1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
4 ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
5 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
6 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
7 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
8 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
9 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
10 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
11 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
12 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
13 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
14 ;;; Copyright © 2018, 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
15 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
16 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
17 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
18 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
19 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
20 ;;; Copyright © 2019, 2020 Wiktor Żelazny <wzelazny@vurv.cz>
21 ;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de>
22 ;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
23 ;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
24 ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
25 ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
26 ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
27 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
28 ;;; Copyright © 2020 Rafael Luque Leiva <rafael.luque@osoco.es>
29 ;;; Copyright © 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org>
30 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
31 ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net>
32 ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
33 ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com>
34 ;;; Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com>
35 ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com>
37 ;;; This file is part of GNU Guix.
39 ;;; GNU Guix is free software; you can redistribute it and/or modify it
40 ;;; under the terms of the GNU General Public License as published by
41 ;;; the Free Software Foundation; either version 3 of the License, or (at
42 ;;; your option) any later version.
44 ;;; GNU Guix is distributed in the hope that it will be useful, but
45 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
46 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
47 ;;; GNU General Public License for more details.
49 ;;; You should have received a copy of the GNU General Public License
50 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
52 (define-module (gnu packages cran)
53 #:use-module ((guix licenses) #:prefix license:)
54 #:use-module (guix packages)
55 #:use-module (guix download)
56 #:use-module (guix git-download)
57 #:use-module (guix utils)
58 #:use-module (guix build-system gnu)
59 #:use-module (guix build-system r)
60 #:use-module (gnu packages)
61 #:use-module (gnu packages algebra)
62 #:use-module (gnu packages autotools)
63 #:use-module (gnu packages base)
64 #:use-module (gnu packages bioinformatics)
65 #:use-module (gnu packages c)
66 #:use-module (gnu packages compression)
67 #:use-module (gnu packages crypto)
68 #:use-module (gnu packages curl)
69 #:use-module (gnu packages databases)
70 #:use-module (gnu packages fontutils)
71 #:use-module (gnu packages fribidi)
72 #:use-module (gnu packages gcc)
73 #:use-module (gnu packages geo)
74 #:use-module (gnu packages ghostscript)
75 #:use-module (gnu packages gl)
76 #:use-module (gnu packages gnome)
77 #:use-module (gnu packages graph)
78 #:use-module (gnu packages gtk)
79 #:use-module (gnu packages haskell-xyz)
80 #:use-module (gnu packages icu4c)
81 #:use-module (gnu packages image)
82 #:use-module (gnu packages imagemagick)
83 #:use-module (gnu packages java)
84 #:use-module (gnu packages javascript)
85 #:use-module (gnu packages libevent)
86 #:use-module (gnu packages lisp-xyz)
87 #:use-module (gnu packages machine-learning)
88 #:use-module (gnu packages maths)
89 #:use-module (gnu packages mpi)
90 #:use-module (gnu packages multiprecision)
91 #:use-module (gnu packages networking)
92 #:use-module (gnu packages node)
93 #:use-module (gnu packages pcre)
94 #:use-module (gnu packages perl)
95 #:use-module (gnu packages pkg-config)
96 #:use-module (gnu packages pulseaudio) ;libsndfile
97 #:use-module (gnu packages python)
98 #:use-module (gnu packages python-xyz)
99 #:use-module (gnu packages sqlite)
100 #:use-module (gnu packages statistics)
101 #:use-module (gnu packages tcl)
102 #:use-module (gnu packages tls)
103 #:use-module (gnu packages version-control)
104 #:use-module (gnu packages web)
105 #:use-module (gnu packages xml)
106 #:use-module (gnu packages xorg))
108 (define-public r-brio
115 (uri (cran-uri "brio" version))
118 "0ai2pqw5zk11r0rl2xshsq095ix1sdp2vjlixz2qxvy27x145ykh"))))
119 (properties `((upstream-name . "brio")))
120 (build-system r-build-system)
121 (home-page "https://github.com/r-lib/brio")
122 (synopsis "Basic R input output")
124 "This package provides functions to handle basic input output. These
125 functions always read and write UTF-8 (8-bit Unicode Transformation Format)
126 files and provide more explicit control over line endings.")
127 (license license:expat)))
129 (define-public r-cachem
136 (uri (cran-uri "cachem" version))
139 "1b1gk837rk9kbfq385ybrrk12ckxwvhjvf0z9635l3vw49wal4mh"))))
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 "09jhwpgd6hg4qyip4r7wzpjz0jr139fyspd5ncriqimp522snqbr"))))
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 "1zcj5y54z1max1df9j2iclm6zlcic4wj684y18wcnmmdwfs51818"))))
216 (properties `((upstream-name . "rticles")))
217 (build-system r-build-system)
219 `(("r-knitr" ,r-knitr)
220 ("r-rmarkdown" ,r-rmarkdown)
221 ("r-tinytex" ,r-tinytex)
224 (home-page "https://github.com/rstudio/rticles")
225 (synopsis "Article formats for R Markdown")
227 "This package provides a suite of custom R Markdown formats and templates
228 for authoring journal articles and conference submissions.")
229 (license license:gpl3)))
231 (define-public r-bezier
237 (uri (cran-uri "bezier" version))
240 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
241 (build-system r-build-system)
242 (home-page "https://cran.r-project.org/web/packages/bezier/")
243 (synopsis "Bezier curve and spline toolkit")
245 "This package is a toolkit for working with Bezier curves and splines.
246 The package provides functions for point generation, arc length estimation,
247 degree elevation and curve fitting.")
248 (license license:gpl2+)))
257 (uri (cran-uri "V8" version))
260 "1g9z22pc8ydx1yhv57ww2d2jg5hvrl7ilwa79x89zgn17jha5j7m"))))
261 (properties `((upstream-name . "V8")))
262 (build-system r-build-system)
265 (modify-phases %standard-phases
266 (add-after 'unpack 'find-v8
267 (lambda* (#:key inputs #:allow-other-keys)
268 (substitute* "configure"
270 (string-append "PKG_LIBS="
271 (assoc-ref inputs "node")
272 "/lib/libnode.so.64\n")))
273 (setenv "INCLUDE_DIR"
275 (assoc-ref inputs "node")
279 (assoc-ref inputs "node") "/lib"))
282 `(("node" ,libnode)))
285 ("r-jsonlite" ,r-jsonlite)
288 `(("r-knitr" ,r-knitr)))
289 (home-page "https://jeroen.cran.dev/V8")
290 (synopsis "Embedded JavaScript and WebAssembly engine for R")
292 "This package provides an R interface to V8: Google's JavaScript and
293 WebAssembly engine.")
294 (license license:expat)))
303 (uri (cran-uri "DOT" version))
306 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
307 (properties `((upstream-name . "DOT")))
308 (build-system r-build-system)
311 (home-page "http://haghish.com/dot")
312 (synopsis "Render and Export DOT Graphs in R")
314 "This package provides tools to render DOT diagram markup language in R
315 and also provides the possibility to export the graphs in PostScript and
316 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
317 programming packages such as @code{knitr} and @code{rmarkdown}.")
318 (license license:expat)))
320 (define-public r-clipr
327 (uri (cran-uri "clipr" version))
330 "1ywa4kipwc2d7na6iiz3wzdah99h6aynnh74yxl3nzl40xxlgbgz"))))
331 (build-system r-build-system)
333 `(("r-knitr" ,r-knitr)))
334 (home-page "https://github.com/mdlincoln/clipr")
335 (synopsis "Read and write from the system clipboard")
337 "This package provides simple utility functions to read from and write to
338 the system clipboards.")
339 (license license:gpl3)))
347 (uri (cran-uri "zoo" version))
350 "1rrw431jwaxd9xljp73f15rhcxvwc0xlyrmr0ghi5fj7a03c932f"))))
351 (build-system r-build-system)
353 `(("r-lattice" ,r-lattice)))
354 (home-page "http://zoo.R-Forge.R-project.org/")
355 (synopsis "S3 infrastructure for regular and irregular time series")
356 (description "This package contains an S3 class with methods for totally
357 ordered indexed observations. It is particularly aimed at irregular time
358 series of numeric vectors/matrices and factors.")
359 (license license:gpl2+)))
361 (define-public r-ggalluvial
363 (name "r-ggalluvial")
367 (uri (cran-uri "ggalluvial" version))
370 "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3"))))
371 (properties `((upstream-name . "ggalluvial")))
372 (build-system r-build-system)
374 `(("r-dplyr" ,r-dplyr)
375 ("r-ggplot2" ,r-ggplot2)
376 ("r-lazyeval" ,r-lazyeval)
379 ("r-tidyselect" ,r-tidyselect)))
381 `(("r-knitr" ,r-knitr)))
382 (home-page "http://corybrunson.github.io/ggalluvial/")
383 (synopsis "Alluvial plots for ggplot2")
384 (description "This package provides alluvial plots for @code{ggplot2}.
385 Alluvial plots use variable-width ribbons and stacked bar plots to represent
386 multi-dimensional or repeated-measures data with categorical or ordinal
388 (license license:gpl3)))
390 (define-public r-ggpmisc
396 (uri (cran-uri "ggpmisc" version))
399 "0kcrh73nwha52vl6z35wafmqs5lsdh2p4nqvi2ir70cv1k5y46zf"))))
400 (build-system r-build-system)
402 `(("r-dplyr" ,r-dplyr)
403 ("r-generics" ,r-generics)
405 ("r-ggplot2" ,r-ggplot2)
406 ("r-gridextra" ,r-gridextra)
407 ("r-lubridate" ,r-lubridate)
408 ("r-magrittr" ,r-magrittr)
411 ("r-polynom" ,r-polynom)
413 ("r-scales" ,r-scales)
414 ("r-splus2r" ,r-splus2r)
415 ("r-stringr" ,r-stringr)
416 ("r-tibble" ,r-tibble)
420 `(("r-knitr" ,r-knitr)))
421 (home-page "https://www.r4photobiology.info/")
422 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
423 (description "This package provides extensions to @code{ggplot2},
424 respecting the grammar of its graphics paradigm.")
425 (license license:gpl2+)))
427 (define-public r-gprofiler
434 (uri (cran-uri "gProfileR" version))
437 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
438 (properties `((upstream-name . "gProfileR")))
439 (build-system r-build-system)
442 ("r-rcurl" ,r-rcurl)))
443 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
444 (synopsis "Interface to the g:Profiler toolkit")
446 "This package provides tools for functional enrichment analysis,
447 gene identifier conversion and mapping homologous genes across related
448 organisms via the @code{g:Profiler} toolkit.")
449 (license license:gpl2+)))
451 (define-public r-gprofiler2
453 (name "r-gprofiler2")
458 (uri (cran-uri "gprofiler2" version))
461 "0q8hl3gdxy34c0181ql405fdklz82nfvmwdcafd5mzf935rjpyjg"))))
462 (properties `((upstream-name . "gprofiler2")))
463 (build-system r-build-system)
465 `(("r-crosstalk" ,r-crosstalk)
467 ("r-ggplot2" ,r-ggplot2)
468 ("r-gridextra" ,r-gridextra)
469 ("r-jsonlite" ,r-jsonlite)
470 ("r-plotly" ,r-plotly)
473 ("r-viridislite" ,r-viridislite)))
474 (native-inputs `(("r-knitr" ,r-knitr)))
475 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
476 (synopsis "Interface to the g:Profiler toolset")
478 "This package provides a toolset for functional enrichment analysis and
479 visualization, gene/protein/SNP identifier conversion and mapping orthologous
480 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
484 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
486 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
488 @item @code{g:Orth}, orthology search across species;
489 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
490 genes and variant effects.
493 This package is an R interface corresponding to the 2019 update of
494 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
496 (license license:gpl2+)))
498 (define-public r-oenb
505 (uri (cran-uri "oenb" version))
508 "1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz"))))
509 (properties `((upstream-name . "oenb")))
510 (build-system r-build-system)
512 `(("r-dplyr" ,r-dplyr)
514 (native-inputs `(("r-knitr" ,r-knitr)))
515 (home-page "https://github.com/franzmohr/oenb")
516 (synopsis "Tools for the OeNB Data Web Service")
518 "Tools to access data from the data web service of the
519 @acronym{OeNB, Oesterreichische Nationalbank},
520 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
521 (license license:gpl2+)))
523 (define-public r-scales
530 (uri (cran-uri "scales" version))
532 (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0"))))
533 (build-system r-build-system)
535 `(("r-farver" ,r-farver)
536 ("r-labeling" ,r-labeling)
537 ("r-lifecycle" ,r-lifecycle)
538 ("r-munsell" ,r-munsell)
539 ("r-rcolorbrewer" ,r-rcolorbrewer)
541 ("r-viridislite" ,r-viridislite)))
542 (home-page "https://github.com/hadley/scales")
543 (synopsis "Scale functions for visualization")
545 "This package provides graphical scales that map data to aesthetics, and
546 provides methods for automatically determining breaks and labels for axes and
548 (license license:expat)))
550 (define-public r-pheatmap
557 (uri (cran-uri "pheatmap" version))
560 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
561 (build-system r-build-system)
563 `(("r-gtable" ,r-gtable)
564 ("r-rcolorbrewer" ,r-rcolorbrewer)
565 ("r-scales" ,r-scales)))
566 (home-page "https://cran.r-project.org/web/packages/pheatmap")
567 (synopsis "Pretty heatmaps")
569 "This package provides an implementation of heatmaps that offers more
570 control over dimensions and appearance.")
571 (license license:gpl2+)))
579 (uri (cran-uri "ecp" version))
582 "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8"))))
583 (build-system r-build-system)
585 `(("r-rcpp" ,r-rcpp)))
586 (home-page "https://cran.r-project.org/web/packages/ecp/")
587 (synopsis "Multiple change-point analysis of multivariate data")
589 "This package implements various procedures for finding multiple
590 change-points. Two methods make use of dynamic programming and pruning, with
591 no distributional assumptions other than the existence of certain absolute
592 moments in one method. Hierarchical and exact search methods are included.
593 All methods return the set of estimated change-points as well as other summary
595 (license license:gpl2+)))
597 (define-public r-ellipsis
604 (uri (cran-uri "ellipsis" version))
607 "1nvmkcca57d9067rcggw1gby80ibx5hplk2myz0cs9zwilaib2jg"))))
608 (build-system r-build-system)
610 `(("r-rlang" ,r-rlang)))
611 (home-page "https://github.com/hadley/ellipsis")
612 (synopsis "Tools for working with additional arguments")
614 "In S3 generics, it's useful to take @code{...} so that methods can have
615 additional arguments. But this flexibility comes at a cost: misspelled
616 arguments will be silently ignored. The @code{ellipsis} package is an
617 experiment that allows a generic to warn if any arguments passed in @code{...}
619 (license license:gpl3)))
628 (uri (cran-uri "grr" version))
631 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
632 (build-system r-build-system)
633 (home-page "https://cran.r-project.org/web/packages/grr")
634 (synopsis "Alternative implementations of base R functions")
636 "This package provides alternative implementations of some base R
637 functions, including @code{sort}, @code{order}, and @code{match}. The
638 functions are simplified but can be faster or have other advantages.")
639 (license license:gpl3)))
641 (define-public r-matrix-utils
643 (name "r-matrix-utils")
648 (uri (cran-uri "Matrix.utils" version))
651 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
652 (properties `((upstream-name . "Matrix.utils")))
653 (build-system r-build-system)
656 ("r-matrix" ,r-matrix)))
657 (home-page "https://github.com/cvarrichio/Matrix.utils")
659 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
661 "This package implements data manipulation methods such as @code{cast},
662 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
664 (license license:gpl3)))
666 (define-public r-mboost
672 (uri (cran-uri "mboost" version))
675 "1dgyc38axfk2a430wsdnnk76xikizkyxf5r0l1kbp6cacrx6idz0"))))
676 (build-system r-build-system)
678 `(("r-lattice" ,r-lattice)
679 ("r-matrix" ,r-matrix)
681 ("r-partykit" ,r-partykit)
682 ("r-quadprog" ,r-quadprog)
684 ("r-survival" ,r-survival)))
685 (home-page "https://github.com/boost-R/mboost")
686 (synopsis "Model-based boosting")
688 "This package provides a functional gradient descent algorithm (boosting)
689 for optimizing general risk functions utilizing component-wise (penalised)
690 least squares estimates or regression trees as base-learners for fitting
691 generalized linear, additive and interaction models to potentially
692 high-dimensional data.")
693 (license license:gpl2)))
695 (define-public r-shadowtext
697 (name "r-shadowtext")
701 (uri (cran-uri "shadowtext" version))
704 "1s1ip8zfr684a3ld7hvf524bhn2j31k6d1wbhh1ni0flsggv2ckf"))))
705 (properties `((upstream-name . "shadowtext")))
706 (build-system r-build-system)
708 `(("r-ggplot2" ,r-ggplot2)
709 ("r-scales" ,r-scales)))
711 `(("r-knitr" ,r-knitr)))
712 (home-page "https://github.com/GuangchuangYu/shadowtext/")
713 (synopsis "Shadow text grob and layer")
714 (description "This package implements @code{shadowtextGrob()} for
715 @code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}.
716 These functions draw text grob with background shadow.")
717 (license license:artistic2.0)))
726 (uri (cran-uri "sys" version))
729 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p"))))
730 (build-system r-build-system)
731 (home-page "https://github.com/jeroen/sys")
732 (synopsis "Powerful and reliable tools for running system commands in R")
734 "This package provides drop-in replacements for the base @code{system2()}
735 function with fine control and consistent behavior across platforms. It
736 supports clean interruption, timeout, background tasks, and streaming STDIN /
737 STDOUT / STDERR over binary or text connections. The package also provides
738 functions for evaluating expressions inside a temporary fork. Such
739 evaluations have no side effects on the main R process, and support reliable
740 interrupts and timeouts. This provides the basis for a sandboxing
742 (license license:expat)))
744 (define-public r-ashr
750 (uri (cran-uri "ashr" version))
753 "1rqb5j30ylaf1h4l66x4jxyn5inrvhc42d90qd5mgkxsq0ghdlr4"))))
754 (properties `((upstream-name . "ashr")))
755 (build-system r-build-system)
757 `(("r-etrunct" ,r-etrunct)
758 ("r-invgamma" ,r-invgamma)
759 ("r-matrix" ,r-matrix)
760 ("r-mixsqp" ,r-mixsqp)
762 ("r-squarem" ,r-squarem)
763 ("r-truncnorm" ,r-truncnorm)))
765 `(("r-knitr" ,r-knitr)))
766 (home-page "https://github.com/stephens999/ashr")
767 (synopsis "Methods for adaptive shrinkage, using empirical bayes")
768 (description "This package implements an empirical Bayes approach for
769 large-scale hypothesis testing and false discovery rate estimation.")
770 (license license:gpl3+)))
772 (define-public r-askpass
779 (uri (cran-uri "askpass" version))
782 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
783 (build-system r-build-system)
784 (propagated-inputs `(("r-sys" ,r-sys)))
785 (home-page "https://github.com/jeroen/askpass")
786 (synopsis "Safe password entry for R")
788 "This package provides cross-platform utilities for prompting the user
789 for credentials or a passphrase, for example to authenticate with a server or
790 read a protected key.")
791 (license license:expat)))
793 (define-public r-vegan
800 (uri (cran-uri "vegan" version))
803 "0aj6m9l1vkh32sar6fyvq4p8j4h2f2f347w1300qnzgaa5lmhfz6"))))
804 (build-system r-build-system)
806 `(("r-knitr" ,r-knitr) ; needed for vignettes
807 ("gfortran" ,gfortran)))
809 `(("r-cluster" ,r-cluster)
810 ("r-lattice" ,r-lattice)
813 ("r-permute" ,r-permute)))
814 (home-page "https://cran.r-project.org/web/packages/vegan")
815 (synopsis "Functions for community ecology")
817 "The vegan package provides tools for descriptive community ecology. It
818 has most basic functions of diversity analysis, community ordination and
819 dissimilarity analysis. Most of its multivariate tools can be used for other
820 data types as well.")
821 (license license:gpl2+)))
823 (define-public r-tidyverse
830 (uri (cran-uri "tidyverse" version))
833 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
834 (build-system r-build-system)
836 `(("r-broom" ,r-broom)
838 ("r-crayon" ,r-crayon)
839 ("r-dbplyr" ,r-dbplyr)
841 ("r-forcats" ,r-forcats)
842 ("r-ggplot2" ,r-ggplot2)
846 ("r-jsonlite" ,r-jsonlite)
847 ("r-lubridate" ,r-lubridate)
848 ("r-magrittr" ,r-magrittr)
849 ("r-modelr" ,r-modelr)
850 ("r-pillar" ,r-pillar)
853 ("r-readxl" ,r-readxl)
854 ("r-reprex" ,r-reprex)
856 ("r-rstudioapi" ,r-rstudioapi)
858 ("r-stringr" ,r-stringr)
859 ("r-tibble" ,r-tibble)
862 (home-page "https://tidyverse.tidyverse.org")
863 (synopsis "Install and load packages from the \"Tidyverse\"")
865 "The @code{tidyverse} is a set of packages that work in harmony because
866 they share common data representations and API design. This package is
867 designed to make it easy to install and load multiple tidyverse packages in a
869 (license license:gpl3)))
871 (define-public r-rvest
878 (uri (cran-uri "rvest" version))
880 (base32 "1yh2p429a0zr8pqmlw5rzf6m797j20j5w6xwxlqq0wrdbnif6bka"))))
881 (build-system r-build-system)
884 ("r-magrittr" ,r-magrittr)
885 ("r-selectr" ,r-selectr)
888 `(("r-knitr" ,r-knitr)))
889 (home-page "https://github.com/hadley/rvest")
890 (synopsis "Simple web scraping for R")
892 "@code{r-rvest} helps you scrape information from web pages. It is
893 designed to work with @code{magrittr} to make it easy to express common web
894 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
895 (license license:gpl3)))
897 (define-public r-selectr
904 (uri (cran-uri "selectr" version))
906 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
907 (build-system r-build-system)
909 `(("r-stringr" ,r-stringr)
911 (home-page "https://sjp.co.nz/projects/selectr/")
912 (synopsis "Translate CSS selectors to XPath expressions")
914 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
915 expression. This allows you to use CSS selectors when working with the XML
916 package as it can only evaluate XPath expressions. Also provided are
917 convenience functions useful for using CSS selectors on XML nodes. This
918 package is a port of the Python package @code{cssselect}.")
919 (license license:bsd-3)))
921 (define-public r-reprex
928 (uri (cran-uri "reprex" version))
931 "07nzx0fdl48jw95ipx17ql0l13q60yl3rjrkj1m375wrc7h1v5nx"))))
932 (build-system r-build-system)
934 `(("r-callr" ,r-callr)
941 ("r-rmarkdown" ,r-rmarkdown)
942 ("r-withr" ,r-withr)))
944 `(("r-knitr" ,r-knitr)))
945 (home-page "https://github.com/tidyverse/reprex")
946 (synopsis "Prepare reproducible R code examples for sharing")
948 "This package provides a convenience wrapper that uses the
949 @code{rmarkdown} package to render small snippets of code to target formats
950 that include both code and output. The goal is to encourage the sharing of
951 small, reproducible, and runnable examples on code-oriented websites or email.
952 @code{reprex} also extracts clean, runnable R code from various common formats,
953 such as copy/paste from an R session.")
954 (license license:expat)))
956 (define-public r-reordercluster
958 (name "r-reordercluster")
962 (uri (cran-uri "ReorderCluster" version))
965 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
966 (build-system r-build-system)
968 `(("r-gplots" ,r-gplots)
970 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
971 (synopsis "Reordering the dendrogram according to the class labels")
972 (description "This package provides tools for performing the leaf reordering
973 for the dendrogram that preserves the hierarchical clustering result and at the
974 same time tries to group instances from the same class together.")
975 (license license:gpl3+)))
977 (define-public r-callr
984 (uri (cran-uri "callr" version))
987 "15l6ppsxdadlnl4fk0f8bvf327n8izk96px5d08m1ay9iij8qcyf"))))
988 (build-system r-build-system)
991 ("r-processx" ,r-processx)))
992 (home-page "https://github.com/r-lib/callr#readme")
993 (synopsis "Call R from R")
995 "It is sometimes useful to perform a computation in a separate R process,
996 without affecting the current R process at all. This package does exactly
998 (license license:expat)))
1000 (define-public r-readxl
1007 (uri (cran-uri "readxl" version))
1010 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
1011 (build-system r-build-system)
1013 `(("r-cellranger" ,r-cellranger)
1014 ("r-progress" ,r-progress)
1016 ("r-tibble" ,r-tibble)))
1017 (home-page "https://readxl.tidyverse.org")
1018 (synopsis "Read Excel files")
1020 "This package lets you import Excel files into R. It supports
1021 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
1022 the embedded @code{RapidXML} C++ library.")
1023 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
1024 ;; 'rapidxml' which is Boost.
1025 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
1027 (define-public r-modelr
1034 (uri (cran-uri "modelr" version))
1037 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
1038 (build-system r-build-system)
1040 `(("r-broom" ,r-broom)
1041 ("r-magrittr" ,r-magrittr)
1042 ("r-purrr" ,r-purrr)
1043 ("r-rlang" ,r-rlang)
1044 ("r-tibble" ,r-tibble)
1045 ("r-tidyr" ,r-tidyr)
1046 ("r-tidyselect" ,r-tidyselect)
1047 ("r-vctrs" ,r-vctrs)))
1048 (home-page "https://github.com/tidyverse/modelr")
1049 (synopsis "Helper functions for modelling in pipelines")
1051 "Functions for modelling that help you seamlessly integrate modelling
1052 into a pipeline of data manipulation and visualisation.")
1053 (license license:gpl3)))
1055 (define-public r-httpuv
1061 (uri (cran-uri "httpuv" version))
1064 "05rir03xwamwfq5691vx0x957sgmr4i8iv5vpx5rv1f74y4wkrhb"))
1065 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
1066 ;; only contains fixes for building on Solaris.
1067 (patches (search-patches "r-httpuv-1.5.5-unvendor-libuv.patch"))
1068 (modules '((guix build utils)))
1071 (delete-file-recursively "src/libuv")
1072 ;; Cannot unbundle http-parser, because it contains local
1075 (build-system r-build-system)
1078 (modify-phases %standard-phases
1079 (add-after 'unpack 'unbundle-libuv
1080 (lambda* (#:key outputs #:allow-other-keys)
1081 (substitute* (find-files "src" "\\.cpp$|\\.h$")
1082 (("\"libuv/include/uv\\.h\"")
1084 ;; Fix https://github.com/rstudio/httpuv/issues/282
1085 (substitute* "src/http.cpp"
1086 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
1087 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);"))
1090 `(("libuv" ,libuv)))
1093 ("r-later" ,r-later)
1094 ("r-promises" ,r-promises)
1096 ("r-rcpp" ,r-rcpp)))
1097 (home-page "https://github.com/rstudio/httpuv")
1098 (synopsis "HTTP and WebSocket server library for R")
1100 "The httpuv package provides low-level socket and protocol support for
1101 handling HTTP and WebSocket requests directly from within R. It is primarily
1102 intended as a building block for other packages, rather than making it
1103 particularly easy to create complete web applications using httpuv alone.")
1104 ;; This package includes third-party code that was originally released
1105 ;; under various non-copyleft licenses. Full licensing information can be
1106 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
1107 (license license:gpl3+)))
1109 (define-public r-jsonlite
1115 (uri (cran-uri "jsonlite" version))
1118 "1lhzcpz9clwq04i5m6jzkvw9x03pwlqrixv4l9xzchjr8d84nd86"))))
1119 (build-system r-build-system)
1121 `(("r-knitr" ,r-knitr)))
1122 (home-page "https://arxiv.org/abs/1403.2805")
1123 (synopsis "Robust, high performance JSON parser and generator for R")
1125 "The jsonlite package provides a fast JSON parser and generator optimized
1126 for statistical data and the web. It offers flexible, robust, high
1127 performance tools for working with JSON in R and is particularly powerful for
1128 building pipelines and interacting with a web API. In addition to converting
1129 JSON data from/to R objects, jsonlite contains functions to stream, validate,
1130 and prettify JSON data. The unit tests included with the package verify that
1131 all edge cases are encoded and decoded consistently for use with dynamic data
1132 in systems and applications.")
1133 (license license:expat)))
1135 (define-public r-servr
1141 (uri (cran-uri "servr" version))
1144 "12fk585hmz735v4hra8da9wld1fmd67byqnf95m7jjyh7l3dmh1z"))))
1145 (build-system r-build-system)
1147 `(("r-httpuv" ,r-httpuv)
1148 ("r-jsonlite" ,r-jsonlite)
1150 ("r-xfun" ,r-xfun)))
1151 (home-page "https://github.com/yihui/servr")
1152 (synopsis "Simple HTTP server to serve static files or dynamic documents")
1154 "Servr provides an HTTP server in R to serve static files, or dynamic
1155 documents that can be converted to HTML files (e.g., R Markdown) under a given
1157 (license license:expat)))
1159 (define-public r-htmltools
1161 (name "r-htmltools")
1165 (uri (cran-uri "htmltools" version))
1168 "1fm4cymz4hz6lds80m9j5q00xy5flkrmfn5dkrn3s3rkzqpyggzh"))))
1169 (build-system r-build-system)
1171 `(("r-base64enc" ,r-base64enc)
1172 ("r-digest" ,r-digest)
1173 ("r-rlang" ,r-rlang)))
1174 (home-page "https://cran.r-project.org/web/packages/htmltools")
1175 (synopsis "R tools for HTML")
1177 "This package provides tools for HTML generation and output in R.")
1178 (license license:expat)))
1180 (define-public r-htmlwidgets
1182 (name "r-htmlwidgets")
1186 (uri (cran-uri "htmlwidgets" version))
1189 "0a8g7wqd3qxnhwkm9c9bkzg29db7gvjiaa5y038ln8nch8qq7981"))))
1190 (build-system r-build-system)
1192 `(("r-htmltools" ,r-htmltools)
1193 ("r-jsonlite" ,r-jsonlite)
1194 ("r-yaml" ,r-yaml)))
1196 `(("r-knitr" ,r-knitr)))
1197 (home-page "https://github.com/ramnathv/htmlwidgets")
1198 (synopsis "HTML Widgets for R")
1200 "HTML widgets is a framework for creating HTML widgets that render in
1201 various contexts including the R console, R Markdown documents, and Shiny web
1203 (license license:expat)))
1205 (define-public r-htmltable
1207 (name "r-htmltable")
1212 (uri (cran-uri "htmlTable" version))
1214 (base32 "1gzh0bdxi55p1ckxv4k0a41b1j0grwv2w3lkqz4c3gkw66dk6ja0"))))
1215 (properties `((upstream-name . "htmlTable")))
1216 (build-system r-build-system)
1218 `(("r-checkmate" ,r-checkmate)
1219 ("r-htmltools" ,r-htmltools)
1220 ("r-htmlwidgets" ,r-htmlwidgets)
1221 ("r-knitr" ,r-knitr)
1222 ("r-magrittr" ,r-magrittr)
1223 ("r-rstudioapi" ,r-rstudioapi)
1224 ("r-stringr" ,r-stringr)))
1226 `(("r-knitr" ,r-knitr)))
1227 (home-page "http://gforge.se/packages/")
1228 (synopsis "Advanced tables for Markdown/HTML")
1230 "This package provides functions to build tables with advanced layout
1231 elements such as row spanners, column spanners, table spanners, zebra
1232 striping, and more. While allowing advanced layout, the underlying
1233 CSS-structure is simple in order to maximize compatibility with word
1234 processors such as LibreOffice. The package also contains a few text
1235 formatting functions that help outputting text compatible with HTML or
1237 (license license:gpl3+)))
1239 (define-public r-curl
1245 (uri (cran-uri "curl" version))
1248 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
1249 (build-system r-build-system)
1252 (modify-phases %standard-phases
1253 ;; The environment variable CURL_CA_BUNDLE is only respected when
1254 ;; running Windows, so we disable the platform checks.
1255 ;; This can be removed once the libcurl has been patched.
1256 (add-after 'unpack 'allow-CURL_CA_BUNDLE
1258 (substitute* "R/onload.R"
1259 (("if \\(!grepl\\(\"mingw\".*")
1261 (substitute* "src/handle.c"
1262 (("/\\* Only set" m)
1264 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
1265 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
1272 `(("pkg-config" ,pkg-config)))
1273 (home-page "https://github.com/jeroenooms/curl")
1274 (synopsis "HTTP client for R")
1276 "The @code{curl()} and @code{curl_download()} functions provide highly
1277 configurable drop-in replacements for base @code{url()} and
1278 @code{download.file()} with better performance, support for encryption, gzip
1279 compression, authentication, and other @code{libcurl} goodies. The core of
1280 the package implements a framework for performing fully customized requests
1281 where data can be processed either in memory, on disk, or streaming via the
1282 callback or connection interfaces.")
1283 (license license:expat)))
1285 (define-public r-hwriter
1292 (uri (cran-uri "hwriter" version))
1295 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
1296 (build-system r-build-system)
1297 (home-page "https://cran.r-project.org/web/packages/hwriter")
1298 (synopsis "Output R objects in HTML format")
1300 "This package provides easy-to-use and versatile functions to output R
1301 objects in HTML format.")
1302 (license license:lgpl2.1+)))
1304 (define-public r-rjson
1311 (uri (cran-uri "rjson" version))
1314 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
1315 (build-system r-build-system)
1316 (home-page "https://cran.r-project.org/web/packages/rjson")
1317 (synopsis "JSON library for R")
1319 "This package provides functions to convert R objects into JSON objects
1321 (license license:gpl2+)))
1323 (define-public r-fastmap
1330 (uri (cran-uri "fastmap" version))
1333 "0aw29hnq3ppn7bsnwg9d9sp84k1cvq30lrmfzqn315n0nhkfa4wi"))))
1334 (properties `((upstream-name . "fastmap")))
1335 (build-system r-build-system)
1336 (home-page "https://r-lib.github.io/fastmap/")
1337 (synopsis "Fast implementation of a key-value store")
1339 "This package provides a fast implementation of a key-value store.
1340 Environments are commonly used as key-value stores, but every time a new key
1341 is used, it is added to R's global symbol table, causing a small amount of
1342 memory leakage. This can be problematic in cases where many different keys
1343 are used. Fastmap avoids this memory leak issue by implementing the map using
1344 data structures in C++.")
1345 (license license:expat)))
1347 (define-public r-fastghquad
1349 (name "r-fastghquad")
1354 (uri (cran-uri "fastGHQuad" version))
1357 "1rjia8wggadr9xwxcmzmal0rc4g6pa3dr5888fbbnb6abl8b2lrj"))))
1358 (properties `((upstream-name . "fastGHQuad")))
1359 (build-system r-build-system)
1361 `(("r-rcpp" ,r-rcpp)))
1362 (home-page "https://github.com/awblocker/fastGHQuad")
1363 (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature")
1365 "This package implements numerically-stable Gauss-Hermite quadrature
1366 rules and utility functions for adaptive GH quadrature.")
1367 (license license:expat)))
1369 (define-public r-rstpm2
1376 (uri (cran-uri "rstpm2" version))
1379 "0c6l3z250b2kn6mh2xyb0bd2y5nsbj11n9xfi51dac9s8xq3v7m4"))))
1380 (properties `((upstream-name . "rstpm2")))
1381 (build-system r-build-system)
1383 `(("r-bbmle" ,r-bbmle)
1385 ("r-desolve" ,r-desolve)
1386 ("r-fastghquad" ,r-fastghquad)
1389 ("r-rcpparmadillo" ,r-rcpparmadillo)
1390 ("r-survival" ,r-survival)))
1392 `(("gfortran" ,gfortran)))
1393 (home-page "https://github.com/mclements/rstpm2")
1394 (synopsis "Link-based survival models")
1396 "This package provides R implementations of @dfn{generalized survival
1397 models} (GSMs), smooth @dfn{accelerated failure time} (AFT) models and Markov
1398 multi-state models.")
1399 ;; One of these licenses
1400 (license (list license:gpl2 license:gpl3))))
1402 ;; This package includes minified JavaScript files. When upgrading please
1403 ;; check that there are no new minified JavaScript files.
1404 (define-public r-jquerylib
1406 (name "r-jquerylib")
1411 (uri (cran-uri "jquerylib" version))
1414 "1s0d6mws13hwkx07jqmry7vp30a05b2p9w7ir68bmkhasidwkzdq"))
1416 '(for-each delete-file
1417 '("inst/lib/jquery-1.12.4.min.js"
1418 "inst/lib/jquery-2.2.4.min.js"
1419 "inst/lib/jquery-3.5.1.min.js")))))
1420 (properties `((upstream-name . "jquerylib")))
1421 (build-system r-build-system)
1423 `(#:modules ((guix build utils)
1424 (guix build r-build-system)
1427 (modify-phases %standard-phases
1428 (add-after 'unpack 'process-javascript
1429 (lambda* (#:key inputs #:allow-other-keys)
1430 (with-directory-excursion "inst/lib/"
1434 `(("jquery-1.12.4.js"
1435 "jquery-1.12.4.min.js")
1437 "jquery-2.2.4.min.js")
1439 "jquery-3.5.1.min.js"))))
1440 (lambda (sources targets)
1441 (for-each (lambda (source target)
1442 (format #t "Processing ~a --> ~a~%"
1444 (invoke "esbuild" source "--minify"
1445 (string-append "--outfile=" target)))
1446 sources targets)))))))))
1448 `(("r-htmltools" ,r-htmltools)))
1450 `(("esbuild" ,esbuild)))
1451 (home-page "https://cran.r-project.org/package=jquerylib")
1452 (synopsis "Obtain jQuery as an HTML dependency object")
1454 "Obtain any major version of jQuery and use it in any webpage generated
1455 by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't
1456 need to use this package directly, but other R packages (e.g. shiny,
1457 rmarkdown, etc.) depend on this package to avoid bundling redundant copies of
1459 (license license:expat)))
1461 (define-public r-sass
1468 (uri (cran-uri "sass" version))
1471 "1cxqwsdyz71mgflqqa65mfr161jlv8q9mshs1y19pxp6pz5wnv0s"))))
1472 (properties `((upstream-name . "sass")))
1473 (build-system r-build-system)
1475 `(("r-digest" ,r-digest)
1477 ("r-htmltools" ,r-htmltools)
1479 ("r-rappdirs" ,r-rappdirs)
1480 ("r-rlang" ,r-rlang)))
1481 (native-inputs `(("r-knitr" ,r-knitr)))
1482 (home-page "https://github.com/rstudio/sass")
1483 (synopsis "Syntactically Awesome Style Sheets (SASS)")
1485 "This package provides an SCSS compiler, powered by the libsass library.
1486 With this, R developers can use variables, inheritance, and functions to
1487 generate dynamic style sheets. The package uses the Sass CSS extension
1488 language, which is stable, powerful, and CSS compatible.")
1489 (license license:expat)))
1491 ;; This package includes minified JavaScript files. When upgrading please
1492 ;; check that there are no new minified JavaScript files.
1493 (define-public r-bslib
1500 (uri (cran-uri "bslib" version))
1503 "0qlpv2lqr3hjykszmnll7vi4zhmrz4rgcfl0sifxc6cha6jy2nac"))
1505 '(for-each delete-file
1506 '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js"
1507 "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js"
1508 "inst/lib/bs-sass/assets/javascripts/bootstrap.min.js"
1509 "inst/lib/bs/dist/js/bootstrap.bundle.min.js")))))
1510 (properties `((upstream-name . "bslib")))
1511 (build-system r-build-system)
1513 `(#:modules ((guix build utils)
1514 (guix build r-build-system)
1517 (modify-phases %standard-phases
1518 (add-after 'unpack 'process-javascript
1519 (lambda* (#:key inputs #:allow-other-keys)
1520 (with-directory-excursion "inst/lib/"
1524 `(("bs-a11y-p/plugins/js/bootstrap-accessibility.js"
1525 "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js")
1526 ("bs-colorpicker/js/bootstrap-colorpicker.js"
1527 "bs-colorpicker/js/bootstrap-colorpicker.min.js")
1528 ("bs-sass/assets/javascripts/bootstrap.js"
1529 "bs-sass/assets/javascripts/bootstrap.min.js")
1530 (,(assoc-ref inputs "js-bootstrap-bundle")
1531 "bs/dist/js/bootstrap.bundle.min.js"))))
1532 (lambda (sources targets)
1533 (for-each (lambda (source target)
1534 (format #t "Processing ~a --> ~a~%"
1536 (invoke "esbuild" source "--minify"
1537 (string-append "--outfile=" target)))
1538 sources targets)))))))))
1540 `(("r-digest" ,r-digest)
1541 ("r-htmltools" ,r-htmltools)
1542 ("r-jquerylib" ,r-jquerylib)
1543 ("r-jsonlite" ,r-jsonlite)
1544 ("r-magrittr" ,r-magrittr)
1545 ("r-rlang" ,r-rlang)
1546 ("r-sass" ,r-sass)))
1548 `(("esbuild" ,esbuild)
1549 ("js-bootstrap-bundle"
1552 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.5.3/dist/js/bootstrap.bundle.js")
1555 "1lcsxj7gcm56va3gck47ggpwzjxrzq27sgjzdw6c54qkp0487sak"))))))
1556 (home-page "https://rstudio.github.io/bslib/")
1557 (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown")
1559 "This package simplifies custom CSS styling of both shiny and rmarkdown
1560 via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their
1561 various Bootswatch themes. An interactive widget is also provided for
1562 previewing themes in real time.")
1563 (license license:expat)))
1565 ;; This package includes minified JavaScript files. When upgrading please
1566 ;; check that there are no new minified JavaScript files.
1567 (define-public r-shiny
1575 (url "https://github.com/rstudio/shiny")
1576 (commit (string-append "v" version))))
1577 (file-name (git-file-name name version))
1580 "0f6cwx5xyqzs40msq271sqhwl8736rwbm7kd1ldkcvxngzr4vlx9"))
1582 '(for-each delete-file
1583 '("inst/www/shared/bootstrap/js/bootstrap.min.js"
1584 "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO
1585 "inst/www/shared/datatables/js/jquery.dataTables.min.js"
1586 "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js"
1587 "inst/www/shared/highlight/highlight.pack.js"
1588 "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js"
1589 "inst/www/shared/jquery.min.js"
1590 "inst/www/shared/jqueryui/jquery-ui.min.js"
1591 "inst/www/shared/legacy/jquery.min.js"
1592 "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js"
1593 "inst/www/shared/selectize/js/selectize.min.js"
1594 "inst/www/shared/shiny.min.js"
1595 "inst/www/shared/showdown/compressed/showdown.js"
1596 "inst/www/shared/strftime/strftime-min.js")))))
1597 (build-system r-build-system)
1599 `(#:modules ((guix build r-build-system)
1600 (guix build minify-build-system)
1603 #:imported-modules (,@%r-build-system-modules
1604 (guix build minify-build-system))
1606 (modify-phases (@ (guix build r-build-system) %standard-phases)
1607 (add-after 'unpack 'replace-bundled-minified-JavaScript
1608 (lambda* (#:key inputs #:allow-other-keys)
1609 (let ((replace-file (lambda (old new)
1610 (format #t "replacing ~a with ~a\n" old new)
1611 (symlink new old))))
1612 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
1613 ;; contain just data. They are not minified code, so we don't
1615 (with-directory-excursion "inst/www/shared"
1616 (replace-file "strftime/strftime-min.js"
1617 (string-append (assoc-ref inputs "js-strftime")
1618 "/share/javascript/strftime.min.js"))
1619 (replace-file "highlight/highlight.pack.js"
1620 (string-append (assoc-ref inputs "js-highlight")
1621 "/share/javascript/highlight.min.js"))
1622 (replace-file "datatables/js/jquery.dataTables.min.js"
1623 (string-append (assoc-ref inputs "js-datatables")
1624 "/share/javascript/jquery.dataTables.min.js"))
1625 (replace-file "selectize/js/selectize.min.js"
1626 (string-append (assoc-ref inputs "js-selectize")
1627 "/share/javascript/selectize.min.js"))
1628 (for-each (match-lambda
1630 (minify source #:target target)))
1631 `(("jqueryui/jquery-ui.js" .
1632 "jqueryui/jquery-ui.min.js")
1633 ("datepicker/js/bootstrap-datepicker.js" .
1634 "datepicker/js/bootstrap-datepicker.min.js")
1635 ("ionrangeslider/js/ion.rangeSlider.js" .
1636 "ionrangeslider/js/ion.rangeSlider.min.js")
1637 ("bootstrap/js/bootstrap.js" .
1638 "bootstrap/js/bootstrap.min.js")
1639 (,(assoc-ref inputs "js-bootstrap-accessibility") .
1640 "bootstrap/accessibility/js/bootstrap-accessibility.min.js")
1645 ("legacy/jquery.js" .
1646 "legacy/jquery.min.js")
1647 ("selectize/accessibility/js/selectize-plugin-a11y.js" .
1648 "selectize/accessibility/js/selectize-plugin-a11y.min.js")
1649 ("showdown/src/showdown.js" .
1650 "showdown/compressed/showdown.js"))))))))))
1652 `(("r-bslib" ,r-bslib)
1653 ("r-cachem" ,r-cachem)
1654 ("r-commonmark" ,r-commonmark)
1655 ("r-crayon" ,r-crayon)
1656 ("r-digest" ,r-digest)
1657 ("r-ellipsis" ,r-ellipsis)
1658 ("r-fastmap" ,r-fastmap)
1660 ("r-htmltools" ,r-htmltools)
1661 ("r-httpuv" ,r-httpuv)
1662 ("r-jsonlite" ,r-jsonlite)
1663 ("r-later" ,r-later)
1664 ("r-lifecycle" ,r-lifecycle)
1666 ("r-promises" ,r-promises)
1668 ("r-rlang" ,r-rlang)
1669 ("r-sourcetools" ,r-sourcetools)
1670 ("r-withr" ,r-withr)
1671 ("r-xtable" ,r-xtable)))
1673 `(("js-datatables" ,js-datatables)
1674 ("js-selectize" ,js-selectize)
1675 ("js-strftime" ,js-strftime)
1676 ("js-highlight" ,js-highlight)))
1678 `(("uglify-js" ,uglify-js)
1679 ("gfortran" ,gfortran)
1680 ("js-bootstrap-accessibility"
1683 (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\
1684 v1.0.7/_site/plugins/js/bootstrap-accessibility.js")
1687 "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8"))))))
1688 (home-page "https://shiny.rstudio.com")
1689 (synopsis "Easy interactive web applications with R")
1691 "Makes it incredibly easy to build interactive web applications
1692 with R. Automatic \"reactive\" binding between inputs and outputs and
1693 extensive prebuilt widgets make it possible to build beautiful,
1694 responsive, and powerful applications with minimal effort.")
1695 (license license:artistic2.0)))
1697 ;; This package includes minified JavaScript files. When upgrading please
1698 ;; check that there are no new minified JavaScript files.
1699 (define-public r-shinytree
1701 (name "r-shinytree")
1706 (uri (cran-uri "shinyTree" version))
1709 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1710 (modules '((guix build utils)))
1713 ;; Delete minified JavaScript
1714 (for-each delete-file
1715 '("inst/www/jsTree-3.3.7/libs/require.js"
1716 "inst/www/jsTree-3.3.7/libs/jquery.js"
1717 "inst/www/jsTree-3.3.7/jstree.min.js"))
1719 (properties `((upstream-name . "shinyTree")))
1720 (build-system r-build-system)
1722 `(#:modules ((guix build utils)
1723 (guix build r-build-system)
1727 (modify-phases %standard-phases
1728 (add-after 'unpack 'replace-minified-javascript
1729 (lambda* (#:key inputs #:allow-other-keys)
1730 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1731 (symlink (string-append (assoc-ref inputs "js-requirejs")
1732 "/share/javascript/require.min.js")
1737 `((,(assoc-ref inputs "js-jquery")
1741 (lambda (sources targets)
1742 (for-each (lambda (source target)
1743 (format #t "Processing ~a --> ~a~%"
1745 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1746 (call-with-output-file target
1748 (dump-port minified port)))))
1752 `(("r-htmlwidgets" ,r-htmlwidgets)
1753 ("r-jsonlite" ,r-jsonlite)
1754 ("r-promises" ,r-promises)
1755 ("r-shiny" ,r-shiny)
1756 ("r-stringr" ,r-stringr)))
1758 `(("js-requirejs" ,js-requirejs)))
1760 `(("uglify-js" ,uglify-js)
1764 (uri "https://code.jquery.com/jquery-3.3.1.js")
1767 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1768 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1769 (synopsis "jsTree bindings for Shiny")
1771 "This package exposes R bindings to jsTree, a JavaScript library that
1772 supports interactive trees, to enable rich, editable trees in Shiny.")
1773 (license license:expat)))
1775 (define-public r-shinydashboard
1777 (name "r-shinydashboard")
1781 (uri (cran-uri "shinydashboard" version))
1784 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1785 (build-system r-build-system)
1786 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1787 ;; Regenerate it from the included sources.
1789 `(#:modules ((guix build utils)
1790 (guix build r-build-system)
1793 (modify-phases %standard-phases
1794 (add-after 'unpack 'generate-minified-javascript
1796 (with-directory-excursion "inst/AdminLTE"
1797 (delete-file "app.min.js")
1798 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1799 (call-with-output-file "app.min.js"
1801 (dump-port minified port))))))))))
1803 `(("r-htmltools" ,r-htmltools)
1804 ("r-promises" ,r-promises)
1805 ("r-shiny" ,r-shiny)))
1807 `(("uglify-js" ,uglify-js)))
1808 (home-page "https://rstudio.github.io/shinydashboard/")
1809 (synopsis "Create dashboards with shiny")
1810 (description "This package provides an extension to the Shiny web
1811 application framework for R, making it easy to create attractive dashboards.")
1812 ;; This package includes software that was released under the Expat
1813 ;; license, but the whole package is released under GPL version 2 or
1815 (license license:gpl2+)))
1817 (define-public r-shinyfiles
1819 (name "r-shinyfiles")
1824 (uri (cran-uri "shinyFiles" version))
1826 (base32 "0rsijlx16vd74r7bd8s9zipy71kgpw19v9s85kxj5bmwc6njmbai"))))
1827 (properties `((upstream-name . "shinyFiles")))
1828 (build-system r-build-system)
1831 ("r-htmltools" ,r-htmltools)
1832 ("r-jsonlite" ,r-jsonlite)
1833 ("r-shiny" ,r-shiny)
1834 ("r-tibble" ,r-tibble)))
1835 (home-page "https://github.com/thomasp85/shinyFiles")
1836 (synopsis "Server-side file system viewer for Shiny")
1838 "This package provides functionality for client-side navigation of the
1839 server side file system in shiny apps. In case the app is running locally
1840 this gives the user direct access to the file system without the need to
1841 \"download\" files to a temporary location. Both file and folder selection as
1842 well as file saving is available.")
1843 (license license:gpl2+)))
1845 (define-public r-shinythemes
1847 (name "r-shinythemes")
1852 (uri (cran-uri "shinythemes" version))
1855 "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip"))))
1856 (properties `((upstream-name . "shinythemes")))
1857 (build-system r-build-system)
1858 (propagated-inputs `(("r-shiny" ,r-shiny)))
1859 (home-page "https://rstudio.github.io/shinythemes/")
1860 (synopsis "Themes for Shiny")
1862 "This package provides themes for use with Shiny. It includes several
1863 Bootstrap themes, which are packaged for use with Shiny applications.")
1864 ;; The package is released under version 3 of the GPL, but it includes
1865 ;; source files that are covered by the Expat license. It also includes
1866 ;; fonts under SIL or the ASL.
1867 (license (list license:gpl3 license:expat
1868 license:silofl1.1 license:asl2.0))))
1870 ;; The package sources include minified variants of d3.js and non-minified
1871 ;; source code of d3-jetpack.
1872 (define-public r-d3r
1879 (uri (cran-uri "d3r" version))
1882 "0kc82vvyfxhxvqfalngn36prn3sxdiinsx04rn99ha6zdc27zp5k"))))
1883 (build-system r-build-system)
1885 `(#:modules ((guix build utils)
1886 (guix build r-build-system)
1889 (modify-phases %standard-phases
1890 (add-after 'unpack 'process-javascript
1891 (lambda* (#:key inputs #:allow-other-keys)
1892 (with-directory-excursion "inst/www/d3/"
1896 `((,(assoc-ref inputs "d3.v3.js")
1897 "v3/dist/d3.min.js")
1898 (,(assoc-ref inputs "d3.v4.js")
1899 "v4/dist/d3.min.js")
1900 (,(assoc-ref inputs "d3.v5.js")
1901 "v5/dist/d3.min.js")
1902 (,(assoc-ref inputs "d3.v6.js")
1903 "v6/dist/d3.min.js"))))
1904 (lambda (sources targets)
1905 (for-each (lambda (source target)
1906 (format #t "Processing ~a --> ~a~%"
1908 (delete-file target)
1909 (invoke "esbuild" source "--minify"
1910 (string-append "--outfile=" target)))
1914 `(("r-dplyr" ,r-dplyr)
1915 ("r-htmltools" ,r-htmltools)
1916 ("r-rlang" ,r-rlang)
1917 ("r-tidyr" ,r-tidyr)))
1919 `(("esbuild" ,esbuild)
1923 (uri "https://d3js.org/d3.v3.js")
1926 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1930 (uri "https://d3js.org/d3.v4.js")
1933 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1937 (uri "https://d3js.org/d3.v5.js")
1940 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))
1944 (uri "https://d3js.org/d3.v6.js")
1947 "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9"))))))
1948 (home-page "https://github.com/timelyportfolio/d3r")
1949 (synopsis "d3.js utilities for R")
1951 "This package provides a suite of functions to help ease the use of the
1952 d3.js visualization library in R. These helpers include
1953 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1954 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1955 R objects into the JSON format that the d3.js library expects.")
1956 (license license:bsd-3)))
1958 ;; We use the latest commit here because the last release was in 2016 while
1959 ;; the latest commit was in 2018.
1960 (define-public r-sankeyd3
1961 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1965 (version (git-version "0.3.2" revision commit))
1970 (url "https://github.com/fbreitwieser/sankeyD3")
1972 (file-name (git-file-name name version))
1975 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1976 (build-system r-build-system)
1979 ("r-htmlwidgets" ,r-htmlwidgets)
1980 ("r-shiny" ,r-shiny)
1981 ("r-magrittr" ,r-magrittr)))
1982 (home-page "https://github.com/fbreitwieser/sankeyD3")
1983 (synopsis "Sankey network graphs from R")
1985 "This package provides an R library to generate Sankey network graphs
1986 in R and Shiny via the D3 visualization library.")
1987 ;; The R code is licensed under GPLv3+. It includes the non-minified
1988 ;; JavaScript source code of d3-sankey, which is released under the
1989 ;; 3-clause BSD license.
1990 (license (list license:gpl3+ license:bsd-3)))))
1992 (define-public r-wesanderson
1994 (name "r-wesanderson")
1999 (uri (cran-uri "wesanderson" version))
2002 "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
2003 (properties `((upstream-name . "wesanderson")))
2004 (build-system r-build-system)
2005 (home-page "https://github.com/karthik/wesanderson")
2006 (synopsis "Wes Anderson color palette generator")
2008 "This package provides color palettes that have been generated mostly
2009 from Wes Anderson movies.")
2010 (license license:expat)))
2012 (define-public r-gg-gap
2019 (uri (cran-uri "gg.gap" version))
2022 "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h"))))
2023 (properties `((upstream-name . "gg.gap")))
2024 (build-system r-build-system)
2026 `(("r-cowplot" ,r-cowplot)
2027 ("r-ggplot2" ,r-ggplot2)))
2028 (home-page "https://github.com/ChrisLou-bioinfo/gg.gap")
2029 (synopsis "Define segments on the y-axis for ggplot2")
2031 "The @code{gg.gap} function enables you to define segments for the y-axis
2032 in a ggplot2 plot.")
2033 (license license:gpl3)))
2035 (define-public r-tablerdash
2037 (name "r-tablerdash")
2042 (uri (cran-uri "tablerDash" version))
2045 "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm"))
2048 ;; Delete minified JavaScript
2049 (for-each delete-file
2050 '("inst/tablerDash-0.1.0/require.min.js"
2051 "inst/bootstrap-4.0.0/bootstrap.bundle.min.js"))
2053 (properties `((upstream-name . "tablerDash")))
2054 (build-system r-build-system)
2056 `(#:modules ((guix build utils)
2057 (guix build r-build-system)
2060 (modify-phases %standard-phases
2061 (add-after 'unpack 'process-javascript
2062 (lambda* (#:key inputs #:allow-other-keys)
2063 (with-directory-excursion "inst"
2067 `((,(assoc-ref inputs "js-requirejs")
2068 "tablerDash-0.1.0/require.min.js")
2069 (,(assoc-ref inputs "js-bootstrap")
2070 "bootstrap-4.0.0/bootstrap.bundle.min.js"))))
2071 (lambda (sources targets)
2072 (for-each (lambda (source target)
2073 (format #t "Processing ~a --> ~a~%"
2075 (invoke "esbuild" source "--minify"
2076 (string-append "--outfile=" target)))
2080 `(("r-htmltools" ,r-htmltools)
2081 ("r-knitr" ,r-knitr)
2082 ("r-shiny" ,r-shiny)))
2084 `(("esbuild" ,esbuild)
2088 (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js")
2091 "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds"))))
2095 (uri "https://raw.githubusercontent.com/twbs/bootstrap/\
2096 v4.0.0/dist/js/bootstrap.bundle.js")
2099 "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj"))))))
2100 (home-page "https://rinterface.github.io/tablerDash/")
2101 (synopsis "Tabler API for Shiny")
2103 "This package provides an R interface to the
2104 @url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap
2105 4 dashboard template. There are different layouts available such as a one
2106 page dashboard or a multi-page template, where the navigation menu is
2107 contained in the navigation bar.")
2108 (license license:gpl2+)))
2110 (define-public r-spelling
2117 (uri (cran-uri "spelling" version))
2120 "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl"))))
2121 (properties `((upstream-name . "spelling")))
2122 (build-system r-build-system)
2124 `(("r-commonmark" ,r-commonmark)
2125 ("r-hunspell" ,r-hunspell)
2126 ("r-knitr" ,r-knitr)
2127 ("r-xml2" ,r-xml2)))
2128 (home-page "https://docs.ropensci.org/spelling/")
2129 (synopsis "Tools for spell checking in R")
2131 "This is an R package for spell checking common document formats
2132 including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes
2133 utilities to automate checking of documentation and vignettes as a unit test
2134 during @code{R CMD check}. Both British and American English are supported
2135 out of the box and other languages can be added. In addition, packages may
2136 define a wordlist to allow custom terminology without having to abuse
2138 (license license:expat)))
2140 (define-public r-crosstalk
2142 (name "r-crosstalk")
2147 (uri (cran-uri "crosstalk" version))
2150 "1n6c6s7a6yxiwvva71x6bzcrim8xprl5s01fqiy61yq0y3vk8cpd"))))
2151 (build-system r-build-system)
2153 `(("r-htmltools" ,r-htmltools)
2154 ("r-jsonlite" ,r-jsonlite)
2155 ("r-lazyeval" ,r-lazyeval)
2157 (home-page "https://rstudio.github.io/crosstalk/")
2158 (synopsis "Inter-widget interactivity for HTML widgets")
2160 "This package provides building blocks for allowing HTML widgets to
2161 communicate with each other, with Shiny or without (i.e. static @code{.html}
2162 files). It currently supports linked brushing and filtering.")
2163 (license license:expat)))
2165 (define-public r-rook
2172 (uri (cran-uri "Rook" version))
2175 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
2176 (properties `((upstream-name . "Rook")))
2177 (build-system r-build-system)
2178 (propagated-inputs `(("r-brew" ,r-brew)))
2179 (home-page "https://cran.r-project.org/web/packages/Rook")
2180 (synopsis "Web server interface for R")
2182 "This package contains the Rook specification and convenience software
2183 for building and running Rook applications. A Rook application is an R
2184 reference class object that implements a @code{call} method or an R closure
2185 that takes exactly one argument, an environment, and returns a list with three
2186 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
2187 (license license:gpl2)))
2189 (define-public r-miniui
2196 (uri (cran-uri "miniUI" version))
2199 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
2200 (properties `((upstream-name . "miniUI")))
2201 (build-system r-build-system)
2203 `(("r-htmltools" ,r-htmltools)
2204 ("r-shiny" ,r-shiny)))
2205 (home-page "https://cran.r-project.org/web/packages/miniUI/")
2206 (synopsis "Shiny UI widgets for small screens")
2208 "This package provides UI widget and layout functions for writing Shiny apps that
2209 work well on small screens.")
2210 (license license:gpl3)))
2212 (define-public r-feather
2219 (uri (cran-uri "feather" version))
2222 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
2223 (build-system r-build-system)
2227 ("r-tibble" ,r-tibble)))
2228 (home-page "https://github.com/wesm/feather")
2229 (synopsis "R Bindings to the Feather API")
2230 (description "Read and write feather files, a lightweight binary columnar
2231 data store designed for maximum speed.")
2232 (license license:asl2.0)))
2234 (define-public r-maps
2241 (uri (cran-uri "maps" version))
2244 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
2245 (build-system r-build-system)
2246 (home-page "https://cran.r-project.org/web/packages/maps")
2247 (synopsis "Draw geographical maps")
2248 (description "This package provides an R module for display of maps.
2249 Projection code and larger maps are in separate packages (@code{mapproj} and
2251 (license license:gpl2)))
2253 (define-public r-mapproj
2260 (uri (cran-uri "mapproj" version))
2263 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
2264 (build-system r-build-system)
2265 (propagated-inputs `(("r-maps" ,r-maps)))
2266 (home-page "https://cran.r-project.org/web/packages/mapproj")
2267 (synopsis "Map projection in R")
2268 (description "This package converts latitude/longitude into projected
2270 (license (list license:gpl2 ; The R interface
2271 (license:non-copyleft ; The C code
2272 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
2273 "Lucent Public License Version 1.02")))))
2275 (define-public r-rgooglemaps
2277 (name "r-rgooglemaps")
2282 (uri (cran-uri "RgoogleMaps" version))
2285 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
2286 (properties `((upstream-name . "RgoogleMaps")))
2287 (build-system r-build-system)
2291 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
2292 (synopsis "Use Google Maps in R")
2293 (description "This package serves two purposes:
2295 @item Provide a comfortable R interface to query the Google server for static
2297 @item Use the map as a background image to overlay plots within R. This
2298 requires proper coordinate scaling.
2300 (license license:gpl2+)))
2302 (define-public r-geosphere
2304 (name "r-geosphere")
2309 (uri (cran-uri "geosphere" version))
2312 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
2313 (build-system r-build-system)
2314 (propagated-inputs `(("r-sp" ,r-sp)))
2315 (home-page "https://cran.r-project.org/web/packages/geosphere")
2316 (synopsis "Spherical trigonometry")
2317 (description "This package computes spherical trigonometry for geographic
2318 applications. That is, compute distances and related measures for angular
2319 (longitude/latitude) locations.")
2320 (license license:gpl3+)))
2322 (define-public r-jpeg
2329 (uri (cran-uri "jpeg" version))
2332 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
2333 (build-system r-build-system)
2334 (inputs `(("libjpeg" ,libjpeg-turbo)))
2335 (home-page "https://www.rforge.net/jpeg/")
2336 (synopsis "Read and write JPEG images with R")
2337 (description "This package provides a way to read, write and display
2338 bitmap images stored in the JPEG format with R. It can read and write both
2339 files and in-memory raw vectors.")
2340 (license license:gpl2+)))
2342 (define-public r-ggmap
2349 (uri (cran-uri "ggmap" version))
2352 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
2353 (build-system r-build-system)
2355 `(("r-bitops" ,r-bitops)
2356 ("r-digest" ,r-digest)
2357 ("r-dplyr" ,r-dplyr)
2358 ("r-ggplot2" ,r-ggplot2)
2362 ("r-magrittr" ,r-magrittr)
2365 ("r-purrr" ,r-purrr)
2366 ("r-rgooglemaps" ,r-rgooglemaps)
2367 ("r-rjson" ,r-rjson)
2368 ("r-scales" ,r-scales)
2369 ("r-stringr" ,r-stringr)
2370 ("r-tibble" ,r-tibble)
2371 ("r-tidyr" ,r-tidyr)))
2372 (home-page "https://github.com/dkahle/ggmap")
2373 (synopsis "Spatial visualization with ggplot2")
2374 (description "This package provides a collection of functions to visualize
2375 spatial data and models on top of static maps from various online sources (e.g
2376 Google Maps and Stamen Maps). It includes tools common to those tasks,
2377 including functions for geolocation and routing.")
2378 (license license:gpl2)))
2380 (define-public r-haven
2387 (uri (cran-uri "haven" version))
2390 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))
2391 (modules '((guix build utils)))
2394 ;; unvendor readstat
2395 (delete-file-recursively "src/readstat")
2397 (build-system r-build-system)
2400 (modify-phases %standard-phases
2401 (add-after 'unpack 'unbundle-readstat
2403 ;; Not required, since we’re not building readstat.
2404 (substitute* "src/Makevars"
2405 (("-lz") "-lreadstat"))
2408 `(("readstat" ,readstat)))
2410 `(("r-knitr" ,r-knitr)))
2412 `(("r-forcats" ,r-forcats)
2415 ("r-rlang" ,r-rlang)
2416 ("r-readr" ,r-readr)
2417 ("r-tibble" ,r-tibble)
2418 ("r-tidyselect" ,r-tidyselect)
2419 ("r-vctrs" ,r-vctrs)))
2420 (home-page "https://haven.tidyverse.org")
2421 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
2423 "This package lets you mport foreign statistical formats into R via the
2424 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
2425 (license license:expat)))
2427 (define-public r-amap
2433 (uri (cran-uri "amap" version))
2436 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
2437 (build-system r-build-system)
2439 `(("gfortran" ,gfortran)))
2440 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
2441 (synopsis "Another multidimensional analysis package")
2442 (description "This package provides tools for clustering and principal
2443 component analysis (with robust methods, and parallelized functions).")
2444 (license license:gpl2+)))
2446 (define-public r-ape
2453 (uri (cran-uri "ape" version))
2456 "1r7fwyz30ippcl1ibqiv1xryf44x5crcks5kx19h146ffj76qcgh"))))
2457 (build-system r-build-system)
2459 `(("r-lattice" ,r-lattice)
2461 ("r-rcpp" ,r-rcpp)))
2462 (home-page "http://ape-package.ird.fr/")
2463 (synopsis "Analyses of phylogenetics and evolution")
2465 "This package provides functions for reading, writing, plotting, and
2466 manipulating phylogenetic trees, analyses of comparative data in a
2467 phylogenetic framework, ancestral character analyses, analyses of
2468 diversification and macroevolution, computing distances from DNA sequences,
2469 and several other tools.")
2470 (license license:gpl2+)))
2472 (define-public r-abbyyr
2479 (uri (cran-uri "abbyyR" version))
2482 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
2483 (properties `((upstream-name . "abbyyR")))
2484 (build-system r-build-system)
2486 `(("r-curl" ,r-curl)
2489 ("r-progress" ,r-progress)
2490 ("r-readr" ,r-readr)
2492 (home-page "https://github.com/soodoku/abbyyR")
2493 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
2495 "This package provides tools to get text from images of text using Abbyy
2496 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
2497 OCR images, barcodes, forms, documents with machine readable zones, e.g.
2498 passports and get the results in a variety of formats including plain text and
2499 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
2500 (license license:expat)))
2502 (define-public r-colorspace
2504 (name "r-colorspace")
2509 (uri (cran-uri "colorspace" version))
2511 (base32 "13h1hara0s6xn16bgkrbd0flszah1yiylwfwxwn2inqqk6pm6sjf"))))
2512 (build-system r-build-system)
2514 `(("r-knitr" ,r-knitr)))
2515 (home-page "https://cran.r-project.org/web/packages/colorspace")
2516 (synopsis "Color space manipulation")
2518 "This package carries out a mapping between assorted color spaces
2519 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
2520 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
2521 colors are provided.")
2522 (license license:bsd-3)))
2524 (define-public r-glue
2531 (uri (cran-uri "glue" version))
2534 "1bgpirdvjrf0da734clrixawvpdap4lpda4g89vais96589m8wwz"))))
2535 (build-system r-build-system)
2536 ;; knitr depends on glue, so we can't add knitr here to build the
2540 `(("r-knitr" ,r-knitr)))
2541 (home-page "https://github.com/tidyverse/glue")
2542 (synopsis "Interpreted string literals")
2544 "This package provides an implementation of interpreted string literals,
2545 inspired by Python's Literal String Interpolation (PEP-0498) and
2546 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
2547 (license license:expat)))
2549 (define-public r-palmerpenguins
2551 (name "r-palmerpenguins")
2556 (uri (cran-uri "palmerpenguins" version))
2559 "0q1k3cdkliq7kwrg1n0vs9b6cjwyfarhlgdijhp9c6riy6y5ik7x"))))
2561 `((upstream-name . "palmerpenguins")))
2562 (build-system r-build-system)
2563 (home-page "https://allisonhorst.github.io/palmerpenguins/")
2564 (synopsis "Palmer Archipelago (Antarctica) penguin data")
2566 "This package includes size measurements, clutch observations, and blood
2567 isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins
2568 observed on islands in the Palmer Archipelago near Palmer Station, Antarctica.
2569 Data were collected and made available by Dr. Kristen Gorman and the Palmer
2570 Station Long Term Ecological Research (LTER) Program.")
2571 (license license:cc0)))
2573 (define-public r-pastecs
2579 (uri (cran-uri "pastecs" version))
2582 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
2583 (build-system r-build-system)
2585 `(("r-boot" ,r-boot)))
2586 (home-page "https://github.com/phgrosjean/pastecs")
2587 (synopsis "Analysis of space-time ecological series")
2589 "This package provides functions for regulation, decomposition and analysis
2590 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
2591 initiative to bring PASSTEC 2000 functionalities to R.")
2592 (license license:gpl2+)))
2594 (define-public r-partykit
2600 (uri (cran-uri "partykit" version))
2603 "15bfhqvx2y4vclnc3sw4v7ggs70pk57b3qk9aqjfvdrx444d2gd4"))))
2604 (build-system r-build-system)
2606 `(("r-formula" ,r-formula)
2608 ("r-libcoin" ,r-libcoin)
2609 ("r-mvtnorm" ,r-mvtnorm)
2610 ("r-rpart" ,r-rpart)
2611 ("r-survival" ,r-survival)))
2612 (home-page "http://partykit.R-Forge.R-project.org/partykit")
2613 (synopsis "Toolkit for recursive partytioning")
2615 "This package provides a toolkit with infrastructure for representing,
2616 summarizing, and visualizing tree-structured regression and classification
2618 (license license:gpl2+)))
2620 (define-public r-plogr
2627 (uri (cran-uri "plogr" version))
2630 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
2631 (build-system r-build-system)
2632 (home-page "https://github.com/krlmlr/plogr")
2633 (synopsis "R bindings for the plog C++ logging library")
2635 "This package provides the header files for a stripped-down version of
2636 the plog header-only C++ logging library, and a method to log to R's standard
2638 (license license:expat)))
2640 (define-public r-pls
2647 (uri (cran-uri "pls" version))
2649 (base32 "0b3ls12w19wc4xkhnsgmb333y9lyzwq3syjc3k8zs1agnw59c7cg"))))
2650 (build-system r-build-system)
2651 (home-page "https://mevik.net/work/software/pls.html")
2652 (synopsis "Partial Least Squares and Principal Component Regression")
2654 "The pls package implements multivariate regression methods: Partial Least
2655 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
2656 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
2659 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
2660 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
2661 @item multi-response models (or @dfn{PLS2})
2662 @item flexible cross-validation
2663 @item Jackknife variance estimates of regression coefficients
2664 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
2665 (R)MSEP, R², and correlation loadings
2666 @item formula interface, modelled after @code{lm()}, with methods for predict,
2667 print, summary, plot, update, etc.
2668 @item extraction functions for coefficients, scores, and loadings
2669 @item MSEP, RMSEP, and R² estimates
2670 @item multiplicative scatter correction (@dfn{MSC})
2672 (license license:gpl2)))
2681 (uri (cran-uri "ps" version))
2683 (base32 "0cdzjqgap108whhsilxllg12m2d05pgksryhrz5bq608bvf7vbc9"))))
2684 (build-system r-build-system)
2685 (home-page "https://ps.r-lib.org")
2686 (synopsis "List, query, and manipulate system processes")
2688 "The ps package implements an API to list, query, and manipulate system
2689 processes. Most of its code is based on the @code{psutil} Python package.")
2690 (license license:bsd-3)))
2692 (define-public r-pkgbuild
2699 (uri (cran-uri "pkgbuild" version))
2701 (base32 "0qx920h2viwjg10va81nj0xja495d8ni6vcc25ggvzki6a6k069f"))))
2702 (build-system r-build-system)
2704 `(("r-callr" ,r-callr)
2706 ("r-crayon" ,r-crayon)
2708 ("r-prettyunits" ,r-prettyunits)
2710 ("r-rprojroot" ,r-rprojroot)
2711 ("r-withr" ,r-withr)))
2712 (home-page "https://github.com/r-pkgs/pkgbuild")
2713 (synopsis "Find tools needed to build R packages")
2715 "This package provides functions used to build R packages. It locates
2716 compilers needed to build R packages on various platforms and ensures the PATH
2717 is configured appropriately so R can use them.")
2718 (license license:gpl3)))
2720 (define-public r-pkgload
2727 (uri (cran-uri "pkgload" version))
2730 "185xr79z2vncq62bni7x4qv3p7dxvnfsbdnnglma0a196hz6pj7v"))))
2731 (build-system r-build-system)
2734 ("r-crayon" ,r-crayon)
2736 ("r-pkgbuild" ,r-pkgbuild)
2737 ("r-rlang" ,r-rlang)
2738 ("r-rprojroot" ,r-rprojroot)
2739 ("r-rstudioapi" ,r-rstudioapi)
2740 ("r-withr" ,r-withr)))
2741 (home-page "https://github.com/r-lib/pkgload")
2742 (synopsis "Simulate package installation and attach")
2744 "This package simulates the process of installing a package and then
2745 attaching it. This is a key part of the @code{devtools} package as it allows
2746 you to rapidly iterate while developing a package.")
2747 (license license:gpl3)))
2749 (define-public r-rcpp
2756 (uri (cran-uri "Rcpp" version))
2758 (base32 "04ph6lm36cmvz01ng53pvvf3jxvzsn9smyflkfc7l3q0pib4gwn9"))))
2759 (build-system r-build-system)
2760 (home-page "http://www.rcpp.org")
2761 (synopsis "Seamless R and C++ integration")
2763 "The Rcpp package provides R functions as well as C++ classes which offer
2764 a seamless integration of R and C++. Many R data types and objects can be
2765 mapped back and forth to C++ equivalents which facilitates both writing of new
2766 code as well as easier integration of third-party libraries. Documentation
2767 about Rcpp is provided by several vignettes included in this package, via the
2768 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
2769 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2770 @code{citation(\"Rcpp\")} for details on these last two.")
2771 (license license:gpl2+)))
2773 (define-public r-rcppthread
2775 (name "r-rcppthread")
2780 (uri (cran-uri "RcppThread" version))
2783 "1xfcxrny779kgknlvnc4j02ifprnakndnkhx8bhy50d39vp4hjjl"))))
2784 (properties `((upstream-name . "RcppThread")))
2785 (build-system r-build-system)
2787 "https://github.com/tnagler/RcppThread")
2788 (synopsis "R threading in C++")
2790 "This package provides a C++11-style thread class and thread pool that can
2791 safely be interrupted from R.")
2792 (license license:expat)))
2794 (define-public r-bindr
2801 (uri (cran-uri "bindr" version))
2804 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
2805 (build-system r-build-system)
2806 (home-page "https://github.com/krlmlr/bindr")
2807 (synopsis "Parametrized active bindings")
2809 "This package provides a simple interface for creating active bindings
2810 where the bound function accepts additional arguments.")
2811 (license license:expat)))
2813 (define-public r-bindrcpp
2820 (uri (cran-uri "bindrcpp" version))
2823 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
2824 (build-system r-build-system)
2826 `(("r-bindr" ,r-bindr)
2827 ("r-plogr" ,r-plogr)
2828 ("r-rcpp" ,r-rcpp)))
2829 (home-page "https://github.com/krlmlr/bindrcpp")
2830 (synopsis "Rcpp interface to active bindings")
2832 "This package provides an easy way to fill an environment with active
2833 bindings that call a C++ function.")
2834 (license license:expat)))
2836 (define-public r-bisquerna
2838 (name "r-bisquerna")
2842 (uri (cran-uri "BisqueRNA" version))
2845 "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2"))))
2846 (properties `((upstream-name . "BisqueRNA")))
2847 (build-system r-build-system)
2849 `(("r-biobase" ,r-biobase)
2850 ("r-limsolve" ,r-limsolve)))
2851 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
2852 (synopsis "Decomposition of bulk expression with single-cell sequencing")
2853 (description "This package provides tools to accurately estimate cell type
2854 abundances from heterogeneous bulk expression. A reference-based method
2855 utilizes single-cell information to generate a signature matrix and
2856 transformation of bulk expression for accurate regression based estimates.
2857 A marker-based method utilizes known cell-specific marker genes to measure
2858 relative abundances across samples.")
2859 (license license:gpl3)))
2861 (define-public r-auc
2868 (uri (cran-uri "AUC" version))
2871 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
2872 (properties `((upstream-name . "AUC")))
2873 (build-system r-build-system)
2874 (home-page "https://cran.r-project.org/web/packages/AUC")
2875 (synopsis "Compute the area under the curve of selected measures")
2877 "This package includes functions to compute the area under the curve of
2878 selected measures: the area under the sensitivity curve (AUSEC), the area
2879 under the specificity curve (AUSPC), the area under the accuracy
2880 curve (AUACC), and the area under the receiver operating characteristic
2881 curve (AUROC). The curves can also be visualized. Support for partial areas
2883 (license license:gpl2+)))
2885 (define-public r-calibrate
2887 (name "r-calibrate")
2892 (uri (cran-uri "calibrate" version))
2894 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
2895 (build-system r-build-system)
2897 `(("r-mass" ,r-mass)))
2898 (home-page "https://cran.r-project.org/web/packages/calibrate")
2899 (synopsis "Calibration of scatterplot and biplot axes")
2901 "This is a package for drawing calibrated scales with tick marks
2902 on (non-orthogonal) variable vectors in scatterplots and biplots.")
2903 (license license:gpl2)))
2905 (define-public r-shape
2912 (uri (cran-uri "shape" version))
2915 "17qqhjyfhxv9la07ykaslb50c8g4d0cgfypx4y91h9i2yjw7jjh9"))))
2916 (build-system r-build-system)
2917 (home-page "https://cran.r-project.org/web/packages/shape")
2918 (synopsis "Functions for plotting graphical shapes")
2920 "This package provides functions for plotting graphical shapes such as
2921 ellipses, circles, cylinders, arrows, ...")
2922 (license license:gpl3+)))
2924 (define-public r-globaloptions
2926 (name "r-globaloptions")
2931 (uri (cran-uri "GlobalOptions" version))
2933 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
2934 (properties `((upstream-name . "GlobalOptions")))
2935 (build-system r-build-system)
2937 `(("r-knitr" ,r-knitr)))
2938 (home-page "https://github.com/jokergoo/GlobalOptions")
2939 (synopsis "Generate functions to get or set global options")
2941 "This package provides more controls on the option values such as
2942 validation and filtering on the values, making options invisible or private.")
2943 (license license:gpl2+)))
2945 (define-public r-circlize
2952 (uri (cran-uri "circlize" version))
2955 "1x2j6a80bb4fly3dm91ias964s1gb1cmzj3lyh69ikwjaam0rdmk"))))
2956 (build-system r-build-system)
2958 `(("r-colorspace" ,r-colorspace)
2959 ("r-globaloptions" ,r-globaloptions)
2960 ("r-shape" ,r-shape)))
2962 `(("r-knitr" ,r-knitr)))
2963 (home-page "https://github.com/jokergoo/circlize")
2964 (synopsis "Circular visualization")
2966 "Circular layout is an efficient way to visualise huge amounts of
2967 information. This package provides an implementation of circular layout
2968 generation in R as well as an enhancement of available software. Its
2969 flexibility is based on the usage of low-level graphics functions such that
2970 self-defined high-level graphics can be easily implemented by users for
2971 specific purposes. Together with the seamless connection between the powerful
2972 computational and visual environment in R, it gives users more convenience and
2973 freedom to design figures for better understanding complex patterns behind
2974 multi-dimensional data.")
2975 (license license:gpl2+)))
2977 (define-public r-powerlaw
2984 (uri (cran-uri "poweRlaw" version))
2986 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2987 (properties `((upstream-name . "poweRlaw")))
2988 (build-system r-build-system)
2990 `(("r-pracma" ,r-pracma)))
2992 `(("r-knitr" ,r-knitr)))
2993 (home-page "https://github.com/csgillespie/poweRlaw")
2994 (synopsis "Tools for the analysis of heavy tailed distributions")
2996 "This package provides an implementation of maximum likelihood estimators
2997 for a variety of heavy tailed distributions, including both the discrete and
2998 continuous power law distributions. Additionally, a goodness-of-fit based
2999 approach is used to estimate the lower cut-off for the scaling region.")
3000 ;; Any of these GPL versions.
3001 (license (list license:gpl2 license:gpl3))))
3003 (define-public r-compare
3010 (uri (cran-uri "compare" version))
3013 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
3014 (build-system r-build-system)
3015 (home-page "https://cran.r-project.org/web/packages/compare")
3016 (synopsis "Comparing objects for differences")
3018 "This package provides functions to compare a model object to a
3019 comparison object. If the objects are not identical, the functions can be
3020 instructed to explore various modifications of the objects (e.g., sorting
3021 rows, dropping names) to see if the modified versions are identical.")
3022 (license license:gpl2+)))
3024 (define-public r-dendextend
3026 (name "r-dendextend")
3031 (uri (cran-uri "dendextend" version))
3034 "0n3qg76apgbqbvxv2yp5qwpy6nx03xmmc9mdfyq4dqblqhdld29p"))))
3035 (build-system r-build-system)
3037 `(("r-ggplot2" ,r-ggplot2)
3038 ("r-magrittr" ,r-magrittr)
3039 ("r-viridis" ,r-viridis)))
3041 `(("r-knitr" ,r-knitr)))
3042 (home-page "https://cran.r-project.org/web/packages/dendextend")
3043 (synopsis "Extending 'dendrogram' functionality in R")
3045 "This package offers a set of functions for extending @code{dendrogram}
3046 objects in R, letting you visualize and compare trees of hierarchical
3047 clusterings. You can adjust a tree's graphical parameters (the color, size,
3048 type, etc of its branches, nodes and labels) and visually and statistically
3049 compare different dendrograms to one another.")
3050 ;; Any of these versions
3051 (license (list license:gpl2 license:gpl3))))
3053 (define-public r-getoptlong
3055 (name "r-getoptlong")
3060 (uri (cran-uri "GetoptLong" version))
3063 "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc"))))
3064 (properties `((upstream-name . "GetoptLong")))
3065 (build-system r-build-system)
3069 `(("r-crayon" ,r-crayon)
3070 ("r-globaloptions" ,r-globaloptions)
3071 ("r-rjson" ,r-rjson)))
3073 `(("r-knitr" ,r-knitr)))
3074 (home-page "https://github.com/jokergoo/GetoptLong")
3075 (synopsis "Parsing command-line arguments and variable interpolation")
3077 "This is yet another command-line argument parser which wraps the
3078 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
3079 use in R. It also provides a simple way for variable interpolation in R.")
3080 (license license:gpl2+)))
3082 (define-public r-fastmatch
3084 (name "r-fastmatch")
3089 (uri (cran-uri "fastmatch" version))
3092 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
3093 (build-system r-build-system)
3094 (home-page "https://www.rforge.net/fastmatch")
3095 (synopsis "Fast match function")
3097 "This package provides a fast @code{match} replacement for cases that
3098 require repeated look-ups. It is slightly faster that R's built-in
3099 @code{match} function on first match against a table, but extremely fast on
3100 any subsequent lookup as it keeps the hash table in memory.")
3101 (license license:gpl2)))
3110 (uri (cran-uri "ff" version))
3113 "1rfj2ff5cxzdp9nvfnbgmswc1jvxz5vkxqgpv6gprwk32a0z3v12"))))
3114 (build-system r-build-system)
3115 (propagated-inputs `(("r-bit" ,r-bit)))
3116 (home-page "http://ff.r-forge.r-project.org/")
3117 (synopsis "Memory-efficient storage of large data on disk and access functions")
3119 "This package provides data structures that are stored on disk but
3120 behave (almost) as if they were in RAM by transparently mapping only a section
3122 ;; error Architecture not supported.
3123 (supported-systems (delete "aarch64-linux" %supported-systems))
3124 (license license:gpl2)))
3126 (define-public r-ffbase
3133 (uri (cran-uri "ffbase" version))
3136 "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk"))))
3137 (build-system r-build-system)
3140 ("r-fastmatch" ,r-fastmatch)
3142 (home-page "https://github.com/edwindj/ffbase")
3143 (synopsis "Basic statistical functions for package 'ff'")
3145 "This package extends the out of memory vectors of @code{ff} with
3146 statistical functions and other utilities to ease their usage.")
3147 (license license:gpl3)))
3149 (define-public r-prettyunits
3151 (name "r-prettyunits")
3156 (uri (cran-uri "prettyunits" version))
3159 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
3160 (build-system r-build-system)
3161 (home-page "https://github.com/gaborcsardi/prettyunits")
3162 (synopsis "Pretty, human readable formatting of quantities")
3164 "This package provides tools for pretty, human readable formatting of
3166 (license license:expat)))
3168 (define-public r-reshape
3175 (uri (cran-uri "reshape" version))
3178 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
3179 (build-system r-build-system)
3181 `(("r-plyr" ,r-plyr)
3182 ("r-rcpp" ,r-rcpp)))
3183 (home-page "http://had.co.nz/reshape")
3184 (synopsis "Flexibly reshape data")
3186 "Flexibly restructure and aggregate data using just two functions:
3187 @code{melt} and @code{cast}. This package provides them.")
3188 (license license:expat)))
3190 (define-public r-restrserve
3192 (name "r-restrserve")
3197 (uri (cran-uri "RestRserve" version))
3199 (base32 "1486hrzj5q5w4nbrsbqlv7vv20ly01y90qc2vygl5syzwvyjd422"))))
3200 (build-system r-build-system)
3202 `(("r-checkmate" ,r-checkmate)
3203 ("r-jsonlite" ,r-jsonlite)
3207 ("r-rserve" ,r-rserve)
3208 ("r-uuid" ,r-uuid)))
3210 `(("r-knitr" ,r-knitr)))
3211 (home-page "https://restrserve.org")
3212 (synopsis "R web API framework")
3214 "RestRserve is an R web API framework for building high-performance AND
3215 robust microservices and app backends. With Rserve backend on UNIX-like
3216 systems it is parallel by design. It will handle incoming requests in
3217 parallel - each request in a separate fork.")
3218 (license license:gpl2+)))
3220 (define-public r-progress
3227 (uri (cran-uri "progress" version))
3230 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
3231 (build-system r-build-system)
3233 `(("r-crayon" ,r-crayon)
3235 ("r-prettyunits" ,r-prettyunits)
3237 (home-page "https://github.com/gaborcsardi/progress")
3238 (synopsis "Terminal progress bars")
3240 "This package provides configurable progress bars. They may include
3241 percentage, elapsed time, and/or the estimated completion time. They work in
3242 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
3243 package also provides a C++ API, that works with or without Rcpp.")
3244 (license license:expat)))
3246 (define-public r-ggally
3253 (uri (cran-uri "GGally" version))
3256 "0lly659kd43cnz1bmmzqj6dbf4v0nm8dhj8xq2wlv9qbnfhq5r9p"))))
3257 (properties `((upstream-name . "GGally")))
3258 (build-system r-build-system)
3260 `(("openssl" ,openssl)))
3262 `(("r-dplyr" ,r-dplyr)
3263 ("r-forcats" ,r-forcats)
3264 ("r-ggplot2" ,r-ggplot2)
3265 ("r-gtable" ,r-gtable)
3266 ("r-lifecycle" ,r-lifecycle)
3268 ("r-progress" ,r-progress)
3269 ("r-rcolorbrewer" ,r-rcolorbrewer)
3270 ("r-reshape" ,r-reshape)
3271 ("r-rlang" ,r-rlang)
3272 ("r-scales" ,r-scales)
3273 ("r-tidyr" ,r-tidyr)))
3274 (home-page "https://ggobi.github.io/ggally")
3275 (synopsis "Extension to ggplot2")
3277 "The R package ggplot2 is a plotting system based on the grammar of
3278 graphics. GGally extends ggplot2 by adding several functions to reduce the
3279 complexity of combining geometric objects with transformed data. Some of
3280 these functions include a pairwise plot matrix, a two group pairwise plot
3281 matrix, a parallel coordinates plot, a survival plot, and several functions to
3283 (license license:gpl2+)))
3285 (define-public r-proxy
3292 (uri (cran-uri "proxy" version))
3295 "1m893djrv6ckadmlx9n5bxfp0ycdh2w63sy6yxfyj1migvc7072f"))))
3296 (build-system r-build-system)
3297 (home-page "https://cran.r-project.org/web/packages/proxy")
3298 (synopsis "Distance and similarity measures")
3300 "This package provides an extensible framework for the efficient
3301 calculation of auto- and cross-proximities, along with implementations of the
3302 most popular ones.")
3303 (license license:gpl2)))
3312 (uri (cran-uri "sp" version))
3314 (base32 "1nh9izsnszzm5kbq461w8bi0yh7fqzb74b2zmpg5qis0slbb5vkb"))))
3315 (build-system r-build-system)
3317 `(("r-lattice" ,r-lattice)))
3318 (home-page "https://cran.r-project.org/web/packages/sp")
3319 (synopsis "Classes and methods for spatial data")
3321 "This package provides classes and methods for spatial data; the classes
3322 document where the spatial location information resides, for 2D or 3D data.
3323 Utility functions are provided, e.g. for plotting data as maps, spatial
3324 selection, as well as methods for retrieving coordinates, for subsetting,
3325 print, summary, etc.")
3326 (license license:gpl2+)))
3328 (define-public r-laplacesdemon
3330 (name "r-laplacesdemon")
3335 (uri (cran-uri "LaplacesDemon" version))
3337 (base32 "1nv1kx86cg8f2s8q15pzskc0lg94bb250p0fhybrx5sjqv1s2lj1"))))
3338 (properties `((upstream-name . "LaplacesDemon")))
3339 (build-system r-build-system)
3340 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
3341 (synopsis "Complete environment for Bayesian inference")
3343 "This package provides a complete environment for Bayesian inference using
3344 a variety of different samplers.")
3345 (license license:expat)))
3347 (define-public r-rmtstat
3354 (uri (cran-uri "RMTstat" version))
3357 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
3358 (properties `((upstream-name . "RMTstat")))
3359 (build-system r-build-system)
3360 (home-page "https://cran.r-project.org/web/packages/RMTstat")
3361 (synopsis "Distributions, statistics and tests derived from random matrix theory")
3363 "This package provides functions for working with the Tracy-Widom laws
3364 and other distributions related to the eigenvalues of large Wishart
3366 (license license:bsd-3)))
3368 (define-public r-rmpi
3374 (uri (cran-uri "Rmpi" version))
3377 "1j8akqjan59yzwx2s1zxc214qyd323fd2i2dhgq0n11mb6ajmq4r"))))
3378 (properties `((upstream-name . "Rmpi")))
3379 (build-system r-build-system)
3381 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
3382 #:phases (modify-phases %standard-phases
3383 (add-before 'install 'mpi-setup
3386 `(("openmpi" ,openmpi)))
3388 `(("pkg-config" ,pkg-config)))
3389 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
3390 (synopsis "R interface to message-passing interface (MPI)")
3392 "This package provides an interface (wrapper) to MPI APIs. It also
3393 provides an interactive R manager and worker environment.")
3394 (license license:gpl2+)))
3396 (define-public r-lmoments
3403 (uri (cran-uri "Lmoments" version))
3406 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
3407 (properties `((upstream-name . "Lmoments")))
3408 (build-system r-build-system)
3410 `(("r-rcpp" ,r-rcpp)
3411 ("r-rcpparmadillo" ,r-rcpparmadillo)))
3412 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
3413 (synopsis "L-moments and quantile mixtures")
3415 "This package contains functions to estimate L-moments and trimmed
3416 L-moments from the data. It also contains functions to estimate the
3417 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
3418 quantile mixture from L-moments and trimmed L-moments.")
3419 (license license:gpl2)))
3421 (define-public r-distillery
3423 (name "r-distillery")
3428 (uri (cran-uri "distillery" version))
3431 "10nhh9p0hp294pp4aav0y0zsmir2qbn05sf3k52rmzmm36q2kc8y"))))
3432 (build-system r-build-system)
3433 (home-page "https://ral.ucar.edu/staff/ericg/")
3434 (synopsis "Functions for confidence intervals and object information")
3436 "This package provides some very simple method functions for confidence
3437 interval calculation and to distill pertinent information from a potentially
3438 complex object; primarily used in common with the packages extRemes and
3440 (license license:gpl2+)))
3442 (define-public r-etrunct
3448 (uri (cran-uri "etrunct" version))
3451 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr"))))
3452 (properties `((upstream-name . "etrunct")))
3453 (build-system r-build-system)
3454 (home-page "https://cran.r-project.org/web/packages/etrunct")
3455 (synopsis "Computes moments of univariate truncated T distribution")
3456 (description "This package computes moments of univariate truncated
3457 T distribution. There is only one exported function, @code{e_trunct},
3458 which should be seen for details.")
3459 (license license:expat)))
3461 (define-public r-extremes
3468 (uri (cran-uri "extRemes" version))
3471 "1b69r3mzl6hp3g3rqxyc77m8r40jyq7c2d87q85af7xqkn6hnxid"))))
3472 (properties `((upstream-name . "extRemes")))
3473 (build-system r-build-system)
3475 `(("r-distillery" ,r-distillery)
3476 ("r-lmoments" ,r-lmoments)))
3477 (home-page "https://www.assessment.ucar.edu/toolkit/")
3478 (synopsis "Extreme value analysis")
3480 "ExtRemes is a suite of functions for carrying out analyses on the
3481 extreme values of a process of interest; be they block maxima over long blocks
3482 or excesses over a high threshold.")
3483 (license license:gpl2+)))
3485 (define-public r-lmtest
3492 (uri (cran-uri "lmtest" version))
3495 "0sr19bmw2cpagfvwg772m79wvl1i2hww1xfr69bzr3rr8pm2r8ij"))))
3496 (build-system r-build-system)
3498 `(("r-zoo" ,r-zoo)))
3500 `(("gfortran" ,gfortran)))
3501 (home-page "https://cran.r-project.org/web/packages/lmtest")
3502 (synopsis "Testing linear regression models")
3504 "This package provides a collection of tests, data sets, and examples for
3505 diagnostic checking in linear regression models. Furthermore, some generic
3506 tools for inference in parametric models are provided.")
3507 ;; Either version is okay
3508 (license (list license:gpl2 license:gpl3))))
3510 (define-public r-idr
3516 (uri (cran-uri "idr" version))
3519 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
3520 (build-system r-build-system)
3521 (home-page "https://cran.r-project.org/web/packages/idr/")
3522 (synopsis "Irreproducible discovery rate")
3524 "This is a package for estimating the copula mixture model and plotting
3525 correspondence curves in \"Measuring reproducibility of high-throughput
3526 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
3527 by Li, Brown, Huang, and Bickel")
3528 (license license:gpl2+)))
3530 (define-public r-inline
3536 (uri (cran-uri "inline" version))
3539 "1wslsn60q959yrr27cwanba43qlpfaxzdli46i9dc26lxfr5fa3r"))))
3540 (build-system r-build-system)
3541 (home-page "https://cran.r-project.org/web/packages/inline")
3542 (synopsis "Functions to inline C, C++, Fortran function calls from R")
3544 "This package provides functionality to dynamically define R functions
3545 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
3546 @code{.Call} calling conventions.")
3547 ;; Any version of the LGPL.
3548 (license license:lgpl3+)))
3550 (define-public r-inum
3556 (uri (cran-uri "inum" version))
3559 "1sz11b4vlpskhmq9vvc1jix63a5g7lij6368w8qbnkjmjd97k7i4"))))
3560 (build-system r-build-system)
3562 `(("r-libcoin" ,r-libcoin)))
3563 (home-page "https://cran.r-project.org/web/packages/inum/")
3564 (synopsis "Interval and enum-type representation of vectors")
3566 "This package provides an enum-type representation of vectors and
3567 representation of intervals, including a method of coercing variables
3569 (license license:gpl2)))
3570 (define-public r-invgamma
3576 (uri (cran-uri "invgamma" version))
3579 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a"))))
3580 (properties `((upstream-name . "invgamma")))
3581 (build-system r-build-system)
3582 (home-page "https://github.com/dkahle/invgamma")
3583 (synopsis "Inverse gamma distribution")
3584 (description "This package provides a light weight implementation of the
3585 standard distribution functions for the inverse gamma distribution, wrapping
3586 those for the gamma distribution in the @code{stats} package.")
3587 (license license:gpl2)))
3589 (define-public r-bdsmatrix
3591 (name "r-bdsmatrix")
3596 (uri (cran-uri "bdsmatrix" version))
3599 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
3600 (properties `((upstream-name . "bdsmatrix")))
3601 (build-system r-build-system)
3602 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
3603 (synopsis "Routines for block diagonal symmetric matrices")
3605 "This package provides procedures to work with block diagonal symmetric
3606 matrices, a special case of sparse matrices.")
3607 (license license:lgpl2.0)))
3609 (define-public r-bbmle
3612 (version "1.0.23.1")
3616 (uri (cran-uri "bbmle" version))
3619 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
3620 (build-system r-build-system)
3622 `(("r-bdsmatrix" ,r-bdsmatrix)
3623 ("r-lattice" ,r-lattice)
3625 ("r-matrix" ,r-matrix)
3626 ("r-mvtnorm" ,r-mvtnorm)
3627 ("r-numderiv" ,r-numderiv)))
3628 (home-page "https://cran.r-project.org/web/packages/bbmle")
3629 (synopsis "Tools for General Maximum Likelihood Estimation")
3631 "This package provides methods and functions for fitting maximum
3632 likelihood models in R. This package modifies and extends the @code{mle}
3633 classes in the @code{stats4} package.")
3634 ;; Any version of the GPL
3635 (license license:gpl2+)))
3637 (define-public r-emdbook
3644 (uri (cran-uri "emdbook" version))
3647 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
3648 (build-system r-build-system)
3650 `(("r-bbmle" ,r-bbmle)
3652 ("r-lattice" ,r-lattice)
3654 ("r-plyr" ,r-plyr)))
3655 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
3656 (synopsis "Support functions and data for \"Ecological Models and Data\"")
3658 "This package provides auxiliary functions and data sets for \"Ecological
3659 Models and Data\", a book presenting maximum likelihood estimation and related
3660 topics for ecologists (ISBN 978-0-691-12522-0).")
3662 (license (list license:gpl2 license:gpl3))))
3664 (define-public r-lpsolve
3671 (uri (cran-uri "lpSolve" version))
3674 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
3675 (properties `((upstream-name . "lpSolve")))
3676 (build-system r-build-system)
3677 (home-page "https://cran.r-project.org/web/packages/lpSolve")
3678 (synopsis "R interface to Lp_solve to solve linear/integer programs")
3680 "Lp_solve is software for solving linear, integer and mixed integer
3681 programs. This implementation supplies a \"wrapper\" function in C and some R
3682 functions that solve general linear/integer problems, assignment problems, and
3683 transportation problems.")
3684 (license license:lgpl2.0)))
3686 (define-public r-limsolve
3693 (uri (cran-uri "limSolve" version))
3696 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
3697 (properties `((upstream-name . "limSolve")))
3698 (build-system r-build-system)
3700 `(("r-lpsolve" ,r-lpsolve)
3702 ("r-quadprog" ,r-quadprog)))
3703 (native-inputs `(("gfortran" ,gfortran)))
3704 (home-page "https://cran.r-project.org/web/packages/limSolve")
3705 (synopsis "Solving linear inverse models")
3707 "This package provides functions that:
3710 @item find the minimum/maximum of a linear or quadratic function,
3711 @item sample an underdetermined or overdetermined system,
3712 @item solve a linear system Ax=B for the unknown x.
3715 It includes banded and tridiagonal linear systems. The package calls Fortran
3716 functions from LINPACK.")
3718 (license (list license:gpl2+ license:gpl3+))))
3720 (define-public r-fitdistrplus
3722 (name "r-fitdistrplus")
3727 (uri (cran-uri "fitdistrplus" version))
3730 "1pjnqx0j26dai2fa4ip56wspmfsrcm9dpmxkg15y9623w5b58vbp"))))
3731 (build-system r-build-system)
3733 `(("r-mass" ,r-mass)
3734 ("r-survival" ,r-survival)))
3736 `(("r-knitr" ,r-knitr)))
3737 (home-page "http://riskassessment.r-forge.r-project.org")
3738 (synopsis "Fitting a parametric distribution from data")
3740 "This package extends the @code{fitdistr} function of the MASS package
3741 with several functions to help the fit of a parametric distribution to
3742 non-censored or censored data. Censored data may contain left-censored,
3743 right-censored and interval-censored values, with several lower and upper
3744 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
3745 provides moment matching (MME), quantile matching (QME) and maximum
3746 goodness-of-fit estimation (MGE) methods (available only for non-censored
3747 data). Weighted versions of MLE, MME and QME are available.")
3748 (license license:gpl2+)))
3750 (define-public r-energy
3757 (uri (cran-uri "energy" version))
3760 "12a7gy681aq3l55iys044cs6sn1s2l5qihghpdl01cvv0ggfh26y"))))
3761 (build-system r-build-system)
3763 `(("r-boot" ,r-boot)
3765 ("r-rcpp" ,r-rcpp)))
3766 (home-page "https://cran.r-project.org/web/packages/energy")
3767 (synopsis "Multivariate inference via the energy of data")
3769 "This package provides e-statistics (energy) tests and statistics for
3770 multivariate and univariate inference, including distance correlation,
3771 one-sample, two-sample, and multi-sample tests for comparing multivariate
3772 distributions, are implemented. Measuring and testing multivariate
3773 independence based on distance correlation, partial distance correlation,
3774 multivariate goodness-of-fit tests, clustering based on energy distance,
3775 testing for multivariate normality, distance components (disco) for
3776 non-parametric analysis of structured data, and other energy
3777 statistics/methods are implemented.")
3778 (license license:gpl2+)))
3780 (define-public r-suppdists
3782 (name "r-suppdists")
3787 (uri (cran-uri "SuppDists" version))
3790 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
3791 (properties `((upstream-name . "SuppDists")))
3792 (build-system r-build-system)
3793 (home-page "https://cran.r-project.org/web/packages/SuppDists")
3794 (synopsis "Supplementary distributions")
3796 "This package provides ten distributions supplementing those built into
3797 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
3798 Spearman's rho, maximum F ratio, the Pearson product moment correlation
3799 coefficient, Johnson distributions, normal scores and generalized
3800 hypergeometric distributions. In addition two random number generators of
3801 George Marsaglia are included.")
3802 (license license:gpl2+)))
3804 (define-public r-ksamples
3811 (uri (cran-uri "kSamples" version))
3814 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
3815 (properties `((upstream-name . "kSamples")))
3816 (build-system r-build-system)
3818 `(("r-suppdists" ,r-suppdists)))
3819 (home-page "https://cran.r-project.org/web/packages/kSamples")
3820 (synopsis "K-Sample rank tests and their combinations")
3822 "This package provides tools to compares k samples using the
3823 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
3824 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
3825 test. It computes asymptotic, simulated or (limited) exact P-values, all
3826 valid under randomization, with or without ties, or conditionally under random
3827 sampling from populations, given the observed tie pattern. Except for Steel's
3828 test and the JT test it also combines these tests across several blocks of
3830 (license license:gpl2+)))
3832 (define-public r-cvst
3839 (uri (cran-uri "CVST" version))
3842 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
3843 (properties `((upstream-name . "CVST")))
3844 (build-system r-build-system)
3846 `(("r-kernlab" ,r-kernlab)
3847 ("r-matrix" ,r-matrix)))
3848 (home-page "https://cran.r-project.org/web/packages/CVST")
3849 (synopsis "Fast cross-validation via sequential testing")
3851 "This package implements the fast cross-validation via sequential
3852 testing (CVST) procedure. CVST is an improved cross-validation procedure
3853 which uses non-parametric testing coupled with sequential analysis to
3854 determine the best parameter set on linearly increasing subsets of the data.
3855 Additionally to the CVST the package contains an implementation of the
3856 ordinary k-fold cross-validation with a flexible and powerful set of helper
3857 objects and methods to handle the overall model selection process. The
3858 implementations of the Cochran's Q test with permutations and the sequential
3859 testing framework of Wald are generic and can therefore also be used in other
3861 (license license:gpl2+)))
3863 (define-public r-squarem
3870 (uri (cran-uri "SQUAREM" version))
3873 "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6"))))
3874 (properties `((upstream-name . "SQUAREM")))
3875 (build-system r-build-system)
3876 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
3877 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
3879 "This package provides algorithms for accelerating the convergence of
3880 slow, monotone sequences from smooth, contraction mapping such as the EM
3881 algorithm. It can be used to accelerate any smooth, linearly convergent
3882 acceleration scheme. A tutorial style introduction to this package is
3883 available in a vignette.")
3884 (license license:gpl2+)))
3886 (define-public r-lava
3893 (uri (cran-uri "lava" version))
3896 "1yiz8y3jhxkszgz9m9fialp9r27hy97xh0imfvs8ziv7dk43y93d"))))
3897 (build-system r-build-system)
3899 `(("r-numderiv" ,r-numderiv)
3900 ("r-squarem" ,r-squarem)
3901 ("r-survival" ,r-survival)))
3903 `(("r-knitr" ,r-knitr)))
3904 (home-page "https://github.com/kkholst/lava")
3905 (synopsis "Latent variable models")
3907 "This package provides tools for the estimation and simulation of latent
3909 (license license:gpl3)))
3911 (define-public r-drr
3918 (uri (cran-uri "DRR" version))
3921 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3922 (properties `((upstream-name . "DRR")))
3923 (build-system r-build-system)
3925 `(("r-cvst" ,r-cvst)
3926 ("r-kernlab" ,r-kernlab)
3927 ("r-matrix" ,r-matrix)))
3928 (home-page "https://cran.r-project.org/web/packages/DRR")
3929 (synopsis "Dimensionality reduction via regression")
3931 "This package provides an implementation of dimensionality reduction via
3932 regression using Kernel Ridge Regression.")
3933 (license license:gpl3)))
3935 (define-public r-prodlim
3938 (version "2019.11.13")
3942 (uri (cran-uri "prodlim" version))
3945 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3946 (build-system r-build-system)
3948 `(("r-kernsmooth" ,r-kernsmooth)
3951 ("r-survival" ,r-survival)))
3952 (home-page "https://cran.r-project.org/web/packages/prodlim")
3953 (synopsis "Product-limit estimation for censored event history analysis")
3955 "This package provides a fast and user-friendly implementation of
3956 nonparametric estimators for censored event history (survival) analysis with
3957 the Kaplan-Meier and Aalen-Johansen methods.")
3958 (license license:gpl2+)))
3960 (define-public r-dimred
3967 (uri (cran-uri "dimRed" version))
3970 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3971 (properties `((upstream-name . "dimRed")))
3972 (build-system r-build-system)
3975 ("r-magrittr" ,r-magrittr)))
3976 (home-page "https://github.com/gdkrmr/dimRed")
3977 (synopsis "Framework for dimensionality reduction")
3979 "This package provides a collection of dimensionality reduction
3980 techniques from R packages and provides a common interface for calling the
3982 (license license:gpl3)))
3984 (define-public r-timedate
3987 (version "3043.102")
3991 (uri (cran-uri "timeDate" version))
3994 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
3995 (properties `((upstream-name . "timeDate")))
3996 (build-system r-build-system)
3997 (home-page "https://www.rmetrics.org")
3998 (synopsis "Chronological and calendar objects")
4000 "This package provides an environment for teaching \"Financial
4001 Engineering and Computational Finance\" and for managing chronological and
4003 (license license:gpl2+)))
4005 (define-public r-magic
4012 (uri (cran-uri "magic" version))
4015 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
4016 (build-system r-build-system)
4018 `(("r-abind" ,r-abind)))
4019 (home-page "https://github.com/RobinHankin/magic.git")
4020 (synopsis "Create and investigate magic squares")
4022 "This package provides a collection of efficient, vectorized algorithms
4023 for the creation and investigation of magic squares and hypercubes, including
4024 a variety of functions for the manipulation and analysis of arbitrarily
4025 dimensioned arrays.")
4026 (license license:gpl2)))
4028 (define-public r-rmysql
4035 (uri (cran-uri "RMySQL" version))
4038 "0cbb5ln9iigl816nzvsls9zil5qlfr8yv2aginapqv6n69nz0srs"))))
4039 (properties `((upstream-name . "RMySQL")))
4040 (build-system r-build-system)
4042 `(("mariadb-dev" ,mariadb "dev")
4045 `(("r-dbi" ,r-dbi)))
4046 (home-page "https://github.com/r-dbi/RMySQL")
4047 (synopsis "Database interface and MySQL driver for R")
4049 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
4050 package contains an old implementation based on legacy code from S-PLUS which
4051 is being phased out. A modern MySQL client based on Rcpp is available from
4052 the RMariaDB package.")
4053 (license license:gpl2)))
4055 (define-public r-rpostgresql
4057 (name "r-rpostgresql")
4062 (uri (cran-uri "RPostgreSQL" version))
4065 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
4066 (properties `((upstream-name . "RPostgreSQL")))
4067 (build-system r-build-system)
4069 `(("postgresql" ,postgresql)))
4071 `(("r-dbi" ,r-dbi)))
4072 (home-page "https://github.com/tomoakin/RPostgreSQL")
4073 (synopsis "R interface to the PostgreSQL database system")
4075 "This package provides a Database Interface (DBI) compliant driver for R
4076 to access PostgreSQL database systems.")
4077 ;; The whole package is released under GPL version 2. It includes code
4078 ;; under the PostgreSQL license.
4079 (license license:gpl2)))
4081 (define-public r-linprog
4088 (uri (cran-uri "linprog" version))
4091 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
4092 (build-system r-build-system)
4093 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
4094 (home-page "http://linprog.r-forge.r-project.org/")
4095 (synopsis "Linear programming and optimization")
4097 "This package can be used to solve Linear Programming / Linear
4098 Optimization problems by using the simplex algorithm.")
4099 (license license:gpl2+)))
4101 (define-public r-geometry
4108 (uri (cran-uri "geometry" version))
4111 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
4112 (build-system r-build-system)
4114 `(("r-magic" ,r-magic)
4115 ("r-linprog" ,r-linprog)
4116 ("r-lpsolve" ,r-lpsolve)
4118 ("r-rcppprogress" ,r-rcppprogress)))
4119 (home-page "http://geometry.r-forge.r-project.org/")
4120 (synopsis "Mesh generator and surface tessellator")
4122 "This package makes the qhull library available in R, in a similar manner
4123 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
4124 intersections about a point, Voronoi diagrams, furthest-site Delaunay
4125 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
4126 and higher dimensions. It implements the Quickhull algorithm for computing
4127 the convex hull. Qhull does not support constrained Delaunay triangulations,
4128 or mesh generation of non-convex objects, but the package does include some R
4129 functions that allow for this. Currently the package only gives access to
4130 Delaunay triangulation and convex hull computation.")
4131 ;; The Qhull sources are included and are distributed under a custom
4132 ;; non-copyleft license. The R sources are released under GPL version 2.
4133 (license (list license:gpl2
4134 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
4136 (define-public r-ddalpha
4143 (uri (cran-uri "ddalpha" version))
4146 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
4147 (build-system r-build-system)
4150 ("r-class" ,r-class)
4151 ("r-geometry" ,r-geometry)
4154 ("r-robustbase" ,r-robustbase)
4155 ("r-sfsmisc" ,r-sfsmisc)))
4157 `(("gfortran" ,gfortran)))
4158 (home-page "https://cran.r-project.org/web/packages/ddalpha")
4159 (synopsis "Depth-Based classification and calculation of data depth")
4161 "This package contains procedures for depth-based supervised learning,
4162 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
4163 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
4164 statistical depth function to a compact low-dimensional space, where the final
4165 classification is done. It also offers an extension to functional data and
4166 routines for calculating certain notions of statistical depth functions. 50
4167 multivariate and 5 functional classification problems are included.")
4168 (license license:gpl2)))
4170 (define-public r-gower
4177 (uri (cran-uri "gower" version))
4180 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
4181 (build-system r-build-system)
4182 (home-page "https://github.com/markvanderloo/gower")
4183 (synopsis "Gower's distance")
4185 "This package provides tools to compute Gower's distance (or similarity)
4186 coefficient between records, and to compute the top-n matches between records.
4187 Core algorithms are executed in parallel on systems supporting OpenMP.")
4188 (license license:gpl3)))
4190 (define-public r-rcpproll
4197 (uri (cran-uri "RcppRoll" version))
4200 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
4201 (properties `((upstream-name . "RcppRoll")))
4202 (build-system r-build-system)
4204 `(("r-rcpp" ,r-rcpp)))
4205 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
4206 (synopsis "Efficient rolling and windowed operations")
4208 "This package provides fast and efficient routines for common rolling /
4209 windowed operations. Routines for the efficient computation of windowed mean,
4210 median, sum, product, minimum, maximum, standard deviation and variance are
4212 (license license:gpl2+)))
4214 (define-public r-ipred
4221 (uri (cran-uri "ipred" version))
4224 "0p9cd2v47h71jbz8q0z6xykkaqpcp0mkpsfmd2bn961n1hfgpa63"))))
4225 (build-system r-build-system)
4227 `(("r-class" ,r-class)
4230 ("r-prodlim" ,r-prodlim)
4231 ("r-rpart" ,r-rpart)
4232 ("r-survival" ,r-survival)))
4233 (home-page "https://cran.r-project.org/web/packages/ipred")
4234 (synopsis "Improved predictors")
4236 "This package provides improved predictive models by indirect
4237 classification and bagging for classification, regression and survival
4238 problems as well as resampling based estimators of prediction error.")
4239 (license license:gpl2+)))
4241 (define-public r-psych
4248 (uri (cran-uri "psych" version))
4251 "0k5dw5nb7kx7f21b0z01dry99qcpnk7iaicv7xq9d35wv2hx8wca"))))
4252 (build-system r-build-system)
4254 `(("r-lattice" ,r-lattice)
4255 ("r-mnormt" ,r-mnormt)
4256 ("r-nlme" ,r-nlme)))
4257 (home-page "https://cran.r-project.org/web/packages/psych/")
4258 (synopsis "Procedures for psychological, psychometric, and personality research")
4260 "This package provides a general purpose toolbox for personality,
4261 psychometric theory and experimental psychology. Functions are primarily for
4262 multivariate analysis and scale construction using factor analysis, principal
4263 component analysis, cluster analysis and reliability analysis, although others
4264 provide basic descriptive statistics. Item Response Theory is done using
4265 factor analysis of tetrachoric and polychoric correlations. Functions for
4266 analyzing data at multiple levels include within and between group statistics,
4267 including correlations and factor analysis. Functions for simulating and
4268 testing particular item and test structures are included. Several functions
4269 serve as a useful front end for structural equation modeling. Graphical
4270 displays of path diagrams, factor analysis and structural equation models are
4271 created using basic graphics.")
4272 (license license:gpl2+)))
4274 (define-public r-generics
4281 (uri (cran-uri "generics" version))
4284 "0qw7r0d2qvlj1pvrlpv30d6akml624ydxkk19hv85iv6pfyx2wdb"))))
4285 (build-system r-build-system)
4286 (home-page "https://github.com/r-lib/generics")
4287 (synopsis "Common S3 generics not provided by base R methods")
4289 "In order to reduce potential package dependencies and conflicts,
4290 generics provides a number of commonly used S3 generics that are not provided
4291 by base R methods related to model fitting.")
4292 (license license:gpl2)))
4294 (define-public r-broom
4301 (uri (cran-uri "broom" version))
4304 "1qjyl5b100bsakm48w1vi3819lkpys7vb86n1sv9h4y2wr1c4jmw"))))
4305 (build-system r-build-system)
4307 `(("r-backports" ,r-backports)
4308 ("r-dplyr" ,r-dplyr)
4309 ("r-ellipsis" ,r-ellipsis)
4310 ("r-generics" ,r-generics)
4312 ("r-purrr" ,r-purrr)
4313 ("r-rlang" ,r-rlang)
4314 ("r-stringr" ,r-stringr)
4315 ("r-tibble" ,r-tibble)
4316 ("r-tidyr" ,r-tidyr)))
4318 `(("r-knitr" ,r-knitr)))
4319 (home-page "https://github.com/tidyverse/broom")
4320 (synopsis "Convert statistical analysis objects into tidy data frames")
4322 "This package provides tools to convert statistical analysis objects from
4323 R into tidy data frames, so that they can more easily be combined, reshaped
4324 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
4325 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
4326 summarizes a model's statistical findings such as coefficients of a
4327 regression; @code{augment}, which adds columns to the original data such as
4328 predictions, residuals and cluster assignments; and @code{glance}, which
4329 provides a one-row summary of model-level statistics.")
4330 (license license:expat)))
4332 (define-public r-recipes
4339 (uri (cran-uri "recipes" version))
4342 "0xif0ak3w90xmfzlxvb5pnzc3scpfl1pyhrjffi3mq4asvsd52l0"))))
4343 (build-system r-build-system)
4345 `(("r-dplyr" ,r-dplyr)
4346 ("r-generics" ,r-generics)
4348 ("r-gower" ,r-gower)
4349 ("r-ipred" ,r-ipred)
4350 ("r-lifecycle" ,r-lifecycle)
4351 ("r-lubridate" ,r-lubridate)
4352 ("r-magrittr" ,r-magrittr)
4353 ("r-matrix" ,r-matrix)
4354 ("r-purrr" ,r-purrr)
4355 ("r-rlang" ,r-rlang)
4356 ("r-tibble" ,r-tibble)
4357 ("r-tidyr" ,r-tidyr)
4358 ("r-tidyselect" ,r-tidyselect)
4359 ("r-timedate" ,r-timedate)
4360 ("r-withr" ,r-withr)))
4362 `(("r-knitr" ,r-knitr)))
4363 (home-page "https://github.com/topepo/recipes")
4364 (synopsis "Preprocessing tools to create design matrices")
4366 "Recipes is an extensible framework to create and preprocess design
4367 matrices. Recipes consist of one or more data manipulation and analysis
4368 \"steps\". Statistical parameters for the steps can be estimated from an
4369 initial data set and then applied to other data sets. The resulting design
4370 matrices can then be used as inputs into statistical or machine learning
4372 (license license:gpl2)))
4374 (define-public r-pdist
4381 (uri (cran-uri "pdist" version))
4384 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
4385 (build-system r-build-system)
4386 (home-page "https://github.com/jeffwong/pdist")
4387 (synopsis "Partitioned distance function")
4389 "Pdist computes the euclidean distance between rows of a matrix X and
4390 rows of another matrix Y. Previously, this could be done by binding the two
4391 matrices together and calling @code{dist}, but this creates unnecessary
4392 computation by computing the distances between a row of X and another row of
4393 X, and likewise for Y. Pdist strictly computes distances across the two
4394 matrices, not within the same matrix, making computations significantly faster
4395 for certain use cases.")
4396 (license license:gpl3+)))
4398 (define-public r-ggrepel
4405 (uri (cran-uri "ggrepel" version))
4408 "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9"))))
4409 (build-system r-build-system)
4411 `(("r-ggplot2" ,r-ggplot2)
4413 ("r-rlang" ,r-rlang)
4414 ("r-scales" ,r-scales)))
4416 `(("r-knitr" ,r-knitr))) ; for vignettes
4417 (home-page "https://github.com/slowkow/ggrepel")
4418 (synopsis "Repulsive text and label geometries for ggplot2")
4420 "This package provides text and label geometries for ggplot2 that help to
4421 avoid overlapping text labels. Labels repel away from each other and away
4422 from the data points.")
4423 (license license:gpl3)))
4425 (define-public r-corrplot
4432 (uri (cran-uri "corrplot" version))
4435 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
4436 (build-system r-build-system)
4437 (home-page "https://github.com/taiyun/corrplot")
4438 (synopsis "Visualization of a correlation matrix")
4440 "This package provides a graphical display of a correlation matrix or
4441 general matrix. It also contains some algorithms to do matrix reordering. In
4442 addition, corrplot is good at details, including choosing color, text labels,
4443 color labels, layout, etc.")
4444 ;; Any version of the GPL
4445 (license license:gpl2+)))
4447 (define-public r-stringdist
4449 (name "r-stringdist")
4454 (uri (cran-uri "stringdist" version))
4456 (base32 "06rzbgw43vzg496xca82pydf3g2rz6iw6h50ai0prbp9hbwrhvfd"))))
4457 (build-system r-build-system)
4458 (home-page "https://github.com/markvanderloo/stringdist")
4459 (synopsis "Approximate string matching and string distance functions")
4461 "This package implements an approximate string matching version of R's
4462 native @code{match} function. It can calculate various string distances based
4463 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment),
4464 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
4465 Jaro-Winkler). An implementation of soundex is provided as well. Distances
4466 can be computed between character vectors while taking proper care of encoding
4467 or between integer vectors representing generic sequences.")
4468 (license license:gpl3+)))
4470 (define-public r-ucminf
4477 (uri (cran-uri "ucminf" version))
4480 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
4481 (build-system r-build-system)
4482 (native-inputs `(("gfortran" ,gfortran)))
4483 (home-page "https://cran.r-project.org/web/packages/ucminf/")
4484 (synopsis "General-purpose unconstrained non-linear optimization")
4486 "This package provides an implementation of an algorithm for
4487 general-purpose unconstrained non-linear optimization. The algorithm is of
4488 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
4489 search with a trust region type monitoring of the input to the line search
4490 algorithm. The interface of @code{ucminf} is designed for easy interchange
4491 with the package @code{optim}.")
4492 (license license:gpl2+)))
4494 (define-public r-useful
4500 (uri (cran-uri "useful" version))
4503 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
4504 (properties `((upstream-name . "useful")))
4505 (build-system r-build-system)
4507 `(("r-assertthat" ,r-assertthat)
4508 ("r-dplyr" ,r-dplyr)
4509 ("r-ggplot2" ,r-ggplot2)
4510 ("r-magrittr" ,r-magrittr)
4511 ("r-matrix" ,r-matrix)
4513 ("r-purrr" ,r-purrr)
4514 ("r-scales" ,r-scales)))
4515 (home-page "https://github.com/jaredlander/useful")
4516 (synopsis "Collection of handy, useful functions")
4517 (description "This package provides a set of little functions that have been
4518 found useful to do little odds and ends such as plotting the results of K-means
4519 clustering, substituting special text characters, viewing parts of a
4520 @code{data.frame}, constructing formulas from text and building design and
4521 response matrices.")
4522 (license license:bsd-3)))
4524 (define-public r-ordinal
4527 (version "2019.12-10")
4531 (uri (cran-uri "ordinal" version))
4534 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
4535 (build-system r-build-system)
4537 `(("r-mass" ,r-mass)
4538 ("r-matrix" ,r-matrix)
4539 ("r-numderiv" ,r-numderiv)
4540 ("r-ucminf" ,r-ucminf)))
4541 (home-page "https://github.com/runehaubo/ordinal")
4542 (synopsis "Regression models for ordinal data")
4544 "This package provides an implementation of cumulative link (mixed)
4545 models also known as ordered regression models, proportional odds models,
4546 proportional hazards models for grouped survival times and ordered models.
4547 Estimation is via maximum likelihood and mixed models are fitted with the
4548 Laplace approximation and adaptive Gauss-Hermite quadrature.")
4549 (license license:gpl2+)))
4551 (define-public r-jomo
4558 (uri (cran-uri "jomo" version))
4561 "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir"))))
4562 (build-system r-build-system)
4564 `(("r-lme4" ,r-lme4)
4566 ("r-ordinal" ,r-ordinal)
4567 ("r-survival" ,r-survival)))
4568 (home-page "https://cran.r-project.org/web/packages/jomo/")
4569 (synopsis "Multilevel Joint Modelling Multiple Imputation")
4571 "Similarly to Schafer's package pan, jomo is a package for multilevel
4572 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
4573 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
4574 possibility of handling binary and categorical data through latent normal
4575 variables, the option to use cluster-specific covariance matrices and to
4576 impute compatibly with the substantive model.")
4577 (license license:gpl2)))
4579 (define-public r-pan
4586 (uri (cran-uri "pan" version))
4589 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
4590 (build-system r-build-system)
4591 (native-inputs `(("gfortran" ,gfortran)))
4592 (home-page "https://cran.r-project.org/web/packages/pan/")
4593 (synopsis "Multiple imputation for multivariate panel or clustered data")
4595 "This package implements multiple imputation for multivariate panel or
4597 (license license:gpl3)))
4599 (define-public r-mitml
4606 (uri (cran-uri "mitml" version))
4609 "1bw92fl6xp3yvawh3nbjzs4hp4alpwj6vnv6lsysd74aqndw447c"))))
4610 (build-system r-build-system)
4612 `(("r-haven" ,r-haven)
4616 `(("r-knitr" ,r-knitr)))
4617 (home-page "https://cran.r-project.org/web/packages/mitml/")
4618 (synopsis "Tools for multiple imputation in multilevel modeling")
4620 "This package provides tools for multiple imputation of missing data in
4621 multilevel modeling. It includes a user-friendly interface to the packages
4622 pan and jomo, and several functions for visualization, data management and the
4623 analysis of multiply imputed data sets.")
4624 (license license:gpl2+)))
4626 (define-public r-mice
4633 (uri (cran-uri "mice" version))
4636 "11cpyqlilakan2pwjzacb9jjlazazsqdngy237nnrj8j6mky822i"))))
4637 (build-system r-build-system)
4639 `(("r-broom" ,r-broom)
4640 ("r-cpp11" ,r-cpp11)
4641 ("r-dplyr" ,r-dplyr)
4642 ("r-generics" ,r-generics)
4643 ("r-lattice" ,r-lattice)
4645 ("r-rlang" ,r-rlang)
4646 ("r-tidyr" ,r-tidyr)))
4647 (home-page "https://cran.r-project.org/web/packages/mice/")
4648 (synopsis "Multivariate imputation by chained equations")
4650 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
4651 implemented by the MICE algorithm as described in @url{Van Buuren and
4652 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
4653 variable has its own imputation model. Built-in imputation models are
4654 provided for continuous data (predictive mean matching, normal), binary
4655 data (logistic regression), unordered categorical data (polytomous logistic
4656 regression) and ordered categorical data (proportional odds). MICE can also
4657 impute continuous two-level data (normal model, pan, second-level variables).
4658 Passive imputation can be used to maintain consistency between variables.
4659 Various diagnostic plots are available to inspect the quality of the
4661 ;; Any of these two versions.
4662 (license (list license:gpl2 license:gpl3))))
4664 (define-public r-truncnorm
4666 (name "r-truncnorm")
4671 (uri (cran-uri "truncnorm" version))
4674 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
4675 (build-system r-build-system)
4676 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
4677 (synopsis "Truncated normal distribution")
4678 (description "This package provides functions for the truncated normal
4679 distribution with mean equal to @code{mean} and standard deviation equal to
4680 @code{sd}. It includes density, distribution, quantile, and expected value
4681 functions, as well as a random generation function.")
4682 (license license:gpl2)))
4684 (define-public r-rsolnp
4691 (uri (cran-uri "Rsolnp" version))
4694 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
4695 (properties `((upstream-name . "Rsolnp")))
4696 (build-system r-build-system)
4698 `(("r-truncnorm" ,r-truncnorm)))
4699 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
4700 (synopsis "General non-linear optimization")
4701 (description "The Rsolnp package implements a general non-linear augmented
4702 Lagrange multiplier method solver, a @dfn{sequential quadratic
4703 programming} (SQP) based solver).")
4704 ;; Any version of the GPL.
4705 (license license:gpl2+)))
4707 (define-public r-hardyweinberg
4709 (name "r-hardyweinberg")
4714 (uri (cran-uri "HardyWeinberg" version))
4717 "0afjz818yvaq3akvgpy4irnlpspd2dj71qkrwj81lm9y36ypwlw6"))))
4718 (properties `((upstream-name . "HardyWeinberg")))
4719 (build-system r-build-system)
4721 `(("r-mice" ,r-mice)
4723 ("r-rsolnp" ,r-rsolnp)))
4724 (home-page "https://cran.r-project.org/package=HardyWeinberg")
4725 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
4727 "This package contains tools for exploring Hardy-Weinberg equilibrium for
4728 diallelic genetic marker data. All classical tests (chi-square, exact,
4729 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
4730 included in the package, as well as functions for power computation and for
4731 the simulation of marker data under equilibrium and disequilibrium. Routines
4732 for dealing with markers on the X-chromosome are included. Functions for
4733 testing equilibrium in the presence of missing data by using multiple
4734 imputation are also provided. Implements several graphics for exploring the
4735 equilibrium status of a large set of diallelic markers: ternary plots with
4736 acceptance regions, log-ratio plots and Q-Q plots.")
4737 (license license:gpl2+)))
4746 (uri (cran-uri "sm" version))
4749 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
4750 (build-system r-build-system)
4751 (native-inputs `(("gfortran" ,gfortran)))
4752 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
4753 (synopsis "Smoothing methods for nonparametric regression and density estimation")
4755 "This is software accompanying the book 'Applied Smoothing Techniques for
4756 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
4757 University Press. It provides smoothing methods for nonparametric regression
4758 and density estimation")
4759 (license license:gpl2+)))
4761 (define-public r-venndiagram
4763 (name "r-venndiagram")
4767 (uri (cran-uri "VennDiagram" version))
4770 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
4771 (properties `((upstream-name . "VennDiagram")))
4772 (build-system r-build-system)
4774 `(("r-futile-logger" ,r-futile-logger)))
4775 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
4776 (synopsis "Generate High-Resolution Venn and Euler Plots")
4778 "This package provides a set of functions to generate high-resolution
4779 Venn and Euler plots. It includes handling for several special cases,
4780 including two-case scaling, and extensive customization of plot shape and
4782 (license license:gpl2+)))
4784 (define-public r-vioplot
4791 (uri (cran-uri "vioplot" version))
4794 "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v"))))
4795 (build-system r-build-system)
4800 `(("r-knitr" ,r-knitr)))
4801 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
4802 (synopsis "Violin plot")
4804 "This package provides a violin plot, which is a combination of a box
4805 plot and a kernel density plot.")
4806 (license license:bsd-3)))
4808 (define-public r-rsofia
4814 ;; This package has been removed from CRAN, so we can
4815 ;; only fetch it from the archives.
4816 (uri (string-append "https://cran.r-project.org/src/"
4817 "contrib/Archive/RSofia/RSofia_"
4821 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
4822 (properties `((upstream-name . "RSofia")))
4823 (build-system r-build-system)
4825 `(("r-rcpp" ,r-rcpp)))
4826 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
4827 (synopsis "Port of sofia-ml to R")
4828 (description "This package is a port of sofia-ml to R. Sofia-ml is a
4829 suite of fast incremental algorithms for machine learning that can be used for
4830 training models for classification or ranking.")
4831 (license license:asl2.0)))
4833 (define-public r-xts
4840 (uri (cran-uri "xts" version))
4843 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
4844 (build-system r-build-system)
4845 (propagated-inputs `(("r-zoo" ,r-zoo)))
4846 (home-page "https://github.com/joshuaulrich/xts")
4847 (synopsis "Extensible time series")
4849 "This package provides for uniform handling of R's different time-based
4850 data classes by extending @code{zoo}, maximizing native format information
4851 preservation and allowing for user-level customization and extension, while
4852 simplifying cross-class interoperability.")
4853 (license license:gpl2+)))
4855 (define-public r-performanceanalytics
4857 (name "r-performanceanalytics")
4862 (uri (cran-uri "PerformanceAnalytics" version))
4865 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
4867 `((upstream-name . "PerformanceAnalytics")))
4868 (build-system r-build-system)
4870 `(("r-quadprog" ,r-quadprog)
4873 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
4874 (synopsis "Econometric tools for performance and risk analysis")
4875 (description "This is a collection of econometric functions for
4876 performance and risk analysis. This package aims to aid practitioners and
4877 researchers in utilizing the latest research in analysis of non-normal return
4878 streams. In general, it is most tested on return (rather than price) data on
4879 a regular scale, but most functions will work with irregular return data as
4880 well, and increasing numbers of functions will work with P&L or price data
4882 ;; Either version may be picked.
4883 (license (list license:gpl2 license:gpl3))))
4885 (define-public r-laeken
4892 (uri (cran-uri "laeken" version))
4895 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
4896 (build-system r-build-system)
4898 `(("r-boot" ,r-boot)
4899 ("r-mass" ,r-mass)))
4900 (home-page "https://cran.r-project.org/web/packages/laeken/")
4901 (synopsis "Estimation of indicators on social exclusion and poverty")
4902 (description "This package provides tools for the estimation of indicators
4903 on social exclusion and poverty, as well as an implementation of Pareto tail
4904 modeling for empirical income distributions.")
4905 (license license:gpl2+)))
4907 (define-public r-vcd
4914 (uri (cran-uri "vcd" version))
4917 "030yyhpzsj4ivwrla7p9kgvmyjh6b8fr7czf678ykxjj64ccnvr3"))))
4918 (build-system r-build-system)
4920 `(("r-colorspace" ,r-colorspace)
4921 ("r-lmtest" ,r-lmtest)
4922 ("r-mass" ,r-mass)))
4923 (home-page "https://cran.r-project.org/web/packages/vcd/")
4924 (synopsis "Visualizing categorical data")
4925 (description "This package provides visualization techniques, data sets,
4926 summary and inference procedures aimed particularly at categorical data.
4927 Special emphasis is given to highly extensible grid graphics. The package was
4928 originally inspired by the book \"Visualizing Categorical Data\" by Michael
4929 Friendly and is now the main support package for a new book, \"Discrete Data
4930 Analysis with R\" by Michael Friendly and David Meyer (2015).")
4931 (license license:gpl2)))
4933 (define-public r-ica
4940 (uri (cran-uri "ica" version))
4943 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
4944 (build-system r-build-system)
4945 (home-page "https://cran.r-project.org/web/packages/ica/")
4946 (synopsis "Independent component analysis")
4947 (description "This package provides tools for @dfn{Independent Component
4948 Analysis} (ICA) using various algorithms: FastICA,
4949 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4950 of Eigenmatrices} (JADE).")
4951 (license license:gpl2+)))
4953 (define-public r-dtw
4960 (uri (cran-uri "dtw" version))
4963 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z"))))
4964 (build-system r-build-system)
4965 (propagated-inputs `(("r-proxy" ,r-proxy)))
4966 (home-page "http://dtw.r-forge.r-project.org/")
4967 (synopsis "Dynamic Time Warping Algorithms")
4968 (description "This package provides a comprehensive implementation of
4969 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4970 optimal (least cumulative distance) alignment between points of two time
4971 series. Common DTW variants covered include local (slope) and global (window)
4972 constraints, subsequence matches, arbitrary distance definitions,
4973 normalizations, minimum variance matching, and so on.")
4974 (license license:gpl2+)))
4976 (define-public r-sdmtools
4979 (version "1.1-221.2")
4983 (uri (cran-uri "SDMTools" version))
4986 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4987 (properties `((upstream-name . "SDMTools")))
4988 (build-system r-build-system)
4989 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4990 (home-page "https://www.rforge.net/SDMTools/")
4991 (synopsis "Species distribution modelling tools")
4992 (description "This package provides a set of tools for post processing
4993 the outcomes of species distribution modeling exercises. It includes novel
4994 methods for comparing models and tracking changes in distributions through
4995 time. It further includes methods for visualizing outcomes, selecting
4996 thresholds, calculating measures of accuracy and landscape fragmentation
4998 (license license:gpl3+)))
5000 (define-public r-scatterplot3d
5002 (name "r-scatterplot3d")
5007 (uri (cran-uri "scatterplot3d" version))
5010 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
5011 (build-system r-build-system)
5012 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
5013 (synopsis "3D scatter plot")
5014 (description "This package provides an implementation of scatter plots for
5015 plotting. a three dimensional point cloud.")
5016 (license license:gpl2)))
5018 (define-public r-ggridges
5025 (uri (cran-uri "ggridges" version))
5028 "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm"))))
5029 (build-system r-build-system)
5031 `(("r-ggplot2" ,r-ggplot2)
5033 ("r-scales" ,r-scales)
5034 ("r-withr" ,r-withr)))
5036 `(("r-knitr" ,r-knitr)))
5037 (home-page "https://github.com/clauswilke/ggridges")
5038 (synopsis "Ridgeline plots in ggplot2")
5040 "Ridgeline plots provide a convenient way of visualizing changes in
5041 distributions over time or space. This package enables the creation of such
5042 plots in @code{ggplot2}.")
5043 (license license:gpl2)))
5045 (define-public r-ggjoy
5052 (uri (cran-uri "ggjoy" version))
5055 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
5056 (build-system r-build-system)
5058 `(("r-ggplot2" ,r-ggplot2)
5059 ("r-ggridges" ,r-ggridges)))
5060 (home-page "https://github.com/clauswilke/ggjoy")
5061 (synopsis "Joyplots in ggplot2")
5062 (description "Joyplots provide a convenient way of visualizing changes in
5063 distributions over time or space. This package enables the creation of such
5064 plots in @code{ggplot2}.")
5065 (license license:gpl2)))
5067 (define-public r-cli
5074 (uri (cran-uri "cli" version))
5077 "1jh64ixn6mg2ap1sx4azrxkjnlsyjbfxyc9zjkx8m9dlakgf4v2i"))))
5078 (build-system r-build-system)
5080 `(("r-assertthat" ,r-assertthat)
5081 ("r-glue" ,r-glue)))
5082 (home-page "https://github.com/r-lib/cli#readme")
5083 (synopsis "Helpers for developing command line interfaces")
5084 (description "This package provides a suite of tools designed to build
5085 attractive command line interfaces (CLIs). It includes tools for drawing
5086 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
5087 (license license:expat)))
5089 (define-public r-argparser
5091 (name "r-argparser")
5096 (uri (cran-uri "argparser" version))
5099 "0xcl0ivsbc4iw8s7027q4cx68j6s5lihbby0xa9pmlv4wjmcvdr6"))))
5100 (build-system r-build-system)
5101 (home-page "https://bitbucket.org/djhshih/argparser")
5102 (synopsis "Command-line argument parser")
5104 "This package provides a cross-platform command-line argument parser
5105 written purely in R with no external dependencies. It is useful with the
5106 Rscript front-end and facilitates turning an R script into an executable
5108 (license license:gpl3+)))
5110 (define-public r-debugme
5117 (uri (cran-uri "debugme" version))
5120 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
5121 (build-system r-build-system)
5122 (propagated-inputs `(("r-crayon" ,r-crayon)))
5123 (home-page "https://github.com/r-lib/debugme#readme")
5124 (synopsis "Debug R packages")
5126 "This package allows the user to specify debug messages as special string
5127 constants, and control debugging of packages via environment variables.")
5128 (license license:expat)))
5130 (define-public r-processx
5137 (uri (cran-uri "processx" version))
5139 (base32 "055v2gdrgqsfy8s672wsq79bqr44b4jjmcbqivx4p2d6lqx10s73"))))
5140 (build-system r-build-system)
5144 (home-page "https://github.com/r-lib/processx3")
5145 (synopsis "Execute and control system processes")
5147 "This package provides portable tools to run system processes in the
5148 background. It can check if a background process is running; wait on a
5149 background process to finish; get the exit status of finished processes; kill
5150 background processes and their children; restart processes. It can read the
5151 standard output and error of the processes, using non-blocking connections.
5152 @code{processx} can poll a process for standard output or error, with a
5153 timeout. It can also poll several processes at once.")
5154 (license license:expat)))
5156 (define-public r-tsp
5163 (uri (cran-uri "TSP" version))
5166 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
5167 (properties `((upstream-name . "TSP")))
5168 (build-system r-build-system)
5169 (propagated-inputs `(("r-foreach" ,r-foreach)))
5170 (home-page "https://cran.r-project.org/web/packages/TSP/")
5171 (synopsis "Traveling salesperson problem (TSP)")
5172 (description "This package provides basic infrastructure and some
5173 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
5174 traveling salesman problem).")
5175 (license license:gpl3)))
5177 (define-public r-qap
5184 (uri (cran-uri "qap" version))
5187 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
5188 (build-system r-build-system)
5189 (native-inputs `(("gfortran" ,gfortran)))
5190 (home-page "https://cran.r-project.org/web/packages/qap/")
5191 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
5192 (description "This package implements heuristics for the @dfn{quadratic
5193 assignment problem} (QAP). Currently only a simulated annealing heuristic is
5195 (license license:gpl3)))
5197 (define-public r-gclus
5204 (uri (cran-uri "gclus" version))
5207 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
5208 (build-system r-build-system)
5209 (propagated-inputs `(("r-cluster" ,r-cluster)))
5210 (home-page "https://cran.r-project.org/web/packages/gclus/")
5211 (synopsis "Clustering graphics")
5212 (description "This package orders panels in scatterplot matrices and
5213 parallel coordinate displays by some merit index. It contains various indices
5214 of merit, ordering functions, and enhanced versions of @code{pairs} and
5215 @code{parcoord} which color panels according to their merit level.")
5216 (license license:gpl2+)))
5218 (define-public r-webshot
5225 (uri (cran-uri "webshot" version))
5228 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
5229 (build-system r-build-system)
5231 `(("r-callr" ,r-callr)
5232 ("r-jsonlite" ,r-jsonlite)
5233 ("r-magrittr" ,r-magrittr)))
5234 (home-page "https://github.com/wch/webshot/")
5235 (synopsis "Take screenshots of web pages")
5237 "Webshot makes it easy to take screenshots of web pages from within R.
5238 It can also run Shiny applications locally and take screenshots of the
5239 application; and it can render and screenshot static as well as interactive R
5240 Markdown documents.")
5241 (license license:gpl2)))
5243 (define-public r-seriation
5245 (name "r-seriation")
5250 (uri (cran-uri "seriation" version))
5253 "1glxn098ar1v96xlwp85kjxzfd1nyfzp2f82x5z3fm87yv57k4lb"))))
5254 (build-system r-build-system)
5256 `(("r-cluster" ,r-cluster)
5257 ("r-colorspace" ,r-colorspace)
5258 ("r-dendextend" ,r-dendextend)
5259 ("r-gclus" ,r-gclus)
5260 ("r-gplots" ,r-gplots)
5263 ("r-registry" ,r-registry)
5265 (native-inputs `(("gfortran" ,gfortran)))
5266 (home-page "https://s2.smu.edu/IDA/seriation/")
5267 (synopsis "Infrastructure for ordering objects using seriation")
5269 "This package provides infrastructure for seriation with an
5270 implementation of several seriation/sequencing techniques to reorder matrices,
5271 dissimilarity matrices, and dendrograms. It also provides (optimally)
5272 reordered heatmaps, color images and clustering visualizations like
5273 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
5275 (license license:gpl3)))
5277 (define-public r-xfun
5284 (uri (cran-uri "xfun" version))
5286 (base32 "18qjs81fn8q2d2drcan8gpgvrbgxgd0b659c92z19kg2h4c1g3k4"))))
5287 (build-system r-build-system)
5288 ;; knitr itself depends on xfun
5291 `(("r-knitr" ,r-knitr)))
5292 (home-page "https://github.com/yihui/xfun")
5293 (synopsis "Miscellaneous functions")
5295 "This package provides miscellaneous functions commonly used in other
5296 packages maintained by Yihui Xie.")
5297 (license license:expat)))
5299 (define-public r-utf8
5306 (uri (cran-uri "utf8" version))
5309 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
5310 (build-system r-build-system)
5311 (home-page "https://github.com/patperry/r-utf8")
5312 (synopsis "Unicode text processing")
5314 "This package provides tools to process and print UTF-8 encoded
5315 international text (Unicode). Input, validate, normalize, encode, format, and
5317 (license license:asl2.0)))
5319 (define-public r-zeallot
5326 (uri (cran-uri "zeallot" version))
5329 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
5330 (build-system r-build-system)
5331 (home-page "https://github.com/nteetor/zeallot")
5332 (synopsis "Multiple, unpacking, and destructuring assignment")
5334 "This package provides a @code{%<-%} operator to perform multiple,
5335 unpacking, and destructuring assignment in R. The operator unpacks the
5336 right-hand side of an assignment into multiple values and assigns these values
5337 to variables on the left-hand side of the assignment.")
5338 (license license:expat)))
5340 (define-public r-vctrs
5347 (uri (cran-uri "vctrs" version))
5350 "09ddxgzyah7lw42hn6n8fynsixf43s10jamsf94d2aidky63czfz"))))
5351 (build-system r-build-system)
5353 `(("r-digest" ,r-digest)
5354 ("r-ellipsis" ,r-ellipsis)
5356 ("r-rlang" ,r-rlang)))
5358 `(("r-knitr" ,r-knitr)))
5359 (home-page "https://github.com/r-lib/vctrs")
5360 (synopsis "Vector helpers")
5362 "There are three main goals to the @code{vctrs} package:
5365 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
5366 @code{length()} and @code{class()}. These definitions are paired with a
5367 framework for type-coercion and size-recycling.
5368 @item To define type- and size-stability as desirable function properties, use
5369 them to analyse existing base function, and to propose better alternatives.
5370 This work has been particularly motivated by thinking about the ideal
5371 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
5372 @item To provide a new @code{vctr} base class that makes it easy to create new
5373 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
5374 a few new @code{vctrs} generics, making implementation considerably simpler
5377 (license license:gpl3)))
5379 (define-public r-pillar
5386 (uri (cran-uri "pillar" version))
5389 "167ji21fx04s2niw5pjq9vzxgagxzsg3gimh8dzr2kl5ljrb5vfd"))))
5390 (build-system r-build-system)
5393 ("r-crayon" ,r-crayon)
5394 ("r-ellipsis" ,r-ellipsis)
5395 ("r-fansi" ,r-fansi)
5396 ("r-lifecycle" ,r-lifecycle)
5397 ("r-rlang" ,r-rlang)
5399 ("r-vctrs" ,r-vctrs)))
5400 (home-page "https://github.com/r-lib/pillar")
5401 (synopsis "Coloured formatting for columns")
5403 "This package provides a @code{pillar} generic designed for formatting
5404 columns of data using the full range of colours provided by modern
5406 (license license:gpl3)))
5408 (define-public r-uuid
5415 (uri (cran-uri "uuid" version))
5418 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
5419 (build-system r-build-system)
5420 (home-page "https://www.rforge.net/uuid")
5421 (synopsis "Tools for generating and handling of UUIDs")
5423 "This package provides tools for generating and handling of
5424 @dfn{Universally Unique Identifiers} (UUIDs).")
5425 (license license:expat)))
5427 (define-public r-tinytex
5434 (uri (cran-uri "tinytex" version))
5437 "0my1412vn5zri01w2myzn268lfwinbhfgdj4bbcib3s48i9djw0n"))))
5438 (build-system r-build-system)
5440 `(("r-xfun" ,r-xfun)))
5441 (home-page "https://github.com/yihui/tinytex")
5442 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
5444 "This package provides helper functions to install and maintain the LaTeX
5445 distribution named TinyTeX, a lightweight, cross-platform, portable, and
5446 easy-to-maintain version of TeX Live. This package also contains helper
5447 functions to compile LaTeX documents, and install missing LaTeX packages
5449 (license license:expat)))
5451 (define-public r-tinytest
5458 (uri (cran-uri "tinytest" version))
5461 "1asryjrah3fj39gg0c6yxgpr142j5bg2n990v7q8r0a5pb8gcr45"))))
5462 (properties `((upstream-name . "tinytest")))
5463 (build-system r-build-system)
5464 (home-page "https://github.com/markvanderloo/tinytest")
5465 (synopsis "Lightweight unit testing framework")
5467 "This package provides a lightweight unit testing framework. Main
5471 @item install tests with the package;
5472 @item test results are treated as data that can be stored and manipulated;
5473 @item test files are R scripts interspersed with test commands, that can be
5475 @item fully automated build-install-test sequence for packages;
5476 @item skip tests when not run locally (e.g. on CRAN);
5477 @item flexible and configurable output printing;
5478 @item compare computed output with output stored with the package;
5479 @item run tests in parallel;
5480 @item extensible by other packages;
5481 @item report side effects.
5484 (license license:gpl3)))
5486 (define-public r-network
5493 (uri (cran-uri "network" version))
5496 "1cgy7vlbinyndl0zkzvnpcmi240wry6iwfb42sz1mj5c9iwkar7b"))))
5497 (build-system r-build-system)
5499 `(("r-magrittr" ,r-magrittr)
5500 ("r-tibble" ,r-tibble)))
5501 (home-page "https://statnet.org/")
5502 (synopsis "Classes for relational data")
5504 "This package provides tools to create and modify network objects. The
5505 @code{network} class can represent a range of relational data types, and
5506 supports arbitrary vertex/edge/graph attributes.")
5507 (license license:gpl2+)))
5509 (define-public r-stabs
5516 (uri (cran-uri "stabs" version))
5519 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q"))))
5520 (build-system r-build-system)
5522 `(("r-knitr" ,r-knitr)))
5523 (home-page "https://github.com/hofnerb/stabs")
5524 (synopsis "Stability selection with error control")
5526 "This package provides resampling procedures to assess the stability of
5527 selected variables with additional finite sample error control for
5528 high-dimensional variable selection procedures such as Lasso or boosting.
5529 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
5530 complementary pairs stability selection with improved error bounds
5531 (Shah & Samworth, 2013) are implemented. The package can be combined with
5532 arbitrary user specified variable selection approaches.")
5533 (license license:gpl2)))
5535 (define-public r-rle
5542 (uri (cran-uri "rle" version))
5545 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40"))))
5546 (properties `((upstream-name . "rle")))
5547 (build-system r-build-system)
5548 (home-page "https://cran.r-project.org/web/packages/rle/")
5549 (synopsis "Common functions for run-length encoded vectors")
5551 "This package provides common @code{base} and @code{stats} methods for
5552 @code{rle} objects, aiming to make it possible to treat them transparently as
5554 (license license:gpl3)))
5556 (define-public r-statnet-common
5558 (name "r-statnet-common")
5563 (uri (cran-uri "statnet.common" version))
5566 "1z89an46xcl1d7dacj4irhk6pkajdz7v85b2347vczwdf622pksf"))))
5568 `((upstream-name . "statnet.common")))
5569 (build-system r-build-system)
5571 `(("r-coda" ,r-coda)
5573 (home-page "https://statnet.org")
5574 (synopsis "R scripts and utilities used by the Statnet software")
5575 (description "This package provides non-statistical utilities used by the
5576 software developed by the Statnet Project.")
5577 (license license:gpl3)))
5579 (define-public r-statcheck
5581 (name "r-statcheck")
5586 (uri (cran-uri "statcheck" version))
5589 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
5590 (build-system r-build-system)
5592 `(("r-ggplot2" ,r-ggplot2)
5594 ("r-rmarkdown" ,r-rmarkdown)))
5595 (home-page "https://cran.r-project.org/web/packages/statcheck/")
5596 (synopsis "Extract statistics from articles and recompute p-values")
5597 (description "This package can automatically extract statistical
5598 null-hypothesis significant testing (NHST) results from articles and recompute
5599 the p-values based on the reported test statistic and degrees of freedom to
5600 detect possible inconsistencies.")
5601 (license license:gpl2)))
5603 (define-public r-sna
5610 (uri (cran-uri "sna" version))
5613 "0ai0v4538d30m4wks5s3lch1yfmx1ml0nnrz7ihs097lv586a09s"))))
5614 (build-system r-build-system)
5616 `(("r-network" ,r-network)
5617 ("r-statnet-common" ,r-statnet-common)))
5618 (home-page "https://statnet.org")
5619 (synopsis "Tools for social network analysis")
5621 "This package provides a range of tools for social network analysis,
5622 including node and graph-level indices, structural distance and covariance
5623 methods, structural equivalence detection, network regression, random graph
5624 generation, and 2D/3D network visualization.")
5625 (license license:gpl2+)))
5627 (define-public r-tfisher
5634 (uri (cran-uri "TFisher" version))
5637 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
5638 (properties `((upstream-name . "TFisher")))
5639 (build-system r-build-system)
5641 `(("r-matrix" ,r-matrix)
5642 ("r-mvtnorm" ,r-mvtnorm)
5644 (home-page "https://cran.r-project.org/web/packages/TFisher/")
5645 (synopsis "Optimal thresholding Fisher's p-value combination method")
5647 "This package provides the @dfn{cumulative distribution function} (CDF),
5648 quantile, and statistical power calculator for a collection of thresholding
5649 Fisher's p-value combination methods, including Fisher's p-value combination
5650 method, truncated product method and, in particular, soft-thresholding
5651 Fisher's p-value combination method which is proven to be optimal in some
5652 context of signal detection. The p-value calculator for the omnibus version
5653 of these tests are also included.")
5654 (license license:gpl2)))
5656 (define-public r-ttr
5663 (uri (cran-uri "TTR" version))
5666 "06vicgbhwpsww09hhha5mbcd0cwip6cvkfbhjjhp950rv64bk1r5"))))
5667 (properties `((upstream-name . "TTR")))
5668 (build-system r-build-system)
5670 `(("r-curl" ,r-curl)
5673 (home-page "https://github.com/joshuaulrich/TTR")
5674 (synopsis "Technical trading rules")
5676 "This package provides functions and data to construct technical trading
5678 (license license:gpl2)))
5680 (define-public r-leaps
5687 (uri (cran-uri "leaps" version))
5690 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
5691 (build-system r-build-system)
5692 (native-inputs `(("gfortran" ,gfortran)))
5693 (home-page "https://cran.r-project.org/web/packages/leaps/")
5694 (synopsis "Regression subset selection")
5696 "This package provides tools for regression subset selection, including
5697 exhaustive search.")
5698 (license license:gpl2+)))
5700 (define-public r-splus2r
5707 (uri (cran-uri "splus2R" version))
5710 "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x"))))
5711 (properties `((upstream-name . "splus2R")))
5712 (build-system r-build-system)
5713 (home-page "https://cran.r-project.org/web/packages/splus2R/")
5714 (synopsis "Supplemental S-PLUS functionality in R")
5716 "Currently there are many functions in S-PLUS that are missing in R. To
5717 facilitate the conversion of S-PLUS packages to R packages, this package
5718 provides some missing S-PLUS functionality in R.")
5719 (license license:gpl2)))
5721 (define-public r-ifultools
5723 (name "r-ifultools")
5728 (uri (cran-uri "ifultools" version))
5731 "0f95vqc47dgssqngznk0rclr72ndbyxc7gdq2cmbksvq7qpn3gg1"))))
5732 (build-system r-build-system)
5734 `(("r-mass" ,r-mass)
5735 ("r-splus2r" ,r-splus2r)))
5736 (home-page "https://cran.r-project.org/web/packages/ifultools/")
5737 (synopsis "Insightful research tools")
5738 (description "This package provides C code used by the wmtsa, fractal, and
5740 (license license:gpl2)))
5742 (define-public r-sapa
5749 (uri (cran-uri "sapa" version))
5752 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
5753 (build-system r-build-system)
5755 `(("r-ifultools" ,r-ifultools)
5756 ("r-splus2r" ,r-splus2r)))
5757 (home-page "https://cran.r-project.org/web/packages/sapa/")
5758 (synopsis "Spectral analysis for physical applications")
5759 (description "This package provides software for the book Spectral
5760 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
5761 Cambridge University Press, 1993.")
5762 (license license:gpl2)))
5764 (define-public r-aggregation
5766 (name "r-aggregation")
5771 (uri (cran-uri "aggregation" version))
5774 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
5775 (build-system r-build-system)
5776 (home-page "https://cran.r-project.org/web/packages/aggregation/")
5777 (synopsis "Methods for p-value aggregation")
5779 "This package contains functionality for performing the following methods
5780 of p-value aggregation: Fisher's method, the Lancaster method (weighted
5781 Fisher's method), and Sidak correction.")
5782 (license license:gpl3)))
5784 (define-public r-quantmod
5791 (uri (cran-uri "quantmod" version))
5794 "0dbcrncv06iqcbkky95dd7l32xq0hhbnkb0kj8wwzym1jf748h5a"))))
5795 (build-system r-build-system)
5797 `(("r-curl" ,r-curl)
5801 (home-page "https://cran.r-project.org/web/packages/quantmod/")
5802 (synopsis "Quantitative financial modelling framework")
5803 (description "This package provides a quantitative financial modelling
5804 framework to allow users to specify, build, trade, and analyse quantitative
5805 financial trading strategies.")
5806 (license license:gpl3)))
5808 (define-public r-tseries
5815 (uri (cran-uri "tseries" version))
5818 "0wa4rcf0igayi1yrwc6wak6d491560p0z89rz32haqlkiiq25gak"))))
5819 (build-system r-build-system)
5821 `(("r-quadprog" ,r-quadprog)
5822 ("r-quantmod" ,r-quantmod)
5825 `(("gfortran" ,gfortran)))
5826 (home-page "https://cran.r-project.org/web/packages/tseries/")
5827 (synopsis "Time series analysis and computational finance")
5829 "This package provides functions relating to time series analysis and
5830 computational finance.")
5831 (license license:gpl2)))
5833 (define-public r-wmtsa
5840 (uri (cran-uri "wmtsa" version))
5843 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
5844 (build-system r-build-system)
5846 `(("r-ifultools" ,r-ifultools)
5848 ("r-splus2r" ,r-splus2r)))
5849 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
5850 (synopsis "Wavelet methods for time series analysis")
5852 "This package provides software to accompany the book \"Wavelet Methods
5853 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
5854 University Press, 2000.")
5855 (license license:gpl2)))
5857 (define-public r-tsa
5864 (uri (cran-uri "TSA" version))
5867 "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb"))))
5868 (properties `((upstream-name . "TSA")))
5869 (build-system r-build-system)
5871 `(("r-leaps" ,r-leaps)
5872 ("r-locfit" ,r-locfit)
5874 ("r-tseries" ,r-tseries)))
5875 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
5876 (synopsis "Time series analysis")
5878 "This package contains R functions and datasets detailed in the book
5879 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
5880 Cryer and Kung-Sik Chan.")
5881 (license license:gpl2+)))
5883 (define-public r-extradistr
5885 (name "r-extradistr")
5890 (uri (cran-uri "extraDistr" version))
5893 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
5894 (properties `((upstream-name . "extraDistr")))
5895 (build-system r-build-system)
5897 `(("r-rcpp" ,r-rcpp)))
5898 (home-page "https://github.com/twolodzko/extraDistr")
5899 (synopsis "Additional univariate and multivariate distributions")
5901 "This package implements density, distribution functions, quantile
5902 functions and random generation functions for a large number of univariate and
5903 multivariate distributions.")
5904 (license license:gpl2)))
5906 (define-public r-fractal
5913 (uri (cran-uri "fractal" version))
5916 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
5917 (build-system r-build-system)
5919 `(("r-ifultools" ,r-ifultools)
5922 ("r-scatterplot3d" ,r-scatterplot3d)
5923 ("r-splus2r" ,r-splus2r)
5924 ("r-wmtsa" ,r-wmtsa)))
5925 (home-page "https://cran.r-project.org/web/packages/fractal/")
5926 (synopsis "Fractal time series modeling and analysis")
5928 "This package provides tools for stochastic fractal and deterministic
5929 chaotic time series analysis.")
5930 (license license:gpl2)))
5932 (define-public r-urca
5939 (uri (cran-uri "urca" version))
5942 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
5943 (build-system r-build-system)
5944 (propagated-inputs `(("r-nlme" ,r-nlme)))
5945 (native-inputs `(("gfortran" ,gfortran)))
5946 (home-page "https://cran.r-project.org/web/packages/urca/")
5947 (synopsis "Unit root and cointegration tests for time series data")
5949 "This package provides unit root and cointegration tests encountered in
5950 applied econometric analysis.")
5951 (license license:gpl2+)))
5953 (define-public r-cubature
5960 (uri (cran-uri "cubature" version))
5963 "006la36gxdikvmdnq4ny7ik7r30id4z3b3fqsl57dpqwkpsbsgrq"))))
5964 (build-system r-build-system)
5966 `(("r-rcpp" ,r-rcpp)))
5968 `(("r-knitr" ,r-knitr)))
5969 (home-page "https://github.com/bnaras/cubature")
5970 (synopsis "Adaptive multivariate integration over hypercubes")
5972 "This package is an R wrapper around the cubature C library for adaptive
5973 multivariate integration over hypercubes. This version provides both
5974 @code{hcubature} and @code{pcubature} routines in addition to a vector
5976 ;; The included cubature C library is released under GPLv2+, but the
5977 ;; wrapper declares the license to be GPLv3+.
5978 (license (list license:gpl2+ license:gpl3+))))
5980 (define-public r-trend
5987 (uri (cran-uri "trend" version))
5990 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
5991 (build-system r-build-system)
5993 `(("r-extradistr" ,r-extradistr)))
5995 `(("gfortran" ,gfortran)))
5996 (home-page "https://cran.r-project.org/web/packages/trend/")
5997 (synopsis "Non-parametric trend tests and change-point detection")
5999 "The analysis of environmental data often requires the detection of
6000 trends and change-points. This package includes tests for trend
6001 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
6002 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
6003 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
6004 correlation trend test), change-point detection (Lanzante's test procedures,
6005 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
6006 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
6007 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
6008 sample Robust Rank-Order Distributional Test.")
6009 (license license:gpl3)))
6011 (define-public r-expm
6018 (uri (cran-uri "expm" version))
6021 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c"))))
6022 (build-system r-build-system)
6023 (propagated-inputs `(("r-matrix" ,r-matrix)))
6024 (native-inputs `(("gfortran" ,gfortran)))
6025 (home-page "https://r-forge.r-project.org/projects/expm/")
6026 (synopsis "Tools for matrix exponentials and related quantities")
6028 "This package provides tools for the computation of the matrix
6029 exponential, logarithm, square root, and related quantities.")
6030 (license license:gpl2+)))
6032 (define-public r-complexplus
6034 (name "r-complexplus")
6039 (uri (cran-uri "complexplus" version))
6042 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
6043 (build-system r-build-system)
6045 `(("r-expm" ,r-expm)
6046 ("r-matrix" ,r-matrix)))
6047 (home-page "https://cran.r-project.org/web/packages/complexplus/")
6048 (synopsis "Functions of complex or real variables")
6050 "This package extends several functions to the complex domain, including
6051 the matrix exponential and logarithm, and the determinant.")
6052 (license license:gpl2)))
6054 (define-public r-phontools
6056 (name "r-phontools")
6061 (uri (cran-uri "phonTools" version))
6064 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
6065 (properties `((upstream-name . "phonTools")))
6066 (build-system r-build-system)
6067 (home-page "http://www.santiagobarreda.com/rscripts.html")
6068 (synopsis "Tools for phonetic and acoustic analyses")
6070 "This package contains tools for the organization, display, and analysis
6071 of the sorts of data frequently encountered in phonetics research and
6072 experimentation, including the easy creation of IPA vowel plots, and the
6073 creation and manipulation of WAVE audio files.")
6074 (license license:bsd-2)))
6083 (uri (cran-uri "np" version))
6086 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
6087 (build-system r-build-system)
6089 `(("r-boot" ,r-boot)
6090 ("r-cubature" ,r-cubature)
6091 ("r-quadprog" ,r-quadprog)
6092 ("r-quantreg" ,r-quantreg)))
6093 (home-page "https://github.com/JeffreyRacine/R-Package-np")
6094 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
6095 (description "This package provides non-parametric (and semi-parametric)
6096 kernel methods that seamlessly handle a mix of continuous, unordered, and
6097 ordered factor data types.")
6098 ;; Any version of the GPL.
6099 (license license:gpl3+)))
6101 (define-public r-powerplus
6103 (name "r-powerplus")
6108 (uri (cran-uri "powerplus" version))
6111 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
6112 (build-system r-build-system)
6114 `(("r-complexplus" ,r-complexplus)
6117 ("r-matrix" ,r-matrix)
6118 ("r-phontools" ,r-phontools)))
6119 (home-page "https://cran.r-project.org/web/packages/powerplus/")
6120 (synopsis "Exponentiation operations")
6122 "This package provides tools for the computation of matrix and scalar
6124 (license license:gpl2)))
6126 (define-public r-egg
6133 (uri (cran-uri "egg" version))
6136 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
6137 (properties `((upstream-name . "egg")))
6138 (build-system r-build-system)
6140 `(("r-ggplot2" ,r-ggplot2)
6141 ("r-gridextra" ,r-gridextra)
6142 ("r-gtable" ,r-gtable)))
6143 (home-page "https://cran.r-project.org/web/packages/egg")
6144 (synopsis "Extensions for ggplot2")
6146 "This package provides miscellaneous functions to help customize ggplot2
6147 objects. High-level functions are provided to post-process ggplot2 layouts
6148 and allow alignment between plot panels, as well as setting panel sizes to
6149 fixed values. Other functions include a custom @code{geom}, and helper
6150 functions to enforce symmetric scales or add tags to facetted plots.")
6151 (license license:gpl3)))
6153 (define-public r-heatmaply
6155 (name "r-heatmaply")
6160 (uri (cran-uri "heatmaply" version))
6163 "0hspfkninwy62sf8gkdcsvwnvl66bbnjs2dpah9rr95a3rsgdp9d"))))
6164 (build-system r-build-system)
6166 `(("r-assertthat" ,r-assertthat)
6167 ("r-colorspace" ,r-colorspace)
6168 ("r-dendextend" ,r-dendextend)
6170 ("r-ggplot2" ,r-ggplot2)
6171 ("r-htmlwidgets" ,r-htmlwidgets)
6172 ("r-magrittr" ,r-magrittr)
6173 ("r-plotly" ,r-plotly)
6174 ("r-rcolorbrewer" ,r-rcolorbrewer)
6175 ("r-reshape2" ,r-reshape2)
6176 ("r-scales" ,r-scales)
6177 ("r-seriation" ,r-seriation)
6178 ("r-viridis" ,r-viridis)
6179 ("r-webshot" ,r-webshot)))
6181 `(("r-knitr" ,r-knitr)))
6182 (home-page "https://cran.r-project.org/package=heatmaply")
6183 (synopsis "Interactive cluster heat maps using plotly")
6185 "This package enables you to create interactive cluster heatmaps that can
6186 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
6187 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
6188 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
6189 a popular graphical method for visualizing high-dimensional data, in which a
6190 table of numbers is encoded as a grid of colored cells. The rows and columns
6191 of the matrix are ordered to highlight patterns and are often accompanied by
6193 ;; Either version of the license.
6194 (license (list license:gpl2 license:gpl3))))
6203 (uri (cran-uri "h5" version))
6206 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
6207 (build-system r-build-system)
6212 `(("which" ,which)))
6214 `(("r-rcpp" ,r-rcpp)))
6215 (home-page "https://github.com/mannau/h5")
6216 (synopsis "Interface to the HDF5 Library")
6218 "This package provides an S4 interface to the HDF5 library supporting
6219 fast storage and retrieval of R-objects like vectors, matrices and arrays to
6220 binary files in a language independent format. The HDF5 format can therefore
6221 be used as an alternative to R's save/load mechanism. Since h5 is able to
6222 access only subsets of stored data it can also handle data sets which do not
6224 (license license:bsd-2)))
6226 (define-public r-cgdsr
6233 (uri (cran-uri "cgdsr" version))
6236 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
6237 (build-system r-build-system)
6239 `(("r-httr" ,r-httr)
6240 ("r-r-methodss3" ,r-r-methodss3)
6241 ("r-r-oo" ,r-r-oo)))
6242 (home-page "https://github.com/cBioPortal/cgdsr")
6243 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
6245 "This package provides a basic set of R functions for querying the Cancer
6246 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
6247 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
6248 (license license:lgpl3)))
6250 (define-public r-import
6257 (uri (cran-uri "import" version))
6260 "018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37"))))
6261 (build-system r-build-system)
6263 `(("r-knitr" ,r-knitr)))
6264 (home-page "https://github.com/smbache/import")
6265 (synopsis "Import mechanism for R")
6267 "This is an alternative mechanism for importing objects from packages.
6268 The syntax allows for importing multiple objects from a package with a single
6269 command in an expressive way. The import package bridges some of the gap
6270 between using @code{library} (or @code{require}) and direct (single-object)
6271 imports. Furthermore the imported objects are not placed in the current
6272 environment. It is also possible to import objects from stand-alone @code{.R}
6274 (license license:expat)))
6276 (define-public r-shinyace
6283 (uri (cran-uri "shinyAce" version))
6286 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
6287 (properties `((upstream-name . "shinyAce")))
6288 (build-system r-build-system)
6290 `(("r-shiny" ,r-shiny)
6291 ("r-jsonlite" ,r-jsonlite)))
6292 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
6293 (synopsis "Ace editor bindings for Shiny")
6295 "This package provides Ace editor bindings to enable a rich text editing
6296 environment within Shiny.")
6297 (license license:expat)))
6299 (define-public r-randomizr
6301 (name "r-randomizr")
6306 (uri (cran-uri "randomizr" version))
6309 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
6310 (properties `((upstream-name . "randomizr")))
6311 (build-system r-build-system)
6313 `(("r-knitr" ,r-knitr)))
6314 (home-page "https://declaredesign.org/r/randomizr/")
6315 (synopsis "Tools for common forms of random assignment and sampling")
6317 "This package provides tools for generating random assignments for common
6318 experimental designs and random samples for common sampling designs.")
6319 (license license:expat)))
6321 (define-public r-base64url
6323 (name "r-base64url")
6328 (uri (cran-uri "base64url" version))
6331 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
6332 (build-system r-build-system)
6334 `(("r-backports" ,r-backports)))
6335 (home-page "https://github.com/mllg/base64url")
6336 (synopsis "Fast and URL-safe base64 encoder and decoder")
6338 "This package provides a URL-safe base64 encoder and decoder. In
6339 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
6340 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
6341 encoder does not fill the string with trailing @code{=}. The resulting
6342 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
6343 and thus are safe to use in URLs or for file names. The package also comes
6344 with a simple base32 encoder/decoder suited for case insensitive file
6346 (license license:gpl3)))
6348 (define-public r-radiant-data
6350 (name "r-radiant-data")
6355 (uri (cran-uri "radiant.data" version))
6358 "08bqqrfvpgyf613ikihwfnzb23l23f5nfs7zynnxbjxc1zfhbpny"))
6359 (modules '((guix build utils)))
6362 ;; Delete files that are under CC-NC-SA.
6363 (delete-file-recursively "inst/app/tools/help")
6365 (properties `((upstream-name . "radiant.data")))
6366 (build-system r-build-system)
6368 `(("r-base64enc" ,r-base64enc)
6369 ("r-broom" ,r-broom)
6372 ("r-dplyr" ,r-dplyr)
6375 ("r-ggplot2" ,r-ggplot2)
6376 ("r-import" ,r-import)
6377 ("r-jsonlite" ,r-jsonlite)
6378 ("r-knitr" ,r-knitr)
6379 ("r-lubridate" ,r-lubridate)
6380 ("r-magrittr" ,r-magrittr)
6381 ("r-markdown" ,r-markdown)
6383 ("r-patchwork" ,r-patchwork)
6384 ("r-plotly" ,r-plotly)
6385 ("r-psych" ,r-psych)
6386 ("r-randomizr" ,r-randomizr)
6387 ("r-readr" ,r-readr)
6388 ("r-readxl" ,r-readxl)
6389 ("r-rlang" ,r-rlang)
6390 ("r-rmarkdown" ,r-rmarkdown)
6391 ("r-rstudioapi" ,r-rstudioapi)
6392 ("r-scales" ,r-scales)
6393 ("r-shiny" ,r-shiny)
6394 ("r-shinyfiles" ,r-shinyfiles)
6395 ("r-shinyace" ,r-shinyace)
6396 ("r-stringi" ,r-stringi)
6397 ("r-tibble" ,r-tibble)
6398 ("r-tidyr" ,r-tidyr)
6399 ("r-writexl" ,r-writexl)))
6400 (home-page "https://github.com/radiant-rstats/radiant.data")
6401 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
6403 "The Radiant Data menu includes interfaces for loading, saving, viewing,
6404 visualizing, summarizing, transforming, and combining data. It also contains
6405 functionality to generate reproducible reports of the analyses conducted in
6407 (license license:agpl3)))
6409 (define-public r-algdesign
6411 (name "r-algdesign")
6416 (uri (cran-uri "AlgDesign" version))
6418 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
6419 (properties `((upstream-name . "AlgDesign")))
6420 (build-system r-build-system)
6421 (home-page "https://github.com/jvbraun/AlgDesign")
6422 (synopsis "Algorithmic experimental design")
6424 "This package provides tools to calculate exact and approximate theory
6425 experimental designs for D, A, and I criteria. Very large designs may be
6426 created. Experimental designs may be blocked or blocked designs created from
6427 a candidate list, using several criteria. The blocking can be done when whole
6428 and within plot factors interact.")
6429 (license license:gpl2+)))
6431 (define-public r-signal
6438 (uri (cran-uri "signal" version))
6441 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
6442 (build-system r-build-system)
6443 (propagated-inputs `(("r-mass" ,r-mass)))
6444 (native-inputs `(("gfortran" ,gfortran)))
6445 (home-page "https://cran.r-project.org/web/packages/signal/")
6446 (synopsis "Signal processing")
6448 "This package provides a set of signal processing functions originally
6449 written for Matlab and GNU Octave. It includes filter generation utilities,
6450 filtering functions, resampling routines, and visualization of filter models.
6451 It also includes interpolation functions.")
6452 (license license:gpl2)))
6454 (define-public r-gsubfn
6461 (uri (cran-uri "gsubfn" version))
6464 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
6465 (build-system r-build-system)
6466 (propagated-inputs `(("r-proto" ,r-proto)))
6467 (home-page "https://code.google.com/archive/p/gsubfn/")
6468 (synopsis "Utilities for strings and function arguments.")
6470 "This package provides @code{gsubfn} which is like @code{gsub} but can
6471 take a replacement function or certain other objects instead of the
6472 replacement string. Matches and back references are input to the replacement
6473 function and replaced by the function output. @code{gsubfn} can be used to
6474 split strings based on content rather than delimiters and for quasi-perl-style
6475 string interpolation. The package also has facilities for translating
6476 formulas to functions and allowing such formulas in function calls instead of
6478 (license license:gpl2+)))
6480 (define-public r-sqldf
6487 (uri (cran-uri "sqldf" version))
6490 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
6491 (build-system r-build-system)
6493 `(("r-chron" ,r-chron)
6495 ("r-gsubfn" ,r-gsubfn)
6496 ("r-proto" ,r-proto)
6497 ("r-rsqlite" ,r-rsqlite)))
6498 (home-page "https://github.com/ggrothendieck/sqldf")
6499 (synopsis "Manipulate R data frames using SQL")
6501 "The @code{sqldf} function is typically passed a single argument which is
6502 an SQL select statement where the table names are ordinary R data frame names.
6503 @code{sqldf} transparently sets up a database, imports the data frames into
6504 that database, performs the SQL statement and returns the result using a
6505 heuristic to determine which class to assign to each column of the returned
6506 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
6507 used to read filtered files into R even if the original files are larger than
6508 R itself can handle.")
6509 (license license:gpl2)))
6511 (define-public r-abind
6518 (uri (cran-uri "abind" version))
6521 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
6522 (build-system r-build-system)
6523 (home-page "https://cran.r-project.org/web/packages/abind/")
6524 (synopsis "Combine multidimensional arrays")
6526 "This package provides tools to combine multidimensional arrays into a
6527 single array. This is a generalization of @code{cbind} and @code{rbind}. It
6528 works with vectors, matrices, and higher-dimensional arrays. It also provides
6529 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
6530 extracting and replacing data in arrays.")
6531 (license license:lgpl2.0+)))
6533 (define-public r-prroc
6540 (uri (cran-uri "PRROC" version))
6543 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
6544 (properties `((upstream-name . "PRROC")))
6545 (build-system r-build-system)
6546 (home-page "https://cran.r-project.org/web/packages/PRROC/")
6547 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
6549 "This package computes the areas under the @dfn{precision-recall} (PR)
6550 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
6551 contrast to other implementations, the interpolation between points of the PR
6552 curve is done by a non-linear piecewise function. In addition to the areas
6553 under the curves, the curves themselves can also be computed and plotted by a
6554 specific S3-method.")
6555 (license license:gpl3)))
6557 (define-public r-vim
6564 (uri (cran-uri "VIM" version))
6567 "1a8aw0ysaf0al95m2la2zx1p3g5mnwqx0x30br1s1dqqkfnv57hz"))))
6568 (properties `((upstream-name . "VIM")))
6569 (build-system r-build-system)
6572 ("r-colorspace" ,r-colorspace)
6573 ("r-data-table" ,r-data-table)
6574 ("r-e1071" ,r-e1071)
6575 ("r-laeken" ,r-laeken)
6576 ("r-magrittr" ,r-magrittr)
6579 ("r-ranger" ,r-ranger)
6581 ("r-robustbase" ,r-robustbase)
6585 `(("r-knitr" ,r-knitr)))
6586 (home-page "https://github.com/alexkowa/VIM")
6587 (synopsis "Visualization and imputation of missing values")
6589 "This package provides tools for the visualization of missing and/or
6590 imputed values are introduced, which can be used for exploring the data and
6591 the structure of the missing and/or imputed values. Depending on this
6592 structure of the missing values, the corresponding methods may help to
6593 identify the mechanism generating the missing values and explore the
6594 data including missing values. In addition, the quality of imputation can be
6595 visually explored using various univariate, bivariate, multiple and
6596 multivariate plot methods.")
6597 (license license:gpl2+)))
6599 (define-public r-fnn
6606 (uri (cran-uri "FNN" version))
6609 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
6610 (properties `((upstream-name . "FNN")))
6611 (build-system r-build-system)
6612 (home-page "https://cran.r-project.org/web/packages/FNN")
6613 (synopsis "Fast nearest neighbor search algorithms and applications")
6615 "This package provides cover-tree and kd-tree fast k-nearest neighbor
6616 search algorithms. Related applications including KNN classification,
6617 regression and information measures are implemented.")
6618 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
6619 ;; later can be used.
6620 (license license:gpl2+)))
6622 (define-public r-smoother
6629 (uri (cran-uri "smoother" version))
6632 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
6633 (build-system r-build-system)
6635 `(("r-ttr" ,r-ttr)))
6636 (home-page "https://cran.r-project.org/web/packages/smoother")
6637 (synopsis "Functions relating to the smoothing of numerical data")
6639 "This package provides a collection of methods for smoothing numerical
6640 data, commencing with a port of the Matlab gaussian window smoothing function.
6641 In addition, several functions typically used in smoothing of financial data
6643 (license license:gpl2)))
6645 (define-public r-riverplot
6647 (name "r-riverplot")
6652 (uri (cran-uri "riverplot" version))
6655 "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj"))))
6656 (build-system r-build-system)
6658 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
6660 `(("r-knitr" ,r-knitr)))
6661 (home-page "https://logfc.wordpress.com")
6662 (synopsis "Sankey or ribbon plots")
6664 "Sankey plots are a type of diagram that is convenient to illustrate how
6665 flow of information, resources etc. separates and joins, much like observing
6666 how rivers split and merge. For example, they can be used to compare
6667 different clusterings. This package provides an implementation of Sankey
6669 (license license:gpl2+)))
6671 (define-public r-dyn
6678 (uri (cran-uri "dyn" version))
6681 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
6682 (build-system r-build-system)
6684 `(("r-zoo" ,r-zoo)))
6685 (home-page "https://cran.r-project.org/web/packages/dyn")
6686 (synopsis "Time series regression")
6688 "This package provides the dyn class interfaces @code{ts}, @code{irts},
6689 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
6690 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
6691 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
6692 @code{randomForest::randomForest()} and other regression functions, allowing
6693 those functions to be used with time series including specifications that may
6694 contain lags, diffs and missing values.")
6696 (license license:gpl2+)))
6698 (define-public r-catdap
6705 (uri (cran-uri "catdap" version))
6708 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
6709 (build-system r-build-system)
6711 `(("gfortran" ,gfortran)))
6712 (home-page "https://cran.r-project.org/web/packages/catdap/")
6713 (synopsis "Tools for categorical data analysis")
6715 "This package provides functions for analyzing multivariate data.
6716 Dependencies of the distribution of the specified variable (response
6717 variable) to other variables (explanatory variables) are derived and
6718 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
6719 (license license:gpl2+)))
6721 (define-public r-arules
6728 (uri (cran-uri "arules" version))
6731 "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm"))))
6732 (build-system r-build-system)
6734 `(("r-matrix" ,r-matrix)))
6735 (home-page "https://github.com/mhahsler/arules")
6736 (synopsis "Mining association rules and frequent itemsets")
6738 "This package provides an infrastructure for representing, manipulating
6739 and analyzing transaction data and patterns (frequent itemsets and association rules).
6740 It also provides C implementations of the association mining algorithms Apriori
6742 (license license:gpl3)))
6744 (define-public r-parsedate
6746 (name "r-parsedate")
6751 (uri (cran-uri "parsedate" version))
6754 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
6755 (build-system r-build-system)
6757 `(("r-rematch2" ,r-rematch2)))
6758 (home-page "https://github.com/gaborcsardi/parsedate")
6760 "Recognize and parse dates in various formats")
6762 "This package provides three functions for dealing with dates:
6763 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
6764 time formats, @code{parse_date} parses dates in unspecified formats,
6765 and @code{format_iso_8601} formats a date in ISO 8601 format.")
6766 (license license:gpl2)))
6768 (define-public r-abc-data
6775 (uri (cran-uri "abc.data" version))
6778 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
6779 (properties `((upstream-name . "abc.data")))
6780 (build-system r-build-system)
6781 (home-page "https://cran.r-project.org/web/packages/abc.data/")
6782 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
6784 "This package contains data which are used by functions of the abc
6785 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
6786 algorithms for performing parameter estimation, model selection, and
6788 (license license:gpl3+)))
6790 (define-public r-abc
6797 (uri (cran-uri "abc" version))
6800 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
6801 (build-system r-build-system)
6803 `(("r-abc-data" ,r-abc-data)
6804 ("r-locfit" ,r-locfit)
6807 ("r-quantreg" ,r-quantreg)))
6808 (home-page "https://cran.r-project.org/web/packages/abc/")
6809 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
6811 "This package implements several @dfn{Approximate Bayesian
6812 Computation} (ABC) algorithms for performing parameter estimation, model
6813 selection, and goodness-of-fit. Cross-validation tools are also available for
6814 measuring the accuracy of ABC estimates, and to calculate the
6815 misclassification probabilities of different models.")
6816 (license license:gpl3+)))
6818 (define-public r-zip
6825 (uri (cran-uri "zip" version))
6828 "0b3wmbx5v0i1scylgk4nli2ljg4p12wx7a1sqljklv9969wl3p8i"))))
6829 (build-system r-build-system)
6830 (home-page "https://github.com/gaborcsardi/zip")
6831 (synopsis "Cross-platform Zip compression")
6833 "This package provides a cross-platform Zip compression library for R.
6834 It is a replacement for the @code{zip} function, that does not require any
6835 additional external tools on any platform.")
6836 (license license:cc0)))
6838 (define-public r-openxlsx
6845 (uri (cran-uri "openxlsx" version))
6848 "0vz4nlrwgsiifrgza8kfd9i1c0ya6plymrgk59vyy2z54vc8kvyd"))))
6849 (build-system r-build-system)
6851 `(("r-rcpp" ,r-rcpp)
6852 ("r-stringi" ,r-stringi)
6855 `(("r-knitr" ,r-knitr)))
6856 (home-page "https://github.com/awalker89/openxlsx")
6857 (synopsis "Read, write and edit XLSX files")
6859 "This package simplifies the creation of Excel @code{.xlsx} files by
6860 providing a high level interface to writing, styling and editing worksheets.
6861 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
6862 and @code{XLConnect} packages with the added benefit of removing the
6863 dependency on Java.")
6864 (license license:gpl3)))
6866 (define-public r-rio
6873 (uri (cran-uri "rio" version))
6876 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
6877 (build-system r-build-system)
6879 `(("r-curl" ,r-curl)
6880 ("r-data-table" ,r-data-table)
6881 ("r-foreign" ,r-foreign)
6882 ("r-haven" ,r-haven)
6883 ("r-openxlsx" ,r-openxlsx)
6884 ("r-readxl" ,r-readxl)
6885 ("r-tibble" ,r-tibble)))
6886 (home-page "https://github.com/leeper/rio")
6887 (synopsis "Swiss-army knife for data I/O")
6889 "This package provides streamlined data import and export infrastructure
6890 by making assumptions that the user is probably willing to make: @code{import}
6891 and @code{export} determine the data structure from the file extension,
6892 reasonable defaults are used for data import and export (e.g.,
6893 @code{stringsAsFactors=FALSE}), web-based import is natively
6894 supported (including from SSL/HTTPS), compressed files can be read directly
6895 without explicit decompression, and fast import packages are used where
6896 appropriate. An additional convenience function, @code{convert}, provides a
6897 simple method for converting between file types.")
6898 (license license:gpl2)))
6900 (define-public r-maptools
6907 (uri (cran-uri "maptools" version))
6910 "0jgf3wg47jdnznxb3ncv4is9ackwviy4lzcyggqwzw3wh6jnvb6s"))))
6911 (build-system r-build-system)
6913 `(("r-foreign" ,r-foreign)
6914 ("r-lattice" ,r-lattice)
6916 (home-page "https://r-forge.r-project.org/projects/maptools/")
6917 (synopsis "Tools for reading and handling spatial objects")
6919 "This package provides a set of tools for manipulating and reading
6920 geographic data, in particular ESRI Shapefiles. It includes binary access to
6921 GSHHG shoreline files. The package also provides interface wrappers for
6922 exchanging spatial objects with other R packages.")
6923 ;; The C source files from shapelib are released under the Expat license.
6924 ;; The R code is released under GPL version 2 or later.
6925 (license (list license:gpl2+
6928 (define-public r-later
6935 (uri (cran-uri "later" version))
6938 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
6939 (build-system r-build-system)
6943 ("r-rlang" ,r-rlang)))
6945 `(("r-knitr" ,r-knitr)))
6946 (home-page "https://github.com/r-lib/later")
6947 (synopsis "Utilities for delaying function execution")
6949 "This package provides tools to execute arbitrary R or C functions some
6950 time after the current time, after the R execution stack has emptied.")
6951 (license license:gpl2+)))
6953 (define-public r-promises
6960 (uri (cran-uri "promises" version))
6963 "002qkhcn3ri6a3w5fizjvdvrjgvqiw8i7rl9jglcnqik5kmwc61p"))))
6964 (build-system r-build-system)
6966 `(("r-later" ,r-later)
6967 ("r-magrittr" ,r-magrittr)
6970 ("r-rlang" ,r-rlang)))
6972 `(("r-knitr" ,r-knitr)))
6973 (home-page "https://rstudio.github.io/promises")
6974 (synopsis "Abstractions for promise-based asynchronous programming")
6976 "This package provides fundamental abstractions for doing asynchronous
6977 programming in R using promises. Asynchronous programming is useful for
6978 allowing a single R process to orchestrate multiple tasks in the background
6979 while also attending to something else. Semantics are similar to JavaScript
6980 promises, but with a syntax that is idiomatic R.")
6981 (license license:expat)))
6983 (define-public r-dosnow
6990 (uri (cran-uri "doSNOW" version))
6993 "0f07b38cl7s61vwzkyqkzzsic9g4sw9k6ndbxk3g90l4ca0d1ljc"))))
6994 (properties `((upstream-name . "doSNOW")))
6995 (build-system r-build-system)
6997 `(("r-foreach" ,r-foreach)
6998 ("r-iterators" ,r-iterators)
6999 ("r-snow" ,r-snow)))
7000 (home-page "https://cran.r-project.org/web/packages/doSNOW")
7001 (synopsis "Foreach parallel adaptor for the snow package")
7003 "This package provides a parallel backend for the @code{%dopar%} function
7004 using the @code{snow} package.")
7005 (license license:gpl2)))
7007 (define-public r-fst
7014 (uri (cran-uri "fst" version))
7017 "0vwclzxww8mw9nnpyj29bn71mrr8jjg7ka03979h9rbzw6d9bjrr"))))
7018 (properties `((upstream-name . "fst")))
7019 (build-system r-build-system)
7020 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7021 (home-page "http://www.fstpackage.org")
7022 (synopsis "Fast serialization of data frames")
7024 "The fst package for R provides a fast, easy and flexible way to
7025 serialize data frames. With access speeds of multiple GB/s, fst is
7026 specifically designed to unlock the potential of high speed solid state disks.
7027 Data frames stored in the fst format have full random access, both in column
7028 and rows. The fst format allows for random access of stored data and
7029 compression with the LZ4 and ZSTD compressors.")
7030 (license license:agpl3)))
7032 (define-public r-snowfall
7035 (version "1.84-6.1")
7038 (uri (cran-uri "snowfall" version))
7040 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
7041 (build-system r-build-system)
7043 `(("r-snow" ,r-snow)))
7044 (home-page "https://cran.r-project.org/web/packages/snowfall/")
7045 (synopsis "Easier cluster computing")
7046 (description "This package is a usability wrapper around snow for easier
7047 development of parallel R programs. This package offers e.g. extended error
7048 checks, and additional functions. All functions work in sequential mode, too,
7049 if no cluster is present or wished. The package is also designed as connector
7050 to the cluster management tool @code{sfCluster}, but can also used without
7052 (license license:gpl2+)))
7054 (define-public r-rgexf
7061 (uri (cran-uri "rgexf" version))
7064 "1vj5ha1qx0xzflchxf25ycys6clfn9y32m1717afzkvhmkwisrra"))
7067 ;; Delete minified JavaScript files
7068 (for-each delete-file
7069 '("inst/gexf-js/js/jquery-2.0.2.min.js"
7070 "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js"
7071 "inst/gexf-js/js/jquery.mousewheel.min.js"))
7073 (properties `((upstream-name . "rgexf")))
7074 (build-system r-build-system)
7076 `(#:modules ((guix build utils)
7077 (guix build r-build-system)
7081 (modify-phases %standard-phases
7082 (add-after 'unpack 'process-javascript
7083 (lambda* (#:key inputs #:allow-other-keys)
7084 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-jquery-ui"))
7085 (with-directory-excursion "inst/gexf-js/js/"
7089 `((,(assoc-ref inputs "js-jquery")
7090 "jquery-2.0.2.min.js")
7091 ("/tmp/jquery-ui-1.10.3/ui/jquery-ui.js"
7092 "jquery-ui-1.10.3.custom.min.js")
7093 (,(assoc-ref inputs "js-jquery-mousewheel")
7094 "jquery.mousewheel.min.js"))))
7095 (lambda (sources targets)
7096 (for-each (lambda (source target)
7097 (format #true "Processing ~a --> ~a~%"
7099 (invoke "esbuild" source "--minify"
7100 (string-append "--outfile=" target)))
7104 `(("r-igraph" ,r-igraph)
7105 ("r-servr" ,r-servr)
7108 `(("r-knitr" ,r-knitr)
7109 ("esbuild" ,esbuild)
7114 (uri "https://code.jquery.com/jquery-2.0.2.js")
7117 "0v818bxpw48gdk8i95qqqij80r9jcgisi2r4ac6xnxca20h0gvfj"))))
7121 (uri "https://jqueryui.com/resources/download/jquery-ui-1.10.3.zip")
7124 "00xpfy0l69nj2yan4s8k65ldsrlfsjkmyw2dwcg93dc8mv454vxx"))))
7125 ("js-jquery-mousewheel"
7128 (uri "https://raw.githubusercontent.com/jquery/jquery-mousewheel/\
7129 3.0.6/jquery.mousewheel.js")
7132 "19lk5xy2s47bx8hsa7j6bg012f8yw6d770g230bcnm559kf4nc6v"))))))
7133 (home-page "https://gvegayon.github.io/rgexf")
7134 (synopsis "Build, import and export GEXF graph files")
7136 "Create, read and write GEXF (Graph Exchange XML Format) graph
7137 files (used in Gephi and others). It allows the user to easily build/read
7138 graph files including attributes, GEXF visual attributes (such as color, size,
7139 and position), network dynamics (for both edges and nodes) and edge weighting.
7140 Users can build/handle graphs element-by-element or massively through
7141 data-frames, visualize the graph on a web browser through gexf-js (a
7142 JavaScript library) and interact with the igraph package.")
7143 (license license:expat)))
7145 (define-public r-data-tree
7147 (name "r-data-tree")
7152 (uri (cran-uri "data.tree" version))
7155 "0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
7156 (properties `((upstream-name . "data.tree")))
7157 (build-system r-build-system)
7160 ("r-stringi" ,r-stringi)))
7162 `(("r-knitr" ,r-knitr)))
7163 (home-page "https://github.com/gluc/data.tree")
7164 (synopsis "General purpose hierarchical data structure")
7166 "Create tree structures from hierarchical data, and traverse the tree in
7167 various orders. Aggregate, cumulate, print, plot, convert to and from
7168 data.frame and more. This is useful for decision trees, machine learning,
7169 finance, conversion from and to JSON, and many other applications.")
7170 (license license:gpl2+)))
7172 (define-public r-collapsibletree
7174 (name "r-collapsibletree")
7179 (uri (cran-uri "collapsibleTree" version))
7182 "0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
7185 ;; Delete minified JavaScript file
7186 (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js")
7189 `((upstream-name . "collapsibleTree")))
7190 (build-system r-build-system)
7193 (modify-phases %standard-phases
7194 (add-after 'unpack 'process-javascript
7195 (lambda* (#:key inputs #:allow-other-keys)
7196 (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/"
7197 (let ((source (assoc-ref inputs "d3.v4.js"))
7198 (target "d3.min.js"))
7199 (format #t "Processing ~a --> ~a~%"
7201 (invoke "esbuild" source "--minify"
7202 (string-append "--outfile=" target)))))))))
7204 `(("r-data-tree" ,r-data-tree)
7205 ("r-htmlwidgets" ,r-htmlwidgets)))
7207 `(("esbuild" ,esbuild)
7211 (uri "https://d3js.org/d3.v4.js")
7214 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
7215 (home-page "https://github.com/AdeelK93/collapsibleTree")
7216 (synopsis "Interactive collapsible tree diagrams using D3.js")
7218 "This is a package for interactive Reingold-Tilford tree diagrams created
7219 using D3.js, where every node can be expanded and collapsed by clicking on it.
7220 Tooltips and color gradients can be mapped to nodes using a numeric column in
7221 the source data frame.")
7222 (license license:gpl3+)))
7224 (define-public r-rappdirs
7231 (uri (cran-uri "rappdirs" version))
7234 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9"))))
7235 (build-system r-build-system)
7236 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
7237 (synopsis "Determine where to save data, caches, and logs")
7239 "This package provides an easy way to determine which directories on the
7240 user's computer should be used to save data, caches and logs. It is a port of
7241 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
7242 (license license:expat)))
7244 (define-public r-rastervis
7246 (name "r-rastervis")
7251 (uri (cran-uri "rasterVis" version))
7254 "0d12h7xqcwy1wps6yya9nzfppbnsxpmbkqmy3a8pvxpg81l632kk"))))
7255 (properties `((upstream-name . "rasterVis")))
7256 (build-system r-build-system)
7258 `(("r-hexbin" ,r-hexbin)
7259 ("r-lattice" ,r-lattice)
7260 ("r-latticeextra" ,r-latticeextra)
7261 ("r-raster" ,r-raster)
7262 ("r-rcolorbrewer" ,r-rcolorbrewer)
7264 ("r-viridislite" ,r-viridislite)
7266 (home-page "https://oscarperpinan.github.io/rastervis/")
7267 (synopsis "Visualization methods for raster data")
7269 "This package provides methods for enhanced visualization and interaction
7270 with raster data. It implements visualization methods for quantitative data
7271 and categorical data, both for univariate and multivariate rasters. It also
7272 provides methods to display spatiotemporal rasters, and vector fields.")
7273 (license license:gpl3)))
7275 (define-public r-rentrez
7282 (uri (cran-uri "rentrez" version))
7285 "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv"))))
7286 (properties `((upstream-name . "rentrez")))
7287 (build-system r-build-system)
7289 `(("r-httr" ,r-httr)
7290 ("r-jsonlite" ,r-jsonlite)
7293 `(("r-knitr" ,r-knitr)))
7294 (home-page "https://docs.ropensci.org/rentrez/")
7295 (synopsis "Entrez in R")
7297 "This package provides an R interface to the NCBI's EUtils API,
7298 allowing users to search databases like GenBank PubMed, process the results of
7299 those searches and pull data into their R sessions.")
7300 (license license:expat)))
7302 (define-public r-renv
7309 (uri (cran-uri "renv" version))
7312 "0wfq1z5glng6jrfxj25mjhp129z6468gaszr9ggks5gp8lrwszzh"))))
7313 (properties `((upstream-name . "renv")))
7314 (build-system r-build-system)
7316 `(("r-knitr" ,r-knitr)))
7317 (home-page "https://rstudio.github.io/renv")
7318 (synopsis "Project environments")
7320 "This package provides a dependency management toolkit for R. Using
7321 renv, you can create and manage project-local R libraries, save the state of
7322 these libraries to a lockfile, and later restore your library as required.
7323 Together, these tools can help make your projects more isolated, portable, and
7325 (license license:expat)))
7327 (define-public r-learnr
7334 (uri (cran-uri "learnr" version))
7337 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
7338 (build-system r-build-system)
7340 `(("r-checkmate" ,r-checkmate)
7341 ("r-ellipsis" ,r-ellipsis)
7342 ("r-evaluate" ,r-evaluate)
7343 ("r-htmltools" ,r-htmltools)
7344 ("r-htmlwidgets" ,r-htmlwidgets)
7345 ("r-jsonlite" ,r-jsonlite)
7346 ("r-knitr" ,r-knitr)
7347 ("r-markdown" ,r-markdown)
7348 ("r-rappdirs" ,r-rappdirs)
7350 ("r-rmarkdown" ,r-rmarkdown)
7351 ("r-rprojroot" ,r-rprojroot)
7352 ("r-shiny" ,r-shiny)
7353 ("r-withr" ,r-withr)))
7354 (home-page "https://rstudio.github.io/learnr/")
7355 (synopsis "Interactive tutorials for R")
7357 "This package provides tools to create interactive tutorials using R
7358 Markdown. Use a combination of narrative, figures, videos, exercises, and
7359 quizzes to create self-paced tutorials for learning about R and R packages.")
7360 (license license:asl2.0)))
7362 (define-public r-analytics
7364 (name "r-analytics")
7369 (uri (cran-uri "analytics" version))
7372 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
7373 (build-system r-build-system)
7376 ("r-cluster" ,r-cluster)
7377 ("r-fractal" ,r-fractal)
7378 ("r-lmtest" ,r-lmtest)
7381 ("r-powerplus" ,r-powerplus)
7382 ("r-robust" ,r-robust)
7383 ("r-trend" ,r-trend)
7387 (home-page "https://cran.r-project.org/web/packages/analytics/")
7388 (synopsis "Collection of data analysis tools")
7390 "This package is a collection of data analysis tools. It includes tools
7391 for regression outlier detection in a fitted linear model, stationary
7392 bootstrap using a truncated geometric distribution, a comprehensive test for
7393 weak stationarity, column means by group, weighted biplots, and a heuristic to
7394 obtain a better initial configuration in non-metric MDS.")
7395 (license license:gpl2)))
7397 (define-public r-reticulate
7399 (name "r-reticulate")
7404 (uri (cran-uri "reticulate" version))
7407 "04w5c9jfxakb4rr2qjynxgagb42khsja3y4dwgxywiplb1d8agxk"))))
7408 (build-system r-build-system)
7409 (inputs `(("python" ,python)))
7411 `(("r-rappdirs" ,r-rappdirs)
7412 ("r-jsonlite" ,r-jsonlite)
7413 ("r-matrix" ,r-matrix)
7414 ("r-rcpp" ,r-rcpp)))
7416 `(("r-knitr" ,r-knitr)))
7417 (home-page "https://github.com/rstudio/reticulate")
7418 (synopsis "R interface to Python")
7420 "This package provides an interface from R to Python modules, classes,
7421 and functions. When calling into Python, R data types are automatically
7422 converted to their equivalent Python types. When values are returned from
7423 Python to R they are converted back to R types.")
7424 (license license:asl2.0)))
7426 (define-public r-bibtex
7433 (uri (cran-uri "bibtex" version))
7436 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv"))))
7437 (build-system r-build-system)
7438 (propagated-inputs `(("r-stringr" ,r-stringr)))
7439 (home-page "https://github.com/romainfrancois/bibtex")
7440 (synopsis "Bibtex parser")
7441 (description "This package provides a utility for R to parse a bibtex
7443 (license license:gpl2+)))
7445 (define-public r-ggseqlogo
7447 (name "r-ggseqlogo")
7452 (uri (cran-uri "ggseqlogo" version))
7455 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
7456 (build-system r-build-system)
7457 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
7458 (home-page "https://github.com/omarwagih/ggseqlogo")
7459 (synopsis "ggplot2 extension for drawing genetic sequence logos")
7461 "The range of functions provided by this package makes it possible to
7462 draw highly versatile genomic sequence logos. Features include, but are not
7463 limited to, modifying colour schemes and fonts used to draw the logo,
7464 generating multiple logo plots, and aiding the visualisation with annotations.
7465 Sequence logos can easily be combined with other ggplot2 plots.")
7466 ;; Unspecified version of the LGPL.
7467 (license license:lgpl3+)))
7469 (define-public r-ggsci
7476 (uri (cran-uri "ggsci" version))
7479 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
7480 (build-system r-build-system)
7482 `(("r-ggplot2" ,r-ggplot2)
7483 ("r-scales" ,r-scales)))
7484 (home-page "https://nanx.me/ggsci/")
7485 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
7487 "This package provides a collection of ggplot2 color palettes inspired by
7488 plots in scientific journals, data visualization libraries, science fiction
7489 movies, and TV shows.")
7490 (license license:gpl3)))
7492 (define-public r-ggsignif
7499 (uri (cran-uri "ggsignif" version))
7502 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
7503 (build-system r-build-system)
7505 `(("r-knitr" ,r-knitr)))
7507 `(("r-ggplot2" ,r-ggplot2)))
7508 (home-page "https://github.com/const-ae/ggsignif")
7509 (synopsis "Significance brackets for ggplot2")
7511 "Enrich your ggplots with group-wise comparisons. This package provides
7512 an easy way to indicate if two groups are significantly different. Commonly
7513 this is shown by a bracket on top connecting the groups of interest which
7514 itself is annotated with the level of significance. The package provides a
7515 single layer that takes the groups for comparison and the test as arguments
7516 and adds the annotation to the plot.")
7517 (license license:gpl3)))
7519 (define-public r-rstatix
7526 (uri (cran-uri "rstatix" version))
7529 "0nwwvxwr4z3j4n9z8cnvwghppc836g47n0ia98chk272qwh8xcpb"))))
7530 (properties `((upstream-name . "rstatix")))
7531 (build-system r-build-system)
7533 `(("r-broom" ,r-broom)
7535 ("r-corrplot" ,r-corrplot)
7536 ("r-dplyr" ,r-dplyr)
7537 ("r-generics" ,r-generics)
7538 ("r-magrittr" ,r-magrittr)
7539 ("r-purrr" ,r-purrr)
7540 ("r-rlang" ,r-rlang)
7541 ("r-tibble" ,r-tibble)
7542 ("r-tidyr" ,r-tidyr)
7543 ("r-tidyselect" ,r-tidyselect)))
7544 (home-page "https://rpkgs.datanovia.com/rstatix/")
7545 (synopsis "Pipe-friendly framework for basic statistical tests")
7547 "This package provides a simple and intuitive pipe-friendly framework,
7548 coherent with the @code{tidyverse} design philosophy, for performing basic
7549 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
7550 correlation analyses. The output of each test is automatically transformed
7551 into a tidy data frame to facilitate visualization. Additional functions are
7552 available for reshaping, reordering, manipulating and visualizing correlation
7554 (license license:gpl2)))
7556 (define-public r-ggpubr
7563 (uri (cran-uri "ggpubr" version))
7566 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
7567 (build-system r-build-system)
7569 `(("r-cowplot" ,r-cowplot)
7570 ("r-dplyr" ,r-dplyr)
7571 ("r-ggplot2" ,r-ggplot2)
7572 ("r-ggrepel" ,r-ggrepel)
7573 ("r-ggsci" ,r-ggsci)
7574 ("r-ggsignif" ,r-ggsignif)
7576 ("r-gridextra" ,r-gridextra)
7577 ("r-magrittr" ,r-magrittr)
7578 ("r-polynom" ,r-polynom)
7579 ("r-purrr" ,r-purrr)
7580 ("r-rlang" ,r-rlang)
7581 ("r-scales" ,r-scales)
7582 ("r-rstatix" ,r-rstatix)
7583 ("r-tibble" ,r-tibble)
7584 ("r-tidyr" ,r-tidyr)))
7585 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
7586 (synopsis "ggplot2-based publication-ready plots")
7588 "The ggplot2 package is an excellent and flexible package for elegant
7589 data visualization in R. However the default generated plots require some
7590 formatting before we can send them for publication. The ggpubr package
7591 provides some easy-to-use functions for creating and customizing ggplot2-based
7592 publication-ready plots.")
7593 (license license:gpl2)))
7595 (define-public r-ellipse
7602 (uri (cran-uri "ellipse" version))
7605 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
7606 (build-system r-build-system)
7607 (home-page "https://cran.r-project.org/web/packages/ellipse/")
7608 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
7610 "This package contains various routines for drawing ellipses and
7611 ellipse-like confidence regions, implementing the plots described in Murdoch
7612 and Chow (1996), A graphical display of large correlation matrices, The
7613 American Statistician 50, 178-180. There are also routines implementing the
7614 profile plots described in Bates and Watts (1988), Nonlinear Regression
7615 Analysis and its Applications.")
7616 (license license:gpl2+)))
7618 (define-public r-flashclust
7620 (name "r-flashclust")
7625 (uri (cran-uri "flashClust" version))
7628 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
7629 (properties `((upstream-name . "flashClust")))
7630 (build-system r-build-system)
7631 (native-inputs `(("gfortran" ,gfortran)))
7632 (home-page "https://cran.r-project.org/web/packages/flashClust/")
7633 (synopsis "Implementation of optimal hierarchical clustering")
7635 "This package provides a fast implementation of hierarchical
7637 (license license:gpl2+)))
7639 (define-public r-factominer
7641 (name "r-factominer")
7646 (uri (cran-uri "FactoMineR" version))
7649 "0lg8n9fxxk46nchnj4pbpqqf4swxfsq7r9jzr36dmd36kb7avqxr"))))
7650 (properties `((upstream-name . "FactoMineR")))
7651 (build-system r-build-system)
7654 ("r-cluster" ,r-cluster)
7656 ("r-ellipse" ,r-ellipse)
7657 ("r-flashclust" ,r-flashclust)
7658 ("r-ggplot2" ,r-ggplot2)
7659 ("r-ggrepel" ,r-ggrepel)
7660 ("r-lattice" ,r-lattice)
7661 ("r-leaps" ,r-leaps)
7663 ("r-scatterplot3d" ,r-scatterplot3d)))
7665 `(("r-knitr" ,r-knitr)))
7666 (home-page "http://factominer.free.fr")
7667 (synopsis "Multivariate exploratory data analysis and data mining")
7669 "This package provides exploratory data analysis methods to summarize,
7670 visualize and describe datasets. The main principal component methods are
7671 available, those with the largest potential in terms of applications:
7672 principal component analysis (PCA) when variables are quantitative,
7673 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
7674 variables are categorical, Multiple Factor Analysis when variables are
7675 structured in groups, etc. and hierarchical cluster analysis.")
7676 (license license:gpl2+)))
7678 (define-public r-factoextra
7680 (name "r-factoextra")
7685 (uri (cran-uri "factoextra" version))
7688 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
7689 (build-system r-build-system)
7691 `(("r-abind" ,r-abind)
7692 ("r-cluster" ,r-cluster)
7693 ("r-dendextend" ,r-dendextend)
7694 ("r-factominer" ,r-factominer)
7695 ("r-ggplot2" ,r-ggplot2)
7696 ("r-ggpubr" ,r-ggpubr)
7697 ("r-ggrepel" ,r-ggrepel)
7698 ("r-reshape2" ,r-reshape2)
7699 ("r-tidyr" ,r-tidyr)))
7700 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
7701 (synopsis "Extract and visualize the results of multivariate data analyses")
7703 "This package provides some easy-to-use functions to extract and
7704 visualize the output of multivariate data analyses, including
7705 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
7706 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
7707 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
7708 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
7709 packages. It contains also functions for simplifying some clustering analysis
7710 steps and provides ggplot2-based elegant data visualization.")
7711 (license license:gpl2)))
7713 (define-public r-fansi
7720 (uri (cran-uri "fansi" version))
7723 "0i7wmaflkjzdbggqv31wnsj3m9imvc6db429vyjk64xrz1ng1vd2"))))
7724 (build-system r-build-system)
7726 `(("r-knitr" ,r-knitr))) ; for vignettes
7727 (home-page "https://github.com/brodieG/fansi")
7728 (synopsis "ANSI control sequence aware string functions")
7730 "This package provides counterparts to R string manipulation functions
7731 that account for the effects of ANSI text formatting control sequences.")
7732 (license license:gpl2+)))
7734 (define-public r-nbclust
7741 (uri (cran-uri "NbClust" version))
7744 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
7745 (properties `((upstream-name . "NbClust")))
7746 (build-system r-build-system)
7747 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
7748 (synopsis "Determine the best number of clusters in a data set")
7750 "NbClust provides 30 indexes for determining the optimal number of
7751 clusters in a data set and offers the best clustering scheme from different
7752 results to the user.")
7753 (license license:gpl2)))
7755 (define-public r-hdf5r
7762 (uri (cran-uri "hdf5r" version))
7765 "0i8m4yjxggrs05slq2afvz2ckl1yc9wq7gd1s7dq2gjn46zkry50"))))
7766 (build-system r-build-system)
7771 `(("r-bit64" ,r-bit64)
7774 `(("r-knitr" ,r-knitr)))
7775 (home-page "https://hhoeflin.github.io/hdf5r")
7776 (synopsis "Interface to the HDF5 binary data format")
7778 "HDF5 is a data model, library and file format for storing and managing
7779 large amounts of data. This package provides a nearly feature complete,
7780 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
7781 functionality is added so that HDF5 objects behave very similar to their
7782 corresponding R counterparts.")
7783 (license license:asl2.0)))
7785 (define-public r-itertools
7787 (name "r-itertools")
7792 (uri (cran-uri "itertools" version))
7795 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
7796 (build-system r-build-system)
7798 `(("r-iterators" ,r-iterators)))
7799 (home-page "https://cran.r-project.org/web/packages/itertools/")
7800 (synopsis "Iterator tools")
7802 "This package provides various tools for creating iterators, many
7803 patterned after functions in the Python @code{itertools} module, and others
7804 patterned after functions in the snow package.")
7805 (license license:gpl2)))
7807 (define-public r-polynom
7814 (uri (cran-uri "polynom" version))
7817 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
7818 (build-system r-build-system)
7819 (home-page "https://cran.r-project.org/web/packages/polynom/")
7820 (synopsis "Functions for univariate polynomial manipulations")
7822 "This package provides a collection of functions to implement a class for
7823 univariate polynomial manipulations.")
7824 (license license:gpl2)))
7826 (define-public r-gbrd
7833 (uri (cran-uri "gbRd" version))
7836 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
7837 (properties `((upstream-name . "gbRd")))
7838 (build-system r-build-system)
7839 (home-page "https://cran.r-project.org/web/packages/gbRd/")
7840 (synopsis "Utilities for processing Rd objects and files")
7842 "This package provides utilities for processing Rd objects and files.
7843 Extract argument descriptions and other parts of the help pages of
7845 (license license:gpl2+)))
7847 (define-public r-rjags
7854 (uri (cran-uri "rjags" version))
7857 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
7858 (build-system r-build-system)
7860 `(("r-coda" ,r-coda)))
7864 `(("pkg-config" ,pkg-config)))
7865 (home-page "http://mcmc-jags.sourceforge.net")
7866 (synopsis "Bayesian graphical models using MCMC")
7868 "This package provides an R interface to the JAGS MCMC library. JAGS is
7869 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
7870 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
7871 (license license:gpl2)))
7873 (define-public r-rbibutils
7875 (name "r-rbibutils")
7880 (uri (cran-uri "rbibutils" version))
7883 "1vfg2188i4dyhrmvnwpsh2la8qkd4wkryz2fpj4cppi1wfz3ml83"))))
7884 (properties `((upstream-name . "rbibutils")))
7885 (build-system r-build-system)
7886 (home-page "https://geobosh.github.io/rbibutils/")
7887 (synopsis "Convert between bibliography formats")
7889 "This package converts between a number of bibliography formats,
7890 including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils
7891 utilities and supports all bibliography formats and character encodings
7892 implemented in bibutils.")
7893 (license license:gpl2)))
7895 (define-public r-rdpack
7902 (uri (cran-uri "Rdpack" version))
7905 "1kmz0kq2z1xl55w22paz98x9jpss06abvicmkslv4zq77kz99q16"))))
7906 (properties `((upstream-name . "Rdpack")))
7907 (build-system r-build-system)
7909 `(("r-rbibutils" ,r-rbibutils)
7910 ("r-gbrd" ,r-gbrd)))
7911 (home-page "https://github.com/GeoBosh/Rdpack")
7912 (synopsis "Update and manipulate Rd documentation objects")
7914 "This package provides functions for manipulation of R documentation
7915 objects, including functions @code{reprompt()} and @code{ereprompt()} for
7916 updating Rd documentation for functions, methods and classes; it also includes
7917 Rd macros for citations and import of references from bibtex files for use in
7918 Rd files and roxygen2 comments, as well as many functions for manipulation of
7919 references and Rd files.")
7920 (license license:gpl2+)))
7922 (define-public r-officer
7929 (uri (cran-uri "officer" version))
7932 "1ls5kp70jfxrzxxb3xrg8sn2fyk6qd7rmx23n5jxi7z7850avjrj"))))
7933 (build-system r-build-system)
7940 `(("r-knitr" ,r-knitr)))
7941 (home-page "https://davidgohel.github.io/officer")
7942 (synopsis "Manipulation of Word and PowerPoint documents")
7944 "This package provides tools to access and manipulate Word and PowerPoint
7945 documents from R. The package focuses on tabular and graphical reporting from
7946 R; it also provides two functions that let users get document content into
7947 data objects. A set of functions lets add and remove images, tables and
7948 paragraphs of text in new or existing documents. When working with PowerPoint
7949 presentations, slides can be added or removed; shapes inside slides can also
7950 be added or removed. When working with Word documents, a cursor can be used
7951 to help insert or delete content at a specific location in the document.")
7952 (license license:gpl3)))
7954 (define-public r-profilemodel
7956 (name "r-profilemodel")
7961 (uri (cran-uri "profileModel" version))
7964 "01m5nb8cmq0aq555pxk2a99182si65hhmn68yn9nal2j3zl2bp4i"))))
7965 (properties `((upstream-name . "profileModel")))
7966 (build-system r-build-system)
7967 (home-page "https://github.com/ikosmidis/profileModel")
7968 (synopsis "Profiling inference functions for various model classes")
7970 "This package provides tools that can be used to calculate, evaluate,
7971 plot and use for inference the profiles of *arbitrary* inference functions for
7972 arbitrary @code{glm}-like fitted models with linear predictors. More information
7973 on the methods that are implemented can be found in Kosmidis (2008)
7974 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
7975 (license license:gpl2+)))
7977 (define-public r-brglm
7984 (uri (cran-uri "brglm" version))
7987 "1v68ma1agwhxar76mfvdfkcnd5h4gmxiz8j491rhdsckg271j7sa"))))
7988 (properties `((upstream-name . "brglm")))
7989 (build-system r-build-system)
7991 `(("r-profilemodel" ,r-profilemodel)))
7992 (home-page "https://github.com/ikosmidis/brglm")
7993 (synopsis "Bias reduction in binomial-response generalized linear models")
7995 "Fit generalized linear models with binomial responses using either an
7996 adjusted-score approach to bias reduction or maximum penalized likelihood
7997 where penalization is by Jeffreys invariant prior. These procedures return
7998 estimates with improved frequentist properties (bias, mean squared error) that
7999 are always finite even in cases where the maximum likelihood estimates are
8000 infinite (data separation). Fitting takes place by fitting generalized linear
8001 models on iteratively updated pseudo-data. The interface is essentially the
8002 same as @code{glm}. More flexibility is provided by the fact that custom
8003 pseudo-data representations can be specified and used for model fitting.
8004 Functions are provided for the construction of confidence intervals for the
8005 reduced-bias estimates.")
8006 (license license:gpl2+)))
8008 (define-public r-entropy
8015 (uri (cran-uri "entropy" version))
8018 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
8019 (properties `((upstream-name . "entropy")))
8020 (build-system r-build-system)
8021 (home-page "https://www.strimmerlab.org/software/entropy/")
8022 (synopsis "Estimation of entropy, mutual information and related quantities")
8024 "This package implements various estimators of entropy, such as the
8025 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
8026 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
8027 estimator. It also offers an R interface to the NSB estimator. Furthermore,
8028 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
8029 mutual information, and chi-squared statistic of independence. In addition
8030 there are functions for discretizing continuous random variables.")
8031 (license license:gpl3+)))
8033 (define-public r-abn
8040 (uri (cran-uri "abn" version))
8043 "17vdrqm6qp5aijg00ah2imj3pqr6cl5r43hgg8dijbrbhznarci6"))))
8044 (build-system r-build-system)
8048 `(("r-lme4" ,r-lme4)
8051 ("r-rcpparmadillo" ,r-rcpparmadillo)
8052 ("r-rjags" ,r-rjags)))
8053 (home-page "https://r-bayesian-networks.org/")
8054 (synopsis "Modelling multivariate data with additive bayesian networks")
8056 "Bayesian network analysis is a form of probabilistic graphical models
8057 which derives from empirical data a directed acyclic graph, DAG, describing
8058 the dependency structure between random variables. An additive Bayesian
8059 network model consists of a form of a DAG where each node comprises a
8060 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
8061 equivalent to Bayesian multivariate regression using graphical modelling, they
8062 generalises the usual multivariable regression, GLM, to multiple dependent
8063 variables. This package provides routines to help determine optimal Bayesian
8064 network models for a given data set, where these models are used to identify
8065 statistical dependencies in messy, complex data.")
8066 (license license:gpl2+)))
8068 (define-public r-acd
8075 (uri (cran-uri "ACD" version))
8078 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
8079 (properties `((upstream-name . "ACD")))
8080 (build-system r-build-system)
8081 (home-page "https://cran.r-project.org/web/packages/ACD/")
8082 (synopsis "Categorical data analysis with complete or missing responses")
8084 "This package provides tools for categorical data analysis with complete
8085 or missing responses.")
8086 (license license:gpl2+)))
8088 (define-public r-acdm
8095 (uri (cran-uri "ACDm" version))
8098 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
8099 (properties `((upstream-name . "ACDm")))
8100 (build-system r-build-system)
8102 `(("r-dplyr" ,r-dplyr)
8103 ("r-ggplot2" ,r-ggplot2)
8105 ("r-rsolnp" ,r-rsolnp)
8107 (home-page "https://cran.r-project.org/web/packages/ACDm/")
8108 (synopsis "Tools for Autoregressive Conditional Duration Models")
8110 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
8111 and Russell, 1998) models. It creates trade, price or volume durations from
8112 transactions (tic) data, performs diurnal adjustments, fits various ACD models
8114 (license license:gpl2+)))
8116 (define-public r-overlap
8123 (uri (cran-uri "overlap" version))
8126 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
8127 (build-system r-build-system)
8128 (home-page "https://cran.r-project.org/web/packages/overlap/")
8129 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
8131 "This package provides functions to fit kernel density functions to data
8132 on temporal activity patterns of animals; estimate coefficients of overlapping
8133 of densities for two species; and calculate bootstrap estimates of confidence
8135 (license license:gpl3+)))
8137 (define-public r-snakecase
8139 (name "r-snakecase")
8144 (uri (cran-uri "snakecase" version))
8147 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
8148 (build-system r-build-system)
8150 `(("r-stringi" ,r-stringi)
8151 ("r-stringr" ,r-stringr)))
8152 (home-page "https://github.com/Tazinho/snakecase")
8153 (synopsis "Convert strings into any case")
8155 "This package provides a consistent, flexible and easy to use tool to
8156 parse and convert strings into cases like snake or camel among others.")
8157 (license license:gpl3)))
8159 (define-public r-prediction
8161 (name "r-prediction")
8166 (uri (cran-uri "prediction" version))
8169 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
8170 (build-system r-build-system)
8172 `(("r-data-table" ,r-data-table)))
8173 (home-page "https://github.com/leeper/prediction")
8174 (synopsis "Tidy, type-safe prediction methods")
8176 "This package provides the @code{prediction()} function, a type-safe
8177 alternative to @code{predict()} that always returns a data frame. The package
8178 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
8179 from the @code{stats} package, as well as numerous other model classes from
8180 other add-on packages.")
8181 (license license:expat)))
8183 (define-public r-insight
8190 (uri (cran-uri "insight" version))
8193 "0gkvcw9d729ql1gfrpxzgrag4xafd0hchrdww215qz11ma1rzy7s"))))
8194 (build-system r-build-system)
8196 `(("r-knitr" ,r-knitr)))
8197 (home-page "https://easystats.github.io/insight/")
8198 (synopsis "Easy access to model information for various model objects")
8200 "This package provides a tool to provide an easy, intuitive and
8201 consistent access to information contained in various R models, like model
8202 formulas, model terms, information about random effects, data that was used to
8203 fit the model or data from response variables. The package mainly revolves
8204 around two types of functions: Functions that find (the names of) information,
8205 starting with @code{find_}, and functions that get the underlying data,
8206 starting with @code{get_}. The package has a consistent syntax and works with
8207 many different model objects, where otherwise functions to access these
8208 information are missing.")
8209 (license license:gpl3)))
8211 (define-public r-sjlabelled
8213 (name "r-sjlabelled")
8218 (uri (cran-uri "sjlabelled" version))
8221 "0d3fsjd2gxchv8mlx9l5pf8xvkmx4pgvizam83f3qss07bmvpzwg"))))
8222 (build-system r-build-system)
8224 `(("r-insight" ,r-insight)))
8226 `(("r-knitr" ,r-knitr)))
8227 (home-page "https://github.com/strengejacke/sjlabelled")
8228 (synopsis "Labelled data utility functions")
8230 "This package provides a collection of functions dealing with labelled
8231 data, like reading and writing data between R and other statistical software
8232 packages. This includes easy ways to get, set or change value and variable
8233 label attributes, to convert labelled vectors into factors or numeric (and
8234 vice versa), or to deal with multiple declared missing values.")
8235 (license license:gpl3)))
8237 (define-public r-sjmisc
8244 (uri (cran-uri "sjmisc" version))
8247 "1nfrkv5jfnwb85blpv7yk7xac1myzi2c30bqcf7xicniknkjwycr"))))
8248 (build-system r-build-system)
8250 `(("r-dplyr" ,r-dplyr)
8251 ("r-insight" ,r-insight)
8252 ("r-magrittr" ,r-magrittr)
8253 ("r-purrr" ,r-purrr)
8254 ("r-rlang" ,r-rlang)
8255 ("r-sjlabelled" ,r-sjlabelled)
8256 ("r-tidyselect" ,r-tidyselect)))
8258 `(("r-knitr" ,r-knitr)))
8259 (home-page "https://github.com/strengejacke/sjmisc")
8260 (synopsis "Data and variable transformation functions")
8262 "This package is a collection of miscellaneous utility functions,
8263 supporting data transformation tasks like recoding, dichotomizing or grouping
8264 variables, setting and replacing missing values. The data transformation
8265 functions also support labelled data, and all integrate seamlessly into a
8266 tidyverse workflow.")
8267 (license license:gpl3)))
8269 (define-public r-nortest
8276 (uri (cran-uri "nortest" version))
8279 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
8280 (build-system r-build-system)
8281 (home-page "https://cran.r-project.org/web/packages/nortest/")
8282 (synopsis "Tests for normality")
8284 "This package provides five omnibus tests for testing the composite
8285 hypothesis of normality.")
8286 (license license:gpl2+)))
8288 (define-public r-moonbook
8295 (uri (cran-uri "moonBook" version))
8298 "0z78pzc8sr2g19xjdd9cmai4iqyifmh79gj8x40ddww6a27dalry"))))
8299 (properties `((upstream-name . "moonBook")))
8300 (build-system r-build-system)
8302 `(("r-magrittr" ,r-magrittr)
8303 ("r-nortest" ,r-nortest)
8304 ("r-sjmisc" ,r-sjmisc)
8305 ("r-stringr" ,r-stringr)
8306 ("r-survival" ,r-survival)
8307 ("r-ztable" ,r-ztable)))
8309 `(("r-knitr" ,r-knitr)))
8310 (home-page "https://github.com/cardiomoon/moonBook")
8311 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
8313 "This package provides several analysis-related functions for the book
8314 entitled \"R statistics and graph for medical articles\" (written in Korean),
8315 version 1, by Keon-Woong Moon with Korean demographic data with several plot
8317 (license license:gpl2)))
8319 (define-public r-flextable
8321 (name "r-flextable")
8326 (uri (cran-uri "flextable" version))
8329 "0as80m19lvajc0vzllq9d9p63zglsm2ph7vdfg3jgk90jp8j76dg"))))
8330 (build-system r-build-system)
8332 `(("r-base64enc" ,r-base64enc)
8333 ("r-data-table" ,r-data-table)
8334 ("r-gdtools" ,r-gdtools)
8335 ("r-htmltools" ,r-htmltools)
8336 ("r-knitr" ,r-knitr)
8337 ("r-officer" ,r-officer)
8338 ("r-rlang" ,r-rlang)
8339 ("r-rmarkdown" ,r-rmarkdown)
8341 ("r-xml2" ,r-xml2)))
8343 `(("r-knitr" ,r-knitr)))
8344 (home-page "https://davidgohel.github.io/flextable")
8345 (synopsis "Functions for tabular reporting")
8347 "This package provides tools to create pretty tables for HTML documents
8348 and other formats. Functions are provided to let users create tables, modify
8349 and format their content. It extends the @code{officer} package and can be
8350 used within R markdown documents when rendering to HTML and to Word
8352 (license license:gpl3)))
8354 (define-public r-writexl
8361 (uri (cran-uri "writexl" version))
8364 "1njdhvh8605wd2j8glrbxfyc36p2n88prpq080jn44s9lgfmbgsb"))))
8365 (build-system r-build-system)
8366 (inputs `(("zlib" ,zlib)))
8367 (home-page "https://github.com/ropensci/writexl")
8368 (synopsis "Export data frames to xlsx format")
8370 "This package provides a data frame to xlsx exporter based on
8372 (license license:bsd-2)))
8374 (define-public r-biasedurn
8376 (name "r-biasedurn")
8381 (uri (cran-uri "BiasedUrn" version))
8384 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
8385 (properties `((upstream-name . "BiasedUrn")))
8386 (build-system r-build-system)
8387 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
8388 (synopsis "Biased Urn model distributions")
8390 "This package provides statistical models of biased sampling in the form
8391 of univariate and multivariate noncentral hypergeometric distributions,
8392 including Wallenius' noncentral hypergeometric distribution and Fisher's
8393 noncentral hypergeometric distribution (also called extended hypergeometric
8395 (license license:gpl3)))
8397 (define-public r-goplot
8404 (uri (cran-uri "GOplot" version))
8407 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
8408 (properties `((upstream-name . "GOplot")))
8409 (build-system r-build-system)
8411 `(("r-ggdendro" ,r-ggdendro)
8412 ("r-ggplot2" ,r-ggplot2)
8413 ("r-gridextra" ,r-gridextra)
8414 ("r-rcolorbrewer" ,r-rcolorbrewer)))
8415 (home-page "https://github.com/wencke/wencke.github.io")
8416 (synopsis "Visualization of functional analysis data")
8418 "This package provides an implementation of multilayered visualizations
8419 for enhanced graphical representation of functional analysis data. It
8420 combines and integrates omics data derived from expression and functional
8421 annotation enrichment analyses. Its plotting functions have been developed
8422 with an hierarchical structure in mind: starting from a general overview to
8423 identify the most enriched categories (modified bar plot, bubble plot) to a
8424 more detailed one displaying different types of relevant information for the
8425 molecules in a given set of categories (circle plot, chord plot, cluster plot,
8426 Venn diagram, heatmap).")
8427 (license license:gpl2)))
8429 (define-public r-getopt
8436 (uri (cran-uri "getopt" version))
8439 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
8440 (build-system r-build-system)
8441 (home-page "https://github.com/trevorld/getopt")
8442 (synopsis "Command-line option processor for R")
8444 "This package is designed to be used with Rscript to write shebang
8445 scripts that accept short and long options. Many users will prefer to
8446 use the packages @code{optparse} or @code{argparse} which add extra
8447 features like automatically generated help options and usage texts,
8448 support for default values, positional argument support, etc.")
8449 (license license:gpl2+)))
8451 (define-public r-findpython
8453 (name "r-findpython")
8458 (uri (cran-uri "findpython" version))
8461 "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar"))))
8462 (build-system r-build-system)
8463 (home-page "https://github.com/trevorld/findpython")
8464 (synopsis "Functions to find an acceptable Python binary")
8466 "This package was designed to find an acceptable Python binary that
8467 matches version and feature constraints.")
8468 (license license:expat)))
8470 ;; This in not the same as "r-argparser"
8471 (define-public r-argparse
8478 (uri (cran-uri "argparse" version))
8481 "1c2r417m1dxk1jhcggv3g4zax5a59k9rqs9jcs6xy2pa2333jqfj"))))
8482 (build-system r-build-system)
8483 (inputs `(("python" ,python)))
8485 `(("r-findpython" ,r-findpython)
8486 ("r-jsonlite" ,r-jsonlite)
8489 `(("r-knitr" ,r-knitr)))
8490 (home-page "https://github.com/trevorld/argparse")
8491 (synopsis "Command line optional and positional argument parser")
8493 "This package provides a command line parser to be used with Rscript to
8494 write shebang scripts that gracefully accept positional and optional arguments
8495 and automatically generate usage notices.")
8496 (license license:gpl2+)))
8498 (define-public r-hash
8505 (uri (cran-uri "hash" version))
8508 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
8509 (build-system r-build-system)
8510 (home-page "https://cran.r-project.org/web/packages/hash/")
8511 (synopsis "Implementation of hash/associated arrays/dictionaries")
8513 "This package implements a data structure similar to hashes in Perl and
8514 dictionaries in Python but with a purposefully R flavor. For objects of
8515 appreciable size, access using hashes outperforms native named lists and
8517 (license license:gpl2+)))
8519 (define-public r-orddom
8526 (uri (cran-uri "orddom" version))
8529 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
8530 (build-system r-build-system)
8531 (propagated-inputs `(("r-psych" ,r-psych)))
8532 (home-page "https://cran.r-project.org/web/packages/orddom/")
8533 (synopsis "Ordinal dominance statistics")
8535 "This package provides tools to compute ordinal, statistics and effect
8536 sizes as an alternative to mean comparison: Cliff's delta or success rate
8537 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
8538 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
8539 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
8540 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
8541 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
8542 Group (Non-)Overlap considerations.")
8543 (license license:gpl2)))
8545 (define-public r-deriv
8552 (uri (cran-uri "Deriv" version))
8555 "1j9sh1w9lsnnhlh59g4ghykyfx46rxh380s8imvm7pzna7rw7c64"))))
8556 (properties `((upstream-name . "Deriv")))
8557 (build-system r-build-system)
8558 (home-page "https://cran.r-project.org/web/packages/Deriv")
8559 (synopsis "Symbolic differentiation")
8561 "This package provides an R-based solution for symbolic differentiation.
8562 It admits user-defined functions as well as function substitution in arguments
8563 of functions to be differentiated. Some symbolic simplification is part of
8565 (license license:gpl3+)))
8567 (define-public r-doby
8574 (uri (cran-uri "doBy" version))
8577 "0r97kwsj6g87m7shgnjc5c9y71jkhiq4xd9q0s2bxl0vl92qqwvg"))))
8578 (properties `((upstream-name . "doBy")))
8579 (build-system r-build-system)
8581 `(("r-broom" ,r-broom)
8582 ("r-deriv" ,r-deriv)
8583 ("r-dplyr" ,r-dplyr)
8584 ("r-ggplot2" ,r-ggplot2)
8585 ("r-magrittr" ,r-magrittr)
8587 ("r-matrix" ,r-matrix)
8588 ("r-pbkrtest" ,r-pbkrtest)
8589 ("r-tibble" ,r-tibble)))
8591 `(("r-knitr" ,r-knitr)))
8592 (home-page "https://people.math.aau.dk/~sorenh/software/doBy/")
8593 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
8595 "This package contains:
8598 @item facilities for working with grouped data: @code{do}
8599 something to data stratified @code{by} some variables.
8600 @item implementations of least-squares means, general linear contrasts, and
8601 @item miscellaneous other utilities.
8603 (license license:gpl2+)))
8605 (define-public r-refgenome
8607 (name "r-refgenome")
8612 (uri (cran-uri "refGenome" version))
8615 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
8616 (properties `((upstream-name . "refGenome")))
8617 (build-system r-build-system)
8621 ("r-rsqlite" ,r-rsqlite)))
8622 (home-page "https://cran.r-project.org/web/packages/refGenome/")
8624 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
8626 "This package contains functionality for importing and managing of
8627 downloaded genome annotation data from the Ensembl genome browser (European
8628 Bioinformatics Institute) and from the UCSC genome browser (University of
8629 California, Santa Cruz) and annotation routines for genomic positions and
8630 splice site positions.")
8631 (license license:gpl2)))
8633 (define-public r-basix
8640 (uri (cran-uri "BASIX" version))
8643 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
8644 (properties `((upstream-name . "BASIX")))
8645 (build-system r-build-system)
8646 (home-page "https://cran.r-project.org/web/packages/BASIX/")
8647 (synopsis "Efficient C/C++ toolset for R")
8649 "BASIX provides some efficient C/C++ implementations of native R
8650 procedures to speed up calculations in R.")
8651 (license license:gpl2)))
8653 (define-public r-blockfest
8655 (name "r-blockfest")
8660 (uri (cran-uri "BlockFeST" version))
8663 "12cbrmgqszlj729zrn9d1d7drbr0iay43knnmrzcxs6v7lfszsx5"))))
8664 (properties `((upstream-name . "BlockFeST")))
8665 (build-system r-build-system)
8666 (propagated-inputs `(("r-basix" ,r-basix)))
8667 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
8668 (synopsis "Bayesian calculation of region-specific fixation index")
8670 "This package provides an R implementation of an extension of the
8671 BayeScan software for codominant markers, adding the option to group
8672 individual SNPs into pre-defined blocks. A typical application of this new
8673 approach is the identification of genomic regions, genes, or gene sets
8674 containing one or more SNPs that evolved under directional selection.")
8675 (license license:gpl2)))
8677 (define-public r-proc
8680 (version "1.17.0.1")
8684 (uri (cran-uri "pROC" version))
8687 "1gd6a47d6bcfd237s3g7r9rws8x2sg7zrvq5k6clpc41zdpp4712"))))
8688 (properties `((upstream-name . "pROC")))
8689 (build-system r-build-system)
8691 `(("r-plyr" ,r-plyr)
8692 ("r-rcpp" ,r-rcpp)))
8693 (home-page "https://web.expasy.org/pROC/")
8694 (synopsis "Display and analyze ROC curves")
8696 "This package provides tools for visualizing, smoothing and comparing
8697 receiver operating characteristic (ROC curves). The area under the
8698 curve (AUC) can be compared with statistical tests based on U-statistics or
8699 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
8700 (license license:gpl3+)))
8702 (define-public r-rootsolve
8704 (name "r-rootsolve")
8709 (uri (cran-uri "rootSolve" version))
8712 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
8713 (properties `((upstream-name . "rootSolve")))
8714 (build-system r-build-system)
8715 (native-inputs `(("gfortran" ,gfortran)))
8716 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
8717 (synopsis "Tools for the analysis of ordinary differential equations")
8719 "This package provides routines to find the root of nonlinear functions,
8720 and to perform steady-state and equilibrium analysis of @dfn{ordinary
8721 differential equations} (ODE). It includes routines that:
8724 @item generate gradient and jacobian matrices (full and banded),
8725 @item find roots of non-linear equations by the Newton-Raphson method,
8726 @item estimate steady-state conditions of a system of (differential) equations
8727 in full, banded or sparse form, using the Newton-Raphson method, or by
8728 dynamically running,
8729 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
8730 and 3-D partial differential equations, that have been converted to ordinary
8731 differential equations by numerical differencing (using the method-of-lines
8734 (license license:gpl2+)))
8736 (define-public r-abcanalysis
8738 (name "r-abcanalysis")
8743 (uri (cran-uri "ABCanalysis" version))
8745 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
8746 (properties `((upstream-name . "ABCanalysis")))
8747 (build-system r-build-system)
8748 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
8749 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
8750 (synopsis "Computed ABC Analysis")
8752 "Multivariate data sets often differ in several factors or derived statistical
8753 parameters, which have to be selected for a valid interpretation. Basing this
8754 selection on traditional statistical limits leads occasionally to the perception
8755 of losing information from a data set. This package provides tools to calculate
8756 these limits on the basis of the mathematical properties of the distribution of
8757 the analyzed items.")
8758 (license license:gpl3)))
8760 (define-public r-slam
8767 (uri (cran-uri "slam" version))
8769 (base32 "1ppsvkph4v1dffxgp12a4wnr9arj7pkmh4qv0and3f6nbz9k42qa"))))
8770 (build-system r-build-system)
8771 (home-page "https://cran.r-project.org/web/packages/slam/")
8772 (synopsis "Sparse lightweight arrays and matrices")
8774 "This package contains data structures and algorithms for sparse arrays and matrices,
8775 based on index arrays and simple triplet representations, respectively.")
8776 (license license:gpl2)))
8778 (define-public r-manipulatewidget
8780 (name "r-manipulatewidget")
8785 (uri (cran-uri "manipulateWidget" version))
8787 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
8789 `((upstream-name . "manipulateWidget")))
8790 (build-system r-build-system)
8792 `(("r-base64enc" ,r-base64enc)
8793 ("r-codetools" ,r-codetools)
8794 ("r-htmltools" ,r-htmltools)
8795 ("r-htmlwidgets" ,r-htmlwidgets)
8796 ("r-knitr" ,r-knitr)
8797 ("r-miniui" ,r-miniui)
8798 ("r-shiny" ,r-shiny)
8799 ("r-webshot" ,r-webshot)))
8800 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
8801 (synopsis "Add even more interactivity to interactive charts")
8803 "This package lets you create in just a few lines of R code a nice user interface to
8804 modify the data or the graphical parameters of one or multiple interactive
8805 charts. It is useful to quickly explore visually some data or for package
8806 developers to generate user interfaces easy to maintain.")
8807 (license license:gpl2+)))
8816 (uri (cran-uri "A3" version))
8818 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
8819 (properties `((upstream-name . "A3")))
8820 (build-system r-build-system)
8822 `(("r-pbapply" ,r-pbapply)
8823 ("r-xtable" ,r-xtable)))
8824 (home-page "https://cran.r-project.org/web/packages/A3/")
8825 (synopsis "Error metrics for predictive models")
8827 "This package supplies tools for tabulating and analyzing the results of predictive
8828 models. The methods employed are applicable to virtually any predictive model
8829 and make comparisons between different methodologies straightforward.")
8830 (license license:gpl2+)))
8832 (define-public r-infotheo
8839 (uri (cran-uri "infotheo" version))
8842 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
8843 (build-system r-build-system)
8844 (home-page "http://homepage.meyerp.com/software")
8845 (synopsis "Information-theoretic measures")
8847 "This package implements various measures of information theory based on
8848 several entropy estimators.")
8849 (license license:gpl3+)))
8851 (define-public r-abcoptim
8858 (uri (cran-uri "ABCoptim" version))
8860 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
8861 (properties `((upstream-name . "ABCoptim")))
8862 (build-system r-build-system)
8863 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
8864 (home-page "https://github.com/gvegayon/ABCoptim/")
8865 (synopsis "Optimization of Artificial Bee Colony algorithm")
8867 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
8868 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
8869 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
8870 algorithms, and uses only common control parameters such as colony size and
8871 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
8872 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
8873 This version is a work-in-progress and is written in R code.")
8874 (license license:expat)))
8876 (define-public r-abcp2
8883 (uri (cran-uri "ABCp2" version))
8885 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
8886 (properties `((upstream-name . "ABCp2")))
8887 (build-system r-build-system)
8888 (propagated-inputs `(("r-mass" ,r-mass)))
8889 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
8890 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
8892 "This package tests the goodness of fit of a distribution of offspring to the Normal,
8893 Poisson, and Gamma distribution and estimates the proportional paternity of the
8894 second male (P2) based on the best fit distribution.")
8895 (license license:gpl2)))
8897 (define-public r-abcrf
8904 (uri (cran-uri "abcrf" version))
8906 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
8907 (build-system r-build-system)
8909 `(("r-doparallel" ,r-doparallel)
8910 ("r-foreach" ,r-foreach)
8912 ("r-matrixstats" ,r-matrixstats)
8913 ("r-ranger" ,r-ranger)
8915 ("r-rcpparmadillo" ,r-rcpparmadillo)
8916 ("r-readr" ,r-readr)
8917 ("r-stringr" ,r-stringr)))
8918 (home-page "https://cran.r-project.org/web/packages/abcrf/")
8919 (synopsis "Approximate bayesian computation via random forests")
8921 "This package performs approximate bayesian computation (ABC) model choice and
8922 parameter inference via random forests. This machine learning tool named random
8923 forests (RF) can conduct selection among the highly complex models covered by
8925 (license license:gpl2+)))
8927 (define-public r-abctools
8934 (uri (cran-uri "abctools" version))
8936 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
8937 (build-system r-build-system)
8940 ("r-abind" ,r-abind)
8941 ("r-hmisc" ,r-hmisc)
8942 ("r-plyr" ,r-plyr)))
8943 (home-page "https://github.com/dennisprangle/abctools/")
8944 (synopsis "Tools for ABC analyses")
8946 "This @code{r-abctools} package provides tools for approximate Bayesian computation
8947 including summary statistic selection and assessing coverage. This includes
8948 recent dimension reduction algorithms to tune the choice of summary statistics,
8949 and coverage methods to tune the choice of threshold.")
8950 (license license:gpl2+)))
8952 (define-public r-ggstance
8959 (uri (cran-uri "ggstance" version))
8961 (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d"))))
8962 (build-system r-build-system)
8964 `(("r-ggplot2" ,r-ggplot2)
8966 ("r-rlang" ,r-rlang)
8967 ("r-withr" ,r-withr)))
8968 (home-page "https://cran.r-project.org/web/packages/ggstance/")
8969 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
8971 "This package is a @code{r-ggplot2} extension that provides flipped components:
8973 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
8974 @item vertical versions of @code{r-ggplot2} positions.
8976 (license license:gpl3)))
8978 (define-public r-mosaiccore
8980 (name "r-mosaiccore")
8985 (uri (cran-uri "mosaicCore" version))
8987 (base32 "1h3ixzna4xy42rdnd89jj0v9q0riy3fnkd33z6l5c0zaidzm58fz"))))
8988 (properties `((upstream-name . "mosaicCore")))
8989 (build-system r-build-system)
8991 `(("r-dplyr" ,r-dplyr)
8993 ("r-rlang" ,r-rlang)
8994 ("r-tidyr" ,r-tidyr)))
8995 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
8996 (synopsis "Common utilities for mosaic family packages")
8998 "Common utilities used in other Mosaic family packages are collected here.")
8999 (license license:gpl2+)))
9001 (define-public r-labelled
9008 (uri (cran-uri "labelled" version))
9011 "1nsb0mh0jg7gggc41b6v55nmfq07g0qn9fy55x4jws5dscs6pdmi"))))
9012 (properties `((upstream-name . "labelled")))
9013 (build-system r-build-system)
9015 `(("r-dplyr" ,r-dplyr)
9016 ("r-haven" ,r-haven)
9017 ("r-lifecycle" ,r-lifecycle)
9018 ("r-pillar" ,r-pillar)
9019 ("r-rlang" ,r-rlang)
9020 ("r-tidyr" ,r-tidyr)
9021 ("r-vctrs" ,r-vctrs)))
9023 `(("r-knitr" ,r-knitr)))
9024 (home-page "http://larmarange.github.io/labelled/")
9025 (synopsis "Manipulating labelled data")
9027 "This package provides useful functions to deal with the
9028 @code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the
9030 (license license:gpl3)))
9032 (define-public r-ggformula
9034 (name "r-ggformula")
9039 (uri (cran-uri "ggformula" version))
9041 (base32 "1ph5jd8svk8hmshi894vmmpq3zwgdmf4yn3gmdlkad68z8jynhsp"))))
9042 (build-system r-build-system)
9044 `(("r-ggforce" ,r-ggforce)
9045 ("r-ggplot2" ,r-ggplot2)
9046 ("r-ggridges" ,r-ggridges)
9047 ("r-ggstance" ,r-ggstance)
9048 ("r-labelled" ,r-labelled)
9049 ("r-magrittr" ,r-magrittr)
9050 ("r-mosaiccore" ,r-mosaiccore)
9051 ("r-rlang" ,r-rlang)
9052 ("r-scales" ,r-scales)
9053 ("r-stringr" ,r-stringr)
9054 ("r-tibble" ,r-tibble)))
9056 `(("r-knitr" ,r-knitr)))
9057 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
9058 (synopsis "Formula interface for the @code{r-ggplot2}")
9060 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
9061 gf_density(), and so on, bring the formula interface to ggplot(). This captures
9062 and extends the excellent simplicity of the lattice-graphics formula interface,
9063 while providing the intuitive capabilities of @code{r-ggplot2}.")
9064 (license license:expat)))
9066 (define-public r-mosaicdata
9068 (name "r-mosaicdata")
9073 (uri (cran-uri "mosaicData" version))
9075 (base32 "0h3f5fgzkzjfgf3ml0qa5j52921y6wy6jgggxmhs31bs8fd4srg4"))))
9076 (properties `((upstream-name . "mosaicData")))
9077 (build-system r-build-system)
9078 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
9079 (synopsis "Data sets for project Mosaic")
9081 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
9082 used to teach mathematics, statistics, computation and modeling.")
9083 (license license:gpl2+)))
9085 (define-public r-raster
9092 (uri (cran-uri "raster" version))
9095 "19g4chd0nyhnz6hc2j0v9ahjcgz64vvja4y3mrj1pfis1dwhsqn6"))))
9096 (build-system r-build-system)
9098 `(("r-rcpp" ,r-rcpp)
9100 (home-page "https://www.rspatial.org/")
9101 (synopsis "Geographic data analysis and modeling")
9103 "The package implements basic and high-level functions for reading,
9104 writing, manipulating, analyzing and modeling of gridded spatial data.
9105 Processing of very large files is supported.")
9106 (license license:gpl3+)))
9108 (define-public r-mosaic
9115 (uri (cran-uri "mosaic" version))
9117 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
9118 (build-system r-build-system)
9120 `(("r-broom" ,r-broom)
9121 ("r-dplyr" ,r-dplyr)
9122 ("r-ggdendro" ,r-ggdendro)
9123 ("r-ggformula" ,r-ggformula)
9124 ("r-ggplot2" ,r-ggplot2)
9125 ("r-ggrepel" ,r-ggrepel)
9127 ("r-gridextra" ,r-gridextra)
9128 ("r-lattice" ,r-lattice)
9129 ("r-latticeextra" ,r-latticeextra)
9130 ("r-lazyeval" ,r-lazyeval)
9132 ("r-matrix" ,r-matrix)
9133 ("r-mosaiccore" ,r-mosaiccore)
9134 ("r-mosaicdata" ,r-mosaicdata)
9135 ("r-readr" ,r-readr)
9136 ("r-tidyr" ,r-tidyr)))
9138 `(("r-knitr" ,r-knitr)))
9139 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
9140 (synopsis "Mathematics, statistics, and computation teaching utilities")
9142 "This package contain data sets and utilities from
9143 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
9144 statistics, computation and modeling. Project MOSAIC is a community of
9145 educators working to tie together aspects of quantitative work that students
9146 in science, technology, engineering and mathematics will need in their
9147 professional lives, but which are usually taught in isolation, if at all.")
9148 (license license:gpl2+)))
9150 (define-public r-abd
9157 (uri (cran-uri "abd" version))
9159 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
9160 (build-system r-build-system)
9162 `(("r-lattice" ,r-lattice)
9163 ("r-mosaic" ,r-mosaic)
9164 ("r-nlme" ,r-nlme)))
9165 (home-page "https://cran.r-project.org/web/packages/abd/")
9166 (synopsis "Analysis of biological data")
9168 "The @code{r-abd} package contains data sets and sample code for the Analysis of
9169 biological data by Michael Whitlock and Dolph Schluter.")
9170 (license license:gpl2)))
9172 (define-public r-svgui
9179 (uri (cran-uri "svGUI" version))
9181 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
9182 (properties `((upstream-name . "svGUI")))
9183 (build-system r-build-system)
9184 (home-page "https://github.com/SciViews/svGUI/")
9185 (synopsis "Functions for managing GUI clients in R")
9187 "The SciViews @code{svGUI} package eases the management of Graphical User
9188 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
9189 centralizes info about GUI elements currently used, and it dispatches GUI
9190 calls to the particular toolkits in use in function of the context.")
9191 (license license:gpl2)))
9193 (define-public r-svdialogs
9195 (name "r-svdialogs")
9200 (uri (cran-uri "svDialogs" version))
9202 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
9203 (properties `((upstream-name . "svDialogs")))
9204 (build-system r-build-system)
9207 ("zenity" ,zenity)))
9209 `(("r-rstudioapi" ,r-rstudioapi)
9210 ("r-svgui" ,r-svgui)))
9211 (home-page "https://github.com/SciViews/svDialogs/")
9212 (synopsis "Portable dialog boxes")
9214 "This package helps to construct standard dialog boxes for your GUI, including
9215 message boxes, input boxes, list, file or directory selection, and others. In
9216 case R cannot display GUI dialog boxes, a simpler command line version of these
9217 interactive elements is also provided as a fallback solution.")
9218 (license license:gpl2)))
9220 (define-public r-abe
9227 (uri (cran-uri "abe" version))
9230 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
9231 (build-system r-build-system)
9232 (home-page "https://cran.r-project.org/web/packages/abe/")
9233 (synopsis "Augmented backward elimination")
9235 "This package performs augmented backward elimination and checks the
9236 stability of the obtained model. Augmented backward elimination combines
9237 significance or information based criteria with the change in estimate to
9238 either select the optimal model for prediction purposes or to serve as a tool
9239 to obtain a practically sound, highly interpretable model.")
9240 (license license:gpl2+)))
9242 (define-public r-abf2
9249 (uri (cran-uri "abf2" version))
9251 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
9252 (build-system r-build-system)
9253 (home-page "https://cran.r-project.org/web/packages/abf2/")
9254 (synopsis "Load gap-free axon @code{r-abf2} files")
9256 "This package loads electrophysiology data from ABF2 files, as created by
9257 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
9258 mode are currently supported.")
9259 (license license:artistic2.0)))
9261 (define-public r-abhgenotyper
9263 (name "r-abhgenotyper")
9268 (uri (cran-uri "ABHgenotypeR" version))
9270 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
9271 (properties `((upstream-name . "ABHgenotypeR")))
9272 (build-system r-build-system)
9274 `(("r-ggplot2" ,r-ggplot2)
9275 ("r-reshape2" ,r-reshape2)))
9276 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
9277 (synopsis "Visualize and manipulate ABH genotypes")
9279 "The @code{r-abhgenotyper} package provides simple imputation,
9280 error-correction and plotting capacities for genotype data. The package is
9281 supposed to serve as an intermediate but independent analysis tool between the
9282 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
9283 not found in either TASSEL or @code{r-qtl} in addition to visualization of
9284 genotypes as \"graphical genotypes\".")
9285 (license license:gpl3)))
9287 (define-public r-furrr
9294 (uri (cran-uri "furrr" version))
9297 "0kfd4hw1yn2mfxzjgiz4r6yi2vsp1j0wy5hdhzd6wha7vi9h7hg5"))))
9298 (build-system r-build-system)
9300 `(("r-ellipsis" ,r-ellipsis)
9301 ("r-future" ,r-future)
9302 ("r-globals" ,r-globals)
9303 ("r-lifecycle" ,r-lifecycle)
9304 ("r-purrr" ,r-purrr)
9305 ("r-rlang" ,r-rlang)
9306 ("r-vctrs" ,r-vctrs)))
9307 (home-page "https://github.com/DavisVaughan/furrr")
9308 (synopsis "Apply mapping functions in parallel using futures")
9310 "This package provides implementations of the family of @code{map()}
9311 functions from the @code{purrr} package that can be resolved using any
9312 @code{future}-supported backend, e.g. parallel on the local machine or
9313 distributed on a compute cluster.")
9314 (license license:lgpl2.1+)))
9316 (define-public r-abjutils
9323 (uri (cran-uri "abjutils" version))
9325 (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd"))))
9326 (build-system r-build-system)
9328 `(("r-dplyr" ,r-dplyr)
9329 ("r-magrittr" ,r-magrittr)
9330 ("r-purrr" ,r-purrr)
9331 ("r-rlang" ,r-rlang)
9332 ("r-rstudioapi" ,r-rstudioapi)
9333 ("r-stringi" ,r-stringi)
9334 ("r-stringr" ,r-stringr)
9335 ("r-tidyr" ,r-tidyr)))
9336 (home-page "https://github.com/abjur/abjutils/")
9337 (synopsis "Collection of tools for jurimetrical analysis")
9339 "This package implements general purpose tools, such as functions for
9340 sampling and basic manipulation of Brazilian lawsuits identification number.
9341 It also implements functions for text cleaning, such as accentuation
9343 (license license:expat)))
9345 (define-public r-abnormality
9347 (name "r-abnormality")
9352 (uri (cran-uri "abnormality" version))
9354 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
9355 (build-system r-build-system)
9357 `(("r-mass" ,r-mass)
9358 ("r-matrix" ,r-matrix)))
9359 (home-page "https://cran.r-project.org/web/packages/abnormality/")
9360 (synopsis "Measure a subject's abnormality with respect to a reference population")
9362 "This package contains functions to implement the methodology and
9363 considerations laid out by Marks et al. in the article \"Measuring abnormality
9364 in high dimensional spaces: applications in biomechanical gait analysis\".
9365 Using high-dimensional datasets to measure a subject's overall level of
9366 abnormality as compared to a reference population is often needed in outcomes
9368 (license license:expat)))
9370 (define-public r-abodoutlier
9372 (name "r-abodoutlier")
9377 (uri (cran-uri "abodOutlier" version))
9379 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
9380 (properties `((upstream-name . "abodOutlier")))
9381 (build-system r-build-system)
9383 `(("r-cluster" ,r-cluster)))
9384 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
9385 (synopsis "Angle-based outlier detection")
9387 "This package performs angle-based outlier detection on a given data
9388 frame. It offers three methods to process data:
9390 @item full but slow implementation using all the data that has cubic
9392 @item a fully randomized method;
9393 @item a method using k-nearest neighbours.
9395 These algorithms are well suited for high dimensional data outlier
9397 (license license:expat)))
9399 (define-public r-abps
9406 (uri (cran-uri "ABPS" version))
9408 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
9409 (properties `((upstream-name . "ABPS")))
9410 (build-system r-build-system)
9411 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
9412 (home-page "https://cran.r-project.org/web/packages/ABPS/")
9413 (synopsis "Abnormal blood profile score to detect blood doping")
9415 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
9416 The ABPS is a part of the Athlete biological passport program of the World
9417 anti-doping agency, which combines several blood parameters into a single
9418 score in order to detect blood doping. The package also contains functions to
9419 calculate other scores used in anti-doping programs, such as the ratio of
9420 hemoglobin to reticulocytes (OFF-score), as well as example data.")
9421 (license license:gpl2+)))
9423 (define-public r-parmigene
9425 (name "r-parmigene")
9430 (uri (cran-uri "parmigene" version))
9433 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
9434 (build-system r-build-system)
9435 (home-page "https://cran.r-project.org/web/packages/parmigene/")
9436 (synopsis "Mutual information estimation for gene network reconstruction")
9438 "This package provides a parallel estimation of the mutual information
9439 based on entropy estimates from k-nearest neighbors distances and algorithms
9440 for the reconstruction of gene regulatory networks.")
9441 (license license:agpl3+)))
9443 (define-public r-pscl
9450 (uri (cran-uri "pscl" version))
9452 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
9453 (build-system r-build-system)
9455 `(("r-mass" ,r-mass)))
9456 (home-page "https://github.com/atahk/pscl/")
9457 (synopsis "Political science computational laboratory")
9459 "The @code{pscl} is an R package providing classes and methods for:
9461 @item Bayesian analysis of roll call data (item-response models);
9462 @item elementary Bayesian statistics;
9463 @item maximum likelihood estimation of zero-inflated and hurdle models for count
9465 @item utility functions.
9467 (license license:gpl2)))
9469 (define-public r-accelmissing
9471 (name "r-accelmissing")
9476 (uri (cran-uri "accelmissing" version))
9478 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
9479 (build-system r-build-system)
9481 `(("r-mice" ,r-mice)
9482 ("r-pscl" ,r-pscl)))
9483 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
9484 (synopsis "Missing value imputation for accelerometer data")
9486 "This package provides a statistical method to impute the missing values in
9487 accelerometer data. The methodology includes both parametric and
9488 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
9489 model. It also provides multiple functions to preprocess the accelerometer data
9490 previous to the missing data imputation. These include detecting the wearing
9491 and the non-wearing time, selecting valid days and subjects, and creating plots.")
9492 (license license:gpl2+)))
9494 (define-public r-mhsmm
9501 (uri (cran-uri "mhsmm" version))
9503 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
9504 (build-system r-build-system)
9505 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
9506 (home-page "https://github.com/jaredo/mhsmm/")
9507 (synopsis "Inference for hidden Markov and semi-Markov models")
9509 "The @code{r-mhsmm} package implements estimation and prediction methods for
9510 hidden Markov and semi-Markov models for multiple observation sequences. Such
9511 techniques are of interest when observed data is thought to be dependent on some
9512 unobserved (or hidden) state. Also, this package is suitable for equidistant
9513 time series data, with multivariate and/or missing data. Allows user defined
9514 emission distributions.")
9515 (license license:gpl2+)))
9517 (define-public r-nleqslv
9524 (uri (cran-uri "nleqslv" version))
9526 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
9527 (build-system r-build-system)
9528 (native-inputs `(("gfortran" ,gfortran)))
9529 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
9530 (synopsis "Solve systems of nonlinear equations")
9532 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
9533 Broyden or a Newton method with a choice of global strategies such as line
9534 search and trust region. There are options for using a numerical or user
9535 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
9536 singular or ill-conditioned Jacobian.")
9537 (license license:gpl2+)))
9539 (define-public r-physicalactivity
9541 (name "r-physicalactivity")
9546 (uri (cran-uri "PhysicalActivity" version))
9548 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40"))))
9550 `((upstream-name . "PhysicalActivity")))
9551 (build-system r-build-system)
9552 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
9553 (synopsis "Procesing accelerometer data for physical activity measurement")
9555 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
9556 for classification of monitor wear and nonwear time intervals in accelerometer
9557 data collected to assess physical activity. The package also contains functions
9558 for making plots of accelerometer data and obtaining the summary of various
9559 information including daily monitor wear time and the mean monitor wear time
9560 during valid days. The revised package version 0.2-1 improved the functions
9561 regarding speed, robustness and add better support for time zones and daylight
9562 saving. In addition, several functions were added:
9564 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
9565 @item the @code{markPAI} can categorize physical activity intensity level based
9566 on user-defined cut-points of accelerometer counts.
9568 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
9569 @code{queryActigraph} functions.")
9570 (license license:gpl3+)))
9572 (define-public r-acc
9579 (uri (cran-uri "acc" version))
9581 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
9582 (build-system r-build-system)
9584 `(("r-circlize" ,r-circlize)
9586 ("r-ggplot2" ,r-ggplot2)
9587 ("r-iterators" ,r-iterators)
9588 ("r-mhsmm" ,r-mhsmm)
9589 ("r-nleqslv" ,r-nleqslv)
9590 ("r-physicalactivity" ,r-physicalactivity)
9592 ("r-r-utils" ,r-r-utils)
9594 ("r-rcpparmadillo" ,r-rcpparmadillo)
9595 ("r-rsqlite" ,r-rsqlite)
9597 (home-page "https://cran.r-project.org/web/packages/acc/")
9598 (synopsis "Exploring accelerometer data")
9600 "This package processes accelerometer data from uni-axial and tri-axial devices
9601 and generates data summaries. Also, includes functions to plot, analyze, and
9602 simulate accelerometer data.")
9603 (license license:gpl2+)))
9605 (define-public r-rbenchmark
9607 (name "r-rbenchmark")
9612 (uri (cran-uri "rbenchmark" version))
9614 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
9615 (build-system r-build-system)
9616 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
9617 (synopsis "Benchmarking routine for R")
9619 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
9620 and is intended to facilitate benchmarking of arbitrary R code. The library
9621 consists of just one function, benchmark, which is a simple wrapper around
9622 system.time. Given a specification of the benchmarking process (counts of
9623 replications, evaluation environment) and an arbitrary number of expressions,
9624 benchmark evaluates each of the expressions in the specified environment,
9625 replicating the evaluation as many times as specified, and returning the results
9626 conveniently wrapped into a data frame.")
9627 (license license:gpl2+)))
9629 (define-public r-mitools
9636 (uri (cran-uri "mitools" version))
9639 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
9640 (build-system r-build-system)
9641 (propagated-inputs `(("r-dbi" ,r-dbi)))
9642 (home-page "https://cran.r-project.org/web/packages/mitools/")
9643 (synopsis "Tools for multiple imputation of missing data")
9645 "This package provides tools to perform analyses and combine results from
9646 multiple-imputation datasets.")
9647 (license license:gpl2)))
9649 (define-public r-mixsqp
9655 (uri (cran-uri "mixsqp" version))
9658 "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q"))))
9659 (properties `((upstream-name . "mixsqp")))
9660 (build-system r-build-system)
9662 `(("r-irlba" ,r-irlba)
9664 ("r-rcpparmadillo" ,r-rcpparmadillo)))
9666 `(("r-knitr" ,r-knitr)))
9667 (home-page "https://github.com/stephenslab/mixsqp")
9669 "Sequential quadratic programming for maximum-likelihood estimation")
9671 "This package provides an optimization method based on sequential
9672 quadratic programming for maximum likelihood estimation of the mixture
9673 proportions in a finite mixture model where the component densities are
9674 known. The algorithm is expected to obtain solutions that are at least
9675 as accurate as the state-of-the-art MOSEK interior-point solver, and they
9676 are expected to arrive at solutions more quickly when the number of
9677 samples is large and the number of mixture components is not too large.")
9678 (license license:expat)))
9680 (define-public r-magick
9687 (uri (cran-uri "magick" version))
9690 "1k4fqhxh2ppynl56fs044wpn4wk6gbv6lwp2x4x7j67zwcv56n36"))))
9691 (build-system r-build-system)
9693 `(("imagemagick" ,imagemagick)
9696 `(("r-curl" ,r-curl)
9697 ("r-magrittr" ,r-magrittr)
9698 ("r-rcpp" ,r-rcpp)))
9700 `(("pkg-config" ,pkg-config)
9701 ("r-knitr" ,r-knitr)))
9702 (home-page "https://github.com/ropensci/magick")
9703 (synopsis "Advanced graphics and image-processing in R")
9705 "This package provides bindings to ImageMagick, a comprehensive image
9706 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
9707 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
9708 operations are vectorized via the Magick++ STL meaning they operate either on
9709 a single frame or a series of frames for working with layers, collages, or
9710 animation. In RStudio, images are automatically previewed when printed to the
9711 console, resulting in an interactive editing environment.")
9712 (license license:expat)))
9714 (define-public r-survey
9721 (uri (cran-uri "survey" version))
9724 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
9725 (build-system r-build-system)
9727 `(("r-lattice" ,r-lattice)
9728 ("r-matrix" ,r-matrix)
9729 ("r-minqa" ,r-minqa)
9730 ("r-mitools" ,r-mitools)
9731 ("r-numderiv" ,r-numderiv)
9732 ("r-survival" ,r-survival)))
9733 (home-page "http://r-survey.r-forge.r-project.org/survey/")
9734 (synopsis "Analysis of complex survey samples")
9736 "This package provides tools for the analysis of complex survey samples.
9737 The provided features include: summary statistics, two-sample tests, rank
9738 tests, generalised linear models, cumulative link models, Cox models,
9739 loglinear models, and general maximum pseudolikelihood estimation for
9740 multistage stratified, cluster-sampled, unequally weighted survey samples;
9741 variances by Taylor series linearisation or replicate weights;
9742 post-stratification, calibration, and raking; two-phase subsampling designs;
9743 graphics; PPS sampling without replacement; principal components, and factor
9745 ;; Either version of the GPL.
9746 (license (list license:gpl2 license:gpl3))))
9748 (define-public r-gee
9755 (uri (cran-uri "gee" version))
9758 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
9759 (properties `((upstream-name . "gee")))
9760 (build-system r-build-system)
9762 `(("gfortran" ,gfortran)))
9763 (home-page "https://cran.r-project.org/web/packages/gee/")
9764 (synopsis "Generalized estimation equation solver")
9766 "This package provides a solver for generalized estimation equations.")
9767 (license license:gpl2)))
9769 (define-public r-tab
9776 (uri (cran-uri "tab" version))
9779 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
9780 (properties `((upstream-name . "tab")))
9781 (build-system r-build-system)
9783 `(("r-dplyr" ,r-dplyr)
9785 ("r-knitr" ,r-knitr)
9787 ("r-survey" ,r-survey)
9788 ("r-survival" ,r-survival)
9789 ("r-xtable" ,r-xtable)))
9790 (home-page "https://cran.r-project.org/web/packages/tab/")
9791 (synopsis "Create summary tables for statistical reports")
9793 "This package contains functions for creating various types of summary
9794 tables, e.g. comparing characteristics across levels of a categorical variable
9795 and summarizing fitted generalized linear models, generalized estimating
9796 equations, and Cox proportional hazards models. Functions are available to
9797 handle data from simple random samples as well as complex surveys.")
9798 (license license:gpl3+)))
9800 (define-public r-dvmisc
9807 (uri (cran-uri "dvmisc" version))
9809 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
9810 (build-system r-build-system)
9812 `(("r-cubature" ,r-cubature)
9813 ("r-data-table" ,r-data-table)
9814 ("r-dplyr" ,r-dplyr)
9815 ("r-ggplot2" ,r-ggplot2)
9817 ("r-mvtnorm" ,r-mvtnorm)
9818 ("r-pracma" ,r-pracma)
9819 ("r-rbenchmark" ,r-rbenchmark)
9821 ("r-survey" ,r-survey)
9823 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
9824 (synopsis "Faster computation of common statistics and miscellaneous functions")
9826 "This package implements faster versions of base R functions (e.g. mean, standard
9827 deviation, covariance, weighted mean), mostly written in C++, along with
9828 miscellaneous functions for various purposes (e.g. create the histogram with
9829 fitted probability density function or probability mass function curve, create
9830 the body mass index groups, assess the linearity assumption in logistic
9832 (license license:gpl2)))
9834 (define-public r-accelerometry
9836 (name "r-accelerometry")
9841 (uri (cran-uri "accelerometry" version))
9843 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
9844 (build-system r-build-system)
9846 `(("r-dvmisc" ,r-dvmisc)
9847 ("r-rcpp" ,r-rcpp)))
9848 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
9849 (synopsis "Functions for processing accelerometer data")
9851 "This package provides a collection of functions that perform operations on
9852 time-series accelerometer data, such as identify the non-wear time, flag minutes
9853 that are part of an activity bout, and find the maximum 10-minute average count
9854 value. The functions are generally very flexible, allowing for a variety of
9855 algorithms to be implemented.")
9856 (license license:gpl3)))
9858 (define-public r-absim
9865 (uri (cran-uri "AbSim" version))
9867 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
9868 (properties `((upstream-name . "AbSim")))
9869 (build-system r-build-system)
9872 ("r-powerlaw" ,r-powerlaw)))
9873 (home-page "https://cran.r-project.org/web/packages/AbSim/")
9874 (synopsis "Time resolved simulations of antibody repertoires")
9876 "This package provides simulation methods for the evolution of antibody repertoires.
9877 The heavy and light chain variable region of both human and C57BL/6 mice can
9878 be simulated in a time-dependent fashion. Both single lineages using one set of
9879 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
9880 with an initial V-D-J recombination event, starting the first phylogenetic tree.
9881 Upon completion, the main loop of the algorithm begins, with each iteration
9882 representing one simulated time step. Various mutation events are possible at
9883 each time step, contributing to a diverse final repertoire.")
9884 (license license:gpl2)))
9886 (define-public r-quic
9893 (uri (cran-uri "QUIC" version))
9895 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
9896 (properties `((upstream-name . "QUIC")))
9897 (build-system r-build-system)
9898 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
9899 (synopsis "Regularized sparse inverse covariance matrix estimation")
9901 "This package implements the regularized Gaussian maximum likelihood
9902 estimation of the inverse of a covariance matrix. It uses Newton's method and
9903 coordinate descent to solve the regularized inverse covariance matrix
9904 estimation problem.")
9905 ;; The project home page states that the release is under GPLv3 or later.
9906 ;; The CRAN page only says GPL-3.
9907 (license license:gpl3+)))
9909 (define-public r-abundant
9916 (uri (cran-uri "abundant" version))
9918 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
9919 (build-system r-build-system)
9921 `(("r-quic" ,r-quic)))
9922 (home-page "https://cran.r-project.org/web/packages/abundant/")
9923 (synopsis "Abundant regression and high-dimensional principal fitted components")
9925 "This package provides tools to fit and predict with the high-dimensional
9926 principal fitted components model. This model is described by Cook, Forzani,
9927 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
9928 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
9929 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
9930 (license license:gpl2+)))
9932 (define-public r-ac3net
9939 (uri (cran-uri "Ac3net" version))
9941 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
9942 (properties `((upstream-name . "Ac3net")))
9943 (build-system r-build-system)
9945 `(("r-data-table" ,r-data-table)))
9946 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
9947 (synopsis "Inferring directional conservative causal core gene networks")
9948 (description "This package infers directional Conservative causal core
9949 (gene) networks (C3NET). This is a version of the algorithm C3NET with
9950 directional network.")
9951 (license license:gpl3+)))
9953 (define-public r-aca
9960 (uri (cran-uri "ACA" version))
9962 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
9963 (properties `((upstream-name . "ACA")))
9964 (build-system r-build-system)
9965 (home-page "https://cran.r-project.org/web/packages/ACA/")
9966 (synopsis "Abrupt change-point or aberration detection in point series")
9968 "This package offers an interactive function for the detection of breakpoints in
9970 ;; Any version of the GPL
9971 (license (list license:gpl2+ license:gpl3+))))
9973 (define-public r-acceptancesampling
9975 (name "r-acceptancesampling")
9980 (uri (cran-uri "AcceptanceSampling" version))
9982 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
9984 `((upstream-name . "AcceptanceSampling")))
9985 (build-system r-build-system)
9986 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
9987 (synopsis "Creation and evaluation of acceptance sampling plans")
9989 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
9990 acceptance sampling plans. Acceptance sampling is a methodology commonly used
9991 in quality control and improvement. International standards of acceptance
9992 sampling provide sampling plans for specific circumstances. The aim of this
9993 package is to provide an easy-to-use interface to visualize single, double or
9994 multiple sampling plans. In addition, methods have been provided to enable the
9995 user to assess sampling plans against pre-specified levels of performance, as
9996 measured by the probability of acceptance for a given level of quality in the
9998 (license license:gpl3+)))
10000 (define-public r-acclma
10007 (uri (cran-uri "ACCLMA" version))
10009 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
10010 (properties `((upstream-name . "ACCLMA")))
10011 (build-system r-build-system)
10012 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
10013 (synopsis "ACC & LMA graph plotting")
10015 "This package contains a function that imports data from a @acronym{CSV,
10016 Comma-Separated Values} file, or uses manually entered data from the format (x,
10017 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
10018 Curve} vs @acronym{LOI, Line of Independence} graph and
10019 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
10020 function is @code{plotLMA} (source file, header) that takes a data set and plots the
10021 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
10022 string) was passed, a manual data entry window is opened. The header parameter
10023 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
10024 a header row or not. The dataset should contain only one independent variable
10025 (x) and one dependent variable (y) and can contain a weight for each
10027 (license license:gpl2)))
10029 (define-public r-aspi
10036 (uri (cran-uri "aspi" version))
10038 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
10039 (build-system r-build-system)
10041 "https://cran.r-project.org/web/packages/aspi/")
10043 "Analysis of symmetry of parasitic infections")
10045 "This package provides tools for the analysis and visualization of bilateral
10046 asymmetry in parasitic infections.")
10047 (license license:gpl3+)))
10049 (define-public r-sandwich
10051 (name "r-sandwich")
10056 (uri (cran-uri "sandwich" version))
10059 "0afm6snak7r11dxyl3qirqdjah6d9pdv4afmxwam1nq9bqxyb3w2"))))
10060 (build-system r-build-system)
10062 `(("r-zoo" ,r-zoo)))
10063 (home-page "https://cran.r-project.org/web/packages/sandwich/")
10064 (synopsis "Robust Covariance Matrix Estimators")
10066 "This package provides model-robust standard error estimators for
10067 cross-sectional, time series, clustered, panel, and longitudinal data.")
10068 ;; Either version of the license.
10069 (license (list license:gpl2 license:gpl3))))
10071 (define-public r-th-data
10078 (uri (cran-uri "TH.data" version))
10081 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
10082 (properties `((upstream-name . "TH.data")))
10083 (build-system r-build-system)
10085 `(("r-mass" ,r-mass)
10086 ("r-survival" ,r-survival)))
10087 (home-page "https://cran.r-project.org/web/packages/TH.data/")
10088 (synopsis "Shared data sets")
10090 "This package contains supporting data sets that are used in other
10091 packages maintained by Torsten Hothorn.")
10092 (license license:gpl3)))
10094 (define-public r-multcomp
10096 (name "r-multcomp")
10101 (uri (cran-uri "multcomp" version))
10104 "1s8qmljawalisggniy7va5l5cicsgvs0lp20c33vxlvyiy0dbb1s"))))
10105 (build-system r-build-system)
10107 `(("r-codetools" ,r-codetools)
10108 ("r-mvtnorm" ,r-mvtnorm)
10109 ("r-sandwich" ,r-sandwich)
10110 ("r-survival" ,r-survival)
10111 ("r-th-data" ,r-th-data)))
10112 (home-page "https://cran.r-project.org/web/packages/multcomp/")
10113 (synopsis "Simultaneous inference in general parametric models")
10115 "Simultaneous tests and confidence intervals for general linear
10116 hypotheses in parametric models, including linear, generalized linear, linear
10117 mixed effects, and survival models. The package includes demos reproducing
10118 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
10119 Hothorn, Westfall, 2010, CRC Press).")
10120 (license license:gpl2)))
10122 (define-public r-emmeans
10129 (uri (cran-uri "emmeans" version))
10132 "1rbh3ls23fazrwpsam5llk3kqdzz2zvsms3i4f1cgn34ky3w8361"))))
10133 (build-system r-build-system)
10135 `(("r-estimability" ,r-estimability)
10136 ("r-mvtnorm" ,r-mvtnorm)
10137 ("r-numderiv" ,r-numderiv)
10139 ("r-xtable" ,r-xtable)))
10141 `(("r-knitr" ,r-knitr)))
10142 (home-page "https://github.com/rvlenth/emmeans")
10143 (synopsis "Estimated marginal means, aka least-squares means")
10145 "This package provides tools to obtain @dfn{estimated marginal
10146 means} (EMMs) for many linear, generalized linear, and mixed models. It can
10147 be used to compute contrasts or linear functions of EMMs, trends, and
10148 comparisons of slopes.")
10149 ;; Either version of the license.
10150 (license (list license:gpl2 license:gpl3))))
10152 (define-public r-pwr
10159 (uri (cran-uri "pwr" version))
10162 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
10163 (build-system r-build-system)
10165 `(("r-knitr" ,r-knitr)))
10166 (home-page "https://github.com/heliosdrm/pwr")
10167 (synopsis "Basic functions for power analysis")
10169 "This package provides power analysis functions along the lines of
10171 (license license:gpl3+)))
10173 (define-public r-libcoin
10180 (uri (cran-uri "libcoin" version))
10182 (base32 "0izgnr4zdrbz3a05b0s28xfly4izp2zslgh282l9ads4skrmj3hl"))))
10183 (build-system r-build-system)
10184 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
10185 (home-page "https://cran.r-project.org/web/packages/libcoin")
10186 (synopsis "Linear test statistics for permutation inference")
10188 "This package provides basic infrastructure for linear test statistics
10189 and permutation inference in the framework of Strasser and Weber (1999).")
10190 (license license:gpl2)))
10192 (define-public r-coin
10199 (uri (cran-uri "coin" version))
10202 "15xvhnbyg34aacn6jfz4bsa1f7wq2ci0hslj8mgymql90k50x1qi"))))
10203 (build-system r-build-system)
10205 `(("r-libcoin" ,r-libcoin)
10206 ("r-matrixstats" ,r-matrixstats)
10207 ("r-modeltools" ,r-modeltools)
10208 ("r-multcomp" ,r-multcomp)
10209 ("r-mvtnorm" ,r-mvtnorm)
10210 ("r-survival" ,r-survival)))
10211 (home-page "http://coin.r-forge.r-project.org")
10212 (synopsis "Conditional inference procedures in a permutation test framework")
10214 "This package provides conditional inference procedures for the general
10215 independence problem including two-sample, K-sample (non-parametric ANOVA),
10216 correlation, censored, ordered and multivariate problems.")
10217 (license license:gpl2)))
10219 (define-public r-bayesplot
10221 (name "r-bayesplot")
10226 (uri (cran-uri "bayesplot" version))
10229 "0j69a78l5z0wyxcz607amaa4jc8kwwvcia9wxyir65b8ks9gj1d6"))))
10230 (build-system r-build-system)
10232 `(("pandoc" ,pandoc)
10233 ("pandoc-citeproc" ,pandoc-citeproc)))
10235 `(("r-knitr" ,r-knitr)))
10237 `(("r-dplyr" ,r-dplyr)
10238 ("r-ggplot2" ,r-ggplot2)
10239 ("r-ggridges" ,r-ggridges)
10241 ("r-reshape2" ,r-reshape2)
10242 ("r-rlang" ,r-rlang)
10243 ("r-tibble" ,r-tibble)
10244 ("r-tidyselect" ,r-tidyselect)))
10245 (home-page "https://mc-stan.org/bayesplot")
10246 (synopsis "Plotting for Bayesian models")
10248 "This package provides plotting functions for posterior analysis, model
10249 checking, and MCMC diagnostics. The package is designed not only to provide
10250 convenient functionality for users, but also a common set of functions that
10251 can be easily used by developers working on a variety of R packages for
10252 Bayesian modeling.")
10253 (license license:gpl3+)))
10255 (define-public r-tmb
10262 (uri (cran-uri "TMB" version))
10265 "0vnjh8d5gnjswil8ld3gbbspy4m5l2pzar1mpj62qxn2mwx0cc4s"))))
10266 (properties `((upstream-name . "TMB")))
10267 (build-system r-build-system)
10269 `(("r-matrix" ,r-matrix)
10270 ("r-rcppeigen" ,r-rcppeigen)))
10271 (home-page "http://tmb-project.org")
10272 (synopsis "Template model builder: a general random effect tool")
10274 "With this tool, a user should be able to quickly implement complex
10275 random effect models through simple C++ templates. The package combines
10276 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
10277 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
10278 from R) to obtain an efficient implementation of the applied Laplace
10279 approximation with exact derivatives. Key features are: Automatic sparseness
10280 detection, parallelism through BLAS and parallel user templates.")
10281 (license license:gpl2)))
10283 (define-public r-sjstats
10290 (uri (cran-uri "sjstats" version))
10292 (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka"))))
10293 (build-system r-build-system)
10295 `(("r-bayestestr" ,r-bayestestr)
10296 ("r-broom" ,r-broom)
10297 ("r-dplyr" ,r-dplyr)
10298 ("r-effectsize" ,r-effectsize)
10299 ("r-emmeans" ,r-emmeans)
10300 ("r-insight" ,r-insight)
10302 ("r-magrittr" ,r-magrittr)
10304 ("r-modelr" ,r-modelr)
10305 ("r-parameters" ,r-parameters)
10306 ("r-performance" ,r-performance)
10307 ("r-purrr" ,r-purrr)
10308 ("r-rlang" ,r-rlang)
10309 ("r-sjlabelled" ,r-sjlabelled)
10310 ("r-sjmisc" ,r-sjmisc)
10311 ("r-tidyr" ,r-tidyr)))
10312 (home-page "https://github.com/strengejacke/sjstats")
10313 (synopsis "Functions for common statistical computations")
10315 "This package provides a collection of convenient functions for common
10316 statistical computations, which are not directly provided by R's @code{base}
10317 or @code{stats} packages. This package aims at providing, first, shortcuts
10318 for statistical measures, which otherwise could only be calculated with
10319 additional effort. Second, these shortcut functions are generic, and can be
10320 applied not only to vectors, but also to other objects as well. The focus of
10321 most functions lies on summary statistics or fit measures for regression
10322 models, including generalized linear models, mixed effects models and Bayesian
10324 (license license:gpl3)))
10326 (define-public r-glmmtmb
10329 (version "1.0.2.1")
10333 (uri (cran-uri "glmmTMB" version))
10336 "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab"))))
10337 (properties `((upstream-name . "glmmTMB")))
10338 (build-system r-build-system)
10340 `(("r-lme4" ,r-lme4)
10341 ("r-matrix" ,r-matrix)
10343 ("r-rcppeigen" ,r-rcppeigen)
10346 `(("r-knitr" ,r-knitr))) ; for vignettes
10347 (home-page "https://github.com/glmmTMB")
10348 (synopsis "Generalized linear mixed models")
10350 "Fit linear and generalized linear mixed models with various extensions,
10351 including zero-inflation. The models are fitted using maximum likelihood
10352 estimation via the Template Model Builder. Random effects are assumed to be
10353 Gaussian on the scale of the linear predictor and are integrated out using the
10354 Laplace approximation. Gradients are calculated using automatic
10356 (license license:agpl3+)))
10358 (define-public r-bayestestr
10360 (name "r-bayestestr")
10365 (uri (cran-uri "bayestestR" version))
10368 "06y7vccgln1882yv04may9p6s915py8nnhg82d5ppbpxzcifi7l4"))))
10369 (properties `((upstream-name . "bayestestR")))
10370 (build-system r-build-system)
10372 `(("r-insight" ,r-insight)))
10374 `(("r-knitr" ,r-knitr)))
10375 (home-page "https://github.com/easystats/bayestestR")
10376 (synopsis "Describe Bayesian models and posterior distributions")
10378 "This package provides utilities to understand and describe posterior
10379 distributions and Bayesian models. It includes point-estimates such as
10380 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
10381 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
10382 ROPE percentage and pd).")
10383 (license license:gpl3)))
10385 (define-public r-performance
10387 (name "r-performance")
10392 (uri (cran-uri "performance" version))
10395 "1z45vy8gg77c2imcspwqf94anzi6c40wwbq0h7hg6zy76jsgvbyj"))))
10396 (build-system r-build-system)
10398 `(("r-bayestestr" ,r-bayestestr)
10399 ("r-insight" ,r-insight)))
10400 (home-page "https://easystats.github.io/performance/")
10401 (synopsis "Assessment of regression models performance")
10403 "This package provides utilities for computing measures to assess model
10404 quality, which are not directly provided by R's @code{base} or @code{stats}
10405 packages. These include e.g. measures like r-squared, intraclass correlation
10406 coefficient, root mean squared error or functions to check models for
10407 overdispersion, singularity or zero-inflation and more. Functions apply to a
10408 large variety of regression models, including generalized linear models, mixed
10409 effects models and Bayesian models.")
10410 (license license:gpl3)))
10412 (define-public r-ggeffects
10414 (name "r-ggeffects")
10419 (uri (cran-uri "ggeffects" version))
10422 "1c5rvycaqp7zp1j6j17c84v8nlpi0w7bhfxmcha4n37m0snk1kgy"))))
10423 (build-system r-build-system)
10425 `(("r-insight" ,r-insight)
10427 ("r-sjlabelled" ,r-sjlabelled)))
10429 `(("r-knitr" ,r-knitr)))
10430 (home-page "https://github.com/strengejacke/ggeffects")
10431 (synopsis "Create tidy data frames of marginal effects for ggplot")
10433 "This package provides tools to compute marginal effects from statistical
10434 models and return the result as tidy data frames. These data frames are ready
10435 to use with the @code{ggplot2} package. Marginal effects can be calculated
10436 for many different models. Interaction terms, splines and polynomial terms
10437 are also supported. The two main functions are @code{ggpredict()} and
10438 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
10439 results using @code{ggplot2}.")
10440 (license license:gpl3)))
10442 (define-public r-effectsize
10444 (name "r-effectsize")
10449 (uri (cran-uri "effectsize" version))
10452 "1hcrnax9wf0nwsb8nv15rxw8yy8w5dak16dw3w5bxi8xnf56lkz2"))))
10453 (properties `((upstream-name . "effectsize")))
10454 (build-system r-build-system)
10456 `(("r-bayestestr" ,r-bayestestr)
10457 ("r-insight" ,r-insight)
10458 ("r-parameters" ,r-parameters)))
10460 `(("r-knitr" ,r-knitr)))
10461 (home-page "https://github.com/easystats/effectsize")
10462 (synopsis "Indices of effect size and standardized parameters")
10464 "This package provides utilities to work with indices of effect size and
10465 standardized parameters for a wide variety of models, allowing computation and
10466 conversion of indices such as Cohen's d, r, odds, etc.")
10467 (license license:gpl3)))
10469 (define-public r-sjplot
10476 (uri (cran-uri "sjPlot" version))
10478 (base32 "1g4qabg654kwdm09ihp4h3mg64a1d7a7gsn6w56rwsidqqaxilq0"))))
10479 (properties `((upstream-name . "sjPlot")))
10480 (build-system r-build-system)
10482 `(("r-bayestestr" ,r-bayestestr)
10483 ("r-dplyr" ,r-dplyr)
10484 ("r-effectsize" ,r-effectsize)
10485 ("r-ggeffects" ,r-ggeffects)
10486 ("r-ggplot2" ,r-ggplot2)
10487 ("r-insight" ,r-insight)
10488 ("r-knitr" ,r-knitr)
10490 ("r-parameters" ,r-parameters)
10491 ("r-performance" ,r-performance)
10492 ("r-purrr" ,r-purrr)
10493 ("r-rlang" ,r-rlang)
10494 ("r-scales" ,r-scales)
10495 ("r-sjlabelled" ,r-sjlabelled)
10496 ("r-sjmisc" ,r-sjmisc)
10497 ("r-sjstats" ,r-sjstats)
10498 ("r-tidyr" ,r-tidyr)))
10500 `(("r-knitr" ,r-knitr)))
10501 (home-page "https://strengejacke.github.io/sjPlot/")
10502 (synopsis "Data visualization for statistics in social science")
10504 "This package represents a collection of plotting and table output
10505 functions for data visualization. Results of various statistical
10506 analyses (that are commonly used in social sciences) can be visualized using
10507 this package, including simple and cross tabulated frequencies, histograms,
10508 box plots, (generalized) linear models, mixed effects models, principal
10509 component analysis and correlation matrices, cluster analyses, scatter plots,
10510 stacked scales, effects plots of regression models (including interaction
10511 terms) and much more. This package supports labelled data.")
10512 (license license:gpl3)))
10514 (define-public r-ini
10521 (uri (cran-uri "ini" version))
10524 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
10525 (build-system r-build-system)
10526 (home-page "https://github.com/dvdscripter/ini")
10527 (synopsis "Read and write configuration files")
10529 "This package provides tools to parse simple @code{.ini} configuration
10530 files to an structured list. Users can manipulate this resulting list with
10531 @code{lapply()} functions. This same structured list can be used to write
10532 back to file after modifications.")
10533 (license license:gpl3)))
10535 (define-public r-gitcreds
10537 (name "r-gitcreds")
10542 (uri (cran-uri "gitcreds" version))
10545 "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi"))))
10546 (properties `((upstream-name . "gitcreds")))
10547 (build-system r-build-system)
10548 (inputs `(("git" ,git-minimal)))
10549 (native-inputs `(("r-knitr" ,r-knitr)))
10550 (home-page "https://github.com/r-lib/gitcreds")
10551 (synopsis "Query git credentials from R")
10553 "Query, set, and delete credentials from the git credential store.
10554 Manage GitHub tokens and other git credentials. This package is to be used by
10555 other packages that need to authenticate to GitHub and/or other git
10557 (license license:expat)))
10559 (define-public r-gh
10566 (uri (cran-uri "gh" version))
10569 "1zvy3ylxvni10lhvmbm9h14mg4wlsbdbzbzviwf28jxss8749219"))))
10570 (build-system r-build-system)
10573 ("r-gitcreds" ,r-gitcreds)
10576 ("r-jsonlite" ,r-jsonlite)))
10578 `(("r-knitr" ,r-knitr)))
10579 (home-page "https://github.com/r-lib/gh#readme")
10580 (synopsis "Access the GitHub API via R")
10582 "This package provides a minimal R client to access the GitHub API.")
10583 (license license:expat)))
10585 (define-public r-fs
10592 (uri (cran-uri "fs" version))
10595 "15rqc3ljmcmgfvadj1j1kq7kvibagxic8sgplhlcdqqxax9idprn"))))
10596 (build-system r-build-system)
10598 `(("r-knitr" ,r-knitr)))
10599 (home-page "https://fs.r-lib.org")
10600 (synopsis "Cross-platform file system operations based on libuv")
10602 "This package provides a cross-platform interface to file system
10603 operations, built on top of the libuv C library.")
10604 (license license:gpl3)))
10606 (define-public r-clisymbols
10608 (name "r-clisymbols")
10613 (uri (cran-uri "clisymbols" version))
10616 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
10617 (build-system r-build-system)
10618 (home-page "https://github.com/gaborcsardi/clisymbols")
10619 (synopsis "Unicode symbols at the R prompt")
10621 "This package provides a small subset of Unicode symbols, that are useful
10622 when building command line applications. They fall back to alternatives on
10623 terminals that do not support Unicode.")
10624 (license license:expat)))
10626 (define-public r-credentials
10628 (name "r-credentials")
10633 (uri (cran-uri "credentials" version))
10636 "1w9zj34xdwz9bszsvhv2cbgq96y5sgxbh7ndn31pgfcpzlkfq6f1"))))
10637 (properties `((upstream-name . "credentials")))
10638 (build-system r-build-system)
10641 (modify-phases %standard-phases
10642 (add-after 'unpack 'setenv-HOME
10644 ;; This is necessary because git looks for $HOME/.gitconfig
10645 (setenv "HOME" "/tmp")
10648 `(("git" ,git-minimal)))
10650 `(("r-askpass" ,r-askpass)
10652 ("r-jsonlite" ,r-jsonlite)
10653 ("r-openssl" ,r-openssl)
10656 `(("r-knitr" ,r-knitr)))
10657 (home-page "https://docs.ropensci.org/credentials/")
10658 (synopsis "Tools for managing SSH and Git credentials")
10660 "This package assists you in setting up and retrieving of HTTPS and SSH
10661 credentials for use with git and other services. For HTTPS remotes the
10662 package interfaces the @command{git-credential} utility which @command{git}
10663 uses to store HTTP usernames and passwords. For SSH remotes this package
10664 provides convenient functions to find or generate appropriate SSH keys. The
10665 package both helps the user to setup a local git installation, and also
10666 provides a back-end for git/ssh client libraries to authenticate with existing
10667 user credentials.")
10668 (license license:expat)))
10670 (define-public r-gert
10677 (uri (cran-uri "gert" version))
10680 "09har6mj7qy813s6dxyzfzmjwg60m8c01yx3q6lfsnvwqzxlqxv8"))))
10681 (properties `((upstream-name . "gert")))
10682 (build-system r-build-system)
10684 `(("libgit2" ,libgit2)
10687 `(("r-askpass" ,r-askpass)
10688 ("r-credentials" ,r-credentials)
10689 ("r-openssl" ,r-openssl)
10690 ("r-rstudioapi" ,r-rstudioapi)
10694 `(("pkg-config" ,pkg-config)
10695 ("r-knitr" ,r-knitr)))
10696 (home-page "https://docs.ropensci.org/gert/")
10697 (synopsis "Simple Git client for R")
10699 "This package provides a simple git client for R based on libgit2 with
10700 support for SSH and HTTPS remotes. All functions in gert use basic R data
10701 types (such as vectors and data-frames) for their arguments and return values.
10702 User credentials are shared with command line git through the
10703 @code{git-credential} store and SSH keys stored on disk or ssh-agent.")
10704 (license license:expat)))
10706 (define-public r-usethis
10713 (uri (cran-uri "usethis" version))
10716 "1j6nzzrm2m6vi1gq0d5kxnnr9d8cy88wpmgigz3inych65x9w9pg"))))
10717 (build-system r-build-system)
10720 ("r-clipr" ,r-clipr)
10721 ("r-crayon" ,r-crayon)
10728 ("r-jsonlite" ,r-jsonlite)
10729 ("r-lifecycle" ,r-lifecycle)
10730 ("r-purrr" ,r-purrr)
10731 ("r-rappdirs" ,r-rappdirs)
10732 ("r-rlang" ,r-rlang)
10733 ("r-rprojroot" ,r-rprojroot)
10734 ("r-rstudioapi" ,r-rstudioapi)
10735 ("r-whisker" ,r-whisker)
10736 ("r-withr" ,r-withr)
10737 ("r-yaml" ,r-yaml)))
10738 (home-page "https://github.com/r-lib/usethis")
10739 (synopsis "Automate R package and project setup")
10741 "This package helps you to automate R package and project setup tasks
10742 that are otherwise performed manually. This includes setting up unit testing,
10743 test coverage, continuous integration, Git, GitHub integration, licenses,
10744 Rcpp, RStudio projects, and more.")
10745 (license license:gpl3)))
10747 (define-public r-sessioninfo
10749 (name "r-sessioninfo")
10754 (uri (cran-uri "sessioninfo" version))
10757 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
10758 (build-system r-build-system)
10761 ("r-withr" ,r-withr)))
10762 (home-page "https://github.com/r-lib/sessioninfo#readme")
10763 (synopsis "R session information")
10765 "This package provides tools to query and print information about the
10766 current R session. It is similar to @code{utils::sessionInfo()}, but includes
10767 more information about packages, and where they were installed from.")
10768 (license license:gpl2)))
10770 (define-public r-remotes
10777 (uri (cran-uri "remotes" version))
10780 "1f1kdw9j1wald3fs8b3n68x1kljy07j60g3aw1aarx26ikyk9whj"))))
10781 (build-system r-build-system)
10783 `(("r-knitr" ,r-knitr)))
10784 (home-page "https://github.com/r-lib/remotes#readme")
10785 (synopsis "R package installation from remote repositories")
10787 "Download and install R packages stored in GitHub, BitBucket, or plain
10788 subversion or git repositories. This package is a lightweight replacement of
10789 the @code{install_*} functions in the @code{devtools} package. Indeed most of
10790 the code was copied over from @code{devtools}.")
10791 (license license:gpl2+)))
10793 (define-public r-xopen
10800 (uri (cran-uri "xopen" version))
10803 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
10804 (build-system r-build-system)
10806 `(("r-processx" ,r-processx)))
10807 (home-page "https://github.com/r-lib/xopen#readme")
10808 (synopsis "Open system files, URLs, anything")
10810 "This package provides a cross-platform solution to open files,
10811 directories or URLs with their associated programs.")
10812 (license license:expat)))
10814 (define-public r-rcmdcheck
10816 (name "r-rcmdcheck")
10821 (uri (cran-uri "rcmdcheck" version))
10824 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
10825 (build-system r-build-system)
10827 `(("r-callr" ,r-callr)
10829 ("r-crayon" ,r-crayon)
10831 ("r-digest" ,r-digest)
10832 ("r-pkgbuild" ,r-pkgbuild)
10833 ("r-prettyunits" ,r-prettyunits)
10835 ("r-rprojroot" ,r-rprojroot)
10836 ("r-sessioninfo" ,r-sessioninfo)
10837 ("r-withr" ,r-withr)
10838 ("r-xopen" ,r-xopen)))
10839 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
10840 (synopsis "Run R CMD check from R and capture results")
10842 "Run @code{R CMD check} from R programmatically, and capture the results
10843 of the individual checks.")
10844 (license license:expat)))
10846 (define-public r-rapportools
10848 (name "r-rapportools")
10853 (uri (cran-uri "rapportools" version))
10856 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
10857 (build-system r-build-system)
10859 `(("r-pander" ,r-pander)
10861 ("r-reshape" ,r-reshape)))
10862 (home-page "https://cran.r-project.org/web/packages/rapportools/")
10863 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
10865 "This package provides helper functions that act as wrappers to more
10866 advanced statistical methods with the advantage of having sane defaults for
10868 (license license:agpl3+)))
10870 (define-public r-pander
10877 (uri (cran-uri "pander" version))
10880 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
10881 (build-system r-build-system)
10883 `(("r-digest" ,r-digest)
10884 ("r-rcpp" ,r-rcpp)))
10885 (home-page "https://rapporter.github.io/pander")
10886 (synopsis "Render R objects into Pandoc's markdown")
10888 "The main aim of the pander R package is to provide a minimal and easy
10889 tool for rendering R objects into Pandoc's markdown. The package is also
10890 capable of exporting/converting complex Pandoc documents (reports) in various
10892 ;; This package is licensed under either the AGPLv3+ or the very rarely
10894 (license license:agpl3+)))
10896 (define-public r-summarytools
10898 (name "r-summarytools")
10903 (uri (cran-uri "summarytools" version))
10906 "0n7rad6bkfn9cb99wbfzbwl5qzch48r0gafhddfcqvyh4fbn2k0j"))))
10907 (build-system r-build-system)
10909 `(("r-base64enc" ,r-base64enc)
10910 ("r-checkmate" ,r-checkmate)
10911 ("r-dplyr" ,r-dplyr)
10912 ("r-htmltools" ,r-htmltools)
10913 ("r-lubridate" ,r-lubridate)
10914 ("r-magick" ,r-magick)
10915 ("r-matrixstats" ,r-matrixstats)
10916 ("r-pander" ,r-pander)
10918 ("r-rapportools" ,r-rapportools)
10919 ("r-tibble" ,r-tibble)
10920 ("r-tidyr" ,r-tidyr)))
10922 `(("r-knitr" ,r-knitr)))
10923 (home-page "https://github.com/dcomtois/summarytools")
10924 (synopsis "Tools to quickly and neatly summarize data")
10926 "This package provides tools for data frame summaries, cross-tabulations,
10927 weight-enabled frequency tables and common univariate statistics in concise
10928 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
10929 good point-of-entry for exploring data, both for experienced and new R
10931 (license license:gpl2)))
10933 (define-public r-lsei
10940 (uri (cran-uri "lsei" version))
10943 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2"))))
10944 (build-system r-build-system)
10946 `(("gfortran" ,gfortran)))
10947 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
10948 (synopsis "Solve regression problems under equality/inequality constraints")
10950 "It contains functions that solve least squares linear regression
10951 problems under linear equality/inequality constraints. Functions for solving
10952 quadratic programming problems are also available, which transform such
10953 problems into least squares ones first.")
10954 (license license:gpl2+)))
10956 (define-public r-npsurv
10963 (uri (cran-uri "npsurv" version))
10966 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw"))))
10967 (build-system r-build-system)
10969 `(("r-lsei" ,r-lsei)))
10970 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
10971 (synopsis "Nonparametric survival analysis")
10973 "This package contains functions for non-parametric survival analysis of
10974 exact and interval-censored observations.")
10975 (license license:gpl2+)))
10977 (define-public r-clusteval
10979 (name "r-clusteval")
10984 (uri (cran-uri "clusteval" version))
10987 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
10988 (build-system r-build-system)
10990 `(("r-mvtnorm" ,r-mvtnorm)
10991 ("r-rcpp" ,r-rcpp)))
10992 (home-page "https://cran.r-project.org/web/packages/clusteval/")
10993 (synopsis "Evaluation of clustering algorithms")
10995 "This R package provides a suite of tools to evaluate clustering
10996 algorithms, clusterings, and individual clusters.")
10997 (license license:expat)))
10999 (define-public r-tweedie
11006 (uri (cran-uri "tweedie" version))
11009 "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0"))))
11010 (build-system r-build-system)
11011 (native-inputs `(("gfortran" ,gfortran)))
11012 (home-page "https://cran.r-project.org/web/packages/tweedie/")
11013 (synopsis "Evaluation of Tweedie exponential family models")
11015 "Maximum likelihood computations for Tweedie families, including the
11016 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
11017 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
11018 and related methods.")
11019 (license license:gpl2+)))
11021 (define-public r-rcppgsl
11028 (uri (cran-uri "RcppGSL" version))
11030 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
11031 (properties `((upstream-name . "RcppGSL")))
11032 (build-system r-build-system)
11034 `(("r-rcpp" ,r-rcpp)
11036 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
11037 (synopsis "Rcpp integration for GSL vectors and matrices")
11039 "The GNU Scientific Library (or GSL) is a collection of numerical
11040 routines for scientific computing. It is particularly useful for C and C++
11041 programs as it provides a standard C interface to a wide range of mathematical
11042 routines. There are over 1000 functions in total with an extensive test
11043 suite. The RcppGSL package provides an easy-to-use interface between GSL data
11044 structures and R using concepts from Rcpp which is itself a package that eases
11045 the interfaces between R and C++.")
11046 (license license:gpl2+)))
11048 (define-public r-mvabund
11055 (uri (cran-uri "mvabund" version))
11058 "0aisvax9d7bk6aykrcdcn1ji618r520mcrkr1i3jnck1qs31z41f"))))
11059 (build-system r-build-system)
11061 `(("r-mass" ,r-mass)
11063 ("r-rcppgsl" ,r-rcppgsl)
11064 ("r-statmod" ,r-statmod)
11065 ("r-tweedie" ,r-tweedie)))
11066 (home-page "https://cran.r-project.org/web/packages/mvabund/")
11067 (synopsis "Statistical methods for analysing multivariate abundance data")
11069 "This package provides a set of tools for displaying, modeling and
11070 analysing multivariate abundance data in community ecology.")
11071 (license license:lgpl2.1+)))
11073 (define-public r-afex
11080 (uri (cran-uri "afex" version))
11083 "0blwqr5ni3psav1dcdmhfi4jy3b4scm5njimqfpr1d81zadvgc6g"))))
11084 (build-system r-build-system)
11088 ("r-lmertest" ,r-lmertest)
11089 ("r-pbkrtest" ,r-pbkrtest)
11090 ("r-reshape2" ,r-reshape2)))
11092 `(("r-knitr" ,r-knitr)))
11093 (home-page "https://afex.singmann.science/")
11094 (synopsis "Analysis of factorial experiments")
11096 "This package provides convenience functions for analyzing factorial
11097 experiments using ANOVA or mixed models.")
11098 (license license:gpl2+)))
11100 (define-public r-lmertest
11102 (name "r-lmertest")
11107 (uri (cran-uri "lmerTest" version))
11110 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim"))))
11111 (properties `((upstream-name . "lmerTest")))
11112 (build-system r-build-system)
11114 `(("r-ggplot2" ,r-ggplot2)
11117 ("r-numderiv" ,r-numderiv)))
11118 (home-page "https://github.com/runehaubo/lmerTestR")
11119 (synopsis "Tests in linear mixed effects models")
11121 "This package provides p-values in type I, II or III anova and summary
11122 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
11123 method. A Kenward-Roger method is also available via the @code{pbkrtest}
11124 package. Model selection methods include step, drop1 and anova-like tables
11125 for random effects (ranova). Methods for Least-Square means (LS-means) and
11126 tests of linear contrasts of fixed effects are also available.")
11127 (license license:gpl2+)))
11129 (define-public r-r2glmm
11136 (uri (cran-uri "r2glmm" version))
11139 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
11140 (build-system r-build-system)
11142 `(("r-afex" ,r-afex)
11143 ("r-data-table" ,r-data-table)
11144 ("r-dplyr" ,r-dplyr)
11145 ("r-ggplot2" ,r-ggplot2)
11146 ("r-gridextra" ,r-gridextra)
11147 ("r-lmertest" ,r-lmertest)
11149 ("r-matrix" ,r-matrix)
11151 ("r-pbkrtest" ,r-pbkrtest)))
11152 (home-page "https://github.com/bcjaeger/r2glmm")
11153 (synopsis "Compute R squared for mixed (multilevel) models")
11155 "This package computes model and semi partial R squared with confidence
11156 limits for the linear and generalized linear mixed model (LMM and GLMM). The
11157 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
11158 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
11160 (license license:gpl2)))
11162 (define-public r-weights
11169 (uri (cran-uri "weights" version))
11172 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
11173 (build-system r-build-system)
11175 `(("r-gdata" ,r-gdata)
11176 ("r-hmisc" ,r-hmisc)
11177 ("r-mice" ,r-mice)))
11179 "https://cran.r-project.org/web/packages/weights/")
11180 (synopsis "Weighting and weighted statistics")
11181 (description "This package Provides a variety of functions for producing
11182 simple weighted statistics, such as weighted Pearson's correlations, partial
11183 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
11184 includes some software for quickly recoding survey data and plotting point
11185 estimates from interaction terms in regressions (and multiply imputed
11186 regressions). NOTE: Weighted partial correlation calculations pulled to
11188 (license license:gpl2+)))
11190 (define-public r-rcppannoy
11192 (name "r-rcppannoy")
11197 (uri (cran-uri "RcppAnnoy" version))
11200 "0n68cf77gz34iq6w6ad87pbqwqam45nxp1gjzns4g6qhf7qdvrz4"))))
11201 (properties `((upstream-name . "RcppAnnoy")))
11202 (build-system r-build-system)
11204 `(("r-rcpp" ,r-rcpp)))
11205 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
11206 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
11208 "Annoy is a small C++ library for Approximate Nearest Neighbors written
11209 for efficient memory usage as well an ability to load from and save to disk.
11210 This package provides an R interface.")
11211 ;; Annoy is released under ASL 2.0, but this wrapper is released under
11213 (license (list license:gpl2+ license:asl2.0))))
11215 (define-public r-rcpphnsw
11217 (name "r-rcpphnsw")
11222 (uri (cran-uri "RcppHNSW" version))
11225 "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
11226 (properties `((upstream-name . "RcppHNSW")))
11227 (build-system r-build-system)
11228 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11229 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
11230 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
11232 "Hnswlib is a C++ library for approximate nearest neighbors. This
11233 package provides a minimal R interface by relying on the Rcpp package.")
11234 ;; hnswlib is released under Version 2.0 of the Apache License.
11235 (license (list license:gpl3 license:asl2.0))))
11237 (define-public r-rcppparallel
11239 (name "r-rcppparallel")
11244 (uri (cran-uri "RcppParallel" version))
11247 "10bg4fw38m64dhy543rwq2nnjjc9y24iggk343xslrb3ij8018lc"))))
11248 (properties `((upstream-name . "RcppParallel")))
11249 (build-system r-build-system)
11250 (home-page "https://rcppcore.github.io/RcppParallel/")
11251 (synopsis "Parallel programming tools for Rcpp")
11253 "This package provides high level functions for parallel programming with
11254 Rcpp. For example, the @code{parallelFor()} function can be used to convert
11255 the work of a standard serial @code{for} loop into a parallel one and the
11256 @code{parallelReduce()} function can be used for accumulating aggregates or
11258 (license license:gpl2)))
11260 (define-public r-ncdf4
11267 (uri (cran-uri "ncdf4" version))
11270 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
11271 (build-system r-build-system)
11273 `(("netcdf" ,netcdf)
11275 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
11276 (synopsis "R interface to Unidata netCDF format data files")
11278 "This package provides a high-level R interface to data files written
11279 using Unidata's netCDF library (version 4 or earlier), which are binary data
11280 files that are portable across platforms and include metadata information in
11281 addition to the data sets. Using this package, netCDF files can be opened and
11282 data sets read in easily. It is also easy to create new netCDF dimensions,
11283 variables, and files, in either version 3 or 4 format, and manipulate existing
11285 (license license:gpl3+)))
11287 (define-public r-biocmanager
11289 (name "r-biocmanager")
11290 (version "1.30.10")
11294 (uri (cran-uri "BiocManager" version))
11296 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
11297 (properties `((upstream-name . "BiocManager")))
11298 (build-system r-build-system)
11299 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
11300 (synopsis "Access the Bioconductor project package repository")
11302 "This package provides a convenient tool to install and update
11303 Bioconductor packages.")
11304 (license license:artistic2.0)))
11306 (define-public r-rgl
11309 (version "0.104.16")
11313 (uri (cran-uri "rgl" version))
11316 "169a8riiam8445nl7rcwn0x92dlwyzh5xldvap6dcxjyjqmjwbdq"))))
11317 (build-system r-build-system)
11319 `(("pkg-config" ,pkg-config)
11320 ("r-knitr" ,r-knitr)))
11322 `(("freetype" ,freetype)
11329 `(("r-crosstalk" ,r-crosstalk)
11330 ("r-htmltools" ,r-htmltools)
11331 ("r-htmlwidgets" ,r-htmlwidgets)
11332 ("r-jsonlite" ,r-jsonlite)
11333 ("r-knitr" ,r-knitr)
11334 ("r-magrittr" ,r-magrittr)
11335 ("r-manipulatewidget" ,r-manipulatewidget)
11336 ("r-shiny" ,r-shiny)))
11337 (home-page "https://r-forge.r-project.org/projects/rgl/")
11338 (synopsis "3D visualization using OpenGL")
11340 "This package provides medium to high level functions for 3D interactive graphics,
11341 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
11342 as functions for constructing representations of geometric
11343 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
11344 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
11345 image formats, including PNG, Postscript, SVG, PGF.")
11346 ;; Any version of the GPL.
11347 (license (list license:gpl2+ license:gpl3+))))
11349 (define-public r-multicool
11351 (name "r-multicool")
11356 (uri (cran-uri "multicool" version))
11359 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
11360 (build-system r-build-system)
11361 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11362 (home-page "https://cran.r-project.org/web/packages/multicool/")
11363 (synopsis "Permutations of multisets in cool-lex order")
11365 "This package provides a set of tools to permute multisets without loops
11366 or hash tables and to generate integer partitions. Cool-lex order is similar
11367 to colexicographical order.")
11368 (license license:gpl2)))
11370 (define-public r-misc3d
11377 (uri (cran-uri "misc3d" version))
11380 "10jf5r1x588vi54bzaqgi9mgcqlkiga2c3jvmqmk3lavc8fjksd1"))))
11381 (build-system r-build-system)
11382 (home-page "https://cran.r-project.org/web/packages/misc3d/")
11383 (synopsis "Miscellaneous 3D Plots")
11385 "This package provides a collection of miscellaneous 3d plots, including
11387 ;; Any version of the GPL.
11388 (license (list license:gpl2+ license:gpl3+))))
11390 (define-public r-ks
11397 (uri (cran-uri "ks" version))
11399 (base32 "1sff6rlpq64lqyvwgral9zbcan30wpgmfb26hw9y6wzypd9gxbz6"))))
11400 (build-system r-build-system)
11403 ("r-kernlab" ,r-kernlab)
11404 ("r-kernsmooth" ,r-kernsmooth)
11405 ("r-matrix" ,r-matrix)
11406 ("r-mclust" ,r-mclust)
11408 ("r-multicool" ,r-multicool)
11409 ("r-mvtnorm" ,r-mvtnorm)
11410 ("r-plot3d" ,r-plot3d)))
11411 (home-page "https://www.mvstat.net/tduong/")
11412 (synopsis "Kernel smoothing")
11414 "This package provides kernel smoothers for univariate and multivariate
11415 data, including density functions, density derivatives, cumulative
11416 distributions, modal clustering, discriminant analysis, and two-sample
11417 hypothesis testing.")
11418 ;; Either version of the GPL.
11419 (license (list license:gpl2 license:gpl3))))
11421 (define-public r-feature
11428 (uri (cran-uri "feature" version))
11431 "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y"))))
11432 (build-system r-build-system)
11435 ("r-plot3d" ,r-plot3d)))
11437 `(("r-knitr" ,r-knitr)))
11438 (home-page "https://www.mvstat.net/tduong/")
11439 (synopsis "Inferential feature significance for kernel density estimation")
11441 "The feature package contains functions to display and compute kernel
11442 density estimates, significant gradient and significant curvature regions.
11443 Significant gradient and/or curvature regions often correspond to significant
11444 features (e.g. local modes).")
11445 ;; Either version of the GPL.
11446 (license (list license:gpl2 license:gpl3))))
11448 (define-public r-arm
11455 (uri (cran-uri "arm" version))
11458 "1grb27vayr2vhyalzfqbhx6p278r7c3l4pzi5nrz3dmnyqrbx1c3"))))
11459 (build-system r-build-system)
11461 `(("r-abind" ,r-abind)
11463 ("r-hmisc" ,r-hmisc)
11466 ("r-matrix" ,r-matrix)
11467 ("r-nlme" ,r-nlme)))
11468 (home-page "https://cran.r-project.org/web/packages/arm/")
11469 (synopsis "Data analysis using regression and multilevel/hierarchical models")
11471 "This package provides functions to accompany A. Gelman and J. Hill,
11472 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
11473 University Press, 2007.")
11474 (license license:gpl3+)))
11476 (define-public r-circular
11478 (name "r-circular")
11483 (uri (cran-uri "circular" version))
11486 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
11487 (build-system r-build-system)
11489 `(("r-boot" ,r-boot)
11490 ("r-mvtnorm" ,r-mvtnorm)))
11492 `(("gfortran" ,gfortran)))
11493 (home-page "https://cran.r-project.org/web/packages/circular/")
11494 (synopsis "Circular statistics")
11496 "This package provides tools for circular statistics, from \"Topics in
11497 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
11499 (license license:gpl2+)))
11501 (define-public r-activity
11503 (name "r-activity")
11508 (uri (cran-uri "activity" version))
11511 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
11512 (build-system r-build-system)
11514 `(("r-circular" ,r-circular)
11515 ("r-insol" ,r-insol)
11516 ("r-pbapply" ,r-pbapply)))
11517 (home-page "https://cran.r-project.org/web/packages/activity/")
11518 (synopsis "Animal activity statistics")
11520 "This package provides functions to fit kernel density functions to
11521 animal activity time data; plot activity distributions; quantify overall
11522 levels of activity; statistically compare activity metrics through
11523 bootstrapping; and evaluate variation in linear variables with time (or other
11524 circular variables).")
11525 (license license:gpl3)))
11527 (define-public r-ouch
11534 (uri (cran-uri "ouch" version))
11537 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
11538 (build-system r-build-system)
11539 (propagated-inputs `(("r-subplex" ,r-subplex)))
11540 (home-page "https://kingaa.github.io/ouch/")
11541 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
11543 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
11544 for evolution along a phylogenetic tree.")
11545 (license license:gpl2+)))
11547 (define-public r-fmsb
11554 (uri (cran-uri "fmsb" version))
11557 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
11558 (build-system r-build-system)
11559 (home-page "http://minato.sip21c.org/msb/")
11560 (synopsis "Functions for medical statistics book with demographic data")
11562 "This package provides several utility functions for the book entitled
11563 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
11564 Japan, 2007) with Japanese demographic data and some demographic analysis
11565 related functions.")
11566 (license license:gpl2+)))
11568 (define-public r-stabledist
11570 (name "r-stabledist")
11575 (uri (cran-uri "stabledist" version))
11578 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
11579 (build-system r-build-system)
11580 (home-page "https://www.rmetrics.org")
11581 (synopsis "Stable distribution functions")
11583 "This package provides density, probability and quantile functions, and
11584 random number generation for (skew) stable distributions, using the
11585 parametrizations of Nolan.")
11586 (license license:gpl2+)))
11588 (define-public r-gsl
11595 (uri (cran-uri "gsl" version))
11598 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
11599 (build-system r-build-system)
11602 (home-page "https://cran.r-project.org/web/packages/gsl")
11603 (synopsis "Wrapper for the GNU Scientific Library")
11605 "This package provides an R wrapper for the special functions and quasi
11606 random number generators of the GNU Scientific Library.")
11607 (license license:gpl2+)))
11609 (define-public r-adgoftest
11611 (name "r-adgoftest")
11616 (uri (cran-uri "ADGofTest" version))
11619 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
11620 (properties `((upstream-name . "ADGofTest")))
11621 (build-system r-build-system)
11622 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
11623 (synopsis "Anderson-Darling GoF test")
11625 "This package provides an implementation of the Anderson-Darling GoF test
11626 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
11627 Anderson-Darling Distribution\".")
11628 ;; Any version of the GPL.
11629 (license license:gpl3+)))
11631 (define-public r-sodium
11638 (uri (cran-uri "sodium" version))
11641 "1zxzi8xvxnhgcd5qrylf08nz1cdq3aslrswjas440qg63ypmbf6w"))))
11642 (properties `((upstream-name . "sodium")))
11643 (build-system r-build-system)
11645 `(("libsodium" ,libsodium)))
11647 `(("pkg-config" ,pkg-config)
11648 ("r-knitr" ,r-knitr)))
11649 (home-page "https://github.com/jeroen/sodium")
11650 (synopsis "R bindings to the libsodium crypto library")
11652 "This package provides bindings to libsodium: a library for encryption,
11653 decryption, signatures, password hashing and more. Sodium uses curve25519, a
11654 Diffie-Hellman function by Daniel Bernstein, which has become very popular
11655 after it was discovered that the NSA had backdoored Dual EC DRBG.")
11656 (license license:expat)))
11658 (define-public r-softimpute
11660 (name "r-softimpute")
11665 (uri (cran-uri "softImpute" version))
11668 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
11669 (properties `((upstream-name . "softImpute")))
11670 (build-system r-build-system)
11672 `(("r-matrix" ,r-matrix)))
11674 `(("gfortran" ,gfortran)))
11675 (home-page "https://cran.r-project.org/web/packages/softImpute")
11676 (synopsis "Matrix completion via iterative soft-thresholded SVD")
11678 "This package provides iterative methods for matrix completion that use
11679 nuclear-norm regularization. The package includes procedures for centering
11680 and scaling rows, columns or both, and for computing low-rank @dfn{single
11681 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
11683 (license license:gpl2)))
11685 (define-public r-fftwtools
11687 (name "r-fftwtools")
11692 (uri (cran-uri "fftwtools" version))
11695 "0h8lyl2i6zq16ir7xnfj9dhyivxvwikm8lml19s8s8jx95z3n9x9"))))
11696 (build-system r-build-system)
11697 (inputs `(("fftw" ,fftw)))
11698 (home-page "https://github.com/krahim/fftwtools")
11699 (synopsis "Wrapper for FFTW3")
11701 "This package provides a wrapper for several FFTW functions. It provides
11702 access to the two-dimensional FFT, the multivariate FFT, and the
11703 one-dimensional real to complex FFT using the FFTW3 library. The package
11704 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
11705 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
11706 The FFT functions have a parameter that allows them to not return the
11707 redundant complex conjugate when the input is real data.")
11708 (license license:gpl2+)))
11710 (define-public r-tiff
11717 (uri (cran-uri "tiff" version))
11720 "1yy4im2lwzhjnnkfwxgkknsajvm83pcwaf370pkgfva2db0xjfv2"))))
11721 (build-system r-build-system)
11723 `(("libtiff" ,libtiff)
11724 ("libjpeg" ,libjpeg-turbo)
11726 (home-page "https://www.rforge.net/tiff/")
11727 (synopsis "Read and write TIFF images")
11729 "This package provides an easy and simple way to read, write and display
11730 bitmap images stored in the TIFF format. It can read and write both files and
11731 in-memory raw vectors.")
11732 ;; Either of these two license versions.
11733 (license (list license:gpl2 license:gpl3))))
11735 (define-public r-nlp
11742 (uri (cran-uri "NLP" version))
11745 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5"))))
11746 (properties `((upstream-name . "NLP")))
11747 (build-system r-build-system)
11748 (home-page "https://cran.r-project.org/web/packages/NLP/")
11749 (synopsis "Natural language processing infrastructure")
11751 "This package provides basic classes and methods for Natural Language
11753 (license license:gpl3)))
11755 (define-public r-tm
11762 (uri (cran-uri "tm" version))
11765 "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi"))))
11766 (properties `((upstream-name . "tm")))
11767 (build-system r-build-system)
11773 ("r-xml2" ,r-xml2)))
11774 (home-page "http://tm.r-forge.r-project.org/")
11775 (synopsis "Text mining package")
11777 "This package provides a framework for text mining applications within R.")
11778 (license license:gpl3)))
11780 (define-public r-waveslim
11782 (name "r-waveslim")
11787 (uri (cran-uri "waveslim" version))
11790 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
11791 (build-system r-build-system)
11793 `(("gfortran" ,gfortran)))
11794 (home-page "http://waveslim.blogspot.com")
11795 (synopsis "Basic wavelet routines for signal processing")
11797 "This package provides basic wavelet routines for time series (1D),
11798 image (2D) and array (3D) analysis. The code provided here is based on
11799 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
11800 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
11801 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
11802 pairs (Selesnick 2001, 2002).")
11803 (license license:bsd-3)))
11805 (define-public r-wordcloud
11807 (name "r-wordcloud")
11812 (uri (cran-uri "wordcloud" version))
11815 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
11816 (build-system r-build-system)
11818 `(("r-rcolorbrewer" ,r-rcolorbrewer)
11820 ;; The "tm" package is only "suggested" according to CRAN, but the
11821 ;; wordcloud package cannot be loaded without it.
11823 (home-page "https://cran.r-project.org/web/packages/wordcloud")
11824 (synopsis "Word clouds")
11826 "This package provides functionality to create pretty word clouds,
11827 visualize differences and similarity between documents, and avoid
11828 over-plotting in scatter plots with text.")
11829 (license license:lgpl2.1)))
11831 (define-public r-colorramps
11833 (name "r-colorramps")
11838 (uri (cran-uri "colorRamps" version))
11841 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
11842 (properties `((upstream-name . "colorRamps")))
11843 (build-system r-build-system)
11844 (home-page "https://cran.r-project.org/web/packages/colorRamps")
11845 (synopsis "Build color tables")
11846 (description "This package provides features to build gradient color
11848 ;; Any version of the GPL
11849 (license license:gpl3+)))
11851 (define-public r-tidytree
11853 (name "r-tidytree")
11858 (uri (cran-uri "tidytree" version))
11860 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
11861 (build-system r-build-system)
11864 ("r-dplyr" ,r-dplyr)
11865 ("r-lazyeval" ,r-lazyeval)
11866 ("r-magrittr" ,r-magrittr)
11867 ("r-rlang" ,r-rlang)
11868 ("r-tibble" ,r-tibble)))
11870 `(("r-knitr" ,r-knitr)))
11871 (home-page "https://github.com/GuangchuangYu/tidytree")
11872 (synopsis "Tidy tool for phylogenetic tree data manipulation")
11874 "Phylogenetic trees generally contain multiple components including nodes,
11875 edges, branches and associated data. This package provides an approach to
11876 convert tree objects to tidy data frames. It also provides tidy interfaces to
11877 manipulate tree data.")
11878 (license license:artistic2.0)))
11880 (define-public r-rvcheck
11887 (uri (cran-uri "rvcheck" version))
11889 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
11890 (build-system r-build-system)
11892 `(("r-biocmanager" ,r-biocmanager)
11893 ("r-rlang" ,r-rlang)))
11894 (home-page "https://cran.r-project.org/web/packages/rvcheck")
11895 (synopsis "R package version check")
11897 "This package provides tools to check the latest release version of R and
11898 R packages (on CRAN, Bioconductor or Github).")
11899 (license license:artistic2.0)))
11901 (define-public r-docopt
11908 (uri (cran-uri "docopt" version))
11911 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
11912 (build-system r-build-system)
11913 (home-page "https://github.com/docopt/docopt.R")
11914 (synopsis "Command-line interface specification language")
11916 "This package enables you to define a command-line interface by just
11917 giving it a description in the specific format.")
11918 (license license:expat)))
11920 (define-public r-sparsesvd
11922 (name "r-sparsesvd")
11927 (uri (cran-uri "sparsesvd" version))
11930 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
11931 (build-system r-build-system)
11932 (propagated-inputs `(("r-matrix" ,r-matrix)))
11933 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
11934 (synopsis "Sparse truncated singular value decomposition")
11936 "This package provides a Wrapper around the SVDLIBC library
11937 for (truncated) singular value decomposition of a sparse matrix. Currently,
11938 only sparse real matrices in Matrix package format are supported.")
11939 ;; SVDLIBC is released under BSD-2. The R interface is released under
11941 (license (list license:bsd-3 license:bsd-2))))
11943 (define-public r-speedglm
11945 (name "r-speedglm")
11950 (uri (cran-uri "speedglm" version))
11953 "0f37w4lj8dpcg1sfkd7cv6qpdkanmb97mnd8zih2fxzv8bpd0rfh"))))
11954 (build-system r-build-system)
11956 `(("r-mass" ,r-mass)
11957 ("r-matrix" ,r-matrix)))
11958 (home-page "https://cran.r-project.org/web/packages/speedglm")
11959 (synopsis "Fit linear and generalized linear models to large data sets")
11961 "This package provides tools for fitting linear models and generalized
11962 linear models to large data sets by updating algorithms.")
11963 ;; Any version of the GPL
11964 (license license:gpl2+)))
11966 (define-public r-densityclust
11968 (name "r-densityclust")
11973 (uri (cran-uri "densityClust" version))
11976 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
11977 (properties `((upstream-name . "densityClust")))
11978 (build-system r-build-system)
11981 ("r-ggplot2" ,r-ggplot2)
11982 ("r-ggrepel" ,r-ggrepel)
11983 ("r-gridextra" ,r-gridextra)
11984 ("r-rcolorbrewer" ,r-rcolorbrewer)
11986 ("r-rtsne" ,r-rtsne)))
11987 (home-page "https://cran.r-project.org/web/packages/densityClust")
11988 (synopsis "Clustering by fast search and find of density peaks")
11990 "This package provides an improved implementation (based on k-nearest
11991 neighbors) of the density peak clustering algorithm, originally described by
11992 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
11993 large datasets (> 100,000 samples) very efficiently.")
11994 (license license:gpl2+)))
11996 (define-public r-combinat
11998 (name "r-combinat")
12003 (uri (cran-uri "combinat" version))
12006 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
12007 (build-system r-build-system)
12008 (home-page "https://cran.r-project.org/web/packages/combinat")
12009 (synopsis "Combinatorics utilities")
12010 (description "This package provides assorted routines for combinatorics.")
12011 (license license:gpl2)))
12013 (define-public r-qlcmatrix
12015 (name "r-qlcmatrix")
12020 (uri (cran-uri "qlcMatrix" version))
12023 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
12024 (properties `((upstream-name . "qlcMatrix")))
12025 (build-system r-build-system)
12027 `(("r-docopt" ,r-docopt)
12028 ("r-matrix" ,r-matrix)
12030 ("r-sparsesvd" ,r-sparsesvd)))
12031 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
12032 (synopsis "Sparse matrix functions for quantitative language comparison")
12034 "This package provides an extension of the functionality of the Matrix
12035 package for using sparse matrices. Some of the functions are very general,
12036 while other are highly specific for the special data format used for
12037 @dfn{quantitative language comparison} (QLC).")
12038 (license license:gpl3)))
12040 (define-public r-ddrtree
12047 (uri (cran-uri "DDRTree" version))
12050 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
12051 (properties `((upstream-name . "DDRTree")))
12052 (build-system r-build-system)
12055 ("r-irlba" ,r-irlba)
12057 ("r-rcppeigen" ,r-rcppeigen)))
12058 (home-page "https://cran.r-project.org/web/packages/DDRTree")
12059 (synopsis "Learning principal graphs with DDRTree")
12061 "This package provides an implementation of the framework of
12062 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
12063 dimensional space while constructs a principal tree which passes through the
12064 middle of the data simultaneously. DDRTree shows superiority to
12065 alternatives (Wishbone, DPT) for inferring the ordering as well as the
12066 intrinsic structure of single cell genomics data. In general, it could be
12067 used to reconstruct the temporal progression as well as the bifurcation
12068 structure of any data type.")
12069 (license license:asl2.0)))
12071 (define-public r-corpcor
12078 (uri (cran-uri "corpcor" version))
12081 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
12082 (build-system r-build-system)
12083 (home-page "http://strimmerlab.org/software/corpcor/")
12084 (synopsis "Efficient estimation of covariance and (partial) correlation")
12086 "This package implements a James-Stein-type shrinkage estimator for the
12087 covariance matrix, with separate shrinkage for variances and correlations.
12088 Furthermore, functions are available for fast singular value decomposition,
12089 for computing the pseudoinverse, and for checking the rank and positive
12090 definiteness of a matrix.")
12091 (license license:gpl3+)))
12093 (define-public r-rspectra
12095 (name "r-rspectra")
12100 (uri (cran-uri "RSpectra" version))
12103 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
12104 (properties `((upstream-name . "RSpectra")))
12105 (build-system r-build-system)
12107 `(("r-matrix" ,r-matrix)
12109 ("r-rcppeigen" ,r-rcppeigen)))
12110 (home-page "https://github.com/yixuan/RSpectra")
12111 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
12113 "This package provides an R interface to the Spectra library for
12114 large-scale eigenvalue and SVD problems. It is typically used to compute a
12115 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
12116 which is usually more efficient than @code{eigen()} if k << n.")
12118 (license license:mpl2.0)))
12120 (define-public r-vbsr
12127 (uri (cran-uri "vbsr" version))
12130 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
12131 (build-system r-build-system)
12132 (home-page "https://cran.r-project.org/web/packages/vbsr")
12133 (synopsis "Variational Bayes spike regression regularized linear models")
12135 "This package provides an efficient algorithm for solving ultra-sparse
12136 regularized regression models using a variational Bayes algorithm with a spike
12137 prior. The algorithm is solved on a path, with coordinate updates, and is
12138 capable of generating very sparse models. Very general model
12139 diagnostics for controlling type-1 errors are also provided.")
12140 (license license:gpl2)))
12142 (define-public r-flare
12149 (uri (cran-uri "flare" version))
12152 "0f992dmgnr6s8g3386i9bjfyf08q8srgw7sjz2yx7snj8znq7251"))))
12153 (build-system r-build-system)
12155 `(("r-igraph" ,r-igraph)
12156 ("r-lattice" ,r-lattice)
12158 ("r-matrix" ,r-matrix)))
12159 (home-page "https://cran.r-project.org/web/packages/flare")
12160 (synopsis "Family of Lasso regression implementations")
12162 "This package provides implementations of a family of Lasso variants
12163 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
12164 high dimensional sparse linear models.")
12165 (license license:gpl2)))
12167 (define-public r-lassopv
12174 (uri (cran-uri "lassopv" version))
12177 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
12178 (build-system r-build-system)
12179 (propagated-inputs `(("r-lars" ,r-lars)))
12180 (home-page "https://github.com/lingfeiwang/lassopv")
12181 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
12183 "This package enables you to estimate the p-values for predictors x
12184 against target variable y in Lasso regression, using the regularization
12185 strength when each predictor enters the active set of regularization path for
12186 the first time as the statistic.")
12187 (license license:gpl3)))
12189 (define-public r-splitstackshape
12191 (name "r-splitstackshape")
12196 (uri (cran-uri "splitstackshape" version))
12199 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
12200 (build-system r-build-system)
12202 `(("r-data-table" ,r-data-table)))
12203 (home-page "https://github.com/mrdwab/splitstackshape")
12204 (synopsis "Stack and reshape datasets after splitting concatenated values")
12206 "Online data collection tools like Google Forms often export
12207 multiple-response questions with data concatenated in cells. The
12208 @code{concat.split} (cSplit) family of functions provided by this package
12209 splits such data into separate cells. This package also includes functions to
12210 stack groups of columns and to reshape wide data, even when the data are
12211 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
12212 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
12214 (license license:gpl3)))
12216 (define-public r-tfmpvalue
12218 (name "r-tfmpvalue")
12223 (uri (cran-uri "TFMPvalue" version))
12226 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
12227 (properties `((upstream-name . "TFMPvalue")))
12228 (build-system r-build-system)
12229 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12230 (home-page "https://github.com/ge11232002/TFMPvalue")
12231 (synopsis "P-value computation for position weight matrices")
12233 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
12234 identification from sequence/alignments, we are interested in the significance
12235 of certain match scores. TFMPvalue provides the accurate calculation of a
12236 p-value with a score threshold for position weight matrices, or the score with
12237 a given p-value. It is an interface to code originally made available by
12238 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
12239 Touzet and Varre (2007).")
12240 (license license:gpl2)))
12242 (define-public r-rnifti
12249 (uri (cran-uri "RNifti" version))
12252 "1zr0q79id62csmc30c7gs4hbmavk8n6p50a981sfz51dczhjj5ny"))))
12253 (properties `((upstream-name . "RNifti")))
12254 (build-system r-build-system)
12255 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
12256 (home-page "https://github.com/jonclayden/RNifti")
12257 (synopsis "Fast R and C++ access to NIfTI images")
12259 "This package provides very fast read and write access to images stored
12260 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
12261 compiled C and interpreted R code. It also provides a C/C++ API that can be
12262 used by other packages.")
12263 (license license:gpl2)))
12265 (define-public r-shades
12272 (uri (cran-uri "shades" version))
12275 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
12276 (build-system r-build-system)
12277 (home-page "https://github.com/jonclayden/shades")
12278 (synopsis "Simple color manipulation")
12280 "This package provides functions for easily manipulating colors,
12281 creating color scales and calculating color distances.")
12282 (license license:bsd-3)))
12284 (define-public r-ore
12291 (uri (cran-uri "ore" version))
12293 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
12294 (build-system r-build-system)
12295 (home-page "https://github.com/jonclayden/ore")
12296 (synopsis "R interface to the Onigmo regular expression library")
12298 "This package provides an alternative to R's built-in functionality for
12299 handling regular expressions, based on the Onigmo library. It offers
12300 first-class compiled regex objects, partial matching and function-based
12301 substitutions, amongst other features.")
12302 (license license:bsd-3)))
12304 (define-public r-reportr
12311 (uri (cran-uri "reportr" version))
12314 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
12315 (build-system r-build-system)
12316 (propagated-inputs `(("r-ore" ,r-ore)))
12317 (home-page "https://github.com/jonclayden/reportr")
12318 (synopsis "General message and error reporting system")
12320 "This package provides a system for reporting messages, which offers
12321 certain useful features over the standard R system, such as the incorporation
12322 of output consolidation, message filtering, assertions, expression
12323 substitution, automatic generation of stack traces for debugging, and
12324 conditional reporting based on the current \"output level\".")
12325 (license license:gpl2)))
12327 (define-public r-tractor-base
12329 (name "r-tractor-base")
12330 (version "3.3.3.1")
12334 (uri (cran-uri "tractor.base" version))
12337 "0w5jw7pf77npkgig7667yikpbwv4dfk1dcq63qm88l409ga2f95p"))))
12338 (properties `((upstream-name . "tractor.base")))
12339 (build-system r-build-system)
12342 ("r-reportr" ,r-reportr)
12343 ("r-rnifti" ,r-rnifti)
12344 ("r-shades" ,r-shades)))
12345 (home-page "https://www.tractor-mri.org.uk")
12346 (synopsis "Read, manipulate and visualize magnetic resonance images")
12348 "This package provides functions for working with magnetic resonance
12349 images. It supports reading and writing of popular file formats (DICOM,
12350 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
12351 visualization; flexible image manipulation; metadata and sparse image
12353 (license license:gpl2)))
12355 (define-public r-grimport
12357 (name "r-grimport")
12362 (uri (cran-uri "grImport" version))
12365 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
12366 (properties `((upstream-name . "grImport")))
12367 (build-system r-build-system)
12369 `(("ghostscript" ,ghostscript)))
12371 `(("r-xml" ,r-xml)))
12372 (home-page "https://cran.r-project.org/web/packages/grImport")
12373 (synopsis "Convert, import, and draw PostScript pictures")
12375 "This package provides functions for converting, importing, and drawing
12376 PostScript pictures in R plots.")
12377 (license license:gpl2+)))
12379 (define-public r-grimport2
12381 (name "r-grimport2")
12386 (uri (cran-uri "grImport2" version))
12389 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
12390 (properties `((upstream-name . "grImport2")))
12391 (build-system r-build-system)
12393 `(("r-base64enc" ,r-base64enc)
12397 (home-page "https://cran.r-project.org/web/packages/grImport2/")
12398 (synopsis "Import SVG graphics")
12400 "This package provides functions for importing external vector images and
12401 drawing them as part of R plots. This package is different from the
12402 @code{grImport} package because, where that package imports PostScript format
12403 images, this package imports SVG format images. Furthermore, this package
12404 imports a specific subset of SVG, so external images must be preprocessed
12405 using a package like @code{rsvg} to produce SVG that this package can import.
12406 SVG features that are not supported by R graphics, such as gradient fills, can
12407 be imported and then exported via the @code{gridSVG} package.")
12408 (license license:gpl2+)))
12410 (define-public r-kohonen
12417 (uri (cran-uri "kohonen" version))
12420 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
12421 (build-system r-build-system)
12423 `(("r-rcpp" ,r-rcpp)))
12424 (home-page "https://cran.r-project.org/web/packages/kohonen")
12425 (synopsis "Supervised and unsupervised self-organising maps")
12427 "This package provides functions to train @dfn{self-organising
12428 maps} (SOMs). Also interrogation of the maps and prediction using trained
12429 maps are supported. The name of the package refers to Teuvo Kohonen, the
12430 inventor of the SOM.")
12431 (license license:gpl2+)))
12433 (define-public r-nnls
12440 (uri (cran-uri "nnls" version))
12443 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
12444 (build-system r-build-system)
12445 (native-inputs `(("gfortran" ,gfortran)))
12446 (home-page "https://cran.r-project.org/web/packages/nnls")
12447 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
12449 "This package provides an R interface to the Lawson-Hanson implementation
12450 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
12451 the combination of non-negative and non-positive constraints.")
12452 (license license:gpl2+)))
12454 (define-public r-iso
12457 (version "0.0-18.1")
12461 (uri (cran-uri "Iso" version))
12464 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
12465 (properties `((upstream-name . "Iso")))
12466 (build-system r-build-system)
12467 (native-inputs `(("gfortran" ,gfortran)))
12468 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
12469 (synopsis "Functions to perform isotonic regression")
12471 "This package provides support for linear order and unimodal
12472 order (univariate) isotonic regression and bivariate isotonic regression with
12473 linear order on both variables.")
12474 (license license:gpl2+)))
12476 (define-public r-chemometricswithr
12478 (name "r-chemometricswithr")
12483 (uri (cran-uri "ChemometricsWithR" version))
12486 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
12488 `((upstream-name . "ChemometricsWithR")))
12489 (build-system r-build-system)
12491 `(("r-devtools" ,r-devtools)
12492 ("r-kohonen" ,r-kohonen)
12495 (home-page "https://github.com/rwehrens/CWR")
12496 (synopsis "Chemometrics with R")
12498 "This package provides functions and scripts used in the book
12499 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
12500 Life Sciences\" by Ron Wehrens, Springer (2011).")
12501 (license license:gpl2+)))
12503 (define-public r-als
12510 (uri (cran-uri "ALS" version))
12513 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
12514 (properties `((upstream-name . "ALS")))
12515 (build-system r-build-system)
12518 ("r-nnls" ,r-nnls)))
12519 (home-page "https://cran.r-project.org/web/packages/ALS")
12520 (synopsis "Multivariate curve resolution alternating least squares")
12522 "Alternating least squares is often used to resolve components
12523 contributing to data with a bilinear structure; the basic technique may be
12524 extended to alternating constrained least squares. This package provides an
12525 implementation of @dfn{multivariate curve resolution alternating least
12526 squares} (MCR-ALS).
12528 Commonly applied constraints include unimodality, non-negativity, and
12529 normalization of components. Several data matrices may be decomposed
12530 simultaneously by assuming that one of the two matrices in the bilinear
12531 decomposition is shared between datasets.")
12532 (license license:gpl2+)))
12534 (define-public r-strucchange
12536 (name "r-strucchange")
12541 (uri (cran-uri "strucchange" version))
12544 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
12545 (build-system r-build-system)
12547 `(("r-sandwich" ,r-sandwich)
12549 (home-page "https://cran.r-project.org/web/packages/strucchange")
12550 (synopsis "Testing, monitoring, and dating structural changes")
12552 "This package provides tools for testing, monitoring and dating
12553 structural changes in (linear) regression models. It features tests/methods
12554 from the generalized fluctuation test framework as well as from the F
12555 test (Chow test) framework. This includes methods to fit, plot and test
12556 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
12557 statistics, respectively. It is possible to monitor incoming data online
12558 using fluctuation processes. Finally, the breakpoints in regression models
12559 with structural changes can be estimated together with confidence intervals.
12560 Emphasis is always given to methods for visualizing the data.")
12561 ;; Either of these two GPL versions
12562 (license (list license:gpl2 license:gpl3))))
12564 (define-public r-pixmap
12571 (uri (cran-uri "pixmap" version))
12574 "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9"))))
12575 (build-system r-build-system)
12576 (home-page "https://cran.r-project.org/web/packages/pixmap")
12577 (synopsis "Tools for bitmap images")
12579 "This package provides functions for importing, exporting, plotting and
12580 other manipulations of bitmapped images.")
12581 (license license:gpl2)))
12583 (define-public r-rapidjsonr
12585 (name "r-rapidjsonr")
12590 (uri (cran-uri "rapidjsonr" version))
12593 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
12594 (build-system r-build-system)
12595 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
12596 (synopsis "JSON parser")
12598 "This package provides JSON parsing capability through the Rapidjson
12600 (license license:expat)))
12602 (define-public r-ontologyindex
12604 (name "r-ontologyindex")
12609 (uri (cran-uri "ontologyIndex" version))
12612 "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k"))))
12613 (properties `((upstream-name . "ontologyIndex")))
12614 (build-system r-build-system)
12616 `(("r-knitr" ,r-knitr)))
12617 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
12618 (synopsis "Functions for processing ontologies in R")
12620 "This package provides functions for reading ontologies into R as lists
12621 and manipulating sets of ontological terms.")
12622 (license license:gpl2+)))
12624 (define-public r-gargle
12631 (uri (cran-uri "gargle" version))
12634 "1fykmiv3x8c9ai31r9wr7qcca51h6kqn9cgwbxvxfj15fhwskh4n"))))
12635 (build-system r-build-system)
12640 ("r-jsonlite" ,r-jsonlite)
12641 ("r-rlang" ,r-rlang)
12642 ("r-withr" ,r-withr)))
12644 `(("r-knitr" ,r-knitr)))
12645 (home-page "https://gargle.r-lib.org")
12646 (synopsis "Utilities for working with Google APIs")
12648 "This package provides utilities for working with Google APIs. This
12649 includes functions and classes for handling common credential types and for
12650 preparing, executing, and processing HTTP requests.")
12651 (license license:expat)))
12653 (define-public r-bigrquery
12655 (name "r-bigrquery")
12660 (uri (cran-uri "bigrquery" version))
12663 "16whccv7f94vf57dvbbrhdskz3nnbmpa11a14kp7aynckldlfy0v"))))
12664 (build-system r-build-system)
12666 `(("r-assertthat" ,r-assertthat)
12667 ("r-bit64" ,r-bit64)
12670 ("r-gargle" ,r-gargle)
12673 ("r-jsonlite" ,r-jsonlite)
12674 ("r-prettyunits" ,r-prettyunits)
12675 ("r-progress" ,r-progress)
12676 ("r-rapidjsonr" ,r-rapidjsonr)
12678 ("r-rlang" ,r-rlang)
12679 ("r-tibble" ,r-tibble)))
12680 (home-page "https://github.com/rstats-db/bigrquery")
12681 (synopsis "R interface to Google's BigQuery API")
12683 "This package provides an R interface to Google's BigQuery database.")
12684 (license license:gpl3)))
12686 (define-public r-gmp
12693 (uri (cran-uri "gmp" version))
12696 "03kzbflgpy5sgnzxmhshs5qv7jjmfc113ybkhxys4z8y7xdv9z3b"))))
12697 (build-system r-build-system)
12700 (modify-phases %standard-phases
12701 (add-after 'unpack 'set-CC
12702 (lambda _ (setenv "CC" "gcc") #t)))))
12703 (inputs `(("gmp" ,gmp)))
12704 (home-page "https://cran.r-project.org/web/packages/gmp")
12705 (synopsis "Multiple precision arithmetic")
12707 "This package supports multiple precision arithmetic (big integers and
12708 rationals, prime number tests, matrix computation), \"arithmetic without
12709 limitations\" using the GNU Multiple Precision library.")
12710 ;; Any version of the GPL.
12711 (license license:gpl3+)))
12713 (define-public r-rmpfr
12720 (uri (cran-uri "Rmpfr" version))
12723 "007pc7fpzl2mcg3qxa2vfjip6m2dr314qjsnybkj3kdj70bszxkl"))))
12724 (properties `((upstream-name . "Rmpfr")))
12725 (build-system r-build-system)
12730 `(("r-gmp" ,r-gmp)))
12732 `(("pkg-config" ,pkg-config)))
12733 (home-page "http://rmpfr.r-forge.r-project.org/")
12734 (synopsis "R bindings to the MPFR library")
12736 "This package supports arithmetic (via S4 classes and methods) for
12737 arbitrary precision floating point numbers, including transcendental
12738 functions. To this end, the package interfaces with the @dfn{Multiple
12739 Precision Floating-Point Reliable} (MPFR) library.")
12740 (license license:gpl2+)))
12742 (define-public r-assertive-base
12744 (name "r-assertive-base")
12749 (uri (cran-uri "assertive.base" version))
12752 "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b"))))
12754 `((upstream-name . "assertive.base")))
12755 (build-system r-build-system)
12756 (home-page "https://bitbucket.org/richierocks/assertive.base")
12757 (synopsis "Core of the assertive package")
12759 "This package provides a minimal set of predicates and assertions used by
12760 the assertive package. This is mainly for use by other package developers who
12761 want to include run-time testing features in their own packages.")
12762 (license license:gpl3+)))
12764 (define-public r-assertive-properties
12766 (name "r-assertive-properties")
12771 (uri (cran-uri "assertive.properties" version))
12774 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
12776 `((upstream-name . "assertive.properties")))
12777 (build-system r-build-system)
12779 `(("r-assertive-base" ,r-assertive-base)))
12780 (home-page "https://bitbucket.org/richierocks/assertive.properties")
12781 (synopsis "Assertions to check properties of variables")
12783 "This package provides a set of predicates and assertions for checking
12784 the properties of variables, such as length, names and attributes. This is
12785 mainly for use by other package developers who want to include run-time
12786 testing features in their own packages.")
12787 (license license:gpl3+)))
12789 (define-public r-assertive-numbers
12791 (name "r-assertive-numbers")
12796 (uri (cran-uri "assertive.numbers" version))
12799 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
12801 `((upstream-name . "assertive.numbers")))
12802 (build-system r-build-system)
12804 `(("r-assertive-base" ,r-assertive-base)))
12805 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
12806 (synopsis "Assertions to check properties of numbers")
12808 "This package provides a set of predicates and assertions for checking
12809 the properties of numbers. This is mainly for use by other package developers
12810 who want to include run-time testing features in their own packages.")
12811 (license license:gpl3+)))
12813 (define-public r-assertive-sets
12815 (name "r-assertive-sets")
12820 (uri (cran-uri "assertive.sets" version))
12823 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
12825 `((upstream-name . "assertive.sets")))
12826 (build-system r-build-system)
12828 `(("r-assertive-base" ,r-assertive-base)))
12829 (home-page "https://bitbucket.org/richierocks/assertive.sets")
12830 (synopsis "Assertions to check properties of sets")
12832 "This package provides a set of predicates and assertions for checking
12833 the properties of sets. This is mainly for use by other package developers
12834 who want to include run-time testing features in their own packages.")
12835 (license license:gpl3+)))
12837 (define-public r-assertive-matrices
12839 (name "r-assertive-matrices")
12844 (uri (cran-uri "assertive.matrices" version))
12847 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
12849 `((upstream-name . "assertive.matrices")))
12850 (build-system r-build-system)
12852 `(("r-assertive-base" ,r-assertive-base)))
12853 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
12854 (synopsis "Assertions to check properties of matrices")
12856 "This package provides a set of predicates and assertions for checking
12857 the properties of matrices. This is mainly for use by other package
12858 developers who want to include run-time testing features in their own
12860 (license license:gpl3+)))
12862 (define-public r-assertive-models
12864 (name "r-assertive-models")
12869 (uri (cran-uri "assertive.models" version))
12872 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
12874 `((upstream-name . "assertive.models")))
12875 (build-system r-build-system)
12877 `(("r-assertive-base" ,r-assertive-base)))
12878 (home-page "https://bitbucket.org/richierocks/assertive.models")
12879 (synopsis "Assertions to check properties of models")
12881 "This package provides a set of predicates and assertions for checking
12882 the properties of models. This is mainly for use by other package developers
12883 who want to include run-time testing features in their own packages.")
12884 (license license:gpl3+)))
12886 (define-public r-assertive-reflection
12888 (name "r-assertive-reflection")
12893 (uri (cran-uri "assertive.reflection" version))
12896 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
12898 `((upstream-name . "assertive.reflection")))
12899 (build-system r-build-system)
12901 `(("r-assertive-base" ,r-assertive-base)))
12902 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
12903 (synopsis "Assertions for checking the state of R")
12905 "This package provides a set of predicates and assertions for checking
12906 the state and capabilities of R, the operating system it is running on, and
12907 the IDE being used. This is mainly for use by other package developers who
12908 want to include run-time testing features in their own packages.")
12909 (license license:gpl3+)))
12911 (define-public r-assertive-types
12913 (name "r-assertive-types")
12918 (uri (cran-uri "assertive.types" version))
12921 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
12923 `((upstream-name . "assertive.types")))
12924 (build-system r-build-system)
12926 `(("r-assertive-base" ,r-assertive-base)
12927 ("r-assertive-properties" ,r-assertive-properties)
12928 ("r-codetools" ,r-codetools)))
12929 (home-page "https://bitbucket.org/richierocks/assertive.types")
12930 (synopsis "Assertions to check types of variables")
12932 "This package provides a set of predicates and assertions for checking
12933 the types of variables. This is mainly for use by other package developers
12934 who want to include run-time testing features in their own packages.")
12935 (license license:gpl3+)))
12937 (define-public r-assertive-files
12939 (name "r-assertive-files")
12944 (uri (cran-uri "assertive.files" version))
12947 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
12949 `((upstream-name . "assertive.files")))
12950 (build-system r-build-system)
12952 `(("r-assertive-base" ,r-assertive-base)
12953 ("r-assertive-numbers" ,r-assertive-numbers)))
12954 (home-page "https://bitbucket.org/richierocks/assertive.files")
12955 (synopsis "Assertions to check properties of files")
12957 "This package provides a set of predicates and assertions for checking
12958 the properties of files and connections. This is mainly for use by other
12959 package developers who want to include run-time testing features in their own
12961 (license license:gpl3+)))
12963 (define-public r-assertive-code
12965 (name "r-assertive-code")
12970 (uri (cran-uri "assertive.code" version))
12973 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
12975 `((upstream-name . "assertive.code")))
12976 (build-system r-build-system)
12978 `(("r-assertive-base" ,r-assertive-base)
12979 ("r-assertive-properties" ,r-assertive-properties)
12980 ("r-assertive-types" ,r-assertive-types)))
12981 (home-page "https://bitbucket.org/richierocks/assertive.code")
12982 (synopsis "Assertions to check properties of code")
12984 "This package provides a set of predicates and assertions for checking
12985 the properties of code. This is mainly for use by other package developers
12986 who want to include run-time testing features in their own packages.")
12987 (license license:gpl3+)))
12989 (define-public r-assertive-datetimes
12991 (name "r-assertive-datetimes")
12996 (uri (cran-uri "assertive.datetimes" version))
12999 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
13001 `((upstream-name . "assertive.datetimes")))
13002 (build-system r-build-system)
13004 `(("r-assertive-base" ,r-assertive-base)
13005 ("r-assertive-types" ,r-assertive-types)))
13006 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
13007 (synopsis "Assertions to check properties of dates and times")
13009 "This package provides a set of predicates and assertions for checking
13010 the properties of dates and times. This is mainly for use by other package
13011 developers who want to include run-time testing features in their own
13013 (license license:gpl3+)))
13015 (define-public r-assertive-strings
13017 (name "r-assertive-strings")
13022 (uri (cran-uri "assertive.strings" version))
13025 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
13027 `((upstream-name . "assertive.strings")))
13028 (build-system r-build-system)
13030 `(("r-assertive-base" ,r-assertive-base)
13031 ("r-assertive-types" ,r-assertive-types)
13032 ("r-stringi" ,r-stringi)))
13033 (home-page "https://bitbucket.org/richierocks/assertive.strings")
13034 (synopsis "Assertions to check properties of strings")
13036 "This package provides a set of predicates and assertions for checking
13037 the properties of strings. This is mainly for use by other package developers
13038 who want to include run-time testing features in their own packages.")
13039 (license license:gpl3+)))
13041 (define-public r-assertive-data-us
13043 (name "r-assertive-data-us")
13048 (uri (cran-uri "assertive.data.us" version))
13051 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
13053 `((upstream-name . "assertive.data.us")))
13054 (build-system r-build-system)
13056 `(("r-assertive-base" ,r-assertive-base)
13057 ("r-assertive-strings" ,r-assertive-strings)))
13058 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
13059 (synopsis "Assertions to check properties of strings")
13061 "This package provides a set of predicates and assertions for checking
13062 the properties of US-specific complex data types. This is mainly for use by
13063 other package developers who want to include run-time testing features in
13064 their own packages.")
13065 (license license:gpl3+)))
13067 (define-public r-assertive-data-uk
13069 (name "r-assertive-data-uk")
13074 (uri (cran-uri "assertive.data.uk" version))
13077 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
13079 `((upstream-name . "assertive.data.uk")))
13080 (build-system r-build-system)
13082 `(("r-assertive-base" ,r-assertive-base)
13083 ("r-assertive-strings" ,r-assertive-strings)))
13084 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
13085 (synopsis "Assertions to check properties of strings")
13087 "This package provides a set of predicates and assertions for checking
13088 the properties of UK-specific complex data types. This is mainly for use by
13089 other package developers who want to include run-time testing features in
13090 their own packages.")
13091 (license license:gpl3+)))
13093 (define-public r-assertive-data
13095 (name "r-assertive-data")
13100 (uri (cran-uri "assertive.data" version))
13103 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
13105 `((upstream-name . "assertive.data")))
13106 (build-system r-build-system)
13108 `(("r-assertive-base" ,r-assertive-base)
13109 ("r-assertive-strings" ,r-assertive-strings)))
13110 (home-page "https://bitbucket.org/richierocks/assertive.data")
13111 (synopsis "Assertions to check properties of data")
13113 "This package provides a set of predicates and assertions for checking
13114 the properties of (country independent) complex data types. This is mainly
13115 for use by other package developers who want to include run-time testing
13116 features in their own packages.")
13117 (license license:gpl3+)))
13119 (define-public r-assertive
13121 (name "r-assertive")
13126 (uri (cran-uri "assertive" version))
13129 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
13130 (build-system r-build-system)
13132 `(("r-assertive-base" ,r-assertive-base)
13133 ("r-assertive-code" ,r-assertive-code)
13134 ("r-assertive-data" ,r-assertive-data)
13135 ("r-assertive-data-uk" ,r-assertive-data-uk)
13136 ("r-assertive-data-us" ,r-assertive-data-us)
13137 ("r-assertive-datetimes" ,r-assertive-datetimes)
13138 ("r-assertive-files" ,r-assertive-files)
13139 ("r-assertive-matrices" ,r-assertive-matrices)
13140 ("r-assertive-models" ,r-assertive-models)
13141 ("r-assertive-numbers" ,r-assertive-numbers)
13142 ("r-assertive-properties" ,r-assertive-properties)
13143 ("r-assertive-reflection" ,r-assertive-reflection)
13144 ("r-assertive-sets" ,r-assertive-sets)
13145 ("r-assertive-strings" ,r-assertive-strings)
13146 ("r-assertive-types" ,r-assertive-types)
13147 ("r-knitr" ,r-knitr)))
13149 `(("r-knitr" ,r-knitr)))
13150 (home-page "https://bitbucket.org/richierocks/assertive")
13151 (synopsis "Readable check functions to ensure code integrity")
13153 "This package provides lots of predicates (@code{is_*} functions) to
13154 check the state of your variables, and assertions (@code{assert_*} functions)
13155 to throw errors if they aren't in the right form.")
13156 (license license:gpl3+)))
13158 (define-public r-dotcall64
13160 (name "r-dotcall64")
13165 (uri (cran-uri "dotCall64" version))
13168 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
13169 (properties `((upstream-name . "dotCall64")))
13170 (build-system r-build-system)
13171 (native-inputs `(("gfortran" ,gfortran)))
13172 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
13173 (synopsis "Enhanced foreign function interface supporting long vectors")
13175 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
13176 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
13177 supports long vectors, arguments of type 64-bit integer, and provides a
13178 mechanism to avoid unnecessary copies of read-only and write-only arguments.
13179 This makes it a convenient and fast interface to C/C++ and Fortran code.")
13180 (license license:gpl2+)))
13182 (define-public r-spam
13189 (uri (cran-uri "spam" version))
13191 (base32 "0p5ycvpry955ldrgbbq3syy91wx9425mddpn8r5m9xwlirjxv3v3"))))
13192 (build-system r-build-system)
13194 `(("r-dotcall64" ,r-dotcall64)))
13196 `(("gfortran" ,gfortran)
13197 ("r-knitr" ,r-knitr)))
13198 (home-page "https://www.math.uzh.ch/pages/spam/")
13199 (synopsis "Sparse matrix algebra")
13201 "This package provides a set of functions for sparse matrix algebra.
13202 Differences with other sparse matrix packages are:
13205 @item it only supports (essentially) one sparse matrix format;
13206 @item it is based on transparent and simple structure(s);
13207 @item it is tailored for MCMC calculations within G(M)RF;
13208 @item and it is fast and scalable (with the extension package @code{spam64}).
13210 ;; Either of these licenses
13211 (license (list license:bsd-3 license:lgpl2.0))))
13213 (define-public r-fields
13220 (uri (cran-uri "fields" version))
13222 (base32 "1nsrgkw9w3mwd3sajyzc06h49gg1s0bkq6xh5b66h1n4jbcx2046"))))
13223 (build-system r-build-system)
13225 `(("r-maps" ,r-maps)
13226 ("r-spam" ,r-spam)))
13228 `(("gfortran" ,gfortran)))
13229 (home-page "https://www.image.ucar.edu/fields")
13230 (synopsis "Tools for spatial data")
13232 "This is a package for curve, surface and function fitting with an
13233 emphasis on splines, spatial data and spatial statistics. The major methods
13234 include cubic, and thin plate splines, Kriging, and compactly supported
13235 covariance functions for large data sets.")
13236 (license license:gpl2+)))
13238 (define-public r-spatialextremes
13240 (name "r-spatialextremes")
13245 (uri (cran-uri "SpatialExtremes" version))
13248 "1mhn1c8n3bmgf0fjyac3wji4790zswzkqliqcv3n8kv9806crb0y"))))
13250 `((upstream-name . "SpatialExtremes")))
13251 (build-system r-build-system)
13253 `(("r-fields" ,r-fields)
13254 ("r-maps" ,r-maps)))
13255 (home-page "http://spatialextremes.r-forge.r-project.org/")
13256 (synopsis "Modelling spatial extremes")
13258 "This package provides tools for the statistical modelling of spatial
13259 extremes using max-stable processes, copula or Bayesian hierarchical models.
13260 More precisely, this package allows (conditional) simulations from various
13261 parametric max-stable models, analysis of the extremal spatial dependence, the
13262 fitting of such processes using composite likelihoods or least square (simple
13263 max-stable processes only), model checking and selection and prediction.")
13264 (license license:gpl2+)))
13266 (define-public r-drc
13273 (uri (cran-uri "drc" version))
13276 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
13277 (build-system r-build-system)
13280 ("r-gtools" ,r-gtools)
13282 ("r-multcomp" ,r-multcomp)
13283 ("r-plotrix" ,r-plotrix)
13284 ("r-scales" ,r-scales)))
13285 (home-page "https://cran.r-project.org/web/packages/drc")
13286 (synopsis "Analysis of dose-response curves")
13288 "This package provides a suite of flexible and versatile model fitting
13289 and after-fitting functions for the analysis of dose-response data.")
13290 (license license:gpl2+)))
13292 (define-public r-rmeta
13299 (uri (cran-uri "rmeta" version))
13302 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
13303 (build-system r-build-system)
13304 (home-page "https://cran.r-project.org/web/packages/rmeta")
13305 (synopsis "Tools for meta-analysis")
13307 "This package provides functions for simple fixed and random effects
13308 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
13309 draws standard summary plots, funnel plots, and computes summaries and tests
13310 for association and heterogeneity.")
13311 (license license:gpl2)))
13313 (define-public r-bootstrap
13315 (name "r-bootstrap")
13320 (uri (cran-uri "bootstrap" version))
13323 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
13324 (build-system r-build-system)
13325 (native-inputs `(("gfortran" ,gfortran)))
13326 (home-page "https://cran.r-project.org/web/packages/bootstrap")
13327 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
13329 "This package provides software and data for the book \"An Introduction
13330 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
13331 This package is primarily provided for projects already based on it, and for
13332 support of the book. New projects should preferentially use the recommended
13333 package \"boot\".")
13334 (license license:bsd-3)))
13336 (define-public r-survivalroc
13338 (name "r-survivalroc")
13343 (uri (cran-uri "survivalROC" version))
13346 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
13347 (properties `((upstream-name . "survivalROC")))
13348 (build-system r-build-system)
13349 (home-page "https://cran.r-project.org/web/packages/survivalROC")
13350 (synopsis "Time-dependent ROC curve estimation from censored survival data")
13352 "Compute time-dependent ROC curve from censored survival data using
13353 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
13354 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
13355 (license license:gpl2+)))
13357 (define-public r-longitudinal
13359 (name "r-longitudinal")
13364 (uri (cran-uri "longitudinal" version))
13367 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
13368 (build-system r-build-system)
13369 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
13370 (home-page "http://strimmerlab.org/software/longitudinal/")
13371 (synopsis "Analysis of multiple time course data")
13373 "This package contains general data structures and functions for
13374 longitudinal data with multiple variables, repeated measurements, and
13375 irregularly spaced time points. It also implements a shrinkage estimator of
13376 dynamical correlation and dynamical covariance.")
13377 (license license:gpl3+)))
13379 (define-public r-genenet
13386 (uri (cran-uri "GeneNet" version))
13389 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
13390 (properties `((upstream-name . "GeneNet")))
13391 (build-system r-build-system)
13393 `(("r-corpcor" ,r-corpcor)
13394 ("r-fdrtool" ,r-fdrtool)
13395 ("r-longitudinal" ,r-longitudinal)))
13396 (home-page "http://strimmerlab.org/software/genenet/")
13397 (synopsis "Modeling and inferring gene networks")
13399 "This package analyzes gene expression (time series) data with focus on
13400 the inference of gene networks. In particular, GeneNet implements the methods
13401 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
13402 for learning large-scale gene association networks (including assignment of
13403 putative directions).")
13404 (license license:gpl3+)))
13406 (define-public r-rbamtools
13408 (name "r-rbamtools")
13409 (version "2.16.17")
13413 (uri (cran-uri "rbamtools" version))
13416 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
13417 (build-system r-build-system)
13418 (inputs `(("zlib" ,zlib)))
13420 `(("r-refgenome" ,r-refgenome)))
13421 (home-page "https://cran.r-project.org/web/packages/rbamtools")
13422 (synopsis "Read and write BAM (binary alignment) files")
13424 "This package provides an R interface to functions of the SAMtools
13426 (license license:artistic2.0)))
13428 (define-public r-protviz
13435 (uri (cran-uri "protViz" version))
13438 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
13439 (properties `((upstream-name . "protViz")))
13440 (build-system r-build-system)
13441 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
13442 (home-page "https://github.com/protViz/protViz/")
13443 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
13445 "This package helps with quality checks, visualizations and analysis of
13446 mass spectrometry data, coming from proteomics experiments. The package is
13447 developed, tested and used at the Functional Genomics Center Zurich, where it
13448 is used mainly for prototyping, teaching, and having fun with proteomics data.
13449 But it can also be used to do data analysis for small scale data sets.")
13450 (license license:gpl3)))
13452 (define-public r-cmprsk
13459 (uri (cran-uri "cmprsk" version))
13461 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
13462 (build-system r-build-system)
13464 `(("r-survival" ,r-survival)))
13466 `(("gfortran" ,gfortran)))
13467 (home-page "https://cran.r-project.org/web/packages/cmprsk")
13468 (synopsis "Subdistribution analysis of competing risks")
13470 "This package provides tool for estimation, testing and regression
13471 modeling of subdistribution functions in competing risks, as described in
13472 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
13473 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
13474 A proportional hazards model for the subdistribution of a competing risk,
13475 JASA, 94:496-509.")
13476 (license license:gpl2+)))
13478 (define-public r-etm
13485 (uri (cran-uri "etm" version))
13488 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
13489 (build-system r-build-system)
13491 `(("r-data-table" ,r-data-table)
13492 ("r-lattice" ,r-lattice)
13494 ("r-rcpparmadillo" ,r-rcpparmadillo)
13495 ("r-survival" ,r-survival)))
13496 (home-page "https://cran.r-project.org/web/packages/etm")
13497 (synopsis "Empirical transition matrix")
13499 "The @dfn{empirical transition matrix} (etm) package estimates
13500 the matrix of transition probabilities for any time-inhomogeneous multistate
13501 model with finite state space using the Aalen-Johansen estimator.")
13502 (license license:expat)))
13504 (define-public r-epi
13511 (uri (cran-uri "Epi" version))
13514 "0wsjvilcivrhy2kh2dcagkzy7bjmfa0sq9xjpv6qb4b0nc0mv089"))))
13515 (properties `((upstream-name . "Epi")))
13516 (build-system r-build-system)
13518 `(("r-cmprsk" ,r-cmprsk)
13519 ("r-data-table" ,r-data-table)
13520 ("r-dplyr" ,r-dplyr)
13523 ("r-matrix" ,r-matrix)
13525 ("r-numderiv" ,r-numderiv)
13527 ("r-purrr" ,r-purrr)
13528 ("r-survival" ,r-survival)
13530 (home-page "https://BendixCarstensen.com/Epi/")
13531 (synopsis "Statistical analysis in epidemiology")
13533 "This package provides functions for demographic and epidemiological
13534 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
13535 particular representation, manipulation and simulation of multistate data -
13536 the Lexis suite of functions, which includes interfaces to the @code{mstate},
13537 @code{etm} and @code{cmprsk} packages. It also contains functions for
13538 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
13539 data and some useful functions for tabulation and plotting, as well as a
13540 number of epidemiological data sets.")
13541 (license license:gpl2)))
13543 (define-public r-ppls
13546 (version "1.6-1.1")
13550 (uri (cran-uri "ppls" version))
13553 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
13554 (build-system r-build-system)
13555 (propagated-inputs `(("r-mass" ,r-mass)))
13556 (home-page "https://cran.r-project.org/web/packages/ppls")
13557 (synopsis "Penalized partial least squares")
13559 "This package contains linear and nonlinear regression methods based on
13560 partial least squares and penalization techniques. Model parameters are
13561 selected via cross-validation, and confidence intervals ans tests for the
13562 regression coefficients can be conducted via jackknifing.")
13563 (license license:gpl2+)))
13565 (define-public r-huge
13568 (version "1.3.4.1")
13572 (uri (cran-uri "huge" version))
13574 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
13575 (build-system r-build-system)
13577 `(("r-igraph" ,r-igraph)
13579 ("r-matrix" ,r-matrix)
13581 ("r-rcppeigen" ,r-rcppeigen)))
13582 (home-page "https://cran.r-project.org/web/packages/huge")
13583 (synopsis "High-dimensional undirected graph estimation")
13585 "This package provides a general framework for high-dimensional
13586 undirected graph estimation. It integrates data preprocessing, neighborhood
13587 screening, graph estimation, and model selection techniques into a pipeline.")
13588 (license license:gpl2)))
13590 (define-public r-parcor
13597 (uri (cran-uri "parcor" version))
13600 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
13601 (build-system r-build-system)
13604 ("r-genenet" ,r-genenet)
13605 ("r-glmnet" ,r-glmnet)
13607 ("r-ppls" ,r-ppls)))
13608 (home-page "https://cran.r-project.org/web/packages/parcor")
13609 (synopsis "Regularized estimation of partial correlation matrices")
13611 "This package estimates the matrix of partial correlations based on
13612 different regularized regression methods: lasso, adaptive lasso, PLS, and
13613 Ridge Regression. In addition, the package provides model selection for
13614 lasso, adaptive lasso and Ridge regression based on cross-validation.")
13615 (license license:gpl2+)))
13617 (define-public r-mcmc
13624 (uri (cran-uri "mcmc" version))
13627 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
13628 (build-system r-build-system)
13629 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
13630 (synopsis "Markov chain Monte Carlo")
13632 "This package simulates continuous distributions of random vectors using
13633 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
13634 function that evaluates the log unnormalized density. Algorithms are random
13635 walk Metropolis algorithm (function @code{metrop}), simulated
13636 tempering (function @code{temper}), and morphometric random walk
13637 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
13638 by change of variable.")
13639 (license license:expat)))
13641 (define-public r-listenv
13648 (uri (cran-uri "listenv" version))
13651 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
13652 (build-system r-build-system)
13654 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13655 (home-page "https://github.com/HenrikBengtsson/listenv")
13656 (synopsis "Environments behaving (almost) as lists")
13658 "This package implements list environments. List environments are
13659 environments that have list-like properties. For instance, the elements of a
13660 list environment are ordered and can be accessed and iterated over using index
13662 (license license:lgpl2.1+)))
13664 (define-public r-globals
13671 (uri (cran-uri "globals" version))
13674 "1wrjiiif6rpc268zz79pvpw33si6n6ffgxdnxmmcracwhb5vqg90"))))
13675 (build-system r-build-system)
13677 `(("r-codetools" ,r-codetools)))
13678 (home-page "https://github.com/HenrikBengtsson/globals")
13679 (synopsis "Identify global objects in R expressions")
13681 "This package provides tools to identify global (\"unknown\" or \"free\")
13682 objects in R expressions by code inspection using various strategies, e.g.
13683 conservative or liberal. The objective of this package is to make it as
13684 simple as possible to identify global objects for the purpose of exporting
13685 them in distributed compute environments.")
13686 (license license:lgpl2.1+)))
13688 (define-public r-parallelly
13690 (name "r-parallelly")
13695 (uri (cran-uri "parallelly" version))
13698 "025whcz55wj9jd73dalkbxh4l2331mqn758glr6hlf472lwf4v1p"))))
13699 (properties `((upstream-name . "parallelly")))
13700 (build-system r-build-system)
13701 (home-page "https://github.com/HenrikBengtsson/parallelly")
13702 (synopsis "Enhancements of the parallel package")
13704 "This package provides utility functions that enhance the @code{parallel}
13705 package and support the built-in parallel backends of the @code{future}
13706 package. For example, @code{availableCores} gives the number of CPU cores
13707 available to your R process as given by R options and environment variables,
13708 including those set by job schedulers on high-performance compute clusters.
13709 If none is set, it will fall back to @code{parallel::detectCores}. Another
13710 example is @code{makeClusterPSOCK}, which is backward compatible with
13711 @code{parallel::makePSOCKcluster} while doing a better job in setting up
13712 remote cluster workers without the need for configuring the firewall to do
13713 port-forwarding to your local computer.")
13714 (license license:lgpl2.1+)))
13716 (define-public r-future
13723 (uri (cran-uri "future" version))
13726 "0bfiy17n5rghxw0702k0vgpjkk13268lniifdlx59flf0q16d7lh"))))
13727 (build-system r-build-system)
13729 `(("r-digest" ,r-digest)
13730 ("r-globals" ,r-globals)
13731 ("r-listenv" ,r-listenv)
13732 ("r-parallelly" ,r-parallelly)))
13734 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13735 (home-page "https://github.com/HenrikBengtsson/future")
13736 (synopsis "Unified parallel and distributed processing in R")
13738 "The purpose of this package is to provide a lightweight and unified
13739 Future API for sequential and parallel processing of R expression via futures.
13740 This package implements sequential, multicore, multisession, and cluster
13741 futures. With these, R expressions can be evaluated on the local machine, in
13742 parallel a set of local machines, or distributed on a mix of local and remote
13743 machines. Extensions to this package implement additional backends for
13744 processing futures via compute cluster schedulers etc. Because of its unified
13745 API, there is no need to modify any code in order to switch from sequential on
13746 the local machine to, say, distributed processing on a remote compute cluster.")
13747 (license license:lgpl2.1+)))
13749 (define-public r-future-apply
13751 (name "r-future-apply")
13756 (uri (cran-uri "future.apply" version))
13759 "1ns5cf80vyabvyz9qp6kpvkg4jycinn7x6v7x6692fgjapdnmyig"))))
13760 (properties `((upstream-name . "future.apply")))
13761 (build-system r-build-system)
13763 `(("r-future" ,r-future)
13764 ("r-globals" ,r-globals)))
13766 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
13767 (home-page "https://github.com/HenrikBengtsson/future.apply")
13768 (synopsis "Apply function to elements in parallel using futures")
13770 "This package provides implementations of @code{apply()},
13771 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
13772 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
13773 can be resolved using any future-supported backend, e.g. parallel on the local
13774 machine or distributed on a compute cluster.")
13775 (license license:gpl2+)))
13777 (define-public r-rsvd
13784 (uri (cran-uri "rsvd" version))
13787 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
13788 (build-system r-build-system)
13790 `(("r-matrix" ,r-matrix)))
13791 (home-page "https://github.com/erichson/rSVD")
13792 (synopsis "Randomized singular value decomposition")
13794 "Low-rank matrix decompositions are fundamental tools and widely used for
13795 data analysis, dimension reduction, and data compression. Classically, highly
13796 accurate deterministic matrix algorithms are used for this task. However, the
13797 emergence of large-scale data has severely challenged our computational
13798 ability to analyze big data. The concept of randomness has been demonstrated
13799 as an effective strategy to quickly produce approximate answers to familiar
13800 problems such as the @dfn{singular value decomposition} (SVD). This package
13801 provides several randomized matrix algorithms such as the randomized singular
13802 value decomposition (@code{rsvd}), randomized principal component
13803 analysis (@code{rpca}), randomized robust principal component
13804 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
13805 and the randomized CUR decomposition (@code{rcur}). In addition several plot
13806 functions are provided.")
13807 (license license:gpl3+)))
13809 (define-public r-sloop
13816 (uri (cran-uri "sloop" version))
13819 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
13820 (build-system r-build-system)
13822 `(("r-codetools" ,r-codetools)
13823 ("r-crayon" ,r-crayon)
13824 ("r-purrr" ,r-purrr)
13825 ("r-rlang" ,r-rlang)
13826 ("r-tibble" ,r-tibble)))
13827 (home-page "https://github.com/r-lib/sloop")
13828 (synopsis "Helpers for object-oriented programming in R")
13830 "This package provides a collection of helper functions designed to
13831 help you to better understand object oriented programming in R, particularly
13833 (license license:gpl3)))
13835 (define-public r-capushe
13842 (uri (cran-uri "capushe" version))
13845 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
13846 (build-system r-build-system)
13847 (propagated-inputs `(("r-mass" ,r-mass)))
13848 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
13849 (synopsis "Calibrating penalties using slope heuristics")
13851 "This package provides tools for the calibration of penalized criteria
13852 for model selection. The calibration methods available are based on the slope
13854 (license license:gpl2+)))
13856 (define-public r-dorng
13863 (uri (cran-uri "doRNG" version))
13866 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
13867 (properties `((upstream-name . "doRNG")))
13868 (build-system r-build-system)
13870 `(("r-foreach" ,r-foreach)
13871 ("r-iterators" ,r-iterators)
13872 ("r-rngtools" ,r-rngtools)))
13873 (home-page "https://renozao.github.io/doRNG/")
13874 (synopsis "Generic reproducible parallel backend for foreach loops")
13876 "This package provides functions to perform reproducible parallel
13877 @code{foreach} loops, using independent random streams as generated by
13878 L'Ecuyer's combined multiple-recursive generator. It enables to easily
13879 convert standard @code{%dopar%} loops into fully reproducible loops,
13880 independently of the number of workers, the task scheduling strategy, or the
13881 chosen parallel environment and associated foreach backend.")
13882 (license license:gpl2+)))
13884 (define-public r-blockmodeling
13886 (name "r-blockmodeling")
13891 (uri (cran-uri "blockmodeling" version))
13894 "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i"))))
13895 (build-system r-build-system)
13897 `(("r-matrix" ,r-matrix)))
13898 (native-inputs `(("gfortran" ,gfortran)))
13899 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
13900 (synopsis "Generalized and classical blockmodeling of valued networks")
13902 "This package is primarily meant as an implementation of generalized
13903 blockmodeling for valued networks. In addition, measures of similarity or
13904 dissimilarity based on structural equivalence and regular equivalence (REGE
13905 algorithms) can be computed and partitioned matrices can be plotted.")
13906 (license license:gpl2+)))
13908 (define-public r-upsetr
13915 (uri (cran-uri "UpSetR" version))
13918 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
13919 (properties `((upstream-name . "UpSetR")))
13920 (build-system r-build-system)
13922 `(("r-ggplot2" ,r-ggplot2)
13923 ("r-gridextra" ,r-gridextra)
13925 ("r-scales" ,r-scales)))
13926 (home-page "https://github.com/hms-dbmi/UpSetR")
13927 (synopsis "Visualize intersecting sets")
13929 "This package provides a more scalable alternative to Venn and Euler
13930 diagrams for visualizing intersecting sets. Create visualizations of
13931 intersecting sets using a novel matrix design, along with visualizations of
13932 several common set, element and attribute related tasks.")
13933 (license license:expat)))
13935 ;; This package includes a JavaScript file, which is not minified. When
13936 ;; upgrading please check that there are no new minified JavaScript files.
13937 (define-public r-shinybs
13944 (uri (cran-uri "shinyBS" version))
13947 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
13948 (properties `((upstream-name . "shinyBS")))
13949 (build-system r-build-system)
13950 ;; The tests spawn Shiny browser apps. They cannot be run
13951 ;; non-interactively.
13952 (arguments '(#:tests? #f))
13954 `(("r-htmltools" ,r-htmltools)
13955 ("r-shiny" ,r-shiny)))
13956 (home-page "https://ebailey78.github.io/shinyBS/")
13957 (synopsis "Twitter Bootstrap components for Shiny")
13959 "This package adds additional Twitter Bootstrap components to Shiny.")
13960 (license license:gpl3)))
13962 (define-public r-shinyjqui
13964 (name "r-shinyjqui")
13969 (uri (cran-uri "shinyjqui" version))
13972 "0n4ijxmkp8x6dwrsxwvx0zgd8b5129cmn6q6rrav38v1q5k8889x"))
13975 (delete-file "inst/www/shinyjqui.min.js")))))
13976 (properties `((upstream-name . "shinyjqui")))
13977 (build-system r-build-system)
13980 (modify-phases %standard-phases
13981 (add-after 'unpack 'process-javascript
13982 (lambda* (#:key inputs #:allow-other-keys)
13983 (with-directory-excursion "inst/www/"
13984 (let ((source "shinyjqui.js")
13985 (target "shinyjqui.min.js"))
13986 (format #true "Processing ~a --> ~a~%"
13988 (invoke "esbuild" source "--minify"
13989 (string-append "--outfile=" target)))))))))
13991 `(("r-htmltools" ,r-htmltools)
13992 ("r-htmlwidgets" ,r-htmlwidgets)
13993 ("r-jsonlite" ,r-jsonlite)
13994 ("r-shiny" ,r-shiny)))
13996 `(("r-knitr" ,r-knitr)
13997 ("esbuild" ,esbuild)))
13998 (home-page "https://github.com/yang-tang/shinyjqui")
13999 (synopsis "jQuery UI interactions and effects for Shiny")
14001 "This is an extension to Shiny that brings interactions and animation
14002 effects from the jQuery UI library.")
14003 (license license:expat)))
14005 (define-public r-outliers
14007 (name "r-outliers")
14012 (uri (cran-uri "outliers" version))
14015 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
14016 (build-system r-build-system)
14017 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
14018 (synopsis "Tests for outliers")
14020 "This package provides a collection of some tests commonly used for
14021 identifying outliers.")
14022 (license license:gpl2+)))
14024 (define-public r-bayesm
14031 (uri (cran-uri "bayesm" version))
14033 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
14034 (build-system r-build-system)
14036 `(("r-rcpp" ,r-rcpp)
14037 ("r-rcpparmadillo" ,r-rcpparmadillo)))
14038 (home-page "http://www.perossi.org/home/bsm-1")
14039 (synopsis "Bayesian inference for marketing/micro-econometrics")
14041 "This package covers many important models used in marketing and
14042 micro-econometrics applications, including Bayes Regression (univariate or
14043 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
14044 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
14045 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
14046 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
14047 Estimation with normal base, Hierarchical Linear Models with normal prior and
14048 covariates, Hierarchical Linear Models with a mixture of normals prior and
14049 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
14050 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
14051 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
14052 analysis of choice-based conjoint data, Bayesian treatment of linear
14053 instrumental variables models, Analysis of Multivariate Ordinal survey data
14054 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
14055 Coefficient Logit Models.")
14056 (license license:gpl2+)))
14058 (define-public r-tensora
14065 (uri (cran-uri "tensorA" version))
14068 "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf"))))
14069 (properties `((upstream-name . "tensorA")))
14070 (build-system r-build-system)
14071 (home-page "http://www.stat.boogaart.de/tensorA")
14072 (synopsis "Advanced tensor arithmetic with named indices")
14074 "This package provides convenience functions for advanced linear algebra
14075 with tensors and computation with datasets of tensors on a higher level
14076 abstraction. It includes Einstein and Riemann summing conventions, dragging,
14077 co- and contravariate indices, and parallel computations on sequences of
14079 (license license:gpl2+)))
14081 (define-public r-rarpack
14088 (uri (cran-uri "rARPACK" version))
14091 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
14092 (properties `((upstream-name . "rARPACK")))
14093 (build-system r-build-system)
14094 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
14095 (home-page "https://github.com/yixuan/rARPACK")
14096 (synopsis "Solvers for large scale eigenvalue and SVD problems")
14098 "This package was previously an R wrapper of the ARPACK library, and now
14099 a shell of the R package RSpectra, an R interface to the Spectra library for
14100 solving large scale eigenvalue/vector problems. The current version of
14101 rARPACK simply imports and exports the functions provided by RSpectra. New
14102 users of rARPACK are advised to switch to the RSpectra package.")
14103 (license license:bsd-3)))
14105 (define-public r-compositions
14107 (name "r-compositions")
14112 (uri (cran-uri "compositions" version))
14115 "03qslsfx11gshls901zlhw47prd55mf16w4mkmd8x1dgiwq938l4"))))
14116 (build-system r-build-system)
14118 `(("r-bayesm" ,r-bayesm)
14120 ("r-robustbase" ,r-robustbase)
14121 ("r-tensora" ,r-tensora)))
14123 `(("r-knitr" ,r-knitr)))
14124 (home-page "http://www.stat.boogaart.de/compositions")
14125 (synopsis "Compositional data analysis")
14127 "This package provides functions for the consistent analysis of
14128 compositional data (e.g. portions of substances) and positive
14129 numbers (e.g. concentrations).")
14130 (license license:gpl2+)))
14132 (define-public r-cobs
14139 (uri (cran-uri "cobs" version))
14142 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
14143 (build-system r-build-system)
14145 `(("r-quantreg" ,r-quantreg)
14146 ("r-sparsem" ,r-sparsem)))
14147 (home-page "https://cran.r-project.org/web/packages/cobs")
14148 (synopsis "Constrained B-Splines (sparse matrix based)")
14150 "This package provides qualitatively constrained (regression) smoothing
14151 splines via linear programming and sparse matrices.")
14152 (license license:gpl2+)))
14154 (define-public r-drimpute
14156 (name "r-drimpute")
14161 (uri (cran-uri "DrImpute" version))
14164 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
14165 (properties `((upstream-name . "DrImpute")))
14166 (build-system r-build-system)
14168 `(("r-rcpp" ,r-rcpp)
14169 ("r-rcpparmadillo" ,r-rcpparmadillo)))
14170 (home-page "https://github.com/ikwak2/DrImpute")
14171 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
14173 "This is an R package for imputing dropout events. Many statistical
14174 methods in cell type identification, visualization and lineage reconstruction
14175 do not account for dropout events. DrImpute can improve the performance of
14176 such software by imputing dropout events.")
14177 (license license:gpl3)))
14179 (define-public r-gamlss-dist
14181 (name "r-gamlss-dist")
14186 (uri (cran-uri "gamlss.dist" version))
14188 (base32 "0nzgq3rnziy0i2zxn88hqy3pakpyin2m2csk9j3zg39si66c6wcq"))))
14189 (properties `((upstream-name . "gamlss.dist")))
14190 (build-system r-build-system)
14191 (propagated-inputs `(("r-mass" ,r-mass)))
14192 (home-page "http://www.gamlss.org/")
14193 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
14195 "This package provides a set of distributions which can be used for
14196 modelling the response variables in Generalized Additive Models for Location
14197 Scale and Shape. The distributions can be continuous, discrete or mixed
14198 distributions. Extra distributions can be created, by transforming, any
14199 continuous distribution defined on the real line, to a distribution defined on
14200 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
14201 transformation, respectively.")
14202 ;; Either version of the GPL.
14203 (license (list license:gpl2 license:gpl3))))
14205 ;; This package includes JavaScript files, which are not minified. When
14206 ;; upgrading please check that there are no new minified JavaScript files.
14207 (define-public r-shinyjs
14214 (uri (cran-uri "shinyjs" version))
14217 "1zzq356dvd8ciajy6r5n4ybgx9xk7ydwv25j86xlcsqznkxdkkf2"))))
14218 (build-system r-build-system)
14220 `(("r-digest" ,r-digest)
14221 ("r-htmltools" ,r-htmltools)
14222 ("r-jsonlite" ,r-jsonlite)
14223 ("r-shiny" ,r-shiny)))
14225 `(("r-knitr" ,r-knitr)))
14226 (home-page "https://deanattali.com/shinyjs")
14227 (synopsis "Improve the user experience of your Shiny apps")
14229 "Perform common useful JavaScript operations in Shiny apps that will
14230 greatly improve your apps without having to know any JavaScript. Examples
14231 include: hiding an element, disabling an input, resetting an input back to its
14232 original value, delaying code execution by a few seconds, and many more useful
14233 functions for both the end user and the developer. Shinyjs can also be used
14234 to easily call your own custom JavaScript functions from R.")
14235 (license license:agpl3+)))
14237 ;; This package includes minified JavaScript files. When upgrading please
14238 ;; check that there are no new minified JavaScript files.
14239 (define-public r-colourpicker
14241 (name "r-colourpicker")
14246 (uri (cran-uri "colourpicker" version))
14249 "1qjispj7i12m02js5cm5xlgn5lyff0kc5ybz6lbknz8q5lkbdyrd"))))
14250 (build-system r-build-system)
14252 `(#:modules ((guix build utils)
14253 (guix build r-build-system)
14257 (modify-phases %standard-phases
14258 (add-after 'unpack 'process-javascript
14259 (lambda* (#:key inputs #:allow-other-keys)
14260 (with-directory-excursion "inst"
14264 `((,(assoc-ref inputs "js-salvattore")
14265 "examples/colourInput/www/salvattore.min.js")
14266 (,(assoc-ref inputs "js-jquery")
14267 "htmlwidgets/lib/jquery/jquery.min.js")
14268 ("www/shared/colourpicker/js/colourpicker.js"
14269 "www/shared/colourpicker/js/colourpicker.min.js"))))
14270 (lambda (sources targets)
14271 (for-each (lambda (source target)
14272 (format #t "Processing ~a --> ~a~%"
14274 (delete-file target)
14275 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14276 (call-with-output-file target
14278 (dump-port minified port)))))
14279 sources targets))))
14282 `(("r-ggplot2" ,r-ggplot2)
14283 ("r-htmltools" ,r-htmltools)
14284 ("r-htmlwidgets" ,r-htmlwidgets)
14285 ("r-jsonlite" ,r-jsonlite)
14286 ("r-miniui" ,r-miniui)
14287 ("r-shiny" ,r-shiny)
14288 ("r-shinyjs" ,r-shinyjs)))
14290 `(("r-knitr" ,r-knitr)
14291 ("uglify-js" ,uglify-js)
14295 (uri "https://code.jquery.com/jquery-3.3.1.js")
14298 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
14302 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
14305 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
14306 (home-page "https://github.com/daattali/colourpicker")
14307 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
14309 "This package provides a color picker that can be used as an input in
14310 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
14311 custom color palettes, and many more options. A plot color helper tool is
14312 available as an RStudio Addin, which helps you pick colors to use in your
14313 plots. A more generic color picker RStudio Addin is also provided to let you
14314 select colors to use in your R code.")
14315 (license license:expat)))
14317 (define-public r-ggextra
14324 (uri (cran-uri "ggExtra" version))
14327 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
14328 (properties `((upstream-name . "ggExtra")))
14329 (build-system r-build-system)
14331 `(("r-colourpicker" ,r-colourpicker)
14332 ("r-ggplot2" ,r-ggplot2)
14333 ("r-gtable" ,r-gtable)
14334 ("r-miniui" ,r-miniui)
14336 ("r-scales" ,r-scales)
14337 ("r-shiny" ,r-shiny)
14338 ("r-shinyjs" ,r-shinyjs)))
14340 `(("r-knitr" ,r-knitr)))
14341 (home-page "https://github.com/daattali/ggExtra")
14342 (synopsis "Marginal histograms for ggplot2 and other enhancements")
14344 "This package is a collection of functions and layers to enhance ggplot2.
14345 The flagship function is @code{ggMarginal()}, which can be used to add
14346 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
14347 (license license:expat)))
14349 (define-public r-minpack-lm
14351 (name "r-minpack-lm")
14356 (uri (cran-uri "minpack.lm" version))
14359 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
14360 (properties `((upstream-name . "minpack.lm")))
14361 (build-system r-build-system)
14362 (native-inputs `(("gfortran" ,gfortran)))
14363 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
14364 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
14366 "The @code{nls.lm} function provides an R interface to @code{lmder} and
14367 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
14368 problems by a modification of the Levenberg-Marquardt algorithm, with support
14369 for lower and upper parameter bounds. The implementation can be used via
14370 @code{nls}-like calls using the @code{nlsLM} function.")
14371 (license license:gpl3)))
14373 (define-public r-moments
14380 (uri (cran-uri "moments" version))
14383 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
14384 (build-system r-build-system)
14385 (home-page "https://cran.r-project.org/web/packages/moments")
14386 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
14388 "This package provides functions to calculate: moments, Pearson's
14389 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
14390 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
14391 (license license:gpl2+)))
14393 (define-public r-msir
14400 (uri (cran-uri "msir" version))
14403 "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84"))))
14404 (build-system r-build-system)
14406 `(("r-mclust" ,r-mclust)))
14408 `(("r-knitr" ,r-knitr)))
14409 (home-page "https://cran.r-project.org/web/packages/msir")
14410 (synopsis "Model-based sliced inverse regression")
14412 "This is an R package for dimension reduction based on finite Gaussian
14413 mixture modeling of inverse regression.")
14414 (license license:gpl2+)))
14416 (define-public r-pbivnorm
14418 (name "r-pbivnorm")
14423 (uri (cran-uri "pbivnorm" version))
14426 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
14427 (build-system r-build-system)
14428 (native-inputs `(("gfortran" ,gfortran)))
14429 (home-page "https://github.com/brentonk/pbivnorm")
14430 (synopsis "Vectorized bivariate normal CDF")
14432 "This package provides a vectorized R function for calculating
14433 probabilities from a standard bivariate normal CDF.")
14434 (license license:gpl2+)))
14436 (define-public r-lavaan
14443 (uri (cran-uri "lavaan" version))
14446 "0ks62wrwghbm1brzmqvr92h5n1295dpc87m1g3xrfx0mkdaqdcdk"))))
14447 (build-system r-build-system)
14449 `(("r-mass" ,r-mass)
14450 ("r-mnormt" ,r-mnormt)
14451 ("r-numderiv" ,r-numderiv)
14452 ("r-pbivnorm" ,r-pbivnorm)))
14453 (home-page "https://lavaan.ugent.be")
14454 (synopsis "Latent variable analysis")
14456 "This package provides tools to fit a variety of latent variable models,
14457 including confirmatory factor analysis, structural equation modeling and
14458 latent growth curve models.")
14459 (license license:gpl2+)))
14461 (define-public r-nonnest2
14463 (name "r-nonnest2")
14468 (uri (cran-uri "nonnest2" version))
14471 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
14472 (build-system r-build-system)
14474 `(("r-compquadform" ,r-compquadform)
14475 ("r-lavaan" ,r-lavaan)
14476 ("r-mvtnorm" ,r-mvtnorm)
14477 ("r-sandwich" ,r-sandwich)))
14479 `(("r-knitr" ,r-knitr)))
14480 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
14481 (synopsis "Tests of non-nested models")
14483 "This package allows for testing of non-nested models. It includes tests
14484 of model distinguishability and of model fit that can be applied to both
14485 nested and non-nested models. The package also includes functionality to
14486 obtain confidence intervals associated with AIC and BIC.")
14487 ;; Either version of the GPL.
14488 (license (list license:gpl2 license:gpl3))))
14490 (define-public r-penalized
14492 (name "r-penalized")
14497 (uri (cran-uri "penalized" version))
14500 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
14501 (build-system r-build-system)
14503 `(("r-rcpp" ,r-rcpp)
14504 ("r-rcpparmadillo" ,r-rcpparmadillo)
14505 ("r-survival" ,r-survival)))
14506 (home-page "https://cran.r-project.org/web/packages/penalized/")
14507 (synopsis "Penalized estimation in GLMs and in the Cox model")
14509 "This package provides tools for fitting possibly high dimensional
14510 penalized regression models. The penalty structure can be any combination of
14511 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
14512 constraint on the regression coefficients. The supported regression models
14513 are linear, logistic and Poisson regression and the Cox Proportional Hazards
14514 model. Cross-validation routines allow optimization of the tuning
14516 (license license:gpl2+)))
14518 (define-public r-zim
14525 (uri (cran-uri "ZIM" version))
14528 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
14529 (properties `((upstream-name . "ZIM")))
14530 (build-system r-build-system)
14531 (propagated-inputs `(("r-mass" ,r-mass)))
14532 (home-page "https://github.com/biostatstudio/ZIM")
14533 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
14535 "Analyze count time series with excess zeros. Two types of statistical
14536 models are supported: Markov regression and state-space models. They are also
14537 known as observation-driven and parameter-driven models respectively in the
14538 time series literature. The functions used for Markov regression or
14539 observation-driven models can also be used to fit ordinary regression models
14540 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
14541 negative binomial (ZINB) assumption. The package also contains miscellaneous
14542 functions to compute density, distribution, quantile, and generate random
14543 numbers from ZIP and ZINB distributions.")
14544 (license license:gpl3)))
14546 (define-public r-nor1mix
14553 (uri (cran-uri "nor1mix" version))
14556 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
14557 (build-system r-build-system)
14558 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
14559 (synopsis "Normal (1-d) mixture models")
14561 "This package provides S3 classes and methods for one-dimensional normal
14562 mixture models, for, e.g., density estimation or clustering algorithms
14563 research and teaching; it provides the widely used Marron-Wand densities. It
14564 also provides tools for efficient random number generation and graphics.")
14565 (license license:gpl2+)))
14567 (define-public r-beanplot
14569 (name "r-beanplot")
14574 (uri (cran-uri "beanplot" version))
14577 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
14578 (build-system r-build-system)
14579 (home-page "https://cran.r-project.org/web/packages/beanplot/")
14580 (synopsis "Visualization via beanplots")
14582 "This package provides beanplots, an alternative to
14583 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
14585 (license license:gpl2)))
14587 (define-public r-pbdzmq
14594 (uri (cran-uri "pbdZMQ" version))
14597 "1v8iv1pzs4j3ics9k9h4xjkv6z1ma2xbqy003xk2lqax6srqi02d"))))
14598 (properties `((upstream-name . "pbdZMQ")))
14599 (build-system r-build-system)
14601 `(("zeromq" ,zeromq)
14604 `(("pkg-config" ,pkg-config)))
14605 (home-page "https://pbdr.org/")
14606 (synopsis "R interface to ZeroMQ")
14608 "ZeroMQ is a well-known library for high-performance asynchronous
14609 messaging in scalable, distributed applications. This package provides high
14610 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
14611 interactive client/server programming frameworks. A few wrapper functions
14612 compatible with @code{rzmq} are also provided.")
14613 (license license:gpl3)))
14615 (define-public r-repr
14622 (uri (cran-uri "repr" version))
14625 "0qimllv9pn8wsl550bjkp5dkknbmr69j85mrwfbbq75m2ga466sk"))))
14626 (build-system r-build-system)
14628 `(("r-base64enc" ,r-base64enc)
14629 ("r-htmltools" ,r-htmltools)
14630 ("r-jsonlite" ,r-jsonlite)
14631 ("r-pillar" ,r-pillar)))
14632 (home-page "https://cran.r-project.org/web/packages/repr/")
14633 (synopsis "Serializable representations")
14635 "This package provides string and binary representations of objects for
14636 several formats and MIME types.")
14637 (license license:gpl3)))
14639 (define-public r-irdisplay
14641 (name "r-irdisplay")
14646 (uri (cran-uri "IRdisplay" version))
14649 "15jbjrihm1mk899357h9xb08iq3xyagds1xb40fmdpkfcmcfqrw9"))))
14650 (properties `((upstream-name . "IRdisplay")))
14651 (build-system r-build-system)
14653 `(("r-repr" ,r-repr)))
14654 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
14655 (synopsis "Jupyter display machinery")
14657 "This package provides an interface to the rich display capabilities of
14658 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
14659 running IRkernel session.")
14660 (license license:expat)))
14662 (define-public r-irkernel
14664 (name "r-irkernel")
14669 (uri (cran-uri "IRkernel" version))
14672 "1y06v3difaiihxfm2abm88nnjzvkla4p346cm1nxmga4iwb2k8gm"))))
14673 (properties `((upstream-name . "IRkernel")))
14674 (build-system r-build-system)
14677 (modify-phases %standard-phases
14678 (add-after 'install 'install-kernelspec
14679 (lambda* (#:key outputs #:allow-other-keys)
14680 (let ((out (assoc-ref outputs "out")))
14681 (setenv "HOME" "/tmp")
14682 (invoke "jupyter" "kernelspec" "install"
14685 (string-append out "/site-library/IRkernel/kernelspec"))
14686 ;; Record the absolute file name of the 'R' executable in
14688 (substitute* (string-append out "/share/jupyter"
14689 "/kernels/ir/kernel.json")
14691 (string-append "[\"" (which "R") "\",")))
14694 `(("jupyter" ,jupyter)))
14696 `(("r-crayon" ,r-crayon)
14697 ("r-digest" ,r-digest)
14698 ("r-evaluate" ,r-evaluate)
14699 ("r-irdisplay" ,r-irdisplay)
14700 ("r-jsonlite" ,r-jsonlite)
14701 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
14702 ("r-minimal" ,r-minimal)
14703 ("r-pbdzmq" ,r-pbdzmq)
14705 ("r-uuid" ,r-uuid)))
14706 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
14707 (synopsis "Native R kernel for Jupyter")
14709 "The R kernel for the Jupyter environment executes R code which the
14710 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
14712 (license license:expat)))
14714 (define-public r-gmodels
14721 (uri (cran-uri "gmodels" version))
14724 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
14725 (build-system r-build-system)
14727 `(("r-gdata" ,r-gdata)
14728 ("r-mass" ,r-mass)))
14729 (home-page "https://cran.r-project.org/web/packages/gmodels/")
14730 (synopsis "Various R programming tools for model fitting")
14732 "This package provides various R programming tools for model fitting.")
14733 (license license:gpl2)))
14735 (define-public r-apcluster
14737 (name "r-apcluster")
14742 (uri (cran-uri "apcluster" version))
14745 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
14746 (build-system r-build-system)
14748 `(("r-matrix" ,r-matrix)
14749 ("r-rcpp" ,r-rcpp)))
14750 (home-page "https://cran.r-project.org/web/packages/apcluster/")
14751 (synopsis "Affinity propagation clustering")
14753 "This package implements affinity propagation clustering introduced by
14754 Frey and Dueck (2007). The package further provides leveraged affinity
14755 propagation and an algorithm for exemplar-based agglomerative clustering that
14756 can also be used to join clusters obtained from affinity propagation. Various
14757 plotting functions are available for analyzing clustering results.")
14758 (license license:gpl2+)))
14760 (define-public r-valr
14767 (uri (cran-uri "valr" version))
14770 "1vbp89zfylgih5acvw7lcx3a0dbbd7dhq7yhywr7kq02737qykdx"))))
14771 (build-system r-build-system)
14773 `(("r-broom" ,r-broom)
14774 ("r-dplyr" ,r-dplyr)
14775 ("r-ggplot2" ,r-ggplot2)
14777 ("r-readr" ,r-readr)
14778 ("r-rlang" ,r-rlang)
14779 ("r-stringr" ,r-stringr)
14780 ("r-tibble" ,r-tibble)))
14782 `(("r-knitr" ,r-knitr)))
14783 (home-page "https://github.com/rnabioco/valr")
14784 (synopsis "Genome interval arithmetic in R")
14786 "This package enables you to read and manipulate genome intervals and
14787 signals. It provides functionality similar to command-line tool suites within
14788 R, enabling interactive analysis and visualization of genome-scale data.")
14789 (license license:expat)))
14791 (define-public r-rematch2
14793 (name "r-rematch2")
14798 (uri (cran-uri "rematch2" version))
14801 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
14802 (build-system r-build-system)
14804 `(("r-tibble" ,r-tibble)))
14805 (home-page "https://github.com/r-lib/rematch2")
14806 (synopsis "Tidy output from regular expression matching")
14808 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
14809 return the match results in tidy data frames.")
14810 (license license:expat)))
14812 (define-public r-picante
14819 (uri (cran-uri "picante" version))
14822 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
14823 (build-system r-build-system)
14827 ("r-vegan" ,r-vegan)))
14828 (home-page "https://cran.r-project.org/web/packages/picante/")
14829 (synopsis "Integrating phylogenies and ecology")
14831 "This package provides functions for phylocom integration, community
14832 analyses, null-models, traits and evolution. It implements numerous
14833 ecophylogenetic approaches including measures of community phylogenetic and
14834 trait diversity, phylogenetic signal, estimation of trait values for
14835 unobserved taxa, null models for community and phylogeny randomizations, and
14836 utility functions for data input/output and phylogeny plotting. A full
14837 description of package functionality and methods are provided by Kembel et
14839 (license license:gpl2)))
14841 (define-public r-reinforcelearn
14843 (name "r-reinforcelearn")
14848 (uri (cran-uri "reinforcelearn" version))
14851 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
14852 (build-system r-build-system)
14854 `(("r-checkmate" ,r-checkmate)
14856 ("r-purrr" ,r-purrr)
14858 (home-page "https://markusdumke.github.io/reinforcelearn")
14859 (synopsis "Reinforcement learning")
14861 "This package implements reinforcement learning environments and
14862 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
14863 can be used with function approximation, eligibility traces (Singh & Sutton,
14864 1996) and experience replay (Mnih et al., 2013).")
14865 (license license:expat)))
14867 (define-public r-lemon
14874 (uri (cran-uri "lemon" version))
14877 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
14878 (build-system r-build-system)
14880 `(("r-ggplot2" ,r-ggplot2)
14881 ("r-gridextra" ,r-gridextra)
14882 ("r-gtable" ,r-gtable)
14883 ("r-knitr" ,r-knitr)
14884 ("r-lattice" ,r-lattice)
14886 ("r-rlang" ,r-rlang)
14887 ("r-scales" ,r-scales)))
14889 `(("r-knitr" ,r-knitr)))
14890 (home-page "https://github.com/stefanedwards/lemon")
14891 (synopsis "Freshen up your ggplot2 plots")
14893 "This package provides functions for working with legends and axis lines
14894 of ggplot2, facets that repeat axis lines on all panels, and some knitr
14896 (license license:gpl3)))
14898 (define-public r-wgaim
14905 (uri (cran-uri "wgaim" version))
14907 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
14908 (build-system r-build-system)
14910 `(("r-ggplot2" ,r-ggplot2)
14912 (home-page "https://cran.r-project.org/web/packages/wgaim")
14913 (synopsis "Whole genome average interval mapping for QTL detection")
14915 "This package integrates sophisticated mixed modelling methods with a
14916 whole genome approach to detecting significant QTL in linkage maps.")
14917 (license license:gpl2+)))
14919 (define-public r-bedr
14926 (uri (cran-uri "bedr" version))
14929 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
14930 (build-system r-build-system)
14932 `(("r-data-table" ,r-data-table)
14933 ("r-r-utils" ,r-r-utils)
14934 ("r-testthat" ,r-testthat)
14935 ("r-venndiagram" ,r-venndiagram)
14938 ("bedtools" ,bedtools)
14939 ("htslib" ,htslib))) ; for tabix
14941 `(("r-knitr" ,r-knitr))) ; for vignettes
14942 (home-page "https://cran.r-project.org/web/packages/bedr")
14943 (synopsis "Genomic region processing")
14945 "This package is for genomic regions processing using command line tools
14946 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
14947 utilities to perform genome arithmetic e.g indexing, formatting and merging.
14948 The bedr package's API enhances access to these tools as well as offers
14949 additional utilities for genomic regions processing.")
14950 (license license:gpl2)))
14952 (define-public r-sets
14959 (uri (cran-uri "sets" version))
14962 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
14963 (properties `((upstream-name . "sets")))
14964 (build-system r-build-system)
14965 (home-page "https://cran.r-project.org/web/packages/sets")
14966 (synopsis "Sets, generalized sets, customizable sets and intervals")
14968 "This package provides data structures and basic operations for ordinary
14969 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
14970 customizable sets, and intervals.")
14971 (license license:gpl2)))
14973 (define-public r-partitions
14975 (name "r-partitions")
14980 (uri (cran-uri "partitions" version))
14983 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
14984 (build-system r-build-system)
14987 ("r-polynom" ,r-polynom)
14988 ("r-sets" ,r-sets)))
14989 (home-page "https://cran.r-project.org/web/packages/partitions")
14990 (synopsis "Additive partitions of integers")
14992 "This package provides tools to enumerates the partitions, unequal
14993 partitions, and restricted partitions of an integer; the three corresponding
14994 partition functions are also given.")
14995 ;; Any version of the GPL
14996 (license license:gpl2+)))
14998 (define-public r-brobdingnag
15000 (name "r-brobdingnag")
15005 (uri (cran-uri "Brobdingnag" version))
15008 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
15009 (properties `((upstream-name . "Brobdingnag")))
15010 (build-system r-build-system)
15011 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
15012 (synopsis "Very large numbers in R")
15014 "This package handles very large numbers in R. Real numbers are held
15015 using their natural logarithms, plus a logical flag indicating sign. The
15016 package includes a vignette that gives a step-by-step introduction to using S4
15018 ;; Any version of the GPL
15019 (license license:gpl2+)))
15021 (define-public r-untb
15028 (uri (cran-uri "untb" version))
15031 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
15032 (build-system r-build-system)
15034 `(("r-brobdingnag" ,r-brobdingnag)
15035 ("r-partitions" ,r-partitions)
15036 ("r-polynom" ,r-polynom)))
15037 (home-page "https://github.com/RobinHankin/untb.git")
15038 (synopsis "Ecological drift under the UNTB")
15040 "This package provides numerical simulations, and visualizations, of
15041 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
15042 (license license:gpl2+)))
15044 (define-public r-stepwise
15046 (name "r-stepwise")
15051 (uri (cran-uri "stepwise" version))
15054 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
15055 (build-system r-build-system)
15056 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
15057 (synopsis "Stepwise detection of recombination breakpoints")
15059 "This package provides a stepwise approach to identifying recombination
15060 breakpoints in a genomic sequence alignment.")
15061 (license license:gpl2+)))
15063 (define-public r-snpmaxsel
15065 (name "r-snpmaxsel")
15070 (uri (cran-uri "SNPmaxsel" version))
15073 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
15074 (properties `((upstream-name . "SNPmaxsel")))
15075 (build-system r-build-system)
15077 `(("r-combinat" ,r-combinat)
15078 ("r-mvtnorm" ,r-mvtnorm)))
15079 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
15080 (synopsis "Maximally selected statistics for SNP data")
15082 "This package implements asymptotic methods related to maximally selected
15083 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
15085 (license license:gpl2+)))
15087 (define-public r-acsnminer
15089 (name "r-acsnminer")
15090 (version "0.16.8.25")
15093 (uri (cran-uri "ACSNMineR" version))
15096 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
15097 (properties `((upstream-name . "ACSNMineR")))
15098 (build-system r-build-system)
15100 `(("r-ggplot2" ,r-ggplot2)
15101 ("r-gridextra" ,r-gridextra)))
15102 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
15103 (synopsis "Gene enrichment analysis")
15105 "This package provides tools to compute and represent gene set enrichment
15106 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
15107 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
15108 enrichment can be run with hypergeometric test or Fisher exact test, and can
15109 use multiple corrections. Visualization of data can be done either by
15110 barplots or heatmaps.")
15111 (license license:gpl2+)))
15113 (define-public r-seqinr
15120 (uri (cran-uri "seqinr" version))
15123 "1z1jipgrn9nrnxlx7bcf8c2chwpa3kfva0zgyb12xbr3kisn166y"))))
15124 (build-system r-build-system)
15126 `(("r-ade4" ,r-ade4)
15127 ("r-segmented" ,r-segmented)))
15130 (home-page "http://seqinr.r-forge.r-project.org/")
15131 (synopsis "Biological sequences retrieval and analysis")
15133 "This package provides tools for exploratory data analysis and data
15134 visualization of biological sequence (DNA and protein) data. It also includes
15135 utilities for sequence data management under the ACNUC system.")
15136 (license license:gpl2+)))
15138 (define-public r-units
15145 (uri (cran-uri "units" version))
15148 "1rdpbkiqcabz00fqzzs98v89v4cgvcd4pb00pwxzkq6vmwmscwrz"))))
15149 (build-system r-build-system)
15151 `(("udunits" ,udunits)))
15153 `(("r-rcpp" ,r-rcpp)))
15155 `(("r-knitr" ,r-knitr)))
15156 (home-page "https://github.com/r-quantities/units/")
15157 (synopsis "Measurement Units for R Vectors")
15159 "This package provides support for measurement units in R vectors,
15160 matrices and arrays: automatic propagation, conversion, derivation and
15161 simplification of units; raising errors in case of unit incompatibility. It
15162 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
15164 (license license:gpl2)))
15166 (define-public r-udunits2
15168 (name "r-udunits2")
15173 (uri (cran-uri "udunits2" version))
15176 "0yav7rm2afcx67xqrknybxgz7x63w78zyxa0xifvc0k2gz0d6mfi"))))
15177 (properties `((upstream-name . "udunits2")))
15178 (build-system r-build-system)
15180 `(("udunits" ,udunits)))
15181 (home-page "https://cran.r-project.org/package=udunits2")
15182 (synopsis "Udunits-2 bindings for R")
15184 "This package provides simple bindings to Unidata's udunits library.")
15185 (license license:gpl2)))
15187 (define-public r-classint
15189 (name "r-classint")
15194 (uri (cran-uri "classInt" version))
15197 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
15198 (properties `((upstream-name . "classInt")))
15199 (build-system r-build-system)
15201 `(("r-class" ,r-class)
15202 ("r-e1071" ,r-e1071)
15203 ("r-kernsmooth" ,r-kernsmooth)))
15205 `(("gfortran" ,gfortran)
15206 ("r-knitr" ,r-knitr)))
15207 (home-page "https://github.com/r-spatial/classInt/")
15208 (synopsis "Choose univariate class intervals")
15210 "This package provides selected commonly used methods for choosing
15211 univariate class intervals for mapping or other graphics purposes.")
15212 (license license:gpl2+)))
15214 (define-public r-spdata
15221 (uri (cran-uri "spData" version))
15224 "1mlsqy9cbilfc80cbdlbgsngvzdkrd9yjdkxnw2b1gzxnj6jcqbs"))))
15225 (properties `((upstream-name . "spData")))
15226 (build-system r-build-system)
15228 `(("r-raster" ,r-raster)
15230 (home-page "https://github.com/Nowosad/spData")
15231 (synopsis "Datasets for spatial analysis")
15233 "This a package containing diverse spatial datasets for demonstrating,
15234 benchmarking and teaching spatial data analysis. It includes R data of class
15235 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
15236 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
15237 of the datasets are designed to illustrate specific analysis techniques.
15238 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
15239 illustrate point pattern analysis techniques.")
15240 (license license:cc0)))
15242 (define-public r-learnbayes
15244 (name "r-learnbayes")
15249 (uri (cran-uri "LearnBayes" version))
15252 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
15253 (properties `((upstream-name . "LearnBayes")))
15254 (build-system r-build-system)
15255 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
15256 (synopsis "Functions for learning Bayesian inference")
15258 "This package provides a collection of functions helpful in learning the
15259 basic tenets of Bayesian statistical inference. It contains functions for
15260 summarizing basic one and two parameter posterior distributions and predictive
15261 distributions. It contains MCMC algorithms for summarizing posterior
15262 distributions defined by the user. It also contains functions for regression
15263 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
15265 (license license:gpl2+)))
15267 (define-public r-deldir
15274 (uri (cran-uri "deldir" version))
15277 "0jfwff5kk0zraspsvbk26lphl3fnrc6xmhl4690hr0a5k177ildm"))))
15278 (build-system r-build-system)
15279 (native-inputs `(("gfortran" ,gfortran)))
15280 (home-page "https://cran.r-project.org/web/packages/deldir")
15281 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
15283 "This package provides tools for calculating the Delaunay triangulation
15284 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
15285 of a planar point set. It plots triangulations and tessellations in various
15286 ways, clips tessellations to sub-windows, calculates perimeters of
15287 tessellations, and summarizes information about the tiles of the
15289 (license license:gpl2+)))
15291 (define-public r-sf
15298 (uri (cran-uri "sf" version))
15301 "175fmnnw11fjhfgjv9sn9b0jfjcqbybpgwsvv99d5yddigvw5jja"))))
15302 (build-system r-build-system)
15310 `(("r-classint" ,r-classint)
15312 ("r-magrittr" ,r-magrittr)
15314 ("r-units" ,r-units)))
15316 `(("pkg-config" ,pkg-config)
15317 ("r-knitr" ,r-knitr)))
15318 (home-page "https://github.com/r-spatial/sf/")
15319 (synopsis "Simple features for R")
15321 "This package provides support for simple features, a standardized way to
15322 encode spatial vector data. It binds to GDAL for reading and writing data, to
15323 GEOS for geometrical operations, and to PROJ for projection conversions and
15324 datum transformations.")
15325 ;; Either of these licenses
15326 (license (list license:gpl2 license:expat))))
15328 (define-public r-spdep
15335 (uri (cran-uri "spdep" version))
15338 "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7"))))
15339 (build-system r-build-system)
15341 `(("r-boot" ,r-boot)
15343 ("r-deldir" ,r-deldir)
15345 ("r-gmodels" ,r-gmodels)
15346 ("r-learnbayes" ,r-learnbayes)
15348 ("r-matrix" ,r-matrix)
15352 ("r-spdata" ,r-spdata)))
15354 `(("r-knitr" ,r-knitr)))
15355 (home-page "https://github.com/r-spatial/spdep/")
15356 (synopsis "Spatial dependence: weighting schemes, statistics and models")
15358 "This package provides a collection of functions to create spatial
15359 weights matrix objects from polygon contiguities, from point patterns by
15360 distance and tessellations, for summarizing these objects, and for permitting
15361 their use in spatial data analysis, including regional aggregation by minimum
15363 (license license:gpl2+)))
15365 (define-public r-adegenet
15367 (name "r-adegenet")
15372 (uri (cran-uri "adegenet" version))
15375 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
15376 (build-system r-build-system)
15378 `(("r-ade4" ,r-ade4)
15381 ("r-dplyr" ,r-dplyr)
15382 ("r-ggplot2" ,r-ggplot2)
15383 ("r-igraph" ,r-igraph)
15385 ("r-reshape2" ,r-reshape2)
15386 ("r-seqinr" ,r-seqinr)
15387 ("r-shiny" ,r-shiny)
15388 ("r-spdep" ,r-spdep)
15389 ("r-vegan" ,r-vegan)))
15390 (home-page "https://github.com/thibautjombart/adegenet")
15391 (synopsis "Exploratory analysis of genetic and genomic data")
15393 "This package provides a toolset for the exploration of genetic and
15394 genomic data. Adegenet provides formal (S4) classes for storing and handling
15395 various genetic data, including genetic markers with varying ploidy and
15396 hierarchical population structure (@code{genind} class), alleles counts by
15397 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
15398 also implements original multivariate methods (DAPC, sPCA), graphics,
15399 statistical tests, simulation tools, distance and similarity measures, and
15400 several spatial methods. A range of both empirical and simulated datasets is
15401 also provided to illustrate various methods.")
15402 (license license:gpl2+)))
15404 (define-public r-pegas
15411 (uri (cran-uri "pegas" version))
15413 (base32 "0lr06gajzdanj8ax91kgpxsj863m367v2s1z5gnxps3999n0xybx"))))
15414 (build-system r-build-system)
15416 `(("r-adegenet" ,r-adegenet)
15418 (home-page "http://ape-package.ird.fr/pegas.html")
15419 (synopsis "Population and evolutionary genetics analysis system")
15421 "This package provides functions for reading, writing, plotting,
15422 analysing, and manipulating allelic and haplotypic data, including from VCF
15423 files, and for the analysis of population nucleotide sequences and
15424 micro-satellites including coalescent analyses, linkage disequilibrium,
15425 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
15426 minimum spanning tree and network, and median-joining networks.")
15427 (license license:gpl2+)))
15429 (define-public r-rmetasim
15431 (name "r-rmetasim")
15436 (uri (cran-uri "rmetasim" version))
15439 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
15440 (build-system r-build-system)
15442 `(("r-ade4" ,r-ade4)
15443 ("r-adegenet" ,r-adegenet)
15444 ("r-gtools" ,r-gtools)
15445 ("r-pegas" ,r-pegas)))
15446 (home-page "https://cran.r-project.org/web/packages/rmetasim")
15447 (synopsis "Individual-based population genetic simulation environment")
15449 "This package provides an interface between R and the metasim simulation
15450 engine. The simulation environment is documented in: Strand, A.(2002),
15451 Metasim 1.0: an individual-based environment for simulating population
15452 genetics of complex population dynamics.")
15454 (license license:gpl2+)))
15456 (define-public r-genetics
15458 (name "r-genetics")
15459 (version "1.3.8.1.2")
15463 (uri (cran-uri "genetics" version))
15466 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
15467 (build-system r-build-system)
15469 `(("r-combinat" ,r-combinat)
15470 ("r-gdata" ,r-gdata)
15471 ("r-gtools" ,r-gtools)
15473 ("r-mvtnorm" ,r-mvtnorm)))
15474 (home-page "https://cran.r-project.org/web/packages/genetics/")
15475 (synopsis "Population genetics")
15477 "This package provides classes and methods for handling genetic data.
15478 It includes classes to represent genotypes and haplotypes at single markers up
15479 to multiple markers on multiple chromosomes. Function include allele
15480 frequencies, flagging homo/heterozygotes, flagging carriers of certain
15481 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
15482 and testing for linkage disequilibrium, ...")
15483 ;; Any GPL version.
15484 (license license:gpl2+)))
15486 (define-public r-snp-plotter
15488 (name "r-snp-plotter")
15493 (uri (cran-uri "snp.plotter" version))
15496 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
15497 (properties `((upstream-name . "snp.plotter")))
15498 (build-system r-build-system)
15499 (propagated-inputs `(("r-genetics" ,r-genetics)))
15500 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
15501 (synopsis "Plot p-values using single SNP and/or haplotype data")
15503 "This package helps you create plots of p-values using single SNP and/or
15504 haplotype data. Main features of the package include options to display a
15505 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
15506 datasets simultaneously. Plots can be created using global and/or individual
15507 haplotype p-values along with single SNP p-values. Images are created as
15508 either PDF/EPS files.")
15509 (license license:gpl2+)))
15511 (define-public r-polspline
15513 (name "r-polspline")
15518 (uri (cran-uri "polspline" version))
15520 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
15521 (build-system r-build-system)
15522 (native-inputs `(("gfortran" ,gfortran)))
15523 (home-page "https://cran.r-project.org/web/packages/polspline/")
15524 (synopsis "Polynomial spline routines")
15526 "This package provides routines for the polynomial spline fitting
15527 routines hazard regression, hazard estimation with flexible tails, logspline,
15528 lspec, polyclass, and polymars.")
15529 (license license:gpl2+)))
15531 (define-public r-rms
15538 (uri (cran-uri "rms" version))
15540 (base32 "1zgfd60lzbakcv7x0i5k3lkw3s0xx5bzssjgangna5lq2j17cdli"))))
15541 (build-system r-build-system)
15543 `(("r-cluster" ,r-cluster)
15544 ("r-digest" ,r-digest)
15545 ("r-ggplot2" ,r-ggplot2)
15546 ("r-hmisc" ,r-hmisc)
15547 ("r-htmltable" ,r-htmltable)
15548 ("r-htmltools" ,r-htmltools)
15549 ("r-lattice" ,r-lattice)
15551 ("r-multcomp" ,r-multcomp)
15553 ("r-polspline" ,r-polspline)
15554 ("r-quantreg" ,r-quantreg)
15555 ("r-rpart" ,r-rpart)
15556 ("r-sparsem" ,r-sparsem)
15557 ("r-survival" ,r-survival)))
15558 (native-inputs `(("gfortran" ,gfortran)))
15559 (home-page "http://biostat.mc.vanderbilt.edu/rms")
15560 (synopsis "Regression modeling strategies")
15562 "This is a package for regression modeling, testing, estimation,
15563 validation, graphics, prediction, and typesetting by storing enhanced model
15564 design attributes in the fit. The rms package is a collection of functions
15565 that assist with and streamline modeling. It also contains functions for
15566 binary and ordinal logistic regression models, ordinal models for continuous Y
15567 with a variety of distribution families, and the Buckley-James multiple
15568 regression model for right-censored responses, and implements penalized
15569 maximum likelihood estimation for logistic and ordinary linear models. The
15570 package works with almost any regression model, but it was especially written
15571 to work with binary or ordinal regression models, Cox regression, accelerated
15572 failure time models, ordinary linear models, the Buckley-James model,
15573 generalized least squares for serially or spatially correlated observations,
15574 generalized linear models, and quantile regression.")
15575 (license license:gpl2+)))
15577 (define-public r-arsenal
15584 (uri (cran-uri "arsenal" version))
15587 "13ql3rb79a764ppsc1sqi8glzzkw79la0j2ahzbxgz7cz879sazy"))))
15588 (properties `((upstream-name . "arsenal")))
15589 (build-system r-build-system)
15590 (propagated-inputs `(("r-knitr" ,r-knitr)))
15591 (native-inputs `(("r-knitr" ,r-knitr)))
15592 (home-page "https://github.com/mayoverse/arsenal")
15593 (synopsis "Functions for large-scale statistical summaries")
15595 "This package provides an arsenal of R functions for large-scale
15596 statistical summaries, which are streamlined to work within the latest
15597 reporting tools in R and RStudio and which use formulas and versatile
15598 summary statistics for summary tables and models. The primary functions
15602 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
15603 levels of one or more categorical variables;
15604 @item @code{paired}, a Table-1-like summary of multiple variable types paired
15605 across two time points;
15606 @item @code{modelsum}, which performs simple model fits on one or more
15607 endpoints for many variables (univariate or adjusted for covariates);
15608 @item @code{freqlist}, a powerful frequency table across many categorical
15610 @item @code{comparedf}, a function for comparing @code{data.frames}; and
15611 @item @code{write2}, a function to output tables to a document.
15614 (license license:gpl2+)))
15616 (define-public r-haplo-stats
15618 (name "r-haplo-stats")
15623 (uri (cran-uri "haplo.stats" version))
15626 "1imz4gs0n57vixwwbirrihpgvn2pyj5da4rgjcjk14n2xkk0nay7"))))
15627 (properties `((upstream-name . "haplo.stats")))
15628 (build-system r-build-system)
15630 `(("r-arsenal" ,r-arsenal)
15633 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
15634 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
15635 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
15637 "This package provides routines for the analysis of indirectly measured
15638 haplotypes. The statistical methods assume that all subjects are unrelated
15639 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
15640 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
15641 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
15642 examples in the vignette.")
15643 (license license:gpl2+)))
15645 (define-public r-bqtl
15652 (uri (cran-uri "bqtl" version))
15655 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
15656 (build-system r-build-system)
15657 (native-inputs `(("gfortran" ,gfortran)))
15658 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
15659 (synopsis "Bayesian QTL mapping toolkit")
15661 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
15662 lines. It includes maximum likelihood and Bayesian tools.")
15663 (license license:gpl2+)))
15665 (define-public r-ibdreg
15672 (uri (cran-uri "ibdreg" version))
15675 "0kgx9iavgm6d6njhki7bm82d6lw2c7kcch2pryd339js2hm0l5gq"))))
15676 (build-system r-build-system)
15677 (home-page "https://www.mayo.edu/research/labs/\
15678 statistical-genetics-genetic-epidemiology/software")
15679 (synopsis "Regression methods for IBD linkage with covariates")
15681 "This package provides a method to test genetic linkage with covariates
15682 by regression methods with response IBD sharing for relative pairs. Account
15683 for correlations of IBD statistics and covariates for relative pairs within
15684 the same pedigree.")
15685 (license license:gpl2+)))
15687 (define-public r-dlmap
15694 (uri (cran-uri "dlmap" version))
15697 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
15698 (build-system r-build-system)
15700 `(("r-ibdreg" ,r-ibdreg)
15704 ("r-wgaim" ,r-wgaim)))
15705 (home-page "https://cran.r-project.org/web/packages/dlmap/")
15706 (synopsis "Detection localization mapping for QTL")
15708 "This is package for QTL mapping in a mixed model framework with separate
15709 detection and localization stages. The first stage detects the number of QTL
15710 on each chromosome based on the genetic variation due to grouped markers on
15711 the chromosome; the second stage uses this information to determine the most
15712 likely QTL positions. The mixed model can accommodate general fixed and
15713 random effects, including spatial effects in field trials and pedigree
15714 effects. It is applicable to backcrosses, doubled haploids, recombinant
15715 inbred lines, F2 intercrosses, and association mapping populations.")
15716 (license license:gpl2)))
15718 (define-public r-hwde
15725 (uri (cran-uri "hwde" version))
15728 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
15729 (build-system r-build-system)
15730 (home-page "https://cran.r-project.org/web/packages/hwde/")
15731 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
15733 "This package fits models for genotypic disequilibria, as described in
15734 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
15735 terms are available that account for first order interactions between loci.
15736 It also implements, for a single locus in a single population, a conditional
15737 exact test for Hardy-Weinberg equilibrium.")
15738 (license license:gpl2+)))
15740 (define-public r-tdthap
15747 (uri (cran-uri "tdthap" version))
15750 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
15751 (build-system r-build-system)
15752 (home-page "https://cran.r-project.org/web/packages/tdthap/")
15753 (synopsis "TDT tests for extended haplotypes")
15755 "Functions and examples are provided for transmission/disequilibrium
15756 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
15757 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
15758 (license license:artistic2.0)))
15760 (define-public r-sparql
15766 (uri (cran-uri "SPARQL" version))
15769 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
15770 (properties `((upstream-name . "SPARQL")))
15771 (build-system r-build-system)
15773 `(("r-rcurl" ,r-rcurl)
15775 (home-page "https://cran.r-project.org/web/packages/SPARQL")
15776 (synopsis "SPARQL client for R")
15777 (description "This package provides an interface to use SPARQL to pose
15778 SELECT or UPDATE queries to an end-point.")
15779 ;; The only license indication is found in the DESCRIPTION file,
15780 ;; which states GPL-3. So we cannot assume GPLv3+.
15781 (license license:gpl3)))
15783 (define-public r-bookdown
15785 (name "r-bookdown")
15789 (uri (cran-uri "bookdown" version))
15792 "0xms1srx9l2mn8xaxnpic0s21y8k56bhwpj45wy7b0yscmxgmh27"))))
15793 (build-system r-build-system)
15795 `(("r-htmltools" ,r-htmltools)
15796 ("r-knitr" ,r-knitr)
15797 ("r-rmarkdown" ,r-rmarkdown)
15798 ("r-tinytex" ,r-tinytex)
15801 ("pandoc" ,pandoc)))
15802 (home-page "https://github.com/rstudio/bookdown")
15803 (synopsis "Authoring books and technical documents with R markdown")
15804 (description "This package provides output formats and utilities for
15805 authoring books and technical documents with R Markdown.")
15806 (license license:gpl3)))
15808 (define-public r-optparse
15810 (name "r-optparse")
15815 (uri (cran-uri "optparse" version))
15818 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
15819 (build-system r-build-system)
15821 `(("r-getopt" ,r-getopt)))
15823 `(("r-knitr" ,r-knitr)))
15824 (home-page "https://github.com/trevorld/optparse")
15825 (synopsis "Command line option parser")
15827 "This package provides a command line parser inspired by Python's
15828 @code{optparse} library to be used with Rscript to write shebang scripts
15829 that accept short and long options.")
15830 (license license:gpl2+)))
15832 (define-public r-kernlab
15839 (uri (cran-uri "kernlab" version))
15841 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
15842 (build-system r-build-system)
15843 (home-page "https://cran.r-project.org/web/packages/kernlab")
15844 (synopsis "Kernel-based machine learning tools")
15846 "This package provides kernel-based machine learning methods for
15847 classification, regression, clustering, novelty detection, quantile regression
15848 and dimensionality reduction. Among other methods @code{kernlab} includes
15849 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
15851 (license license:gpl2)))
15853 (define-public r-hierfstat
15855 (name "r-hierfstat")
15860 (uri (cran-uri "hierfstat" version))
15863 "0dp8k1z5a8gqnax99y1hwfvxilzf4n2i751zr0z6ihrzirsvb3m3"))))
15864 (build-system r-build-system)
15866 `(("r-ade4" ,r-ade4)
15867 ("r-adegenet" ,r-adegenet)
15868 ("r-gaston" ,r-gaston)
15869 ("r-gtools" ,r-gtools)))
15871 `(("r-knitr" ,r-knitr)))
15872 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
15873 (synopsis "Estimation and tests of hierarchical F-statistics")
15875 "This package allows the estimation of hierarchical F-statistics from
15876 haploid or diploid genetic data with any numbers of levels in the hierarchy,
15877 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
15878 are also given to test via randomisations the significance of each F and
15879 variance components, using the likelihood-ratio statistics G.")
15880 (license license:gpl2+)))
15882 (define-public r-hapassoc
15884 (name "r-hapassoc")
15889 (uri (cran-uri "hapassoc" version))
15892 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
15893 (build-system r-build-system)
15894 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
15895 (synopsis "Inference of trait associations with SNP haplotypes")
15897 "Hapassoc performs likelihood inference of trait associations with
15898 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
15899 functions are developed primarily for data collected in cohort or
15900 cross-sectional studies. They can accommodate uncertain haplotype phase and
15901 handle missing genotypes at some SNPs.")
15902 (license license:gpl2)))
15904 (define-public r-sampling
15906 (name "r-sampling")
15911 (uri (cran-uri "sampling" version))
15914 "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz"))))
15915 (build-system r-build-system)
15917 `(("r-lpsolve" ,r-lpsolve)
15918 ("r-mass" ,r-mass)))
15919 (home-page "https://cran.r-project.org/web/packages/sampling/")
15920 (synopsis "Survey sampling")
15922 "This package provides functions for drawing and calibrating samples.")
15923 (license license:gpl2+)))
15925 (define-public r-r2html
15932 (uri (cran-uri "R2HTML" version))
15935 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
15936 (properties `((upstream-name . "R2HTML")))
15937 (build-system r-build-system)
15938 (home-page "https://github.com/nalimilan/R2HTML")
15939 (synopsis "HTML export for R objects")
15941 "This package includes HTML functions and methods to write in an HTML
15942 file. Thus, making HTML reports is easy. It includes a function that allows
15943 redirection on the fly, which appears to be very useful for teaching purposes,
15944 as the student can keep a copy of the produced output to keep all that they
15945 did during the course. The package comes with a vignette describing how to
15946 write HTML reports for statistical analysis. Finally, a driver for Sweave
15947 parses HTML flat files containing R code and to automatically write
15948 the corresponding outputs (tables and graphs).")
15949 (license license:gpl2+)))
15951 (define-public r-rjava
15958 (uri (cran-uri "rJava" version))
15961 "1x3mihyqzr61j52rwaqciw43mkjzmhib4s6qf57v6xj40ksqh5jv"))))
15962 (properties `((upstream-name . "rJava")))
15963 (build-system r-build-system)
15965 `(#:modules ((guix build utils)
15966 (guix build r-build-system)
15969 (modify-phases %standard-phases
15970 (add-after 'unpack 'set-JAVA_HOME
15971 (lambda* (#:key inputs #:allow-other-keys)
15972 (let ((jdk (assoc-ref inputs "jdk")))
15973 (setenv "JAVA_HOME" jdk)
15974 (setenv "JAVA" (which "java"))
15975 (setenv "JAR" (which "jar"))
15976 (setenv "JAVAC" (which "javac"))
15977 (setenv "JAVAH" (which "javah"))
15978 (setenv "JAVA_CPPFLAGS"
15979 (string-append "-I" jdk "/include "
15980 "-I" jdk "/include/linux"))
15981 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
15982 ((lib) (setenv "JAVA_LIBS" lib))
15983 (_ (error "Could not find libjvm.so"))))
15987 ("jdk" ,icedtea-8 "jdk")
15990 (home-page "https://www.rforge.net/rJava/")
15991 (synopsis "Low-Level R to Java interface")
15993 "This package provides a low-level interface to the Java VM very much
15994 like .C/.Call and friends. It allows the creation of objects, calling methods
15995 and accessing fields.")
15996 (license license:gpl2)))
15998 (define-public r-svmisc
16005 (uri (cran-uri "svMisc" version))
16008 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
16009 (properties `((upstream-name . "svMisc")))
16010 (build-system r-build-system)
16011 (home-page "https://github.com/SciViews/svMisc")
16012 (synopsis "Miscellaneous functions for SciViews")
16014 "This package provides miscellaneous functions for SciViews or general
16015 use, including tools to manage a temporary environment attached to the search
16016 path for temporary variables you do not want to @code{save()} or
16017 @code{load()}; test the current platform; showing progress bars, etc.")
16018 (license license:gpl2)))
16020 (define-public r-xyz
16027 (uri (cran-uri "xyz" version))
16030 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
16031 (build-system r-build-system)
16033 `(("r-rcpp" ,r-rcpp)))
16034 (home-page "https://cran.r-project.org/web/packages/xyz/")
16035 (synopsis "Algorithm for fast interaction search in high-dimensional data")
16037 "High dimensional interaction search by brute force requires a quadratic
16038 computational cost in the number of variables. The xyz algorithm provably
16039 finds strong interactions in almost linear time. For details of the algorithm
16040 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
16041 interaction search in high-dimensional data.")
16042 ;; Any version of the GPL.
16043 (license license:gpl2+)))
16045 (define-public r-rttf2pt1
16047 (name "r-rttf2pt1")
16052 (uri (cran-uri "Rttf2pt1" version))
16055 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
16056 (properties `((upstream-name . "Rttf2pt1")))
16057 (build-system r-build-system)
16058 (home-page "https://github.com/wch/Rttf2pt1")
16059 (synopsis "Font conversion utility")
16061 "This package contains the program @code{ttf2pt1}, for use with the
16062 @code{extrafont} package.")
16063 ;; Most of the files are covered under the Expat license. Some files are
16064 ;; covered under BSD-3. Deviations for individual files are recorded in
16065 ;; the LICENSE file.
16066 (license (list license:bsd-3 license:expat
16067 (license:non-copyleft "file://LICENSE")))))
16069 (define-public r-extrafontdb
16071 (name "r-extrafontdb")
16076 (uri (cran-uri "extrafontdb" version))
16079 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
16080 (build-system r-build-system)
16081 (home-page "https://github.com/wch/extrafontdb")
16082 (synopsis "Database for the extrafont package")
16084 "This package holds the database for the @code{extrafont} package.")
16085 (license license:gpl2)))
16087 (define-public r-extrafont
16089 (name "r-extrafont")
16094 (uri (cran-uri "extrafont" version))
16097 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
16098 (build-system r-build-system)
16100 `(("r-extrafontdb" ,r-extrafontdb)
16101 ("r-rttf2pt1" ,r-rttf2pt1)))
16102 (home-page "https://github.com/wch/extrafont")
16103 (synopsis "Tools for using fonts in R")
16105 "The extrafont package makes it easier to use fonts other than the basic
16106 PostScript fonts that R uses. Fonts that are imported into extrafont can be
16107 used with PDF or PostScript output files. There are two hurdles for using
16108 fonts in PDF (or Postscript) output files:
16111 @item Making R aware of the font and the dimensions of the characters.
16112 @item Embedding the fonts in the PDF file so that the PDF can be displayed
16113 properly on a device that doesn't have the font. This is usually needed if
16114 you want to print the PDF file or share it with others.
16117 The extrafont package makes both of these things easier.")
16118 (license license:gpl2)))
16120 (define-public r-xkcd
16127 (uri (cran-uri "xkcd" version))
16130 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
16131 (build-system r-build-system)
16133 `(("r-extrafont" ,r-extrafont)
16134 ("r-ggplot2" ,r-ggplot2)
16135 ("r-hmisc" ,r-hmisc)))
16136 (home-page "https://cran.r-project.org/web/packages/xkcd/")
16137 (synopsis "Plot ggplot2 graphics in the XKCD style")
16139 "This package provides the means to plot ggplot2 graphs in the style of
16140 the XKCD web comic.")
16141 (license license:gpl3)))
16143 (define-public r-msigdbr
16150 (uri (cran-uri "msigdbr" version))
16153 "1rc2p9vw57pn4prmfgay4w18qd53ggq7wxfsi9kp7w25ciip1dq1"))))
16154 (build-system r-build-system)
16156 `(("r-dplyr" ,r-dplyr)
16157 ("r-magrittr" ,r-magrittr)
16158 ("r-rlang" ,r-rlang)
16159 ("r-tibble" ,r-tibble)
16160 ("r-tidyselect" ,r-tidyselect)))
16162 `(("r-knitr" ,r-knitr)))
16163 (home-page "https://github.com/igordot/msigdbr")
16164 (synopsis "MSigDB gene sets for multiple organisms")
16166 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
16167 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
16168 software in a standard R data frame with key-value pairs. Included are the
16169 original human gene symbols and Entrez IDs as well as the equivalents for
16170 various frequently studied model organisms such as mouse, rat, pig, fly, and
16172 ;; The package is covered under the Expat license, but the upstream MSigDB
16173 ;; files are made available under the Creative Commons Attribution 4.0
16174 ;; International license.
16175 (license (list license:expat license:cc-by4.0))))
16177 (define-public r-gridgraphics
16179 (name "r-gridgraphics")
16184 (uri (cran-uri "gridGraphics" version))
16187 "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219"))))
16188 (properties `((upstream-name . "gridGraphics")))
16189 (build-system r-build-system)
16190 (home-page "https://github.com/pmur002/gridgraphics")
16191 (synopsis "Redraw base graphics using @code{grid} graphics")
16193 "This package provides functions to convert a page of plots drawn with
16194 the @code{graphics} package into identical output drawn with the @code{grid}
16195 package. The result looks like the original @code{graphics}-based plot, but
16196 consists of @code{grid} grobs and viewports that can then be manipulated with
16197 @code{grid} functions (e.g., edit grobs and revisit viewports).")
16198 (license license:gpl2+)))
16200 (define-public r-farver
16207 (uri (cran-uri "farver" version))
16210 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
16211 (build-system r-build-system)
16212 (home-page "https://github.com/thomasp85/farver")
16213 (synopsis "Vectorized color conversion and comparison")
16215 "The encoding of color can be handled in many different ways, using
16216 different color spaces. As different color spaces have different uses,
16217 efficient conversion between these representations are important. This
16218 package provides a set of functions that gives access to very fast color space
16219 conversion and comparisons implemented in C++, and offers 100-fold speed
16220 improvements over the @code{convertColor} function in the @code{grDevices}
16222 (license license:expat)))
16224 (define-public r-ggplotify
16226 (name "r-ggplotify")
16231 (uri (cran-uri "ggplotify" version))
16234 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
16235 (build-system r-build-system)
16237 `(("r-ggplot2" ,r-ggplot2)
16238 ("r-gridgraphics" ,r-gridgraphics)
16239 ("r-rvcheck" ,r-rvcheck)))
16241 `(("r-knitr" ,r-knitr)))
16242 (home-page "https://github.com/GuangchuangYu/ggplotify")
16243 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
16245 "This package provides tools to convert plot function calls (using
16246 expression or formula) to @code{grob} or @code{ggplot} objects that are
16247 compatible with the @code{grid} and @code{ggplot2} environment. With this
16248 package, we are able to e.g. use @code{cowplot} to align plots produced by
16249 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
16250 converting them to @code{ggplot} objects.")
16251 (license license:artistic2.0)))
16253 (define-public r-triebeard
16255 (name "r-triebeard")
16260 (uri (cran-uri "triebeard" version))
16263 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
16264 (build-system r-build-system)
16265 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16266 (home-page "https://github.com/Ironholds/triebeard/")
16267 (synopsis "Radix trees in Rcpp")
16269 "Radix trees, or tries, are key-value data structures optimized for
16270 efficient lookups, similar in purpose to hash tables. This package provides
16271 an implementation of radix trees for use in R programming and in developing
16272 packages with Rcpp.")
16273 (license license:expat)))
16275 (define-public r-tweenr
16282 (uri (cran-uri "tweenr" version))
16285 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
16286 (build-system r-build-system)
16288 `(("r-farver" ,r-farver)
16289 ("r-magrittr" ,r-magrittr)
16291 ("r-rlang" ,r-rlang)))
16292 (home-page "https://github.com/thomasp85/tweenr")
16293 (synopsis "Interpolate data for smooth animations")
16295 "In order to create smooth animation between states of data, tweening is
16296 necessary. This package provides a range of functions for creating tweened
16297 data that can be used as basis for animation. Furthermore it adds a number of
16298 vectorized interpolaters for common R data types such as numeric, date and
16300 (license license:expat)))
16302 (define-public r-polyclip
16304 (name "r-polyclip")
16309 (uri (cran-uri "polyclip" version))
16312 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
16313 (build-system r-build-system)
16314 (native-inputs `(("pkg-config" ,pkg-config)))
16315 (home-page "http://www.angusj.com/delphi/clipper.php")
16316 (synopsis "Polygon clipping")
16318 "This package provides an R port of the library Clipper. It performs
16319 polygon clipping operations (intersection, union, set minus, set difference)
16320 for polygonal regions of arbitrary complexity, including holes. It computes
16321 offset polygons (spatial buffer zones, morphological dilations, Minkowski
16322 dilations) for polygonal regions and polygonal lines. It computes the
16323 Minkowski Sum of general polygons. There is a function for removing
16324 self-intersections from polygon data.")
16325 (license license:boost1.0)))
16327 (define-public r-urltools
16329 (name "r-urltools")
16334 (uri (cran-uri "urltools" version))
16337 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
16338 (build-system r-build-system)
16340 `(("r-rcpp" ,r-rcpp)
16341 ("r-triebeard" ,r-triebeard)))
16342 (home-page "https://github.com/Ironholds/urltools/")
16343 (synopsis "Vectorized tools for URL handling and parsing")
16345 "This package provides a toolkit for all URL-handling needs, including
16346 encoding and decoding, parsing, parameter extraction and modification. All
16347 functions are designed to be both fast and entirely vectorized. It is
16348 intended to be useful for people dealing with web-related datasets, such as
16349 server-side logs, although may be useful for other situations involving large
16351 (license license:expat)))
16353 (define-public r-ggforce
16360 (uri (cran-uri "ggforce" version))
16363 "1lplxyq5bgx90dgaimhynpcywag1gp6vlsy7q52ay1nfc35qmkjc"))))
16364 (build-system r-build-system)
16366 `(("r-ggplot2" ,r-ggplot2)
16367 ("r-gtable" ,r-gtable)
16369 ("r-polyclip" ,r-polyclip)
16371 ("r-rcppeigen" ,r-rcppeigen)
16372 ("r-rlang" ,r-rlang)
16373 ("r-scales" ,r-scales)
16374 ("r-tidyselect" ,r-tidyselect)
16375 ("r-tweenr" ,r-tweenr)
16376 ("r-withr" ,r-withr)))
16377 (home-page "https://ggforce.data-imaginist.com")
16378 (synopsis "Accelerating ggplot2")
16380 "The aim of the ggplot2 package is to aid in visual data investigations.
16381 This focus has led to a lack of facilities for composing specialized plots.
16382 Thi package aims to be a collection of mainly new statistics and geometries
16383 that fills this gap.")
16384 (license license:expat)))
16386 (define-public r-europepmc
16388 (name "r-europepmc")
16393 (uri (cran-uri "europepmc" version))
16396 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
16397 (build-system r-build-system)
16399 `(("r-dplyr" ,r-dplyr)
16401 ("r-jsonlite" ,r-jsonlite)
16403 ("r-progress" ,r-progress)
16404 ("r-purrr" ,r-purrr)
16405 ("r-rlang" ,r-rlang)
16406 ("r-tibble" ,r-tibble)
16407 ("r-tidyr" ,r-tidyr)
16408 ("r-urltools" ,r-urltools)
16409 ("r-xml2" ,r-xml2)))
16411 `(("r-knitr" ,r-knitr)))
16412 (home-page "https://github.com/ropensci/europepmc/")
16413 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
16415 "This package provides an R Client for the
16416 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
16417 Service}. It gives access to both metadata on life science literature and
16418 open access full texts. Europe PMC indexes all PubMed content and other
16419 literature sources including Agricola, a bibliographic database of citations
16420 to the agricultural literature, or Biological Patents. In addition to
16421 bibliographic metadata, the client allows users to fetch citations and
16422 reference lists. Links between life-science literature and other EBI
16423 databases, including ENA, PDB or ChEMBL are also accessible.")
16424 (license license:gpl3)))
16426 (define-public r-ggraph
16433 (uri (cran-uri "ggraph" version))
16436 "1j3xf4fsv0i0gbppdrw4yprfyk53wx6s8nvnkipi2ywbm7cr4q4w"))))
16437 (build-system r-build-system)
16439 `(("r-digest" ,r-digest)
16440 ("r-dplyr" ,r-dplyr)
16441 ("r-ggforce" ,r-ggforce)
16442 ("r-ggplot2" ,r-ggplot2)
16443 ("r-ggrepel" ,r-ggrepel)
16444 ("r-graphlayouts" ,r-graphlayouts)
16445 ("r-gtable" ,r-gtable)
16446 ("r-igraph" ,r-igraph)
16449 ("r-rlang" ,r-rlang)
16450 ("r-scales" ,r-scales)
16451 ("r-tidygraph" ,r-tidygraph)
16452 ("r-viridis" ,r-viridis)
16453 ("r-withr" ,r-withr)))
16455 `(("r-knitr" ,r-knitr)))
16456 (home-page "https://cran.r-project.org/web/packages/ggraph/")
16457 (synopsis "Implementation of grammar of graphics for graphs and networks")
16459 "The grammar of graphics as implemented in ggplot2 is a poor fit for
16460 graph and network visualizations due to its reliance on tabular data input.
16461 The ggraph package is an extension of the ggplot2 API tailored to graph
16462 visualizations and provides the same flexible approach to building up plots
16464 (license license:gpl3)))
16466 (define-public r-varselrf
16468 (name "r-varselrf")
16473 (uri (cran-uri "varSelRF" version))
16476 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
16477 (properties `((upstream-name . "varSelRF")))
16478 (build-system r-build-system)
16480 `(("r-randomforest" ,r-randomforest)))
16481 (home-page "https://www.ligarto.org/rdiaz/software/software")
16482 (synopsis "Variable selection using random forests")
16484 "This package provides tools for the variable selection from random
16485 forests using both backwards variable elimination (for the selection of small
16486 sets of non-redundant variables) and selection based on the importance
16487 spectrum (somewhat similar to scree plots; for the selection of large,
16488 potentially highly-correlated variables). The main applications are in
16489 high-dimensional data (e.g., microarray data, and other genomics and
16490 proteomics applications).")
16491 (license license:gpl2+)))
16493 (define-public r-pamr
16500 (uri (cran-uri "pamr" version))
16503 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
16504 (build-system r-build-system)
16506 `(("r-cluster" ,r-cluster)
16507 ("r-survival" ,r-survival)))
16508 (native-inputs `(("gfortran" ,gfortran)))
16509 (home-page "https://cran.r-project.org/web/packages/pamr/")
16510 (synopsis "Prediction Analysis for Microarrays")
16512 "This package provides some functions for sample classification in
16514 (license license:gpl2)))
16516 (define-public r-rda
16519 (version "1.0.2-2.1")
16523 (uri (cran-uri "rda" version))
16526 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
16527 (build-system r-build-system)
16528 (home-page "https://cran.r-project.org/web/packages/rda/")
16529 (synopsis "Shrunken centroids regularized discriminant analysis")
16531 "This package provides tools for shrunken centroids regularized
16532 discriminant analysis for the purpose of classifying high dimensional data.")
16533 (license license:gpl2+)))
16535 (define-public r-ggvis
16542 (uri (cran-uri "ggvis" version))
16545 "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy"))))
16546 (build-system r-build-system)
16548 `(("r-assertthat" ,r-assertthat)
16549 ("r-dplyr" ,r-dplyr)
16550 ("r-htmltools" ,r-htmltools)
16551 ("r-jsonlite" ,r-jsonlite)
16552 ("r-magrittr" ,r-magrittr)
16553 ("r-rlang" ,r-rlang)
16554 ("r-shiny" ,r-shiny)))
16555 (home-page "https://ggvis.rstudio.com/")
16556 (synopsis "Interactive grammar of graphics")
16558 "This package is a data visualization package for R providing an
16559 implementation of an interactive grammar of graphics, taking the best parts of
16560 ggplot2, combining them with the reactive framework of Shiny and drawing web
16561 graphics using Vega.")
16562 (license license:gpl2)))
16564 (define-public r-gbm
16571 (uri (cran-uri "gbm" version))
16574 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
16575 (build-system r-build-system)
16577 `(("r-lattice" ,r-lattice)
16578 ("r-survival" ,r-survival)))
16580 `(("r-knitr" ,r-knitr)))
16581 (home-page "https://github.com/gbm-developers/gbm")
16582 (synopsis "Generalized boosted regression models")
16584 "This package is an implementation of extensions to Freund and Schapire's
16585 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
16586 regression methods for least squares, absolute loss, t-distribution loss,
16587 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
16588 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
16589 and Learning to Rank measures (LambdaMart).")
16590 (license license:gpl2+)))
16592 (define-public r-threejs
16599 (uri (cran-uri "threejs" version))
16602 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
16603 (build-system r-build-system)
16605 `(#:modules ((guix build utils)
16606 (guix build r-build-system)
16610 (modify-phases %standard-phases
16611 (add-after 'unpack 'process-javascript
16612 (lambda* (#:key inputs #:allow-other-keys)
16613 (with-directory-excursion "inst"
16617 `((,(assoc-ref inputs "js-jquery")
16618 "htmlwidgets/lib/jquery/jquery.min.js")
16619 (,(assoc-ref inputs "js-threejs-111")
16620 "htmlwidgets/lib/threejs-111/three.min.js"))))
16621 (lambda (sources targets)
16622 (for-each (lambda (source target)
16623 (format #t "Processing ~a --> ~a~%"
16625 (delete-file target)
16626 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16627 (call-with-output-file target
16629 (dump-port minified port)))))
16630 sources targets))))
16633 `(("r-base64enc" ,r-base64enc)
16634 ("r-crosstalk" ,r-crosstalk)
16635 ("r-htmlwidgets" ,r-htmlwidgets)
16636 ("r-igraph" ,r-igraph)))
16638 `(("uglify-js" ,uglify-js)
16642 (uri "https://code.jquery.com/jquery-1.12.4.js")
16645 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
16649 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
16652 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
16653 (home-page "https://bwlewis.github.io/rthreejs")
16654 (synopsis "Interactive 3D scatter plots, networks and globes")
16656 "Create interactive 3D scatter plots, network plots, and globes in R
16657 using the three.js visualization library.")
16658 (license license:expat)))
16660 (define-public r-mlbench
16667 (uri (cran-uri "mlbench" version))
16670 "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi"))))
16671 (build-system r-build-system)
16672 (home-page "https://cran.r-project.org/web/packages/mlbench/")
16673 (synopsis "Machine learning benchmark problems")
16675 "This package provides a collection of artificial and real-world machine
16676 learning benchmark problems, including, e.g., several data sets from the UCI
16678 (license license:gpl2)))
16680 (define-public r-mpm
16687 (uri (cran-uri "mpm" version))
16690 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
16691 (build-system r-build-system)
16693 `(("r-kernsmooth" ,r-kernsmooth)
16694 ("r-mass" ,r-mass)))
16695 (home-page "http://mpm.r-forge.r-project.org")
16696 (synopsis "Multivariate projection methods")
16698 "This is a package for exploratory graphical analysis of multivariate
16699 data, specifically gene expression data with different projection methods:
16700 principal component analysis, correspondence analysis, spectral map
16702 (license license:gpl2+)))
16704 (define-public r-png
16710 (uri (cran-uri "png" version))
16713 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
16714 (build-system r-build-system)
16716 `(("libpng" ,libpng)
16718 (home-page "https://www.rforge.net/png/")
16719 (synopsis "Read and write PNG images")
16721 "This package provides an easy and simple way to read, write and display
16722 bitmap images stored in the PNG format. It can read and write both files and
16723 in-memory raw vectors.")
16724 ;; Any of these GPL versions.
16725 (license (list license:gpl2 license:gpl3))))
16727 (define-public r-ggcorrplot
16729 (name "r-ggcorrplot")
16734 (uri (cran-uri "ggcorrplot" version))
16737 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
16738 (build-system r-build-system)
16740 `(("r-ggplot2" ,r-ggplot2)
16741 ("r-reshape2" ,r-reshape2)))
16742 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
16743 (synopsis "Visualization of a correlation matrix using ggplot2")
16745 "The ggcorrplot package can be used to visualize easily a correlation
16746 matrix using ggplot2. It provides a solution for reordering the correlation
16747 matrix and displays the significance level on the plot. It also includes a
16748 function for computing a matrix of correlation p-values.")
16749 (license license:gpl2)))
16751 (define-public r-gridtext
16753 (name "r-gridtext")
16758 (uri (cran-uri "gridtext" version))
16761 "131kw7nkfwksviwfifd2kk7lyvhxzzzv1nnj8rahkr3dik3akk61"))))
16762 (properties `((upstream-name . "gridtext")))
16763 (build-system r-build-system)
16765 `(("r-jpeg" ,r-jpeg)
16766 ("r-markdown" ,r-markdown)
16769 ("r-rcurl" ,r-rcurl)
16770 ("r-rlang" ,r-rlang)
16771 ("r-stringr" ,r-stringr)
16772 ("r-xml2" ,r-xml2)))
16773 (home-page "https://wilkelab.org/gridtext/")
16774 (synopsis "Improved text rendering support for Grid graphics")
16776 "This package provides support for rendering of formatted text using Grid
16777 graphics. Text can be formatted via a minimal subset of Markdown, HTML, and
16778 inline CSS directives, and it can be rendered both with and without word
16780 (license license:expat)))
16782 (define-public r-ggtext
16789 (uri (cran-uri "ggtext" version))
16792 "0n19dlcys8v7myfyckr6dnq0kx79k3sbh8nwx1jsx8pgzfbi8a2b"))))
16793 (properties `((upstream-name . "ggtext")))
16794 (build-system r-build-system)
16796 `(("r-ggplot2" ,r-ggplot2)
16797 ("r-gridtext" ,r-gridtext)
16798 ("r-rlang" ,r-rlang)
16799 ("r-scales" ,r-scales)))
16800 (native-inputs `(("r-knitr" ,r-knitr)))
16801 (home-page "https://wilkelab.org/ggtext/")
16802 (synopsis "Improved text rendering support for ggplot2")
16804 "This package provides a ggplot2 extension that enables the rendering of
16805 complex formatted plot labels (titles, subtitles, facet labels, axis labels,
16806 etc.). Text boxes with automatic word wrap are also supported.")
16807 (license license:gpl2)))
16809 ;; This package includes minified JavaScript files. When upgrading please
16810 ;; check that there are no new minified JavaScript files.
16811 (define-public r-flexdashboard
16813 (name "r-flexdashboard")
16818 (uri (cran-uri "flexdashboard" version))
16821 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
16822 (modules '((guix build utils)))
16825 ;; Delete bundled minified JavaScript files
16826 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
16827 (delete-file "inst/www/sly/sly.min.js")
16828 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
16829 (delete-file "inst/www/prism/prism.js")
16831 (build-system r-build-system)
16833 `(#:modules ((guix build utils)
16834 (guix build r-build-system)
16838 (ice-9 textual-ports))
16840 (modify-phases %standard-phases
16841 (add-after 'unpack 'process-javascript
16842 (lambda* (#:key inputs #:allow-other-keys)
16843 (with-directory-excursion "inst"
16844 ;; Concatenate all components of prism.js
16845 (let ((contents (string-join
16846 (map (lambda (name)
16847 (call-with-input-file
16848 (assoc-ref inputs name)
16852 "js-prism-line-numbers"))
16854 (call-with-output-file "prism-src.js"
16855 (cut display contents <>)))
16859 `(("www/stickytableheaders/jquery.stickytableheaders.js"
16860 "www/stickytableheaders/jquery.stickytableheaders.min.js")
16862 "www/sly/sly.min.js")
16864 "www/prism/prism.js")
16865 (,(assoc-ref inputs "js-raphael")
16866 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
16867 (,(assoc-ref inputs "js-featherlight")
16868 "www/featherlight/featherlight.min.js"))))
16869 (lambda (sources targets)
16870 (for-each (lambda (source target)
16871 (format #t "Processing ~a --> ~a~%"
16873 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16874 (call-with-output-file target
16876 (dump-port minified port)))))
16877 sources targets))))
16880 `(("r-htmltools" ,r-htmltools)
16881 ("r-htmlwidgets" ,r-htmlwidgets)
16882 ("r-jsonlite" ,r-jsonlite)
16883 ("r-knitr" ,r-knitr)
16884 ("r-rmarkdown" ,r-rmarkdown)
16885 ("r-shiny" ,r-shiny)))
16887 `(("uglify-js" ,uglify-js)
16891 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
16894 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
16898 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
16901 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
16905 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
16908 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
16909 ("js-prism-line-numbers"
16912 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
16915 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
16919 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
16922 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
16923 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
16924 (synopsis "R Markdown format for flexible dashboards")
16926 "This package provides an R Markdown format for converting an R Markdown
16927 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
16928 of its components to the containing web page.")
16929 (license license:expat)))
16931 (define-public r-preseqr
16938 (uri (cran-uri "preseqR" version))
16941 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
16942 (properties `((upstream-name . "preseqR")))
16943 (build-system r-build-system)
16945 `(("r-polynom" ,r-polynom)))
16946 (home-page "https://cran.r-project.org/web/packages/preseqR/")
16947 (synopsis "Predicting species accumulation curves")
16949 "This package can be used to predict the r-species accumulation
16950 curve (r-SAC), which is the number of species represented at least r times as
16951 a function of the sampling effort. When r = 1, the curve is known as the
16952 species accumulation curve, or the library complexity curve in high-throughput
16953 genomic sequencing. The package includes both parametric and nonparametric
16954 methods, as described by Deng C, et al. (2018).")
16955 (license license:gpl3)))
16957 (define-public r-mapplots
16959 (name "r-mapplots")
16964 (uri (cran-uri "mapplots" version))
16967 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
16968 (build-system r-build-system)
16969 (home-page "https://cran.r-project.org/web/packages/mapplots/")
16970 (synopsis "Data visualization on maps")
16972 "This package helps you create simple maps; add sub-plots like pie plots
16973 to a map or any other plot; format, plot and export gridded data. The package
16974 was developed for displaying fisheries data but most functions can be used for
16975 more generic data visualisation.")
16976 (license license:gpl2+)))
16978 (define-public r-pmcmr
16985 (uri (cran-uri "PMCMR" version))
16988 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
16989 (properties `((upstream-name . "PMCMR")))
16990 (build-system r-build-system)
16991 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
16992 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
16994 "This is a deprecated package for calculating pairwise multiple
16995 comparisons of mean rank sums. This package is superseded by the novel
16996 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
16997 compatibility of dependent packages for some time.")
16998 (license license:gpl3+)))
17000 (define-public r-downloader
17002 (name "r-downloader")
17007 (uri (cran-uri "downloader" version))
17010 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
17011 (build-system r-build-system)
17013 `(("r-digest" ,r-digest)))
17014 (home-page "https://github.com/wch/downloader")
17015 (synopsis "Download files over HTTP and HTTPS")
17017 "This package provides a wrapper for the @code{download.file} function,
17018 making it possible to download files over HTTPS across platforms. The
17019 @code{RCurl} package provides this functionality (and much more) but has
17020 external dependencies. This package has is implemented purely in R.")
17021 (license license:gpl2)))
17023 (define-public r-rex
17030 (uri (cran-uri "rex" version))
17033 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
17034 (build-system r-build-system)
17036 `(("r-lazyeval" ,r-lazyeval)))
17038 `(("r-knitr" ,r-knitr)))
17039 (home-page "https://github.com/kevinushey/rex")
17040 (synopsis "Friendly regular expressions")
17042 "This package provides a friendly interface for the construction of
17043 regular expressions. Regular expressions are a very powerful feature, however
17044 they are often difficult to interpret. Rex allows you to build complex
17045 regular expressions from human readable expressions")
17046 (license license:expat)))
17048 (define-public r-xmlparsedata
17050 (name "r-xmlparsedata")
17055 (uri (cran-uri "xmlparsedata" version))
17058 "177vfyjrqfi3wam8scpsradap1lv35yc25xq745dr7gabg116yrq"))))
17059 (properties `((upstream-name . "xmlparsedata")))
17060 (build-system r-build-system)
17061 (home-page "https://github.com/r-lib/xmlparsedata#readme")
17062 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
17064 "This package provides tools to convert the output of
17065 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
17066 @code{XPath}, and is easier to manipulate in general.")
17067 (license license:expat)))
17069 (define-public r-cyclocomp
17071 (name "r-cyclocomp")
17076 (uri (cran-uri "cyclocomp" version))
17079 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
17080 (properties `((upstream-name . "cyclocomp")))
17081 (build-system r-build-system)
17083 `(("r-callr" ,r-callr)
17084 ("r-crayon" ,r-crayon)
17086 ("r-remotes" ,r-remotes)
17087 ("r-withr" ,r-withr)))
17088 (home-page "https://github.com/MangoTheCat/cyclocomp")
17089 (synopsis "Cyclomatic complexity of R code")
17091 "Cyclomatic complexity is a software metric, used to indicate the
17092 complexity of a program. It is a quantitative measure of the number of
17093 linearly independent paths through a program's source code. This package
17094 provides tools to compute this metric.")
17095 (license license:expat)))
17097 (define-public r-lintr
17104 (uri (cran-uri "lintr" version))
17107 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
17108 (properties `((upstream-name . "lintr")))
17109 (build-system r-build-system)
17111 `(("r-codetools" ,r-codetools)
17112 ("r-crayon" ,r-crayon)
17113 ("r-cyclocomp" ,r-cyclocomp)
17114 ("r-digest" ,r-digest)
17116 ("r-jsonlite" ,r-jsonlite)
17117 ("r-knitr" ,r-knitr)
17119 ("r-rstudioapi" ,r-rstudioapi)
17120 ("r-testthat" ,r-testthat)
17122 ("r-xmlparsedata" ,r-xmlparsedata)))
17123 (home-page "https://github.com/jimhester/lintr")
17124 (synopsis "Linter for R code")
17125 (description "This package checks adherence to a given style, syntax
17126 errors and possible semantic issues. It supports on the fly checking of R
17127 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
17128 (license license:expat)))
17130 (define-public r-sctransform
17132 (name "r-sctransform")
17137 (uri (cran-uri "sctransform" version))
17140 "1p3m6i28nlxh6r609syn88cwlbdpl3dw44dy3gsijk2ibq20mfsx"))))
17141 (build-system r-build-system)
17143 `(("r-future" ,r-future)
17144 ("r-future-apply" ,r-future-apply)
17145 ("r-ggplot2" ,r-ggplot2)
17146 ("r-gridextra" ,r-gridextra)
17148 ("r-matrix" ,r-matrix)
17149 ("r-matrixstats" ,r-matrixstats)
17151 ("r-rcpparmadillo" ,r-rcpparmadillo)
17152 ("r-reshape2" ,r-reshape2)))
17153 (home-page "https://github.com/ChristophH/sctransform")
17154 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
17156 "This package provides a normalization method for single-cell UMI count
17157 data using a variance stabilizing transformation. The transformation is based
17158 on a negative binomial regression model with regularized parameters. As part
17159 of the same regression framework, this package also provides functions for
17160 batch correction, and data correction.")
17161 (license license:gpl3)))
17163 (define-public r-styler
17170 (uri (cran-uri "styler" version))
17173 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
17174 (build-system r-build-system)
17176 `(("r-backports" ,r-backports)
17178 ("r-magrittr" ,r-magrittr)
17179 ("r-purrr" ,r-purrr)
17180 ("r-r-cache" ,r-r-cache)
17181 ("r-rematch2" ,r-rematch2)
17182 ("r-rlang" ,r-rlang)
17183 ("r-rprojroot" ,r-rprojroot)
17184 ("r-tibble" ,r-tibble)
17185 ("r-withr" ,r-withr)
17186 ("r-xfun" ,r-xfun)))
17187 (home-page "https://github.com/r-lib/styler")
17188 (synopsis "Non-invasive pretty printing of R code")
17190 "This is a package for pretty-printing R code without changing the user's
17191 formatting intent.")
17192 (license license:gpl3)))
17194 (define-public r-scrime
17201 (uri (cran-uri "scrime" version))
17204 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
17205 (build-system r-build-system)
17206 (home-page "https://cran.r-project.org/web/packages/scrime/")
17207 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
17209 "This package provides tools for the analysis of high-dimensional data
17210 developed/implemented at the group \"Statistical Complexity Reduction In
17211 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
17212 the functions can also be applied to other types of categorical data.")
17213 (license license:gpl2)))
17215 (define-public r-pbmcapply
17217 (name "r-pbmcapply")
17222 (uri (cran-uri "pbmcapply" version))
17225 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
17226 (build-system r-build-system)
17227 (home-page "https://github.com/kvnkuang/pbmcapply")
17228 (synopsis "Track the progress of apply procedures with a progress bar")
17230 "This light-weight package helps you track and visualize the progress of
17231 parallel versions of vectorized R functions of the @code{mc*apply} family.")
17232 (license license:expat)))
17234 (define-public r-blme
17241 (uri (cran-uri "blme" version))
17244 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7"))))
17245 (build-system r-build-system)
17246 (propagated-inputs `(("r-lme4" ,r-lme4)))
17247 (home-page "https://github.com/vdorie/blme")
17248 (synopsis "Bayesian linear mixed-effects models")
17250 "This package provides tools for maximum a posteriori estimation for
17251 linear and generalized linear mixed-effects models in a Bayesian setting. It
17252 extends the lme4 package.")
17253 (license license:gpl2+)))
17255 (define-public r-batchtools
17257 (name "r-batchtools")
17262 (uri (cran-uri "batchtools" version))
17265 "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52"))))
17266 (build-system r-build-system)
17268 `(("r-backports" ,r-backports)
17269 ("r-base64url" ,r-base64url)
17271 ("r-checkmate" ,r-checkmate)
17272 ("r-data-table" ,r-data-table)
17273 ("r-digest" ,r-digest)
17275 ("r-progress" ,r-progress)
17277 ("r-rappdirs" ,r-rappdirs)
17278 ("r-stringi" ,r-stringi)
17279 ("r-withr" ,r-withr)))
17281 `(("r-knitr" ,r-knitr)))
17282 (home-page "https://github.com/mllg/batchtools")
17283 (synopsis "Tools for computation on batch systems")
17285 "As a successor of the packages BatchJobs and BatchExperiments, this
17286 package provides a parallel implementation of the Map function for high
17287 performance computing systems managed by various schedulers. A multicore and
17288 socket mode allow the parallelization on a local machines, and multiple
17289 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
17290 the package provides an abstraction mechanism to define large-scale computer
17291 experiments in a well-organized and reproducible way.")
17292 (license license:lgpl3)))
17294 (define-public r-clue
17301 (uri (cran-uri "clue" version))
17304 "1rwwxlnpl1k0n4k96vxc9zajw9kb4syqwzj76fvaf0qim8p6ddia"))))
17305 (build-system r-build-system)
17306 (propagated-inputs `(("r-cluster" ,r-cluster)))
17307 (home-page "https://cran.r-project.org/web/packages/clue/")
17308 (synopsis "Tools for analyzing cluster ensembles")
17309 (description "Cluster ensembles are collections of individual solutions to
17310 a given clustering problem which are useful or necessary to consider in a wide
17311 range of applications. This R package provides an extensible computational
17312 environment for creating and analyzing cluster ensembles, with basic data
17313 structures for representing partitions and hierarchies, and facilities for
17314 computing on them, including methods for measuring proximity and obtaining
17315 consensus and secondary clusterings.")
17316 (license license:gpl2)))
17318 (define-public r-sitmo
17325 (uri (cran-uri "sitmo" version))
17328 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
17329 (build-system r-build-system)
17330 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17331 (home-page "https://github.com/coatless/sitmo/")
17332 (synopsis "Parallel pseudo random number generator header files")
17334 "This package provides two high quality and fast PPRNGs that may be used
17335 in an OpenMP parallel environment. In addition, there is a generator for one
17336 dimensional low-discrepancy sequence.")
17337 (license license:expat)))
17339 (define-public r-dqrng
17346 (uri (cran-uri "dqrng" version))
17349 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
17350 (build-system r-build-system)
17354 ("r-sitmo" ,r-sitmo)))
17355 (home-page "https://www.daqana.org/dqrng")
17356 (synopsis "Fast pseudo random number generators")
17358 "Several fast random number generators are provided as C++ header-only
17359 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
17360 Additionally, fast functions for generating random numbers according to a
17361 uniform, normal and exponential distribution are included. The latter two use
17362 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
17363 functions are exported to R and as a C++ interface and are enabled for use
17364 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
17365 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
17366 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
17367 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
17368 ;; whole is distributed under the terms of the AGPL 3.
17369 (license license:agpl3)))
17371 (define-public r-ingredients
17373 (name "r-ingredients")
17378 (uri (cran-uri "ingredients" version))
17381 "0w46h1f28y5ypqm3ypsvk7yk9v7k8p21f1pzjl3ima8r1ivmhv12"))))
17382 (properties `((upstream-name . "ingredients")))
17383 (build-system r-build-system)
17385 `(("r-ggplot2" ,r-ggplot2)
17386 ("r-gridextra" ,r-gridextra)
17387 ("r-scales" ,r-scales)))
17388 (native-inputs `(("r-knitr" ,r-knitr)))
17389 (home-page "https://ModelOriented.github.io/ingredients/")
17390 (synopsis "Effects and importances of model ingredients")
17392 "This is a collection of tools for assessment of feature importance and
17393 feature effects. Key functions are:
17396 @item @code{feature_importance()} for assessment of global level feature
17398 @item @code{ceteris_paribus()} for calculation of the what-if plots,
17399 @item @code{partial_dependence()} for partial dependence plots,
17400 @item @code{conditional_dependence()} for conditional dependence plots,
17401 @item @code{accumulated_dependence()} for accumulated local effects plots,
17402 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
17403 aggregation of ceteris paribus profiles,
17404 @item generic @code{print()} and @code{plot()} for better usability of
17405 selected explainers,
17406 @item generic @code{plotD3()} for interactive, D3 based explanations, and
17407 @item generic @code{describe()} for explanations in natural language.
17409 (license license:gpl3)))
17411 (define-public r-ibreakdown
17413 (name "r-ibreakdown")
17418 (uri (cran-uri "iBreakDown" version))
17421 "1bfl5bh0x6z5a0cmdmx68sap9zdxa3kwdnyk57csxapc362yz108"))))
17422 (properties `((upstream-name . "iBreakDown")))
17423 (build-system r-build-system)
17424 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
17425 (native-inputs `(("r-knitr" ,r-knitr)))
17426 (home-page "https://ModelOriented.github.io/iBreakDown/")
17427 (synopsis "Model agnostic instance level variable attributions")
17429 "This package provides a model agnostic tool for decomposition of
17430 predictions from black boxes. It supports additive attributions and
17431 attributions with interactions. The Break Down Table shows contributions of
17432 every variable to a final prediction. The Break Down Plot presents variable
17433 contributions in a concise graphical way. This package works for
17434 classification and regression models.")
17435 (license license:gpl3)))
17437 (define-public r-dae
17444 (uri (cran-uri "dae" version))
17447 "126w1lb9pz8mb2ajl2vz5dj798nbifp0dypnzfgcwixif5g5bpqi"))))
17448 (build-system r-build-system)
17450 `(("r-ggplot2" ,r-ggplot2)
17451 ("r-plyr" ,r-plyr)))
17453 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
17454 (home-page "http://chris.brien.name")
17455 (synopsis "Functions useful in the design and ANOVA of experiments")
17457 "This package provides functions useful in the design and ANOVA of
17458 experiments. The content falls into the following groupings:
17462 @item factor manipulation functions,
17463 @item design functions,
17464 @item ANOVA functions,
17465 @item matrix functions,
17466 @item projector and canonical efficiency functions, and
17467 @item miscellaneous functions.
17470 There is a vignette called @code{DesignNotes} describing how to use the design
17471 functions for randomizing and assessing designs. The ANOVA functions
17472 facilitate the extraction of information when the @code{Error} function has
17473 been used in the call to @code{aov}.")
17474 (license license:gpl2)))
17476 (define-public r-dalex
17483 (uri (cran-uri "DALEX" version))
17486 "1hiknx55d91abyfj3w4a2xxin7f1q8h5k0041m7w93xjdc4kis98"))))
17487 (properties `((upstream-name . "DALEX")))
17488 (build-system r-build-system)
17490 `(("r-ggplot2" ,r-ggplot2)
17491 ("r-ibreakdown" ,r-ibreakdown)
17492 ("r-ingredients" ,r-ingredients)))
17493 (home-page "https://pbiecek.github.io/DALEX/")
17494 (synopsis "Descriptive machine learning explanations")
17496 "Machine Learning models are widely used and have various applications in
17497 classification or regression. Models created with boosting, bagging, stacking
17498 or similar techniques are often used due to their high performance, but such
17499 black-box models usually lack interpretability. The DALEX package contains
17500 various explainers that help to understand the link between input variables
17501 and model output.")
17502 ;; Any version of the GPL
17503 (license license:gpl3+)))
17505 (define-public r-enrichr
17512 (uri (cran-uri "enrichR" version))
17515 "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3"))))
17516 (properties `((upstream-name . "enrichR")))
17517 (build-system r-build-system)
17519 `(("r-ggplot2" ,r-ggplot2)
17521 ("r-rjson" ,r-rjson)))
17523 `(("r-knitr" ,r-knitr)))
17524 (home-page "https://cran.r-project.org/web/packages/enrichR/")
17525 (synopsis "R Interface to Enrichr database for analyzing gene sets")
17527 "This package provides an R interface to all Enrichr databases, a
17528 web-based tool for analyzing gene sets and returns any enrichment of common
17529 annotated biological functions.")
17530 (license license:gpl2+)))
17532 (define-public r-plot3d
17539 (uri (cran-uri "plot3D" version))
17542 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
17543 (properties `((upstream-name . "plot3D")))
17544 (build-system r-build-system)
17545 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
17546 (home-page "https://cran.r-project.org/web/packages/plot3D")
17547 (synopsis "Plot multi-dimensional data")
17549 "This package provides functions for viewing 2D and 3D data, including
17550 perspective plots, slice plots, surface plots, scatter plots, etc. It
17551 includes data sets from oceanography.")
17552 (license license:gpl3+)))
17554 (define-public r-ggfortify
17556 (name "r-ggfortify")
17561 (uri (cran-uri "ggfortify" version))
17564 "1wfm7l9bz6msh7rflgfv9dgbxh1ikz2ay0v7sgk9nkc24y6lhbpk"))))
17565 (build-system r-build-system)
17567 `(("r-dplyr" ,r-dplyr)
17568 ("r-ggplot2" ,r-ggplot2)
17569 ("r-gridextra" ,r-gridextra)
17570 ("r-scales" ,r-scales)
17571 ("r-stringr" ,r-stringr)
17572 ("r-tibble" ,r-tibble)
17573 ("r-tidyr" ,r-tidyr)))
17575 `(("r-knitr" ,r-knitr)))
17576 (home-page "https://github.com/sinhrks/ggfortify")
17577 (synopsis "Data visualization tools for statistical analysis results")
17579 "This package provides unified plotting tools for statistics commonly
17580 used, such as GLM, time series, PCA families, clustering and survival
17581 analysis. The package offers a single plotting interface for these analysis
17582 results and plots in a unified style using the @code{ggplot2} package.")
17583 (license license:gpl2)))
17585 (define-public r-refmanager
17587 (name "r-refmanager")
17592 (uri (cran-uri "RefManageR" version))
17595 "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps"))))
17596 (properties `((upstream-name . "RefManageR")))
17597 (build-system r-build-system)
17599 `(("r-httr" ,r-httr)
17600 ("r-jsonlite" ,r-jsonlite)
17601 ("r-lubridate" ,r-lubridate)
17603 ("r-stringr" ,r-stringr)
17604 ("r-xml2" ,r-xml2)))
17606 `(("r-knitr" ,r-knitr)))
17607 (home-page "https://github.com/ropensci/RefManageR/")
17608 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
17610 "This package provides tools for importing and working with bibliographic
17611 references. It greatly enhances the @code{bibentry} class by providing a
17612 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
17613 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
17614 by various formats for name lists (author by last names, translator by full
17615 names, etc.). Entries can be updated, combined, sorted, printed in a number
17616 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
17617 into R and converted to @code{BibEntry} objects.")
17618 ;; Any of these licenses may be picked.
17619 (license (list license:gpl2 license:gpl3 license:bsd-3))))
17621 (define-public r-citr
17628 (uri (cran-uri "citr" version))
17631 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
17632 (build-system r-build-system)
17634 `(("r-assertthat" ,r-assertthat)
17637 ("r-miniui" ,r-miniui)
17638 ("r-refmanager" ,r-refmanager)
17639 ("r-rstudioapi" ,r-rstudioapi)
17640 ("r-shiny" ,r-shiny)
17641 ("r-shinyjs" ,r-shinyjs)
17642 ("r-yaml" ,r-yaml)))
17643 (home-page "https://github.com/crsh/citr")
17644 (synopsis "RStudio add-in to insert Markdown citations")
17646 "This package provides functions and an RStudio add-in that search a
17647 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
17648 the current document.")
17649 (license license:expat)))
17651 (define-public r-xgboost
17654 (version "1.3.2.1")
17658 (uri (cran-uri "xgboost" version))
17661 "117q8xqm82589517fi8xicd8724v9c0wnq3qpl84h6nm3aw65x1g"))))
17662 (build-system r-build-system)
17664 `(("r-data-table" ,r-data-table)
17665 ("r-magrittr" ,r-magrittr)
17666 ("r-matrix" ,r-matrix)))
17668 `(("r-knitr" ,r-knitr)))
17669 (home-page "https://github.com/dmlc/xgboost")
17670 (synopsis "Extreme gradient boosting")
17672 "This package provides an R interface to Extreme Gradient Boosting, which
17673 is an efficient implementation of the gradient boosting framework from Chen
17674 and Guestrin (2016). The package includes efficient linear model solver and
17675 tree learning algorithms. The package can automatically do parallel
17676 computation on a single machine. It supports various objective functions,
17677 including regression, classification and ranking. The package is made to be
17678 extensible, so that users are also allowed to define their own objectives
17680 (license license:asl2.0)))
17682 (define-public r-umap
17685 (version "0.2.7.0")
17689 (uri (cran-uri "umap" version))
17692 "191vpy84s0bar06y9z1qx43x2kc4qp7lmrcmd0cvz2pnzq722jab"))))
17693 (build-system r-build-system)
17695 `(("r-openssl" ,r-openssl)
17697 ("r-reticulate" ,r-reticulate)
17698 ("r-rspectra" ,r-rspectra)))
17700 `(("r-knitr" ,r-knitr)))
17701 (home-page "https://github.com/tkonopka/umap")
17702 (synopsis "Uniform manifold approximation and projection")
17704 "Uniform manifold approximation and projection is a technique for
17705 dimension reduction. This package provides an interface to the UMAP algorithm
17706 in R, including a translation of the original algorithm into R.")
17707 (license license:expat)))
17709 (define-public r-uwot
17716 (uri (cran-uri "uwot" version))
17719 "08vxh085wnrxgwy35ksb4cr7ccjvd98pyr2zlgarqryfgc1bdqbf"))))
17720 (build-system r-build-system)
17722 `(("r-dqrng" ,r-dqrng)
17724 ("r-irlba" ,r-irlba)
17725 ("r-matrix" ,r-matrix)
17727 ("r-rcppannoy" ,r-rcppannoy)
17728 ("r-rcppprogress" ,r-rcppprogress)
17729 ("r-rspectra" ,r-rspectra)))
17730 (home-page "https://github.com/jlmelville/uwot")
17731 (synopsis "Uniform manifold approximation and projection")
17733 "This package provides an implementation of the Uniform Manifold
17734 Approximation and Projection dimensionality reduction by McInnes et
17735 al. (2018). It also provides means to transform new data and to carry out
17736 supervised dimensionality reduction. An implementation of the related
17737 LargeVis method of Tang et al. (2016) is also provided.")
17738 (license license:gpl3)))
17740 (define-public r-kableextra
17742 (name "r-kableextra")
17747 (uri (cran-uri "kableExtra" version))
17750 "1zixccpgy9x95fgzfgxc43pm020c80c21flch71klc3zzzsq53gf"))))
17751 (properties `((upstream-name . "kableExtra")))
17752 (build-system r-build-system)
17754 `(("r-digest" ,r-digest)
17756 ("r-htmltools" ,r-htmltools)
17757 ("r-knitr" ,r-knitr)
17758 ("r-magrittr" ,r-magrittr)
17759 ("r-rmarkdown" ,r-rmarkdown)
17760 ("r-rstudioapi" ,r-rstudioapi)
17761 ("r-rvest" ,r-rvest)
17762 ("r-scales" ,r-scales)
17763 ("r-stringr" ,r-stringr)
17764 ("r-viridislite" ,r-viridislite)
17765 ("r-webshot" ,r-webshot)
17766 ("r-xml2" ,r-xml2)))
17768 `(("r-knitr" ,r-knitr)))
17769 (home-page "https://haozhu233.github.io/kableExtra/")
17770 (synopsis "Construct complex tables with pipe syntax")
17772 "Build complex HTML or LaTeX tables using @code{kable()} from
17773 @code{knitr} and the piping syntax from @code{magrittr}. The function
17774 @code{kable()} is a light weight table generator coming from @code{knitr}.
17775 This package simplifies the way to manipulate the HTML or LaTeX codes
17776 generated by @code{kable()} and allows users to construct complex tables and
17777 customize styles using a readable syntax.")
17778 (license license:expat)))
17780 (define-public r-glasso
17787 (uri (cran-uri "glasso" version))
17789 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
17790 (build-system r-build-system)
17791 (native-inputs `(("gfortran" ,gfortran)))
17792 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
17793 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
17795 "This is a package for estimation of a sparse inverse covariance matrix
17796 using a lasso (L1) penalty. Facilities are provided for estimates along a
17797 path of values for the regularization parameter.")
17798 (license license:gpl2)))
17800 (define-public r-rhpcblasctl
17802 (name "r-rhpcblasctl")
17803 (version "0.20-137")
17807 (uri (cran-uri "RhpcBLASctl" version))
17810 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
17811 (properties `((upstream-name . "RhpcBLASctl")))
17812 (build-system r-build-system)
17813 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
17814 (synopsis "Control the number of threads on BLAS")
17816 "This package allows you to control the number of threads the BLAS
17817 library uses. It is also possible to control the number of threads in
17819 (license license:agpl3+)))
17821 (define-public r-lda
17828 (uri (cran-uri "lda" version))
17831 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
17832 (build-system r-build-system)
17833 (home-page "https://cran.r-project.org/web/packages/lda/")
17834 (synopsis "Collapsed Gibbs sampling methods for topic models")
17836 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
17837 related models. This includes (but is not limited to) sLDA, corrLDA, and the
17838 mixed-membership stochastic blockmodel. Inference for all of these models is
17839 implemented via a fast collapsed Gibbs sampler written in C. Utility
17840 functions for reading/writing data typically used in topic models, as well as
17841 tools for examining posterior distributions are also included.")
17842 ;; Any version of the LGPL
17843 (license license:lgpl3+)))
17845 (define-public r-rann-l1
17852 (uri (cran-uri "RANN.L1" version))
17855 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
17856 (properties `((upstream-name . "RANN.L1")))
17857 (build-system r-build-system)
17858 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
17859 (synopsis "Fast nearest neighbour search using L1 metric")
17861 "This package provides tools to find the k nearest neighbours for every
17862 point in a given dataset in O(N log N) time using Arya and Mount's ANN
17863 library. There is support for approximate as well as exact searches, fixed
17864 radius searches and @code{bd} as well as @code{kd} trees. The distance is
17865 computed using the L1 (Manhattan, taxicab) metric.")
17866 (license license:gpl3+)))
17868 (define-public r-leiden
17875 (uri (cran-uri "leiden" version))
17878 "14iqn5iqcya6bqbjvjivpd7q9gwc323sj29y7ssrbhb3sz9982bp"))))
17879 (properties `((upstream-name . "leiden")))
17880 (build-system r-build-system)
17882 `(("r-igraph" ,r-igraph)
17883 ("r-matrix" ,r-matrix)
17884 ("r-reticulate" ,r-reticulate)))
17886 `(("r-knitr" ,r-knitr)))
17887 (home-page "https://github.com/TomKellyGenetics/leiden")
17888 (synopsis "R implementation of Leiden clustering algorithm")
17890 "This package implements the Python @code{leidenalg} module to be called
17891 in R. It enables clustering using the Leiden algorithm for partitioning a
17892 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
17893 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
17894 (license license:gpl3)))
17896 (define-public r-patchwork
17898 (name "r-patchwork")
17903 (uri (cran-uri "patchwork" version))
17906 "10glgkf58lcykcwda1hj6xdps02m3i247qynk6s2jmwljagps3fg"))))
17907 (build-system r-build-system)
17909 `(("r-ggplot2" ,r-ggplot2)
17910 ("r-gtable" ,r-gtable)))
17912 `(("r-knitr" ,r-knitr)))
17913 (home-page "https://github.com/thomasp85/patchwork")
17914 (synopsis "Compose ggplot2 plots")
17916 "The @code{ggplot2} package provides a strong API for sequentially
17917 building up a plot, but does not concern itself with composition of multiple
17918 plots. Patchwork is a package that expands the API to allow for arbitrarily
17919 complex composition of plots by providing mathematical operators for combining
17921 (license license:expat)))
17923 (define-public r-liger
17930 (uri (git-reference
17931 (url "https://github.com/MacoskoLab/liger")
17932 (commit (string-append "v" version))))
17933 (file-name (git-file-name name version))
17936 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
17937 (modules '((guix build utils)))
17940 (delete-file "inst/java/ModularityOptimizer.jar")
17942 (build-system r-build-system)
17945 (modify-phases %standard-phases
17946 (add-after 'unpack 'build-java-part
17947 (lambda* (#:key inputs #:allow-other-keys)
17948 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
17949 (for-each (lambda (file) (invoke "javac" file))
17950 (find-files "." "\\.java$"))
17951 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
17952 (find-files "." "\\.class$"))
17955 `(("r-cowplot" ,r-cowplot)
17956 ("r-dosnow" ,r-dosnow)
17957 ("r-dplyr" ,r-dplyr)
17959 ("r-foreach" ,r-foreach)
17960 ("r-ggplot2" ,r-ggplot2)
17961 ("r-ggrepel" ,r-ggrepel)
17962 ("r-hmisc" ,r-hmisc)
17964 ("r-irlba" ,r-irlba)
17965 ("r-matrix" ,r-matrix)
17966 ("r-mclust" ,r-mclust)
17967 ("r-patchwork" ,r-patchwork)
17969 ("r-rann-l1" ,r-rann-l1)
17971 ("r-rcpparmadillo" ,r-rcpparmadillo)
17972 ("r-riverplot" ,r-riverplot)
17973 ("r-rtsne" ,r-rtsne)
17974 ("r-snow" ,r-snow)))
17976 `(("jdk" ,icedtea "jdk")
17977 ;; See https://github.com/MacoskoLab/liger/issues/96
17978 ;; The optimizer is released under the Expat license.
17982 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
17985 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
17987 ("r-knitr" ,r-knitr))) ; for vignettes
17988 (home-page "https://github.com/MacoskoLab/liger")
17989 (synopsis "Integrate and analyze multiple single-cell datasets")
17991 "LIGER is a package for integrating and analyzing multiple single-cell
17992 datasets, developed and maintained by the Macosko lab. It relies on
17993 integrative non-negative matrix factorization to identify shared and
17994 dataset-specific factors.")
17995 (license license:gpl3)))
17997 (define-public r-harmony
18004 (uri (git-reference
18005 (url "https://github.com/immunogenomics/harmony")
18007 (file-name (git-file-name name version))
18010 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
18011 (modules '((guix build utils)))
18014 (for-each delete-file '("config.status" "configure"))
18016 (build-system r-build-system)
18018 `(("r-cowplot" ,r-cowplot)
18019 ("r-dplyr" ,r-dplyr)
18020 ("r-ggplot2" ,r-ggplot2)
18021 ("r-irlba" ,r-irlba)
18022 ("r-matrix" ,r-matrix)
18024 ("r-rcpparmadillo" ,r-rcpparmadillo)
18025 ("r-rcppprogress" ,r-rcppprogress)
18026 ("r-rlang" ,r-rlang)
18027 ("r-tibble" ,r-tibble)
18028 ("r-tidyr" ,r-tidyr)))
18030 `(("autoconf" ,autoconf)))
18031 (home-page "https://github.com/immunogenomics/harmony")
18032 (synopsis "Integration of single cell sequencing data")
18034 "This package provides an implementation of the Harmony algorithm for
18035 single cell integration, described in Korsunsky et al
18036 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
18037 function and interfaces to external frameworks.")
18038 (license license:gpl3)))
18040 (define-public r-covr
18047 (uri (cran-uri "covr" version))
18049 (base32 "0v5cv3cw2kpdr6wxmkbd3wclavr17zipypdcb10hhmpa4cvgqk55"))))
18050 (properties `((upstream-name . "covr")))
18051 (build-system r-build-system)
18053 `(("r-crayon" ,r-crayon)
18054 ("r-digest" ,r-digest)
18056 ("r-jsonlite" ,r-jsonlite)
18058 ("r-withr" ,r-withr)
18059 ("r-yaml" ,r-yaml)))
18061 `(("r-knitr" ,r-knitr))) ; for vignettes
18062 (home-page "https://github.com/r-lib/covr")
18063 (synopsis "Test coverage for R packages")
18065 "Thisp package enables you to track and report code coverage for your
18066 package and (optionally) upload the results to a coverage service. Code
18067 coverage is a measure of the amount of code being exercised by a set of tests.
18068 It is an indirect measure of test quality and completeness. This package is
18069 compatible with any testing methodology or framework and tracks coverage of
18070 both R code and compiled C/C++/FORTRAN code.")
18071 (license license:gpl3)))
18073 (define-public r-systemfonts
18075 (name "r-systemfonts")
18080 (uri (cran-uri "systemfonts" version))
18083 "15x7qx8iigkybgz6b6s66i3mh75vgynzpd50nw05wflfwzcv87a0"))))
18084 (properties `((upstream-name . "systemfonts")))
18085 (build-system r-build-system)
18087 `(("r-cpp11" ,r-cpp11)))
18089 `(("fontconfig" ,fontconfig)
18092 `(("pkg-config" ,pkg-config)
18093 ("r-knitr" ,r-knitr)))
18094 (home-page "https://github.com/r-lib/systemfonts")
18095 (synopsis "System native font finding")
18097 "This package provides system native access to the font catalogue. As
18098 font handling varies between systems it is difficult to correctly locate
18099 installed fonts across different operating systems. The 'systemfonts' package
18100 provides bindings to the native libraries for finding font files that can then
18101 be used further by e.g. graphic devices.")
18102 (license license:expat)))
18104 (define-public r-graphlayouts
18106 (name "r-graphlayouts")
18111 (uri (cran-uri "graphlayouts" version))
18114 "05v7ss18bflhqa4ipsca8iw2ln8ddbaiyrizx2a5cwq81g5qq3rq"))))
18115 (properties `((upstream-name . "graphlayouts")))
18116 (build-system r-build-system)
18118 `(("r-igraph" ,r-igraph)
18120 ("r-rcpparmadillo" ,r-rcpparmadillo)))
18121 (home-page "https://github.com/schochastics/graphlayouts")
18122 (synopsis "Additional layout algorithms for network visualizations")
18124 "This package provides several layout algorithms to visualize networks
18125 which are not part of the igraph library. Most are based on the concept of
18126 stress majorization by Gansner et al. (2004)
18127 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
18128 emphasize hidden group structures in networks or focus on specific nodes.")
18129 (license license:expat)))
18131 (define-public r-terra
18138 (uri (cran-uri "terra" version))
18141 "1vsh55sq56shc8s2vmkl27yvrdbrbn3l6jrigqf2hmvppkb2jsbg"))))
18142 (properties `((upstream-name . "terra")))
18143 (build-system r-build-system)
18148 ("sqlite" ,sqlite) ; needed for proj
18151 `(("r-raster" ,r-raster)
18152 ("r-rcpp" ,r-rcpp)))
18154 `(("pkg-config" ,pkg-config)))
18155 (home-page "https://rspatial.org/terra")
18156 (synopsis "Spatial data analysis")
18158 "This package provides methods for spatial data analysis, especially
18159 raster data. The included methods allow for low-level data manipulation as
18160 well as high-level global, local, zonal, and focal computation. The predict
18161 and interpolate methods facilitate the use of regression type (interpolation,
18162 machine learning) models for spatial prediction. Processing of very large
18163 files is supported.")
18164 (license license:gpl3+)))
18166 (define-public r-tidygraph
18168 (name "r-tidygraph")
18173 (uri (cran-uri "tidygraph" version))
18176 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
18177 (properties `((upstream-name . "tidygraph")))
18178 (build-system r-build-system)
18180 `(("r-dplyr" ,r-dplyr)
18181 ("r-igraph" ,r-igraph)
18182 ("r-magrittr" ,r-magrittr)
18183 ("r-pillar" ,r-pillar)
18186 ("r-rlang" ,r-rlang)
18187 ("r-tibble" ,r-tibble)
18188 ("r-tidyr" ,r-tidyr)))
18189 (home-page "https://github.com/thomasp85/tidygraph")
18190 (synopsis "Tidy API for graph manipulation")
18192 "This package provides a graph implementation that can be thought of as
18193 two tidy data frames describing node and edge data respectively. It provides
18194 an approach to manipulate these two virtual data frames using the API defined
18195 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
18196 common graph algorithms.")
18197 (license license:expat)))
18199 (define-public r-soupx
18200 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
18204 (version (git-version "0.3.1" revision commit))
18208 (uri (git-reference
18209 (url "https://github.com/constantAmateur/SoupX")
18211 (file-name (git-file-name name version))
18214 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
18215 (properties `((upstream-name . "SoupX")))
18216 (build-system r-build-system)
18218 `(("r-ggplot2" ,r-ggplot2)
18219 ("r-matrix" ,r-matrix)
18220 ("r-seurat" ,r-seurat)))
18221 (home-page "https://github.com/constantAmateur/SoupX")
18222 (synopsis "Single cell mRNA Soup eXterminator")
18224 "This package provides a package for quantifying, profiling and
18225 removing cell free mRNA contamination (the \"soup\") from droplet based single
18226 cell RNA-seq experiments.")
18227 (license license:gpl2))))
18229 (define-public r-assertr
18236 (uri (cran-uri "assertr" version))
18239 "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650"))))
18240 (build-system r-build-system)
18242 `(("r-dplyr" ,r-dplyr)
18244 ("r-rlang" ,r-rlang)))
18246 `(("r-knitr" ,r-knitr))) ; needed for vignette
18247 (home-page "https://github.com/ropensci/assertr")
18248 (synopsis "Assertive programming for R analysis pipelines")
18250 "This package provides functionality to assert conditions that have to be
18251 met so that errors in data used in analysis pipelines can fail quickly. It is
18252 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
18254 (license license:expat)))
18256 (define-public r-parameters
18258 (name "r-parameters")
18263 (uri (cran-uri "parameters" version))
18266 "020k3vxnp0vjrlkcxx5vj30vag474hw48zxzw9315whsq4hhhbqc"))))
18267 (properties `((upstream-name . "parameters")))
18268 (build-system r-build-system)
18270 `(("r-bayestestr" ,r-bayestestr)
18271 ("r-insight" ,r-insight)))
18273 `(("r-knitr" ,r-knitr)))
18274 (home-page "https://cran.r-project.org/web/packages/parameters")
18275 (synopsis "Processing of model parameters")
18277 "This package provides utilities for processing the parameters of various
18278 statistical models. Beyond computing p values, CIs, and other indices for a
18279 wide variety of models, this package implements features like standardization
18280 or bootstrapping of parameters and models, feature reduction (feature
18281 extraction and variable selection) as well as conversion between indices of
18283 (license license:gpl3)))
18285 (define-public r-rgdal
18292 (uri (cran-uri "rgdal" version))
18294 (base32 "0vnb7kw762y349pda4aq1hx0smafylmn3635l963qykfji5p99cw"))))
18295 (properties `((upstream-name . "rgdal")))
18296 (build-system r-build-system)
18304 `(("pkg-config" ,pkg-config)
18305 ("r-knitr" ,r-knitr)))
18306 (home-page "http://rgdal.r-forge.r-project.org")
18307 (synopsis "Bindings for the Geospatial Data Abstraction Library")
18309 "This package provides bindings to the Geospatial Data Abstraction
18310 Library (GDAL) and access to projection/transformation operations from the
18312 (license license:gpl2+)))
18314 (define-public r-insol
18321 (uri (cran-uri "insol" version))
18324 "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3"))))
18325 (properties `((upstream-name . "insol")))
18326 (build-system r-build-system)
18328 `(("r-raster" ,r-raster)))
18330 `(("gfortran" ,gfortran)))
18331 (home-page "https://meteoexploration.com/R/insol/index.html")
18332 (synopsis "Tools for calculating solar radiation")
18334 "This package provides functions to compute insolation on tilted
18335 surfaces, computes atmospheric transmittance and related parameters such as:
18336 Earth radius vector, declination, sunset and sunrise, daylength, equation of
18337 time, vector in the direction of the sun, vector normal to surface, and some
18338 atmospheric physics.")
18339 (license license:gpl2+)))
18341 (define-public r-lifecycle
18343 (name "r-lifecycle")
18348 (uri (cran-uri "lifecycle" version))
18351 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
18352 (properties `((upstream-name . "lifecycle")))
18353 (build-system r-build-system)
18355 `(("r-glue" ,r-glue)
18356 ("r-rlang" ,r-rlang)))
18358 `(("r-knitr" ,r-knitr))) ; for vignettes
18359 (home-page "https://github.com/r-lib/lifecycle")
18360 (synopsis "Manage the life cycle of your package functions")
18362 "Manage the life cycle of your exported functions with shared
18363 conventions, documentation badges, and non-invasive deprecation warnings. The
18364 lifecycle package defines four development stages (experimental, maturing,
18365 stable, and questioning) and three deprecation stages (soft-deprecated,
18366 deprecated, and defunct). It makes it easy to insert badges corresponding to
18367 these stages in your documentation. Usage of deprecated functions are
18368 signalled with increasing levels of non-invasive verbosity.")
18369 (license license:gpl3)))
18371 (define-public r-assertable
18373 (name "r-assertable")
18378 (uri (cran-uri "assertable" version))
18381 "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4"))))
18382 (build-system r-build-system)
18384 `(("r-data-table" ,r-data-table)))
18386 `(("r-knitr" ,r-knitr)))
18387 (home-page "https://cran.r-project.org/web/packages/assertable/")
18388 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
18389 (description "This package provides simple, flexible assertions on
18390 data.frame or data.table objects with verbose output for vetting. While other
18391 assertion packages apply towards more general use-cases, @code{assertable} is
18392 tailored towards tabular data. It includes functions to check variable names
18393 and values, whether the dataset contains all combinations of a given set of
18394 unique identifiers, and whether it is a certain length. In addition,
18395 @code{assertable} includes utility functions to check the existence of target
18396 files and to efficiently import multiple tabular data files into one
18398 (license license:gpl3)))
18400 (define-public r-quadprog
18402 (name "r-quadprog")
18407 (uri (cran-uri "quadprog" version))
18409 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
18410 (build-system r-build-system)
18412 `(("gfortran" ,gfortran)))
18413 (home-page "https://cran.r-project.org/web/packages/quadprog")
18414 (synopsis "Functions to solve quadratic programming problems")
18416 "This package contains routines and documentation for solving quadratic
18417 programming problems.")
18418 (license license:gpl3+)))
18420 (define-public r-desolve
18427 (uri (cran-uri "deSolve" version))
18429 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
18430 (properties `((upstream-name . "deSolve")))
18431 (build-system r-build-system)
18433 `(("gfortran" ,gfortran)))
18434 (home-page "https://desolve.r-forge.r-project.org/")
18435 (synopsis "Solvers for initial value problems of differential equations")
18436 (description "This package provides functions that solve initial value
18437 problems of a system of first-order @dfn{ordinary differential
18438 equations} (ODE), of @dfn{partial differential equations} (PDE), of
18439 @dfn{differential algebraic equations} (DAE), and of delay differential
18440 equations. The functions provide an interface to the FORTRAN functions
18441 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
18442 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
18443 C-implementation of solvers of the Runge-Kutta family with fixed or variable
18444 time steps. The package contains routines designed for solving ODEs resulting
18445 from 1-D, 2-D and 3-D partial differential equations that have been converted
18446 to ODEs by numerical differencing.")
18447 (license license:gpl2+)))
18449 (define-public r-pracma
18455 (uri (cran-uri "pracma" version))
18457 (base32 "0g5r5ir5k43ba0ngnsanp108k479l2dnsjd5w6idk1d34ivqs7yg"))))
18458 (build-system r-build-system)
18459 (home-page "https://cran.r-project.org/web/packages/pracma/")
18460 (synopsis "Practical numerical math functions")
18461 (description "This package provides functions for numerical analysis and
18462 linear algebra, numerical optimization, differential equations, plus some
18463 special functions. It uses Matlab function names where appropriate to simplify
18465 (license license:gpl3+)))
18467 (define-public r-subplex
18474 (uri (cran-uri "subplex" version))
18477 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
18478 (build-system r-build-system)
18480 `(("gfortran" ,gfortran)))
18481 (home-page "https://cran.r-project.org/web/packages/subplex")
18482 (synopsis "Unconstrained optimization using the subplex algorithm")
18484 "This package implements the Subplex optimization algorithm.
18485 It solves unconstrained optimization problems using a simplex method on
18486 subspaces. The method is well suited for optimizing objective functions that
18487 are noisy or are discontinuous at the solution.")
18488 (license license:gpl3+)))
18490 (define-public r-txtplot
18497 (uri (cran-uri "txtplot" version))
18500 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
18501 (build-system r-build-system)
18502 (home-page "https://cran.r-project.org/web/packages/txtplot/")
18503 (synopsis "Text-based plotting")
18504 (description "This package provides functions to produce rudimentary ASCII
18505 graphics directly in the terminal window. This package provides a basic
18506 plotting function (and equivalents of curve, density, acf and barplot) as well
18507 as a boxplot function.")
18508 (license license:lgpl3+)))
18510 (define-public r-bio3d
18517 (uri (cran-uri "bio3d" version))
18520 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
18521 (properties `((upstream-name . "bio3d")))
18522 (build-system r-build-system)
18523 (inputs `(("zlib" ,zlib)))
18524 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
18525 (home-page "http://thegrantlab.org/bio3d/")
18526 (synopsis "Biological structure analysis")
18528 "This package provides utilities to process, organize and explore protein
18529 structure, sequence and dynamics data. Features include the ability to read
18530 and write structure, sequence and dynamic trajectory data, perform sequence
18531 and structure database searches, data summaries, atom selection, alignment,
18532 superposition, rigid core identification, clustering, torsion analysis,
18533 distance matrix analysis, structure and sequence conservation analysis, normal
18534 mode analysis, principal component analysis of heterogeneous structure data,
18535 and correlation network analysis from normal mode and molecular dynamics data.
18536 In addition, various utility functions are provided to enable the statistical
18537 and graphical power of the R environment to work with biological sequence and
18539 (license license:gpl2+)))
18541 (define-public r-bios2cor
18543 (name "r-bios2cor")
18548 (uri (cran-uri "Bios2cor" version))
18551 "1wkj9vr33m9jilidil9jpw5rzr3pf7gkimxdvch22ks4bgkx7l1w"))))
18552 (properties `((upstream-name . "Bios2cor")))
18553 (build-system r-build-system)
18555 `(("r-bigmemory" ,r-bigmemory)
18556 ("r-bio3d" ,r-bio3d)
18557 ("r-circular" ,r-circular)
18558 ("r-igraph" ,r-igraph)))
18559 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
18560 (synopsis "From biological sequences and simulations to correlation analysis")
18562 "This package provides utilities for computation and analysis of
18563 correlation/covariation in multiple sequence alignments and in side chain
18564 motions during molecular dynamics simulations. Features include the
18565 computation of correlation/covariation scores using a variety of scoring
18566 functions between either sequence positions in alignments or side chain
18567 dihedral angles in molecular dynamics simulations and utilities to analyze the
18568 correlation/covariation matrix through a variety of tools including network
18569 representation and principal components analysis. In addition, several
18570 utility functions are based on the R graphical environment to provide friendly
18571 tools for help in data interpretation.")
18572 (license license:gpl2+)))
18574 ;; This package includes minified JavaScript files. When upgrading please
18575 ;; check that there are no new minified JavaScript files.
18576 (define-public r-networkd3
18578 (name "r-networkd3")
18583 (uri (cran-uri "networkD3" version))
18586 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
18589 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
18591 (properties `((upstream-name . "networkD3")))
18592 (build-system r-build-system)
18594 `(#:modules ((guix build utils)
18595 (guix build r-build-system)
18599 (modify-phases %standard-phases
18600 (add-after 'unpack 'process-javascript
18601 (lambda* (#:key inputs #:allow-other-keys)
18602 (with-directory-excursion "inst/htmlwidgets/lib/"
18606 `((,(assoc-ref inputs "d3.v4.js")
18607 "d3-4.5.0/d3.min.js"))))
18608 (lambda (sources targets)
18609 (for-each (lambda (source target)
18610 (format #t "Processing ~a --> ~a~%"
18612 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
18613 (call-with-output-file target
18615 (dump-port minified port)))))
18616 sources targets))))
18619 `(("uglify-js" ,uglify-js)
18620 ;; NOTE: Make sure that this version of d3 is still valid when
18621 ;; upgrading the package.
18625 (uri "https://d3js.org/d3.v4.js")
18628 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
18630 `(("r-htmlwidgets" ,r-htmlwidgets)
18631 ("r-igraph" ,r-igraph)
18632 ("r-magrittr" ,r-magrittr)))
18633 (home-page "https://cran.r-project.org/package=networkD3")
18634 (synopsis "D3 JavaScript network graphs from R")
18636 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
18638 (license license:gpl3+)))
18640 (define-public r-aasea
18647 (uri (cran-uri "aaSEA" version))
18650 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
18651 (properties `((upstream-name . "aaSEA")))
18652 (build-system r-build-system)
18654 `(("r-bios2cor" ,r-bios2cor)
18656 ("r-hmisc" ,r-hmisc)
18657 ("r-magrittr" ,r-magrittr)
18658 ("r-networkd3" ,r-networkd3)
18659 ("r-plotly" ,r-plotly)
18660 ("r-seqinr" ,r-seqinr)
18661 ("r-shiny" ,r-shiny)
18662 ("r-shinydashboard" ,r-shinydashboard)))
18663 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
18664 (synopsis "Amino acid substitution effect analyzer")
18666 "Given a protein multiple sequence alignment, it is a daunting task to
18667 assess the effects of substitutions along sequence length. The aaSEA package
18668 is intended to help researchers to rapidly analyze property changes caused by
18669 single, multiple and correlated amino acid substitutions in proteins.")
18670 (license license:gpl3)))
18672 (define-public r-abacus
18679 (uri (cran-uri "ABACUS" version))
18682 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
18683 (properties `((upstream-name . "ABACUS")))
18684 (build-system r-build-system)
18686 `(("r-ggplot2" ,r-ggplot2)
18687 ("r-shiny" ,r-shiny)))
18688 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
18689 (synopsis "Apps-based activities for communicating and understanding statistics")
18691 "This package provides a set of Shiny apps for effective communication
18692 and understanding in statistics. The current version includes properties of
18693 normal distribution, properties of sampling distribution, one-sample z and t
18694 tests, two samples independent (unpaired) t test and analysis of variance.")
18695 (license license:gpl3)))
18697 (define-public r-abc-rap
18704 (uri (cran-uri "ABC.RAP" version))
18707 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
18708 (properties `((upstream-name . "ABC.RAP")))
18709 (build-system r-build-system)
18710 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
18711 (synopsis "Array-based CpG region analysis pipeline")
18713 "This package aims to identify candidate genes that are differentially
18714 methylated between cases and controls. It applies Student's t-test and delta
18715 beta analysis to identify candidate genes containing multiple CpG sites.")
18716 (license license:gpl3)))
18718 (define-public r-abcadm
18725 (uri (cran-uri "abcADM" version))
18728 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
18729 (properties `((upstream-name . "abcADM")))
18730 (build-system r-build-system)
18733 ("r-rcpp" ,r-rcpp)))
18734 (home-page "https://cran.r-project.org/web/packages/abcADM/")
18735 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
18737 "This package provides tools to estimate parameters of accumulated
18738 damage (load duration) models based on failure time data under a Bayesian
18739 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
18740 long-term reliability under stochastic load profiles.")
18741 (license license:gpl3)))
18743 (define-public r-rglpk
18750 (uri (cran-uri "Rglpk" version))
18753 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
18754 (properties `((upstream-name . "Rglpk")))
18755 (build-system r-build-system)
18757 `(("r-slam" ,r-slam)))
18760 (home-page "https://r-forge.r-project.org/projects/rglp/")
18761 (synopsis "R interface to the GNU Linear Programming Kit")
18763 "This package provides an R interface to the GNU Linear Programming Kit,
18764 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
18765 integer linear programming} (MILP) and other related problems.")
18767 (license (list license:gpl2 license:gpl3))))
18769 (define-public r-abcdefba
18771 (name "r-abcdefba")
18776 (uri (cran-uri "abcdeFBA" version))
18779 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
18780 (properties `((upstream-name . "abcdeFBA")))
18781 (build-system r-build-system)
18783 `(("r-corrplot" ,r-corrplot)
18784 ("r-lattice" ,r-lattice)
18786 ("r-rglpk" ,r-rglpk)))
18787 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
18788 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
18790 "This package provides functions for Constraint Based Simulation using
18791 Flux Balance Analysis and informative analysis of the data generated during
18793 (license license:gpl2)))
18795 (define-public r-abcrlda
18802 (uri (cran-uri "abcrlda" version))
18805 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
18806 (properties `((upstream-name . "abcrlda")))
18807 (build-system r-build-system)
18808 (home-page "https://ieeexplore.ieee.org/document/8720003/")
18809 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
18811 "This package offers methods to perform @dfn{asymptotically
18812 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
18813 cost-sensitive binary classification. The bias-correction is an estimate of
18814 the bias term added to regularized discriminant analysis that minimizes the
18816 (license license:gpl3)))
18818 (define-public r-abemus
18825 (uri (cran-uri "abemus" version))
18828 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
18829 (properties `((upstream-name . "abemus")))
18830 (build-system r-build-system)
18832 `(("r-data-table" ,r-data-table)))
18833 (home-page "https://cran.r-project.org/web/packages/abemus/")
18834 (synopsis "Adaptive base error model in ultra-deep sequencing data")
18836 "This package provides an implementation of @dfn{Adaptive Base Error
18837 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
18838 platform-specific genetic knowledge and empirical signal to readily detect and
18839 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
18840 cell free DNA} (cfDNA).")
18841 (license license:gpl3)))
18843 ;; This package includes minified JavaScript files. When upgrading please
18844 ;; check that there are no new minified JavaScript files.
18845 (define-public r-rintrojs
18847 (name "r-rintrojs")
18852 (uri (cran-uri "rintrojs" version))
18855 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
18856 (properties `((upstream-name . "rintrojs")))
18857 (build-system r-build-system)
18859 `(#:modules ((guix build utils)
18860 (guix build r-build-system)
18864 (modify-phases %standard-phases
18865 (add-after 'unpack 'process-javascript
18866 (lambda* (#:key inputs #:allow-other-keys)
18867 (with-directory-excursion "inst/javascript/introjs/"
18871 `((,(assoc-ref inputs "intro.js")
18873 (lambda (sources targets)
18874 (for-each (lambda (source target)
18875 (format #t "Processing ~a --> ~a~%"
18877 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
18878 (call-with-output-file target
18880 (dump-port minified port)))))
18881 sources targets))))
18884 `(("uglify-js" ,uglify-js)
18888 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
18891 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
18893 `(("r-jsonlite" ,r-jsonlite)
18894 ("r-shiny" ,r-shiny)))
18895 (home-page "https://github.com/carlganz/rintrojs")
18896 (synopsis "Wrapper for the Intro.js library")
18898 "This package provides a wrapper for the @url{http://www.introjs.com,
18899 Intro.js} library. This package makes it easy to include step-by-step
18900 introductions, and clickable hints in a Shiny application. It supports both
18901 static introductions in the UI, and programmatic introductions from the
18903 (license license:agpl3+)))
18905 (define-public r-sysfonts
18907 (name "r-sysfonts")
18912 (uri (cran-uri "sysfonts" version))
18915 "00kbazxw6zd1kakfshffdj928krca53bw9k78k0zar40mbqxiwd5"))))
18916 (properties `((upstream-name . "sysfonts")))
18917 (build-system r-build-system)
18919 `(("freetype" ,freetype)
18923 `(("pkg-config" ,pkg-config)))
18924 (home-page "https://github.com/yixuan/sysfonts")
18925 (synopsis "Loading fonts into R")
18927 "This is a package to simplify loading of system fonts and Google Fonts
18928 into R, in order to support other packages.")
18929 (license license:gpl2)))
18931 (define-public r-showtextdb
18933 (name "r-showtextdb")
18938 (uri (cran-uri "showtextdb" version))
18941 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
18942 (properties `((upstream-name . "showtextdb")))
18943 (build-system r-build-system)
18945 `(("r-sysfonts" ,r-sysfonts)))
18946 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
18947 (synopsis "Font files for the 'showtext' package")
18949 "This package provides font files that can be used by the @code{showtext}
18951 (license license:asl2.0)))
18953 (define-public r-showtext
18955 (name "r-showtext")
18960 (uri (cran-uri "showtext" version))
18963 "0y5mw6ffk92r7b22irrfhdmj4hxfl0d1wjxj14hznbapc4qm6f0z"))))
18964 (properties `((upstream-name . "showtext")))
18965 (build-system r-build-system)
18967 `(("freetype" ,freetype)
18971 `(("r-showtextdb" ,r-showtextdb)
18972 ("r-sysfonts" ,r-sysfonts)))
18974 `(("pkg-config" ,pkg-config)
18975 ("r-knitr" ,r-knitr)))
18976 (home-page "https://github.com/yixuan/showtext")
18977 (synopsis "Using fonts more easily in R graphs")
18979 "This package aims to make it easy to use various types of
18980 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
18981 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
18982 will be converted into polygons or raster images, hence after the plot has
18983 been created, it no longer relies on the font files. No external software
18984 such as Ghostscript is needed to use this package.")
18985 (license license:asl2.0)))
18987 (define-public r-emojifont
18989 (name "r-emojifont")
18994 (uri (cran-uri "emojifont" version))
18997 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
18998 (properties `((upstream-name . "emojifont")))
18999 (build-system r-build-system)
19001 `(("r-ggplot2" ,r-ggplot2)
19002 ("r-proto" ,r-proto)
19003 ("r-showtext" ,r-showtext)
19004 ("r-sysfonts" ,r-sysfonts)))
19005 (home-page "https://guangchuangyu.github.io/emojifont")
19006 (synopsis "Emoji and Font Awesome in R graphics")
19008 "This package enables the use of emoji and the Font Awesome glyphs in
19009 both base and ggplot2 graphics.")
19010 (license license:artistic2.0)))
19012 (define-public r-abstractr
19014 (name "r-abstractr")
19019 (uri (cran-uri "abstractr" version))
19022 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
19023 (properties `((upstream-name . "abstractr")))
19024 (build-system r-build-system)
19026 `(("r-colourpicker" ,r-colourpicker)
19027 ("r-emojifont" ,r-emojifont)
19028 ("r-ggplot2" ,r-ggplot2)
19029 ("r-gridextra" ,r-gridextra)
19030 ("r-rintrojs" ,r-rintrojs)
19031 ("r-shiny" ,r-shiny)
19032 ("r-shinythemes" ,r-shinythemes)))
19033 (home-page "https://matt-kumar.shinyapps.io/portfolio")
19034 (synopsis "R-Shiny application for creating visual abstracts")
19036 "This package provides an R Shiny application to create visual abstracts
19037 for original research. A variety of user defined options and formatting are
19039 (license license:gpl3)))
19041 (define-public r-qgam
19048 (uri (cran-uri "qgam" version))
19051 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
19052 (properties `((upstream-name . "qgam")))
19053 (build-system r-build-system)
19055 `(("r-doparallel" ,r-doparallel)
19058 ("r-shiny" ,r-shiny)))
19059 (native-inputs `(("r-knitr" ,r-knitr)))
19060 (home-page "https://cran.r-project.org/web/packages/qgam/")
19061 (synopsis "Smooth additive quantile regression models")
19063 "This package provides smooth additive quantile regression models, fitted
19064 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
19065 the smoothing parameters are estimated automatically by marginal loss
19066 minimization, while the regression coefficients are estimated using either
19067 PIRLS or Newton algorithm. The learning rate is determined so that the
19068 Bayesian credible intervals of the estimated effects have approximately the
19069 correct coverage. The main function is @code{qgam()} which is similar to
19070 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
19071 regression models.")
19072 (license license:gpl2+)))
19074 (define-public r-abtest
19081 (uri (cran-uri "abtest" version))
19084 "1ak0m4jd1grriwg4pn3aqf1468qma6rjn5kqjh8izx7zl29jd07v"))))
19085 (properties `((upstream-name . "abtest")))
19086 (build-system r-build-system)
19088 `(("r-matrix" ,r-matrix)
19089 ("r-mvtnorm" ,r-mvtnorm)
19090 ("r-plotrix" ,r-plotrix)
19092 ("r-rcolorbrewer" ,r-rcolorbrewer)
19095 ("r-truncnorm" ,r-truncnorm)))
19096 (home-page "https://cran.r-project.org/web/packages/abtest/")
19097 (synopsis "Bayesian A/B testing")
19099 "This package provides functions for Bayesian A/B testing including prior
19100 elicitation options based on Kass and Vaidyanathan (1992)
19101 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
19102 (license license:gpl2+)))
19104 (define-public r-accept
19111 (uri (cran-uri "accept" version))
19114 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
19115 (properties `((upstream-name . "accept")))
19116 (build-system r-build-system)
19118 `(("r-dplyr" ,r-dplyr)
19119 ("r-extrafont" ,r-extrafont)
19121 ("r-plotly" ,r-plotly)
19122 ("r-stringr" ,r-stringr)
19123 ("r-viridis" ,r-viridis)))
19124 (home-page "https://cran.r-project.org/web/packages/accept/")
19125 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
19127 "This package allows clinicians to predict the rate and severity of
19128 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
19129 Disease} (COPD) patients, based on the clinical prediction model published in
19130 Adibi et al. (2019) @url{doi:10.1101/651901}.")
19131 (license license:gpl3)))
19133 (define-public r-smpracticals
19135 (name "r-smpracticals")
19140 (uri (cran-uri "SMPracticals" version))
19143 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
19144 (properties `((upstream-name . "SMPracticals")))
19145 (build-system r-build-system)
19147 `(("r-ellipse" ,r-ellipse)
19150 ("r-survival" ,r-survival)))
19151 (home-page "http://statwww.epfl.ch/davison/SM/")
19152 (synopsis "Practicals for use with Davison (2003) Statistical Models")
19154 "This package contains the datasets and a few functions for use with the
19155 practicals outlined in Appendix A of the book Statistical Models (Davison,
19156 2003, Cambridge University Press). The practicals themselves can be found at
19157 @url{http://statwww.epfl.ch/davison/SM/}.")
19158 (license license:gpl2+)))
19160 (define-public r-fgui
19167 (uri (cran-uri "fgui" version))
19170 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
19171 (properties `((upstream-name . "fgui")))
19172 (build-system r-build-system)
19174 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
19175 (synopsis "Create GUI for R functions")
19177 "Rapidly create a GUI for a function you created by automatically
19178 creating widgets for arguments of the function. This package automatically
19179 parses help routines for context-sensitive help to these arguments. The
19180 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
19181 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
19182 incorporated into the interface for greater customization for the more
19184 ;; Any version of the GPL.
19185 (license (list license:gpl2+ license:gpl3+))))
19187 (define-public r-tcltk2
19194 (uri (cran-uri "tcltk2" version))
19197 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
19198 (properties `((upstream-name . "tcltk2")))
19199 (build-system r-build-system)
19203 (home-page "https://www.sciviews.org/SciViews-R")
19204 (synopsis "Tcl/Tk additions")
19206 "This package provides a series of additional Tcl commands and Tk widgets
19207 with style and various functions to supplement the tcltk package")
19208 (license license:lgpl3)))
19210 (define-public r-accrual
19217 (uri (cran-uri "accrual" version))
19220 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
19221 (properties `((upstream-name . "accrual")))
19222 (build-system r-build-system)
19224 `(("r-fgui" ,r-fgui)
19225 ("r-smpracticals" ,r-smpracticals)
19226 ("r-tcltk2" ,r-tcltk2)))
19227 (home-page "https://cran.r-project.org/web/packages/accrual/")
19228 (synopsis "Bayesian accrual prediction")
19230 "Subject recruitment for medical research is challenging. Slow patient
19231 accrual leads to delay in research. Accrual monitoring during the process of
19232 recruitment is critical. Researchers need reliable tools to manage the
19233 accrual rate. This package provides an implementation of a Bayesian method
19234 that integrates researcher's experience on previous trials and data from the
19235 current study, providing reliable prediction on accrual rate for clinical
19236 studies. It provides functions for Bayesian accrual prediction which can be
19237 easily used by statisticians and clinical researchers.")
19238 (license license:gpl2)))
19240 (define-public r-accrued
19247 (uri (cran-uri "accrued" version))
19250 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
19251 (properties `((upstream-name . "accrued")))
19252 (build-system r-build-system)
19253 (home-page "https://cran.r-project.org/web/packages/accrued/")
19254 (synopsis "Data quality visualization tools for partially accruing data")
19256 "This is a package for visualizing data quality of partially accruing
19258 (license license:gpl3)))
19260 (define-public r-mda
19267 (uri (cran-uri "mda" version))
19270 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
19271 (properties `((upstream-name . "mda")))
19272 (build-system r-build-system)
19273 (propagated-inputs `(("r-class" ,r-class)))
19274 (native-inputs `(("gfortran" ,gfortran)))
19275 (home-page "https://cran.r-project.org/web/packages/mda/")
19276 (synopsis "Mixture and flexible discriminant analysis")
19278 "This is a package for mixture and flexible discriminant analysis,
19279 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
19280 (license license:gpl2)))
19282 (define-public r-elasticnet
19284 (name "r-elasticnet")
19289 (uri (cran-uri "elasticnet" version))
19292 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
19293 (properties `((upstream-name . "elasticnet")))
19294 (build-system r-build-system)
19296 `(("r-lars" ,r-lars)))
19297 (home-page "http://users.stat.umn.edu/~zouxx019/")
19298 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
19300 "This package provides functions for fitting the entire solution path of
19301 the Elastic-Net and also provides functions for estimating sparse Principal
19302 Components. The Lasso solution paths can be computed by the same function.")
19303 (license license:gpl2+)))
19305 (define-public r-sparselda
19307 (name "r-sparselda")
19312 (uri (cran-uri "sparseLDA" version))
19315 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
19316 (properties `((upstream-name . "sparseLDA")))
19317 (build-system r-build-system)
19319 `(("r-elasticnet" ,r-elasticnet)
19322 (home-page "https://www.imm.dtu.dk/~lkhc/")
19323 (synopsis "Sparse discriminant analysis")
19325 "This package performs sparse linear discriminant analysis for Gaussians
19326 and mixture of Gaussian models.")
19327 (license license:gpl2+)))
19329 (define-public r-accsda
19336 (uri (cran-uri "accSDA" version))
19339 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
19340 (properties `((upstream-name . "accSDA")))
19341 (build-system r-build-system)
19343 `(("r-ggplot2" ,r-ggplot2)
19344 ("r-ggthemes" ,r-ggthemes)
19345 ("r-gridextra" ,r-gridextra)
19347 ("r-rarpack" ,r-rarpack)
19348 ("r-sparselda" ,r-sparselda)))
19349 (home-page "https://github.com/gumeo/accSDA/wiki")
19350 (synopsis "Accelerated sparse discriminant analysis")
19352 "This package provides an implementation of sparse linear discriminant
19353 analysis, which is a supervised classification method for multiple classes.
19354 Various novel optimization approaches to this problem are implemented
19355 including @dfn{alternating direction method of multipliers} (ADMM),
19356 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
19357 Functions for performing cross validation are also supplied along with basic
19358 prediction and plotting functions. @dfn{Sparse zero variance
19359 discriminant} (SZVD) analysis is also included in the package.")
19360 (license license:gpl2+)))
19362 (define-public r-ace2fastq
19364 (name "r-ace2fastq")
19369 (uri (cran-uri "ace2fastq" version))
19372 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
19373 (properties `((upstream-name . "ace2fastq")))
19374 (build-system r-build-system)
19376 `(("r-stringr" ,r-stringr)))
19377 (home-page "https://github.com/c5sire/ace2fastq")
19378 (synopsis "ACE file to FASTQ converter")
19380 "The ACE file format is used in genomics to store contigs from sequencing
19381 machines. This tools converts it into FASTQ format. Both formats contain the
19382 sequence characters and their corresponding quality information. Unlike the
19383 FASTQ file, the ACE file stores the quality values numerically. The
19384 conversion algorithm uses the standard Sanger formula. The package
19385 facilitates insertion into pipelines, and content inspection.")
19386 (license license:gpl3)))
19388 (define-public r-rngwell
19395 (uri (cran-uri "rngWELL" version))
19398 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
19399 (properties `((upstream-name . "rngWELL")))
19400 (build-system r-build-system)
19401 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
19402 (synopsis "Toolbox for WELL random number generators")
19404 "This is a dedicated package to WELL pseudo random generators, which were
19405 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
19406 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
19407 (license license:bsd-3)))
19409 (define-public r-randtoolbox
19411 (name "r-randtoolbox")
19416 (uri (cran-uri "randtoolbox" version))
19419 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
19420 (properties `((upstream-name . "randtoolbox")))
19421 (build-system r-build-system)
19423 `(("r-rngwell" ,r-rngwell)))
19425 `(("gfortran" ,gfortran)))
19426 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
19427 (synopsis "Toolbox for pseudo and quasi random number generation")
19429 "This package provides
19432 @item pseudo random generators, such as general linear
19433 congruential generators, multiple recursive generators and generalized
19434 feedback shift register (SF-Mersenne Twister algorithm and WELL
19437 @item quasi random generators, such as the Torus algorithm, the Sobol
19438 sequence, the Halton sequence (including the Van der Corput sequence), and
19440 @item some generator tests: the gap test, the serial test, the poker test.
19443 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
19444 (license license:bsd-3)))
19446 (define-public r-lhs
19453 (uri (cran-uri "lhs" version))
19456 "1p4h03qlijs2a59wfd4rlvdlb9i87pw2zm8xsjd6yzz8vlm9yglh"))))
19457 (properties `((upstream-name . "lhs")))
19458 (build-system r-build-system)
19459 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19461 `(("r-knitr" ,r-knitr)))
19462 (home-page "https://github.com/bertcarnell/lhs")
19463 (synopsis "Latin Hypercube Samples")
19465 "This package provides a number of methods for creating and augmenting
19466 Latin Hypercube Samples.")
19467 (license license:gpl3)))
19469 (define-public r-acebayes
19471 (name "r-acebayes")
19476 (uri (cran-uri "acebayes" version))
19479 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73"))))
19480 (properties `((upstream-name . "acebayes")))
19481 (build-system r-build-system)
19483 `(("r-compare" ,r-compare)
19485 ("r-randtoolbox" ,r-randtoolbox)
19487 ("r-rcpparmadillo" ,r-rcpparmadillo)))
19488 (home-page "https://cran.r-project.org/web/packages/acebayes/")
19489 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
19491 "Finding an optimal Bayesian experimental design involves maximizing an
19492 objective function given by the expectation of some appropriately chosen
19493 utility function with respect to the joint distribution of unknown
19494 quantities (including responses). This objective function is usually not
19495 available in closed form and the design space can be continuous and of high
19496 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
19497 to maximise an approximation to the expectation of the utility function.")
19498 (license license:gpl2)))
19500 (define-public r-acet
19507 (uri (cran-uri "ACEt" version))
19510 "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4"))))
19511 (properties `((upstream-name . "ACEt")))
19512 (build-system r-build-system)
19517 ("r-rcpparmadillo" ,r-rcpparmadillo)))
19518 (home-page "https://cran.r-project.org/web/packages/ACEt/")
19519 (synopsis "Estimating dynamic heritability and twin model comparison")
19521 "This package supports twin models that are able to estimate the dynamic
19522 behaviour of the variance components in the classical twin models with respect
19523 to age using B-splines and P-splines.")
19524 (license license:gpl2+)))
19526 (define-public r-acfmperiod
19528 (name "r-acfmperiod")
19533 (uri (cran-uri "acfMPeriod" version))
19536 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
19537 (properties `((upstream-name . "acfMPeriod")))
19538 (build-system r-build-system)
19540 `(("r-mass" ,r-mass)))
19541 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
19542 (synopsis "Estimation of the ACF from the M-periodogram")
19544 "This package support non-robust and robust computations of the sample
19545 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
19546 univariate and multivariate processes. The methodology consists in reversing
19547 the diagonalization procedure involving the periodogram or the
19548 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
19549 ACOVF or the ACF as discussed in Fuller (1995)
19550 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
19551 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
19552 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
19553 (license license:gpl2+)))
19555 (define-public r-gamlss-data
19557 (name "r-gamlss-data")
19562 (uri (cran-uri "gamlss.data" version))
19565 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
19566 (properties `((upstream-name . "gamlss.data")))
19567 (build-system r-build-system)
19568 (home-page "http://www.gamlss.org/")
19569 (synopsis "GAMLSS data")
19571 "This package provides data used as examples to demonstrate GAMLSS
19573 ;; Either version of the license
19574 (license (list license:gpl2 license:gpl3))))
19576 (define-public r-gamlss
19583 (uri (cran-uri "gamlss" version))
19586 "1q82md0439si0n7vqbbbdk45sjr0ad7i8mgrn3kwnr4h213pb4nk"))))
19587 (properties `((upstream-name . "gamlss")))
19588 (build-system r-build-system)
19590 `(("r-gamlss-data" ,r-gamlss-data)
19591 ("r-gamlss-dist" ,r-gamlss-dist)
19594 ("r-survival" ,r-survival)))
19595 (home-page "http://www.gamlss.org/")
19596 (synopsis "Generalized additive models for location scale and shape")
19598 "This package provides functions for fitting the generalized additive
19599 models for location scale and shape introduced by Rigby and
19600 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
19601 use a distributional regression approach where all the parameters of the
19602 conditional distribution of the response variable are modelled using
19603 explanatory variables.")
19604 ;; Either version of the license
19605 (license (list license:gpl2 license:gpl3))))
19607 (define-public r-acid
19614 (uri (cran-uri "acid" version))
19617 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
19618 (properties `((upstream-name . "acid")))
19619 (build-system r-build-system)
19621 `(("r-gamlss" ,r-gamlss)
19622 ("r-gamlss-dist" ,r-gamlss-dist)
19623 ("r-hmisc" ,r-hmisc)))
19624 (home-page "https://cran.r-project.org/web/packages/acid/")
19625 (synopsis "Analysing conditional income distributions")
19627 "This package provides functions for the analysis of income distributions
19628 for subgroups of the population as defined by a set of variables like age,
19629 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
19630 distribution as well as functions for moments, inequality measures, entropy
19631 measures and polarisation measures of income distributions. This package thus
19632 aides the analysis of income inequality by offering tools for the exploratory
19633 analysis of income distributions at the disaggregated level.")
19634 (license license:gpl3)))
19636 (define-public r-acm4r
19643 (uri (cran-uri "acm4r" version))
19646 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
19647 (properties `((upstream-name . "acm4r")))
19648 (build-system r-build-system)
19649 (propagated-inputs `(("r-mass" ,r-mass)))
19650 (home-page "https://cran.r-project.org/web/packages/acm4r/")
19651 (synopsis "Align-and-count method comparisons of RFLP data")
19653 "This is a package to compare sequence fragment lengths or molecular
19654 weights from pairs of lanes. The number of matching bands in the
19655 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
19656 the align-and-count method.")
19657 ;; Any version of the GPL
19658 (license (list license:gpl2+ license:gpl3+))))
19660 (define-public r-filelock
19662 (name "r-filelock")
19667 (uri (cran-uri "filelock" version))
19670 "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc"))))
19671 (properties `((upstream-name . "filelock")))
19672 (build-system r-build-system)
19673 (home-page "https://github.com/r-lib/filelock")
19674 (synopsis "Portable file locking")
19676 "This library lets you place an exclusive or shared lock on a file using
19677 the appropriate system call provided by the underlying operating system.")
19678 (license license:expat)))
19680 (define-public r-filematrix
19682 (name "r-filematrix")
19687 (uri (cran-uri "filematrix" version))
19690 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
19691 (properties `((upstream-name . "filematrix")))
19692 (build-system r-build-system)
19693 ;; These inputs are needed for vignettes
19695 `(("r-knitr" ,r-knitr)
19696 ("r-rmarkdown" ,r-rmarkdown)
19697 ("pandoc-citeproc" ,pandoc-citeproc)))
19698 (home-page "https://github.com/andreyshabalin/filematrix")
19699 (synopsis "File-backed matrix class with convenient read and write access")
19701 "This package provides an interface for working with large matrices
19702 stored in files, not in computer memory. It supports multiple non-character
19703 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
19704 byte real values). Access to parts of the matrix is done by indexing, exactly
19705 as with usual R matrices. It supports very large matrices; the package has
19706 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
19707 columns, ad allows for quick addition of extra columns to a filematrix.")
19708 (license license:lgpl3)))
19710 (define-public r-acmeeqtl
19712 (name "r-acmeeqtl")
19717 (uri (cran-uri "ACMEeqtl" version))
19720 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
19721 (properties `((upstream-name . "ACMEeqtl")))
19722 (build-system r-build-system)
19724 `(("r-filematrix" ,r-filematrix)))
19725 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
19726 (synopsis "Estimation of interpretable eQTL effect sizes")
19728 "This package provides a non-linear model, termed ACME, that reflects a
19729 parsimonious biological model for allelic contributions of cis-acting eQTLs.
19730 With non-linear least-squares algorithm the maximum likelihood parameters can
19731 be estimated. The ACME model provides interpretable effect size estimates and
19732 p-values with well controlled Type-I error.")
19733 (license license:lgpl3)))
19735 (define-public r-acmer
19742 (uri (cran-uri "acmeR" version))
19745 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
19746 (properties `((upstream-name . "acmeR")))
19747 (build-system r-build-system)
19748 (propagated-inputs `(("r-foreign" ,r-foreign)))
19749 (home-page "https://cran.r-project.org/web/packages/acmeR/")
19750 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
19752 "This package provides an implementation of the ACME estimator, described
19753 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
19754 Mortality at Wind Turbines. Unlike most other models, this estimator supports
19755 decreasing-hazard Weibull model for persistence; decreasing search proficiency
19756 as carcasses age; variable bleed-through at successive searches; and interval
19757 mortality estimates. The package provides, based on search data, functions
19758 for estimating the mortality inflation factor in Frequentist and Bayesian
19760 (license license:expat)))
19762 (define-public r-r-huge
19769 (uri (cran-uri "R.huge" version))
19772 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
19773 (properties `((upstream-name . "R.huge")))
19774 (build-system r-build-system)
19776 `(("r-r-methodss3" ,r-r-methodss3)
19778 ("r-r-utils" ,r-r-utils)))
19779 (home-page "https://github.com/HenrikBengtsson/R.huge")
19780 (synopsis "Methods for accessing huge amounts of data")
19782 "This is a deprecated package for accessing huge amounts of data.
19783 Cross-platform alternatives are the following packages: bigmemory (CRAN),
19784 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
19785 the @code{aroma.affymetrix} package.")
19786 (license license:lgpl2.1+)))
19788 (define-public r-r-filesets
19790 (name "r-r-filesets")
19795 (uri (cran-uri "R.filesets" version))
19798 "08xv8b3c81nf54viyr3w912al18483k5gfnjpg7bxbdfk70dfzbh"))))
19799 (properties `((upstream-name . "R.filesets")))
19800 (build-system r-build-system)
19802 `(("r-digest" ,r-digest)
19803 ("r-r-cache" ,r-r-cache)
19804 ("r-r-methodss3" ,r-r-methodss3)
19806 ("r-r-utils" ,r-r-utils)))
19807 (home-page "https://github.com/HenrikBengtsson/R.filesets")
19808 (synopsis "Easy handling of and access to files")
19810 "This package provides classes and methods to locate, setup, subset,
19811 navigate and iterate file sets, i.e. sets of files located in one or more
19812 directories on the file system. The API is designed such that these classes
19813 can be extended via inheritance to provide a richer API for special file
19814 formats. Moreover, a specific name format is defined such that filenames and
19815 directories can be considered to have full names which consists of a name
19816 followed by comma-separated tags. This adds additional flexibility to
19817 identify file sets and individual files.")
19818 (license license:lgpl2.1+)))
19820 (define-public r-r-devices
19822 (name "r-r-devices")
19827 (uri (cran-uri "R.devices" version))
19830 "1djz6vm1b7sjvx1q319dl47gbnz9kvipaxcz9i0spyp094lv3m62"))))
19831 (properties `((upstream-name . "R.devices")))
19832 (build-system r-build-system)
19834 `(("r-base64enc" ,r-base64enc)
19835 ("r-r-methodss3" ,r-r-methodss3)
19837 ("r-r-utils" ,r-r-utils)))
19838 (home-page "https://github.com/HenrikBengtsson/R.devices")
19839 (synopsis "Unified handling of graphics devices")
19841 "This package provides functions for creating plots and image files in a
19842 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
19843 Default device options as well as scales and aspect ratios are controlled in a
19844 uniform way across all device types. Switching output format requires minimal
19845 changes in code. This package is ideal for large-scale batch processing,
19846 because it will never leave open graphics devices or incomplete image files
19847 behind, even on errors or user interrupts.")
19848 (license license:lgpl2.1+)))
19850 (define-public r-acnr
19857 (uri (cran-uri "acnr" version))
19860 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
19861 (properties `((upstream-name . "acnr")))
19862 (build-system r-build-system)
19863 (home-page "https://github.com/mpierrejean/acnr")
19864 (synopsis "Annotated copy-number regions")
19866 "This package provides SNP array data from different types of copy-number
19867 regions. These regions were identified manually by the authors of the package
19868 and may be used to generate realistic data sets with known truth.")
19869 (license license:lgpl2.1+)))
19871 (define-public r-acopula
19878 (uri (cran-uri "acopula" version))
19881 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
19882 (properties `((upstream-name . "acopula")))
19883 (build-system r-build-system)
19884 (home-page "https://cran.r-project.org/web/packages/acopula/")
19885 (synopsis "Modelling dependence with multivariate Archimax copulas")
19887 "Archimax copulas are a mixture of Archimedean and EV copulas. This
19888 package provides definitions of several parametric families of generator and
19889 dependence function, computes CDF and PDF, estimates parameters, tests for
19890 goodness of fit, generates random sample and checks copula properties for
19891 custom constructs. In the 2-dimensional case explicit formulas for density
19892 are used, contrary to higher dimensions when all derivatives are linearly
19893 approximated. Several non-archimax families (normal, FGM, Plackett) are
19894 provided as well.")
19895 (license license:gpl2)))
19897 (define-public r-tuner
19904 (uri (cran-uri "tuneR" version))
19907 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
19908 (properties `((upstream-name . "tuneR")))
19909 (build-system r-build-system)
19910 (propagated-inputs `(("r-signal" ,r-signal)))
19911 (home-page "https://cran.r-project.org/web/packages/tuneR/")
19912 (synopsis "Analysis of music and speech")
19914 "This is a package for the analysis of music and speech. Analyze music
19915 and speech, extract features like MFCCs, handle wave files and their
19916 representation in various ways, read MP3, read MIDI, perform steps of a
19917 transcription, ...")
19918 ;; Either of these versions.
19919 (license (list license:gpl2 license:gpl3))))
19921 (define-public r-seewave
19928 (uri (cran-uri "seewave" version))
19931 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
19932 (properties `((upstream-name . "seewave")))
19933 (build-system r-build-system)
19935 `(("libsndfile" ,libsndfile)))
19937 `(("r-tuner" ,r-tuner)))
19938 (home-page "http://rug.mnhn.fr/seewave")
19939 (synopsis "Sound analysis and synthesis")
19941 "This package provides functions for analysing, manipulating, displaying,
19942 editing and synthesizing time waves (particularly sound). This package
19943 processes time analysis (oscillograms and envelopes), spectral content,
19944 resonance quality factor, entropy, cross correlation and autocorrelation,
19945 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
19946 and 3D spectrograms and many other analyses.")
19947 (license license:gpl2+)))
19949 (define-public r-acousticndlcoder
19951 (name "r-acousticndlcoder")
19956 (uri (cran-uri "AcousticNDLCodeR" version))
19959 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
19961 `((upstream-name . "AcousticNDLCodeR")))
19962 (build-system r-build-system)
19964 `(("r-seewave" ,r-seewave)
19965 ("r-tuner" ,r-tuner)
19967 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
19968 (synopsis "Coding sound files for use with NDL")
19970 "Make acoustic cues to use with the R package @code{ndl}.
19971 The package implements functions used in the PLoS ONE paper \"Words from
19972 spontaneous conversational speech can be recognized with human-like accuracy
19973 by an error-driven learning algorithm that discriminates between meanings
19974 straight from smart acoustic features, bypassing the phoneme as recognition
19975 unit.\" @url{doi:10.1371/journal.pone.0174623}")
19976 (license license:gpl2+)))
19978 (define-public r-acp
19985 (uri (cran-uri "acp" version))
19988 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
19989 (properties `((upstream-name . "acp")))
19990 (build-system r-build-system)
19992 `(("r-quantmod" ,r-quantmod)
19993 ("r-tseries" ,r-tseries)))
19994 (home-page "https://cran.r-project.org/web/packages/acp/")
19995 (synopsis "Autoregressive conditional Poisson")
19997 "This package supports the analysis of count data exhibiting
19998 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
19999 model (ACP(p,q)) proposed by Heinen (2003).")
20000 (license license:gpl2)))
20002 (define-public r-ada
20009 (uri (cran-uri "ada" version))
20012 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
20013 (properties `((upstream-name . "ada")))
20014 (build-system r-build-system)
20015 (propagated-inputs `(("r-rpart" ,r-rpart)))
20016 (home-page "https://cran.r-project.org/web/packages/ada/")
20017 (synopsis "Stochastic boosting")
20019 "This package provides a straightforward, well-documented, and broad
20020 boosting routine for classification, ideally suited for small to
20021 moderate-sized data sets. It performs discrete, real, and gentle boost under
20022 both exponential and logistic loss on a given data set.")
20023 ;; Any version of the GPL.
20024 (license (list license:gpl2+ license:gpl3+))))
20026 (define-public r-genalg
20033 (uri (cran-uri "genalg" version))
20036 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
20037 (properties `((upstream-name . "genalg")))
20038 (build-system r-build-system)
20039 (home-page "https://github.com/egonw/genalg")
20040 (synopsis "R based genetic algorithm")
20042 "This package provides an R based genetic algorithm for binary and
20043 floating point chromosomes.")
20044 (license license:gpl2)))
20046 (define-public r-kernelfactory
20048 (name "r-kernelfactory")
20053 (uri (cran-uri "kernelFactory" version))
20056 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
20057 (properties `((upstream-name . "kernelFactory")))
20058 (build-system r-build-system)
20061 ("r-genalg" ,r-genalg)
20062 ("r-kernlab" ,r-kernlab)
20063 ("r-randomforest" ,r-randomforest)))
20064 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
20065 (synopsis "Ensemble of kernel machines")
20067 "Kernel factory is an ensemble method where each base classifier (random
20068 forest) is fit on the kernel matrix of a subset of the training data.")
20069 (license license:gpl2+)))
20071 (define-public r-dummies
20078 (uri (cran-uri "dummies" version))
20081 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
20082 (properties `((upstream-name . "dummies")))
20083 (build-system r-build-system)
20084 (home-page "https://decisionpatterns.com")
20085 (synopsis "Create dummy/indicator variables flexibly and efficiently")
20087 "This package lets you expand factors, characters and other eligible
20088 classes into dummy/indicator variables.")
20089 (license license:gpl2+)))
20091 (define-public r-acrm
20098 (uri (cran-uri "aCRM" version))
20101 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
20102 (properties `((upstream-name . "aCRM")))
20103 (build-system r-build-system)
20106 ("r-dummies" ,r-dummies)
20107 ("r-kernelfactory" ,r-kernelfactory)
20108 ("r-randomforest" ,r-randomforest)))
20109 (home-page "https://cran.r-project.org/web/packages/aCRM/")
20110 (synopsis "Convenience functions for analytical customer relationship management")
20112 "This package provides convenience functions for data preparation and
20113 modeling often used in @dfn{analytical customer relationship
20114 management} (aCRM).")
20115 (license license:gpl2+)))
20117 (define-public r-treeclust
20119 (name "r-treeclust")
20124 (uri (cran-uri "treeClust" version))
20127 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
20128 (properties `((upstream-name . "treeClust")))
20129 (build-system r-build-system)
20131 `(("r-cluster" ,r-cluster)
20132 ("r-rpart" ,r-rpart)))
20133 (home-page "https://cran.r-project.org/web/packages/treeClust/")
20134 (synopsis "Cluster distances through trees")
20136 "This package provides tools to create a measure of inter-point
20137 dissimilarity useful for clustering mixed data, and, optionally, perform the
20139 (license license:gpl2+)))
20141 (define-public r-acrosstic
20143 (name "r-acrosstic")
20148 (uri (cran-uri "AcrossTic" version))
20151 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
20152 (properties `((upstream-name . "AcrossTic")))
20153 (build-system r-build-system)
20155 `(("r-lpsolve" ,r-lpsolve)
20156 ("r-treeclust" ,r-treeclust)))
20157 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
20158 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
20160 "This is a package for constructing minimum-cost regular spanning
20161 subgraph as part of a non-parametric two-sample test for equality of
20163 (license license:gpl2+)))
20165 (define-public r-acrt
20172 (uri (cran-uri "acrt" version))
20175 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
20176 (properties `((upstream-name . "acrt")))
20177 (build-system r-build-system)
20179 `(("r-rcpp" ,r-rcpp)
20180 ("r-rcppeigen" ,r-rcppeigen)
20181 ("r-sandwich" ,r-sandwich)))
20182 (home-page "https://cran.r-project.org/web/packages/acrt/")
20183 (synopsis "Autocorrelation robust testing")
20185 "This package provides functions for testing affine hypotheses on the
20186 regression coefficient vector in regression models with autocorrelated
20188 (license license:gpl2)))
20190 (define-public r-acs
20197 (uri (cran-uri "acs" version))
20200 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
20201 (properties `((upstream-name . "acs")))
20202 (build-system r-build-system)
20204 `(("r-httr" ,r-httr)
20207 ("r-stringr" ,r-stringr)
20209 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
20210 (synopsis "Work with data from the US Census")
20212 "This package provides a general toolkit for downloading, managing,
20213 analyzing, and presenting data from the
20214 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
20215 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
20216 American Community Survey (ACS). Confidence intervals provided with ACS data
20217 are converted to standard errors to be bundled with estimates in complex
20218 @code{acs} objects. The package provides new methods to conduct standard
20219 operations on @code{acs} objects and present/plot data in statistically
20220 appropriate ways.")
20221 (license license:gpl3)))
20223 (define-public r-acss-data
20225 (name "r-acss-data")
20230 (uri (cran-uri "acss.data" version))
20233 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
20234 (properties `((upstream-name . "acss.data")))
20235 (build-system r-build-system)
20236 (home-page "http://complexitycalculator.com/methodology.html")
20237 (synopsis "Data for algorithmic complexity of short strings")
20239 "This is a data only package providing the algorithmic complexity of
20240 short strings, computed using the coding theorem method. For a given set of
20241 symbols in a string, all possible or a large number of random samples of
20242 Turing machines with a given number of states (e.g., 5) and number of symbols
20243 corresponding to the number of symbols in the strings were simulated until
20244 they reached a halting state or failed to end. This package contains data on
20245 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
20246 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
20247 distribution of the halting states.")
20248 (license license:gpl2+)))
20250 (define-public r-acss
20257 (uri (cran-uri "acss" version))
20260 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
20261 (properties `((upstream-name . "acss")))
20262 (build-system r-build-system)
20264 `(("r-acss-data" ,r-acss-data)
20266 (home-page "http://complexitycalculator.com/methodology.html")
20267 (synopsis "Algorithmic complexity for short strings")
20269 "The main purpose of this package is to provide the algorithmic
20270 complexity for short strings, an approximation of the Kolmogorov Complexity of
20271 a short string using the coding theorem method. While the database containing
20272 the complexity is provided in the data only package @code{acss.data}, this
20273 package provides functions accessing the data such as @code{prob_random}
20274 returning the posterior probability that a given string was produced by a
20275 random process. In addition, two traditional (but problematic) measures of
20276 complexity are also provided: entropy and change complexity.")
20277 (license license:gpl2+)))
20279 (define-public r-acswr
20286 (uri (cran-uri "ACSWR" version))
20289 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
20290 (properties `((upstream-name . "ACSWR")))
20291 (build-system r-build-system)
20293 `(("r-mass" ,r-mass)))
20294 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
20295 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
20297 "This is a companion package for the book \"A Course in Statistics with
20298 R\" (ISBN 978-1-119-15272-9.)")
20299 (license license:gpl2)))
20301 (define-public r-alabama
20304 (version "2015.3-1")
20308 (uri (cran-uri "alabama" version))
20311 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
20312 (properties `((upstream-name . "alabama")))
20313 (build-system r-build-system)
20314 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
20315 (home-page "https://cran.r-project.org/web/packages/alabama/")
20316 (synopsis "Constrained nonlinear optimization")
20318 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
20319 Algorithm; it is used for optimizing smooth nonlinear objective functions with
20320 constraints. Linear or nonlinear equality and inequality constraints are
20322 (license license:gpl2+)))
20324 (define-public r-gdina
20331 (uri (cran-uri "GDINA" version))
20334 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
20335 (properties `((upstream-name . "GDINA")))
20336 (build-system r-build-system)
20338 `(("r-alabama" ,r-alabama)
20339 ("r-ggplot2" ,r-ggplot2)
20341 ("r-nloptr" ,r-nloptr)
20342 ("r-numderiv" ,r-numderiv)
20344 ("r-rcpparmadillo" ,r-rcpparmadillo)
20345 ("r-rsolnp" ,r-rsolnp)
20346 ("r-shiny" ,r-shiny)
20347 ("r-shinydashboard" ,r-shinydashboard)))
20349 `(("r-knitr" ,r-knitr)))
20350 (home-page "https://github.com/Wenchao-Ma/GDINA")
20351 (synopsis "Generalized DINA model framework")
20353 "This package provides a set of psychometric tools for cognitive
20354 diagnosis modeling based on the generalized deterministic inputs, noisy and
20355 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
20356 and its extensions, including the sequential G-DINA model by Ma and de la
20357 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
20358 polytomous G-DINA model by Chen and de la Torre
20359 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
20360 distribution can be independent, saturated, higher-order, loglinear smoothed
20361 or structured. Q-matrix validation, item and model fit statistics, model
20362 comparison at test and item level and differential item functioning can also
20363 be conducted. A graphical user interface is also provided.")
20364 (license license:gpl3)))
20366 (define-public r-actcd
20373 (uri (cran-uri "ACTCD" version))
20376 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
20377 (properties `((upstream-name . "ACTCD")))
20378 (build-system r-build-system)
20380 `(("r-gdina" ,r-gdina)
20381 ("r-r-methodss3" ,r-r-methodss3)))
20383 `(("gfortran" ,gfortran)))
20384 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
20385 (synopsis "Asymptotic classification theory for cognitive diagnosis")
20387 "This is a package supporting cluster analysis for cognitive diagnosis
20388 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
20389 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
20390 sum-scores, cluster analysis techniques can be used to classify examinees into
20391 latent classes based on their attribute patterns. In addition to the
20392 algorithms used to classify data, three labeling approaches are proposed to
20393 label clusters so that examinees' attribute profiles can be obtained.")
20394 (license license:gpl2+)))
20396 (define-public r-ineq
20403 (uri (cran-uri "ineq" version))
20406 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
20407 (properties `((upstream-name . "ineq")))
20408 (build-system r-build-system)
20409 (home-page "https://cran.r-project.org/web/packages/ineq/")
20410 (synopsis "Measuring inequality, concentration, and poverty")
20412 "This package provides tools for measuring inequality, concentration, and
20413 poverty measures. It provides both empirical and theoretical Lorenz curves.")
20414 ;; Either of these two versions.
20415 (license (list license:gpl2 license:gpl3))))
20417 (define-public r-actfrag
20424 (uri (cran-uri "ActFrag" version))
20427 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
20428 (properties `((upstream-name . "ActFrag")))
20429 (build-system r-build-system)
20431 `(("r-accelerometry" ,r-accelerometry)
20432 ("r-dplyr" ,r-dplyr)
20434 ("r-survival" ,r-survival)
20435 ("r-tidyr" ,r-tidyr)))
20436 (home-page "https://github.com/junruidi/ActFrag")
20437 (synopsis "Activity fragmentation metrics extraction")
20439 "This package provides functions to extract commonly used fragmentation
20440 metrics to quantify time accumulation strategies based on minute level
20441 actigraphy-measured activity counts data.")
20442 (license license:gpl3)))
20444 (define-public r-ash
20451 (uri (cran-uri "ash" version))
20454 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb"))))
20455 (properties `((upstream-name . "ash")))
20456 (build-system r-build-system)
20457 (native-inputs `(("gfortran" ,gfortran)))
20458 (home-page "https://cran.r-project.org/web/packages/ash/")
20459 (synopsis "David Scott's ASH routines")
20461 "This package provides David Scott's ASH routines ported from S-PLUS to
20463 (license license:gpl2+)))
20465 (define-public r-hdrcde
20472 (uri (cran-uri "hdrcde" version))
20475 "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3"))))
20476 (properties `((upstream-name . "hdrcde")))
20477 (build-system r-build-system)
20480 ("r-ggplot2" ,r-ggplot2)
20481 ("r-kernsmooth" ,r-kernsmooth)
20483 ("r-locfit" ,r-locfit)
20484 ("r-rcolorbrewer" ,r-rcolorbrewer)))
20485 (native-inputs `(("gfortran" ,gfortran)))
20486 (home-page "http://pkg.robjhyndman.com/hdrcde")
20487 (synopsis "Highest density regions and conditional density estimation")
20489 "This is a package for the computation of highest density regions in one
20490 and two dimensions, kernel estimation of univariate density functions
20491 conditional on one covariate, and multimodal regression.")
20492 (license license:gpl3)))
20494 (define-public r-rainbow
20501 (uri (cran-uri "rainbow" version))
20504 "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3"))))
20505 (properties `((upstream-name . "rainbow")))
20506 (build-system r-build-system)
20508 `(("r-cluster" ,r-cluster)
20509 ("r-colorspace" ,r-colorspace)
20510 ("r-hdrcde" ,r-hdrcde)
20513 ("r-pcapp" ,r-pcapp)))
20514 (home-page "https://cran.r-project.org/web/packages/rainbow/")
20515 (synopsis "Bagplots, boxplots and rainbow plots for functional data")
20517 "This is a package for visualizing functional data and identifying
20518 functional outliers with bagplots, boxplots and rainbow plots.")
20519 (license license:gpl3)))
20521 (define-public r-fds
20528 (uri (cran-uri "fds" version))
20531 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0"))))
20532 (properties `((upstream-name . "fds")))
20533 (build-system r-build-system)
20535 `(("r-rainbow" ,r-rainbow)
20536 ("r-rcurl" ,r-rcurl)))
20537 (home-page "https://cran.r-project.org/web/packages/fds/")
20538 (synopsis "Functional data sets")
20539 (description "This package contains a list of functional time series,
20540 sliced functional time series, and functional data sets. Functional time
20541 series is a special type of functional data observed over time. Sliced
20542 functional time series is a special type of functional time series with a time
20543 variable observed over time.")
20544 (license license:gpl2+)))
20546 (define-public r-fda
20553 (uri (cran-uri "fda" version))
20556 "0yjrjsv55bcwqn2yxjgj3hn17wfvjvgngfw9xv3w802i52yz9gf8"))))
20557 (properties `((upstream-name . "fda")))
20558 (build-system r-build-system)
20561 ("r-matrix" ,r-matrix)))
20562 (home-page "https://www.functionaldata.org")
20563 (synopsis "Functional data analysis")
20565 "These functions were developed to support functional data analysis as
20566 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
20567 Analysis. The package includes data sets and script files working many
20569 (license license:gpl2+)))
20571 (define-public r-actigraphy
20573 (name "r-actigraphy")
20578 (uri (cran-uri "Actigraphy" version))
20581 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
20582 (properties `((upstream-name . "Actigraphy")))
20583 (build-system r-build-system)
20585 `(("r-fda" ,r-fda)))
20586 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
20587 (synopsis "Actigraphy data analysis")
20589 "This package provides tools for functional linear modeling and analysis
20590 of actigraphy data.")
20591 (license license:asl2.0)))
20593 (define-public r-activedriver
20595 (name "r-activedriver")
20600 (uri (cran-uri "ActiveDriver" version))
20603 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
20604 (properties `((upstream-name . "ActiveDriver")))
20605 (build-system r-build-system)
20607 `(("r-mass" ,r-mass)))
20608 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
20609 (synopsis "Tools for finding cancer driver proteins")
20611 "This package provides a mutation analysis tool that discovers cancer
20612 driver genes with frequent mutations in protein signalling sites such as
20613 post-translational modifications (phosphorylation, ubiquitination, etc). The
20614 Poisson generalized linear regression model identifies genes where cancer
20615 mutations in signalling sites are more frequent than expected from the
20616 sequence of the entire gene. Integration of mutations with signalling
20617 information helps find new driver genes and propose candidate mechanisms to
20619 (license license:gpl2+)))
20621 (define-public r-activitycounts
20623 (name "r-activitycounts")
20628 (uri (cran-uri "activityCounts" version))
20631 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
20633 `((upstream-name . "activityCounts")))
20634 (build-system r-build-system)
20636 `(("r-lubridate" ,r-lubridate)
20637 ("r-magrittr" ,r-magrittr)
20638 ("r-seewave" ,r-seewave)
20639 ("r-signal" ,r-signal)
20640 ("r-tibble" ,r-tibble)))
20641 (home-page "https://github.com/walkabillylab/activityCounts")
20642 (synopsis "Generate ActiLife counts")
20644 "ActiLife generates activity counts from data collected by Actigraph
20645 accelerometers. Actigraph is one of the most common research-grade
20646 accelerometers. There is considerable research validating and developing
20647 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
20648 counts are proprietary and difficult to implement if researchers use different
20649 accelerometer brands. The code creates ActiLife counts from raw acceleration
20650 data for different accelerometer brands.")
20651 (license license:gpl3)))
20653 (define-public r-activityindex
20655 (name "r-activityindex")
20660 (uri (cran-uri "ActivityIndex" version))
20663 "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5"))))
20664 (properties `((upstream-name . "ActivityIndex")))
20665 (build-system r-build-system)
20667 `(("r-data-table" ,r-data-table)
20668 ("r-matrixstats" ,r-matrixstats)
20669 ("r-r-utils" ,r-r-utils)))
20671 `(("r-knitr" ,r-knitr)))
20672 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
20673 (synopsis "Activity Index calculation using raw accelerometry data")
20675 "This is a package to read raw accelerometry from GT3X+ accelerometry
20676 data and plain table data to calculate the Activity Index from Bai et
20677 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
20678 (license license:gpl3)))
20680 (define-public r-activpal
20682 (name "r-activpal")
20687 (uri (cran-uri "activPAL" version))
20690 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
20691 (properties `((upstream-name . "activPAL")))
20692 (build-system r-build-system)
20694 `(("r-devtools" ,r-devtools)
20695 ("r-dplyr" ,r-dplyr)
20696 ("r-ggplot2" ,r-ggplot2)
20697 ("r-lubridate" ,r-lubridate)
20698 ("r-magrittr" ,r-magrittr)
20699 ("r-tidyr" ,r-tidyr)))
20700 (home-page "https://cran.r-project.org/web/packages/activPAL")
20701 (synopsis "Processing and chart generation from activPAL events files")
20703 "This package contains functions to generate pre-defined summary
20704 statistics from activPAL events files. The package also contains functions to
20705 produce informative graphics that visualize physical activity behaviour and
20706 trends. This includes generating graphs that align physical activity
20707 behaviour with additional time based observations described by other data
20708 sets, such as sleep diaries and continuous glucose monitoring data.")
20709 (license license:gpl3)))
20711 (define-public r-activpalprocessing
20713 (name "r-activpalprocessing")
20718 (uri (cran-uri "activpalProcessing" version))
20721 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
20723 `((upstream-name . "activpalProcessing")))
20724 (build-system r-build-system)
20726 `(("r-chron" ,r-chron)))
20727 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
20728 (synopsis "Process activPAL events files")
20730 "This package performs estimation of physical activity and sedentary
20731 behavior variables from activPAL events files.")
20732 ;; Either version of the GPL.
20733 (license (list license:gpl2 license:gpl3))))
20735 (define-public r-actogrammr
20737 (name "r-actogrammr")
20742 (uri (cran-uri "actogrammr" version))
20745 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
20746 (properties `((upstream-name . "actogrammr")))
20747 (build-system r-build-system)
20749 `(("r-dplyr" ,r-dplyr)
20750 ("r-ggplot2" ,r-ggplot2)
20751 ("r-lubridate" ,r-lubridate)
20752 ("r-readr" ,r-readr)
20753 ("r-tidyr" ,r-tidyr)))
20754 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
20755 (synopsis "Read in activity data and plot actograms")
20757 "Read in activity measurements from standard file formats used by
20758 circadian rhythm researchers, currently only ClockLab format, and process and
20759 plot the data. The central type of plot is the actogram, as first described
20760 in \"Activity and distribution of certain wild mice in relation to biotic
20761 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
20762 (license license:gpl3)))
20764 (define-public r-expint
20771 (uri (cran-uri "expint" version))
20774 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
20775 (properties `((upstream-name . "expint")))
20776 (build-system r-build-system)
20777 (home-page "https://gitlab.com/vigou3/expint")
20778 (synopsis "Exponential integral and incomplete Gamma function")
20780 "This package provides the exponential integrals @code{E_1(x)},
20781 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
20782 function @code{G(a, x)} defined for negative values of its first argument.
20783 The package also gives easy access to the underlying C routines through an
20784 API; see the package vignette for details.")
20785 (license license:gpl2+)))
20787 (define-public r-actuar
20794 (uri (cran-uri "actuar" version))
20797 "0sxn1mskh7x164f1vbrqnadgxnq7y2p3a9mlmqc0sp6cqkw9lhp9"))))
20798 (properties `((upstream-name . "actuar")))
20799 (build-system r-build-system)
20800 (propagated-inputs `(("r-expint" ,r-expint)))
20801 (home-page "https://gitlab.com/vigou3/actuar")
20802 (synopsis "Actuarial functions and heavy tailed distributions")
20804 "This package provides functions and data sets for actuarial science:
20805 modeling of loss distributions; risk theory and ruin theory; simulation of
20806 compound models, discrete mixtures and compound hierarchical models;
20807 credibility theory. It boasts support for many additional probability
20808 distributions to model insurance loss amounts and loss frequency: 19
20809 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
20810 distribution; zero-truncated and zero-modified extensions of the standard
20811 discrete distributions. It also supports phase-type distributions commonly
20812 used to compute ruin probabilities.")
20813 (license license:gpl2+)))
20815 (define-public r-bmp
20822 (uri (cran-uri "bmp" version))
20825 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
20826 (properties `((upstream-name . "bmp")))
20827 (build-system r-build-system)
20828 (home-page "https://cran.r-project.org/web/packages/bmp/")
20829 (synopsis "Read Bitmap (BMP) images")
20831 "This package provides pure R tools to read BMP format images. It is
20832 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
20833 (license license:gpl2+)))
20835 (define-public r-readbitmap
20837 (name "r-readbitmap")
20842 (uri (cran-uri "readbitmap" version))
20845 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
20846 (properties `((upstream-name . "readbitmap")))
20847 (build-system r-build-system)
20849 `(("libjpeg" ,libjpeg-turbo)
20850 ("libpng" ,libpng)))
20855 ("r-tiff" ,r-tiff)))
20856 (home-page "https://github.com/jefferis/readbitmap")
20857 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
20859 "This package provides tools to identify and read BMP, JPEG, PNG, and
20860 TIFF format bitmap images. Identification defaults to the use of the magic
20861 number embedded in the file rather than the file extension.")
20862 (license license:gpl2+)))
20864 (define-public r-imager
20871 (uri (cran-uri "imager" version))
20874 "1wxvbv803222gjrf1ys6a349xlnmmdw3kqgi93piq9gq7lahihvg"))))
20875 (properties `((upstream-name . "imager")))
20876 (build-system r-build-system)
20879 ("libtiff" ,libtiff)
20883 `(("r-downloader" ,r-downloader)
20884 ("r-igraph" ,r-igraph)
20886 ("r-magrittr" ,r-magrittr)
20888 ("r-purrr" ,r-purrr)
20890 ("r-readbitmap" ,r-readbitmap)
20891 ("r-stringr" ,r-stringr)))
20893 `(("pkg-config" ,pkg-config)
20894 ("r-knitr" ,r-knitr)))
20895 (home-page "https://dahtah.github.io/imager/")
20896 (synopsis "Image processing library")
20898 "This is a package for fast image processing for images in up to 4
20899 dimensions (two spatial dimensions, one time/depth dimension, one color
20900 dimension). It provides most traditional image processing tools (filtering,
20901 morphology, transformations, etc.) as well as various functions for easily
20902 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
20903 simple, modern C++ library for image processing.")
20904 (license license:lgpl3)))
20906 (define-public r-acuityview
20908 (name "r-acuityview")
20913 (uri (cran-uri "AcuityView" version))
20916 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
20917 (properties `((upstream-name . "AcuityView")))
20918 (build-system r-build-system)
20920 `(("r-fftwtools" ,r-fftwtools)
20921 ("r-imager" ,r-imager)
20922 ("r-plotrix" ,r-plotrix)))
20923 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
20924 (synopsis "Display scenes as seen by an animal with less acute vision")
20926 "This package provides a simple method for representing a visual scene as
20927 it may be seen by an animal with less acute vision.")
20928 (license license:gpl2+)))
20930 (define-public r-caret
20937 (uri (cran-uri "caret" version))
20940 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
20941 (build-system r-build-system)
20943 `(("r-foreach" ,r-foreach)
20944 ("r-ggplot2" ,r-ggplot2)
20945 ("r-lattice" ,r-lattice)
20946 ("r-modelmetrics" ,r-modelmetrics)
20950 ("r-recipes" ,r-recipes)
20951 ("r-reshape2" ,r-reshape2)
20952 ("r-withr" ,r-withr)))
20954 `(("r-knitr" ,r-knitr)))
20955 (home-page "https://github.com/topepo/caret")
20956 (synopsis "Classification and regression training")
20958 "This package provides miscellaneous functions for training and plotting
20959 classification and regression models.")
20960 (license license:gpl2+)))
20962 (define-public r-adabag
20969 (uri (cran-uri "adabag" version))
20972 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
20973 (properties `((upstream-name . "adabag")))
20974 (build-system r-build-system)
20976 `(("r-caret" ,r-caret)
20977 ("r-doparallel" ,r-doparallel)
20978 ("r-foreach" ,r-foreach)
20979 ("r-rpart" ,r-rpart)))
20980 (home-page "https://cran.r-project.org/web/packages/adabag/")
20981 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
20983 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
20984 Breiman's Bagging algorithm using classification trees as individual
20985 classifiers. Once these classifiers have been trained, they can be used to
20986 predict on new data. Also, cross validation estimation of the error can be
20988 (license license:gpl2+)))
20990 (define-public r-adagio
20997 (uri (cran-uri "adagio" version))
21000 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
21001 (properties `((upstream-name . "adagio")))
21002 (build-system r-build-system)
21003 (native-inputs `(("gfortran" ,gfortran)))
21004 (home-page "https://cran.r-project.org/web/packages/adagio/")
21005 (synopsis "Discrete and global optimization routines")
21007 "This package provides methods and algorithms for discrete optimization,
21008 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
21009 Hooke-Jeeves minimization, and some (evolutionary) global optimization
21011 (license license:gpl3+)))
21013 (define-public r-univoutl
21015 (name "r-univoutl")
21020 (uri (cran-uri "univOutl" version))
21023 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
21024 (properties `((upstream-name . "univOutl")))
21025 (build-system r-build-system)
21027 `(("r-hmisc" ,r-hmisc)
21028 ("r-robustbase" ,r-robustbase)))
21029 (home-page "https://github.com/marcellodo/univOutl")
21030 (synopsis "Detection of univariate outliers")
21032 "This package provides well-known outlier detection techniques in the
21033 univariate case. Methods to deal with skewed distribution are included too.
21034 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
21035 historical data is implemented as well. When available, survey weights can be
21036 used in outliers detection.")
21037 (license license:gpl2+)))
21039 (define-public r-tolerance
21041 (name "r-tolerance")
21046 (uri (cran-uri "tolerance" version))
21049 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
21050 (properties `((upstream-name . "tolerance")))
21051 (build-system r-build-system)
21053 `(("r-mass" ,r-mass)
21055 (home-page "https://cran.r-project.org/web/packages/tolerance/")
21056 (synopsis "Statistical tolerance intervals and regions")
21058 "This package provides functions for estimating tolerance
21059 limits (intervals) for various univariate distributions (binomial, Cauchy,
21060 discrete Pareto, exponential, two-parameter exponential, extreme value,
21061 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
21062 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
21063 Bayesian normal tolerance limits, multivariate normal tolerance regions,
21064 nonparametric tolerance intervals, tolerance bands for regression
21065 settings (linear regression, nonlinear regression, nonparametric regression,
21066 and multivariate regression), and analysis of variance tolerance intervals.
21067 Visualizations are also available for most of these settings.")
21068 (license license:gpl2+)))
21070 (define-public r-additivitytests
21072 (name "r-additivitytests")
21077 (uri (cran-uri "additivityTests" version))
21080 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
21082 `((upstream-name . "additivityTests")))
21083 (build-system r-build-system)
21084 (home-page "https://github.com/simecek/additivityTests")
21085 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
21087 "This package provides an implementation of the Tukey, Mandel,
21088 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
21089 (license license:gpl3)))
21091 (define-public r-flexclust
21093 (name "r-flexclust")
21098 (uri (cran-uri "flexclust" version))
21101 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
21102 (properties `((upstream-name . "flexclust")))
21103 (build-system r-build-system)
21105 `(("r-class" ,r-class)
21106 ("r-lattice" ,r-lattice)
21107 ("r-modeltools" ,r-modeltools)))
21108 (home-page "https://cran.r-project.org/web/packages/flexclust/")
21109 (synopsis "Flexible cluster algorithms")
21111 "The main function @code{kcca} implements a general framework for
21112 k-centroids cluster analysis supporting arbitrary distance measures and
21113 centroid computation. Further cluster methods include hard competitive
21114 learning, neural gas, and QT clustering. There are numerous visualization
21115 methods for cluster results (neighborhood graphs, convex cluster hulls,
21116 barcharts of centroids, ...), and bootstrap methods for the analysis of
21117 cluster stability.")
21118 (license license:gpl2)))
21120 (define-public r-biclust
21127 (uri (cran-uri "biclust" version))
21130 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
21131 (properties `((upstream-name . "biclust")))
21132 (build-system r-build-system)
21134 `(("r-additivitytests" ,r-additivitytests)
21135 ("r-colorspace" ,r-colorspace)
21136 ("r-flexclust" ,r-flexclust)
21137 ("r-ggplot2" ,r-ggplot2)
21138 ("r-lattice" ,r-lattice)
21140 ("r-tidyr" ,r-tidyr)))
21141 (home-page "https://cran.r-project.org/web/packages/biclust/")
21142 (synopsis "BiCluster algorithms")
21144 "The main function @code{biclust()} provides several algorithms to find
21145 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
21146 In addition, the package provides methods for data
21147 preprocessing (normalization and discretization), visualization, and
21148 validation of bicluster solutions.")
21149 (license license:gpl3)))
21151 (define-public r-icge
21158 (uri (cran-uri "ICGE" version))
21161 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
21162 (properties `((upstream-name . "ICGE")))
21163 (build-system r-build-system)
21165 `(("r-cluster" ,r-cluster)
21166 ("r-mass" ,r-mass)))
21167 (home-page "https://cran.r-project.org/web/packages/ICGE/")
21168 (synopsis "Cluster estimation and identification of atypical units")
21170 "ICGE is a package that helps to estimate the number of real clusters in
21171 data as well as to identify atypical units. The underlying methods are based
21172 on distances rather than on unit x variables.")
21173 (license license:gpl2+)))
21175 (define-public r-depth
21178 (version "2.1-1.1")
21182 (uri (cran-uri "depth" version))
21185 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
21186 (properties `((upstream-name . "depth")))
21187 (build-system r-build-system)
21189 `(("r-abind" ,r-abind)
21190 ("r-circular" ,r-circular)
21193 `(("gfortran" ,gfortran)))
21194 (home-page "https://cran.r-project.org/web/packages/depth/")
21195 (synopsis "Nonparametric depth functions for multivariate analysis")
21197 "This package provides tools for depth functions methodology applied to
21198 multivariate analysis. Besides allowing calculation of depth values and
21199 depth-based location estimators, the package includes functions or drawing
21200 contour plots and perspective plots of depth functions. Euclidean and
21201 spherical depths are supported.")
21202 (license license:gpl2)))
21204 (define-public r-archetypes
21206 (name "r-archetypes")
21207 (version "2.2-0.1")
21211 (uri (cran-uri "archetypes" version))
21214 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
21215 (properties `((upstream-name . "archetypes")))
21216 (build-system r-build-system)
21218 `(("r-modeltools" ,r-modeltools)
21219 ("r-nnls" ,r-nnls)))
21220 (home-page "https://cran.r-project.org/web/packages/archetypes")
21221 (synopsis "Archetypal analysis")
21223 "The main function @code{archetypes} implements a framework for
21224 archetypal analysis supporting arbitrary problem solving mechanisms for the
21225 different conceptual parts of the algorithm.")
21226 (license license:gpl2+)))
21228 (define-public r-shapes
21235 (uri (cran-uri "shapes" version))
21238 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
21239 (properties `((upstream-name . "shapes")))
21240 (build-system r-build-system)
21242 `(("r-mass" ,r-mass)
21243 ("r-minpack-lm" ,r-minpack-lm)
21245 ("r-scatterplot3d" ,r-scatterplot3d)))
21246 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
21247 (synopsis "Statistical shape analysis")
21249 "This package provides routines for the statistical analysis of landmark
21250 shapes, including Procrustes analysis, graphical displays, principal
21251 components analysis, permutation and bootstrap tests, thin-plate spline
21252 transformation grids and comparing covariance matrices. See Dryden, I.L. and
21253 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
21254 Edition), John Wiley and Sons.")
21255 (license license:gpl2)))
21257 (define-public r-anthropometry
21259 (name "r-anthropometry")
21264 (uri (cran-uri "Anthropometry" version))
21267 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
21268 (properties `((upstream-name . "Anthropometry")))
21269 (build-system r-build-system)
21271 `(("r-archetypes" ,r-archetypes)
21272 ("r-biclust" ,r-biclust)
21273 ("r-cluster" ,r-cluster)
21274 ("r-depth" ,r-depth)
21279 ("r-shapes" ,r-shapes)))
21281 `(("r-knitr" ,r-knitr)))
21282 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
21283 (synopsis "Statistical methods for anthropometric data")
21285 "This package provides statistical methods especially developed to
21286 analyze anthropometric data. These methods are aimed at providing effective
21287 solutions to some commons problems related to Ergonomics and Anthropometry.
21288 They are based on clustering, the statistical concept of data depth,
21289 statistical shape analysis and archetypal analysis.")
21290 (license license:gpl2+)))
21292 (define-public r-adamethods
21294 (name "r-adamethods")
21299 (uri (cran-uri "adamethods" version))
21302 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
21303 (properties `((upstream-name . "adamethods")))
21304 (build-system r-build-system)
21306 `(("r-anthropometry" ,r-anthropometry)
21307 ("r-archetypes" ,r-archetypes)
21309 ("r-foreach" ,r-foreach)
21311 ("r-tolerance" ,r-tolerance)
21312 ("r-univoutl" ,r-univoutl)))
21313 (home-page "https://cran.r-project.org/web/packages/adamethods/")
21314 (synopsis "Archetypoid algorithms and anomaly detection")
21316 "This package is a collection of several algorithms to obtain
21317 archetypoids with small and large databases and with both classical
21318 multivariate data and functional data (univariate and multivariate). Some of
21319 these algorithms also detect anomalies (outliers).")
21320 (license license:gpl2+)))
21322 (define-public r-idpmisc
21329 (uri (cran-uri "IDPmisc" version))
21332 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
21333 (properties `((upstream-name . "IDPmisc")))
21334 (build-system r-build-system)
21336 `(("r-lattice" ,r-lattice)))
21337 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
21338 (synopsis "Functions for data analyses and visualization")
21340 "This package provides different high-level graphics functions for
21341 displaying large datasets, displaying circular data in a very flexible way,
21342 finding local maxima, brewing color ramps, drawing nice arrows, zooming
21343 2D-plots, creating figures with differently colored margin and plot region.
21344 In addition, the package contains auxiliary functions for data manipulation
21345 like omitting observations with irregular values or selecting data by logical
21346 vectors, which include NAs. Other functions are especially useful in
21347 spectroscopy and analyses of environmental data: robust baseline fitting,
21348 finding peaks in spectra, converting humidity measures.")
21349 (license license:gpl3+)))
21351 (define-public r-qqman
21358 (uri (cran-uri "qqman" version))
21361 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
21362 (properties `((upstream-name . "qqman")))
21363 (build-system r-build-system)
21365 `(("r-calibrate" ,r-calibrate)))
21366 (home-page "https://cran.r-project.org/web/packages/qqman/")
21367 (synopsis "Q-Q and Manhattan plots for GWAS data")
21369 "This package allows you to create Q-Q and Manhattan plots for GWAS data
21370 from PLINK results.")
21371 (license license:gpl3)))
21373 (define-public r-ggplot-multistats
21375 (name "r-ggplot-multistats")
21380 (uri (cran-uri "ggplot.multistats" version))
21383 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
21385 `((upstream-name . "ggplot.multistats")))
21386 (build-system r-build-system)
21388 `(("r-ggplot2" ,r-ggplot2)
21389 ("r-hexbin" ,r-hexbin)
21390 ("r-rlang" ,r-rlang)
21391 ("r-scales" ,r-scales)))
21392 (home-page "https://github.com/flying-sheep/ggplot.multistats")
21393 (synopsis "Multiple summary statistics for binned stats/geometries")
21395 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
21396 which functions similar to its singular form, but allows the use of multiple
21397 statistics per bin. Those statistics can be mapped to multiple bin
21399 (license license:gpl3)))
21401 (define-public r-knn-covertree
21403 (name "r-knn-covertree")
21408 (uri (cran-uri "knn.covertree" version))
21411 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
21412 (properties `((upstream-name . "knn.covertree")))
21413 (build-system r-build-system)
21415 `(("r-matrix" ,r-matrix)
21417 ("r-rcppeigen" ,r-rcppeigen)))
21418 (home-page "https://github.com/flying-sheep/knn.covertree")
21419 (synopsis "Accurate kNN Implementation with multiple distance measures")
21421 "Similarly to the FNN package, this package allows calculation of the k
21422 nearest neighbors (kNN) of a data matrix. The implementation is based on
21423 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
21424 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
21425 (license license:agpl3+)))
21427 (define-public r-poibin
21434 (uri (cran-uri "poibin" version))
21437 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
21438 (properties `((upstream-name . "poibin")))
21439 (build-system r-build-system)
21440 (home-page "https://cran.r-project.org/web/packages/poibin/")
21441 (synopsis "Poisson binomial distribution")
21443 "This package provides an implementation of both the exact and
21444 approximation methods for computing the @dfn{cumulative distribution
21445 function} (CDF) of the Poisson binomial distribution. It also provides the
21446 @dfn{probability mass function} (PMF), quantile function, and random number
21447 generation for the Poisson binomial distribution.")
21448 (license license:gpl2)))
21450 (define-public r-diagram
21457 (uri (cran-uri "diagram" version))
21460 "1r3lyl0h7mk9cfg8smr3jydfkjdawaphnxibkxfjqa7029vkxh79"))))
21461 (properties `((upstream-name . "diagram")))
21462 (build-system r-build-system)
21464 `(("r-shape" ,r-shape)))
21465 (home-page "https://cran.r-project.org/web/packages/diagram/")
21466 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
21468 "This package provides tools to visualize simple graphs (networks) based
21469 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
21470 electrical networks, etc. It also includes supporting material for the book
21471 \"A practical guide to ecological modelling - using R as a simulation
21472 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
21473 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
21474 Francesca Mazzia (2012).")
21475 (license license:gpl2+)))
21477 (define-public r-lim
21484 (uri (cran-uri "LIM" version))
21487 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
21488 (properties `((upstream-name . "LIM")))
21489 (build-system r-build-system)
21491 `(("r-diagram" ,r-diagram)
21492 ("r-limsolve" ,r-limsolve)))
21493 (home-page "https://cran.r-project.org/web/packages/LIM/")
21494 (synopsis "Linear inverse model examples and solution methods")
21496 "This package provides functions that read and solve linear inverse
21497 problems (food web problems, linear programming problems).")
21498 (license license:gpl2+)))
21500 (define-public r-shinycssloaders
21502 (name "r-shinycssloaders")
21507 (uri (cran-uri "shinycssloaders" version))
21510 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
21512 `((upstream-name . "shinycssloaders")))
21513 (build-system r-build-system)
21515 `(("r-digest" ,r-digest)
21517 ("r-shiny" ,r-shiny)))
21518 (home-page "https://github.com/andrewsali/shinycssloaders")
21519 (synopsis "Add CSS loading animations to Shiny outputs")
21521 "This package provides tools to create a lightweight Shiny wrapper for
21522 the css-loaders created by Luke Hass
21523 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
21524 automatically show a loader when the output is (re)calculating.")
21525 (license license:gpl3)))
21527 (define-public r-rsvg
21534 (uri (cran-uri "rsvg" version))
21537 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
21538 (properties `((upstream-name . "rsvg")))
21539 (build-system r-build-system)
21541 `(("librsvg" ,librsvg)
21544 `(("pkg-config" ,pkg-config)
21545 ("r-knitr" ,r-knitr)))
21546 (home-page "https://github.com/jeroen/rsvg#readme")
21547 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
21549 "This package allows you to render vector-based SVG images into
21550 high-quality custom-size bitmap arrays using the librsvg2 library. The
21551 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
21552 addition, the package can convert images directly to various formats such as
21553 PDF or PostScript.")
21554 (license license:expat)))
21556 (define-public r-influencer
21558 (name "r-influencer")
21563 (uri (cran-uri "influenceR" version))
21566 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
21567 (properties `((upstream-name . "influenceR")))
21568 (build-system r-build-system)
21570 `(("r-igraph" ,r-igraph)
21571 ("r-matrix" ,r-matrix)))
21572 (home-page "https://github.com/rcc-uchicago/influenceR")
21573 (synopsis "Tools to quantify structural importance of nodes in a network")
21575 "This package provides functionality to compute various node centrality
21576 measures on networks. Included are functions to compute betweenness
21577 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
21578 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
21579 algorithm to identify key players, and Valente's bridging metric. The
21580 betweenness, Key Players, and bridging implementations are parallelized with
21582 (license license:gpl2)))
21584 (define-public r-emplik
21591 (uri (cran-uri "emplik" version))
21594 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
21595 (properties `((upstream-name . "emplik")))
21596 (build-system r-build-system)
21598 `(("r-quantreg" ,r-quantreg)))
21599 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
21600 (synopsis "Empirical likelihood ratio for censored/truncated data")
21602 "This package provides empirical likelihood ratio tests for
21603 means/quantiles/hazards from possibly censored and/or truncated data. It also
21605 (license license:gpl2+)))
21607 (define-public r-imputeyn
21609 (name "r-imputeyn")
21614 (uri (cran-uri "imputeYn" version))
21617 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
21618 (properties `((upstream-name . "imputeYn")))
21619 (build-system r-build-system)
21621 `(("r-boot" ,r-boot)
21622 ("r-emplik" ,r-emplik)
21623 ("r-mvtnorm" ,r-mvtnorm)
21624 ("r-quadprog" ,r-quadprog)
21625 ("r-survival" ,r-survival)))
21626 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
21627 (synopsis "Impute last largest censored observation under weighted least squares")
21629 "This package allows for the imputation of the last largest censored
21630 observantions. This method brings less bias and more efficient estimates for
21632 (license license:gpl2)))
21634 (define-public r-adapenetclass
21636 (name "r-adapenetclass")
21641 (uri (cran-uri "AdapEnetClass" version))
21644 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
21645 (properties `((upstream-name . "AdapEnetClass")))
21646 (build-system r-build-system)
21648 `(("r-glmnet" ,r-glmnet)
21649 ("r-imputeyn" ,r-imputeyn)
21651 ("r-quadprog" ,r-quadprog)))
21652 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
21653 (synopsis "Class of adaptive elastic net methods for censored data")
21655 "This package provides methods for variable selection for AFT models.")
21656 (license license:gpl2)))
21658 (define-public r-flock
21665 (uri (cran-uri "flock" version))
21668 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
21669 (properties `((upstream-name . "flock")))
21670 (build-system r-build-system)
21671 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
21672 (home-page "https://cran.r-project.org/web/packages/flock/")
21673 (synopsis "Process synchronization using file locks")
21675 "This package implements synchronization between R processes (spawned by
21676 using the @code{parallel} package for instance) using file locks. It supports
21677 both exclusive and shared locking.")
21678 (license license:asl2.0)))
21680 (define-public r-archivist
21682 (name "r-archivist")
21687 (uri (cran-uri "archivist" version))
21690 "0sk16bcafgswrvwh39ysbgm6jvsg20yil4pdsg3wsp81nnsrb43k"))))
21691 (properties `((upstream-name . "archivist")))
21692 (build-system r-build-system)
21695 ("r-digest" ,r-digest)
21696 ("r-flock" ,r-flock)
21698 ("r-lubridate" ,r-lubridate)
21699 ("r-magrittr" ,r-magrittr)
21700 ("r-rcurl" ,r-rcurl)
21701 ("r-rsqlite" ,r-rsqlite)))
21703 `(("r-knitr" ,r-knitr)))
21704 (home-page "https://pbiecek.github.io/archivist/")
21705 (synopsis "Tools for storing, restoring and searching for R objects")
21707 "Data exploration and modelling is a process in which a lot of data
21708 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
21709 statistical models, different versions of data sets and different versions of
21710 results. Archivist helps to store and manage artifacts created in R. It
21711 allows you to store selected artifacts as binary files together with their
21712 metadata and relations. Archivist allows sharing artifacts with others. It
21713 can look for already created artifacts by using its class, name, date of the
21714 creation or other properties. It also makes it easy to restore such
21716 (license license:gpl2)))
21718 (define-public r-versions
21720 (name "r-versions")
21725 (uri (cran-uri "versions" version))
21728 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
21729 (properties `((upstream-name . "versions")))
21730 (build-system r-build-system)
21731 (home-page "https://cran.r-project.org/web/packages/versions/")
21732 (synopsis "Query and install specific versions of CRAN packages")
21734 "This package allows you to install specified versions of R packages
21735 hosted on CRAN and provides functions to list available versions and the
21736 versions of currently installed packages.")
21737 (license license:bsd-3)))
21739 (define-public r-adapr
21746 (uri (cran-uri "adapr" version))
21749 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
21750 (properties `((upstream-name . "adapr")))
21751 (build-system r-build-system)
21753 `(("r-archivist" ,r-archivist)
21754 ("r-devtools" ,r-devtools)
21755 ("r-digest" ,r-digest)
21756 ("r-doparallel" ,r-doparallel)
21757 ("r-gdata" ,r-gdata)
21758 ("r-ggplot2" ,r-ggplot2)
21759 ("r-git2r" ,r-git2r)
21760 ("r-igraph" ,r-igraph)
21761 ("r-knitr" ,r-knitr)
21762 ("r-plotly" ,r-plotly)
21764 ("r-rmarkdown" ,r-rmarkdown)
21765 ("r-shiny" ,r-shiny)
21766 ("r-shinydashboard" ,r-shinydashboard)
21767 ("r-versions" ,r-versions)))
21768 (home-page "https://cran.r-project.org/web/packages/adapr/")
21769 (synopsis "Implementation of an accountable data analysis process")
21771 "This package tracks reading and writing within R scripts that are
21772 organized into a directed acyclic graph. It contains an interactive Shiny
21773 application @code{adaprApp()}. It uses Git and file hashes to track version
21774 histories of inputs and outputs.")
21775 (license license:lgpl2.0)))
21777 (define-public r-adapsamp
21779 (name "r-adapsamp")
21784 (uri (cran-uri "AdapSamp" version))
21787 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
21788 (properties `((upstream-name . "AdapSamp")))
21789 (build-system r-build-system)
21790 (propagated-inputs `(("r-pracma" ,r-pracma)))
21791 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
21792 (synopsis "Adaptive sampling algorithms")
21794 "For distributions whose probability density functions are log-concave,
21795 the adaptive rejection sampling algorithm can be used to build envelope
21796 functions for sampling. For others, the modified adaptive rejection sampling
21797 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
21798 adaptive slice sampling algorithm can be used. This R package mainly includes
21799 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
21800 @code{rASS()}. These functions can realize sampling based on the algorithms
21802 (license license:gpl2)))
21804 (define-public r-adaptalint
21806 (name "r-adaptalint")
21811 (uri (cran-uri "adaptalint" version))
21814 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
21815 (properties `((upstream-name . "adaptalint")))
21816 (build-system r-build-system)
21818 `(("r-dplyr" ,r-dplyr)
21819 ("r-lintr" ,r-lintr)
21820 ("r-purrr" ,r-purrr)))
21821 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
21822 (synopsis "Check R code style")
21824 "This package provides tools to infer the code style (which style rules
21825 are followed and which ones are not) from one package and use it to check
21826 another. This makes it easier to find and correct the most important problems
21828 (license license:gpl3)))
21830 (define-public r-fracdiff
21832 (name "r-fracdiff")
21837 (uri (cran-uri "fracdiff" version))
21840 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
21841 (properties `((upstream-name . "fracdiff")))
21842 (build-system r-build-system)
21843 (home-page "https://github.com/mmaechler/fracdiff")
21845 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
21847 "This package provides tools for the maximum likelihood estimation of the
21848 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
21849 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
21850 (license license:gpl2+)))
21852 (define-public r-forecast
21854 (name "r-forecast")
21859 (uri (cran-uri "forecast" version))
21862 "0vrql5d4v28890np2m6ws1nr1fcl6frs1bz74vfkihkixcmkl3j9"))))
21863 (properties `((upstream-name . "forecast")))
21864 (build-system r-build-system)
21866 `(("r-colorspace" ,r-colorspace)
21867 ("r-fracdiff" ,r-fracdiff)
21868 ("r-ggplot2" ,r-ggplot2)
21869 ("r-lmtest" ,r-lmtest)
21870 ("r-magrittr" ,r-magrittr)
21873 ("r-rcpparmadillo" ,r-rcpparmadillo)
21874 ("r-timedate" ,r-timedate)
21875 ("r-tseries" ,r-tseries)
21879 `(("r-knitr" ,r-knitr))) ; needed for vignettes
21880 (home-page "https://pkg.robjhyndman.com/forecast/")
21881 (synopsis "Forecasting functions for time series and linear models")
21883 "This package provides methods and tools for displaying and analysing
21884 univariate time series forecasts including exponential smoothing via state
21885 space models and automatic ARIMA modelling.")
21886 (license license:gpl3)))
21888 (define-public r-xmisc
21895 (uri (cran-uri "Xmisc" version))
21898 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
21899 (properties `((upstream-name . "Xmisc")))
21900 (build-system r-build-system)
21901 (home-page "https://cran.r-project.org/package=Xmisc")
21903 "Xiaobei's miscellaneous classes and functions")
21905 "This package provides Xiaobei's miscellaneous classes and functions,
21906 which are useful when developing R packages for @dfn{object oriented
21907 programming} (OOP) using R Reference Class.")
21908 (license license:gpl2+)))
21910 (define-public r-proxyc
21917 (uri (cran-uri "proxyC" version))
21920 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
21921 (properties `((upstream-name . "proxyC")))
21922 (build-system r-build-system)
21924 `(("r-matrix" ,r-matrix)
21926 ("r-rcpparmadillo" ,r-rcpparmadillo)
21927 ("r-rcppparallel" ,r-rcppparallel)))
21928 (home-page "https://cran.r-project.org/package=proxyC")
21929 (synopsis "Compute proximity in large sparse matrices")
21931 "This package provides efficient tools to compute the proximity between
21932 rows or columns of large matrices. Functions are optimised for large sparse
21933 matrices using the Armadillo and Intel TBB libraries. Among several built-in
21934 similarity/distance measures, computation of correlation, cosine similarity
21935 and Euclidean distance is particularly fast.")
21936 (license license:gpl3)))
21938 (define-public r-isocodes
21940 (name "r-isocodes")
21941 (version "2020.12.04")
21945 (uri (cran-uri "ISOcodes" version))
21948 "18373rkhmwm7y2drvfbhrxkqw9d23avf0ndvh0fg00z4djvddkjx"))))
21949 (properties `((upstream-name . "ISOcodes")))
21950 (build-system r-build-system)
21951 (home-page "https://cran.r-project.org/package=ISOcodes")
21952 (synopsis "Selected ISO codes")
21954 "This package provides ISO language, territory, currency, script and
21955 character codes. It provides ISO 639 language codes, ISO 3166 territory
21956 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
21957 character codes as well as the UN M.49 area codes.")
21958 (license license:gpl2)))
21960 (define-public r-stopwords
21962 (name "r-stopwords")
21967 (uri (cran-uri "stopwords" version))
21970 "1f862y30c4r0phamlp7shzkpxg0vh3i410xy0336w310hv3wqsxn"))))
21971 (properties `((upstream-name . "stopwords")))
21972 (build-system r-build-system)
21974 `(("r-isocodes" ,r-isocodes)))
21975 (home-page "https://github.com/quanteda/stopwords")
21976 (synopsis "Multilingual stopword lists")
21978 "This package provides multiple sources of stopwords, for use in text
21979 analysis and natural language processing.")
21980 (license license:expat)))
21982 (define-public r-spacyr
21989 (uri (cran-uri "spacyr" version))
21992 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
21993 (properties `((upstream-name . "spacyr")))
21994 (build-system r-build-system)
21996 `(("r-data-table" ,r-data-table)
21997 ("r-reticulate" ,r-reticulate)))
21998 (home-page "https://spacyr.quanteda.io")
21999 (synopsis "R wrapper for the spaCy NLP library")
22001 "This package provides an R wrapper to the Python @dfn{natural language
22002 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
22003 (license license:gpl3)))
22005 (define-public r-snowballc
22007 (name "r-snowballc")
22012 (uri (cran-uri "SnowballC" version))
22015 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
22016 (properties `((upstream-name . "SnowballC")))
22017 (build-system r-build-system)
22018 (home-page "https://r-forge.r-project.org/projects/r-temis/")
22019 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
22021 "This package provides an R interface to the C @code{libstemmer} library
22022 that implements Porter's word stemming algorithm for collapsing words to a
22023 common root to aid comparison of vocabulary. Currently supported languages
22024 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
22025 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
22026 (license license:bsd-3)))
22028 (define-public r-quanteda
22030 (name "r-quanteda")
22035 (uri (cran-uri "quanteda" version))
22038 "13rjwgmg5v1dbryrs9ifyy76s5ib6wrbrm2y5af44vhf1h6p9cvy"))))
22039 (properties `((upstream-name . "quanteda")))
22040 (build-system r-build-system)
22042 `(("r-data-table" ,r-data-table)
22043 ("r-digest" ,r-digest)
22044 ("r-extrafont" ,r-extrafont)
22045 ("r-fastmatch" ,r-fastmatch)
22046 ("r-ggplot2" ,r-ggplot2)
22047 ("r-ggrepel" ,r-ggrepel)
22048 ("r-jsonlite" ,r-jsonlite)
22049 ("r-magrittr" ,r-magrittr)
22050 ("r-matrix" ,r-matrix)
22051 ("r-network" ,r-network)
22052 ("r-proxyc" ,r-proxyc)
22054 ("r-rcpparmadillo" ,r-rcpparmadillo)
22055 ("r-rcppparallel" ,r-rcppparallel)
22057 ("r-snowballc" ,r-snowballc)
22058 ("r-stopwords" ,r-stopwords)
22059 ("r-stringi" ,r-stringi)
22061 ("r-yaml" ,r-yaml)))
22063 `(("r-knitr" ,r-knitr)))
22064 (home-page "https://quanteda.io")
22065 (synopsis "Quantitative analysis of textual data")
22067 "This package provides a fast, flexible, and comprehensive framework for
22068 quantitative text analysis in R. It provides functionality for corpus
22069 management, creating and manipulating tokens and ngrams, exploring keywords in
22070 context, forming and manipulating sparse matrices of documents by features and
22071 feature co-occurrences, analyzing keywords, computing feature similarities and
22072 distances, applying content dictionaries, applying supervised and unsupervised
22073 machine learning, visually representing text and text analyses, and more.")
22074 (license license:gpl3)))
22076 (define-public r-topicmodels
22078 (name "r-topicmodels")
22083 (uri (cran-uri "topicmodels" version))
22086 "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g"))))
22087 (properties `((upstream-name . "topicmodels")))
22088 (build-system r-build-system)
22092 `(("r-modeltools" ,r-modeltools)
22095 (home-page "https://cran.r-project.org/package=topicmodels")
22096 (synopsis "Topic models")
22098 "This package provides an interface to the C code for @dfn{Latent
22099 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
22100 David M. Blei and co-authors and the C++ code for fitting LDA models using
22101 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
22102 (license license:gpl2)))
22104 (define-public r-stm
22111 (uri (cran-uri "stm" version))
22114 "0qwq4nin2n9fjd06852r8k7arvcgh46kcfb3lm21swgx6j8bgrhb"))))
22115 (properties `((upstream-name . "stm")))
22116 (build-system r-build-system)
22118 `(("r-data-table" ,r-data-table)
22119 ("r-glmnet" ,r-glmnet)
22121 ("r-matrix" ,r-matrix)
22122 ("r-matrixstats" ,r-matrixstats)
22123 ("r-quadprog" ,r-quadprog)
22124 ("r-quanteda" ,r-quanteda)
22126 ("r-rcpparmadillo" ,r-rcpparmadillo)
22128 ("r-stringr" ,r-stringr)))
22129 (home-page "http://www.structuraltopicmodel.com/")
22130 (synopsis "Estimation of the Structural Topic Model")
22132 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
22133 topic models with document-level covariates. The package also includes tools
22134 for model selection, visualization, and estimation of topic-covariate
22136 (license license:expat)))
22138 (define-public r-polycor
22145 (uri (cran-uri "polycor" version))
22148 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
22149 (properties `((upstream-name . "polycor")))
22150 (build-system r-build-system)
22152 `(("r-matrix" ,r-matrix)
22153 ("r-mvtnorm" ,r-mvtnorm)))
22154 (home-page "https://r-forge.r-project.org/projects/polycor/")
22155 (synopsis "Polychoric and polyserial correlations")
22157 "This package provides tools to compute polychoric and polyserial
22158 correlations by quick \"two-step\" methods or ML, optionally with standard
22159 errors; tetrachoric and biserial correlations are special cases.")
22160 (license license:gpl2+)))
22162 (define-public r-msm
22169 (uri (cran-uri "msm" version))
22172 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
22173 (properties `((upstream-name . "msm")))
22174 (build-system r-build-system)
22176 `(("r-expm" ,r-expm)
22177 ("r-mvtnorm" ,r-mvtnorm)
22178 ("r-survival" ,r-survival)))
22179 (home-page "https://github.com/chjackson/msm")
22180 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
22182 "This package provides functions for fitting continuous-time Markov and
22183 hidden Markov multi-state models to longitudinal data. It was designed for
22184 processes observed at arbitrary times in continuous time (panel data) but some
22185 other observation schemes are supported. Both Markov transition rates and the
22186 hidden Markov output process can be modelled in terms of covariates, which may
22187 be constant or piecewise-constant in time.")
22188 (license license:gpl2+)))
22190 (define-public r-ltm
22197 (uri (cran-uri "ltm" version))
22200 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
22201 (properties `((upstream-name . "ltm")))
22202 (build-system r-build-system)
22204 `(("r-mass" ,r-mass)
22206 ("r-polycor" ,r-polycor)))
22207 (home-page "https://github.com/drizopoulos/ltm")
22208 (synopsis "Latent trait models under IRT")
22210 "This is a package supporting the analysis of multivariate dichotomous
22211 and polytomous data using latent trait models under the Item Response Theory
22212 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
22213 Three-Parameter, the Graded Response, and the Generalized Partial Credit
22215 (license license:gpl2+)))
22217 (define-public r-mi
22224 (uri (cran-uri "mi" version))
22227 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
22228 (properties `((upstream-name . "mi")))
22229 (build-system r-build-system)
22232 ("r-matrix" ,r-matrix)))
22233 (home-page "http://www.stat.columbia.edu/~gelman/")
22234 (synopsis "Missing data imputation and model checking")
22236 "This package provides functions for data manipulation, imputing missing
22237 values in an approximate Bayesian framework, diagnostics of the models used to
22238 generate the imputations, confidence-building mechanisms to validate some of
22239 the assumptions of the imputation algorithm, and functions to analyze multiply
22240 imputed data sets with the appropriate degree of sampling uncertainty.")
22241 (license license:gpl2+)))
22243 (define-public r-matrixcalc
22245 (name "r-matrixcalc")
22250 (uri (cran-uri "matrixcalc" version))
22253 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
22254 (properties `((upstream-name . "matrixcalc")))
22255 (build-system r-build-system)
22256 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
22257 (synopsis "Collection of functions for matrix calculations")
22259 "This package provides a collection of functions to support matrix
22260 calculations for probability, econometric and numerical analysis. There are
22261 additional functions that are comparable to APL functions which are useful for
22262 actuarial models such as pension mathematics.")
22263 (license license:gpl2+)))
22265 (define-public r-sem
22272 (uri (cran-uri "sem" version))
22275 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
22276 (properties `((upstream-name . "sem")))
22277 (build-system r-build-system)
22279 `(("r-boot" ,r-boot)
22281 ("r-matrixcalc" ,r-matrixcalc)
22283 (home-page "https://cran.r-project.org/package=sem")
22284 (synopsis "Structural equation models")
22286 "This package provides functions for fitting general linear structural
22287 equation models (with observed and latent variables) using the RAM approach,
22288 and for fitting structural equations in observed-variable models by two-stage
22290 (license license:gpl2+)))
22292 (define-public r-semtools
22294 (name "r-semtools")
22299 (uri (cran-uri "semTools" version))
22302 "15kban4ds2mssxqslm126b89p8biya14c9m68sqk61vzvx5dm2vq"))))
22303 (properties `((upstream-name . "semTools")))
22304 (build-system r-build-system)
22306 `(("r-lavaan" ,r-lavaan)))
22307 (home-page "https://github.com/simsem/semTools/wiki")
22308 (synopsis "Useful tools for structural equation modeling")
22310 "This package provides useful tools for structural equation modeling.")
22311 (license license:gpl2+)))
22313 (define-public r-regsem
22320 (uri (cran-uri "regsem" version))
22323 "14nrzyrkrijdrr4jwkri5zra2wh36w68wy6xs600l2z1633h2lmn"))))
22324 (properties `((upstream-name . "regsem")))
22325 (build-system r-build-system)
22327 `(("r-lavaan" ,r-lavaan)
22329 ("r-rcpparmadillo" ,r-rcpparmadillo)
22330 ("r-rsolnp" ,r-rsolnp)))
22332 `(("r-knitr" ,r-knitr)))
22333 (home-page "https://cran.r-project.org/package=regsem")
22334 (synopsis "Regularized structural equation modeling")
22336 "This package uses both ridge and lasso penalties (and extensions) to
22337 penalize specific parameters in structural equation models. The package
22338 offers additional cost functions, cross validation, and other extensions
22339 beyond traditional structural equation models. It also contains a function to
22340 perform @dfn{exploratory mediation} (XMed).")
22341 (license license:gpl2+)))
22343 (define-public r-stanheaders
22345 (name "r-stanheaders")
22346 (version "2.21.0-7")
22350 (uri (cran-uri "StanHeaders" version))
22353 "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17"))))
22354 (properties `((upstream-name . "StanHeaders")))
22355 (build-system r-build-system)
22356 (inputs `(("pandoc" ,pandoc)))
22358 `(("r-rcppeigen" ,r-rcppeigen)
22359 ("r-rcppparallel" ,r-rcppparallel)))
22361 `(("gfortran" ,gfortran)
22362 ("r-knitr" ,r-knitr))) ; for vignettes
22363 (home-page "https://mc-stan.org/")
22364 (synopsis "C++ header files for Stan")
22366 "The C++ header files of the Stan project are provided by this package.
22367 There is a shared object containing part of the @code{CVODES} library, but it
22368 is not accessible from R. @code{r-stanheaders} is only useful for developers
22369 who want to utilize the @code{LinkingTo} directive of their package's
22370 DESCRIPTION file to build on the Stan library without incurring unnecessary
22373 The Stan project develops a probabilistic programming language that implements
22374 full or approximate Bayesian statistical inference via Markov Chain Monte
22375 Carlo or variational methods and implements (optionally penalized) maximum
22376 likelihood estimation via optimization. The Stan library includes an advanced
22377 automatic differentiation scheme, templated statistical and linear algebra
22378 functions that can handle the automatically differentiable scalar types (and
22379 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
22380 package provides user-facing R functions to parse, compile, test, estimate,
22381 and analyze Stan models.")
22382 (license license:bsd-3)))
22384 (define-public r-rpf
22391 (uri (cran-uri "rpf" version))
22394 "0kz7i7g3l16irz6bxgnkxdmmd931m1fk6rl72dvs21ir5brr010l"))))
22395 (properties `((upstream-name . "rpf")))
22396 (build-system r-build-system)
22398 `(("r-lifecycle" ,r-lifecycle)
22399 ("r-mvtnorm" ,r-mvtnorm)
22401 ("r-rcppeigen" ,r-rcppeigen)))
22403 `(("r-knitr" ,r-knitr)))
22404 (home-page "https://github.com/jpritikin/rpf")
22405 (synopsis "Response probability functions")
22407 "The purpose of this package is to factor out logic and math common to
22408 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
22409 core support code suitable for more specialized IRT packages to build upon.
22410 Complete access to optimized C functions is made available with
22411 @code{R_RegisterCCallable()}.")
22412 (license license:gpl3+)))
22414 (define-public r-openmx
22421 (uri (cran-uri "OpenMx" version))
22424 "0gyjps0l3ig90piccgd04s63cz65kk5i5l9iyakps4bv27h1lzwm"))))
22425 (properties `((upstream-name . "OpenMx")))
22426 (build-system r-build-system)
22429 ("r-digest" ,r-digest)
22430 ("r-lifecycle" ,r-lifecycle)
22432 ("r-matrix" ,r-matrix)
22434 ("r-rcppeigen" ,r-rcppeigen)
22436 ("r-stanheaders" ,r-stanheaders)))
22437 (native-inputs `(("gfortran" ,gfortran)))
22438 (home-page "http://openmx.ssri.psu.edu")
22439 (synopsis "Extended structural equation modelling")
22441 "This package allows for the estimation of a wide variety of advanced
22442 multivariate statistical models. It consists of a library of functions and
22443 optimizers that allow you to quickly and flexibly define an SEM model and
22444 estimate parameters given observed data.")
22445 (license license:asl2.0)))
22447 (define-public r-kutils
22454 (uri (cran-uri "kutils" version))
22457 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
22458 (properties `((upstream-name . "kutils")))
22459 (build-system r-build-system)
22461 `(("r-foreign" ,r-foreign)
22462 ("r-openxlsx" ,r-openxlsx)
22464 ("r-runit" ,r-runit)
22465 ("r-xtable" ,r-xtable)))
22466 (home-page "https://cran.r-project.org/package=kutils")
22467 (synopsis "Project management tools")
22469 "This package provides tools for data importation, recoding, and
22470 inspection. There are functions to create new project folders, R code
22471 templates, create uniquely named output directories, and to quickly obtain a
22472 visual summary for each variable in a data frame. The main feature here is
22473 the systematic implementation of the \"variable key\" framework for data
22474 importation and recoding.")
22475 (license license:gpl2)))
22477 (define-public r-rockchalk
22479 (name "r-rockchalk")
22480 (version "1.8.144")
22484 (uri (cran-uri "rockchalk" version))
22487 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
22488 (properties `((upstream-name . "rockchalk")))
22489 (build-system r-build-system)
22491 `(("r-cardata" ,r-cardata)
22492 ("r-kutils" ,r-kutils)
22494 ("r-mass" ,r-mass)))
22495 (home-page "https://cran.r-project.org/package=rockchalk")
22496 (synopsis "Regression estimation and presentation")
22498 "This package provides a collection of functions for interpretation and
22499 presentation of regression analysis. These functions are used to produce the
22500 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
22501 includes regression diagnostics, regression tables, and plots of interactions
22502 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
22503 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
22504 fairly comprehensive overview.")
22505 (license license:gpl3+)))
22507 (define-public r-lisreltor
22509 (name "r-lisreltor")
22514 (uri (cran-uri "lisrelToR" version))
22517 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
22518 (properties `((upstream-name . "lisrelToR")))
22519 (build-system r-build-system)
22520 (home-page "https://cran.r-project.org/package=lisrelToR")
22521 (synopsis "Import output from LISREL into R")
22523 "This is an unofficial package aimed at automating the import of LISREL
22525 (license license:gpl2)))
22527 (define-public r-bdgraph
22534 (uri (cran-uri "BDgraph" version))
22537 "05q6dbvdnxmh7myvw60zqcqx16f80i8d6qa4y7xnfkx02l9lwiyc"))))
22538 (properties `((upstream-name . "BDgraph")))
22539 (build-system r-build-system)
22541 `(("r-igraph" ,r-igraph)))
22542 (home-page "https://www.uva.nl/profile/a.mohammadi")
22543 (synopsis "Bayesian structure learning in graphical models")
22545 "This package provides statistical tools for Bayesian structure learning
22546 in undirected graphical models for continuous, discrete, and mixed data. It
22547 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
22548 on a continuous-time birth-death process.")
22549 (license license:gpl2+)))
22551 (define-public r-d3network
22553 (name "r-d3network")
22554 (version "0.5.2.1")
22558 (uri (cran-uri "d3Network" version))
22561 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
22562 (properties `((upstream-name . "d3Network")))
22563 (build-system r-build-system)
22565 `(("r-plyr" ,r-plyr)
22566 ("r-rjson" ,r-rjson)
22567 ("r-whisker" ,r-whisker)))
22568 (home-page "http://christophergandrud.github.io/d3Network/")
22569 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
22571 "This package is intended to make it easy to create D3 JavaScript
22572 network, tree, dendrogram, and Sankey graphs from R using data frames.")
22573 (license license:gpl3+)))
22575 (define-public r-qgraph
22582 (uri (cran-uri "qgraph" version))
22585 "153bqfmsrghkg7598nfr57r3cxv6dn6ir084njl2sqq5np0sj9di"))))
22586 (properties `((upstream-name . "qgraph")))
22587 (build-system r-build-system)
22589 `(("r-abind" ,r-abind)
22590 ("r-colorspace" ,r-colorspace)
22591 ("r-corpcor" ,r-corpcor)
22592 ("r-dplyr" ,r-dplyr)
22593 ("r-fdrtool" ,r-fdrtool)
22594 ("r-ggplot2" ,r-ggplot2)
22595 ("r-glasso" ,r-glasso)
22596 ("r-gtools" ,r-gtools)
22597 ("r-hmisc" ,r-hmisc)
22598 ("r-igraph" ,r-igraph)
22600 ("r-lavaan" ,r-lavaan)
22601 ("r-matrix" ,r-matrix)
22602 ("r-pbapply" ,r-pbapply)
22605 ("r-psych" ,r-psych)
22607 ("r-reshape2" ,r-reshape2)))
22608 (home-page "http://sachaepskamp.com/qgraph/")
22609 (synopsis "Weighted network visualization and analysis")
22611 "This package implements tools for weighted network visualization and
22612 analysis, as well as Gaussian graphical model computation. It contains graph
22613 plotting methods, and tools for psychometric data visualization and graphical
22614 model estimation. See Epskamp et al. (2012)
22615 @url{doi:10.18637/jss.v048.i04}.")
22616 (license license:gpl2)))
22618 (define-public r-semplot
22625 (uri (cran-uri "semPlot" version))
22628 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
22629 (properties `((upstream-name . "semPlot")))
22630 (build-system r-build-system)
22632 `(("r-colorspace" ,r-colorspace)
22633 ("r-corpcor" ,r-corpcor)
22634 ("r-igraph" ,r-igraph)
22635 ("r-lavaan" ,r-lavaan)
22636 ("r-lisreltor" ,r-lisreltor)
22637 ("r-openmx" ,r-openmx)
22639 ("r-qgraph" ,r-qgraph)
22640 ("r-regsem" ,r-regsem)
22641 ("r-rockchalk" ,r-rockchalk)
22644 (home-page "https://github.com/SachaEpskamp/semPlot")
22645 (synopsis "Unified visualizations of structural equation models")
22647 "Structural equation modeling (SEM) has a long history of representing
22648 models graphically as path diagrams. The semPlot package for R fills the gap
22649 between advanced, but time-consuming, graphical software and the limited
22650 graphics produced automatically by SEM software. In addition, semPlot offers
22651 more functionality than drawing path diagrams: it can act as a common ground
22652 for importing SEM results into R. Any result usable as input to semPlot can
22653 also be represented in any of the three popular SEM frame-works, as well as
22654 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
22655 (license license:gpl2)))
22657 (define-public r-cdm
22664 (uri (cran-uri "CDM" version))
22667 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
22668 (properties `((upstream-name . "CDM")))
22669 (build-system r-build-system)
22671 `(("r-mvtnorm" ,r-mvtnorm)
22672 ("r-polycor" ,r-polycor)
22674 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22676 "https://github.com/alexanderrobitzsch/CDM")
22677 (synopsis "Cognitive diagnosis modeling")
22679 "This package provides functions for cognitive diagnosis modeling and
22680 multidimensional item response modeling for dichotomous and polytomous item
22681 responses. It enables the estimation of the DINA and DINO model, the multiple
22682 group (polytomous) GDINA model, the multiple choice DINA model, the general
22683 diagnostic model (GDM), the structured latent class model (SLCA), and
22684 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
22685 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
22686 estimation and the package structure. For tutorials on how to use the CDM
22687 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
22688 well as Ravand and Robitzsch (2015).")
22689 (license license:gpl2+)))
22691 (define-public r-tam
22698 (uri (cran-uri "TAM" version))
22701 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
22702 (properties `((upstream-name . "TAM")))
22703 (build-system r-build-system)
22707 ("r-rcpparmadillo" ,r-rcpparmadillo)))
22708 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
22709 (synopsis "Test analysis modules")
22711 "This package includes tools for marginal maximum likelihood estimation
22712 and joint maximum likelihood estimation for unidimensional and
22713 multidimensional item response models. The package functionality covers the
22714 Rasch model, 2PL model, 3PL model, generalized partial credit model,
22715 multi-faceted Rasch model, nominal item response model, structured latent
22716 class model, mixture distribution IRT models, and located latent class models.
22717 Latent regression models and plausible value imputation are also supported.")
22718 (license license:gpl2+)))
22720 (define-public r-erm
22727 (uri (cran-uri "eRm" version))
22730 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
22731 (properties `((upstream-name . "eRm")))
22732 (build-system r-build-system)
22734 `(("r-colorspace" ,r-colorspace)
22735 ("r-lattice" ,r-lattice)
22737 ("r-matrix" ,r-matrix)
22738 ("r-psych" ,r-psych)))
22739 (native-inputs `(("gfortran" ,gfortran)))
22740 (home-page "https://cran.r-project.org/package=eRm")
22741 (synopsis "Extended Rasch modeling")
22743 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
22744 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
22745 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
22746 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
22747 data matrix. Additional features are the ML estimation of the person
22748 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
22749 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
22750 infit and outfit measures, ICC and other plots, automated stepwise item
22751 elimination, and a simulation module for various binary data matrices.")
22752 (license license:gpl3)))
22754 (define-public r-irtoys
22761 (uri (cran-uri "irtoys" version))
22764 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
22765 (properties `((upstream-name . "irtoys")))
22766 (build-system r-build-system)
22770 (home-page "https://cran.r-project.org/package=irtoys")
22771 (synopsis "Collection of functions related to Item Response Theory (IRT)")
22773 "This package provides a collection of functions useful in learning and
22774 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
22775 programs. It provides basic CTT analysis, a simple common interface to the
22776 estimation of item parameters in IRT models for binary responses with three
22777 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
22778 EAP, WLE, plausible values), item and person fit statistics, scaling
22779 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
22780 array of parametric and non-parametric (kernel) plots. It estimates and plots
22781 Haberman's interaction model when all items are dichotomously scored.")
22782 (license license:gpl2+)))
22784 (define-public r-iheatmapr
22786 (name "r-iheatmapr")
22791 (uri (cran-uri "iheatmapr" version))
22794 "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx"))))
22795 (properties `((upstream-name . "iheatmapr")))
22796 (build-system r-build-system)
22798 `(("r-fastcluster" ,r-fastcluster)
22799 ("r-ggdendro" ,r-ggdendro)
22800 ("r-htmlwidgets" ,r-htmlwidgets)
22801 ("r-jsonlite" ,r-jsonlite)
22802 ("r-knitr" ,r-knitr)
22803 ("r-magrittr" ,r-magrittr)
22804 ("r-rcolorbrewer" ,r-rcolorbrewer)
22805 ("r-scales" ,r-scales)))
22807 `(("r-knitr" ,r-knitr)))
22808 (home-page "https://docs.ropensci.org/iheatmapr")
22809 (synopsis "Interactive, Complex Heatmaps")
22811 "iheatmapr is an R package for building complex, interactive heatmaps
22812 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
22813 subplots along the rows or columns of the main heatmap add more information
22814 about each row or column. For example, a one column additional heatmap may
22815 indicate what group a particular row or column belongs to. Complex heatmaps
22816 may also include multiple side by side heatmaps which show different types of
22817 data for the same conditions. Interactivity can improve complex heatmaps by
22818 providing tooltips with information about each cell and enabling zooming into
22819 interesting features. iheatmapr uses the plotly library for interactivity.")
22820 (license license:expat)))
22822 (define-public r-packrat
22829 (uri (cran-uri "packrat" version))
22832 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
22833 (properties `((upstream-name . "packrat")))
22834 (build-system r-build-system)
22835 (home-page "https://github.com/rstudio/packrat/")
22836 (synopsis "Dependency management R projects")
22838 "This package provides a dependency manager for R projects that allows
22839 you to manage the R packages your project depends on in an isolated, portable,
22840 and reproducible way.")
22841 (license license:gpl2)))
22843 (define-public r-rsconnect
22845 (name "r-rsconnect")
22850 (uri (cran-uri "rsconnect" version))
22853 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
22854 (properties `((upstream-name . "rsconnect")))
22855 (build-system r-build-system)
22857 `(("r-curl" ,r-curl)
22858 ("r-digest" ,r-digest)
22859 ("r-jsonlite" ,r-jsonlite)
22860 ("r-openssl" ,r-openssl)
22861 ("r-packrat" ,r-packrat)
22862 ("r-rstudioapi" ,r-rstudioapi)
22863 ("r-yaml" ,r-yaml)))
22864 (home-page "https://github.com/rstudio/rsconnect")
22865 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
22867 "This package provides a programmatic deployment interface for RPubs,
22868 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
22869 documents, Shiny applications, Plumber APIs, plots, and static web content.")
22870 (license license:gpl2)))
22872 ;; This package includes minified JavaScript files. When upgrading please
22873 ;; check that there are no new minified JavaScript files.
22874 (define-public r-dygraphs
22876 (name "r-dygraphs")
22877 (version "1.1.1.6")
22881 (uri (cran-uri "dygraphs" version))
22884 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
22885 (properties `((upstream-name . "dygraphs")))
22886 (build-system r-build-system)
22888 `(#:modules ((guix build utils)
22889 (guix build r-build-system)
22893 (modify-phases %standard-phases
22894 (add-after 'unpack 'process-javascript
22895 (lambda* (#:key inputs #:allow-other-keys)
22896 (with-directory-excursion "inst/htmlwidgets/lib/"
22900 `(("dygraphs/dygraph-combined-dev.js"
22901 "dygraph-combined.js")
22902 (,(assoc-ref inputs "js-jquery")
22903 "jquery/jquery.min.js")
22904 (,(assoc-ref inputs "js-fquarter")
22905 "fquarter/moment-fquarter.min.js"))))
22906 (lambda (sources targets)
22907 (for-each (lambda (source target)
22908 (format #t "Processing ~a --> ~a~%"
22910 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
22911 (call-with-output-file target
22913 (dump-port minified port)))))
22914 sources targets))))
22917 `(("uglify-js" ,uglify-js)
22918 ;; They actually use version 1.11.1, but this more recent version
22919 ;; should be just fine.
22923 (uri "https://code.jquery.com/jquery-1.12.4.js")
22926 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
22930 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
22931 "moment-fquarter/1.0.1/moment-fquarter.js"))
22934 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
22936 `(("r-htmltools" ,r-htmltools)
22937 ("r-htmlwidgets" ,r-htmlwidgets)
22938 ("r-magrittr" ,r-magrittr)
22941 (home-page "https://github.com/rstudio/dygraphs")
22942 (synopsis "Interface to Dygraphs interactive time series charting library")
22944 "This package provides an R interface to the dygraphs JavaScript charting
22945 library (a copy of which is included in the package). It provides rich
22946 facilities for charting time-series data in R, including highly configurable
22947 series- and axis-display and interactive features like zoom/pan and
22948 series/point highlighting.")
22949 (license license:expat)))
22951 (define-public r-shinystan
22953 (name "r-shinystan")
22958 (uri (cran-uri "shinystan" version))
22961 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
22962 (properties `((upstream-name . "shinystan")))
22963 (build-system r-build-system)
22965 `(("r-bayesplot" ,r-bayesplot)
22966 ("r-colourpicker" ,r-colourpicker)
22968 ("r-dygraphs" ,r-dygraphs)
22969 ("r-ggplot2" ,r-ggplot2)
22970 ("r-gridextra" ,r-gridextra)
22971 ("r-gtools" ,r-gtools)
22972 ("r-markdown" ,r-markdown)
22973 ("r-reshape2" ,r-reshape2)
22974 ("r-rsconnect" ,r-rsconnect)
22975 ("r-rstan" ,r-rstan)
22976 ("r-shiny" ,r-shiny)
22977 ("r-shinyjs" ,r-shinyjs)
22978 ("r-shinythemes" ,r-shinythemes)
22979 ("r-threejs" ,r-threejs)
22980 ("r-xtable" ,r-xtable)
22982 (home-page "https://mc-stan.org/")
22983 (synopsis "Interactive visual and numerical analysis for Bayesian models")
22985 "This package provides a graphical user interface for interactive
22986 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
22987 for analyzing a posterior sample. The interface is powered by the Shiny web
22988 application framework and works with the output of MCMC programs written in
22989 any programming language (and has extended functionality for Stan models fit
22990 using the @code{rstan} and @code{rstanarm} packages).")
22991 (license license:gpl3+)))
22993 (define-public r-rstantools
22995 (name "r-rstantools")
23000 (uri (cran-uri "rstantools" version))
23003 "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
23004 (properties `((upstream-name . "rstantools")))
23005 (build-system r-build-system)
23006 (inputs `(("pandoc" ,pandoc)))
23008 `(("r-desc" ,r-desc)
23010 ("r-rcppparallel" ,r-rcppparallel)))
23012 `(("r-knitr" ,r-knitr)))
23013 (home-page "https://mc-stan.org/rstantools/")
23014 (synopsis "Tools for developing R packages interfacing with Stan")
23016 "This package provides various tools for developers of R packages
23017 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
23018 up the required package structure, S3 generics and default methods to unify
23019 function naming across Stan-based R packages, and vignettes with
23020 recommendations for developers.")
23021 (license license:gpl3+)))
23023 (define-public r-loo
23030 (uri (cran-uri "loo" version))
23032 (base32 "0l2v8zpashqbnck3qx5lp1gqjcfphzky8mxyw5gfk9wk99mzn8dw"))))
23033 (properties `((upstream-name . "loo")))
23034 (build-system r-build-system)
23036 `(("pandoc" ,pandoc)
23037 ("pandoc-citeproc" ,pandoc-citeproc)))
23039 `(("r-checkmate" ,r-checkmate)
23040 ("r-matrixstats" ,r-matrixstats)))
23042 `(("r-knitr" ,r-knitr)))
23043 (home-page "https://mc-stan.org/loo/")
23044 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
23046 "This package provides an implementation of efficient approximate
23047 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
23048 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
23049 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
23050 procedure for regularizing importance weights. As a byproduct of the
23051 calculations, we also obtain approximate standard errors for estimated
23052 predictive errors and for the comparison of predictive errors between models.
23053 The package also provides methods for using stacking and other model weighting
23054 techniques to average Bayesian predictive distributions.")
23055 (license license:gpl3+)))
23057 (define-public r-rstan
23064 (uri (cran-uri "rstan" version))
23067 "0jh58qfrksd2j9w2zy4bajryivgp36m3xdb9mjrjqbk1ib9h83p3"))))
23068 (properties `((upstream-name . "rstan")))
23069 (build-system r-build-system)
23072 (modify-phases %standard-phases
23073 (add-before 'install 'set-timezone
23074 ;; This package is picky about timezones.
23075 (lambda* (#:key inputs #:allow-other-keys)
23076 (setenv "TZ" "UTC+1")
23078 (string-append (assoc-ref inputs "tzdata")
23079 "/share/zoneinfo"))
23082 `(("tzdata" ,tzdata-for-tests)
23084 ("r-knitr" ,r-knitr)))
23087 ("r-ggplot2" ,r-ggplot2)
23088 ("r-gridextra" ,r-gridextra)
23089 ("r-inline" ,r-inline)
23091 ("r-pkgbuild" ,r-pkgbuild)
23093 ("r-rcppeigen" ,r-rcppeigen)
23094 ("r-rcppparallel" ,r-rcppparallel)
23095 ("r-stanheaders" ,r-stanheaders)
23097 ("r-withr" ,r-withr)))
23098 (home-page "https://discourse.mc-stan.org/")
23099 (synopsis "R interface to Stan")
23101 "User-facing R functions are provided to parse, compile, test, estimate,
23102 and analyze Stan models by accessing the header-only Stan library provided by
23103 the StanHeaders package. The Stan project develops a probabilistic
23104 programming language that implements full Bayesian statistical inference via
23105 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
23106 approximation, and (optionally penalized) maximum likelihood estimation via
23107 optimization. In all three cases, automatic differentiation is used to
23108 quickly and accurately evaluate gradients without burdening the user with the
23109 need to derive the partial derivatives.")
23110 (license license:gpl3+)))
23112 (define-public r-rstanarm
23114 (name "r-rstanarm")
23119 (uri (cran-uri "rstanarm" version))
23122 "04ggzak3f7jaxza3dxyrmxp5b48qcgyspy22ykbhr03g4hzp7jk8"))))
23123 (properties `((upstream-name . "rstanarm")))
23124 (build-system r-build-system)
23126 `(("pandoc" ,pandoc)
23127 ("pandoc-citeproc" ,pandoc-citeproc)))
23129 `(("r-bayesplot" ,r-bayesplot)
23131 ("r-ggplot2" ,r-ggplot2)
23134 ("r-matrix" ,r-matrix)
23137 ("r-rcppeigen" ,r-rcppeigen)
23138 ("r-rcppparallel" ,r-rcppparallel)
23139 ("r-rstan" ,r-rstan)
23140 ("r-rstantools" ,r-rstantools)
23141 ("r-shinystan" ,r-shinystan)
23142 ("r-stanheaders" ,r-stanheaders)
23143 ("r-survival" ,r-survival)))
23145 `(("r-knitr" ,r-knitr)))
23146 (home-page "https://mc-stan.org/rstanarm/")
23147 (synopsis "Bayesian applied regression modeling via Stan")
23149 "This package estimates previously compiled regression models using the
23150 @code{rstan} package, which provides the R interface to the Stan C++ library
23151 for Bayesian estimation. Users specify models via the customary R syntax with
23152 a formula and @code{data.frame} plus some additional arguments for priors.")
23153 (license license:gpl3+)))
23155 (define-public r-kendall
23162 (uri (cran-uri "Kendall" version))
23165 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
23166 (properties `((upstream-name . "Kendall")))
23167 (build-system r-build-system)
23169 `(("r-boot" ,r-boot)))
23171 `(("gfortran" ,gfortran)))
23172 (home-page "https://cran.r-project.org/web/packages/Kendall/")
23173 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
23175 "This package computes the Kendall rank correlation and Mann-Kendall
23177 (license license:gpl2+)))
23179 (define-public r-keyring
23186 (uri (cran-uri "keyring" version))
23189 "1hpfd4hbx43i39l995rg86kfxi7wlyla1gv8mwcdr4xx7z122zzq"))))
23190 (properties `((upstream-name . "keyring")))
23191 (build-system r-build-system)
23193 `(("r-assertthat" ,r-assertthat)
23194 ("r-filelock" ,r-filelock)
23195 ("r-getpass" ,r-getpass)
23196 ("r-openssl" ,r-openssl)
23198 ("r-rappdirs" ,r-rappdirs)
23199 ("r-sodium" ,r-sodium)
23200 ("r-yaml" ,r-yaml)))
23201 (native-inputs `(("pkg-config" ,pkg-config)))
23202 (home-page "https://github.com/r-lib/keyring")
23203 (synopsis "Access the system credential store from R")
23205 "This package provides a platform-independent API to access the operating
23206 system's credential store. It currently supports Keychain on macOS,
23207 Credential Store on Windows, the Secret Service API on GNU/Linux, and a
23208 simple, platform independent store implemented with environment variables.
23209 Additional storage back-ends can be added easily.")
23210 (license license:expat)))
23212 (define-public r-zyp
23215 (version "0.10-1.1")
23219 (uri (cran-uri "zyp" version))
23222 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
23223 (properties `((upstream-name . "zyp")))
23224 (build-system r-build-system)
23226 `(("r-kendall" ,r-kendall)))
23227 (home-page "https://cran.r-project.org/web/packages/zyp/")
23228 (synopsis "Zhang + Yue-Pilon Trends Package")
23230 "This package contains an efficient implementation of Sen's slope
23231 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
23232 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
23234 (license license:lgpl2.1)))
23236 (define-public r-rlinsolve
23238 (name "r-rlinsolve")
23243 (uri (cran-uri "Rlinsolve" version))
23246 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
23247 (properties `((upstream-name . "Rlinsolve")))
23248 (build-system r-build-system)
23250 `(("r-matrix" ,r-matrix)
23252 ("r-rcpparmadillo" ,r-rcpparmadillo)
23253 ("r-rdpack" ,r-rdpack)))
23254 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
23255 (synopsis "Iterative solvers for (sparse) linear system of equations")
23257 "Solving a system of linear equations is one of the most fundamental
23258 computational problems for many fields of mathematical studies, such as
23259 regression problems from statistics or numerical partial differential
23260 equations. This package provides basic stationary iterative solvers such as
23261 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
23262 Nonstationary, also known as Krylov subspace methods are also provided.
23263 Sparse matrix computation is also supported in that solving large and sparse
23264 linear systems can be manageable using the @code{Matrix} package along with
23265 @code{RcppArmadillo}.")
23266 (license license:gpl3+)))
23268 (define-public r-zvcv
23275 (uri (cran-uri "ZVCV" version))
23278 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
23279 (properties `((upstream-name . "ZVCV")))
23280 (build-system r-build-system)
23282 `(("r-abind" ,r-abind)
23284 ("r-dplyr" ,r-dplyr)
23285 ("r-glmnet" ,r-glmnet)
23286 ("r-magrittr" ,r-magrittr)
23287 ("r-mvtnorm" ,r-mvtnorm)
23289 ("r-rcpparmadillo" ,r-rcpparmadillo)
23290 ("r-rlinsolve" ,r-rlinsolve)))
23291 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
23292 (synopsis "Zero-Variance Control Variates")
23294 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
23295 to reduce the variance of Monte Carlo estimators of expectations using the
23296 derivatives of the log target. Once the derivatives are available, the only
23297 additional computational effort is in solving a linear regression problem.
23298 This method has been extended to higher dimensions using regularisation. This
23299 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
23300 samples, derivatives and function evaluations are available. Additional
23301 functions for applying ZV-CV to two estimators for the normalising constant of
23302 the posterior distribution in Bayesian statistics are also supplied.")
23303 (license license:gpl2+)))
23305 (define-public r-ztype
23312 (uri (cran-uri "ztype" version))
23315 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
23316 (properties `((upstream-name . "ztype")))
23317 (build-system r-build-system)
23319 `(("r-assertthat" ,r-assertthat)
23320 ("r-dplyr" ,r-dplyr)
23321 ("r-ggplot2" ,r-ggplot2)
23322 ("r-lubridate" ,r-lubridate)
23323 ("r-magrittr" ,r-magrittr)
23324 ("r-rvest" ,r-rvest)
23325 ("r-stringr" ,r-stringr)))
23326 (home-page "https://cran.r-project.org/web/packages/ztype/")
23327 (synopsis "Run a Ztype game loaded with R functions")
23329 "How fast can you type R functions on your keyboard? Find out by running
23330 a @code{zty.pe} game: export R functions as instructions to type to destroy
23331 opponents' vessels.")
23332 (license license:gpl3)))
23334 (define-public r-zseq
23341 (uri (cran-uri "Zseq" version))
23344 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
23345 (properties `((upstream-name . "Zseq")))
23346 (build-system r-build-system)
23348 `(("r-gmp" ,r-gmp)))
23349 (home-page "https://cran.r-project.org/web/packages/Zseq/")
23350 (synopsis "Integer sequence generator")
23352 "This package generates well-known integer sequences. The @code{gmp}
23353 package is adopted for computing with arbitrarily large numbers. Every
23354 function has a hyperlink to its corresponding item in the @dfn{On-Line
23355 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
23356 (license license:gpl3+)))
23358 (define-public r-isoband
23365 (uri (cran-uri "isoband" version))
23368 "1zkzdc39dpw2z59bjck27nimz9a2vskmw0f7wb17s53dvy7k3lzr"))))
23369 (properties `((upstream-name . "isoband")))
23370 (build-system r-build-system)
23372 `(("r-testthat" ,r-testthat)))
23374 `(("r-knitr" ,r-knitr)))
23375 (home-page "https://github.com/wilkelab/isoband")
23376 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
23378 "This package provides a fast C++ implementation to generate contour
23379 lines (isolines) and contour polygons (isobands) from regularly spaced grids
23380 containing elevation data.")
23381 (license license:expat)))
23383 (define-public r-ppcor
23390 (uri (cran-uri "ppcor" version))
23393 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
23394 (properties `((upstream-name . "ppcor")))
23395 (build-system r-build-system)
23397 `(("r-mass" ,r-mass)))
23398 (home-page "https://cran.r-project.org/web/packages/ppcor/")
23399 (synopsis "Partial and semi-partial correlation")
23401 "This package provides users not only with a function to readily
23402 calculate the higher-order partial and semi-partial correlations but also with
23403 statistics and p-values of the correlation coefficients.")
23404 (license license:gpl2)))
23406 (define-public r-hrbrthemes
23408 (name "r-hrbrthemes")
23413 (uri (cran-uri "hrbrthemes" version))
23415 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
23416 (properties `((upstream-name . "hrbrthemes")))
23417 (build-system r-build-system)
23419 `(("r-extrafont" ,r-extrafont)
23420 ("r-gdtools" ,r-gdtools)
23421 ("r-ggplot2" ,r-ggplot2)
23422 ("r-htmltools" ,r-htmltools)
23423 ("r-knitr" ,r-knitr)
23424 ("r-magrittr" ,r-magrittr)
23425 ("r-rmarkdown" ,r-rmarkdown)
23426 ("r-scales" ,r-scales)))
23428 `(("r-knitr" ,r-knitr)))
23429 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
23430 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
23432 "This package provides a compilation of extra @code{ggplot2} themes,
23433 scales and utilities, including a spell check function for plot label fields
23434 and an overall emphasis on typography.")
23435 (license license:expat)))
23437 (define-public r-crochet
23444 (uri (cran-uri "crochet" version))
23447 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
23448 (build-system r-build-system)
23450 `(("r-knitr" ,r-knitr)))
23451 (home-page "https://github.com/agrueneberg/crochet")
23452 (synopsis "Implementation Helper for Matrix-Like Types")
23454 "Functions to help implement the extraction / subsetting / indexing
23455 function @code{[} and replacement function @code{[<-} of custom matrix-like
23456 types (based on S3, S4, etc.), modeled as closely to the base matrix class
23457 as possible (with tests to prove it).")
23458 (license license:expat)))
23460 (define-public r-boa
23463 (version "1.1.8-2")
23467 (uri (cran-uri "boa" version))
23470 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
23471 (properties `((upstream-name . "boa")))
23472 (build-system r-build-system)
23473 (home-page "https://www.jstatsoft.org/v21/i11")
23474 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
23476 "This package provides a menu-driven program and library of functions for
23477 carrying out convergence diagnostics and statistical and graphical analysis of
23478 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
23479 (license license:gpl2+)))
23481 (define-public r-httpcode
23483 (name "r-httpcode")
23487 (uri (cran-uri "httpcode" version))
23490 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
23491 (build-system r-build-system)
23492 (home-page "https://github.com/sckott/httpcode")
23493 (synopsis "HTTP status code helper")
23494 (description "@code{httpcode} provides functionality for finding and
23495 explaining the meaning of @code{HTTP} status codes. Functions are included for
23496 searching for codes by full or partial number, by message, and to get
23497 appropriate dog and cat images for many status codes.")
23498 (license license:expat)))
23500 (define-public r-latex2exp
23502 (name "r-latex2exp")
23506 (uri (cran-uri "latex2exp" version))
23509 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
23510 (build-system r-build-system)
23512 `(("r-stringr" ,r-stringr)
23513 ("r-magrittr" ,r-magrittr)))
23514 (home-page "https://github.com/stefano-meschiari/latex2exp/")
23515 (synopsis "Use LaTeX expressions in plots")
23516 (description "@code{latex2exp} parses and converts LaTeX math formulas to
23517 R's plotmath expressions, used to enter mathematical formulas and symbols to be
23518 rendered as text, axis labels, etc. throughout R's plotting system.")
23519 (license license:expat)))
23521 (define-public r-oai
23527 (uri (cran-uri "oai" version))
23530 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
23531 (build-system r-build-system)
23533 `(("r-xml2" ,r-xml2)
23536 ("r-stringr" ,r-stringr)
23537 ("r-tibble" ,r-tibble)))
23538 (home-page "https://github.com/ropensci/oai/")
23539 (synopsis "General purpose OAI-PMH services client")
23540 (description "@code{oai} provides a general purpose client to work with
23541 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
23542 service. Functions are provided to work with the OAI-PMH verbs:
23543 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
23544 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
23545 (license license:expat)))
23547 (define-public r-argon2
23554 (uri (cran-uri "argon2" version))
23557 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
23558 (properties `((upstream-name . "argon2")))
23559 (build-system r-build-system)
23560 (home-page "https://github.com/wrathematics/argon2")
23561 (synopsis "Secure password hashing based on the argon2 algorithm")
23563 "This package provides utilities for secure password hashing via the
23564 argon2 algorithm.")
23565 (license license:bsd-2)))
23567 (define-public r-getpass
23574 (uri (cran-uri "getPass" version))
23577 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
23578 (properties `((upstream-name . "getPass")))
23579 (build-system r-build-system)
23581 `(("r-rstudioapi" ,r-rstudioapi)))
23582 (home-page "https://github.com/wrathematics/getPass")
23583 (synopsis "Masked user input")
23585 "This package provides a micro-package for reading \"passwords\", i.e.
23586 reading user input with masking, so that the input is not displayed as it is
23587 typed. Currently, RStudio, the command line (every OS), and any platform
23588 where tcltk is present are supported.")
23589 (license license:bsd-2)))
23591 (define-public r-remoter
23598 (uri (cran-uri "remoter" version))
23601 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
23602 (properties `((upstream-name . "remoter")))
23603 (build-system r-build-system)
23605 `(("r-argon2" ,r-argon2)
23606 ("r-getpass" ,r-getpass)
23607 ("r-pbdzmq" ,r-pbdzmq)
23609 (home-page "https://github.com/RBigData/remoter")
23610 (synopsis "Control a remote R session from a local one")
23612 "This package provides a set of utilities for client/server computing
23613 with R, controlling a remote R session (the server) from a local one (the
23615 (license license:bsd-2)))
23617 (define-public r-asd
23624 (uri (cran-uri "asd" version))
23627 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
23628 (properties `((upstream-name . "asd")))
23629 (build-system r-build-system)
23631 `(("r-mvtnorm" ,r-mvtnorm)))
23632 (home-page "https://cran.r-project.org/web/packages/asd")
23633 (synopsis "Simulations for Adaptive Seamless Designs")
23635 "This package provdes means to run simulations for adaptive seamless
23636 designs with and without early outcomes for treatment selection and
23637 subpopulation type designs.")
23638 (license license:gpl3)))
23640 (define-public r-nbconvertr
23642 (name "r-nbconvertr")
23647 (uri (cran-uri "nbconvertR" version))
23650 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
23651 (properties `((upstream-name . "nbconvertR")))
23652 (build-system r-build-system)
23654 `(("jupyter" ,python-nbconvert)
23655 ("pandoc" ,pandoc)))
23656 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
23657 (synopsis "Vignette engine wrapping Jupyter notebooks")
23659 "This package calls the Jupyter script @code{nbconvert} to create
23660 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
23661 containing rich text, code, and its output. Code cells can be edited and
23662 evaluated interactively.")
23663 (license license:gpl3)))
23665 (define-public r-bridgesampling
23667 (name "r-bridgesampling")
23672 (uri (cran-uri "bridgesampling" version))
23675 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
23677 `((upstream-name . "bridgesampling")))
23678 (build-system r-build-system)
23680 `(("r-brobdingnag" ,r-brobdingnag)
23682 ("r-matrix" ,r-matrix)
23683 ("r-mvtnorm" ,r-mvtnorm)
23684 ("r-scales" ,r-scales)
23685 ("r-stringr" ,r-stringr)))
23687 `(("r-knitr" ,r-knitr)))
23688 (home-page "https://github.com/quentingronau/bridgesampling")
23689 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
23691 "This package provides functions for estimating marginal likelihoods,
23692 Bayes factors, posterior model probabilities, and normalizing constants in
23693 general, via different versions of bridge sampling.")
23694 (license license:gpl2+)))
23696 (define-public r-tea
23703 (uri (cran-uri "tea" version))
23706 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
23708 `((upstream-name . "tea")))
23709 (build-system r-build-system)
23711 `(("r-matrix" ,r-matrix)))
23712 (home-page "https://cran.r-project.org/web/packages/tea/")
23713 (synopsis "Threshold estimation approaches")
23715 "This package provides different approaches for selecting the threshold
23716 in generalized Pareto distributions. Most of them are based on minimizing the
23717 AMSE-criterion or at least by reducing the bias of the assumed GPD-model.
23718 Others are heuristically motivated by searching for stable sample paths, i.e.
23719 a nearly constant region of the tail index estimator with respect to k, which
23720 is the number of data in the tail. The third class is motivated by graphical
23721 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
23722 is also implemented here.")
23723 (license license:gpl3)))
23725 (define-public r-awsmethods
23727 (name "r-awsmethods")
23732 (uri (cran-uri "awsMethods" version))
23735 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
23737 `((upstream-name . "awsMethods")))
23738 (build-system r-build-system)
23739 (home-page "http://www.wias-berlin.de/software/imaging/")
23740 (synopsis "Class and methods definitions")
23742 "This package defines the generic method @code{extract} and provides
23743 @code{openMP} support as needed in several packages like
23744 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
23745 (license license:gpl2+)))
23747 (define-public r-aws
23754 (uri (cran-uri "aws" version))
23757 "1fhm87iax6bkvd4vszvjbcqw3b2drs11rjxr7zf2w4sgc72svaz8"))))
23759 `((upstream-name . "aws")))
23760 (build-system r-build-system)
23762 `(("r-awsmethods" ,r-awsmethods)
23765 `(("gfortran" ,gfortran)))
23766 (home-page "https://cran.r-project.org/web/packages/aws/")
23767 (synopsis "Adaptive weights smoothing")
23769 "This package provides a collection of R-functions implementing adaptive
23770 smoothing procedures in 1D, 2D and 3D. This includes the
23771 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
23772 Confidence Intervals} (ICI), variational approaches, and a non-local means
23774 (license license:gpl2+)))
23776 (define-public r-sgloptim
23778 (name "r-sgloptim")
23783 (uri (cran-uri "sglOptim" version))
23786 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
23788 `((upstream-name . "sglOptim")))
23789 (build-system r-build-system)
23792 ("r-doparallel" ,r-doparallel)
23793 ("r-foreach" ,r-foreach)
23794 ("r-matrix" ,r-matrix)
23796 ("r-rcpparmadillo" ,r-rcpparmadillo)
23797 ("r-rcppprogress" ,r-rcppprogress)))
23799 `(("r-knitr" ,r-knitr)))
23800 (home-page "https://github.com/nielsrhansen/sglOptim")
23801 (synopsis "Generic sparse group Lasso solver")
23803 "This package provides a fast generic solver for sparse group lasso
23804 optimization problems. The loss (objective) function must be defined in a C++
23805 module. The optimization problem is solved using a coordinate gradient
23806 descent algorithm. Convergence of the algorithm is established and the
23807 algorithm is applicable to a broad class of loss functions. Use of parallel
23808 computing for cross validation and subsampling is supported through the
23809 @code{foreach} and @code{doParallel} packages.")
23810 (license license:gpl2+)))
23812 (define-public r-grouped
23819 (uri (cran-uri "grouped" version))
23822 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
23824 `((upstream-name . "grouped")))
23825 (build-system r-build-system)
23827 `(("r-mass" ,r-mass)))
23828 (home-page "https://cran.r-project.org/web/packages/grouped/")
23829 (synopsis "Regression analysis of grouped and coarse data")
23831 "This package provides regression models for grouped and coarse data,
23832 under the coarsened at random assumption.")
23833 (license license:gpl2+)))
23835 (define-public r-stam
23842 (uri (cran-uri "stam" version))
23845 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
23847 `((upstream-name . "stam")))
23848 (build-system r-build-system)
23852 (home-page "https://cran.r-project.org/web/packages/stam")
23853 (synopsis "Spatio-temporal analysis and modelling")
23855 "This package provides various methods to conduct Spatio-Temporal
23856 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
23857 Inferred Spatio-Temporal Modelling.")
23858 (license license:gpl2+)))
23860 (define-public r-dcv
23867 (uri (cran-uri "dcv" version))
23870 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
23872 `((upstream-name . "dcv")))
23873 (build-system r-build-system)
23875 `(("r-lmtest" ,r-lmtest)))
23876 (home-page "https://cran.r-project.org/web/packages/dcv/")
23877 (synopsis "Conventional cross-validation statistics for climate-growth model")
23879 "This package performs several conventional cross-validation statistical
23880 methods for climate-growth model in the climate reconstruction from tree
23881 rings, including Sign Test statistic, Reduction of Error statistic, Product
23882 Mean Test, Durbin-Watson statistic etc.")
23883 (license license:gpl2)))
23885 (define-public r-rcdd
23892 (uri (cran-uri "rcdd" version))
23895 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
23897 `((upstream-name . "rcdd")))
23898 (build-system r-build-system)
23901 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
23902 (synopsis "Computational geometry")
23904 "This package converts back and forth between two representations of a
23905 convex polytope: as solution of a set of linear equalities and inequalities
23906 and as convex hull of set of points and rays. Also does linear programming
23907 and redundant generator elimination. All functions can use exact
23908 infinite-precision rational arithmetic.")
23909 (license license:gpl2)))
23911 (define-public r-rxnat
23918 (uri (cran-uri "Rxnat" version))
23921 "00fl68pa0c2vy4xlny67pn41lzgm7b97wgg3dwm6z35izca62l11"))))
23923 `((upstream-name . "Rxnat")))
23924 (build-system r-build-system)
23926 `(("r-dplyr" ,r-dplyr)
23928 ("r-rcurl" ,r-rcurl)
23929 ("r-tibble" ,r-tibble)))
23931 `(("r-knitr" ,r-knitr)))
23932 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
23933 (synopsis "Queries and extracts images from neuroimaging datasets")
23935 "This package allows communication with the Extensible Neuroimaging
23936 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
23938 (license license:gpl2)))
23940 (define-public r-rserve
23947 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
23948 version ".tar.gz"))
23951 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
23952 (build-system r-build-system)
23955 (modify-phases %standard-phases
23956 (add-before 'install 'install-server-binary
23957 ;; Makevars tries to install to R's store directory.
23958 (lambda* (#:key outputs #:allow-other-keys)
23959 (let* ((out (assoc-ref outputs "out"))
23960 (bin (string-append out "/bin")))
23961 (substitute* "src/Makevars.in"
23962 (("\\$\\(R_HOME\\)") out))
23963 (mkdir-p bin)))))))
23965 `(("r-checkmate" ,r-checkmate)
23967 ("r-jsonlite" ,r-jsonlite)
23968 ("r-knitr" ,r-knitr)
23971 ("r-uuid" ,r-uuid)))
23973 `(("openssl" ,openssl)
23975 (home-page "https://github.com/s-u/Rserve")
23977 "Server providing access to R from many languages and systems")
23979 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
23980 binary requests to be sent to R. Every connection has a separate workspace
23981 and working directory. Client-side implementations are available for popular
23982 languages such as C/C++ and Java, allowing any application to use facilities
23983 of R without the need of linking to R code. Rserve supports remote
23984 connection, user authentication and file transfer. A simple R client is
23985 included in this package as well.")
23986 (license license:gpl2)))
23988 (define-public r-gamm4
23995 (uri (cran-uri "gamm4" version))
23998 "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap"))))
23999 (properties `((upstream-name . "gamm4")))
24000 (build-system r-build-system)
24002 `(("r-lme4" ,r-lme4)
24003 ("r-matrix" ,r-matrix)
24004 ("r-mgcv" ,r-mgcv)))
24005 (home-page "https://cran.r-project.org/web/packages/gamm4/")
24006 (synopsis "Generalized additive mixed models using mgcv and lme4")
24008 "Estimate generalized additive mixed models via a version of function
24009 @code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor
24011 (license license:gpl2+)))
24013 (define-public r-optimx
24016 (version "2020-4.2")
24020 (uri (cran-uri "optimx" version))
24023 "00bi2sr2hr7x6cfwlsn7hz2r56lcyv9naa8vmfcgr1r269fc50b3"))))
24024 (properties `((upstream-name . "optimx")))
24025 (build-system r-build-system)
24026 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
24027 (native-inputs `(("r-knitr" ,r-knitr)))
24028 (home-page "https://cran.r-project.org/web/packages/optimx/")
24029 (synopsis "Expanded replacement and extension of the optim function")
24031 "This package provides a replacement and extension of the @code{optim}
24032 function to call to several function minimization codes in R in a single
24033 statement. These methods handle smooth, possibly box constrained functions of
24034 several or many parameters. Note that the function @code{optimr} was prepared
24035 to simplify the incorporation of minimization codes going forward. This
24036 package also implements some utility codes and some extra solvers, including
24037 safeguarded Newton methods. Many methods previously separate are now included
24039 (license license:gpl2)))
24041 (define-public r-projpred
24043 (name "r-projpred")
24048 (uri (cran-uri "projpred" version))
24051 "0nx514mrfh3gv854pr71w5x3zgdnn0kinf5nh7z90q3h7ysry2mg"))))
24052 (properties `((upstream-name . "projpred")))
24053 (build-system r-build-system)
24055 `(("r-dplyr" ,r-dplyr)
24056 ("r-gamm4" ,r-gamm4)
24057 ("r-ggplot2" ,r-ggplot2)
24060 ("r-magrittr" ,r-magrittr)
24063 ("r-optimx" ,r-optimx)
24065 ("r-rcpparmadillo" ,r-rcpparmadillo)
24066 ("r-rngtools" ,r-rngtools)
24067 ("r-rstantools" ,r-rstantools)
24068 ("r-tidyverse" ,r-tidyverse)))
24069 (native-inputs `(("r-knitr" ,r-knitr)))
24070 (home-page "https://mc-stan.org/projpred/")
24071 (synopsis "Projection predictive feature selection")
24073 "This package performs projection predictive feature selection for
24074 generalized linear models and generalized linear and additive multilevel
24075 models. The package is compatible with the @code{rstanarm} and @code{brms}
24076 packages, but other reference models can also be used. See the package
24077 vignette for more information and examples.")
24078 (license license:gpl3)))
24080 (define-public r-brms
24087 (uri (cran-uri "brms" version))
24090 "0mzwihhgmn405l6zq11a180q4k3chggj9qj0j7q838b9vrszg59j"))))
24091 (properties `((upstream-name . "brms")))
24092 (build-system r-build-system)
24094 `(("r-abind" ,r-abind)
24095 ("r-backports" ,r-backports)
24096 ("r-bayesplot" ,r-bayesplot)
24097 ("r-bridgesampling" ,r-bridgesampling)
24099 ("r-future" ,r-future)
24100 ("r-ggplot2" ,r-ggplot2)
24103 ("r-matrix" ,r-matrix)
24104 ("r-matrixstats" ,r-matrixstats)
24106 ("r-nleqslv" ,r-nleqslv)
24108 ("r-projpred" ,r-projpred)
24110 ("r-rstan" ,r-rstan)
24111 ("r-rstantools" ,r-rstantools)
24112 ("r-shinystan" ,r-shinystan)))
24113 (native-inputs `(("r-knitr" ,r-knitr)))
24115 "https://github.com/paul-buerkner/brms")
24117 "Bayesian Regression Models using 'Stan'")
24119 "Fit Bayesian generalized (non-)linear multivariate multilevel models
24120 using 'Stan' for full Bayesian inference. A wide range of distributions and
24121 link functions are supported, allowing users to fit -- among others -- linear,
24122 robust linear, count data, survival, response times, ordinal, zero-inflated,
24123 hurdle, and even self-defined mixture models all in a multilevel context.
24124 Further modeling options include non-linear and smooth terms, auto-correlation
24125 structures, censored data, meta-analytic standard errors, and quite a few
24126 more. In addition, all parameters of the response distribution can be
24127 predicted in order to perform distributional regression. Prior specifications
24128 are flexible and explicitly encourage users to apply prior distributions that
24129 actually reflect their beliefs. Model fit can easily be assessed and compared
24130 with posterior predictive checks and leave-one-out cross-validation.")
24131 (license license:gpl2)))
24133 (define-public r-mstate
24140 (uri (cran-uri "mstate" version))
24143 "11i3p7fph8nbnfis1m7rdrq32qryaajv2wrkxk1x6k17zkh4rq6i"))))
24144 (properties `((upstream-name . "mstate")))
24145 (build-system r-build-system)
24147 `(("r-data-table" ,r-data-table)
24148 ("r-lattice" ,r-lattice)
24149 ("r-magrittr" ,r-magrittr)
24150 ("r-rcolorbrewer" ,r-rcolorbrewer)
24151 ("r-rlang" ,r-rlang)
24152 ("r-survival" ,r-survival)
24153 ("r-viridis" ,r-viridis)))
24155 `(("r-knitr" ,r-knitr)))
24157 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
24159 "Data Preparation, Estimation and Prediction in Multi-State Models")
24161 "Contains functions for data preparation, descriptives, hazard estimation
24162 and prediction with Aalen-Johansen or simulation in competing risks and
24163 multi-state models.")
24164 (license license:gpl2+)))
24166 (define-public r-scatterpie
24168 (name "r-scatterpie")
24173 (uri (cran-uri "scatterpie" version))
24176 "0h48l0699lpfagv09f53yismir84945m56qwzk52lc7wxyvkfcp1"))))
24177 (properties `((upstream-name . "scatterpie")))
24178 (build-system r-build-system)
24180 `(("r-ggforce" ,r-ggforce)
24181 ("r-ggplot2" ,r-ggplot2)
24182 ("r-rlang" ,r-rlang)
24183 ("r-rvcheck" ,r-rvcheck)
24184 ("r-tidyr" ,r-tidyr)))
24186 `(("r-knitr" ,r-knitr)))
24187 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
24188 (synopsis "Scatter pie plot")
24190 "This package creates scatterpie plots, especially useful for plotting
24192 (license license:artistic2.0)))
24194 (define-public r-scrypt
24201 (uri (cran-uri "scrypt" version))
24204 "14iblgbp9v2by8fjbrpsd59iknp5babcz7j3yv1yxxzcwyb6wrrm"))))
24205 (properties `((upstream-name . "scrypt")))
24206 (build-system r-build-system)
24208 `(("r-rcpp" ,r-rcpp)))
24209 (home-page "https://github.com/rstudio/rscrypt")
24210 (synopsis "Key derivation functions for R based on Scrypt")
24212 "This package provides functions for working with the scrypt key
24213 derivation functions. Scrypt is a password-based key derivation function
24214 created by Colin Percival. The algorithm was specifically designed to make it
24215 costly to perform large-scale custom hardware attacks by requiring large
24216 amounts of memory.")
24217 (license license:bsd-2)))
24219 (define-public r-boruta
24226 (uri (cran-uri "Boruta" version))
24229 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
24230 (properties `((upstream-name . "Boruta")))
24231 (build-system r-build-system)
24232 (propagated-inputs `(("r-ranger" ,r-ranger)))
24233 (home-page "https://gitlab.com/mbq/Boruta/")
24234 (synopsis "Wrapper algorithm for all relevant feature selection")
24236 "This package provides an all relevant feature selection wrapper
24237 algorithm. It finds relevant features by comparing original attributes'
24238 importance with importance achievable at random, estimated using their
24239 permuted copies (shadows).")
24240 (license license:gpl2+)))
24242 (define-public r-directlabels
24244 (name "r-directlabels")
24245 (version "2021.1.13")
24249 (uri (cran-uri "directlabels" version))
24252 "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w"))))
24253 (build-system r-build-system)
24255 `(("r-quadprog" ,r-quadprog)))
24257 `(("r-knitr" ,r-knitr)))
24258 (home-page "http://directlabels.r-forge.r-project.org/")
24259 (synopsis "Direct labels for multicolor plots")
24261 "This package provides an extensible framework for automatically placing
24262 direct labels onto multicolor plots. Label positions are described using
24263 positioning methods that can be re-used across several different plots. There
24264 are heuristics for examining @code{trellis} and @code{ggplot} objects and
24265 inferring an appropriate positioning method.")
24266 (license license:gpl3)))
24268 (define-public r-lsd
24275 (uri (cran-uri "LSD" version))
24277 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
24278 (properties `((upstream-name . "LSD")))
24279 (build-system r-build-system)
24280 (home-page "https://cran.r-project.org/web/packages/LSD/")
24281 (synopsis "Lots of superior depictions tool creates colorful plots")
24283 "This package creates lots of colorful plots in a multitude of variations.
24284 Try a demo of the LSD by running @code{demotour()}.")
24286 (license (list license:gpl2 license:gpl3))))
24288 (define-public r-phylogram
24290 (name "r-phylogram")
24295 (uri (cran-uri "phylogram" version))
24297 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
24298 (properties `((upstream-name . "phylogram")))
24299 (build-system r-build-system)
24300 (propagated-inputs `(("r-ape" ,r-ape)))
24301 (home-page "https://github.com/ropensci/phylogram/")
24302 (synopsis "Dendrograms for evolutionary analysis")
24304 "The @code{r-phylogram} package is a tool for for developing phylogenetic
24305 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
24306 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
24307 as well as several tools for command-line tree manipulation and import/export
24308 via Newick parenthetic text. This improves accessibility to the comprehensive
24309 range of object-specific analytical and tree-visualization functions found
24310 across a wide array of bioinformatic R packages.")
24311 (license license:gpl3)))
24313 (define-public r-kmer
24320 (uri (cran-uri "kmer" version))
24322 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
24323 (properties `((upstream-name . "kmer")))
24324 (build-system r-build-system)
24326 `(("r-openssl" ,r-openssl)
24327 ("r-phylogram" ,r-phylogram)
24328 ("r-rcpp" ,r-rcpp)))
24329 (home-page "https://github.com/shaunpwilkinson/kmer/")
24330 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
24332 "@code{r-kmer} is an R package for rapidly computing distance matrices
24333 and clustering large sequence datasets using fast alignment-free k-mer
24334 counting and recursive k-means partitioning.")
24335 (license license:gpl3)))
24337 (define-public r-hardhat
24344 (uri (cran-uri "hardhat" version))
24347 "1b7f9i9fy39j9n03g40vd6nzgq9fgq914xg3svf84najlknvjzly"))))
24348 (properties `((upstream-name . "hardhat")))
24349 (build-system r-build-system)
24351 `(("r-glue" ,r-glue)
24352 ("r-rlang" ,r-rlang)
24353 ("r-tibble" ,r-tibble)
24354 ("r-vctrs" ,r-vctrs)))
24356 `(("r-knitr" ,r-knitr)))
24357 (home-page "https://github.com/tidymodels/hardhat")
24358 (synopsis "Construct modeling packages")
24360 "Building modeling packages is hard. A large amount of effort generally
24361 goes into providing an implementation for a new method that is efficient,
24362 fast, and correct, but often less emphasis is put on the user interface. A
24363 good interface requires specialized knowledge about S3 methods and formulas,
24364 which the average package developer might not have. The goal of
24365 @code{hardhat} is to reduce the burden around building new modeling packages
24366 by providing functionality for preprocessing, predicting, and validating
24368 (license license:expat)))
24370 (define-public r-lightgbm
24372 (name "r-lightgbm")
24377 (uri (cran-uri "lightgbm" version))
24380 "1pwsh6j9ksahh58b15j5ij56bsc6syy3z4k4a5zhy5n7829rz555"))))
24381 (properties `((upstream-name . "lightgbm")))
24382 (build-system r-build-system)
24384 `(("r-data-table" ,r-data-table)
24385 ("r-jsonlite" ,r-jsonlite)
24386 ("r-matrix" ,r-matrix)
24388 (home-page "https://github.com/Microsoft/LightGBM")
24389 (synopsis "Light gradient boosting machine")
24391 "Tree based algorithms can be improved by introducing boosting
24392 frameworks. LightGBM is one such framework, based on Ke, Guolin et
24393 al. (2017). This package offers an R interface to work with it. It is
24394 designed to be distributed and efficient with the following goals:
24397 @item Faster training speed and higher efficiency;
24398 @item lower memory usage;
24399 @item better accuracy;
24400 @item parallel learning supported; and
24401 @item capable of handling large-scale data.
24404 (license license:expat)))
24406 (define-public r-shapforxgboost
24408 (name "r-shapforxgboost")
24413 (uri (cran-uri "SHAPforxgboost" version))
24416 "0jgyss9bawl7sf4dwa75sn7ld3mvrrr0z2074lbkq3f5qb9gwsly"))))
24418 `((upstream-name . "SHAPforxgboost")))
24419 (build-system r-build-system)
24421 `(("r-bbmisc" ,r-bbmisc)
24422 ("r-data-table" ,r-data-table)
24423 ("r-ggextra" ,r-ggextra)
24424 ("r-ggforce" ,r-ggforce)
24425 ("r-ggplot2" ,r-ggplot2)
24426 ("r-ggpubr" ,r-ggpubr)
24427 ("r-lightgbm" ,r-lightgbm)
24428 ("r-rcolorbrewer" ,r-rcolorbrewer)
24429 ("r-xgboost" ,r-xgboost)))
24430 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
24431 (synopsis "SHAP Plots for XGBoost")
24433 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
24434 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
24435 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
24436 and force plot. It relies on the @code{XGBoost} package to produce SHAP
24438 (license license:expat)))
24440 (define-public r-rismed
24447 (uri (cran-uri "RISmed" version))
24450 "0nwixhngi4r2f73362salivsmsf7l52bm13jqvhdq8mfiigm80vd"))))
24451 (properties `((upstream-name . "RISmed")))
24452 (build-system r-build-system)
24453 (home-page "https://cran.r-project.org/web/packages/RISmed")
24454 (synopsis "Download content from NCBI databases")
24456 "This package provides a set of tools to extract bibliographic
24457 content from the National Center for Biotechnology Information (NCBI)
24458 databases, including PubMed. The name RISmed is a portmanteau of
24459 RIS (for Research Information Systems, a common tag format for
24460 bibliographic data) and PubMed.")
24461 (license license:gpl2+)))
24463 (define-public r-semver
24470 (uri (cran-uri "semver" version))
24473 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
24474 (properties `((upstream-name . "semver")))
24475 (build-system r-build-system)
24477 `(("r-assertthat" ,r-assertthat)
24478 ("r-rcpp" ,r-rcpp)))
24479 (native-inputs `(("r-knitr" ,r-knitr)))
24480 (home-page "https://github.com/johndharrison/semver")
24481 (synopsis "Parser for Semantic Versioning 2.0.0")
24483 "This package provides tools and functions for parsing, rendering and
24484 operating on semantic version strings. Semantic versioning is a simple set of
24485 rules and requirements that dictate how version numbers are assigned and
24486 incremented as outlined at @url{http://semver.org}.")
24487 (license license:expat)))
24489 (define-public r-binman
24496 (uri (cran-uri "binman" version))
24499 "00l7m98h41r67gf0qxqis3vx63j7wylnk9vlgcyk41szkrz8ikkc"))))
24500 (properties `((upstream-name . "binman")))
24501 (build-system r-build-system)
24503 `(("r-assertthat" ,r-assertthat)
24505 ("r-jsonlite" ,r-jsonlite)
24506 ("r-rappdirs" ,r-rappdirs)
24507 ("r-semver" ,r-semver)
24509 ("r-yaml" ,r-yaml)))
24510 (native-inputs `(("r-knitr" ,r-knitr)))
24511 (home-page "https://github.com/ropensci/binman")
24512 (synopsis "Binary download manager")
24514 "This package provides tools and functions for managing the download of
24515 binary files. Binary repositories are defined in the YAML format. Defining
24516 new pre-download, download and post-download templates allow additional
24517 repositories to be added.")
24518 (license license:expat)))
24520 (define-public r-wdman
24527 (uri (cran-uri "wdman" version))
24530 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
24531 (properties `((upstream-name . "wdman")))
24532 (build-system r-build-system)
24534 `(("r-assertthat" ,r-assertthat)
24535 ("r-binman" ,r-binman)
24536 ("r-processx" ,r-processx)
24537 ("r-semver" ,r-semver)
24538 ("r-yaml" ,r-yaml)))
24539 (native-inputs `(("r-knitr" ,r-knitr)))
24540 (home-page "https://docs.ropensci.org/wdman/")
24541 (synopsis "Webdriver/Selenium binary manager")
24543 "There are a number of binary files associated with the
24544 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
24545 @url{https://sites.google.com/a/chromium.org/chromedriver/},
24546 @url{https://github.com/mozilla/geckodriver},
24547 @url{http://phantomjs.org/download.html}, and
24548 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
24549 more information). This package provides functions to download these binaries
24550 and to manage processes involving them.")
24551 (license license:expat)))
24553 (define-public r-rselenium
24555 (name "r-rselenium")
24560 (uri (cran-uri "RSelenium" version))
24563 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
24564 (properties `((upstream-name . "RSelenium")))
24565 (build-system r-build-system)
24567 `(("r-binman" ,r-binman)
24568 ("r-catools" ,r-catools)
24570 ("r-openssl" ,r-openssl)
24571 ("r-wdman" ,r-wdman)
24573 (native-inputs `(("r-knitr" ,r-knitr)))
24574 (home-page "https://docs.ropensci.org/RSelenium/")
24575 (synopsis "R bindings for Selenium WebDriver")
24577 "This package provides a set of R bindings for the Selenium 2.0
24578 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
24579 information) using the @code{JsonWireProtocol} (see
24580 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
24581 information). Selenium 2.0 WebDriver allows driving a web browser natively as
24582 a user would either locally or on a remote machine using the Selenium server
24583 it marks a leap forward in terms of web browser automation. Selenium
24584 automates web browsers (commonly referred to as browsers). Using RSelenium
24585 you can automate browsers locally or remotely.")
24586 (license license:agpl3+)))
24588 (define-public r-conquer
24595 (uri (cran-uri "conquer" version))
24598 "1zvlsrbmrij011mcdi3qngs1al2lhrdiyknxnk0w1zhzrra62bsl"))))
24599 (properties `((upstream-name . "conquer")))
24600 (build-system r-build-system)
24602 `(("r-matrix" ,r-matrix)
24603 ("r-matrixstats" ,r-matrixstats)
24605 ("r-rcpparmadillo" ,r-rcpparmadillo)))
24606 (home-page "https://github.com/XiaoouPan/conquer")
24607 (synopsis "Convolution-type smoothed quantile regression")
24609 "This package provides fast and accurate convolution-type smoothed
24610 quantile regression, implemented using Barzilai-Borwein gradient descent with
24611 a Huber regression warm start. Confidence intervals for regression
24612 coefficients are constructed using multiplier bootstrap.")
24613 (license license:gpl3)))
24615 (define-public r-fastshap
24617 (name "r-fastshap")
24622 (uri (cran-uri "fastshap" version))
24625 "08f25ib5mry6h8lvj0g3clc9kfl5g2wdd8x8bw455wwmbcm6x5vg"))))
24626 (properties `((upstream-name . "fastshap")))
24627 (build-system r-build-system)
24629 `(("r-abind" ,r-abind)
24630 ("r-ggplot2" ,r-ggplot2)
24631 ("r-gridextra" ,r-gridextra)
24632 ("r-matrixstats" ,r-matrixstats)
24635 ("r-rcpparmadillo" ,r-rcpparmadillo)
24636 ("r-tibble" ,r-tibble)))
24637 (home-page "https://github.com/bgreenwell/fastshap")
24638 (synopsis "Fast approximate Shapley values")
24640 "This package computes fast (relative to other implementations)
24641 approximate Shapley values for any supervised learning model. Shapley values
24642 help to explain the predictions from any black box model using ideas from game
24643 theory; see @url{Strumbel and Kononenko (2014),
24644 doi.org/10.1007/s10115-013-0679-x} for details.")
24645 (license license:gpl2+)))
24647 (define-public r-metrics
24654 (uri (cran-uri "Metrics" version))
24657 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
24658 (properties `((upstream-name . "Metrics")))
24659 (build-system r-build-system)
24660 (home-page "https://github.com/mfrasco/Metrics")
24661 (synopsis "Evaluation metrics for machine learning")
24663 "This package provides an implementation of evaluation metrics in R that
24664 are commonly used in supervised machine learning. It implements metrics for
24665 regression, time series, binary classification, classification, and
24666 information retrieval problems. It has zero dependencies and a consistent,
24667 simple interface for all functions.")
24668 (license license:bsd-3)))
24670 (define-public r-iml
24677 (uri (cran-uri "iml" version))
24680 "0xm3q42qahq798ilgg050df0mahhbdfd3fx3i7cpx606h38si0x7"))))
24681 (properties `((upstream-name . "iml")))
24682 (build-system r-build-system)
24684 `(("r-checkmate" ,r-checkmate)
24685 ("r-data-table" ,r-data-table)
24686 ("r-formula" ,r-formula)
24687 ("r-future" ,r-future)
24688 ("r-future-apply" ,r-future-apply)
24689 ("r-ggplot2" ,r-ggplot2)
24690 ("r-gridextra" ,r-gridextra)
24691 ("r-metrics" ,r-metrics)
24692 ("r-prediction" ,r-prediction)
24694 (native-inputs `(("r-knitr" ,r-knitr)))
24695 (home-page "https://github.com/christophM/iml")
24696 (synopsis "Interpretable machine learning")
24698 "This package provides interpretability methods to analyze the behavior
24699 and predictions of any machine learning model. Implemented methods are:
24702 @item Feature importance described by Fisher et al. (2018),
24703 @item accumulated local effects plots described by Apley (2018),
24704 @item partial dependence plots described by Friedman (2001),
24705 @item individual conditional expectation ('ice') plots described by Goldstein
24706 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
24707 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
24708 @item the Shapley Value described by Strumbelj et. al (2014)
24709 @url{https://doi.org/10.1007/s10115-013-0679-x},
24710 @item feature interactions described by Friedman et. al
24711 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
24714 (license license:expat)))
24716 (define-public r-goftest
24723 (uri (cran-uri "goftest" version))
24726 "0ivnkqhv5xgiv05dm648nngacymd8x8g0fyppv3bc0mhcqk9k5z4"))))
24727 (properties `((upstream-name . "goftest")))
24728 (build-system r-build-system)
24729 (home-page "https://github.com/baddstats/goftest")
24730 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
24732 "This package provides Cramer-Von Mises and Anderson-Darling tests of
24733 goodness-of-fit for continuous univariate distributions, using efficient
24735 (license license:gpl2+)))
24737 (define-public r-tensor
24744 (uri (cran-uri "tensor" version))
24747 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
24748 (properties `((upstream-name . "tensor")))
24749 (build-system r-build-system)
24750 (home-page "https://cran.r-project.org/web/packages/tensor/")
24751 (synopsis "Tensor product of arrays")
24753 "The tensor product of two arrays is notionally an outer product of the
24754 arrays collapsed in specific extents by summing along the appropriate
24755 diagonals. This package allows you to compute the tensor product of arrays.")
24756 (license license:gpl2+)))
24758 (define-public r-spatstat-utils
24760 (name "r-spatstat-utils")
24765 (uri (cran-uri "spatstat.utils" version))
24768 "1li0vksxpkvgyx3j2wi40kj5687vwakkfdix6icm6g01a0lb2m5d"))))
24770 `((upstream-name . "spatstat.utils")))
24771 (build-system r-build-system)
24772 (home-page "http://www.spatstat.org")
24773 (synopsis "Utility functions for spatstat")
24775 "This package contains utility functions for the @code{spatstat} package
24776 which may also be useful for other purposes.")
24777 (license license:gpl2+)))
24779 (define-public r-spatstat-data
24781 (name "r-spatstat-data")
24786 (uri (cran-uri "spatstat.data" version))
24789 "1z1jb1yzb7qhfg55dhzcrdvn5x8hpg9xif0hpnapddbmhxd1hbb7"))))
24790 (properties `((upstream-name . "spatstat.data")))
24791 (build-system r-build-system)
24793 `(("r-matrix" ,r-matrix)
24794 ("r-spatstat-utils" ,r-spatstat-utils)))
24795 (home-page "http://www.spatstat.org")
24796 (synopsis "Datasets for spatstat")
24798 "This package contains all the datasets for the @code{spatstat}
24800 (license license:gpl2+)))
24802 (define-public r-spatstat
24804 (name "r-spatstat")
24809 (uri (cran-uri "spatstat" version))
24812 "06jmxfs9kz9qqi3ichfgn8dglwb87kq2nl578p83za5psv8cfgya"))))
24813 (properties `((upstream-name . "spatstat")))
24814 (build-system r-build-system)
24816 `(("r-abind" ,r-abind)
24817 ("r-deldir" ,r-deldir)
24818 ("r-goftest" ,r-goftest)
24819 ("r-matrix" ,r-matrix)
24822 ("r-polyclip" ,r-polyclip)
24823 ("r-rpart" ,r-rpart)
24824 ("r-spatstat-data" ,r-spatstat-data)
24825 ("r-spatstat-utils" ,r-spatstat-utils)
24826 ("r-tensor" ,r-tensor)))
24827 (home-page "http://www.spatstat.org")
24828 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
24830 "This package provides a comprehensive toolbox for analysing Spatial
24831 Point Patterns. It is focused mainly on two-dimensional point patterns,
24832 including multitype/marked points, in any spatial region. It also supports
24833 three-dimensional point patterns, space-time point patterns in any number of
24834 dimensions, point patterns on a linear network, and patterns of other
24835 geometrical objects. It supports spatial covariate data such as pixel images
24836 and contains over 2000 functions for plotting spatial data, exploratory data
24837 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
24838 formal inference.")
24839 (license license:gpl2+)))
24841 (define-public r-gaston
24848 (uri (cran-uri "gaston" version))
24851 "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i"))))
24852 (properties `((upstream-name . "gaston")))
24853 (build-system r-build-system)
24854 (inputs `(("zlib" ,zlib)))
24856 `(("r-rcpp" ,r-rcpp)
24857 ("r-rcppeigen" ,r-rcppeigen)
24858 ("r-rcppparallel" ,r-rcppparallel)))
24859 (native-inputs `(("r-knitr" ,r-knitr)))
24860 (home-page "https://cran.r-project.org/web/packages/gaston/")
24861 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
24863 "This is a package for the manipulation of genetic data (SNPs).
24864 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
24865 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
24866 for linear mixed models (AIREML).")
24867 (license license:gpl3)))
24869 (define-public r-cpp11
24876 (uri (cran-uri "cpp11" version))
24879 "118i8s7978vl9xyhnb47wcbd6rcc6b958mq2w8s3rdsd4pxv62gz"))))
24880 (properties `((upstream-name . "cpp11")))
24881 (build-system r-build-system)
24882 (native-inputs `(("r-knitr" ,r-knitr)))
24883 (home-page "https://github.com/r-lib/cpp11")
24884 (synopsis "C++11 Interface for R's C Interface")
24886 "This package provides a header only, C++11 interface to R's C interface.
24887 Compared to other approaches @code{cpp11} strives to be safe against long
24888 jumps from the C API as well as C++ exceptions, conform to normal R function
24889 semantics and supports interaction with @code{ALTREP} vectors.")
24890 (license license:expat)))
24892 (define-public r-rcppziggurat
24894 (name "r-rcppziggurat")
24899 (uri (cran-uri "RcppZiggurat" version))
24902 "0wgd1v2p7zajnbrjf3hfi56p3pk3ld6iwkanbb04bjbnlif2ay4w"))))
24903 (properties `((upstream-name . "RcppZiggurat")))
24904 (build-system r-build-system)
24906 `(("r-rcpp" ,r-rcpp)
24907 ("r-rcppgsl" ,r-rcppgsl)))
24908 (native-inputs `(("r-knitr" ,r-knitr)))
24909 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
24910 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
24912 "The Ziggurat generator for normally distributed random numbers,
24913 originally proposed by Marsaglia and Tsang (2000,
24914 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
24915 times starting with Leong et al (2005,
24916 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
24917 aggregation for comparing different implementations in order to provide a
24918 'faster but good enough' alternative for use with R and C++ code.")
24919 (license license:gpl2+)))
24921 (define-public r-rfast
24928 (uri (cran-uri "Rfast" version))
24931 "1cq3mcg49hsvqhwn6f4dgsx7f8ma4qnwr5n6s7m22qy57rg31958"))))
24932 (properties `((upstream-name . "Rfast")))
24933 (build-system r-build-system)
24935 `(("r-rcpp" ,r-rcpp)
24936 ("r-rcpparmadillo" ,r-rcpparmadillo)
24937 ("r-rcppziggurat" ,r-rcppziggurat)))
24938 (home-page "https://github.com/RfastOfficial/Rfast")
24939 (synopsis "Collection of efficient and fast R functions")
24941 "This package provides a collection of fast (utility) functions for data
24942 analysis. Column- and row- wise means, medians, variances, minimums,
24943 maximums, many t, F and G-square tests, many regressions (normal, logistic,
24944 Poisson), are some of the many fast functions.")
24945 (license license:gpl2+)))
24947 (define-public r-clusterr
24949 (name "r-clusterr")
24954 (uri (cran-uri "ClusterR" version))
24957 "1ky172bk15a78hky77vl60j7c81nq2495sxjrv53is25nkac7sjm"))))
24958 (properties `((upstream-name . "ClusterR")))
24959 (build-system r-build-system)
24961 `(("r-ggplot2" ,r-ggplot2)
24963 ("r-gtools" ,r-gtools)
24965 ("r-rcpparmadillo" ,r-rcpparmadillo)))
24966 (native-inputs `(("r-knitr" ,r-knitr)))
24967 (home-page "https://github.com/mlampros/ClusterR")
24968 (synopsis "Clustering")
24970 "This package provides Gaussian mixture models, k-means,
24971 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
24972 option to plot, validate, predict (new data) and estimate the optimal number
24973 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
24974 the computationally intensive parts of the functions. For more information,
24978 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
24979 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
24980 @url{https://doi.org/10.18637/jss.v001.i04};
24981 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
24982 Library, @url{https://doi.org/10.1145/1772690.1772862};
24983 @item \"Armadillo: a template-based C++ library
24984 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
24985 Software, @url{https://doi.org/10.21105/joss.00026};
24986 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
24987 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
24988 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
24991 (license license:gpl3)))
24993 (define-public r-spectrum
24995 (name "r-spectrum")
25000 (uri (cran-uri "Spectrum" version))
25003 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
25004 (properties `((upstream-name . "Spectrum")))
25005 (build-system r-build-system)
25007 `(("r-clusterr" ,r-clusterr)
25008 ("r-diptest" ,r-diptest)
25009 ("r-ggplot2" ,r-ggplot2)
25010 ("r-rfast" ,r-rfast)))
25011 (native-inputs `(("r-knitr" ,r-knitr)))
25012 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
25013 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
25015 "This package provides a self-tuning spectral clustering method for
25016 single or multi-view data. Spectrum uses a new type of adaptive density aware
25017 kernel that strengthens connections in the graph based on common nearest
25018 neighbours. It uses a tensor product graph data integration and diffusion
25019 procedure to integrate different data sources and reduce noise. Spectrum uses
25020 either the eigengap or multimodality gap heuristics to determine the number of
25021 clusters. The method is sufficiently flexible so that a wide range of
25022 Gaussian and non-Gaussian structures can be clustered with automatic selection
25024 (license license:agpl3+)))
25026 (define-public r-nabor
25033 (uri (cran-uri "nabor" version))
25036 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
25037 (properties `((upstream-name . "nabor")))
25038 (build-system r-build-system)
25042 ("r-rcppeigen" ,r-rcppeigen)))
25043 (home-page "https://cran.r-project.org/web/packages/nabor/")
25044 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
25046 "This package provides an R wrapper for libnabo, an exact or approximate
25047 k nearest neighbour library which is optimised for low dimensional
25048 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
25049 designed as a drop-in replacement for the RANN function @code{nn2}. In
25050 addition, objects which include the k-d tree search structure can be returned
25051 to speed up repeated queries of the same set of target points.")
25052 (license license:bsd-3)))
25054 (define-public r-muhaz
25057 (version "1.2.6.1")
25061 (uri (cran-uri "muhaz" version))
25064 "08qh43zx6h3yby44q2vxphfvmfdmqxpgyp0734yn341sy9n8pkkk"))))
25065 (properties `((upstream-name . "muhaz")))
25066 (build-system r-build-system)
25068 `(("r-survival" ,r-survival)))
25070 `(("gfortran" ,gfortran)))
25071 (home-page "https://cran.r-project.org/web/packages/muhaz/")
25072 (synopsis "Hazard function estimation in survival analysis")
25074 "This package produces a smooth estimate of the hazard function for
25076 ;; Any version of the GPL.
25077 (license license:gpl3+)))
25079 (define-public r-flexsurv
25081 (name "r-flexsurv")
25086 (uri (cran-uri "flexsurv" version))
25089 "0x7p1rv51pplfyyzcg63ssb8z56mig7y0363hkr0219w3cvyq9nr"))))
25090 (properties `((upstream-name . "flexsurv")))
25091 (build-system r-build-system)
25093 `(("r-desolve" ,r-desolve)
25094 ("r-mstate" ,r-mstate)
25095 ("r-muhaz" ,r-muhaz)
25096 ("r-mvtnorm" ,r-mvtnorm)
25097 ("r-quadprog" ,r-quadprog)
25099 ("r-survival" ,r-survival)
25100 ("r-tibble" ,r-tibble)
25101 ("r-tidyr" ,r-tidyr)))
25103 `(("r-knitr" ,r-knitr)))
25104 (home-page "https://github.com/chjackson/flexsurv-dev")
25105 (synopsis "Flexible parametric survival and multi-state models")
25107 "This package provides flexible parametric models for time-to-event data,
25108 including the Royston-Parmar spline model, generalized gamma and generalized F
25109 distributions. Any user-defined parametric distribution can be fitted, given
25110 at least an R function defining the probability density or hazard. There are
25111 also tools for fitting and predicting from fully parametric multi-state
25113 (license license:gpl2+)))
25115 (define-public r-transphylo
25117 (name "r-transphylo")
25122 (uri (cran-uri "TransPhylo" version))
25125 "1506c97y8dnhd0c38rgvmg70q0l3xmmn07mjglhnw7hi5n5y9mv9"))))
25126 (properties `((upstream-name . "TransPhylo")))
25127 (build-system r-build-system)
25130 ("r-rcpp" ,r-rcpp)))
25132 `(("r-knitr" ,r-knitr)))
25133 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
25134 (synopsis "Inference of transmission tree from a dated phylogeny")
25136 "This is a package to infer transmission trees from a dated phylogeny.
25137 It includes methods to simulate and analyze outbreaks. The methodology is
25138 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
25139 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
25140 (license license:gpl2+)))
25142 (define-public r-km-ci
25149 (uri (cran-uri "km.ci" version))
25152 "1l6kw8jppaa1802yc5pbfwwgac56nhwc9p076ivylhms4w7cdf8v"))))
25153 (properties `((upstream-name . "km.ci")))
25154 (build-system r-build-system)
25156 `(("r-survival" ,r-survival)))
25157 (home-page "https://cran.r-project.org/web/packages/km.ci/")
25158 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
25160 "This package computes various @dfn{confidence intervals} (CI) for the
25161 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
25162 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
25163 Nair and Hall and Wellner.")
25164 (license license:gpl2+)))
25166 (define-public r-kmsurv
25173 (uri (cran-uri "KMsurv" version))
25176 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
25177 (properties `((upstream-name . "KMsurv")))
25178 (build-system r-build-system)
25179 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
25180 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
25182 "This package provides data sets and functions for Klein and Moeschberger
25183 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
25185 (license license:gpl3+)))
25187 (define-public r-survmisc
25189 (name "r-survmisc")
25194 (uri (cran-uri "survMisc" version))
25197 "00nvvl8gz4477ab24rd0xvfksm8msv8h021b9ld5c9cizc41n2bm"))))
25198 (properties `((upstream-name . "survMisc")))
25199 (build-system r-build-system)
25201 `(("r-data-table" ,r-data-table)
25202 ("r-ggplot2" ,r-ggplot2)
25203 ("r-gridextra" ,r-gridextra)
25204 ("r-km-ci" ,r-km-ci)
25205 ("r-kmsurv" ,r-kmsurv)
25206 ("r-knitr" ,r-knitr)
25207 ("r-survival" ,r-survival)
25208 ("r-xtable" ,r-xtable)
25211 `(("r-knitr" ,r-knitr)))
25212 (home-page "https://cran.r-project.org/web/packages/survMisc/")
25213 (synopsis "Miscellaneous functions for survival data")
25215 "This package provides a collection of functions to help in the analysis
25216 of right-censored survival data. These extend the methods available in
25217 the @code{survival} package.")
25218 (license license:gpl2)))
25220 (define-public r-exactranktests
25222 (name "r-exactranktests")
25227 (uri (cran-uri "exactRankTests" version))
25230 "1154dkcid3njhamdp87qs9bnx7l8bdqkcjsds9q9f2xmizs9x8gw"))))
25232 `((upstream-name . "exactRankTests")))
25233 (build-system r-build-system)
25234 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
25235 (synopsis "Exact distributions for rank and permutation tests")
25237 "This package computes exact conditional p-values and quantiles using an
25238 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
25239 (license license:gpl2+)))
25241 (define-public r-maxstat
25248 (uri (cran-uri "maxstat" version))
25251 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
25252 (properties `((upstream-name . "maxstat")))
25253 (build-system r-build-system)
25255 `(("r-exactranktests" ,r-exactranktests)
25256 ("r-mvtnorm" ,r-mvtnorm)))
25257 (home-page "https://cran.r-project.org/web/packages/maxstat/")
25258 (synopsis "Maximally selected rank statistics")
25260 "This package provides maximally selected rank statistics with several
25261 p-value approximations.")
25262 (license license:gpl2+)))
25264 (define-public r-survminer
25266 (name "r-survminer")
25271 (uri (cran-uri "survminer" version))
25274 "1niysd89mxb2a6ncvzm1s6xgfvq3psba65af0whh2p56r2hwrwff"))))
25275 (properties `((upstream-name . "survminer")))
25276 (build-system r-build-system)
25278 `(("r-broom" ,r-broom)
25279 ("r-dplyr" ,r-dplyr)
25280 ("r-ggplot2" ,r-ggplot2)
25281 ("r-ggpubr" ,r-ggpubr)
25282 ("r-gridextra" ,r-gridextra)
25283 ("r-magrittr" ,r-magrittr)
25284 ("r-maxstat" ,r-maxstat)
25285 ("r-purrr" ,r-purrr)
25286 ("r-rlang" ,r-rlang)
25287 ("r-scales" ,r-scales)
25288 ("r-survival" ,r-survival)
25289 ("r-survmisc" ,r-survmisc)
25290 ("r-tibble" ,r-tibble)
25291 ("r-tidyr" ,r-tidyr)))
25293 `(("r-knitr" ,r-knitr)))
25294 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
25295 (synopsis "Drawing survival curves using ggplot2")
25297 "This package contains the function @code{ggsurvplot()} for easily
25298 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
25299 risk' table and 'censoring count plot'. Other functions are also available to
25300 plot adjusted curves for Cox model and to visually examine Cox model
25302 (license license:gpl2)))
25304 (define-public r-forge
25311 (uri (cran-uri "forge" version))
25314 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
25315 (properties `((upstream-name . "forge")))
25316 (build-system r-build-system)
25318 `(("r-magrittr" ,r-magrittr)
25319 ("r-rlang" ,r-rlang)))
25320 (home-page "https://cran.r-project.org/web/packages/forge/")
25321 (synopsis "Cast values into shape")
25323 "This package provides helper functions with a consistent interface to
25324 coerce and verify the types and shapes of values for input checking.")
25325 (license license:asl2.0)))
25327 (define-public r-config
25334 (uri (cran-uri "config" version))
25337 "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l"))))
25338 (properties `((upstream-name . "config")))
25339 (build-system r-build-system)
25341 `(("r-yaml" ,r-yaml)))
25343 `(("r-knitr" ,r-knitr)))
25344 (home-page "https://github.com/rstudio/config")
25345 (synopsis "Manage environment specific configuration values")
25347 "This package lets you manage configuration values across multiple
25348 environments (e.g. development, test, production). It reads values using a
25349 function that determines the current environment and returns the appropriate
25351 (license license:gpl3)))
25353 (define-public r-adaptivesparsity
25355 (name "r-adaptivesparsity")
25359 (uri (cran-uri "AdaptiveSparsity" version))
25362 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
25364 `((upstream-name . "AdaptiveSparsity")))
25365 (build-system r-build-system)
25368 (modify-phases %standard-phases
25369 (add-after 'unpack 'link-against-armadillo
25371 (substitute* "src/Makevars"
25372 (("PKG_LIBS=" prefix)
25373 (string-append prefix "-larmadillo")))
25376 `(("r-mass" ,r-mass)
25377 ("r-matrix" ,r-matrix)
25379 ("r-rcpparmadillo" ,r-rcpparmadillo)))
25381 `(("armadillo" ,armadillo)))
25382 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
25383 (synopsis "Adaptive sparsity models")
25385 "This package implements the Figueiredo machine learning algorithm for
25386 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
25387 geometric models.")
25388 (license license:lgpl3+)))
25390 (define-public r-diffusionmap
25392 (name "r-diffusionmap")
25397 (uri (cran-uri "diffusionMap" version))
25400 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
25401 (properties `((upstream-name . "diffusionMap")))
25402 (build-system r-build-system)
25404 `(("r-igraph" ,r-igraph)
25405 ("r-matrix" ,r-matrix)
25406 ("r-scatterplot3d" ,r-scatterplot3d)))
25407 (home-page "https://www.r-project.org")
25408 (synopsis "Diffusion map")
25409 (description "This package implements the diffusion map method of data
25410 parametrization, including creation and visualization of diffusion maps,
25411 clustering with diffusion K-means and regression using the adaptive regression
25413 (license license:gpl2)))
25415 (define-public r-igraph
25422 (uri (cran-uri "igraph" version))
25425 "0vf7wrx77cdiav8724cw8gchrn0y9wvywphf5km4pa7xcqhsf3b4"))))
25426 (build-system r-build-system)
25428 `(("gfortran" ,gfortran)))
25432 ("libxml2" ,libxml2)
25435 `(("r-magrittr" ,r-magrittr)
25436 ("r-matrix" ,r-matrix)
25437 ("r-pkgconfig" ,r-pkgconfig)))
25438 (home-page "https://igraph.org")
25439 (synopsis "Network analysis and visualization")
25441 "This package provides routines for simple graphs and network analysis.
25442 It can handle large graphs very well and provides functions for generating
25443 random and regular graphs, graph visualization, centrality methods and much
25445 (license license:gpl2+)))
25447 (define-public r-workflows
25449 (name "r-workflows")
25454 (uri (cran-uri "workflows" version))
25457 "1mk0pnmpqlhf143mvj9rwvjrrshirz6s83s5hbfalhnyw7hzkfb9"))))
25458 (properties `((upstream-name . "workflows")))
25459 (build-system r-build-system)
25462 ("r-ellipsis" ,r-ellipsis)
25463 ("r-generics" ,r-generics)
25465 ("r-hardhat" ,r-hardhat)
25466 ("r-parsnip" ,r-parsnip)
25467 ("r-rlang" ,r-rlang)
25468 ("r-tidyselect" ,r-tidyselect)))
25470 `(("r-knitr" ,r-knitr)))
25471 (home-page "https://github.com/tidymodels/workflows")
25472 (synopsis "Modeling workflows")
25474 "A workflow is an object that can bundle together your pre-processing,
25475 modeling, and post-processing requests. For example, if you have a
25476 @code{recipe} and @code{parsnip} model, these can be combined into a
25477 workflow. The advantages are:
25480 @item You don’t have to keep track of separate objects in your workspace.
25481 @item The recipe prepping and model fitting can be executed using a single
25482 call to @code{fit()}.
25483 @item If you have custom tuning parameter settings, these can be defined using
25484 a simpler interface when combined with @code{tune}.
25485 @item In the future, workflows will be able to add post-processing operations,
25486 such as modifying the probability cutoff for two-class models.
25489 (license license:expat)))
25491 (define-public r-gpfit
25498 (uri (cran-uri "GPfit" version))
25501 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
25502 (properties `((upstream-name . "GPfit")))
25503 (build-system r-build-system)
25505 `(("r-lattice" ,r-lattice)
25507 (home-page "https://cran.r-project.org/web/packages/GPfit/")
25508 (synopsis "Gaussian Processes modeling")
25510 "This package provides a computationally stable approach of fitting a
25511 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
25512 (license license:gpl2)))
25514 (define-public r-yardstick
25516 (name "r-yardstick")
25521 (uri (cran-uri "yardstick" version))
25524 "1yrvlhn4gxyn9f20z5yv3xam0j0a8z362jwa32r33r0g0jk5z2fq"))))
25525 (properties `((upstream-name . "yardstick")))
25526 (build-system r-build-system)
25528 `(("r-dplyr" ,r-dplyr)
25529 ("r-generics" ,r-generics)
25531 ("r-rlang" ,r-rlang)
25532 ("r-tidyselect" ,r-tidyselect)))
25534 `(("r-knitr" ,r-knitr)))
25535 (home-page "https://github.com/tidymodels/yardstick")
25536 (synopsis "Tidy characterizations of model performance")
25538 "This package provides tidy tools for quantifying how well a model fits
25539 to a data set such as confusion matrices, class probability curve summaries,
25540 and regression metrics (e.g., RMSE).")
25541 (license license:gpl2)))
25543 (define-public r-warp
25550 (uri (cran-uri "warp" version))
25553 "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
25554 (properties `((upstream-name . "warp")))
25555 (build-system r-build-system)
25556 (native-inputs `(("r-knitr" ,r-knitr)))
25557 (home-page "https://github.com/DavisVaughan/warp")
25558 (synopsis "Group dates")
25560 "This package provides tooling to group dates by a variety of periods
25561 including: yearly, monthly, by second, by week of the month, and more. The
25562 groups are defined in such a way that they also represent the distance between
25563 dates in terms of the period. This extracts valuable information that can be
25564 used in further calculations that rely on a specific temporal spacing between
25566 (license license:expat)))
25568 (define-public r-slider
25575 (uri (cran-uri "slider" version))
25578 "1x4jwfxam4czfkb1s5qds5krfw1h2p5a4rh6f5z4yvhsv0d81xck"))))
25579 (properties `((upstream-name . "slider")))
25580 (build-system r-build-system)
25582 `(("r-glue" ,r-glue)
25583 ("r-rlang" ,r-rlang)
25584 ("r-vctrs" ,r-vctrs)
25585 ("r-warp" ,r-warp)))
25586 (native-inputs `(("r-knitr" ,r-knitr)))
25587 (home-page "https://github.com/DavisVaughan/slider")
25588 (synopsis "Sliding window functions")
25590 "This package provides type-stable rolling window functions over any R
25591 data type. Cumulative and expanding windows are also supported. For more
25592 advanced usage, an index can be used as a secondary vector that defines how
25593 sliding windows are to be created.")
25594 (license license:expat)))
25596 (define-public r-rsample
25603 (uri (cran-uri "rsample" version))
25606 "1psmxk16d4bz1v05x0gb9hn4brkdjxw8hjbxmj62snichnix3q3i"))))
25607 (properties `((upstream-name . "rsample")))
25608 (build-system r-build-system)
25610 `(("r-dplyr" ,r-dplyr)
25611 ("r-ellipsis" ,r-ellipsis)
25612 ("r-furrr" ,r-furrr)
25613 ("r-generics" ,r-generics)
25614 ("r-modeldata" ,r-modeldata)
25615 ("r-purrr" ,r-purrr)
25616 ("r-rlang" ,r-rlang)
25617 ("r-slider" ,r-slider)
25618 ("r-tibble" ,r-tibble)
25619 ("r-tidyr" ,r-tidyr)
25620 ("r-tidyselect" ,r-tidyselect)
25621 ("r-vctrs" ,r-vctrs)))
25623 `(("r-knitr" ,r-knitr)))
25624 (home-page "https://rsample.tidymodels.org")
25625 (synopsis "General resampling infrastructure")
25627 "This package provides classes and functions to create and summarize
25628 different types of resampling objects (e.g. bootstrap, cross-validation).")
25629 (license license:gpl2)))
25631 (define-public r-dicedesign
25633 (name "r-dicedesign")
25638 (uri (cran-uri "DiceDesign" version))
25641 "11s1m543kxd6gv4amh8z6pph1n67sj9sfwm6hjy83wfs65syf5vp"))))
25642 (properties `((upstream-name . "DiceDesign")))
25643 (build-system r-build-system)
25644 (home-page "http://dice.emse.fr/")
25645 (synopsis "Designs of computer experiments")
25647 "This package provides tools to create some specific @code{Space-Filling
25648 Design} (SFD) and to test their quality.")
25649 (license license:gpl3)))
25651 (define-public r-dials
25658 (uri (cran-uri "dials" version))
25661 "0g9wj2py4wz703rh4p7hk8qxqnkm7zyrypv4qz4vaqziazjsmxks"))))
25662 (properties `((upstream-name . "dials")))
25663 (build-system r-build-system)
25665 `(("r-dicedesign" ,r-dicedesign)
25666 ("r-dplyr" ,r-dplyr)
25668 ("r-purrr" ,r-purrr)
25669 ("r-rlang" ,r-rlang)
25670 ("r-scales" ,r-scales)
25671 ("r-tibble" ,r-tibble)
25672 ("r-vctrs" ,r-vctrs)
25673 ("r-withr" ,r-withr)))
25674 (native-inputs `(("r-knitr" ,r-knitr)))
25675 (home-page "https://dials.tidymodels.org/")
25676 (synopsis "Tools for creating tuning parameter values")
25678 "Many models contain tuning parameters (i.e. parameters that cannot be
25679 directly estimated from the data). These tools can be used to define objects
25680 for creating, simulating, or validating values for such parameters.")
25681 (license license:gpl2)))
25683 (define-public r-tune
25690 (uri (cran-uri "tune" version))
25693 "0ja7rjkjj88v3ngrc6izcz2qh9qv4s8abgcafmvx2ihgz99hds37"))))
25694 (properties `((upstream-name . "tune")))
25695 (build-system r-build-system)
25698 ("r-dials" ,r-dials)
25699 ("r-dplyr" ,r-dplyr)
25700 ("r-foreach" ,r-foreach)
25701 ("r-generics" ,r-generics)
25702 ("r-ggplot2" ,r-ggplot2)
25704 ("r-gpfit" ,r-gpfit)
25705 ("r-hardhat" ,r-hardhat)
25706 ("r-parsnip" ,r-parsnip)
25707 ("r-purrr" ,r-purrr)
25708 ("r-recipes" ,r-recipes)
25709 ("r-rlang" ,r-rlang)
25710 ("r-rsample" ,r-rsample)
25711 ("r-tibble" ,r-tibble)
25712 ("r-tidyr" ,r-tidyr)
25713 ("r-vctrs" ,r-vctrs)
25714 ("r-workflows" ,r-workflows)
25715 ("r-yardstick" ,r-yardstick)))
25716 (home-page "https://github.com/tidymodels/tune")
25717 (synopsis "Tidy tuning tools")
25719 "The ability to tune models is important. @code{tune} contains functions
25720 and classes to be used in conjunction with other @code{tidymodels} packages
25721 for finding reasonable values of hyper-parameters in models, pre-processing
25722 methods, and post-processing steps.")
25723 (license license:expat)))
25725 (define-public r-tidyposterior
25727 (name "r-tidyposterior")
25732 (uri (cran-uri "tidyposterior" version))
25735 "0wsv800w056ziqbnwal7ncmdy4li8cn5yrdx07w35b7j8kl4mwhg"))))
25736 (properties `((upstream-name . "tidyposterior")))
25737 (build-system r-build-system)
25739 `(("r-dplyr" ,r-dplyr)
25740 ("r-generics" ,r-generics)
25741 ("r-ggplot2" ,r-ggplot2)
25742 ("r-lifecycle" ,r-lifecycle)
25743 ("r-purrr" ,r-purrr)
25744 ("r-rlang" ,r-rlang)
25745 ("r-rsample" ,r-rsample)
25746 ("r-rstanarm" ,r-rstanarm)
25747 ("r-tibble" ,r-tibble)
25748 ("r-tidyr" ,r-tidyr)
25749 ("r-vctrs" ,r-vctrs)))
25751 `(("r-knitr" ,r-knitr)))
25752 (home-page "https://tidyposterior.tidymodels.org")
25753 (synopsis "Bayesian analysis to compare models using resampling statistics")
25755 "This package can be used to conduct post hoc analyses of resampling
25756 results generated by models. For example, if two models are evaluated with
25757 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
25758 are 10 paired statistics. These can be used to make comparisons between
25759 models without involving a test set.")
25760 (license license:gpl2)))
25762 (define-public r-tidypredict
25764 (name "r-tidypredict")
25769 (uri (cran-uri "tidypredict" version))
25772 "0fff349pkksss8h1k2qza78l81ha6avx63pxziv6dfa8h62qmrdy"))))
25773 (properties `((upstream-name . "tidypredict")))
25774 (build-system r-build-system)
25776 `(("r-dplyr" ,r-dplyr)
25777 ("r-generics" ,r-generics)
25778 ("r-knitr" ,r-knitr)
25779 ("r-purrr" ,r-purrr)
25780 ("r-rlang" ,r-rlang)
25781 ("r-stringr" ,r-stringr)
25782 ("r-tibble" ,r-tibble)
25783 ("r-tidyr" ,r-tidyr)))
25785 `(("r-knitr" ,r-knitr)))
25786 (home-page "https://tidypredict.tidymodels.org")
25787 (synopsis "Run predictions inside the database")
25789 "This package parses a fitted R model object, and returns a formula in
25790 Tidy Eval code that calculates the predictions. It works with several
25791 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
25792 final SQL translation of the algorithm. It currently supports @code{lm()},
25793 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
25794 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
25795 (license license:gpl3)))
25797 (define-public r-janeaustenr
25799 (name "r-janeaustenr")
25804 (uri (cran-uri "janeaustenr" version))
25807 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
25808 (properties `((upstream-name . "janeaustenr")))
25809 (build-system r-build-system)
25810 (home-page "https://github.com/juliasilge/janeaustenr")
25811 (synopsis "Jane Austen's complete novels")
25813 "This package provides the full texts for Jane Austen's six completed
25814 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
25815 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
25816 and \"Persuasion\".")
25817 (license license:expat)))
25819 (define-public r-tokenizers
25821 (name "r-tokenizers")
25826 (uri (cran-uri "tokenizers" version))
25829 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
25830 (properties `((upstream-name . "tokenizers")))
25831 (build-system r-build-system)
25833 `(("r-rcpp" ,r-rcpp)
25834 ("r-snowballc" ,r-snowballc)
25835 ("r-stringi" ,r-stringi)))
25837 `(("r-knitr" ,r-knitr)))
25838 (home-page "https://lincolnmullen.com/software/tokenizers/")
25839 (synopsis "Fast, consistent tokenization of natural language text")
25841 "This is a package for converting natural language text into tokens.
25842 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
25843 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
25844 Treebank, regular expressions, as well as functions for counting characters,
25845 words, and sentences, and a function for splitting longer texts into separate
25846 documents, each with the same number of words. The tokenizers have a
25847 consistent interface, and the package is built on the @code{stringi} and
25848 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
25849 (license license:expat)))
25851 (define-public r-hunspell
25853 (name "r-hunspell")
25858 (uri (cran-uri "hunspell" version))
25861 "0ql6y05d4xxpm468rslb0wxdp1x9l3flxzmb5w6pjg617f8vpv8z"))))
25862 (properties `((upstream-name . "hunspell")))
25863 (build-system r-build-system)
25865 `(("r-digest" ,r-digest)
25866 ("r-rcpp" ,r-rcpp)))
25868 `(("r-knitr" ,r-knitr)))
25869 (home-page "https://github.com/ropensci/hunspell#readme")
25870 (synopsis "High-performance stemmer, tokenizer, and spell checker")
25872 "This package provides a low-level spell checker and morphological
25873 analyzer based on the famous @code{hunspell} library. The package can analyze
25874 or check individual words as well as parse text, LaTeX, HTML or XML documents.
25875 For a more user-friendly interface use the @code{spelling} package which
25876 builds on this package to automate checking of files, documentation and
25877 vignettes in all common formats.")
25878 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
25879 ;; MPL; in addition to these licenses the rest of the R wrapper is also
25880 ;; available under the Expat license.
25881 (license (list license:gpl2
25886 (define-public r-tidytext
25888 (name "r-tidytext")
25893 (uri (cran-uri "tidytext" version))
25896 "1icbfw4zkbs9sp6vk814mw2zzm0bc0d7af92vhriqxaga0gbwdkx"))))
25897 (properties `((upstream-name . "tidytext")))
25898 (build-system r-build-system)
25900 `(("r-dplyr" ,r-dplyr)
25901 ("r-generics" ,r-generics)
25902 ("r-hunspell" ,r-hunspell)
25903 ("r-janeaustenr" ,r-janeaustenr)
25904 ("r-lifecycle" ,r-lifecycle)
25905 ("r-matrix" ,r-matrix)
25906 ("r-purrr" ,r-purrr)
25907 ("r-rlang" ,r-rlang)
25908 ("r-stringr" ,r-stringr)
25909 ("r-tibble" ,r-tibble)
25910 ("r-tokenizers" ,r-tokenizers)
25911 ("r-vctrs" ,r-vctrs)))
25913 `(("r-knitr" ,r-knitr)))
25914 (home-page "https://github.com/juliasilge/tidytext")
25915 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
25917 "This is a package for text mining for word processing and sentiment
25918 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
25919 (license license:expat)))
25921 (define-public r-parsnip
25928 (uri (cran-uri "parsnip" version))
25931 "0c12lyfxqsdprqlcmgy421py38z28h88d68pxb1c4fw14v1c2d06"))))
25932 (properties `((upstream-name . "parsnip")))
25933 (build-system r-build-system)
25935 `(("r-dplyr" ,r-dplyr)
25936 ("r-generics" ,r-generics)
25937 ("r-globals" ,r-globals)
25939 ("r-magrittr" ,r-magrittr)
25940 ("r-prettyunits" ,r-prettyunits)
25941 ("r-purrr" ,r-purrr)
25942 ("r-rlang" ,r-rlang)
25943 ("r-tibble" ,r-tibble)
25944 ("r-tidyr" ,r-tidyr)
25945 ("r-vctrs" ,r-vctrs)))
25947 `(("r-knitr" ,r-knitr)))
25948 (home-page "https://parsnip.tidymodels.org")
25949 (synopsis "Common API to modeling and analysis functions")
25951 "This package provides a common interface to allow users to specify a
25952 model without having to remember the different argument names across different
25953 functions or computational engines (e.g. R, Spark, Stan, etc).")
25954 (license license:gpl2)))
25956 (define-public r-infer
25963 (uri (cran-uri "infer" version))
25966 "0wvvgqjhyv7ql98cjzqad61wbmk7xrqd1ybk894jr5cmza13c8w2"))))
25967 (properties `((upstream-name . "infer")))
25968 (build-system r-build-system)
25970 `(("r-dplyr" ,r-dplyr)
25971 ("r-ggplot2" ,r-ggplot2)
25973 ("r-magrittr" ,r-magrittr)
25974 ("r-purrr" ,r-purrr)
25975 ("r-rlang" ,r-rlang)
25976 ("r-tibble" ,r-tibble)))
25978 `(("r-knitr" ,r-knitr)))
25979 (home-page "https://github.com/tidymodels/infer")
25980 (synopsis "Tidy statistical inference")
25982 "The objective of this package is to perform inference using an
25983 expressive statistical grammar that coheres with the Tidy design framework.")
25984 (license license:cc0)))
25986 (define-public r-modeldata
25988 (name "r-modeldata")
25993 (uri (cran-uri "modeldata" version))
25996 "0lbvmicvhw560jn9qk5dywrl6mgj1rf7zh7p86lf97c6bmz0zp2r"))))
25997 (properties `((upstream-name . "modeldata")))
25998 (build-system r-build-system)
25999 (home-page "https://modeldata.tidymodels.org")
26000 (synopsis "Data sets useful for modeling packages")
26002 "This package provides data sets used for demonstrating or testing
26003 model-related packages.")
26004 (license license:expat)))
26006 (define-public r-tidymodels
26008 (name "r-tidymodels")
26013 (uri (cran-uri "tidymodels" version))
26016 "09njrl655sh82xrzckgg56a6ndfrjla5fy8675wj4jsj14jpv0fw"))))
26017 (properties `((upstream-name . "tidymodels")))
26018 (build-system r-build-system)
26020 `(("r-broom" ,r-broom)
26022 ("r-dials" ,r-dials)
26023 ("r-dplyr" ,r-dplyr)
26024 ("r-ggplot2" ,r-ggplot2)
26025 ("r-infer" ,r-infer)
26026 ("r-magrittr" ,r-magrittr)
26027 ("r-modeldata" ,r-modeldata)
26028 ("r-parsnip" ,r-parsnip)
26029 ("r-purrr" ,r-purrr)
26030 ("r-recipes" ,r-recipes)
26031 ("r-rlang" ,r-rlang)
26032 ("r-rsample" ,r-rsample)
26033 ("r-rstudioapi" ,r-rstudioapi)
26034 ("r-tibble" ,r-tibble)
26035 ("r-tidyr" ,r-tidyr)
26037 ("r-workflows" ,r-workflows)
26038 ("r-yardstick" ,r-yardstick)))
26040 `(("r-knitr" ,r-knitr)
26041 ("r-rmarkdown" ,r-rmarkdown)
26043 ("pandoc-citeproc" ,pandoc-citeproc))) ; for vignettes
26044 (home-page "https://github.com/tidymodels/tidymodels")
26045 (synopsis "Tidy collection for modeling and statistical analysis")
26047 "The tidy modeling \"verse\" is a collection of packages for modeling and
26048 statistical analysis that share the underlying design philosophy, grammar, and
26049 data structures of the tidyverse.")
26050 (license license:gpl3)))
26052 (define-public r-mlecens
26059 (uri (cran-uri "MLEcens" version))
26062 "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))
26063 (properties `((upstream-name . "MLEcens")))
26064 (build-system r-build-system)
26065 (home-page "http://stat.ethz.ch/~maathuis/")
26066 (synopsis "Computation of the MLE for bivariate (interval) censored data")
26068 "This package contains functions to compute the nonparametric
26069 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
26070 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
26071 To be more precise, we consider the situation where we observe a set of
26072 rectangles that are known to contain the unobservable realizations of (X,Y).
26073 We compute the MLE based on such a set of rectangles. The methods can also be
26074 used for univariate censored data (see data set @code{cosmesis}), and for
26075 censored data with competing risks (see data set @code{menopause}). The
26076 package also provides functions to visualize the observed data and the MLE.")
26077 (license license:gpl2+)))
26079 (define-public r-metafor
26086 (uri (cran-uri "metafor" version))
26089 "1b599fxk7s0brkchmx698fr5k4g1kzkia2rnlvhg349ffs5nfjmn"))))
26090 (properties `((upstream-name . "metafor")))
26091 (build-system r-build-system)
26093 `(("r-matrix" ,r-matrix)
26094 ("r-nlme" ,r-nlme)))
26095 (home-page "https://cran.r-project.org/web/packages/metafor/")
26096 (synopsis "Meta-analysis package for R")
26098 "This package provides a comprehensive collection of functions for
26099 conducting meta-analyses in R. The package includes functions to calculate
26100 various effect sizes or outcome measures, fit fixed-, random-, and
26101 mixed-effects models to such data, carry out moderator and meta-regression
26102 analyses, and create various types of meta-analytical plots (e.g., forest,
26103 funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial
26104 and person-time data, the package also provides functions that implement
26105 specialized methods, including the Mantel-Haenszel method, Peto's method, and
26106 a variety of suitable generalized linear (mixed-effects) models (i.e.
26107 mixed-effects logistic and Poisson regression models). Finally, the package
26108 provides functionality for fitting meta-analytic multivariate/multilevel
26109 models that account for non-independent sampling errors and/or true
26110 effects (e.g. due to the inclusion of multiple treatment studies, multiple
26111 endpoints, or other forms of clustering). Network meta-analyses and
26112 meta-analyses accounting for known correlation structures (e.g. due to
26113 phylogenetic relatedness) can also be conducted.")
26114 (license license:gpl2+)))
26116 (define-public r-altmeta
26123 (uri (cran-uri "altmeta" version))
26126 "0z252lbsknqp33i0b0xf5r7spr535iq47bv40vgip6nsqhgrl7b0"))))
26127 (properties `((upstream-name . "altmeta")))
26128 (build-system r-build-system)
26130 `(("r-coda" ,r-coda)
26132 ("r-matrix" ,r-matrix)
26133 ("r-metafor" ,r-metafor)
26134 ("r-rjags" ,r-rjags)))
26135 (home-page "https://cran.r-project.org/web/packages/altmeta/")
26136 (synopsis "Alternative meta-analysis methods")
26138 "This package provides alternative statistical methods for meta-analysis,
26142 @item bivariate generalized linear mixed models for synthesizing odds ratios,
26143 relative risks, and risk differences
26144 @item heterogeneity tests and measures that are robust to outliers;
26145 @item measures, tests, and visualization tools for publication bias or
26146 small-study effects;
26147 @item meta-analysis of diagnostic tests for synthesizing sensitivities,
26148 specificities, etc.;
26149 @item meta-analysis methods for synthesizing proportions;
26150 @item models for multivariate meta-analysis.
26153 (license license:gpl2+)))
26155 (define-public r-perm
26158 (version "1.0-0.0")
26162 (uri (cran-uri "perm" version))
26165 "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk"))))
26166 (properties `((upstream-name . "perm")))
26167 (build-system r-build-system)
26168 (home-page "https://cran.r-project.org/web/packages/perm/")
26169 (synopsis "Exact or asymptotic permutation tests")
26171 "This package provides several methods for performing permutation tests.
26172 It has three main functions, to perform linear permutation tests. These tests
26173 are tests where the test statistic is the sum of the product of a
26174 covariate (usually group indicator) and the scores.")
26175 ;; Any version of the GPL
26176 (license license:gpl2+)))
26178 (define-public r-qtl
26185 (uri (cran-uri "qtl" version))
26188 "0hffirsvw9j82cdx6l7vhqn3a7ab52claqjlinv3lswl1nsfg93b"))))
26189 (build-system r-build-system)
26190 (home-page "https://rqtl.org/")
26191 (synopsis "R package for analyzing QTL experiments in genetics")
26192 (description "R/qtl is an extension library for the R statistics system.
26193 It is used to analyze experimental crosses for identifying genes contributing
26194 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
26196 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
26197 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
26199 (license license:gpl3)))
26201 (define-public r-qtl2
26207 (uri (cran-uri "qtl2" version))
26209 (base32 "1558khh0zkwm0rdk87krv9836krvwv5h7ymlz9bsrgcvypyr9186"))))
26210 (build-system r-build-system)
26212 `(("r-data-table" ,r-data-table)
26213 ("r-jsonlite" ,r-jsonlite)
26215 ("r-rcppeigen" ,r-rcppeigen)
26216 ("r-rsqlite" ,r-rsqlite)
26217 ("r-yaml" ,r-yaml)))
26218 (home-page "https://kbroman.org/qtl2/")
26219 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
26221 "This package provides a set of tools to perform @dfn{Quantitative Trait
26222 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
26223 @code{R/qtl} package to better handle high-dimensional data and complex cross
26224 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
26225 (license license:gpl3)))
26227 (define-public r-seqminer
26229 (name "r-seqminer")
26234 (uri (cran-uri "seqminer" version))
26237 "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
26238 (build-system r-build-system)
26241 (home-page "http://seqminer.genomic.codes")
26242 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
26244 "This package provides tools to integrate nucleotide sequencing
26245 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
26246 ;; Any version of the GPL is acceptable
26247 (license (list license:gpl2+ license:gpl3+))))
26249 (define-public r-maldiquant
26251 (name "r-maldiquant")
26256 (uri (cran-uri "MALDIquant" version))
26259 "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
26260 (properties `((upstream-name . "MALDIquant")))
26261 (build-system r-build-system)
26262 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
26263 (synopsis "Quantitative analysis of mass spectrometry data")
26265 "This package provides a complete analysis pipeline for matrix-assisted
26266 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
26267 two-dimensional mass spectrometry data. In addition to commonly used plotting
26268 and processing methods it includes distinctive features, namely baseline
26269 subtraction methods such as morphological filters (TopHat) or the
26270 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
26271 alignment using warping functions, handling of replicated measurements as well
26272 as allowing spectra with different resolutions.")
26273 (license license:gpl3+)))
26275 (define-public r-scattermore
26277 (name "r-scattermore")
26282 (uri (cran-uri "scattermore" version))
26285 "18nzlprmphkvjg946h10h2qq0wbkmv2526p8di6k2xl4gccq0qpk"))))
26286 (properties `((upstream-name . "scattermore")))
26287 (build-system r-build-system)
26289 `(("r-ggplot2" ,r-ggplot2)
26290 ("r-scales" ,r-scales)))
26291 (home-page "https://github.com/exaexa/scattermore")
26292 (synopsis "Scatterplots with more points")
26294 "This package provides C-based tools for converting large scatterplot
26295 data to rasters. It speeds up plotting of data with millions of points.")
26296 (license license:gpl3+)))
26298 (define-public r-seuratobject
26300 (name "r-seuratobject")
26305 (uri (cran-uri "SeuratObject" version))
26308 "03k27z7g76wy7mfja2cpxq183xk0906k9gxb2j6p1zw341gv4gii"))))
26309 (properties `((upstream-name . "SeuratObject")))
26310 (build-system r-build-system)
26312 `(("r-matrix" ,r-matrix)
26314 ("r-rcppeigen" ,r-rcppeigen)
26315 ("r-rlang" ,r-rlang)
26316 ("r-sctransform" ,r-sctransform)))
26317 (home-page "https://satijalab.org/seurat")
26318 (synopsis "Data structures for single cell data")
26320 "This package defines S4 classes for single-cell genomic data and
26321 associated information, such as dimensionality reduction embeddings,
26322 nearest-neighbor graphs, and spatially-resolved coordinates. It provides data
26323 access methods and R-native hooks to ensure the Seurat object is familiar to
26325 (license license:gpl3)))
26327 (define-public r-seurat
26333 (uri (cran-uri "Seurat" version))
26336 "1mp3py00bmzj4541d8ry5sfzkpfzvnl9dpa8n4qhakd13dl30xdn"))))
26337 (properties `((upstream-name . "Seurat")))
26338 (build-system r-build-system)
26340 `(("r-cluster" ,r-cluster)
26341 ("r-cowplot" ,r-cowplot)
26342 ("r-fitdistrplus" ,r-fitdistrplus)
26343 ("r-future" ,r-future)
26344 ("r-future-apply" ,r-future-apply)
26345 ("r-ggplot2" ,r-ggplot2)
26346 ("r-ggrepel" ,r-ggrepel)
26347 ("r-ggridges" ,r-ggridges)
26350 ("r-igraph" ,r-igraph)
26351 ("r-irlba" ,r-irlba)
26352 ("r-jsonlite" ,r-jsonlite)
26353 ("r-kernsmooth" ,r-kernsmooth)
26354 ("r-leiden" ,r-leiden)
26355 ("r-lmtest" ,r-lmtest)
26357 ("r-matrix" ,r-matrix)
26358 ("r-matrixstats" ,r-matrixstats)
26359 ("r-miniui" ,r-miniui)
26360 ("r-patchwork" ,r-patchwork)
26361 ("r-pbapply" ,r-pbapply)
26362 ("r-plotly" ,r-plotly)
26365 ("r-rcolorbrewer" ,r-rcolorbrewer)
26367 ("r-rcppannoy" ,r-rcppannoy)
26368 ("r-rcppeigen" ,r-rcppeigen)
26369 ("r-rcppprogress" ,r-rcppprogress)
26370 ("r-reticulate" ,r-reticulate)
26371 ("r-rlang" ,r-rlang)
26373 ("r-rtsne" ,r-rtsne)
26374 ("r-scales" ,r-scales)
26375 ("r-scattermore" ,r-scattermore)
26376 ("r-sctransform" ,r-sctransform)
26377 ("r-seuratobject" ,r-seuratobject)
26378 ("r-shiny" ,r-shiny)
26379 ("r-spatstat" ,r-spatstat)
26380 ("r-tibble" ,r-tibble)
26381 ("r-uwot" ,r-uwot)))
26382 (home-page "http://www.satijalab.org/seurat")
26383 (synopsis "Seurat is an R toolkit for single cell genomics")
26385 "This package is an R package designed for QC, analysis, and
26386 exploration of single cell RNA-seq data. It easily enables widely-used
26387 analytical techniques, including the identification of highly variable genes,
26388 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
26389 algorithms; density clustering, hierarchical clustering, k-means, and the
26390 discovery of differentially expressed genes and markers.")
26391 (license license:gpl3)))
26393 (define-public r-phangorn
26395 (name "r-phangorn")
26400 (uri (cran-uri "phangorn" version))
26403 "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
26404 (build-system r-build-system)
26407 ("r-fastmatch" ,r-fastmatch)
26408 ("r-igraph" ,r-igraph)
26409 ("r-magrittr" ,r-magrittr)
26410 ("r-matrix" ,r-matrix)
26411 ("r-quadprog" ,r-quadprog)
26412 ("r-rcpp" ,r-rcpp)))
26413 (home-page "https://github.com/KlausVigo/phangorn")
26414 (synopsis "Phylogenetic analysis in R")
26416 "Phangorn is a package for phylogenetic analysis in R. It supports
26417 estimation of phylogenetic trees and networks using Maximum Likelihood,
26418 Maximum Parsimony, distance methods and Hadamard conjugation.")
26419 (license license:gpl2+)))
26421 (define-public r-diversitree
26423 (name "r-diversitree")
26428 (uri (cran-uri "diversitree" version))
26431 "1sk3sgn5hi04978s5s7gy6pzp28g3v9rglmiamlgs96c9wyyyff7"))))
26432 (build-system r-build-system)
26434 `(("gfortran" ,gfortran)))
26435 (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
26438 ("r-desolve" ,r-desolve)
26440 ("r-subplex" ,r-subplex)))
26441 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
26442 (synopsis "Comparative 'phylogenetic' analyses of diversification")
26443 (description "This package contains a number of comparative \"phylogenetic\"
26444 methods, mostly focusing on analysing diversification and character evolution.
26445 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
26446 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
26447 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
26448 include Markov models of discrete and continuous trait evolution and constant
26449 rate speciation and extinction.")
26450 (license license:gpl2+)))
26452 (define-public r-absfiltergsea
26454 (name "r-absfiltergsea")
26459 (uri (cran-uri "AbsFilterGSEA" version))
26461 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
26462 (properties `((upstream-name . "AbsFilterGSEA")))
26463 (build-system r-build-system)
26465 `(("r-biobase" ,r-biobase)
26466 ("r-deseq" ,r-deseq)
26467 ("r-limma" ,r-limma)
26469 ("r-rcpparmadillo" ,r-rcpparmadillo)))
26470 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
26471 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
26473 "This package provides a function that performs gene-permuting of a gene-set
26474 enrichment analysis (GSEA) calculation with or without the absolute filtering.
26475 Without filtering, users can perform (original) two-tailed or one-tailed
26477 (license license:gpl2)))
26479 (define-public r-calculus
26481 (name "r-calculus")
26486 (uri (cran-uri "calculus" version))
26489 "1wa5ap89cfcp0ancj9ivx5s2y0wqr2vmp9y115g7f6g772jwhscj"))))
26490 (properties `((upstream-name . "calculus")))
26491 (build-system r-build-system)
26493 `(("r-rcpp" ,r-rcpp)))
26495 `(("r-knitr" ,r-knitr)))
26496 (home-page "https://github.com/eguidotti/calculus")
26497 (synopsis "High dimensional numerical and symbolic calculus")
26499 "Efficient C++ optimized functions for numerical and symbolic calculus.
26500 It includes basic symbolic arithmetic, tensor calculus, Einstein summing
26501 convention, fast computation of the Levi-Civita symbol and generalized
26502 Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
26503 accurate high-order derivatives, differential operators (Gradient, Jacobian,
26504 Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
26505 orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
26506 parabolic or user defined by custom scale factors.")
26507 (license license:gpl3)))
26509 (define-public r-decon
26516 (uri (cran-uri "decon" version))
26519 "1v4l0xq29rm8mks354g40g9jxn0didzlxg3g7z08m0gvj29zdj7s"))))
26520 (properties `((upstream-name . "decon")))
26521 (build-system r-build-system)
26523 `(("gfortran" ,gfortran)))
26525 "https://cran.r-project.org/web/packages/decon/")
26526 (synopsis "Deconvolution Estimation in Measurement Error Models")
26528 "This package contains a collection of functions to deal with
26529 nonparametric measurement error problems using deconvolution
26530 kernel methods. We focus two measurement error models in the
26531 package: (1) an additive measurement error model, where the
26532 goal is to estimate the density or distribution function from
26533 contaminated data; (2) nonparametric regression model with
26534 errors-in-variables. The R functions allow the measurement errors
26535 to be either homoscedastic or heteroscedastic. To make the
26536 deconvolution estimators computationally more efficient in R,
26537 we adapt the \"Fast Fourier Transform\" (FFT) algorithm for
26538 density estimation with error-free data to the deconvolution
26539 kernel estimation. Several methods for the selection of the
26540 data-driven smoothing parameter are also provided in the package.
26541 See details in: Wang, X.F. and Wang, B. (2011). Deconvolution
26542 estimation in measurement error models: The R package decon.
26543 Journal of Statistical Software, 39(10), 1-24.")
26544 (license license:gpl3+)))
26546 (define-public r-locpol
26553 (uri (cran-uri "locpol" version))
26556 "1p915n0l09kbwkly627074jslxl01yssp1rf0c7sygvsw6sgy5lm"))))
26557 (properties `((upstream-name . "locpol")))
26558 (build-system r-build-system)
26560 "https://cran.r-project.org/web/packages/locpol/")
26561 (synopsis "Kernel Local Polynomial Regression")
26563 "Computes local polynomial estimators for the regression and
26564 also density. It comprises several different utilities to handle
26565 kernel estimators.")
26566 (license license:gpl2+)))
26568 (define-public r-lpme
26575 (uri (cran-uri "lpme" version))
26578 "0si90nkgl8bqk8yvd2igdsrngiwqh8891072pfpzipifnd0f5448"))))
26579 (properties `((upstream-name . "lpme")))
26580 (build-system r-build-system)
26582 `(("r-decon" ,r-decon)
26583 ("r-flexmix" ,r-flexmix)
26584 ("r-locpol" ,r-locpol)
26586 ("r-rcpparmadillo" ,r-rcpparmadillo)))
26588 "https://cran.r-project.org/web/packages/lpme/")
26589 (synopsis "Nonparametric Estimation of Measurement Error Models")
26591 "Provide nonparametric methods for mean regression model,
26592 modal regression and conditional density estimation in the
26593 presence/absence of measurement error. Bandwidth selection is
26594 also provided for each method.")
26595 (license license:gpl2+)))
26597 (define-public r-aws-signature
26599 (name "r-aws-signature")
26604 (uri (cran-uri "aws.signature" version))
26607 "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp"))))
26608 (properties `((upstream-name . "aws.signature")))
26609 (build-system r-build-system)
26611 `(("r-base64enc" ,r-base64enc)
26612 ("r-digest" ,r-digest)))
26613 (home-page "https://github.com/cloudyr/aws.signature")
26614 (synopsis "Amazon Web Services Request Signatures")
26616 "This package generates version 2 and 4 request signatures for Amazon Web
26617 Services (AWS) and provides a mechanism for retrieving credentials from
26618 environment variables, AWS credentials files, and EC2 instance metadata. For
26619 use on EC2 instances, the package 'aws.ec2metadata' is suggested.")
26620 (license license:gpl2+)))
26622 (define-public r-aws-s3
26629 (uri (cran-uri "aws.s3" version))
26632 "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx"))))
26633 (properties `((upstream-name . "aws.s3")))
26634 (build-system r-build-system)
26636 `(("r-aws-signature" ,r-aws-signature)
26637 ("r-base64enc" ,r-base64enc)
26639 ("r-digest" ,r-digest)
26641 ("r-xml2" ,r-xml2)))
26642 (home-page "https://github.com/cloudyr/aws.s3")
26643 (synopsis "AWS S3 Client Package")
26645 "This package provides a simple client package for the Amazon Web
26646 Services (AWS) Simple Storage Service (S3) REST API.")
26647 (license license:gpl2+)))
26649 (define-public r-lgr
26655 (uri (cran-uri "lgr" version))
26658 "0k4kacjk7swm3gmdpha1rg44xb29vzvhvx48jhpb78glj5c9phyr"))))
26659 (build-system r-build-system)
26663 `(("r-knitr" ,r-knitr)))
26664 (home-page "https://s-fleck.github.io/lgr/")
26665 (synopsis "Fully featured logging framework")
26666 (description "This package offers a flexible, feature-rich yet
26667 light-weight logging framework based on @code{R6} classes. It supports
26668 hierarchical loggers, custom log levels, arbitrary data fields in log events,
26669 logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as
26670 well as email and push notifications.")
26671 (license license:expat)))
26673 (define-public r-mlr3measures
26675 (name "r-mlr3measures")
26679 (uri (cran-uri "mlr3measures" version))
26682 "18jk4kdj9771r16smz7xhmmiilcdg1qlavln5hrpvkx780zh3hj6"))))
26683 (build-system r-build-system)
26685 `(("r-checkmate" ,r-checkmate)
26686 ("r-prroc" ,r-prroc)))
26687 (home-page "https://mlr3measures.mlr-org.com/")
26688 (synopsis "Performance measures for mlr3")
26689 (description "This package implements multiple performance measures for
26690 supervised learning. It includes over 40 measures for regression and
26691 classification. Additionally, meta information about the performance measures
26692 can be queried, e.g. what the best and worst possible performances scores
26694 (license license:lgpl3)))
26696 (define-public r-mlr3misc
26698 (name "r-mlr3misc")
26702 (uri (cran-uri "mlr3misc" version))
26705 "19k3l2d6wnqvdng0m7p54rrlvwl5457lcy7bg82m2bbpqxi8qch3"))))
26706 (build-system r-build-system)
26708 `(("r-backports" ,r-backports)
26709 ("r-checkmate" ,r-checkmate)
26710 ("r-data-table" ,r-data-table)
26712 (home-page "https://mlr3misc.mlr-org.com/")
26713 (synopsis "Helper functions for mlr3")
26714 (description "@code{mlr3misc} provides frequently used helper functions
26715 and assertions used in @code{mlr3} and its companion packages. It comes with
26716 helper functions for functional programming, for printing, to work with
26717 @code{data.table}, as well as some generally useful @code{R6} classes. This
26718 package also supersedes the package @code{BBmisc}.")
26719 (license license:lgpl3)))
26721 (define-public r-paradox
26727 (uri (cran-uri "paradox" version))
26730 "1fz6sdwvvifm4qbmwgm27dil278mswvcfw8bbsvli5v4l1ghw8kj"))))
26731 (build-system r-build-system)
26733 `(("r-backports" ,r-backports)
26734 ("r-checkmate" ,r-checkmate)
26735 ("r-data-table" ,r-data-table)
26736 ("r-mlr3misc" ,r-mlr3misc)
26738 (home-page "https://paradox.mlr-org.com/")
26739 (synopsis "Define and work with parameter spaces for complex algorithms")
26740 (description "With this package it is possible to define parameter spaces,
26741 constraints and dependencies for arbitrary algorithms, and to program on such
26742 spaces. It also includes statistical designs and random samplers. Objects are
26743 implemented as @code{R6} classes.")
26744 (license license:lgpl3)))
26746 (define-public r-mlr3
26752 (uri (cran-uri "mlr3" version))
26755 "1arqijbbmhv57mj8kyq30zxykah83ab1d1c7gs0cxs0xhfwln66g"))))
26756 (build-system r-build-system)
26759 ("r-backports" ,r-backports)
26760 ("r-checkmate" ,r-checkmate)
26761 ("r-data-table" ,r-data-table)
26762 ("r-digest" ,r-digest)
26763 ("r-future-apply" ,r-future-apply)
26765 ("r-mlbench" ,r-mlbench)
26766 ("r-mlr3measures" ,r-mlr3measures)
26767 ("r-mlr3misc" ,r-mlr3misc)
26768 ("r-paradox" ,r-paradox)
26769 ("r-uuid" ,r-uuid)))
26770 (home-page "https://mlr3.mlr-org.com/")
26771 (synopsis "Machine Learning in R - Next Generation")
26772 (description "@code{mlr3} enables efficient, object-oriented programming
26773 on the building blocks of machine learning. It provides @code{R6} objects for
26774 tasks, learners, resamplings, and measures. The package is geared towards
26775 scalability and larger datasets by supporting parallelization and out-of-memory
26776 data-backends like databases. While @code{mlr3} focuses on the core
26777 computational operations, add-on packages provide additional functionality.")
26778 (license license:lgpl3)))
26780 (define-public r-mlr3learners
26782 (name "r-mlr3learners")
26786 (uri (cran-uri "mlr3learners" version))
26789 "1wxlpzz3hpkn77n4ag1v868dmp140j1pmrhynsv5xfgk9fg0w7ri"))))
26790 (build-system r-build-system)
26792 `(("r-data-table" ,r-data-table)
26794 ("r-mlr3misc" ,r-mlr3misc)
26795 ("r-paradox" ,r-paradox)
26797 (home-page "https://mlr3learners.mlr-org.com/")
26798 (synopsis "Recommended Learners for @code{mlr3}")
26799 (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba}
26800 with interfaces to essential machine learning packages on CRAN. This includes,
26801 but is not limited to: (penalized) linear and logistic regression, linear and
26802 quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support
26803 vector machines, and gradient boosting.")
26804 (license license:lgpl3)))
26806 (define-public r-bbotk
26813 (uri (cran-uri "bbotk" version))
26816 "0kbjbwwq1fdfpl4xzy08hz4qvhjjchvz58icxq0dlbsmdyqwhwv0"))))
26817 (properties `((upstream-name . "bbotk")))
26818 (build-system r-build-system)
26820 `(("r-checkmate" ,r-checkmate)
26821 ("r-data-table" ,r-data-table)
26823 ("r-mlr3misc" ,r-mlr3misc)
26824 ("r-paradox" ,r-paradox)
26827 `(("r-knitr" ,r-knitr)))
26828 (home-page "https://bbotk.mlr-org.com")
26829 (synopsis "Black-Box Optimization Toolkit")
26830 (description "This package provides a common framework for optimization of
26831 black-box functions for other packages, e.g. @code{mlr3}. It offers various
26832 optimization methods e.g. grid search, random search and generalized simulated
26834 (license license:lgpl3)))
26836 (define-public r-mlr3tuning
26838 (name "r-mlr3tuning")
26842 (uri (cran-uri "mlr3tuning" version))
26845 "0kxf9wl1jnwyrj2zfmiz12w2594407y44m0xxwp9b2lrwxk31wm7"))))
26846 (build-system r-build-system)
26848 `(("r-bbotk" ,r-bbotk)
26849 ("r-checkmate" ,r-checkmate)
26850 ("r-data-table" ,r-data-table)
26853 ("r-mlr3misc" ,r-mlr3misc)
26854 ("r-paradox" ,r-paradox)
26856 (home-page "https://mlr3tuning.mlr-org.com/")
26857 (synopsis "Tuning for @code{mlr3}")
26858 (description "@code{mlr3tuning} implements methods for hyperparameter
26859 tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various
26860 termination criteria can be set and combined. The class @code{AutoTuner} provides a
26861 convenient way to perform nested resampling in combination with @code{mlr3}.")
26862 (license license:lgpl3)))
26864 (define-public r-fontliberation
26866 (name "r-fontliberation")
26871 (uri (cran-uri "fontLiberation" version))
26874 "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc"))))
26876 `((upstream-name . "fontLiberation")))
26877 (build-system r-build-system)
26878 (home-page "https://cran.r-project.org/package=fontLiberation")
26879 (synopsis "Liberation fonts")
26881 "This package provides a placeholder for the Liberation fontset intended
26882 for the fontquiver package. This fontset covers the 12 combinations of
26883 families (sans, serif, mono) and faces (plain, bold, italic, bold italic)
26884 supported in R graphics devices.")
26885 (license license:silofl1.1)))
26887 (define-public r-fontbitstreamvera
26889 (name "r-fontbitstreamvera")
26894 (uri (cran-uri "fontBitstreamVera" version))
26897 "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j"))))
26899 `((upstream-name . "fontBitstreamVera")))
26900 (build-system r-build-system)
26901 (home-page "https://cran.r-project.org/package=fontBitstreamVera")
26902 (synopsis "Fonts for fontquiver")
26904 "This package is a placeholder for the Bitstream Vera font. It is
26905 intended for the fontquiver package.")
26907 (license:fsdg-compatible
26908 "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts"
26909 "The Font Software may be sold as part of a larger software package but
26910 no copy of one or more of the Font Software typefaces may be sold by
26913 (define-public r-fontquiver
26915 (name "r-fontquiver")
26920 (uri (cran-uri "fontquiver" version))
26923 "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm"))))
26924 (properties `((upstream-name . "fontquiver")))
26925 (build-system r-build-system)
26927 `(("r-fontbitstreamvera" ,r-fontbitstreamvera)
26928 ("r-fontliberation" ,r-fontliberation)))
26929 (home-page "https://cran.r-project.org/package=fontquiver")
26930 (synopsis "Set of installed fonts")
26932 "This package provides a set of fonts. This is useful when you want to
26933 avoid system fonts to make sure your outputs are reproducible.")
26934 (license license:gpl3)))
26936 (define-public r-freetypeharfbuzz
26938 (name "r-freetypeharfbuzz")
26943 (uri (cran-uri "freetypeharfbuzz" version))
26946 "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7"))))
26948 `((upstream-name . "freetypeharfbuzz")))
26949 (build-system r-build-system)
26952 (modify-phases %standard-phases
26953 (add-after 'unpack 'prepare-static-libraries
26954 (lambda* (#:key inputs #:allow-other-keys)
26955 (mkdir-p "src/target/include")
26956 (let ((freetype (assoc-ref inputs "static-freetype"))
26957 (harfbuzz (assoc-ref inputs "static-harfbuzz")))
26958 (substitute* "src/Makevars.in"
26959 (("include @MK_FILE@") "") ; do not build static libs
26960 (("^HB_STATIC_LIB =.*")
26961 (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n"))
26962 (("^FT_STATIC_LIB =.*")
26963 (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n")))
26964 (copy-recursively (string-append freetype "/include")
26965 "src/target/include")
26966 (copy-recursively (string-append harfbuzz "/include")
26967 "src/target/include")))))))
26969 `(("r-fontquiver" ,r-fontquiver)))
26970 ;; This may defeat the purpose of this package as our versions of freetype
26971 ;; and harfbuzz obviously differ from the tarballs offered by this
26972 ;; project. On the other hand, Guix arguably does a better job at
26973 ;; "ensur[ing] deterministic computation".
26975 `(("static-freetype"
26977 (inherit (static-package freetype))
26979 `(#:configure-flags
26980 (list "--enable-static=yes"
26985 "--without-harfbuzz")))))
26988 (inherit (static-package harfbuzz))
26990 `(#:tests? #false ; fail because shared library is disabled
26992 (list "--enable-static=yes"
26993 "--enable-shared=no"
26995 "--with-freetype=yes"
26998 "--without-fontconfig"
26999 "--without-glib")))))))
27002 (home-page "https://cran.r-project.org/package=freetypeharfbuzz")
27003 (synopsis "Deterministic computation of text box metrics")
27005 "Unlike other tools that dynamically link to the Cairo stack,
27006 freetypeharfbuzz is statically linked to specific versions of the FreeType and
27007 harfbuzz libraries. This ensures deterministic computation of text box
27008 extents for situations where reproducible results are crucial (for instance
27009 unit tests of graphics).")
27010 (license license:gpl3)))
27012 (define-public r-vdiffr
27019 (uri (cran-uri "vdiffr" version))
27022 "0i0xdr8dakbkkgrhp0zvlnv3rxhc8h5naqq416mr5zv9q8i4p8jc"))
27025 (delete-file "inst/htmlwidgets/lib/jquery.min.js")))))
27026 (properties `((upstream-name . "vdiffr")))
27027 (build-system r-build-system)
27030 (modify-phases %standard-phases
27031 (add-after 'unpack 'process-javascript
27032 (lambda* (#:key inputs #:allow-other-keys)
27033 (with-directory-excursion "inst/htmlwidgets/lib/"
27034 (let ((source (assoc-ref inputs "js-jquery"))
27035 (target "jquery.min.js"))
27036 (format #true "Processing ~a --> ~a~%"
27038 (invoke "esbuild" source "--minify"
27039 (string-append "--outfile=" target)))))))))
27041 `(("freetype" ,freetype)
27042 ("harfbuzz" ,harfbuzz)))
27045 ("r-devtools" ,r-devtools)
27046 ("r-diffobj" ,r-diffobj)
27047 ("r-fontquiver" ,r-fontquiver)
27048 ("r-freetypeharfbuzz" ,r-freetypeharfbuzz)
27049 ("r-gdtools" ,r-gdtools)
27051 ("r-htmltools" ,r-htmltools)
27052 ("r-htmlwidgets" ,r-htmlwidgets)
27053 ("r-purrr" ,r-purrr)
27056 ("r-rlang" ,r-rlang)
27057 ("r-shiny" ,r-shiny)
27058 ("r-testthat" ,r-testthat)
27059 ("r-usethis" ,r-usethis)
27060 ("r-xml2" ,r-xml2)))
27062 `(("esbuild" ,esbuild)
27066 (uri "https://code.jquery.com/jquery-1.12.4.js")
27069 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))))
27070 (home-page "https://github.com/r-lib/vdiffr")
27071 (synopsis "Visual regression testing and graphical diffing")
27073 "This package is an extension to the testthat package that makes it easy
27074 to add graphical unit tests. It provides a Shiny application to manage the
27076 (license license:gpl3)))
27078 (define-public r-highlight
27080 (name "r-highlight")
27085 (uri (cran-uri "highlight" version))
27088 "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf"))))
27089 (properties `((upstream-name . "highlight")))
27090 (build-system r-build-system)
27091 (home-page "https://github.com/hadley/highlight")
27092 (synopsis "Syntax highlighter for R code")
27094 "This package provides a syntax highlighter for R code based on the
27095 results of the R parser. It supports rendering in HTML and LaTeX markup. It
27096 includes a custom Sweave driver performing syntax highlighting of R code
27098 (license license:gpl3+)))
27100 (define-public r-clustree
27102 (name "r-clustree")
27107 (uri (cran-uri "clustree" version))
27110 "0lxydy2f83qqd5dhlp2l546jax759l43b29j6g82079yzg1szwsz"))))
27111 (properties `((upstream-name . "clustree")))
27112 (build-system r-build-system)
27114 `(("r-checkmate" ,r-checkmate)
27115 ("r-dplyr" ,r-dplyr)
27116 ("r-ggplot2" ,r-ggplot2)
27117 ("r-ggraph" ,r-ggraph)
27118 ("r-ggrepel" ,r-ggrepel)
27119 ("r-igraph" ,r-igraph)
27120 ("r-rlang" ,r-rlang)
27121 ("r-tidygraph" ,r-tidygraph)
27122 ("r-viridis" ,r-viridis)))
27124 `(("r-knitr" ,r-knitr)))
27125 (home-page "https://github.com/lazappi/clustree")
27126 (synopsis "Visualize clusterings at different resolutions")
27128 "Deciding what resolution to use can be a difficult question when
27129 approaching a clustering analysis. One way to approach this problem is to
27130 look at how samples move as the number of clusters increases. This package
27131 allows you to produce clustering trees, a visualization for interrogating
27132 clusterings as resolution increases.")
27133 (license license:gpl3)))
27135 (define-public r-textshaping
27137 (name "r-textshaping")
27142 (uri (cran-uri "textshaping" version))
27145 "053pbw45by96q62kjfnyc3d0ssar9svssrdqy6a09kdmdh75xdar"))))
27146 (properties `((upstream-name . "textshaping")))
27147 (build-system r-build-system)
27149 `(("freetype" ,freetype)
27150 ("fribidi" ,fribidi)
27151 ("harfbuzz" ,harfbuzz)
27154 `(("r-cpp11" ,r-cpp11)
27155 ("r-systemfonts" ,r-systemfonts)))
27157 `(("pkg-config" ,pkg-config)
27158 ("r-knitr" ,r-knitr)))
27159 (home-page "https://github.com/r-lib/textshaping")
27160 (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping")
27162 "This package provides access to the text shaping functionality in the
27163 HarfBuzz library and the bidirectional algorithm in the Fribidi library. This
27164 is a low-level utility package mainly for graphic devices that expands upon
27165 the font tool-set provided by the @code{systemfonts} package.")
27166 (license license:expat)))
27168 (define-public r-ragg
27175 (uri (cran-uri "ragg" version))
27178 "0443dhfi7bjfpap041vrnslw3ql3vpsxx18raz2w9nfdb7id8lsc"))))
27179 (properties `((upstream-name . "ragg")))
27180 (build-system r-build-system)
27182 `(("freetype" ,freetype)
27183 ("libjpeg" ,libjpeg-turbo)
27185 ("libtiff" ,libtiff)
27188 `(("r-systemfonts" ,r-systemfonts)
27189 ("r-textshaping" ,r-textshaping)))
27191 `(("pkg-config" ,pkg-config)))
27192 (home-page "https://ragg.r-lib.org")
27193 (synopsis "Graphic devices based on AGG")
27195 "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D
27196 drawing library. The ragg package provides a set of graphic devices based on
27197 AGG to use as alternative to the raster devices provided through the
27198 @code{grDevices} package.")
27199 (license license:expat)))
27201 (define-public r-downlit
27208 (uri (cran-uri "downlit" version))
27211 "0z4fz7c9kyd9v72wl3iqs2wxspi975d6b0rgjr9lvg8a18maa9z6"))))
27212 (properties `((upstream-name . "downlit")))
27213 (build-system r-build-system)
27215 `(("r-brio" ,r-brio)
27216 ("r-digest" ,r-digest)
27217 ("r-evaluate" ,r-evaluate)
27218 ("r-fansi" ,r-fansi)
27219 ("r-rlang" ,r-rlang)
27220 ("r-vctrs" ,r-vctrs)
27221 ("r-yaml" ,r-yaml)))
27222 (home-page "https://downlit.r-lib.org/")
27223 (synopsis "Syntax highlighting and automatic linking")
27225 "This package provides syntax highlighting of R code, specifically
27226 designed for the needs of RMarkdown packages like @code{pkgdown},
27227 @code{hugodown}, and @code{bookdown}. It includes linking of function calls
27228 to their documentation on the web, and automatic translation of ANSI escapes
27229 in output to the equivalent HTML.")
27230 (license license:expat)))
27232 (define-public r-pkgdown
27239 (uri (cran-uri "pkgdown" version))
27242 "1k31biyvxkv3xjc1yy3nzb9wfza3vbx97fv17nly5a6vlv7zqbs4"))))
27243 (properties `((upstream-name . "pkgdown")))
27244 (build-system r-build-system)
27245 (inputs `(("pandoc" ,pandoc)))
27247 `(("r-callr" ,r-callr)
27248 ("r-crayon" ,r-crayon)
27250 ("r-digest" ,r-digest)
27251 ("r-downlit" ,r-downlit)
27254 ("r-magrittr" ,r-magrittr)
27255 ("r-memoise" ,r-memoise)
27256 ("r-openssl" ,r-openssl)
27257 ("r-purrr" ,r-purrr)
27259 ("r-rematch2" ,r-rematch2)
27260 ("r-rlang" ,r-rlang)
27261 ("r-rmarkdown" ,r-rmarkdown)
27262 ("r-tibble" ,r-tibble)
27263 ("r-whisker" ,r-whisker)
27264 ("r-withr" ,r-withr)
27266 ("r-yaml" ,r-yaml)))
27268 `(("r-knitr" ,r-knitr)))
27269 (home-page "https://pkgdown.r-lib.org")
27270 (synopsis "Make static HTML documentation for an R package")
27272 "The goal of this package is to generate an attractive and useful website
27273 from a source package. @code{pkgdown} converts your documentation, vignettes,
27274 README file, and more to HTML making it easy to share information about your
27276 (license license:expat)))