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 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-shiny
1355 (url "https://github.com/rstudio/shiny")
1356 (commit (string-append "v" version))))
1357 (file-name (git-file-name name version))
1360 "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs"))))
1361 (build-system r-build-system)
1363 `(#:modules ((guix build r-build-system)
1364 (guix build minify-build-system)
1367 #:imported-modules (,@%r-build-system-modules
1368 (guix build minify-build-system))
1370 (modify-phases (@ (guix build r-build-system) %standard-phases)
1371 (add-after 'unpack 'replace-bundled-minified-JavaScript
1372 (lambda* (#:key inputs #:allow-other-keys)
1373 (let ((replace-file (lambda (old new)
1374 (format #t "replacing ~a with ~a\n" old new)
1376 (symlink new old))))
1377 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
1378 ;; contain just data. They are not minified code, so we don't
1380 (with-directory-excursion "inst/www/shared"
1381 (replace-file "bootstrap/shim/respond.min.js"
1382 (string-append (assoc-ref inputs "js-respond")
1383 "/share/javascript/respond.min.js"))
1384 (replace-file "bootstrap/shim/html5shiv.min.js"
1385 (string-append (assoc-ref inputs "js-html5shiv")
1386 "/share/javascript/html5shiv.min.js"))
1387 (replace-file "json2-min.js"
1388 (string-append (assoc-ref inputs "js-json2")
1389 "/share/javascript/json2-min.js"))
1390 (replace-file "strftime/strftime-min.js"
1391 (string-append (assoc-ref inputs "js-strftime")
1392 "/share/javascript/strftime.min.js"))
1393 (replace-file "highlight/highlight.pack.js"
1394 (string-append (assoc-ref inputs "js-highlight")
1395 "/share/javascript/highlight.min.js"))
1396 (replace-file "datatables/js/jquery.dataTables.min.js"
1397 (string-append (assoc-ref inputs "js-datatables")
1398 "/share/javascript/jquery.dataTables.min.js"))
1399 (replace-file "selectize/js/selectize.min.js"
1400 (string-append (assoc-ref inputs "js-selectize")
1401 "/share/javascript/selectize.min.js"))
1402 (replace-file "selectize/js/es5-shim.min.js"
1403 (string-append (assoc-ref inputs "js-es5-shim")
1404 "/share/javascript/es5-shim.min.js"))
1405 (for-each (match-lambda
1407 (delete-file target)
1408 (minify source #:target target)))
1409 '(("jqueryui/jquery-ui.js" .
1410 "jqueryui/jquery-ui.min.js")
1411 ("datepicker/js/bootstrap-datepicker.js" .
1412 "datepicker/js/bootstrap-datepicker.min.js")
1413 ("ionrangeslider/js/ion.rangeSlider.js" .
1414 "ionrangeslider/js/ion.rangeSlider.min.js")
1415 ("bootstrap/js/bootstrap.js" .
1416 "bootstrap/js/bootstrap.min.js")
1421 ("legacy/jquery.js" .
1422 "legacy/jquery.min.js")
1423 ("showdown/src/showdown.js" .
1424 "showdown/compressed/showdown.js")))))
1427 `(("r-crayon" ,r-crayon)
1428 ("r-digest" ,r-digest)
1429 ("r-fastmap" ,r-fastmap)
1430 ("r-htmltools" ,r-htmltools)
1431 ("r-httpuv" ,r-httpuv)
1432 ("r-jsonlite" ,r-jsonlite)
1433 ("r-later" ,r-later)
1435 ("r-promises" ,r-promises)
1437 ("r-rlang" ,r-rlang)
1438 ("r-sourcetools" ,r-sourcetools)
1439 ("r-withr" ,r-withr)
1440 ("r-xtable" ,r-xtable)))
1442 `(("js-datatables" ,js-datatables)
1443 ("js-html5shiv" ,js-html5shiv)
1444 ("js-json2" ,js-json2)
1445 ("js-respond" ,js-respond)
1446 ("js-selectize" ,js-selectize)
1447 ("js-strftime" ,js-strftime)
1448 ("js-highlight" ,js-highlight)
1449 ("js-es5-shim" ,js-es5-shim)))
1451 `(("uglify-js" ,uglify-js)
1452 ("gfortran" ,gfortran)))
1453 (home-page "http://shiny.rstudio.com")
1454 (synopsis "Easy interactive web applications with R")
1456 "Makes it incredibly easy to build interactive web applications
1457 with R. Automatic \"reactive\" binding between inputs and outputs and
1458 extensive prebuilt widgets make it possible to build beautiful,
1459 responsive, and powerful applications with minimal effort.")
1460 (license license:artistic2.0)))
1462 ;; This package includes minified JavaScript files. When upgrading please
1463 ;; check that there are no new minified JavaScript files.
1464 (define-public r-shinytree
1466 (name "r-shinytree")
1471 (uri (cran-uri "shinyTree" version))
1474 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1475 (modules '((guix build utils)))
1478 ;; Delete minified JavaScript
1479 (for-each delete-file
1480 '("inst/www/jsTree-3.3.7/libs/require.js"
1481 "inst/www/jsTree-3.3.7/libs/jquery.js"
1482 "inst/www/jsTree-3.3.7/jstree.min.js"))
1484 (properties `((upstream-name . "shinyTree")))
1485 (build-system r-build-system)
1487 `(#:modules ((guix build utils)
1488 (guix build r-build-system)
1492 (modify-phases %standard-phases
1493 (add-after 'unpack 'replace-minified-javascript
1494 (lambda* (#:key inputs #:allow-other-keys)
1495 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1496 (symlink (string-append (assoc-ref inputs "js-requirejs")
1497 "/share/javascript/require.min.js")
1502 `((,(assoc-ref inputs "js-jquery")
1506 (lambda (sources targets)
1507 (for-each (lambda (source target)
1508 (format #t "Processing ~a --> ~a~%"
1510 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1511 (call-with-output-file target
1513 (dump-port minified port)))))
1517 `(("r-htmlwidgets" ,r-htmlwidgets)
1518 ("r-jsonlite" ,r-jsonlite)
1519 ("r-promises" ,r-promises)
1520 ("r-shiny" ,r-shiny)
1521 ("r-stringr" ,r-stringr)))
1523 `(("js-requirejs" ,js-requirejs)))
1525 `(("uglify-js" ,uglify-js)
1529 (uri "https://code.jquery.com/jquery-3.3.1.js")
1532 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1533 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1534 (synopsis "jsTree bindings for Shiny")
1536 "This package exposes R bindings to jsTree, a JavaScript library that
1537 supports interactive trees, to enable rich, editable trees in Shiny.")
1538 (license license:expat)))
1540 (define-public r-shinydashboard
1542 (name "r-shinydashboard")
1546 (uri (cran-uri "shinydashboard" version))
1549 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1550 (build-system r-build-system)
1551 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1552 ;; Regenerate it from the included sources.
1554 `(#:modules ((guix build utils)
1555 (guix build r-build-system)
1558 (modify-phases %standard-phases
1559 (add-after 'unpack 'generate-minified-javascript
1561 (with-directory-excursion "inst/AdminLTE"
1562 (delete-file "app.min.js")
1563 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1564 (call-with-output-file "app.min.js"
1566 (dump-port minified port))))))))))
1568 `(("r-htmltools" ,r-htmltools)
1569 ("r-promises" ,r-promises)
1570 ("r-shiny" ,r-shiny)))
1572 `(("uglify-js" ,uglify-js)))
1573 (home-page "https://rstudio.github.io/shinydashboard/")
1574 (synopsis "Create dashboards with shiny")
1575 (description "This package provides an extension to the Shiny web
1576 application framework for R, making it easy to create attractive dashboards.")
1577 ;; This package includes software that was released under the Expat
1578 ;; license, but the whole package is released under GPL version 2 or
1580 (license license:gpl2+)))
1582 (define-public r-shinyfiles
1584 (name "r-shinyfiles")
1589 (uri (cran-uri "shinyFiles" version))
1591 (base32 "0rsijlx16vd74r7bd8s9zipy71kgpw19v9s85kxj5bmwc6njmbai"))))
1592 (properties `((upstream-name . "shinyFiles")))
1593 (build-system r-build-system)
1596 ("r-htmltools" ,r-htmltools)
1597 ("r-jsonlite" ,r-jsonlite)
1598 ("r-shiny" ,r-shiny)
1599 ("r-tibble" ,r-tibble)))
1600 (home-page "https://github.com/thomasp85/shinyFiles")
1601 (synopsis "Server-side file system viewer for Shiny")
1603 "This package provides functionality for client-side navigation of the
1604 server side file system in shiny apps. In case the app is running locally
1605 this gives the user direct access to the file system without the need to
1606 \"download\" files to a temporary location. Both file and folder selection as
1607 well as file saving is available.")
1608 (license license:gpl2+)))
1610 (define-public r-shinythemes
1612 (name "r-shinythemes")
1617 (uri (cran-uri "shinythemes" version))
1620 "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip"))))
1621 (properties `((upstream-name . "shinythemes")))
1622 (build-system r-build-system)
1623 (propagated-inputs `(("r-shiny" ,r-shiny)))
1624 (home-page "https://rstudio.github.io/shinythemes/")
1625 (synopsis "Themes for Shiny")
1627 "This package provides themes for use with Shiny. It includes several
1628 Bootstrap themes, which are packaged for use with Shiny applications.")
1629 ;; The package is released under version 3 of the GPL, but it includes
1630 ;; source files that are covered by the Expat license. It also includes
1631 ;; fonts under SIL or the ASL.
1632 (license (list license:gpl3 license:expat
1633 license:silofl1.1 license:asl2.0))))
1635 ;; The package sources include minified variants of d3.js and non-minified
1636 ;; source code of d3-jetpack.
1637 (define-public r-d3r
1644 (uri (cran-uri "d3r" version))
1647 "0kc82vvyfxhxvqfalngn36prn3sxdiinsx04rn99ha6zdc27zp5k"))))
1648 (build-system r-build-system)
1650 `(#:modules ((guix build utils)
1651 (guix build r-build-system)
1654 (modify-phases %standard-phases
1655 (add-after 'unpack 'process-javascript
1656 (lambda* (#:key inputs #:allow-other-keys)
1657 (with-directory-excursion "inst/www/d3/"
1661 `((,(assoc-ref inputs "d3.v3.js")
1662 "v3/dist/d3.min.js")
1663 (,(assoc-ref inputs "d3.v4.js")
1664 "v4/dist/d3.min.js")
1665 (,(assoc-ref inputs "d3.v5.js")
1666 "v5/dist/d3.min.js")
1667 (,(assoc-ref inputs "d3.v6.js")
1668 "v6/dist/d3.min.js"))))
1669 (lambda (sources targets)
1670 (for-each (lambda (source target)
1671 (format #t "Processing ~a --> ~a~%"
1673 (delete-file target)
1674 (invoke "esbuild" source "--minify"
1675 (string-append "--outfile=" target)))
1679 `(("r-dplyr" ,r-dplyr)
1680 ("r-htmltools" ,r-htmltools)
1681 ("r-rlang" ,r-rlang)
1682 ("r-tidyr" ,r-tidyr)))
1684 `(("esbuild" ,esbuild)
1688 (uri "https://d3js.org/d3.v3.js")
1691 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1695 (uri "https://d3js.org/d3.v4.js")
1698 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1702 (uri "https://d3js.org/d3.v5.js")
1705 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))
1709 (uri "https://d3js.org/d3.v6.js")
1712 "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9"))))))
1713 (home-page "https://github.com/timelyportfolio/d3r")
1714 (synopsis "d3.js utilities for R")
1716 "This package provides a suite of functions to help ease the use of the
1717 d3.js visualization library in R. These helpers include
1718 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1719 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1720 R objects into the JSON format that the d3.js library expects.")
1721 (license license:bsd-3)))
1723 ;; We use the latest commit here because the last release was in 2016 while
1724 ;; the latest commit was in 2018.
1725 (define-public r-sankeyd3
1726 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1730 (version (git-version "0.3.2" revision commit))
1735 (url "https://github.com/fbreitwieser/sankeyD3")
1737 (file-name (git-file-name name version))
1740 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1741 (build-system r-build-system)
1744 ("r-htmlwidgets" ,r-htmlwidgets)
1745 ("r-shiny" ,r-shiny)
1746 ("r-magrittr" ,r-magrittr)))
1747 (home-page "https://github.com/fbreitwieser/sankeyD3")
1748 (synopsis "Sankey network graphs from R")
1750 "This package provides an R library to generate Sankey network graphs
1751 in R and Shiny via the D3 visualization library.")
1752 ;; The R code is licensed under GPLv3+. It includes the non-minified
1753 ;; JavaScript source code of d3-sankey, which is released under the
1754 ;; 3-clause BSD license.
1755 (license (list license:gpl3+ license:bsd-3)))))
1757 (define-public r-wesanderson
1759 (name "r-wesanderson")
1764 (uri (cran-uri "wesanderson" version))
1767 "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
1768 (properties `((upstream-name . "wesanderson")))
1769 (build-system r-build-system)
1770 (home-page "https://github.com/karthik/wesanderson")
1771 (synopsis "Wes Anderson color palette generator")
1773 "This package provides color palettes that have been generated mostly
1774 from Wes Anderson movies.")
1775 (license license:expat)))
1777 (define-public r-tablerdash
1779 (name "r-tablerdash")
1784 (uri (cran-uri "tablerDash" version))
1787 "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm"))
1790 ;; Delete minified JavaScript
1791 (for-each delete-file
1792 '("inst/tablerDash-0.1.0/require.min.js"
1793 "inst/bootstrap-4.0.0/bootstrap.bundle.min.js"))
1795 (properties `((upstream-name . "tablerDash")))
1796 (build-system r-build-system)
1798 `(#:modules ((guix build utils)
1799 (guix build r-build-system)
1802 (modify-phases %standard-phases
1803 (add-after 'unpack 'process-javascript
1804 (lambda* (#:key inputs #:allow-other-keys)
1805 (with-directory-excursion "inst"
1809 `((,(assoc-ref inputs "js-requirejs")
1810 "tablerDash-0.1.0/require.min.js")
1811 (,(assoc-ref inputs "js-bootstrap")
1812 "bootstrap-4.0.0/bootstrap.bundle.min.js"))))
1813 (lambda (sources targets)
1814 (for-each (lambda (source target)
1815 (format #t "Processing ~a --> ~a~%"
1817 (invoke "esbuild" source "--minify"
1818 (string-append "--outfile=" target)))
1822 `(("r-htmltools" ,r-htmltools)
1823 ("r-knitr" ,r-knitr)
1824 ("r-shiny" ,r-shiny)))
1826 `(("esbuild" ,esbuild)
1830 (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js")
1833 "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds"))))
1837 (uri "https://raw.githubusercontent.com/twbs/bootstrap/\
1838 v4.0.0/dist/js/bootstrap.bundle.js")
1841 "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj"))))))
1842 (home-page "https://rinterface.github.io/tablerDash/")
1843 (synopsis "Tabler API for Shiny")
1845 "This package provides an R interface to the
1846 @url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap
1847 4 dashboard template. There are different layouts available such as a one
1848 page dashboard or a multi-page template, where the navigation menu is
1849 contained in the navigation bar.")
1850 (license license:gpl2+)))
1852 (define-public r-spelling
1859 (uri (cran-uri "spelling" version))
1862 "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl"))))
1863 (properties `((upstream-name . "spelling")))
1864 (build-system r-build-system)
1866 `(("r-commonmark" ,r-commonmark)
1867 ("r-hunspell" ,r-hunspell)
1868 ("r-knitr" ,r-knitr)
1869 ("r-xml2" ,r-xml2)))
1870 (home-page "https://docs.ropensci.org/spelling/")
1871 (synopsis "Tools for spell checking in R")
1873 "This is an R package for spell checking common document formats
1874 including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes
1875 utilities to automate checking of documentation and vignettes as a unit test
1876 during @code{R CMD check}. Both British and American English are supported
1877 out of the box and other languages can be added. In addition, packages may
1878 define a wordlist to allow custom terminology without having to abuse
1880 (license license:expat)))
1882 (define-public r-crosstalk
1884 (name "r-crosstalk")
1889 (uri (cran-uri "crosstalk" version))
1892 "1n6c6s7a6yxiwvva71x6bzcrim8xprl5s01fqiy61yq0y3vk8cpd"))))
1893 (build-system r-build-system)
1895 `(("r-htmltools" ,r-htmltools)
1896 ("r-jsonlite" ,r-jsonlite)
1897 ("r-lazyeval" ,r-lazyeval)
1899 (home-page "https://rstudio.github.io/crosstalk/")
1900 (synopsis "Inter-widget interactivity for HTML widgets")
1902 "This package provides building blocks for allowing HTML widgets to
1903 communicate with each other, with Shiny or without (i.e. static @code{.html}
1904 files). It currently supports linked brushing and filtering.")
1905 (license license:expat)))
1907 (define-public r-rook
1914 (uri (cran-uri "Rook" version))
1917 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1918 (properties `((upstream-name . "Rook")))
1919 (build-system r-build-system)
1920 (propagated-inputs `(("r-brew" ,r-brew)))
1921 (home-page "https://cran.r-project.org/web/packages/Rook")
1922 (synopsis "Web server interface for R")
1924 "This package contains the Rook specification and convenience software
1925 for building and running Rook applications. A Rook application is an R
1926 reference class object that implements a @code{call} method or an R closure
1927 that takes exactly one argument, an environment, and returns a list with three
1928 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1929 (license license:gpl2)))
1931 (define-public r-miniui
1938 (uri (cran-uri "miniUI" version))
1941 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1942 (properties `((upstream-name . "miniUI")))
1943 (build-system r-build-system)
1945 `(("r-htmltools" ,r-htmltools)
1946 ("r-shiny" ,r-shiny)))
1947 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1948 (synopsis "Shiny UI widgets for small screens")
1950 "This package provides UI widget and layout functions for writing Shiny apps that
1951 work well on small screens.")
1952 (license license:gpl3)))
1954 (define-public r-feather
1961 (uri (cran-uri "feather" version))
1964 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1965 (build-system r-build-system)
1969 ("r-tibble" ,r-tibble)))
1970 (home-page "https://github.com/wesm/feather")
1971 (synopsis "R Bindings to the Feather API")
1972 (description "Read and write feather files, a lightweight binary columnar
1973 data store designed for maximum speed.")
1974 (license license:asl2.0)))
1976 (define-public r-maps
1983 (uri (cran-uri "maps" version))
1986 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1987 (build-system r-build-system)
1988 (home-page "https://cran.r-project.org/web/packages/maps")
1989 (synopsis "Draw geographical maps")
1990 (description "This package provides an R module for display of maps.
1991 Projection code and larger maps are in separate packages (@code{mapproj} and
1993 (license license:gpl2)))
1995 (define-public r-mapproj
2002 (uri (cran-uri "mapproj" version))
2005 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
2006 (build-system r-build-system)
2007 (propagated-inputs `(("r-maps" ,r-maps)))
2008 (home-page "https://cran.r-project.org/web/packages/mapproj")
2009 (synopsis "Map projection in R")
2010 (description "This package converts latitude/longitude into projected
2012 (license (list license:gpl2 ; The R interface
2013 (license:non-copyleft ; The C code
2014 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
2015 "Lucent Public License Version 1.02")))))
2017 (define-public r-rgooglemaps
2019 (name "r-rgooglemaps")
2024 (uri (cran-uri "RgoogleMaps" version))
2027 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
2028 (properties `((upstream-name . "RgoogleMaps")))
2029 (build-system r-build-system)
2033 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
2034 (synopsis "Use Google Maps in R")
2035 (description "This package serves two purposes:
2037 @item Provide a comfortable R interface to query the Google server for static
2039 @item Use the map as a background image to overlay plots within R. This
2040 requires proper coordinate scaling.
2042 (license license:gpl2+)))
2044 (define-public r-geosphere
2046 (name "r-geosphere")
2051 (uri (cran-uri "geosphere" version))
2054 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
2055 (build-system r-build-system)
2056 (propagated-inputs `(("r-sp" ,r-sp)))
2057 (home-page "https://cran.r-project.org/web/packages/geosphere")
2058 (synopsis "Spherical trigonometry")
2059 (description "This package computes spherical trigonometry for geographic
2060 applications. That is, compute distances and related measures for angular
2061 (longitude/latitude) locations.")
2062 (license license:gpl3+)))
2064 (define-public r-jpeg
2071 (uri (cran-uri "jpeg" version))
2074 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
2075 (build-system r-build-system)
2076 (inputs `(("libjpeg" ,libjpeg-turbo)))
2077 (home-page "https://www.rforge.net/jpeg/")
2078 (synopsis "Read and write JPEG images with R")
2079 (description "This package provides a way to read, write and display
2080 bitmap images stored in the JPEG format with R. It can read and write both
2081 files and in-memory raw vectors.")
2082 (license license:gpl2+)))
2084 (define-public r-ggmap
2091 (uri (cran-uri "ggmap" version))
2094 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
2095 (build-system r-build-system)
2097 `(("r-bitops" ,r-bitops)
2098 ("r-digest" ,r-digest)
2099 ("r-dplyr" ,r-dplyr)
2100 ("r-ggplot2" ,r-ggplot2)
2104 ("r-magrittr" ,r-magrittr)
2107 ("r-purrr" ,r-purrr)
2108 ("r-rgooglemaps" ,r-rgooglemaps)
2109 ("r-rjson" ,r-rjson)
2110 ("r-scales" ,r-scales)
2111 ("r-stringr" ,r-stringr)
2112 ("r-tibble" ,r-tibble)
2113 ("r-tidyr" ,r-tidyr)))
2114 (home-page "https://github.com/dkahle/ggmap")
2115 (synopsis "Spatial visualization with ggplot2")
2116 (description "This package provides a collection of functions to visualize
2117 spatial data and models on top of static maps from various online sources (e.g
2118 Google Maps and Stamen Maps). It includes tools common to those tasks,
2119 including functions for geolocation and routing.")
2120 (license license:gpl2)))
2122 (define-public r-haven
2129 (uri (cran-uri "haven" version))
2132 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))))
2133 (build-system r-build-system)
2137 `(("r-knitr" ,r-knitr)))
2139 `(("r-forcats" ,r-forcats)
2142 ("r-rlang" ,r-rlang)
2143 ("r-readr" ,r-readr)
2144 ("r-tibble" ,r-tibble)
2145 ("r-tidyselect" ,r-tidyselect)
2146 ("r-vctrs" ,r-vctrs)))
2147 (home-page "https://haven.tidyverse.org")
2148 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
2150 "This package lets you mport foreign statistical formats into R via the
2151 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
2152 (license license:expat)))
2154 (define-public r-amap
2160 (uri (cran-uri "amap" version))
2163 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
2164 (build-system r-build-system)
2166 `(("gfortran" ,gfortran)))
2167 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
2168 (synopsis "Another multidimensional analysis package")
2169 (description "This package provides tools for clustering and principal
2170 component analysis (with robust methods, and parallelized functions).")
2171 (license license:gpl2+)))
2173 (define-public r-ape
2180 (uri (cran-uri "ape" version))
2183 "1r7fwyz30ippcl1ibqiv1xryf44x5crcks5kx19h146ffj76qcgh"))))
2184 (build-system r-build-system)
2186 `(("r-lattice" ,r-lattice)
2188 ("r-rcpp" ,r-rcpp)))
2189 (home-page "http://ape-package.ird.fr/")
2190 (synopsis "Analyses of phylogenetics and evolution")
2192 "This package provides functions for reading, writing, plotting, and
2193 manipulating phylogenetic trees, analyses of comparative data in a
2194 phylogenetic framework, ancestral character analyses, analyses of
2195 diversification and macroevolution, computing distances from DNA sequences,
2196 and several other tools.")
2197 (license license:gpl2+)))
2199 (define-public r-abbyyr
2206 (uri (cran-uri "abbyyR" version))
2209 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
2210 (properties `((upstream-name . "abbyyR")))
2211 (build-system r-build-system)
2213 `(("r-curl" ,r-curl)
2216 ("r-progress" ,r-progress)
2217 ("r-readr" ,r-readr)
2219 (home-page "https://github.com/soodoku/abbyyR")
2220 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
2222 "This package provides tools to get text from images of text using Abbyy
2223 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
2224 OCR images, barcodes, forms, documents with machine readable zones, e.g.
2225 passports and get the results in a variety of formats including plain text and
2226 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
2227 (license license:expat)))
2229 (define-public r-colorspace
2231 (name "r-colorspace")
2236 (uri (cran-uri "colorspace" version))
2238 (base32 "13h1hara0s6xn16bgkrbd0flszah1yiylwfwxwn2inqqk6pm6sjf"))))
2239 (build-system r-build-system)
2241 `(("r-knitr" ,r-knitr)))
2242 (home-page "https://cran.r-project.org/web/packages/colorspace")
2243 (synopsis "Color space manipulation")
2245 "This package carries out a mapping between assorted color spaces
2246 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
2247 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
2248 colors are provided.")
2249 (license license:bsd-3)))
2251 (define-public r-glue
2258 (uri (cran-uri "glue" version))
2261 "1bgpirdvjrf0da734clrixawvpdap4lpda4g89vais96589m8wwz"))))
2262 (build-system r-build-system)
2263 ;; knitr depends on glue, so we can't add knitr here to build the
2267 `(("r-knitr" ,r-knitr)))
2268 (home-page "https://github.com/tidyverse/glue")
2269 (synopsis "Interpreted string literals")
2271 "This package provides an implementation of interpreted string literals,
2272 inspired by Python's Literal String Interpolation (PEP-0498) and
2273 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
2274 (license license:expat)))
2276 (define-public r-pastecs
2282 (uri (cran-uri "pastecs" version))
2285 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
2286 (build-system r-build-system)
2288 `(("r-boot" ,r-boot)))
2289 (home-page "http://www.sciviews.org/pastecs")
2290 (synopsis "Analysis of space-time ecological series")
2292 "This package provides functions for regulation, decomposition and analysis
2293 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
2294 initiative to bring PASSTEC 2000 functionalities to R.")
2295 (license license:gpl2+)))
2297 (define-public r-partykit
2303 (uri (cran-uri "partykit" version))
2306 "15d5g89winndv8cy8jjjxy87fliafp5zyb8b58czrijwcmagg50l"))))
2307 (build-system r-build-system)
2309 `(("r-formula" ,r-formula)
2311 ("r-libcoin" ,r-libcoin)
2312 ("r-mvtnorm" ,r-mvtnorm)
2313 ("r-rpart" ,r-rpart)
2314 ("r-survival" ,r-survival)))
2315 (home-page "http://partykit.R-Forge.R-project.org/partykit")
2316 (synopsis "Toolkit for recursive partytioning")
2318 "This package provides a toolkit with infrastructure for representing,
2319 summarizing, and visualizing tree-structured regression and classification
2321 (license license:gpl2+)))
2323 (define-public r-plogr
2330 (uri (cran-uri "plogr" version))
2333 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
2334 (build-system r-build-system)
2335 (home-page "https://github.com/krlmlr/plogr")
2336 (synopsis "R bindings for the plog C++ logging library")
2338 "This package provides the header files for a stripped-down version of
2339 the plog header-only C++ logging library, and a method to log to R's standard
2341 (license license:expat)))
2343 (define-public r-pls
2350 (uri (cran-uri "pls" version))
2352 (base32 "0b3ls12w19wc4xkhnsgmb333y9lyzwq3syjc3k8zs1agnw59c7cg"))))
2353 (build-system r-build-system)
2354 (home-page "https://mevik.net/work/software/pls.html")
2355 (synopsis "Partial Least Squares and Principal Component Regression")
2357 "The pls package implements multivariate regression methods: Partial Least
2358 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
2359 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
2362 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
2363 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
2364 @item multi-response models (or @dfn{PLS2})
2365 @item flexible cross-validation
2366 @item Jackknife variance estimates of regression coefficients
2367 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
2368 (R)MSEP, R², and correlation loadings
2369 @item formula interface, modelled after @code{lm()}, with methods for predict,
2370 print, summary, plot, update, etc.
2371 @item extraction functions for coefficients, scores, and loadings
2372 @item MSEP, RMSEP, and R² estimates
2373 @item multiplicative scatter correction (@dfn{MSC})
2375 (license license:gpl2)))
2384 (uri (cran-uri "ps" version))
2386 (base32 "15pyz94b0z6ibrjp25np5nd4z20whnnr35wsavdgwmsmynba2qbl"))))
2387 (build-system r-build-system)
2388 (home-page "https://ps.r-lib.org")
2389 (synopsis "List, query, and manipulate system processes")
2391 "The ps package implements an API to list, query, and manipulate system
2392 processes. Most of its code is based on the @code{psutil} Python package.")
2393 (license license:bsd-3)))
2395 (define-public r-pkgbuild
2402 (uri (cran-uri "pkgbuild" version))
2404 (base32 "0qx920h2viwjg10va81nj0xja495d8ni6vcc25ggvzki6a6k069f"))))
2405 (build-system r-build-system)
2407 `(("r-callr" ,r-callr)
2409 ("r-crayon" ,r-crayon)
2411 ("r-prettyunits" ,r-prettyunits)
2413 ("r-rprojroot" ,r-rprojroot)
2414 ("r-withr" ,r-withr)))
2415 (home-page "https://github.com/r-pkgs/pkgbuild")
2416 (synopsis "Find tools needed to build R packages")
2418 "This package provides functions used to build R packages. It locates
2419 compilers needed to build R packages on various platforms and ensures the PATH
2420 is configured appropriately so R can use them.")
2421 (license license:gpl3)))
2423 (define-public r-pkgload
2430 (uri (cran-uri "pkgload" version))
2433 "03bv8xq4s6s7m34y1kjs99jzlb95vwrfi76mbnhmzcx2pc6ld78q"))))
2434 (build-system r-build-system)
2437 ("r-crayon" ,r-crayon)
2439 ("r-pkgbuild" ,r-pkgbuild)
2440 ("r-rlang" ,r-rlang)
2441 ("r-rprojroot" ,r-rprojroot)
2442 ("r-rstudioapi" ,r-rstudioapi)
2443 ("r-withr" ,r-withr)))
2444 (home-page "https://github.com/r-lib/pkgload")
2445 (synopsis "Simulate package installation and attach")
2447 "This package simulates the process of installing a package and then
2448 attaching it. This is a key part of the @code{devtools} package as it allows
2449 you to rapidly iterate while developing a package.")
2450 (license license:gpl3)))
2452 (define-public r-rcpp
2459 (uri (cran-uri "Rcpp" version))
2461 (base32 "04ph6lm36cmvz01ng53pvvf3jxvzsn9smyflkfc7l3q0pib4gwn9"))))
2462 (build-system r-build-system)
2463 (home-page "http://www.rcpp.org")
2464 (synopsis "Seamless R and C++ integration")
2466 "The Rcpp package provides R functions as well as C++ classes which offer
2467 a seamless integration of R and C++. Many R data types and objects can be
2468 mapped back and forth to C++ equivalents which facilitates both writing of new
2469 code as well as easier integration of third-party libraries. Documentation
2470 about Rcpp is provided by several vignettes included in this package, via the
2471 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
2472 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2473 @code{citation(\"Rcpp\")} for details on these last two.")
2474 (license license:gpl2+)))
2476 (define-public r-bindr
2483 (uri (cran-uri "bindr" version))
2486 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
2487 (build-system r-build-system)
2488 (home-page "https://github.com/krlmlr/bindr")
2489 (synopsis "Parametrized active bindings")
2491 "This package provides a simple interface for creating active bindings
2492 where the bound function accepts additional arguments.")
2493 (license license:expat)))
2495 (define-public r-bindrcpp
2502 (uri (cran-uri "bindrcpp" version))
2505 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
2506 (build-system r-build-system)
2508 `(("r-bindr" ,r-bindr)
2509 ("r-plogr" ,r-plogr)
2510 ("r-rcpp" ,r-rcpp)))
2511 (home-page "https://github.com/krlmlr/bindrcpp")
2512 (synopsis "Rcpp interface to active bindings")
2514 "This package provides an easy way to fill an environment with active
2515 bindings that call a C++ function.")
2516 (license license:expat)))
2518 (define-public r-bisquerna
2520 (name "r-bisquerna")
2524 (uri (cran-uri "BisqueRNA" version))
2527 "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
2528 (properties `((upstream-name . "BisqueRNA")))
2529 (build-system r-build-system)
2531 `(("r-biobase" ,r-biobase)
2532 ("r-limsolve" ,r-limsolve)))
2533 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
2534 (synopsis "Decomposition of bulk expression with single-cell sequencing")
2535 (description "This package provides tools to accurately estimate cell type
2536 abundances from heterogeneous bulk expression. A reference-based method
2537 utilizes single-cell information to generate a signature matrix and
2538 transformation of bulk expression for accurate regression based estimates.
2539 A marker-based method utilizes known cell-specific marker genes to measure
2540 relative abundances across samples.")
2541 (license license:gpl3)))
2543 (define-public r-auc
2550 (uri (cran-uri "AUC" version))
2553 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
2554 (properties `((upstream-name . "AUC")))
2555 (build-system r-build-system)
2556 (home-page "https://cran.r-project.org/web/packages/AUC")
2557 (synopsis "Compute the area under the curve of selected measures")
2559 "This package includes functions to compute the area under the curve of
2560 selected measures: the area under the sensitivity curve (AUSEC), the area
2561 under the specificity curve (AUSPC), the area under the accuracy
2562 curve (AUACC), and the area under the receiver operating characteristic
2563 curve (AUROC). The curves can also be visualized. Support for partial areas
2565 (license license:gpl2+)))
2567 (define-public r-calibrate
2569 (name "r-calibrate")
2574 (uri (cran-uri "calibrate" version))
2576 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
2577 (build-system r-build-system)
2579 `(("r-mass" ,r-mass)))
2580 (home-page "https://cran.r-project.org/web/packages/calibrate")
2581 (synopsis "Calibration of scatterplot and biplot axes")
2583 "This is a package for drawing calibrated scales with tick marks
2584 on (non-orthogonal) variable vectors in scatterplots and biplots.")
2585 (license license:gpl2)))
2587 (define-public r-shape
2594 (uri (cran-uri "shape" version))
2597 "17qqhjyfhxv9la07ykaslb50c8g4d0cgfypx4y91h9i2yjw7jjh9"))))
2598 (build-system r-build-system)
2599 (home-page "https://cran.r-project.org/web/packages/shape")
2600 (synopsis "Functions for plotting graphical shapes")
2602 "This package provides functions for plotting graphical shapes such as
2603 ellipses, circles, cylinders, arrows, ...")
2604 (license license:gpl3+)))
2606 (define-public r-globaloptions
2608 (name "r-globaloptions")
2613 (uri (cran-uri "GlobalOptions" version))
2615 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
2616 (properties `((upstream-name . "GlobalOptions")))
2617 (build-system r-build-system)
2619 `(("r-knitr" ,r-knitr)))
2620 (home-page "https://github.com/jokergoo/GlobalOptions")
2621 (synopsis "Generate functions to get or set global options")
2623 "This package provides more controls on the option values such as
2624 validation and filtering on the values, making options invisible or private.")
2625 (license license:gpl2+)))
2627 (define-public r-circlize
2634 (uri (cran-uri "circlize" version))
2637 "1x2j6a80bb4fly3dm91ias964s1gb1cmzj3lyh69ikwjaam0rdmk"))))
2638 (build-system r-build-system)
2640 `(("r-colorspace" ,r-colorspace)
2641 ("r-globaloptions" ,r-globaloptions)
2642 ("r-shape" ,r-shape)))
2644 `(("r-knitr" ,r-knitr)))
2645 (home-page "https://github.com/jokergoo/circlize")
2646 (synopsis "Circular visualization")
2648 "Circular layout is an efficient way to visualise huge amounts of
2649 information. This package provides an implementation of circular layout
2650 generation in R as well as an enhancement of available software. Its
2651 flexibility is based on the usage of low-level graphics functions such that
2652 self-defined high-level graphics can be easily implemented by users for
2653 specific purposes. Together with the seamless connection between the powerful
2654 computational and visual environment in R, it gives users more convenience and
2655 freedom to design figures for better understanding complex patterns behind
2656 multi-dimensional data.")
2657 (license license:gpl2+)))
2659 (define-public r-powerlaw
2666 (uri (cran-uri "poweRlaw" version))
2668 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2669 (properties `((upstream-name . "poweRlaw")))
2670 (build-system r-build-system)
2672 `(("r-pracma" ,r-pracma)))
2674 `(("r-knitr" ,r-knitr)))
2675 (home-page "https://github.com/csgillespie/poweRlaw")
2676 (synopsis "Tools for the analysis of heavy tailed distributions")
2678 "This package provides an implementation of maximum likelihood estimators
2679 for a variety of heavy tailed distributions, including both the discrete and
2680 continuous power law distributions. Additionally, a goodness-of-fit based
2681 approach is used to estimate the lower cut-off for the scaling region.")
2682 ;; Any of these GPL versions.
2683 (license (list license:gpl2 license:gpl3))))
2685 (define-public r-compare
2692 (uri (cran-uri "compare" version))
2695 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
2696 (build-system r-build-system)
2697 (home-page "https://cran.r-project.org/web/packages/compare")
2698 (synopsis "Comparing objects for differences")
2700 "This package provides functions to compare a model object to a
2701 comparison object. If the objects are not identical, the functions can be
2702 instructed to explore various modifications of the objects (e.g., sorting
2703 rows, dropping names) to see if the modified versions are identical.")
2704 (license license:gpl2+)))
2706 (define-public r-dendextend
2708 (name "r-dendextend")
2713 (uri (cran-uri "dendextend" version))
2716 "0n3qg76apgbqbvxv2yp5qwpy6nx03xmmc9mdfyq4dqblqhdld29p"))))
2717 (build-system r-build-system)
2719 `(("r-ggplot2" ,r-ggplot2)
2720 ("r-magrittr" ,r-magrittr)
2721 ("r-viridis" ,r-viridis)))
2723 `(("r-knitr" ,r-knitr)))
2724 (home-page "https://cran.r-project.org/web/packages/dendextend")
2725 (synopsis "Extending 'dendrogram' functionality in R")
2727 "This package offers a set of functions for extending @code{dendrogram}
2728 objects in R, letting you visualize and compare trees of hierarchical
2729 clusterings. You can adjust a tree's graphical parameters (the color, size,
2730 type, etc of its branches, nodes and labels) and visually and statistically
2731 compare different dendrograms to one another.")
2732 ;; Any of these versions
2733 (license (list license:gpl2 license:gpl3))))
2735 (define-public r-getoptlong
2737 (name "r-getoptlong")
2742 (uri (cran-uri "GetoptLong" version))
2745 "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc"))))
2746 (properties `((upstream-name . "GetoptLong")))
2747 (build-system r-build-system)
2751 `(("r-crayon" ,r-crayon)
2752 ("r-globaloptions" ,r-globaloptions)
2753 ("r-rjson" ,r-rjson)))
2755 `(("r-knitr" ,r-knitr)))
2756 (home-page "https://github.com/jokergoo/GetoptLong")
2757 (synopsis "Parsing command-line arguments and variable interpolation")
2759 "This is yet another command-line argument parser which wraps the
2760 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
2761 use in R. It also provides a simple way for variable interpolation in R.")
2762 (license license:gpl2+)))
2764 (define-public r-fastmatch
2766 (name "r-fastmatch")
2771 (uri (cran-uri "fastmatch" version))
2774 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
2775 (build-system r-build-system)
2776 (home-page "https://www.rforge.net/fastmatch")
2777 (synopsis "Fast match function")
2779 "This package provides a fast @code{match} replacement for cases that
2780 require repeated look-ups. It is slightly faster that R's built-in
2781 @code{match} function on first match against a table, but extremely fast on
2782 any subsequent lookup as it keeps the hash table in memory.")
2783 (license license:gpl2)))
2792 (uri (cran-uri "ff" version))
2795 "1rfj2ff5cxzdp9nvfnbgmswc1jvxz5vkxqgpv6gprwk32a0z3v12"))))
2796 (build-system r-build-system)
2797 (propagated-inputs `(("r-bit" ,r-bit)))
2798 (home-page "http://ff.r-forge.r-project.org/")
2799 (synopsis "Memory-efficient storage of large data on disk and access functions")
2801 "This package provides data structures that are stored on disk but
2802 behave (almost) as if they were in RAM by transparently mapping only a section
2804 ;; error Architecture not supported.
2805 (supported-systems (delete "aarch64-linux" %supported-systems))
2806 (license license:gpl2)))
2808 (define-public r-ffbase
2815 (uri (cran-uri "ffbase" version))
2818 "0knl0vnh8w4q3ry24gp4fd55ipnaj9hb1rwm31fs119kgmh3gd8x"))))
2819 (build-system r-build-system)
2822 ("r-fastmatch" ,r-fastmatch)
2824 (home-page "https://github.com/edwindj/ffbase")
2825 (synopsis "Basic statistical functions for package 'ff'")
2827 "This package extends the out of memory vectors of @code{ff} with
2828 statistical functions and other utilities to ease their usage.")
2829 (license license:gpl3)))
2831 (define-public r-prettyunits
2833 (name "r-prettyunits")
2838 (uri (cran-uri "prettyunits" version))
2841 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
2842 (build-system r-build-system)
2843 (home-page "https://github.com/gaborcsardi/prettyunits")
2844 (synopsis "Pretty, human readable formatting of quantities")
2846 "This package provides tools for pretty, human readable formatting of
2848 (license license:expat)))
2850 (define-public r-reshape
2857 (uri (cran-uri "reshape" version))
2860 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2861 (build-system r-build-system)
2863 `(("r-plyr" ,r-plyr)
2864 ("r-rcpp" ,r-rcpp)))
2865 (home-page "http://had.co.nz/reshape")
2866 (synopsis "Flexibly reshape data")
2868 "Flexibly restructure and aggregate data using just two functions:
2869 @code{melt} and @code{cast}. This package provides them.")
2870 (license license:expat)))
2872 (define-public r-restrserve
2874 (name "r-restrserve")
2879 (uri (cran-uri "RestRserve" version))
2881 (base32 "1486hrzj5q5w4nbrsbqlv7vv20ly01y90qc2vygl5syzwvyjd422"))))
2882 (build-system r-build-system)
2884 `(("r-checkmate" ,r-checkmate)
2885 ("r-jsonlite" ,r-jsonlite)
2889 ("r-rserve" ,r-rserve)
2890 ("r-uuid" ,r-uuid)))
2892 `(("r-knitr" ,r-knitr)))
2893 (home-page "https://restrserve.org")
2894 (synopsis "R web API framework")
2896 "RestRserve is an R web API framework for building high-performance AND
2897 robust microservices and app backends. With Rserve backend on UNIX-like
2898 systems it is parallel by design. It will handle incoming requests in
2899 parallel - each request in a separate fork.")
2900 (license license:gpl2+)))
2902 (define-public r-progress
2909 (uri (cran-uri "progress" version))
2912 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2913 (build-system r-build-system)
2915 `(("r-crayon" ,r-crayon)
2917 ("r-prettyunits" ,r-prettyunits)
2919 (home-page "https://github.com/gaborcsardi/progress")
2920 (synopsis "Terminal progress bars")
2922 "This package provides configurable progress bars. They may include
2923 percentage, elapsed time, and/or the estimated completion time. They work in
2924 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2925 package also provides a C++ API, that works with or without Rcpp.")
2926 (license license:expat)))
2928 (define-public r-ggally
2935 (uri (cran-uri "GGally" version))
2938 "0lvcvlc8p2cii7rqx7m81f7cv3kk9mlf7cbbgv7l75g7ljw8dyvz"))))
2939 (properties `((upstream-name . "GGally")))
2940 (build-system r-build-system)
2942 `(("openssl" ,openssl)))
2944 `(("r-dplyr" ,r-dplyr)
2945 ("r-forcats" ,r-forcats)
2946 ("r-ggplot2" ,r-ggplot2)
2947 ("r-gtable" ,r-gtable)
2948 ("r-lifecycle" ,r-lifecycle)
2950 ("r-progress" ,r-progress)
2951 ("r-rcolorbrewer" ,r-rcolorbrewer)
2952 ("r-reshape" ,r-reshape)
2953 ("r-rlang" ,r-rlang)
2954 ("r-scales" ,r-scales)
2955 ("r-tidyr" ,r-tidyr)))
2956 (home-page "https://ggobi.github.io/ggally")
2957 (synopsis "Extension to ggplot2")
2959 "The R package ggplot2 is a plotting system based on the grammar of
2960 graphics. GGally extends ggplot2 by adding several functions to reduce the
2961 complexity of combining geometric objects with transformed data. Some of
2962 these functions include a pairwise plot matrix, a two group pairwise plot
2963 matrix, a parallel coordinates plot, a survival plot, and several functions to
2965 (license license:gpl2+)))
2967 (define-public r-proxy
2974 (uri (cran-uri "proxy" version))
2977 "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
2978 (build-system r-build-system)
2979 (home-page "https://cran.r-project.org/web/packages/proxy")
2980 (synopsis "Distance and similarity measures")
2982 "This package provides an extensible framework for the efficient
2983 calculation of auto- and cross-proximities, along with implementations of the
2984 most popular ones.")
2985 (license license:gpl2)))
2994 (uri (cran-uri "sp" version))
2996 (base32 "1nh9izsnszzm5kbq461w8bi0yh7fqzb74b2zmpg5qis0slbb5vkb"))))
2997 (build-system r-build-system)
2999 `(("r-lattice" ,r-lattice)))
3000 (home-page "https://cran.r-project.org/web/packages/sp")
3001 (synopsis "Classes and methods for spatial data")
3003 "This package provides classes and methods for spatial data; the classes
3004 document where the spatial location information resides, for 2D or 3D data.
3005 Utility functions are provided, e.g. for plotting data as maps, spatial
3006 selection, as well as methods for retrieving coordinates, for subsetting,
3007 print, summary, etc.")
3008 (license license:gpl2+)))
3010 (define-public r-laplacesdemon
3012 (name "r-laplacesdemon")
3017 (uri (cran-uri "LaplacesDemon" version))
3019 (base32 "1nv1kx86cg8f2s8q15pzskc0lg94bb250p0fhybrx5sjqv1s2lj1"))))
3020 (properties `((upstream-name . "LaplacesDemon")))
3021 (build-system r-build-system)
3022 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
3023 (synopsis "Complete environment for Bayesian inference")
3025 "This package provides a complete environment for Bayesian inference using
3026 a variety of different samplers.")
3027 (license license:expat)))
3029 (define-public r-rmtstat
3036 (uri (cran-uri "RMTstat" version))
3039 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
3040 (properties `((upstream-name . "RMTstat")))
3041 (build-system r-build-system)
3042 (home-page "https://cran.r-project.org/web/packages/RMTstat")
3043 (synopsis "Distributions, statistics and tests derived from random matrix theory")
3045 "This package provides functions for working with the Tracy-Widom laws
3046 and other distributions related to the eigenvalues of large Wishart
3048 (license license:bsd-3)))
3050 (define-public r-rmpi
3056 (uri (cran-uri "Rmpi" version))
3059 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
3060 (properties `((upstream-name . "Rmpi")))
3061 (build-system r-build-system)
3063 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
3064 #:phases (modify-phases %standard-phases
3065 (add-before 'install 'mpi-setup
3068 `(("openmpi" ,openmpi)))
3070 `(("pkg-config" ,pkg-config)))
3071 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
3072 (synopsis "R interface to message-passing interface (MPI)")
3074 "This package provides an interface (wrapper) to MPI APIs. It also
3075 provides an interactive R manager and worker environment.")
3076 (license license:gpl2+)))
3078 (define-public r-lmoments
3085 (uri (cran-uri "Lmoments" version))
3088 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
3089 (properties `((upstream-name . "Lmoments")))
3090 (build-system r-build-system)
3092 `(("r-rcpp" ,r-rcpp)
3093 ("r-rcpparmadillo" ,r-rcpparmadillo)))
3094 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
3095 (synopsis "L-moments and quantile mixtures")
3097 "This package contains functions to estimate L-moments and trimmed
3098 L-moments from the data. It also contains functions to estimate the
3099 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
3100 quantile mixture from L-moments and trimmed L-moments.")
3101 (license license:gpl2)))
3103 (define-public r-distillery
3105 (name "r-distillery")
3110 (uri (cran-uri "distillery" version))
3113 "10nhh9p0hp294pp4aav0y0zsmir2qbn05sf3k52rmzmm36q2kc8y"))))
3114 (build-system r-build-system)
3115 (home-page "https://ral.ucar.edu/staff/ericg/")
3116 (synopsis "Functions for confidence intervals and object information")
3118 "This package provides some very simple method functions for confidence
3119 interval calculation and to distill pertinent information from a potentially
3120 complex object; primarily used in common with the packages extRemes and
3122 (license license:gpl2+)))
3124 (define-public r-etrunct
3130 (uri (cran-uri "etrunct" version))
3133 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr"))))
3134 (properties `((upstream-name . "etrunct")))
3135 (build-system r-build-system)
3136 (home-page "https://cran.r-project.org/web/packages/etrunct")
3137 (synopsis "Computes moments of univariate truncated T distribution")
3138 (description "This package computes moments of univariate truncated
3139 T distribution. There is only one exported function, @code{e_trunct},
3140 which should be seen for details.")
3141 (license license:expat)))
3143 (define-public r-extremes
3150 (uri (cran-uri "extRemes" version))
3153 "1b69r3mzl6hp3g3rqxyc77m8r40jyq7c2d87q85af7xqkn6hnxid"))))
3154 (properties `((upstream-name . "extRemes")))
3155 (build-system r-build-system)
3157 `(("r-distillery" ,r-distillery)
3158 ("r-lmoments" ,r-lmoments)))
3159 (home-page "https://www.assessment.ucar.edu/toolkit/")
3160 (synopsis "Extreme value analysis")
3162 "ExtRemes is a suite of functions for carrying out analyses on the
3163 extreme values of a process of interest; be they block maxima over long blocks
3164 or excesses over a high threshold.")
3165 (license license:gpl2+)))
3167 (define-public r-lmtest
3174 (uri (cran-uri "lmtest" version))
3177 "0sr19bmw2cpagfvwg772m79wvl1i2hww1xfr69bzr3rr8pm2r8ij"))))
3178 (build-system r-build-system)
3180 `(("r-zoo" ,r-zoo)))
3182 `(("gfortran" ,gfortran)))
3183 (home-page "https://cran.r-project.org/web/packages/lmtest")
3184 (synopsis "Testing linear regression models")
3186 "This package provides a collection of tests, data sets, and examples for
3187 diagnostic checking in linear regression models. Furthermore, some generic
3188 tools for inference in parametric models are provided.")
3189 ;; Either version is okay
3190 (license (list license:gpl2 license:gpl3))))
3192 (define-public r-idr
3198 (uri (cran-uri "idr" version))
3201 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
3202 (build-system r-build-system)
3203 (home-page "https://cran.r-project.org/web/packages/idr/")
3204 (synopsis "Irreproducible discovery rate")
3206 "This is a package for estimating the copula mixture model and plotting
3207 correspondence curves in \"Measuring reproducibility of high-throughput
3208 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
3209 by Li, Brown, Huang, and Bickel")
3210 (license license:gpl2+)))
3212 (define-public r-inline
3218 (uri (cran-uri "inline" version))
3221 "1wslsn60q959yrr27cwanba43qlpfaxzdli46i9dc26lxfr5fa3r"))))
3222 (build-system r-build-system)
3223 (home-page "https://cran.r-project.org/web/packages/inline")
3224 (synopsis "Functions to inline C, C++, Fortran function calls from R")
3226 "This package provides functionality to dynamically define R functions
3227 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
3228 @code{.Call} calling conventions.")
3229 ;; Any version of the LGPL.
3230 (license license:lgpl3+)))
3232 (define-public r-inum
3238 (uri (cran-uri "inum" version))
3241 "1sz11b4vlpskhmq9vvc1jix63a5g7lij6368w8qbnkjmjd97k7i4"))))
3242 (build-system r-build-system)
3244 `(("r-libcoin" ,r-libcoin)))
3245 (home-page "https://cran.r-project.org/web/packages/inum/")
3246 (synopsis "Interval and enum-type representation of vectors")
3248 "This package provides an enum-type representation of vectors and
3249 representation of intervals, including a method of coercing variables
3251 (license license:gpl2)))
3252 (define-public r-invgamma
3258 (uri (cran-uri "invgamma" version))
3261 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a"))))
3262 (properties `((upstream-name . "invgamma")))
3263 (build-system r-build-system)
3264 (home-page "https://github.com/dkahle/invgamma")
3265 (synopsis "Inverse gamma distribution")
3266 (description "This package provides a light weight implementation of the
3267 standard distribution functions for the inverse gamma distribution, wrapping
3268 those for the gamma distribution in the @code{stats} package.")
3269 (license license:gpl2)))
3271 (define-public r-bdsmatrix
3273 (name "r-bdsmatrix")
3278 (uri (cran-uri "bdsmatrix" version))
3281 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
3282 (properties `((upstream-name . "bdsmatrix")))
3283 (build-system r-build-system)
3284 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
3285 (synopsis "Routines for block diagonal symmetric matrices")
3287 "This package provides procedures to work with block diagonal symmetric
3288 matrices, a special case of sparse matrices.")
3289 (license license:lgpl2.0)))
3291 (define-public r-bbmle
3294 (version "1.0.23.1")
3298 (uri (cran-uri "bbmle" version))
3301 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
3302 (build-system r-build-system)
3304 `(("r-bdsmatrix" ,r-bdsmatrix)
3305 ("r-lattice" ,r-lattice)
3307 ("r-matrix" ,r-matrix)
3308 ("r-mvtnorm" ,r-mvtnorm)
3309 ("r-numderiv" ,r-numderiv)))
3310 (home-page "https://cran.r-project.org/web/packages/bbmle")
3311 (synopsis "Tools for General Maximum Likelihood Estimation")
3313 "This package provides methods and functions for fitting maximum
3314 likelihood models in R. This package modifies and extends the @code{mle}
3315 classes in the @code{stats4} package.")
3316 ;; Any version of the GPL
3317 (license license:gpl2+)))
3319 (define-public r-emdbook
3326 (uri (cran-uri "emdbook" version))
3329 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
3330 (build-system r-build-system)
3332 `(("r-bbmle" ,r-bbmle)
3334 ("r-lattice" ,r-lattice)
3336 ("r-plyr" ,r-plyr)))
3337 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
3338 (synopsis "Support functions and data for \"Ecological Models and Data\"")
3340 "This package provides auxiliary functions and data sets for \"Ecological
3341 Models and Data\", a book presenting maximum likelihood estimation and related
3342 topics for ecologists (ISBN 978-0-691-12522-0).")
3344 (license (list license:gpl2 license:gpl3))))
3346 (define-public r-lpsolve
3353 (uri (cran-uri "lpSolve" version))
3356 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
3357 (properties `((upstream-name . "lpSolve")))
3358 (build-system r-build-system)
3359 (home-page "https://cran.r-project.org/web/packages/lpSolve")
3360 (synopsis "R interface to Lp_solve to solve linear/integer programs")
3362 "Lp_solve is software for solving linear, integer and mixed integer
3363 programs. This implementation supplies a \"wrapper\" function in C and some R
3364 functions that solve general linear/integer problems, assignment problems, and
3365 transportation problems.")
3366 (license license:lgpl2.0)))
3368 (define-public r-limsolve
3375 (uri (cran-uri "limSolve" version))
3378 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
3379 (properties `((upstream-name . "limSolve")))
3380 (build-system r-build-system)
3382 `(("r-lpsolve" ,r-lpsolve)
3384 ("r-quadprog" ,r-quadprog)))
3385 (native-inputs `(("gfortran" ,gfortran)))
3386 (home-page "https://cran.r-project.org/web/packages/limSolve")
3387 (synopsis "Solving linear inverse models")
3389 "This package provides functions that:
3392 @item find the minimum/maximum of a linear or quadratic function,
3393 @item sample an underdetermined or overdetermined system,
3394 @item solve a linear system Ax=B for the unknown x.
3397 It includes banded and tridiagonal linear systems. The package calls Fortran
3398 functions from LINPACK.")
3400 (license (list license:gpl2+ license:gpl3+))))
3402 (define-public r-fitdistrplus
3404 (name "r-fitdistrplus")
3409 (uri (cran-uri "fitdistrplus" version))
3412 "1pjnqx0j26dai2fa4ip56wspmfsrcm9dpmxkg15y9623w5b58vbp"))))
3413 (build-system r-build-system)
3415 `(("r-mass" ,r-mass)
3416 ("r-survival" ,r-survival)))
3418 `(("r-knitr" ,r-knitr)))
3419 (home-page "http://riskassessment.r-forge.r-project.org")
3420 (synopsis "Fitting a parametric distribution from data")
3422 "This package extends the @code{fitdistr} function of the MASS package
3423 with several functions to help the fit of a parametric distribution to
3424 non-censored or censored data. Censored data may contain left-censored,
3425 right-censored and interval-censored values, with several lower and upper
3426 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
3427 provides moment matching (MME), quantile matching (QME) and maximum
3428 goodness-of-fit estimation (MGE) methods (available only for non-censored
3429 data). Weighted versions of MLE, MME and QME are available.")
3430 (license license:gpl2+)))
3432 (define-public r-energy
3439 (uri (cran-uri "energy" version))
3442 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
3443 (build-system r-build-system)
3445 `(("r-boot" ,r-boot)
3446 ("r-rcpp" ,r-rcpp)))
3447 (home-page "https://cran.r-project.org/web/packages/energy")
3448 (synopsis "Multivariate inference via the energy of data")
3450 "This package provides e-statistics (energy) tests and statistics for
3451 multivariate and univariate inference, including distance correlation,
3452 one-sample, two-sample, and multi-sample tests for comparing multivariate
3453 distributions, are implemented. Measuring and testing multivariate
3454 independence based on distance correlation, partial distance correlation,
3455 multivariate goodness-of-fit tests, clustering based on energy distance,
3456 testing for multivariate normality, distance components (disco) for
3457 non-parametric analysis of structured data, and other energy
3458 statistics/methods are implemented.")
3459 (license license:gpl2+)))
3461 (define-public r-suppdists
3463 (name "r-suppdists")
3468 (uri (cran-uri "SuppDists" version))
3471 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
3472 (properties `((upstream-name . "SuppDists")))
3473 (build-system r-build-system)
3474 (home-page "https://cran.r-project.org/web/packages/SuppDists")
3475 (synopsis "Supplementary distributions")
3477 "This package provides ten distributions supplementing those built into
3478 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
3479 Spearman's rho, maximum F ratio, the Pearson product moment correlation
3480 coefficient, Johnson distributions, normal scores and generalized
3481 hypergeometric distributions. In addition two random number generators of
3482 George Marsaglia are included.")
3483 (license license:gpl2+)))
3485 (define-public r-ksamples
3492 (uri (cran-uri "kSamples" version))
3495 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
3496 (properties `((upstream-name . "kSamples")))
3497 (build-system r-build-system)
3499 `(("r-suppdists" ,r-suppdists)))
3500 (home-page "https://cran.r-project.org/web/packages/kSamples")
3501 (synopsis "K-Sample rank tests and their combinations")
3503 "This package provides tools to compares k samples using the
3504 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
3505 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
3506 test. It computes asymptotic, simulated or (limited) exact P-values, all
3507 valid under randomization, with or without ties, or conditionally under random
3508 sampling from populations, given the observed tie pattern. Except for Steel's
3509 test and the JT test it also combines these tests across several blocks of
3511 (license license:gpl2+)))
3513 (define-public r-cvst
3520 (uri (cran-uri "CVST" version))
3523 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
3524 (properties `((upstream-name . "CVST")))
3525 (build-system r-build-system)
3527 `(("r-kernlab" ,r-kernlab)
3528 ("r-matrix" ,r-matrix)))
3529 (home-page "https://cran.r-project.org/web/packages/CVST")
3530 (synopsis "Fast cross-validation via sequential testing")
3532 "This package implements the fast cross-validation via sequential
3533 testing (CVST) procedure. CVST is an improved cross-validation procedure
3534 which uses non-parametric testing coupled with sequential analysis to
3535 determine the best parameter set on linearly increasing subsets of the data.
3536 Additionally to the CVST the package contains an implementation of the
3537 ordinary k-fold cross-validation with a flexible and powerful set of helper
3538 objects and methods to handle the overall model selection process. The
3539 implementations of the Cochran's Q test with permutations and the sequential
3540 testing framework of Wald are generic and can therefore also be used in other
3542 (license license:gpl2+)))
3544 (define-public r-squarem
3551 (uri (cran-uri "SQUAREM" version))
3554 "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6"))))
3555 (properties `((upstream-name . "SQUAREM")))
3556 (build-system r-build-system)
3557 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
3558 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
3560 "This package provides algorithms for accelerating the convergence of
3561 slow, monotone sequences from smooth, contraction mapping such as the EM
3562 algorithm. It can be used to accelerate any smooth, linearly convergent
3563 acceleration scheme. A tutorial style introduction to this package is
3564 available in a vignette.")
3565 (license license:gpl2+)))
3567 (define-public r-lava
3574 (uri (cran-uri "lava" version))
3577 "1yiz8y3jhxkszgz9m9fialp9r27hy97xh0imfvs8ziv7dk43y93d"))))
3578 (build-system r-build-system)
3580 `(("r-numderiv" ,r-numderiv)
3581 ("r-squarem" ,r-squarem)
3582 ("r-survival" ,r-survival)))
3584 `(("r-knitr" ,r-knitr)))
3585 (home-page "https://github.com/kkholst/lava")
3586 (synopsis "Latent variable models")
3588 "This package provides tools for the estimation and simulation of latent
3590 (license license:gpl3)))
3592 (define-public r-drr
3599 (uri (cran-uri "DRR" version))
3602 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3603 (properties `((upstream-name . "DRR")))
3604 (build-system r-build-system)
3606 `(("r-cvst" ,r-cvst)
3607 ("r-kernlab" ,r-kernlab)
3608 ("r-matrix" ,r-matrix)))
3609 (home-page "https://cran.r-project.org/web/packages/DRR")
3610 (synopsis "Dimensionality reduction via regression")
3612 "This package provides an implementation of dimensionality reduction via
3613 regression using Kernel Ridge Regression.")
3614 (license license:gpl3)))
3616 (define-public r-prodlim
3619 (version "2019.11.13")
3623 (uri (cran-uri "prodlim" version))
3626 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3627 (build-system r-build-system)
3629 `(("r-kernsmooth" ,r-kernsmooth)
3632 ("r-survival" ,r-survival)))
3633 (home-page "https://cran.r-project.org/web/packages/prodlim")
3634 (synopsis "Product-limit estimation for censored event history analysis")
3636 "This package provides a fast and user-friendly implementation of
3637 nonparametric estimators for censored event history (survival) analysis with
3638 the Kaplan-Meier and Aalen-Johansen methods.")
3639 (license license:gpl2+)))
3641 (define-public r-dimred
3648 (uri (cran-uri "dimRed" version))
3651 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3652 (properties `((upstream-name . "dimRed")))
3653 (build-system r-build-system)
3656 ("r-magrittr" ,r-magrittr)))
3657 (home-page "https://github.com/gdkrmr/dimRed")
3658 (synopsis "Framework for dimensionality reduction")
3660 "This package provides a collection of dimensionality reduction
3661 techniques from R packages and provides a common interface for calling the
3663 (license license:gpl3)))
3665 (define-public r-timedate
3668 (version "3043.102")
3672 (uri (cran-uri "timeDate" version))
3675 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
3676 (properties `((upstream-name . "timeDate")))
3677 (build-system r-build-system)
3678 (home-page "https://www.rmetrics.org")
3679 (synopsis "Chronological and calendar objects")
3681 "This package provides an environment for teaching \"Financial
3682 Engineering and Computational Finance\" and for managing chronological and
3684 (license license:gpl2+)))
3686 (define-public r-magic
3693 (uri (cran-uri "magic" version))
3696 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
3697 (build-system r-build-system)
3699 `(("r-abind" ,r-abind)))
3700 (home-page "https://github.com/RobinHankin/magic.git")
3701 (synopsis "Create and investigate magic squares")
3703 "This package provides a collection of efficient, vectorized algorithms
3704 for the creation and investigation of magic squares and hypercubes, including
3705 a variety of functions for the manipulation and analysis of arbitrarily
3706 dimensioned arrays.")
3707 (license license:gpl2)))
3709 (define-public r-rmysql
3716 (uri (cran-uri "RMySQL" version))
3719 "0cbb5ln9iigl816nzvsls9zil5qlfr8yv2aginapqv6n69nz0srs"))))
3720 (properties `((upstream-name . "RMySQL")))
3721 (build-system r-build-system)
3723 `(("mariadb-dev" ,mariadb "dev")
3726 `(("r-dbi" ,r-dbi)))
3727 (home-page "https://github.com/r-dbi/RMySQL")
3728 (synopsis "Database interface and MySQL driver for R")
3730 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
3731 package contains an old implementation based on legacy code from S-PLUS which
3732 is being phased out. A modern MySQL client based on Rcpp is available from
3733 the RMariaDB package.")
3734 (license license:gpl2)))
3736 (define-public r-rpostgresql
3738 (name "r-rpostgresql")
3743 (uri (cran-uri "RPostgreSQL" version))
3746 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
3747 (properties `((upstream-name . "RPostgreSQL")))
3748 (build-system r-build-system)
3750 `(("postgresql" ,postgresql)))
3752 `(("r-dbi" ,r-dbi)))
3753 (home-page "https://github.com/tomoakin/RPostgreSQL")
3754 (synopsis "R interface to the PostgreSQL database system")
3756 "This package provides a Database Interface (DBI) compliant driver for R
3757 to access PostgreSQL database systems.")
3758 ;; The whole package is released under GPL version 2. It includes code
3759 ;; under the PostgreSQL license.
3760 (license license:gpl2)))
3762 (define-public r-linprog
3769 (uri (cran-uri "linprog" version))
3772 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
3773 (build-system r-build-system)
3774 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
3775 (home-page "http://linprog.r-forge.r-project.org/")
3776 (synopsis "Linear programming and optimization")
3778 "This package can be used to solve Linear Programming / Linear
3779 Optimization problems by using the simplex algorithm.")
3780 (license license:gpl2+)))
3782 (define-public r-geometry
3789 (uri (cran-uri "geometry" version))
3792 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
3793 (build-system r-build-system)
3795 `(("r-magic" ,r-magic)
3796 ("r-linprog" ,r-linprog)
3797 ("r-lpsolve" ,r-lpsolve)
3799 ("r-rcppprogress" ,r-rcppprogress)))
3800 (home-page "http://geometry.r-forge.r-project.org/")
3801 (synopsis "Mesh generator and surface tessellator")
3803 "This package makes the qhull library available in R, in a similar manner
3804 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
3805 intersections about a point, Voronoi diagrams, furthest-site Delaunay
3806 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
3807 and higher dimensions. It implements the Quickhull algorithm for computing
3808 the convex hull. Qhull does not support constrained Delaunay triangulations,
3809 or mesh generation of non-convex objects, but the package does include some R
3810 functions that allow for this. Currently the package only gives access to
3811 Delaunay triangulation and convex hull computation.")
3812 ;; The Qhull sources are included and are distributed under a custom
3813 ;; non-copyleft license. The R sources are released under GPL version 2.
3814 (license (list license:gpl2
3815 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
3817 (define-public r-ddalpha
3824 (uri (cran-uri "ddalpha" version))
3827 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
3828 (build-system r-build-system)
3831 ("r-class" ,r-class)
3832 ("r-geometry" ,r-geometry)
3835 ("r-robustbase" ,r-robustbase)
3836 ("r-sfsmisc" ,r-sfsmisc)))
3838 `(("gfortran" ,gfortran)))
3839 (home-page "https://cran.r-project.org/web/packages/ddalpha")
3840 (synopsis "Depth-Based classification and calculation of data depth")
3842 "This package contains procedures for depth-based supervised learning,
3843 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
3844 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
3845 statistical depth function to a compact low-dimensional space, where the final
3846 classification is done. It also offers an extension to functional data and
3847 routines for calculating certain notions of statistical depth functions. 50
3848 multivariate and 5 functional classification problems are included.")
3849 (license license:gpl2)))
3851 (define-public r-gower
3858 (uri (cran-uri "gower" version))
3861 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
3862 (build-system r-build-system)
3863 (home-page "https://github.com/markvanderloo/gower")
3864 (synopsis "Gower's distance")
3866 "This package provides tools to compute Gower's distance (or similarity)
3867 coefficient between records, and to compute the top-n matches between records.
3868 Core algorithms are executed in parallel on systems supporting OpenMP.")
3869 (license license:gpl3)))
3871 (define-public r-rcpproll
3878 (uri (cran-uri "RcppRoll" version))
3881 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
3882 (properties `((upstream-name . "RcppRoll")))
3883 (build-system r-build-system)
3885 `(("r-rcpp" ,r-rcpp)))
3886 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
3887 (synopsis "Efficient rolling and windowed operations")
3889 "This package provides fast and efficient routines for common rolling /
3890 windowed operations. Routines for the efficient computation of windowed mean,
3891 median, sum, product, minimum, maximum, standard deviation and variance are
3893 (license license:gpl2+)))
3895 (define-public r-ipred
3902 (uri (cran-uri "ipred" version))
3905 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
3906 (build-system r-build-system)
3908 `(("r-class" ,r-class)
3911 ("r-prodlim" ,r-prodlim)
3912 ("r-rpart" ,r-rpart)
3913 ("r-survival" ,r-survival)))
3914 (home-page "https://cran.r-project.org/web/packages/ipred")
3915 (synopsis "Improved predictors")
3917 "This package provides improved predictive models by indirect
3918 classification and bagging for classification, regression and survival
3919 problems as well as resampling based estimators of prediction error.")
3920 (license license:gpl2+)))
3922 (define-public r-psych
3929 (uri (cran-uri "psych" version))
3932 "0k5dw5nb7kx7f21b0z01dry99qcpnk7iaicv7xq9d35wv2hx8wca"))))
3933 (build-system r-build-system)
3935 `(("r-lattice" ,r-lattice)
3936 ("r-mnormt" ,r-mnormt)
3937 ("r-nlme" ,r-nlme)))
3938 (home-page "https://cran.r-project.org/web/packages/psych/")
3939 (synopsis "Procedures for psychological, psychometric, and personality research")
3941 "This package provides a general purpose toolbox for personality,
3942 psychometric theory and experimental psychology. Functions are primarily for
3943 multivariate analysis and scale construction using factor analysis, principal
3944 component analysis, cluster analysis and reliability analysis, although others
3945 provide basic descriptive statistics. Item Response Theory is done using
3946 factor analysis of tetrachoric and polychoric correlations. Functions for
3947 analyzing data at multiple levels include within and between group statistics,
3948 including correlations and factor analysis. Functions for simulating and
3949 testing particular item and test structures are included. Several functions
3950 serve as a useful front end for structural equation modeling. Graphical
3951 displays of path diagrams, factor analysis and structural equation models are
3952 created using basic graphics.")
3953 (license license:gpl2+)))
3955 (define-public r-generics
3962 (uri (cran-uri "generics" version))
3965 "0qw7r0d2qvlj1pvrlpv30d6akml624ydxkk19hv85iv6pfyx2wdb"))))
3966 (build-system r-build-system)
3967 (home-page "https://github.com/r-lib/generics")
3968 (synopsis "Common S3 generics not provided by base R methods")
3970 "In order to reduce potential package dependencies and conflicts,
3971 generics provides a number of commonly used S3 generics that are not provided
3972 by base R methods related to model fitting.")
3973 (license license:gpl2)))
3975 (define-public r-broom
3982 (uri (cran-uri "broom" version))
3985 "1zwdgv59a5c4mdcfn3anvsf83ymi11ij6k9nssw3aqzirp6fwg3w"))))
3986 (build-system r-build-system)
3988 `(("r-backports" ,r-backports)
3989 ("r-dplyr" ,r-dplyr)
3990 ("r-ellipsis" ,r-ellipsis)
3991 ("r-generics" ,r-generics)
3993 ("r-purrr" ,r-purrr)
3994 ("r-rlang" ,r-rlang)
3995 ("r-stringr" ,r-stringr)
3996 ("r-tibble" ,r-tibble)
3997 ("r-tidyr" ,r-tidyr)))
3999 `(("r-knitr" ,r-knitr)))
4000 (home-page "https://github.com/tidyverse/broom")
4001 (synopsis "Convert statistical analysis objects into tidy data frames")
4003 "This package provides tools to convert statistical analysis objects from
4004 R into tidy data frames, so that they can more easily be combined, reshaped
4005 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
4006 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
4007 summarizes a model's statistical findings such as coefficients of a
4008 regression; @code{augment}, which adds columns to the original data such as
4009 predictions, residuals and cluster assignments; and @code{glance}, which
4010 provides a one-row summary of model-level statistics.")
4011 (license license:expat)))
4013 (define-public r-recipes
4020 (uri (cran-uri "recipes" version))
4023 "0xif0ak3w90xmfzlxvb5pnzc3scpfl1pyhrjffi3mq4asvsd52l0"))))
4024 (build-system r-build-system)
4026 `(("r-dplyr" ,r-dplyr)
4027 ("r-generics" ,r-generics)
4029 ("r-gower" ,r-gower)
4030 ("r-ipred" ,r-ipred)
4031 ("r-lifecycle" ,r-lifecycle)
4032 ("r-lubridate" ,r-lubridate)
4033 ("r-magrittr" ,r-magrittr)
4034 ("r-matrix" ,r-matrix)
4035 ("r-purrr" ,r-purrr)
4036 ("r-rlang" ,r-rlang)
4037 ("r-tibble" ,r-tibble)
4038 ("r-tidyr" ,r-tidyr)
4039 ("r-tidyselect" ,r-tidyselect)
4040 ("r-timedate" ,r-timedate)
4041 ("r-withr" ,r-withr)))
4043 `(("r-knitr" ,r-knitr)))
4044 (home-page "https://github.com/topepo/recipes")
4045 (synopsis "Preprocessing tools to create design matrices")
4047 "Recipes is an extensible framework to create and preprocess design
4048 matrices. Recipes consist of one or more data manipulation and analysis
4049 \"steps\". Statistical parameters for the steps can be estimated from an
4050 initial data set and then applied to other data sets. The resulting design
4051 matrices can then be used as inputs into statistical or machine learning
4053 (license license:gpl2)))
4055 (define-public r-pdist
4062 (uri (cran-uri "pdist" version))
4065 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
4066 (build-system r-build-system)
4067 (home-page "https://github.com/jeffwong/pdist")
4068 (synopsis "Partitioned distance function")
4070 "Pdist computes the euclidean distance between rows of a matrix X and
4071 rows of another matrix Y. Previously, this could be done by binding the two
4072 matrices together and calling @code{dist}, but this creates unnecessary
4073 computation by computing the distances between a row of X and another row of
4074 X, and likewise for Y. Pdist strictly computes distances across the two
4075 matrices, not within the same matrix, making computations significantly faster
4076 for certain use cases.")
4077 (license license:gpl3+)))
4079 (define-public r-ggrepel
4086 (uri (cran-uri "ggrepel" version))
4089 "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9"))))
4090 (build-system r-build-system)
4092 `(("r-ggplot2" ,r-ggplot2)
4094 ("r-rlang" ,r-rlang)
4095 ("r-scales" ,r-scales)))
4097 `(("r-knitr" ,r-knitr))) ; for vignettes
4098 (home-page "https://github.com/slowkow/ggrepel")
4099 (synopsis "Repulsive text and label geometries for ggplot2")
4101 "This package provides text and label geometries for ggplot2 that help to
4102 avoid overlapping text labels. Labels repel away from each other and away
4103 from the data points.")
4104 (license license:gpl3)))
4106 (define-public r-corrplot
4113 (uri (cran-uri "corrplot" version))
4116 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
4117 (build-system r-build-system)
4118 (home-page "https://github.com/taiyun/corrplot")
4119 (synopsis "Visualization of a correlation matrix")
4121 "This package provides a graphical display of a correlation matrix or
4122 general matrix. It also contains some algorithms to do matrix reordering. In
4123 addition, corrplot is good at details, including choosing color, text labels,
4124 color labels, layout, etc.")
4125 ;; Any version of the GPL
4126 (license license:gpl2+)))
4128 (define-public r-stringdist
4130 (name "r-stringdist")
4135 (uri (cran-uri "stringdist" version))
4137 (base32 "06rzbgw43vzg496xca82pydf3g2rz6iw6h50ai0prbp9hbwrhvfd"))))
4138 (build-system r-build-system)
4139 (home-page "https://github.com/markvanderloo/stringdist")
4140 (synopsis "Approximate string matching and string distance functions")
4142 "This package implements an approximate string matching version of R's
4143 native @code{match} function. It can calculate various string distances based
4144 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment),
4145 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
4146 Jaro-Winkler). An implementation of soundex is provided as well. Distances
4147 can be computed between character vectors while taking proper care of encoding
4148 or between integer vectors representing generic sequences.")
4149 (license license:gpl3+)))
4151 (define-public r-ucminf
4158 (uri (cran-uri "ucminf" version))
4161 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
4162 (build-system r-build-system)
4163 (native-inputs `(("gfortran" ,gfortran)))
4164 (home-page "https://cran.r-project.org/web/packages/ucminf/")
4165 (synopsis "General-purpose unconstrained non-linear optimization")
4167 "This package provides an implementation of an algorithm for
4168 general-purpose unconstrained non-linear optimization. The algorithm is of
4169 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
4170 search with a trust region type monitoring of the input to the line search
4171 algorithm. The interface of @code{ucminf} is designed for easy interchange
4172 with the package @code{optim}.")
4173 (license license:gpl2+)))
4175 (define-public r-useful
4181 (uri (cran-uri "useful" version))
4184 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
4185 (properties `((upstream-name . "useful")))
4186 (build-system r-build-system)
4188 `(("r-assertthat" ,r-assertthat)
4189 ("r-dplyr" ,r-dplyr)
4190 ("r-ggplot2" ,r-ggplot2)
4191 ("r-magrittr" ,r-magrittr)
4192 ("r-matrix" ,r-matrix)
4194 ("r-purrr" ,r-purrr)
4195 ("r-scales" ,r-scales)))
4196 (home-page "https://github.com/jaredlander/useful")
4197 (synopsis "Collection of handy, useful functions")
4198 (description "This package provides a set of little functions that have been
4199 found useful to do little odds and ends such as plotting the results of K-means
4200 clustering, substituting special text characters, viewing parts of a
4201 @code{data.frame}, constructing formulas from text and building design and
4202 response matrices.")
4203 (license license:bsd-3)))
4205 (define-public r-ordinal
4208 (version "2019.12-10")
4212 (uri (cran-uri "ordinal" version))
4215 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
4216 (build-system r-build-system)
4218 `(("r-mass" ,r-mass)
4219 ("r-matrix" ,r-matrix)
4220 ("r-numderiv" ,r-numderiv)
4221 ("r-ucminf" ,r-ucminf)))
4222 (home-page "https://github.com/runehaubo/ordinal")
4223 (synopsis "Regression models for ordinal data")
4225 "This package provides an implementation of cumulative link (mixed)
4226 models also known as ordered regression models, proportional odds models,
4227 proportional hazards models for grouped survival times and ordered models.
4228 Estimation is via maximum likelihood and mixed models are fitted with the
4229 Laplace approximation and adaptive Gauss-Hermite quadrature.")
4230 (license license:gpl2+)))
4232 (define-public r-jomo
4239 (uri (cran-uri "jomo" version))
4242 "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir"))))
4243 (build-system r-build-system)
4245 `(("r-lme4" ,r-lme4)
4247 ("r-ordinal" ,r-ordinal)
4248 ("r-survival" ,r-survival)))
4249 (home-page "https://cran.r-project.org/web/packages/jomo/")
4250 (synopsis "Multilevel Joint Modelling Multiple Imputation")
4252 "Similarly to Schafer's package pan, jomo is a package for multilevel
4253 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
4254 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
4255 possibility of handling binary and categorical data through latent normal
4256 variables, the option to use cluster-specific covariance matrices and to
4257 impute compatibly with the substantive model.")
4258 (license license:gpl2)))
4260 (define-public r-pan
4267 (uri (cran-uri "pan" version))
4270 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
4271 (build-system r-build-system)
4272 (native-inputs `(("gfortran" ,gfortran)))
4273 (home-page "https://cran.r-project.org/web/packages/pan/")
4274 (synopsis "Multiple imputation for multivariate panel or clustered data")
4276 "This package implements multiple imputation for multivariate panel or
4278 (license license:gpl3)))
4280 (define-public r-mitml
4287 (uri (cran-uri "mitml" version))
4290 "1bw92fl6xp3yvawh3nbjzs4hp4alpwj6vnv6lsysd74aqndw447c"))))
4291 (build-system r-build-system)
4293 `(("r-haven" ,r-haven)
4297 `(("r-knitr" ,r-knitr)))
4298 (home-page "https://cran.r-project.org/web/packages/mitml/")
4299 (synopsis "Tools for multiple imputation in multilevel modeling")
4301 "This package provides tools for multiple imputation of missing data in
4302 multilevel modeling. It includes a user-friendly interface to the packages
4303 pan and jomo, and several functions for visualization, data management and the
4304 analysis of multiply imputed data sets.")
4305 (license license:gpl2+)))
4307 (define-public r-mice
4314 (uri (cran-uri "mice" version))
4317 "11cpyqlilakan2pwjzacb9jjlazazsqdngy237nnrj8j6mky822i"))))
4318 (build-system r-build-system)
4320 `(("r-broom" ,r-broom)
4321 ("r-cpp11" ,r-cpp11)
4322 ("r-dplyr" ,r-dplyr)
4323 ("r-generics" ,r-generics)
4324 ("r-lattice" ,r-lattice)
4326 ("r-rlang" ,r-rlang)
4327 ("r-tidyr" ,r-tidyr)))
4328 (home-page "https://cran.r-project.org/web/packages/mice/")
4329 (synopsis "Multivariate imputation by chained equations")
4331 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
4332 implemented by the MICE algorithm as described in @url{Van Buuren and
4333 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
4334 variable has its own imputation model. Built-in imputation models are
4335 provided for continuous data (predictive mean matching, normal), binary
4336 data (logistic regression), unordered categorical data (polytomous logistic
4337 regression) and ordered categorical data (proportional odds). MICE can also
4338 impute continuous two-level data (normal model, pan, second-level variables).
4339 Passive imputation can be used to maintain consistency between variables.
4340 Various diagnostic plots are available to inspect the quality of the
4342 ;; Any of these two versions.
4343 (license (list license:gpl2 license:gpl3))))
4345 (define-public r-truncnorm
4347 (name "r-truncnorm")
4352 (uri (cran-uri "truncnorm" version))
4355 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
4356 (build-system r-build-system)
4357 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
4358 (synopsis "Truncated normal distribution")
4359 (description "This package provides functions for the truncated normal
4360 distribution with mean equal to @code{mean} and standard deviation equal to
4361 @code{sd}. It includes density, distribution, quantile, and expected value
4362 functions, as well as a random generation function.")
4363 (license license:gpl2)))
4365 (define-public r-rsolnp
4372 (uri (cran-uri "Rsolnp" version))
4375 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
4376 (properties `((upstream-name . "Rsolnp")))
4377 (build-system r-build-system)
4379 `(("r-truncnorm" ,r-truncnorm)))
4380 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
4381 (synopsis "General non-linear optimization")
4382 (description "The Rsolnp package implements a general non-linear augmented
4383 Lagrange multiplier method solver, a @dfn{sequential quadratic
4384 programming} (SQP) based solver).")
4385 ;; Any version of the GPL.
4386 (license license:gpl2+)))
4388 (define-public r-hardyweinberg
4390 (name "r-hardyweinberg")
4395 (uri (cran-uri "HardyWeinberg" version))
4398 "0afjz818yvaq3akvgpy4irnlpspd2dj71qkrwj81lm9y36ypwlw6"))))
4399 (properties `((upstream-name . "HardyWeinberg")))
4400 (build-system r-build-system)
4402 `(("r-mice" ,r-mice)
4404 ("r-rsolnp" ,r-rsolnp)))
4405 (home-page "https://cran.r-project.org/package=HardyWeinberg")
4406 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
4408 "This package contains tools for exploring Hardy-Weinberg equilibrium for
4409 diallelic genetic marker data. All classical tests (chi-square, exact,
4410 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
4411 included in the package, as well as functions for power computation and for
4412 the simulation of marker data under equilibrium and disequilibrium. Routines
4413 for dealing with markers on the X-chromosome are included. Functions for
4414 testing equilibrium in the presence of missing data by using multiple
4415 imputation are also provided. Implements several graphics for exploring the
4416 equilibrium status of a large set of diallelic markers: ternary plots with
4417 acceptance regions, log-ratio plots and Q-Q plots.")
4418 (license license:gpl2+)))
4427 (uri (cran-uri "sm" version))
4430 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
4431 (build-system r-build-system)
4432 (native-inputs `(("gfortran" ,gfortran)))
4433 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
4434 (synopsis "Smoothing methods for nonparametric regression and density estimation")
4436 "This is software accompanying the book 'Applied Smoothing Techniques for
4437 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
4438 University Press. It provides smoothing methods for nonparametric regression
4439 and density estimation")
4440 (license license:gpl2+)))
4442 (define-public r-venndiagram
4444 (name "r-venndiagram")
4448 (uri (cran-uri "VennDiagram" version))
4451 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
4452 (properties `((upstream-name . "VennDiagram")))
4453 (build-system r-build-system)
4455 `(("r-futile-logger" ,r-futile-logger)))
4456 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
4457 (synopsis "Generate High-Resolution Venn and Euler Plots")
4459 "This package provides a set of functions to generate high-resolution
4460 Venn and Euler plots. It includes handling for several special cases,
4461 including two-case scaling, and extensive customization of plot shape and
4463 (license license:gpl2+)))
4465 (define-public r-vioplot
4472 (uri (cran-uri "vioplot" version))
4475 "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v"))))
4476 (build-system r-build-system)
4481 `(("r-knitr" ,r-knitr)))
4482 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
4483 (synopsis "Violin plot")
4485 "This package provides a violin plot, which is a combination of a box
4486 plot and a kernel density plot.")
4487 (license license:bsd-3)))
4489 (define-public r-rsofia
4495 ;; This package has been removed from CRAN, so we can
4496 ;; only fetch it from the archives.
4497 (uri (string-append "https://cran.r-project.org/src/"
4498 "contrib/Archive/RSofia/RSofia_"
4502 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
4503 (properties `((upstream-name . "RSofia")))
4504 (build-system r-build-system)
4506 `(("r-rcpp" ,r-rcpp)))
4507 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
4508 (synopsis "Port of sofia-ml to R")
4509 (description "This package is a port of sofia-ml to R. Sofia-ml is a
4510 suite of fast incremental algorithms for machine learning that can be used for
4511 training models for classification or ranking.")
4512 (license license:asl2.0)))
4514 (define-public r-xts
4521 (uri (cran-uri "xts" version))
4524 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
4525 (build-system r-build-system)
4526 (propagated-inputs `(("r-zoo" ,r-zoo)))
4527 (home-page "https://github.com/joshuaulrich/xts")
4528 (synopsis "Extensible time series")
4530 "This package provides for uniform handling of R's different time-based
4531 data classes by extending @code{zoo}, maximizing native format information
4532 preservation and allowing for user-level customization and extension, while
4533 simplifying cross-class interoperability.")
4534 (license license:gpl2+)))
4536 (define-public r-performanceanalytics
4538 (name "r-performanceanalytics")
4543 (uri (cran-uri "PerformanceAnalytics" version))
4546 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
4548 `((upstream-name . "PerformanceAnalytics")))
4549 (build-system r-build-system)
4551 `(("r-quadprog" ,r-quadprog)
4554 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
4555 (synopsis "Econometric tools for performance and risk analysis")
4556 (description "This is a collection of econometric functions for
4557 performance and risk analysis. This package aims to aid practitioners and
4558 researchers in utilizing the latest research in analysis of non-normal return
4559 streams. In general, it is most tested on return (rather than price) data on
4560 a regular scale, but most functions will work with irregular return data as
4561 well, and increasing numbers of functions will work with P&L or price data
4563 ;; Either version may be picked.
4564 (license (list license:gpl2 license:gpl3))))
4566 (define-public r-laeken
4573 (uri (cran-uri "laeken" version))
4576 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
4577 (build-system r-build-system)
4579 `(("r-boot" ,r-boot)
4580 ("r-mass" ,r-mass)))
4581 (home-page "https://cran.r-project.org/web/packages/laeken/")
4582 (synopsis "Estimation of indicators on social exclusion and poverty")
4583 (description "This package provides tools for the estimation of indicators
4584 on social exclusion and poverty, as well as an implementation of Pareto tail
4585 modeling for empirical income distributions.")
4586 (license license:gpl2+)))
4588 (define-public r-vcd
4595 (uri (cran-uri "vcd" version))
4598 "030yyhpzsj4ivwrla7p9kgvmyjh6b8fr7czf678ykxjj64ccnvr3"))))
4599 (build-system r-build-system)
4601 `(("r-colorspace" ,r-colorspace)
4602 ("r-lmtest" ,r-lmtest)
4603 ("r-mass" ,r-mass)))
4604 (home-page "https://cran.r-project.org/web/packages/vcd/")
4605 (synopsis "Visualizing categorical data")
4606 (description "This package provides visualization techniques, data sets,
4607 summary and inference procedures aimed particularly at categorical data.
4608 Special emphasis is given to highly extensible grid graphics. The package was
4609 originally inspired by the book \"Visualizing Categorical Data\" by Michael
4610 Friendly and is now the main support package for a new book, \"Discrete Data
4611 Analysis with R\" by Michael Friendly and David Meyer (2015).")
4612 (license license:gpl2)))
4614 (define-public r-ica
4621 (uri (cran-uri "ica" version))
4624 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
4625 (build-system r-build-system)
4626 (home-page "https://cran.r-project.org/web/packages/ica/")
4627 (synopsis "Independent component analysis")
4628 (description "This package provides tools for @dfn{Independent Component
4629 Analysis} (ICA) using various algorithms: FastICA,
4630 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4631 of Eigenmatrices} (JADE).")
4632 (license license:gpl2+)))
4634 (define-public r-dtw
4641 (uri (cran-uri "dtw" version))
4644 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z"))))
4645 (build-system r-build-system)
4646 (propagated-inputs `(("r-proxy" ,r-proxy)))
4647 (home-page "http://dtw.r-forge.r-project.org/")
4648 (synopsis "Dynamic Time Warping Algorithms")
4649 (description "This package provides a comprehensive implementation of
4650 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4651 optimal (least cumulative distance) alignment between points of two time
4652 series. Common DTW variants covered include local (slope) and global (window)
4653 constraints, subsequence matches, arbitrary distance definitions,
4654 normalizations, minimum variance matching, and so on.")
4655 (license license:gpl2+)))
4657 (define-public r-sdmtools
4660 (version "1.1-221.2")
4664 (uri (cran-uri "SDMTools" version))
4667 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4668 (properties `((upstream-name . "SDMTools")))
4669 (build-system r-build-system)
4670 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4671 (home-page "https://www.rforge.net/SDMTools/")
4672 (synopsis "Species distribution modelling tools")
4673 (description "This package provides a set of tools for post processing
4674 the outcomes of species distribution modeling exercises. It includes novel
4675 methods for comparing models and tracking changes in distributions through
4676 time. It further includes methods for visualizing outcomes, selecting
4677 thresholds, calculating measures of accuracy and landscape fragmentation
4679 (license license:gpl3+)))
4681 (define-public r-scatterplot3d
4683 (name "r-scatterplot3d")
4688 (uri (cran-uri "scatterplot3d" version))
4691 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
4692 (build-system r-build-system)
4693 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
4694 (synopsis "3D scatter plot")
4695 (description "This package provides an implementation of scatter plots for
4696 plotting. a three dimensional point cloud.")
4697 (license license:gpl2)))
4699 (define-public r-ggridges
4706 (uri (cran-uri "ggridges" version))
4709 "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm"))))
4710 (build-system r-build-system)
4712 `(("r-ggplot2" ,r-ggplot2)
4714 ("r-scales" ,r-scales)
4715 ("r-withr" ,r-withr)))
4717 `(("r-knitr" ,r-knitr)))
4718 (home-page "https://github.com/clauswilke/ggridges")
4719 (synopsis "Ridgeline plots in ggplot2")
4721 "Ridgeline plots provide a convenient way of visualizing changes in
4722 distributions over time or space. This package enables the creation of such
4723 plots in @code{ggplot2}.")
4724 (license license:gpl2)))
4726 (define-public r-ggjoy
4733 (uri (cran-uri "ggjoy" version))
4736 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
4737 (build-system r-build-system)
4739 `(("r-ggplot2" ,r-ggplot2)
4740 ("r-ggridges" ,r-ggridges)))
4741 (home-page "https://github.com/clauswilke/ggjoy")
4742 (synopsis "Joyplots in ggplot2")
4743 (description "Joyplots provide a convenient way of visualizing changes in
4744 distributions over time or space. This package enables the creation of such
4745 plots in @code{ggplot2}.")
4746 (license license:gpl2)))
4748 (define-public r-cli
4755 (uri (cran-uri "cli" version))
4758 "128bx3bds0dnkixc4frbky11rz1ilnvdfzz9mggajj690i11b62q"))))
4759 (build-system r-build-system)
4761 `(("r-assertthat" ,r-assertthat)
4762 ("r-glue" ,r-glue)))
4763 (home-page "https://github.com/r-lib/cli#readme")
4764 (synopsis "Helpers for developing command line interfaces")
4765 (description "This package provides a suite of tools designed to build
4766 attractive command line interfaces (CLIs). It includes tools for drawing
4767 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
4768 (license license:expat)))
4770 (define-public r-argparser
4772 (name "r-argparser")
4777 (uri (cran-uri "argparser" version))
4780 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
4781 (build-system r-build-system)
4782 (home-page "https://bitbucket.org/djhshih/argparser")
4783 (synopsis "Command-line argument parser")
4785 "This package provides a cross-platform command-line argument parser
4786 written purely in R with no external dependencies. It is useful with the
4787 Rscript front-end and facilitates turning an R script into an executable
4789 (license license:gpl3+)))
4791 (define-public r-debugme
4798 (uri (cran-uri "debugme" version))
4801 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
4802 (build-system r-build-system)
4803 (propagated-inputs `(("r-crayon" ,r-crayon)))
4804 (home-page "https://github.com/r-lib/debugme#readme")
4805 (synopsis "Debug R packages")
4807 "This package allows the user to specify debug messages as special string
4808 constants, and control debugging of packages via environment variables.")
4809 (license license:expat)))
4811 (define-public r-processx
4818 (uri (cran-uri "processx" version))
4820 (base32 "055v2gdrgqsfy8s672wsq79bqr44b4jjmcbqivx4p2d6lqx10s73"))))
4821 (build-system r-build-system)
4825 (home-page "https://github.com/r-lib/processx3")
4826 (synopsis "Execute and control system processes")
4828 "This package provides portable tools to run system processes in the
4829 background. It can check if a background process is running; wait on a
4830 background process to finish; get the exit status of finished processes; kill
4831 background processes and their children; restart processes. It can read the
4832 standard output and error of the processes, using non-blocking connections.
4833 @code{processx} can poll a process for standard output or error, with a
4834 timeout. It can also poll several processes at once.")
4835 (license license:expat)))
4837 (define-public r-tsp
4844 (uri (cran-uri "TSP" version))
4847 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
4848 (properties `((upstream-name . "TSP")))
4849 (build-system r-build-system)
4850 (propagated-inputs `(("r-foreach" ,r-foreach)))
4851 (home-page "https://cran.r-project.org/web/packages/TSP/")
4852 (synopsis "Traveling salesperson problem (TSP)")
4853 (description "This package provides basic infrastructure and some
4854 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
4855 traveling salesman problem).")
4856 (license license:gpl3)))
4858 (define-public r-qap
4865 (uri (cran-uri "qap" version))
4868 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
4869 (build-system r-build-system)
4870 (native-inputs `(("gfortran" ,gfortran)))
4871 (home-page "https://cran.r-project.org/web/packages/qap/")
4872 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
4873 (description "This package implements heuristics for the @dfn{quadratic
4874 assignment problem} (QAP). Currently only a simulated annealing heuristic is
4876 (license license:gpl3)))
4878 (define-public r-gclus
4885 (uri (cran-uri "gclus" version))
4888 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
4889 (build-system r-build-system)
4890 (propagated-inputs `(("r-cluster" ,r-cluster)))
4891 (home-page "https://cran.r-project.org/web/packages/gclus/")
4892 (synopsis "Clustering graphics")
4893 (description "This package orders panels in scatterplot matrices and
4894 parallel coordinate displays by some merit index. It contains various indices
4895 of merit, ordering functions, and enhanced versions of @code{pairs} and
4896 @code{parcoord} which color panels according to their merit level.")
4897 (license license:gpl2+)))
4899 (define-public r-webshot
4906 (uri (cran-uri "webshot" version))
4909 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
4910 (build-system r-build-system)
4912 `(("r-callr" ,r-callr)
4913 ("r-jsonlite" ,r-jsonlite)
4914 ("r-magrittr" ,r-magrittr)))
4915 (home-page "https://github.com/wch/webshot/")
4916 (synopsis "Take screenshots of web pages")
4918 "Webshot makes it easy to take screenshots of web pages from within R.
4919 It can also run Shiny applications locally and take screenshots of the
4920 application; and it can render and screenshot static as well as interactive R
4921 Markdown documents.")
4922 (license license:gpl2)))
4924 (define-public r-seriation
4926 (name "r-seriation")
4931 (uri (cran-uri "seriation" version))
4934 "1glxn098ar1v96xlwp85kjxzfd1nyfzp2f82x5z3fm87yv57k4lb"))))
4935 (build-system r-build-system)
4937 `(("r-cluster" ,r-cluster)
4938 ("r-colorspace" ,r-colorspace)
4939 ("r-dendextend" ,r-dendextend)
4940 ("r-gclus" ,r-gclus)
4941 ("r-gplots" ,r-gplots)
4944 ("r-registry" ,r-registry)
4946 (native-inputs `(("gfortran" ,gfortran)))
4947 (home-page "https://s2.smu.edu/IDA/seriation/")
4948 (synopsis "Infrastructure for ordering objects using seriation")
4950 "This package provides infrastructure for seriation with an
4951 implementation of several seriation/sequencing techniques to reorder matrices,
4952 dissimilarity matrices, and dendrograms. It also provides (optimally)
4953 reordered heatmaps, color images and clustering visualizations like
4954 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4956 (license license:gpl3)))
4958 (define-public r-xfun
4965 (uri (cran-uri "xfun" version))
4967 (base32 "18qjs81fn8q2d2drcan8gpgvrbgxgd0b659c92z19kg2h4c1g3k4"))))
4968 (build-system r-build-system)
4969 ;; knitr itself depends on xfun
4972 `(("r-knitr" ,r-knitr)))
4973 (home-page "https://github.com/yihui/xfun")
4974 (synopsis "Miscellaneous functions")
4976 "This package provides miscellaneous functions commonly used in other
4977 packages maintained by Yihui Xie.")
4978 (license license:expat)))
4980 (define-public r-utf8
4987 (uri (cran-uri "utf8" version))
4990 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4991 (build-system r-build-system)
4992 (home-page "https://github.com/patperry/r-utf8")
4993 (synopsis "Unicode text processing")
4995 "This package provides tools to process and print UTF-8 encoded
4996 international text (Unicode). Input, validate, normalize, encode, format, and
4998 (license license:asl2.0)))
5000 (define-public r-zeallot
5007 (uri (cran-uri "zeallot" version))
5010 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
5011 (build-system r-build-system)
5012 (home-page "https://github.com/nteetor/zeallot")
5013 (synopsis "Multiple, unpacking, and destructuring assignment")
5015 "This package provides a @code{%<-%} operator to perform multiple,
5016 unpacking, and destructuring assignment in R. The operator unpacks the
5017 right-hand side of an assignment into multiple values and assigns these values
5018 to variables on the left-hand side of the assignment.")
5019 (license license:expat)))
5021 (define-public r-vctrs
5028 (uri (cran-uri "vctrs" version))
5031 "09ddxgzyah7lw42hn6n8fynsixf43s10jamsf94d2aidky63czfz"))))
5032 (build-system r-build-system)
5034 `(("r-digest" ,r-digest)
5035 ("r-ellipsis" ,r-ellipsis)
5037 ("r-rlang" ,r-rlang)))
5039 `(("r-knitr" ,r-knitr)))
5040 (home-page "https://github.com/r-lib/vctrs")
5041 (synopsis "Vector helpers")
5043 "There are three main goals to the @code{vctrs} package:
5046 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
5047 @code{length()} and @code{class()}. These definitions are paired with a
5048 framework for type-coercion and size-recycling.
5049 @item To define type- and size-stability as desirable function properties, use
5050 them to analyse existing base function, and to propose better alternatives.
5051 This work has been particularly motivated by thinking about the ideal
5052 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
5053 @item To provide a new @code{vctr} base class that makes it easy to create new
5054 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
5055 a few new @code{vctrs} generics, making implementation considerably simpler
5058 (license license:gpl3)))
5060 (define-public r-pillar
5067 (uri (cran-uri "pillar" version))
5070 "167ji21fx04s2niw5pjq9vzxgagxzsg3gimh8dzr2kl5ljrb5vfd"))))
5071 (build-system r-build-system)
5074 ("r-crayon" ,r-crayon)
5075 ("r-ellipsis" ,r-ellipsis)
5076 ("r-fansi" ,r-fansi)
5077 ("r-lifecycle" ,r-lifecycle)
5078 ("r-rlang" ,r-rlang)
5080 ("r-vctrs" ,r-vctrs)))
5081 (home-page "https://github.com/r-lib/pillar")
5082 (synopsis "Coloured formatting for columns")
5084 "This package provides a @code{pillar} generic designed for formatting
5085 columns of data using the full range of colours provided by modern
5087 (license license:gpl3)))
5089 (define-public r-uuid
5096 (uri (cran-uri "uuid" version))
5099 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
5100 (build-system r-build-system)
5101 (home-page "https://www.rforge.net/uuid")
5102 (synopsis "Tools for generating and handling of UUIDs")
5104 "This package provides tools for generating and handling of
5105 @dfn{Universally Unique Identifiers} (UUIDs).")
5106 (license license:expat)))
5108 (define-public r-tinytex
5115 (uri (cran-uri "tinytex" version))
5118 "0my1412vn5zri01w2myzn268lfwinbhfgdj4bbcib3s48i9djw0n"))))
5119 (build-system r-build-system)
5121 `(("r-xfun" ,r-xfun)))
5122 (home-page "https://github.com/yihui/tinytex")
5123 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
5125 "This package provides helper functions to install and maintain the LaTeX
5126 distribution named TinyTeX, a lightweight, cross-platform, portable, and
5127 easy-to-maintain version of TeX Live. This package also contains helper
5128 functions to compile LaTeX documents, and install missing LaTeX packages
5130 (license license:expat)))
5132 (define-public r-tinytest
5139 (uri (cran-uri "tinytest" version))
5142 "1asryjrah3fj39gg0c6yxgpr142j5bg2n990v7q8r0a5pb8gcr45"))))
5143 (properties `((upstream-name . "tinytest")))
5144 (build-system r-build-system)
5145 (home-page "https://github.com/markvanderloo/tinytest")
5146 (synopsis "Lightweight unit testing framework")
5148 "This package provides a lightweight unit testing framework. Main
5152 @item install tests with the package;
5153 @item test results are treated as data that can be stored and manipulated;
5154 @item test files are R scripts interspersed with test commands, that can be
5156 @item fully automated build-install-test sequence for packages;
5157 @item skip tests when not run locally (e.g. on CRAN);
5158 @item flexible and configurable output printing;
5159 @item compare computed output with output stored with the package;
5160 @item run tests in parallel;
5161 @item extensible by other packages;
5162 @item report side effects.
5165 (license license:gpl3)))
5167 (define-public r-network
5174 (uri (cran-uri "network" version))
5177 "1cgy7vlbinyndl0zkzvnpcmi240wry6iwfb42sz1mj5c9iwkar7b"))))
5178 (build-system r-build-system)
5180 `(("r-magrittr" ,r-magrittr)
5181 ("r-tibble" ,r-tibble)))
5182 (home-page "https://statnet.org/")
5183 (synopsis "Classes for relational data")
5185 "This package provides tools to create and modify network objects. The
5186 @code{network} class can represent a range of relational data types, and
5187 supports arbitrary vertex/edge/graph attributes.")
5188 (license license:gpl2+)))
5190 (define-public r-stabs
5197 (uri (cran-uri "stabs" version))
5200 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q"))))
5201 (build-system r-build-system)
5203 `(("r-knitr" ,r-knitr)))
5204 (home-page "https://github.com/hofnerb/stabs")
5205 (synopsis "Stability selection with error control")
5207 "This package provides resampling procedures to assess the stability of
5208 selected variables with additional finite sample error control for
5209 high-dimensional variable selection procedures such as Lasso or boosting.
5210 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
5211 complementary pairs stability selection with improved error bounds
5212 (Shah & Samworth, 2013) are implemented. The package can be combined with
5213 arbitrary user specified variable selection approaches.")
5214 (license license:gpl2)))
5216 (define-public r-rle
5223 (uri (cran-uri "rle" version))
5226 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40"))))
5227 (properties `((upstream-name . "rle")))
5228 (build-system r-build-system)
5229 (home-page "https://cran.r-project.org/web/packages/rle/")
5230 (synopsis "Common functions for run-length encoded vectors")
5232 "This package provides common @code{base} and @code{stats} methods for
5233 @code{rle} objects, aiming to make it possible to treat them transparently as
5235 (license license:gpl3)))
5237 (define-public r-statnet-common
5239 (name "r-statnet-common")
5244 (uri (cran-uri "statnet.common" version))
5247 "1z89an46xcl1d7dacj4irhk6pkajdz7v85b2347vczwdf622pksf"))))
5249 `((upstream-name . "statnet.common")))
5250 (build-system r-build-system)
5252 `(("r-coda" ,r-coda)
5254 (home-page "https://statnet.org")
5255 (synopsis "R scripts and utilities used by the Statnet software")
5256 (description "This package provides non-statistical utilities used by the
5257 software developed by the Statnet Project.")
5258 (license license:gpl3)))
5260 (define-public r-statcheck
5262 (name "r-statcheck")
5267 (uri (cran-uri "statcheck" version))
5270 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
5271 (build-system r-build-system)
5273 `(("r-ggplot2" ,r-ggplot2)
5275 ("r-rmarkdown" ,r-rmarkdown)))
5276 (home-page "https://cran.r-project.org/web/packages/statcheck/")
5277 (synopsis "Extract statistics from articles and recompute p-values")
5278 (description "This package can automatically extract statistical
5279 null-hypothesis significant testing (NHST) results from articles and recompute
5280 the p-values based on the reported test statistic and degrees of freedom to
5281 detect possible inconsistencies.")
5282 (license license:gpl2)))
5284 (define-public r-sna
5291 (uri (cran-uri "sna" version))
5294 "0ai0v4538d30m4wks5s3lch1yfmx1ml0nnrz7ihs097lv586a09s"))))
5295 (build-system r-build-system)
5297 `(("r-network" ,r-network)
5298 ("r-statnet-common" ,r-statnet-common)))
5299 (home-page "https://statnet.org")
5300 (synopsis "Tools for social network analysis")
5302 "This package provides a range of tools for social network analysis,
5303 including node and graph-level indices, structural distance and covariance
5304 methods, structural equivalence detection, network regression, random graph
5305 generation, and 2D/3D network visualization.")
5306 (license license:gpl2+)))
5308 (define-public r-tfisher
5315 (uri (cran-uri "TFisher" version))
5318 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
5319 (properties `((upstream-name . "TFisher")))
5320 (build-system r-build-system)
5322 `(("r-matrix" ,r-matrix)
5323 ("r-mvtnorm" ,r-mvtnorm)
5325 (home-page "https://cran.r-project.org/web/packages/TFisher/")
5326 (synopsis "Optimal thresholding Fisher's p-value combination method")
5328 "This package provides the @dfn{cumulative distribution function} (CDF),
5329 quantile, and statistical power calculator for a collection of thresholding
5330 Fisher's p-value combination methods, including Fisher's p-value combination
5331 method, truncated product method and, in particular, soft-thresholding
5332 Fisher's p-value combination method which is proven to be optimal in some
5333 context of signal detection. The p-value calculator for the omnibus version
5334 of these tests are also included.")
5335 (license license:gpl2)))
5337 (define-public r-ttr
5344 (uri (cran-uri "TTR" version))
5347 "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5"))))
5348 (properties `((upstream-name . "TTR")))
5349 (build-system r-build-system)
5351 `(("r-curl" ,r-curl)
5354 (home-page "https://github.com/joshuaulrich/TTR")
5355 (synopsis "Technical trading rules")
5357 "This package provides functions and data to construct technical trading
5359 (license license:gpl2)))
5361 (define-public r-leaps
5368 (uri (cran-uri "leaps" version))
5371 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
5372 (build-system r-build-system)
5373 (native-inputs `(("gfortran" ,gfortran)))
5374 (home-page "https://cran.r-project.org/web/packages/leaps/")
5375 (synopsis "Regression subset selection")
5377 "This package provides tools for regression subset selection, including
5378 exhaustive search.")
5379 (license license:gpl2+)))
5381 (define-public r-splus2r
5388 (uri (cran-uri "splus2R" version))
5391 "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x"))))
5392 (properties `((upstream-name . "splus2R")))
5393 (build-system r-build-system)
5394 (home-page "https://cran.r-project.org/web/packages/splus2R/")
5395 (synopsis "Supplemental S-PLUS functionality in R")
5397 "Currently there are many functions in S-PLUS that are missing in R. To
5398 facilitate the conversion of S-PLUS packages to R packages, this package
5399 provides some missing S-PLUS functionality in R.")
5400 (license license:gpl2)))
5402 (define-public r-ifultools
5404 (name "r-ifultools")
5409 (uri (cran-uri "ifultools" version))
5412 "0f95vqc47dgssqngznk0rclr72ndbyxc7gdq2cmbksvq7qpn3gg1"))))
5413 (build-system r-build-system)
5415 `(("r-mass" ,r-mass)
5416 ("r-splus2r" ,r-splus2r)))
5417 (home-page "https://cran.r-project.org/web/packages/ifultools/")
5418 (synopsis "Insightful research tools")
5419 (description "This package provides C code used by the wmtsa, fractal, and
5421 (license license:gpl2)))
5423 (define-public r-sapa
5430 (uri (cran-uri "sapa" version))
5433 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
5434 (build-system r-build-system)
5436 `(("r-ifultools" ,r-ifultools)
5437 ("r-splus2r" ,r-splus2r)))
5438 (home-page "https://cran.r-project.org/web/packages/sapa/")
5439 (synopsis "Spectral analysis for physical applications")
5440 (description "This package provides software for the book Spectral
5441 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
5442 Cambridge University Press, 1993.")
5443 (license license:gpl2)))
5445 (define-public r-aggregation
5447 (name "r-aggregation")
5452 (uri (cran-uri "aggregation" version))
5455 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
5456 (build-system r-build-system)
5457 (home-page "https://cran.r-project.org/web/packages/aggregation/")
5458 (synopsis "Methods for p-value aggregation")
5460 "This package contains functionality for performing the following methods
5461 of p-value aggregation: Fisher's method, the Lancaster method (weighted
5462 Fisher's method), and Sidak correction.")
5463 (license license:gpl3)))
5465 (define-public r-quantmod
5472 (uri (cran-uri "quantmod" version))
5475 "0dbcrncv06iqcbkky95dd7l32xq0hhbnkb0kj8wwzym1jf748h5a"))))
5476 (build-system r-build-system)
5478 `(("r-curl" ,r-curl)
5482 (home-page "https://cran.r-project.org/web/packages/quantmod/")
5483 (synopsis "Quantitative financial modelling framework")
5484 (description "This package provides a quantitative financial modelling
5485 framework to allow users to specify, build, trade, and analyse quantitative
5486 financial trading strategies.")
5487 (license license:gpl3)))
5489 (define-public r-tseries
5496 (uri (cran-uri "tseries" version))
5499 "0wa4rcf0igayi1yrwc6wak6d491560p0z89rz32haqlkiiq25gak"))))
5500 (build-system r-build-system)
5502 `(("r-quadprog" ,r-quadprog)
5503 ("r-quantmod" ,r-quantmod)
5506 `(("gfortran" ,gfortran)))
5507 (home-page "https://cran.r-project.org/web/packages/tseries/")
5508 (synopsis "Time series analysis and computational finance")
5510 "This package provides functions relating to time series analysis and
5511 computational finance.")
5512 (license license:gpl2)))
5514 (define-public r-wmtsa
5521 (uri (cran-uri "wmtsa" version))
5524 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
5525 (build-system r-build-system)
5527 `(("r-ifultools" ,r-ifultools)
5529 ("r-splus2r" ,r-splus2r)))
5530 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
5531 (synopsis "Wavelet methods for time series analysis")
5533 "This package provides software to accompany the book \"Wavelet Methods
5534 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
5535 University Press, 2000.")
5536 (license license:gpl2)))
5538 (define-public r-tsa
5545 (uri (cran-uri "TSA" version))
5548 "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb"))))
5549 (properties `((upstream-name . "TSA")))
5550 (build-system r-build-system)
5552 `(("r-leaps" ,r-leaps)
5553 ("r-locfit" ,r-locfit)
5555 ("r-tseries" ,r-tseries)))
5556 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
5557 (synopsis "Time series analysis")
5559 "This package contains R functions and datasets detailed in the book
5560 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
5561 Cryer and Kung-Sik Chan.")
5562 (license license:gpl2+)))
5564 (define-public r-extradistr
5566 (name "r-extradistr")
5571 (uri (cran-uri "extraDistr" version))
5574 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
5575 (properties `((upstream-name . "extraDistr")))
5576 (build-system r-build-system)
5578 `(("r-rcpp" ,r-rcpp)))
5579 (home-page "https://github.com/twolodzko/extraDistr")
5580 (synopsis "Additional univariate and multivariate distributions")
5582 "This package implements density, distribution functions, quantile
5583 functions and random generation functions for a large number of univariate and
5584 multivariate distributions.")
5585 (license license:gpl2)))
5587 (define-public r-fractal
5594 (uri (cran-uri "fractal" version))
5597 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
5598 (build-system r-build-system)
5600 `(("r-ifultools" ,r-ifultools)
5603 ("r-scatterplot3d" ,r-scatterplot3d)
5604 ("r-splus2r" ,r-splus2r)
5605 ("r-wmtsa" ,r-wmtsa)))
5606 (home-page "https://cran.r-project.org/web/packages/fractal/")
5607 (synopsis "Fractal time series modeling and analysis")
5609 "This package provides tools for stochastic fractal and deterministic
5610 chaotic time series analysis.")
5611 (license license:gpl2)))
5613 (define-public r-urca
5620 (uri (cran-uri "urca" version))
5623 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
5624 (build-system r-build-system)
5625 (propagated-inputs `(("r-nlme" ,r-nlme)))
5626 (native-inputs `(("gfortran" ,gfortran)))
5627 (home-page "https://cran.r-project.org/web/packages/urca/")
5628 (synopsis "Unit root and cointegration tests for time series data")
5630 "This package provides unit root and cointegration tests encountered in
5631 applied econometric analysis.")
5632 (license license:gpl2+)))
5634 (define-public r-cubature
5641 (uri (cran-uri "cubature" version))
5644 "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq"))))
5645 (build-system r-build-system)
5647 `(("r-rcpp" ,r-rcpp)))
5649 `(("r-knitr" ,r-knitr)))
5650 (home-page "https://github.com/bnaras/cubature")
5651 (synopsis "Adaptive multivariate integration over hypercubes")
5653 "This package is an R wrapper around the cubature C library for adaptive
5654 multivariate integration over hypercubes. This version provides both
5655 @code{hcubature} and @code{pcubature} routines in addition to a vector
5657 ;; The included cubature C library is released under GPLv2+, but the
5658 ;; wrapper declares the license to be GPLv3+.
5659 (license (list license:gpl2+ license:gpl3+))))
5661 (define-public r-trend
5668 (uri (cran-uri "trend" version))
5671 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
5672 (build-system r-build-system)
5674 `(("r-extradistr" ,r-extradistr)))
5676 `(("gfortran" ,gfortran)))
5677 (home-page "https://cran.r-project.org/web/packages/trend/")
5678 (synopsis "Non-parametric trend tests and change-point detection")
5680 "The analysis of environmental data often requires the detection of
5681 trends and change-points. This package includes tests for trend
5682 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
5683 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
5684 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
5685 correlation trend test), change-point detection (Lanzante's test procedures,
5686 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
5687 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
5688 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
5689 sample Robust Rank-Order Distributional Test.")
5690 (license license:gpl3)))
5692 (define-public r-expm
5699 (uri (cran-uri "expm" version))
5702 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c"))))
5703 (build-system r-build-system)
5704 (propagated-inputs `(("r-matrix" ,r-matrix)))
5705 (native-inputs `(("gfortran" ,gfortran)))
5706 (home-page "https://r-forge.r-project.org/projects/expm/")
5707 (synopsis "Tools for matrix exponentials and related quantities")
5709 "This package provides tools for the computation of the matrix
5710 exponential, logarithm, square root, and related quantities.")
5711 (license license:gpl2+)))
5713 (define-public r-complexplus
5715 (name "r-complexplus")
5720 (uri (cran-uri "complexplus" version))
5723 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
5724 (build-system r-build-system)
5726 `(("r-expm" ,r-expm)
5727 ("r-matrix" ,r-matrix)))
5728 (home-page "https://cran.r-project.org/web/packages/complexplus/")
5729 (synopsis "Functions of complex or real variables")
5731 "This package extends several functions to the complex domain, including
5732 the matrix exponential and logarithm, and the determinant.")
5733 (license license:gpl2)))
5735 (define-public r-phontools
5737 (name "r-phontools")
5742 (uri (cran-uri "phonTools" version))
5745 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
5746 (properties `((upstream-name . "phonTools")))
5747 (build-system r-build-system)
5748 (home-page "http://www.santiagobarreda.com/rscripts.html")
5749 (synopsis "Tools for phonetic and acoustic analyses")
5751 "This package contains tools for the organization, display, and analysis
5752 of the sorts of data frequently encountered in phonetics research and
5753 experimentation, including the easy creation of IPA vowel plots, and the
5754 creation and manipulation of WAVE audio files.")
5755 (license license:bsd-2)))
5764 (uri (cran-uri "np" version))
5767 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
5768 (build-system r-build-system)
5770 `(("r-boot" ,r-boot)
5771 ("r-cubature" ,r-cubature)
5772 ("r-quadprog" ,r-quadprog)
5773 ("r-quantreg" ,r-quantreg)))
5774 (home-page "https://github.com/JeffreyRacine/R-Package-np")
5775 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
5776 (description "This package provides non-parametric (and semi-parametric)
5777 kernel methods that seamlessly handle a mix of continuous, unordered, and
5778 ordered factor data types.")
5779 ;; Any version of the GPL.
5780 (license license:gpl3+)))
5782 (define-public r-powerplus
5784 (name "r-powerplus")
5789 (uri (cran-uri "powerplus" version))
5792 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
5793 (build-system r-build-system)
5795 `(("r-complexplus" ,r-complexplus)
5798 ("r-matrix" ,r-matrix)
5799 ("r-phontools" ,r-phontools)))
5800 (home-page "https://cran.r-project.org/web/packages/powerplus/")
5801 (synopsis "Exponentiation operations")
5803 "This package provides tools for the computation of matrix and scalar
5805 (license license:gpl2)))
5807 (define-public r-egg
5814 (uri (cran-uri "egg" version))
5817 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
5818 (properties `((upstream-name . "egg")))
5819 (build-system r-build-system)
5821 `(("r-ggplot2" ,r-ggplot2)
5822 ("r-gridextra" ,r-gridextra)
5823 ("r-gtable" ,r-gtable)))
5824 (home-page "https://cran.r-project.org/web/packages/egg")
5825 (synopsis "Extensions for ggplot2")
5827 "This package provides miscellaneous functions to help customize ggplot2
5828 objects. High-level functions are provided to post-process ggplot2 layouts
5829 and allow alignment between plot panels, as well as setting panel sizes to
5830 fixed values. Other functions include a custom @code{geom}, and helper
5831 functions to enforce symmetric scales or add tags to facetted plots.")
5832 (license license:gpl3)))
5834 (define-public r-heatmaply
5836 (name "r-heatmaply")
5841 (uri (cran-uri "heatmaply" version))
5844 "0hspfkninwy62sf8gkdcsvwnvl66bbnjs2dpah9rr95a3rsgdp9d"))))
5845 (build-system r-build-system)
5847 `(("r-assertthat" ,r-assertthat)
5848 ("r-colorspace" ,r-colorspace)
5849 ("r-dendextend" ,r-dendextend)
5851 ("r-ggplot2" ,r-ggplot2)
5852 ("r-htmlwidgets" ,r-htmlwidgets)
5853 ("r-magrittr" ,r-magrittr)
5854 ("r-plotly" ,r-plotly)
5855 ("r-rcolorbrewer" ,r-rcolorbrewer)
5856 ("r-reshape2" ,r-reshape2)
5857 ("r-scales" ,r-scales)
5858 ("r-seriation" ,r-seriation)
5859 ("r-viridis" ,r-viridis)
5860 ("r-webshot" ,r-webshot)))
5862 `(("r-knitr" ,r-knitr)))
5863 (home-page "https://cran.r-project.org/package=heatmaply")
5864 (synopsis "Interactive cluster heat maps using plotly")
5866 "This package enables you to create interactive cluster heatmaps that can
5867 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
5868 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
5869 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
5870 a popular graphical method for visualizing high-dimensional data, in which a
5871 table of numbers is encoded as a grid of colored cells. The rows and columns
5872 of the matrix are ordered to highlight patterns and are often accompanied by
5874 ;; Either version of the license.
5875 (license (list license:gpl2 license:gpl3))))
5884 (uri (cran-uri "h5" version))
5887 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
5888 (build-system r-build-system)
5893 `(("which" ,which)))
5895 `(("r-rcpp" ,r-rcpp)))
5896 (home-page "https://github.com/mannau/h5")
5897 (synopsis "Interface to the HDF5 Library")
5899 "This package provides an S4 interface to the HDF5 library supporting
5900 fast storage and retrieval of R-objects like vectors, matrices and arrays to
5901 binary files in a language independent format. The HDF5 format can therefore
5902 be used as an alternative to R's save/load mechanism. Since h5 is able to
5903 access only subsets of stored data it can also handle data sets which do not
5905 (license license:bsd-2)))
5907 (define-public r-cgdsr
5914 (uri (cran-uri "cgdsr" version))
5917 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
5918 (build-system r-build-system)
5920 `(("r-httr" ,r-httr)
5921 ("r-r-methodss3" ,r-r-methodss3)
5922 ("r-r-oo" ,r-r-oo)))
5923 (home-page "https://github.com/cBioPortal/cgdsr")
5924 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
5926 "This package provides a basic set of R functions for querying the Cancer
5927 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
5928 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
5929 (license license:lgpl3)))
5931 (define-public r-import
5938 (uri (cran-uri "import" version))
5941 "018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37"))))
5942 (build-system r-build-system)
5944 `(("r-knitr" ,r-knitr)))
5945 (home-page "https://github.com/smbache/import")
5946 (synopsis "Import mechanism for R")
5948 "This is an alternative mechanism for importing objects from packages.
5949 The syntax allows for importing multiple objects from a package with a single
5950 command in an expressive way. The import package bridges some of the gap
5951 between using @code{library} (or @code{require}) and direct (single-object)
5952 imports. Furthermore the imported objects are not placed in the current
5953 environment. It is also possible to import objects from stand-alone @code{.R}
5955 (license license:expat)))
5957 (define-public r-shinyace
5964 (uri (cran-uri "shinyAce" version))
5967 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
5968 (properties `((upstream-name . "shinyAce")))
5969 (build-system r-build-system)
5971 `(("r-shiny" ,r-shiny)
5972 ("r-jsonlite" ,r-jsonlite)))
5973 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
5974 (synopsis "Ace editor bindings for Shiny")
5976 "This package provides Ace editor bindings to enable a rich text editing
5977 environment within Shiny.")
5978 (license license:expat)))
5980 (define-public r-randomizr
5982 (name "r-randomizr")
5987 (uri (cran-uri "randomizr" version))
5990 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
5991 (properties `((upstream-name . "randomizr")))
5992 (build-system r-build-system)
5994 `(("r-knitr" ,r-knitr)))
5995 (home-page "https://declaredesign.org/r/randomizr/")
5996 (synopsis "Tools for common forms of random assignment and sampling")
5998 "This package provides tools for generating random assignments for common
5999 experimental designs and random samples for common sampling designs.")
6000 (license license:expat)))
6002 (define-public r-base64url
6004 (name "r-base64url")
6009 (uri (cran-uri "base64url" version))
6012 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
6013 (build-system r-build-system)
6015 `(("r-backports" ,r-backports)))
6016 (home-page "https://github.com/mllg/base64url")
6017 (synopsis "Fast and URL-safe base64 encoder and decoder")
6019 "This package provides a URL-safe base64 encoder and decoder. In
6020 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
6021 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
6022 encoder does not fill the string with trailing @code{=}. The resulting
6023 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
6024 and thus are safe to use in URLs or for file names. The package also comes
6025 with a simple base32 encoder/decoder suited for case insensitive file
6027 (license license:gpl3)))
6029 (define-public r-radiant-data
6031 (name "r-radiant-data")
6036 (uri (cran-uri "radiant.data" version))
6039 "08bqqrfvpgyf613ikihwfnzb23l23f5nfs7zynnxbjxc1zfhbpny"))
6040 (modules '((guix build utils)))
6043 ;; Delete files that are under CC-NC-SA.
6044 (delete-file-recursively "inst/app/tools/help")
6046 (properties `((upstream-name . "radiant.data")))
6047 (build-system r-build-system)
6049 `(("r-base64enc" ,r-base64enc)
6050 ("r-broom" ,r-broom)
6053 ("r-dplyr" ,r-dplyr)
6056 ("r-ggplot2" ,r-ggplot2)
6057 ("r-import" ,r-import)
6058 ("r-jsonlite" ,r-jsonlite)
6059 ("r-knitr" ,r-knitr)
6060 ("r-lubridate" ,r-lubridate)
6061 ("r-magrittr" ,r-magrittr)
6062 ("r-markdown" ,r-markdown)
6064 ("r-patchwork" ,r-patchwork)
6065 ("r-plotly" ,r-plotly)
6066 ("r-psych" ,r-psych)
6067 ("r-randomizr" ,r-randomizr)
6068 ("r-readr" ,r-readr)
6069 ("r-readxl" ,r-readxl)
6070 ("r-rlang" ,r-rlang)
6071 ("r-rmarkdown" ,r-rmarkdown)
6072 ("r-rstudioapi" ,r-rstudioapi)
6073 ("r-scales" ,r-scales)
6074 ("r-shiny" ,r-shiny)
6075 ("r-shinyfiles" ,r-shinyfiles)
6076 ("r-shinyace" ,r-shinyace)
6077 ("r-stringi" ,r-stringi)
6078 ("r-tibble" ,r-tibble)
6079 ("r-tidyr" ,r-tidyr)
6080 ("r-writexl" ,r-writexl)))
6081 (home-page "https://github.com/radiant-rstats/radiant.data")
6082 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
6084 "The Radiant Data menu includes interfaces for loading, saving, viewing,
6085 visualizing, summarizing, transforming, and combining data. It also contains
6086 functionality to generate reproducible reports of the analyses conducted in
6088 (license license:agpl3)))
6090 (define-public r-algdesign
6092 (name "r-algdesign")
6097 (uri (cran-uri "AlgDesign" version))
6099 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
6100 (properties `((upstream-name . "AlgDesign")))
6101 (build-system r-build-system)
6102 (home-page "https://github.com/jvbraun/AlgDesign")
6103 (synopsis "Algorithmic experimental design")
6105 "This package provides tools to calculate exact and approximate theory
6106 experimental designs for D, A, and I criteria. Very large designs may be
6107 created. Experimental designs may be blocked or blocked designs created from
6108 a candidate list, using several criteria. The blocking can be done when whole
6109 and within plot factors interact.")
6110 (license license:gpl2+)))
6112 (define-public r-signal
6119 (uri (cran-uri "signal" version))
6122 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
6123 (build-system r-build-system)
6124 (propagated-inputs `(("r-mass" ,r-mass)))
6125 (native-inputs `(("gfortran" ,gfortran)))
6126 (home-page "https://cran.r-project.org/web/packages/signal/")
6127 (synopsis "Signal processing")
6129 "This package provides a set of signal processing functions originally
6130 written for Matlab and GNU Octave. It includes filter generation utilities,
6131 filtering functions, resampling routines, and visualization of filter models.
6132 It also includes interpolation functions.")
6133 (license license:gpl2)))
6135 (define-public r-gsubfn
6142 (uri (cran-uri "gsubfn" version))
6145 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
6146 (build-system r-build-system)
6147 (propagated-inputs `(("r-proto" ,r-proto)))
6148 (home-page "https://code.google.com/archive/p/gsubfn/")
6149 (synopsis "Utilities for strings and function arguments.")
6151 "This package provides @code{gsubfn} which is like @code{gsub} but can
6152 take a replacement function or certain other objects instead of the
6153 replacement string. Matches and back references are input to the replacement
6154 function and replaced by the function output. @code{gsubfn} can be used to
6155 split strings based on content rather than delimiters and for quasi-perl-style
6156 string interpolation. The package also has facilities for translating
6157 formulas to functions and allowing such formulas in function calls instead of
6159 (license license:gpl2+)))
6161 (define-public r-sqldf
6168 (uri (cran-uri "sqldf" version))
6171 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
6172 (build-system r-build-system)
6174 `(("r-chron" ,r-chron)
6176 ("r-gsubfn" ,r-gsubfn)
6177 ("r-proto" ,r-proto)
6178 ("r-rsqlite" ,r-rsqlite)))
6179 (home-page "https://github.com/ggrothendieck/sqldf")
6180 (synopsis "Manipulate R data frames using SQL")
6182 "The @code{sqldf} function is typically passed a single argument which is
6183 an SQL select statement where the table names are ordinary R data frame names.
6184 @code{sqldf} transparently sets up a database, imports the data frames into
6185 that database, performs the SQL statement and returns the result using a
6186 heuristic to determine which class to assign to each column of the returned
6187 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
6188 used to read filtered files into R even if the original files are larger than
6189 R itself can handle.")
6190 (license license:gpl2)))
6192 (define-public r-abind
6199 (uri (cran-uri "abind" version))
6202 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
6203 (build-system r-build-system)
6204 (home-page "https://cran.r-project.org/web/packages/abind/")
6205 (synopsis "Combine multidimensional arrays")
6207 "This package provides tools to combine multidimensional arrays into a
6208 single array. This is a generalization of @code{cbind} and @code{rbind}. It
6209 works with vectors, matrices, and higher-dimensional arrays. It also provides
6210 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
6211 extracting and replacing data in arrays.")
6212 (license license:lgpl2.0+)))
6214 (define-public r-prroc
6221 (uri (cran-uri "PRROC" version))
6224 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
6225 (properties `((upstream-name . "PRROC")))
6226 (build-system r-build-system)
6227 (home-page "https://cran.r-project.org/web/packages/PRROC/")
6228 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
6230 "This package computes the areas under the @dfn{precision-recall} (PR)
6231 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
6232 contrast to other implementations, the interpolation between points of the PR
6233 curve is done by a non-linear piecewise function. In addition to the areas
6234 under the curves, the curves themselves can also be computed and plotted by a
6235 specific S3-method.")
6236 (license license:gpl3)))
6238 (define-public r-vim
6245 (uri (cran-uri "VIM" version))
6248 "1a8aw0ysaf0al95m2la2zx1p3g5mnwqx0x30br1s1dqqkfnv57hz"))))
6249 (properties `((upstream-name . "VIM")))
6250 (build-system r-build-system)
6253 ("r-colorspace" ,r-colorspace)
6254 ("r-data-table" ,r-data-table)
6255 ("r-e1071" ,r-e1071)
6256 ("r-laeken" ,r-laeken)
6257 ("r-magrittr" ,r-magrittr)
6260 ("r-ranger" ,r-ranger)
6262 ("r-robustbase" ,r-robustbase)
6266 `(("r-knitr" ,r-knitr)))
6267 (home-page "https://github.com/alexkowa/VIM")
6268 (synopsis "Visualization and imputation of missing values")
6270 "This package provides tools for the visualization of missing and/or
6271 imputed values are introduced, which can be used for exploring the data and
6272 the structure of the missing and/or imputed values. Depending on this
6273 structure of the missing values, the corresponding methods may help to
6274 identify the mechanism generating the missing values and explore the
6275 data including missing values. In addition, the quality of imputation can be
6276 visually explored using various univariate, bivariate, multiple and
6277 multivariate plot methods.")
6278 (license license:gpl2+)))
6280 (define-public r-fnn
6287 (uri (cran-uri "FNN" version))
6290 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
6291 (properties `((upstream-name . "FNN")))
6292 (build-system r-build-system)
6293 (home-page "https://cran.r-project.org/web/packages/FNN")
6294 (synopsis "Fast nearest neighbor search algorithms and applications")
6296 "This package provides cover-tree and kd-tree fast k-nearest neighbor
6297 search algorithms. Related applications including KNN classification,
6298 regression and information measures are implemented.")
6299 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
6300 ;; later can be used.
6301 (license license:gpl2+)))
6303 (define-public r-smoother
6310 (uri (cran-uri "smoother" version))
6313 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
6314 (build-system r-build-system)
6316 `(("r-ttr" ,r-ttr)))
6317 (home-page "https://cran.r-project.org/web/packages/smoother")
6318 (synopsis "Functions relating to the smoothing of numerical data")
6320 "This package provides a collection of methods for smoothing numerical
6321 data, commencing with a port of the Matlab gaussian window smoothing function.
6322 In addition, several functions typically used in smoothing of financial data
6324 (license license:gpl2)))
6326 (define-public r-riverplot
6328 (name "r-riverplot")
6333 (uri (cran-uri "riverplot" version))
6336 "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj"))))
6337 (build-system r-build-system)
6339 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
6341 `(("r-knitr" ,r-knitr)))
6342 (home-page "https://logfc.wordpress.com")
6343 (synopsis "Sankey or ribbon plots")
6345 "Sankey plots are a type of diagram that is convenient to illustrate how
6346 flow of information, resources etc. separates and joins, much like observing
6347 how rivers split and merge. For example, they can be used to compare
6348 different clusterings. This package provides an implementation of Sankey
6350 (license license:gpl2+)))
6352 (define-public r-dyn
6359 (uri (cran-uri "dyn" version))
6362 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
6363 (build-system r-build-system)
6365 `(("r-zoo" ,r-zoo)))
6366 (home-page "https://cran.r-project.org/web/packages/dyn")
6367 (synopsis "Time series regression")
6369 "This package provides the dyn class interfaces @code{ts}, @code{irts},
6370 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
6371 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
6372 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
6373 @code{randomForest::randomForest()} and other regression functions, allowing
6374 those functions to be used with time series including specifications that may
6375 contain lags, diffs and missing values.")
6377 (license license:gpl2+)))
6379 (define-public r-catdap
6386 (uri (cran-uri "catdap" version))
6389 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
6390 (build-system r-build-system)
6392 `(("gfortran" ,gfortran)))
6393 (home-page "https://cran.r-project.org/web/packages/catdap/")
6394 (synopsis "Tools for categorical data analysis")
6396 "This package provides functions for analyzing multivariate data.
6397 Dependencies of the distribution of the specified variable (response
6398 variable) to other variables (explanatory variables) are derived and
6399 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
6400 (license license:gpl2+)))
6402 (define-public r-arules
6409 (uri (cran-uri "arules" version))
6412 "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm"))))
6413 (build-system r-build-system)
6415 `(("r-matrix" ,r-matrix)))
6416 (home-page "https://github.com/mhahsler/arules")
6417 (synopsis "Mining association rules and frequent itemsets")
6419 "This package provides an infrastructure for representing, manipulating
6420 and analyzing transaction data and patterns (frequent itemsets and association rules).
6421 It also provides C implementations of the association mining algorithms Apriori
6423 (license license:gpl3)))
6425 (define-public r-parsedate
6427 (name "r-parsedate")
6432 (uri (cran-uri "parsedate" version))
6435 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
6436 (build-system r-build-system)
6438 `(("r-rematch2" ,r-rematch2)))
6439 (home-page "https://github.com/gaborcsardi/parsedate")
6441 "Recognize and parse dates in various formats")
6443 "This package provides three functions for dealing with dates:
6444 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
6445 time formats, @code{parse_date} parses dates in unspecified formats,
6446 and @code{format_iso_8601} formats a date in ISO 8601 format.")
6447 (license license:gpl2)))
6449 (define-public r-abc-data
6456 (uri (cran-uri "abc.data" version))
6459 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
6460 (properties `((upstream-name . "abc.data")))
6461 (build-system r-build-system)
6462 (home-page "https://cran.r-project.org/web/packages/abc.data/")
6463 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
6465 "This package contains data which are used by functions of the abc
6466 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
6467 algorithms for performing parameter estimation, model selection, and
6469 (license license:gpl3+)))
6471 (define-public r-abc
6478 (uri (cran-uri "abc" version))
6481 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
6482 (build-system r-build-system)
6484 `(("r-abc-data" ,r-abc-data)
6485 ("r-locfit" ,r-locfit)
6488 ("r-quantreg" ,r-quantreg)))
6489 (home-page "https://cran.r-project.org/web/packages/abc/")
6490 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
6492 "This package implements several @dfn{Approximate Bayesian
6493 Computation} (ABC) algorithms for performing parameter estimation, model
6494 selection, and goodness-of-fit. Cross-validation tools are also available for
6495 measuring the accuracy of ABC estimates, and to calculate the
6496 misclassification probabilities of different models.")
6497 (license license:gpl3+)))
6499 (define-public r-zip
6506 (uri (cran-uri "zip" version))
6509 "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i"))))
6510 (build-system r-build-system)
6511 (home-page "https://github.com/gaborcsardi/zip")
6512 (synopsis "Cross-platform Zip compression")
6514 "This package provides a cross-platform Zip compression library for R.
6515 It is a replacement for the @code{zip} function, that does not require any
6516 additional external tools on any platform.")
6517 (license license:cc0)))
6519 (define-public r-openxlsx
6526 (uri (cran-uri "openxlsx" version))
6529 "0vz4nlrwgsiifrgza8kfd9i1c0ya6plymrgk59vyy2z54vc8kvyd"))))
6530 (build-system r-build-system)
6532 `(("r-rcpp" ,r-rcpp)
6533 ("r-stringi" ,r-stringi)
6536 `(("r-knitr" ,r-knitr)))
6537 (home-page "https://github.com/awalker89/openxlsx")
6538 (synopsis "Read, write and edit XLSX files")
6540 "This package simplifies the creation of Excel @code{.xlsx} files by
6541 providing a high level interface to writing, styling and editing worksheets.
6542 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
6543 and @code{XLConnect} packages with the added benefit of removing the
6544 dependency on Java.")
6545 (license license:gpl3)))
6547 (define-public r-rio
6554 (uri (cran-uri "rio" version))
6557 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
6558 (build-system r-build-system)
6560 `(("r-curl" ,r-curl)
6561 ("r-data-table" ,r-data-table)
6562 ("r-foreign" ,r-foreign)
6563 ("r-haven" ,r-haven)
6564 ("r-openxlsx" ,r-openxlsx)
6565 ("r-readxl" ,r-readxl)
6566 ("r-tibble" ,r-tibble)))
6567 (home-page "https://github.com/leeper/rio")
6568 (synopsis "Swiss-army knife for data I/O")
6570 "This package provides streamlined data import and export infrastructure
6571 by making assumptions that the user is probably willing to make: @code{import}
6572 and @code{export} determine the data structure from the file extension,
6573 reasonable defaults are used for data import and export (e.g.,
6574 @code{stringsAsFactors=FALSE}), web-based import is natively
6575 supported (including from SSL/HTTPS), compressed files can be read directly
6576 without explicit decompression, and fast import packages are used where
6577 appropriate. An additional convenience function, @code{convert}, provides a
6578 simple method for converting between file types.")
6579 (license license:gpl2)))
6581 (define-public r-maptools
6588 (uri (cran-uri "maptools" version))
6591 "0jgf3wg47jdnznxb3ncv4is9ackwviy4lzcyggqwzw3wh6jnvb6s"))))
6592 (build-system r-build-system)
6594 `(("r-foreign" ,r-foreign)
6595 ("r-lattice" ,r-lattice)
6597 (home-page "https://r-forge.r-project.org/projects/maptools/")
6598 (synopsis "Tools for reading and handling spatial objects")
6600 "This package provides a set of tools for manipulating and reading
6601 geographic data, in particular ESRI Shapefiles. It includes binary access to
6602 GSHHG shoreline files. The package also provides interface wrappers for
6603 exchanging spatial objects with other R packages.")
6604 ;; The C source files from shapelib are released under the Expat license.
6605 ;; The R code is released under GPL version 2 or later.
6606 (license (list license:gpl2+
6609 (define-public r-later
6616 (uri (cran-uri "later" version))
6619 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
6620 (build-system r-build-system)
6624 ("r-rlang" ,r-rlang)))
6626 `(("r-knitr" ,r-knitr)))
6627 (home-page "https://github.com/r-lib/later")
6628 (synopsis "Utilities for delaying function execution")
6630 "This package provides tools to execute arbitrary R or C functions some
6631 time after the current time, after the R execution stack has emptied.")
6632 (license license:gpl2+)))
6634 (define-public r-promises
6641 (uri (cran-uri "promises" version))
6644 "002qkhcn3ri6a3w5fizjvdvrjgvqiw8i7rl9jglcnqik5kmwc61p"))))
6645 (build-system r-build-system)
6647 `(("r-later" ,r-later)
6648 ("r-magrittr" ,r-magrittr)
6651 ("r-rlang" ,r-rlang)))
6653 `(("r-knitr" ,r-knitr)))
6654 (home-page "https://rstudio.github.io/promises")
6655 (synopsis "Abstractions for promise-based asynchronous programming")
6657 "This package provides fundamental abstractions for doing asynchronous
6658 programming in R using promises. Asynchronous programming is useful for
6659 allowing a single R process to orchestrate multiple tasks in the background
6660 while also attending to something else. Semantics are similar to JavaScript
6661 promises, but with a syntax that is idiomatic R.")
6662 (license license:expat)))
6664 (define-public r-dosnow
6671 (uri (cran-uri "doSNOW" version))
6674 "0f07b38cl7s61vwzkyqkzzsic9g4sw9k6ndbxk3g90l4ca0d1ljc"))))
6675 (properties `((upstream-name . "doSNOW")))
6676 (build-system r-build-system)
6678 `(("r-foreach" ,r-foreach)
6679 ("r-iterators" ,r-iterators)
6680 ("r-snow" ,r-snow)))
6681 (home-page "https://cran.r-project.org/web/packages/doSNOW")
6682 (synopsis "Foreach parallel adaptor for the snow package")
6684 "This package provides a parallel backend for the @code{%dopar%} function
6685 using the @code{snow} package.")
6686 (license license:gpl2)))
6688 (define-public r-fst
6695 (uri (cran-uri "fst" version))
6698 "0vwclzxww8mw9nnpyj29bn71mrr8jjg7ka03979h9rbzw6d9bjrr"))))
6699 (properties `((upstream-name . "fst")))
6700 (build-system r-build-system)
6701 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
6702 (home-page "http://www.fstpackage.org")
6703 (synopsis "Fast serialization of data frames")
6705 "The fst package for R provides a fast, easy and flexible way to
6706 serialize data frames. With access speeds of multiple GB/s, fst is
6707 specifically designed to unlock the potential of high speed solid state disks.
6708 Data frames stored in the fst format have full random access, both in column
6709 and rows. The fst format allows for random access of stored data and
6710 compression with the LZ4 and ZSTD compressors.")
6711 (license license:agpl3)))
6713 (define-public r-snowfall
6716 (version "1.84-6.1")
6719 (uri (cran-uri "snowfall" version))
6721 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
6722 (build-system r-build-system)
6724 `(("r-snow" ,r-snow)))
6725 (home-page "https://cran.r-project.org/web/packages/snowfall/")
6726 (synopsis "Easier cluster computing")
6727 (description "This package is a usability wrapper around snow for easier
6728 development of parallel R programs. This package offers e.g. extended error
6729 checks, and additional functions. All functions work in sequential mode, too,
6730 if no cluster is present or wished. The package is also designed as connector
6731 to the cluster management tool @code{sfCluster}, but can also used without
6733 (license license:gpl2+)))
6735 (define-public r-rgexf
6742 (uri (cran-uri "rgexf" version))
6745 "1vj5ha1qx0xzflchxf25ycys6clfn9y32m1717afzkvhmkwisrra"))
6748 ;; Delete minified JavaScript files
6749 (for-each delete-file
6750 '("inst/gexf-js/js/jquery-2.0.2.min.js"
6751 "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js"
6752 "inst/gexf-js/js/jquery.mousewheel.min.js"))
6754 (properties `((upstream-name . "rgexf")))
6755 (build-system r-build-system)
6757 `(#:modules ((guix build utils)
6758 (guix build r-build-system)
6762 (modify-phases %standard-phases
6763 (add-after 'unpack 'process-javascript
6764 (lambda* (#:key inputs #:allow-other-keys)
6765 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-jquery-ui"))
6766 (with-directory-excursion "inst/gexf-js/js/"
6770 `((,(assoc-ref inputs "js-jquery")
6771 "jquery-2.0.2.min.js")
6772 ("/tmp/jquery-ui-1.10.3/ui/jquery-ui.js"
6773 "jquery-ui-1.10.3.custom.min.js")
6774 (,(assoc-ref inputs "js-jquery-mousewheel")
6775 "jquery.mousewheel.min.js"))))
6776 (lambda (sources targets)
6777 (for-each (lambda (source target)
6778 (format #true "Processing ~a --> ~a~%"
6780 (invoke "esbuild" source "--minify"
6781 (string-append "--outfile=" target)))
6785 `(("r-igraph" ,r-igraph)
6786 ("r-servr" ,r-servr)
6789 `(("r-knitr" ,r-knitr)
6790 ("esbuild" ,esbuild)
6795 (uri "https://code.jquery.com/jquery-2.0.2.js")
6798 "0v818bxpw48gdk8i95qqqij80r9jcgisi2r4ac6xnxca20h0gvfj"))))
6802 (uri "https://jqueryui.com/resources/download/jquery-ui-1.10.3.zip")
6805 "00xpfy0l69nj2yan4s8k65ldsrlfsjkmyw2dwcg93dc8mv454vxx"))))
6806 ("js-jquery-mousewheel"
6809 (uri "https://raw.githubusercontent.com/jquery/jquery-mousewheel/\
6810 3.0.6/jquery.mousewheel.js")
6813 "19lk5xy2s47bx8hsa7j6bg012f8yw6d770g230bcnm559kf4nc6v"))))))
6814 (home-page "https://gvegayon.github.io/rgexf")
6815 (synopsis "Build, import and export GEXF graph files")
6817 "Create, read and write GEXF (Graph Exchange XML Format) graph
6818 files (used in Gephi and others). It allows the user to easily build/read
6819 graph files including attributes, GEXF visual attributes (such as color, size,
6820 and position), network dynamics (for both edges and nodes) and edge weighting.
6821 Users can build/handle graphs element-by-element or massively through
6822 data-frames, visualize the graph on a web browser through gexf-js (a
6823 JavaScript library) and interact with the igraph package.")
6824 (license license:expat)))
6826 (define-public r-data-tree
6828 (name "r-data-tree")
6833 (uri (cran-uri "data.tree" version))
6836 "0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
6837 (properties `((upstream-name . "data.tree")))
6838 (build-system r-build-system)
6841 ("r-stringi" ,r-stringi)))
6843 `(("r-knitr" ,r-knitr)))
6844 (home-page "http://github.com/gluc/data.tree")
6845 (synopsis "General purpose hierarchical data structure")
6847 "Create tree structures from hierarchical data, and traverse the tree in
6848 various orders. Aggregate, cumulate, print, plot, convert to and from
6849 data.frame and more. This is useful for decision trees, machine learning,
6850 finance, conversion from and to JSON, and many other applications.")
6851 (license license:gpl2+)))
6853 (define-public r-collapsibletree
6855 (name "r-collapsibletree")
6860 (uri (cran-uri "collapsibleTree" version))
6863 "0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
6866 ;; Delete minified JavaScript file
6867 (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js")
6870 `((upstream-name . "collapsibleTree")))
6871 (build-system r-build-system)
6874 (modify-phases %standard-phases
6875 (add-after 'unpack 'process-javascript
6876 (lambda* (#:key inputs #:allow-other-keys)
6877 (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/"
6878 (let ((source (assoc-ref inputs "d3.v4.js"))
6879 (target "d3.min.js"))
6880 (format #t "Processing ~a --> ~a~%"
6882 (invoke "esbuild" source "--minify"
6883 (string-append "--outfile=" target)))))))))
6885 `(("r-data-tree" ,r-data-tree)
6886 ("r-htmlwidgets" ,r-htmlwidgets)))
6888 `(("esbuild" ,esbuild)
6892 (uri "https://d3js.org/d3.v4.js")
6895 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
6896 (home-page "https://github.com/AdeelK93/collapsibleTree")
6897 (synopsis "Interactive collapsible tree diagrams using D3.js")
6899 "This is a package for interactive Reingold-Tilford tree diagrams created
6900 using D3.js, where every node can be expanded and collapsed by clicking on it.
6901 Tooltips and color gradients can be mapped to nodes using a numeric column in
6902 the source data frame.")
6903 (license license:gpl3+)))
6905 (define-public r-rappdirs
6912 (uri (cran-uri "rappdirs" version))
6915 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9"))))
6916 (build-system r-build-system)
6917 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
6918 (synopsis "Determine where to save data, caches, and logs")
6920 "This package provides an easy way to determine which directories on the
6921 user's computer should be used to save data, caches and logs. It is a port of
6922 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
6923 (license license:expat)))
6925 (define-public r-rastervis
6927 (name "r-rastervis")
6932 (uri (cran-uri "rasterVis" version))
6935 "0d12h7xqcwy1wps6yya9nzfppbnsxpmbkqmy3a8pvxpg81l632kk"))))
6936 (properties `((upstream-name . "rasterVis")))
6937 (build-system r-build-system)
6939 `(("r-hexbin" ,r-hexbin)
6940 ("r-lattice" ,r-lattice)
6941 ("r-latticeextra" ,r-latticeextra)
6942 ("r-raster" ,r-raster)
6943 ("r-rcolorbrewer" ,r-rcolorbrewer)
6945 ("r-viridislite" ,r-viridislite)
6947 (home-page "https://oscarperpinan.github.io/rastervis/")
6948 (synopsis "Visualization methods for raster data")
6950 "This package provides methods for enhanced visualization and interaction
6951 with raster data. It implements visualization methods for quantitative data
6952 and categorical data, both for univariate and multivariate rasters. It also
6953 provides methods to display spatiotemporal rasters, and vector fields.")
6954 (license license:gpl3)))
6956 (define-public r-rentrez
6963 (uri (cran-uri "rentrez" version))
6966 "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv"))))
6967 (properties `((upstream-name . "rentrez")))
6968 (build-system r-build-system)
6970 `(("r-httr" ,r-httr)
6971 ("r-jsonlite" ,r-jsonlite)
6974 `(("r-knitr" ,r-knitr)))
6975 (home-page "https://docs.ropensci.org/rentrez/")
6976 (synopsis "Entrez in R")
6978 "This package provides an R interface to the NCBI's EUtils API,
6979 allowing users to search databases like GenBank PubMed, process the results of
6980 those searches and pull data into their R sessions.")
6981 (license license:expat)))
6983 (define-public r-renv
6990 (uri (cran-uri "renv" version))
6993 "0wfq1z5glng6jrfxj25mjhp129z6468gaszr9ggks5gp8lrwszzh"))))
6994 (properties `((upstream-name . "renv")))
6995 (build-system r-build-system)
6997 `(("r-knitr" ,r-knitr)))
6998 (home-page "https://rstudio.github.io/renv")
6999 (synopsis "Project environments")
7001 "This package provides a dependency management toolkit for R. Using
7002 renv, you can create and manage project-local R libraries, save the state of
7003 these libraries to a lockfile, and later restore your library as required.
7004 Together, these tools can help make your projects more isolated, portable, and
7006 (license license:expat)))
7008 (define-public r-learnr
7015 (uri (cran-uri "learnr" version))
7018 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
7019 (build-system r-build-system)
7021 `(("r-checkmate" ,r-checkmate)
7022 ("r-ellipsis" ,r-ellipsis)
7023 ("r-evaluate" ,r-evaluate)
7024 ("r-htmltools" ,r-htmltools)
7025 ("r-htmlwidgets" ,r-htmlwidgets)
7026 ("r-jsonlite" ,r-jsonlite)
7027 ("r-knitr" ,r-knitr)
7028 ("r-markdown" ,r-markdown)
7029 ("r-rappdirs" ,r-rappdirs)
7031 ("r-rmarkdown" ,r-rmarkdown)
7032 ("r-rprojroot" ,r-rprojroot)
7033 ("r-shiny" ,r-shiny)
7034 ("r-withr" ,r-withr)))
7035 (home-page "https://rstudio.github.io/learnr/")
7036 (synopsis "Interactive tutorials for R")
7038 "This package provides tools to create interactive tutorials using R
7039 Markdown. Use a combination of narrative, figures, videos, exercises, and
7040 quizzes to create self-paced tutorials for learning about R and R packages.")
7041 (license license:asl2.0)))
7043 (define-public r-analytics
7045 (name "r-analytics")
7050 (uri (cran-uri "analytics" version))
7053 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
7054 (build-system r-build-system)
7057 ("r-cluster" ,r-cluster)
7058 ("r-fractal" ,r-fractal)
7059 ("r-lmtest" ,r-lmtest)
7062 ("r-powerplus" ,r-powerplus)
7063 ("r-robust" ,r-robust)
7064 ("r-trend" ,r-trend)
7068 (home-page "https://cran.r-project.org/web/packages/analytics/")
7069 (synopsis "Collection of data analysis tools")
7071 "This package is a collection of data analysis tools. It includes tools
7072 for regression outlier detection in a fitted linear model, stationary
7073 bootstrap using a truncated geometric distribution, a comprehensive test for
7074 weak stationarity, column means by group, weighted biplots, and a heuristic to
7075 obtain a better initial configuration in non-metric MDS.")
7076 (license license:gpl2)))
7078 (define-public r-reticulate
7080 (name "r-reticulate")
7085 (uri (cran-uri "reticulate" version))
7088 "04w5c9jfxakb4rr2qjynxgagb42khsja3y4dwgxywiplb1d8agxk"))))
7089 (build-system r-build-system)
7090 (inputs `(("python" ,python)))
7092 `(("r-rappdirs" ,r-rappdirs)
7093 ("r-jsonlite" ,r-jsonlite)
7094 ("r-matrix" ,r-matrix)
7095 ("r-rcpp" ,r-rcpp)))
7097 `(("r-knitr" ,r-knitr)))
7098 (home-page "https://github.com/rstudio/reticulate")
7099 (synopsis "R interface to Python")
7101 "This package provides an interface from R to Python modules, classes,
7102 and functions. When calling into Python, R data types are automatically
7103 converted to their equivalent Python types. When values are returned from
7104 Python to R they are converted back to R types.")
7105 (license license:asl2.0)))
7107 (define-public r-bibtex
7114 (uri (cran-uri "bibtex" version))
7117 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv"))))
7118 (build-system r-build-system)
7119 (propagated-inputs `(("r-stringr" ,r-stringr)))
7120 (home-page "https://github.com/romainfrancois/bibtex")
7121 (synopsis "Bibtex parser")
7122 (description "This package provides a utility for R to parse a bibtex
7124 (license license:gpl2+)))
7126 (define-public r-ggseqlogo
7128 (name "r-ggseqlogo")
7133 (uri (cran-uri "ggseqlogo" version))
7136 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
7137 (build-system r-build-system)
7138 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
7139 (home-page "https://github.com/omarwagih/ggseqlogo")
7140 (synopsis "ggplot2 extension for drawing genetic sequence logos")
7142 "The range of functions provided by this package makes it possible to
7143 draw highly versatile genomic sequence logos. Features include, but are not
7144 limited to, modifying colour schemes and fonts used to draw the logo,
7145 generating multiple logo plots, and aiding the visualisation with annotations.
7146 Sequence logos can easily be combined with other ggplot2 plots.")
7147 ;; Unspecified version of the LGPL.
7148 (license license:lgpl3+)))
7150 (define-public r-ggsci
7157 (uri (cran-uri "ggsci" version))
7160 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
7161 (build-system r-build-system)
7163 `(("r-ggplot2" ,r-ggplot2)
7164 ("r-scales" ,r-scales)))
7165 (home-page "https://nanx.me/ggsci/")
7166 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
7168 "This package provides a collection of ggplot2 color palettes inspired by
7169 plots in scientific journals, data visualization libraries, science fiction
7170 movies, and TV shows.")
7171 (license license:gpl3)))
7173 (define-public r-ggsignif
7180 (uri (cran-uri "ggsignif" version))
7183 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
7184 (build-system r-build-system)
7186 `(("r-knitr" ,r-knitr)))
7188 `(("r-ggplot2" ,r-ggplot2)))
7189 (home-page "https://github.com/const-ae/ggsignif")
7190 (synopsis "Significance brackets for ggplot2")
7192 "Enrich your ggplots with group-wise comparisons. This package provides
7193 an easy way to indicate if two groups are significantly different. Commonly
7194 this is shown by a bracket on top connecting the groups of interest which
7195 itself is annotated with the level of significance. The package provides a
7196 single layer that takes the groups for comparison and the test as arguments
7197 and adds the annotation to the plot.")
7198 (license license:gpl3)))
7200 (define-public r-rstatix
7207 (uri (cran-uri "rstatix" version))
7210 "0nwwvxwr4z3j4n9z8cnvwghppc836g47n0ia98chk272qwh8xcpb"))))
7211 (properties `((upstream-name . "rstatix")))
7212 (build-system r-build-system)
7214 `(("r-broom" ,r-broom)
7216 ("r-corrplot" ,r-corrplot)
7217 ("r-dplyr" ,r-dplyr)
7218 ("r-generics" ,r-generics)
7219 ("r-magrittr" ,r-magrittr)
7220 ("r-purrr" ,r-purrr)
7221 ("r-rlang" ,r-rlang)
7222 ("r-tibble" ,r-tibble)
7223 ("r-tidyr" ,r-tidyr)
7224 ("r-tidyselect" ,r-tidyselect)))
7225 (home-page "https://rpkgs.datanovia.com/rstatix/")
7226 (synopsis "Pipe-friendly framework for basic statistical tests")
7228 "This package provides a simple and intuitive pipe-friendly framework,
7229 coherent with the @code{tidyverse} design philosophy, for performing basic
7230 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
7231 correlation analyses. The output of each test is automatically transformed
7232 into a tidy data frame to facilitate visualization. Additional functions are
7233 available for reshaping, reordering, manipulating and visualizing correlation
7235 (license license:gpl2)))
7237 (define-public r-ggpubr
7244 (uri (cran-uri "ggpubr" version))
7247 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
7248 (build-system r-build-system)
7250 `(("r-cowplot" ,r-cowplot)
7251 ("r-dplyr" ,r-dplyr)
7252 ("r-ggplot2" ,r-ggplot2)
7253 ("r-ggrepel" ,r-ggrepel)
7254 ("r-ggsci" ,r-ggsci)
7255 ("r-ggsignif" ,r-ggsignif)
7257 ("r-gridextra" ,r-gridextra)
7258 ("r-magrittr" ,r-magrittr)
7259 ("r-polynom" ,r-polynom)
7260 ("r-purrr" ,r-purrr)
7261 ("r-rlang" ,r-rlang)
7262 ("r-scales" ,r-scales)
7263 ("r-rstatix" ,r-rstatix)
7264 ("r-tibble" ,r-tibble)
7265 ("r-tidyr" ,r-tidyr)))
7266 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
7267 (synopsis "ggplot2-based publication-ready plots")
7269 "The ggplot2 package is an excellent and flexible package for elegant
7270 data visualization in R. However the default generated plots require some
7271 formatting before we can send them for publication. The ggpubr package
7272 provides some easy-to-use functions for creating and customizing ggplot2-based
7273 publication-ready plots.")
7274 (license license:gpl2)))
7276 (define-public r-ellipse
7283 (uri (cran-uri "ellipse" version))
7286 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
7287 (build-system r-build-system)
7288 (home-page "https://cran.r-project.org/web/packages/ellipse/")
7289 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
7291 "This package contains various routines for drawing ellipses and
7292 ellipse-like confidence regions, implementing the plots described in Murdoch
7293 and Chow (1996), A graphical display of large correlation matrices, The
7294 American Statistician 50, 178-180. There are also routines implementing the
7295 profile plots described in Bates and Watts (1988), Nonlinear Regression
7296 Analysis and its Applications.")
7297 (license license:gpl2+)))
7299 (define-public r-flashclust
7301 (name "r-flashclust")
7306 (uri (cran-uri "flashClust" version))
7309 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
7310 (properties `((upstream-name . "flashClust")))
7311 (build-system r-build-system)
7312 (native-inputs `(("gfortran" ,gfortran)))
7313 (home-page "https://cran.r-project.org/web/packages/flashClust/")
7314 (synopsis "Implementation of optimal hierarchical clustering")
7316 "This package provides a fast implementation of hierarchical
7318 (license license:gpl2+)))
7320 (define-public r-factominer
7322 (name "r-factominer")
7327 (uri (cran-uri "FactoMineR" version))
7330 "0lg8n9fxxk46nchnj4pbpqqf4swxfsq7r9jzr36dmd36kb7avqxr"))))
7331 (properties `((upstream-name . "FactoMineR")))
7332 (build-system r-build-system)
7335 ("r-cluster" ,r-cluster)
7337 ("r-ellipse" ,r-ellipse)
7338 ("r-flashclust" ,r-flashclust)
7339 ("r-ggplot2" ,r-ggplot2)
7340 ("r-ggrepel" ,r-ggrepel)
7341 ("r-lattice" ,r-lattice)
7342 ("r-leaps" ,r-leaps)
7344 ("r-scatterplot3d" ,r-scatterplot3d)))
7346 `(("r-knitr" ,r-knitr)))
7347 (home-page "http://factominer.free.fr")
7348 (synopsis "Multivariate exploratory data analysis and data mining")
7350 "This package provides exploratory data analysis methods to summarize,
7351 visualize and describe datasets. The main principal component methods are
7352 available, those with the largest potential in terms of applications:
7353 principal component analysis (PCA) when variables are quantitative,
7354 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
7355 variables are categorical, Multiple Factor Analysis when variables are
7356 structured in groups, etc. and hierarchical cluster analysis.")
7357 (license license:gpl2+)))
7359 (define-public r-factoextra
7361 (name "r-factoextra")
7366 (uri (cran-uri "factoextra" version))
7369 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
7370 (build-system r-build-system)
7372 `(("r-abind" ,r-abind)
7373 ("r-cluster" ,r-cluster)
7374 ("r-dendextend" ,r-dendextend)
7375 ("r-factominer" ,r-factominer)
7376 ("r-ggplot2" ,r-ggplot2)
7377 ("r-ggpubr" ,r-ggpubr)
7378 ("r-ggrepel" ,r-ggrepel)
7379 ("r-reshape2" ,r-reshape2)
7380 ("r-tidyr" ,r-tidyr)))
7381 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
7382 (synopsis "Extract and visualize the results of multivariate data analyses")
7384 "This package provides some easy-to-use functions to extract and
7385 visualize the output of multivariate data analyses, including
7386 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
7387 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
7388 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
7389 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
7390 packages. It contains also functions for simplifying some clustering analysis
7391 steps and provides ggplot2-based elegant data visualization.")
7392 (license license:gpl2)))
7394 (define-public r-fansi
7401 (uri (cran-uri "fansi" version))
7404 "0i7wmaflkjzdbggqv31wnsj3m9imvc6db429vyjk64xrz1ng1vd2"))))
7405 (build-system r-build-system)
7407 `(("r-knitr" ,r-knitr))) ; for vignettes
7408 (home-page "https://github.com/brodieG/fansi")
7409 (synopsis "ANSI control sequence aware string functions")
7411 "This package provides counterparts to R string manipulation functions
7412 that account for the effects of ANSI text formatting control sequences.")
7413 (license license:gpl2+)))
7415 (define-public r-nbclust
7422 (uri (cran-uri "NbClust" version))
7425 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
7426 (properties `((upstream-name . "NbClust")))
7427 (build-system r-build-system)
7428 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
7429 (synopsis "Determine the best number of clusters in a data set")
7431 "NbClust provides 30 indexes for determining the optimal number of
7432 clusters in a data set and offers the best clustering scheme from different
7433 results to the user.")
7434 (license license:gpl2)))
7436 (define-public r-hdf5r
7443 (uri (cran-uri "hdf5r" version))
7446 "0i8m4yjxggrs05slq2afvz2ckl1yc9wq7gd1s7dq2gjn46zkry50"))))
7447 (build-system r-build-system)
7452 `(("r-bit64" ,r-bit64)
7455 `(("r-knitr" ,r-knitr)))
7456 (home-page "https://hhoeflin.github.io/hdf5r")
7457 (synopsis "Interface to the HDF5 binary data format")
7459 "HDF5 is a data model, library and file format for storing and managing
7460 large amounts of data. This package provides a nearly feature complete,
7461 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
7462 functionality is added so that HDF5 objects behave very similar to their
7463 corresponding R counterparts.")
7464 (license license:asl2.0)))
7466 (define-public r-itertools
7468 (name "r-itertools")
7473 (uri (cran-uri "itertools" version))
7476 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
7477 (build-system r-build-system)
7479 `(("r-iterators" ,r-iterators)))
7480 (home-page "https://cran.r-project.org/web/packages/itertools/")
7481 (synopsis "Iterator tools")
7483 "This package provides various tools for creating iterators, many
7484 patterned after functions in the Python @code{itertools} module, and others
7485 patterned after functions in the snow package.")
7486 (license license:gpl2)))
7488 (define-public r-polynom
7495 (uri (cran-uri "polynom" version))
7498 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
7499 (build-system r-build-system)
7500 (home-page "https://cran.r-project.org/web/packages/polynom/")
7501 (synopsis "Functions for univariate polynomial manipulations")
7503 "This package provides a collection of functions to implement a class for
7504 univariate polynomial manipulations.")
7505 (license license:gpl2)))
7507 (define-public r-gbrd
7514 (uri (cran-uri "gbRd" version))
7517 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
7518 (properties `((upstream-name . "gbRd")))
7519 (build-system r-build-system)
7520 (home-page "https://cran.r-project.org/web/packages/gbRd/")
7521 (synopsis "Utilities for processing Rd objects and files")
7523 "This package provides utilities for processing Rd objects and files.
7524 Extract argument descriptions and other parts of the help pages of
7526 (license license:gpl2+)))
7528 (define-public r-rjags
7535 (uri (cran-uri "rjags" version))
7538 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
7539 (build-system r-build-system)
7541 `(("r-coda" ,r-coda)))
7545 `(("pkg-config" ,pkg-config)))
7546 (home-page "http://mcmc-jags.sourceforge.net")
7547 (synopsis "Bayesian graphical models using MCMC")
7549 "This package provides an R interface to the JAGS MCMC library. JAGS is
7550 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
7551 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
7552 (license license:gpl2)))
7554 (define-public r-rbibutils
7556 (name "r-rbibutils")
7561 (uri (cran-uri "rbibutils" version))
7564 "1vfg2188i4dyhrmvnwpsh2la8qkd4wkryz2fpj4cppi1wfz3ml83"))))
7565 (properties `((upstream-name . "rbibutils")))
7566 (build-system r-build-system)
7567 (home-page "https://geobosh.github.io/rbibutils/")
7568 (synopsis "Convert between bibliography formats")
7570 "This package converts between a number of bibliography formats,
7571 including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils
7572 utilities and supports all bibliography formats and character encodings
7573 implemented in bibutils.")
7574 (license license:gpl2)))
7576 (define-public r-rdpack
7583 (uri (cran-uri "Rdpack" version))
7586 "1kmz0kq2z1xl55w22paz98x9jpss06abvicmkslv4zq77kz99q16"))))
7587 (properties `((upstream-name . "Rdpack")))
7588 (build-system r-build-system)
7590 `(("r-rbibutils" ,r-rbibutils)
7591 ("r-gbrd" ,r-gbrd)))
7592 (home-page "https://github.com/GeoBosh/Rdpack")
7593 (synopsis "Update and manipulate Rd documentation objects")
7595 "This package provides functions for manipulation of R documentation
7596 objects, including functions @code{reprompt()} and @code{ereprompt()} for
7597 updating Rd documentation for functions, methods and classes; it also includes
7598 Rd macros for citations and import of references from bibtex files for use in
7599 Rd files and roxygen2 comments, as well as many functions for manipulation of
7600 references and Rd files.")
7601 (license license:gpl2+)))
7603 (define-public r-officer
7610 (uri (cran-uri "officer" version))
7613 "1ls5kp70jfxrzxxb3xrg8sn2fyk6qd7rmx23n5jxi7z7850avjrj"))))
7614 (build-system r-build-system)
7621 `(("r-knitr" ,r-knitr)))
7622 (home-page "https://davidgohel.github.io/officer")
7623 (synopsis "Manipulation of Word and PowerPoint documents")
7625 "This package provides tools to access and manipulate Word and PowerPoint
7626 documents from R. The package focuses on tabular and graphical reporting from
7627 R; it also provides two functions that let users get document content into
7628 data objects. A set of functions lets add and remove images, tables and
7629 paragraphs of text in new or existing documents. When working with PowerPoint
7630 presentations, slides can be added or removed; shapes inside slides can also
7631 be added or removed. When working with Word documents, a cursor can be used
7632 to help insert or delete content at a specific location in the document.")
7633 (license license:gpl3)))
7635 (define-public r-profilemodel
7637 (name "r-profilemodel")
7642 (uri (cran-uri "profileModel" version))
7645 "01m5nb8cmq0aq555pxk2a99182si65hhmn68yn9nal2j3zl2bp4i"))))
7646 (properties `((upstream-name . "profileModel")))
7647 (build-system r-build-system)
7648 (home-page "https://github.com/ikosmidis/profileModel")
7649 (synopsis "Profiling inference functions for various model classes")
7651 "This package provides tools that can be used to calculate, evaluate,
7652 plot and use for inference the profiles of *arbitrary* inference functions for
7653 arbitrary @code{glm}-like fitted models with linear predictors. More information
7654 on the methods that are implemented can be found in Kosmidis (2008)
7655 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
7656 (license license:gpl2+)))
7658 (define-public r-brglm
7665 (uri (cran-uri "brglm" version))
7668 "1v68ma1agwhxar76mfvdfkcnd5h4gmxiz8j491rhdsckg271j7sa"))))
7669 (properties `((upstream-name . "brglm")))
7670 (build-system r-build-system)
7672 `(("r-profilemodel" ,r-profilemodel)))
7673 (home-page "https://github.com/ikosmidis/brglm")
7674 (synopsis "Bias reduction in binomial-response generalized linear models")
7676 "Fit generalized linear models with binomial responses using either an
7677 adjusted-score approach to bias reduction or maximum penalized likelihood
7678 where penalization is by Jeffreys invariant prior. These procedures return
7679 estimates with improved frequentist properties (bias, mean squared error) that
7680 are always finite even in cases where the maximum likelihood estimates are
7681 infinite (data separation). Fitting takes place by fitting generalized linear
7682 models on iteratively updated pseudo-data. The interface is essentially the
7683 same as @code{glm}. More flexibility is provided by the fact that custom
7684 pseudo-data representations can be specified and used for model fitting.
7685 Functions are provided for the construction of confidence intervals for the
7686 reduced-bias estimates.")
7687 (license license:gpl2+)))
7689 (define-public r-entropy
7696 (uri (cran-uri "entropy" version))
7699 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
7700 (properties `((upstream-name . "entropy")))
7701 (build-system r-build-system)
7702 (home-page "https://www.strimmerlab.org/software/entropy/")
7703 (synopsis "Estimation of entropy, mutual information and related quantities")
7705 "This package implements various estimators of entropy, such as the
7706 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
7707 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
7708 estimator. It also offers an R interface to the NSB estimator. Furthermore,
7709 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
7710 mutual information, and chi-squared statistic of independence. In addition
7711 there are functions for discretizing continuous random variables.")
7712 (license license:gpl3+)))
7714 (define-public r-abn
7721 (uri (cran-uri "abn" version))
7724 "17vdrqm6qp5aijg00ah2imj3pqr6cl5r43hgg8dijbrbhznarci6"))))
7725 (build-system r-build-system)
7729 `(("r-lme4" ,r-lme4)
7732 ("r-rcpparmadillo" ,r-rcpparmadillo)
7733 ("r-rjags" ,r-rjags)))
7734 (home-page "https://r-bayesian-networks.org/")
7735 (synopsis "Modelling multivariate data with additive bayesian networks")
7737 "Bayesian network analysis is a form of probabilistic graphical models
7738 which derives from empirical data a directed acyclic graph, DAG, describing
7739 the dependency structure between random variables. An additive Bayesian
7740 network model consists of a form of a DAG where each node comprises a
7741 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
7742 equivalent to Bayesian multivariate regression using graphical modelling, they
7743 generalises the usual multivariable regression, GLM, to multiple dependent
7744 variables. This package provides routines to help determine optimal Bayesian
7745 network models for a given data set, where these models are used to identify
7746 statistical dependencies in messy, complex data.")
7747 (license license:gpl2+)))
7749 (define-public r-acd
7756 (uri (cran-uri "ACD" version))
7759 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
7760 (properties `((upstream-name . "ACD")))
7761 (build-system r-build-system)
7762 (home-page "https://cran.r-project.org/web/packages/ACD/")
7763 (synopsis "Categorical data analysis with complete or missing responses")
7765 "This package provides tools for categorical data analysis with complete
7766 or missing responses.")
7767 (license license:gpl2+)))
7769 (define-public r-acdm
7776 (uri (cran-uri "ACDm" version))
7779 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
7780 (properties `((upstream-name . "ACDm")))
7781 (build-system r-build-system)
7783 `(("r-dplyr" ,r-dplyr)
7784 ("r-ggplot2" ,r-ggplot2)
7786 ("r-rsolnp" ,r-rsolnp)
7788 (home-page "https://cran.r-project.org/web/packages/ACDm/")
7789 (synopsis "Tools for Autoregressive Conditional Duration Models")
7791 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
7792 and Russell, 1998) models. It creates trade, price or volume durations from
7793 transactions (tic) data, performs diurnal adjustments, fits various ACD models
7795 (license license:gpl2+)))
7797 (define-public r-overlap
7804 (uri (cran-uri "overlap" version))
7807 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
7808 (build-system r-build-system)
7809 (home-page "https://cran.r-project.org/web/packages/overlap/")
7810 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
7812 "This package provides functions to fit kernel density functions to data
7813 on temporal activity patterns of animals; estimate coefficients of overlapping
7814 of densities for two species; and calculate bootstrap estimates of confidence
7816 (license license:gpl3+)))
7818 (define-public r-snakecase
7820 (name "r-snakecase")
7825 (uri (cran-uri "snakecase" version))
7828 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
7829 (build-system r-build-system)
7831 `(("r-stringi" ,r-stringi)
7832 ("r-stringr" ,r-stringr)))
7833 (home-page "https://github.com/Tazinho/snakecase")
7834 (synopsis "Convert strings into any case")
7836 "This package provides a consistent, flexible and easy to use tool to
7837 parse and convert strings into cases like snake or camel among others.")
7838 (license license:gpl3)))
7840 (define-public r-prediction
7842 (name "r-prediction")
7847 (uri (cran-uri "prediction" version))
7850 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
7851 (build-system r-build-system)
7853 `(("r-data-table" ,r-data-table)))
7854 (home-page "https://github.com/leeper/prediction")
7855 (synopsis "Tidy, type-safe prediction methods")
7857 "This package provides the @code{prediction()} function, a type-safe
7858 alternative to @code{predict()} that always returns a data frame. The package
7859 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
7860 from the @code{stats} package, as well as numerous other model classes from
7861 other add-on packages.")
7862 (license license:expat)))
7864 (define-public r-insight
7871 (uri (cran-uri "insight" version))
7874 "0gkvcw9d729ql1gfrpxzgrag4xafd0hchrdww215qz11ma1rzy7s"))))
7875 (build-system r-build-system)
7877 `(("r-knitr" ,r-knitr)))
7878 (home-page "https://easystats.github.io/insight/")
7879 (synopsis "Easy access to model information for various model objects")
7881 "This package provides a tool to provide an easy, intuitive and
7882 consistent access to information contained in various R models, like model
7883 formulas, model terms, information about random effects, data that was used to
7884 fit the model or data from response variables. The package mainly revolves
7885 around two types of functions: Functions that find (the names of) information,
7886 starting with @code{find_}, and functions that get the underlying data,
7887 starting with @code{get_}. The package has a consistent syntax and works with
7888 many different model objects, where otherwise functions to access these
7889 information are missing.")
7890 (license license:gpl3)))
7892 (define-public r-sjlabelled
7894 (name "r-sjlabelled")
7899 (uri (cran-uri "sjlabelled" version))
7902 "0d3fsjd2gxchv8mlx9l5pf8xvkmx4pgvizam83f3qss07bmvpzwg"))))
7903 (build-system r-build-system)
7905 `(("r-insight" ,r-insight)))
7907 `(("r-knitr" ,r-knitr)))
7908 (home-page "https://github.com/strengejacke/sjlabelled")
7909 (synopsis "Labelled data utility functions")
7911 "This package provides a collection of functions dealing with labelled
7912 data, like reading and writing data between R and other statistical software
7913 packages. This includes easy ways to get, set or change value and variable
7914 label attributes, to convert labelled vectors into factors or numeric (and
7915 vice versa), or to deal with multiple declared missing values.")
7916 (license license:gpl3)))
7918 (define-public r-sjmisc
7925 (uri (cran-uri "sjmisc" version))
7928 "1nfrkv5jfnwb85blpv7yk7xac1myzi2c30bqcf7xicniknkjwycr"))))
7929 (build-system r-build-system)
7931 `(("r-dplyr" ,r-dplyr)
7932 ("r-insight" ,r-insight)
7933 ("r-magrittr" ,r-magrittr)
7934 ("r-purrr" ,r-purrr)
7935 ("r-rlang" ,r-rlang)
7936 ("r-sjlabelled" ,r-sjlabelled)
7937 ("r-tidyselect" ,r-tidyselect)))
7939 `(("r-knitr" ,r-knitr)))
7940 (home-page "https://github.com/strengejacke/sjmisc")
7941 (synopsis "Data and variable transformation functions")
7943 "This package is a collection of miscellaneous utility functions,
7944 supporting data transformation tasks like recoding, dichotomizing or grouping
7945 variables, setting and replacing missing values. The data transformation
7946 functions also support labelled data, and all integrate seamlessly into a
7947 tidyverse workflow.")
7948 (license license:gpl3)))
7950 (define-public r-nortest
7957 (uri (cran-uri "nortest" version))
7960 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
7961 (build-system r-build-system)
7962 (home-page "https://cran.r-project.org/web/packages/nortest/")
7963 (synopsis "Tests for normality")
7965 "This package provides five omnibus tests for testing the composite
7966 hypothesis of normality.")
7967 (license license:gpl2+)))
7969 (define-public r-moonbook
7976 (uri (cran-uri "moonBook" version))
7979 "0z78pzc8sr2g19xjdd9cmai4iqyifmh79gj8x40ddww6a27dalry"))))
7980 (properties `((upstream-name . "moonBook")))
7981 (build-system r-build-system)
7983 `(("r-magrittr" ,r-magrittr)
7984 ("r-nortest" ,r-nortest)
7985 ("r-sjmisc" ,r-sjmisc)
7986 ("r-stringr" ,r-stringr)
7987 ("r-survival" ,r-survival)
7988 ("r-ztable" ,r-ztable)))
7990 `(("r-knitr" ,r-knitr)))
7991 (home-page "https://github.com/cardiomoon/moonBook")
7992 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
7994 "This package provides several analysis-related functions for the book
7995 entitled \"R statistics and graph for medical articles\" (written in Korean),
7996 version 1, by Keon-Woong Moon with Korean demographic data with several plot
7998 (license license:gpl2)))
8000 (define-public r-flextable
8002 (name "r-flextable")
8007 (uri (cran-uri "flextable" version))
8010 "0as80m19lvajc0vzllq9d9p63zglsm2ph7vdfg3jgk90jp8j76dg"))))
8011 (build-system r-build-system)
8013 `(("r-base64enc" ,r-base64enc)
8014 ("r-data-table" ,r-data-table)
8015 ("r-gdtools" ,r-gdtools)
8016 ("r-htmltools" ,r-htmltools)
8017 ("r-knitr" ,r-knitr)
8018 ("r-officer" ,r-officer)
8019 ("r-rlang" ,r-rlang)
8020 ("r-rmarkdown" ,r-rmarkdown)
8022 ("r-xml2" ,r-xml2)))
8024 `(("r-knitr" ,r-knitr)))
8025 (home-page "https://davidgohel.github.io/flextable")
8026 (synopsis "Functions for tabular reporting")
8028 "This package provides tools to create pretty tables for HTML documents
8029 and other formats. Functions are provided to let users create tables, modify
8030 and format their content. It extends the @code{officer} package and can be
8031 used within R markdown documents when rendering to HTML and to Word
8033 (license license:gpl3)))
8035 (define-public r-writexl
8042 (uri (cran-uri "writexl" version))
8045 "1njdhvh8605wd2j8glrbxfyc36p2n88prpq080jn44s9lgfmbgsb"))))
8046 (build-system r-build-system)
8047 (inputs `(("zlib" ,zlib)))
8048 (home-page "https://github.com/ropensci/writexl")
8049 (synopsis "Export data frames to xlsx format")
8051 "This package provides a data frame to xlsx exporter based on
8053 (license license:bsd-2)))
8055 (define-public r-biasedurn
8057 (name "r-biasedurn")
8062 (uri (cran-uri "BiasedUrn" version))
8065 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
8066 (properties `((upstream-name . "BiasedUrn")))
8067 (build-system r-build-system)
8068 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
8069 (synopsis "Biased Urn model distributions")
8071 "This package provides statistical models of biased sampling in the form
8072 of univariate and multivariate noncentral hypergeometric distributions,
8073 including Wallenius' noncentral hypergeometric distribution and Fisher's
8074 noncentral hypergeometric distribution (also called extended hypergeometric
8076 (license license:gpl3)))
8078 (define-public r-goplot
8085 (uri (cran-uri "GOplot" version))
8088 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
8089 (properties `((upstream-name . "GOplot")))
8090 (build-system r-build-system)
8092 `(("r-ggdendro" ,r-ggdendro)
8093 ("r-ggplot2" ,r-ggplot2)
8094 ("r-gridextra" ,r-gridextra)
8095 ("r-rcolorbrewer" ,r-rcolorbrewer)))
8096 (home-page "https://github.com/wencke/wencke.github.io")
8097 (synopsis "Visualization of functional analysis data")
8099 "This package provides an implementation of multilayered visualizations
8100 for enhanced graphical representation of functional analysis data. It
8101 combines and integrates omics data derived from expression and functional
8102 annotation enrichment analyses. Its plotting functions have been developed
8103 with an hierarchical structure in mind: starting from a general overview to
8104 identify the most enriched categories (modified bar plot, bubble plot) to a
8105 more detailed one displaying different types of relevant information for the
8106 molecules in a given set of categories (circle plot, chord plot, cluster plot,
8107 Venn diagram, heatmap).")
8108 (license license:gpl2)))
8110 (define-public r-getopt
8117 (uri (cran-uri "getopt" version))
8120 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
8121 (build-system r-build-system)
8122 (home-page "https://github.com/trevorld/getopt")
8123 (synopsis "Command-line option processor for R")
8125 "This package is designed to be used with Rscript to write shebang
8126 scripts that accept short and long options. Many users will prefer to
8127 use the packages @code{optparse} or @code{argparse} which add extra
8128 features like automatically generated help options and usage texts,
8129 support for default values, positional argument support, etc.")
8130 (license license:gpl2+)))
8132 (define-public r-findpython
8134 (name "r-findpython")
8139 (uri (cran-uri "findpython" version))
8142 "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar"))))
8143 (build-system r-build-system)
8144 (home-page "https://github.com/trevorld/findpython")
8145 (synopsis "Functions to find an acceptable Python binary")
8147 "This package was designed to find an acceptable Python binary that
8148 matches version and feature constraints.")
8149 (license license:expat)))
8151 ;; This in not the same as "r-argparser"
8152 (define-public r-argparse
8159 (uri (cran-uri "argparse" version))
8162 "1c2r417m1dxk1jhcggv3g4zax5a59k9rqs9jcs6xy2pa2333jqfj"))))
8163 (build-system r-build-system)
8164 (inputs `(("python" ,python)))
8166 `(("r-findpython" ,r-findpython)
8167 ("r-jsonlite" ,r-jsonlite)
8170 `(("r-knitr" ,r-knitr)))
8171 (home-page "https://github.com/trevorld/argparse")
8172 (synopsis "Command line optional and positional argument parser")
8174 "This package provides a command line parser to be used with Rscript to
8175 write shebang scripts that gracefully accept positional and optional arguments
8176 and automatically generate usage notices.")
8177 (license license:gpl2+)))
8179 (define-public r-hash
8186 (uri (cran-uri "hash" version))
8189 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
8190 (build-system r-build-system)
8191 (home-page "https://cran.r-project.org/web/packages/hash/")
8192 (synopsis "Implementation of hash/associated arrays/dictionaries")
8194 "This package implements a data structure similar to hashes in Perl and
8195 dictionaries in Python but with a purposefully R flavor. For objects of
8196 appreciable size, access using hashes outperforms native named lists and
8198 (license license:gpl2+)))
8200 (define-public r-orddom
8207 (uri (cran-uri "orddom" version))
8210 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
8211 (build-system r-build-system)
8212 (propagated-inputs `(("r-psych" ,r-psych)))
8213 (home-page "https://cran.r-project.org/web/packages/orddom/")
8214 (synopsis "Ordinal dominance statistics")
8216 "This package provides tools to compute ordinal, statistics and effect
8217 sizes as an alternative to mean comparison: Cliff's delta or success rate
8218 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
8219 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
8220 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
8221 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
8222 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
8223 Group (Non-)Overlap considerations.")
8224 (license license:gpl2)))
8226 (define-public r-deriv
8233 (uri (cran-uri "Deriv" version))
8236 "1j9sh1w9lsnnhlh59g4ghykyfx46rxh380s8imvm7pzna7rw7c64"))))
8237 (properties `((upstream-name . "Deriv")))
8238 (build-system r-build-system)
8239 (home-page "https://cran.r-project.org/web/packages/Deriv")
8240 (synopsis "Symbolic differentiation")
8242 "This package provides an R-based solution for symbolic differentiation.
8243 It admits user-defined functions as well as function substitution in arguments
8244 of functions to be differentiated. Some symbolic simplification is part of
8246 (license license:gpl3+)))
8248 (define-public r-doby
8255 (uri (cran-uri "doBy" version))
8258 "0r97kwsj6g87m7shgnjc5c9y71jkhiq4xd9q0s2bxl0vl92qqwvg"))))
8259 (properties `((upstream-name . "doBy")))
8260 (build-system r-build-system)
8262 `(("r-broom" ,r-broom)
8263 ("r-deriv" ,r-deriv)
8264 ("r-dplyr" ,r-dplyr)
8265 ("r-ggplot2" ,r-ggplot2)
8266 ("r-magrittr" ,r-magrittr)
8268 ("r-matrix" ,r-matrix)
8269 ("r-pbkrtest" ,r-pbkrtest)
8270 ("r-tibble" ,r-tibble)))
8272 `(("r-knitr" ,r-knitr)))
8273 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
8274 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
8276 "This package contains:
8279 @item facilities for working with grouped data: @code{do}
8280 something to data stratified @code{by} some variables.
8281 @item implementations of least-squares means, general linear contrasts, and
8282 @item miscellaneous other utilities.
8284 (license license:gpl2+)))
8286 (define-public r-refgenome
8288 (name "r-refgenome")
8293 (uri (cran-uri "refGenome" version))
8296 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
8297 (properties `((upstream-name . "refGenome")))
8298 (build-system r-build-system)
8302 ("r-rsqlite" ,r-rsqlite)))
8303 (home-page "https://cran.r-project.org/web/packages/refGenome/")
8305 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
8307 "This package contains functionality for importing and managing of
8308 downloaded genome annotation data from the Ensembl genome browser (European
8309 Bioinformatics Institute) and from the UCSC genome browser (University of
8310 California, Santa Cruz) and annotation routines for genomic positions and
8311 splice site positions.")
8312 (license license:gpl2)))
8314 (define-public r-basix
8321 (uri (cran-uri "BASIX" version))
8324 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
8325 (properties `((upstream-name . "BASIX")))
8326 (build-system r-build-system)
8327 (home-page "https://cran.r-project.org/web/packages/BASIX/")
8328 (synopsis "Efficient C/C++ toolset for R")
8330 "BASIX provides some efficient C/C++ implementations of native R
8331 procedures to speed up calculations in R.")
8332 (license license:gpl2)))
8334 (define-public r-blockfest
8336 (name "r-blockfest")
8341 (uri (cran-uri "BlockFeST" version))
8344 "12cbrmgqszlj729zrn9d1d7drbr0iay43knnmrzcxs6v7lfszsx5"))))
8345 (properties `((upstream-name . "BlockFeST")))
8346 (build-system r-build-system)
8347 (propagated-inputs `(("r-basix" ,r-basix)))
8348 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
8349 (synopsis "Bayesian calculation of region-specific fixation index")
8351 "This package provides an R implementation of an extension of the
8352 BayeScan software for codominant markers, adding the option to group
8353 individual SNPs into pre-defined blocks. A typical application of this new
8354 approach is the identification of genomic regions, genes, or gene sets
8355 containing one or more SNPs that evolved under directional selection.")
8356 (license license:gpl2)))
8358 (define-public r-proc
8361 (version "1.17.0.1")
8365 (uri (cran-uri "pROC" version))
8368 "1gd6a47d6bcfd237s3g7r9rws8x2sg7zrvq5k6clpc41zdpp4712"))))
8369 (properties `((upstream-name . "pROC")))
8370 (build-system r-build-system)
8372 `(("r-plyr" ,r-plyr)
8373 ("r-rcpp" ,r-rcpp)))
8374 (home-page "https://web.expasy.org/pROC/")
8375 (synopsis "Display and analyze ROC curves")
8377 "This package provides tools for visualizing, smoothing and comparing
8378 receiver operating characteristic (ROC curves). The area under the
8379 curve (AUC) can be compared with statistical tests based on U-statistics or
8380 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
8381 (license license:gpl3+)))
8383 (define-public r-rootsolve
8385 (name "r-rootsolve")
8390 (uri (cran-uri "rootSolve" version))
8393 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
8394 (properties `((upstream-name . "rootSolve")))
8395 (build-system r-build-system)
8396 (native-inputs `(("gfortran" ,gfortran)))
8397 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
8398 (synopsis "Tools for the analysis of ordinary differential equations")
8400 "This package provides routines to find the root of nonlinear functions,
8401 and to perform steady-state and equilibrium analysis of @dfn{ordinary
8402 differential equations} (ODE). It includes routines that:
8405 @item generate gradient and jacobian matrices (full and banded),
8406 @item find roots of non-linear equations by the Newton-Raphson method,
8407 @item estimate steady-state conditions of a system of (differential) equations
8408 in full, banded or sparse form, using the Newton-Raphson method, or by
8409 dynamically running,
8410 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
8411 and 3-D partial differential equations, that have been converted to ordinary
8412 differential equations by numerical differencing (using the method-of-lines
8415 (license license:gpl2+)))
8417 (define-public r-abcanalysis
8419 (name "r-abcanalysis")
8424 (uri (cran-uri "ABCanalysis" version))
8426 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
8427 (properties `((upstream-name . "ABCanalysis")))
8428 (build-system r-build-system)
8429 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
8430 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
8431 (synopsis "Computed ABC Analysis")
8433 "Multivariate data sets often differ in several factors or derived statistical
8434 parameters, which have to be selected for a valid interpretation. Basing this
8435 selection on traditional statistical limits leads occasionally to the perception
8436 of losing information from a data set. This package provides tools to calculate
8437 these limits on the basis of the mathematical properties of the distribution of
8438 the analyzed items.")
8439 (license license:gpl3)))
8441 (define-public r-slam
8448 (uri (cran-uri "slam" version))
8450 (base32 "1ppsvkph4v1dffxgp12a4wnr9arj7pkmh4qv0and3f6nbz9k42qa"))))
8451 (build-system r-build-system)
8452 (home-page "https://cran.r-project.org/web/packages/slam/")
8453 (synopsis "Sparse lightweight arrays and matrices")
8455 "This package contains data structures and algorithms for sparse arrays and matrices,
8456 based on index arrays and simple triplet representations, respectively.")
8457 (license license:gpl2)))
8459 (define-public r-manipulatewidget
8461 (name "r-manipulatewidget")
8466 (uri (cran-uri "manipulateWidget" version))
8468 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
8470 `((upstream-name . "manipulateWidget")))
8471 (build-system r-build-system)
8473 `(("r-base64enc" ,r-base64enc)
8474 ("r-codetools" ,r-codetools)
8475 ("r-htmltools" ,r-htmltools)
8476 ("r-htmlwidgets" ,r-htmlwidgets)
8477 ("r-knitr" ,r-knitr)
8478 ("r-miniui" ,r-miniui)
8479 ("r-shiny" ,r-shiny)
8480 ("r-webshot" ,r-webshot)))
8481 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
8482 (synopsis "Add even more interactivity to interactive charts")
8484 "This package lets you create in just a few lines of R code a nice user interface to
8485 modify the data or the graphical parameters of one or multiple interactive
8486 charts. It is useful to quickly explore visually some data or for package
8487 developers to generate user interfaces easy to maintain.")
8488 (license license:gpl2+)))
8497 (uri (cran-uri "A3" version))
8499 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
8500 (properties `((upstream-name . "A3")))
8501 (build-system r-build-system)
8503 `(("r-pbapply" ,r-pbapply)
8504 ("r-xtable" ,r-xtable)))
8505 (home-page "https://cran.r-project.org/web/packages/A3/")
8506 (synopsis "Error metrics for predictive models")
8508 "This package supplies tools for tabulating and analyzing the results of predictive
8509 models. The methods employed are applicable to virtually any predictive model
8510 and make comparisons between different methodologies straightforward.")
8511 (license license:gpl2+)))
8513 (define-public r-infotheo
8520 (uri (cran-uri "infotheo" version))
8523 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
8524 (build-system r-build-system)
8525 (home-page "http://homepage.meyerp.com/software")
8526 (synopsis "Information-theoretic measures")
8528 "This package implements various measures of information theory based on
8529 several entropy estimators.")
8530 (license license:gpl3+)))
8532 (define-public r-abcoptim
8539 (uri (cran-uri "ABCoptim" version))
8541 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
8542 (properties `((upstream-name . "ABCoptim")))
8543 (build-system r-build-system)
8544 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
8545 (home-page "https://github.com/gvegayon/ABCoptim/")
8546 (synopsis "Optimization of Artificial Bee Colony algorithm")
8548 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
8549 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
8550 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
8551 algorithms, and uses only common control parameters such as colony size and
8552 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
8553 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
8554 This version is a work-in-progress and is written in R code.")
8555 (license license:expat)))
8557 (define-public r-abcp2
8564 (uri (cran-uri "ABCp2" version))
8566 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
8567 (properties `((upstream-name . "ABCp2")))
8568 (build-system r-build-system)
8569 (propagated-inputs `(("r-mass" ,r-mass)))
8570 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
8571 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
8573 "This package tests the goodness of fit of a distribution of offspring to the Normal,
8574 Poisson, and Gamma distribution and estimates the proportional paternity of the
8575 second male (P2) based on the best fit distribution.")
8576 (license license:gpl2)))
8578 (define-public r-abcrf
8585 (uri (cran-uri "abcrf" version))
8587 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
8588 (build-system r-build-system)
8590 `(("r-doparallel" ,r-doparallel)
8591 ("r-foreach" ,r-foreach)
8593 ("r-matrixstats" ,r-matrixstats)
8594 ("r-ranger" ,r-ranger)
8596 ("r-rcpparmadillo" ,r-rcpparmadillo)
8597 ("r-readr" ,r-readr)
8598 ("r-stringr" ,r-stringr)))
8599 (home-page "https://cran.r-project.org/web/packages/abcrf/")
8600 (synopsis "Approximate bayesian computation via random forests")
8602 "This package performs approximate bayesian computation (ABC) model choice and
8603 parameter inference via random forests. This machine learning tool named random
8604 forests (RF) can conduct selection among the highly complex models covered by
8606 (license license:gpl2+)))
8608 (define-public r-abctools
8615 (uri (cran-uri "abctools" version))
8617 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
8618 (build-system r-build-system)
8621 ("r-abind" ,r-abind)
8622 ("r-hmisc" ,r-hmisc)
8623 ("r-plyr" ,r-plyr)))
8624 (home-page "https://github.com/dennisprangle/abctools/")
8625 (synopsis "Tools for ABC analyses")
8627 "This @code{r-abctools} package provides tools for approximate Bayesian computation
8628 including summary statistic selection and assessing coverage. This includes
8629 recent dimension reduction algorithms to tune the choice of summary statistics,
8630 and coverage methods to tune the choice of threshold.")
8631 (license license:gpl2+)))
8633 (define-public r-ggstance
8640 (uri (cran-uri "ggstance" version))
8642 (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d"))))
8643 (build-system r-build-system)
8645 `(("r-ggplot2" ,r-ggplot2)
8647 ("r-rlang" ,r-rlang)
8648 ("r-withr" ,r-withr)))
8649 (home-page "https://cran.r-project.org/web/packages/ggstance/")
8650 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
8652 "This package is a @code{r-ggplot2} extension that provides flipped components:
8654 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
8655 @item vertical versions of @code{r-ggplot2} positions.
8657 (license license:gpl3)))
8659 (define-public r-mosaiccore
8661 (name "r-mosaiccore")
8666 (uri (cran-uri "mosaicCore" version))
8668 (base32 "1h3ixzna4xy42rdnd89jj0v9q0riy3fnkd33z6l5c0zaidzm58fz"))))
8669 (properties `((upstream-name . "mosaicCore")))
8670 (build-system r-build-system)
8672 `(("r-dplyr" ,r-dplyr)
8674 ("r-rlang" ,r-rlang)
8675 ("r-tidyr" ,r-tidyr)))
8676 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
8677 (synopsis "Common utilities for mosaic family packages")
8679 "Common utilities used in other Mosaic family packages are collected here.")
8680 (license license:gpl2+)))
8682 (define-public r-labelled
8689 (uri (cran-uri "labelled" version))
8692 "1nsb0mh0jg7gggc41b6v55nmfq07g0qn9fy55x4jws5dscs6pdmi"))))
8693 (properties `((upstream-name . "labelled")))
8694 (build-system r-build-system)
8696 `(("r-dplyr" ,r-dplyr)
8697 ("r-haven" ,r-haven)
8698 ("r-lifecycle" ,r-lifecycle)
8699 ("r-pillar" ,r-pillar)
8700 ("r-rlang" ,r-rlang)
8701 ("r-tidyr" ,r-tidyr)
8702 ("r-vctrs" ,r-vctrs)))
8704 `(("r-knitr" ,r-knitr)))
8705 (home-page "http://larmarange.github.io/labelled/")
8706 (synopsis "Manipulating labelled data")
8708 "This package provides useful functions to deal with the
8709 @code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the
8711 (license license:gpl3)))
8713 (define-public r-ggformula
8715 (name "r-ggformula")
8720 (uri (cran-uri "ggformula" version))
8722 (base32 "1ph5jd8svk8hmshi894vmmpq3zwgdmf4yn3gmdlkad68z8jynhsp"))))
8723 (build-system r-build-system)
8725 `(("r-ggforce" ,r-ggforce)
8726 ("r-ggplot2" ,r-ggplot2)
8727 ("r-ggridges" ,r-ggridges)
8728 ("r-ggstance" ,r-ggstance)
8729 ("r-labelled" ,r-labelled)
8730 ("r-magrittr" ,r-magrittr)
8731 ("r-mosaiccore" ,r-mosaiccore)
8732 ("r-rlang" ,r-rlang)
8733 ("r-scales" ,r-scales)
8734 ("r-stringr" ,r-stringr)
8735 ("r-tibble" ,r-tibble)))
8737 `(("r-knitr" ,r-knitr)))
8738 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
8739 (synopsis "Formula interface for the @code{r-ggplot2}")
8741 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
8742 gf_density(), and so on, bring the formula interface to ggplot(). This captures
8743 and extends the excellent simplicity of the lattice-graphics formula interface,
8744 while providing the intuitive capabilities of @code{r-ggplot2}.")
8745 (license license:expat)))
8747 (define-public r-mosaicdata
8749 (name "r-mosaicdata")
8754 (uri (cran-uri "mosaicData" version))
8756 (base32 "0h3f5fgzkzjfgf3ml0qa5j52921y6wy6jgggxmhs31bs8fd4srg4"))))
8757 (properties `((upstream-name . "mosaicData")))
8758 (build-system r-build-system)
8759 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
8760 (synopsis "Data sets for project Mosaic")
8762 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
8763 used to teach mathematics, statistics, computation and modeling.")
8764 (license license:gpl2+)))
8766 (define-public r-raster
8773 (uri (cran-uri "raster" version))
8776 "19g4chd0nyhnz6hc2j0v9ahjcgz64vvja4y3mrj1pfis1dwhsqn6"))))
8777 (build-system r-build-system)
8779 `(("r-rcpp" ,r-rcpp)
8781 (home-page "https://www.rspatial.org/")
8782 (synopsis "Geographic data analysis and modeling")
8784 "The package implements basic and high-level functions for reading,
8785 writing, manipulating, analyzing and modeling of gridded spatial data.
8786 Processing of very large files is supported.")
8787 (license license:gpl3+)))
8789 (define-public r-mosaic
8796 (uri (cran-uri "mosaic" version))
8798 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
8799 (build-system r-build-system)
8801 `(("r-broom" ,r-broom)
8802 ("r-dplyr" ,r-dplyr)
8803 ("r-ggdendro" ,r-ggdendro)
8804 ("r-ggformula" ,r-ggformula)
8805 ("r-ggplot2" ,r-ggplot2)
8806 ("r-ggrepel" ,r-ggrepel)
8808 ("r-gridextra" ,r-gridextra)
8809 ("r-lattice" ,r-lattice)
8810 ("r-latticeextra" ,r-latticeextra)
8811 ("r-lazyeval" ,r-lazyeval)
8813 ("r-matrix" ,r-matrix)
8814 ("r-mosaiccore" ,r-mosaiccore)
8815 ("r-mosaicdata" ,r-mosaicdata)
8816 ("r-readr" ,r-readr)
8817 ("r-tidyr" ,r-tidyr)))
8819 `(("r-knitr" ,r-knitr)))
8820 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
8821 (synopsis "Mathematics, statistics, and computation teaching utilities")
8823 "This package contain data sets and utilities from
8824 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
8825 statistics, computation and modeling. Project MOSAIC is a community of
8826 educators working to tie together aspects of quantitative work that students
8827 in science, technology, engineering and mathematics will need in their
8828 professional lives, but which are usually taught in isolation, if at all.")
8829 (license license:gpl2+)))
8831 (define-public r-abd
8838 (uri (cran-uri "abd" version))
8840 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
8841 (build-system r-build-system)
8843 `(("r-lattice" ,r-lattice)
8844 ("r-mosaic" ,r-mosaic)
8845 ("r-nlme" ,r-nlme)))
8846 (home-page "https://cran.r-project.org/web/packages/abd/")
8847 (synopsis "Analysis of biological data")
8849 "The @code{r-abd} package contains data sets and sample code for the Analysis of
8850 biological data by Michael Whitlock and Dolph Schluter.")
8851 (license license:gpl2)))
8853 (define-public r-svgui
8860 (uri (cran-uri "svGUI" version))
8862 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
8863 (properties `((upstream-name . "svGUI")))
8864 (build-system r-build-system)
8865 (home-page "https://github.com/SciViews/svGUI/")
8866 (synopsis "Functions for managing GUI clients in R")
8868 "The SciViews @code{svGUI} package eases the management of Graphical User
8869 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
8870 centralizes info about GUI elements currently used, and it dispatches GUI
8871 calls to the particular toolkits in use in function of the context.")
8872 (license license:gpl2)))
8874 (define-public r-svdialogs
8876 (name "r-svdialogs")
8881 (uri (cran-uri "svDialogs" version))
8883 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
8884 (properties `((upstream-name . "svDialogs")))
8885 (build-system r-build-system)
8888 ("zenity" ,zenity)))
8890 `(("r-rstudioapi" ,r-rstudioapi)
8891 ("r-svgui" ,r-svgui)))
8892 (home-page "https://github.com/SciViews/svDialogs/")
8893 (synopsis "Portable dialog boxes")
8895 "This package helps to construct standard dialog boxes for your GUI, including
8896 message boxes, input boxes, list, file or directory selection, and others. In
8897 case R cannot display GUI dialog boxes, a simpler command line version of these
8898 interactive elements is also provided as a fallback solution.")
8899 (license license:gpl2)))
8901 (define-public r-abe
8908 (uri (cran-uri "abe" version))
8911 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
8912 (build-system r-build-system)
8913 (home-page "https://cran.r-project.org/web/packages/abe/")
8914 (synopsis "Augmented backward elimination")
8916 "This package performs augmented backward elimination and checks the
8917 stability of the obtained model. Augmented backward elimination combines
8918 significance or information based criteria with the change in estimate to
8919 either select the optimal model for prediction purposes or to serve as a tool
8920 to obtain a practically sound, highly interpretable model.")
8921 (license license:gpl2+)))
8923 (define-public r-abf2
8930 (uri (cran-uri "abf2" version))
8932 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
8933 (build-system r-build-system)
8934 (home-page "https://cran.r-project.org/web/packages/abf2/")
8935 (synopsis "Load gap-free axon @code{r-abf2} files")
8937 "This package loads electrophysiology data from ABF2 files, as created by
8938 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
8939 mode are currently supported.")
8940 (license license:artistic2.0)))
8942 (define-public r-abhgenotyper
8944 (name "r-abhgenotyper")
8949 (uri (cran-uri "ABHgenotypeR" version))
8951 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
8952 (properties `((upstream-name . "ABHgenotypeR")))
8953 (build-system r-build-system)
8955 `(("r-ggplot2" ,r-ggplot2)
8956 ("r-reshape2" ,r-reshape2)))
8957 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
8958 (synopsis "Visualize and manipulate ABH genotypes")
8960 "The @code{r-abhgenotyper} package provides simple imputation,
8961 error-correction and plotting capacities for genotype data. The package is
8962 supposed to serve as an intermediate but independent analysis tool between the
8963 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
8964 not found in either TASSEL or @code{r-qtl} in addition to visualization of
8965 genotypes as \"graphical genotypes\".")
8966 (license license:gpl3)))
8968 (define-public r-furrr
8975 (uri (cran-uri "furrr" version))
8978 "0kfd4hw1yn2mfxzjgiz4r6yi2vsp1j0wy5hdhzd6wha7vi9h7hg5"))))
8979 (build-system r-build-system)
8981 `(("r-ellipsis" ,r-ellipsis)
8982 ("r-future" ,r-future)
8983 ("r-globals" ,r-globals)
8984 ("r-lifecycle" ,r-lifecycle)
8985 ("r-purrr" ,r-purrr)
8986 ("r-rlang" ,r-rlang)
8987 ("r-vctrs" ,r-vctrs)))
8988 (home-page "https://github.com/DavisVaughan/furrr")
8989 (synopsis "Apply mapping functions in parallel using futures")
8991 "This package provides implementations of the family of @code{map()}
8992 functions from the @code{purrr} package that can be resolved using any
8993 @code{future}-supported backend, e.g. parallel on the local machine or
8994 distributed on a compute cluster.")
8995 (license license:lgpl2.1+)))
8997 (define-public r-abjutils
9004 (uri (cran-uri "abjutils" version))
9006 (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd"))))
9007 (build-system r-build-system)
9009 `(("r-dplyr" ,r-dplyr)
9010 ("r-magrittr" ,r-magrittr)
9011 ("r-purrr" ,r-purrr)
9012 ("r-rlang" ,r-rlang)
9013 ("r-rstudioapi" ,r-rstudioapi)
9014 ("r-stringi" ,r-stringi)
9015 ("r-stringr" ,r-stringr)
9016 ("r-tidyr" ,r-tidyr)))
9017 (home-page "https://github.com/abjur/abjutils/")
9018 (synopsis "Collection of tools for jurimetrical analysis")
9020 "This package implements general purpose tools, such as functions for
9021 sampling and basic manipulation of Brazilian lawsuits identification number.
9022 It also implements functions for text cleaning, such as accentuation
9024 (license license:expat)))
9026 (define-public r-abnormality
9028 (name "r-abnormality")
9033 (uri (cran-uri "abnormality" version))
9035 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
9036 (build-system r-build-system)
9038 `(("r-mass" ,r-mass)
9039 ("r-matrix" ,r-matrix)))
9040 (home-page "https://cran.r-project.org/web/packages/abnormality/")
9041 (synopsis "Measure a subject's abnormality with respect to a reference population")
9043 "This package contains functions to implement the methodology and
9044 considerations laid out by Marks et al. in the article \"Measuring abnormality
9045 in high dimensional spaces: applications in biomechanical gait analysis\".
9046 Using high-dimensional datasets to measure a subject's overall level of
9047 abnormality as compared to a reference population is often needed in outcomes
9049 (license license:expat)))
9051 (define-public r-abodoutlier
9053 (name "r-abodoutlier")
9058 (uri (cran-uri "abodOutlier" version))
9060 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
9061 (properties `((upstream-name . "abodOutlier")))
9062 (build-system r-build-system)
9064 `(("r-cluster" ,r-cluster)))
9065 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
9066 (synopsis "Angle-based outlier detection")
9068 "This package performs angle-based outlier detection on a given data
9069 frame. It offers three methods to process data:
9071 @item full but slow implementation using all the data that has cubic
9073 @item a fully randomized method;
9074 @item a method using k-nearest neighbours.
9076 These algorithms are well suited for high dimensional data outlier
9078 (license license:expat)))
9080 (define-public r-abps
9087 (uri (cran-uri "ABPS" version))
9089 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
9090 (properties `((upstream-name . "ABPS")))
9091 (build-system r-build-system)
9092 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
9093 (home-page "https://cran.r-project.org/web/packages/ABPS/")
9094 (synopsis "Abnormal blood profile score to detect blood doping")
9096 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
9097 The ABPS is a part of the Athlete biological passport program of the World
9098 anti-doping agency, which combines several blood parameters into a single
9099 score in order to detect blood doping. The package also contains functions to
9100 calculate other scores used in anti-doping programs, such as the ratio of
9101 hemoglobin to reticulocytes (OFF-score), as well as example data.")
9102 (license license:gpl2+)))
9104 (define-public r-parmigene
9106 (name "r-parmigene")
9111 (uri (cran-uri "parmigene" version))
9114 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
9115 (build-system r-build-system)
9116 (home-page "https://cran.r-project.org/web/packages/parmigene/")
9117 (synopsis "Mutual information estimation for gene network reconstruction")
9119 "This package provides a parallel estimation of the mutual information
9120 based on entropy estimates from k-nearest neighbors distances and algorithms
9121 for the reconstruction of gene regulatory networks.")
9122 (license license:agpl3+)))
9124 (define-public r-pscl
9131 (uri (cran-uri "pscl" version))
9133 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
9134 (build-system r-build-system)
9136 `(("r-mass" ,r-mass)))
9137 (home-page "https://github.com/atahk/pscl/")
9138 (synopsis "Political science computational laboratory")
9140 "The @code{pscl} is an R package providing classes and methods for:
9142 @item Bayesian analysis of roll call data (item-response models);
9143 @item elementary Bayesian statistics;
9144 @item maximum likelihood estimation of zero-inflated and hurdle models for count
9146 @item utility functions.
9148 (license license:gpl2)))
9150 (define-public r-accelmissing
9152 (name "r-accelmissing")
9157 (uri (cran-uri "accelmissing" version))
9159 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
9160 (build-system r-build-system)
9162 `(("r-mice" ,r-mice)
9163 ("r-pscl" ,r-pscl)))
9164 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
9165 (synopsis "Missing value imputation for accelerometer data")
9167 "This package provides a statistical method to impute the missing values in
9168 accelerometer data. The methodology includes both parametric and
9169 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
9170 model. It also provides multiple functions to preprocess the accelerometer data
9171 previous to the missing data imputation. These include detecting the wearing
9172 and the non-wearing time, selecting valid days and subjects, and creating plots.")
9173 (license license:gpl2+)))
9175 (define-public r-mhsmm
9182 (uri (cran-uri "mhsmm" version))
9184 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
9185 (build-system r-build-system)
9186 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
9187 (home-page "https://github.com/jaredo/mhsmm/")
9188 (synopsis "Inference for hidden Markov and semi-Markov models")
9190 "The @code{r-mhsmm} package implements estimation and prediction methods for
9191 hidden Markov and semi-Markov models for multiple observation sequences. Such
9192 techniques are of interest when observed data is thought to be dependent on some
9193 unobserved (or hidden) state. Also, this package is suitable for equidistant
9194 time series data, with multivariate and/or missing data. Allows user defined
9195 emission distributions.")
9196 (license license:gpl2+)))
9198 (define-public r-nleqslv
9205 (uri (cran-uri "nleqslv" version))
9207 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
9208 (build-system r-build-system)
9209 (native-inputs `(("gfortran" ,gfortran)))
9210 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
9211 (synopsis "Solve systems of nonlinear equations")
9213 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
9214 Broyden or a Newton method with a choice of global strategies such as line
9215 search and trust region. There are options for using a numerical or user
9216 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
9217 singular or ill-conditioned Jacobian.")
9218 (license license:gpl2+)))
9220 (define-public r-physicalactivity
9222 (name "r-physicalactivity")
9227 (uri (cran-uri "PhysicalActivity" version))
9229 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40"))))
9231 `((upstream-name . "PhysicalActivity")))
9232 (build-system r-build-system)
9233 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
9234 (synopsis "Procesing accelerometer data for physical activity measurement")
9236 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
9237 for classification of monitor wear and nonwear time intervals in accelerometer
9238 data collected to assess physical activity. The package also contains functions
9239 for making plots of accelerometer data and obtaining the summary of various
9240 information including daily monitor wear time and the mean monitor wear time
9241 during valid days. The revised package version 0.2-1 improved the functions
9242 regarding speed, robustness and add better support for time zones and daylight
9243 saving. In addition, several functions were added:
9245 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
9246 @item the @code{markPAI} can categorize physical activity intensity level based
9247 on user-defined cut-points of accelerometer counts.
9249 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
9250 @code{queryActigraph} functions.")
9251 (license license:gpl3+)))
9253 (define-public r-acc
9260 (uri (cran-uri "acc" version))
9262 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
9263 (build-system r-build-system)
9265 `(("r-circlize" ,r-circlize)
9267 ("r-ggplot2" ,r-ggplot2)
9268 ("r-iterators" ,r-iterators)
9269 ("r-mhsmm" ,r-mhsmm)
9270 ("r-nleqslv" ,r-nleqslv)
9271 ("r-physicalactivity" ,r-physicalactivity)
9273 ("r-r-utils" ,r-r-utils)
9275 ("r-rcpparmadillo" ,r-rcpparmadillo)
9276 ("r-rsqlite" ,r-rsqlite)
9278 (home-page "https://cran.r-project.org/web/packages/acc/")
9279 (synopsis "Exploring accelerometer data")
9281 "This package processes accelerometer data from uni-axial and tri-axial devices
9282 and generates data summaries. Also, includes functions to plot, analyze, and
9283 simulate accelerometer data.")
9284 (license license:gpl2+)))
9286 (define-public r-rbenchmark
9288 (name "r-rbenchmark")
9293 (uri (cran-uri "rbenchmark" version))
9295 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
9296 (build-system r-build-system)
9297 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
9298 (synopsis "Benchmarking routine for R")
9300 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
9301 and is intended to facilitate benchmarking of arbitrary R code. The library
9302 consists of just one function, benchmark, which is a simple wrapper around
9303 system.time. Given a specification of the benchmarking process (counts of
9304 replications, evaluation environment) and an arbitrary number of expressions,
9305 benchmark evaluates each of the expressions in the specified environment,
9306 replicating the evaluation as many times as specified, and returning the results
9307 conveniently wrapped into a data frame.")
9308 (license license:gpl2+)))
9310 (define-public r-mitools
9317 (uri (cran-uri "mitools" version))
9320 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
9321 (build-system r-build-system)
9322 (propagated-inputs `(("r-dbi" ,r-dbi)))
9323 (home-page "https://cran.r-project.org/web/packages/mitools/")
9324 (synopsis "Tools for multiple imputation of missing data")
9326 "This package provides tools to perform analyses and combine results from
9327 multiple-imputation datasets.")
9328 (license license:gpl2)))
9330 (define-public r-mixsqp
9336 (uri (cran-uri "mixsqp" version))
9339 "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q"))))
9340 (properties `((upstream-name . "mixsqp")))
9341 (build-system r-build-system)
9343 `(("r-irlba" ,r-irlba)
9345 ("r-rcpparmadillo" ,r-rcpparmadillo)))
9347 `(("r-knitr" ,r-knitr)))
9348 (home-page "https://github.com/stephenslab/mixsqp")
9350 "Sequential quadratic programming for maximum-likelihood estimation")
9352 "This package provides an optimization method based on sequential
9353 quadratic programming for maximum likelihood estimation of the mixture
9354 proportions in a finite mixture model where the component densities are
9355 known. The algorithm is expected to obtain solutions that are at least
9356 as accurate as the state-of-the-art MOSEK interior-point solver, and they
9357 are expected to arrive at solutions more quickly when the number of
9358 samples is large and the number of mixture components is not too large.")
9359 (license license:expat)))
9361 (define-public r-magick
9368 (uri (cran-uri "magick" version))
9371 "1k4fqhxh2ppynl56fs044wpn4wk6gbv6lwp2x4x7j67zwcv56n36"))))
9372 (build-system r-build-system)
9374 `(("imagemagick" ,imagemagick)
9377 `(("r-curl" ,r-curl)
9378 ("r-magrittr" ,r-magrittr)
9379 ("r-rcpp" ,r-rcpp)))
9381 `(("pkg-config" ,pkg-config)
9382 ("r-knitr" ,r-knitr)))
9383 (home-page "https://github.com/ropensci/magick")
9384 (synopsis "Advanced graphics and image-processing in R")
9386 "This package provides bindings to ImageMagick, a comprehensive image
9387 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
9388 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
9389 operations are vectorized via the Magick++ STL meaning they operate either on
9390 a single frame or a series of frames for working with layers, collages, or
9391 animation. In RStudio, images are automatically previewed when printed to the
9392 console, resulting in an interactive editing environment.")
9393 (license license:expat)))
9395 (define-public r-survey
9402 (uri (cran-uri "survey" version))
9405 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
9406 (build-system r-build-system)
9408 `(("r-lattice" ,r-lattice)
9409 ("r-matrix" ,r-matrix)
9410 ("r-minqa" ,r-minqa)
9411 ("r-mitools" ,r-mitools)
9412 ("r-numderiv" ,r-numderiv)
9413 ("r-survival" ,r-survival)))
9414 (home-page "http://r-survey.r-forge.r-project.org/survey/")
9415 (synopsis "Analysis of complex survey samples")
9417 "This package provides tools for the analysis of complex survey samples.
9418 The provided features include: summary statistics, two-sample tests, rank
9419 tests, generalised linear models, cumulative link models, Cox models,
9420 loglinear models, and general maximum pseudolikelihood estimation for
9421 multistage stratified, cluster-sampled, unequally weighted survey samples;
9422 variances by Taylor series linearisation or replicate weights;
9423 post-stratification, calibration, and raking; two-phase subsampling designs;
9424 graphics; PPS sampling without replacement; principal components, and factor
9426 ;; Either version of the GPL.
9427 (license (list license:gpl2 license:gpl3))))
9429 (define-public r-gee
9436 (uri (cran-uri "gee" version))
9439 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
9440 (properties `((upstream-name . "gee")))
9441 (build-system r-build-system)
9443 `(("gfortran" ,gfortran)))
9444 (home-page "https://cran.r-project.org/web/packages/gee/")
9445 (synopsis "Generalized estimation equation solver")
9447 "This package provides a solver for generalized estimation equations.")
9448 (license license:gpl2)))
9450 (define-public r-tab
9457 (uri (cran-uri "tab" version))
9460 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
9461 (properties `((upstream-name . "tab")))
9462 (build-system r-build-system)
9464 `(("r-dplyr" ,r-dplyr)
9466 ("r-knitr" ,r-knitr)
9468 ("r-survey" ,r-survey)
9469 ("r-survival" ,r-survival)
9470 ("r-xtable" ,r-xtable)))
9471 (home-page "https://cran.r-project.org/web/packages/tab/")
9472 (synopsis "Create summary tables for statistical reports")
9474 "This package contains functions for creating various types of summary
9475 tables, e.g. comparing characteristics across levels of a categorical variable
9476 and summarizing fitted generalized linear models, generalized estimating
9477 equations, and Cox proportional hazards models. Functions are available to
9478 handle data from simple random samples as well as complex surveys.")
9479 (license license:gpl3+)))
9481 (define-public r-dvmisc
9488 (uri (cran-uri "dvmisc" version))
9490 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
9491 (build-system r-build-system)
9493 `(("r-cubature" ,r-cubature)
9494 ("r-data-table" ,r-data-table)
9495 ("r-dplyr" ,r-dplyr)
9496 ("r-ggplot2" ,r-ggplot2)
9498 ("r-mvtnorm" ,r-mvtnorm)
9499 ("r-pracma" ,r-pracma)
9500 ("r-rbenchmark" ,r-rbenchmark)
9502 ("r-survey" ,r-survey)
9504 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
9505 (synopsis "Faster computation of common statistics and miscellaneous functions")
9507 "This package implements faster versions of base R functions (e.g. mean, standard
9508 deviation, covariance, weighted mean), mostly written in C++, along with
9509 miscellaneous functions for various purposes (e.g. create the histogram with
9510 fitted probability density function or probability mass function curve, create
9511 the body mass index groups, assess the linearity assumption in logistic
9513 (license license:gpl2)))
9515 (define-public r-accelerometry
9517 (name "r-accelerometry")
9522 (uri (cran-uri "accelerometry" version))
9524 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
9525 (build-system r-build-system)
9527 `(("r-dvmisc" ,r-dvmisc)
9528 ("r-rcpp" ,r-rcpp)))
9529 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
9530 (synopsis "Functions for processing accelerometer data")
9532 "This package provides a collection of functions that perform operations on
9533 time-series accelerometer data, such as identify the non-wear time, flag minutes
9534 that are part of an activity bout, and find the maximum 10-minute average count
9535 value. The functions are generally very flexible, allowing for a variety of
9536 algorithms to be implemented.")
9537 (license license:gpl3)))
9539 (define-public r-absim
9546 (uri (cran-uri "AbSim" version))
9548 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
9549 (properties `((upstream-name . "AbSim")))
9550 (build-system r-build-system)
9553 ("r-powerlaw" ,r-powerlaw)))
9554 (home-page "https://cran.r-project.org/web/packages/AbSim/")
9555 (synopsis "Time resolved simulations of antibody repertoires")
9557 "This package provides simulation methods for the evolution of antibody repertoires.
9558 The heavy and light chain variable region of both human and C57BL/6 mice can
9559 be simulated in a time-dependent fashion. Both single lineages using one set of
9560 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
9561 with an initial V-D-J recombination event, starting the first phylogenetic tree.
9562 Upon completion, the main loop of the algorithm begins, with each iteration
9563 representing one simulated time step. Various mutation events are possible at
9564 each time step, contributing to a diverse final repertoire.")
9565 (license license:gpl2)))
9567 (define-public r-quic
9574 (uri (cran-uri "QUIC" version))
9576 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
9577 (properties `((upstream-name . "QUIC")))
9578 (build-system r-build-system)
9579 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
9580 (synopsis "Regularized sparse inverse covariance matrix estimation")
9582 "This package implements the regularized Gaussian maximum likelihood
9583 estimation of the inverse of a covariance matrix. It uses Newton's method and
9584 coordinate descent to solve the regularized inverse covariance matrix
9585 estimation problem.")
9586 ;; The project home page states that the release is under GPLv3 or later.
9587 ;; The CRAN page only says GPL-3.
9588 (license license:gpl3+)))
9590 (define-public r-abundant
9597 (uri (cran-uri "abundant" version))
9599 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
9600 (build-system r-build-system)
9602 `(("r-quic" ,r-quic)))
9603 (home-page "https://cran.r-project.org/web/packages/abundant/")
9604 (synopsis "Abundant regression and high-dimensional principal fitted components")
9606 "This package provides tools to fit and predict with the high-dimensional
9607 principal fitted components model. This model is described by Cook, Forzani,
9608 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
9609 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
9610 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
9611 (license license:gpl2+)))
9613 (define-public r-ac3net
9620 (uri (cran-uri "Ac3net" version))
9622 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
9623 (properties `((upstream-name . "Ac3net")))
9624 (build-system r-build-system)
9626 `(("r-data-table" ,r-data-table)))
9627 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
9628 (synopsis "Inferring directional conservative causal core gene networks")
9629 (description "This package infers directional Conservative causal core
9630 (gene) networks (C3NET). This is a version of the algorithm C3NET with
9631 directional network.")
9632 (license license:gpl3+)))
9634 (define-public r-aca
9641 (uri (cran-uri "ACA" version))
9643 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
9644 (properties `((upstream-name . "ACA")))
9645 (build-system r-build-system)
9646 (home-page "https://cran.r-project.org/web/packages/ACA/")
9647 (synopsis "Abrupt change-point or aberration detection in point series")
9649 "This package offers an interactive function for the detection of breakpoints in
9651 ;; Any version of the GPL
9652 (license (list license:gpl2+ license:gpl3+))))
9654 (define-public r-acceptancesampling
9656 (name "r-acceptancesampling")
9661 (uri (cran-uri "AcceptanceSampling" version))
9663 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
9665 `((upstream-name . "AcceptanceSampling")))
9666 (build-system r-build-system)
9667 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
9668 (synopsis "Creation and evaluation of acceptance sampling plans")
9670 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
9671 acceptance sampling plans. Acceptance sampling is a methodology commonly used
9672 in quality control and improvement. International standards of acceptance
9673 sampling provide sampling plans for specific circumstances. The aim of this
9674 package is to provide an easy-to-use interface to visualize single, double or
9675 multiple sampling plans. In addition, methods have been provided to enable the
9676 user to assess sampling plans against pre-specified levels of performance, as
9677 measured by the probability of acceptance for a given level of quality in the
9679 (license license:gpl3+)))
9681 (define-public r-acclma
9688 (uri (cran-uri "ACCLMA" version))
9690 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
9691 (properties `((upstream-name . "ACCLMA")))
9692 (build-system r-build-system)
9693 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
9694 (synopsis "ACC & LMA graph plotting")
9696 "This package contains a function that imports data from a @acronym{CSV,
9697 Comma-Separated Values} file, or uses manually entered data from the format (x,
9698 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
9699 Curve} vs @acronym{LOI, Line of Independence} graph and
9700 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
9701 function is @code{plotLMA} (source file, header) that takes a data set and plots the
9702 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
9703 string) was passed, a manual data entry window is opened. The header parameter
9704 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
9705 a header row or not. The dataset should contain only one independent variable
9706 (x) and one dependent variable (y) and can contain a weight for each
9708 (license license:gpl2)))
9710 (define-public r-aspi
9717 (uri (cran-uri "aspi" version))
9719 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
9720 (build-system r-build-system)
9722 "https://cran.r-project.org/web/packages/aspi/")
9724 "Analysis of symmetry of parasitic infections")
9726 "This package provides tools for the analysis and visualization of bilateral
9727 asymmetry in parasitic infections.")
9728 (license license:gpl3+)))
9730 (define-public r-sandwich
9737 (uri (cran-uri "sandwich" version))
9740 "0afm6snak7r11dxyl3qirqdjah6d9pdv4afmxwam1nq9bqxyb3w2"))))
9741 (build-system r-build-system)
9743 `(("r-zoo" ,r-zoo)))
9744 (home-page "https://cran.r-project.org/web/packages/sandwich/")
9745 (synopsis "Robust Covariance Matrix Estimators")
9747 "This package provides model-robust standard error estimators for
9748 cross-sectional, time series, clustered, panel, and longitudinal data.")
9749 ;; Either version of the license.
9750 (license (list license:gpl2 license:gpl3))))
9752 (define-public r-th-data
9759 (uri (cran-uri "TH.data" version))
9762 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
9763 (properties `((upstream-name . "TH.data")))
9764 (build-system r-build-system)
9766 `(("r-mass" ,r-mass)
9767 ("r-survival" ,r-survival)))
9768 (home-page "https://cran.r-project.org/web/packages/TH.data/")
9769 (synopsis "Shared data sets")
9771 "This package contains supporting data sets that are used in other
9772 packages maintained by Torsten Hothorn.")
9773 (license license:gpl3)))
9775 (define-public r-multcomp
9782 (uri (cran-uri "multcomp" version))
9785 "1s8qmljawalisggniy7va5l5cicsgvs0lp20c33vxlvyiy0dbb1s"))))
9786 (build-system r-build-system)
9788 `(("r-codetools" ,r-codetools)
9789 ("r-mvtnorm" ,r-mvtnorm)
9790 ("r-sandwich" ,r-sandwich)
9791 ("r-survival" ,r-survival)
9792 ("r-th-data" ,r-th-data)))
9793 (home-page "https://cran.r-project.org/web/packages/multcomp/")
9794 (synopsis "Simultaneous inference in general parametric models")
9796 "Simultaneous tests and confidence intervals for general linear
9797 hypotheses in parametric models, including linear, generalized linear, linear
9798 mixed effects, and survival models. The package includes demos reproducing
9799 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
9800 Hothorn, Westfall, 2010, CRC Press).")
9801 (license license:gpl2)))
9803 (define-public r-emmeans
9810 (uri (cran-uri "emmeans" version))
9813 "1rbh3ls23fazrwpsam5llk3kqdzz2zvsms3i4f1cgn34ky3w8361"))))
9814 (build-system r-build-system)
9816 `(("r-estimability" ,r-estimability)
9817 ("r-mvtnorm" ,r-mvtnorm)
9818 ("r-numderiv" ,r-numderiv)
9820 ("r-xtable" ,r-xtable)))
9822 `(("r-knitr" ,r-knitr)))
9823 (home-page "https://github.com/rvlenth/emmeans")
9824 (synopsis "Estimated marginal means, aka least-squares means")
9826 "This package provides tools to obtain @dfn{estimated marginal
9827 means} (EMMs) for many linear, generalized linear, and mixed models. It can
9828 be used to compute contrasts or linear functions of EMMs, trends, and
9829 comparisons of slopes.")
9830 ;; Either version of the license.
9831 (license (list license:gpl2 license:gpl3))))
9833 (define-public r-pwr
9840 (uri (cran-uri "pwr" version))
9843 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
9844 (build-system r-build-system)
9846 `(("r-knitr" ,r-knitr)))
9847 (home-page "https://github.com/heliosdrm/pwr")
9848 (synopsis "Basic functions for power analysis")
9850 "This package provides power analysis functions along the lines of
9852 (license license:gpl3+)))
9854 (define-public r-libcoin
9861 (uri (cran-uri "libcoin" version))
9863 (base32 "0izgnr4zdrbz3a05b0s28xfly4izp2zslgh282l9ads4skrmj3hl"))))
9864 (build-system r-build-system)
9865 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
9866 (home-page "https://cran.r-project.org/web/packages/libcoin")
9867 (synopsis "Linear test statistics for permutation inference")
9869 "This package provides basic infrastructure for linear test statistics
9870 and permutation inference in the framework of Strasser and Weber (1999).")
9871 (license license:gpl2)))
9873 (define-public r-coin
9880 (uri (cran-uri "coin" version))
9883 "15xvhnbyg34aacn6jfz4bsa1f7wq2ci0hslj8mgymql90k50x1qi"))))
9884 (build-system r-build-system)
9886 `(("r-libcoin" ,r-libcoin)
9887 ("r-matrixstats" ,r-matrixstats)
9888 ("r-modeltools" ,r-modeltools)
9889 ("r-multcomp" ,r-multcomp)
9890 ("r-mvtnorm" ,r-mvtnorm)
9891 ("r-survival" ,r-survival)))
9892 (home-page "http://coin.r-forge.r-project.org")
9893 (synopsis "Conditional inference procedures in a permutation test framework")
9895 "This package provides conditional inference procedures for the general
9896 independence problem including two-sample, K-sample (non-parametric ANOVA),
9897 correlation, censored, ordered and multivariate problems.")
9898 (license license:gpl2)))
9900 (define-public r-bayesplot
9902 (name "r-bayesplot")
9907 (uri (cran-uri "bayesplot" version))
9910 "0j69a78l5z0wyxcz607amaa4jc8kwwvcia9wxyir65b8ks9gj1d6"))))
9911 (build-system r-build-system)
9913 `(("pandoc" ,pandoc)
9914 ("pandoc-citeproc" ,pandoc-citeproc)))
9916 `(("r-knitr" ,r-knitr)))
9918 `(("r-dplyr" ,r-dplyr)
9919 ("r-ggplot2" ,r-ggplot2)
9920 ("r-ggridges" ,r-ggridges)
9922 ("r-reshape2" ,r-reshape2)
9923 ("r-rlang" ,r-rlang)
9924 ("r-tibble" ,r-tibble)
9925 ("r-tidyselect" ,r-tidyselect)))
9926 (home-page "https://mc-stan.org/bayesplot")
9927 (synopsis "Plotting for Bayesian models")
9929 "This package provides plotting functions for posterior analysis, model
9930 checking, and MCMC diagnostics. The package is designed not only to provide
9931 convenient functionality for users, but also a common set of functions that
9932 can be easily used by developers working on a variety of R packages for
9933 Bayesian modeling.")
9934 (license license:gpl3+)))
9936 (define-public r-tmb
9943 (uri (cran-uri "TMB" version))
9946 "0vnjh8d5gnjswil8ld3gbbspy4m5l2pzar1mpj62qxn2mwx0cc4s"))))
9947 (properties `((upstream-name . "TMB")))
9948 (build-system r-build-system)
9950 `(("r-matrix" ,r-matrix)
9951 ("r-rcppeigen" ,r-rcppeigen)))
9952 (home-page "http://tmb-project.org")
9953 (synopsis "Template model builder: a general random effect tool")
9955 "With this tool, a user should be able to quickly implement complex
9956 random effect models through simple C++ templates. The package combines
9957 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
9958 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
9959 from R) to obtain an efficient implementation of the applied Laplace
9960 approximation with exact derivatives. Key features are: Automatic sparseness
9961 detection, parallelism through BLAS and parallel user templates.")
9962 (license license:gpl2)))
9964 (define-public r-sjstats
9971 (uri (cran-uri "sjstats" version))
9973 (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka"))))
9974 (build-system r-build-system)
9976 `(("r-bayestestr" ,r-bayestestr)
9977 ("r-broom" ,r-broom)
9978 ("r-dplyr" ,r-dplyr)
9979 ("r-effectsize" ,r-effectsize)
9980 ("r-emmeans" ,r-emmeans)
9981 ("r-insight" ,r-insight)
9983 ("r-magrittr" ,r-magrittr)
9985 ("r-modelr" ,r-modelr)
9986 ("r-parameters" ,r-parameters)
9987 ("r-performance" ,r-performance)
9988 ("r-purrr" ,r-purrr)
9989 ("r-rlang" ,r-rlang)
9990 ("r-sjlabelled" ,r-sjlabelled)
9991 ("r-sjmisc" ,r-sjmisc)
9992 ("r-tidyr" ,r-tidyr)))
9993 (home-page "https://github.com/strengejacke/sjstats")
9994 (synopsis "Functions for common statistical computations")
9996 "This package provides a collection of convenient functions for common
9997 statistical computations, which are not directly provided by R's @code{base}
9998 or @code{stats} packages. This package aims at providing, first, shortcuts
9999 for statistical measures, which otherwise could only be calculated with
10000 additional effort. Second, these shortcut functions are generic, and can be
10001 applied not only to vectors, but also to other objects as well. The focus of
10002 most functions lies on summary statistics or fit measures for regression
10003 models, including generalized linear models, mixed effects models and Bayesian
10005 (license license:gpl3)))
10007 (define-public r-glmmtmb
10010 (version "1.0.2.1")
10014 (uri (cran-uri "glmmTMB" version))
10017 "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab"))))
10018 (properties `((upstream-name . "glmmTMB")))
10019 (build-system r-build-system)
10021 `(("r-lme4" ,r-lme4)
10022 ("r-matrix" ,r-matrix)
10024 ("r-rcppeigen" ,r-rcppeigen)
10027 `(("r-knitr" ,r-knitr))) ; for vignettes
10028 (home-page "https://github.com/glmmTMB")
10029 (synopsis "Generalized linear mixed models")
10031 "Fit linear and generalized linear mixed models with various extensions,
10032 including zero-inflation. The models are fitted using maximum likelihood
10033 estimation via the Template Model Builder. Random effects are assumed to be
10034 Gaussian on the scale of the linear predictor and are integrated out using the
10035 Laplace approximation. Gradients are calculated using automatic
10037 (license license:agpl3+)))
10039 (define-public r-bayestestr
10041 (name "r-bayestestr")
10046 (uri (cran-uri "bayestestR" version))
10049 "06y7vccgln1882yv04may9p6s915py8nnhg82d5ppbpxzcifi7l4"))))
10050 (properties `((upstream-name . "bayestestR")))
10051 (build-system r-build-system)
10053 `(("r-insight" ,r-insight)))
10055 `(("r-knitr" ,r-knitr)))
10056 (home-page "https://github.com/easystats/bayestestR")
10057 (synopsis "Describe Bayesian models and posterior distributions")
10059 "This package provides utilities to understand and describe posterior
10060 distributions and Bayesian models. It includes point-estimates such as
10061 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
10062 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
10063 ROPE percentage and pd).")
10064 (license license:gpl3)))
10066 (define-public r-performance
10068 (name "r-performance")
10073 (uri (cran-uri "performance" version))
10076 "1z45vy8gg77c2imcspwqf94anzi6c40wwbq0h7hg6zy76jsgvbyj"))))
10077 (build-system r-build-system)
10079 `(("r-bayestestr" ,r-bayestestr)
10080 ("r-insight" ,r-insight)))
10081 (home-page "https://easystats.github.io/performance/")
10082 (synopsis "Assessment of regression models performance")
10084 "This package provides utilities for computing measures to assess model
10085 quality, which are not directly provided by R's @code{base} or @code{stats}
10086 packages. These include e.g. measures like r-squared, intraclass correlation
10087 coefficient, root mean squared error or functions to check models for
10088 overdispersion, singularity or zero-inflation and more. Functions apply to a
10089 large variety of regression models, including generalized linear models, mixed
10090 effects models and Bayesian models.")
10091 (license license:gpl3)))
10093 (define-public r-ggeffects
10095 (name "r-ggeffects")
10100 (uri (cran-uri "ggeffects" version))
10103 "1c5rvycaqp7zp1j6j17c84v8nlpi0w7bhfxmcha4n37m0snk1kgy"))))
10104 (build-system r-build-system)
10106 `(("r-insight" ,r-insight)
10108 ("r-sjlabelled" ,r-sjlabelled)))
10110 `(("r-knitr" ,r-knitr)))
10111 (home-page "https://github.com/strengejacke/ggeffects")
10112 (synopsis "Create tidy data frames of marginal effects for ggplot")
10114 "This package provides tools to compute marginal effects from statistical
10115 models and return the result as tidy data frames. These data frames are ready
10116 to use with the @code{ggplot2} package. Marginal effects can be calculated
10117 for many different models. Interaction terms, splines and polynomial terms
10118 are also supported. The two main functions are @code{ggpredict()} and
10119 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
10120 results using @code{ggplot2}.")
10121 (license license:gpl3)))
10123 (define-public r-effectsize
10125 (name "r-effectsize")
10130 (uri (cran-uri "effectsize" version))
10133 "1hcrnax9wf0nwsb8nv15rxw8yy8w5dak16dw3w5bxi8xnf56lkz2"))))
10134 (properties `((upstream-name . "effectsize")))
10135 (build-system r-build-system)
10137 `(("r-bayestestr" ,r-bayestestr)
10138 ("r-insight" ,r-insight)
10139 ("r-parameters" ,r-parameters)))
10141 `(("r-knitr" ,r-knitr)))
10142 (home-page "https://github.com/easystats/effectsize")
10143 (synopsis "Indices of effect size and standardized parameters")
10145 "This package provides utilities to work with indices of effect size and
10146 standardized parameters for a wide variety of models, allowing computation and
10147 conversion of indices such as Cohen's d, r, odds, etc.")
10148 (license license:gpl3)))
10150 (define-public r-sjplot
10157 (uri (cran-uri "sjPlot" version))
10159 (base32 "1g4qabg654kwdm09ihp4h3mg64a1d7a7gsn6w56rwsidqqaxilq0"))))
10160 (properties `((upstream-name . "sjPlot")))
10161 (build-system r-build-system)
10163 `(("r-bayestestr" ,r-bayestestr)
10164 ("r-dplyr" ,r-dplyr)
10165 ("r-effectsize" ,r-effectsize)
10166 ("r-ggeffects" ,r-ggeffects)
10167 ("r-ggplot2" ,r-ggplot2)
10168 ("r-insight" ,r-insight)
10169 ("r-knitr" ,r-knitr)
10171 ("r-parameters" ,r-parameters)
10172 ("r-performance" ,r-performance)
10173 ("r-purrr" ,r-purrr)
10174 ("r-rlang" ,r-rlang)
10175 ("r-scales" ,r-scales)
10176 ("r-sjlabelled" ,r-sjlabelled)
10177 ("r-sjmisc" ,r-sjmisc)
10178 ("r-sjstats" ,r-sjstats)
10179 ("r-tidyr" ,r-tidyr)))
10181 `(("r-knitr" ,r-knitr)))
10182 (home-page "https://strengejacke.github.io/sjPlot/")
10183 (synopsis "Data visualization for statistics in social science")
10185 "This package represents a collection of plotting and table output
10186 functions for data visualization. Results of various statistical
10187 analyses (that are commonly used in social sciences) can be visualized using
10188 this package, including simple and cross tabulated frequencies, histograms,
10189 box plots, (generalized) linear models, mixed effects models, principal
10190 component analysis and correlation matrices, cluster analyses, scatter plots,
10191 stacked scales, effects plots of regression models (including interaction
10192 terms) and much more. This package supports labelled data.")
10193 (license license:gpl3)))
10195 (define-public r-ini
10202 (uri (cran-uri "ini" version))
10205 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
10206 (build-system r-build-system)
10207 (home-page "https://github.com/dvdscripter/ini")
10208 (synopsis "Read and write configuration files")
10210 "This package provides tools to parse simple @code{.ini} configuration
10211 files to an structured list. Users can manipulate this resulting list with
10212 @code{lapply()} functions. This same structured list can be used to write
10213 back to file after modifications.")
10214 (license license:gpl3)))
10216 (define-public r-gitcreds
10218 (name "r-gitcreds")
10223 (uri (cran-uri "gitcreds" version))
10226 "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi"))))
10227 (properties `((upstream-name . "gitcreds")))
10228 (build-system r-build-system)
10229 (inputs `(("git" ,git-minimal)))
10230 (native-inputs `(("r-knitr" ,r-knitr)))
10231 (home-page "https://github.com/r-lib/gitcreds")
10232 (synopsis "Query git credentials from R")
10234 "Query, set, and delete credentials from the git credential store.
10235 Manage GitHub tokens and other git credentials. This package is to be used by
10236 other packages that need to authenticate to GitHub and/or other git
10238 (license license:expat)))
10240 (define-public r-gh
10247 (uri (cran-uri "gh" version))
10250 "1zvy3ylxvni10lhvmbm9h14mg4wlsbdbzbzviwf28jxss8749219"))))
10251 (build-system r-build-system)
10254 ("r-gitcreds" ,r-gitcreds)
10257 ("r-jsonlite" ,r-jsonlite)))
10259 `(("r-knitr" ,r-knitr)))
10260 (home-page "https://github.com/r-lib/gh#readme")
10261 (synopsis "Access the GitHub API via R")
10263 "This package provides a minimal R client to access the GitHub API.")
10264 (license license:expat)))
10266 (define-public r-fs
10273 (uri (cran-uri "fs" version))
10276 "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn"))))
10277 (build-system r-build-system)
10279 `(("r-knitr" ,r-knitr)))
10280 (home-page "https://fs.r-lib.org")
10281 (synopsis "Cross-platform file system operations based on libuv")
10283 "This package provides a cross-platform interface to file system
10284 operations, built on top of the libuv C library.")
10285 (license license:gpl3)))
10287 (define-public r-clisymbols
10289 (name "r-clisymbols")
10294 (uri (cran-uri "clisymbols" version))
10297 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
10298 (build-system r-build-system)
10299 (home-page "https://github.com/gaborcsardi/clisymbols")
10300 (synopsis "Unicode symbols at the R prompt")
10302 "This package provides a small subset of Unicode symbols, that are useful
10303 when building command line applications. They fall back to alternatives on
10304 terminals that do not support Unicode.")
10305 (license license:expat)))
10307 (define-public r-credentials
10309 (name "r-credentials")
10314 (uri (cran-uri "credentials" version))
10317 "1w9zj34xdwz9bszsvhv2cbgq96y5sgxbh7ndn31pgfcpzlkfq6f1"))))
10318 (properties `((upstream-name . "credentials")))
10319 (build-system r-build-system)
10322 (modify-phases %standard-phases
10323 (add-after 'unpack 'setenv-HOME
10325 ;; This is necessary because git looks for $HOME/.gitconfig
10326 (setenv "HOME" "/tmp")
10329 `(("git" ,git-minimal)))
10331 `(("r-askpass" ,r-askpass)
10333 ("r-jsonlite" ,r-jsonlite)
10334 ("r-openssl" ,r-openssl)
10337 `(("r-knitr" ,r-knitr)))
10338 (home-page "https://docs.ropensci.org/credentials/")
10339 (synopsis "Tools for managing SSH and Git credentials")
10341 "This package assists you in setting up and retrieving of HTTPS and SSH
10342 credentials for use with git and other services. For HTTPS remotes the
10343 package interfaces the @command{git-credential} utility which @command{git}
10344 uses to store HTTP usernames and passwords. For SSH remotes this package
10345 provides convenient functions to find or generate appropriate SSH keys. The
10346 package both helps the user to setup a local git installation, and also
10347 provides a back-end for git/ssh client libraries to authenticate with existing
10348 user credentials.")
10349 (license license:expat)))
10351 (define-public r-gert
10358 (uri (cran-uri "gert" version))
10361 "09har6mj7qy813s6dxyzfzmjwg60m8c01yx3q6lfsnvwqzxlqxv8"))))
10362 (properties `((upstream-name . "gert")))
10363 (build-system r-build-system)
10365 `(("libgit2" ,libgit2)
10368 `(("r-askpass" ,r-askpass)
10369 ("r-credentials" ,r-credentials)
10370 ("r-openssl" ,r-openssl)
10371 ("r-rstudioapi" ,r-rstudioapi)
10375 `(("pkg-config" ,pkg-config)
10376 ("r-knitr" ,r-knitr)))
10377 (home-page "https://docs.ropensci.org/gert/")
10378 (synopsis "Simple Git client for R")
10380 "This package provides a simple git client for R based on libgit2 with
10381 support for SSH and HTTPS remotes. All functions in gert use basic R data
10382 types (such as vectors and data-frames) for their arguments and return values.
10383 User credentials are shared with command line git through the
10384 @code{git-credential} store and SSH keys stored on disk or ssh-agent.")
10385 (license license:expat)))
10387 (define-public r-usethis
10394 (uri (cran-uri "usethis" version))
10397 "1j6nzzrm2m6vi1gq0d5kxnnr9d8cy88wpmgigz3inych65x9w9pg"))))
10398 (build-system r-build-system)
10401 ("r-clipr" ,r-clipr)
10402 ("r-crayon" ,r-crayon)
10409 ("r-jsonlite" ,r-jsonlite)
10410 ("r-lifecycle" ,r-lifecycle)
10411 ("r-purrr" ,r-purrr)
10412 ("r-rappdirs" ,r-rappdirs)
10413 ("r-rlang" ,r-rlang)
10414 ("r-rprojroot" ,r-rprojroot)
10415 ("r-rstudioapi" ,r-rstudioapi)
10416 ("r-whisker" ,r-whisker)
10417 ("r-withr" ,r-withr)
10418 ("r-yaml" ,r-yaml)))
10419 (home-page "https://github.com/r-lib/usethis")
10420 (synopsis "Automate R package and project setup")
10422 "This package helps you to automate R package and project setup tasks
10423 that are otherwise performed manually. This includes setting up unit testing,
10424 test coverage, continuous integration, Git, GitHub integration, licenses,
10425 Rcpp, RStudio projects, and more.")
10426 (license license:gpl3)))
10428 (define-public r-sessioninfo
10430 (name "r-sessioninfo")
10435 (uri (cran-uri "sessioninfo" version))
10438 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
10439 (build-system r-build-system)
10442 ("r-withr" ,r-withr)))
10443 (home-page "https://github.com/r-lib/sessioninfo#readme")
10444 (synopsis "R session information")
10446 "This package provides tools to query and print information about the
10447 current R session. It is similar to @code{utils::sessionInfo()}, but includes
10448 more information about packages, and where they were installed from.")
10449 (license license:gpl2)))
10451 (define-public r-remotes
10458 (uri (cran-uri "remotes" version))
10461 "1f1kdw9j1wald3fs8b3n68x1kljy07j60g3aw1aarx26ikyk9whj"))))
10462 (build-system r-build-system)
10464 `(("r-knitr" ,r-knitr)))
10465 (home-page "https://github.com/r-lib/remotes#readme")
10466 (synopsis "R package installation from remote repositories")
10468 "Download and install R packages stored in GitHub, BitBucket, or plain
10469 subversion or git repositories. This package is a lightweight replacement of
10470 the @code{install_*} functions in the @code{devtools} package. Indeed most of
10471 the code was copied over from @code{devtools}.")
10472 (license license:gpl2+)))
10474 (define-public r-xopen
10481 (uri (cran-uri "xopen" version))
10484 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
10485 (build-system r-build-system)
10487 `(("r-processx" ,r-processx)))
10488 (home-page "https://github.com/r-lib/xopen#readme")
10489 (synopsis "Open system files, URLs, anything")
10491 "This package provides a cross-platform solution to open files,
10492 directories or URLs with their associated programs.")
10493 (license license:expat)))
10495 (define-public r-rcmdcheck
10497 (name "r-rcmdcheck")
10502 (uri (cran-uri "rcmdcheck" version))
10505 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
10506 (build-system r-build-system)
10508 `(("r-callr" ,r-callr)
10510 ("r-crayon" ,r-crayon)
10512 ("r-digest" ,r-digest)
10513 ("r-pkgbuild" ,r-pkgbuild)
10514 ("r-prettyunits" ,r-prettyunits)
10516 ("r-rprojroot" ,r-rprojroot)
10517 ("r-sessioninfo" ,r-sessioninfo)
10518 ("r-withr" ,r-withr)
10519 ("r-xopen" ,r-xopen)))
10520 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
10521 (synopsis "Run R CMD check from R and capture results")
10523 "Run @code{R CMD check} from R programmatically, and capture the results
10524 of the individual checks.")
10525 (license license:expat)))
10527 (define-public r-rapportools
10529 (name "r-rapportools")
10534 (uri (cran-uri "rapportools" version))
10537 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
10538 (build-system r-build-system)
10540 `(("r-pander" ,r-pander)
10542 ("r-reshape" ,r-reshape)))
10543 (home-page "https://cran.r-project.org/web/packages/rapportools/")
10544 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
10546 "This package provides helper functions that act as wrappers to more
10547 advanced statistical methods with the advantage of having sane defaults for
10549 (license license:agpl3+)))
10551 (define-public r-pander
10558 (uri (cran-uri "pander" version))
10561 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
10562 (build-system r-build-system)
10564 `(("r-digest" ,r-digest)
10565 ("r-rcpp" ,r-rcpp)))
10566 (home-page "https://rapporter.github.io/pander")
10567 (synopsis "Render R objects into Pandoc's markdown")
10569 "The main aim of the pander R package is to provide a minimal and easy
10570 tool for rendering R objects into Pandoc's markdown. The package is also
10571 capable of exporting/converting complex Pandoc documents (reports) in various
10573 ;; This package is licensed under either the AGPLv3+ or the very rarely
10575 (license license:agpl3+)))
10577 (define-public r-summarytools
10579 (name "r-summarytools")
10584 (uri (cran-uri "summarytools" version))
10587 "0n7rad6bkfn9cb99wbfzbwl5qzch48r0gafhddfcqvyh4fbn2k0j"))))
10588 (build-system r-build-system)
10590 `(("r-base64enc" ,r-base64enc)
10591 ("r-checkmate" ,r-checkmate)
10592 ("r-dplyr" ,r-dplyr)
10593 ("r-htmltools" ,r-htmltools)
10594 ("r-lubridate" ,r-lubridate)
10595 ("r-magick" ,r-magick)
10596 ("r-matrixstats" ,r-matrixstats)
10597 ("r-pander" ,r-pander)
10599 ("r-rapportools" ,r-rapportools)
10600 ("r-tibble" ,r-tibble)
10601 ("r-tidyr" ,r-tidyr)))
10603 `(("r-knitr" ,r-knitr)))
10604 (home-page "https://github.com/dcomtois/summarytools")
10605 (synopsis "Tools to quickly and neatly summarize data")
10607 "This package provides tools for data frame summaries, cross-tabulations,
10608 weight-enabled frequency tables and common univariate statistics in concise
10609 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
10610 good point-of-entry for exploring data, both for experienced and new R
10612 (license license:gpl2)))
10614 (define-public r-lsei
10621 (uri (cran-uri "lsei" version))
10624 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2"))))
10625 (build-system r-build-system)
10627 `(("gfortran" ,gfortran)))
10628 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
10629 (synopsis "Solve regression problems under equality/inequality constraints")
10631 "It contains functions that solve least squares linear regression
10632 problems under linear equality/inequality constraints. Functions for solving
10633 quadratic programming problems are also available, which transform such
10634 problems into least squares ones first.")
10635 (license license:gpl2+)))
10637 (define-public r-npsurv
10644 (uri (cran-uri "npsurv" version))
10647 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw"))))
10648 (build-system r-build-system)
10650 `(("r-lsei" ,r-lsei)))
10651 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
10652 (synopsis "Nonparametric survival analysis")
10654 "This package contains functions for non-parametric survival analysis of
10655 exact and interval-censored observations.")
10656 (license license:gpl2+)))
10658 (define-public r-clusteval
10660 (name "r-clusteval")
10665 (uri (cran-uri "clusteval" version))
10668 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
10669 (build-system r-build-system)
10671 `(("r-mvtnorm" ,r-mvtnorm)
10672 ("r-rcpp" ,r-rcpp)))
10673 (home-page "https://cran.r-project.org/web/packages/clusteval/")
10674 (synopsis "Evaluation of clustering algorithms")
10676 "This R package provides a suite of tools to evaluate clustering
10677 algorithms, clusterings, and individual clusters.")
10678 (license license:expat)))
10680 (define-public r-tweedie
10687 (uri (cran-uri "tweedie" version))
10690 "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0"))))
10691 (build-system r-build-system)
10692 (native-inputs `(("gfortran" ,gfortran)))
10693 (home-page "https://cran.r-project.org/web/packages/tweedie/")
10694 (synopsis "Evaluation of Tweedie exponential family models")
10696 "Maximum likelihood computations for Tweedie families, including the
10697 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
10698 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
10699 and related methods.")
10700 (license license:gpl2+)))
10702 (define-public r-rcppgsl
10709 (uri (cran-uri "RcppGSL" version))
10711 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
10712 (properties `((upstream-name . "RcppGSL")))
10713 (build-system r-build-system)
10715 `(("r-rcpp" ,r-rcpp)
10717 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
10718 (synopsis "Rcpp integration for GSL vectors and matrices")
10720 "The GNU Scientific Library (or GSL) is a collection of numerical
10721 routines for scientific computing. It is particularly useful for C and C++
10722 programs as it provides a standard C interface to a wide range of mathematical
10723 routines. There are over 1000 functions in total with an extensive test
10724 suite. The RcppGSL package provides an easy-to-use interface between GSL data
10725 structures and R using concepts from Rcpp which is itself a package that eases
10726 the interfaces between R and C++.")
10727 (license license:gpl2+)))
10729 (define-public r-mvabund
10736 (uri (cran-uri "mvabund" version))
10739 "0aisvax9d7bk6aykrcdcn1ji618r520mcrkr1i3jnck1qs31z41f"))))
10740 (build-system r-build-system)
10742 `(("r-mass" ,r-mass)
10744 ("r-rcppgsl" ,r-rcppgsl)
10745 ("r-statmod" ,r-statmod)
10746 ("r-tweedie" ,r-tweedie)))
10747 (home-page "https://cran.r-project.org/web/packages/mvabund/")
10748 (synopsis "Statistical methods for analysing multivariate abundance data")
10750 "This package provides a set of tools for displaying, modeling and
10751 analysing multivariate abundance data in community ecology.")
10752 (license license:lgpl2.1+)))
10754 (define-public r-afex
10761 (uri (cran-uri "afex" version))
10764 "0blwqr5ni3psav1dcdmhfi4jy3b4scm5njimqfpr1d81zadvgc6g"))))
10765 (build-system r-build-system)
10769 ("r-lmertest" ,r-lmertest)
10770 ("r-pbkrtest" ,r-pbkrtest)
10771 ("r-reshape2" ,r-reshape2)))
10773 `(("r-knitr" ,r-knitr)))
10774 (home-page "https://afex.singmann.science/")
10775 (synopsis "Analysis of factorial experiments")
10777 "This package provides convenience functions for analyzing factorial
10778 experiments using ANOVA or mixed models.")
10779 (license license:gpl2+)))
10781 (define-public r-lmertest
10783 (name "r-lmertest")
10788 (uri (cran-uri "lmerTest" version))
10791 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim"))))
10792 (properties `((upstream-name . "lmerTest")))
10793 (build-system r-build-system)
10795 `(("r-ggplot2" ,r-ggplot2)
10798 ("r-numderiv" ,r-numderiv)))
10799 (home-page "https://github.com/runehaubo/lmerTestR")
10800 (synopsis "Tests in linear mixed effects models")
10802 "This package provides p-values in type I, II or III anova and summary
10803 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
10804 method. A Kenward-Roger method is also available via the @code{pbkrtest}
10805 package. Model selection methods include step, drop1 and anova-like tables
10806 for random effects (ranova). Methods for Least-Square means (LS-means) and
10807 tests of linear contrasts of fixed effects are also available.")
10808 (license license:gpl2+)))
10810 (define-public r-r2glmm
10817 (uri (cran-uri "r2glmm" version))
10820 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
10821 (build-system r-build-system)
10823 `(("r-afex" ,r-afex)
10824 ("r-data-table" ,r-data-table)
10825 ("r-dplyr" ,r-dplyr)
10826 ("r-ggplot2" ,r-ggplot2)
10827 ("r-gridextra" ,r-gridextra)
10828 ("r-lmertest" ,r-lmertest)
10830 ("r-matrix" ,r-matrix)
10832 ("r-pbkrtest" ,r-pbkrtest)))
10833 (home-page "https://github.com/bcjaeger/r2glmm")
10834 (synopsis "Compute R squared for mixed (multilevel) models")
10836 "This package computes model and semi partial R squared with confidence
10837 limits for the linear and generalized linear mixed model (LMM and GLMM). The
10838 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
10839 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
10841 (license license:gpl2)))
10843 (define-public r-weights
10850 (uri (cran-uri "weights" version))
10853 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
10854 (build-system r-build-system)
10856 `(("r-gdata" ,r-gdata)
10857 ("r-hmisc" ,r-hmisc)
10858 ("r-mice" ,r-mice)))
10860 "https://cran.r-project.org/web/packages/weights/")
10861 (synopsis "Weighting and weighted statistics")
10862 (description "This package Provides a variety of functions for producing
10863 simple weighted statistics, such as weighted Pearson's correlations, partial
10864 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
10865 includes some software for quickly recoding survey data and plotting point
10866 estimates from interaction terms in regressions (and multiply imputed
10867 regressions). NOTE: Weighted partial correlation calculations pulled to
10869 (license license:gpl2+)))
10871 (define-public r-rcppannoy
10873 (name "r-rcppannoy")
10878 (uri (cran-uri "RcppAnnoy" version))
10881 "0n68cf77gz34iq6w6ad87pbqwqam45nxp1gjzns4g6qhf7qdvrz4"))))
10882 (properties `((upstream-name . "RcppAnnoy")))
10883 (build-system r-build-system)
10885 `(("r-rcpp" ,r-rcpp)))
10886 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
10887 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
10889 "Annoy is a small C++ library for Approximate Nearest Neighbors written
10890 for efficient memory usage as well an ability to load from and save to disk.
10891 This package provides an R interface.")
10892 ;; Annoy is released under ASL 2.0, but this wrapper is released under
10894 (license (list license:gpl2+ license:asl2.0))))
10896 (define-public r-rcpphnsw
10898 (name "r-rcpphnsw")
10903 (uri (cran-uri "RcppHNSW" version))
10906 "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
10907 (properties `((upstream-name . "RcppHNSW")))
10908 (build-system r-build-system)
10909 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10910 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
10911 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
10913 "Hnswlib is a C++ library for approximate nearest neighbors. This
10914 package provides a minimal R interface by relying on the Rcpp package.")
10915 ;; hnswlib is released under Version 2.0 of the Apache License.
10916 (license (list license:gpl3 license:asl2.0))))
10918 (define-public r-rcppparallel
10920 (name "r-rcppparallel")
10925 (uri (cran-uri "RcppParallel" version))
10928 "10bg4fw38m64dhy543rwq2nnjjc9y24iggk343xslrb3ij8018lc"))))
10929 (properties `((upstream-name . "RcppParallel")))
10930 (build-system r-build-system)
10931 (home-page "https://rcppcore.github.io/RcppParallel/")
10932 (synopsis "Parallel programming tools for Rcpp")
10934 "This package provides high level functions for parallel programming with
10935 Rcpp. For example, the @code{parallelFor()} function can be used to convert
10936 the work of a standard serial @code{for} loop into a parallel one and the
10937 @code{parallelReduce()} function can be used for accumulating aggregates or
10939 (license license:gpl2)))
10941 (define-public r-ncdf4
10948 (uri (cran-uri "ncdf4" version))
10951 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
10952 (build-system r-build-system)
10954 `(("netcdf" ,netcdf)
10956 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
10957 (synopsis "R interface to Unidata netCDF format data files")
10959 "This package provides a high-level R interface to data files written
10960 using Unidata's netCDF library (version 4 or earlier), which are binary data
10961 files that are portable across platforms and include metadata information in
10962 addition to the data sets. Using this package, netCDF files can be opened and
10963 data sets read in easily. It is also easy to create new netCDF dimensions,
10964 variables, and files, in either version 3 or 4 format, and manipulate existing
10966 (license license:gpl3+)))
10968 (define-public r-biocmanager
10970 (name "r-biocmanager")
10971 (version "1.30.10")
10975 (uri (cran-uri "BiocManager" version))
10977 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
10978 (properties `((upstream-name . "BiocManager")))
10979 (build-system r-build-system)
10980 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
10981 (synopsis "Access the Bioconductor project package repository")
10983 "This package provides a convenient tool to install and update
10984 Bioconductor packages.")
10985 (license license:artistic2.0)))
10987 (define-public r-rgl
10990 (version "0.104.16")
10994 (uri (cran-uri "rgl" version))
10997 "169a8riiam8445nl7rcwn0x92dlwyzh5xldvap6dcxjyjqmjwbdq"))))
10998 (build-system r-build-system)
11000 `(("pkg-config" ,pkg-config)
11001 ("r-knitr" ,r-knitr)))
11003 `(("freetype" ,freetype)
11010 `(("r-crosstalk" ,r-crosstalk)
11011 ("r-htmltools" ,r-htmltools)
11012 ("r-htmlwidgets" ,r-htmlwidgets)
11013 ("r-jsonlite" ,r-jsonlite)
11014 ("r-knitr" ,r-knitr)
11015 ("r-magrittr" ,r-magrittr)
11016 ("r-manipulatewidget" ,r-manipulatewidget)
11017 ("r-shiny" ,r-shiny)))
11018 (home-page "https://r-forge.r-project.org/projects/rgl/")
11019 (synopsis "3D visualization using OpenGL")
11021 "This package provides medium to high level functions for 3D interactive graphics,
11022 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
11023 as functions for constructing representations of geometric
11024 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
11025 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
11026 image formats, including PNG, Postscript, SVG, PGF.")
11027 ;; Any version of the GPL.
11028 (license (list license:gpl2+ license:gpl3+))))
11030 (define-public r-multicool
11032 (name "r-multicool")
11037 (uri (cran-uri "multicool" version))
11040 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
11041 (build-system r-build-system)
11042 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11043 (home-page "https://cran.r-project.org/web/packages/multicool/")
11044 (synopsis "Permutations of multisets in cool-lex order")
11046 "This package provides a set of tools to permute multisets without loops
11047 or hash tables and to generate integer partitions. Cool-lex order is similar
11048 to colexicographical order.")
11049 (license license:gpl2)))
11051 (define-public r-misc3d
11058 (uri (cran-uri "misc3d" version))
11061 "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1"))))
11062 (build-system r-build-system)
11063 (home-page "https://cran.r-project.org/web/packages/misc3d/")
11064 (synopsis "Miscellaneous 3D Plots")
11066 "This package provides a collection of miscellaneous 3d plots, including
11068 ;; Any version of the GPL.
11069 (license (list license:gpl2+ license:gpl3+))))
11071 (define-public r-ks
11078 (uri (cran-uri "ks" version))
11080 (base32 "1sff6rlpq64lqyvwgral9zbcan30wpgmfb26hw9y6wzypd9gxbz6"))))
11081 (build-system r-build-system)
11084 ("r-kernlab" ,r-kernlab)
11085 ("r-kernsmooth" ,r-kernsmooth)
11086 ("r-matrix" ,r-matrix)
11087 ("r-mclust" ,r-mclust)
11089 ("r-multicool" ,r-multicool)
11090 ("r-mvtnorm" ,r-mvtnorm)
11091 ("r-plot3d" ,r-plot3d)))
11092 (home-page "http://www.mvstat.net/tduong/")
11093 (synopsis "Kernel smoothing")
11095 "This package provides kernel smoothers for univariate and multivariate
11096 data, including density functions, density derivatives, cumulative
11097 distributions, modal clustering, discriminant analysis, and two-sample
11098 hypothesis testing.")
11099 ;; Either version of the GPL.
11100 (license (list license:gpl2 license:gpl3))))
11102 (define-public r-feature
11109 (uri (cran-uri "feature" version))
11112 "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y"))))
11113 (build-system r-build-system)
11116 ("r-plot3d" ,r-plot3d)))
11118 `(("r-knitr" ,r-knitr)))
11119 (home-page "http://www.mvstat.net/tduong/")
11120 (synopsis "Inferential feature significance for kernel density estimation")
11122 "The feature package contains functions to display and compute kernel
11123 density estimates, significant gradient and significant curvature regions.
11124 Significant gradient and/or curvature regions often correspond to significant
11125 features (e.g. local modes).")
11126 ;; Either version of the GPL.
11127 (license (list license:gpl2 license:gpl3))))
11129 (define-public r-arm
11136 (uri (cran-uri "arm" version))
11139 "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3"))))
11140 (build-system r-build-system)
11142 `(("r-abind" ,r-abind)
11144 ("r-hmisc" ,r-hmisc)
11147 ("r-matrix" ,r-matrix)
11148 ("r-nlme" ,r-nlme)))
11149 (home-page "https://cran.r-project.org/web/packages/arm/")
11150 (synopsis "Data analysis using regression and multilevel/hierarchical models")
11152 "This package provides functions to accompany A. Gelman and J. Hill,
11153 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
11154 University Press, 2007.")
11155 (license license:gpl3+)))
11157 (define-public r-circular
11159 (name "r-circular")
11164 (uri (cran-uri "circular" version))
11167 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
11168 (build-system r-build-system)
11170 `(("r-boot" ,r-boot)
11171 ("r-mvtnorm" ,r-mvtnorm)))
11173 `(("gfortran" ,gfortran)))
11174 (home-page "https://cran.r-project.org/web/packages/circular/")
11175 (synopsis "Circular statistics")
11177 "This package provides tools for circular statistics, from \"Topics in
11178 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
11180 (license license:gpl2+)))
11182 (define-public r-activity
11184 (name "r-activity")
11189 (uri (cran-uri "activity" version))
11192 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
11193 (build-system r-build-system)
11195 `(("r-circular" ,r-circular)
11196 ("r-insol" ,r-insol)
11197 ("r-pbapply" ,r-pbapply)))
11198 (home-page "https://cran.r-project.org/web/packages/activity/")
11199 (synopsis "Animal activity statistics")
11201 "This package provides functions to fit kernel density functions to
11202 animal activity time data; plot activity distributions; quantify overall
11203 levels of activity; statistically compare activity metrics through
11204 bootstrapping; and evaluate variation in linear variables with time (or other
11205 circular variables).")
11206 (license license:gpl3)))
11208 (define-public r-ouch
11215 (uri (cran-uri "ouch" version))
11218 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
11219 (build-system r-build-system)
11220 (propagated-inputs `(("r-subplex" ,r-subplex)))
11221 (home-page "https://kingaa.github.io/ouch/")
11222 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
11224 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
11225 for evolution along a phylogenetic tree.")
11226 (license license:gpl2+)))
11228 (define-public r-fmsb
11235 (uri (cran-uri "fmsb" version))
11238 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
11239 (build-system r-build-system)
11240 (home-page "http://minato.sip21c.org/msb/")
11241 (synopsis "Functions for medical statistics book with demographic data")
11243 "This package provides several utility functions for the book entitled
11244 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
11245 Japan, 2007) with Japanese demographic data and some demographic analysis
11246 related functions.")
11247 (license license:gpl2+)))
11249 (define-public r-stabledist
11251 (name "r-stabledist")
11256 (uri (cran-uri "stabledist" version))
11259 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
11260 (build-system r-build-system)
11261 (home-page "https://www.rmetrics.org")
11262 (synopsis "Stable distribution functions")
11264 "This package provides density, probability and quantile functions, and
11265 random number generation for (skew) stable distributions, using the
11266 parametrizations of Nolan.")
11267 (license license:gpl2+)))
11269 (define-public r-gsl
11276 (uri (cran-uri "gsl" version))
11279 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
11280 (build-system r-build-system)
11283 (home-page "https://cran.r-project.org/web/packages/gsl")
11284 (synopsis "Wrapper for the GNU Scientific Library")
11286 "This package provides an R wrapper for the special functions and quasi
11287 random number generators of the GNU Scientific Library.")
11288 (license license:gpl2+)))
11290 (define-public r-adgoftest
11292 (name "r-adgoftest")
11297 (uri (cran-uri "ADGofTest" version))
11300 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
11301 (properties `((upstream-name . "ADGofTest")))
11302 (build-system r-build-system)
11303 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
11304 (synopsis "Anderson-Darling GoF test")
11306 "This package provides an implementation of the Anderson-Darling GoF test
11307 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
11308 Anderson-Darling Distribution\".")
11309 ;; Any version of the GPL.
11310 (license license:gpl3+)))
11312 (define-public r-sodium
11319 (uri (cran-uri "sodium" version))
11322 "1zxzi8xvxnhgcd5qrylf08nz1cdq3aslrswjas440qg63ypmbf6w"))))
11323 (properties `((upstream-name . "sodium")))
11324 (build-system r-build-system)
11326 `(("libsodium" ,libsodium)))
11328 `(("pkg-config" ,pkg-config)
11329 ("r-knitr" ,r-knitr)))
11330 (home-page "https://github.com/jeroen/sodium")
11331 (synopsis "R bindings to the libsodium crypto library")
11333 "This package provides bindings to libsodium: a library for encryption,
11334 decryption, signatures, password hashing and more. Sodium uses curve25519, a
11335 Diffie-Hellman function by Daniel Bernstein, which has become very popular
11336 after it was discovered that the NSA had backdoored Dual EC DRBG.")
11337 (license license:expat)))
11339 (define-public r-softimpute
11341 (name "r-softimpute")
11346 (uri (cran-uri "softImpute" version))
11349 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
11350 (properties `((upstream-name . "softImpute")))
11351 (build-system r-build-system)
11353 `(("r-matrix" ,r-matrix)))
11355 `(("gfortran" ,gfortran)))
11356 (home-page "https://cran.r-project.org/web/packages/softImpute")
11357 (synopsis "Matrix completion via iterative soft-thresholded SVD")
11359 "This package provides iterative methods for matrix completion that use
11360 nuclear-norm regularization. The package includes procedures for centering
11361 and scaling rows, columns or both, and for computing low-rank @dfn{single
11362 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
11364 (license license:gpl2)))
11366 (define-public r-fftwtools
11368 (name "r-fftwtools")
11373 (uri (cran-uri "fftwtools" version))
11376 "0h8lyl2i6zq16ir7xnfj9dhyivxvwikm8lml19s8s8jx95z3n9x9"))))
11377 (build-system r-build-system)
11378 (inputs `(("fftw" ,fftw)))
11379 (home-page "https://github.com/krahim/fftwtools")
11380 (synopsis "Wrapper for FFTW3")
11382 "This package provides a wrapper for several FFTW functions. It provides
11383 access to the two-dimensional FFT, the multivariate FFT, and the
11384 one-dimensional real to complex FFT using the FFTW3 library. The package
11385 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
11386 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
11387 The FFT functions have a parameter that allows them to not return the
11388 redundant complex conjugate when the input is real data.")
11389 (license license:gpl2+)))
11391 (define-public r-tiff
11398 (uri (cran-uri "tiff" version))
11401 "1yy4im2lwzhjnnkfwxgkknsajvm83pcwaf370pkgfva2db0xjfv2"))))
11402 (build-system r-build-system)
11404 `(("libtiff" ,libtiff)
11405 ("libjpeg" ,libjpeg-turbo)
11407 (home-page "https://www.rforge.net/tiff/")
11408 (synopsis "Read and write TIFF images")
11410 "This package provides an easy and simple way to read, write and display
11411 bitmap images stored in the TIFF format. It can read and write both files and
11412 in-memory raw vectors.")
11413 ;; Either of these two license versions.
11414 (license (list license:gpl2 license:gpl3))))
11416 (define-public r-nlp
11423 (uri (cran-uri "NLP" version))
11426 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5"))))
11427 (properties `((upstream-name . "NLP")))
11428 (build-system r-build-system)
11429 (home-page "https://cran.r-project.org/web/packages/NLP/")
11430 (synopsis "Natural language processing infrastructure")
11432 "This package provides basic classes and methods for Natural Language
11434 (license license:gpl3)))
11436 (define-public r-tm
11443 (uri (cran-uri "tm" version))
11446 "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi"))))
11447 (properties `((upstream-name . "tm")))
11448 (build-system r-build-system)
11454 ("r-xml2" ,r-xml2)))
11455 (home-page "http://tm.r-forge.r-project.org/")
11456 (synopsis "Text mining package")
11458 "This package provides a framework for text mining applications within R.")
11459 (license license:gpl3)))
11461 (define-public r-waveslim
11463 (name "r-waveslim")
11468 (uri (cran-uri "waveslim" version))
11471 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
11472 (build-system r-build-system)
11474 `(("gfortran" ,gfortran)))
11475 (home-page "http://waveslim.blogspot.com")
11476 (synopsis "Basic wavelet routines for signal processing")
11478 "This package provides basic wavelet routines for time series (1D),
11479 image (2D) and array (3D) analysis. The code provided here is based on
11480 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
11481 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
11482 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
11483 pairs (Selesnick 2001, 2002).")
11484 (license license:bsd-3)))
11486 (define-public r-wordcloud
11488 (name "r-wordcloud")
11493 (uri (cran-uri "wordcloud" version))
11496 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
11497 (build-system r-build-system)
11499 `(("r-rcolorbrewer" ,r-rcolorbrewer)
11501 ;; The "tm" package is only "suggested" according to CRAN, but the
11502 ;; wordcloud package cannot be loaded without it.
11504 (home-page "https://cran.r-project.org/web/packages/wordcloud")
11505 (synopsis "Word clouds")
11507 "This package provides functionality to create pretty word clouds,
11508 visualize differences and similarity between documents, and avoid
11509 over-plotting in scatter plots with text.")
11510 (license license:lgpl2.1)))
11512 (define-public r-colorramps
11514 (name "r-colorramps")
11519 (uri (cran-uri "colorRamps" version))
11522 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
11523 (properties `((upstream-name . "colorRamps")))
11524 (build-system r-build-system)
11525 (home-page "https://cran.r-project.org/web/packages/colorRamps")
11526 (synopsis "Build color tables")
11527 (description "This package provides features to build gradient color
11529 ;; Any version of the GPL
11530 (license license:gpl3+)))
11532 (define-public r-tidytree
11534 (name "r-tidytree")
11539 (uri (cran-uri "tidytree" version))
11541 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
11542 (build-system r-build-system)
11545 ("r-dplyr" ,r-dplyr)
11546 ("r-lazyeval" ,r-lazyeval)
11547 ("r-magrittr" ,r-magrittr)
11548 ("r-rlang" ,r-rlang)
11549 ("r-tibble" ,r-tibble)))
11551 `(("r-knitr" ,r-knitr)))
11552 (home-page "https://github.com/GuangchuangYu/tidytree")
11553 (synopsis "Tidy tool for phylogenetic tree data manipulation")
11555 "Phylogenetic trees generally contain multiple components including nodes,
11556 edges, branches and associated data. This package provides an approach to
11557 convert tree objects to tidy data frames. It also provides tidy interfaces to
11558 manipulate tree data.")
11559 (license license:artistic2.0)))
11561 (define-public r-rvcheck
11568 (uri (cran-uri "rvcheck" version))
11570 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
11571 (build-system r-build-system)
11573 `(("r-biocmanager" ,r-biocmanager)
11574 ("r-rlang" ,r-rlang)))
11575 (home-page "https://cran.r-project.org/web/packages/rvcheck")
11576 (synopsis "R package version check")
11578 "This package provides tools to check the latest release version of R and
11579 R packages (on CRAN, Bioconductor or Github).")
11580 (license license:artistic2.0)))
11582 (define-public r-docopt
11589 (uri (cran-uri "docopt" version))
11592 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
11593 (build-system r-build-system)
11594 (home-page "https://github.com/docopt/docopt.R")
11595 (synopsis "Command-line interface specification language")
11597 "This package enables you to define a command-line interface by just
11598 giving it a description in the specific format.")
11599 (license license:expat)))
11601 (define-public r-sparsesvd
11603 (name "r-sparsesvd")
11608 (uri (cran-uri "sparsesvd" version))
11611 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
11612 (build-system r-build-system)
11613 (propagated-inputs `(("r-matrix" ,r-matrix)))
11614 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
11615 (synopsis "Sparse truncated singular value decomposition")
11617 "This package provides a Wrapper around the SVDLIBC library
11618 for (truncated) singular value decomposition of a sparse matrix. Currently,
11619 only sparse real matrices in Matrix package format are supported.")
11620 ;; SVDLIBC is released under BSD-2. The R interface is released under
11622 (license (list license:bsd-3 license:bsd-2))))
11624 (define-public r-speedglm
11626 (name "r-speedglm")
11631 (uri (cran-uri "speedglm" version))
11634 "0f37w4lj8dpcg1sfkd7cv6qpdkanmb97mnd8zih2fxzv8bpd0rfh"))))
11635 (build-system r-build-system)
11637 `(("r-mass" ,r-mass)
11638 ("r-matrix" ,r-matrix)))
11639 (home-page "https://cran.r-project.org/web/packages/speedglm")
11640 (synopsis "Fit linear and generalized linear models to large data sets")
11642 "This package provides tools for fitting linear models and generalized
11643 linear models to large data sets by updating algorithms.")
11644 ;; Any version of the GPL
11645 (license license:gpl2+)))
11647 (define-public r-densityclust
11649 (name "r-densityclust")
11654 (uri (cran-uri "densityClust" version))
11657 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
11658 (properties `((upstream-name . "densityClust")))
11659 (build-system r-build-system)
11662 ("r-ggplot2" ,r-ggplot2)
11663 ("r-ggrepel" ,r-ggrepel)
11664 ("r-gridextra" ,r-gridextra)
11665 ("r-rcolorbrewer" ,r-rcolorbrewer)
11667 ("r-rtsne" ,r-rtsne)))
11668 (home-page "https://cran.r-project.org/web/packages/densityClust")
11669 (synopsis "Clustering by fast search and find of density peaks")
11671 "This package provides an improved implementation (based on k-nearest
11672 neighbors) of the density peak clustering algorithm, originally described by
11673 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
11674 large datasets (> 100,000 samples) very efficiently.")
11675 (license license:gpl2+)))
11677 (define-public r-combinat
11679 (name "r-combinat")
11684 (uri (cran-uri "combinat" version))
11687 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
11688 (build-system r-build-system)
11689 (home-page "https://cran.r-project.org/web/packages/combinat")
11690 (synopsis "Combinatorics utilities")
11691 (description "This package provides assorted routines for combinatorics.")
11692 (license license:gpl2)))
11694 (define-public r-qlcmatrix
11696 (name "r-qlcmatrix")
11701 (uri (cran-uri "qlcMatrix" version))
11704 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
11705 (properties `((upstream-name . "qlcMatrix")))
11706 (build-system r-build-system)
11708 `(("r-docopt" ,r-docopt)
11709 ("r-matrix" ,r-matrix)
11711 ("r-sparsesvd" ,r-sparsesvd)))
11712 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
11713 (synopsis "Sparse matrix functions for quantitative language comparison")
11715 "This package provides an extension of the functionality of the Matrix
11716 package for using sparse matrices. Some of the functions are very general,
11717 while other are highly specific for the special data format used for
11718 @dfn{quantitative language comparison} (QLC).")
11719 (license license:gpl3)))
11721 (define-public r-ddrtree
11728 (uri (cran-uri "DDRTree" version))
11731 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
11732 (properties `((upstream-name . "DDRTree")))
11733 (build-system r-build-system)
11736 ("r-irlba" ,r-irlba)
11738 ("r-rcppeigen" ,r-rcppeigen)))
11739 (home-page "https://cran.r-project.org/web/packages/DDRTree")
11740 (synopsis "Learning principal graphs with DDRTree")
11742 "This package provides an implementation of the framework of
11743 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
11744 dimensional space while constructs a principal tree which passes through the
11745 middle of the data simultaneously. DDRTree shows superiority to
11746 alternatives (Wishbone, DPT) for inferring the ordering as well as the
11747 intrinsic structure of single cell genomics data. In general, it could be
11748 used to reconstruct the temporal progression as well as the bifurcation
11749 structure of any data type.")
11750 (license license:asl2.0)))
11752 (define-public r-corpcor
11759 (uri (cran-uri "corpcor" version))
11762 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
11763 (build-system r-build-system)
11764 (home-page "http://strimmerlab.org/software/corpcor/")
11765 (synopsis "Efficient estimation of covariance and (partial) correlation")
11767 "This package implements a James-Stein-type shrinkage estimator for the
11768 covariance matrix, with separate shrinkage for variances and correlations.
11769 Furthermore, functions are available for fast singular value decomposition,
11770 for computing the pseudoinverse, and for checking the rank and positive
11771 definiteness of a matrix.")
11772 (license license:gpl3+)))
11774 (define-public r-rspectra
11776 (name "r-rspectra")
11781 (uri (cran-uri "RSpectra" version))
11784 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
11785 (properties `((upstream-name . "RSpectra")))
11786 (build-system r-build-system)
11788 `(("r-matrix" ,r-matrix)
11790 ("r-rcppeigen" ,r-rcppeigen)))
11791 (home-page "https://github.com/yixuan/RSpectra")
11792 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
11794 "This package provides an R interface to the Spectra library for
11795 large-scale eigenvalue and SVD problems. It is typically used to compute a
11796 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
11797 which is usually more efficient than @code{eigen()} if k << n.")
11799 (license license:mpl2.0)))
11801 (define-public r-vbsr
11808 (uri (cran-uri "vbsr" version))
11811 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
11812 (build-system r-build-system)
11813 (home-page "https://cran.r-project.org/web/packages/vbsr")
11814 (synopsis "Variational Bayes spike regression regularized linear models")
11816 "This package provides an efficient algorithm for solving ultra-sparse
11817 regularized regression models using a variational Bayes algorithm with a spike
11818 prior. The algorithm is solved on a path, with coordinate updates, and is
11819 capable of generating very sparse models. Very general model
11820 diagnostics for controlling type-1 errors are also provided.")
11821 (license license:gpl2)))
11823 (define-public r-flare
11830 (uri (cran-uri "flare" version))
11833 "0f992dmgnr6s8g3386i9bjfyf08q8srgw7sjz2yx7snj8znq7251"))))
11834 (build-system r-build-system)
11836 `(("r-igraph" ,r-igraph)
11837 ("r-lattice" ,r-lattice)
11839 ("r-matrix" ,r-matrix)))
11840 (home-page "https://cran.r-project.org/web/packages/flare")
11841 (synopsis "Family of Lasso regression implementations")
11843 "This package provides implementations of a family of Lasso variants
11844 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
11845 high dimensional sparse linear models.")
11846 (license license:gpl2)))
11848 (define-public r-lassopv
11855 (uri (cran-uri "lassopv" version))
11858 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
11859 (build-system r-build-system)
11860 (propagated-inputs `(("r-lars" ,r-lars)))
11861 (home-page "https://github.com/lingfeiwang/lassopv")
11862 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
11864 "This package enables you to estimate the p-values for predictors x
11865 against target variable y in Lasso regression, using the regularization
11866 strength when each predictor enters the active set of regularization path for
11867 the first time as the statistic.")
11868 (license license:gpl3)))
11870 (define-public r-splitstackshape
11872 (name "r-splitstackshape")
11877 (uri (cran-uri "splitstackshape" version))
11880 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
11881 (build-system r-build-system)
11883 `(("r-data-table" ,r-data-table)))
11884 (home-page "https://github.com/mrdwab/splitstackshape")
11885 (synopsis "Stack and reshape datasets after splitting concatenated values")
11887 "Online data collection tools like Google Forms often export
11888 multiple-response questions with data concatenated in cells. The
11889 @code{concat.split} (cSplit) family of functions provided by this package
11890 splits such data into separate cells. This package also includes functions to
11891 stack groups of columns and to reshape wide data, even when the data are
11892 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
11893 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
11895 (license license:gpl3)))
11897 (define-public r-tfmpvalue
11899 (name "r-tfmpvalue")
11904 (uri (cran-uri "TFMPvalue" version))
11907 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
11908 (properties `((upstream-name . "TFMPvalue")))
11909 (build-system r-build-system)
11910 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11911 (home-page "https://github.com/ge11232002/TFMPvalue")
11912 (synopsis "P-value computation for position weight matrices")
11914 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
11915 identification from sequence/alignments, we are interested in the significance
11916 of certain match scores. TFMPvalue provides the accurate calculation of a
11917 p-value with a score threshold for position weight matrices, or the score with
11918 a given p-value. It is an interface to code originally made available by
11919 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
11920 Touzet and Varre (2007).")
11921 (license license:gpl2)))
11923 (define-public r-rnifti
11930 (uri (cran-uri "RNifti" version))
11933 "1zr0q79id62csmc30c7gs4hbmavk8n6p50a981sfz51dczhjj5ny"))))
11934 (properties `((upstream-name . "RNifti")))
11935 (build-system r-build-system)
11936 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11937 (home-page "https://github.com/jonclayden/RNifti")
11938 (synopsis "Fast R and C++ access to NIfTI images")
11940 "This package provides very fast read and write access to images stored
11941 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
11942 compiled C and interpreted R code. It also provides a C/C++ API that can be
11943 used by other packages.")
11944 (license license:gpl2)))
11946 (define-public r-shades
11953 (uri (cran-uri "shades" version))
11956 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
11957 (build-system r-build-system)
11958 (home-page "https://github.com/jonclayden/shades")
11959 (synopsis "Simple color manipulation")
11961 "This package provides functions for easily manipulating colors,
11962 creating color scales and calculating color distances.")
11963 (license license:bsd-3)))
11965 (define-public r-ore
11972 (uri (cran-uri "ore" version))
11974 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
11975 (build-system r-build-system)
11976 (home-page "https://github.com/jonclayden/ore")
11977 (synopsis "R interface to the Onigmo regular expression library")
11979 "This package provides an alternative to R's built-in functionality for
11980 handling regular expressions, based on the Onigmo library. It offers
11981 first-class compiled regex objects, partial matching and function-based
11982 substitutions, amongst other features.")
11983 (license license:bsd-3)))
11985 (define-public r-reportr
11992 (uri (cran-uri "reportr" version))
11995 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
11996 (build-system r-build-system)
11997 (propagated-inputs `(("r-ore" ,r-ore)))
11998 (home-page "https://github.com/jonclayden/reportr")
11999 (synopsis "General message and error reporting system")
12001 "This package provides a system for reporting messages, which offers
12002 certain useful features over the standard R system, such as the incorporation
12003 of output consolidation, message filtering, assertions, expression
12004 substitution, automatic generation of stack traces for debugging, and
12005 conditional reporting based on the current \"output level\".")
12006 (license license:gpl2)))
12008 (define-public r-tractor-base
12010 (name "r-tractor-base")
12011 (version "3.3.3.1")
12015 (uri (cran-uri "tractor.base" version))
12018 "0w5jw7pf77npkgig7667yikpbwv4dfk1dcq63qm88l409ga2f95p"))))
12019 (properties `((upstream-name . "tractor.base")))
12020 (build-system r-build-system)
12023 ("r-reportr" ,r-reportr)
12024 ("r-rnifti" ,r-rnifti)
12025 ("r-shades" ,r-shades)))
12026 (home-page "https://www.tractor-mri.org.uk")
12027 (synopsis "Read, manipulate and visualize magnetic resonance images")
12029 "This package provides functions for working with magnetic resonance
12030 images. It supports reading and writing of popular file formats (DICOM,
12031 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
12032 visualization; flexible image manipulation; metadata and sparse image
12034 (license license:gpl2)))
12036 (define-public r-grimport
12038 (name "r-grimport")
12043 (uri (cran-uri "grImport" version))
12046 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
12047 (properties `((upstream-name . "grImport")))
12048 (build-system r-build-system)
12050 `(("ghostscript" ,ghostscript)))
12052 `(("r-xml" ,r-xml)))
12053 (home-page "https://cran.r-project.org/web/packages/grImport")
12054 (synopsis "Convert, import, and draw PostScript pictures")
12056 "This package provides functions for converting, importing, and drawing
12057 PostScript pictures in R plots.")
12058 (license license:gpl2+)))
12060 (define-public r-grimport2
12062 (name "r-grimport2")
12067 (uri (cran-uri "grImport2" version))
12070 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
12071 (properties `((upstream-name . "grImport2")))
12072 (build-system r-build-system)
12074 `(("r-base64enc" ,r-base64enc)
12078 (home-page "https://cran.r-project.org/web/packages/grImport2/")
12079 (synopsis "Import SVG graphics")
12081 "This package provides functions for importing external vector images and
12082 drawing them as part of R plots. This package is different from the
12083 @code{grImport} package because, where that package imports PostScript format
12084 images, this package imports SVG format images. Furthermore, this package
12085 imports a specific subset of SVG, so external images must be preprocessed
12086 using a package like @code{rsvg} to produce SVG that this package can import.
12087 SVG features that are not supported by R graphics, such as gradient fills, can
12088 be imported and then exported via the @code{gridSVG} package.")
12089 (license license:gpl2+)))
12091 (define-public r-kohonen
12098 (uri (cran-uri "kohonen" version))
12101 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
12102 (build-system r-build-system)
12104 `(("r-rcpp" ,r-rcpp)))
12105 (home-page "https://cran.r-project.org/web/packages/kohonen")
12106 (synopsis "Supervised and unsupervised self-organising maps")
12108 "This package provides functions to train @dfn{self-organising
12109 maps} (SOMs). Also interrogation of the maps and prediction using trained
12110 maps are supported. The name of the package refers to Teuvo Kohonen, the
12111 inventor of the SOM.")
12112 (license license:gpl2+)))
12114 (define-public r-nnls
12121 (uri (cran-uri "nnls" version))
12124 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
12125 (build-system r-build-system)
12126 (native-inputs `(("gfortran" ,gfortran)))
12127 (home-page "https://cran.r-project.org/web/packages/nnls")
12128 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
12130 "This package provides an R interface to the Lawson-Hanson implementation
12131 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
12132 the combination of non-negative and non-positive constraints.")
12133 (license license:gpl2+)))
12135 (define-public r-iso
12138 (version "0.0-18.1")
12142 (uri (cran-uri "Iso" version))
12145 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
12146 (properties `((upstream-name . "Iso")))
12147 (build-system r-build-system)
12148 (native-inputs `(("gfortran" ,gfortran)))
12149 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
12150 (synopsis "Functions to perform isotonic regression")
12152 "This package provides support for linear order and unimodal
12153 order (univariate) isotonic regression and bivariate isotonic regression with
12154 linear order on both variables.")
12155 (license license:gpl2+)))
12157 (define-public r-chemometricswithr
12159 (name "r-chemometricswithr")
12164 (uri (cran-uri "ChemometricsWithR" version))
12167 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
12169 `((upstream-name . "ChemometricsWithR")))
12170 (build-system r-build-system)
12172 `(("r-devtools" ,r-devtools)
12173 ("r-kohonen" ,r-kohonen)
12176 (home-page "https://github.com/rwehrens/CWR")
12177 (synopsis "Chemometrics with R")
12179 "This package provides functions and scripts used in the book
12180 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
12181 Life Sciences\" by Ron Wehrens, Springer (2011).")
12182 (license license:gpl2+)))
12184 (define-public r-als
12191 (uri (cran-uri "ALS" version))
12194 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
12195 (properties `((upstream-name . "ALS")))
12196 (build-system r-build-system)
12199 ("r-nnls" ,r-nnls)))
12200 (home-page "https://cran.r-project.org/web/packages/ALS")
12201 (synopsis "Multivariate curve resolution alternating least squares")
12203 "Alternating least squares is often used to resolve components
12204 contributing to data with a bilinear structure; the basic technique may be
12205 extended to alternating constrained least squares. This package provides an
12206 implementation of @dfn{multivariate curve resolution alternating least
12207 squares} (MCR-ALS).
12209 Commonly applied constraints include unimodality, non-negativity, and
12210 normalization of components. Several data matrices may be decomposed
12211 simultaneously by assuming that one of the two matrices in the bilinear
12212 decomposition is shared between datasets.")
12213 (license license:gpl2+)))
12215 (define-public r-strucchange
12217 (name "r-strucchange")
12222 (uri (cran-uri "strucchange" version))
12225 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
12226 (build-system r-build-system)
12228 `(("r-sandwich" ,r-sandwich)
12230 (home-page "https://cran.r-project.org/web/packages/strucchange")
12231 (synopsis "Testing, monitoring, and dating structural changes")
12233 "This package provides tools for testing, monitoring and dating
12234 structural changes in (linear) regression models. It features tests/methods
12235 from the generalized fluctuation test framework as well as from the F
12236 test (Chow test) framework. This includes methods to fit, plot and test
12237 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
12238 statistics, respectively. It is possible to monitor incoming data online
12239 using fluctuation processes. Finally, the breakpoints in regression models
12240 with structural changes can be estimated together with confidence intervals.
12241 Emphasis is always given to methods for visualizing the data.")
12242 ;; Either of these two GPL versions
12243 (license (list license:gpl2 license:gpl3))))
12245 (define-public r-pixmap
12252 (uri (cran-uri "pixmap" version))
12255 "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9"))))
12256 (build-system r-build-system)
12257 (home-page "https://cran.r-project.org/web/packages/pixmap")
12258 (synopsis "Tools for bitmap images")
12260 "This package provides functions for importing, exporting, plotting and
12261 other manipulations of bitmapped images.")
12262 (license license:gpl2)))
12264 (define-public r-rapidjsonr
12266 (name "r-rapidjsonr")
12271 (uri (cran-uri "rapidjsonr" version))
12274 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
12275 (build-system r-build-system)
12276 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
12277 (synopsis "JSON parser")
12279 "This package provides JSON parsing capability through the Rapidjson
12281 (license license:expat)))
12283 (define-public r-ontologyindex
12285 (name "r-ontologyindex")
12290 (uri (cran-uri "ontologyIndex" version))
12293 "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k"))))
12294 (properties `((upstream-name . "ontologyIndex")))
12295 (build-system r-build-system)
12297 `(("r-knitr" ,r-knitr)))
12298 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
12299 (synopsis "Functions for processing ontologies in R")
12301 "This package provides functions for reading ontologies into R as lists
12302 and manipulating sets of ontological terms.")
12303 (license license:gpl2+)))
12305 (define-public r-gargle
12312 (uri (cran-uri "gargle" version))
12315 "1fykmiv3x8c9ai31r9wr7qcca51h6kqn9cgwbxvxfj15fhwskh4n"))))
12316 (build-system r-build-system)
12321 ("r-jsonlite" ,r-jsonlite)
12322 ("r-rlang" ,r-rlang)
12323 ("r-withr" ,r-withr)))
12325 `(("r-knitr" ,r-knitr)))
12326 (home-page "https://gargle.r-lib.org")
12327 (synopsis "Utilities for working with Google APIs")
12329 "This package provides utilities for working with Google APIs. This
12330 includes functions and classes for handling common credential types and for
12331 preparing, executing, and processing HTTP requests.")
12332 (license license:expat)))
12334 (define-public r-bigrquery
12336 (name "r-bigrquery")
12341 (uri (cran-uri "bigrquery" version))
12344 "16whccv7f94vf57dvbbrhdskz3nnbmpa11a14kp7aynckldlfy0v"))))
12345 (build-system r-build-system)
12347 `(("r-assertthat" ,r-assertthat)
12348 ("r-bit64" ,r-bit64)
12351 ("r-gargle" ,r-gargle)
12354 ("r-jsonlite" ,r-jsonlite)
12355 ("r-prettyunits" ,r-prettyunits)
12356 ("r-progress" ,r-progress)
12357 ("r-rapidjsonr" ,r-rapidjsonr)
12359 ("r-rlang" ,r-rlang)
12360 ("r-tibble" ,r-tibble)))
12361 (home-page "https://github.com/rstats-db/bigrquery")
12362 (synopsis "R interface to Google's BigQuery API")
12364 "This package provides an R interface to Google's BigQuery database.")
12365 (license license:gpl3)))
12367 (define-public r-gmp
12374 (uri (cran-uri "gmp" version))
12377 "03kzbflgpy5sgnzxmhshs5qv7jjmfc113ybkhxys4z8y7xdv9z3b"))))
12378 (build-system r-build-system)
12381 (modify-phases %standard-phases
12382 (add-after 'unpack 'set-CC
12383 (lambda _ (setenv "CC" "gcc") #t)))))
12384 (inputs `(("gmp" ,gmp)))
12385 (home-page "https://cran.r-project.org/web/packages/gmp")
12386 (synopsis "Multiple precision arithmetic")
12388 "This package supports multiple precision arithmetic (big integers and
12389 rationals, prime number tests, matrix computation), \"arithmetic without
12390 limitations\" using the GNU Multiple Precision library.")
12391 ;; Any version of the GPL.
12392 (license license:gpl3+)))
12394 (define-public r-rmpfr
12401 (uri (cran-uri "Rmpfr" version))
12404 "007pc7fpzl2mcg3qxa2vfjip6m2dr314qjsnybkj3kdj70bszxkl"))))
12405 (properties `((upstream-name . "Rmpfr")))
12406 (build-system r-build-system)
12411 `(("r-gmp" ,r-gmp)))
12413 `(("pkg-config" ,pkg-config)))
12414 (home-page "http://rmpfr.r-forge.r-project.org/")
12415 (synopsis "R bindings to the MPFR library")
12417 "This package supports arithmetic (via S4 classes and methods) for
12418 arbitrary precision floating point numbers, including transcendental
12419 functions. To this end, the package interfaces with the @dfn{Multiple
12420 Precision Floating-Point Reliable} (MPFR) library.")
12421 (license license:gpl2+)))
12423 (define-public r-assertive-base
12425 (name "r-assertive-base")
12430 (uri (cran-uri "assertive.base" version))
12433 "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b"))))
12435 `((upstream-name . "assertive.base")))
12436 (build-system r-build-system)
12437 (home-page "https://bitbucket.org/richierocks/assertive.base")
12438 (synopsis "Core of the assertive package")
12440 "This package provides a minimal set of predicates and assertions used by
12441 the assertive package. This is mainly for use by other package developers who
12442 want to include run-time testing features in their own packages.")
12443 (license license:gpl3+)))
12445 (define-public r-assertive-properties
12447 (name "r-assertive-properties")
12452 (uri (cran-uri "assertive.properties" version))
12455 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
12457 `((upstream-name . "assertive.properties")))
12458 (build-system r-build-system)
12460 `(("r-assertive-base" ,r-assertive-base)))
12461 (home-page "https://bitbucket.org/richierocks/assertive.properties")
12462 (synopsis "Assertions to check properties of variables")
12464 "This package provides a set of predicates and assertions for checking
12465 the properties of variables, such as length, names and attributes. This is
12466 mainly for use by other package developers who want to include run-time
12467 testing features in their own packages.")
12468 (license license:gpl3+)))
12470 (define-public r-assertive-numbers
12472 (name "r-assertive-numbers")
12477 (uri (cran-uri "assertive.numbers" version))
12480 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
12482 `((upstream-name . "assertive.numbers")))
12483 (build-system r-build-system)
12485 `(("r-assertive-base" ,r-assertive-base)))
12486 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
12487 (synopsis "Assertions to check properties of numbers")
12489 "This package provides a set of predicates and assertions for checking
12490 the properties of numbers. This is mainly for use by other package developers
12491 who want to include run-time testing features in their own packages.")
12492 (license license:gpl3+)))
12494 (define-public r-assertive-sets
12496 (name "r-assertive-sets")
12501 (uri (cran-uri "assertive.sets" version))
12504 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
12506 `((upstream-name . "assertive.sets")))
12507 (build-system r-build-system)
12509 `(("r-assertive-base" ,r-assertive-base)))
12510 (home-page "https://bitbucket.org/richierocks/assertive.sets")
12511 (synopsis "Assertions to check properties of sets")
12513 "This package provides a set of predicates and assertions for checking
12514 the properties of sets. This is mainly for use by other package developers
12515 who want to include run-time testing features in their own packages.")
12516 (license license:gpl3+)))
12518 (define-public r-assertive-matrices
12520 (name "r-assertive-matrices")
12525 (uri (cran-uri "assertive.matrices" version))
12528 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
12530 `((upstream-name . "assertive.matrices")))
12531 (build-system r-build-system)
12533 `(("r-assertive-base" ,r-assertive-base)))
12534 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
12535 (synopsis "Assertions to check properties of matrices")
12537 "This package provides a set of predicates and assertions for checking
12538 the properties of matrices. This is mainly for use by other package
12539 developers who want to include run-time testing features in their own
12541 (license license:gpl3+)))
12543 (define-public r-assertive-models
12545 (name "r-assertive-models")
12550 (uri (cran-uri "assertive.models" version))
12553 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
12555 `((upstream-name . "assertive.models")))
12556 (build-system r-build-system)
12558 `(("r-assertive-base" ,r-assertive-base)))
12559 (home-page "https://bitbucket.org/richierocks/assertive.models")
12560 (synopsis "Assertions to check properties of models")
12562 "This package provides a set of predicates and assertions for checking
12563 the properties of models. This is mainly for use by other package developers
12564 who want to include run-time testing features in their own packages.")
12565 (license license:gpl3+)))
12567 (define-public r-assertive-reflection
12569 (name "r-assertive-reflection")
12574 (uri (cran-uri "assertive.reflection" version))
12577 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
12579 `((upstream-name . "assertive.reflection")))
12580 (build-system r-build-system)
12582 `(("r-assertive-base" ,r-assertive-base)))
12583 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
12584 (synopsis "Assertions for checking the state of R")
12586 "This package provides a set of predicates and assertions for checking
12587 the state and capabilities of R, the operating system it is running on, and
12588 the IDE being used. This is mainly for use by other package developers who
12589 want to include run-time testing features in their own packages.")
12590 (license license:gpl3+)))
12592 (define-public r-assertive-types
12594 (name "r-assertive-types")
12599 (uri (cran-uri "assertive.types" version))
12602 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
12604 `((upstream-name . "assertive.types")))
12605 (build-system r-build-system)
12607 `(("r-assertive-base" ,r-assertive-base)
12608 ("r-assertive-properties" ,r-assertive-properties)
12609 ("r-codetools" ,r-codetools)))
12610 (home-page "https://bitbucket.org/richierocks/assertive.types")
12611 (synopsis "Assertions to check types of variables")
12613 "This package provides a set of predicates and assertions for checking
12614 the types of variables. This is mainly for use by other package developers
12615 who want to include run-time testing features in their own packages.")
12616 (license license:gpl3+)))
12618 (define-public r-assertive-files
12620 (name "r-assertive-files")
12625 (uri (cran-uri "assertive.files" version))
12628 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
12630 `((upstream-name . "assertive.files")))
12631 (build-system r-build-system)
12633 `(("r-assertive-base" ,r-assertive-base)
12634 ("r-assertive-numbers" ,r-assertive-numbers)))
12635 (home-page "https://bitbucket.org/richierocks/assertive.files")
12636 (synopsis "Assertions to check properties of files")
12638 "This package provides a set of predicates and assertions for checking
12639 the properties of files and connections. This is mainly for use by other
12640 package developers who want to include run-time testing features in their own
12642 (license license:gpl3+)))
12644 (define-public r-assertive-code
12646 (name "r-assertive-code")
12651 (uri (cran-uri "assertive.code" version))
12654 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
12656 `((upstream-name . "assertive.code")))
12657 (build-system r-build-system)
12659 `(("r-assertive-base" ,r-assertive-base)
12660 ("r-assertive-properties" ,r-assertive-properties)
12661 ("r-assertive-types" ,r-assertive-types)))
12662 (home-page "https://bitbucket.org/richierocks/assertive.code")
12663 (synopsis "Assertions to check properties of code")
12665 "This package provides a set of predicates and assertions for checking
12666 the properties of code. This is mainly for use by other package developers
12667 who want to include run-time testing features in their own packages.")
12668 (license license:gpl3+)))
12670 (define-public r-assertive-datetimes
12672 (name "r-assertive-datetimes")
12677 (uri (cran-uri "assertive.datetimes" version))
12680 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
12682 `((upstream-name . "assertive.datetimes")))
12683 (build-system r-build-system)
12685 `(("r-assertive-base" ,r-assertive-base)
12686 ("r-assertive-types" ,r-assertive-types)))
12687 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
12688 (synopsis "Assertions to check properties of dates and times")
12690 "This package provides a set of predicates and assertions for checking
12691 the properties of dates and times. This is mainly for use by other package
12692 developers who want to include run-time testing features in their own
12694 (license license:gpl3+)))
12696 (define-public r-assertive-strings
12698 (name "r-assertive-strings")
12703 (uri (cran-uri "assertive.strings" version))
12706 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
12708 `((upstream-name . "assertive.strings")))
12709 (build-system r-build-system)
12711 `(("r-assertive-base" ,r-assertive-base)
12712 ("r-assertive-types" ,r-assertive-types)
12713 ("r-stringi" ,r-stringi)))
12714 (home-page "https://bitbucket.org/richierocks/assertive.strings")
12715 (synopsis "Assertions to check properties of strings")
12717 "This package provides a set of predicates and assertions for checking
12718 the properties of strings. This is mainly for use by other package developers
12719 who want to include run-time testing features in their own packages.")
12720 (license license:gpl3+)))
12722 (define-public r-assertive-data-us
12724 (name "r-assertive-data-us")
12729 (uri (cran-uri "assertive.data.us" version))
12732 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
12734 `((upstream-name . "assertive.data.us")))
12735 (build-system r-build-system)
12737 `(("r-assertive-base" ,r-assertive-base)
12738 ("r-assertive-strings" ,r-assertive-strings)))
12739 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
12740 (synopsis "Assertions to check properties of strings")
12742 "This package provides a set of predicates and assertions for checking
12743 the properties of US-specific complex data types. This is mainly for use by
12744 other package developers who want to include run-time testing features in
12745 their own packages.")
12746 (license license:gpl3+)))
12748 (define-public r-assertive-data-uk
12750 (name "r-assertive-data-uk")
12755 (uri (cran-uri "assertive.data.uk" version))
12758 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
12760 `((upstream-name . "assertive.data.uk")))
12761 (build-system r-build-system)
12763 `(("r-assertive-base" ,r-assertive-base)
12764 ("r-assertive-strings" ,r-assertive-strings)))
12765 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
12766 (synopsis "Assertions to check properties of strings")
12768 "This package provides a set of predicates and assertions for checking
12769 the properties of UK-specific complex data types. This is mainly for use by
12770 other package developers who want to include run-time testing features in
12771 their own packages.")
12772 (license license:gpl3+)))
12774 (define-public r-assertive-data
12776 (name "r-assertive-data")
12781 (uri (cran-uri "assertive.data" version))
12784 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
12786 `((upstream-name . "assertive.data")))
12787 (build-system r-build-system)
12789 `(("r-assertive-base" ,r-assertive-base)
12790 ("r-assertive-strings" ,r-assertive-strings)))
12791 (home-page "https://bitbucket.org/richierocks/assertive.data")
12792 (synopsis "Assertions to check properties of data")
12794 "This package provides a set of predicates and assertions for checking
12795 the properties of (country independent) complex data types. This is mainly
12796 for use by other package developers who want to include run-time testing
12797 features in their own packages.")
12798 (license license:gpl3+)))
12800 (define-public r-assertive
12802 (name "r-assertive")
12807 (uri (cran-uri "assertive" version))
12810 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
12811 (build-system r-build-system)
12813 `(("r-assertive-base" ,r-assertive-base)
12814 ("r-assertive-code" ,r-assertive-code)
12815 ("r-assertive-data" ,r-assertive-data)
12816 ("r-assertive-data-uk" ,r-assertive-data-uk)
12817 ("r-assertive-data-us" ,r-assertive-data-us)
12818 ("r-assertive-datetimes" ,r-assertive-datetimes)
12819 ("r-assertive-files" ,r-assertive-files)
12820 ("r-assertive-matrices" ,r-assertive-matrices)
12821 ("r-assertive-models" ,r-assertive-models)
12822 ("r-assertive-numbers" ,r-assertive-numbers)
12823 ("r-assertive-properties" ,r-assertive-properties)
12824 ("r-assertive-reflection" ,r-assertive-reflection)
12825 ("r-assertive-sets" ,r-assertive-sets)
12826 ("r-assertive-strings" ,r-assertive-strings)
12827 ("r-assertive-types" ,r-assertive-types)
12828 ("r-knitr" ,r-knitr)))
12830 `(("r-knitr" ,r-knitr)))
12831 (home-page "https://bitbucket.org/richierocks/assertive")
12832 (synopsis "Readable check functions to ensure code integrity")
12834 "This package provides lots of predicates (@code{is_*} functions) to
12835 check the state of your variables, and assertions (@code{assert_*} functions)
12836 to throw errors if they aren't in the right form.")
12837 (license license:gpl3+)))
12839 (define-public r-dotcall64
12841 (name "r-dotcall64")
12846 (uri (cran-uri "dotCall64" version))
12849 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
12850 (properties `((upstream-name . "dotCall64")))
12851 (build-system r-build-system)
12852 (native-inputs `(("gfortran" ,gfortran)))
12853 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
12854 (synopsis "Enhanced foreign function interface supporting long vectors")
12856 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
12857 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
12858 supports long vectors, arguments of type 64-bit integer, and provides a
12859 mechanism to avoid unnecessary copies of read-only and write-only arguments.
12860 This makes it a convenient and fast interface to C/C++ and Fortran code.")
12861 (license license:gpl2+)))
12863 (define-public r-spam
12870 (uri (cran-uri "spam" version))
12872 (base32 "0p5ycvpry955ldrgbbq3syy91wx9425mddpn8r5m9xwlirjxv3v3"))))
12873 (build-system r-build-system)
12875 `(("r-dotcall64" ,r-dotcall64)))
12877 `(("gfortran" ,gfortran)
12878 ("r-knitr" ,r-knitr)))
12879 (home-page "https://www.math.uzh.ch/pages/spam/")
12880 (synopsis "Sparse matrix algebra")
12882 "This package provides a set of functions for sparse matrix algebra.
12883 Differences with other sparse matrix packages are:
12886 @item it only supports (essentially) one sparse matrix format;
12887 @item it is based on transparent and simple structure(s);
12888 @item it is tailored for MCMC calculations within G(M)RF;
12889 @item and it is fast and scalable (with the extension package @code{spam64}).
12891 ;; Either of these licenses
12892 (license (list license:bsd-3 license:lgpl2.0))))
12894 (define-public r-fields
12901 (uri (cran-uri "fields" version))
12903 (base32 "1nsrgkw9w3mwd3sajyzc06h49gg1s0bkq6xh5b66h1n4jbcx2046"))))
12904 (build-system r-build-system)
12906 `(("r-maps" ,r-maps)
12907 ("r-spam" ,r-spam)))
12909 `(("gfortran" ,gfortran)))
12910 (home-page "https://www.image.ucar.edu/fields")
12911 (synopsis "Tools for spatial data")
12913 "This is a package for curve, surface and function fitting with an
12914 emphasis on splines, spatial data and spatial statistics. The major methods
12915 include cubic, and thin plate splines, Kriging, and compactly supported
12916 covariance functions for large data sets.")
12917 (license license:gpl2+)))
12919 (define-public r-spatialextremes
12921 (name "r-spatialextremes")
12926 (uri (cran-uri "SpatialExtremes" version))
12929 "1mhn1c8n3bmgf0fjyac3wji4790zswzkqliqcv3n8kv9806crb0y"))))
12931 `((upstream-name . "SpatialExtremes")))
12932 (build-system r-build-system)
12934 `(("r-fields" ,r-fields)
12935 ("r-maps" ,r-maps)))
12936 (home-page "http://spatialextremes.r-forge.r-project.org/")
12937 (synopsis "Modelling spatial extremes")
12939 "This package provides tools for the statistical modelling of spatial
12940 extremes using max-stable processes, copula or Bayesian hierarchical models.
12941 More precisely, this package allows (conditional) simulations from various
12942 parametric max-stable models, analysis of the extremal spatial dependence, the
12943 fitting of such processes using composite likelihoods or least square (simple
12944 max-stable processes only), model checking and selection and prediction.")
12945 (license license:gpl2+)))
12947 (define-public r-drc
12954 (uri (cran-uri "drc" version))
12957 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
12958 (build-system r-build-system)
12961 ("r-gtools" ,r-gtools)
12963 ("r-multcomp" ,r-multcomp)
12964 ("r-plotrix" ,r-plotrix)
12965 ("r-scales" ,r-scales)))
12966 (home-page "https://cran.r-project.org/web/packages/drc")
12967 (synopsis "Analysis of dose-response curves")
12969 "This package provides a suite of flexible and versatile model fitting
12970 and after-fitting functions for the analysis of dose-response data.")
12971 (license license:gpl2+)))
12973 (define-public r-rmeta
12980 (uri (cran-uri "rmeta" version))
12983 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
12984 (build-system r-build-system)
12985 (home-page "https://cran.r-project.org/web/packages/rmeta")
12986 (synopsis "Tools for meta-analysis")
12988 "This package provides functions for simple fixed and random effects
12989 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
12990 draws standard summary plots, funnel plots, and computes summaries and tests
12991 for association and heterogeneity.")
12992 (license license:gpl2)))
12994 (define-public r-bootstrap
12996 (name "r-bootstrap")
13001 (uri (cran-uri "bootstrap" version))
13004 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
13005 (build-system r-build-system)
13006 (native-inputs `(("gfortran" ,gfortran)))
13007 (home-page "https://cran.r-project.org/web/packages/bootstrap")
13008 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
13010 "This package provides software and data for the book \"An Introduction
13011 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
13012 This package is primarily provided for projects already based on it, and for
13013 support of the book. New projects should preferentially use the recommended
13014 package \"boot\".")
13015 (license license:bsd-3)))
13017 (define-public r-survivalroc
13019 (name "r-survivalroc")
13024 (uri (cran-uri "survivalROC" version))
13027 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
13028 (properties `((upstream-name . "survivalROC")))
13029 (build-system r-build-system)
13030 (home-page "https://cran.r-project.org/web/packages/survivalROC")
13031 (synopsis "Time-dependent ROC curve estimation from censored survival data")
13033 "Compute time-dependent ROC curve from censored survival data using
13034 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
13035 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
13036 (license license:gpl2+)))
13038 (define-public r-longitudinal
13040 (name "r-longitudinal")
13045 (uri (cran-uri "longitudinal" version))
13048 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
13049 (build-system r-build-system)
13050 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
13051 (home-page "http://strimmerlab.org/software/longitudinal/")
13052 (synopsis "Analysis of multiple time course data")
13054 "This package contains general data structures and functions for
13055 longitudinal data with multiple variables, repeated measurements, and
13056 irregularly spaced time points. It also implements a shrinkage estimator of
13057 dynamical correlation and dynamical covariance.")
13058 (license license:gpl3+)))
13060 (define-public r-genenet
13067 (uri (cran-uri "GeneNet" version))
13070 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
13071 (properties `((upstream-name . "GeneNet")))
13072 (build-system r-build-system)
13074 `(("r-corpcor" ,r-corpcor)
13075 ("r-fdrtool" ,r-fdrtool)
13076 ("r-longitudinal" ,r-longitudinal)))
13077 (home-page "http://strimmerlab.org/software/genenet/")
13078 (synopsis "Modeling and inferring gene networks")
13080 "This package analyzes gene expression (time series) data with focus on
13081 the inference of gene networks. In particular, GeneNet implements the methods
13082 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
13083 for learning large-scale gene association networks (including assignment of
13084 putative directions).")
13085 (license license:gpl3+)))
13087 (define-public r-rbamtools
13089 (name "r-rbamtools")
13090 (version "2.16.17")
13094 (uri (cran-uri "rbamtools" version))
13097 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
13098 (build-system r-build-system)
13099 (inputs `(("zlib" ,zlib)))
13101 `(("r-refgenome" ,r-refgenome)))
13102 (home-page "https://cran.r-project.org/web/packages/rbamtools")
13103 (synopsis "Read and write BAM (binary alignment) files")
13105 "This package provides an R interface to functions of the SAMtools
13107 (license license:artistic2.0)))
13109 (define-public r-protviz
13116 (uri (cran-uri "protViz" version))
13119 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
13120 (properties `((upstream-name . "protViz")))
13121 (build-system r-build-system)
13122 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
13123 (home-page "https://github.com/protViz/protViz/")
13124 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
13126 "This package helps with quality checks, visualizations and analysis of
13127 mass spectrometry data, coming from proteomics experiments. The package is
13128 developed, tested and used at the Functional Genomics Center Zurich, where it
13129 is used mainly for prototyping, teaching, and having fun with proteomics data.
13130 But it can also be used to do data analysis for small scale data sets.")
13131 (license license:gpl3)))
13133 (define-public r-cmprsk
13140 (uri (cran-uri "cmprsk" version))
13142 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
13143 (build-system r-build-system)
13145 `(("r-survival" ,r-survival)))
13147 `(("gfortran" ,gfortran)))
13148 (home-page "https://cran.r-project.org/web/packages/cmprsk")
13149 (synopsis "Subdistribution analysis of competing risks")
13151 "This package provides tool for estimation, testing and regression
13152 modeling of subdistribution functions in competing risks, as described in
13153 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
13154 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
13155 A proportional hazards model for the subdistribution of a competing risk,
13156 JASA, 94:496-509.")
13157 (license license:gpl2+)))
13159 (define-public r-etm
13166 (uri (cran-uri "etm" version))
13169 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
13170 (build-system r-build-system)
13172 `(("r-data-table" ,r-data-table)
13173 ("r-lattice" ,r-lattice)
13175 ("r-rcpparmadillo" ,r-rcpparmadillo)
13176 ("r-survival" ,r-survival)))
13177 (home-page "https://cran.r-project.org/web/packages/etm")
13178 (synopsis "Empirical transition matrix")
13180 "The @dfn{empirical transition matrix} (etm) package estimates
13181 the matrix of transition probabilities for any time-inhomogeneous multistate
13182 model with finite state space using the Aalen-Johansen estimator.")
13183 (license license:expat)))
13185 (define-public r-epi
13192 (uri (cran-uri "Epi" version))
13195 "0wsjvilcivrhy2kh2dcagkzy7bjmfa0sq9xjpv6qb4b0nc0mv089"))))
13196 (properties `((upstream-name . "Epi")))
13197 (build-system r-build-system)
13199 `(("r-cmprsk" ,r-cmprsk)
13200 ("r-data-table" ,r-data-table)
13201 ("r-dplyr" ,r-dplyr)
13204 ("r-matrix" ,r-matrix)
13206 ("r-numderiv" ,r-numderiv)
13208 ("r-purrr" ,r-purrr)
13209 ("r-survival" ,r-survival)
13211 (home-page "https://BendixCarstensen.com/Epi/")
13212 (synopsis "Statistical analysis in epidemiology")
13214 "This package provides functions for demographic and epidemiological
13215 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
13216 particular representation, manipulation and simulation of multistate data -
13217 the Lexis suite of functions, which includes interfaces to the @code{mstate},
13218 @code{etm} and @code{cmprsk} packages. It also contains functions for
13219 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
13220 data and some useful functions for tabulation and plotting, as well as a
13221 number of epidemiological data sets.")
13222 (license license:gpl2)))
13224 (define-public r-ppls
13227 (version "1.6-1.1")
13231 (uri (cran-uri "ppls" version))
13234 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
13235 (build-system r-build-system)
13236 (propagated-inputs `(("r-mass" ,r-mass)))
13237 (home-page "https://cran.r-project.org/web/packages/ppls")
13238 (synopsis "Penalized partial least squares")
13240 "This package contains linear and nonlinear regression methods based on
13241 partial least squares and penalization techniques. Model parameters are
13242 selected via cross-validation, and confidence intervals ans tests for the
13243 regression coefficients can be conducted via jackknifing.")
13244 (license license:gpl2+)))
13246 (define-public r-huge
13249 (version "1.3.4.1")
13253 (uri (cran-uri "huge" version))
13255 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
13256 (build-system r-build-system)
13258 `(("r-igraph" ,r-igraph)
13260 ("r-matrix" ,r-matrix)
13262 ("r-rcppeigen" ,r-rcppeigen)))
13263 (home-page "https://cran.r-project.org/web/packages/huge")
13264 (synopsis "High-dimensional undirected graph estimation")
13266 "This package provides a general framework for high-dimensional
13267 undirected graph estimation. It integrates data preprocessing, neighborhood
13268 screening, graph estimation, and model selection techniques into a pipeline.")
13269 (license license:gpl2)))
13271 (define-public r-parcor
13278 (uri (cran-uri "parcor" version))
13281 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
13282 (build-system r-build-system)
13285 ("r-genenet" ,r-genenet)
13286 ("r-glmnet" ,r-glmnet)
13288 ("r-ppls" ,r-ppls)))
13289 (home-page "https://cran.r-project.org/web/packages/parcor")
13290 (synopsis "Regularized estimation of partial correlation matrices")
13292 "This package estimates the matrix of partial correlations based on
13293 different regularized regression methods: lasso, adaptive lasso, PLS, and
13294 Ridge Regression. In addition, the package provides model selection for
13295 lasso, adaptive lasso and Ridge regression based on cross-validation.")
13296 (license license:gpl2+)))
13298 (define-public r-mcmc
13305 (uri (cran-uri "mcmc" version))
13308 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
13309 (build-system r-build-system)
13310 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
13311 (synopsis "Markov chain Monte Carlo")
13313 "This package simulates continuous distributions of random vectors using
13314 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
13315 function that evaluates the log unnormalized density. Algorithms are random
13316 walk Metropolis algorithm (function @code{metrop}), simulated
13317 tempering (function @code{temper}), and morphometric random walk
13318 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
13319 by change of variable.")
13320 (license license:expat)))
13322 (define-public r-listenv
13329 (uri (cran-uri "listenv" version))
13332 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
13333 (build-system r-build-system)
13335 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13336 (home-page "https://github.com/HenrikBengtsson/listenv")
13337 (synopsis "Environments behaving (almost) as lists")
13339 "This package implements list environments. List environments are
13340 environments that have list-like properties. For instance, the elements of a
13341 list environment are ordered and can be accessed and iterated over using index
13343 (license license:lgpl2.1+)))
13345 (define-public r-globals
13352 (uri (cran-uri "globals" version))
13355 "1wrjiiif6rpc268zz79pvpw33si6n6ffgxdnxmmcracwhb5vqg90"))))
13356 (build-system r-build-system)
13358 `(("r-codetools" ,r-codetools)))
13359 (home-page "https://github.com/HenrikBengtsson/globals")
13360 (synopsis "Identify global objects in R expressions")
13362 "This package provides tools to identify global (\"unknown\" or \"free\")
13363 objects in R expressions by code inspection using various strategies, e.g.
13364 conservative or liberal. The objective of this package is to make it as
13365 simple as possible to identify global objects for the purpose of exporting
13366 them in distributed compute environments.")
13367 (license license:lgpl2.1+)))
13369 (define-public r-parallelly
13371 (name "r-parallelly")
13376 (uri (cran-uri "parallelly" version))
13379 "025whcz55wj9jd73dalkbxh4l2331mqn758glr6hlf472lwf4v1p"))))
13380 (properties `((upstream-name . "parallelly")))
13381 (build-system r-build-system)
13382 (home-page "https://github.com/HenrikBengtsson/parallelly")
13383 (synopsis "Enhancements of the parallel package")
13385 "This package provides utility functions that enhance the @code{parallel}
13386 package and support the built-in parallel backends of the @code{future}
13387 package. For example, @code{availableCores} gives the number of CPU cores
13388 available to your R process as given by R options and environment variables,
13389 including those set by job schedulers on high-performance compute clusters.
13390 If none is set, it will fall back to @code{parallel::detectCores}. Another
13391 example is @code{makeClusterPSOCK}, which is backward compatible with
13392 @code{parallel::makePSOCKcluster} while doing a better job in setting up
13393 remote cluster workers without the need for configuring the firewall to do
13394 port-forwarding to your local computer.")
13395 (license license:lgpl2.1+)))
13397 (define-public r-future
13404 (uri (cran-uri "future" version))
13407 "0bfiy17n5rghxw0702k0vgpjkk13268lniifdlx59flf0q16d7lh"))))
13408 (build-system r-build-system)
13410 `(("r-digest" ,r-digest)
13411 ("r-globals" ,r-globals)
13412 ("r-listenv" ,r-listenv)
13413 ("r-parallelly" ,r-parallelly)))
13415 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13416 (home-page "https://github.com/HenrikBengtsson/future")
13417 (synopsis "Unified parallel and distributed processing in R")
13419 "The purpose of this package is to provide a lightweight and unified
13420 Future API for sequential and parallel processing of R expression via futures.
13421 This package implements sequential, multicore, multisession, and cluster
13422 futures. With these, R expressions can be evaluated on the local machine, in
13423 parallel a set of local machines, or distributed on a mix of local and remote
13424 machines. Extensions to this package implement additional backends for
13425 processing futures via compute cluster schedulers etc. Because of its unified
13426 API, there is no need to modify any code in order to switch from sequential on
13427 the local machine to, say, distributed processing on a remote compute cluster.")
13428 (license license:lgpl2.1+)))
13430 (define-public r-future-apply
13432 (name "r-future-apply")
13437 (uri (cran-uri "future.apply" version))
13440 "1ns5cf80vyabvyz9qp6kpvkg4jycinn7x6v7x6692fgjapdnmyig"))))
13441 (properties `((upstream-name . "future.apply")))
13442 (build-system r-build-system)
13444 `(("r-future" ,r-future)
13445 ("r-globals" ,r-globals)))
13447 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13448 (home-page "https://github.com/HenrikBengtsson/future.apply")
13449 (synopsis "Apply function to elements in parallel using futures")
13451 "This package provides implementations of @code{apply()},
13452 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
13453 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
13454 can be resolved using any future-supported backend, e.g. parallel on the local
13455 machine or distributed on a compute cluster.")
13456 (license license:gpl2+)))
13458 (define-public r-rsvd
13465 (uri (cran-uri "rsvd" version))
13468 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
13469 (build-system r-build-system)
13471 `(("r-matrix" ,r-matrix)))
13472 (home-page "https://github.com/erichson/rSVD")
13473 (synopsis "Randomized singular value decomposition")
13475 "Low-rank matrix decompositions are fundamental tools and widely used for
13476 data analysis, dimension reduction, and data compression. Classically, highly
13477 accurate deterministic matrix algorithms are used for this task. However, the
13478 emergence of large-scale data has severely challenged our computational
13479 ability to analyze big data. The concept of randomness has been demonstrated
13480 as an effective strategy to quickly produce approximate answers to familiar
13481 problems such as the @dfn{singular value decomposition} (SVD). This package
13482 provides several randomized matrix algorithms such as the randomized singular
13483 value decomposition (@code{rsvd}), randomized principal component
13484 analysis (@code{rpca}), randomized robust principal component
13485 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
13486 and the randomized CUR decomposition (@code{rcur}). In addition several plot
13487 functions are provided.")
13488 (license license:gpl3+)))
13490 (define-public r-sloop
13497 (uri (cran-uri "sloop" version))
13500 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
13501 (build-system r-build-system)
13503 `(("r-codetools" ,r-codetools)
13504 ("r-crayon" ,r-crayon)
13505 ("r-purrr" ,r-purrr)
13506 ("r-rlang" ,r-rlang)
13507 ("r-tibble" ,r-tibble)))
13508 (home-page "https://github.com/r-lib/sloop")
13509 (synopsis "Helpers for object-oriented programming in R")
13511 "This package provides a collection of helper functions designed to
13512 help you to better understand object oriented programming in R, particularly
13514 (license license:gpl3)))
13516 (define-public r-capushe
13523 (uri (cran-uri "capushe" version))
13526 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
13527 (build-system r-build-system)
13528 (propagated-inputs `(("r-mass" ,r-mass)))
13529 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
13530 (synopsis "Calibrating penalties using slope heuristics")
13532 "This package provides tools for the calibration of penalized criteria
13533 for model selection. The calibration methods available are based on the slope
13535 (license license:gpl2+)))
13537 (define-public r-dorng
13544 (uri (cran-uri "doRNG" version))
13547 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
13548 (properties `((upstream-name . "doRNG")))
13549 (build-system r-build-system)
13551 `(("r-foreach" ,r-foreach)
13552 ("r-iterators" ,r-iterators)
13553 ("r-rngtools" ,r-rngtools)))
13554 (home-page "https://renozao.github.io/doRNG/")
13555 (synopsis "Generic reproducible parallel backend for foreach loops")
13557 "This package provides functions to perform reproducible parallel
13558 @code{foreach} loops, using independent random streams as generated by
13559 L'Ecuyer's combined multiple-recursive generator. It enables to easily
13560 convert standard @code{%dopar%} loops into fully reproducible loops,
13561 independently of the number of workers, the task scheduling strategy, or the
13562 chosen parallel environment and associated foreach backend.")
13563 (license license:gpl2+)))
13565 (define-public r-blockmodeling
13567 (name "r-blockmodeling")
13572 (uri (cran-uri "blockmodeling" version))
13575 "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i"))))
13576 (build-system r-build-system)
13578 `(("r-matrix" ,r-matrix)))
13579 (native-inputs `(("gfortran" ,gfortran)))
13580 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
13581 (synopsis "Generalized and classical blockmodeling of valued networks")
13583 "This package is primarily meant as an implementation of generalized
13584 blockmodeling for valued networks. In addition, measures of similarity or
13585 dissimilarity based on structural equivalence and regular equivalence (REGE
13586 algorithms) can be computed and partitioned matrices can be plotted.")
13587 (license license:gpl2+)))
13589 (define-public r-upsetr
13596 (uri (cran-uri "UpSetR" version))
13599 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
13600 (properties `((upstream-name . "UpSetR")))
13601 (build-system r-build-system)
13603 `(("r-ggplot2" ,r-ggplot2)
13604 ("r-gridextra" ,r-gridextra)
13606 ("r-scales" ,r-scales)))
13607 (home-page "https://github.com/hms-dbmi/UpSetR")
13608 (synopsis "Visualize intersecting sets")
13610 "This package provides a more scalable alternative to Venn and Euler
13611 diagrams for visualizing intersecting sets. Create visualizations of
13612 intersecting sets using a novel matrix design, along with visualizations of
13613 several common set, element and attribute related tasks.")
13614 (license license:expat)))
13616 ;; This package includes a JavaScript file, which is not minified. When
13617 ;; upgrading please check that there are no new minified JavaScript files.
13618 (define-public r-shinybs
13625 (uri (cran-uri "shinyBS" version))
13628 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
13629 (properties `((upstream-name . "shinyBS")))
13630 (build-system r-build-system)
13631 ;; The tests spawn Shiny browser apps. They cannot be run
13632 ;; non-interactively.
13633 (arguments '(#:tests? #f))
13635 `(("r-htmltools" ,r-htmltools)
13636 ("r-shiny" ,r-shiny)))
13637 (home-page "https://ebailey78.github.io/shinyBS/")
13638 (synopsis "Twitter Bootstrap components for Shiny")
13640 "This package adds additional Twitter Bootstrap components to Shiny.")
13641 (license license:gpl3)))
13643 (define-public r-shinyjqui
13645 (name "r-shinyjqui")
13650 (uri (cran-uri "shinyjqui" version))
13653 "0n4ijxmkp8x6dwrsxwvx0zgd8b5129cmn6q6rrav38v1q5k8889x"))
13656 (delete-file "inst/www/shinyjqui.min.js")))))
13657 (properties `((upstream-name . "shinyjqui")))
13658 (build-system r-build-system)
13661 (modify-phases %standard-phases
13662 (add-after 'unpack 'process-javascript
13663 (lambda* (#:key inputs #:allow-other-keys)
13664 (with-directory-excursion "inst/www/"
13665 (let ((source "shinyjqui.js")
13666 (target "shinyjqui.min.js"))
13667 (format #true "Processing ~a --> ~a~%"
13669 (invoke "esbuild" source "--minify"
13670 (string-append "--outfile=" target)))))))))
13672 `(("r-htmltools" ,r-htmltools)
13673 ("r-htmlwidgets" ,r-htmlwidgets)
13674 ("r-jsonlite" ,r-jsonlite)
13675 ("r-shiny" ,r-shiny)))
13677 `(("r-knitr" ,r-knitr)
13678 ("esbuild" ,esbuild)))
13679 (home-page "https://github.com/yang-tang/shinyjqui")
13680 (synopsis "jQuery UI interactions and effects for Shiny")
13682 "This is an extension to Shiny that brings interactions and animation
13683 effects from the jQuery UI library.")
13684 (license license:expat)))
13686 (define-public r-outliers
13688 (name "r-outliers")
13693 (uri (cran-uri "outliers" version))
13696 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
13697 (build-system r-build-system)
13698 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
13699 (synopsis "Tests for outliers")
13701 "This package provides a collection of some tests commonly used for
13702 identifying outliers.")
13703 (license license:gpl2+)))
13705 (define-public r-bayesm
13712 (uri (cran-uri "bayesm" version))
13714 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
13715 (build-system r-build-system)
13717 `(("r-rcpp" ,r-rcpp)
13718 ("r-rcpparmadillo" ,r-rcpparmadillo)))
13719 (home-page "http://www.perossi.org/home/bsm-1")
13720 (synopsis "Bayesian inference for marketing/micro-econometrics")
13722 "This package covers many important models used in marketing and
13723 micro-econometrics applications, including Bayes Regression (univariate or
13724 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
13725 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
13726 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
13727 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
13728 Estimation with normal base, Hierarchical Linear Models with normal prior and
13729 covariates, Hierarchical Linear Models with a mixture of normals prior and
13730 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
13731 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
13732 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
13733 analysis of choice-based conjoint data, Bayesian treatment of linear
13734 instrumental variables models, Analysis of Multivariate Ordinal survey data
13735 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
13736 Coefficient Logit Models.")
13737 (license license:gpl2+)))
13739 (define-public r-tensora
13746 (uri (cran-uri "tensorA" version))
13749 "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf"))))
13750 (properties `((upstream-name . "tensorA")))
13751 (build-system r-build-system)
13752 (home-page "http://www.stat.boogaart.de/tensorA")
13753 (synopsis "Advanced tensor arithmetic with named indices")
13755 "This package provides convenience functions for advanced linear algebra
13756 with tensors and computation with datasets of tensors on a higher level
13757 abstraction. It includes Einstein and Riemann summing conventions, dragging,
13758 co- and contravariate indices, and parallel computations on sequences of
13760 (license license:gpl2+)))
13762 (define-public r-rarpack
13769 (uri (cran-uri "rARPACK" version))
13772 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
13773 (properties `((upstream-name . "rARPACK")))
13774 (build-system r-build-system)
13775 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
13776 (home-page "https://github.com/yixuan/rARPACK")
13777 (synopsis "Solvers for large scale eigenvalue and SVD problems")
13779 "This package was previously an R wrapper of the ARPACK library, and now
13780 a shell of the R package RSpectra, an R interface to the Spectra library for
13781 solving large scale eigenvalue/vector problems. The current version of
13782 rARPACK simply imports and exports the functions provided by RSpectra. New
13783 users of rARPACK are advised to switch to the RSpectra package.")
13784 (license license:bsd-3)))
13786 (define-public r-compositions
13788 (name "r-compositions")
13793 (uri (cran-uri "compositions" version))
13796 "03qslsfx11gshls901zlhw47prd55mf16w4mkmd8x1dgiwq938l4"))))
13797 (build-system r-build-system)
13799 `(("r-bayesm" ,r-bayesm)
13801 ("r-robustbase" ,r-robustbase)
13802 ("r-tensora" ,r-tensora)))
13804 `(("r-knitr" ,r-knitr)))
13805 (home-page "http://www.stat.boogaart.de/compositions")
13806 (synopsis "Compositional data analysis")
13808 "This package provides functions for the consistent analysis of
13809 compositional data (e.g. portions of substances) and positive
13810 numbers (e.g. concentrations).")
13811 (license license:gpl2+)))
13813 (define-public r-cobs
13820 (uri (cran-uri "cobs" version))
13823 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
13824 (build-system r-build-system)
13826 `(("r-quantreg" ,r-quantreg)
13827 ("r-sparsem" ,r-sparsem)))
13828 (home-page "https://cran.r-project.org/web/packages/cobs")
13829 (synopsis "Constrained B-Splines (sparse matrix based)")
13831 "This package provides qualitatively constrained (regression) smoothing
13832 splines via linear programming and sparse matrices.")
13833 (license license:gpl2+)))
13835 (define-public r-drimpute
13837 (name "r-drimpute")
13842 (uri (cran-uri "DrImpute" version))
13845 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
13846 (properties `((upstream-name . "DrImpute")))
13847 (build-system r-build-system)
13849 `(("r-rcpp" ,r-rcpp)
13850 ("r-rcpparmadillo" ,r-rcpparmadillo)))
13851 (home-page "https://github.com/ikwak2/DrImpute")
13852 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
13854 "This is an R package for imputing dropout events. Many statistical
13855 methods in cell type identification, visualization and lineage reconstruction
13856 do not account for dropout events. DrImpute can improve the performance of
13857 such software by imputing dropout events.")
13858 (license license:gpl3)))
13860 (define-public r-gamlss-dist
13862 (name "r-gamlss-dist")
13867 (uri (cran-uri "gamlss.dist" version))
13869 (base32 "0nzgq3rnziy0i2zxn88hqy3pakpyin2m2csk9j3zg39si66c6wcq"))))
13870 (properties `((upstream-name . "gamlss.dist")))
13871 (build-system r-build-system)
13872 (propagated-inputs `(("r-mass" ,r-mass)))
13873 (home-page "http://www.gamlss.org/")
13874 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
13876 "This package provides a set of distributions which can be used for
13877 modelling the response variables in Generalized Additive Models for Location
13878 Scale and Shape. The distributions can be continuous, discrete or mixed
13879 distributions. Extra distributions can be created, by transforming, any
13880 continuous distribution defined on the real line, to a distribution defined on
13881 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
13882 transformation, respectively.")
13883 ;; Either version of the GPL.
13884 (license (list license:gpl2 license:gpl3))))
13886 ;; This package includes JavaScript files, which are not minified. When
13887 ;; upgrading please check that there are no new minified JavaScript files.
13888 (define-public r-shinyjs
13895 (uri (cran-uri "shinyjs" version))
13898 "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2"))))
13899 (build-system r-build-system)
13901 `(("r-digest" ,r-digest)
13902 ("r-htmltools" ,r-htmltools)
13903 ("r-jsonlite" ,r-jsonlite)
13904 ("r-shiny" ,r-shiny)))
13906 `(("r-knitr" ,r-knitr)))
13907 (home-page "https://deanattali.com/shinyjs")
13908 (synopsis "Improve the user experience of your Shiny apps")
13910 "Perform common useful JavaScript operations in Shiny apps that will
13911 greatly improve your apps without having to know any JavaScript. Examples
13912 include: hiding an element, disabling an input, resetting an input back to its
13913 original value, delaying code execution by a few seconds, and many more useful
13914 functions for both the end user and the developer. Shinyjs can also be used
13915 to easily call your own custom JavaScript functions from R.")
13916 (license license:agpl3+)))
13918 ;; This package includes minified JavaScript files. When upgrading please
13919 ;; check that there are no new minified JavaScript files.
13920 (define-public r-colourpicker
13922 (name "r-colourpicker")
13927 (uri (cran-uri "colourpicker" version))
13930 "1qjispj7i12m02js5cm5xlgn5lyff0kc5ybz6lbknz8q5lkbdyrd"))))
13931 (build-system r-build-system)
13933 `(#:modules ((guix build utils)
13934 (guix build r-build-system)
13938 (modify-phases %standard-phases
13939 (add-after 'unpack 'process-javascript
13940 (lambda* (#:key inputs #:allow-other-keys)
13941 (with-directory-excursion "inst"
13945 `((,(assoc-ref inputs "js-salvattore")
13946 "examples/colourInput/www/salvattore.min.js")
13947 (,(assoc-ref inputs "js-jquery")
13948 "htmlwidgets/lib/jquery/jquery.min.js")
13949 ("www/shared/colourpicker/js/colourpicker.js"
13950 "www/shared/colourpicker/js/colourpicker.min.js"))))
13951 (lambda (sources targets)
13952 (for-each (lambda (source target)
13953 (format #t "Processing ~a --> ~a~%"
13955 (delete-file target)
13956 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
13957 (call-with-output-file target
13959 (dump-port minified port)))))
13960 sources targets))))
13963 `(("r-ggplot2" ,r-ggplot2)
13964 ("r-htmltools" ,r-htmltools)
13965 ("r-htmlwidgets" ,r-htmlwidgets)
13966 ("r-jsonlite" ,r-jsonlite)
13967 ("r-miniui" ,r-miniui)
13968 ("r-shiny" ,r-shiny)
13969 ("r-shinyjs" ,r-shinyjs)))
13971 `(("r-knitr" ,r-knitr)
13972 ("uglify-js" ,uglify-js)
13976 (uri "https://code.jquery.com/jquery-3.3.1.js")
13979 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
13983 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
13986 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
13987 (home-page "https://github.com/daattali/colourpicker")
13988 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
13990 "This package provides a color picker that can be used as an input in
13991 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
13992 custom color palettes, and many more options. A plot color helper tool is
13993 available as an RStudio Addin, which helps you pick colors to use in your
13994 plots. A more generic color picker RStudio Addin is also provided to let you
13995 select colors to use in your R code.")
13996 (license license:expat)))
13998 (define-public r-ggextra
14005 (uri (cran-uri "ggExtra" version))
14008 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
14009 (properties `((upstream-name . "ggExtra")))
14010 (build-system r-build-system)
14012 `(("r-colourpicker" ,r-colourpicker)
14013 ("r-ggplot2" ,r-ggplot2)
14014 ("r-gtable" ,r-gtable)
14015 ("r-miniui" ,r-miniui)
14017 ("r-scales" ,r-scales)
14018 ("r-shiny" ,r-shiny)
14019 ("r-shinyjs" ,r-shinyjs)))
14021 `(("r-knitr" ,r-knitr)))
14022 (home-page "https://github.com/daattali/ggExtra")
14023 (synopsis "Marginal histograms for ggplot2 and other enhancements")
14025 "This package is a collection of functions and layers to enhance ggplot2.
14026 The flagship function is @code{ggMarginal()}, which can be used to add
14027 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
14028 (license license:expat)))
14030 (define-public r-minpack-lm
14032 (name "r-minpack-lm")
14037 (uri (cran-uri "minpack.lm" version))
14040 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
14041 (properties `((upstream-name . "minpack.lm")))
14042 (build-system r-build-system)
14043 (native-inputs `(("gfortran" ,gfortran)))
14044 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
14045 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
14047 "The @code{nls.lm} function provides an R interface to @code{lmder} and
14048 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
14049 problems by a modification of the Levenberg-Marquardt algorithm, with support
14050 for lower and upper parameter bounds. The implementation can be used via
14051 @code{nls}-like calls using the @code{nlsLM} function.")
14052 (license license:gpl3)))
14054 (define-public r-moments
14061 (uri (cran-uri "moments" version))
14064 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
14065 (build-system r-build-system)
14066 (home-page "https://cran.r-project.org/web/packages/moments")
14067 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
14069 "This package provides functions to calculate: moments, Pearson's
14070 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
14071 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
14072 (license license:gpl2+)))
14074 (define-public r-msir
14081 (uri (cran-uri "msir" version))
14084 "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84"))))
14085 (build-system r-build-system)
14087 `(("r-mclust" ,r-mclust)))
14089 `(("r-knitr" ,r-knitr)))
14090 (home-page "https://cran.r-project.org/web/packages/msir")
14091 (synopsis "Model-based sliced inverse regression")
14093 "This is an R package for dimension reduction based on finite Gaussian
14094 mixture modeling of inverse regression.")
14095 (license license:gpl2+)))
14097 (define-public r-pbivnorm
14099 (name "r-pbivnorm")
14104 (uri (cran-uri "pbivnorm" version))
14107 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
14108 (build-system r-build-system)
14109 (native-inputs `(("gfortran" ,gfortran)))
14110 (home-page "https://github.com/brentonk/pbivnorm")
14111 (synopsis "Vectorized bivariate normal CDF")
14113 "This package provides a vectorized R function for calculating
14114 probabilities from a standard bivariate normal CDF.")
14115 (license license:gpl2+)))
14117 (define-public r-lavaan
14124 (uri (cran-uri "lavaan" version))
14127 "0ks62wrwghbm1brzmqvr92h5n1295dpc87m1g3xrfx0mkdaqdcdk"))))
14128 (build-system r-build-system)
14130 `(("r-mass" ,r-mass)
14131 ("r-mnormt" ,r-mnormt)
14132 ("r-numderiv" ,r-numderiv)
14133 ("r-pbivnorm" ,r-pbivnorm)))
14134 (home-page "http://lavaan.ugent.be")
14135 (synopsis "Latent variable analysis")
14137 "This package provides tools to fit a variety of latent variable models,
14138 including confirmatory factor analysis, structural equation modeling and
14139 latent growth curve models.")
14140 (license license:gpl2+)))
14142 (define-public r-nonnest2
14144 (name "r-nonnest2")
14149 (uri (cran-uri "nonnest2" version))
14152 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
14153 (build-system r-build-system)
14155 `(("r-compquadform" ,r-compquadform)
14156 ("r-lavaan" ,r-lavaan)
14157 ("r-mvtnorm" ,r-mvtnorm)
14158 ("r-sandwich" ,r-sandwich)))
14160 `(("r-knitr" ,r-knitr)))
14161 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
14162 (synopsis "Tests of non-nested models")
14164 "This package allows for testing of non-nested models. It includes tests
14165 of model distinguishability and of model fit that can be applied to both
14166 nested and non-nested models. The package also includes functionality to
14167 obtain confidence intervals associated with AIC and BIC.")
14168 ;; Either version of the GPL.
14169 (license (list license:gpl2 license:gpl3))))
14171 (define-public r-penalized
14173 (name "r-penalized")
14178 (uri (cran-uri "penalized" version))
14181 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
14182 (build-system r-build-system)
14184 `(("r-rcpp" ,r-rcpp)
14185 ("r-rcpparmadillo" ,r-rcpparmadillo)
14186 ("r-survival" ,r-survival)))
14187 (home-page "https://cran.r-project.org/web/packages/penalized/")
14188 (synopsis "Penalized estimation in GLMs and in the Cox model")
14190 "This package provides tools for fitting possibly high dimensional
14191 penalized regression models. The penalty structure can be any combination of
14192 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
14193 constraint on the regression coefficients. The supported regression models
14194 are linear, logistic and Poisson regression and the Cox Proportional Hazards
14195 model. Cross-validation routines allow optimization of the tuning
14197 (license license:gpl2+)))
14199 (define-public r-zim
14206 (uri (cran-uri "ZIM" version))
14209 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
14210 (properties `((upstream-name . "ZIM")))
14211 (build-system r-build-system)
14212 (propagated-inputs `(("r-mass" ,r-mass)))
14213 (home-page "https://github.com/biostatstudio/ZIM")
14214 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
14216 "Analyze count time series with excess zeros. Two types of statistical
14217 models are supported: Markov regression and state-space models. They are also
14218 known as observation-driven and parameter-driven models respectively in the
14219 time series literature. The functions used for Markov regression or
14220 observation-driven models can also be used to fit ordinary regression models
14221 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
14222 negative binomial (ZINB) assumption. The package also contains miscellaneous
14223 functions to compute density, distribution, quantile, and generate random
14224 numbers from ZIP and ZINB distributions.")
14225 (license license:gpl3)))
14227 (define-public r-nor1mix
14234 (uri (cran-uri "nor1mix" version))
14237 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
14238 (build-system r-build-system)
14239 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
14240 (synopsis "Normal (1-d) mixture models")
14242 "This package provides S3 classes and methods for one-dimensional normal
14243 mixture models, for, e.g., density estimation or clustering algorithms
14244 research and teaching; it provides the widely used Marron-Wand densities. It
14245 also provides tools for efficient random number generation and graphics.")
14246 (license license:gpl2+)))
14248 (define-public r-beanplot
14250 (name "r-beanplot")
14255 (uri (cran-uri "beanplot" version))
14258 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
14259 (build-system r-build-system)
14260 (home-page "https://cran.r-project.org/web/packages/beanplot/")
14261 (synopsis "Visualization via beanplots")
14263 "This package provides beanplots, an alternative to
14264 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
14266 (license license:gpl2)))
14268 (define-public r-pbdzmq
14275 (uri (cran-uri "pbdZMQ" version))
14278 "1v8iv1pzs4j3ics9k9h4xjkv6z1ma2xbqy003xk2lqax6srqi02d"))))
14279 (properties `((upstream-name . "pbdZMQ")))
14280 (build-system r-build-system)
14282 `(("zeromq" ,zeromq)
14285 `(("pkg-config" ,pkg-config)))
14286 (home-page "https://pbdr.org/")
14287 (synopsis "R interface to ZeroMQ")
14289 "ZeroMQ is a well-known library for high-performance asynchronous
14290 messaging in scalable, distributed applications. This package provides high
14291 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
14292 interactive client/server programming frameworks. A few wrapper functions
14293 compatible with @code{rzmq} are also provided.")
14294 (license license:gpl3)))
14296 (define-public r-repr
14303 (uri (cran-uri "repr" version))
14306 "0qimllv9pn8wsl550bjkp5dkknbmr69j85mrwfbbq75m2ga466sk"))))
14307 (build-system r-build-system)
14309 `(("r-base64enc" ,r-base64enc)
14310 ("r-htmltools" ,r-htmltools)
14311 ("r-jsonlite" ,r-jsonlite)
14312 ("r-pillar" ,r-pillar)))
14313 (home-page "https://cran.r-project.org/web/packages/repr/")
14314 (synopsis "Serializable representations")
14316 "This package provides string and binary representations of objects for
14317 several formats and MIME types.")
14318 (license license:gpl3)))
14320 (define-public r-irdisplay
14322 (name "r-irdisplay")
14327 (uri (cran-uri "IRdisplay" version))
14330 "15jbjrihm1mk899357h9xb08iq3xyagds1xb40fmdpkfcmcfqrw9"))))
14331 (properties `((upstream-name . "IRdisplay")))
14332 (build-system r-build-system)
14334 `(("r-repr" ,r-repr)))
14335 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
14336 (synopsis "Jupyter display machinery")
14338 "This package provides an interface to the rich display capabilities of
14339 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
14340 running IRkernel session.")
14341 (license license:expat)))
14343 (define-public r-irkernel
14345 (name "r-irkernel")
14350 (uri (cran-uri "IRkernel" version))
14353 "1y06v3difaiihxfm2abm88nnjzvkla4p346cm1nxmga4iwb2k8gm"))))
14354 (properties `((upstream-name . "IRkernel")))
14355 (build-system r-build-system)
14358 (modify-phases %standard-phases
14359 (add-after 'install 'install-kernelspec
14360 (lambda* (#:key outputs #:allow-other-keys)
14361 (let ((out (assoc-ref outputs "out")))
14362 (setenv "HOME" "/tmp")
14363 (invoke "jupyter" "kernelspec" "install"
14366 (string-append out "/site-library/IRkernel/kernelspec"))
14367 ;; Record the absolute file name of the 'R' executable in
14369 (substitute* (string-append out "/share/jupyter"
14370 "/kernels/ir/kernel.json")
14372 (string-append "[\"" (which "R") "\",")))
14375 `(("jupyter" ,jupyter)))
14377 `(("r-crayon" ,r-crayon)
14378 ("r-digest" ,r-digest)
14379 ("r-evaluate" ,r-evaluate)
14380 ("r-irdisplay" ,r-irdisplay)
14381 ("r-jsonlite" ,r-jsonlite)
14382 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
14383 ("r-minimal" ,r-minimal)
14384 ("r-pbdzmq" ,r-pbdzmq)
14386 ("r-uuid" ,r-uuid)))
14387 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
14388 (synopsis "Native R kernel for Jupyter")
14390 "The R kernel for the Jupyter environment executes R code which the
14391 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
14393 (license license:expat)))
14395 (define-public r-gmodels
14402 (uri (cran-uri "gmodels" version))
14405 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
14406 (build-system r-build-system)
14408 `(("r-gdata" ,r-gdata)
14409 ("r-mass" ,r-mass)))
14410 (home-page "https://cran.r-project.org/web/packages/gmodels/")
14411 (synopsis "Various R programming tools for model fitting")
14413 "This package provides various R programming tools for model fitting.")
14414 (license license:gpl2)))
14416 (define-public r-apcluster
14418 (name "r-apcluster")
14423 (uri (cran-uri "apcluster" version))
14426 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
14427 (build-system r-build-system)
14429 `(("r-matrix" ,r-matrix)
14430 ("r-rcpp" ,r-rcpp)))
14431 (home-page "https://cran.r-project.org/web/packages/apcluster/")
14432 (synopsis "Affinity propagation clustering")
14434 "This package implements affinity propagation clustering introduced by
14435 Frey and Dueck (2007). The package further provides leveraged affinity
14436 propagation and an algorithm for exemplar-based agglomerative clustering that
14437 can also be used to join clusters obtained from affinity propagation. Various
14438 plotting functions are available for analyzing clustering results.")
14439 (license license:gpl2+)))
14441 (define-public r-valr
14448 (uri (cran-uri "valr" version))
14451 "1vbp89zfylgih5acvw7lcx3a0dbbd7dhq7yhywr7kq02737qykdx"))))
14452 (build-system r-build-system)
14454 `(("r-broom" ,r-broom)
14455 ("r-dplyr" ,r-dplyr)
14456 ("r-ggplot2" ,r-ggplot2)
14458 ("r-readr" ,r-readr)
14459 ("r-rlang" ,r-rlang)
14460 ("r-stringr" ,r-stringr)
14461 ("r-tibble" ,r-tibble)))
14463 `(("r-knitr" ,r-knitr)))
14464 (home-page "https://github.com/rnabioco/valr")
14465 (synopsis "Genome interval arithmetic in R")
14467 "This package enables you to read and manipulate genome intervals and
14468 signals. It provides functionality similar to command-line tool suites within
14469 R, enabling interactive analysis and visualization of genome-scale data.")
14470 (license license:expat)))
14472 (define-public r-rematch2
14474 (name "r-rematch2")
14479 (uri (cran-uri "rematch2" version))
14482 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
14483 (build-system r-build-system)
14485 `(("r-tibble" ,r-tibble)))
14486 (home-page "https://github.com/r-lib/rematch2")
14487 (synopsis "Tidy output from regular expression matching")
14489 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
14490 return the match results in tidy data frames.")
14491 (license license:expat)))
14493 (define-public r-picante
14500 (uri (cran-uri "picante" version))
14503 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
14504 (build-system r-build-system)
14508 ("r-vegan" ,r-vegan)))
14509 (home-page "https://cran.r-project.org/web/packages/picante/")
14510 (synopsis "Integrating phylogenies and ecology")
14512 "This package provides functions for phylocom integration, community
14513 analyses, null-models, traits and evolution. It implements numerous
14514 ecophylogenetic approaches including measures of community phylogenetic and
14515 trait diversity, phylogenetic signal, estimation of trait values for
14516 unobserved taxa, null models for community and phylogeny randomizations, and
14517 utility functions for data input/output and phylogeny plotting. A full
14518 description of package functionality and methods are provided by Kembel et
14520 (license license:gpl2)))
14522 (define-public r-reinforcelearn
14524 (name "r-reinforcelearn")
14529 (uri (cran-uri "reinforcelearn" version))
14532 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
14533 (build-system r-build-system)
14535 `(("r-checkmate" ,r-checkmate)
14537 ("r-purrr" ,r-purrr)
14539 (home-page "https://markusdumke.github.io/reinforcelearn")
14540 (synopsis "Reinforcement learning")
14542 "This package implements reinforcement learning environments and
14543 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
14544 can be used with function approximation, eligibility traces (Singh & Sutton,
14545 1996) and experience replay (Mnih et al., 2013).")
14546 (license license:expat)))
14548 (define-public r-lemon
14555 (uri (cran-uri "lemon" version))
14558 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
14559 (build-system r-build-system)
14561 `(("r-ggplot2" ,r-ggplot2)
14562 ("r-gridextra" ,r-gridextra)
14563 ("r-gtable" ,r-gtable)
14564 ("r-knitr" ,r-knitr)
14565 ("r-lattice" ,r-lattice)
14567 ("r-rlang" ,r-rlang)
14568 ("r-scales" ,r-scales)))
14570 `(("r-knitr" ,r-knitr)))
14571 (home-page "https://github.com/stefanedwards/lemon")
14572 (synopsis "Freshen up your ggplot2 plots")
14574 "This package provides functions for working with legends and axis lines
14575 of ggplot2, facets that repeat axis lines on all panels, and some knitr
14577 (license license:gpl3)))
14579 (define-public r-wgaim
14586 (uri (cran-uri "wgaim" version))
14588 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
14589 (build-system r-build-system)
14591 `(("r-ggplot2" ,r-ggplot2)
14593 (home-page "https://cran.r-project.org/web/packages/wgaim")
14594 (synopsis "Whole genome average interval mapping for QTL detection")
14596 "This package integrates sophisticated mixed modelling methods with a
14597 whole genome approach to detecting significant QTL in linkage maps.")
14598 (license license:gpl2+)))
14600 (define-public r-bedr
14607 (uri (cran-uri "bedr" version))
14610 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
14611 (build-system r-build-system)
14613 `(("r-data-table" ,r-data-table)
14614 ("r-r-utils" ,r-r-utils)
14615 ("r-testthat" ,r-testthat)
14616 ("r-venndiagram" ,r-venndiagram)
14619 ("bedtools" ,bedtools)
14620 ("htslib" ,htslib))) ; for tabix
14622 `(("r-knitr" ,r-knitr))) ; for vignettes
14623 (home-page "https://cran.r-project.org/web/packages/bedr")
14624 (synopsis "Genomic region processing")
14626 "This package is for genomic regions processing using command line tools
14627 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
14628 utilities to perform genome arithmetic e.g indexing, formatting and merging.
14629 The bedr package's API enhances access to these tools as well as offers
14630 additional utilities for genomic regions processing.")
14631 (license license:gpl2)))
14633 (define-public r-sets
14640 (uri (cran-uri "sets" version))
14643 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
14644 (properties `((upstream-name . "sets")))
14645 (build-system r-build-system)
14646 (home-page "https://cran.r-project.org/web/packages/sets")
14647 (synopsis "Sets, generalized sets, customizable sets and intervals")
14649 "This package provides data structures and basic operations for ordinary
14650 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
14651 customizable sets, and intervals.")
14652 (license license:gpl2)))
14654 (define-public r-partitions
14656 (name "r-partitions")
14661 (uri (cran-uri "partitions" version))
14664 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
14665 (build-system r-build-system)
14668 ("r-polynom" ,r-polynom)
14669 ("r-sets" ,r-sets)))
14670 (home-page "https://cran.r-project.org/web/packages/partitions")
14671 (synopsis "Additive partitions of integers")
14673 "This package provides tools to enumerates the partitions, unequal
14674 partitions, and restricted partitions of an integer; the three corresponding
14675 partition functions are also given.")
14676 ;; Any version of the GPL
14677 (license license:gpl2+)))
14679 (define-public r-brobdingnag
14681 (name "r-brobdingnag")
14686 (uri (cran-uri "Brobdingnag" version))
14689 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
14690 (properties `((upstream-name . "Brobdingnag")))
14691 (build-system r-build-system)
14692 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
14693 (synopsis "Very large numbers in R")
14695 "This package handles very large numbers in R. Real numbers are held
14696 using their natural logarithms, plus a logical flag indicating sign. The
14697 package includes a vignette that gives a step-by-step introduction to using S4
14699 ;; Any version of the GPL
14700 (license license:gpl2+)))
14702 (define-public r-untb
14709 (uri (cran-uri "untb" version))
14712 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
14713 (build-system r-build-system)
14715 `(("r-brobdingnag" ,r-brobdingnag)
14716 ("r-partitions" ,r-partitions)
14717 ("r-polynom" ,r-polynom)))
14718 (home-page "https://github.com/RobinHankin/untb.git")
14719 (synopsis "Ecological drift under the UNTB")
14721 "This package provides numerical simulations, and visualizations, of
14722 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
14723 (license license:gpl2+)))
14725 (define-public r-stepwise
14727 (name "r-stepwise")
14732 (uri (cran-uri "stepwise" version))
14735 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
14736 (build-system r-build-system)
14737 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
14738 (synopsis "Stepwise detection of recombination breakpoints")
14740 "This package provides a stepwise approach to identifying recombination
14741 breakpoints in a genomic sequence alignment.")
14742 (license license:gpl2+)))
14744 (define-public r-snpmaxsel
14746 (name "r-snpmaxsel")
14751 (uri (cran-uri "SNPmaxsel" version))
14754 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
14755 (properties `((upstream-name . "SNPmaxsel")))
14756 (build-system r-build-system)
14758 `(("r-combinat" ,r-combinat)
14759 ("r-mvtnorm" ,r-mvtnorm)))
14760 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
14761 (synopsis "Maximally selected statistics for SNP data")
14763 "This package implements asymptotic methods related to maximally selected
14764 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
14766 (license license:gpl2+)))
14768 (define-public r-acsnminer
14770 (name "r-acsnminer")
14771 (version "0.16.8.25")
14774 (uri (cran-uri "ACSNMineR" version))
14777 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
14778 (properties `((upstream-name . "ACSNMineR")))
14779 (build-system r-build-system)
14781 `(("r-ggplot2" ,r-ggplot2)
14782 ("r-gridextra" ,r-gridextra)))
14783 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
14784 (synopsis "Gene enrichment analysis")
14786 "This package provides tools to compute and represent gene set enrichment
14787 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
14788 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
14789 enrichment can be run with hypergeometric test or Fisher exact test, and can
14790 use multiple corrections. Visualization of data can be done either by
14791 barplots or heatmaps.")
14792 (license license:gpl2+)))
14794 (define-public r-seqinr
14801 (uri (cran-uri "seqinr" version))
14804 "1z1jipgrn9nrnxlx7bcf8c2chwpa3kfva0zgyb12xbr3kisn166y"))))
14805 (build-system r-build-system)
14807 `(("r-ade4" ,r-ade4)
14808 ("r-segmented" ,r-segmented)))
14811 (home-page "http://seqinr.r-forge.r-project.org/")
14812 (synopsis "Biological sequences retrieval and analysis")
14814 "This package provides tools for exploratory data analysis and data
14815 visualization of biological sequence (DNA and protein) data. It also includes
14816 utilities for sequence data management under the ACNUC system.")
14817 (license license:gpl2+)))
14819 (define-public r-units
14826 (uri (cran-uri "units" version))
14829 "1rdpbkiqcabz00fqzzs98v89v4cgvcd4pb00pwxzkq6vmwmscwrz"))))
14830 (build-system r-build-system)
14832 `(("udunits" ,udunits)))
14834 `(("r-rcpp" ,r-rcpp)))
14836 `(("r-knitr" ,r-knitr)))
14837 (home-page "https://github.com/r-quantities/units/")
14838 (synopsis "Measurement Units for R Vectors")
14840 "This package provides support for measurement units in R vectors,
14841 matrices and arrays: automatic propagation, conversion, derivation and
14842 simplification of units; raising errors in case of unit incompatibility. It
14843 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
14845 (license license:gpl2)))
14847 (define-public r-udunits2
14849 (name "r-udunits2")
14854 (uri (cran-uri "udunits2" version))
14857 "0yav7rm2afcx67xqrknybxgz7x63w78zyxa0xifvc0k2gz0d6mfi"))))
14858 (properties `((upstream-name . "udunits2")))
14859 (build-system r-build-system)
14861 `(("udunits" ,udunits)))
14862 (home-page "https://cran.r-project.org/package=udunits2")
14863 (synopsis "Udunits-2 bindings for R")
14865 "This package provides simple bindings to Unidata's udunits library.")
14866 (license license:gpl2)))
14868 (define-public r-classint
14870 (name "r-classint")
14875 (uri (cran-uri "classInt" version))
14878 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
14879 (properties `((upstream-name . "classInt")))
14880 (build-system r-build-system)
14882 `(("r-class" ,r-class)
14883 ("r-e1071" ,r-e1071)
14884 ("r-kernsmooth" ,r-kernsmooth)))
14886 `(("gfortran" ,gfortran)
14887 ("r-knitr" ,r-knitr)))
14888 (home-page "https://github.com/r-spatial/classInt/")
14889 (synopsis "Choose univariate class intervals")
14891 "This package provides selected commonly used methods for choosing
14892 univariate class intervals for mapping or other graphics purposes.")
14893 (license license:gpl2+)))
14895 (define-public r-spdata
14902 (uri (cran-uri "spData" version))
14905 "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs"))))
14906 (properties `((upstream-name . "spData")))
14907 (build-system r-build-system)
14909 `(("r-raster" ,r-raster)
14911 (home-page "https://github.com/Nowosad/spData")
14912 (synopsis "Datasets for spatial analysis")
14914 "This a package containing diverse spatial datasets for demonstrating,
14915 benchmarking and teaching spatial data analysis. It includes R data of class
14916 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
14917 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
14918 of the datasets are designed to illustrate specific analysis techniques.
14919 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
14920 illustrate point pattern analysis techniques.")
14921 (license license:cc0)))
14923 (define-public r-learnbayes
14925 (name "r-learnbayes")
14930 (uri (cran-uri "LearnBayes" version))
14933 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
14934 (properties `((upstream-name . "LearnBayes")))
14935 (build-system r-build-system)
14936 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
14937 (synopsis "Functions for learning Bayesian inference")
14939 "This package provides a collection of functions helpful in learning the
14940 basic tenets of Bayesian statistical inference. It contains functions for
14941 summarizing basic one and two parameter posterior distributions and predictive
14942 distributions. It contains MCMC algorithms for summarizing posterior
14943 distributions defined by the user. It also contains functions for regression
14944 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
14946 (license license:gpl2+)))
14948 (define-public r-deldir
14955 (uri (cran-uri "deldir" version))
14958 "0jfwff5kk0zraspsvbk26lphl3fnrc6xmhl4690hr0a5k177ildm"))))
14959 (build-system r-build-system)
14960 (native-inputs `(("gfortran" ,gfortran)))
14961 (home-page "https://cran.r-project.org/web/packages/deldir")
14962 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
14964 "This package provides tools for calculating the Delaunay triangulation
14965 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
14966 of a planar point set. It plots triangulations and tessellations in various
14967 ways, clips tessellations to sub-windows, calculates perimeters of
14968 tessellations, and summarizes information about the tiles of the
14970 (license license:gpl2+)))
14972 (define-public r-sf
14979 (uri (cran-uri "sf" version))
14982 "175fmnnw11fjhfgjv9sn9b0jfjcqbybpgwsvv99d5yddigvw5jja"))))
14983 (build-system r-build-system)
14991 `(("r-classint" ,r-classint)
14993 ("r-magrittr" ,r-magrittr)
14995 ("r-units" ,r-units)))
14997 `(("pkg-config" ,pkg-config)
14998 ("r-knitr" ,r-knitr)))
14999 (home-page "https://github.com/r-spatial/sf/")
15000 (synopsis "Simple features for R")
15002 "This package provides support for simple features, a standardized way to
15003 encode spatial vector data. It binds to GDAL for reading and writing data, to
15004 GEOS for geometrical operations, and to PROJ for projection conversions and
15005 datum transformations.")
15006 ;; Either of these licenses
15007 (license (list license:gpl2 license:expat))))
15009 (define-public r-spdep
15016 (uri (cran-uri "spdep" version))
15019 "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7"))))
15020 (build-system r-build-system)
15022 `(("r-boot" ,r-boot)
15024 ("r-deldir" ,r-deldir)
15026 ("r-gmodels" ,r-gmodels)
15027 ("r-learnbayes" ,r-learnbayes)
15029 ("r-matrix" ,r-matrix)
15033 ("r-spdata" ,r-spdata)))
15035 `(("r-knitr" ,r-knitr)))
15036 (home-page "https://github.com/r-spatial/spdep/")
15037 (synopsis "Spatial dependence: weighting schemes, statistics and models")
15039 "This package provides a collection of functions to create spatial
15040 weights matrix objects from polygon contiguities, from point patterns by
15041 distance and tessellations, for summarizing these objects, and for permitting
15042 their use in spatial data analysis, including regional aggregation by minimum
15044 (license license:gpl2+)))
15046 (define-public r-adegenet
15048 (name "r-adegenet")
15053 (uri (cran-uri "adegenet" version))
15056 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
15057 (build-system r-build-system)
15059 `(("r-ade4" ,r-ade4)
15062 ("r-dplyr" ,r-dplyr)
15063 ("r-ggplot2" ,r-ggplot2)
15064 ("r-igraph" ,r-igraph)
15066 ("r-reshape2" ,r-reshape2)
15067 ("r-seqinr" ,r-seqinr)
15068 ("r-shiny" ,r-shiny)
15069 ("r-spdep" ,r-spdep)
15070 ("r-vegan" ,r-vegan)))
15071 (home-page "https://github.com/thibautjombart/adegenet")
15072 (synopsis "Exploratory analysis of genetic and genomic data")
15074 "This package provides a toolset for the exploration of genetic and
15075 genomic data. Adegenet provides formal (S4) classes for storing and handling
15076 various genetic data, including genetic markers with varying ploidy and
15077 hierarchical population structure (@code{genind} class), alleles counts by
15078 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
15079 also implements original multivariate methods (DAPC, sPCA), graphics,
15080 statistical tests, simulation tools, distance and similarity measures, and
15081 several spatial methods. A range of both empirical and simulated datasets is
15082 also provided to illustrate various methods.")
15083 (license license:gpl2+)))
15085 (define-public r-pegas
15092 (uri (cran-uri "pegas" version))
15094 (base32 "0lr06gajzdanj8ax91kgpxsj863m367v2s1z5gnxps3999n0xybx"))))
15095 (build-system r-build-system)
15097 `(("r-adegenet" ,r-adegenet)
15099 (home-page "http://ape-package.ird.fr/pegas.html")
15100 (synopsis "Population and evolutionary genetics analysis system")
15102 "This package provides functions for reading, writing, plotting,
15103 analysing, and manipulating allelic and haplotypic data, including from VCF
15104 files, and for the analysis of population nucleotide sequences and
15105 micro-satellites including coalescent analyses, linkage disequilibrium,
15106 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
15107 minimum spanning tree and network, and median-joining networks.")
15108 (license license:gpl2+)))
15110 (define-public r-rmetasim
15112 (name "r-rmetasim")
15117 (uri (cran-uri "rmetasim" version))
15120 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
15121 (build-system r-build-system)
15123 `(("r-ade4" ,r-ade4)
15124 ("r-adegenet" ,r-adegenet)
15125 ("r-gtools" ,r-gtools)
15126 ("r-pegas" ,r-pegas)))
15127 (home-page "https://cran.r-project.org/web/packages/rmetasim")
15128 (synopsis "Individual-based population genetic simulation environment")
15130 "This package provides an interface between R and the metasim simulation
15131 engine. The simulation environment is documented in: Strand, A.(2002),
15132 Metasim 1.0: an individual-based environment for simulating population
15133 genetics of complex population dynamics.")
15135 (license license:gpl2+)))
15137 (define-public r-genetics
15139 (name "r-genetics")
15140 (version "1.3.8.1.2")
15144 (uri (cran-uri "genetics" version))
15147 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
15148 (build-system r-build-system)
15150 `(("r-combinat" ,r-combinat)
15151 ("r-gdata" ,r-gdata)
15152 ("r-gtools" ,r-gtools)
15154 ("r-mvtnorm" ,r-mvtnorm)))
15155 (home-page "https://cran.r-project.org/web/packages/genetics/")
15156 (synopsis "Population genetics")
15158 "This package provides classes and methods for handling genetic data.
15159 It includes classes to represent genotypes and haplotypes at single markers up
15160 to multiple markers on multiple chromosomes. Function include allele
15161 frequencies, flagging homo/heterozygotes, flagging carriers of certain
15162 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
15163 and testing for linkage disequilibrium, ...")
15164 ;; Any GPL version.
15165 (license license:gpl2+)))
15167 (define-public r-snp-plotter
15169 (name "r-snp-plotter")
15174 (uri (cran-uri "snp.plotter" version))
15177 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
15178 (properties `((upstream-name . "snp.plotter")))
15179 (build-system r-build-system)
15180 (propagated-inputs `(("r-genetics" ,r-genetics)))
15181 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
15182 (synopsis "Plot p-values using single SNP and/or haplotype data")
15184 "This package helps you create plots of p-values using single SNP and/or
15185 haplotype data. Main features of the package include options to display a
15186 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
15187 datasets simultaneously. Plots can be created using global and/or individual
15188 haplotype p-values along with single SNP p-values. Images are created as
15189 either PDF/EPS files.")
15190 (license license:gpl2+)))
15192 (define-public r-polspline
15194 (name "r-polspline")
15199 (uri (cran-uri "polspline" version))
15201 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
15202 (build-system r-build-system)
15203 (native-inputs `(("gfortran" ,gfortran)))
15204 (home-page "https://cran.r-project.org/web/packages/polspline/")
15205 (synopsis "Polynomial spline routines")
15207 "This package provides routines for the polynomial spline fitting
15208 routines hazard regression, hazard estimation with flexible tails, logspline,
15209 lspec, polyclass, and polymars.")
15210 (license license:gpl2+)))
15212 (define-public r-rms
15219 (uri (cran-uri "rms" version))
15221 (base32 "1zgfd60lzbakcv7x0i5k3lkw3s0xx5bzssjgangna5lq2j17cdli"))))
15222 (build-system r-build-system)
15224 `(("r-cluster" ,r-cluster)
15225 ("r-digest" ,r-digest)
15226 ("r-ggplot2" ,r-ggplot2)
15227 ("r-hmisc" ,r-hmisc)
15228 ("r-htmltable" ,r-htmltable)
15229 ("r-htmltools" ,r-htmltools)
15230 ("r-lattice" ,r-lattice)
15232 ("r-multcomp" ,r-multcomp)
15234 ("r-polspline" ,r-polspline)
15235 ("r-quantreg" ,r-quantreg)
15236 ("r-rpart" ,r-rpart)
15237 ("r-sparsem" ,r-sparsem)
15238 ("r-survival" ,r-survival)))
15239 (native-inputs `(("gfortran" ,gfortran)))
15240 (home-page "http://biostat.mc.vanderbilt.edu/rms")
15241 (synopsis "Regression modeling strategies")
15243 "This is a package for regression modeling, testing, estimation,
15244 validation, graphics, prediction, and typesetting by storing enhanced model
15245 design attributes in the fit. The rms package is a collection of functions
15246 that assist with and streamline modeling. It also contains functions for
15247 binary and ordinal logistic regression models, ordinal models for continuous Y
15248 with a variety of distribution families, and the Buckley-James multiple
15249 regression model for right-censored responses, and implements penalized
15250 maximum likelihood estimation for logistic and ordinary linear models. The
15251 package works with almost any regression model, but it was especially written
15252 to work with binary or ordinal regression models, Cox regression, accelerated
15253 failure time models, ordinary linear models, the Buckley-James model,
15254 generalized least squares for serially or spatially correlated observations,
15255 generalized linear models, and quantile regression.")
15256 (license license:gpl2+)))
15258 (define-public r-arsenal
15265 (uri (cran-uri "arsenal" version))
15268 "13ql3rb79a764ppsc1sqi8glzzkw79la0j2ahzbxgz7cz879sazy"))))
15269 (properties `((upstream-name . "arsenal")))
15270 (build-system r-build-system)
15271 (propagated-inputs `(("r-knitr" ,r-knitr)))
15272 (native-inputs `(("r-knitr" ,r-knitr)))
15273 (home-page "https://github.com/mayoverse/arsenal")
15274 (synopsis "Functions for large-scale statistical summaries")
15276 "This package provides an arsenal of R functions for large-scale
15277 statistical summaries, which are streamlined to work within the latest
15278 reporting tools in R and RStudio and which use formulas and versatile
15279 summary statistics for summary tables and models. The primary functions
15283 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
15284 levels of one or more categorical variables;
15285 @item @code{paired}, a Table-1-like summary of multiple variable types paired
15286 across two time points;
15287 @item @code{modelsum}, which performs simple model fits on one or more
15288 endpoints for many variables (univariate or adjusted for covariates);
15289 @item @code{freqlist}, a powerful frequency table across many categorical
15291 @item @code{comparedf}, a function for comparing @code{data.frames}; and
15292 @item @code{write2}, a function to output tables to a document.
15295 (license license:gpl2+)))
15297 (define-public r-haplo-stats
15299 (name "r-haplo-stats")
15304 (uri (cran-uri "haplo.stats" version))
15307 "1imz4gs0n57vixwwbirrihpgvn2pyj5da4rgjcjk14n2xkk0nay7"))))
15308 (properties `((upstream-name . "haplo.stats")))
15309 (build-system r-build-system)
15311 `(("r-arsenal" ,r-arsenal)
15314 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
15315 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
15316 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
15318 "This package provides routines for the analysis of indirectly measured
15319 haplotypes. The statistical methods assume that all subjects are unrelated
15320 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
15321 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
15322 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
15323 examples in the vignette.")
15324 (license license:gpl2+)))
15326 (define-public r-bqtl
15333 (uri (cran-uri "bqtl" version))
15336 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
15337 (build-system r-build-system)
15338 (native-inputs `(("gfortran" ,gfortran)))
15339 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
15340 (synopsis "Bayesian QTL mapping toolkit")
15342 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
15343 lines. It includes maximum likelihood and Bayesian tools.")
15344 (license license:gpl2+)))
15346 (define-public r-ibdreg
15353 (uri (cran-uri "ibdreg" version))
15356 "0kgx9iavgm6d6njhki7bm82d6lw2c7kcch2pryd339js2hm0l5gq"))))
15357 (build-system r-build-system)
15358 (home-page "https://www.mayo.edu/research/labs/\
15359 statistical-genetics-genetic-epidemiology/software")
15360 (synopsis "Regression methods for IBD linkage with covariates")
15362 "This package provides a method to test genetic linkage with covariates
15363 by regression methods with response IBD sharing for relative pairs. Account
15364 for correlations of IBD statistics and covariates for relative pairs within
15365 the same pedigree.")
15366 (license license:gpl2+)))
15368 (define-public r-dlmap
15375 (uri (cran-uri "dlmap" version))
15378 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
15379 (build-system r-build-system)
15381 `(("r-ibdreg" ,r-ibdreg)
15385 ("r-wgaim" ,r-wgaim)))
15386 (home-page "https://cran.r-project.org/web/packages/dlmap/")
15387 (synopsis "Detection localization mapping for QTL")
15389 "This is package for QTL mapping in a mixed model framework with separate
15390 detection and localization stages. The first stage detects the number of QTL
15391 on each chromosome based on the genetic variation due to grouped markers on
15392 the chromosome; the second stage uses this information to determine the most
15393 likely QTL positions. The mixed model can accommodate general fixed and
15394 random effects, including spatial effects in field trials and pedigree
15395 effects. It is applicable to backcrosses, doubled haploids, recombinant
15396 inbred lines, F2 intercrosses, and association mapping populations.")
15397 (license license:gpl2)))
15399 (define-public r-hwde
15406 (uri (cran-uri "hwde" version))
15409 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
15410 (build-system r-build-system)
15411 (home-page "https://cran.r-project.org/web/packages/hwde/")
15412 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
15414 "This package fits models for genotypic disequilibria, as described in
15415 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
15416 terms are available that account for first order interactions between loci.
15417 It also implements, for a single locus in a single population, a conditional
15418 exact test for Hardy-Weinberg equilibrium.")
15419 (license license:gpl2+)))
15421 (define-public r-tdthap
15428 (uri (cran-uri "tdthap" version))
15431 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
15432 (build-system r-build-system)
15433 (home-page "https://cran.r-project.org/web/packages/tdthap/")
15434 (synopsis "TDT tests for extended haplotypes")
15436 "Functions and examples are provided for transmission/disequilibrium
15437 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
15438 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
15439 (license license:artistic2.0)))
15441 (define-public r-sparql
15447 (uri (cran-uri "SPARQL" version))
15450 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
15451 (properties `((upstream-name . "SPARQL")))
15452 (build-system r-build-system)
15454 `(("r-rcurl" ,r-rcurl)
15456 (home-page "https://cran.r-project.org/web/packages/SPARQL")
15457 (synopsis "SPARQL client for R")
15458 (description "This package provides an interface to use SPARQL to pose
15459 SELECT or UPDATE queries to an end-point.")
15460 ;; The only license indication is found in the DESCRIPTION file,
15461 ;; which states GPL-3. So we cannot assume GPLv3+.
15462 (license license:gpl3)))
15464 (define-public r-bookdown
15466 (name "r-bookdown")
15470 (uri (cran-uri "bookdown" version))
15473 "0xms1srx9l2mn8xaxnpic0s21y8k56bhwpj45wy7b0yscmxgmh27"))))
15474 (build-system r-build-system)
15476 `(("r-htmltools" ,r-htmltools)
15477 ("r-knitr" ,r-knitr)
15478 ("r-rmarkdown" ,r-rmarkdown)
15479 ("r-tinytex" ,r-tinytex)
15482 ("pandoc" ,pandoc)))
15483 (home-page "https://github.com/rstudio/bookdown")
15484 (synopsis "Authoring books and technical documents with R markdown")
15485 (description "This package provides output formats and utilities for
15486 authoring books and technical documents with R Markdown.")
15487 (license license:gpl3)))
15489 (define-public r-optparse
15491 (name "r-optparse")
15496 (uri (cran-uri "optparse" version))
15499 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
15500 (build-system r-build-system)
15502 `(("r-getopt" ,r-getopt)))
15504 `(("r-knitr" ,r-knitr)))
15505 (home-page "https://github.com/trevorld/optparse")
15506 (synopsis "Command line option parser")
15508 "This package provides a command line parser inspired by Python's
15509 @code{optparse} library to be used with Rscript to write shebang scripts
15510 that accept short and long options.")
15511 (license license:gpl2+)))
15513 (define-public r-kernlab
15520 (uri (cran-uri "kernlab" version))
15522 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
15523 (build-system r-build-system)
15524 (home-page "https://cran.r-project.org/web/packages/kernlab")
15525 (synopsis "Kernel-based machine learning tools")
15527 "This package provides kernel-based machine learning methods for
15528 classification, regression, clustering, novelty detection, quantile regression
15529 and dimensionality reduction. Among other methods @code{kernlab} includes
15530 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
15532 (license license:gpl2)))
15534 (define-public r-hierfstat
15536 (name "r-hierfstat")
15541 (uri (cran-uri "hierfstat" version))
15544 "0dp8k1z5a8gqnax99y1hwfvxilzf4n2i751zr0z6ihrzirsvb3m3"))))
15545 (build-system r-build-system)
15547 `(("r-ade4" ,r-ade4)
15548 ("r-adegenet" ,r-adegenet)
15549 ("r-gaston" ,r-gaston)
15550 ("r-gtools" ,r-gtools)))
15552 `(("r-knitr" ,r-knitr)))
15553 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
15554 (synopsis "Estimation and tests of hierarchical F-statistics")
15556 "This package allows the estimation of hierarchical F-statistics from
15557 haploid or diploid genetic data with any numbers of levels in the hierarchy,
15558 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
15559 are also given to test via randomisations the significance of each F and
15560 variance components, using the likelihood-ratio statistics G.")
15561 (license license:gpl2+)))
15563 (define-public r-hapassoc
15565 (name "r-hapassoc")
15570 (uri (cran-uri "hapassoc" version))
15573 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
15574 (build-system r-build-system)
15575 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
15576 (synopsis "Inference of trait associations with SNP haplotypes")
15578 "Hapassoc performs likelihood inference of trait associations with
15579 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
15580 functions are developed primarily for data collected in cohort or
15581 cross-sectional studies. They can accommodate uncertain haplotype phase and
15582 handle missing genotypes at some SNPs.")
15583 (license license:gpl2)))
15585 (define-public r-sampling
15587 (name "r-sampling")
15592 (uri (cran-uri "sampling" version))
15595 "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz"))))
15596 (build-system r-build-system)
15598 `(("r-lpsolve" ,r-lpsolve)
15599 ("r-mass" ,r-mass)))
15600 (home-page "https://cran.r-project.org/web/packages/sampling/")
15601 (synopsis "Survey sampling")
15603 "This package provides functions for drawing and calibrating samples.")
15604 (license license:gpl2+)))
15606 (define-public r-r2html
15613 (uri (cran-uri "R2HTML" version))
15616 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
15617 (properties `((upstream-name . "R2HTML")))
15618 (build-system r-build-system)
15619 (home-page "https://github.com/nalimilan/R2HTML")
15620 (synopsis "HTML export for R objects")
15622 "This package includes HTML functions and methods to write in an HTML
15623 file. Thus, making HTML reports is easy. It includes a function that allows
15624 redirection on the fly, which appears to be very useful for teaching purposes,
15625 as the student can keep a copy of the produced output to keep all that they
15626 did during the course. The package comes with a vignette describing how to
15627 write HTML reports for statistical analysis. Finally, a driver for Sweave
15628 parses HTML flat files containing R code and to automatically write
15629 the corresponding outputs (tables and graphs).")
15630 (license license:gpl2+)))
15632 (define-public r-rjava
15639 (uri (cran-uri "rJava" version))
15642 "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv"))))
15643 (properties `((upstream-name . "rJava")))
15644 (build-system r-build-system)
15646 `(#:modules ((guix build utils)
15647 (guix build r-build-system)
15650 (modify-phases %standard-phases
15651 (add-after 'unpack 'set-JAVA_HOME
15652 (lambda* (#:key inputs #:allow-other-keys)
15653 (let ((jdk (assoc-ref inputs "jdk")))
15654 (setenv "JAVA_HOME" jdk)
15655 (setenv "JAVA" (which "java"))
15656 (setenv "JAR" (which "jar"))
15657 (setenv "JAVAC" (which "javac"))
15658 (setenv "JAVAH" (which "javah"))
15659 (setenv "JAVA_CPPFLAGS"
15660 (string-append "-I" jdk "/include "
15661 "-I" jdk "/include/linux"))
15662 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
15663 ((lib) (setenv "JAVA_LIBS" lib))
15664 (_ (error "Could not find libjvm.so"))))
15668 ("jdk" ,icedtea-8 "jdk")
15671 (home-page "https://www.rforge.net/rJava/")
15672 (synopsis "Low-Level R to Java interface")
15674 "This package provides a low-level interface to the Java VM very much
15675 like .C/.Call and friends. It allows the creation of objects, calling methods
15676 and accessing fields.")
15677 (license license:gpl2)))
15679 (define-public r-svmisc
15686 (uri (cran-uri "svMisc" version))
15689 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
15690 (properties `((upstream-name . "svMisc")))
15691 (build-system r-build-system)
15692 (home-page "https://github.com/SciViews/svMisc")
15693 (synopsis "Miscellaneous functions for SciViews")
15695 "This package provides miscellaneous functions for SciViews or general
15696 use, including tools to manage a temporary environment attached to the search
15697 path for temporary variables you do not want to @code{save()} or
15698 @code{load()}; test the current platform; showing progress bars, etc.")
15699 (license license:gpl2)))
15701 (define-public r-xyz
15708 (uri (cran-uri "xyz" version))
15711 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
15712 (build-system r-build-system)
15714 `(("r-rcpp" ,r-rcpp)))
15715 (home-page "https://cran.r-project.org/web/packages/xyz/")
15716 (synopsis "Algorithm for fast interaction search in high-dimensional data")
15718 "High dimensional interaction search by brute force requires a quadratic
15719 computational cost in the number of variables. The xyz algorithm provably
15720 finds strong interactions in almost linear time. For details of the algorithm
15721 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
15722 interaction search in high-dimensional data.")
15723 ;; Any version of the GPL.
15724 (license license:gpl2+)))
15726 (define-public r-rttf2pt1
15728 (name "r-rttf2pt1")
15733 (uri (cran-uri "Rttf2pt1" version))
15736 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
15737 (properties `((upstream-name . "Rttf2pt1")))
15738 (build-system r-build-system)
15739 (home-page "https://github.com/wch/Rttf2pt1")
15740 (synopsis "Font conversion utility")
15742 "This package contains the program @code{ttf2pt1}, for use with the
15743 @code{extrafont} package.")
15744 ;; Most of the files are covered under the Expat license. Some files are
15745 ;; covered under BSD-3. Deviations for individual files are recorded in
15746 ;; the LICENSE file.
15747 (license (list license:bsd-3 license:expat
15748 (license:non-copyleft "file://LICENSE")))))
15750 (define-public r-extrafontdb
15752 (name "r-extrafontdb")
15757 (uri (cran-uri "extrafontdb" version))
15760 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
15761 (build-system r-build-system)
15762 (home-page "https://github.com/wch/extrafontdb")
15763 (synopsis "Database for the extrafont package")
15765 "This package holds the database for the @code{extrafont} package.")
15766 (license license:gpl2)))
15768 (define-public r-extrafont
15770 (name "r-extrafont")
15775 (uri (cran-uri "extrafont" version))
15778 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
15779 (build-system r-build-system)
15781 `(("r-extrafontdb" ,r-extrafontdb)
15782 ("r-rttf2pt1" ,r-rttf2pt1)))
15783 (home-page "https://github.com/wch/extrafont")
15784 (synopsis "Tools for using fonts in R")
15786 "The extrafont package makes it easier to use fonts other than the basic
15787 PostScript fonts that R uses. Fonts that are imported into extrafont can be
15788 used with PDF or PostScript output files. There are two hurdles for using
15789 fonts in PDF (or Postscript) output files:
15792 @item Making R aware of the font and the dimensions of the characters.
15793 @item Embedding the fonts in the PDF file so that the PDF can be displayed
15794 properly on a device that doesn't have the font. This is usually needed if
15795 you want to print the PDF file or share it with others.
15798 The extrafont package makes both of these things easier.")
15799 (license license:gpl2)))
15801 (define-public r-xkcd
15808 (uri (cran-uri "xkcd" version))
15811 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
15812 (build-system r-build-system)
15814 `(("r-extrafont" ,r-extrafont)
15815 ("r-ggplot2" ,r-ggplot2)
15816 ("r-hmisc" ,r-hmisc)))
15817 (home-page "https://cran.r-project.org/web/packages/xkcd/")
15818 (synopsis "Plot ggplot2 graphics in the XKCD style")
15820 "This package provides the means to plot ggplot2 graphs in the style of
15821 the XKCD web comic.")
15822 (license license:gpl3)))
15824 (define-public r-msigdbr
15831 (uri (cran-uri "msigdbr" version))
15834 "1rc2p9vw57pn4prmfgay4w18qd53ggq7wxfsi9kp7w25ciip1dq1"))))
15835 (build-system r-build-system)
15837 `(("r-dplyr" ,r-dplyr)
15838 ("r-magrittr" ,r-magrittr)
15839 ("r-rlang" ,r-rlang)
15840 ("r-tibble" ,r-tibble)
15841 ("r-tidyselect" ,r-tidyselect)))
15843 `(("r-knitr" ,r-knitr)))
15844 (home-page "https://github.com/igordot/msigdbr")
15845 (synopsis "MSigDB gene sets for multiple organisms")
15847 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
15848 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
15849 software in a standard R data frame with key-value pairs. Included are the
15850 original human gene symbols and Entrez IDs as well as the equivalents for
15851 various frequently studied model organisms such as mouse, rat, pig, fly, and
15853 ;; The package is covered under the Expat license, but the upstream MSigDB
15854 ;; files are made available under the Creative Commons Attribution 4.0
15855 ;; International license.
15856 (license (list license:expat license:cc-by4.0))))
15858 (define-public r-gridgraphics
15860 (name "r-gridgraphics")
15865 (uri (cran-uri "gridGraphics" version))
15868 "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219"))))
15869 (properties `((upstream-name . "gridGraphics")))
15870 (build-system r-build-system)
15871 (home-page "https://github.com/pmur002/gridgraphics")
15872 (synopsis "Redraw base graphics using @code{grid} graphics")
15874 "This package provides functions to convert a page of plots drawn with
15875 the @code{graphics} package into identical output drawn with the @code{grid}
15876 package. The result looks like the original @code{graphics}-based plot, but
15877 consists of @code{grid} grobs and viewports that can then be manipulated with
15878 @code{grid} functions (e.g., edit grobs and revisit viewports).")
15879 (license license:gpl2+)))
15881 (define-public r-farver
15888 (uri (cran-uri "farver" version))
15891 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
15892 (build-system r-build-system)
15893 (home-page "https://github.com/thomasp85/farver")
15894 (synopsis "Vectorized color conversion and comparison")
15896 "The encoding of color can be handled in many different ways, using
15897 different color spaces. As different color spaces have different uses,
15898 efficient conversion between these representations are important. This
15899 package provides a set of functions that gives access to very fast color space
15900 conversion and comparisons implemented in C++, and offers 100-fold speed
15901 improvements over the @code{convertColor} function in the @code{grDevices}
15903 (license license:expat)))
15905 (define-public r-ggplotify
15907 (name "r-ggplotify")
15912 (uri (cran-uri "ggplotify" version))
15915 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
15916 (build-system r-build-system)
15918 `(("r-ggplot2" ,r-ggplot2)
15919 ("r-gridgraphics" ,r-gridgraphics)
15920 ("r-rvcheck" ,r-rvcheck)))
15922 `(("r-knitr" ,r-knitr)))
15923 (home-page "https://github.com/GuangchuangYu/ggplotify")
15924 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
15926 "This package provides tools to convert plot function calls (using
15927 expression or formula) to @code{grob} or @code{ggplot} objects that are
15928 compatible with the @code{grid} and @code{ggplot2} environment. With this
15929 package, we are able to e.g. use @code{cowplot} to align plots produced by
15930 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
15931 converting them to @code{ggplot} objects.")
15932 (license license:artistic2.0)))
15934 (define-public r-triebeard
15936 (name "r-triebeard")
15941 (uri (cran-uri "triebeard" version))
15944 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
15945 (build-system r-build-system)
15946 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15947 (home-page "https://github.com/Ironholds/triebeard/")
15948 (synopsis "Radix trees in Rcpp")
15950 "Radix trees, or tries, are key-value data structures optimized for
15951 efficient lookups, similar in purpose to hash tables. This package provides
15952 an implementation of radix trees for use in R programming and in developing
15953 packages with Rcpp.")
15954 (license license:expat)))
15956 (define-public r-tweenr
15963 (uri (cran-uri "tweenr" version))
15966 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
15967 (build-system r-build-system)
15969 `(("r-farver" ,r-farver)
15970 ("r-magrittr" ,r-magrittr)
15972 ("r-rlang" ,r-rlang)))
15973 (home-page "https://github.com/thomasp85/tweenr")
15974 (synopsis "Interpolate data for smooth animations")
15976 "In order to create smooth animation between states of data, tweening is
15977 necessary. This package provides a range of functions for creating tweened
15978 data that can be used as basis for animation. Furthermore it adds a number of
15979 vectorized interpolaters for common R data types such as numeric, date and
15981 (license license:expat)))
15983 (define-public r-polyclip
15985 (name "r-polyclip")
15990 (uri (cran-uri "polyclip" version))
15993 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
15994 (build-system r-build-system)
15995 (native-inputs `(("pkg-config" ,pkg-config)))
15996 (home-page "http://www.angusj.com/delphi/clipper.php")
15997 (synopsis "Polygon clipping")
15999 "This package provides an R port of the library Clipper. It performs
16000 polygon clipping operations (intersection, union, set minus, set difference)
16001 for polygonal regions of arbitrary complexity, including holes. It computes
16002 offset polygons (spatial buffer zones, morphological dilations, Minkowski
16003 dilations) for polygonal regions and polygonal lines. It computes the
16004 Minkowski Sum of general polygons. There is a function for removing
16005 self-intersections from polygon data.")
16006 (license license:boost1.0)))
16008 (define-public r-urltools
16010 (name "r-urltools")
16015 (uri (cran-uri "urltools" version))
16018 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
16019 (build-system r-build-system)
16021 `(("r-rcpp" ,r-rcpp)
16022 ("r-triebeard" ,r-triebeard)))
16023 (home-page "https://github.com/Ironholds/urltools/")
16024 (synopsis "Vectorized tools for URL handling and parsing")
16026 "This package provides a toolkit for all URL-handling needs, including
16027 encoding and decoding, parsing, parameter extraction and modification. All
16028 functions are designed to be both fast and entirely vectorized. It is
16029 intended to be useful for people dealing with web-related datasets, such as
16030 server-side logs, although may be useful for other situations involving large
16032 (license license:expat)))
16034 (define-public r-ggforce
16041 (uri (cran-uri "ggforce" version))
16044 "1lplxyq5bgx90dgaimhynpcywag1gp6vlsy7q52ay1nfc35qmkjc"))))
16045 (build-system r-build-system)
16047 `(("r-ggplot2" ,r-ggplot2)
16048 ("r-gtable" ,r-gtable)
16050 ("r-polyclip" ,r-polyclip)
16052 ("r-rcppeigen" ,r-rcppeigen)
16053 ("r-rlang" ,r-rlang)
16054 ("r-scales" ,r-scales)
16055 ("r-tidyselect" ,r-tidyselect)
16056 ("r-tweenr" ,r-tweenr)
16057 ("r-withr" ,r-withr)))
16058 (home-page "https://ggforce.data-imaginist.com")
16059 (synopsis "Accelerating ggplot2")
16061 "The aim of the ggplot2 package is to aid in visual data investigations.
16062 This focus has led to a lack of facilities for composing specialized plots.
16063 Thi package aims to be a collection of mainly new statistics and geometries
16064 that fills this gap.")
16065 (license license:expat)))
16067 (define-public r-europepmc
16069 (name "r-europepmc")
16074 (uri (cran-uri "europepmc" version))
16077 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
16078 (build-system r-build-system)
16080 `(("r-dplyr" ,r-dplyr)
16082 ("r-jsonlite" ,r-jsonlite)
16084 ("r-progress" ,r-progress)
16085 ("r-purrr" ,r-purrr)
16086 ("r-rlang" ,r-rlang)
16087 ("r-tibble" ,r-tibble)
16088 ("r-tidyr" ,r-tidyr)
16089 ("r-urltools" ,r-urltools)
16090 ("r-xml2" ,r-xml2)))
16092 `(("r-knitr" ,r-knitr)))
16093 (home-page "https://github.com/ropensci/europepmc/")
16094 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
16096 "This package provides an R Client for the
16097 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
16098 Service}. It gives access to both metadata on life science literature and
16099 open access full texts. Europe PMC indexes all PubMed content and other
16100 literature sources including Agricola, a bibliographic database of citations
16101 to the agricultural literature, or Biological Patents. In addition to
16102 bibliographic metadata, the client allows users to fetch citations and
16103 reference lists. Links between life-science literature and other EBI
16104 databases, including ENA, PDB or ChEMBL are also accessible.")
16105 (license license:gpl3)))
16107 (define-public r-ggraph
16114 (uri (cran-uri "ggraph" version))
16117 "1j3xf4fsv0i0gbppdrw4yprfyk53wx6s8nvnkipi2ywbm7cr4q4w"))))
16118 (build-system r-build-system)
16120 `(("r-digest" ,r-digest)
16121 ("r-dplyr" ,r-dplyr)
16122 ("r-ggforce" ,r-ggforce)
16123 ("r-ggplot2" ,r-ggplot2)
16124 ("r-ggrepel" ,r-ggrepel)
16125 ("r-graphlayouts" ,r-graphlayouts)
16126 ("r-gtable" ,r-gtable)
16127 ("r-igraph" ,r-igraph)
16130 ("r-rlang" ,r-rlang)
16131 ("r-scales" ,r-scales)
16132 ("r-tidygraph" ,r-tidygraph)
16133 ("r-viridis" ,r-viridis)
16134 ("r-withr" ,r-withr)))
16136 `(("r-knitr" ,r-knitr)))
16137 (home-page "https://cran.r-project.org/web/packages/ggraph/")
16138 (synopsis "Implementation of grammar of graphics for graphs and networks")
16140 "The grammar of graphics as implemented in ggplot2 is a poor fit for
16141 graph and network visualizations due to its reliance on tabular data input.
16142 The ggraph package is an extension of the ggplot2 API tailored to graph
16143 visualizations and provides the same flexible approach to building up plots
16145 (license license:gpl3)))
16147 (define-public r-varselrf
16149 (name "r-varselrf")
16154 (uri (cran-uri "varSelRF" version))
16157 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
16158 (properties `((upstream-name . "varSelRF")))
16159 (build-system r-build-system)
16161 `(("r-randomforest" ,r-randomforest)))
16162 (home-page "https://www.ligarto.org/rdiaz/software/software")
16163 (synopsis "Variable selection using random forests")
16165 "This package provides tools for the variable selection from random
16166 forests using both backwards variable elimination (for the selection of small
16167 sets of non-redundant variables) and selection based on the importance
16168 spectrum (somewhat similar to scree plots; for the selection of large,
16169 potentially highly-correlated variables). The main applications are in
16170 high-dimensional data (e.g., microarray data, and other genomics and
16171 proteomics applications).")
16172 (license license:gpl2+)))
16174 (define-public r-pamr
16181 (uri (cran-uri "pamr" version))
16184 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
16185 (build-system r-build-system)
16187 `(("r-cluster" ,r-cluster)
16188 ("r-survival" ,r-survival)))
16189 (native-inputs `(("gfortran" ,gfortran)))
16190 (home-page "https://cran.r-project.org/web/packages/pamr/")
16191 (synopsis "Prediction Analysis for Microarrays")
16193 "This package provides some functions for sample classification in
16195 (license license:gpl2)))
16197 (define-public r-rda
16200 (version "1.0.2-2.1")
16204 (uri (cran-uri "rda" version))
16207 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
16208 (build-system r-build-system)
16209 (home-page "https://cran.r-project.org/web/packages/rda/")
16210 (synopsis "Shrunken centroids regularized discriminant analysis")
16212 "This package provides tools for shrunken centroids regularized
16213 discriminant analysis for the purpose of classifying high dimensional data.")
16214 (license license:gpl2+)))
16216 (define-public r-ggvis
16223 (uri (cran-uri "ggvis" version))
16226 "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy"))))
16227 (build-system r-build-system)
16229 `(("r-assertthat" ,r-assertthat)
16230 ("r-dplyr" ,r-dplyr)
16231 ("r-htmltools" ,r-htmltools)
16232 ("r-jsonlite" ,r-jsonlite)
16233 ("r-magrittr" ,r-magrittr)
16234 ("r-rlang" ,r-rlang)
16235 ("r-shiny" ,r-shiny)))
16236 (home-page "https://ggvis.rstudio.com/")
16237 (synopsis "Interactive grammar of graphics")
16239 "This package is a data visualization package for R providing an
16240 implementation of an interactive grammar of graphics, taking the best parts of
16241 ggplot2, combining them with the reactive framework of Shiny and drawing web
16242 graphics using Vega.")
16243 (license license:gpl2)))
16245 (define-public r-gbm
16252 (uri (cran-uri "gbm" version))
16255 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
16256 (build-system r-build-system)
16258 `(("r-lattice" ,r-lattice)
16259 ("r-survival" ,r-survival)))
16261 `(("r-knitr" ,r-knitr)))
16262 (home-page "https://github.com/gbm-developers/gbm")
16263 (synopsis "Generalized boosted regression models")
16265 "This package is an implementation of extensions to Freund and Schapire's
16266 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
16267 regression methods for least squares, absolute loss, t-distribution loss,
16268 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
16269 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
16270 and Learning to Rank measures (LambdaMart).")
16271 (license license:gpl2+)))
16273 (define-public r-threejs
16280 (uri (cran-uri "threejs" version))
16283 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
16284 (build-system r-build-system)
16286 `(#:modules ((guix build utils)
16287 (guix build r-build-system)
16291 (modify-phases %standard-phases
16292 (add-after 'unpack 'process-javascript
16293 (lambda* (#:key inputs #:allow-other-keys)
16294 (with-directory-excursion "inst"
16298 `((,(assoc-ref inputs "js-jquery")
16299 "htmlwidgets/lib/jquery/jquery.min.js")
16300 (,(assoc-ref inputs "js-threejs-111")
16301 "htmlwidgets/lib/threejs-111/three.min.js"))))
16302 (lambda (sources targets)
16303 (for-each (lambda (source target)
16304 (format #t "Processing ~a --> ~a~%"
16306 (delete-file target)
16307 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16308 (call-with-output-file target
16310 (dump-port minified port)))))
16311 sources targets))))
16314 `(("r-base64enc" ,r-base64enc)
16315 ("r-crosstalk" ,r-crosstalk)
16316 ("r-htmlwidgets" ,r-htmlwidgets)
16317 ("r-igraph" ,r-igraph)))
16319 `(("uglify-js" ,uglify-js)
16323 (uri "https://code.jquery.com/jquery-1.12.4.js")
16326 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
16330 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
16333 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
16334 (home-page "https://bwlewis.github.io/rthreejs")
16335 (synopsis "Interactive 3D scatter plots, networks and globes")
16337 "Create interactive 3D scatter plots, network plots, and globes in R
16338 using the three.js visualization library.")
16339 (license license:expat)))
16341 (define-public r-mlbench
16348 (uri (cran-uri "mlbench" version))
16351 "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi"))))
16352 (build-system r-build-system)
16353 (home-page "https://cran.r-project.org/web/packages/mlbench/")
16354 (synopsis "Machine learning benchmark problems")
16356 "This package provides a collection of artificial and real-world machine
16357 learning benchmark problems, including, e.g., several data sets from the UCI
16359 (license license:gpl2)))
16361 (define-public r-mpm
16368 (uri (cran-uri "mpm" version))
16371 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
16372 (build-system r-build-system)
16374 `(("r-kernsmooth" ,r-kernsmooth)
16375 ("r-mass" ,r-mass)))
16376 (home-page "http://mpm.r-forge.r-project.org")
16377 (synopsis "Multivariate projection methods")
16379 "This is a package for exploratory graphical analysis of multivariate
16380 data, specifically gene expression data with different projection methods:
16381 principal component analysis, correspondence analysis, spectral map
16383 (license license:gpl2+)))
16385 (define-public r-png
16391 (uri (cran-uri "png" version))
16394 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
16395 (build-system r-build-system)
16397 `(("libpng" ,libpng)
16399 (home-page "https://www.rforge.net/png/")
16400 (synopsis "Read and write PNG images")
16402 "This package provides an easy and simple way to read, write and display
16403 bitmap images stored in the PNG format. It can read and write both files and
16404 in-memory raw vectors.")
16405 ;; Any of these GPL versions.
16406 (license (list license:gpl2 license:gpl3))))
16408 (define-public r-ggcorrplot
16410 (name "r-ggcorrplot")
16415 (uri (cran-uri "ggcorrplot" version))
16418 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
16419 (build-system r-build-system)
16421 `(("r-ggplot2" ,r-ggplot2)
16422 ("r-reshape2" ,r-reshape2)))
16423 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
16424 (synopsis "Visualization of a correlation matrix using ggplot2")
16426 "The ggcorrplot package can be used to visualize easily a correlation
16427 matrix using ggplot2. It provides a solution for reordering the correlation
16428 matrix and displays the significance level on the plot. It also includes a
16429 function for computing a matrix of correlation p-values.")
16430 (license license:gpl2)))
16432 ;; This package includes minified JavaScript files. When upgrading please
16433 ;; check that there are no new minified JavaScript files.
16434 (define-public r-flexdashboard
16436 (name "r-flexdashboard")
16441 (uri (cran-uri "flexdashboard" version))
16444 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
16445 (modules '((guix build utils)))
16448 ;; Delete bundled minified JavaScript files
16449 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
16450 (delete-file "inst/www/sly/sly.min.js")
16451 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
16452 (delete-file "inst/www/prism/prism.js")
16454 (build-system r-build-system)
16456 `(#:modules ((guix build utils)
16457 (guix build r-build-system)
16461 (ice-9 textual-ports))
16463 (modify-phases %standard-phases
16464 (add-after 'unpack 'process-javascript
16465 (lambda* (#:key inputs #:allow-other-keys)
16466 (with-directory-excursion "inst"
16467 ;; Concatenate all components of prism.js
16468 (let ((contents (string-join
16469 (map (lambda (name)
16470 (call-with-input-file
16471 (assoc-ref inputs name)
16475 "js-prism-line-numbers"))
16477 (call-with-output-file "prism-src.js"
16478 (cut display contents <>)))
16482 `(("www/stickytableheaders/jquery.stickytableheaders.js"
16483 "www/stickytableheaders/jquery.stickytableheaders.min.js")
16485 "www/sly/sly.min.js")
16487 "www/prism/prism.js")
16488 (,(assoc-ref inputs "js-raphael")
16489 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
16490 (,(assoc-ref inputs "js-featherlight")
16491 "www/featherlight/featherlight.min.js"))))
16492 (lambda (sources targets)
16493 (for-each (lambda (source target)
16494 (format #t "Processing ~a --> ~a~%"
16496 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16497 (call-with-output-file target
16499 (dump-port minified port)))))
16500 sources targets))))
16503 `(("r-htmltools" ,r-htmltools)
16504 ("r-htmlwidgets" ,r-htmlwidgets)
16505 ("r-jsonlite" ,r-jsonlite)
16506 ("r-knitr" ,r-knitr)
16507 ("r-rmarkdown" ,r-rmarkdown)
16508 ("r-shiny" ,r-shiny)))
16510 `(("uglify-js" ,uglify-js)
16514 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
16517 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
16521 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
16524 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
16528 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
16531 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
16532 ("js-prism-line-numbers"
16535 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
16538 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
16542 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
16545 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
16546 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
16547 (synopsis "R Markdown format for flexible dashboards")
16549 "This package provides an R Markdown format for converting an R Markdown
16550 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
16551 of its components to the containing web page.")
16552 (license license:expat)))
16554 (define-public r-preseqr
16561 (uri (cran-uri "preseqR" version))
16564 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
16565 (properties `((upstream-name . "preseqR")))
16566 (build-system r-build-system)
16568 `(("r-polynom" ,r-polynom)))
16569 (home-page "https://cran.r-project.org/web/packages/preseqR/")
16570 (synopsis "Predicting species accumulation curves")
16572 "This package can be used to predict the r-species accumulation
16573 curve (r-SAC), which is the number of species represented at least r times as
16574 a function of the sampling effort. When r = 1, the curve is known as the
16575 species accumulation curve, or the library complexity curve in high-throughput
16576 genomic sequencing. The package includes both parametric and nonparametric
16577 methods, as described by Deng C, et al. (2018).")
16578 (license license:gpl3)))
16580 (define-public r-mapplots
16582 (name "r-mapplots")
16587 (uri (cran-uri "mapplots" version))
16590 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
16591 (build-system r-build-system)
16592 (home-page "https://cran.r-project.org/web/packages/mapplots/")
16593 (synopsis "Data visualization on maps")
16595 "This package helps you create simple maps; add sub-plots like pie plots
16596 to a map or any other plot; format, plot and export gridded data. The package
16597 was developed for displaying fisheries data but most functions can be used for
16598 more generic data visualisation.")
16599 (license license:gpl2+)))
16601 (define-public r-pmcmr
16608 (uri (cran-uri "PMCMR" version))
16611 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
16612 (properties `((upstream-name . "PMCMR")))
16613 (build-system r-build-system)
16614 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
16615 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
16617 "This is a deprecated package for calculating pairwise multiple
16618 comparisons of mean rank sums. This package is superseded by the novel
16619 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
16620 compatibility of dependent packages for some time.")
16621 (license license:gpl3+)))
16623 (define-public r-downloader
16625 (name "r-downloader")
16630 (uri (cran-uri "downloader" version))
16633 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
16634 (build-system r-build-system)
16636 `(("r-digest" ,r-digest)))
16637 (home-page "https://github.com/wch/downloader")
16638 (synopsis "Download files over HTTP and HTTPS")
16640 "This package provides a wrapper for the @code{download.file} function,
16641 making it possible to download files over HTTPS across platforms. The
16642 @code{RCurl} package provides this functionality (and much more) but has
16643 external dependencies. This package has is implemented purely in R.")
16644 (license license:gpl2)))
16646 (define-public r-rex
16653 (uri (cran-uri "rex" version))
16656 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
16657 (build-system r-build-system)
16659 `(("r-lazyeval" ,r-lazyeval)))
16661 `(("r-knitr" ,r-knitr)))
16662 (home-page "https://github.com/kevinushey/rex")
16663 (synopsis "Friendly regular expressions")
16665 "This package provides a friendly interface for the construction of
16666 regular expressions. Regular expressions are a very powerful feature, however
16667 they are often difficult to interpret. Rex allows you to build complex
16668 regular expressions from human readable expressions")
16669 (license license:expat)))
16671 (define-public r-xmlparsedata
16673 (name "r-xmlparsedata")
16678 (uri (cran-uri "xmlparsedata" version))
16681 "177vfyjrqfi3wam8scpsradap1lv35yc25xq745dr7gabg116yrq"))))
16682 (properties `((upstream-name . "xmlparsedata")))
16683 (build-system r-build-system)
16684 (home-page "https://github.com/r-lib/xmlparsedata#readme")
16685 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
16687 "This package provides tools to convert the output of
16688 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
16689 @code{XPath}, and is easier to manipulate in general.")
16690 (license license:expat)))
16692 (define-public r-cyclocomp
16694 (name "r-cyclocomp")
16699 (uri (cran-uri "cyclocomp" version))
16702 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
16703 (properties `((upstream-name . "cyclocomp")))
16704 (build-system r-build-system)
16706 `(("r-callr" ,r-callr)
16707 ("r-crayon" ,r-crayon)
16709 ("r-remotes" ,r-remotes)
16710 ("r-withr" ,r-withr)))
16711 (home-page "https://github.com/MangoTheCat/cyclocomp")
16712 (synopsis "Cyclomatic complexity of R code")
16714 "Cyclomatic complexity is a software metric, used to indicate the
16715 complexity of a program. It is a quantitative measure of the number of
16716 linearly independent paths through a program's source code. This package
16717 provides tools to compute this metric.")
16718 (license license:expat)))
16720 (define-public r-lintr
16727 (uri (cran-uri "lintr" version))
16730 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
16731 (properties `((upstream-name . "lintr")))
16732 (build-system r-build-system)
16734 `(("r-codetools" ,r-codetools)
16735 ("r-crayon" ,r-crayon)
16736 ("r-cyclocomp" ,r-cyclocomp)
16737 ("r-digest" ,r-digest)
16739 ("r-jsonlite" ,r-jsonlite)
16740 ("r-knitr" ,r-knitr)
16742 ("r-rstudioapi" ,r-rstudioapi)
16743 ("r-testthat" ,r-testthat)
16745 ("r-xmlparsedata" ,r-xmlparsedata)))
16746 (home-page "https://github.com/jimhester/lintr")
16747 (synopsis "Linter for R code")
16748 (description "This package checks adherence to a given style, syntax
16749 errors and possible semantic issues. It supports on the fly checking of R
16750 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
16751 (license license:expat)))
16753 (define-public r-sctransform
16755 (name "r-sctransform")
16760 (uri (cran-uri "sctransform" version))
16763 "1p3m6i28nlxh6r609syn88cwlbdpl3dw44dy3gsijk2ibq20mfsx"))))
16764 (build-system r-build-system)
16766 `(("r-future" ,r-future)
16767 ("r-future-apply" ,r-future-apply)
16768 ("r-ggplot2" ,r-ggplot2)
16769 ("r-gridextra" ,r-gridextra)
16771 ("r-matrix" ,r-matrix)
16772 ("r-matrixstats" ,r-matrixstats)
16774 ("r-rcpparmadillo" ,r-rcpparmadillo)
16775 ("r-reshape2" ,r-reshape2)))
16776 (home-page "https://github.com/ChristophH/sctransform")
16777 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
16779 "This package provides a normalization method for single-cell UMI count
16780 data using a variance stabilizing transformation. The transformation is based
16781 on a negative binomial regression model with regularized parameters. As part
16782 of the same regression framework, this package also provides functions for
16783 batch correction, and data correction.")
16784 (license license:gpl3)))
16786 (define-public r-styler
16793 (uri (cran-uri "styler" version))
16796 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
16797 (build-system r-build-system)
16799 `(("r-backports" ,r-backports)
16801 ("r-magrittr" ,r-magrittr)
16802 ("r-purrr" ,r-purrr)
16803 ("r-r-cache" ,r-r-cache)
16804 ("r-rematch2" ,r-rematch2)
16805 ("r-rlang" ,r-rlang)
16806 ("r-rprojroot" ,r-rprojroot)
16807 ("r-tibble" ,r-tibble)
16808 ("r-withr" ,r-withr)
16809 ("r-xfun" ,r-xfun)))
16810 (home-page "https://github.com/r-lib/styler")
16811 (synopsis "Non-invasive pretty printing of R code")
16813 "This is a package for pretty-printing R code without changing the user's
16814 formatting intent.")
16815 (license license:gpl3)))
16817 (define-public r-scrime
16824 (uri (cran-uri "scrime" version))
16827 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
16828 (build-system r-build-system)
16829 (home-page "https://cran.r-project.org/web/packages/scrime/")
16830 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
16832 "This package provides tools for the analysis of high-dimensional data
16833 developed/implemented at the group \"Statistical Complexity Reduction In
16834 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
16835 the functions can also be applied to other types of categorical data.")
16836 (license license:gpl2)))
16838 (define-public r-pbmcapply
16840 (name "r-pbmcapply")
16845 (uri (cran-uri "pbmcapply" version))
16848 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
16849 (build-system r-build-system)
16850 (home-page "https://github.com/kvnkuang/pbmcapply")
16851 (synopsis "Track the progress of apply procedures with a progress bar")
16853 "This light-weight package helps you track and visualize the progress of
16854 parallel versions of vectorized R functions of the @code{mc*apply} family.")
16855 (license license:expat)))
16857 (define-public r-blme
16864 (uri (cran-uri "blme" version))
16867 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7"))))
16868 (build-system r-build-system)
16869 (propagated-inputs `(("r-lme4" ,r-lme4)))
16870 (home-page "https://github.com/vdorie/blme")
16871 (synopsis "Bayesian linear mixed-effects models")
16873 "This package provides tools for maximum a posteriori estimation for
16874 linear and generalized linear mixed-effects models in a Bayesian setting. It
16875 extends the lme4 package.")
16876 (license license:gpl2+)))
16878 (define-public r-batchtools
16880 (name "r-batchtools")
16885 (uri (cran-uri "batchtools" version))
16888 "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52"))))
16889 (build-system r-build-system)
16891 `(("r-backports" ,r-backports)
16892 ("r-base64url" ,r-base64url)
16894 ("r-checkmate" ,r-checkmate)
16895 ("r-data-table" ,r-data-table)
16896 ("r-digest" ,r-digest)
16898 ("r-progress" ,r-progress)
16900 ("r-rappdirs" ,r-rappdirs)
16901 ("r-stringi" ,r-stringi)
16902 ("r-withr" ,r-withr)))
16904 `(("r-knitr" ,r-knitr)))
16905 (home-page "https://github.com/mllg/batchtools")
16906 (synopsis "Tools for computation on batch systems")
16908 "As a successor of the packages BatchJobs and BatchExperiments, this
16909 package provides a parallel implementation of the Map function for high
16910 performance computing systems managed by various schedulers. A multicore and
16911 socket mode allow the parallelization on a local machines, and multiple
16912 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
16913 the package provides an abstraction mechanism to define large-scale computer
16914 experiments in a well-organized and reproducible way.")
16915 (license license:lgpl3)))
16917 (define-public r-clue
16924 (uri (cran-uri "clue" version))
16927 "1rwwxlnpl1k0n4k96vxc9zajw9kb4syqwzj76fvaf0qim8p6ddia"))))
16928 (build-system r-build-system)
16929 (propagated-inputs `(("r-cluster" ,r-cluster)))
16930 (home-page "https://cran.r-project.org/web/packages/clue/")
16931 (synopsis "Tools for analyzing cluster ensembles")
16932 (description "Cluster ensembles are collections of individual solutions to
16933 a given clustering problem which are useful or necessary to consider in a wide
16934 range of applications. This R package provides an extensible computational
16935 environment for creating and analyzing cluster ensembles, with basic data
16936 structures for representing partitions and hierarchies, and facilities for
16937 computing on them, including methods for measuring proximity and obtaining
16938 consensus and secondary clusterings.")
16939 (license license:gpl2)))
16941 (define-public r-sitmo
16948 (uri (cran-uri "sitmo" version))
16951 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
16952 (build-system r-build-system)
16953 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16954 (home-page "https://github.com/coatless/sitmo/")
16955 (synopsis "Parallel pseudo random number generator header files")
16957 "This package provides two high quality and fast PPRNGs that may be used
16958 in an OpenMP parallel environment. In addition, there is a generator for one
16959 dimensional low-discrepancy sequence.")
16960 (license license:expat)))
16962 (define-public r-dqrng
16969 (uri (cran-uri "dqrng" version))
16972 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
16973 (build-system r-build-system)
16977 ("r-sitmo" ,r-sitmo)))
16978 (home-page "https://www.daqana.org/dqrng")
16979 (synopsis "Fast pseudo random number generators")
16981 "Several fast random number generators are provided as C++ header-only
16982 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
16983 Additionally, fast functions for generating random numbers according to a
16984 uniform, normal and exponential distribution are included. The latter two use
16985 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
16986 functions are exported to R and as a C++ interface and are enabled for use
16987 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
16988 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
16989 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
16990 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
16991 ;; whole is distributed under the terms of the AGPL 3.
16992 (license license:agpl3)))
16994 (define-public r-ingredients
16996 (name "r-ingredients")
17001 (uri (cran-uri "ingredients" version))
17004 "0w46h1f28y5ypqm3ypsvk7yk9v7k8p21f1pzjl3ima8r1ivmhv12"))))
17005 (properties `((upstream-name . "ingredients")))
17006 (build-system r-build-system)
17008 `(("r-ggplot2" ,r-ggplot2)
17009 ("r-gridextra" ,r-gridextra)
17010 ("r-scales" ,r-scales)))
17011 (native-inputs `(("r-knitr" ,r-knitr)))
17012 (home-page "https://ModelOriented.github.io/ingredients/")
17013 (synopsis "Effects and importances of model ingredients")
17015 "This is a collection of tools for assessment of feature importance and
17016 feature effects. Key functions are:
17019 @item @code{feature_importance()} for assessment of global level feature
17021 @item @code{ceteris_paribus()} for calculation of the what-if plots,
17022 @item @code{partial_dependence()} for partial dependence plots,
17023 @item @code{conditional_dependence()} for conditional dependence plots,
17024 @item @code{accumulated_dependence()} for accumulated local effects plots,
17025 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
17026 aggregation of ceteris paribus profiles,
17027 @item generic @code{print()} and @code{plot()} for better usability of
17028 selected explainers,
17029 @item generic @code{plotD3()} for interactive, D3 based explanations, and
17030 @item generic @code{describe()} for explanations in natural language.
17032 (license license:gpl3)))
17034 (define-public r-ibreakdown
17036 (name "r-ibreakdown")
17041 (uri (cran-uri "iBreakDown" version))
17044 "1bfl5bh0x6z5a0cmdmx68sap9zdxa3kwdnyk57csxapc362yz108"))))
17045 (properties `((upstream-name . "iBreakDown")))
17046 (build-system r-build-system)
17047 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
17048 (native-inputs `(("r-knitr" ,r-knitr)))
17049 (home-page "https://ModelOriented.github.io/iBreakDown/")
17050 (synopsis "Model agnostic instance level variable attributions")
17052 "This package provides a model agnostic tool for decomposition of
17053 predictions from black boxes. It supports additive attributions and
17054 attributions with interactions. The Break Down Table shows contributions of
17055 every variable to a final prediction. The Break Down Plot presents variable
17056 contributions in a concise graphical way. This package works for
17057 classification and regression models.")
17058 (license license:gpl3)))
17060 (define-public r-dae
17067 (uri (cran-uri "dae" version))
17070 "126w1lb9pz8mb2ajl2vz5dj798nbifp0dypnzfgcwixif5g5bpqi"))))
17071 (build-system r-build-system)
17073 `(("r-ggplot2" ,r-ggplot2)
17074 ("r-plyr" ,r-plyr)))
17076 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
17077 (home-page "http://chris.brien.name")
17078 (synopsis "Functions useful in the design and ANOVA of experiments")
17080 "This package provides functions useful in the design and ANOVA of
17081 experiments. The content falls into the following groupings:
17085 @item factor manipulation functions,
17086 @item design functions,
17087 @item ANOVA functions,
17088 @item matrix functions,
17089 @item projector and canonical efficiency functions, and
17090 @item miscellaneous functions.
17093 There is a vignette called @code{DesignNotes} describing how to use the design
17094 functions for randomizing and assessing designs. The ANOVA functions
17095 facilitate the extraction of information when the @code{Error} function has
17096 been used in the call to @code{aov}.")
17097 (license license:gpl2)))
17099 (define-public r-dalex
17106 (uri (cran-uri "DALEX" version))
17109 "1hiknx55d91abyfj3w4a2xxin7f1q8h5k0041m7w93xjdc4kis98"))))
17110 (properties `((upstream-name . "DALEX")))
17111 (build-system r-build-system)
17113 `(("r-ggplot2" ,r-ggplot2)
17114 ("r-ibreakdown" ,r-ibreakdown)
17115 ("r-ingredients" ,r-ingredients)))
17116 (home-page "https://pbiecek.github.io/DALEX/")
17117 (synopsis "Descriptive machine learning explanations")
17119 "Machine Learning models are widely used and have various applications in
17120 classification or regression. Models created with boosting, bagging, stacking
17121 or similar techniques are often used due to their high performance, but such
17122 black-box models usually lack interpretability. The DALEX package contains
17123 various explainers that help to understand the link between input variables
17124 and model output.")
17125 ;; Any version of the GPL
17126 (license license:gpl3+)))
17128 (define-public r-enrichr
17135 (uri (cran-uri "enrichR" version))
17138 "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3"))))
17139 (properties `((upstream-name . "enrichR")))
17140 (build-system r-build-system)
17142 `(("r-ggplot2" ,r-ggplot2)
17144 ("r-rjson" ,r-rjson)))
17146 `(("r-knitr" ,r-knitr)))
17147 (home-page "https://cran.r-project.org/web/packages/enrichR/")
17148 (synopsis "R Interface to Enrichr database for analyzing gene sets")
17150 "This package provides an R interface to all Enrichr databases, a
17151 web-based tool for analyzing gene sets and returns any enrichment of common
17152 annotated biological functions.")
17153 (license license:gpl2+)))
17155 (define-public r-plot3d
17162 (uri (cran-uri "plot3D" version))
17165 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
17166 (properties `((upstream-name . "plot3D")))
17167 (build-system r-build-system)
17168 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
17169 (home-page "https://cran.r-project.org/web/packages/plot3D")
17170 (synopsis "Plot multi-dimensional data")
17172 "This package provides functions for viewing 2D and 3D data, including
17173 perspective plots, slice plots, surface plots, scatter plots, etc. It
17174 includes data sets from oceanography.")
17175 (license license:gpl3+)))
17177 (define-public r-ggfortify
17179 (name "r-ggfortify")
17184 (uri (cran-uri "ggfortify" version))
17187 "1wfm7l9bz6msh7rflgfv9dgbxh1ikz2ay0v7sgk9nkc24y6lhbpk"))))
17188 (build-system r-build-system)
17190 `(("r-dplyr" ,r-dplyr)
17191 ("r-ggplot2" ,r-ggplot2)
17192 ("r-gridextra" ,r-gridextra)
17193 ("r-scales" ,r-scales)
17194 ("r-stringr" ,r-stringr)
17195 ("r-tibble" ,r-tibble)
17196 ("r-tidyr" ,r-tidyr)))
17198 `(("r-knitr" ,r-knitr)))
17199 (home-page "https://github.com/sinhrks/ggfortify")
17200 (synopsis "Data visualization tools for statistical analysis results")
17202 "This package provides unified plotting tools for statistics commonly
17203 used, such as GLM, time series, PCA families, clustering and survival
17204 analysis. The package offers a single plotting interface for these analysis
17205 results and plots in a unified style using the @code{ggplot2} package.")
17206 (license license:gpl2)))
17208 (define-public r-refmanager
17210 (name "r-refmanager")
17215 (uri (cran-uri "RefManageR" version))
17218 "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps"))))
17219 (properties `((upstream-name . "RefManageR")))
17220 (build-system r-build-system)
17222 `(("r-httr" ,r-httr)
17223 ("r-jsonlite" ,r-jsonlite)
17224 ("r-lubridate" ,r-lubridate)
17226 ("r-stringr" ,r-stringr)
17227 ("r-xml2" ,r-xml2)))
17229 `(("r-knitr" ,r-knitr)))
17230 (home-page "https://github.com/ropensci/RefManageR/")
17231 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
17233 "This package provides tools for importing and working with bibliographic
17234 references. It greatly enhances the @code{bibentry} class by providing a
17235 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
17236 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
17237 by various formats for name lists (author by last names, translator by full
17238 names, etc.). Entries can be updated, combined, sorted, printed in a number
17239 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
17240 into R and converted to @code{BibEntry} objects.")
17241 ;; Any of these licenses may be picked.
17242 (license (list license:gpl2 license:gpl3 license:bsd-3))))
17244 (define-public r-citr
17251 (uri (cran-uri "citr" version))
17254 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
17255 (build-system r-build-system)
17257 `(("r-assertthat" ,r-assertthat)
17260 ("r-miniui" ,r-miniui)
17261 ("r-refmanager" ,r-refmanager)
17262 ("r-rstudioapi" ,r-rstudioapi)
17263 ("r-shiny" ,r-shiny)
17264 ("r-shinyjs" ,r-shinyjs)
17265 ("r-yaml" ,r-yaml)))
17266 (home-page "https://github.com/crsh/citr")
17267 (synopsis "RStudio add-in to insert Markdown citations")
17269 "This package provides functions and an RStudio add-in that search a
17270 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
17271 the current document.")
17272 (license license:expat)))
17274 (define-public r-xgboost
17277 (version "1.3.2.1")
17281 (uri (cran-uri "xgboost" version))
17284 "117q8xqm82589517fi8xicd8724v9c0wnq3qpl84h6nm3aw65x1g"))))
17285 (build-system r-build-system)
17287 `(("r-data-table" ,r-data-table)
17288 ("r-magrittr" ,r-magrittr)
17289 ("r-matrix" ,r-matrix)))
17291 `(("r-knitr" ,r-knitr)))
17292 (home-page "https://github.com/dmlc/xgboost")
17293 (synopsis "Extreme gradient boosting")
17295 "This package provides an R interface to Extreme Gradient Boosting, which
17296 is an efficient implementation of the gradient boosting framework from Chen
17297 and Guestrin (2016). The package includes efficient linear model solver and
17298 tree learning algorithms. The package can automatically do parallel
17299 computation on a single machine. It supports various objective functions,
17300 including regression, classification and ranking. The package is made to be
17301 extensible, so that users are also allowed to define their own objectives
17303 (license license:asl2.0)))
17305 (define-public r-umap
17308 (version "0.2.7.0")
17312 (uri (cran-uri "umap" version))
17315 "191vpy84s0bar06y9z1qx43x2kc4qp7lmrcmd0cvz2pnzq722jab"))))
17316 (build-system r-build-system)
17318 `(("r-openssl" ,r-openssl)
17320 ("r-reticulate" ,r-reticulate)
17321 ("r-rspectra" ,r-rspectra)))
17323 `(("r-knitr" ,r-knitr)))
17324 (home-page "https://github.com/tkonopka/umap")
17325 (synopsis "Uniform manifold approximation and projection")
17327 "Uniform manifold approximation and projection is a technique for
17328 dimension reduction. This package provides an interface to the UMAP algorithm
17329 in R, including a translation of the original algorithm into R.")
17330 (license license:expat)))
17332 (define-public r-uwot
17339 (uri (cran-uri "uwot" version))
17342 "08vxh085wnrxgwy35ksb4cr7ccjvd98pyr2zlgarqryfgc1bdqbf"))))
17343 (build-system r-build-system)
17345 `(("r-dqrng" ,r-dqrng)
17347 ("r-irlba" ,r-irlba)
17348 ("r-matrix" ,r-matrix)
17350 ("r-rcppannoy" ,r-rcppannoy)
17351 ("r-rcppprogress" ,r-rcppprogress)
17352 ("r-rspectra" ,r-rspectra)))
17353 (home-page "https://github.com/jlmelville/uwot")
17354 (synopsis "Uniform manifold approximation and projection")
17356 "This package provides an implementation of the Uniform Manifold
17357 Approximation and Projection dimensionality reduction by McInnes et
17358 al. (2018). It also provides means to transform new data and to carry out
17359 supervised dimensionality reduction. An implementation of the related
17360 LargeVis method of Tang et al. (2016) is also provided.")
17361 (license license:gpl3)))
17363 (define-public r-kableextra
17365 (name "r-kableextra")
17370 (uri (cran-uri "kableExtra" version))
17373 "1zixccpgy9x95fgzfgxc43pm020c80c21flch71klc3zzzsq53gf"))))
17374 (properties `((upstream-name . "kableExtra")))
17375 (build-system r-build-system)
17377 `(("r-digest" ,r-digest)
17379 ("r-htmltools" ,r-htmltools)
17380 ("r-knitr" ,r-knitr)
17381 ("r-magrittr" ,r-magrittr)
17382 ("r-rmarkdown" ,r-rmarkdown)
17383 ("r-rstudioapi" ,r-rstudioapi)
17384 ("r-rvest" ,r-rvest)
17385 ("r-scales" ,r-scales)
17386 ("r-stringr" ,r-stringr)
17387 ("r-viridislite" ,r-viridislite)
17388 ("r-webshot" ,r-webshot)
17389 ("r-xml2" ,r-xml2)))
17391 `(("r-knitr" ,r-knitr)))
17392 (home-page "https://haozhu233.github.io/kableExtra/")
17393 (synopsis "Construct complex tables with pipe syntax")
17395 "Build complex HTML or LaTeX tables using @code{kable()} from
17396 @code{knitr} and the piping syntax from @code{magrittr}. The function
17397 @code{kable()} is a light weight table generator coming from @code{knitr}.
17398 This package simplifies the way to manipulate the HTML or LaTeX codes
17399 generated by @code{kable()} and allows users to construct complex tables and
17400 customize styles using a readable syntax.")
17401 (license license:expat)))
17403 (define-public r-glasso
17410 (uri (cran-uri "glasso" version))
17412 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
17413 (build-system r-build-system)
17414 (native-inputs `(("gfortran" ,gfortran)))
17415 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
17416 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
17418 "This is a package for estimation of a sparse inverse covariance matrix
17419 using a lasso (L1) penalty. Facilities are provided for estimates along a
17420 path of values for the regularization parameter.")
17421 (license license:gpl2)))
17423 (define-public r-rhpcblasctl
17425 (name "r-rhpcblasctl")
17426 (version "0.20-137")
17430 (uri (cran-uri "RhpcBLASctl" version))
17433 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
17434 (properties `((upstream-name . "RhpcBLASctl")))
17435 (build-system r-build-system)
17436 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
17437 (synopsis "Control the number of threads on BLAS")
17439 "This package allows you to control the number of threads the BLAS
17440 library uses. It is also possible to control the number of threads in
17442 (license license:agpl3+)))
17444 (define-public r-lda
17451 (uri (cran-uri "lda" version))
17454 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
17455 (build-system r-build-system)
17456 (home-page "https://cran.r-project.org/web/packages/lda/")
17457 (synopsis "Collapsed Gibbs sampling methods for topic models")
17459 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
17460 related models. This includes (but is not limited to) sLDA, corrLDA, and the
17461 mixed-membership stochastic blockmodel. Inference for all of these models is
17462 implemented via a fast collapsed Gibbs sampler written in C. Utility
17463 functions for reading/writing data typically used in topic models, as well as
17464 tools for examining posterior distributions are also included.")
17465 ;; Any version of the LGPL
17466 (license license:lgpl3+)))
17468 (define-public r-rann-l1
17475 (uri (cran-uri "RANN.L1" version))
17478 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
17479 (properties `((upstream-name . "RANN.L1")))
17480 (build-system r-build-system)
17481 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
17482 (synopsis "Fast nearest neighbour search using L1 metric")
17484 "This package provides tools to find the k nearest neighbours for every
17485 point in a given dataset in O(N log N) time using Arya and Mount's ANN
17486 library. There is support for approximate as well as exact searches, fixed
17487 radius searches and @code{bd} as well as @code{kd} trees. The distance is
17488 computed using the L1 (Manhattan, taxicab) metric.")
17489 (license license:gpl3+)))
17491 (define-public r-leiden
17498 (uri (cran-uri "leiden" version))
17501 "14iqn5iqcya6bqbjvjivpd7q9gwc323sj29y7ssrbhb3sz9982bp"))))
17502 (properties `((upstream-name . "leiden")))
17503 (build-system r-build-system)
17505 `(("r-igraph" ,r-igraph)
17506 ("r-matrix" ,r-matrix)
17507 ("r-reticulate" ,r-reticulate)))
17509 `(("r-knitr" ,r-knitr)))
17510 (home-page "https://github.com/TomKellyGenetics/leiden")
17511 (synopsis "R implementation of Leiden clustering algorithm")
17513 "This package implements the Python @code{leidenalg} module to be called
17514 in R. It enables clustering using the Leiden algorithm for partitioning a
17515 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
17516 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
17517 (license license:gpl3)))
17519 (define-public r-patchwork
17521 (name "r-patchwork")
17526 (uri (cran-uri "patchwork" version))
17529 "10glgkf58lcykcwda1hj6xdps02m3i247qynk6s2jmwljagps3fg"))))
17530 (build-system r-build-system)
17532 `(("r-ggplot2" ,r-ggplot2)
17533 ("r-gtable" ,r-gtable)))
17535 `(("r-knitr" ,r-knitr)))
17536 (home-page "https://github.com/thomasp85/patchwork")
17537 (synopsis "Compose ggplot2 plots")
17539 "The @code{ggplot2} package provides a strong API for sequentially
17540 building up a plot, but does not concern itself with composition of multiple
17541 plots. Patchwork is a package that expands the API to allow for arbitrarily
17542 complex composition of plots by providing mathematical operators for combining
17544 (license license:expat)))
17546 (define-public r-liger
17553 (uri (git-reference
17554 (url "https://github.com/MacoskoLab/liger")
17555 (commit (string-append "v" version))))
17556 (file-name (git-file-name name version))
17559 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
17560 (modules '((guix build utils)))
17563 (delete-file "inst/java/ModularityOptimizer.jar")
17565 (build-system r-build-system)
17568 (modify-phases %standard-phases
17569 (add-after 'unpack 'build-java-part
17570 (lambda* (#:key inputs #:allow-other-keys)
17571 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
17572 (for-each (lambda (file) (invoke "javac" file))
17573 (find-files "." "\\.java$"))
17574 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
17575 (find-files "." "\\.class$"))
17578 `(("r-cowplot" ,r-cowplot)
17579 ("r-dosnow" ,r-dosnow)
17580 ("r-dplyr" ,r-dplyr)
17582 ("r-foreach" ,r-foreach)
17583 ("r-ggplot2" ,r-ggplot2)
17584 ("r-ggrepel" ,r-ggrepel)
17585 ("r-hmisc" ,r-hmisc)
17587 ("r-irlba" ,r-irlba)
17588 ("r-matrix" ,r-matrix)
17589 ("r-mclust" ,r-mclust)
17590 ("r-patchwork" ,r-patchwork)
17592 ("r-rann-l1" ,r-rann-l1)
17594 ("r-rcpparmadillo" ,r-rcpparmadillo)
17595 ("r-riverplot" ,r-riverplot)
17596 ("r-rtsne" ,r-rtsne)
17597 ("r-snow" ,r-snow)))
17599 `(("jdk" ,icedtea "jdk")
17600 ;; See https://github.com/MacoskoLab/liger/issues/96
17601 ;; The optimizer is released under the Expat license.
17605 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
17608 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
17610 ("r-knitr" ,r-knitr))) ; for vignettes
17611 (home-page "https://github.com/MacoskoLab/liger")
17612 (synopsis "Integrate and analyze multiple single-cell datasets")
17614 "LIGER is a package for integrating and analyzing multiple single-cell
17615 datasets, developed and maintained by the Macosko lab. It relies on
17616 integrative non-negative matrix factorization to identify shared and
17617 dataset-specific factors.")
17618 (license license:gpl3)))
17620 (define-public r-harmony
17627 (uri (git-reference
17628 (url "https://github.com/immunogenomics/harmony")
17630 (file-name (git-file-name name version))
17633 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
17634 (modules '((guix build utils)))
17637 (for-each delete-file '("config.status" "configure"))
17639 (build-system r-build-system)
17641 `(("r-cowplot" ,r-cowplot)
17642 ("r-dplyr" ,r-dplyr)
17643 ("r-ggplot2" ,r-ggplot2)
17644 ("r-irlba" ,r-irlba)
17645 ("r-matrix" ,r-matrix)
17647 ("r-rcpparmadillo" ,r-rcpparmadillo)
17648 ("r-rcppprogress" ,r-rcppprogress)
17649 ("r-rlang" ,r-rlang)
17650 ("r-tibble" ,r-tibble)
17651 ("r-tidyr" ,r-tidyr)))
17653 `(("autoconf" ,autoconf)))
17654 (home-page "https://github.com/immunogenomics/harmony")
17655 (synopsis "Integration of single cell sequencing data")
17657 "This package provides an implementation of the Harmony algorithm for
17658 single cell integration, described in Korsunsky et al
17659 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
17660 function and interfaces to external frameworks.")
17661 (license license:gpl3)))
17663 (define-public r-covr
17670 (uri (cran-uri "covr" version))
17672 (base32 "0v5cv3cw2kpdr6wxmkbd3wclavr17zipypdcb10hhmpa4cvgqk55"))))
17673 (properties `((upstream-name . "covr")))
17674 (build-system r-build-system)
17676 `(("r-crayon" ,r-crayon)
17677 ("r-digest" ,r-digest)
17679 ("r-jsonlite" ,r-jsonlite)
17681 ("r-withr" ,r-withr)
17682 ("r-yaml" ,r-yaml)))
17684 `(("r-knitr" ,r-knitr))) ; for vignettes
17685 (home-page "https://github.com/r-lib/covr")
17686 (synopsis "Test coverage for R packages")
17688 "Thisp package enables you to track and report code coverage for your
17689 package and (optionally) upload the results to a coverage service. Code
17690 coverage is a measure of the amount of code being exercised by a set of tests.
17691 It is an indirect measure of test quality and completeness. This package is
17692 compatible with any testing methodology or framework and tracks coverage of
17693 both R code and compiled C/C++/FORTRAN code.")
17694 (license license:gpl3)))
17696 (define-public r-systemfonts
17698 (name "r-systemfonts")
17703 (uri (cran-uri "systemfonts" version))
17706 "15x7qx8iigkybgz6b6s66i3mh75vgynzpd50nw05wflfwzcv87a0"))))
17707 (properties `((upstream-name . "systemfonts")))
17708 (build-system r-build-system)
17710 `(("r-cpp11" ,r-cpp11)))
17712 `(("fontconfig" ,fontconfig)
17715 `(("pkg-config" ,pkg-config)
17716 ("r-knitr" ,r-knitr)))
17717 (home-page "https://github.com/r-lib/systemfonts")
17718 (synopsis "System native font finding")
17720 "This package provides system native access to the font catalogue. As
17721 font handling varies between systems it is difficult to correctly locate
17722 installed fonts across different operating systems. The 'systemfonts' package
17723 provides bindings to the native libraries for finding font files that can then
17724 be used further by e.g. graphic devices.")
17725 (license license:expat)))
17727 (define-public r-graphlayouts
17729 (name "r-graphlayouts")
17734 (uri (cran-uri "graphlayouts" version))
17737 "05v7ss18bflhqa4ipsca8iw2ln8ddbaiyrizx2a5cwq81g5qq3rq"))))
17738 (properties `((upstream-name . "graphlayouts")))
17739 (build-system r-build-system)
17741 `(("r-igraph" ,r-igraph)
17743 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17744 (home-page "https://github.com/schochastics/graphlayouts")
17745 (synopsis "Additional layout algorithms for network visualizations")
17747 "This package provides several layout algorithms to visualize networks
17748 which are not part of the igraph library. Most are based on the concept of
17749 stress majorization by Gansner et al. (2004)
17750 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
17751 emphasize hidden group structures in networks or focus on specific nodes.")
17752 (license license:expat)))
17754 (define-public r-tidygraph
17756 (name "r-tidygraph")
17761 (uri (cran-uri "tidygraph" version))
17764 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
17765 (properties `((upstream-name . "tidygraph")))
17766 (build-system r-build-system)
17768 `(("r-dplyr" ,r-dplyr)
17769 ("r-igraph" ,r-igraph)
17770 ("r-magrittr" ,r-magrittr)
17771 ("r-pillar" ,r-pillar)
17774 ("r-rlang" ,r-rlang)
17775 ("r-tibble" ,r-tibble)
17776 ("r-tidyr" ,r-tidyr)))
17777 (home-page "https://github.com/thomasp85/tidygraph")
17778 (synopsis "Tidy API for graph manipulation")
17780 "This package provides a graph implementation that can be thought of as
17781 two tidy data frames describing node and edge data respectively. It provides
17782 an approach to manipulate these two virtual data frames using the API defined
17783 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
17784 common graph algorithms.")
17785 (license license:expat)))
17787 (define-public r-soupx
17788 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
17792 (version (git-version "0.3.1" revision commit))
17796 (uri (git-reference
17797 (url "https://github.com/constantAmateur/SoupX")
17799 (file-name (git-file-name name version))
17802 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
17803 (properties `((upstream-name . "SoupX")))
17804 (build-system r-build-system)
17806 `(("r-ggplot2" ,r-ggplot2)
17807 ("r-matrix" ,r-matrix)
17808 ("r-seurat" ,r-seurat)))
17809 (home-page "https://github.com/constantAmateur/SoupX")
17810 (synopsis "Single cell mRNA Soup eXterminator")
17812 "This package provides a package for quantifying, profiling and
17813 removing cell free mRNA contamination (the \"soup\") from droplet based single
17814 cell RNA-seq experiments.")
17815 (license license:gpl2))))
17817 (define-public r-assertr
17824 (uri (cran-uri "assertr" version))
17827 "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650"))))
17828 (build-system r-build-system)
17830 `(("r-dplyr" ,r-dplyr)
17832 ("r-rlang" ,r-rlang)))
17834 `(("r-knitr" ,r-knitr))) ; needed for vignette
17835 (home-page "https://github.com/ropensci/assertr")
17836 (synopsis "Assertive programming for R analysis pipelines")
17838 "This package provides functionality to assert conditions that have to be
17839 met so that errors in data used in analysis pipelines can fail quickly. It is
17840 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
17842 (license license:expat)))
17844 (define-public r-parameters
17846 (name "r-parameters")
17851 (uri (cran-uri "parameters" version))
17854 "020k3vxnp0vjrlkcxx5vj30vag474hw48zxzw9315whsq4hhhbqc"))))
17855 (properties `((upstream-name . "parameters")))
17856 (build-system r-build-system)
17858 `(("r-bayestestr" ,r-bayestestr)
17859 ("r-insight" ,r-insight)))
17861 `(("r-knitr" ,r-knitr)))
17862 (home-page "https://cran.r-project.org/web/packages/parameters")
17863 (synopsis "Processing of model parameters")
17865 "This package provides utilities for processing the parameters of various
17866 statistical models. Beyond computing p values, CIs, and other indices for a
17867 wide variety of models, this package implements features like standardization
17868 or bootstrapping of parameters and models, feature reduction (feature
17869 extraction and variable selection) as well as conversion between indices of
17871 (license license:gpl3)))
17873 (define-public r-rgdal
17880 (uri (cran-uri "rgdal" version))
17882 (base32 "1cii2azm3zv5l6fn33xzwahp8349z3pb2769vpdxkf7734dxggvg"))))
17883 (properties `((upstream-name . "rgdal")))
17884 (build-system r-build-system)
17892 `(("pkg-config" ,pkg-config)
17893 ("r-knitr" ,r-knitr)))
17894 (home-page "http://rgdal.r-forge.r-project.org")
17895 (synopsis "Bindings for the Geospatial Data Abstraction Library")
17897 "This package provides bindings to the Geospatial Data Abstraction
17898 Library (GDAL) and access to projection/transformation operations from the
17900 (license license:gpl2+)))
17902 (define-public r-insol
17909 (uri (cran-uri "insol" version))
17912 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
17913 (properties `((upstream-name . "insol")))
17914 (build-system r-build-system)
17916 `(("r-raster" ,r-raster)))
17918 `(("gfortran" ,gfortran)))
17919 (home-page "https://meteoexploration.com/R/insol/index.html")
17920 (synopsis "Tools for calculating solar radiation")
17922 "This package provides functions to compute insolation on tilted
17923 surfaces, computes atmospheric transmittance and related parameters such as:
17924 Earth radius vector, declination, sunset and sunrise, daylength, equation of
17925 time, vector in the direction of the sun, vector normal to surface, and some
17926 atmospheric physics.")
17927 (license license:gpl2+)))
17929 (define-public r-lifecycle
17931 (name "r-lifecycle")
17936 (uri (cran-uri "lifecycle" version))
17939 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
17940 (properties `((upstream-name . "lifecycle")))
17941 (build-system r-build-system)
17943 `(("r-glue" ,r-glue)
17944 ("r-rlang" ,r-rlang)))
17946 `(("r-knitr" ,r-knitr))) ; for vignettes
17947 (home-page "https://github.com/r-lib/lifecycle")
17948 (synopsis "Manage the life cycle of your package functions")
17950 "Manage the life cycle of your exported functions with shared
17951 conventions, documentation badges, and non-invasive deprecation warnings. The
17952 lifecycle package defines four development stages (experimental, maturing,
17953 stable, and questioning) and three deprecation stages (soft-deprecated,
17954 deprecated, and defunct). It makes it easy to insert badges corresponding to
17955 these stages in your documentation. Usage of deprecated functions are
17956 signalled with increasing levels of non-invasive verbosity.")
17957 (license license:gpl3)))
17959 (define-public r-assertable
17961 (name "r-assertable")
17966 (uri (cran-uri "assertable" version))
17969 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
17970 (build-system r-build-system)
17972 `(("r-data-table" ,r-data-table)))
17973 (home-page "https://cran.r-project.org/web/packages/assertable/")
17974 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
17975 (description "This package provides simple, flexible assertions on
17976 data.frame or data.table objects with verbose output for vetting. While other
17977 assertion packages apply towards more general use-cases, @code{assertable} is
17978 tailored towards tabular data. It includes functions to check variable names
17979 and values, whether the dataset contains all combinations of a given set of
17980 unique identifiers, and whether it is a certain length. In addition,
17981 @code{assertable} includes utility functions to check the existence of target
17982 files and to efficiently import multiple tabular data files into one
17984 (license license:gpl3)))
17986 (define-public r-quadprog
17988 (name "r-quadprog")
17993 (uri (cran-uri "quadprog" version))
17995 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
17996 (build-system r-build-system)
17998 `(("gfortran" ,gfortran)))
17999 (home-page "https://cran.r-project.org/web/packages/quadprog")
18000 (synopsis "Functions to solve quadratic programming problems")
18002 "This package contains routines and documentation for solving quadratic
18003 programming problems.")
18004 (license license:gpl3+)))
18006 (define-public r-desolve
18013 (uri (cran-uri "deSolve" version))
18015 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
18016 (properties `((upstream-name . "deSolve")))
18017 (build-system r-build-system)
18019 `(("gfortran" ,gfortran)))
18020 (home-page "https://desolve.r-forge.r-project.org/")
18021 (synopsis "Solvers for initial value problems of differential equations")
18022 (description "This package provides functions that solve initial value
18023 problems of a system of first-order @dfn{ordinary differential
18024 equations} (ODE), of @dfn{partial differential equations} (PDE), of
18025 @dfn{differential algebraic equations} (DAE), and of delay differential
18026 equations. The functions provide an interface to the FORTRAN functions
18027 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
18028 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
18029 C-implementation of solvers of the Runge-Kutta family with fixed or variable
18030 time steps. The package contains routines designed for solving ODEs resulting
18031 from 1-D, 2-D and 3-D partial differential equations that have been converted
18032 to ODEs by numerical differencing.")
18033 (license license:gpl2+)))
18035 (define-public r-pracma
18041 (uri (cran-uri "pracma" version))
18043 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
18044 (build-system r-build-system)
18045 (home-page "https://cran.r-project.org/web/packages/pracma/")
18046 (synopsis "Practical numerical math functions")
18047 (description "This package provides functions for numerical analysis and
18048 linear algebra, numerical optimization, differential equations, plus some
18049 special functions. It uses Matlab function names where appropriate to simplify
18051 (license license:gpl3+)))
18053 (define-public r-subplex
18060 (uri (cran-uri "subplex" version))
18063 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
18064 (build-system r-build-system)
18066 `(("gfortran" ,gfortran)))
18067 (home-page "https://cran.r-project.org/web/packages/subplex")
18068 (synopsis "Unconstrained optimization using the subplex algorithm")
18070 "This package implements the Subplex optimization algorithm.
18071 It solves unconstrained optimization problems using a simplex method on
18072 subspaces. The method is well suited for optimizing objective functions that
18073 are noisy or are discontinuous at the solution.")
18074 (license license:gpl3+)))
18076 (define-public r-txtplot
18083 (uri (cran-uri "txtplot" version))
18086 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
18087 (build-system r-build-system)
18088 (home-page "https://cran.r-project.org/web/packages/txtplot/")
18089 (synopsis "Text-based plotting")
18090 (description "This package provides functions to produce rudimentary ASCII
18091 graphics directly in the terminal window. This package provides a basic
18092 plotting function (and equivalents of curve, density, acf and barplot) as well
18093 as a boxplot function.")
18094 (license license:lgpl3+)))
18096 (define-public r-bio3d
18103 (uri (cran-uri "bio3d" version))
18106 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
18107 (properties `((upstream-name . "bio3d")))
18108 (build-system r-build-system)
18109 (inputs `(("zlib" ,zlib)))
18110 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
18111 (home-page "http://thegrantlab.org/bio3d/")
18112 (synopsis "Biological structure analysis")
18114 "This package provides utilities to process, organize and explore protein
18115 structure, sequence and dynamics data. Features include the ability to read
18116 and write structure, sequence and dynamic trajectory data, perform sequence
18117 and structure database searches, data summaries, atom selection, alignment,
18118 superposition, rigid core identification, clustering, torsion analysis,
18119 distance matrix analysis, structure and sequence conservation analysis, normal
18120 mode analysis, principal component analysis of heterogeneous structure data,
18121 and correlation network analysis from normal mode and molecular dynamics data.
18122 In addition, various utility functions are provided to enable the statistical
18123 and graphical power of the R environment to work with biological sequence and
18125 (license license:gpl2+)))
18127 (define-public r-bios2cor
18129 (name "r-bios2cor")
18134 (uri (cran-uri "Bios2cor" version))
18137 "1wkj9vr33m9jilidil9jpw5rzr3pf7gkimxdvch22ks4bgkx7l1w"))))
18138 (properties `((upstream-name . "Bios2cor")))
18139 (build-system r-build-system)
18141 `(("r-bigmemory" ,r-bigmemory)
18142 ("r-bio3d" ,r-bio3d)
18143 ("r-circular" ,r-circular)
18144 ("r-igraph" ,r-igraph)))
18145 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
18146 (synopsis "From biological sequences and simulations to correlation analysis")
18148 "This package provides utilities for computation and analysis of
18149 correlation/covariation in multiple sequence alignments and in side chain
18150 motions during molecular dynamics simulations. Features include the
18151 computation of correlation/covariation scores using a variety of scoring
18152 functions between either sequence positions in alignments or side chain
18153 dihedral angles in molecular dynamics simulations and utilities to analyze the
18154 correlation/covariation matrix through a variety of tools including network
18155 representation and principal components analysis. In addition, several
18156 utility functions are based on the R graphical environment to provide friendly
18157 tools for help in data interpretation.")
18158 (license license:gpl2+)))
18160 ;; This package includes minified JavaScript files. When upgrading please
18161 ;; check that there are no new minified JavaScript files.
18162 (define-public r-networkd3
18164 (name "r-networkd3")
18169 (uri (cran-uri "networkD3" version))
18172 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
18175 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
18177 (properties `((upstream-name . "networkD3")))
18178 (build-system r-build-system)
18180 `(#:modules ((guix build utils)
18181 (guix build r-build-system)
18185 (modify-phases %standard-phases
18186 (add-after 'unpack 'process-javascript
18187 (lambda* (#:key inputs #:allow-other-keys)
18188 (with-directory-excursion "inst/htmlwidgets/lib/"
18192 `((,(assoc-ref inputs "d3.v4.js")
18193 "d3-4.5.0/d3.min.js"))))
18194 (lambda (sources targets)
18195 (for-each (lambda (source target)
18196 (format #t "Processing ~a --> ~a~%"
18198 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
18199 (call-with-output-file target
18201 (dump-port minified port)))))
18202 sources targets))))
18205 `(("uglify-js" ,uglify-js)
18206 ;; NOTE: Make sure that this version of d3 is still valid when
18207 ;; upgrading the package.
18211 (uri "https://d3js.org/d3.v4.js")
18214 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
18216 `(("r-htmlwidgets" ,r-htmlwidgets)
18217 ("r-igraph" ,r-igraph)
18218 ("r-magrittr" ,r-magrittr)))
18219 (home-page "https://cran.r-project.org/package=networkD3")
18220 (synopsis "D3 JavaScript network graphs from R")
18222 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
18224 (license license:gpl3+)))
18226 (define-public r-aasea
18233 (uri (cran-uri "aaSEA" version))
18236 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
18237 (properties `((upstream-name . "aaSEA")))
18238 (build-system r-build-system)
18240 `(("r-bios2cor" ,r-bios2cor)
18242 ("r-hmisc" ,r-hmisc)
18243 ("r-magrittr" ,r-magrittr)
18244 ("r-networkd3" ,r-networkd3)
18245 ("r-plotly" ,r-plotly)
18246 ("r-seqinr" ,r-seqinr)
18247 ("r-shiny" ,r-shiny)
18248 ("r-shinydashboard" ,r-shinydashboard)))
18249 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
18250 (synopsis "Amino acid substitution effect analyzer")
18252 "Given a protein multiple sequence alignment, it is a daunting task to
18253 assess the effects of substitutions along sequence length. The aaSEA package
18254 is intended to help researchers to rapidly analyze property changes caused by
18255 single, multiple and correlated amino acid substitutions in proteins.")
18256 (license license:gpl3)))
18258 (define-public r-abacus
18265 (uri (cran-uri "ABACUS" version))
18268 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
18269 (properties `((upstream-name . "ABACUS")))
18270 (build-system r-build-system)
18272 `(("r-ggplot2" ,r-ggplot2)
18273 ("r-shiny" ,r-shiny)))
18274 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
18275 (synopsis "Apps-based activities for communicating and understanding statistics")
18277 "This package provides a set of Shiny apps for effective communication
18278 and understanding in statistics. The current version includes properties of
18279 normal distribution, properties of sampling distribution, one-sample z and t
18280 tests, two samples independent (unpaired) t test and analysis of variance.")
18281 (license license:gpl3)))
18283 (define-public r-abc-rap
18290 (uri (cran-uri "ABC.RAP" version))
18293 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
18294 (properties `((upstream-name . "ABC.RAP")))
18295 (build-system r-build-system)
18296 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
18297 (synopsis "Array-based CpG region analysis pipeline")
18299 "This package aims to identify candidate genes that are differentially
18300 methylated between cases and controls. It applies Student's t-test and delta
18301 beta analysis to identify candidate genes containing multiple CpG sites.")
18302 (license license:gpl3)))
18304 (define-public r-abcadm
18311 (uri (cran-uri "abcADM" version))
18314 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
18315 (properties `((upstream-name . "abcADM")))
18316 (build-system r-build-system)
18319 ("r-rcpp" ,r-rcpp)))
18320 (home-page "https://cran.r-project.org/web/packages/abcADM/")
18321 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
18323 "This package provides tools to estimate parameters of accumulated
18324 damage (load duration) models based on failure time data under a Bayesian
18325 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
18326 long-term reliability under stochastic load profiles.")
18327 (license license:gpl3)))
18329 (define-public r-rglpk
18336 (uri (cran-uri "Rglpk" version))
18339 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
18340 (properties `((upstream-name . "Rglpk")))
18341 (build-system r-build-system)
18343 `(("r-slam" ,r-slam)))
18346 (home-page "https://r-forge.r-project.org/projects/rglp/")
18347 (synopsis "R interface to the GNU Linear Programming Kit")
18349 "This package provides an R interface to the GNU Linear Programming Kit,
18350 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
18351 integer linear programming} (MILP) and other related problems.")
18353 (license (list license:gpl2 license:gpl3))))
18355 (define-public r-abcdefba
18357 (name "r-abcdefba")
18362 (uri (cran-uri "abcdeFBA" version))
18365 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
18366 (properties `((upstream-name . "abcdeFBA")))
18367 (build-system r-build-system)
18369 `(("r-corrplot" ,r-corrplot)
18370 ("r-lattice" ,r-lattice)
18372 ("r-rglpk" ,r-rglpk)))
18373 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
18374 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
18376 "This package provides functions for Constraint Based Simulation using
18377 Flux Balance Analysis and informative analysis of the data generated during
18379 (license license:gpl2)))
18381 (define-public r-abcrlda
18388 (uri (cran-uri "abcrlda" version))
18391 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
18392 (properties `((upstream-name . "abcrlda")))
18393 (build-system r-build-system)
18394 (home-page "https://ieeexplore.ieee.org/document/8720003/")
18395 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
18397 "This package offers methods to perform @dfn{asymptotically
18398 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
18399 cost-sensitive binary classification. The bias-correction is an estimate of
18400 the bias term added to regularized discriminant analysis that minimizes the
18402 (license license:gpl3)))
18404 (define-public r-abemus
18411 (uri (cran-uri "abemus" version))
18414 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
18415 (properties `((upstream-name . "abemus")))
18416 (build-system r-build-system)
18418 `(("r-data-table" ,r-data-table)))
18419 (home-page "https://cran.r-project.org/web/packages/abemus/")
18420 (synopsis "Adaptive base error model in ultra-deep sequencing data")
18422 "This package provides an implementation of @dfn{Adaptive Base Error
18423 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
18424 platform-specific genetic knowledge and empirical signal to readily detect and
18425 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
18426 cell free DNA} (cfDNA).")
18427 (license license:gpl3)))
18429 ;; This package includes minified JavaScript files. When upgrading please
18430 ;; check that there are no new minified JavaScript files.
18431 (define-public r-rintrojs
18433 (name "r-rintrojs")
18438 (uri (cran-uri "rintrojs" version))
18441 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
18442 (properties `((upstream-name . "rintrojs")))
18443 (build-system r-build-system)
18445 `(#:modules ((guix build utils)
18446 (guix build r-build-system)
18450 (modify-phases %standard-phases
18451 (add-after 'unpack 'process-javascript
18452 (lambda* (#:key inputs #:allow-other-keys)
18453 (with-directory-excursion "inst/javascript/introjs/"
18457 `((,(assoc-ref inputs "intro.js")
18459 (lambda (sources targets)
18460 (for-each (lambda (source target)
18461 (format #t "Processing ~a --> ~a~%"
18463 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
18464 (call-with-output-file target
18466 (dump-port minified port)))))
18467 sources targets))))
18470 `(("uglify-js" ,uglify-js)
18474 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
18477 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
18479 `(("r-jsonlite" ,r-jsonlite)
18480 ("r-shiny" ,r-shiny)))
18481 (home-page "https://github.com/carlganz/rintrojs")
18482 (synopsis "Wrapper for the Intro.js library")
18484 "This package provides a wrapper for the @url{http://www.introjs.com,
18485 Intro.js} library. This package makes it easy to include step-by-step
18486 introductions, and clickable hints in a Shiny application. It supports both
18487 static introductions in the UI, and programmatic introductions from the
18489 (license license:agpl3+)))
18491 (define-public r-sysfonts
18493 (name "r-sysfonts")
18498 (uri (cran-uri "sysfonts" version))
18501 "00kbazxw6zd1kakfshffdj928krca53bw9k78k0zar40mbqxiwd5"))))
18502 (properties `((upstream-name . "sysfonts")))
18503 (build-system r-build-system)
18505 `(("freetype" ,freetype)
18509 `(("pkg-config" ,pkg-config)))
18510 (home-page "https://github.com/yixuan/sysfonts")
18511 (synopsis "Loading fonts into R")
18513 "This is a package to simplify loading of system fonts and Google Fonts
18514 into R, in order to support other packages.")
18515 (license license:gpl2)))
18517 (define-public r-showtextdb
18519 (name "r-showtextdb")
18524 (uri (cran-uri "showtextdb" version))
18527 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
18528 (properties `((upstream-name . "showtextdb")))
18529 (build-system r-build-system)
18531 `(("r-sysfonts" ,r-sysfonts)))
18532 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
18533 (synopsis "Font files for the 'showtext' package")
18535 "This package provides font files that can be used by the @code{showtext}
18537 (license license:asl2.0)))
18539 (define-public r-showtext
18541 (name "r-showtext")
18546 (uri (cran-uri "showtext" version))
18549 "0y5mw6ffk92r7b22irrfhdmj4hxfl0d1wjxj14hznbapc4qm6f0z"))))
18550 (properties `((upstream-name . "showtext")))
18551 (build-system r-build-system)
18553 `(("freetype" ,freetype)
18557 `(("r-showtextdb" ,r-showtextdb)
18558 ("r-sysfonts" ,r-sysfonts)))
18560 `(("pkg-config" ,pkg-config)
18561 ("r-knitr" ,r-knitr)))
18562 (home-page "https://github.com/yixuan/showtext")
18563 (synopsis "Using fonts more easily in R graphs")
18565 "This package aims to make it easy to use various types of
18566 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
18567 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
18568 will be converted into polygons or raster images, hence after the plot has
18569 been created, it no longer relies on the font files. No external software
18570 such as Ghostscript is needed to use this package.")
18571 (license license:asl2.0)))
18573 (define-public r-emojifont
18575 (name "r-emojifont")
18580 (uri (cran-uri "emojifont" version))
18583 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
18584 (properties `((upstream-name . "emojifont")))
18585 (build-system r-build-system)
18587 `(("r-ggplot2" ,r-ggplot2)
18588 ("r-proto" ,r-proto)
18589 ("r-showtext" ,r-showtext)
18590 ("r-sysfonts" ,r-sysfonts)))
18591 (home-page "https://guangchuangyu.github.io/emojifont")
18592 (synopsis "Emoji and Font Awesome in R graphics")
18594 "This package enables the use of emoji and the Font Awesome glyphs in
18595 both base and ggplot2 graphics.")
18596 (license license:artistic2.0)))
18598 (define-public r-abstractr
18600 (name "r-abstractr")
18605 (uri (cran-uri "abstractr" version))
18608 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
18609 (properties `((upstream-name . "abstractr")))
18610 (build-system r-build-system)
18612 `(("r-colourpicker" ,r-colourpicker)
18613 ("r-emojifont" ,r-emojifont)
18614 ("r-ggplot2" ,r-ggplot2)
18615 ("r-gridextra" ,r-gridextra)
18616 ("r-rintrojs" ,r-rintrojs)
18617 ("r-shiny" ,r-shiny)
18618 ("r-shinythemes" ,r-shinythemes)))
18619 (home-page "https://matt-kumar.shinyapps.io/portfolio")
18620 (synopsis "R-Shiny application for creating visual abstracts")
18622 "This package provides an R Shiny application to create visual abstracts
18623 for original research. A variety of user defined options and formatting are
18625 (license license:gpl3)))
18627 (define-public r-qgam
18634 (uri (cran-uri "qgam" version))
18637 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
18638 (properties `((upstream-name . "qgam")))
18639 (build-system r-build-system)
18641 `(("r-doparallel" ,r-doparallel)
18644 ("r-shiny" ,r-shiny)))
18645 (native-inputs `(("r-knitr" ,r-knitr)))
18646 (home-page "https://cran.r-project.org/web/packages/qgam/")
18647 (synopsis "Smooth additive quantile regression models")
18649 "This package provides smooth additive quantile regression models, fitted
18650 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
18651 the smoothing parameters are estimated automatically by marginal loss
18652 minimization, while the regression coefficients are estimated using either
18653 PIRLS or Newton algorithm. The learning rate is determined so that the
18654 Bayesian credible intervals of the estimated effects have approximately the
18655 correct coverage. The main function is @code{qgam()} which is similar to
18656 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
18657 regression models.")
18658 (license license:gpl2+)))
18660 (define-public r-abtest
18667 (uri (cran-uri "abtest" version))
18670 "1ak0m4jd1grriwg4pn3aqf1468qma6rjn5kqjh8izx7zl29jd07v"))))
18671 (properties `((upstream-name . "abtest")))
18672 (build-system r-build-system)
18674 `(("r-matrix" ,r-matrix)
18675 ("r-mvtnorm" ,r-mvtnorm)
18676 ("r-plotrix" ,r-plotrix)
18678 ("r-rcolorbrewer" ,r-rcolorbrewer)
18681 ("r-truncnorm" ,r-truncnorm)))
18682 (home-page "https://cran.r-project.org/web/packages/abtest/")
18683 (synopsis "Bayesian A/B testing")
18685 "This package provides functions for Bayesian A/B testing including prior
18686 elicitation options based on Kass and Vaidyanathan (1992)
18687 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
18688 (license license:gpl2+)))
18690 (define-public r-accept
18697 (uri (cran-uri "accept" version))
18700 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
18701 (properties `((upstream-name . "accept")))
18702 (build-system r-build-system)
18704 `(("r-dplyr" ,r-dplyr)
18705 ("r-extrafont" ,r-extrafont)
18707 ("r-plotly" ,r-plotly)
18708 ("r-stringr" ,r-stringr)
18709 ("r-viridis" ,r-viridis)))
18710 (home-page "https://cran.r-project.org/web/packages/accept/")
18711 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
18713 "This package allows clinicians to predict the rate and severity of
18714 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
18715 Disease} (COPD) patients, based on the clinical prediction model published in
18716 Adibi et al. (2019) @url{doi:10.1101/651901}.")
18717 (license license:gpl3)))
18719 (define-public r-smpracticals
18721 (name "r-smpracticals")
18726 (uri (cran-uri "SMPracticals" version))
18729 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
18730 (properties `((upstream-name . "SMPracticals")))
18731 (build-system r-build-system)
18733 `(("r-ellipse" ,r-ellipse)
18736 ("r-survival" ,r-survival)))
18737 (home-page "http://statwww.epfl.ch/davison/SM/")
18738 (synopsis "Practicals for use with Davison (2003) Statistical Models")
18740 "This package contains the datasets and a few functions for use with the
18741 practicals outlined in Appendix A of the book Statistical Models (Davison,
18742 2003, Cambridge University Press). The practicals themselves can be found at
18743 @url{http://statwww.epfl.ch/davison/SM/}.")
18744 (license license:gpl2+)))
18746 (define-public r-fgui
18753 (uri (cran-uri "fgui" version))
18756 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
18757 (properties `((upstream-name . "fgui")))
18758 (build-system r-build-system)
18760 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
18761 (synopsis "Create GUI for R functions")
18763 "Rapidly create a GUI for a function you created by automatically
18764 creating widgets for arguments of the function. This package automatically
18765 parses help routines for context-sensitive help to these arguments. The
18766 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
18767 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
18768 incorporated into the interface for greater customization for the more
18770 ;; Any version of the GPL.
18771 (license (list license:gpl2+ license:gpl3+))))
18773 (define-public r-tcltk2
18780 (uri (cran-uri "tcltk2" version))
18783 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
18784 (properties `((upstream-name . "tcltk2")))
18785 (build-system r-build-system)
18789 (home-page "https://www.sciviews.org/SciViews-R")
18790 (synopsis "Tcl/Tk additions")
18792 "This package provides a series of additional Tcl commands and Tk widgets
18793 with style and various functions to supplement the tcltk package")
18794 (license license:lgpl3)))
18796 (define-public r-accrual
18803 (uri (cran-uri "accrual" version))
18806 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
18807 (properties `((upstream-name . "accrual")))
18808 (build-system r-build-system)
18810 `(("r-fgui" ,r-fgui)
18811 ("r-smpracticals" ,r-smpracticals)
18812 ("r-tcltk2" ,r-tcltk2)))
18813 (home-page "https://cran.r-project.org/web/packages/accrual/")
18814 (synopsis "Bayesian accrual prediction")
18816 "Subject recruitment for medical research is challenging. Slow patient
18817 accrual leads to delay in research. Accrual monitoring during the process of
18818 recruitment is critical. Researchers need reliable tools to manage the
18819 accrual rate. This package provides an implementation of a Bayesian method
18820 that integrates researcher's experience on previous trials and data from the
18821 current study, providing reliable prediction on accrual rate for clinical
18822 studies. It provides functions for Bayesian accrual prediction which can be
18823 easily used by statisticians and clinical researchers.")
18824 (license license:gpl2)))
18826 (define-public r-accrued
18833 (uri (cran-uri "accrued" version))
18836 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
18837 (properties `((upstream-name . "accrued")))
18838 (build-system r-build-system)
18839 (home-page "https://cran.r-project.org/web/packages/accrued/")
18840 (synopsis "Data quality visualization tools for partially accruing data")
18842 "This is a package for visualizing data quality of partially accruing
18844 (license license:gpl3)))
18846 (define-public r-mda
18853 (uri (cran-uri "mda" version))
18856 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
18857 (properties `((upstream-name . "mda")))
18858 (build-system r-build-system)
18859 (propagated-inputs `(("r-class" ,r-class)))
18860 (native-inputs `(("gfortran" ,gfortran)))
18861 (home-page "https://cran.r-project.org/web/packages/mda/")
18862 (synopsis "Mixture and flexible discriminant analysis")
18864 "This is a package for mixture and flexible discriminant analysis,
18865 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
18866 (license license:gpl2)))
18868 (define-public r-elasticnet
18870 (name "r-elasticnet")
18875 (uri (cran-uri "elasticnet" version))
18878 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
18879 (properties `((upstream-name . "elasticnet")))
18880 (build-system r-build-system)
18882 `(("r-lars" ,r-lars)))
18883 (home-page "http://users.stat.umn.edu/~zouxx019/")
18884 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
18886 "This package provides functions for fitting the entire solution path of
18887 the Elastic-Net and also provides functions for estimating sparse Principal
18888 Components. The Lasso solution paths can be computed by the same function.")
18889 (license license:gpl2+)))
18891 (define-public r-sparselda
18893 (name "r-sparselda")
18898 (uri (cran-uri "sparseLDA" version))
18901 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
18902 (properties `((upstream-name . "sparseLDA")))
18903 (build-system r-build-system)
18905 `(("r-elasticnet" ,r-elasticnet)
18908 (home-page "https://www.imm.dtu.dk/~lkhc/")
18909 (synopsis "Sparse discriminant analysis")
18911 "This package performs sparse linear discriminant analysis for Gaussians
18912 and mixture of Gaussian models.")
18913 (license license:gpl2+)))
18915 (define-public r-accsda
18922 (uri (cran-uri "accSDA" version))
18925 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
18926 (properties `((upstream-name . "accSDA")))
18927 (build-system r-build-system)
18929 `(("r-ggplot2" ,r-ggplot2)
18930 ("r-ggthemes" ,r-ggthemes)
18931 ("r-gridextra" ,r-gridextra)
18933 ("r-rarpack" ,r-rarpack)
18934 ("r-sparselda" ,r-sparselda)))
18935 (home-page "https://github.com/gumeo/accSDA/wiki")
18936 (synopsis "Accelerated sparse discriminant analysis")
18938 "This package provides an implementation of sparse linear discriminant
18939 analysis, which is a supervised classification method for multiple classes.
18940 Various novel optimization approaches to this problem are implemented
18941 including @dfn{alternating direction method of multipliers} (ADMM),
18942 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
18943 Functions for performing cross validation are also supplied along with basic
18944 prediction and plotting functions. @dfn{Sparse zero variance
18945 discriminant} (SZVD) analysis is also included in the package.")
18946 (license license:gpl2+)))
18948 (define-public r-ace2fastq
18950 (name "r-ace2fastq")
18955 (uri (cran-uri "ace2fastq" version))
18958 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
18959 (properties `((upstream-name . "ace2fastq")))
18960 (build-system r-build-system)
18962 `(("r-stringr" ,r-stringr)))
18963 (home-page "https://github.com/c5sire/ace2fastq")
18964 (synopsis "ACE file to FASTQ converter")
18966 "The ACE file format is used in genomics to store contigs from sequencing
18967 machines. This tools converts it into FASTQ format. Both formats contain the
18968 sequence characters and their corresponding quality information. Unlike the
18969 FASTQ file, the ACE file stores the quality values numerically. The
18970 conversion algorithm uses the standard Sanger formula. The package
18971 facilitates insertion into pipelines, and content inspection.")
18972 (license license:gpl3)))
18974 (define-public r-rngwell
18981 (uri (cran-uri "rngWELL" version))
18984 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
18985 (properties `((upstream-name . "rngWELL")))
18986 (build-system r-build-system)
18987 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
18988 (synopsis "Toolbox for WELL random number generators")
18990 "This is a dedicated package to WELL pseudo random generators, which were
18991 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
18992 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
18993 (license license:bsd-3)))
18995 (define-public r-randtoolbox
18997 (name "r-randtoolbox")
19002 (uri (cran-uri "randtoolbox" version))
19005 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
19006 (properties `((upstream-name . "randtoolbox")))
19007 (build-system r-build-system)
19009 `(("r-rngwell" ,r-rngwell)))
19011 `(("gfortran" ,gfortran)))
19012 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
19013 (synopsis "Toolbox for pseudo and quasi random number generation")
19015 "This package provides
19018 @item pseudo random generators, such as general linear
19019 congruential generators, multiple recursive generators and generalized
19020 feedback shift register (SF-Mersenne Twister algorithm and WELL
19023 @item quasi random generators, such as the Torus algorithm, the Sobol
19024 sequence, the Halton sequence (including the Van der Corput sequence), and
19026 @item some generator tests: the gap test, the serial test, the poker test.
19029 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
19030 (license license:bsd-3)))
19032 (define-public r-lhs
19039 (uri (cran-uri "lhs" version))
19042 "1p4h03qlijs2a59wfd4rlvdlb9i87pw2zm8xsjd6yzz8vlm9yglh"))))
19043 (properties `((upstream-name . "lhs")))
19044 (build-system r-build-system)
19045 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19047 `(("r-knitr" ,r-knitr)))
19048 (home-page "https://github.com/bertcarnell/lhs")
19049 (synopsis "Latin Hypercube Samples")
19051 "This package provides a number of methods for creating and augmenting
19052 Latin Hypercube Samples.")
19053 (license license:gpl3)))
19055 (define-public r-acebayes
19057 (name "r-acebayes")
19062 (uri (cran-uri "acebayes" version))
19065 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73"))))
19066 (properties `((upstream-name . "acebayes")))
19067 (build-system r-build-system)
19069 `(("r-compare" ,r-compare)
19071 ("r-randtoolbox" ,r-randtoolbox)
19073 ("r-rcpparmadillo" ,r-rcpparmadillo)))
19074 (home-page "https://cran.r-project.org/web/packages/acebayes/")
19075 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
19077 "Finding an optimal Bayesian experimental design involves maximizing an
19078 objective function given by the expectation of some appropriately chosen
19079 utility function with respect to the joint distribution of unknown
19080 quantities (including responses). This objective function is usually not
19081 available in closed form and the design space can be continuous and of high
19082 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
19083 to maximise an approximation to the expectation of the utility function.")
19084 (license license:gpl2)))
19086 (define-public r-acet
19093 (uri (cran-uri "ACEt" version))
19096 "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4"))))
19097 (properties `((upstream-name . "ACEt")))
19098 (build-system r-build-system)
19103 ("r-rcpparmadillo" ,r-rcpparmadillo)))
19104 (home-page "https://cran.r-project.org/web/packages/ACEt/")
19105 (synopsis "Estimating dynamic heritability and twin model comparison")
19107 "This package supports twin models that are able to estimate the dynamic
19108 behaviour of the variance components in the classical twin models with respect
19109 to age using B-splines and P-splines.")
19110 (license license:gpl2+)))
19112 (define-public r-acfmperiod
19114 (name "r-acfmperiod")
19119 (uri (cran-uri "acfMPeriod" version))
19122 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
19123 (properties `((upstream-name . "acfMPeriod")))
19124 (build-system r-build-system)
19126 `(("r-mass" ,r-mass)))
19127 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
19128 (synopsis "Estimation of the ACF from the M-periodogram")
19130 "This package support non-robust and robust computations of the sample
19131 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
19132 univariate and multivariate processes. The methodology consists in reversing
19133 the diagonalization procedure involving the periodogram or the
19134 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
19135 ACOVF or the ACF as discussed in Fuller (1995)
19136 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
19137 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
19138 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
19139 (license license:gpl2+)))
19141 (define-public r-gamlss-data
19143 (name "r-gamlss-data")
19148 (uri (cran-uri "gamlss.data" version))
19151 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
19152 (properties `((upstream-name . "gamlss.data")))
19153 (build-system r-build-system)
19154 (home-page "http://www.gamlss.org/")
19155 (synopsis "GAMLSS data")
19157 "This package provides data used as examples to demonstrate GAMLSS
19159 ;; Either version of the license
19160 (license (list license:gpl2 license:gpl3))))
19162 (define-public r-gamlss
19169 (uri (cran-uri "gamlss" version))
19172 "1q82md0439si0n7vqbbbdk45sjr0ad7i8mgrn3kwnr4h213pb4nk"))))
19173 (properties `((upstream-name . "gamlss")))
19174 (build-system r-build-system)
19176 `(("r-gamlss-data" ,r-gamlss-data)
19177 ("r-gamlss-dist" ,r-gamlss-dist)
19180 ("r-survival" ,r-survival)))
19181 (home-page "http://www.gamlss.org/")
19182 (synopsis "Generalized additive models for location scale and shape")
19184 "This package provides functions for fitting the generalized additive
19185 models for location scale and shape introduced by Rigby and
19186 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
19187 use a distributional regression approach where all the parameters of the
19188 conditional distribution of the response variable are modelled using
19189 explanatory variables.")
19190 ;; Either version of the license
19191 (license (list license:gpl2 license:gpl3))))
19193 (define-public r-acid
19200 (uri (cran-uri "acid" version))
19203 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
19204 (properties `((upstream-name . "acid")))
19205 (build-system r-build-system)
19207 `(("r-gamlss" ,r-gamlss)
19208 ("r-gamlss-dist" ,r-gamlss-dist)
19209 ("r-hmisc" ,r-hmisc)))
19210 (home-page "https://cran.r-project.org/web/packages/acid/")
19211 (synopsis "Analysing conditional income distributions")
19213 "This package provides functions for the analysis of income distributions
19214 for subgroups of the population as defined by a set of variables like age,
19215 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
19216 distribution as well as functions for moments, inequality measures, entropy
19217 measures and polarisation measures of income distributions. This package thus
19218 aides the analysis of income inequality by offering tools for the exploratory
19219 analysis of income distributions at the disaggregated level.")
19220 (license license:gpl3)))
19222 (define-public r-acm4r
19229 (uri (cran-uri "acm4r" version))
19232 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
19233 (properties `((upstream-name . "acm4r")))
19234 (build-system r-build-system)
19235 (propagated-inputs `(("r-mass" ,r-mass)))
19236 (home-page "https://cran.r-project.org/web/packages/acm4r/")
19237 (synopsis "Align-and-count method comparisons of RFLP data")
19239 "This is a package to compare sequence fragment lengths or molecular
19240 weights from pairs of lanes. The number of matching bands in the
19241 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
19242 the align-and-count method.")
19243 ;; Any version of the GPL
19244 (license (list license:gpl2+ license:gpl3+))))
19246 (define-public r-filelock
19248 (name "r-filelock")
19253 (uri (cran-uri "filelock" version))
19256 "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc"))))
19257 (properties `((upstream-name . "filelock")))
19258 (build-system r-build-system)
19259 (home-page "https://github.com/r-lib/filelock")
19260 (synopsis "Portable file locking")
19262 "This library lets you place an exclusive or shared lock on a file using
19263 the appropriate system call provided by the underlying operating system.")
19264 (license license:expat)))
19266 (define-public r-filematrix
19268 (name "r-filematrix")
19273 (uri (cran-uri "filematrix" version))
19276 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
19277 (properties `((upstream-name . "filematrix")))
19278 (build-system r-build-system)
19279 ;; These inputs are needed for vignettes
19281 `(("r-knitr" ,r-knitr)
19282 ("r-rmarkdown" ,r-rmarkdown)
19283 ("pandoc-citeproc" ,pandoc-citeproc)))
19284 (home-page "https://github.com/andreyshabalin/filematrix")
19285 (synopsis "File-backed matrix class with convenient read and write access")
19287 "This package provides an interface for working with large matrices
19288 stored in files, not in computer memory. It supports multiple non-character
19289 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
19290 byte real values). Access to parts of the matrix is done by indexing, exactly
19291 as with usual R matrices. It supports very large matrices; the package has
19292 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
19293 columns, ad allows for quick addition of extra columns to a filematrix.")
19294 (license license:lgpl3)))
19296 (define-public r-acmeeqtl
19298 (name "r-acmeeqtl")
19303 (uri (cran-uri "ACMEeqtl" version))
19306 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
19307 (properties `((upstream-name . "ACMEeqtl")))
19308 (build-system r-build-system)
19310 `(("r-filematrix" ,r-filematrix)))
19311 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
19312 (synopsis "Estimation of interpretable eQTL effect sizes")
19314 "This package provides a non-linear model, termed ACME, that reflects a
19315 parsimonious biological model for allelic contributions of cis-acting eQTLs.
19316 With non-linear least-squares algorithm the maximum likelihood parameters can
19317 be estimated. The ACME model provides interpretable effect size estimates and
19318 p-values with well controlled Type-I error.")
19319 (license license:lgpl3)))
19321 (define-public r-acmer
19328 (uri (cran-uri "acmeR" version))
19331 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
19332 (properties `((upstream-name . "acmeR")))
19333 (build-system r-build-system)
19334 (propagated-inputs `(("r-foreign" ,r-foreign)))
19335 (home-page "https://cran.r-project.org/web/packages/acmeR/")
19336 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
19338 "This package provides an implementation of the ACME estimator, described
19339 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
19340 Mortality at Wind Turbines. Unlike most other models, this estimator supports
19341 decreasing-hazard Weibull model for persistence; decreasing search proficiency
19342 as carcasses age; variable bleed-through at successive searches; and interval
19343 mortality estimates. The package provides, based on search data, functions
19344 for estimating the mortality inflation factor in Frequentist and Bayesian
19346 (license license:expat)))
19348 (define-public r-r-huge
19355 (uri (cran-uri "R.huge" version))
19358 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
19359 (properties `((upstream-name . "R.huge")))
19360 (build-system r-build-system)
19362 `(("r-r-methodss3" ,r-r-methodss3)
19364 ("r-r-utils" ,r-r-utils)))
19365 (home-page "https://github.com/HenrikBengtsson/R.huge")
19366 (synopsis "Methods for accessing huge amounts of data")
19368 "This is a deprecated package for accessing huge amounts of data.
19369 Cross-platform alternatives are the following packages: bigmemory (CRAN),
19370 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
19371 the @code{aroma.affymetrix} package.")
19372 (license license:lgpl2.1+)))
19374 (define-public r-r-filesets
19376 (name "r-r-filesets")
19381 (uri (cran-uri "R.filesets" version))
19384 "08xv8b3c81nf54viyr3w912al18483k5gfnjpg7bxbdfk70dfzbh"))))
19385 (properties `((upstream-name . "R.filesets")))
19386 (build-system r-build-system)
19388 `(("r-digest" ,r-digest)
19389 ("r-r-cache" ,r-r-cache)
19390 ("r-r-methodss3" ,r-r-methodss3)
19392 ("r-r-utils" ,r-r-utils)))
19393 (home-page "https://github.com/HenrikBengtsson/R.filesets")
19394 (synopsis "Easy handling of and access to files")
19396 "This package provides classes and methods to locate, setup, subset,
19397 navigate and iterate file sets, i.e. sets of files located in one or more
19398 directories on the file system. The API is designed such that these classes
19399 can be extended via inheritance to provide a richer API for special file
19400 formats. Moreover, a specific name format is defined such that filenames and
19401 directories can be considered to have full names which consists of a name
19402 followed by comma-separated tags. This adds additional flexibility to
19403 identify file sets and individual files.")
19404 (license license:lgpl2.1+)))
19406 (define-public r-r-devices
19408 (name "r-r-devices")
19413 (uri (cran-uri "R.devices" version))
19416 "1djz6vm1b7sjvx1q319dl47gbnz9kvipaxcz9i0spyp094lv3m62"))))
19417 (properties `((upstream-name . "R.devices")))
19418 (build-system r-build-system)
19420 `(("r-base64enc" ,r-base64enc)
19421 ("r-r-methodss3" ,r-r-methodss3)
19423 ("r-r-utils" ,r-r-utils)))
19424 (home-page "https://github.com/HenrikBengtsson/R.devices")
19425 (synopsis "Unified handling of graphics devices")
19427 "This package provides functions for creating plots and image files in a
19428 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
19429 Default device options as well as scales and aspect ratios are controlled in a
19430 uniform way across all device types. Switching output format requires minimal
19431 changes in code. This package is ideal for large-scale batch processing,
19432 because it will never leave open graphics devices or incomplete image files
19433 behind, even on errors or user interrupts.")
19434 (license license:lgpl2.1+)))
19436 (define-public r-acnr
19443 (uri (cran-uri "acnr" version))
19446 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
19447 (properties `((upstream-name . "acnr")))
19448 (build-system r-build-system)
19449 (home-page "https://github.com/mpierrejean/acnr")
19450 (synopsis "Annotated copy-number regions")
19452 "This package provides SNP array data from different types of copy-number
19453 regions. These regions were identified manually by the authors of the package
19454 and may be used to generate realistic data sets with known truth.")
19455 (license license:lgpl2.1+)))
19457 (define-public r-acopula
19464 (uri (cran-uri "acopula" version))
19467 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
19468 (properties `((upstream-name . "acopula")))
19469 (build-system r-build-system)
19470 (home-page "https://cran.r-project.org/web/packages/acopula/")
19471 (synopsis "Modelling dependence with multivariate Archimax copulas")
19473 "Archimax copulas are a mixture of Archimedean and EV copulas. This
19474 package provides definitions of several parametric families of generator and
19475 dependence function, computes CDF and PDF, estimates parameters, tests for
19476 goodness of fit, generates random sample and checks copula properties for
19477 custom constructs. In the 2-dimensional case explicit formulas for density
19478 are used, contrary to higher dimensions when all derivatives are linearly
19479 approximated. Several non-archimax families (normal, FGM, Plackett) are
19480 provided as well.")
19481 (license license:gpl2)))
19483 (define-public r-tuner
19490 (uri (cran-uri "tuneR" version))
19493 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
19494 (properties `((upstream-name . "tuneR")))
19495 (build-system r-build-system)
19496 (propagated-inputs `(("r-signal" ,r-signal)))
19497 (home-page "https://cran.r-project.org/web/packages/tuneR/")
19498 (synopsis "Analysis of music and speech")
19500 "This is a package for the analysis of music and speech. Analyze music
19501 and speech, extract features like MFCCs, handle wave files and their
19502 representation in various ways, read MP3, read MIDI, perform steps of a
19503 transcription, ...")
19504 ;; Either of these versions.
19505 (license (list license:gpl2 license:gpl3))))
19507 (define-public r-seewave
19514 (uri (cran-uri "seewave" version))
19517 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
19518 (properties `((upstream-name . "seewave")))
19519 (build-system r-build-system)
19521 `(("libsndfile" ,libsndfile)))
19523 `(("r-tuner" ,r-tuner)))
19524 (home-page "http://rug.mnhn.fr/seewave")
19525 (synopsis "Sound analysis and synthesis")
19527 "This package provides functions for analysing, manipulating, displaying,
19528 editing and synthesizing time waves (particularly sound). This package
19529 processes time analysis (oscillograms and envelopes), spectral content,
19530 resonance quality factor, entropy, cross correlation and autocorrelation,
19531 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
19532 and 3D spectrograms and many other analyses.")
19533 (license license:gpl2+)))
19535 (define-public r-acousticndlcoder
19537 (name "r-acousticndlcoder")
19542 (uri (cran-uri "AcousticNDLCodeR" version))
19545 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
19547 `((upstream-name . "AcousticNDLCodeR")))
19548 (build-system r-build-system)
19550 `(("r-seewave" ,r-seewave)
19551 ("r-tuner" ,r-tuner)
19553 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
19554 (synopsis "Coding sound files for use with NDL")
19556 "Make acoustic cues to use with the R package @code{ndl}.
19557 The package implements functions used in the PLoS ONE paper \"Words from
19558 spontaneous conversational speech can be recognized with human-like accuracy
19559 by an error-driven learning algorithm that discriminates between meanings
19560 straight from smart acoustic features, bypassing the phoneme as recognition
19561 unit.\" @url{doi:10.1371/journal.pone.0174623}")
19562 (license license:gpl2+)))
19564 (define-public r-acp
19571 (uri (cran-uri "acp" version))
19574 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
19575 (properties `((upstream-name . "acp")))
19576 (build-system r-build-system)
19578 `(("r-quantmod" ,r-quantmod)
19579 ("r-tseries" ,r-tseries)))
19580 (home-page "https://cran.r-project.org/web/packages/acp/")
19581 (synopsis "Autoregressive conditional Poisson")
19583 "This package supports the analysis of count data exhibiting
19584 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
19585 model (ACP(p,q)) proposed by Heinen (2003).")
19586 (license license:gpl2)))
19588 (define-public r-ada
19595 (uri (cran-uri "ada" version))
19598 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
19599 (properties `((upstream-name . "ada")))
19600 (build-system r-build-system)
19601 (propagated-inputs `(("r-rpart" ,r-rpart)))
19602 (home-page "https://cran.r-project.org/web/packages/ada/")
19603 (synopsis "Stochastic boosting")
19605 "This package provides a straightforward, well-documented, and broad
19606 boosting routine for classification, ideally suited for small to
19607 moderate-sized data sets. It performs discrete, real, and gentle boost under
19608 both exponential and logistic loss on a given data set.")
19609 ;; Any version of the GPL.
19610 (license (list license:gpl2+ license:gpl3+))))
19612 (define-public r-genalg
19619 (uri (cran-uri "genalg" version))
19622 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
19623 (properties `((upstream-name . "genalg")))
19624 (build-system r-build-system)
19625 (home-page "https://github.com/egonw/genalg")
19626 (synopsis "R based genetic algorithm")
19628 "This package provides an R based genetic algorithm for binary and
19629 floating point chromosomes.")
19630 (license license:gpl2)))
19632 (define-public r-kernelfactory
19634 (name "r-kernelfactory")
19639 (uri (cran-uri "kernelFactory" version))
19642 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
19643 (properties `((upstream-name . "kernelFactory")))
19644 (build-system r-build-system)
19647 ("r-genalg" ,r-genalg)
19648 ("r-kernlab" ,r-kernlab)
19649 ("r-randomforest" ,r-randomforest)))
19650 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
19651 (synopsis "Ensemble of kernel machines")
19653 "Kernel factory is an ensemble method where each base classifier (random
19654 forest) is fit on the kernel matrix of a subset of the training data.")
19655 (license license:gpl2+)))
19657 (define-public r-dummies
19664 (uri (cran-uri "dummies" version))
19667 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
19668 (properties `((upstream-name . "dummies")))
19669 (build-system r-build-system)
19670 (home-page "https://decisionpatterns.com")
19671 (synopsis "Create dummy/indicator variables flexibly and efficiently")
19673 "This package lets you expand factors, characters and other eligible
19674 classes into dummy/indicator variables.")
19675 (license license:gpl2+)))
19677 (define-public r-acrm
19684 (uri (cran-uri "aCRM" version))
19687 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
19688 (properties `((upstream-name . "aCRM")))
19689 (build-system r-build-system)
19692 ("r-dummies" ,r-dummies)
19693 ("r-kernelfactory" ,r-kernelfactory)
19694 ("r-randomforest" ,r-randomforest)))
19695 (home-page "https://cran.r-project.org/web/packages/aCRM/")
19696 (synopsis "Convenience functions for analytical customer relationship management")
19698 "This package provides convenience functions for data preparation and
19699 modeling often used in @dfn{analytical customer relationship
19700 management} (aCRM).")
19701 (license license:gpl2+)))
19703 (define-public r-treeclust
19705 (name "r-treeclust")
19710 (uri (cran-uri "treeClust" version))
19713 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
19714 (properties `((upstream-name . "treeClust")))
19715 (build-system r-build-system)
19717 `(("r-cluster" ,r-cluster)
19718 ("r-rpart" ,r-rpart)))
19719 (home-page "https://cran.r-project.org/web/packages/treeClust/")
19720 (synopsis "Cluster distances through trees")
19722 "This package provides tools to create a measure of inter-point
19723 dissimilarity useful for clustering mixed data, and, optionally, perform the
19725 (license license:gpl2+)))
19727 (define-public r-acrosstic
19729 (name "r-acrosstic")
19734 (uri (cran-uri "AcrossTic" version))
19737 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
19738 (properties `((upstream-name . "AcrossTic")))
19739 (build-system r-build-system)
19741 `(("r-lpsolve" ,r-lpsolve)
19742 ("r-treeclust" ,r-treeclust)))
19743 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
19744 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
19746 "This is a package for constructing minimum-cost regular spanning
19747 subgraph as part of a non-parametric two-sample test for equality of
19749 (license license:gpl2+)))
19751 (define-public r-acrt
19758 (uri (cran-uri "acrt" version))
19761 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
19762 (properties `((upstream-name . "acrt")))
19763 (build-system r-build-system)
19765 `(("r-rcpp" ,r-rcpp)
19766 ("r-rcppeigen" ,r-rcppeigen)
19767 ("r-sandwich" ,r-sandwich)))
19768 (home-page "https://cran.r-project.org/web/packages/acrt/")
19769 (synopsis "Autocorrelation robust testing")
19771 "This package provides functions for testing affine hypotheses on the
19772 regression coefficient vector in regression models with autocorrelated
19774 (license license:gpl2)))
19776 (define-public r-acs
19783 (uri (cran-uri "acs" version))
19786 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
19787 (properties `((upstream-name . "acs")))
19788 (build-system r-build-system)
19790 `(("r-httr" ,r-httr)
19793 ("r-stringr" ,r-stringr)
19795 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
19796 (synopsis "Work with data from the US Census")
19798 "This package provides a general toolkit for downloading, managing,
19799 analyzing, and presenting data from the
19800 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
19801 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
19802 American Community Survey (ACS). Confidence intervals provided with ACS data
19803 are converted to standard errors to be bundled with estimates in complex
19804 @code{acs} objects. The package provides new methods to conduct standard
19805 operations on @code{acs} objects and present/plot data in statistically
19806 appropriate ways.")
19807 (license license:gpl3)))
19809 (define-public r-acss-data
19811 (name "r-acss-data")
19816 (uri (cran-uri "acss.data" version))
19819 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
19820 (properties `((upstream-name . "acss.data")))
19821 (build-system r-build-system)
19822 (home-page "http://complexitycalculator.com/methodology.html")
19823 (synopsis "Data for algorithmic complexity of short strings")
19825 "This is a data only package providing the algorithmic complexity of
19826 short strings, computed using the coding theorem method. For a given set of
19827 symbols in a string, all possible or a large number of random samples of
19828 Turing machines with a given number of states (e.g., 5) and number of symbols
19829 corresponding to the number of symbols in the strings were simulated until
19830 they reached a halting state or failed to end. This package contains data on
19831 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
19832 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
19833 distribution of the halting states.")
19834 (license license:gpl2+)))
19836 (define-public r-acss
19843 (uri (cran-uri "acss" version))
19846 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
19847 (properties `((upstream-name . "acss")))
19848 (build-system r-build-system)
19850 `(("r-acss-data" ,r-acss-data)
19852 (home-page "http://complexitycalculator.com/methodology.html")
19853 (synopsis "Algorithmic complexity for short strings")
19855 "The main purpose of this package is to provide the algorithmic
19856 complexity for short strings, an approximation of the Kolmogorov Complexity of
19857 a short string using the coding theorem method. While the database containing
19858 the complexity is provided in the data only package @code{acss.data}, this
19859 package provides functions accessing the data such as @code{prob_random}
19860 returning the posterior probability that a given string was produced by a
19861 random process. In addition, two traditional (but problematic) measures of
19862 complexity are also provided: entropy and change complexity.")
19863 (license license:gpl2+)))
19865 (define-public r-acswr
19872 (uri (cran-uri "ACSWR" version))
19875 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
19876 (properties `((upstream-name . "ACSWR")))
19877 (build-system r-build-system)
19879 `(("r-mass" ,r-mass)))
19880 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
19881 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
19883 "This is a companion package for the book \"A Course in Statistics with
19884 R\" (ISBN 978-1-119-15272-9.)")
19885 (license license:gpl2)))
19887 (define-public r-alabama
19890 (version "2015.3-1")
19894 (uri (cran-uri "alabama" version))
19897 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
19898 (properties `((upstream-name . "alabama")))
19899 (build-system r-build-system)
19900 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
19901 (home-page "https://cran.r-project.org/web/packages/alabama/")
19902 (synopsis "Constrained nonlinear optimization")
19904 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
19905 Algorithm; it is used for optimizing smooth nonlinear objective functions with
19906 constraints. Linear or nonlinear equality and inequality constraints are
19908 (license license:gpl2+)))
19910 (define-public r-gdina
19917 (uri (cran-uri "GDINA" version))
19920 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
19921 (properties `((upstream-name . "GDINA")))
19922 (build-system r-build-system)
19924 `(("r-alabama" ,r-alabama)
19925 ("r-ggplot2" ,r-ggplot2)
19927 ("r-nloptr" ,r-nloptr)
19928 ("r-numderiv" ,r-numderiv)
19930 ("r-rcpparmadillo" ,r-rcpparmadillo)
19931 ("r-rsolnp" ,r-rsolnp)
19932 ("r-shiny" ,r-shiny)
19933 ("r-shinydashboard" ,r-shinydashboard)))
19935 `(("r-knitr" ,r-knitr)))
19936 (home-page "https://github.com/Wenchao-Ma/GDINA")
19937 (synopsis "Generalized DINA model framework")
19939 "This package provides a set of psychometric tools for cognitive
19940 diagnosis modeling based on the generalized deterministic inputs, noisy and
19941 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
19942 and its extensions, including the sequential G-DINA model by Ma and de la
19943 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
19944 polytomous G-DINA model by Chen and de la Torre
19945 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
19946 distribution can be independent, saturated, higher-order, loglinear smoothed
19947 or structured. Q-matrix validation, item and model fit statistics, model
19948 comparison at test and item level and differential item functioning can also
19949 be conducted. A graphical user interface is also provided.")
19950 (license license:gpl3)))
19952 (define-public r-actcd
19959 (uri (cran-uri "ACTCD" version))
19962 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
19963 (properties `((upstream-name . "ACTCD")))
19964 (build-system r-build-system)
19966 `(("r-gdina" ,r-gdina)
19967 ("r-r-methodss3" ,r-r-methodss3)))
19969 `(("gfortran" ,gfortran)))
19970 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
19971 (synopsis "Asymptotic classification theory for cognitive diagnosis")
19973 "This is a package supporting cluster analysis for cognitive diagnosis
19974 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
19975 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
19976 sum-scores, cluster analysis techniques can be used to classify examinees into
19977 latent classes based on their attribute patterns. In addition to the
19978 algorithms used to classify data, three labeling approaches are proposed to
19979 label clusters so that examinees' attribute profiles can be obtained.")
19980 (license license:gpl2+)))
19982 (define-public r-ineq
19989 (uri (cran-uri "ineq" version))
19992 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
19993 (properties `((upstream-name . "ineq")))
19994 (build-system r-build-system)
19995 (home-page "https://cran.r-project.org/web/packages/ineq/")
19996 (synopsis "Measuring inequality, concentration, and poverty")
19998 "This package provides tools for measuring inequality, concentration, and
19999 poverty measures. It provides both empirical and theoretical Lorenz curves.")
20000 ;; Either of these two versions.
20001 (license (list license:gpl2 license:gpl3))))
20003 (define-public r-actfrag
20010 (uri (cran-uri "ActFrag" version))
20013 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
20014 (properties `((upstream-name . "ActFrag")))
20015 (build-system r-build-system)
20017 `(("r-accelerometry" ,r-accelerometry)
20018 ("r-dplyr" ,r-dplyr)
20020 ("r-survival" ,r-survival)
20021 ("r-tidyr" ,r-tidyr)))
20022 (home-page "https://github.com/junruidi/ActFrag")
20023 (synopsis "Activity fragmentation metrics extraction")
20025 "This package provides functions to extract commonly used fragmentation
20026 metrics to quantify time accumulation strategies based on minute level
20027 actigraphy-measured activity counts data.")
20028 (license license:gpl3)))
20030 (define-public r-ash
20037 (uri (cran-uri "ash" version))
20040 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb"))))
20041 (properties `((upstream-name . "ash")))
20042 (build-system r-build-system)
20043 (native-inputs `(("gfortran" ,gfortran)))
20044 (home-page "https://cran.r-project.org/web/packages/ash/")
20045 (synopsis "David Scott's ASH routines")
20047 "This package provides David Scott's ASH routines ported from S-PLUS to
20049 (license license:gpl2+)))
20051 (define-public r-hdrcde
20058 (uri (cran-uri "hdrcde" version))
20061 "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3"))))
20062 (properties `((upstream-name . "hdrcde")))
20063 (build-system r-build-system)
20066 ("r-ggplot2" ,r-ggplot2)
20067 ("r-kernsmooth" ,r-kernsmooth)
20069 ("r-locfit" ,r-locfit)
20070 ("r-rcolorbrewer" ,r-rcolorbrewer)))
20071 (native-inputs `(("gfortran" ,gfortran)))
20072 (home-page "http://pkg.robjhyndman.com/hdrcde")
20073 (synopsis "Highest density regions and conditional density estimation")
20075 "This is a package for the computation of highest density regions in one
20076 and two dimensions, kernel estimation of univariate density functions
20077 conditional on one covariate, and multimodal regression.")
20078 (license license:gpl3)))
20080 (define-public r-rainbow
20087 (uri (cran-uri "rainbow" version))
20090 "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3"))))
20091 (properties `((upstream-name . "rainbow")))
20092 (build-system r-build-system)
20094 `(("r-cluster" ,r-cluster)
20095 ("r-colorspace" ,r-colorspace)
20096 ("r-hdrcde" ,r-hdrcde)
20099 ("r-pcapp" ,r-pcapp)))
20100 (home-page "https://cran.r-project.org/web/packages/rainbow/")
20101 (synopsis "Bagplots, boxplots and rainbow plots for functional data")
20103 "This is a package for visualizing functional data and identifying
20104 functional outliers with bagplots, boxplots and rainbow plots.")
20105 (license license:gpl3)))
20107 (define-public r-fds
20114 (uri (cran-uri "fds" version))
20117 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0"))))
20118 (properties `((upstream-name . "fds")))
20119 (build-system r-build-system)
20121 `(("r-rainbow" ,r-rainbow)
20122 ("r-rcurl" ,r-rcurl)))
20123 (home-page "https://cran.r-project.org/web/packages/fds/")
20124 (synopsis "Functional data sets")
20125 (description "This package contains a list of functional time series,
20126 sliced functional time series, and functional data sets. Functional time
20127 series is a special type of functional data observed over time. Sliced
20128 functional time series is a special type of functional time series with a time
20129 variable observed over time.")
20130 (license license:gpl2+)))
20132 (define-public r-fda
20139 (uri (cran-uri "fda" version))
20142 "0yjrjsv55bcwqn2yxjgj3hn17wfvjvgngfw9xv3w802i52yz9gf8"))))
20143 (properties `((upstream-name . "fda")))
20144 (build-system r-build-system)
20147 ("r-matrix" ,r-matrix)))
20148 (home-page "https://www.functionaldata.org")
20149 (synopsis "Functional data analysis")
20151 "These functions were developed to support functional data analysis as
20152 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
20153 Analysis. The package includes data sets and script files working many
20155 (license license:gpl2+)))
20157 (define-public r-actigraphy
20159 (name "r-actigraphy")
20164 (uri (cran-uri "Actigraphy" version))
20167 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
20168 (properties `((upstream-name . "Actigraphy")))
20169 (build-system r-build-system)
20171 `(("r-fda" ,r-fda)))
20172 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
20173 (synopsis "Actigraphy data analysis")
20175 "This package provides tools for functional linear modeling and analysis
20176 of actigraphy data.")
20177 (license license:asl2.0)))
20179 (define-public r-activedriver
20181 (name "r-activedriver")
20186 (uri (cran-uri "ActiveDriver" version))
20189 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
20190 (properties `((upstream-name . "ActiveDriver")))
20191 (build-system r-build-system)
20193 `(("r-mass" ,r-mass)))
20194 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
20195 (synopsis "Tools for finding cancer driver proteins")
20197 "This package provides a mutation analysis tool that discovers cancer
20198 driver genes with frequent mutations in protein signalling sites such as
20199 post-translational modifications (phosphorylation, ubiquitination, etc). The
20200 Poisson generalized linear regression model identifies genes where cancer
20201 mutations in signalling sites are more frequent than expected from the
20202 sequence of the entire gene. Integration of mutations with signalling
20203 information helps find new driver genes and propose candidate mechanisms to
20205 (license license:gpl2+)))
20207 (define-public r-activitycounts
20209 (name "r-activitycounts")
20214 (uri (cran-uri "activityCounts" version))
20217 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
20219 `((upstream-name . "activityCounts")))
20220 (build-system r-build-system)
20222 `(("r-lubridate" ,r-lubridate)
20223 ("r-magrittr" ,r-magrittr)
20224 ("r-seewave" ,r-seewave)
20225 ("r-signal" ,r-signal)
20226 ("r-tibble" ,r-tibble)))
20227 (home-page "https://github.com/walkabillylab/activityCounts")
20228 (synopsis "Generate ActiLife counts")
20230 "ActiLife generates activity counts from data collected by Actigraph
20231 accelerometers. Actigraph is one of the most common research-grade
20232 accelerometers. There is considerable research validating and developing
20233 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
20234 counts are proprietary and difficult to implement if researchers use different
20235 accelerometer brands. The code creates ActiLife counts from raw acceleration
20236 data for different accelerometer brands.")
20237 (license license:gpl3)))
20239 (define-public r-activityindex
20241 (name "r-activityindex")
20246 (uri (cran-uri "ActivityIndex" version))
20249 "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5"))))
20250 (properties `((upstream-name . "ActivityIndex")))
20251 (build-system r-build-system)
20253 `(("r-data-table" ,r-data-table)
20254 ("r-matrixstats" ,r-matrixstats)
20255 ("r-r-utils" ,r-r-utils)))
20257 `(("r-knitr" ,r-knitr)))
20258 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
20259 (synopsis "Activity Index calculation using raw accelerometry data")
20261 "This is a package to read raw accelerometry from GT3X+ accelerometry
20262 data and plain table data to calculate the Activity Index from Bai et
20263 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
20264 (license license:gpl3)))
20266 (define-public r-activpal
20268 (name "r-activpal")
20273 (uri (cran-uri "activPAL" version))
20276 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
20277 (properties `((upstream-name . "activPAL")))
20278 (build-system r-build-system)
20280 `(("r-devtools" ,r-devtools)
20281 ("r-dplyr" ,r-dplyr)
20282 ("r-ggplot2" ,r-ggplot2)
20283 ("r-lubridate" ,r-lubridate)
20284 ("r-magrittr" ,r-magrittr)
20285 ("r-tidyr" ,r-tidyr)))
20286 (home-page "https://cran.r-project.org/web/packages/activPAL")
20287 (synopsis "Processing and chart generation from activPAL events files")
20289 "This package contains functions to generate pre-defined summary
20290 statistics from activPAL events files. The package also contains functions to
20291 produce informative graphics that visualize physical activity behaviour and
20292 trends. This includes generating graphs that align physical activity
20293 behaviour with additional time based observations described by other data
20294 sets, such as sleep diaries and continuous glucose monitoring data.")
20295 (license license:gpl3)))
20297 (define-public r-activpalprocessing
20299 (name "r-activpalprocessing")
20304 (uri (cran-uri "activpalProcessing" version))
20307 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
20309 `((upstream-name . "activpalProcessing")))
20310 (build-system r-build-system)
20312 `(("r-chron" ,r-chron)))
20313 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
20314 (synopsis "Process activPAL events files")
20316 "This package performs estimation of physical activity and sedentary
20317 behavior variables from activPAL events files.")
20318 ;; Either version of the GPL.
20319 (license (list license:gpl2 license:gpl3))))
20321 (define-public r-actogrammr
20323 (name "r-actogrammr")
20328 (uri (cran-uri "actogrammr" version))
20331 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
20332 (properties `((upstream-name . "actogrammr")))
20333 (build-system r-build-system)
20335 `(("r-dplyr" ,r-dplyr)
20336 ("r-ggplot2" ,r-ggplot2)
20337 ("r-lubridate" ,r-lubridate)
20338 ("r-readr" ,r-readr)
20339 ("r-tidyr" ,r-tidyr)))
20340 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
20341 (synopsis "Read in activity data and plot actograms")
20343 "Read in activity measurements from standard file formats used by
20344 circadian rhythm researchers, currently only ClockLab format, and process and
20345 plot the data. The central type of plot is the actogram, as first described
20346 in \"Activity and distribution of certain wild mice in relation to biotic
20347 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
20348 (license license:gpl3)))
20350 (define-public r-expint
20357 (uri (cran-uri "expint" version))
20360 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
20361 (properties `((upstream-name . "expint")))
20362 (build-system r-build-system)
20363 (home-page "https://gitlab.com/vigou3/expint")
20364 (synopsis "Exponential integral and incomplete Gamma function")
20366 "This package provides the exponential integrals @code{E_1(x)},
20367 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
20368 function @code{G(a, x)} defined for negative values of its first argument.
20369 The package also gives easy access to the underlying C routines through an
20370 API; see the package vignette for details.")
20371 (license license:gpl2+)))
20373 (define-public r-actuar
20380 (uri (cran-uri "actuar" version))
20383 "15a8axb2ym46j8vlm7icwnsc950p8m66hp0armha7drk0725y77k"))))
20384 (properties `((upstream-name . "actuar")))
20385 (build-system r-build-system)
20386 (propagated-inputs `(("r-expint" ,r-expint)))
20387 (home-page "https://gitlab.com/vigou3/actuar")
20388 (synopsis "Actuarial functions and heavy tailed distributions")
20390 "This package provides functions and data sets for actuarial science:
20391 modeling of loss distributions; risk theory and ruin theory; simulation of
20392 compound models, discrete mixtures and compound hierarchical models;
20393 credibility theory. It boasts support for many additional probability
20394 distributions to model insurance loss amounts and loss frequency: 19
20395 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
20396 distribution; zero-truncated and zero-modified extensions of the standard
20397 discrete distributions. It also supports phase-type distributions commonly
20398 used to compute ruin probabilities.")
20399 (license license:gpl2+)))
20401 (define-public r-bmp
20408 (uri (cran-uri "bmp" version))
20411 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
20412 (properties `((upstream-name . "bmp")))
20413 (build-system r-build-system)
20414 (home-page "https://cran.r-project.org/web/packages/bmp/")
20415 (synopsis "Read Bitmap (BMP) images")
20417 "This package provides pure R tools to read BMP format images. It is
20418 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
20419 (license license:gpl2+)))
20421 (define-public r-readbitmap
20423 (name "r-readbitmap")
20428 (uri (cran-uri "readbitmap" version))
20431 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
20432 (properties `((upstream-name . "readbitmap")))
20433 (build-system r-build-system)
20435 `(("libjpeg" ,libjpeg-turbo)
20436 ("libpng" ,libpng)))
20441 ("r-tiff" ,r-tiff)))
20442 (home-page "https://github.com/jefferis/readbitmap")
20443 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
20445 "This package provides tools to identify and read BMP, JPEG, PNG, and
20446 TIFF format bitmap images. Identification defaults to the use of the magic
20447 number embedded in the file rather than the file extension.")
20448 (license license:gpl2+)))
20450 (define-public r-imager
20457 (uri (cran-uri "imager" version))
20460 "1wxvbv803222gjrf1ys6a349xlnmmdw3kqgi93piq9gq7lahihvg"))))
20461 (properties `((upstream-name . "imager")))
20462 (build-system r-build-system)
20465 ("libtiff" ,libtiff)
20469 `(("r-downloader" ,r-downloader)
20470 ("r-igraph" ,r-igraph)
20472 ("r-magrittr" ,r-magrittr)
20474 ("r-purrr" ,r-purrr)
20476 ("r-readbitmap" ,r-readbitmap)
20477 ("r-stringr" ,r-stringr)))
20479 `(("pkg-config" ,pkg-config)
20480 ("r-knitr" ,r-knitr)))
20481 (home-page "https://dahtah.github.io/imager/")
20482 (synopsis "Image processing library")
20484 "This is a package for fast image processing for images in up to 4
20485 dimensions (two spatial dimensions, one time/depth dimension, one color
20486 dimension). It provides most traditional image processing tools (filtering,
20487 morphology, transformations, etc.) as well as various functions for easily
20488 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
20489 simple, modern C++ library for image processing.")
20490 (license license:lgpl3)))
20492 (define-public r-acuityview
20494 (name "r-acuityview")
20499 (uri (cran-uri "AcuityView" version))
20502 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
20503 (properties `((upstream-name . "AcuityView")))
20504 (build-system r-build-system)
20506 `(("r-fftwtools" ,r-fftwtools)
20507 ("r-imager" ,r-imager)
20508 ("r-plotrix" ,r-plotrix)))
20509 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
20510 (synopsis "Display scenes as seen by an animal with less acute vision")
20512 "This package provides a simple method for representing a visual scene as
20513 it may be seen by an animal with less acute vision.")
20514 (license license:gpl2+)))
20516 (define-public r-caret
20523 (uri (cran-uri "caret" version))
20526 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
20527 (build-system r-build-system)
20529 `(("r-foreach" ,r-foreach)
20530 ("r-ggplot2" ,r-ggplot2)
20531 ("r-lattice" ,r-lattice)
20532 ("r-modelmetrics" ,r-modelmetrics)
20536 ("r-recipes" ,r-recipes)
20537 ("r-reshape2" ,r-reshape2)
20538 ("r-withr" ,r-withr)))
20540 `(("r-knitr" ,r-knitr)))
20541 (home-page "https://github.com/topepo/caret")
20542 (synopsis "Classification and regression training")
20544 "This package provides miscellaneous functions for training and plotting
20545 classification and regression models.")
20546 (license license:gpl2+)))
20548 (define-public r-adabag
20555 (uri (cran-uri "adabag" version))
20558 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
20559 (properties `((upstream-name . "adabag")))
20560 (build-system r-build-system)
20562 `(("r-caret" ,r-caret)
20563 ("r-doparallel" ,r-doparallel)
20564 ("r-foreach" ,r-foreach)
20565 ("r-rpart" ,r-rpart)))
20566 (home-page "https://cran.r-project.org/web/packages/adabag/")
20567 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
20569 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
20570 Breiman's Bagging algorithm using classification trees as individual
20571 classifiers. Once these classifiers have been trained, they can be used to
20572 predict on new data. Also, cross validation estimation of the error can be
20574 (license license:gpl2+)))
20576 (define-public r-adagio
20583 (uri (cran-uri "adagio" version))
20586 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
20587 (properties `((upstream-name . "adagio")))
20588 (build-system r-build-system)
20589 (native-inputs `(("gfortran" ,gfortran)))
20590 (home-page "https://cran.r-project.org/web/packages/adagio/")
20591 (synopsis "Discrete and global optimization routines")
20593 "This package provides methods and algorithms for discrete optimization,
20594 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
20595 Hooke-Jeeves minimization, and some (evolutionary) global optimization
20597 (license license:gpl3+)))
20599 (define-public r-univoutl
20601 (name "r-univoutl")
20606 (uri (cran-uri "univOutl" version))
20609 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
20610 (properties `((upstream-name . "univOutl")))
20611 (build-system r-build-system)
20613 `(("r-hmisc" ,r-hmisc)
20614 ("r-robustbase" ,r-robustbase)))
20615 (home-page "https://github.com/marcellodo/univOutl")
20616 (synopsis "Detection of univariate outliers")
20618 "This package provides well-known outlier detection techniques in the
20619 univariate case. Methods to deal with skewed distribution are included too.
20620 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
20621 historical data is implemented as well. When available, survey weights can be
20622 used in outliers detection.")
20623 (license license:gpl2+)))
20625 (define-public r-tolerance
20627 (name "r-tolerance")
20632 (uri (cran-uri "tolerance" version))
20635 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
20636 (properties `((upstream-name . "tolerance")))
20637 (build-system r-build-system)
20639 `(("r-mass" ,r-mass)
20641 (home-page "https://cran.r-project.org/web/packages/tolerance/")
20642 (synopsis "Statistical tolerance intervals and regions")
20644 "This package provides functions for estimating tolerance
20645 limits (intervals) for various univariate distributions (binomial, Cauchy,
20646 discrete Pareto, exponential, two-parameter exponential, extreme value,
20647 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
20648 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
20649 Bayesian normal tolerance limits, multivariate normal tolerance regions,
20650 nonparametric tolerance intervals, tolerance bands for regression
20651 settings (linear regression, nonlinear regression, nonparametric regression,
20652 and multivariate regression), and analysis of variance tolerance intervals.
20653 Visualizations are also available for most of these settings.")
20654 (license license:gpl2+)))
20656 (define-public r-additivitytests
20658 (name "r-additivitytests")
20663 (uri (cran-uri "additivityTests" version))
20666 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
20668 `((upstream-name . "additivityTests")))
20669 (build-system r-build-system)
20670 (home-page "https://github.com/simecek/additivityTests")
20671 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
20673 "This package provides an implementation of the Tukey, Mandel,
20674 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
20675 (license license:gpl3)))
20677 (define-public r-flexclust
20679 (name "r-flexclust")
20684 (uri (cran-uri "flexclust" version))
20687 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
20688 (properties `((upstream-name . "flexclust")))
20689 (build-system r-build-system)
20691 `(("r-class" ,r-class)
20692 ("r-lattice" ,r-lattice)
20693 ("r-modeltools" ,r-modeltools)))
20694 (home-page "https://cran.r-project.org/web/packages/flexclust/")
20695 (synopsis "Flexible cluster algorithms")
20697 "The main function @code{kcca} implements a general framework for
20698 k-centroids cluster analysis supporting arbitrary distance measures and
20699 centroid computation. Further cluster methods include hard competitive
20700 learning, neural gas, and QT clustering. There are numerous visualization
20701 methods for cluster results (neighborhood graphs, convex cluster hulls,
20702 barcharts of centroids, ...), and bootstrap methods for the analysis of
20703 cluster stability.")
20704 (license license:gpl2)))
20706 (define-public r-biclust
20713 (uri (cran-uri "biclust" version))
20716 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
20717 (properties `((upstream-name . "biclust")))
20718 (build-system r-build-system)
20720 `(("r-additivitytests" ,r-additivitytests)
20721 ("r-colorspace" ,r-colorspace)
20722 ("r-flexclust" ,r-flexclust)
20723 ("r-ggplot2" ,r-ggplot2)
20724 ("r-lattice" ,r-lattice)
20726 ("r-tidyr" ,r-tidyr)))
20727 (home-page "https://cran.r-project.org/web/packages/biclust/")
20728 (synopsis "BiCluster algorithms")
20730 "The main function @code{biclust()} provides several algorithms to find
20731 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
20732 In addition, the package provides methods for data
20733 preprocessing (normalization and discretization), visualization, and
20734 validation of bicluster solutions.")
20735 (license license:gpl3)))
20737 (define-public r-icge
20744 (uri (cran-uri "ICGE" version))
20747 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
20748 (properties `((upstream-name . "ICGE")))
20749 (build-system r-build-system)
20751 `(("r-cluster" ,r-cluster)
20752 ("r-mass" ,r-mass)))
20753 (home-page "https://cran.r-project.org/web/packages/ICGE/")
20754 (synopsis "Cluster estimation and identification of atypical units")
20756 "ICGE is a package that helps to estimate the number of real clusters in
20757 data as well as to identify atypical units. The underlying methods are based
20758 on distances rather than on unit x variables.")
20759 (license license:gpl2+)))
20761 (define-public r-depth
20764 (version "2.1-1.1")
20768 (uri (cran-uri "depth" version))
20771 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
20772 (properties `((upstream-name . "depth")))
20773 (build-system r-build-system)
20775 `(("r-abind" ,r-abind)
20776 ("r-circular" ,r-circular)
20779 `(("gfortran" ,gfortran)))
20780 (home-page "https://cran.r-project.org/web/packages/depth/")
20781 (synopsis "Nonparametric depth functions for multivariate analysis")
20783 "This package provides tools for depth functions methodology applied to
20784 multivariate analysis. Besides allowing calculation of depth values and
20785 depth-based location estimators, the package includes functions or drawing
20786 contour plots and perspective plots of depth functions. Euclidean and
20787 spherical depths are supported.")
20788 (license license:gpl2)))
20790 (define-public r-archetypes
20792 (name "r-archetypes")
20793 (version "2.2-0.1")
20797 (uri (cran-uri "archetypes" version))
20800 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
20801 (properties `((upstream-name . "archetypes")))
20802 (build-system r-build-system)
20804 `(("r-modeltools" ,r-modeltools)
20805 ("r-nnls" ,r-nnls)))
20806 (home-page "https://cran.r-project.org/web/packages/archetypes")
20807 (synopsis "Archetypal analysis")
20809 "The main function @code{archetypes} implements a framework for
20810 archetypal analysis supporting arbitrary problem solving mechanisms for the
20811 different conceptual parts of the algorithm.")
20812 (license license:gpl2+)))
20814 (define-public r-shapes
20821 (uri (cran-uri "shapes" version))
20824 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
20825 (properties `((upstream-name . "shapes")))
20826 (build-system r-build-system)
20828 `(("r-mass" ,r-mass)
20829 ("r-minpack-lm" ,r-minpack-lm)
20831 ("r-scatterplot3d" ,r-scatterplot3d)))
20832 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
20833 (synopsis "Statistical shape analysis")
20835 "This package provides routines for the statistical analysis of landmark
20836 shapes, including Procrustes analysis, graphical displays, principal
20837 components analysis, permutation and bootstrap tests, thin-plate spline
20838 transformation grids and comparing covariance matrices. See Dryden, I.L. and
20839 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
20840 Edition), John Wiley and Sons.")
20841 (license license:gpl2)))
20843 (define-public r-anthropometry
20845 (name "r-anthropometry")
20850 (uri (cran-uri "Anthropometry" version))
20853 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
20854 (properties `((upstream-name . "Anthropometry")))
20855 (build-system r-build-system)
20857 `(("r-archetypes" ,r-archetypes)
20858 ("r-biclust" ,r-biclust)
20859 ("r-cluster" ,r-cluster)
20860 ("r-depth" ,r-depth)
20865 ("r-shapes" ,r-shapes)))
20867 `(("r-knitr" ,r-knitr)))
20868 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
20869 (synopsis "Statistical methods for anthropometric data")
20871 "This package provides statistical methods especially developed to
20872 analyze anthropometric data. These methods are aimed at providing effective
20873 solutions to some commons problems related to Ergonomics and Anthropometry.
20874 They are based on clustering, the statistical concept of data depth,
20875 statistical shape analysis and archetypal analysis.")
20876 (license license:gpl2+)))
20878 (define-public r-adamethods
20880 (name "r-adamethods")
20885 (uri (cran-uri "adamethods" version))
20888 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
20889 (properties `((upstream-name . "adamethods")))
20890 (build-system r-build-system)
20892 `(("r-anthropometry" ,r-anthropometry)
20893 ("r-archetypes" ,r-archetypes)
20895 ("r-foreach" ,r-foreach)
20897 ("r-tolerance" ,r-tolerance)
20898 ("r-univoutl" ,r-univoutl)))
20899 (home-page "https://cran.r-project.org/web/packages/adamethods/")
20900 (synopsis "Archetypoid algorithms and anomaly detection")
20902 "This package is a collection of several algorithms to obtain
20903 archetypoids with small and large databases and with both classical
20904 multivariate data and functional data (univariate and multivariate). Some of
20905 these algorithms also detect anomalies (outliers).")
20906 (license license:gpl2+)))
20908 (define-public r-idpmisc
20915 (uri (cran-uri "IDPmisc" version))
20918 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
20919 (properties `((upstream-name . "IDPmisc")))
20920 (build-system r-build-system)
20922 `(("r-lattice" ,r-lattice)))
20923 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
20924 (synopsis "Functions for data analyses and visualization")
20926 "This package provides different high-level graphics functions for
20927 displaying large datasets, displaying circular data in a very flexible way,
20928 finding local maxima, brewing color ramps, drawing nice arrows, zooming
20929 2D-plots, creating figures with differently colored margin and plot region.
20930 In addition, the package contains auxiliary functions for data manipulation
20931 like omitting observations with irregular values or selecting data by logical
20932 vectors, which include NAs. Other functions are especially useful in
20933 spectroscopy and analyses of environmental data: robust baseline fitting,
20934 finding peaks in spectra, converting humidity measures.")
20935 (license license:gpl3+)))
20937 (define-public r-qqman
20944 (uri (cran-uri "qqman" version))
20947 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
20948 (properties `((upstream-name . "qqman")))
20949 (build-system r-build-system)
20951 `(("r-calibrate" ,r-calibrate)))
20952 (home-page "https://cran.r-project.org/web/packages/qqman/")
20953 (synopsis "Q-Q and Manhattan plots for GWAS data")
20955 "This package allows you to create Q-Q and Manhattan plots for GWAS data
20956 from PLINK results.")
20957 (license license:gpl3)))
20959 (define-public r-ggplot-multistats
20961 (name "r-ggplot-multistats")
20966 (uri (cran-uri "ggplot.multistats" version))
20969 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
20971 `((upstream-name . "ggplot.multistats")))
20972 (build-system r-build-system)
20974 `(("r-ggplot2" ,r-ggplot2)
20975 ("r-hexbin" ,r-hexbin)
20976 ("r-rlang" ,r-rlang)
20977 ("r-scales" ,r-scales)))
20978 (home-page "https://github.com/flying-sheep/ggplot.multistats")
20979 (synopsis "Multiple summary statistics for binned stats/geometries")
20981 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
20982 which functions similar to its singular form, but allows the use of multiple
20983 statistics per bin. Those statistics can be mapped to multiple bin
20985 (license license:gpl3)))
20987 (define-public r-knn-covertree
20989 (name "r-knn-covertree")
20994 (uri (cran-uri "knn.covertree" version))
20997 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
20998 (properties `((upstream-name . "knn.covertree")))
20999 (build-system r-build-system)
21001 `(("r-matrix" ,r-matrix)
21003 ("r-rcppeigen" ,r-rcppeigen)))
21004 (home-page "https://github.com/flying-sheep/knn.covertree")
21005 (synopsis "Accurate kNN Implementation with multiple distance measures")
21007 "Similarly to the FNN package, this package allows calculation of the k
21008 nearest neighbors (kNN) of a data matrix. The implementation is based on
21009 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
21010 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
21011 (license license:agpl3+)))
21013 (define-public r-poibin
21020 (uri (cran-uri "poibin" version))
21023 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
21024 (properties `((upstream-name . "poibin")))
21025 (build-system r-build-system)
21026 (home-page "https://cran.r-project.org/web/packages/poibin/")
21027 (synopsis "Poisson binomial distribution")
21029 "This package provides an implementation of both the exact and
21030 approximation methods for computing the @dfn{cumulative distribution
21031 function} (CDF) of the Poisson binomial distribution. It also provides the
21032 @dfn{probability mass function} (PMF), quantile function, and random number
21033 generation for the Poisson binomial distribution.")
21034 (license license:gpl2)))
21036 (define-public r-diagram
21043 (uri (cran-uri "diagram" version))
21046 "1r3lyl0h7mk9cfg8smr3jydfkjdawaphnxibkxfjqa7029vkxh79"))))
21047 (properties `((upstream-name . "diagram")))
21048 (build-system r-build-system)
21050 `(("r-shape" ,r-shape)))
21051 (home-page "https://cran.r-project.org/web/packages/diagram/")
21052 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
21054 "This package provides tools to visualize simple graphs (networks) based
21055 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
21056 electrical networks, etc. It also includes supporting material for the book
21057 \"A practical guide to ecological modelling - using R as a simulation
21058 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
21059 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
21060 Francesca Mazzia (2012).")
21061 (license license:gpl2+)))
21063 (define-public r-lim
21070 (uri (cran-uri "LIM" version))
21073 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
21074 (properties `((upstream-name . "LIM")))
21075 (build-system r-build-system)
21077 `(("r-diagram" ,r-diagram)
21078 ("r-limsolve" ,r-limsolve)))
21079 (home-page "https://cran.r-project.org/web/packages/LIM/")
21080 (synopsis "Linear inverse model examples and solution methods")
21082 "This package provides functions that read and solve linear inverse
21083 problems (food web problems, linear programming problems).")
21084 (license license:gpl2+)))
21086 (define-public r-shinycssloaders
21088 (name "r-shinycssloaders")
21093 (uri (cran-uri "shinycssloaders" version))
21096 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
21098 `((upstream-name . "shinycssloaders")))
21099 (build-system r-build-system)
21101 `(("r-digest" ,r-digest)
21103 ("r-shiny" ,r-shiny)))
21104 (home-page "https://github.com/andrewsali/shinycssloaders")
21105 (synopsis "Add CSS loading animations to Shiny outputs")
21107 "This package provides tools to create a lightweight Shiny wrapper for
21108 the css-loaders created by Luke Hass
21109 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
21110 automatically show a loader when the output is (re)calculating.")
21111 (license license:gpl3)))
21113 (define-public r-rsvg
21120 (uri (cran-uri "rsvg" version))
21123 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
21124 (properties `((upstream-name . "rsvg")))
21125 (build-system r-build-system)
21127 `(("librsvg" ,librsvg)
21130 `(("pkg-config" ,pkg-config)
21131 ("r-knitr" ,r-knitr)))
21132 (home-page "https://github.com/jeroen/rsvg#readme")
21133 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
21135 "This package allows you to render vector-based SVG images into
21136 high-quality custom-size bitmap arrays using the librsvg2 library. The
21137 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
21138 addition, the package can convert images directly to various formats such as
21139 PDF or PostScript.")
21140 (license license:expat)))
21142 (define-public r-influencer
21144 (name "r-influencer")
21149 (uri (cran-uri "influenceR" version))
21152 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
21153 (properties `((upstream-name . "influenceR")))
21154 (build-system r-build-system)
21156 `(("r-igraph" ,r-igraph)
21157 ("r-matrix" ,r-matrix)))
21158 (home-page "https://github.com/rcc-uchicago/influenceR")
21159 (synopsis "Tools to quantify structural importance of nodes in a network")
21161 "This package provides functionality to compute various node centrality
21162 measures on networks. Included are functions to compute betweenness
21163 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
21164 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
21165 algorithm to identify key players, and Valente's bridging metric. The
21166 betweenness, Key Players, and bridging implementations are parallelized with
21168 (license license:gpl2)))
21170 (define-public r-emplik
21177 (uri (cran-uri "emplik" version))
21180 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
21181 (properties `((upstream-name . "emplik")))
21182 (build-system r-build-system)
21184 `(("r-quantreg" ,r-quantreg)))
21185 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
21186 (synopsis "Empirical likelihood ratio for censored/truncated data")
21188 "This package provides empirical likelihood ratio tests for
21189 means/quantiles/hazards from possibly censored and/or truncated data. It also
21191 (license license:gpl2+)))
21193 (define-public r-imputeyn
21195 (name "r-imputeyn")
21200 (uri (cran-uri "imputeYn" version))
21203 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
21204 (properties `((upstream-name . "imputeYn")))
21205 (build-system r-build-system)
21207 `(("r-boot" ,r-boot)
21208 ("r-emplik" ,r-emplik)
21209 ("r-mvtnorm" ,r-mvtnorm)
21210 ("r-quadprog" ,r-quadprog)
21211 ("r-survival" ,r-survival)))
21212 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
21213 (synopsis "Impute last largest censored observation under weighted least squares")
21215 "This package allows for the imputation of the last largest censored
21216 observantions. This method brings less bias and more efficient estimates for
21218 (license license:gpl2)))
21220 (define-public r-adapenetclass
21222 (name "r-adapenetclass")
21227 (uri (cran-uri "AdapEnetClass" version))
21230 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
21231 (properties `((upstream-name . "AdapEnetClass")))
21232 (build-system r-build-system)
21234 `(("r-glmnet" ,r-glmnet)
21235 ("r-imputeyn" ,r-imputeyn)
21237 ("r-quadprog" ,r-quadprog)))
21238 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
21239 (synopsis "Class of adaptive elastic net methods for censored data")
21241 "This package provides methods for variable selection for AFT models.")
21242 (license license:gpl2)))
21244 (define-public r-flock
21251 (uri (cran-uri "flock" version))
21254 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
21255 (properties `((upstream-name . "flock")))
21256 (build-system r-build-system)
21257 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
21258 (home-page "https://cran.r-project.org/web/packages/flock/")
21259 (synopsis "Process synchronization using file locks")
21261 "This package implements synchronization between R processes (spawned by
21262 using the @code{parallel} package for instance) using file locks. It supports
21263 both exclusive and shared locking.")
21264 (license license:asl2.0)))
21266 (define-public r-archivist
21268 (name "r-archivist")
21273 (uri (cran-uri "archivist" version))
21276 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
21277 (properties `((upstream-name . "archivist")))
21278 (build-system r-build-system)
21281 ("r-digest" ,r-digest)
21282 ("r-flock" ,r-flock)
21284 ("r-lubridate" ,r-lubridate)
21285 ("r-magrittr" ,r-magrittr)
21286 ("r-rcurl" ,r-rcurl)
21287 ("r-rsqlite" ,r-rsqlite)))
21288 (home-page "https://pbiecek.github.io/archivist/")
21289 (synopsis "Tools for storing, restoring and searching for R objects")
21291 "Data exploration and modelling is a process in which a lot of data
21292 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
21293 statistical models, different versions of data sets and different versions of
21294 results. Archivist helps to store and manage artifacts created in R. It
21295 allows you to store selected artifacts as binary files together with their
21296 metadata and relations. Archivist allows sharing artifacts with others. It
21297 can look for already created artifacts by using its class, name, date of the
21298 creation or other properties. It also makes it easy to restore such
21300 (license license:gpl2)))
21302 (define-public r-versions
21304 (name "r-versions")
21309 (uri (cran-uri "versions" version))
21312 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
21313 (properties `((upstream-name . "versions")))
21314 (build-system r-build-system)
21315 (home-page "https://cran.r-project.org/web/packages/versions/")
21316 (synopsis "Query and install specific versions of CRAN packages")
21318 "This package allows you to install specified versions of R packages
21319 hosted on CRAN and provides functions to list available versions and the
21320 versions of currently installed packages.")
21321 (license license:bsd-3)))
21323 (define-public r-adapr
21330 (uri (cran-uri "adapr" version))
21333 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
21334 (properties `((upstream-name . "adapr")))
21335 (build-system r-build-system)
21337 `(("r-archivist" ,r-archivist)
21338 ("r-devtools" ,r-devtools)
21339 ("r-digest" ,r-digest)
21340 ("r-doparallel" ,r-doparallel)
21341 ("r-gdata" ,r-gdata)
21342 ("r-ggplot2" ,r-ggplot2)
21343 ("r-git2r" ,r-git2r)
21344 ("r-igraph" ,r-igraph)
21345 ("r-knitr" ,r-knitr)
21346 ("r-plotly" ,r-plotly)
21348 ("r-rmarkdown" ,r-rmarkdown)
21349 ("r-shiny" ,r-shiny)
21350 ("r-shinydashboard" ,r-shinydashboard)
21351 ("r-versions" ,r-versions)))
21352 (home-page "https://cran.r-project.org/web/packages/adapr/")
21353 (synopsis "Implementation of an accountable data analysis process")
21355 "This package tracks reading and writing within R scripts that are
21356 organized into a directed acyclic graph. It contains an interactive Shiny
21357 application @code{adaprApp()}. It uses Git and file hashes to track version
21358 histories of inputs and outputs.")
21359 (license license:lgpl2.0)))
21361 (define-public r-adapsamp
21363 (name "r-adapsamp")
21368 (uri (cran-uri "AdapSamp" version))
21371 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
21372 (properties `((upstream-name . "AdapSamp")))
21373 (build-system r-build-system)
21374 (propagated-inputs `(("r-pracma" ,r-pracma)))
21375 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
21376 (synopsis "Adaptive sampling algorithms")
21378 "For distributions whose probability density functions are log-concave,
21379 the adaptive rejection sampling algorithm can be used to build envelope
21380 functions for sampling. For others, the modified adaptive rejection sampling
21381 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
21382 adaptive slice sampling algorithm can be used. This R package mainly includes
21383 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
21384 @code{rASS()}. These functions can realize sampling based on the algorithms
21386 (license license:gpl2)))
21388 (define-public r-adaptalint
21390 (name "r-adaptalint")
21395 (uri (cran-uri "adaptalint" version))
21398 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
21399 (properties `((upstream-name . "adaptalint")))
21400 (build-system r-build-system)
21402 `(("r-dplyr" ,r-dplyr)
21403 ("r-lintr" ,r-lintr)
21404 ("r-purrr" ,r-purrr)))
21405 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
21406 (synopsis "Check R code style")
21408 "This package provides tools to infer the code style (which style rules
21409 are followed and which ones are not) from one package and use it to check
21410 another. This makes it easier to find and correct the most important problems
21412 (license license:gpl3)))
21414 (define-public r-fracdiff
21416 (name "r-fracdiff")
21421 (uri (cran-uri "fracdiff" version))
21424 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
21425 (properties `((upstream-name . "fracdiff")))
21426 (build-system r-build-system)
21427 (home-page "https://github.com/mmaechler/fracdiff")
21429 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
21431 "This package provides tools for the maximum likelihood estimation of the
21432 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
21433 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
21434 (license license:gpl2+)))
21436 (define-public r-forecast
21438 (name "r-forecast")
21443 (uri (cran-uri "forecast" version))
21446 "0vrql5d4v28890np2m6ws1nr1fcl6frs1bz74vfkihkixcmkl3j9"))))
21447 (properties `((upstream-name . "forecast")))
21448 (build-system r-build-system)
21450 `(("r-colorspace" ,r-colorspace)
21451 ("r-fracdiff" ,r-fracdiff)
21452 ("r-ggplot2" ,r-ggplot2)
21453 ("r-lmtest" ,r-lmtest)
21454 ("r-magrittr" ,r-magrittr)
21457 ("r-rcpparmadillo" ,r-rcpparmadillo)
21458 ("r-timedate" ,r-timedate)
21459 ("r-tseries" ,r-tseries)
21463 `(("r-knitr" ,r-knitr))) ; needed for vignettes
21464 (home-page "https://pkg.robjhyndman.com/forecast/")
21465 (synopsis "Forecasting functions for time series and linear models")
21467 "This package provides methods and tools for displaying and analysing
21468 univariate time series forecasts including exponential smoothing via state
21469 space models and automatic ARIMA modelling.")
21470 (license license:gpl3)))
21472 (define-public r-xmisc
21479 (uri (cran-uri "Xmisc" version))
21482 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
21483 (properties `((upstream-name . "Xmisc")))
21484 (build-system r-build-system)
21485 (home-page "https://cran.r-project.org/package=Xmisc")
21487 "Xiaobei's miscellaneous classes and functions")
21489 "This package provides Xiaobei's miscellaneous classes and functions,
21490 which are useful when developing R packages for @dfn{object oriented
21491 programming} (OOP) using R Reference Class.")
21492 (license license:gpl2+)))
21494 (define-public r-proxyc
21501 (uri (cran-uri "proxyC" version))
21504 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
21505 (properties `((upstream-name . "proxyC")))
21506 (build-system r-build-system)
21508 `(("r-matrix" ,r-matrix)
21510 ("r-rcpparmadillo" ,r-rcpparmadillo)
21511 ("r-rcppparallel" ,r-rcppparallel)))
21512 (home-page "https://cran.r-project.org/package=proxyC")
21513 (synopsis "Compute proximity in large sparse matrices")
21515 "This package provides efficient tools to compute the proximity between
21516 rows or columns of large matrices. Functions are optimised for large sparse
21517 matrices using the Armadillo and Intel TBB libraries. Among several built-in
21518 similarity/distance measures, computation of correlation, cosine similarity
21519 and Euclidean distance is particularly fast.")
21520 (license license:gpl3)))
21522 (define-public r-isocodes
21524 (name "r-isocodes")
21525 (version "2020.12.04")
21529 (uri (cran-uri "ISOcodes" version))
21532 "18373rkhmwm7y2drvfbhrxkqw9d23avf0ndvh0fg00z4djvddkjx"))))
21533 (properties `((upstream-name . "ISOcodes")))
21534 (build-system r-build-system)
21535 (home-page "https://cran.r-project.org/package=ISOcodes")
21536 (synopsis "Selected ISO codes")
21538 "This package provides ISO language, territory, currency, script and
21539 character codes. It provides ISO 639 language codes, ISO 3166 territory
21540 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
21541 character codes as well as the UN M.49 area codes.")
21542 (license license:gpl2)))
21544 (define-public r-stopwords
21546 (name "r-stopwords")
21551 (uri (cran-uri "stopwords" version))
21554 "1g2p8gsj7xjck7idcwczgc7fmv72lzwjw00qarrj0cv44kypmiq8"))))
21555 (properties `((upstream-name . "stopwords")))
21556 (build-system r-build-system)
21558 `(("r-desc" ,r-desc)
21559 ("r-isocodes" ,r-isocodes)
21560 ("r-usethis" ,r-usethis)))
21561 (home-page "https://github.com/quanteda/stopwords")
21562 (synopsis "Multilingual stopword lists")
21564 "This package provides multiple sources of stopwords, for use in text
21565 analysis and natural language processing.")
21566 (license license:expat)))
21568 (define-public r-spacyr
21575 (uri (cran-uri "spacyr" version))
21578 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
21579 (properties `((upstream-name . "spacyr")))
21580 (build-system r-build-system)
21582 `(("r-data-table" ,r-data-table)
21583 ("r-reticulate" ,r-reticulate)))
21584 (home-page "https://spacyr.quanteda.io")
21585 (synopsis "R wrapper for the spaCy NLP library")
21587 "This package provides an R wrapper to the Python @dfn{natural language
21588 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
21589 (license license:gpl3)))
21591 (define-public r-snowballc
21593 (name "r-snowballc")
21598 (uri (cran-uri "SnowballC" version))
21601 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
21602 (properties `((upstream-name . "SnowballC")))
21603 (build-system r-build-system)
21604 (home-page "https://r-forge.r-project.org/projects/r-temis/")
21605 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
21607 "This package provides an R interface to the C @code{libstemmer} library
21608 that implements Porter's word stemming algorithm for collapsing words to a
21609 common root to aid comparison of vocabulary. Currently supported languages
21610 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
21611 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
21612 (license license:bsd-3)))
21614 (define-public r-quanteda
21616 (name "r-quanteda")
21621 (uri (cran-uri "quanteda" version))
21624 "13rjwgmg5v1dbryrs9ifyy76s5ib6wrbrm2y5af44vhf1h6p9cvy"))))
21625 (properties `((upstream-name . "quanteda")))
21626 (build-system r-build-system)
21628 `(("r-data-table" ,r-data-table)
21629 ("r-digest" ,r-digest)
21630 ("r-extrafont" ,r-extrafont)
21631 ("r-fastmatch" ,r-fastmatch)
21632 ("r-ggplot2" ,r-ggplot2)
21633 ("r-ggrepel" ,r-ggrepel)
21634 ("r-jsonlite" ,r-jsonlite)
21635 ("r-magrittr" ,r-magrittr)
21636 ("r-matrix" ,r-matrix)
21637 ("r-network" ,r-network)
21638 ("r-proxyc" ,r-proxyc)
21640 ("r-rcpparmadillo" ,r-rcpparmadillo)
21641 ("r-rcppparallel" ,r-rcppparallel)
21643 ("r-snowballc" ,r-snowballc)
21644 ("r-stopwords" ,r-stopwords)
21645 ("r-stringi" ,r-stringi)
21647 ("r-yaml" ,r-yaml)))
21649 `(("r-knitr" ,r-knitr)))
21650 (home-page "https://quanteda.io")
21651 (synopsis "Quantitative analysis of textual data")
21653 "This package provides a fast, flexible, and comprehensive framework for
21654 quantitative text analysis in R. It provides functionality for corpus
21655 management, creating and manipulating tokens and ngrams, exploring keywords in
21656 context, forming and manipulating sparse matrices of documents by features and
21657 feature co-occurrences, analyzing keywords, computing feature similarities and
21658 distances, applying content dictionaries, applying supervised and unsupervised
21659 machine learning, visually representing text and text analyses, and more.")
21660 (license license:gpl3)))
21662 (define-public r-topicmodels
21664 (name "r-topicmodels")
21669 (uri (cran-uri "topicmodels" version))
21672 "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
21673 (properties `((upstream-name . "topicmodels")))
21674 (build-system r-build-system)
21678 `(("r-modeltools" ,r-modeltools)
21681 (home-page "https://cran.r-project.org/package=topicmodels")
21682 (synopsis "Topic models")
21684 "This package provides an interface to the C code for @dfn{Latent
21685 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
21686 David M. Blei and co-authors and the C++ code for fitting LDA models using
21687 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
21688 (license license:gpl2)))
21690 (define-public r-stm
21697 (uri (cran-uri "stm" version))
21700 "0qwq4nin2n9fjd06852r8k7arvcgh46kcfb3lm21swgx6j8bgrhb"))))
21701 (properties `((upstream-name . "stm")))
21702 (build-system r-build-system)
21704 `(("r-data-table" ,r-data-table)
21705 ("r-glmnet" ,r-glmnet)
21707 ("r-matrix" ,r-matrix)
21708 ("r-matrixstats" ,r-matrixstats)
21709 ("r-quadprog" ,r-quadprog)
21710 ("r-quanteda" ,r-quanteda)
21712 ("r-rcpparmadillo" ,r-rcpparmadillo)
21714 ("r-stringr" ,r-stringr)))
21715 (home-page "http://www.structuraltopicmodel.com/")
21716 (synopsis "Estimation of the Structural Topic Model")
21718 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
21719 topic models with document-level covariates. The package also includes tools
21720 for model selection, visualization, and estimation of topic-covariate
21722 (license license:expat)))
21724 (define-public r-polycor
21731 (uri (cran-uri "polycor" version))
21734 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
21735 (properties `((upstream-name . "polycor")))
21736 (build-system r-build-system)
21738 `(("r-matrix" ,r-matrix)
21739 ("r-mvtnorm" ,r-mvtnorm)))
21740 (home-page "https://r-forge.r-project.org/projects/polycor/")
21741 (synopsis "Polychoric and polyserial correlations")
21743 "This package provides tools to compute polychoric and polyserial
21744 correlations by quick \"two-step\" methods or ML, optionally with standard
21745 errors; tetrachoric and biserial correlations are special cases.")
21746 (license license:gpl2+)))
21748 (define-public r-msm
21755 (uri (cran-uri "msm" version))
21758 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
21759 (properties `((upstream-name . "msm")))
21760 (build-system r-build-system)
21762 `(("r-expm" ,r-expm)
21763 ("r-mvtnorm" ,r-mvtnorm)
21764 ("r-survival" ,r-survival)))
21765 (home-page "https://github.com/chjackson/msm")
21766 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
21768 "This package provides functions for fitting continuous-time Markov and
21769 hidden Markov multi-state models to longitudinal data. It was designed for
21770 processes observed at arbitrary times in continuous time (panel data) but some
21771 other observation schemes are supported. Both Markov transition rates and the
21772 hidden Markov output process can be modelled in terms of covariates, which may
21773 be constant or piecewise-constant in time.")
21774 (license license:gpl2+)))
21776 (define-public r-ltm
21783 (uri (cran-uri "ltm" version))
21786 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
21787 (properties `((upstream-name . "ltm")))
21788 (build-system r-build-system)
21790 `(("r-mass" ,r-mass)
21792 ("r-polycor" ,r-polycor)))
21793 (home-page "https://github.com/drizopoulos/ltm")
21794 (synopsis "Latent trait models under IRT")
21796 "This is a package supporting the analysis of multivariate dichotomous
21797 and polytomous data using latent trait models under the Item Response Theory
21798 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
21799 Three-Parameter, the Graded Response, and the Generalized Partial Credit
21801 (license license:gpl2+)))
21803 (define-public r-mi
21810 (uri (cran-uri "mi" version))
21813 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
21814 (properties `((upstream-name . "mi")))
21815 (build-system r-build-system)
21818 ("r-matrix" ,r-matrix)))
21819 (home-page "http://www.stat.columbia.edu/~gelman/")
21820 (synopsis "Missing data imputation and model checking")
21822 "This package provides functions for data manipulation, imputing missing
21823 values in an approximate Bayesian framework, diagnostics of the models used to
21824 generate the imputations, confidence-building mechanisms to validate some of
21825 the assumptions of the imputation algorithm, and functions to analyze multiply
21826 imputed data sets with the appropriate degree of sampling uncertainty.")
21827 (license license:gpl2+)))
21829 (define-public r-matrixcalc
21831 (name "r-matrixcalc")
21836 (uri (cran-uri "matrixcalc" version))
21839 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
21840 (properties `((upstream-name . "matrixcalc")))
21841 (build-system r-build-system)
21842 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
21843 (synopsis "Collection of functions for matrix calculations")
21845 "This package provides a collection of functions to support matrix
21846 calculations for probability, econometric and numerical analysis. There are
21847 additional functions that are comparable to APL functions which are useful for
21848 actuarial models such as pension mathematics.")
21849 (license license:gpl2+)))
21851 (define-public r-sem
21858 (uri (cran-uri "sem" version))
21861 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
21862 (properties `((upstream-name . "sem")))
21863 (build-system r-build-system)
21865 `(("r-boot" ,r-boot)
21867 ("r-matrixcalc" ,r-matrixcalc)
21869 (home-page "https://cran.r-project.org/package=sem")
21870 (synopsis "Structural equation models")
21872 "This package provides functions for fitting general linear structural
21873 equation models (with observed and latent variables) using the RAM approach,
21874 and for fitting structural equations in observed-variable models by two-stage
21876 (license license:gpl2+)))
21878 (define-public r-semtools
21880 (name "r-semtools")
21885 (uri (cran-uri "semTools" version))
21888 "15kban4ds2mssxqslm126b89p8biya14c9m68sqk61vzvx5dm2vq"))))
21889 (properties `((upstream-name . "semTools")))
21890 (build-system r-build-system)
21892 `(("r-lavaan" ,r-lavaan)))
21893 (home-page "https://github.com/simsem/semTools/wiki")
21894 (synopsis "Useful tools for structural equation modeling")
21896 "This package provides useful tools for structural equation modeling.")
21897 (license license:gpl2+)))
21899 (define-public r-regsem
21906 (uri (cran-uri "regsem" version))
21909 "14nrzyrkrijdrr4jwkri5zra2wh36w68wy6xs600l2z1633h2lmn"))))
21910 (properties `((upstream-name . "regsem")))
21911 (build-system r-build-system)
21913 `(("r-lavaan" ,r-lavaan)
21915 ("r-rcpparmadillo" ,r-rcpparmadillo)
21916 ("r-rsolnp" ,r-rsolnp)))
21918 `(("r-knitr" ,r-knitr)))
21919 (home-page "https://cran.r-project.org/package=regsem")
21920 (synopsis "Regularized structural equation modeling")
21922 "This package uses both ridge and lasso penalties (and extensions) to
21923 penalize specific parameters in structural equation models. The package
21924 offers additional cost functions, cross validation, and other extensions
21925 beyond traditional structural equation models. It also contains a function to
21926 perform @dfn{exploratory mediation} (XMed).")
21927 (license license:gpl2+)))
21929 (define-public r-stanheaders
21931 (name "r-stanheaders")
21932 (version "2.21.0-7")
21936 (uri (cran-uri "StanHeaders" version))
21939 "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17"))))
21940 (properties `((upstream-name . "StanHeaders")))
21941 (build-system r-build-system)
21942 (inputs `(("pandoc" ,pandoc)))
21944 `(("r-rcppeigen" ,r-rcppeigen)
21945 ("r-rcppparallel" ,r-rcppparallel)))
21947 `(("gfortran" ,gfortran)
21948 ("r-knitr" ,r-knitr))) ; for vignettes
21949 (home-page "https://mc-stan.org/")
21950 (synopsis "C++ header files for Stan")
21952 "The C++ header files of the Stan project are provided by this package.
21953 There is a shared object containing part of the @code{CVODES} library, but it
21954 is not accessible from R. @code{r-stanheaders} is only useful for developers
21955 who want to utilize the @code{LinkingTo} directive of their package's
21956 DESCRIPTION file to build on the Stan library without incurring unnecessary
21959 The Stan project develops a probabilistic programming language that implements
21960 full or approximate Bayesian statistical inference via Markov Chain Monte
21961 Carlo or variational methods and implements (optionally penalized) maximum
21962 likelihood estimation via optimization. The Stan library includes an advanced
21963 automatic differentiation scheme, templated statistical and linear algebra
21964 functions that can handle the automatically differentiable scalar types (and
21965 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
21966 package provides user-facing R functions to parse, compile, test, estimate,
21967 and analyze Stan models.")
21968 (license license:bsd-3)))
21970 (define-public r-rpf
21977 (uri (cran-uri "rpf" version))
21980 "0kz7i7g3l16irz6bxgnkxdmmd931m1fk6rl72dvs21ir5brr010l"))))
21981 (properties `((upstream-name . "rpf")))
21982 (build-system r-build-system)
21984 `(("r-lifecycle" ,r-lifecycle)
21985 ("r-mvtnorm" ,r-mvtnorm)
21987 ("r-rcppeigen" ,r-rcppeigen)))
21989 `(("r-knitr" ,r-knitr)))
21990 (home-page "https://github.com/jpritikin/rpf")
21991 (synopsis "Response probability functions")
21993 "The purpose of this package is to factor out logic and math common to
21994 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
21995 core support code suitable for more specialized IRT packages to build upon.
21996 Complete access to optimized C functions is made available with
21997 @code{R_RegisterCCallable()}.")
21998 (license license:gpl3+)))
22000 (define-public r-openmx
22007 (uri (cran-uri "OpenMx" version))
22010 "0gyjps0l3ig90piccgd04s63cz65kk5i5l9iyakps4bv27h1lzwm"))))
22011 (properties `((upstream-name . "OpenMx")))
22012 (build-system r-build-system)
22015 ("r-digest" ,r-digest)
22016 ("r-lifecycle" ,r-lifecycle)
22018 ("r-matrix" ,r-matrix)
22020 ("r-rcppeigen" ,r-rcppeigen)
22022 ("r-stanheaders" ,r-stanheaders)))
22023 (native-inputs `(("gfortran" ,gfortran)))
22024 (home-page "http://openmx.ssri.psu.edu")
22025 (synopsis "Extended structural equation modelling")
22027 "This package allows for the estimation of a wide variety of advanced
22028 multivariate statistical models. It consists of a library of functions and
22029 optimizers that allow you to quickly and flexibly define an SEM model and
22030 estimate parameters given observed data.")
22031 (license license:asl2.0)))
22033 (define-public r-kutils
22040 (uri (cran-uri "kutils" version))
22043 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
22044 (properties `((upstream-name . "kutils")))
22045 (build-system r-build-system)
22047 `(("r-foreign" ,r-foreign)
22048 ("r-openxlsx" ,r-openxlsx)
22050 ("r-runit" ,r-runit)
22051 ("r-xtable" ,r-xtable)))
22052 (home-page "https://cran.r-project.org/package=kutils")
22053 (synopsis "Project management tools")
22055 "This package provides tools for data importation, recoding, and
22056 inspection. There are functions to create new project folders, R code
22057 templates, create uniquely named output directories, and to quickly obtain a
22058 visual summary for each variable in a data frame. The main feature here is
22059 the systematic implementation of the \"variable key\" framework for data
22060 importation and recoding.")
22061 (license license:gpl2)))
22063 (define-public r-rockchalk
22065 (name "r-rockchalk")
22066 (version "1.8.144")
22070 (uri (cran-uri "rockchalk" version))
22073 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
22074 (properties `((upstream-name . "rockchalk")))
22075 (build-system r-build-system)
22077 `(("r-cardata" ,r-cardata)
22078 ("r-kutils" ,r-kutils)
22080 ("r-mass" ,r-mass)))
22081 (home-page "https://cran.r-project.org/package=rockchalk")
22082 (synopsis "Regression estimation and presentation")
22084 "This package provides a collection of functions for interpretation and
22085 presentation of regression analysis. These functions are used to produce the
22086 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
22087 includes regression diagnostics, regression tables, and plots of interactions
22088 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
22089 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
22090 fairly comprehensive overview.")
22091 (license license:gpl3+)))
22093 (define-public r-lisreltor
22095 (name "r-lisreltor")
22100 (uri (cran-uri "lisrelToR" version))
22103 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
22104 (properties `((upstream-name . "lisrelToR")))
22105 (build-system r-build-system)
22106 (home-page "https://cran.r-project.org/package=lisrelToR")
22107 (synopsis "Import output from LISREL into R")
22109 "This is an unofficial package aimed at automating the import of LISREL
22111 (license license:gpl2)))
22113 (define-public r-bdgraph
22120 (uri (cran-uri "BDgraph" version))
22123 "05q6dbvdnxmh7myvw60zqcqx16f80i8d6qa4y7xnfkx02l9lwiyc"))))
22124 (properties `((upstream-name . "BDgraph")))
22125 (build-system r-build-system)
22127 `(("r-igraph" ,r-igraph)))
22128 (home-page "https://www.uva.nl/profile/a.mohammadi")
22129 (synopsis "Bayesian structure learning in graphical models")
22131 "This package provides statistical tools for Bayesian structure learning
22132 in undirected graphical models for continuous, discrete, and mixed data. It
22133 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
22134 on a continuous-time birth-death process.")
22135 (license license:gpl2+)))
22137 (define-public r-d3network
22139 (name "r-d3network")
22140 (version "0.5.2.1")
22144 (uri (cran-uri "d3Network" version))
22147 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
22148 (properties `((upstream-name . "d3Network")))
22149 (build-system r-build-system)
22151 `(("r-plyr" ,r-plyr)
22152 ("r-rjson" ,r-rjson)
22153 ("r-whisker" ,r-whisker)))
22154 (home-page "http://christophergandrud.github.io/d3Network/")
22155 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
22157 "This package is intended to make it easy to create D3 JavaScript
22158 network, tree, dendrogram, and Sankey graphs from R using data frames.")
22159 (license license:gpl3+)))
22161 (define-public r-qgraph
22168 (uri (cran-uri "qgraph" version))
22171 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
22172 (properties `((upstream-name . "qgraph")))
22173 (build-system r-build-system)
22175 `(("r-abind" ,r-abind)
22176 ("r-bdgraph" ,r-bdgraph)
22177 ("r-colorspace" ,r-colorspace)
22178 ("r-corpcor" ,r-corpcor)
22179 ("r-d3network" ,r-d3network)
22180 ("r-dplyr" ,r-dplyr)
22181 ("r-fdrtool" ,r-fdrtool)
22182 ("r-ggplot2" ,r-ggplot2)
22183 ("r-ggraph" ,r-ggraph)
22184 ("r-glasso" ,r-glasso)
22185 ("r-gtools" ,r-gtools)
22186 ("r-hmisc" ,r-hmisc)
22188 ("r-igraph" ,r-igraph)
22190 ("r-lavaan" ,r-lavaan)
22191 ("r-matrix" ,r-matrix)
22192 ("r-pbapply" ,r-pbapply)
22195 ("r-psych" ,r-psych)
22197 ("r-reshape2" ,r-reshape2)
22198 ("r-tidygraph" ,r-tidygraph)))
22199 (home-page "http://sachaepskamp.com/qgraph/")
22200 (synopsis "Weighted network visualization and analysis")
22202 "This package implements tools for weighted network visualization and
22203 analysis, as well as Gaussian graphical model computation. It contains graph
22204 plotting methods, and tools for psychometric data visualization and graphical
22205 model estimation. See Epskamp et al. (2012)
22206 @url{doi:10.18637/jss.v048.i04}.")
22207 (license license:gpl2)))
22209 (define-public r-semplot
22216 (uri (cran-uri "semPlot" version))
22219 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
22220 (properties `((upstream-name . "semPlot")))
22221 (build-system r-build-system)
22223 `(("r-colorspace" ,r-colorspace)
22224 ("r-corpcor" ,r-corpcor)
22225 ("r-igraph" ,r-igraph)
22226 ("r-lavaan" ,r-lavaan)
22227 ("r-lisreltor" ,r-lisreltor)
22228 ("r-openmx" ,r-openmx)
22230 ("r-qgraph" ,r-qgraph)
22231 ("r-regsem" ,r-regsem)
22232 ("r-rockchalk" ,r-rockchalk)
22235 (home-page "https://github.com/SachaEpskamp/semPlot")
22236 (synopsis "Unified visualizations of structural equation models")
22238 "Structural equation modeling (SEM) has a long history of representing
22239 models graphically as path diagrams. The semPlot package for R fills the gap
22240 between advanced, but time-consuming, graphical software and the limited
22241 graphics produced automatically by SEM software. In addition, semPlot offers
22242 more functionality than drawing path diagrams: it can act as a common ground
22243 for importing SEM results into R. Any result usable as input to semPlot can
22244 also be represented in any of the three popular SEM frame-works, as well as
22245 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
22246 (license license:gpl2)))
22248 (define-public r-cdm
22255 (uri (cran-uri "CDM" version))
22258 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
22259 (properties `((upstream-name . "CDM")))
22260 (build-system r-build-system)
22262 `(("r-mvtnorm" ,r-mvtnorm)
22263 ("r-polycor" ,r-polycor)
22265 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22267 "https://github.com/alexanderrobitzsch/CDM")
22268 (synopsis "Cognitive diagnosis modeling")
22270 "This package provides functions for cognitive diagnosis modeling and
22271 multidimensional item response modeling for dichotomous and polytomous item
22272 responses. It enables the estimation of the DINA and DINO model, the multiple
22273 group (polytomous) GDINA model, the multiple choice DINA model, the general
22274 diagnostic model (GDM), the structured latent class model (SLCA), and
22275 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
22276 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
22277 estimation and the package structure. For tutorials on how to use the CDM
22278 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
22279 well as Ravand and Robitzsch (2015).")
22280 (license license:gpl2+)))
22282 (define-public r-tam
22289 (uri (cran-uri "TAM" version))
22292 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
22293 (properties `((upstream-name . "TAM")))
22294 (build-system r-build-system)
22298 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22299 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
22300 (synopsis "Test analysis modules")
22302 "This package includes tools for marginal maximum likelihood estimation
22303 and joint maximum likelihood estimation for unidimensional and
22304 multidimensional item response models. The package functionality covers the
22305 Rasch model, 2PL model, 3PL model, generalized partial credit model,
22306 multi-faceted Rasch model, nominal item response model, structured latent
22307 class model, mixture distribution IRT models, and located latent class models.
22308 Latent regression models and plausible value imputation are also supported.")
22309 (license license:gpl2+)))
22311 (define-public r-erm
22318 (uri (cran-uri "eRm" version))
22321 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
22322 (properties `((upstream-name . "eRm")))
22323 (build-system r-build-system)
22325 `(("r-colorspace" ,r-colorspace)
22326 ("r-lattice" ,r-lattice)
22328 ("r-matrix" ,r-matrix)
22329 ("r-psych" ,r-psych)))
22330 (native-inputs `(("gfortran" ,gfortran)))
22331 (home-page "https://cran.r-project.org/package=eRm")
22332 (synopsis "Extended Rasch modeling")
22334 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
22335 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
22336 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
22337 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
22338 data matrix. Additional features are the ML estimation of the person
22339 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
22340 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
22341 infit and outfit measures, ICC and other plots, automated stepwise item
22342 elimination, and a simulation module for various binary data matrices.")
22343 (license license:gpl3)))
22345 (define-public r-irtoys
22352 (uri (cran-uri "irtoys" version))
22355 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
22356 (properties `((upstream-name . "irtoys")))
22357 (build-system r-build-system)
22361 (home-page "https://cran.r-project.org/package=irtoys")
22362 (synopsis "Collection of functions related to Item Response Theory (IRT)")
22364 "This package provides a collection of functions useful in learning and
22365 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
22366 programs. It provides basic CTT analysis, a simple common interface to the
22367 estimation of item parameters in IRT models for binary responses with three
22368 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
22369 EAP, WLE, plausible values), item and person fit statistics, scaling
22370 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
22371 array of parametric and non-parametric (kernel) plots. It estimates and plots
22372 Haberman's interaction model when all items are dichotomously scored.")
22373 (license license:gpl2+)))
22375 (define-public r-iheatmapr
22377 (name "r-iheatmapr")
22382 (uri (cran-uri "iheatmapr" version))
22385 "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx"))))
22386 (properties `((upstream-name . "iheatmapr")))
22387 (build-system r-build-system)
22389 `(("r-fastcluster" ,r-fastcluster)
22390 ("r-ggdendro" ,r-ggdendro)
22391 ("r-htmlwidgets" ,r-htmlwidgets)
22392 ("r-jsonlite" ,r-jsonlite)
22393 ("r-knitr" ,r-knitr)
22394 ("r-magrittr" ,r-magrittr)
22395 ("r-rcolorbrewer" ,r-rcolorbrewer)
22396 ("r-scales" ,r-scales)))
22398 `(("r-knitr" ,r-knitr)))
22399 (home-page "https://docs.ropensci.org/iheatmapr")
22400 (synopsis "Interactive, Complex Heatmaps")
22402 "iheatmapr is an R package for building complex, interactive heatmaps
22403 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
22404 subplots along the rows or columns of the main heatmap add more information
22405 about each row or column. For example, a one column additional heatmap may
22406 indicate what group a particular row or column belongs to. Complex heatmaps
22407 may also include multiple side by side heatmaps which show different types of
22408 data for the same conditions. Interactivity can improve complex heatmaps by
22409 providing tooltips with information about each cell and enabling zooming into
22410 interesting features. iheatmapr uses the plotly library for interactivity.")
22411 (license license:expat)))
22413 (define-public r-packrat
22420 (uri (cran-uri "packrat" version))
22423 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
22424 (properties `((upstream-name . "packrat")))
22425 (build-system r-build-system)
22426 (home-page "https://github.com/rstudio/packrat/")
22427 (synopsis "Dependency management R projects")
22429 "This package provides a dependency manager for R projects that allows
22430 you to manage the R packages your project depends on in an isolated, portable,
22431 and reproducible way.")
22432 (license license:gpl2)))
22434 (define-public r-rsconnect
22436 (name "r-rsconnect")
22441 (uri (cran-uri "rsconnect" version))
22444 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
22445 (properties `((upstream-name . "rsconnect")))
22446 (build-system r-build-system)
22448 `(("r-curl" ,r-curl)
22449 ("r-digest" ,r-digest)
22450 ("r-jsonlite" ,r-jsonlite)
22451 ("r-openssl" ,r-openssl)
22452 ("r-packrat" ,r-packrat)
22453 ("r-rstudioapi" ,r-rstudioapi)
22454 ("r-yaml" ,r-yaml)))
22455 (home-page "https://github.com/rstudio/rsconnect")
22456 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
22458 "This package provides a programmatic deployment interface for RPubs,
22459 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
22460 documents, Shiny applications, Plumber APIs, plots, and static web content.")
22461 (license license:gpl2)))
22463 ;; This package includes minified JavaScript files. When upgrading please
22464 ;; check that there are no new minified JavaScript files.
22465 (define-public r-dygraphs
22467 (name "r-dygraphs")
22468 (version "1.1.1.6")
22472 (uri (cran-uri "dygraphs" version))
22475 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
22476 (properties `((upstream-name . "dygraphs")))
22477 (build-system r-build-system)
22479 `(#:modules ((guix build utils)
22480 (guix build r-build-system)
22484 (modify-phases %standard-phases
22485 (add-after 'unpack 'process-javascript
22486 (lambda* (#:key inputs #:allow-other-keys)
22487 (with-directory-excursion "inst/htmlwidgets/lib/"
22491 `(("dygraphs/dygraph-combined-dev.js"
22492 "dygraph-combined.js")
22493 (,(assoc-ref inputs "js-jquery")
22494 "jquery/jquery.min.js")
22495 (,(assoc-ref inputs "js-fquarter")
22496 "fquarter/moment-fquarter.min.js"))))
22497 (lambda (sources targets)
22498 (for-each (lambda (source target)
22499 (format #t "Processing ~a --> ~a~%"
22501 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
22502 (call-with-output-file target
22504 (dump-port minified port)))))
22505 sources targets))))
22508 `(("uglify-js" ,uglify-js)
22509 ;; They actually use version 1.11.1, but this more recent version
22510 ;; should be just fine.
22514 (uri "https://code.jquery.com/jquery-1.12.4.js")
22517 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
22521 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
22522 "moment-fquarter/1.0.1/moment-fquarter.js"))
22525 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
22527 `(("r-htmltools" ,r-htmltools)
22528 ("r-htmlwidgets" ,r-htmlwidgets)
22529 ("r-magrittr" ,r-magrittr)
22532 (home-page "https://github.com/rstudio/dygraphs")
22533 (synopsis "Interface to Dygraphs interactive time series charting library")
22535 "This package provides an R interface to the dygraphs JavaScript charting
22536 library (a copy of which is included in the package). It provides rich
22537 facilities for charting time-series data in R, including highly configurable
22538 series- and axis-display and interactive features like zoom/pan and
22539 series/point highlighting.")
22540 (license license:expat)))
22542 (define-public r-shinystan
22544 (name "r-shinystan")
22549 (uri (cran-uri "shinystan" version))
22552 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
22553 (properties `((upstream-name . "shinystan")))
22554 (build-system r-build-system)
22556 `(("r-bayesplot" ,r-bayesplot)
22557 ("r-colourpicker" ,r-colourpicker)
22559 ("r-dygraphs" ,r-dygraphs)
22560 ("r-ggplot2" ,r-ggplot2)
22561 ("r-gridextra" ,r-gridextra)
22562 ("r-gtools" ,r-gtools)
22563 ("r-markdown" ,r-markdown)
22564 ("r-reshape2" ,r-reshape2)
22565 ("r-rsconnect" ,r-rsconnect)
22566 ("r-rstan" ,r-rstan)
22567 ("r-shiny" ,r-shiny)
22568 ("r-shinyjs" ,r-shinyjs)
22569 ("r-shinythemes" ,r-shinythemes)
22570 ("r-threejs" ,r-threejs)
22571 ("r-xtable" ,r-xtable)
22573 (home-page "https://mc-stan.org/")
22574 (synopsis "Interactive visual and numerical analysis for Bayesian models")
22576 "This package provides a graphical user interface for interactive
22577 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
22578 for analyzing a posterior sample. The interface is powered by the Shiny web
22579 application framework and works with the output of MCMC programs written in
22580 any programming language (and has extended functionality for Stan models fit
22581 using the @code{rstan} and @code{rstanarm} packages).")
22582 (license license:gpl3+)))
22584 (define-public r-rstantools
22586 (name "r-rstantools")
22591 (uri (cran-uri "rstantools" version))
22594 "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
22595 (properties `((upstream-name . "rstantools")))
22596 (build-system r-build-system)
22597 (inputs `(("pandoc" ,pandoc)))
22599 `(("r-desc" ,r-desc)
22601 ("r-rcppparallel" ,r-rcppparallel)))
22603 `(("r-knitr" ,r-knitr)))
22604 (home-page "https://mc-stan.org/rstantools/")
22605 (synopsis "Tools for developing R packages interfacing with Stan")
22607 "This package provides various tools for developers of R packages
22608 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
22609 up the required package structure, S3 generics and default methods to unify
22610 function naming across Stan-based R packages, and vignettes with
22611 recommendations for developers.")
22612 (license license:gpl3+)))
22614 (define-public r-loo
22621 (uri (cran-uri "loo" version))
22623 (base32 "0l2v8zpashqbnck3qx5lp1gqjcfphzky8mxyw5gfk9wk99mzn8dw"))))
22624 (properties `((upstream-name . "loo")))
22625 (build-system r-build-system)
22627 `(("pandoc" ,pandoc)
22628 ("pandoc-citeproc" ,pandoc-citeproc)))
22630 `(("r-checkmate" ,r-checkmate)
22631 ("r-matrixstats" ,r-matrixstats)))
22633 `(("r-knitr" ,r-knitr)))
22634 (home-page "https://mc-stan.org/loo/")
22635 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
22637 "This package provides an implementation of efficient approximate
22638 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
22639 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
22640 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
22641 procedure for regularizing importance weights. As a byproduct of the
22642 calculations, we also obtain approximate standard errors for estimated
22643 predictive errors and for the comparison of predictive errors between models.
22644 The package also provides methods for using stacking and other model weighting
22645 techniques to average Bayesian predictive distributions.")
22646 (license license:gpl3+)))
22648 (define-public r-rstan
22655 (uri (cran-uri "rstan" version))
22658 "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3"))))
22659 (properties `((upstream-name . "rstan")))
22660 (build-system r-build-system)
22663 (modify-phases %standard-phases
22664 (add-before 'install 'set-timezone
22665 ;; This package is picky about timezones.
22666 (lambda* (#:key inputs #:allow-other-keys)
22667 (setenv "TZ" "UTC+1")
22669 (string-append (assoc-ref inputs "tzdata")
22670 "/share/zoneinfo"))
22673 `(("tzdata" ,tzdata-for-tests)
22675 ("r-knitr" ,r-knitr)))
22678 ("r-ggplot2" ,r-ggplot2)
22679 ("r-gridextra" ,r-gridextra)
22680 ("r-inline" ,r-inline)
22682 ("r-pkgbuild" ,r-pkgbuild)
22684 ("r-rcppeigen" ,r-rcppeigen)
22685 ("r-rcppparallel" ,r-rcppparallel)
22686 ("r-stanheaders" ,r-stanheaders)
22688 ("r-withr" ,r-withr)))
22689 (home-page "https://discourse.mc-stan.org/")
22690 (synopsis "R interface to Stan")
22692 "User-facing R functions are provided to parse, compile, test, estimate,
22693 and analyze Stan models by accessing the header-only Stan library provided by
22694 the StanHeaders package. The Stan project develops a probabilistic
22695 programming language that implements full Bayesian statistical inference via
22696 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
22697 approximation, and (optionally penalized) maximum likelihood estimation via
22698 optimization. In all three cases, automatic differentiation is used to
22699 quickly and accurately evaluate gradients without burdening the user with the
22700 need to derive the partial derivatives.")
22701 (license license:gpl3+)))
22703 (define-public r-rstanarm
22705 (name "r-rstanarm")
22710 (uri (cran-uri "rstanarm" version))
22713 "04ggzak3f7jaxza3dxyrmxp5b48qcgyspy22ykbhr03g4hzp7jk8"))))
22714 (properties `((upstream-name . "rstanarm")))
22715 (build-system r-build-system)
22717 `(("pandoc" ,pandoc)
22718 ("pandoc-citeproc" ,pandoc-citeproc)))
22720 `(("r-bayesplot" ,r-bayesplot)
22722 ("r-ggplot2" ,r-ggplot2)
22725 ("r-matrix" ,r-matrix)
22728 ("r-rcppeigen" ,r-rcppeigen)
22729 ("r-rcppparallel" ,r-rcppparallel)
22730 ("r-rstan" ,r-rstan)
22731 ("r-rstantools" ,r-rstantools)
22732 ("r-shinystan" ,r-shinystan)
22733 ("r-stanheaders" ,r-stanheaders)
22734 ("r-survival" ,r-survival)))
22736 `(("r-knitr" ,r-knitr)))
22737 (home-page "https://mc-stan.org/rstanarm/")
22738 (synopsis "Bayesian applied regression modeling via Stan")
22740 "This package estimates previously compiled regression models using the
22741 @code{rstan} package, which provides the R interface to the Stan C++ library
22742 for Bayesian estimation. Users specify models via the customary R syntax with
22743 a formula and @code{data.frame} plus some additional arguments for priors.")
22744 (license license:gpl3+)))
22746 (define-public r-kendall
22753 (uri (cran-uri "Kendall" version))
22756 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
22757 (properties `((upstream-name . "Kendall")))
22758 (build-system r-build-system)
22760 `(("r-boot" ,r-boot)))
22762 `(("gfortran" ,gfortran)))
22763 (home-page "https://cran.r-project.org/web/packages/Kendall/")
22764 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
22766 "This package computes the Kendall rank correlation and Mann-Kendall
22768 (license license:gpl2+)))
22770 (define-public r-keyring
22777 (uri (cran-uri "keyring" version))
22780 "1hpfd4hbx43i39l995rg86kfxi7wlyla1gv8mwcdr4xx7z122zzq"))))
22781 (properties `((upstream-name . "keyring")))
22782 (build-system r-build-system)
22784 `(("r-assertthat" ,r-assertthat)
22785 ("r-filelock" ,r-filelock)
22786 ("r-getpass" ,r-getpass)
22787 ("r-openssl" ,r-openssl)
22789 ("r-rappdirs" ,r-rappdirs)
22790 ("r-sodium" ,r-sodium)
22791 ("r-yaml" ,r-yaml)))
22792 (native-inputs `(("pkg-config" ,pkg-config)))
22793 (home-page "https://github.com/r-lib/keyring")
22794 (synopsis "Access the system credential store from R")
22796 "This package provides a platform-independent API to access the operating
22797 system's credential store. It currently supports Keychain on macOS,
22798 Credential Store on Windows, the Secret Service API on GNU/Linux, and a
22799 simple, platform independent store implemented with environment variables.
22800 Additional storage back-ends can be added easily.")
22801 (license license:expat)))
22803 (define-public r-zyp
22806 (version "0.10-1.1")
22810 (uri (cran-uri "zyp" version))
22813 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
22814 (properties `((upstream-name . "zyp")))
22815 (build-system r-build-system)
22817 `(("r-kendall" ,r-kendall)))
22818 (home-page "https://cran.r-project.org/web/packages/zyp/")
22819 (synopsis "Zhang + Yue-Pilon Trends Package")
22821 "This package contains an efficient implementation of Sen's slope
22822 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
22823 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
22825 (license license:lgpl2.1)))
22827 (define-public r-rlinsolve
22829 (name "r-rlinsolve")
22834 (uri (cran-uri "Rlinsolve" version))
22837 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
22838 (properties `((upstream-name . "Rlinsolve")))
22839 (build-system r-build-system)
22841 `(("r-matrix" ,r-matrix)
22843 ("r-rcpparmadillo" ,r-rcpparmadillo)
22844 ("r-rdpack" ,r-rdpack)))
22845 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
22846 (synopsis "Iterative solvers for (sparse) linear system of equations")
22848 "Solving a system of linear equations is one of the most fundamental
22849 computational problems for many fields of mathematical studies, such as
22850 regression problems from statistics or numerical partial differential
22851 equations. This package provides basic stationary iterative solvers such as
22852 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
22853 Nonstationary, also known as Krylov subspace methods are also provided.
22854 Sparse matrix computation is also supported in that solving large and sparse
22855 linear systems can be manageable using the @code{Matrix} package along with
22856 @code{RcppArmadillo}.")
22857 (license license:gpl3+)))
22859 (define-public r-zvcv
22866 (uri (cran-uri "ZVCV" version))
22869 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
22870 (properties `((upstream-name . "ZVCV")))
22871 (build-system r-build-system)
22873 `(("r-abind" ,r-abind)
22875 ("r-dplyr" ,r-dplyr)
22876 ("r-glmnet" ,r-glmnet)
22877 ("r-magrittr" ,r-magrittr)
22878 ("r-mvtnorm" ,r-mvtnorm)
22880 ("r-rcpparmadillo" ,r-rcpparmadillo)
22881 ("r-rlinsolve" ,r-rlinsolve)))
22882 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
22883 (synopsis "Zero-Variance Control Variates")
22885 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
22886 to reduce the variance of Monte Carlo estimators of expectations using the
22887 derivatives of the log target. Once the derivatives are available, the only
22888 additional computational effort is in solving a linear regression problem.
22889 This method has been extended to higher dimensions using regularisation. This
22890 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
22891 samples, derivatives and function evaluations are available. Additional
22892 functions for applying ZV-CV to two estimators for the normalising constant of
22893 the posterior distribution in Bayesian statistics are also supplied.")
22894 (license license:gpl2+)))
22896 (define-public r-ztype
22903 (uri (cran-uri "ztype" version))
22906 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
22907 (properties `((upstream-name . "ztype")))
22908 (build-system r-build-system)
22910 `(("r-assertthat" ,r-assertthat)
22911 ("r-dplyr" ,r-dplyr)
22912 ("r-ggplot2" ,r-ggplot2)
22913 ("r-lubridate" ,r-lubridate)
22914 ("r-magrittr" ,r-magrittr)
22915 ("r-rvest" ,r-rvest)
22916 ("r-stringr" ,r-stringr)))
22917 (home-page "https://cran.r-project.org/web/packages/ztype/")
22918 (synopsis "Run a Ztype game loaded with R functions")
22920 "How fast can you type R functions on your keyboard? Find out by running
22921 a @code{zty.pe} game: export R functions as instructions to type to destroy
22922 opponents' vessels.")
22923 (license license:gpl3)))
22925 (define-public r-zseq
22932 (uri (cran-uri "Zseq" version))
22935 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
22936 (properties `((upstream-name . "Zseq")))
22937 (build-system r-build-system)
22939 `(("r-gmp" ,r-gmp)))
22940 (home-page "https://cran.r-project.org/web/packages/Zseq/")
22941 (synopsis "Integer sequence generator")
22943 "This package generates well-known integer sequences. The @code{gmp}
22944 package is adopted for computing with arbitrarily large numbers. Every
22945 function has a hyperlink to its corresponding item in the @dfn{On-Line
22946 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
22947 (license license:gpl3+)))
22949 (define-public r-isoband
22956 (uri (cran-uri "isoband" version))
22959 "1zkzdc39dpw2z59bjck27nimz9a2vskmw0f7wb17s53dvy7k3lzr"))))
22960 (properties `((upstream-name . "isoband")))
22961 (build-system r-build-system)
22963 `(("r-testthat" ,r-testthat)))
22965 `(("r-knitr" ,r-knitr)))
22966 (home-page "https://github.com/wilkelab/isoband")
22967 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
22969 "This package provides a fast C++ implementation to generate contour
22970 lines (isolines) and contour polygons (isobands) from regularly spaced grids
22971 containing elevation data.")
22972 (license license:expat)))
22974 (define-public r-ppcor
22981 (uri (cran-uri "ppcor" version))
22984 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
22985 (properties `((upstream-name . "ppcor")))
22986 (build-system r-build-system)
22988 `(("r-mass" ,r-mass)))
22989 (home-page "https://cran.r-project.org/web/packages/ppcor/")
22990 (synopsis "Partial and semi-partial correlation")
22992 "This package provides users not only with a function to readily
22993 calculate the higher-order partial and semi-partial correlations but also with
22994 statistics and p-values of the correlation coefficients.")
22995 (license license:gpl2)))
22997 (define-public r-hrbrthemes
22999 (name "r-hrbrthemes")
23004 (uri (cran-uri "hrbrthemes" version))
23006 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
23007 (properties `((upstream-name . "hrbrthemes")))
23008 (build-system r-build-system)
23010 `(("r-extrafont" ,r-extrafont)
23011 ("r-gdtools" ,r-gdtools)
23012 ("r-ggplot2" ,r-ggplot2)
23013 ("r-htmltools" ,r-htmltools)
23014 ("r-knitr" ,r-knitr)
23015 ("r-magrittr" ,r-magrittr)
23016 ("r-rmarkdown" ,r-rmarkdown)
23017 ("r-scales" ,r-scales)))
23019 `(("r-knitr" ,r-knitr)))
23020 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
23021 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
23023 "This package provides a compilation of extra @code{ggplot2} themes,
23024 scales and utilities, including a spell check function for plot label fields
23025 and an overall emphasis on typography.")
23026 (license license:expat)))
23028 (define-public r-crochet
23035 (uri (cran-uri "crochet" version))
23038 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
23039 (build-system r-build-system)
23041 `(("r-knitr" ,r-knitr)))
23042 (home-page "https://github.com/agrueneberg/crochet")
23043 (synopsis "Implementation Helper for Matrix-Like Types")
23045 "Functions to help implement the extraction / subsetting / indexing
23046 function @code{[} and replacement function @code{[<-} of custom matrix-like
23047 types (based on S3, S4, etc.), modeled as closely to the base matrix class
23048 as possible (with tests to prove it).")
23049 (license license:expat)))
23051 (define-public r-boa
23054 (version "1.1.8-2")
23058 (uri (cran-uri "boa" version))
23061 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
23062 (properties `((upstream-name . "boa")))
23063 (build-system r-build-system)
23064 (home-page "http://www.jstatsoft.org/v21/i11")
23065 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
23067 "This package provides a menu-driven program and library of functions for
23068 carrying out convergence diagnostics and statistical and graphical analysis of
23069 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
23070 (license license:gpl2+)))
23072 (define-public r-httpcode
23074 (name "r-httpcode")
23078 (uri (cran-uri "httpcode" version))
23081 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
23082 (build-system r-build-system)
23083 (home-page "https://github.com/sckott/httpcode")
23084 (synopsis "HTTP status code helper")
23085 (description "@code{httpcode} provides functionality for finding and
23086 explaining the meaning of @code{HTTP} status codes. Functions are included for
23087 searching for codes by full or partial number, by message, and to get
23088 appropriate dog and cat images for many status codes.")
23089 (license license:expat)))
23091 (define-public r-latex2exp
23093 (name "r-latex2exp")
23097 (uri (cran-uri "latex2exp" version))
23100 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
23101 (build-system r-build-system)
23103 `(("r-stringr" ,r-stringr)
23104 ("r-magrittr" ,r-magrittr)))
23105 (home-page "https://github.com/stefano-meschiari/latex2exp/")
23106 (synopsis "Use LaTeX expressions in plots")
23107 (description "@code{latex2exp} parses and converts LaTeX math formulas to
23108 R's plotmath expressions, used to enter mathematical formulas and symbols to be
23109 rendered as text, axis labels, etc. throughout R's plotting system.")
23110 (license license:expat)))
23112 (define-public r-oai
23118 (uri (cran-uri "oai" version))
23121 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
23122 (build-system r-build-system)
23124 `(("r-xml2" ,r-xml2)
23127 ("r-stringr" ,r-stringr)
23128 ("r-tibble" ,r-tibble)))
23129 (home-page "https://github.com/ropensci/oai/")
23130 (synopsis "General purpose OAI-PMH services client")
23131 (description "@code{oai} provides a general purpose client to work with
23132 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
23133 service. Functions are provided to work with the OAI-PMH verbs:
23134 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
23135 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
23136 (license license:expat)))
23138 (define-public r-argon2
23145 (uri (cran-uri "argon2" version))
23148 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
23149 (properties `((upstream-name . "argon2")))
23150 (build-system r-build-system)
23151 (home-page "https://github.com/wrathematics/argon2")
23152 (synopsis "Secure password hashing based on the argon2 algorithm")
23154 "This package provides utilities for secure password hashing via the
23155 argon2 algorithm.")
23156 (license license:bsd-2)))
23158 (define-public r-getpass
23165 (uri (cran-uri "getPass" version))
23168 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
23169 (properties `((upstream-name . "getPass")))
23170 (build-system r-build-system)
23172 `(("r-rstudioapi" ,r-rstudioapi)))
23173 (home-page "https://github.com/wrathematics/getPass")
23174 (synopsis "Masked user input")
23176 "This package provides a micro-package for reading \"passwords\", i.e.
23177 reading user input with masking, so that the input is not displayed as it is
23178 typed. Currently, RStudio, the command line (every OS), and any platform
23179 where tcltk is present are supported.")
23180 (license license:bsd-2)))
23182 (define-public r-remoter
23189 (uri (cran-uri "remoter" version))
23192 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
23193 (properties `((upstream-name . "remoter")))
23194 (build-system r-build-system)
23196 `(("r-argon2" ,r-argon2)
23197 ("r-getpass" ,r-getpass)
23198 ("r-pbdzmq" ,r-pbdzmq)
23200 (home-page "https://github.com/RBigData/remoter")
23201 (synopsis "Control a remote R session from a local one")
23203 "This package provides a set of utilities for client/server computing
23204 with R, controlling a remote R session (the server) from a local one (the
23206 (license license:bsd-2)))
23208 (define-public r-asd
23215 (uri (cran-uri "asd" version))
23218 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
23219 (properties `((upstream-name . "asd")))
23220 (build-system r-build-system)
23222 `(("r-mvtnorm" ,r-mvtnorm)))
23223 (home-page "https://cran.r-project.org/web/packages/asd")
23224 (synopsis "Simulations for Adaptive Seamless Designs")
23226 "This package provdes means to run simulations for adaptive seamless
23227 designs with and without early outcomes for treatment selection and
23228 subpopulation type designs.")
23229 (license license:gpl3)))
23231 (define-public r-nbconvertr
23233 (name "r-nbconvertr")
23238 (uri (cran-uri "nbconvertR" version))
23241 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
23242 (properties `((upstream-name . "nbconvertR")))
23243 (build-system r-build-system)
23245 `(("jupyter" ,python-nbconvert)
23246 ("pandoc" ,pandoc)))
23247 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
23248 (synopsis "Vignette engine wrapping Jupyter notebooks")
23250 "This package calls the Jupyter script @code{nbconvert} to create
23251 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
23252 containing rich text, code, and its output. Code cells can be edited and
23253 evaluated interactively.")
23254 (license license:gpl3)))
23256 (define-public r-bridgesampling
23258 (name "r-bridgesampling")
23263 (uri (cran-uri "bridgesampling" version))
23266 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
23268 `((upstream-name . "bridgesampling")))
23269 (build-system r-build-system)
23271 `(("r-brobdingnag" ,r-brobdingnag)
23273 ("r-matrix" ,r-matrix)
23274 ("r-mvtnorm" ,r-mvtnorm)
23275 ("r-scales" ,r-scales)
23276 ("r-stringr" ,r-stringr)))
23278 `(("r-knitr" ,r-knitr)))
23279 (home-page "https://github.com/quentingronau/bridgesampling")
23280 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
23282 "This package provides functions for estimating marginal likelihoods,
23283 Bayes factors, posterior model probabilities, and normalizing constants in
23284 general, via different versions of bridge sampling.")
23285 (license license:gpl2+)))
23287 (define-public r-tea
23294 (uri (cran-uri "tea" version))
23297 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
23299 `((upstream-name . "tea")))
23300 (build-system r-build-system)
23302 `(("r-matrix" ,r-matrix)))
23303 (home-page "https://cran.r-project.org/web/packages/tea/")
23304 (synopsis "Threshold estimation approaches")
23306 "This package provides different approaches for selecting the threshold
23307 in generalized Pareto distributions. Most of them are based on minimizing the
23308 AMSE-criterion or at least by reducing the bias of the assumed GPD-model.
23309 Others are heuristically motivated by searching for stable sample paths, i.e.
23310 a nearly constant region of the tail index estimator with respect to k, which
23311 is the number of data in the tail. The third class is motivated by graphical
23312 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
23313 is also implemented here.")
23314 (license license:gpl3)))
23316 (define-public r-awsmethods
23318 (name "r-awsmethods")
23323 (uri (cran-uri "awsMethods" version))
23326 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
23328 `((upstream-name . "awsMethods")))
23329 (build-system r-build-system)
23330 (home-page "http://www.wias-berlin.de/software/imaging/")
23331 (synopsis "Class and methods definitions")
23333 "This package defines the generic method @code{extract} and provides
23334 @code{openMP} support as needed in several packages like
23335 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
23336 (license license:gpl2+)))
23338 (define-public r-aws
23345 (uri (cran-uri "aws" version))
23348 "1fhm87iax6bkvd4vszvjbcqw3b2drs11rjxr7zf2w4sgc72svaz8"))))
23350 `((upstream-name . "aws")))
23351 (build-system r-build-system)
23353 `(("r-awsmethods" ,r-awsmethods)
23356 `(("gfortran" ,gfortran)))
23357 (home-page "https://cran.r-project.org/web/packages/aws/")
23358 (synopsis "Adaptive weights smoothing")
23360 "This package provides a collection of R-functions implementing adaptive
23361 smoothing procedures in 1D, 2D and 3D. This includes the
23362 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
23363 Confidence Intervals} (ICI), variational approaches, and a non-local means
23365 (license license:gpl2+)))
23367 (define-public r-sgloptim
23369 (name "r-sgloptim")
23374 (uri (cran-uri "sglOptim" version))
23377 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
23379 `((upstream-name . "sglOptim")))
23380 (build-system r-build-system)
23383 ("r-doparallel" ,r-doparallel)
23384 ("r-foreach" ,r-foreach)
23385 ("r-matrix" ,r-matrix)
23387 ("r-rcpparmadillo" ,r-rcpparmadillo)
23388 ("r-rcppprogress" ,r-rcppprogress)))
23390 `(("r-knitr" ,r-knitr)))
23391 (home-page "https://github.com/nielsrhansen/sglOptim")
23392 (synopsis "Generic sparse group Lasso solver")
23394 "This package provides a fast generic solver for sparse group lasso
23395 optimization problems. The loss (objective) function must be defined in a C++
23396 module. The optimization problem is solved using a coordinate gradient
23397 descent algorithm. Convergence of the algorithm is established and the
23398 algorithm is applicable to a broad class of loss functions. Use of parallel
23399 computing for cross validation and subsampling is supported through the
23400 @code{foreach} and @code{doParallel} packages.")
23401 (license license:gpl2+)))
23403 (define-public r-grouped
23410 (uri (cran-uri "grouped" version))
23413 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
23415 `((upstream-name . "grouped")))
23416 (build-system r-build-system)
23418 `(("r-mass" ,r-mass)))
23419 (home-page "https://cran.r-project.org/web/packages/grouped/")
23420 (synopsis "Regression analysis of grouped and coarse data")
23422 "This package provides regression models for grouped and coarse data,
23423 under the coarsened at random assumption.")
23424 (license license:gpl2+)))
23426 (define-public r-stam
23433 (uri (cran-uri "stam" version))
23436 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
23438 `((upstream-name . "stam")))
23439 (build-system r-build-system)
23443 (home-page "https://cran.r-project.org/web/packages/stam")
23444 (synopsis "Spatio-temporal analysis and modelling")
23446 "This package provides various methods to conduct Spatio-Temporal
23447 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
23448 Inferred Spatio-Temporal Modelling.")
23449 (license license:gpl2+)))
23451 (define-public r-dcv
23458 (uri (cran-uri "dcv" version))
23461 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
23463 `((upstream-name . "dcv")))
23464 (build-system r-build-system)
23466 `(("r-lmtest" ,r-lmtest)))
23467 (home-page "https://cran.r-project.org/web/packages/dcv/")
23468 (synopsis "Conventional cross-validation statistics for climate-growth model")
23470 "This package performs several conventional cross-validation statistical
23471 methods for climate-growth model in the climate reconstruction from tree
23472 rings, including Sign Test statistic, Reduction of Error statistic, Product
23473 Mean Test, Durbin-Watson statistic etc.")
23474 (license license:gpl2)))
23476 (define-public r-rcdd
23483 (uri (cran-uri "rcdd" version))
23486 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
23488 `((upstream-name . "rcdd")))
23489 (build-system r-build-system)
23492 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
23493 (synopsis "Computational geometry")
23495 "This package converts back and forth between two representations of a
23496 convex polytope: as solution of a set of linear equalities and inequalities
23497 and as convex hull of set of points and rays. Also does linear programming
23498 and redundant generator elimination. All functions can use exact
23499 infinite-precision rational arithmetic.")
23500 (license license:gpl2)))
23502 (define-public r-rxnat
23509 (uri (cran-uri "Rxnat" version))
23512 "00fl68pa0c2vy4xlny67pn41lzgm7b97wgg3dwm6z35izca62l11"))))
23514 `((upstream-name . "Rxnat")))
23515 (build-system r-build-system)
23517 `(("r-dplyr" ,r-dplyr)
23519 ("r-rcurl" ,r-rcurl)
23520 ("r-tibble" ,r-tibble)))
23522 `(("r-knitr" ,r-knitr)))
23523 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
23524 (synopsis "Queries and extracts images from neuroimaging datasets")
23526 "This package allows communication with the Extensible Neuroimaging
23527 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
23529 (license license:gpl2)))
23531 (define-public r-rserve
23538 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
23539 version ".tar.gz"))
23542 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
23543 (build-system r-build-system)
23545 `(("r-checkmate" ,r-checkmate)
23547 ("r-jsonlite" ,r-jsonlite)
23548 ("r-knitr" ,r-knitr)
23551 ("r-uuid" ,r-uuid)))
23553 `(("openssl" ,openssl)
23555 (home-page "https://github.com/s-u/Rserve")
23557 "Server providing access to R from many languages and systems")
23559 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
23560 binary requests to be sent to R. Every connection has a separate workspace
23561 and working directory. Client-side implementations are available for popular
23562 languages such as C/C++ and Java, allowing any application to use facilities
23563 of R without the need of linking to R code. Rserve supports remote
23564 connection, user authentication and file transfer. A simple R client is
23565 included in this package as well.")
23566 (license license:gpl2)))
23568 (define-public r-gamm4
23575 (uri (cran-uri "gamm4" version))
23578 "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap"))))
23579 (properties `((upstream-name . "gamm4")))
23580 (build-system r-build-system)
23582 `(("r-lme4" ,r-lme4)
23583 ("r-matrix" ,r-matrix)
23584 ("r-mgcv" ,r-mgcv)))
23585 (home-page "https://cran.r-project.org/web/packages/gamm4/")
23586 (synopsis "Generalized additive mixed models using mgcv and lme4")
23588 "Estimate generalized additive mixed models via a version of function
23589 @code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor
23591 (license license:gpl2+)))
23593 (define-public r-optimx
23596 (version "2020-4.2")
23600 (uri (cran-uri "optimx" version))
23603 "00bi2sr2hr7x6cfwlsn7hz2r56lcyv9naa8vmfcgr1r269fc50b3"))))
23604 (properties `((upstream-name . "optimx")))
23605 (build-system r-build-system)
23606 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
23607 (native-inputs `(("r-knitr" ,r-knitr)))
23608 (home-page "https://cran.r-project.org/web/packages/optimx/")
23609 (synopsis "Expanded replacement and extension of the optim function")
23611 "This package provides a replacement and extension of the @code{optim}
23612 function to call to several function minimization codes in R in a single
23613 statement. These methods handle smooth, possibly box constrained functions of
23614 several or many parameters. Note that the function @code{optimr} was prepared
23615 to simplify the incorporation of minimization codes going forward. This
23616 package also implements some utility codes and some extra solvers, including
23617 safeguarded Newton methods. Many methods previously separate are now included
23619 (license license:gpl2)))
23621 (define-public r-projpred
23623 (name "r-projpred")
23628 (uri (cran-uri "projpred" version))
23631 "0nx514mrfh3gv854pr71w5x3zgdnn0kinf5nh7z90q3h7ysry2mg"))))
23632 (properties `((upstream-name . "projpred")))
23633 (build-system r-build-system)
23635 `(("r-dplyr" ,r-dplyr)
23636 ("r-gamm4" ,r-gamm4)
23637 ("r-ggplot2" ,r-ggplot2)
23640 ("r-magrittr" ,r-magrittr)
23643 ("r-optimx" ,r-optimx)
23645 ("r-rcpparmadillo" ,r-rcpparmadillo)
23646 ("r-rngtools" ,r-rngtools)
23647 ("r-rstantools" ,r-rstantools)
23648 ("r-tidyverse" ,r-tidyverse)))
23649 (native-inputs `(("r-knitr" ,r-knitr)))
23650 (home-page "https://mc-stan.org/projpred/")
23651 (synopsis "Projection predictive feature selection")
23653 "This package performs projection predictive feature selection for
23654 generalized linear models and generalized linear and additive multilevel
23655 models. The package is compatible with the @code{rstanarm} and @code{brms}
23656 packages, but other reference models can also be used. See the package
23657 vignette for more information and examples.")
23658 (license license:gpl3)))
23660 (define-public r-brms
23667 (uri (cran-uri "brms" version))
23670 "0mzwihhgmn405l6zq11a180q4k3chggj9qj0j7q838b9vrszg59j"))))
23671 (properties `((upstream-name . "brms")))
23672 (build-system r-build-system)
23674 `(("r-abind" ,r-abind)
23675 ("r-backports" ,r-backports)
23676 ("r-bayesplot" ,r-bayesplot)
23677 ("r-bridgesampling" ,r-bridgesampling)
23679 ("r-future" ,r-future)
23680 ("r-ggplot2" ,r-ggplot2)
23683 ("r-matrix" ,r-matrix)
23684 ("r-matrixstats" ,r-matrixstats)
23686 ("r-nleqslv" ,r-nleqslv)
23688 ("r-projpred" ,r-projpred)
23690 ("r-rstan" ,r-rstan)
23691 ("r-rstantools" ,r-rstantools)
23692 ("r-shinystan" ,r-shinystan)))
23693 (native-inputs `(("r-knitr" ,r-knitr)))
23695 "https://github.com/paul-buerkner/brms")
23697 "Bayesian Regression Models using 'Stan'")
23699 "Fit Bayesian generalized (non-)linear multivariate multilevel models
23700 using 'Stan' for full Bayesian inference. A wide range of distributions and
23701 link functions are supported, allowing users to fit -- among others -- linear,
23702 robust linear, count data, survival, response times, ordinal, zero-inflated,
23703 hurdle, and even self-defined mixture models all in a multilevel context.
23704 Further modeling options include non-linear and smooth terms, auto-correlation
23705 structures, censored data, meta-analytic standard errors, and quite a few
23706 more. In addition, all parameters of the response distribution can be
23707 predicted in order to perform distributional regression. Prior specifications
23708 are flexible and explicitly encourage users to apply prior distributions that
23709 actually reflect their beliefs. Model fit can easily be assessed and compared
23710 with posterior predictive checks and leave-one-out cross-validation.")
23711 (license license:gpl2)))
23713 (define-public r-mstate
23720 (uri (cran-uri "mstate" version))
23723 "11i3p7fph8nbnfis1m7rdrq32qryaajv2wrkxk1x6k17zkh4rq6i"))))
23724 (properties `((upstream-name . "mstate")))
23725 (build-system r-build-system)
23727 `(("r-data-table" ,r-data-table)
23728 ("r-lattice" ,r-lattice)
23729 ("r-magrittr" ,r-magrittr)
23730 ("r-rcolorbrewer" ,r-rcolorbrewer)
23731 ("r-rlang" ,r-rlang)
23732 ("r-survival" ,r-survival)
23733 ("r-viridis" ,r-viridis)))
23735 `(("r-knitr" ,r-knitr)))
23737 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
23739 "Data Preparation, Estimation and Prediction in Multi-State Models")
23741 "Contains functions for data preparation, descriptives, hazard estimation
23742 and prediction with Aalen-Johansen or simulation in competing risks and
23743 multi-state models.")
23744 (license license:gpl2+)))
23746 (define-public r-scatterpie
23748 (name "r-scatterpie")
23753 (uri (cran-uri "scatterpie" version))
23756 "0h48l0699lpfagv09f53yismir84945m56qwzk52lc7wxyvkfcp1"))))
23757 (properties `((upstream-name . "scatterpie")))
23758 (build-system r-build-system)
23760 `(("r-ggforce" ,r-ggforce)
23761 ("r-ggplot2" ,r-ggplot2)
23762 ("r-rlang" ,r-rlang)
23763 ("r-rvcheck" ,r-rvcheck)
23764 ("r-tidyr" ,r-tidyr)))
23766 `(("r-knitr" ,r-knitr)))
23767 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
23768 (synopsis "Scatter pie plot")
23770 "This package creates scatterpie plots, especially useful for plotting
23772 (license license:artistic2.0)))
23774 (define-public r-scrypt
23781 (uri (cran-uri "scrypt" version))
23784 "14iblgbp9v2by8fjbrpsd59iknp5babcz7j3yv1yxxzcwyb6wrrm"))))
23785 (properties `((upstream-name . "scrypt")))
23786 (build-system r-build-system)
23788 `(("r-rcpp" ,r-rcpp)))
23789 (home-page "https://github.com/rstudio/rscrypt")
23790 (synopsis "Key derivation functions for R based on Scrypt")
23792 "This package provides functions for working with the scrypt key
23793 derivation functions. Scrypt is a password-based key derivation function
23794 created by Colin Percival. The algorithm was specifically designed to make it
23795 costly to perform large-scale custom hardware attacks by requiring large
23796 amounts of memory.")
23797 (license license:bsd-2)))
23799 (define-public r-boruta
23806 (uri (cran-uri "Boruta" version))
23809 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
23810 (properties `((upstream-name . "Boruta")))
23811 (build-system r-build-system)
23812 (propagated-inputs `(("r-ranger" ,r-ranger)))
23813 (home-page "https://gitlab.com/mbq/Boruta/")
23814 (synopsis "Wrapper algorithm for all relevant feature selection")
23816 "This package provides an all relevant feature selection wrapper
23817 algorithm. It finds relevant features by comparing original attributes'
23818 importance with importance achievable at random, estimated using their
23819 permuted copies (shadows).")
23820 (license license:gpl2+)))
23822 (define-public r-directlabels
23824 (name "r-directlabels")
23825 (version "2021.1.13")
23829 (uri (cran-uri "directlabels" version))
23832 "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w"))))
23833 (build-system r-build-system)
23835 `(("r-quadprog" ,r-quadprog)))
23837 `(("r-knitr" ,r-knitr)))
23838 (home-page "http://directlabels.r-forge.r-project.org/")
23839 (synopsis "Direct labels for multicolor plots")
23841 "This package provides an extensible framework for automatically placing
23842 direct labels onto multicolor plots. Label positions are described using
23843 positioning methods that can be re-used across several different plots. There
23844 are heuristics for examining @code{trellis} and @code{ggplot} objects and
23845 inferring an appropriate positioning method.")
23846 (license license:gpl3)))
23848 (define-public r-lsd
23855 (uri (cran-uri "LSD" version))
23857 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
23858 (properties `((upstream-name . "LSD")))
23859 (build-system r-build-system)
23860 (home-page "https://cran.r-project.org/web/packages/LSD/")
23861 (synopsis "Lots of superior depictions tool creates colorful plots")
23863 "This package creates lots of colorful plots in a multitude of variations.
23864 Try a demo of the LSD by running @code{demotour()}.")
23866 (license (list license:gpl2 license:gpl3))))
23868 (define-public r-phylogram
23870 (name "r-phylogram")
23875 (uri (cran-uri "phylogram" version))
23877 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
23878 (properties `((upstream-name . "phylogram")))
23879 (build-system r-build-system)
23880 (propagated-inputs `(("r-ape" ,r-ape)))
23881 (home-page "https://github.com/ropensci/phylogram/")
23882 (synopsis "Dendrograms for evolutionary analysis")
23884 "The @code{r-phylogram} package is a tool for for developing phylogenetic
23885 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
23886 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
23887 as well as several tools for command-line tree manipulation and import/export
23888 via Newick parenthetic text. This improves accessibility to the comprehensive
23889 range of object-specific analytical and tree-visualization functions found
23890 across a wide array of bioinformatic R packages.")
23891 (license license:gpl3)))
23893 (define-public r-kmer
23900 (uri (cran-uri "kmer" version))
23902 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
23903 (properties `((upstream-name . "kmer")))
23904 (build-system r-build-system)
23906 `(("r-openssl" ,r-openssl)
23907 ("r-phylogram" ,r-phylogram)
23908 ("r-rcpp" ,r-rcpp)))
23909 (home-page "https://github.com/shaunpwilkinson/kmer/")
23910 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
23912 "@code{r-kmer} is an R package for rapidly computing distance matrices
23913 and clustering large sequence datasets using fast alignment-free k-mer
23914 counting and recursive k-means partitioning.")
23915 (license license:gpl3)))
23917 (define-public r-hardhat
23924 (uri (cran-uri "hardhat" version))
23927 "1b7f9i9fy39j9n03g40vd6nzgq9fgq914xg3svf84najlknvjzly"))))
23928 (properties `((upstream-name . "hardhat")))
23929 (build-system r-build-system)
23931 `(("r-glue" ,r-glue)
23932 ("r-rlang" ,r-rlang)
23933 ("r-tibble" ,r-tibble)
23934 ("r-vctrs" ,r-vctrs)))
23936 `(("r-knitr" ,r-knitr)))
23937 (home-page "https://github.com/tidymodels/hardhat")
23938 (synopsis "Construct modeling packages")
23940 "Building modeling packages is hard. A large amount of effort generally
23941 goes into providing an implementation for a new method that is efficient,
23942 fast, and correct, but often less emphasis is put on the user interface. A
23943 good interface requires specialized knowledge about S3 methods and formulas,
23944 which the average package developer might not have. The goal of
23945 @code{hardhat} is to reduce the burden around building new modeling packages
23946 by providing functionality for preprocessing, predicting, and validating
23948 (license license:expat)))
23950 (define-public r-lightgbm
23952 (name "r-lightgbm")
23957 (uri (cran-uri "lightgbm" version))
23960 "1pwsh6j9ksahh58b15j5ij56bsc6syy3z4k4a5zhy5n7829rz555"))))
23961 (properties `((upstream-name . "lightgbm")))
23962 (build-system r-build-system)
23964 `(("r-data-table" ,r-data-table)
23965 ("r-jsonlite" ,r-jsonlite)
23966 ("r-matrix" ,r-matrix)
23968 (home-page "https://github.com/Microsoft/LightGBM")
23969 (synopsis "Light gradient boosting machine")
23971 "Tree based algorithms can be improved by introducing boosting
23972 frameworks. LightGBM is one such framework, based on Ke, Guolin et
23973 al. (2017). This package offers an R interface to work with it. It is
23974 designed to be distributed and efficient with the following goals:
23977 @item Faster training speed and higher efficiency;
23978 @item lower memory usage;
23979 @item better accuracy;
23980 @item parallel learning supported; and
23981 @item capable of handling large-scale data.
23984 (license license:expat)))
23986 (define-public r-shapforxgboost
23988 (name "r-shapforxgboost")
23993 (uri (cran-uri "SHAPforxgboost" version))
23996 "0jgyss9bawl7sf4dwa75sn7ld3mvrrr0z2074lbkq3f5qb9gwsly"))))
23998 `((upstream-name . "SHAPforxgboost")))
23999 (build-system r-build-system)
24001 `(("r-bbmisc" ,r-bbmisc)
24002 ("r-data-table" ,r-data-table)
24003 ("r-ggextra" ,r-ggextra)
24004 ("r-ggforce" ,r-ggforce)
24005 ("r-ggplot2" ,r-ggplot2)
24006 ("r-ggpubr" ,r-ggpubr)
24007 ("r-lightgbm" ,r-lightgbm)
24008 ("r-rcolorbrewer" ,r-rcolorbrewer)
24009 ("r-xgboost" ,r-xgboost)))
24010 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
24011 (synopsis "SHAP Plots for XGBoost")
24013 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
24014 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
24015 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
24016 and force plot. It relies on the @code{XGBoost} package to produce SHAP
24018 (license license:expat)))
24020 (define-public r-rismed
24027 (uri (cran-uri "RISmed" version))
24030 "0nwixhngi4r2f73362salivsmsf7l52bm13jqvhdq8mfiigm80vd"))))
24031 (properties `((upstream-name . "RISmed")))
24032 (build-system r-build-system)
24033 (home-page "https://cran.r-project.org/web/packages/RISmed")
24034 (synopsis "Download content from NCBI databases")
24036 "This package provides a set of tools to extract bibliographic
24037 content from the National Center for Biotechnology Information (NCBI)
24038 databases, including PubMed. The name RISmed is a portmanteau of
24039 RIS (for Research Information Systems, a common tag format for
24040 bibliographic data) and PubMed.")
24041 (license license:gpl2+)))
24043 (define-public r-semver
24050 (uri (cran-uri "semver" version))
24053 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
24054 (properties `((upstream-name . "semver")))
24055 (build-system r-build-system)
24057 `(("r-assertthat" ,r-assertthat)
24058 ("r-rcpp" ,r-rcpp)))
24059 (native-inputs `(("r-knitr" ,r-knitr)))
24060 (home-page "https://github.com/johndharrison/semver")
24061 (synopsis "Parser for Semantic Versioning 2.0.0")
24063 "This package provides tools and functions for parsing, rendering and
24064 operating on semantic version strings. Semantic versioning is a simple set of
24065 rules and requirements that dictate how version numbers are assigned and
24066 incremented as outlined at @url{http://semver.org}.")
24067 (license license:expat)))
24069 (define-public r-binman
24076 (uri (cran-uri "binman" version))
24079 "00l7m98h41r67gf0qxqis3vx63j7wylnk9vlgcyk41szkrz8ikkc"))))
24080 (properties `((upstream-name . "binman")))
24081 (build-system r-build-system)
24083 `(("r-assertthat" ,r-assertthat)
24085 ("r-jsonlite" ,r-jsonlite)
24086 ("r-rappdirs" ,r-rappdirs)
24087 ("r-semver" ,r-semver)
24089 ("r-yaml" ,r-yaml)))
24090 (native-inputs `(("r-knitr" ,r-knitr)))
24091 (home-page "https://github.com/ropensci/binman")
24092 (synopsis "Binary download manager")
24094 "This package provides tools and functions for managing the download of
24095 binary files. Binary repositories are defined in the YAML format. Defining
24096 new pre-download, download and post-download templates allow additional
24097 repositories to be added.")
24098 (license license:expat)))
24100 (define-public r-wdman
24107 (uri (cran-uri "wdman" version))
24110 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
24111 (properties `((upstream-name . "wdman")))
24112 (build-system r-build-system)
24114 `(("r-assertthat" ,r-assertthat)
24115 ("r-binman" ,r-binman)
24116 ("r-processx" ,r-processx)
24117 ("r-semver" ,r-semver)
24118 ("r-yaml" ,r-yaml)))
24119 (native-inputs `(("r-knitr" ,r-knitr)))
24120 (home-page "https://docs.ropensci.org/wdman/")
24121 (synopsis "Webdriver/Selenium binary manager")
24123 "There are a number of binary files associated with the
24124 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
24125 @url{https://sites.google.com/a/chromium.org/chromedriver/},
24126 @url{https://github.com/mozilla/geckodriver},
24127 @url{http://phantomjs.org/download.html}, and
24128 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
24129 more information). This package provides functions to download these binaries
24130 and to manage processes involving them.")
24131 (license license:expat)))
24133 (define-public r-rselenium
24135 (name "r-rselenium")
24140 (uri (cran-uri "RSelenium" version))
24143 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
24144 (properties `((upstream-name . "RSelenium")))
24145 (build-system r-build-system)
24147 `(("r-binman" ,r-binman)
24148 ("r-catools" ,r-catools)
24150 ("r-openssl" ,r-openssl)
24151 ("r-wdman" ,r-wdman)
24153 (native-inputs `(("r-knitr" ,r-knitr)))
24154 (home-page "https://docs.ropensci.org/RSelenium/")
24155 (synopsis "R bindings for Selenium WebDriver")
24157 "This package provides a set of R bindings for the Selenium 2.0
24158 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
24159 information) using the @code{JsonWireProtocol} (see
24160 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
24161 information). Selenium 2.0 WebDriver allows driving a web browser natively as
24162 a user would either locally or on a remote machine using the Selenium server
24163 it marks a leap forward in terms of web browser automation. Selenium
24164 automates web browsers (commonly referred to as browsers). Using RSelenium
24165 you can automate browsers locally or remotely.")
24166 (license license:agpl3+)))
24168 (define-public r-conquer
24175 (uri (cran-uri "conquer" version))
24178 "1zvlsrbmrij011mcdi3qngs1al2lhrdiyknxnk0w1zhzrra62bsl"))))
24179 (properties `((upstream-name . "conquer")))
24180 (build-system r-build-system)
24182 `(("r-matrix" ,r-matrix)
24183 ("r-matrixstats" ,r-matrixstats)
24185 ("r-rcpparmadillo" ,r-rcpparmadillo)))
24186 (home-page "https://github.com/XiaoouPan/conquer")
24187 (synopsis "Convolution-type smoothed quantile regression")
24189 "This package provides fast and accurate convolution-type smoothed
24190 quantile regression, implemented using Barzilai-Borwein gradient descent with
24191 a Huber regression warm start. Confidence intervals for regression
24192 coefficients are constructed using multiplier bootstrap.")
24193 (license license:gpl3)))
24195 (define-public r-fastshap
24197 (name "r-fastshap")
24202 (uri (cran-uri "fastshap" version))
24205 "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg"))))
24206 (properties `((upstream-name . "fastshap")))
24207 (build-system r-build-system)
24209 `(("r-abind" ,r-abind)
24210 ("r-ggplot2" ,r-ggplot2)
24211 ("r-gridextra" ,r-gridextra)
24212 ("r-matrixstats" ,r-matrixstats)
24215 ("r-rcpparmadillo" ,r-rcpparmadillo)
24216 ("r-tibble" ,r-tibble)))
24217 (home-page "https://github.com/bgreenwell/fastshap")
24218 (synopsis "Fast approximate Shapley values")
24220 "This package computes fast (relative to other implementations)
24221 approximate Shapley values for any supervised learning model. Shapley values
24222 help to explain the predictions from any black box model using ideas from game
24223 theory; see @url{Strumbel and Kononenko (2014),
24224 doi.org/10.1007/s10115-013-0679-x} for details.")
24225 (license license:gpl2+)))
24227 (define-public r-metrics
24234 (uri (cran-uri "Metrics" version))
24237 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
24238 (properties `((upstream-name . "Metrics")))
24239 (build-system r-build-system)
24240 (home-page "https://github.com/mfrasco/Metrics")
24241 (synopsis "Evaluation metrics for machine learning")
24243 "This package provides an implementation of evaluation metrics in R that
24244 are commonly used in supervised machine learning. It implements metrics for
24245 regression, time series, binary classification, classification, and
24246 information retrieval problems. It has zero dependencies and a consistent,
24247 simple interface for all functions.")
24248 (license license:bsd-3)))
24250 (define-public r-iml
24257 (uri (cran-uri "iml" version))
24260 "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7"))))
24261 (properties `((upstream-name . "iml")))
24262 (build-system r-build-system)
24264 `(("r-checkmate" ,r-checkmate)
24265 ("r-data-table" ,r-data-table)
24266 ("r-formula" ,r-formula)
24267 ("r-future" ,r-future)
24268 ("r-future-apply" ,r-future-apply)
24269 ("r-ggplot2" ,r-ggplot2)
24270 ("r-gridextra" ,r-gridextra)
24271 ("r-metrics" ,r-metrics)
24272 ("r-prediction" ,r-prediction)
24274 (native-inputs `(("r-knitr" ,r-knitr)))
24275 (home-page "https://github.com/christophM/iml")
24276 (synopsis "Interpretable machine learning")
24278 "This package provides interpretability methods to analyze the behavior
24279 and predictions of any machine learning model. Implemented methods are:
24282 @item Feature importance described by Fisher et al. (2018),
24283 @item accumulated local effects plots described by Apley (2018),
24284 @item partial dependence plots described by Friedman (2001),
24285 @item individual conditional expectation ('ice') plots described by Goldstein
24286 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
24287 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
24288 @item the Shapley Value described by Strumbelj et. al (2014)
24289 @url{https://doi.org/10.1007/s10115-013-0679-x},
24290 @item feature interactions described by Friedman et. al
24291 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
24294 (license license:expat)))
24296 (define-public r-goftest
24303 (uri (cran-uri "goftest" version))
24306 "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4"))))
24307 (properties `((upstream-name . "goftest")))
24308 (build-system r-build-system)
24309 (home-page "https://github.com/baddstats/goftest")
24310 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
24312 "This package provides Cramer-Von Mises and Anderson-Darling tests of
24313 goodness-of-fit for continuous univariate distributions, using efficient
24315 (license license:gpl2+)))
24317 (define-public r-tensor
24324 (uri (cran-uri "tensor" version))
24327 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
24328 (properties `((upstream-name . "tensor")))
24329 (build-system r-build-system)
24330 (home-page "https://cran.r-project.org/web/packages/tensor/")
24331 (synopsis "Tensor product of arrays")
24333 "The tensor product of two arrays is notionally an outer product of the
24334 arrays collapsed in specific extents by summing along the appropriate
24335 diagonals. This package allows you to compute the tensor product of arrays.")
24336 (license license:gpl2+)))
24338 (define-public r-spatstat-utils
24340 (name "r-spatstat-utils")
24345 (uri (cran-uri "spatstat.utils" version))
24348 "066f35017wpbz9plwc14gji3ddq4a1h2lx4mcgxajrcrk0zl3hk2"))))
24350 `((upstream-name . "spatstat.utils")))
24351 (build-system r-build-system)
24352 (home-page "http://www.spatstat.org")
24353 (synopsis "Utility functions for spatstat")
24355 "This package contains utility functions for the @code{spatstat} package
24356 which may also be useful for other purposes.")
24357 (license license:gpl2+)))
24359 (define-public r-spatstat-data
24361 (name "r-spatstat-data")
24366 (uri (cran-uri "spatstat.data" version))
24369 "0by10dx72jjn6rvgrdj4xwh4zg6vxi4cp536aq4b6drb7za95hdv"))))
24370 (properties `((upstream-name . "spatstat.data")))
24371 (build-system r-build-system)
24373 `(("r-matrix" ,r-matrix)
24374 ("r-spatstat-utils" ,r-spatstat-utils)))
24375 (home-page "http://www.spatstat.org")
24376 (synopsis "Datasets for spatstat")
24378 "This package contains all the datasets for the @code{spatstat}
24380 (license license:gpl2+)))
24382 (define-public r-spatstat
24384 (name "r-spatstat")
24389 (uri (cran-uri "spatstat" version))
24392 "06jmxfs9kz9qqi3ichfgn8dglwb87kq2nl578p83za5psv8cfgya"))))
24393 (properties `((upstream-name . "spatstat")))
24394 (build-system r-build-system)
24396 `(("r-abind" ,r-abind)
24397 ("r-deldir" ,r-deldir)
24398 ("r-goftest" ,r-goftest)
24399 ("r-matrix" ,r-matrix)
24402 ("r-polyclip" ,r-polyclip)
24403 ("r-rpart" ,r-rpart)
24404 ("r-spatstat-data" ,r-spatstat-data)
24405 ("r-spatstat-utils" ,r-spatstat-utils)
24406 ("r-tensor" ,r-tensor)))
24407 (home-page "http://www.spatstat.org")
24408 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
24410 "This package provides a comprehensive toolbox for analysing Spatial
24411 Point Patterns. It is focused mainly on two-dimensional point patterns,
24412 including multitype/marked points, in any spatial region. It also supports
24413 three-dimensional point patterns, space-time point patterns in any number of
24414 dimensions, point patterns on a linear network, and patterns of other
24415 geometrical objects. It supports spatial covariate data such as pixel images
24416 and contains over 2000 functions for plotting spatial data, exploratory data
24417 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
24418 formal inference.")
24419 (license license:gpl2+)))
24421 (define-public r-gaston
24428 (uri (cran-uri "gaston" version))
24431 "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i"))))
24432 (properties `((upstream-name . "gaston")))
24433 (build-system r-build-system)
24434 (inputs `(("zlib" ,zlib)))
24436 `(("r-rcpp" ,r-rcpp)
24437 ("r-rcppeigen" ,r-rcppeigen)
24438 ("r-rcppparallel" ,r-rcppparallel)))
24439 (native-inputs `(("r-knitr" ,r-knitr)))
24440 (home-page "https://cran.r-project.org/web/packages/gaston/")
24441 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
24443 "This is a package for the manipulation of genetic data (SNPs).
24444 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
24445 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
24446 for linear mixed models (AIREML).")
24447 (license license:gpl3)))
24449 (define-public r-cpp11
24456 (uri (cran-uri "cpp11" version))
24459 "081f3b98mcxyilqsxbzzdnj2x6v7xycprrw7r5934163q0397vvg"))))
24460 (properties `((upstream-name . "cpp11")))
24461 (build-system r-build-system)
24462 (native-inputs `(("r-knitr" ,r-knitr)))
24463 (home-page "https://github.com/r-lib/cpp11")
24464 (synopsis "C++11 Interface for R's C Interface")
24466 "This package provides a header only, C++11 interface to R's C interface.
24467 Compared to other approaches @code{cpp11} strives to be safe against long
24468 jumps from the C API as well as C++ exceptions, conform to normal R function
24469 semantics and supports interaction with @code{ALTREP} vectors.")
24470 (license license:expat)))
24472 (define-public r-rcppziggurat
24474 (name "r-rcppziggurat")
24479 (uri (cran-uri "RcppZiggurat" version))
24482 "0wgd1v2p7zajnbrjf3hfi56p3pk3ld6iwkanbb04bjbnlif2ay4w"))))
24483 (properties `((upstream-name . "RcppZiggurat")))
24484 (build-system r-build-system)
24486 `(("r-rcpp" ,r-rcpp)
24487 ("r-rcppgsl" ,r-rcppgsl)))
24488 (native-inputs `(("r-knitr" ,r-knitr)))
24489 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
24490 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
24492 "The Ziggurat generator for normally distributed random numbers,
24493 originally proposed by Marsaglia and Tsang (2000,
24494 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
24495 times starting with Leong et al (2005,
24496 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
24497 aggregation for comparing different implementations in order to provide a
24498 'faster but good enough' alternative for use with R and C++ code.")
24499 (license license:gpl2+)))
24501 (define-public r-rfast
24508 (uri (cran-uri "Rfast" version))
24511 "1cq3mcg49hsvqhwn6f4dgsx7f8ma4qnwr5n6s7m22qy57rg31958"))))
24512 (properties `((upstream-name . "Rfast")))
24513 (build-system r-build-system)
24515 `(("r-rcpp" ,r-rcpp)
24516 ("r-rcpparmadillo" ,r-rcpparmadillo)
24517 ("r-rcppziggurat" ,r-rcppziggurat)))
24518 (home-page "https://github.com/RfastOfficial/Rfast")
24519 (synopsis "Collection of efficient and fast R functions")
24521 "This package provides a collection of fast (utility) functions for data
24522 analysis. Column- and row- wise means, medians, variances, minimums,
24523 maximums, many t, F and G-square tests, many regressions (normal, logistic,
24524 Poisson), are some of the many fast functions.")
24525 (license license:gpl2+)))
24527 (define-public r-clusterr
24529 (name "r-clusterr")
24534 (uri (cran-uri "ClusterR" version))
24537 "1ky172bk15a78hky77vl60j7c81nq2495sxjrv53is25nkac7sjm"))))
24538 (properties `((upstream-name . "ClusterR")))
24539 (build-system r-build-system)
24541 `(("r-ggplot2" ,r-ggplot2)
24543 ("r-gtools" ,r-gtools)
24545 ("r-rcpparmadillo" ,r-rcpparmadillo)))
24546 (native-inputs `(("r-knitr" ,r-knitr)))
24547 (home-page "https://github.com/mlampros/ClusterR")
24548 (synopsis "Clustering")
24550 "This package provides Gaussian mixture models, k-means,
24551 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
24552 option to plot, validate, predict (new data) and estimate the optimal number
24553 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
24554 the computationally intensive parts of the functions. For more information,
24558 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
24559 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
24560 @url{https://doi.org/10.18637/jss.v001.i04};
24561 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
24562 Library, @url{https://doi.org/10.1145/1772690.1772862};
24563 @item \"Armadillo: a template-based C++ library
24564 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
24565 Software, @url{https://doi.org/10.21105/joss.00026};
24566 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
24567 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
24568 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
24571 (license license:gpl3)))
24573 (define-public r-spectrum
24575 (name "r-spectrum")
24580 (uri (cran-uri "Spectrum" version))
24583 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
24584 (properties `((upstream-name . "Spectrum")))
24585 (build-system r-build-system)
24587 `(("r-clusterr" ,r-clusterr)
24588 ("r-diptest" ,r-diptest)
24589 ("r-ggplot2" ,r-ggplot2)
24590 ("r-rfast" ,r-rfast)))
24591 (native-inputs `(("r-knitr" ,r-knitr)))
24592 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
24593 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
24595 "This package provides a self-tuning spectral clustering method for
24596 single or multi-view data. Spectrum uses a new type of adaptive density aware
24597 kernel that strengthens connections in the graph based on common nearest
24598 neighbours. It uses a tensor product graph data integration and diffusion
24599 procedure to integrate different data sources and reduce noise. Spectrum uses
24600 either the eigengap or multimodality gap heuristics to determine the number of
24601 clusters. The method is sufficiently flexible so that a wide range of
24602 Gaussian and non-Gaussian structures can be clustered with automatic selection
24604 (license license:agpl3+)))
24606 (define-public r-nabor
24613 (uri (cran-uri "nabor" version))
24616 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
24617 (properties `((upstream-name . "nabor")))
24618 (build-system r-build-system)
24622 ("r-rcppeigen" ,r-rcppeigen)))
24623 (home-page "https://cran.r-project.org/web/packages/nabor/")
24624 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
24626 "This package provides an R wrapper for libnabo, an exact or approximate
24627 k nearest neighbour library which is optimised for low dimensional
24628 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
24629 designed as a drop-in replacement for the RANN function @code{nn2}. In
24630 addition, objects which include the k-d tree search structure can be returned
24631 to speed up repeated queries of the same set of target points.")
24632 (license license:bsd-3)))
24634 (define-public r-muhaz
24637 (version "1.2.6.1")
24641 (uri (cran-uri "muhaz" version))
24644 "08qh43zx6h3yby44q2vxphfvmfdmqxpgyp0734yn341sy9n8pkkk"))))
24645 (properties `((upstream-name . "muhaz")))
24646 (build-system r-build-system)
24648 `(("r-survival" ,r-survival)))
24650 `(("gfortran" ,gfortran)))
24651 (home-page "https://cran.r-project.org/web/packages/muhaz/")
24652 (synopsis "Hazard function estimation in survival analysis")
24654 "This package produces a smooth estimate of the hazard function for
24656 ;; Any version of the GPL.
24657 (license license:gpl3+)))
24659 (define-public r-flexsurv
24661 (name "r-flexsurv")
24666 (uri (cran-uri "flexsurv" version))
24669 "0x7p1rv51pplfyyzcg63ssb8z56mig7y0363hkr0219w3cvyq9nr"))))
24670 (properties `((upstream-name . "flexsurv")))
24671 (build-system r-build-system)
24673 `(("r-desolve" ,r-desolve)
24674 ("r-mstate" ,r-mstate)
24675 ("r-muhaz" ,r-muhaz)
24676 ("r-mvtnorm" ,r-mvtnorm)
24677 ("r-quadprog" ,r-quadprog)
24679 ("r-survival" ,r-survival)
24680 ("r-tibble" ,r-tibble)
24681 ("r-tidyr" ,r-tidyr)))
24683 `(("r-knitr" ,r-knitr)))
24684 (home-page "https://github.com/chjackson/flexsurv-dev")
24685 (synopsis "Flexible parametric survival and multi-state models")
24687 "This package provides flexible parametric models for time-to-event data,
24688 including the Royston-Parmar spline model, generalized gamma and generalized F
24689 distributions. Any user-defined parametric distribution can be fitted, given
24690 at least an R function defining the probability density or hazard. There are
24691 also tools for fitting and predicting from fully parametric multi-state
24693 (license license:gpl2+)))
24695 (define-public r-transphylo
24697 (name "r-transphylo")
24702 (uri (cran-uri "TransPhylo" version))
24705 "1506c97y8dnhd0c38rgvmg70q0l3xmmn07mjglhnw7hi5n5y9mv9"))))
24706 (properties `((upstream-name . "TransPhylo")))
24707 (build-system r-build-system)
24710 ("r-rcpp" ,r-rcpp)))
24712 `(("r-knitr" ,r-knitr)))
24713 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
24714 (synopsis "Inference of transmission tree from a dated phylogeny")
24716 "This is a package to infer transmission trees from a dated phylogeny.
24717 It includes methods to simulate and analyze outbreaks. The methodology is
24718 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
24719 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
24720 (license license:gpl2+)))
24722 (define-public r-km-ci
24729 (uri (cran-uri "km.ci" version))
24732 "1l6kw8jppaa1802yc5pbfwwgac56nhwc9p076ivylhms4w7cdf8v"))))
24733 (properties `((upstream-name . "km.ci")))
24734 (build-system r-build-system)
24736 `(("r-survival" ,r-survival)))
24737 (home-page "https://cran.r-project.org/web/packages/km.ci/")
24738 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
24740 "This package computes various @dfn{confidence intervals} (CI) for the
24741 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
24742 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
24743 Nair and Hall and Wellner.")
24744 (license license:gpl2+)))
24746 (define-public r-kmsurv
24753 (uri (cran-uri "KMsurv" version))
24756 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
24757 (properties `((upstream-name . "KMsurv")))
24758 (build-system r-build-system)
24759 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
24760 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
24762 "This package provides data sets and functions for Klein and Moeschberger
24763 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
24765 (license license:gpl3+)))
24767 (define-public r-survmisc
24769 (name "r-survmisc")
24774 (uri (cran-uri "survMisc" version))
24777 "00nvvl8gz4477ab24rd0xvfksm8msv8h021b9ld5c9cizc41n2bm"))))
24778 (properties `((upstream-name . "survMisc")))
24779 (build-system r-build-system)
24781 `(("r-data-table" ,r-data-table)
24782 ("r-ggplot2" ,r-ggplot2)
24783 ("r-gridextra" ,r-gridextra)
24784 ("r-km-ci" ,r-km-ci)
24785 ("r-kmsurv" ,r-kmsurv)
24786 ("r-knitr" ,r-knitr)
24787 ("r-survival" ,r-survival)
24788 ("r-xtable" ,r-xtable)
24791 `(("r-knitr" ,r-knitr)))
24792 (home-page "https://cran.r-project.org/web/packages/survMisc/")
24793 (synopsis "Miscellaneous functions for survival data")
24795 "This package provides a collection of functions to help in the analysis
24796 of right-censored survival data. These extend the methods available in
24797 the @code{survival} package.")
24798 (license license:gpl2)))
24800 (define-public r-exactranktests
24802 (name "r-exactranktests")
24807 (uri (cran-uri "exactRankTests" version))
24810 "1154dkcid3njhamdp87qs9bnx7l8bdqkcjsds9q9f2xmizs9x8gw"))))
24812 `((upstream-name . "exactRankTests")))
24813 (build-system r-build-system)
24814 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
24815 (synopsis "Exact distributions for rank and permutation tests")
24817 "This package computes exact conditional p-values and quantiles using an
24818 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
24819 (license license:gpl2+)))
24821 (define-public r-maxstat
24828 (uri (cran-uri "maxstat" version))
24831 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
24832 (properties `((upstream-name . "maxstat")))
24833 (build-system r-build-system)
24835 `(("r-exactranktests" ,r-exactranktests)
24836 ("r-mvtnorm" ,r-mvtnorm)))
24837 (home-page "https://cran.r-project.org/web/packages/maxstat/")
24838 (synopsis "Maximally selected rank statistics")
24840 "This package provides maximally selected rank statistics with several
24841 p-value approximations.")
24842 (license license:gpl2+)))
24844 (define-public r-survminer
24846 (name "r-survminer")
24851 (uri (cran-uri "survminer" version))
24854 "1niysd89mxb2a6ncvzm1s6xgfvq3psba65af0whh2p56r2hwrwff"))))
24855 (properties `((upstream-name . "survminer")))
24856 (build-system r-build-system)
24858 `(("r-broom" ,r-broom)
24859 ("r-dplyr" ,r-dplyr)
24860 ("r-ggplot2" ,r-ggplot2)
24861 ("r-ggpubr" ,r-ggpubr)
24862 ("r-gridextra" ,r-gridextra)
24863 ("r-magrittr" ,r-magrittr)
24864 ("r-maxstat" ,r-maxstat)
24865 ("r-purrr" ,r-purrr)
24866 ("r-rlang" ,r-rlang)
24867 ("r-scales" ,r-scales)
24868 ("r-survival" ,r-survival)
24869 ("r-survmisc" ,r-survmisc)
24870 ("r-tibble" ,r-tibble)
24871 ("r-tidyr" ,r-tidyr)))
24873 `(("r-knitr" ,r-knitr)))
24874 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
24875 (synopsis "Drawing survival curves using ggplot2")
24877 "This package contains the function @code{ggsurvplot()} for easily
24878 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
24879 risk' table and 'censoring count plot'. Other functions are also available to
24880 plot adjusted curves for Cox model and to visually examine Cox model
24882 (license license:gpl2)))
24884 (define-public r-forge
24891 (uri (cran-uri "forge" version))
24894 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
24895 (properties `((upstream-name . "forge")))
24896 (build-system r-build-system)
24898 `(("r-magrittr" ,r-magrittr)
24899 ("r-rlang" ,r-rlang)))
24900 (home-page "https://cran.r-project.org/web/packages/forge/")
24901 (synopsis "Cast values into shape")
24903 "This package provides helper functions with a consistent interface to
24904 coerce and verify the types and shapes of values for input checking.")
24905 (license license:asl2.0)))
24907 (define-public r-config
24914 (uri (cran-uri "config" version))
24917 "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l"))))
24918 (properties `((upstream-name . "config")))
24919 (build-system r-build-system)
24921 `(("r-yaml" ,r-yaml)))
24923 `(("r-knitr" ,r-knitr)))
24924 (home-page "https://github.com/rstudio/config")
24925 (synopsis "Manage environment specific configuration values")
24927 "This package lets you manage configuration values across multiple
24928 environments (e.g. development, test, production). It reads values using a
24929 function that determines the current environment and returns the appropriate
24931 (license license:gpl3)))
24933 (define-public r-adaptivesparsity
24935 (name "r-adaptivesparsity")
24939 (uri (cran-uri "AdaptiveSparsity" version))
24942 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
24944 `((upstream-name . "AdaptiveSparsity")))
24945 (build-system r-build-system)
24948 (modify-phases %standard-phases
24949 (add-after 'unpack 'link-against-armadillo
24951 (substitute* "src/Makevars"
24952 (("PKG_LIBS=" prefix)
24953 (string-append prefix "-larmadillo")))
24956 `(("r-mass" ,r-mass)
24957 ("r-matrix" ,r-matrix)
24959 ("r-rcpparmadillo" ,r-rcpparmadillo)))
24961 `(("armadillo" ,armadillo)))
24962 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
24963 (synopsis "Adaptive sparsity models")
24965 "This package implements the Figueiredo machine learning algorithm for
24966 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
24967 geometric models.")
24968 (license license:lgpl3+)))
24970 (define-public r-diffusionmap
24972 (name "r-diffusionmap")
24977 (uri (cran-uri "diffusionMap" version))
24980 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
24981 (properties `((upstream-name . "diffusionMap")))
24982 (build-system r-build-system)
24984 `(("r-igraph" ,r-igraph)
24985 ("r-matrix" ,r-matrix)
24986 ("r-scatterplot3d" ,r-scatterplot3d)))
24987 (home-page "https://www.r-project.org")
24988 (synopsis "Diffusion map")
24989 (description "This package implements the diffusion map method of data
24990 parametrization, including creation and visualization of diffusion maps,
24991 clustering with diffusion K-means and regression using the adaptive regression
24993 (license license:gpl2)))
24995 (define-public r-igraph
25002 (uri (cran-uri "igraph" version))
25005 "0vf7wrx77cdiav8724cw8gchrn0y9wvywphf5km4pa7xcqhsf3b4"))))
25006 (build-system r-build-system)
25008 `(("gfortran" ,gfortran)))
25012 ("libxml2" ,libxml2)
25015 `(("r-magrittr" ,r-magrittr)
25016 ("r-matrix" ,r-matrix)
25017 ("r-pkgconfig" ,r-pkgconfig)))
25018 (home-page "https://igraph.org")
25019 (synopsis "Network analysis and visualization")
25021 "This package provides routines for simple graphs and network analysis.
25022 It can handle large graphs very well and provides functions for generating
25023 random and regular graphs, graph visualization, centrality methods and much
25025 (license license:gpl2+)))
25027 (define-public r-workflows
25029 (name "r-workflows")
25034 (uri (cran-uri "workflows" version))
25037 "1mk0pnmpqlhf143mvj9rwvjrrshirz6s83s5hbfalhnyw7hzkfb9"))))
25038 (properties `((upstream-name . "workflows")))
25039 (build-system r-build-system)
25042 ("r-ellipsis" ,r-ellipsis)
25043 ("r-generics" ,r-generics)
25045 ("r-hardhat" ,r-hardhat)
25046 ("r-parsnip" ,r-parsnip)
25047 ("r-rlang" ,r-rlang)
25048 ("r-tidyselect" ,r-tidyselect)))
25050 `(("r-knitr" ,r-knitr)))
25051 (home-page "https://github.com/tidymodels/workflows")
25052 (synopsis "Modeling workflows")
25054 "A workflow is an object that can bundle together your pre-processing,
25055 modeling, and post-processing requests. For example, if you have a
25056 @code{recipe} and @code{parsnip} model, these can be combined into a
25057 workflow. The advantages are:
25060 @item You don’t have to keep track of separate objects in your workspace.
25061 @item The recipe prepping and model fitting can be executed using a single
25062 call to @code{fit()}.
25063 @item If you have custom tuning parameter settings, these can be defined using
25064 a simpler interface when combined with @code{tune}.
25065 @item In the future, workflows will be able to add post-processing operations,
25066 such as modifying the probability cutoff for two-class models.
25069 (license license:expat)))
25071 (define-public r-gpfit
25078 (uri (cran-uri "GPfit" version))
25081 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
25082 (properties `((upstream-name . "GPfit")))
25083 (build-system r-build-system)
25085 `(("r-lattice" ,r-lattice)
25087 (home-page "https://cran.r-project.org/web/packages/GPfit/")
25088 (synopsis "Gaussian Processes modeling")
25090 "This package provides a computationally stable approach of fitting a
25091 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
25092 (license license:gpl2)))
25094 (define-public r-yardstick
25096 (name "r-yardstick")
25101 (uri (cran-uri "yardstick" version))
25104 "1yrvlhn4gxyn9f20z5yv3xam0j0a8z362jwa32r33r0g0jk5z2fq"))))
25105 (properties `((upstream-name . "yardstick")))
25106 (build-system r-build-system)
25108 `(("r-dplyr" ,r-dplyr)
25109 ("r-generics" ,r-generics)
25111 ("r-rlang" ,r-rlang)
25112 ("r-tidyselect" ,r-tidyselect)))
25114 `(("r-knitr" ,r-knitr)))
25115 (home-page "https://github.com/tidymodels/yardstick")
25116 (synopsis "Tidy characterizations of model performance")
25118 "This package provides tidy tools for quantifying how well a model fits
25119 to a data set such as confusion matrices, class probability curve summaries,
25120 and regression metrics (e.g., RMSE).")
25121 (license license:gpl2)))
25123 (define-public r-warp
25130 (uri (cran-uri "warp" version))
25133 "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
25134 (properties `((upstream-name . "warp")))
25135 (build-system r-build-system)
25136 (native-inputs `(("r-knitr" ,r-knitr)))
25137 (home-page "https://github.com/DavisVaughan/warp")
25138 (synopsis "Group dates")
25140 "This package provides tooling to group dates by a variety of periods
25141 including: yearly, monthly, by second, by week of the month, and more. The
25142 groups are defined in such a way that they also represent the distance between
25143 dates in terms of the period. This extracts valuable information that can be
25144 used in further calculations that rely on a specific temporal spacing between
25146 (license license:expat)))
25148 (define-public r-slider
25155 (uri (cran-uri "slider" version))
25158 "1x4jwfxam4czfkb1s5qds5krfw1h2p5a4rh6f5z4yvhsv0d81xck"))))
25159 (properties `((upstream-name . "slider")))
25160 (build-system r-build-system)
25162 `(("r-glue" ,r-glue)
25163 ("r-rlang" ,r-rlang)
25164 ("r-vctrs" ,r-vctrs)
25165 ("r-warp" ,r-warp)))
25166 (native-inputs `(("r-knitr" ,r-knitr)))
25167 (home-page "https://github.com/DavisVaughan/slider")
25168 (synopsis "Sliding window functions")
25170 "This package provides type-stable rolling window functions over any R
25171 data type. Cumulative and expanding windows are also supported. For more
25172 advanced usage, an index can be used as a secondary vector that defines how
25173 sliding windows are to be created.")
25174 (license license:expat)))
25176 (define-public r-rsample
25183 (uri (cran-uri "rsample" version))
25186 "1psmxk16d4bz1v05x0gb9hn4brkdjxw8hjbxmj62snichnix3q3i"))))
25187 (properties `((upstream-name . "rsample")))
25188 (build-system r-build-system)
25190 `(("r-dplyr" ,r-dplyr)
25191 ("r-ellipsis" ,r-ellipsis)
25192 ("r-furrr" ,r-furrr)
25193 ("r-generics" ,r-generics)
25194 ("r-modeldata" ,r-modeldata)
25195 ("r-purrr" ,r-purrr)
25196 ("r-rlang" ,r-rlang)
25197 ("r-slider" ,r-slider)
25198 ("r-tibble" ,r-tibble)
25199 ("r-tidyr" ,r-tidyr)
25200 ("r-tidyselect" ,r-tidyselect)
25201 ("r-vctrs" ,r-vctrs)))
25203 `(("r-knitr" ,r-knitr)))
25204 (home-page "https://rsample.tidymodels.org")
25205 (synopsis "General resampling infrastructure")
25207 "This package provides classes and functions to create and summarize
25208 different types of resampling objects (e.g. bootstrap, cross-validation).")
25209 (license license:gpl2)))
25211 (define-public r-dicedesign
25213 (name "r-dicedesign")
25218 (uri (cran-uri "DiceDesign" version))
25221 "11s1m543kxd6gv4amh8z6pph1n67sj9sfwm6hjy83wfs65syf5vp"))))
25222 (properties `((upstream-name . "DiceDesign")))
25223 (build-system r-build-system)
25224 (home-page "http://dice.emse.fr/")
25225 (synopsis "Designs of computer experiments")
25227 "This package provides tools to create some specific @code{Space-Filling
25228 Design} (SFD) and to test their quality.")
25229 (license license:gpl3)))
25231 (define-public r-dials
25238 (uri (cran-uri "dials" version))
25241 "0g9wj2py4wz703rh4p7hk8qxqnkm7zyrypv4qz4vaqziazjsmxks"))))
25242 (properties `((upstream-name . "dials")))
25243 (build-system r-build-system)
25245 `(("r-dicedesign" ,r-dicedesign)
25246 ("r-dplyr" ,r-dplyr)
25248 ("r-purrr" ,r-purrr)
25249 ("r-rlang" ,r-rlang)
25250 ("r-scales" ,r-scales)
25251 ("r-tibble" ,r-tibble)
25252 ("r-vctrs" ,r-vctrs)
25253 ("r-withr" ,r-withr)))
25254 (native-inputs `(("r-knitr" ,r-knitr)))
25255 (home-page "https://dials.tidymodels.org/")
25256 (synopsis "Tools for creating tuning parameter values")
25258 "Many models contain tuning parameters (i.e. parameters that cannot be
25259 directly estimated from the data). These tools can be used to define objects
25260 for creating, simulating, or validating values for such parameters.")
25261 (license license:gpl2)))
25263 (define-public r-tune
25270 (uri (cran-uri "tune" version))
25273 "0ja7rjkjj88v3ngrc6izcz2qh9qv4s8abgcafmvx2ihgz99hds37"))))
25274 (properties `((upstream-name . "tune")))
25275 (build-system r-build-system)
25278 ("r-dials" ,r-dials)
25279 ("r-dplyr" ,r-dplyr)
25280 ("r-foreach" ,r-foreach)
25281 ("r-generics" ,r-generics)
25282 ("r-ggplot2" ,r-ggplot2)
25284 ("r-gpfit" ,r-gpfit)
25285 ("r-hardhat" ,r-hardhat)
25286 ("r-parsnip" ,r-parsnip)
25287 ("r-purrr" ,r-purrr)
25288 ("r-recipes" ,r-recipes)
25289 ("r-rlang" ,r-rlang)
25290 ("r-rsample" ,r-rsample)
25291 ("r-tibble" ,r-tibble)
25292 ("r-tidyr" ,r-tidyr)
25293 ("r-vctrs" ,r-vctrs)
25294 ("r-workflows" ,r-workflows)
25295 ("r-yardstick" ,r-yardstick)))
25296 (home-page "https://github.com/tidymodels/tune")
25297 (synopsis "Tidy tuning tools")
25299 "The ability to tune models is important. @code{tune} contains functions
25300 and classes to be used in conjunction with other @code{tidymodels} packages
25301 for finding reasonable values of hyper-parameters in models, pre-processing
25302 methods, and post-processing steps.")
25303 (license license:expat)))
25305 (define-public r-tidyposterior
25307 (name "r-tidyposterior")
25312 (uri (cran-uri "tidyposterior" version))
25315 "0wsv800w056ziqbnwal7ncmdy4li8cn5yrdx07w35b7j8kl4mwhg"))))
25316 (properties `((upstream-name . "tidyposterior")))
25317 (build-system r-build-system)
25319 `(("r-dplyr" ,r-dplyr)
25320 ("r-generics" ,r-generics)
25321 ("r-ggplot2" ,r-ggplot2)
25322 ("r-lifecycle" ,r-lifecycle)
25323 ("r-purrr" ,r-purrr)
25324 ("r-rlang" ,r-rlang)
25325 ("r-rsample" ,r-rsample)
25326 ("r-rstanarm" ,r-rstanarm)
25327 ("r-tibble" ,r-tibble)
25328 ("r-tidyr" ,r-tidyr)
25329 ("r-vctrs" ,r-vctrs)))
25331 `(("r-knitr" ,r-knitr)))
25332 (home-page "https://tidyposterior.tidymodels.org")
25333 (synopsis "Bayesian analysis to compare models using resampling statistics")
25335 "This package can be used to conduct post hoc analyses of resampling
25336 results generated by models. For example, if two models are evaluated with
25337 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
25338 are 10 paired statistics. These can be used to make comparisons between
25339 models without involving a test set.")
25340 (license license:gpl2)))
25342 (define-public r-tidypredict
25344 (name "r-tidypredict")
25349 (uri (cran-uri "tidypredict" version))
25352 "0fff349pkksss8h1k2qza78l81ha6avx63pxziv6dfa8h62qmrdy"))))
25353 (properties `((upstream-name . "tidypredict")))
25354 (build-system r-build-system)
25356 `(("r-dplyr" ,r-dplyr)
25357 ("r-generics" ,r-generics)
25358 ("r-knitr" ,r-knitr)
25359 ("r-purrr" ,r-purrr)
25360 ("r-rlang" ,r-rlang)
25361 ("r-stringr" ,r-stringr)
25362 ("r-tibble" ,r-tibble)
25363 ("r-tidyr" ,r-tidyr)))
25365 `(("r-knitr" ,r-knitr)))
25366 (home-page "https://tidypredict.tidymodels.org")
25367 (synopsis "Run predictions inside the database")
25369 "This package parses a fitted R model object, and returns a formula in
25370 Tidy Eval code that calculates the predictions. It works with several
25371 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
25372 final SQL translation of the algorithm. It currently supports @code{lm()},
25373 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
25374 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
25375 (license license:gpl3)))
25377 (define-public r-janeaustenr
25379 (name "r-janeaustenr")
25384 (uri (cran-uri "janeaustenr" version))
25387 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
25388 (properties `((upstream-name . "janeaustenr")))
25389 (build-system r-build-system)
25390 (home-page "https://github.com/juliasilge/janeaustenr")
25391 (synopsis "Jane Austen's complete novels")
25393 "This package provides the full texts for Jane Austen's six completed
25394 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
25395 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
25396 and \"Persuasion\".")
25397 (license license:expat)))
25399 (define-public r-tokenizers
25401 (name "r-tokenizers")
25406 (uri (cran-uri "tokenizers" version))
25409 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
25410 (properties `((upstream-name . "tokenizers")))
25411 (build-system r-build-system)
25413 `(("r-rcpp" ,r-rcpp)
25414 ("r-snowballc" ,r-snowballc)
25415 ("r-stringi" ,r-stringi)))
25417 `(("r-knitr" ,r-knitr)))
25418 (home-page "https://lincolnmullen.com/software/tokenizers/")
25419 (synopsis "Fast, consistent tokenization of natural language text")
25421 "This is a package for converting natural language text into tokens.
25422 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
25423 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
25424 Treebank, regular expressions, as well as functions for counting characters,
25425 words, and sentences, and a function for splitting longer texts into separate
25426 documents, each with the same number of words. The tokenizers have a
25427 consistent interface, and the package is built on the @code{stringi} and
25428 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
25429 (license license:expat)))
25431 (define-public r-hunspell
25433 (name "r-hunspell")
25438 (uri (cran-uri "hunspell" version))
25441 "0ql6y05d4xxpm468rslb0wxdp1x9l3flxzmb5w6pjg617f8vpv8z"))))
25442 (properties `((upstream-name . "hunspell")))
25443 (build-system r-build-system)
25445 `(("r-digest" ,r-digest)
25446 ("r-rcpp" ,r-rcpp)))
25448 `(("r-knitr" ,r-knitr)))
25449 (home-page "https://github.com/ropensci/hunspell#readme")
25450 (synopsis "High-performance stemmer, tokenizer, and spell checker")
25452 "This package provides a low-level spell checker and morphological
25453 analyzer based on the famous @code{hunspell} library. The package can analyze
25454 or check individual words as well as parse text, LaTeX, HTML or XML documents.
25455 For a more user-friendly interface use the @code{spelling} package which
25456 builds on this package to automate checking of files, documentation and
25457 vignettes in all common formats.")
25458 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
25459 ;; MPL; in addition to these licenses the rest of the R wrapper is also
25460 ;; available under the Expat license.
25461 (license (list license:gpl2
25466 (define-public r-tidytext
25468 (name "r-tidytext")
25473 (uri (cran-uri "tidytext" version))
25476 "1icbfw4zkbs9sp6vk814mw2zzm0bc0d7af92vhriqxaga0gbwdkx"))))
25477 (properties `((upstream-name . "tidytext")))
25478 (build-system r-build-system)
25480 `(("r-dplyr" ,r-dplyr)
25481 ("r-generics" ,r-generics)
25482 ("r-hunspell" ,r-hunspell)
25483 ("r-janeaustenr" ,r-janeaustenr)
25484 ("r-lifecycle" ,r-lifecycle)
25485 ("r-matrix" ,r-matrix)
25486 ("r-purrr" ,r-purrr)
25487 ("r-rlang" ,r-rlang)
25488 ("r-stringr" ,r-stringr)
25489 ("r-tibble" ,r-tibble)
25490 ("r-tokenizers" ,r-tokenizers)
25491 ("r-vctrs" ,r-vctrs)))
25493 `(("r-knitr" ,r-knitr)))
25494 (home-page "https://github.com/juliasilge/tidytext")
25495 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
25497 "This is a package for text mining for word processing and sentiment
25498 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
25499 (license license:expat)))
25501 (define-public r-parsnip
25508 (uri (cran-uri "parsnip" version))
25511 "0c12lyfxqsdprqlcmgy421py38z28h88d68pxb1c4fw14v1c2d06"))))
25512 (properties `((upstream-name . "parsnip")))
25513 (build-system r-build-system)
25515 `(("r-dplyr" ,r-dplyr)
25516 ("r-generics" ,r-generics)
25517 ("r-globals" ,r-globals)
25519 ("r-magrittr" ,r-magrittr)
25520 ("r-prettyunits" ,r-prettyunits)
25521 ("r-purrr" ,r-purrr)
25522 ("r-rlang" ,r-rlang)
25523 ("r-tibble" ,r-tibble)
25524 ("r-tidyr" ,r-tidyr)
25525 ("r-vctrs" ,r-vctrs)))
25527 `(("r-knitr" ,r-knitr)))
25528 (home-page "https://parsnip.tidymodels.org")
25529 (synopsis "Common API to modeling and analysis functions")
25531 "This package provides a common interface to allow users to specify a
25532 model without having to remember the different argument names across different
25533 functions or computational engines (e.g. R, Spark, Stan, etc).")
25534 (license license:gpl2)))
25536 (define-public r-infer
25543 (uri (cran-uri "infer" version))
25546 "0wvvgqjhyv7ql98cjzqad61wbmk7xrqd1ybk894jr5cmza13c8w2"))))
25547 (properties `((upstream-name . "infer")))
25548 (build-system r-build-system)
25550 `(("r-dplyr" ,r-dplyr)
25551 ("r-ggplot2" ,r-ggplot2)
25553 ("r-magrittr" ,r-magrittr)
25554 ("r-purrr" ,r-purrr)
25555 ("r-rlang" ,r-rlang)
25556 ("r-tibble" ,r-tibble)))
25558 `(("r-knitr" ,r-knitr)))
25559 (home-page "https://github.com/tidymodels/infer")
25560 (synopsis "Tidy statistical inference")
25562 "The objective of this package is to perform inference using an
25563 expressive statistical grammar that coheres with the Tidy design framework.")
25564 (license license:cc0)))
25566 (define-public r-modeldata
25568 (name "r-modeldata")
25573 (uri (cran-uri "modeldata" version))
25576 "0lbvmicvhw560jn9qk5dywrl6mgj1rf7zh7p86lf97c6bmz0zp2r"))))
25577 (properties `((upstream-name . "modeldata")))
25578 (build-system r-build-system)
25579 (home-page "https://modeldata.tidymodels.org")
25580 (synopsis "Data sets useful for modeling packages")
25582 "This package provides data sets used for demonstrating or testing
25583 model-related packages.")
25584 (license license:expat)))
25586 (define-public r-tidymodels
25588 (name "r-tidymodels")
25593 (uri (cran-uri "tidymodels" version))
25596 "09njrl655sh82xrzckgg56a6ndfrjla5fy8675wj4jsj14jpv0fw"))))
25597 (properties `((upstream-name . "tidymodels")))
25598 (build-system r-build-system)
25600 `(("r-broom" ,r-broom)
25602 ("r-dials" ,r-dials)
25603 ("r-dplyr" ,r-dplyr)
25604 ("r-ggplot2" ,r-ggplot2)
25605 ("r-infer" ,r-infer)
25606 ("r-magrittr" ,r-magrittr)
25607 ("r-modeldata" ,r-modeldata)
25608 ("r-parsnip" ,r-parsnip)
25609 ("r-purrr" ,r-purrr)
25610 ("r-recipes" ,r-recipes)
25611 ("r-rlang" ,r-rlang)
25612 ("r-rsample" ,r-rsample)
25613 ("r-rstudioapi" ,r-rstudioapi)
25614 ("r-tibble" ,r-tibble)
25615 ("r-tidyr" ,r-tidyr)
25617 ("r-workflows" ,r-workflows)
25618 ("r-yardstick" ,r-yardstick)))
25620 `(("r-knitr" ,r-knitr)
25621 ("r-rmarkdown" ,r-rmarkdown)
25623 ("pandoc-citeproc" ,pandoc-citeproc))) ; for vignettes
25624 (home-page "https://github.com/tidymodels/tidymodels")
25625 (synopsis "Tidy collection for modeling and statistical analysis")
25627 "The tidy modeling \"verse\" is a collection of packages for modeling and
25628 statistical analysis that share the underlying design philosophy, grammar, and
25629 data structures of the tidyverse.")
25630 (license license:gpl3)))
25632 (define-public r-mlecens
25639 (uri (cran-uri "MLEcens" version))
25642 "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))
25643 (properties `((upstream-name . "MLEcens")))
25644 (build-system r-build-system)
25645 (home-page "http://stat.ethz.ch/~maathuis/")
25646 (synopsis "Computation of the MLE for bivariate (interval) censored data")
25648 "This package contains functions to compute the nonparametric
25649 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
25650 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
25651 To be more precise, we consider the situation where we observe a set of
25652 rectangles that are known to contain the unobservable realizations of (X,Y).
25653 We compute the MLE based on such a set of rectangles. The methods can also be
25654 used for univariate censored data (see data set @code{cosmesis}), and for
25655 censored data with competing risks (see data set @code{menopause}). The
25656 package also provides functions to visualize the observed data and the MLE.")
25657 (license license:gpl2+)))
25659 (define-public r-metafor
25666 (uri (cran-uri "metafor" version))
25669 "1b599fxk7s0brkchmx698fr5k4g1kzkia2rnlvhg349ffs5nfjmn"))))
25670 (properties `((upstream-name . "metafor")))
25671 (build-system r-build-system)
25673 `(("r-matrix" ,r-matrix)
25674 ("r-nlme" ,r-nlme)))
25675 (home-page "https://cran.r-project.org/web/packages/metafor/")
25676 (synopsis "Meta-analysis package for R")
25678 "This package provides a comprehensive collection of functions for
25679 conducting meta-analyses in R. The package includes functions to calculate
25680 various effect sizes or outcome measures, fit fixed-, random-, and
25681 mixed-effects models to such data, carry out moderator and meta-regression
25682 analyses, and create various types of meta-analytical plots (e.g., forest,
25683 funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial
25684 and person-time data, the package also provides functions that implement
25685 specialized methods, including the Mantel-Haenszel method, Peto's method, and
25686 a variety of suitable generalized linear (mixed-effects) models (i.e.
25687 mixed-effects logistic and Poisson regression models). Finally, the package
25688 provides functionality for fitting meta-analytic multivariate/multilevel
25689 models that account for non-independent sampling errors and/or true
25690 effects (e.g. due to the inclusion of multiple treatment studies, multiple
25691 endpoints, or other forms of clustering). Network meta-analyses and
25692 meta-analyses accounting for known correlation structures (e.g. due to
25693 phylogenetic relatedness) can also be conducted.")
25694 (license license:gpl2+)))
25696 (define-public r-altmeta
25703 (uri (cran-uri "altmeta" version))
25706 "0z252lbsknqp33i0b0xf5r7spr535iq47bv40vgip6nsqhgrl7b0"))))
25707 (properties `((upstream-name . "altmeta")))
25708 (build-system r-build-system)
25710 `(("r-coda" ,r-coda)
25712 ("r-matrix" ,r-matrix)
25713 ("r-metafor" ,r-metafor)
25714 ("r-rjags" ,r-rjags)))
25715 (home-page "https://cran.r-project.org/web/packages/altmeta/")
25716 (synopsis "Alternative meta-analysis methods")
25718 "This package provides alternative statistical methods for meta-analysis,
25722 @item bivariate generalized linear mixed models for synthesizing odds ratios,
25723 relative risks, and risk differences
25724 @item heterogeneity tests and measures that are robust to outliers;
25725 @item measures, tests, and visualization tools for publication bias or
25726 small-study effects;
25727 @item meta-analysis of diagnostic tests for synthesizing sensitivities,
25728 specificities, etc.;
25729 @item meta-analysis methods for synthesizing proportions;
25730 @item models for multivariate meta-analysis.
25733 (license license:gpl2+)))
25735 (define-public r-perm
25738 (version "1.0-0.0")
25742 (uri (cran-uri "perm" version))
25745 "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk"))))
25746 (properties `((upstream-name . "perm")))
25747 (build-system r-build-system)
25748 (home-page "https://cran.r-project.org/web/packages/perm/")
25749 (synopsis "Exact or asymptotic permutation tests")
25751 "This package provides several methods for performing permutation tests.
25752 It has three main functions, to perform linear permutation tests. These tests
25753 are tests where the test statistic is the sum of the product of a
25754 covariate (usually group indicator) and the scores.")
25755 ;; Any version of the GPL
25756 (license license:gpl2+)))
25758 (define-public r-qtl
25765 (uri (cran-uri "qtl" version))
25768 "0hffirsvw9j82cdx6l7vhqn3a7ab52claqjlinv3lswl1nsfg93b"))))
25769 (build-system r-build-system)
25770 (home-page "https://rqtl.org/")
25771 (synopsis "R package for analyzing QTL experiments in genetics")
25772 (description "R/qtl is an extension library for the R statistics system.
25773 It is used to analyze experimental crosses for identifying genes contributing
25774 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
25776 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
25777 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
25779 (license license:gpl3)))
25781 (define-public r-qtl2
25787 (uri (cran-uri "qtl2" version))
25789 (base32 "1558khh0zkwm0rdk87krv9836krvwv5h7ymlz9bsrgcvypyr9186"))))
25790 (build-system r-build-system)
25792 `(("r-data-table" ,r-data-table)
25793 ("r-jsonlite" ,r-jsonlite)
25795 ("r-rcppeigen" ,r-rcppeigen)
25796 ("r-rsqlite" ,r-rsqlite)
25797 ("r-yaml" ,r-yaml)))
25798 (home-page "https://kbroman.org/qtl2/")
25799 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
25801 "This package provides a set of tools to perform @dfn{Quantitative Trait
25802 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
25803 @code{R/qtl} package to better handle high-dimensional data and complex cross
25804 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
25805 (license license:gpl3)))
25807 (define-public r-seqminer
25809 (name "r-seqminer")
25814 (uri (cran-uri "seqminer" version))
25817 "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
25818 (build-system r-build-system)
25821 (home-page "http://seqminer.genomic.codes")
25822 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
25824 "This package provides tools to integrate nucleotide sequencing
25825 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
25826 ;; Any version of the GPL is acceptable
25827 (license (list license:gpl2+ license:gpl3+))))
25829 (define-public r-maldiquant
25831 (name "r-maldiquant")
25836 (uri (cran-uri "MALDIquant" version))
25839 "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
25840 (properties `((upstream-name . "MALDIquant")))
25841 (build-system r-build-system)
25842 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
25843 (synopsis "Quantitative analysis of mass spectrometry data")
25845 "This package provides a complete analysis pipeline for matrix-assisted
25846 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
25847 two-dimensional mass spectrometry data. In addition to commonly used plotting
25848 and processing methods it includes distinctive features, namely baseline
25849 subtraction methods such as morphological filters (TopHat) or the
25850 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
25851 alignment using warping functions, handling of replicated measurements as well
25852 as allowing spectra with different resolutions.")
25853 (license license:gpl3+)))
25855 (define-public r-scattermore
25857 (name "r-scattermore")
25862 (uri (cran-uri "scattermore" version))
25865 "18nzlprmphkvjg946h10h2qq0wbkmv2526p8di6k2xl4gccq0qpk"))))
25866 (properties `((upstream-name . "scattermore")))
25867 (build-system r-build-system)
25869 `(("r-ggplot2" ,r-ggplot2)
25870 ("r-scales" ,r-scales)))
25871 (home-page "https://github.com/exaexa/scattermore")
25872 (synopsis "Scatterplots with more points")
25874 "This package provides C-based tools for converting large scatterplot
25875 data to rasters. It speeds up plotting of data with millions of points.")
25876 (license license:gpl3+)))
25878 (define-public r-seuratobject
25880 (name "r-seuratobject")
25885 (uri (cran-uri "SeuratObject" version))
25888 "03k27z7g76wy7mfja2cpxq183xk0906k9gxb2j6p1zw341gv4gii"))))
25889 (properties `((upstream-name . "SeuratObject")))
25890 (build-system r-build-system)
25892 `(("r-matrix" ,r-matrix)
25894 ("r-rcppeigen" ,r-rcppeigen)
25895 ("r-rlang" ,r-rlang)
25896 ("r-sctransform" ,r-sctransform)))
25897 (home-page "https://satijalab.org/seurat")
25898 (synopsis "Data structures for single cell data")
25900 "This package defines S4 classes for single-cell genomic data and
25901 associated information, such as dimensionality reduction embeddings,
25902 nearest-neighbor graphs, and spatially-resolved coordinates. It provides data
25903 access methods and R-native hooks to ensure the Seurat object is familiar to
25905 (license license:gpl3)))
25907 (define-public r-seurat
25913 (uri (cran-uri "Seurat" version))
25916 "11rzc7h2ad8z8k5r1sbz4d7y4rl3080qp2hh7vibwmipbkvlial3"))))
25917 (properties `((upstream-name . "Seurat")))
25918 (build-system r-build-system)
25920 `(("r-cluster" ,r-cluster)
25921 ("r-cowplot" ,r-cowplot)
25922 ("r-fitdistrplus" ,r-fitdistrplus)
25923 ("r-future" ,r-future)
25924 ("r-future-apply" ,r-future-apply)
25925 ("r-ggplot2" ,r-ggplot2)
25926 ("r-ggrepel" ,r-ggrepel)
25927 ("r-ggridges" ,r-ggridges)
25930 ("r-igraph" ,r-igraph)
25931 ("r-irlba" ,r-irlba)
25932 ("r-jsonlite" ,r-jsonlite)
25933 ("r-kernsmooth" ,r-kernsmooth)
25934 ("r-leiden" ,r-leiden)
25935 ("r-lmtest" ,r-lmtest)
25937 ("r-matrix" ,r-matrix)
25938 ("r-matrixstats" ,r-matrixstats)
25939 ("r-miniui" ,r-miniui)
25940 ("r-patchwork" ,r-patchwork)
25941 ("r-pbapply" ,r-pbapply)
25942 ("r-plotly" ,r-plotly)
25945 ("r-rcolorbrewer" ,r-rcolorbrewer)
25947 ("r-rcppannoy" ,r-rcppannoy)
25948 ("r-rcppeigen" ,r-rcppeigen)
25949 ("r-rcppprogress" ,r-rcppprogress)
25950 ("r-reticulate" ,r-reticulate)
25951 ("r-rlang" ,r-rlang)
25954 ("r-rtsne" ,r-rtsne)
25955 ("r-scales" ,r-scales)
25956 ("r-scattermore" ,r-scattermore)
25957 ("r-sctransform" ,r-sctransform)
25958 ("r-shiny" ,r-shiny)
25959 ("r-spatstat" ,r-spatstat)
25960 ("r-tibble" ,r-tibble)
25961 ("r-uwot" ,r-uwot)))
25962 (home-page "http://www.satijalab.org/seurat")
25963 (synopsis "Seurat is an R toolkit for single cell genomics")
25965 "This package is an R package designed for QC, analysis, and
25966 exploration of single cell RNA-seq data. It easily enables widely-used
25967 analytical techniques, including the identification of highly variable genes,
25968 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
25969 algorithms; density clustering, hierarchical clustering, k-means, and the
25970 discovery of differentially expressed genes and markers.")
25971 (license license:gpl3)))
25973 (define-public r-phangorn
25975 (name "r-phangorn")
25980 (uri (cran-uri "phangorn" version))
25983 "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
25984 (build-system r-build-system)
25987 ("r-fastmatch" ,r-fastmatch)
25988 ("r-igraph" ,r-igraph)
25989 ("r-magrittr" ,r-magrittr)
25990 ("r-matrix" ,r-matrix)
25991 ("r-quadprog" ,r-quadprog)
25992 ("r-rcpp" ,r-rcpp)))
25993 (home-page "https://github.com/KlausVigo/phangorn")
25994 (synopsis "Phylogenetic analysis in R")
25996 "Phangorn is a package for phylogenetic analysis in R. It supports
25997 estimation of phylogenetic trees and networks using Maximum Likelihood,
25998 Maximum Parsimony, distance methods and Hadamard conjugation.")
25999 (license license:gpl2+)))
26001 (define-public r-diversitree
26003 (name "r-diversitree")
26008 (uri (cran-uri "diversitree" version))
26011 "1sk3sgn5hi04978s5s7gy6pzp28g3v9rglmiamlgs96c9wyyyff7"))))
26012 (build-system r-build-system)
26014 `(("gfortran" ,gfortran)))
26015 (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
26018 ("r-desolve" ,r-desolve)
26020 ("r-subplex" ,r-subplex)))
26021 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
26022 (synopsis "Comparative 'phylogenetic' analyses of diversification")
26023 (description "This package contains a number of comparative \"phylogenetic\"
26024 methods, mostly focusing on analysing diversification and character evolution.
26025 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
26026 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
26027 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
26028 include Markov models of discrete and continuous trait evolution and constant
26029 rate speciation and extinction.")
26030 (license license:gpl2+)))
26032 (define-public r-absfiltergsea
26034 (name "r-absfiltergsea")
26039 (uri (cran-uri "AbsFilterGSEA" version))
26041 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
26042 (properties `((upstream-name . "AbsFilterGSEA")))
26043 (build-system r-build-system)
26045 `(("r-biobase" ,r-biobase)
26046 ("r-deseq" ,r-deseq)
26047 ("r-limma" ,r-limma)
26049 ("r-rcpparmadillo" ,r-rcpparmadillo)))
26050 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
26051 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
26053 "This package provides a function that performs gene-permuting of a gene-set
26054 enrichment analysis (GSEA) calculation with or without the absolute filtering.
26055 Without filtering, users can perform (original) two-tailed or one-tailed
26057 (license license:gpl2)))
26059 (define-public r-calculus
26061 (name "r-calculus")
26066 (uri (cran-uri "calculus" version))
26069 "1wa5ap89cfcp0ancj9ivx5s2y0wqr2vmp9y115g7f6g772jwhscj"))))
26070 (properties `((upstream-name . "calculus")))
26071 (build-system r-build-system)
26073 `(("r-rcpp" ,r-rcpp)))
26075 `(("r-knitr" ,r-knitr)))
26076 (home-page "https://github.com/eguidotti/calculus")
26077 (synopsis "High dimensional numerical and symbolic calculus")
26079 "Efficient C++ optimized functions for numerical and symbolic calculus.
26080 It includes basic symbolic arithmetic, tensor calculus, Einstein summing
26081 convention, fast computation of the Levi-Civita symbol and generalized
26082 Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
26083 accurate high-order derivatives, differential operators (Gradient, Jacobian,
26084 Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
26085 orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
26086 parabolic or user defined by custom scale factors.")
26087 (license license:gpl3)))
26089 (define-public r-decon
26096 (uri (cran-uri "decon" version))
26099 "1v4l0xq29rm8mks354g40g9jxn0didzlxg3g7z08m0gvj29zdj7s"))))
26100 (properties `((upstream-name . "decon")))
26101 (build-system r-build-system)
26103 `(("gfortran" ,gfortran)))
26105 "https://cran.r-project.org/web/packages/decon/")
26106 (synopsis "Deconvolution Estimation in Measurement Error Models")
26108 "This package contains a collection of functions to deal with
26109 nonparametric measurement error problems using deconvolution
26110 kernel methods. We focus two measurement error models in the
26111 package: (1) an additive measurement error model, where the
26112 goal is to estimate the density or distribution function from
26113 contaminated data; (2) nonparametric regression model with
26114 errors-in-variables. The R functions allow the measurement errors
26115 to be either homoscedastic or heteroscedastic. To make the
26116 deconvolution estimators computationally more efficient in R,
26117 we adapt the \"Fast Fourier Transform\" (FFT) algorithm for
26118 density estimation with error-free data to the deconvolution
26119 kernel estimation. Several methods for the selection of the
26120 data-driven smoothing parameter are also provided in the package.
26121 See details in: Wang, X.F. and Wang, B. (2011). Deconvolution
26122 estimation in measurement error models: The R package decon.
26123 Journal of Statistical Software, 39(10), 1-24.")
26124 (license license:gpl3+)))
26126 (define-public r-locpol
26133 (uri (cran-uri "locpol" version))
26136 "1p915n0l09kbwkly627074jslxl01yssp1rf0c7sygvsw6sgy5lm"))))
26137 (properties `((upstream-name . "locpol")))
26138 (build-system r-build-system)
26140 "https://cran.r-project.org/web/packages/locpol/")
26141 (synopsis "Kernel Local Polynomial Regression")
26143 "Computes local polynomial estimators for the regression and
26144 also density. It comprises several different utilities to handle
26145 kernel estimators.")
26146 (license license:gpl2+)))
26148 (define-public r-lpme
26155 (uri (cran-uri "lpme" version))
26158 "0si90nkgl8bqk8yvd2igdsrngiwqh8891072pfpzipifnd0f5448"))))
26159 (properties `((upstream-name . "lpme")))
26160 (build-system r-build-system)
26162 `(("r-decon" ,r-decon)
26163 ("r-flexmix" ,r-flexmix)
26164 ("r-locpol" ,r-locpol)
26166 ("r-rcpparmadillo" ,r-rcpparmadillo)))
26168 "https://cran.r-project.org/web/packages/lpme/")
26169 (synopsis "Nonparametric Estimation of Measurement Error Models")
26171 "Provide nonparametric methods for mean regression model,
26172 modal regression and conditional density estimation in the
26173 presence/absence of measurement error. Bandwidth selection is
26174 also provided for each method.")
26175 (license license:gpl2+)))
26177 (define-public r-aws-signature
26179 (name "r-aws-signature")
26184 (uri (cran-uri "aws.signature" version))
26187 "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp"))))
26188 (properties `((upstream-name . "aws.signature")))
26189 (build-system r-build-system)
26191 `(("r-base64enc" ,r-base64enc)
26192 ("r-digest" ,r-digest)))
26193 (home-page "https://github.com/cloudyr/aws.signature")
26194 (synopsis "Amazon Web Services Request Signatures")
26196 "This package generates version 2 and 4 request signatures for Amazon Web
26197 Services (AWS) and provides a mechanism for retrieving credentials from
26198 environment variables, AWS credentials files, and EC2 instance metadata. For
26199 use on EC2 instances, the package 'aws.ec2metadata' is suggested.")
26200 (license license:gpl2+)))
26202 (define-public r-aws-s3
26209 (uri (cran-uri "aws.s3" version))
26212 "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx"))))
26213 (properties `((upstream-name . "aws.s3")))
26214 (build-system r-build-system)
26216 `(("r-aws-signature" ,r-aws-signature)
26217 ("r-base64enc" ,r-base64enc)
26219 ("r-digest" ,r-digest)
26221 ("r-xml2" ,r-xml2)))
26222 (home-page "https://github.com/cloudyr/aws.s3")
26223 (synopsis "AWS S3 Client Package")
26225 "This package provides a simple client package for the Amazon Web
26226 Services (AWS) Simple Storage Service (S3) REST API.")
26227 (license license:gpl2+)))
26229 (define-public r-lgr
26235 (uri (cran-uri "lgr" version))
26238 "0k4kacjk7swm3gmdpha1rg44xb29vzvhvx48jhpb78glj5c9phyr"))))
26239 (build-system r-build-system)
26243 `(("r-knitr" ,r-knitr)))
26244 (home-page "https://s-fleck.github.io/lgr/")
26245 (synopsis "Fully featured logging framework")
26246 (description "This package offers a flexible, feature-rich yet
26247 light-weight logging framework based on @code{R6} classes. It supports
26248 hierarchical loggers, custom log levels, arbitrary data fields in log events,
26249 logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as
26250 well as email and push notifications.")
26251 (license license:expat)))
26253 (define-public r-mlr3measures
26255 (name "r-mlr3measures")
26259 (uri (cran-uri "mlr3measures" version))
26262 "18jk4kdj9771r16smz7xhmmiilcdg1qlavln5hrpvkx780zh3hj6"))))
26263 (build-system r-build-system)
26265 `(("r-checkmate" ,r-checkmate)
26266 ("r-prroc" ,r-prroc)))
26267 (home-page "https://mlr3measures.mlr-org.com/")
26268 (synopsis "Performance measures for mlr3")
26269 (description "This package implements multiple performance measures for
26270 supervised learning. It includes over 40 measures for regression and
26271 classification. Additionally, meta information about the performance measures
26272 can be queried, e.g. what the best and worst possible performances scores
26274 (license license:lgpl3)))
26276 (define-public r-mlr3misc
26278 (name "r-mlr3misc")
26282 (uri (cran-uri "mlr3misc" version))
26285 "19k3l2d6wnqvdng0m7p54rrlvwl5457lcy7bg82m2bbpqxi8qch3"))))
26286 (build-system r-build-system)
26288 `(("r-backports" ,r-backports)
26289 ("r-checkmate" ,r-checkmate)
26290 ("r-data-table" ,r-data-table)
26292 (home-page "https://mlr3misc.mlr-org.com/")
26293 (synopsis "Helper functions for mlr3")
26294 (description "@code{mlr3misc} provides frequently used helper functions
26295 and assertions used in @code{mlr3} and its companion packages. It comes with
26296 helper functions for functional programming, for printing, to work with
26297 @code{data.table}, as well as some generally useful @code{R6} classes. This
26298 package also supersedes the package @code{BBmisc}.")
26299 (license license:lgpl3)))
26301 (define-public r-paradox
26307 (uri (cran-uri "paradox" version))
26310 "1zv0q411wcwigkf4yggs3w2gz48lvv3jhnrddrv40qih8b70ywi3"))))
26311 (build-system r-build-system)
26313 `(("r-backports" ,r-backports)
26314 ("r-checkmate" ,r-checkmate)
26315 ("r-data-table" ,r-data-table)
26316 ("r-mlr3misc" ,r-mlr3misc)
26318 (home-page "https://paradox.mlr-org.com/")
26319 (synopsis "Define and work with parameter spaces for complex algorithms")
26320 (description "With this package it is possible to define parameter spaces,
26321 constraints and dependencies for arbitrary algorithms, and to program on such
26322 spaces. It also includes statistical designs and random samplers. Objects are
26323 implemented as @code{R6} classes.")
26324 (license license:lgpl3)))
26326 (define-public r-mlr3
26332 (uri (cran-uri "mlr3" version))
26335 "0gg7rrzxwrnpg6sgm0aa6bmfwmqv3d3za0ghnqrnibg33p9ynpgb"))))
26336 (build-system r-build-system)
26339 ("r-backports" ,r-backports)
26340 ("r-checkmate" ,r-checkmate)
26341 ("r-data-table" ,r-data-table)
26342 ("r-digest" ,r-digest)
26343 ("r-future-apply" ,r-future-apply)
26345 ("r-mlbench" ,r-mlbench)
26346 ("r-mlr3measures" ,r-mlr3measures)
26347 ("r-mlr3misc" ,r-mlr3misc)
26348 ("r-paradox" ,r-paradox)
26349 ("r-uuid" ,r-uuid)))
26350 (home-page "https://mlr3.mlr-org.com/")
26351 (synopsis "Machine Learning in R - Next Generation")
26352 (description "@code{mlr3} enables efficient, object-oriented programming
26353 on the building blocks of machine learning. It provides @code{R6} objects for
26354 tasks, learners, resamplings, and measures. The package is geared towards
26355 scalability and larger datasets by supporting parallelization and out-of-memory
26356 data-backends like databases. While @code{mlr3} focuses on the core
26357 computational operations, add-on packages provide additional functionality.")
26358 (license license:lgpl3)))
26360 (define-public r-mlr3learners
26362 (name "r-mlr3learners")
26366 (uri (cran-uri "mlr3learners" version))
26369 "1wxlpzz3hpkn77n4ag1v868dmp140j1pmrhynsv5xfgk9fg0w7ri"))))
26370 (build-system r-build-system)
26372 `(("r-data-table" ,r-data-table)
26374 ("r-mlr3misc" ,r-mlr3misc)
26375 ("r-paradox" ,r-paradox)
26377 (home-page "https://mlr3learners.mlr-org.com/")
26378 (synopsis "Recommended Learners for @code{mlr3}")
26379 (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba}
26380 with interfaces to essential machine learning packages on CRAN. This includes,
26381 but is not limited to: (penalized) linear and logistic regression, linear and
26382 quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support
26383 vector machines, and gradient boosting.")
26384 (license license:lgpl3)))
26386 (define-public r-bbotk
26393 (uri (cran-uri "bbotk" version))
26396 "06iz6gyymcxkbjiw049v1dk3vjfni646z247q08i2s0x59sqfqxv"))))
26397 (properties `((upstream-name . "bbotk")))
26398 (build-system r-build-system)
26400 `(("r-checkmate" ,r-checkmate)
26401 ("r-data-table" ,r-data-table)
26403 ("r-mlr3misc" ,r-mlr3misc)
26404 ("r-paradox" ,r-paradox)
26406 (home-page "https://bbotk.mlr-org.com")
26407 (synopsis "Black-Box Optimization Toolkit")
26408 (description "This package provides a common framework for optimization of
26409 black-box functions for other packages, e.g. @code{mlr3}. It offers various
26410 optimization methods e.g. grid search, random search and generalized simulated
26412 (license license:lgpl3)))
26414 (define-public r-mlr3tuning
26416 (name "r-mlr3tuning")
26420 (uri (cran-uri "mlr3tuning" version))
26423 "1pn80qjxzj2pivgs6qgairci6yh1bdnl2zbgl9ykdip2rqzv6r6m"))))
26424 (build-system r-build-system)
26426 `(("r-bbotk" ,r-bbotk)
26427 ("r-checkmate" ,r-checkmate)
26428 ("r-data-table" ,r-data-table)
26431 ("r-mlr3misc" ,r-mlr3misc)
26432 ("r-paradox" ,r-paradox)
26434 (home-page "https://mlr3tuning.mlr-org.com/")
26435 (synopsis "Tuning for @code{mlr3}")
26436 (description "@code{mlr3tuning} implements methods for hyperparameter
26437 tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various
26438 termination criteria can be set and combined. The class @code{AutoTuner} provides a
26439 convenient way to perform nested resampling in combination with @code{mlr3}.")
26440 (license license:lgpl3)))
26442 (define-public r-fontliberation
26444 (name "r-fontliberation")
26449 (uri (cran-uri "fontLiberation" version))
26452 "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc"))))
26454 `((upstream-name . "fontLiberation")))
26455 (build-system r-build-system)
26456 (home-page "https://cran.r-project.org/package=fontLiberation")
26457 (synopsis "Liberation fonts")
26459 "This package provides a placeholder for the Liberation fontset intended
26460 for the fontquiver package. This fontset covers the 12 combinations of
26461 families (sans, serif, mono) and faces (plain, bold, italic, bold italic)
26462 supported in R graphics devices.")
26463 (license license:silofl1.1)))
26465 (define-public r-fontbitstreamvera
26467 (name "r-fontbitstreamvera")
26472 (uri (cran-uri "fontBitstreamVera" version))
26475 "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j"))))
26477 `((upstream-name . "fontBitstreamVera")))
26478 (build-system r-build-system)
26479 (home-page "https://cran.r-project.org/package=fontBitstreamVera")
26480 (synopsis "Fonts for fontquiver")
26482 "This package is a placeholder for the Bitstream Vera font. It is
26483 intended for the fontquiver package.")
26485 (license:fsdg-compatible
26486 "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts"
26487 "The Font Software may be sold as part of a larger software package but
26488 no copy of one or more of the Font Software typefaces may be sold by
26491 (define-public r-fontquiver
26493 (name "r-fontquiver")
26498 (uri (cran-uri "fontquiver" version))
26501 "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm"))))
26502 (properties `((upstream-name . "fontquiver")))
26503 (build-system r-build-system)
26505 `(("r-fontbitstreamvera" ,r-fontbitstreamvera)
26506 ("r-fontliberation" ,r-fontliberation)))
26507 (home-page "https://cran.r-project.org/package=fontquiver")
26508 (synopsis "Set of installed fonts")
26510 "This package provides a set of fonts. This is useful when you want to
26511 avoid system fonts to make sure your outputs are reproducible.")
26512 (license license:gpl3)))
26514 (define-public r-freetypeharfbuzz
26516 (name "r-freetypeharfbuzz")
26521 (uri (cran-uri "freetypeharfbuzz" version))
26524 "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7"))))
26526 `((upstream-name . "freetypeharfbuzz")))
26527 (build-system r-build-system)
26530 (modify-phases %standard-phases
26531 (add-after 'unpack 'prepare-static-libraries
26532 (lambda* (#:key inputs #:allow-other-keys)
26533 (mkdir-p "src/target/include")
26534 (let ((freetype (assoc-ref inputs "static-freetype"))
26535 (harfbuzz (assoc-ref inputs "static-harfbuzz")))
26536 (substitute* "src/Makevars.in"
26537 (("include @MK_FILE@") "") ; do not build static libs
26538 (("^HB_STATIC_LIB =.*")
26539 (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n"))
26540 (("^FT_STATIC_LIB =.*")
26541 (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n")))
26542 (copy-recursively (string-append freetype "/include")
26543 "src/target/include")
26544 (copy-recursively (string-append harfbuzz "/include")
26545 "src/target/include")))))))
26547 `(("r-fontquiver" ,r-fontquiver)))
26548 ;; This may defeat the purpose of this package as our versions of freetype
26549 ;; and harfbuzz obviously differ from the tarballs offered by this
26550 ;; project. On the other hand, Guix arguably does a better job at
26551 ;; "ensur[ing] deterministic computation".
26553 `(("static-freetype"
26555 (inherit (static-package freetype))
26557 `(#:configure-flags
26558 (list "--enable-static=yes"
26563 "--without-harfbuzz")))))
26566 (inherit (static-package harfbuzz))
26568 `(#:tests? #false ; fail because shared library is disabled
26570 (list "--enable-static=yes"
26571 "--enable-shared=no"
26573 "--with-freetype=yes"
26576 "--without-fontconfig"
26577 "--without-glib")))))))
26580 (home-page "https://cran.r-project.org/package=freetypeharfbuzz")
26581 (synopsis "Deterministic computation of text box metrics")
26583 "Unlike other tools that dynamically link to the Cairo stack,
26584 freetypeharfbuzz is statically linked to specific versions of the FreeType and
26585 harfbuzz libraries. This ensures deterministic computation of text box
26586 extents for situations where reproducible results are crucial (for instance
26587 unit tests of graphics).")
26588 (license license:gpl3)))
26590 (define-public r-vdiffr
26597 (uri (cran-uri "vdiffr" version))
26600 "0i0xdr8dakbkkgrhp0zvlnv3rxhc8h5naqq416mr5zv9q8i4p8jc"))
26603 (delete-file "inst/htmlwidgets/lib/jquery.min.js")))))
26604 (properties `((upstream-name . "vdiffr")))
26605 (build-system r-build-system)
26608 (modify-phases %standard-phases
26609 (add-after 'unpack 'process-javascript
26610 (lambda* (#:key inputs #:allow-other-keys)
26611 (with-directory-excursion "inst/htmlwidgets/lib/"
26612 (let ((source (assoc-ref inputs "js-jquery"))
26613 (target "jquery.min.js"))
26614 (format #true "Processing ~a --> ~a~%"
26616 (invoke "esbuild" source "--minify"
26617 (string-append "--outfile=" target)))))))))
26619 `(("freetype" ,freetype)
26620 ("harfbuzz" ,harfbuzz)))
26623 ("r-devtools" ,r-devtools)
26624 ("r-diffobj" ,r-diffobj)
26625 ("r-fontquiver" ,r-fontquiver)
26626 ("r-freetypeharfbuzz" ,r-freetypeharfbuzz)
26627 ("r-gdtools" ,r-gdtools)
26629 ("r-htmltools" ,r-htmltools)
26630 ("r-htmlwidgets" ,r-htmlwidgets)
26631 ("r-purrr" ,r-purrr)
26634 ("r-rlang" ,r-rlang)
26635 ("r-shiny" ,r-shiny)
26636 ("r-testthat" ,r-testthat)
26637 ("r-usethis" ,r-usethis)
26638 ("r-xml2" ,r-xml2)))
26640 `(("esbuild" ,esbuild)
26644 (uri "https://code.jquery.com/jquery-1.12.4.js")
26647 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))))
26648 (home-page "https://github.com/r-lib/vdiffr")
26649 (synopsis "Visual regression testing and graphical diffing")
26651 "This package is an extension to the testthat package that makes it easy
26652 to add graphical unit tests. It provides a Shiny application to manage the
26654 (license license:gpl3)))
26656 (define-public r-highlight
26658 (name "r-highlight")
26663 (uri (cran-uri "highlight" version))
26666 "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf"))))
26667 (properties `((upstream-name . "highlight")))
26668 (build-system r-build-system)
26669 (home-page "https://github.com/hadley/highlight")
26670 (synopsis "Syntax highlighter for R code")
26672 "This package provides a syntax highlighter for R code based on the
26673 results of the R parser. It supports rendering in HTML and LaTeX markup. It
26674 includes a custom Sweave driver performing syntax highlighting of R code
26676 (license license:gpl3+)))
26678 (define-public r-clustree
26680 (name "r-clustree")
26685 (uri (cran-uri "clustree" version))
26688 "0lxydy2f83qqd5dhlp2l546jax759l43b29j6g82079yzg1szwsz"))))
26689 (properties `((upstream-name . "clustree")))
26690 (build-system r-build-system)
26692 `(("r-checkmate" ,r-checkmate)
26693 ("r-dplyr" ,r-dplyr)
26694 ("r-ggplot2" ,r-ggplot2)
26695 ("r-ggraph" ,r-ggraph)
26696 ("r-ggrepel" ,r-ggrepel)
26697 ("r-igraph" ,r-igraph)
26698 ("r-rlang" ,r-rlang)
26699 ("r-tidygraph" ,r-tidygraph)
26700 ("r-viridis" ,r-viridis)))
26702 `(("r-knitr" ,r-knitr)))
26703 (home-page "https://github.com/lazappi/clustree")
26704 (synopsis "Visualize clusterings at different resolutions")
26706 "Deciding what resolution to use can be a difficult question when
26707 approaching a clustering analysis. One way to approach this problem is to
26708 look at how samples move as the number of clusters increases. This package
26709 allows you to produce clustering trees, a visualization for interrogating
26710 clusterings as resolution increases.")
26711 (license license:gpl3)))
26713 (define-public r-textshaping
26715 (name "r-textshaping")
26720 (uri (cran-uri "textshaping" version))
26723 "053pbw45by96q62kjfnyc3d0ssar9svssrdqy6a09kdmdh75xdar"))))
26724 (properties `((upstream-name . "textshaping")))
26725 (build-system r-build-system)
26727 `(("freetype" ,freetype)
26728 ("fribidi" ,fribidi)
26729 ("harfbuzz" ,harfbuzz)
26732 `(("r-cpp11" ,r-cpp11)
26733 ("r-systemfonts" ,r-systemfonts)))
26735 `(("pkg-config" ,pkg-config)
26736 ("r-knitr" ,r-knitr)))
26737 (home-page "https://github.com/r-lib/textshaping")
26738 (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping")
26740 "This package provides access to the text shaping functionality in the
26741 HarfBuzz library and the bidirectional algorithm in the Fribidi library. This
26742 is a low-level utility package mainly for graphic devices that expands upon
26743 the font tool-set provided by the @code{systemfonts} package.")
26744 (license license:expat)))
26746 (define-public r-ragg
26753 (uri (cran-uri "ragg" version))
26756 "0443dhfi7bjfpap041vrnslw3ql3vpsxx18raz2w9nfdb7id8lsc"))))
26757 (properties `((upstream-name . "ragg")))
26758 (build-system r-build-system)
26760 `(("freetype" ,freetype)
26761 ("libjpeg" ,libjpeg-turbo)
26763 ("libtiff" ,libtiff)
26766 `(("r-systemfonts" ,r-systemfonts)
26767 ("r-textshaping" ,r-textshaping)))
26769 `(("pkg-config" ,pkg-config)))
26770 (home-page "https://ragg.r-lib.org")
26771 (synopsis "Graphic devices based on AGG")
26773 "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D
26774 drawing library. The ragg package provides a set of graphic devices based on
26775 AGG to use as alternative to the raster devices provided through the
26776 @code{grDevices} package.")
26777 (license license:expat)))
26779 (define-public r-downlit
26786 (uri (cran-uri "downlit" version))
26789 "0z4fz7c9kyd9v72wl3iqs2wxspi975d6b0rgjr9lvg8a18maa9z6"))))
26790 (properties `((upstream-name . "downlit")))
26791 (build-system r-build-system)
26793 `(("r-brio" ,r-brio)
26794 ("r-digest" ,r-digest)
26795 ("r-evaluate" ,r-evaluate)
26796 ("r-fansi" ,r-fansi)
26797 ("r-rlang" ,r-rlang)
26798 ("r-vctrs" ,r-vctrs)
26799 ("r-yaml" ,r-yaml)))
26800 (home-page "https://downlit.r-lib.org/")
26801 (synopsis "Syntax highlighting and automatic linking")
26803 "This package provides syntax highlighting of R code, specifically
26804 designed for the needs of RMarkdown packages like @code{pkgdown},
26805 @code{hugodown}, and @code{bookdown}. It includes linking of function calls
26806 to their documentation on the web, and automatic translation of ANSI escapes
26807 in output to the equivalent HTML.")
26808 (license license:expat)))
26810 (define-public r-pkgdown
26817 (uri (cran-uri "pkgdown" version))
26820 "1k31biyvxkv3xjc1yy3nzb9wfza3vbx97fv17nly5a6vlv7zqbs4"))))
26821 (properties `((upstream-name . "pkgdown")))
26822 (build-system r-build-system)
26823 (inputs `(("pandoc" ,pandoc)))
26825 `(("r-callr" ,r-callr)
26826 ("r-crayon" ,r-crayon)
26828 ("r-digest" ,r-digest)
26829 ("r-downlit" ,r-downlit)
26832 ("r-magrittr" ,r-magrittr)
26833 ("r-memoise" ,r-memoise)
26834 ("r-openssl" ,r-openssl)
26835 ("r-purrr" ,r-purrr)
26837 ("r-rematch2" ,r-rematch2)
26838 ("r-rlang" ,r-rlang)
26839 ("r-rmarkdown" ,r-rmarkdown)
26840 ("r-tibble" ,r-tibble)
26841 ("r-whisker" ,r-whisker)
26842 ("r-withr" ,r-withr)
26844 ("r-yaml" ,r-yaml)))
26846 `(("r-knitr" ,r-knitr)))
26847 (home-page "https://pkgdown.r-lib.org")
26848 (synopsis "Make static HTML documentation for an R package")
26850 "The goal of this package is to generate an attractive and useful website
26851 from a source package. @code{pkgdown} converts your documentation, vignettes,
26852 README file, and more to HTML making it easy to share information about your
26854 (license license:expat)))