
16566 the inference of gene networks. In particular, GeneNet implements the methods
16567 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
16568 for learning large-scale gene association networks (including assignment of
16569 putative directions).")
16570 (license license:gpl3+)))
16572 (define-public r-rbamtools
16574 (name "r-rbamtools")
16575 (version "2.16.17")
16579 (uri (cran-uri "rbamtools" version))
16582 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
16583 (build-system r-build-system)
16584 (inputs (list zlib))
16586 (list r-refgenome))
16587 (home-page "https://cran.r-project.org/web/packages/rbamtools")
16588 (synopsis "Read and write BAM (binary alignment) files")
16590 "This package provides an R interface to functions of the SAMtools
16592 (license license:artistic2.0)))
16594 (define-public r-profvis
16600 (uri (cran-uri "profvis" version))
16603 "1f86m426pcf90l29hf4hkirzf8f38dihk52bxbdq2gvrrdili5s3"))
16604 (modules '((guix build utils)))
16606 '(with-directory-excursion "inst/htmlwidgets/lib"
16607 (for-each delete-file
16608 (list "highlight/highlight.js" ;from rmarkdown
16609 "jquery/jquery.min.js" ;version 1.12.4
16610 "d3/d3.min.js")))))) ;version 3.5.6
16611 (properties `((upstream-name . "profvis")))
16612 (build-system r-build-system)
16615 (modify-phases %standard-phases
16616 (add-after 'unpack 'process-javascript
16617 (lambda* (#:key inputs #:allow-other-keys)
16618 (with-directory-excursion "inst/htmlwidgets/lib/"
16621 inputs "/site-library/rmarkdown/rmd/h/highlightjs/highlight.js")
16622 "highlight/highlight.js")
16624 `((,(assoc-ref inputs "js-jquery")
16625 . "jquery/jquery.min.js")
16626 (,(assoc-ref inputs "js-d3")
16627 . "d3/d3.min.js"))))
16628 (for-each (lambda (source target)
16629 (format #true "Processing ~a --> ~a~%"
16631 (invoke "esbuild" source "--minify"
16632 (string-append "--outfile=" target)))
16634 (map cdr mapping)))))))))
16636 `(("esbuild" ,esbuild)
16637 ("r-rmarkdown" ,r-rmarkdown)
16641 (uri "https://raw.githubusercontent.com/d3/d3/v3.5.6/d3.js")
16644 "17qlbwn7vgx335gciq6zp2ib6zg1r9lfa6p1bd9g0ds0xbcsbvgd"))))
16648 (uri "https://code.jquery.com/jquery-1.12.4.js")
16651 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))))
16652 (propagated-inputs (list r-htmlwidgets r-stringr))
16653 (home-page "https://rstudio.github.io/profvis/")
16654 (synopsis "Interactive visualizations for profiling R code")
16655 (description "This package provides interactive visualizations for
16656 profiling R code.")
16657 (license license:gpl3)))
16659 (define-public r-protviz
16666 (uri (cran-uri "protViz" version))
16669 "0f6jwzcqi0w37hvg3i5dlk0c3anpkqh54ibf94vaf17r8sykr4nw"))))
16670 (properties `((upstream-name . "protViz")))
16671 (build-system r-build-system)
16672 (propagated-inputs (list r-rcpp))
16673 (home-page "https://github.com/protViz/protViz/")
16674 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
16676 "This package helps with quality checks, visualizations and analysis of
16677 mass spectrometry data, coming from proteomics experiments. The package is
16678 developed, tested and used at the Functional Genomics Center Zurich, where it
16679 is used mainly for prototyping, teaching, and having fun with proteomics data.
16680 But it can also be used to do data analysis for small scale data sets.")
16681 (license license:gpl3)))
16683 (define-public r-cmprsk
16690 (uri (cran-uri "cmprsk" version))
16692 (base32 "050f24l5ab1ds9824c7yjahimf6pg8ih2k83jzpzfb0n5k5jfh44"))))
16693 (build-system r-build-system)
16698 (home-page "https://cran.r-project.org/web/packages/cmprsk")
16699 (synopsis "Subdistribution analysis of competing risks")
16701 "This package provides tool for estimation, testing and regression
16702 modeling of subdistribution functions in competing risks, as described in
16703 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
16704 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
16705 A proportional hazards model for the subdistribution of a competing risk,
16706 JASA, 94:496-509.")
16707 (license license:gpl2+)))
16709 (define-public r-etm
16716 (uri (cran-uri "etm" version))
16719 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
16720 (build-system r-build-system)
16722 (list r-data-table r-lattice r-rcpp r-rcpparmadillo r-survival))
16723 (home-page "https://cran.r-project.org/web/packages/etm")
16724 (synopsis "Empirical transition matrix")
16726 "The @dfn{empirical transition matrix} (etm) package estimates
16727 the matrix of transition probabilities for any time-inhomogeneous multistate
16728 model with finite state space using the Aalen-Johansen estimator.")
16729 (license license:expat)))
16731 (define-public r-epi
16738 (uri (cran-uri "Epi" version))
16741 "1dkdx000cvy2rgxq3w6ppl3j9h7mwmcqg5xqsqh5hr3aks845pwx"))))
16742 (properties `((upstream-name . "Epi")))
16743 (build-system r-build-system)
16757 (home-page "https://BendixCarstensen.com/Epi/")
16758 (synopsis "Statistical analysis in epidemiology")
16760 "This package provides functions for demographic and epidemiological
16761 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
16762 particular representation, manipulation and simulation of multistate data -
16763 the Lexis suite of functions, which includes interfaces to the @code{mstate},
16764 @code{etm} and @code{cmprsk} packages. It also contains functions for
16765 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
16766 data and some useful functions for tabulation and plotting, as well as a
16767 number of epidemiological data sets.")
16768 (license license:gpl2)))
16770 (define-public r-ppls
16773 (version "1.6-1.1")
16777 (uri (cran-uri "ppls" version))
16780 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
16781 (build-system r-build-system)
16782 (propagated-inputs (list r-mass))
16783 (home-page "https://cran.r-project.org/web/packages/ppls")
16784 (synopsis "Penalized partial least squares")
16786 "This package contains linear and nonlinear regression methods based on
16787 partial least squares and penalization techniques. Model parameters are
16788 selected via cross-validation, and confidence intervals ans tests for the
16789 regression coefficients can be conducted via jackknifing.")
16790 (license license:gpl2+)))
16792 (define-public r-huge
16799 (uri (cran-uri "huge" version))
16801 (base32 "1sl457a1lndrx98y2j9a2smanawx2iqlhl82iand0g3p5xp8ch4j"))))
16802 (build-system r-build-system)
16804 (list r-igraph r-mass r-matrix r-rcpp r-rcppeigen))
16805 (home-page "https://cran.r-project.org/web/packages/huge")
16806 (synopsis "High-dimensional undirected graph estimation")
16808 "This package provides a general framework for high-dimensional
16809 undirected graph estimation. It integrates data preprocessing, neighborhood
16810 screening, graph estimation, and model selection techniques into a pipeline.")
16811 (license license:gpl2)))
16813 (define-public r-parcor
16820 (uri (cran-uri "parcor" version))
16823 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
16824 (build-system r-build-system)
16826 (list r-epi r-genenet r-glmnet r-mass r-ppls))
16827 (home-page "https://cran.r-project.org/web/packages/parcor")
16828 (synopsis "Regularized estimation of partial correlation matrices")
16830 "This package estimates the matrix of partial correlations based on
16831 different regularized regression methods: lasso, adaptive lasso, PLS, and
16832 Ridge Regression. In addition, the package provides model selection for
16833 lasso, adaptive lasso and Ridge regression based on cross-validation.")
16834 (license license:gpl2+)))
16836 (define-public r-mcmc
16843 (uri (cran-uri "mcmc" version))
16846 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
16847 (build-system r-build-system)
16848 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
16849 (synopsis "Markov chain Monte Carlo")
16851 "This package simulates continuous distributions of random vectors using
16852 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
16853 function that evaluates the log unnormalized density. Algorithms are random
16854 walk Metropolis algorithm (function @code{metrop}), simulated
16855 tempering (function @code{temper}), and morphometric random walk
16856 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
16857 by change of variable.")
16858 (license license:expat)))
16860 (define-public r-listenv
16867 (uri (cran-uri "listenv" version))
16870 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
16871 (build-system r-build-system)
16874 (modify-phases %standard-phases
16875 (add-after 'unpack 'set-HOME
16876 (lambda _ (setenv "HOME" "/tmp"))))))
16878 (list r-r-rsp)) ; vignette builder
16879 (home-page "https://github.com/HenrikBengtsson/listenv")
16880 (synopsis "Environments behaving (almost) as lists")
16882 "This package implements list environments. List environments are
16883 environments that have list-like properties. For instance, the elements of a
16884 list environment are ordered and can be accessed and iterated over using index
16886 (license license:lgpl2.1+)))
16888 (define-public r-globals
16895 (uri (cran-uri "globals" version))
16898 "158y39qv99f1kc2i7w8d4lm2ls96plb43fzamz31im9xb9bkmxpp"))))
16899 (build-system r-build-system)
16901 (list r-codetools))
16902 (home-page "https://github.com/HenrikBengtsson/globals")
16903 (synopsis "Identify global objects in R expressions")
16905 "This package provides tools to identify global (\"unknown\" or \"free\")
16906 objects in R expressions by code inspection using various strategies, e.g.
16907 conservative or liberal. The objective of this package is to make it as
16908 simple as possible to identify global objects for the purpose of exporting
16909 them in distributed compute environments.")
16910 (license license:lgpl2.1+)))
16912 (define-public r-parallelly
16914 (name "r-parallelly")
16919 (uri (cran-uri "parallelly" version))
16922 "146a9i999vrflr4g1fph1pgkl4bq0dw102bjw8pp1zy7kbsqbiii"))))
16923 (properties `((upstream-name . "parallelly")))
16924 (build-system r-build-system)
16925 (home-page "https://github.com/HenrikBengtsson/parallelly")
16926 (synopsis "Enhancements of the parallel package")
16928 "This package provides utility functions that enhance the @code{parallel}
16929 package and support the built-in parallel backends of the @code{future}
16930 package. For example, @code{availableCores} gives the number of CPU cores
16931 available to your R process as given by R options and environment variables,
16932 including those set by job schedulers on high-performance compute clusters.
16933 If none is set, it will fall back to @code{parallel::detectCores}. Another
16934 example is @code{makeClusterPSOCK}, which is backward compatible with
16935 @code{parallel::makePSOCKcluster} while doing a better job in setting up
16936 remote cluster workers without the need for configuring the firewall to do
16937 port-forwarding to your local computer.")
16938 (license license:lgpl2.1+)))
16940 (define-public r-future
16947 (uri (cran-uri "future" version))
16950 "1xhv0nf97yxxxsmxczyqqbnb4yn5sfn5vzvhm9dmw9csrmmadpbg"))))
16951 (build-system r-build-system)
16954 (modify-phases %standard-phases
16955 (add-after 'unpack 'set-HOME
16956 (lambda _ (setenv "HOME" "/tmp"))))))
16958 (list r-digest r-globals r-listenv r-parallelly))
16960 (list r-r-rsp)) ; vignette builder
16961 (home-page "https://github.com/HenrikBengtsson/future")
16962 (synopsis "Unified parallel and distributed processing in R")
16964 "The purpose of this package is to provide a lightweight and unified
16965 Future API for sequential and parallel processing of R expression via futures.
16966 This package implements sequential, multicore, multisession, and cluster
16967 futures. With these, R expressions can be evaluated on the local machine, in
16968 parallel a set of local machines, or distributed on a mix of local and remote
16969 machines. Extensions to this package implement additional backends for
16970 processing futures via compute cluster schedulers etc. Because of its unified
16971 API, there is no need to modify any code in order to switch from sequential on
16972 the local machine to, say, distributed processing on a remote compute cluster.")
16973 (license license:lgpl2.1+)))
16975 (define-public r-future-apply
16977 (name "r-future-apply")
16982 (uri (cran-uri "future.apply" version))
16985 "0cr141mamjxby79sww02493yal9lahslvp3a3ic7f856rbawq8jg"))))
16986 (properties `((upstream-name . "future.apply")))
16987 (build-system r-build-system)
16990 (modify-phases %standard-phases
16991 (add-after 'unpack 'set-HOME
16992 (lambda _ (setenv "HOME" "/tmp"))))))
16994 (list r-future r-globals))
16996 (list r-r-rsp)) ; vignette builder
16997 (home-page "https://github.com/HenrikBengtsson/future.apply")
16998 (synopsis "Apply function to elements in parallel using futures")
17000 "This package provides implementations of @code{apply()},
17001 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
17002 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
17003 can be resolved using any future-supported backend, e.g. parallel on the local
17004 machine or distributed on a compute cluster.")
17005 (license license:gpl2+)))
17007 (define-public r-rsvd
17014 (uri (cran-uri "rsvd" version))
17017 "07p2hjmpcwcsang8z9sjkpy94rydcin7m3hyvcgzgm5cd6w8c1p4"))))
17018 (build-system r-build-system)
17021 (home-page "https://github.com/erichson/rSVD")
17022 (synopsis "Randomized singular value decomposition")
17024 "Low-rank matrix decompositions are fundamental tools and widely used for
17025 data analysis, dimension reduction, and data compression. Classically, highly
17026 accurate deterministic matrix algorithms are used for this task. However, the
17027 emergence of large-scale data has severely challenged our computational
17028 ability to analyze big data. The concept of randomness has been demonstrated
17029 as an effective strategy to quickly produce approximate answers to familiar
17030 problems such as the @dfn{singular value decomposition} (SVD). This package
17031 provides several randomized matrix algorithms such as the randomized singular
17032 value decomposition (@code{rsvd}), randomized principal component
17033 analysis (@code{rpca}), randomized robust principal component
17034 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
17035 and the randomized CUR decomposition (@code{rcur}). In addition several plot
17036 functions are provided.")
17037 (license license:gpl3+)))
17039 (define-public r-sloop
17046 (uri (cran-uri "sloop" version))
17049 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
17050 (build-system r-build-system)
17052 (list r-codetools r-crayon r-purrr r-rlang r-tibble))
17053 (home-page "https://github.com/r-lib/sloop")
17054 (synopsis "Helpers for object-oriented programming in R")
17056 "This package provides a collection of helper functions designed to
17057 help you to better understand object oriented programming in R, particularly
17059 (license license:gpl3)))
17061 (define-public r-capushe
17068 (uri (cran-uri "capushe" version))
17071 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
17072 (build-system r-build-system)
17073 (propagated-inputs (list r-mass))
17074 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
17075 (synopsis "Calibrating penalties using slope heuristics")
17077 "This package provides tools for the calibration of penalized criteria
17078 for model selection. The calibration methods available are based on the slope
17080 (license license:gpl2+)))
17082 (define-public r-dorng
17089 (uri (cran-uri "doRNG" version))
17092 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
17093 (properties `((upstream-name . "doRNG")))
17094 (build-system r-build-system)
17096 (list r-foreach r-iterators r-rngtools))
17097 (home-page "https://renozao.github.io/doRNG/")
17098 (synopsis "Generic reproducible parallel backend for foreach loops")
17100 "This package provides functions to perform reproducible parallel
17101 @code{foreach} loops, using independent random streams as generated by
17102 L'Ecuyer's combined multiple-recursive generator. It enables to easily
17103 convert standard @code{%dopar%} loops into fully reproducible loops,
17104 independently of the number of workers, the task scheduling strategy, or the
17105 chosen parallel environment and associated foreach backend.")
17106 (license license:gpl2+)))
17108 (define-public r-blockmodeling
17110 (name "r-blockmodeling")
17115 (uri (cran-uri "blockmodeling" version))
17118 "19mxmxsnl6rrh85p0sak91vcaw4dz2cnm70hdzfwnvdrr695yw2z"))))
17119 (build-system r-build-system)
17122 (native-inputs (list gfortran))
17123 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
17124 (synopsis "Generalized and classical blockmodeling of valued networks")
17126 "This package is primarily meant as an implementation of generalized
17127 blockmodeling for valued networks. In addition, measures of similarity or
17128 dissimilarity based on structural equivalence and regular equivalence (REGE
17129 algorithms) can be computed and partitioned matrices can be plotted.")
17130 (license license:gpl2+)))
17132 (define-public r-upsetr
17139 (uri (cran-uri "UpSetR" version))
17142 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
17143 (properties `((upstream-name . "UpSetR")))
17144 (build-system r-build-system)
17146 (list r-ggplot2 r-gridextra r-plyr r-scales))
17147 (home-page "https://github.com/hms-dbmi/UpSetR")
17148 (synopsis "Visualize intersecting sets")
17150 "This package provides a more scalable alternative to Venn and Euler
17151 diagrams for visualizing intersecting sets. Create visualizations of
17152 intersecting sets using a novel matrix design, along with visualizations of
17153 several common set, element and attribute related tasks.")
17154 (license license:expat)))
17156 ;; This package includes a JavaScript file, which is not minified. When
17157 ;; upgrading please check that there are no new minified JavaScript files.
17158 (define-public r-shinybs
17165 (uri (cran-uri "shinyBS" version))
17168 "0h51685a9qll4agayldjyryi60ih969219ibg071slv0613p5v8a"))))
17169 (properties `((upstream-name . "shinyBS")))
17170 (build-system r-build-system)
17171 ;; The tests spawn Shiny browser apps. They cannot be run
17172 ;; non-interactively.
17173 (arguments '(#:tests? #f))
17175 (list r-htmltools r-shiny))
17176 (home-page "https://ebailey78.github.io/shinyBS/")
17177 (synopsis "Twitter Bootstrap components for Shiny")
17179 "This package adds additional Twitter Bootstrap components to Shiny.")
17180 (license license:gpl3)))
17182 (define-public r-shinyjqui
17184 (name "r-shinyjqui")
17189 (uri (cran-uri "shinyjqui" version))
17192 "135gwz7syyb6pbn0lkvmq0v1c6r1zivavnqhi1rnzbbzlysi27v1"))
17194 '(for-each delete-file
17195 (list "inst/www/shinyjqui.min.js"
17196 "inst/www/jquery.ui.touch-punch.min.js")))))
17197 (properties `((upstream-name . "shinyjqui")))
17198 (build-system r-build-system)
17201 (modify-phases %standard-phases
17202 (add-after 'unpack 'process-javascript
17203 (lambda* (#:key inputs #:allow-other-keys)
17204 (with-directory-excursion "inst/www"
17206 `((,(string-append (assoc-ref inputs "js-jquery.ui.touch-punch")
17207 "/jquery.ui.touch-punch.js")
17208 . "jquery.ui.touch-punch.min.js")
17210 . "shinyjqui.min.js"))))
17211 (for-each (lambda (source target)
17212 (format #true "Processing ~a --> ~a~%"
17214 (invoke "esbuild" source "--minify"
17215 (string-append "--outfile=" target)))
17217 (map cdr mapping)))))))))
17219 (list r-htmltools r-htmlwidgets r-jsonlite r-rlang r-shiny))
17221 `(("r-knitr" ,r-knitr)
17222 ("esbuild" ,esbuild)
17223 ("js-jquery.ui.touch-punch"
17226 (uri (git-reference
17227 (url "https://github.com/furf/jquery-ui-touch-punch")
17228 (commit "8f7559b6e65cdc3ee3648d5fe76d38c653f87ff5")))
17231 "1lzywp2q9hwx6d5fqjla95vp7ra2lahr5dam7lsqjmch9d98r48q"))))))
17232 (home-page "https://github.com/yang-tang/shinyjqui")
17233 (synopsis "jQuery UI interactions and effects for Shiny")
17235 "This is an extension to Shiny that brings interactions and animation
17236 effects from the jQuery UI library.")
17237 (license license:expat)))
17239 (define-public r-shinymanager
17241 (name "r-shinymanager")
17242 (version "1.0.410")
17246 (uri (cran-uri "shinymanager" version))
17248 (base32 "0nl672dgwj34wm4i3pxk28lv6qw9xsgg3hm0h78q3zdgk8a33kdn"))))
17249 (properties `((upstream-name . "shinymanager")))
17250 (build-system r-build-system)
17252 (list r-billboarder
17262 (native-inputs (list r-knitr))
17263 (home-page "https://github.com/datastorm-open/shinymanager")
17264 (synopsis "Authentication management for Shiny applications")
17266 "This package provides simple and secure authentication mechanism for
17267 single Shiny applications. Credentials are stored in an encrypted SQLite
17269 (license license:gpl3)))
17271 (define-public r-outliers
17273 (name "r-outliers")
17278 (uri (cran-uri "outliers" version))
17281 "1yrmwvjjb0a6sbx940k9svf23cykcxz8rrwcgyic7lpgzbrdfcfc"))))
17282 (build-system r-build-system)
17283 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
17284 (synopsis "Tests for outliers")
17286 "This package provides a collection of some tests commonly used for
17287 identifying outliers.")
17288 (license license:gpl2+)))
17290 (define-public r-bayesm
17297 (uri (cran-uri "bayesm" version))
17299 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
17300 (build-system r-build-system)
17302 (list r-rcpp r-rcpparmadillo))
17303 (home-page "http://www.perossi.org/home/bsm-1")
17304 (synopsis "Bayesian inference for marketing/micro-econometrics")
17306 "This package covers many important models used in marketing and
17307 micro-econometrics applications, including Bayes Regression (univariate or
17308 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
17309 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
17310 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
17311 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
17312 Estimation with normal base, Hierarchical Linear Models with normal prior and
17313 covariates, Hierarchical Linear Models with a mixture of normals prior and
17314 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
17315 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
17316 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
17317 analysis of choice-based conjoint data, Bayesian treatment of linear
17318 instrumental variables models, Analysis of Multivariate Ordinal survey data
17319 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
17320 Coefficient Logit Models.")
17321 (license license:gpl2+)))
17323 (define-public r-tensora
17330 (uri (cran-uri "tensorA" version))
17333 "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf"))))
17334 (properties `((upstream-name . "tensorA")))
17335 (build-system r-build-system)
17336 (home-page "http://www.stat.boogaart.de/tensorA")
17337 (synopsis "Advanced tensor arithmetic with named indices")
17339 "This package provides convenience functions for advanced linear algebra
17340 with tensors and computation with datasets of tensors on a higher level
17341 abstraction. It includes Einstein and Riemann summing conventions, dragging,
17342 co- and contravariate indices, and parallel computations on sequences of
17344 (license license:gpl2+)))
17346 (define-public r-rarpack
17353 (uri (cran-uri "rARPACK" version))
17356 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
17357 (properties `((upstream-name . "rARPACK")))
17358 (build-system r-build-system)
17359 (propagated-inputs (list r-rspectra))
17360 (home-page "https://github.com/yixuan/rARPACK")
17361 (synopsis "Solvers for large scale eigenvalue and SVD problems")
17363 "This package was previously an R wrapper of the ARPACK library, and now
17364 a shell of the R package RSpectra, an R interface to the Spectra library for
17365 solving large scale eigenvalue/vector problems. The current version of
17366 rARPACK simply imports and exports the functions provided by RSpectra. New
17367 users of rARPACK are advised to switch to the RSpectra package.")
17368 (license license:bsd-3)))
17370 (define-public r-compositions
17372 (name "r-compositions")
17377 (uri (cran-uri "compositions" version))
17380 "1bqg0qqzsf92q0jb7hdjycr54bwv8rk7ajhvxgch5yslyqxpm73v"))))
17381 (build-system r-build-system)
17383 (list r-bayesm r-mass r-robustbase r-tensora))
17386 (home-page "http://www.stat.boogaart.de/compositions")
17387 (synopsis "Compositional data analysis")
17389 "This package provides functions for the consistent analysis of
17390 compositional data (e.g. portions of substances) and positive
17391 numbers (e.g. concentrations).")
17392 (license license:gpl2+)))
17394 (define-public r-cobs
17401 (uri (cran-uri "cobs" version))
17404 "04f6a6gp11p93j2k35mbrfqgjx5qsgi3dj1085a5v5s0z6l7vbkz"))))
17405 (build-system r-build-system)
17407 (list r-quantreg r-sparsem))
17408 (home-page "https://cran.r-project.org/web/packages/cobs")
17409 (synopsis "Constrained B-Splines (sparse matrix based)")
17411 "This package provides qualitatively constrained (regression) smoothing
17412 splines via linear programming and sparse matrices.")
17413 (license license:gpl2+)))
17415 (define-public r-drimpute
17417 (name "r-drimpute")
17422 (uri (cran-uri "DrImpute" version))
17425 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
17426 (properties `((upstream-name . "DrImpute")))
17427 (build-system r-build-system)
17429 (list r-rcpp r-rcpparmadillo))
17430 (home-page "https://github.com/ikwak2/DrImpute")
17431 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
17433 "This is an R package for imputing dropout events. Many statistical
17434 methods in cell type identification, visualization and lineage reconstruction
17435 do not account for dropout events. DrImpute can improve the performance of
17436 such software by imputing dropout events.")
17437 (license license:gpl3)))
17439 (define-public r-gamlss-dist
17441 (name "r-gamlss-dist")
17446 (uri (cran-uri "gamlss.dist" version))
17448 (base32 "03m275qvrmpzmc10hs48277kxp503riz8sz6xk9pkpj8n7gsz20g"))))
17449 (properties `((upstream-name . "gamlss.dist")))
17450 (build-system r-build-system)
17451 (propagated-inputs (list r-mass))
17452 (home-page "http://www.gamlss.org/")
17453 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
17455 "This package provides a set of distributions which can be used for
17456 modelling the response variables in Generalized Additive Models for Location
17457 Scale and Shape. The distributions can be continuous, discrete or mixed
17458 distributions. Extra distributions can be created, by transforming, any
17459 continuous distribution defined on the real line, to a distribution defined on
17460 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
17461 transformation, respectively.")
17462 ;; Either version of the GPL.
17463 (license (list license:gpl2 license:gpl3))))
17465 ;; This package includes JavaScript files, which are not minified. When
17466 ;; upgrading please check that there are no new minified JavaScript files.
17467 (define-public r-shinyjs
17474 (uri (cran-uri "shinyjs" version))
17477 "1id9gsrkr28xl80a8794in17rxmmz06zqvd5hlns7mqz3fzhrhky"))))
17478 (build-system r-build-system)
17480 (list r-digest r-jsonlite r-shiny))
17483 (home-page "https://deanattali.com/shinyjs")
17484 (synopsis "Improve the user experience of your Shiny apps")
17486 "Perform common useful JavaScript operations in Shiny apps that will
17487 greatly improve your apps without having to know any JavaScript. Examples
17488 include: hiding an element, disabling an input, resetting an input back to its
17489 original value, delaying code execution by a few seconds, and many more useful
17490 functions for both the end user and the developer. Shinyjs can also be used
17491 to easily call your own custom JavaScript functions from R.")
17492 (license license:agpl3+)))
17494 ;; This package includes minified JavaScript files. When upgrading please
17495 ;; check that there are no new minified JavaScript files.
17496 (define-public r-colourpicker
17498 (name "r-colourpicker")
17503 (uri (cran-uri "colourpicker" version))
17506 "12k3m2s49pc1p2hzd4zqqzzdf94q7hhqz7zgp8w908a6w3p80b5w"))))
17507 (build-system r-build-system)
17510 (modify-phases %standard-phases
17511 (add-after 'unpack 'process-javascript
17512 (lambda* (#:key inputs #:allow-other-keys)
17513 (with-directory-excursion "inst"
17515 `((,(assoc-ref inputs "js-salvattore")
17516 . "examples/colourInput/www/salvattore.min.js")
17517 (,(assoc-ref inputs "js-jquery")
17518 . "htmlwidgets/lib/jquery/jquery.min.js")
17519 ("www/shared/colourpicker/js/colourpicker.js"
17520 . "www/shared/colourpicker/js/colourpicker.min.js"))))
17521 (for-each (lambda (source target)
17522 (format #true "Processing ~a --> ~a~%"
17524 (delete-file target)
17525 (invoke "esbuild" source "--minify"
17526 (string-append "--outfile=" target)))
17528 (map cdr mapping)))))))))
17538 `(("esbuild" ,esbuild)
17542 (uri "https://code.jquery.com/jquery-3.6.1.js")
17545 "1lm4zcpvqdi7qi2s7bgci2z74wazq0z0bdvjmlrqbhmfrpk42ffz"))))
17549 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
17552 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
17553 (home-page "https://github.com/daattali/colourpicker")
17554 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
17556 "This package provides a color picker that can be used as an input in
17557 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
17558 custom color palettes, and many more options. A plot color helper tool is
17559 available as an RStudio Addin, which helps you pick colors to use in your
17560 plots. A more generic color picker RStudio Addin is also provided to let you
17561 select colors to use in your R code.")
17562 (license license:expat)))
17564 (define-public r-ggextra
17571 (uri (cran-uri "ggExtra" version))
17574 "1rd3qv6ah3zphr1jicjhgxms73vi496mjnxnsrcgl7z8nyxmas6w"))))
17575 (properties `((upstream-name . "ggExtra")))
17576 (build-system r-build-system)
17578 (list r-colourpicker
17588 (home-page "https://github.com/daattali/ggExtra")
17589 (synopsis "Marginal histograms for ggplot2 and other enhancements")
17591 "This package is a collection of functions and layers to enhance ggplot2.
17592 The flagship function is @code{ggMarginal()}, which can be used to add
17593 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
17594 (license license:expat)))
17596 (define-public r-minpack-lm
17598 (name "r-minpack-lm")
17603 (uri (cran-uri "minpack.lm" version))
17606 "11yz6hk2r33571d16kq01cb1x6sgdzi6jmksqlrm8mr84l95c2f7"))))
17607 (properties `((upstream-name . "minpack.lm")))
17608 (build-system r-build-system)
17609 (native-inputs (list gfortran))
17610 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
17611 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
17613 "The @code{nls.lm} function provides an R interface to @code{lmder} and
17614 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
17615 problems by a modification of the Levenberg-Marquardt algorithm, with support
17616 for lower and upper parameter bounds. The implementation can be used via
17617 @code{nls}-like calls using the @code{nlsLM} function.")
17618 (license license:gpl3)))
17620 (define-public r-moments
17627 (uri (cran-uri "moments" version))
17630 "0r6qf3i1rzh2822bx1p0h8mh91gsbgg6asl2rzh2l4ys094bilif"))))
17631 (build-system r-build-system)
17632 (home-page "https://cran.r-project.org/web/packages/moments")
17633 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
17635 "This package provides functions to calculate: moments, Pearson's
17636 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
17637 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
17638 (license license:gpl2+)))
17640 (define-public r-msir
17647 (uri (cran-uri "msir" version))
17650 "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84"))))
17651 (build-system r-build-system)
17656 (home-page "https://cran.r-project.org/web/packages/msir")
17657 (synopsis "Model-based sliced inverse regression")
17659 "This is an R package for dimension reduction based on finite Gaussian
17660 mixture modeling of inverse regression.")
17661 (license license:gpl2+)))
17663 (define-public r-pbivnorm
17665 (name "r-pbivnorm")
17670 (uri (cran-uri "pbivnorm" version))
17673 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
17674 (build-system r-build-system)
17675 (native-inputs (list gfortran))
17676 (home-page "https://github.com/brentonk/pbivnorm")
17677 (synopsis "Vectorized bivariate normal CDF")
17679 "This package provides a vectorized R function for calculating
17680 probabilities from a standard bivariate normal CDF.")
17681 (license license:gpl2+)))
17683 (define-public r-lavaan
17690 (uri (cran-uri "lavaan" version))
17693 "17h79pnww1mihvlp6ap0r6d8wnly9bwszj13l5dkby0284z2fj40"))))
17694 (build-system r-build-system)
17696 (list r-mass r-mnormt r-numderiv r-pbivnorm))
17697 (home-page "https://lavaan.ugent.be")
17698 (synopsis "Latent variable analysis")
17700 "This package provides tools to fit a variety of latent variable models,
17701 including confirmatory factor analysis, structural equation modeling and
17702 latent growth curve models.")
17703 (license license:gpl2+)))
17705 (define-public r-nonnest2
17707 (name "r-nonnest2")
17712 (uri (cran-uri "nonnest2" version))
17715 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
17716 (build-system r-build-system)
17718 (list r-compquadform r-lavaan r-mvtnorm r-sandwich))
17721 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
17722 (synopsis "Tests of non-nested models")
17724 "This package allows for testing of non-nested models. It includes tests
17725 of model distinguishability and of model fit that can be applied to both
17726 nested and non-nested models. The package also includes functionality to
17727 obtain confidence intervals associated with AIC and BIC.")
17728 ;; Either version of the GPL.
17729 (license (list license:gpl2 license:gpl3))))
17731 (define-public r-penalized
17733 (name "r-penalized")
17738 (uri (cran-uri "penalized" version))
17741 "08badmgygppbqzay20qijyww028yw6s8dyd8ijcp8g4r9rn8xqyq"))))
17742 (build-system r-build-system)
17744 (list r-rcpp r-rcpparmadillo r-survival))
17745 (home-page "https://cran.r-project.org/web/packages/penalized/")
17746 (synopsis "Penalized estimation in GLMs and in the Cox model")
17748 "This package provides tools for fitting possibly high dimensional
17749 penalized regression models. The penalty structure can be any combination of
17750 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
17751 constraint on the regression coefficients. The supported regression models
17752 are linear, logistic and Poisson regression and the Cox Proportional Hazards
17753 model. Cross-validation routines allow optimization of the tuning
17755 (license license:gpl2+)))
17757 (define-public r-zim
17764 (uri (cran-uri "ZIM" version))
17767 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
17768 (properties `((upstream-name . "ZIM")))
17769 (build-system r-build-system)
17770 (propagated-inputs (list r-mass))
17771 (home-page "https://github.com/biostatstudio/ZIM")
17772 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
17774 "Analyze count time series with excess zeros. Two types of statistical
17775 models are supported: Markov regression and state-space models. They are also
17776 known as observation-driven and parameter-driven models respectively in the
17777 time series literature. The functions used for Markov regression or
17778 observation-driven models can also be used to fit ordinary regression models
17779 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
17780 negative binomial (ZINB) assumption. The package also contains miscellaneous
17781 functions to compute density, distribution, quantile, and generate random
17782 numbers from ZIP and ZINB distributions.")
17783 (license license:gpl3)))
17785 (define-public r-nor1mix
17792 (uri (cran-uri "nor1mix" version))
17795 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
17796 (build-system r-build-system)
17797 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
17798 (synopsis "Normal (1-d) mixture models")
17800 "This package provides S3 classes and methods for one-dimensional normal
17801 mixture models, for, e.g., density estimation or clustering algorithms
17802 research and teaching; it provides the widely used Marron-Wand densities. It
17803 also provides tools for efficient random number generation and graphics.")
17804 (license license:gpl2+)))
17806 (define-public r-beanplot
17808 (name "r-beanplot")
17813 (uri (cran-uri "beanplot" version))
17816 "1b8mvlcsv5l9g08ag92hndsvk8jmgxvznhzgazc8y4296kp8l5a9"))))
17817 (build-system r-build-system)
17818 (home-page "https://cran.r-project.org/web/packages/beanplot/")
17819 (synopsis "Visualization via beanplots")
17821 "This package provides beanplots, an alternative to
17822 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
17824 (license license:gpl2)))
17826 (define-public r-pbdzmq
17833 (uri (cran-uri "pbdZMQ" version))
17836 "0rala2aqyva4cjpih8xbqq1nxhwfgbkcdwb1c3h5jjp5dv7lrvgd"))))
17837 (properties `((upstream-name . "pbdZMQ")))
17838 (build-system r-build-system)
17840 (list zeromq zlib))
17843 (home-page "https://pbdr.org/")
17844 (synopsis "R interface to ZeroMQ")
17846 "ZeroMQ is a well-known library for high-performance asynchronous
17847 messaging in scalable, distributed applications. This package provides high
17848 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
17849 interactive client/server programming frameworks. A few wrapper functions
17850 compatible with @code{rzmq} are also provided.")
17851 (license license:gpl3)))
17853 (define-public r-repr
17860 (uri (cran-uri "repr" version))
17863 "0h3h14ybamcbwmm31ib66fx13v75vkzn4bn2v26n2h097sl9qybg"))))
17864 (build-system r-build-system)
17866 (list r-base64enc r-htmltools r-jsonlite r-pillar))
17867 (home-page "https://cran.r-project.org/web/packages/repr/")
17868 (synopsis "Serializable representations")
17870 "This package provides string and binary representations of objects for
17871 several formats and MIME types.")
17872 (license license:gpl3)))
17874 (define-public r-irdisplay
17876 (name "r-irdisplay")
17881 (uri (cran-uri "IRdisplay" version))
17884 "0awdiv4rr93y8jb1d64sm1iy37ywyniqm7w98yv6qm0zz47h7sw3"))))
17885 (properties `((upstream-name . "IRdisplay")))
17886 (build-system r-build-system)
17889 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
17890 (synopsis "Jupyter display machinery")
17892 "This package provides an interface to the rich display capabilities of
17893 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
17894 running IRkernel session.")
17895 (license license:expat)))
17897 (define-public r-irkernel
17899 (name "r-irkernel")
17904 (uri (cran-uri "IRkernel" version))
17907 "00qrmsywpzw2hfp88020zjaijma7q4hqm9h2cz53rywdjzywnzss"))))
17908 (properties `((upstream-name . "IRkernel")))
17909 (build-system r-build-system)
17912 (modify-phases %standard-phases
17913 (add-after 'install 'install-kernelspec
17914 (lambda* (#:key outputs #:allow-other-keys)
17915 (let ((out (assoc-ref outputs "out")))
17916 (setenv "HOME" "/tmp")
17917 (invoke "jupyter" "kernelspec" "install"
17920 (string-append out "/site-library/IRkernel/kernelspec"))
17921 ;; Record the absolute file name of the 'R' executable in
17923 (substitute* (string-append out "/share/jupyter"
17924 "/kernels/ir/kernel.json")
17926 (string-append "[\"" (which "R") "\",")))
17936 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
17941 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
17942 (synopsis "Native R kernel for Jupyter")
17944 "The R kernel for the Jupyter environment executes R code which the
17945 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
17947 (license license:expat)))
17949 (define-public r-gmodels
17952 (version "2.18.1.1")
17956 (uri (cran-uri "gmodels" version))
17959 "158y7yh4maawn9vki8cq4sil48xib2bbpl6qgj5gvlkw3c14hzfs"))))
17960 (build-system r-build-system)
17962 (list r-gdata r-mass))
17963 (home-page "https://cran.r-project.org/web/packages/gmodels/")
17964 (synopsis "Various R programming tools for model fitting")
17966 "This package provides various R programming tools for model fitting.")
17967 (license license:gpl2)))
17969 (define-public r-apcluster
17971 (name "r-apcluster")
17976 (uri (cran-uri "apcluster" version))
17979 "1820j1xjlbmw6j2fwwv2g806dqpk5qrbbaqsrbrn6igql8pzf552"))))
17980 (build-system r-build-system)
17982 (list r-matrix r-rcpp))
17983 (native-inputs (list r-knitr))
17984 (home-page "https://cran.r-project.org/web/packages/apcluster/")
17985 (synopsis "Affinity propagation clustering")
17987 "This package implements affinity propagation clustering introduced by
17988 Frey and Dueck (2007). The package further provides leveraged affinity
17989 propagation and an algorithm for exemplar-based agglomerative clustering that
17990 can also be used to join clusters obtained from affinity propagation. Various
17991 plotting functions are available for analyzing clustering results.")
17992 (license license:gpl2+)))
17994 (define-public r-rematch2
17996 (name "r-rematch2")
18001 (uri (cran-uri "rematch2" version))
18004 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
18005 (build-system r-build-system)
18008 (home-page "https://github.com/r-lib/rematch2")
18009 (synopsis "Tidy output from regular expression matching")
18011 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
18012 return the match results in tidy data frames.")
18013 (license license:expat)))
18015 (define-public r-picante
18022 (uri (cran-uri "picante" version))
18025 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
18026 (build-system r-build-system)
18028 (list r-ape r-nlme r-vegan))
18029 (home-page "https://cran.r-project.org/web/packages/picante/")
18030 (synopsis "Integrating phylogenies and ecology")
18032 "This package provides functions for phylocom integration, community
18033 analyses, null-models, traits and evolution. It implements numerous
18034 ecophylogenetic approaches including measures of community phylogenetic and
18035 trait diversity, phylogenetic signal, estimation of trait values for
18036 unobserved taxa, null models for community and phylogeny randomizations, and
18037 utility functions for data input/output and phylogeny plotting. A full
18038 description of package functionality and methods are provided by Kembel et
18040 (license license:gpl2)))
18042 (define-public r-reinforcelearn
18044 (name "r-reinforcelearn")
18049 (uri (cran-uri "reinforcelearn" version))
18052 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
18053 (build-system r-build-system)
18055 (list r-checkmate r-nnet r-purrr r-r6))
18056 (home-page "https://markusdumke.github.io/reinforcelearn")
18057 (synopsis "Reinforcement learning")
18059 "This package implements reinforcement learning environments and
18060 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
18061 can be used with function approximation, eligibility traces (Singh & Sutton,
18062 1996) and experience replay (Mnih et al., 2013).")
18063 (license license:expat)))
18065 (define-public r-lemon
18072 (uri (cran-uri "lemon" version))
18075 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
18076 (build-system r-build-system)
18088 (home-page "https://github.com/stefanedwards/lemon")
18089 (synopsis "Freshen up your ggplot2 plots")
18091 "This package provides functions for working with legends and axis lines
18092 of ggplot2, facets that repeat axis lines on all panels, and some knitr
18094 (license license:gpl3)))
18096 (define-public r-wgaim
18103 (uri (cran-uri "wgaim" version))
18105 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
18106 (build-system r-build-system)
18108 (list r-ggplot2 r-qtl))
18109 (home-page "https://cran.r-project.org/web/packages/wgaim")
18110 (synopsis "Whole genome average interval mapping for QTL detection")
18112 "This package integrates sophisticated mixed modelling methods with a
18113 whole genome approach to detecting significant QTL in linkage maps.")
18114 (license license:gpl2+)))
18116 (define-public r-bedr
18123 (uri (cran-uri "bedr" version))
18126 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
18127 (build-system r-build-system)
18136 htslib)) ; for tabix
18138 (list r-knitr)) ; for vignettes
18139 (home-page "https://cran.r-project.org/web/packages/bedr")
18140 (synopsis "Genomic region processing")
18142 "This package is for genomic regions processing using command line tools
18143 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
18144 utilities to perform genome arithmetic e.g indexing, formatting and merging.
18145 The bedr package's API enhances access to these tools as well as offers
18146 additional utilities for genomic regions processing.")
18147 (license license:gpl2)))
18149 (define-public r-sets
18156 (uri (cran-uri "sets" version))
18159 "1h1a03b1850kh5hd3gxbspx2nxqxvk2gb0wm0s60b70qb6zg0csp"))))
18160 (properties `((upstream-name . "sets")))
18161 (build-system r-build-system)
18162 (home-page "https://cran.r-project.org/web/packages/sets")
18163 (synopsis "Sets, generalized sets, customizable sets and intervals")
18165 "This package provides data structures and basic operations for ordinary
18166 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
18167 customizable sets, and intervals.")
18168 (license license:gpl2)))
18170 (define-public r-partitions
18172 (name "r-partitions")
18177 (uri (cran-uri "partitions" version))
18180 "1kxiy1wl7dr39kyfg2y9hd67s32knd83r2jsb7j9p3vg8iqq7yqb"))))
18181 (build-system r-build-system)
18183 (list r-gmp r-mathjaxr r-polynom r-rdpack r-sets))
18184 (home-page "https://cran.r-project.org/web/packages/partitions")
18185 (synopsis "Additive partitions of integers")
18187 "This package provides tools to enumerates the partitions, unequal
18188 partitions, and restricted partitions of an integer; the three corresponding
18189 partition functions are also given.")
18190 ;; Any version of the GPL
18191 (license license:gpl2+)))
18193 (define-public r-brobdingnag
18195 (name "r-brobdingnag")
18200 (uri (cran-uri "Brobdingnag" version))
18203 "07p9416rdzfyiigbglxjpbcg7pfly9nw19yn2mwg98621cjjs0gr"))))
18204 (properties `((upstream-name . "Brobdingnag")))
18205 (build-system r-build-system)
18206 (propagated-inputs (list r-matrix))
18207 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
18208 (synopsis "Very large numbers in R")
18210 "This package handles very large numbers in R. Real numbers are held
18211 using their natural logarithms, plus a logical flag indicating sign. The
18212 package includes a vignette that gives a step-by-step introduction to using S4
18214 ;; Any version of the GPL
18215 (license license:gpl2+)))
18217 (define-public r-untb
18224 (uri (cran-uri "untb" version))
18227 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
18228 (build-system r-build-system)
18230 (list r-brobdingnag r-partitions r-polynom))
18231 (home-page "https://github.com/RobinHankin/untb.git")
18232 (synopsis "Ecological drift under the UNTB")
18234 "This package provides numerical simulations, and visualizations, of
18235 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
18236 (license license:gpl2+)))
18238 (define-public r-stepwise
18240 (name "r-stepwise")
18245 (uri (cran-uri "stepwise" version))
18248 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
18249 (build-system r-build-system)
18250 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
18251 (synopsis "Stepwise detection of recombination breakpoints")
18253 "This package provides a stepwise approach to identifying recombination
18254 breakpoints in a genomic sequence alignment.")
18255 (license license:gpl2+)))
18257 (define-public r-snpmaxsel
18259 (name "r-snpmaxsel")
18264 (uri (cran-uri "SNPmaxsel" version))
18267 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
18268 (properties `((upstream-name . "SNPmaxsel")))
18269 (build-system r-build-system)
18271 (list r-combinat r-mvtnorm))
18272 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
18273 (synopsis "Maximally selected statistics for SNP data")
18275 "This package implements asymptotic methods related to maximally selected
18276 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
18278 (license license:gpl2+)))
18280 (define-public r-acsnminer
18282 (name "r-acsnminer")
18283 (version "0.16.8.25")
18286 (uri (cran-uri "ACSNMineR" version))
18289 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
18290 (properties `((upstream-name . "ACSNMineR")))
18291 (build-system r-build-system)
18293 (list r-ggplot2 r-gridextra))
18294 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
18295 (synopsis "Gene enrichment analysis")
18297 "This package provides tools to compute and represent gene set enrichment
18298 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
18299 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
18300 enrichment can be run with hypergeometric test or Fisher exact test, and can
18301 use multiple corrections. Visualization of data can be done either by
18302 barplots or heatmaps.")
18303 (license license:gpl2+)))
18305 (define-public r-seqinr
18312 (uri (cran-uri "seqinr" version))
18315 "0cj07b7km5mla63qhbkxg1mnqq6vh79lsyyfpnbm29gw68w2bwy4"))))
18316 (build-system r-build-system)
18318 (list r-ade4 r-segmented))
18321 (home-page "http://seqinr.r-forge.r-project.org/")
18322 (synopsis "Biological sequences retrieval and analysis")
18324 "This package provides tools for exploratory data analysis and data
18325 visualization of biological sequence (DNA and protein) data. It also includes
18326 utilities for sequence data management under the ACNUC system.")
18327 (license license:gpl2+)))
18329 (define-public r-units
18336 (uri (cran-uri "units" version))
18339 "06mjprqi06xprj6185k5cmrrdl025x0pd1r6a4x3s74ciq9zwilw"))))
18340 (build-system r-build-system)
18347 (home-page "https://github.com/r-quantities/units/")
18348 (synopsis "Measurement Units for R Vectors")
18350 "This package provides support for measurement units in R vectors,
18351 matrices and arrays: automatic propagation, conversion, derivation and
18352 simplification of units; raising errors in case of unit incompatibility. It
18353 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
18355 (license license:gpl2)))
18357 (define-public r-udunits2
18359 (name "r-udunits2")
18360 (version "0.13.2.1")
18364 (uri (cran-uri "udunits2" version))
18367 "00prsy8m41v1camcsz94d7gm8qab2mdnwl3x0dyhz4r49b02jm4z"))))
18368 (properties `((upstream-name . "udunits2")))
18369 (build-system r-build-system)
18372 (home-page "https://cran.r-project.org/package=udunits2")
18373 (synopsis "Udunits-2 bindings for R")
18375 "This package provides simple bindings to Unidata's udunits library.")
18376 (license license:gpl2)))
18378 (define-public r-classint
18380 (name "r-classint")
18385 (uri (cran-uri "classInt" version))
18388 "1csrrb93lzy1pajs91qd0vyvl218jyskcksa43xfrfvibdzn3sba"))))
18389 (properties `((upstream-name . "classInt")))
18390 (build-system r-build-system)
18392 (list r-class r-e1071 r-kernsmooth))
18394 (list gfortran r-knitr))
18395 (home-page "https://github.com/r-spatial/classInt/")
18396 (synopsis "Choose univariate class intervals")
18398 "This package provides selected commonly used methods for choosing
18399 univariate class intervals for mapping or other graphics purposes.")
18400 (license license:gpl2+)))
18402 (define-public r-spdata
18409 (uri (cran-uri "spData" version))
18412 "07whxr039cxvk2nn65jada3i8vqqw34lgca9j17ah8chy9r0m73f"))))
18413 (properties `((upstream-name . "spData")))
18414 (build-system r-build-system)
18417 (home-page "https://github.com/Nowosad/spData")
18418 (synopsis "Datasets for spatial analysis")
18420 "This a package containing diverse spatial datasets for demonstrating,
18421 benchmarking and teaching spatial data analysis. It includes R data of class
18422 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
18423 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
18424 of the datasets are designed to illustrate specific analysis techniques.
18425 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
18426 illustrate point pattern analysis techniques.")
18427 (license license:cc0)))
18429 (define-public r-learnbayes
18431 (name "r-learnbayes")
18436 (uri (cran-uri "LearnBayes" version))
18439 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
18440 (properties `((upstream-name . "LearnBayes")))
18441 (build-system r-build-system)
18442 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
18443 (synopsis "Functions for learning Bayesian inference")
18445 "This package provides a collection of functions helpful in learning the
18446 basic tenets of Bayesian statistical inference. It contains functions for
18447 summarizing basic one and two parameter posterior distributions and predictive
18448 distributions. It contains MCMC algorithms for summarizing posterior
18449 distributions defined by the user. It also contains functions for regression
18450 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
18452 (license license:gpl2+)))
18454 (define-public r-deldir
18461 (uri (cran-uri "deldir" version))
18464 "1igq0l2knsbhizncgydcsidgkvvlwwlkrifbcdyhnzk0bhrdixkd"))))
18465 (build-system r-build-system)
18466 (native-inputs (list gfortran))
18467 (home-page "https://cran.r-project.org/web/packages/deldir")
18468 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
18470 "This package provides tools for calculating the Delaunay triangulation
18471 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
18472 of a planar point set. It plots triangulations and tessellations in various
18473 ways, clips tessellations to sub-windows, calculates perimeters of
18474 tessellations, and summarizes information about the tiles of the
18476 (license license:gpl2+)))
18478 (define-public r-wk
18485 (uri (cran-uri "wk" version))
18488 "1pm2293xqcgjckghbf6q9sk7jh74njiynq3wqq1dbwigiz9jfhz2"))))
18489 (properties `((upstream-name . "wk")))
18490 (build-system r-build-system)
18491 (home-page "https://paleolimbot.github.io/wk/")
18492 (synopsis "Lightweight well-known geometry parsing")
18494 "This package provides a minimal R and C++ API for parsing well-known
18495 binary and well-known text representation of geometries to and from R-native
18496 formats. Well-known binary is compact and fast to parse; well-known text is
18497 human-readable and is useful for writing tests. These formats are only useful
18498 in R if the information they contain can be accessed in R, for which
18499 high-performance functions are provided here.")
18500 (license license:expat)))
18502 (define-public r-s2
18509 (uri (cran-uri "s2" version))
18512 "05n459rp5b1wk826sq3c5d2z1xwgkpfp8m1jnfshvs4gadlfkap3"))))
18513 (properties `((upstream-name . "s2")))
18514 (build-system r-build-system)
18518 `(modify-phases %standard-phases
18519 ;; We don't want to convert -lssl to -l:libssl.so.1.1; there is only
18520 ;; one libssl.so anyway and the -l:* thing breaks linking.
18521 (add-after 'unpack 'undo-library-versioning
18523 (substitute* "configure"
18524 (("PKG_LIBS_VERSIONED=.*")
18525 "PKG_LIBS_VERSIONED=\"${PKG_LIBS}\"\n")))))))
18527 (list r-rcpp r-wk))
18532 (home-page "https://r-spatial.github.io/s2/")
18533 (synopsis "Spherical geometry operators using the S2 geometry library")
18535 "This package provides R bindings for Google's s2 library for geometric
18536 calculations on the sphere. High-performance constructors and exporters
18537 provide high compatibility with existing spatial packages, transformers
18538 construct new geometries from existing geometries, predicates provide a means
18539 to select geometries based on spatial relationships, and accessors extract
18540 information about geometries.")
18541 (license license:asl2.0)))
18543 (define-public r-sf
18550 (uri (cran-uri "sf" version))
18553 "0cl7m47ar3iw95rpwpmjl23frdbscxa15q39mlzmwswxwy871p1x"))))
18554 (build-system r-build-system)
18556 (list gdal geos proj sqlite zlib))
18565 (list pkg-config r-knitr))
18566 (home-page "https://github.com/r-spatial/sf/")
18567 (synopsis "Simple features for R")
18569 "This package provides support for simple features, a standardized way to
18570 encode spatial vector data. It binds to GDAL for reading and writing data, to
18571 GEOS for geometrical operations, and to PROJ for projection conversions and
18572 datum transformations.")
18573 ;; Either of these licenses
18574 (license (list license:gpl2 license:expat))))
18576 (define-public r-sftime
18582 (uri (cran-uri "sftime" version))
18585 "1ymi60ag8kqb3293bdcvb83zwsgrz000ylifjvlpzzmh1xsisanq"))))
18586 (properties `((upstream-name . "sftime")))
18587 (build-system r-build-system)
18588 (propagated-inputs (list r-sf))
18589 (native-inputs (list r-knitr))
18590 (home-page "https://cran.r-project.org/package=sftime")
18591 (synopsis "Simple feature objects that have a time column")
18593 "This package provides classes and methods for spatial objects
18594 that have a registered time column, in particular for irregular
18595 spatiotemporal data. The @code{time} column can be of any type, but
18596 needs to be ordinal. Regularly laid out spatiotemporal data (vector
18597 or raster data cubes) are handled by package stars'.")
18598 (license license:asl2.0)))
18600 (define-public r-spdep
18606 (uri (cran-uri "spdep" version))
18609 "1slykkgvn7blj59lbzj0g0r0dqlcbp0gwnw43sihlbdz4m45kb4x"))
18611 '(for-each delete-file '("inst/doc/CO69.html"
18615 "inst/doc/nb_sf.html"
18617 "inst/doc/nb_sf.Rmd"
18618 "inst/doc/sids.html"
18619 "inst/doc/sids.R")))))
18620 (build-system r-build-system)
18632 (home-page "https://github.com/r-spatial/spdep/")
18633 (synopsis "Spatial dependence: weighting schemes, statistics and models")
18635 "This package provides a collection of functions to create spatial
18636 weights matrix objects from polygon contiguities, from point patterns by
18637 distance and tessellations, for summarizing these objects, and for permitting
18638 their use in spatial data analysis, including regional aggregation by minimum
18640 (license license:gpl2+)))
18642 (define-public r-adegenet
18644 (name "r-adegenet")
18649 (uri (cran-uri "adegenet" version))
18652 "09ahgz1ddsdn30fmi5kimdcrcnw18ryqpjcixhyp4xz0xwz2rmw0"))))
18653 (build-system r-build-system)
18666 (home-page "https://github.com/thibautjombart/adegenet")
18667 (synopsis "Exploratory analysis of genetic and genomic data")
18669 "This package provides a toolset for the exploration of genetic and
18670 genomic data. Adegenet provides formal (S4) classes for storing and handling
18671 various genetic data, including genetic markers with varying ploidy and
18672 hierarchical population structure (@code{genind} class), alleles counts by
18673 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
18674 also implements original multivariate methods (DAPC, sPCA), graphics,
18675 statistical tests, simulation tools, distance and similarity measures, and
18676 several spatial methods. A range of both empirical and simulated datasets is
18677 also provided to illustrate various methods.")
18678 (license license:gpl2+)))
18680 (define-public r-pegas
18687 (uri (cran-uri "pegas" version))
18689 (base32 "0ngd0laqbs139ji9hm9kwsm9rm56agw2yyfcplxgqva936l93fl7"))))
18690 (build-system r-build-system)
18693 (home-page "http://ape-package.ird.fr/pegas.html")
18694 (synopsis "Population and evolutionary genetics analysis system")
18696 "This package provides functions for reading, writing, plotting,
18697 analysing, and manipulating allelic and haplotypic data, including from VCF
18698 files, and for the analysis of population nucleotide sequences and
18699 micro-satellites including coalescent analyses, linkage disequilibrium,
18700 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
18701 minimum spanning tree and network, and median-joining networks.")
18702 (license license:gpl2+)))
18704 (define-public r-rmetasim
18706 (name "r-rmetasim")
18711 (uri (cran-uri "rmetasim" version))
18714 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
18715 (build-system r-build-system)
18717 (list r-ade4 r-adegenet r-gtools r-pegas))
18718 (home-page "https://cran.r-project.org/web/packages/rmetasim")
18719 (synopsis "Individual-based population genetic simulation environment")
18721 "This package provides an interface between R and the metasim simulation
18722 engine. The simulation environment is documented in: Strand, A.(2002),
18723 Metasim 1.0: an individual-based environment for simulating population
18724 genetics of complex population dynamics.")
18726 (license license:gpl2+)))
18728 (define-public r-genetics
18730 (name "r-genetics")
18731 (version "1.3.8.1.3")
18735 (uri (cran-uri "genetics" version))
18738 "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy"))))
18739 (build-system r-build-system)
18741 (list r-combinat r-gdata r-gtools r-mass r-mvtnorm))
18742 (home-page "https://cran.r-project.org/web/packages/genetics/")
18743 (synopsis "Population genetics")
18745 "This package provides classes and methods for handling genetic data.
18746 It includes classes to represent genotypes and haplotypes at single markers up
18747 to multiple markers on multiple chromosomes. Function include allele
18748 frequencies, flagging homo/heterozygotes, flagging carriers of certain
18749 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
18750 and testing for linkage disequilibrium, ...")
18751 ;; Any GPL version.
18752 (license license:gpl2+)))
18754 (define-public r-snp-plotter
18756 (name "r-snp-plotter")
18761 (uri (cran-uri "snp.plotter" version))
18764 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
18765 (properties `((upstream-name . "snp.plotter")))
18766 (build-system r-build-system)
18767 (propagated-inputs (list r-genetics))
18768 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
18769 (synopsis "Plot p-values using single SNP and/or haplotype data")
18771 "This package helps you create plots of p-values using single SNP and/or
18772 haplotype data. Main features of the package include options to display a
18773 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
18774 datasets simultaneously. Plots can be created using global and/or individual
18775 haplotype p-values along with single SNP p-values. Images are created as
18776 either PDF/EPS files.")
18777 (license license:gpl2+)))
18779 (define-public r-polspline
18781 (name "r-polspline")
18786 (uri (cran-uri "polspline" version))
18788 (base32 "1dd1jwiaglkkhajzvqfkd1x5r3wzjlk5ww0yxzmns0s1kr74i4k9"))))
18789 (build-system r-build-system)
18790 (native-inputs (list gfortran))
18791 (home-page "https://cran.r-project.org/web/packages/polspline/")
18792 (synopsis "Polynomial spline routines")
18794 "This package provides routines for the polynomial spline fitting
18795 routines hazard regression, hazard estimation with flexible tails, logspline,
18796 lspec, polyclass, and polymars.")
18797 (license license:gpl2+)))
18799 (define-public r-rms
18806 (uri (cran-uri "rms" version))
18808 (base32 "1yfk800q4mgmrjkh0hqjkiv907sr1bi1jaigrj8l6pmg1mkynhbc"))))
18809 (build-system r-build-system)
18826 (native-inputs (list gfortran))
18827 (home-page "http://biostat.mc.vanderbilt.edu/rms")
18828 (synopsis "Regression modeling strategies")
18830 "This is a package for regression modeling, testing, estimation,
18831 validation, graphics, prediction, and typesetting by storing enhanced model
18832 design attributes in the fit. The rms package is a collection of functions
18833 that assist with and streamline modeling. It also contains functions for
18834 binary and ordinal logistic regression models, ordinal models for continuous Y
18835 with a variety of distribution families, and the Buckley-James multiple
18836 regression model for right-censored responses, and implements penalized
18837 maximum likelihood estimation for logistic and ordinary linear models. The
18838 package works with almost any regression model, but it was especially written
18839 to work with binary or ordinal regression models, Cox regression, accelerated
18840 failure time models, ordinary linear models, the Buckley-James model,
18841 generalized least squares for serially or spatially correlated observations,
18842 generalized linear models, and quantile regression.")
18843 (license license:gpl2+)))
18845 (define-public r-arsenal
18852 (uri (cran-uri "arsenal" version))
18855 "0qvs3ld28djnjnggdhqjwq8sbv8zz322qahlvf7dnx35yqf6xkms"))))
18856 (properties `((upstream-name . "arsenal")))
18857 (build-system r-build-system)
18858 (propagated-inputs (list r-knitr))
18859 (native-inputs (list r-knitr))
18860 (home-page "https://github.com/mayoverse/arsenal")
18861 (synopsis "Functions for large-scale statistical summaries")
18863 "This package provides an arsenal of R functions for large-scale
18864 statistical summaries, which are streamlined to work within the latest
18865 reporting tools in R and RStudio and which use formulas and versatile
18866 summary statistics for summary tables and models. The primary functions
18870 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
18871 levels of one or more categorical variables;
18872 @item @code{paired}, a Table-1-like summary of multiple variable types paired
18873 across two time points;
18874 @item @code{modelsum}, which performs simple model fits on one or more
18875 endpoints for many variables (univariate or adjusted for covariates);
18876 @item @code{freqlist}, a powerful frequency table across many categorical
18878 @item @code{comparedf}, a function for comparing @code{data.frames}; and
18879 @item @code{write2}, a function to output tables to a document.
18882 (license license:gpl2+)))
18884 (define-public r-haplo-stats
18886 (name "r-haplo-stats")
18891 (uri (cran-uri "haplo.stats" version))
18894 "0np9kw4f30xbvwr4f79g909ilis5n273ridmlwyzjxiskiry6mx0"))))
18895 (properties `((upstream-name . "haplo.stats")))
18896 (build-system r-build-system)
18898 (list r-arsenal r-rms))
18900 (list r-r-rsp)) ; for vignettes
18901 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
18902 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
18904 "This package provides routines for the analysis of indirectly measured
18905 haplotypes. The statistical methods assume that all subjects are unrelated
18906 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
18907 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
18908 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
18909 examples in the vignette.")
18910 (license license:gpl2+)))
18912 (define-public r-bqtl
18919 (uri (cran-uri "bqtl" version))
18922 "1xlkgyhlgrwqfzph4sbhh49pjzfnw5zdr3y4786rsnr3faksnxns"))))
18923 (build-system r-build-system)
18924 (native-inputs (list gfortran))
18925 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
18926 (synopsis "Bayesian QTL mapping toolkit")
18928 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
18929 lines. It includes maximum likelihood and Bayesian tools.")
18930 (license license:gpl2+)))
18932 (define-public r-ibdreg
18939 (uri (cran-uri "ibdreg" version))
18942 "1x8z0vr2cmdks12hxfm0wwxskb0cr669w5j5rpa2ln8q704yy41g"))))
18943 (build-system r-build-system)
18944 (home-page "https://www.mayo.edu/research/labs/\
18945 statistical-genetics-genetic-epidemiology/software")
18946 (synopsis "Regression methods for IBD linkage with covariates")
18948 "This package provides a method to test genetic linkage with covariates
18949 by regression methods with response IBD sharing for relative pairs. Account
18950 for correlations of IBD statistics and covariates for relative pairs within
18951 the same pedigree.")
18952 (license license:gpl2+)))
18954 (define-public r-dlmap
18961 (uri (cran-uri "dlmap" version))
18964 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
18965 (build-system r-build-system)
18967 (list r-ibdreg r-mgcv r-nlme r-qtl r-wgaim))
18968 (home-page "https://cran.r-project.org/web/packages/dlmap/")
18969 (synopsis "Detection localization mapping for QTL")
18971 "This is package for QTL mapping in a mixed model framework with separate
18972 detection and localization stages. The first stage detects the number of QTL
18973 on each chromosome based on the genetic variation due to grouped markers on
18974 the chromosome; the second stage uses this information to determine the most
18975 likely QTL positions. The mixed model can accommodate general fixed and
18976 random effects, including spatial effects in field trials and pedigree
18977 effects. It is applicable to backcrosses, doubled haploids, recombinant
18978 inbred lines, F2 intercrosses, and association mapping populations.")
18979 (license license:gpl2)))
18981 (define-public r-hwde
18988 (uri (cran-uri "hwde" version))
18991 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
18992 (build-system r-build-system)
18993 (home-page "https://cran.r-project.org/web/packages/hwde/")
18994 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
18996 "This package fits models for genotypic disequilibria, as described in
18997 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
18998 terms are available that account for first order interactions between loci.
18999 It also implements, for a single locus in a single population, a conditional
19000 exact test for Hardy-Weinberg equilibrium.")
19001 (license license:gpl2+)))
19003 (define-public r-tdthap
19010 (uri (cran-uri "tdthap" version))
19013 "0x67k50vly92b9n5hpqp4hy87kh8r6nzadsj8xzz4lvcmb4vb6mq"))))
19014 (build-system r-build-system)
19015 (home-page "https://cran.r-project.org/web/packages/tdthap/")
19016 (synopsis "TDT tests for extended haplotypes")
19018 "Functions and examples are provided for transmission/disequilibrium
19019 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
19020 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
19021 (license license:artistic2.0)))
19023 (define-public r-sparql
19029 (uri (cran-uri "SPARQL" version))
19032 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
19033 (properties `((upstream-name . "SPARQL")))
19034 (build-system r-build-system)
19036 (list r-rcurl r-xml))
19037 (home-page "https://cran.r-project.org/web/packages/SPARQL")
19038 (synopsis "SPARQL client for R")
19039 (description "This package provides an interface to use SPARQL to pose
19040 SELECT or UPDATE queries to an end-point.")
19041 ;; The only license indication is found in the DESCRIPTION file,
19042 ;; which states GPL-3. So we cannot assume GPLv3+.
19043 (license license:gpl3)))
19045 (define-public r-bookdown
19047 (name "r-bookdown")
19051 (uri (cran-uri "bookdown" version))
19054 "08zpky94bdbjsbhi90pymxpczpfkjxwbx7p1v7ip8raw9b23skjv"))))
19055 (build-system r-build-system)
19065 ;; We cannot add knitr because this package depends on xfun, which is an
19070 (home-page "https://github.com/rstudio/bookdown")
19071 (synopsis "Authoring books and technical documents with R markdown")
19072 (description "This package provides output formats and utilities for
19073 authoring books and technical documents with R Markdown.")
19074 (license license:gpl3)))
19076 (define-public r-optparse
19078 (name "r-optparse")
19083 (uri (cran-uri "optparse" version))
19086 "1v87db7fm494dwxvdsnl1m2kj84nplq7pkh0g41najhx0npy31v2"))))
19087 (build-system r-build-system)
19092 (home-page "https://github.com/trevorld/optparse")
19093 (synopsis "Command line option parser")
19095 "This package provides a command line parser inspired by Python's
19096 @code{optparse} library to be used with Rscript to write shebang scripts
19097 that accept short and long options.")
19098 (license license:gpl2+)))
19100 (define-public r-kernlab
19107 (uri (cran-uri "kernlab" version))
19109 (base32 "12i7ffc1aacyy7bpjc0w60wwivn88wri8jz43h77irn5q5jwcnbk"))))
19110 (build-system r-build-system)
19111 (home-page "https://cran.r-project.org/web/packages/kernlab")
19112 (synopsis "Kernel-based machine learning tools")
19114 "This package provides kernel-based machine learning methods for
19115 classification, regression, clustering, novelty detection, quantile regression
19116 and dimensionality reduction. Among other methods @code{kernlab} includes
19117 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
19119 (license license:gpl2)))
19121 (define-public r-hierfstat
19123 (name "r-hierfstat")
19128 (uri (cran-uri "hierfstat" version))
19131 "0nyb5091lr8ma9vydbssyx9503601rynlrbldv98mmrmh74h6v41"))))
19132 (build-system r-build-system)
19134 (list r-ade4 r-adegenet r-gaston r-gtools))
19137 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
19138 (synopsis "Estimation and tests of hierarchical F-statistics")
19140 "This package allows the estimation of hierarchical F-statistics from
19141 haploid or diploid genetic data with any numbers of levels in the hierarchy,
19142 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
19143 are also given to test via randomisations the significance of each F and
19144 variance components, using the likelihood-ratio statistics G.")
19145 (license license:gpl2+)))
19147 (define-public r-hapassoc
19149 (name "r-hapassoc")
19154 (uri (cran-uri "hapassoc" version))
19157 "09ijc4sbw743z74fzklmvig11ndkycg6j86k4214wfsj1yj6j9x6"))))
19158 (build-system r-build-system)
19159 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
19160 (synopsis "Inference of trait associations with SNP haplotypes")
19162 "Hapassoc performs likelihood inference of trait associations with
19163 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
19164 functions are developed primarily for data collected in cohort or
19165 cross-sectional studies. They can accommodate uncertain haplotype phase and
19166 handle missing genotypes at some SNPs.")
19167 (license license:gpl2)))
19169 (define-public r-sampling
19171 (name "r-sampling")
19176 (uri (cran-uri "sampling" version))
19179 "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz"))))
19180 (build-system r-build-system)
19182 (list r-lpsolve r-mass))
19183 (home-page "https://cran.r-project.org/web/packages/sampling/")
19184 (synopsis "Survey sampling")
19186 "This package provides functions for drawing and calibrating samples.")
19187 (license license:gpl2+)))
19189 (define-public r-r2html
19196 (uri (cran-uri "R2HTML" version))
19199 "12qg9rp1j26h2f48dfg5k9jds26ycacv3f3ymk686ks43hd1hzja"))))
19200 (properties `((upstream-name . "R2HTML")))
19201 (build-system r-build-system)
19202 (home-page "https://github.com/nalimilan/R2HTML")
19203 (synopsis "HTML export for R objects")
19205 "This package includes HTML functions and methods to write in an HTML
19206 file. Thus, making HTML reports is easy. It includes a function that allows
19207 redirection on the fly, which appears to be very useful for teaching purposes,
19208 as the student can keep a copy of the produced output to keep all that they
19209 did during the course. The package comes with a vignette describing how to
19210 write HTML reports for statistical analysis. Finally, a driver for Sweave
19211 parses HTML flat files containing R code and to automatically write
19212 the corresponding outputs (tables and graphs).")
19213 (license license:gpl2+)))
19215 (define-public r-rjava
19222 (uri (cran-uri "rJava" version))
19225 "1ijqhvnb8ab38cp9pwdf7zq7xqqlm6x94gkrab2dd98p6d4x1472"))))
19226 (properties `((upstream-name . "rJava")))
19227 (build-system r-build-system)
19229 `(#:modules ((guix build utils)
19230 (guix build r-build-system)
19233 (modify-phases %standard-phases
19234 (add-after 'unpack 'set-JAVA_HOME
19235 (lambda* (#:key inputs #:allow-other-keys)
19236 (let ((jdk (assoc-ref inputs "jdk")))
19237 (setenv "JAVA_HOME" jdk)
19238 (setenv "JAVA" (which "java"))
19239 (setenv "JAR" (which "jar"))
19240 (setenv "JAVAC" (which "javac"))
19241 (setenv "JAVAH" (which "javah"))
19242 (setenv "JAVA_CPPFLAGS"
19243 (string-append "-I" jdk "/include "
19244 "-I" jdk "/include/linux"))
19245 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
19246 ((lib) (setenv "JAVA_LIBS" lib))
19247 (_ (error "Could not find libjvm.so"))))
19251 ("jdk" ,icedtea-8 "jdk")
19253 (home-page "https://www.rforge.net/rJava/")
19254 (synopsis "Low-Level R to Java interface")
19256 "This package provides a low-level interface to the Java VM very much
19257 like .C/.Call and friends. It allows the creation of objects, calling methods
19258 and accessing fields.")
19259 (license license:gpl2)))
19261 (define-public r-svmisc
19268 (uri (cran-uri "svMisc" version))
19271 "1r3kih5bnr4plnzdn5f2gg3xl3krgyl7gkdlf58a2l8vk13j3m9d"))))
19272 (properties `((upstream-name . "svMisc")))
19273 (build-system r-build-system)
19276 (home-page "https://github.com/SciViews/svMisc")
19277 (synopsis "Miscellaneous functions for SciViews")
19279 "This package provides miscellaneous functions for SciViews or general
19280 use, including tools to manage a temporary environment attached to the search
19281 path for temporary variables you do not want to @code{save()} or
19282 @code{load()}; test the current platform; showing progress bars, etc.")
19283 (license license:gpl2)))
19285 (define-public r-xyz
19292 (uri (cran-uri "xyz" version))
19295 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
19296 (build-system r-build-system)
19299 (home-page "https://cran.r-project.org/web/packages/xyz/")
19300 (synopsis "Algorithm for fast interaction search in high-dimensional data")
19302 "High dimensional interaction search by brute force requires a quadratic
19303 computational cost in the number of variables. The xyz algorithm provably
19304 finds strong interactions in almost linear time. For details of the algorithm
19305 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
19306 interaction search in high-dimensional data.")
19307 ;; Any version of the GPL.
19308 (license license:gpl2+)))
19310 (define-public r-rttf2pt1
19312 (name "r-rttf2pt1")
19317 (uri (cran-uri "Rttf2pt1" version))
19320 "1fbls9hy4s0hdszg449bpapx2mhknwiasvr15djf9f1hm0b2908p"))))
19321 (properties `((upstream-name . "Rttf2pt1")))
19322 (build-system r-build-system)
19323 (home-page "https://github.com/wch/Rttf2pt1")
19324 (synopsis "Font conversion utility")
19326 "This package contains the program @code{ttf2pt1}, for use with the
19327 @code{extrafont} package.")
19328 ;; Most of the files are covered under the Expat license. Some files are
19329 ;; covered under BSD-3. Deviations for individual files are recorded in
19330 ;; the LICENSE file.
19331 (license (list license:bsd-3 license:expat
19332 (license:non-copyleft "file://LICENSE")))))
19334 (define-public r-extrafontdb
19336 (name "r-extrafontdb")
19341 (uri (cran-uri "extrafontdb" version))
19344 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
19345 (build-system r-build-system)
19346 (home-page "https://github.com/wch/extrafontdb")
19347 (synopsis "Database for the extrafont package")
19349 "This package holds the database for the @code{extrafont} package.")
19350 (license license:gpl2)))
19352 (define-public r-extrafont
19354 (name "r-extrafont")
19359 (uri (cran-uri "extrafont" version))
19362 "0mx810mld67vb1w3wkl4fhpjmkq32lgpq5x1c0a9rf8li5wskrj4"))))
19363 (build-system r-build-system)
19365 (list r-extrafontdb r-rttf2pt1))
19366 (home-page "https://github.com/wch/extrafont")
19367 (synopsis "Tools for using fonts in R")
19369 "The extrafont package makes it easier to use fonts other than the basic
19370 PostScript fonts that R uses. Fonts that are imported into extrafont can be
19371 used with PDF or PostScript output files. There are two hurdles for using
19372 fonts in PDF (or Postscript) output files:
19375 @item Making R aware of the font and the dimensions of the characters.
19376 @item Embedding the fonts in the PDF file so that the PDF can be displayed
19377 properly on a device that doesn't have the font. This is usually needed if
19378 you want to print the PDF file or share it with others.
19381 The extrafont package makes both of these things easier.")
19382 (license license:gpl2)))
19384 (define-public r-xkcd
19391 (uri (cran-uri "xkcd" version))
19394 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
19395 (build-system r-build-system)
19397 (list r-extrafont r-ggplot2 r-hmisc))
19398 (home-page "https://cran.r-project.org/web/packages/xkcd/")
19399 (synopsis "Plot ggplot2 graphics in the XKCD style")
19401 "This package provides the means to plot ggplot2 graphs in the style of
19402 the XKCD web comic.")
19403 (license license:gpl3)))
19405 (define-public r-babelgene
19407 (name "r-babelgene")
19412 (uri (cran-uri "babelgene" version))
19415 "1ql5r1chl5ajzy9ppcnk755ia3m2a8n08m837dnm2ll3nzf02rnf"))))
19416 (properties `((upstream-name . "babelgene")))
19417 (build-system r-build-system)
19419 (list r-dplyr r-rlang))
19423 "https://igordot.github.io/babelgene/")
19424 (synopsis "Gene orthologs for model organisms in a Tidy data format")
19426 "Genomic analysis of model organisms often requires the use of databases
19427 based on human data or making comparisons to patient-derived resources. This
19428 requires converting genes between human and non-human analogues. The
19429 babelgene R package provides predicted gene orthologs/homologs for frequently
19430 studied model organisms in an R-friendly tidy/long format. The package
19431 integrates orthology assertion predictions sourced from multiple databases as
19432 compiled by the HGNC Comparison of Orthology Predictions (HCOP).")
19433 (license license:expat)))
19435 (define-public r-msigdbr
19442 (uri (cran-uri "msigdbr" version))
19445 "1jna9bkq0a7r6f8nhxziyiw75kfhsyh1rv7sx5d4551mvxxlhc6w"))))
19446 (build-system r-build-system)
19456 (home-page "https://github.com/igordot/msigdbr")
19457 (synopsis "MSigDB gene sets for multiple organisms")
19459 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
19460 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
19461 software in a standard R data frame with key-value pairs. Included are the
19462 original human gene symbols and Entrez IDs as well as the equivalents for
19463 various frequently studied model organisms such as mouse, rat, pig, fly, and
19465 ;; The package is covered under the Expat license, but the upstream MSigDB
19466 ;; files are made available under the Creative Commons Attribution 4.0
19467 ;; International license.
19468 (license (list license:expat license:cc-by4.0))))
19470 (define-public r-gridgraphics
19472 (name "r-gridgraphics")
19477 (uri (cran-uri "gridGraphics" version))
19480 "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219"))))
19481 (properties `((upstream-name . "gridGraphics")))
19482 (build-system r-build-system)
19483 (home-page "https://github.com/pmur002/gridgraphics")
19484 (synopsis "Redraw base graphics using @code{grid} graphics")
19486 "This package provides functions to convert a page of plots drawn with
19487 the @code{graphics} package into identical output drawn with the @code{grid}
19488 package. The result looks like the original @code{graphics}-based plot, but
19489 consists of @code{grid} grobs and viewports that can then be manipulated with
19490 @code{grid} functions (e.g., edit grobs and revisit viewports).")
19491 (license license:gpl2+)))
19493 (define-public r-farver
19500 (uri (cran-uri "farver" version))
19503 "1klnr73fhm7n46q85in1v9gi99y6rcdzzg4h4wvnbx23lxndmkqd"))))
19504 (build-system r-build-system)
19505 (home-page "https://github.com/thomasp85/farver")
19506 (synopsis "Vectorized color conversion and comparison")
19508 "The encoding of color can be handled in many different ways, using
19509 different color spaces. As different color spaces have different uses,
19510 efficient conversion between these representations are important. This
19511 package provides a set of functions that gives access to very fast color space
19512 conversion and comparisons implemented in C++, and offers 100-fold speed
19513 improvements over the @code{convertColor} function in the @code{grDevices}
19515 (license license:expat)))
19517 (define-public r-yulab-utils
19519 (name "r-yulab-utils")
19524 (uri (cran-uri "yulab.utils" version))
19527 "0sq5wc0mp84h6fs4wa2smvf7dcn0p0xarzb2ljvqc3p4vb2lvkbf"))))
19528 (properties `((upstream-name . "yulab.utils")))
19529 (build-system r-build-system)
19530 (home-page "https://cran.r-project.org/package=yulab.utils")
19531 (synopsis "Supporting functions for packages maintained by YuLab-SMU")
19533 "Miscellaneous functions commonly used by YuLab-SMU, such as
19534 @code{install_zip_gh} to install R packages from Github ZIP files.")
19535 (license license:artistic2.0)))
19537 (define-public r-ggplotify
19539 (name "r-ggplotify")
19544 (uri (cran-uri "ggplotify" version))
19547 "12mk3fa8fdjxj7xxz21jkr7h91w5wdgwjqhszcz1qffwsgb773qp"))))
19548 (build-system r-build-system)
19550 (list r-ggplot2 r-gridgraphics r-yulab-utils))
19553 (home-page "https://github.com/GuangchuangYu/ggplotify")
19554 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
19556 "This package provides tools to convert plot function calls (using
19557 expression or formula) to @code{grob} or @code{ggplot} objects that are
19558 compatible with the @code{grid} and @code{ggplot2} environment. With this
19559 package, we are able to e.g. use @code{cowplot} to align plots produced by
19560 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
19561 converting them to @code{ggplot} objects.")
19562 (license license:artistic2.0)))
19564 (define-public r-triebeard
19566 (name "r-triebeard")
19571 (uri (cran-uri "triebeard" version))
19574 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
19575 (build-system r-build-system)
19576 (propagated-inputs (list r-rcpp))
19577 (home-page "https://github.com/Ironholds/triebeard/")
19578 (synopsis "Radix trees in Rcpp")
19580 "Radix trees, or tries, are key-value data structures optimized for
19581 efficient lookups, similar in purpose to hash tables. This package provides
19582 an implementation of radix trees for use in R programming and in developing
19583 packages with Rcpp.")
19584 (license license:expat)))
19586 (define-public r-tweenr
19593 (uri (cran-uri "tweenr" version))
19596 "1wqzcsxlz1isb1j0v5g6dgvd40q3q9qlahvgcgiq0j4d87nzvfv4"))))
19597 (build-system r-build-system)
19601 '(modify-phases %standard-phases
19602 (add-after 'unpack 'build-reproducibly
19604 (substitute* "R/aaa.R"
19605 (("BASEDATETIME <- Sys.time.*")
19606 "BASEDATETIME <- structure(0, class = c(\"POSIXct\", \"POSIXt\"))\n")))))))
19608 (list r-cpp11 r-farver r-magrittr r-rlang r-vctrs))
19609 (home-page "https://github.com/thomasp85/tweenr")
19610 (synopsis "Interpolate data for smooth animations")
19612 "In order to create smooth animation between states of data, tweening is
19613 necessary. This package provides a range of functions for creating tweened
19614 data that can be used as basis for animation. Furthermore it adds a number of
19615 vectorized interpolaters for common R data types such as numeric, date and
19617 (license license:expat)))
19619 (define-public r-polyclip
19621 (name "r-polyclip")
19626 (uri (cran-uri "polyclip" version))
19629 "0mkg5v045an49c3j279vvabm7p4d9jsnzlfp96dpblvihxvwkll4"))))
19630 (build-system r-build-system)
19631 (native-inputs (list pkg-config))
19632 (home-page "http://www.angusj.com/delphi/clipper.php")
19633 (synopsis "Polygon clipping")
19635 "This package provides an R port of the library Clipper. It performs
19636 polygon clipping operations (intersection, union, set minus, set difference)
19637 for polygonal regions of arbitrary complexity, including holes. It computes
19638 offset polygons (spatial buffer zones, morphological dilations, Minkowski
19639 dilations) for polygonal regions and polygonal lines. It computes the
19640 Minkowski Sum of general polygons. There is a function for removing
19641 self-intersections from polygon data.")
19642 (license license:boost1.0)))
19644 (define-public r-urlchecker
19646 (name "r-urlchecker")
19650 (uri (cran-uri "urlchecker" version))
19653 "06034lb94krbzawqg5xklwcksvyyzl3qy355f66baj5pw7dms5k2"))))
19654 (properties `((upstream-name . "urlchecker")))
19655 (build-system r-build-system)
19656 (propagated-inputs (list r-cli r-curl r-xml2))
19657 (home-page "https://github.com/r-lib/urlchecker")
19658 (synopsis "Run CRAN URL checks from older R versions")
19660 "This package provides the URL checking tools available in R 4.1+ as a
19661 package for earlier versions of R. It also uses concurrent requests so can be
19662 much faster than the serial versions.")
19663 (license license:gpl3)))
19665 (define-public r-urltools
19667 (name "r-urltools")
19672 (uri (cran-uri "urltools" version))
19675 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
19676 (build-system r-build-system)
19678 (list r-rcpp r-triebeard))
19679 (home-page "https://github.com/Ironholds/urltools/")
19680 (synopsis "Vectorized tools for URL handling and parsing")
19682 "This package provides a toolkit for all URL-handling needs, including
19683 encoding and decoding, parsing, parameter extraction and modification. All
19684 functions are designed to be both fast and entirely vectorized. It is
19685 intended to be useful for people dealing with web-related datasets, such as
19686 server-side logs, although may be useful for other situations involving large
19688 (license license:expat)))
19690 (define-public r-ggforce
19697 (uri (cran-uri "ggforce" version))
19700 "0wqq8l7lq96k4w0vq12jcg7clvgia8s35jjbqq1s0py4cgxijhml"))))
19701 (build-system r-build-system)
19718 (home-page "https://ggforce.data-imaginist.com")
19719 (synopsis "Accelerating ggplot2")
19721 "The aim of the ggplot2 package is to aid in visual data investigations.
19722 This focus has led to a lack of facilities for composing specialized plots.
19723 This package aims to be a collection of mainly new statistics and geometries
19724 that fills this gap.")
19725 (license license:expat)))
19727 (define-public r-eulerr
19733 (uri (cran-uri "eulerr" version))
19736 "0lldp2319qd08y87f862gx8a77rvikcnkmdl9xgx4glynfs3hk19"))))
19737 (properties `((upstream-name . "eulerr")))
19738 (build-system r-build-system)
19745 (native-inputs (list r-knitr))
19746 (home-page "https://github.com/jolars/eulerr")
19747 (synopsis "Area-proportional Euler and Venn diagrams with ellipses")
19749 "This package generates area-proportional Euler diagrams using
19750 numerical optimization. An Euler diagram is a generalization of a
19751 Venn diagram, relaxing the criterion that all interactions need to be
19752 represented. Diagrams may be fit with ellipses and circles via a wide
19753 range of inputs and can be visualized in numerous ways.")
19754 (license license:gpl3)))
19756 (define-public r-europepmc
19758 (name "r-europepmc")
19763 (uri (cran-uri "europepmc" version))
19766 "16japbndid34shqg8n0bmjrxn84xmhrylvz832zclcllm6i93fn1"))))
19767 (build-system r-build-system)
19782 (home-page "https://github.com/ropensci/europepmc/")
19783 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
19785 "This package provides an R Client for the
19786 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
19787 Service}. It gives access to both metadata on life science literature and
19788 open access full texts. Europe PMC indexes all PubMed content and other
19789 literature sources including Agricola, a bibliographic database of citations
19790 to the agricultural literature, or Biological Patents. In addition to
19791 bibliographic metadata, the client allows users to fetch citations and
19792 reference lists. Links between life-science literature and other EBI
19793 databases, including ENA, PDB or ChEMBL are also accessible.")
19794 (license license:gpl3)))
19796 (define-public r-ggraph
19803 (uri (cran-uri "ggraph" version))
19806 "07sw4h94dzbs44dcvvj80g8v8252k4iw8pkmzdrk4qagvhidnvv8"))))
19807 (build-system r-build-system)
19829 (home-page "https://cran.r-project.org/web/packages/ggraph/")
19830 (synopsis "Implementation of grammar of graphics for graphs and networks")
19832 "The grammar of graphics as implemented in ggplot2 is a poor fit for
19833 graph and network visualizations due to its reliance on tabular data input.
19834 The ggraph package is an extension of the ggplot2 API tailored to graph
19835 visualizations and provides the same flexible approach to building up plots
19837 (license license:gpl3)))
19839 (define-public r-gkmsvm
19846 (uri (cran-uri "gkmSVM" version))
19849 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
19850 (properties `((upstream-name . "gkmSVM")))
19851 (build-system r-build-system)
19853 (list r-kernlab r-rcpp r-rocr r-seqinr))
19854 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
19855 (synopsis "Gapped-kmer support vector machine")
19857 "This R package provides tools for training gapped-kmer SVM classifiers
19858 for DNA and protein sequences. This package supports several sequence
19859 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
19860 (license license:gpl2+)))
19862 (define-public r-varselrf
19864 (name "r-varselrf")
19869 (uri (cran-uri "varSelRF" version))
19872 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
19873 (properties `((upstream-name . "varSelRF")))
19874 (build-system r-build-system)
19876 (list r-randomforest))
19877 (home-page "https://www.ligarto.org/rdiaz/software/software")
19878 (synopsis "Variable selection using random forests")
19880 "This package provides tools for the variable selection from random
19881 forests using both backwards variable elimination (for the selection of small
19882 sets of non-redundant variables) and selection based on the importance
19883 spectrum (somewhat similar to scree plots; for the selection of large,
19884 potentially highly-correlated variables). The main applications are in
19885 high-dimensional data (e.g., microarray data, and other genomics and
19886 proteomics applications).")
19887 (license license:gpl2+)))
19889 (define-public r-pamr
19896 (uri (cran-uri "pamr" version))
19899 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
19900 (build-system r-build-system)
19902 (list r-cluster r-survival))
19903 (native-inputs (list gfortran))
19904 (home-page "https://cran.r-project.org/web/packages/pamr/")
19905 (synopsis "Prediction Analysis for Microarrays")
19907 "This package provides some functions for sample classification in
19909 (license license:gpl2)))
19911 (define-public r-rda
19914 (version "1.0.2-2.1")
19918 (uri (cran-uri "rda" version))
19921 "17ll0idnms4bcpbl65xnl8zfnwsk9ww0rg5z8qqh4ahk5qdab8zf"))))
19922 (build-system r-build-system)
19923 (home-page "https://cran.r-project.org/web/packages/rda/")
19924 (synopsis "Shrunken centroids regularized discriminant analysis")
19926 "This package provides tools for shrunken centroids regularized
19927 discriminant analysis for the purpose of classifying high dimensional data.")
19928 (license license:gpl2+)))
19930 (define-public r-ggvis
19937 (uri (cran-uri "ggvis" version))
19940 "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy"))))
19941 (build-system r-build-system)
19950 (home-page "https://ggvis.rstudio.com/")
19951 (synopsis "Interactive grammar of graphics")
19953 "This package is a data visualization package for R providing an
19954 implementation of an interactive grammar of graphics, taking the best parts of
19955 ggplot2, combining them with the reactive framework of Shiny and drawing web
19956 graphics using Vega.")
19957 (license license:gpl2)))
19959 (define-public r-gbm
19962 (version "2.1.8.1")
19966 (uri (cran-uri "gbm" version))
19969 "02z85d7zp3i5x8r8q005hyw2rx1ck7lw81q7a3lqwraj8l95c94d"))))
19970 (build-system r-build-system)
19972 (list r-lattice r-survival))
19975 (home-page "https://github.com/gbm-developers/gbm")
19976 (synopsis "Generalized boosted regression models")
19978 "This package is an implementation of extensions to Freund and Schapire's
19979 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
19980 regression methods for least squares, absolute loss, t-distribution loss,
19981 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
19982 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
19983 and Learning to Rank measures (LambdaMart).")
19984 (license license:gpl2+)))
19986 (define-public r-threejs
19993 (uri (cran-uri "threejs" version))
19996 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
19997 (build-system r-build-system)
19999 `(#:modules ((guix build utils)
20000 (guix build r-build-system)
20004 (modify-phases %standard-phases
20005 (add-after 'unpack 'process-javascript
20006 (lambda* (#:key inputs #:allow-other-keys)
20007 (with-directory-excursion "inst"
20011 `((,(assoc-ref inputs "js-jquery")
20012 "htmlwidgets/lib/jquery/jquery.min.js")
20013 (,(assoc-ref inputs "js-threejs-111")
20014 "htmlwidgets/lib/threejs-111/three.min.js"))))
20015 (lambda (sources targets)
20016 (for-each (lambda (source target)
20017 (format #t "Processing ~a --> ~a~%"
20019 (delete-file target)
20020 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
20021 (call-with-output-file target
20023 (dump-port minified port)))))
20024 sources targets))))
20027 (list r-base64enc r-crosstalk r-htmlwidgets r-igraph))
20029 `(("uglifyjs" ,node-uglify-js)
20033 (uri "https://code.jquery.com/jquery-1.12.4.js")
20036 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
20040 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
20043 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
20044 (home-page "https://bwlewis.github.io/rthreejs")
20045 (synopsis "Interactive 3D scatter plots, networks and globes")
20047 "Create interactive 3D scatter plots, network plots, and globes in R
20048 using the three.js visualization library.")
20049 (license license:expat)))
20051 (define-public r-mlbench
20058 (uri (cran-uri "mlbench" version))
20061 "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi"))))
20062 (build-system r-build-system)
20063 (home-page "https://cran.r-project.org/web/packages/mlbench/")
20064 (synopsis "Machine learning benchmark problems")
20066 "This package provides a collection of artificial and real-world machine
20067 learning benchmark problems, including, e.g., several data sets from the UCI
20069 (license license:gpl2)))
20071 (define-public r-mpm
20078 (uri (cran-uri "mpm" version))
20081 "1jpv2ddmw7aarqbbyfys1yb840arw33319wnny3v2hk84hldmayj"))))
20082 (build-system r-build-system)
20084 (list r-kernsmooth r-mass))
20085 (home-page "http://mpm.r-forge.r-project.org")
20086 (synopsis "Multivariate projection methods")
20088 "This is a package for exploratory graphical analysis of multivariate
20089 data, specifically gene expression data with different projection methods:
20090 principal component analysis, correspondence analysis, spectral map
20092 (license license:gpl2+)))
20094 (define-public r-png
20100 (uri (cran-uri "png" version))
20103 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
20104 (build-system r-build-system)
20106 (list libpng zlib))
20107 (home-page "https://www.rforge.net/png/")
20108 (synopsis "Read and write PNG images")
20110 "This package provides an easy and simple way to read, write and display
20111 bitmap images stored in the PNG format. It can read and write both files and
20112 in-memory raw vectors.")
20113 ;; Any of these GPL versions.
20114 (license (list license:gpl2 license:gpl3))))
20116 (define-public r-ggcorrplot
20118 (name "r-ggcorrplot")
20123 (uri (cran-uri "ggcorrplot" version))
20126 "186a0mpdpipp24fjbd52l1gdgpqm6vl83ff8069d8nngyqbrx0jr"))))
20127 (build-system r-build-system)
20129 (list r-ggplot2 r-reshape2))
20130 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
20131 (synopsis "Visualization of a correlation matrix using ggplot2")
20133 "The ggcorrplot package can be used to visualize easily a correlation
20134 matrix using ggplot2. It provides a solution for reordering the correlation
20135 matrix and displays the significance level on the plot. It also includes a
20136 function for computing a matrix of correlation p-values.")
20137 (license license:gpl2)))
20139 (define-public r-ggfun
20146 (uri (cran-uri "ggfun" version))
20149 "0x71p3mm0sw72hv92368wy2yiy7zv826p3kddpwndqv1bywmyfx8"))))
20150 (properties `((upstream-name . "ggfun")))
20151 (build-system r-build-system)
20153 (list r-ggplot2 r-rlang))
20154 (native-inputs (list r-knitr))
20155 (home-page "https://cran.r-project.org/package=ggfun")
20156 (synopsis "Miscellaneous functions for ggplot2")
20158 "This package provides useful functions to edit ggplot object (e.g.,
20159 setting fonts for theme and layers, adding rounded rectangle as background for
20160 each of the legends).")
20161 (license license:artistic2.0)))
20163 (define-public r-gridtext
20165 (name "r-gridtext")
20170 (uri (cran-uri "gridtext" version))
20173 "0f7i2qb8fawi8agy2iz2c173kfwj7cbb5ikjix64nmzqc5j7363d"))))
20174 (properties `((upstream-name . "gridtext")))
20175 (build-system r-build-system)
20185 (home-page "https://wilkelab.org/gridtext/")
20186 (synopsis "Improved text rendering support for Grid graphics")
20188 "This package provides support for rendering of formatted text using Grid
20189 graphics. Text can be formatted via a minimal subset of Markdown, HTML, and
20190 inline CSS directives, and it can be rendered both with and without word
20192 (license license:expat)))
20194 (define-public r-ggghost
20200 (uri (cran-uri "ggghost" version))
20203 "0kvsjadxxdf6yvzk4a6yqkg02q1ysslvf3m0a369bdim396z4hnv"))))
20204 (properties `((upstream-name . "ggghost")))
20205 (build-system r-build-system)
20206 (propagated-inputs (list r-animation r-ggplot2))
20207 (home-page "https://github.com/jonocarroll/ggghost")
20208 (synopsis "Capture the spirit of your ggplot2 calls")
20210 "This package lets you create a reproducible @code{ggplot2} object by
20211 storing the data and calls.")
20212 (license license:gpl3+)))
20214 (define-public r-ggtext
20221 (uri (cran-uri "ggtext" version))
20224 "10vrrxviv4yp9lqsanqvwsvbj64vn66hwm1w7860x1g58hf1g0l7"))))
20225 (properties `((upstream-name . "ggtext")))
20226 (build-system r-build-system)
20228 (list r-ggplot2 r-gridtext r-rlang r-scales))
20229 (native-inputs (list r-knitr))
20230 (home-page "https://wilkelab.org/ggtext/")
20231 (synopsis "Improved text rendering support for ggplot2")
20233 "This package provides a ggplot2 extension that enables the rendering of
20234 complex formatted plot labels (titles, subtitles, facet labels, axis labels,
20235 etc.). Text boxes with automatic word wrap are also supported.")
20236 (license license:gpl2)))
20238 (define-public r-ggthemeassist
20240 (name "r-ggthemeassist")
20244 (uri (cran-uri "ggThemeAssist" version))
20247 "1biw91a8p13h62v4w3yim6ghr98khmyhb3qd0h04asf91vvmpxbv"))))
20248 (properties `((upstream-name . "ggThemeAssist")))
20249 (build-system r-build-system)
20256 (home-page "https://github.com/calligross/ggthemeassist")
20257 (synopsis "Add-in to customize ggplot2 themes")
20259 "This package provides an Rstudio add-in that delivers a graphical
20260 interface for editing @code{ggplot2} theme elements.")
20261 (license license:gpl3)))
20263 ;; This package includes minified JavaScript files. When upgrading please
20264 ;; check that there are no new minified JavaScript files.
20265 (define-public r-flexdashboard
20267 (name "r-flexdashboard")
20272 (uri (cran-uri "flexdashboard" version))
20275 "0bvw2ca6xxscia4hvq505qvjf6zkgpsqv86f1s78aknzwr9jsikm"))
20276 (modules '((guix build utils)))
20279 ;; Delete bundled minified JavaScript files
20280 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
20281 (delete-file "inst/www/sly/sly.min.js")
20282 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
20283 (delete-file "inst/www/prism/prism.js")
20284 (delete-file "inst/www/featherlight/featherlight.min.js")))))
20285 (build-system r-build-system)
20287 `(#:modules ((guix build utils)
20288 (guix build r-build-system)
20292 (ice-9 textual-ports))
20294 (modify-phases %standard-phases
20295 (add-after 'unpack 'process-javascript
20296 (lambda* (#:key inputs #:allow-other-keys)
20297 (with-directory-excursion "inst"
20298 ;; Concatenate all components of prism.js
20299 (let ((contents (string-join
20300 (map (lambda (name)
20301 (call-with-input-file
20302 (assoc-ref inputs name)
20306 "js-prism-line-numbers"))
20308 (call-with-output-file "prism-src.js"
20309 (cut display contents <>)))
20313 `(("www/stickytableheaders/jquery.stickytableheaders.js"
20314 "www/stickytableheaders/jquery.stickytableheaders.min.js")
20316 "www/sly/sly.min.js")
20318 "www/prism/prism.js")
20319 (,(assoc-ref inputs "js-raphael")
20320 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
20321 (,(assoc-ref inputs "js-featherlight")
20322 "www/featherlight/featherlight.min.js"))))
20323 (lambda (sources targets)
20324 (for-each (lambda (source target)
20325 (format #t "Processing ~a --> ~a~%"
20327 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
20328 (call-with-output-file target
20330 (dump-port minified port)))))
20331 sources targets)))))))))
20343 `(("uglifyjs" ,node-uglify-js)
20347 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
20350 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
20354 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
20357 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
20361 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
20364 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
20365 ("js-prism-line-numbers"
20368 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
20371 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
20375 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
20378 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
20379 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
20380 (synopsis "R Markdown format for flexible dashboards")
20382 "This package provides an R Markdown format for converting an R Markdown
20383 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
20384 of its components to the containing web page.")
20385 (license license:expat)))
20387 (define-public r-preseqr
20394 (uri (cran-uri "preseqR" version))
20397 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
20398 (properties `((upstream-name . "preseqR")))
20399 (build-system r-build-system)
20402 (home-page "https://cran.r-project.org/web/packages/preseqR/")
20403 (synopsis "Predicting species accumulation curves")
20405 "This package can be used to predict the r-species accumulation
20406 curve (r-SAC), which is the number of species represented at least r times as
20407 a function of the sampling effort. When r = 1, the curve is known as the
20408 species accumulation curve, or the library complexity curve in high-throughput
20409 genomic sequencing. The package includes both parametric and nonparametric
20410 methods, as described by Deng C, et al. (2018).")
20411 (license license:gpl3)))
20413 (define-public r-mapplots
20415 (name "r-mapplots")
20420 (uri (cran-uri "mapplots" version))
20423 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
20424 (build-system r-build-system)
20425 (home-page "https://cran.r-project.org/web/packages/mapplots/")
20426 (synopsis "Data visualization on maps")
20428 "This package helps you create simple maps; add sub-plots like pie plots
20429 to a map or any other plot; format, plot and export gridded data. The package
20430 was developed for displaying fisheries data but most functions can be used for
20431 more generic data visualisation.")
20432 (license license:gpl2+)))
20434 (define-public r-pmcmr
20441 (uri (cran-uri "PMCMR" version))
20444 "05n13pp5yff6pzk4ry07crddfaj3jlglrd1vkcnacyd8jpaxkd77"))))
20445 (properties `((upstream-name . "PMCMR")))
20446 (build-system r-build-system)
20447 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
20448 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
20450 "This is a deprecated package for calculating pairwise multiple
20451 comparisons of mean rank sums. This package is superseded by the novel
20452 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
20453 compatibility of dependent packages for some time.")
20454 (license license:gpl3+)))
20456 (define-public r-downloader
20458 (name "r-downloader")
20463 (uri (cran-uri "downloader" version))
20466 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
20467 (build-system r-build-system)
20470 (home-page "https://github.com/wch/downloader")
20471 (synopsis "Download files over HTTP and HTTPS")
20473 "This package provides a wrapper for the @code{download.file} function,
20474 making it possible to download files over HTTPS across platforms. The
20475 @code{RCurl} package provides this functionality (and much more) but has
20476 external dependencies. This package has is implemented purely in R.")
20477 (license license:gpl2)))
20479 (define-public r-aplot
20486 (uri (cran-uri "aplot" version))
20489 "17256cdn46cii97s0h2zmah9vs116ybnih78734lpkn7kmvdfcfr"))))
20490 (properties `((upstream-name . "aplot")))
20491 (build-system r-build-system)
20498 (home-page "https://github.com/YuLab-SMU/aplot")
20499 (synopsis "Decorate a ggplot with associated information")
20501 "Users may want to align plots with associated information that requires
20502 axes to be exactly matched in subplots, e.g. hierarchical clustering with a
20503 heatmap. This package provides utilities to align associated subplots to a
20504 main plot at different sides (left, right, top and bottom) with axes exactly
20506 (license license:artistic2.0)))
20508 (define-public r-ggnewscale
20510 (name "r-ggnewscale")
20515 (uri (cran-uri "ggnewscale" version))
20518 "004p5ai6rc5y8f6966k894jzw9v3m4zy36z50yapig7c85lzmzn7"))))
20519 (properties `((upstream-name . "ggnewscale")))
20520 (build-system r-build-system)
20523 (home-page "https://cran.r-project.org/package=ggnewscale")
20524 (synopsis "Multiple fill and color scales in ggplot2")
20526 "This package lets you use multiple fill and color scales in ggplot2.")
20527 (license license:gpl3)))
20529 (define-public r-ggpointdensity
20531 (name "r-ggpointdensity")
20536 (uri (cran-uri "ggpointdensity" version))
20539 "0c9a14j3b0hvamqylhzldw2hjdxmfbllwahjkf3gg2rw337ld9iy"))))
20541 `((upstream-name . "ggpointdensity")))
20542 (build-system r-build-system)
20545 (home-page "https://github.com/LKremer/ggpointdensity")
20546 (synopsis "Cross between a 2D density plot and a scatter plot")
20548 "This package provides a cross between a 2D density plot and a scatter
20549 plot, implemented as a ggplot2 @code{geom}. Points in the scatter plot are
20550 colored by the number of neighboring points. This is useful to visualize the
20551 2D-distribution of points in case of overplotting.")
20552 (license license:gpl3)))
20554 (define-public r-arrow
20561 (uri (cran-uri "arrow" version))
20564 "04qsj68zsqcwkv1ryp4l0is474siyi1b64dy41fr74ryj7mbamg8"))))
20565 (properties `((upstream-name . "arrow")))
20566 (build-system r-build-system)
20568 (list `(,apache-arrow "lib") zlib))
20580 (list pkg-config r-knitr))
20581 (home-page "https://github.com/apache/arrow/")
20582 (synopsis "R integration to Apache Arrow")
20584 "Apache Arrow is a cross-language development platform for in-memory
20585 data. It specifies a standardized language-independent columnar memory format
20586 for flat and hierarchical data, organized for efficient analytic operations on
20587 modern hardware. This package provides an R interface to the Arrow C++
20589 (license license:asl2.0)))
20591 (define-public r-rex
20598 (uri (cran-uri "rex" version))
20601 "1mmzlc3j7xa0rbjxa369f4sr0iw3gq58g8fmjjxbsjvfq14ychmg"))))
20602 (build-system r-build-system)
20607 (home-page "https://github.com/kevinushey/rex")
20608 (synopsis "Friendly regular expressions")
20610 "This package provides a friendly interface for the construction of
20611 regular expressions. Regular expressions are a very powerful feature, however
20612 they are often difficult to interpret. Rex allows you to build complex
20613 regular expressions from human readable expressions")
20614 (license license:expat)))
20616 (define-public r-mlapi
20623 (uri (cran-uri "mlapi" version))
20626 "1qyiii6x9b89i4pd4yi2zd23aabpmnpj18gqi5va0zy0l8r7kknr"))))
20627 (properties `((upstream-name . "mlapi")))
20628 (build-system r-build-system)
20630 (list r-matrix r-r6))
20633 (home-page "https://cran.r-project.org/package=mlapi")
20634 (synopsis "Abstract classes for building scikit-learn like API")
20636 "This package provides R6 abstract classes for building machine learning
20637 models with a scikit-learn like API. Scikit-learn is a popular module for the
20638 Python programming language whose design became a de facto standard in
20639 industry for machine learning tasks.")
20640 (license license:expat)))
20642 (define-public r-float
20649 (uri (cran-uri "float" version))
20652 "0m7bf3548vlgkk1c78jyrgj72ngwg0gsccap2iqinm3l3qrm4zbs"))))
20653 (properties `((upstream-name . "float")))
20654 (build-system r-build-system)
20657 (home-page "https://github.com/wrathematics/float")
20658 (synopsis "32-bit floats")
20660 "R comes with a suite of utilities for linear algebra with
20661 \"numeric\" (double precision) vectors/matrices. However, sometimes single
20662 precision (or less!) is more than enough for a particular task. This package
20663 extends R's linear algebra facilities to include 32-bit float (single
20664 precision) data. Float vectors/matrices have half the precision of their
20665 \"numeric\"-type counterparts but are generally faster to numerically operate
20666 on, for a performance vs accuracy trade-off.")
20667 (license license:bsd-2)))
20669 (define-public r-rsparse
20676 (uri (cran-uri "rsparse" version))
20679 "15kdllm2lh6xdlv4j0ljyj5pczhx26s9d8cac7953zbb0sd45chz"))))
20680 (properties `((upstream-name . "rsparse")))
20681 (build-system r-build-system)
20691 (home-page "https://github.com/rexyai/rsparse")
20692 (synopsis "Statistical learning on sparse matrices")
20694 "This package implements many algorithms for statistical learning on
20695 sparse matrices: matrix factorizations, matrix completion, elastic net
20696 regressions, factorization machines. The rsparse package also enhances the
20697 Matrix package by providing methods for multithreaded <sparse, dense> matrix
20698 products and native slicing of the sparse matrices in @dfn{Compressed Sparse
20699 Row} (CSR) format.")
20700 (license license:gpl2+)))
20702 (define-public r-text2vec
20704 (name "r-text2vec")
20709 (uri (cran-uri "text2vec" version))
20712 "1as58w1hb6h0hpncwcr2nx9a8bj5fy6bfllx2a8ck8hal764iach"))))
20713 (properties `((upstream-name . "text2vec")))
20714 (build-system r-build-system)
20727 (home-page "http://text2vec.org")
20728 (synopsis "Text mining framework for R")
20730 "This package provides fast and memory-friendly tools for text
20731 vectorization, topic modeling (LDA, LSA), word embeddings (GloVe),
20732 similarities. It provides a source-agnostic streaming API, which allows
20733 researchers to perform analysis of collections of documents which are larger
20734 than available RAM. All core functions are parallelized to benefit from
20735 multicore machines.")
20736 (license license:gpl2+)))
20738 (define-public r-mcmcpack
20740 (name "r-mcmcpack")
20745 (uri (cran-uri "MCMCpack" version))
20748 "1cwdjn43b9hxpxf9mnas583myhk6r2258mh57f0zsc8bd4hbl56b"))))
20749 (properties `((upstream-name . "MCMCpack")))
20750 (build-system r-build-system)
20752 (list r-coda r-lattice r-mass r-mcmc r-quantreg))
20753 (home-page "https://cran.r-project.org/package=MCMCpack")
20754 (synopsis "Markov Chain Monte Carlo (MCMC) package")
20756 "This package contains functions to perform Bayesian inference using
20757 posterior simulation for a number of statistical models. Most simulation is
20758 done in compiled C++ written in the Scythe Statistical Library. All models
20759 return @code{coda} @code{mcmc} objects that can then be summarized using the
20760 @code{coda} package. Some useful utility functions such as density functions,
20761 pseudo-random number generators for statistical distributions, a general
20762 purpose Metropolis sampling algorithm, and tools for visualization are
20764 (license license:gpl3)))
20766 (define-public r-xmlparsedata
20768 (name "r-xmlparsedata")
20773 (uri (cran-uri "xmlparsedata" version))
20776 "1c6bnz3ng1qw7sfip8wq3a4dn36a4d6rbja0sadn0a4pbsmk8q3n"))))
20777 (properties `((upstream-name . "xmlparsedata")))
20778 (build-system r-build-system)
20779 (home-page "https://github.com/r-lib/xmlparsedata#readme")
20780 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
20782 "This package provides tools to convert the output of
20783 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
20784 @code{XPath}, and is easier to manipulate in general.")
20785 (license license:expat)))
20787 (define-public r-cyclocomp
20789 (name "r-cyclocomp")
20794 (uri (cran-uri "cyclocomp" version))
20797 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
20798 (properties `((upstream-name . "cyclocomp")))
20799 (build-system r-build-system)
20801 (list r-callr r-crayon r-desc r-remotes r-withr))
20802 (home-page "https://github.com/MangoTheCat/cyclocomp")
20803 (synopsis "Cyclomatic complexity of R code")
20805 "Cyclomatic complexity is a software metric, used to indicate the
20806 complexity of a program. It is a quantitative measure of the number of
20807 linearly independent paths through a program's source code. This package
20808 provides tools to compute this metric.")
20809 (license license:expat)))
20811 (define-public r-lintr
20818 (uri (cran-uri "lintr" version))
20821 "1j9l5lsa88hl5b3lw1789868pm0m2sbahyqayj9213d7zspp0slz"))))
20822 (properties `((upstream-name . "lintr")))
20823 (build-system r-build-system)
20836 (native-inputs (list r-knitr))
20837 (home-page "https://github.com/jimhester/lintr")
20838 (synopsis "Linter for R code")
20839 (description "This package checks adherence to a given style, syntax
20840 errors and possible semantic issues. It supports on the fly checking of R
20841 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
20842 (license license:expat)))
20844 (define-public r-sctransform
20846 (name "r-sctransform")
20851 (uri (cran-uri "sctransform" version))
20854 "02vfgv6v3knmn5nxadjyjkzqmni1sgaf3f9ywm7d0knn0pgmd3n0"))))
20855 (build-system r-build-system)
20870 (home-page "https://github.com/ChristophH/sctransform")
20871 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
20873 "This package provides a normalization method for single-cell UMI count
20874 data using a variance stabilizing transformation. The transformation is based
20875 on a negative binomial regression model with regularized parameters. As part
20876 of the same regression framework, this package also provides functions for
20877 batch correction, and data correction.")
20878 (license license:gpl3)))
20880 (define-public r-styler
20887 (uri (cran-uri "styler" version))
20890 "1iw4nj68aj4psysrpyy7s6g3r3vhpfk8s05n6d20m2qmmk0p92sg"))))
20891 (build-system r-build-system)
20892 ;; This is needed by R.cache.
20895 (modify-phases %standard-phases
20896 (add-after 'unpack 'set-HOME
20897 (lambda _ (setenv "HOME" "/tmp"))))))
20909 (home-page "https://github.com/r-lib/styler")
20910 (synopsis "Non-invasive pretty printing of R code")
20912 "This is a package for pretty-printing R code without changing the user's
20913 formatting intent.")
20914 (license license:gpl3)))
20916 (define-public r-scrime
20923 (uri (cran-uri "scrime" version))
20926 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
20927 (build-system r-build-system)
20928 (home-page "https://cran.r-project.org/web/packages/scrime/")
20929 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
20931 "This package provides tools for the analysis of high-dimensional data
20932 developed/implemented at the group \"Statistical Complexity Reduction In
20933 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
20934 the functions can also be applied to other types of categorical data.")
20935 (license license:gpl2)))
20937 (define-public r-pbmcapply
20939 (name "r-pbmcapply")
20944 (uri (cran-uri "pbmcapply" version))
20947 "1p8jf7c4k45482w72sr0jw4jkz787krrxai3sl6jz5l4lda2iz3z"))))
20948 (build-system r-build-system)
20949 (home-page "https://github.com/kvnkuang/pbmcapply")
20950 (synopsis "Track the progress of apply procedures with a progress bar")
20952 "This light-weight package helps you track and visualize the progress of
20953 parallel versions of vectorized R functions of the @code{mc*apply} family.")
20954 (license license:expat)))
20956 (define-public r-blme
20963 (uri (cran-uri "blme" version))
20966 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7"))))
20967 (build-system r-build-system)
20968 (propagated-inputs (list r-lme4))
20969 (home-page "https://github.com/vdorie/blme")
20970 (synopsis "Bayesian linear mixed-effects models")
20972 "This package provides tools for maximum a posteriori estimation for
20973 linear and generalized linear mixed-effects models in a Bayesian setting. It
20974 extends the lme4 package.")
20975 (license license:gpl2+)))
20977 (define-public r-batchtools
20979 (name "r-batchtools")
20984 (uri (cran-uri "batchtools" version))
20987 "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52"))))
20988 (build-system r-build-system)
21004 (home-page "https://github.com/mllg/batchtools")
21005 (synopsis "Tools for computation on batch systems")
21007 "As a successor of the packages BatchJobs and BatchExperiments, this
21008 package provides a parallel implementation of the Map function for high
21009 performance computing systems managed by various schedulers. A multicore and
21010 socket mode allow the parallelization on a local machines, and multiple
21011 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
21012 the package provides an abstraction mechanism to define large-scale computer
21013 experiments in a well-organized and reproducible way.")
21014 (license license:lgpl3)))
21016 (define-public r-clue
21023 (uri (cran-uri "clue" version))
21026 "1lhybs6rhq8zs7q15ahng7c93liiygr64i2zwg3ya6maqji3ynjp"))))
21027 (build-system r-build-system)
21028 (propagated-inputs (list r-cluster))
21029 (home-page "https://cran.r-project.org/web/packages/clue/")
21030 (synopsis "Tools for analyzing cluster ensembles")
21031 (description "Cluster ensembles are collections of individual solutions to
21032 a given clustering problem which are useful or necessary to consider in a wide
21033 range of applications. This R package provides an extensible computational
21034 environment for creating and analyzing cluster ensembles, with basic data
21035 structures for representing partitions and hierarchies, and facilities for
21036 computing on them, including methods for measuring proximity and obtaining
21037 consensus and secondary clusterings.")
21038 (license license:gpl2)))
21040 (define-public r-sitmo
21047 (uri (cran-uri "sitmo" version))
21050 "1hm89zi38ldgbskyx1cn7gm87yqy7zrxli8q05a36y1ndvazi3j4"))))
21051 (build-system r-build-system)
21052 (propagated-inputs (list r-rcpp))
21055 (home-page "https://github.com/coatless/sitmo/")
21056 (synopsis "Parallel pseudo random number generator header files")
21058 "This package provides two high quality and fast PPRNGs that may be used
21059 in an OpenMP parallel environment. In addition, there is a generator for one
21060 dimensional low-discrepancy sequence.")
21061 (license license:expat)))
21063 (define-public r-dqrng
21070 (uri (cran-uri "dqrng" version))
21073 "1fwsldqcri2lccna4icbmmlqic3w4xyjm7rn0xmikrsw4kzapvjb"))))
21074 (build-system r-build-system)
21076 (list r-bh r-rcpp r-sitmo))
21079 (home-page "https://www.daqana.org/dqrng")
21080 (synopsis "Fast pseudo random number generators")
21082 "Several fast random number generators are provided as C++ header-only
21083 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
21084 Additionally, fast functions for generating random numbers according to a
21085 uniform, normal and exponential distribution are included. The latter two use
21086 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
21087 functions are exported to R and as a C++ interface and are enabled for use
21088 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
21089 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
21090 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
21091 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
21092 ;; whole is distributed under the terms of the AGPL 3.
21093 (license license:agpl3)))
21095 (define-public r-ingredients
21097 (name "r-ingredients")
21102 (uri (cran-uri "ingredients" version))
21105 "11bv4l4fn9kr7y2nfzrwnaya8fi9w3nwcm9vzlqb7dva83rkqbsc"))))
21106 (properties `((upstream-name . "ingredients")))
21107 (build-system r-build-system)
21109 (list r-ggplot2 r-gridextra r-scales))
21110 (native-inputs (list r-knitr))
21111 (home-page "https://ModelOriented.github.io/ingredients/")
21112 (synopsis "Effects and importances of model ingredients")
21114 "This is a collection of tools for assessment of feature importance and
21115 feature effects. Key functions are:
21118 @item @code{feature_importance()} for assessment of global level feature
21120 @item @code{ceteris_paribus()} for calculation of the what-if plots,
21121 @item @code{partial_dependence()} for partial dependence plots,
21122 @item @code{conditional_dependence()} for conditional dependence plots,
21123 @item @code{accumulated_dependence()} for accumulated local effects plots,
21124 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
21125 aggregation of ceteris paribus profiles,
21126 @item generic @code{print()} and @code{plot()} for better usability of
21127 selected explainers,
21128 @item generic @code{plotD3()} for interactive, D3 based explanations, and
21129 @item generic @code{describe()} for explanations in natural language.
21131 (license license:gpl3)))
21133 (define-public r-ibreakdown
21135 (name "r-ibreakdown")
21140 (uri (cran-uri "iBreakDown" version))
21143 "00jzrndb3ahsv6ihp2pvs732n9cc944m83vdinrl9v1pxd82prkh"))))
21144 (properties `((upstream-name . "iBreakDown")))
21145 (build-system r-build-system)
21146 (propagated-inputs (list r-ggplot2))
21147 (native-inputs (list r-knitr))
21148 (home-page "https://ModelOriented.github.io/iBreakDown/")
21149 (synopsis "Model agnostic instance level variable attributions")
21151 "This package provides a model agnostic tool for decomposition of
21152 predictions from black boxes. It supports additive attributions and
21153 attributions with interactions. The Break Down Table shows contributions of
21154 every variable to a final prediction. The Break Down Plot presents variable
21155 contributions in a concise graphical way. This package works for
21156 classification and regression models.")
21157 (license license:gpl3)))
21159 (define-public r-dae
21166 (uri (cran-uri "dae" version))
21169 "0mq94ah21p1glvsbvdmi2p7nlgz1bvq7w3rz2z3mdqq18kz6nkjw"))))
21170 (build-system r-build-system)
21172 (list r-ggplot2 r-plyr))
21174 (list r-r-rsp)) ; vignette builder
21175 (home-page "http://chris.brien.name")
21176 (synopsis "Functions useful in the design and ANOVA of experiments")
21178 "This package provides functions useful in the design and ANOVA of
21179 experiments. The content falls into the following groupings:
21183 @item factor manipulation functions,
21184 @item design functions,
21185 @item ANOVA functions,
21186 @item matrix functions,
21187 @item projector and canonical efficiency functions, and
21188 @item miscellaneous functions.
21191 There is a vignette called @code{DesignNotes} describing how to use the design
21192 functions for randomizing and assessing designs. The ANOVA functions
21193 facilitate the extraction of information when the @code{Error} function has
21194 been used in the call to @code{aov}.")
21195 (license license:gpl2)))
21197 (define-public r-dalex
21204 (uri (cran-uri "DALEX" version))
21207 "1m19ibv8rpghqm4vr8nrvarrjkm9rxw6jx8xl3hzrqnnmf2xifqr"))))
21208 (properties `((upstream-name . "DALEX")))
21209 (build-system r-build-system)
21211 (list r-ggplot2 r-ibreakdown r-ingredients))
21212 (home-page "https://pbiecek.github.io/DALEX/")
21213 (synopsis "Descriptive machine learning explanations")
21215 "Machine Learning models are widely used and have various applications in
21216 classification or regression. Models created with boosting, bagging, stacking
21217 or similar techniques are often used due to their high performance, but such
21218 black-box models usually lack interpretability. The DALEX package contains
21219 various explainers that help to understand the link between input variables
21220 and model output.")
21221 ;; Any version of the GPL
21222 (license license:gpl3+)))
21224 (define-public r-enrichr
21231 (uri (cran-uri "enrichR" version))
21234 "0ad7jp398prvmm2fym07268qhv40mg67dx55ml4ayqkwxwffr1i9"))))
21235 (properties `((upstream-name . "enrichR")))
21236 (build-system r-build-system)
21238 (list r-curl r-ggplot2 r-httr r-rjson))
21241 (home-page "https://cran.r-project.org/web/packages/enrichR/")
21242 (synopsis "R Interface to Enrichr database for analyzing gene sets")
21244 "This package provides an R interface to all Enrichr databases, a
21245 web-based tool for analyzing gene sets and returns any enrichment of common
21246 annotated biological functions.")
21247 (license license:gpl2+)))
21249 (define-public r-plot3d
21256 (uri (cran-uri "plot3D" version))
21259 "1h59zlsyzbjylaziwavppl9bjmnba4iiq34772y3dys6fqclajnh"))))
21260 (properties `((upstream-name . "plot3D")))
21261 (build-system r-build-system)
21262 (propagated-inputs (list r-misc3d))
21263 (home-page "https://cran.r-project.org/web/packages/plot3D")
21264 (synopsis "Plot multi-dimensional data")
21266 "This package provides functions for viewing 2D and 3D data, including
21267 perspective plots, slice plots, surface plots, scatter plots, etc. It
21268 includes data sets from oceanography.")
21269 (license license:gpl3+)))
21271 (define-public r-ggfortify
21273 (name "r-ggfortify")
21278 (uri (cran-uri "ggfortify" version))
21281 "038m74azpy43869ax1yi6wxbl1kr59iaxl8raiikjg749vcx6njw"))))
21282 (build-system r-build-system)
21293 (home-page "https://github.com/sinhrks/ggfortify")
21294 (synopsis "Data visualization tools for statistical analysis results")
21296 "This package provides unified plotting tools for statistics commonly
21297 used, such as GLM, time series, PCA families, clustering and survival
21298 analysis. The package offers a single plotting interface for these analysis
21299 results and plots in a unified style using the @code{ggplot2} package.")
21300 (license license:gpl2)))
21302 (define-public r-refmanager
21304 (name "r-refmanager")
21309 (uri (cran-uri "RefManageR" version))
21312 "1kjd66gp2z9fzrnyr1bqfd9p58q0bin3a187z9b56hiqmdjhyc78"))))
21313 (properties `((upstream-name . "RefManageR")))
21314 (build-system r-build-system)
21325 (home-page "https://github.com/ropensci/RefManageR/")
21326 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
21328 "This package provides tools for importing and working with bibliographic
21329 references. It greatly enhances the @code{bibentry} class by providing a
21330 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
21331 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
21332 by various formats for name lists (author by last names, translator by full
21333 names, etc.). Entries can be updated, combined, sorted, printed in a number
21334 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
21335 into R and converted to @code{BibEntry} objects.")
21336 ;; Any of these licenses may be picked.
21337 (license (list license:gpl2 license:gpl3 license:bsd-3))))
21339 (define-public r-citr
21346 (uri (cran-uri "citr" version))
21349 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
21350 (build-system r-build-system)
21361 (home-page "https://github.com/crsh/citr")
21362 (synopsis "RStudio add-in to insert Markdown citations")
21364 "This package provides functions and an RStudio add-in that search a
21365 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
21366 the current document.")
21367 (license license:expat)))
21369 (define-public r-xgboost
21372 (version "1.6.0.1")
21376 (uri (cran-uri "xgboost" version))
21379 "1gafjv6vcpny03lqw8s68xszalsylniavaqwsbzh46vyk4h9mscs"))))
21380 (build-system r-build-system)
21382 (list r-data-table r-jsonlite r-matrix))
21385 (home-page "https://github.com/dmlc/xgboost")
21386 (synopsis "Extreme gradient boosting")
21388 "This package provides an R interface to Extreme Gradient Boosting, which
21389 is an efficient implementation of the gradient boosting framework from Chen
21390 and Guestrin (2016). The package includes efficient linear model solver and
21391 tree learning algorithms. The package can automatically do parallel
21392 computation on a single machine. It supports various objective functions,
21393 including regression, classification and ranking. The package is made to be
21394 extensible, so that users are also allowed to define their own objectives
21396 (license license:asl2.0)))
21398 (define-public r-umap
21401 (version "0.2.9.0")
21405 (uri (cran-uri "umap" version))
21408 "1282v09kpds83mlr7kz06k8a40ji15hw85p30vrnp1g6w64w26sm"))))
21409 (build-system r-build-system)
21411 (list r-matrix r-openssl r-rcpp r-reticulate r-rspectra))
21414 (home-page "https://github.com/tkonopka/umap")
21415 (synopsis "Uniform manifold approximation and projection")
21417 "Uniform manifold approximation and projection is a technique for
21418 dimension reduction. This package provides an interface to the UMAP algorithm
21419 in R, including a translation of the original algorithm into R.")
21420 (license license:expat)))
21422 (define-public r-uwot
21429 (uri (cran-uri "uwot" version))
21432 "1q4z98w3pkc51vrcpmwaibnwmlm17zjcnh0qlx660wky5ccyh5l0"))))
21433 (build-system r-build-system)
21442 (home-page "https://github.com/jlmelville/uwot")
21443 (synopsis "Uniform manifold approximation and projection")
21445 "This package provides an implementation of the Uniform Manifold
21446 Approximation and Projection dimensionality reduction by McInnes et
21447 al. (2018). It also provides means to transform new data and to carry out
21448 supervised dimensionality reduction. An implementation of the related
21449 LargeVis method of Tang et al. (2016) is also provided.")
21450 (license license:gpl3)))
21452 (define-public r-kableextra
21454 (name "r-kableextra")
21459 (uri (cran-uri "kableExtra" version))
21462 "1c5vzy95cbz36jwyssr927qicrayifinv861rvnmg4nghb1gl7q9"))))
21463 (properties `((upstream-name . "kableExtra")))
21464 (build-system r-build-system)
21482 (home-page "https://haozhu233.github.io/kableExtra/")
21483 (synopsis "Construct complex tables with pipe syntax")
21485 "Build complex HTML or LaTeX tables using @code{kable()} from
21486 @code{knitr} and the piping syntax from @code{magrittr}. The function
21487 @code{kable()} is a light weight table generator coming from @code{knitr}.
21488 This package simplifies the way to manipulate the HTML or LaTeX codes
21489 generated by @code{kable()} and allows users to construct complex tables and
21490 customize styles using a readable syntax.")
21491 (license license:expat)))
21493 (define-public r-glasso
21500 (uri (cran-uri "glasso" version))
21502 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
21503 (build-system r-build-system)
21504 (native-inputs (list gfortran))
21505 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
21506 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
21508 "This is a package for estimation of a sparse inverse covariance matrix
21509 using a lasso (L1) penalty. Facilities are provided for estimates along a
21510 path of values for the regularization parameter.")
21511 (license license:gpl2)))
21513 (define-public r-gldex
21516 (version "2.0.0.9.2")
21519 (uri (cran-uri "GLDEX" version))
21522 "0pikq5aywky77sbbkga7s0ww3ywlarx336rgpyiigr72fmjvb289"))))
21523 (properties `((upstream-name . "GLDEX")))
21524 (build-system r-build-system)
21525 (propagated-inputs (list r-cluster r-spacefillr))
21526 (home-page "https://cran.r-project.org/package=GLDEX")
21527 (synopsis "Fitting single and mixture of generalised lambda distributions")
21529 "@code{GLDEX} offers fitting algorithms corresponding to two major
21530 objectives. One is to provide a smoothing device to fit distributions to data
21531 using the weighted and unweighted discretised approach based on the bin width
21532 of the histogram. The other is to provide a definitive fit to the data set
21533 using the maximum likelihood and quantile matching estimation. Other methods
21534 such as moment matching, starship method, and L moment matching are also
21535 provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample
21536 tests and comparing mean, variance, skewness and kurtosis of the data with the
21537 fitted distribution.")
21538 (license license:gpl3+)))
21540 (define-public r-rhpcblasctl
21542 (name "r-rhpcblasctl")
21543 (version "0.21-247.1")
21547 (uri (cran-uri "RhpcBLASctl" version))
21550 "0scpr6jq25xx7wmqyc380ann4h536ll0g7wblikk25yqvpamzrav"))))
21551 (properties `((upstream-name . "RhpcBLASctl")))
21552 (build-system r-build-system)
21553 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
21554 (synopsis "Control the number of threads on BLAS")
21556 "This package allows you to control the number of threads the BLAS
21557 library uses. It is also possible to control the number of threads in
21559 (license license:agpl3+)))
21561 (define-public r-lda
21568 (uri (cran-uri "lda" version))
21571 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
21572 (build-system r-build-system)
21573 (home-page "https://cran.r-project.org/web/packages/lda/")
21574 (synopsis "Collapsed Gibbs sampling methods for topic models")
21576 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
21577 related models. This includes (but is not limited to) sLDA, corrLDA, and the
21578 mixed-membership stochastic blockmodel. Inference for all of these models is
21579 implemented via a fast collapsed Gibbs sampler written in C. Utility
21580 functions for reading/writing data typically used in topic models, as well as
21581 tools for examining posterior distributions are also included.")
21582 ;; Any version of the LGPL
21583 (license license:lgpl3+)))
21585 (define-public r-rann-l1
21592 (uri (cran-uri "RANN.L1" version))
21595 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
21596 (properties `((upstream-name . "RANN.L1")))
21597 (build-system r-build-system)
21598 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
21599 (synopsis "Fast nearest neighbour search using L1 metric")
21601 "This package provides tools to find the k nearest neighbours for every
21602 point in a given dataset in O(N log N) time using Arya and Mount's ANN
21603 library. There is support for approximate as well as exact searches, fixed
21604 radius searches and @code{bd} as well as @code{kd} trees. The distance is
21605 computed using the L1 (Manhattan, taxicab) metric.")
21606 (license license:gpl3+)))
21608 (define-public r-leiden
21615 (uri (cran-uri "leiden" version))
21618 "0f09k3mhb0di2cz1q95y6qd3rqh7xdybn0dpnd4ifqhfhr5lnika"))))
21619 (properties `((upstream-name . "leiden")))
21620 (build-system r-build-system)
21622 (list r-igraph r-matrix r-reticulate))
21625 (home-page "https://github.com/TomKellyGenetics/leiden")
21626 (synopsis "R implementation of Leiden clustering algorithm")
21628 "This package implements the Python @code{leidenalg} module to be called
21629 in R. It enables clustering using the Leiden algorithm for partitioning a
21630 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
21631 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
21632 (license license:gpl3)))
21634 (define-public r-patchwork
21636 (name "r-patchwork")
21641 (uri (cran-uri "patchwork" version))
21644 "0xw9mh1qakj131nw98icxrxwvdlwy2ngwvmagrqr3m84sz9dbffs"))))
21645 (build-system r-build-system)
21647 (list r-ggplot2 r-gtable))
21650 (home-page "https://github.com/thomasp85/patchwork")
21651 (synopsis "Compose ggplot2 plots")
21653 "The @code{ggplot2} package provides a strong API for sequentially
21654 building up a plot, but does not concern itself with composition of multiple
21655 plots. Patchwork is a package that expands the API to allow for arbitrarily
21656 complex composition of plots by providing mathematical operators for combining
21658 (license license:expat)))
21660 (define-public r-liger
21667 (uri (git-reference
21668 (url "https://github.com/MacoskoLab/liger")
21669 (commit (string-append "v" version))))
21670 (file-name (git-file-name name version))
21673 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
21674 (modules '((guix build utils)))
21677 (delete-file "inst/java/ModularityOptimizer.jar")
21679 (build-system r-build-system)
21682 (modify-phases %standard-phases
21683 (add-after 'unpack 'build-java-part
21684 (lambda* (#:key inputs #:allow-other-keys)
21685 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
21686 (for-each (lambda (file) (invoke "javac" file))
21687 (find-files "." "\\.java$"))
21688 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
21689 (find-files "." "\\.class$"))
21713 `(("jdk" ,icedtea "jdk")
21714 ;; See https://github.com/MacoskoLab/liger/issues/96
21715 ;; The optimizer is released under the Expat license.
21719 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
21722 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
21724 ("r-knitr" ,r-knitr))) ; for vignettes
21725 (home-page "https://github.com/MacoskoLab/liger")
21726 (synopsis "Integrate and analyze multiple single-cell datasets")
21728 "LIGER is a package for integrating and analyzing multiple single-cell
21729 datasets, developed and maintained by the Macosko lab. It relies on
21730 integrative non-negative matrix factorization to identify shared and
21731 dataset-specific factors.")
21732 (license license:gpl3)))
21734 (define-public r-harmony
21741 (uri (git-reference
21742 (url "https://github.com/immunogenomics/harmony")
21744 (file-name (git-file-name name version))
21747 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
21748 (modules '((guix build utils)))
21751 (for-each delete-file '("config.status" "configure"))
21753 (build-system r-build-system)
21768 (home-page "https://github.com/immunogenomics/harmony")
21769 (synopsis "Integration of single cell sequencing data")
21771 "This package provides an implementation of the Harmony algorithm for
21772 single cell integration, described in Korsunsky et al
21773 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
21774 function and interfaces to external frameworks.")
21775 (license license:gpl3)))
21777 (define-public r-covr
21784 (uri (cran-uri "covr" version))
21786 (base32 "0mqiqmbwq5f083lda208nqd4ya0f912bkkya2i62fkqsii1ibgpz"))))
21787 (properties `((upstream-name . "covr")))
21788 (build-system r-build-system)
21798 (list r-knitr)) ; for vignettes
21799 (home-page "https://github.com/r-lib/covr")
21800 (synopsis "Test coverage for R packages")
21802 "Thisp package enables you to track and report code coverage for your
21803 package and (optionally) upload the results to a coverage service. Code
21804 coverage is a measure of the amount of code being exercised by a set of tests.
21805 It is an indirect measure of test quality and completeness. This package is
21806 compatible with any testing methodology or framework and tracks coverage of
21807 both R code and compiled C/C++/FORTRAN code.")
21808 (license license:gpl3)))
21810 (define-public r-systemfonts
21812 (name "r-systemfonts")
21817 (uri (cran-uri "systemfonts" version))
21820 "1h44bal845jp7ya8i7ff1kz1n3wklkb00jk6hb9lgwa2p5snqxpg"))))
21821 (properties `((upstream-name . "systemfonts")))
21822 (build-system r-build-system)
21826 (list fontconfig freetype zlib))
21828 (list pkg-config r-knitr))
21829 (home-page "https://github.com/r-lib/systemfonts")
21830 (synopsis "System native font finding")
21832 "This package provides system native access to the font catalogue. As
21833 font handling varies between systems it is difficult to correctly locate
21834 installed fonts across different operating systems. The 'systemfonts' package
21835 provides bindings to the native libraries for finding font files that can then
21836 be used further by e.g. graphic devices.")
21837 (license license:expat)))
21839 (define-public r-graphlayouts
21841 (name "r-graphlayouts")
21846 (uri (cran-uri "graphlayouts" version))
21849 "08a4cpy0n90hw8xzmxck13hp76yh40r0njb2m7mwdldljkbybr7r"))))
21850 (properties `((upstream-name . "graphlayouts")))
21851 (build-system r-build-system)
21853 (list r-igraph r-rcpp r-rcpparmadillo))
21854 (home-page "https://github.com/schochastics/graphlayouts")
21855 (synopsis "Additional layout algorithms for network visualizations")
21857 "This package provides several layout algorithms to visualize networks
21858 which are not part of the igraph library. Most are based on the concept of
21859 stress majorization by Gansner et al. (2004)
21860 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
21861 emphasize hidden group structures in networks or focus on specific nodes.")
21862 (license license:expat)))
21864 (define-public r-terra
21871 (uri (cran-uri "terra" version))
21874 "00mwigymvsqf7r3swbkdw8fwqzr05ddk84fhyhr16lfa4118z26v"))))
21875 (properties `((upstream-name . "terra")))
21876 (build-system r-build-system)
21881 sqlite ; needed for proj
21887 (home-page "https://rspatial.org/terra")
21888 (synopsis "Spatial data analysis")
21890 "This package provides methods for spatial data analysis, especially
21891 raster data. The included methods allow for low-level data manipulation as
21892 well as high-level global, local, zonal, and focal computation. The predict
21893 and interpolate methods facilitate the use of regression type (interpolation,
21894 machine learning) models for spatial prediction. Processing of very large
21895 files is supported.")
21896 (license license:gpl3+)))
21898 (define-public r-tidygraph
21900 (name "r-tidygraph")
21905 (uri (cran-uri "tidygraph" version))
21908 "0w34jfldjkynbkyinmi1vdrfjhjrs47hm599mbnx4sxmnpbclmfm"))))
21909 (properties `((upstream-name . "tidygraph")))
21910 (build-system r-build-system)
21922 (home-page "https://github.com/thomasp85/tidygraph")
21923 (synopsis "Tidy API for graph manipulation")
21925 "This package provides a graph implementation that can be thought of as
21926 two tidy data frames describing node and edge data respectively. It provides
21927 an approach to manipulate these two virtual data frames using the API defined
21928 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
21929 common graph algorithms.")
21930 (license license:expat)))
21932 (define-public r-soupx
21933 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
21937 (version (git-version "0.3.1" revision commit))
21941 (uri (git-reference
21942 (url "https://github.com/constantAmateur/SoupX")
21944 (file-name (git-file-name name version))
21947 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
21948 (properties `((upstream-name . "SoupX")))
21949 (build-system r-build-system)
21951 (list r-ggplot2 r-matrix r-seurat))
21952 (home-page "https://github.com/constantAmateur/SoupX")
21953 (synopsis "Single cell mRNA Soup eXterminator")
21955 "This package provides a package for quantifying, profiling and
21956 removing cell free mRNA contamination (the \"soup\") from droplet based single
21957 cell RNA-seq experiments.")
21958 (license license:gpl2))))
21960 (define-public r-assertr
21967 (uri (cran-uri "assertr" version))
21970 "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650"))))
21971 (build-system r-build-system)
21973 (list r-dplyr r-mass r-rlang))
21975 (list r-knitr)) ; needed for vignette
21976 (home-page "https://github.com/ropensci/assertr")
21977 (synopsis "Assertive programming for R analysis pipelines")
21979 "This package provides functionality to assert conditions that have to be
21980 met so that errors in data used in analysis pipelines can fail quickly. It is
21981 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
21983 (license license:expat)))
21985 (define-public r-parameters
21987 (name "r-parameters")
21992 (uri (cran-uri "parameters" version))
21995 "10cl8vgcjncnry6qkkr41yyh8ngxxn81hwqqqix9g7pwpbf3c2mf"))))
21996 (properties `((upstream-name . "parameters")))
21997 (build-system r-build-system)
21999 (list r-bayestestr r-datawizard r-insight))
22002 (home-page "https://cran.r-project.org/web/packages/parameters")
22003 (synopsis "Processing of model parameters")
22005 "This package provides utilities for processing the parameters of various
22006 statistical models. Beyond computing p values, CIs, and other indices for a
22007 wide variety of models, this package implements features like standardization
22008 or bootstrapping of parameters and models, feature reduction (feature
22009 extraction and variable selection) as well as conversion between indices of
22011 (license license:gpl3)))
22013 (define-public r-rgdal
22020 (uri (cran-uri "rgdal" version))
22022 (base32 "1vbkyhw8nd7dw1r53qisphav31x6zvpbzilvnlvbjbj9hzhs90s5"))))
22023 (properties `((upstream-name . "rgdal")))
22024 (build-system r-build-system)
22026 (list gdal proj zlib))
22030 (list pkg-config r-knitr))
22031 (home-page "http://rgdal.r-forge.r-project.org")
22032 (synopsis "Bindings for the Geospatial Data Abstraction Library")
22034 "This package provides bindings to the Geospatial Data Abstraction
22035 Library (GDAL) and access to projection/transformation operations from the
22037 (license license:gpl2+)))
22039 (define-public r-insol
22046 (uri (cran-uri "insol" version))
22049 "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3"))))
22050 (properties `((upstream-name . "insol")))
22051 (build-system r-build-system)
22056 (home-page "https://meteoexploration.com/R/insol/index.html")
22057 (synopsis "Tools for calculating solar radiation")
22059 "This package provides functions to compute insolation on tilted
22060 surfaces, computes atmospheric transmittance and related parameters such as:
22061 Earth radius vector, declination, sunset and sunrise, daylength, equation of
22062 time, vector in the direction of the sun, vector normal to surface, and some
22063 atmospheric physics.")
22064 (license license:gpl2+)))
22066 (define-public r-lifecycle
22068 (name "r-lifecycle")
22073 (uri (cran-uri "lifecycle" version))
22076 "1hk9mblhap429fk77qpgc4hv0j91q5wpahi0y76w118m471zsnb4"))))
22077 (properties `((upstream-name . "lifecycle")))
22078 (build-system r-build-system)
22080 (list r-cli r-glue r-rlang))
22082 (list r-knitr)) ; for vignettes
22083 (home-page "https://github.com/r-lib/lifecycle")
22084 (synopsis "Manage the life cycle of your package functions")
22086 "Manage the life cycle of your exported functions with shared
22087 conventions, documentation badges, and non-invasive deprecation warnings. The
22088 lifecycle package defines four development stages (experimental, maturing,
22089 stable, and questioning) and three deprecation stages (soft-deprecated,
22090 deprecated, and defunct). It makes it easy to insert badges corresponding to
22091 these stages in your documentation. Usage of deprecated functions are
22092 signalled with increasing levels of non-invasive verbosity.")
22093 (license license:gpl3)))
22095 (define-public r-assertable
22097 (name "r-assertable")
22102 (uri (cran-uri "assertable" version))
22105 "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4"))))
22106 (build-system r-build-system)
22108 (list r-data-table))
22111 (home-page "https://cran.r-project.org/web/packages/assertable/")
22112 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
22113 (description "This package provides simple, flexible assertions on
22114 data.frame or data.table objects with verbose output for vetting. While other
22115 assertion packages apply towards more general use-cases, @code{assertable} is
22116 tailored towards tabular data. It includes functions to check variable names
22117 and values, whether the dataset contains all combinations of a given set of
22118 unique identifiers, and whether it is a certain length. In addition,
22119 @code{assertable} includes utility functions to check the existence of target
22120 files and to efficiently import multiple tabular data files into one
22122 (license license:gpl3)))
22124 (define-public r-quadprog
22126 (name "r-quadprog")
22131 (uri (cran-uri "quadprog" version))
22133 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
22134 (build-system r-build-system)
22137 (home-page "https://cran.r-project.org/web/packages/quadprog")
22138 (synopsis "Functions to solve quadratic programming problems")
22140 "This package contains routines and documentation for solving quadratic
22141 programming problems.")
22142 (license license:gpl3+)))
22144 (define-public r-desolve
22151 (uri (cran-uri "deSolve" version))
22153 (base32 "08czbjvq07ax6q3k303w37q8lq50547cdx7yhp32mqnx8igk0m12"))))
22154 (properties `((upstream-name . "deSolve")))
22155 (build-system r-build-system)
22158 (home-page "https://desolve.r-forge.r-project.org/")
22159 (synopsis "Solvers for initial value problems of differential equations")
22160 (description "This package provides functions that solve initial value
22161 problems of a system of first-order @dfn{ordinary differential
22162 equations} (ODE), of @dfn{partial differential equations} (PDE), of
22163 @dfn{differential algebraic equations} (DAE), and of delay differential
22164 equations. The functions provide an interface to the FORTRAN functions
22165 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
22166 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
22167 C-implementation of solvers of the Runge-Kutta family with fixed or variable
22168 time steps. The package contains routines designed for solving ODEs resulting
22169 from 1-D, 2-D and 3-D partial differential equations that have been converted
22170 to ODEs by numerical differencing.")
22171 (license license:gpl2+)))
22173 (define-public r-pmcmrplus
22175 (name "r-pmcmrplus")
22180 (uri (cran-uri "PMCMRplus" version))
22182 (base32 "1mvj3cwrdkl3frk7fvh6l7v7yya5p3xm4z0qhc4fvykxdmb92ivz"))))
22183 (properties `((upstream-name . "PMCMRplus")))
22184 (build-system r-build-system)
22185 (inputs (list gmp))
22195 (native-inputs (list gfortran r-knitr))
22196 (home-page "https://cran.r-project.org/package=PMCMRplus")
22197 (synopsis "Calculate pairwise multiple comparisons of mean rank sums extended")
22199 "This package provides multiple pairwise tests.")
22200 (license license:gpl3+)))
22202 (define-public r-pracma
22208 (uri (cran-uri "pracma" version))
22210 (base32 "05lwx2yx7f45cr5amzbjv3b2p6ibspjxl0aglq2dga6rvxzk6l0x"))))
22211 (build-system r-build-system)
22212 (home-page "https://cran.r-project.org/web/packages/pracma/")
22213 (synopsis "Practical numerical math functions")
22214 (description "This package provides functions for numerical analysis and
22215 linear algebra, numerical optimization, differential equations, plus some
22216 special functions. It uses Matlab function names where appropriate to simplify
22218 (license license:gpl3+)))
22220 (define-public r-subplex
22227 (uri (cran-uri "subplex" version))
22230 "19g5bd39gmcn27xdsklkzxg99x1r5v5q8zcw1iwry31qj24ivhrv"))))
22231 (build-system r-build-system)
22234 (home-page "https://cran.r-project.org/web/packages/subplex")
22235 (synopsis "Unconstrained optimization using the subplex algorithm")
22237 "This package implements the Subplex optimization algorithm.
22238 It solves unconstrained optimization problems using a simplex method on
22239 subspaces. The method is well suited for optimizing objective functions that
22240 are noisy or are discontinuous at the solution.")
22241 (license license:gpl3+)))
22243 (define-public r-txtplot
22250 (uri (cran-uri "txtplot" version))
22253 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
22254 (build-system r-build-system)
22255 (home-page "https://cran.r-project.org/web/packages/txtplot/")
22256 (synopsis "Text-based plotting")
22257 (description "This package provides functions to produce rudimentary ASCII
22258 graphics directly in the terminal window. This package provides a basic
22259 plotting function (and equivalents of curve, density, acf and barplot) as well
22260 as a boxplot function.")
22261 (license license:lgpl3+)))
22263 (define-public r-bio3d
22270 (uri (cran-uri "bio3d" version))
22273 "1scxzmh22ca0nmpkvapsdcmq3n06j2wy74ljz1g27r1k1p0ylm2n"))))
22274 (properties `((upstream-name . "bio3d")))
22275 (build-system r-build-system)
22276 (inputs (list zlib))
22277 (propagated-inputs (list r-rcpp))
22280 (home-page "http://thegrantlab.org/bio3d/")
22281 (synopsis "Biological structure analysis")
22283 "This package provides utilities to process, organize and explore protein
22284 structure, sequence and dynamics data. Features include the ability to read
22285 and write structure, sequence and dynamic trajectory data, perform sequence
22286 and structure database searches, data summaries, atom selection, alignment,
22287 superposition, rigid core identification, clustering, torsion analysis,
22288 distance matrix analysis, structure and sequence conservation analysis, normal
22289 mode analysis, principal component analysis of heterogeneous structure data,
22290 and correlation network analysis from normal mode and molecular dynamics data.
22291 In addition, various utility functions are provided to enable the statistical
22292 and graphical power of the R environment to work with biological sequence and
22294 (license license:gpl2+)))
22296 (define-public r-bios2cor
22298 (name "r-bios2cor")
22303 (uri (cran-uri "Bios2cor" version))
22306 "0xj7ab9a463p4a67y0hlv6mfd08xf8didkn2mwrfa7gxjqqvix4z"))))
22307 (properties `((upstream-name . "Bios2cor")))
22308 (build-system r-build-system)
22310 (list r-bigmemory r-bio3d r-circular r-igraph))
22311 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
22312 (synopsis "From biological sequences and simulations to correlation analysis")
22314 "This package provides utilities for computation and analysis of
22315 correlation/covariation in multiple sequence alignments and in side chain
22316 motions during molecular dynamics simulations. Features include the
22317 computation of correlation/covariation scores using a variety of scoring
22318 functions between either sequence positions in alignments or side chain
22319 dihedral angles in molecular dynamics simulations and utilities to analyze the
22320 correlation/covariation matrix through a variety of tools including network
22321 representation and principal components analysis. In addition, several
22322 utility functions are based on the R graphical environment to provide friendly
22323 tools for help in data interpretation.")
22324 (license license:gpl2+)))
22326 ;; This package includes minified JavaScript files. When upgrading please
22327 ;; check that there are no new minified JavaScript files.
22328 (define-public r-networkd3
22330 (name "r-networkd3")
22335 (uri (cran-uri "networkD3" version))
22338 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
22341 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
22343 (properties `((upstream-name . "networkD3")))
22344 (build-system r-build-system)
22346 `(#:modules ((guix build utils)
22347 (guix build r-build-system)
22351 (modify-phases %standard-phases
22352 (add-after 'unpack 'process-javascript
22353 (lambda* (#:key inputs #:allow-other-keys)
22354 (with-directory-excursion "inst/htmlwidgets/lib/"
22358 `((,(assoc-ref inputs "d3.v4.js")
22359 "d3-4.5.0/d3.min.js"))))
22360 (lambda (sources targets)
22361 (for-each (lambda (source target)
22362 (format #t "Processing ~a --> ~a~%"
22364 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
22365 (call-with-output-file target
22367 (dump-port minified port)))))
22368 sources targets))))
22371 `(("uglifyjs" ,node-uglify-js)
22372 ;; NOTE: Make sure that this version of d3 is still valid when
22373 ;; upgrading the package.
22377 (uri "https://d3js.org/d3.v4.js")
22380 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
22382 (list r-htmlwidgets r-igraph r-magrittr))
22383 (home-page "https://cran.r-project.org/package=networkD3")
22384 (synopsis "D3 JavaScript network graphs from R")
22386 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
22388 (license license:gpl3+)))
22390 (define-public r-aasea
22397 (uri (cran-uri "aaSEA" version))
22400 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
22401 (properties `((upstream-name . "aaSEA")))
22402 (build-system r-build-system)
22413 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
22414 (synopsis "Amino acid substitution effect analyzer")
22416 "Given a protein multiple sequence alignment, it is a daunting task to
22417 assess the effects of substitutions along sequence length. The aaSEA package
22418 is intended to help researchers to rapidly analyze property changes caused by
22419 single, multiple and correlated amino acid substitutions in proteins.")
22420 (license license:gpl3)))
22422 (define-public r-abacus
22429 (uri (cran-uri "ABACUS" version))
22432 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
22433 (properties `((upstream-name . "ABACUS")))
22434 (build-system r-build-system)
22436 (list r-ggplot2 r-shiny))
22437 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
22438 (synopsis "Apps-based activities for communicating and understanding statistics")
22440 "This package provides a set of Shiny apps for effective communication
22441 and understanding in statistics. The current version includes properties of
22442 normal distribution, properties of sampling distribution, one-sample z and t
22443 tests, two samples independent (unpaired) t test and analysis of variance.")
22444 (license license:gpl3)))
22446 (define-public r-abc-rap
22453 (uri (cran-uri "ABC.RAP" version))
22456 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
22457 (properties `((upstream-name . "ABC.RAP")))
22458 (build-system r-build-system)
22459 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
22460 (synopsis "Array-based CpG region analysis pipeline")
22462 "This package aims to identify candidate genes that are differentially
22463 methylated between cases and controls. It applies Student's t-test and delta
22464 beta analysis to identify candidate genes containing multiple CpG sites.")
22465 (license license:gpl3)))
22467 (define-public r-abcadm
22474 (uri (cran-uri "abcADM" version))
22477 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
22478 (properties `((upstream-name . "abcADM")))
22479 (build-system r-build-system)
22481 (list r-bh r-rcpp))
22482 (home-page "https://cran.r-project.org/web/packages/abcADM/")
22483 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
22485 "This package provides tools to estimate parameters of accumulated
22486 damage (load duration) models based on failure time data under a Bayesian
22487 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
22488 long-term reliability under stochastic load profiles.")
22489 (license license:gpl3)))
22491 (define-public r-rglpk
22498 (uri (cran-uri "Rglpk" version))
22501 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
22502 (properties `((upstream-name . "Rglpk")))
22503 (build-system r-build-system)
22508 (home-page "https://r-forge.r-project.org/projects/rglp/")
22509 (synopsis "R interface to the GNU Linear Programming Kit")
22511 "This package provides an R interface to the GNU Linear Programming Kit,
22512 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
22513 integer linear programming} (MILP) and other related problems.")
22515 (license (list license:gpl2 license:gpl3))))
22517 (define-public r-abcdefba
22519 (name "r-abcdefba")
22524 (uri (cran-uri "abcdeFBA" version))
22527 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
22528 (properties `((upstream-name . "abcdeFBA")))
22529 (build-system r-build-system)
22531 (list r-corrplot r-lattice r-rgl r-rglpk))
22532 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
22533 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
22535 "This package provides functions for Constraint Based Simulation using
22536 Flux Balance Analysis and informative analysis of the data generated during
22538 (license license:gpl2)))
22540 (define-public r-abcrlda
22547 (uri (cran-uri "abcrlda" version))
22550 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
22551 (properties `((upstream-name . "abcrlda")))
22552 (build-system r-build-system)
22553 (home-page "https://ieeexplore.ieee.org/document/8720003/")
22554 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
22556 "This package offers methods to perform @dfn{asymptotically
22557 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
22558 cost-sensitive binary classification. The bias-correction is an estimate of
22559 the bias term added to regularized discriminant analysis that minimizes the
22561 (license license:gpl3)))
22563 (define-public r-abemus
22570 (uri (cran-uri "abemus" version))
22573 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
22574 (properties `((upstream-name . "abemus")))
22575 (build-system r-build-system)
22577 (list r-data-table))
22578 (home-page "https://cran.r-project.org/web/packages/abemus/")
22579 (synopsis "Adaptive base error model in ultra-deep sequencing data")
22581 "This package provides an implementation of @dfn{Adaptive Base Error
22582 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
22583 platform-specific genetic knowledge and empirical signal to readily detect and
22584 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
22585 cell free DNA} (cfDNA).")
22586 (license license:gpl3)))
22588 ;; This package includes minified JavaScript files. When upgrading please
22589 ;; check that there are no new minified JavaScript files.
22590 (define-public r-rintrojs
22592 (name "r-rintrojs")
22597 (uri (cran-uri "rintrojs" version))
22600 "19lpq421hrs1wc9bnimbwxx35p8bbzil3x1h9l28gjayn4djmjsh"))
22602 '(delete-file "inst/javascript/introjs/intro.min.js"))))
22603 (properties `((upstream-name . "rintrojs")))
22604 (build-system r-build-system)
22607 (modify-phases %standard-phases
22608 (add-after 'unpack 'process-javascript
22609 (lambda* (#:key inputs #:allow-other-keys)
22610 (with-directory-excursion "inst/javascript/introjs/"
22611 (let ((source (assoc-ref inputs "intro.js"))
22612 (target "intro.min.js"))
22613 (format #true "Processing ~a --> ~a~%"
22615 (invoke "esbuild" source "--minify"
22616 (string-append "--outfile=" target)))))))))
22618 `(("esbuild" ,esbuild)
22622 (uri "https://cdn.jsdelivr.net/npm/intro.js@3.2.1/intro.js")
22625 "0vh5n7hqqyx2pdvlqq6xadfqibcn78h5961rwhpf817kpxfzv8v7"))))))
22627 (list r-jsonlite r-shiny))
22628 (home-page "https://github.com/carlganz/rintrojs")
22629 (synopsis "Wrapper for the Intro.js library")
22631 "This package provides a wrapper for the @url{http://www.introjs.com,
22632 Intro.js} library. This package makes it easy to include step-by-step
22633 introductions, and clickable hints in a Shiny application. It supports both
22634 static introductions in the UI, and programmatic introductions from the
22636 ;; The intro.js library is licensed under Expat.
22637 (license (list license:agpl3+ license:expat))))
22639 (define-public r-sysfonts
22641 (name "r-sysfonts")
22646 (uri (cran-uri "sysfonts" version))
22649 "1fq5dn4l09sgrbznfz9cakf4vgc3761zwicvqaazh0s8mzbaicpn"))))
22650 (properties `((upstream-name . "sysfonts")))
22651 (build-system r-build-system)
22653 (list freetype libpng zlib))
22656 (home-page "https://github.com/yixuan/sysfonts")
22657 (synopsis "Loading fonts into R")
22659 "This is a package to simplify loading of system fonts and Google Fonts
22660 into R, in order to support other packages.")
22661 (license license:gpl2)))
22663 (define-public r-showtextdb
22665 (name "r-showtextdb")
22670 (uri (cran-uri "showtextdb" version))
22673 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
22674 (properties `((upstream-name . "showtextdb")))
22675 (build-system r-build-system)
22678 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
22679 (synopsis "Font files for the 'showtext' package")
22681 "This package provides font files that can be used by the @code{showtext}
22683 (license license:asl2.0)))
22685 (define-public r-showtext
22687 (name "r-showtext")
22692 (uri (cran-uri "showtext" version))
22695 "1larnqxn9nanbqiadm35ah5hh89xrzm4fdj9pfc93zzzhlfrvhb3"))))
22696 (properties `((upstream-name . "showtext")))
22697 (build-system r-build-system)
22699 (list freetype libpng zlib))
22701 (list r-showtextdb r-sysfonts))
22703 (list pkg-config r-knitr))
22704 (home-page "https://github.com/yixuan/showtext")
22705 (synopsis "Using fonts more easily in R graphs")
22707 "This package aims to make it easy to use various types of
22708 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
22709 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
22710 will be converted into polygons or raster images, hence after the plot has
22711 been created, it no longer relies on the font files. No external software
22712 such as Ghostscript is needed to use this package.")
22713 (license license:asl2.0)))
22715 (define-public r-emojifont
22717 (name "r-emojifont")
22722 (uri (cran-uri "emojifont" version))
22725 "1hhrwilv36hd9gs1kcl2zsi6519md0h9aixjrm6lfclxvz8r6k1i"))))
22726 (properties `((upstream-name . "emojifont")))
22727 (build-system r-build-system)
22729 (list r-ggplot2 r-proto r-showtext r-sysfonts))
22732 (home-page "https://guangchuangyu.github.io/emojifont")
22733 (synopsis "Emoji and Font Awesome in R graphics")
22735 "This package enables the use of emoji and the Font Awesome glyphs in
22736 both base and ggplot2 graphics.")
22737 (license license:artistic2.0)))
22739 (define-public r-abstractr
22741 (name "r-abstractr")
22746 (uri (cran-uri "abstractr" version))
22749 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
22750 (properties `((upstream-name . "abstractr")))
22751 (build-system r-build-system)
22753 (list r-colourpicker
22760 (home-page "https://matt-kumar.shinyapps.io/portfolio")
22761 (synopsis "R-Shiny application for creating visual abstracts")
22763 "This package provides an R Shiny application to create visual abstracts
22764 for original research. A variety of user defined options and formatting are
22766 (license license:gpl3)))
22768 (define-public r-qgam
22775 (uri (cran-uri "qgam" version))
22778 "1jyamamdffaks89rspyhmg18b4iik0nb1j0vgqzvfnm890514cvn"))))
22779 (properties `((upstream-name . "qgam")))
22780 (build-system r-build-system)
22782 (list r-doparallel r-mgcv r-plyr r-shiny))
22783 (native-inputs (list r-knitr))
22784 (home-page "https://cran.r-project.org/web/packages/qgam/")
22785 (synopsis "Smooth additive quantile regression models")
22787 "This package provides smooth additive quantile regression models, fitted
22788 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
22789 the smoothing parameters are estimated automatically by marginal loss
22790 minimization, while the regression coefficients are estimated using either
22791 PIRLS or Newton algorithm. The learning rate is determined so that the
22792 Bayesian credible intervals of the estimated effects have approximately the
22793 correct coverage. The main function is @code{qgam()} which is similar to
22794 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
22795 regression models.")
22796 (license license:gpl2+)))
22798 (define-public r-abtest
22805 (uri (cran-uri "abtest" version))
22808 "0jz2ry5364p8h8xlk5a5sycn8xlpxd1iasfg99bcr4jqzd92jfqg"))))
22809 (properties `((upstream-name . "abtest")))
22810 (build-system r-build-system)
22820 (home-page "https://cran.r-project.org/web/packages/abtest/")
22821 (synopsis "Bayesian A/B testing")
22823 "This package provides functions for Bayesian A/B testing including prior
22824 elicitation options based on Kass and Vaidyanathan (1992)
22825 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
22826 (license license:gpl2+)))
22828 (define-public r-reldist
22835 (uri (cran-uri "reldist" version))
22838 "17kbqqapqmckghv7jizibmicv3bzbycfr3mz4xg3yjp3c2bap4r6"))))
22839 (properties `((upstream-name . "reldist")))
22840 (build-system r-build-system)
22842 (list r-densestbayes r-mgcv))
22843 (home-page "http://www.stat.ucla.edu/~handcock/RelDist")
22844 (synopsis "Relative distribution methods")
22846 "This package provides tools for the comparison of distributions. This
22847 includes nonparametric estimation of the relative distribution PDF and CDF and
22848 numerical summaries as described in \"Relative Distribution Methods in the
22849 Social Sciences\" by Mark S. Handcock and Martina Morris, Springer-Verlag,
22850 1999, Springer-Verlag, ISBN 0387987789.")
22851 ;; See also https://cran.r-project.org/web/packages/reldist/LICENSE for
22852 ;; attribution requirements.
22853 (license license:gpl3)))
22855 (define-public r-accept
22862 (uri (cran-uri "accept" version))
22865 "0risdxw17jk3d56q40a78slb1rcj93b6kz71hn5hbwr0iih722gr"))))
22866 (properties `((upstream-name . "accept")))
22867 (build-system r-build-system)
22869 (list r-dplyr r-reldist))
22870 (home-page "https://cran.r-project.org/web/packages/accept/")
22871 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
22873 "This package allows clinicians to predict the rate and severity of
22874 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
22875 Disease} (COPD) patients, based on the clinical prediction model published in
22876 Adibi et al. (2019) @url{doi:10.1101/651901}.")
22877 (license license:gpl3)))
22879 (define-public r-smpracticals
22881 (name "r-smpracticals")
22886 (uri (cran-uri "SMPracticals" version))
22889 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
22890 (properties `((upstream-name . "SMPracticals")))
22891 (build-system r-build-system)
22893 (list r-ellipse r-mass r-nlme r-survival))
22894 (home-page "http://statwww.epfl.ch/davison/SM/")
22895 (synopsis "Practicals for use with Davison (2003) Statistical Models")
22897 "This package contains the datasets and a few functions for use with the
22898 practicals outlined in Appendix A of the book Statistical Models (Davison,
22899 2003, Cambridge University Press). The practicals themselves can be found at
22900 @url{http://statwww.epfl.ch/davison/SM/}.")
22901 (license license:gpl2+)))
22903 (define-public r-fgui
22910 (uri (cran-uri "fgui" version))
22913 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
22914 (properties `((upstream-name . "fgui")))
22915 (build-system r-build-system)
22917 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
22918 (synopsis "Create GUI for R functions")
22920 "Rapidly create a GUI for a function you created by automatically
22921 creating widgets for arguments of the function. This package automatically
22922 parses help routines for context-sensitive help to these arguments. The
22923 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
22924 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
22925 incorporated into the interface for greater customization for the more
22927 ;; Any version of the GPL.
22928 (license (list license:gpl2+ license:gpl3+))))
22930 (define-public r-tcltk2
22937 (uri (cran-uri "tcltk2" version))
22940 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
22941 (properties `((upstream-name . "tcltk2")))
22942 (build-system r-build-system)
22945 (home-page "https://www.sciviews.org/SciViews-R")
22946 (synopsis "Tcl/Tk additions")
22948 "This package provides a series of additional Tcl commands and Tk widgets
22949 with style and various functions to supplement the tcltk package")
22950 (license license:lgpl3)))
22952 (define-public r-accrual
22959 (uri (cran-uri "accrual" version))
22962 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
22963 (properties `((upstream-name . "accrual")))
22964 (build-system r-build-system)
22966 (list r-fgui r-smpracticals r-tcltk2))
22967 (home-page "https://cran.r-project.org/web/packages/accrual/")
22968 (synopsis "Bayesian accrual prediction")
22970 "Subject recruitment for medical research is challenging. Slow patient
22971 accrual leads to delay in research. Accrual monitoring during the process of
22972 recruitment is critical. Researchers need reliable tools to manage the
22973 accrual rate. This package provides an implementation of a Bayesian method
22974 that integrates researcher's experience on previous trials and data from the
22975 current study, providing reliable prediction on accrual rate for clinical
22976 studies. It provides functions for Bayesian accrual prediction which can be
22977 easily used by statisticians and clinical researchers.")
22978 (license license:gpl2)))
22980 (define-public r-accrued
22987 (uri (cran-uri "accrued" version))
22990 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
22991 (properties `((upstream-name . "accrued")))
22992 (build-system r-build-system)
22993 (home-page "https://cran.r-project.org/web/packages/accrued/")
22994 (synopsis "Data quality visualization tools for partially accruing data")
22996 "This is a package for visualizing data quality of partially accruing
22998 (license license:gpl3)))
23000 (define-public r-mda
23007 (uri (cran-uri "mda" version))
23010 "0qw4scc2w7jmnxssj5w2mdxb9rrl4dscqn54gplzm1gk2yf419mx"))))
23011 (properties `((upstream-name . "mda")))
23012 (build-system r-build-system)
23013 (propagated-inputs (list r-class))
23014 (native-inputs (list gfortran))
23015 (home-page "https://cran.r-project.org/web/packages/mda/")
23016 (synopsis "Mixture and flexible discriminant analysis")
23018 "This is a package for mixture and flexible discriminant analysis,
23019 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
23020 (license license:gpl2)))
23022 (define-public r-elasticnet
23024 (name "r-elasticnet")
23029 (uri (cran-uri "elasticnet" version))
23032 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
23033 (properties `((upstream-name . "elasticnet")))
23034 (build-system r-build-system)
23037 (home-page "http://users.stat.umn.edu/~zouxx019/")
23038 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
23040 "This package provides functions for fitting the entire solution path of
23041 the Elastic-Net and also provides functions for estimating sparse Principal
23042 Components. The Lasso solution paths can be computed by the same function.")
23043 (license license:gpl2+)))
23045 (define-public r-sparselda
23047 (name "r-sparselda")
23052 (uri (cran-uri "sparseLDA" version))
23055 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
23056 (properties `((upstream-name . "sparseLDA")))
23057 (build-system r-build-system)
23059 (list r-elasticnet r-mass r-mda))
23060 (home-page "https://www.imm.dtu.dk/~lkhc/")
23061 (synopsis "Sparse discriminant analysis")
23063 "This package performs sparse linear discriminant analysis for Gaussians
23064 and mixture of Gaussian models.")
23065 (license license:gpl2+)))
23067 (define-public r-accsda
23074 (uri (cran-uri "accSDA" version))
23077 "0jf4x5j9y7a3mvf2ghjp6bxdq1s5jh2sx3x3ar6f3lyzzvrnls4v"))))
23078 (properties `((upstream-name . "accSDA")))
23079 (build-system r-build-system)
23085 (home-page "https://github.com/gumeo/accSDA/wiki")
23086 (synopsis "Accelerated sparse discriminant analysis")
23088 "This package provides an implementation of sparse linear discriminant
23089 analysis, which is a supervised classification method for multiple classes.
23090 Various novel optimization approaches to this problem are implemented
23091 including @dfn{alternating direction method of multipliers} (ADMM),
23092 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
23093 Functions for performing cross validation are also supplied along with basic
23094 prediction and plotting functions. @dfn{Sparse zero variance
23095 discriminant} (SZVD) analysis is also included in the package.")
23096 (license license:gpl2+)))
23098 (define-public r-ace2fastq
23100 (name "r-ace2fastq")
23105 (uri (cran-uri "ace2fastq" version))
23108 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
23109 (properties `((upstream-name . "ace2fastq")))
23110 (build-system r-build-system)
23113 (home-page "https://github.com/c5sire/ace2fastq")
23114 (synopsis "ACE file to FASTQ converter")
23116 "The ACE file format is used in genomics to store contigs from sequencing
23117 machines. This tools converts it into FASTQ format. Both formats contain the
23118 sequence characters and their corresponding quality information. Unlike the
23119 FASTQ file, the ACE file stores the quality values numerically. The
23120 conversion algorithm uses the standard Sanger formula. The package
23121 facilitates insertion into pipelines, and content inspection.")
23122 (license license:gpl3)))
23124 (define-public r-rngwell
23131 (uri (cran-uri "rngWELL" version))
23134 "0f1dxxaimfb0fww8ym9ciqf6q760ai46wxldl37m5mfpd57ca00c"))))
23135 (properties `((upstream-name . "rngWELL")))
23136 (build-system r-build-system)
23137 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
23138 (synopsis "Toolbox for WELL random number generators")
23140 "This is a dedicated package to WELL pseudo random generators, which were
23141 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
23142 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
23143 (license license:bsd-3)))
23145 (define-public r-rnmf
23151 (uri (cran-uri "rNMF" version))
23154 "1nz6h0j5ywdh48m0swmhp34hbkycd7n13rclrxaw85qi9wc42597"))))
23155 (build-system r-build-system)
23157 (list r-knitr r-nnls))
23158 (home-page "https://cran.r-project.org/web/packages/rNMF/")
23159 (synopsis "Robust nonnegative matrix factorization")
23161 "This package provides an implementation of robust nonnegative matrix
23162 factorization (rNMF). The rNMF algorithm decomposes a nonnegative high
23163 dimension data matrix into the product of two low rank nonnegative matrices,
23164 while detecting and trimming outliers. The main function is @code{rnmf()}.
23165 The package also includes a visualization tool, @code{see()}, that arranges
23166 and prints vectorized images.")
23167 (license license:gpl2+)))
23169 (define-public r-randtoolbox
23171 (name "r-randtoolbox")
23176 (uri (cran-uri "randtoolbox" version))
23179 "0mvafd2gm1jpg19gdn6bw8668pqghi0xmcb56rl4fwamg8jg09xn"))))
23180 (properties `((upstream-name . "randtoolbox")))
23181 (build-system r-build-system)
23184 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
23185 (synopsis "Toolbox for pseudo and quasi random number generation")
23187 "This package provides
23190 @item pseudo random generators, such as general linear
23191 congruential generators, multiple recursive generators and generalized
23192 feedback shift register (SF-Mersenne Twister algorithm and WELL
23195 @item quasi random generators, such as the Torus algorithm, the Sobol
23196 sequence, the Halton sequence (including the Van der Corput sequence), and
23198 @item some generator tests: the gap test, the serial test, the poker test.
23201 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
23202 (license license:bsd-3)))
23204 (define-public r-lhs
23211 (uri (cran-uri "lhs" version))
23214 "0fb3bc3s5pbwg92qkjbg7v8ah36wm6qs05vf098hwjakr7f6yg3s"))))
23215 (properties `((upstream-name . "lhs")))
23216 (build-system r-build-system)
23217 (propagated-inputs (list r-rcpp))
23220 (home-page "https://github.com/bertcarnell/lhs")
23221 (synopsis "Latin Hypercube Samples")
23223 "This package provides a number of methods for creating and augmenting
23224 Latin Hypercube Samples.")
23225 (license license:gpl3)))
23227 (define-public r-acebayes
23229 (name "r-acebayes")
23234 (uri (cran-uri "acebayes" version))
23237 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73"))))
23238 (properties `((upstream-name . "acebayes")))
23239 (build-system r-build-system)
23241 (list r-compare r-lhs r-randtoolbox r-rcpp r-rcpparmadillo))
23242 (home-page "https://cran.r-project.org/web/packages/acebayes/")
23243 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
23245 "Finding an optimal Bayesian experimental design involves maximizing an
23246 objective function given by the expectation of some appropriately chosen
23247 utility function with respect to the joint distribution of unknown
23248 quantities (including responses). This objective function is usually not
23249 available in closed form and the design space can be continuous and of high
23250 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
23251 to maximise an approximation to the expectation of the utility function.")
23252 (license license:gpl2)))
23254 (define-public r-acet
23261 (uri (cran-uri "ACEt" version))
23264 "0583c9dg2yf01zf5p0bf24zipkm8yp7rwhn1dxyw2d0v881bbli6"))))
23265 (properties `((upstream-name . "ACEt")))
23266 (build-system r-build-system)
23268 (list r-bh r-mass r-rcpp r-rcpparmadillo))
23269 (native-inputs (list r-knitr))
23270 (home-page "https://cran.r-project.org/web/packages/ACEt/")
23271 (synopsis "Estimating dynamic heritability and twin model comparison")
23273 "This package supports twin models that are able to estimate the dynamic
23274 behaviour of the variance components in the classical twin models with respect
23275 to age using B-splines and P-splines.")
23276 (license license:gpl2+)))
23278 (define-public r-acfmperiod
23280 (name "r-acfmperiod")
23285 (uri (cran-uri "acfMPeriod" version))
23288 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
23289 (properties `((upstream-name . "acfMPeriod")))
23290 (build-system r-build-system)
23293 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
23294 (synopsis "Estimation of the ACF from the M-periodogram")
23296 "This package support non-robust and robust computations of the sample
23297 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
23298 univariate and multivariate processes. The methodology consists in reversing
23299 the diagonalization procedure involving the periodogram or the
23300 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
23301 ACOVF or the ACF as discussed in Fuller (1995)
23302 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
23303 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
23304 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
23305 (license license:gpl2+)))
23307 (define-public r-gamlss-data
23309 (name "r-gamlss-data")
23314 (uri (cran-uri "gamlss.data" version))
23317 "07mpdl4h9rwmnpl9jmsn6ig8ji11an6pyjfsvg62h2alapwbdcyv"))))
23318 (properties `((upstream-name . "gamlss.data")))
23319 (build-system r-build-system)
23320 (home-page "http://www.gamlss.org/")
23321 (synopsis "GAMLSS data")
23323 "This package provides data used as examples to demonstrate GAMLSS
23325 ;; Either version of the license
23326 (license (list license:gpl2 license:gpl3))))
23328 (define-public r-gamlss
23335 (uri (cran-uri "gamlss" version))
23338 "0xih19zqgpjl5qv5j38ana6x29y84shn2jfl2lk4kaw3q7yx86b6"))))
23339 (properties `((upstream-name . "gamlss")))
23340 (build-system r-build-system)
23342 (list r-gamlss-data r-gamlss-dist r-mass r-nlme r-survival))
23343 (home-page "http://www.gamlss.org/")
23344 (synopsis "Generalized additive models for location scale and shape")
23346 "This package provides functions for fitting the generalized additive
23347 models for location scale and shape introduced by Rigby and
23348 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
23349 use a distributional regression approach where all the parameters of the
23350 conditional distribution of the response variable are modelled using
23351 explanatory variables.")
23352 ;; Either version of the license
23353 (license (list license:gpl2 license:gpl3))))
23355 (define-public r-acid
23362 (uri (cran-uri "acid" version))
23365 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
23366 (properties `((upstream-name . "acid")))
23367 (build-system r-build-system)
23369 (list r-gamlss r-gamlss-dist r-hmisc))
23370 (home-page "https://cran.r-project.org/web/packages/acid/")
23371 (synopsis "Analysing conditional income distributions")
23373 "This package provides functions for the analysis of income distributions
23374 for subgroups of the population as defined by a set of variables like age,
23375 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
23376 distribution as well as functions for moments, inequality measures, entropy
23377 measures and polarisation measures of income distributions. This package thus
23378 aides the analysis of income inequality by offering tools for the exploratory
23379 analysis of income distributions at the disaggregated level.")
23380 (license license:gpl3)))
23382 (define-public r-acm4r
23389 (uri (cran-uri "acm4r" version))
23392 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
23393 (properties `((upstream-name . "acm4r")))
23394 (build-system r-build-system)
23395 (propagated-inputs (list r-mass))
23396 (home-page "https://cran.r-project.org/web/packages/acm4r/")
23397 (synopsis "Align-and-count method comparisons of RFLP data")
23399 "This is a package to compare sequence fragment lengths or molecular
23400 weights from pairs of lanes. The number of matching bands in the
23401 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
23402 the align-and-count method.")
23403 ;; Any version of the GPL
23404 (license (list license:gpl2+ license:gpl3+))))
23406 (define-public r-filelock
23408 (name "r-filelock")
23413 (uri (cran-uri "filelock" version))
23416 "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc"))))
23417 (properties `((upstream-name . "filelock")))
23418 (build-system r-build-system)
23419 (home-page "https://github.com/r-lib/filelock")
23420 (synopsis "Portable file locking")
23422 "This library lets you place an exclusive or shared lock on a file using
23423 the appropriate system call provided by the underlying operating system.")
23424 (license license:expat)))
23426 (define-public r-filematrix
23428 (name "r-filematrix")
23433 (uri (cran-uri "filematrix" version))
23436 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
23437 (properties `((upstream-name . "filematrix")))
23438 (build-system r-build-system)
23439 ;; These inputs are needed for vignettes
23441 (list r-knitr r-rmarkdown))
23442 (home-page "https://github.com/andreyshabalin/filematrix")
23443 (synopsis "File-backed matrix class with convenient read and write access")
23445 "This package provides an interface for working with large matrices
23446 stored in files, not in computer memory. It supports multiple non-character
23447 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
23448 byte real values). Access to parts of the matrix is done by indexing, exactly
23449 as with usual R matrices. It supports very large matrices; the package has
23450 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
23451 columns, ad allows for quick addition of extra columns to a filematrix.")
23452 (license license:lgpl3)))
23454 (define-public r-acmeeqtl
23456 (name "r-acmeeqtl")
23461 (uri (cran-uri "ACMEeqtl" version))
23464 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
23465 (properties `((upstream-name . "ACMEeqtl")))
23466 (build-system r-build-system)
23468 (list r-filematrix))
23469 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
23470 (synopsis "Estimation of interpretable eQTL effect sizes")
23472 "This package provides a non-linear model, termed ACME, that reflects a
23473 parsimonious biological model for allelic contributions of cis-acting eQTLs.
23474 With non-linear least-squares algorithm the maximum likelihood parameters can
23475 be estimated. The ACME model provides interpretable effect size estimates and
23476 p-values with well controlled Type-I error.")
23477 (license license:lgpl3)))
23479 (define-public r-acmer
23486 (uri (cran-uri "acmeR" version))
23489 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
23490 (properties `((upstream-name . "acmeR")))
23491 (build-system r-build-system)
23492 (propagated-inputs (list r-foreign))
23493 (home-page "https://cran.r-project.org/web/packages/acmeR/")
23494 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
23496 "This package provides an implementation of the ACME estimator, described
23497 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
23498 Mortality at Wind Turbines. Unlike most other models, this estimator supports
23499 decreasing-hazard Weibull model for persistence; decreasing search proficiency
23500 as carcasses age; variable bleed-through at successive searches; and interval
23501 mortality estimates. The package provides, based on search data, functions
23502 for estimating the mortality inflation factor in Frequentist and Bayesian
23504 (license license:expat)))
23506 (define-public r-r-huge
23513 (uri (cran-uri "R.huge" version))
23516 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
23517 (properties `((upstream-name . "R.huge")))
23518 (build-system r-build-system)
23520 (list r-r-methodss3 r-r-oo r-r-utils))
23521 (home-page "https://github.com/HenrikBengtsson/R.huge")
23522 (synopsis "Methods for accessing huge amounts of data")
23524 "This is a deprecated package for accessing huge amounts of data.
23525 Cross-platform alternatives are the following packages: bigmemory (CRAN),
23526 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
23527 the @code{aroma.affymetrix} package.")
23528 (license license:lgpl2.1+)))
23530 (define-public r-r-filesets
23532 (name "r-r-filesets")
23537 (uri (cran-uri "R.filesets" version))
23540 "14dngx6ffhfvlaixpvlq890nwgil6zyaw8wy3dlcrv001wynzmms"))))
23541 (properties `((upstream-name . "R.filesets")))
23542 (build-system r-build-system)
23545 (modify-phases %standard-phases
23546 (add-after 'unpack 'set-HOME
23547 (lambda _ (setenv "HOME" "/tmp"))))))
23549 (list r-digest r-r-cache r-r-methodss3 r-r-oo r-r-utils))
23550 (home-page "https://github.com/HenrikBengtsson/R.filesets")
23551 (synopsis "Easy handling of and access to files")
23553 "This package provides classes and methods to locate, setup, subset,
23554 navigate and iterate file sets, i.e. sets of files located in one or more
23555 directories on the file system. The API is designed such that these classes
23556 can be extended via inheritance to provide a richer API for special file
23557 formats. Moreover, a specific name format is defined such that filenames and
23558 directories can be considered to have full names which consists of a name
23559 followed by comma-separated tags. This adds additional flexibility to
23560 identify file sets and individual files.")
23561 (license license:lgpl2.1+)))
23563 (define-public r-r-devices
23565 (name "r-r-devices")
23570 (uri (cran-uri "R.devices" version))
23573 "02cwdhb9m97gxi4pki4kasc5j3a12r7yzsychzzk9h0ijc1mfziv"))))
23574 (properties `((upstream-name . "R.devices")))
23575 (build-system r-build-system)
23577 (list r-base64enc r-r-methodss3 r-r-oo r-r-utils))
23578 (home-page "https://github.com/HenrikBengtsson/R.devices")
23579 (synopsis "Unified handling of graphics devices")
23581 "This package provides functions for creating plots and image files in a
23582 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
23583 Default device options as well as scales and aspect ratios are controlled in a
23584 uniform way across all device types. Switching output format requires minimal
23585 changes in code. This package is ideal for large-scale batch processing,
23586 because it will never leave open graphics devices or incomplete image files
23587 behind, even on errors or user interrupts.")
23588 (license license:lgpl2.1+)))
23590 (define-public r-acnr
23597 (uri (cran-uri "acnr" version))
23600 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
23601 (properties `((upstream-name . "acnr")))
23602 (build-system r-build-system)
23603 (home-page "https://github.com/mpierrejean/acnr")
23604 (synopsis "Annotated copy-number regions")
23606 "This package provides SNP array data from different types of copy-number
23607 regions. These regions were identified manually by the authors of the package
23608 and may be used to generate realistic data sets with known truth.")
23609 (license license:lgpl2.1+)))
23611 (define-public r-acopula
23618 (uri (cran-uri "acopula" version))
23621 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
23622 (properties `((upstream-name . "acopula")))
23623 (build-system r-build-system)
23624 (home-page "https://cran.r-project.org/web/packages/acopula/")
23625 (synopsis "Modelling dependence with multivariate Archimax copulas")
23627 "Archimax copulas are a mixture of Archimedean and EV copulas. This
23628 package provides definitions of several parametric families of generator and
23629 dependence function, computes CDF and PDF, estimates parameters, tests for
23630 goodness of fit, generates random sample and checks copula properties for
23631 custom constructs. In the 2-dimensional case explicit formulas for density
23632 are used, contrary to higher dimensions when all derivatives are linearly
23633 approximated. Several non-archimax families (normal, FGM, Plackett) are
23634 provided as well.")
23635 (license license:gpl2)))
23637 (define-public r-tuner
23644 (uri (cran-uri "tuneR" version))
23647 "1mfkhxprqkj5v2z23g0bj8mwdp6q5fj1krk5ggr79359bd1nl7pf"))))
23648 (properties `((upstream-name . "tuneR")))
23649 (build-system r-build-system)
23650 (propagated-inputs (list r-signal))
23651 (home-page "https://cran.r-project.org/web/packages/tuneR/")
23652 (synopsis "Analysis of music and speech")
23654 "This is a package for the analysis of music and speech. Analyze music
23655 and speech, extract features like MFCCs, handle wave files and their
23656 representation in various ways, read MP3, read MIDI, perform steps of a
23657 transcription, ...")
23658 ;; Either of these versions.
23659 (license (list license:gpl2 license:gpl3))))
23661 (define-public r-seewave
23668 (uri (cran-uri "seewave" version))
23671 "0bi1l47l3846c18k6h2vrv0xp9xh00n544a578jrndahzrj1hfwl"))))
23672 (properties `((upstream-name . "seewave")))
23673 (build-system r-build-system)
23678 (home-page "http://rug.mnhn.fr/seewave")
23679 (synopsis "Sound analysis and synthesis")
23681 "This package provides functions for analysing, manipulating, displaying,
23682 editing and synthesizing time waves (particularly sound). This package
23683 processes time analysis (oscillograms and envelopes), spectral content,
23684 resonance quality factor, entropy, cross correlation and autocorrelation,
23685 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
23686 and 3D spectrograms and many other analyses.")
23687 (license license:gpl2+)))
23689 (define-public r-acousticndlcoder
23691 (name "r-acousticndlcoder")
23696 (uri (cran-uri "AcousticNDLCodeR" version))
23699 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
23701 `((upstream-name . "AcousticNDLCodeR")))
23702 (build-system r-build-system)
23704 (list r-seewave r-tuner r-zoo))
23705 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
23706 (synopsis "Coding sound files for use with NDL")
23708 "Make acoustic cues to use with the R package @code{ndl}.
23709 The package implements functions used in the PLoS ONE paper \"Words from
23710 spontaneous conversational speech can be recognized with human-like accuracy
23711 by an error-driven learning algorithm that discriminates between meanings
23712 straight from smart acoustic features, bypassing the phoneme as recognition
23713 unit.\" @url{doi:10.1371/journal.pone.0174623}")
23714 (license license:gpl2+)))
23716 (define-public r-acp
23723 (uri (cran-uri "acp" version))
23726 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
23727 (properties `((upstream-name . "acp")))
23728 (build-system r-build-system)
23730 (list r-quantmod r-tseries))
23731 (home-page "https://cran.r-project.org/web/packages/acp/")
23732 (synopsis "Autoregressive conditional Poisson")
23734 "This package supports the analysis of count data exhibiting
23735 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
23736 model (ACP(p,q)) proposed by Heinen (2003).")
23737 (license license:gpl2)))
23739 (define-public r-ada
23746 (uri (cran-uri "ada" version))
23749 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
23750 (properties `((upstream-name . "ada")))
23751 (build-system r-build-system)
23752 (propagated-inputs (list r-rpart))
23753 (home-page "https://cran.r-project.org/web/packages/ada/")
23754 (synopsis "Stochastic boosting")
23756 "This package provides a straightforward, well-documented, and broad
23757 boosting routine for classification, ideally suited for small to
23758 moderate-sized data sets. It performs discrete, real, and gentle boost under
23759 both exponential and logistic loss on a given data set.")
23760 ;; Any version of the GPL.
23761 (license (list license:gpl2+ license:gpl3+))))
23763 (define-public r-genalg
23770 (uri (cran-uri "genalg" version))
23773 "1y4qz1s85zpd1r3259gr542arssf2vpd4drhy0wnq5q47ignrvna"))))
23774 (properties `((upstream-name . "genalg")))
23775 (build-system r-build-system)
23776 (home-page "https://github.com/egonw/genalg")
23777 (synopsis "R based genetic algorithm")
23779 "This package provides an R based genetic algorithm for binary and
23780 floating point chromosomes.")
23781 (license license:gpl2)))
23783 (define-public r-kernelfactory
23785 (name "r-kernelfactory")
23790 (uri (cran-uri "kernelFactory" version))
23793 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
23794 (properties `((upstream-name . "kernelFactory")))
23795 (build-system r-build-system)
23797 (list r-auc r-genalg r-kernlab r-randomforest))
23798 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
23799 (synopsis "Ensemble of kernel machines")
23801 "Kernel factory is an ensemble method where each base classifier (random
23802 forest) is fit on the kernel matrix of a subset of the training data.")
23803 (license license:gpl2+)))
23805 (define-public r-dummies
23812 (uri (cran-uri "dummies" version))
23815 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
23816 (properties `((upstream-name . "dummies")))
23817 (build-system r-build-system)
23818 (home-page "https://decisionpatterns.com")
23819 (synopsis "Create dummy/indicator variables flexibly and efficiently")
23821 "This package lets you expand factors, characters and other eligible
23822 classes into dummy/indicator variables.")
23823 (license license:gpl2+)))
23825 (define-public r-acrm
23832 (uri (cran-uri "aCRM" version))
23835 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
23836 (properties `((upstream-name . "aCRM")))
23837 (build-system r-build-system)
23839 (list r-ada r-dummies r-kernelfactory r-randomforest))
23840 (home-page "https://cran.r-project.org/web/packages/aCRM/")
23841 (synopsis "Convenience functions for analytical customer relationship management")
23843 "This package provides convenience functions for data preparation and
23844 modeling often used in @dfn{analytical customer relationship
23845 management} (aCRM).")
23846 (license license:gpl2+)))
23848 (define-public r-tree
23854 (uri (cran-uri "tree" version))
23857 "1q3jgkhl5d4d8c396cyvkw60094p0z0a3x7xwhdbi8gl4c2c65ss"))))
23858 (build-system r-build-system)
23859 (home-page "https://cran.r-project.org/web/packages/tree/")
23860 (synopsis "Classification and regression trees")
23861 (description "This package provides procedures to work with classification
23862 and regression trees.")
23863 (license license:gpl2+)))
23865 (define-public r-treeclust
23867 (name "r-treeclust")
23872 (uri (cran-uri "treeClust" version))
23875 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
23876 (properties `((upstream-name . "treeClust")))
23877 (build-system r-build-system)
23879 (list r-cluster r-rpart))
23880 (home-page "https://cran.r-project.org/web/packages/treeClust/")
23881 (synopsis "Cluster distances through trees")
23883 "This package provides tools to create a measure of inter-point
23884 dissimilarity useful for clustering mixed data, and, optionally, perform the
23886 (license license:gpl2+)))
23888 (define-public r-acrosstic
23890 (name "r-acrosstic")
23895 (uri (cran-uri "AcrossTic" version))
23898 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
23899 (properties `((upstream-name . "AcrossTic")))
23900 (build-system r-build-system)
23902 (list r-lpsolve r-treeclust))
23903 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
23904 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
23906 "This is a package for constructing minimum-cost regular spanning
23907 subgraph as part of a non-parametric two-sample test for equality of
23909 (license license:gpl2+)))
23911 (define-public r-acrt
23918 (uri (cran-uri "acrt" version))
23921 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
23922 (properties `((upstream-name . "acrt")))
23923 (build-system r-build-system)
23925 (list r-rcpp r-rcppeigen r-sandwich))
23926 (home-page "https://cran.r-project.org/web/packages/acrt/")
23927 (synopsis "Autocorrelation robust testing")
23929 "This package provides functions for testing affine hypotheses on the
23930 regression coefficient vector in regression models with autocorrelated
23932 (license license:gpl2)))
23934 (define-public r-acs
23941 (uri (cran-uri "acs" version))
23944 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
23945 (properties `((upstream-name . "acs")))
23946 (build-system r-build-system)
23948 (list r-httr r-plyr r-rcpp r-stringr r-xml))
23949 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
23950 (synopsis "Work with data from the US Census")
23952 "This package provides a general toolkit for downloading, managing,
23953 analyzing, and presenting data from the
23954 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
23955 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
23956 American Community Survey (ACS). Confidence intervals provided with ACS data
23957 are converted to standard errors to be bundled with estimates in complex
23958 @code{acs} objects. The package provides new methods to conduct standard
23959 operations on @code{acs} objects and present/plot data in statistically
23960 appropriate ways.")
23961 (license license:gpl3)))
23963 (define-public r-acss-data
23965 (name "r-acss-data")
23970 (uri (cran-uri "acss.data" version))
23973 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
23974 (properties `((upstream-name . "acss.data")))
23975 (build-system r-build-system)
23976 (home-page "http://complexitycalculator.com/methodology.html")
23977 (synopsis "Data for algorithmic complexity of short strings")
23979 "This is a data only package providing the algorithmic complexity of
23980 short strings, computed using the coding theorem method. For a given set of
23981 symbols in a string, all possible or a large number of random samples of
23982 Turing machines with a given number of states (e.g., 5) and number of symbols
23983 corresponding to the number of symbols in the strings were simulated until
23984 they reached a halting state or failed to end. This package contains data on
23985 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
23986 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
23987 distribution of the halting states.")
23988 (license license:gpl2+)))
23990 (define-public r-acss
23997 (uri (cran-uri "acss" version))
24000 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
24001 (properties `((upstream-name . "acss")))
24002 (build-system r-build-system)
24004 (list r-acss-data r-zoo))
24005 (home-page "http://complexitycalculator.com/methodology.html")
24006 (synopsis "Algorithmic complexity for short strings")
24008 "The main purpose of this package is to provide the algorithmic
24009 complexity for short strings, an approximation of the Kolmogorov Complexity of
24010 a short string using the coding theorem method. While the database containing
24011 the complexity is provided in the data only package @code{acss.data}, this
24012 package provides functions accessing the data such as @code{prob_random}
24013 returning the posterior probability that a given string was produced by a
24014 random process. In addition, two traditional (but problematic) measures of
24015 complexity are also provided: entropy and change complexity.")
24016 (license license:gpl2+)))
24018 (define-public r-acswr
24025 (uri (cran-uri "ACSWR" version))
24028 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
24029 (properties `((upstream-name . "ACSWR")))
24030 (build-system r-build-system)
24033 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
24034 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
24036 "This is a companion package for the book \"A Course in Statistics with
24037 R\" (ISBN 978-1-119-15272-9.)")
24038 (license license:gpl2)))
24040 (define-public r-alabama
24043 (version "2022.4-1")
24047 (uri (cran-uri "alabama" version))
24050 "0v6kl6ndm8wvp9xzya3x4gj5kh03qgx13x5vyzn410wsndcjiim8"))))
24051 (properties `((upstream-name . "alabama")))
24052 (build-system r-build-system)
24053 (propagated-inputs (list r-numderiv))
24054 (home-page "https://cran.r-project.org/web/packages/alabama/")
24055 (synopsis "Constrained nonlinear optimization")
24057 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
24058 Algorithm; it is used for optimizing smooth nonlinear objective functions with
24059 constraints. Linear or nonlinear equality and inequality constraints are
24061 (license license:gpl2+)))
24063 (define-public r-gdina
24070 (uri (cran-uri "GDINA" version))
24073 "0bwg9sfsqs5nsqwhjnbb631fbhj0mx2dc4c185qkym9cjb5lfkm9"))))
24074 (properties `((upstream-name . "GDINA")))
24075 (build-system r-build-system)
24089 (home-page "https://github.com/Wenchao-Ma/GDINA")
24090 (synopsis "Generalized DINA model framework")
24092 "This package provides a set of psychometric tools for cognitive
24093 diagnosis modeling based on the generalized deterministic inputs, noisy and
24094 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
24095 and its extensions, including the sequential G-DINA model by Ma and de la
24096 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
24097 polytomous G-DINA model by Chen and de la Torre
24098 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
24099 distribution can be independent, saturated, higher-order, loglinear smoothed
24100 or structured. Q-matrix validation, item and model fit statistics, model
24101 comparison at test and item level and differential item functioning can also
24102 be conducted. A graphical user interface is also provided.")
24103 (license license:gpl3)))
24105 (define-public r-actcd
24112 (uri (cran-uri "ACTCD" version))
24115 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
24116 (properties `((upstream-name . "ACTCD")))
24117 (build-system r-build-system)
24119 (list r-gdina r-r-methodss3))
24122 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
24123 (synopsis "Asymptotic classification theory for cognitive diagnosis")
24125 "This is a package supporting cluster analysis for cognitive diagnosis
24126 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
24127 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
24128 sum-scores, cluster analysis techniques can be used to classify examinees into
24129 latent classes based on their attribute patterns. In addition to the
24130 algorithms used to classify data, three labeling approaches are proposed to
24131 label clusters so that examinees' attribute profiles can be obtained.")
24132 (license license:gpl2+)))
24134 (define-public r-ineq
24141 (uri (cran-uri "ineq" version))
24144 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
24145 (properties `((upstream-name . "ineq")))
24146 (build-system r-build-system)
24147 (home-page "https://cran.r-project.org/web/packages/ineq/")
24148 (synopsis "Measuring inequality, concentration, and poverty")
24150 "This package provides tools for measuring inequality, concentration, and
24151 poverty measures. It provides both empirical and theoretical Lorenz curves.")
24152 ;; Either of these two versions.
24153 (license (list license:gpl2 license:gpl3))))
24155 (define-public r-actfrag
24162 (uri (cran-uri "ActFrag" version))
24165 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
24166 (properties `((upstream-name . "ActFrag")))
24167 (build-system r-build-system)
24169 (list r-accelerometry r-dplyr r-ineq r-survival r-tidyr))
24170 (home-page "https://github.com/junruidi/ActFrag")
24171 (synopsis "Activity fragmentation metrics extraction")
24173 "This package provides functions to extract commonly used fragmentation
24174 metrics to quantify time accumulation strategies based on minute level
24175 actigraphy-measured activity counts data.")
24176 (license license:gpl3)))
24178 (define-public r-ash
24185 (uri (cran-uri "ash" version))
24188 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb"))))
24189 (properties `((upstream-name . "ash")))
24190 (build-system r-build-system)
24191 (native-inputs (list gfortran))
24192 (home-page "https://cran.r-project.org/web/packages/ash/")
24193 (synopsis "David Scott's ASH routines")
24195 "This package provides David Scott's ASH routines ported from S-PLUS to
24197 (license license:gpl2+)))
24199 (define-public r-hdrcde
24206 (uri (cran-uri "hdrcde" version))
24209 "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3"))))
24210 (properties `((upstream-name . "hdrcde")))
24211 (build-system r-build-system)
24219 (native-inputs (list gfortran))
24220 (home-page "http://pkg.robjhyndman.com/hdrcde")
24221 (synopsis "Highest density regions and conditional density estimation")
24223 "This is a package for the computation of highest density regions in one
24224 and two dimensions, kernel estimation of univariate density functions
24225 conditional on one covariate, and multimodal regression.")
24226 (license license:gpl3)))
24228 (define-public r-rainbow
24235 (uri (cran-uri "rainbow" version))
24238 "1cldipi3cb55d434wv03ymwygbisfwgq2b84gwwkgqpfal2xk78m"))))
24239 (properties `((upstream-name . "rainbow")))
24240 (build-system r-build-system)
24248 (home-page "https://cran.r-project.org/web/packages/rainbow/")
24249 (synopsis "Bagplots, boxplots and rainbow plots for functional data")
24251 "This is a package for visualizing functional data and identifying
24252 functional outliers with bagplots, boxplots and rainbow plots.")
24253 (license license:gpl3)))
24255 (define-public r-fds
24262 (uri (cran-uri "fds" version))
24265 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0"))))
24266 (properties `((upstream-name . "fds")))
24267 (build-system r-build-system)
24269 (list r-rainbow r-rcurl))
24270 (home-page "https://cran.r-project.org/web/packages/fds/")
24271 (synopsis "Functional data sets")
24272 (description "This package contains a list of functional time series,
24273 sliced functional time series, and functional data sets. Functional time
24274 series is a special type of functional data observed over time. Sliced
24275 functional time series is a special type of functional time series with a time
24276 variable observed over time.")
24277 (license license:gpl2+)))
24279 (define-public r-fda
24286 (uri (cran-uri "fda" version))
24289 "1wdq35acxavarh7qrxxmdpcjc9jcs56mp3p9rbb4qa35ziv5fi0l"))))
24290 (properties `((upstream-name . "fda")))
24291 (build-system r-build-system)
24293 (list r-desolve r-fds))
24296 (home-page "https://www.functionaldata.org")
24297 (synopsis "Functional data analysis")
24299 "These functions were developed to support functional data analysis as
24300 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
24301 Analysis. The package includes data sets and script files working many
24303 (license license:gpl2+)))
24305 (define-public r-actigraphy
24307 (name "r-actigraphy")
24312 (uri (cran-uri "Actigraphy" version))
24315 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
24316 (properties `((upstream-name . "Actigraphy")))
24317 (build-system r-build-system)
24320 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
24321 (synopsis "Actigraphy data analysis")
24323 "This package provides tools for functional linear modeling and analysis
24324 of actigraphy data.")
24325 (license license:asl2.0)))
24327 (define-public r-activedriver
24329 (name "r-activedriver")
24334 (uri (cran-uri "ActiveDriver" version))
24337 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
24338 (properties `((upstream-name . "ActiveDriver")))
24339 (build-system r-build-system)
24342 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
24343 (synopsis "Tools for finding cancer driver proteins")
24345 "This package provides a mutation analysis tool that discovers cancer
24346 driver genes with frequent mutations in protein signalling sites such as
24347 post-translational modifications (phosphorylation, ubiquitination, etc). The
24348 Poisson generalized linear regression model identifies genes where cancer
24349 mutations in signalling sites are more frequent than expected from the
24350 sequence of the entire gene. Integration of mutations with signalling
24351 information helps find new driver genes and propose candidate mechanisms to
24353 (license license:gpl2+)))
24355 (define-public r-activitycounts
24357 (name "r-activitycounts")
24362 (uri (cran-uri "activityCounts" version))
24365 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
24367 `((upstream-name . "activityCounts")))
24368 (build-system r-build-system)
24370 (list r-lubridate r-magrittr r-seewave r-signal r-tibble))
24371 (home-page "https://github.com/walkabillylab/activityCounts")
24372 (synopsis "Generate ActiLife counts")
24374 "ActiLife generates activity counts from data collected by Actigraph
24375 accelerometers. Actigraph is one of the most common research-grade
24376 accelerometers. There is considerable research validating and developing
24377 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
24378 counts are proprietary and difficult to implement if researchers use different
24379 accelerometer brands. The code creates ActiLife counts from raw acceleration
24380 data for different accelerometer brands.")
24381 (license license:gpl3)))
24383 (define-public r-activityindex
24385 (name "r-activityindex")
24390 (uri (cran-uri "ActivityIndex" version))
24393 "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5"))))
24394 (properties `((upstream-name . "ActivityIndex")))
24395 (build-system r-build-system)
24397 (list r-data-table r-matrixstats r-r-utils))
24400 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
24401 (synopsis "Activity Index calculation using raw accelerometry data")
24403 "This is a package to read raw accelerometry from GT3X+ accelerometry
24404 data and plain table data to calculate the Activity Index from Bai et
24405 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
24406 (license license:gpl3)))
24408 (define-public r-activpal
24410 (name "r-activpal")
24415 (uri (cran-uri "activPAL" version))
24418 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
24419 (properties `((upstream-name . "activPAL")))
24420 (build-system r-build-system)
24428 (home-page "https://cran.r-project.org/web/packages/activPAL")
24429 (synopsis "Processing and chart generation from activPAL events files")
24431 "This package contains functions to generate pre-defined summary
24432 statistics from activPAL events files. The package also contains functions to
24433 produce informative graphics that visualize physical activity behaviour and
24434 trends. This includes generating graphs that align physical activity
24435 behaviour with additional time based observations described by other data
24436 sets, such as sleep diaries and continuous glucose monitoring data.")
24437 (license license:gpl3)))
24439 (define-public r-activpalprocessing
24441 (name "r-activpalprocessing")
24446 (uri (cran-uri "activpalProcessing" version))
24449 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
24451 `((upstream-name . "activpalProcessing")))
24452 (build-system r-build-system)
24455 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
24456 (synopsis "Process activPAL events files")
24458 "This package performs estimation of physical activity and sedentary
24459 behavior variables from activPAL events files.")
24460 ;; Either version of the GPL.
24461 (license (list license:gpl2 license:gpl3))))
24463 (define-public r-actogrammr
24465 (name "r-actogrammr")
24470 (uri (cran-uri "actogrammr" version))
24473 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
24474 (properties `((upstream-name . "actogrammr")))
24475 (build-system r-build-system)
24477 (list r-dplyr r-ggplot2 r-lubridate r-readr r-tidyr))
24478 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
24479 (synopsis "Read in activity data and plot actograms")
24481 "Read in activity measurements from standard file formats used by
24482 circadian rhythm researchers, currently only ClockLab format, and process and
24483 plot the data. The central type of plot is the actogram, as first described
24484 in \"Activity and distribution of certain wild mice in relation to biotic
24485 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
24486 (license license:gpl3)))
24488 (define-public r-expint
24495 (uri (cran-uri "expint" version))
24498 "1cn6c84pqf8bgk109qm4znn186h6s6cpll3d11cw144h0vh4yr8j"))))
24499 (properties `((upstream-name . "expint")))
24500 (build-system r-build-system)
24501 (home-page "https://gitlab.com/vigou3/expint")
24502 (synopsis "Exponential integral and incomplete Gamma function")
24504 "This package provides the exponential integrals @code{E_1(x)},
24505 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
24506 function @code{G(a, x)} defined for negative values of its first argument.
24507 The package also gives easy access to the underlying C routines through an
24508 API; see the package vignette for details.")
24509 (license license:gpl2+)))
24511 (define-public r-actuar
24518 (uri (cran-uri "actuar" version))
24521 "16nyhn0aw2mb8915ycr46rjvg9pbcps7zxs2sgvdws9kzm027mpj"))))
24522 (properties `((upstream-name . "actuar")))
24523 (build-system r-build-system)
24524 (propagated-inputs (list r-expint))
24525 (home-page "https://gitlab.com/vigou3/actuar")
24526 (synopsis "Actuarial functions and heavy tailed distributions")
24528 "This package provides functions and data sets for actuarial science:
24529 modeling of loss distributions; risk theory and ruin theory; simulation of
24530 compound models, discrete mixtures and compound hierarchical models;
24531 credibility theory. It boasts support for many additional probability
24532 distributions to model insurance loss amounts and loss frequency: 19
24533 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
24534 distribution; zero-truncated and zero-modified extensions of the standard
24535 discrete distributions. It also supports phase-type distributions commonly
24536 used to compute ruin probabilities.")
24537 (license license:gpl2+)))
24539 (define-public r-bmp
24546 (uri (cran-uri "bmp" version))
24549 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
24550 (properties `((upstream-name . "bmp")))
24551 (build-system r-build-system)
24552 (home-page "https://cran.r-project.org/web/packages/bmp/")
24553 (synopsis "Read Bitmap (BMP) images")
24555 "This package provides pure R tools to read BMP format images. It is
24556 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
24557 (license license:gpl2+)))
24559 (define-public r-readbitmap
24561 (name "r-readbitmap")
24566 (uri (cran-uri "readbitmap" version))
24569 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
24570 (properties `((upstream-name . "readbitmap")))
24571 (build-system r-build-system)
24573 (list libjpeg-turbo libpng))
24575 (list r-bmp r-jpeg r-png r-tiff))
24576 (home-page "https://github.com/jefferis/readbitmap")
24577 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
24579 "This package provides tools to identify and read BMP, JPEG, PNG, and
24580 TIFF format bitmap images. Identification defaults to the use of the magic
24581 number embedded in the file rather than the file extension.")
24582 (license license:gpl2+)))
24584 (define-public r-imager
24587 (version "0.42.13")
24591 (uri (cran-uri "imager" version))
24594 "0zygnmxwbbmj5i2l2affzdz90xvsa7b5pbkzkhjbm40is69rh2nr"))))
24595 (properties `((upstream-name . "imager")))
24596 (build-system r-build-system)
24598 (list fftw libtiff libx11 zlib))
24610 (list pkg-config r-knitr))
24611 (home-page "https://dahtah.github.io/imager/")
24612 (synopsis "Image processing library")
24614 "This is a package for fast image processing for images in up to 4
24615 dimensions (two spatial dimensions, one time/depth dimension, one color
24616 dimension). It provides most traditional image processing tools (filtering,
24617 morphology, transformations, etc.) as well as various functions for easily
24618 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
24619 simple, modern C++ library for image processing.")
24620 (license license:lgpl3)))
24622 (define-public r-acuityview
24624 (name "r-acuityview")
24629 (uri (cran-uri "AcuityView" version))
24632 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
24633 (properties `((upstream-name . "AcuityView")))
24634 (build-system r-build-system)
24636 (list r-fftwtools r-imager r-plotrix))
24637 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
24638 (synopsis "Display scenes as seen by an animal with less acute vision")
24640 "This package provides a simple method for representing a visual scene as
24641 it may be seen by an animal with less acute vision.")
24642 (license license:gpl2+)))
24644 (define-public r-caret
24651 (uri (cran-uri "caret" version))
24654 "01sa1h9pc3a062pwm0rxadvg9qxszwcylya7llv08fcxhy46n5ac"))))
24655 (build-system r-build-system)
24670 (home-page "https://github.com/topepo/caret")
24671 (synopsis "Classification and regression training")
24673 "This package provides miscellaneous functions for training and plotting
24674 classification and regression models.")
24675 (license license:gpl2+)))
24677 (define-public r-adabag
24684 (uri (cran-uri "adabag" version))
24687 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
24688 (properties `((upstream-name . "adabag")))
24689 (build-system r-build-system)
24691 (list r-caret r-doparallel r-foreach r-rpart))
24692 (home-page "https://cran.r-project.org/web/packages/adabag/")
24693 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
24695 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
24696 Breiman's Bagging algorithm using classification trees as individual
24697 classifiers. Once these classifiers have been trained, they can be used to
24698 predict on new data. Also, cross validation estimation of the error can be
24700 (license license:gpl2+)))
24702 (define-public r-adagio
24709 (uri (cran-uri "adagio" version))
24712 "0icwr3cark67jyg9zzqwyv9q4fs0j0xgb5i7nkwv9s7y5dlldl0b"))))
24713 (properties `((upstream-name . "adagio")))
24714 (build-system r-build-system)
24717 (home-page "https://cran.r-project.org/web/packages/adagio/")
24718 (synopsis "Discrete and global optimization routines")
24720 "This package provides methods and algorithms for discrete optimization,
24721 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
24722 Hooke-Jeeves minimization, and some (evolutionary) global optimization
24724 (license license:gpl3+)))
24726 (define-public r-univoutl
24728 (name "r-univoutl")
24733 (uri (cran-uri "univOutl" version))
24736 "1kp014bhs8v02fp7misrj4fpfp2na9lg45p5zqvlfaypnm5imsr9"))))
24737 (properties `((upstream-name . "univOutl")))
24738 (build-system r-build-system)
24740 (list r-hmisc r-robustbase))
24741 (home-page "https://github.com/marcellodo/univOutl")
24742 (synopsis "Detection of univariate outliers")
24744 "This package provides well-known outlier detection techniques in the
24745 univariate case. Methods to deal with skewed distribution are included too.
24746 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
24747 historical data is implemented as well. When available, survey weights can be
24748 used in outliers detection.")
24749 (license license:gpl2+)))
24751 (define-public r-tolerance
24753 (name "r-tolerance")
24758 (uri (cran-uri "tolerance" version))
24761 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
24762 (properties `((upstream-name . "tolerance")))
24763 (build-system r-build-system)
24765 (list r-mass r-rgl))
24766 (home-page "https://cran.r-project.org/web/packages/tolerance/")
24767 (synopsis "Statistical tolerance intervals and regions")
24769 "This package provides functions for estimating tolerance
24770 limits (intervals) for various univariate distributions (binomial, Cauchy,
24771 discrete Pareto, exponential, two-parameter exponential, extreme value,
24772 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
24773 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
24774 Bayesian normal tolerance limits, multivariate normal tolerance regions,
24775 nonparametric tolerance intervals, tolerance bands for regression
24776 settings (linear regression, nonlinear regression, nonparametric regression,
24777 and multivariate regression), and analysis of variance tolerance intervals.
24778 Visualizations are also available for most of these settings.")
24779 (license license:gpl2+)))
24781 ;; Keep this in sync with the liblantern package.
24782 (define-public r-torch
24789 (uri (cran-uri "torch" version))
24791 (base32 "1iylnz0hsi00q7hngi2h24kg3nvjjg10z6iarqhp3wylsasgjs1f"))))
24792 (properties `((upstream-name . "torch")))
24793 (build-system r-build-system)
24797 (let ((python-version (version-major+minor (package-version python))))
24798 #~(modify-phases %standard-phases
24799 (add-after 'install 'link-libraries
24800 (lambda* (#:key inputs #:allow-other-keys)
24801 (let ((deps (string-append #$output "/site-library/torch/deps"))
24802 (site-packages (string-append "/lib/python"
24804 "/site-packages")))
24808 inputs (string-append site-packages "/torch/lib/libtorch.so"))
24809 (string-append deps "/libtorch.so"))
24812 inputs "/lib/liblantern.so")
24813 (string-append deps "/liblantern.so")))))))))
24815 (list python-pytorch-for-r-torch
24828 (native-inputs (list r-knitr))
24829 (home-page "https://torch.mlverse.org/docs")
24830 (synopsis "Tensors and neural networks with GPU acceleration")
24832 "This package provides functionality to define and train neural networks
24833 similar to PyTorch but written entirely in R using the libtorch library. It
24834 also supports low-level tensor operations and GPU acceleration.")
24835 (license license:expat)))
24837 (define-public r-additivitytests
24839 (name "r-additivitytests")
24840 (version "1.1-4.1")
24844 (uri (cran-uri "additivityTests" version))
24847 "00kzfv86z6kk0gvbz9mg3p6xi5fb8cn74rhslr17rdpd02md0884"))))
24849 `((upstream-name . "additivityTests")))
24850 (build-system r-build-system)
24851 (native-inputs (list r-knitr))
24852 (home-page "https://github.com/simecek/additivityTests")
24853 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
24855 "This package provides an implementation of the Tukey, Mandel,
24856 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
24857 (license license:gpl3)))
24859 (define-public r-flexclust
24861 (name "r-flexclust")
24866 (uri (cran-uri "flexclust" version))
24869 "13akk3w6a76jpws5v9108c3hdmb8i6gm0sc06lr2hqly0pgpfyfn"))))
24870 (properties `((upstream-name . "flexclust")))
24871 (build-system r-build-system)
24873 (list r-class r-lattice r-modeltools))
24874 (home-page "https://cran.r-project.org/web/packages/flexclust/")
24875 (synopsis "Flexible cluster algorithms")
24877 "The main function @code{kcca} implements a general framework for
24878 k-centroids cluster analysis supporting arbitrary distance measures and
24879 centroid computation. Further cluster methods include hard competitive
24880 learning, neural gas, and QT clustering. There are numerous visualization
24881 methods for cluster results (neighborhood graphs, convex cluster hulls,
24882 barcharts of centroids, ...), and bootstrap methods for the analysis of
24883 cluster stability.")
24884 (license license:gpl2)))
24886 (define-public r-biclust
24893 (uri (cran-uri "biclust" version))
24896 "0lgyc2f04dhr65cwga78pradxsdzgjrpp8vphchqn60ab1z95dlp"))))
24897 (properties `((upstream-name . "biclust")))
24898 (build-system r-build-system)
24900 (list r-additivitytests
24907 (home-page "https://cran.r-project.org/web/packages/biclust/")
24908 (synopsis "BiCluster algorithms")
24910 "The main function @code{biclust()} provides several algorithms to find
24911 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
24912 In addition, the package provides methods for data
24913 preprocessing (normalization and discretization), visualization, and
24914 validation of bicluster solutions.")
24915 (license license:gpl3)))
24917 (define-public r-icge
24924 (uri (cran-uri "ICGE" version))
24927 "13p9v0g5qda8bpj3sj9p277l7idv4jscrsszg2kn080dapp3cppp"))))
24928 (properties `((upstream-name . "ICGE")))
24929 (build-system r-build-system)
24931 (list r-cluster r-fastcluster r-mass))
24932 (home-page "https://cran.r-project.org/web/packages/ICGE/")
24933 (synopsis "Cluster estimation and identification of atypical units")
24935 "ICGE is a package that helps to estimate the number of real clusters in
24936 data as well as to identify atypical units. The underlying methods are based
24937 on distances rather than on unit x variables.")
24938 (license license:gpl2+)))
24940 (define-public r-depth
24943 (version "2.1-1.1")
24947 (uri (cran-uri "depth" version))
24950 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
24951 (properties `((upstream-name . "depth")))
24952 (build-system r-build-system)
24954 (list r-abind r-circular r-rgl))
24957 (home-page "https://cran.r-project.org/web/packages/depth/")
24958 (synopsis "Nonparametric depth functions for multivariate analysis")
24960 "This package provides tools for depth functions methodology applied to
24961 multivariate analysis. Besides allowing calculation of depth values and
24962 depth-based location estimators, the package includes functions or drawing
24963 contour plots and perspective plots of depth functions. Euclidean and
24964 spherical depths are supported.")
24965 (license license:gpl2)))
24967 (define-public r-archetypes
24969 (name "r-archetypes")
24970 (version "2.2-0.1")
24974 (uri (cran-uri "archetypes" version))
24977 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
24978 (properties `((upstream-name . "archetypes")))
24979 (build-system r-build-system)
24981 (list r-modeltools r-nnls))
24982 (home-page "https://cran.r-project.org/web/packages/archetypes")
24983 (synopsis "Archetypal analysis")
24985 "The main function @code{archetypes} implements a framework for
24986 archetypal analysis supporting arbitrary problem solving mechanisms for the
24987 different conceptual parts of the algorithm.")
24988 (license license:gpl2+)))
24990 (define-public r-shapes
24997 (uri (cran-uri "shapes" version))
25000 "1p9fr95zk3q2v277c5ksb0nh26mcpzwjzjb2lmag51z6hck8cb66"))))
25001 (properties `((upstream-name . "shapes")))
25002 (build-system r-build-system)
25004 (list r-mass r-minpack-lm r-rgl r-scatterplot3d))
25005 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
25006 (synopsis "Statistical shape analysis")
25008 "This package provides routines for the statistical analysis of landmark
25009 shapes, including Procrustes analysis, graphical displays, principal
25010 components analysis, permutation and bootstrap tests, thin-plate spline
25011 transformation grids and comparing covariance matrices. See Dryden, I.L. and
25012 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
25013 Edition), John Wiley and Sons.")
25014 (license license:gpl2)))
25016 (define-public r-animation
25018 (name "r-animation")
25022 (uri (cran-uri "animation" version))
25025 "0sg4sz5lkn85yzpcg22xkr7921cbnh7g74nlp9imjy7c0hdqyhc8"))
25027 '(for-each delete-file
25028 '("inst/misc/scianimator/js/jquery.scianimator.min.js"
25029 "inst/misc/scianimator/js/jquery-1.4.4.min.js")))))
25030 (properties `((upstream-name . "animation")))
25031 (build-system r-build-system)
25035 '(modify-phases %standard-phases
25036 (add-after 'unpack 'process-javascript
25037 (lambda* (#:key inputs #:allow-other-keys)
25038 (with-directory-excursion "inst/misc/"
25039 (symlink (search-input-file
25041 "share/javascript/jquery.scianimator.min.js")
25042 "scianimator/js/jquery.scianimator.min.js")
25043 (invoke "esbuild" (assoc-ref inputs "js-jquery")
25045 (string-append "--outfile="
25046 "scianimator/js/jquery-1.4.4.min.js"))))))))
25047 (propagated-inputs (list r-magick))
25048 (inputs (list js-scianimator))
25050 `(("esbuild" ,esbuild)
25054 (uri "https://code.jquery.com/jquery-1.4.4.js")
25057 "10nl4smq63vrfb0c3n0fknm1zw7ss8gicy6wc6jb6l3rmyad075k"))))))
25058 (home-page "https://yihui.org/animation/")
25059 (synopsis "Gallery of animations and utilities to create animations")
25061 "This package provides functions for animations in statistics, covering
25062 topics in probability theory, mathematical statistics, multivariate
25063 statistics, non-parametric statistics, sampling survey, linear models, time
25064 series, computational statistics, data mining and machine learning. These
25065 functions may be helpful in teaching statistics and data analysis. Also
25066 provided in this package are a series of functions to save animations to
25067 various formats, e.g. GIF, HTML pages, PDF, and videos. PDF animations can be
25068 inserted into Sweave / @code{knitr} easily.")
25069 (license (list license:gpl2+ license:gpl3+))))
25071 (define-public r-anthropometry
25073 (name "r-anthropometry")
25078 (uri (cran-uri "Anthropometry" version))
25081 "0vxjlzxv16bygw8n57f25msq5bd1dydg41my92ximah0nzzvbg41"))))
25082 (properties `((upstream-name . "Anthropometry")))
25083 (build-system r-build-system)
25096 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
25097 (synopsis "Statistical methods for anthropometric data")
25099 "This package provides statistical methods especially developed to
25100 analyze anthropometric data. These methods are aimed at providing effective
25101 solutions to some commons problems related to Ergonomics and Anthropometry.
25102 They are based on clustering, the statistical concept of data depth,
25103 statistical shape analysis and archetypal analysis.")
25104 (license license:gpl2+)))
25106 (define-public r-anndata
25109 (version "0.7.5.5")
25113 (uri (cran-uri "anndata" version))
25115 (base32 "1ync82qp0v6zszibz8bwhlyknf99v3iki8cwq4n4vwmg9z7hrb54"))))
25116 (properties `((upstream-name . "anndata")))
25117 (build-system r-build-system)
25118 (propagated-inputs (list r-assertthat r-matrix r-r6 r-reticulate))
25119 (native-inputs (list r-knitr))
25120 (home-page "https://anndata.dynverse.org")
25121 (synopsis "Anndata for R")
25123 "This package provides a reticulate wrapper for the Python package
25124 @code{anndata}. It provides a scalable way of keeping track of data and
25125 learned annotations. It is used to read from and write to the h5ad file
25127 (license license:expat)))
25129 (define-public r-adamethods
25131 (name "r-adamethods")
25136 (uri (cran-uri "adamethods" version))
25139 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
25140 (properties `((upstream-name . "adamethods")))
25141 (build-system r-build-system)
25143 (list r-anthropometry
25150 (home-page "https://cran.r-project.org/web/packages/adamethods/")
25151 (synopsis "Archetypoid algorithms and anomaly detection")
25153 "This package is a collection of several algorithms to obtain
25154 archetypoids with small and large databases and with both classical
25155 multivariate data and functional data (univariate and multivariate). Some of
25156 these algorithms also detect anomalies (outliers).")
25157 (license license:gpl2+)))
25159 (define-public r-idpmisc
25166 (uri (cran-uri "IDPmisc" version))
25169 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
25170 (properties `((upstream-name . "IDPmisc")))
25171 (build-system r-build-system)
25174 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
25175 (synopsis "Functions for data analyses and visualization")
25177 "This package provides different high-level graphics functions for
25178 displaying large datasets, displaying circular data in a very flexible way,
25179 finding local maxima, brewing color ramps, drawing nice arrows, zooming
25180 2D-plots, creating figures with differently colored margin and plot region.
25181 In addition, the package contains auxiliary functions for data manipulation
25182 like omitting observations with irregular values or selecting data by logical
25183 vectors, which include NAs. Other functions are especially useful in
25184 spectroscopy and analyses of environmental data: robust baseline fitting,
25185 finding peaks in spectra, converting humidity measures.")
25186 (license license:gpl3+)))
25188 (define-public r-qqconf
25194 (uri (cran-uri "qqconf" version))
25197 "11sh0q5bwmqdygqd1gspx7xc5mysj18whz11afnz6s1m820snhhw"))))
25198 (properties `((upstream-name . "qqconf")))
25199 (build-system r-build-system)
25200 (inputs (list fftw))
25205 (native-inputs (list pkg-config r-knitr))
25206 (home-page "https://github.com/eweine/qqconf")
25207 (synopsis "Create simultaneous testing bands for QQ-plots")
25209 "This package provides functionality for creating Quantile-Quantile (QQ) and
25210 Probability-Probability (PP) plots with simultaneous testing bands to asses
25211 significance of sample deviation from a reference distribution.")
25212 (license license:gpl3)))
25214 (define-public r-qqman
25221 (uri (cran-uri "qqman" version))
25224 "1a6qp5wv9bvwjchfw8x4jh48hkynlnfr21a8vqgnswldvwbq7njq"))))
25225 (properties `((upstream-name . "qqman")))
25226 (build-system r-build-system)
25228 (list r-calibrate))
25231 (home-page "https://cran.r-project.org/web/packages/qqman/")
25232 (synopsis "Q-Q and Manhattan plots for GWAS data")
25234 "This package allows you to create Q-Q and Manhattan plots for GWAS data
25235 from PLINK results.")
25236 (license license:gpl3)))
25238 (define-public r-gghighlight
25240 (name "r-gghighlight")
25245 (uri (cran-uri "gghighlight" version))
25247 (base32 "0vfcn3gg6j7g20n2z1iwr94jnpqn0zl5j9jfc8bnbsrmz49dzqpd"))))
25248 (properties `((upstream-name . "gghighlight")))
25249 (build-system r-build-system)
25251 (list r-dplyr r-ggplot2 r-ggrepel r-lifecycle r-purrr r-rlang r-tibble))
25252 (native-inputs (list r-knitr))
25253 (home-page "https://github.com/yutannihilation/gghighlight/")
25254 (synopsis "Highlight lines and points in ggplot2")
25255 (description "Suppose we have data that has so many series that it is hard
25256 to identify them by their colors as the differences are so subtle. With
25257 gghighlight we can highlight those lines that match certain criteria. The
25258 result is a usual @code{ggplot} object, so it is fully customizable and can be
25259 used with custom themes and facets.")
25260 (license license:expat)))
25262 (define-public r-ggplot-multistats
25264 (name "r-ggplot-multistats")
25269 (uri (cran-uri "ggplot.multistats" version))
25272 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
25274 `((upstream-name . "ggplot.multistats")))
25275 (build-system r-build-system)
25277 (list r-ggplot2 r-hexbin r-rlang r-scales))
25278 (home-page "https://github.com/flying-sheep/ggplot.multistats")
25279 (synopsis "Multiple summary statistics for binned stats/geometries")
25281 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
25282 which functions similar to its singular form, but allows the use of multiple
25283 statistics per bin. Those statistics can be mapped to multiple bin
25285 (license license:gpl3)))
25287 (define-public r-knn-covertree
25289 (name "r-knn-covertree")
25294 (uri (cran-uri "knn.covertree" version))
25297 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
25298 (properties `((upstream-name . "knn.covertree")))
25299 (build-system r-build-system)
25301 (list r-matrix r-rcpp r-rcppeigen))
25302 (home-page "https://github.com/flying-sheep/knn.covertree")
25303 (synopsis "Accurate kNN Implementation with multiple distance measures")
25305 "Similarly to the FNN package, this package allows calculation of the k
25306 nearest neighbors (kNN) of a data matrix. The implementation is based on
25307 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
25308 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
25309 (license license:agpl3+)))
25311 (define-public r-poibin
25318 (uri (cran-uri "poibin" version))
25321 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
25322 (properties `((upstream-name . "poibin")))
25323 (build-system r-build-system)
25324 (home-page "https://cran.r-project.org/web/packages/poibin/")
25325 (synopsis "Poisson binomial distribution")
25327 "This package provides an implementation of both the exact and
25328 approximation methods for computing the @dfn{cumulative distribution
25329 function} (CDF) of the Poisson binomial distribution. It also provides the
25330 @dfn{probability mass function} (PMF), quantile function, and random number
25331 generation for the Poisson binomial distribution.")
25332 (license license:gpl2)))
25334 (define-public r-diagram
25341 (uri (cran-uri "diagram" version))
25344 "1r3lyl0h7mk9cfg8smr3jydfkjdawaphnxibkxfjqa7029vkxh79"))))
25345 (properties `((upstream-name . "diagram")))
25346 (build-system r-build-system)
25349 (home-page "https://cran.r-project.org/web/packages/diagram/")
25350 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
25352 "This package provides tools to visualize simple graphs (networks) based
25353 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
25354 electrical networks, etc. It also includes supporting material for the book
25355 \"A practical guide to ecological modelling - using R as a simulation
25356 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
25357 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
25358 Francesca Mazzia (2012).")
25359 (license license:gpl2+)))
25361 (define-public r-lim
25368 (uri (cran-uri "LIM" version))
25371 "0d9bgyd0mnag8wds993dsvlbpkhyakydlzwc3nghxzv2n8504hjj"))))
25372 (properties `((upstream-name . "LIM")))
25373 (build-system r-build-system)
25375 (list r-diagram r-limsolve))
25376 (home-page "https://cran.r-project.org/web/packages/LIM/")
25377 (synopsis "Linear inverse model examples and solution methods")
25379 "This package provides functions that read and solve linear inverse
25380 problems (food web problems, linear programming problems).")
25381 (license license:gpl2+)))
25383 (define-public r-shinycssloaders
25385 (name "r-shinycssloaders")
25390 (uri (cran-uri "shinycssloaders" version))
25393 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
25395 `((upstream-name . "shinycssloaders")))
25396 (build-system r-build-system)
25398 (list r-digest r-glue r-shiny))
25399 (home-page "https://github.com/andrewsali/shinycssloaders")
25400 (synopsis "Add CSS loading animations to Shiny outputs")
25402 "This package provides tools to create a lightweight Shiny wrapper for
25403 the css-loaders created by Luke Hass
25404 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
25405 automatically show a loader when the output is (re)calculating.")
25406 (license license:gpl3)))
25408 (define-public r-rsvg
25415 (uri (cran-uri "rsvg" version))
25418 "1lx84x5dnxj1xdsidwfg9i6fkay7ldarwrbg0gl0f02wajf8ifsz"))))
25419 (properties `((upstream-name . "rsvg")))
25420 (build-system r-build-system)
25422 (list librsvg zlib))
25424 (list pkg-config r-knitr))
25425 (home-page "https://github.com/jeroen/rsvg#readme")
25426 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
25428 "This package allows you to render vector-based SVG images into
25429 high-quality custom-size bitmap arrays using the librsvg2 library. The
25430 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
25431 addition, the package can convert images directly to various formats such as
25432 PDF or PostScript.")
25433 (license license:expat)))
25435 (define-public r-influencer
25437 (name "r-influencer")
25438 (version "0.1.0.1")
25442 (uri (cran-uri "influenceR" version))
25445 "0rj7rm236vn3v8302nwl12s0kvpv6xpdbm3q3gxk7vgwfl8nzi33"))))
25446 (properties `((upstream-name . "influenceR")))
25447 (build-system r-build-system)
25449 (list r-igraph r-matrix))
25450 (home-page "https://github.com/rcc-uchicago/influenceR")
25451 (synopsis "Tools to quantify structural importance of nodes in a network")
25453 "This package provides functionality to compute various node centrality
25454 measures on networks. Included are functions to compute betweenness
25455 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
25456 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
25457 algorithm to identify key players, and Valente's bridging metric. The
25458 betweenness, Key Players, and bridging implementations are parallelized with
25460 (license license:gpl2)))
25462 (define-public r-emplik
25469 (uri (cran-uri "emplik" version))
25472 "039kz7703ri91j2i93dr8ixap7i63sr72id9zp74cm7ws9pd1b27"))))
25473 (properties `((upstream-name . "emplik")))
25474 (build-system r-build-system)
25477 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
25478 (synopsis "Empirical likelihood ratio for censored/truncated data")
25480 "This package provides empirical likelihood ratio tests for
25481 means/quantiles/hazards from possibly censored and/or truncated data. It also
25483 (license license:gpl2+)))
25485 (define-public r-imputeyn
25487 (name "r-imputeyn")
25492 (uri (cran-uri "imputeYn" version))
25495 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
25496 (properties `((upstream-name . "imputeYn")))
25497 (build-system r-build-system)
25499 (list r-boot r-emplik r-mvtnorm r-quadprog r-survival))
25500 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
25501 (synopsis "Impute last largest censored observation under weighted least squares")
25503 "This package allows for the imputation of the last largest censored
25504 observantions. This method brings less bias and more efficient estimates for
25506 (license license:gpl2)))
25508 (define-public r-adapenetclass
25510 (name "r-adapenetclass")
25515 (uri (cran-uri "AdapEnetClass" version))
25518 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
25519 (properties `((upstream-name . "AdapEnetClass")))
25520 (build-system r-build-system)
25522 (list r-glmnet r-imputeyn r-lars r-quadprog))
25523 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
25524 (synopsis "Class of adaptive elastic net methods for censored data")
25526 "This package provides methods for variable selection for AFT models.")
25527 (license license:gpl2)))
25529 (define-public r-flock
25536 (uri (cran-uri "flock" version))
25539 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
25540 (properties `((upstream-name . "flock")))
25541 (build-system r-build-system)
25542 (propagated-inputs (list r-rcpp))
25543 (home-page "https://cran.r-project.org/web/packages/flock/")
25544 (synopsis "Process synchronization using file locks")
25546 "This package implements synchronization between R processes (spawned by
25547 using the @code{parallel} package for instance) using file locks. It supports
25548 both exclusive and shared locking.")
25549 (license license:asl2.0)))
25551 (define-public r-archivist
25553 (name "r-archivist")
25558 (uri (cran-uri "archivist" version))
25561 "0q1qysack30xzxdbvvi56rk7r85hsj4ghls9r70ki7bl3rqwr4c9"))))
25562 (properties `((upstream-name . "archivist")))
25563 (build-system r-build-system)
25575 (home-page "https://pbiecek.github.io/archivist/")
25576 (synopsis "Tools for storing, restoring and searching for R objects")
25578 "Data exploration and modelling is a process in which a lot of data
25579 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
25580 statistical models, different versions of data sets and different versions of
25581 results. Archivist helps to store and manage artifacts created in R. It
25582 allows you to store selected artifacts as binary files together with their
25583 metadata and relations. Archivist allows sharing artifacts with others. It
25584 can look for already created artifacts by using its class, name, date of the
25585 creation or other properties. It also makes it easy to restore such
25587 (license license:gpl2)))
25589 (define-public r-versions
25591 (name "r-versions")
25596 (uri (cran-uri "versions" version))
25599 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
25600 (properties `((upstream-name . "versions")))
25601 (build-system r-build-system)
25602 (home-page "https://cran.r-project.org/web/packages/versions/")
25603 (synopsis "Query and install specific versions of CRAN packages")
25605 "This package allows you to install specified versions of R packages
25606 hosted on CRAN and provides functions to list available versions and the
25607 versions of currently installed packages.")
25608 (license license:bsd-3)))
25610 (define-public r-adapr
25617 (uri (cran-uri "adapr" version))
25620 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
25621 (properties `((upstream-name . "adapr")))
25622 (build-system r-build-system)
25639 (home-page "https://cran.r-project.org/web/packages/adapr/")
25640 (synopsis "Implementation of an accountable data analysis process")
25642 "This package tracks reading and writing within R scripts that are
25643 organized into a directed acyclic graph. It contains an interactive Shiny
25644 application @code{adaprApp()}. It uses Git and file hashes to track version
25645 histories of inputs and outputs.")
25646 (license license:lgpl2.0)))
25648 (define-public r-adapsamp
25650 (name "r-adapsamp")
25655 (uri (cran-uri "AdapSamp" version))
25658 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
25659 (properties `((upstream-name . "AdapSamp")))
25660 (build-system r-build-system)
25661 (propagated-inputs (list r-pracma))
25662 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
25663 (synopsis "Adaptive sampling algorithms")
25665 "For distributions whose probability density functions are log-concave,
25666 the adaptive rejection sampling algorithm can be used to build envelope
25667 functions for sampling. For others, the modified adaptive rejection sampling
25668 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
25669 adaptive slice sampling algorithm can be used. This R package mainly includes
25670 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
25671 @code{rASS()}. These functions can realize sampling based on the algorithms
25673 (license license:gpl2)))
25675 (define-public r-adaptalint
25677 (name "r-adaptalint")
25682 (uri (cran-uri "adaptalint" version))
25685 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
25686 (properties `((upstream-name . "adaptalint")))
25687 (build-system r-build-system)
25689 (list r-dplyr r-lintr r-purrr))
25690 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
25691 (synopsis "Check R code style")
25693 "This package provides tools to infer the code style (which style rules
25694 are followed and which ones are not) from one package and use it to check
25695 another. This makes it easier to find and correct the most important problems
25697 (license license:gpl3)))
25699 (define-public r-fracdiff
25701 (name "r-fracdiff")
25706 (uri (cran-uri "fracdiff" version))
25709 "0dzl011c92skf7hmx1zvdwsrashmfkxy9p2wig35nzr8609qhpxc"))))
25710 (properties `((upstream-name . "fracdiff")))
25711 (build-system r-build-system)
25712 (home-page "https://github.com/mmaechler/fracdiff")
25714 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
25716 "This package provides tools for the maximum likelihood estimation of the
25717 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
25718 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
25719 (license license:gpl2+)))
25721 (define-public r-forecast
25723 (name "r-forecast")
25728 (uri (cran-uri "forecast" version))
25731 "1pfq2b1ppkbg3a9bag4jrfsjclf0c7mdqbhf1l08h6fqv6lbl82r"))))
25732 (properties `((upstream-name . "forecast")))
25733 (build-system r-build-system)
25749 (list r-knitr)) ; needed for vignettes
25750 (home-page "https://pkg.robjhyndman.com/forecast/")
25751 (synopsis "Forecasting functions for time series and linear models")
25753 "This package provides methods and tools for displaying and analysing
25754 univariate time series forecasts including exponential smoothing via state
25755 space models and automatic ARIMA modelling.")
25756 (license license:gpl3)))
25758 (define-public r-forestplot
25760 (name "r-forestplot")
25764 (uri (cran-uri "forestplot" version))
25767 "0xk30mpb87sab2afnk2j474qjjf4j6x1ifh9j5n7w690f481iqqb"))))
25768 (properties `((upstream-name . "forestplot")))
25769 (build-system r-build-system)
25771 (list r-abind r-checkmate))
25772 (native-inputs (list r-knitr))
25773 (home-page "https://gforge.se/packages/")
25774 (synopsis "Advanced forest plot using @code{grid} graphics")
25776 "This package provides a forest plot that allows for multiple
25777 confidence intervals per row, custom fonts for each text element,
25778 custom confidence intervals, text mixed with expressions, and more.
25779 The aim is to extend the use of forest plots beyond meta-analyses.
25780 This is a more general version of the original @code{rmeta} package's
25781 @code{forestplot()} function and relies heavily on the @code{grid}
25783 (license license:gpl2)))
25785 (define-public r-formattable
25787 (name "r-formattable")
25792 (uri (cran-uri "formattable" version))
25794 (base32 "1vdxi0xmg019qyzjrp8bkjxciz245jcxsrkhfzd44ynqcwi4s3ag"))))
25795 (properties `((upstream-name . "formattable")))
25796 (build-system r-build-system)
25798 (list r-htmltools r-htmlwidgets r-lifecycle r-rmarkdown))
25801 (home-page "https://github.com/renkun-ken/formattable")
25802 (synopsis "Print vectors and data frames with text fromatting")
25804 "This R package provides functions to create formattable vectors and data
25805 frames. @emph{Formattable} vectors are printed with text formatting, and
25806 formattable data frames are printed with multiple types of formatting in HTML
25807 to improve the readability of data presented in tabular form rendered in web
25809 (license license:expat)))
25811 (define-public r-xmisc
25818 (uri (cran-uri "Xmisc" version))
25821 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
25822 (properties `((upstream-name . "Xmisc")))
25823 (build-system r-build-system)
25824 (home-page "https://cran.r-project.org/package=Xmisc")
25826 "Xiaobei's miscellaneous classes and functions")
25828 "This package provides Xiaobei's miscellaneous classes and functions,
25829 which are useful when developing R packages for @dfn{object oriented
25830 programming} (OOP) using R Reference Class.")
25831 (license license:gpl2+)))
25833 (define-public r-proxyc
25840 (uri (cran-uri "proxyC" version))
25843 "00p3604ny6qax5rr1865c27hfp90v2vga0xcrp3bb81xcfadl99y"))))
25844 (properties `((upstream-name . "proxyC")))
25845 (build-system r-build-system)
25846 (native-inputs (list r-knitr))
25848 (list r-matrix r-rcpp r-rcpparmadillo r-rcppparallel))
25849 (home-page "https://cran.r-project.org/package=proxyC")
25850 (synopsis "Compute proximity in large sparse matrices")
25852 "This package provides efficient tools to compute the proximity between
25853 rows or columns of large matrices. Functions are optimised for large sparse
25854 matrices using the Armadillo and Intel TBB libraries. Among several built-in
25855 similarity/distance measures, computation of correlation, cosine similarity
25856 and Euclidean distance is particularly fast.")
25857 (license license:gpl3)))
25859 (define-public r-isocodes
25861 (name "r-isocodes")
25862 (version "2022.09.29")
25866 (uri (cran-uri "ISOcodes" version))
25869 "1rag5mb3bbyxp8n32rhfyy752cy9hh5j80lp9xljj70scvglzbjb"))))
25870 (properties `((upstream-name . "ISOcodes")))
25871 (build-system r-build-system)
25872 (home-page "https://cran.r-project.org/package=ISOcodes")
25873 (synopsis "Selected ISO codes")
25875 "This package provides ISO language, territory, currency, script and
25876 character codes. It provides ISO 639 language codes, ISO 3166 territory
25877 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
25878 character codes as well as the UN M.49 area codes.")
25879 (license license:gpl2)))
25881 (define-public r-stopwords
25883 (name "r-stopwords")
25888 (uri (cran-uri "stopwords" version))
25891 "1ci1cgxrcvlhhplximsfv0plvjdbcd5kv0nphxnpildsn5m1rv65"))))
25892 (properties `((upstream-name . "stopwords")))
25893 (build-system r-build-system)
25896 (home-page "https://github.com/quanteda/stopwords")
25897 (synopsis "Multilingual stopword lists")
25899 "This package provides multiple sources of stopwords, for use in text
25900 analysis and natural language processing.")
25901 (license license:expat)))
25903 (define-public r-spacyr
25910 (uri (cran-uri "spacyr" version))
25913 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
25914 (properties `((upstream-name . "spacyr")))
25915 (build-system r-build-system)
25917 (list r-data-table r-reticulate))
25918 (home-page "https://spacyr.quanteda.io")
25919 (synopsis "R wrapper for the spaCy NLP library")
25921 "This package provides an R wrapper to the Python @dfn{natural language
25922 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
25923 (license license:gpl3)))
25925 (define-public r-snowballc
25927 (name "r-snowballc")
25932 (uri (cran-uri "SnowballC" version))
25935 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
25936 (properties `((upstream-name . "SnowballC")))
25937 (build-system r-build-system)
25938 (home-page "https://r-forge.r-project.org/projects/r-temis/")
25939 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
25941 "This package provides an R interface to the C @code{libstemmer} library
25942 that implements Porter's word stemming algorithm for collapsing words to a
25943 common root to aid comparison of vocabulary. Currently supported languages
25944 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
25945 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
25946 (license license:bsd-3)))
25948 (define-public r-quanteda
25950 (name "r-quanteda")
25955 (uri (cran-uri "quanteda" version))
25958 "1blk9nhydvqyyz0kzhph7nh7ahcjzflmgyr4sv8fx5bpmn4hwjzk"))))
25959 (properties `((upstream-name . "quanteda")))
25960 (build-system r-build-system)
25975 (home-page "https://quanteda.io")
25976 (synopsis "Quantitative analysis of textual data")
25978 "This package provides a fast, flexible, and comprehensive framework for
25979 quantitative text analysis in R. It provides functionality for corpus
25980 management, creating and manipulating tokens and ngrams, exploring keywords in
25981 context, forming and manipulating sparse matrices of documents by features and
25982 feature co-occurrences, analyzing keywords, computing feature similarities and
25983 distances, applying content dictionaries, applying supervised and unsupervised
25984 machine learning, visually representing text and text analyses, and more.")
25985 (license license:gpl3)))
25987 (define-public r-topicmodels
25989 (name "r-topicmodels")
25994 (uri (cran-uri "topicmodels" version))
25997 "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g"))))
25998 (properties `((upstream-name . "topicmodels")))
25999 (build-system r-build-system)
26003 (list r-modeltools r-slam r-tm))
26004 (home-page "https://cran.r-project.org/package=topicmodels")
26005 (synopsis "Topic models")
26007 "This package provides an interface to the C code for @dfn{Latent
26008 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
26009 David M. Blei and co-authors and the C++ code for fitting LDA models using
26010 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
26011 (license license:gpl2)))
26013 (define-public r-stm
26020 (uri (cran-uri "stm" version))
26023 "0qwq4nin2n9fjd06852r8k7arvcgh46kcfb3lm21swgx6j8bgrhb"))))
26024 (properties `((upstream-name . "stm")))
26025 (build-system r-build-system)
26038 (home-page "http://www.structuraltopicmodel.com/")
26039 (synopsis "Estimation of the Structural Topic Model")
26041 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
26042 topic models with document-level covariates. The package also includes tools
26043 for model selection, visualization, and estimation of topic-covariate
26045 (license license:expat)))
26047 (define-public r-polycor
26054 (uri (cran-uri "polycor" version))
26057 "0285rvx8238qp8dix0jq0cqq7ks8h6cjwsscbc7dx4n9nph56pzh"))))
26058 (properties `((upstream-name . "polycor")))
26059 (build-system r-build-system)
26061 (list r-admisc r-matrix r-mvtnorm))
26062 (home-page "https://r-forge.r-project.org/projects/polycor/")
26063 (synopsis "Polychoric and polyserial correlations")
26065 "This package provides tools to compute polychoric and polyserial
26066 correlations by quick \"two-step\" methods or ML, optionally with standard
26067 errors; tetrachoric and biserial correlations are special cases.")
26068 (license license:gpl2+)))
26070 (define-public r-msm
26077 (uri (cran-uri "msm" version))
26080 "08vhazswyxr3y1zb9y60mbg3bappzlizxml8s08p65mh82xxkz5f"))))
26081 (properties `((upstream-name . "msm")))
26082 (build-system r-build-system)
26084 (list r-expm r-mvtnorm r-survival))
26085 (home-page "https://github.com/chjackson/msm")
26086 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
26088 "This package provides functions for fitting continuous-time Markov and
26089 hidden Markov multi-state models to longitudinal data. It was designed for
26090 processes observed at arbitrary times in continuous time (panel data) but some
26091 other observation schemes are supported. Both Markov transition rates and the
26092 hidden Markov output process can be modelled in terms of covariates, which may
26093 be constant or piecewise-constant in time.")
26094 (license license:gpl2+)))
26096 (define-public r-ltm
26103 (uri (cran-uri "ltm" version))
26106 "0vhgbk6j0z3limsrbjkjkpfn2whiaij5j4jf1gg66mjs9dlylap1"))))
26107 (properties `((upstream-name . "ltm")))
26108 (build-system r-build-system)
26110 (list r-mass r-msm r-polycor))
26111 (home-page "https://github.com/drizopoulos/ltm")
26112 (synopsis "Latent trait models under IRT")
26114 "This is a package supporting the analysis of multivariate dichotomous
26115 and polytomous data using latent trait models under the Item Response Theory
26116 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
26117 Three-Parameter, the Graded Response, and the Generalized Partial Credit
26119 (license license:gpl2+)))
26121 (define-public r-mi
26128 (uri (cran-uri "mi" version))
26131 "11f75ivnax6p48mp2pasprws488cm2daym87sw2mcrywvf89fyjd"))))
26132 (properties `((upstream-name . "mi")))
26133 (build-system r-build-system)
26135 (list r-arm r-matrix))
26138 (home-page "http://www.stat.columbia.edu/~gelman/")
26139 (synopsis "Missing data imputation and model checking")
26141 "This package provides functions for data manipulation, imputing missing
26142 values in an approximate Bayesian framework, diagnostics of the models used to
26143 generate the imputations, confidence-building mechanisms to validate some of
26144 the assumptions of the imputation algorithm, and functions to analyze multiply
26145 imputed data sets with the appropriate degree of sampling uncertainty.")
26146 (license license:gpl2+)))
26148 (define-public r-matrixcalc
26150 (name "r-matrixcalc")
26155 (uri (cran-uri "matrixcalc" version))
26158 "09pk0ym6qzribxc6v18cpb6478i4r4kzxpkljjbb3n323zqx5iqb"))))
26159 (properties `((upstream-name . "matrixcalc")))
26160 (build-system r-build-system)
26161 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
26162 (synopsis "Collection of functions for matrix calculations")
26164 "This package provides a collection of functions to support matrix
26165 calculations for probability, econometric and numerical analysis. There are
26166 additional functions that are comparable to APL functions which are useful for
26167 actuarial models such as pension mathematics.")
26168 (license license:gpl2+)))
26170 (define-public r-matrixextra
26172 (name "r-matrixextra")
26177 (uri (cran-uri "MatrixExtra" version))
26179 (base32 "1s8y8zp9k7rsnyi1d8ghi4brjbbdwxijc9chhla24qm3fi6np33a"))))
26180 (properties `((upstream-name . "MatrixExtra")))
26181 (build-system r-build-system)
26183 (list r-float r-matrix r-rcpp r-rhpcblasctl))
26186 (home-page "https://github.com/david-cortes/MatrixExtra")
26187 (synopsis "Extra methods for sparse matrices")
26189 "This package extends sparse matrix and vector classes from the Matrix
26190 package by providing:
26193 @item Methods and operators that work natively on CSR formats (compressed
26194 sparse row, a.k.a. @code{RsparseMatrix}) such as slicing/sub-setting,
26195 assignment, @code{rbind()}, mathematical operators for CSR and COO such as
26196 addition or @code{sqrt()}, and methods such as @code{diag()};
26197 @item Multi-threaded matrix multiplication and cross-product for many
26198 @code{<sparse, dense>} types, including the @code{float32} type from
26200 @item Coercion methods between pairs of classes which are not present in
26201 @code{Matrix}, such as from @code{dgCMatrix} to @code{ngRMatrix}, as well as
26202 convenience conversion functions;
26203 @item Utility functions for sparse matrices such as sorting the indices or
26204 removing zero-valued entries;
26205 @item Fast transposes that work by outputting in the opposite storage format;
26206 @item Faster replacements for many @code{Matrix} methods for all sparse types,
26207 such as slicing and elementwise multiplication.
26208 @item Convenience functions for sparse objects, such as @code{mapSparse} or a
26209 shorter @code{show} method.
26212 (license license:gpl2+)))
26214 (define-public r-sem
26221 (uri (cran-uri "sem" version))
26224 "05hk72zxvyv6kkjhk5y6qw253c64108az7030z8j1sz8wq03n0md"))))
26225 (properties `((upstream-name . "sem")))
26226 (build-system r-build-system)
26228 (list r-boot r-mass r-mi))
26229 (home-page "https://cran.r-project.org/package=sem")
26230 (synopsis "Structural equation models")
26232 "This package provides functions for fitting general linear structural
26233 equation models (with observed and latent variables) using the RAM approach,
26234 and for fitting structural equations in observed-variable models by two-stage
26236 (license license:gpl2+)))
26238 (define-public r-semtools
26240 (name "r-semtools")
26245 (uri (cran-uri "semTools" version))
26248 "1wnakz76c4mgkwvx3iycmvgrzqys860jg9zpkba0ln5c08ycw8pm"))))
26249 (properties `((upstream-name . "semTools")))
26250 (build-system r-build-system)
26252 (list r-lavaan r-pbivnorm))
26253 (home-page "https://github.com/simsem/semTools/wiki")
26254 (synopsis "Useful tools for structural equation modeling")
26256 "This package provides useful tools for structural equation modeling.")
26257 (license license:gpl2+)))
26259 (define-public r-regsem
26266 (uri (cran-uri "regsem" version))
26269 "0vpizmdml55naxmhy9nfcm9ylhy15p9na7l0c6z3rvk29ck3g3sw"))))
26270 (properties `((upstream-name . "regsem")))
26271 (build-system r-build-system)
26273 (list r-lavaan r-rcpp r-rcpparmadillo r-rsolnp))
26276 (home-page "https://cran.r-project.org/package=regsem")
26277 (synopsis "Regularized structural equation modeling")
26279 "This package uses both ridge and lasso penalties (and extensions) to
26280 penalize specific parameters in structural equation models. The package
26281 offers additional cost functions, cross validation, and other extensions
26282 beyond traditional structural equation models. It also contains a function to
26283 perform @dfn{exploratory mediation} (XMed).")
26284 (license license:gpl2+)))
26286 (define-public r-stanheaders
26288 (name "r-stanheaders")
26289 (version "2.21.0-7")
26293 (uri (cran-uri "StanHeaders" version))
26296 "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17"))))
26297 (properties `((upstream-name . "StanHeaders")))
26298 (build-system r-build-system)
26299 (inputs (list pandoc))
26301 (list r-rcppeigen r-rcppparallel))
26303 (list gfortran r-knitr)) ; for vignettes
26304 (home-page "https://mc-stan.org/")
26305 (synopsis "C++ header files for Stan")
26307 "The C++ header files of the Stan project are provided by this package.
26308 There is a shared object containing part of the @code{CVODES} library, but it
26309 is not accessible from R. @code{r-stanheaders} is only useful for developers
26310 who want to utilize the @code{LinkingTo} directive of their package's
26311 DESCRIPTION file to build on the Stan library without incurring unnecessary
26314 The Stan project develops a probabilistic programming language that implements
26315 full or approximate Bayesian statistical inference via Markov Chain Monte
26316 Carlo or variational methods and implements (optionally penalized) maximum
26317 likelihood estimation via optimization. The Stan library includes an advanced
26318 automatic differentiation scheme, templated statistical and linear algebra
26319 functions that can handle the automatically differentiable scalar types (and
26320 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
26321 package provides user-facing R functions to parse, compile, test, estimate,
26322 and analyze Stan models.")
26323 (license license:bsd-3)))
26325 (define-public r-rpf
26332 (uri (cran-uri "rpf" version))
26335 "1yr1i7kswq57mcxv05lh7bvbicz1djqxcl6f13dlgsf3ww56gzg1"))))
26336 (properties `((upstream-name . "rpf")))
26337 (build-system r-build-system)
26339 (list r-lifecycle r-mvtnorm r-rcpp r-rcppeigen))
26342 (home-page "https://github.com/jpritikin/rpf")
26343 (synopsis "Response probability functions")
26345 "The purpose of this package is to factor out logic and math common to
26346 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
26347 core support code suitable for more specialized IRT packages to build upon.
26348 Complete access to optimized C functions is made available with
26349 @code{R_RegisterCCallable()}.")
26350 (license license:gpl3+)))
26352 (define-public r-openmx
26359 (uri (cran-uri "OpenMx" version))
26362 "0ki3n2i9b9880mpfxazmd6zrblzl1jngi10qnbxxvxik1x2mq3vy"))))
26363 (properties `((upstream-name . "OpenMx")))
26364 (build-system r-build-system)
26376 (native-inputs (list r-knitr gfortran))
26377 (home-page "http://openmx.ssri.psu.edu")
26378 (synopsis "Extended structural equation modelling")
26380 "This package allows for the estimation of a wide variety of advanced
26381 multivariate statistical models. It consists of a library of functions and
26382 optimizers that allow you to quickly and flexibly define an SEM model and
26383 estimate parameters given observed data.")
26384 (license license:asl2.0)))
26386 (define-public r-kutils
26393 (uri (cran-uri "kutils" version))
26396 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
26397 (properties `((upstream-name . "kutils")))
26398 (build-system r-build-system)
26400 (list r-foreign r-openxlsx r-plyr r-runit r-xtable))
26401 (home-page "https://cran.r-project.org/package=kutils")
26402 (synopsis "Project management tools")
26404 "This package provides tools for data importation, recoding, and
26405 inspection. There are functions to create new project folders, R code
26406 templates, create uniquely named output directories, and to quickly obtain a
26407 visual summary for each variable in a data frame. The main feature here is
26408 the systematic implementation of the \"variable key\" framework for data
26409 importation and recoding.")
26410 (license license:gpl2)))
26412 (define-public r-rockchalk
26414 (name "r-rockchalk")
26415 (version "1.8.157")
26419 (uri (cran-uri "rockchalk" version))
26422 "13g2rdnxazqfgy653d7vj6w79b2vgnd7bbz0sqn9k4qiig59jh41"))))
26423 (properties `((upstream-name . "rockchalk")))
26424 (build-system r-build-system)
26426 (list r-cardata r-kutils r-lme4 r-mass))
26427 (home-page "https://cran.r-project.org/package=rockchalk")
26428 (synopsis "Regression estimation and presentation")
26430 "This package provides a collection of functions for interpretation and
26431 presentation of regression analysis. These functions are used to produce the
26432 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
26433 includes regression diagnostics, regression tables, and plots of interactions
26434 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
26435 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
26436 fairly comprehensive overview.")
26437 (license license:gpl3+)))
26439 (define-public r-lisreltor
26441 (name "r-lisreltor")
26446 (uri (cran-uri "lisrelToR" version))
26449 "0i51v0x87277ly0kggdd594w6q4zq62b4n7xs9r25j08bzs82nfk"))))
26450 (properties `((upstream-name . "lisrelToR")))
26451 (build-system r-build-system)
26452 (home-page "https://cran.r-project.org/package=lisrelToR")
26453 (synopsis "Import output from LISREL into R")
26455 "This is an unofficial package aimed at automating the import of LISREL
26457 (license license:gpl2)))
26459 (define-public r-bdgraph
26466 (uri (cran-uri "BDgraph" version))
26469 "1s148fvvg1c0n4swsvcinlwckj86jys5nvwp4wlyzh3aw9siyqz7"))))
26470 (properties `((upstream-name . "BDgraph")))
26471 (build-system r-build-system)
26473 (list r-ggplot2 r-igraph r-proc))
26476 (home-page "https://www.uva.nl/profile/a.mohammadi")
26477 (synopsis "Bayesian structure learning in graphical models")
26479 "This package provides statistical tools for Bayesian structure learning
26480 in undirected graphical models for continuous, discrete, and mixed data. It
26481 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
26482 on a continuous-time birth-death process.")
26483 (license license:gpl2+)))
26485 (define-public r-bundesligr
26487 (name "r-bundesligr")
26491 (uri (cran-uri "bundesligR" version))
26494 "0dnhbh9jh7dfbk7mfh8msq4ys5kakalr0kwkycycrb2q8rd049vp"))))
26495 (properties `((upstream-name . "bundesligR")))
26496 (build-system r-build-system)
26497 (home-page "https://github.com/ottlngr/bundesligR")
26498 (synopsis "All final tables of the Bundesliga")
26500 "This package provides all final tables of Germany's highest football
26501 league, the Bundesliga. It contains data from 1964 to 2016.")
26502 (license license:gpl3)))
26504 (define-public r-d3network
26506 (name "r-d3network")
26507 (version "0.5.2.1")
26511 (uri (cran-uri "d3Network" version))
26514 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
26515 (properties `((upstream-name . "d3Network")))
26516 (build-system r-build-system)
26518 (list r-plyr r-rjson r-whisker))
26519 (home-page "http://christophergandrud.github.io/d3Network/")
26520 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
26522 "This package is intended to make it easy to create D3 JavaScript
26523 network, tree, dendrogram, and Sankey graphs from R using data frames.")
26524 (license license:gpl3+)))
26526 (define-public r-qgraph
26533 (uri (cran-uri "qgraph" version))
26536 "0r225b7rnsv6wz41ij0msmqr1xy0iqxh9dbsvjixbi1hvgv91wds"))))
26537 (properties `((upstream-name . "qgraph")))
26538 (build-system r-build-system)
26558 (home-page "http://sachaepskamp.com/qgraph/")
26559 (synopsis "Weighted network visualization and analysis")
26561 "This package implements tools for weighted network visualization and
26562 analysis, as well as Gaussian graphical model computation. It contains graph
26563 plotting methods, and tools for psychometric data visualization and graphical
26564 model estimation. See Epskamp et al. (2012)
26565 @url{doi:10.18637/jss.v048.i04}.")
26566 (license license:gpl2)))
26568 (define-public r-semplot
26575 (uri (cran-uri "semPlot" version))
26578 "0s9bp4pfsllg1k4x8a36yw82fw432dyz0xvmvi8dw9l12q3jkx8i"))))
26579 (properties `((upstream-name . "semPlot")))
26580 (build-system r-build-system)
26593 (home-page "https://github.com/SachaEpskamp/semPlot")
26594 (synopsis "Unified visualizations of structural equation models")
26596 "Structural equation modeling (SEM) has a long history of representing
26597 models graphically as path diagrams. The semPlot package for R fills the gap
26598 between advanced, but time-consuming, graphical software and the limited
26599 graphics produced automatically by SEM software. In addition, semPlot offers
26600 more functionality than drawing path diagrams: it can act as a common ground
26601 for importing SEM results into R. Any result usable as input to semPlot can
26602 also be represented in any of the three popular SEM frame-works, as well as
26603 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
26604 (license license:gpl2)))
26606 (define-public r-cdm
26613 (uri (cran-uri "CDM" version))
26616 "1lcq3i5rlyqkc12c26kj0x4fm2gh1jsisp6kbf59y3hjdkiqajhl"))))
26617 (properties `((upstream-name . "CDM")))
26618 (build-system r-build-system)
26620 (list r-mvtnorm r-polycor r-rcpp r-rcpparmadillo))
26622 "https://github.com/alexanderrobitzsch/CDM")
26623 (synopsis "Cognitive diagnosis modeling")
26625 "This package provides functions for cognitive diagnosis modeling and
26626 multidimensional item response modeling for dichotomous and polytomous item
26627 responses. It enables the estimation of the DINA and DINO model, the multiple
26628 group (polytomous) GDINA model, the multiple choice DINA model, the general
26629 diagnostic model (GDM), the structured latent class model (SLCA), and
26630 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
26631 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
26632 estimation and the package structure. For tutorials on how to use the CDM
26633 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
26634 well as Ravand and Robitzsch (2015).")
26635 (license license:gpl2+)))
26637 (define-public r-tam
26644 (uri (cran-uri "TAM" version))
26647 "0b81d0g4j94yrfzj019jffxrk1aw24iscddp60kjbkrl5p7qy38g"))))
26648 (properties `((upstream-name . "TAM")))
26649 (build-system r-build-system)
26651 (list r-cdm r-rcpp r-rcpparmadillo))
26652 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
26653 (synopsis "Test analysis modules")
26655 "This package includes tools for marginal maximum likelihood estimation
26656 and joint maximum likelihood estimation for unidimensional and
26657 multidimensional item response models. The package functionality covers the
26658 Rasch model, 2PL model, 3PL model, generalized partial credit model,
26659 multi-faceted Rasch model, nominal item response model, structured latent
26660 class model, mixture distribution IRT models, and located latent class models.
26661 Latent regression models and plausible value imputation are also supported.")
26662 (license license:gpl2+)))
26664 (define-public r-erm
26671 (uri (cran-uri "eRm" version))
26674 "0smym010kswc5vx90qr3x1vl16xj1x1i54rvrj006dc4agc1vmlk"))))
26675 (properties `((upstream-name . "eRm")))
26676 (build-system r-build-system)
26678 (list r-colorspace r-lattice r-mass r-matrix r-psych))
26679 (native-inputs (list gfortran))
26680 (home-page "https://cran.r-project.org/package=eRm")
26681 (synopsis "Extended Rasch modeling")
26683 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
26684 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
26685 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
26686 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
26687 data matrix. Additional features are the ML estimation of the person
26688 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
26689 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
26690 infit and outfit measures, ICC and other plots, automated stepwise item
26691 elimination, and a simulation module for various binary data matrices.")
26692 (license license:gpl3)))
26694 (define-public r-irtoys
26701 (uri (cran-uri "irtoys" version))
26704 "1qshz6czykgf53mq6xiswzv5xsjwrkrinpfkf1yavql4v08hs82b"))))
26705 (properties `((upstream-name . "irtoys")))
26706 (build-system r-build-system)
26711 (home-page "https://cran.r-project.org/package=irtoys")
26712 (synopsis "Collection of functions related to Item Response Theory (IRT)")
26714 "This package provides a collection of functions useful in learning and
26715 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
26716 programs. It provides basic CTT analysis, a simple common interface to the
26717 estimation of item parameters in IRT models for binary responses with three
26718 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
26719 EAP, WLE, plausible values), item and person fit statistics, scaling
26720 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
26721 array of parametric and non-parametric (kernel) plots. It estimates and plots
26722 Haberman's interaction model when all items are dichotomously scored.")
26723 (license license:gpl2+)))
26725 (define-public r-iheatmapr
26727 (name "r-iheatmapr")
26732 (uri (cran-uri "iheatmapr" version))
26735 "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx"))))
26736 (properties `((upstream-name . "iheatmapr")))
26737 (build-system r-build-system)
26739 (list r-fastcluster
26749 (home-page "https://docs.ropensci.org/iheatmapr")
26750 (synopsis "Interactive, Complex Heatmaps")
26752 "iheatmapr is an R package for building complex, interactive heatmaps
26753 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
26754 subplots along the rows or columns of the main heatmap add more information
26755 about each row or column. For example, a one column additional heatmap may
26756 indicate what group a particular row or column belongs to. Complex heatmaps
26757 may also include multiple side by side heatmaps which show different types of
26758 data for the same conditions. Interactivity can improve complex heatmaps by
26759 providing tooltips with information about each cell and enabling zooming into
26760 interesting features. iheatmapr uses the plotly library for interactivity.")
26761 (license license:expat)))
26763 (define-public r-packrat
26770 (uri (cran-uri "packrat" version))
26773 "1ni3xn51xifdb2bya5z54jn4nxgss6f23b3hn126j2kaz80h7ns5"))))
26774 (properties `((upstream-name . "packrat")))
26775 (build-system r-build-system)
26776 (home-page "https://github.com/rstudio/packrat/")
26777 (synopsis "Dependency management R projects")
26779 "This package provides a dependency manager for R projects that allows
26780 you to manage the R packages your project depends on in an isolated, portable,
26781 and reproducible way.")
26782 (license license:gpl2)))
26784 (define-public r-rsconnect
26786 (name "r-rsconnect")
26791 (uri (cran-uri "rsconnect" version))
26794 "1q0njv25xiri4ql9mfrzlwdf3l3xg9xjjj2wva9rbniafx3skf95"))))
26795 (properties `((upstream-name . "rsconnect")))
26796 (build-system r-build-system)
26805 (home-page "https://github.com/rstudio/rsconnect")
26806 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
26808 "This package provides a programmatic deployment interface for RPubs,
26809 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
26810 documents, Shiny applications, Plumber APIs, plots, and static web content.")
26811 (license license:gpl2)))
26813 ;; This package includes minified JavaScript files. When upgrading please
26814 ;; check that there are no new minified JavaScript files.
26815 (define-public r-dygraphs
26817 (name "r-dygraphs")
26818 (version "1.1.1.6")
26822 (uri (cran-uri "dygraphs" version))
26825 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
26826 (properties `((upstream-name . "dygraphs")))
26827 (build-system r-build-system)
26829 `(#:modules ((guix build utils)
26830 (guix build r-build-system)
26834 (modify-phases %standard-phases
26835 (add-after 'unpack 'process-javascript
26836 (lambda* (#:key inputs #:allow-other-keys)
26837 (with-directory-excursion "inst/htmlwidgets/lib/"
26841 `(("dygraphs/dygraph-combined-dev.js"
26842 "dygraph-combined.js")
26843 (,(assoc-ref inputs "js-jquery")
26844 "jquery/jquery.min.js")
26845 (,(assoc-ref inputs "js-fquarter")
26846 "fquarter/moment-fquarter.min.js"))))
26847 (lambda (sources targets)
26848 (for-each (lambda (source target)
26849 (format #t "Processing ~a --> ~a~%"
26851 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
26852 (call-with-output-file target
26854 (dump-port minified port)))))
26855 sources targets))))
26858 `(("uglifyjs" ,node-uglify-js)
26859 ;; They actually use version 1.11.1, but this more recent version
26860 ;; should be just fine.
26864 (uri "https://code.jquery.com/jquery-1.12.4.js")
26867 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
26871 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
26872 "moment-fquarter/1.0.1/moment-fquarter.js"))
26875 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
26877 (list r-htmltools r-htmlwidgets r-magrittr r-xts r-zoo))
26878 (home-page "https://github.com/rstudio/dygraphs")
26879 (synopsis "Interface to Dygraphs interactive time series charting library")
26881 "This package provides an R interface to the dygraphs JavaScript charting
26882 library (a copy of which is included in the package). It provides rich
26883 facilities for charting time-series data in R, including highly configurable
26884 series- and axis-display and interactive features like zoom/pan and
26885 series/point highlighting.")
26886 (license license:expat)))
26888 (define-public r-shinystan
26890 (name "r-shinystan")
26895 (uri (cran-uri "shinystan" version))
26898 "0afm703zriyqprz1zvypir80lq2ylfff3qvj5i7p9n365mm8b150"))))
26899 (properties `((upstream-name . "shinystan")))
26900 (build-system r-build-system)
26918 (home-page "https://mc-stan.org/")
26919 (synopsis "Interactive visual and numerical analysis for Bayesian models")
26921 "This package provides a graphical user interface for interactive
26922 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
26923 for analyzing a posterior sample. The interface is powered by the Shiny web
26924 application framework and works with the output of MCMC programs written in
26925 any programming language (and has extended functionality for Stan models fit
26926 using the @code{rstan} and @code{rstanarm} packages).")
26927 (license license:gpl3+)))
26929 (define-public r-rstantools
26931 (name "r-rstantools")
26936 (uri (cran-uri "rstantools" version))
26939 "1dsfgi02hps878n3vimfdbzpm4gr5n3ccrmnc61ncrqcp6p0p0fb"))))
26940 (properties `((upstream-name . "rstantools")))
26941 (build-system r-build-system)
26942 (inputs (list pandoc))
26944 (list r-desc r-rcpp r-rcppparallel))
26947 (home-page "https://mc-stan.org/rstantools/")
26948 (synopsis "Tools for developing R packages interfacing with Stan")
26950 "This package provides various tools for developers of R packages
26951 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
26952 up the required package structure, S3 generics and default methods to unify
26953 function naming across Stan-based R packages, and vignettes with
26954 recommendations for developers.")
26955 (license license:gpl3+)))
26957 (define-public r-loo
26964 (uri (cran-uri "loo" version))
26966 (base32 "1wa5hxk7lkr88mway6b7xd5arrkkl2ldl9rf0v1nqwp8lia2ysl6"))))
26967 (properties `((upstream-name . "loo")))
26968 (build-system r-build-system)
26972 (list r-checkmate r-matrixstats))
26975 (home-page "https://mc-stan.org/loo/")
26976 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
26978 "This package provides an implementation of efficient approximate
26979 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
26980 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
26981 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
26982 procedure for regularizing importance weights. As a byproduct of the
26983 calculations, we also obtain approximate standard errors for estimated
26984 predictive errors and for the comparison of predictive errors between models.
26985 The package also provides methods for using stacking and other model weighting
26986 techniques to average Bayesian predictive distributions.")
26987 (license license:gpl3+)))
26989 (define-public r-rstan
26996 (uri (cran-uri "rstan" version))
26999 "0ibd3pj2pvd7658sdg95fa2yhfmxz9gy0cjwcrdr546k209j55a4"))))
27000 (properties `((upstream-name . "rstan")))
27001 (build-system r-build-system)
27004 (modify-phases %standard-phases
27005 (add-before 'install 'set-timezone
27006 ;; This package is picky about timezones.
27007 (lambda* (#:key inputs #:allow-other-keys)
27008 (setenv "TZ" "UTC+1")
27010 (search-input-directory inputs
27011 "share/zoneinfo")))))))
27013 (list tzdata-for-tests pandoc r-knitr))
27025 (home-page "https://discourse.mc-stan.org/")
27026 (synopsis "R interface to Stan")
27028 "User-facing R functions are provided to parse, compile, test, estimate,
27029 and analyze Stan models by accessing the header-only Stan library provided by
27030 the StanHeaders package. The Stan project develops a probabilistic
27031 programming language that implements full Bayesian statistical inference via
27032 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
27033 approximation, and (optionally penalized) maximum likelihood estimation via
27034 optimization. In all three cases, automatic differentiation is used to
27035 quickly and accurately evaluate gradients without burdening the user with the
27036 need to derive the partial derivatives.")
27037 (license license:gpl3+)))
27039 (define-public r-rstanarm
27041 (name "r-rstanarm")
27046 (uri (cran-uri "rstanarm" version))
27049 "19rj396q84maxnd9d2xcd5rblg3310xn7sqbd6k18kwf3dvd7wp9"))))
27050 (properties `((upstream-name . "rstanarm")))
27051 (build-system r-build-system)
27072 (home-page "https://mc-stan.org/rstanarm/")
27073 (synopsis "Bayesian applied regression modeling via Stan")
27075 "This package estimates previously compiled regression models using the
27076 @code{rstan} package, which provides the R interface to the Stan C++ library
27077 for Bayesian estimation. Users specify models via the customary R syntax with
27078 a formula and @code{data.frame} plus some additional arguments for priors.")
27079 (license license:gpl3+)))
27081 (define-public r-kendall
27088 (uri (cran-uri "Kendall" version))
27091 "1xmk95l4i3kj9jn0xh1chi2rj322k29jq14ra5pa7316gwf9vx2m"))))
27092 (properties `((upstream-name . "Kendall")))
27093 (build-system r-build-system)
27098 (home-page "https://cran.r-project.org/web/packages/Kendall/")
27099 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
27101 "This package computes the Kendall rank correlation and Mann-Kendall
27103 (license license:gpl2+)))
27105 (define-public r-keyring
27112 (uri (cran-uri "keyring" version))
27115 "113rjhihqfhxdihnf6nwqbsknlnm8pqyhvnyxx624gyajl9mn3a7"))))
27116 (properties `((upstream-name . "keyring")))
27117 (build-system r-build-system)
27127 (native-inputs (list pkg-config))
27128 (home-page "https://github.com/r-lib/keyring")
27129 (synopsis "Access the system credential store from R")
27131 "This package provides a platform-independent API to access the operating
27132 system's credential store. It currently supports Keychain on macOS,
27133 Credential Store on Windows, the Secret Service API on GNU/Linux, and a
27134 simple, platform independent store implemented with environment variables.
27135 Additional storage back-ends can be added easily.")
27136 (license license:expat)))
27138 (define-public r-zyp
27141 (version "0.10-1.1")
27145 (uri (cran-uri "zyp" version))
27148 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
27149 (properties `((upstream-name . "zyp")))
27150 (build-system r-build-system)
27153 (home-page "https://cran.r-project.org/web/packages/zyp/")
27154 (synopsis "Zhang + Yue-Pilon Trends Package")
27156 "This package contains an efficient implementation of Sen's slope
27157 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
27158 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
27160 (license license:lgpl2.1)))
27162 (define-public r-rlecuyer
27164 (name "r-rlecuyer")
27168 (uri (cran-uri "rlecuyer" version))
27171 "09mniai7v8gapr6hd3zm8sm3vi1zcyhgym389904ykb2yx7l68s7"))))
27172 (properties `((upstream-name . "rlecuyer")))
27173 (build-system r-build-system)
27175 "https://www.iro.umontreal.ca/~lecuyer/myftp/papers/streams00.pdf")
27176 (synopsis "R interface to RNG with multiple streams")
27178 "This package provides an interface to the C implementation of the random
27179 number generator with multiple independent streams developed by L'Ecuyer et
27180 al (2002). The main purpose of this package is to enable the use of this
27181 random number generator in parallel R applications.")
27182 (license license:gpl2+)))
27184 (define-public r-rlinsolve
27186 (name "r-rlinsolve")
27191 (uri (cran-uri "Rlinsolve" version))
27194 "1xv500n1480qyakw0isanw1s5ywykhc207hqja4804s5s2m8zfjw"))))
27195 (properties `((upstream-name . "Rlinsolve")))
27196 (build-system r-build-system)
27198 (list r-matrix r-rcpp r-rcpparmadillo r-rdpack))
27199 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
27200 (synopsis "Iterative solvers for (sparse) linear system of equations")
27202 "Solving a system of linear equations is one of the most fundamental
27203 computational problems for many fields of mathematical studies, such as
27204 regression problems from statistics or numerical partial differential
27205 equations. This package provides basic stationary iterative solvers such as
27206 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
27207 Nonstationary, also known as Krylov subspace methods are also provided.
27208 Sparse matrix computation is also supported in that solving large and sparse
27209 linear systems can be manageable using the @code{Matrix} package along with
27210 @code{RcppArmadillo}.")
27211 (license license:gpl3+)))
27213 (define-public r-zvcv
27220 (uri (cran-uri "ZVCV" version))
27223 "0gc76j9i8fkm2v638nyzzb1qxl4zmapbspkkaffb8gi5qyjja448"))))
27224 (properties `((upstream-name . "ZVCV")))
27225 (build-system r-build-system)
27236 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
27237 (synopsis "Zero-Variance Control Variates")
27239 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
27240 to reduce the variance of Monte Carlo estimators of expectations using the
27241 derivatives of the log target. Once the derivatives are available, the only
27242 additional computational effort is in solving a linear regression problem.
27243 This method has been extended to higher dimensions using regularisation. This
27244 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
27245 samples, derivatives and function evaluations are available. Additional
27246 functions for applying ZV-CV to two estimators for the normalising constant of
27247 the posterior distribution in Bayesian statistics are also supplied.")
27248 (license license:gpl2+)))
27250 (define-public r-ztype
27257 (uri (cran-uri "ztype" version))
27260 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
27261 (properties `((upstream-name . "ztype")))
27262 (build-system r-build-system)
27271 (home-page "https://cran.r-project.org/web/packages/ztype/")
27272 (synopsis "Run a Ztype game loaded with R functions")
27274 "How fast can you type R functions on your keyboard? Find out by running
27275 a @code{zty.pe} game: export R functions as instructions to type to destroy
27276 opponents' vessels.")
27277 (license license:gpl3)))
27279 (define-public r-zseq
27286 (uri (cran-uri "Zseq" version))
27289 "0xp7qi5kjg8xmci9wrfvmygjmz8gbhq60fl9bvk8rnka6s4ppkrc"))))
27290 (properties `((upstream-name . "Zseq")))
27291 (build-system r-build-system)
27294 (home-page "https://cran.r-project.org/web/packages/Zseq/")
27295 (synopsis "Integer sequence generator")
27297 "This package generates well-known integer sequences. The @code{gmp}
27298 package is adopted for computing with arbitrarily large numbers. Every
27299 function has a hyperlink to its corresponding item in the @dfn{On-Line
27300 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
27301 (license license:gpl3+)))
27303 (define-public r-isoband
27310 (uri (cran-uri "isoband" version))
27313 "18s3mdzl9y8v5fpvdy6iyqp3j57kw8bwhgan94373xjkaya61r17"))))
27314 (properties `((upstream-name . "isoband")))
27315 (build-system r-build-system)
27318 (home-page "https://github.com/wilkelab/isoband")
27319 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
27321 "This package provides a fast C++ implementation to generate contour
27322 lines (isolines) and contour polygons (isobands) from regularly spaced grids
27323 containing elevation data.")
27324 (license license:expat)))
27326 (define-public r-ppcor
27333 (uri (cran-uri "ppcor" version))
27336 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
27337 (properties `((upstream-name . "ppcor")))
27338 (build-system r-build-system)
27341 (home-page "https://cran.r-project.org/web/packages/ppcor/")
27342 (synopsis "Partial and semi-partial correlation")
27344 "This package provides users not only with a function to readily
27345 calculate the higher-order partial and semi-partial correlations but also with
27346 statistics and p-values of the correlation coefficients.")
27347 (license license:gpl2)))
27349 (define-public r-hrbrthemes
27351 (name "r-hrbrthemes")
27356 (uri (cran-uri "hrbrthemes" version))
27358 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
27359 (properties `((upstream-name . "hrbrthemes")))
27360 (build-system r-build-system)
27372 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
27373 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
27375 "This package provides a compilation of extra @code{ggplot2} themes,
27376 scales and utilities, including a spell check function for plot label fields
27377 and an overall emphasis on typography.")
27378 (license license:expat)))
27380 (define-public r-crochet
27387 (uri (cran-uri "crochet" version))
27390 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
27391 (build-system r-build-system)
27394 (home-page "https://github.com/agrueneberg/crochet")
27395 (synopsis "Implementation Helper for Matrix-Like Types")
27397 "Functions to help implement the extraction / subsetting / indexing
27398 function @code{[} and replacement function @code{[<-} of custom matrix-like
27399 types (based on S3, S4, etc.), modeled as closely to the base matrix class
27400 as possible (with tests to prove it).")
27401 (license license:expat)))
27403 (define-public r-boa
27406 (version "1.1.8-2")
27410 (uri (cran-uri "boa" version))
27413 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
27414 (properties `((upstream-name . "boa")))
27415 (build-system r-build-system)
27416 (home-page "https://www.jstatsoft.org/v21/i11")
27417 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
27419 "This package provides a menu-driven program and library of functions for
27420 carrying out convergence diagnostics and statistical and graphical analysis of
27421 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
27422 (license license:gpl2+)))
27424 (define-public r-httpcode
27426 (name "r-httpcode")
27430 (uri (cran-uri "httpcode" version))
27433 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
27434 (build-system r-build-system)
27435 (home-page "https://github.com/sckott/httpcode")
27436 (synopsis "HTTP status code helper")
27437 (description "@code{httpcode} provides functionality for finding and
27438 explaining the meaning of @code{HTTP} status codes. Functions are included for
27439 searching for codes by full or partial number, by message, and to get
27440 appropriate dog and cat images for many status codes.")
27441 (license license:expat)))
27443 (define-public r-latex2exp
27445 (name "r-latex2exp")
27449 (uri (cran-uri "latex2exp" version))
27452 "153br3xflvnnxqhkhm1wgwb2664bw08alhslgdcgjdk73clafhla"))))
27453 (build-system r-build-system)
27455 (list r-stringr r-magrittr))
27458 (home-page "https://github.com/stefano-meschiari/latex2exp/")
27459 (synopsis "Use LaTeX expressions in plots")
27460 (description "@code{latex2exp} parses and converts LaTeX math formulas to
27461 R's plotmath expressions, used to enter mathematical formulas and symbols to be
27462 rendered as text, axis labels, etc. throughout R's plotting system.")
27463 (license license:expat)))
27465 (define-public r-oai
27471 (uri (cran-uri "oai" version))
27474 "1zcbcxhw692s0y6izvwazyzhgx0iwsxsbcan2nk0mb7n11p7bypb"))))
27475 (build-system r-build-system)
27477 (list r-xml2 r-httr r-plyr r-stringr r-tibble))
27480 (home-page "https://github.com/ropensci/oai/")
27481 (synopsis "General purpose OAI-PMH services client")
27482 (description "@code{oai} provides a general purpose client to work with
27483 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
27484 service. Functions are provided to work with the OAI-PMH verbs:
27485 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
27486 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
27487 (license license:expat)))
27489 (define-public r-argon2
27496 (uri (cran-uri "argon2" version))
27499 "09hzl0wz0lw2v7g64rdv0lij2hq36zl37a6rmxwvinmjdzijcsyw"))))
27500 (properties `((upstream-name . "argon2")))
27501 (build-system r-build-system)
27502 (home-page "https://github.com/wrathematics/argon2")
27503 (synopsis "Secure password hashing based on the argon2 algorithm")
27505 "This package provides utilities for secure password hashing via the
27506 argon2 algorithm.")
27507 (license license:bsd-2)))
27509 (define-public r-getpass
27516 (uri (cran-uri "getPass" version))
27519 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
27520 (properties `((upstream-name . "getPass")))
27521 (build-system r-build-system)
27523 (list r-rstudioapi))
27524 (home-page "https://github.com/wrathematics/getPass")
27525 (synopsis "Masked user input")
27527 "This package provides a micro-package for reading \"passwords\", i.e.
27528 reading user input with masking, so that the input is not displayed as it is
27529 typed. Currently, RStudio, the command line (every OS), and any platform
27530 where tcltk is present are supported.")
27531 (license license:bsd-2)))
27533 (define-public r-remoter
27540 (uri (cran-uri "remoter" version))
27543 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
27544 (properties `((upstream-name . "remoter")))
27545 (build-system r-build-system)
27547 (list r-argon2 r-getpass r-pbdzmq r-png))
27548 (home-page "https://github.com/RBigData/remoter")
27549 (synopsis "Control a remote R session from a local one")
27551 "This package provides a set of utilities for client/server computing
27552 with R, controlling a remote R session (the server) from a local one (the
27554 (license license:bsd-2)))
27556 (define-public r-asd
27563 (uri (cran-uri "asd" version))
27566 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
27567 (properties `((upstream-name . "asd")))
27568 (build-system r-build-system)
27571 (home-page "https://cran.r-project.org/web/packages/asd")
27572 (synopsis "Simulations for Adaptive Seamless Designs")
27574 "This package provdes means to run simulations for adaptive seamless
27575 designs with and without early outcomes for treatment selection and
27576 subpopulation type designs.")
27577 (license license:gpl3)))
27579 (define-public r-nbconvertr
27581 (name "r-nbconvertr")
27586 (uri (cran-uri "nbconvertR" version))
27589 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
27590 (properties `((upstream-name . "nbconvertR")))
27591 (build-system r-build-system)
27593 (list python-nbconvert pandoc))
27594 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
27595 (synopsis "Vignette engine wrapping Jupyter notebooks")
27597 "This package calls the Jupyter script @code{nbconvert} to create
27598 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
27599 containing rich text, code, and its output. Code cells can be edited and
27600 evaluated interactively.")
27601 (license license:gpl3)))
27603 (define-public r-bridgesampling
27605 (name "r-bridgesampling")
27610 (uri (cran-uri "bridgesampling" version))
27613 "0sry1xwiv4y52k44hq6z8y2kysp5kxgl4dix3m94svg3ladd7v2l"))))
27615 `((upstream-name . "bridgesampling")))
27616 (build-system r-build-system)
27618 (list r-brobdingnag
27626 (home-page "https://github.com/quentingronau/bridgesampling")
27627 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
27629 "This package provides functions for estimating marginal likelihoods,
27630 Bayes factors, posterior model probabilities, and normalizing constants in
27631 general, via different versions of bridge sampling.")
27632 (license license:gpl2+)))
27634 (define-public r-tea
27641 (uri (cran-uri "tea" version))
27644 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
27646 `((upstream-name . "tea")))
27647 (build-system r-build-system)
27650 (home-page "https://cran.r-project.org/web/packages/tea/")
27651 (synopsis "Threshold estimation approaches")
27653 "This package provides different approaches for selecting the threshold
27654 in generalized Pareto distributions. Most of them are based on minimizing the
27655 AMSE-criterion or at least by reducing the bias of the assumed GPD-model.
27656 Others are heuristically motivated by searching for stable sample paths, i.e.
27657 a nearly constant region of the tail index estimator with respect to k, which
27658 is the number of data in the tail. The third class is motivated by graphical
27659 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
27660 is also implemented here.")
27661 (license license:gpl3)))
27663 (define-public r-awsmethods
27665 (name "r-awsmethods")
27670 (uri (cran-uri "awsMethods" version))
27673 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
27675 `((upstream-name . "awsMethods")))
27676 (build-system r-build-system)
27677 (home-page "http://www.wias-berlin.de/software/imaging/")
27678 (synopsis "Class and methods definitions")
27680 "This package defines the generic method @code{extract} and provides
27681 @code{openMP} support as needed in several packages like
27682 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
27683 (license license:gpl2+)))
27685 (define-public r-aws
27692 (uri (cran-uri "aws" version))
27695 "1fhm87iax6bkvd4vszvjbcqw3b2drs11rjxr7zf2w4sgc72svaz8"))))
27697 `((upstream-name . "aws")))
27698 (build-system r-build-system)
27700 (list r-awsmethods r-gsl))
27703 (home-page "https://cran.r-project.org/web/packages/aws/")
27704 (synopsis "Adaptive weights smoothing")
27706 "This package provides a collection of R-functions implementing adaptive
27707 smoothing procedures in 1D, 2D and 3D. This includes the
27708 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
27709 Confidence Intervals} (ICI), variational approaches, and a non-local means
27711 (license license:gpl2+)))
27713 (define-public r-sgloptim
27715 (name "r-sgloptim")
27720 (uri (cran-uri "sglOptim" version))
27723 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
27725 `((upstream-name . "sglOptim")))
27726 (build-system r-build-system)
27737 (home-page "https://github.com/nielsrhansen/sglOptim")
27738 (synopsis "Generic sparse group Lasso solver")
27740 "This package provides a fast generic solver for sparse group lasso
27741 optimization problems. The loss (objective) function must be defined in a C++
27742 module. The optimization problem is solved using a coordinate gradient
27743 descent algorithm. Convergence of the algorithm is established and the
27744 algorithm is applicable to a broad class of loss functions. Use of parallel
27745 computing for cross validation and subsampling is supported through the
27746 @code{foreach} and @code{doParallel} packages.")
27747 (license license:gpl2+)))
27749 (define-public r-grouped
27756 (uri (cran-uri "grouped" version))
27759 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
27761 `((upstream-name . "grouped")))
27762 (build-system r-build-system)
27765 (home-page "https://cran.r-project.org/web/packages/grouped/")
27766 (synopsis "Regression analysis of grouped and coarse data")
27768 "This package provides regression models for grouped and coarse data,
27769 under the coarsened at random assumption.")
27770 (license license:gpl2+)))
27772 (define-public r-stam
27779 (uri (cran-uri "stam" version))
27782 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
27784 `((upstream-name . "stam")))
27785 (build-system r-build-system)
27788 (home-page "https://cran.r-project.org/web/packages/stam")
27789 (synopsis "Spatio-temporal analysis and modelling")
27791 "This package provides various methods to conduct Spatio-Temporal
27792 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
27793 Inferred Spatio-Temporal Modelling.")
27794 (license license:gpl2+)))
27796 (define-public r-dcv
27803 (uri (cran-uri "dcv" version))
27806 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
27808 `((upstream-name . "dcv")))
27809 (build-system r-build-system)
27812 (home-page "https://cran.r-project.org/web/packages/dcv/")
27813 (synopsis "Conventional cross-validation statistics for climate-growth model")
27815 "This package performs several conventional cross-validation statistical
27816 methods for climate-growth model in the climate reconstruction from tree
27817 rings, including Sign Test statistic, Reduction of Error statistic, Product
27818 Mean Test, Durbin-Watson statistic etc.")
27819 (license license:gpl2)))
27821 (define-public r-rcdd
27828 (uri (cran-uri "rcdd" version))
27831 "0zxx0qvv26ba30jkm8mvca4h59rqklay4jwazpcw7h9dzp4189jr"))))
27833 `((upstream-name . "rcdd")))
27834 (build-system r-build-system)
27837 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
27838 (synopsis "Computational geometry")
27840 "This package converts back and forth between two representations of a
27841 convex polytope: as solution of a set of linear equalities and inequalities
27842 and as convex hull of set of points and rays. Also does linear programming
27843 and redundant generator elimination. All functions can use exact
27844 infinite-precision rational arithmetic.")
27845 (license license:gpl2)))
27847 (define-public r-rxnat
27854 (uri (cran-uri "Rxnat" version))
27857 "0siylypjd8cgcmr2c443w8krg8sgr5gz4zapbinanp8vsfzivdv2"))))
27859 `((upstream-name . "Rxnat")))
27860 (build-system r-build-system)
27862 (list r-httr r-rcurl r-tibble))
27865 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
27866 (synopsis "Queries and extracts images from neuroimaging datasets")
27868 "This package allows communication with the Extensible Neuroimaging
27869 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
27871 (license license:gpl2)))
27873 (define-public r-rserve
27880 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
27881 version ".tar.gz"))
27884 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
27885 (build-system r-build-system)
27888 (modify-phases %standard-phases
27889 (add-before 'install 'install-server-binary
27890 ;; Makevars tries to install to R's store directory.
27891 (lambda* (#:key outputs #:allow-other-keys)
27892 (let* ((out (assoc-ref outputs "out"))
27893 (bin (string-append out "/bin")))
27894 (substitute* "src/Makevars.in"
27895 (("\\$\\(R_HOME\\)") out))
27896 (mkdir-p bin)))))))
27906 (list openssl zlib))
27907 (home-page "https://github.com/s-u/Rserve")
27909 "Server providing access to R from many languages and systems")
27911 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
27912 binary requests to be sent to R. Every connection has a separate workspace
27913 and working directory. Client-side implementations are available for popular
27914 languages such as C/C++ and Java, allowing any application to use facilities
27915 of R without the need of linking to R code. Rserve supports remote
27916 connection, user authentication and file transfer. A simple R client is
27917 included in this package as well.")
27918 (license license:gpl2)))
27920 (define-public r-gamm4
27927 (uri (cran-uri "gamm4" version))
27930 "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap"))))
27931 (properties `((upstream-name . "gamm4")))
27932 (build-system r-build-system)
27934 (list r-lme4 r-matrix r-mgcv))
27935 (home-page "https://cran.r-project.org/web/packages/gamm4/")
27936 (synopsis "Generalized additive mixed models using mgcv and lme4")
27938 "Estimate generalized additive mixed models via a version of function
27939 @code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor
27941 (license license:gpl2+)))
27943 (define-public r-optimx
27946 (version "2022-4.30")
27950 (uri (cran-uri "optimx" version))
27953 "045ls1vl1392ihwln6mngz0zg2w93ym1m607vfrg8v1949x8isgb"))))
27954 (properties `((upstream-name . "optimx")))
27955 (build-system r-build-system)
27956 (propagated-inputs (list r-numderiv))
27957 (native-inputs (list r-knitr))
27958 (home-page "https://cran.r-project.org/web/packages/optimx/")
27959 (synopsis "Expanded replacement and extension of the optim function")
27961 "This package provides a replacement and extension of the @code{optim}
27962 function to call to several function minimization codes in R in a single
27963 statement. These methods handle smooth, possibly box constrained functions of
27964 several or many parameters. Note that the function @code{optimr} was prepared
27965 to simplify the incorporation of minimization codes going forward. This
27966 package also implements some utility codes and some extra solvers, including
27967 safeguarded Newton methods. Many methods previously separate are now included
27969 (license license:gpl2)))
27971 (define-public r-projpred
27973 (name "r-projpred")
27978 (uri (cran-uri "projpred" version))
27981 "1bbjrjaj6zzb1ph69x16i40fj2j6cg8vzmmw2rchsn0ygphaq9b8"))))
27982 (properties `((upstream-name . "projpred")))
27983 (build-system r-build-system)
27997 (native-inputs (list r-knitr))
27998 (home-page "https://mc-stan.org/projpred/")
27999 (synopsis "Projection predictive feature selection")
28001 "This package performs projection predictive feature selection for
28002 generalized linear models and generalized linear and additive multilevel
28003 models. The package is compatible with the @code{rstanarm} and @code{brms}
28004 packages, but other reference models can also be used. See the package
28005 vignette for more information and examples.")
28006 (license license:gpl3)))
28008 (define-public r-distributional
28010 (name "r-distributional")
28015 (uri (cran-uri "distributional" version))
28018 "0pr34yq6igb7ciqss2ldwa7gc55xvla040x8rkd8m2hcrz5mczkj"))))
28020 `((upstream-name . "distributional")))
28021 (build-system r-build-system)
28032 (home-page "https://pkg.mitchelloharawild.com/distributional/")
28033 (synopsis "Vectorized probability distributions")
28035 "This package provides vectorized distribution objects with tools for
28036 manipulating, visualizing, and using probability distributions. It was
28037 designed to allow model prediction outputs to return distributions rather than
28038 their parameters, allowing users to directly interact with predictive
28039 distributions in a data-oriented workflow. In addition to providing generic
28040 replacements for p/d/q/r functions, other useful statistics can be computed
28041 including means, variances, intervals, and highest density regions.")
28042 (license license:gpl3)))
28044 (define-public r-posterior
28046 (name "r-posterior")
28051 (uri (cran-uri "posterior" version))
28054 "0yjdjdr4ifssnml1niqyxs6jsqpci8rx8va0pinyhjx2j017h03h"))))
28055 (properties `((upstream-name . "posterior")))
28056 (build-system r-build-system)
28069 (home-page "https://mc-stan.org/posterior/")
28070 (synopsis "Tools for working with posterior distributions")
28072 "This package provides useful tools for both users and developers of
28073 packages for fitting Bayesian models or working with output from Bayesian
28074 models. The primary goals of the package are to:
28077 @item Efficiently convert between many different useful formats of
28078 draws (samples) from posterior or prior distributions.
28080 @item Provide consistent methods for operations commonly performed on draws,
28081 for example, subsetting, binding, or mutating draws.
28083 @item Provide various summaries of draws in convenient formats.
28085 @item Provide lightweight implementations of state of the art posterior
28086 inference diagnostics.
28089 (license license:bsd-3)))
28091 (define-public r-brms
28098 (uri (cran-uri "brms" version))
28101 "04g10yx66izpghrqip5h9i0w0bds4xw2vlhp6crydi6i7kh4p4b3"))))
28102 (properties `((upstream-name . "brms")))
28103 (build-system r-build-system)
28124 (native-inputs (list r-knitr))
28126 "https://github.com/paul-buerkner/brms")
28128 "Bayesian Regression Models using 'Stan'")
28130 "Fit Bayesian generalized (non-)linear multivariate multilevel models
28131 using 'Stan' for full Bayesian inference. A wide range of distributions and
28132 link functions are supported, allowing users to fit -- among others -- linear,
28133 robust linear, count data, survival, response times, ordinal, zero-inflated,
28134 hurdle, and even self-defined mixture models all in a multilevel context.
28135 Further modeling options include non-linear and smooth terms, auto-correlation
28136 structures, censored data, meta-analytic standard errors, and quite a few
28137 more. In addition, all parameters of the response distribution can be
28138 predicted in order to perform distributional regression. Prior specifications
28139 are flexible and explicitly encourage users to apply prior distributions that
28140 actually reflect their beliefs. Model fit can easily be assessed and compared
28141 with posterior predictive checks and leave-one-out cross-validation.")
28142 (license license:gpl2)))
28144 (define-public r-mstate
28151 (uri (cran-uri "mstate" version))
28154 "054dzrd5b0xjjjl7862q3aq1jwgrxbkqz7zpvbdirqsld3zksirw"))))
28155 (properties `((upstream-name . "mstate")))
28156 (build-system r-build-system)
28167 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
28169 "Data Preparation, Estimation and Prediction in Multi-State Models")
28171 "Contains functions for data preparation, descriptives, hazard estimation
28172 and prediction with Aalen-Johansen or simulation in competing risks and
28173 multi-state models.")
28174 (license license:gpl2+)))
28176 (define-public r-scatterpie
28178 (name "r-scatterpie")
28183 (uri (cran-uri "scatterpie" version))
28186 "183ji1q0wr8fswdrgaw161fvgh8y7j4x9xacf09s2gz6icxcdk56"))))
28187 (properties `((upstream-name . "scatterpie")))
28188 (build-system r-build-system)
28190 (list r-ggforce r-ggfun r-ggplot2 r-rlang r-tidyr))
28193 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
28194 (synopsis "Scatter pie plot")
28196 "This package creates scatterpie plots, especially useful for plotting
28198 (license license:artistic2.0)))
28200 (define-public r-scrypt
28207 (uri (cran-uri "scrypt" version))
28210 "12q9d4m7flbvlgssvjh1ga4jswkmqjfshf6pna6qk6v087gmzdsj"))))
28211 (properties `((upstream-name . "scrypt")))
28212 (build-system r-build-system)
28215 (home-page "https://github.com/rstudio/rscrypt")
28216 (synopsis "Key derivation functions for R based on Scrypt")
28218 "This package provides functions for working with the scrypt key
28219 derivation functions. Scrypt is a password-based key derivation function
28220 created by Colin Percival. The algorithm was specifically designed to make it
28221 costly to perform large-scale custom hardware attacks by requiring large
28222 amounts of memory.")
28223 (license license:bsd-2)))
28225 (define-public r-boruta
28232 (uri (cran-uri "Boruta" version))
28235 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
28236 (properties `((upstream-name . "Boruta")))
28237 (build-system r-build-system)
28238 (propagated-inputs (list r-ranger))
28239 (home-page "https://gitlab.com/mbq/Boruta/")
28240 (synopsis "Wrapper algorithm for all relevant feature selection")
28242 "This package provides an all relevant feature selection wrapper
28243 algorithm. It finds relevant features by comparing original attributes'
28244 importance with importance achievable at random, estimated using their
28245 permuted copies (shadows).")
28246 (license license:gpl2+)))
28248 (define-public r-directlabels
28250 (name "r-directlabels")
28251 (version "2021.1.13")
28255 (uri (cran-uri "directlabels" version))
28258 "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w"))))
28259 (build-system r-build-system)
28264 (home-page "http://directlabels.r-forge.r-project.org/")
28265 (synopsis "Direct labels for multicolor plots")
28267 "This package provides an extensible framework for automatically placing
28268 direct labels onto multicolor plots. Label positions are described using
28269 positioning methods that can be re-used across several different plots. There
28270 are heuristics for examining @code{trellis} and @code{ggplot} objects and
28271 inferring an appropriate positioning method.")
28272 (license license:gpl3)))
28274 (define-public r-lsd
28281 (uri (cran-uri "LSD" version))
28283 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
28284 (properties `((upstream-name . "LSD")))
28285 (build-system r-build-system)
28286 (home-page "https://cran.r-project.org/web/packages/LSD/")
28287 (synopsis "Lots of superior depictions tool creates colorful plots")
28289 "This package creates lots of colorful plots in a multitude of variations.
28290 Try a demo of the LSD by running @code{demotour()}.")
28292 (license (list license:gpl2 license:gpl3))))
28294 (define-public r-phylogram
28296 (name "r-phylogram")
28301 (uri (cran-uri "phylogram" version))
28303 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
28304 (properties `((upstream-name . "phylogram")))
28305 (build-system r-build-system)
28306 (propagated-inputs (list r-ape))
28307 (home-page "https://github.com/ropensci/phylogram/")
28308 (synopsis "Dendrograms for evolutionary analysis")
28310 "The @code{r-phylogram} package is a tool for for developing phylogenetic
28311 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
28312 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
28313 as well as several tools for command-line tree manipulation and import/export
28314 via Newick parenthetic text. This improves accessibility to the comprehensive
28315 range of object-specific analytical and tree-visualization functions found
28316 across a wide array of bioinformatic R packages.")
28317 (license license:gpl3)))
28319 (define-public r-kmer
28326 (uri (cran-uri "kmer" version))
28328 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
28329 (properties `((upstream-name . "kmer")))
28330 (build-system r-build-system)
28332 (list r-openssl r-phylogram r-rcpp))
28333 (home-page "https://github.com/shaunpwilkinson/kmer/")
28334 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
28336 "@code{r-kmer} is an R package for rapidly computing distance matrices
28337 and clustering large sequence datasets using fast alignment-free k-mer
28338 counting and recursive k-means partitioning.")
28339 (license license:gpl3)))
28341 (define-public r-hardhat
28348 (uri (cran-uri "hardhat" version))
28351 "0y5dxpd4gsrs365x1v4qf2vq7hq2qb6f6x50dyj29xmmn760wcpr"))))
28352 (properties `((upstream-name . "hardhat")))
28353 (build-system r-build-system)
28355 (list r-glue r-rlang r-tibble r-vctrs))
28358 (home-page "https://github.com/tidymodels/hardhat")
28359 (synopsis "Construct modeling packages")
28361 "Building modeling packages is hard. A large amount of effort generally
28362 goes into providing an implementation for a new method that is efficient,
28363 fast, and correct, but often less emphasis is put on the user interface. A
28364 good interface requires specialized knowledge about S3 methods and formulas,
28365 which the average package developer might not have. The goal of
28366 @code{hardhat} is to reduce the burden around building new modeling packages
28367 by providing functionality for preprocessing, predicting, and validating
28369 (license license:expat)))
28371 (define-public r-lightgbm
28373 (name "r-lightgbm")
28378 (uri (cran-uri "lightgbm" version))
28381 "1a4nacdpsqd5mr7jnw1g9nyn8w7p0hskfm07cy8yrj3h8a5hmcz8"))))
28382 (properties `((upstream-name . "lightgbm")))
28383 (build-system r-build-system)
28385 (list r-data-table r-jsonlite r-matrix r-r6))
28386 (home-page "https://github.com/Microsoft/LightGBM")
28387 (synopsis "Light gradient boosting machine")
28389 "Tree based algorithms can be improved by introducing boosting
28390 frameworks. LightGBM is one such framework, based on Ke, Guolin et
28391 al. (2017). This package offers an R interface to work with it. It is
28392 designed to be distributed and efficient with the following goals:
28395 @item Faster training speed and higher efficiency;
28396 @item lower memory usage;
28397 @item better accuracy;
28398 @item parallel learning supported; and
28399 @item capable of handling large-scale data.
28402 (license license:expat)))
28404 (define-public r-shapforxgboost
28406 (name "r-shapforxgboost")
28411 (uri (cran-uri "SHAPforxgboost" version))
28414 "106nsf02b1w3yshb55lwnyw1rl1a60162v2wk8znjz3b4ln3mqj5"))))
28416 `((upstream-name . "SHAPforxgboost")))
28417 (build-system r-build-system)
28429 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
28430 (synopsis "SHAP Plots for XGBoost")
28432 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
28433 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
28434 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
28435 and force plot. It relies on the @code{XGBoost} package to produce SHAP
28437 (license license:expat)))
28439 (define-public r-rismed
28446 (uri (cran-uri "RISmed" version))
28449 "0vpi88gzi9r85v6nhjz9jbw671zkrmyazwna2z881346wfyr3l8b"))))
28450 (properties `((upstream-name . "RISmed")))
28451 (build-system r-build-system)
28453 (list r-httr r-xml2))
28454 (home-page "https://cran.r-project.org/web/packages/RISmed")
28455 (synopsis "Download content from NCBI databases")
28457 "This package provides a set of tools to extract bibliographic
28458 content from the National Center for Biotechnology Information (NCBI)
28459 databases, including PubMed. The name RISmed is a portmanteau of
28460 RIS (for Research Information Systems, a common tag format for
28461 bibliographic data) and PubMed.")
28462 (license license:gpl2+)))
28464 (define-public r-semver
28471 (uri (cran-uri "semver" version))
28474 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
28475 (properties `((upstream-name . "semver")))
28476 (build-system r-build-system)
28478 (list r-assertthat r-rcpp))
28479 (native-inputs (list r-knitr))
28480 (home-page "https://github.com/johndharrison/semver")
28481 (synopsis "Parser for Semantic Versioning 2.0.0")
28483 "This package provides tools and functions for parsing, rendering and
28484 operating on semantic version strings. Semantic versioning is a simple set of
28485 rules and requirements that dictate how version numbers are assigned and
28486 incremented as outlined at @url{http://semver.org}.")
28487 (license license:expat)))
28489 (define-public r-binman
28496 (uri (cran-uri "binman" version))
28499 "1xz9ky3axidm0fp518rj80ma6q14ybyvashil79hhkk3iqmx0lhw"))))
28500 (properties `((upstream-name . "binman")))
28501 (build-system r-build-system)
28510 (native-inputs (list r-knitr))
28511 (home-page "https://github.com/ropensci/binman")
28512 (synopsis "Binary download manager")
28514 "This package provides tools and functions for managing the download of
28515 binary files. Binary repositories are defined in the YAML format. Defining
28516 new pre-download, download and post-download templates allow additional
28517 repositories to be added.")
28518 (license license:expat)))
28520 (define-public r-wdman
28527 (uri (cran-uri "wdman" version))
28530 "0n0wwb9ip6qc8qzdxn4dsqfbc8b3f607n8l6jigryd7g83ibnbp6"))))
28531 (properties `((upstream-name . "wdman")))
28532 (build-system r-build-system)
28534 (list r-assertthat r-binman r-processx r-semver r-yaml))
28535 (native-inputs (list r-knitr))
28536 (home-page "https://docs.ropensci.org/wdman/")
28537 (synopsis "Webdriver/Selenium binary manager")
28539 "There are a number of binary files associated with the
28540 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
28541 @url{https://sites.google.com/a/chromium.org/chromedriver/},
28542 @url{https://github.com/mozilla/geckodriver},
28543 @url{http://phantomjs.org/download.html}, and
28544 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
28545 more information). This package provides functions to download these binaries
28546 and to manage processes involving them.")
28547 (license license:expat)))
28549 (define-public r-rselenium
28551 (name "r-rselenium")
28556 (uri (cran-uri "RSelenium" version))
28559 "18hd0gfpblg9ij99ik7ccc60q9dxha89n5rrwrrzx498c5sscjg2"))))
28560 (properties `((upstream-name . "RSelenium")))
28561 (build-system r-build-system)
28566 (native-inputs (list r-knitr))
28567 (home-page "https://docs.ropensci.org/RSelenium/")
28568 (synopsis "R bindings for Selenium WebDriver")
28570 "This package provides a set of R bindings for the Selenium 2.0
28571 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
28572 information) using the @code{JsonWireProtocol} (see
28573 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
28574 information). Selenium 2.0 WebDriver allows driving a web browser natively as
28575 a user would either locally or on a remote machine using the Selenium server
28576 it marks a leap forward in terms of web browser automation. Selenium
28577 automates web browsers (commonly referred to as browsers). Using RSelenium
28578 you can automate browsers locally or remotely.")
28579 (license license:agpl3+)))
28581 (define-public r-conquer
28588 (uri (cran-uri "conquer" version))
28591 "1mdwm0aanq4rx3042djvs0l2vkdx6zbzvrjfyfb9dhv0gfs8mhhl"))))
28592 (properties `((upstream-name . "conquer")))
28593 (build-system r-build-system)
28595 (list r-matrix r-matrixstats r-rcpp r-rcpparmadillo))
28596 (home-page "https://github.com/XiaoouPan/conquer")
28597 (synopsis "Convolution-type smoothed quantile regression")
28599 "This package provides fast and accurate convolution-type smoothed
28600 quantile regression, implemented using Barzilai-Borwein gradient descent with
28601 a Huber regression warm start. Confidence intervals for regression
28602 coefficients are constructed using multiplier bootstrap.")
28603 (license license:gpl3)))
28605 (define-public r-fastshap
28607 (name "r-fastshap")
28612 (uri (cran-uri "fastshap" version))
28615 "0gxch67i3bj6m8nb94m5hswq058w6n1q9war4dy2qnimlv7cmhdv"))))
28616 (properties `((upstream-name . "fastshap")))
28617 (build-system r-build-system)
28627 (home-page "https://github.com/bgreenwell/fastshap")
28628 (synopsis "Fast approximate Shapley values")
28630 "This package computes fast (relative to other implementations)
28631 approximate Shapley values for any supervised learning model. Shapley values
28632 help to explain the predictions from any black box model using ideas from game
28633 theory; see @url{Strumbel and Kononenko (2014),
28634 doi.org/10.1007/s10115-013-0679-x} for details.")
28635 (license license:gpl2+)))
28637 (define-public r-memuse
28643 (uri (cran-uri "memuse" version))
28646 "1wvwnjaaiv2647561z2b55dss35033ildx4kk8hzxfzgsjmdpsgm"))))
28647 (properties `((upstream-name . "memuse")))
28648 (build-system r-build-system)
28649 (home-page "https://github.com/shinra-dev/memuse")
28650 (synopsis "Memory Estimation Utilities")
28652 "This package provides procedures to answer the following questions:
28653 How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is
28654 your current R session using? How much ram do you even have?")
28655 (license license:bsd-2)))
28657 (define-public r-metrics
28664 (uri (cran-uri "Metrics" version))
28667 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
28668 (properties `((upstream-name . "Metrics")))
28669 (build-system r-build-system)
28670 (home-page "https://github.com/mfrasco/Metrics")
28671 (synopsis "Evaluation metrics for machine learning")
28673 "This package provides an implementation of evaluation metrics in R that
28674 are commonly used in supervised machine learning. It implements metrics for
28675 regression, time series, binary classification, classification, and
28676 information retrieval problems. It has zero dependencies and a consistent,
28677 simple interface for all functions.")
28678 (license license:bsd-3)))
28680 (define-public r-iml
28687 (uri (cran-uri "iml" version))
28690 "0fi37lv9czaxcc123f6r57607shqhs83ks96n2n0b93dl1qs0j52"))))
28691 (properties `((upstream-name . "iml")))
28692 (build-system r-build-system)
28703 (native-inputs (list r-knitr))
28704 (home-page "https://github.com/christophM/iml")
28705 (synopsis "Interpretable machine learning")
28707 "This package provides interpretability methods to analyze the behavior
28708 and predictions of any machine learning model. Implemented methods are:
28711 @item Feature importance described by Fisher et al. (2018),
28712 @item accumulated local effects plots described by Apley (2018),
28713 @item partial dependence plots described by Friedman (2001),
28714 @item individual conditional expectation ('ice') plots described by Goldstein
28715 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
28716 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
28717 @item the Shapley Value described by Strumbelj et. al (2014)
28718 @url{https://doi.org/10.1007/s10115-013-0679-x},
28719 @item feature interactions described by Friedman et. al
28720 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
28723 (license license:expat)))
28725 (define-public r-goftest
28732 (uri (cran-uri "goftest" version))
28735 "06bz6k7smr4jbvzmb73qc5fkf4my59w5gbl18wlmpkkymsv78prs"))))
28736 (properties `((upstream-name . "goftest")))
28737 (build-system r-build-system)
28738 (home-page "https://github.com/baddstats/goftest")
28739 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
28741 "This package provides Cramer-Von Mises and Anderson-Darling tests of
28742 goodness-of-fit for continuous univariate distributions, using efficient
28744 (license license:gpl2+)))
28746 (define-public r-tensor
28753 (uri (cran-uri "tensor" version))
28756 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
28757 (properties `((upstream-name . "tensor")))
28758 (build-system r-build-system)
28759 (home-page "https://cran.r-project.org/web/packages/tensor/")
28760 (synopsis "Tensor product of arrays")
28762 "The tensor product of two arrays is notionally an outer product of the
28763 arrays collapsed in specific extents by summing along the appropriate
28764 diagonals. This package allows you to compute the tensor product of arrays.")
28765 (license license:gpl2+)))
28767 (define-public r-spatstat-utils
28769 (name "r-spatstat-utils")
28774 (uri (cran-uri "spatstat.utils" version))
28777 "06mrw3nc2pqz4897i7wqy04mdfnn6drggv8mr92r3zb4cn0cg8fb"))))
28779 `((upstream-name . "spatstat.utils")))
28780 (build-system r-build-system)
28781 (home-page "http://www.spatstat.org")
28782 (synopsis "Utility functions for spatstat")
28784 "This package contains utility functions for the @code{spatstat} package
28785 which may also be useful for other purposes.")
28786 (license license:gpl2+)))
28788 (define-public r-spatstat-sparse
28790 (name "r-spatstat-sparse")
28795 (uri (cran-uri "spatstat.sparse" version))
28798 "1lhsa1gjahz6sp1yrlch0d01rnayyw8hip382vghyxljfly0mglr"))))
28800 `((upstream-name . "spatstat.sparse")))
28801 (build-system r-build-system)
28803 (list r-abind r-matrix r-spatstat-utils r-tensor))
28804 (home-page "http://spatstat.org/")
28805 (synopsis "Sparse three-dimensional arrays and linear algebra utilities")
28807 "This package defines sparse three-dimensional arrays and supports
28808 standard operations on them. The package also includes utility functions for
28809 matrix calculations that are common in statistics, such as quadratic forms.")
28810 (license license:gpl2+)))
28812 (define-public r-spatstat-data
28814 (name "r-spatstat-data")
28819 (uri (cran-uri "spatstat.data" version))
28822 "0mvh33sk2sfhfk276j088adzldrg8p6pd5avl2j21428i250byfg"))))
28823 (properties `((upstream-name . "spatstat.data")))
28824 (build-system r-build-system)
28826 (list r-matrix r-spatstat-utils))
28827 (home-page "http://www.spatstat.org")
28828 (synopsis "Datasets for spatstat")
28830 "This package contains all the datasets for the @code{spatstat}
28832 (license license:gpl2+)))
28834 (define-public r-spatstat-geom
28836 (name "r-spatstat-geom")
28841 (uri (cran-uri "spatstat.geom" version))
28844 "111wj507i2mxi0ak8sj468w26pr2f7hgv3ssmbf0qjkp1v35cnvf"))))
28845 (properties `((upstream-name . "spatstat.geom")))
28846 (build-system r-build-system)
28848 (list r-deldir r-polyclip r-spatstat-data r-spatstat-utils))
28849 (home-page "http://spatstat.org/")
28850 (synopsis "Geometrical functionality of the spatstat package")
28852 "This is a subset of the original spatstat package, containing the
28853 user-level code from spatstat which performs geometrical operations, except
28854 for the geometry of linear networks.")
28855 (license license:gpl2+)))
28857 (define-public r-spatstat-core
28859 (name "r-spatstat-core")
28864 (uri (cran-uri "spatstat.core" version))
28867 "0fyi8y1z919nzn47kaviln7gflhcp5qdi3gfvf7nwkdix3pkk373"))))
28868 (properties `((upstream-name . "spatstat.core")))
28869 (build-system r-build-system)
28883 (home-page "http://spatstat.org/")
28884 (synopsis "Core functionality of the spatstat package")
28886 "This is a subset of the original spatstat package, containing all of the
28887 user-level code from spatstat, except for the code for linear networks.")
28888 (license license:gpl2+)))
28890 (define-public r-spatstat-linnet
28892 (name "r-spatstat-linnet")
28897 (uri (cran-uri "spatstat.linnet" version))
28900 "0y1py6x0xbw4ad3pjwcspi4ysgfh61f5fd79787zzgyyh2va8y4w"))))
28902 `((upstream-name . "spatstat.linnet")))
28903 (build-system r-build-system)
28912 (home-page "http://spatstat.org/")
28913 (synopsis "Linear networks functionality of the spatstat package")
28915 "This is a subset of the spatstat package, containing its functionality
28916 for spatial data on a linear network.")
28917 (license license:gpl2+)))
28919 (define-public r-spatstat-random
28921 (name "r-spatstat-random")
28926 (uri (cran-uri "spatstat.random" version))
28928 (base32 "0kb01s8k67ydcfqcnz3i55vpiksihh4xsg0w2p2bclxxkpdvpw25"))))
28929 (properties `((upstream-name . "spatstat.random")))
28930 (build-system r-build-system)
28931 (propagated-inputs (list r-spatstat-data r-spatstat-geom r-spatstat-utils))
28932 (home-page "http://spatstat.org/")
28933 (synopsis "Random Generation Functionality for the 'spatstat' Family")
28935 "This package provides functionality for random generation of spatial
28936 data in the spatstat family of packages. It generates random spatial patterns
28937 of points according to many simple rules (complete spatial randomness,
28938 Poisson, binomial, random grid, systematic, cell), randomised alteration of
28939 patterns (thinning, random shift, jittering), simulated realisations of random
28940 point processes (simple sequential inhibition, Matern inhibition models,
28941 Matern cluster process, Neyman-Scott cluster processes, log-Gaussian Cox
28942 processes, product shot noise cluster processes) and simulation of Gibbs point
28943 processes (Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs
28945 (license license:gpl2+)))
28947 (define-public r-spatstat
28949 (name "r-spatstat")
28954 (uri (cran-uri "spatstat" version))
28957 "1nlrp7660y68axlm4pczc5rxbdhbbac1ylh69azr4swj1gbzi82f"))))
28958 (properties `((upstream-name . "spatstat")))
28959 (build-system r-build-system)
28961 (list r-spatstat-core r-spatstat-data r-spatstat-geom
28962 r-spatstat-linnet r-spatstat-random r-spatstat-utils))
28963 (home-page "http://www.spatstat.org")
28964 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
28966 "This package provides a comprehensive toolbox for analysing Spatial
28967 Point Patterns. It is focused mainly on two-dimensional point patterns,
28968 including multitype/marked points, in any spatial region. It also supports
28969 three-dimensional point patterns, space-time point patterns in any number of
28970 dimensions, point patterns on a linear network, and patterns of other
28971 geometrical objects. It supports spatial covariate data such as pixel images
28972 and contains over 2000 functions for plotting spatial data, exploratory data
28973 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
28974 formal inference.")
28975 (license license:gpl2+)))
28977 (define-public r-gaston
28984 (uri (cran-uri "gaston" version))
28987 "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i"))))
28988 (properties `((upstream-name . "gaston")))
28989 (build-system r-build-system)
28990 (inputs (list zlib))
28992 (list r-rcpp r-rcppeigen r-rcppparallel))
28993 (native-inputs (list r-knitr))
28994 (home-page "https://cran.r-project.org/web/packages/gaston/")
28995 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
28997 "This is a package for the manipulation of genetic data (SNPs).
28998 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
28999 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
29000 for linear mixed models (AIREML).")
29001 (license license:gpl3)))
29003 (define-public r-cpp11
29010 (uri (cran-uri "cpp11" version))
29013 "1wcq4lq7xa62xn6zsg6r8nf6vdlvnlwxgfqndb7vnvd8f54hx9pi"))))
29014 (properties `((upstream-name . "cpp11")))
29015 (build-system r-build-system)
29016 (native-inputs (list r-knitr))
29017 (home-page "https://github.com/r-lib/cpp11")
29018 (synopsis "C++11 Interface for R's C Interface")
29020 "This package provides a header only, C++11 interface to R's C interface.
29021 Compared to other approaches @code{cpp11} strives to be safe against long
29022 jumps from the C API as well as C++ exceptions, conform to normal R function
29023 semantics and supports interaction with @code{ALTREP} vectors.")
29024 (license license:expat)))
29026 (define-public r-rcpptoml
29028 (name "r-rcpptoml")
29033 (uri (cran-uri "RcppTOML" version))
29035 (base32 "0h8517ipwqhqkhcfiyqmvsb585g01p0ra0azbpzyxip6pq6g029g"))))
29036 (properties `((upstream-name . "RcppTOML")))
29037 (build-system r-build-system)
29038 (propagated-inputs (list r-rcpp))
29039 (home-page "http://dirk.eddelbuettel.com/code/rcpp.toml.html")
29040 (synopsis "Rcpp bindings to TOML parser")
29042 "The TOML configuration format specifies an excellent format suitable for
29043 both human editing as well as the common uses of a machine-readable format.
29044 This package provides Rcpp bindings to a TOML parser.")
29045 (license license:gpl2+)))
29047 (define-public r-rcppziggurat
29049 (name "r-rcppziggurat")
29054 (uri (cran-uri "RcppZiggurat" version))
29057 "0wgd1v2p7zajnbrjf3hfi56p3pk3ld6iwkanbb04bjbnlif2ay4w"))))
29058 (properties `((upstream-name . "RcppZiggurat")))
29059 (build-system r-build-system)
29061 (list r-rcpp r-rcppgsl))
29062 (native-inputs (list r-knitr))
29063 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
29064 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
29066 "The Ziggurat generator for normally distributed random numbers,
29067 originally proposed by Marsaglia and Tsang (2000,
29068 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
29069 times starting with Leong et al (2005,
29070 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
29071 aggregation for comparing different implementations in order to provide a
29072 'faster but good enough' alternative for use with R and C++ code.")
29073 (license license:gpl2+)))
29075 (define-public r-rfast
29082 (uri (cran-uri "Rfast" version))
29085 "0zxykq021h57mq0n6giqbx8ncjsdly0arhmaj3fcp3yfcxf4ns9l"))))
29086 (properties `((upstream-name . "Rfast")))
29087 (build-system r-build-system)
29089 (list r-rcpp r-rcpparmadillo r-rcppziggurat))
29090 (home-page "https://github.com/RfastOfficial/Rfast")
29091 (synopsis "Collection of efficient and fast R functions")
29093 "This package provides a collection of fast (utility) functions for data
29094 analysis. Column- and row- wise means, medians, variances, minimums,
29095 maximums, many t, F and G-square tests, many regressions (normal, logistic,
29096 Poisson), are some of the many fast functions.")
29097 (license license:gpl2+)))
29099 (define-public r-rffc
29105 (uri (string-append
29106 "https://download.r-forge.r-project.org/src/contrib/"
29107 "rfFC_" version ".tar.gz"))
29110 "05x9wgzsmx4vb12lmcspymgmpb2xw8bwryb8ysg7vzg2nkh0ma3g"))))
29111 (build-system r-build-system)
29113 (list r-randomforest))
29114 (home-page "https://r-forge.r-project.org/projects/rffc/")
29115 (synopsis "Random Forest Feature Contributions")
29116 (description "This package provides functions for extracting feature
29117 contributions from a random forest model from package @code{randomForest}.
29118 Feature contributions provide detailed information about the relationship
29119 between data variables and the predicted value returned by random forest
29121 (license license:gpl2)))
29123 (define-public r-clusterr
29125 (name "r-clusterr")
29130 (uri (cran-uri "ClusterR" version))
29133 "1sl218scrf5s02v54bmmk2sz1vrnlq16c14c0lcg1n7x8d76sgk6"))))
29134 (properties `((upstream-name . "ClusterR")))
29135 (build-system r-build-system)
29143 (native-inputs (list r-knitr))
29144 (home-page "https://github.com/mlampros/ClusterR")
29145 (synopsis "Clustering")
29147 "This package provides Gaussian mixture models, k-means,
29148 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
29149 option to plot, validate, predict (new data) and estimate the optimal number
29150 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
29151 the computationally intensive parts of the functions. For more information,
29155 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
29156 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
29157 @url{https://doi.org/10.18637/jss.v001.i04};
29158 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
29159 Library, @url{https://doi.org/10.1145/1772690.1772862};
29160 @item \"Armadillo: a template-based C++ library
29161 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
29162 Software, @url{https://doi.org/10.21105/joss.00026};
29163 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
29164 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
29165 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
29168 (license license:gpl3)))
29170 (define-public r-spectrum
29172 (name "r-spectrum")
29177 (uri (cran-uri "Spectrum" version))
29180 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
29181 (properties `((upstream-name . "Spectrum")))
29182 (build-system r-build-system)
29184 (list r-clusterr r-diptest r-ggplot2 r-rfast))
29185 (native-inputs (list r-knitr))
29186 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
29187 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
29189 "This package provides a self-tuning spectral clustering method for
29190 single or multi-view data. Spectrum uses a new type of adaptive density aware
29191 kernel that strengthens connections in the graph based on common nearest
29192 neighbours. It uses a tensor product graph data integration and diffusion
29193 procedure to integrate different data sources and reduce noise. Spectrum uses
29194 either the eigengap or multimodality gap heuristics to determine the number of
29195 clusters. The method is sufficiently flexible so that a wide range of
29196 Gaussian and non-Gaussian structures can be clustered with automatic selection
29198 (license license:agpl3+)))
29200 (define-public r-nabor
29207 (uri (cran-uri "nabor" version))
29210 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
29211 (properties `((upstream-name . "nabor")))
29212 (build-system r-build-system)
29214 (list r-bh r-rcpp r-rcppeigen))
29215 (home-page "https://cran.r-project.org/web/packages/nabor/")
29216 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
29218 "This package provides an R wrapper for libnabo, an exact or approximate
29219 k nearest neighbour library which is optimised for low dimensional
29220 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
29221 designed as a drop-in replacement for the RANN function @code{nn2}. In
29222 addition, objects which include the k-d tree search structure can be returned
29223 to speed up repeated queries of the same set of target points.")
29224 (license license:bsd-3)))
29226 (define-public r-naturalsort
29228 (name "r-naturalsort")
29232 (uri (cran-uri "naturalsort" version))
29235 "0mz801y9mzld9ypp3xmsjw2d8l9q97sdnv09wrci9xi3yg2sjf6d"))))
29236 (build-system r-build-system)
29237 (home-page "https://cran.r-project.org/web/packages/naturalsort/")
29238 (synopsis "Natural ordering")
29239 (description "This package provides functions related to human natural
29240 ordering. It handles adjacent digits in a character sequence as a number
29241 so that natural sort function arranges a character vector by their numbers,
29242 not digit characters.")
29243 (license license:bsd-3)))
29245 (define-public r-visdat
29251 (uri (cran-uri "visdat" version))
29254 "1ikqp29nncbw1xlwyb9dqqgcdk9q0bs3wxhnhnjpb11vcjv7cz2j"))))
29255 (build-system r-build-system)
29267 (home-page "https://visdat.njtierney.com/")
29268 (synopsis "Preliminary Visualisation of Data")
29269 (description "This package provides procedures to create preliminary exploratory
29270 data visualisations of an entire dataset to identify problems or unexpected features
29271 using @code{ggplot2}.")
29272 (license license:expat)))
29274 (define-public r-muhaz
29277 (version "1.2.6.4")
29281 (uri (cran-uri "muhaz" version))
29284 "1ddy8ayr4rdhzcipdvxdwd7z5g9hfp0ppacl7xf6f2612cn1185g"))))
29285 (properties `((upstream-name . "muhaz")))
29286 (build-system r-build-system)
29291 (home-page "https://cran.r-project.org/web/packages/muhaz/")
29292 (synopsis "Hazard function estimation in survival analysis")
29294 "This package produces a smooth estimate of the hazard function for
29296 ;; Any version of the GPL.
29297 (license license:gpl3+)))
29299 (define-public r-flexsurv
29301 (name "r-flexsurv")
29306 (uri (cran-uri "flexsurv" version))
29309 "0244amsyf2izih6008n2535r3ddksgdnys8pyslrcb1c09spmjrw"))))
29310 (properties `((upstream-name . "flexsurv")))
29311 (build-system r-build-system)
29336 (home-page "https://github.com/chjackson/flexsurv-dev")
29337 (synopsis "Flexible parametric survival and multi-state models")
29339 "This package provides flexible parametric models for time-to-event data,
29340 including the Royston-Parmar spline model, generalized gamma and generalized F
29341 distributions. Any user-defined parametric distribution can be fitted, given
29342 at least an R function defining the probability density or hazard. There are
29343 also tools for fitting and predicting from fully parametric multi-state
29345 (license license:gpl2+)))
29347 (define-public r-transphylo
29349 (name "r-transphylo")
29354 (uri (cran-uri "TransPhylo" version))
29357 "0g92kwi1nlmpc8m4pc9kv9xhczryr2kn9icfr3js7da7vy8g50xy"))))
29358 (properties `((upstream-name . "TransPhylo")))
29359 (build-system r-build-system)
29361 (list r-ape r-rcpp))
29364 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
29365 (synopsis "Inference of transmission tree from a dated phylogeny")
29367 "This is a package to infer transmission trees from a dated phylogeny.
29368 It includes methods to simulate and analyze outbreaks. The methodology is
29369 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
29370 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
29371 (license license:gpl2+)))
29373 (define-public r-km-ci
29380 (uri (cran-uri "km.ci" version))
29383 "18sc9vhbdgks8lhk2nfxkkayh8j4j227hl63fm5p04f7z4wm6wc1"))))
29384 (properties `((upstream-name . "km.ci")))
29385 (build-system r-build-system)
29388 (home-page "https://cran.r-project.org/web/packages/km.ci/")
29389 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
29391 "This package computes various @dfn{confidence intervals} (CI) for the
29392 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
29393 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
29394 Nair and Hall and Wellner.")
29395 (license license:gpl2+)))
29397 (define-public r-kmsurv
29404 (uri (cran-uri "KMsurv" version))
29407 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
29408 (properties `((upstream-name . "KMsurv")))
29409 (build-system r-build-system)
29410 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
29411 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
29413 "This package provides data sets and functions for Klein and Moeschberger
29414 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
29416 (license license:gpl3+)))
29418 (define-public r-survmisc
29420 (name "r-survmisc")
29425 (uri (cran-uri "survMisc" version))
29428 "014cf7sfndmib9jmj0p3h67sr750k2pvw7m865zwdpvlqddi44fr"))))
29429 (properties `((upstream-name . "survMisc")))
29430 (build-system r-build-system)
29443 (home-page "https://cran.r-project.org/web/packages/survMisc/")
29444 (synopsis "Miscellaneous functions for survival data")
29446 "This package provides a collection of functions to help in the analysis
29447 of right-censored survival data. These extend the methods available in
29448 the @code{survival} package.")
29449 (license license:gpl2)))
29451 (define-public r-exactranktests
29453 (name "r-exactranktests")
29458 (uri (cran-uri "exactRankTests" version))
29461 "1qv9i57chhz8xiv0j8r47rbigyqs72fa7ssz99inyc0s8gzskd3y"))))
29463 `((upstream-name . "exactRankTests")))
29464 (build-system r-build-system)
29465 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
29466 (synopsis "Exact distributions for rank and permutation tests")
29468 "This package computes exact conditional p-values and quantiles using an
29469 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
29470 (license license:gpl2+)))
29472 (define-public r-maxstat
29479 (uri (cran-uri "maxstat" version))
29482 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
29483 (properties `((upstream-name . "maxstat")))
29484 (build-system r-build-system)
29486 (list r-exactranktests r-mvtnorm))
29487 (home-page "https://cran.r-project.org/web/packages/maxstat/")
29488 (synopsis "Maximally selected rank statistics")
29490 "This package provides maximally selected rank statistics with several
29491 p-value approximations.")
29492 (license license:gpl2+)))
29494 (define-public r-survminer
29496 (name "r-survminer")
29501 (uri (cran-uri "survminer" version))
29504 "0byh0wxdbjfwdrzsnqv4xlmnik6lj0vkkzfxy7lssk8dv5zmj7nz"))))
29505 (properties `((upstream-name . "survminer")))
29506 (build-system r-build-system)
29525 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
29526 (synopsis "Drawing survival curves using ggplot2")
29528 "This package contains the function @code{ggsurvplot()} for easily
29529 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
29530 risk' table and 'censoring count plot'. Other functions are also available to
29531 plot adjusted curves for Cox model and to visually examine Cox model
29533 (license license:gpl2)))
29535 (define-public r-forge
29542 (uri (cran-uri "forge" version))
29545 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
29546 (properties `((upstream-name . "forge")))
29547 (build-system r-build-system)
29549 (list r-magrittr r-rlang))
29550 (home-page "https://cran.r-project.org/web/packages/forge/")
29551 (synopsis "Cast values into shape")
29553 "This package provides helper functions with a consistent interface to
29554 coerce and verify the types and shapes of values for input checking.")
29555 (license license:asl2.0)))
29557 (define-public r-config
29564 (uri (cran-uri "config" version))
29567 "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l"))))
29568 (properties `((upstream-name . "config")))
29569 (build-system r-build-system)
29574 (home-page "https://github.com/rstudio/config")
29575 (synopsis "Manage environment specific configuration values")
29577 "This package lets you manage configuration values across multiple
29578 environments (e.g. development, test, production). It reads values using a
29579 function that determines the current environment and returns the appropriate
29581 (license license:gpl3)))
29583 (define-public r-confintr
29585 (name "r-confintr")
29589 (uri (cran-uri "confintr" version))
29592 "1zpprv5ysmnqn83xdsixsm6jhsi1gck32z6x60gp0y8xs25mwcbg"))))
29593 (properties `((upstream-name . "confintr")))
29594 (build-system r-build-system)
29595 (propagated-inputs (list r-boot))
29596 (native-inputs (list r-knitr))
29597 (home-page "https://github.com/mayer79/confintr")
29598 (synopsis "Confidence intervals")
29600 "This package calculates classic and/or bootstrap confidence intervals
29601 for many parameters such as the population mean, variance, @dfn{interquartile
29602 range} (IQR), @dfn{median absolute deviation} (MAD), skewness, kurtosis,
29603 Cramer's V, odds ratio, R-squared, quantiles (including median), proportions,
29604 different types of correlation measures, difference in means, quantiles and
29605 medians. Many of the classic confidence intervals are described in Smithson,
29606 M. (2003, ISBN: 978-0761924999). Bootstrap confidence intervals are
29607 calculated with the R package @code{boot}. Both one- and two-sided intervals
29609 (license license:gpl2+)))
29611 (define-public r-adaptivesparsity
29613 (name "r-adaptivesparsity")
29617 (uri (cran-uri "AdaptiveSparsity" version))
29620 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
29622 `((upstream-name . "AdaptiveSparsity")))
29623 (build-system r-build-system)
29626 (modify-phases %standard-phases
29627 (add-after 'unpack 'link-against-armadillo
29629 (substitute* "src/Makevars"
29630 (("PKG_LIBS=" prefix)
29631 (string-append prefix "-larmadillo")))
29634 (list r-mass r-matrix r-rcpp r-rcpparmadillo))
29637 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
29638 (synopsis "Adaptive sparsity models")
29640 "This package implements the Figueiredo machine learning algorithm for
29641 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
29642 geometric models.")
29643 (license license:lgpl3+)))
29645 (define-public r-add2ggplot
29647 (name "r-add2ggplot")
29652 (uri (cran-uri "add2ggplot" version))
29654 (base32 "0c94i1cfp2pvplvxmfvvz2fyj026r1jnax05mrzrc7ppnqzy25y0"))))
29655 (properties `((upstream-name . "add2ggplot")))
29656 (build-system r-build-system)
29658 (list r-ggplot2 r-magick r-magrittr r-rcolorbrewer r-zeallot))
29659 (native-inputs (list r-knitr))
29660 (home-page "https://github.com/JiaxiangBU/add2ggplot")
29661 (synopsis "Extension for ggplot2")
29662 (description "This package provides tools to create themes and color
29663 palettes for the package ggplot2.")
29664 (license license:expat)))
29666 (define-public r-diffusionmap
29668 (name "r-diffusionmap")
29673 (uri (cran-uri "diffusionMap" version))
29676 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
29677 (properties `((upstream-name . "diffusionMap")))
29678 (build-system r-build-system)
29680 (list r-igraph r-matrix r-scatterplot3d))
29681 (home-page "https://www.r-project.org")
29682 (synopsis "Diffusion map")
29683 (description "This package implements the diffusion map method of data
29684 parametrization, including creation and visualization of diffusion maps,
29685 clustering with diffusion K-means and regression using the adaptive regression
29687 (license license:gpl2)))
29689 (define-public r-igraph
29696 (uri (cran-uri "igraph" version))
29699 "1m4vbc1v2wvjn9df7w9ax0zpr3ys566bqazcakx7vddmnrkmsqcy"))))
29700 (build-system r-build-system)
29704 (list gmp glpk libxml2 zlib))
29706 (list r-magrittr r-matrix r-pkgconfig r-rlang))
29707 (home-page "https://igraph.org")
29708 (synopsis "Network analysis and visualization")
29710 "This package provides routines for simple graphs and network analysis.
29711 It can handle large graphs very well and provides functions for generating
29712 random and regular graphs, graph visualization, centrality methods and much
29714 (license license:gpl2+)))
29716 (define-public r-workflows
29718 (name "r-workflows")
29723 (uri (cran-uri "workflows" version))
29726 "0l5v5qmgj1qv2bk50kv59k2nydh1r97hmqffyxkfpkh2121b2qaq"))))
29727 (properties `((upstream-name . "workflows")))
29728 (build-system r-build-system)
29741 (home-page "https://github.com/tidymodels/workflows")
29742 (synopsis "Modeling workflows")
29744 "A workflow is an object that can bundle together your pre-processing,
29745 modeling, and post-processing requests. For example, if you have a
29746 @code{recipe} and @code{parsnip} model, these can be combined into a
29747 workflow. The advantages are:
29750 @item You don’t have to keep track of separate objects in your workspace.
29751 @item The recipe prepping and model fitting can be executed using a single
29752 call to @code{fit()}.
29753 @item If you have custom tuning parameter settings, these can be defined using
29754 a simpler interface when combined with @code{tune}.
29755 @item In the future, workflows will be able to add post-processing operations,
29756 such as modifying the probability cutoff for two-class models.
29759 (license license:expat)))
29761 (define-public r-lobstr
29768 (uri (cran-uri "lobstr" version))
29771 "060p7b7i2qx09d7nf0kdl85r9j886fivrkrsl2bn10cggvnk7icv"))))
29772 (properties `((upstream-name . "lobstr")))
29773 (build-system r-build-system)
29779 (home-page "https://github.com/r-lib/lobstr")
29780 (synopsis "Visualize R data structures with trees")
29782 "This package provides a set of tools for inspecting and understanding R
29783 data structures inspired by @code{str}. It includes @code{ast} for
29784 visualizing abstract syntax trees, @code{ref} for showing shared references,
29785 @code{cst} for showing call stack trees, and @code{obj_size} for computing
29787 (license license:gpl3)))
29789 (define-public r-gpfit
29796 (uri (cran-uri "GPfit" version))
29799 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
29800 (properties `((upstream-name . "GPfit")))
29801 (build-system r-build-system)
29803 (list r-lattice r-lhs))
29804 (home-page "https://cran.r-project.org/web/packages/GPfit/")
29805 (synopsis "Gaussian Processes modeling")
29807 "This package provides a computationally stable approach of fitting a
29808 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
29809 (license license:gpl2)))
29811 (define-public r-yardstick
29813 (name "r-yardstick")
29818 (uri (cran-uri "yardstick" version))
29821 "0bcirq9mp7c6kwx563nnsd4lk33xk0rfaakj1xj5r8pzmrcgbikj"))))
29822 (properties `((upstream-name . "yardstick")))
29823 (build-system r-build-system)
29833 (home-page "https://github.com/tidymodels/yardstick")
29834 (synopsis "Tidy characterizations of model performance")
29836 "This package provides tidy tools for quantifying how well a model fits
29837 to a data set such as confusion matrices, class probability curve summaries,
29838 and regression metrics (e.g., RMSE).")
29839 (license license:gpl2)))
29841 (define-public r-warp
29848 (uri (cran-uri "warp" version))
29851 "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
29852 (properties `((upstream-name . "warp")))
29853 (build-system r-build-system)
29854 (native-inputs (list r-knitr))
29855 (home-page "https://github.com/DavisVaughan/warp")
29856 (synopsis "Group dates")
29858 "This package provides tooling to group dates by a variety of periods
29859 including: yearly, monthly, by second, by week of the month, and more. The
29860 groups are defined in such a way that they also represent the distance between
29861 dates in terms of the period. This extracts valuable information that can be
29862 used in further calculations that rely on a specific temporal spacing between
29864 (license license:expat)))
29866 (define-public r-scico
29873 (uri (cran-uri "scico" version))
29875 (base32 "1f2czfhzdpi5dqjbxvbrrcnxjpylc5zzghj70ihlh2agq3n9hw5g"))))
29876 (properties `((upstream-name . "scico")))
29877 (build-system r-build-system)
29878 (propagated-inputs (list r-scales))
29879 (home-page "https://github.com/thomasp85/scico")
29880 (synopsis "Colour Palettes Based on the Scientific Colour-Maps")
29882 "This package provides colour choice in information visualisation. It
29883 important in order to avoid being mislead by inherent bias in the used colour
29884 palette. This package provides access to the perceptually uniform and
29885 colour-blindness friendly palettes developed by Fabio Crameri and released
29886 under the \"Scientific Colour-Maps\" moniker. The package contains 24
29887 different palettes and includes both diverging and sequential types.")
29888 (license license:expat)))
29890 (define-public r-slider
29897 (uri (cran-uri "slider" version))
29900 "1vxk2bc33svwcki2j8zr5jcxswh27i0fqgzjw2a5a1pp9dh3fmd3"))))
29901 (properties `((upstream-name . "slider")))
29902 (build-system r-build-system)
29904 (list r-ellipsis r-glue r-rlang r-vctrs r-warp))
29905 (native-inputs (list r-knitr))
29906 (home-page "https://github.com/DavisVaughan/slider")
29907 (synopsis "Sliding window functions")
29909 "This package provides type-stable rolling window functions over any R
29910 data type. Cumulative and expanding windows are also supported. For more
29911 advanced usage, an index can be used as a secondary vector that defines how
29912 sliding windows are to be created.")
29913 (license license:expat)))
29915 (define-public r-rlist
29918 (version "0.4.6.2")
29922 (uri (cran-uri "rlist" version))
29924 (base32 "15q99rhbbjq8zd976yjmfnny45dd5fg2p2dv1sljg2kwi66nbppb"))))
29925 (properties `((upstream-name . "rlist")))
29926 (build-system r-build-system)
29927 (propagated-inputs (list r-data-table r-jsonlite r-xml r-yaml))
29928 (home-page "https://renkun-ken.github.io/rlist/")
29929 (synopsis "Toolbox for Non-Tabular Data Manipulation")
29931 "This package provides a set of functions for data manipulation with
29932 list objects, including mapping, filtering, grouping, sorting, updating,
29933 searching, and other useful functions. Most functions are designed to be
29934 pipeline friendly so that data processing with lists can be chained.")
29935 (license license:expat)))
29937 (define-public r-rsample
29944 (uri (cran-uri "rsample" version))
29947 "1iy61riwjch9z4m6k7whsrkl80sk9sww5lf1np4iq4vdfq6w01jb"))))
29948 (properties `((upstream-name . "rsample")))
29949 (build-system r-build-system)
29966 (home-page "https://rsample.tidymodels.org")
29967 (synopsis "General resampling infrastructure")
29969 "This package provides classes and functions to create and summarize
29970 different types of resampling objects (e.g. bootstrap, cross-validation).")
29971 (license license:gpl2)))
29973 (define-public r-dicedesign
29975 (name "r-dicedesign")
29980 (uri (cran-uri "DiceDesign" version))
29983 "1a8ixa65xgyfri03cviic8qi2plbhdyz8m02bwif8w94w0q3ghlk"))))
29984 (properties `((upstream-name . "DiceDesign")))
29985 (build-system r-build-system)
29986 (home-page "http://dice.emse.fr/")
29987 (synopsis "Designs of computer experiments")
29989 "This package provides tools to create some specific @code{Space-Filling
29990 Design} (SFD) and to test their quality.")
29991 (license license:gpl3)))
29993 (define-public r-dials
30000 (uri (cran-uri "dials" version))
30003 "0flpd7bxknsscv0gk6c7zz1aid9y3z6sibkvjp9zcyc5wnqldrvj"))))
30004 (properties `((upstream-name . "dials")))
30005 (build-system r-build-system)
30019 (native-inputs (list r-knitr))
30020 (home-page "https://dials.tidymodels.org/")
30021 (synopsis "Tools for creating tuning parameter values")
30023 "Many models contain tuning parameters (i.e. parameters that cannot be
30024 directly estimated from the data). These tools can be used to define objects
30025 for creating, simulating, or validating values for such parameters.")
30026 (license license:gpl2)))
30028 (define-public r-tune
30035 (uri (cran-uri "tune" version))
30038 "044bz8g3p8vj97w9ycpiw39iakzghxbqzmb4lxqpplpxymc8ybkm"))))
30039 (properties `((upstream-name . "tune")))
30040 (build-system r-build-system)
30064 (home-page "https://github.com/tidymodels/tune")
30065 (synopsis "Tidy tuning tools")
30067 "The ability to tune models is important. @code{tune} contains functions
30068 and classes to be used in conjunction with other @code{tidymodels} packages
30069 for finding reasonable values of hyper-parameters in models, pre-processing
30070 methods, and post-processing steps.")
30071 (license license:expat)))
30073 (define-public r-workflowsets
30075 (name "r-workflowsets")
30080 (uri (cran-uri "workflowsets" version))
30083 "12wj0m6kqnjh8k5k14kqh40wf14gzyg5l3shhbpr2lvk87l9ssqq"))))
30084 (properties `((upstream-name . "workflowsets")))
30085 (build-system r-build-system)
30108 (home-page "https://github.com/tidymodels/workflowsets")
30109 (synopsis "Create a collection of tidymodels workflows")
30111 "A workflow is a combination of a model and preprocessors (e.g, a
30112 formula, recipe, etc.). In order to try different combinations of these, an
30113 object can be created that contains many workflows. There are functions to
30114 create workflows en masse as well as training them and visualizing the
30116 (license license:expat)))
30118 (define-public r-tidyposterior
30120 (name "r-tidyposterior")
30125 (uri (cran-uri "tidyposterior" version))
30128 "19cyyhh417i5xcchb8kq3iycaf4y7aznr7y9r004h2k2vk3svc86"))))
30129 (properties `((upstream-name . "tidyposterior")))
30130 (build-system r-build-system)
30146 (home-page "https://tidyposterior.tidymodels.org")
30147 (synopsis "Bayesian analysis to compare models using resampling statistics")
30149 "This package can be used to conduct post hoc analyses of resampling
30150 results generated by models. For example, if two models are evaluated with
30151 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
30152 are 10 paired statistics. These can be used to make comparisons between
30153 models without involving a test set.")
30154 (license license:gpl2)))
30156 (define-public r-tidypredict
30158 (name "r-tidypredict")
30163 (uri (cran-uri "tidypredict" version))
30166 "0x0r36zvny4rqgndx7iqh39yhr53gl4d8wd8wpvdcgg35q6z02z2"))))
30167 (properties `((upstream-name . "tidypredict")))
30168 (build-system r-build-system)
30180 (home-page "https://tidypredict.tidymodels.org")
30181 (synopsis "Run predictions inside the database")
30183 "This package parses a fitted R model object, and returns a formula in
30184 Tidy Eval code that calculates the predictions. It works with several
30185 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
30186 final SQL translation of the algorithm. It currently supports @code{lm()},
30187 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
30188 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
30189 (license license:gpl3)))
30191 (define-public r-janeaustenr
30193 (name "r-janeaustenr")
30198 (uri (cran-uri "janeaustenr" version))
30201 "1ap8p1lpbj2wz90mpf1vbyzhv2spzv03bi8lwzpsir2y77hjxhxl"))))
30202 (properties `((upstream-name . "janeaustenr")))
30203 (build-system r-build-system)
30204 (home-page "https://github.com/juliasilge/janeaustenr")
30205 (synopsis "Jane Austen's complete novels")
30207 "This package provides the full texts for Jane Austen's six completed
30208 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
30209 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
30210 and \"Persuasion\".")
30211 (license license:expat)))
30213 (define-public r-janitor
30219 (uri (cran-uri "janitor" version))
30222 "09nqm957m2f54y2l30619b58x4i7gxwvr2lwg5kly5xy1ya1a1nn"))))
30223 (properties `((upstream-name . "janitor")))
30224 (build-system r-build-system)
30237 (native-inputs (list r-knitr))
30238 (home-page "https://github.com/sfirke/janitor")
30239 (synopsis "Simple tools for examining and cleaning dirty data")
30241 "The main janitor functions can: perfectly format @code{data.frame column}
30242 names; provide quick counts of variable combinations (i.e., frequency tables
30243 and crosstabs); and isolate duplicate records. Other janitor functions nicely
30244 format the tabulation results. These tabulate-and-report functions
30245 approximate popular features of SPSS and Excel. This package follows the
30246 principles of the \"tidyverse\" and works well with the pipe function
30247 @code{%>%}. janitor was built with beginning-to-intermediate R users in mind
30248 and is optimized for user-friendliness. Advanced R users can already do
30249 everything covered here, but with janitor they can do it faster and save their
30250 thinking for the fun stuff.")
30251 (license license:expat)))
30253 (define-public r-tokenizers
30255 (name "r-tokenizers")
30260 (uri (cran-uri "tokenizers" version))
30263 "01s2bx35r8kc7c68jnhcbrk963v2mhd21gmf630w7i4xnx46nvb2"))))
30264 (properties `((upstream-name . "tokenizers")))
30265 (build-system r-build-system)
30267 (list r-rcpp r-snowballc r-stringi))
30270 (home-page "https://lincolnmullen.com/software/tokenizers/")
30271 (synopsis "Fast, consistent tokenization of natural language text")
30273 "This is a package for converting natural language text into tokens.
30274 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
30275 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
30276 Treebank, regular expressions, as well as functions for counting characters,
30277 words, and sentences, and a function for splitting longer texts into separate
30278 documents, each with the same number of words. The tokenizers have a
30279 consistent interface, and the package is built on the @code{stringi} and
30280 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
30281 (license license:expat)))
30283 (define-public r-hunspell
30285 (name "r-hunspell")
30290 (uri (cran-uri "hunspell" version))
30293 "0kij39rhsx7s4lfddy6745f1zjyi003srj14ckjpbhkcyxamk8jy"))))
30294 (properties `((upstream-name . "hunspell")))
30295 (build-system r-build-system)
30297 (list r-digest r-rcpp))
30300 (home-page "https://github.com/ropensci/hunspell#readme")
30301 (synopsis "High-performance stemmer, tokenizer, and spell checker")
30303 "This package provides a low-level spell checker and morphological
30304 analyzer based on the famous @code{hunspell} library. The package can analyze
30305 or check individual words as well as parse text, LaTeX, HTML or XML documents.
30306 For a more user-friendly interface use the @code{spelling} package which
30307 builds on this package to automate checking of files, documentation and
30308 vignettes in all common formats.")
30309 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
30310 ;; MPL; in addition to these licenses the rest of the R wrapper is also
30311 ;; available under the Expat license.
30312 (license (list license:gpl2
30317 (define-public r-tidytext
30319 (name "r-tidytext")
30324 (uri (cran-uri "tidytext" version))
30327 "0mk75wdiy4mixj1xlksw9ns4ajlj8ak90sgchjcg1zb90qp7gg56"))))
30328 (properties `((upstream-name . "tidytext")))
30329 (build-system r-build-system)
30345 (home-page "https://github.com/juliasilge/tidytext")
30346 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
30348 "This is a package for text mining for word processing and sentiment
30349 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
30350 (license license:expat)))
30352 (define-public r-parsnip
30359 (uri (cran-uri "parsnip" version))
30362 "171crglp6ncy41iyb60gj6xp7zn2vnbffgbgpszrahf6j2hhxvw4"))))
30363 (properties `((upstream-name . "parsnip")))
30364 (build-system r-build-system)
30385 (home-page "https://parsnip.tidymodels.org")
30386 (synopsis "Common API to modeling and analysis functions")
30388 "This package provides a common interface to allow users to specify a
30389 model without having to remember the different argument names across different
30390 functions or computational engines (e.g. R, Spark, Stan, etc).")
30391 (license license:gpl2)))
30393 (define-public r-infer
30400 (uri (cran-uri "infer" version))
30403 "1m5srhcmkh8wq12pvy57g3g703wilkl8r3gmm5s7lbj103iz7v8b"))))
30404 (properties `((upstream-name . "infer")))
30405 (build-system r-build-system)
30420 (home-page "https://github.com/tidymodels/infer")
30421 (synopsis "Tidy statistical inference")
30423 "The objective of this package is to perform inference using an
30424 expressive statistical grammar that coheres with the Tidy design framework.")
30425 (license license:cc0)))
30427 (define-public r-modeldata
30429 (name "r-modeldata")
30434 (uri (cran-uri "modeldata" version))
30437 "0ik4r25l69brkf0l248bln1kicy7dpi6mziwn19by8rq3f8fylhy"))))
30438 (properties `((upstream-name . "modeldata")))
30439 (build-system r-build-system)
30446 (home-page "https://modeldata.tidymodels.org")
30447 (synopsis "Data sets useful for modeling packages")
30449 "This package provides data sets used for demonstrating or testing
30450 model-related packages.")
30451 (license license:expat)))
30453 (define-public r-conflicted
30455 (name "r-conflicted")
30460 (uri (cran-uri "conflicted" version))
30463 "1qg9ar114r98wm0pnf65mss4v2ksq3924rlpm13mqp4s3p6j9yi4"))))
30464 (properties `((upstream-name . "conflicted")))
30465 (build-system r-build-system)
30467 (list r-memoise r-rlang))
30468 (home-page "https://github.com/r-lib/conflicted")
30469 (synopsis "Alternative conflict resolution strategy")
30471 "R's default conflict management system gives the most recently loaded
30472 package precedence. This can make it hard to detect conflicts, particularly
30473 when they arise because a package update creates ambiguity that did not
30474 previously exist. The @code{conflicted} package takes a different approach,
30475 making every conflict an error and forcing you to choose which function to
30477 (license license:gpl3)))
30479 (define-public r-tidymodels
30481 (name "r-tidymodels")
30486 (uri (cran-uri "tidymodels" version))
30489 "1zqdq7zwmhc19zs77x27l5ja01rhj01v8dw182j8jhy49h0alyz3"))))
30490 (properties `((upstream-name . "tidymodels")))
30491 (build-system r-build-system)
30516 (home-page "https://github.com/tidymodels/tidymodels")
30517 (synopsis "Tidy collection for modeling and statistical analysis")
30519 "The tidy modeling \"verse\" is a collection of packages for modeling and
30520 statistical analysis that share the underlying design philosophy, grammar, and
30521 data structures of the tidyverse.")
30522 (license license:gpl3)))
30524 (define-public r-lsa
30531 (uri (cran-uri "lsa" version))
30534 "16k1g0kh3yaw7azg76aqf3hn3b6jgqg92xx0syai8l0my9ci2zzh"))))
30535 (properties `((upstream-name . "lsa")))
30536 (build-system r-build-system)
30538 (list r-snowballc))
30539 (home-page "https://cran.r-project.org/package=lsa")
30540 (synopsis "Latent semantic analysis")
30542 "The basic idea of latent semantic analysis (LSA) is, that text do have a
30543 higher order (=latent semantic) structure which, however, is obscured by word
30544 usage (e.g. through the use of synonyms or polysemy). By using conceptual
30545 indices that are derived statistically via a truncated singular value
30546 decomposition (a two-mode factor analysis) over a given document-term matrix,
30547 this variability problem can be overcome.")
30548 (license license:gpl2+)))
30550 (define-public r-mlecens
30557 (uri (cran-uri "MLEcens" version))
30560 "1kdnm5ilfn5fclry3f1d518761hykrqgjhv69kc881r2fpcfa1lv"))))
30561 (properties `((upstream-name . "MLEcens")))
30562 (build-system r-build-system)
30563 (home-page "http://stat.ethz.ch/~maathuis/")
30564 (synopsis "Computation of the MLE for bivariate (interval) censored data")
30566 "This package contains functions to compute the nonparametric
30567 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
30568 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
30569 To be more precise, we consider the situation where we observe a set of
30570 rectangles that are known to contain the unobservable realizations of (X,Y).
30571 We compute the MLE based on such a set of rectangles. The methods can also be
30572 used for univariate censored data (see data set @code{cosmesis}), and for
30573 censored data with competing risks (see data set @code{menopause}). The
30574 package also provides functions to visualize the observed data and the MLE.")
30575 (license license:gpl2+)))
30577 (define-public r-metafor
30584 (uri (cran-uri "metafor" version))
30587 "05053cvk65fh2p4wrmygkvgqvrl73kz22rdbxsjxhi21jmzmg56n"))))
30588 (properties `((upstream-name . "metafor")))
30589 (build-system r-build-system)
30591 (list r-mathjaxr r-matrix r-metadat r-nlme r-pbapply))
30592 (home-page "https://cran.r-project.org/web/packages/metafor/")
30593 (synopsis "Meta-analysis package for R")
30595 "This package provides a comprehensive collection of functions for
30596 conducting meta-analyses in R. The package includes functions to calculate
30597 various effect sizes or outcome measures, fit fixed-, random-, and
30598 mixed-effects models to such data, carry out moderator and meta-regression
30599 analyses, and create various types of meta-analytical plots (e.g., forest,
30600 funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial
30601 and person-time data, the package also provides functions that implement
30602 specialized methods, including the Mantel-Haenszel method, Peto's method, and
30603 a variety of suitable generalized linear (mixed-effects) models (i.e.
30604 mixed-effects logistic and Poisson regression models). Finally, the package
30605 provides functionality for fitting meta-analytic multivariate/multilevel
30606 models that account for non-independent sampling errors and/or true
30607 effects (e.g. due to the inclusion of multiple treatment studies, multiple
30608 endpoints, or other forms of clustering). Network meta-analyses and
30609 meta-analyses accounting for known correlation structures (e.g. due to
30610 phylogenetic relatedness) can also be conducted.")
30611 (license license:gpl2+)))
30613 (define-public r-altmeta
30620 (uri (cran-uri "altmeta" version))
30623 "01v308389wqzp35icrp9ssb4y4gxwjzl600qw47c6rmm6s2mxzjh"))))
30624 (properties `((upstream-name . "altmeta")))
30625 (build-system r-build-system)
30627 (list r-coda r-lme4 r-matrix r-metafor r-rjags))
30628 (home-page "https://cran.r-project.org/web/packages/altmeta/")
30629 (synopsis "Alternative meta-analysis methods")
30631 "This package provides alternative statistical methods for meta-analysis,
30635 @item bivariate generalized linear mixed models for synthesizing odds ratios,
30636 relative risks, and risk differences
30637 @item heterogeneity tests and measures that are robust to outliers;
30638 @item measures, tests, and visualization tools for publication bias or
30639 small-study effects;
30640 @item meta-analysis of diagnostic tests for synthesizing sensitivities,
30641 specificities, etc.;
30642 @item meta-analysis methods for synthesizing proportions;
30643 @item models for multivariate meta-analysis.
30646 (license license:gpl2+)))
30648 (define-public r-perm
30651 (version "1.0-0.2")
30655 (uri (cran-uri "perm" version))
30658 "182ac1y91yzb34zwdcmx5fdfr5z0cha0gx2bgk36gwxhgfc994kj"))))
30659 (properties `((upstream-name . "perm")))
30660 (build-system r-build-system)
30661 (home-page "https://cran.r-project.org/web/packages/perm/")
30662 (synopsis "Exact or asymptotic permutation tests")
30664 "This package provides several methods for performing permutation tests.
30665 It has three main functions, to perform linear permutation tests. These tests
30666 are tests where the test statistic is the sum of the product of a
30667 covariate (usually group indicator) and the scores.")
30668 ;; Any version of the GPL
30669 (license license:gpl2+)))
30671 (define-public r-qtl
30678 (uri (cran-uri "qtl" version))
30681 "0q49g3ar1451whsl6ig7kz4mg8s9zxlcvgkj4ivyw4995wbwc2ij"))))
30682 (build-system r-build-system)
30683 (home-page "https://rqtl.org/")
30684 (synopsis "R package for analyzing QTL experiments in genetics")
30685 (description "R/qtl is an extension library for the R statistics system.
30686 It is used to analyze experimental crosses for identifying genes contributing
30687 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
30689 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
30690 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
30692 (license license:gpl3)))
30694 (define-public r-qtl2
30700 (uri (cran-uri "qtl2" version))
30702 (base32 "0ppc6dzlq77mppxc6bczai9gi40jrbxd1466y2cn2s8a4ah1jg9y"))))
30703 (build-system r-build-system)
30711 (home-page "https://kbroman.org/qtl2/")
30712 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
30714 "This package provides a set of tools to perform @dfn{Quantitative Trait
30715 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
30716 @code{R/qtl} package to better handle high-dimensional data and complex cross
30717 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
30718 (license license:gpl3)))
30720 (define-public r-seqminer
30722 (name "r-seqminer")
30727 (uri (cran-uri "seqminer" version))
30730 "1mbx1hw9dhgry7hhan43g6aiz2lyd5api7wxq3fwajyzjrc6p1g8"))))
30731 (build-system r-build-system)
30734 (home-page "http://seqminer.genomic.codes")
30735 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
30737 "This package provides tools to integrate nucleotide sequencing
30738 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
30739 ;; Any version of the GPL is acceptable
30740 (license (list license:gpl2+ license:gpl3+))))
30742 (define-public r-maldiquant
30744 (name "r-maldiquant")
30749 (uri (cran-uri "MALDIquant" version))
30752 "1y1g3819ss06dry70kfhg2syddw71682qmzkcyppfsma6hhghw87"))))
30753 (properties `((upstream-name . "MALDIquant")))
30754 (build-system r-build-system)
30757 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
30758 (synopsis "Quantitative analysis of mass spectrometry data")
30760 "This package provides a complete analysis pipeline for matrix-assisted
30761 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
30762 two-dimensional mass spectrometry data. In addition to commonly used plotting
30763 and processing methods it includes distinctive features, namely baseline
30764 subtraction methods such as morphological filters (TopHat) or the
30765 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
30766 alignment using warping functions, handling of replicated measurements as well
30767 as allowing spectra with different resolutions.")
30768 (license license:gpl3+)))
30770 (define-public r-scattermore
30772 (name "r-scattermore")
30777 (uri (cran-uri "scattermore" version))
30780 "1rgqm7r1k7j3h2y4i6d1a2y8fzivfcbmr7dj9d367c0w4vc77pfv"))))
30781 (properties `((upstream-name . "scattermore")))
30782 (build-system r-build-system)
30784 (list r-ggplot2 r-scales))
30785 (home-page "https://github.com/exaexa/scattermore")
30786 (synopsis "Scatterplots with more points")
30788 "This package provides C-based tools for converting large scatterplot
30789 data to rasters. It speeds up plotting of data with millions of points.")
30790 (license license:gpl3+)))
30792 (define-public r-seuratobject
30794 (name "r-seuratobject")
30799 (uri (cran-uri "SeuratObject" version))
30802 "03bd4fazcafaf5mp37cf9w6bxm9zwrlxkrqm9bjdnwxm07slanba"))))
30803 (properties `((upstream-name . "SeuratObject")))
30804 (build-system r-build-system)
30815 (home-page "https://satijalab.org/seurat")
30816 (synopsis "Data structures for single cell data")
30818 "This package defines S4 classes for single-cell genomic data and
30819 associated information, such as dimensionality reduction embeddings,
30820 nearest-neighbor graphs, and spatially-resolved coordinates. It provides data
30821 access methods and R-native hooks to ensure the Seurat object is familiar to
30823 (license license:gpl3)))
30825 (define-public r-seurat
30831 (uri (cran-uri "Seurat" version))
30834 "1vzb2k21nnzlky5dbf586wnixffz7wc9ncrpbgdw8md2kcmd58r2"))))
30835 (properties `((upstream-name . "Seurat")))
30836 (build-system r-build-system)
30881 (home-page "http://www.satijalab.org/seurat")
30882 (synopsis "Seurat is an R toolkit for single cell genomics")
30884 "This package is an R package designed for QC, analysis, and
30885 exploration of single cell RNA-seq data. It easily enables widely-used
30886 analytical techniques, including the identification of highly variable genes,
30887 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
30888 algorithms; density clustering, hierarchical clustering, k-means, and the
30889 discovery of differentially expressed genes and markers.")
30890 (license license:gpl3)))
30892 (define-public r-seuratdisk
30893 (let ((commit "163f1aade5bac38ed1e9e9c912283a7e74781610")
30896 (name "r-seuratdisk")
30897 (version (git-version "0.0.0.9019" revision commit))
30901 (uri (git-reference
30902 (url "https://github.com/mojaveazure/seurat-disk")
30904 (file-name (git-file-name name version))
30906 (base32 "1d1v8qi6kknzy5fj6bl8akwy74h5h143i00lyidsnqjbwp9n4qnw"))))
30907 (properties `((upstream-name . "SeuratDisk")))
30908 (build-system r-build-system)
30922 (home-page "https://github.com/mojaveazure/seurat-disk")
30923 (synopsis "Interfaces for HDF5-based single cell file formats")
30925 "The h5Seurat file format is specifically designed for the storage and
30926 analysis of multi-modal single-cell and spatially-resolved expression
30927 experiments, for example, from CITE-seq or 10X Visium technologies. It holds
30928 all molecular information and associated metadata, including (for example)
30929 nearest-neighbor graphs, dimensional reduction information, spatial
30930 coordinates and image data, and cluster labels. This package also supports
30931 rapid and on-disk conversion between h5Seurat and AnnData objects, with the
30932 goal of enhancing interoperability between Seurat and Scanpy.")
30933 (license license:gpl3))))
30935 (define-public r-seuratdata
30936 (let ((commit "b59556b24d7d6728a5744c9c715dd5f7f32ed7a5")
30939 (name "r-seuratdata")
30940 (version (git-version "0.2.1" revision commit))
30944 (uri (git-reference
30945 (url "https://github.com/satijalab/seurat-data")
30947 (file-name (git-file-name name version))
30949 (base32 "1xfdmdmgn4r0z6w4cxa98ic6xk8i6qz054r215dvqbjs1vydsbf9"))))
30950 (properties `((upstream-name . "SeuratData")))
30951 (build-system r-build-system)
30954 (modify-phases %standard-phases
30955 ;; When there is no HOME directory, this package will fail to load
30956 ;; the included list of packages.
30957 (add-after 'unpack 'set-HOME
30958 (lambda _ (setenv "HOME" "/tmp"))))))
30960 (list r-cli r-crayon r-rappdirs))
30961 (home-page "https://github.com/satijalab/seurat-data")
30962 (synopsis "Install and manage Seurat datasets")
30964 "Single cell RNA sequencing datasets can be large, consisting of
30965 matrices that contain expression data for several thousand features across
30966 several thousand cells. This package is designed to easily install, manage,
30967 and learn about various single-cell datasets, provided Seurat objects and
30968 distributed as independent packages.")
30969 (license license:gpl3))))
30971 (define-public r-phangorn
30973 (name "r-phangorn")
30978 (uri (cran-uri "phangorn" version))
30981 "1kjxp352jdk1amxpk9jrql490d0qy79zm65y8szyxrm1adqghlyi"))))
30982 (build-system r-build-system)
30994 (home-page "https://github.com/KlausVigo/phangorn")
30995 (synopsis "Phylogenetic analysis in R")
30997 "Phangorn is a package for phylogenetic analysis in R. It supports
30998 estimation of phylogenetic trees and networks using Maximum Likelihood,
30999 Maximum Parsimony, distance methods and Hadamard conjugation.")
31000 (license license:gpl2+)))
31002 (define-public r-diversitree
31004 (name "r-diversitree")
31009 (uri (cran-uri "diversitree" version))
31012 "0rzrk7xsn4gy271pbcw3azndhx0c06bmsgrg6libjmlfnmq6j8sc"))))
31013 (build-system r-build-system)
31016 (inputs (list fftw gsl))
31018 (list r-ape r-desolve r-rcpp r-subplex))
31019 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
31020 (synopsis "Comparative 'phylogenetic' analyses of diversification")
31021 (description "This package contains a number of comparative \"phylogenetic\"
31022 methods, mostly focusing on analysing diversification and character evolution.
31023 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
31024 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
31025 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
31026 include Markov models of discrete and continuous trait evolution and constant
31027 rate speciation and extinction.")
31028 (license license:gpl2+)))
31030 (define-public r-calculus
31032 (name "r-calculus")
31037 (uri (cran-uri "calculus" version))
31040 "18w64jp6ah2q09242bsnszjl2adqmcs4b0w44ixrc74rjjxwp1cd"))))
31041 (properties `((upstream-name . "calculus")))
31042 (build-system r-build-system)
31047 (home-page "https://github.com/eguidotti/calculus")
31048 (synopsis "High dimensional numerical and symbolic calculus")
31050 "Efficient C++ optimized functions for numerical and symbolic calculus.
31051 It includes basic symbolic arithmetic, tensor calculus, Einstein summing
31052 convention, fast computation of the Levi-Civita symbol and generalized
31053 Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
31054 accurate high-order derivatives, differential operators (Gradient, Jacobian,
31055 Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
31056 orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
31057 parabolic or user defined by custom scale factors.")
31058 (license license:gpl3)))
31060 (define-public r-decon
31067 (uri (cran-uri "decon" version))
31070 "036cv56wf42q2p3d5h15hbrp5rc29xxy20qwv4k1qzhkq6hmw0qs"))))
31071 (properties `((upstream-name . "decon")))
31072 (build-system r-build-system)
31076 "https://cran.r-project.org/web/packages/decon/")
31077 (synopsis "Deconvolution Estimation in Measurement Error Models")
31079 "This package contains a collection of functions to deal with
31080 nonparametric measurement error problems using deconvolution
31081 kernel methods. We focus two measurement error models in the
31082 package: (1) an additive measurement error model, where the
31083 goal is to estimate the density or distribution function from
31084 contaminated data; (2) nonparametric regression model with
31085 errors-in-variables. The R functions allow the measurement errors
31086 to be either homoscedastic or heteroscedastic. To make the
31087 deconvolution estimators computationally more efficient in R,
31088 we adapt the \"Fast Fourier Transform\" (FFT) algorithm for
31089 density estimation with error-free data to the deconvolution
31090 kernel estimation. Several methods for the selection of the
31091 data-driven smoothing parameter are also provided in the package.
31092 See details in: Wang, X.F. and Wang, B. (2011). Deconvolution
31093 estimation in measurement error models: The R package decon.
31094 Journal of Statistical Software, 39(10), 1-24.")
31095 (license license:gpl3+)))
31097 (define-public r-densestbayes
31099 (name "r-densestbayes")
31100 (version "1.0-2.1")
31104 (uri (cran-uri "densEstBayes" version))
31106 (base32 "1pzmgn65lv91zg1588qhwczy9f2zgciknlc4l072mvh2i7hncw2b"))))
31107 (properties `((upstream-name . "densEstBayes")))
31108 (build-system r-build-system)
31120 (home-page "https://cran.r-project.org/package=densEstBayes")
31121 (synopsis "Density estimation via Bayesian inference engines")
31123 "Bayesian density estimates for univariate continuous random samples are
31124 provided using the Bayesian inference engine paradigm. The engine options
31125 are: Hamiltonian Monte Carlo, the no U-turn sampler, semiparametric mean field
31126 variational Bayes and slice sampling. The methodology is described in Wand
31127 and Yu (2020), arXiv:2009.06182.")
31128 (license license:gpl2+)))
31130 (define-public r-locpol
31137 (uri (cran-uri "locpol" version))
31140 "1p915n0l09kbwkly627074jslxl01yssp1rf0c7sygvsw6sgy5lm"))))
31141 (properties `((upstream-name . "locpol")))
31142 (build-system r-build-system)
31144 "https://cran.r-project.org/web/packages/locpol/")
31145 (synopsis "Kernel Local Polynomial Regression")
31147 "Computes local polynomial estimators for the regression and
31148 also density. It comprises several different utilities to handle
31149 kernel estimators.")
31150 (license license:gpl2+)))
31152 (define-public r-lpme
31159 (uri (cran-uri "lpme" version))
31162 "1ch11cwjci98m7952p9wdsh9fj5y1mjya6ayq0q4wmbm824qfpzb"))))
31163 (properties `((upstream-name . "lpme")))
31164 (build-system r-build-system)
31166 (list r-decon r-flexmix r-locpol r-rcpp r-rcpparmadillo))
31168 "https://cran.r-project.org/web/packages/lpme/")
31169 (synopsis "Nonparametric Estimation of Measurement Error Models")
31171 "Provide nonparametric methods for mean regression model,
31172 modal regression and conditional density estimation in the
31173 presence/absence of measurement error. Bandwidth selection is
31174 also provided for each method.")
31175 (license license:gpl2+)))
31177 (define-public r-aws-signature
31179 (name "r-aws-signature")
31184 (uri (cran-uri "aws.signature" version))
31187 "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp"))))
31188 (properties `((upstream-name . "aws.signature")))
31189 (build-system r-build-system)
31191 (list r-base64enc r-digest))
31192 (home-page "https://github.com/cloudyr/aws.signature")
31193 (synopsis "Amazon Web Services Request Signatures")
31195 "This package generates version 2 and 4 request signatures for Amazon Web
31196 Services (AWS) and provides a mechanism for retrieving credentials from
31197 environment variables, AWS credentials files, and EC2 instance metadata. For
31198 use on EC2 instances, the package 'aws.ec2metadata' is suggested.")
31199 (license license:gpl2+)))
31201 (define-public r-aws-s3
31208 (uri (cran-uri "aws.s3" version))
31211 "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx"))))
31212 (properties `((upstream-name . "aws.s3")))
31213 (build-system r-build-system)
31215 (list r-aws-signature
31221 (home-page "https://github.com/cloudyr/aws.s3")
31222 (synopsis "AWS S3 Client Package")
31224 "This package provides a simple client package for the Amazon Web
31225 Services (AWS) Simple Storage Service (S3) REST API.")
31226 (license license:gpl2+)))
31228 (define-public r-lgr
31234 (uri (cran-uri "lgr" version))
31237 "09x1vw6cnc1c0p0ylcz1q1vcxyaf1kljhh7ni3gl5jm19zii2h4c"))))
31238 (build-system r-build-system)
31243 (home-page "https://s-fleck.github.io/lgr/")
31244 (synopsis "Fully featured logging framework")
31245 (description "This package offers a flexible, feature-rich yet
31246 light-weight logging framework based on @code{R6} classes. It supports
31247 hierarchical loggers, custom log levels, arbitrary data fields in log events,
31248 logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as
31249 well as email and push notifications.")
31250 (license license:expat)))
31252 (define-public r-mhg
31259 (uri (cran-uri "mHG" version))
31262 "1rz5ncrvvv9h9grls15apa63v2nh9j87fmp4mwjjil37jx6a5zki"))))
31263 (properties `((upstream-name . "mHG")))
31264 (build-system r-build-system)
31265 (home-page "https://cran.r-project.org/package=mHG")
31266 (synopsis "Minimum-hypergeometric test")
31268 "This package runs a minimum-hypergeometric (mHG) test as described in
31269 \"Discovering Motifs in Ranked Lists of DNA Sequences\" by Eran Eden.")
31270 (license license:gpl2)))
31272 (define-public r-mlr3measures
31274 (name "r-mlr3measures")
31278 (uri (cran-uri "mlr3measures" version))
31281 "0k0i1xx63lds1870p2ljy1dlp2i376gdd0sq9s4xiqljqjb8va57"))))
31282 (build-system r-build-system)
31284 (list r-checkmate r-prroc))
31285 (home-page "https://mlr3measures.mlr-org.com/")
31286 (synopsis "Performance measures for mlr3")
31287 (description "This package implements multiple performance measures for
31288 supervised learning. It includes over 40 measures for regression and
31289 classification. Additionally, meta information about the performance measures
31290 can be queried, e.g. what the best and worst possible performances scores
31292 (license license:lgpl3)))
31294 (define-public r-mlr3misc
31296 (name "r-mlr3misc")
31300 (uri (cran-uri "mlr3misc" version))
31303 "0haxj0zlflalw10nhdwmk45qsl164bgyjgnm101l2wybw795ixfi"))))
31304 (build-system r-build-system)
31306 (list r-backports r-checkmate r-data-table r-digest r-r6))
31307 (home-page "https://mlr3misc.mlr-org.com/")
31308 (synopsis "Helper functions for mlr3")
31309 (description "@code{mlr3misc} provides frequently used helper functions
31310 and assertions used in @code{mlr3} and its companion packages. It comes with
31311 helper functions for functional programming, for printing, to work with
31312 @code{data.table}, as well as some generally useful @code{R6} classes. This
31313 package also supersedes the package @code{BBmisc}.")
31314 (license license:lgpl3)))
31316 (define-public r-mlr3pipelines
31318 (name "r-mlr3pipelines")
31322 (uri (cran-uri "mlr3pipelines" version))
31325 "09pk3dwjcg5rbpwa1k21srdpvf2dlxq4b5p71cvkha85jx2gdgh6"))))
31326 (build-system r-build-system)
31338 (home-page "https://mlr3pipelines.mlr-org.com/")
31339 (synopsis "Preprocessing Operators and Pipelines for @code{mlr3}")
31340 (description "@code{mlr3pipelines} enriches @code{mlr3} with a diverse
31341 set of pipelining operators (PipeOps) that can be composed into graphs.
31342 Operations exist for data preprocessing, model fitting, and ensemble learning.
31343 Graphs can themselves be treated as @code{mlr3} Learners and can therefore be
31344 resampled, benchmarked, and tuned.")
31345 (license license:lgpl3)))
31347 (define-public r-mlr3ordinal
31348 (let ((commit "736e3a39be6b7088b650297cc6d90208ec58c0d7")
31351 (name "r-mlr3ordinal")
31352 (version (git-version "0.1.0-9000" revision commit))
31355 (uri (git-reference
31356 (url "https://github.com/mlr-org/mlr3ordinal")
31358 (file-name (git-file-name name version))
31361 "0ipf6n4m6giicn0x7f3lrfmbqkhw8zkz32hzq2xf209wndkqhqm1"))))
31362 (build-system r-build-system)
31373 (home-page "https://mlr3ordinal.mlr-org.com/")
31374 (synopsis "Ordinal Regression for mlr3")
31375 (description "This package extends @code{mlr3} with support for
31376 performing ordinal regression.")
31377 (license license:expat))))
31379 (define-public r-paradox
31385 (uri (cran-uri "paradox" version))
31388 "08h92wk8splf0w3rach9zbk3xz13phgcd1yybmgbs0sj4vx93whd"))))
31389 (build-system r-build-system)
31391 (list r-backports r-checkmate r-data-table r-mlr3misc r-r6))
31392 (home-page "https://paradox.mlr-org.com/")
31393 (synopsis "Define and work with parameter spaces for complex algorithms")
31394 (description "With this package it is possible to define parameter spaces,
31395 constraints and dependencies for arbitrary algorithms, and to program on such
31396 spaces. It also includes statistical designs and random samplers. Objects are
31397 implemented as @code{R6} classes.")
31398 (license license:lgpl3)))
31400 (define-public r-mlr3
31406 (uri (cran-uri "mlr3" version))
31409 "0cnyby4947g1w0h45nd3ld5zr4k19xrwp565mq1hnqkjwmyjsgdj"))))
31410 (build-system r-build-system)
31427 (home-page "https://mlr3.mlr-org.com/")
31428 (synopsis "Machine Learning in R - Next Generation")
31429 (description "@code{mlr3} enables efficient, object-oriented programming
31430 on the building blocks of machine learning. It provides @code{R6} objects for
31431 tasks, learners, resamplings, and measures. The package is geared towards
31432 scalability and larger datasets by supporting parallelization and out-of-memory
31433 data-backends like databases. While @code{mlr3} focuses on the core
31434 computational operations, add-on packages provide additional functionality.")
31435 (license license:lgpl3)))
31437 (define-public r-mlr3learners
31439 (name "r-mlr3learners")
31443 (uri (cran-uri "mlr3learners" version))
31446 "0sa2qjvhvjzsfssln9ah08zknzdcps1z28xzgkdfgi6dj25a0y3k"))))
31447 (build-system r-build-system)
31455 (home-page "https://mlr3learners.mlr-org.com/")
31456 (synopsis "Recommended Learners for @code{mlr3}")
31457 (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba}
31458 with interfaces to essential machine learning packages on CRAN. This includes,
31459 but is not limited to: (penalized) linear and logistic regression, linear and
31460 quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support
31461 vector machines, and gradient boosting.")
31462 (license license:lgpl3)))
31464 (define-public r-bbotk
31471 (uri (cran-uri "bbotk" version))
31474 "0ingnvfps46bysi8k2rqnvlh577bzk6fih6hcf20mjspdxx1as3v"))))
31475 (properties `((upstream-name . "bbotk")))
31476 (build-system r-build-system)
31486 (home-page "https://bbotk.mlr-org.com")
31487 (synopsis "Black-Box Optimization Toolkit")
31488 (description "This package provides a common framework for optimization of
31489 black-box functions for other packages, e.g. @code{mlr3}. It offers various
31490 optimization methods e.g. grid search, random search and generalized simulated
31492 (license license:lgpl3)))
31494 (define-public r-mlr3tuning
31496 (name "r-mlr3tuning")
31500 (uri (cran-uri "mlr3tuning" version))
31503 "13p0gcnl8sxvn3ig526pscl63g1dx7l5i9sfzi2yyrddg8vgik4g"))))
31504 (build-system r-build-system)
31514 (home-page "https://mlr3tuning.mlr-org.com/")
31515 (synopsis "Tuning for @code{mlr3}")
31516 (description "@code{mlr3tuning} implements methods for hyperparameter
31517 tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various
31518 termination criteria can be set and combined. The class @code{AutoTuner} provides a
31519 convenient way to perform nested resampling in combination with @code{mlr3}.")
31520 (license license:lgpl3)))
31522 (define-public r-fontliberation
31524 (name "r-fontliberation")
31529 (uri (cran-uri "fontLiberation" version))
31532 "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc"))))
31534 `((upstream-name . "fontLiberation")))
31535 (build-system r-build-system)
31536 (home-page "https://cran.r-project.org/package=fontLiberation")
31537 (synopsis "Liberation fonts")
31539 "This package provides a placeholder for the Liberation fontset intended
31540 for the fontquiver package. This fontset covers the 12 combinations of
31541 families (sans, serif, mono) and faces (plain, bold, italic, bold italic)
31542 supported in R graphics devices.")
31543 (license license:silofl1.1)))
31545 (define-public r-fontbitstreamvera
31547 (name "r-fontbitstreamvera")
31552 (uri (cran-uri "fontBitstreamVera" version))
31555 "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j"))))
31557 `((upstream-name . "fontBitstreamVera")))
31558 (build-system r-build-system)
31559 (home-page "https://cran.r-project.org/package=fontBitstreamVera")
31560 (synopsis "Fonts for fontquiver")
31562 "This package is a placeholder for the Bitstream Vera font. It is
31563 intended for the fontquiver package.")
31565 (license:fsdg-compatible
31566 "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts"
31567 "The Font Software may be sold as part of a larger software package but
31568 no copy of one or more of the Font Software typefaces may be sold by
31571 (define-public r-fontquiver
31573 (name "r-fontquiver")
31578 (uri (cran-uri "fontquiver" version))
31581 "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm"))))
31582 (properties `((upstream-name . "fontquiver")))
31583 (build-system r-build-system)
31585 (list r-fontbitstreamvera r-fontliberation))
31586 (home-page "https://cran.r-project.org/package=fontquiver")
31587 (synopsis "Set of installed fonts")
31589 "This package provides a set of fonts. This is useful when you want to
31590 avoid system fonts to make sure your outputs are reproducible.")
31591 (license license:gpl3)))
31593 (define-public r-freetypeharfbuzz
31595 (name "r-freetypeharfbuzz")
31600 (uri (cran-uri "freetypeharfbuzz" version))
31603 "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7"))))
31605 `((upstream-name . "freetypeharfbuzz")))
31606 (build-system r-build-system)
31609 (modify-phases %standard-phases
31610 (add-after 'unpack 'prepare-static-libraries
31611 (lambda* (#:key inputs #:allow-other-keys)
31612 (mkdir-p "src/target/include")
31613 (let ((freetype (assoc-ref inputs "static-freetype"))
31614 (harfbuzz (assoc-ref inputs "static-harfbuzz")))
31615 (substitute* "src/Makevars.in"
31616 (("include @MK_FILE@") "") ; do not build static libs
31617 (("^HB_STATIC_LIB =.*")
31618 (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n"))
31619 (("^FT_STATIC_LIB =.*")
31620 (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n")))
31621 (copy-recursively (string-append freetype "/include")
31622 "src/target/include")
31623 (copy-recursively (string-append harfbuzz "/include")
31624 "src/target/include")))))))
31626 (list r-fontquiver))
31627 ;; This may defeat the purpose of this package as our versions of freetype
31628 ;; and harfbuzz obviously differ from the tarballs offered by this
31629 ;; project. On the other hand, Guix arguably does a better job at
31630 ;; "ensur[ing] deterministic computation".
31632 `(("static-freetype"
31634 (inherit (static-package freetype))
31636 `(#:configure-flags
31637 (list "--enable-static=yes"
31642 "--without-harfbuzz")))))
31645 (inherit (static-package harfbuzz))
31647 `(#:tests? #false ; fail because shared library is disabled
31649 (list "--enable-static=yes"
31650 "--enable-shared=no"
31652 "--with-freetype=yes"
31655 "--without-fontconfig"
31656 "--without-glib")))))))
31659 (home-page "https://cran.r-project.org/package=freetypeharfbuzz")
31660 (synopsis "Deterministic computation of text box metrics")
31662 "Unlike other tools that dynamically link to the Cairo stack,
31663 freetypeharfbuzz is statically linked to specific versions of the FreeType and
31664 harfbuzz libraries. This ensures deterministic computation of text box
31665 extents for situations where reproducible results are crucial (for instance
31666 unit tests of graphics).")
31667 (license license:gpl3)))
31669 (define-public r-vdiffr
31676 (uri (cran-uri "vdiffr" version))
31679 "1z8nn8yh6jfzb9r7ylmigwh1p30lrclqm6khmp323qqphzmzfdwy"))))
31680 (properties `((upstream-name . "vdiffr")))
31681 (build-system r-build-system)
31683 (list libpng zlib))
31693 (home-page "https://github.com/r-lib/vdiffr")
31694 (synopsis "Visual regression testing and graphical diffing")
31696 "This package is an extension to the testthat package that makes it easy
31697 to add graphical unit tests. It provides a Shiny application to manage the
31699 (license license:gpl3)))
31701 (define-public r-highlight
31703 (name "r-highlight")
31708 (uri (cran-uri "highlight" version))
31711 "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf"))))
31712 (properties `((upstream-name . "highlight")))
31713 (build-system r-build-system)
31714 (home-page "https://github.com/hadley/highlight")
31715 (synopsis "Syntax highlighter for R code")
31717 "This package provides a syntax highlighter for R code based on the
31718 results of the R parser. It supports rendering in HTML and LaTeX markup. It
31719 includes a custom Sweave driver performing syntax highlighting of R code
31721 (license license:gpl3+)))
31723 (define-public r-clustree
31725 (name "r-clustree")
31730 (uri (cran-uri "clustree" version))
31733 "1haam13aifak8fladyxwa0gz56anj1zfczfjgs07gbw90kf6azx8"))))
31734 (properties `((upstream-name . "clustree")))
31735 (build-system r-build-system)
31748 (home-page "https://github.com/lazappi/clustree")
31749 (synopsis "Visualize clusterings at different resolutions")
31751 "Deciding what resolution to use can be a difficult question when
31752 approaching a clustering analysis. One way to approach this problem is to
31753 look at how samples move as the number of clusters increases. This package
31754 allows you to produce clustering trees, a visualization for interrogating
31755 clusterings as resolution increases.")
31756 (license license:gpl3)))
31758 (define-public r-textshaping
31760 (name "r-textshaping")
31765 (uri (cran-uri "textshaping" version))
31768 "1niaj1dh09rqrg9hrh98ddnc0f2nkyq9iizv24lcwm9gjs3w1ql0"))))
31769 (properties `((upstream-name . "textshaping")))
31770 (build-system r-build-system)
31772 (list freetype fribidi harfbuzz zlib))
31774 (list r-cpp11 r-systemfonts))
31776 (list pkg-config r-knitr))
31777 (home-page "https://github.com/r-lib/textshaping")
31778 (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping")
31780 "This package provides access to the text shaping functionality in the
31781 HarfBuzz library and the bidirectional algorithm in the Fribidi library. This
31782 is a low-level utility package mainly for graphic devices that expands upon
31783 the font tool-set provided by the @code{systemfonts} package.")
31784 (license license:expat)))
31786 (define-public r-ragg
31793 (uri (cran-uri "ragg" version))
31796 "1k8dd08a2f3dg4zrq37cfvljqg413snhzmd0440amvrfd9iyaiy5"))))
31797 (properties `((upstream-name . "ragg")))
31798 (build-system r-build-system)
31800 (list freetype libjpeg-turbo libpng libtiff zlib))
31802 (list r-systemfonts r-textshaping))
31805 (home-page "https://ragg.r-lib.org")
31806 (synopsis "Graphic devices based on AGG")
31808 "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D
31809 drawing library. The ragg package provides a set of graphic devices based on
31810 AGG to use as alternative to the raster devices provided through the
31811 @code{grDevices} package.")
31812 (license license:expat)))
31814 (define-public r-downlit
31821 (uri (cran-uri "downlit" version))
31824 "0g3yncj3gmaqsc6cw7g9slgvd0kfk2414yz5m1dilk8h15lzdprk"))))
31825 (properties `((upstream-name . "downlit")))
31826 (build-system r-build-system)
31838 (home-page "https://downlit.r-lib.org/")
31839 (synopsis "Syntax highlighting and automatic linking")
31841 "This package provides syntax highlighting of R code, specifically
31842 designed for the needs of RMarkdown packages like @code{pkgdown},
31843 @code{hugodown}, and @code{bookdown}. It includes linking of function calls
31844 to their documentation on the web, and automatic translation of ANSI escapes
31845 in output to the equivalent HTML.")
31846 (license license:expat)))
31848 (define-public r-pkgdown
31855 (uri (cran-uri "pkgdown" version))
31858 "0sbz3kzd0hbdnszylsb281arldn2z1c9yxifhj4zv2dilp46b6nj"))))
31859 (properties `((upstream-name . "pkgdown")))
31860 (build-system r-build-system)
31861 (inputs (list pandoc))
31885 (home-page "https://pkgdown.r-lib.org")
31886 (synopsis "Make static HTML documentation for an R package")
31888 "The goal of this package is to generate an attractive and useful website
31889 from a source package. @code{pkgdown} converts your documentation, vignettes,
31890 README file, and more to HTML making it easy to share information about your
31892 (license license:expat)))
31894 (define-public r-prereg
31901 (uri (cran-uri "prereg" version))
31904 "039nrl5cirsx1ysh214dr6xnn1h6h3f90im6k9dgmzfksxdqigpw"))))
31905 (properties `((upstream-name . "prereg")))
31906 (build-system r-build-system)
31909 ;; The package provides a custom LaTex template in
31910 ;; inst/rmd/prereg_form.tex, which depends on these packages:
31914 texlive-generic-iftex
31915 texlive-latex-fancyhdr
31916 texlive-latex-fancyvrb
31917 texlive-latex-geometry
31918 texlive-latex-graphics
31919 texlive-latex-threeparttable
31920 texlive-latex-titlesec
31921 texlive-latex-upquote
31923 texlive-polyglossia
31927 (texlive-updmap.cfg (list texlive-amsfonts texlive-lm))))
31928 (home-page "https://github.com/crsh/prereg")
31930 "R Markdown Templates to preregister Scientific Studies")
31932 "This package provides a collection of templates to author
31933 preregistration documents for scientific studies in PDF format.")
31934 (license license:gpl3)))
31936 (define-public r-ez
31943 (uri (cran-uri "ez" version))
31946 "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq"))))
31947 (properties `((upstream-name . "ez")))
31948 (build-system r-build-system)
31960 (home-page "https://github.com/mike-lawrence/ez")
31961 (synopsis "Easy Analysis and Visualization of Factorial Experiments")
31963 "Facilitates easy analysis of factorial experiments, including purely
31964 within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss designs,
31965 and mixed within-and-between-Ss designs. The functions in this package aim to
31966 provide simple, intuitive and consistent specification of data analysis and
31967 visualization. Visualization functions also include design visualization for
31968 pre-analysis data auditing, and correlation matrix visualization. Finally,
31969 this package includes functions for non-parametric analysis, including
31970 permutation tests and bootstrap resampling. The bootstrap function obtains
31971 predictions either by cell means or by more advanced/powerful mixed effects
31972 models, yielding predictions and confidence intervals that may be easily
31973 visualized at any level of the experiment's design.")
31974 (license license:gpl2+)))
31976 (define-public r-qdapregex
31978 (name "r-qdapregex")
31983 (uri (cran-uri "qdapRegex" version))
31986 "1hdilycwrvi0q6cx7k8vg87bamm2xsafjkya5x4smxysm5k1r4qb"))))
31987 (properties `((upstream-name . "qdapRegex")))
31988 (build-system r-build-system)
31989 (propagated-inputs (list r-stringi))
31991 "https://trinker.github.com/qdapRegex/")
31993 "Regular Expression Removal, Extraction, and Replacement Tools")
31995 "This package provides a collection of regular expression tools
31996 associated with the @code{qdap} package that may be useful outside of the
31997 context of discourse analysis. Tools include removal/extraction/replacement of
31998 abbreviations, dates, dollar amounts, email addresses, hash tags, numbers,
31999 percentages, citations, person tags, phone numbers, times, and zip codes.")
32000 (license license:gpl2)))
32002 (define-public r-mgsub
32009 (uri (cran-uri "mgsub" version))
32012 "1mci6x65h94qiz9cwikx2inbrwkykv43zbs8abfbx416zrh2bbn9"))))
32013 (properties `((upstream-name . "mgsub")))
32014 (build-system r-build-system)
32015 (native-inputs (list r-knitr))
32017 "https://cran.r-project.org/package=mgsub")
32019 "Safe, Multiple, Simultaneous String Substitution")
32021 "Designed to enable simultaneous substitution in strings in a safe
32022 fashion. Safe means it does not rely on placeholders (which can cause errors
32023 in same length matches).")
32024 (license license:expat)))
32026 (define-public r-textshape
32028 (name "r-textshape")
32033 (uri (cran-uri "textshape" version))
32036 "0k9injxykgj2qprc7dygd7gafvcbh3r9x84qzaa1al21pk0dz7ds"))))
32037 (properties `((upstream-name . "textshape")))
32038 (build-system r-build-system)
32040 (list r-data-table r-slam r-stringi))
32041 (home-page "https://github.com/trinker/textshape")
32042 (synopsis "Tools for Reshaping Text")
32044 "Tools that can be used to reshape and restructure text data.")
32045 (license license:gpl2)))
32047 (define-public r-syuzhet
32054 (uri (cran-uri "syuzhet" version))
32057 "16iccqdbw02iw82nah6kwz3gwfghi864j2y698n4b9dyc386ijzv"))))
32058 (properties `((upstream-name . "syuzhet")))
32059 (build-system r-build-system)
32068 (native-inputs (list r-knitr))
32069 (home-page "https://github.com/mjockers/syuzhet")
32071 "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text")
32073 "Extracts sentiment and sentiment-derived plot arcs from text using a
32074 variety of sentiment dictionaries conveniently packaged for consumption by R
32075 users. Implemented dictionaries include @dfn{syuzhet} (default) developed in the
32076 Nebraska Literary Lab, @dfn{afinn} developed by Finn Arup Nielsen, @dfn{bing}
32077 developed by Minqing Hu and Bing Liu, and @dfn{nrc} developed by Mohammad, Saif
32078 M. and Turney, Peter D. Applicable references are available in
32079 @file{README.md} and in the documentation for the @code{get_sentiment}
32080 function. The package also provides a hack for implementing Stanford's coreNLP
32081 sentiment parser. The package provides several methods for plot arc
32083 (license license:gpl3)))
32085 (define-public r-lexicon
32092 (uri (cran-uri "lexicon" version))
32095 "0x7rscsh6par2lj11sby7bmz41cxn63iiw51lgh29z09cg8j606c"))))
32096 (properties `((upstream-name . "lexicon")))
32097 (build-system r-build-system)
32099 (list r-data-table r-syuzhet))
32100 (home-page "https://github.com/trinker/lexicon")
32101 (synopsis "Lexicons for Text Analysis")
32103 "This package provides a collection of lexical hash tables, dictionaries,
32105 (license license:gpl3)))
32107 (define-public r-english
32114 (uri (cran-uri "english" version))
32117 "1g3nmy5p8wj3ix1vp1qmkmy3dyqisrw0md8cjrx4klqkp0wqlms9"))))
32118 (properties `((upstream-name . "english")))
32119 (build-system r-build-system)
32120 (native-inputs (list r-knitr))
32122 "https://cran.r-project.org/package=english")
32123 (synopsis "Translate Integers into English")
32125 "Allow numbers to be presented in an English language version, one, two,
32126 three, ... Ordinals are also available, first, second, third, ... and
32127 indefinite article choice, \"a\" or \"an\".")
32128 (license license:gpl2)))
32130 (define-public r-textclean
32132 (name "r-textclean")
32137 (uri (cran-uri "textclean" version))
32140 "0kgjh6c4f14qkjc4fds7q7rpf4nkma3p0igm54fplmm3p853nvrz"))))
32141 (properties `((upstream-name . "textclean")))
32142 (build-system r-build-system)
32153 "https://github.com/trinker/textclean")
32154 (synopsis "Text Cleaning Tools")
32156 "Tools to clean and process text. Tools are geared at checking for
32157 substrings that are not optimal for analysis and replacing or removing them
32158 (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen,
32159 Kumar, Ostendorf, & Richards (2001) @url{doi:10.1006/csla.2001.0169}) or
32160 extracting them into new variables. For example, emoticons are often used in
32161 text but not always easily handled by analysis algorithms. The
32162 @code{replace_emoticon()} function replaces emoticons with word equivalents.")
32163 (license license:gpl2)))
32165 (define-public r-striprtf
32167 (name "r-striprtf")
32172 (uri (cran-uri "striprtf" version))
32175 "0dqcsh3fb8j0mmmxvxjl77rryhmrjm7a3scqvk2xkgxk4xq6q316"))))
32176 (properties `((upstream-name . "striprtf")))
32177 (build-system r-build-system)
32179 (list r-magrittr r-rcpp r-stringr))
32180 (home-page "https://github.com/kota7/striprtf")
32181 (synopsis "Extract Text from RTF File")
32183 "Extracts plain text from @dfn{Rich Text Format} (RTF) file.")
32184 (license license:expat)))
32186 (define-public r-ndjson
32193 (uri (cran-uri "ndjson" version))
32196 "18j5bibranvbv84hvbsg6glmvhfancdsf2w6j99n3nw53bcgb12d"))
32197 (modules '((guix build utils)))
32200 ;; unvendor gzstream
32201 (for-each delete-file '("src/gzstream.cpp" "src/gzstream.h"))
32203 (properties `((upstream-name . "ndjson")))
32204 (build-system r-build-system)
32207 (modify-phases %standard-phases
32208 (add-after 'unpack 'use-system-gzstream
32209 (lambda* (#:key inputs #:allow-other-keys)
32210 (substitute* "src/Makevars"
32211 (("PKG_LIBS = " all)
32212 (string-append all "-lgzstream ")))
32214 (inputs (list zlib gzstream))
32216 (list r-data-table r-rcpp r-tibble))
32217 (home-page "https://gitlab.com/hrbrmstr/ndjson")
32219 "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader")
32221 "@dfn{Streaming JSON} (ndjson) has one JSON record per-line and many
32222 modern ndjson files contain large numbers of records. These constructs may not
32223 be columnar in nature, but it is often useful to read in these files and
32224 \"flatten\" the structure out to enable working with the data in an R
32225 @code{data.frame}-like context. Functions are provided that make it possible
32226 to read in plain ndjson files or compressed (@code{gz}) ndjson files and either
32227 validate the format of the records or create \"flat\" @code{data.table}
32228 structures from them.")
32229 (license license:expat)))
32231 (define-public r-streamr
32238 (uri (cran-uri "streamR" version))
32241 "1clx3b0j2515r1nmnl6ki7qw5n54q3x2jvqv3zrc00kq71mlj7ix"))))
32242 (properties `((upstream-name . "streamR")))
32243 (build-system r-build-system)
32245 (list r-ndjson r-rcurl r-rjson))
32247 "https://cran.r-project.org/package=streamR")
32249 "Access to Twitter Streaming API via R")
32251 "This package provides functions to access Twitter's filter, sample, and
32252 user streams, and to parse the output into data frames.")
32253 (license license:gpl2)))
32255 (define-public r-readods
32262 (uri (cran-uri "readODS" version))
32265 "1hi217ab7hp15jsbzi5ak57cqf8jn2rv78bnn74q72gn9mrfra7n"))))
32266 (properties `((upstream-name . "readODS")))
32267 (build-system r-build-system)
32269 (list r-cellranger r-readr r-stringi r-xml2))
32270 (native-inputs (list r-knitr))
32272 "https://cran.r-project.org/package=readODS")
32273 (synopsis "Read and Write ODS Files")
32275 "Import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame.
32276 Also support writing data frame into ODS file.")
32277 (license license:gpl3)))
32279 (define-public r-qpdf
32286 (uri (cran-uri "qpdf" version))
32289 "0x2n9b4avnm0p1cz6i90a3p6qjpwr68g4v0xa8d1rr3gbgqfraf8"))
32290 (modules '((guix build utils)))
32293 ;; unvendor libqpdf
32294 (delete-file-recursively "src/libqpdf")
32295 (delete-file-recursively "src/include/qpdf")))))
32296 (properties `((upstream-name . "qpdf")))
32297 (build-system r-build-system)
32300 (modify-phases %standard-phases
32301 (add-after 'unpack 'configure
32302 (lambda _ (setenv "EXTERNAL_QPDF" "1"))))))
32304 (list libjpeg-turbo qpdf zlib))
32306 (list r-askpass r-curl r-rcpp))
32307 (native-inputs (list pkg-config))
32308 (home-page "https://github.com/ropensci/qpdf")
32310 "Split, Combine and Compress PDF Files")
32312 "Content-preserving transformations transformations of PDF files such as
32313 split, combine, and compress. This package interfaces directly to the
32314 @code{qpdf} C++ API and does not require any command line utilities. Note that
32315 @code{qpdf} does not read actual content from PDF files: to extract text and
32316 data you need the @code{pdftools} package.")
32317 (license license:asl2.0)))
32319 (define-public r-pbdmpi
32325 (uri (cran-uri "pbdMPI" version))
32328 "0r6kbrvc0z4mb2dhrz1iqdyx0c03f682b5xfi1igp7z3rszd1va1"))))
32329 (properties `((upstream-name . "pbdMPI")))
32330 (build-system r-build-system)
32333 (modify-phases %standard-phases
32334 (add-before 'install 'mpi-setup
32335 ,%openmpi-setup))))
32336 (inputs (list openmpi))
32337 (propagated-inputs (list r-float r-rlecuyer))
32338 (native-inputs (list pkg-config))
32339 (home-page "https://pbdr.org/")
32340 (synopsis "Programming with Big Data -- Interface to MPI")
32342 "This package provides an efficient interface to MPI by utilizing S4
32343 classes and methods with a focus on @dfn{Single Program/Multiple Data} (SPMD)
32344 parallel programming style, which is intended for batch parallel execution.")
32345 (license license:mpl2.0)))
32347 (define-public r-pdftools
32349 (name "r-pdftools")
32354 (uri (cran-uri "pdftools" version))
32357 "012s98ghj3mk0adghbx2nyrwnja0707ym13nhjpjwj4xd7bll7s5"))))
32358 (properties `((upstream-name . "pdftools")))
32359 (build-system r-build-system)
32360 (inputs (list zlib poppler))
32361 (propagated-inputs (list r-qpdf r-rcpp))
32362 (native-inputs (list pkg-config))
32363 (home-page "https://docs.ropensci.org/pdftools/")
32364 (synopsis "Text Extraction, Rendering and Converting of PDF Documents")
32366 "This package provides utilities based on @code{libpoppler} for
32367 extracting text, fonts, attachments and metadata from a PDF file. It also
32368 supports high quality rendering of PDF documents into PNG, JPEG, TIFF format,
32369 or into raw bitmap vectors for further processing in R.")
32370 (license license:expat)))
32372 (define-public r-antiword
32374 (name "r-antiword")
32379 (uri (cran-uri "antiword" version))
32382 "123v8zlczwh6fr1v3x7dl3885xlmddq1bqlcxih8zh07w0hlk1k2"))
32383 (modules '((guix build utils)))
32386 ;; unvendor libantiword
32387 (delete-file-recursively "src")
32389 (properties `((upstream-name . "antiword")))
32390 (build-system r-build-system)
32393 (modify-phases %standard-phases
32394 (add-after 'unpack 'use-system-antiword
32395 (lambda* (#:key inputs #:allow-other-keys)
32396 (substitute* "R/antiword.R"
32397 (("system.file\\(\"bin\", package = \"antiword\"\\)")
32398 (string-append "\"" (assoc-ref inputs "antiword") "/bin\"")))
32400 (inputs (list antiword))
32401 (propagated-inputs (list r-sys))
32403 "https://github.com/ropensci/antiword#readme")
32405 "Extract Text from Microsoft Word Documents")
32407 "Wraps the @code{AntiWord} utility to extract text from Microsoft Word
32408 documents. The utility only supports the old @code{doc} format, not the new
32409 xml based @code{docx} format. Use the @code{xml2} package to read the
32411 (license license:gpl2)))
32413 (define-public r-readtext
32415 (name "r-readtext")
32420 (uri (cran-uri "readtext" version))
32423 "0k782h5hns5v5h8a6qyfqck2hc15nq0awg8bsp196q4zviv5jw3c"))))
32424 (properties `((upstream-name . "readtext")))
32425 (build-system r-build-system)
32440 (native-inputs (list r-knitr))
32442 "https://github.com/quanteda/readtext")
32444 "Import and Handling for Plain and Formatted Text Files")
32446 "This package provides functions for importing and handling text files
32447 and formatted text files with additional meta-data, such including @code{.csv},
32448 @code{.tab}, @code{.json}, @code{.xml}, @code{.html}, @code{.pdf}, @code{.doc},
32449 @code{.docx}, @code{.rtf}, @code{.xls}, @code{.xlsx}, and others.")
32450 (license license:gpl3)))
32452 (define-public r-packcircles
32454 (name "r-packcircles")
32459 (uri (cran-uri "packcircles" version))
32462 "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk"))))
32463 (properties `((upstream-name . "packcircles")))
32464 (build-system r-build-system)
32465 (propagated-inputs (list r-rcpp))
32466 (native-inputs (list r-knitr))
32468 "https://github.com/mbedward/packcircles")
32469 (synopsis "Circle Packing")
32471 "Algorithms to find arrangements of non-overlapping circles.")
32472 (license license:expat)))
32474 ;; Cannot unbundle liblwgeom, because PostGIS does not support building it on
32476 (define-public r-lwgeom
32483 (uri (cran-uri "lwgeom" version))
32486 "1a0s15rliqd4zr6pyj76xln41f64s9yfwblk074342zvvbps5ck9"))))
32487 (properties `((upstream-name . "lwgeom")))
32488 (build-system r-build-system)
32490 (list geos proj sqlite zlib))
32492 (list r-rcpp r-sf r-units))
32493 (native-inputs (list pkg-config))
32494 (home-page "https://github.com/r-spatial/lwgeom/")
32495 (synopsis "Bindings to Selected 'liblwgeom' Functions for Simple Features")
32497 "Access to selected functions found in
32498 @url{https://github.com/postgis/postgis/tree/master/liblwgeom,liblwgeom}, the
32499 light-weight geometry library used by @url{http://postgis.net/,PostGIS}.")
32500 (license license:gpl2)))
32502 (define-public r-stars
32509 (uri (cran-uri "stars" version))
32512 "0qcli9bangpym4yp96yfibd5f4li5qw1622jnbvzfd9n8aakqhg0"))))
32513 (properties `((upstream-name . "stars")))
32514 (build-system r-build-system)
32522 (native-inputs (list r-knitr))
32523 (home-page "https://r-spatial.github.io/stars/")
32525 "Spatiotemporal Arrays, Raster and Vector Data Cubes")
32527 "Reading, manipulating, writing and plotting spatiotemporal arrays
32528 (raster and vector data cubes) in @code{R}, using @code{GDAL} bindings provided
32529 by @code{sf}, and @code{NetCDF} bindings by @code{ncmeta} and @code{RNetCDF}.")
32530 (license license:asl2.0)))
32532 (define-public r-tmaptools
32534 (name "r-tmaptools")
32539 (uri (cran-uri "tmaptools" version))
32542 "0bal3czrdr93qig8s5cf5szld5vjbbks67rismfhlkmlgw6wp2gx"))))
32543 (properties `((upstream-name . "tmaptools")))
32544 (build-system r-build-system)
32556 "https://github.com/mtennekes/tmaptools")
32557 (synopsis "Thematic Map Tools")
32559 "Set of tools for reading and processing spatial data. The aim is to
32560 supply the workflow to create thematic maps. This package also facilitates
32561 @code{tmap}, the package for visualizing thematic maps.")
32562 (license license:gpl3)))
32564 (define-public r-rworldmap
32566 (name "r-rworldmap")
32571 (uri (cran-uri "rworldmap" version))
32574 "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk"))))
32575 (properties `((upstream-name . "rworldmap")))
32576 (build-system r-build-system)
32578 (list r-fields r-maptools r-sp))
32580 "https://github.com/AndySouth/rworldmap/")
32581 (synopsis "Mapping Global Data")
32583 "Enables mapping of country level and gridded user datasets.")
32584 (license license:gpl2+)))
32586 (define-public r-rtweet
32593 (uri (cran-uri "rtweet" version))
32596 "1dhdq2c2zl88h29caqpm7zh2i5970q7rfg98zf2xb7x4zak7bq9x"))))
32597 (properties `((upstream-name . "rtweet")))
32598 (build-system r-build-system)
32609 (native-inputs (list r-knitr))
32610 (home-page "https://docs.ropensci.org/rtweet/")
32611 (synopsis "Collect Twitter data")
32613 "This package implements tools designed to collect and organize Twitter
32614 data via @url{https://developer.twitter.com/en/docs,Twitter's REST and stream
32615 Application Program Interfaces (API)}.")
32616 (license license:expat)))
32618 (define-public r-intervals
32620 (name "r-intervals")
32625 (uri (cran-uri "intervals" version))
32628 "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb"))))
32629 (properties `((upstream-name . "intervals")))
32630 (build-system r-build-system)
32631 (home-page "https://github.com/edzer/intervals")
32633 "Tools for Working with Points and Intervals")
32635 "Tools for working with and comparing sets of points and intervals.")
32636 (license license:artistic2.0)))
32638 (define-public r-eyelinker
32640 (name "r-eyelinker")
32645 (uri (cran-uri "eyelinker" version))
32648 "0wijd45p6j2qal6wnj7zywks8p9v3m9cmyp7axmk44mrjdjx2i71"))))
32649 (properties `((upstream-name . "eyelinker")))
32650 (build-system r-build-system)
32652 (list r-intervals r-readr r-stringi r-stringr r-tibble))
32653 (native-inputs (list r-knitr))
32655 "https://github.com/a-hurst/eyelinker")
32657 "Import ASC Files from EyeLink Eye Trackers")
32659 "Imports plain-text ASC data files from EyeLink eye trackers into
32660 (relatively) tidy data frames for analysis and visualization.")
32661 (license license:gpl3)))
32663 (define-public r-btm
32670 (uri (cran-uri "BTM" version))
32673 "0ab0wr8nbwn1w1j9hpwfz52lm1sw0qk93713y9k0hpm3pw9dq4jr"))))
32674 (properties `((upstream-name . "BTM")))
32675 (build-system r-build-system)
32676 (propagated-inputs (list r-rcpp))
32677 (home-page "https://github.com/bnosac/BTM")
32678 (synopsis "Biterm Topic Models for Short Text")
32680 "Biterm Topic Models find topics in collections of short texts. It is a
32681 word co-occurrence based topic model that learns topics by modeling word-word
32682 co-occurrences patterns which are called biterms. This in contrast to
32683 traditional topic models like Latent Dirichlet Allocation and Probabilistic
32684 Latent Semantic Analysis which are word-document co-occurrence topic models. A
32685 biterm consists of two words co-occurring in the same short text window. This
32686 context window can for example be a twitter message, a short answer on a
32687 survey, a sentence of a text or a document identifier. The techniques are
32688 explained in detail in the paper 'A Biterm Topic Model For Short Text' by
32689 Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013)
32690 @url{https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/\
32692 (license license:asl2.0)))
32694 (define-public r-delaporte
32696 (name "r-delaporte")
32701 (uri (cran-uri "Delaporte" version))
32704 "1d1jkbxlwnqznh9pkjpkr7np2nmqzjvrdmlb210y1lb08mqmb73w"))))
32705 (properties `((upstream-name . "Delaporte")))
32706 (build-system r-build-system)
32707 (native-inputs (list gfortran))
32708 (home-page "https://github.com/aadler/Delaporte")
32709 (synopsis "Statistical functions for the Delaporte distribution")
32711 "This package provides probability mass, distribution, quantile,
32712 random-variate generation, and method-of-moments parameter-estimation
32713 functions for the Delaporte distribution with parameterization based on
32714 Vose (2008). The Delaporte is a discrete probability distribution which can
32715 be considered the convolution of a negative binomial distribution with a
32716 Poisson distribution. Alternatively, it can be considered a counting
32717 distribution with both Poisson and negative binomial components. It has been
32718 studied in actuarial science as a frequency distribution which has more
32719 variability than the Poisson, but less than the negative binomial.")
32720 (license license:bsd-2)))
32722 (define-public r-rjsonio
32725 (version "1.3-1.6")
32729 (uri (cran-uri "RJSONIO" version))
32732 "17x0ayk7daprbc8w2hvb2jl9mfnw4dic9yc3sr5adcjqfzmcklc2"))))
32733 (properties `((upstream-name . "RJSONIO")))
32734 (build-system r-build-system)
32735 (home-page "https://cran.r-project.org/package=RJSONIO")
32736 (synopsis "Serialize R objects to JSON")
32738 "This is a package that allows conversion to and from data in JavaScript
32739 Object Notation (JSON) format. This allows R objects to be inserted into
32740 Javascript/ECMAScript/ActionScript code and allows R programmers to read and
32741 convert JSON content to R objects. This is an alternative to the @code{rjson}
32743 (license license:bsd-3)))
32745 (define-public r-revgeo
32752 (uri (cran-uri "revgeo" version))
32755 "1ns7d1817475lriss6wwgvdm6lj760p40yxqaifla13c2xb73a55"))))
32756 (properties `((upstream-name . "revgeo")))
32757 (build-system r-build-system)
32759 (list r-rcurl r-rjsonio))
32760 (home-page "https://cran.r-project.org/package=revgeo")
32761 (synopsis "Reverse geocoding")
32763 "The @code{revgeo} procedure allows you to use the Photon geocoder for
32764 OpenStreetMap, Google Maps, and Bing to reverse geocode coordinate pairs with
32766 (license license:gpl3+)))
32768 (define-public r-qpcr
32775 (uri (cran-uri "qpcR" version))
32778 "1r01q7jv3w59yx1gc0qw91rq7rvdhqsi8y57sqqkmwyqfw2x2vsv"))))
32779 (properties `((upstream-name . "qpcR")))
32780 (build-system r-build-system)
32782 (list r-mass r-matrix r-minpack-lm r-rgl r-robustbase))
32783 (home-page "https://cran.r-project.org/package=qpcR")
32784 (synopsis "Modelling and analysis of real-time PCR data")
32786 "This is a package for model fitting, optimal model selection and
32787 calculation of various features that are essential in the analysis of
32788 quantitative real-time polymerase chain reaction (qPCR).")
32789 (license license:gpl2+)))
32791 (define-public r-textplot
32793 (name "r-textplot")
32798 (uri (cran-uri "textplot" version))
32801 "1ag2h365zsx0fxbl05s2yfhf1q13p40akvbqg4qwsb5ynh2a56bf"))))
32802 (properties `((upstream-name . "textplot")))
32803 (build-system r-build-system)
32805 (list r-data-table r-lattice r-matrix))
32806 (native-inputs (list r-knitr))
32807 (home-page "https://github.com/bnosac/textplot")
32808 (synopsis "Text Plots")
32810 "Visualise complex relations in texts. This is done by providing
32811 functionalities for displaying text co-occurrence networks, text correlation
32812 networks, dependency relationships as well as text clustering. Feel free to
32813 join the effort of providing interesting text visualisations.")
32814 (license license:gpl2)))
32816 (define-public r-gsa
32823 (uri (cran-uri "GSA" version))
32826 "1f1mrxxdbdlnibgav6nsvbpniz2x3km2svc0hf43spb4zicn0z8p"))))
32827 (properties `((upstream-name . "GSA")))
32828 (build-system r-build-system)
32829 (home-page "https://statweb.stanford.edu/~tibs/GSA/")
32830 (synopsis "Gene set analysis")
32831 (description "This package lets you determine the significance of
32832 pre-defined sets of genes with respect to an outcome variable, such as a group
32833 indicator, a quantitative variable or a survival time.")
32834 ;; Any version of the LGPL
32835 (license license:lgpl3+)))
32837 (define-public r-gsalib
32844 (uri (cran-uri "gsalib" version))
32847 "145zyc2sqa0acn9crilpw5njms7w7ca3jgl499lhsahlb6ws98rx"))))
32848 (build-system r-build-system)
32849 (home-page "https://cran.r-project.org/web/packages/gsalib")
32850 (synopsis "Utility functions for GATK")
32851 (description "This package contains utility functions used by the Genome
32852 Analysis Toolkit (GATK) to load tables and plot data. The GATK is a toolkit
32853 for variant discovery in high-throughput sequencing data.")
32854 (license license:expat)))
32856 (define-public r-randomforestsrc
32858 (name "r-randomforestsrc")
32863 (uri (cran-uri "randomForestSRC" version))
32866 "05ifvj49jv0n5p6k46milpgj9r10sc5aw23fypyyibdgwpwvwixw"))))
32868 `((upstream-name . "randomForestSRC")))
32869 (build-system r-build-system)
32870 (home-page "https://cran.r-project.org/web/packages/randomForestSRC/")
32871 (synopsis "Random forests for survival, regression, and classification")
32873 "This package implements fast OpenMP parallel computing of Breiman's
32874 random forests for survival, competing risks, regression and classification
32875 based on Ishwaran and Kogalur's popular random survival forests (RSF) package.
32876 It handles missing data and now includes multivariate, unsupervised forests,
32877 quantile regression and solutions for class imbalanced data. It provides a
32878 fast interface using subsampling and confidence regions for variable
32880 (license license:gpl3+)))
32882 (define-public r-contfrac
32884 (name "r-contfrac")
32889 (uri (cran-uri "contfrac" version))
32892 "0sq5c7ny235yrkv2xc4insgxby6rvzc1qsj8h301cd2if3lwbgwm"))))
32893 (properties `((upstream-name . "contfrac")))
32894 (build-system r-build-system)
32896 "https://github.com/RobinHankin/contfrac")
32897 (synopsis "Continued Fractions")
32899 "Various utilities for evaluating continued fractions.")
32900 (license license:gpl2)))
32902 (define-public r-elliptic
32904 (name "r-elliptic")
32909 (uri (cran-uri "elliptic" version))
32912 "1dhba0yfxjd5rlqsxp5a7s2hclfkla9wigsr39dlma67l6qjjmxn"))))
32913 (properties `((upstream-name . "elliptic")))
32914 (build-system r-build-system)
32915 (inputs (list pari-gp))
32916 (propagated-inputs (list r-mass))
32918 "https://github.com/RobinHankin/elliptic")
32920 "Weierstrass and Jacobi Elliptic Functions")
32922 "A suite of elliptic and related functions including Weierstrass and
32923 Jacobi forms. Also includes various tools for manipulating and visualizing
32924 complex functions.")
32925 (license license:gpl2)))
32927 (define-public r-hypergeo
32929 (name "r-hypergeo")
32934 (uri (cran-uri "hypergeo" version))
32937 "13jdiy216znwhr91iqnh03mvkmyscw439syb3h4i67dd78sphnvd"))))
32938 (properties `((upstream-name . "hypergeo")))
32939 (build-system r-build-system)
32941 (list r-contfrac r-desolve r-elliptic))
32943 "https://cran.r-project.org/web/packages/hypergeo/")
32944 (synopsis "The Gauss Hypergeometric Function")
32946 "The Gaussian hypergeometric function for complex numbers.")
32947 (license license:gpl2)))
32949 (define-public r-gganimate
32951 (name "r-gganimate")
32956 (uri (cran-uri "gganimate" version))
32959 "1jabs9qr0319w508kdsk5nmzfhl6nzykpp1by7l639yfvrfqcbd1"))))
32960 (properties `((upstream-name . "gganimate")))
32961 (build-system r-build-system)
32964 (modify-phases %standard-phases
32965 (add-after 'unpack 'absolute-paths
32966 (lambda* (#:key inputs #:allow-other-keys)
32967 (substitute* "R/renderers.R"
32969 (string-append "'" (assoc-ref inputs "ffmpeg") "/bin/ffmpeg'"))))))))
32971 ;; For video output.
32981 ;; For GIF/SVG output. gifski is faster, but depends on Rust.
32983 ;; For HTML output.
32986 (native-inputs (list r-knitr))
32987 (home-page "https://gganimate.com")
32988 (synopsis "Grammar of Animated Graphics")
32990 "This package extends the grammar of graphics as implemented by
32991 @code{ggplot2} to include the description of animation. It does this by
32992 providing a range of new grammar classes that can be added to the plot object
32993 in order to customise how it should change with time.")
32994 (license license:expat)))
32996 ;; This library bundles ‘date’ from (gnu packages calendar). We cannot unbundle
32997 ;; it, because its C++ libtz.so is built with different compiler flags than
32999 (define-public r-tzdb
33006 (uri (cran-uri "tzdb" version))
33009 "0f3h4zaf9f4l371k6nc1mq6z2f9aj1vaf2inni8jnsds3zng16b0"))))
33010 (properties `((upstream-name . "tzdb")))
33011 (build-system r-build-system)
33012 (propagated-inputs (list r-cpp11))
33013 (home-page "https://github.com/r-lib/tzdb")
33014 (synopsis "Time Zone Database Information")
33016 "This package provides an up-to-date copy of the Internet Assigned
33017 Numbers Authority (IANA) Time Zone Database. It is updated periodically to
33018 reflect changes made by political bodies to time zone boundaries, UTC offsets,
33019 and daylight saving time rules. Additionally, this package provides a C++
33020 interface for working with the @code{date} library. @code{date} provides
33021 comprehensive support for working with dates and date-times, which this package
33022 exposes to make it easier for other R packages to utilize. Headers are
33023 provided for calendar specific calculations, along with a limited interface for
33024 time zone manipulations.")
33025 (license license:expat)))
33027 (define-public r-vroom
33034 (uri (cran-uri "vroom" version))
33037 "1plz20x6s01gkkcac51lhx4r2s024pgh778ri7y25hkiiwacp1yh"))))
33038 (properties `((upstream-name . "vroom")))
33039 (build-system r-build-system)
33055 (native-inputs (list r-knitr))
33056 (home-page "https://vroom.r-lib.org")
33058 "Read and Write Rectangular Text Data")
33060 "This package reads and writes data files like @acronym{CSV},
33061 @acronym{TSV} and @acronym{FWF}. When reading it uses a quick initial indexing
33062 step, then reads the values lazily, so only the data you actually use needs to
33063 be read. The writer formats the data in parallel and writes to disk
33064 asynchronously from formatting.")
33065 (license license:expat)))
33067 (define-public r-rmisc
33073 (uri (cran-uri "Rmisc" version))
33076 "1h6jb0xwkyhm9lwm7nj9bhrb5dhrsifvkpqkrd594j1lz74dar8x"))))
33077 (build-system r-build-system)
33079 (list r-plyr r-lattice))
33080 (home-page "https://cran.r-project.org/web/packages/Rmisc/")
33081 (synopsis "Ryan Miscellaneous")
33082 (description "The Rmisc library contains functions for data analysis and
33083 utility operations.")
33084 (license license:gpl3)))
33086 (define-public r-rsq
33092 (uri (cran-uri "rsq" version))
33095 "1r628srxhhf7b51lnj4qrzgbqajkm0ls47a9rzjkvmfq4ax5i73f"))))
33096 (properties `((upstream-name . "rsq")))
33097 (build-system r-build-system)
33104 (home-page "https://cran.r-project.org/package=rsq")
33105 (synopsis "R-squared and related measures")
33107 "Calculate generalized R-squared, partial R-squared, and partial correlation
33108 coefficients for generalized linear (mixed) models (including quasi models
33109 with well defined variance functions).")
33110 (license license:gpl2)))
33112 (define-public r-webutils
33114 (name "r-webutils")
33119 (uri (cran-uri "webutils" version))
33121 (base32 "16a6ds0fnb6y8i1r9ba1hf1ydb53am57s070b3hi5jmrs84b9qik"))))
33122 (properties `((upstream-name . "webutils")))
33123 (build-system r-build-system)
33125 (list r-curl r-jsonlite))
33126 (home-page "https://github.com/jeroen/webutils")
33127 (synopsis "Utility functions for developing web applications")
33129 "This package parses HTTP request data in @code{application/json},
33130 @code{multipart/form-data}, or @code{application/x-www-form-urlencoded}
33131 format. It includes an example of hosting and parsing HTML form data in R
33132 using either @code{httpuv} or @code{Rhttpd}.")
33133 (license license:expat)))
33135 (define-public r-protolite
33137 (name "r-protolite")
33142 (uri (cran-uri "protolite" version))
33144 (base32 "0g1r3lzmvx1w44qzqzdvxfn21zmz11srlp6cr76kd7pd5wzjv82p"))))
33145 (properties `((upstream-name . "protolite")))
33146 (build-system r-build-system)
33150 (list r-jsonlite r-rcpp))
33152 (list protobuf pkg-config))
33153 (home-page "https://github.com/jeroen/protolite")
33154 (synopsis "Highly optimized protocol buffer serializers")
33156 "This package provides pure C++ implementations for reading and writing
33157 several common data formats based on Google protocol-buffers. It currently
33158 supports @code{rexp.proto} for serialized R objects, @code{geobuf.proto} for
33159 binary geojson, and @code{mvt.proto} for vector tiles. This package uses the
33160 auto-generated C++ code by protobuf-compiler, hence the entire serialization
33161 is optimized at compile time. The @code{RProtoBuf} package on the other hand
33162 uses the protobuf runtime library to provide a general-purpose toolkit for
33163 reading and writing arbitrary protocol-buffer data in R.")
33164 (license license:expat)))
33166 (define-public r-opencpu
33173 (uri (cran-uri "opencpu" version))
33175 (base32 "1h0s7fbifyf4h1296sdk3amij0m6s12wq32mbky7xg4nz8wj29ni"))))
33176 (properties `((upstream-name . "opencpu")))
33177 (build-system r-build-system)
33197 (home-page "https://www.opencpu.org")
33198 (synopsis "API for embedded scientific computing")
33200 "This package provides a system for embedded scientific computing and
33201 reproducible research with R. The OpenCPU server exposes a simple but
33202 powerful HTTP API for RPC and data interchange with R. This provides a
33203 reliable and scalable foundation for statistical services or building R web
33204 applications. The OpenCPU server runs either as a single-user development
33205 server within the interactive R session, or as a multi-user stack based on
33207 (license license:asl2.0)))
33209 (define-public r-exactextractr
33211 (name "r-exactextractr")
33216 (uri (cran-uri "exactextractr" version))
33219 "13di9s0lv9kdv2p3hp9ksrr0rh98z6m998pj5a1xq9zl6iakankh"))))
33220 (properties `((upstream-name . "exactextractr")))
33221 (build-system r-build-system)
33222 (inputs (list geos))
33224 (list r-raster r-rcpp r-sf))
33227 (home-page "https://isciences.gitlab.io/exactextractr/")
33228 (synopsis "Fast extraction from raster datasets using polygons")
33230 "This package provides a replacement for the @code{extract} function from
33231 the @code{raster} package that is suitable for extracting raster values using
33232 @code{sf} polygons.")
33233 (license license:asl2.0)))
33235 (define-public r-stringfish
33237 (name "r-stringfish")
33242 (uri (cran-uri "stringfish" version))
33245 "0ddpsi7z0kzqgbq9y646pk9afclq0r7ak22zsdh0i93ni0x71c9l"))))
33246 (properties `((upstream-name . "stringfish")))
33247 (build-system r-build-system)
33249 (list r-rcpp r-rcppparallel))
33251 (list pkg-config r-knitr))
33252 (home-page "https://github.com/traversc/stringfish")
33253 (synopsis "Alternative string implementation")
33255 "This package provides an extendable, performant and multithreaded
33256 @code{alt-string} implementation backed by C++ vectors and strings.")
33257 (license license:gpl3)))
33259 (define-public r-rapiserialize
33261 (name "r-rapiserialize")
33266 (uri (cran-uri "RApiSerialize" version))
33269 "02k0l8bi849b2102ysb102xky4p84i9v2r4w6fab7bgf32wvph4w"))))
33270 (properties `((upstream-name . "RApiSerialize")))
33271 (build-system r-build-system)
33273 "https://cran.r-project.org/package=RApiSerialize")
33274 (synopsis "R API serialization")
33276 "This package provides other packages with access to the internal R
33277 serialization code. Access to this code is provided at the C function level
33278 by using the registration of native function mechanism. Client packages
33279 simply include a single header file RApiSerializeAPI.h provided by this
33281 (license license:gpl2+)))
33283 (define-public r-qs
33290 (uri (cran-uri "qs" version))
33293 "0cx5k0mzn6bm8ff58yrqz3hjidxcawxgqbpijnynvin1m4395i4j"))))
33294 (properties `((upstream-name . "qs")))
33295 (build-system r-build-system)
33296 (inputs (list zlib))
33298 (list r-rapiserialize r-rcpp r-stringfish))
33300 (list pkg-config r-knitr))
33301 (home-page "https://github.com/traversc/qs")
33302 (synopsis "Quick serialization of R objects")
33304 "This package provides functions for quickly writing and reading any R
33305 object to and from disk.")
33306 (license license:gpl3)))
33308 (define-public r-rgeos
33315 (uri (cran-uri "rgeos" version))
33318 "1m73y0nwrdwsjrl48c4fg1kdqnh79835brnmxv9ak01ndbzcp45b"))))
33319 (properties `((upstream-name . "rgeos")))
33320 (build-system r-build-system)
33325 (home-page "https://cran.r-project.org/package=rgeos")
33326 (synopsis "Interface to Geometry Engine (GEOS)")
33328 "This package provides an R interface to Geometry Engine (GEOS) using the
33329 C API for topology operations on geometries.")
33330 (license license:gpl2+)))
33332 (define-public r-tfruns
33339 (uri (cran-uri "tfruns" version))
33342 "1xk7dl51xd1h54798xwycvxmn77jv80in61hanm36zk0024wpxg8"))))
33343 (properties `((upstream-name . "tfruns")))
33344 (build-system r-build-system)
33356 (native-inputs (list r-knitr))
33357 (home-page "https://github.com/rstudio/tfruns")
33358 (synopsis "Training run tools for TensorFlow")
33360 "Create and manage unique directories for each TensorFlow training run.
33361 This package provides a unique, time stamped directory for each run along with
33362 functions to retrieve the directory of the latest run or latest several
33364 (license license:asl2.0)))
33366 (define-public r-tfautograph
33368 (name "r-tfautograph")
33373 (uri (cran-uri "tfautograph" version))
33376 "0fmaq1ggjyxgf2ss7qb8jk74sfwc3s1vc123pd5glclxcy1ib0j2"))))
33377 (properties `((upstream-name . "tfautograph")))
33378 (build-system r-build-system)
33379 (inputs (list tensorflow))
33381 (list r-backports r-reticulate))
33382 (home-page "https://t-kalinowski.github.io/tfautograph/")
33383 (synopsis "Autograph R for Tensorflow")
33385 "This package lets you translate R control flow expressions into
33386 Tensorflow graphs.")
33387 (license license:gpl3)))
33389 (define-public r-tensorflow
33391 (name "r-tensorflow")
33396 (uri (cran-uri "tensorflow" version))
33399 "12c6ndxx4g6fqjakpzp9pgl29ghswhqyr6q9jahpk0cawizh2znj"))))
33400 (properties `((upstream-name . "tensorflow")))
33401 (build-system r-build-system)
33402 (inputs (list tensorflow))
33411 (home-page "https://github.com/rstudio/tensorflow")
33412 (synopsis "R interface to TensorFlow")
33414 "R interface to TensorFlow a library for numerical computation using data
33415 flow graphs. Nodes in the graph represent mathematical operations, while the
33416 graph edges represent the multidimensional data arrays (tensors) communicated
33418 (license license:asl2.0)))
33420 (define-public r-keras
33427 (uri (cran-uri "keras" version))
33430 "06513d1fp7cxk4v03xm9lhgj6xmp9dqqvw3lnzwbzjwdkfj948yc"))))
33431 (properties `((upstream-name . "keras")))
33432 (build-system r-build-system)
33444 (native-inputs (list r-knitr))
33445 (home-page "https://keras.rstudio.com")
33446 (synopsis "R Interface to 'Keras'")
33448 "This package provides an interface to Keras, a high-level neural
33449 networks API. Keras was developed with a focus on enabling fast
33450 experimentation, supports both convolution based networks and recurrent
33451 networks (as well as combinations of the two), and runs seamlessly on both CPU
33453 (license license:expat)))
33455 (define-public r-zzlite
33462 (uri (cran-uri "zzlite" version))
33465 "0vi1slx2s4r5zf82lazqv0c3m12xq73wlgsbz6af4y00h0bkr3ps"))))
33466 (properties `((upstream-name . "zzlite")))
33467 (build-system r-build-system)
33469 (list r-httr r-jsonlite))
33472 (home-page "https://cran.r-project.org/package=zzlite")
33473 (synopsis "Wrapper for the Zamzar file conversion API")
33475 "This package provides a minor collection of HTTP wrappers for the Zamzar
33476 file conversion API. The wrappers makes it easy to utilize the API and thus
33477 convert between more than 100 different file formats (ranging from audio
33478 files, images, movie formats, etc., etc.) through an R session.")
33479 (license license:gpl3)))
33481 (define-public r-ztree
33488 (uri (cran-uri "zTree" version))
33491 "005zk6wpchpss6865ki35yawgf668pn70163ah97rnfkhfaswm6y"))))
33492 (properties `((upstream-name . "zTree")))
33493 (build-system r-build-system)
33496 (home-page "https://cran.r-project.org/package=zTree")
33497 (synopsis "Functions to import data from z-Tree into R")
33499 "This package provides tools for reading @code{.xls} and @code{.sbj}
33500 files which are written by the proprietary program z-Tree for developing and
33501 carrying out economic experiments.")
33502 (license license:gpl3)))
33504 (define-public r-distributionutils
33506 (name "r-distributionutils")
33511 (uri (cran-uri "DistributionUtils" version))
33514 "08vq54pyqxlqsj6q6gsg5ikqa0z3x842j52ld5dxaq272p6xchvl"))))
33516 `((upstream-name . "DistributionUtils")))
33517 (build-system r-build-system)
33520 (home-page "https://cran.r-project.org/package=DistributionUtils")
33521 (synopsis "Distribution utilities")
33523 "This package provides utilities for dealing with distributions.
33524 Functionality includes sample skewness and kurtosis, log-histogram, tail
33525 plots, moments by integration, changing the point about which a moment is
33526 calculated, functions for testing distributions using inversion tests and the
33527 Massart inequality. Also included is an implementation of the incomplete
33528 Bessel K function.")
33529 (license license:gpl2+)))
33531 (define-public r-ztpln
33538 (uri (cran-uri "ztpln" version))
33541 "1b22m72a8117yrgq5k1gzsrbx6yrsrj7bpd49lh7x3vbaz56c0wr"))))
33542 (properties `((upstream-name . "ztpln")))
33543 (build-system r-build-system)
33545 (list r-distributionutils r-mixtools r-rcpp r-rcppeigen
33549 (home-page "https://github.com/mattocci27/ztpln")
33550 (synopsis "Zero-truncated Poisson lognormal distribution")
33552 "This package provides functions for obtaining the density, random
33553 variates and maximum likelihood estimates of the Zero-truncated Poisson
33554 lognormal distribution and their mixture distribution.")
33555 (license license:expat)))
33557 (define-public r-zscorer
33564 (uri (cran-uri "zscorer" version))
33567 "0aijhs0fyird5gq68x4dxchb02mxa7ijk10k9zjhngghxbjj7iqn"))))
33568 (properties `((upstream-name . "zscorer")))
33569 (build-system r-build-system)
33574 (home-page "https://github.com/nutriverse/zscorer")
33575 (synopsis "Child Anthropometry z-Score Calculator")
33577 "This package provides a tool for calculating z-scores and centiles for
33578 weight-for-age, length/height-for-age, weight-for-length/height, BMI-for-age,
33579 head circumference-for-age, age circumference-for-age, subscapular
33580 skinfold-for-age, triceps skinfold-for-age based on the WHO Child Growth
33582 (license license:agpl3+)))
33584 (define-public r-zra
33591 (uri (cran-uri "ZRA" version))
33594 "1sx1q5yf68hhlb5j1hicpj594rmgajqr25llg7ax416j0m2rnagi"))))
33595 (properties `((upstream-name . "ZRA")))
33596 (build-system r-build-system)
33598 (list r-dygraphs r-forecast))
33599 (home-page "https://cran.r-project.org/package=ZRA")
33600 (synopsis "Dynamic plots for time series forecasting")
33602 "This package combines a forecast of a time series, using the function @code{forecast},
33603 with the dynamic plots from @code{dygraphs}.")
33604 (license license:gpl2+)))
33606 (define-public r-rfigshare
33608 (name "r-rfigshare")
33613 (uri (cran-uri "rfigshare" version))
33616 "10shwl1y9220m7ld5w9fjsjzy5yg8myrz9cz97ps9z2bw7bvka5j"))))
33617 (properties `((upstream-name . "rfigshare")))
33618 (build-system r-build-system)
33628 (home-page "https://github.com/ropensci/rfigshare")
33629 (synopsis "R Interface to figshare")
33631 "This package provides an interface to figshare, a scientific repository
33632 to archive and assign DOIs to data, software, figures, and more.")
33633 (license license:cc0)))
33635 (define-public r-dismo
33642 (uri (cran-uri "dismo" version))
33645 "17dwk4fv9l903fp38ab9arc4dfyrj1sbllfxlybkdwm9lpsn1qv6"))))
33646 (properties `((upstream-name . "dismo")))
33647 (build-system r-build-system)
33649 (list r-raster r-rcpp r-sp r-terra))
33650 (home-page "https://rspatial.org/raster/sdm/")
33651 (synopsis "Species distribution modeling")
33653 "This package provides methods for species distribution modeling, i.e.,
33654 predicting the environmental similarity of any site to that of the locations
33655 of known occurrences of a species.")
33656 (license license:gpl3+)))
33658 (define-public r-zoon
33665 (uri (cran-uri "zoon" version))
33668 "02y29vr2yn8al69km8faiqrwjrc1r3hsvw3dg8lwjr65cxw1krip"))))
33669 (properties `((upstream-name . "zoon")))
33670 (build-system r-build-system)
33685 (home-page "https://github.com/zoonproject/zoon")
33686 (synopsis "Reproducible, accessible and shareable species distribution modelling")
33688 "This package reads user submitted modules from an online repository,
33689 runs full species distribution modelling workflows and returns output that is
33690 fully reproducible.")
33691 (license license:bsd-3)))
33693 (define-public r-paws-common
33695 (name "r-paws-common")
33700 (uri (cran-uri "paws.common" version))
33703 "12dz3giv1xajdqq79s5gin9kw4x74w2iaw62ha6ssf8whrc3wmh5"))))
33704 (properties `((upstream-name . "paws.common")))
33705 (build-system r-build-system)
33714 (home-page "https://cran.r-project.org/package=paws.common")
33715 (synopsis "Paws low-level Amazon Web Services API")
33717 "This package provides functions for making low-level API requests to
33718 Amazon Web Services. The functions handle building, signing, and sending
33719 requests, and receiving responses. They are designed to help build
33720 higher-level interfaces to individual services, such as Simple Storage
33722 (license license:asl2.0)))
33724 (define-public r-paws-customer-engagement
33726 (name "r-paws-customer-engagement")
33731 (uri (cran-uri "paws.customer.engagement" version))
33734 "0ac6hzn4ilfjhzdmc9x80999fl18cz16mky31qd3y09m93w2xkdj"))))
33736 `((upstream-name . "paws.customer.engagement")))
33737 (build-system r-build-system)
33739 (list r-paws-common))
33740 (home-page "https://github.com/paws-r/paws")
33741 (synopsis "Amazon Web Services customer engagement services")
33743 "This package provides an interface to Amazon Web Services customer
33744 engagement services, including Simple Email Service, Connect contact center
33745 service, and more.")
33746 (license license:asl2.0)))
33748 (define-public r-paws-cost-management
33750 (name "r-paws-cost-management")
33755 (uri (cran-uri "paws.cost.management" version))
33758 "0in4f8ygw5g2v6vl3lz2y0v51llglh8b1ymbd04d54xxlgn83knh"))))
33760 `((upstream-name . "paws.cost.management")))
33761 (build-system r-build-system)
33763 (list r-paws-common))
33764 (home-page "https://github.com/paws-r/paws")
33765 (synopsis "Amazon Web Services cost management services")
33767 "This package provides an interface to Amazon Web Services cost
33768 management services, including cost and usage reports, budgets, pricing, and
33770 (license license:asl2.0)))
33772 (define-public r-paws-developer-tools
33774 (name "r-paws-developer-tools")
33779 (uri (cran-uri "paws.developer.tools" version))
33781 (base32 "16gb8g8s67al7qdd95fbigxqkih9a9p7slkyf3cga42wb6miiby2"))))
33782 (properties `((upstream-name . "paws.developer.tools")))
33783 (build-system r-build-system)
33785 (list r-paws-common))
33786 (home-page "https://github.com/paws-r/paws")
33787 (synopsis "Amazon Web Services developer tools services")
33789 "This package provides an interface to Amazon Web Services developer
33790 tools services, including version control, continuous integration and
33791 deployment, and more.")
33792 (license license:asl2.0)))
33794 (define-public r-paws-end-user-computing
33796 (name "r-paws-end-user-computing")
33801 (uri (cran-uri "paws.end.user.computing" version))
33803 (base32 "1xxsz86nx128sizym9np8vldzkbym0p3i6vcy94kq1y0cylaicv3"))))
33804 (properties `((upstream-name . "paws.end.user.computing")))
33805 (build-system r-build-system)
33807 (list r-paws-common))
33808 (home-page "https://github.com/paws-r/paws")
33809 (synopsis "Amazon Web Services end user computing services")
33811 "This package provides an interface to Amazon Web Services end user
33812 computing services, including collaborative document editing, mobile intranet,
33814 (license license:asl2.0)))
33816 (define-public r-paws-application-integration
33818 (name "r-paws-application-integration")
33823 (uri (cran-uri "paws.application.integration" version))
33826 "0llyd9hc679pad1ih0rcc38q5xxpzinhwrl8cvrkgsjgbc3agq42"))))
33828 `((upstream-name . "paws.application.integration")))
33829 (build-system r-build-system)
33831 (list r-paws-common))
33832 (home-page "https://github.com/paws-r/paws")
33833 (synopsis "Amazon Web Services application integration services")
33835 "This package provides an interface to Amazon Web Services application
33836 integration services, including Simple Queue Service (SQS) message queue,
33837 Simple Notification Service (SNS) publish/subscribe messaging, and more.")
33838 (license license:asl2.0)))
33840 (define-public r-paws-security-identity
33842 (name "r-paws-security-identity")
33847 (uri (cran-uri "paws.security.identity" version))
33850 "092lz2ipn5iqr593x7ra8c0bj64yf6315mdc3llgwrjyb4vfxif9"))))
33852 `((upstream-name . "paws.security.identity")))
33853 (build-system r-build-system)
33855 (list r-paws-common))
33856 (home-page "https://github.com/paws-r/paws")
33857 (synopsis "Amazon Web Services security, identity, and compliance services")
33859 "This package provides an interface to Amazon Web Services security,
33860 identity, and compliance services, including the Identity and Access
33861 Management (IAM) service for managing access to services and resources, and
33863 (license license:asl2.0)))
33865 (define-public r-paws-analytics
33867 (name "r-paws-analytics")
33872 (uri (cran-uri "paws.analytics" version))
33875 "04gnaxmj21l312xkrsd9bisi0bz9h6h5fyhwlqylcxi077z1yb2g"))))
33877 `((upstream-name . "paws.analytics")))
33878 (build-system r-build-system)
33880 (list r-paws-common))
33881 (home-page "https://github.com/paws-r/paws")
33882 (synopsis "Amazon Web Services analytics services")
33884 "This package provides an interface to Amazon Web Services analytics
33885 services, including Elastic MapReduce Hadoop and Spark big data service,
33886 Elasticsearch search engine, and more.")
33887 (license license:asl2.0)))
33889 (define-public r-paws-machine-learning
33891 (name "r-paws-machine-learning")
33896 (uri (cran-uri "paws.machine.learning" version))
33899 "01w2y5952pk50xjbzby2pc51xrkrzjpfxbmii1b10cl2xgzfkxsa"))))
33901 `((upstream-name . "paws.machine.learning")))
33902 (build-system r-build-system)
33904 (list r-paws-common))
33905 (home-page "https://github.com/paws-r/paws")
33906 (synopsis "Amazon Web Services machine learning services")
33908 "This package provides an interface to Amazon Web Services machine
33909 learning services, including SageMaker managed machine learning service,
33910 natural language processing, speech recognition, translation, and more.")
33911 (license license:asl2.0)))
33913 (define-public r-paws-management
33915 (name "r-paws-management")
33920 (uri (cran-uri "paws.management" version))
33923 "09k7wg0jlj40zs2yb3vldffpkdcjg7ap98n7c5lxr5plpca08swg"))))
33925 `((upstream-name . "paws.management")))
33926 (build-system r-build-system)
33928 (list r-paws-common))
33929 (home-page "https://github.com/paws-r/paws")
33930 (synopsis "Amazon Web Services management and governance services")
33932 "This package provides an interface to Amazon Web Services management and
33933 governance services, including CloudWatch application and infrastructure
33934 monitoring, Auto Scaling for automatically scaling resources, and more.")
33935 (license license:asl2.0)))
33937 (define-public r-paws-networking
33939 (name "r-paws-networking")
33944 (uri (cran-uri "paws.networking" version))
33947 "02hxaa5nlj70mdggh379ij3fn09xm8h5ldzsyf45c342prpl6zwj"))))
33949 `((upstream-name . "paws.networking")))
33950 (build-system r-build-system)
33952 (list r-paws-common))
33953 (home-page "https://github.com/paws-r/paws")
33954 (synopsis "Amazon Web Services networking and content delivery services")
33956 "This package provides an interface to Amazon Web Services networking and
33957 content delivery services, including Route 53 Domain Name System service,
33958 CloudFront content delivery, load balancing, and more.")
33959 (license license:asl2.0)))
33961 (define-public r-paws-database
33963 (name "r-paws-database")
33968 (uri (cran-uri "paws.database" version))
33971 "08jpwz95fw3f68j0wxh2lg57nn60khflldab0ryhkkbcw1iy0qyz"))))
33972 (properties `((upstream-name . "paws.database")))
33973 (build-system r-build-system)
33975 (list r-paws-common))
33976 (home-page "https://github.com/paws-r/paws")
33978 "Amazon Web Services Database Services")
33980 "This package provides an interface to Amazon Web Services database
33981 services, including Relational Database Service (RDS), DynamoDB NoSQL
33982 database, and more.")
33983 (license license:asl2.0)))
33985 (define-public r-paws-storage
33987 (name "r-paws-storage")
33992 (uri (cran-uri "paws.storage" version))
33995 "06m887vpqp5d6k3zxdlga599dsv8v3rladk7xqaxqnld1f17am04"))))
33996 (properties `((upstream-name . "paws.storage")))
33997 (build-system r-build-system)
33999 (list r-paws-common))
34000 (home-page "https://github.com/paws-r/paws")
34001 (synopsis "Amazon Web Services storage services")
34003 "This package provides an interface to Amazon Web Services storage
34004 services, including Simple Storage Service (S3).")
34005 (license license:asl2.0)))
34007 (define-public r-paws-compute
34009 (name "r-paws-compute")
34014 (uri (cran-uri "paws.compute" version))
34017 "1s7g4y2h763xf32p08drs3ygkfqb2zjikkgxb7yl91gk13zp7kjm"))))
34018 (properties `((upstream-name . "paws.compute")))
34019 (build-system r-build-system)
34021 (list r-paws-common))
34022 (home-page "https://github.com/paws-r/paws")
34023 (synopsis "Amazon Web Services compute services")
34025 "This package provides an interface to Amazon Web Services compute
34026 services, including Elastic Compute Cloud (EC2), Lambda
34027 functions-as-a-service, containers, batch processing, and more.")
34028 (license license:asl2.0)))
34030 (define-public r-paws
34037 (uri (cran-uri "paws" version))
34040 "0kn1z045r106fwqcaz52hb02bhrcblh479cajfjiq480s1iljcw6"))))
34041 (properties `((upstream-name . "paws")))
34042 (build-system r-build-system)
34044 (list r-paws-analytics
34045 r-paws-application-integration
34047 r-paws-cost-management
34048 r-paws-customer-engagement
34050 r-paws-developer-tools
34051 r-paws-end-user-computing
34052 r-paws-machine-learning
34055 r-paws-security-identity
34057 (home-page "https://github.com/paws-r/paws")
34058 (synopsis "Amazon Web Services software development kit")
34060 "This package provides an interface to Amazon Web Services, including
34061 storage, database, and compute services, such as Simple Storage Service (S3),
34062 DynamoDB NoSQL database, and Lambda functions-as-a-service.")
34063 (license license:asl2.0)))
34065 (define-public r-zoomgroupstats
34067 (name "r-zoomgroupstats")
34072 (uri (cran-uri "zoomGroupStats" version))
34075 "0gndiq92cy6gi7f833hdjvqii3cn83wz5rjvygcvjl3dw4pwv966"))))
34077 `((upstream-name . "zoomGroupStats")))
34078 (build-system r-build-system)
34089 (native-inputs (list r-knitr))
34090 (home-page "http://zoomgroupstats.org")
34091 (synopsis "Analyze text, audio, and video from Zoom meetings")
34093 "This package provides utilities for processing and analyzing the files
34094 that are exported from a recorded Zoom meeting. This includes analyzing data
34095 captured through video cameras and microphones, the text-based chat, and
34096 meta-data. You can analyze aspects of the conversation among meeting
34097 participants and their emotional expressions throughout the meeting.")
34098 (license license:expat)))
34100 (define-public r-zoom
34107 (uri (cran-uri "zoom" version))
34110 "05ikad4j1qi5y8mn77n9bw7d6ic3api9d7mbcn855w8xcc69ja4q"))))
34111 (properties `((upstream-name . "zoom")))
34112 (build-system r-build-system)
34113 (home-page "https://github.com/cbarbu/R-package-zoom")
34114 (synopsis "Spatial data visualization tool")
34116 "This package provides @code{zm}, a utility that allows you to
34117 zoom/navigate any plot when called with any active plot.")
34118 (license license:gpl3+)))
34120 (define-public r-zoolog
34127 (uri (cran-uri "zoolog" version))
34130 "06g44gjk9w73996n4h1a2q8kcd6q2mvm1vhx0iq0785gvrz18pj9"))))
34131 (properties `((upstream-name . "zoolog")))
34132 (build-system r-build-system)
34134 (list r-rdpack r-stringi))
34137 (home-page "https://josempozo.github.io/zoolog/")
34138 (synopsis "Zooarchaeological analysis with log-ratios")
34140 "This package includes functions and reference data to generate and
34141 manipulate log-ratios (also known as @dfn{log size index} (LSI) values) from
34142 measurements obtained on zooarchaeological material. Log ratios are used to
34143 compare the relative (rather than the absolute) dimensions of animals from
34144 archaeological contexts. The zoolog package is also able to seamlessly
34145 integrate data and references with heterogeneous nomenclature, which is
34146 internally managed by a zoolog thesaurus.")
34147 (license license:gpl3)))
34149 (define-public r-filehash
34151 (name "r-filehash")
34156 (uri (cran-uri "filehash" version))
34159 "1ga17smgjd4qsnf5a7qk0giwhpc5969ylqj520favs1k6b4y557k"))))
34160 (properties `((upstream-name . "filehash")))
34161 (build-system r-build-system)
34162 (home-page "http://github.com/rdpeng/filehash")
34163 (synopsis "Simple key-value database")
34165 "This package implements a simple key-value style database where
34166 character string keys are associated with data values that are stored on the
34167 disk. A simple interface is provided for inserting, retrieving, and deleting
34168 data from the database. Utilities are provided that allow filehash databases
34169 to be treated much like environments and lists are already used in R. These
34170 utilities are provided to encourage interactive and exploratory analysis on
34172 (license license:gpl2+)))
34174 (define-public r-mlearning
34176 (name "r-mlearning")
34181 (uri (cran-uri "mlearning" version))
34184 "1zjnh4gcw068li1bks60gazn3205xhmqz67hbkb1san33lmlxya3"))))
34185 (properties `((upstream-name . "mlearning")))
34186 (build-system r-build-system)
34194 (home-page "http://www.sciviews.org/zooimage")
34195 (synopsis "Machine learning algorithms with unified interface")
34197 "This package provides a unified interface to various machine learning
34198 algorithms. Confusion matrices are provided too.")
34199 (license license:gpl2+)))
34201 (define-public r-zooimage
34203 (name "r-zooimage")
34208 (uri (cran-uri "zooimage" version))
34211 "0ck8w0zb9l1n9xvjwqshq9q9l8pigy3yslq2hnfbgcwk17kk9mp8"))))
34212 (properties `((upstream-name . "zooimage")))
34213 (build-system r-build-system)
34227 (home-page "http://www.sciviews.org/zooimage")
34228 (synopsis "Analysis of numerical plankton images")
34230 "This package provides a solution for analyzing digital images of
34231 plankton. In combination with ImageJ, an image analysis system, it processes
34232 digital images, measures individuals, trains for automatic classification of
34233 taxa, and finally, measures plankton samples (abundances, total and partial
34234 size spectra or biomasses, etc.).")
34235 (license license:gpl2+)))
34237 (define-public r-zooarch
34244 (uri (cran-uri "zooaRch" version))
34247 "0grc378xppv0303sf4flfqz5002vq5a23nzbq4bsff41rww7dihc"))))
34248 (properties `((upstream-name . "zooaRch")))
34249 (build-system r-build-system)
34250 (propagated-inputs (list r-ggplot2))
34251 (native-inputs (list r-knitr))
34253 "https://cran.r-project.org/package=zooaRch")
34255 "Analytical Tools for Zooarchaeological Data")
34257 "The analysis and inference of faunal remains recovered from
34258 archaeological sites concerns the field of zooarchaeology. The zooaRch
34259 package provides analytical tools to make inferences on zooarchaeological
34260 data. Functions in this package allow users to read, manipulate, visualize,
34261 and analyze zooarchaeological data.")
34262 (license license:gpl2+)))
34264 (define-public r-zonebuilder
34266 (name "r-zonebuilder")
34271 (uri (cran-uri "zonebuilder" version))
34274 "0mxf3dz0d6bi5wwjilqivdxhy5ypnq5svky8zygha0clv45l4dmn"))))
34275 (properties `((upstream-name . "zonebuilder")))
34276 (build-system r-build-system)
34278 (list r-rcolorbrewer r-sf))
34281 (home-page "https://github.com/zonebuilders/zonebuilder")
34282 (synopsis "Create and explore geographic zoning systems")
34284 "This package provides functions, documentation and example data to help
34285 divide geographic space into discrete polygons (zones). The functions are
34286 motivated by research into the merits of different zoning systems. A flexible
34287 @code{ClockBoard} zoning system is provided, which breaks-up space by
34288 concentric rings and radial lines emanating from a central point.")
34289 (license license:gpl3)))
34291 (define-public r-zonator
34298 (uri (cran-uri "zonator" version))
34301 "1plxchpd4ypp36phl13pi9yvlrqi3lk83lv5rldrhdqynhcgfw2k"))))
34302 (properties `((upstream-name . "zonator")))
34303 (build-system r-build-system)
34305 (list r-ggplot2 r-raster r-rcolorbrewer r-reshape2 r-rgdal))
34306 (native-inputs (list r-knitr))
34307 (home-page "https://cbig.github.io/zonator/")
34308 (synopsis "Utilities for Zonation spatial conservation prioritization")
34310 "Create new analysis setups and deal with results of Zonation
34311 conservation prioritization software.")
34312 (license license:bsd-2)))
34314 (define-public r-mmwrweek
34316 (name "r-mmwrweek")
34321 (uri (cran-uri "MMWRweek" version))
34324 "1l1ks44v52iggw9nhs56lfj6804yab5b17k8fzrc6h1kvj3vda0s"))))
34325 (properties `((upstream-name . "MMWRweek")))
34326 (build-system r-build-system)
34327 (home-page "http://wwwn.cdc.gov/nndss/document/MMWR_Week_overview.pdf")
34328 (synopsis "Convert dates to MMWR day, week, and year")
34330 "The first day of any MMWR week is Sunday. MMWR week numbering is
34331 sequential beginning with 1 and incrementing with each week to a maximum of 52
34332 or 53. MMWR week #1 of an MMWR year is the first week of the year that has at
34333 least four days in the calendar year. This package provides functionality to
34334 convert dates to MMWR day, week, and year and the reverse.")
34335 (license license:gpl2+)))
34337 (define-public r-cccd
34344 (uri (cran-uri "cccd" version))
34346 (base32 "0cxh19jqappc6zq9nz3m40ybdmsp12mf7yvflsz96wks3ly2ld4y"))))
34347 (properties `((upstream-name . "cccd")))
34348 (build-system r-build-system)
34349 (propagated-inputs (list r-deldir r-fnn r-igraph r-proxy))
34350 (home-page "https://cran.r-project.org/package=cccd")
34351 (synopsis "Class cover catch digraphs")
34353 "This package provides tools to create Class Cover Catch Digraphs,
34354 neighborhood graphs, and relatives.")
34355 (license license:gpl2+)))
34357 (define-public r-crul
34364 (uri (cran-uri "crul" version))
34367 "0b8y12wb5kjylr8b4a2iarb5rpw1ydinw3lxp2ssq91pidyn2n40"))))
34368 (properties `((upstream-name . "crul")))
34369 (build-system r-build-system)
34377 (native-inputs (list r-knitr))
34378 (home-page "https://github.com/ropensci/crul")
34379 (synopsis "HTTP client")
34381 "This package provides a simple HTTP client, with tools for making HTTP
34382 requests, and mocking HTTP requests. The package is built on R6, and takes
34383 inspiration from Ruby's @code{faraday} gem.")
34384 (license license:expat)))
34386 (define-public r-gistr
34393 (uri (cran-uri "gistr" version))
34396 "0ac9ikrdg6i8xvlma0gizvsdva46408lk7hvsgkqirhy2ljy02hp"))))
34397 (properties `((upstream-name . "gistr")))
34398 (build-system r-build-system)
34408 (native-inputs (list r-knitr))
34409 (home-page "https://github.com/ropensci/gistr")
34410 (synopsis "Work with Gists in browser")
34412 "This package allows the user to create new Github gists, update gists
34413 with new files, rename files, delete files, get and delete gists, star and
34414 un-star them, fork them, open a gist in your default browser, get an embed
34415 code for a gist, list gist commits, and get rate limit information when
34417 (license license:expat)))
34419 (define-public r-rbokeh
34426 (uri (cran-uri "rbokeh" version))
34429 "1h2fpzqf17pw9d09r1g1iyxsj5qma4fsk8vnar7f1z4fjyypvi6q"))
34431 '(for-each delete-file '("inst/htmlwidgets/lib/bokehjs/bokeh-widgets.min.js"
34432 "inst/htmlwidgets/lib/bokehjs/bokeh.min.js")))))
34433 (properties `((upstream-name . "rbokeh")))
34434 (build-system r-build-system)
34437 (modify-phases %standard-phases
34438 (add-after 'unpack 'process-javascript
34439 (lambda* (#:key inputs #:allow-other-keys)
34440 (with-directory-excursion "inst/htmlwidgets/lib/bokehjs"
34442 `((,(assoc-ref inputs "js-bokeh-widgets")
34443 . "bokeh-widgets.min.js")
34444 (,(assoc-ref inputs "js-bokeh")
34445 . "bokeh.min.js"))))
34446 (for-each (lambda (source target)
34447 (format #true "Processing ~a --> ~a~%"
34449 (invoke "esbuild" source "--minify"
34450 (string-append "--outfile=" target)))
34452 (map cdr mapping)))))))))
34464 ;; Version 0.12.15 is mentioned in lib/htmlwidgets/rbokeh.yaml.
34466 `(("esbuild" ,esbuild)
34467 ("js-bokeh-widgets"
34470 (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh-widgets.js")
34473 "07v9lrkfcbdznpb10qqwi4m660zp65g85vlnfw7kn83zmkxkhhxy"))))
34477 (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh.js")
34480 "1pq0059aad7d2jv50nv9449p3w0gbkxkl0mhblc76m5d9qjqav2q"))))
34481 ("r-knitr" ,r-knitr)))
34482 (home-page "https://cran.r-project.org/web/packages/rbokeh/")
34483 (synopsis "R interface for the Bokeh visualization library")
34485 "This package provides a native R plotting library that provides a
34486 flexible declarative interface for creating interactive web-based graphics,
34487 backed by the @url{https://bokeh.pydata.org/, Bokeh visualization library}.")
34488 (license license:expat)))
34490 (define-public r-fauxpas
34497 (uri (cran-uri "fauxpas" version))
34500 "129fzqb7wsskbn50s8x0marr4wm8jrns6hiycqcsk166k3dnyyy8"))))
34501 (properties `((upstream-name . "fauxpas")))
34502 (build-system r-build-system)
34504 (list r-httpcode r-r6 r-whisker))
34507 (home-page "https://docs.ropensci.org/fauxpas")
34508 (synopsis "HTTP error helpers")
34510 "This package provides HTTP error helpers. Methods are included for
34511 general purpose HTTP error handling, as well as individual methods for every
34512 HTTP status code, both via status code numbers as well as their descriptive
34513 names. It supports the ability to adjust behavior to stop, message or
34514 warning. It includes the ability to use a custom whisker template to have any
34515 configuration of status code, short description, and verbose message.")
34516 (license license:expat)))
34518 (define-public r-webmockr
34520 (name "r-webmockr")
34525 (uri (cran-uri "webmockr" version))
34528 "06lqv3v095i51xsac8bvkjgd58l6a5azamchiip8m2y7q0nm4iw9"))))
34529 (properties `((upstream-name . "webmockr")))
34530 (build-system r-build-system)
34540 (home-page "https://github.com/ropensci/webmockr")
34541 (synopsis "Stubbing and setting expectations on HTTP Requests")
34543 "This is a package for stubbing and setting expectations on HTTP
34544 requests. It includes tools for stubbing HTTP requests, including expected
34545 request conditions and response conditions. You can match on HTTP method,
34546 query parameters, request body, headers and more. It can be used for unit
34547 tests or outside of a testing context.")
34548 (license license:expat)))
34550 (define-public r-iotools
34557 (uri (cran-uri "iotools" version))
34559 (base32 "07q0z0kszm1xx5hfhisfliyrcsxd8dc5mx0a2bwwnv5l1xzmix17"))))
34560 (properties `((upstream-name . "iotools")))
34561 (build-system r-build-system)
34562 (home-page "https://www.rforge.net/iotools")
34563 (synopsis "I/O tools for streaming")
34564 (description "This package provides basic I/O tools for streaming and data
34567 (license license:gpl3)))
34569 (define-public r-wordspace
34571 (name "r-wordspace")
34576 (uri (cran-uri "wordspace" version))
34578 (base32 "17fqd4zrsklv2ik3lg00x66yasfh1kyhs3k9ri6lrk56wwv6hzb2"))))
34579 (properties `((upstream-name . "wordspace")))
34580 (build-system r-build-system)
34582 (list r-cluster r-iotools r-mass r-matrix r-rcpp r-sparsesvd))
34583 (native-inputs (list r-knitr))
34584 (home-page "https://wordspace.r-forge.r-project.org/")
34585 (synopsis "Distributional semantic models in R")
34587 "The wordspace package turns R into an interactive laboratory for
34588 empirical research on @dfn{distributional semantic models} (DSM). It consists
34589 of a small set of carefully designed functions, most of which
34592 @item encapsulate non-trivial R operations in a user-friendly manner or
34593 @item provide efficient and memory-lean C implementations of key operations.
34596 (license license:gpl3)))
34598 (define-public r-maxlik
34605 (uri (cran-uri "maxLik" version))
34607 (base32 "0pdigfpyiqacj2ydhpn5w1h89dz1ydk0syzs25lsgdi40sz0bvkw"))))
34608 (properties `((upstream-name . "maxLik")))
34609 (build-system r-build-system)
34610 (propagated-inputs (list r-generics r-misctools r-sandwich))
34611 (home-page "https://cran.r-project.org/package=maxLik")
34612 (synopsis "Maximum Likelihood Estimation and related tools")
34614 "This package provides functions for @dfn{Maximum Likelihood} (ML) estimation,
34615 non-linear optimization, and related tools. It includes a unified way to call
34616 different optimizers, and classes and methods to handle the results from the
34617 Maximum Likelihood viewpoint. It also includes a number of convenience tools
34618 for testing and developing your own models.")
34619 (license license:gpl2+)))
34621 (define-public r-misctools
34623 (name "r-misctools")
34628 (uri (cran-uri "miscTools" version))
34630 (base32 "16pwfxpyl0zv3hjxx2kjchkg7p6kbj0s2rrpskj7rkhjr9imlg5y"))))
34631 (properties `((upstream-name . "miscTools")))
34632 (build-system r-build-system)
34633 (propagated-inputs (list r-digest))
34634 (home-page "http://www.micEcon.org")
34635 (synopsis "Miscellaneous tools and utilities")
34637 "This package provides miscellaneous small tools and utilities. Many of
34638 them facilitate the work with matrices, e.g. inserting rows or columns,
34639 creating symmetric matrices, or checking for semidefiniteness. Other tools
34640 facilitate the work with regression models, e.g. extracting the standard
34641 errors, obtaining the number of (estimated) parameters, or calculating
34642 R-squared values.")
34643 (license license:gpl2+)))
34645 (define-public r-mockery
34652 (uri (cran-uri "mockery" version))
34655 "0sj77m9vgn4bzb8c8nq93xb9lm8ih8rcb7sfccripraibibg3jcz"))))
34656 (properties `((upstream-name . "mockery")))
34657 (build-system r-build-system)
34662 (home-page "https://github.com/jfiksel/mockery")
34663 (synopsis "Mocking library for R")
34665 "The two main functionalities of this package are creating mock
34666 objects (functions) and selectively intercepting calls to a given function
34667 that originate in some other function. It can be used with any testing
34668 framework available for R. Mock objects can be injected with either this
34669 package's own @code{stub} function or a similar @code{with_mock} facility
34670 present in the @code{testthat} package.")
34671 (license license:expat)))
34673 (define-public r-zoltr
34680 (uri (cran-uri "zoltr" version))
34683 "12zh7y3pwidclscgvd0b0iaqq9j5y8mc8xd6pz4vs0jy5qs3ahar"))))
34684 (properties `((upstream-name . "zoltr")))
34685 (build-system r-build-system)
34697 (native-inputs (list r-knitr))
34698 (home-page "https://github.com/reichlab/zoltr")
34699 (synopsis "Interface to the Zoltar forecast repository API")
34701 "Zoltar is a website that provides a repository of model forecast results
34702 in a standardized format and a central location. It supports storing,
34703 retrieving, comparing, and analyzing time series forecasts for prediction
34704 challenges of interest to the modeling community. This package provides
34705 functions for working with the Zoltar API, including connecting and
34706 authenticating, getting information about projects, models, and forecasts,
34707 deleting and uploading forecast data, and downloading scores.")
34708 (license license:gpl3)))
34710 (define-public r-zoib
34717 (uri (cran-uri "zoib" version))
34720 "0inm7f2pc68ksqxvq12xp9jc99vj7ydylvs24ip12nksbj5k1n8f"))))
34721 (properties `((upstream-name . "zoib")))
34722 (build-system r-build-system)
34724 (list r-abind r-coda r-formula r-rjags))
34725 (home-page "https://www.r-project.org")
34726 (synopsis "Bayesian inference for beta regression")
34728 "This package lets you fit beta regression and zero-or-one inflated beta
34729 regression and obtain Bayesian inference of the model via the Markov Chain
34730 Monte Carlo approach implemented in JAGS.")
34731 (license license:gpl3+)))
34733 (define-public r-logger
34740 (uri (cran-uri "logger" version))
34742 (base32 "08kym5i5fvbf5xhh9qdszp4jdgyc7j7zpnwzy68wabqz73aff6sg"))))
34743 (properties `((upstream-name . "logger")))
34744 (build-system r-build-system)
34745 (native-inputs (list r-knitr))
34746 (home-page "https://daroczig.github.io/logger/")
34747 (synopsis "Lightweight and flexible logging utility")
34749 "Inspired by the the @code{futile.logger} R package and @code{logging}
34750 Python module, this utility provides a flexible and extensible way of
34751 formatting and delivering log messages with low overhead.")
34752 (license license:agpl3+)))
34754 (define-public r-fasterize
34756 (name "r-fasterize")
34761 (uri (cran-uri "fasterize" version))
34763 (base32 "10bzl77c1b9jhcn1xp467qzp2n8c7s3wpxn53qjh1nwvbri5kd32"))))
34764 (properties `((upstream-name . "fasterize")))
34765 (build-system r-build-system)
34767 (list r-raster r-rcpp r-rcpparmadillo r-sp))
34768 (native-inputs (list r-knitr))
34769 (home-page "https://github.com/ecohealthalliance/fasterize")
34770 (synopsis "Fast Polygon to Raster Conversion")
34772 "This package provides a drop-in replacement for @code{rasterize} from
34773 the @code{raster} package that takes sf-type objects, and is much faster.
34774 There is support for the main options provided by the @code{rasterize}
34775 function, including setting the field used and background value, and
34776 options for aggregating multi-layer rasters.")
34777 (license license:expat)))
34779 (define-public r-bien
34786 (uri (cran-uri "BIEN" version))
34788 (base32 "0s98n6zbf48vssd3h63k6kashcxv1kawcb026n0ngsfpc5dv6i48"))))
34789 (properties `((upstream-name . "BIEN")))
34790 (build-system r-build-system)
34805 (home-page "https://cran.r-project.org/package=BIEN")
34806 (synopsis "Tools for accessing the BIEN database")
34808 "This package provides tools for accessing the Botanical Information and
34809 Ecology Network (BIEN) database. The BIEN database contains cleaned and
34810 standardized botanical data including occurrence, trait, plot and taxonomic
34811 data. This package provides functions that query the BIEN database by
34812 constructing and executing optimized SQL queries.")
34813 (license license:expat)))
34815 (define-public r-varhandle
34817 (name "r-varhandle")
34822 (uri (cran-uri "varhandle" version))
34824 (base32 "1l42d0s6fbjjc9l28a2m3myxkrx2c0p0b9yj8wjjjgilw19yc3lv"))))
34825 (properties `((upstream-name . "varhandle")))
34826 (build-system r-build-system)
34827 (home-page "https://bitbucket.org/mehrad_mahmoudian/varhandle")
34828 (synopsis "Functions for robust variable handling")
34830 "This package contains some functions to help users (especially data
34831 explorers) to make more sense of their variables and take the most out of
34832 variables and hardware resources. Functions in this package are supposed to
34833 be efficient and easy to use.")
34834 (license license:gpl2+)))
34836 (define-public r-ggh4x
34843 (uri (cran-uri "ggh4x" version))
34846 "11mskrby3gyjhkvnkcwl2ar1bdh4h45y48dfnm4kzgc7nwvdl3ia"))))
34847 (properties `((upstream-name . "ggh4x")))
34848 (build-system r-build-system)
34859 (home-page "https://github.com/teunbrand/ggh4x")
34860 (synopsis "Extension for ggplot2")
34861 (description "This package is a @code{ggplot2} extension. It provides some
34862 utility functions that do not entirely fit within the grammar of graphics
34863 concept. The package extends @code{ggpplots} facets through customisation, by
34864 setting individual scales per panel, resizing panels and providing nested
34865 facets. It also allows multiple colour, fill scales per plot and hosts a
34866 smaller collection of stats, geoms and axis guides.")
34867 (license license:expat)))
34869 (define-public r-gghalves
34871 (name "r-gghalves")
34876 (uri (cran-uri "gghalves" version))
34879 "1lj4c38fzxwg8gy57ymf00lqjdplb7v2a0lnd262c1d5cavqiws4"))))
34880 (properties `((upstream-name . "gghalves")))
34881 (build-system r-build-system)
34883 (list r-ggplot2 r-gtable))
34886 (home-page "https://github.com/erocoar/gghalves")
34887 (synopsis "Compose half-half plots using your favourite geoms")
34888 (description "This package provides a @code{ggplot2} extension for easy
34889 plotting of half-half geom combinations. Think half boxplot and half
34890 jitterplot, or half violinplot and half dotplot.")
34891 (license license:expat)))
34893 (define-public r-zoeppritz
34895 (name "r-zoeppritz")
34899 (uri (cran-uri "zoeppritz" version))
34902 "1711szx9zz17q6pfinyzlyrw7m9772c8ywlixqar2l165bkjalgm"))))
34903 (properties `((upstream-name . "zoeppritz")))
34904 (build-system r-build-system)
34905 (home-page "https://cran.r-project.org/package=zoeppritz")
34906 (synopsis "Seismic reflection and scattering coefficients for waves")
34908 "The @code{r-zoeppritz} package calculates and plots scattering matrix
34909 coefficients or scattering amplitudes, for seismological P and S-waves at an
34911 (license license:gpl2+)))
34913 (define-public r-metadat
34919 (uri (cran-uri "metadat" version))
34922 "1f7mb3pw5d0akr09jjva06ay223izhpzbr21bapnw99x1kiybk7h"))))
34923 (properties `((upstream-name . "metadat")))
34924 (build-system r-build-system)
34925 (propagated-inputs (list r-mathjaxr))
34926 (home-page "https://github.com/wviechtb/metadat")
34927 (synopsis "Meta-Analysis Datasets")
34929 "This package provides a collection of meta-analysis datasets for teaching
34930 purposes, illustrating/testing meta-analytic methods, and validating published
34932 (license license:gpl2+)))
34934 (define-public r-mathjaxr
34936 (name "r-mathjaxr")
34940 (uri (cran-uri "mathjaxr" version))
34943 "0yf1sfkb2kjsplipl2v4k2gp20li9xzsynclg228sy0v243pdi7c"))
34944 (modules '((guix build utils)))
34947 (delete-file-recursively "src/mathjax/es5/input")
34948 (delete-file-recursively "src/mathjax/es5/output")
34949 (delete-file "src/mathjax/es5/tex-chtml-full.js")))))
34950 (properties `((upstream-name . "mathjaxr")))
34951 (build-system r-build-system)
34955 `(modify-phases %standard-phases
34956 (add-after 'unpack 'use-js-mathjax
34957 (lambda* (#:key inputs #:allow-other-keys)
34959 (search-input-directory
34960 inputs "/share/javascript/mathjax/es5/output")
34961 "src/mathjax/es5/output")
34963 (search-input-directory
34964 inputs "/share/javascript/mathjax/es5/input")
34965 "src/mathjax/es5/input")
34968 inputs "/share/javascript/mathjax/es5/tex-chtml-full.js")
34969 "src/mathjax/es5/tex-chtml-full.js"))))))
34971 (list js-mathjax-for-r-mathjaxr))
34972 (home-page "https://github.com/wviechtb/mathjaxr")
34973 (synopsis "Use Mathjax in Rd Files")
34975 "This package provides MathJax and macros to enable its use within Rd files
34976 for rendering equations in the HTML help files.")
34977 (license (list license:asl2.0 license:gpl3))))
34979 (define-public r-spacefillr
34981 (name "r-spacefillr")
34985 (uri (cran-uri "spacefillr" version))
34988 "0c4yasc1zizjmhd2ciyz86lg76fsrxvl19yjkb2fmkda9rmnc0bf"))))
34989 (properties `((upstream-name . "spacefillr")))
34990 (build-system r-build-system)
34991 (propagated-inputs (list r-rcpp))
34992 (home-page "https://github.com/tylermorganwall/spacefillr")
34993 (synopsis "Space-Filling Random and Quasi-Random Sequences")
34995 "@code{spacefillr} enables generation of random and quasi-random
34996 space-filling sequences. It supports the following sequences: Halton, Sobol,
34997 Owen-scrambled Sobol, Owen-scrambled Sobol with errors distributed as blue
34998 noise, progressive jittered, progressive multi-jittered (PMJ), PMJ with blue
34999 noise, PMJ02, and PMJ02 with blue noise. The package also includes a C++
35001 (license license:expat)))
35003 (define-public r-spacetime
35005 (name "r-spacetime")
35009 (uri (cran-uri "spacetime" version))
35012 "0nacy8a9mbxh22q248zxhnlcfrmgj9yslrgc3kj35zscmcks15s2"))))
35013 (properties `((upstream-name . "spacetime")))
35014 (build-system r-build-system)
35015 (propagated-inputs (list r-lattice r-sp r-zoo r-xts r-intervals))
35016 (native-inputs (list r-knitr))
35017 (home-page "https://github.com/edzer/spacetime/")
35018 (synopsis "Classes and methods for spatio-temporal data")
35020 "@command{spacetime} provides classes and methods for spatio-temporal
35021 data, including space-time regular lattices, sparse lattices, irregular data,
35022 and trajectories; utility functions for plotting data as map sequences (lattice
35023 or animation) or multiple time series; methods for spatial and temporal
35024 matching or aggregation, retrieving coordinates, print, summary, etc.")
35025 (license license:gpl2+)))
35027 (define-public r-gstat
35033 (uri (cran-uri "gstat" version))
35036 "0vrdiyjav92wbbms8ljmv1i0l8cdjblfnmhyrsd1a7v0z93fp9jp"))))
35037 (properties `((upstream-name . "gstat")))
35038 (build-system r-build-system)
35048 (home-page "https://github.com/r-spatial/gstat/")
35049 (synopsis "Spatial and spatio-temporal geostatistical modelling,
35050 prediction and simulation")
35052 "This package enables variogram modelling, including: simple,
35053 ordinary and universal point or block (co)kriging; spatio-temporal
35054 kriging; and sequential Gaussian or indicator (co)simulation. It
35055 includes variogram and variogram map plotting utility functions, and
35056 supports @command{sf} and @command{stars}.")
35057 (license license:gpl2+)))
35059 (define-public r-automap
35065 (uri (cran-uri "automap" version))
35068 "0jz0p28gmx9cpzv4cz0xhbml3w1inf2nsd2ynbhmfxg5rm2f7dca"))))
35069 (properties `((upstream-name . "automap")))
35070 (build-system r-build-system)
35071 (propagated-inputs (list r-ggplot2
35077 (home-page "https://cran.r-project.org/package=automap")
35078 (synopsis "Automatic interpolation package")
35080 "@command{automap} performs an automatic interpolation by automatically
35081 estimating the variogram and then calling @command{gstat}.")
35082 (license (list license:gpl2+ license:gpl3+))))
35084 (define-public r-cartogram
35086 (name "r-cartogram")
35090 (uri (cran-uri "cartogram" version))
35093 "0kz8hwdr5n8llkylwaixnb66f4pzaxxniz57spxhqizmi6qay7yd"))))
35094 (properties `((upstream-name . "cartogram")))
35095 (build-system r-build-system)
35096 (propagated-inputs (list r-packcircles r-sf))
35097 (home-page "https://github.com/sjewo/cartogram/")
35098 (synopsis "Create cartograms with R")
35099 (description "This package enables construction of continuous and
35100 non-contiguous area cartograms.")
35101 (license license:gpl3)))
35103 (define-public r-measurements
35105 (name "r-measurements")
35109 (uri (cran-uri "measurements" version))
35112 "1kihavs9vgxwqjm9z1zjjngkmcwfsv8dg7nn9nrv5r06k5hv8bz6"))))
35113 (properties `((upstream-name . "measurements")))
35114 (build-system r-build-system)
35115 (home-page "https://cran.r-project.org/web/packages/measurements/")
35116 (synopsis "Tools for units of measurement")
35118 "This package provides a collection of tools to make working with physical
35119 measurements easier. One can convert between metric and imperial units, or
35120 calculate a dimension's unknown value from other dimensions' measurements.")
35121 (license license:gpl3)))
35123 (define-public r-sungeo
35126 (version "0.2.288")
35129 (uri (cran-uri "SUNGEO" version))
35132 "0c8y0ngx1020rw2v00rxmq8syd72f41ckik5sg7gigg7d80gi31w"))
35133 (modules '((guix build utils)))
35135 ;; Fortunately, the package does not actually use
35136 ;; rmapshaper, which has got a js/node dependency.
35137 ;; The only occurrence is in R/point2poly_tess.R,
35138 ;; where it is commented out.
35139 (substitute* "DESCRIPTION"
35140 (("rmapshaper,") ""))
35141 (substitute* "NAMESPACE"
35142 (("importFrom\\(rmapshaper,ms_dissolve\\)
35145 (properties `((upstream-name . "SUNGEO")))
35146 (build-system r-build-system)
35147 (propagated-inputs (list r-automap
35165 (home-page "https://github.com/zhukovyuri/SUNGEO/")
35166 (synopsis "Sub-National Geospatial Data Archive: Geoprocessing Toolkit")
35168 "Tools for integrating spatially-misaligned GIS datasets. Part of the
35169 Sub-National Geospatial Data Archive System.")
35170 (license license:gpl2)))
35173 ;;; Avoid adding new packages to the end of this file. To reduce the chances
35174 ;;; of a merge conflict, place them above by existing packages with similar
35175 ;;; functionality or similar names.