1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 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 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 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 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 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 Simon Tournier <zimon.toutoune@gmail.com>
35 ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com>
37 ;;; This file is part of GNU Guix.
39 ;;; GNU Guix is free software; you can redistribute it and/or modify it
40 ;;; under the terms of the GNU General Public License as published by
41 ;;; the Free Software Foundation; either version 3 of the License, or (at
42 ;;; your option) any later version.
44 ;;; GNU Guix is distributed in the hope that it will be useful, but
45 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
46 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
47 ;;; GNU General Public License for more details.
49 ;;; You should have received a copy of the GNU General Public License
50 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
52 (define-module (gnu packages cran)
53 #:use-module ((guix licenses) #:prefix license:)
54 #:use-module (guix packages)
55 #:use-module (guix download)
56 #:use-module (guix git-download)
57 #:use-module (guix utils)
58 #:use-module (guix build-system gnu)
59 #:use-module (guix build-system r)
60 #:use-module (gnu packages)
61 #:use-module (gnu packages algebra)
62 #:use-module (gnu packages autotools)
63 #:use-module (gnu packages base)
64 #:use-module (gnu packages bioinformatics)
65 #:use-module (gnu packages c)
66 #:use-module (gnu packages compression)
67 #:use-module (gnu packages crypto)
68 #:use-module (gnu packages curl)
69 #:use-module (gnu packages databases)
70 #:use-module (gnu packages fontutils)
71 #:use-module (gnu packages fribidi)
72 #:use-module (gnu packages gcc)
73 #:use-module (gnu packages geo)
74 #:use-module (gnu packages ghostscript)
75 #:use-module (gnu packages gl)
76 #:use-module (gnu packages gnome)
77 #:use-module (gnu packages graph)
78 #:use-module (gnu packages gtk)
79 #:use-module (gnu packages haskell-xyz)
80 #:use-module (gnu packages icu4c)
81 #:use-module (gnu packages image)
82 #:use-module (gnu packages imagemagick)
83 #:use-module (gnu packages java)
84 #:use-module (gnu packages javascript)
85 #:use-module (gnu packages libevent)
86 #:use-module (gnu packages lisp-xyz)
87 #:use-module (gnu packages machine-learning)
88 #:use-module (gnu packages maths)
89 #:use-module (gnu packages mpi)
90 #:use-module (gnu packages multiprecision)
91 #:use-module (gnu packages networking)
92 #:use-module (gnu packages node)
93 #:use-module (gnu packages pcre)
94 #:use-module (gnu packages perl)
95 #:use-module (gnu packages pkg-config)
96 #:use-module (gnu packages pulseaudio) ;libsndfile
97 #:use-module (gnu packages python)
98 #:use-module (gnu packages python-xyz)
99 #:use-module (gnu packages sqlite)
100 #:use-module (gnu packages statistics)
101 #:use-module (gnu packages tcl)
102 #:use-module (gnu packages tls)
103 #:use-module (gnu packages version-control)
104 #:use-module (gnu packages web)
105 #:use-module (gnu packages xml)
106 #:use-module (gnu packages xorg))
108 (define-public r-brio
115 (uri (cran-uri "brio" version))
118 "0ai2pqw5zk11r0rl2xshsq095ix1sdp2vjlixz2qxvy27x145ykh"))))
119 (properties `((upstream-name . "brio")))
120 (build-system r-build-system)
121 (home-page "https://github.com/r-lib/brio")
122 (synopsis "Basic R input output")
124 "This package provides functions to handle basic input output. These
125 functions always read and write UTF-8 (8-bit Unicode Transformation Format)
126 files and provide more explicit control over line endings.")
127 (license license:expat)))
129 (define-public r-cachem
136 (uri (cran-uri "cachem" version))
139 "0y3jb96lyn3vc3nq8gs9x669w3xp69vdg5xc69qy0l356r39gp3r"))))
140 (properties `((upstream-name . "cachem")))
141 (build-system r-build-system)
143 `(("r-fastmap" ,r-fastmap)
144 ("r-rlang" ,r-rlang)))
145 (home-page "https://cachem.r-lib.org/")
146 (synopsis "Cache R objects with automatic pruning")
148 "This package provides key-value stores with automatic pruning. Caches
149 can limit either their total size or the age of the oldest object (or both),
150 automatically pruning objects to maintain the constraints.")
151 (license license:expat)))
153 (define-public r-diffobj
160 (uri (cran-uri "diffobj" version))
163 "1x3d5sk8mk0s2d7dq8wxi1zv6krlx33n22ls2jwnb58b8xrmakj1"))))
164 (properties `((upstream-name . "diffobj")))
165 (build-system r-build-system)
166 (propagated-inputs `(("r-crayon" ,r-crayon)))
167 (native-inputs `(("r-knitr" ,r-knitr)))
168 (home-page "https://github.com/brodieG/diffobj")
169 (synopsis "Diffs for R objects")
171 "Generate a colorized diff of two R objects for an intuitive
172 visualization of their differences.")
173 (license license:gpl2+)))
175 (define-public r-waldo
182 (uri (cran-uri "waldo" version))
185 "0lsw8p4wiggqm9fvh5vgmf0ms0npcg3hcwyzlg5ahv5yx4pv5fhz"))))
186 (properties `((upstream-name . "waldo")))
187 (build-system r-build-system)
190 ("r-diffobj" ,r-diffobj)
193 ("r-rematch2" ,r-rematch2)
195 ("r-tibble" ,r-tibble)))
196 (home-page "https://github.com/r-lib/waldo")
197 (synopsis "Find differences between R objects")
199 "Compare complex R objects and reveal the key differences. This package
200 was designed particularly for use in testing packages where being able to
201 quickly isolate key differences makes understanding test failures much
203 (license license:expat)))
205 (define-public r-rticles
212 (uri (cran-uri "rticles" version))
215 "1srczjy9dqw06glrv95798xsg462kfbbwm3yk1fv1zhpz9jhakwv"))))
216 (properties `((upstream-name . "rticles")))
217 (build-system r-build-system)
219 `(("r-knitr" ,r-knitr)
220 ("r-rmarkdown" ,r-rmarkdown)
221 ("r-tinytex" ,r-tinytex)
224 (home-page "https://github.com/rstudio/rticles")
225 (synopsis "Article formats for R Markdown")
227 "This package provides a suite of custom R Markdown formats and templates
228 for authoring journal articles and conference submissions.")
229 (license license:gpl3)))
231 (define-public r-bezier
237 (uri (cran-uri "bezier" version))
240 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
241 (build-system r-build-system)
242 (home-page "https://cran.r-project.org/web/packages/bezier/")
243 (synopsis "Bezier curve and spline toolkit")
245 "This package is a toolkit for working with Bezier curves and splines.
246 The package provides functions for point generation, arc length estimation,
247 degree elevation and curve fitting.")
248 (license license:gpl2+)))
257 (uri (cran-uri "V8" version))
260 "1g9z22pc8ydx1yhv57ww2d2jg5hvrl7ilwa79x89zgn17jha5j7m"))))
261 (properties `((upstream-name . "V8")))
262 (build-system r-build-system)
265 (modify-phases %standard-phases
266 (add-after 'unpack 'find-v8
267 (lambda* (#:key inputs #:allow-other-keys)
268 (substitute* "configure"
270 (string-append "PKG_LIBS="
271 (assoc-ref inputs "node")
272 "/lib/libnode.so.64\n")))
273 (setenv "INCLUDE_DIR"
275 (assoc-ref inputs "node")
279 (assoc-ref inputs "node") "/lib"))
282 `(("node" ,libnode)))
285 ("r-jsonlite" ,r-jsonlite)
288 `(("r-knitr" ,r-knitr)))
289 (home-page "https://jeroen.cran.dev/V8")
290 (synopsis "Embedded JavaScript and WebAssembly engine for R")
292 "This package provides an R interface to V8: Google's JavaScript and
293 WebAssembly engine.")
294 (license license:expat)))
303 (uri (cran-uri "DOT" version))
306 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
307 (properties `((upstream-name . "DOT")))
308 (build-system r-build-system)
311 (home-page "http://haghish.com/dot")
312 (synopsis "Render and Export DOT Graphs in R")
314 "This package provides tools to render DOT diagram markup language in R
315 and also provides the possibility to export the graphs in PostScript and
316 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
317 programming packages such as @code{knitr} and @code{rmarkdown}.")
318 (license license:expat)))
320 (define-public r-clipr
327 (uri (cran-uri "clipr" version))
330 "1ywa4kipwc2d7na6iiz3wzdah99h6aynnh74yxl3nzl40xxlgbgz"))))
331 (build-system r-build-system)
333 `(("r-knitr" ,r-knitr)))
334 (home-page "https://github.com/mdlincoln/clipr")
335 (synopsis "Read and write from the system clipboard")
337 "This package provides simple utility functions to read from and write to
338 the system clipboards.")
339 (license license:gpl3)))
347 (uri (cran-uri "zoo" version))
350 "1rrw431jwaxd9xljp73f15rhcxvwc0xlyrmr0ghi5fj7a03c932f"))))
351 (build-system r-build-system)
353 `(("r-lattice" ,r-lattice)))
354 (home-page "http://zoo.R-Forge.R-project.org/")
355 (synopsis "S3 infrastructure for regular and irregular time series")
356 (description "This package contains an S3 class with methods for totally
357 ordered indexed observations. It is particularly aimed at irregular time
358 series of numeric vectors/matrices and factors.")
359 (license license:gpl2+)))
361 (define-public r-ggalluvial
363 (name "r-ggalluvial")
367 (uri (cran-uri "ggalluvial" version))
370 "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3"))))
371 (properties `((upstream-name . "ggalluvial")))
372 (build-system r-build-system)
374 `(("r-dplyr" ,r-dplyr)
375 ("r-ggplot2" ,r-ggplot2)
376 ("r-lazyeval" ,r-lazyeval)
379 ("r-tidyselect" ,r-tidyselect)))
381 `(("r-knitr" ,r-knitr)))
382 (home-page "http://corybrunson.github.io/ggalluvial/")
383 (synopsis "Alluvial plots for ggplot2")
384 (description "This package provides alluvial plots for @code{ggplot2}.
385 Alluvial plots use variable-width ribbons and stacked bar plots to represent
386 multi-dimensional or repeated-measures data with categorical or ordinal
388 (license license:gpl3)))
390 (define-public r-ggpmisc
396 (uri (cran-uri "ggpmisc" version))
399 "0kcrh73nwha52vl6z35wafmqs5lsdh2p4nqvi2ir70cv1k5y46zf"))))
400 (build-system r-build-system)
402 `(("r-dplyr" ,r-dplyr)
403 ("r-generics" ,r-generics)
405 ("r-ggplot2" ,r-ggplot2)
406 ("r-gridextra" ,r-gridextra)
407 ("r-lubridate" ,r-lubridate)
408 ("r-magrittr" ,r-magrittr)
411 ("r-polynom" ,r-polynom)
413 ("r-scales" ,r-scales)
414 ("r-splus2r" ,r-splus2r)
415 ("r-stringr" ,r-stringr)
416 ("r-tibble" ,r-tibble)
420 `(("r-knitr" ,r-knitr)))
421 (home-page "https://www.r4photobiology.info/")
422 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
423 (description "This package provides extensions to @code{ggplot2},
424 respecting the grammar of its graphics paradigm.")
425 (license license:gpl2+)))
427 (define-public r-gprofiler
434 (uri (cran-uri "gProfileR" version))
437 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
438 (properties `((upstream-name . "gProfileR")))
439 (build-system r-build-system)
442 ("r-rcurl" ,r-rcurl)))
443 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
444 (synopsis "Interface to the g:Profiler toolkit")
446 "This package provides tools for functional enrichment analysis,
447 gene identifier conversion and mapping homologous genes across related
448 organisms via the @code{g:Profiler} toolkit.")
449 (license license:gpl2+)))
451 (define-public r-gprofiler2
453 (name "r-gprofiler2")
458 (uri (cran-uri "gprofiler2" version))
461 "0q8hl3gdxy34c0181ql405fdklz82nfvmwdcafd5mzf935rjpyjg"))))
462 (properties `((upstream-name . "gprofiler2")))
463 (build-system r-build-system)
465 `(("r-crosstalk" ,r-crosstalk)
467 ("r-ggplot2" ,r-ggplot2)
468 ("r-gridextra" ,r-gridextra)
469 ("r-jsonlite" ,r-jsonlite)
470 ("r-plotly" ,r-plotly)
473 ("r-viridislite" ,r-viridislite)))
474 (native-inputs `(("r-knitr" ,r-knitr)))
475 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
476 (synopsis "Interface to the g:Profiler toolset")
478 "This package provides a toolset for functional enrichment analysis and
479 visualization, gene/protein/SNP identifier conversion and mapping orthologous
480 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
484 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
486 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
488 @item @code{g:Orth}, orthology search across species;
489 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
490 genes and variant effects.
493 This package is an R interface corresponding to the 2019 update of
494 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
496 (license license:gpl2+)))
498 (define-public r-oenb
505 (uri (cran-uri "oenb" version))
508 "1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz"))))
509 (properties `((upstream-name . "oenb")))
510 (build-system r-build-system)
512 `(("r-dplyr" ,r-dplyr)
514 (native-inputs `(("r-knitr" ,r-knitr)))
515 (home-page "https://github.com/franzmohr/oenb")
516 (synopsis "Tools for the OeNB Data Web Service")
518 "Tools to access data from the data web service of the
519 @acronym{OeNB, Oesterreichische Nationalbank},
520 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
521 (license license:gpl2+)))
523 (define-public r-scales
530 (uri (cran-uri "scales" version))
532 (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0"))))
533 (build-system r-build-system)
535 `(("r-farver" ,r-farver)
536 ("r-labeling" ,r-labeling)
537 ("r-lifecycle" ,r-lifecycle)
538 ("r-munsell" ,r-munsell)
539 ("r-rcolorbrewer" ,r-rcolorbrewer)
541 ("r-viridislite" ,r-viridislite)))
542 (home-page "https://github.com/hadley/scales")
543 (synopsis "Scale functions for visualization")
545 "This package provides graphical scales that map data to aesthetics, and
546 provides methods for automatically determining breaks and labels for axes and
548 (license license:expat)))
550 (define-public r-pheatmap
557 (uri (cran-uri "pheatmap" version))
560 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
561 (build-system r-build-system)
563 `(("r-gtable" ,r-gtable)
564 ("r-rcolorbrewer" ,r-rcolorbrewer)
565 ("r-scales" ,r-scales)))
566 (home-page "https://cran.r-project.org/web/packages/pheatmap")
567 (synopsis "Pretty heatmaps")
569 "This package provides an implementation of heatmaps that offers more
570 control over dimensions and appearance.")
571 (license license:gpl2+)))
579 (uri (cran-uri "ecp" version))
582 "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8"))))
583 (build-system r-build-system)
585 `(("r-rcpp" ,r-rcpp)))
586 (home-page "https://cran.r-project.org/web/packages/ecp/")
587 (synopsis "Multiple change-point analysis of multivariate data")
589 "This package implements various procedures for finding multiple
590 change-points. Two methods make use of dynamic programming and pruning, with
591 no distributional assumptions other than the existence of certain absolute
592 moments in one method. Hierarchical and exact search methods are included.
593 All methods return the set of estimated change-points as well as other summary
595 (license license:gpl2+)))
597 (define-public r-ellipsis
604 (uri (cran-uri "ellipsis" version))
607 "1nvmkcca57d9067rcggw1gby80ibx5hplk2myz0cs9zwilaib2jg"))))
608 (build-system r-build-system)
610 `(("r-rlang" ,r-rlang)))
611 (home-page "https://github.com/hadley/ellipsis")
612 (synopsis "Tools for working with additional arguments")
614 "In S3 generics, it's useful to take @code{...} so that methods can have
615 additional arguments. But this flexibility comes at a cost: misspelled
616 arguments will be silently ignored. The @code{ellipsis} package is an
617 experiment that allows a generic to warn if any arguments passed in @code{...}
619 (license license:gpl3)))
628 (uri (cran-uri "grr" version))
631 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
632 (build-system r-build-system)
633 (home-page "https://cran.r-project.org/web/packages/grr")
634 (synopsis "Alternative implementations of base R functions")
636 "This package provides alternative implementations of some base R
637 functions, including @code{sort}, @code{order}, and @code{match}. The
638 functions are simplified but can be faster or have other advantages.")
639 (license license:gpl3)))
641 (define-public r-matrix-utils
643 (name "r-matrix-utils")
648 (uri (cran-uri "Matrix.utils" version))
651 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
652 (properties `((upstream-name . "Matrix.utils")))
653 (build-system r-build-system)
656 ("r-matrix" ,r-matrix)))
657 (home-page "https://github.com/cvarrichio/Matrix.utils")
659 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
661 "This package implements data manipulation methods such as @code{cast},
662 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
664 (license license:gpl3)))
666 (define-public r-mboost
672 (uri (cran-uri "mboost" version))
675 "1dgyc38axfk2a430wsdnnk76xikizkyxf5r0l1kbp6cacrx6idz0"))))
676 (build-system r-build-system)
678 `(("r-lattice" ,r-lattice)
679 ("r-matrix" ,r-matrix)
681 ("r-partykit" ,r-partykit)
682 ("r-quadprog" ,r-quadprog)
684 ("r-survival" ,r-survival)))
685 (home-page "https://github.com/boost-R/mboost")
686 (synopsis "Model-based boosting")
688 "This package provides a functional gradient descent algorithm (boosting)
689 for optimizing general risk functions utilizing component-wise (penalised)
690 least squares estimates or regression trees as base-learners for fitting
691 generalized linear, additive and interaction models to potentially
692 high-dimensional data.")
693 (license license:gpl2)))
695 (define-public r-shadowtext
697 (name "r-shadowtext")
701 (uri (cran-uri "shadowtext" version))
704 "1s1ip8zfr684a3ld7hvf524bhn2j31k6d1wbhh1ni0flsggv2ckf"))))
705 (properties `((upstream-name . "shadowtext")))
706 (build-system r-build-system)
708 `(("r-ggplot2" ,r-ggplot2)
709 ("r-scales" ,r-scales)))
711 `(("r-knitr" ,r-knitr)))
712 (home-page "https://github.com/GuangchuangYu/shadowtext/")
713 (synopsis "Shadow text grob and layer")
714 (description "This package implements @code{shadowtextGrob()} for
715 @code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}.
716 These functions draw text grob with background shadow.")
717 (license license:artistic2.0)))
726 (uri (cran-uri "sys" version))
729 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p"))))
730 (build-system r-build-system)
731 (home-page "https://github.com/jeroen/sys")
732 (synopsis "Powerful and reliable tools for running system commands in R")
734 "This package provides drop-in replacements for the base @code{system2()}
735 function with fine control and consistent behavior across platforms. It
736 supports clean interruption, timeout, background tasks, and streaming STDIN /
737 STDOUT / STDERR over binary or text connections. The package also provides
738 functions for evaluating expressions inside a temporary fork. Such
739 evaluations have no side effects on the main R process, and support reliable
740 interrupts and timeouts. This provides the basis for a sandboxing
742 (license license:expat)))
744 (define-public r-ashr
750 (uri (cran-uri "ashr" version))
753 "1rqb5j30ylaf1h4l66x4jxyn5inrvhc42d90qd5mgkxsq0ghdlr4"))))
754 (properties `((upstream-name . "ashr")))
755 (build-system r-build-system)
757 `(("r-etrunct" ,r-etrunct)
758 ("r-invgamma" ,r-invgamma)
759 ("r-matrix" ,r-matrix)
760 ("r-mixsqp" ,r-mixsqp)
762 ("r-squarem" ,r-squarem)
763 ("r-truncnorm" ,r-truncnorm)))
765 `(("r-knitr" ,r-knitr)))
766 (home-page "https://github.com/stephens999/ashr")
767 (synopsis "Methods for adaptive shrinkage, using empirical bayes")
768 (description "This package implements an empirical Bayes approach for
769 large-scale hypothesis testing and false discovery rate estimation.")
770 (license license:gpl3+)))
772 (define-public r-askpass
779 (uri (cran-uri "askpass" version))
782 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
783 (build-system r-build-system)
784 (propagated-inputs `(("r-sys" ,r-sys)))
785 (home-page "https://github.com/jeroen/askpass")
786 (synopsis "Safe password entry for R")
788 "This package provides cross-platform utilities for prompting the user
789 for credentials or a passphrase, for example to authenticate with a server or
790 read a protected key.")
791 (license license:expat)))
793 (define-public r-vegan
800 (uri (cran-uri "vegan" version))
803 "0aj6m9l1vkh32sar6fyvq4p8j4h2f2f347w1300qnzgaa5lmhfz6"))))
804 (build-system r-build-system)
806 `(("r-knitr" ,r-knitr) ; needed for vignettes
807 ("gfortran" ,gfortran)))
809 `(("r-cluster" ,r-cluster)
810 ("r-lattice" ,r-lattice)
813 ("r-permute" ,r-permute)))
814 (home-page "https://cran.r-project.org/web/packages/vegan")
815 (synopsis "Functions for community ecology")
817 "The vegan package provides tools for descriptive community ecology. It
818 has most basic functions of diversity analysis, community ordination and
819 dissimilarity analysis. Most of its multivariate tools can be used for other
820 data types as well.")
821 (license license:gpl2+)))
823 (define-public r-tidyverse
830 (uri (cran-uri "tidyverse" version))
833 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
834 (build-system r-build-system)
836 `(("r-broom" ,r-broom)
838 ("r-crayon" ,r-crayon)
839 ("r-dbplyr" ,r-dbplyr)
841 ("r-forcats" ,r-forcats)
842 ("r-ggplot2" ,r-ggplot2)
846 ("r-jsonlite" ,r-jsonlite)
847 ("r-lubridate" ,r-lubridate)
848 ("r-magrittr" ,r-magrittr)
849 ("r-modelr" ,r-modelr)
850 ("r-pillar" ,r-pillar)
853 ("r-readxl" ,r-readxl)
854 ("r-reprex" ,r-reprex)
856 ("r-rstudioapi" ,r-rstudioapi)
858 ("r-stringr" ,r-stringr)
859 ("r-tibble" ,r-tibble)
862 (home-page "https://tidyverse.tidyverse.org")
863 (synopsis "Install and load packages from the \"Tidyverse\"")
865 "The @code{tidyverse} is a set of packages that work in harmony because
866 they share common data representations and API design. This package is
867 designed to make it easy to install and load multiple tidyverse packages in a
869 (license license:gpl3)))
871 (define-public r-rvest
878 (uri (cran-uri "rvest" version))
880 (base32 "1yh2p429a0zr8pqmlw5rzf6m797j20j5w6xwxlqq0wrdbnif6bka"))))
881 (build-system r-build-system)
884 ("r-magrittr" ,r-magrittr)
885 ("r-selectr" ,r-selectr)
888 `(("r-knitr" ,r-knitr)))
889 (home-page "https://github.com/hadley/rvest")
890 (synopsis "Simple web scraping for R")
892 "@code{r-rvest} helps you scrape information from web pages. It is
893 designed to work with @code{magrittr} to make it easy to express common web
894 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
895 (license license:gpl3)))
897 (define-public r-selectr
904 (uri (cran-uri "selectr" version))
906 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
907 (build-system r-build-system)
909 `(("r-stringr" ,r-stringr)
911 (home-page "https://sjp.co.nz/projects/selectr/")
912 (synopsis "Translate CSS selectors to XPath expressions")
914 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
915 expression. This allows you to use CSS selectors when working with the XML
916 package as it can only evaluate XPath expressions. Also provided are
917 convenience functions useful for using CSS selectors on XML nodes. This
918 package is a port of the Python package @code{cssselect}.")
919 (license license:bsd-3)))
921 (define-public r-reprex
928 (uri (cran-uri "reprex" version))
931 "07nzx0fdl48jw95ipx17ql0l13q60yl3rjrkj1m375wrc7h1v5nx"))))
932 (build-system r-build-system)
934 `(("r-callr" ,r-callr)
941 ("r-rmarkdown" ,r-rmarkdown)
942 ("r-withr" ,r-withr)))
944 `(("r-knitr" ,r-knitr)))
945 (home-page "https://github.com/tidyverse/reprex")
946 (synopsis "Prepare reproducible R code examples for sharing")
948 "This package provides a convenience wrapper that uses the
949 @code{rmarkdown} package to render small snippets of code to target formats
950 that include both code and output. The goal is to encourage the sharing of
951 small, reproducible, and runnable examples on code-oriented websites or email.
952 @code{reprex} also extracts clean, runnable R code from various common formats,
953 such as copy/paste from an R session.")
954 (license license:expat)))
956 (define-public r-reordercluster
958 (name "r-reordercluster")
962 (uri (cran-uri "ReorderCluster" version))
965 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
966 (build-system r-build-system)
968 `(("r-gplots" ,r-gplots)
970 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
971 (synopsis "Reordering the dendrogram according to the class labels")
972 (description "This package provides tools for performing the leaf reordering
973 for the dendrogram that preserves the hierarchical clustering result and at the
974 same time tries to group instances from the same class together.")
975 (license license:gpl3+)))
977 (define-public r-callr
984 (uri (cran-uri "callr" version))
987 "15l6ppsxdadlnl4fk0f8bvf327n8izk96px5d08m1ay9iij8qcyf"))))
988 (build-system r-build-system)
991 ("r-processx" ,r-processx)))
992 (home-page "https://github.com/r-lib/callr#readme")
993 (synopsis "Call R from R")
995 "It is sometimes useful to perform a computation in a separate R process,
996 without affecting the current R process at all. This package does exactly
998 (license license:expat)))
1000 (define-public r-readxl
1007 (uri (cran-uri "readxl" version))
1010 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
1011 (build-system r-build-system)
1013 `(("r-cellranger" ,r-cellranger)
1014 ("r-progress" ,r-progress)
1016 ("r-tibble" ,r-tibble)))
1017 (home-page "https://readxl.tidyverse.org")
1018 (synopsis "Read Excel files")
1020 "This package lets you import Excel files into R. It supports
1021 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
1022 the embedded @code{RapidXML} C++ library.")
1023 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
1024 ;; 'rapidxml' which is Boost.
1025 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
1027 (define-public r-modelr
1034 (uri (cran-uri "modelr" version))
1037 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
1038 (build-system r-build-system)
1040 `(("r-broom" ,r-broom)
1041 ("r-magrittr" ,r-magrittr)
1042 ("r-purrr" ,r-purrr)
1043 ("r-rlang" ,r-rlang)
1044 ("r-tibble" ,r-tibble)
1045 ("r-tidyr" ,r-tidyr)
1046 ("r-tidyselect" ,r-tidyselect)
1047 ("r-vctrs" ,r-vctrs)))
1048 (home-page "https://github.com/tidyverse/modelr")
1049 (synopsis "Helper functions for modelling in pipelines")
1051 "Functions for modelling that help you seamlessly integrate modelling
1052 into a pipeline of data manipulation and visualisation.")
1053 (license license:gpl3)))
1055 (define-public r-httpuv
1061 (uri (cran-uri "httpuv" version))
1064 "05rir03xwamwfq5691vx0x957sgmr4i8iv5vpx5rv1f74y4wkrhb"))
1065 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
1066 ;; only contains fixes for building on Solaris.
1067 (patches (search-patches "r-httpuv-1.5.5-unvendor-libuv.patch"))
1068 (modules '((guix build utils)))
1071 (delete-file-recursively "src/libuv")
1072 ;; Cannot unbundle http-parser, because it contains local
1075 (build-system r-build-system)
1078 (modify-phases %standard-phases
1079 (add-after 'unpack 'unbundle-libuv
1080 (lambda* (#:key outputs #:allow-other-keys)
1081 (substitute* (find-files "src" "\\.cpp$|\\.h$")
1082 (("\"libuv/include/uv\\.h\"")
1084 ;; Fix https://github.com/rstudio/httpuv/issues/282
1085 (substitute* "src/http.cpp"
1086 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
1087 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);"))
1090 `(("libuv" ,libuv)))
1093 ("r-later" ,r-later)
1094 ("r-promises" ,r-promises)
1096 ("r-rcpp" ,r-rcpp)))
1097 (home-page "https://github.com/rstudio/httpuv")
1098 (synopsis "HTTP and WebSocket server library for R")
1100 "The httpuv package provides low-level socket and protocol support for
1101 handling HTTP and WebSocket requests directly from within R. It is primarily
1102 intended as a building block for other packages, rather than making it
1103 particularly easy to create complete web applications using httpuv alone.")
1104 ;; This package includes third-party code that was originally released
1105 ;; under various non-copyleft licenses. Full licensing information can be
1106 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
1107 (license license:gpl3+)))
1109 (define-public r-jsonlite
1115 (uri (cran-uri "jsonlite" version))
1118 "1lhzcpz9clwq04i5m6jzkvw9x03pwlqrixv4l9xzchjr8d84nd86"))))
1119 (build-system r-build-system)
1121 `(("r-knitr" ,r-knitr)))
1122 (home-page "https://arxiv.org/abs/1403.2805")
1123 (synopsis "Robust, high performance JSON parser and generator for R")
1125 "The jsonlite package provides a fast JSON parser and generator optimized
1126 for statistical data and the web. It offers flexible, robust, high
1127 performance tools for working with JSON in R and is particularly powerful for
1128 building pipelines and interacting with a web API. In addition to converting
1129 JSON data from/to R objects, jsonlite contains functions to stream, validate,
1130 and prettify JSON data. The unit tests included with the package verify that
1131 all edge cases are encoded and decoded consistently for use with dynamic data
1132 in systems and applications.")
1133 (license license:expat)))
1135 (define-public r-servr
1141 (uri (cran-uri "servr" version))
1144 "12fk585hmz735v4hra8da9wld1fmd67byqnf95m7jjyh7l3dmh1z"))))
1145 (build-system r-build-system)
1147 `(("r-httpuv" ,r-httpuv)
1148 ("r-jsonlite" ,r-jsonlite)
1150 ("r-xfun" ,r-xfun)))
1151 (home-page "https://github.com/yihui/servr")
1152 (synopsis "Simple HTTP server to serve static files or dynamic documents")
1154 "Servr provides an HTTP server in R to serve static files, or dynamic
1155 documents that can be converted to HTML files (e.g., R Markdown) under a given
1157 (license license:expat)))
1159 (define-public r-htmltools
1161 (name "r-htmltools")
1165 (uri (cran-uri "htmltools" version))
1168 "1fm4cymz4hz6lds80m9j5q00xy5flkrmfn5dkrn3s3rkzqpyggzh"))))
1169 (build-system r-build-system)
1171 `(("r-base64enc" ,r-base64enc)
1172 ("r-digest" ,r-digest)
1173 ("r-rlang" ,r-rlang)))
1174 (home-page "https://cran.r-project.org/web/packages/htmltools")
1175 (synopsis "R tools for HTML")
1177 "This package provides tools for HTML generation and output in R.")
1178 (license license:expat)))
1180 (define-public r-htmlwidgets
1182 (name "r-htmlwidgets")
1186 (uri (cran-uri "htmlwidgets" version))
1189 "0a8g7wqd3qxnhwkm9c9bkzg29db7gvjiaa5y038ln8nch8qq7981"))))
1190 (build-system r-build-system)
1192 `(("r-htmltools" ,r-htmltools)
1193 ("r-jsonlite" ,r-jsonlite)
1194 ("r-yaml" ,r-yaml)))
1196 `(("r-knitr" ,r-knitr)))
1197 (home-page "https://github.com/ramnathv/htmlwidgets")
1198 (synopsis "HTML Widgets for R")
1200 "HTML widgets is a framework for creating HTML widgets that render in
1201 various contexts including the R console, R Markdown documents, and Shiny web
1203 (license license:expat)))
1205 (define-public r-htmltable
1207 (name "r-htmltable")
1212 (uri (cran-uri "htmlTable" version))
1214 (base32 "1gzh0bdxi55p1ckxv4k0a41b1j0grwv2w3lkqz4c3gkw66dk6ja0"))))
1215 (properties `((upstream-name . "htmlTable")))
1216 (build-system r-build-system)
1218 `(("r-checkmate" ,r-checkmate)
1219 ("r-htmltools" ,r-htmltools)
1220 ("r-htmlwidgets" ,r-htmlwidgets)
1221 ("r-knitr" ,r-knitr)
1222 ("r-magrittr" ,r-magrittr)
1223 ("r-rstudioapi" ,r-rstudioapi)
1224 ("r-stringr" ,r-stringr)))
1226 `(("r-knitr" ,r-knitr)))
1227 (home-page "http://gforge.se/packages/")
1228 (synopsis "Advanced tables for Markdown/HTML")
1230 "This package provides functions to build tables with advanced layout
1231 elements such as row spanners, column spanners, table spanners, zebra
1232 striping, and more. While allowing advanced layout, the underlying
1233 CSS-structure is simple in order to maximize compatibility with word
1234 processors such as LibreOffice. The package also contains a few text
1235 formatting functions that help outputting text compatible with HTML or
1237 (license license:gpl3+)))
1239 (define-public r-curl
1245 (uri (cran-uri "curl" version))
1248 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
1249 (build-system r-build-system)
1252 (modify-phases %standard-phases
1253 ;; The environment variable CURL_CA_BUNDLE is only respected when
1254 ;; running Windows, so we disable the platform checks.
1255 ;; This can be removed once the libcurl has been patched.
1256 (add-after 'unpack 'allow-CURL_CA_BUNDLE
1258 (substitute* "R/onload.R"
1259 (("if \\(!grepl\\(\"mingw\".*")
1261 (substitute* "src/handle.c"
1262 (("/\\* Only set" m)
1264 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
1265 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
1272 `(("pkg-config" ,pkg-config)))
1273 (home-page "https://github.com/jeroenooms/curl")
1274 (synopsis "HTTP client for R")
1276 "The @code{curl()} and @code{curl_download()} functions provide highly
1277 configurable drop-in replacements for base @code{url()} and
1278 @code{download.file()} with better performance, support for encryption, gzip
1279 compression, authentication, and other @code{libcurl} goodies. The core of
1280 the package implements a framework for performing fully customized requests
1281 where data can be processed either in memory, on disk, or streaming via the
1282 callback or connection interfaces.")
1283 (license license:expat)))
1285 (define-public r-hwriter
1292 (uri (cran-uri "hwriter" version))
1295 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
1296 (build-system r-build-system)
1297 (home-page "https://cran.r-project.org/web/packages/hwriter")
1298 (synopsis "Output R objects in HTML format")
1300 "This package provides easy-to-use and versatile functions to output R
1301 objects in HTML format.")
1302 (license license:lgpl2.1+)))
1304 (define-public r-rjson
1311 (uri (cran-uri "rjson" version))
1314 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
1315 (build-system r-build-system)
1316 (home-page "https://cran.r-project.org/web/packages/rjson")
1317 (synopsis "JSON library for R")
1319 "This package provides functions to convert R objects into JSON objects
1321 (license license:gpl2+)))
1323 (define-public r-fastmap
1330 (uri (cran-uri "fastmap" version))
1333 "0aw29hnq3ppn7bsnwg9d9sp84k1cvq30lrmfzqn315n0nhkfa4wi"))))
1334 (properties `((upstream-name . "fastmap")))
1335 (build-system r-build-system)
1336 (home-page "https://r-lib.github.io/fastmap/")
1337 (synopsis "Fast implementation of a key-value store")
1339 "This package provides a fast implementation of a key-value store.
1340 Environments are commonly used as key-value stores, but every time a new key
1341 is used, it is added to R's global symbol table, causing a small amount of
1342 memory leakage. This can be problematic in cases where many different keys
1343 are used. Fastmap avoids this memory leak issue by implementing the map using
1344 data structures in C++.")
1345 (license license:expat)))
1347 (define-public r-fastghquad
1349 (name "r-fastghquad")
1354 (uri (cran-uri "fastGHQuad" version))
1357 "1rjia8wggadr9xwxcmzmal0rc4g6pa3dr5888fbbnb6abl8b2lrj"))))
1358 (properties `((upstream-name . "fastGHQuad")))
1359 (build-system r-build-system)
1361 `(("r-rcpp" ,r-rcpp)))
1362 (home-page "https://github.com/awblocker/fastGHQuad")
1363 (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature")
1365 "This package implements numerically-stable Gauss-Hermite quadrature
1366 rules and utility functions for adaptive GH quadrature.")
1367 (license license:expat)))
1369 (define-public r-rstpm2
1376 (uri (cran-uri "rstpm2" version))
1379 "0c6l3z250b2kn6mh2xyb0bd2y5nsbj11n9xfi51dac9s8xq3v7m4"))))
1380 (properties `((upstream-name . "rstpm2")))
1381 (build-system r-build-system)
1383 `(("r-bbmle" ,r-bbmle)
1385 ("r-desolve" ,r-desolve)
1386 ("r-fastghquad" ,r-fastghquad)
1389 ("r-rcpparmadillo" ,r-rcpparmadillo)
1390 ("r-survival" ,r-survival)))
1392 `(("gfortran" ,gfortran)))
1393 (home-page "https://github.com/mclements/rstpm2")
1394 (synopsis "Link-based survival models")
1396 "This package provides R implementations of @dfn{generalized survival
1397 models} (GSMs), smooth @dfn{accelerated failure time} (AFT) models and Markov
1398 multi-state models.")
1399 ;; One of these licenses
1400 (license (list license:gpl2 license:gpl3))))
1402 ;; This package includes minified JavaScript files. When upgrading please
1403 ;; check that there are no new minified JavaScript files.
1404 (define-public r-jquerylib
1406 (name "r-jquerylib")
1411 (uri (cran-uri "jquerylib" version))
1414 "1s0d6mws13hwkx07jqmry7vp30a05b2p9w7ir68bmkhasidwkzdq"))
1416 '(for-each delete-file
1417 '("inst/lib/jquery-1.12.4.min.js"
1418 "inst/lib/jquery-2.2.4.min.js"
1419 "inst/lib/jquery-3.5.1.min.js")))))
1420 (properties `((upstream-name . "jquerylib")))
1421 (build-system r-build-system)
1423 `(#:modules ((guix build utils)
1424 (guix build r-build-system)
1427 (modify-phases %standard-phases
1428 (add-after 'unpack 'process-javascript
1429 (lambda* (#:key inputs #:allow-other-keys)
1430 (with-directory-excursion "inst/lib/"
1434 `(("jquery-1.12.4.js"
1435 "jquery-1.12.4.min.js")
1437 "jquery-2.2.4.min.js")
1439 "jquery-3.5.1.min.js"))))
1440 (lambda (sources targets)
1441 (for-each (lambda (source target)
1442 (format #t "Processing ~a --> ~a~%"
1444 (invoke "esbuild" source "--minify"
1445 (string-append "--outfile=" target)))
1446 sources targets)))))))))
1448 `(("r-htmltools" ,r-htmltools)))
1450 `(("esbuild" ,esbuild)))
1451 (home-page "https://cran.r-project.org/package=jquerylib")
1452 (synopsis "Obtain jQuery as an HTML dependency object")
1454 "Obtain any major version of jQuery and use it in any webpage generated
1455 by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't
1456 need to use this package directly, but other R packages (e.g. shiny,
1457 rmarkdown, etc.) depend on this package to avoid bundling redundant copies of
1459 (license license:expat)))
1461 (define-public r-sass
1468 (uri (cran-uri "sass" version))
1471 "1cxqwsdyz71mgflqqa65mfr161jlv8q9mshs1y19pxp6pz5wnv0s"))))
1472 (properties `((upstream-name . "sass")))
1473 (build-system r-build-system)
1475 `(("r-digest" ,r-digest)
1477 ("r-htmltools" ,r-htmltools)
1479 ("r-rappdirs" ,r-rappdirs)
1480 ("r-rlang" ,r-rlang)))
1481 (native-inputs `(("r-knitr" ,r-knitr)))
1482 (home-page "https://github.com/rstudio/sass")
1483 (synopsis "Syntactically Awesome Style Sheets (SASS)")
1485 "This package provides an SCSS compiler, powered by the libsass library.
1486 With this, R developers can use variables, inheritance, and functions to
1487 generate dynamic style sheets. The package uses the Sass CSS extension
1488 language, which is stable, powerful, and CSS compatible.")
1489 (license license:expat)))
1491 ;; This package includes minified JavaScript files. When upgrading please
1492 ;; check that there are no new minified JavaScript files.
1493 (define-public r-bslib
1500 (uri (cran-uri "bslib" version))
1503 "0qlpv2lqr3hjykszmnll7vi4zhmrz4rgcfl0sifxc6cha6jy2nac"))
1505 '(for-each delete-file
1506 '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js"
1507 "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js"
1508 "inst/lib/bs-sass/assets/javascripts/bootstrap.min.js"
1509 "inst/lib/bs/dist/js/bootstrap.bundle.min.js")))))
1510 (properties `((upstream-name . "bslib")))
1511 (build-system r-build-system)
1513 `(#:modules ((guix build utils)
1514 (guix build r-build-system)
1517 (modify-phases %standard-phases
1518 (add-after 'unpack 'process-javascript
1519 (lambda* (#:key inputs #:allow-other-keys)
1520 (with-directory-excursion "inst/lib/"
1524 `(("bs-a11y-p/plugins/js/bootstrap-accessibility.js"
1525 "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js")
1526 ("bs-colorpicker/js/bootstrap-colorpicker.js"
1527 "bs-colorpicker/js/bootstrap-colorpicker.min.js")
1528 ("bs-sass/assets/javascripts/bootstrap.js"
1529 "bs-sass/assets/javascripts/bootstrap.min.js")
1530 (,(assoc-ref inputs "js-bootstrap-bundle")
1531 "bs/dist/js/bootstrap.bundle.min.js"))))
1532 (lambda (sources targets)
1533 (for-each (lambda (source target)
1534 (format #t "Processing ~a --> ~a~%"
1536 (invoke "esbuild" source "--minify"
1537 (string-append "--outfile=" target)))
1538 sources targets)))))))))
1540 `(("r-digest" ,r-digest)
1541 ("r-htmltools" ,r-htmltools)
1542 ("r-jquerylib" ,r-jquerylib)
1543 ("r-jsonlite" ,r-jsonlite)
1544 ("r-magrittr" ,r-magrittr)
1545 ("r-rlang" ,r-rlang)
1546 ("r-sass" ,r-sass)))
1548 `(("esbuild" ,esbuild)
1549 ("js-bootstrap-bundle"
1552 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.5.3/dist/js/bootstrap.bundle.js")
1555 "1lcsxj7gcm56va3gck47ggpwzjxrzq27sgjzdw6c54qkp0487sak"))))))
1556 (home-page "https://rstudio.github.io/bslib/")
1557 (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown")
1559 "This package simplifies custom CSS styling of both shiny and rmarkdown
1560 via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their
1561 various Bootswatch themes. An interactive widget is also provided for
1562 previewing themes in real time.")
1563 (license license:expat)))
1565 ;; This package includes minified JavaScript files. When upgrading please
1566 ;; check that there are no new minified JavaScript files.
1567 (define-public r-shiny
1575 (url "https://github.com/rstudio/shiny")
1576 (commit (string-append "v" version))))
1577 (file-name (git-file-name name version))
1580 "0f6cwx5xyqzs40msq271sqhwl8736rwbm7kd1ldkcvxngzr4vlx9"))
1582 '(for-each delete-file
1583 '("inst/www/shared/bootstrap/js/bootstrap.min.js"
1584 "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO
1585 "inst/www/shared/datatables/js/jquery.dataTables.min.js"
1586 "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js"
1587 "inst/www/shared/highlight/highlight.pack.js"
1588 "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js"
1589 "inst/www/shared/jquery.min.js"
1590 "inst/www/shared/jqueryui/jquery-ui.min.js"
1591 "inst/www/shared/legacy/jquery.min.js"
1592 "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js"
1593 "inst/www/shared/selectize/js/selectize.min.js"
1594 "inst/www/shared/shiny.min.js"
1595 "inst/www/shared/showdown/compressed/showdown.js"
1596 "inst/www/shared/strftime/strftime-min.js")))))
1597 (build-system r-build-system)
1599 `(#:modules ((guix build r-build-system)
1600 (guix build minify-build-system)
1603 #:imported-modules (,@%r-build-system-modules
1604 (guix build minify-build-system))
1606 (modify-phases (@ (guix build r-build-system) %standard-phases)
1607 (add-after 'unpack 'replace-bundled-minified-JavaScript
1608 (lambda* (#:key inputs #:allow-other-keys)
1609 (let ((replace-file (lambda (old new)
1610 (format #t "replacing ~a with ~a\n" old new)
1611 (symlink new old))))
1612 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
1613 ;; contain just data. They are not minified code, so we don't
1615 (with-directory-excursion "inst/www/shared"
1616 (replace-file "strftime/strftime-min.js"
1617 (string-append (assoc-ref inputs "js-strftime")
1618 "/share/javascript/strftime.min.js"))
1619 (replace-file "highlight/highlight.pack.js"
1620 (string-append (assoc-ref inputs "js-highlight")
1621 "/share/javascript/highlight.min.js"))
1622 (replace-file "datatables/js/jquery.dataTables.min.js"
1623 (string-append (assoc-ref inputs "js-datatables")
1624 "/share/javascript/jquery.dataTables.min.js"))
1625 (replace-file "selectize/js/selectize.min.js"
1626 (string-append (assoc-ref inputs "js-selectize")
1627 "/share/javascript/selectize.min.js"))
1628 (for-each (match-lambda
1630 (minify source #:target target)))
1631 `(("jqueryui/jquery-ui.js" .
1632 "jqueryui/jquery-ui.min.js")
1633 ("datepicker/js/bootstrap-datepicker.js" .
1634 "datepicker/js/bootstrap-datepicker.min.js")
1635 ("ionrangeslider/js/ion.rangeSlider.js" .
1636 "ionrangeslider/js/ion.rangeSlider.min.js")
1637 ("bootstrap/js/bootstrap.js" .
1638 "bootstrap/js/bootstrap.min.js")
1639 (,(assoc-ref inputs "js-bootstrap-accessibility") .
1640 "bootstrap/accessibility/js/bootstrap-accessibility.min.js")
1645 ("legacy/jquery.js" .
1646 "legacy/jquery.min.js")
1647 ("selectize/accessibility/js/selectize-plugin-a11y.js" .
1648 "selectize/accessibility/js/selectize-plugin-a11y.min.js")
1649 ("showdown/src/showdown.js" .
1650 "showdown/compressed/showdown.js"))))))))))
1652 `(("r-bslib" ,r-bslib)
1653 ("r-cachem" ,r-cachem)
1654 ("r-commonmark" ,r-commonmark)
1655 ("r-crayon" ,r-crayon)
1656 ("r-digest" ,r-digest)
1657 ("r-ellipsis" ,r-ellipsis)
1658 ("r-fastmap" ,r-fastmap)
1660 ("r-htmltools" ,r-htmltools)
1661 ("r-httpuv" ,r-httpuv)
1662 ("r-jsonlite" ,r-jsonlite)
1663 ("r-later" ,r-later)
1664 ("r-lifecycle" ,r-lifecycle)
1666 ("r-promises" ,r-promises)
1668 ("r-rlang" ,r-rlang)
1669 ("r-sourcetools" ,r-sourcetools)
1670 ("r-withr" ,r-withr)
1671 ("r-xtable" ,r-xtable)))
1673 `(("js-datatables" ,js-datatables)
1674 ("js-selectize" ,js-selectize)
1675 ("js-strftime" ,js-strftime)
1676 ("js-highlight" ,js-highlight)))
1678 `(("uglify-js" ,uglify-js)
1679 ("gfortran" ,gfortran)
1680 ("js-bootstrap-accessibility"
1683 (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\
1684 v1.0.7/_site/plugins/js/bootstrap-accessibility.js")
1687 "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8"))))))
1688 (home-page "https://shiny.rstudio.com")
1689 (synopsis "Easy interactive web applications with R")
1691 "Makes it incredibly easy to build interactive web applications
1692 with R. Automatic \"reactive\" binding between inputs and outputs and
1693 extensive prebuilt widgets make it possible to build beautiful,
1694 responsive, and powerful applications with minimal effort.")
1695 (license license:artistic2.0)))
1697 ;; This package includes minified JavaScript files. When upgrading please
1698 ;; check that there are no new minified JavaScript files.
1699 (define-public r-shinytree
1701 (name "r-shinytree")
1706 (uri (cran-uri "shinyTree" version))
1709 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1710 (modules '((guix build utils)))
1713 ;; Delete minified JavaScript
1714 (for-each delete-file
1715 '("inst/www/jsTree-3.3.7/libs/require.js"
1716 "inst/www/jsTree-3.3.7/libs/jquery.js"
1717 "inst/www/jsTree-3.3.7/jstree.min.js"))
1719 (properties `((upstream-name . "shinyTree")))
1720 (build-system r-build-system)
1722 `(#:modules ((guix build utils)
1723 (guix build r-build-system)
1727 (modify-phases %standard-phases
1728 (add-after 'unpack 'replace-minified-javascript
1729 (lambda* (#:key inputs #:allow-other-keys)
1730 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1731 (symlink (string-append (assoc-ref inputs "js-requirejs")
1732 "/share/javascript/require.min.js")
1737 `((,(assoc-ref inputs "js-jquery")
1741 (lambda (sources targets)
1742 (for-each (lambda (source target)
1743 (format #t "Processing ~a --> ~a~%"
1745 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1746 (call-with-output-file target
1748 (dump-port minified port)))))
1752 `(("r-htmlwidgets" ,r-htmlwidgets)
1753 ("r-jsonlite" ,r-jsonlite)
1754 ("r-promises" ,r-promises)
1755 ("r-shiny" ,r-shiny)
1756 ("r-stringr" ,r-stringr)))
1758 `(("js-requirejs" ,js-requirejs)))
1760 `(("uglify-js" ,uglify-js)
1764 (uri "https://code.jquery.com/jquery-3.3.1.js")
1767 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1768 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1769 (synopsis "jsTree bindings for Shiny")
1771 "This package exposes R bindings to jsTree, a JavaScript library that
1772 supports interactive trees, to enable rich, editable trees in Shiny.")
1773 (license license:expat)))
1775 (define-public r-shinydashboard
1777 (name "r-shinydashboard")
1781 (uri (cran-uri "shinydashboard" version))
1784 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1785 (build-system r-build-system)
1786 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1787 ;; Regenerate it from the included sources.
1789 `(#:modules ((guix build utils)
1790 (guix build r-build-system)
1793 (modify-phases %standard-phases
1794 (add-after 'unpack 'generate-minified-javascript
1796 (with-directory-excursion "inst/AdminLTE"
1797 (delete-file "app.min.js")
1798 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1799 (call-with-output-file "app.min.js"
1801 (dump-port minified port))))))))))
1803 `(("r-htmltools" ,r-htmltools)
1804 ("r-promises" ,r-promises)
1805 ("r-shiny" ,r-shiny)))
1807 `(("uglify-js" ,uglify-js)))
1808 (home-page "https://rstudio.github.io/shinydashboard/")
1809 (synopsis "Create dashboards with shiny")
1810 (description "This package provides an extension to the Shiny web
1811 application framework for R, making it easy to create attractive dashboards.")
1812 ;; This package includes software that was released under the Expat
1813 ;; license, but the whole package is released under GPL version 2 or
1815 (license license:gpl2+)))
1817 (define-public r-shinyfiles
1819 (name "r-shinyfiles")
1824 (uri (cran-uri "shinyFiles" version))
1826 (base32 "0rsijlx16vd74r7bd8s9zipy71kgpw19v9s85kxj5bmwc6njmbai"))))
1827 (properties `((upstream-name . "shinyFiles")))
1828 (build-system r-build-system)
1831 ("r-htmltools" ,r-htmltools)
1832 ("r-jsonlite" ,r-jsonlite)
1833 ("r-shiny" ,r-shiny)
1834 ("r-tibble" ,r-tibble)))
1835 (home-page "https://github.com/thomasp85/shinyFiles")
1836 (synopsis "Server-side file system viewer for Shiny")
1838 "This package provides functionality for client-side navigation of the
1839 server side file system in shiny apps. In case the app is running locally
1840 this gives the user direct access to the file system without the need to
1841 \"download\" files to a temporary location. Both file and folder selection as
1842 well as file saving is available.")
1843 (license license:gpl2+)))
1845 (define-public r-shinythemes
1847 (name "r-shinythemes")
1852 (uri (cran-uri "shinythemes" version))
1855 "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip"))))
1856 (properties `((upstream-name . "shinythemes")))
1857 (build-system r-build-system)
1858 (propagated-inputs `(("r-shiny" ,r-shiny)))
1859 (home-page "https://rstudio.github.io/shinythemes/")
1860 (synopsis "Themes for Shiny")
1862 "This package provides themes for use with Shiny. It includes several
1863 Bootstrap themes, which are packaged for use with Shiny applications.")
1864 ;; The package is released under version 3 of the GPL, but it includes
1865 ;; source files that are covered by the Expat license. It also includes
1866 ;; fonts under SIL or the ASL.
1867 (license (list license:gpl3 license:expat
1868 license:silofl1.1 license:asl2.0))))
1870 ;; The package sources include minified variants of d3.js and non-minified
1871 ;; source code of d3-jetpack.
1872 (define-public r-d3r
1879 (uri (cran-uri "d3r" version))
1882 "0kc82vvyfxhxvqfalngn36prn3sxdiinsx04rn99ha6zdc27zp5k"))))
1883 (build-system r-build-system)
1885 `(#:modules ((guix build utils)
1886 (guix build r-build-system)
1889 (modify-phases %standard-phases
1890 (add-after 'unpack 'process-javascript
1891 (lambda* (#:key inputs #:allow-other-keys)
1892 (with-directory-excursion "inst/www/d3/"
1896 `((,(assoc-ref inputs "d3.v3.js")
1897 "v3/dist/d3.min.js")
1898 (,(assoc-ref inputs "d3.v4.js")
1899 "v4/dist/d3.min.js")
1900 (,(assoc-ref inputs "d3.v5.js")
1901 "v5/dist/d3.min.js")
1902 (,(assoc-ref inputs "d3.v6.js")
1903 "v6/dist/d3.min.js"))))
1904 (lambda (sources targets)
1905 (for-each (lambda (source target)
1906 (format #t "Processing ~a --> ~a~%"
1908 (delete-file target)
1909 (invoke "esbuild" source "--minify"
1910 (string-append "--outfile=" target)))
1914 `(("r-dplyr" ,r-dplyr)
1915 ("r-htmltools" ,r-htmltools)
1916 ("r-rlang" ,r-rlang)
1917 ("r-tidyr" ,r-tidyr)))
1919 `(("esbuild" ,esbuild)
1923 (uri "https://d3js.org/d3.v3.js")
1926 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1930 (uri "https://d3js.org/d3.v4.js")
1933 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1937 (uri "https://d3js.org/d3.v5.js")
1940 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))
1944 (uri "https://d3js.org/d3.v6.js")
1947 "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9"))))))
1948 (home-page "https://github.com/timelyportfolio/d3r")
1949 (synopsis "d3.js utilities for R")
1951 "This package provides a suite of functions to help ease the use of the
1952 d3.js visualization library in R. These helpers include
1953 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1954 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1955 R objects into the JSON format that the d3.js library expects.")
1956 (license license:bsd-3)))
1958 ;; We use the latest commit here because the last release was in 2016 while
1959 ;; the latest commit was in 2018.
1960 (define-public r-sankeyd3
1961 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1965 (version (git-version "0.3.2" revision commit))
1970 (url "https://github.com/fbreitwieser/sankeyD3")
1972 (file-name (git-file-name name version))
1975 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1976 (build-system r-build-system)
1979 ("r-htmlwidgets" ,r-htmlwidgets)
1980 ("r-shiny" ,r-shiny)
1981 ("r-magrittr" ,r-magrittr)))
1982 (home-page "https://github.com/fbreitwieser/sankeyD3")
1983 (synopsis "Sankey network graphs from R")
1985 "This package provides an R library to generate Sankey network graphs
1986 in R and Shiny via the D3 visualization library.")
1987 ;; The R code is licensed under GPLv3+. It includes the non-minified
1988 ;; JavaScript source code of d3-sankey, which is released under the
1989 ;; 3-clause BSD license.
1990 (license (list license:gpl3+ license:bsd-3)))))
1992 (define-public r-wesanderson
1994 (name "r-wesanderson")
1999 (uri (cran-uri "wesanderson" version))
2002 "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
2003 (properties `((upstream-name . "wesanderson")))
2004 (build-system r-build-system)
2005 (home-page "https://github.com/karthik/wesanderson")
2006 (synopsis "Wes Anderson color palette generator")
2008 "This package provides color palettes that have been generated mostly
2009 from Wes Anderson movies.")
2010 (license license:expat)))
2012 (define-public r-gg-gap
2019 (uri (cran-uri "gg.gap" version))
2022 "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h"))))
2023 (properties `((upstream-name . "gg.gap")))
2024 (build-system r-build-system)
2026 `(("r-cowplot" ,r-cowplot)
2027 ("r-ggplot2" ,r-ggplot2)))
2028 (home-page "https://github.com/ChrisLou-bioinfo/gg.gap")
2029 (synopsis "Define segments on the y-axis for ggplot2")
2031 "The @code{gg.gap} function enables you to define segments for the y-axis
2032 in a ggplot2 plot.")
2033 (license license:gpl3)))
2035 (define-public r-tablerdash
2037 (name "r-tablerdash")
2042 (uri (cran-uri "tablerDash" version))
2045 "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm"))
2048 ;; Delete minified JavaScript
2049 (for-each delete-file
2050 '("inst/tablerDash-0.1.0/require.min.js"
2051 "inst/bootstrap-4.0.0/bootstrap.bundle.min.js"))
2053 (properties `((upstream-name . "tablerDash")))
2054 (build-system r-build-system)
2056 `(#:modules ((guix build utils)
2057 (guix build r-build-system)
2060 (modify-phases %standard-phases
2061 (add-after 'unpack 'process-javascript
2062 (lambda* (#:key inputs #:allow-other-keys)
2063 (with-directory-excursion "inst"
2067 `((,(assoc-ref inputs "js-requirejs")
2068 "tablerDash-0.1.0/require.min.js")
2069 (,(assoc-ref inputs "js-bootstrap")
2070 "bootstrap-4.0.0/bootstrap.bundle.min.js"))))
2071 (lambda (sources targets)
2072 (for-each (lambda (source target)
2073 (format #t "Processing ~a --> ~a~%"
2075 (invoke "esbuild" source "--minify"
2076 (string-append "--outfile=" target)))
2080 `(("r-htmltools" ,r-htmltools)
2081 ("r-knitr" ,r-knitr)
2082 ("r-shiny" ,r-shiny)))
2084 `(("esbuild" ,esbuild)
2088 (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js")
2091 "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds"))))
2095 (uri "https://raw.githubusercontent.com/twbs/bootstrap/\
2096 v4.0.0/dist/js/bootstrap.bundle.js")
2099 "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj"))))))
2100 (home-page "https://rinterface.github.io/tablerDash/")
2101 (synopsis "Tabler API for Shiny")
2103 "This package provides an R interface to the
2104 @url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap
2105 4 dashboard template. There are different layouts available such as a one
2106 page dashboard or a multi-page template, where the navigation menu is
2107 contained in the navigation bar.")
2108 (license license:gpl2+)))
2110 (define-public r-spelling
2117 (uri (cran-uri "spelling" version))
2120 "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl"))))
2121 (properties `((upstream-name . "spelling")))
2122 (build-system r-build-system)
2124 `(("r-commonmark" ,r-commonmark)
2125 ("r-hunspell" ,r-hunspell)
2126 ("r-knitr" ,r-knitr)
2127 ("r-xml2" ,r-xml2)))
2128 (home-page "https://docs.ropensci.org/spelling/")
2129 (synopsis "Tools for spell checking in R")
2131 "This is an R package for spell checking common document formats
2132 including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes
2133 utilities to automate checking of documentation and vignettes as a unit test
2134 during @code{R CMD check}. Both British and American English are supported
2135 out of the box and other languages can be added. In addition, packages may
2136 define a wordlist to allow custom terminology without having to abuse
2138 (license license:expat)))
2140 (define-public r-crosstalk
2142 (name "r-crosstalk")
2147 (uri (cran-uri "crosstalk" version))
2150 "1n6c6s7a6yxiwvva71x6bzcrim8xprl5s01fqiy61yq0y3vk8cpd"))))
2151 (build-system r-build-system)
2153 `(("r-htmltools" ,r-htmltools)
2154 ("r-jsonlite" ,r-jsonlite)
2155 ("r-lazyeval" ,r-lazyeval)
2157 (home-page "https://rstudio.github.io/crosstalk/")
2158 (synopsis "Inter-widget interactivity for HTML widgets")
2160 "This package provides building blocks for allowing HTML widgets to
2161 communicate with each other, with Shiny or without (i.e. static @code{.html}
2162 files). It currently supports linked brushing and filtering.")
2163 (license license:expat)))
2165 (define-public r-rook
2172 (uri (cran-uri "Rook" version))
2175 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
2176 (properties `((upstream-name . "Rook")))
2177 (build-system r-build-system)
2178 (propagated-inputs `(("r-brew" ,r-brew)))
2179 (home-page "https://cran.r-project.org/web/packages/Rook")
2180 (synopsis "Web server interface for R")
2182 "This package contains the Rook specification and convenience software
2183 for building and running Rook applications. A Rook application is an R
2184 reference class object that implements a @code{call} method or an R closure
2185 that takes exactly one argument, an environment, and returns a list with three
2186 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
2187 (license license:gpl2)))
2189 (define-public r-miniui
2196 (uri (cran-uri "miniUI" version))
2199 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
2200 (properties `((upstream-name . "miniUI")))
2201 (build-system r-build-system)
2203 `(("r-htmltools" ,r-htmltools)
2204 ("r-shiny" ,r-shiny)))
2205 (home-page "https://cran.r-project.org/web/packages/miniUI/")
2206 (synopsis "Shiny UI widgets for small screens")
2208 "This package provides UI widget and layout functions for writing Shiny apps that
2209 work well on small screens.")
2210 (license license:gpl3)))
2212 (define-public r-feather
2219 (uri (cran-uri "feather" version))
2222 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
2223 (build-system r-build-system)
2227 ("r-tibble" ,r-tibble)))
2228 (home-page "https://github.com/wesm/feather")
2229 (synopsis "R Bindings to the Feather API")
2230 (description "Read and write feather files, a lightweight binary columnar
2231 data store designed for maximum speed.")
2232 (license license:asl2.0)))
2234 (define-public r-maps
2241 (uri (cran-uri "maps" version))
2244 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
2245 (build-system r-build-system)
2246 (home-page "https://cran.r-project.org/web/packages/maps")
2247 (synopsis "Draw geographical maps")
2248 (description "This package provides an R module for display of maps.
2249 Projection code and larger maps are in separate packages (@code{mapproj} and
2251 (license license:gpl2)))
2253 (define-public r-mapproj
2260 (uri (cran-uri "mapproj" version))
2263 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
2264 (build-system r-build-system)
2265 (propagated-inputs `(("r-maps" ,r-maps)))
2266 (home-page "https://cran.r-project.org/web/packages/mapproj")
2267 (synopsis "Map projection in R")
2268 (description "This package converts latitude/longitude into projected
2270 (license (list license:gpl2 ; The R interface
2271 (license:non-copyleft ; The C code
2272 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
2273 "Lucent Public License Version 1.02")))))
2275 (define-public r-rgooglemaps
2277 (name "r-rgooglemaps")
2282 (uri (cran-uri "RgoogleMaps" version))
2285 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
2286 (properties `((upstream-name . "RgoogleMaps")))
2287 (build-system r-build-system)
2291 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
2292 (synopsis "Use Google Maps in R")
2293 (description "This package serves two purposes:
2295 @item Provide a comfortable R interface to query the Google server for static
2297 @item Use the map as a background image to overlay plots within R. This
2298 requires proper coordinate scaling.
2300 (license license:gpl2+)))
2302 (define-public r-geosphere
2304 (name "r-geosphere")
2309 (uri (cran-uri "geosphere" version))
2312 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
2313 (build-system r-build-system)
2314 (propagated-inputs `(("r-sp" ,r-sp)))
2315 (home-page "https://cran.r-project.org/web/packages/geosphere")
2316 (synopsis "Spherical trigonometry")
2317 (description "This package computes spherical trigonometry for geographic
2318 applications. That is, compute distances and related measures for angular
2319 (longitude/latitude) locations.")
2320 (license license:gpl3+)))
2322 (define-public r-jpeg
2329 (uri (cran-uri "jpeg" version))
2332 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
2333 (build-system r-build-system)
2334 (inputs `(("libjpeg" ,libjpeg-turbo)))
2335 (home-page "https://www.rforge.net/jpeg/")
2336 (synopsis "Read and write JPEG images with R")
2337 (description "This package provides a way to read, write and display
2338 bitmap images stored in the JPEG format with R. It can read and write both
2339 files and in-memory raw vectors.")
2340 (license license:gpl2+)))
2342 (define-public r-ggmap
2349 (uri (cran-uri "ggmap" version))
2352 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
2353 (build-system r-build-system)
2355 `(("r-bitops" ,r-bitops)
2356 ("r-digest" ,r-digest)
2357 ("r-dplyr" ,r-dplyr)
2358 ("r-ggplot2" ,r-ggplot2)
2362 ("r-magrittr" ,r-magrittr)
2365 ("r-purrr" ,r-purrr)
2366 ("r-rgooglemaps" ,r-rgooglemaps)
2367 ("r-rjson" ,r-rjson)
2368 ("r-scales" ,r-scales)
2369 ("r-stringr" ,r-stringr)
2370 ("r-tibble" ,r-tibble)
2371 ("r-tidyr" ,r-tidyr)))
2372 (home-page "https://github.com/dkahle/ggmap")
2373 (synopsis "Spatial visualization with ggplot2")
2374 (description "This package provides a collection of functions to visualize
2375 spatial data and models on top of static maps from various online sources (e.g
2376 Google Maps and Stamen Maps). It includes tools common to those tasks,
2377 including functions for geolocation and routing.")
2378 (license license:gpl2)))
2380 (define-public r-haven
2387 (uri (cran-uri "haven" version))
2390 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))
2391 (modules '((guix build utils)))
2394 ;; unvendor readstat
2395 (delete-file-recursively "src/readstat")
2397 (build-system r-build-system)
2400 (modify-phases %standard-phases
2401 (add-after 'unpack 'unbundle-readstat
2403 ;; Not required, since we’re not building readstat.
2404 (substitute* "src/Makevars"
2405 (("-lz") "-lreadstat"))
2408 `(("readstat" ,readstat)))
2410 `(("r-knitr" ,r-knitr)))
2412 `(("r-forcats" ,r-forcats)
2415 ("r-rlang" ,r-rlang)
2416 ("r-readr" ,r-readr)
2417 ("r-tibble" ,r-tibble)
2418 ("r-tidyselect" ,r-tidyselect)
2419 ("r-vctrs" ,r-vctrs)))
2420 (home-page "https://haven.tidyverse.org")
2421 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
2423 "This package lets you mport foreign statistical formats into R via the
2424 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
2425 (license license:expat)))
2427 (define-public r-amap
2433 (uri (cran-uri "amap" version))
2436 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
2437 (build-system r-build-system)
2439 `(("gfortran" ,gfortran)))
2440 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
2441 (synopsis "Another multidimensional analysis package")
2442 (description "This package provides tools for clustering and principal
2443 component analysis (with robust methods, and parallelized functions).")
2444 (license license:gpl2+)))
2446 (define-public r-ape
2453 (uri (cran-uri "ape" version))
2456 "1r7fwyz30ippcl1ibqiv1xryf44x5crcks5kx19h146ffj76qcgh"))))
2457 (build-system r-build-system)
2459 `(("r-lattice" ,r-lattice)
2461 ("r-rcpp" ,r-rcpp)))
2462 (home-page "http://ape-package.ird.fr/")
2463 (synopsis "Analyses of phylogenetics and evolution")
2465 "This package provides functions for reading, writing, plotting, and
2466 manipulating phylogenetic trees, analyses of comparative data in a
2467 phylogenetic framework, ancestral character analyses, analyses of
2468 diversification and macroevolution, computing distances from DNA sequences,
2469 and several other tools.")
2470 (license license:gpl2+)))
2472 (define-public r-abbyyr
2479 (uri (cran-uri "abbyyR" version))
2482 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
2483 (properties `((upstream-name . "abbyyR")))
2484 (build-system r-build-system)
2486 `(("r-curl" ,r-curl)
2489 ("r-progress" ,r-progress)
2490 ("r-readr" ,r-readr)
2492 (home-page "https://github.com/soodoku/abbyyR")
2493 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
2495 "This package provides tools to get text from images of text using Abbyy
2496 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
2497 OCR images, barcodes, forms, documents with machine readable zones, e.g.
2498 passports and get the results in a variety of formats including plain text and
2499 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
2500 (license license:expat)))
2502 (define-public r-colorspace
2504 (name "r-colorspace")
2509 (uri (cran-uri "colorspace" version))
2511 (base32 "13h1hara0s6xn16bgkrbd0flszah1yiylwfwxwn2inqqk6pm6sjf"))))
2512 (build-system r-build-system)
2514 `(("r-knitr" ,r-knitr)))
2515 (home-page "https://cran.r-project.org/web/packages/colorspace")
2516 (synopsis "Color space manipulation")
2518 "This package carries out a mapping between assorted color spaces
2519 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
2520 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
2521 colors are provided.")
2522 (license license:bsd-3)))
2524 (define-public r-glue
2531 (uri (cran-uri "glue" version))
2534 "1bgpirdvjrf0da734clrixawvpdap4lpda4g89vais96589m8wwz"))))
2535 (build-system r-build-system)
2536 ;; knitr depends on glue, so we can't add knitr here to build the
2540 `(("r-knitr" ,r-knitr)))
2541 (home-page "https://github.com/tidyverse/glue")
2542 (synopsis "Interpreted string literals")
2544 "This package provides an implementation of interpreted string literals,
2545 inspired by Python's Literal String Interpolation (PEP-0498) and
2546 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
2547 (license license:expat)))
2549 (define-public r-palmerpenguins
2551 (name "r-palmerpenguins")
2556 (uri (cran-uri "palmerpenguins" version))
2559 "0q1k3cdkliq7kwrg1n0vs9b6cjwyfarhlgdijhp9c6riy6y5ik7x"))))
2561 `((upstream-name . "palmerpenguins")))
2562 (build-system r-build-system)
2563 (home-page "https://allisonhorst.github.io/palmerpenguins/")
2564 (synopsis "Palmer Archipelago (Antarctica) penguin data")
2566 "This package includes size measurements, clutch observations, and blood
2567 isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins
2568 observed on islands in the Palmer Archipelago near Palmer Station, Antarctica.
2569 Data were collected and made available by Dr. Kristen Gorman and the Palmer
2570 Station Long Term Ecological Research (LTER) Program.")
2571 (license license:cc0)))
2573 (define-public r-pastecs
2579 (uri (cran-uri "pastecs" version))
2582 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
2583 (build-system r-build-system)
2585 `(("r-boot" ,r-boot)))
2586 (home-page "https://github.com/phgrosjean/pastecs")
2587 (synopsis "Analysis of space-time ecological series")
2589 "This package provides functions for regulation, decomposition and analysis
2590 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
2591 initiative to bring PASSTEC 2000 functionalities to R.")
2592 (license license:gpl2+)))
2594 (define-public r-partykit
2600 (uri (cran-uri "partykit" version))
2603 "15d5g89winndv8cy8jjjxy87fliafp5zyb8b58czrijwcmagg50l"))))
2604 (build-system r-build-system)
2606 `(("r-formula" ,r-formula)
2608 ("r-libcoin" ,r-libcoin)
2609 ("r-mvtnorm" ,r-mvtnorm)
2610 ("r-rpart" ,r-rpart)
2611 ("r-survival" ,r-survival)))
2612 (home-page "http://partykit.R-Forge.R-project.org/partykit")
2613 (synopsis "Toolkit for recursive partytioning")
2615 "This package provides a toolkit with infrastructure for representing,
2616 summarizing, and visualizing tree-structured regression and classification
2618 (license license:gpl2+)))
2620 (define-public r-plogr
2627 (uri (cran-uri "plogr" version))
2630 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
2631 (build-system r-build-system)
2632 (home-page "https://github.com/krlmlr/plogr")
2633 (synopsis "R bindings for the plog C++ logging library")
2635 "This package provides the header files for a stripped-down version of
2636 the plog header-only C++ logging library, and a method to log to R's standard
2638 (license license:expat)))
2640 (define-public r-pls
2647 (uri (cran-uri "pls" version))
2649 (base32 "0b3ls12w19wc4xkhnsgmb333y9lyzwq3syjc3k8zs1agnw59c7cg"))))
2650 (build-system r-build-system)
2651 (home-page "https://mevik.net/work/software/pls.html")
2652 (synopsis "Partial Least Squares and Principal Component Regression")
2654 "The pls package implements multivariate regression methods: Partial Least
2655 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
2656 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
2659 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
2660 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
2661 @item multi-response models (or @dfn{PLS2})
2662 @item flexible cross-validation
2663 @item Jackknife variance estimates of regression coefficients
2664 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
2665 (R)MSEP, R², and correlation loadings
2666 @item formula interface, modelled after @code{lm()}, with methods for predict,
2667 print, summary, plot, update, etc.
2668 @item extraction functions for coefficients, scores, and loadings
2669 @item MSEP, RMSEP, and R² estimates
2670 @item multiplicative scatter correction (@dfn{MSC})
2672 (license license:gpl2)))
2681 (uri (cran-uri "ps" version))
2683 (base32 "15pyz94b0z6ibrjp25np5nd4z20whnnr35wsavdgwmsmynba2qbl"))))
2684 (build-system r-build-system)
2685 (home-page "https://ps.r-lib.org")
2686 (synopsis "List, query, and manipulate system processes")
2688 "The ps package implements an API to list, query, and manipulate system
2689 processes. Most of its code is based on the @code{psutil} Python package.")
2690 (license license:bsd-3)))
2692 (define-public r-pkgbuild
2699 (uri (cran-uri "pkgbuild" version))
2701 (base32 "0qx920h2viwjg10va81nj0xja495d8ni6vcc25ggvzki6a6k069f"))))
2702 (build-system r-build-system)
2704 `(("r-callr" ,r-callr)
2706 ("r-crayon" ,r-crayon)
2708 ("r-prettyunits" ,r-prettyunits)
2710 ("r-rprojroot" ,r-rprojroot)
2711 ("r-withr" ,r-withr)))
2712 (home-page "https://github.com/r-pkgs/pkgbuild")
2713 (synopsis "Find tools needed to build R packages")
2715 "This package provides functions used to build R packages. It locates
2716 compilers needed to build R packages on various platforms and ensures the PATH
2717 is configured appropriately so R can use them.")
2718 (license license:gpl3)))
2720 (define-public r-pkgload
2727 (uri (cran-uri "pkgload" version))
2730 "03bv8xq4s6s7m34y1kjs99jzlb95vwrfi76mbnhmzcx2pc6ld78q"))))
2731 (build-system r-build-system)
2734 ("r-crayon" ,r-crayon)
2736 ("r-pkgbuild" ,r-pkgbuild)
2737 ("r-rlang" ,r-rlang)
2738 ("r-rprojroot" ,r-rprojroot)
2739 ("r-rstudioapi" ,r-rstudioapi)
2740 ("r-withr" ,r-withr)))
2741 (home-page "https://github.com/r-lib/pkgload")
2742 (synopsis "Simulate package installation and attach")
2744 "This package simulates the process of installing a package and then
2745 attaching it. This is a key part of the @code{devtools} package as it allows
2746 you to rapidly iterate while developing a package.")
2747 (license license:gpl3)))
2749 (define-public r-rcpp
2756 (uri (cran-uri "Rcpp" version))
2758 (base32 "04ph6lm36cmvz01ng53pvvf3jxvzsn9smyflkfc7l3q0pib4gwn9"))))
2759 (build-system r-build-system)
2760 (home-page "http://www.rcpp.org")
2761 (synopsis "Seamless R and C++ integration")
2763 "The Rcpp package provides R functions as well as C++ classes which offer
2764 a seamless integration of R and C++. Many R data types and objects can be
2765 mapped back and forth to C++ equivalents which facilitates both writing of new
2766 code as well as easier integration of third-party libraries. Documentation
2767 about Rcpp is provided by several vignettes included in this package, via the
2768 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
2769 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2770 @code{citation(\"Rcpp\")} for details on these last two.")
2771 (license license:gpl2+)))
2773 (define-public r-rcppthread
2775 (name "r-rcppthread")
2780 (uri (cran-uri "RcppThread" version))
2783 "1xfcxrny779kgknlvnc4j02ifprnakndnkhx8bhy50d39vp4hjjl"))))
2784 (properties `((upstream-name . "RcppThread")))
2785 (build-system r-build-system)
2787 "https://github.com/tnagler/RcppThread")
2788 (synopsis "R threading in C++")
2790 "This package provides a C++11-style thread class and thread pool that can
2791 safely be interrupted from R.")
2792 (license license:expat)))
2794 (define-public r-bindr
2801 (uri (cran-uri "bindr" version))
2804 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
2805 (build-system r-build-system)
2806 (home-page "https://github.com/krlmlr/bindr")
2807 (synopsis "Parametrized active bindings")
2809 "This package provides a simple interface for creating active bindings
2810 where the bound function accepts additional arguments.")
2811 (license license:expat)))
2813 (define-public r-bindrcpp
2820 (uri (cran-uri "bindrcpp" version))
2823 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
2824 (build-system r-build-system)
2826 `(("r-bindr" ,r-bindr)
2827 ("r-plogr" ,r-plogr)
2828 ("r-rcpp" ,r-rcpp)))
2829 (home-page "https://github.com/krlmlr/bindrcpp")
2830 (synopsis "Rcpp interface to active bindings")
2832 "This package provides an easy way to fill an environment with active
2833 bindings that call a C++ function.")
2834 (license license:expat)))
2836 (define-public r-bisquerna
2838 (name "r-bisquerna")
2842 (uri (cran-uri "BisqueRNA" version))
2845 "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
2846 (properties `((upstream-name . "BisqueRNA")))
2847 (build-system r-build-system)
2849 `(("r-biobase" ,r-biobase)
2850 ("r-limsolve" ,r-limsolve)))
2851 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
2852 (synopsis "Decomposition of bulk expression with single-cell sequencing")
2853 (description "This package provides tools to accurately estimate cell type
2854 abundances from heterogeneous bulk expression. A reference-based method
2855 utilizes single-cell information to generate a signature matrix and
2856 transformation of bulk expression for accurate regression based estimates.
2857 A marker-based method utilizes known cell-specific marker genes to measure
2858 relative abundances across samples.")
2859 (license license:gpl3)))
2861 (define-public r-auc
2868 (uri (cran-uri "AUC" version))
2871 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
2872 (properties `((upstream-name . "AUC")))
2873 (build-system r-build-system)
2874 (home-page "https://cran.r-project.org/web/packages/AUC")
2875 (synopsis "Compute the area under the curve of selected measures")
2877 "This package includes functions to compute the area under the curve of
2878 selected measures: the area under the sensitivity curve (AUSEC), the area
2879 under the specificity curve (AUSPC), the area under the accuracy
2880 curve (AUACC), and the area under the receiver operating characteristic
2881 curve (AUROC). The curves can also be visualized. Support for partial areas
2883 (license license:gpl2+)))
2885 (define-public r-calibrate
2887 (name "r-calibrate")
2892 (uri (cran-uri "calibrate" version))
2894 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
2895 (build-system r-build-system)
2897 `(("r-mass" ,r-mass)))
2898 (home-page "https://cran.r-project.org/web/packages/calibrate")
2899 (synopsis "Calibration of scatterplot and biplot axes")
2901 "This is a package for drawing calibrated scales with tick marks
2902 on (non-orthogonal) variable vectors in scatterplots and biplots.")
2903 (license license:gpl2)))
2905 (define-public r-shape
2912 (uri (cran-uri "shape" version))
2915 "17qqhjyfhxv9la07ykaslb50c8g4d0cgfypx4y91h9i2yjw7jjh9"))))
2916 (build-system r-build-system)
2917 (home-page "https://cran.r-project.org/web/packages/shape")
2918 (synopsis "Functions for plotting graphical shapes")
2920 "This package provides functions for plotting graphical shapes such as
2921 ellipses, circles, cylinders, arrows, ...")
2922 (license license:gpl3+)))
2924 (define-public r-globaloptions
2926 (name "r-globaloptions")
2931 (uri (cran-uri "GlobalOptions" version))
2933 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
2934 (properties `((upstream-name . "GlobalOptions")))
2935 (build-system r-build-system)
2937 `(("r-knitr" ,r-knitr)))
2938 (home-page "https://github.com/jokergoo/GlobalOptions")
2939 (synopsis "Generate functions to get or set global options")
2941 "This package provides more controls on the option values such as
2942 validation and filtering on the values, making options invisible or private.")
2943 (license license:gpl2+)))
2945 (define-public r-circlize
2952 (uri (cran-uri "circlize" version))
2955 "1x2j6a80bb4fly3dm91ias964s1gb1cmzj3lyh69ikwjaam0rdmk"))))
2956 (build-system r-build-system)
2958 `(("r-colorspace" ,r-colorspace)
2959 ("r-globaloptions" ,r-globaloptions)
2960 ("r-shape" ,r-shape)))
2962 `(("r-knitr" ,r-knitr)))
2963 (home-page "https://github.com/jokergoo/circlize")
2964 (synopsis "Circular visualization")
2966 "Circular layout is an efficient way to visualise huge amounts of
2967 information. This package provides an implementation of circular layout
2968 generation in R as well as an enhancement of available software. Its
2969 flexibility is based on the usage of low-level graphics functions such that
2970 self-defined high-level graphics can be easily implemented by users for
2971 specific purposes. Together with the seamless connection between the powerful
2972 computational and visual environment in R, it gives users more convenience and
2973 freedom to design figures for better understanding complex patterns behind
2974 multi-dimensional data.")
2975 (license license:gpl2+)))
2977 (define-public r-powerlaw
2984 (uri (cran-uri "poweRlaw" version))
2986 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2987 (properties `((upstream-name . "poweRlaw")))
2988 (build-system r-build-system)
2990 `(("r-pracma" ,r-pracma)))
2992 `(("r-knitr" ,r-knitr)))
2993 (home-page "https://github.com/csgillespie/poweRlaw")
2994 (synopsis "Tools for the analysis of heavy tailed distributions")
2996 "This package provides an implementation of maximum likelihood estimators
2997 for a variety of heavy tailed distributions, including both the discrete and
2998 continuous power law distributions. Additionally, a goodness-of-fit based
2999 approach is used to estimate the lower cut-off for the scaling region.")
3000 ;; Any of these GPL versions.
3001 (license (list license:gpl2 license:gpl3))))
3003 (define-public r-compare
3010 (uri (cran-uri "compare" version))
3013 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
3014 (build-system r-build-system)
3015 (home-page "https://cran.r-project.org/web/packages/compare")
3016 (synopsis "Comparing objects for differences")
3018 "This package provides functions to compare a model object to a
3019 comparison object. If the objects are not identical, the functions can be
3020 instructed to explore various modifications of the objects (e.g., sorting
3021 rows, dropping names) to see if the modified versions are identical.")
3022 (license license:gpl2+)))
3024 (define-public r-dendextend
3026 (name "r-dendextend")
3031 (uri (cran-uri "dendextend" version))
3034 "0n3qg76apgbqbvxv2yp5qwpy6nx03xmmc9mdfyq4dqblqhdld29p"))))
3035 (build-system r-build-system)
3037 `(("r-ggplot2" ,r-ggplot2)
3038 ("r-magrittr" ,r-magrittr)
3039 ("r-viridis" ,r-viridis)))
3041 `(("r-knitr" ,r-knitr)))
3042 (home-page "https://cran.r-project.org/web/packages/dendextend")
3043 (synopsis "Extending 'dendrogram' functionality in R")
3045 "This package offers a set of functions for extending @code{dendrogram}
3046 objects in R, letting you visualize and compare trees of hierarchical
3047 clusterings. You can adjust a tree's graphical parameters (the color, size,
3048 type, etc of its branches, nodes and labels) and visually and statistically
3049 compare different dendrograms to one another.")
3050 ;; Any of these versions
3051 (license (list license:gpl2 license:gpl3))))
3053 (define-public r-getoptlong
3055 (name "r-getoptlong")
3060 (uri (cran-uri "GetoptLong" version))
3063 "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc"))))
3064 (properties `((upstream-name . "GetoptLong")))
3065 (build-system r-build-system)
3069 `(("r-crayon" ,r-crayon)
3070 ("r-globaloptions" ,r-globaloptions)
3071 ("r-rjson" ,r-rjson)))
3073 `(("r-knitr" ,r-knitr)))
3074 (home-page "https://github.com/jokergoo/GetoptLong")
3075 (synopsis "Parsing command-line arguments and variable interpolation")
3077 "This is yet another command-line argument parser which wraps the
3078 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
3079 use in R. It also provides a simple way for variable interpolation in R.")
3080 (license license:gpl2+)))
3082 (define-public r-fastmatch
3084 (name "r-fastmatch")
3089 (uri (cran-uri "fastmatch" version))
3092 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
3093 (build-system r-build-system)
3094 (home-page "https://www.rforge.net/fastmatch")
3095 (synopsis "Fast match function")
3097 "This package provides a fast @code{match} replacement for cases that
3098 require repeated look-ups. It is slightly faster that R's built-in
3099 @code{match} function on first match against a table, but extremely fast on
3100 any subsequent lookup as it keeps the hash table in memory.")
3101 (license license:gpl2)))
3110 (uri (cran-uri "ff" version))
3113 "1rfj2ff5cxzdp9nvfnbgmswc1jvxz5vkxqgpv6gprwk32a0z3v12"))))
3114 (build-system r-build-system)
3115 (propagated-inputs `(("r-bit" ,r-bit)))
3116 (home-page "http://ff.r-forge.r-project.org/")
3117 (synopsis "Memory-efficient storage of large data on disk and access functions")
3119 "This package provides data structures that are stored on disk but
3120 behave (almost) as if they were in RAM by transparently mapping only a section
3122 ;; error Architecture not supported.
3123 (supported-systems (delete "aarch64-linux" %supported-systems))
3124 (license license:gpl2)))
3126 (define-public r-ffbase
3133 (uri (cran-uri "ffbase" version))
3136 "0knl0vnh8w4q3ry24gp4fd55ipnaj9hb1rwm31fs119kgmh3gd8x"))))
3137 (build-system r-build-system)
3140 ("r-fastmatch" ,r-fastmatch)
3142 (home-page "https://github.com/edwindj/ffbase")
3143 (synopsis "Basic statistical functions for package 'ff'")
3145 "This package extends the out of memory vectors of @code{ff} with
3146 statistical functions and other utilities to ease their usage.")
3147 (license license:gpl3)))
3149 (define-public r-prettyunits
3151 (name "r-prettyunits")
3156 (uri (cran-uri "prettyunits" version))
3159 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
3160 (build-system r-build-system)
3161 (home-page "https://github.com/gaborcsardi/prettyunits")
3162 (synopsis "Pretty, human readable formatting of quantities")
3164 "This package provides tools for pretty, human readable formatting of
3166 (license license:expat)))
3168 (define-public r-reshape
3175 (uri (cran-uri "reshape" version))
3178 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
3179 (build-system r-build-system)
3181 `(("r-plyr" ,r-plyr)
3182 ("r-rcpp" ,r-rcpp)))
3183 (home-page "http://had.co.nz/reshape")
3184 (synopsis "Flexibly reshape data")
3186 "Flexibly restructure and aggregate data using just two functions:
3187 @code{melt} and @code{cast}. This package provides them.")
3188 (license license:expat)))
3190 (define-public r-restrserve
3192 (name "r-restrserve")
3197 (uri (cran-uri "RestRserve" version))
3199 (base32 "1486hrzj5q5w4nbrsbqlv7vv20ly01y90qc2vygl5syzwvyjd422"))))
3200 (build-system r-build-system)
3202 `(("r-checkmate" ,r-checkmate)
3203 ("r-jsonlite" ,r-jsonlite)
3207 ("r-rserve" ,r-rserve)
3208 ("r-uuid" ,r-uuid)))
3210 `(("r-knitr" ,r-knitr)))
3211 (home-page "https://restrserve.org")
3212 (synopsis "R web API framework")
3214 "RestRserve is an R web API framework for building high-performance AND
3215 robust microservices and app backends. With Rserve backend on UNIX-like
3216 systems it is parallel by design. It will handle incoming requests in
3217 parallel - each request in a separate fork.")
3218 (license license:gpl2+)))
3220 (define-public r-progress
3227 (uri (cran-uri "progress" version))
3230 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
3231 (build-system r-build-system)
3233 `(("r-crayon" ,r-crayon)
3235 ("r-prettyunits" ,r-prettyunits)
3237 (home-page "https://github.com/gaborcsardi/progress")
3238 (synopsis "Terminal progress bars")
3240 "This package provides configurable progress bars. They may include
3241 percentage, elapsed time, and/or the estimated completion time. They work in
3242 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
3243 package also provides a C++ API, that works with or without Rcpp.")
3244 (license license:expat)))
3246 (define-public r-ggally
3253 (uri (cran-uri "GGally" version))
3256 "0lvcvlc8p2cii7rqx7m81f7cv3kk9mlf7cbbgv7l75g7ljw8dyvz"))))
3257 (properties `((upstream-name . "GGally")))
3258 (build-system r-build-system)
3260 `(("openssl" ,openssl)))
3262 `(("r-dplyr" ,r-dplyr)
3263 ("r-forcats" ,r-forcats)
3264 ("r-ggplot2" ,r-ggplot2)
3265 ("r-gtable" ,r-gtable)
3266 ("r-lifecycle" ,r-lifecycle)
3268 ("r-progress" ,r-progress)
3269 ("r-rcolorbrewer" ,r-rcolorbrewer)
3270 ("r-reshape" ,r-reshape)
3271 ("r-rlang" ,r-rlang)
3272 ("r-scales" ,r-scales)
3273 ("r-tidyr" ,r-tidyr)))
3274 (home-page "https://ggobi.github.io/ggally")
3275 (synopsis "Extension to ggplot2")
3277 "The R package ggplot2 is a plotting system based on the grammar of
3278 graphics. GGally extends ggplot2 by adding several functions to reduce the
3279 complexity of combining geometric objects with transformed data. Some of
3280 these functions include a pairwise plot matrix, a two group pairwise plot
3281 matrix, a parallel coordinates plot, a survival plot, and several functions to
3283 (license license:gpl2+)))
3285 (define-public r-proxy
3292 (uri (cran-uri "proxy" version))
3295 "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
3296 (build-system r-build-system)
3297 (home-page "https://cran.r-project.org/web/packages/proxy")
3298 (synopsis "Distance and similarity measures")
3300 "This package provides an extensible framework for the efficient
3301 calculation of auto- and cross-proximities, along with implementations of the
3302 most popular ones.")
3303 (license license:gpl2)))
3312 (uri (cran-uri "sp" version))
3314 (base32 "1nh9izsnszzm5kbq461w8bi0yh7fqzb74b2zmpg5qis0slbb5vkb"))))
3315 (build-system r-build-system)
3317 `(("r-lattice" ,r-lattice)))
3318 (home-page "https://cran.r-project.org/web/packages/sp")
3319 (synopsis "Classes and methods for spatial data")
3321 "This package provides classes and methods for spatial data; the classes
3322 document where the spatial location information resides, for 2D or 3D data.
3323 Utility functions are provided, e.g. for plotting data as maps, spatial
3324 selection, as well as methods for retrieving coordinates, for subsetting,
3325 print, summary, etc.")
3326 (license license:gpl2+)))
3328 (define-public r-laplacesdemon
3330 (name "r-laplacesdemon")
3335 (uri (cran-uri "LaplacesDemon" version))
3337 (base32 "1nv1kx86cg8f2s8q15pzskc0lg94bb250p0fhybrx5sjqv1s2lj1"))))
3338 (properties `((upstream-name . "LaplacesDemon")))
3339 (build-system r-build-system)
3340 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
3341 (synopsis "Complete environment for Bayesian inference")
3343 "This package provides a complete environment for Bayesian inference using
3344 a variety of different samplers.")
3345 (license license:expat)))
3347 (define-public r-rmtstat
3354 (uri (cran-uri "RMTstat" version))
3357 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
3358 (properties `((upstream-name . "RMTstat")))
3359 (build-system r-build-system)
3360 (home-page "https://cran.r-project.org/web/packages/RMTstat")
3361 (synopsis "Distributions, statistics and tests derived from random matrix theory")
3363 "This package provides functions for working with the Tracy-Widom laws
3364 and other distributions related to the eigenvalues of large Wishart
3366 (license license:bsd-3)))
3368 (define-public r-rmpi
3374 (uri (cran-uri "Rmpi" version))
3377 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
3378 (properties `((upstream-name . "Rmpi")))
3379 (build-system r-build-system)
3381 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
3382 #:phases (modify-phases %standard-phases
3383 (add-before 'install 'mpi-setup
3386 `(("openmpi" ,openmpi)))
3388 `(("pkg-config" ,pkg-config)))
3389 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
3390 (synopsis "R interface to message-passing interface (MPI)")
3392 "This package provides an interface (wrapper) to MPI APIs. It also
3393 provides an interactive R manager and worker environment.")
3394 (license license:gpl2+)))
3396 (define-public r-lmoments
3403 (uri (cran-uri "Lmoments" version))
3406 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
3407 (properties `((upstream-name . "Lmoments")))
3408 (build-system r-build-system)
3410 `(("r-rcpp" ,r-rcpp)
3411 ("r-rcpparmadillo" ,r-rcpparmadillo)))
3412 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
3413 (synopsis "L-moments and quantile mixtures")
3415 "This package contains functions to estimate L-moments and trimmed
3416 L-moments from the data. It also contains functions to estimate the
3417 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
3418 quantile mixture from L-moments and trimmed L-moments.")
3419 (license license:gpl2)))
3421 (define-public r-distillery
3423 (name "r-distillery")
3428 (uri (cran-uri "distillery" version))
3431 "10nhh9p0hp294pp4aav0y0zsmir2qbn05sf3k52rmzmm36q2kc8y"))))
3432 (build-system r-build-system)
3433 (home-page "https://ral.ucar.edu/staff/ericg/")
3434 (synopsis "Functions for confidence intervals and object information")
3436 "This package provides some very simple method functions for confidence
3437 interval calculation and to distill pertinent information from a potentially
3438 complex object; primarily used in common with the packages extRemes and
3440 (license license:gpl2+)))
3442 (define-public r-etrunct
3448 (uri (cran-uri "etrunct" version))
3451 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr"))))
3452 (properties `((upstream-name . "etrunct")))
3453 (build-system r-build-system)
3454 (home-page "https://cran.r-project.org/web/packages/etrunct")
3455 (synopsis "Computes moments of univariate truncated T distribution")
3456 (description "This package computes moments of univariate truncated
3457 T distribution. There is only one exported function, @code{e_trunct},
3458 which should be seen for details.")
3459 (license license:expat)))
3461 (define-public r-extremes
3468 (uri (cran-uri "extRemes" version))
3471 "1b69r3mzl6hp3g3rqxyc77m8r40jyq7c2d87q85af7xqkn6hnxid"))))
3472 (properties `((upstream-name . "extRemes")))
3473 (build-system r-build-system)
3475 `(("r-distillery" ,r-distillery)
3476 ("r-lmoments" ,r-lmoments)))
3477 (home-page "https://www.assessment.ucar.edu/toolkit/")
3478 (synopsis "Extreme value analysis")
3480 "ExtRemes is a suite of functions for carrying out analyses on the
3481 extreme values of a process of interest; be they block maxima over long blocks
3482 or excesses over a high threshold.")
3483 (license license:gpl2+)))
3485 (define-public r-lmtest
3492 (uri (cran-uri "lmtest" version))
3495 "0sr19bmw2cpagfvwg772m79wvl1i2hww1xfr69bzr3rr8pm2r8ij"))))
3496 (build-system r-build-system)
3498 `(("r-zoo" ,r-zoo)))
3500 `(("gfortran" ,gfortran)))
3501 (home-page "https://cran.r-project.org/web/packages/lmtest")
3502 (synopsis "Testing linear regression models")
3504 "This package provides a collection of tests, data sets, and examples for
3505 diagnostic checking in linear regression models. Furthermore, some generic
3506 tools for inference in parametric models are provided.")
3507 ;; Either version is okay
3508 (license (list license:gpl2 license:gpl3))))
3510 (define-public r-idr
3516 (uri (cran-uri "idr" version))
3519 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
3520 (build-system r-build-system)
3521 (home-page "https://cran.r-project.org/web/packages/idr/")
3522 (synopsis "Irreproducible discovery rate")
3524 "This is a package for estimating the copula mixture model and plotting
3525 correspondence curves in \"Measuring reproducibility of high-throughput
3526 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
3527 by Li, Brown, Huang, and Bickel")
3528 (license license:gpl2+)))
3530 (define-public r-inline
3536 (uri (cran-uri "inline" version))
3539 "1wslsn60q959yrr27cwanba43qlpfaxzdli46i9dc26lxfr5fa3r"))))
3540 (build-system r-build-system)
3541 (home-page "https://cran.r-project.org/web/packages/inline")
3542 (synopsis "Functions to inline C, C++, Fortran function calls from R")
3544 "This package provides functionality to dynamically define R functions
3545 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
3546 @code{.Call} calling conventions.")
3547 ;; Any version of the LGPL.
3548 (license license:lgpl3+)))
3550 (define-public r-inum
3556 (uri (cran-uri "inum" version))
3559 "1sz11b4vlpskhmq9vvc1jix63a5g7lij6368w8qbnkjmjd97k7i4"))))
3560 (build-system r-build-system)
3562 `(("r-libcoin" ,r-libcoin)))
3563 (home-page "https://cran.r-project.org/web/packages/inum/")
3564 (synopsis "Interval and enum-type representation of vectors")
3566 "This package provides an enum-type representation of vectors and
3567 representation of intervals, including a method of coercing variables
3569 (license license:gpl2)))
3570 (define-public r-invgamma
3576 (uri (cran-uri "invgamma" version))
3579 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a"))))
3580 (properties `((upstream-name . "invgamma")))
3581 (build-system r-build-system)
3582 (home-page "https://github.com/dkahle/invgamma")
3583 (synopsis "Inverse gamma distribution")
3584 (description "This package provides a light weight implementation of the
3585 standard distribution functions for the inverse gamma distribution, wrapping
3586 those for the gamma distribution in the @code{stats} package.")
3587 (license license:gpl2)))
3589 (define-public r-bdsmatrix
3591 (name "r-bdsmatrix")
3596 (uri (cran-uri "bdsmatrix" version))
3599 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
3600 (properties `((upstream-name . "bdsmatrix")))
3601 (build-system r-build-system)
3602 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
3603 (synopsis "Routines for block diagonal symmetric matrices")
3605 "This package provides procedures to work with block diagonal symmetric
3606 matrices, a special case of sparse matrices.")
3607 (license license:lgpl2.0)))
3609 (define-public r-bbmle
3612 (version "1.0.23.1")
3616 (uri (cran-uri "bbmle" version))
3619 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
3620 (build-system r-build-system)
3622 `(("r-bdsmatrix" ,r-bdsmatrix)
3623 ("r-lattice" ,r-lattice)
3625 ("r-matrix" ,r-matrix)
3626 ("r-mvtnorm" ,r-mvtnorm)
3627 ("r-numderiv" ,r-numderiv)))
3628 (home-page "https://cran.r-project.org/web/packages/bbmle")
3629 (synopsis "Tools for General Maximum Likelihood Estimation")
3631 "This package provides methods and functions for fitting maximum
3632 likelihood models in R. This package modifies and extends the @code{mle}
3633 classes in the @code{stats4} package.")
3634 ;; Any version of the GPL
3635 (license license:gpl2+)))
3637 (define-public r-emdbook
3644 (uri (cran-uri "emdbook" version))
3647 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
3648 (build-system r-build-system)
3650 `(("r-bbmle" ,r-bbmle)
3652 ("r-lattice" ,r-lattice)
3654 ("r-plyr" ,r-plyr)))
3655 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
3656 (synopsis "Support functions and data for \"Ecological Models and Data\"")
3658 "This package provides auxiliary functions and data sets for \"Ecological
3659 Models and Data\", a book presenting maximum likelihood estimation and related
3660 topics for ecologists (ISBN 978-0-691-12522-0).")
3662 (license (list license:gpl2 license:gpl3))))
3664 (define-public r-lpsolve
3671 (uri (cran-uri "lpSolve" version))
3674 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
3675 (properties `((upstream-name . "lpSolve")))
3676 (build-system r-build-system)
3677 (home-page "https://cran.r-project.org/web/packages/lpSolve")
3678 (synopsis "R interface to Lp_solve to solve linear/integer programs")
3680 "Lp_solve is software for solving linear, integer and mixed integer
3681 programs. This implementation supplies a \"wrapper\" function in C and some R
3682 functions that solve general linear/integer problems, assignment problems, and
3683 transportation problems.")
3684 (license license:lgpl2.0)))
3686 (define-public r-limsolve
3693 (uri (cran-uri "limSolve" version))
3696 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
3697 (properties `((upstream-name . "limSolve")))
3698 (build-system r-build-system)
3700 `(("r-lpsolve" ,r-lpsolve)
3702 ("r-quadprog" ,r-quadprog)))
3703 (native-inputs `(("gfortran" ,gfortran)))
3704 (home-page "https://cran.r-project.org/web/packages/limSolve")
3705 (synopsis "Solving linear inverse models")
3707 "This package provides functions that:
3710 @item find the minimum/maximum of a linear or quadratic function,
3711 @item sample an underdetermined or overdetermined system,
3712 @item solve a linear system Ax=B for the unknown x.
3715 It includes banded and tridiagonal linear systems. The package calls Fortran
3716 functions from LINPACK.")
3718 (license (list license:gpl2+ license:gpl3+))))
3720 (define-public r-fitdistrplus
3722 (name "r-fitdistrplus")
3727 (uri (cran-uri "fitdistrplus" version))
3730 "1pjnqx0j26dai2fa4ip56wspmfsrcm9dpmxkg15y9623w5b58vbp"))))
3731 (build-system r-build-system)
3733 `(("r-mass" ,r-mass)
3734 ("r-survival" ,r-survival)))
3736 `(("r-knitr" ,r-knitr)))
3737 (home-page "http://riskassessment.r-forge.r-project.org")
3738 (synopsis "Fitting a parametric distribution from data")
3740 "This package extends the @code{fitdistr} function of the MASS package
3741 with several functions to help the fit of a parametric distribution to
3742 non-censored or censored data. Censored data may contain left-censored,
3743 right-censored and interval-censored values, with several lower and upper
3744 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
3745 provides moment matching (MME), quantile matching (QME) and maximum
3746 goodness-of-fit estimation (MGE) methods (available only for non-censored
3747 data). Weighted versions of MLE, MME and QME are available.")
3748 (license license:gpl2+)))
3750 (define-public r-energy
3757 (uri (cran-uri "energy" version))
3760 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
3761 (build-system r-build-system)
3763 `(("r-boot" ,r-boot)
3764 ("r-rcpp" ,r-rcpp)))
3765 (home-page "https://cran.r-project.org/web/packages/energy")
3766 (synopsis "Multivariate inference via the energy of data")
3768 "This package provides e-statistics (energy) tests and statistics for
3769 multivariate and univariate inference, including distance correlation,
3770 one-sample, two-sample, and multi-sample tests for comparing multivariate
3771 distributions, are implemented. Measuring and testing multivariate
3772 independence based on distance correlation, partial distance correlation,
3773 multivariate goodness-of-fit tests, clustering based on energy distance,
3774 testing for multivariate normality, distance components (disco) for
3775 non-parametric analysis of structured data, and other energy
3776 statistics/methods are implemented.")
3777 (license license:gpl2+)))
3779 (define-public r-suppdists
3781 (name "r-suppdists")
3786 (uri (cran-uri "SuppDists" version))
3789 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
3790 (properties `((upstream-name . "SuppDists")))
3791 (build-system r-build-system)
3792 (home-page "https://cran.r-project.org/web/packages/SuppDists")
3793 (synopsis "Supplementary distributions")
3795 "This package provides ten distributions supplementing those built into
3796 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
3797 Spearman's rho, maximum F ratio, the Pearson product moment correlation
3798 coefficient, Johnson distributions, normal scores and generalized
3799 hypergeometric distributions. In addition two random number generators of
3800 George Marsaglia are included.")
3801 (license license:gpl2+)))
3803 (define-public r-ksamples
3810 (uri (cran-uri "kSamples" version))
3813 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
3814 (properties `((upstream-name . "kSamples")))
3815 (build-system r-build-system)
3817 `(("r-suppdists" ,r-suppdists)))
3818 (home-page "https://cran.r-project.org/web/packages/kSamples")
3819 (synopsis "K-Sample rank tests and their combinations")
3821 "This package provides tools to compares k samples using the
3822 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
3823 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
3824 test. It computes asymptotic, simulated or (limited) exact P-values, all
3825 valid under randomization, with or without ties, or conditionally under random
3826 sampling from populations, given the observed tie pattern. Except for Steel's
3827 test and the JT test it also combines these tests across several blocks of
3829 (license license:gpl2+)))
3831 (define-public r-cvst
3838 (uri (cran-uri "CVST" version))
3841 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
3842 (properties `((upstream-name . "CVST")))
3843 (build-system r-build-system)
3845 `(("r-kernlab" ,r-kernlab)
3846 ("r-matrix" ,r-matrix)))
3847 (home-page "https://cran.r-project.org/web/packages/CVST")
3848 (synopsis "Fast cross-validation via sequential testing")
3850 "This package implements the fast cross-validation via sequential
3851 testing (CVST) procedure. CVST is an improved cross-validation procedure
3852 which uses non-parametric testing coupled with sequential analysis to
3853 determine the best parameter set on linearly increasing subsets of the data.
3854 Additionally to the CVST the package contains an implementation of the
3855 ordinary k-fold cross-validation with a flexible and powerful set of helper
3856 objects and methods to handle the overall model selection process. The
3857 implementations of the Cochran's Q test with permutations and the sequential
3858 testing framework of Wald are generic and can therefore also be used in other
3860 (license license:gpl2+)))
3862 (define-public r-squarem
3869 (uri (cran-uri "SQUAREM" version))
3872 "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6"))))
3873 (properties `((upstream-name . "SQUAREM")))
3874 (build-system r-build-system)
3875 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
3876 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
3878 "This package provides algorithms for accelerating the convergence of
3879 slow, monotone sequences from smooth, contraction mapping such as the EM
3880 algorithm. It can be used to accelerate any smooth, linearly convergent
3881 acceleration scheme. A tutorial style introduction to this package is
3882 available in a vignette.")
3883 (license license:gpl2+)))
3885 (define-public r-lava
3892 (uri (cran-uri "lava" version))
3895 "1yiz8y3jhxkszgz9m9fialp9r27hy97xh0imfvs8ziv7dk43y93d"))))
3896 (build-system r-build-system)
3898 `(("r-numderiv" ,r-numderiv)
3899 ("r-squarem" ,r-squarem)
3900 ("r-survival" ,r-survival)))
3902 `(("r-knitr" ,r-knitr)))
3903 (home-page "https://github.com/kkholst/lava")
3904 (synopsis "Latent variable models")
3906 "This package provides tools for the estimation and simulation of latent
3908 (license license:gpl3)))
3910 (define-public r-drr
3917 (uri (cran-uri "DRR" version))
3920 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3921 (properties `((upstream-name . "DRR")))
3922 (build-system r-build-system)
3924 `(("r-cvst" ,r-cvst)
3925 ("r-kernlab" ,r-kernlab)
3926 ("r-matrix" ,r-matrix)))
3927 (home-page "https://cran.r-project.org/web/packages/DRR")
3928 (synopsis "Dimensionality reduction via regression")
3930 "This package provides an implementation of dimensionality reduction via
3931 regression using Kernel Ridge Regression.")
3932 (license license:gpl3)))
3934 (define-public r-prodlim
3937 (version "2019.11.13")
3941 (uri (cran-uri "prodlim" version))
3944 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3945 (build-system r-build-system)
3947 `(("r-kernsmooth" ,r-kernsmooth)
3950 ("r-survival" ,r-survival)))
3951 (home-page "https://cran.r-project.org/web/packages/prodlim")
3952 (synopsis "Product-limit estimation for censored event history analysis")
3954 "This package provides a fast and user-friendly implementation of
3955 nonparametric estimators for censored event history (survival) analysis with
3956 the Kaplan-Meier and Aalen-Johansen methods.")
3957 (license license:gpl2+)))
3959 (define-public r-dimred
3966 (uri (cran-uri "dimRed" version))
3969 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3970 (properties `((upstream-name . "dimRed")))
3971 (build-system r-build-system)
3974 ("r-magrittr" ,r-magrittr)))
3975 (home-page "https://github.com/gdkrmr/dimRed")
3976 (synopsis "Framework for dimensionality reduction")
3978 "This package provides a collection of dimensionality reduction
3979 techniques from R packages and provides a common interface for calling the
3981 (license license:gpl3)))
3983 (define-public r-timedate
3986 (version "3043.102")
3990 (uri (cran-uri "timeDate" version))
3993 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
3994 (properties `((upstream-name . "timeDate")))
3995 (build-system r-build-system)
3996 (home-page "https://www.rmetrics.org")
3997 (synopsis "Chronological and calendar objects")
3999 "This package provides an environment for teaching \"Financial
4000 Engineering and Computational Finance\" and for managing chronological and
4002 (license license:gpl2+)))
4004 (define-public r-magic
4011 (uri (cran-uri "magic" version))
4014 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
4015 (build-system r-build-system)
4017 `(("r-abind" ,r-abind)))
4018 (home-page "https://github.com/RobinHankin/magic.git")
4019 (synopsis "Create and investigate magic squares")
4021 "This package provides a collection of efficient, vectorized algorithms
4022 for the creation and investigation of magic squares and hypercubes, including
4023 a variety of functions for the manipulation and analysis of arbitrarily
4024 dimensioned arrays.")
4025 (license license:gpl2)))
4027 (define-public r-rmysql
4034 (uri (cran-uri "RMySQL" version))
4037 "0cbb5ln9iigl816nzvsls9zil5qlfr8yv2aginapqv6n69nz0srs"))))
4038 (properties `((upstream-name . "RMySQL")))
4039 (build-system r-build-system)
4041 `(("mariadb-dev" ,mariadb "dev")
4044 `(("r-dbi" ,r-dbi)))
4045 (home-page "https://github.com/r-dbi/RMySQL")
4046 (synopsis "Database interface and MySQL driver for R")
4048 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
4049 package contains an old implementation based on legacy code from S-PLUS which
4050 is being phased out. A modern MySQL client based on Rcpp is available from
4051 the RMariaDB package.")
4052 (license license:gpl2)))
4054 (define-public r-rpostgresql
4056 (name "r-rpostgresql")
4061 (uri (cran-uri "RPostgreSQL" version))
4064 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
4065 (properties `((upstream-name . "RPostgreSQL")))
4066 (build-system r-build-system)
4068 `(("postgresql" ,postgresql)))
4070 `(("r-dbi" ,r-dbi)))
4071 (home-page "https://github.com/tomoakin/RPostgreSQL")
4072 (synopsis "R interface to the PostgreSQL database system")
4074 "This package provides a Database Interface (DBI) compliant driver for R
4075 to access PostgreSQL database systems.")
4076 ;; The whole package is released under GPL version 2. It includes code
4077 ;; under the PostgreSQL license.
4078 (license license:gpl2)))
4080 (define-public r-linprog
4087 (uri (cran-uri "linprog" version))
4090 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
4091 (build-system r-build-system)
4092 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
4093 (home-page "http://linprog.r-forge.r-project.org/")
4094 (synopsis "Linear programming and optimization")
4096 "This package can be used to solve Linear Programming / Linear
4097 Optimization problems by using the simplex algorithm.")
4098 (license license:gpl2+)))
4100 (define-public r-geometry
4107 (uri (cran-uri "geometry" version))
4110 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
4111 (build-system r-build-system)
4113 `(("r-magic" ,r-magic)
4114 ("r-linprog" ,r-linprog)
4115 ("r-lpsolve" ,r-lpsolve)
4117 ("r-rcppprogress" ,r-rcppprogress)))
4118 (home-page "http://geometry.r-forge.r-project.org/")
4119 (synopsis "Mesh generator and surface tessellator")
4121 "This package makes the qhull library available in R, in a similar manner
4122 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
4123 intersections about a point, Voronoi diagrams, furthest-site Delaunay
4124 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
4125 and higher dimensions. It implements the Quickhull algorithm for computing
4126 the convex hull. Qhull does not support constrained Delaunay triangulations,
4127 or mesh generation of non-convex objects, but the package does include some R
4128 functions that allow for this. Currently the package only gives access to
4129 Delaunay triangulation and convex hull computation.")
4130 ;; The Qhull sources are included and are distributed under a custom
4131 ;; non-copyleft license. The R sources are released under GPL version 2.
4132 (license (list license:gpl2
4133 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
4135 (define-public r-ddalpha
4142 (uri (cran-uri "ddalpha" version))
4145 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
4146 (build-system r-build-system)
4149 ("r-class" ,r-class)
4150 ("r-geometry" ,r-geometry)
4153 ("r-robustbase" ,r-robustbase)
4154 ("r-sfsmisc" ,r-sfsmisc)))
4156 `(("gfortran" ,gfortran)))
4157 (home-page "https://cran.r-project.org/web/packages/ddalpha")
4158 (synopsis "Depth-Based classification and calculation of data depth")
4160 "This package contains procedures for depth-based supervised learning,
4161 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
4162 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
4163 statistical depth function to a compact low-dimensional space, where the final
4164 classification is done. It also offers an extension to functional data and
4165 routines for calculating certain notions of statistical depth functions. 50
4166 multivariate and 5 functional classification problems are included.")
4167 (license license:gpl2)))
4169 (define-public r-gower
4176 (uri (cran-uri "gower" version))
4179 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
4180 (build-system r-build-system)
4181 (home-page "https://github.com/markvanderloo/gower")
4182 (synopsis "Gower's distance")
4184 "This package provides tools to compute Gower's distance (or similarity)
4185 coefficient between records, and to compute the top-n matches between records.
4186 Core algorithms are executed in parallel on systems supporting OpenMP.")
4187 (license license:gpl3)))
4189 (define-public r-rcpproll
4196 (uri (cran-uri "RcppRoll" version))
4199 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
4200 (properties `((upstream-name . "RcppRoll")))
4201 (build-system r-build-system)
4203 `(("r-rcpp" ,r-rcpp)))
4204 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
4205 (synopsis "Efficient rolling and windowed operations")
4207 "This package provides fast and efficient routines for common rolling /
4208 windowed operations. Routines for the efficient computation of windowed mean,
4209 median, sum, product, minimum, maximum, standard deviation and variance are
4211 (license license:gpl2+)))
4213 (define-public r-ipred
4220 (uri (cran-uri "ipred" version))
4223 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
4224 (build-system r-build-system)
4226 `(("r-class" ,r-class)
4229 ("r-prodlim" ,r-prodlim)
4230 ("r-rpart" ,r-rpart)
4231 ("r-survival" ,r-survival)))
4232 (home-page "https://cran.r-project.org/web/packages/ipred")
4233 (synopsis "Improved predictors")
4235 "This package provides improved predictive models by indirect
4236 classification and bagging for classification, regression and survival
4237 problems as well as resampling based estimators of prediction error.")
4238 (license license:gpl2+)))
4240 (define-public r-psych
4247 (uri (cran-uri "psych" version))
4250 "0k5dw5nb7kx7f21b0z01dry99qcpnk7iaicv7xq9d35wv2hx8wca"))))
4251 (build-system r-build-system)
4253 `(("r-lattice" ,r-lattice)
4254 ("r-mnormt" ,r-mnormt)
4255 ("r-nlme" ,r-nlme)))
4256 (home-page "https://cran.r-project.org/web/packages/psych/")
4257 (synopsis "Procedures for psychological, psychometric, and personality research")
4259 "This package provides a general purpose toolbox for personality,
4260 psychometric theory and experimental psychology. Functions are primarily for
4261 multivariate analysis and scale construction using factor analysis, principal
4262 component analysis, cluster analysis and reliability analysis, although others
4263 provide basic descriptive statistics. Item Response Theory is done using
4264 factor analysis of tetrachoric and polychoric correlations. Functions for
4265 analyzing data at multiple levels include within and between group statistics,
4266 including correlations and factor analysis. Functions for simulating and
4267 testing particular item and test structures are included. Several functions
4268 serve as a useful front end for structural equation modeling. Graphical
4269 displays of path diagrams, factor analysis and structural equation models are
4270 created using basic graphics.")
4271 (license license:gpl2+)))
4273 (define-public r-generics
4280 (uri (cran-uri "generics" version))
4283 "0qw7r0d2qvlj1pvrlpv30d6akml624ydxkk19hv85iv6pfyx2wdb"))))
4284 (build-system r-build-system)
4285 (home-page "https://github.com/r-lib/generics")
4286 (synopsis "Common S3 generics not provided by base R methods")
4288 "In order to reduce potential package dependencies and conflicts,
4289 generics provides a number of commonly used S3 generics that are not provided
4290 by base R methods related to model fitting.")
4291 (license license:gpl2)))
4293 (define-public r-broom
4300 (uri (cran-uri "broom" version))
4303 "1zwdgv59a5c4mdcfn3anvsf83ymi11ij6k9nssw3aqzirp6fwg3w"))))
4304 (build-system r-build-system)
4306 `(("r-backports" ,r-backports)
4307 ("r-dplyr" ,r-dplyr)
4308 ("r-ellipsis" ,r-ellipsis)
4309 ("r-generics" ,r-generics)
4311 ("r-purrr" ,r-purrr)
4312 ("r-rlang" ,r-rlang)
4313 ("r-stringr" ,r-stringr)
4314 ("r-tibble" ,r-tibble)
4315 ("r-tidyr" ,r-tidyr)))
4317 `(("r-knitr" ,r-knitr)))
4318 (home-page "https://github.com/tidyverse/broom")
4319 (synopsis "Convert statistical analysis objects into tidy data frames")
4321 "This package provides tools to convert statistical analysis objects from
4322 R into tidy data frames, so that they can more easily be combined, reshaped
4323 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
4324 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
4325 summarizes a model's statistical findings such as coefficients of a
4326 regression; @code{augment}, which adds columns to the original data such as
4327 predictions, residuals and cluster assignments; and @code{glance}, which
4328 provides a one-row summary of model-level statistics.")
4329 (license license:expat)))
4331 (define-public r-recipes
4338 (uri (cran-uri "recipes" version))
4341 "0xif0ak3w90xmfzlxvb5pnzc3scpfl1pyhrjffi3mq4asvsd52l0"))))
4342 (build-system r-build-system)
4344 `(("r-dplyr" ,r-dplyr)
4345 ("r-generics" ,r-generics)
4347 ("r-gower" ,r-gower)
4348 ("r-ipred" ,r-ipred)
4349 ("r-lifecycle" ,r-lifecycle)
4350 ("r-lubridate" ,r-lubridate)
4351 ("r-magrittr" ,r-magrittr)
4352 ("r-matrix" ,r-matrix)
4353 ("r-purrr" ,r-purrr)
4354 ("r-rlang" ,r-rlang)
4355 ("r-tibble" ,r-tibble)
4356 ("r-tidyr" ,r-tidyr)
4357 ("r-tidyselect" ,r-tidyselect)
4358 ("r-timedate" ,r-timedate)
4359 ("r-withr" ,r-withr)))
4361 `(("r-knitr" ,r-knitr)))
4362 (home-page "https://github.com/topepo/recipes")
4363 (synopsis "Preprocessing tools to create design matrices")
4365 "Recipes is an extensible framework to create and preprocess design
4366 matrices. Recipes consist of one or more data manipulation and analysis
4367 \"steps\". Statistical parameters for the steps can be estimated from an
4368 initial data set and then applied to other data sets. The resulting design
4369 matrices can then be used as inputs into statistical or machine learning
4371 (license license:gpl2)))
4373 (define-public r-pdist
4380 (uri (cran-uri "pdist" version))
4383 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
4384 (build-system r-build-system)
4385 (home-page "https://github.com/jeffwong/pdist")
4386 (synopsis "Partitioned distance function")
4388 "Pdist computes the euclidean distance between rows of a matrix X and
4389 rows of another matrix Y. Previously, this could be done by binding the two
4390 matrices together and calling @code{dist}, but this creates unnecessary
4391 computation by computing the distances between a row of X and another row of
4392 X, and likewise for Y. Pdist strictly computes distances across the two
4393 matrices, not within the same matrix, making computations significantly faster
4394 for certain use cases.")
4395 (license license:gpl3+)))
4397 (define-public r-ggrepel
4404 (uri (cran-uri "ggrepel" version))
4407 "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9"))))
4408 (build-system r-build-system)
4410 `(("r-ggplot2" ,r-ggplot2)
4412 ("r-rlang" ,r-rlang)
4413 ("r-scales" ,r-scales)))
4415 `(("r-knitr" ,r-knitr))) ; for vignettes
4416 (home-page "https://github.com/slowkow/ggrepel")
4417 (synopsis "Repulsive text and label geometries for ggplot2")
4419 "This package provides text and label geometries for ggplot2 that help to
4420 avoid overlapping text labels. Labels repel away from each other and away
4421 from the data points.")
4422 (license license:gpl3)))
4424 (define-public r-corrplot
4431 (uri (cran-uri "corrplot" version))
4434 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
4435 (build-system r-build-system)
4436 (home-page "https://github.com/taiyun/corrplot")
4437 (synopsis "Visualization of a correlation matrix")
4439 "This package provides a graphical display of a correlation matrix or
4440 general matrix. It also contains some algorithms to do matrix reordering. In
4441 addition, corrplot is good at details, including choosing color, text labels,
4442 color labels, layout, etc.")
4443 ;; Any version of the GPL
4444 (license license:gpl2+)))
4446 (define-public r-stringdist
4448 (name "r-stringdist")
4453 (uri (cran-uri "stringdist" version))
4455 (base32 "06rzbgw43vzg496xca82pydf3g2rz6iw6h50ai0prbp9hbwrhvfd"))))
4456 (build-system r-build-system)
4457 (home-page "https://github.com/markvanderloo/stringdist")
4458 (synopsis "Approximate string matching and string distance functions")
4460 "This package implements an approximate string matching version of R's
4461 native @code{match} function. It can calculate various string distances based
4462 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment),
4463 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
4464 Jaro-Winkler). An implementation of soundex is provided as well. Distances
4465 can be computed between character vectors while taking proper care of encoding
4466 or between integer vectors representing generic sequences.")
4467 (license license:gpl3+)))
4469 (define-public r-ucminf
4476 (uri (cran-uri "ucminf" version))
4479 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
4480 (build-system r-build-system)
4481 (native-inputs `(("gfortran" ,gfortran)))
4482 (home-page "https://cran.r-project.org/web/packages/ucminf/")
4483 (synopsis "General-purpose unconstrained non-linear optimization")
4485 "This package provides an implementation of an algorithm for
4486 general-purpose unconstrained non-linear optimization. The algorithm is of
4487 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
4488 search with a trust region type monitoring of the input to the line search
4489 algorithm. The interface of @code{ucminf} is designed for easy interchange
4490 with the package @code{optim}.")
4491 (license license:gpl2+)))
4493 (define-public r-useful
4499 (uri (cran-uri "useful" version))
4502 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
4503 (properties `((upstream-name . "useful")))
4504 (build-system r-build-system)
4506 `(("r-assertthat" ,r-assertthat)
4507 ("r-dplyr" ,r-dplyr)
4508 ("r-ggplot2" ,r-ggplot2)
4509 ("r-magrittr" ,r-magrittr)
4510 ("r-matrix" ,r-matrix)
4512 ("r-purrr" ,r-purrr)
4513 ("r-scales" ,r-scales)))
4514 (home-page "https://github.com/jaredlander/useful")
4515 (synopsis "Collection of handy, useful functions")
4516 (description "This package provides a set of little functions that have been
4517 found useful to do little odds and ends such as plotting the results of K-means
4518 clustering, substituting special text characters, viewing parts of a
4519 @code{data.frame}, constructing formulas from text and building design and
4520 response matrices.")
4521 (license license:bsd-3)))
4523 (define-public r-ordinal
4526 (version "2019.12-10")
4530 (uri (cran-uri "ordinal" version))
4533 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
4534 (build-system r-build-system)
4536 `(("r-mass" ,r-mass)
4537 ("r-matrix" ,r-matrix)
4538 ("r-numderiv" ,r-numderiv)
4539 ("r-ucminf" ,r-ucminf)))
4540 (home-page "https://github.com/runehaubo/ordinal")
4541 (synopsis "Regression models for ordinal data")
4543 "This package provides an implementation of cumulative link (mixed)
4544 models also known as ordered regression models, proportional odds models,
4545 proportional hazards models for grouped survival times and ordered models.
4546 Estimation is via maximum likelihood and mixed models are fitted with the
4547 Laplace approximation and adaptive Gauss-Hermite quadrature.")
4548 (license license:gpl2+)))
4550 (define-public r-jomo
4557 (uri (cran-uri "jomo" version))
4560 "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir"))))
4561 (build-system r-build-system)
4563 `(("r-lme4" ,r-lme4)
4565 ("r-ordinal" ,r-ordinal)
4566 ("r-survival" ,r-survival)))
4567 (home-page "https://cran.r-project.org/web/packages/jomo/")
4568 (synopsis "Multilevel Joint Modelling Multiple Imputation")
4570 "Similarly to Schafer's package pan, jomo is a package for multilevel
4571 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
4572 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
4573 possibility of handling binary and categorical data through latent normal
4574 variables, the option to use cluster-specific covariance matrices and to
4575 impute compatibly with the substantive model.")
4576 (license license:gpl2)))
4578 (define-public r-pan
4585 (uri (cran-uri "pan" version))
4588 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
4589 (build-system r-build-system)
4590 (native-inputs `(("gfortran" ,gfortran)))
4591 (home-page "https://cran.r-project.org/web/packages/pan/")
4592 (synopsis "Multiple imputation for multivariate panel or clustered data")
4594 "This package implements multiple imputation for multivariate panel or
4596 (license license:gpl3)))
4598 (define-public r-mitml
4605 (uri (cran-uri "mitml" version))
4608 "1bw92fl6xp3yvawh3nbjzs4hp4alpwj6vnv6lsysd74aqndw447c"))))
4609 (build-system r-build-system)
4611 `(("r-haven" ,r-haven)
4615 `(("r-knitr" ,r-knitr)))
4616 (home-page "https://cran.r-project.org/web/packages/mitml/")
4617 (synopsis "Tools for multiple imputation in multilevel modeling")
4619 "This package provides tools for multiple imputation of missing data in
4620 multilevel modeling. It includes a user-friendly interface to the packages
4621 pan and jomo, and several functions for visualization, data management and the
4622 analysis of multiply imputed data sets.")
4623 (license license:gpl2+)))
4625 (define-public r-mice
4632 (uri (cran-uri "mice" version))
4635 "11cpyqlilakan2pwjzacb9jjlazazsqdngy237nnrj8j6mky822i"))))
4636 (build-system r-build-system)
4638 `(("r-broom" ,r-broom)
4639 ("r-cpp11" ,r-cpp11)
4640 ("r-dplyr" ,r-dplyr)
4641 ("r-generics" ,r-generics)
4642 ("r-lattice" ,r-lattice)
4644 ("r-rlang" ,r-rlang)
4645 ("r-tidyr" ,r-tidyr)))
4646 (home-page "https://cran.r-project.org/web/packages/mice/")
4647 (synopsis "Multivariate imputation by chained equations")
4649 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
4650 implemented by the MICE algorithm as described in @url{Van Buuren and
4651 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
4652 variable has its own imputation model. Built-in imputation models are
4653 provided for continuous data (predictive mean matching, normal), binary
4654 data (logistic regression), unordered categorical data (polytomous logistic
4655 regression) and ordered categorical data (proportional odds). MICE can also
4656 impute continuous two-level data (normal model, pan, second-level variables).
4657 Passive imputation can be used to maintain consistency between variables.
4658 Various diagnostic plots are available to inspect the quality of the
4660 ;; Any of these two versions.
4661 (license (list license:gpl2 license:gpl3))))
4663 (define-public r-truncnorm
4665 (name "r-truncnorm")
4670 (uri (cran-uri "truncnorm" version))
4673 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
4674 (build-system r-build-system)
4675 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
4676 (synopsis "Truncated normal distribution")
4677 (description "This package provides functions for the truncated normal
4678 distribution with mean equal to @code{mean} and standard deviation equal to
4679 @code{sd}. It includes density, distribution, quantile, and expected value
4680 functions, as well as a random generation function.")
4681 (license license:gpl2)))
4683 (define-public r-rsolnp
4690 (uri (cran-uri "Rsolnp" version))
4693 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
4694 (properties `((upstream-name . "Rsolnp")))
4695 (build-system r-build-system)
4697 `(("r-truncnorm" ,r-truncnorm)))
4698 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
4699 (synopsis "General non-linear optimization")
4700 (description "The Rsolnp package implements a general non-linear augmented
4701 Lagrange multiplier method solver, a @dfn{sequential quadratic
4702 programming} (SQP) based solver).")
4703 ;; Any version of the GPL.
4704 (license license:gpl2+)))
4706 (define-public r-hardyweinberg
4708 (name "r-hardyweinberg")
4713 (uri (cran-uri "HardyWeinberg" version))
4716 "0afjz818yvaq3akvgpy4irnlpspd2dj71qkrwj81lm9y36ypwlw6"))))
4717 (properties `((upstream-name . "HardyWeinberg")))
4718 (build-system r-build-system)
4720 `(("r-mice" ,r-mice)
4722 ("r-rsolnp" ,r-rsolnp)))
4723 (home-page "https://cran.r-project.org/package=HardyWeinberg")
4724 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
4726 "This package contains tools for exploring Hardy-Weinberg equilibrium for
4727 diallelic genetic marker data. All classical tests (chi-square, exact,
4728 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
4729 included in the package, as well as functions for power computation and for
4730 the simulation of marker data under equilibrium and disequilibrium. Routines
4731 for dealing with markers on the X-chromosome are included. Functions for
4732 testing equilibrium in the presence of missing data by using multiple
4733 imputation are also provided. Implements several graphics for exploring the
4734 equilibrium status of a large set of diallelic markers: ternary plots with
4735 acceptance regions, log-ratio plots and Q-Q plots.")
4736 (license license:gpl2+)))
4745 (uri (cran-uri "sm" version))
4748 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
4749 (build-system r-build-system)
4750 (native-inputs `(("gfortran" ,gfortran)))
4751 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
4752 (synopsis "Smoothing methods for nonparametric regression and density estimation")
4754 "This is software accompanying the book 'Applied Smoothing Techniques for
4755 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
4756 University Press. It provides smoothing methods for nonparametric regression
4757 and density estimation")
4758 (license license:gpl2+)))
4760 (define-public r-venndiagram
4762 (name "r-venndiagram")
4766 (uri (cran-uri "VennDiagram" version))
4769 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
4770 (properties `((upstream-name . "VennDiagram")))
4771 (build-system r-build-system)
4773 `(("r-futile-logger" ,r-futile-logger)))
4774 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
4775 (synopsis "Generate High-Resolution Venn and Euler Plots")
4777 "This package provides a set of functions to generate high-resolution
4778 Venn and Euler plots. It includes handling for several special cases,
4779 including two-case scaling, and extensive customization of plot shape and
4781 (license license:gpl2+)))
4783 (define-public r-vioplot
4790 (uri (cran-uri "vioplot" version))
4793 "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v"))))
4794 (build-system r-build-system)
4799 `(("r-knitr" ,r-knitr)))
4800 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
4801 (synopsis "Violin plot")
4803 "This package provides a violin plot, which is a combination of a box
4804 plot and a kernel density plot.")
4805 (license license:bsd-3)))
4807 (define-public r-rsofia
4813 ;; This package has been removed from CRAN, so we can
4814 ;; only fetch it from the archives.
4815 (uri (string-append "https://cran.r-project.org/src/"
4816 "contrib/Archive/RSofia/RSofia_"
4820 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
4821 (properties `((upstream-name . "RSofia")))
4822 (build-system r-build-system)
4824 `(("r-rcpp" ,r-rcpp)))
4825 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
4826 (synopsis "Port of sofia-ml to R")
4827 (description "This package is a port of sofia-ml to R. Sofia-ml is a
4828 suite of fast incremental algorithms for machine learning that can be used for
4829 training models for classification or ranking.")
4830 (license license:asl2.0)))
4832 (define-public r-xts
4839 (uri (cran-uri "xts" version))
4842 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
4843 (build-system r-build-system)
4844 (propagated-inputs `(("r-zoo" ,r-zoo)))
4845 (home-page "https://github.com/joshuaulrich/xts")
4846 (synopsis "Extensible time series")
4848 "This package provides for uniform handling of R's different time-based
4849 data classes by extending @code{zoo}, maximizing native format information
4850 preservation and allowing for user-level customization and extension, while
4851 simplifying cross-class interoperability.")
4852 (license license:gpl2+)))
4854 (define-public r-performanceanalytics
4856 (name "r-performanceanalytics")
4861 (uri (cran-uri "PerformanceAnalytics" version))
4864 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
4866 `((upstream-name . "PerformanceAnalytics")))
4867 (build-system r-build-system)
4869 `(("r-quadprog" ,r-quadprog)
4872 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
4873 (synopsis "Econometric tools for performance and risk analysis")
4874 (description "This is a collection of econometric functions for
4875 performance and risk analysis. This package aims to aid practitioners and
4876 researchers in utilizing the latest research in analysis of non-normal return
4877 streams. In general, it is most tested on return (rather than price) data on
4878 a regular scale, but most functions will work with irregular return data as
4879 well, and increasing numbers of functions will work with P&L or price data
4881 ;; Either version may be picked.
4882 (license (list license:gpl2 license:gpl3))))
4884 (define-public r-laeken
4891 (uri (cran-uri "laeken" version))
4894 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
4895 (build-system r-build-system)
4897 `(("r-boot" ,r-boot)
4898 ("r-mass" ,r-mass)))
4899 (home-page "https://cran.r-project.org/web/packages/laeken/")
4900 (synopsis "Estimation of indicators on social exclusion and poverty")
4901 (description "This package provides tools for the estimation of indicators
4902 on social exclusion and poverty, as well as an implementation of Pareto tail
4903 modeling for empirical income distributions.")
4904 (license license:gpl2+)))
4906 (define-public r-vcd
4913 (uri (cran-uri "vcd" version))
4916 "030yyhpzsj4ivwrla7p9kgvmyjh6b8fr7czf678ykxjj64ccnvr3"))))
4917 (build-system r-build-system)
4919 `(("r-colorspace" ,r-colorspace)
4920 ("r-lmtest" ,r-lmtest)
4921 ("r-mass" ,r-mass)))
4922 (home-page "https://cran.r-project.org/web/packages/vcd/")
4923 (synopsis "Visualizing categorical data")
4924 (description "This package provides visualization techniques, data sets,
4925 summary and inference procedures aimed particularly at categorical data.
4926 Special emphasis is given to highly extensible grid graphics. The package was
4927 originally inspired by the book \"Visualizing Categorical Data\" by Michael
4928 Friendly and is now the main support package for a new book, \"Discrete Data
4929 Analysis with R\" by Michael Friendly and David Meyer (2015).")
4930 (license license:gpl2)))
4932 (define-public r-ica
4939 (uri (cran-uri "ica" version))
4942 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
4943 (build-system r-build-system)
4944 (home-page "https://cran.r-project.org/web/packages/ica/")
4945 (synopsis "Independent component analysis")
4946 (description "This package provides tools for @dfn{Independent Component
4947 Analysis} (ICA) using various algorithms: FastICA,
4948 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4949 of Eigenmatrices} (JADE).")
4950 (license license:gpl2+)))
4952 (define-public r-dtw
4959 (uri (cran-uri "dtw" version))
4962 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z"))))
4963 (build-system r-build-system)
4964 (propagated-inputs `(("r-proxy" ,r-proxy)))
4965 (home-page "http://dtw.r-forge.r-project.org/")
4966 (synopsis "Dynamic Time Warping Algorithms")
4967 (description "This package provides a comprehensive implementation of
4968 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4969 optimal (least cumulative distance) alignment between points of two time
4970 series. Common DTW variants covered include local (slope) and global (window)
4971 constraints, subsequence matches, arbitrary distance definitions,
4972 normalizations, minimum variance matching, and so on.")
4973 (license license:gpl2+)))
4975 (define-public r-sdmtools
4978 (version "1.1-221.2")
4982 (uri (cran-uri "SDMTools" version))
4985 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4986 (properties `((upstream-name . "SDMTools")))
4987 (build-system r-build-system)
4988 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4989 (home-page "https://www.rforge.net/SDMTools/")
4990 (synopsis "Species distribution modelling tools")
4991 (description "This package provides a set of tools for post processing
4992 the outcomes of species distribution modeling exercises. It includes novel
4993 methods for comparing models and tracking changes in distributions through
4994 time. It further includes methods for visualizing outcomes, selecting
4995 thresholds, calculating measures of accuracy and landscape fragmentation
4997 (license license:gpl3+)))
4999 (define-public r-scatterplot3d
5001 (name "r-scatterplot3d")
5006 (uri (cran-uri "scatterplot3d" version))
5009 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
5010 (build-system r-build-system)
5011 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
5012 (synopsis "3D scatter plot")
5013 (description "This package provides an implementation of scatter plots for
5014 plotting. a three dimensional point cloud.")
5015 (license license:gpl2)))
5017 (define-public r-ggridges
5024 (uri (cran-uri "ggridges" version))
5027 "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm"))))
5028 (build-system r-build-system)
5030 `(("r-ggplot2" ,r-ggplot2)
5032 ("r-scales" ,r-scales)
5033 ("r-withr" ,r-withr)))
5035 `(("r-knitr" ,r-knitr)))
5036 (home-page "https://github.com/clauswilke/ggridges")
5037 (synopsis "Ridgeline plots in ggplot2")
5039 "Ridgeline plots provide a convenient way of visualizing changes in
5040 distributions over time or space. This package enables the creation of such
5041 plots in @code{ggplot2}.")
5042 (license license:gpl2)))
5044 (define-public r-ggjoy
5051 (uri (cran-uri "ggjoy" version))
5054 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
5055 (build-system r-build-system)
5057 `(("r-ggplot2" ,r-ggplot2)
5058 ("r-ggridges" ,r-ggridges)))
5059 (home-page "https://github.com/clauswilke/ggjoy")
5060 (synopsis "Joyplots in ggplot2")
5061 (description "Joyplots provide a convenient way of visualizing changes in
5062 distributions over time or space. This package enables the creation of such
5063 plots in @code{ggplot2}.")
5064 (license license:gpl2)))
5066 (define-public r-cli
5073 (uri (cran-uri "cli" version))
5076 "128bx3bds0dnkixc4frbky11rz1ilnvdfzz9mggajj690i11b62q"))))
5077 (build-system r-build-system)
5079 `(("r-assertthat" ,r-assertthat)
5080 ("r-glue" ,r-glue)))
5081 (home-page "https://github.com/r-lib/cli#readme")
5082 (synopsis "Helpers for developing command line interfaces")
5083 (description "This package provides a suite of tools designed to build
5084 attractive command line interfaces (CLIs). It includes tools for drawing
5085 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
5086 (license license:expat)))
5088 (define-public r-argparser
5090 (name "r-argparser")
5095 (uri (cran-uri "argparser" version))
5098 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
5099 (build-system r-build-system)
5100 (home-page "https://bitbucket.org/djhshih/argparser")
5101 (synopsis "Command-line argument parser")
5103 "This package provides a cross-platform command-line argument parser
5104 written purely in R with no external dependencies. It is useful with the
5105 Rscript front-end and facilitates turning an R script into an executable
5107 (license license:gpl3+)))
5109 (define-public r-debugme
5116 (uri (cran-uri "debugme" version))
5119 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
5120 (build-system r-build-system)
5121 (propagated-inputs `(("r-crayon" ,r-crayon)))
5122 (home-page "https://github.com/r-lib/debugme#readme")
5123 (synopsis "Debug R packages")
5125 "This package allows the user to specify debug messages as special string
5126 constants, and control debugging of packages via environment variables.")
5127 (license license:expat)))
5129 (define-public r-processx
5136 (uri (cran-uri "processx" version))
5138 (base32 "055v2gdrgqsfy8s672wsq79bqr44b4jjmcbqivx4p2d6lqx10s73"))))
5139 (build-system r-build-system)
5143 (home-page "https://github.com/r-lib/processx3")
5144 (synopsis "Execute and control system processes")
5146 "This package provides portable tools to run system processes in the
5147 background. It can check if a background process is running; wait on a
5148 background process to finish; get the exit status of finished processes; kill
5149 background processes and their children; restart processes. It can read the
5150 standard output and error of the processes, using non-blocking connections.
5151 @code{processx} can poll a process for standard output or error, with a
5152 timeout. It can also poll several processes at once.")
5153 (license license:expat)))
5155 (define-public r-tsp
5162 (uri (cran-uri "TSP" version))
5165 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
5166 (properties `((upstream-name . "TSP")))
5167 (build-system r-build-system)
5168 (propagated-inputs `(("r-foreach" ,r-foreach)))
5169 (home-page "https://cran.r-project.org/web/packages/TSP/")
5170 (synopsis "Traveling salesperson problem (TSP)")
5171 (description "This package provides basic infrastructure and some
5172 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
5173 traveling salesman problem).")
5174 (license license:gpl3)))
5176 (define-public r-qap
5183 (uri (cran-uri "qap" version))
5186 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
5187 (build-system r-build-system)
5188 (native-inputs `(("gfortran" ,gfortran)))
5189 (home-page "https://cran.r-project.org/web/packages/qap/")
5190 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
5191 (description "This package implements heuristics for the @dfn{quadratic
5192 assignment problem} (QAP). Currently only a simulated annealing heuristic is
5194 (license license:gpl3)))
5196 (define-public r-gclus
5203 (uri (cran-uri "gclus" version))
5206 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
5207 (build-system r-build-system)
5208 (propagated-inputs `(("r-cluster" ,r-cluster)))
5209 (home-page "https://cran.r-project.org/web/packages/gclus/")
5210 (synopsis "Clustering graphics")
5211 (description "This package orders panels in scatterplot matrices and
5212 parallel coordinate displays by some merit index. It contains various indices
5213 of merit, ordering functions, and enhanced versions of @code{pairs} and
5214 @code{parcoord} which color panels according to their merit level.")
5215 (license license:gpl2+)))
5217 (define-public r-webshot
5224 (uri (cran-uri "webshot" version))
5227 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
5228 (build-system r-build-system)
5230 `(("r-callr" ,r-callr)
5231 ("r-jsonlite" ,r-jsonlite)
5232 ("r-magrittr" ,r-magrittr)))
5233 (home-page "https://github.com/wch/webshot/")
5234 (synopsis "Take screenshots of web pages")
5236 "Webshot makes it easy to take screenshots of web pages from within R.
5237 It can also run Shiny applications locally and take screenshots of the
5238 application; and it can render and screenshot static as well as interactive R
5239 Markdown documents.")
5240 (license license:gpl2)))
5242 (define-public r-seriation
5244 (name "r-seriation")
5249 (uri (cran-uri "seriation" version))
5252 "1glxn098ar1v96xlwp85kjxzfd1nyfzp2f82x5z3fm87yv57k4lb"))))
5253 (build-system r-build-system)
5255 `(("r-cluster" ,r-cluster)
5256 ("r-colorspace" ,r-colorspace)
5257 ("r-dendextend" ,r-dendextend)
5258 ("r-gclus" ,r-gclus)
5259 ("r-gplots" ,r-gplots)
5262 ("r-registry" ,r-registry)
5264 (native-inputs `(("gfortran" ,gfortran)))
5265 (home-page "https://s2.smu.edu/IDA/seriation/")
5266 (synopsis "Infrastructure for ordering objects using seriation")
5268 "This package provides infrastructure for seriation with an
5269 implementation of several seriation/sequencing techniques to reorder matrices,
5270 dissimilarity matrices, and dendrograms. It also provides (optimally)
5271 reordered heatmaps, color images and clustering visualizations like
5272 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
5274 (license license:gpl3)))
5276 (define-public r-xfun
5283 (uri (cran-uri "xfun" version))
5285 (base32 "18qjs81fn8q2d2drcan8gpgvrbgxgd0b659c92z19kg2h4c1g3k4"))))
5286 (build-system r-build-system)
5287 ;; knitr itself depends on xfun
5290 `(("r-knitr" ,r-knitr)))
5291 (home-page "https://github.com/yihui/xfun")
5292 (synopsis "Miscellaneous functions")
5294 "This package provides miscellaneous functions commonly used in other
5295 packages maintained by Yihui Xie.")
5296 (license license:expat)))
5298 (define-public r-utf8
5305 (uri (cran-uri "utf8" version))
5308 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
5309 (build-system r-build-system)
5310 (home-page "https://github.com/patperry/r-utf8")
5311 (synopsis "Unicode text processing")
5313 "This package provides tools to process and print UTF-8 encoded
5314 international text (Unicode). Input, validate, normalize, encode, format, and
5316 (license license:asl2.0)))
5318 (define-public r-zeallot
5325 (uri (cran-uri "zeallot" version))
5328 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
5329 (build-system r-build-system)
5330 (home-page "https://github.com/nteetor/zeallot")
5331 (synopsis "Multiple, unpacking, and destructuring assignment")
5333 "This package provides a @code{%<-%} operator to perform multiple,
5334 unpacking, and destructuring assignment in R. The operator unpacks the
5335 right-hand side of an assignment into multiple values and assigns these values
5336 to variables on the left-hand side of the assignment.")
5337 (license license:expat)))
5339 (define-public r-vctrs
5346 (uri (cran-uri "vctrs" version))
5349 "09ddxgzyah7lw42hn6n8fynsixf43s10jamsf94d2aidky63czfz"))))
5350 (build-system r-build-system)
5352 `(("r-digest" ,r-digest)
5353 ("r-ellipsis" ,r-ellipsis)
5355 ("r-rlang" ,r-rlang)))
5357 `(("r-knitr" ,r-knitr)))
5358 (home-page "https://github.com/r-lib/vctrs")
5359 (synopsis "Vector helpers")
5361 "There are three main goals to the @code{vctrs} package:
5364 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
5365 @code{length()} and @code{class()}. These definitions are paired with a
5366 framework for type-coercion and size-recycling.
5367 @item To define type- and size-stability as desirable function properties, use
5368 them to analyse existing base function, and to propose better alternatives.
5369 This work has been particularly motivated by thinking about the ideal
5370 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
5371 @item To provide a new @code{vctr} base class that makes it easy to create new
5372 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
5373 a few new @code{vctrs} generics, making implementation considerably simpler
5376 (license license:gpl3)))
5378 (define-public r-pillar
5385 (uri (cran-uri "pillar" version))
5388 "167ji21fx04s2niw5pjq9vzxgagxzsg3gimh8dzr2kl5ljrb5vfd"))))
5389 (build-system r-build-system)
5392 ("r-crayon" ,r-crayon)
5393 ("r-ellipsis" ,r-ellipsis)
5394 ("r-fansi" ,r-fansi)
5395 ("r-lifecycle" ,r-lifecycle)
5396 ("r-rlang" ,r-rlang)
5398 ("r-vctrs" ,r-vctrs)))
5399 (home-page "https://github.com/r-lib/pillar")
5400 (synopsis "Coloured formatting for columns")
5402 "This package provides a @code{pillar} generic designed for formatting
5403 columns of data using the full range of colours provided by modern
5405 (license license:gpl3)))
5407 (define-public r-uuid
5414 (uri (cran-uri "uuid" version))
5417 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
5418 (build-system r-build-system)
5419 (home-page "https://www.rforge.net/uuid")
5420 (synopsis "Tools for generating and handling of UUIDs")
5422 "This package provides tools for generating and handling of
5423 @dfn{Universally Unique Identifiers} (UUIDs).")
5424 (license license:expat)))
5426 (define-public r-tinytex
5433 (uri (cran-uri "tinytex" version))
5436 "0my1412vn5zri01w2myzn268lfwinbhfgdj4bbcib3s48i9djw0n"))))
5437 (build-system r-build-system)
5439 `(("r-xfun" ,r-xfun)))
5440 (home-page "https://github.com/yihui/tinytex")
5441 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
5443 "This package provides helper functions to install and maintain the LaTeX
5444 distribution named TinyTeX, a lightweight, cross-platform, portable, and
5445 easy-to-maintain version of TeX Live. This package also contains helper
5446 functions to compile LaTeX documents, and install missing LaTeX packages
5448 (license license:expat)))
5450 (define-public r-tinytest
5457 (uri (cran-uri "tinytest" version))
5460 "1asryjrah3fj39gg0c6yxgpr142j5bg2n990v7q8r0a5pb8gcr45"))))
5461 (properties `((upstream-name . "tinytest")))
5462 (build-system r-build-system)
5463 (home-page "https://github.com/markvanderloo/tinytest")
5464 (synopsis "Lightweight unit testing framework")
5466 "This package provides a lightweight unit testing framework. Main
5470 @item install tests with the package;
5471 @item test results are treated as data that can be stored and manipulated;
5472 @item test files are R scripts interspersed with test commands, that can be
5474 @item fully automated build-install-test sequence for packages;
5475 @item skip tests when not run locally (e.g. on CRAN);
5476 @item flexible and configurable output printing;
5477 @item compare computed output with output stored with the package;
5478 @item run tests in parallel;
5479 @item extensible by other packages;
5480 @item report side effects.
5483 (license license:gpl3)))
5485 (define-public r-network
5492 (uri (cran-uri "network" version))
5495 "1cgy7vlbinyndl0zkzvnpcmi240wry6iwfb42sz1mj5c9iwkar7b"))))
5496 (build-system r-build-system)
5498 `(("r-magrittr" ,r-magrittr)
5499 ("r-tibble" ,r-tibble)))
5500 (home-page "https://statnet.org/")
5501 (synopsis "Classes for relational data")
5503 "This package provides tools to create and modify network objects. The
5504 @code{network} class can represent a range of relational data types, and
5505 supports arbitrary vertex/edge/graph attributes.")
5506 (license license:gpl2+)))
5508 (define-public r-stabs
5515 (uri (cran-uri "stabs" version))
5518 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q"))))
5519 (build-system r-build-system)
5521 `(("r-knitr" ,r-knitr)))
5522 (home-page "https://github.com/hofnerb/stabs")
5523 (synopsis "Stability selection with error control")
5525 "This package provides resampling procedures to assess the stability of
5526 selected variables with additional finite sample error control for
5527 high-dimensional variable selection procedures such as Lasso or boosting.
5528 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
5529 complementary pairs stability selection with improved error bounds
5530 (Shah & Samworth, 2013) are implemented. The package can be combined with
5531 arbitrary user specified variable selection approaches.")
5532 (license license:gpl2)))
5534 (define-public r-rle
5541 (uri (cran-uri "rle" version))
5544 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40"))))
5545 (properties `((upstream-name . "rle")))
5546 (build-system r-build-system)
5547 (home-page "https://cran.r-project.org/web/packages/rle/")
5548 (synopsis "Common functions for run-length encoded vectors")
5550 "This package provides common @code{base} and @code{stats} methods for
5551 @code{rle} objects, aiming to make it possible to treat them transparently as
5553 (license license:gpl3)))
5555 (define-public r-statnet-common
5557 (name "r-statnet-common")
5562 (uri (cran-uri "statnet.common" version))
5565 "1z89an46xcl1d7dacj4irhk6pkajdz7v85b2347vczwdf622pksf"))))
5567 `((upstream-name . "statnet.common")))
5568 (build-system r-build-system)
5570 `(("r-coda" ,r-coda)
5572 (home-page "https://statnet.org")
5573 (synopsis "R scripts and utilities used by the Statnet software")
5574 (description "This package provides non-statistical utilities used by the
5575 software developed by the Statnet Project.")
5576 (license license:gpl3)))
5578 (define-public r-statcheck
5580 (name "r-statcheck")
5585 (uri (cran-uri "statcheck" version))
5588 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
5589 (build-system r-build-system)
5591 `(("r-ggplot2" ,r-ggplot2)
5593 ("r-rmarkdown" ,r-rmarkdown)))
5594 (home-page "https://cran.r-project.org/web/packages/statcheck/")
5595 (synopsis "Extract statistics from articles and recompute p-values")
5596 (description "This package can automatically extract statistical
5597 null-hypothesis significant testing (NHST) results from articles and recompute
5598 the p-values based on the reported test statistic and degrees of freedom to
5599 detect possible inconsistencies.")
5600 (license license:gpl2)))
5602 (define-public r-sna
5609 (uri (cran-uri "sna" version))
5612 "0ai0v4538d30m4wks5s3lch1yfmx1ml0nnrz7ihs097lv586a09s"))))
5613 (build-system r-build-system)
5615 `(("r-network" ,r-network)
5616 ("r-statnet-common" ,r-statnet-common)))
5617 (home-page "https://statnet.org")
5618 (synopsis "Tools for social network analysis")
5620 "This package provides a range of tools for social network analysis,
5621 including node and graph-level indices, structural distance and covariance
5622 methods, structural equivalence detection, network regression, random graph
5623 generation, and 2D/3D network visualization.")
5624 (license license:gpl2+)))
5626 (define-public r-tfisher
5633 (uri (cran-uri "TFisher" version))
5636 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
5637 (properties `((upstream-name . "TFisher")))
5638 (build-system r-build-system)
5640 `(("r-matrix" ,r-matrix)
5641 ("r-mvtnorm" ,r-mvtnorm)
5643 (home-page "https://cran.r-project.org/web/packages/TFisher/")
5644 (synopsis "Optimal thresholding Fisher's p-value combination method")
5646 "This package provides the @dfn{cumulative distribution function} (CDF),
5647 quantile, and statistical power calculator for a collection of thresholding
5648 Fisher's p-value combination methods, including Fisher's p-value combination
5649 method, truncated product method and, in particular, soft-thresholding
5650 Fisher's p-value combination method which is proven to be optimal in some
5651 context of signal detection. The p-value calculator for the omnibus version
5652 of these tests are also included.")
5653 (license license:gpl2)))
5655 (define-public r-ttr
5662 (uri (cran-uri "TTR" version))
5665 "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5"))))
5666 (properties `((upstream-name . "TTR")))
5667 (build-system r-build-system)
5669 `(("r-curl" ,r-curl)
5672 (home-page "https://github.com/joshuaulrich/TTR")
5673 (synopsis "Technical trading rules")
5675 "This package provides functions and data to construct technical trading
5677 (license license:gpl2)))
5679 (define-public r-leaps
5686 (uri (cran-uri "leaps" version))
5689 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
5690 (build-system r-build-system)
5691 (native-inputs `(("gfortran" ,gfortran)))
5692 (home-page "https://cran.r-project.org/web/packages/leaps/")
5693 (synopsis "Regression subset selection")
5695 "This package provides tools for regression subset selection, including
5696 exhaustive search.")
5697 (license license:gpl2+)))
5699 (define-public r-splus2r
5706 (uri (cran-uri "splus2R" version))
5709 "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x"))))
5710 (properties `((upstream-name . "splus2R")))
5711 (build-system r-build-system)
5712 (home-page "https://cran.r-project.org/web/packages/splus2R/")
5713 (synopsis "Supplemental S-PLUS functionality in R")
5715 "Currently there are many functions in S-PLUS that are missing in R. To
5716 facilitate the conversion of S-PLUS packages to R packages, this package
5717 provides some missing S-PLUS functionality in R.")
5718 (license license:gpl2)))
5720 (define-public r-ifultools
5722 (name "r-ifultools")
5727 (uri (cran-uri "ifultools" version))
5730 "0f95vqc47dgssqngznk0rclr72ndbyxc7gdq2cmbksvq7qpn3gg1"))))
5731 (build-system r-build-system)
5733 `(("r-mass" ,r-mass)
5734 ("r-splus2r" ,r-splus2r)))
5735 (home-page "https://cran.r-project.org/web/packages/ifultools/")
5736 (synopsis "Insightful research tools")
5737 (description "This package provides C code used by the wmtsa, fractal, and
5739 (license license:gpl2)))
5741 (define-public r-sapa
5748 (uri (cran-uri "sapa" version))
5751 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
5752 (build-system r-build-system)
5754 `(("r-ifultools" ,r-ifultools)
5755 ("r-splus2r" ,r-splus2r)))
5756 (home-page "https://cran.r-project.org/web/packages/sapa/")
5757 (synopsis "Spectral analysis for physical applications")
5758 (description "This package provides software for the book Spectral
5759 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
5760 Cambridge University Press, 1993.")
5761 (license license:gpl2)))
5763 (define-public r-aggregation
5765 (name "r-aggregation")
5770 (uri (cran-uri "aggregation" version))
5773 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
5774 (build-system r-build-system)
5775 (home-page "https://cran.r-project.org/web/packages/aggregation/")
5776 (synopsis "Methods for p-value aggregation")
5778 "This package contains functionality for performing the following methods
5779 of p-value aggregation: Fisher's method, the Lancaster method (weighted
5780 Fisher's method), and Sidak correction.")
5781 (license license:gpl3)))
5783 (define-public r-quantmod
5790 (uri (cran-uri "quantmod" version))
5793 "0dbcrncv06iqcbkky95dd7l32xq0hhbnkb0kj8wwzym1jf748h5a"))))
5794 (build-system r-build-system)
5796 `(("r-curl" ,r-curl)
5800 (home-page "https://cran.r-project.org/web/packages/quantmod/")
5801 (synopsis "Quantitative financial modelling framework")
5802 (description "This package provides a quantitative financial modelling
5803 framework to allow users to specify, build, trade, and analyse quantitative
5804 financial trading strategies.")
5805 (license license:gpl3)))
5807 (define-public r-tseries
5814 (uri (cran-uri "tseries" version))
5817 "0wa4rcf0igayi1yrwc6wak6d491560p0z89rz32haqlkiiq25gak"))))
5818 (build-system r-build-system)
5820 `(("r-quadprog" ,r-quadprog)
5821 ("r-quantmod" ,r-quantmod)
5824 `(("gfortran" ,gfortran)))
5825 (home-page "https://cran.r-project.org/web/packages/tseries/")
5826 (synopsis "Time series analysis and computational finance")
5828 "This package provides functions relating to time series analysis and
5829 computational finance.")
5830 (license license:gpl2)))
5832 (define-public r-wmtsa
5839 (uri (cran-uri "wmtsa" version))
5842 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
5843 (build-system r-build-system)
5845 `(("r-ifultools" ,r-ifultools)
5847 ("r-splus2r" ,r-splus2r)))
5848 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
5849 (synopsis "Wavelet methods for time series analysis")
5851 "This package provides software to accompany the book \"Wavelet Methods
5852 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
5853 University Press, 2000.")
5854 (license license:gpl2)))
5856 (define-public r-tsa
5863 (uri (cran-uri "TSA" version))
5866 "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb"))))
5867 (properties `((upstream-name . "TSA")))
5868 (build-system r-build-system)
5870 `(("r-leaps" ,r-leaps)
5871 ("r-locfit" ,r-locfit)
5873 ("r-tseries" ,r-tseries)))
5874 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
5875 (synopsis "Time series analysis")
5877 "This package contains R functions and datasets detailed in the book
5878 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
5879 Cryer and Kung-Sik Chan.")
5880 (license license:gpl2+)))
5882 (define-public r-extradistr
5884 (name "r-extradistr")
5889 (uri (cran-uri "extraDistr" version))
5892 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
5893 (properties `((upstream-name . "extraDistr")))
5894 (build-system r-build-system)
5896 `(("r-rcpp" ,r-rcpp)))
5897 (home-page "https://github.com/twolodzko/extraDistr")
5898 (synopsis "Additional univariate and multivariate distributions")
5900 "This package implements density, distribution functions, quantile
5901 functions and random generation functions for a large number of univariate and
5902 multivariate distributions.")
5903 (license license:gpl2)))
5905 (define-public r-fractal
5912 (uri (cran-uri "fractal" version))
5915 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
5916 (build-system r-build-system)
5918 `(("r-ifultools" ,r-ifultools)
5921 ("r-scatterplot3d" ,r-scatterplot3d)
5922 ("r-splus2r" ,r-splus2r)
5923 ("r-wmtsa" ,r-wmtsa)))
5924 (home-page "https://cran.r-project.org/web/packages/fractal/")
5925 (synopsis "Fractal time series modeling and analysis")
5927 "This package provides tools for stochastic fractal and deterministic
5928 chaotic time series analysis.")
5929 (license license:gpl2)))
5931 (define-public r-urca
5938 (uri (cran-uri "urca" version))
5941 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
5942 (build-system r-build-system)
5943 (propagated-inputs `(("r-nlme" ,r-nlme)))
5944 (native-inputs `(("gfortran" ,gfortran)))
5945 (home-page "https://cran.r-project.org/web/packages/urca/")
5946 (synopsis "Unit root and cointegration tests for time series data")
5948 "This package provides unit root and cointegration tests encountered in
5949 applied econometric analysis.")
5950 (license license:gpl2+)))
5952 (define-public r-cubature
5959 (uri (cran-uri "cubature" version))
5962 "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq"))))
5963 (build-system r-build-system)
5965 `(("r-rcpp" ,r-rcpp)))
5967 `(("r-knitr" ,r-knitr)))
5968 (home-page "https://github.com/bnaras/cubature")
5969 (synopsis "Adaptive multivariate integration over hypercubes")
5971 "This package is an R wrapper around the cubature C library for adaptive
5972 multivariate integration over hypercubes. This version provides both
5973 @code{hcubature} and @code{pcubature} routines in addition to a vector
5975 ;; The included cubature C library is released under GPLv2+, but the
5976 ;; wrapper declares the license to be GPLv3+.
5977 (license (list license:gpl2+ license:gpl3+))))
5979 (define-public r-trend
5986 (uri (cran-uri "trend" version))
5989 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
5990 (build-system r-build-system)
5992 `(("r-extradistr" ,r-extradistr)))
5994 `(("gfortran" ,gfortran)))
5995 (home-page "https://cran.r-project.org/web/packages/trend/")
5996 (synopsis "Non-parametric trend tests and change-point detection")
5998 "The analysis of environmental data often requires the detection of
5999 trends and change-points. This package includes tests for trend
6000 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
6001 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
6002 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
6003 correlation trend test), change-point detection (Lanzante's test procedures,
6004 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
6005 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
6006 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
6007 sample Robust Rank-Order Distributional Test.")
6008 (license license:gpl3)))
6010 (define-public r-expm
6017 (uri (cran-uri "expm" version))
6020 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c"))))
6021 (build-system r-build-system)
6022 (propagated-inputs `(("r-matrix" ,r-matrix)))
6023 (native-inputs `(("gfortran" ,gfortran)))
6024 (home-page "https://r-forge.r-project.org/projects/expm/")
6025 (synopsis "Tools for matrix exponentials and related quantities")
6027 "This package provides tools for the computation of the matrix
6028 exponential, logarithm, square root, and related quantities.")
6029 (license license:gpl2+)))
6031 (define-public r-complexplus
6033 (name "r-complexplus")
6038 (uri (cran-uri "complexplus" version))
6041 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
6042 (build-system r-build-system)
6044 `(("r-expm" ,r-expm)
6045 ("r-matrix" ,r-matrix)))
6046 (home-page "https://cran.r-project.org/web/packages/complexplus/")
6047 (synopsis "Functions of complex or real variables")
6049 "This package extends several functions to the complex domain, including
6050 the matrix exponential and logarithm, and the determinant.")
6051 (license license:gpl2)))
6053 (define-public r-phontools
6055 (name "r-phontools")
6060 (uri (cran-uri "phonTools" version))
6063 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
6064 (properties `((upstream-name . "phonTools")))
6065 (build-system r-build-system)
6066 (home-page "http://www.santiagobarreda.com/rscripts.html")
6067 (synopsis "Tools for phonetic and acoustic analyses")
6069 "This package contains tools for the organization, display, and analysis
6070 of the sorts of data frequently encountered in phonetics research and
6071 experimentation, including the easy creation of IPA vowel plots, and the
6072 creation and manipulation of WAVE audio files.")
6073 (license license:bsd-2)))
6082 (uri (cran-uri "np" version))
6085 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
6086 (build-system r-build-system)
6088 `(("r-boot" ,r-boot)
6089 ("r-cubature" ,r-cubature)
6090 ("r-quadprog" ,r-quadprog)
6091 ("r-quantreg" ,r-quantreg)))
6092 (home-page "https://github.com/JeffreyRacine/R-Package-np")
6093 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
6094 (description "This package provides non-parametric (and semi-parametric)
6095 kernel methods that seamlessly handle a mix of continuous, unordered, and
6096 ordered factor data types.")
6097 ;; Any version of the GPL.
6098 (license license:gpl3+)))
6100 (define-public r-powerplus
6102 (name "r-powerplus")
6107 (uri (cran-uri "powerplus" version))
6110 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
6111 (build-system r-build-system)
6113 `(("r-complexplus" ,r-complexplus)
6116 ("r-matrix" ,r-matrix)
6117 ("r-phontools" ,r-phontools)))
6118 (home-page "https://cran.r-project.org/web/packages/powerplus/")
6119 (synopsis "Exponentiation operations")
6121 "This package provides tools for the computation of matrix and scalar
6123 (license license:gpl2)))
6125 (define-public r-egg
6132 (uri (cran-uri "egg" version))
6135 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
6136 (properties `((upstream-name . "egg")))
6137 (build-system r-build-system)
6139 `(("r-ggplot2" ,r-ggplot2)
6140 ("r-gridextra" ,r-gridextra)
6141 ("r-gtable" ,r-gtable)))
6142 (home-page "https://cran.r-project.org/web/packages/egg")
6143 (synopsis "Extensions for ggplot2")
6145 "This package provides miscellaneous functions to help customize ggplot2
6146 objects. High-level functions are provided to post-process ggplot2 layouts
6147 and allow alignment between plot panels, as well as setting panel sizes to
6148 fixed values. Other functions include a custom @code{geom}, and helper
6149 functions to enforce symmetric scales or add tags to facetted plots.")
6150 (license license:gpl3)))
6152 (define-public r-heatmaply
6154 (name "r-heatmaply")
6159 (uri (cran-uri "heatmaply" version))
6162 "0hspfkninwy62sf8gkdcsvwnvl66bbnjs2dpah9rr95a3rsgdp9d"))))
6163 (build-system r-build-system)
6165 `(("r-assertthat" ,r-assertthat)
6166 ("r-colorspace" ,r-colorspace)
6167 ("r-dendextend" ,r-dendextend)
6169 ("r-ggplot2" ,r-ggplot2)
6170 ("r-htmlwidgets" ,r-htmlwidgets)
6171 ("r-magrittr" ,r-magrittr)
6172 ("r-plotly" ,r-plotly)
6173 ("r-rcolorbrewer" ,r-rcolorbrewer)
6174 ("r-reshape2" ,r-reshape2)
6175 ("r-scales" ,r-scales)
6176 ("r-seriation" ,r-seriation)
6177 ("r-viridis" ,r-viridis)
6178 ("r-webshot" ,r-webshot)))
6180 `(("r-knitr" ,r-knitr)))
6181 (home-page "https://cran.r-project.org/package=heatmaply")
6182 (synopsis "Interactive cluster heat maps using plotly")
6184 "This package enables you to create interactive cluster heatmaps that can
6185 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
6186 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
6187 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
6188 a popular graphical method for visualizing high-dimensional data, in which a
6189 table of numbers is encoded as a grid of colored cells. The rows and columns
6190 of the matrix are ordered to highlight patterns and are often accompanied by
6192 ;; Either version of the license.
6193 (license (list license:gpl2 license:gpl3))))
6202 (uri (cran-uri "h5" version))
6205 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
6206 (build-system r-build-system)
6211 `(("which" ,which)))
6213 `(("r-rcpp" ,r-rcpp)))
6214 (home-page "https://github.com/mannau/h5")
6215 (synopsis "Interface to the HDF5 Library")
6217 "This package provides an S4 interface to the HDF5 library supporting
6218 fast storage and retrieval of R-objects like vectors, matrices and arrays to
6219 binary files in a language independent format. The HDF5 format can therefore
6220 be used as an alternative to R's save/load mechanism. Since h5 is able to
6221 access only subsets of stored data it can also handle data sets which do not
6223 (license license:bsd-2)))
6225 (define-public r-cgdsr
6232 (uri (cran-uri "cgdsr" version))
6235 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
6236 (build-system r-build-system)
6238 `(("r-httr" ,r-httr)
6239 ("r-r-methodss3" ,r-r-methodss3)
6240 ("r-r-oo" ,r-r-oo)))
6241 (home-page "https://github.com/cBioPortal/cgdsr")
6242 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
6244 "This package provides a basic set of R functions for querying the Cancer
6245 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
6246 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
6247 (license license:lgpl3)))
6249 (define-public r-import
6256 (uri (cran-uri "import" version))
6259 "018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37"))))
6260 (build-system r-build-system)
6262 `(("r-knitr" ,r-knitr)))
6263 (home-page "https://github.com/smbache/import")
6264 (synopsis "Import mechanism for R")
6266 "This is an alternative mechanism for importing objects from packages.
6267 The syntax allows for importing multiple objects from a package with a single
6268 command in an expressive way. The import package bridges some of the gap
6269 between using @code{library} (or @code{require}) and direct (single-object)
6270 imports. Furthermore the imported objects are not placed in the current
6271 environment. It is also possible to import objects from stand-alone @code{.R}
6273 (license license:expat)))
6275 (define-public r-shinyace
6282 (uri (cran-uri "shinyAce" version))
6285 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
6286 (properties `((upstream-name . "shinyAce")))
6287 (build-system r-build-system)
6289 `(("r-shiny" ,r-shiny)
6290 ("r-jsonlite" ,r-jsonlite)))
6291 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
6292 (synopsis "Ace editor bindings for Shiny")
6294 "This package provides Ace editor bindings to enable a rich text editing
6295 environment within Shiny.")
6296 (license license:expat)))
6298 (define-public r-randomizr
6300 (name "r-randomizr")
6305 (uri (cran-uri "randomizr" version))
6308 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
6309 (properties `((upstream-name . "randomizr")))
6310 (build-system r-build-system)
6312 `(("r-knitr" ,r-knitr)))
6313 (home-page "https://declaredesign.org/r/randomizr/")
6314 (synopsis "Tools for common forms of random assignment and sampling")
6316 "This package provides tools for generating random assignments for common
6317 experimental designs and random samples for common sampling designs.")
6318 (license license:expat)))
6320 (define-public r-base64url
6322 (name "r-base64url")
6327 (uri (cran-uri "base64url" version))
6330 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
6331 (build-system r-build-system)
6333 `(("r-backports" ,r-backports)))
6334 (home-page "https://github.com/mllg/base64url")
6335 (synopsis "Fast and URL-safe base64 encoder and decoder")
6337 "This package provides a URL-safe base64 encoder and decoder. In
6338 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
6339 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
6340 encoder does not fill the string with trailing @code{=}. The resulting
6341 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
6342 and thus are safe to use in URLs or for file names. The package also comes
6343 with a simple base32 encoder/decoder suited for case insensitive file
6345 (license license:gpl3)))
6347 (define-public r-radiant-data
6349 (name "r-radiant-data")
6354 (uri (cran-uri "radiant.data" version))
6357 "08bqqrfvpgyf613ikihwfnzb23l23f5nfs7zynnxbjxc1zfhbpny"))
6358 (modules '((guix build utils)))
6361 ;; Delete files that are under CC-NC-SA.
6362 (delete-file-recursively "inst/app/tools/help")
6364 (properties `((upstream-name . "radiant.data")))
6365 (build-system r-build-system)
6367 `(("r-base64enc" ,r-base64enc)
6368 ("r-broom" ,r-broom)
6371 ("r-dplyr" ,r-dplyr)
6374 ("r-ggplot2" ,r-ggplot2)
6375 ("r-import" ,r-import)
6376 ("r-jsonlite" ,r-jsonlite)
6377 ("r-knitr" ,r-knitr)
6378 ("r-lubridate" ,r-lubridate)
6379 ("r-magrittr" ,r-magrittr)
6380 ("r-markdown" ,r-markdown)
6382 ("r-patchwork" ,r-patchwork)
6383 ("r-plotly" ,r-plotly)
6384 ("r-psych" ,r-psych)
6385 ("r-randomizr" ,r-randomizr)
6386 ("r-readr" ,r-readr)
6387 ("r-readxl" ,r-readxl)
6388 ("r-rlang" ,r-rlang)
6389 ("r-rmarkdown" ,r-rmarkdown)
6390 ("r-rstudioapi" ,r-rstudioapi)
6391 ("r-scales" ,r-scales)
6392 ("r-shiny" ,r-shiny)
6393 ("r-shinyfiles" ,r-shinyfiles)
6394 ("r-shinyace" ,r-shinyace)
6395 ("r-stringi" ,r-stringi)
6396 ("r-tibble" ,r-tibble)
6397 ("r-tidyr" ,r-tidyr)
6398 ("r-writexl" ,r-writexl)))
6399 (home-page "https://github.com/radiant-rstats/radiant.data")
6400 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
6402 "The Radiant Data menu includes interfaces for loading, saving, viewing,
6403 visualizing, summarizing, transforming, and combining data. It also contains
6404 functionality to generate reproducible reports of the analyses conducted in
6406 (license license:agpl3)))
6408 (define-public r-algdesign
6410 (name "r-algdesign")
6415 (uri (cran-uri "AlgDesign" version))
6417 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
6418 (properties `((upstream-name . "AlgDesign")))
6419 (build-system r-build-system)
6420 (home-page "https://github.com/jvbraun/AlgDesign")
6421 (synopsis "Algorithmic experimental design")
6423 "This package provides tools to calculate exact and approximate theory
6424 experimental designs for D, A, and I criteria. Very large designs may be
6425 created. Experimental designs may be blocked or blocked designs created from
6426 a candidate list, using several criteria. The blocking can be done when whole
6427 and within plot factors interact.")
6428 (license license:gpl2+)))
6430 (define-public r-signal
6437 (uri (cran-uri "signal" version))
6440 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
6441 (build-system r-build-system)
6442 (propagated-inputs `(("r-mass" ,r-mass)))
6443 (native-inputs `(("gfortran" ,gfortran)))
6444 (home-page "https://cran.r-project.org/web/packages/signal/")
6445 (synopsis "Signal processing")
6447 "This package provides a set of signal processing functions originally
6448 written for Matlab and GNU Octave. It includes filter generation utilities,
6449 filtering functions, resampling routines, and visualization of filter models.
6450 It also includes interpolation functions.")
6451 (license license:gpl2)))
6453 (define-public r-gsubfn
6460 (uri (cran-uri "gsubfn" version))
6463 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
6464 (build-system r-build-system)
6465 (propagated-inputs `(("r-proto" ,r-proto)))
6466 (home-page "https://code.google.com/archive/p/gsubfn/")
6467 (synopsis "Utilities for strings and function arguments.")
6469 "This package provides @code{gsubfn} which is like @code{gsub} but can
6470 take a replacement function or certain other objects instead of the
6471 replacement string. Matches and back references are input to the replacement
6472 function and replaced by the function output. @code{gsubfn} can be used to
6473 split strings based on content rather than delimiters and for quasi-perl-style
6474 string interpolation. The package also has facilities for translating
6475 formulas to functions and allowing such formulas in function calls instead of
6477 (license license:gpl2+)))
6479 (define-public r-sqldf
6486 (uri (cran-uri "sqldf" version))
6489 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
6490 (build-system r-build-system)
6492 `(("r-chron" ,r-chron)
6494 ("r-gsubfn" ,r-gsubfn)
6495 ("r-proto" ,r-proto)
6496 ("r-rsqlite" ,r-rsqlite)))
6497 (home-page "https://github.com/ggrothendieck/sqldf")
6498 (synopsis "Manipulate R data frames using SQL")
6500 "The @code{sqldf} function is typically passed a single argument which is
6501 an SQL select statement where the table names are ordinary R data frame names.
6502 @code{sqldf} transparently sets up a database, imports the data frames into
6503 that database, performs the SQL statement and returns the result using a
6504 heuristic to determine which class to assign to each column of the returned
6505 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
6506 used to read filtered files into R even if the original files are larger than
6507 R itself can handle.")
6508 (license license:gpl2)))
6510 (define-public r-abind
6517 (uri (cran-uri "abind" version))
6520 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
6521 (build-system r-build-system)
6522 (home-page "https://cran.r-project.org/web/packages/abind/")
6523 (synopsis "Combine multidimensional arrays")
6525 "This package provides tools to combine multidimensional arrays into a
6526 single array. This is a generalization of @code{cbind} and @code{rbind}. It
6527 works with vectors, matrices, and higher-dimensional arrays. It also provides
6528 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
6529 extracting and replacing data in arrays.")
6530 (license license:lgpl2.0+)))
6532 (define-public r-prroc
6539 (uri (cran-uri "PRROC" version))
6542 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
6543 (properties `((upstream-name . "PRROC")))
6544 (build-system r-build-system)
6545 (home-page "https://cran.r-project.org/web/packages/PRROC/")
6546 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
6548 "This package computes the areas under the @dfn{precision-recall} (PR)
6549 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
6550 contrast to other implementations, the interpolation between points of the PR
6551 curve is done by a non-linear piecewise function. In addition to the areas
6552 under the curves, the curves themselves can also be computed and plotted by a
6553 specific S3-method.")
6554 (license license:gpl3)))
6556 (define-public r-vim
6563 (uri (cran-uri "VIM" version))
6566 "1a8aw0ysaf0al95m2la2zx1p3g5mnwqx0x30br1s1dqqkfnv57hz"))))
6567 (properties `((upstream-name . "VIM")))
6568 (build-system r-build-system)
6571 ("r-colorspace" ,r-colorspace)
6572 ("r-data-table" ,r-data-table)
6573 ("r-e1071" ,r-e1071)
6574 ("r-laeken" ,r-laeken)
6575 ("r-magrittr" ,r-magrittr)
6578 ("r-ranger" ,r-ranger)
6580 ("r-robustbase" ,r-robustbase)
6584 `(("r-knitr" ,r-knitr)))
6585 (home-page "https://github.com/alexkowa/VIM")
6586 (synopsis "Visualization and imputation of missing values")
6588 "This package provides tools for the visualization of missing and/or
6589 imputed values are introduced, which can be used for exploring the data and
6590 the structure of the missing and/or imputed values. Depending on this
6591 structure of the missing values, the corresponding methods may help to
6592 identify the mechanism generating the missing values and explore the
6593 data including missing values. In addition, the quality of imputation can be
6594 visually explored using various univariate, bivariate, multiple and
6595 multivariate plot methods.")
6596 (license license:gpl2+)))
6598 (define-public r-fnn
6605 (uri (cran-uri "FNN" version))
6608 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
6609 (properties `((upstream-name . "FNN")))
6610 (build-system r-build-system)
6611 (home-page "https://cran.r-project.org/web/packages/FNN")
6612 (synopsis "Fast nearest neighbor search algorithms and applications")
6614 "This package provides cover-tree and kd-tree fast k-nearest neighbor
6615 search algorithms. Related applications including KNN classification,
6616 regression and information measures are implemented.")
6617 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
6618 ;; later can be used.
6619 (license license:gpl2+)))
6621 (define-public r-smoother
6628 (uri (cran-uri "smoother" version))
6631 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
6632 (build-system r-build-system)
6634 `(("r-ttr" ,r-ttr)))
6635 (home-page "https://cran.r-project.org/web/packages/smoother")
6636 (synopsis "Functions relating to the smoothing of numerical data")
6638 "This package provides a collection of methods for smoothing numerical
6639 data, commencing with a port of the Matlab gaussian window smoothing function.
6640 In addition, several functions typically used in smoothing of financial data
6642 (license license:gpl2)))
6644 (define-public r-riverplot
6646 (name "r-riverplot")
6651 (uri (cran-uri "riverplot" version))
6654 "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj"))))
6655 (build-system r-build-system)
6657 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
6659 `(("r-knitr" ,r-knitr)))
6660 (home-page "https://logfc.wordpress.com")
6661 (synopsis "Sankey or ribbon plots")
6663 "Sankey plots are a type of diagram that is convenient to illustrate how
6664 flow of information, resources etc. separates and joins, much like observing
6665 how rivers split and merge. For example, they can be used to compare
6666 different clusterings. This package provides an implementation of Sankey
6668 (license license:gpl2+)))
6670 (define-public r-dyn
6677 (uri (cran-uri "dyn" version))
6680 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
6681 (build-system r-build-system)
6683 `(("r-zoo" ,r-zoo)))
6684 (home-page "https://cran.r-project.org/web/packages/dyn")
6685 (synopsis "Time series regression")
6687 "This package provides the dyn class interfaces @code{ts}, @code{irts},
6688 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
6689 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
6690 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
6691 @code{randomForest::randomForest()} and other regression functions, allowing
6692 those functions to be used with time series including specifications that may
6693 contain lags, diffs and missing values.")
6695 (license license:gpl2+)))
6697 (define-public r-catdap
6704 (uri (cran-uri "catdap" version))
6707 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
6708 (build-system r-build-system)
6710 `(("gfortran" ,gfortran)))
6711 (home-page "https://cran.r-project.org/web/packages/catdap/")
6712 (synopsis "Tools for categorical data analysis")
6714 "This package provides functions for analyzing multivariate data.
6715 Dependencies of the distribution of the specified variable (response
6716 variable) to other variables (explanatory variables) are derived and
6717 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
6718 (license license:gpl2+)))
6720 (define-public r-arules
6727 (uri (cran-uri "arules" version))
6730 "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm"))))
6731 (build-system r-build-system)
6733 `(("r-matrix" ,r-matrix)))
6734 (home-page "https://github.com/mhahsler/arules")
6735 (synopsis "Mining association rules and frequent itemsets")
6737 "This package provides an infrastructure for representing, manipulating
6738 and analyzing transaction data and patterns (frequent itemsets and association rules).
6739 It also provides C implementations of the association mining algorithms Apriori
6741 (license license:gpl3)))
6743 (define-public r-parsedate
6745 (name "r-parsedate")
6750 (uri (cran-uri "parsedate" version))
6753 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
6754 (build-system r-build-system)
6756 `(("r-rematch2" ,r-rematch2)))
6757 (home-page "https://github.com/gaborcsardi/parsedate")
6759 "Recognize and parse dates in various formats")
6761 "This package provides three functions for dealing with dates:
6762 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
6763 time formats, @code{parse_date} parses dates in unspecified formats,
6764 and @code{format_iso_8601} formats a date in ISO 8601 format.")
6765 (license license:gpl2)))
6767 (define-public r-abc-data
6774 (uri (cran-uri "abc.data" version))
6777 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
6778 (properties `((upstream-name . "abc.data")))
6779 (build-system r-build-system)
6780 (home-page "https://cran.r-project.org/web/packages/abc.data/")
6781 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
6783 "This package contains data which are used by functions of the abc
6784 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
6785 algorithms for performing parameter estimation, model selection, and
6787 (license license:gpl3+)))
6789 (define-public r-abc
6796 (uri (cran-uri "abc" version))
6799 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
6800 (build-system r-build-system)
6802 `(("r-abc-data" ,r-abc-data)
6803 ("r-locfit" ,r-locfit)
6806 ("r-quantreg" ,r-quantreg)))
6807 (home-page "https://cran.r-project.org/web/packages/abc/")
6808 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
6810 "This package implements several @dfn{Approximate Bayesian
6811 Computation} (ABC) algorithms for performing parameter estimation, model
6812 selection, and goodness-of-fit. Cross-validation tools are also available for
6813 measuring the accuracy of ABC estimates, and to calculate the
6814 misclassification probabilities of different models.")
6815 (license license:gpl3+)))
6817 (define-public r-zip
6824 (uri (cran-uri "zip" version))
6827 "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i"))))
6828 (build-system r-build-system)
6829 (home-page "https://github.com/gaborcsardi/zip")
6830 (synopsis "Cross-platform Zip compression")
6832 "This package provides a cross-platform Zip compression library for R.
6833 It is a replacement for the @code{zip} function, that does not require any
6834 additional external tools on any platform.")
6835 (license license:cc0)))
6837 (define-public r-openxlsx
6844 (uri (cran-uri "openxlsx" version))
6847 "0vz4nlrwgsiifrgza8kfd9i1c0ya6plymrgk59vyy2z54vc8kvyd"))))
6848 (build-system r-build-system)
6850 `(("r-rcpp" ,r-rcpp)
6851 ("r-stringi" ,r-stringi)
6854 `(("r-knitr" ,r-knitr)))
6855 (home-page "https://github.com/awalker89/openxlsx")
6856 (synopsis "Read, write and edit XLSX files")
6858 "This package simplifies the creation of Excel @code{.xlsx} files by
6859 providing a high level interface to writing, styling and editing worksheets.
6860 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
6861 and @code{XLConnect} packages with the added benefit of removing the
6862 dependency on Java.")
6863 (license license:gpl3)))
6865 (define-public r-rio
6872 (uri (cran-uri "rio" version))
6875 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
6876 (build-system r-build-system)
6878 `(("r-curl" ,r-curl)
6879 ("r-data-table" ,r-data-table)
6880 ("r-foreign" ,r-foreign)
6881 ("r-haven" ,r-haven)
6882 ("r-openxlsx" ,r-openxlsx)
6883 ("r-readxl" ,r-readxl)
6884 ("r-tibble" ,r-tibble)))
6885 (home-page "https://github.com/leeper/rio")
6886 (synopsis "Swiss-army knife for data I/O")
6888 "This package provides streamlined data import and export infrastructure
6889 by making assumptions that the user is probably willing to make: @code{import}
6890 and @code{export} determine the data structure from the file extension,
6891 reasonable defaults are used for data import and export (e.g.,
6892 @code{stringsAsFactors=FALSE}), web-based import is natively
6893 supported (including from SSL/HTTPS), compressed files can be read directly
6894 without explicit decompression, and fast import packages are used where
6895 appropriate. An additional convenience function, @code{convert}, provides a
6896 simple method for converting between file types.")
6897 (license license:gpl2)))
6899 (define-public r-maptools
6906 (uri (cran-uri "maptools" version))
6909 "0jgf3wg47jdnznxb3ncv4is9ackwviy4lzcyggqwzw3wh6jnvb6s"))))
6910 (build-system r-build-system)
6912 `(("r-foreign" ,r-foreign)
6913 ("r-lattice" ,r-lattice)
6915 (home-page "https://r-forge.r-project.org/projects/maptools/")
6916 (synopsis "Tools for reading and handling spatial objects")
6918 "This package provides a set of tools for manipulating and reading
6919 geographic data, in particular ESRI Shapefiles. It includes binary access to
6920 GSHHG shoreline files. The package also provides interface wrappers for
6921 exchanging spatial objects with other R packages.")
6922 ;; The C source files from shapelib are released under the Expat license.
6923 ;; The R code is released under GPL version 2 or later.
6924 (license (list license:gpl2+
6927 (define-public r-later
6934 (uri (cran-uri "later" version))
6937 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
6938 (build-system r-build-system)
6942 ("r-rlang" ,r-rlang)))
6944 `(("r-knitr" ,r-knitr)))
6945 (home-page "https://github.com/r-lib/later")
6946 (synopsis "Utilities for delaying function execution")
6948 "This package provides tools to execute arbitrary R or C functions some
6949 time after the current time, after the R execution stack has emptied.")
6950 (license license:gpl2+)))
6952 (define-public r-promises
6959 (uri (cran-uri "promises" version))
6962 "002qkhcn3ri6a3w5fizjvdvrjgvqiw8i7rl9jglcnqik5kmwc61p"))))
6963 (build-system r-build-system)
6965 `(("r-later" ,r-later)
6966 ("r-magrittr" ,r-magrittr)
6969 ("r-rlang" ,r-rlang)))
6971 `(("r-knitr" ,r-knitr)))
6972 (home-page "https://rstudio.github.io/promises")
6973 (synopsis "Abstractions for promise-based asynchronous programming")
6975 "This package provides fundamental abstractions for doing asynchronous
6976 programming in R using promises. Asynchronous programming is useful for
6977 allowing a single R process to orchestrate multiple tasks in the background
6978 while also attending to something else. Semantics are similar to JavaScript
6979 promises, but with a syntax that is idiomatic R.")
6980 (license license:expat)))
6982 (define-public r-dosnow
6989 (uri (cran-uri "doSNOW" version))
6992 "0f07b38cl7s61vwzkyqkzzsic9g4sw9k6ndbxk3g90l4ca0d1ljc"))))
6993 (properties `((upstream-name . "doSNOW")))
6994 (build-system r-build-system)
6996 `(("r-foreach" ,r-foreach)
6997 ("r-iterators" ,r-iterators)
6998 ("r-snow" ,r-snow)))
6999 (home-page "https://cran.r-project.org/web/packages/doSNOW")
7000 (synopsis "Foreach parallel adaptor for the snow package")
7002 "This package provides a parallel backend for the @code{%dopar%} function
7003 using the @code{snow} package.")
7004 (license license:gpl2)))
7006 (define-public r-fst
7013 (uri (cran-uri "fst" version))
7016 "0vwclzxww8mw9nnpyj29bn71mrr8jjg7ka03979h9rbzw6d9bjrr"))))
7017 (properties `((upstream-name . "fst")))
7018 (build-system r-build-system)
7019 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7020 (home-page "http://www.fstpackage.org")
7021 (synopsis "Fast serialization of data frames")
7023 "The fst package for R provides a fast, easy and flexible way to
7024 serialize data frames. With access speeds of multiple GB/s, fst is
7025 specifically designed to unlock the potential of high speed solid state disks.
7026 Data frames stored in the fst format have full random access, both in column
7027 and rows. The fst format allows for random access of stored data and
7028 compression with the LZ4 and ZSTD compressors.")
7029 (license license:agpl3)))
7031 (define-public r-snowfall
7034 (version "1.84-6.1")
7037 (uri (cran-uri "snowfall" version))
7039 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
7040 (build-system r-build-system)
7042 `(("r-snow" ,r-snow)))
7043 (home-page "https://cran.r-project.org/web/packages/snowfall/")
7044 (synopsis "Easier cluster computing")
7045 (description "This package is a usability wrapper around snow for easier
7046 development of parallel R programs. This package offers e.g. extended error
7047 checks, and additional functions. All functions work in sequential mode, too,
7048 if no cluster is present or wished. The package is also designed as connector
7049 to the cluster management tool @code{sfCluster}, but can also used without
7051 (license license:gpl2+)))
7053 (define-public r-rgexf
7060 (uri (cran-uri "rgexf" version))
7063 "1vj5ha1qx0xzflchxf25ycys6clfn9y32m1717afzkvhmkwisrra"))
7066 ;; Delete minified JavaScript files
7067 (for-each delete-file
7068 '("inst/gexf-js/js/jquery-2.0.2.min.js"
7069 "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js"
7070 "inst/gexf-js/js/jquery.mousewheel.min.js"))
7072 (properties `((upstream-name . "rgexf")))
7073 (build-system r-build-system)
7075 `(#:modules ((guix build utils)
7076 (guix build r-build-system)
7080 (modify-phases %standard-phases
7081 (add-after 'unpack 'process-javascript
7082 (lambda* (#:key inputs #:allow-other-keys)
7083 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-jquery-ui"))
7084 (with-directory-excursion "inst/gexf-js/js/"
7088 `((,(assoc-ref inputs "js-jquery")
7089 "jquery-2.0.2.min.js")
7090 ("/tmp/jquery-ui-1.10.3/ui/jquery-ui.js"
7091 "jquery-ui-1.10.3.custom.min.js")
7092 (,(assoc-ref inputs "js-jquery-mousewheel")
7093 "jquery.mousewheel.min.js"))))
7094 (lambda (sources targets)
7095 (for-each (lambda (source target)
7096 (format #true "Processing ~a --> ~a~%"
7098 (invoke "esbuild" source "--minify"
7099 (string-append "--outfile=" target)))
7103 `(("r-igraph" ,r-igraph)
7104 ("r-servr" ,r-servr)
7107 `(("r-knitr" ,r-knitr)
7108 ("esbuild" ,esbuild)
7113 (uri "https://code.jquery.com/jquery-2.0.2.js")
7116 "0v818bxpw48gdk8i95qqqij80r9jcgisi2r4ac6xnxca20h0gvfj"))))
7120 (uri "https://jqueryui.com/resources/download/jquery-ui-1.10.3.zip")
7123 "00xpfy0l69nj2yan4s8k65ldsrlfsjkmyw2dwcg93dc8mv454vxx"))))
7124 ("js-jquery-mousewheel"
7127 (uri "https://raw.githubusercontent.com/jquery/jquery-mousewheel/\
7128 3.0.6/jquery.mousewheel.js")
7131 "19lk5xy2s47bx8hsa7j6bg012f8yw6d770g230bcnm559kf4nc6v"))))))
7132 (home-page "https://gvegayon.github.io/rgexf")
7133 (synopsis "Build, import and export GEXF graph files")
7135 "Create, read and write GEXF (Graph Exchange XML Format) graph
7136 files (used in Gephi and others). It allows the user to easily build/read
7137 graph files including attributes, GEXF visual attributes (such as color, size,
7138 and position), network dynamics (for both edges and nodes) and edge weighting.
7139 Users can build/handle graphs element-by-element or massively through
7140 data-frames, visualize the graph on a web browser through gexf-js (a
7141 JavaScript library) and interact with the igraph package.")
7142 (license license:expat)))
7144 (define-public r-data-tree
7146 (name "r-data-tree")
7151 (uri (cran-uri "data.tree" version))
7154 "0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
7155 (properties `((upstream-name . "data.tree")))
7156 (build-system r-build-system)
7159 ("r-stringi" ,r-stringi)))
7161 `(("r-knitr" ,r-knitr)))
7162 (home-page "https://github.com/gluc/data.tree")
7163 (synopsis "General purpose hierarchical data structure")
7165 "Create tree structures from hierarchical data, and traverse the tree in
7166 various orders. Aggregate, cumulate, print, plot, convert to and from
7167 data.frame and more. This is useful for decision trees, machine learning,
7168 finance, conversion from and to JSON, and many other applications.")
7169 (license license:gpl2+)))
7171 (define-public r-collapsibletree
7173 (name "r-collapsibletree")
7178 (uri (cran-uri "collapsibleTree" version))
7181 "0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
7184 ;; Delete minified JavaScript file
7185 (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js")
7188 `((upstream-name . "collapsibleTree")))
7189 (build-system r-build-system)
7192 (modify-phases %standard-phases
7193 (add-after 'unpack 'process-javascript
7194 (lambda* (#:key inputs #:allow-other-keys)
7195 (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/"
7196 (let ((source (assoc-ref inputs "d3.v4.js"))
7197 (target "d3.min.js"))
7198 (format #t "Processing ~a --> ~a~%"
7200 (invoke "esbuild" source "--minify"
7201 (string-append "--outfile=" target)))))))))
7203 `(("r-data-tree" ,r-data-tree)
7204 ("r-htmlwidgets" ,r-htmlwidgets)))
7206 `(("esbuild" ,esbuild)
7210 (uri "https://d3js.org/d3.v4.js")
7213 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
7214 (home-page "https://github.com/AdeelK93/collapsibleTree")
7215 (synopsis "Interactive collapsible tree diagrams using D3.js")
7217 "This is a package for interactive Reingold-Tilford tree diagrams created
7218 using D3.js, where every node can be expanded and collapsed by clicking on it.
7219 Tooltips and color gradients can be mapped to nodes using a numeric column in
7220 the source data frame.")
7221 (license license:gpl3+)))
7223 (define-public r-rappdirs
7230 (uri (cran-uri "rappdirs" version))
7233 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9"))))
7234 (build-system r-build-system)
7235 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
7236 (synopsis "Determine where to save data, caches, and logs")
7238 "This package provides an easy way to determine which directories on the
7239 user's computer should be used to save data, caches and logs. It is a port of
7240 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
7241 (license license:expat)))
7243 (define-public r-rastervis
7245 (name "r-rastervis")
7250 (uri (cran-uri "rasterVis" version))
7253 "0d12h7xqcwy1wps6yya9nzfppbnsxpmbkqmy3a8pvxpg81l632kk"))))
7254 (properties `((upstream-name . "rasterVis")))
7255 (build-system r-build-system)
7257 `(("r-hexbin" ,r-hexbin)
7258 ("r-lattice" ,r-lattice)
7259 ("r-latticeextra" ,r-latticeextra)
7260 ("r-raster" ,r-raster)
7261 ("r-rcolorbrewer" ,r-rcolorbrewer)
7263 ("r-viridislite" ,r-viridislite)
7265 (home-page "https://oscarperpinan.github.io/rastervis/")
7266 (synopsis "Visualization methods for raster data")
7268 "This package provides methods for enhanced visualization and interaction
7269 with raster data. It implements visualization methods for quantitative data
7270 and categorical data, both for univariate and multivariate rasters. It also
7271 provides methods to display spatiotemporal rasters, and vector fields.")
7272 (license license:gpl3)))
7274 (define-public r-rentrez
7281 (uri (cran-uri "rentrez" version))
7284 "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv"))))
7285 (properties `((upstream-name . "rentrez")))
7286 (build-system r-build-system)
7288 `(("r-httr" ,r-httr)
7289 ("r-jsonlite" ,r-jsonlite)
7292 `(("r-knitr" ,r-knitr)))
7293 (home-page "https://docs.ropensci.org/rentrez/")
7294 (synopsis "Entrez in R")
7296 "This package provides an R interface to the NCBI's EUtils API,
7297 allowing users to search databases like GenBank PubMed, process the results of
7298 those searches and pull data into their R sessions.")
7299 (license license:expat)))
7301 (define-public r-renv
7308 (uri (cran-uri "renv" version))
7311 "0wfq1z5glng6jrfxj25mjhp129z6468gaszr9ggks5gp8lrwszzh"))))
7312 (properties `((upstream-name . "renv")))
7313 (build-system r-build-system)
7315 `(("r-knitr" ,r-knitr)))
7316 (home-page "https://rstudio.github.io/renv")
7317 (synopsis "Project environments")
7319 "This package provides a dependency management toolkit for R. Using
7320 renv, you can create and manage project-local R libraries, save the state of
7321 these libraries to a lockfile, and later restore your library as required.
7322 Together, these tools can help make your projects more isolated, portable, and
7324 (license license:expat)))
7326 (define-public r-learnr
7333 (uri (cran-uri "learnr" version))
7336 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
7337 (build-system r-build-system)
7339 `(("r-checkmate" ,r-checkmate)
7340 ("r-ellipsis" ,r-ellipsis)
7341 ("r-evaluate" ,r-evaluate)
7342 ("r-htmltools" ,r-htmltools)
7343 ("r-htmlwidgets" ,r-htmlwidgets)
7344 ("r-jsonlite" ,r-jsonlite)
7345 ("r-knitr" ,r-knitr)
7346 ("r-markdown" ,r-markdown)
7347 ("r-rappdirs" ,r-rappdirs)
7349 ("r-rmarkdown" ,r-rmarkdown)
7350 ("r-rprojroot" ,r-rprojroot)
7351 ("r-shiny" ,r-shiny)
7352 ("r-withr" ,r-withr)))
7353 (home-page "https://rstudio.github.io/learnr/")
7354 (synopsis "Interactive tutorials for R")
7356 "This package provides tools to create interactive tutorials using R
7357 Markdown. Use a combination of narrative, figures, videos, exercises, and
7358 quizzes to create self-paced tutorials for learning about R and R packages.")
7359 (license license:asl2.0)))
7361 (define-public r-analytics
7363 (name "r-analytics")
7368 (uri (cran-uri "analytics" version))
7371 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
7372 (build-system r-build-system)
7375 ("r-cluster" ,r-cluster)
7376 ("r-fractal" ,r-fractal)
7377 ("r-lmtest" ,r-lmtest)
7380 ("r-powerplus" ,r-powerplus)
7381 ("r-robust" ,r-robust)
7382 ("r-trend" ,r-trend)
7386 (home-page "https://cran.r-project.org/web/packages/analytics/")
7387 (synopsis "Collection of data analysis tools")
7389 "This package is a collection of data analysis tools. It includes tools
7390 for regression outlier detection in a fitted linear model, stationary
7391 bootstrap using a truncated geometric distribution, a comprehensive test for
7392 weak stationarity, column means by group, weighted biplots, and a heuristic to
7393 obtain a better initial configuration in non-metric MDS.")
7394 (license license:gpl2)))
7396 (define-public r-reticulate
7398 (name "r-reticulate")
7403 (uri (cran-uri "reticulate" version))
7406 "04w5c9jfxakb4rr2qjynxgagb42khsja3y4dwgxywiplb1d8agxk"))))
7407 (build-system r-build-system)
7408 (inputs `(("python" ,python)))
7410 `(("r-rappdirs" ,r-rappdirs)
7411 ("r-jsonlite" ,r-jsonlite)
7412 ("r-matrix" ,r-matrix)
7413 ("r-rcpp" ,r-rcpp)))
7415 `(("r-knitr" ,r-knitr)))
7416 (home-page "https://github.com/rstudio/reticulate")
7417 (synopsis "R interface to Python")
7419 "This package provides an interface from R to Python modules, classes,
7420 and functions. When calling into Python, R data types are automatically
7421 converted to their equivalent Python types. When values are returned from
7422 Python to R they are converted back to R types.")
7423 (license license:asl2.0)))
7425 (define-public r-bibtex
7432 (uri (cran-uri "bibtex" version))
7435 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv"))))
7436 (build-system r-build-system)
7437 (propagated-inputs `(("r-stringr" ,r-stringr)))
7438 (home-page "https://github.com/romainfrancois/bibtex")
7439 (synopsis "Bibtex parser")
7440 (description "This package provides a utility for R to parse a bibtex
7442 (license license:gpl2+)))
7444 (define-public r-ggseqlogo
7446 (name "r-ggseqlogo")
7451 (uri (cran-uri "ggseqlogo" version))
7454 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
7455 (build-system r-build-system)
7456 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
7457 (home-page "https://github.com/omarwagih/ggseqlogo")
7458 (synopsis "ggplot2 extension for drawing genetic sequence logos")
7460 "The range of functions provided by this package makes it possible to
7461 draw highly versatile genomic sequence logos. Features include, but are not
7462 limited to, modifying colour schemes and fonts used to draw the logo,
7463 generating multiple logo plots, and aiding the visualisation with annotations.
7464 Sequence logos can easily be combined with other ggplot2 plots.")
7465 ;; Unspecified version of the LGPL.
7466 (license license:lgpl3+)))
7468 (define-public r-ggsci
7475 (uri (cran-uri "ggsci" version))
7478 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
7479 (build-system r-build-system)
7481 `(("r-ggplot2" ,r-ggplot2)
7482 ("r-scales" ,r-scales)))
7483 (home-page "https://nanx.me/ggsci/")
7484 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
7486 "This package provides a collection of ggplot2 color palettes inspired by
7487 plots in scientific journals, data visualization libraries, science fiction
7488 movies, and TV shows.")
7489 (license license:gpl3)))
7491 (define-public r-ggsignif
7498 (uri (cran-uri "ggsignif" version))
7501 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
7502 (build-system r-build-system)
7504 `(("r-knitr" ,r-knitr)))
7506 `(("r-ggplot2" ,r-ggplot2)))
7507 (home-page "https://github.com/const-ae/ggsignif")
7508 (synopsis "Significance brackets for ggplot2")
7510 "Enrich your ggplots with group-wise comparisons. This package provides
7511 an easy way to indicate if two groups are significantly different. Commonly
7512 this is shown by a bracket on top connecting the groups of interest which
7513 itself is annotated with the level of significance. The package provides a
7514 single layer that takes the groups for comparison and the test as arguments
7515 and adds the annotation to the plot.")
7516 (license license:gpl3)))
7518 (define-public r-rstatix
7525 (uri (cran-uri "rstatix" version))
7528 "0nwwvxwr4z3j4n9z8cnvwghppc836g47n0ia98chk272qwh8xcpb"))))
7529 (properties `((upstream-name . "rstatix")))
7530 (build-system r-build-system)
7532 `(("r-broom" ,r-broom)
7534 ("r-corrplot" ,r-corrplot)
7535 ("r-dplyr" ,r-dplyr)
7536 ("r-generics" ,r-generics)
7537 ("r-magrittr" ,r-magrittr)
7538 ("r-purrr" ,r-purrr)
7539 ("r-rlang" ,r-rlang)
7540 ("r-tibble" ,r-tibble)
7541 ("r-tidyr" ,r-tidyr)
7542 ("r-tidyselect" ,r-tidyselect)))
7543 (home-page "https://rpkgs.datanovia.com/rstatix/")
7544 (synopsis "Pipe-friendly framework for basic statistical tests")
7546 "This package provides a simple and intuitive pipe-friendly framework,
7547 coherent with the @code{tidyverse} design philosophy, for performing basic
7548 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
7549 correlation analyses. The output of each test is automatically transformed
7550 into a tidy data frame to facilitate visualization. Additional functions are
7551 available for reshaping, reordering, manipulating and visualizing correlation
7553 (license license:gpl2)))
7555 (define-public r-ggpubr
7562 (uri (cran-uri "ggpubr" version))
7565 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
7566 (build-system r-build-system)
7568 `(("r-cowplot" ,r-cowplot)
7569 ("r-dplyr" ,r-dplyr)
7570 ("r-ggplot2" ,r-ggplot2)
7571 ("r-ggrepel" ,r-ggrepel)
7572 ("r-ggsci" ,r-ggsci)
7573 ("r-ggsignif" ,r-ggsignif)
7575 ("r-gridextra" ,r-gridextra)
7576 ("r-magrittr" ,r-magrittr)
7577 ("r-polynom" ,r-polynom)
7578 ("r-purrr" ,r-purrr)
7579 ("r-rlang" ,r-rlang)
7580 ("r-scales" ,r-scales)
7581 ("r-rstatix" ,r-rstatix)
7582 ("r-tibble" ,r-tibble)
7583 ("r-tidyr" ,r-tidyr)))
7584 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
7585 (synopsis "ggplot2-based publication-ready plots")
7587 "The ggplot2 package is an excellent and flexible package for elegant
7588 data visualization in R. However the default generated plots require some
7589 formatting before we can send them for publication. The ggpubr package
7590 provides some easy-to-use functions for creating and customizing ggplot2-based
7591 publication-ready plots.")
7592 (license license:gpl2)))
7594 (define-public r-ellipse
7601 (uri (cran-uri "ellipse" version))
7604 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
7605 (build-system r-build-system)
7606 (home-page "https://cran.r-project.org/web/packages/ellipse/")
7607 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
7609 "This package contains various routines for drawing ellipses and
7610 ellipse-like confidence regions, implementing the plots described in Murdoch
7611 and Chow (1996), A graphical display of large correlation matrices, The
7612 American Statistician 50, 178-180. There are also routines implementing the
7613 profile plots described in Bates and Watts (1988), Nonlinear Regression
7614 Analysis and its Applications.")
7615 (license license:gpl2+)))
7617 (define-public r-flashclust
7619 (name "r-flashclust")
7624 (uri (cran-uri "flashClust" version))
7627 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
7628 (properties `((upstream-name . "flashClust")))
7629 (build-system r-build-system)
7630 (native-inputs `(("gfortran" ,gfortran)))
7631 (home-page "https://cran.r-project.org/web/packages/flashClust/")
7632 (synopsis "Implementation of optimal hierarchical clustering")
7634 "This package provides a fast implementation of hierarchical
7636 (license license:gpl2+)))
7638 (define-public r-factominer
7640 (name "r-factominer")
7645 (uri (cran-uri "FactoMineR" version))
7648 "0lg8n9fxxk46nchnj4pbpqqf4swxfsq7r9jzr36dmd36kb7avqxr"))))
7649 (properties `((upstream-name . "FactoMineR")))
7650 (build-system r-build-system)
7653 ("r-cluster" ,r-cluster)
7655 ("r-ellipse" ,r-ellipse)
7656 ("r-flashclust" ,r-flashclust)
7657 ("r-ggplot2" ,r-ggplot2)
7658 ("r-ggrepel" ,r-ggrepel)
7659 ("r-lattice" ,r-lattice)
7660 ("r-leaps" ,r-leaps)
7662 ("r-scatterplot3d" ,r-scatterplot3d)))
7664 `(("r-knitr" ,r-knitr)))
7665 (home-page "http://factominer.free.fr")
7666 (synopsis "Multivariate exploratory data analysis and data mining")
7668 "This package provides exploratory data analysis methods to summarize,
7669 visualize and describe datasets. The main principal component methods are
7670 available, those with the largest potential in terms of applications:
7671 principal component analysis (PCA) when variables are quantitative,
7672 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
7673 variables are categorical, Multiple Factor Analysis when variables are
7674 structured in groups, etc. and hierarchical cluster analysis.")
7675 (license license:gpl2+)))
7677 (define-public r-factoextra
7679 (name "r-factoextra")
7684 (uri (cran-uri "factoextra" version))
7687 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
7688 (build-system r-build-system)
7690 `(("r-abind" ,r-abind)
7691 ("r-cluster" ,r-cluster)
7692 ("r-dendextend" ,r-dendextend)
7693 ("r-factominer" ,r-factominer)
7694 ("r-ggplot2" ,r-ggplot2)
7695 ("r-ggpubr" ,r-ggpubr)
7696 ("r-ggrepel" ,r-ggrepel)
7697 ("r-reshape2" ,r-reshape2)
7698 ("r-tidyr" ,r-tidyr)))
7699 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
7700 (synopsis "Extract and visualize the results of multivariate data analyses")
7702 "This package provides some easy-to-use functions to extract and
7703 visualize the output of multivariate data analyses, including
7704 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
7705 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
7706 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
7707 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
7708 packages. It contains also functions for simplifying some clustering analysis
7709 steps and provides ggplot2-based elegant data visualization.")
7710 (license license:gpl2)))
7712 (define-public r-fansi
7719 (uri (cran-uri "fansi" version))
7722 "0i7wmaflkjzdbggqv31wnsj3m9imvc6db429vyjk64xrz1ng1vd2"))))
7723 (build-system r-build-system)
7725 `(("r-knitr" ,r-knitr))) ; for vignettes
7726 (home-page "https://github.com/brodieG/fansi")
7727 (synopsis "ANSI control sequence aware string functions")
7729 "This package provides counterparts to R string manipulation functions
7730 that account for the effects of ANSI text formatting control sequences.")
7731 (license license:gpl2+)))
7733 (define-public r-nbclust
7740 (uri (cran-uri "NbClust" version))
7743 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
7744 (properties `((upstream-name . "NbClust")))
7745 (build-system r-build-system)
7746 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
7747 (synopsis "Determine the best number of clusters in a data set")
7749 "NbClust provides 30 indexes for determining the optimal number of
7750 clusters in a data set and offers the best clustering scheme from different
7751 results to the user.")
7752 (license license:gpl2)))
7754 (define-public r-hdf5r
7761 (uri (cran-uri "hdf5r" version))
7764 "0i8m4yjxggrs05slq2afvz2ckl1yc9wq7gd1s7dq2gjn46zkry50"))))
7765 (build-system r-build-system)
7770 `(("r-bit64" ,r-bit64)
7773 `(("r-knitr" ,r-knitr)))
7774 (home-page "https://hhoeflin.github.io/hdf5r")
7775 (synopsis "Interface to the HDF5 binary data format")
7777 "HDF5 is a data model, library and file format for storing and managing
7778 large amounts of data. This package provides a nearly feature complete,
7779 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
7780 functionality is added so that HDF5 objects behave very similar to their
7781 corresponding R counterparts.")
7782 (license license:asl2.0)))
7784 (define-public r-itertools
7786 (name "r-itertools")
7791 (uri (cran-uri "itertools" version))
7794 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
7795 (build-system r-build-system)
7797 `(("r-iterators" ,r-iterators)))
7798 (home-page "https://cran.r-project.org/web/packages/itertools/")
7799 (synopsis "Iterator tools")
7801 "This package provides various tools for creating iterators, many
7802 patterned after functions in the Python @code{itertools} module, and others
7803 patterned after functions in the snow package.")
7804 (license license:gpl2)))
7806 (define-public r-polynom
7813 (uri (cran-uri "polynom" version))
7816 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
7817 (build-system r-build-system)
7818 (home-page "https://cran.r-project.org/web/packages/polynom/")
7819 (synopsis "Functions for univariate polynomial manipulations")
7821 "This package provides a collection of functions to implement a class for
7822 univariate polynomial manipulations.")
7823 (license license:gpl2)))
7825 (define-public r-gbrd
7832 (uri (cran-uri "gbRd" version))
7835 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
7836 (properties `((upstream-name . "gbRd")))
7837 (build-system r-build-system)
7838 (home-page "https://cran.r-project.org/web/packages/gbRd/")
7839 (synopsis "Utilities for processing Rd objects and files")
7841 "This package provides utilities for processing Rd objects and files.
7842 Extract argument descriptions and other parts of the help pages of
7844 (license license:gpl2+)))
7846 (define-public r-rjags
7853 (uri (cran-uri "rjags" version))
7856 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
7857 (build-system r-build-system)
7859 `(("r-coda" ,r-coda)))
7863 `(("pkg-config" ,pkg-config)))
7864 (home-page "http://mcmc-jags.sourceforge.net")
7865 (synopsis "Bayesian graphical models using MCMC")
7867 "This package provides an R interface to the JAGS MCMC library. JAGS is
7868 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
7869 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
7870 (license license:gpl2)))
7872 (define-public r-rbibutils
7874 (name "r-rbibutils")
7879 (uri (cran-uri "rbibutils" version))
7882 "1vfg2188i4dyhrmvnwpsh2la8qkd4wkryz2fpj4cppi1wfz3ml83"))))
7883 (properties `((upstream-name . "rbibutils")))
7884 (build-system r-build-system)
7885 (home-page "https://geobosh.github.io/rbibutils/")
7886 (synopsis "Convert between bibliography formats")
7888 "This package converts between a number of bibliography formats,
7889 including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils
7890 utilities and supports all bibliography formats and character encodings
7891 implemented in bibutils.")
7892 (license license:gpl2)))
7894 (define-public r-rdpack
7901 (uri (cran-uri "Rdpack" version))
7904 "1kmz0kq2z1xl55w22paz98x9jpss06abvicmkslv4zq77kz99q16"))))
7905 (properties `((upstream-name . "Rdpack")))
7906 (build-system r-build-system)
7908 `(("r-rbibutils" ,r-rbibutils)
7909 ("r-gbrd" ,r-gbrd)))
7910 (home-page "https://github.com/GeoBosh/Rdpack")
7911 (synopsis "Update and manipulate Rd documentation objects")
7913 "This package provides functions for manipulation of R documentation
7914 objects, including functions @code{reprompt()} and @code{ereprompt()} for
7915 updating Rd documentation for functions, methods and classes; it also includes
7916 Rd macros for citations and import of references from bibtex files for use in
7917 Rd files and roxygen2 comments, as well as many functions for manipulation of
7918 references and Rd files.")
7919 (license license:gpl2+)))
7921 (define-public r-officer
7928 (uri (cran-uri "officer" version))
7931 "1ls5kp70jfxrzxxb3xrg8sn2fyk6qd7rmx23n5jxi7z7850avjrj"))))
7932 (build-system r-build-system)
7939 `(("r-knitr" ,r-knitr)))
7940 (home-page "https://davidgohel.github.io/officer")
7941 (synopsis "Manipulation of Word and PowerPoint documents")
7943 "This package provides tools to access and manipulate Word and PowerPoint
7944 documents from R. The package focuses on tabular and graphical reporting from
7945 R; it also provides two functions that let users get document content into
7946 data objects. A set of functions lets add and remove images, tables and
7947 paragraphs of text in new or existing documents. When working with PowerPoint
7948 presentations, slides can be added or removed; shapes inside slides can also
7949 be added or removed. When working with Word documents, a cursor can be used
7950 to help insert or delete content at a specific location in the document.")
7951 (license license:gpl3)))
7953 (define-public r-profilemodel
7955 (name "r-profilemodel")
7960 (uri (cran-uri "profileModel" version))
7963 "01m5nb8cmq0aq555pxk2a99182si65hhmn68yn9nal2j3zl2bp4i"))))
7964 (properties `((upstream-name . "profileModel")))
7965 (build-system r-build-system)
7966 (home-page "https://github.com/ikosmidis/profileModel")
7967 (synopsis "Profiling inference functions for various model classes")
7969 "This package provides tools that can be used to calculate, evaluate,
7970 plot and use for inference the profiles of *arbitrary* inference functions for
7971 arbitrary @code{glm}-like fitted models with linear predictors. More information
7972 on the methods that are implemented can be found in Kosmidis (2008)
7973 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
7974 (license license:gpl2+)))
7976 (define-public r-brglm
7983 (uri (cran-uri "brglm" version))
7986 "1v68ma1agwhxar76mfvdfkcnd5h4gmxiz8j491rhdsckg271j7sa"))))
7987 (properties `((upstream-name . "brglm")))
7988 (build-system r-build-system)
7990 `(("r-profilemodel" ,r-profilemodel)))
7991 (home-page "https://github.com/ikosmidis/brglm")
7992 (synopsis "Bias reduction in binomial-response generalized linear models")
7994 "Fit generalized linear models with binomial responses using either an
7995 adjusted-score approach to bias reduction or maximum penalized likelihood
7996 where penalization is by Jeffreys invariant prior. These procedures return
7997 estimates with improved frequentist properties (bias, mean squared error) that
7998 are always finite even in cases where the maximum likelihood estimates are
7999 infinite (data separation). Fitting takes place by fitting generalized linear
8000 models on iteratively updated pseudo-data. The interface is essentially the
8001 same as @code{glm}. More flexibility is provided by the fact that custom
8002 pseudo-data representations can be specified and used for model fitting.
8003 Functions are provided for the construction of confidence intervals for the
8004 reduced-bias estimates.")
8005 (license license:gpl2+)))
8007 (define-public r-entropy
8014 (uri (cran-uri "entropy" version))
8017 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
8018 (properties `((upstream-name . "entropy")))
8019 (build-system r-build-system)
8020 (home-page "https://www.strimmerlab.org/software/entropy/")
8021 (synopsis "Estimation of entropy, mutual information and related quantities")
8023 "This package implements various estimators of entropy, such as the
8024 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
8025 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
8026 estimator. It also offers an R interface to the NSB estimator. Furthermore,
8027 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
8028 mutual information, and chi-squared statistic of independence. In addition
8029 there are functions for discretizing continuous random variables.")
8030 (license license:gpl3+)))
8032 (define-public r-abn
8039 (uri (cran-uri "abn" version))
8042 "17vdrqm6qp5aijg00ah2imj3pqr6cl5r43hgg8dijbrbhznarci6"))))
8043 (build-system r-build-system)
8047 `(("r-lme4" ,r-lme4)
8050 ("r-rcpparmadillo" ,r-rcpparmadillo)
8051 ("r-rjags" ,r-rjags)))
8052 (home-page "https://r-bayesian-networks.org/")
8053 (synopsis "Modelling multivariate data with additive bayesian networks")
8055 "Bayesian network analysis is a form of probabilistic graphical models
8056 which derives from empirical data a directed acyclic graph, DAG, describing
8057 the dependency structure between random variables. An additive Bayesian
8058 network model consists of a form of a DAG where each node comprises a
8059 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
8060 equivalent to Bayesian multivariate regression using graphical modelling, they
8061 generalises the usual multivariable regression, GLM, to multiple dependent
8062 variables. This package provides routines to help determine optimal Bayesian
8063 network models for a given data set, where these models are used to identify
8064 statistical dependencies in messy, complex data.")
8065 (license license:gpl2+)))
8067 (define-public r-acd
8074 (uri (cran-uri "ACD" version))
8077 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
8078 (properties `((upstream-name . "ACD")))
8079 (build-system r-build-system)
8080 (home-page "https://cran.r-project.org/web/packages/ACD/")
8081 (synopsis "Categorical data analysis with complete or missing responses")
8083 "This package provides tools for categorical data analysis with complete
8084 or missing responses.")
8085 (license license:gpl2+)))
8087 (define-public r-acdm
8094 (uri (cran-uri "ACDm" version))
8097 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
8098 (properties `((upstream-name . "ACDm")))
8099 (build-system r-build-system)
8101 `(("r-dplyr" ,r-dplyr)
8102 ("r-ggplot2" ,r-ggplot2)
8104 ("r-rsolnp" ,r-rsolnp)
8106 (home-page "https://cran.r-project.org/web/packages/ACDm/")
8107 (synopsis "Tools for Autoregressive Conditional Duration Models")
8109 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
8110 and Russell, 1998) models. It creates trade, price or volume durations from
8111 transactions (tic) data, performs diurnal adjustments, fits various ACD models
8113 (license license:gpl2+)))
8115 (define-public r-overlap
8122 (uri (cran-uri "overlap" version))
8125 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
8126 (build-system r-build-system)
8127 (home-page "https://cran.r-project.org/web/packages/overlap/")
8128 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
8130 "This package provides functions to fit kernel density functions to data
8131 on temporal activity patterns of animals; estimate coefficients of overlapping
8132 of densities for two species; and calculate bootstrap estimates of confidence
8134 (license license:gpl3+)))
8136 (define-public r-snakecase
8138 (name "r-snakecase")
8143 (uri (cran-uri "snakecase" version))
8146 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
8147 (build-system r-build-system)
8149 `(("r-stringi" ,r-stringi)
8150 ("r-stringr" ,r-stringr)))
8151 (home-page "https://github.com/Tazinho/snakecase")
8152 (synopsis "Convert strings into any case")
8154 "This package provides a consistent, flexible and easy to use tool to
8155 parse and convert strings into cases like snake or camel among others.")
8156 (license license:gpl3)))
8158 (define-public r-prediction
8160 (name "r-prediction")
8165 (uri (cran-uri "prediction" version))
8168 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
8169 (build-system r-build-system)
8171 `(("r-data-table" ,r-data-table)))
8172 (home-page "https://github.com/leeper/prediction")
8173 (synopsis "Tidy, type-safe prediction methods")
8175 "This package provides the @code{prediction()} function, a type-safe
8176 alternative to @code{predict()} that always returns a data frame. The package
8177 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
8178 from the @code{stats} package, as well as numerous other model classes from
8179 other add-on packages.")
8180 (license license:expat)))
8182 (define-public r-insight
8189 (uri (cran-uri "insight" version))
8192 "0gkvcw9d729ql1gfrpxzgrag4xafd0hchrdww215qz11ma1rzy7s"))))
8193 (build-system r-build-system)
8195 `(("r-knitr" ,r-knitr)))
8196 (home-page "https://easystats.github.io/insight/")
8197 (synopsis "Easy access to model information for various model objects")
8199 "This package provides a tool to provide an easy, intuitive and
8200 consistent access to information contained in various R models, like model
8201 formulas, model terms, information about random effects, data that was used to
8202 fit the model or data from response variables. The package mainly revolves
8203 around two types of functions: Functions that find (the names of) information,
8204 starting with @code{find_}, and functions that get the underlying data,
8205 starting with @code{get_}. The package has a consistent syntax and works with
8206 many different model objects, where otherwise functions to access these
8207 information are missing.")
8208 (license license:gpl3)))
8210 (define-public r-sjlabelled
8212 (name "r-sjlabelled")
8217 (uri (cran-uri "sjlabelled" version))
8220 "0d3fsjd2gxchv8mlx9l5pf8xvkmx4pgvizam83f3qss07bmvpzwg"))))
8221 (build-system r-build-system)
8223 `(("r-insight" ,r-insight)))
8225 `(("r-knitr" ,r-knitr)))
8226 (home-page "https://github.com/strengejacke/sjlabelled")
8227 (synopsis "Labelled data utility functions")
8229 "This package provides a collection of functions dealing with labelled
8230 data, like reading and writing data between R and other statistical software
8231 packages. This includes easy ways to get, set or change value and variable
8232 label attributes, to convert labelled vectors into factors or numeric (and
8233 vice versa), or to deal with multiple declared missing values.")
8234 (license license:gpl3)))
8236 (define-public r-sjmisc
8243 (uri (cran-uri "sjmisc" version))
8246 "1nfrkv5jfnwb85blpv7yk7xac1myzi2c30bqcf7xicniknkjwycr"))))
8247 (build-system r-build-system)
8249 `(("r-dplyr" ,r-dplyr)
8250 ("r-insight" ,r-insight)
8251 ("r-magrittr" ,r-magrittr)
8252 ("r-purrr" ,r-purrr)
8253 ("r-rlang" ,r-rlang)
8254 ("r-sjlabelled" ,r-sjlabelled)
8255 ("r-tidyselect" ,r-tidyselect)))
8257 `(("r-knitr" ,r-knitr)))
8258 (home-page "https://github.com/strengejacke/sjmisc")
8259 (synopsis "Data and variable transformation functions")
8261 "This package is a collection of miscellaneous utility functions,
8262 supporting data transformation tasks like recoding, dichotomizing or grouping
8263 variables, setting and replacing missing values. The data transformation
8264 functions also support labelled data, and all integrate seamlessly into a
8265 tidyverse workflow.")
8266 (license license:gpl3)))
8268 (define-public r-nortest
8275 (uri (cran-uri "nortest" version))
8278 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
8279 (build-system r-build-system)
8280 (home-page "https://cran.r-project.org/web/packages/nortest/")
8281 (synopsis "Tests for normality")
8283 "This package provides five omnibus tests for testing the composite
8284 hypothesis of normality.")
8285 (license license:gpl2+)))
8287 (define-public r-moonbook
8294 (uri (cran-uri "moonBook" version))
8297 "0z78pzc8sr2g19xjdd9cmai4iqyifmh79gj8x40ddww6a27dalry"))))
8298 (properties `((upstream-name . "moonBook")))
8299 (build-system r-build-system)
8301 `(("r-magrittr" ,r-magrittr)
8302 ("r-nortest" ,r-nortest)
8303 ("r-sjmisc" ,r-sjmisc)
8304 ("r-stringr" ,r-stringr)
8305 ("r-survival" ,r-survival)
8306 ("r-ztable" ,r-ztable)))
8308 `(("r-knitr" ,r-knitr)))
8309 (home-page "https://github.com/cardiomoon/moonBook")
8310 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
8312 "This package provides several analysis-related functions for the book
8313 entitled \"R statistics and graph for medical articles\" (written in Korean),
8314 version 1, by Keon-Woong Moon with Korean demographic data with several plot
8316 (license license:gpl2)))
8318 (define-public r-flextable
8320 (name "r-flextable")
8325 (uri (cran-uri "flextable" version))
8328 "0as80m19lvajc0vzllq9d9p63zglsm2ph7vdfg3jgk90jp8j76dg"))))
8329 (build-system r-build-system)
8331 `(("r-base64enc" ,r-base64enc)
8332 ("r-data-table" ,r-data-table)
8333 ("r-gdtools" ,r-gdtools)
8334 ("r-htmltools" ,r-htmltools)
8335 ("r-knitr" ,r-knitr)
8336 ("r-officer" ,r-officer)
8337 ("r-rlang" ,r-rlang)
8338 ("r-rmarkdown" ,r-rmarkdown)
8340 ("r-xml2" ,r-xml2)))
8342 `(("r-knitr" ,r-knitr)))
8343 (home-page "https://davidgohel.github.io/flextable")
8344 (synopsis "Functions for tabular reporting")
8346 "This package provides tools to create pretty tables for HTML documents
8347 and other formats. Functions are provided to let users create tables, modify
8348 and format their content. It extends the @code{officer} package and can be
8349 used within R markdown documents when rendering to HTML and to Word
8351 (license license:gpl3)))
8353 (define-public r-writexl
8360 (uri (cran-uri "writexl" version))
8363 "1njdhvh8605wd2j8glrbxfyc36p2n88prpq080jn44s9lgfmbgsb"))))
8364 (build-system r-build-system)
8365 (inputs `(("zlib" ,zlib)))
8366 (home-page "https://github.com/ropensci/writexl")
8367 (synopsis "Export data frames to xlsx format")
8369 "This package provides a data frame to xlsx exporter based on
8371 (license license:bsd-2)))
8373 (define-public r-biasedurn
8375 (name "r-biasedurn")
8380 (uri (cran-uri "BiasedUrn" version))
8383 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
8384 (properties `((upstream-name . "BiasedUrn")))
8385 (build-system r-build-system)
8386 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
8387 (synopsis "Biased Urn model distributions")
8389 "This package provides statistical models of biased sampling in the form
8390 of univariate and multivariate noncentral hypergeometric distributions,
8391 including Wallenius' noncentral hypergeometric distribution and Fisher's
8392 noncentral hypergeometric distribution (also called extended hypergeometric
8394 (license license:gpl3)))
8396 (define-public r-goplot
8403 (uri (cran-uri "GOplot" version))
8406 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
8407 (properties `((upstream-name . "GOplot")))
8408 (build-system r-build-system)
8410 `(("r-ggdendro" ,r-ggdendro)
8411 ("r-ggplot2" ,r-ggplot2)
8412 ("r-gridextra" ,r-gridextra)
8413 ("r-rcolorbrewer" ,r-rcolorbrewer)))
8414 (home-page "https://github.com/wencke/wencke.github.io")
8415 (synopsis "Visualization of functional analysis data")
8417 "This package provides an implementation of multilayered visualizations
8418 for enhanced graphical representation of functional analysis data. It
8419 combines and integrates omics data derived from expression and functional
8420 annotation enrichment analyses. Its plotting functions have been developed
8421 with an hierarchical structure in mind: starting from a general overview to
8422 identify the most enriched categories (modified bar plot, bubble plot) to a
8423 more detailed one displaying different types of relevant information for the
8424 molecules in a given set of categories (circle plot, chord plot, cluster plot,
8425 Venn diagram, heatmap).")
8426 (license license:gpl2)))
8428 (define-public r-getopt
8435 (uri (cran-uri "getopt" version))
8438 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
8439 (build-system r-build-system)
8440 (home-page "https://github.com/trevorld/getopt")
8441 (synopsis "Command-line option processor for R")
8443 "This package is designed to be used with Rscript to write shebang
8444 scripts that accept short and long options. Many users will prefer to
8445 use the packages @code{optparse} or @code{argparse} which add extra
8446 features like automatically generated help options and usage texts,
8447 support for default values, positional argument support, etc.")
8448 (license license:gpl2+)))
8450 (define-public r-findpython
8452 (name "r-findpython")
8457 (uri (cran-uri "findpython" version))
8460 "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar"))))
8461 (build-system r-build-system)
8462 (home-page "https://github.com/trevorld/findpython")
8463 (synopsis "Functions to find an acceptable Python binary")
8465 "This package was designed to find an acceptable Python binary that
8466 matches version and feature constraints.")
8467 (license license:expat)))
8469 ;; This in not the same as "r-argparser"
8470 (define-public r-argparse
8477 (uri (cran-uri "argparse" version))
8480 "1c2r417m1dxk1jhcggv3g4zax5a59k9rqs9jcs6xy2pa2333jqfj"))))
8481 (build-system r-build-system)
8482 (inputs `(("python" ,python)))
8484 `(("r-findpython" ,r-findpython)
8485 ("r-jsonlite" ,r-jsonlite)
8488 `(("r-knitr" ,r-knitr)))
8489 (home-page "https://github.com/trevorld/argparse")
8490 (synopsis "Command line optional and positional argument parser")
8492 "This package provides a command line parser to be used with Rscript to
8493 write shebang scripts that gracefully accept positional and optional arguments
8494 and automatically generate usage notices.")
8495 (license license:gpl2+)))
8497 (define-public r-hash
8504 (uri (cran-uri "hash" version))
8507 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
8508 (build-system r-build-system)
8509 (home-page "https://cran.r-project.org/web/packages/hash/")
8510 (synopsis "Implementation of hash/associated arrays/dictionaries")
8512 "This package implements a data structure similar to hashes in Perl and
8513 dictionaries in Python but with a purposefully R flavor. For objects of
8514 appreciable size, access using hashes outperforms native named lists and
8516 (license license:gpl2+)))
8518 (define-public r-orddom
8525 (uri (cran-uri "orddom" version))
8528 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
8529 (build-system r-build-system)
8530 (propagated-inputs `(("r-psych" ,r-psych)))
8531 (home-page "https://cran.r-project.org/web/packages/orddom/")
8532 (synopsis "Ordinal dominance statistics")
8534 "This package provides tools to compute ordinal, statistics and effect
8535 sizes as an alternative to mean comparison: Cliff's delta or success rate
8536 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
8537 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
8538 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
8539 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
8540 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
8541 Group (Non-)Overlap considerations.")
8542 (license license:gpl2)))
8544 (define-public r-deriv
8551 (uri (cran-uri "Deriv" version))
8554 "1j9sh1w9lsnnhlh59g4ghykyfx46rxh380s8imvm7pzna7rw7c64"))))
8555 (properties `((upstream-name . "Deriv")))
8556 (build-system r-build-system)
8557 (home-page "https://cran.r-project.org/web/packages/Deriv")
8558 (synopsis "Symbolic differentiation")
8560 "This package provides an R-based solution for symbolic differentiation.
8561 It admits user-defined functions as well as function substitution in arguments
8562 of functions to be differentiated. Some symbolic simplification is part of
8564 (license license:gpl3+)))
8566 (define-public r-doby
8573 (uri (cran-uri "doBy" version))
8576 "0r97kwsj6g87m7shgnjc5c9y71jkhiq4xd9q0s2bxl0vl92qqwvg"))))
8577 (properties `((upstream-name . "doBy")))
8578 (build-system r-build-system)
8580 `(("r-broom" ,r-broom)
8581 ("r-deriv" ,r-deriv)
8582 ("r-dplyr" ,r-dplyr)
8583 ("r-ggplot2" ,r-ggplot2)
8584 ("r-magrittr" ,r-magrittr)
8586 ("r-matrix" ,r-matrix)
8587 ("r-pbkrtest" ,r-pbkrtest)
8588 ("r-tibble" ,r-tibble)))
8590 `(("r-knitr" ,r-knitr)))
8591 (home-page "https://people.math.aau.dk/~sorenh/software/doBy/")
8592 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
8594 "This package contains:
8597 @item facilities for working with grouped data: @code{do}
8598 something to data stratified @code{by} some variables.
8599 @item implementations of least-squares means, general linear contrasts, and
8600 @item miscellaneous other utilities.
8602 (license license:gpl2+)))
8604 (define-public r-refgenome
8606 (name "r-refgenome")
8611 (uri (cran-uri "refGenome" version))
8614 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
8615 (properties `((upstream-name . "refGenome")))
8616 (build-system r-build-system)
8620 ("r-rsqlite" ,r-rsqlite)))
8621 (home-page "https://cran.r-project.org/web/packages/refGenome/")
8623 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
8625 "This package contains functionality for importing and managing of
8626 downloaded genome annotation data from the Ensembl genome browser (European
8627 Bioinformatics Institute) and from the UCSC genome browser (University of
8628 California, Santa Cruz) and annotation routines for genomic positions and
8629 splice site positions.")
8630 (license license:gpl2)))
8632 (define-public r-basix
8639 (uri (cran-uri "BASIX" version))
8642 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
8643 (properties `((upstream-name . "BASIX")))
8644 (build-system r-build-system)
8645 (home-page "https://cran.r-project.org/web/packages/BASIX/")
8646 (synopsis "Efficient C/C++ toolset for R")
8648 "BASIX provides some efficient C/C++ implementations of native R
8649 procedures to speed up calculations in R.")
8650 (license license:gpl2)))
8652 (define-public r-blockfest
8654 (name "r-blockfest")
8659 (uri (cran-uri "BlockFeST" version))
8662 "12cbrmgqszlj729zrn9d1d7drbr0iay43knnmrzcxs6v7lfszsx5"))))
8663 (properties `((upstream-name . "BlockFeST")))
8664 (build-system r-build-system)
8665 (propagated-inputs `(("r-basix" ,r-basix)))
8666 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
8667 (synopsis "Bayesian calculation of region-specific fixation index")
8669 "This package provides an R implementation of an extension of the
8670 BayeScan software for codominant markers, adding the option to group
8671 individual SNPs into pre-defined blocks. A typical application of this new
8672 approach is the identification of genomic regions, genes, or gene sets
8673 containing one or more SNPs that evolved under directional selection.")
8674 (license license:gpl2)))
8676 (define-public r-proc
8679 (version "1.17.0.1")
8683 (uri (cran-uri "pROC" version))
8686 "1gd6a47d6bcfd237s3g7r9rws8x2sg7zrvq5k6clpc41zdpp4712"))))
8687 (properties `((upstream-name . "pROC")))
8688 (build-system r-build-system)
8690 `(("r-plyr" ,r-plyr)
8691 ("r-rcpp" ,r-rcpp)))
8692 (home-page "https://web.expasy.org/pROC/")
8693 (synopsis "Display and analyze ROC curves")
8695 "This package provides tools for visualizing, smoothing and comparing
8696 receiver operating characteristic (ROC curves). The area under the
8697 curve (AUC) can be compared with statistical tests based on U-statistics or
8698 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
8699 (license license:gpl3+)))
8701 (define-public r-rootsolve
8703 (name "r-rootsolve")
8708 (uri (cran-uri "rootSolve" version))
8711 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
8712 (properties `((upstream-name . "rootSolve")))
8713 (build-system r-build-system)
8714 (native-inputs `(("gfortran" ,gfortran)))
8715 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
8716 (synopsis "Tools for the analysis of ordinary differential equations")
8718 "This package provides routines to find the root of nonlinear functions,
8719 and to perform steady-state and equilibrium analysis of @dfn{ordinary
8720 differential equations} (ODE). It includes routines that:
8723 @item generate gradient and jacobian matrices (full and banded),
8724 @item find roots of non-linear equations by the Newton-Raphson method,
8725 @item estimate steady-state conditions of a system of (differential) equations
8726 in full, banded or sparse form, using the Newton-Raphson method, or by
8727 dynamically running,
8728 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
8729 and 3-D partial differential equations, that have been converted to ordinary
8730 differential equations by numerical differencing (using the method-of-lines
8733 (license license:gpl2+)))
8735 (define-public r-abcanalysis
8737 (name "r-abcanalysis")
8742 (uri (cran-uri "ABCanalysis" version))
8744 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
8745 (properties `((upstream-name . "ABCanalysis")))
8746 (build-system r-build-system)
8747 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
8748 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
8749 (synopsis "Computed ABC Analysis")
8751 "Multivariate data sets often differ in several factors or derived statistical
8752 parameters, which have to be selected for a valid interpretation. Basing this
8753 selection on traditional statistical limits leads occasionally to the perception
8754 of losing information from a data set. This package provides tools to calculate
8755 these limits on the basis of the mathematical properties of the distribution of
8756 the analyzed items.")
8757 (license license:gpl3)))
8759 (define-public r-slam
8766 (uri (cran-uri "slam" version))
8768 (base32 "1ppsvkph4v1dffxgp12a4wnr9arj7pkmh4qv0and3f6nbz9k42qa"))))
8769 (build-system r-build-system)
8770 (home-page "https://cran.r-project.org/web/packages/slam/")
8771 (synopsis "Sparse lightweight arrays and matrices")
8773 "This package contains data structures and algorithms for sparse arrays and matrices,
8774 based on index arrays and simple triplet representations, respectively.")
8775 (license license:gpl2)))
8777 (define-public r-manipulatewidget
8779 (name "r-manipulatewidget")
8784 (uri (cran-uri "manipulateWidget" version))
8786 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
8788 `((upstream-name . "manipulateWidget")))
8789 (build-system r-build-system)
8791 `(("r-base64enc" ,r-base64enc)
8792 ("r-codetools" ,r-codetools)
8793 ("r-htmltools" ,r-htmltools)
8794 ("r-htmlwidgets" ,r-htmlwidgets)
8795 ("r-knitr" ,r-knitr)
8796 ("r-miniui" ,r-miniui)
8797 ("r-shiny" ,r-shiny)
8798 ("r-webshot" ,r-webshot)))
8799 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
8800 (synopsis "Add even more interactivity to interactive charts")
8802 "This package lets you create in just a few lines of R code a nice user interface to
8803 modify the data or the graphical parameters of one or multiple interactive
8804 charts. It is useful to quickly explore visually some data or for package
8805 developers to generate user interfaces easy to maintain.")
8806 (license license:gpl2+)))
8815 (uri (cran-uri "A3" version))
8817 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
8818 (properties `((upstream-name . "A3")))
8819 (build-system r-build-system)
8821 `(("r-pbapply" ,r-pbapply)
8822 ("r-xtable" ,r-xtable)))
8823 (home-page "https://cran.r-project.org/web/packages/A3/")
8824 (synopsis "Error metrics for predictive models")
8826 "This package supplies tools for tabulating and analyzing the results of predictive
8827 models. The methods employed are applicable to virtually any predictive model
8828 and make comparisons between different methodologies straightforward.")
8829 (license license:gpl2+)))
8831 (define-public r-infotheo
8838 (uri (cran-uri "infotheo" version))
8841 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
8842 (build-system r-build-system)
8843 (home-page "http://homepage.meyerp.com/software")
8844 (synopsis "Information-theoretic measures")
8846 "This package implements various measures of information theory based on
8847 several entropy estimators.")
8848 (license license:gpl3+)))
8850 (define-public r-abcoptim
8857 (uri (cran-uri "ABCoptim" version))
8859 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
8860 (properties `((upstream-name . "ABCoptim")))
8861 (build-system r-build-system)
8862 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
8863 (home-page "https://github.com/gvegayon/ABCoptim/")
8864 (synopsis "Optimization of Artificial Bee Colony algorithm")
8866 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
8867 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
8868 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
8869 algorithms, and uses only common control parameters such as colony size and
8870 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
8871 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
8872 This version is a work-in-progress and is written in R code.")
8873 (license license:expat)))
8875 (define-public r-abcp2
8882 (uri (cran-uri "ABCp2" version))
8884 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
8885 (properties `((upstream-name . "ABCp2")))
8886 (build-system r-build-system)
8887 (propagated-inputs `(("r-mass" ,r-mass)))
8888 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
8889 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
8891 "This package tests the goodness of fit of a distribution of offspring to the Normal,
8892 Poisson, and Gamma distribution and estimates the proportional paternity of the
8893 second male (P2) based on the best fit distribution.")
8894 (license license:gpl2)))
8896 (define-public r-abcrf
8903 (uri (cran-uri "abcrf" version))
8905 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
8906 (build-system r-build-system)
8908 `(("r-doparallel" ,r-doparallel)
8909 ("r-foreach" ,r-foreach)
8911 ("r-matrixstats" ,r-matrixstats)
8912 ("r-ranger" ,r-ranger)
8914 ("r-rcpparmadillo" ,r-rcpparmadillo)
8915 ("r-readr" ,r-readr)
8916 ("r-stringr" ,r-stringr)))
8917 (home-page "https://cran.r-project.org/web/packages/abcrf/")
8918 (synopsis "Approximate bayesian computation via random forests")
8920 "This package performs approximate bayesian computation (ABC) model choice and
8921 parameter inference via random forests. This machine learning tool named random
8922 forests (RF) can conduct selection among the highly complex models covered by
8924 (license license:gpl2+)))
8926 (define-public r-abctools
8933 (uri (cran-uri "abctools" version))
8935 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
8936 (build-system r-build-system)
8939 ("r-abind" ,r-abind)
8940 ("r-hmisc" ,r-hmisc)
8941 ("r-plyr" ,r-plyr)))
8942 (home-page "https://github.com/dennisprangle/abctools/")
8943 (synopsis "Tools for ABC analyses")
8945 "This @code{r-abctools} package provides tools for approximate Bayesian computation
8946 including summary statistic selection and assessing coverage. This includes
8947 recent dimension reduction algorithms to tune the choice of summary statistics,
8948 and coverage methods to tune the choice of threshold.")
8949 (license license:gpl2+)))
8951 (define-public r-ggstance
8958 (uri (cran-uri "ggstance" version))
8960 (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d"))))
8961 (build-system r-build-system)
8963 `(("r-ggplot2" ,r-ggplot2)
8965 ("r-rlang" ,r-rlang)
8966 ("r-withr" ,r-withr)))
8967 (home-page "https://cran.r-project.org/web/packages/ggstance/")
8968 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
8970 "This package is a @code{r-ggplot2} extension that provides flipped components:
8972 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
8973 @item vertical versions of @code{r-ggplot2} positions.
8975 (license license:gpl3)))
8977 (define-public r-mosaiccore
8979 (name "r-mosaiccore")
8984 (uri (cran-uri "mosaicCore" version))
8986 (base32 "1h3ixzna4xy42rdnd89jj0v9q0riy3fnkd33z6l5c0zaidzm58fz"))))
8987 (properties `((upstream-name . "mosaicCore")))
8988 (build-system r-build-system)
8990 `(("r-dplyr" ,r-dplyr)
8992 ("r-rlang" ,r-rlang)
8993 ("r-tidyr" ,r-tidyr)))
8994 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
8995 (synopsis "Common utilities for mosaic family packages")
8997 "Common utilities used in other Mosaic family packages are collected here.")
8998 (license license:gpl2+)))
9000 (define-public r-labelled
9007 (uri (cran-uri "labelled" version))
9010 "1nsb0mh0jg7gggc41b6v55nmfq07g0qn9fy55x4jws5dscs6pdmi"))))
9011 (properties `((upstream-name . "labelled")))
9012 (build-system r-build-system)
9014 `(("r-dplyr" ,r-dplyr)
9015 ("r-haven" ,r-haven)
9016 ("r-lifecycle" ,r-lifecycle)
9017 ("r-pillar" ,r-pillar)
9018 ("r-rlang" ,r-rlang)
9019 ("r-tidyr" ,r-tidyr)
9020 ("r-vctrs" ,r-vctrs)))
9022 `(("r-knitr" ,r-knitr)))
9023 (home-page "http://larmarange.github.io/labelled/")
9024 (synopsis "Manipulating labelled data")
9026 "This package provides useful functions to deal with the
9027 @code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the
9029 (license license:gpl3)))
9031 (define-public r-ggformula
9033 (name "r-ggformula")
9038 (uri (cran-uri "ggformula" version))
9040 (base32 "1ph5jd8svk8hmshi894vmmpq3zwgdmf4yn3gmdlkad68z8jynhsp"))))
9041 (build-system r-build-system)
9043 `(("r-ggforce" ,r-ggforce)
9044 ("r-ggplot2" ,r-ggplot2)
9045 ("r-ggridges" ,r-ggridges)
9046 ("r-ggstance" ,r-ggstance)
9047 ("r-labelled" ,r-labelled)
9048 ("r-magrittr" ,r-magrittr)
9049 ("r-mosaiccore" ,r-mosaiccore)
9050 ("r-rlang" ,r-rlang)
9051 ("r-scales" ,r-scales)
9052 ("r-stringr" ,r-stringr)
9053 ("r-tibble" ,r-tibble)))
9055 `(("r-knitr" ,r-knitr)))
9056 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
9057 (synopsis "Formula interface for the @code{r-ggplot2}")
9059 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
9060 gf_density(), and so on, bring the formula interface to ggplot(). This captures
9061 and extends the excellent simplicity of the lattice-graphics formula interface,
9062 while providing the intuitive capabilities of @code{r-ggplot2}.")
9063 (license license:expat)))
9065 (define-public r-mosaicdata
9067 (name "r-mosaicdata")
9072 (uri (cran-uri "mosaicData" version))
9074 (base32 "0h3f5fgzkzjfgf3ml0qa5j52921y6wy6jgggxmhs31bs8fd4srg4"))))
9075 (properties `((upstream-name . "mosaicData")))
9076 (build-system r-build-system)
9077 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
9078 (synopsis "Data sets for project Mosaic")
9080 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
9081 used to teach mathematics, statistics, computation and modeling.")
9082 (license license:gpl2+)))
9084 (define-public r-raster
9091 (uri (cran-uri "raster" version))
9094 "19g4chd0nyhnz6hc2j0v9ahjcgz64vvja4y3mrj1pfis1dwhsqn6"))))
9095 (build-system r-build-system)
9097 `(("r-rcpp" ,r-rcpp)
9099 (home-page "https://www.rspatial.org/")
9100 (synopsis "Geographic data analysis and modeling")
9102 "The package implements basic and high-level functions for reading,
9103 writing, manipulating, analyzing and modeling of gridded spatial data.
9104 Processing of very large files is supported.")
9105 (license license:gpl3+)))
9107 (define-public r-mosaic
9114 (uri (cran-uri "mosaic" version))
9116 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
9117 (build-system r-build-system)
9119 `(("r-broom" ,r-broom)
9120 ("r-dplyr" ,r-dplyr)
9121 ("r-ggdendro" ,r-ggdendro)
9122 ("r-ggformula" ,r-ggformula)
9123 ("r-ggplot2" ,r-ggplot2)
9124 ("r-ggrepel" ,r-ggrepel)
9126 ("r-gridextra" ,r-gridextra)
9127 ("r-lattice" ,r-lattice)
9128 ("r-latticeextra" ,r-latticeextra)
9129 ("r-lazyeval" ,r-lazyeval)
9131 ("r-matrix" ,r-matrix)
9132 ("r-mosaiccore" ,r-mosaiccore)
9133 ("r-mosaicdata" ,r-mosaicdata)
9134 ("r-readr" ,r-readr)
9135 ("r-tidyr" ,r-tidyr)))
9137 `(("r-knitr" ,r-knitr)))
9138 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
9139 (synopsis "Mathematics, statistics, and computation teaching utilities")
9141 "This package contain data sets and utilities from
9142 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
9143 statistics, computation and modeling. Project MOSAIC is a community of
9144 educators working to tie together aspects of quantitative work that students
9145 in science, technology, engineering and mathematics will need in their
9146 professional lives, but which are usually taught in isolation, if at all.")
9147 (license license:gpl2+)))
9149 (define-public r-abd
9156 (uri (cran-uri "abd" version))
9158 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
9159 (build-system r-build-system)
9161 `(("r-lattice" ,r-lattice)
9162 ("r-mosaic" ,r-mosaic)
9163 ("r-nlme" ,r-nlme)))
9164 (home-page "https://cran.r-project.org/web/packages/abd/")
9165 (synopsis "Analysis of biological data")
9167 "The @code{r-abd} package contains data sets and sample code for the Analysis of
9168 biological data by Michael Whitlock and Dolph Schluter.")
9169 (license license:gpl2)))
9171 (define-public r-svgui
9178 (uri (cran-uri "svGUI" version))
9180 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
9181 (properties `((upstream-name . "svGUI")))
9182 (build-system r-build-system)
9183 (home-page "https://github.com/SciViews/svGUI/")
9184 (synopsis "Functions for managing GUI clients in R")
9186 "The SciViews @code{svGUI} package eases the management of Graphical User
9187 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
9188 centralizes info about GUI elements currently used, and it dispatches GUI
9189 calls to the particular toolkits in use in function of the context.")
9190 (license license:gpl2)))
9192 (define-public r-svdialogs
9194 (name "r-svdialogs")
9199 (uri (cran-uri "svDialogs" version))
9201 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
9202 (properties `((upstream-name . "svDialogs")))
9203 (build-system r-build-system)
9206 ("zenity" ,zenity)))
9208 `(("r-rstudioapi" ,r-rstudioapi)
9209 ("r-svgui" ,r-svgui)))
9210 (home-page "https://github.com/SciViews/svDialogs/")
9211 (synopsis "Portable dialog boxes")
9213 "This package helps to construct standard dialog boxes for your GUI, including
9214 message boxes, input boxes, list, file or directory selection, and others. In
9215 case R cannot display GUI dialog boxes, a simpler command line version of these
9216 interactive elements is also provided as a fallback solution.")
9217 (license license:gpl2)))
9219 (define-public r-abe
9226 (uri (cran-uri "abe" version))
9229 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
9230 (build-system r-build-system)
9231 (home-page "https://cran.r-project.org/web/packages/abe/")
9232 (synopsis "Augmented backward elimination")
9234 "This package performs augmented backward elimination and checks the
9235 stability of the obtained model. Augmented backward elimination combines
9236 significance or information based criteria with the change in estimate to
9237 either select the optimal model for prediction purposes or to serve as a tool
9238 to obtain a practically sound, highly interpretable model.")
9239 (license license:gpl2+)))
9241 (define-public r-abf2
9248 (uri (cran-uri "abf2" version))
9250 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
9251 (build-system r-build-system)
9252 (home-page "https://cran.r-project.org/web/packages/abf2/")
9253 (synopsis "Load gap-free axon @code{r-abf2} files")
9255 "This package loads electrophysiology data from ABF2 files, as created by
9256 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
9257 mode are currently supported.")
9258 (license license:artistic2.0)))
9260 (define-public r-abhgenotyper
9262 (name "r-abhgenotyper")
9267 (uri (cran-uri "ABHgenotypeR" version))
9269 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
9270 (properties `((upstream-name . "ABHgenotypeR")))
9271 (build-system r-build-system)
9273 `(("r-ggplot2" ,r-ggplot2)
9274 ("r-reshape2" ,r-reshape2)))
9275 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
9276 (synopsis "Visualize and manipulate ABH genotypes")
9278 "The @code{r-abhgenotyper} package provides simple imputation,
9279 error-correction and plotting capacities for genotype data. The package is
9280 supposed to serve as an intermediate but independent analysis tool between the
9281 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
9282 not found in either TASSEL or @code{r-qtl} in addition to visualization of
9283 genotypes as \"graphical genotypes\".")
9284 (license license:gpl3)))
9286 (define-public r-furrr
9293 (uri (cran-uri "furrr" version))
9296 "0kfd4hw1yn2mfxzjgiz4r6yi2vsp1j0wy5hdhzd6wha7vi9h7hg5"))))
9297 (build-system r-build-system)
9299 `(("r-ellipsis" ,r-ellipsis)
9300 ("r-future" ,r-future)
9301 ("r-globals" ,r-globals)
9302 ("r-lifecycle" ,r-lifecycle)
9303 ("r-purrr" ,r-purrr)
9304 ("r-rlang" ,r-rlang)
9305 ("r-vctrs" ,r-vctrs)))
9306 (home-page "https://github.com/DavisVaughan/furrr")
9307 (synopsis "Apply mapping functions in parallel using futures")
9309 "This package provides implementations of the family of @code{map()}
9310 functions from the @code{purrr} package that can be resolved using any
9311 @code{future}-supported backend, e.g. parallel on the local machine or
9312 distributed on a compute cluster.")
9313 (license license:lgpl2.1+)))
9315 (define-public r-abjutils
9322 (uri (cran-uri "abjutils" version))
9324 (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd"))))
9325 (build-system r-build-system)
9327 `(("r-dplyr" ,r-dplyr)
9328 ("r-magrittr" ,r-magrittr)
9329 ("r-purrr" ,r-purrr)
9330 ("r-rlang" ,r-rlang)
9331 ("r-rstudioapi" ,r-rstudioapi)
9332 ("r-stringi" ,r-stringi)
9333 ("r-stringr" ,r-stringr)
9334 ("r-tidyr" ,r-tidyr)))
9335 (home-page "https://github.com/abjur/abjutils/")
9336 (synopsis "Collection of tools for jurimetrical analysis")
9338 "This package implements general purpose tools, such as functions for
9339 sampling and basic manipulation of Brazilian lawsuits identification number.
9340 It also implements functions for text cleaning, such as accentuation
9342 (license license:expat)))
9344 (define-public r-abnormality
9346 (name "r-abnormality")
9351 (uri (cran-uri "abnormality" version))
9353 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
9354 (build-system r-build-system)
9356 `(("r-mass" ,r-mass)
9357 ("r-matrix" ,r-matrix)))
9358 (home-page "https://cran.r-project.org/web/packages/abnormality/")
9359 (synopsis "Measure a subject's abnormality with respect to a reference population")
9361 "This package contains functions to implement the methodology and
9362 considerations laid out by Marks et al. in the article \"Measuring abnormality
9363 in high dimensional spaces: applications in biomechanical gait analysis\".
9364 Using high-dimensional datasets to measure a subject's overall level of
9365 abnormality as compared to a reference population is often needed in outcomes
9367 (license license:expat)))
9369 (define-public r-abodoutlier
9371 (name "r-abodoutlier")
9376 (uri (cran-uri "abodOutlier" version))
9378 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
9379 (properties `((upstream-name . "abodOutlier")))
9380 (build-system r-build-system)
9382 `(("r-cluster" ,r-cluster)))
9383 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
9384 (synopsis "Angle-based outlier detection")
9386 "This package performs angle-based outlier detection on a given data
9387 frame. It offers three methods to process data:
9389 @item full but slow implementation using all the data that has cubic
9391 @item a fully randomized method;
9392 @item a method using k-nearest neighbours.
9394 These algorithms are well suited for high dimensional data outlier
9396 (license license:expat)))
9398 (define-public r-abps
9405 (uri (cran-uri "ABPS" version))
9407 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
9408 (properties `((upstream-name . "ABPS")))
9409 (build-system r-build-system)
9410 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
9411 (home-page "https://cran.r-project.org/web/packages/ABPS/")
9412 (synopsis "Abnormal blood profile score to detect blood doping")
9414 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
9415 The ABPS is a part of the Athlete biological passport program of the World
9416 anti-doping agency, which combines several blood parameters into a single
9417 score in order to detect blood doping. The package also contains functions to
9418 calculate other scores used in anti-doping programs, such as the ratio of
9419 hemoglobin to reticulocytes (OFF-score), as well as example data.")
9420 (license license:gpl2+)))
9422 (define-public r-parmigene
9424 (name "r-parmigene")
9429 (uri (cran-uri "parmigene" version))
9432 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
9433 (build-system r-build-system)
9434 (home-page "https://cran.r-project.org/web/packages/parmigene/")
9435 (synopsis "Mutual information estimation for gene network reconstruction")
9437 "This package provides a parallel estimation of the mutual information
9438 based on entropy estimates from k-nearest neighbors distances and algorithms
9439 for the reconstruction of gene regulatory networks.")
9440 (license license:agpl3+)))
9442 (define-public r-pscl
9449 (uri (cran-uri "pscl" version))
9451 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
9452 (build-system r-build-system)
9454 `(("r-mass" ,r-mass)))
9455 (home-page "https://github.com/atahk/pscl/")
9456 (synopsis "Political science computational laboratory")
9458 "The @code{pscl} is an R package providing classes and methods for:
9460 @item Bayesian analysis of roll call data (item-response models);
9461 @item elementary Bayesian statistics;
9462 @item maximum likelihood estimation of zero-inflated and hurdle models for count
9464 @item utility functions.
9466 (license license:gpl2)))
9468 (define-public r-accelmissing
9470 (name "r-accelmissing")
9475 (uri (cran-uri "accelmissing" version))
9477 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
9478 (build-system r-build-system)
9480 `(("r-mice" ,r-mice)
9481 ("r-pscl" ,r-pscl)))
9482 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
9483 (synopsis "Missing value imputation for accelerometer data")
9485 "This package provides a statistical method to impute the missing values in
9486 accelerometer data. The methodology includes both parametric and
9487 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
9488 model. It also provides multiple functions to preprocess the accelerometer data
9489 previous to the missing data imputation. These include detecting the wearing
9490 and the non-wearing time, selecting valid days and subjects, and creating plots.")
9491 (license license:gpl2+)))
9493 (define-public r-mhsmm
9500 (uri (cran-uri "mhsmm" version))
9502 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
9503 (build-system r-build-system)
9504 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
9505 (home-page "https://github.com/jaredo/mhsmm/")
9506 (synopsis "Inference for hidden Markov and semi-Markov models")
9508 "The @code{r-mhsmm} package implements estimation and prediction methods for
9509 hidden Markov and semi-Markov models for multiple observation sequences. Such
9510 techniques are of interest when observed data is thought to be dependent on some
9511 unobserved (or hidden) state. Also, this package is suitable for equidistant
9512 time series data, with multivariate and/or missing data. Allows user defined
9513 emission distributions.")
9514 (license license:gpl2+)))
9516 (define-public r-nleqslv
9523 (uri (cran-uri "nleqslv" version))
9525 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
9526 (build-system r-build-system)
9527 (native-inputs `(("gfortran" ,gfortran)))
9528 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
9529 (synopsis "Solve systems of nonlinear equations")
9531 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
9532 Broyden or a Newton method with a choice of global strategies such as line
9533 search and trust region. There are options for using a numerical or user
9534 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
9535 singular or ill-conditioned Jacobian.")
9536 (license license:gpl2+)))
9538 (define-public r-physicalactivity
9540 (name "r-physicalactivity")
9545 (uri (cran-uri "PhysicalActivity" version))
9547 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40"))))
9549 `((upstream-name . "PhysicalActivity")))
9550 (build-system r-build-system)
9551 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
9552 (synopsis "Procesing accelerometer data for physical activity measurement")
9554 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
9555 for classification of monitor wear and nonwear time intervals in accelerometer
9556 data collected to assess physical activity. The package also contains functions
9557 for making plots of accelerometer data and obtaining the summary of various
9558 information including daily monitor wear time and the mean monitor wear time
9559 during valid days. The revised package version 0.2-1 improved the functions
9560 regarding speed, robustness and add better support for time zones and daylight
9561 saving. In addition, several functions were added:
9563 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
9564 @item the @code{markPAI} can categorize physical activity intensity level based
9565 on user-defined cut-points of accelerometer counts.
9567 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
9568 @code{queryActigraph} functions.")
9569 (license license:gpl3+)))
9571 (define-public r-acc
9578 (uri (cran-uri "acc" version))
9580 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
9581 (build-system r-build-system)
9583 `(("r-circlize" ,r-circlize)
9585 ("r-ggplot2" ,r-ggplot2)
9586 ("r-iterators" ,r-iterators)
9587 ("r-mhsmm" ,r-mhsmm)
9588 ("r-nleqslv" ,r-nleqslv)
9589 ("r-physicalactivity" ,r-physicalactivity)
9591 ("r-r-utils" ,r-r-utils)
9593 ("r-rcpparmadillo" ,r-rcpparmadillo)
9594 ("r-rsqlite" ,r-rsqlite)
9596 (home-page "https://cran.r-project.org/web/packages/acc/")
9597 (synopsis "Exploring accelerometer data")
9599 "This package processes accelerometer data from uni-axial and tri-axial devices
9600 and generates data summaries. Also, includes functions to plot, analyze, and
9601 simulate accelerometer data.")
9602 (license license:gpl2+)))
9604 (define-public r-rbenchmark
9606 (name "r-rbenchmark")
9611 (uri (cran-uri "rbenchmark" version))
9613 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
9614 (build-system r-build-system)
9615 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
9616 (synopsis "Benchmarking routine for R")
9618 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
9619 and is intended to facilitate benchmarking of arbitrary R code. The library
9620 consists of just one function, benchmark, which is a simple wrapper around
9621 system.time. Given a specification of the benchmarking process (counts of
9622 replications, evaluation environment) and an arbitrary number of expressions,
9623 benchmark evaluates each of the expressions in the specified environment,
9624 replicating the evaluation as many times as specified, and returning the results
9625 conveniently wrapped into a data frame.")
9626 (license license:gpl2+)))
9628 (define-public r-mitools
9635 (uri (cran-uri "mitools" version))
9638 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
9639 (build-system r-build-system)
9640 (propagated-inputs `(("r-dbi" ,r-dbi)))
9641 (home-page "https://cran.r-project.org/web/packages/mitools/")
9642 (synopsis "Tools for multiple imputation of missing data")
9644 "This package provides tools to perform analyses and combine results from
9645 multiple-imputation datasets.")
9646 (license license:gpl2)))
9648 (define-public r-mixsqp
9654 (uri (cran-uri "mixsqp" version))
9657 "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q"))))
9658 (properties `((upstream-name . "mixsqp")))
9659 (build-system r-build-system)
9661 `(("r-irlba" ,r-irlba)
9663 ("r-rcpparmadillo" ,r-rcpparmadillo)))
9665 `(("r-knitr" ,r-knitr)))
9666 (home-page "https://github.com/stephenslab/mixsqp")
9668 "Sequential quadratic programming for maximum-likelihood estimation")
9670 "This package provides an optimization method based on sequential
9671 quadratic programming for maximum likelihood estimation of the mixture
9672 proportions in a finite mixture model where the component densities are
9673 known. The algorithm is expected to obtain solutions that are at least
9674 as accurate as the state-of-the-art MOSEK interior-point solver, and they
9675 are expected to arrive at solutions more quickly when the number of
9676 samples is large and the number of mixture components is not too large.")
9677 (license license:expat)))
9679 (define-public r-magick
9686 (uri (cran-uri "magick" version))
9689 "1k4fqhxh2ppynl56fs044wpn4wk6gbv6lwp2x4x7j67zwcv56n36"))))
9690 (build-system r-build-system)
9692 `(("imagemagick" ,imagemagick)
9695 `(("r-curl" ,r-curl)
9696 ("r-magrittr" ,r-magrittr)
9697 ("r-rcpp" ,r-rcpp)))
9699 `(("pkg-config" ,pkg-config)
9700 ("r-knitr" ,r-knitr)))
9701 (home-page "https://github.com/ropensci/magick")
9702 (synopsis "Advanced graphics and image-processing in R")
9704 "This package provides bindings to ImageMagick, a comprehensive image
9705 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
9706 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
9707 operations are vectorized via the Magick++ STL meaning they operate either on
9708 a single frame or a series of frames for working with layers, collages, or
9709 animation. In RStudio, images are automatically previewed when printed to the
9710 console, resulting in an interactive editing environment.")
9711 (license license:expat)))
9713 (define-public r-survey
9720 (uri (cran-uri "survey" version))
9723 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
9724 (build-system r-build-system)
9726 `(("r-lattice" ,r-lattice)
9727 ("r-matrix" ,r-matrix)
9728 ("r-minqa" ,r-minqa)
9729 ("r-mitools" ,r-mitools)
9730 ("r-numderiv" ,r-numderiv)
9731 ("r-survival" ,r-survival)))
9732 (home-page "http://r-survey.r-forge.r-project.org/survey/")
9733 (synopsis "Analysis of complex survey samples")
9735 "This package provides tools for the analysis of complex survey samples.
9736 The provided features include: summary statistics, two-sample tests, rank
9737 tests, generalised linear models, cumulative link models, Cox models,
9738 loglinear models, and general maximum pseudolikelihood estimation for
9739 multistage stratified, cluster-sampled, unequally weighted survey samples;
9740 variances by Taylor series linearisation or replicate weights;
9741 post-stratification, calibration, and raking; two-phase subsampling designs;
9742 graphics; PPS sampling without replacement; principal components, and factor
9744 ;; Either version of the GPL.
9745 (license (list license:gpl2 license:gpl3))))
9747 (define-public r-gee
9754 (uri (cran-uri "gee" version))
9757 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
9758 (properties `((upstream-name . "gee")))
9759 (build-system r-build-system)
9761 `(("gfortran" ,gfortran)))
9762 (home-page "https://cran.r-project.org/web/packages/gee/")
9763 (synopsis "Generalized estimation equation solver")
9765 "This package provides a solver for generalized estimation equations.")
9766 (license license:gpl2)))
9768 (define-public r-tab
9775 (uri (cran-uri "tab" version))
9778 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
9779 (properties `((upstream-name . "tab")))
9780 (build-system r-build-system)
9782 `(("r-dplyr" ,r-dplyr)
9784 ("r-knitr" ,r-knitr)
9786 ("r-survey" ,r-survey)
9787 ("r-survival" ,r-survival)
9788 ("r-xtable" ,r-xtable)))
9789 (home-page "https://cran.r-project.org/web/packages/tab/")
9790 (synopsis "Create summary tables for statistical reports")
9792 "This package contains functions for creating various types of summary
9793 tables, e.g. comparing characteristics across levels of a categorical variable
9794 and summarizing fitted generalized linear models, generalized estimating
9795 equations, and Cox proportional hazards models. Functions are available to
9796 handle data from simple random samples as well as complex surveys.")
9797 (license license:gpl3+)))
9799 (define-public r-dvmisc
9806 (uri (cran-uri "dvmisc" version))
9808 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
9809 (build-system r-build-system)
9811 `(("r-cubature" ,r-cubature)
9812 ("r-data-table" ,r-data-table)
9813 ("r-dplyr" ,r-dplyr)
9814 ("r-ggplot2" ,r-ggplot2)
9816 ("r-mvtnorm" ,r-mvtnorm)
9817 ("r-pracma" ,r-pracma)
9818 ("r-rbenchmark" ,r-rbenchmark)
9820 ("r-survey" ,r-survey)
9822 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
9823 (synopsis "Faster computation of common statistics and miscellaneous functions")
9825 "This package implements faster versions of base R functions (e.g. mean, standard
9826 deviation, covariance, weighted mean), mostly written in C++, along with
9827 miscellaneous functions for various purposes (e.g. create the histogram with
9828 fitted probability density function or probability mass function curve, create
9829 the body mass index groups, assess the linearity assumption in logistic
9831 (license license:gpl2)))
9833 (define-public r-accelerometry
9835 (name "r-accelerometry")
9840 (uri (cran-uri "accelerometry" version))
9842 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
9843 (build-system r-build-system)
9845 `(("r-dvmisc" ,r-dvmisc)
9846 ("r-rcpp" ,r-rcpp)))
9847 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
9848 (synopsis "Functions for processing accelerometer data")
9850 "This package provides a collection of functions that perform operations on
9851 time-series accelerometer data, such as identify the non-wear time, flag minutes
9852 that are part of an activity bout, and find the maximum 10-minute average count
9853 value. The functions are generally very flexible, allowing for a variety of
9854 algorithms to be implemented.")
9855 (license license:gpl3)))
9857 (define-public r-absim
9864 (uri (cran-uri "AbSim" version))
9866 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
9867 (properties `((upstream-name . "AbSim")))
9868 (build-system r-build-system)
9871 ("r-powerlaw" ,r-powerlaw)))
9872 (home-page "https://cran.r-project.org/web/packages/AbSim/")
9873 (synopsis "Time resolved simulations of antibody repertoires")
9875 "This package provides simulation methods for the evolution of antibody repertoires.
9876 The heavy and light chain variable region of both human and C57BL/6 mice can
9877 be simulated in a time-dependent fashion. Both single lineages using one set of
9878 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
9879 with an initial V-D-J recombination event, starting the first phylogenetic tree.
9880 Upon completion, the main loop of the algorithm begins, with each iteration
9881 representing one simulated time step. Various mutation events are possible at
9882 each time step, contributing to a diverse final repertoire.")
9883 (license license:gpl2)))
9885 (define-public r-quic
9892 (uri (cran-uri "QUIC" version))
9894 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
9895 (properties `((upstream-name . "QUIC")))
9896 (build-system r-build-system)
9897 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
9898 (synopsis "Regularized sparse inverse covariance matrix estimation")
9900 "This package implements the regularized Gaussian maximum likelihood
9901 estimation of the inverse of a covariance matrix. It uses Newton's method and
9902 coordinate descent to solve the regularized inverse covariance matrix
9903 estimation problem.")
9904 ;; The project home page states that the release is under GPLv3 or later.
9905 ;; The CRAN page only says GPL-3.
9906 (license license:gpl3+)))
9908 (define-public r-abundant
9915 (uri (cran-uri "abundant" version))
9917 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
9918 (build-system r-build-system)
9920 `(("r-quic" ,r-quic)))
9921 (home-page "https://cran.r-project.org/web/packages/abundant/")
9922 (synopsis "Abundant regression and high-dimensional principal fitted components")
9924 "This package provides tools to fit and predict with the high-dimensional
9925 principal fitted components model. This model is described by Cook, Forzani,
9926 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
9927 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
9928 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
9929 (license license:gpl2+)))
9931 (define-public r-ac3net
9938 (uri (cran-uri "Ac3net" version))
9940 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
9941 (properties `((upstream-name . "Ac3net")))
9942 (build-system r-build-system)
9944 `(("r-data-table" ,r-data-table)))
9945 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
9946 (synopsis "Inferring directional conservative causal core gene networks")
9947 (description "This package infers directional Conservative causal core
9948 (gene) networks (C3NET). This is a version of the algorithm C3NET with
9949 directional network.")
9950 (license license:gpl3+)))
9952 (define-public r-aca
9959 (uri (cran-uri "ACA" version))
9961 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
9962 (properties `((upstream-name . "ACA")))
9963 (build-system r-build-system)
9964 (home-page "https://cran.r-project.org/web/packages/ACA/")
9965 (synopsis "Abrupt change-point or aberration detection in point series")
9967 "This package offers an interactive function for the detection of breakpoints in
9969 ;; Any version of the GPL
9970 (license (list license:gpl2+ license:gpl3+))))
9972 (define-public r-acceptancesampling
9974 (name "r-acceptancesampling")
9979 (uri (cran-uri "AcceptanceSampling" version))
9981 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
9983 `((upstream-name . "AcceptanceSampling")))
9984 (build-system r-build-system)
9985 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
9986 (synopsis "Creation and evaluation of acceptance sampling plans")
9988 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
9989 acceptance sampling plans. Acceptance sampling is a methodology commonly used
9990 in quality control and improvement. International standards of acceptance
9991 sampling provide sampling plans for specific circumstances. The aim of this
9992 package is to provide an easy-to-use interface to visualize single, double or
9993 multiple sampling plans. In addition, methods have been provided to enable the
9994 user to assess sampling plans against pre-specified levels of performance, as
9995 measured by the probability of acceptance for a given level of quality in the
9997 (license license:gpl3+)))
9999 (define-public r-acclma
10006 (uri (cran-uri "ACCLMA" version))
10008 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
10009 (properties `((upstream-name . "ACCLMA")))
10010 (build-system r-build-system)
10011 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
10012 (synopsis "ACC & LMA graph plotting")
10014 "This package contains a function that imports data from a @acronym{CSV,
10015 Comma-Separated Values} file, or uses manually entered data from the format (x,
10016 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
10017 Curve} vs @acronym{LOI, Line of Independence} graph and
10018 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
10019 function is @code{plotLMA} (source file, header) that takes a data set and plots the
10020 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
10021 string) was passed, a manual data entry window is opened. The header parameter
10022 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
10023 a header row or not. The dataset should contain only one independent variable
10024 (x) and one dependent variable (y) and can contain a weight for each
10026 (license license:gpl2)))
10028 (define-public r-aspi
10035 (uri (cran-uri "aspi" version))
10037 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
10038 (build-system r-build-system)
10040 "https://cran.r-project.org/web/packages/aspi/")
10042 "Analysis of symmetry of parasitic infections")
10044 "This package provides tools for the analysis and visualization of bilateral
10045 asymmetry in parasitic infections.")
10046 (license license:gpl3+)))
10048 (define-public r-sandwich
10050 (name "r-sandwich")
10055 (uri (cran-uri "sandwich" version))
10058 "0afm6snak7r11dxyl3qirqdjah6d9pdv4afmxwam1nq9bqxyb3w2"))))
10059 (build-system r-build-system)
10061 `(("r-zoo" ,r-zoo)))
10062 (home-page "https://cran.r-project.org/web/packages/sandwich/")
10063 (synopsis "Robust Covariance Matrix Estimators")
10065 "This package provides model-robust standard error estimators for
10066 cross-sectional, time series, clustered, panel, and longitudinal data.")
10067 ;; Either version of the license.
10068 (license (list license:gpl2 license:gpl3))))
10070 (define-public r-th-data
10077 (uri (cran-uri "TH.data" version))
10080 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
10081 (properties `((upstream-name . "TH.data")))
10082 (build-system r-build-system)
10084 `(("r-mass" ,r-mass)
10085 ("r-survival" ,r-survival)))
10086 (home-page "https://cran.r-project.org/web/packages/TH.data/")
10087 (synopsis "Shared data sets")
10089 "This package contains supporting data sets that are used in other
10090 packages maintained by Torsten Hothorn.")
10091 (license license:gpl3)))
10093 (define-public r-multcomp
10095 (name "r-multcomp")
10100 (uri (cran-uri "multcomp" version))
10103 "1s8qmljawalisggniy7va5l5cicsgvs0lp20c33vxlvyiy0dbb1s"))))
10104 (build-system r-build-system)
10106 `(("r-codetools" ,r-codetools)
10107 ("r-mvtnorm" ,r-mvtnorm)
10108 ("r-sandwich" ,r-sandwich)
10109 ("r-survival" ,r-survival)
10110 ("r-th-data" ,r-th-data)))
10111 (home-page "https://cran.r-project.org/web/packages/multcomp/")
10112 (synopsis "Simultaneous inference in general parametric models")
10114 "Simultaneous tests and confidence intervals for general linear
10115 hypotheses in parametric models, including linear, generalized linear, linear
10116 mixed effects, and survival models. The package includes demos reproducing
10117 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
10118 Hothorn, Westfall, 2010, CRC Press).")
10119 (license license:gpl2)))
10121 (define-public r-emmeans
10128 (uri (cran-uri "emmeans" version))
10131 "1rbh3ls23fazrwpsam5llk3kqdzz2zvsms3i4f1cgn34ky3w8361"))))
10132 (build-system r-build-system)
10134 `(("r-estimability" ,r-estimability)
10135 ("r-mvtnorm" ,r-mvtnorm)
10136 ("r-numderiv" ,r-numderiv)
10138 ("r-xtable" ,r-xtable)))
10140 `(("r-knitr" ,r-knitr)))
10141 (home-page "https://github.com/rvlenth/emmeans")
10142 (synopsis "Estimated marginal means, aka least-squares means")
10144 "This package provides tools to obtain @dfn{estimated marginal
10145 means} (EMMs) for many linear, generalized linear, and mixed models. It can
10146 be used to compute contrasts or linear functions of EMMs, trends, and
10147 comparisons of slopes.")
10148 ;; Either version of the license.
10149 (license (list license:gpl2 license:gpl3))))
10151 (define-public r-pwr
10158 (uri (cran-uri "pwr" version))
10161 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
10162 (build-system r-build-system)
10164 `(("r-knitr" ,r-knitr)))
10165 (home-page "https://github.com/heliosdrm/pwr")
10166 (synopsis "Basic functions for power analysis")
10168 "This package provides power analysis functions along the lines of
10170 (license license:gpl3+)))
10172 (define-public r-libcoin
10179 (uri (cran-uri "libcoin" version))
10181 (base32 "0izgnr4zdrbz3a05b0s28xfly4izp2zslgh282l9ads4skrmj3hl"))))
10182 (build-system r-build-system)
10183 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
10184 (home-page "https://cran.r-project.org/web/packages/libcoin")
10185 (synopsis "Linear test statistics for permutation inference")
10187 "This package provides basic infrastructure for linear test statistics
10188 and permutation inference in the framework of Strasser and Weber (1999).")
10189 (license license:gpl2)))
10191 (define-public r-coin
10198 (uri (cran-uri "coin" version))
10201 "15xvhnbyg34aacn6jfz4bsa1f7wq2ci0hslj8mgymql90k50x1qi"))))
10202 (build-system r-build-system)
10204 `(("r-libcoin" ,r-libcoin)
10205 ("r-matrixstats" ,r-matrixstats)
10206 ("r-modeltools" ,r-modeltools)
10207 ("r-multcomp" ,r-multcomp)
10208 ("r-mvtnorm" ,r-mvtnorm)
10209 ("r-survival" ,r-survival)))
10210 (home-page "http://coin.r-forge.r-project.org")
10211 (synopsis "Conditional inference procedures in a permutation test framework")
10213 "This package provides conditional inference procedures for the general
10214 independence problem including two-sample, K-sample (non-parametric ANOVA),
10215 correlation, censored, ordered and multivariate problems.")
10216 (license license:gpl2)))
10218 (define-public r-bayesplot
10220 (name "r-bayesplot")
10225 (uri (cran-uri "bayesplot" version))
10228 "0j69a78l5z0wyxcz607amaa4jc8kwwvcia9wxyir65b8ks9gj1d6"))))
10229 (build-system r-build-system)
10231 `(("pandoc" ,pandoc)
10232 ("pandoc-citeproc" ,pandoc-citeproc)))
10234 `(("r-knitr" ,r-knitr)))
10236 `(("r-dplyr" ,r-dplyr)
10237 ("r-ggplot2" ,r-ggplot2)
10238 ("r-ggridges" ,r-ggridges)
10240 ("r-reshape2" ,r-reshape2)
10241 ("r-rlang" ,r-rlang)
10242 ("r-tibble" ,r-tibble)
10243 ("r-tidyselect" ,r-tidyselect)))
10244 (home-page "https://mc-stan.org/bayesplot")
10245 (synopsis "Plotting for Bayesian models")
10247 "This package provides plotting functions for posterior analysis, model
10248 checking, and MCMC diagnostics. The package is designed not only to provide
10249 convenient functionality for users, but also a common set of functions that
10250 can be easily used by developers working on a variety of R packages for
10251 Bayesian modeling.")
10252 (license license:gpl3+)))
10254 (define-public r-tmb
10261 (uri (cran-uri "TMB" version))
10264 "0vnjh8d5gnjswil8ld3gbbspy4m5l2pzar1mpj62qxn2mwx0cc4s"))))
10265 (properties `((upstream-name . "TMB")))
10266 (build-system r-build-system)
10268 `(("r-matrix" ,r-matrix)
10269 ("r-rcppeigen" ,r-rcppeigen)))
10270 (home-page "http://tmb-project.org")
10271 (synopsis "Template model builder: a general random effect tool")
10273 "With this tool, a user should be able to quickly implement complex
10274 random effect models through simple C++ templates. The package combines
10275 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
10276 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
10277 from R) to obtain an efficient implementation of the applied Laplace
10278 approximation with exact derivatives. Key features are: Automatic sparseness
10279 detection, parallelism through BLAS and parallel user templates.")
10280 (license license:gpl2)))
10282 (define-public r-sjstats
10289 (uri (cran-uri "sjstats" version))
10291 (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka"))))
10292 (build-system r-build-system)
10294 `(("r-bayestestr" ,r-bayestestr)
10295 ("r-broom" ,r-broom)
10296 ("r-dplyr" ,r-dplyr)
10297 ("r-effectsize" ,r-effectsize)
10298 ("r-emmeans" ,r-emmeans)
10299 ("r-insight" ,r-insight)
10301 ("r-magrittr" ,r-magrittr)
10303 ("r-modelr" ,r-modelr)
10304 ("r-parameters" ,r-parameters)
10305 ("r-performance" ,r-performance)
10306 ("r-purrr" ,r-purrr)
10307 ("r-rlang" ,r-rlang)
10308 ("r-sjlabelled" ,r-sjlabelled)
10309 ("r-sjmisc" ,r-sjmisc)
10310 ("r-tidyr" ,r-tidyr)))
10311 (home-page "https://github.com/strengejacke/sjstats")
10312 (synopsis "Functions for common statistical computations")
10314 "This package provides a collection of convenient functions for common
10315 statistical computations, which are not directly provided by R's @code{base}
10316 or @code{stats} packages. This package aims at providing, first, shortcuts
10317 for statistical measures, which otherwise could only be calculated with
10318 additional effort. Second, these shortcut functions are generic, and can be
10319 applied not only to vectors, but also to other objects as well. The focus of
10320 most functions lies on summary statistics or fit measures for regression
10321 models, including generalized linear models, mixed effects models and Bayesian
10323 (license license:gpl3)))
10325 (define-public r-glmmtmb
10328 (version "1.0.2.1")
10332 (uri (cran-uri "glmmTMB" version))
10335 "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab"))))
10336 (properties `((upstream-name . "glmmTMB")))
10337 (build-system r-build-system)
10339 `(("r-lme4" ,r-lme4)
10340 ("r-matrix" ,r-matrix)
10342 ("r-rcppeigen" ,r-rcppeigen)
10345 `(("r-knitr" ,r-knitr))) ; for vignettes
10346 (home-page "https://github.com/glmmTMB")
10347 (synopsis "Generalized linear mixed models")
10349 "Fit linear and generalized linear mixed models with various extensions,
10350 including zero-inflation. The models are fitted using maximum likelihood
10351 estimation via the Template Model Builder. Random effects are assumed to be
10352 Gaussian on the scale of the linear predictor and are integrated out using the
10353 Laplace approximation. Gradients are calculated using automatic
10355 (license license:agpl3+)))
10357 (define-public r-bayestestr
10359 (name "r-bayestestr")
10364 (uri (cran-uri "bayestestR" version))
10367 "06y7vccgln1882yv04may9p6s915py8nnhg82d5ppbpxzcifi7l4"))))
10368 (properties `((upstream-name . "bayestestR")))
10369 (build-system r-build-system)
10371 `(("r-insight" ,r-insight)))
10373 `(("r-knitr" ,r-knitr)))
10374 (home-page "https://github.com/easystats/bayestestR")
10375 (synopsis "Describe Bayesian models and posterior distributions")
10377 "This package provides utilities to understand and describe posterior
10378 distributions and Bayesian models. It includes point-estimates such as
10379 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
10380 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
10381 ROPE percentage and pd).")
10382 (license license:gpl3)))
10384 (define-public r-performance
10386 (name "r-performance")
10391 (uri (cran-uri "performance" version))
10394 "1z45vy8gg77c2imcspwqf94anzi6c40wwbq0h7hg6zy76jsgvbyj"))))
10395 (build-system r-build-system)
10397 `(("r-bayestestr" ,r-bayestestr)
10398 ("r-insight" ,r-insight)))
10399 (home-page "https://easystats.github.io/performance/")
10400 (synopsis "Assessment of regression models performance")
10402 "This package provides utilities for computing measures to assess model
10403 quality, which are not directly provided by R's @code{base} or @code{stats}
10404 packages. These include e.g. measures like r-squared, intraclass correlation
10405 coefficient, root mean squared error or functions to check models for
10406 overdispersion, singularity or zero-inflation and more. Functions apply to a
10407 large variety of regression models, including generalized linear models, mixed
10408 effects models and Bayesian models.")
10409 (license license:gpl3)))
10411 (define-public r-ggeffects
10413 (name "r-ggeffects")
10418 (uri (cran-uri "ggeffects" version))
10421 "1c5rvycaqp7zp1j6j17c84v8nlpi0w7bhfxmcha4n37m0snk1kgy"))))
10422 (build-system r-build-system)
10424 `(("r-insight" ,r-insight)
10426 ("r-sjlabelled" ,r-sjlabelled)))
10428 `(("r-knitr" ,r-knitr)))
10429 (home-page "https://github.com/strengejacke/ggeffects")
10430 (synopsis "Create tidy data frames of marginal effects for ggplot")
10432 "This package provides tools to compute marginal effects from statistical
10433 models and return the result as tidy data frames. These data frames are ready
10434 to use with the @code{ggplot2} package. Marginal effects can be calculated
10435 for many different models. Interaction terms, splines and polynomial terms
10436 are also supported. The two main functions are @code{ggpredict()} and
10437 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
10438 results using @code{ggplot2}.")
10439 (license license:gpl3)))
10441 (define-public r-effectsize
10443 (name "r-effectsize")
10448 (uri (cran-uri "effectsize" version))
10451 "1hcrnax9wf0nwsb8nv15rxw8yy8w5dak16dw3w5bxi8xnf56lkz2"))))
10452 (properties `((upstream-name . "effectsize")))
10453 (build-system r-build-system)
10455 `(("r-bayestestr" ,r-bayestestr)
10456 ("r-insight" ,r-insight)
10457 ("r-parameters" ,r-parameters)))
10459 `(("r-knitr" ,r-knitr)))
10460 (home-page "https://github.com/easystats/effectsize")
10461 (synopsis "Indices of effect size and standardized parameters")
10463 "This package provides utilities to work with indices of effect size and
10464 standardized parameters for a wide variety of models, allowing computation and
10465 conversion of indices such as Cohen's d, r, odds, etc.")
10466 (license license:gpl3)))
10468 (define-public r-sjplot
10475 (uri (cran-uri "sjPlot" version))
10477 (base32 "1g4qabg654kwdm09ihp4h3mg64a1d7a7gsn6w56rwsidqqaxilq0"))))
10478 (properties `((upstream-name . "sjPlot")))
10479 (build-system r-build-system)
10481 `(("r-bayestestr" ,r-bayestestr)
10482 ("r-dplyr" ,r-dplyr)
10483 ("r-effectsize" ,r-effectsize)
10484 ("r-ggeffects" ,r-ggeffects)
10485 ("r-ggplot2" ,r-ggplot2)
10486 ("r-insight" ,r-insight)
10487 ("r-knitr" ,r-knitr)
10489 ("r-parameters" ,r-parameters)
10490 ("r-performance" ,r-performance)
10491 ("r-purrr" ,r-purrr)
10492 ("r-rlang" ,r-rlang)
10493 ("r-scales" ,r-scales)
10494 ("r-sjlabelled" ,r-sjlabelled)
10495 ("r-sjmisc" ,r-sjmisc)
10496 ("r-sjstats" ,r-sjstats)
10497 ("r-tidyr" ,r-tidyr)))
10499 `(("r-knitr" ,r-knitr)))
10500 (home-page "https://strengejacke.github.io/sjPlot/")
10501 (synopsis "Data visualization for statistics in social science")
10503 "This package represents a collection of plotting and table output
10504 functions for data visualization. Results of various statistical
10505 analyses (that are commonly used in social sciences) can be visualized using
10506 this package, including simple and cross tabulated frequencies, histograms,
10507 box plots, (generalized) linear models, mixed effects models, principal
10508 component analysis and correlation matrices, cluster analyses, scatter plots,
10509 stacked scales, effects plots of regression models (including interaction
10510 terms) and much more. This package supports labelled data.")
10511 (license license:gpl3)))
10513 (define-public r-ini
10520 (uri (cran-uri "ini" version))
10523 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
10524 (build-system r-build-system)
10525 (home-page "https://github.com/dvdscripter/ini")
10526 (synopsis "Read and write configuration files")
10528 "This package provides tools to parse simple @code{.ini} configuration
10529 files to an structured list. Users can manipulate this resulting list with
10530 @code{lapply()} functions. This same structured list can be used to write
10531 back to file after modifications.")
10532 (license license:gpl3)))
10534 (define-public r-gitcreds
10536 (name "r-gitcreds")
10541 (uri (cran-uri "gitcreds" version))
10544 "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi"))))
10545 (properties `((upstream-name . "gitcreds")))
10546 (build-system r-build-system)
10547 (inputs `(("git" ,git-minimal)))
10548 (native-inputs `(("r-knitr" ,r-knitr)))
10549 (home-page "https://github.com/r-lib/gitcreds")
10550 (synopsis "Query git credentials from R")
10552 "Query, set, and delete credentials from the git credential store.
10553 Manage GitHub tokens and other git credentials. This package is to be used by
10554 other packages that need to authenticate to GitHub and/or other git
10556 (license license:expat)))
10558 (define-public r-gh
10565 (uri (cran-uri "gh" version))
10568 "1zvy3ylxvni10lhvmbm9h14mg4wlsbdbzbzviwf28jxss8749219"))))
10569 (build-system r-build-system)
10572 ("r-gitcreds" ,r-gitcreds)
10575 ("r-jsonlite" ,r-jsonlite)))
10577 `(("r-knitr" ,r-knitr)))
10578 (home-page "https://github.com/r-lib/gh#readme")
10579 (synopsis "Access the GitHub API via R")
10581 "This package provides a minimal R client to access the GitHub API.")
10582 (license license:expat)))
10584 (define-public r-fs
10591 (uri (cran-uri "fs" version))
10594 "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn"))))
10595 (build-system r-build-system)
10597 `(("r-knitr" ,r-knitr)))
10598 (home-page "https://fs.r-lib.org")
10599 (synopsis "Cross-platform file system operations based on libuv")
10601 "This package provides a cross-platform interface to file system
10602 operations, built on top of the libuv C library.")
10603 (license license:gpl3)))
10605 (define-public r-clisymbols
10607 (name "r-clisymbols")
10612 (uri (cran-uri "clisymbols" version))
10615 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
10616 (build-system r-build-system)
10617 (home-page "https://github.com/gaborcsardi/clisymbols")
10618 (synopsis "Unicode symbols at the R prompt")
10620 "This package provides a small subset of Unicode symbols, that are useful
10621 when building command line applications. They fall back to alternatives on
10622 terminals that do not support Unicode.")
10623 (license license:expat)))
10625 (define-public r-credentials
10627 (name "r-credentials")
10632 (uri (cran-uri "credentials" version))
10635 "1w9zj34xdwz9bszsvhv2cbgq96y5sgxbh7ndn31pgfcpzlkfq6f1"))))
10636 (properties `((upstream-name . "credentials")))
10637 (build-system r-build-system)
10640 (modify-phases %standard-phases
10641 (add-after 'unpack 'setenv-HOME
10643 ;; This is necessary because git looks for $HOME/.gitconfig
10644 (setenv "HOME" "/tmp")
10647 `(("git" ,git-minimal)))
10649 `(("r-askpass" ,r-askpass)
10651 ("r-jsonlite" ,r-jsonlite)
10652 ("r-openssl" ,r-openssl)
10655 `(("r-knitr" ,r-knitr)))
10656 (home-page "https://docs.ropensci.org/credentials/")
10657 (synopsis "Tools for managing SSH and Git credentials")
10659 "This package assists you in setting up and retrieving of HTTPS and SSH
10660 credentials for use with git and other services. For HTTPS remotes the
10661 package interfaces the @command{git-credential} utility which @command{git}
10662 uses to store HTTP usernames and passwords. For SSH remotes this package
10663 provides convenient functions to find or generate appropriate SSH keys. The
10664 package both helps the user to setup a local git installation, and also
10665 provides a back-end for git/ssh client libraries to authenticate with existing
10666 user credentials.")
10667 (license license:expat)))
10669 (define-public r-gert
10676 (uri (cran-uri "gert" version))
10679 "09har6mj7qy813s6dxyzfzmjwg60m8c01yx3q6lfsnvwqzxlqxv8"))))
10680 (properties `((upstream-name . "gert")))
10681 (build-system r-build-system)
10683 `(("libgit2" ,libgit2)
10686 `(("r-askpass" ,r-askpass)
10687 ("r-credentials" ,r-credentials)
10688 ("r-openssl" ,r-openssl)
10689 ("r-rstudioapi" ,r-rstudioapi)
10693 `(("pkg-config" ,pkg-config)
10694 ("r-knitr" ,r-knitr)))
10695 (home-page "https://docs.ropensci.org/gert/")
10696 (synopsis "Simple Git client for R")
10698 "This package provides a simple git client for R based on libgit2 with
10699 support for SSH and HTTPS remotes. All functions in gert use basic R data
10700 types (such as vectors and data-frames) for their arguments and return values.
10701 User credentials are shared with command line git through the
10702 @code{git-credential} store and SSH keys stored on disk or ssh-agent.")
10703 (license license:expat)))
10705 (define-public r-usethis
10712 (uri (cran-uri "usethis" version))
10715 "1j6nzzrm2m6vi1gq0d5kxnnr9d8cy88wpmgigz3inych65x9w9pg"))))
10716 (build-system r-build-system)
10719 ("r-clipr" ,r-clipr)
10720 ("r-crayon" ,r-crayon)
10727 ("r-jsonlite" ,r-jsonlite)
10728 ("r-lifecycle" ,r-lifecycle)
10729 ("r-purrr" ,r-purrr)
10730 ("r-rappdirs" ,r-rappdirs)
10731 ("r-rlang" ,r-rlang)
10732 ("r-rprojroot" ,r-rprojroot)
10733 ("r-rstudioapi" ,r-rstudioapi)
10734 ("r-whisker" ,r-whisker)
10735 ("r-withr" ,r-withr)
10736 ("r-yaml" ,r-yaml)))
10737 (home-page "https://github.com/r-lib/usethis")
10738 (synopsis "Automate R package and project setup")
10740 "This package helps you to automate R package and project setup tasks
10741 that are otherwise performed manually. This includes setting up unit testing,
10742 test coverage, continuous integration, Git, GitHub integration, licenses,
10743 Rcpp, RStudio projects, and more.")
10744 (license license:gpl3)))
10746 (define-public r-sessioninfo
10748 (name "r-sessioninfo")
10753 (uri (cran-uri "sessioninfo" version))
10756 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
10757 (build-system r-build-system)
10760 ("r-withr" ,r-withr)))
10761 (home-page "https://github.com/r-lib/sessioninfo#readme")
10762 (synopsis "R session information")
10764 "This package provides tools to query and print information about the
10765 current R session. It is similar to @code{utils::sessionInfo()}, but includes
10766 more information about packages, and where they were installed from.")
10767 (license license:gpl2)))
10769 (define-public r-remotes
10776 (uri (cran-uri "remotes" version))
10779 "1f1kdw9j1wald3fs8b3n68x1kljy07j60g3aw1aarx26ikyk9whj"))))
10780 (build-system r-build-system)
10782 `(("r-knitr" ,r-knitr)))
10783 (home-page "https://github.com/r-lib/remotes#readme")
10784 (synopsis "R package installation from remote repositories")
10786 "Download and install R packages stored in GitHub, BitBucket, or plain
10787 subversion or git repositories. This package is a lightweight replacement of
10788 the @code{install_*} functions in the @code{devtools} package. Indeed most of
10789 the code was copied over from @code{devtools}.")
10790 (license license:gpl2+)))
10792 (define-public r-xopen
10799 (uri (cran-uri "xopen" version))
10802 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
10803 (build-system r-build-system)
10805 `(("r-processx" ,r-processx)))
10806 (home-page "https://github.com/r-lib/xopen#readme")
10807 (synopsis "Open system files, URLs, anything")
10809 "This package provides a cross-platform solution to open files,
10810 directories or URLs with their associated programs.")
10811 (license license:expat)))
10813 (define-public r-rcmdcheck
10815 (name "r-rcmdcheck")
10820 (uri (cran-uri "rcmdcheck" version))
10823 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
10824 (build-system r-build-system)
10826 `(("r-callr" ,r-callr)
10828 ("r-crayon" ,r-crayon)
10830 ("r-digest" ,r-digest)
10831 ("r-pkgbuild" ,r-pkgbuild)
10832 ("r-prettyunits" ,r-prettyunits)
10834 ("r-rprojroot" ,r-rprojroot)
10835 ("r-sessioninfo" ,r-sessioninfo)
10836 ("r-withr" ,r-withr)
10837 ("r-xopen" ,r-xopen)))
10838 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
10839 (synopsis "Run R CMD check from R and capture results")
10841 "Run @code{R CMD check} from R programmatically, and capture the results
10842 of the individual checks.")
10843 (license license:expat)))
10845 (define-public r-rapportools
10847 (name "r-rapportools")
10852 (uri (cran-uri "rapportools" version))
10855 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
10856 (build-system r-build-system)
10858 `(("r-pander" ,r-pander)
10860 ("r-reshape" ,r-reshape)))
10861 (home-page "https://cran.r-project.org/web/packages/rapportools/")
10862 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
10864 "This package provides helper functions that act as wrappers to more
10865 advanced statistical methods with the advantage of having sane defaults for
10867 (license license:agpl3+)))
10869 (define-public r-pander
10876 (uri (cran-uri "pander" version))
10879 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
10880 (build-system r-build-system)
10882 `(("r-digest" ,r-digest)
10883 ("r-rcpp" ,r-rcpp)))
10884 (home-page "https://rapporter.github.io/pander")
10885 (synopsis "Render R objects into Pandoc's markdown")
10887 "The main aim of the pander R package is to provide a minimal and easy
10888 tool for rendering R objects into Pandoc's markdown. The package is also
10889 capable of exporting/converting complex Pandoc documents (reports) in various
10891 ;; This package is licensed under either the AGPLv3+ or the very rarely
10893 (license license:agpl3+)))
10895 (define-public r-summarytools
10897 (name "r-summarytools")
10902 (uri (cran-uri "summarytools" version))
10905 "0n7rad6bkfn9cb99wbfzbwl5qzch48r0gafhddfcqvyh4fbn2k0j"))))
10906 (build-system r-build-system)
10908 `(("r-base64enc" ,r-base64enc)
10909 ("r-checkmate" ,r-checkmate)
10910 ("r-dplyr" ,r-dplyr)
10911 ("r-htmltools" ,r-htmltools)
10912 ("r-lubridate" ,r-lubridate)
10913 ("r-magick" ,r-magick)
10914 ("r-matrixstats" ,r-matrixstats)
10915 ("r-pander" ,r-pander)
10917 ("r-rapportools" ,r-rapportools)
10918 ("r-tibble" ,r-tibble)
10919 ("r-tidyr" ,r-tidyr)))
10921 `(("r-knitr" ,r-knitr)))
10922 (home-page "https://github.com/dcomtois/summarytools")
10923 (synopsis "Tools to quickly and neatly summarize data")
10925 "This package provides tools for data frame summaries, cross-tabulations,
10926 weight-enabled frequency tables and common univariate statistics in concise
10927 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
10928 good point-of-entry for exploring data, both for experienced and new R
10930 (license license:gpl2)))
10932 (define-public r-lsei
10939 (uri (cran-uri "lsei" version))
10942 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2"))))
10943 (build-system r-build-system)
10945 `(("gfortran" ,gfortran)))
10946 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
10947 (synopsis "Solve regression problems under equality/inequality constraints")
10949 "It contains functions that solve least squares linear regression
10950 problems under linear equality/inequality constraints. Functions for solving
10951 quadratic programming problems are also available, which transform such
10952 problems into least squares ones first.")
10953 (license license:gpl2+)))
10955 (define-public r-npsurv
10962 (uri (cran-uri "npsurv" version))
10965 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw"))))
10966 (build-system r-build-system)
10968 `(("r-lsei" ,r-lsei)))
10969 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
10970 (synopsis "Nonparametric survival analysis")
10972 "This package contains functions for non-parametric survival analysis of
10973 exact and interval-censored observations.")
10974 (license license:gpl2+)))
10976 (define-public r-clusteval
10978 (name "r-clusteval")
10983 (uri (cran-uri "clusteval" version))
10986 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
10987 (build-system r-build-system)
10989 `(("r-mvtnorm" ,r-mvtnorm)
10990 ("r-rcpp" ,r-rcpp)))
10991 (home-page "https://cran.r-project.org/web/packages/clusteval/")
10992 (synopsis "Evaluation of clustering algorithms")
10994 "This R package provides a suite of tools to evaluate clustering
10995 algorithms, clusterings, and individual clusters.")
10996 (license license:expat)))
10998 (define-public r-tweedie
11005 (uri (cran-uri "tweedie" version))
11008 "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0"))))
11009 (build-system r-build-system)
11010 (native-inputs `(("gfortran" ,gfortran)))
11011 (home-page "https://cran.r-project.org/web/packages/tweedie/")
11012 (synopsis "Evaluation of Tweedie exponential family models")
11014 "Maximum likelihood computations for Tweedie families, including the
11015 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
11016 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
11017 and related methods.")
11018 (license license:gpl2+)))
11020 (define-public r-rcppgsl
11027 (uri (cran-uri "RcppGSL" version))
11029 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
11030 (properties `((upstream-name . "RcppGSL")))
11031 (build-system r-build-system)
11033 `(("r-rcpp" ,r-rcpp)
11035 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
11036 (synopsis "Rcpp integration for GSL vectors and matrices")
11038 "The GNU Scientific Library (or GSL) is a collection of numerical
11039 routines for scientific computing. It is particularly useful for C and C++
11040 programs as it provides a standard C interface to a wide range of mathematical
11041 routines. There are over 1000 functions in total with an extensive test
11042 suite. The RcppGSL package provides an easy-to-use interface between GSL data
11043 structures and R using concepts from Rcpp which is itself a package that eases
11044 the interfaces between R and C++.")
11045 (license license:gpl2+)))
11047 (define-public r-mvabund
11054 (uri (cran-uri "mvabund" version))
11057 "0aisvax9d7bk6aykrcdcn1ji618r520mcrkr1i3jnck1qs31z41f"))))
11058 (build-system r-build-system)
11060 `(("r-mass" ,r-mass)
11062 ("r-rcppgsl" ,r-rcppgsl)
11063 ("r-statmod" ,r-statmod)
11064 ("r-tweedie" ,r-tweedie)))
11065 (home-page "https://cran.r-project.org/web/packages/mvabund/")
11066 (synopsis "Statistical methods for analysing multivariate abundance data")
11068 "This package provides a set of tools for displaying, modeling and
11069 analysing multivariate abundance data in community ecology.")
11070 (license license:lgpl2.1+)))
11072 (define-public r-afex
11079 (uri (cran-uri "afex" version))
11082 "0blwqr5ni3psav1dcdmhfi4jy3b4scm5njimqfpr1d81zadvgc6g"))))
11083 (build-system r-build-system)
11087 ("r-lmertest" ,r-lmertest)
11088 ("r-pbkrtest" ,r-pbkrtest)
11089 ("r-reshape2" ,r-reshape2)))
11091 `(("r-knitr" ,r-knitr)))
11092 (home-page "https://afex.singmann.science/")
11093 (synopsis "Analysis of factorial experiments")
11095 "This package provides convenience functions for analyzing factorial
11096 experiments using ANOVA or mixed models.")
11097 (license license:gpl2+)))
11099 (define-public r-lmertest
11101 (name "r-lmertest")
11106 (uri (cran-uri "lmerTest" version))
11109 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim"))))
11110 (properties `((upstream-name . "lmerTest")))
11111 (build-system r-build-system)
11113 `(("r-ggplot2" ,r-ggplot2)
11116 ("r-numderiv" ,r-numderiv)))
11117 (home-page "https://github.com/runehaubo/lmerTestR")
11118 (synopsis "Tests in linear mixed effects models")
11120 "This package provides p-values in type I, II or III anova and summary
11121 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
11122 method. A Kenward-Roger method is also available via the @code{pbkrtest}
11123 package. Model selection methods include step, drop1 and anova-like tables
11124 for random effects (ranova). Methods for Least-Square means (LS-means) and
11125 tests of linear contrasts of fixed effects are also available.")
11126 (license license:gpl2+)))
11128 (define-public r-r2glmm
11135 (uri (cran-uri "r2glmm" version))
11138 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
11139 (build-system r-build-system)
11141 `(("r-afex" ,r-afex)
11142 ("r-data-table" ,r-data-table)
11143 ("r-dplyr" ,r-dplyr)
11144 ("r-ggplot2" ,r-ggplot2)
11145 ("r-gridextra" ,r-gridextra)
11146 ("r-lmertest" ,r-lmertest)
11148 ("r-matrix" ,r-matrix)
11150 ("r-pbkrtest" ,r-pbkrtest)))
11151 (home-page "https://github.com/bcjaeger/r2glmm")
11152 (synopsis "Compute R squared for mixed (multilevel) models")
11154 "This package computes model and semi partial R squared with confidence
11155 limits for the linear and generalized linear mixed model (LMM and GLMM). The
11156 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
11157 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
11159 (license license:gpl2)))
11161 (define-public r-weights
11168 (uri (cran-uri "weights" version))
11171 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
11172 (build-system r-build-system)
11174 `(("r-gdata" ,r-gdata)
11175 ("r-hmisc" ,r-hmisc)
11176 ("r-mice" ,r-mice)))
11178 "https://cran.r-project.org/web/packages/weights/")
11179 (synopsis "Weighting and weighted statistics")
11180 (description "This package Provides a variety of functions for producing
11181 simple weighted statistics, such as weighted Pearson's correlations, partial
11182 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
11183 includes some software for quickly recoding survey data and plotting point
11184 estimates from interaction terms in regressions (and multiply imputed
11185 regressions). NOTE: Weighted partial correlation calculations pulled to
11187 (license license:gpl2+)))
11189 (define-public r-rcppannoy
11191 (name "r-rcppannoy")
11196 (uri (cran-uri "RcppAnnoy" version))
11199 "0n68cf77gz34iq6w6ad87pbqwqam45nxp1gjzns4g6qhf7qdvrz4"))))
11200 (properties `((upstream-name . "RcppAnnoy")))
11201 (build-system r-build-system)
11203 `(("r-rcpp" ,r-rcpp)))
11204 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
11205 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
11207 "Annoy is a small C++ library for Approximate Nearest Neighbors written
11208 for efficient memory usage as well an ability to load from and save to disk.
11209 This package provides an R interface.")
11210 ;; Annoy is released under ASL 2.0, but this wrapper is released under
11212 (license (list license:gpl2+ license:asl2.0))))
11214 (define-public r-rcpphnsw
11216 (name "r-rcpphnsw")
11221 (uri (cran-uri "RcppHNSW" version))
11224 "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
11225 (properties `((upstream-name . "RcppHNSW")))
11226 (build-system r-build-system)
11227 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11228 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
11229 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
11231 "Hnswlib is a C++ library for approximate nearest neighbors. This
11232 package provides a minimal R interface by relying on the Rcpp package.")
11233 ;; hnswlib is released under Version 2.0 of the Apache License.
11234 (license (list license:gpl3 license:asl2.0))))
11236 (define-public r-rcppparallel
11238 (name "r-rcppparallel")
11243 (uri (cran-uri "RcppParallel" version))
11246 "10bg4fw38m64dhy543rwq2nnjjc9y24iggk343xslrb3ij8018lc"))))
11247 (properties `((upstream-name . "RcppParallel")))
11248 (build-system r-build-system)
11249 (home-page "https://rcppcore.github.io/RcppParallel/")
11250 (synopsis "Parallel programming tools for Rcpp")
11252 "This package provides high level functions for parallel programming with
11253 Rcpp. For example, the @code{parallelFor()} function can be used to convert
11254 the work of a standard serial @code{for} loop into a parallel one and the
11255 @code{parallelReduce()} function can be used for accumulating aggregates or
11257 (license license:gpl2)))
11259 (define-public r-ncdf4
11266 (uri (cran-uri "ncdf4" version))
11269 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
11270 (build-system r-build-system)
11272 `(("netcdf" ,netcdf)
11274 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
11275 (synopsis "R interface to Unidata netCDF format data files")
11277 "This package provides a high-level R interface to data files written
11278 using Unidata's netCDF library (version 4 or earlier), which are binary data
11279 files that are portable across platforms and include metadata information in
11280 addition to the data sets. Using this package, netCDF files can be opened and
11281 data sets read in easily. It is also easy to create new netCDF dimensions,
11282 variables, and files, in either version 3 or 4 format, and manipulate existing
11284 (license license:gpl3+)))
11286 (define-public r-biocmanager
11288 (name "r-biocmanager")
11289 (version "1.30.10")
11293 (uri (cran-uri "BiocManager" version))
11295 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
11296 (properties `((upstream-name . "BiocManager")))
11297 (build-system r-build-system)
11298 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
11299 (synopsis "Access the Bioconductor project package repository")
11301 "This package provides a convenient tool to install and update
11302 Bioconductor packages.")
11303 (license license:artistic2.0)))
11305 (define-public r-rgl
11308 (version "0.104.16")
11312 (uri (cran-uri "rgl" version))
11315 "169a8riiam8445nl7rcwn0x92dlwyzh5xldvap6dcxjyjqmjwbdq"))))
11316 (build-system r-build-system)
11318 `(("pkg-config" ,pkg-config)
11319 ("r-knitr" ,r-knitr)))
11321 `(("freetype" ,freetype)
11328 `(("r-crosstalk" ,r-crosstalk)
11329 ("r-htmltools" ,r-htmltools)
11330 ("r-htmlwidgets" ,r-htmlwidgets)
11331 ("r-jsonlite" ,r-jsonlite)
11332 ("r-knitr" ,r-knitr)
11333 ("r-magrittr" ,r-magrittr)
11334 ("r-manipulatewidget" ,r-manipulatewidget)
11335 ("r-shiny" ,r-shiny)))
11336 (home-page "https://r-forge.r-project.org/projects/rgl/")
11337 (synopsis "3D visualization using OpenGL")
11339 "This package provides medium to high level functions for 3D interactive graphics,
11340 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
11341 as functions for constructing representations of geometric
11342 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
11343 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
11344 image formats, including PNG, Postscript, SVG, PGF.")
11345 ;; Any version of the GPL.
11346 (license (list license:gpl2+ license:gpl3+))))
11348 (define-public r-multicool
11350 (name "r-multicool")
11355 (uri (cran-uri "multicool" version))
11358 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
11359 (build-system r-build-system)
11360 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11361 (home-page "https://cran.r-project.org/web/packages/multicool/")
11362 (synopsis "Permutations of multisets in cool-lex order")
11364 "This package provides a set of tools to permute multisets without loops
11365 or hash tables and to generate integer partitions. Cool-lex order is similar
11366 to colexicographical order.")
11367 (license license:gpl2)))
11369 (define-public r-misc3d
11376 (uri (cran-uri "misc3d" version))
11379 "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1"))))
11380 (build-system r-build-system)
11381 (home-page "https://cran.r-project.org/web/packages/misc3d/")
11382 (synopsis "Miscellaneous 3D Plots")
11384 "This package provides a collection of miscellaneous 3d plots, including
11386 ;; Any version of the GPL.
11387 (license (list license:gpl2+ license:gpl3+))))
11389 (define-public r-ks
11396 (uri (cran-uri "ks" version))
11398 (base32 "1sff6rlpq64lqyvwgral9zbcan30wpgmfb26hw9y6wzypd9gxbz6"))))
11399 (build-system r-build-system)
11402 ("r-kernlab" ,r-kernlab)
11403 ("r-kernsmooth" ,r-kernsmooth)
11404 ("r-matrix" ,r-matrix)
11405 ("r-mclust" ,r-mclust)
11407 ("r-multicool" ,r-multicool)
11408 ("r-mvtnorm" ,r-mvtnorm)
11409 ("r-plot3d" ,r-plot3d)))
11410 (home-page "https://www.mvstat.net/tduong/")
11411 (synopsis "Kernel smoothing")
11413 "This package provides kernel smoothers for univariate and multivariate
11414 data, including density functions, density derivatives, cumulative
11415 distributions, modal clustering, discriminant analysis, and two-sample
11416 hypothesis testing.")
11417 ;; Either version of the GPL.
11418 (license (list license:gpl2 license:gpl3))))
11420 (define-public r-feature
11427 (uri (cran-uri "feature" version))
11430 "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y"))))
11431 (build-system r-build-system)
11434 ("r-plot3d" ,r-plot3d)))
11436 `(("r-knitr" ,r-knitr)))
11437 (home-page "https://www.mvstat.net/tduong/")
11438 (synopsis "Inferential feature significance for kernel density estimation")
11440 "The feature package contains functions to display and compute kernel
11441 density estimates, significant gradient and significant curvature regions.
11442 Significant gradient and/or curvature regions often correspond to significant
11443 features (e.g. local modes).")
11444 ;; Either version of the GPL.
11445 (license (list license:gpl2 license:gpl3))))
11447 (define-public r-arm
11454 (uri (cran-uri "arm" version))
11457 "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3"))))
11458 (build-system r-build-system)
11460 `(("r-abind" ,r-abind)
11462 ("r-hmisc" ,r-hmisc)
11465 ("r-matrix" ,r-matrix)
11466 ("r-nlme" ,r-nlme)))
11467 (home-page "https://cran.r-project.org/web/packages/arm/")
11468 (synopsis "Data analysis using regression and multilevel/hierarchical models")
11470 "This package provides functions to accompany A. Gelman and J. Hill,
11471 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
11472 University Press, 2007.")
11473 (license license:gpl3+)))
11475 (define-public r-circular
11477 (name "r-circular")
11482 (uri (cran-uri "circular" version))
11485 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
11486 (build-system r-build-system)
11488 `(("r-boot" ,r-boot)
11489 ("r-mvtnorm" ,r-mvtnorm)))
11491 `(("gfortran" ,gfortran)))
11492 (home-page "https://cran.r-project.org/web/packages/circular/")
11493 (synopsis "Circular statistics")
11495 "This package provides tools for circular statistics, from \"Topics in
11496 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
11498 (license license:gpl2+)))
11500 (define-public r-activity
11502 (name "r-activity")
11507 (uri (cran-uri "activity" version))
11510 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
11511 (build-system r-build-system)
11513 `(("r-circular" ,r-circular)
11514 ("r-insol" ,r-insol)
11515 ("r-pbapply" ,r-pbapply)))
11516 (home-page "https://cran.r-project.org/web/packages/activity/")
11517 (synopsis "Animal activity statistics")
11519 "This package provides functions to fit kernel density functions to
11520 animal activity time data; plot activity distributions; quantify overall
11521 levels of activity; statistically compare activity metrics through
11522 bootstrapping; and evaluate variation in linear variables with time (or other
11523 circular variables).")
11524 (license license:gpl3)))
11526 (define-public r-ouch
11533 (uri (cran-uri "ouch" version))
11536 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
11537 (build-system r-build-system)
11538 (propagated-inputs `(("r-subplex" ,r-subplex)))
11539 (home-page "https://kingaa.github.io/ouch/")
11540 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
11542 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
11543 for evolution along a phylogenetic tree.")
11544 (license license:gpl2+)))
11546 (define-public r-fmsb
11553 (uri (cran-uri "fmsb" version))
11556 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
11557 (build-system r-build-system)
11558 (home-page "http://minato.sip21c.org/msb/")
11559 (synopsis "Functions for medical statistics book with demographic data")
11561 "This package provides several utility functions for the book entitled
11562 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
11563 Japan, 2007) with Japanese demographic data and some demographic analysis
11564 related functions.")
11565 (license license:gpl2+)))
11567 (define-public r-stabledist
11569 (name "r-stabledist")
11574 (uri (cran-uri "stabledist" version))
11577 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
11578 (build-system r-build-system)
11579 (home-page "https://www.rmetrics.org")
11580 (synopsis "Stable distribution functions")
11582 "This package provides density, probability and quantile functions, and
11583 random number generation for (skew) stable distributions, using the
11584 parametrizations of Nolan.")
11585 (license license:gpl2+)))
11587 (define-public r-gsl
11594 (uri (cran-uri "gsl" version))
11597 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
11598 (build-system r-build-system)
11601 (home-page "https://cran.r-project.org/web/packages/gsl")
11602 (synopsis "Wrapper for the GNU Scientific Library")
11604 "This package provides an R wrapper for the special functions and quasi
11605 random number generators of the GNU Scientific Library.")
11606 (license license:gpl2+)))
11608 (define-public r-adgoftest
11610 (name "r-adgoftest")
11615 (uri (cran-uri "ADGofTest" version))
11618 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
11619 (properties `((upstream-name . "ADGofTest")))
11620 (build-system r-build-system)
11621 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
11622 (synopsis "Anderson-Darling GoF test")
11624 "This package provides an implementation of the Anderson-Darling GoF test
11625 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
11626 Anderson-Darling Distribution\".")
11627 ;; Any version of the GPL.
11628 (license license:gpl3+)))
11630 (define-public r-sodium
11637 (uri (cran-uri "sodium" version))
11640 "1zxzi8xvxnhgcd5qrylf08nz1cdq3aslrswjas440qg63ypmbf6w"))))
11641 (properties `((upstream-name . "sodium")))
11642 (build-system r-build-system)
11644 `(("libsodium" ,libsodium)))
11646 `(("pkg-config" ,pkg-config)
11647 ("r-knitr" ,r-knitr)))
11648 (home-page "https://github.com/jeroen/sodium")
11649 (synopsis "R bindings to the libsodium crypto library")
11651 "This package provides bindings to libsodium: a library for encryption,
11652 decryption, signatures, password hashing and more. Sodium uses curve25519, a
11653 Diffie-Hellman function by Daniel Bernstein, which has become very popular
11654 after it was discovered that the NSA had backdoored Dual EC DRBG.")
11655 (license license:expat)))
11657 (define-public r-softimpute
11659 (name "r-softimpute")
11664 (uri (cran-uri "softImpute" version))
11667 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
11668 (properties `((upstream-name . "softImpute")))
11669 (build-system r-build-system)
11671 `(("r-matrix" ,r-matrix)))
11673 `(("gfortran" ,gfortran)))
11674 (home-page "https://cran.r-project.org/web/packages/softImpute")
11675 (synopsis "Matrix completion via iterative soft-thresholded SVD")
11677 "This package provides iterative methods for matrix completion that use
11678 nuclear-norm regularization. The package includes procedures for centering
11679 and scaling rows, columns or both, and for computing low-rank @dfn{single
11680 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
11682 (license license:gpl2)))
11684 (define-public r-fftwtools
11686 (name "r-fftwtools")
11691 (uri (cran-uri "fftwtools" version))
11694 "0h8lyl2i6zq16ir7xnfj9dhyivxvwikm8lml19s8s8jx95z3n9x9"))))
11695 (build-system r-build-system)
11696 (inputs `(("fftw" ,fftw)))
11697 (home-page "https://github.com/krahim/fftwtools")
11698 (synopsis "Wrapper for FFTW3")
11700 "This package provides a wrapper for several FFTW functions. It provides
11701 access to the two-dimensional FFT, the multivariate FFT, and the
11702 one-dimensional real to complex FFT using the FFTW3 library. The package
11703 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
11704 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
11705 The FFT functions have a parameter that allows them to not return the
11706 redundant complex conjugate when the input is real data.")
11707 (license license:gpl2+)))
11709 (define-public r-tiff
11716 (uri (cran-uri "tiff" version))
11719 "1yy4im2lwzhjnnkfwxgkknsajvm83pcwaf370pkgfva2db0xjfv2"))))
11720 (build-system r-build-system)
11722 `(("libtiff" ,libtiff)
11723 ("libjpeg" ,libjpeg-turbo)
11725 (home-page "https://www.rforge.net/tiff/")
11726 (synopsis "Read and write TIFF images")
11728 "This package provides an easy and simple way to read, write and display
11729 bitmap images stored in the TIFF format. It can read and write both files and
11730 in-memory raw vectors.")
11731 ;; Either of these two license versions.
11732 (license (list license:gpl2 license:gpl3))))
11734 (define-public r-nlp
11741 (uri (cran-uri "NLP" version))
11744 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5"))))
11745 (properties `((upstream-name . "NLP")))
11746 (build-system r-build-system)
11747 (home-page "https://cran.r-project.org/web/packages/NLP/")
11748 (synopsis "Natural language processing infrastructure")
11750 "This package provides basic classes and methods for Natural Language
11752 (license license:gpl3)))
11754 (define-public r-tm
11761 (uri (cran-uri "tm" version))
11764 "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi"))))
11765 (properties `((upstream-name . "tm")))
11766 (build-system r-build-system)
11772 ("r-xml2" ,r-xml2)))
11773 (home-page "http://tm.r-forge.r-project.org/")
11774 (synopsis "Text mining package")
11776 "This package provides a framework for text mining applications within R.")
11777 (license license:gpl3)))
11779 (define-public r-waveslim
11781 (name "r-waveslim")
11786 (uri (cran-uri "waveslim" version))
11789 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
11790 (build-system r-build-system)
11792 `(("gfortran" ,gfortran)))
11793 (home-page "http://waveslim.blogspot.com")
11794 (synopsis "Basic wavelet routines for signal processing")
11796 "This package provides basic wavelet routines for time series (1D),
11797 image (2D) and array (3D) analysis. The code provided here is based on
11798 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
11799 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
11800 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
11801 pairs (Selesnick 2001, 2002).")
11802 (license license:bsd-3)))
11804 (define-public r-wordcloud
11806 (name "r-wordcloud")
11811 (uri (cran-uri "wordcloud" version))
11814 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
11815 (build-system r-build-system)
11817 `(("r-rcolorbrewer" ,r-rcolorbrewer)
11819 ;; The "tm" package is only "suggested" according to CRAN, but the
11820 ;; wordcloud package cannot be loaded without it.
11822 (home-page "https://cran.r-project.org/web/packages/wordcloud")
11823 (synopsis "Word clouds")
11825 "This package provides functionality to create pretty word clouds,
11826 visualize differences and similarity between documents, and avoid
11827 over-plotting in scatter plots with text.")
11828 (license license:lgpl2.1)))
11830 (define-public r-colorramps
11832 (name "r-colorramps")
11837 (uri (cran-uri "colorRamps" version))
11840 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
11841 (properties `((upstream-name . "colorRamps")))
11842 (build-system r-build-system)
11843 (home-page "https://cran.r-project.org/web/packages/colorRamps")
11844 (synopsis "Build color tables")
11845 (description "This package provides features to build gradient color
11847 ;; Any version of the GPL
11848 (license license:gpl3+)))
11850 (define-public r-tidytree
11852 (name "r-tidytree")
11857 (uri (cran-uri "tidytree" version))
11859 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
11860 (build-system r-build-system)
11863 ("r-dplyr" ,r-dplyr)
11864 ("r-lazyeval" ,r-lazyeval)
11865 ("r-magrittr" ,r-magrittr)
11866 ("r-rlang" ,r-rlang)
11867 ("r-tibble" ,r-tibble)))
11869 `(("r-knitr" ,r-knitr)))
11870 (home-page "https://github.com/GuangchuangYu/tidytree")
11871 (synopsis "Tidy tool for phylogenetic tree data manipulation")
11873 "Phylogenetic trees generally contain multiple components including nodes,
11874 edges, branches and associated data. This package provides an approach to
11875 convert tree objects to tidy data frames. It also provides tidy interfaces to
11876 manipulate tree data.")
11877 (license license:artistic2.0)))
11879 (define-public r-rvcheck
11886 (uri (cran-uri "rvcheck" version))
11888 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
11889 (build-system r-build-system)
11891 `(("r-biocmanager" ,r-biocmanager)
11892 ("r-rlang" ,r-rlang)))
11893 (home-page "https://cran.r-project.org/web/packages/rvcheck")
11894 (synopsis "R package version check")
11896 "This package provides tools to check the latest release version of R and
11897 R packages (on CRAN, Bioconductor or Github).")
11898 (license license:artistic2.0)))
11900 (define-public r-docopt
11907 (uri (cran-uri "docopt" version))
11910 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
11911 (build-system r-build-system)
11912 (home-page "https://github.com/docopt/docopt.R")
11913 (synopsis "Command-line interface specification language")
11915 "This package enables you to define a command-line interface by just
11916 giving it a description in the specific format.")
11917 (license license:expat)))
11919 (define-public r-sparsesvd
11921 (name "r-sparsesvd")
11926 (uri (cran-uri "sparsesvd" version))
11929 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
11930 (build-system r-build-system)
11931 (propagated-inputs `(("r-matrix" ,r-matrix)))
11932 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
11933 (synopsis "Sparse truncated singular value decomposition")
11935 "This package provides a Wrapper around the SVDLIBC library
11936 for (truncated) singular value decomposition of a sparse matrix. Currently,
11937 only sparse real matrices in Matrix package format are supported.")
11938 ;; SVDLIBC is released under BSD-2. The R interface is released under
11940 (license (list license:bsd-3 license:bsd-2))))
11942 (define-public r-speedglm
11944 (name "r-speedglm")
11949 (uri (cran-uri "speedglm" version))
11952 "0f37w4lj8dpcg1sfkd7cv6qpdkanmb97mnd8zih2fxzv8bpd0rfh"))))
11953 (build-system r-build-system)
11955 `(("r-mass" ,r-mass)
11956 ("r-matrix" ,r-matrix)))
11957 (home-page "https://cran.r-project.org/web/packages/speedglm")
11958 (synopsis "Fit linear and generalized linear models to large data sets")
11960 "This package provides tools for fitting linear models and generalized
11961 linear models to large data sets by updating algorithms.")
11962 ;; Any version of the GPL
11963 (license license:gpl2+)))
11965 (define-public r-densityclust
11967 (name "r-densityclust")
11972 (uri (cran-uri "densityClust" version))
11975 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
11976 (properties `((upstream-name . "densityClust")))
11977 (build-system r-build-system)
11980 ("r-ggplot2" ,r-ggplot2)
11981 ("r-ggrepel" ,r-ggrepel)
11982 ("r-gridextra" ,r-gridextra)
11983 ("r-rcolorbrewer" ,r-rcolorbrewer)
11985 ("r-rtsne" ,r-rtsne)))
11986 (home-page "https://cran.r-project.org/web/packages/densityClust")
11987 (synopsis "Clustering by fast search and find of density peaks")
11989 "This package provides an improved implementation (based on k-nearest
11990 neighbors) of the density peak clustering algorithm, originally described by
11991 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
11992 large datasets (> 100,000 samples) very efficiently.")
11993 (license license:gpl2+)))
11995 (define-public r-combinat
11997 (name "r-combinat")
12002 (uri (cran-uri "combinat" version))
12005 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
12006 (build-system r-build-system)
12007 (home-page "https://cran.r-project.org/web/packages/combinat")
12008 (synopsis "Combinatorics utilities")
12009 (description "This package provides assorted routines for combinatorics.")
12010 (license license:gpl2)))
12012 (define-public r-qlcmatrix
12014 (name "r-qlcmatrix")
12019 (uri (cran-uri "qlcMatrix" version))
12022 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
12023 (properties `((upstream-name . "qlcMatrix")))
12024 (build-system r-build-system)
12026 `(("r-docopt" ,r-docopt)
12027 ("r-matrix" ,r-matrix)
12029 ("r-sparsesvd" ,r-sparsesvd)))
12030 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
12031 (synopsis "Sparse matrix functions for quantitative language comparison")
12033 "This package provides an extension of the functionality of the Matrix
12034 package for using sparse matrices. Some of the functions are very general,
12035 while other are highly specific for the special data format used for
12036 @dfn{quantitative language comparison} (QLC).")
12037 (license license:gpl3)))
12039 (define-public r-ddrtree
12046 (uri (cran-uri "DDRTree" version))
12049 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
12050 (properties `((upstream-name . "DDRTree")))
12051 (build-system r-build-system)
12054 ("r-irlba" ,r-irlba)
12056 ("r-rcppeigen" ,r-rcppeigen)))
12057 (home-page "https://cran.r-project.org/web/packages/DDRTree")
12058 (synopsis "Learning principal graphs with DDRTree")
12060 "This package provides an implementation of the framework of
12061 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
12062 dimensional space while constructs a principal tree which passes through the
12063 middle of the data simultaneously. DDRTree shows superiority to
12064 alternatives (Wishbone, DPT) for inferring the ordering as well as the
12065 intrinsic structure of single cell genomics data. In general, it could be
12066 used to reconstruct the temporal progression as well as the bifurcation
12067 structure of any data type.")
12068 (license license:asl2.0)))
12070 (define-public r-corpcor
12077 (uri (cran-uri "corpcor" version))
12080 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
12081 (build-system r-build-system)
12082 (home-page "http://strimmerlab.org/software/corpcor/")
12083 (synopsis "Efficient estimation of covariance and (partial) correlation")
12085 "This package implements a James-Stein-type shrinkage estimator for the
12086 covariance matrix, with separate shrinkage for variances and correlations.
12087 Furthermore, functions are available for fast singular value decomposition,
12088 for computing the pseudoinverse, and for checking the rank and positive
12089 definiteness of a matrix.")
12090 (license license:gpl3+)))
12092 (define-public r-rspectra
12094 (name "r-rspectra")
12099 (uri (cran-uri "RSpectra" version))
12102 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
12103 (properties `((upstream-name . "RSpectra")))
12104 (build-system r-build-system)
12106 `(("r-matrix" ,r-matrix)
12108 ("r-rcppeigen" ,r-rcppeigen)))
12109 (home-page "https://github.com/yixuan/RSpectra")
12110 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
12112 "This package provides an R interface to the Spectra library for
12113 large-scale eigenvalue and SVD problems. It is typically used to compute a
12114 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
12115 which is usually more efficient than @code{eigen()} if k << n.")
12117 (license license:mpl2.0)))
12119 (define-public r-vbsr
12126 (uri (cran-uri "vbsr" version))
12129 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
12130 (build-system r-build-system)
12131 (home-page "https://cran.r-project.org/web/packages/vbsr")
12132 (synopsis "Variational Bayes spike regression regularized linear models")
12134 "This package provides an efficient algorithm for solving ultra-sparse
12135 regularized regression models using a variational Bayes algorithm with a spike
12136 prior. The algorithm is solved on a path, with coordinate updates, and is
12137 capable of generating very sparse models. Very general model
12138 diagnostics for controlling type-1 errors are also provided.")
12139 (license license:gpl2)))
12141 (define-public r-flare
12148 (uri (cran-uri "flare" version))
12151 "0f992dmgnr6s8g3386i9bjfyf08q8srgw7sjz2yx7snj8znq7251"))))
12152 (build-system r-build-system)
12154 `(("r-igraph" ,r-igraph)
12155 ("r-lattice" ,r-lattice)
12157 ("r-matrix" ,r-matrix)))
12158 (home-page "https://cran.r-project.org/web/packages/flare")
12159 (synopsis "Family of Lasso regression implementations")
12161 "This package provides implementations of a family of Lasso variants
12162 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
12163 high dimensional sparse linear models.")
12164 (license license:gpl2)))
12166 (define-public r-lassopv
12173 (uri (cran-uri "lassopv" version))
12176 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
12177 (build-system r-build-system)
12178 (propagated-inputs `(("r-lars" ,r-lars)))
12179 (home-page "https://github.com/lingfeiwang/lassopv")
12180 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
12182 "This package enables you to estimate the p-values for predictors x
12183 against target variable y in Lasso regression, using the regularization
12184 strength when each predictor enters the active set of regularization path for
12185 the first time as the statistic.")
12186 (license license:gpl3)))
12188 (define-public r-splitstackshape
12190 (name "r-splitstackshape")
12195 (uri (cran-uri "splitstackshape" version))
12198 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
12199 (build-system r-build-system)
12201 `(("r-data-table" ,r-data-table)))
12202 (home-page "https://github.com/mrdwab/splitstackshape")
12203 (synopsis "Stack and reshape datasets after splitting concatenated values")
12205 "Online data collection tools like Google Forms often export
12206 multiple-response questions with data concatenated in cells. The
12207 @code{concat.split} (cSplit) family of functions provided by this package
12208 splits such data into separate cells. This package also includes functions to
12209 stack groups of columns and to reshape wide data, even when the data are
12210 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
12211 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
12213 (license license:gpl3)))
12215 (define-public r-tfmpvalue
12217 (name "r-tfmpvalue")
12222 (uri (cran-uri "TFMPvalue" version))
12225 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
12226 (properties `((upstream-name . "TFMPvalue")))
12227 (build-system r-build-system)
12228 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12229 (home-page "https://github.com/ge11232002/TFMPvalue")
12230 (synopsis "P-value computation for position weight matrices")
12232 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
12233 identification from sequence/alignments, we are interested in the significance
12234 of certain match scores. TFMPvalue provides the accurate calculation of a
12235 p-value with a score threshold for position weight matrices, or the score with
12236 a given p-value. It is an interface to code originally made available by
12237 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
12238 Touzet and Varre (2007).")
12239 (license license:gpl2)))
12241 (define-public r-rnifti
12248 (uri (cran-uri "RNifti" version))
12251 "1zr0q79id62csmc30c7gs4hbmavk8n6p50a981sfz51dczhjj5ny"))))
12252 (properties `((upstream-name . "RNifti")))
12253 (build-system r-build-system)
12254 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12255 (home-page "https://github.com/jonclayden/RNifti")
12256 (synopsis "Fast R and C++ access to NIfTI images")
12258 "This package provides very fast read and write access to images stored
12259 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
12260 compiled C and interpreted R code. It also provides a C/C++ API that can be
12261 used by other packages.")
12262 (license license:gpl2)))
12264 (define-public r-shades
12271 (uri (cran-uri "shades" version))
12274 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
12275 (build-system r-build-system)
12276 (home-page "https://github.com/jonclayden/shades")
12277 (synopsis "Simple color manipulation")
12279 "This package provides functions for easily manipulating colors,
12280 creating color scales and calculating color distances.")
12281 (license license:bsd-3)))
12283 (define-public r-ore
12290 (uri (cran-uri "ore" version))
12292 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
12293 (build-system r-build-system)
12294 (home-page "https://github.com/jonclayden/ore")
12295 (synopsis "R interface to the Onigmo regular expression library")
12297 "This package provides an alternative to R's built-in functionality for
12298 handling regular expressions, based on the Onigmo library. It offers
12299 first-class compiled regex objects, partial matching and function-based
12300 substitutions, amongst other features.")
12301 (license license:bsd-3)))
12303 (define-public r-reportr
12310 (uri (cran-uri "reportr" version))
12313 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
12314 (build-system r-build-system)
12315 (propagated-inputs `(("r-ore" ,r-ore)))
12316 (home-page "https://github.com/jonclayden/reportr")
12317 (synopsis "General message and error reporting system")
12319 "This package provides a system for reporting messages, which offers
12320 certain useful features over the standard R system, such as the incorporation
12321 of output consolidation, message filtering, assertions, expression
12322 substitution, automatic generation of stack traces for debugging, and
12323 conditional reporting based on the current \"output level\".")
12324 (license license:gpl2)))
12326 (define-public r-tractor-base
12328 (name "r-tractor-base")
12329 (version "3.3.3.1")
12333 (uri (cran-uri "tractor.base" version))
12336 "0w5jw7pf77npkgig7667yikpbwv4dfk1dcq63qm88l409ga2f95p"))))
12337 (properties `((upstream-name . "tractor.base")))
12338 (build-system r-build-system)
12341 ("r-reportr" ,r-reportr)
12342 ("r-rnifti" ,r-rnifti)
12343 ("r-shades" ,r-shades)))
12344 (home-page "https://www.tractor-mri.org.uk")
12345 (synopsis "Read, manipulate and visualize magnetic resonance images")
12347 "This package provides functions for working with magnetic resonance
12348 images. It supports reading and writing of popular file formats (DICOM,
12349 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
12350 visualization; flexible image manipulation; metadata and sparse image
12352 (license license:gpl2)))
12354 (define-public r-grimport
12356 (name "r-grimport")
12361 (uri (cran-uri "grImport" version))
12364 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
12365 (properties `((upstream-name . "grImport")))
12366 (build-system r-build-system)
12368 `(("ghostscript" ,ghostscript)))
12370 `(("r-xml" ,r-xml)))
12371 (home-page "https://cran.r-project.org/web/packages/grImport")
12372 (synopsis "Convert, import, and draw PostScript pictures")
12374 "This package provides functions for converting, importing, and drawing
12375 PostScript pictures in R plots.")
12376 (license license:gpl2+)))
12378 (define-public r-grimport2
12380 (name "r-grimport2")
12385 (uri (cran-uri "grImport2" version))
12388 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
12389 (properties `((upstream-name . "grImport2")))
12390 (build-system r-build-system)
12392 `(("r-base64enc" ,r-base64enc)
12396 (home-page "https://cran.r-project.org/web/packages/grImport2/")
12397 (synopsis "Import SVG graphics")
12399 "This package provides functions for importing external vector images and
12400 drawing them as part of R plots. This package is different from the
12401 @code{grImport} package because, where that package imports PostScript format
12402 images, this package imports SVG format images. Furthermore, this package
12403 imports a specific subset of SVG, so external images must be preprocessed
12404 using a package like @code{rsvg} to produce SVG that this package can import.
12405 SVG features that are not supported by R graphics, such as gradient fills, can
12406 be imported and then exported via the @code{gridSVG} package.")
12407 (license license:gpl2+)))
12409 (define-public r-kohonen
12416 (uri (cran-uri "kohonen" version))
12419 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
12420 (build-system r-build-system)
12422 `(("r-rcpp" ,r-rcpp)))
12423 (home-page "https://cran.r-project.org/web/packages/kohonen")
12424 (synopsis "Supervised and unsupervised self-organising maps")
12426 "This package provides functions to train @dfn{self-organising
12427 maps} (SOMs). Also interrogation of the maps and prediction using trained
12428 maps are supported. The name of the package refers to Teuvo Kohonen, the
12429 inventor of the SOM.")
12430 (license license:gpl2+)))
12432 (define-public r-nnls
12439 (uri (cran-uri "nnls" version))
12442 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
12443 (build-system r-build-system)
12444 (native-inputs `(("gfortran" ,gfortran)))
12445 (home-page "https://cran.r-project.org/web/packages/nnls")
12446 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
12448 "This package provides an R interface to the Lawson-Hanson implementation
12449 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
12450 the combination of non-negative and non-positive constraints.")
12451 (license license:gpl2+)))
12453 (define-public r-iso
12456 (version "0.0-18.1")
12460 (uri (cran-uri "Iso" version))
12463 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
12464 (properties `((upstream-name . "Iso")))
12465 (build-system r-build-system)
12466 (native-inputs `(("gfortran" ,gfortran)))
12467 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
12468 (synopsis "Functions to perform isotonic regression")
12470 "This package provides support for linear order and unimodal
12471 order (univariate) isotonic regression and bivariate isotonic regression with
12472 linear order on both variables.")
12473 (license license:gpl2+)))
12475 (define-public r-chemometricswithr
12477 (name "r-chemometricswithr")
12482 (uri (cran-uri "ChemometricsWithR" version))
12485 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
12487 `((upstream-name . "ChemometricsWithR")))
12488 (build-system r-build-system)
12490 `(("r-devtools" ,r-devtools)
12491 ("r-kohonen" ,r-kohonen)
12494 (home-page "https://github.com/rwehrens/CWR")
12495 (synopsis "Chemometrics with R")
12497 "This package provides functions and scripts used in the book
12498 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
12499 Life Sciences\" by Ron Wehrens, Springer (2011).")
12500 (license license:gpl2+)))
12502 (define-public r-als
12509 (uri (cran-uri "ALS" version))
12512 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
12513 (properties `((upstream-name . "ALS")))
12514 (build-system r-build-system)
12517 ("r-nnls" ,r-nnls)))
12518 (home-page "https://cran.r-project.org/web/packages/ALS")
12519 (synopsis "Multivariate curve resolution alternating least squares")
12521 "Alternating least squares is often used to resolve components
12522 contributing to data with a bilinear structure; the basic technique may be
12523 extended to alternating constrained least squares. This package provides an
12524 implementation of @dfn{multivariate curve resolution alternating least
12525 squares} (MCR-ALS).
12527 Commonly applied constraints include unimodality, non-negativity, and
12528 normalization of components. Several data matrices may be decomposed
12529 simultaneously by assuming that one of the two matrices in the bilinear
12530 decomposition is shared between datasets.")
12531 (license license:gpl2+)))
12533 (define-public r-strucchange
12535 (name "r-strucchange")
12540 (uri (cran-uri "strucchange" version))
12543 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
12544 (build-system r-build-system)
12546 `(("r-sandwich" ,r-sandwich)
12548 (home-page "https://cran.r-project.org/web/packages/strucchange")
12549 (synopsis "Testing, monitoring, and dating structural changes")
12551 "This package provides tools for testing, monitoring and dating
12552 structural changes in (linear) regression models. It features tests/methods
12553 from the generalized fluctuation test framework as well as from the F
12554 test (Chow test) framework. This includes methods to fit, plot and test
12555 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
12556 statistics, respectively. It is possible to monitor incoming data online
12557 using fluctuation processes. Finally, the breakpoints in regression models
12558 with structural changes can be estimated together with confidence intervals.
12559 Emphasis is always given to methods for visualizing the data.")
12560 ;; Either of these two GPL versions
12561 (license (list license:gpl2 license:gpl3))))
12563 (define-public r-pixmap
12570 (uri (cran-uri "pixmap" version))
12573 "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9"))))
12574 (build-system r-build-system)
12575 (home-page "https://cran.r-project.org/web/packages/pixmap")
12576 (synopsis "Tools for bitmap images")
12578 "This package provides functions for importing, exporting, plotting and
12579 other manipulations of bitmapped images.")
12580 (license license:gpl2)))
12582 (define-public r-rapidjsonr
12584 (name "r-rapidjsonr")
12589 (uri (cran-uri "rapidjsonr" version))
12592 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
12593 (build-system r-build-system)
12594 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
12595 (synopsis "JSON parser")
12597 "This package provides JSON parsing capability through the Rapidjson
12599 (license license:expat)))
12601 (define-public r-ontologyindex
12603 (name "r-ontologyindex")
12608 (uri (cran-uri "ontologyIndex" version))
12611 "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k"))))
12612 (properties `((upstream-name . "ontologyIndex")))
12613 (build-system r-build-system)
12615 `(("r-knitr" ,r-knitr)))
12616 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
12617 (synopsis "Functions for processing ontologies in R")
12619 "This package provides functions for reading ontologies into R as lists
12620 and manipulating sets of ontological terms.")
12621 (license license:gpl2+)))
12623 (define-public r-gargle
12630 (uri (cran-uri "gargle" version))
12633 "1fykmiv3x8c9ai31r9wr7qcca51h6kqn9cgwbxvxfj15fhwskh4n"))))
12634 (build-system r-build-system)
12639 ("r-jsonlite" ,r-jsonlite)
12640 ("r-rlang" ,r-rlang)
12641 ("r-withr" ,r-withr)))
12643 `(("r-knitr" ,r-knitr)))
12644 (home-page "https://gargle.r-lib.org")
12645 (synopsis "Utilities for working with Google APIs")
12647 "This package provides utilities for working with Google APIs. This
12648 includes functions and classes for handling common credential types and for
12649 preparing, executing, and processing HTTP requests.")
12650 (license license:expat)))
12652 (define-public r-bigrquery
12654 (name "r-bigrquery")
12659 (uri (cran-uri "bigrquery" version))
12662 "16whccv7f94vf57dvbbrhdskz3nnbmpa11a14kp7aynckldlfy0v"))))
12663 (build-system r-build-system)
12665 `(("r-assertthat" ,r-assertthat)
12666 ("r-bit64" ,r-bit64)
12669 ("r-gargle" ,r-gargle)
12672 ("r-jsonlite" ,r-jsonlite)
12673 ("r-prettyunits" ,r-prettyunits)
12674 ("r-progress" ,r-progress)
12675 ("r-rapidjsonr" ,r-rapidjsonr)
12677 ("r-rlang" ,r-rlang)
12678 ("r-tibble" ,r-tibble)))
12679 (home-page "https://github.com/rstats-db/bigrquery")
12680 (synopsis "R interface to Google's BigQuery API")
12682 "This package provides an R interface to Google's BigQuery database.")
12683 (license license:gpl3)))
12685 (define-public r-gmp
12692 (uri (cran-uri "gmp" version))
12695 "03kzbflgpy5sgnzxmhshs5qv7jjmfc113ybkhxys4z8y7xdv9z3b"))))
12696 (build-system r-build-system)
12699 (modify-phases %standard-phases
12700 (add-after 'unpack 'set-CC
12701 (lambda _ (setenv "CC" "gcc") #t)))))
12702 (inputs `(("gmp" ,gmp)))
12703 (home-page "https://cran.r-project.org/web/packages/gmp")
12704 (synopsis "Multiple precision arithmetic")
12706 "This package supports multiple precision arithmetic (big integers and
12707 rationals, prime number tests, matrix computation), \"arithmetic without
12708 limitations\" using the GNU Multiple Precision library.")
12709 ;; Any version of the GPL.
12710 (license license:gpl3+)))
12712 (define-public r-rmpfr
12719 (uri (cran-uri "Rmpfr" version))
12722 "007pc7fpzl2mcg3qxa2vfjip6m2dr314qjsnybkj3kdj70bszxkl"))))
12723 (properties `((upstream-name . "Rmpfr")))
12724 (build-system r-build-system)
12729 `(("r-gmp" ,r-gmp)))
12731 `(("pkg-config" ,pkg-config)))
12732 (home-page "http://rmpfr.r-forge.r-project.org/")
12733 (synopsis "R bindings to the MPFR library")
12735 "This package supports arithmetic (via S4 classes and methods) for
12736 arbitrary precision floating point numbers, including transcendental
12737 functions. To this end, the package interfaces with the @dfn{Multiple
12738 Precision Floating-Point Reliable} (MPFR) library.")
12739 (license license:gpl2+)))
12741 (define-public r-assertive-base
12743 (name "r-assertive-base")
12748 (uri (cran-uri "assertive.base" version))
12751 "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b"))))
12753 `((upstream-name . "assertive.base")))
12754 (build-system r-build-system)
12755 (home-page "https://bitbucket.org/richierocks/assertive.base")
12756 (synopsis "Core of the assertive package")
12758 "This package provides a minimal set of predicates and assertions used by
12759 the assertive package. This is mainly for use by other package developers who
12760 want to include run-time testing features in their own packages.")
12761 (license license:gpl3+)))
12763 (define-public r-assertive-properties
12765 (name "r-assertive-properties")
12770 (uri (cran-uri "assertive.properties" version))
12773 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
12775 `((upstream-name . "assertive.properties")))
12776 (build-system r-build-system)
12778 `(("r-assertive-base" ,r-assertive-base)))
12779 (home-page "https://bitbucket.org/richierocks/assertive.properties")
12780 (synopsis "Assertions to check properties of variables")
12782 "This package provides a set of predicates and assertions for checking
12783 the properties of variables, such as length, names and attributes. This is
12784 mainly for use by other package developers who want to include run-time
12785 testing features in their own packages.")
12786 (license license:gpl3+)))
12788 (define-public r-assertive-numbers
12790 (name "r-assertive-numbers")
12795 (uri (cran-uri "assertive.numbers" version))
12798 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
12800 `((upstream-name . "assertive.numbers")))
12801 (build-system r-build-system)
12803 `(("r-assertive-base" ,r-assertive-base)))
12804 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
12805 (synopsis "Assertions to check properties of numbers")
12807 "This package provides a set of predicates and assertions for checking
12808 the properties of numbers. This is mainly for use by other package developers
12809 who want to include run-time testing features in their own packages.")
12810 (license license:gpl3+)))
12812 (define-public r-assertive-sets
12814 (name "r-assertive-sets")
12819 (uri (cran-uri "assertive.sets" version))
12822 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
12824 `((upstream-name . "assertive.sets")))
12825 (build-system r-build-system)
12827 `(("r-assertive-base" ,r-assertive-base)))
12828 (home-page "https://bitbucket.org/richierocks/assertive.sets")
12829 (synopsis "Assertions to check properties of sets")
12831 "This package provides a set of predicates and assertions for checking
12832 the properties of sets. This is mainly for use by other package developers
12833 who want to include run-time testing features in their own packages.")
12834 (license license:gpl3+)))
12836 (define-public r-assertive-matrices
12838 (name "r-assertive-matrices")
12843 (uri (cran-uri "assertive.matrices" version))
12846 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
12848 `((upstream-name . "assertive.matrices")))
12849 (build-system r-build-system)
12851 `(("r-assertive-base" ,r-assertive-base)))
12852 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
12853 (synopsis "Assertions to check properties of matrices")
12855 "This package provides a set of predicates and assertions for checking
12856 the properties of matrices. This is mainly for use by other package
12857 developers who want to include run-time testing features in their own
12859 (license license:gpl3+)))
12861 (define-public r-assertive-models
12863 (name "r-assertive-models")
12868 (uri (cran-uri "assertive.models" version))
12871 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
12873 `((upstream-name . "assertive.models")))
12874 (build-system r-build-system)
12876 `(("r-assertive-base" ,r-assertive-base)))
12877 (home-page "https://bitbucket.org/richierocks/assertive.models")
12878 (synopsis "Assertions to check properties of models")
12880 "This package provides a set of predicates and assertions for checking
12881 the properties of models. This is mainly for use by other package developers
12882 who want to include run-time testing features in their own packages.")
12883 (license license:gpl3+)))
12885 (define-public r-assertive-reflection
12887 (name "r-assertive-reflection")
12892 (uri (cran-uri "assertive.reflection" version))
12895 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
12897 `((upstream-name . "assertive.reflection")))
12898 (build-system r-build-system)
12900 `(("r-assertive-base" ,r-assertive-base)))
12901 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
12902 (synopsis "Assertions for checking the state of R")
12904 "This package provides a set of predicates and assertions for checking
12905 the state and capabilities of R, the operating system it is running on, and
12906 the IDE being used. This is mainly for use by other package developers who
12907 want to include run-time testing features in their own packages.")
12908 (license license:gpl3+)))
12910 (define-public r-assertive-types
12912 (name "r-assertive-types")
12917 (uri (cran-uri "assertive.types" version))
12920 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
12922 `((upstream-name . "assertive.types")))
12923 (build-system r-build-system)
12925 `(("r-assertive-base" ,r-assertive-base)
12926 ("r-assertive-properties" ,r-assertive-properties)
12927 ("r-codetools" ,r-codetools)))
12928 (home-page "https://bitbucket.org/richierocks/assertive.types")
12929 (synopsis "Assertions to check types of variables")
12931 "This package provides a set of predicates and assertions for checking
12932 the types of variables. This is mainly for use by other package developers
12933 who want to include run-time testing features in their own packages.")
12934 (license license:gpl3+)))
12936 (define-public r-assertive-files
12938 (name "r-assertive-files")
12943 (uri (cran-uri "assertive.files" version))
12946 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
12948 `((upstream-name . "assertive.files")))
12949 (build-system r-build-system)
12951 `(("r-assertive-base" ,r-assertive-base)
12952 ("r-assertive-numbers" ,r-assertive-numbers)))
12953 (home-page "https://bitbucket.org/richierocks/assertive.files")
12954 (synopsis "Assertions to check properties of files")
12956 "This package provides a set of predicates and assertions for checking
12957 the properties of files and connections. This is mainly for use by other
12958 package developers who want to include run-time testing features in their own
12960 (license license:gpl3+)))
12962 (define-public r-assertive-code
12964 (name "r-assertive-code")
12969 (uri (cran-uri "assertive.code" version))
12972 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
12974 `((upstream-name . "assertive.code")))
12975 (build-system r-build-system)
12977 `(("r-assertive-base" ,r-assertive-base)
12978 ("r-assertive-properties" ,r-assertive-properties)
12979 ("r-assertive-types" ,r-assertive-types)))
12980 (home-page "https://bitbucket.org/richierocks/assertive.code")
12981 (synopsis "Assertions to check properties of code")
12983 "This package provides a set of predicates and assertions for checking
12984 the properties of code. This is mainly for use by other package developers
12985 who want to include run-time testing features in their own packages.")
12986 (license license:gpl3+)))
12988 (define-public r-assertive-datetimes
12990 (name "r-assertive-datetimes")
12995 (uri (cran-uri "assertive.datetimes" version))
12998 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
13000 `((upstream-name . "assertive.datetimes")))
13001 (build-system r-build-system)
13003 `(("r-assertive-base" ,r-assertive-base)
13004 ("r-assertive-types" ,r-assertive-types)))
13005 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
13006 (synopsis "Assertions to check properties of dates and times")
13008 "This package provides a set of predicates and assertions for checking
13009 the properties of dates and times. This is mainly for use by other package
13010 developers who want to include run-time testing features in their own
13012 (license license:gpl3+)))
13014 (define-public r-assertive-strings
13016 (name "r-assertive-strings")
13021 (uri (cran-uri "assertive.strings" version))
13024 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
13026 `((upstream-name . "assertive.strings")))
13027 (build-system r-build-system)
13029 `(("r-assertive-base" ,r-assertive-base)
13030 ("r-assertive-types" ,r-assertive-types)
13031 ("r-stringi" ,r-stringi)))
13032 (home-page "https://bitbucket.org/richierocks/assertive.strings")
13033 (synopsis "Assertions to check properties of strings")
13035 "This package provides a set of predicates and assertions for checking
13036 the properties of strings. This is mainly for use by other package developers
13037 who want to include run-time testing features in their own packages.")
13038 (license license:gpl3+)))
13040 (define-public r-assertive-data-us
13042 (name "r-assertive-data-us")
13047 (uri (cran-uri "assertive.data.us" version))
13050 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
13052 `((upstream-name . "assertive.data.us")))
13053 (build-system r-build-system)
13055 `(("r-assertive-base" ,r-assertive-base)
13056 ("r-assertive-strings" ,r-assertive-strings)))
13057 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
13058 (synopsis "Assertions to check properties of strings")
13060 "This package provides a set of predicates and assertions for checking
13061 the properties of US-specific complex data types. This is mainly for use by
13062 other package developers who want to include run-time testing features in
13063 their own packages.")
13064 (license license:gpl3+)))
13066 (define-public r-assertive-data-uk
13068 (name "r-assertive-data-uk")
13073 (uri (cran-uri "assertive.data.uk" version))
13076 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
13078 `((upstream-name . "assertive.data.uk")))
13079 (build-system r-build-system)
13081 `(("r-assertive-base" ,r-assertive-base)
13082 ("r-assertive-strings" ,r-assertive-strings)))
13083 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
13084 (synopsis "Assertions to check properties of strings")
13086 "This package provides a set of predicates and assertions for checking
13087 the properties of UK-specific complex data types. This is mainly for use by
13088 other package developers who want to include run-time testing features in
13089 their own packages.")
13090 (license license:gpl3+)))
13092 (define-public r-assertive-data
13094 (name "r-assertive-data")
13099 (uri (cran-uri "assertive.data" version))
13102 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
13104 `((upstream-name . "assertive.data")))
13105 (build-system r-build-system)
13107 `(("r-assertive-base" ,r-assertive-base)
13108 ("r-assertive-strings" ,r-assertive-strings)))
13109 (home-page "https://bitbucket.org/richierocks/assertive.data")
13110 (synopsis "Assertions to check properties of data")
13112 "This package provides a set of predicates and assertions for checking
13113 the properties of (country independent) complex data types. This is mainly
13114 for use by other package developers who want to include run-time testing
13115 features in their own packages.")
13116 (license license:gpl3+)))
13118 (define-public r-assertive
13120 (name "r-assertive")
13125 (uri (cran-uri "assertive" version))
13128 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
13129 (build-system r-build-system)
13131 `(("r-assertive-base" ,r-assertive-base)
13132 ("r-assertive-code" ,r-assertive-code)
13133 ("r-assertive-data" ,r-assertive-data)
13134 ("r-assertive-data-uk" ,r-assertive-data-uk)
13135 ("r-assertive-data-us" ,r-assertive-data-us)
13136 ("r-assertive-datetimes" ,r-assertive-datetimes)
13137 ("r-assertive-files" ,r-assertive-files)
13138 ("r-assertive-matrices" ,r-assertive-matrices)
13139 ("r-assertive-models" ,r-assertive-models)
13140 ("r-assertive-numbers" ,r-assertive-numbers)
13141 ("r-assertive-properties" ,r-assertive-properties)
13142 ("r-assertive-reflection" ,r-assertive-reflection)
13143 ("r-assertive-sets" ,r-assertive-sets)
13144 ("r-assertive-strings" ,r-assertive-strings)
13145 ("r-assertive-types" ,r-assertive-types)
13146 ("r-knitr" ,r-knitr)))
13148 `(("r-knitr" ,r-knitr)))
13149 (home-page "https://bitbucket.org/richierocks/assertive")
13150 (synopsis "Readable check functions to ensure code integrity")
13152 "This package provides lots of predicates (@code{is_*} functions) to
13153 check the state of your variables, and assertions (@code{assert_*} functions)
13154 to throw errors if they aren't in the right form.")
13155 (license license:gpl3+)))
13157 (define-public r-dotcall64
13159 (name "r-dotcall64")
13164 (uri (cran-uri "dotCall64" version))
13167 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
13168 (properties `((upstream-name . "dotCall64")))
13169 (build-system r-build-system)
13170 (native-inputs `(("gfortran" ,gfortran)))
13171 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
13172 (synopsis "Enhanced foreign function interface supporting long vectors")
13174 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
13175 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
13176 supports long vectors, arguments of type 64-bit integer, and provides a
13177 mechanism to avoid unnecessary copies of read-only and write-only arguments.
13178 This makes it a convenient and fast interface to C/C++ and Fortran code.")
13179 (license license:gpl2+)))
13181 (define-public r-spam
13188 (uri (cran-uri "spam" version))
13190 (base32 "0p5ycvpry955ldrgbbq3syy91wx9425mddpn8r5m9xwlirjxv3v3"))))
13191 (build-system r-build-system)
13193 `(("r-dotcall64" ,r-dotcall64)))
13195 `(("gfortran" ,gfortran)
13196 ("r-knitr" ,r-knitr)))
13197 (home-page "https://www.math.uzh.ch/pages/spam/")
13198 (synopsis "Sparse matrix algebra")
13200 "This package provides a set of functions for sparse matrix algebra.
13201 Differences with other sparse matrix packages are:
13204 @item it only supports (essentially) one sparse matrix format;
13205 @item it is based on transparent and simple structure(s);
13206 @item it is tailored for MCMC calculations within G(M)RF;
13207 @item and it is fast and scalable (with the extension package @code{spam64}).
13209 ;; Either of these licenses
13210 (license (list license:bsd-3 license:lgpl2.0))))
13212 (define-public r-fields
13219 (uri (cran-uri "fields" version))
13221 (base32 "1nsrgkw9w3mwd3sajyzc06h49gg1s0bkq6xh5b66h1n4jbcx2046"))))
13222 (build-system r-build-system)
13224 `(("r-maps" ,r-maps)
13225 ("r-spam" ,r-spam)))
13227 `(("gfortran" ,gfortran)))
13228 (home-page "https://www.image.ucar.edu/fields")
13229 (synopsis "Tools for spatial data")
13231 "This is a package for curve, surface and function fitting with an
13232 emphasis on splines, spatial data and spatial statistics. The major methods
13233 include cubic, and thin plate splines, Kriging, and compactly supported
13234 covariance functions for large data sets.")
13235 (license license:gpl2+)))
13237 (define-public r-spatialextremes
13239 (name "r-spatialextremes")
13244 (uri (cran-uri "SpatialExtremes" version))
13247 "1mhn1c8n3bmgf0fjyac3wji4790zswzkqliqcv3n8kv9806crb0y"))))
13249 `((upstream-name . "SpatialExtremes")))
13250 (build-system r-build-system)
13252 `(("r-fields" ,r-fields)
13253 ("r-maps" ,r-maps)))
13254 (home-page "http://spatialextremes.r-forge.r-project.org/")
13255 (synopsis "Modelling spatial extremes")
13257 "This package provides tools for the statistical modelling of spatial
13258 extremes using max-stable processes, copula or Bayesian hierarchical models.
13259 More precisely, this package allows (conditional) simulations from various
13260 parametric max-stable models, analysis of the extremal spatial dependence, the
13261 fitting of such processes using composite likelihoods or least square (simple
13262 max-stable processes only), model checking and selection and prediction.")
13263 (license license:gpl2+)))
13265 (define-public r-drc
13272 (uri (cran-uri "drc" version))
13275 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
13276 (build-system r-build-system)
13279 ("r-gtools" ,r-gtools)
13281 ("r-multcomp" ,r-multcomp)
13282 ("r-plotrix" ,r-plotrix)
13283 ("r-scales" ,r-scales)))
13284 (home-page "https://cran.r-project.org/web/packages/drc")
13285 (synopsis "Analysis of dose-response curves")
13287 "This package provides a suite of flexible and versatile model fitting
13288 and after-fitting functions for the analysis of dose-response data.")
13289 (license license:gpl2+)))
13291 (define-public r-rmeta
13298 (uri (cran-uri "rmeta" version))
13301 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
13302 (build-system r-build-system)
13303 (home-page "https://cran.r-project.org/web/packages/rmeta")
13304 (synopsis "Tools for meta-analysis")
13306 "This package provides functions for simple fixed and random effects
13307 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
13308 draws standard summary plots, funnel plots, and computes summaries and tests
13309 for association and heterogeneity.")
13310 (license license:gpl2)))
13312 (define-public r-bootstrap
13314 (name "r-bootstrap")
13319 (uri (cran-uri "bootstrap" version))
13322 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
13323 (build-system r-build-system)
13324 (native-inputs `(("gfortran" ,gfortran)))
13325 (home-page "https://cran.r-project.org/web/packages/bootstrap")
13326 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
13328 "This package provides software and data for the book \"An Introduction
13329 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
13330 This package is primarily provided for projects already based on it, and for
13331 support of the book. New projects should preferentially use the recommended
13332 package \"boot\".")
13333 (license license:bsd-3)))
13335 (define-public r-survivalroc
13337 (name "r-survivalroc")
13342 (uri (cran-uri "survivalROC" version))
13345 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
13346 (properties `((upstream-name . "survivalROC")))
13347 (build-system r-build-system)
13348 (home-page "https://cran.r-project.org/web/packages/survivalROC")
13349 (synopsis "Time-dependent ROC curve estimation from censored survival data")
13351 "Compute time-dependent ROC curve from censored survival data using
13352 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
13353 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
13354 (license license:gpl2+)))
13356 (define-public r-longitudinal
13358 (name "r-longitudinal")
13363 (uri (cran-uri "longitudinal" version))
13366 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
13367 (build-system r-build-system)
13368 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
13369 (home-page "http://strimmerlab.org/software/longitudinal/")
13370 (synopsis "Analysis of multiple time course data")
13372 "This package contains general data structures and functions for
13373 longitudinal data with multiple variables, repeated measurements, and
13374 irregularly spaced time points. It also implements a shrinkage estimator of
13375 dynamical correlation and dynamical covariance.")
13376 (license license:gpl3+)))
13378 (define-public r-genenet
13385 (uri (cran-uri "GeneNet" version))
13388 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
13389 (properties `((upstream-name . "GeneNet")))
13390 (build-system r-build-system)
13392 `(("r-corpcor" ,r-corpcor)
13393 ("r-fdrtool" ,r-fdrtool)
13394 ("r-longitudinal" ,r-longitudinal)))
13395 (home-page "http://strimmerlab.org/software/genenet/")
13396 (synopsis "Modeling and inferring gene networks")
13398 "This package analyzes gene expression (time series) data with focus on
13399 the inference of gene networks. In particular, GeneNet implements the methods
13400 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
13401 for learning large-scale gene association networks (including assignment of
13402 putative directions).")
13403 (license license:gpl3+)))
13405 (define-public r-rbamtools
13407 (name "r-rbamtools")
13408 (version "2.16.17")
13412 (uri (cran-uri "rbamtools" version))
13415 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
13416 (build-system r-build-system)
13417 (inputs `(("zlib" ,zlib)))
13419 `(("r-refgenome" ,r-refgenome)))
13420 (home-page "https://cran.r-project.org/web/packages/rbamtools")
13421 (synopsis "Read and write BAM (binary alignment) files")
13423 "This package provides an R interface to functions of the SAMtools
13425 (license license:artistic2.0)))
13427 (define-public r-protviz
13434 (uri (cran-uri "protViz" version))
13437 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
13438 (properties `((upstream-name . "protViz")))
13439 (build-system r-build-system)
13440 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
13441 (home-page "https://github.com/protViz/protViz/")
13442 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
13444 "This package helps with quality checks, visualizations and analysis of
13445 mass spectrometry data, coming from proteomics experiments. The package is
13446 developed, tested and used at the Functional Genomics Center Zurich, where it
13447 is used mainly for prototyping, teaching, and having fun with proteomics data.
13448 But it can also be used to do data analysis for small scale data sets.")
13449 (license license:gpl3)))
13451 (define-public r-cmprsk
13458 (uri (cran-uri "cmprsk" version))
13460 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
13461 (build-system r-build-system)
13463 `(("r-survival" ,r-survival)))
13465 `(("gfortran" ,gfortran)))
13466 (home-page "https://cran.r-project.org/web/packages/cmprsk")
13467 (synopsis "Subdistribution analysis of competing risks")
13469 "This package provides tool for estimation, testing and regression
13470 modeling of subdistribution functions in competing risks, as described in
13471 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
13472 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
13473 A proportional hazards model for the subdistribution of a competing risk,
13474 JASA, 94:496-509.")
13475 (license license:gpl2+)))
13477 (define-public r-etm
13484 (uri (cran-uri "etm" version))
13487 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
13488 (build-system r-build-system)
13490 `(("r-data-table" ,r-data-table)
13491 ("r-lattice" ,r-lattice)
13493 ("r-rcpparmadillo" ,r-rcpparmadillo)
13494 ("r-survival" ,r-survival)))
13495 (home-page "https://cran.r-project.org/web/packages/etm")
13496 (synopsis "Empirical transition matrix")
13498 "The @dfn{empirical transition matrix} (etm) package estimates
13499 the matrix of transition probabilities for any time-inhomogeneous multistate
13500 model with finite state space using the Aalen-Johansen estimator.")
13501 (license license:expat)))
13503 (define-public r-epi
13510 (uri (cran-uri "Epi" version))
13513 "0wsjvilcivrhy2kh2dcagkzy7bjmfa0sq9xjpv6qb4b0nc0mv089"))))
13514 (properties `((upstream-name . "Epi")))
13515 (build-system r-build-system)
13517 `(("r-cmprsk" ,r-cmprsk)
13518 ("r-data-table" ,r-data-table)
13519 ("r-dplyr" ,r-dplyr)
13522 ("r-matrix" ,r-matrix)
13524 ("r-numderiv" ,r-numderiv)
13526 ("r-purrr" ,r-purrr)
13527 ("r-survival" ,r-survival)
13529 (home-page "https://BendixCarstensen.com/Epi/")
13530 (synopsis "Statistical analysis in epidemiology")
13532 "This package provides functions for demographic and epidemiological
13533 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
13534 particular representation, manipulation and simulation of multistate data -
13535 the Lexis suite of functions, which includes interfaces to the @code{mstate},
13536 @code{etm} and @code{cmprsk} packages. It also contains functions for
13537 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
13538 data and some useful functions for tabulation and plotting, as well as a
13539 number of epidemiological data sets.")
13540 (license license:gpl2)))
13542 (define-public r-ppls
13545 (version "1.6-1.1")
13549 (uri (cran-uri "ppls" version))
13552 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
13553 (build-system r-build-system)
13554 (propagated-inputs `(("r-mass" ,r-mass)))
13555 (home-page "https://cran.r-project.org/web/packages/ppls")
13556 (synopsis "Penalized partial least squares")
13558 "This package contains linear and nonlinear regression methods based on
13559 partial least squares and penalization techniques. Model parameters are
13560 selected via cross-validation, and confidence intervals ans tests for the
13561 regression coefficients can be conducted via jackknifing.")
13562 (license license:gpl2+)))
13564 (define-public r-huge
13567 (version "1.3.4.1")
13571 (uri (cran-uri "huge" version))
13573 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
13574 (build-system r-build-system)
13576 `(("r-igraph" ,r-igraph)
13578 ("r-matrix" ,r-matrix)
13580 ("r-rcppeigen" ,r-rcppeigen)))
13581 (home-page "https://cran.r-project.org/web/packages/huge")
13582 (synopsis "High-dimensional undirected graph estimation")
13584 "This package provides a general framework for high-dimensional
13585 undirected graph estimation. It integrates data preprocessing, neighborhood
13586 screening, graph estimation, and model selection techniques into a pipeline.")
13587 (license license:gpl2)))
13589 (define-public r-parcor
13596 (uri (cran-uri "parcor" version))
13599 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
13600 (build-system r-build-system)
13603 ("r-genenet" ,r-genenet)
13604 ("r-glmnet" ,r-glmnet)
13606 ("r-ppls" ,r-ppls)))
13607 (home-page "https://cran.r-project.org/web/packages/parcor")
13608 (synopsis "Regularized estimation of partial correlation matrices")
13610 "This package estimates the matrix of partial correlations based on
13611 different regularized regression methods: lasso, adaptive lasso, PLS, and
13612 Ridge Regression. In addition, the package provides model selection for
13613 lasso, adaptive lasso and Ridge regression based on cross-validation.")
13614 (license license:gpl2+)))
13616 (define-public r-mcmc
13623 (uri (cran-uri "mcmc" version))
13626 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
13627 (build-system r-build-system)
13628 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
13629 (synopsis "Markov chain Monte Carlo")
13631 "This package simulates continuous distributions of random vectors using
13632 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
13633 function that evaluates the log unnormalized density. Algorithms are random
13634 walk Metropolis algorithm (function @code{metrop}), simulated
13635 tempering (function @code{temper}), and morphometric random walk
13636 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
13637 by change of variable.")
13638 (license license:expat)))
13640 (define-public r-listenv
13647 (uri (cran-uri "listenv" version))
13650 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
13651 (build-system r-build-system)
13653 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13654 (home-page "https://github.com/HenrikBengtsson/listenv")
13655 (synopsis "Environments behaving (almost) as lists")
13657 "This package implements list environments. List environments are
13658 environments that have list-like properties. For instance, the elements of a
13659 list environment are ordered and can be accessed and iterated over using index
13661 (license license:lgpl2.1+)))
13663 (define-public r-globals
13670 (uri (cran-uri "globals" version))
13673 "1wrjiiif6rpc268zz79pvpw33si6n6ffgxdnxmmcracwhb5vqg90"))))
13674 (build-system r-build-system)
13676 `(("r-codetools" ,r-codetools)))
13677 (home-page "https://github.com/HenrikBengtsson/globals")
13678 (synopsis "Identify global objects in R expressions")
13680 "This package provides tools to identify global (\"unknown\" or \"free\")
13681 objects in R expressions by code inspection using various strategies, e.g.
13682 conservative or liberal. The objective of this package is to make it as
13683 simple as possible to identify global objects for the purpose of exporting
13684 them in distributed compute environments.")
13685 (license license:lgpl2.1+)))
13687 (define-public r-parallelly
13689 (name "r-parallelly")
13694 (uri (cran-uri "parallelly" version))
13697 "025whcz55wj9jd73dalkbxh4l2331mqn758glr6hlf472lwf4v1p"))))
13698 (properties `((upstream-name . "parallelly")))
13699 (build-system r-build-system)
13700 (home-page "https://github.com/HenrikBengtsson/parallelly")
13701 (synopsis "Enhancements of the parallel package")
13703 "This package provides utility functions that enhance the @code{parallel}
13704 package and support the built-in parallel backends of the @code{future}
13705 package. For example, @code{availableCores} gives the number of CPU cores
13706 available to your R process as given by R options and environment variables,
13707 including those set by job schedulers on high-performance compute clusters.
13708 If none is set, it will fall back to @code{parallel::detectCores}. Another
13709 example is @code{makeClusterPSOCK}, which is backward compatible with
13710 @code{parallel::makePSOCKcluster} while doing a better job in setting up
13711 remote cluster workers without the need for configuring the firewall to do
13712 port-forwarding to your local computer.")
13713 (license license:lgpl2.1+)))
13715 (define-public r-future
13722 (uri (cran-uri "future" version))
13725 "0bfiy17n5rghxw0702k0vgpjkk13268lniifdlx59flf0q16d7lh"))))
13726 (build-system r-build-system)
13728 `(("r-digest" ,r-digest)
13729 ("r-globals" ,r-globals)
13730 ("r-listenv" ,r-listenv)
13731 ("r-parallelly" ,r-parallelly)))
13733 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13734 (home-page "https://github.com/HenrikBengtsson/future")
13735 (synopsis "Unified parallel and distributed processing in R")
13737 "The purpose of this package is to provide a lightweight and unified
13738 Future API for sequential and parallel processing of R expression via futures.
13739 This package implements sequential, multicore, multisession, and cluster
13740 futures. With these, R expressions can be evaluated on the local machine, in
13741 parallel a set of local machines, or distributed on a mix of local and remote
13742 machines. Extensions to this package implement additional backends for
13743 processing futures via compute cluster schedulers etc. Because of its unified
13744 API, there is no need to modify any code in order to switch from sequential on
13745 the local machine to, say, distributed processing on a remote compute cluster.")
13746 (license license:lgpl2.1+)))
13748 (define-public r-future-apply
13750 (name "r-future-apply")
13755 (uri (cran-uri "future.apply" version))
13758 "1ns5cf80vyabvyz9qp6kpvkg4jycinn7x6v7x6692fgjapdnmyig"))))
13759 (properties `((upstream-name . "future.apply")))
13760 (build-system r-build-system)
13762 `(("r-future" ,r-future)
13763 ("r-globals" ,r-globals)))
13765 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13766 (home-page "https://github.com/HenrikBengtsson/future.apply")
13767 (synopsis "Apply function to elements in parallel using futures")
13769 "This package provides implementations of @code{apply()},
13770 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
13771 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
13772 can be resolved using any future-supported backend, e.g. parallel on the local
13773 machine or distributed on a compute cluster.")
13774 (license license:gpl2+)))
13776 (define-public r-rsvd
13783 (uri (cran-uri "rsvd" version))
13786 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
13787 (build-system r-build-system)
13789 `(("r-matrix" ,r-matrix)))
13790 (home-page "https://github.com/erichson/rSVD")
13791 (synopsis "Randomized singular value decomposition")
13793 "Low-rank matrix decompositions are fundamental tools and widely used for
13794 data analysis, dimension reduction, and data compression. Classically, highly
13795 accurate deterministic matrix algorithms are used for this task. However, the
13796 emergence of large-scale data has severely challenged our computational
13797 ability to analyze big data. The concept of randomness has been demonstrated
13798 as an effective strategy to quickly produce approximate answers to familiar
13799 problems such as the @dfn{singular value decomposition} (SVD). This package
13800 provides several randomized matrix algorithms such as the randomized singular
13801 value decomposition (@code{rsvd}), randomized principal component
13802 analysis (@code{rpca}), randomized robust principal component
13803 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
13804 and the randomized CUR decomposition (@code{rcur}). In addition several plot
13805 functions are provided.")
13806 (license license:gpl3+)))
13808 (define-public r-sloop
13815 (uri (cran-uri "sloop" version))
13818 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
13819 (build-system r-build-system)
13821 `(("r-codetools" ,r-codetools)
13822 ("r-crayon" ,r-crayon)
13823 ("r-purrr" ,r-purrr)
13824 ("r-rlang" ,r-rlang)
13825 ("r-tibble" ,r-tibble)))
13826 (home-page "https://github.com/r-lib/sloop")
13827 (synopsis "Helpers for object-oriented programming in R")
13829 "This package provides a collection of helper functions designed to
13830 help you to better understand object oriented programming in R, particularly
13832 (license license:gpl3)))
13834 (define-public r-capushe
13841 (uri (cran-uri "capushe" version))
13844 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
13845 (build-system r-build-system)
13846 (propagated-inputs `(("r-mass" ,r-mass)))
13847 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
13848 (synopsis "Calibrating penalties using slope heuristics")
13850 "This package provides tools for the calibration of penalized criteria
13851 for model selection. The calibration methods available are based on the slope
13853 (license license:gpl2+)))
13855 (define-public r-dorng
13862 (uri (cran-uri "doRNG" version))
13865 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
13866 (properties `((upstream-name . "doRNG")))
13867 (build-system r-build-system)
13869 `(("r-foreach" ,r-foreach)
13870 ("r-iterators" ,r-iterators)
13871 ("r-rngtools" ,r-rngtools)))
13872 (home-page "https://renozao.github.io/doRNG/")
13873 (synopsis "Generic reproducible parallel backend for foreach loops")
13875 "This package provides functions to perform reproducible parallel
13876 @code{foreach} loops, using independent random streams as generated by
13877 L'Ecuyer's combined multiple-recursive generator. It enables to easily
13878 convert standard @code{%dopar%} loops into fully reproducible loops,
13879 independently of the number of workers, the task scheduling strategy, or the
13880 chosen parallel environment and associated foreach backend.")
13881 (license license:gpl2+)))
13883 (define-public r-blockmodeling
13885 (name "r-blockmodeling")
13890 (uri (cran-uri "blockmodeling" version))
13893 "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i"))))
13894 (build-system r-build-system)
13896 `(("r-matrix" ,r-matrix)))
13897 (native-inputs `(("gfortran" ,gfortran)))
13898 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
13899 (synopsis "Generalized and classical blockmodeling of valued networks")
13901 "This package is primarily meant as an implementation of generalized
13902 blockmodeling for valued networks. In addition, measures of similarity or
13903 dissimilarity based on structural equivalence and regular equivalence (REGE
13904 algorithms) can be computed and partitioned matrices can be plotted.")
13905 (license license:gpl2+)))
13907 (define-public r-upsetr
13914 (uri (cran-uri "UpSetR" version))
13917 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
13918 (properties `((upstream-name . "UpSetR")))
13919 (build-system r-build-system)
13921 `(("r-ggplot2" ,r-ggplot2)
13922 ("r-gridextra" ,r-gridextra)
13924 ("r-scales" ,r-scales)))
13925 (home-page "https://github.com/hms-dbmi/UpSetR")
13926 (synopsis "Visualize intersecting sets")
13928 "This package provides a more scalable alternative to Venn and Euler
13929 diagrams for visualizing intersecting sets. Create visualizations of
13930 intersecting sets using a novel matrix design, along with visualizations of
13931 several common set, element and attribute related tasks.")
13932 (license license:expat)))
13934 ;; This package includes a JavaScript file, which is not minified. When
13935 ;; upgrading please check that there are no new minified JavaScript files.
13936 (define-public r-shinybs
13943 (uri (cran-uri "shinyBS" version))
13946 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
13947 (properties `((upstream-name . "shinyBS")))
13948 (build-system r-build-system)
13949 ;; The tests spawn Shiny browser apps. They cannot be run
13950 ;; non-interactively.
13951 (arguments '(#:tests? #f))
13953 `(("r-htmltools" ,r-htmltools)
13954 ("r-shiny" ,r-shiny)))
13955 (home-page "https://ebailey78.github.io/shinyBS/")
13956 (synopsis "Twitter Bootstrap components for Shiny")
13958 "This package adds additional Twitter Bootstrap components to Shiny.")
13959 (license license:gpl3)))
13961 (define-public r-shinyjqui
13963 (name "r-shinyjqui")
13968 (uri (cran-uri "shinyjqui" version))
13971 "0n4ijxmkp8x6dwrsxwvx0zgd8b5129cmn6q6rrav38v1q5k8889x"))
13974 (delete-file "inst/www/shinyjqui.min.js")))))
13975 (properties `((upstream-name . "shinyjqui")))
13976 (build-system r-build-system)
13979 (modify-phases %standard-phases
13980 (add-after 'unpack 'process-javascript
13981 (lambda* (#:key inputs #:allow-other-keys)
13982 (with-directory-excursion "inst/www/"
13983 (let ((source "shinyjqui.js")
13984 (target "shinyjqui.min.js"))
13985 (format #true "Processing ~a --> ~a~%"
13987 (invoke "esbuild" source "--minify"
13988 (string-append "--outfile=" target)))))))))
13990 `(("r-htmltools" ,r-htmltools)
13991 ("r-htmlwidgets" ,r-htmlwidgets)
13992 ("r-jsonlite" ,r-jsonlite)
13993 ("r-shiny" ,r-shiny)))
13995 `(("r-knitr" ,r-knitr)
13996 ("esbuild" ,esbuild)))
13997 (home-page "https://github.com/yang-tang/shinyjqui")
13998 (synopsis "jQuery UI interactions and effects for Shiny")
14000 "This is an extension to Shiny that brings interactions and animation
14001 effects from the jQuery UI library.")
14002 (license license:expat)))
14004 (define-public r-outliers
14006 (name "r-outliers")
14011 (uri (cran-uri "outliers" version))
14014 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
14015 (build-system r-build-system)
14016 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
14017 (synopsis "Tests for outliers")
14019 "This package provides a collection of some tests commonly used for
14020 identifying outliers.")
14021 (license license:gpl2+)))
14023 (define-public r-bayesm
14030 (uri (cran-uri "bayesm" version))
14032 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
14033 (build-system r-build-system)
14035 `(("r-rcpp" ,r-rcpp)
14036 ("r-rcpparmadillo" ,r-rcpparmadillo)))
14037 (home-page "http://www.perossi.org/home/bsm-1")
14038 (synopsis "Bayesian inference for marketing/micro-econometrics")
14040 "This package covers many important models used in marketing and
14041 micro-econometrics applications, including Bayes Regression (univariate or
14042 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
14043 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
14044 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
14045 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
14046 Estimation with normal base, Hierarchical Linear Models with normal prior and
14047 covariates, Hierarchical Linear Models with a mixture of normals prior and
14048 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
14049 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
14050 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
14051 analysis of choice-based conjoint data, Bayesian treatment of linear
14052 instrumental variables models, Analysis of Multivariate Ordinal survey data
14053 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
14054 Coefficient Logit Models.")
14055 (license license:gpl2+)))
14057 (define-public r-tensora
14064 (uri (cran-uri "tensorA" version))
14067 "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf"))))
14068 (properties `((upstream-name . "tensorA")))
14069 (build-system r-build-system)
14070 (home-page "http://www.stat.boogaart.de/tensorA")
14071 (synopsis "Advanced tensor arithmetic with named indices")
14073 "This package provides convenience functions for advanced linear algebra
14074 with tensors and computation with datasets of tensors on a higher level
14075 abstraction. It includes Einstein and Riemann summing conventions, dragging,
14076 co- and contravariate indices, and parallel computations on sequences of
14078 (license license:gpl2+)))
14080 (define-public r-rarpack
14087 (uri (cran-uri "rARPACK" version))
14090 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
14091 (properties `((upstream-name . "rARPACK")))
14092 (build-system r-build-system)
14093 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
14094 (home-page "https://github.com/yixuan/rARPACK")
14095 (synopsis "Solvers for large scale eigenvalue and SVD problems")
14097 "This package was previously an R wrapper of the ARPACK library, and now
14098 a shell of the R package RSpectra, an R interface to the Spectra library for
14099 solving large scale eigenvalue/vector problems. The current version of
14100 rARPACK simply imports and exports the functions provided by RSpectra. New
14101 users of rARPACK are advised to switch to the RSpectra package.")
14102 (license license:bsd-3)))
14104 (define-public r-compositions
14106 (name "r-compositions")
14111 (uri (cran-uri "compositions" version))
14114 "03qslsfx11gshls901zlhw47prd55mf16w4mkmd8x1dgiwq938l4"))))
14115 (build-system r-build-system)
14117 `(("r-bayesm" ,r-bayesm)
14119 ("r-robustbase" ,r-robustbase)
14120 ("r-tensora" ,r-tensora)))
14122 `(("r-knitr" ,r-knitr)))
14123 (home-page "http://www.stat.boogaart.de/compositions")
14124 (synopsis "Compositional data analysis")
14126 "This package provides functions for the consistent analysis of
14127 compositional data (e.g. portions of substances) and positive
14128 numbers (e.g. concentrations).")
14129 (license license:gpl2+)))
14131 (define-public r-cobs
14138 (uri (cran-uri "cobs" version))
14141 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
14142 (build-system r-build-system)
14144 `(("r-quantreg" ,r-quantreg)
14145 ("r-sparsem" ,r-sparsem)))
14146 (home-page "https://cran.r-project.org/web/packages/cobs")
14147 (synopsis "Constrained B-Splines (sparse matrix based)")
14149 "This package provides qualitatively constrained (regression) smoothing
14150 splines via linear programming and sparse matrices.")
14151 (license license:gpl2+)))
14153 (define-public r-drimpute
14155 (name "r-drimpute")
14160 (uri (cran-uri "DrImpute" version))
14163 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
14164 (properties `((upstream-name . "DrImpute")))
14165 (build-system r-build-system)
14167 `(("r-rcpp" ,r-rcpp)
14168 ("r-rcpparmadillo" ,r-rcpparmadillo)))
14169 (home-page "https://github.com/ikwak2/DrImpute")
14170 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
14172 "This is an R package for imputing dropout events. Many statistical
14173 methods in cell type identification, visualization and lineage reconstruction
14174 do not account for dropout events. DrImpute can improve the performance of
14175 such software by imputing dropout events.")
14176 (license license:gpl3)))
14178 (define-public r-gamlss-dist
14180 (name "r-gamlss-dist")
14185 (uri (cran-uri "gamlss.dist" version))
14187 (base32 "0nzgq3rnziy0i2zxn88hqy3pakpyin2m2csk9j3zg39si66c6wcq"))))
14188 (properties `((upstream-name . "gamlss.dist")))
14189 (build-system r-build-system)
14190 (propagated-inputs `(("r-mass" ,r-mass)))
14191 (home-page "http://www.gamlss.org/")
14192 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
14194 "This package provides a set of distributions which can be used for
14195 modelling the response variables in Generalized Additive Models for Location
14196 Scale and Shape. The distributions can be continuous, discrete or mixed
14197 distributions. Extra distributions can be created, by transforming, any
14198 continuous distribution defined on the real line, to a distribution defined on
14199 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
14200 transformation, respectively.")
14201 ;; Either version of the GPL.
14202 (license (list license:gpl2 license:gpl3))))
14204 ;; This package includes JavaScript files, which are not minified. When
14205 ;; upgrading please check that there are no new minified JavaScript files.
14206 (define-public r-shinyjs
14213 (uri (cran-uri "shinyjs" version))
14216 "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2"))))
14217 (build-system r-build-system)
14219 `(("r-digest" ,r-digest)
14220 ("r-htmltools" ,r-htmltools)
14221 ("r-jsonlite" ,r-jsonlite)
14222 ("r-shiny" ,r-shiny)))
14224 `(("r-knitr" ,r-knitr)))
14225 (home-page "https://deanattali.com/shinyjs")
14226 (synopsis "Improve the user experience of your Shiny apps")
14228 "Perform common useful JavaScript operations in Shiny apps that will
14229 greatly improve your apps without having to know any JavaScript. Examples
14230 include: hiding an element, disabling an input, resetting an input back to its
14231 original value, delaying code execution by a few seconds, and many more useful
14232 functions for both the end user and the developer. Shinyjs can also be used
14233 to easily call your own custom JavaScript functions from R.")
14234 (license license:agpl3+)))
14236 ;; This package includes minified JavaScript files. When upgrading please
14237 ;; check that there are no new minified JavaScript files.
14238 (define-public r-colourpicker
14240 (name "r-colourpicker")
14245 (uri (cran-uri "colourpicker" version))
14248 "1qjispj7i12m02js5cm5xlgn5lyff0kc5ybz6lbknz8q5lkbdyrd"))))
14249 (build-system r-build-system)
14251 `(#:modules ((guix build utils)
14252 (guix build r-build-system)
14256 (modify-phases %standard-phases
14257 (add-after 'unpack 'process-javascript
14258 (lambda* (#:key inputs #:allow-other-keys)
14259 (with-directory-excursion "inst"
14263 `((,(assoc-ref inputs "js-salvattore")
14264 "examples/colourInput/www/salvattore.min.js")
14265 (,(assoc-ref inputs "js-jquery")
14266 "htmlwidgets/lib/jquery/jquery.min.js")
14267 ("www/shared/colourpicker/js/colourpicker.js"
14268 "www/shared/colourpicker/js/colourpicker.min.js"))))
14269 (lambda (sources targets)
14270 (for-each (lambda (source target)
14271 (format #t "Processing ~a --> ~a~%"
14273 (delete-file target)
14274 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14275 (call-with-output-file target
14277 (dump-port minified port)))))
14278 sources targets))))
14281 `(("r-ggplot2" ,r-ggplot2)
14282 ("r-htmltools" ,r-htmltools)
14283 ("r-htmlwidgets" ,r-htmlwidgets)
14284 ("r-jsonlite" ,r-jsonlite)
14285 ("r-miniui" ,r-miniui)
14286 ("r-shiny" ,r-shiny)
14287 ("r-shinyjs" ,r-shinyjs)))
14289 `(("r-knitr" ,r-knitr)
14290 ("uglify-js" ,uglify-js)
14294 (uri "https://code.jquery.com/jquery-3.3.1.js")
14297 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
14301 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
14304 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
14305 (home-page "https://github.com/daattali/colourpicker")
14306 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
14308 "This package provides a color picker that can be used as an input in
14309 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
14310 custom color palettes, and many more options. A plot color helper tool is
14311 available as an RStudio Addin, which helps you pick colors to use in your
14312 plots. A more generic color picker RStudio Addin is also provided to let you
14313 select colors to use in your R code.")
14314 (license license:expat)))
14316 (define-public r-ggextra
14323 (uri (cran-uri "ggExtra" version))
14326 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
14327 (properties `((upstream-name . "ggExtra")))
14328 (build-system r-build-system)
14330 `(("r-colourpicker" ,r-colourpicker)
14331 ("r-ggplot2" ,r-ggplot2)
14332 ("r-gtable" ,r-gtable)
14333 ("r-miniui" ,r-miniui)
14335 ("r-scales" ,r-scales)
14336 ("r-shiny" ,r-shiny)
14337 ("r-shinyjs" ,r-shinyjs)))
14339 `(("r-knitr" ,r-knitr)))
14340 (home-page "https://github.com/daattali/ggExtra")
14341 (synopsis "Marginal histograms for ggplot2 and other enhancements")
14343 "This package is a collection of functions and layers to enhance ggplot2.
14344 The flagship function is @code{ggMarginal()}, which can be used to add
14345 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
14346 (license license:expat)))
14348 (define-public r-minpack-lm
14350 (name "r-minpack-lm")
14355 (uri (cran-uri "minpack.lm" version))
14358 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
14359 (properties `((upstream-name . "minpack.lm")))
14360 (build-system r-build-system)
14361 (native-inputs `(("gfortran" ,gfortran)))
14362 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
14363 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
14365 "The @code{nls.lm} function provides an R interface to @code{lmder} and
14366 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
14367 problems by a modification of the Levenberg-Marquardt algorithm, with support
14368 for lower and upper parameter bounds. The implementation can be used via
14369 @code{nls}-like calls using the @code{nlsLM} function.")
14370 (license license:gpl3)))
14372 (define-public r-moments
14379 (uri (cran-uri "moments" version))
14382 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
14383 (build-system r-build-system)
14384 (home-page "https://cran.r-project.org/web/packages/moments")
14385 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
14387 "This package provides functions to calculate: moments, Pearson's
14388 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
14389 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
14390 (license license:gpl2+)))
14392 (define-public r-msir
14399 (uri (cran-uri "msir" version))
14402 "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84"))))
14403 (build-system r-build-system)
14405 `(("r-mclust" ,r-mclust)))
14407 `(("r-knitr" ,r-knitr)))
14408 (home-page "https://cran.r-project.org/web/packages/msir")
14409 (synopsis "Model-based sliced inverse regression")
14411 "This is an R package for dimension reduction based on finite Gaussian
14412 mixture modeling of inverse regression.")
14413 (license license:gpl2+)))
14415 (define-public r-pbivnorm
14417 (name "r-pbivnorm")
14422 (uri (cran-uri "pbivnorm" version))
14425 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
14426 (build-system r-build-system)
14427 (native-inputs `(("gfortran" ,gfortran)))
14428 (home-page "https://github.com/brentonk/pbivnorm")
14429 (synopsis "Vectorized bivariate normal CDF")
14431 "This package provides a vectorized R function for calculating
14432 probabilities from a standard bivariate normal CDF.")
14433 (license license:gpl2+)))
14435 (define-public r-lavaan
14442 (uri (cran-uri "lavaan" version))
14445 "0ks62wrwghbm1brzmqvr92h5n1295dpc87m1g3xrfx0mkdaqdcdk"))))
14446 (build-system r-build-system)
14448 `(("r-mass" ,r-mass)
14449 ("r-mnormt" ,r-mnormt)
14450 ("r-numderiv" ,r-numderiv)
14451 ("r-pbivnorm" ,r-pbivnorm)))
14452 (home-page "https://lavaan.ugent.be")
14453 (synopsis "Latent variable analysis")
14455 "This package provides tools to fit a variety of latent variable models,
14456 including confirmatory factor analysis, structural equation modeling and
14457 latent growth curve models.")
14458 (license license:gpl2+)))
14460 (define-public r-nonnest2
14462 (name "r-nonnest2")
14467 (uri (cran-uri "nonnest2" version))
14470 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
14471 (build-system r-build-system)
14473 `(("r-compquadform" ,r-compquadform)
14474 ("r-lavaan" ,r-lavaan)
14475 ("r-mvtnorm" ,r-mvtnorm)
14476 ("r-sandwich" ,r-sandwich)))
14478 `(("r-knitr" ,r-knitr)))
14479 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
14480 (synopsis "Tests of non-nested models")
14482 "This package allows for testing of non-nested models. It includes tests
14483 of model distinguishability and of model fit that can be applied to both
14484 nested and non-nested models. The package also includes functionality to
14485 obtain confidence intervals associated with AIC and BIC.")
14486 ;; Either version of the GPL.
14487 (license (list license:gpl2 license:gpl3))))
14489 (define-public r-penalized
14491 (name "r-penalized")
14496 (uri (cran-uri "penalized" version))
14499 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
14500 (build-system r-build-system)
14502 `(("r-rcpp" ,r-rcpp)
14503 ("r-rcpparmadillo" ,r-rcpparmadillo)
14504 ("r-survival" ,r-survival)))
14505 (home-page "https://cran.r-project.org/web/packages/penalized/")
14506 (synopsis "Penalized estimation in GLMs and in the Cox model")
14508 "This package provides tools for fitting possibly high dimensional
14509 penalized regression models. The penalty structure can be any combination of
14510 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
14511 constraint on the regression coefficients. The supported regression models
14512 are linear, logistic and Poisson regression and the Cox Proportional Hazards
14513 model. Cross-validation routines allow optimization of the tuning
14515 (license license:gpl2+)))
14517 (define-public r-zim
14524 (uri (cran-uri "ZIM" version))
14527 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
14528 (properties `((upstream-name . "ZIM")))
14529 (build-system r-build-system)
14530 (propagated-inputs `(("r-mass" ,r-mass)))
14531 (home-page "https://github.com/biostatstudio/ZIM")
14532 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
14534 "Analyze count time series with excess zeros. Two types of statistical
14535 models are supported: Markov regression and state-space models. They are also
14536 known as observation-driven and parameter-driven models respectively in the
14537 time series literature. The functions used for Markov regression or
14538 observation-driven models can also be used to fit ordinary regression models
14539 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
14540 negative binomial (ZINB) assumption. The package also contains miscellaneous
14541 functions to compute density, distribution, quantile, and generate random
14542 numbers from ZIP and ZINB distributions.")
14543 (license license:gpl3)))
14545 (define-public r-nor1mix
14552 (uri (cran-uri "nor1mix" version))
14555 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
14556 (build-system r-build-system)
14557 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
14558 (synopsis "Normal (1-d) mixture models")
14560 "This package provides S3 classes and methods for one-dimensional normal
14561 mixture models, for, e.g., density estimation or clustering algorithms
14562 research and teaching; it provides the widely used Marron-Wand densities. It
14563 also provides tools for efficient random number generation and graphics.")
14564 (license license:gpl2+)))
14566 (define-public r-beanplot
14568 (name "r-beanplot")
14573 (uri (cran-uri "beanplot" version))
14576 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
14577 (build-system r-build-system)
14578 (home-page "https://cran.r-project.org/web/packages/beanplot/")
14579 (synopsis "Visualization via beanplots")
14581 "This package provides beanplots, an alternative to
14582 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
14584 (license license:gpl2)))
14586 (define-public r-pbdzmq
14593 (uri (cran-uri "pbdZMQ" version))
14596 "1v8iv1pzs4j3ics9k9h4xjkv6z1ma2xbqy003xk2lqax6srqi02d"))))
14597 (properties `((upstream-name . "pbdZMQ")))
14598 (build-system r-build-system)
14600 `(("zeromq" ,zeromq)
14603 `(("pkg-config" ,pkg-config)))
14604 (home-page "https://pbdr.org/")
14605 (synopsis "R interface to ZeroMQ")
14607 "ZeroMQ is a well-known library for high-performance asynchronous
14608 messaging in scalable, distributed applications. This package provides high
14609 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
14610 interactive client/server programming frameworks. A few wrapper functions
14611 compatible with @code{rzmq} are also provided.")
14612 (license license:gpl3)))
14614 (define-public r-repr
14621 (uri (cran-uri "repr" version))
14624 "0qimllv9pn8wsl550bjkp5dkknbmr69j85mrwfbbq75m2ga466sk"))))
14625 (build-system r-build-system)
14627 `(("r-base64enc" ,r-base64enc)
14628 ("r-htmltools" ,r-htmltools)
14629 ("r-jsonlite" ,r-jsonlite)
14630 ("r-pillar" ,r-pillar)))
14631 (home-page "https://cran.r-project.org/web/packages/repr/")
14632 (synopsis "Serializable representations")
14634 "This package provides string and binary representations of objects for
14635 several formats and MIME types.")
14636 (license license:gpl3)))
14638 (define-public r-irdisplay
14640 (name "r-irdisplay")
14645 (uri (cran-uri "IRdisplay" version))
14648 "15jbjrihm1mk899357h9xb08iq3xyagds1xb40fmdpkfcmcfqrw9"))))
14649 (properties `((upstream-name . "IRdisplay")))
14650 (build-system r-build-system)
14652 `(("r-repr" ,r-repr)))
14653 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
14654 (synopsis "Jupyter display machinery")
14656 "This package provides an interface to the rich display capabilities of
14657 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
14658 running IRkernel session.")
14659 (license license:expat)))
14661 (define-public r-irkernel
14663 (name "r-irkernel")
14668 (uri (cran-uri "IRkernel" version))
14671 "1y06v3difaiihxfm2abm88nnjzvkla4p346cm1nxmga4iwb2k8gm"))))
14672 (properties `((upstream-name . "IRkernel")))
14673 (build-system r-build-system)
14676 (modify-phases %standard-phases
14677 (add-after 'install 'install-kernelspec
14678 (lambda* (#:key outputs #:allow-other-keys)
14679 (let ((out (assoc-ref outputs "out")))
14680 (setenv "HOME" "/tmp")
14681 (invoke "jupyter" "kernelspec" "install"
14684 (string-append out "/site-library/IRkernel/kernelspec"))
14685 ;; Record the absolute file name of the 'R' executable in
14687 (substitute* (string-append out "/share/jupyter"
14688 "/kernels/ir/kernel.json")
14690 (string-append "[\"" (which "R") "\",")))
14693 `(("jupyter" ,jupyter)))
14695 `(("r-crayon" ,r-crayon)
14696 ("r-digest" ,r-digest)
14697 ("r-evaluate" ,r-evaluate)
14698 ("r-irdisplay" ,r-irdisplay)
14699 ("r-jsonlite" ,r-jsonlite)
14700 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
14701 ("r-minimal" ,r-minimal)
14702 ("r-pbdzmq" ,r-pbdzmq)
14704 ("r-uuid" ,r-uuid)))
14705 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
14706 (synopsis "Native R kernel for Jupyter")
14708 "The R kernel for the Jupyter environment executes R code which the
14709 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
14711 (license license:expat)))
14713 (define-public r-gmodels
14720 (uri (cran-uri "gmodels" version))
14723 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
14724 (build-system r-build-system)
14726 `(("r-gdata" ,r-gdata)
14727 ("r-mass" ,r-mass)))
14728 (home-page "https://cran.r-project.org/web/packages/gmodels/")
14729 (synopsis "Various R programming tools for model fitting")
14731 "This package provides various R programming tools for model fitting.")
14732 (license license:gpl2)))
14734 (define-public r-apcluster
14736 (name "r-apcluster")
14741 (uri (cran-uri "apcluster" version))
14744 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
14745 (build-system r-build-system)
14747 `(("r-matrix" ,r-matrix)
14748 ("r-rcpp" ,r-rcpp)))
14749 (home-page "https://cran.r-project.org/web/packages/apcluster/")
14750 (synopsis "Affinity propagation clustering")
14752 "This package implements affinity propagation clustering introduced by
14753 Frey and Dueck (2007). The package further provides leveraged affinity
14754 propagation and an algorithm for exemplar-based agglomerative clustering that
14755 can also be used to join clusters obtained from affinity propagation. Various
14756 plotting functions are available for analyzing clustering results.")
14757 (license license:gpl2+)))
14759 (define-public r-valr
14766 (uri (cran-uri "valr" version))
14769 "1vbp89zfylgih5acvw7lcx3a0dbbd7dhq7yhywr7kq02737qykdx"))))
14770 (build-system r-build-system)
14772 `(("r-broom" ,r-broom)
14773 ("r-dplyr" ,r-dplyr)
14774 ("r-ggplot2" ,r-ggplot2)
14776 ("r-readr" ,r-readr)
14777 ("r-rlang" ,r-rlang)
14778 ("r-stringr" ,r-stringr)
14779 ("r-tibble" ,r-tibble)))
14781 `(("r-knitr" ,r-knitr)))
14782 (home-page "https://github.com/rnabioco/valr")
14783 (synopsis "Genome interval arithmetic in R")
14785 "This package enables you to read and manipulate genome intervals and
14786 signals. It provides functionality similar to command-line tool suites within
14787 R, enabling interactive analysis and visualization of genome-scale data.")
14788 (license license:expat)))
14790 (define-public r-rematch2
14792 (name "r-rematch2")
14797 (uri (cran-uri "rematch2" version))
14800 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
14801 (build-system r-build-system)
14803 `(("r-tibble" ,r-tibble)))
14804 (home-page "https://github.com/r-lib/rematch2")
14805 (synopsis "Tidy output from regular expression matching")
14807 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
14808 return the match results in tidy data frames.")
14809 (license license:expat)))
14811 (define-public r-picante
14818 (uri (cran-uri "picante" version))
14821 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
14822 (build-system r-build-system)
14826 ("r-vegan" ,r-vegan)))
14827 (home-page "https://cran.r-project.org/web/packages/picante/")
14828 (synopsis "Integrating phylogenies and ecology")
14830 "This package provides functions for phylocom integration, community
14831 analyses, null-models, traits and evolution. It implements numerous
14832 ecophylogenetic approaches including measures of community phylogenetic and
14833 trait diversity, phylogenetic signal, estimation of trait values for
14834 unobserved taxa, null models for community and phylogeny randomizations, and
14835 utility functions for data input/output and phylogeny plotting. A full
14836 description of package functionality and methods are provided by Kembel et
14838 (license license:gpl2)))
14840 (define-public r-reinforcelearn
14842 (name "r-reinforcelearn")
14847 (uri (cran-uri "reinforcelearn" version))
14850 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
14851 (build-system r-build-system)
14853 `(("r-checkmate" ,r-checkmate)
14855 ("r-purrr" ,r-purrr)
14857 (home-page "https://markusdumke.github.io/reinforcelearn")
14858 (synopsis "Reinforcement learning")
14860 "This package implements reinforcement learning environments and
14861 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
14862 can be used with function approximation, eligibility traces (Singh & Sutton,
14863 1996) and experience replay (Mnih et al., 2013).")
14864 (license license:expat)))
14866 (define-public r-lemon
14873 (uri (cran-uri "lemon" version))
14876 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
14877 (build-system r-build-system)
14879 `(("r-ggplot2" ,r-ggplot2)
14880 ("r-gridextra" ,r-gridextra)
14881 ("r-gtable" ,r-gtable)
14882 ("r-knitr" ,r-knitr)
14883 ("r-lattice" ,r-lattice)
14885 ("r-rlang" ,r-rlang)
14886 ("r-scales" ,r-scales)))
14888 `(("r-knitr" ,r-knitr)))
14889 (home-page "https://github.com/stefanedwards/lemon")
14890 (synopsis "Freshen up your ggplot2 plots")
14892 "This package provides functions for working with legends and axis lines
14893 of ggplot2, facets that repeat axis lines on all panels, and some knitr
14895 (license license:gpl3)))
14897 (define-public r-wgaim
14904 (uri (cran-uri "wgaim" version))
14906 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
14907 (build-system r-build-system)
14909 `(("r-ggplot2" ,r-ggplot2)
14911 (home-page "https://cran.r-project.org/web/packages/wgaim")
14912 (synopsis "Whole genome average interval mapping for QTL detection")
14914 "This package integrates sophisticated mixed modelling methods with a
14915 whole genome approach to detecting significant QTL in linkage maps.")
14916 (license license:gpl2+)))
14918 (define-public r-bedr
14925 (uri (cran-uri "bedr" version))
14928 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
14929 (build-system r-build-system)
14931 `(("r-data-table" ,r-data-table)
14932 ("r-r-utils" ,r-r-utils)
14933 ("r-testthat" ,r-testthat)
14934 ("r-venndiagram" ,r-venndiagram)
14937 ("bedtools" ,bedtools)
14938 ("htslib" ,htslib))) ; for tabix
14940 `(("r-knitr" ,r-knitr))) ; for vignettes
14941 (home-page "https://cran.r-project.org/web/packages/bedr")
14942 (synopsis "Genomic region processing")
14944 "This package is for genomic regions processing using command line tools
14945 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
14946 utilities to perform genome arithmetic e.g indexing, formatting and merging.
14947 The bedr package's API enhances access to these tools as well as offers
14948 additional utilities for genomic regions processing.")
14949 (license license:gpl2)))
14951 (define-public r-sets
14958 (uri (cran-uri "sets" version))
14961 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
14962 (properties `((upstream-name . "sets")))
14963 (build-system r-build-system)
14964 (home-page "https://cran.r-project.org/web/packages/sets")
14965 (synopsis "Sets, generalized sets, customizable sets and intervals")
14967 "This package provides data structures and basic operations for ordinary
14968 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
14969 customizable sets, and intervals.")
14970 (license license:gpl2)))
14972 (define-public r-partitions
14974 (name "r-partitions")
14979 (uri (cran-uri "partitions" version))
14982 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
14983 (build-system r-build-system)
14986 ("r-polynom" ,r-polynom)
14987 ("r-sets" ,r-sets)))
14988 (home-page "https://cran.r-project.org/web/packages/partitions")
14989 (synopsis "Additive partitions of integers")
14991 "This package provides tools to enumerates the partitions, unequal
14992 partitions, and restricted partitions of an integer; the three corresponding
14993 partition functions are also given.")
14994 ;; Any version of the GPL
14995 (license license:gpl2+)))
14997 (define-public r-brobdingnag
14999 (name "r-brobdingnag")
15004 (uri (cran-uri "Brobdingnag" version))
15007 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
15008 (properties `((upstream-name . "Brobdingnag")))
15009 (build-system r-build-system)
15010 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
15011 (synopsis "Very large numbers in R")
15013 "This package handles very large numbers in R. Real numbers are held
15014 using their natural logarithms, plus a logical flag indicating sign. The
15015 package includes a vignette that gives a step-by-step introduction to using S4
15017 ;; Any version of the GPL
15018 (license license:gpl2+)))
15020 (define-public r-untb
15027 (uri (cran-uri "untb" version))
15030 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
15031 (build-system r-build-system)
15033 `(("r-brobdingnag" ,r-brobdingnag)
15034 ("r-partitions" ,r-partitions)
15035 ("r-polynom" ,r-polynom)))
15036 (home-page "https://github.com/RobinHankin/untb.git")
15037 (synopsis "Ecological drift under the UNTB")
15039 "This package provides numerical simulations, and visualizations, of
15040 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
15041 (license license:gpl2+)))
15043 (define-public r-stepwise
15045 (name "r-stepwise")
15050 (uri (cran-uri "stepwise" version))
15053 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
15054 (build-system r-build-system)
15055 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
15056 (synopsis "Stepwise detection of recombination breakpoints")
15058 "This package provides a stepwise approach to identifying recombination
15059 breakpoints in a genomic sequence alignment.")
15060 (license license:gpl2+)))
15062 (define-public r-snpmaxsel
15064 (name "r-snpmaxsel")
15069 (uri (cran-uri "SNPmaxsel" version))
15072 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
15073 (properties `((upstream-name . "SNPmaxsel")))
15074 (build-system r-build-system)
15076 `(("r-combinat" ,r-combinat)
15077 ("r-mvtnorm" ,r-mvtnorm)))
15078 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
15079 (synopsis "Maximally selected statistics for SNP data")
15081 "This package implements asymptotic methods related to maximally selected
15082 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
15084 (license license:gpl2+)))
15086 (define-public r-acsnminer
15088 (name "r-acsnminer")
15089 (version "0.16.8.25")
15092 (uri (cran-uri "ACSNMineR" version))
15095 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
15096 (properties `((upstream-name . "ACSNMineR")))
15097 (build-system r-build-system)
15099 `(("r-ggplot2" ,r-ggplot2)
15100 ("r-gridextra" ,r-gridextra)))
15101 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
15102 (synopsis "Gene enrichment analysis")
15104 "This package provides tools to compute and represent gene set enrichment
15105 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
15106 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
15107 enrichment can be run with hypergeometric test or Fisher exact test, and can
15108 use multiple corrections. Visualization of data can be done either by
15109 barplots or heatmaps.")
15110 (license license:gpl2+)))
15112 (define-public r-seqinr
15119 (uri (cran-uri "seqinr" version))
15122 "1z1jipgrn9nrnxlx7bcf8c2chwpa3kfva0zgyb12xbr3kisn166y"))))
15123 (build-system r-build-system)
15125 `(("r-ade4" ,r-ade4)
15126 ("r-segmented" ,r-segmented)))
15129 (home-page "http://seqinr.r-forge.r-project.org/")
15130 (synopsis "Biological sequences retrieval and analysis")
15132 "This package provides tools for exploratory data analysis and data
15133 visualization of biological sequence (DNA and protein) data. It also includes
15134 utilities for sequence data management under the ACNUC system.")
15135 (license license:gpl2+)))
15137 (define-public r-units
15144 (uri (cran-uri "units" version))
15147 "1rdpbkiqcabz00fqzzs98v89v4cgvcd4pb00pwxzkq6vmwmscwrz"))))
15148 (build-system r-build-system)
15150 `(("udunits" ,udunits)))
15152 `(("r-rcpp" ,r-rcpp)))
15154 `(("r-knitr" ,r-knitr)))
15155 (home-page "https://github.com/r-quantities/units/")
15156 (synopsis "Measurement Units for R Vectors")
15158 "This package provides support for measurement units in R vectors,
15159 matrices and arrays: automatic propagation, conversion, derivation and
15160 simplification of units; raising errors in case of unit incompatibility. It
15161 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
15163 (license license:gpl2)))
15165 (define-public r-udunits2
15167 (name "r-udunits2")
15172 (uri (cran-uri "udunits2" version))
15175 "0yav7rm2afcx67xqrknybxgz7x63w78zyxa0xifvc0k2gz0d6mfi"))))
15176 (properties `((upstream-name . "udunits2")))
15177 (build-system r-build-system)
15179 `(("udunits" ,udunits)))
15180 (home-page "https://cran.r-project.org/package=udunits2")
15181 (synopsis "Udunits-2 bindings for R")
15183 "This package provides simple bindings to Unidata's udunits library.")
15184 (license license:gpl2)))
15186 (define-public r-classint
15188 (name "r-classint")
15193 (uri (cran-uri "classInt" version))
15196 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
15197 (properties `((upstream-name . "classInt")))
15198 (build-system r-build-system)
15200 `(("r-class" ,r-class)
15201 ("r-e1071" ,r-e1071)
15202 ("r-kernsmooth" ,r-kernsmooth)))
15204 `(("gfortran" ,gfortran)
15205 ("r-knitr" ,r-knitr)))
15206 (home-page "https://github.com/r-spatial/classInt/")
15207 (synopsis "Choose univariate class intervals")
15209 "This package provides selected commonly used methods for choosing
15210 univariate class intervals for mapping or other graphics purposes.")
15211 (license license:gpl2+)))
15213 (define-public r-spdata
15220 (uri (cran-uri "spData" version))
15223 "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs"))))
15224 (properties `((upstream-name . "spData")))
15225 (build-system r-build-system)
15227 `(("r-raster" ,r-raster)
15229 (home-page "https://github.com/Nowosad/spData")
15230 (synopsis "Datasets for spatial analysis")
15232 "This a package containing diverse spatial datasets for demonstrating,
15233 benchmarking and teaching spatial data analysis. It includes R data of class
15234 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
15235 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
15236 of the datasets are designed to illustrate specific analysis techniques.
15237 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
15238 illustrate point pattern analysis techniques.")
15239 (license license:cc0)))
15241 (define-public r-learnbayes
15243 (name "r-learnbayes")
15248 (uri (cran-uri "LearnBayes" version))
15251 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
15252 (properties `((upstream-name . "LearnBayes")))
15253 (build-system r-build-system)
15254 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
15255 (synopsis "Functions for learning Bayesian inference")
15257 "This package provides a collection of functions helpful in learning the
15258 basic tenets of Bayesian statistical inference. It contains functions for
15259 summarizing basic one and two parameter posterior distributions and predictive
15260 distributions. It contains MCMC algorithms for summarizing posterior
15261 distributions defined by the user. It also contains functions for regression
15262 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
15264 (license license:gpl2+)))
15266 (define-public r-deldir
15273 (uri (cran-uri "deldir" version))
15276 "0jfwff5kk0zraspsvbk26lphl3fnrc6xmhl4690hr0a5k177ildm"))))
15277 (build-system r-build-system)
15278 (native-inputs `(("gfortran" ,gfortran)))
15279 (home-page "https://cran.r-project.org/web/packages/deldir")
15280 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
15282 "This package provides tools for calculating the Delaunay triangulation
15283 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
15284 of a planar point set. It plots triangulations and tessellations in various
15285 ways, clips tessellations to sub-windows, calculates perimeters of
15286 tessellations, and summarizes information about the tiles of the
15288 (license license:gpl2+)))
15290 (define-public r-sf
15297 (uri (cran-uri "sf" version))
15300 "175fmnnw11fjhfgjv9sn9b0jfjcqbybpgwsvv99d5yddigvw5jja"))))
15301 (build-system r-build-system)
15309 `(("r-classint" ,r-classint)
15311 ("r-magrittr" ,r-magrittr)
15313 ("r-units" ,r-units)))
15315 `(("pkg-config" ,pkg-config)
15316 ("r-knitr" ,r-knitr)))
15317 (home-page "https://github.com/r-spatial/sf/")
15318 (synopsis "Simple features for R")
15320 "This package provides support for simple features, a standardized way to
15321 encode spatial vector data. It binds to GDAL for reading and writing data, to
15322 GEOS for geometrical operations, and to PROJ for projection conversions and
15323 datum transformations.")
15324 ;; Either of these licenses
15325 (license (list license:gpl2 license:expat))))
15327 (define-public r-spdep
15334 (uri (cran-uri "spdep" version))
15337 "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7"))))
15338 (build-system r-build-system)
15340 `(("r-boot" ,r-boot)
15342 ("r-deldir" ,r-deldir)
15344 ("r-gmodels" ,r-gmodels)
15345 ("r-learnbayes" ,r-learnbayes)
15347 ("r-matrix" ,r-matrix)
15351 ("r-spdata" ,r-spdata)))
15353 `(("r-knitr" ,r-knitr)))
15354 (home-page "https://github.com/r-spatial/spdep/")
15355 (synopsis "Spatial dependence: weighting schemes, statistics and models")
15357 "This package provides a collection of functions to create spatial
15358 weights matrix objects from polygon contiguities, from point patterns by
15359 distance and tessellations, for summarizing these objects, and for permitting
15360 their use in spatial data analysis, including regional aggregation by minimum
15362 (license license:gpl2+)))
15364 (define-public r-adegenet
15366 (name "r-adegenet")
15371 (uri (cran-uri "adegenet" version))
15374 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
15375 (build-system r-build-system)
15377 `(("r-ade4" ,r-ade4)
15380 ("r-dplyr" ,r-dplyr)
15381 ("r-ggplot2" ,r-ggplot2)
15382 ("r-igraph" ,r-igraph)
15384 ("r-reshape2" ,r-reshape2)
15385 ("r-seqinr" ,r-seqinr)
15386 ("r-shiny" ,r-shiny)
15387 ("r-spdep" ,r-spdep)
15388 ("r-vegan" ,r-vegan)))
15389 (home-page "https://github.com/thibautjombart/adegenet")
15390 (synopsis "Exploratory analysis of genetic and genomic data")
15392 "This package provides a toolset for the exploration of genetic and
15393 genomic data. Adegenet provides formal (S4) classes for storing and handling
15394 various genetic data, including genetic markers with varying ploidy and
15395 hierarchical population structure (@code{genind} class), alleles counts by
15396 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
15397 also implements original multivariate methods (DAPC, sPCA), graphics,
15398 statistical tests, simulation tools, distance and similarity measures, and
15399 several spatial methods. A range of both empirical and simulated datasets is
15400 also provided to illustrate various methods.")
15401 (license license:gpl2+)))
15403 (define-public r-pegas
15410 (uri (cran-uri "pegas" version))
15412 (base32 "0lr06gajzdanj8ax91kgpxsj863m367v2s1z5gnxps3999n0xybx"))))
15413 (build-system r-build-system)
15415 `(("r-adegenet" ,r-adegenet)
15417 (home-page "http://ape-package.ird.fr/pegas.html")
15418 (synopsis "Population and evolutionary genetics analysis system")
15420 "This package provides functions for reading, writing, plotting,
15421 analysing, and manipulating allelic and haplotypic data, including from VCF
15422 files, and for the analysis of population nucleotide sequences and
15423 micro-satellites including coalescent analyses, linkage disequilibrium,
15424 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
15425 minimum spanning tree and network, and median-joining networks.")
15426 (license license:gpl2+)))
15428 (define-public r-rmetasim
15430 (name "r-rmetasim")
15435 (uri (cran-uri "rmetasim" version))
15438 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
15439 (build-system r-build-system)
15441 `(("r-ade4" ,r-ade4)
15442 ("r-adegenet" ,r-adegenet)
15443 ("r-gtools" ,r-gtools)
15444 ("r-pegas" ,r-pegas)))
15445 (home-page "https://cran.r-project.org/web/packages/rmetasim")
15446 (synopsis "Individual-based population genetic simulation environment")
15448 "This package provides an interface between R and the metasim simulation
15449 engine. The simulation environment is documented in: Strand, A.(2002),
15450 Metasim 1.0: an individual-based environment for simulating population
15451 genetics of complex population dynamics.")
15453 (license license:gpl2+)))
15455 (define-public r-genetics
15457 (name "r-genetics")
15458 (version "1.3.8.1.2")
15462 (uri (cran-uri "genetics" version))
15465 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
15466 (build-system r-build-system)
15468 `(("r-combinat" ,r-combinat)
15469 ("r-gdata" ,r-gdata)
15470 ("r-gtools" ,r-gtools)
15472 ("r-mvtnorm" ,r-mvtnorm)))
15473 (home-page "https://cran.r-project.org/web/packages/genetics/")
15474 (synopsis "Population genetics")
15476 "This package provides classes and methods for handling genetic data.
15477 It includes classes to represent genotypes and haplotypes at single markers up
15478 to multiple markers on multiple chromosomes. Function include allele
15479 frequencies, flagging homo/heterozygotes, flagging carriers of certain
15480 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
15481 and testing for linkage disequilibrium, ...")
15482 ;; Any GPL version.
15483 (license license:gpl2+)))
15485 (define-public r-snp-plotter
15487 (name "r-snp-plotter")
15492 (uri (cran-uri "snp.plotter" version))
15495 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
15496 (properties `((upstream-name . "snp.plotter")))
15497 (build-system r-build-system)
15498 (propagated-inputs `(("r-genetics" ,r-genetics)))
15499 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
15500 (synopsis "Plot p-values using single SNP and/or haplotype data")
15502 "This package helps you create plots of p-values using single SNP and/or
15503 haplotype data. Main features of the package include options to display a
15504 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
15505 datasets simultaneously. Plots can be created using global and/or individual
15506 haplotype p-values along with single SNP p-values. Images are created as
15507 either PDF/EPS files.")
15508 (license license:gpl2+)))
15510 (define-public r-polspline
15512 (name "r-polspline")
15517 (uri (cran-uri "polspline" version))
15519 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
15520 (build-system r-build-system)
15521 (native-inputs `(("gfortran" ,gfortran)))
15522 (home-page "https://cran.r-project.org/web/packages/polspline/")
15523 (synopsis "Polynomial spline routines")
15525 "This package provides routines for the polynomial spline fitting
15526 routines hazard regression, hazard estimation with flexible tails, logspline,
15527 lspec, polyclass, and polymars.")
15528 (license license:gpl2+)))
15530 (define-public r-rms
15537 (uri (cran-uri "rms" version))
15539 (base32 "1zgfd60lzbakcv7x0i5k3lkw3s0xx5bzssjgangna5lq2j17cdli"))))
15540 (build-system r-build-system)
15542 `(("r-cluster" ,r-cluster)
15543 ("r-digest" ,r-digest)
15544 ("r-ggplot2" ,r-ggplot2)
15545 ("r-hmisc" ,r-hmisc)
15546 ("r-htmltable" ,r-htmltable)
15547 ("r-htmltools" ,r-htmltools)
15548 ("r-lattice" ,r-lattice)
15550 ("r-multcomp" ,r-multcomp)
15552 ("r-polspline" ,r-polspline)
15553 ("r-quantreg" ,r-quantreg)
15554 ("r-rpart" ,r-rpart)
15555 ("r-sparsem" ,r-sparsem)
15556 ("r-survival" ,r-survival)))
15557 (native-inputs `(("gfortran" ,gfortran)))
15558 (home-page "http://biostat.mc.vanderbilt.edu/rms")
15559 (synopsis "Regression modeling strategies")
15561 "This is a package for regression modeling, testing, estimation,
15562 validation, graphics, prediction, and typesetting by storing enhanced model
15563 design attributes in the fit. The rms package is a collection of functions
15564 that assist with and streamline modeling. It also contains functions for
15565 binary and ordinal logistic regression models, ordinal models for continuous Y
15566 with a variety of distribution families, and the Buckley-James multiple
15567 regression model for right-censored responses, and implements penalized
15568 maximum likelihood estimation for logistic and ordinary linear models. The
15569 package works with almost any regression model, but it was especially written
15570 to work with binary or ordinal regression models, Cox regression, accelerated
15571 failure time models, ordinary linear models, the Buckley-James model,
15572 generalized least squares for serially or spatially correlated observations,
15573 generalized linear models, and quantile regression.")
15574 (license license:gpl2+)))
15576 (define-public r-arsenal
15583 (uri (cran-uri "arsenal" version))
15586 "13ql3rb79a764ppsc1sqi8glzzkw79la0j2ahzbxgz7cz879sazy"))))
15587 (properties `((upstream-name . "arsenal")))
15588 (build-system r-build-system)
15589 (propagated-inputs `(("r-knitr" ,r-knitr)))
15590 (native-inputs `(("r-knitr" ,r-knitr)))
15591 (home-page "https://github.com/mayoverse/arsenal")
15592 (synopsis "Functions for large-scale statistical summaries")
15594 "This package provides an arsenal of R functions for large-scale
15595 statistical summaries, which are streamlined to work within the latest
15596 reporting tools in R and RStudio and which use formulas and versatile
15597 summary statistics for summary tables and models. The primary functions
15601 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
15602 levels of one or more categorical variables;
15603 @item @code{paired}, a Table-1-like summary of multiple variable types paired
15604 across two time points;
15605 @item @code{modelsum}, which performs simple model fits on one or more
15606 endpoints for many variables (univariate or adjusted for covariates);
15607 @item @code{freqlist}, a powerful frequency table across many categorical
15609 @item @code{comparedf}, a function for comparing @code{data.frames}; and
15610 @item @code{write2}, a function to output tables to a document.
15613 (license license:gpl2+)))
15615 (define-public r-haplo-stats
15617 (name "r-haplo-stats")
15622 (uri (cran-uri "haplo.stats" version))
15625 "1imz4gs0n57vixwwbirrihpgvn2pyj5da4rgjcjk14n2xkk0nay7"))))
15626 (properties `((upstream-name . "haplo.stats")))
15627 (build-system r-build-system)
15629 `(("r-arsenal" ,r-arsenal)
15632 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
15633 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
15634 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
15636 "This package provides routines for the analysis of indirectly measured
15637 haplotypes. The statistical methods assume that all subjects are unrelated
15638 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
15639 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
15640 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
15641 examples in the vignette.")
15642 (license license:gpl2+)))
15644 (define-public r-bqtl
15651 (uri (cran-uri "bqtl" version))
15654 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
15655 (build-system r-build-system)
15656 (native-inputs `(("gfortran" ,gfortran)))
15657 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
15658 (synopsis "Bayesian QTL mapping toolkit")
15660 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
15661 lines. It includes maximum likelihood and Bayesian tools.")
15662 (license license:gpl2+)))
15664 (define-public r-ibdreg
15671 (uri (cran-uri "ibdreg" version))
15674 "0kgx9iavgm6d6njhki7bm82d6lw2c7kcch2pryd339js2hm0l5gq"))))
15675 (build-system r-build-system)
15676 (home-page "https://www.mayo.edu/research/labs/\
15677 statistical-genetics-genetic-epidemiology/software")
15678 (synopsis "Regression methods for IBD linkage with covariates")
15680 "This package provides a method to test genetic linkage with covariates
15681 by regression methods with response IBD sharing for relative pairs. Account
15682 for correlations of IBD statistics and covariates for relative pairs within
15683 the same pedigree.")
15684 (license license:gpl2+)))
15686 (define-public r-dlmap
15693 (uri (cran-uri "dlmap" version))
15696 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
15697 (build-system r-build-system)
15699 `(("r-ibdreg" ,r-ibdreg)
15703 ("r-wgaim" ,r-wgaim)))
15704 (home-page "https://cran.r-project.org/web/packages/dlmap/")
15705 (synopsis "Detection localization mapping for QTL")
15707 "This is package for QTL mapping in a mixed model framework with separate
15708 detection and localization stages. The first stage detects the number of QTL
15709 on each chromosome based on the genetic variation due to grouped markers on
15710 the chromosome; the second stage uses this information to determine the most
15711 likely QTL positions. The mixed model can accommodate general fixed and
15712 random effects, including spatial effects in field trials and pedigree
15713 effects. It is applicable to backcrosses, doubled haploids, recombinant
15714 inbred lines, F2 intercrosses, and association mapping populations.")
15715 (license license:gpl2)))
15717 (define-public r-hwde
15724 (uri (cran-uri "hwde" version))
15727 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
15728 (build-system r-build-system)
15729 (home-page "https://cran.r-project.org/web/packages/hwde/")
15730 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
15732 "This package fits models for genotypic disequilibria, as described in
15733 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
15734 terms are available that account for first order interactions between loci.
15735 It also implements, for a single locus in a single population, a conditional
15736 exact test for Hardy-Weinberg equilibrium.")
15737 (license license:gpl2+)))
15739 (define-public r-tdthap
15746 (uri (cran-uri "tdthap" version))
15749 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
15750 (build-system r-build-system)
15751 (home-page "https://cran.r-project.org/web/packages/tdthap/")
15752 (synopsis "TDT tests for extended haplotypes")
15754 "Functions and examples are provided for transmission/disequilibrium
15755 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
15756 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
15757 (license license:artistic2.0)))
15759 (define-public r-sparql
15765 (uri (cran-uri "SPARQL" version))
15768 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
15769 (properties `((upstream-name . "SPARQL")))
15770 (build-system r-build-system)
15772 `(("r-rcurl" ,r-rcurl)
15774 (home-page "https://cran.r-project.org/web/packages/SPARQL")
15775 (synopsis "SPARQL client for R")
15776 (description "This package provides an interface to use SPARQL to pose
15777 SELECT or UPDATE queries to an end-point.")
15778 ;; The only license indication is found in the DESCRIPTION file,
15779 ;; which states GPL-3. So we cannot assume GPLv3+.
15780 (license license:gpl3)))
15782 (define-public r-bookdown
15784 (name "r-bookdown")
15788 (uri (cran-uri "bookdown" version))
15791 "0xms1srx9l2mn8xaxnpic0s21y8k56bhwpj45wy7b0yscmxgmh27"))))
15792 (build-system r-build-system)
15794 `(("r-htmltools" ,r-htmltools)
15795 ("r-knitr" ,r-knitr)
15796 ("r-rmarkdown" ,r-rmarkdown)
15797 ("r-tinytex" ,r-tinytex)
15800 ("pandoc" ,pandoc)))
15801 (home-page "https://github.com/rstudio/bookdown")
15802 (synopsis "Authoring books and technical documents with R markdown")
15803 (description "This package provides output formats and utilities for
15804 authoring books and technical documents with R Markdown.")
15805 (license license:gpl3)))
15807 (define-public r-optparse
15809 (name "r-optparse")
15814 (uri (cran-uri "optparse" version))
15817 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
15818 (build-system r-build-system)
15820 `(("r-getopt" ,r-getopt)))
15822 `(("r-knitr" ,r-knitr)))
15823 (home-page "https://github.com/trevorld/optparse")
15824 (synopsis "Command line option parser")
15826 "This package provides a command line parser inspired by Python's
15827 @code{optparse} library to be used with Rscript to write shebang scripts
15828 that accept short and long options.")
15829 (license license:gpl2+)))
15831 (define-public r-kernlab
15838 (uri (cran-uri "kernlab" version))
15840 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
15841 (build-system r-build-system)
15842 (home-page "https://cran.r-project.org/web/packages/kernlab")
15843 (synopsis "Kernel-based machine learning tools")
15845 "This package provides kernel-based machine learning methods for
15846 classification, regression, clustering, novelty detection, quantile regression
15847 and dimensionality reduction. Among other methods @code{kernlab} includes
15848 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
15850 (license license:gpl2)))
15852 (define-public r-hierfstat
15854 (name "r-hierfstat")
15859 (uri (cran-uri "hierfstat" version))
15862 "0dp8k1z5a8gqnax99y1hwfvxilzf4n2i751zr0z6ihrzirsvb3m3"))))
15863 (build-system r-build-system)
15865 `(("r-ade4" ,r-ade4)
15866 ("r-adegenet" ,r-adegenet)
15867 ("r-gaston" ,r-gaston)
15868 ("r-gtools" ,r-gtools)))
15870 `(("r-knitr" ,r-knitr)))
15871 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
15872 (synopsis "Estimation and tests of hierarchical F-statistics")
15874 "This package allows the estimation of hierarchical F-statistics from
15875 haploid or diploid genetic data with any numbers of levels in the hierarchy,
15876 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
15877 are also given to test via randomisations the significance of each F and
15878 variance components, using the likelihood-ratio statistics G.")
15879 (license license:gpl2+)))
15881 (define-public r-hapassoc
15883 (name "r-hapassoc")
15888 (uri (cran-uri "hapassoc" version))
15891 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
15892 (build-system r-build-system)
15893 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
15894 (synopsis "Inference of trait associations with SNP haplotypes")
15896 "Hapassoc performs likelihood inference of trait associations with
15897 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
15898 functions are developed primarily for data collected in cohort or
15899 cross-sectional studies. They can accommodate uncertain haplotype phase and
15900 handle missing genotypes at some SNPs.")
15901 (license license:gpl2)))
15903 (define-public r-sampling
15905 (name "r-sampling")
15910 (uri (cran-uri "sampling" version))
15913 "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz"))))
15914 (build-system r-build-system)
15916 `(("r-lpsolve" ,r-lpsolve)
15917 ("r-mass" ,r-mass)))
15918 (home-page "https://cran.r-project.org/web/packages/sampling/")
15919 (synopsis "Survey sampling")
15921 "This package provides functions for drawing and calibrating samples.")
15922 (license license:gpl2+)))
15924 (define-public r-r2html
15931 (uri (cran-uri "R2HTML" version))
15934 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
15935 (properties `((upstream-name . "R2HTML")))
15936 (build-system r-build-system)
15937 (home-page "https://github.com/nalimilan/R2HTML")
15938 (synopsis "HTML export for R objects")
15940 "This package includes HTML functions and methods to write in an HTML
15941 file. Thus, making HTML reports is easy. It includes a function that allows
15942 redirection on the fly, which appears to be very useful for teaching purposes,
15943 as the student can keep a copy of the produced output to keep all that they
15944 did during the course. The package comes with a vignette describing how to
15945 write HTML reports for statistical analysis. Finally, a driver for Sweave
15946 parses HTML flat files containing R code and to automatically write
15947 the corresponding outputs (tables and graphs).")
15948 (license license:gpl2+)))
15950 (define-public r-rjava
15957 (uri (cran-uri "rJava" version))
15960 "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv"))))
15961 (properties `((upstream-name . "rJava")))
15962 (build-system r-build-system)
15964 `(#:modules ((guix build utils)
15965 (guix build r-build-system)
15968 (modify-phases %standard-phases
15969 (add-after 'unpack 'set-JAVA_HOME
15970 (lambda* (#:key inputs #:allow-other-keys)
15971 (let ((jdk (assoc-ref inputs "jdk")))
15972 (setenv "JAVA_HOME" jdk)
15973 (setenv "JAVA" (which "java"))
15974 (setenv "JAR" (which "jar"))
15975 (setenv "JAVAC" (which "javac"))
15976 (setenv "JAVAH" (which "javah"))
15977 (setenv "JAVA_CPPFLAGS"
15978 (string-append "-I" jdk "/include "
15979 "-I" jdk "/include/linux"))
15980 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
15981 ((lib) (setenv "JAVA_LIBS" lib))
15982 (_ (error "Could not find libjvm.so"))))
15986 ("jdk" ,icedtea-8 "jdk")
15989 (home-page "https://www.rforge.net/rJava/")
15990 (synopsis "Low-Level R to Java interface")
15992 "This package provides a low-level interface to the Java VM very much
15993 like .C/.Call and friends. It allows the creation of objects, calling methods
15994 and accessing fields.")
15995 (license license:gpl2)))
15997 (define-public r-svmisc
16004 (uri (cran-uri "svMisc" version))
16007 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
16008 (properties `((upstream-name . "svMisc")))
16009 (build-system r-build-system)
16010 (home-page "https://github.com/SciViews/svMisc")
16011 (synopsis "Miscellaneous functions for SciViews")
16013 "This package provides miscellaneous functions for SciViews or general
16014 use, including tools to manage a temporary environment attached to the search
16015 path for temporary variables you do not want to @code{save()} or
16016 @code{load()}; test the current platform; showing progress bars, etc.")
16017 (license license:gpl2)))
16019 (define-public r-xyz
16026 (uri (cran-uri "xyz" version))
16029 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
16030 (build-system r-build-system)
16032 `(("r-rcpp" ,r-rcpp)))
16033 (home-page "https://cran.r-project.org/web/packages/xyz/")
16034 (synopsis "Algorithm for fast interaction search in high-dimensional data")
16036 "High dimensional interaction search by brute force requires a quadratic
16037 computational cost in the number of variables. The xyz algorithm provably
16038 finds strong interactions in almost linear time. For details of the algorithm
16039 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
16040 interaction search in high-dimensional data.")
16041 ;; Any version of the GPL.
16042 (license license:gpl2+)))
16044 (define-public r-rttf2pt1
16046 (name "r-rttf2pt1")
16051 (uri (cran-uri "Rttf2pt1" version))
16054 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
16055 (properties `((upstream-name . "Rttf2pt1")))
16056 (build-system r-build-system)
16057 (home-page "https://github.com/wch/Rttf2pt1")
16058 (synopsis "Font conversion utility")
16060 "This package contains the program @code{ttf2pt1}, for use with the
16061 @code{extrafont} package.")
16062 ;; Most of the files are covered under the Expat license. Some files are
16063 ;; covered under BSD-3. Deviations for individual files are recorded in
16064 ;; the LICENSE file.
16065 (license (list license:bsd-3 license:expat
16066 (license:non-copyleft "file://LICENSE")))))
16068 (define-public r-extrafontdb
16070 (name "r-extrafontdb")
16075 (uri (cran-uri "extrafontdb" version))
16078 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
16079 (build-system r-build-system)
16080 (home-page "https://github.com/wch/extrafontdb")
16081 (synopsis "Database for the extrafont package")
16083 "This package holds the database for the @code{extrafont} package.")
16084 (license license:gpl2)))
16086 (define-public r-extrafont
16088 (name "r-extrafont")
16093 (uri (cran-uri "extrafont" version))
16096 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
16097 (build-system r-build-system)
16099 `(("r-extrafontdb" ,r-extrafontdb)
16100 ("r-rttf2pt1" ,r-rttf2pt1)))
16101 (home-page "https://github.com/wch/extrafont")
16102 (synopsis "Tools for using fonts in R")
16104 "The extrafont package makes it easier to use fonts other than the basic
16105 PostScript fonts that R uses. Fonts that are imported into extrafont can be
16106 used with PDF or PostScript output files. There are two hurdles for using
16107 fonts in PDF (or Postscript) output files:
16110 @item Making R aware of the font and the dimensions of the characters.
16111 @item Embedding the fonts in the PDF file so that the PDF can be displayed
16112 properly on a device that doesn't have the font. This is usually needed if
16113 you want to print the PDF file or share it with others.
16116 The extrafont package makes both of these things easier.")
16117 (license license:gpl2)))
16119 (define-public r-xkcd
16126 (uri (cran-uri "xkcd" version))
16129 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
16130 (build-system r-build-system)
16132 `(("r-extrafont" ,r-extrafont)
16133 ("r-ggplot2" ,r-ggplot2)
16134 ("r-hmisc" ,r-hmisc)))
16135 (home-page "https://cran.r-project.org/web/packages/xkcd/")
16136 (synopsis "Plot ggplot2 graphics in the XKCD style")
16138 "This package provides the means to plot ggplot2 graphs in the style of
16139 the XKCD web comic.")
16140 (license license:gpl3)))
16142 (define-public r-msigdbr
16149 (uri (cran-uri "msigdbr" version))
16152 "1rc2p9vw57pn4prmfgay4w18qd53ggq7wxfsi9kp7w25ciip1dq1"))))
16153 (build-system r-build-system)
16155 `(("r-dplyr" ,r-dplyr)
16156 ("r-magrittr" ,r-magrittr)
16157 ("r-rlang" ,r-rlang)
16158 ("r-tibble" ,r-tibble)
16159 ("r-tidyselect" ,r-tidyselect)))
16161 `(("r-knitr" ,r-knitr)))
16162 (home-page "https://github.com/igordot/msigdbr")
16163 (synopsis "MSigDB gene sets for multiple organisms")
16165 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
16166 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
16167 software in a standard R data frame with key-value pairs. Included are the
16168 original human gene symbols and Entrez IDs as well as the equivalents for
16169 various frequently studied model organisms such as mouse, rat, pig, fly, and
16171 ;; The package is covered under the Expat license, but the upstream MSigDB
16172 ;; files are made available under the Creative Commons Attribution 4.0
16173 ;; International license.
16174 (license (list license:expat license:cc-by4.0))))
16176 (define-public r-gridgraphics
16178 (name "r-gridgraphics")
16183 (uri (cran-uri "gridGraphics" version))
16186 "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219"))))
16187 (properties `((upstream-name . "gridGraphics")))
16188 (build-system r-build-system)
16189 (home-page "https://github.com/pmur002/gridgraphics")
16190 (synopsis "Redraw base graphics using @code{grid} graphics")
16192 "This package provides functions to convert a page of plots drawn with
16193 the @code{graphics} package into identical output drawn with the @code{grid}
16194 package. The result looks like the original @code{graphics}-based plot, but
16195 consists of @code{grid} grobs and viewports that can then be manipulated with
16196 @code{grid} functions (e.g., edit grobs and revisit viewports).")
16197 (license license:gpl2+)))
16199 (define-public r-farver
16206 (uri (cran-uri "farver" version))
16209 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
16210 (build-system r-build-system)
16211 (home-page "https://github.com/thomasp85/farver")
16212 (synopsis "Vectorized color conversion and comparison")
16214 "The encoding of color can be handled in many different ways, using
16215 different color spaces. As different color spaces have different uses,
16216 efficient conversion between these representations are important. This
16217 package provides a set of functions that gives access to very fast color space
16218 conversion and comparisons implemented in C++, and offers 100-fold speed
16219 improvements over the @code{convertColor} function in the @code{grDevices}
16221 (license license:expat)))
16223 (define-public r-ggplotify
16225 (name "r-ggplotify")
16230 (uri (cran-uri "ggplotify" version))
16233 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
16234 (build-system r-build-system)
16236 `(("r-ggplot2" ,r-ggplot2)
16237 ("r-gridgraphics" ,r-gridgraphics)
16238 ("r-rvcheck" ,r-rvcheck)))
16240 `(("r-knitr" ,r-knitr)))
16241 (home-page "https://github.com/GuangchuangYu/ggplotify")
16242 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
16244 "This package provides tools to convert plot function calls (using
16245 expression or formula) to @code{grob} or @code{ggplot} objects that are
16246 compatible with the @code{grid} and @code{ggplot2} environment. With this
16247 package, we are able to e.g. use @code{cowplot} to align plots produced by
16248 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
16249 converting them to @code{ggplot} objects.")
16250 (license license:artistic2.0)))
16252 (define-public r-triebeard
16254 (name "r-triebeard")
16259 (uri (cran-uri "triebeard" version))
16262 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
16263 (build-system r-build-system)
16264 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16265 (home-page "https://github.com/Ironholds/triebeard/")
16266 (synopsis "Radix trees in Rcpp")
16268 "Radix trees, or tries, are key-value data structures optimized for
16269 efficient lookups, similar in purpose to hash tables. This package provides
16270 an implementation of radix trees for use in R programming and in developing
16271 packages with Rcpp.")
16272 (license license:expat)))
16274 (define-public r-tweenr
16281 (uri (cran-uri "tweenr" version))
16284 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
16285 (build-system r-build-system)
16287 `(("r-farver" ,r-farver)
16288 ("r-magrittr" ,r-magrittr)
16290 ("r-rlang" ,r-rlang)))
16291 (home-page "https://github.com/thomasp85/tweenr")
16292 (synopsis "Interpolate data for smooth animations")
16294 "In order to create smooth animation between states of data, tweening is
16295 necessary. This package provides a range of functions for creating tweened
16296 data that can be used as basis for animation. Furthermore it adds a number of
16297 vectorized interpolaters for common R data types such as numeric, date and
16299 (license license:expat)))
16301 (define-public r-polyclip
16303 (name "r-polyclip")
16308 (uri (cran-uri "polyclip" version))
16311 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
16312 (build-system r-build-system)
16313 (native-inputs `(("pkg-config" ,pkg-config)))
16314 (home-page "http://www.angusj.com/delphi/clipper.php")
16315 (synopsis "Polygon clipping")
16317 "This package provides an R port of the library Clipper. It performs
16318 polygon clipping operations (intersection, union, set minus, set difference)
16319 for polygonal regions of arbitrary complexity, including holes. It computes
16320 offset polygons (spatial buffer zones, morphological dilations, Minkowski
16321 dilations) for polygonal regions and polygonal lines. It computes the
16322 Minkowski Sum of general polygons. There is a function for removing
16323 self-intersections from polygon data.")
16324 (license license:boost1.0)))
16326 (define-public r-urltools
16328 (name "r-urltools")
16333 (uri (cran-uri "urltools" version))
16336 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
16337 (build-system r-build-system)
16339 `(("r-rcpp" ,r-rcpp)
16340 ("r-triebeard" ,r-triebeard)))
16341 (home-page "https://github.com/Ironholds/urltools/")
16342 (synopsis "Vectorized tools for URL handling and parsing")
16344 "This package provides a toolkit for all URL-handling needs, including
16345 encoding and decoding, parsing, parameter extraction and modification. All
16346 functions are designed to be both fast and entirely vectorized. It is
16347 intended to be useful for people dealing with web-related datasets, such as
16348 server-side logs, although may be useful for other situations involving large
16350 (license license:expat)))
16352 (define-public r-ggforce
16359 (uri (cran-uri "ggforce" version))
16362 "1lplxyq5bgx90dgaimhynpcywag1gp6vlsy7q52ay1nfc35qmkjc"))))
16363 (build-system r-build-system)
16365 `(("r-ggplot2" ,r-ggplot2)
16366 ("r-gtable" ,r-gtable)
16368 ("r-polyclip" ,r-polyclip)
16370 ("r-rcppeigen" ,r-rcppeigen)
16371 ("r-rlang" ,r-rlang)
16372 ("r-scales" ,r-scales)
16373 ("r-tidyselect" ,r-tidyselect)
16374 ("r-tweenr" ,r-tweenr)
16375 ("r-withr" ,r-withr)))
16376 (home-page "https://ggforce.data-imaginist.com")
16377 (synopsis "Accelerating ggplot2")
16379 "The aim of the ggplot2 package is to aid in visual data investigations.
16380 This focus has led to a lack of facilities for composing specialized plots.
16381 Thi package aims to be a collection of mainly new statistics and geometries
16382 that fills this gap.")
16383 (license license:expat)))
16385 (define-public r-europepmc
16387 (name "r-europepmc")
16392 (uri (cran-uri "europepmc" version))
16395 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
16396 (build-system r-build-system)
16398 `(("r-dplyr" ,r-dplyr)
16400 ("r-jsonlite" ,r-jsonlite)
16402 ("r-progress" ,r-progress)
16403 ("r-purrr" ,r-purrr)
16404 ("r-rlang" ,r-rlang)
16405 ("r-tibble" ,r-tibble)
16406 ("r-tidyr" ,r-tidyr)
16407 ("r-urltools" ,r-urltools)
16408 ("r-xml2" ,r-xml2)))
16410 `(("r-knitr" ,r-knitr)))
16411 (home-page "https://github.com/ropensci/europepmc/")
16412 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
16414 "This package provides an R Client for the
16415 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
16416 Service}. It gives access to both metadata on life science literature and
16417 open access full texts. Europe PMC indexes all PubMed content and other
16418 literature sources including Agricola, a bibliographic database of citations
16419 to the agricultural literature, or Biological Patents. In addition to
16420 bibliographic metadata, the client allows users to fetch citations and
16421 reference lists. Links between life-science literature and other EBI
16422 databases, including ENA, PDB or ChEMBL are also accessible.")
16423 (license license:gpl3)))
16425 (define-public r-ggraph
16432 (uri (cran-uri "ggraph" version))
16435 "1j3xf4fsv0i0gbppdrw4yprfyk53wx6s8nvnkipi2ywbm7cr4q4w"))))
16436 (build-system r-build-system)
16438 `(("r-digest" ,r-digest)
16439 ("r-dplyr" ,r-dplyr)
16440 ("r-ggforce" ,r-ggforce)
16441 ("r-ggplot2" ,r-ggplot2)
16442 ("r-ggrepel" ,r-ggrepel)
16443 ("r-graphlayouts" ,r-graphlayouts)
16444 ("r-gtable" ,r-gtable)
16445 ("r-igraph" ,r-igraph)
16448 ("r-rlang" ,r-rlang)
16449 ("r-scales" ,r-scales)
16450 ("r-tidygraph" ,r-tidygraph)
16451 ("r-viridis" ,r-viridis)
16452 ("r-withr" ,r-withr)))
16454 `(("r-knitr" ,r-knitr)))
16455 (home-page "https://cran.r-project.org/web/packages/ggraph/")
16456 (synopsis "Implementation of grammar of graphics for graphs and networks")
16458 "The grammar of graphics as implemented in ggplot2 is a poor fit for
16459 graph and network visualizations due to its reliance on tabular data input.
16460 The ggraph package is an extension of the ggplot2 API tailored to graph
16461 visualizations and provides the same flexible approach to building up plots
16463 (license license:gpl3)))
16465 (define-public r-varselrf
16467 (name "r-varselrf")
16472 (uri (cran-uri "varSelRF" version))
16475 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
16476 (properties `((upstream-name . "varSelRF")))
16477 (build-system r-build-system)
16479 `(("r-randomforest" ,r-randomforest)))
16480 (home-page "https://www.ligarto.org/rdiaz/software/software")
16481 (synopsis "Variable selection using random forests")
16483 "This package provides tools for the variable selection from random
16484 forests using both backwards variable elimination (for the selection of small
16485 sets of non-redundant variables) and selection based on the importance
16486 spectrum (somewhat similar to scree plots; for the selection of large,
16487 potentially highly-correlated variables). The main applications are in
16488 high-dimensional data (e.g., microarray data, and other genomics and
16489 proteomics applications).")
16490 (license license:gpl2+)))
16492 (define-public r-pamr
16499 (uri (cran-uri "pamr" version))
16502 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
16503 (build-system r-build-system)
16505 `(("r-cluster" ,r-cluster)
16506 ("r-survival" ,r-survival)))
16507 (native-inputs `(("gfortran" ,gfortran)))
16508 (home-page "https://cran.r-project.org/web/packages/pamr/")
16509 (synopsis "Prediction Analysis for Microarrays")
16511 "This package provides some functions for sample classification in
16513 (license license:gpl2)))
16515 (define-public r-rda
16518 (version "1.0.2-2.1")
16522 (uri (cran-uri "rda" version))
16525 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
16526 (build-system r-build-system)
16527 (home-page "https://cran.r-project.org/web/packages/rda/")
16528 (synopsis "Shrunken centroids regularized discriminant analysis")
16530 "This package provides tools for shrunken centroids regularized
16531 discriminant analysis for the purpose of classifying high dimensional data.")
16532 (license license:gpl2+)))
16534 (define-public r-ggvis
16541 (uri (cran-uri "ggvis" version))
16544 "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy"))))
16545 (build-system r-build-system)
16547 `(("r-assertthat" ,r-assertthat)
16548 ("r-dplyr" ,r-dplyr)
16549 ("r-htmltools" ,r-htmltools)
16550 ("r-jsonlite" ,r-jsonlite)
16551 ("r-magrittr" ,r-magrittr)
16552 ("r-rlang" ,r-rlang)
16553 ("r-shiny" ,r-shiny)))
16554 (home-page "https://ggvis.rstudio.com/")
16555 (synopsis "Interactive grammar of graphics")
16557 "This package is a data visualization package for R providing an
16558 implementation of an interactive grammar of graphics, taking the best parts of
16559 ggplot2, combining them with the reactive framework of Shiny and drawing web
16560 graphics using Vega.")
16561 (license license:gpl2)))
16563 (define-public r-gbm
16570 (uri (cran-uri "gbm" version))
16573 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
16574 (build-system r-build-system)
16576 `(("r-lattice" ,r-lattice)
16577 ("r-survival" ,r-survival)))
16579 `(("r-knitr" ,r-knitr)))
16580 (home-page "https://github.com/gbm-developers/gbm")
16581 (synopsis "Generalized boosted regression models")
16583 "This package is an implementation of extensions to Freund and Schapire's
16584 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
16585 regression methods for least squares, absolute loss, t-distribution loss,
16586 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
16587 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
16588 and Learning to Rank measures (LambdaMart).")
16589 (license license:gpl2+)))
16591 (define-public r-threejs
16598 (uri (cran-uri "threejs" version))
16601 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
16602 (build-system r-build-system)
16604 `(#:modules ((guix build utils)
16605 (guix build r-build-system)
16609 (modify-phases %standard-phases
16610 (add-after 'unpack 'process-javascript
16611 (lambda* (#:key inputs #:allow-other-keys)
16612 (with-directory-excursion "inst"
16616 `((,(assoc-ref inputs "js-jquery")
16617 "htmlwidgets/lib/jquery/jquery.min.js")
16618 (,(assoc-ref inputs "js-threejs-111")
16619 "htmlwidgets/lib/threejs-111/three.min.js"))))
16620 (lambda (sources targets)
16621 (for-each (lambda (source target)
16622 (format #t "Processing ~a --> ~a~%"
16624 (delete-file target)
16625 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16626 (call-with-output-file target
16628 (dump-port minified port)))))
16629 sources targets))))
16632 `(("r-base64enc" ,r-base64enc)
16633 ("r-crosstalk" ,r-crosstalk)
16634 ("r-htmlwidgets" ,r-htmlwidgets)
16635 ("r-igraph" ,r-igraph)))
16637 `(("uglify-js" ,uglify-js)
16641 (uri "https://code.jquery.com/jquery-1.12.4.js")
16644 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
16648 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
16651 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
16652 (home-page "https://bwlewis.github.io/rthreejs")
16653 (synopsis "Interactive 3D scatter plots, networks and globes")
16655 "Create interactive 3D scatter plots, network plots, and globes in R
16656 using the three.js visualization library.")
16657 (license license:expat)))
16659 (define-public r-mlbench
16666 (uri (cran-uri "mlbench" version))
16669 "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi"))))
16670 (build-system r-build-system)
16671 (home-page "https://cran.r-project.org/web/packages/mlbench/")
16672 (synopsis "Machine learning benchmark problems")
16674 "This package provides a collection of artificial and real-world machine
16675 learning benchmark problems, including, e.g., several data sets from the UCI
16677 (license license:gpl2)))
16679 (define-public r-mpm
16686 (uri (cran-uri "mpm" version))
16689 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
16690 (build-system r-build-system)
16692 `(("r-kernsmooth" ,r-kernsmooth)
16693 ("r-mass" ,r-mass)))
16694 (home-page "http://mpm.r-forge.r-project.org")
16695 (synopsis "Multivariate projection methods")
16697 "This is a package for exploratory graphical analysis of multivariate
16698 data, specifically gene expression data with different projection methods:
16699 principal component analysis, correspondence analysis, spectral map
16701 (license license:gpl2+)))
16703 (define-public r-png
16709 (uri (cran-uri "png" version))
16712 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
16713 (build-system r-build-system)
16715 `(("libpng" ,libpng)
16717 (home-page "https://www.rforge.net/png/")
16718 (synopsis "Read and write PNG images")
16720 "This package provides an easy and simple way to read, write and display
16721 bitmap images stored in the PNG format. It can read and write both files and
16722 in-memory raw vectors.")
16723 ;; Any of these GPL versions.
16724 (license (list license:gpl2 license:gpl3))))
16726 (define-public r-ggcorrplot
16728 (name "r-ggcorrplot")
16733 (uri (cran-uri "ggcorrplot" version))
16736 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
16737 (build-system r-build-system)
16739 `(("r-ggplot2" ,r-ggplot2)
16740 ("r-reshape2" ,r-reshape2)))
16741 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
16742 (synopsis "Visualization of a correlation matrix using ggplot2")
16744 "The ggcorrplot package can be used to visualize easily a correlation
16745 matrix using ggplot2. It provides a solution for reordering the correlation
16746 matrix and displays the significance level on the plot. It also includes a
16747 function for computing a matrix of correlation p-values.")
16748 (license license:gpl2)))
16750 (define-public r-gridtext
16752 (name "r-gridtext")
16757 (uri (cran-uri "gridtext" version))
16760 "131kw7nkfwksviwfifd2kk7lyvhxzzzv1nnj8rahkr3dik3akk61"))))
16761 (properties `((upstream-name . "gridtext")))
16762 (build-system r-build-system)
16764 `(("r-jpeg" ,r-jpeg)
16765 ("r-markdown" ,r-markdown)
16768 ("r-rcurl" ,r-rcurl)
16769 ("r-rlang" ,r-rlang)
16770 ("r-stringr" ,r-stringr)
16771 ("r-xml2" ,r-xml2)))
16772 (home-page "https://wilkelab.org/gridtext/")
16773 (synopsis "Improved text rendering support for Grid graphics")
16775 "This package provides support for rendering of formatted text using Grid
16776 graphics. Text can be formatted via a minimal subset of Markdown, HTML, and
16777 inline CSS directives, and it can be rendered both with and without word
16779 (license license:expat)))
16781 (define-public r-ggtext
16788 (uri (cran-uri "ggtext" version))
16791 "0n19dlcys8v7myfyckr6dnq0kx79k3sbh8nwx1jsx8pgzfbi8a2b"))))
16792 (properties `((upstream-name . "ggtext")))
16793 (build-system r-build-system)
16795 `(("r-ggplot2" ,r-ggplot2)
16796 ("r-gridtext" ,r-gridtext)
16797 ("r-rlang" ,r-rlang)
16798 ("r-scales" ,r-scales)))
16799 (native-inputs `(("r-knitr" ,r-knitr)))
16800 (home-page "https://wilkelab.org/ggtext/")
16801 (synopsis "Improved text rendering support for ggplot2")
16803 "This package provides a ggplot2 extension that enables the rendering of
16804 complex formatted plot labels (titles, subtitles, facet labels, axis labels,
16805 etc.). Text boxes with automatic word wrap are also supported.")
16806 (license license:gpl2)))
16808 ;; This package includes minified JavaScript files. When upgrading please
16809 ;; check that there are no new minified JavaScript files.
16810 (define-public r-flexdashboard
16812 (name "r-flexdashboard")
16817 (uri (cran-uri "flexdashboard" version))
16820 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
16821 (modules '((guix build utils)))
16824 ;; Delete bundled minified JavaScript files
16825 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
16826 (delete-file "inst/www/sly/sly.min.js")
16827 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
16828 (delete-file "inst/www/prism/prism.js")
16830 (build-system r-build-system)
16832 `(#:modules ((guix build utils)
16833 (guix build r-build-system)
16837 (ice-9 textual-ports))
16839 (modify-phases %standard-phases
16840 (add-after 'unpack 'process-javascript
16841 (lambda* (#:key inputs #:allow-other-keys)
16842 (with-directory-excursion "inst"
16843 ;; Concatenate all components of prism.js
16844 (let ((contents (string-join
16845 (map (lambda (name)
16846 (call-with-input-file
16847 (assoc-ref inputs name)
16851 "js-prism-line-numbers"))
16853 (call-with-output-file "prism-src.js"
16854 (cut display contents <>)))
16858 `(("www/stickytableheaders/jquery.stickytableheaders.js"
16859 "www/stickytableheaders/jquery.stickytableheaders.min.js")
16861 "www/sly/sly.min.js")
16863 "www/prism/prism.js")
16864 (,(assoc-ref inputs "js-raphael")
16865 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
16866 (,(assoc-ref inputs "js-featherlight")
16867 "www/featherlight/featherlight.min.js"))))
16868 (lambda (sources targets)
16869 (for-each (lambda (source target)
16870 (format #t "Processing ~a --> ~a~%"
16872 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16873 (call-with-output-file target
16875 (dump-port minified port)))))
16876 sources targets))))
16879 `(("r-htmltools" ,r-htmltools)
16880 ("r-htmlwidgets" ,r-htmlwidgets)
16881 ("r-jsonlite" ,r-jsonlite)
16882 ("r-knitr" ,r-knitr)
16883 ("r-rmarkdown" ,r-rmarkdown)
16884 ("r-shiny" ,r-shiny)))
16886 `(("uglify-js" ,uglify-js)
16890 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
16893 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
16897 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
16900 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
16904 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
16907 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
16908 ("js-prism-line-numbers"
16911 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
16914 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
16918 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
16921 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
16922 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
16923 (synopsis "R Markdown format for flexible dashboards")
16925 "This package provides an R Markdown format for converting an R Markdown
16926 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
16927 of its components to the containing web page.")
16928 (license license:expat)))
16930 (define-public r-preseqr
16937 (uri (cran-uri "preseqR" version))
16940 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
16941 (properties `((upstream-name . "preseqR")))
16942 (build-system r-build-system)
16944 `(("r-polynom" ,r-polynom)))
16945 (home-page "https://cran.r-project.org/web/packages/preseqR/")
16946 (synopsis "Predicting species accumulation curves")
16948 "This package can be used to predict the r-species accumulation
16949 curve (r-SAC), which is the number of species represented at least r times as
16950 a function of the sampling effort. When r = 1, the curve is known as the
16951 species accumulation curve, or the library complexity curve in high-throughput
16952 genomic sequencing. The package includes both parametric and nonparametric
16953 methods, as described by Deng C, et al. (2018).")
16954 (license license:gpl3)))
16956 (define-public r-mapplots
16958 (name "r-mapplots")
16963 (uri (cran-uri "mapplots" version))
16966 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
16967 (build-system r-build-system)
16968 (home-page "https://cran.r-project.org/web/packages/mapplots/")
16969 (synopsis "Data visualization on maps")
16971 "This package helps you create simple maps; add sub-plots like pie plots
16972 to a map or any other plot; format, plot and export gridded data. The package
16973 was developed for displaying fisheries data but most functions can be used for
16974 more generic data visualisation.")
16975 (license license:gpl2+)))
16977 (define-public r-pmcmr
16984 (uri (cran-uri "PMCMR" version))
16987 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
16988 (properties `((upstream-name . "PMCMR")))
16989 (build-system r-build-system)
16990 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
16991 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
16993 "This is a deprecated package for calculating pairwise multiple
16994 comparisons of mean rank sums. This package is superseded by the novel
16995 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
16996 compatibility of dependent packages for some time.")
16997 (license license:gpl3+)))
16999 (define-public r-downloader
17001 (name "r-downloader")
17006 (uri (cran-uri "downloader" version))
17009 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
17010 (build-system r-build-system)
17012 `(("r-digest" ,r-digest)))
17013 (home-page "https://github.com/wch/downloader")
17014 (synopsis "Download files over HTTP and HTTPS")
17016 "This package provides a wrapper for the @code{download.file} function,
17017 making it possible to download files over HTTPS across platforms. The
17018 @code{RCurl} package provides this functionality (and much more) but has
17019 external dependencies. This package has is implemented purely in R.")
17020 (license license:gpl2)))
17022 (define-public r-rex
17029 (uri (cran-uri "rex" version))
17032 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
17033 (build-system r-build-system)
17035 `(("r-lazyeval" ,r-lazyeval)))
17037 `(("r-knitr" ,r-knitr)))
17038 (home-page "https://github.com/kevinushey/rex")
17039 (synopsis "Friendly regular expressions")
17041 "This package provides a friendly interface for the construction of
17042 regular expressions. Regular expressions are a very powerful feature, however
17043 they are often difficult to interpret. Rex allows you to build complex
17044 regular expressions from human readable expressions")
17045 (license license:expat)))
17047 (define-public r-xmlparsedata
17049 (name "r-xmlparsedata")
17054 (uri (cran-uri "xmlparsedata" version))
17057 "177vfyjrqfi3wam8scpsradap1lv35yc25xq745dr7gabg116yrq"))))
17058 (properties `((upstream-name . "xmlparsedata")))
17059 (build-system r-build-system)
17060 (home-page "https://github.com/r-lib/xmlparsedata#readme")
17061 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
17063 "This package provides tools to convert the output of
17064 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
17065 @code{XPath}, and is easier to manipulate in general.")
17066 (license license:expat)))
17068 (define-public r-cyclocomp
17070 (name "r-cyclocomp")
17075 (uri (cran-uri "cyclocomp" version))
17078 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
17079 (properties `((upstream-name . "cyclocomp")))
17080 (build-system r-build-system)
17082 `(("r-callr" ,r-callr)
17083 ("r-crayon" ,r-crayon)
17085 ("r-remotes" ,r-remotes)
17086 ("r-withr" ,r-withr)))
17087 (home-page "https://github.com/MangoTheCat/cyclocomp")
17088 (synopsis "Cyclomatic complexity of R code")
17090 "Cyclomatic complexity is a software metric, used to indicate the
17091 complexity of a program. It is a quantitative measure of the number of
17092 linearly independent paths through a program's source code. This package
17093 provides tools to compute this metric.")
17094 (license license:expat)))
17096 (define-public r-lintr
17103 (uri (cran-uri "lintr" version))
17106 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
17107 (properties `((upstream-name . "lintr")))
17108 (build-system r-build-system)
17110 `(("r-codetools" ,r-codetools)
17111 ("r-crayon" ,r-crayon)
17112 ("r-cyclocomp" ,r-cyclocomp)
17113 ("r-digest" ,r-digest)
17115 ("r-jsonlite" ,r-jsonlite)
17116 ("r-knitr" ,r-knitr)
17118 ("r-rstudioapi" ,r-rstudioapi)
17119 ("r-testthat" ,r-testthat)
17121 ("r-xmlparsedata" ,r-xmlparsedata)))
17122 (home-page "https://github.com/jimhester/lintr")
17123 (synopsis "Linter for R code")
17124 (description "This package checks adherence to a given style, syntax
17125 errors and possible semantic issues. It supports on the fly checking of R
17126 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
17127 (license license:expat)))
17129 (define-public r-sctransform
17131 (name "r-sctransform")
17136 (uri (cran-uri "sctransform" version))
17139 "1p3m6i28nlxh6r609syn88cwlbdpl3dw44dy3gsijk2ibq20mfsx"))))
17140 (build-system r-build-system)
17142 `(("r-future" ,r-future)
17143 ("r-future-apply" ,r-future-apply)
17144 ("r-ggplot2" ,r-ggplot2)
17145 ("r-gridextra" ,r-gridextra)
17147 ("r-matrix" ,r-matrix)
17148 ("r-matrixstats" ,r-matrixstats)
17150 ("r-rcpparmadillo" ,r-rcpparmadillo)
17151 ("r-reshape2" ,r-reshape2)))
17152 (home-page "https://github.com/ChristophH/sctransform")
17153 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
17155 "This package provides a normalization method for single-cell UMI count
17156 data using a variance stabilizing transformation. The transformation is based
17157 on a negative binomial regression model with regularized parameters. As part
17158 of the same regression framework, this package also provides functions for
17159 batch correction, and data correction.")
17160 (license license:gpl3)))
17162 (define-public r-styler
17169 (uri (cran-uri "styler" version))
17172 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
17173 (build-system r-build-system)
17175 `(("r-backports" ,r-backports)
17177 ("r-magrittr" ,r-magrittr)
17178 ("r-purrr" ,r-purrr)
17179 ("r-r-cache" ,r-r-cache)
17180 ("r-rematch2" ,r-rematch2)
17181 ("r-rlang" ,r-rlang)
17182 ("r-rprojroot" ,r-rprojroot)
17183 ("r-tibble" ,r-tibble)
17184 ("r-withr" ,r-withr)
17185 ("r-xfun" ,r-xfun)))
17186 (home-page "https://github.com/r-lib/styler")
17187 (synopsis "Non-invasive pretty printing of R code")
17189 "This is a package for pretty-printing R code without changing the user's
17190 formatting intent.")
17191 (license license:gpl3)))
17193 (define-public r-scrime
17200 (uri (cran-uri "scrime" version))
17203 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
17204 (build-system r-build-system)
17205 (home-page "https://cran.r-project.org/web/packages/scrime/")
17206 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
17208 "This package provides tools for the analysis of high-dimensional data
17209 developed/implemented at the group \"Statistical Complexity Reduction In
17210 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
17211 the functions can also be applied to other types of categorical data.")
17212 (license license:gpl2)))
17214 (define-public r-pbmcapply
17216 (name "r-pbmcapply")
17221 (uri (cran-uri "pbmcapply" version))
17224 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
17225 (build-system r-build-system)
17226 (home-page "https://github.com/kvnkuang/pbmcapply")
17227 (synopsis "Track the progress of apply procedures with a progress bar")
17229 "This light-weight package helps you track and visualize the progress of
17230 parallel versions of vectorized R functions of the @code{mc*apply} family.")
17231 (license license:expat)))
17233 (define-public r-blme
17240 (uri (cran-uri "blme" version))
17243 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7"))))
17244 (build-system r-build-system)
17245 (propagated-inputs `(("r-lme4" ,r-lme4)))
17246 (home-page "https://github.com/vdorie/blme")
17247 (synopsis "Bayesian linear mixed-effects models")
17249 "This package provides tools for maximum a posteriori estimation for
17250 linear and generalized linear mixed-effects models in a Bayesian setting. It
17251 extends the lme4 package.")
17252 (license license:gpl2+)))
17254 (define-public r-batchtools
17256 (name "r-batchtools")
17261 (uri (cran-uri "batchtools" version))
17264 "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52"))))
17265 (build-system r-build-system)
17267 `(("r-backports" ,r-backports)
17268 ("r-base64url" ,r-base64url)
17270 ("r-checkmate" ,r-checkmate)
17271 ("r-data-table" ,r-data-table)
17272 ("r-digest" ,r-digest)
17274 ("r-progress" ,r-progress)
17276 ("r-rappdirs" ,r-rappdirs)
17277 ("r-stringi" ,r-stringi)
17278 ("r-withr" ,r-withr)))
17280 `(("r-knitr" ,r-knitr)))
17281 (home-page "https://github.com/mllg/batchtools")
17282 (synopsis "Tools for computation on batch systems")
17284 "As a successor of the packages BatchJobs and BatchExperiments, this
17285 package provides a parallel implementation of the Map function for high
17286 performance computing systems managed by various schedulers. A multicore and
17287 socket mode allow the parallelization on a local machines, and multiple
17288 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
17289 the package provides an abstraction mechanism to define large-scale computer
17290 experiments in a well-organized and reproducible way.")
17291 (license license:lgpl3)))
17293 (define-public r-clue
17300 (uri (cran-uri "clue" version))
17303 "1rwwxlnpl1k0n4k96vxc9zajw9kb4syqwzj76fvaf0qim8p6ddia"))))
17304 (build-system r-build-system)
17305 (propagated-inputs `(("r-cluster" ,r-cluster)))
17306 (home-page "https://cran.r-project.org/web/packages/clue/")
17307 (synopsis "Tools for analyzing cluster ensembles")
17308 (description "Cluster ensembles are collections of individual solutions to
17309 a given clustering problem which are useful or necessary to consider in a wide
17310 range of applications. This R package provides an extensible computational
17311 environment for creating and analyzing cluster ensembles, with basic data
17312 structures for representing partitions and hierarchies, and facilities for
17313 computing on them, including methods for measuring proximity and obtaining
17314 consensus and secondary clusterings.")
17315 (license license:gpl2)))
17317 (define-public r-sitmo
17324 (uri (cran-uri "sitmo" version))
17327 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
17328 (build-system r-build-system)
17329 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17330 (home-page "https://github.com/coatless/sitmo/")
17331 (synopsis "Parallel pseudo random number generator header files")
17333 "This package provides two high quality and fast PPRNGs that may be used
17334 in an OpenMP parallel environment. In addition, there is a generator for one
17335 dimensional low-discrepancy sequence.")
17336 (license license:expat)))
17338 (define-public r-dqrng
17345 (uri (cran-uri "dqrng" version))
17348 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
17349 (build-system r-build-system)
17353 ("r-sitmo" ,r-sitmo)))
17354 (home-page "https://www.daqana.org/dqrng")
17355 (synopsis "Fast pseudo random number generators")
17357 "Several fast random number generators are provided as C++ header-only
17358 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
17359 Additionally, fast functions for generating random numbers according to a
17360 uniform, normal and exponential distribution are included. The latter two use
17361 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
17362 functions are exported to R and as a C++ interface and are enabled for use
17363 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
17364 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
17365 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
17366 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
17367 ;; whole is distributed under the terms of the AGPL 3.
17368 (license license:agpl3)))
17370 (define-public r-ingredients
17372 (name "r-ingredients")
17377 (uri (cran-uri "ingredients" version))
17380 "0w46h1f28y5ypqm3ypsvk7yk9v7k8p21f1pzjl3ima8r1ivmhv12"))))
17381 (properties `((upstream-name . "ingredients")))
17382 (build-system r-build-system)
17384 `(("r-ggplot2" ,r-ggplot2)
17385 ("r-gridextra" ,r-gridextra)
17386 ("r-scales" ,r-scales)))
17387 (native-inputs `(("r-knitr" ,r-knitr)))
17388 (home-page "https://ModelOriented.github.io/ingredients/")
17389 (synopsis "Effects and importances of model ingredients")
17391 "This is a collection of tools for assessment of feature importance and
17392 feature effects. Key functions are:
17395 @item @code{feature_importance()} for assessment of global level feature
17397 @item @code{ceteris_paribus()} for calculation of the what-if plots,
17398 @item @code{partial_dependence()} for partial dependence plots,
17399 @item @code{conditional_dependence()} for conditional dependence plots,
17400 @item @code{accumulated_dependence()} for accumulated local effects plots,
17401 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
17402 aggregation of ceteris paribus profiles,
17403 @item generic @code{print()} and @code{plot()} for better usability of
17404 selected explainers,
17405 @item generic @code{plotD3()} for interactive, D3 based explanations, and
17406 @item generic @code{describe()} for explanations in natural language.
17408 (license license:gpl3)))
17410 (define-public r-ibreakdown
17412 (name "r-ibreakdown")
17417 (uri (cran-uri "iBreakDown" version))
17420 "1bfl5bh0x6z5a0cmdmx68sap9zdxa3kwdnyk57csxapc362yz108"))))
17421 (properties `((upstream-name . "iBreakDown")))
17422 (build-system r-build-system)
17423 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
17424 (native-inputs `(("r-knitr" ,r-knitr)))
17425 (home-page "https://ModelOriented.github.io/iBreakDown/")
17426 (synopsis "Model agnostic instance level variable attributions")
17428 "This package provides a model agnostic tool for decomposition of
17429 predictions from black boxes. It supports additive attributions and
17430 attributions with interactions. The Break Down Table shows contributions of
17431 every variable to a final prediction. The Break Down Plot presents variable
17432 contributions in a concise graphical way. This package works for
17433 classification and regression models.")
17434 (license license:gpl3)))
17436 (define-public r-dae
17443 (uri (cran-uri "dae" version))
17446 "126w1lb9pz8mb2ajl2vz5dj798nbifp0dypnzfgcwixif5g5bpqi"))))
17447 (build-system r-build-system)
17449 `(("r-ggplot2" ,r-ggplot2)
17450 ("r-plyr" ,r-plyr)))
17452 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
17453 (home-page "http://chris.brien.name")
17454 (synopsis "Functions useful in the design and ANOVA of experiments")
17456 "This package provides functions useful in the design and ANOVA of
17457 experiments. The content falls into the following groupings:
17461 @item factor manipulation functions,
17462 @item design functions,
17463 @item ANOVA functions,
17464 @item matrix functions,
17465 @item projector and canonical efficiency functions, and
17466 @item miscellaneous functions.
17469 There is a vignette called @code{DesignNotes} describing how to use the design
17470 functions for randomizing and assessing designs. The ANOVA functions
17471 facilitate the extraction of information when the @code{Error} function has
17472 been used in the call to @code{aov}.")
17473 (license license:gpl2)))
17475 (define-public r-dalex
17482 (uri (cran-uri "DALEX" version))
17485 "1hiknx55d91abyfj3w4a2xxin7f1q8h5k0041m7w93xjdc4kis98"))))
17486 (properties `((upstream-name . "DALEX")))
17487 (build-system r-build-system)
17489 `(("r-ggplot2" ,r-ggplot2)
17490 ("r-ibreakdown" ,r-ibreakdown)
17491 ("r-ingredients" ,r-ingredients)))
17492 (home-page "https://pbiecek.github.io/DALEX/")
17493 (synopsis "Descriptive machine learning explanations")
17495 "Machine Learning models are widely used and have various applications in
17496 classification or regression. Models created with boosting, bagging, stacking
17497 or similar techniques are often used due to their high performance, but such
17498 black-box models usually lack interpretability. The DALEX package contains
17499 various explainers that help to understand the link between input variables
17500 and model output.")
17501 ;; Any version of the GPL
17502 (license license:gpl3+)))
17504 (define-public r-enrichr
17511 (uri (cran-uri "enrichR" version))
17514 "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3"))))
17515 (properties `((upstream-name . "enrichR")))
17516 (build-system r-build-system)
17518 `(("r-ggplot2" ,r-ggplot2)
17520 ("r-rjson" ,r-rjson)))
17522 `(("r-knitr" ,r-knitr)))
17523 (home-page "https://cran.r-project.org/web/packages/enrichR/")
17524 (synopsis "R Interface to Enrichr database for analyzing gene sets")
17526 "This package provides an R interface to all Enrichr databases, a
17527 web-based tool for analyzing gene sets and returns any enrichment of common
17528 annotated biological functions.")
17529 (license license:gpl2+)))
17531 (define-public r-plot3d
17538 (uri (cran-uri "plot3D" version))
17541 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
17542 (properties `((upstream-name . "plot3D")))
17543 (build-system r-build-system)
17544 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
17545 (home-page "https://cran.r-project.org/web/packages/plot3D")
17546 (synopsis "Plot multi-dimensional data")
17548 "This package provides functions for viewing 2D and 3D data, including
17549 perspective plots, slice plots, surface plots, scatter plots, etc. It
17550 includes data sets from oceanography.")
17551 (license license:gpl3+)))
17553 (define-public r-ggfortify
17555 (name "r-ggfortify")
17560 (uri (cran-uri "ggfortify" version))
17563 "1wfm7l9bz6msh7rflgfv9dgbxh1ikz2ay0v7sgk9nkc24y6lhbpk"))))
17564 (build-system r-build-system)
17566 `(("r-dplyr" ,r-dplyr)
17567 ("r-ggplot2" ,r-ggplot2)
17568 ("r-gridextra" ,r-gridextra)
17569 ("r-scales" ,r-scales)
17570 ("r-stringr" ,r-stringr)
17571 ("r-tibble" ,r-tibble)
17572 ("r-tidyr" ,r-tidyr)))
17574 `(("r-knitr" ,r-knitr)))
17575 (home-page "https://github.com/sinhrks/ggfortify")
17576 (synopsis "Data visualization tools for statistical analysis results")
17578 "This package provides unified plotting tools for statistics commonly
17579 used, such as GLM, time series, PCA families, clustering and survival
17580 analysis. The package offers a single plotting interface for these analysis
17581 results and plots in a unified style using the @code{ggplot2} package.")
17582 (license license:gpl2)))
17584 (define-public r-refmanager
17586 (name "r-refmanager")
17591 (uri (cran-uri "RefManageR" version))
17594 "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps"))))
17595 (properties `((upstream-name . "RefManageR")))
17596 (build-system r-build-system)
17598 `(("r-httr" ,r-httr)
17599 ("r-jsonlite" ,r-jsonlite)
17600 ("r-lubridate" ,r-lubridate)
17602 ("r-stringr" ,r-stringr)
17603 ("r-xml2" ,r-xml2)))
17605 `(("r-knitr" ,r-knitr)))
17606 (home-page "https://github.com/ropensci/RefManageR/")
17607 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
17609 "This package provides tools for importing and working with bibliographic
17610 references. It greatly enhances the @code{bibentry} class by providing a
17611 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
17612 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
17613 by various formats for name lists (author by last names, translator by full
17614 names, etc.). Entries can be updated, combined, sorted, printed in a number
17615 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
17616 into R and converted to @code{BibEntry} objects.")
17617 ;; Any of these licenses may be picked.
17618 (license (list license:gpl2 license:gpl3 license:bsd-3))))
17620 (define-public r-citr
17627 (uri (cran-uri "citr" version))
17630 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
17631 (build-system r-build-system)
17633 `(("r-assertthat" ,r-assertthat)
17636 ("r-miniui" ,r-miniui)
17637 ("r-refmanager" ,r-refmanager)
17638 ("r-rstudioapi" ,r-rstudioapi)
17639 ("r-shiny" ,r-shiny)
17640 ("r-shinyjs" ,r-shinyjs)
17641 ("r-yaml" ,r-yaml)))
17642 (home-page "https://github.com/crsh/citr")
17643 (synopsis "RStudio add-in to insert Markdown citations")
17645 "This package provides functions and an RStudio add-in that search a
17646 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
17647 the current document.")
17648 (license license:expat)))
17650 (define-public r-xgboost
17653 (version "1.3.2.1")
17657 (uri (cran-uri "xgboost" version))
17660 "117q8xqm82589517fi8xicd8724v9c0wnq3qpl84h6nm3aw65x1g"))))
17661 (build-system r-build-system)
17663 `(("r-data-table" ,r-data-table)
17664 ("r-magrittr" ,r-magrittr)
17665 ("r-matrix" ,r-matrix)))
17667 `(("r-knitr" ,r-knitr)))
17668 (home-page "https://github.com/dmlc/xgboost")
17669 (synopsis "Extreme gradient boosting")
17671 "This package provides an R interface to Extreme Gradient Boosting, which
17672 is an efficient implementation of the gradient boosting framework from Chen
17673 and Guestrin (2016). The package includes efficient linear model solver and
17674 tree learning algorithms. The package can automatically do parallel
17675 computation on a single machine. It supports various objective functions,
17676 including regression, classification and ranking. The package is made to be
17677 extensible, so that users are also allowed to define their own objectives
17679 (license license:asl2.0)))
17681 (define-public r-umap
17684 (version "0.2.7.0")
17688 (uri (cran-uri "umap" version))
17691 "191vpy84s0bar06y9z1qx43x2kc4qp7lmrcmd0cvz2pnzq722jab"))))
17692 (build-system r-build-system)
17694 `(("r-openssl" ,r-openssl)
17696 ("r-reticulate" ,r-reticulate)
17697 ("r-rspectra" ,r-rspectra)))
17699 `(("r-knitr" ,r-knitr)))
17700 (home-page "https://github.com/tkonopka/umap")
17701 (synopsis "Uniform manifold approximation and projection")
17703 "Uniform manifold approximation and projection is a technique for
17704 dimension reduction. This package provides an interface to the UMAP algorithm
17705 in R, including a translation of the original algorithm into R.")
17706 (license license:expat)))
17708 (define-public r-uwot
17715 (uri (cran-uri "uwot" version))
17718 "08vxh085wnrxgwy35ksb4cr7ccjvd98pyr2zlgarqryfgc1bdqbf"))))
17719 (build-system r-build-system)
17721 `(("r-dqrng" ,r-dqrng)
17723 ("r-irlba" ,r-irlba)
17724 ("r-matrix" ,r-matrix)
17726 ("r-rcppannoy" ,r-rcppannoy)
17727 ("r-rcppprogress" ,r-rcppprogress)
17728 ("r-rspectra" ,r-rspectra)))
17729 (home-page "https://github.com/jlmelville/uwot")
17730 (synopsis "Uniform manifold approximation and projection")
17732 "This package provides an implementation of the Uniform Manifold
17733 Approximation and Projection dimensionality reduction by McInnes et
17734 al. (2018). It also provides means to transform new data and to carry out
17735 supervised dimensionality reduction. An implementation of the related
17736 LargeVis method of Tang et al. (2016) is also provided.")
17737 (license license:gpl3)))
17739 (define-public r-kableextra
17741 (name "r-kableextra")
17746 (uri (cran-uri "kableExtra" version))
17749 "1zixccpgy9x95fgzfgxc43pm020c80c21flch71klc3zzzsq53gf"))))
17750 (properties `((upstream-name . "kableExtra")))
17751 (build-system r-build-system)
17753 `(("r-digest" ,r-digest)
17755 ("r-htmltools" ,r-htmltools)
17756 ("r-knitr" ,r-knitr)
17757 ("r-magrittr" ,r-magrittr)
17758 ("r-rmarkdown" ,r-rmarkdown)
17759 ("r-rstudioapi" ,r-rstudioapi)
17760 ("r-rvest" ,r-rvest)
17761 ("r-scales" ,r-scales)
17762 ("r-stringr" ,r-stringr)
17763 ("r-viridislite" ,r-viridislite)
17764 ("r-webshot" ,r-webshot)
17765 ("r-xml2" ,r-xml2)))
17767 `(("r-knitr" ,r-knitr)))
17768 (home-page "https://haozhu233.github.io/kableExtra/")
17769 (synopsis "Construct complex tables with pipe syntax")
17771 "Build complex HTML or LaTeX tables using @code{kable()} from
17772 @code{knitr} and the piping syntax from @code{magrittr}. The function
17773 @code{kable()} is a light weight table generator coming from @code{knitr}.
17774 This package simplifies the way to manipulate the HTML or LaTeX codes
17775 generated by @code{kable()} and allows users to construct complex tables and
17776 customize styles using a readable syntax.")
17777 (license license:expat)))
17779 (define-public r-glasso
17786 (uri (cran-uri "glasso" version))
17788 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
17789 (build-system r-build-system)
17790 (native-inputs `(("gfortran" ,gfortran)))
17791 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
17792 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
17794 "This is a package for estimation of a sparse inverse covariance matrix
17795 using a lasso (L1) penalty. Facilities are provided for estimates along a
17796 path of values for the regularization parameter.")
17797 (license license:gpl2)))
17799 (define-public r-rhpcblasctl
17801 (name "r-rhpcblasctl")
17802 (version "0.20-137")
17806 (uri (cran-uri "RhpcBLASctl" version))
17809 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
17810 (properties `((upstream-name . "RhpcBLASctl")))
17811 (build-system r-build-system)
17812 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
17813 (synopsis "Control the number of threads on BLAS")
17815 "This package allows you to control the number of threads the BLAS
17816 library uses. It is also possible to control the number of threads in
17818 (license license:agpl3+)))
17820 (define-public r-lda
17827 (uri (cran-uri "lda" version))
17830 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
17831 (build-system r-build-system)
17832 (home-page "https://cran.r-project.org/web/packages/lda/")
17833 (synopsis "Collapsed Gibbs sampling methods for topic models")
17835 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
17836 related models. This includes (but is not limited to) sLDA, corrLDA, and the
17837 mixed-membership stochastic blockmodel. Inference for all of these models is
17838 implemented via a fast collapsed Gibbs sampler written in C. Utility
17839 functions for reading/writing data typically used in topic models, as well as
17840 tools for examining posterior distributions are also included.")
17841 ;; Any version of the LGPL
17842 (license license:lgpl3+)))
17844 (define-public r-rann-l1
17851 (uri (cran-uri "RANN.L1" version))
17854 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
17855 (properties `((upstream-name . "RANN.L1")))
17856 (build-system r-build-system)
17857 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
17858 (synopsis "Fast nearest neighbour search using L1 metric")
17860 "This package provides tools to find the k nearest neighbours for every
17861 point in a given dataset in O(N log N) time using Arya and Mount's ANN
17862 library. There is support for approximate as well as exact searches, fixed
17863 radius searches and @code{bd} as well as @code{kd} trees. The distance is
17864 computed using the L1 (Manhattan, taxicab) metric.")
17865 (license license:gpl3+)))
17867 (define-public r-leiden
17874 (uri (cran-uri "leiden" version))
17877 "14iqn5iqcya6bqbjvjivpd7q9gwc323sj29y7ssrbhb3sz9982bp"))))
17878 (properties `((upstream-name . "leiden")))
17879 (build-system r-build-system)
17881 `(("r-igraph" ,r-igraph)
17882 ("r-matrix" ,r-matrix)
17883 ("r-reticulate" ,r-reticulate)))
17885 `(("r-knitr" ,r-knitr)))
17886 (home-page "https://github.com/TomKellyGenetics/leiden")
17887 (synopsis "R implementation of Leiden clustering algorithm")
17889 "This package implements the Python @code{leidenalg} module to be called
17890 in R. It enables clustering using the Leiden algorithm for partitioning a
17891 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
17892 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
17893 (license license:gpl3)))
17895 (define-public r-patchwork
17897 (name "r-patchwork")
17902 (uri (cran-uri "patchwork" version))
17905 "10glgkf58lcykcwda1hj6xdps02m3i247qynk6s2jmwljagps3fg"))))
17906 (build-system r-build-system)
17908 `(("r-ggplot2" ,r-ggplot2)
17909 ("r-gtable" ,r-gtable)))
17911 `(("r-knitr" ,r-knitr)))
17912 (home-page "https://github.com/thomasp85/patchwork")
17913 (synopsis "Compose ggplot2 plots")
17915 "The @code{ggplot2} package provides a strong API for sequentially
17916 building up a plot, but does not concern itself with composition of multiple
17917 plots. Patchwork is a package that expands the API to allow for arbitrarily
17918 complex composition of plots by providing mathematical operators for combining
17920 (license license:expat)))
17922 (define-public r-liger
17929 (uri (git-reference
17930 (url "https://github.com/MacoskoLab/liger")
17931 (commit (string-append "v" version))))
17932 (file-name (git-file-name name version))
17935 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
17936 (modules '((guix build utils)))
17939 (delete-file "inst/java/ModularityOptimizer.jar")
17941 (build-system r-build-system)
17944 (modify-phases %standard-phases
17945 (add-after 'unpack 'build-java-part
17946 (lambda* (#:key inputs #:allow-other-keys)
17947 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
17948 (for-each (lambda (file) (invoke "javac" file))
17949 (find-files "." "\\.java$"))
17950 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
17951 (find-files "." "\\.class$"))
17954 `(("r-cowplot" ,r-cowplot)
17955 ("r-dosnow" ,r-dosnow)
17956 ("r-dplyr" ,r-dplyr)
17958 ("r-foreach" ,r-foreach)
17959 ("r-ggplot2" ,r-ggplot2)
17960 ("r-ggrepel" ,r-ggrepel)
17961 ("r-hmisc" ,r-hmisc)
17963 ("r-irlba" ,r-irlba)
17964 ("r-matrix" ,r-matrix)
17965 ("r-mclust" ,r-mclust)
17966 ("r-patchwork" ,r-patchwork)
17968 ("r-rann-l1" ,r-rann-l1)
17970 ("r-rcpparmadillo" ,r-rcpparmadillo)
17971 ("r-riverplot" ,r-riverplot)
17972 ("r-rtsne" ,r-rtsne)
17973 ("r-snow" ,r-snow)))
17975 `(("jdk" ,icedtea "jdk")
17976 ;; See https://github.com/MacoskoLab/liger/issues/96
17977 ;; The optimizer is released under the Expat license.
17981 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
17984 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
17986 ("r-knitr" ,r-knitr))) ; for vignettes
17987 (home-page "https://github.com/MacoskoLab/liger")
17988 (synopsis "Integrate and analyze multiple single-cell datasets")
17990 "LIGER is a package for integrating and analyzing multiple single-cell
17991 datasets, developed and maintained by the Macosko lab. It relies on
17992 integrative non-negative matrix factorization to identify shared and
17993 dataset-specific factors.")
17994 (license license:gpl3)))
17996 (define-public r-harmony
18003 (uri (git-reference
18004 (url "https://github.com/immunogenomics/harmony")
18006 (file-name (git-file-name name version))
18009 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
18010 (modules '((guix build utils)))
18013 (for-each delete-file '("config.status" "configure"))
18015 (build-system r-build-system)
18017 `(("r-cowplot" ,r-cowplot)
18018 ("r-dplyr" ,r-dplyr)
18019 ("r-ggplot2" ,r-ggplot2)
18020 ("r-irlba" ,r-irlba)
18021 ("r-matrix" ,r-matrix)
18023 ("r-rcpparmadillo" ,r-rcpparmadillo)
18024 ("r-rcppprogress" ,r-rcppprogress)
18025 ("r-rlang" ,r-rlang)
18026 ("r-tibble" ,r-tibble)
18027 ("r-tidyr" ,r-tidyr)))
18029 `(("autoconf" ,autoconf)))
18030 (home-page "https://github.com/immunogenomics/harmony")
18031 (synopsis "Integration of single cell sequencing data")
18033 "This package provides an implementation of the Harmony algorithm for
18034 single cell integration, described in Korsunsky et al
18035 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
18036 function and interfaces to external frameworks.")
18037 (license license:gpl3)))
18039 (define-public r-covr
18046 (uri (cran-uri "covr" version))
18048 (base32 "0v5cv3cw2kpdr6wxmkbd3wclavr17zipypdcb10hhmpa4cvgqk55"))))
18049 (properties `((upstream-name . "covr")))
18050 (build-system r-build-system)
18052 `(("r-crayon" ,r-crayon)
18053 ("r-digest" ,r-digest)
18055 ("r-jsonlite" ,r-jsonlite)
18057 ("r-withr" ,r-withr)
18058 ("r-yaml" ,r-yaml)))
18060 `(("r-knitr" ,r-knitr))) ; for vignettes
18061 (home-page "https://github.com/r-lib/covr")
18062 (synopsis "Test coverage for R packages")
18064 "Thisp package enables you to track and report code coverage for your
18065 package and (optionally) upload the results to a coverage service. Code
18066 coverage is a measure of the amount of code being exercised by a set of tests.
18067 It is an indirect measure of test quality and completeness. This package is
18068 compatible with any testing methodology or framework and tracks coverage of
18069 both R code and compiled C/C++/FORTRAN code.")
18070 (license license:gpl3)))
18072 (define-public r-systemfonts
18074 (name "r-systemfonts")
18079 (uri (cran-uri "systemfonts" version))
18082 "15x7qx8iigkybgz6b6s66i3mh75vgynzpd50nw05wflfwzcv87a0"))))
18083 (properties `((upstream-name . "systemfonts")))
18084 (build-system r-build-system)
18086 `(("r-cpp11" ,r-cpp11)))
18088 `(("fontconfig" ,fontconfig)
18091 `(("pkg-config" ,pkg-config)
18092 ("r-knitr" ,r-knitr)))
18093 (home-page "https://github.com/r-lib/systemfonts")
18094 (synopsis "System native font finding")
18096 "This package provides system native access to the font catalogue. As
18097 font handling varies between systems it is difficult to correctly locate
18098 installed fonts across different operating systems. The 'systemfonts' package
18099 provides bindings to the native libraries for finding font files that can then
18100 be used further by e.g. graphic devices.")
18101 (license license:expat)))
18103 (define-public r-graphlayouts
18105 (name "r-graphlayouts")
18110 (uri (cran-uri "graphlayouts" version))
18113 "05v7ss18bflhqa4ipsca8iw2ln8ddbaiyrizx2a5cwq81g5qq3rq"))))
18114 (properties `((upstream-name . "graphlayouts")))
18115 (build-system r-build-system)
18117 `(("r-igraph" ,r-igraph)
18119 ("r-rcpparmadillo" ,r-rcpparmadillo)))
18120 (home-page "https://github.com/schochastics/graphlayouts")
18121 (synopsis "Additional layout algorithms for network visualizations")
18123 "This package provides several layout algorithms to visualize networks
18124 which are not part of the igraph library. Most are based on the concept of
18125 stress majorization by Gansner et al. (2004)
18126 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
18127 emphasize hidden group structures in networks or focus on specific nodes.")
18128 (license license:expat)))
18130 (define-public r-terra
18137 (uri (cran-uri "terra" version))
18140 "1vsh55sq56shc8s2vmkl27yvrdbrbn3l6jrigqf2hmvppkb2jsbg"))))
18141 (properties `((upstream-name . "terra")))
18142 (build-system r-build-system)
18147 ("sqlite" ,sqlite) ; needed for proj
18150 `(("r-raster" ,r-raster)
18151 ("r-rcpp" ,r-rcpp)))
18153 `(("pkg-config" ,pkg-config)))
18154 (home-page "https://rspatial.org/terra")
18155 (synopsis "Spatial data analysis")
18157 "This package provides methods for spatial data analysis, especially
18158 raster data. The included methods allow for low-level data manipulation as
18159 well as high-level global, local, zonal, and focal computation. The predict
18160 and interpolate methods facilitate the use of regression type (interpolation,
18161 machine learning) models for spatial prediction. Processing of very large
18162 files is supported.")
18163 (license license:gpl3+)))
18165 (define-public r-tidygraph
18167 (name "r-tidygraph")
18172 (uri (cran-uri "tidygraph" version))
18175 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
18176 (properties `((upstream-name . "tidygraph")))
18177 (build-system r-build-system)
18179 `(("r-dplyr" ,r-dplyr)
18180 ("r-igraph" ,r-igraph)
18181 ("r-magrittr" ,r-magrittr)
18182 ("r-pillar" ,r-pillar)
18185 ("r-rlang" ,r-rlang)
18186 ("r-tibble" ,r-tibble)
18187 ("r-tidyr" ,r-tidyr)))
18188 (home-page "https://github.com/thomasp85/tidygraph")
18189 (synopsis "Tidy API for graph manipulation")
18191 "This package provides a graph implementation that can be thought of as
18192 two tidy data frames describing node and edge data respectively. It provides
18193 an approach to manipulate these two virtual data frames using the API defined
18194 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
18195 common graph algorithms.")
18196 (license license:expat)))
18198 (define-public r-soupx
18199 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
18203 (version (git-version "0.3.1" revision commit))
18207 (uri (git-reference
18208 (url "https://github.com/constantAmateur/SoupX")
18210 (file-name (git-file-name name version))
18213 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
18214 (properties `((upstream-name . "SoupX")))
18215 (build-system r-build-system)
18217 `(("r-ggplot2" ,r-ggplot2)
18218 ("r-matrix" ,r-matrix)
18219 ("r-seurat" ,r-seurat)))
18220 (home-page "https://github.com/constantAmateur/SoupX")
18221 (synopsis "Single cell mRNA Soup eXterminator")
18223 "This package provides a package for quantifying, profiling and
18224 removing cell free mRNA contamination (the \"soup\") from droplet based single
18225 cell RNA-seq experiments.")
18226 (license license:gpl2))))
18228 (define-public r-assertr
18235 (uri (cran-uri "assertr" version))
18238 "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650"))))
18239 (build-system r-build-system)
18241 `(("r-dplyr" ,r-dplyr)
18243 ("r-rlang" ,r-rlang)))
18245 `(("r-knitr" ,r-knitr))) ; needed for vignette
18246 (home-page "https://github.com/ropensci/assertr")
18247 (synopsis "Assertive programming for R analysis pipelines")
18249 "This package provides functionality to assert conditions that have to be
18250 met so that errors in data used in analysis pipelines can fail quickly. It is
18251 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
18253 (license license:expat)))
18255 (define-public r-parameters
18257 (name "r-parameters")
18262 (uri (cran-uri "parameters" version))
18265 "020k3vxnp0vjrlkcxx5vj30vag474hw48zxzw9315whsq4hhhbqc"))))
18266 (properties `((upstream-name . "parameters")))
18267 (build-system r-build-system)
18269 `(("r-bayestestr" ,r-bayestestr)
18270 ("r-insight" ,r-insight)))
18272 `(("r-knitr" ,r-knitr)))
18273 (home-page "https://cran.r-project.org/web/packages/parameters")
18274 (synopsis "Processing of model parameters")
18276 "This package provides utilities for processing the parameters of various
18277 statistical models. Beyond computing p values, CIs, and other indices for a
18278 wide variety of models, this package implements features like standardization
18279 or bootstrapping of parameters and models, feature reduction (feature
18280 extraction and variable selection) as well as conversion between indices of
18282 (license license:gpl3)))
18284 (define-public r-rgdal
18291 (uri (cran-uri "rgdal" version))
18293 (base32 "0vnb7kw762y349pda4aq1hx0smafylmn3635l963qykfji5p99cw"))))
18294 (properties `((upstream-name . "rgdal")))
18295 (build-system r-build-system)
18303 `(("pkg-config" ,pkg-config)
18304 ("r-knitr" ,r-knitr)))
18305 (home-page "http://rgdal.r-forge.r-project.org")
18306 (synopsis "Bindings for the Geospatial Data Abstraction Library")
18308 "This package provides bindings to the Geospatial Data Abstraction
18309 Library (GDAL) and access to projection/transformation operations from the
18311 (license license:gpl2+)))
18313 (define-public r-insol
18320 (uri (cran-uri "insol" version))
18323 "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3"))))
18324 (properties `((upstream-name . "insol")))
18325 (build-system r-build-system)
18327 `(("r-raster" ,r-raster)))
18329 `(("gfortran" ,gfortran)))
18330 (home-page "https://meteoexploration.com/R/insol/index.html")
18331 (synopsis "Tools for calculating solar radiation")
18333 "This package provides functions to compute insolation on tilted
18334 surfaces, computes atmospheric transmittance and related parameters such as:
18335 Earth radius vector, declination, sunset and sunrise, daylength, equation of
18336 time, vector in the direction of the sun, vector normal to surface, and some
18337 atmospheric physics.")
18338 (license license:gpl2+)))
18340 (define-public r-lifecycle
18342 (name "r-lifecycle")
18347 (uri (cran-uri "lifecycle" version))
18350 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
18351 (properties `((upstream-name . "lifecycle")))
18352 (build-system r-build-system)
18354 `(("r-glue" ,r-glue)
18355 ("r-rlang" ,r-rlang)))
18357 `(("r-knitr" ,r-knitr))) ; for vignettes
18358 (home-page "https://github.com/r-lib/lifecycle")
18359 (synopsis "Manage the life cycle of your package functions")
18361 "Manage the life cycle of your exported functions with shared
18362 conventions, documentation badges, and non-invasive deprecation warnings. The
18363 lifecycle package defines four development stages (experimental, maturing,
18364 stable, and questioning) and three deprecation stages (soft-deprecated,
18365 deprecated, and defunct). It makes it easy to insert badges corresponding to
18366 these stages in your documentation. Usage of deprecated functions are
18367 signalled with increasing levels of non-invasive verbosity.")
18368 (license license:gpl3)))
18370 (define-public r-assertable
18372 (name "r-assertable")
18377 (uri (cran-uri "assertable" version))
18380 "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4"))))
18381 (build-system r-build-system)
18383 `(("r-data-table" ,r-data-table)))
18385 `(("r-knitr" ,r-knitr)))
18386 (home-page "https://cran.r-project.org/web/packages/assertable/")
18387 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
18388 (description "This package provides simple, flexible assertions on
18389 data.frame or data.table objects with verbose output for vetting. While other
18390 assertion packages apply towards more general use-cases, @code{assertable} is
18391 tailored towards tabular data. It includes functions to check variable names
18392 and values, whether the dataset contains all combinations of a given set of
18393 unique identifiers, and whether it is a certain length. In addition,
18394 @code{assertable} includes utility functions to check the existence of target
18395 files and to efficiently import multiple tabular data files into one
18397 (license license:gpl3)))
18399 (define-public r-quadprog
18401 (name "r-quadprog")
18406 (uri (cran-uri "quadprog" version))
18408 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
18409 (build-system r-build-system)
18411 `(("gfortran" ,gfortran)))
18412 (home-page "https://cran.r-project.org/web/packages/quadprog")
18413 (synopsis "Functions to solve quadratic programming problems")
18415 "This package contains routines and documentation for solving quadratic
18416 programming problems.")
18417 (license license:gpl3+)))
18419 (define-public r-desolve
18426 (uri (cran-uri "deSolve" version))
18428 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
18429 (properties `((upstream-name . "deSolve")))
18430 (build-system r-build-system)
18432 `(("gfortran" ,gfortran)))
18433 (home-page "https://desolve.r-forge.r-project.org/")
18434 (synopsis "Solvers for initial value problems of differential equations")
18435 (description "This package provides functions that solve initial value
18436 problems of a system of first-order @dfn{ordinary differential
18437 equations} (ODE), of @dfn{partial differential equations} (PDE), of
18438 @dfn{differential algebraic equations} (DAE), and of delay differential
18439 equations. The functions provide an interface to the FORTRAN functions
18440 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
18441 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
18442 C-implementation of solvers of the Runge-Kutta family with fixed or variable
18443 time steps. The package contains routines designed for solving ODEs resulting
18444 from 1-D, 2-D and 3-D partial differential equations that have been converted
18445 to ODEs by numerical differencing.")
18446 (license license:gpl2+)))
18448 (define-public r-pracma
18454 (uri (cran-uri "pracma" version))
18456 (base32 "0g5r5ir5k43ba0ngnsanp108k479l2dnsjd5w6idk1d34ivqs7yg"))))
18457 (build-system r-build-system)
18458 (home-page "https://cran.r-project.org/web/packages/pracma/")
18459 (synopsis "Practical numerical math functions")
18460 (description "This package provides functions for numerical analysis and
18461 linear algebra, numerical optimization, differential equations, plus some
18462 special functions. It uses Matlab function names where appropriate to simplify
18464 (license license:gpl3+)))
18466 (define-public r-subplex
18473 (uri (cran-uri "subplex" version))
18476 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
18477 (build-system r-build-system)
18479 `(("gfortran" ,gfortran)))
18480 (home-page "https://cran.r-project.org/web/packages/subplex")
18481 (synopsis "Unconstrained optimization using the subplex algorithm")
18483 "This package implements the Subplex optimization algorithm.
18484 It solves unconstrained optimization problems using a simplex method on
18485 subspaces. The method is well suited for optimizing objective functions that
18486 are noisy or are discontinuous at the solution.")
18487 (license license:gpl3+)))
18489 (define-public r-txtplot
18496 (uri (cran-uri "txtplot" version))
18499 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
18500 (build-system r-build-system)
18501 (home-page "https://cran.r-project.org/web/packages/txtplot/")
18502 (synopsis "Text-based plotting")
18503 (description "This package provides functions to produce rudimentary ASCII
18504 graphics directly in the terminal window. This package provides a basic
18505 plotting function (and equivalents of curve, density, acf and barplot) as well
18506 as a boxplot function.")
18507 (license license:lgpl3+)))
18509 (define-public r-bio3d
18516 (uri (cran-uri "bio3d" version))
18519 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
18520 (properties `((upstream-name . "bio3d")))
18521 (build-system r-build-system)
18522 (inputs `(("zlib" ,zlib)))
18523 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
18524 (home-page "http://thegrantlab.org/bio3d/")
18525 (synopsis "Biological structure analysis")
18527 "This package provides utilities to process, organize and explore protein
18528 structure, sequence and dynamics data. Features include the ability to read
18529 and write structure, sequence and dynamic trajectory data, perform sequence
18530 and structure database searches, data summaries, atom selection, alignment,
18531 superposition, rigid core identification, clustering, torsion analysis,
18532 distance matrix analysis, structure and sequence conservation analysis, normal
18533 mode analysis, principal component analysis of heterogeneous structure data,
18534 and correlation network analysis from normal mode and molecular dynamics data.
18535 In addition, various utility functions are provided to enable the statistical
18536 and graphical power of the R environment to work with biological sequence and
18538 (license license:gpl2+)))
18540 (define-public r-bios2cor
18542 (name "r-bios2cor")
18547 (uri (cran-uri "Bios2cor" version))
18550 "1wkj9vr33m9jilidil9jpw5rzr3pf7gkimxdvch22ks4bgkx7l1w"))))
18551 (properties `((upstream-name . "Bios2cor")))
18552 (build-system r-build-system)
18554 `(("r-bigmemory" ,r-bigmemory)
18555 ("r-bio3d" ,r-bio3d)
18556 ("r-circular" ,r-circular)
18557 ("r-igraph" ,r-igraph)))
18558 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
18559 (synopsis "From biological sequences and simulations to correlation analysis")
18561 "This package provides utilities for computation and analysis of
18562 correlation/covariation in multiple sequence alignments and in side chain
18563 motions during molecular dynamics simulations. Features include the
18564 computation of correlation/covariation scores using a variety of scoring
18565 functions between either sequence positions in alignments or side chain
18566 dihedral angles in molecular dynamics simulations and utilities to analyze the
18567 correlation/covariation matrix through a variety of tools including network
18568 representation and principal components analysis. In addition, several
18569 utility functions are based on the R graphical environment to provide friendly
18570 tools for help in data interpretation.")
18571 (license license:gpl2+)))
18573 ;; This package includes minified JavaScript files. When upgrading please
18574 ;; check that there are no new minified JavaScript files.
18575 (define-public r-networkd3
18577 (name "r-networkd3")
18582 (uri (cran-uri "networkD3" version))
18585 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
18588 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
18590 (properties `((upstream-name . "networkD3")))
18591 (build-system r-build-system)
18593 `(#:modules ((guix build utils)
18594 (guix build r-build-system)
18598 (modify-phases %standard-phases
18599 (add-after 'unpack 'process-javascript
18600 (lambda* (#:key inputs #:allow-other-keys)
18601 (with-directory-excursion "inst/htmlwidgets/lib/"
18605 `((,(assoc-ref inputs "d3.v4.js")
18606 "d3-4.5.0/d3.min.js"))))
18607 (lambda (sources targets)
18608 (for-each (lambda (source target)
18609 (format #t "Processing ~a --> ~a~%"
18611 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
18612 (call-with-output-file target
18614 (dump-port minified port)))))
18615 sources targets))))
18618 `(("uglify-js" ,uglify-js)
18619 ;; NOTE: Make sure that this version of d3 is still valid when
18620 ;; upgrading the package.
18624 (uri "https://d3js.org/d3.v4.js")
18627 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
18629 `(("r-htmlwidgets" ,r-htmlwidgets)
18630 ("r-igraph" ,r-igraph)
18631 ("r-magrittr" ,r-magrittr)))
18632 (home-page "https://cran.r-project.org/package=networkD3")
18633 (synopsis "D3 JavaScript network graphs from R")
18635 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
18637 (license license:gpl3+)))
18639 (define-public r-aasea
18646 (uri (cran-uri "aaSEA" version))
18649 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
18650 (properties `((upstream-name . "aaSEA")))
18651 (build-system r-build-system)
18653 `(("r-bios2cor" ,r-bios2cor)
18655 ("r-hmisc" ,r-hmisc)
18656 ("r-magrittr" ,r-magrittr)
18657 ("r-networkd3" ,r-networkd3)
18658 ("r-plotly" ,r-plotly)
18659 ("r-seqinr" ,r-seqinr)
18660 ("r-shiny" ,r-shiny)
18661 ("r-shinydashboard" ,r-shinydashboard)))
18662 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
18663 (synopsis "Amino acid substitution effect analyzer")
18665 "Given a protein multiple sequence alignment, it is a daunting task to
18666 assess the effects of substitutions along sequence length. The aaSEA package
18667 is intended to help researchers to rapidly analyze property changes caused by
18668 single, multiple and correlated amino acid substitutions in proteins.")
18669 (license license:gpl3)))
18671 (define-public r-abacus
18678 (uri (cran-uri "ABACUS" version))
18681 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
18682 (properties `((upstream-name . "ABACUS")))
18683 (build-system r-build-system)
18685 `(("r-ggplot2" ,r-ggplot2)
18686 ("r-shiny" ,r-shiny)))
18687 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
18688 (synopsis "Apps-based activities for communicating and understanding statistics")
18690 "This package provides a set of Shiny apps for effective communication
18691 and understanding in statistics. The current version includes properties of
18692 normal distribution, properties of sampling distribution, one-sample z and t
18693 tests, two samples independent (unpaired) t test and analysis of variance.")
18694 (license license:gpl3)))
18696 (define-public r-abc-rap
18703 (uri (cran-uri "ABC.RAP" version))
18706 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
18707 (properties `((upstream-name . "ABC.RAP")))
18708 (build-system r-build-system)
18709 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
18710 (synopsis "Array-based CpG region analysis pipeline")
18712 "This package aims to identify candidate genes that are differentially
18713 methylated between cases and controls. It applies Student's t-test and delta
18714 beta analysis to identify candidate genes containing multiple CpG sites.")
18715 (license license:gpl3)))
18717 (define-public r-abcadm
18724 (uri (cran-uri "abcADM" version))
18727 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
18728 (properties `((upstream-name . "abcADM")))
18729 (build-system r-build-system)
18732 ("r-rcpp" ,r-rcpp)))
18733 (home-page "https://cran.r-project.org/web/packages/abcADM/")
18734 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
18736 "This package provides tools to estimate parameters of accumulated
18737 damage (load duration) models based on failure time data under a Bayesian
18738 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
18739 long-term reliability under stochastic load profiles.")
18740 (license license:gpl3)))
18742 (define-public r-rglpk
18749 (uri (cran-uri "Rglpk" version))
18752 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
18753 (properties `((upstream-name . "Rglpk")))
18754 (build-system r-build-system)
18756 `(("r-slam" ,r-slam)))
18759 (home-page "https://r-forge.r-project.org/projects/rglp/")
18760 (synopsis "R interface to the GNU Linear Programming Kit")
18762 "This package provides an R interface to the GNU Linear Programming Kit,
18763 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
18764 integer linear programming} (MILP) and other related problems.")
18766 (license (list license:gpl2 license:gpl3))))
18768 (define-public r-abcdefba
18770 (name "r-abcdefba")
18775 (uri (cran-uri "abcdeFBA" version))
18778 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
18779 (properties `((upstream-name . "abcdeFBA")))
18780 (build-system r-build-system)
18782 `(("r-corrplot" ,r-corrplot)
18783 ("r-lattice" ,r-lattice)
18785 ("r-rglpk" ,r-rglpk)))
18786 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
18787 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
18789 "This package provides functions for Constraint Based Simulation using
18790 Flux Balance Analysis and informative analysis of the data generated during
18792 (license license:gpl2)))
18794 (define-public r-abcrlda
18801 (uri (cran-uri "abcrlda" version))
18804 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
18805 (properties `((upstream-name . "abcrlda")))
18806 (build-system r-build-system)
18807 (home-page "https://ieeexplore.ieee.org/document/8720003/")
18808 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
18810 "This package offers methods to perform @dfn{asymptotically
18811 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
18812 cost-sensitive binary classification. The bias-correction is an estimate of
18813 the bias term added to regularized discriminant analysis that minimizes the
18815 (license license:gpl3)))
18817 (define-public r-abemus
18824 (uri (cran-uri "abemus" version))
18827 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
18828 (properties `((upstream-name . "abemus")))
18829 (build-system r-build-system)
18831 `(("r-data-table" ,r-data-table)))
18832 (home-page "https://cran.r-project.org/web/packages/abemus/")
18833 (synopsis "Adaptive base error model in ultra-deep sequencing data")
18835 "This package provides an implementation of @dfn{Adaptive Base Error
18836 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
18837 platform-specific genetic knowledge and empirical signal to readily detect and
18838 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
18839 cell free DNA} (cfDNA).")
18840 (license license:gpl3)))
18842 ;; This package includes minified JavaScript files. When upgrading please
18843 ;; check that there are no new minified JavaScript files.
18844 (define-public r-rintrojs
18846 (name "r-rintrojs")
18851 (uri (cran-uri "rintrojs" version))
18854 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
18855 (properties `((upstream-name . "rintrojs")))
18856 (build-system r-build-system)
18858 `(#:modules ((guix build utils)
18859 (guix build r-build-system)
18863 (modify-phases %standard-phases
18864 (add-after 'unpack 'process-javascript
18865 (lambda* (#:key inputs #:allow-other-keys)
18866 (with-directory-excursion "inst/javascript/introjs/"
18870 `((,(assoc-ref inputs "intro.js")
18872 (lambda (sources targets)
18873 (for-each (lambda (source target)
18874 (format #t "Processing ~a --> ~a~%"
18876 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
18877 (call-with-output-file target
18879 (dump-port minified port)))))
18880 sources targets))))
18883 `(("uglify-js" ,uglify-js)
18887 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
18890 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
18892 `(("r-jsonlite" ,r-jsonlite)
18893 ("r-shiny" ,r-shiny)))
18894 (home-page "https://github.com/carlganz/rintrojs")
18895 (synopsis "Wrapper for the Intro.js library")
18897 "This package provides a wrapper for the @url{http://www.introjs.com,
18898 Intro.js} library. This package makes it easy to include step-by-step
18899 introductions, and clickable hints in a Shiny application. It supports both
18900 static introductions in the UI, and programmatic introductions from the
18902 (license license:agpl3+)))
18904 (define-public r-sysfonts
18906 (name "r-sysfonts")
18911 (uri (cran-uri "sysfonts" version))
18914 "00kbazxw6zd1kakfshffdj928krca53bw9k78k0zar40mbqxiwd5"))))
18915 (properties `((upstream-name . "sysfonts")))
18916 (build-system r-build-system)
18918 `(("freetype" ,freetype)
18922 `(("pkg-config" ,pkg-config)))
18923 (home-page "https://github.com/yixuan/sysfonts")
18924 (synopsis "Loading fonts into R")
18926 "This is a package to simplify loading of system fonts and Google Fonts
18927 into R, in order to support other packages.")
18928 (license license:gpl2)))
18930 (define-public r-showtextdb
18932 (name "r-showtextdb")
18937 (uri (cran-uri "showtextdb" version))
18940 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
18941 (properties `((upstream-name . "showtextdb")))
18942 (build-system r-build-system)
18944 `(("r-sysfonts" ,r-sysfonts)))
18945 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
18946 (synopsis "Font files for the 'showtext' package")
18948 "This package provides font files that can be used by the @code{showtext}
18950 (license license:asl2.0)))
18952 (define-public r-showtext
18954 (name "r-showtext")
18959 (uri (cran-uri "showtext" version))
18962 "0y5mw6ffk92r7b22irrfhdmj4hxfl0d1wjxj14hznbapc4qm6f0z"))))
18963 (properties `((upstream-name . "showtext")))
18964 (build-system r-build-system)
18966 `(("freetype" ,freetype)
18970 `(("r-showtextdb" ,r-showtextdb)
18971 ("r-sysfonts" ,r-sysfonts)))
18973 `(("pkg-config" ,pkg-config)
18974 ("r-knitr" ,r-knitr)))
18975 (home-page "https://github.com/yixuan/showtext")
18976 (synopsis "Using fonts more easily in R graphs")
18978 "This package aims to make it easy to use various types of
18979 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
18980 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
18981 will be converted into polygons or raster images, hence after the plot has
18982 been created, it no longer relies on the font files. No external software
18983 such as Ghostscript is needed to use this package.")
18984 (license license:asl2.0)))
18986 (define-public r-emojifont
18988 (name "r-emojifont")
18993 (uri (cran-uri "emojifont" version))
18996 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
18997 (properties `((upstream-name . "emojifont")))
18998 (build-system r-build-system)
19000 `(("r-ggplot2" ,r-ggplot2)
19001 ("r-proto" ,r-proto)
19002 ("r-showtext" ,r-showtext)
19003 ("r-sysfonts" ,r-sysfonts)))
19004 (home-page "https://guangchuangyu.github.io/emojifont")
19005 (synopsis "Emoji and Font Awesome in R graphics")
19007 "This package enables the use of emoji and the Font Awesome glyphs in
19008 both base and ggplot2 graphics.")
19009 (license license:artistic2.0)))
19011 (define-public r-abstractr
19013 (name "r-abstractr")
19018 (uri (cran-uri "abstractr" version))
19021 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
19022 (properties `((upstream-name . "abstractr")))
19023 (build-system r-build-system)
19025 `(("r-colourpicker" ,r-colourpicker)
19026 ("r-emojifont" ,r-emojifont)
19027 ("r-ggplot2" ,r-ggplot2)
19028 ("r-gridextra" ,r-gridextra)
19029 ("r-rintrojs" ,r-rintrojs)
19030 ("r-shiny" ,r-shiny)
19031 ("r-shinythemes" ,r-shinythemes)))
19032 (home-page "https://matt-kumar.shinyapps.io/portfolio")
19033 (synopsis "R-Shiny application for creating visual abstracts")
19035 "This package provides an R Shiny application to create visual abstracts
19036 for original research. A variety of user defined options and formatting are
19038 (license license:gpl3)))
19040 (define-public r-qgam
19047 (uri (cran-uri "qgam" version))
19050 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
19051 (properties `((upstream-name . "qgam")))
19052 (build-system r-build-system)
19054 `(("r-doparallel" ,r-doparallel)
19057 ("r-shiny" ,r-shiny)))
19058 (native-inputs `(("r-knitr" ,r-knitr)))
19059 (home-page "https://cran.r-project.org/web/packages/qgam/")
19060 (synopsis "Smooth additive quantile regression models")
19062 "This package provides smooth additive quantile regression models, fitted
19063 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
19064 the smoothing parameters are estimated automatically by marginal loss
19065 minimization, while the regression coefficients are estimated using either
19066 PIRLS or Newton algorithm. The learning rate is determined so that the
19067 Bayesian credible intervals of the estimated effects have approximately the
19068 correct coverage. The main function is @code{qgam()} which is similar to
19069 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
19070 regression models.")
19071 (license license:gpl2+)))
19073 (define-public r-abtest
19080 (uri (cran-uri "abtest" version))
19083 "1ak0m4jd1grriwg4pn3aqf1468qma6rjn5kqjh8izx7zl29jd07v"))))
19084 (properties `((upstream-name . "abtest")))
19085 (build-system r-build-system)
19087 `(("r-matrix" ,r-matrix)
19088 ("r-mvtnorm" ,r-mvtnorm)
19089 ("r-plotrix" ,r-plotrix)
19091 ("r-rcolorbrewer" ,r-rcolorbrewer)
19094 ("r-truncnorm" ,r-truncnorm)))
19095 (home-page "https://cran.r-project.org/web/packages/abtest/")
19096 (synopsis "Bayesian A/B testing")
19098 "This package provides functions for Bayesian A/B testing including prior
19099 elicitation options based on Kass and Vaidyanathan (1992)
19100 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
19101 (license license:gpl2+)))
19103 (define-public r-accept
19110 (uri (cran-uri "accept" version))
19113 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
19114 (properties `((upstream-name . "accept")))
19115 (build-system r-build-system)
19117 `(("r-dplyr" ,r-dplyr)
19118 ("r-extrafont" ,r-extrafont)
19120 ("r-plotly" ,r-plotly)
19121 ("r-stringr" ,r-stringr)
19122 ("r-viridis" ,r-viridis)))
19123 (home-page "https://cran.r-project.org/web/packages/accept/")
19124 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
19126 "This package allows clinicians to predict the rate and severity of
19127 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
19128 Disease} (COPD) patients, based on the clinical prediction model published in
19129 Adibi et al. (2019) @url{doi:10.1101/651901}.")
19130 (license license:gpl3)))
19132 (define-public r-smpracticals
19134 (name "r-smpracticals")
19139 (uri (cran-uri "SMPracticals" version))
19142 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
19143 (properties `((upstream-name . "SMPracticals")))
19144 (build-system r-build-system)
19146 `(("r-ellipse" ,r-ellipse)
19149 ("r-survival" ,r-survival)))
19150 (home-page "http://statwww.epfl.ch/davison/SM/")
19151 (synopsis "Practicals for use with Davison (2003) Statistical Models")
19153 "This package contains the datasets and a few functions for use with the
19154 practicals outlined in Appendix A of the book Statistical Models (Davison,
19155 2003, Cambridge University Press). The practicals themselves can be found at
19156 @url{http://statwww.epfl.ch/davison/SM/}.")
19157 (license license:gpl2+)))
19159 (define-public r-fgui
19166 (uri (cran-uri "fgui" version))
19169 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
19170 (properties `((upstream-name . "fgui")))
19171 (build-system r-build-system)
19173 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
19174 (synopsis "Create GUI for R functions")
19176 "Rapidly create a GUI for a function you created by automatically
19177 creating widgets for arguments of the function. This package automatically
19178 parses help routines for context-sensitive help to these arguments. The
19179 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
19180 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
19181 incorporated into the interface for greater customization for the more
19183 ;; Any version of the GPL.
19184 (license (list license:gpl2+ license:gpl3+))))
19186 (define-public r-tcltk2
19193 (uri (cran-uri "tcltk2" version))
19196 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
19197 (properties `((upstream-name . "tcltk2")))
19198 (build-system r-build-system)
19202 (home-page "https://www.sciviews.org/SciViews-R")
19203 (synopsis "Tcl/Tk additions")
19205 "This package provides a series of additional Tcl commands and Tk widgets
19206 with style and various functions to supplement the tcltk package")
19207 (license license:lgpl3)))
19209 (define-public r-accrual
19216 (uri (cran-uri "accrual" version))
19219 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
19220 (properties `((upstream-name . "accrual")))
19221 (build-system r-build-system)
19223 `(("r-fgui" ,r-fgui)
19224 ("r-smpracticals" ,r-smpracticals)
19225 ("r-tcltk2" ,r-tcltk2)))
19226 (home-page "https://cran.r-project.org/web/packages/accrual/")
19227 (synopsis "Bayesian accrual prediction")
19229 "Subject recruitment for medical research is challenging. Slow patient
19230 accrual leads to delay in research. Accrual monitoring during the process of
19231 recruitment is critical. Researchers need reliable tools to manage the
19232 accrual rate. This package provides an implementation of a Bayesian method
19233 that integrates researcher's experience on previous trials and data from the
19234 current study, providing reliable prediction on accrual rate for clinical
19235 studies. It provides functions for Bayesian accrual prediction which can be
19236 easily used by statisticians and clinical researchers.")
19237 (license license:gpl2)))
19239 (define-public r-accrued
19246 (uri (cran-uri "accrued" version))
19249 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
19250 (properties `((upstream-name . "accrued")))
19251 (build-system r-build-system)
19252 (home-page "https://cran.r-project.org/web/packages/accrued/")
19253 (synopsis "Data quality visualization tools for partially accruing data")
19255 "This is a package for visualizing data quality of partially accruing
19257 (license license:gpl3)))
19259 (define-public r-mda
19266 (uri (cran-uri "mda" version))
19269 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
19270 (properties `((upstream-name . "mda")))
19271 (build-system r-build-system)
19272 (propagated-inputs `(("r-class" ,r-class)))
19273 (native-inputs `(("gfortran" ,gfortran)))
19274 (home-page "https://cran.r-project.org/web/packages/mda/")
19275 (synopsis "Mixture and flexible discriminant analysis")
19277 "This is a package for mixture and flexible discriminant analysis,
19278 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
19279 (license license:gpl2)))
19281 (define-public r-elasticnet
19283 (name "r-elasticnet")
19288 (uri (cran-uri "elasticnet" version))
19291 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
19292 (properties `((upstream-name . "elasticnet")))
19293 (build-system r-build-system)
19295 `(("r-lars" ,r-lars)))
19296 (home-page "http://users.stat.umn.edu/~zouxx019/")
19297 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
19299 "This package provides functions for fitting the entire solution path of
19300 the Elastic-Net and also provides functions for estimating sparse Principal
19301 Components. The Lasso solution paths can be computed by the same function.")
19302 (license license:gpl2+)))
19304 (define-public r-sparselda
19306 (name "r-sparselda")
19311 (uri (cran-uri "sparseLDA" version))
19314 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
19315 (properties `((upstream-name . "sparseLDA")))
19316 (build-system r-build-system)
19318 `(("r-elasticnet" ,r-elasticnet)
19321 (home-page "https://www.imm.dtu.dk/~lkhc/")
19322 (synopsis "Sparse discriminant analysis")
19324 "This package performs sparse linear discriminant analysis for Gaussians
19325 and mixture of Gaussian models.")
19326 (license license:gpl2+)))
19328 (define-public r-accsda
19335 (uri (cran-uri "accSDA" version))
19338 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
19339 (properties `((upstream-name . "accSDA")))
19340 (build-system r-build-system)
19342 `(("r-ggplot2" ,r-ggplot2)
19343 ("r-ggthemes" ,r-ggthemes)
19344 ("r-gridextra" ,r-gridextra)
19346 ("r-rarpack" ,r-rarpack)
19347 ("r-sparselda" ,r-sparselda)))
19348 (home-page "https://github.com/gumeo/accSDA/wiki")
19349 (synopsis "Accelerated sparse discriminant analysis")
19351 "This package provides an implementation of sparse linear discriminant
19352 analysis, which is a supervised classification method for multiple classes.
19353 Various novel optimization approaches to this problem are implemented
19354 including @dfn{alternating direction method of multipliers} (ADMM),
19355 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
19356 Functions for performing cross validation are also supplied along with basic
19357 prediction and plotting functions. @dfn{Sparse zero variance
19358 discriminant} (SZVD) analysis is also included in the package.")
19359 (license license:gpl2+)))
19361 (define-public r-ace2fastq
19363 (name "r-ace2fastq")
19368 (uri (cran-uri "ace2fastq" version))
19371 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
19372 (properties `((upstream-name . "ace2fastq")))
19373 (build-system r-build-system)
19375 `(("r-stringr" ,r-stringr)))
19376 (home-page "https://github.com/c5sire/ace2fastq")
19377 (synopsis "ACE file to FASTQ converter")
19379 "The ACE file format is used in genomics to store contigs from sequencing
19380 machines. This tools converts it into FASTQ format. Both formats contain the
19381 sequence characters and their corresponding quality information. Unlike the
19382 FASTQ file, the ACE file stores the quality values numerically. The
19383 conversion algorithm uses the standard Sanger formula. The package
19384 facilitates insertion into pipelines, and content inspection.")
19385 (license license:gpl3)))
19387 (define-public r-rngwell
19394 (uri (cran-uri "rngWELL" version))
19397 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
19398 (properties `((upstream-name . "rngWELL")))
19399 (build-system r-build-system)
19400 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
19401 (synopsis "Toolbox for WELL random number generators")
19403 "This is a dedicated package to WELL pseudo random generators, which were
19404 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
19405 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
19406 (license license:bsd-3)))
19408 (define-public r-randtoolbox
19410 (name "r-randtoolbox")
19415 (uri (cran-uri "randtoolbox" version))
19418 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
19419 (properties `((upstream-name . "randtoolbox")))
19420 (build-system r-build-system)
19422 `(("r-rngwell" ,r-rngwell)))
19424 `(("gfortran" ,gfortran)))
19425 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
19426 (synopsis "Toolbox for pseudo and quasi random number generation")
19428 "This package provides
19431 @item pseudo random generators, such as general linear
19432 congruential generators, multiple recursive generators and generalized
19433 feedback shift register (SF-Mersenne Twister algorithm and WELL
19436 @item quasi random generators, such as the Torus algorithm, the Sobol
19437 sequence, the Halton sequence (including the Van der Corput sequence), and
19439 @item some generator tests: the gap test, the serial test, the poker test.
19442 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
19443 (license license:bsd-3)))
19445 (define-public r-lhs
19452 (uri (cran-uri "lhs" version))
19455 "1p4h03qlijs2a59wfd4rlvdlb9i87pw2zm8xsjd6yzz8vlm9yglh"))))
19456 (properties `((upstream-name . "lhs")))
19457 (build-system r-build-system)
19458 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19460 `(("r-knitr" ,r-knitr)))
19461 (home-page "https://github.com/bertcarnell/lhs")
19462 (synopsis "Latin Hypercube Samples")
19464 "This package provides a number of methods for creating and augmenting
19465 Latin Hypercube Samples.")
19466 (license license:gpl3)))
19468 (define-public r-acebayes
19470 (name "r-acebayes")
19475 (uri (cran-uri "acebayes" version))
19478 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73"))))
19479 (properties `((upstream-name . "acebayes")))
19480 (build-system r-build-system)
19482 `(("r-compare" ,r-compare)
19484 ("r-randtoolbox" ,r-randtoolbox)
19486 ("r-rcpparmadillo" ,r-rcpparmadillo)))
19487 (home-page "https://cran.r-project.org/web/packages/acebayes/")
19488 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
19490 "Finding an optimal Bayesian experimental design involves maximizing an
19491 objective function given by the expectation of some appropriately chosen
19492 utility function with respect to the joint distribution of unknown
19493 quantities (including responses). This objective function is usually not
19494 available in closed form and the design space can be continuous and of high
19495 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
19496 to maximise an approximation to the expectation of the utility function.")
19497 (license license:gpl2)))
19499 (define-public r-acet
19506 (uri (cran-uri "ACEt" version))
19509 "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4"))))
19510 (properties `((upstream-name . "ACEt")))
19511 (build-system r-build-system)
19516 ("r-rcpparmadillo" ,r-rcpparmadillo)))
19517 (home-page "https://cran.r-project.org/web/packages/ACEt/")
19518 (synopsis "Estimating dynamic heritability and twin model comparison")
19520 "This package supports twin models that are able to estimate the dynamic
19521 behaviour of the variance components in the classical twin models with respect
19522 to age using B-splines and P-splines.")
19523 (license license:gpl2+)))
19525 (define-public r-acfmperiod
19527 (name "r-acfmperiod")
19532 (uri (cran-uri "acfMPeriod" version))
19535 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
19536 (properties `((upstream-name . "acfMPeriod")))
19537 (build-system r-build-system)
19539 `(("r-mass" ,r-mass)))
19540 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
19541 (synopsis "Estimation of the ACF from the M-periodogram")
19543 "This package support non-robust and robust computations of the sample
19544 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
19545 univariate and multivariate processes. The methodology consists in reversing
19546 the diagonalization procedure involving the periodogram or the
19547 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
19548 ACOVF or the ACF as discussed in Fuller (1995)
19549 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
19550 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
19551 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
19552 (license license:gpl2+)))
19554 (define-public r-gamlss-data
19556 (name "r-gamlss-data")
19561 (uri (cran-uri "gamlss.data" version))
19564 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
19565 (properties `((upstream-name . "gamlss.data")))
19566 (build-system r-build-system)
19567 (home-page "http://www.gamlss.org/")
19568 (synopsis "GAMLSS data")
19570 "This package provides data used as examples to demonstrate GAMLSS
19572 ;; Either version of the license
19573 (license (list license:gpl2 license:gpl3))))
19575 (define-public r-gamlss
19582 (uri (cran-uri "gamlss" version))
19585 "1q82md0439si0n7vqbbbdk45sjr0ad7i8mgrn3kwnr4h213pb4nk"))))
19586 (properties `((upstream-name . "gamlss")))
19587 (build-system r-build-system)
19589 `(("r-gamlss-data" ,r-gamlss-data)
19590 ("r-gamlss-dist" ,r-gamlss-dist)
19593 ("r-survival" ,r-survival)))
19594 (home-page "http://www.gamlss.org/")
19595 (synopsis "Generalized additive models for location scale and shape")
19597 "This package provides functions for fitting the generalized additive
19598 models for location scale and shape introduced by Rigby and
19599 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
19600 use a distributional regression approach where all the parameters of the
19601 conditional distribution of the response variable are modelled using
19602 explanatory variables.")
19603 ;; Either version of the license
19604 (license (list license:gpl2 license:gpl3))))
19606 (define-public r-acid
19613 (uri (cran-uri "acid" version))
19616 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
19617 (properties `((upstream-name . "acid")))
19618 (build-system r-build-system)
19620 `(("r-gamlss" ,r-gamlss)
19621 ("r-gamlss-dist" ,r-gamlss-dist)
19622 ("r-hmisc" ,r-hmisc)))
19623 (home-page "https://cran.r-project.org/web/packages/acid/")
19624 (synopsis "Analysing conditional income distributions")
19626 "This package provides functions for the analysis of income distributions
19627 for subgroups of the population as defined by a set of variables like age,
19628 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
19629 distribution as well as functions for moments, inequality measures, entropy
19630 measures and polarisation measures of income distributions. This package thus
19631 aides the analysis of income inequality by offering tools for the exploratory
19632 analysis of income distributions at the disaggregated level.")
19633 (license license:gpl3)))
19635 (define-public r-acm4r
19642 (uri (cran-uri "acm4r" version))
19645 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
19646 (properties `((upstream-name . "acm4r")))
19647 (build-system r-build-system)
19648 (propagated-inputs `(("r-mass" ,r-mass)))
19649 (home-page "https://cran.r-project.org/web/packages/acm4r/")
19650 (synopsis "Align-and-count method comparisons of RFLP data")
19652 "This is a package to compare sequence fragment lengths or molecular
19653 weights from pairs of lanes. The number of matching bands in the
19654 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
19655 the align-and-count method.")
19656 ;; Any version of the GPL
19657 (license (list license:gpl2+ license:gpl3+))))
19659 (define-public r-filelock
19661 (name "r-filelock")
19666 (uri (cran-uri "filelock" version))
19669 "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc"))))
19670 (properties `((upstream-name . "filelock")))
19671 (build-system r-build-system)
19672 (home-page "https://github.com/r-lib/filelock")
19673 (synopsis "Portable file locking")
19675 "This library lets you place an exclusive or shared lock on a file using
19676 the appropriate system call provided by the underlying operating system.")
19677 (license license:expat)))
19679 (define-public r-filematrix
19681 (name "r-filematrix")
19686 (uri (cran-uri "filematrix" version))
19689 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
19690 (properties `((upstream-name . "filematrix")))
19691 (build-system r-build-system)
19692 ;; These inputs are needed for vignettes
19694 `(("r-knitr" ,r-knitr)
19695 ("r-rmarkdown" ,r-rmarkdown)
19696 ("pandoc-citeproc" ,pandoc-citeproc)))
19697 (home-page "https://github.com/andreyshabalin/filematrix")
19698 (synopsis "File-backed matrix class with convenient read and write access")
19700 "This package provides an interface for working with large matrices
19701 stored in files, not in computer memory. It supports multiple non-character
19702 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
19703 byte real values). Access to parts of the matrix is done by indexing, exactly
19704 as with usual R matrices. It supports very large matrices; the package has
19705 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
19706 columns, ad allows for quick addition of extra columns to a filematrix.")
19707 (license license:lgpl3)))
19709 (define-public r-acmeeqtl
19711 (name "r-acmeeqtl")
19716 (uri (cran-uri "ACMEeqtl" version))
19719 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
19720 (properties `((upstream-name . "ACMEeqtl")))
19721 (build-system r-build-system)
19723 `(("r-filematrix" ,r-filematrix)))
19724 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
19725 (synopsis "Estimation of interpretable eQTL effect sizes")
19727 "This package provides a non-linear model, termed ACME, that reflects a
19728 parsimonious biological model for allelic contributions of cis-acting eQTLs.
19729 With non-linear least-squares algorithm the maximum likelihood parameters can
19730 be estimated. The ACME model provides interpretable effect size estimates and
19731 p-values with well controlled Type-I error.")
19732 (license license:lgpl3)))
19734 (define-public r-acmer
19741 (uri (cran-uri "acmeR" version))
19744 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
19745 (properties `((upstream-name . "acmeR")))
19746 (build-system r-build-system)
19747 (propagated-inputs `(("r-foreign" ,r-foreign)))
19748 (home-page "https://cran.r-project.org/web/packages/acmeR/")
19749 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
19751 "This package provides an implementation of the ACME estimator, described
19752 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
19753 Mortality at Wind Turbines. Unlike most other models, this estimator supports
19754 decreasing-hazard Weibull model for persistence; decreasing search proficiency
19755 as carcasses age; variable bleed-through at successive searches; and interval
19756 mortality estimates. The package provides, based on search data, functions
19757 for estimating the mortality inflation factor in Frequentist and Bayesian
19759 (license license:expat)))
19761 (define-public r-r-huge
19768 (uri (cran-uri "R.huge" version))
19771 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
19772 (properties `((upstream-name . "R.huge")))
19773 (build-system r-build-system)
19775 `(("r-r-methodss3" ,r-r-methodss3)
19777 ("r-r-utils" ,r-r-utils)))
19778 (home-page "https://github.com/HenrikBengtsson/R.huge")
19779 (synopsis "Methods for accessing huge amounts of data")
19781 "This is a deprecated package for accessing huge amounts of data.
19782 Cross-platform alternatives are the following packages: bigmemory (CRAN),
19783 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
19784 the @code{aroma.affymetrix} package.")
19785 (license license:lgpl2.1+)))
19787 (define-public r-r-filesets
19789 (name "r-r-filesets")
19794 (uri (cran-uri "R.filesets" version))
19797 "08xv8b3c81nf54viyr3w912al18483k5gfnjpg7bxbdfk70dfzbh"))))
19798 (properties `((upstream-name . "R.filesets")))
19799 (build-system r-build-system)
19801 `(("r-digest" ,r-digest)
19802 ("r-r-cache" ,r-r-cache)
19803 ("r-r-methodss3" ,r-r-methodss3)
19805 ("r-r-utils" ,r-r-utils)))
19806 (home-page "https://github.com/HenrikBengtsson/R.filesets")
19807 (synopsis "Easy handling of and access to files")
19809 "This package provides classes and methods to locate, setup, subset,
19810 navigate and iterate file sets, i.e. sets of files located in one or more
19811 directories on the file system. The API is designed such that these classes
19812 can be extended via inheritance to provide a richer API for special file
19813 formats. Moreover, a specific name format is defined such that filenames and
19814 directories can be considered to have full names which consists of a name
19815 followed by comma-separated tags. This adds additional flexibility to
19816 identify file sets and individual files.")
19817 (license license:lgpl2.1+)))
19819 (define-public r-r-devices
19821 (name "r-r-devices")
19826 (uri (cran-uri "R.devices" version))
19829 "1djz6vm1b7sjvx1q319dl47gbnz9kvipaxcz9i0spyp094lv3m62"))))
19830 (properties `((upstream-name . "R.devices")))
19831 (build-system r-build-system)
19833 `(("r-base64enc" ,r-base64enc)
19834 ("r-r-methodss3" ,r-r-methodss3)
19836 ("r-r-utils" ,r-r-utils)))
19837 (home-page "https://github.com/HenrikBengtsson/R.devices")
19838 (synopsis "Unified handling of graphics devices")
19840 "This package provides functions for creating plots and image files in a
19841 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
19842 Default device options as well as scales and aspect ratios are controlled in a
19843 uniform way across all device types. Switching output format requires minimal
19844 changes in code. This package is ideal for large-scale batch processing,
19845 because it will never leave open graphics devices or incomplete image files
19846 behind, even on errors or user interrupts.")
19847 (license license:lgpl2.1+)))
19849 (define-public r-acnr
19856 (uri (cran-uri "acnr" version))
19859 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
19860 (properties `((upstream-name . "acnr")))
19861 (build-system r-build-system)
19862 (home-page "https://github.com/mpierrejean/acnr")
19863 (synopsis "Annotated copy-number regions")
19865 "This package provides SNP array data from different types of copy-number
19866 regions. These regions were identified manually by the authors of the package
19867 and may be used to generate realistic data sets with known truth.")
19868 (license license:lgpl2.1+)))
19870 (define-public r-acopula
19877 (uri (cran-uri "acopula" version))
19880 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
19881 (properties `((upstream-name . "acopula")))
19882 (build-system r-build-system)
19883 (home-page "https://cran.r-project.org/web/packages/acopula/")
19884 (synopsis "Modelling dependence with multivariate Archimax copulas")
19886 "Archimax copulas are a mixture of Archimedean and EV copulas. This
19887 package provides definitions of several parametric families of generator and
19888 dependence function, computes CDF and PDF, estimates parameters, tests for
19889 goodness of fit, generates random sample and checks copula properties for
19890 custom constructs. In the 2-dimensional case explicit formulas for density
19891 are used, contrary to higher dimensions when all derivatives are linearly
19892 approximated. Several non-archimax families (normal, FGM, Plackett) are
19893 provided as well.")
19894 (license license:gpl2)))
19896 (define-public r-tuner
19903 (uri (cran-uri "tuneR" version))
19906 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
19907 (properties `((upstream-name . "tuneR")))
19908 (build-system r-build-system)
19909 (propagated-inputs `(("r-signal" ,r-signal)))
19910 (home-page "https://cran.r-project.org/web/packages/tuneR/")
19911 (synopsis "Analysis of music and speech")
19913 "This is a package for the analysis of music and speech. Analyze music
19914 and speech, extract features like MFCCs, handle wave files and their
19915 representation in various ways, read MP3, read MIDI, perform steps of a
19916 transcription, ...")
19917 ;; Either of these versions.
19918 (license (list license:gpl2 license:gpl3))))
19920 (define-public r-seewave
19927 (uri (cran-uri "seewave" version))
19930 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
19931 (properties `((upstream-name . "seewave")))
19932 (build-system r-build-system)
19934 `(("libsndfile" ,libsndfile)))
19936 `(("r-tuner" ,r-tuner)))
19937 (home-page "http://rug.mnhn.fr/seewave")
19938 (synopsis "Sound analysis and synthesis")
19940 "This package provides functions for analysing, manipulating, displaying,
19941 editing and synthesizing time waves (particularly sound). This package
19942 processes time analysis (oscillograms and envelopes), spectral content,
19943 resonance quality factor, entropy, cross correlation and autocorrelation,
19944 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
19945 and 3D spectrograms and many other analyses.")
19946 (license license:gpl2+)))
19948 (define-public r-acousticndlcoder
19950 (name "r-acousticndlcoder")
19955 (uri (cran-uri "AcousticNDLCodeR" version))
19958 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
19960 `((upstream-name . "AcousticNDLCodeR")))
19961 (build-system r-build-system)
19963 `(("r-seewave" ,r-seewave)
19964 ("r-tuner" ,r-tuner)
19966 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
19967 (synopsis "Coding sound files for use with NDL")
19969 "Make acoustic cues to use with the R package @code{ndl}.
19970 The package implements functions used in the PLoS ONE paper \"Words from
19971 spontaneous conversational speech can be recognized with human-like accuracy
19972 by an error-driven learning algorithm that discriminates between meanings
19973 straight from smart acoustic features, bypassing the phoneme as recognition
19974 unit.\" @url{doi:10.1371/journal.pone.0174623}")
19975 (license license:gpl2+)))
19977 (define-public r-acp
19984 (uri (cran-uri "acp" version))
19987 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
19988 (properties `((upstream-name . "acp")))
19989 (build-system r-build-system)
19991 `(("r-quantmod" ,r-quantmod)
19992 ("r-tseries" ,r-tseries)))
19993 (home-page "https://cran.r-project.org/web/packages/acp/")
19994 (synopsis "Autoregressive conditional Poisson")
19996 "This package supports the analysis of count data exhibiting
19997 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
19998 model (ACP(p,q)) proposed by Heinen (2003).")
19999 (license license:gpl2)))
20001 (define-public r-ada
20008 (uri (cran-uri "ada" version))
20011 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
20012 (properties `((upstream-name . "ada")))
20013 (build-system r-build-system)
20014 (propagated-inputs `(("r-rpart" ,r-rpart)))
20015 (home-page "https://cran.r-project.org/web/packages/ada/")
20016 (synopsis "Stochastic boosting")
20018 "This package provides a straightforward, well-documented, and broad
20019 boosting routine for classification, ideally suited for small to
20020 moderate-sized data sets. It performs discrete, real, and gentle boost under
20021 both exponential and logistic loss on a given data set.")
20022 ;; Any version of the GPL.
20023 (license (list license:gpl2+ license:gpl3+))))
20025 (define-public r-genalg
20032 (uri (cran-uri "genalg" version))
20035 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
20036 (properties `((upstream-name . "genalg")))
20037 (build-system r-build-system)
20038 (home-page "https://github.com/egonw/genalg")
20039 (synopsis "R based genetic algorithm")
20041 "This package provides an R based genetic algorithm for binary and
20042 floating point chromosomes.")
20043 (license license:gpl2)))
20045 (define-public r-kernelfactory
20047 (name "r-kernelfactory")
20052 (uri (cran-uri "kernelFactory" version))
20055 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
20056 (properties `((upstream-name . "kernelFactory")))
20057 (build-system r-build-system)
20060 ("r-genalg" ,r-genalg)
20061 ("r-kernlab" ,r-kernlab)
20062 ("r-randomforest" ,r-randomforest)))
20063 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
20064 (synopsis "Ensemble of kernel machines")
20066 "Kernel factory is an ensemble method where each base classifier (random
20067 forest) is fit on the kernel matrix of a subset of the training data.")
20068 (license license:gpl2+)))
20070 (define-public r-dummies
20077 (uri (cran-uri "dummies" version))
20080 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
20081 (properties `((upstream-name . "dummies")))
20082 (build-system r-build-system)
20083 (home-page "https://decisionpatterns.com")
20084 (synopsis "Create dummy/indicator variables flexibly and efficiently")
20086 "This package lets you expand factors, characters and other eligible
20087 classes into dummy/indicator variables.")
20088 (license license:gpl2+)))
20090 (define-public r-acrm
20097 (uri (cran-uri "aCRM" version))
20100 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
20101 (properties `((upstream-name . "aCRM")))
20102 (build-system r-build-system)
20105 ("r-dummies" ,r-dummies)
20106 ("r-kernelfactory" ,r-kernelfactory)
20107 ("r-randomforest" ,r-randomforest)))
20108 (home-page "https://cran.r-project.org/web/packages/aCRM/")
20109 (synopsis "Convenience functions for analytical customer relationship management")
20111 "This package provides convenience functions for data preparation and
20112 modeling often used in @dfn{analytical customer relationship
20113 management} (aCRM).")
20114 (license license:gpl2+)))
20116 (define-public r-treeclust
20118 (name "r-treeclust")
20123 (uri (cran-uri "treeClust" version))
20126 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
20127 (properties `((upstream-name . "treeClust")))
20128 (build-system r-build-system)
20130 `(("r-cluster" ,r-cluster)
20131 ("r-rpart" ,r-rpart)))
20132 (home-page "https://cran.r-project.org/web/packages/treeClust/")
20133 (synopsis "Cluster distances through trees")
20135 "This package provides tools to create a measure of inter-point
20136 dissimilarity useful for clustering mixed data, and, optionally, perform the
20138 (license license:gpl2+)))
20140 (define-public r-acrosstic
20142 (name "r-acrosstic")
20147 (uri (cran-uri "AcrossTic" version))
20150 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
20151 (properties `((upstream-name . "AcrossTic")))
20152 (build-system r-build-system)
20154 `(("r-lpsolve" ,r-lpsolve)
20155 ("r-treeclust" ,r-treeclust)))
20156 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
20157 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
20159 "This is a package for constructing minimum-cost regular spanning
20160 subgraph as part of a non-parametric two-sample test for equality of
20162 (license license:gpl2+)))
20164 (define-public r-acrt
20171 (uri (cran-uri "acrt" version))
20174 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
20175 (properties `((upstream-name . "acrt")))
20176 (build-system r-build-system)
20178 `(("r-rcpp" ,r-rcpp)
20179 ("r-rcppeigen" ,r-rcppeigen)
20180 ("r-sandwich" ,r-sandwich)))
20181 (home-page "https://cran.r-project.org/web/packages/acrt/")
20182 (synopsis "Autocorrelation robust testing")
20184 "This package provides functions for testing affine hypotheses on the
20185 regression coefficient vector in regression models with autocorrelated
20187 (license license:gpl2)))
20189 (define-public r-acs
20196 (uri (cran-uri "acs" version))
20199 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
20200 (properties `((upstream-name . "acs")))
20201 (build-system r-build-system)
20203 `(("r-httr" ,r-httr)
20206 ("r-stringr" ,r-stringr)
20208 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
20209 (synopsis "Work with data from the US Census")
20211 "This package provides a general toolkit for downloading, managing,
20212 analyzing, and presenting data from the
20213 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
20214 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
20215 American Community Survey (ACS). Confidence intervals provided with ACS data
20216 are converted to standard errors to be bundled with estimates in complex
20217 @code{acs} objects. The package provides new methods to conduct standard
20218 operations on @code{acs} objects and present/plot data in statistically
20219 appropriate ways.")
20220 (license license:gpl3)))
20222 (define-public r-acss-data
20224 (name "r-acss-data")
20229 (uri (cran-uri "acss.data" version))
20232 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
20233 (properties `((upstream-name . "acss.data")))
20234 (build-system r-build-system)
20235 (home-page "http://complexitycalculator.com/methodology.html")
20236 (synopsis "Data for algorithmic complexity of short strings")
20238 "This is a data only package providing the algorithmic complexity of
20239 short strings, computed using the coding theorem method. For a given set of
20240 symbols in a string, all possible or a large number of random samples of
20241 Turing machines with a given number of states (e.g., 5) and number of symbols
20242 corresponding to the number of symbols in the strings were simulated until
20243 they reached a halting state or failed to end. This package contains data on
20244 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
20245 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
20246 distribution of the halting states.")
20247 (license license:gpl2+)))
20249 (define-public r-acss
20256 (uri (cran-uri "acss" version))
20259 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
20260 (properties `((upstream-name . "acss")))
20261 (build-system r-build-system)
20263 `(("r-acss-data" ,r-acss-data)
20265 (home-page "http://complexitycalculator.com/methodology.html")
20266 (synopsis "Algorithmic complexity for short strings")
20268 "The main purpose of this package is to provide the algorithmic
20269 complexity for short strings, an approximation of the Kolmogorov Complexity of
20270 a short string using the coding theorem method. While the database containing
20271 the complexity is provided in the data only package @code{acss.data}, this
20272 package provides functions accessing the data such as @code{prob_random}
20273 returning the posterior probability that a given string was produced by a
20274 random process. In addition, two traditional (but problematic) measures of
20275 complexity are also provided: entropy and change complexity.")
20276 (license license:gpl2+)))
20278 (define-public r-acswr
20285 (uri (cran-uri "ACSWR" version))
20288 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
20289 (properties `((upstream-name . "ACSWR")))
20290 (build-system r-build-system)
20292 `(("r-mass" ,r-mass)))
20293 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
20294 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
20296 "This is a companion package for the book \"A Course in Statistics with
20297 R\" (ISBN 978-1-119-15272-9.)")
20298 (license license:gpl2)))
20300 (define-public r-alabama
20303 (version "2015.3-1")
20307 (uri (cran-uri "alabama" version))
20310 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
20311 (properties `((upstream-name . "alabama")))
20312 (build-system r-build-system)
20313 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
20314 (home-page "https://cran.r-project.org/web/packages/alabama/")
20315 (synopsis "Constrained nonlinear optimization")
20317 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
20318 Algorithm; it is used for optimizing smooth nonlinear objective functions with
20319 constraints. Linear or nonlinear equality and inequality constraints are
20321 (license license:gpl2+)))
20323 (define-public r-gdina
20330 (uri (cran-uri "GDINA" version))
20333 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
20334 (properties `((upstream-name . "GDINA")))
20335 (build-system r-build-system)
20337 `(("r-alabama" ,r-alabama)
20338 ("r-ggplot2" ,r-ggplot2)
20340 ("r-nloptr" ,r-nloptr)
20341 ("r-numderiv" ,r-numderiv)
20343 ("r-rcpparmadillo" ,r-rcpparmadillo)
20344 ("r-rsolnp" ,r-rsolnp)
20345 ("r-shiny" ,r-shiny)
20346 ("r-shinydashboard" ,r-shinydashboard)))
20348 `(("r-knitr" ,r-knitr)))
20349 (home-page "https://github.com/Wenchao-Ma/GDINA")
20350 (synopsis "Generalized DINA model framework")
20352 "This package provides a set of psychometric tools for cognitive
20353 diagnosis modeling based on the generalized deterministic inputs, noisy and
20354 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
20355 and its extensions, including the sequential G-DINA model by Ma and de la
20356 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
20357 polytomous G-DINA model by Chen and de la Torre
20358 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
20359 distribution can be independent, saturated, higher-order, loglinear smoothed
20360 or structured. Q-matrix validation, item and model fit statistics, model
20361 comparison at test and item level and differential item functioning can also
20362 be conducted. A graphical user interface is also provided.")
20363 (license license:gpl3)))
20365 (define-public r-actcd
20372 (uri (cran-uri "ACTCD" version))
20375 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
20376 (properties `((upstream-name . "ACTCD")))
20377 (build-system r-build-system)
20379 `(("r-gdina" ,r-gdina)
20380 ("r-r-methodss3" ,r-r-methodss3)))
20382 `(("gfortran" ,gfortran)))
20383 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
20384 (synopsis "Asymptotic classification theory for cognitive diagnosis")
20386 "This is a package supporting cluster analysis for cognitive diagnosis
20387 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
20388 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
20389 sum-scores, cluster analysis techniques can be used to classify examinees into
20390 latent classes based on their attribute patterns. In addition to the
20391 algorithms used to classify data, three labeling approaches are proposed to
20392 label clusters so that examinees' attribute profiles can be obtained.")
20393 (license license:gpl2+)))
20395 (define-public r-ineq
20402 (uri (cran-uri "ineq" version))
20405 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
20406 (properties `((upstream-name . "ineq")))
20407 (build-system r-build-system)
20408 (home-page "https://cran.r-project.org/web/packages/ineq/")
20409 (synopsis "Measuring inequality, concentration, and poverty")
20411 "This package provides tools for measuring inequality, concentration, and
20412 poverty measures. It provides both empirical and theoretical Lorenz curves.")
20413 ;; Either of these two versions.
20414 (license (list license:gpl2 license:gpl3))))
20416 (define-public r-actfrag
20423 (uri (cran-uri "ActFrag" version))
20426 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
20427 (properties `((upstream-name . "ActFrag")))
20428 (build-system r-build-system)
20430 `(("r-accelerometry" ,r-accelerometry)
20431 ("r-dplyr" ,r-dplyr)
20433 ("r-survival" ,r-survival)
20434 ("r-tidyr" ,r-tidyr)))
20435 (home-page "https://github.com/junruidi/ActFrag")
20436 (synopsis "Activity fragmentation metrics extraction")
20438 "This package provides functions to extract commonly used fragmentation
20439 metrics to quantify time accumulation strategies based on minute level
20440 actigraphy-measured activity counts data.")
20441 (license license:gpl3)))
20443 (define-public r-ash
20450 (uri (cran-uri "ash" version))
20453 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb"))))
20454 (properties `((upstream-name . "ash")))
20455 (build-system r-build-system)
20456 (native-inputs `(("gfortran" ,gfortran)))
20457 (home-page "https://cran.r-project.org/web/packages/ash/")
20458 (synopsis "David Scott's ASH routines")
20460 "This package provides David Scott's ASH routines ported from S-PLUS to
20462 (license license:gpl2+)))
20464 (define-public r-hdrcde
20471 (uri (cran-uri "hdrcde" version))
20474 "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3"))))
20475 (properties `((upstream-name . "hdrcde")))
20476 (build-system r-build-system)
20479 ("r-ggplot2" ,r-ggplot2)
20480 ("r-kernsmooth" ,r-kernsmooth)
20482 ("r-locfit" ,r-locfit)
20483 ("r-rcolorbrewer" ,r-rcolorbrewer)))
20484 (native-inputs `(("gfortran" ,gfortran)))
20485 (home-page "http://pkg.robjhyndman.com/hdrcde")
20486 (synopsis "Highest density regions and conditional density estimation")
20488 "This is a package for the computation of highest density regions in one
20489 and two dimensions, kernel estimation of univariate density functions
20490 conditional on one covariate, and multimodal regression.")
20491 (license license:gpl3)))
20493 (define-public r-rainbow
20500 (uri (cran-uri "rainbow" version))
20503 "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3"))))
20504 (properties `((upstream-name . "rainbow")))
20505 (build-system r-build-system)
20507 `(("r-cluster" ,r-cluster)
20508 ("r-colorspace" ,r-colorspace)
20509 ("r-hdrcde" ,r-hdrcde)
20512 ("r-pcapp" ,r-pcapp)))
20513 (home-page "https://cran.r-project.org/web/packages/rainbow/")
20514 (synopsis "Bagplots, boxplots and rainbow plots for functional data")
20516 "This is a package for visualizing functional data and identifying
20517 functional outliers with bagplots, boxplots and rainbow plots.")
20518 (license license:gpl3)))
20520 (define-public r-fds
20527 (uri (cran-uri "fds" version))
20530 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0"))))
20531 (properties `((upstream-name . "fds")))
20532 (build-system r-build-system)
20534 `(("r-rainbow" ,r-rainbow)
20535 ("r-rcurl" ,r-rcurl)))
20536 (home-page "https://cran.r-project.org/web/packages/fds/")
20537 (synopsis "Functional data sets")
20538 (description "This package contains a list of functional time series,
20539 sliced functional time series, and functional data sets. Functional time
20540 series is a special type of functional data observed over time. Sliced
20541 functional time series is a special type of functional time series with a time
20542 variable observed over time.")
20543 (license license:gpl2+)))
20545 (define-public r-fda
20552 (uri (cran-uri "fda" version))
20555 "0yjrjsv55bcwqn2yxjgj3hn17wfvjvgngfw9xv3w802i52yz9gf8"))))
20556 (properties `((upstream-name . "fda")))
20557 (build-system r-build-system)
20560 ("r-matrix" ,r-matrix)))
20561 (home-page "https://www.functionaldata.org")
20562 (synopsis "Functional data analysis")
20564 "These functions were developed to support functional data analysis as
20565 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
20566 Analysis. The package includes data sets and script files working many
20568 (license license:gpl2+)))
20570 (define-public r-actigraphy
20572 (name "r-actigraphy")
20577 (uri (cran-uri "Actigraphy" version))
20580 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
20581 (properties `((upstream-name . "Actigraphy")))
20582 (build-system r-build-system)
20584 `(("r-fda" ,r-fda)))
20585 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
20586 (synopsis "Actigraphy data analysis")
20588 "This package provides tools for functional linear modeling and analysis
20589 of actigraphy data.")
20590 (license license:asl2.0)))
20592 (define-public r-activedriver
20594 (name "r-activedriver")
20599 (uri (cran-uri "ActiveDriver" version))
20602 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
20603 (properties `((upstream-name . "ActiveDriver")))
20604 (build-system r-build-system)
20606 `(("r-mass" ,r-mass)))
20607 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
20608 (synopsis "Tools for finding cancer driver proteins")
20610 "This package provides a mutation analysis tool that discovers cancer
20611 driver genes with frequent mutations in protein signalling sites such as
20612 post-translational modifications (phosphorylation, ubiquitination, etc). The
20613 Poisson generalized linear regression model identifies genes where cancer
20614 mutations in signalling sites are more frequent than expected from the
20615 sequence of the entire gene. Integration of mutations with signalling
20616 information helps find new driver genes and propose candidate mechanisms to
20618 (license license:gpl2+)))
20620 (define-public r-activitycounts
20622 (name "r-activitycounts")
20627 (uri (cran-uri "activityCounts" version))
20630 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
20632 `((upstream-name . "activityCounts")))
20633 (build-system r-build-system)
20635 `(("r-lubridate" ,r-lubridate)
20636 ("r-magrittr" ,r-magrittr)
20637 ("r-seewave" ,r-seewave)
20638 ("r-signal" ,r-signal)
20639 ("r-tibble" ,r-tibble)))
20640 (home-page "https://github.com/walkabillylab/activityCounts")
20641 (synopsis "Generate ActiLife counts")
20643 "ActiLife generates activity counts from data collected by Actigraph
20644 accelerometers. Actigraph is one of the most common research-grade
20645 accelerometers. There is considerable research validating and developing
20646 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
20647 counts are proprietary and difficult to implement if researchers use different
20648 accelerometer brands. The code creates ActiLife counts from raw acceleration
20649 data for different accelerometer brands.")
20650 (license license:gpl3)))
20652 (define-public r-activityindex
20654 (name "r-activityindex")
20659 (uri (cran-uri "ActivityIndex" version))
20662 "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5"))))
20663 (properties `((upstream-name . "ActivityIndex")))
20664 (build-system r-build-system)
20666 `(("r-data-table" ,r-data-table)
20667 ("r-matrixstats" ,r-matrixstats)
20668 ("r-r-utils" ,r-r-utils)))
20670 `(("r-knitr" ,r-knitr)))
20671 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
20672 (synopsis "Activity Index calculation using raw accelerometry data")
20674 "This is a package to read raw accelerometry from GT3X+ accelerometry
20675 data and plain table data to calculate the Activity Index from Bai et
20676 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
20677 (license license:gpl3)))
20679 (define-public r-activpal
20681 (name "r-activpal")
20686 (uri (cran-uri "activPAL" version))
20689 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
20690 (properties `((upstream-name . "activPAL")))
20691 (build-system r-build-system)
20693 `(("r-devtools" ,r-devtools)
20694 ("r-dplyr" ,r-dplyr)
20695 ("r-ggplot2" ,r-ggplot2)
20696 ("r-lubridate" ,r-lubridate)
20697 ("r-magrittr" ,r-magrittr)
20698 ("r-tidyr" ,r-tidyr)))
20699 (home-page "https://cran.r-project.org/web/packages/activPAL")
20700 (synopsis "Processing and chart generation from activPAL events files")
20702 "This package contains functions to generate pre-defined summary
20703 statistics from activPAL events files. The package also contains functions to
20704 produce informative graphics that visualize physical activity behaviour and
20705 trends. This includes generating graphs that align physical activity
20706 behaviour with additional time based observations described by other data
20707 sets, such as sleep diaries and continuous glucose monitoring data.")
20708 (license license:gpl3)))
20710 (define-public r-activpalprocessing
20712 (name "r-activpalprocessing")
20717 (uri (cran-uri "activpalProcessing" version))
20720 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
20722 `((upstream-name . "activpalProcessing")))
20723 (build-system r-build-system)
20725 `(("r-chron" ,r-chron)))
20726 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
20727 (synopsis "Process activPAL events files")
20729 "This package performs estimation of physical activity and sedentary
20730 behavior variables from activPAL events files.")
20731 ;; Either version of the GPL.
20732 (license (list license:gpl2 license:gpl3))))
20734 (define-public r-actogrammr
20736 (name "r-actogrammr")
20741 (uri (cran-uri "actogrammr" version))
20744 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
20745 (properties `((upstream-name . "actogrammr")))
20746 (build-system r-build-system)
20748 `(("r-dplyr" ,r-dplyr)
20749 ("r-ggplot2" ,r-ggplot2)
20750 ("r-lubridate" ,r-lubridate)
20751 ("r-readr" ,r-readr)
20752 ("r-tidyr" ,r-tidyr)))
20753 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
20754 (synopsis "Read in activity data and plot actograms")
20756 "Read in activity measurements from standard file formats used by
20757 circadian rhythm researchers, currently only ClockLab format, and process and
20758 plot the data. The central type of plot is the actogram, as first described
20759 in \"Activity and distribution of certain wild mice in relation to biotic
20760 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
20761 (license license:gpl3)))
20763 (define-public r-expint
20770 (uri (cran-uri "expint" version))
20773 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
20774 (properties `((upstream-name . "expint")))
20775 (build-system r-build-system)
20776 (home-page "https://gitlab.com/vigou3/expint")
20777 (synopsis "Exponential integral and incomplete Gamma function")
20779 "This package provides the exponential integrals @code{E_1(x)},
20780 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
20781 function @code{G(a, x)} defined for negative values of its first argument.
20782 The package also gives easy access to the underlying C routines through an
20783 API; see the package vignette for details.")
20784 (license license:gpl2+)))
20786 (define-public r-actuar
20793 (uri (cran-uri "actuar" version))
20796 "0sxn1mskh7x164f1vbrqnadgxnq7y2p3a9mlmqc0sp6cqkw9lhp9"))))
20797 (properties `((upstream-name . "actuar")))
20798 (build-system r-build-system)
20799 (propagated-inputs `(("r-expint" ,r-expint)))
20800 (home-page "https://gitlab.com/vigou3/actuar")
20801 (synopsis "Actuarial functions and heavy tailed distributions")
20803 "This package provides functions and data sets for actuarial science:
20804 modeling of loss distributions; risk theory and ruin theory; simulation of
20805 compound models, discrete mixtures and compound hierarchical models;
20806 credibility theory. It boasts support for many additional probability
20807 distributions to model insurance loss amounts and loss frequency: 19
20808 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
20809 distribution; zero-truncated and zero-modified extensions of the standard
20810 discrete distributions. It also supports phase-type distributions commonly
20811 used to compute ruin probabilities.")
20812 (license license:gpl2+)))
20814 (define-public r-bmp
20821 (uri (cran-uri "bmp" version))
20824 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
20825 (properties `((upstream-name . "bmp")))
20826 (build-system r-build-system)
20827 (home-page "https://cran.r-project.org/web/packages/bmp/")
20828 (synopsis "Read Bitmap (BMP) images")
20830 "This package provides pure R tools to read BMP format images. It is
20831 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
20832 (license license:gpl2+)))
20834 (define-public r-readbitmap
20836 (name "r-readbitmap")
20841 (uri (cran-uri "readbitmap" version))
20844 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
20845 (properties `((upstream-name . "readbitmap")))
20846 (build-system r-build-system)
20848 `(("libjpeg" ,libjpeg-turbo)
20849 ("libpng" ,libpng)))
20854 ("r-tiff" ,r-tiff)))
20855 (home-page "https://github.com/jefferis/readbitmap")
20856 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
20858 "This package provides tools to identify and read BMP, JPEG, PNG, and
20859 TIFF format bitmap images. Identification defaults to the use of the magic
20860 number embedded in the file rather than the file extension.")
20861 (license license:gpl2+)))
20863 (define-public r-imager
20870 (uri (cran-uri "imager" version))
20873 "1wxvbv803222gjrf1ys6a349xlnmmdw3kqgi93piq9gq7lahihvg"))))
20874 (properties `((upstream-name . "imager")))
20875 (build-system r-build-system)
20878 ("libtiff" ,libtiff)
20882 `(("r-downloader" ,r-downloader)
20883 ("r-igraph" ,r-igraph)
20885 ("r-magrittr" ,r-magrittr)
20887 ("r-purrr" ,r-purrr)
20889 ("r-readbitmap" ,r-readbitmap)
20890 ("r-stringr" ,r-stringr)))
20892 `(("pkg-config" ,pkg-config)
20893 ("r-knitr" ,r-knitr)))
20894 (home-page "https://dahtah.github.io/imager/")
20895 (synopsis "Image processing library")
20897 "This is a package for fast image processing for images in up to 4
20898 dimensions (two spatial dimensions, one time/depth dimension, one color
20899 dimension). It provides most traditional image processing tools (filtering,
20900 morphology, transformations, etc.) as well as various functions for easily
20901 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
20902 simple, modern C++ library for image processing.")
20903 (license license:lgpl3)))
20905 (define-public r-acuityview
20907 (name "r-acuityview")
20912 (uri (cran-uri "AcuityView" version))
20915 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
20916 (properties `((upstream-name . "AcuityView")))
20917 (build-system r-build-system)
20919 `(("r-fftwtools" ,r-fftwtools)
20920 ("r-imager" ,r-imager)
20921 ("r-plotrix" ,r-plotrix)))
20922 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
20923 (synopsis "Display scenes as seen by an animal with less acute vision")
20925 "This package provides a simple method for representing a visual scene as
20926 it may be seen by an animal with less acute vision.")
20927 (license license:gpl2+)))
20929 (define-public r-caret
20936 (uri (cran-uri "caret" version))
20939 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
20940 (build-system r-build-system)
20942 `(("r-foreach" ,r-foreach)
20943 ("r-ggplot2" ,r-ggplot2)
20944 ("r-lattice" ,r-lattice)
20945 ("r-modelmetrics" ,r-modelmetrics)
20949 ("r-recipes" ,r-recipes)
20950 ("r-reshape2" ,r-reshape2)
20951 ("r-withr" ,r-withr)))
20953 `(("r-knitr" ,r-knitr)))
20954 (home-page "https://github.com/topepo/caret")
20955 (synopsis "Classification and regression training")
20957 "This package provides miscellaneous functions for training and plotting
20958 classification and regression models.")
20959 (license license:gpl2+)))
20961 (define-public r-adabag
20968 (uri (cran-uri "adabag" version))
20971 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
20972 (properties `((upstream-name . "adabag")))
20973 (build-system r-build-system)
20975 `(("r-caret" ,r-caret)
20976 ("r-doparallel" ,r-doparallel)
20977 ("r-foreach" ,r-foreach)
20978 ("r-rpart" ,r-rpart)))
20979 (home-page "https://cran.r-project.org/web/packages/adabag/")
20980 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
20982 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
20983 Breiman's Bagging algorithm using classification trees as individual
20984 classifiers. Once these classifiers have been trained, they can be used to
20985 predict on new data. Also, cross validation estimation of the error can be
20987 (license license:gpl2+)))
20989 (define-public r-adagio
20996 (uri (cran-uri "adagio" version))
20999 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
21000 (properties `((upstream-name . "adagio")))
21001 (build-system r-build-system)
21002 (native-inputs `(("gfortran" ,gfortran)))
21003 (home-page "https://cran.r-project.org/web/packages/adagio/")
21004 (synopsis "Discrete and global optimization routines")
21006 "This package provides methods and algorithms for discrete optimization,
21007 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
21008 Hooke-Jeeves minimization, and some (evolutionary) global optimization
21010 (license license:gpl3+)))
21012 (define-public r-univoutl
21014 (name "r-univoutl")
21019 (uri (cran-uri "univOutl" version))
21022 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
21023 (properties `((upstream-name . "univOutl")))
21024 (build-system r-build-system)
21026 `(("r-hmisc" ,r-hmisc)
21027 ("r-robustbase" ,r-robustbase)))
21028 (home-page "https://github.com/marcellodo/univOutl")
21029 (synopsis "Detection of univariate outliers")
21031 "This package provides well-known outlier detection techniques in the
21032 univariate case. Methods to deal with skewed distribution are included too.
21033 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
21034 historical data is implemented as well. When available, survey weights can be
21035 used in outliers detection.")
21036 (license license:gpl2+)))
21038 (define-public r-tolerance
21040 (name "r-tolerance")
21045 (uri (cran-uri "tolerance" version))
21048 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
21049 (properties `((upstream-name . "tolerance")))
21050 (build-system r-build-system)
21052 `(("r-mass" ,r-mass)
21054 (home-page "https://cran.r-project.org/web/packages/tolerance/")
21055 (synopsis "Statistical tolerance intervals and regions")
21057 "This package provides functions for estimating tolerance
21058 limits (intervals) for various univariate distributions (binomial, Cauchy,
21059 discrete Pareto, exponential, two-parameter exponential, extreme value,
21060 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
21061 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
21062 Bayesian normal tolerance limits, multivariate normal tolerance regions,
21063 nonparametric tolerance intervals, tolerance bands for regression
21064 settings (linear regression, nonlinear regression, nonparametric regression,
21065 and multivariate regression), and analysis of variance tolerance intervals.
21066 Visualizations are also available for most of these settings.")
21067 (license license:gpl2+)))
21069 (define-public r-additivitytests
21071 (name "r-additivitytests")
21076 (uri (cran-uri "additivityTests" version))
21079 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
21081 `((upstream-name . "additivityTests")))
21082 (build-system r-build-system)
21083 (home-page "https://github.com/simecek/additivityTests")
21084 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
21086 "This package provides an implementation of the Tukey, Mandel,
21087 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
21088 (license license:gpl3)))
21090 (define-public r-flexclust
21092 (name "r-flexclust")
21097 (uri (cran-uri "flexclust" version))
21100 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
21101 (properties `((upstream-name . "flexclust")))
21102 (build-system r-build-system)
21104 `(("r-class" ,r-class)
21105 ("r-lattice" ,r-lattice)
21106 ("r-modeltools" ,r-modeltools)))
21107 (home-page "https://cran.r-project.org/web/packages/flexclust/")
21108 (synopsis "Flexible cluster algorithms")
21110 "The main function @code{kcca} implements a general framework for
21111 k-centroids cluster analysis supporting arbitrary distance measures and
21112 centroid computation. Further cluster methods include hard competitive
21113 learning, neural gas, and QT clustering. There are numerous visualization
21114 methods for cluster results (neighborhood graphs, convex cluster hulls,
21115 barcharts of centroids, ...), and bootstrap methods for the analysis of
21116 cluster stability.")
21117 (license license:gpl2)))
21119 (define-public r-biclust
21126 (uri (cran-uri "biclust" version))
21129 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
21130 (properties `((upstream-name . "biclust")))
21131 (build-system r-build-system)
21133 `(("r-additivitytests" ,r-additivitytests)
21134 ("r-colorspace" ,r-colorspace)
21135 ("r-flexclust" ,r-flexclust)
21136 ("r-ggplot2" ,r-ggplot2)
21137 ("r-lattice" ,r-lattice)
21139 ("r-tidyr" ,r-tidyr)))
21140 (home-page "https://cran.r-project.org/web/packages/biclust/")
21141 (synopsis "BiCluster algorithms")
21143 "The main function @code{biclust()} provides several algorithms to find
21144 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
21145 In addition, the package provides methods for data
21146 preprocessing (normalization and discretization), visualization, and
21147 validation of bicluster solutions.")
21148 (license license:gpl3)))
21150 (define-public r-icge
21157 (uri (cran-uri "ICGE" version))
21160 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
21161 (properties `((upstream-name . "ICGE")))
21162 (build-system r-build-system)
21164 `(("r-cluster" ,r-cluster)
21165 ("r-mass" ,r-mass)))
21166 (home-page "https://cran.r-project.org/web/packages/ICGE/")
21167 (synopsis "Cluster estimation and identification of atypical units")
21169 "ICGE is a package that helps to estimate the number of real clusters in
21170 data as well as to identify atypical units. The underlying methods are based
21171 on distances rather than on unit x variables.")
21172 (license license:gpl2+)))
21174 (define-public r-depth
21177 (version "2.1-1.1")
21181 (uri (cran-uri "depth" version))
21184 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
21185 (properties `((upstream-name . "depth")))
21186 (build-system r-build-system)
21188 `(("r-abind" ,r-abind)
21189 ("r-circular" ,r-circular)
21192 `(("gfortran" ,gfortran)))
21193 (home-page "https://cran.r-project.org/web/packages/depth/")
21194 (synopsis "Nonparametric depth functions for multivariate analysis")
21196 "This package provides tools for depth functions methodology applied to
21197 multivariate analysis. Besides allowing calculation of depth values and
21198 depth-based location estimators, the package includes functions or drawing
21199 contour plots and perspective plots of depth functions. Euclidean and
21200 spherical depths are supported.")
21201 (license license:gpl2)))
21203 (define-public r-archetypes
21205 (name "r-archetypes")
21206 (version "2.2-0.1")
21210 (uri (cran-uri "archetypes" version))
21213 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
21214 (properties `((upstream-name . "archetypes")))
21215 (build-system r-build-system)
21217 `(("r-modeltools" ,r-modeltools)
21218 ("r-nnls" ,r-nnls)))
21219 (home-page "https://cran.r-project.org/web/packages/archetypes")
21220 (synopsis "Archetypal analysis")
21222 "The main function @code{archetypes} implements a framework for
21223 archetypal analysis supporting arbitrary problem solving mechanisms for the
21224 different conceptual parts of the algorithm.")
21225 (license license:gpl2+)))
21227 (define-public r-shapes
21234 (uri (cran-uri "shapes" version))
21237 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
21238 (properties `((upstream-name . "shapes")))
21239 (build-system r-build-system)
21241 `(("r-mass" ,r-mass)
21242 ("r-minpack-lm" ,r-minpack-lm)
21244 ("r-scatterplot3d" ,r-scatterplot3d)))
21245 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
21246 (synopsis "Statistical shape analysis")
21248 "This package provides routines for the statistical analysis of landmark
21249 shapes, including Procrustes analysis, graphical displays, principal
21250 components analysis, permutation and bootstrap tests, thin-plate spline
21251 transformation grids and comparing covariance matrices. See Dryden, I.L. and
21252 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
21253 Edition), John Wiley and Sons.")
21254 (license license:gpl2)))
21256 (define-public r-anthropometry
21258 (name "r-anthropometry")
21263 (uri (cran-uri "Anthropometry" version))
21266 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
21267 (properties `((upstream-name . "Anthropometry")))
21268 (build-system r-build-system)
21270 `(("r-archetypes" ,r-archetypes)
21271 ("r-biclust" ,r-biclust)
21272 ("r-cluster" ,r-cluster)
21273 ("r-depth" ,r-depth)
21278 ("r-shapes" ,r-shapes)))
21280 `(("r-knitr" ,r-knitr)))
21281 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
21282 (synopsis "Statistical methods for anthropometric data")
21284 "This package provides statistical methods especially developed to
21285 analyze anthropometric data. These methods are aimed at providing effective
21286 solutions to some commons problems related to Ergonomics and Anthropometry.
21287 They are based on clustering, the statistical concept of data depth,
21288 statistical shape analysis and archetypal analysis.")
21289 (license license:gpl2+)))
21291 (define-public r-adamethods
21293 (name "r-adamethods")
21298 (uri (cran-uri "adamethods" version))
21301 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
21302 (properties `((upstream-name . "adamethods")))
21303 (build-system r-build-system)
21305 `(("r-anthropometry" ,r-anthropometry)
21306 ("r-archetypes" ,r-archetypes)
21308 ("r-foreach" ,r-foreach)
21310 ("r-tolerance" ,r-tolerance)
21311 ("r-univoutl" ,r-univoutl)))
21312 (home-page "https://cran.r-project.org/web/packages/adamethods/")
21313 (synopsis "Archetypoid algorithms and anomaly detection")
21315 "This package is a collection of several algorithms to obtain
21316 archetypoids with small and large databases and with both classical
21317 multivariate data and functional data (univariate and multivariate). Some of
21318 these algorithms also detect anomalies (outliers).")
21319 (license license:gpl2+)))
21321 (define-public r-idpmisc
21328 (uri (cran-uri "IDPmisc" version))
21331 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
21332 (properties `((upstream-name . "IDPmisc")))
21333 (build-system r-build-system)
21335 `(("r-lattice" ,r-lattice)))
21336 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
21337 (synopsis "Functions for data analyses and visualization")
21339 "This package provides different high-level graphics functions for
21340 displaying large datasets, displaying circular data in a very flexible way,
21341 finding local maxima, brewing color ramps, drawing nice arrows, zooming
21342 2D-plots, creating figures with differently colored margin and plot region.
21343 In addition, the package contains auxiliary functions for data manipulation
21344 like omitting observations with irregular values or selecting data by logical
21345 vectors, which include NAs. Other functions are especially useful in
21346 spectroscopy and analyses of environmental data: robust baseline fitting,
21347 finding peaks in spectra, converting humidity measures.")
21348 (license license:gpl3+)))
21350 (define-public r-qqman
21357 (uri (cran-uri "qqman" version))
21360 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
21361 (properties `((upstream-name . "qqman")))
21362 (build-system r-build-system)
21364 `(("r-calibrate" ,r-calibrate)))
21365 (home-page "https://cran.r-project.org/web/packages/qqman/")
21366 (synopsis "Q-Q and Manhattan plots for GWAS data")
21368 "This package allows you to create Q-Q and Manhattan plots for GWAS data
21369 from PLINK results.")
21370 (license license:gpl3)))
21372 (define-public r-ggplot-multistats
21374 (name "r-ggplot-multistats")
21379 (uri (cran-uri "ggplot.multistats" version))
21382 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
21384 `((upstream-name . "ggplot.multistats")))
21385 (build-system r-build-system)
21387 `(("r-ggplot2" ,r-ggplot2)
21388 ("r-hexbin" ,r-hexbin)
21389 ("r-rlang" ,r-rlang)
21390 ("r-scales" ,r-scales)))
21391 (home-page "https://github.com/flying-sheep/ggplot.multistats")
21392 (synopsis "Multiple summary statistics for binned stats/geometries")
21394 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
21395 which functions similar to its singular form, but allows the use of multiple
21396 statistics per bin. Those statistics can be mapped to multiple bin
21398 (license license:gpl3)))
21400 (define-public r-knn-covertree
21402 (name "r-knn-covertree")
21407 (uri (cran-uri "knn.covertree" version))
21410 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
21411 (properties `((upstream-name . "knn.covertree")))
21412 (build-system r-build-system)
21414 `(("r-matrix" ,r-matrix)
21416 ("r-rcppeigen" ,r-rcppeigen)))
21417 (home-page "https://github.com/flying-sheep/knn.covertree")
21418 (synopsis "Accurate kNN Implementation with multiple distance measures")
21420 "Similarly to the FNN package, this package allows calculation of the k
21421 nearest neighbors (kNN) of a data matrix. The implementation is based on
21422 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
21423 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
21424 (license license:agpl3+)))
21426 (define-public r-poibin
21433 (uri (cran-uri "poibin" version))
21436 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
21437 (properties `((upstream-name . "poibin")))
21438 (build-system r-build-system)
21439 (home-page "https://cran.r-project.org/web/packages/poibin/")
21440 (synopsis "Poisson binomial distribution")
21442 "This package provides an implementation of both the exact and
21443 approximation methods for computing the @dfn{cumulative distribution
21444 function} (CDF) of the Poisson binomial distribution. It also provides the
21445 @dfn{probability mass function} (PMF), quantile function, and random number
21446 generation for the Poisson binomial distribution.")
21447 (license license:gpl2)))
21449 (define-public r-diagram
21456 (uri (cran-uri "diagram" version))
21459 "1r3lyl0h7mk9cfg8smr3jydfkjdawaphnxibkxfjqa7029vkxh79"))))
21460 (properties `((upstream-name . "diagram")))
21461 (build-system r-build-system)
21463 `(("r-shape" ,r-shape)))
21464 (home-page "https://cran.r-project.org/web/packages/diagram/")
21465 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
21467 "This package provides tools to visualize simple graphs (networks) based
21468 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
21469 electrical networks, etc. It also includes supporting material for the book
21470 \"A practical guide to ecological modelling - using R as a simulation
21471 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
21472 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
21473 Francesca Mazzia (2012).")
21474 (license license:gpl2+)))
21476 (define-public r-lim
21483 (uri (cran-uri "LIM" version))
21486 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
21487 (properties `((upstream-name . "LIM")))
21488 (build-system r-build-system)
21490 `(("r-diagram" ,r-diagram)
21491 ("r-limsolve" ,r-limsolve)))
21492 (home-page "https://cran.r-project.org/web/packages/LIM/")
21493 (synopsis "Linear inverse model examples and solution methods")
21495 "This package provides functions that read and solve linear inverse
21496 problems (food web problems, linear programming problems).")
21497 (license license:gpl2+)))
21499 (define-public r-shinycssloaders
21501 (name "r-shinycssloaders")
21506 (uri (cran-uri "shinycssloaders" version))
21509 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
21511 `((upstream-name . "shinycssloaders")))
21512 (build-system r-build-system)
21514 `(("r-digest" ,r-digest)
21516 ("r-shiny" ,r-shiny)))
21517 (home-page "https://github.com/andrewsali/shinycssloaders")
21518 (synopsis "Add CSS loading animations to Shiny outputs")
21520 "This package provides tools to create a lightweight Shiny wrapper for
21521 the css-loaders created by Luke Hass
21522 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
21523 automatically show a loader when the output is (re)calculating.")
21524 (license license:gpl3)))
21526 (define-public r-rsvg
21533 (uri (cran-uri "rsvg" version))
21536 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
21537 (properties `((upstream-name . "rsvg")))
21538 (build-system r-build-system)
21540 `(("librsvg" ,librsvg)
21543 `(("pkg-config" ,pkg-config)
21544 ("r-knitr" ,r-knitr)))
21545 (home-page "https://github.com/jeroen/rsvg#readme")
21546 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
21548 "This package allows you to render vector-based SVG images into
21549 high-quality custom-size bitmap arrays using the librsvg2 library. The
21550 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
21551 addition, the package can convert images directly to various formats such as
21552 PDF or PostScript.")
21553 (license license:expat)))
21555 (define-public r-influencer
21557 (name "r-influencer")
21562 (uri (cran-uri "influenceR" version))
21565 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
21566 (properties `((upstream-name . "influenceR")))
21567 (build-system r-build-system)
21569 `(("r-igraph" ,r-igraph)
21570 ("r-matrix" ,r-matrix)))
21571 (home-page "https://github.com/rcc-uchicago/influenceR")
21572 (synopsis "Tools to quantify structural importance of nodes in a network")
21574 "This package provides functionality to compute various node centrality
21575 measures on networks. Included are functions to compute betweenness
21576 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
21577 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
21578 algorithm to identify key players, and Valente's bridging metric. The
21579 betweenness, Key Players, and bridging implementations are parallelized with
21581 (license license:gpl2)))
21583 (define-public r-emplik
21590 (uri (cran-uri "emplik" version))
21593 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
21594 (properties `((upstream-name . "emplik")))
21595 (build-system r-build-system)
21597 `(("r-quantreg" ,r-quantreg)))
21598 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
21599 (synopsis "Empirical likelihood ratio for censored/truncated data")
21601 "This package provides empirical likelihood ratio tests for
21602 means/quantiles/hazards from possibly censored and/or truncated data. It also
21604 (license license:gpl2+)))
21606 (define-public r-imputeyn
21608 (name "r-imputeyn")
21613 (uri (cran-uri "imputeYn" version))
21616 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
21617 (properties `((upstream-name . "imputeYn")))
21618 (build-system r-build-system)
21620 `(("r-boot" ,r-boot)
21621 ("r-emplik" ,r-emplik)
21622 ("r-mvtnorm" ,r-mvtnorm)
21623 ("r-quadprog" ,r-quadprog)
21624 ("r-survival" ,r-survival)))
21625 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
21626 (synopsis "Impute last largest censored observation under weighted least squares")
21628 "This package allows for the imputation of the last largest censored
21629 observantions. This method brings less bias and more efficient estimates for
21631 (license license:gpl2)))
21633 (define-public r-adapenetclass
21635 (name "r-adapenetclass")
21640 (uri (cran-uri "AdapEnetClass" version))
21643 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
21644 (properties `((upstream-name . "AdapEnetClass")))
21645 (build-system r-build-system)
21647 `(("r-glmnet" ,r-glmnet)
21648 ("r-imputeyn" ,r-imputeyn)
21650 ("r-quadprog" ,r-quadprog)))
21651 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
21652 (synopsis "Class of adaptive elastic net methods for censored data")
21654 "This package provides methods for variable selection for AFT models.")
21655 (license license:gpl2)))
21657 (define-public r-flock
21664 (uri (cran-uri "flock" version))
21667 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
21668 (properties `((upstream-name . "flock")))
21669 (build-system r-build-system)
21670 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
21671 (home-page "https://cran.r-project.org/web/packages/flock/")
21672 (synopsis "Process synchronization using file locks")
21674 "This package implements synchronization between R processes (spawned by
21675 using the @code{parallel} package for instance) using file locks. It supports
21676 both exclusive and shared locking.")
21677 (license license:asl2.0)))
21679 (define-public r-archivist
21681 (name "r-archivist")
21686 (uri (cran-uri "archivist" version))
21689 "0sk16bcafgswrvwh39ysbgm6jvsg20yil4pdsg3wsp81nnsrb43k"))))
21690 (properties `((upstream-name . "archivist")))
21691 (build-system r-build-system)
21694 ("r-digest" ,r-digest)
21695 ("r-flock" ,r-flock)
21697 ("r-lubridate" ,r-lubridate)
21698 ("r-magrittr" ,r-magrittr)
21699 ("r-rcurl" ,r-rcurl)
21700 ("r-rsqlite" ,r-rsqlite)))
21702 `(("r-knitr" ,r-knitr)))
21703 (home-page "https://pbiecek.github.io/archivist/")
21704 (synopsis "Tools for storing, restoring and searching for R objects")
21706 "Data exploration and modelling is a process in which a lot of data
21707 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
21708 statistical models, different versions of data sets and different versions of
21709 results. Archivist helps to store and manage artifacts created in R. It
21710 allows you to store selected artifacts as binary files together with their
21711 metadata and relations. Archivist allows sharing artifacts with others. It
21712 can look for already created artifacts by using its class, name, date of the
21713 creation or other properties. It also makes it easy to restore such
21715 (license license:gpl2)))
21717 (define-public r-versions
21719 (name "r-versions")
21724 (uri (cran-uri "versions" version))
21727 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
21728 (properties `((upstream-name . "versions")))
21729 (build-system r-build-system)
21730 (home-page "https://cran.r-project.org/web/packages/versions/")
21731 (synopsis "Query and install specific versions of CRAN packages")
21733 "This package allows you to install specified versions of R packages
21734 hosted on CRAN and provides functions to list available versions and the
21735 versions of currently installed packages.")
21736 (license license:bsd-3)))
21738 (define-public r-adapr
21745 (uri (cran-uri "adapr" version))
21748 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
21749 (properties `((upstream-name . "adapr")))
21750 (build-system r-build-system)
21752 `(("r-archivist" ,r-archivist)
21753 ("r-devtools" ,r-devtools)
21754 ("r-digest" ,r-digest)
21755 ("r-doparallel" ,r-doparallel)
21756 ("r-gdata" ,r-gdata)
21757 ("r-ggplot2" ,r-ggplot2)
21758 ("r-git2r" ,r-git2r)
21759 ("r-igraph" ,r-igraph)
21760 ("r-knitr" ,r-knitr)
21761 ("r-plotly" ,r-plotly)
21763 ("r-rmarkdown" ,r-rmarkdown)
21764 ("r-shiny" ,r-shiny)
21765 ("r-shinydashboard" ,r-shinydashboard)
21766 ("r-versions" ,r-versions)))
21767 (home-page "https://cran.r-project.org/web/packages/adapr/")
21768 (synopsis "Implementation of an accountable data analysis process")
21770 "This package tracks reading and writing within R scripts that are
21771 organized into a directed acyclic graph. It contains an interactive Shiny
21772 application @code{adaprApp()}. It uses Git and file hashes to track version
21773 histories of inputs and outputs.")
21774 (license license:lgpl2.0)))
21776 (define-public r-adapsamp
21778 (name "r-adapsamp")
21783 (uri (cran-uri "AdapSamp" version))
21786 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
21787 (properties `((upstream-name . "AdapSamp")))
21788 (build-system r-build-system)
21789 (propagated-inputs `(("r-pracma" ,r-pracma)))
21790 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
21791 (synopsis "Adaptive sampling algorithms")
21793 "For distributions whose probability density functions are log-concave,
21794 the adaptive rejection sampling algorithm can be used to build envelope
21795 functions for sampling. For others, the modified adaptive rejection sampling
21796 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
21797 adaptive slice sampling algorithm can be used. This R package mainly includes
21798 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
21799 @code{rASS()}. These functions can realize sampling based on the algorithms
21801 (license license:gpl2)))
21803 (define-public r-adaptalint
21805 (name "r-adaptalint")
21810 (uri (cran-uri "adaptalint" version))
21813 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
21814 (properties `((upstream-name . "adaptalint")))
21815 (build-system r-build-system)
21817 `(("r-dplyr" ,r-dplyr)
21818 ("r-lintr" ,r-lintr)
21819 ("r-purrr" ,r-purrr)))
21820 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
21821 (synopsis "Check R code style")
21823 "This package provides tools to infer the code style (which style rules
21824 are followed and which ones are not) from one package and use it to check
21825 another. This makes it easier to find and correct the most important problems
21827 (license license:gpl3)))
21829 (define-public r-fracdiff
21831 (name "r-fracdiff")
21836 (uri (cran-uri "fracdiff" version))
21839 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
21840 (properties `((upstream-name . "fracdiff")))
21841 (build-system r-build-system)
21842 (home-page "https://github.com/mmaechler/fracdiff")
21844 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
21846 "This package provides tools for the maximum likelihood estimation of the
21847 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
21848 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
21849 (license license:gpl2+)))
21851 (define-public r-forecast
21853 (name "r-forecast")
21858 (uri (cran-uri "forecast" version))
21861 "0vrql5d4v28890np2m6ws1nr1fcl6frs1bz74vfkihkixcmkl3j9"))))
21862 (properties `((upstream-name . "forecast")))
21863 (build-system r-build-system)
21865 `(("r-colorspace" ,r-colorspace)
21866 ("r-fracdiff" ,r-fracdiff)
21867 ("r-ggplot2" ,r-ggplot2)
21868 ("r-lmtest" ,r-lmtest)
21869 ("r-magrittr" ,r-magrittr)
21872 ("r-rcpparmadillo" ,r-rcpparmadillo)
21873 ("r-timedate" ,r-timedate)
21874 ("r-tseries" ,r-tseries)
21878 `(("r-knitr" ,r-knitr))) ; needed for vignettes
21879 (home-page "https://pkg.robjhyndman.com/forecast/")
21880 (synopsis "Forecasting functions for time series and linear models")
21882 "This package provides methods and tools for displaying and analysing
21883 univariate time series forecasts including exponential smoothing via state
21884 space models and automatic ARIMA modelling.")
21885 (license license:gpl3)))
21887 (define-public r-xmisc
21894 (uri (cran-uri "Xmisc" version))
21897 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
21898 (properties `((upstream-name . "Xmisc")))
21899 (build-system r-build-system)
21900 (home-page "https://cran.r-project.org/package=Xmisc")
21902 "Xiaobei's miscellaneous classes and functions")
21904 "This package provides Xiaobei's miscellaneous classes and functions,
21905 which are useful when developing R packages for @dfn{object oriented
21906 programming} (OOP) using R Reference Class.")
21907 (license license:gpl2+)))
21909 (define-public r-proxyc
21916 (uri (cran-uri "proxyC" version))
21919 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
21920 (properties `((upstream-name . "proxyC")))
21921 (build-system r-build-system)
21923 `(("r-matrix" ,r-matrix)
21925 ("r-rcpparmadillo" ,r-rcpparmadillo)
21926 ("r-rcppparallel" ,r-rcppparallel)))
21927 (home-page "https://cran.r-project.org/package=proxyC")
21928 (synopsis "Compute proximity in large sparse matrices")
21930 "This package provides efficient tools to compute the proximity between
21931 rows or columns of large matrices. Functions are optimised for large sparse
21932 matrices using the Armadillo and Intel TBB libraries. Among several built-in
21933 similarity/distance measures, computation of correlation, cosine similarity
21934 and Euclidean distance is particularly fast.")
21935 (license license:gpl3)))
21937 (define-public r-isocodes
21939 (name "r-isocodes")
21940 (version "2020.12.04")
21944 (uri (cran-uri "ISOcodes" version))
21947 "18373rkhmwm7y2drvfbhrxkqw9d23avf0ndvh0fg00z4djvddkjx"))))
21948 (properties `((upstream-name . "ISOcodes")))
21949 (build-system r-build-system)
21950 (home-page "https://cran.r-project.org/package=ISOcodes")
21951 (synopsis "Selected ISO codes")
21953 "This package provides ISO language, territory, currency, script and
21954 character codes. It provides ISO 639 language codes, ISO 3166 territory
21955 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
21956 character codes as well as the UN M.49 area codes.")
21957 (license license:gpl2)))
21959 (define-public r-stopwords
21961 (name "r-stopwords")
21966 (uri (cran-uri "stopwords" version))
21969 "1f862y30c4r0phamlp7shzkpxg0vh3i410xy0336w310hv3wqsxn"))))
21970 (properties `((upstream-name . "stopwords")))
21971 (build-system r-build-system)
21973 `(("r-isocodes" ,r-isocodes)))
21974 (home-page "https://github.com/quanteda/stopwords")
21975 (synopsis "Multilingual stopword lists")
21977 "This package provides multiple sources of stopwords, for use in text
21978 analysis and natural language processing.")
21979 (license license:expat)))
21981 (define-public r-spacyr
21988 (uri (cran-uri "spacyr" version))
21991 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
21992 (properties `((upstream-name . "spacyr")))
21993 (build-system r-build-system)
21995 `(("r-data-table" ,r-data-table)
21996 ("r-reticulate" ,r-reticulate)))
21997 (home-page "https://spacyr.quanteda.io")
21998 (synopsis "R wrapper for the spaCy NLP library")
22000 "This package provides an R wrapper to the Python @dfn{natural language
22001 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
22002 (license license:gpl3)))
22004 (define-public r-snowballc
22006 (name "r-snowballc")
22011 (uri (cran-uri "SnowballC" version))
22014 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
22015 (properties `((upstream-name . "SnowballC")))
22016 (build-system r-build-system)
22017 (home-page "https://r-forge.r-project.org/projects/r-temis/")
22018 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
22020 "This package provides an R interface to the C @code{libstemmer} library
22021 that implements Porter's word stemming algorithm for collapsing words to a
22022 common root to aid comparison of vocabulary. Currently supported languages
22023 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
22024 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
22025 (license license:bsd-3)))
22027 (define-public r-quanteda
22029 (name "r-quanteda")
22034 (uri (cran-uri "quanteda" version))
22037 "13rjwgmg5v1dbryrs9ifyy76s5ib6wrbrm2y5af44vhf1h6p9cvy"))))
22038 (properties `((upstream-name . "quanteda")))
22039 (build-system r-build-system)
22041 `(("r-data-table" ,r-data-table)
22042 ("r-digest" ,r-digest)
22043 ("r-extrafont" ,r-extrafont)
22044 ("r-fastmatch" ,r-fastmatch)
22045 ("r-ggplot2" ,r-ggplot2)
22046 ("r-ggrepel" ,r-ggrepel)
22047 ("r-jsonlite" ,r-jsonlite)
22048 ("r-magrittr" ,r-magrittr)
22049 ("r-matrix" ,r-matrix)
22050 ("r-network" ,r-network)
22051 ("r-proxyc" ,r-proxyc)
22053 ("r-rcpparmadillo" ,r-rcpparmadillo)
22054 ("r-rcppparallel" ,r-rcppparallel)
22056 ("r-snowballc" ,r-snowballc)
22057 ("r-stopwords" ,r-stopwords)
22058 ("r-stringi" ,r-stringi)
22060 ("r-yaml" ,r-yaml)))
22062 `(("r-knitr" ,r-knitr)))
22063 (home-page "https://quanteda.io")
22064 (synopsis "Quantitative analysis of textual data")
22066 "This package provides a fast, flexible, and comprehensive framework for
22067 quantitative text analysis in R. It provides functionality for corpus
22068 management, creating and manipulating tokens and ngrams, exploring keywords in
22069 context, forming and manipulating sparse matrices of documents by features and
22070 feature co-occurrences, analyzing keywords, computing feature similarities and
22071 distances, applying content dictionaries, applying supervised and unsupervised
22072 machine learning, visually representing text and text analyses, and more.")
22073 (license license:gpl3)))
22075 (define-public r-topicmodels
22077 (name "r-topicmodels")
22082 (uri (cran-uri "topicmodels" version))
22085 "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g"))))
22086 (properties `((upstream-name . "topicmodels")))
22087 (build-system r-build-system)
22091 `(("r-modeltools" ,r-modeltools)
22094 (home-page "https://cran.r-project.org/package=topicmodels")
22095 (synopsis "Topic models")
22097 "This package provides an interface to the C code for @dfn{Latent
22098 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
22099 David M. Blei and co-authors and the C++ code for fitting LDA models using
22100 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
22101 (license license:gpl2)))
22103 (define-public r-stm
22110 (uri (cran-uri "stm" version))
22113 "0qwq4nin2n9fjd06852r8k7arvcgh46kcfb3lm21swgx6j8bgrhb"))))
22114 (properties `((upstream-name . "stm")))
22115 (build-system r-build-system)
22117 `(("r-data-table" ,r-data-table)
22118 ("r-glmnet" ,r-glmnet)
22120 ("r-matrix" ,r-matrix)
22121 ("r-matrixstats" ,r-matrixstats)
22122 ("r-quadprog" ,r-quadprog)
22123 ("r-quanteda" ,r-quanteda)
22125 ("r-rcpparmadillo" ,r-rcpparmadillo)
22127 ("r-stringr" ,r-stringr)))
22128 (home-page "http://www.structuraltopicmodel.com/")
22129 (synopsis "Estimation of the Structural Topic Model")
22131 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
22132 topic models with document-level covariates. The package also includes tools
22133 for model selection, visualization, and estimation of topic-covariate
22135 (license license:expat)))
22137 (define-public r-polycor
22144 (uri (cran-uri "polycor" version))
22147 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
22148 (properties `((upstream-name . "polycor")))
22149 (build-system r-build-system)
22151 `(("r-matrix" ,r-matrix)
22152 ("r-mvtnorm" ,r-mvtnorm)))
22153 (home-page "https://r-forge.r-project.org/projects/polycor/")
22154 (synopsis "Polychoric and polyserial correlations")
22156 "This package provides tools to compute polychoric and polyserial
22157 correlations by quick \"two-step\" methods or ML, optionally with standard
22158 errors; tetrachoric and biserial correlations are special cases.")
22159 (license license:gpl2+)))
22161 (define-public r-msm
22168 (uri (cran-uri "msm" version))
22171 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
22172 (properties `((upstream-name . "msm")))
22173 (build-system r-build-system)
22175 `(("r-expm" ,r-expm)
22176 ("r-mvtnorm" ,r-mvtnorm)
22177 ("r-survival" ,r-survival)))
22178 (home-page "https://github.com/chjackson/msm")
22179 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
22181 "This package provides functions for fitting continuous-time Markov and
22182 hidden Markov multi-state models to longitudinal data. It was designed for
22183 processes observed at arbitrary times in continuous time (panel data) but some
22184 other observation schemes are supported. Both Markov transition rates and the
22185 hidden Markov output process can be modelled in terms of covariates, which may
22186 be constant or piecewise-constant in time.")
22187 (license license:gpl2+)))
22189 (define-public r-ltm
22196 (uri (cran-uri "ltm" version))
22199 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
22200 (properties `((upstream-name . "ltm")))
22201 (build-system r-build-system)
22203 `(("r-mass" ,r-mass)
22205 ("r-polycor" ,r-polycor)))
22206 (home-page "https://github.com/drizopoulos/ltm")
22207 (synopsis "Latent trait models under IRT")
22209 "This is a package supporting the analysis of multivariate dichotomous
22210 and polytomous data using latent trait models under the Item Response Theory
22211 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
22212 Three-Parameter, the Graded Response, and the Generalized Partial Credit
22214 (license license:gpl2+)))
22216 (define-public r-mi
22223 (uri (cran-uri "mi" version))
22226 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
22227 (properties `((upstream-name . "mi")))
22228 (build-system r-build-system)
22231 ("r-matrix" ,r-matrix)))
22232 (home-page "http://www.stat.columbia.edu/~gelman/")
22233 (synopsis "Missing data imputation and model checking")
22235 "This package provides functions for data manipulation, imputing missing
22236 values in an approximate Bayesian framework, diagnostics of the models used to
22237 generate the imputations, confidence-building mechanisms to validate some of
22238 the assumptions of the imputation algorithm, and functions to analyze multiply
22239 imputed data sets with the appropriate degree of sampling uncertainty.")
22240 (license license:gpl2+)))
22242 (define-public r-matrixcalc
22244 (name "r-matrixcalc")
22249 (uri (cran-uri "matrixcalc" version))
22252 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
22253 (properties `((upstream-name . "matrixcalc")))
22254 (build-system r-build-system)
22255 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
22256 (synopsis "Collection of functions for matrix calculations")
22258 "This package provides a collection of functions to support matrix
22259 calculations for probability, econometric and numerical analysis. There are
22260 additional functions that are comparable to APL functions which are useful for
22261 actuarial models such as pension mathematics.")
22262 (license license:gpl2+)))
22264 (define-public r-sem
22271 (uri (cran-uri "sem" version))
22274 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
22275 (properties `((upstream-name . "sem")))
22276 (build-system r-build-system)
22278 `(("r-boot" ,r-boot)
22280 ("r-matrixcalc" ,r-matrixcalc)
22282 (home-page "https://cran.r-project.org/package=sem")
22283 (synopsis "Structural equation models")
22285 "This package provides functions for fitting general linear structural
22286 equation models (with observed and latent variables) using the RAM approach,
22287 and for fitting structural equations in observed-variable models by two-stage
22289 (license license:gpl2+)))
22291 (define-public r-semtools
22293 (name "r-semtools")
22298 (uri (cran-uri "semTools" version))
22301 "15kban4ds2mssxqslm126b89p8biya14c9m68sqk61vzvx5dm2vq"))))
22302 (properties `((upstream-name . "semTools")))
22303 (build-system r-build-system)
22305 `(("r-lavaan" ,r-lavaan)))
22306 (home-page "https://github.com/simsem/semTools/wiki")
22307 (synopsis "Useful tools for structural equation modeling")
22309 "This package provides useful tools for structural equation modeling.")
22310 (license license:gpl2+)))
22312 (define-public r-regsem
22319 (uri (cran-uri "regsem" version))
22322 "14nrzyrkrijdrr4jwkri5zra2wh36w68wy6xs600l2z1633h2lmn"))))
22323 (properties `((upstream-name . "regsem")))
22324 (build-system r-build-system)
22326 `(("r-lavaan" ,r-lavaan)
22328 ("r-rcpparmadillo" ,r-rcpparmadillo)
22329 ("r-rsolnp" ,r-rsolnp)))
22331 `(("r-knitr" ,r-knitr)))
22332 (home-page "https://cran.r-project.org/package=regsem")
22333 (synopsis "Regularized structural equation modeling")
22335 "This package uses both ridge and lasso penalties (and extensions) to
22336 penalize specific parameters in structural equation models. The package
22337 offers additional cost functions, cross validation, and other extensions
22338 beyond traditional structural equation models. It also contains a function to
22339 perform @dfn{exploratory mediation} (XMed).")
22340 (license license:gpl2+)))
22342 (define-public r-stanheaders
22344 (name "r-stanheaders")
22345 (version "2.21.0-7")
22349 (uri (cran-uri "StanHeaders" version))
22352 "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17"))))
22353 (properties `((upstream-name . "StanHeaders")))
22354 (build-system r-build-system)
22355 (inputs `(("pandoc" ,pandoc)))
22357 `(("r-rcppeigen" ,r-rcppeigen)
22358 ("r-rcppparallel" ,r-rcppparallel)))
22360 `(("gfortran" ,gfortran)
22361 ("r-knitr" ,r-knitr))) ; for vignettes
22362 (home-page "https://mc-stan.org/")
22363 (synopsis "C++ header files for Stan")
22365 "The C++ header files of the Stan project are provided by this package.
22366 There is a shared object containing part of the @code{CVODES} library, but it
22367 is not accessible from R. @code{r-stanheaders} is only useful for developers
22368 who want to utilize the @code{LinkingTo} directive of their package's
22369 DESCRIPTION file to build on the Stan library without incurring unnecessary
22372 The Stan project develops a probabilistic programming language that implements
22373 full or approximate Bayesian statistical inference via Markov Chain Monte
22374 Carlo or variational methods and implements (optionally penalized) maximum
22375 likelihood estimation via optimization. The Stan library includes an advanced
22376 automatic differentiation scheme, templated statistical and linear algebra
22377 functions that can handle the automatically differentiable scalar types (and
22378 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
22379 package provides user-facing R functions to parse, compile, test, estimate,
22380 and analyze Stan models.")
22381 (license license:bsd-3)))
22383 (define-public r-rpf
22390 (uri (cran-uri "rpf" version))
22393 "0kz7i7g3l16irz6bxgnkxdmmd931m1fk6rl72dvs21ir5brr010l"))))
22394 (properties `((upstream-name . "rpf")))
22395 (build-system r-build-system)
22397 `(("r-lifecycle" ,r-lifecycle)
22398 ("r-mvtnorm" ,r-mvtnorm)
22400 ("r-rcppeigen" ,r-rcppeigen)))
22402 `(("r-knitr" ,r-knitr)))
22403 (home-page "https://github.com/jpritikin/rpf")
22404 (synopsis "Response probability functions")
22406 "The purpose of this package is to factor out logic and math common to
22407 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
22408 core support code suitable for more specialized IRT packages to build upon.
22409 Complete access to optimized C functions is made available with
22410 @code{R_RegisterCCallable()}.")
22411 (license license:gpl3+)))
22413 (define-public r-openmx
22420 (uri (cran-uri "OpenMx" version))
22423 "0gyjps0l3ig90piccgd04s63cz65kk5i5l9iyakps4bv27h1lzwm"))))
22424 (properties `((upstream-name . "OpenMx")))
22425 (build-system r-build-system)
22428 ("r-digest" ,r-digest)
22429 ("r-lifecycle" ,r-lifecycle)
22431 ("r-matrix" ,r-matrix)
22433 ("r-rcppeigen" ,r-rcppeigen)
22435 ("r-stanheaders" ,r-stanheaders)))
22436 (native-inputs `(("gfortran" ,gfortran)))
22437 (home-page "http://openmx.ssri.psu.edu")
22438 (synopsis "Extended structural equation modelling")
22440 "This package allows for the estimation of a wide variety of advanced
22441 multivariate statistical models. It consists of a library of functions and
22442 optimizers that allow you to quickly and flexibly define an SEM model and
22443 estimate parameters given observed data.")
22444 (license license:asl2.0)))
22446 (define-public r-kutils
22453 (uri (cran-uri "kutils" version))
22456 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
22457 (properties `((upstream-name . "kutils")))
22458 (build-system r-build-system)
22460 `(("r-foreign" ,r-foreign)
22461 ("r-openxlsx" ,r-openxlsx)
22463 ("r-runit" ,r-runit)
22464 ("r-xtable" ,r-xtable)))
22465 (home-page "https://cran.r-project.org/package=kutils")
22466 (synopsis "Project management tools")
22468 "This package provides tools for data importation, recoding, and
22469 inspection. There are functions to create new project folders, R code
22470 templates, create uniquely named output directories, and to quickly obtain a
22471 visual summary for each variable in a data frame. The main feature here is
22472 the systematic implementation of the \"variable key\" framework for data
22473 importation and recoding.")
22474 (license license:gpl2)))
22476 (define-public r-rockchalk
22478 (name "r-rockchalk")
22479 (version "1.8.144")
22483 (uri (cran-uri "rockchalk" version))
22486 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
22487 (properties `((upstream-name . "rockchalk")))
22488 (build-system r-build-system)
22490 `(("r-cardata" ,r-cardata)
22491 ("r-kutils" ,r-kutils)
22493 ("r-mass" ,r-mass)))
22494 (home-page "https://cran.r-project.org/package=rockchalk")
22495 (synopsis "Regression estimation and presentation")
22497 "This package provides a collection of functions for interpretation and
22498 presentation of regression analysis. These functions are used to produce the
22499 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
22500 includes regression diagnostics, regression tables, and plots of interactions
22501 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
22502 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
22503 fairly comprehensive overview.")
22504 (license license:gpl3+)))
22506 (define-public r-lisreltor
22508 (name "r-lisreltor")
22513 (uri (cran-uri "lisrelToR" version))
22516 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
22517 (properties `((upstream-name . "lisrelToR")))
22518 (build-system r-build-system)
22519 (home-page "https://cran.r-project.org/package=lisrelToR")
22520 (synopsis "Import output from LISREL into R")
22522 "This is an unofficial package aimed at automating the import of LISREL
22524 (license license:gpl2)))
22526 (define-public r-bdgraph
22533 (uri (cran-uri "BDgraph" version))
22536 "05q6dbvdnxmh7myvw60zqcqx16f80i8d6qa4y7xnfkx02l9lwiyc"))))
22537 (properties `((upstream-name . "BDgraph")))
22538 (build-system r-build-system)
22540 `(("r-igraph" ,r-igraph)))
22541 (home-page "https://www.uva.nl/profile/a.mohammadi")
22542 (synopsis "Bayesian structure learning in graphical models")
22544 "This package provides statistical tools for Bayesian structure learning
22545 in undirected graphical models for continuous, discrete, and mixed data. It
22546 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
22547 on a continuous-time birth-death process.")
22548 (license license:gpl2+)))
22550 (define-public r-d3network
22552 (name "r-d3network")
22553 (version "0.5.2.1")
22557 (uri (cran-uri "d3Network" version))
22560 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
22561 (properties `((upstream-name . "d3Network")))
22562 (build-system r-build-system)
22564 `(("r-plyr" ,r-plyr)
22565 ("r-rjson" ,r-rjson)
22566 ("r-whisker" ,r-whisker)))
22567 (home-page "http://christophergandrud.github.io/d3Network/")
22568 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
22570 "This package is intended to make it easy to create D3 JavaScript
22571 network, tree, dendrogram, and Sankey graphs from R using data frames.")
22572 (license license:gpl3+)))
22574 (define-public r-qgraph
22581 (uri (cran-uri "qgraph" version))
22584 "153bqfmsrghkg7598nfr57r3cxv6dn6ir084njl2sqq5np0sj9di"))))
22585 (properties `((upstream-name . "qgraph")))
22586 (build-system r-build-system)
22588 `(("r-abind" ,r-abind)
22589 ("r-colorspace" ,r-colorspace)
22590 ("r-corpcor" ,r-corpcor)
22591 ("r-dplyr" ,r-dplyr)
22592 ("r-fdrtool" ,r-fdrtool)
22593 ("r-ggplot2" ,r-ggplot2)
22594 ("r-glasso" ,r-glasso)
22595 ("r-gtools" ,r-gtools)
22596 ("r-hmisc" ,r-hmisc)
22597 ("r-igraph" ,r-igraph)
22599 ("r-lavaan" ,r-lavaan)
22600 ("r-matrix" ,r-matrix)
22601 ("r-pbapply" ,r-pbapply)
22604 ("r-psych" ,r-psych)
22606 ("r-reshape2" ,r-reshape2)))
22607 (home-page "http://sachaepskamp.com/qgraph/")
22608 (synopsis "Weighted network visualization and analysis")
22610 "This package implements tools for weighted network visualization and
22611 analysis, as well as Gaussian graphical model computation. It contains graph
22612 plotting methods, and tools for psychometric data visualization and graphical
22613 model estimation. See Epskamp et al. (2012)
22614 @url{doi:10.18637/jss.v048.i04}.")
22615 (license license:gpl2)))
22617 (define-public r-semplot
22624 (uri (cran-uri "semPlot" version))
22627 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
22628 (properties `((upstream-name . "semPlot")))
22629 (build-system r-build-system)
22631 `(("r-colorspace" ,r-colorspace)
22632 ("r-corpcor" ,r-corpcor)
22633 ("r-igraph" ,r-igraph)
22634 ("r-lavaan" ,r-lavaan)
22635 ("r-lisreltor" ,r-lisreltor)
22636 ("r-openmx" ,r-openmx)
22638 ("r-qgraph" ,r-qgraph)
22639 ("r-regsem" ,r-regsem)
22640 ("r-rockchalk" ,r-rockchalk)
22643 (home-page "https://github.com/SachaEpskamp/semPlot")
22644 (synopsis "Unified visualizations of structural equation models")
22646 "Structural equation modeling (SEM) has a long history of representing
22647 models graphically as path diagrams. The semPlot package for R fills the gap
22648 between advanced, but time-consuming, graphical software and the limited
22649 graphics produced automatically by SEM software. In addition, semPlot offers
22650 more functionality than drawing path diagrams: it can act as a common ground
22651 for importing SEM results into R. Any result usable as input to semPlot can
22652 also be represented in any of the three popular SEM frame-works, as well as
22653 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
22654 (license license:gpl2)))
22656 (define-public r-cdm
22663 (uri (cran-uri "CDM" version))
22666 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
22667 (properties `((upstream-name . "CDM")))
22668 (build-system r-build-system)
22670 `(("r-mvtnorm" ,r-mvtnorm)
22671 ("r-polycor" ,r-polycor)
22673 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22675 "https://github.com/alexanderrobitzsch/CDM")
22676 (synopsis "Cognitive diagnosis modeling")
22678 "This package provides functions for cognitive diagnosis modeling and
22679 multidimensional item response modeling for dichotomous and polytomous item
22680 responses. It enables the estimation of the DINA and DINO model, the multiple
22681 group (polytomous) GDINA model, the multiple choice DINA model, the general
22682 diagnostic model (GDM), the structured latent class model (SLCA), and
22683 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
22684 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
22685 estimation and the package structure. For tutorials on how to use the CDM
22686 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
22687 well as Ravand and Robitzsch (2015).")
22688 (license license:gpl2+)))
22690 (define-public r-tam
22697 (uri (cran-uri "TAM" version))
22700 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
22701 (properties `((upstream-name . "TAM")))
22702 (build-system r-build-system)
22706 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22707 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
22708 (synopsis "Test analysis modules")
22710 "This package includes tools for marginal maximum likelihood estimation
22711 and joint maximum likelihood estimation for unidimensional and
22712 multidimensional item response models. The package functionality covers the
22713 Rasch model, 2PL model, 3PL model, generalized partial credit model,
22714 multi-faceted Rasch model, nominal item response model, structured latent
22715 class model, mixture distribution IRT models, and located latent class models.
22716 Latent regression models and plausible value imputation are also supported.")
22717 (license license:gpl2+)))
22719 (define-public r-erm
22726 (uri (cran-uri "eRm" version))
22729 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
22730 (properties `((upstream-name . "eRm")))
22731 (build-system r-build-system)
22733 `(("r-colorspace" ,r-colorspace)
22734 ("r-lattice" ,r-lattice)
22736 ("r-matrix" ,r-matrix)
22737 ("r-psych" ,r-psych)))
22738 (native-inputs `(("gfortran" ,gfortran)))
22739 (home-page "https://cran.r-project.org/package=eRm")
22740 (synopsis "Extended Rasch modeling")
22742 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
22743 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
22744 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
22745 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
22746 data matrix. Additional features are the ML estimation of the person
22747 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
22748 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
22749 infit and outfit measures, ICC and other plots, automated stepwise item
22750 elimination, and a simulation module for various binary data matrices.")
22751 (license license:gpl3)))
22753 (define-public r-irtoys
22760 (uri (cran-uri "irtoys" version))
22763 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
22764 (properties `((upstream-name . "irtoys")))
22765 (build-system r-build-system)
22769 (home-page "https://cran.r-project.org/package=irtoys")
22770 (synopsis "Collection of functions related to Item Response Theory (IRT)")
22772 "This package provides a collection of functions useful in learning and
22773 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
22774 programs. It provides basic CTT analysis, a simple common interface to the
22775 estimation of item parameters in IRT models for binary responses with three
22776 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
22777 EAP, WLE, plausible values), item and person fit statistics, scaling
22778 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
22779 array of parametric and non-parametric (kernel) plots. It estimates and plots
22780 Haberman's interaction model when all items are dichotomously scored.")
22781 (license license:gpl2+)))
22783 (define-public r-iheatmapr
22785 (name "r-iheatmapr")
22790 (uri (cran-uri "iheatmapr" version))
22793 "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx"))))
22794 (properties `((upstream-name . "iheatmapr")))
22795 (build-system r-build-system)
22797 `(("r-fastcluster" ,r-fastcluster)
22798 ("r-ggdendro" ,r-ggdendro)
22799 ("r-htmlwidgets" ,r-htmlwidgets)
22800 ("r-jsonlite" ,r-jsonlite)
22801 ("r-knitr" ,r-knitr)
22802 ("r-magrittr" ,r-magrittr)
22803 ("r-rcolorbrewer" ,r-rcolorbrewer)
22804 ("r-scales" ,r-scales)))
22806 `(("r-knitr" ,r-knitr)))
22807 (home-page "https://docs.ropensci.org/iheatmapr")
22808 (synopsis "Interactive, Complex Heatmaps")
22810 "iheatmapr is an R package for building complex, interactive heatmaps
22811 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
22812 subplots along the rows or columns of the main heatmap add more information
22813 about each row or column. For example, a one column additional heatmap may
22814 indicate what group a particular row or column belongs to. Complex heatmaps
22815 may also include multiple side by side heatmaps which show different types of
22816 data for the same conditions. Interactivity can improve complex heatmaps by
22817 providing tooltips with information about each cell and enabling zooming into
22818 interesting features. iheatmapr uses the plotly library for interactivity.")
22819 (license license:expat)))
22821 (define-public r-packrat
22828 (uri (cran-uri "packrat" version))
22831 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
22832 (properties `((upstream-name . "packrat")))
22833 (build-system r-build-system)
22834 (home-page "https://github.com/rstudio/packrat/")
22835 (synopsis "Dependency management R projects")
22837 "This package provides a dependency manager for R projects that allows
22838 you to manage the R packages your project depends on in an isolated, portable,
22839 and reproducible way.")
22840 (license license:gpl2)))
22842 (define-public r-rsconnect
22844 (name "r-rsconnect")
22849 (uri (cran-uri "rsconnect" version))
22852 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
22853 (properties `((upstream-name . "rsconnect")))
22854 (build-system r-build-system)
22856 `(("r-curl" ,r-curl)
22857 ("r-digest" ,r-digest)
22858 ("r-jsonlite" ,r-jsonlite)
22859 ("r-openssl" ,r-openssl)
22860 ("r-packrat" ,r-packrat)
22861 ("r-rstudioapi" ,r-rstudioapi)
22862 ("r-yaml" ,r-yaml)))
22863 (home-page "https://github.com/rstudio/rsconnect")
22864 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
22866 "This package provides a programmatic deployment interface for RPubs,
22867 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
22868 documents, Shiny applications, Plumber APIs, plots, and static web content.")
22869 (license license:gpl2)))
22871 ;; This package includes minified JavaScript files. When upgrading please
22872 ;; check that there are no new minified JavaScript files.
22873 (define-public r-dygraphs
22875 (name "r-dygraphs")
22876 (version "1.1.1.6")
22880 (uri (cran-uri "dygraphs" version))
22883 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
22884 (properties `((upstream-name . "dygraphs")))
22885 (build-system r-build-system)
22887 `(#:modules ((guix build utils)
22888 (guix build r-build-system)
22892 (modify-phases %standard-phases
22893 (add-after 'unpack 'process-javascript
22894 (lambda* (#:key inputs #:allow-other-keys)
22895 (with-directory-excursion "inst/htmlwidgets/lib/"
22899 `(("dygraphs/dygraph-combined-dev.js"
22900 "dygraph-combined.js")
22901 (,(assoc-ref inputs "js-jquery")
22902 "jquery/jquery.min.js")
22903 (,(assoc-ref inputs "js-fquarter")
22904 "fquarter/moment-fquarter.min.js"))))
22905 (lambda (sources targets)
22906 (for-each (lambda (source target)
22907 (format #t "Processing ~a --> ~a~%"
22909 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
22910 (call-with-output-file target
22912 (dump-port minified port)))))
22913 sources targets))))
22916 `(("uglify-js" ,uglify-js)
22917 ;; They actually use version 1.11.1, but this more recent version
22918 ;; should be just fine.
22922 (uri "https://code.jquery.com/jquery-1.12.4.js")
22925 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
22929 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
22930 "moment-fquarter/1.0.1/moment-fquarter.js"))
22933 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
22935 `(("r-htmltools" ,r-htmltools)
22936 ("r-htmlwidgets" ,r-htmlwidgets)
22937 ("r-magrittr" ,r-magrittr)
22940 (home-page "https://github.com/rstudio/dygraphs")
22941 (synopsis "Interface to Dygraphs interactive time series charting library")
22943 "This package provides an R interface to the dygraphs JavaScript charting
22944 library (a copy of which is included in the package). It provides rich
22945 facilities for charting time-series data in R, including highly configurable
22946 series- and axis-display and interactive features like zoom/pan and
22947 series/point highlighting.")
22948 (license license:expat)))
22950 (define-public r-shinystan
22952 (name "r-shinystan")
22957 (uri (cran-uri "shinystan" version))
22960 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
22961 (properties `((upstream-name . "shinystan")))
22962 (build-system r-build-system)
22964 `(("r-bayesplot" ,r-bayesplot)
22965 ("r-colourpicker" ,r-colourpicker)
22967 ("r-dygraphs" ,r-dygraphs)
22968 ("r-ggplot2" ,r-ggplot2)
22969 ("r-gridextra" ,r-gridextra)
22970 ("r-gtools" ,r-gtools)
22971 ("r-markdown" ,r-markdown)
22972 ("r-reshape2" ,r-reshape2)
22973 ("r-rsconnect" ,r-rsconnect)
22974 ("r-rstan" ,r-rstan)
22975 ("r-shiny" ,r-shiny)
22976 ("r-shinyjs" ,r-shinyjs)
22977 ("r-shinythemes" ,r-shinythemes)
22978 ("r-threejs" ,r-threejs)
22979 ("r-xtable" ,r-xtable)
22981 (home-page "https://mc-stan.org/")
22982 (synopsis "Interactive visual and numerical analysis for Bayesian models")
22984 "This package provides a graphical user interface for interactive
22985 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
22986 for analyzing a posterior sample. The interface is powered by the Shiny web
22987 application framework and works with the output of MCMC programs written in
22988 any programming language (and has extended functionality for Stan models fit
22989 using the @code{rstan} and @code{rstanarm} packages).")
22990 (license license:gpl3+)))
22992 (define-public r-rstantools
22994 (name "r-rstantools")
22999 (uri (cran-uri "rstantools" version))
23002 "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
23003 (properties `((upstream-name . "rstantools")))
23004 (build-system r-build-system)
23005 (inputs `(("pandoc" ,pandoc)))
23007 `(("r-desc" ,r-desc)
23009 ("r-rcppparallel" ,r-rcppparallel)))
23011 `(("r-knitr" ,r-knitr)))
23012 (home-page "https://mc-stan.org/rstantools/")
23013 (synopsis "Tools for developing R packages interfacing with Stan")
23015 "This package provides various tools for developers of R packages
23016 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
23017 up the required package structure, S3 generics and default methods to unify
23018 function naming across Stan-based R packages, and vignettes with
23019 recommendations for developers.")
23020 (license license:gpl3+)))
23022 (define-public r-loo
23029 (uri (cran-uri "loo" version))
23031 (base32 "0l2v8zpashqbnck3qx5lp1gqjcfphzky8mxyw5gfk9wk99mzn8dw"))))
23032 (properties `((upstream-name . "loo")))
23033 (build-system r-build-system)
23035 `(("pandoc" ,pandoc)
23036 ("pandoc-citeproc" ,pandoc-citeproc)))
23038 `(("r-checkmate" ,r-checkmate)
23039 ("r-matrixstats" ,r-matrixstats)))
23041 `(("r-knitr" ,r-knitr)))
23042 (home-page "https://mc-stan.org/loo/")
23043 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
23045 "This package provides an implementation of efficient approximate
23046 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
23047 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
23048 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
23049 procedure for regularizing importance weights. As a byproduct of the
23050 calculations, we also obtain approximate standard errors for estimated
23051 predictive errors and for the comparison of predictive errors between models.
23052 The package also provides methods for using stacking and other model weighting
23053 techniques to average Bayesian predictive distributions.")
23054 (license license:gpl3+)))
23056 (define-public r-rstan
23063 (uri (cran-uri "rstan" version))
23066 "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3"))))
23067 (properties `((upstream-name . "rstan")))
23068 (build-system r-build-system)
23071 (modify-phases %standard-phases
23072 (add-before 'install 'set-timezone
23073 ;; This package is picky about timezones.
23074 (lambda* (#:key inputs #:allow-other-keys)
23075 (setenv "TZ" "UTC+1")
23077 (string-append (assoc-ref inputs "tzdata")
23078 "/share/zoneinfo"))
23081 `(("tzdata" ,tzdata-for-tests)
23083 ("r-knitr" ,r-knitr)))
23086 ("r-ggplot2" ,r-ggplot2)
23087 ("r-gridextra" ,r-gridextra)
23088 ("r-inline" ,r-inline)
23090 ("r-pkgbuild" ,r-pkgbuild)
23092 ("r-rcppeigen" ,r-rcppeigen)
23093 ("r-rcppparallel" ,r-rcppparallel)
23094 ("r-stanheaders" ,r-stanheaders)
23096 ("r-withr" ,r-withr)))
23097 (home-page "https://discourse.mc-stan.org/")
23098 (synopsis "R interface to Stan")
23100 "User-facing R functions are provided to parse, compile, test, estimate,
23101 and analyze Stan models by accessing the header-only Stan library provided by
23102 the StanHeaders package. The Stan project develops a probabilistic
23103 programming language that implements full Bayesian statistical inference via
23104 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
23105 approximation, and (optionally penalized) maximum likelihood estimation via
23106 optimization. In all three cases, automatic differentiation is used to
23107 quickly and accurately evaluate gradients without burdening the user with the
23108 need to derive the partial derivatives.")
23109 (license license:gpl3+)))
23111 (define-public r-rstanarm
23113 (name "r-rstanarm")
23118 (uri (cran-uri "rstanarm" version))
23121 "04ggzak3f7jaxza3dxyrmxp5b48qcgyspy22ykbhr03g4hzp7jk8"))))
23122 (properties `((upstream-name . "rstanarm")))
23123 (build-system r-build-system)
23125 `(("pandoc" ,pandoc)
23126 ("pandoc-citeproc" ,pandoc-citeproc)))
23128 `(("r-bayesplot" ,r-bayesplot)
23130 ("r-ggplot2" ,r-ggplot2)
23133 ("r-matrix" ,r-matrix)
23136 ("r-rcppeigen" ,r-rcppeigen)
23137 ("r-rcppparallel" ,r-rcppparallel)
23138 ("r-rstan" ,r-rstan)
23139 ("r-rstantools" ,r-rstantools)
23140 ("r-shinystan" ,r-shinystan)
23141 ("r-stanheaders" ,r-stanheaders)
23142 ("r-survival" ,r-survival)))
23144 `(("r-knitr" ,r-knitr)))
23145 (home-page "https://mc-stan.org/rstanarm/")
23146 (synopsis "Bayesian applied regression modeling via Stan")
23148 "This package estimates previously compiled regression models using the
23149 @code{rstan} package, which provides the R interface to the Stan C++ library
23150 for Bayesian estimation. Users specify models via the customary R syntax with
23151 a formula and @code{data.frame} plus some additional arguments for priors.")
23152 (license license:gpl3+)))
23154 (define-public r-kendall
23161 (uri (cran-uri "Kendall" version))
23164 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
23165 (properties `((upstream-name . "Kendall")))
23166 (build-system r-build-system)
23168 `(("r-boot" ,r-boot)))
23170 `(("gfortran" ,gfortran)))
23171 (home-page "https://cran.r-project.org/web/packages/Kendall/")
23172 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
23174 "This package computes the Kendall rank correlation and Mann-Kendall
23176 (license license:gpl2+)))
23178 (define-public r-keyring
23185 (uri (cran-uri "keyring" version))
23188 "1hpfd4hbx43i39l995rg86kfxi7wlyla1gv8mwcdr4xx7z122zzq"))))
23189 (properties `((upstream-name . "keyring")))
23190 (build-system r-build-system)
23192 `(("r-assertthat" ,r-assertthat)
23193 ("r-filelock" ,r-filelock)
23194 ("r-getpass" ,r-getpass)
23195 ("r-openssl" ,r-openssl)
23197 ("r-rappdirs" ,r-rappdirs)
23198 ("r-sodium" ,r-sodium)
23199 ("r-yaml" ,r-yaml)))
23200 (native-inputs `(("pkg-config" ,pkg-config)))
23201 (home-page "https://github.com/r-lib/keyring")
23202 (synopsis "Access the system credential store from R")
23204 "This package provides a platform-independent API to access the operating
23205 system's credential store. It currently supports Keychain on macOS,
23206 Credential Store on Windows, the Secret Service API on GNU/Linux, and a
23207 simple, platform independent store implemented with environment variables.
23208 Additional storage back-ends can be added easily.")
23209 (license license:expat)))
23211 (define-public r-zyp
23214 (version "0.10-1.1")
23218 (uri (cran-uri "zyp" version))
23221 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
23222 (properties `((upstream-name . "zyp")))
23223 (build-system r-build-system)
23225 `(("r-kendall" ,r-kendall)))
23226 (home-page "https://cran.r-project.org/web/packages/zyp/")
23227 (synopsis "Zhang + Yue-Pilon Trends Package")
23229 "This package contains an efficient implementation of Sen's slope
23230 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
23231 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
23233 (license license:lgpl2.1)))
23235 (define-public r-rlinsolve
23237 (name "r-rlinsolve")
23242 (uri (cran-uri "Rlinsolve" version))
23245 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
23246 (properties `((upstream-name . "Rlinsolve")))
23247 (build-system r-build-system)
23249 `(("r-matrix" ,r-matrix)
23251 ("r-rcpparmadillo" ,r-rcpparmadillo)
23252 ("r-rdpack" ,r-rdpack)))
23253 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
23254 (synopsis "Iterative solvers for (sparse) linear system of equations")
23256 "Solving a system of linear equations is one of the most fundamental
23257 computational problems for many fields of mathematical studies, such as
23258 regression problems from statistics or numerical partial differential
23259 equations. This package provides basic stationary iterative solvers such as
23260 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
23261 Nonstationary, also known as Krylov subspace methods are also provided.
23262 Sparse matrix computation is also supported in that solving large and sparse
23263 linear systems can be manageable using the @code{Matrix} package along with
23264 @code{RcppArmadillo}.")
23265 (license license:gpl3+)))
23267 (define-public r-zvcv
23274 (uri (cran-uri "ZVCV" version))
23277 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
23278 (properties `((upstream-name . "ZVCV")))
23279 (build-system r-build-system)
23281 `(("r-abind" ,r-abind)
23283 ("r-dplyr" ,r-dplyr)
23284 ("r-glmnet" ,r-glmnet)
23285 ("r-magrittr" ,r-magrittr)
23286 ("r-mvtnorm" ,r-mvtnorm)
23288 ("r-rcpparmadillo" ,r-rcpparmadillo)
23289 ("r-rlinsolve" ,r-rlinsolve)))
23290 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
23291 (synopsis "Zero-Variance Control Variates")
23293 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
23294 to reduce the variance of Monte Carlo estimators of expectations using the
23295 derivatives of the log target. Once the derivatives are available, the only
23296 additional computational effort is in solving a linear regression problem.
23297 This method has been extended to higher dimensions using regularisation. This
23298 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
23299 samples, derivatives and function evaluations are available. Additional
23300 functions for applying ZV-CV to two estimators for the normalising constant of
23301 the posterior distribution in Bayesian statistics are also supplied.")
23302 (license license:gpl2+)))
23304 (define-public r-ztype
23311 (uri (cran-uri "ztype" version))
23314 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
23315 (properties `((upstream-name . "ztype")))
23316 (build-system r-build-system)
23318 `(("r-assertthat" ,r-assertthat)
23319 ("r-dplyr" ,r-dplyr)
23320 ("r-ggplot2" ,r-ggplot2)
23321 ("r-lubridate" ,r-lubridate)
23322 ("r-magrittr" ,r-magrittr)
23323 ("r-rvest" ,r-rvest)
23324 ("r-stringr" ,r-stringr)))
23325 (home-page "https://cran.r-project.org/web/packages/ztype/")
23326 (synopsis "Run a Ztype game loaded with R functions")
23328 "How fast can you type R functions on your keyboard? Find out by running
23329 a @code{zty.pe} game: export R functions as instructions to type to destroy
23330 opponents' vessels.")
23331 (license license:gpl3)))
23333 (define-public r-zseq
23340 (uri (cran-uri "Zseq" version))
23343 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
23344 (properties `((upstream-name . "Zseq")))
23345 (build-system r-build-system)
23347 `(("r-gmp" ,r-gmp)))
23348 (home-page "https://cran.r-project.org/web/packages/Zseq/")
23349 (synopsis "Integer sequence generator")
23351 "This package generates well-known integer sequences. The @code{gmp}
23352 package is adopted for computing with arbitrarily large numbers. Every
23353 function has a hyperlink to its corresponding item in the @dfn{On-Line
23354 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
23355 (license license:gpl3+)))
23357 (define-public r-isoband
23364 (uri (cran-uri "isoband" version))
23367 "1zkzdc39dpw2z59bjck27nimz9a2vskmw0f7wb17s53dvy7k3lzr"))))
23368 (properties `((upstream-name . "isoband")))
23369 (build-system r-build-system)
23371 `(("r-testthat" ,r-testthat)))
23373 `(("r-knitr" ,r-knitr)))
23374 (home-page "https://github.com/wilkelab/isoband")
23375 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
23377 "This package provides a fast C++ implementation to generate contour
23378 lines (isolines) and contour polygons (isobands) from regularly spaced grids
23379 containing elevation data.")
23380 (license license:expat)))
23382 (define-public r-ppcor
23389 (uri (cran-uri "ppcor" version))
23392 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
23393 (properties `((upstream-name . "ppcor")))
23394 (build-system r-build-system)
23396 `(("r-mass" ,r-mass)))
23397 (home-page "https://cran.r-project.org/web/packages/ppcor/")
23398 (synopsis "Partial and semi-partial correlation")
23400 "This package provides users not only with a function to readily
23401 calculate the higher-order partial and semi-partial correlations but also with
23402 statistics and p-values of the correlation coefficients.")
23403 (license license:gpl2)))
23405 (define-public r-hrbrthemes
23407 (name "r-hrbrthemes")
23412 (uri (cran-uri "hrbrthemes" version))
23414 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
23415 (properties `((upstream-name . "hrbrthemes")))
23416 (build-system r-build-system)
23418 `(("r-extrafont" ,r-extrafont)
23419 ("r-gdtools" ,r-gdtools)
23420 ("r-ggplot2" ,r-ggplot2)
23421 ("r-htmltools" ,r-htmltools)
23422 ("r-knitr" ,r-knitr)
23423 ("r-magrittr" ,r-magrittr)
23424 ("r-rmarkdown" ,r-rmarkdown)
23425 ("r-scales" ,r-scales)))
23427 `(("r-knitr" ,r-knitr)))
23428 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
23429 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
23431 "This package provides a compilation of extra @code{ggplot2} themes,
23432 scales and utilities, including a spell check function for plot label fields
23433 and an overall emphasis on typography.")
23434 (license license:expat)))
23436 (define-public r-crochet
23443 (uri (cran-uri "crochet" version))
23446 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
23447 (build-system r-build-system)
23449 `(("r-knitr" ,r-knitr)))
23450 (home-page "https://github.com/agrueneberg/crochet")
23451 (synopsis "Implementation Helper for Matrix-Like Types")
23453 "Functions to help implement the extraction / subsetting / indexing
23454 function @code{[} and replacement function @code{[<-} of custom matrix-like
23455 types (based on S3, S4, etc.), modeled as closely to the base matrix class
23456 as possible (with tests to prove it).")
23457 (license license:expat)))
23459 (define-public r-boa
23462 (version "1.1.8-2")
23466 (uri (cran-uri "boa" version))
23469 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
23470 (properties `((upstream-name . "boa")))
23471 (build-system r-build-system)
23472 (home-page "https://www.jstatsoft.org/v21/i11")
23473 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
23475 "This package provides a menu-driven program and library of functions for
23476 carrying out convergence diagnostics and statistical and graphical analysis of
23477 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
23478 (license license:gpl2+)))
23480 (define-public r-httpcode
23482 (name "r-httpcode")
23486 (uri (cran-uri "httpcode" version))
23489 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
23490 (build-system r-build-system)
23491 (home-page "https://github.com/sckott/httpcode")
23492 (synopsis "HTTP status code helper")
23493 (description "@code{httpcode} provides functionality for finding and
23494 explaining the meaning of @code{HTTP} status codes. Functions are included for
23495 searching for codes by full or partial number, by message, and to get
23496 appropriate dog and cat images for many status codes.")
23497 (license license:expat)))
23499 (define-public r-latex2exp
23501 (name "r-latex2exp")
23505 (uri (cran-uri "latex2exp" version))
23508 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
23509 (build-system r-build-system)
23511 `(("r-stringr" ,r-stringr)
23512 ("r-magrittr" ,r-magrittr)))
23513 (home-page "https://github.com/stefano-meschiari/latex2exp/")
23514 (synopsis "Use LaTeX expressions in plots")
23515 (description "@code{latex2exp} parses and converts LaTeX math formulas to
23516 R's plotmath expressions, used to enter mathematical formulas and symbols to be
23517 rendered as text, axis labels, etc. throughout R's plotting system.")
23518 (license license:expat)))
23520 (define-public r-oai
23526 (uri (cran-uri "oai" version))
23529 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
23530 (build-system r-build-system)
23532 `(("r-xml2" ,r-xml2)
23535 ("r-stringr" ,r-stringr)
23536 ("r-tibble" ,r-tibble)))
23537 (home-page "https://github.com/ropensci/oai/")
23538 (synopsis "General purpose OAI-PMH services client")
23539 (description "@code{oai} provides a general purpose client to work with
23540 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
23541 service. Functions are provided to work with the OAI-PMH verbs:
23542 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
23543 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
23544 (license license:expat)))
23546 (define-public r-argon2
23553 (uri (cran-uri "argon2" version))
23556 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
23557 (properties `((upstream-name . "argon2")))
23558 (build-system r-build-system)
23559 (home-page "https://github.com/wrathematics/argon2")
23560 (synopsis "Secure password hashing based on the argon2 algorithm")
23562 "This package provides utilities for secure password hashing via the
23563 argon2 algorithm.")
23564 (license license:bsd-2)))
23566 (define-public r-getpass
23573 (uri (cran-uri "getPass" version))
23576 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
23577 (properties `((upstream-name . "getPass")))
23578 (build-system r-build-system)
23580 `(("r-rstudioapi" ,r-rstudioapi)))
23581 (home-page "https://github.com/wrathematics/getPass")
23582 (synopsis "Masked user input")
23584 "This package provides a micro-package for reading \"passwords\", i.e.
23585 reading user input with masking, so that the input is not displayed as it is
23586 typed. Currently, RStudio, the command line (every OS), and any platform
23587 where tcltk is present are supported.")
23588 (license license:bsd-2)))
23590 (define-public r-remoter
23597 (uri (cran-uri "remoter" version))
23600 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
23601 (properties `((upstream-name . "remoter")))
23602 (build-system r-build-system)
23604 `(("r-argon2" ,r-argon2)
23605 ("r-getpass" ,r-getpass)
23606 ("r-pbdzmq" ,r-pbdzmq)
23608 (home-page "https://github.com/RBigData/remoter")
23609 (synopsis "Control a remote R session from a local one")
23611 "This package provides a set of utilities for client/server computing
23612 with R, controlling a remote R session (the server) from a local one (the
23614 (license license:bsd-2)))
23616 (define-public r-asd
23623 (uri (cran-uri "asd" version))
23626 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
23627 (properties `((upstream-name . "asd")))
23628 (build-system r-build-system)
23630 `(("r-mvtnorm" ,r-mvtnorm)))
23631 (home-page "https://cran.r-project.org/web/packages/asd")
23632 (synopsis "Simulations for Adaptive Seamless Designs")
23634 "This package provdes means to run simulations for adaptive seamless
23635 designs with and without early outcomes for treatment selection and
23636 subpopulation type designs.")
23637 (license license:gpl3)))
23639 (define-public r-nbconvertr
23641 (name "r-nbconvertr")
23646 (uri (cran-uri "nbconvertR" version))
23649 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
23650 (properties `((upstream-name . "nbconvertR")))
23651 (build-system r-build-system)
23653 `(("jupyter" ,python-nbconvert)
23654 ("pandoc" ,pandoc)))
23655 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
23656 (synopsis "Vignette engine wrapping Jupyter notebooks")
23658 "This package calls the Jupyter script @code{nbconvert} to create
23659 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
23660 containing rich text, code, and its output. Code cells can be edited and
23661 evaluated interactively.")
23662 (license license:gpl3)))
23664 (define-public r-bridgesampling
23666 (name "r-bridgesampling")
23671 (uri (cran-uri "bridgesampling" version))
23674 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
23676 `((upstream-name . "bridgesampling")))
23677 (build-system r-build-system)
23679 `(("r-brobdingnag" ,r-brobdingnag)
23681 ("r-matrix" ,r-matrix)
23682 ("r-mvtnorm" ,r-mvtnorm)
23683 ("r-scales" ,r-scales)
23684 ("r-stringr" ,r-stringr)))
23686 `(("r-knitr" ,r-knitr)))
23687 (home-page "https://github.com/quentingronau/bridgesampling")
23688 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
23690 "This package provides functions for estimating marginal likelihoods,
23691 Bayes factors, posterior model probabilities, and normalizing constants in
23692 general, via different versions of bridge sampling.")
23693 (license license:gpl2+)))
23695 (define-public r-tea
23702 (uri (cran-uri "tea" version))
23705 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
23707 `((upstream-name . "tea")))
23708 (build-system r-build-system)
23710 `(("r-matrix" ,r-matrix)))
23711 (home-page "https://cran.r-project.org/web/packages/tea/")
23712 (synopsis "Threshold estimation approaches")
23714 "This package provides different approaches for selecting the threshold
23715 in generalized Pareto distributions. Most of them are based on minimizing the
23716 AMSE-criterion or at least by reducing the bias of the assumed GPD-model.
23717 Others are heuristically motivated by searching for stable sample paths, i.e.
23718 a nearly constant region of the tail index estimator with respect to k, which
23719 is the number of data in the tail. The third class is motivated by graphical
23720 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
23721 is also implemented here.")
23722 (license license:gpl3)))
23724 (define-public r-awsmethods
23726 (name "r-awsmethods")
23731 (uri (cran-uri "awsMethods" version))
23734 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
23736 `((upstream-name . "awsMethods")))
23737 (build-system r-build-system)
23738 (home-page "http://www.wias-berlin.de/software/imaging/")
23739 (synopsis "Class and methods definitions")
23741 "This package defines the generic method @code{extract} and provides
23742 @code{openMP} support as needed in several packages like
23743 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
23744 (license license:gpl2+)))
23746 (define-public r-aws
23753 (uri (cran-uri "aws" version))
23756 "1fhm87iax6bkvd4vszvjbcqw3b2drs11rjxr7zf2w4sgc72svaz8"))))
23758 `((upstream-name . "aws")))
23759 (build-system r-build-system)
23761 `(("r-awsmethods" ,r-awsmethods)
23764 `(("gfortran" ,gfortran)))
23765 (home-page "https://cran.r-project.org/web/packages/aws/")
23766 (synopsis "Adaptive weights smoothing")
23768 "This package provides a collection of R-functions implementing adaptive
23769 smoothing procedures in 1D, 2D and 3D. This includes the
23770 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
23771 Confidence Intervals} (ICI), variational approaches, and a non-local means
23773 (license license:gpl2+)))
23775 (define-public r-sgloptim
23777 (name "r-sgloptim")
23782 (uri (cran-uri "sglOptim" version))
23785 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
23787 `((upstream-name . "sglOptim")))
23788 (build-system r-build-system)
23791 ("r-doparallel" ,r-doparallel)
23792 ("r-foreach" ,r-foreach)
23793 ("r-matrix" ,r-matrix)
23795 ("r-rcpparmadillo" ,r-rcpparmadillo)
23796 ("r-rcppprogress" ,r-rcppprogress)))
23798 `(("r-knitr" ,r-knitr)))
23799 (home-page "https://github.com/nielsrhansen/sglOptim")
23800 (synopsis "Generic sparse group Lasso solver")
23802 "This package provides a fast generic solver for sparse group lasso
23803 optimization problems. The loss (objective) function must be defined in a C++
23804 module. The optimization problem is solved using a coordinate gradient
23805 descent algorithm. Convergence of the algorithm is established and the
23806 algorithm is applicable to a broad class of loss functions. Use of parallel
23807 computing for cross validation and subsampling is supported through the
23808 @code{foreach} and @code{doParallel} packages.")
23809 (license license:gpl2+)))
23811 (define-public r-grouped
23818 (uri (cran-uri "grouped" version))
23821 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
23823 `((upstream-name . "grouped")))
23824 (build-system r-build-system)
23826 `(("r-mass" ,r-mass)))
23827 (home-page "https://cran.r-project.org/web/packages/grouped/")
23828 (synopsis "Regression analysis of grouped and coarse data")
23830 "This package provides regression models for grouped and coarse data,
23831 under the coarsened at random assumption.")
23832 (license license:gpl2+)))
23834 (define-public r-stam
23841 (uri (cran-uri "stam" version))
23844 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
23846 `((upstream-name . "stam")))
23847 (build-system r-build-system)
23851 (home-page "https://cran.r-project.org/web/packages/stam")
23852 (synopsis "Spatio-temporal analysis and modelling")
23854 "This package provides various methods to conduct Spatio-Temporal
23855 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
23856 Inferred Spatio-Temporal Modelling.")
23857 (license license:gpl2+)))
23859 (define-public r-dcv
23866 (uri (cran-uri "dcv" version))
23869 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
23871 `((upstream-name . "dcv")))
23872 (build-system r-build-system)
23874 `(("r-lmtest" ,r-lmtest)))
23875 (home-page "https://cran.r-project.org/web/packages/dcv/")
23876 (synopsis "Conventional cross-validation statistics for climate-growth model")
23878 "This package performs several conventional cross-validation statistical
23879 methods for climate-growth model in the climate reconstruction from tree
23880 rings, including Sign Test statistic, Reduction of Error statistic, Product
23881 Mean Test, Durbin-Watson statistic etc.")
23882 (license license:gpl2)))
23884 (define-public r-rcdd
23891 (uri (cran-uri "rcdd" version))
23894 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
23896 `((upstream-name . "rcdd")))
23897 (build-system r-build-system)
23900 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
23901 (synopsis "Computational geometry")
23903 "This package converts back and forth between two representations of a
23904 convex polytope: as solution of a set of linear equalities and inequalities
23905 and as convex hull of set of points and rays. Also does linear programming
23906 and redundant generator elimination. All functions can use exact
23907 infinite-precision rational arithmetic.")
23908 (license license:gpl2)))
23910 (define-public r-rxnat
23917 (uri (cran-uri "Rxnat" version))
23920 "00fl68pa0c2vy4xlny67pn41lzgm7b97wgg3dwm6z35izca62l11"))))
23922 `((upstream-name . "Rxnat")))
23923 (build-system r-build-system)
23925 `(("r-dplyr" ,r-dplyr)
23927 ("r-rcurl" ,r-rcurl)
23928 ("r-tibble" ,r-tibble)))
23930 `(("r-knitr" ,r-knitr)))
23931 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
23932 (synopsis "Queries and extracts images from neuroimaging datasets")
23934 "This package allows communication with the Extensible Neuroimaging
23935 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
23937 (license license:gpl2)))
23939 (define-public r-rserve
23946 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
23947 version ".tar.gz"))
23950 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
23951 (build-system r-build-system)
23954 (modify-phases %standard-phases
23955 (add-before 'install 'install-server-binary
23956 ;; Makevars tries to install to R's store directory.
23957 (lambda* (#:key outputs #:allow-other-keys)
23958 (let* ((out (assoc-ref outputs "out"))
23959 (bin (string-append out "/bin")))
23960 (substitute* "src/Makevars.in"
23961 (("\\$\\(R_HOME\\)") out))
23962 (mkdir-p bin)))))))
23964 `(("r-checkmate" ,r-checkmate)
23966 ("r-jsonlite" ,r-jsonlite)
23967 ("r-knitr" ,r-knitr)
23970 ("r-uuid" ,r-uuid)))
23972 `(("openssl" ,openssl)
23974 (home-page "https://github.com/s-u/Rserve")
23976 "Server providing access to R from many languages and systems")
23978 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
23979 binary requests to be sent to R. Every connection has a separate workspace
23980 and working directory. Client-side implementations are available for popular
23981 languages such as C/C++ and Java, allowing any application to use facilities
23982 of R without the need of linking to R code. Rserve supports remote
23983 connection, user authentication and file transfer. A simple R client is
23984 included in this package as well.")
23985 (license license:gpl2)))
23987 (define-public r-gamm4
23994 (uri (cran-uri "gamm4" version))
23997 "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap"))))
23998 (properties `((upstream-name . "gamm4")))
23999 (build-system r-build-system)
24001 `(("r-lme4" ,r-lme4)
24002 ("r-matrix" ,r-matrix)
24003 ("r-mgcv" ,r-mgcv)))
24004 (home-page "https://cran.r-project.org/web/packages/gamm4/")
24005 (synopsis "Generalized additive mixed models using mgcv and lme4")
24007 "Estimate generalized additive mixed models via a version of function
24008 @code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor
24010 (license license:gpl2+)))
24012 (define-public r-optimx
24015 (version "2020-4.2")
24019 (uri (cran-uri "optimx" version))
24022 "00bi2sr2hr7x6cfwlsn7hz2r56lcyv9naa8vmfcgr1r269fc50b3"))))
24023 (properties `((upstream-name . "optimx")))
24024 (build-system r-build-system)
24025 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
24026 (native-inputs `(("r-knitr" ,r-knitr)))
24027 (home-page "https://cran.r-project.org/web/packages/optimx/")
24028 (synopsis "Expanded replacement and extension of the optim function")
24030 "This package provides a replacement and extension of the @code{optim}
24031 function to call to several function minimization codes in R in a single
24032 statement. These methods handle smooth, possibly box constrained functions of
24033 several or many parameters. Note that the function @code{optimr} was prepared
24034 to simplify the incorporation of minimization codes going forward. This
24035 package also implements some utility codes and some extra solvers, including
24036 safeguarded Newton methods. Many methods previously separate are now included
24038 (license license:gpl2)))
24040 (define-public r-projpred
24042 (name "r-projpred")
24047 (uri (cran-uri "projpred" version))
24050 "0nx514mrfh3gv854pr71w5x3zgdnn0kinf5nh7z90q3h7ysry2mg"))))
24051 (properties `((upstream-name . "projpred")))
24052 (build-system r-build-system)
24054 `(("r-dplyr" ,r-dplyr)
24055 ("r-gamm4" ,r-gamm4)
24056 ("r-ggplot2" ,r-ggplot2)
24059 ("r-magrittr" ,r-magrittr)
24062 ("r-optimx" ,r-optimx)
24064 ("r-rcpparmadillo" ,r-rcpparmadillo)
24065 ("r-rngtools" ,r-rngtools)
24066 ("r-rstantools" ,r-rstantools)
24067 ("r-tidyverse" ,r-tidyverse)))
24068 (native-inputs `(("r-knitr" ,r-knitr)))
24069 (home-page "https://mc-stan.org/projpred/")
24070 (synopsis "Projection predictive feature selection")
24072 "This package performs projection predictive feature selection for
24073 generalized linear models and generalized linear and additive multilevel
24074 models. The package is compatible with the @code{rstanarm} and @code{brms}
24075 packages, but other reference models can also be used. See the package
24076 vignette for more information and examples.")
24077 (license license:gpl3)))
24079 (define-public r-brms
24086 (uri (cran-uri "brms" version))
24089 "0mzwihhgmn405l6zq11a180q4k3chggj9qj0j7q838b9vrszg59j"))))
24090 (properties `((upstream-name . "brms")))
24091 (build-system r-build-system)
24093 `(("r-abind" ,r-abind)
24094 ("r-backports" ,r-backports)
24095 ("r-bayesplot" ,r-bayesplot)
24096 ("r-bridgesampling" ,r-bridgesampling)
24098 ("r-future" ,r-future)
24099 ("r-ggplot2" ,r-ggplot2)
24102 ("r-matrix" ,r-matrix)
24103 ("r-matrixstats" ,r-matrixstats)
24105 ("r-nleqslv" ,r-nleqslv)
24107 ("r-projpred" ,r-projpred)
24109 ("r-rstan" ,r-rstan)
24110 ("r-rstantools" ,r-rstantools)
24111 ("r-shinystan" ,r-shinystan)))
24112 (native-inputs `(("r-knitr" ,r-knitr)))
24114 "https://github.com/paul-buerkner/brms")
24116 "Bayesian Regression Models using 'Stan'")
24118 "Fit Bayesian generalized (non-)linear multivariate multilevel models
24119 using 'Stan' for full Bayesian inference. A wide range of distributions and
24120 link functions are supported, allowing users to fit -- among others -- linear,
24121 robust linear, count data, survival, response times, ordinal, zero-inflated,
24122 hurdle, and even self-defined mixture models all in a multilevel context.
24123 Further modeling options include non-linear and smooth terms, auto-correlation
24124 structures, censored data, meta-analytic standard errors, and quite a few
24125 more. In addition, all parameters of the response distribution can be
24126 predicted in order to perform distributional regression. Prior specifications
24127 are flexible and explicitly encourage users to apply prior distributions that
24128 actually reflect their beliefs. Model fit can easily be assessed and compared
24129 with posterior predictive checks and leave-one-out cross-validation.")
24130 (license license:gpl2)))
24132 (define-public r-mstate
24139 (uri (cran-uri "mstate" version))
24142 "11i3p7fph8nbnfis1m7rdrq32qryaajv2wrkxk1x6k17zkh4rq6i"))))
24143 (properties `((upstream-name . "mstate")))
24144 (build-system r-build-system)
24146 `(("r-data-table" ,r-data-table)
24147 ("r-lattice" ,r-lattice)
24148 ("r-magrittr" ,r-magrittr)
24149 ("r-rcolorbrewer" ,r-rcolorbrewer)
24150 ("r-rlang" ,r-rlang)
24151 ("r-survival" ,r-survival)
24152 ("r-viridis" ,r-viridis)))
24154 `(("r-knitr" ,r-knitr)))
24156 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
24158 "Data Preparation, Estimation and Prediction in Multi-State Models")
24160 "Contains functions for data preparation, descriptives, hazard estimation
24161 and prediction with Aalen-Johansen or simulation in competing risks and
24162 multi-state models.")
24163 (license license:gpl2+)))
24165 (define-public r-scatterpie
24167 (name "r-scatterpie")
24172 (uri (cran-uri "scatterpie" version))
24175 "0h48l0699lpfagv09f53yismir84945m56qwzk52lc7wxyvkfcp1"))))
24176 (properties `((upstream-name . "scatterpie")))
24177 (build-system r-build-system)
24179 `(("r-ggforce" ,r-ggforce)
24180 ("r-ggplot2" ,r-ggplot2)
24181 ("r-rlang" ,r-rlang)
24182 ("r-rvcheck" ,r-rvcheck)
24183 ("r-tidyr" ,r-tidyr)))
24185 `(("r-knitr" ,r-knitr)))
24186 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
24187 (synopsis "Scatter pie plot")
24189 "This package creates scatterpie plots, especially useful for plotting
24191 (license license:artistic2.0)))
24193 (define-public r-scrypt
24200 (uri (cran-uri "scrypt" version))
24203 "14iblgbp9v2by8fjbrpsd59iknp5babcz7j3yv1yxxzcwyb6wrrm"))))
24204 (properties `((upstream-name . "scrypt")))
24205 (build-system r-build-system)
24207 `(("r-rcpp" ,r-rcpp)))
24208 (home-page "https://github.com/rstudio/rscrypt")
24209 (synopsis "Key derivation functions for R based on Scrypt")
24211 "This package provides functions for working with the scrypt key
24212 derivation functions. Scrypt is a password-based key derivation function
24213 created by Colin Percival. The algorithm was specifically designed to make it
24214 costly to perform large-scale custom hardware attacks by requiring large
24215 amounts of memory.")
24216 (license license:bsd-2)))
24218 (define-public r-boruta
24225 (uri (cran-uri "Boruta" version))
24228 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
24229 (properties `((upstream-name . "Boruta")))
24230 (build-system r-build-system)
24231 (propagated-inputs `(("r-ranger" ,r-ranger)))
24232 (home-page "https://gitlab.com/mbq/Boruta/")
24233 (synopsis "Wrapper algorithm for all relevant feature selection")
24235 "This package provides an all relevant feature selection wrapper
24236 algorithm. It finds relevant features by comparing original attributes'
24237 importance with importance achievable at random, estimated using their
24238 permuted copies (shadows).")
24239 (license license:gpl2+)))
24241 (define-public r-directlabels
24243 (name "r-directlabels")
24244 (version "2021.1.13")
24248 (uri (cran-uri "directlabels" version))
24251 "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w"))))
24252 (build-system r-build-system)
24254 `(("r-quadprog" ,r-quadprog)))
24256 `(("r-knitr" ,r-knitr)))
24257 (home-page "http://directlabels.r-forge.r-project.org/")
24258 (synopsis "Direct labels for multicolor plots")
24260 "This package provides an extensible framework for automatically placing
24261 direct labels onto multicolor plots. Label positions are described using
24262 positioning methods that can be re-used across several different plots. There
24263 are heuristics for examining @code{trellis} and @code{ggplot} objects and
24264 inferring an appropriate positioning method.")
24265 (license license:gpl3)))
24267 (define-public r-lsd
24274 (uri (cran-uri "LSD" version))
24276 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
24277 (properties `((upstream-name . "LSD")))
24278 (build-system r-build-system)
24279 (home-page "https://cran.r-project.org/web/packages/LSD/")
24280 (synopsis "Lots of superior depictions tool creates colorful plots")
24282 "This package creates lots of colorful plots in a multitude of variations.
24283 Try a demo of the LSD by running @code{demotour()}.")
24285 (license (list license:gpl2 license:gpl3))))
24287 (define-public r-phylogram
24289 (name "r-phylogram")
24294 (uri (cran-uri "phylogram" version))
24296 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
24297 (properties `((upstream-name . "phylogram")))
24298 (build-system r-build-system)
24299 (propagated-inputs `(("r-ape" ,r-ape)))
24300 (home-page "https://github.com/ropensci/phylogram/")
24301 (synopsis "Dendrograms for evolutionary analysis")
24303 "The @code{r-phylogram} package is a tool for for developing phylogenetic
24304 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
24305 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
24306 as well as several tools for command-line tree manipulation and import/export
24307 via Newick parenthetic text. This improves accessibility to the comprehensive
24308 range of object-specific analytical and tree-visualization functions found
24309 across a wide array of bioinformatic R packages.")
24310 (license license:gpl3)))
24312 (define-public r-kmer
24319 (uri (cran-uri "kmer" version))
24321 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
24322 (properties `((upstream-name . "kmer")))
24323 (build-system r-build-system)
24325 `(("r-openssl" ,r-openssl)
24326 ("r-phylogram" ,r-phylogram)
24327 ("r-rcpp" ,r-rcpp)))
24328 (home-page "https://github.com/shaunpwilkinson/kmer/")
24329 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
24331 "@code{r-kmer} is an R package for rapidly computing distance matrices
24332 and clustering large sequence datasets using fast alignment-free k-mer
24333 counting and recursive k-means partitioning.")
24334 (license license:gpl3)))
24336 (define-public r-hardhat
24343 (uri (cran-uri "hardhat" version))
24346 "1b7f9i9fy39j9n03g40vd6nzgq9fgq914xg3svf84najlknvjzly"))))
24347 (properties `((upstream-name . "hardhat")))
24348 (build-system r-build-system)
24350 `(("r-glue" ,r-glue)
24351 ("r-rlang" ,r-rlang)
24352 ("r-tibble" ,r-tibble)
24353 ("r-vctrs" ,r-vctrs)))
24355 `(("r-knitr" ,r-knitr)))
24356 (home-page "https://github.com/tidymodels/hardhat")
24357 (synopsis "Construct modeling packages")
24359 "Building modeling packages is hard. A large amount of effort generally
24360 goes into providing an implementation for a new method that is efficient,
24361 fast, and correct, but often less emphasis is put on the user interface. A
24362 good interface requires specialized knowledge about S3 methods and formulas,
24363 which the average package developer might not have. The goal of
24364 @code{hardhat} is to reduce the burden around building new modeling packages
24365 by providing functionality for preprocessing, predicting, and validating
24367 (license license:expat)))
24369 (define-public r-lightgbm
24371 (name "r-lightgbm")
24376 (uri (cran-uri "lightgbm" version))
24379 "1pwsh6j9ksahh58b15j5ij56bsc6syy3z4k4a5zhy5n7829rz555"))))
24380 (properties `((upstream-name . "lightgbm")))
24381 (build-system r-build-system)
24383 `(("r-data-table" ,r-data-table)
24384 ("r-jsonlite" ,r-jsonlite)
24385 ("r-matrix" ,r-matrix)
24387 (home-page "https://github.com/Microsoft/LightGBM")
24388 (synopsis "Light gradient boosting machine")
24390 "Tree based algorithms can be improved by introducing boosting
24391 frameworks. LightGBM is one such framework, based on Ke, Guolin et
24392 al. (2017). This package offers an R interface to work with it. It is
24393 designed to be distributed and efficient with the following goals:
24396 @item Faster training speed and higher efficiency;
24397 @item lower memory usage;
24398 @item better accuracy;
24399 @item parallel learning supported; and
24400 @item capable of handling large-scale data.
24403 (license license:expat)))
24405 (define-public r-shapforxgboost
24407 (name "r-shapforxgboost")
24412 (uri (cran-uri "SHAPforxgboost" version))
24415 "0jgyss9bawl7sf4dwa75sn7ld3mvrrr0z2074lbkq3f5qb9gwsly"))))
24417 `((upstream-name . "SHAPforxgboost")))
24418 (build-system r-build-system)
24420 `(("r-bbmisc" ,r-bbmisc)
24421 ("r-data-table" ,r-data-table)
24422 ("r-ggextra" ,r-ggextra)
24423 ("r-ggforce" ,r-ggforce)
24424 ("r-ggplot2" ,r-ggplot2)
24425 ("r-ggpubr" ,r-ggpubr)
24426 ("r-lightgbm" ,r-lightgbm)
24427 ("r-rcolorbrewer" ,r-rcolorbrewer)
24428 ("r-xgboost" ,r-xgboost)))
24429 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
24430 (synopsis "SHAP Plots for XGBoost")
24432 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
24433 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
24434 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
24435 and force plot. It relies on the @code{XGBoost} package to produce SHAP
24437 (license license:expat)))
24439 (define-public r-rismed
24446 (uri (cran-uri "RISmed" version))
24449 "0nwixhngi4r2f73362salivsmsf7l52bm13jqvhdq8mfiigm80vd"))))
24450 (properties `((upstream-name . "RISmed")))
24451 (build-system r-build-system)
24452 (home-page "https://cran.r-project.org/web/packages/RISmed")
24453 (synopsis "Download content from NCBI databases")
24455 "This package provides a set of tools to extract bibliographic
24456 content from the National Center for Biotechnology Information (NCBI)
24457 databases, including PubMed. The name RISmed is a portmanteau of
24458 RIS (for Research Information Systems, a common tag format for
24459 bibliographic data) and PubMed.")
24460 (license license:gpl2+)))
24462 (define-public r-semver
24469 (uri (cran-uri "semver" version))
24472 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
24473 (properties `((upstream-name . "semver")))
24474 (build-system r-build-system)
24476 `(("r-assertthat" ,r-assertthat)
24477 ("r-rcpp" ,r-rcpp)))
24478 (native-inputs `(("r-knitr" ,r-knitr)))
24479 (home-page "https://github.com/johndharrison/semver")
24480 (synopsis "Parser for Semantic Versioning 2.0.0")
24482 "This package provides tools and functions for parsing, rendering and
24483 operating on semantic version strings. Semantic versioning is a simple set of
24484 rules and requirements that dictate how version numbers are assigned and
24485 incremented as outlined at @url{http://semver.org}.")
24486 (license license:expat)))
24488 (define-public r-binman
24495 (uri (cran-uri "binman" version))
24498 "00l7m98h41r67gf0qxqis3vx63j7wylnk9vlgcyk41szkrz8ikkc"))))
24499 (properties `((upstream-name . "binman")))
24500 (build-system r-build-system)
24502 `(("r-assertthat" ,r-assertthat)
24504 ("r-jsonlite" ,r-jsonlite)
24505 ("r-rappdirs" ,r-rappdirs)
24506 ("r-semver" ,r-semver)
24508 ("r-yaml" ,r-yaml)))
24509 (native-inputs `(("r-knitr" ,r-knitr)))
24510 (home-page "https://github.com/ropensci/binman")
24511 (synopsis "Binary download manager")
24513 "This package provides tools and functions for managing the download of
24514 binary files. Binary repositories are defined in the YAML format. Defining
24515 new pre-download, download and post-download templates allow additional
24516 repositories to be added.")
24517 (license license:expat)))
24519 (define-public r-wdman
24526 (uri (cran-uri "wdman" version))
24529 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
24530 (properties `((upstream-name . "wdman")))
24531 (build-system r-build-system)
24533 `(("r-assertthat" ,r-assertthat)
24534 ("r-binman" ,r-binman)
24535 ("r-processx" ,r-processx)
24536 ("r-semver" ,r-semver)
24537 ("r-yaml" ,r-yaml)))
24538 (native-inputs `(("r-knitr" ,r-knitr)))
24539 (home-page "https://docs.ropensci.org/wdman/")
24540 (synopsis "Webdriver/Selenium binary manager")
24542 "There are a number of binary files associated with the
24543 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
24544 @url{https://sites.google.com/a/chromium.org/chromedriver/},
24545 @url{https://github.com/mozilla/geckodriver},
24546 @url{http://phantomjs.org/download.html}, and
24547 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
24548 more information). This package provides functions to download these binaries
24549 and to manage processes involving them.")
24550 (license license:expat)))
24552 (define-public r-rselenium
24554 (name "r-rselenium")
24559 (uri (cran-uri "RSelenium" version))
24562 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
24563 (properties `((upstream-name . "RSelenium")))
24564 (build-system r-build-system)
24566 `(("r-binman" ,r-binman)
24567 ("r-catools" ,r-catools)
24569 ("r-openssl" ,r-openssl)
24570 ("r-wdman" ,r-wdman)
24572 (native-inputs `(("r-knitr" ,r-knitr)))
24573 (home-page "https://docs.ropensci.org/RSelenium/")
24574 (synopsis "R bindings for Selenium WebDriver")
24576 "This package provides a set of R bindings for the Selenium 2.0
24577 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
24578 information) using the @code{JsonWireProtocol} (see
24579 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
24580 information). Selenium 2.0 WebDriver allows driving a web browser natively as
24581 a user would either locally or on a remote machine using the Selenium server
24582 it marks a leap forward in terms of web browser automation. Selenium
24583 automates web browsers (commonly referred to as browsers). Using RSelenium
24584 you can automate browsers locally or remotely.")
24585 (license license:agpl3+)))
24587 (define-public r-conquer
24594 (uri (cran-uri "conquer" version))
24597 "1zvlsrbmrij011mcdi3qngs1al2lhrdiyknxnk0w1zhzrra62bsl"))))
24598 (properties `((upstream-name . "conquer")))
24599 (build-system r-build-system)
24601 `(("r-matrix" ,r-matrix)
24602 ("r-matrixstats" ,r-matrixstats)
24604 ("r-rcpparmadillo" ,r-rcpparmadillo)))
24605 (home-page "https://github.com/XiaoouPan/conquer")
24606 (synopsis "Convolution-type smoothed quantile regression")
24608 "This package provides fast and accurate convolution-type smoothed
24609 quantile regression, implemented using Barzilai-Borwein gradient descent with
24610 a Huber regression warm start. Confidence intervals for regression
24611 coefficients are constructed using multiplier bootstrap.")
24612 (license license:gpl3)))
24614 (define-public r-fastshap
24616 (name "r-fastshap")
24621 (uri (cran-uri "fastshap" version))
24624 "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg"))))
24625 (properties `((upstream-name . "fastshap")))
24626 (build-system r-build-system)
24628 `(("r-abind" ,r-abind)
24629 ("r-ggplot2" ,r-ggplot2)
24630 ("r-gridextra" ,r-gridextra)
24631 ("r-matrixstats" ,r-matrixstats)
24634 ("r-rcpparmadillo" ,r-rcpparmadillo)
24635 ("r-tibble" ,r-tibble)))
24636 (home-page "https://github.com/bgreenwell/fastshap")
24637 (synopsis "Fast approximate Shapley values")
24639 "This package computes fast (relative to other implementations)
24640 approximate Shapley values for any supervised learning model. Shapley values
24641 help to explain the predictions from any black box model using ideas from game
24642 theory; see @url{Strumbel and Kononenko (2014),
24643 doi.org/10.1007/s10115-013-0679-x} for details.")
24644 (license license:gpl2+)))
24646 (define-public r-metrics
24653 (uri (cran-uri "Metrics" version))
24656 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
24657 (properties `((upstream-name . "Metrics")))
24658 (build-system r-build-system)
24659 (home-page "https://github.com/mfrasco/Metrics")
24660 (synopsis "Evaluation metrics for machine learning")
24662 "This package provides an implementation of evaluation metrics in R that
24663 are commonly used in supervised machine learning. It implements metrics for
24664 regression, time series, binary classification, classification, and
24665 information retrieval problems. It has zero dependencies and a consistent,
24666 simple interface for all functions.")
24667 (license license:bsd-3)))
24669 (define-public r-iml
24676 (uri (cran-uri "iml" version))
24679 "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7"))))
24680 (properties `((upstream-name . "iml")))
24681 (build-system r-build-system)
24683 `(("r-checkmate" ,r-checkmate)
24684 ("r-data-table" ,r-data-table)
24685 ("r-formula" ,r-formula)
24686 ("r-future" ,r-future)
24687 ("r-future-apply" ,r-future-apply)
24688 ("r-ggplot2" ,r-ggplot2)
24689 ("r-gridextra" ,r-gridextra)
24690 ("r-metrics" ,r-metrics)
24691 ("r-prediction" ,r-prediction)
24693 (native-inputs `(("r-knitr" ,r-knitr)))
24694 (home-page "https://github.com/christophM/iml")
24695 (synopsis "Interpretable machine learning")
24697 "This package provides interpretability methods to analyze the behavior
24698 and predictions of any machine learning model. Implemented methods are:
24701 @item Feature importance described by Fisher et al. (2018),
24702 @item accumulated local effects plots described by Apley (2018),
24703 @item partial dependence plots described by Friedman (2001),
24704 @item individual conditional expectation ('ice') plots described by Goldstein
24705 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
24706 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
24707 @item the Shapley Value described by Strumbelj et. al (2014)
24708 @url{https://doi.org/10.1007/s10115-013-0679-x},
24709 @item feature interactions described by Friedman et. al
24710 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
24713 (license license:expat)))
24715 (define-public r-goftest
24722 (uri (cran-uri "goftest" version))
24725 "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4"))))
24726 (properties `((upstream-name . "goftest")))
24727 (build-system r-build-system)
24728 (home-page "https://github.com/baddstats/goftest")
24729 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
24731 "This package provides Cramer-Von Mises and Anderson-Darling tests of
24732 goodness-of-fit for continuous univariate distributions, using efficient
24734 (license license:gpl2+)))
24736 (define-public r-tensor
24743 (uri (cran-uri "tensor" version))
24746 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
24747 (properties `((upstream-name . "tensor")))
24748 (build-system r-build-system)
24749 (home-page "https://cran.r-project.org/web/packages/tensor/")
24750 (synopsis "Tensor product of arrays")
24752 "The tensor product of two arrays is notionally an outer product of the
24753 arrays collapsed in specific extents by summing along the appropriate
24754 diagonals. This package allows you to compute the tensor product of arrays.")
24755 (license license:gpl2+)))
24757 (define-public r-spatstat-utils
24759 (name "r-spatstat-utils")
24764 (uri (cran-uri "spatstat.utils" version))
24767 "1li0vksxpkvgyx3j2wi40kj5687vwakkfdix6icm6g01a0lb2m5d"))))
24769 `((upstream-name . "spatstat.utils")))
24770 (build-system r-build-system)
24771 (home-page "http://www.spatstat.org")
24772 (synopsis "Utility functions for spatstat")
24774 "This package contains utility functions for the @code{spatstat} package
24775 which may also be useful for other purposes.")
24776 (license license:gpl2+)))
24778 (define-public r-spatstat-data
24780 (name "r-spatstat-data")
24785 (uri (cran-uri "spatstat.data" version))
24788 "1z1jb1yzb7qhfg55dhzcrdvn5x8hpg9xif0hpnapddbmhxd1hbb7"))))
24789 (properties `((upstream-name . "spatstat.data")))
24790 (build-system r-build-system)
24792 `(("r-matrix" ,r-matrix)
24793 ("r-spatstat-utils" ,r-spatstat-utils)))
24794 (home-page "http://www.spatstat.org")
24795 (synopsis "Datasets for spatstat")
24797 "This package contains all the datasets for the @code{spatstat}
24799 (license license:gpl2+)))
24801 (define-public r-spatstat
24803 (name "r-spatstat")
24808 (uri (cran-uri "spatstat" version))
24811 "06jmxfs9kz9qqi3ichfgn8dglwb87kq2nl578p83za5psv8cfgya"))))
24812 (properties `((upstream-name . "spatstat")))
24813 (build-system r-build-system)
24815 `(("r-abind" ,r-abind)
24816 ("r-deldir" ,r-deldir)
24817 ("r-goftest" ,r-goftest)
24818 ("r-matrix" ,r-matrix)
24821 ("r-polyclip" ,r-polyclip)
24822 ("r-rpart" ,r-rpart)
24823 ("r-spatstat-data" ,r-spatstat-data)
24824 ("r-spatstat-utils" ,r-spatstat-utils)
24825 ("r-tensor" ,r-tensor)))
24826 (home-page "http://www.spatstat.org")
24827 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
24829 "This package provides a comprehensive toolbox for analysing Spatial
24830 Point Patterns. It is focused mainly on two-dimensional point patterns,
24831 including multitype/marked points, in any spatial region. It also supports
24832 three-dimensional point patterns, space-time point patterns in any number of
24833 dimensions, point patterns on a linear network, and patterns of other
24834 geometrical objects. It supports spatial covariate data such as pixel images
24835 and contains over 2000 functions for plotting spatial data, exploratory data
24836 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
24837 formal inference.")
24838 (license license:gpl2+)))
24840 (define-public r-gaston
24847 (uri (cran-uri "gaston" version))
24850 "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i"))))
24851 (properties `((upstream-name . "gaston")))
24852 (build-system r-build-system)
24853 (inputs `(("zlib" ,zlib)))
24855 `(("r-rcpp" ,r-rcpp)
24856 ("r-rcppeigen" ,r-rcppeigen)
24857 ("r-rcppparallel" ,r-rcppparallel)))
24858 (native-inputs `(("r-knitr" ,r-knitr)))
24859 (home-page "https://cran.r-project.org/web/packages/gaston/")
24860 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
24862 "This is a package for the manipulation of genetic data (SNPs).
24863 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
24864 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
24865 for linear mixed models (AIREML).")
24866 (license license:gpl3)))
24868 (define-public r-cpp11
24875 (uri (cran-uri "cpp11" version))
24878 "118i8s7978vl9xyhnb47wcbd6rcc6b958mq2w8s3rdsd4pxv62gz"))))
24879 (properties `((upstream-name . "cpp11")))
24880 (build-system r-build-system)
24881 (native-inputs `(("r-knitr" ,r-knitr)))
24882 (home-page "https://github.com/r-lib/cpp11")
24883 (synopsis "C++11 Interface for R's C Interface")
24885 "This package provides a header only, C++11 interface to R's C interface.
24886 Compared to other approaches @code{cpp11} strives to be safe against long
24887 jumps from the C API as well as C++ exceptions, conform to normal R function
24888 semantics and supports interaction with @code{ALTREP} vectors.")
24889 (license license:expat)))
24891 (define-public r-rcppziggurat
24893 (name "r-rcppziggurat")
24898 (uri (cran-uri "RcppZiggurat" version))
24901 "0wgd1v2p7zajnbrjf3hfi56p3pk3ld6iwkanbb04bjbnlif2ay4w"))))
24902 (properties `((upstream-name . "RcppZiggurat")))
24903 (build-system r-build-system)
24905 `(("r-rcpp" ,r-rcpp)
24906 ("r-rcppgsl" ,r-rcppgsl)))
24907 (native-inputs `(("r-knitr" ,r-knitr)))
24908 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
24909 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
24911 "The Ziggurat generator for normally distributed random numbers,
24912 originally proposed by Marsaglia and Tsang (2000,
24913 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
24914 times starting with Leong et al (2005,
24915 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
24916 aggregation for comparing different implementations in order to provide a
24917 'faster but good enough' alternative for use with R and C++ code.")
24918 (license license:gpl2+)))
24920 (define-public r-rfast
24927 (uri (cran-uri "Rfast" version))
24930 "1cq3mcg49hsvqhwn6f4dgsx7f8ma4qnwr5n6s7m22qy57rg31958"))))
24931 (properties `((upstream-name . "Rfast")))
24932 (build-system r-build-system)
24934 `(("r-rcpp" ,r-rcpp)
24935 ("r-rcpparmadillo" ,r-rcpparmadillo)
24936 ("r-rcppziggurat" ,r-rcppziggurat)))
24937 (home-page "https://github.com/RfastOfficial/Rfast")
24938 (synopsis "Collection of efficient and fast R functions")
24940 "This package provides a collection of fast (utility) functions for data
24941 analysis. Column- and row- wise means, medians, variances, minimums,
24942 maximums, many t, F and G-square tests, many regressions (normal, logistic,
24943 Poisson), are some of the many fast functions.")
24944 (license license:gpl2+)))
24946 (define-public r-clusterr
24948 (name "r-clusterr")
24953 (uri (cran-uri "ClusterR" version))
24956 "1ky172bk15a78hky77vl60j7c81nq2495sxjrv53is25nkac7sjm"))))
24957 (properties `((upstream-name . "ClusterR")))
24958 (build-system r-build-system)
24960 `(("r-ggplot2" ,r-ggplot2)
24962 ("r-gtools" ,r-gtools)
24964 ("r-rcpparmadillo" ,r-rcpparmadillo)))
24965 (native-inputs `(("r-knitr" ,r-knitr)))
24966 (home-page "https://github.com/mlampros/ClusterR")
24967 (synopsis "Clustering")
24969 "This package provides Gaussian mixture models, k-means,
24970 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
24971 option to plot, validate, predict (new data) and estimate the optimal number
24972 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
24973 the computationally intensive parts of the functions. For more information,
24977 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
24978 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
24979 @url{https://doi.org/10.18637/jss.v001.i04};
24980 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
24981 Library, @url{https://doi.org/10.1145/1772690.1772862};
24982 @item \"Armadillo: a template-based C++ library
24983 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
24984 Software, @url{https://doi.org/10.21105/joss.00026};
24985 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
24986 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
24987 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
24990 (license license:gpl3)))
24992 (define-public r-spectrum
24994 (name "r-spectrum")
24999 (uri (cran-uri "Spectrum" version))
25002 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
25003 (properties `((upstream-name . "Spectrum")))
25004 (build-system r-build-system)
25006 `(("r-clusterr" ,r-clusterr)
25007 ("r-diptest" ,r-diptest)
25008 ("r-ggplot2" ,r-ggplot2)
25009 ("r-rfast" ,r-rfast)))
25010 (native-inputs `(("r-knitr" ,r-knitr)))
25011 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
25012 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
25014 "This package provides a self-tuning spectral clustering method for
25015 single or multi-view data. Spectrum uses a new type of adaptive density aware
25016 kernel that strengthens connections in the graph based on common nearest
25017 neighbours. It uses a tensor product graph data integration and diffusion
25018 procedure to integrate different data sources and reduce noise. Spectrum uses
25019 either the eigengap or multimodality gap heuristics to determine the number of
25020 clusters. The method is sufficiently flexible so that a wide range of
25021 Gaussian and non-Gaussian structures can be clustered with automatic selection
25023 (license license:agpl3+)))
25025 (define-public r-nabor
25032 (uri (cran-uri "nabor" version))
25035 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
25036 (properties `((upstream-name . "nabor")))
25037 (build-system r-build-system)
25041 ("r-rcppeigen" ,r-rcppeigen)))
25042 (home-page "https://cran.r-project.org/web/packages/nabor/")
25043 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
25045 "This package provides an R wrapper for libnabo, an exact or approximate
25046 k nearest neighbour library which is optimised for low dimensional
25047 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
25048 designed as a drop-in replacement for the RANN function @code{nn2}. In
25049 addition, objects which include the k-d tree search structure can be returned
25050 to speed up repeated queries of the same set of target points.")
25051 (license license:bsd-3)))
25053 (define-public r-muhaz
25056 (version "1.2.6.1")
25060 (uri (cran-uri "muhaz" version))
25063 "08qh43zx6h3yby44q2vxphfvmfdmqxpgyp0734yn341sy9n8pkkk"))))
25064 (properties `((upstream-name . "muhaz")))
25065 (build-system r-build-system)
25067 `(("r-survival" ,r-survival)))
25069 `(("gfortran" ,gfortran)))
25070 (home-page "https://cran.r-project.org/web/packages/muhaz/")
25071 (synopsis "Hazard function estimation in survival analysis")
25073 "This package produces a smooth estimate of the hazard function for
25075 ;; Any version of the GPL.
25076 (license license:gpl3+)))
25078 (define-public r-flexsurv
25080 (name "r-flexsurv")
25085 (uri (cran-uri "flexsurv" version))
25088 "0x7p1rv51pplfyyzcg63ssb8z56mig7y0363hkr0219w3cvyq9nr"))))
25089 (properties `((upstream-name . "flexsurv")))
25090 (build-system r-build-system)
25092 `(("r-desolve" ,r-desolve)
25093 ("r-mstate" ,r-mstate)
25094 ("r-muhaz" ,r-muhaz)
25095 ("r-mvtnorm" ,r-mvtnorm)
25096 ("r-quadprog" ,r-quadprog)
25098 ("r-survival" ,r-survival)
25099 ("r-tibble" ,r-tibble)
25100 ("r-tidyr" ,r-tidyr)))
25102 `(("r-knitr" ,r-knitr)))
25103 (home-page "https://github.com/chjackson/flexsurv-dev")
25104 (synopsis "Flexible parametric survival and multi-state models")
25106 "This package provides flexible parametric models for time-to-event data,
25107 including the Royston-Parmar spline model, generalized gamma and generalized F
25108 distributions. Any user-defined parametric distribution can be fitted, given
25109 at least an R function defining the probability density or hazard. There are
25110 also tools for fitting and predicting from fully parametric multi-state
25112 (license license:gpl2+)))
25114 (define-public r-transphylo
25116 (name "r-transphylo")
25121 (uri (cran-uri "TransPhylo" version))
25124 "1506c97y8dnhd0c38rgvmg70q0l3xmmn07mjglhnw7hi5n5y9mv9"))))
25125 (properties `((upstream-name . "TransPhylo")))
25126 (build-system r-build-system)
25129 ("r-rcpp" ,r-rcpp)))
25131 `(("r-knitr" ,r-knitr)))
25132 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
25133 (synopsis "Inference of transmission tree from a dated phylogeny")
25135 "This is a package to infer transmission trees from a dated phylogeny.
25136 It includes methods to simulate and analyze outbreaks. The methodology is
25137 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
25138 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
25139 (license license:gpl2+)))
25141 (define-public r-km-ci
25148 (uri (cran-uri "km.ci" version))
25151 "1l6kw8jppaa1802yc5pbfwwgac56nhwc9p076ivylhms4w7cdf8v"))))
25152 (properties `((upstream-name . "km.ci")))
25153 (build-system r-build-system)
25155 `(("r-survival" ,r-survival)))
25156 (home-page "https://cran.r-project.org/web/packages/km.ci/")
25157 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
25159 "This package computes various @dfn{confidence intervals} (CI) for the
25160 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
25161 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
25162 Nair and Hall and Wellner.")
25163 (license license:gpl2+)))
25165 (define-public r-kmsurv
25172 (uri (cran-uri "KMsurv" version))
25175 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
25176 (properties `((upstream-name . "KMsurv")))
25177 (build-system r-build-system)
25178 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
25179 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
25181 "This package provides data sets and functions for Klein and Moeschberger
25182 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
25184 (license license:gpl3+)))
25186 (define-public r-survmisc
25188 (name "r-survmisc")
25193 (uri (cran-uri "survMisc" version))
25196 "00nvvl8gz4477ab24rd0xvfksm8msv8h021b9ld5c9cizc41n2bm"))))
25197 (properties `((upstream-name . "survMisc")))
25198 (build-system r-build-system)
25200 `(("r-data-table" ,r-data-table)
25201 ("r-ggplot2" ,r-ggplot2)
25202 ("r-gridextra" ,r-gridextra)
25203 ("r-km-ci" ,r-km-ci)
25204 ("r-kmsurv" ,r-kmsurv)
25205 ("r-knitr" ,r-knitr)
25206 ("r-survival" ,r-survival)
25207 ("r-xtable" ,r-xtable)
25210 `(("r-knitr" ,r-knitr)))
25211 (home-page "https://cran.r-project.org/web/packages/survMisc/")
25212 (synopsis "Miscellaneous functions for survival data")
25214 "This package provides a collection of functions to help in the analysis
25215 of right-censored survival data. These extend the methods available in
25216 the @code{survival} package.")
25217 (license license:gpl2)))
25219 (define-public r-exactranktests
25221 (name "r-exactranktests")
25226 (uri (cran-uri "exactRankTests" version))
25229 "1154dkcid3njhamdp87qs9bnx7l8bdqkcjsds9q9f2xmizs9x8gw"))))
25231 `((upstream-name . "exactRankTests")))
25232 (build-system r-build-system)
25233 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
25234 (synopsis "Exact distributions for rank and permutation tests")
25236 "This package computes exact conditional p-values and quantiles using an
25237 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
25238 (license license:gpl2+)))
25240 (define-public r-maxstat
25247 (uri (cran-uri "maxstat" version))
25250 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
25251 (properties `((upstream-name . "maxstat")))
25252 (build-system r-build-system)
25254 `(("r-exactranktests" ,r-exactranktests)
25255 ("r-mvtnorm" ,r-mvtnorm)))
25256 (home-page "https://cran.r-project.org/web/packages/maxstat/")
25257 (synopsis "Maximally selected rank statistics")
25259 "This package provides maximally selected rank statistics with several
25260 p-value approximations.")
25261 (license license:gpl2+)))
25263 (define-public r-survminer
25265 (name "r-survminer")
25270 (uri (cran-uri "survminer" version))
25273 "1niysd89mxb2a6ncvzm1s6xgfvq3psba65af0whh2p56r2hwrwff"))))
25274 (properties `((upstream-name . "survminer")))
25275 (build-system r-build-system)
25277 `(("r-broom" ,r-broom)
25278 ("r-dplyr" ,r-dplyr)
25279 ("r-ggplot2" ,r-ggplot2)
25280 ("r-ggpubr" ,r-ggpubr)
25281 ("r-gridextra" ,r-gridextra)
25282 ("r-magrittr" ,r-magrittr)
25283 ("r-maxstat" ,r-maxstat)
25284 ("r-purrr" ,r-purrr)
25285 ("r-rlang" ,r-rlang)
25286 ("r-scales" ,r-scales)
25287 ("r-survival" ,r-survival)
25288 ("r-survmisc" ,r-survmisc)
25289 ("r-tibble" ,r-tibble)
25290 ("r-tidyr" ,r-tidyr)))
25292 `(("r-knitr" ,r-knitr)))
25293 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
25294 (synopsis "Drawing survival curves using ggplot2")
25296 "This package contains the function @code{ggsurvplot()} for easily
25297 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
25298 risk' table and 'censoring count plot'. Other functions are also available to
25299 plot adjusted curves for Cox model and to visually examine Cox model
25301 (license license:gpl2)))
25303 (define-public r-forge
25310 (uri (cran-uri "forge" version))
25313 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
25314 (properties `((upstream-name . "forge")))
25315 (build-system r-build-system)
25317 `(("r-magrittr" ,r-magrittr)
25318 ("r-rlang" ,r-rlang)))
25319 (home-page "https://cran.r-project.org/web/packages/forge/")
25320 (synopsis "Cast values into shape")
25322 "This package provides helper functions with a consistent interface to
25323 coerce and verify the types and shapes of values for input checking.")
25324 (license license:asl2.0)))
25326 (define-public r-config
25333 (uri (cran-uri "config" version))
25336 "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l"))))
25337 (properties `((upstream-name . "config")))
25338 (build-system r-build-system)
25340 `(("r-yaml" ,r-yaml)))
25342 `(("r-knitr" ,r-knitr)))
25343 (home-page "https://github.com/rstudio/config")
25344 (synopsis "Manage environment specific configuration values")
25346 "This package lets you manage configuration values across multiple
25347 environments (e.g. development, test, production). It reads values using a
25348 function that determines the current environment and returns the appropriate
25350 (license license:gpl3)))
25352 (define-public r-adaptivesparsity
25354 (name "r-adaptivesparsity")
25358 (uri (cran-uri "AdaptiveSparsity" version))
25361 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
25363 `((upstream-name . "AdaptiveSparsity")))
25364 (build-system r-build-system)
25367 (modify-phases %standard-phases
25368 (add-after 'unpack 'link-against-armadillo
25370 (substitute* "src/Makevars"
25371 (("PKG_LIBS=" prefix)
25372 (string-append prefix "-larmadillo")))
25375 `(("r-mass" ,r-mass)
25376 ("r-matrix" ,r-matrix)
25378 ("r-rcpparmadillo" ,r-rcpparmadillo)))
25380 `(("armadillo" ,armadillo)))
25381 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
25382 (synopsis "Adaptive sparsity models")
25384 "This package implements the Figueiredo machine learning algorithm for
25385 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
25386 geometric models.")
25387 (license license:lgpl3+)))
25389 (define-public r-diffusionmap
25391 (name "r-diffusionmap")
25396 (uri (cran-uri "diffusionMap" version))
25399 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
25400 (properties `((upstream-name . "diffusionMap")))
25401 (build-system r-build-system)
25403 `(("r-igraph" ,r-igraph)
25404 ("r-matrix" ,r-matrix)
25405 ("r-scatterplot3d" ,r-scatterplot3d)))
25406 (home-page "https://www.r-project.org")
25407 (synopsis "Diffusion map")
25408 (description "This package implements the diffusion map method of data
25409 parametrization, including creation and visualization of diffusion maps,
25410 clustering with diffusion K-means and regression using the adaptive regression
25412 (license license:gpl2)))
25414 (define-public r-igraph
25421 (uri (cran-uri "igraph" version))
25424 "0vf7wrx77cdiav8724cw8gchrn0y9wvywphf5km4pa7xcqhsf3b4"))))
25425 (build-system r-build-system)
25427 `(("gfortran" ,gfortran)))
25431 ("libxml2" ,libxml2)
25434 `(("r-magrittr" ,r-magrittr)
25435 ("r-matrix" ,r-matrix)
25436 ("r-pkgconfig" ,r-pkgconfig)))
25437 (home-page "https://igraph.org")
25438 (synopsis "Network analysis and visualization")
25440 "This package provides routines for simple graphs and network analysis.
25441 It can handle large graphs very well and provides functions for generating
25442 random and regular graphs, graph visualization, centrality methods and much
25444 (license license:gpl2+)))
25446 (define-public r-workflows
25448 (name "r-workflows")
25453 (uri (cran-uri "workflows" version))
25456 "1mk0pnmpqlhf143mvj9rwvjrrshirz6s83s5hbfalhnyw7hzkfb9"))))
25457 (properties `((upstream-name . "workflows")))
25458 (build-system r-build-system)
25461 ("r-ellipsis" ,r-ellipsis)
25462 ("r-generics" ,r-generics)
25464 ("r-hardhat" ,r-hardhat)
25465 ("r-parsnip" ,r-parsnip)
25466 ("r-rlang" ,r-rlang)
25467 ("r-tidyselect" ,r-tidyselect)))
25469 `(("r-knitr" ,r-knitr)))
25470 (home-page "https://github.com/tidymodels/workflows")
25471 (synopsis "Modeling workflows")
25473 "A workflow is an object that can bundle together your pre-processing,
25474 modeling, and post-processing requests. For example, if you have a
25475 @code{recipe} and @code{parsnip} model, these can be combined into a
25476 workflow. The advantages are:
25479 @item You don’t have to keep track of separate objects in your workspace.
25480 @item The recipe prepping and model fitting can be executed using a single
25481 call to @code{fit()}.
25482 @item If you have custom tuning parameter settings, these can be defined using
25483 a simpler interface when combined with @code{tune}.
25484 @item In the future, workflows will be able to add post-processing operations,
25485 such as modifying the probability cutoff for two-class models.
25488 (license license:expat)))
25490 (define-public r-gpfit
25497 (uri (cran-uri "GPfit" version))
25500 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
25501 (properties `((upstream-name . "GPfit")))
25502 (build-system r-build-system)
25504 `(("r-lattice" ,r-lattice)
25506 (home-page "https://cran.r-project.org/web/packages/GPfit/")
25507 (synopsis "Gaussian Processes modeling")
25509 "This package provides a computationally stable approach of fitting a
25510 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
25511 (license license:gpl2)))
25513 (define-public r-yardstick
25515 (name "r-yardstick")
25520 (uri (cran-uri "yardstick" version))
25523 "1yrvlhn4gxyn9f20z5yv3xam0j0a8z362jwa32r33r0g0jk5z2fq"))))
25524 (properties `((upstream-name . "yardstick")))
25525 (build-system r-build-system)
25527 `(("r-dplyr" ,r-dplyr)
25528 ("r-generics" ,r-generics)
25530 ("r-rlang" ,r-rlang)
25531 ("r-tidyselect" ,r-tidyselect)))
25533 `(("r-knitr" ,r-knitr)))
25534 (home-page "https://github.com/tidymodels/yardstick")
25535 (synopsis "Tidy characterizations of model performance")
25537 "This package provides tidy tools for quantifying how well a model fits
25538 to a data set such as confusion matrices, class probability curve summaries,
25539 and regression metrics (e.g., RMSE).")
25540 (license license:gpl2)))
25542 (define-public r-warp
25549 (uri (cran-uri "warp" version))
25552 "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
25553 (properties `((upstream-name . "warp")))
25554 (build-system r-build-system)
25555 (native-inputs `(("r-knitr" ,r-knitr)))
25556 (home-page "https://github.com/DavisVaughan/warp")
25557 (synopsis "Group dates")
25559 "This package provides tooling to group dates by a variety of periods
25560 including: yearly, monthly, by second, by week of the month, and more. The
25561 groups are defined in such a way that they also represent the distance between
25562 dates in terms of the period. This extracts valuable information that can be
25563 used in further calculations that rely on a specific temporal spacing between
25565 (license license:expat)))
25567 (define-public r-slider
25574 (uri (cran-uri "slider" version))
25577 "1x4jwfxam4czfkb1s5qds5krfw1h2p5a4rh6f5z4yvhsv0d81xck"))))
25578 (properties `((upstream-name . "slider")))
25579 (build-system r-build-system)
25581 `(("r-glue" ,r-glue)
25582 ("r-rlang" ,r-rlang)
25583 ("r-vctrs" ,r-vctrs)
25584 ("r-warp" ,r-warp)))
25585 (native-inputs `(("r-knitr" ,r-knitr)))
25586 (home-page "https://github.com/DavisVaughan/slider")
25587 (synopsis "Sliding window functions")
25589 "This package provides type-stable rolling window functions over any R
25590 data type. Cumulative and expanding windows are also supported. For more
25591 advanced usage, an index can be used as a secondary vector that defines how
25592 sliding windows are to be created.")
25593 (license license:expat)))
25595 (define-public r-rsample
25602 (uri (cran-uri "rsample" version))
25605 "1psmxk16d4bz1v05x0gb9hn4brkdjxw8hjbxmj62snichnix3q3i"))))
25606 (properties `((upstream-name . "rsample")))
25607 (build-system r-build-system)
25609 `(("r-dplyr" ,r-dplyr)
25610 ("r-ellipsis" ,r-ellipsis)
25611 ("r-furrr" ,r-furrr)
25612 ("r-generics" ,r-generics)
25613 ("r-modeldata" ,r-modeldata)
25614 ("r-purrr" ,r-purrr)
25615 ("r-rlang" ,r-rlang)
25616 ("r-slider" ,r-slider)
25617 ("r-tibble" ,r-tibble)
25618 ("r-tidyr" ,r-tidyr)
25619 ("r-tidyselect" ,r-tidyselect)
25620 ("r-vctrs" ,r-vctrs)))
25622 `(("r-knitr" ,r-knitr)))
25623 (home-page "https://rsample.tidymodels.org")
25624 (synopsis "General resampling infrastructure")
25626 "This package provides classes and functions to create and summarize
25627 different types of resampling objects (e.g. bootstrap, cross-validation).")
25628 (license license:gpl2)))
25630 (define-public r-dicedesign
25632 (name "r-dicedesign")
25637 (uri (cran-uri "DiceDesign" version))
25640 "11s1m543kxd6gv4amh8z6pph1n67sj9sfwm6hjy83wfs65syf5vp"))))
25641 (properties `((upstream-name . "DiceDesign")))
25642 (build-system r-build-system)
25643 (home-page "http://dice.emse.fr/")
25644 (synopsis "Designs of computer experiments")
25646 "This package provides tools to create some specific @code{Space-Filling
25647 Design} (SFD) and to test their quality.")
25648 (license license:gpl3)))
25650 (define-public r-dials
25657 (uri (cran-uri "dials" version))
25660 "0g9wj2py4wz703rh4p7hk8qxqnkm7zyrypv4qz4vaqziazjsmxks"))))
25661 (properties `((upstream-name . "dials")))
25662 (build-system r-build-system)
25664 `(("r-dicedesign" ,r-dicedesign)
25665 ("r-dplyr" ,r-dplyr)
25667 ("r-purrr" ,r-purrr)
25668 ("r-rlang" ,r-rlang)
25669 ("r-scales" ,r-scales)
25670 ("r-tibble" ,r-tibble)
25671 ("r-vctrs" ,r-vctrs)
25672 ("r-withr" ,r-withr)))
25673 (native-inputs `(("r-knitr" ,r-knitr)))
25674 (home-page "https://dials.tidymodels.org/")
25675 (synopsis "Tools for creating tuning parameter values")
25677 "Many models contain tuning parameters (i.e. parameters that cannot be
25678 directly estimated from the data). These tools can be used to define objects
25679 for creating, simulating, or validating values for such parameters.")
25680 (license license:gpl2)))
25682 (define-public r-tune
25689 (uri (cran-uri "tune" version))
25692 "0ja7rjkjj88v3ngrc6izcz2qh9qv4s8abgcafmvx2ihgz99hds37"))))
25693 (properties `((upstream-name . "tune")))
25694 (build-system r-build-system)
25697 ("r-dials" ,r-dials)
25698 ("r-dplyr" ,r-dplyr)
25699 ("r-foreach" ,r-foreach)
25700 ("r-generics" ,r-generics)
25701 ("r-ggplot2" ,r-ggplot2)
25703 ("r-gpfit" ,r-gpfit)
25704 ("r-hardhat" ,r-hardhat)
25705 ("r-parsnip" ,r-parsnip)
25706 ("r-purrr" ,r-purrr)
25707 ("r-recipes" ,r-recipes)
25708 ("r-rlang" ,r-rlang)
25709 ("r-rsample" ,r-rsample)
25710 ("r-tibble" ,r-tibble)
25711 ("r-tidyr" ,r-tidyr)
25712 ("r-vctrs" ,r-vctrs)
25713 ("r-workflows" ,r-workflows)
25714 ("r-yardstick" ,r-yardstick)))
25715 (home-page "https://github.com/tidymodels/tune")
25716 (synopsis "Tidy tuning tools")
25718 "The ability to tune models is important. @code{tune} contains functions
25719 and classes to be used in conjunction with other @code{tidymodels} packages
25720 for finding reasonable values of hyper-parameters in models, pre-processing
25721 methods, and post-processing steps.")
25722 (license license:expat)))
25724 (define-public r-tidyposterior
25726 (name "r-tidyposterior")
25731 (uri (cran-uri "tidyposterior" version))
25734 "0wsv800w056ziqbnwal7ncmdy4li8cn5yrdx07w35b7j8kl4mwhg"))))
25735 (properties `((upstream-name . "tidyposterior")))
25736 (build-system r-build-system)
25738 `(("r-dplyr" ,r-dplyr)
25739 ("r-generics" ,r-generics)
25740 ("r-ggplot2" ,r-ggplot2)
25741 ("r-lifecycle" ,r-lifecycle)
25742 ("r-purrr" ,r-purrr)
25743 ("r-rlang" ,r-rlang)
25744 ("r-rsample" ,r-rsample)
25745 ("r-rstanarm" ,r-rstanarm)
25746 ("r-tibble" ,r-tibble)
25747 ("r-tidyr" ,r-tidyr)
25748 ("r-vctrs" ,r-vctrs)))
25750 `(("r-knitr" ,r-knitr)))
25751 (home-page "https://tidyposterior.tidymodels.org")
25752 (synopsis "Bayesian analysis to compare models using resampling statistics")
25754 "This package can be used to conduct post hoc analyses of resampling
25755 results generated by models. For example, if two models are evaluated with
25756 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
25757 are 10 paired statistics. These can be used to make comparisons between
25758 models without involving a test set.")
25759 (license license:gpl2)))
25761 (define-public r-tidypredict
25763 (name "r-tidypredict")
25768 (uri (cran-uri "tidypredict" version))
25771 "0fff349pkksss8h1k2qza78l81ha6avx63pxziv6dfa8h62qmrdy"))))
25772 (properties `((upstream-name . "tidypredict")))
25773 (build-system r-build-system)
25775 `(("r-dplyr" ,r-dplyr)
25776 ("r-generics" ,r-generics)
25777 ("r-knitr" ,r-knitr)
25778 ("r-purrr" ,r-purrr)
25779 ("r-rlang" ,r-rlang)
25780 ("r-stringr" ,r-stringr)
25781 ("r-tibble" ,r-tibble)
25782 ("r-tidyr" ,r-tidyr)))
25784 `(("r-knitr" ,r-knitr)))
25785 (home-page "https://tidypredict.tidymodels.org")
25786 (synopsis "Run predictions inside the database")
25788 "This package parses a fitted R model object, and returns a formula in
25789 Tidy Eval code that calculates the predictions. It works with several
25790 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
25791 final SQL translation of the algorithm. It currently supports @code{lm()},
25792 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
25793 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
25794 (license license:gpl3)))
25796 (define-public r-janeaustenr
25798 (name "r-janeaustenr")
25803 (uri (cran-uri "janeaustenr" version))
25806 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
25807 (properties `((upstream-name . "janeaustenr")))
25808 (build-system r-build-system)
25809 (home-page "https://github.com/juliasilge/janeaustenr")
25810 (synopsis "Jane Austen's complete novels")
25812 "This package provides the full texts for Jane Austen's six completed
25813 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
25814 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
25815 and \"Persuasion\".")
25816 (license license:expat)))
25818 (define-public r-tokenizers
25820 (name "r-tokenizers")
25825 (uri (cran-uri "tokenizers" version))
25828 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
25829 (properties `((upstream-name . "tokenizers")))
25830 (build-system r-build-system)
25832 `(("r-rcpp" ,r-rcpp)
25833 ("r-snowballc" ,r-snowballc)
25834 ("r-stringi" ,r-stringi)))
25836 `(("r-knitr" ,r-knitr)))
25837 (home-page "https://lincolnmullen.com/software/tokenizers/")
25838 (synopsis "Fast, consistent tokenization of natural language text")
25840 "This is a package for converting natural language text into tokens.
25841 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
25842 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
25843 Treebank, regular expressions, as well as functions for counting characters,
25844 words, and sentences, and a function for splitting longer texts into separate
25845 documents, each with the same number of words. The tokenizers have a
25846 consistent interface, and the package is built on the @code{stringi} and
25847 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
25848 (license license:expat)))
25850 (define-public r-hunspell
25852 (name "r-hunspell")
25857 (uri (cran-uri "hunspell" version))
25860 "0ql6y05d4xxpm468rslb0wxdp1x9l3flxzmb5w6pjg617f8vpv8z"))))
25861 (properties `((upstream-name . "hunspell")))
25862 (build-system r-build-system)
25864 `(("r-digest" ,r-digest)
25865 ("r-rcpp" ,r-rcpp)))
25867 `(("r-knitr" ,r-knitr)))
25868 (home-page "https://github.com/ropensci/hunspell#readme")
25869 (synopsis "High-performance stemmer, tokenizer, and spell checker")
25871 "This package provides a low-level spell checker and morphological
25872 analyzer based on the famous @code{hunspell} library. The package can analyze
25873 or check individual words as well as parse text, LaTeX, HTML or XML documents.
25874 For a more user-friendly interface use the @code{spelling} package which
25875 builds on this package to automate checking of files, documentation and
25876 vignettes in all common formats.")
25877 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
25878 ;; MPL; in addition to these licenses the rest of the R wrapper is also
25879 ;; available under the Expat license.
25880 (license (list license:gpl2
25885 (define-public r-tidytext
25887 (name "r-tidytext")
25892 (uri (cran-uri "tidytext" version))
25895 "1icbfw4zkbs9sp6vk814mw2zzm0bc0d7af92vhriqxaga0gbwdkx"))))
25896 (properties `((upstream-name . "tidytext")))
25897 (build-system r-build-system)
25899 `(("r-dplyr" ,r-dplyr)
25900 ("r-generics" ,r-generics)
25901 ("r-hunspell" ,r-hunspell)
25902 ("r-janeaustenr" ,r-janeaustenr)
25903 ("r-lifecycle" ,r-lifecycle)
25904 ("r-matrix" ,r-matrix)
25905 ("r-purrr" ,r-purrr)
25906 ("r-rlang" ,r-rlang)
25907 ("r-stringr" ,r-stringr)
25908 ("r-tibble" ,r-tibble)
25909 ("r-tokenizers" ,r-tokenizers)
25910 ("r-vctrs" ,r-vctrs)))
25912 `(("r-knitr" ,r-knitr)))
25913 (home-page "https://github.com/juliasilge/tidytext")
25914 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
25916 "This is a package for text mining for word processing and sentiment
25917 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
25918 (license license:expat)))
25920 (define-public r-parsnip
25927 (uri (cran-uri "parsnip" version))
25930 "0c12lyfxqsdprqlcmgy421py38z28h88d68pxb1c4fw14v1c2d06"))))
25931 (properties `((upstream-name . "parsnip")))
25932 (build-system r-build-system)
25934 `(("r-dplyr" ,r-dplyr)
25935 ("r-generics" ,r-generics)
25936 ("r-globals" ,r-globals)
25938 ("r-magrittr" ,r-magrittr)
25939 ("r-prettyunits" ,r-prettyunits)
25940 ("r-purrr" ,r-purrr)
25941 ("r-rlang" ,r-rlang)
25942 ("r-tibble" ,r-tibble)
25943 ("r-tidyr" ,r-tidyr)
25944 ("r-vctrs" ,r-vctrs)))
25946 `(("r-knitr" ,r-knitr)))
25947 (home-page "https://parsnip.tidymodels.org")
25948 (synopsis "Common API to modeling and analysis functions")
25950 "This package provides a common interface to allow users to specify a
25951 model without having to remember the different argument names across different
25952 functions or computational engines (e.g. R, Spark, Stan, etc).")
25953 (license license:gpl2)))
25955 (define-public r-infer
25962 (uri (cran-uri "infer" version))
25965 "0wvvgqjhyv7ql98cjzqad61wbmk7xrqd1ybk894jr5cmza13c8w2"))))
25966 (properties `((upstream-name . "infer")))
25967 (build-system r-build-system)
25969 `(("r-dplyr" ,r-dplyr)
25970 ("r-ggplot2" ,r-ggplot2)
25972 ("r-magrittr" ,r-magrittr)
25973 ("r-purrr" ,r-purrr)
25974 ("r-rlang" ,r-rlang)
25975 ("r-tibble" ,r-tibble)))
25977 `(("r-knitr" ,r-knitr)))
25978 (home-page "https://github.com/tidymodels/infer")
25979 (synopsis "Tidy statistical inference")
25981 "The objective of this package is to perform inference using an
25982 expressive statistical grammar that coheres with the Tidy design framework.")
25983 (license license:cc0)))
25985 (define-public r-modeldata
25987 (name "r-modeldata")
25992 (uri (cran-uri "modeldata" version))
25995 "0lbvmicvhw560jn9qk5dywrl6mgj1rf7zh7p86lf97c6bmz0zp2r"))))
25996 (properties `((upstream-name . "modeldata")))
25997 (build-system r-build-system)
25998 (home-page "https://modeldata.tidymodels.org")
25999 (synopsis "Data sets useful for modeling packages")
26001 "This package provides data sets used for demonstrating or testing
26002 model-related packages.")
26003 (license license:expat)))
26005 (define-public r-tidymodels
26007 (name "r-tidymodels")
26012 (uri (cran-uri "tidymodels" version))
26015 "09njrl655sh82xrzckgg56a6ndfrjla5fy8675wj4jsj14jpv0fw"))))
26016 (properties `((upstream-name . "tidymodels")))
26017 (build-system r-build-system)
26019 `(("r-broom" ,r-broom)
26021 ("r-dials" ,r-dials)
26022 ("r-dplyr" ,r-dplyr)
26023 ("r-ggplot2" ,r-ggplot2)
26024 ("r-infer" ,r-infer)
26025 ("r-magrittr" ,r-magrittr)
26026 ("r-modeldata" ,r-modeldata)
26027 ("r-parsnip" ,r-parsnip)
26028 ("r-purrr" ,r-purrr)
26029 ("r-recipes" ,r-recipes)
26030 ("r-rlang" ,r-rlang)
26031 ("r-rsample" ,r-rsample)
26032 ("r-rstudioapi" ,r-rstudioapi)
26033 ("r-tibble" ,r-tibble)
26034 ("r-tidyr" ,r-tidyr)
26036 ("r-workflows" ,r-workflows)
26037 ("r-yardstick" ,r-yardstick)))
26039 `(("r-knitr" ,r-knitr)
26040 ("r-rmarkdown" ,r-rmarkdown)
26042 ("pandoc-citeproc" ,pandoc-citeproc))) ; for vignettes
26043 (home-page "https://github.com/tidymodels/tidymodels")
26044 (synopsis "Tidy collection for modeling and statistical analysis")
26046 "The tidy modeling \"verse\" is a collection of packages for modeling and
26047 statistical analysis that share the underlying design philosophy, grammar, and
26048 data structures of the tidyverse.")
26049 (license license:gpl3)))
26051 (define-public r-mlecens
26058 (uri (cran-uri "MLEcens" version))
26061 "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))
26062 (properties `((upstream-name . "MLEcens")))
26063 (build-system r-build-system)
26064 (home-page "http://stat.ethz.ch/~maathuis/")
26065 (synopsis "Computation of the MLE for bivariate (interval) censored data")
26067 "This package contains functions to compute the nonparametric
26068 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
26069 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
26070 To be more precise, we consider the situation where we observe a set of
26071 rectangles that are known to contain the unobservable realizations of (X,Y).
26072 We compute the MLE based on such a set of rectangles. The methods can also be
26073 used for univariate censored data (see data set @code{cosmesis}), and for
26074 censored data with competing risks (see data set @code{menopause}). The
26075 package also provides functions to visualize the observed data and the MLE.")
26076 (license license:gpl2+)))
26078 (define-public r-metafor
26085 (uri (cran-uri "metafor" version))
26088 "1b599fxk7s0brkchmx698fr5k4g1kzkia2rnlvhg349ffs5nfjmn"))))
26089 (properties `((upstream-name . "metafor")))
26090 (build-system r-build-system)
26092 `(("r-matrix" ,r-matrix)
26093 ("r-nlme" ,r-nlme)))
26094 (home-page "https://cran.r-project.org/web/packages/metafor/")
26095 (synopsis "Meta-analysis package for R")
26097 "This package provides a comprehensive collection of functions for
26098 conducting meta-analyses in R. The package includes functions to calculate
26099 various effect sizes or outcome measures, fit fixed-, random-, and
26100 mixed-effects models to such data, carry out moderator and meta-regression
26101 analyses, and create various types of meta-analytical plots (e.g., forest,
26102 funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial
26103 and person-time data, the package also provides functions that implement
26104 specialized methods, including the Mantel-Haenszel method, Peto's method, and
26105 a variety of suitable generalized linear (mixed-effects) models (i.e.
26106 mixed-effects logistic and Poisson regression models). Finally, the package
26107 provides functionality for fitting meta-analytic multivariate/multilevel
26108 models that account for non-independent sampling errors and/or true
26109 effects (e.g. due to the inclusion of multiple treatment studies, multiple
26110 endpoints, or other forms of clustering). Network meta-analyses and
26111 meta-analyses accounting for known correlation structures (e.g. due to
26112 phylogenetic relatedness) can also be conducted.")
26113 (license license:gpl2+)))
26115 (define-public r-altmeta
26122 (uri (cran-uri "altmeta" version))
26125 "0z252lbsknqp33i0b0xf5r7spr535iq47bv40vgip6nsqhgrl7b0"))))
26126 (properties `((upstream-name . "altmeta")))
26127 (build-system r-build-system)
26129 `(("r-coda" ,r-coda)
26131 ("r-matrix" ,r-matrix)
26132 ("r-metafor" ,r-metafor)
26133 ("r-rjags" ,r-rjags)))
26134 (home-page "https://cran.r-project.org/web/packages/altmeta/")
26135 (synopsis "Alternative meta-analysis methods")
26137 "This package provides alternative statistical methods for meta-analysis,
26141 @item bivariate generalized linear mixed models for synthesizing odds ratios,
26142 relative risks, and risk differences
26143 @item heterogeneity tests and measures that are robust to outliers;
26144 @item measures, tests, and visualization tools for publication bias or
26145 small-study effects;
26146 @item meta-analysis of diagnostic tests for synthesizing sensitivities,
26147 specificities, etc.;
26148 @item meta-analysis methods for synthesizing proportions;
26149 @item models for multivariate meta-analysis.
26152 (license license:gpl2+)))
26154 (define-public r-perm
26157 (version "1.0-0.0")
26161 (uri (cran-uri "perm" version))
26164 "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk"))))
26165 (properties `((upstream-name . "perm")))
26166 (build-system r-build-system)
26167 (home-page "https://cran.r-project.org/web/packages/perm/")
26168 (synopsis "Exact or asymptotic permutation tests")
26170 "This package provides several methods for performing permutation tests.
26171 It has three main functions, to perform linear permutation tests. These tests
26172 are tests where the test statistic is the sum of the product of a
26173 covariate (usually group indicator) and the scores.")
26174 ;; Any version of the GPL
26175 (license license:gpl2+)))
26177 (define-public r-qtl
26184 (uri (cran-uri "qtl" version))
26187 "0hffirsvw9j82cdx6l7vhqn3a7ab52claqjlinv3lswl1nsfg93b"))))
26188 (build-system r-build-system)
26189 (home-page "https://rqtl.org/")
26190 (synopsis "R package for analyzing QTL experiments in genetics")
26191 (description "R/qtl is an extension library for the R statistics system.
26192 It is used to analyze experimental crosses for identifying genes contributing
26193 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
26195 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
26196 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
26198 (license license:gpl3)))
26200 (define-public r-qtl2
26206 (uri (cran-uri "qtl2" version))
26208 (base32 "1558khh0zkwm0rdk87krv9836krvwv5h7ymlz9bsrgcvypyr9186"))))
26209 (build-system r-build-system)
26211 `(("r-data-table" ,r-data-table)
26212 ("r-jsonlite" ,r-jsonlite)
26214 ("r-rcppeigen" ,r-rcppeigen)
26215 ("r-rsqlite" ,r-rsqlite)
26216 ("r-yaml" ,r-yaml)))
26217 (home-page "https://kbroman.org/qtl2/")
26218 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
26220 "This package provides a set of tools to perform @dfn{Quantitative Trait
26221 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
26222 @code{R/qtl} package to better handle high-dimensional data and complex cross
26223 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
26224 (license license:gpl3)))
26226 (define-public r-seqminer
26228 (name "r-seqminer")
26233 (uri (cran-uri "seqminer" version))
26236 "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
26237 (build-system r-build-system)
26240 (home-page "http://seqminer.genomic.codes")
26241 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
26243 "This package provides tools to integrate nucleotide sequencing
26244 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
26245 ;; Any version of the GPL is acceptable
26246 (license (list license:gpl2+ license:gpl3+))))
26248 (define-public r-maldiquant
26250 (name "r-maldiquant")
26255 (uri (cran-uri "MALDIquant" version))
26258 "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
26259 (properties `((upstream-name . "MALDIquant")))
26260 (build-system r-build-system)
26261 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
26262 (synopsis "Quantitative analysis of mass spectrometry data")
26264 "This package provides a complete analysis pipeline for matrix-assisted
26265 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
26266 two-dimensional mass spectrometry data. In addition to commonly used plotting
26267 and processing methods it includes distinctive features, namely baseline
26268 subtraction methods such as morphological filters (TopHat) or the
26269 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
26270 alignment using warping functions, handling of replicated measurements as well
26271 as allowing spectra with different resolutions.")
26272 (license license:gpl3+)))
26274 (define-public r-scattermore
26276 (name "r-scattermore")
26281 (uri (cran-uri "scattermore" version))
26284 "18nzlprmphkvjg946h10h2qq0wbkmv2526p8di6k2xl4gccq0qpk"))))
26285 (properties `((upstream-name . "scattermore")))
26286 (build-system r-build-system)
26288 `(("r-ggplot2" ,r-ggplot2)
26289 ("r-scales" ,r-scales)))
26290 (home-page "https://github.com/exaexa/scattermore")
26291 (synopsis "Scatterplots with more points")
26293 "This package provides C-based tools for converting large scatterplot
26294 data to rasters. It speeds up plotting of data with millions of points.")
26295 (license license:gpl3+)))
26297 (define-public r-seuratobject
26299 (name "r-seuratobject")
26304 (uri (cran-uri "SeuratObject" version))
26307 "03k27z7g76wy7mfja2cpxq183xk0906k9gxb2j6p1zw341gv4gii"))))
26308 (properties `((upstream-name . "SeuratObject")))
26309 (build-system r-build-system)
26311 `(("r-matrix" ,r-matrix)
26313 ("r-rcppeigen" ,r-rcppeigen)
26314 ("r-rlang" ,r-rlang)
26315 ("r-sctransform" ,r-sctransform)))
26316 (home-page "https://satijalab.org/seurat")
26317 (synopsis "Data structures for single cell data")
26319 "This package defines S4 classes for single-cell genomic data and
26320 associated information, such as dimensionality reduction embeddings,
26321 nearest-neighbor graphs, and spatially-resolved coordinates. It provides data
26322 access methods and R-native hooks to ensure the Seurat object is familiar to
26324 (license license:gpl3)))
26326 (define-public r-seurat
26332 (uri (cran-uri "Seurat" version))
26335 "1mp3py00bmzj4541d8ry5sfzkpfzvnl9dpa8n4qhakd13dl30xdn"))))
26336 (properties `((upstream-name . "Seurat")))
26337 (build-system r-build-system)
26339 `(("r-cluster" ,r-cluster)
26340 ("r-cowplot" ,r-cowplot)
26341 ("r-fitdistrplus" ,r-fitdistrplus)
26342 ("r-future" ,r-future)
26343 ("r-future-apply" ,r-future-apply)
26344 ("r-ggplot2" ,r-ggplot2)
26345 ("r-ggrepel" ,r-ggrepel)
26346 ("r-ggridges" ,r-ggridges)
26349 ("r-igraph" ,r-igraph)
26350 ("r-irlba" ,r-irlba)
26351 ("r-jsonlite" ,r-jsonlite)
26352 ("r-kernsmooth" ,r-kernsmooth)
26353 ("r-leiden" ,r-leiden)
26354 ("r-lmtest" ,r-lmtest)
26356 ("r-matrix" ,r-matrix)
26357 ("r-matrixstats" ,r-matrixstats)
26358 ("r-miniui" ,r-miniui)
26359 ("r-patchwork" ,r-patchwork)
26360 ("r-pbapply" ,r-pbapply)
26361 ("r-plotly" ,r-plotly)
26364 ("r-rcolorbrewer" ,r-rcolorbrewer)
26366 ("r-rcppannoy" ,r-rcppannoy)
26367 ("r-rcppeigen" ,r-rcppeigen)
26368 ("r-rcppprogress" ,r-rcppprogress)
26369 ("r-reticulate" ,r-reticulate)
26370 ("r-rlang" ,r-rlang)
26372 ("r-rtsne" ,r-rtsne)
26373 ("r-scales" ,r-scales)
26374 ("r-scattermore" ,r-scattermore)
26375 ("r-sctransform" ,r-sctransform)
26376 ("r-seuratobject" ,r-seuratobject)
26377 ("r-shiny" ,r-shiny)
26378 ("r-spatstat" ,r-spatstat)
26379 ("r-tibble" ,r-tibble)
26380 ("r-uwot" ,r-uwot)))
26381 (home-page "http://www.satijalab.org/seurat")
26382 (synopsis "Seurat is an R toolkit for single cell genomics")
26384 "This package is an R package designed for QC, analysis, and
26385 exploration of single cell RNA-seq data. It easily enables widely-used
26386 analytical techniques, including the identification of highly variable genes,
26387 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
26388 algorithms; density clustering, hierarchical clustering, k-means, and the
26389 discovery of differentially expressed genes and markers.")
26390 (license license:gpl3)))
26392 (define-public r-phangorn
26394 (name "r-phangorn")
26399 (uri (cran-uri "phangorn" version))
26402 "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
26403 (build-system r-build-system)
26406 ("r-fastmatch" ,r-fastmatch)
26407 ("r-igraph" ,r-igraph)
26408 ("r-magrittr" ,r-magrittr)
26409 ("r-matrix" ,r-matrix)
26410 ("r-quadprog" ,r-quadprog)
26411 ("r-rcpp" ,r-rcpp)))
26412 (home-page "https://github.com/KlausVigo/phangorn")
26413 (synopsis "Phylogenetic analysis in R")
26415 "Phangorn is a package for phylogenetic analysis in R. It supports
26416 estimation of phylogenetic trees and networks using Maximum Likelihood,
26417 Maximum Parsimony, distance methods and Hadamard conjugation.")
26418 (license license:gpl2+)))
26420 (define-public r-diversitree
26422 (name "r-diversitree")
26427 (uri (cran-uri "diversitree" version))
26430 "1sk3sgn5hi04978s5s7gy6pzp28g3v9rglmiamlgs96c9wyyyff7"))))
26431 (build-system r-build-system)
26433 `(("gfortran" ,gfortran)))
26434 (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
26437 ("r-desolve" ,r-desolve)
26439 ("r-subplex" ,r-subplex)))
26440 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
26441 (synopsis "Comparative 'phylogenetic' analyses of diversification")
26442 (description "This package contains a number of comparative \"phylogenetic\"
26443 methods, mostly focusing on analysing diversification and character evolution.
26444 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
26445 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
26446 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
26447 include Markov models of discrete and continuous trait evolution and constant
26448 rate speciation and extinction.")
26449 (license license:gpl2+)))
26451 (define-public r-absfiltergsea
26453 (name "r-absfiltergsea")
26458 (uri (cran-uri "AbsFilterGSEA" version))
26460 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
26461 (properties `((upstream-name . "AbsFilterGSEA")))
26462 (build-system r-build-system)
26464 `(("r-biobase" ,r-biobase)
26465 ("r-deseq" ,r-deseq)
26466 ("r-limma" ,r-limma)
26468 ("r-rcpparmadillo" ,r-rcpparmadillo)))
26469 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
26470 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
26472 "This package provides a function that performs gene-permuting of a gene-set
26473 enrichment analysis (GSEA) calculation with or without the absolute filtering.
26474 Without filtering, users can perform (original) two-tailed or one-tailed
26476 (license license:gpl2)))
26478 (define-public r-calculus
26480 (name "r-calculus")
26485 (uri (cran-uri "calculus" version))
26488 "1wa5ap89cfcp0ancj9ivx5s2y0wqr2vmp9y115g7f6g772jwhscj"))))
26489 (properties `((upstream-name . "calculus")))
26490 (build-system r-build-system)
26492 `(("r-rcpp" ,r-rcpp)))
26494 `(("r-knitr" ,r-knitr)))
26495 (home-page "https://github.com/eguidotti/calculus")
26496 (synopsis "High dimensional numerical and symbolic calculus")
26498 "Efficient C++ optimized functions for numerical and symbolic calculus.
26499 It includes basic symbolic arithmetic, tensor calculus, Einstein summing
26500 convention, fast computation of the Levi-Civita symbol and generalized
26501 Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
26502 accurate high-order derivatives, differential operators (Gradient, Jacobian,
26503 Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
26504 orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
26505 parabolic or user defined by custom scale factors.")
26506 (license license:gpl3)))
26508 (define-public r-decon
26515 (uri (cran-uri "decon" version))
26518 "1v4l0xq29rm8mks354g40g9jxn0didzlxg3g7z08m0gvj29zdj7s"))))
26519 (properties `((upstream-name . "decon")))
26520 (build-system r-build-system)
26522 `(("gfortran" ,gfortran)))
26524 "https://cran.r-project.org/web/packages/decon/")
26525 (synopsis "Deconvolution Estimation in Measurement Error Models")
26527 "This package contains a collection of functions to deal with
26528 nonparametric measurement error problems using deconvolution
26529 kernel methods. We focus two measurement error models in the
26530 package: (1) an additive measurement error model, where the
26531 goal is to estimate the density or distribution function from
26532 contaminated data; (2) nonparametric regression model with
26533 errors-in-variables. The R functions allow the measurement errors
26534 to be either homoscedastic or heteroscedastic. To make the
26535 deconvolution estimators computationally more efficient in R,
26536 we adapt the \"Fast Fourier Transform\" (FFT) algorithm for
26537 density estimation with error-free data to the deconvolution
26538 kernel estimation. Several methods for the selection of the
26539 data-driven smoothing parameter are also provided in the package.
26540 See details in: Wang, X.F. and Wang, B. (2011). Deconvolution
26541 estimation in measurement error models: The R package decon.
26542 Journal of Statistical Software, 39(10), 1-24.")
26543 (license license:gpl3+)))
26545 (define-public r-locpol
26552 (uri (cran-uri "locpol" version))
26555 "1p915n0l09kbwkly627074jslxl01yssp1rf0c7sygvsw6sgy5lm"))))
26556 (properties `((upstream-name . "locpol")))
26557 (build-system r-build-system)
26559 "https://cran.r-project.org/web/packages/locpol/")
26560 (synopsis "Kernel Local Polynomial Regression")
26562 "Computes local polynomial estimators for the regression and
26563 also density. It comprises several different utilities to handle
26564 kernel estimators.")
26565 (license license:gpl2+)))
26567 (define-public r-lpme
26574 (uri (cran-uri "lpme" version))
26577 "0si90nkgl8bqk8yvd2igdsrngiwqh8891072pfpzipifnd0f5448"))))
26578 (properties `((upstream-name . "lpme")))
26579 (build-system r-build-system)
26581 `(("r-decon" ,r-decon)
26582 ("r-flexmix" ,r-flexmix)
26583 ("r-locpol" ,r-locpol)
26585 ("r-rcpparmadillo" ,r-rcpparmadillo)))
26587 "https://cran.r-project.org/web/packages/lpme/")
26588 (synopsis "Nonparametric Estimation of Measurement Error Models")
26590 "Provide nonparametric methods for mean regression model,
26591 modal regression and conditional density estimation in the
26592 presence/absence of measurement error. Bandwidth selection is
26593 also provided for each method.")
26594 (license license:gpl2+)))
26596 (define-public r-aws-signature
26598 (name "r-aws-signature")
26603 (uri (cran-uri "aws.signature" version))
26606 "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp"))))
26607 (properties `((upstream-name . "aws.signature")))
26608 (build-system r-build-system)
26610 `(("r-base64enc" ,r-base64enc)
26611 ("r-digest" ,r-digest)))
26612 (home-page "https://github.com/cloudyr/aws.signature")
26613 (synopsis "Amazon Web Services Request Signatures")
26615 "This package generates version 2 and 4 request signatures for Amazon Web
26616 Services (AWS) and provides a mechanism for retrieving credentials from
26617 environment variables, AWS credentials files, and EC2 instance metadata. For
26618 use on EC2 instances, the package 'aws.ec2metadata' is suggested.")
26619 (license license:gpl2+)))
26621 (define-public r-aws-s3
26628 (uri (cran-uri "aws.s3" version))
26631 "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx"))))
26632 (properties `((upstream-name . "aws.s3")))
26633 (build-system r-build-system)
26635 `(("r-aws-signature" ,r-aws-signature)
26636 ("r-base64enc" ,r-base64enc)
26638 ("r-digest" ,r-digest)
26640 ("r-xml2" ,r-xml2)))
26641 (home-page "https://github.com/cloudyr/aws.s3")
26642 (synopsis "AWS S3 Client Package")
26644 "This package provides a simple client package for the Amazon Web
26645 Services (AWS) Simple Storage Service (S3) REST API.")
26646 (license license:gpl2+)))
26648 (define-public r-lgr
26654 (uri (cran-uri "lgr" version))
26657 "0k4kacjk7swm3gmdpha1rg44xb29vzvhvx48jhpb78glj5c9phyr"))))
26658 (build-system r-build-system)
26662 `(("r-knitr" ,r-knitr)))
26663 (home-page "https://s-fleck.github.io/lgr/")
26664 (synopsis "Fully featured logging framework")
26665 (description "This package offers a flexible, feature-rich yet
26666 light-weight logging framework based on @code{R6} classes. It supports
26667 hierarchical loggers, custom log levels, arbitrary data fields in log events,
26668 logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as
26669 well as email and push notifications.")
26670 (license license:expat)))
26672 (define-public r-mlr3measures
26674 (name "r-mlr3measures")
26678 (uri (cran-uri "mlr3measures" version))
26681 "18jk4kdj9771r16smz7xhmmiilcdg1qlavln5hrpvkx780zh3hj6"))))
26682 (build-system r-build-system)
26684 `(("r-checkmate" ,r-checkmate)
26685 ("r-prroc" ,r-prroc)))
26686 (home-page "https://mlr3measures.mlr-org.com/")
26687 (synopsis "Performance measures for mlr3")
26688 (description "This package implements multiple performance measures for
26689 supervised learning. It includes over 40 measures for regression and
26690 classification. Additionally, meta information about the performance measures
26691 can be queried, e.g. what the best and worst possible performances scores
26693 (license license:lgpl3)))
26695 (define-public r-mlr3misc
26697 (name "r-mlr3misc")
26701 (uri (cran-uri "mlr3misc" version))
26704 "19k3l2d6wnqvdng0m7p54rrlvwl5457lcy7bg82m2bbpqxi8qch3"))))
26705 (build-system r-build-system)
26707 `(("r-backports" ,r-backports)
26708 ("r-checkmate" ,r-checkmate)
26709 ("r-data-table" ,r-data-table)
26711 (home-page "https://mlr3misc.mlr-org.com/")
26712 (synopsis "Helper functions for mlr3")
26713 (description "@code{mlr3misc} provides frequently used helper functions
26714 and assertions used in @code{mlr3} and its companion packages. It comes with
26715 helper functions for functional programming, for printing, to work with
26716 @code{data.table}, as well as some generally useful @code{R6} classes. This
26717 package also supersedes the package @code{BBmisc}.")
26718 (license license:lgpl3)))
26720 (define-public r-paradox
26726 (uri (cran-uri "paradox" version))
26729 "1fz6sdwvvifm4qbmwgm27dil278mswvcfw8bbsvli5v4l1ghw8kj"))))
26730 (build-system r-build-system)
26732 `(("r-backports" ,r-backports)
26733 ("r-checkmate" ,r-checkmate)
26734 ("r-data-table" ,r-data-table)
26735 ("r-mlr3misc" ,r-mlr3misc)
26737 (home-page "https://paradox.mlr-org.com/")
26738 (synopsis "Define and work with parameter spaces for complex algorithms")
26739 (description "With this package it is possible to define parameter spaces,
26740 constraints and dependencies for arbitrary algorithms, and to program on such
26741 spaces. It also includes statistical designs and random samplers. Objects are
26742 implemented as @code{R6} classes.")
26743 (license license:lgpl3)))
26745 (define-public r-mlr3
26751 (uri (cran-uri "mlr3" version))
26754 "1arqijbbmhv57mj8kyq30zxykah83ab1d1c7gs0cxs0xhfwln66g"))))
26755 (build-system r-build-system)
26758 ("r-backports" ,r-backports)
26759 ("r-checkmate" ,r-checkmate)
26760 ("r-data-table" ,r-data-table)
26761 ("r-digest" ,r-digest)
26762 ("r-future-apply" ,r-future-apply)
26764 ("r-mlbench" ,r-mlbench)
26765 ("r-mlr3measures" ,r-mlr3measures)
26766 ("r-mlr3misc" ,r-mlr3misc)
26767 ("r-paradox" ,r-paradox)
26768 ("r-uuid" ,r-uuid)))
26769 (home-page "https://mlr3.mlr-org.com/")
26770 (synopsis "Machine Learning in R - Next Generation")
26771 (description "@code{mlr3} enables efficient, object-oriented programming
26772 on the building blocks of machine learning. It provides @code{R6} objects for
26773 tasks, learners, resamplings, and measures. The package is geared towards
26774 scalability and larger datasets by supporting parallelization and out-of-memory
26775 data-backends like databases. While @code{mlr3} focuses on the core
26776 computational operations, add-on packages provide additional functionality.")
26777 (license license:lgpl3)))
26779 (define-public r-mlr3learners
26781 (name "r-mlr3learners")
26785 (uri (cran-uri "mlr3learners" version))
26788 "1wxlpzz3hpkn77n4ag1v868dmp140j1pmrhynsv5xfgk9fg0w7ri"))))
26789 (build-system r-build-system)
26791 `(("r-data-table" ,r-data-table)
26793 ("r-mlr3misc" ,r-mlr3misc)
26794 ("r-paradox" ,r-paradox)
26796 (home-page "https://mlr3learners.mlr-org.com/")
26797 (synopsis "Recommended Learners for @code{mlr3}")
26798 (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba}
26799 with interfaces to essential machine learning packages on CRAN. This includes,
26800 but is not limited to: (penalized) linear and logistic regression, linear and
26801 quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support
26802 vector machines, and gradient boosting.")
26803 (license license:lgpl3)))
26805 (define-public r-bbotk
26812 (uri (cran-uri "bbotk" version))
26815 "0kbjbwwq1fdfpl4xzy08hz4qvhjjchvz58icxq0dlbsmdyqwhwv0"))))
26816 (properties `((upstream-name . "bbotk")))
26817 (build-system r-build-system)
26819 `(("r-checkmate" ,r-checkmate)
26820 ("r-data-table" ,r-data-table)
26822 ("r-mlr3misc" ,r-mlr3misc)
26823 ("r-paradox" ,r-paradox)
26826 `(("r-knitr" ,r-knitr)))
26827 (home-page "https://bbotk.mlr-org.com")
26828 (synopsis "Black-Box Optimization Toolkit")
26829 (description "This package provides a common framework for optimization of
26830 black-box functions for other packages, e.g. @code{mlr3}. It offers various
26831 optimization methods e.g. grid search, random search and generalized simulated
26833 (license license:lgpl3)))
26835 (define-public r-mlr3tuning
26837 (name "r-mlr3tuning")
26841 (uri (cran-uri "mlr3tuning" version))
26844 "0kxf9wl1jnwyrj2zfmiz12w2594407y44m0xxwp9b2lrwxk31wm7"))))
26845 (build-system r-build-system)
26847 `(("r-bbotk" ,r-bbotk)
26848 ("r-checkmate" ,r-checkmate)
26849 ("r-data-table" ,r-data-table)
26852 ("r-mlr3misc" ,r-mlr3misc)
26853 ("r-paradox" ,r-paradox)
26855 (home-page "https://mlr3tuning.mlr-org.com/")
26856 (synopsis "Tuning for @code{mlr3}")
26857 (description "@code{mlr3tuning} implements methods for hyperparameter
26858 tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various
26859 termination criteria can be set and combined. The class @code{AutoTuner} provides a
26860 convenient way to perform nested resampling in combination with @code{mlr3}.")
26861 (license license:lgpl3)))
26863 (define-public r-fontliberation
26865 (name "r-fontliberation")
26870 (uri (cran-uri "fontLiberation" version))
26873 "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc"))))
26875 `((upstream-name . "fontLiberation")))
26876 (build-system r-build-system)
26877 (home-page "https://cran.r-project.org/package=fontLiberation")
26878 (synopsis "Liberation fonts")
26880 "This package provides a placeholder for the Liberation fontset intended
26881 for the fontquiver package. This fontset covers the 12 combinations of
26882 families (sans, serif, mono) and faces (plain, bold, italic, bold italic)
26883 supported in R graphics devices.")
26884 (license license:silofl1.1)))
26886 (define-public r-fontbitstreamvera
26888 (name "r-fontbitstreamvera")
26893 (uri (cran-uri "fontBitstreamVera" version))
26896 "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j"))))
26898 `((upstream-name . "fontBitstreamVera")))
26899 (build-system r-build-system)
26900 (home-page "https://cran.r-project.org/package=fontBitstreamVera")
26901 (synopsis "Fonts for fontquiver")
26903 "This package is a placeholder for the Bitstream Vera font. It is
26904 intended for the fontquiver package.")
26906 (license:fsdg-compatible
26907 "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts"
26908 "The Font Software may be sold as part of a larger software package but
26909 no copy of one or more of the Font Software typefaces may be sold by
26912 (define-public r-fontquiver
26914 (name "r-fontquiver")
26919 (uri (cran-uri "fontquiver" version))
26922 "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm"))))
26923 (properties `((upstream-name . "fontquiver")))
26924 (build-system r-build-system)
26926 `(("r-fontbitstreamvera" ,r-fontbitstreamvera)
26927 ("r-fontliberation" ,r-fontliberation)))
26928 (home-page "https://cran.r-project.org/package=fontquiver")
26929 (synopsis "Set of installed fonts")
26931 "This package provides a set of fonts. This is useful when you want to
26932 avoid system fonts to make sure your outputs are reproducible.")
26933 (license license:gpl3)))
26935 (define-public r-freetypeharfbuzz
26937 (name "r-freetypeharfbuzz")
26942 (uri (cran-uri "freetypeharfbuzz" version))
26945 "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7"))))
26947 `((upstream-name . "freetypeharfbuzz")))
26948 (build-system r-build-system)
26951 (modify-phases %standard-phases
26952 (add-after 'unpack 'prepare-static-libraries
26953 (lambda* (#:key inputs #:allow-other-keys)
26954 (mkdir-p "src/target/include")
26955 (let ((freetype (assoc-ref inputs "static-freetype"))
26956 (harfbuzz (assoc-ref inputs "static-harfbuzz")))
26957 (substitute* "src/Makevars.in"
26958 (("include @MK_FILE@") "") ; do not build static libs
26959 (("^HB_STATIC_LIB =.*")
26960 (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n"))
26961 (("^FT_STATIC_LIB =.*")
26962 (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n")))
26963 (copy-recursively (string-append freetype "/include")
26964 "src/target/include")
26965 (copy-recursively (string-append harfbuzz "/include")
26966 "src/target/include")))))))
26968 `(("r-fontquiver" ,r-fontquiver)))
26969 ;; This may defeat the purpose of this package as our versions of freetype
26970 ;; and harfbuzz obviously differ from the tarballs offered by this
26971 ;; project. On the other hand, Guix arguably does a better job at
26972 ;; "ensur[ing] deterministic computation".
26974 `(("static-freetype"
26976 (inherit (static-package freetype))
26978 `(#:configure-flags
26979 (list "--enable-static=yes"
26984 "--without-harfbuzz")))))
26987 (inherit (static-package harfbuzz))
26989 `(#:tests? #false ; fail because shared library is disabled
26991 (list "--enable-static=yes"
26992 "--enable-shared=no"
26994 "--with-freetype=yes"
26997 "--without-fontconfig"
26998 "--without-glib")))))))
27001 (home-page "https://cran.r-project.org/package=freetypeharfbuzz")
27002 (synopsis "Deterministic computation of text box metrics")
27004 "Unlike other tools that dynamically link to the Cairo stack,
27005 freetypeharfbuzz is statically linked to specific versions of the FreeType and
27006 harfbuzz libraries. This ensures deterministic computation of text box
27007 extents for situations where reproducible results are crucial (for instance
27008 unit tests of graphics).")
27009 (license license:gpl3)))
27011 (define-public r-vdiffr
27018 (uri (cran-uri "vdiffr" version))
27021 "0i0xdr8dakbkkgrhp0zvlnv3rxhc8h5naqq416mr5zv9q8i4p8jc"))
27024 (delete-file "inst/htmlwidgets/lib/jquery.min.js")))))
27025 (properties `((upstream-name . "vdiffr")))
27026 (build-system r-build-system)
27029 (modify-phases %standard-phases
27030 (add-after 'unpack 'process-javascript
27031 (lambda* (#:key inputs #:allow-other-keys)
27032 (with-directory-excursion "inst/htmlwidgets/lib/"
27033 (let ((source (assoc-ref inputs "js-jquery"))
27034 (target "jquery.min.js"))
27035 (format #true "Processing ~a --> ~a~%"
27037 (invoke "esbuild" source "--minify"
27038 (string-append "--outfile=" target)))))))))
27040 `(("freetype" ,freetype)
27041 ("harfbuzz" ,harfbuzz)))
27044 ("r-devtools" ,r-devtools)
27045 ("r-diffobj" ,r-diffobj)
27046 ("r-fontquiver" ,r-fontquiver)
27047 ("r-freetypeharfbuzz" ,r-freetypeharfbuzz)
27048 ("r-gdtools" ,r-gdtools)
27050 ("r-htmltools" ,r-htmltools)
27051 ("r-htmlwidgets" ,r-htmlwidgets)
27052 ("r-purrr" ,r-purrr)
27055 ("r-rlang" ,r-rlang)
27056 ("r-shiny" ,r-shiny)
27057 ("r-testthat" ,r-testthat)
27058 ("r-usethis" ,r-usethis)
27059 ("r-xml2" ,r-xml2)))
27061 `(("esbuild" ,esbuild)
27065 (uri "https://code.jquery.com/jquery-1.12.4.js")
27068 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))))
27069 (home-page "https://github.com/r-lib/vdiffr")
27070 (synopsis "Visual regression testing and graphical diffing")
27072 "This package is an extension to the testthat package that makes it easy
27073 to add graphical unit tests. It provides a Shiny application to manage the
27075 (license license:gpl3)))
27077 (define-public r-highlight
27079 (name "r-highlight")
27084 (uri (cran-uri "highlight" version))
27087 "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf"))))
27088 (properties `((upstream-name . "highlight")))
27089 (build-system r-build-system)
27090 (home-page "https://github.com/hadley/highlight")
27091 (synopsis "Syntax highlighter for R code")
27093 "This package provides a syntax highlighter for R code based on the
27094 results of the R parser. It supports rendering in HTML and LaTeX markup. It
27095 includes a custom Sweave driver performing syntax highlighting of R code
27097 (license license:gpl3+)))
27099 (define-public r-clustree
27101 (name "r-clustree")
27106 (uri (cran-uri "clustree" version))
27109 "0lxydy2f83qqd5dhlp2l546jax759l43b29j6g82079yzg1szwsz"))))
27110 (properties `((upstream-name . "clustree")))
27111 (build-system r-build-system)
27113 `(("r-checkmate" ,r-checkmate)
27114 ("r-dplyr" ,r-dplyr)
27115 ("r-ggplot2" ,r-ggplot2)
27116 ("r-ggraph" ,r-ggraph)
27117 ("r-ggrepel" ,r-ggrepel)
27118 ("r-igraph" ,r-igraph)
27119 ("r-rlang" ,r-rlang)
27120 ("r-tidygraph" ,r-tidygraph)
27121 ("r-viridis" ,r-viridis)))
27123 `(("r-knitr" ,r-knitr)))
27124 (home-page "https://github.com/lazappi/clustree")
27125 (synopsis "Visualize clusterings at different resolutions")
27127 "Deciding what resolution to use can be a difficult question when
27128 approaching a clustering analysis. One way to approach this problem is to
27129 look at how samples move as the number of clusters increases. This package
27130 allows you to produce clustering trees, a visualization for interrogating
27131 clusterings as resolution increases.")
27132 (license license:gpl3)))
27134 (define-public r-textshaping
27136 (name "r-textshaping")
27141 (uri (cran-uri "textshaping" version))
27144 "053pbw45by96q62kjfnyc3d0ssar9svssrdqy6a09kdmdh75xdar"))))
27145 (properties `((upstream-name . "textshaping")))
27146 (build-system r-build-system)
27148 `(("freetype" ,freetype)
27149 ("fribidi" ,fribidi)
27150 ("harfbuzz" ,harfbuzz)
27153 `(("r-cpp11" ,r-cpp11)
27154 ("r-systemfonts" ,r-systemfonts)))
27156 `(("pkg-config" ,pkg-config)
27157 ("r-knitr" ,r-knitr)))
27158 (home-page "https://github.com/r-lib/textshaping")
27159 (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping")
27161 "This package provides access to the text shaping functionality in the
27162 HarfBuzz library and the bidirectional algorithm in the Fribidi library. This
27163 is a low-level utility package mainly for graphic devices that expands upon
27164 the font tool-set provided by the @code{systemfonts} package.")
27165 (license license:expat)))
27167 (define-public r-ragg
27174 (uri (cran-uri "ragg" version))
27177 "0443dhfi7bjfpap041vrnslw3ql3vpsxx18raz2w9nfdb7id8lsc"))))
27178 (properties `((upstream-name . "ragg")))
27179 (build-system r-build-system)
27181 `(("freetype" ,freetype)
27182 ("libjpeg" ,libjpeg-turbo)
27184 ("libtiff" ,libtiff)
27187 `(("r-systemfonts" ,r-systemfonts)
27188 ("r-textshaping" ,r-textshaping)))
27190 `(("pkg-config" ,pkg-config)))
27191 (home-page "https://ragg.r-lib.org")
27192 (synopsis "Graphic devices based on AGG")
27194 "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D
27195 drawing library. The ragg package provides a set of graphic devices based on
27196 AGG to use as alternative to the raster devices provided through the
27197 @code{grDevices} package.")
27198 (license license:expat)))
27200 (define-public r-downlit
27207 (uri (cran-uri "downlit" version))
27210 "0z4fz7c9kyd9v72wl3iqs2wxspi975d6b0rgjr9lvg8a18maa9z6"))))
27211 (properties `((upstream-name . "downlit")))
27212 (build-system r-build-system)
27214 `(("r-brio" ,r-brio)
27215 ("r-digest" ,r-digest)
27216 ("r-evaluate" ,r-evaluate)
27217 ("r-fansi" ,r-fansi)
27218 ("r-rlang" ,r-rlang)
27219 ("r-vctrs" ,r-vctrs)
27220 ("r-yaml" ,r-yaml)))
27221 (home-page "https://downlit.r-lib.org/")
27222 (synopsis "Syntax highlighting and automatic linking")
27224 "This package provides syntax highlighting of R code, specifically
27225 designed for the needs of RMarkdown packages like @code{pkgdown},
27226 @code{hugodown}, and @code{bookdown}. It includes linking of function calls
27227 to their documentation on the web, and automatic translation of ANSI escapes
27228 in output to the equivalent HTML.")
27229 (license license:expat)))
27231 (define-public r-pkgdown
27238 (uri (cran-uri "pkgdown" version))
27241 "1k31biyvxkv3xjc1yy3nzb9wfza3vbx97fv17nly5a6vlv7zqbs4"))))
27242 (properties `((upstream-name . "pkgdown")))
27243 (build-system r-build-system)
27244 (inputs `(("pandoc" ,pandoc)))
27246 `(("r-callr" ,r-callr)
27247 ("r-crayon" ,r-crayon)
27249 ("r-digest" ,r-digest)
27250 ("r-downlit" ,r-downlit)
27253 ("r-magrittr" ,r-magrittr)
27254 ("r-memoise" ,r-memoise)
27255 ("r-openssl" ,r-openssl)
27256 ("r-purrr" ,r-purrr)
27258 ("r-rematch2" ,r-rematch2)
27259 ("r-rlang" ,r-rlang)
27260 ("r-rmarkdown" ,r-rmarkdown)
27261 ("r-tibble" ,r-tibble)
27262 ("r-whisker" ,r-whisker)
27263 ("r-withr" ,r-withr)
27265 ("r-yaml" ,r-yaml)))
27267 `(("r-knitr" ,r-knitr)))
27268 (home-page "https://pkgdown.r-lib.org")
27269 (synopsis "Make static HTML documentation for an R package")
27271 "The goal of this package is to generate an attractive and useful website
27272 from a source package. @code{pkgdown} converts your documentation, vignettes,
27273 README file, and more to HTML making it easy to share information about your
27275 (license license:expat)))